Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold36
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 140008
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5341 original size:9 final size:9
Alignment explanation
Indices: 5329--5362 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
5319 AAAATATTAG
5329 GTTTTGTGA
1 GTTTTGTGA
5338 GTTTTGTGA
1 GTTTTGTGA
5347 GTTTTGTGA
1 GTTTTGTGA
5356 GTTTTGT
1 GTTTTGT
5363 TAGTATTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.32, T:0.59
Consensus pattern (9 bp):
GTTTTGTGA
Left flanking sequence: Indices 4829 -- 5328
AATTGAGAGAAAAAATATCCACGGTGCTCTGCACGAATGCGGAAACTTCTATACAAGTACATCGC
AACTAATGTGCCAATAGATGTACCTCCGCATATTATGCTTCAACTGACGATTATTTACCATCAGG
TCGATTGTAACTCTTCTCTATTTCCCTGCTATATTTCATTACATGTACGAAGAAGTGTATCCATG
CAGACTTACGGCCCAGACAGCAGTGAATGACTTTTTCAGTAGACGAATCTCCGGCTTGAAAGTTG
AGGAAAAGTATCACTATGCGATCCGCAGCTTAGACTTCACTAGTGGAATGTTGTGCTAGTATCGG
AATGCGGAGTCGGGTGTGTAAAAATATTTTTGAGCTCATCCTTTTCTGAGCAAGCCACTTTCGCG
ACAATTACGGCATCATAAGAACTCACACACGCCTTTTTTGTGGTTACGCAAGTGCTCGCGCTAGA
GTGATGTCGAGAAATCAGACGCGCATCAAATCAACAAAATATTAG
Right flanking sequence: Indices 5363 -- 5862
TAGTATTGGTAACATTTAGAGCAAACAAATCCAACAGAGCCGAGTACCGCAAATACACATGGTGC
ATGTAGGAAATATGGAAAATAGATGGAAACTATACAAAGCGAATATTGAAAAGTTTAAATTGACT
ACTTCGTGTGTTACGTCATCAAGCCACAAGCCTGAATTAGGTTTGAGGACATCAAAATGCAATAA
ATTAGGTAATAAAAATTTGCCGAAATTCCGTGGCTTATTGTTTGCACTTCGGACGATCGGCGCAG
ACATGGTGAGTAAGCCTAGTGAAATAGTCGATTCACTATCAAATTCCACTCTCATAGATATACAT
GTCCCAAAGTAACGAGCATATTGCACAGATGCGTAGAAAATTTAATAGCTGCATATTTTGCCGCC
AACGCACCAACGCACCAACCAACGCACGGCGGAGCTAGCCGACGAATTGTTTATTTATCGAGTCA
ACCTGAAACATGGAAGTCAGGAAATTCTACTTCTGTGAGACCAGC
Found at i:6140 original size:13 final size:13
Alignment explanation
Indices: 6122--6146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6112 TCTTTTTCCA
6122 TTTTTTTTCACTC
1 TTTTTTTTCACTC
6135 TTTTTTTTCACT
1 TTTTTTTTCACT
6147 TTTCCTCCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCACTC
Left flanking sequence: Indices 5622 -- 6121
GACATGGTGAGTAAGCCTAGTGAAATAGTCGATTCACTATCAAATTCCACTCTCATAGATATACA
TGTCCCAAAGTAACGAGCATATTGCACAGATGCGTAGAAAATTTAATAGCTGCATATTTTGCCGC
CAACGCACCAACGCACCAACCAACGCACGGCGGAGCTAGCCGACGAATTGTTTATTTATCGAGTC
