Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1064
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3046
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:831 original size:186 final size:186
Alignment explanation
Indices: 508--1020 Score: 866
Period size: 186 Copynumber: 2.8 Consensus size: 186
498 GATTTTGCGT
* * * * ** * *
508 TTTAAAATGACACCTTTTCTGCCTCTAAAGAGAAATGAGAGTTGTTTTAAAGCTTAAGCCAGGTA
1 TTTAATATCACACCTTTTCGGTCTCTGGAGAGAAATGTGAGTTGTTTTAAAGCTTAATCCAGGTA
573 ATTTAGGATTGTTGAAGTCAGAGGGAGCTCACACAAATGATGGGAGACGGCTCAGAATTTTTTTA
66 ATTTAGGATTGTTGAAGTCAGAGGGAGCTCACACAAATGATGGGAGACGGCTCAGAATTTTTTTA
638 TTGCTGGATCAGTTTCAGGGAGGTCTTGAAATTTTACGCATTTTGATGGATCGAGA
131 TTGCTGGATCAGTTTCAGGGAGGTCTTGAAATTTTACGCATTTTGATGGATCGAGA
694 TTTAATATCACACCTTTTCGGTCTCTGGAGAGAAATGTGAGTTGTTTTAAAGCTTAATCCAGGTA
1 TTTAATATCACACCTTTTCGGTCTCTGGAGAGAAATGTGAGTTGTTTTAAAGCTTAATCCAGGTA
759 ATTTAGGATTGTTGAAGTCAGAGGGAGCTCACACAAATGATGGGAGACGGCTCAGAATTTTTTTA
66 ATTTAGGATTGTTGAAGTCAGAGGGAGCTCACACAAATGATGGGAGACGGCTCAGAATTTTTTTA
824 TTGCTGGATCAGTTTCAGGGAGGTCTTGAAATTTTACGCATTTTGATGGATCGAGA
131 TTGCTGGATCAGTTTCAGGGAGGTCTTGAAATTTTACGCATTTTGATGGATCGAGA
*
880 TTTAATATCACACCTTTTCGGTCTCTGGAGAGAAATGTGAGTTGTTTTAAAGCTTAATCCATGT-
1 TTTAATATCACACCTTTTCGGTCTCTGGAGAGAAATGTGAGTTGTTTTAAAGCTTAATCCAGGTA
* * * * * *
944 ATTTCAGGATTGGTGAAGTCAGAGGAAGCTCAAATAAATGATGGGAGACGGCTAAGAAATTTTTT
66 ATTT-AGGATTGTTGAAGTCAGAGGGAGCTCACACAAATGATGGGAGACGGCTCAGAATTTTTTT
*
1009 ATTACTGGATCA
130 ATTGCTGGATCA
1021 CTTGTAGGCC
Statistics
Matches: 310, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
185 4 0.01
186 306 0.99
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (186 bp):
TTTAATATCACACCTTTTCGGTCTCTGGAGAGAAATGTGAGTTGTTTTAAAGCTTAATCCAGGTA
ATTTAGGATTGTTGAAGTCAGAGGGAGCTCACACAAATGATGGGAGACGGCTCAGAATTTTTTTA
TTGCTGGATCAGTTTCAGGGAGGTCTTGAAATTTTACGCATTTTGATGGATCGAGA
Found at i:1625 original size:185 final size:183
Alignment explanation
Indices: 1245--1730 Score: 514
Period size: 185 Copynumber: 2.6 Consensus size: 183
1235 CAAACGTTTT
* ** * *
1245 ATCAAAACTAAAACTCTAATAACTCTTAAAATAATCGTTCCCAAAGTGTCAGAGATGATTCTCCA
1 ATCAAAACTGAAACTCTAATAACT-TTAAAATAATCGTTCCTGAAGTGTCAGAGATGTTTCTCTA
* * * * * **
1310 GCTAGTACTGACTGTAAAATATACTTATTAACCGTTGAATCCGATTGCAAGAGCCAAAGACTTTT
