Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold714
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: 32230
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:16611 original size:21 final size:21
Alignment explanation
Indices: 16585--16625 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16575 ATCTGCTCAA
* *
16585 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
16606 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
16626 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:21218 original size:13 final size:14
Alignment explanation
Indices: 21186--21233 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
21176 GCAAAAGCTG
21186 GAGAAATGAAAGAGA
1 GAGAAA-GAAAGAGA
*
21201 GAGAAAGAAGGAGA
1 GAGAAAGAAAGAGA
*
21215 -AGAAAGAAAAAGA
1 GAGAAAGAAAGAGA
*
21228 AAGAAA
1 GAGAAA
21234 ACGAAAGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 11 0.38
14 12 0.41
15 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
GAGAAAGAAAGAGA
Found at i:21232 original size:10 final size:10
Alignment explanation
Indices: 21204--21312 Score: 107
Period size: 10 Copynumber: 11.0 Consensus size: 10
21194 AAAGAGAGAG
21204 AAAG-AAGGA
1 AAAGAAAGGA
* *
21213 GAAGAAAGAA
1 AAAGAAAGGA
21223 AAAGAAA-GA
1 AAAGAAAGGA
21232 AAACGAAAGGA
1 AAA-GAAAGGA
*
21243 AAGGAAAGGA
1 AAAGAAAGGA
*
21253 AAGGAAAGGA
1 AAAGAAAGGA
* *
21263 GAAGAAAGAA
1 AAAGAAAGGA
21273 AAAGAAA-GA
1 AAAGAAAGGA
21282 AAAGGAAAGGA
1 AAA-GAAAGGA
*
21293 GAAGAAAGGA
1 AAAGAAAGGA
*
21303 AAGGAAAGGA
1 AAAGAAAGGA
21313 GGAGAAGAAG
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
9 11 0.13
10 63 0.77
11 8 0.10
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (10 bp):
AAAGAAAGGA
Found at i:21246 original size:5 final size:5
Alignment explanation
Indices: 21216--21312 Score: 99
Period size: 5 Copynumber: 19.4 Consensus size: 5
21206 AGAAGGAGAA
* * * *
21216 GAAAG AAAAA GAAAG AAAAC GAAAG GAAAG GAAAG GAAAG GAAAG GAGAA-
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GA-AAG
* * *
21266 GAAAG AAAAA GAAAG AAAAG GAAAG GAGAA- GAAAG GAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GA-AAG GAAAG GAAAG GAAAG GA
21313 GGAGAAGAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
4 4 0.05
5 66 0.89
6 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:21250 original size:30 final size:30
Alignment explanation
Indices: 21208--21310 Score: 127
Period size: 30 Copynumber: 3.4 Consensus size: 30
21198 AGAGAGAAAG
* * * *
21208 AAGGAGAA-GAAAGAAAAAGAAAGAAAACGA
1 AAGGA-AAGGAAAGAAAAGGAAAGGAGAAGA
*
21238 AAGGAAAGGAAAGGAAAGGAAAGGAGAAGA
1 AAGGAAAGGAAAGAAAAGGAAAGGAGAAGA
* *
21268 AAGAAAAAGAAAGAAAAGGAAAGGAGAAGA
1 AAGGAAAGGAAAGAAAAGGAAAGGAGAAGA
21298 AAGGAAAGGAAAG
1 AAGGAAAGGAAAG
21311 GAGGAGAAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (30 bp):
AAGGAAAGGAAAGAAAAGGAAAGGAGAAGA
Found at i:21267 original size:50 final size:50
Alignment explanation
Indices: 21208--21318 Score: 188
Period size: 50 Copynumber: 2.2 Consensus size: 50
21198 AGAGAGAAAG
21208 AAGGAGAAGAAAGAAAAAGAAAGAAAACGAAAGGA-AAGGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGAAAACGAAAGGAGAA-GAAAGGAAAGGA