AACCTGAAACATGGAAGTCAGGAAATTCTACTTCTGTGAGACCAGCTACTACAGGCGGTCGCATT
CGTAAGAAGAAAATTCCTGCAAGCACTCTTTTGAATGGGTCATGAGAAACGTCCGGTGCTCGGAA
TCGCCCTTCTTGCGAACCTTCGAAACAAAACAGATTCATGATAAGCACAATTTGAGTAACACCCA
TAGATTTTTCCAGACTCAAAAAAATCTCCCGAACCGAGAATCGAACTCGGATCTCCCGCGTGACA
AGCGGAGATACTAACCGTTATACTATCCGGGAACCTCTTTTTCCA
Right flanking sequence: Indices 6147 -- 6646
TTTCCTCCTTTTTTTTTCTTCACTTTTCCTGAACATTAACTAGATACTTAGAAAATTAACGGCAT
GCGTCTTGTATGGGGAACCGTTGATTGGAGAAAAACCCATTGCATTTGTCATGACATGTGTGTCA
TGGTATTTGGTTGGCTTATGTTTTACAGTCAGATCTTACGTATCTAAGTACGTAGTTAGCAAATT
ATATGGAAAAAAAAAAAAATGTCAGCTTCAAGGCAGGGGTTTAGCGAGTTCCCCCCTAACCGCTT
GACCCAAGATGTTCTTTTCGAGATGGCCCGGTTTCTCCGCGCCGTCTTCCTCTTACGGAAAGAGA
CACAACTTTCAAACAGCGCCCCCTAGCCCGTCACTGAAGGCCATTTGAAAGAGTAGATTAAGAAC
AAATTGGAATACATCAAGACGGGTAGAGGCATGGCATGATCGATGATTTGAGACCAAAAAACGAA
AAAATCAAAAAAATCGAAAAAACCCAAATTAAACAATTCGAATTT
Found at i:68528 original size:15 final size:16
Alignment explanation
Indices: 68508--68592 Score: 117
Period size: 15 Copynumber: 5.6 Consensus size: 16
68498 TGTTGCACTT
68508 TCCTTGG-CAGCCTTC
1 TCCTTGGCCAGCCTTC
*
68523 TCCTTGGTC-GCCTTC
1 TCCTTGGCCAGCCTTC
68538 TCCTTGG-CAGCCTTC
1 TCCTTGGCCAGCCTTC
*
68553 TCCTCGGCCA-CCTTC
1 TCCTTGGCCAGCCTTC
68568 TCCTTGGCCA-CCTTC
1 TCCTTGGCCAGCCTTC
68583 TCCTTGGCCA
1 TCCTTGGCCA
68593 CTCTGATCAT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
14 1 0.02
15 61 0.94
16 3 0.05
ACGTcount: A:0.06, C:0.44, G:0.18, T:0.33
Consensus pattern (16 bp):
TCCTTGGCCAGCCTTC
Left flanking sequence: Indices 68008 -- 68507
TTTTACTCATGGGATTGATTTCTCTTTGGTGGGGGATGCTTTTCATGACCAATGTATACTTCCAC
TCAATCCTTGAAAAGTTTGTTGGTTTGGTGTTTGGTTTTGCGGCCATCATACCCATCTACATACT
CCCACGTTGGCTTCAGCCCCCAGTTGAGCCTGAAAGGCAAAAGCAAGCATAGAATGGCTCAAAAA
TCATGTAATCGAGATGTATATACTAATTAATGATGAACTATAGATTTTCGGCAACTGGTTCTTCA
ACTGCAGGTCTATTCTCAGTAGCCTTTGATGAGATACGAAGCTTTTCTAATCGCTTCTCTAAGTC
GGCCTCGCTAATTTGTGTTTCAGATGAGCCGGTGTCTTCGGTCATACCTCCTCTATGCAGATCAT
TGGTTACGGGTTCCTTCGTACTTCGCTCAGCCTCTTCTTTCTTTGCACGTTCATCAAGACTGTAC
TCCGTAGTCGCATTTTCCTTGGCCATCATAGCTTGTGTTGCACTT
Right flanking sequence: Indices 68593 -- 69092
CTCTGATCATTGTCTCTTCTCGGAGCATTCGATCAAATTCGTCATCGACTTCAGCCTCAGCGGCT
