Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold437
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: 39550
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:380 original size:17 final size:16
Alignment explanation
Indices: 358--395 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
348 ACAATAATAT
358 AAAATAATGATATGTAC
1 AAAATAAT-ATATGTAC
375 AAAAT-ATATATGTAC
1 AAAATAATATATGTAC
*
390 ATAATA
1 AAAATA
396 TAGTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 12 0.63
16 2 0.11
17 5 0.26
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (16 bp):
AAAATAATATATGTAC
Found at i:387 original size:15 final size:15
Alignment explanation
Indices: 367--414 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
357 TAAAATAATG
367 ATATGTACAAAATAT
1 ATATGTACAAAATAT
*
382 ATATGTACATAATAT
1 ATATGTACAAAATAT
*
397 AGT-TATA-AAAATAT
1 A-TATGTACAAAATAT
411 ATAT
1 ATAT
415 TAAATTCGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 18 0.64
16 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (15 bp):
ATATGTACAAAATAT
Found at i:1486 original size:30 final size:30
Alignment explanation
Indices: 1434--1544 Score: 134
Period size: 30 Copynumber: 3.7 Consensus size: 30
1424 TTTTTAAAAA
* *
1434 TTTA-GGGTTAAAATGTAATTTAAGGAAAG
1 TTTAGGGGTCAAAATGAAATTTAAGGAAAG
* * *
1463 TTTAGGGGTCTAAGTGAAATTTAAAGAAAG
1 TTTAGGGGTCAAAATGAAATTTAAGGAAAG
* *
1493 TTTAAGGGTCAAAATGAAATTTAAGAAAAG
1 TTTAGGGGTCAAAATGAAATTTAAGGAAAG
* *
1523 TTTAGGGGTAAAAATGTAATTT
1 TTTAGGGGTCAAAATGAAATTT
1545 TTATTTTTTG
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 4 0.06
30 64 0.94
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.32
Consensus pattern (30 bp):
TTTAGGGGTCAAAATGAAATTTAAGGAAAG
Found at i:1544 original size:60 final size:57
Alignment explanation
Indices: 1416--1544 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 57
1406 TTCTGGGGCT
* * * * **
1416 AAATGTAATTTTTAAAAATTTAGGGTTAAAATGTAATTTAAGGAAAGTTTAGGGGTCT
1 AAATGTAA-TTTAAAAAATTTAGGGTCAAAATGAAATTTAAGAAAAGTTTAGGGGTAA
* *
1474 AAGTGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTTAAGAAAAGTTTAGGGGTAA
1 AAATGTAATTTAAA-AAA-TTT-AGGGTCAAAATGAAATTTAAGAAAAGTTTAGGGGTAA
1534 AAATGTAATTT
1 AAATGTAATTT
1545 TTATTTTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
57 5 0.09
58 9 0.16
59 3 0.05
60 41 0.71
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (57 bp):
AAATGTAATTTAAAAAATTTAGGGTCAAAATGAAATTTAAGAAAAGTTTAGGGGTAA
Found at i:1856 original size:78 final size:77
Alignment explanation
Indices: 1725--2053 Score: 302
Period size: 78 Copynumber: 4.3 Consensus size: 77
1715 TCATTCTTTA
* * * * *
1725 TTGAAAAACAAAAAAAATTGAAAATAGCTC-GGGATGCGACCTGAAGTTCAACTCACCTCTCG-A
1 TTGAAAAAC--AAAAAATTGAAAATACCTCAGCG-TGTGACCTGAGGCTCAACTCACCTCTCGCA
1788 ATTATGAGTTGATCTT
63 A-TATGAGTTGATCTT
*
1804 TTGAAAAAGCAAAAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTTAACTCACCTCTC-CAAT
1 TTGAAAAA-CAAAAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAAT
*
1868 ATGAGTTGATTTTT
65 ATGAGTTGA-TCTT
* * * * * **
1882 TTGAAAGAC-AGAAATTGAAAATACCTCA--ATGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
1 TTGAAAAACAAAAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
1944 TGAGTTGA-CTT
66 TGAGTTGATCTT
* * * * *
1955 TTAAAAAAAAAAATAGGAATTGAAATTACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGT
1 TT-GAAAAACAAA-A--AATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGC
*
2018 AATATGAATTGAT-TT
62 AATATGAGTTGATCTT
*
2033 TTGAAAAAC-ATAAATTGAAAA
1 TTGAAAAACAAAAAATTGAAAA
2054 ACGGAAATCG
Statistics
Matches: 205, Mismatches: 32, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
73 12 0.06
74 26 0.13
75 15 0.07
76 20 0.10
77 16 0.08
78 102 0.50
79 10 0.05
80 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (77 bp):
TTGAAAAACAAAAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATCTT
Found at i:2179 original size:89 final size:87
Alignment explanation
Indices: 1963--2381 Score: 551
Period size: 87 Copynumber: 4.8 Consensus size: 87
1953 TTTTAAAAAA
* * * * * *
1963 AAAAATAGGAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGTAATATGAATT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
2028 GATTTTTGAAAAACATAAATTG
66 GATTTTTGAAAAACATAAATTG
* * * * *
2050 AAAAACGGAAATCGAAAATACCTCAACGTGTCTTGAGGCTCAATTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
2115 GATTTTTGAAAAATATAGATTGG
66 GATTTTTGAAAAACATAAATT-G
2138 AAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 -AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