*
21258 AAGGAGAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGAAAACGAAAGGAGAAGAAAGGAAAGGA
*
21308 AAGGAGGAGAA
1 AAGGAGAAGAA
21319 GAAGAGGGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 56 0.97
51 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (50 bp):
AAGGAGAAGAAAGAAAAAGAAAGAAAACGAAAGGAGAAGAAAGGAAAGGA
Found at i:21335 original size:23 final size:23
Alignment explanation
Indices: 21246--21321 Score: 89
Period size: 25 Copynumber: 3.1 Consensus size: 23
21236 GAAAGGAAAG
*
21246 GAAAGGAAAGGAAAGGAGAAGAAA
1 GAAAGGAAAGGAAAGGAGGAG-AA
* *
21270 GAAAAAGAAAGAAAAGGAAAGGAGAA
1 G-AAAGGAAAGGAAAGG--AGGAGAA
21296 GAAAGGAAAGGAAAGGAGGAGAA
1 GAAAGGAAAGGAAAGGAGGAGAA
21319 GAA
1 GAA
21322 GAGGGAGGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 10 0.23
24 1 0.02
25 26 0.59
26 3 0.07
27 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (23 bp):
GAAAGGAAAGGAAAGGAGGAGAA
Found at i:21690 original size:26 final size:26
Alignment explanation
Indices: 21661--21710 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
21651 ATATTCACCG
*
21661 AAAATAATAAAATCCGAAAATAATGT
1 AAAATAATAAAATACGAAAATAATGT
21687 AAAATAATAAAATACGAAAATAAT
1 AAAATAATAAAATACGAAAATAAT
21711 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (26 bp):
AAAATAATAAAATACGAAAATAATGT
Found at i:22276 original size:156 final size:155
Alignment explanation
Indices: 21677--22408 Score: 974
Period size: 156 Copynumber: 4.7 Consensus size: 155
21667 ATAAAATCCG
*
21677 AAAATAATGTAAAATAATAAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAG
1 AAAATAATGTAAAATAATAAAATTA-GAAAATAATAT-TTTTTATTGAAAGTAATAAAATTCGGG
* * * * *
21741 AAAAAAAAAAGAACAAAGGGCCGAAGTAAAGGTTATTTTTTG-AAATTTATTTAAAAGATACTGT
64 AAAAAAATACGAACAAAGGGCCGAAGTAAGGGTT-TTTTTTGTAAATTTATTTAAAAAATACT-A
21805 AAATTAATACATTTCAAACATAATGTACT
127 AAATTAATACATTTCAAACATAATGTACT
* * *
21834 AAAATAATGTAAAATAATAAAATTAGAAAATAGTA-TATTT-TT-AAAGTAATAAAATCCGGAGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATTTTTTATTGAAAGTAATAAAATTCGG-GA
* * ** *
21896 AAAAAATACGAACAAAGGGCCGAAATAAGGG-CTTTTTACTAAA-TTATTTTAACAAAACAC-AA
65 AAAAAATACGAACAAAGGGCCGAAGTAAGGGTTTTTTTTGTAAATTTA-TTTAA-AAAATACTAA
21958 TTAATTAATACATTTCAAACATAATGTACT
128 --AATTAATACATTTCAAACATAATGTACT
21988 AAAATAATG-----TAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATAT-TTTTTATTGAAAGTAATAAAATTCGGGA
* *
22048 AAAAAATACGAACAAAGGGCCGAAGTAA-GGTTTTTTTTGTAAATTTACTTAAAAAATACAATAA
65 AAAAAATACGAACAAAGGGCCGAAGTAAGGGTTTTTTTTGTAAATTTATTTAAAAAATACTA-AA
*
22112 ATTAATACATTTCAAATATAATGTACT
129 ATTAATACATTTCAAACATAATGTACT
* *
22139 AAACTAATGTAAAATAATAAAATTAGAAAATAATATTTTTTATTGAAAGTAATAAAATTCGGGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATTTTTTATTGAAAGTAATAAAATTCGGGAA
22204 AAAAATACGAACAAAGGGCCGAAGTAAGGGTTTTTTTTGTAAATTTATTTAAAAAAGATACTAAA
66 AAAAATACGAACAAAGGGCCGAAGTAAGGGTTTTTTTTGTAAATTTATTT-AAAAA-ATACTAAA
* *
22269 ATT-ATACATTTCAAATATAATGTAAT
129 ATTAATACATTTCAAACATAATGTACT
* ** * *
22295 AAACTAATGTAAAATAATAAAATTAGAAAATAATATTTTTTATTGAAAGTAATAAAAACCAGTAA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATTTTTTATTGAAAGTAATAAAATTCGGGAA