TCGTCAATGTTGACCTCCGCAAGACGAGCCCCTACTTCATCAATCTTGGACATCTCCTCCACAAT
GCTATCCTTGACTGCATCGACATCATCGGTATTCAATCGGTCGTTGTAGTACTTCATGGCTTCAG
CTGCGTCTTGCATCGCGTCCATCACCACCACATTCAGCTGACTCTCGTCTAGTTTCATCATCACC
AGGCGTAGTTGAGATTCCGAGGACATGCCCTGGTCAAGCAGCTGTAAAACACGCTTTTTGAGTCG
CAACAAATGCTTGATTCGAGCTTCAGGGGCTTTTGTTTTCACTAAATCACGAGTCTTCTTCTCTA
ACCGGCTCAATTCGGCTGCGAGTCCCTCATTCCTCTTGGTAGTCGCCTGGCATGCGTTCTTAACA
TCAATAAAAGTCTTTTCGCTATCGGTGATCTCCAGGGAGTTAAGC
Found at i:68542 original size:30 final size:30
Alignment explanation
Indices: 68508--68593 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
68498 TGTTGCACTT
* *
68508 TCCTTGGCAGCCTTCTCCTTGGTCGCCTTC
1 TCCTTGGCAGCCTTCTCCTTGGCCACCTTC
*
68538 TCCTTGGCAGCCTTCTCCTCGGCCACCTTC
1 TCCTTGGCAGCCTTCTCCTTGGCCACCTTC
68568 TCCTTGGCCA-CCTTCTCCTTGGCCAC
1 TCCTTGG-CAGCCTTCTCCTTGGCCAC
68594 TCTGATCATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 49 0.96
31 2 0.04
ACGTcount: A:0.06, C:0.44, G:0.17, T:0.33
Consensus pattern (30 bp):
TCCTTGGCAGCCTTCTCCTTGGCCACCTTC
Left flanking sequence: Indices 68008 -- 68507
TTTTACTCATGGGATTGATTTCTCTTTGGTGGGGGATGCTTTTCATGACCAATGTATACTTCCAC
TCAATCCTTGAAAAGTTTGTTGGTTTGGTGTTTGGTTTTGCGGCCATCATACCCATCTACATACT
CCCACGTTGGCTTCAGCCCCCAGTTGAGCCTGAAAGGCAAAAGCAAGCATAGAATGGCTCAAAAA
TCATGTAATCGAGATGTATATACTAATTAATGATGAACTATAGATTTTCGGCAACTGGTTCTTCA
ACTGCAGGTCTATTCTCAGTAGCCTTTGATGAGATACGAAGCTTTTCTAATCGCTTCTCTAAGTC
GGCCTCGCTAATTTGTGTTTCAGATGAGCCGGTGTCTTCGGTCATACCTCCTCTATGCAGATCAT
TGGTTACGGGTTCCTTCGTACTTCGCTCAGCCTCTTCTTTCTTTGCACGTTCATCAAGACTGTAC
TCCGTAGTCGCATTTTCCTTGGCCATCATAGCTTGTGTTGCACTT
Right flanking sequence: Indices 68594 -- 69093
TCTGATCATTGTCTCTTCTCGGAGCATTCGATCAAATTCGTCATCGACTTCAGCCTCAGCGGCTT
CGTCAATGTTGACCTCCGCAAGACGAGCCCCTACTTCATCAATCTTGGACATCTCCTCCACAATG
CTATCCTTGACTGCATCGACATCATCGGTATTCAATCGGTCGTTGTAGTACTTCATGGCTTCAGC
TGCGTCTTGCATCGCGTCCATCACCACCACATTCAGCTGACTCTCGTCTAGTTTCATCATCACCA
GGCGTAGTTGAGATTCCGAGGACATGCCCTGGTCAAGCAGCTGTAAAACACGCTTTTTGAGTCGC
AACAAATGCTTGATTCGAGCTTCAGGGGCTTTTGTTTTCACTAAATCACGAGTCTTCTTCTCTAA
CCGGCTCAATTCGGCTGCGAGTCCCTCATTCCTCTTGGTAGTCGCCTGGCATGCGTTCTTAACAT
CAATAAAAGTCTTTTCGCTATCGGTGATCTCCAGGGAGTTAAGCT
Found at i:77589 original size:15 final size:12
Alignment explanation
