Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: C10589
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: 5540
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Found at i:1665 original size:22 final size:22
Alignment explanation
Indices: 1635--1678 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1625 GAGCTCGGCA
1635 TGCTGGTGCCGGTGGTGGTGAT
1 TGCTGGTGCCGGTGGTGGTGAT
* *
1657 TGCTTGTGCGGGTGGTGGTGAT
1 TGCTGGTGCCGGTGGTGGTGAT
1679 GCCGAGGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.05, C:0.11, G:0.50, T:0.34
Consensus pattern (22 bp):
TGCTGGTGCCGGTGGTGGTGAT
Left flanking sequence: Indices 1135 -- 1634
CCATACTTTTTGAAGGTCGTCGAGCGCGGTGTCGGTGTGATGTTGCCGCTGGTGTTTGTCACCTG
TACGCTGGACGACACTCTGGGCGCGATCATGATTGAGGACGAGCTGGGCTGCGTCATGTACGGCT
ACGAGGTGTTGGGCGCAGAGCAGTTGGTGAATGGGTGCACTGTCGCTGTGCATGGAGTAGCGGGG
AAGTGGGGTTTTGAGGTGTTGGAAGTGGTCCATCCACAGCCTATAGCGCTGAGGACCTGGAAGGC
GATTGCCGACGGCGATACCGCCAGCATTCTCCGCCTCGAAGTCTTGAAACAGTACGTGTTGGGTG
AGACCGGCGACCCGCACCGGACATGGCTTATCGCCGAAGTGGTGGTGGGCGACCTGATCGCCGCC
AAACACGAAGTGGTTACCGACTCATTCCTGTCTTCCAACAACAACGGTCTGAAAATACCCTGAAG
TTCTCGCCCACATCACTGGCCAAGTTCGACGCCTGGAGCTCGGCA
Right flanking sequence: Indices 1679 -- 2178
GCCGAGGACCCTTGATCCTGCAGTAATCTGCTGGCCCCAGGCGCTGTTGCACCGGTCAGTGATGT
CCCGTGCCGCCAGGCTGCAGGGATTCACCCGGTTGACCAACCCCCAGTATTTGCATGTGTCCACT
AACATCTCTCCTCAGCGGATGTTGCTCAGTTCTGGGCATAACATGGCGGACATGTAGATTCATAG
TTTCTAGGCTTTTATAAGGATAATATACATACTCCATTACACGAAGACGATGGCGGAGAGTACTG
TGATGGCCACGGAGTGCGTGGCCCAGTTCAGAGGCAACCGACCGGTTGGTGGGTACATGTGTCGG
CCGCCGCCTTAGCGCCCAGCGTTAGGAGGGGCAGTGCACAACGCCCTCAAGCCCCAGCTGTAGTG
GCTGGTCTACGACGCGGGCGCCGGCGATAGCGCCCAGGAACCGGGCAGGCACGCTGACAGTGTCG
TCCTTGACATGCCAAAATAAGGAAATGTCGTCGGAGAAGGGTGAC
Found at i:3342 original size:30 final size:30
Alignment explanation
Indices: 3306--3364 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3296 GGATCGCTTG
*
3306 GACCGAATTGATGCTAGGTTAGAGAAATTA
1 GACCGAATCGATGCTAGGTTAGAGAAATTA
3336 GACCGAATCGATGCTAGGTTAGAGAAATT
1 GACCGAATCGATGCTAGGTTAGAGAAATT
3365 GGAACGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (30 bp):
GACCGAATCGATGCTAGGTTAGAGAAATTA
Left flanking sequence: Indices 2806 -- 3305
