Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold60
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: 37761
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3418 original size:18 final size:18
Alignment explanation
Indices: 3395--3429 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3385 CTTGGCCAAC
3395 TTCTTGATCAACTTCTTG
1 TTCTTGATCAACTTCTTG
*
3413 TTCTTGTTCAACTTCTT
1 TTCTTGATCAACTTCTT
3430 CAAGTCCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.23, G:0.09, T:0.54
Consensus pattern (18 bp):
TTCTTGATCAACTTCTTG
Left flanking sequence: Indices 2895 -- 3394
TGAGTATCTACCGCATTTATATTAGTTTTCACCTTTTATTTGGCTTCTCACTTCCCCTCATCTCC
ACCCTCTTTGATCTCCGCGTGAAAATTTTTCTACAGTGTATCCGTGATTAATGACGTTCCTATTA
TTATACAAATTAACCGAAAATCTAGTAGATCTTCTGGGGGGGACCCATGGTCGACTTGATAACGA
AACCGCCAACGTTCTGCCAGTTCTTCTTCAACAAAGAAACCAAGAAGTTAGCGGCCATCAAGACC
TGGTTGACGATAATGTCCTCCTCCATCTCAACGTGACCAACGGCAACAGACATACACAAGACCTT
CTTCAACTGGAACTTGATGGTGGACTTGACGTCCTGGACCTTACCGTACAAGTCGTCGTTGTGAG
ACACGGGGGTGGGGAACTTACCAGCCTTGGACAAACCAGGACCCAACAAACGGGGGATCTGCTTA
ATCAAGACCTCGGAAGCGACGAAGGCGTTGTACTTCTTGGCCAAC
Right flanking sequence: Indices 3430 -- 3929
CAAGTCCTCAACCGACATGGCGTCAATACCAATAGACTTGGCACGGTCAACGTCGAAAGCGTCAC
CGAACAAGCAGATAGACATGTTGGGACGGGGGACCTCGGGGAGTCTCAACGAACCAGCGAAACGC
TTGTCTCTCTGGGGGTCGTAGTTCTTCAACGAAGCCTGCAACTCGATGGACTCGAGAAAGTTTCT
AGGCTTGGTCTCCTTAGAGTACTTGATGATCTCTTGGACCTTGGCGCGAACCTCGGAGCTGGGCA
ATTTCGACATGTTACTTGTCTTCCAATGTAAAAACTTTGGTAAAGAGGTACCCCTTCCCGCACGA
TTTTTTTTTCACCGGGCGTCTGCGCCATCGGAGCAGACTGCAGACAATGCTAGGGTTAACAACCC
TAATCACGTGAGTGACAAAACGGGTAATATTCACGGGGTAAGGGGGTCCAATGGCTAAAATAAGT
GGTGGAAACGTCAAATTTAGAGGAACGTAGCAGCTAGTGGCGTAT
Found at i:5830 original size:17 final size:16
Alignment explanation
Indices: 5808--5840 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5798 CAAAACACGA
5808 CTCACCACTAGCTCAT
1 CTCACCACTAGCTCAT
5824 NCTCACCACTAGCTCAT
1 -CTCACCACTAGCTCAT
5841 GAGCGAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.42, G:0.06, T:0.24
Consensus pattern (16 bp):
CTCACCACTAGCTCAT
Left flanking sequence: Indices 5308 -- 5807
GAGCGGGGGATCAATCCCGGCCATTGTCATCCATAAACCAAGCCGAAGAGCCGATGGCTCGTACC