Indices: 77553--77596 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
77543 GTGTTCTGAC
77553 GAGCTGGATGAT
1 GAGCTGGATGAT
77565 GAGCTGGATGAT
1 GAGCTGGATGAT
77577 GAGCTGGATGAT
1 GAGCTGGATGAT
77589 GAGCTGGA
1 GAGCTGGA
77597 GGAACTGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.43, T:0.23
Consensus pattern (12 bp):
GAGCTGGATGAT
Left flanking sequence: Indices 77053 -- 77552
CTACTATCCCAGACCTGCGGATTGCGCGTATTGAGGGTTTGTTGGACTTTGGAGAAAGAGAGTTT
GGCATTCCTCAGTTGGTAGACATCACCGACTTTCGAAAGGATGTGCCTGATGAAAAGTGTTTGTT
GCCCTACATTTTGGAGCTACATCGCCAATTTGCTAGCGAGAACGTTTTAATTCCCAAAAGTGCAA
AACCTGGGTTGCCTTTGGGCCACGAGGTTAAAGTAAACGACAAGGAGACGACAAACCTTTCCAAG
AATCAGGGACATCTGATGGTTCAAGAGTTGGTTCGCAAATTGTCCGCAGGCTCGCTGGTAGAGCT
TGAGACTAACACGACAACTGAAACGATGAACACTAAACACGAACCAGGCGTTGAGTCATTCTCCG
GTGATGCTCCGCCGGAGACACCCAACAATAATGCTCCGCGTAAAGAGGATAATCAAAGTATACTT
GGGCATCTGGATGATGCGGGTAATTTGGAGCTGGGGTGTTCTGAC
Right flanking sequence: Indices 77597 -- 78096
GGAACTGGGAGATGATCTGGACCATCTGGACGGTCTGGATTGTGATCTGGAAAAGCCTGTCAAAA
TAAATTCAACTCAGAAGTGCCCAGCACATGGGCAACTACTCAATGGGCCACACACCCCAAGAACG
GACCGAAGTAAAAAAGTTGTGTCTTTTGCCTCGCCCGAGCACGATAGTGATGCGTCTAGTGAGGG
CTCTGCCGAGCTGTCCGAGGACGATGCCACATCTAGTTCGGAGTCTGGGTCAGAAACCCTGACAC
TTGGCGACAGCGCCGAACCGATCGGTGACGACAATAGCACACTTGCAAGTCTGGTTACTAGTCAA
GCCCCTAAACTCACATTCAAGCAACGTATGGGGATGGTCTTCAAAAAGATCAACAATCCCCTCTG
AATCAGAAGAACCTGAGCTCGATCTGAAATACGTGCAAGCTTCTCCTGTTGAACCAATCACTTAC
GACTTCAACACCACTAATGATCTCGTCTACGTGTTAGTGGCGACC
Found at i:77604 original size:21 final size:23
Alignment explanation
Indices: 77556--77617 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
77546 TTCTGACGAG
*
77556 CTGGATGATGAGCTGGATGATGAG
1 CTGGATGATGAGCTGGATGA-GAA
77580 CTGGATGATGAGCTGGA-G-GAA
1 CTGGATGATGAGCTGGATGAGAA
*
77601 CTGGGA-GATGATCTGGA
1 CT-GGATGATGAGCTGGA
77618 CCATCTGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.40
22 3 0.09
23 1 0.03
24 17 0.49
ACGTcount: A:0.26, C:0.10, G:0.42, T:0.23
Consensus pattern (23 bp):
CTGGATGATGAGCTGGATGAGAA
Left flanking sequence: Indices 77056 -- 77555
CTATCCCAGACCTGCGGATTGCGCGTATTGAGGGTTTGTTGGACTTTGGAGAAAGAGAGTTTGGC
ATTCCTCAGTTGGTAGACATCACCGACTTTCGAAAGGATGTGCCTGATGAAAAGTGTTTGTTGCC