65 GCTAGTACTAACTGTAAAATATACTTATTGACCGTTGAAACCG-TTTCAAAAGCCAAAGACGATT
* * * * * *
1375 TTTAAGAATTAATTTTTTACGTCAAGTTGAGAGAATTGCAAATTTTACGTGATTC
129 TTTAAGAACTAATTTTTTACGTCAAGTGGAGAGAAATGCAAAATTTAAGAGATTC
* *
1430 ATCGAAACTGAAACTCTAATAACTTTCAAAATAATCGTTCCTGAAGTGTCAGAGATGTTTCTCTG
1 ATCAAAACTGAAACTCTAATAACTTT-AAAATAATCGTTCCTGAAGTGTCAGAGATGTTTCTCTA
* * * *
1495 GCTAGTACTAACAT-TGAAATATGCTTATTGACCGTTGAAACCGTTTTCAAAAGCCATAGAGGAT
65 GCTAGTACTAAC-TGTAAAATATACTTATTGACCGTTGAAACCG-TTTCAAAAGCCAAAGACGAT
* * * * * *
1559 TTTTGAG-ACTGATTTTTTAACGTGAAGTGGAGA-AAATGTAAGAATTTAAGAGCTTG
128 TTTTAAGAACTAATTTTTT-ACGTCAAGTGGAGAGAAATGCAA-AATTTAAGAGATTC
* * * *
1615 ATCAAAACTGAAACTCTAATAATTTTTTAATTAATCGTTCCTTG-AGTGGCAGAG-TAGTTTCTC
1 ATCAAAACTGAAACTCTAATAA-CTTTAAAATAATCGTTCC-TGAAGTGTCAGAGAT-GTTTCTC
* **
1678 TAGTTAGTACTAACTGTAAAATATACTTATTGAAGGTTGAAACCGTTTCAAAA
63 TAGCTAGTACTAACTGTAAAATATACTTATTGACCGTTGAAACCGTTTCAAAA
1731 TGGAAGGAGA
Statistics
Matches: 251, Mismatches: 42, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
184 27 0.11
185 218 0.87
186 6 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATCAAAACTGAAACTCTAATAACTTTAAAATAATCGTTCCTGAAGTGTCAGAGATGTTTCTCTAG
CTAGTACTAACTGTAAAATATACTTATTGACCGTTGAAACCGTTTCAAAAGCCAAAGACGATTTT
TAAGAACTAATTTTTTACGTCAAGTGGAGAGAAATGCAAAATTTAAGAGATTC
Found at i:2747 original size:112 final size:113
Alignment explanation
Indices: 2608--2833 Score: 436
Period size: 112 Copynumber: 2.0 Consensus size: 113
2598 GTGTACCTTG
2608 AACGAGCGGCTTTTTTGGATCGCCACAGAGCTTTCTGTTCTCCACTTGTGGTTTGAGAGGTTCAC
1 AACGAGCGGC-TTTTTGGATCGCCACAGAGCTTTCTGTTCTCCACTTGTGGTTTGAGAGGTTCAC
2673 GTCCCTTCAATTTGTGACTGTTAAACAAGTTATTTGTCTCTCTTTCATC
65 GTCCCTTCAATTTGTGACTGTTAAACAAGTTATTTGTCTCTCTTTCATC
2722 AACGAGCGGC-TTTTGGATCGCCACAGAGCTTTCTGTTCTCCACTTGTGGTTTGAGAGGTTCACG
1 AACGAGCGGCTTTTTGGATCGCCACAGAGCTTTCTGTTCTCCACTTGTGGTTTGAGAGGTTCACG
2786 TCCCTTCAATTTGTGACTGTTAAACAAGTTATTTGTCTCTCTTTCATC
66 TCCCTTCAATTTGTGACTGTTAAACAAGTTATTTGTCTCTCTTTCATC
2834 GATTTCATTT
Statistics
Matches: 112, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 102 0.91
114 10 0.09
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (113 bp):
AACGAGCGGCTTTTTGGATCGCCACAGAGCTTTCTGTTCTCCACTTGTGGTTTGAGAGGTTCACG
TCCCTTCAATTTGTGACTGTTAAACAAGTTATTTGTCTCTCTTTCATC
Done.