* **
22360 AAAAATACGAACAAAGGGCCGAAATAAGGG-TTTTTTACTAAATTTATTT
66 AAAAATACGAACAAAGGGCCGAAGTAAGGGTTTTTTTTGTAAATTTATTT
22409 TGAAGTTGCA
Statistics
Matches: 515, Mismatches: 37, Indels: 48
0.86 0.06 0.08
Matches are distributed among these distances:
149 20 0.04
151 47 0.09
152 54 0.10
153 43 0.08
154 73 0.14
155 76 0.15
156 154 0.30
157 41 0.08
158 7 0.01
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (155 bp):
AAAATAATGTAAAATAATAAAATTAGAAAATAATATTTTTTATTGAAAGTAATAAAATTCGGGAA
AAAAATACGAACAAAGGGCCGAAGTAAGGGTTTTTTTTGTAAATTTATTTAAAAAATACTAAAAT
TAATACATTTCAAACATAATGTACT
Found at i:26604 original size:43 final size:41
Alignment explanation
Indices: 26542--26848 Score: 269
Period size: 43 Copynumber: 7.2 Consensus size: 41
26532 ATAAATAAAA
* * * *
26542 GCCGCTAAAAATCATGACCTTTAGCGGCGCATTTCTCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGACGC-TTTC-CACAAAC
* * *
26585 GCCGCTAAAGACCAAGACCTTTAGTGGCACTTTAACCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGACGCTTT--CCACAAAC
* *
26628 GCTGCTAAAGACCAAGACCTTTAGCGACGCTTTTCTCACAAAT
1 GCCGCTAAAGACCAAGACCTTTAGCGACGC-TTTC-CACAAAC
*
26671 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAACCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGACGCTTT--CCACAAAC
* * * * *
26714 GCCGCTATAGAACATGAGCTTTAGCGCCGCTTTTCCCACAAA-
1 GCCGCTAAAGACCAAGACCTTTAGCGACGC-TTT-CCACAAAC
* *
26756 --CGCTAAAGACCAAGACCTTTAACGAAGCTTTAACCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGACGCTTT--CCACAAAC
* * * * *
26797 GCTGCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGACGC-TTT-CCACAAAC
26840 GCCGCTAAA
1 GCCGCTAAA
26849 AGTACAACTC
Statistics
Matches: 217, Mismatches: 35, Indels: 24
0.79 0.13 0.09
Matches are distributed among these distances:
39 3 0.01
40 28 0.13
42 7 0.03
43 168 0.77
44 11 0.05
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (41 bp):
GCCGCTAAAGACCAAGACCTTTAGCGACGCTTTCCACAAAC
Found at i:26650 original size:86 final size:86
Alignment explanation
Indices: 26545--26848 Score: 402
Period size: 86 Copynumber: 3.6 Consensus size: 86
26535 AATAAAAGCC
* *
26545 GCTAAA-AATCATGACCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
1 GCTAAAGAA-CATGACCTTTAGCGACGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
*
26609 TGGCACTTTAACCACAAACGCT
65 AGGCACTTTAACCACAAACGCT
* * * *
26631 GCTAAAGACCAAGACCTTTAGCGACGCTTTTCTCACAAATGCCGCTAAAGACCAAGACCTTTAGC
1 GCTAAAGAACATGACCTTTAGCGACGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAGA
* *
26696 GGCGCTTTAACCACAAACGCC
66 GGCACTTTAACCACAAACGCT
* * * *
26717 GCTATAGAACATGAGCTTTAGCGCCGCTTTTCCCACAAA---CGCTAAAGACCAAGACCTTTA-A
1 GCTAAAGAACATGACCTTTAGCGACGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAGA
* *
26778 CGAAGCTTTAACCACAAACGCT
66 GGCA-CTTTAACCACAAACGCT
* *
26800 GCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAACGCCGCTAAA
1 GCTAAAGAACATGACCTTTAGCGACGCTTTTCTCACAAACGCCGCTAAA
26849 AGTACAACTC
Statistics
Matches: 189, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
82 1 0.01
83 71 0.38
86 116 0.61
87 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (86 bp):