CTACATTTTGGAGCTACATCGCCAATTTGCTAGCGAGAACGTTTTAATTCCCAAAAGTGCAAAAC
CTGGGTTGCCTTTGGGCCACGAGGTTAAAGTAAACGACAAGGAGACGACAAACCTTTCCAAGAAT
CAGGGACATCTGATGGTTCAAGAGTTGGTTCGCAAATTGTCCGCAGGCTCGCTGGTAGAGCTTGA
GACTAACACGACAACTGAAACGATGAACACTAAACACGAACCAGGCGTTGAGTCATTCTCCGGTG
ATGCTCCGCCGGAGACACCCAACAATAATGCTCCGCGTAAAGAGGATAATCAAAGTATACTTGGG
CATCTGGATGATGCGGGTAATTTGGAGCTGGGGTGTTCTGACGAG
Right flanking sequence: Indices 77618 -- 78117
CCATCTGGACGGTCTGGATTGTGATCTGGAAAAGCCTGTCAAAATAAATTCAACTCAGAAGTGCC
CAGCACATGGGCAACTACTCAATGGGCCACACACCCCAAGAACGGACCGAAGTAAAAAAGTTGTG
TCTTTTGCCTCGCCCGAGCACGATAGTGATGCGTCTAGTGAGGGCTCTGCCGAGCTGTCCGAGGA
CGATGCCACATCTAGTTCGGAGTCTGGGTCAGAAACCCTGACACTTGGCGACAGCGCCGAACCGA
TCGGTGACGACAATAGCACACTTGCAAGTCTGGTTACTAGTCAAGCCCCTAAACTCACATTCAAG
CAACGTATGGGGATGGTCTTCAAAAAGATCAACAATCCCCTCTGAATCAGAAGAACCTGAGCTCG
ATCTGAAATACGTGCAAGCTTCTCCTGTTGAACCAATCACTTACGACTTCAACACCACTAATGAT
CTCGTCTACGTGTTAGTGGCGACCCGCAACCTTCGTGCAAAATAT
Found at i:104402 original size:6 final size:6
Alignment explanation
Indices: 104393--104445 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
104383 TCAGGACGAG
* * * * *
104393 GAGGAA GAGGAA GACGAA GAGGAA GACGAA GAAGAA GAGGAG GAGGAC
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
104441 GAGGA
1 GAGGA
104446 GGACGAAGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.47, C:0.06, G:0.47, T:0.00
Consensus pattern (6 bp):
GAGGAA
Left flanking sequence: Indices 103893 -- 104392
TATTTTGGAAGATTCCAACGTATTTTAGTTGTTGGTTTTGAGCCCATAACTAAACCCGCGATGCC
TACGCAGTCTACCTCATCACTTACCTAACCAGACTCGTTATCTCCCACATCCAAATTATGGCTAA
GAAGAGCGCAAAAGGGGATGATCTCCTTTTGACCATCGACAGTGATGACGAACAAAATGTCTACG
AGAAGGTGAATCTGGATAGTGAGTCCGAGACTGAGGCTCCACTCCCCAAAAAGGCCAAGAAGAGT
AAGAAGGGCAAAAAGGCGGCTCAGCCTGAGCCAGAGGCCGAAGACAAAGAGGCAGCTGACTTGAA
CCCCGACTTTCAATTCATTGTGGAGGGTGGCATGGCCTCTTCTCGTTTCGATGGCTGGGATTTTG
CTGGCGATGAGAAGACTGGTCGGAAGGACGTTGATTTGGATGGCATCTTGCGTCGGAAAGGTGGC
TTGGTAAACCAAATGACTGGTGAAGAGGAGGCTCCTCAGGACGAG
Right flanking sequence: Indices 104446 -- 104945
GGACGAAGCCGAGGAAGACGACGACGACGAAGCCGAAGAGGCCAACGGCGAGGACGAAGACGACC
TTGCCATGGACGGCTTTGGTATGGGTGTTCAGGCTGAGGCAGAGGAAGCCGAGGATGATGAGGAG
GCCGAAGCTGAGGAGGAGCAAGCCTCCGAAGACGAAGCCCCAGTTGAGGCTGACATGGATGAGGA
