Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold40
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: 6026
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Found at i:2184 original size:27 final size:27
Alignment explanation
Indices: 2123--2185 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2113 CACCACGCTA
* **
2123 GACGACGCAGTGGGGCGCGATCATGGTC
1 GACGACG-AGTGGGCCGCGATCATGCAC
*
2151 GAGGACGAGCTGGGCCGCG-TCATGCAC
1 GACGACGAG-TGGGCCGCGATCATGCAC
2178 GACGACGA
1 GACGACGA
2186 CGTGTTGGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.21, C:0.27, G:0.41, T:0.11
Consensus pattern (27 bp):
GACGACGAGTGGGCCGCGATCATGCAC
Left flanking sequence: Indices 1623 -- 2122
CATAGCAGCGGGAGCTGTTGGTGTTTCTTGTTGCTGGGTTGCTCATAGAAGGGTGGCAGAGATTC
ACCCTGTCGCAGGTGTGGGAGCTCAAGGGATTGTTCATGACCTTCGGGCTTCTTGTTACCTCAGG
TTGTCCGCATCGTGATGATGTATTGTGAGTTCTGCTTGCTCAAAGTGGCCCAGGTGTTGACGCTT
CTGATAGTGGGGCTTTCCGAGGAAGTGTTGTCAATCGTGGTGATGGCGTTGGAGCTTGGCCATTG
GATGAGCGGATCCGAAATTGCCTGGTTATTTGACGTTGACGAACGTTGCCTGGTACAACATCTTC
CGCCACGGATGCCGAGGAGCCACGACGTTGGCGTTTGTTGACGACGAGCTGAGGCCGAGCGAAGA
CTAAGCTCCACATCATGTCAATATGCGGCGCATGTCAGCTGCCGAACCTTTTGGAGGTCGTCGAG
TACGGCGTTGCTGTGGTGTTGCCGCTGGTGCCTGCCACCACGCTA
Right flanking sequence: Indices 2186 -- 2685
CGTGTTGGGCGCGGAGCAGTTGGTGACGGGGTGCACCGCCGTTGTGCTTGGATTAGCGGGGACTC
AGGGGTTTTGAGTTGTTGGACGTGGACCATCCGTAGCAGATAGCGCTAGAGGACCCGGTAGGCGA
TTGCCGACGGCGATACCGCTAGCGACCTCCGTCTCAAACTCTTGAAACAGTACGTGTTGGGCGAG
ACTGGCGACCCGCACCTGGCATGGCTAACCGCCGAGGTGGTGGTGGGCGACCTGATCGCCGCCAA
ACACGAAGTGGTCACCTACTCATTCCTCTCTTCCAACAACAACGGTCTGAAAACACCCTGAAGAT
CTCGCCCGCGTCCCTGGCCAAGTTCGACGCCTGGGTACTGGAGCTATGCATGCTGGTGCCGGTGG
TGGTGATGCCGAGGACCCTTGATCCTTCAATGGTCTACTGGACCCAGGCGCTGTTGCACCGGTCA
GTAATGCCCCGTGCCGCCAGGCGGCAAGGTTTCACCCGGTTGACT
Found at i:4008 original size:5 final size:5
Alignment explanation
Indices: 3995--4052 Score: 73
Period size: 5 Copynumber: 11.6 Consensus size: 5
3985 ACTCAACTTC
* * *
3995 CTCCA CTCCC CTCCC CTCCA CTCCA CTCCC CTCCA CTCCA CTCCA CTACC-
1 CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CT-CCA
4045 CTCCA CTC
1 CTCCA CTC
4053 TCCTTCTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
4 2 0.04
5 43 0.91
6 2 0.04