GGTAGACTAGCCAACCAAATCCGATGAGTAATGCAGCACACTAAACCAGTAGAAACGTACTCCCC
TCAATCATGAATGCGCAAGGACTACCGACACTCGAAACCGACCCCCAACCACCTTCCTCGGCTTC
AGGTCACGAGCGACGGTGCCGCCTACACGTGGCTCGTTATCCCCTCTCTACGTCACCTCTTTCAT
GTCGTCTCGGCTGTTGACTACCTCTCCGGGCTCGCTTCTTATCTCTCAGGGCACACAACCCCGAT
ACCCACCGCCGGACCAATTGGCTCGCTCCACACCCACCCAATCGCTACACAACTCCACAACTAAC
TTCCGATAAGACCCCACTACACCCCCCGACCACCTAAAAACCCCTTTCCCTTCCCCTTACCCGAC
CCCACCGGCCCCCTTCTCTTCGCTACGCGATCAAACAAAACACGA
Right flanking sequence: Indices 5841 -- 6340
GAGCGAGCCGGCCCCGTACAACAACTCCGACGATGAGGACGGGCCCACCCAGATGGCCGACGACT
TTGTGTCGTTCCCCACCATCCCCGATCCCGAGCAAGAACAGCGGGGCACCTTCAAACGCATCTTC
ACCAACACCATCCGCAAGGTCACCACCAATGCCACCAACTTAGTGCCCAACTACAGCCCGCGCGC
GGATTACGAGCCAAAGGTCGACTCGATAGACCTCGAAGAAGACGAGGACGAGGGCCCTGTGGTTG
CTGCGCCACCTCCAGCGCCCCTGCCGCCTCCTCCGGCGTCTCTGCCCGTTCCACCCGAACCACTG
CCACCAGCGACGCTACCGCCTGCGCCACCGGCCCCGGCACCGCTGCCAGTGGCCCACAGCGTGGC
TGCAACCTCAACCAACGACGACGACAGCATTGTCGACCCCGGACGGGTCGCGGCAGACAACCGGA
GTTTGCGGTTGCTCTCGCACCACCAGCCCATGACCAGGCCCACCA
Found at i:30035 original size:11 final size:11
Alignment explanation
Indices: 30019--30061 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
30009 TCCGGTATGA
*
30019 TGACTCCCATT
1 TGACTCCCACT
30030 TGACTCCCACT
1 TGACTCCCACT
30041 TGACTCCCACT
1 TGACTCCCACT
30052 TGACTCCCAC
1 TGACTCCCAC
30062 CTGCGTCCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.19, C:0.44, G:0.09, T:0.28
Consensus pattern (11 bp):
TGACTCCCACT
Left flanking sequence: Indices 29519 -- 30018
TATCAATTTACAACCTCGGCGACTTCCGAGTCGGCACCCTTACACCAAGTTAAAATTCACACATG
ATTGCAGGAGCTGGATAGAATACGACGGTTGTAGGGTGTTGCCTCTAGGTGCGAGCTCTAGAGAC
ACCGCCTCCTAGATTGTCGATGGCACGACGCGTACCAGGGTGCACCTATCAGCATATTGCCAAGA
TTCCCAGAGACTTTAAGCTCGCCTAATCGCCCCGAATAGAACATTTCTTTCTCATTTGTGGGGTA
TAACCTTTGAGGGACGCCTTAGACCAAAGCCCTGACGCGTATTGCATGATCCCGAAAGCCTCGAG
GCAACGAGCACCTGAGACAACGAACACCTCATGCAAACACTAAACCCCGCCGTATTCCGTGGGCC
CTTCTTTGAAATGTTGTCTACGTTATGATTCCGTAAAGATCCTTAGTCTTGAAAGCAAGGTAATG
CCGCGTTTCGCAAGACAATAATTCTCCGAGACATATCCGGTATGA
Right flanking sequence: Indices 30062 -- 30561
CTGCGTCCGAACAAAGATCCAGGCGGTCGTCATCGCTTACGGCTTCTCCGGGAGCACATTCAGAC