GCATGGAGACGACGAGGAGAAGGAGGATGTTGAGGACCTGGCCGAGGCTATCAAGGAGTTTTACG
ACACCGAGGAGCCTGCTACCAAGCAGAAGCACACTCTGTTTAACTCATTGCAGTTGTCCCGTCCC
GTGCTCAAGGGGTTGGCGCAGCTTGGATACACGAAGCCGCTGCCGATTCAGAGTGCCGCCATCCC
GATTGGTTTGCTTGGTAAAGACATCGTCGCGGGTGCCCAGACTGGTTCCGGTAAGACCGCAGCAT
TCATGATTCCCATTATCGAGCGGTTGGTATTCAAGCCGGCAAAGG
Found at i:104478 original size:24 final size:24
Alignment explanation
Indices: 104432--104481 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
104422 AGAAGAAGAG
* * *
104432 GAGGAGGACGAGGAGGACGAAGCC
1 GAGGAAGACGACGACGACGAAGCC
104456 GAGGAAGACGACGACGACGAAGCC
1 GAGGAAGACGACGACGACGAAGCC
104480 GA
1 GA
104482 AGAGGCCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.44, T:0.00
Consensus pattern (24 bp):
GAGGAAGACGACGACGACGAAGCC
Left flanking sequence: Indices 103932 -- 104431
GAGCCCATAACTAAACCCGCGATGCCTACGCAGTCTACCTCATCACTTACCTAACCAGACTCGTT
ATCTCCCACATCCAAATTATGGCTAAGAAGAGCGCAAAAGGGGATGATCTCCTTTTGACCATCGA
CAGTGATGACGAACAAAATGTCTACGAGAAGGTGAATCTGGATAGTGAGTCCGAGACTGAGGCTC
CACTCCCCAAAAAGGCCAAGAAGAGTAAGAAGGGCAAAAAGGCGGCTCAGCCTGAGCCAGAGGCC
GAAGACAAAGAGGCAGCTGACTTGAACCCCGACTTTCAATTCATTGTGGAGGGTGGCATGGCCTC
TTCTCGTTTCGATGGCTGGGATTTTGCTGGCGATGAGAAGACTGGTCGGAAGGACGTTGATTTGG
ATGGCATCTTGCGTCGGAAAGGTGGCTTGGTAAACCAAATGACTGGTGAAGAGGAGGCTCCTCAG
GACGAGGAGGAAGAGGAAGACGAAGAGGAAGACGAAGAAGAAGAG
Right flanking sequence: Indices 104482 -- 104981
AGAGGCCAACGGCGAGGACGAAGACGACCTTGCCATGGACGGCTTTGGTATGGGTGTTCAGGCTG
AGGCAGAGGAAGCCGAGGATGATGAGGAGGCCGAAGCTGAGGAGGAGCAAGCCTCCGAAGACGAA
GCCCCAGTTGAGGCTGACATGGATGAGGAGCATGGAGACGACGAGGAGAAGGAGGATGTTGAGGA
CCTGGCCGAGGCTATCAAGGAGTTTTACGACACCGAGGAGCCTGCTACCAAGCAGAAGCACACTC
TGTTTAACTCATTGCAGTTGTCCCGTCCCGTGCTCAAGGGGTTGGCGCAGCTTGGATACACGAAG
CCGCTGCCGATTCAGAGTGCCGCCATCCCGATTGGTTTGCTTGGTAAAGACATCGTCGCGGGTGC
CCAGACTGGTTCCGGTAAGACCGCAGCATTCATGATTCCCATTATCGAGCGGTTGGTATTCAAGC
CGGCAAAGGGGGCTCTGACCCGAGTGATCATCTTGACCCCTACTC
Found at i:110608 original size:18 final size:18
Alignment explanation
Indices: 110581--110619 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
110571 TCAAAAGGGC
*
110581 CAGGGGCAGC-AGCCTCAG
1 CAGGGACAGCAAG-CTCAG
110599 CAGGGACAGCAAGCTCAG
1 CAGGGACAGCAAGCTCAG
110617 CAG
1 CAG