ACGTcount: A:0.14, C:0.66, G:0.00, T:0.21
Consensus pattern (5 bp):
CTCCA
Left flanking sequence: Indices 3495 -- 3994
GTGGGGTGAAACGTAAACCCCAGCTGCATGTCAAGCATTATCGAGACCGTTTTGGGGTTTTTGGC
GGTGCTAGTTAGCCCGAGCTTGGCGCCGGTCATTTTGTTGTGGACTATGGTATCGTCAAGCACCA
CGATGGGGAAACTAAGGTTGCCCACTAACGAGTTACCTTCGCTTTCGTCAACGGGACACCGGTAG
CCCTTATAGTTCACCATATAAAAACCGAAAATGGCTCTTCAAACAGCCTGTATCGATGAGGTAGC
CGTGCTTGTCGCCGGTTACGTTATTTCATGCCCGCTACGTCAGCGAGAACCAACGCAGGTACAGC
AGAGGATCTGGCGCATACGATGATAGCAACCGTCCACCATGTCTGGGAAGAGAACGAGCAGTTTA
GGGTTTTATCAGCTTCCATATACCACCAAAATCAAAGCCATATTTTTACGAGTAGATACGATGCC
ATCTTTTTGTAGATACGAATGCTTTCCACATTAGGACTCAACTTC
Right flanking sequence: Indices 4053 -- 4552
TCCTTCTCCTCCGTTCCATATTCCCCTAACTACACACCACCTCTCCGCCGCTCAAATCAAATGAG
ATGCTCGGGCCATGGCCCAATCCCCTTCTTCTCCATATTAGTAATAAACCAGTCGTTTACGAACG
ACACCAACAGAAGCACAAACATGTTGCGCTCGTTGATCCGGTTGTAATCGTGCTGGGTGACAATC
CCCTCCTCCTTGGCCGCCTTGGGCGTCTGGTGCCGTGGCCAAACTCCGCGTACACCAAGTCCTCA
ATCCCGTGCATCAGGTCGTAGCGAATGTCCTCCCGCTCAATGCCAAGGAACCGGTTGCCGATCAG
CCGCTAGTACTTGAAGTAGCGGTAGATCTACCCGCCAAGGATGGTGGTCTTTTTGTTGAACGACG
CCGTCAGCGCCTTGGAGGAGGTTCTCACCTCCTTGAAAACGTTTCTCGTGCTCTGCACCAACTCG
TGGTGCTGGCGGTTGGTGCGGAGGTGGTCTGGGTAGATGTGCTTG
Found at i:4014 original size:15 final size:15
Alignment explanation
Indices: 3994--4052 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
3984 GACTCAACTT
*
3994 CCTCCACTCCCCTCC
1 CCTCCACTCCACTCC
4009 CCTCCACTCCACTCC
1 CCTCCACTCCACTCC
4024 CCTCCACTCCACTCC
1 CCTCCACTCCACTCC
*
4039 ACTACC-CTCCACTC
1 CCT-CCACTCCACTC
4053 TCCTTCTCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
15 39 0.95
16 2 0.05
ACGTcount: A:0.14, C:0.66, G:0.00, T:0.20
Consensus pattern (15 bp):
CCTCCACTCCACTCC
Left flanking sequence: Indices 3494 -- 3993
GGTGGGGTGAAACGTAAACCCCAGCTGCATGTCAAGCATTATCGAGACCGTTTTGGGGTTTTTGG
CGGTGCTAGTTAGCCCGAGCTTGGCGCCGGTCATTTTGTTGTGGACTATGGTATCGTCAAGCACC
ACGATGGGGAAACTAAGGTTGCCCACTAACGAGTTACCTTCGCTTTCGTCAACGGGACACCGGTA
GCCCTTATAGTTCACCATATAAAAACCGAAAATGGCTCTTCAAACAGCCTGTATCGATGAGGTAG
CCGTGCTTGTCGCCGGTTACGTTATTTCATGCCCGCTACGTCAGCGAGAACCAACGCAGGTACAG
CAGAGGATCTGGCGCATACGATGATAGCAACCGTCCACCATGTCTGGGAAGAGAACGAGCAGTTT
AGGGTTTTATCAGCTTCCATATACCACCAAAATCAAAGCCATATTTTTACGAGTAGATACGATGC