GCTAAAGAACATGACCTTTAGCGACGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAGA
GGCACTTTAACCACAAACGCT
Found at i:26864 original size:169 final size:169
Alignment explanation
Indices: 26554--26872 Score: 432
Period size: 169 Copynumber: 1.9 Consensus size: 169
26544 CGCTAAAAAT
* * ** *
26554 CATGACCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAGTGGCACTTTA
1 CATGACCTTTAGCGCCGCATTTCCCACAAA--CCGCTAAAGACCAAGACCTTTAGACGAACTTTA
* * *
26619 ACCACAAACGCTGCTAAAGACCAAGACCTTTAGCGACGCTTTTCTCACAAATGCCGCTAAAGACC
64 ACCACAAACGCTGCTAAAGAACAAGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGACC
26684 AAGACCTTTAGCGGCGCTTTAACCACAAACGCCGCTATAGAA
129 AAGACCTTTAGCGGCG-TTTAACCACAAACGCCGCTATAGAA
* *
26726 CATGAGCTTTAGCGCCGCTTTTCCCACAAA-CGCTAAAGACCAAGACCTTTA-ACGAAGCTTTAA
1 CATGACCTTTAGCGCCGCATTTCCCACAAACCGCTAAAGACCAAGACCTTTAGACGAA-CTTTAA
* *
26789 CCACAAACGCTGCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAAGTA-
65 CCACAAACGCTGCTAAAGAACAAGACCTTTAGCGACGCTTTTATCACAAACGCCGCT-AAAG-AC
26853 C-A-ACTCTTTAGCGGCGTTTA
128 CAAGAC-CTTTAGCGGCGTTTA
26873 TAAAAAACGC
Statistics
Matches: 131, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
168 8 0.06
169 91 0.69
170 5 0.04
171 1 0.01
172 26 0.20
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (169 bp):
CATGACCTTTAGCGCCGCATTTCCCACAAACCGCTAAAGACCAAGACCTTTAGACGAACTTTAAC
CACAAACGCTGCTAAAGAACAAGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGACCAA
GACCTTTAGCGGCGTTTAACCACAAACGCCGCTATAGAA
Found at i:27841 original size:40 final size:40
Alignment explanation
Indices: 27778--27861 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
27768 TAGCTTGAAC
* * *
27778 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
27818 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
27858 ATCA
1 ATCA
27862 TGTATAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:28027 original size:77 final size:77
Alignment explanation
Indices: 27891--28034 Score: 182
Period size: 77 Copynumber: 1.9 Consensus size: 77
27881 CAAAAAATTA
* * * * ** *
27891 GCAAAAATTAACAATTCATGTATAATGTATTTACCAAAAACTGGACCAACTTGTCAATTTTTTAT
1 GCAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACCAAATTGTCAATTTTTTAT
27956 AACATTTTAAAT
66 AACATTTTAAAT
* * *
27968 GCAACAAATTAACAATACAAGT-TCATATATTCACCAAAAACCAGACTAAATTTTCAATTTTTTA
1 GCAA-AAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACCAAATTGTCAATTTTTTA
28032 TAA
65 TAA
28035 AATAAGAGGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 41 0.73
78 15 0.27
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (77 bp):
GCAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACCAAATTGTCAATTTTTTAT
AACATTTTAAAT
Found at i:32013 original size:15 final size:15
Alignment explanation
Indices: 31977--32022 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
31967 TTATTAACTT
* *
31977 TTTAAAAATCTAATA
1 TTTAAATATCAAATA
*
31992 TTTAAATATCAAATG
1 TTTAAATATCAAATA
32007 TTTAAAT-T-AAATA
1 TTTAAATATCAAATA
32020 TTT
1 TTT
32023 TTTAGTCACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 7 0.26
14 1 0.04
15 19 0.70
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (15 bp):
TTTAAATATCAAATA
Done.