TCGGCTCATCAAACAGCCCGGGATCCATTACCCTCGCAATGACGTAGGCGTACGTAGGCGTACCC
GTCCGCTTACGGATTTTTGTGCCCGCAACATCAGGGAGAAAACGCAGGTACAGCCGGGGGAATCC
GGCGCATATAATAATAGCGTCCACCACGTCTGGGAAAAGAACGAGCGATTTAGGGTTTCGTTCGC
TCCAATATATCTGGTTATACATCTAACCAAGTACGGTAACCATCTAACCACGAGGTAGTTATCGA
CATCAGACCACAATAGGTTATACAAAACCACATTCCTGCATATTTTTGGAGTATATCACCCAATT
CCATAACCGTATTCCGTACTTTCGAACTGAAAAAACATATTCCATGGCTGAGAACGACAAGAAAT
TCACCAACGGTGCCGTTGCCCCCTTCGCTACTGACCCTGAAGTCGGGTCGCGACATGATGAGGCG
GAAATTTCTCTCAACTCCTTTATGGTCAAGATTGTGGATCGCTTG
Right flanking sequence: Indices 3365 -- 3864
GGAACGAAATTACGCGCGCTTGGGTAACCTTGAGCAGCATTTCGCCAACCTTTTCACTTATAGTA
GTACCCCAGTATTCCTGGACTATACCCCTTCCGAGGATTCTGTCGACGACTCTGATTTGCCCACA
CCAGTATTCCTGGACTACACCCCCTCCGAGGATTCTGTCGACGACTCTTGTTTGTCCACACCTTC
CTCTGCCAATGCCTCGGCTCTGCATGTGCCGACGGACACTGCACCTGACACGACTGGCCCCAAAC
GATCCAAAGAAGACTTTGGTCACAATGAGAACCCTTTTGCTGGTAGGCTCCCCGATGATCTCATC
GACCGCTCTGTTCCTGAATTGATCGACTGGATTGATTCCTGTACTGACCTTGTTCGTGAAGCTGA
GATCAACAATACCGAGGCGAAACTCAAGTACCAACTTAACGCGTCTTTTGCCCCGTACGTGAGAC
GCCACAACCCCCACGTGAAATTTGACCCCAACCTTCGTGTGAGTG
Found at i:3528 original size:60 final size:60
Alignment explanation
Indices: 3435--3556 Score: 201
Period size: 60 Copynumber: 2.0 Consensus size: 60
3425 TAGTAGTACC
* *
3435 CCAGTATTCCTGGACTATACCCCTTCCGAGGATTCTGTCGACGACTC-TGATTTGCCCACA
1 CCAGTATTCCTGGACTACACCCCCTCCGAGGATTCTGTCGACGACTCTTG-TTTGCCCACA
*
3495 CCAGTATTCCTGGACTACACCCCCTCCGAGGATTCTGTCGACGACTCTTGTTTGTCCACA
1 CCAGTATTCCTGGACTACACCCCCTCCGAGGATTCTGTCGACGACTCTTGTTTGCCCACA
3555 CC
1 CC
3557 TTCCTCTGCC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 56 0.97
61 2 0.03
ACGTcount: A:0.19, C:0.35, G:0.18, T:0.28
Consensus pattern (60 bp):
CCAGTATTCCTGGACTACACCCCCTCCGAGGATTCTGTCGACGACTCTTGTTTGCCCACA
Left flanking sequence: Indices 2935 -- 3434
CGGCGCATATAATAATAGCGTCCACCACGTCTGGGAAAAGAACGAGCGATTTAGGGTTTCGTTCG
CTCCAATATATCTGGTTATACATCTAACCAAGTACGGTAACCATCTAACCACGAGGTAGTTATCG
ACATCAGACCACAATAGGTTATACAAAACCACATTCCTGCATATTTTTGGAGTATATCACCCAAT
TCCATAACCGTATTCCGTACTTTCGAACTGAAAAAACATATTCCATGGCTGAGAACGACAAGAAA
TTCACCAACGGTGCCGTTGCCCCCTTCGCTACTGACCCTGAAGTCGGGTCGCGACATGATGAGGC
GGAAATTTCTCTCAACTCCTTTATGGTCAAGATTGTGGATCGCTTGGACCGAATTGATGCTAGGT