110620 CCGAAGTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.28, C:0.31, G:0.36, T:0.05
Consensus pattern (18 bp):
CAGGGACAGCAAGCTCAG
Left flanking sequence: Indices 110081 -- 110580
AGCTGCAGCTGCTTACCAAGTACCTGTACCAGGCGATCGAGAAGTTCTTCCAGTCGTACCCCGAC
CCGTCGGTGGCCAACAAGGACGTCAAGGGGGTGCCGCGCGAGGCGGTGCTTGACCCTCGCCAGCT
GTACCAGTTGTTGTCGCTGCAGCGGTTTGCCTTGGGCGACCGTGTGATCTATGTGCACGACCTGG
GCAAGGTTCCGATGTTGTCAAAGGGCACAGTAGCGCTGATCATCACTCTTGGTGCCAAGACGCTG
TTGGGGGTGATCTTCGATAAGGAGTTGTTGAACGGTAGCACCATGCACGGCAAGCTTGCAACCAA
GCGCGGCATGCTGATCGACTCGCTGTTGGTGTTGAACTTGAGCAACCGCCAGTTCGTGTACCACT
CGAAGGCGCTGAAGAACCAGAAGGCTCGGGTGGCCCAGAGCGTCAACCAGACCTATGGCAAGCCC
CAGAAGGCTCCCCAGCGGGCTCTGACTCCCAAGGGTCAAAAGGGC
Right flanking sequence: Indices 110620 -- 111119
CCGAAGTCTCAGCAGAAGCCCAAGCCCAAGGGCAAGGGCAAAACCCCGCCTCCCCAACCTCAGAA
CGGTAACACCGAGCCTCAGAGCGAAGTCAACGCGAAGCAATCGCACGAGCTTCTTCTGATTCTTA
AGGGTCTGTCCAAGGACTCGAAGGACTCCAAGGACTCCAACGCAAAGGAGGAGCCACAGGAGGAG
CCGTCGAGCCAACAGAACCCTGCAGTGGCCAACCCGAACGCCATCAAGCTGATCTACGGGCAGAT
TTACTCCAACGTGATGAGTGAGGGCCAGATGCCGGTGCCGCAGATGTACATGCCCCCTCCCGGGC
AGTTCCCGCCGCAGATGATGCCGATGGTGCCTGGAGTCCCTGTGCCTCCGCAGTTCTACCAGCAG
CCTCCTCCGGGCCAGTTCTACCAGCCGTACGGCCAGCCCCCGCAGCAGCCTCAGCAGCCACAACA
GCCGCAACAACCCCACCCTCAGCAGCAGCAGCAGTCCCAGCAGCG
Found at i:110775 original size:9 final size:9
Alignment explanation
Indices: 110758--110789 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
110748 TAAGGGTCTG
110758 TCCAAGGAC
1 TCCAAGGAC
*
110767 TCGAAGGAC
1 TCCAAGGAC
110776 TCCAAGGAC
1 TCCAAGGAC
110785 TCCAA
1 TCCAA
110790 CGCAAAGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.12
Consensus pattern (9 bp):
TCCAAGGAC
Left flanking sequence: Indices 110258 -- 110757
TCTATGTGCACGACCTGGGCAAGGTTCCGATGTTGTCAAAGGGCACAGTAGCGCTGATCATCACT
CTTGGTGCCAAGACGCTGTTGGGGGTGATCTTCGATAAGGAGTTGTTGAACGGTAGCACCATGCA
CGGCAAGCTTGCAACCAAGCGCGGCATGCTGATCGACTCGCTGTTGGTGTTGAACTTGAGCAACC
GCCAGTTCGTGTACCACTCGAAGGCGCTGAAGAACCAGAAGGCTCGGGTGGCCCAGAGCGTCAAC
CAGACCTATGGCAAGCCCCAGAAGGCTCCCCAGCGGGCTCTGACTCCCAAGGGTCAAAAGGGCCA
GGGGCAGCAGCCTCAGCAGGGACAGCAAGCTCAGCAGCCGAAGTCTCAGCAGAAGCCCAAGCCCA
AGGGCAAGGGCAAAACCCCGCCTCCCCAACCTCAGAACGGTAACACCGAGCCTCAGAGCGAAGTC
