Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1100
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: 14908
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Found at i:319 original size:27 final size:27
Alignment explanation
Indices: 260--361 Score: 129
Period size: 27 Copynumber: 3.8 Consensus size: 27
250 TTTCTTCACA
*
260 ATCGGGGACACTCCAA-CCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
286 ATCGGGGATACTCCAACCCTCG-TAATC
1 ATCGGGGATACTCCAACCC-CGTTAATC
*
313 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTA-ATC
*
341 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
362 ACTTATTCTC
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
26 17 0.25
27 29 0.43
28 22 0.32
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:598 original size:50 final size:51
Alignment explanation
Indices: 344--612 Score: 241
Period size: 50 Copynumber: 5.3 Consensus size: 51
334 TTATTTCTGA
* * * *
344 GGGGATACTCCAACCCCGA-CTTA-TTCTCAAAATATCGA-TTTTCATAATC
1 GGGGATACTCCAACTCCGATTTTATTTC-CAAAATACCAATTTTTCATAATC
* * * * * * *
393 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTT-TTC-ATAATC
* *
446 GGGGATACTCCAATTCCGATTTTATTTCCAAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACTCCGATTTTATTTCC--AAAATACCAATTTTTCATAATC
* * *
499 -GGGATACTCCAA-TCCTGGTTTTATTTTC--AA-ACGCAATTTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GATTTTATTTCCAAAATAC-CAATTTTT-C-ATAATC
549 GGGGATACT-CAACTCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
*
599 GAGGATACTCCAAC
1 GGGGATACTCCAAC
613 CTCGTTATTT
Statistics
Matches: 177, Mismatches: 26, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
47 2 0.01
48 10 0.06
49 19 0.11
50 40 0.23
51 23 0.13
52 34 0.19
53 36 0.20
54 2 0.01
55 11 0.06
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:632 original size:28 final size:28
Alignment explanation
Indices: 596--672 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
586 ATTTTTCATA
* * *
596 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
624 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
652 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
673 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:701 original size:106 final size:105
Alignment explanation
Indices: 549--750 Score: 246
Period size: 106 Copynumber: 1.9 Consensus size: 105
539 TCCTTTAATC
* * *
549 GGGGATACTCAACTCCGATTTTATTTCCAAAATACCAATTTTTCATAATCGAGGATACTCCAACC
1 GGGGATACTCAACCCCGACTTTATTTCCAAAATACCAATTTCTCATAATCGAGGATACTCCAACC
*
614 TCGTTA-TTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCGTTATTTTCA--GGGGATACTCCAACCCCGTTACTTCCGA
* *** * * *
655 GGGGATACTCCAACCCCGGCTTTA-TTCCAAAATATTGATTTCTCATAATTGGGGGTACTCCAAC
1 GGGGATACT-CAACCCCGACTTTATTTCCAAAATACCAATTTCTCATAATCGAGGATACTCCAAC
*
719 CCCGTTATTTTCGAGGGGATACTCCAATCCCG
65 CCCGTTATTTTC-AGGGGATACTCCAACCCCG
751 ATTTTTTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
106 65 0.80
107 15 0.19
108 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (105 bp):
GGGGATACTCAACCCCGACTTTATTTCCAAAATACCAATTTCTCATAATCGAGGATACTCCAACC
CCGTTATTTTCAGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:13227 original size:9 final size:9
Alignment explanation
Indices: 13209--13276 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
13199 CCTTCTCTTC
13209 AAAAAA-AA
1 AAAAAAGAA
13217 AAAAAAGAA
1 AAAAAAGAA
13226 AAAAAA-AA
1 AAAAAAGAA
*
13234 AAACAAAAAA
1 AAA-AAAGAA
*
13244 AACAAAACAA
1 AA-AAAAGAA
*
13254 AGAAAAAGAG
1 A-AAAAAGAA
*
13264 AGAAAAGAA
1 AAAAAAGAA
13273 AAAA
1 AAAA
13277 CCTACTTAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 11 0.22
9 20 0.41
10 16 0.33
11 2 0.04
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:13229 original size:14 final size:14
Alignment explanation
Indices: 13210--13260 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
13200 CTTCTCTTCA
*