CATCTTTTTGTAGATACGAATGCTTTCCACATTAGGACTCAACTT
Right flanking sequence: Indices 4053 -- 4552
TCCTTCTCCTCCGTTCCATATTCCCCTAACTACACACCACCTCTCCGCCGCTCAAATCAAATGAG
ATGCTCGGGCCATGGCCCAATCCCCTTCTTCTCCATATTAGTAATAAACCAGTCGTTTACGAACG
ACACCAACAGAAGCACAAACATGTTGCGCTCGTTGATCCGGTTGTAATCGTGCTGGGTGACAATC
CCCTCCTCCTTGGCCGCCTTGGGCGTCTGGTGCCGTGGCCAAACTCCGCGTACACCAAGTCCTCA
ATCCCGTGCATCAGGTCGTAGCGAATGTCCTCCCGCTCAATGCCAAGGAACCGGTTGCCGATCAG
CCGCTAGTACTTGAAGTAGCGGTAGATCTACCCGCCAAGGATGGTGGTCTTTTTGTTGAACGACG
CCGTCAGCGCCTTGGAGGAGGTTCTCACCTCCTTGAAAACGTTTCTCGTGCTCTGCACCAACTCG
TGGTGCTGGCGGTTGGTGCGGAGGTGGTCTGGGTAGATGTGCTTG
Found at i:4020 original size:20 final size:20
Alignment explanation
Indices: 3995--4052 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3985 ACTCAACTTC
*
3995 CTCCACTCCCCTCCCCTCCA
1 CTCCACTCCCCTCCACTCCA
4015 CTCCACTCCCCTCCACTCCA
1 CTCCACTCCCCTCCACTCCA
*
4035 CTCCACTACCCTCCACTC
1 CTCCACTCCCCTCCACTC
4053 TCCTTCTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.14, C:0.66, G:0.00, T:0.21
Consensus pattern (20 bp):
CTCCACTCCCCTCCACTCCA
Left flanking sequence: Indices 3495 -- 3994
GTGGGGTGAAACGTAAACCCCAGCTGCATGTCAAGCATTATCGAGACCGTTTTGGGGTTTTTGGC
GGTGCTAGTTAGCCCGAGCTTGGCGCCGGTCATTTTGTTGTGGACTATGGTATCGTCAAGCACCA
CGATGGGGAAACTAAGGTTGCCCACTAACGAGTTACCTTCGCTTTCGTCAACGGGACACCGGTAG
CCCTTATAGTTCACCATATAAAAACCGAAAATGGCTCTTCAAACAGCCTGTATCGATGAGGTAGC
CGTGCTTGTCGCCGGTTACGTTATTTCATGCCCGCTACGTCAGCGAGAACCAACGCAGGTACAGC
AGAGGATCTGGCGCATACGATGATAGCAACCGTCCACCATGTCTGGGAAGAGAACGAGCAGTTTA
GGGTTTTATCAGCTTCCATATACCACCAAAATCAAAGCCATATTTTTACGAGTAGATACGATGCC
ATCTTTTTGTAGATACGAATGCTTTCCACATTAGGACTCAACTTC
Right flanking sequence: Indices 4053 -- 4552
TCCTTCTCCTCCGTTCCATATTCCCCTAACTACACACCACCTCTCCGCCGCTCAAATCAAATGAG
ATGCTCGGGCCATGGCCCAATCCCCTTCTTCTCCATATTAGTAATAAACCAGTCGTTTACGAACG
ACACCAACAGAAGCACAAACATGTTGCGCTCGTTGATCCGGTTGTAATCGTGCTGGGTGACAATC
CCCTCCTCCTTGGCCGCCTTGGGCGTCTGGTGCCGTGGCCAAACTCCGCGTACACCAAGTCCTCA
ATCCCGTGCATCAGGTCGTAGCGAATGTCCTCCCGCTCAATGCCAAGGAACCGGTTGCCGATCAG
CCGCTAGTACTTGAAGTAGCGGTAGATCTACCCGCCAAGGATGGTGGTCTTTTTGTTGAACGACG
CCGTCAGCGCCTTGGAGGAGGTTCTCACCTCCTTGAAAACGTTTCTCGTGCTCTGCACCAACTCG
TGGTGCTGGCGGTTGGTGCGGAGGTGGTCTGGGTAGATGTGCTTG
Done.