ACTCGCAATTATCCGTGGGAACCTAAATGGGGCGATTCCTCCACTCCGTAGTGGAAATAATTACG
ATGTCAATACCATCGTGTTGGTATTATTGACTCAAAATCAGTCGATTCGTCAGTCAAATTGAGAT
TTGACGGGATCGCCCCACTATTTAAACGTTCGGCTGTAGTCTAGATCGGTCCCCGGGTCATCAGC
CACCCTGGCATTAGCTGTTTCGCTAGAAGTTGTTGCTTTTTCTTGGATCTACACGTAGCGAATAC
GGTGGAAAAACGCCTAAATTACCCGTTTGGGATGAGCGCAACGGTTGCCACTAAAAATAAACGGC
TGTATAGAGTCCGCGCTGGCTGTATAGAGTCCGGACTATTTGTATAGAGTCCGCACTGAGCTGTA
TAGAGTCCGTGTCGGGCACCGCCTCCGCCCATATCCGGACGGGCG
Found at i:30474 original size:20 final size:20
Alignment explanation
Indices: 30449--30525 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
30439 AAAAATAAAC
30449 GGCTGTATAGAGTCCGCGCT
1 GGCTGTATAGAGTCCGCGCT
30469 GGCTGTATAGAGTCCG-GACT
1 GGCTGTATAGAGTCCGCG-CT
*** *
30489 ATTTGTATAGAGTCCGCACT
1 GGCTGTATAGAGTCCGCGCT
30509 GAGCTGTATAGAGTCCG
1 G-GCTGTATAGAGTCCG
30526 TGTCGGGCAC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 33 0.70
21 13 0.28
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (20 bp):
GGCTGTATAGAGTCCGCGCT
Left flanking sequence: Indices 29949 -- 30448
CCTTAGTCTTGAAAGCAAGGTAATGCCGCGTTTCGCAAGACAATAATTCTCCGAGACATATCCGG
TATGATGACTCCCATTTGACTCCCACTTGACTCCCACTTGACTCCCACCTGCGTCCGAACAAAGA
TCCAGGCGGTCGTCATCGCTTACGGCTTCTCCGGGAGCACATTCAGACACTCGCAATTATCCGTG
GGAACCTAAATGGGGCGATTCCTCCACTCCGTAGTGGAAATAATTACGATGTCAATACCATCGTG
TTGGTATTATTGACTCAAAATCAGTCGATTCGTCAGTCAAATTGAGATTTGACGGGATCGCCCCA
CTATTTAAACGTTCGGCTGTAGTCTAGATCGGTCCCCGGGTCATCAGCCACCCTGGCATTAGCTG
TTTCGCTAGAAGTTGTTGCTTTTTCTTGGATCTACACGTAGCGAATACGGTGGAAAAACGCCTAA
ATTACCCGTTTGGGATGAGCGCAACGGTTGCCACTAAAAATAAAC
Right flanking sequence: Indices 30526 -- 31025
TGTCGGGCACCGCCTCCGCCCATATCCGGACGGGCGGTCCGATGTATGGCTTATTCGGGGGTGCG
TTTCCACCCACCTGAAACTCACTGACCTCTAGCTATAGTGATTTTCGAGCTAAAGGGGGTCAAAC
CGGCTTGAATGAAAGCCACTCGCAACACTGGCTCACCCTAGCTTTCCCCGCTGCCCTCCACCTTC
TGTTGCTCTCTCATTACTAATTCATTTTGACTCTAGGTGAAAATTTTCCCGGGCATCGAATATTA
TTTATGCACCCTGCCACCATTGCGGGATTGGTTTTCCTACGGCTGAAGCGATGGCTGCTGTTTGA
AACGCTCTAGCGACACCGGGCAAACGCTTCGTTGATGGGAAAGGTCTCCCGCAACTACCTTCCCA
GTTTCAACTCGTTACTCTCGGCGGTTTTTCTTGGATTTGAATGTTCCCCCCCTCGCTAGCATTTC
TTTTGTCGTATATAGACTGAGATCGGGACCGGCGCAGGGATAGAC
Done.