TAGAGAAATTAGACCGAATCGATGCTAGGTTAGAGAAATTGGAACGAAATTACGCGCGCTTGGGT
AACCTTGAGCAGCATTTCGCCAACCTTTTCACTTATAGTAGTACC
Right flanking sequence: Indices 3557 -- 4056
TTCCTCTGCCAATGCCTCGGCTCTGCATGTGCCGACGGACACTGCACCTGACACGACTGGCCCCA
AACGATCCAAAGAAGACTTTGGTCACAATGAGAACCCTTTTGCTGGTAGGCTCCCCGATGATCTC
ATCGACCGCTCTGTTCCTGAATTGATCGACTGGATTGATTCCTGTACTGACCTTGTTCGTGAAGC
TGAGATCAACAATACCGAGGCGAAACTCAAGTACCAACTTAACGCGTCTTTTGCCCCGTACGTGA
GACGCCACAACCCCCACGTGAAATTTGACCCCAACCTTCGTGTGAGTGAATATTTTGCTCAAGCC
CGGCTTGCCTTGATGGATTCCCCCAAAATGTTCAACCACTACATTACCGCGATTGGAGTGAGACC
TCTCCAGCAGGCCATGCTATACAACCATACTTGGTTCAACGACTTCTCAATCACTCTCACCAAGC
TTCTGGACGACATTCGTTACATGAGCCCCACAAAGGTCCATGCCA
Found at i:4260 original size:15 final size:15
Alignment explanation
Indices: 4240--4293 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
4230 AATCTCCCGC
4240 TATAGCAACAACTCG
1 TATAGCAACAACTCG
4255 TATAGCAACAACTCG
1 TATAGCAACAACTCG
*
4270 TATGGCAACAACTCG
1 TATAGCAACAACTCG
*
4285 TATGGCAAC
1 TATAGCAAC
4294 TGGCAATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (15 bp):
TATAGCAACAACTCG
Left flanking sequence: Indices 3740 -- 4239
TGTTCGTGAAGCTGAGATCAACAATACCGAGGCGAAACTCAAGTACCAACTTAACGCGTCTTTTG
CCCCGTACGTGAGACGCCACAACCCCCACGTGAAATTTGACCCCAACCTTCGTGTGAGTGAATAT
TTTGCTCAAGCCCGGCTTGCCTTGATGGATTCCCCCAAAATGTTCAACCACTACATTACCGCGAT
TGGAGTGAGACCTCTCCAGCAGGCCATGCTATACAACCATACTTGGTTCAACGACTTCTCAATCA
CTCTCACCAAGCTTCTGGACGACATTCGTTACATGAGCCCCACAAAGGTCCATGCCATTGGTACT
ACTCTCTTTGCTTACCGACTTTCACTTTCCATGGATCTTAAGCTTGAACTTTACCCGGCTATTTC
TTTCTTCAGTGACTGTAACATGCAAACACAAGAGACCGTCAGTGCTCGCGCCCCGATCATGATCA
TGTCAGTCGTTAACGCCGTATCCACTATCCGGAACAATCTCCCGC
Right flanking sequence: Indices 4294 -- 4793
TGGCAATGAATTCTCTGGCACCGGGAATTGTTTTCACAATTGTGGCTCCAGACCACCCACAAGTC
CAAATAAGCGTGGAGGATTCAACTAACTGAGCGAAACACGAACTTACCCTTAGAAAATATGCAGA
ACGCCTTTTAATGACGAGACACAGCGCGCAATACCTAGCTACAGGTAAGTTTAGCGACGAACTCT
TCGCTCTAAACCTATTTGCCTACTATAATATTGCTGCTGATTTCCTAATTGCCCTGACAGATACT
ATTTTGACTGATTTTACCCCGAAACCACAGCACTATGATGCCACCAACGGCACACCAATACTCGC
GACGGGCTAAAGCACTTTTACCATCTGTGACACTAAGGGCCACAAGGCTCATTTCGAGACTGCTC
TTGTTTCCCACACACCTGGATATCTGAGTGCTATATACCCCGCTGATTGAGGCATGTTTGCTTCA
CCAAGGCAATGTAACCAAGGCAGAACCGACTCCACCACATGCCCC
Done.