AACGCGAAGCAATCGCACGAGCTTCTTCTGATTCTTAAGGGTCTG
Right flanking sequence: Indices 110790 -- 111289
CGCAAAGGAGGAGCCACAGGAGGAGCCGTCGAGCCAACAGAACCCTGCAGTGGCCAACCCGAACG
CCATCAAGCTGATCTACGGGCAGATTTACTCCAACGTGATGAGTGAGGGCCAGATGCCGGTGCCG
CAGATGTACATGCCCCCTCCCGGGCAGTTCCCGCCGCAGATGATGCCGATGGTGCCTGGAGTCCC
TGTGCCTCCGCAGTTCTACCAGCAGCCTCCTCCGGGCCAGTTCTACCAGCCGTACGGCCAGCCCC
CGCAGCAGCCTCAGCAGCCACAACAGCCGCAACAACCCCACCCTCAGCAGCAGCAGCAGTCCCAG
CAGCGGCCTTCTGAAAACGGCCGTGGCAGAGGTGGTGCTCGCGGGCGCGGTGGTGCTCGGGGACG
TGGCAGCAACCGCGGTCGTGGTGGTCGTCGGGGATCTCCTGCTCCCAAGCCGGCCCCTGCTTCTG
CGCAATGACCGTGTACGATTCTTACATTGTAATTATATTTCACCC
Found at i:127730 original size:31 final size:31
Alignment explanation
Indices: 127668--127730 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
127658 CAACCTCAAT
*
127668 TGAAGACGCACCGTTGAAGGCACCCGCCATC
1 TGAAGACGCACCGTTGAAGGCACCCACCATC
* *
127699 TGAAGAGGCACCGTTGAAGGCACCCATCATC
1 TGAAGACGCACCGTTGAAGGCACCCACCATC
127730 T
1 T
127731 ATCATCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.16
Consensus pattern (31 bp):
TGAAGACGCACCGTTGAAGGCACCCACCATC
Left flanking sequence: Indices 127168 -- 127667
TCAGCTAACAAAACCGCCGATTATCATTTCAGGAGGAAGGTTCTCTGGTAATTATGCTTCTCCTT
CGCCTTAGTGGGGTACATGATTCCCTAAGTCGCATCATGTCGTTAGCCCAGCAAAAGAAAAATGT
GCCAAGAAGCCCATGTCGGCCTATGAAAGCAATCACGTTACGCGTGTCTAGGCAATAGATGCTGA
GAAATCATTTATTGTTTGAACGTTCCCTGAGGTTCTTTGTTGGTATTAGCAGTGCTCATAATGTT
CGAGCGATTTCCACGGTCAGTCATGCAAACACGTGACTTGAAACGTAGATTATTGCGATAAACAA
ACTTGTAGGACGTTGAATGAAGGCATTCTATCGAAGCATTTGAGACTTGGTATGACTTGAAAGTT
CAGTTTGGTGCTGGGTAACGAAATAGTTGTTGTCATGCCCACAGAACAGATGAAAGTATTTCCAT
CTACAACGACTTGCGGGGCGGTCATCAAAGTCAGCCAACCTCAAT
Right flanking sequence: Indices 127731 -- 128230
ATCATCTGTTGACAATTGATCGCGAGATATATGATGGTCAGGAGCCCTGTCACAAGTTTAAATAT
CAGTGTAAACAAAAGATCGACCCTTATGAGTCTGTTACTGAAGGAGATTGAGCGGAAAGAACGCA
TGTTGGCGCAAGTCAAAAGGATGGCAGAAGATACGGAGACCTTCGTGAACGACCTAGACGCTGTC
GGGAGTAGGTTGGACTTGATGGGATCCAGCACAGAACAGATGAACCTTTTACTAGCAAATTGGAA
AATGACCACACGGGCCATGTACCTTGGGAGTGCTGCACAGGGGCGACATACAGAGGCTGATTTTG
AAGCTGGTAGAGCTCTCCCCGAGCAATTGGTGCGAATTCCCTTGGGCACAGAGCAGGAAGTTGGC
GACGACGAAAAAGCCGATGAGGGGTCAGGGGACGCGGTAGGGGACGAGTCGATTGAAGAAACAGC
TAGTAAATTAGCTGAGGTAGGTTAGTCTGAAAGCATTGCAAGTGA
Done.