13210 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAC
13224 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
*
13238 AAAAAAAACAAAAC
1 AAAAAAAAAAAAAC
13252 AAAGAAAAA
1 AAA-AAAAA
13261 GAGAGAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 29 0.85
15 5 0.15
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:13229 original size:15 final size:15
Alignment explanation
Indices: 13209--13276 Score: 75
Period size: 15 Copynumber: 4.4 Consensus size: 15
13199 CCTTCTCTTC
13209 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
13224 AAAAAAAAAAAAACA-
1 AAAAAAAAAAAAA-AG
13239 AAAAAAACAAAACAAAG
1 AAAAAAA-AAAA-AAAG
* * *
13256 AAAAAGAGAGAAAAG
1 AAAAAAAAAAAAAAG
13271 AAAAAA
1 AAAAAA
13277 CCTACTTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 29 0.64
16 8 0.18
17 8 0.18
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:13276 original size:1 final size:1
Alignment explanation
Indices: 13209--13260 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
13199 CCTTCTCTTC
* * * * *
13209 AAAAAAAAAAAAAAGAAAAAAAAAAAAACAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13261 GAGAGAAAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:14385 original size:55 final size:54
Alignment explanation
Indices: 14247--14908 Score: 887
Period size: 53 Copynumber: 12.2 Consensus size: 54
14237 TCCGCTTTTT
14247 AGTCC-CAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
*
14300 AGTCCTCAAAGAGCAGGACACCT-TTCAAAG-CCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACTTT-C
*
14354 AGTCCTACAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCT-CAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* *
14410 AGTCCCCAAAGAGCAGGACACCCTCTTAAAG-CCACACAAGTTGGTGGCAACCTTC
1 AGTCCTCAAAGAGCAGGACA-CCTCTTAAAGCCCACACAAGTTGGTGGC-ACTTTC
* *
14465 AGTCCTCAAAGAGCAGGACACCT-TTCAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTT-C
*
14519 AGTCC-CAAAGAGCAGGACACCTCTTAAAGCCCA-ACAAGTTGGTGGCATTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
*
14571 AGTCCTC-AA-AGCAGGGACACCTCTT-AAGCCCA-ACACGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCA-GGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
*
14623 AGTCCTCAAAGAGCAGGACA-CTTTTAAAG-CCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
14676 AGTCCTCAAA-AGCGAGGACACCT-TTAAAGCCCACACAAAGTTGGTGGCA-TTGTCC
1 AGTCCTCAAAGAGC-AGGACACCTCTTAAAGCCCACAC-AAGTTGGTGGCACTT-T-C
14731 AGTCCTCAAAGAGCAGGACACCTCTT-AA-CCCACAC-AGTTGGTGGCCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG-CA-CTTTC
*
14784 AGTCCCCAAAGAGGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGA-GCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
*
14840 AGTCCTCAAAGAGCAGGACACC-CTTTCAAAGCCCACACAAGTTGGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTC-TT-AAAGCCCACACAAGTT-GGTGGCACTTT-C
14897 AGTCCTCAAAGA
1 AGTCCTCAAAGA
Statistics
Matches: 553, Mismatches: 18, Indels: 72
0.86 0.03 0.11
Matches are distributed among these distances:
51 24 0.04
52 49 0.09
53 139 0.25
54 99 0.18
55 123 0.22
56 87 0.16
57 32 0.06
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (54 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
Found at i:14806 original size:27 final size:27
Alignment explanation
Indices: 14776--14867 Score: 66
Period size: 27 Copynumber: 3.3 Consensus size: 27
14766 AGTTGGTGGC
14776 CACCTTTCAGTCCCCAAAGAGGCAGGA
1 CACCTTTCAGTCCCCAAAGAGGCAGGA
* * *
14803 CACCTCTTAAAG-CCCACACAAGTTGG-TGG-
1 CACCT-TT-CAGTCCC-CA-AAG-AGGCAGGA
*
14832 CACCTTTCAGTCCTCAAAGA-GCAGGA
1 CACCTTTCAGTCCCCAAAGAGGCAGGA
14858 CACCCTTTCA
1 CA-CCTTTCA
14868 AAGCCCACAC
Statistics
Matches: 49, Mismatches: 7, Indels: 18
0.66 0.09 0.24
Matches are distributed among these distances:
24 1 0.02
25 2 0.04
26 5 0.10
27 16 0.33
28 9 0.18
29 9 0.18
30 5 0.10
31 2 0.04
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (27 bp):
CACCTTTCAGTCCCCAAAGAGGCAGGA
Done.