2203 TGA--TTT-AAAAACAGT-CATT-
65 TGATTTTTGAAAAACA-TAAATTG
* * * *
2222 AAGAACAGAAATTAAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAATT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
2287 GATTTTTGCAAAATATAAATTG
66 GATTTTTGAAAAACATAAATTG
* * * *
2309 CAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTC
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
2374 GACTTTTT
66 GA-TTTTT
2382 TTTTGACAAA
Statistics
Matches: 288, Mismatches: 35, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
83 63 0.22
85 4 0.01
86 17 0.06
87 136 0.47
88 6 0.02
89 62 0.22
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAACATAAATTG
Found at i:2311 original size:14 final size:14
Alignment explanation
Indices: 2292--2322 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2282 GAATTGATTT
*
2292 TTGCAAAATATAAA
1 TTGCAAAACATAAA
2306 TTGCAAAACATAAA
1 TTGCAAAACATAAA
2320 TTG
1 TTG
2323 AAATTACCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (14 bp):
TTGCAAAACATAAA
Found at i:2348 original size:259 final size:242
Alignment explanation
Indices: 1817--2453 Score: 737
Period size: 259 Copynumber: 2.6 Consensus size: 242
1807 AAAAAGCAAA
* * * *
1817 AAATTGAAAATACCTCAGCGTGTGACCTGAGGCTTAACTCACCTCTC-CAATATGAGTTGA---T
1 AAATCGAAAATACCTCAACGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGACTTT
* ** * *
1878 TTTTTTGAAAGACAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
64 TTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAAT
* * * *
1943 ATGAGTTGACTTTTAAAAAAAAAAATAGGAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACT
129 ATGAGTTGAC-TTTAAAAAAAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACT
* *
2008 CACCTCTCGTAATATGAATTGATTTTTGAAAAACATAAATTGAAAAACGG
193 CACCTCTCGCAATATGAATTGATTTTTGAAAAACATAAATTGAAAAACAG
* * *
2058 AAATCGAAAATACCTCAACGTGTCTTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA-TTTTT
1 AAATCGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGACTTTTT
2122 GAAAAATATAGATTGGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
66 ------T-T---TT-G-AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
* *
2187 CTCTCGCAATATGAGTTGA-TTTAAAAACAGTCATTAAGAACAGAAATTAAAAATACCTCAGTGT
119 TTCTCGCAATATGAGTTGACTTTAAAAA-A---A--AA-AACAGAAATTAAAAATACCTCAGCGT
* * * *
2251 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTGCAAAATATAAATTGCAAAACA
177 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTGAAAAACATAAATTGAAAAACA
*
2316 T
242 G
* * *
2317 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGACTTTTT
1 AAATCGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGACTTTTT
* * * * *
2382 TTTTGACAAACAGTAATTGAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATAT
66 TTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATAT
2447 GAGTTGA
131 GAGTTGA
2454 ATTTTGAAAA
Statistics
Matches: 338, Mismatches: 35, Indels: 39
0.82 0.08 0.09
Matches are distributed among these distances:
239 19 0.06
240 13 0.04
241 21 0.06
242 3 0.01
248 62 0.18
249 2 0.01
250 2 0.01
252 10 0.03
253 3 0.01
254 62 0.18
256 1 0.00
258 2 0.01
259 133 0.39
260 5 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (242 bp):
AAATCGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGACTTTTT
TTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATAT
GAGTTGACTTTAAAAAAAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCAC
CTCTCGCAATATGAATTGATTTTTGAAAAACATAAATTGAAAAACAG
Found at i:14560 original size:17 final size:19
Alignment explanation
Indices: 14538--14581 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
14528 ACAATAATAT
14538 AAAATA-AT-GATATGTAC
1 AAAATATATAGATATGTAC
*
14555 AAAATATATATATATGTAC
1 AAAATATATAGATATGTAC
*
14574 ATAATATA
1 AAAATATA
14582 GTTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 15 0.65
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAATATATAGATATGTAC
Found at i:15657 original size:30 final size:30
Alignment explanation
Indices: 15585--15699 Score: 81
Period size: 30 Copynumber: 3.9 Consensus size: 30
15575 TAATTTTTAG
* * *
15585 AAAA-TTTAA-GGTTAAAATGGAATTTAAG
1 AAAAGTTTAAGGGTCAAAATGAAATTTAAA
* * * * *
15613 GAAATTTTAGGGGTCTAAGTGAAATTTAAA
1 AAAAGTTTAAGGGTCAAAATGAAATTTAAA
* **
15643 AAAAGTTTAAGGGTCAAAATTAAATTTAGG
1 AAAAGTTTAAGGGTCAAAATGAAATTTAAA
** * *
15673 AAAAGTTTGGGGGTAAAAATGTAATTT
1 AAAAGTTTAAGGGTCAAAATGAAATTT
15700 TTATTTTTTG
Statistics
Matches: 65, Mismatches: 20, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
28 3 0.05
29 4 0.06
30 58 0.89
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (30 bp):
AAAAGTTTAAGGGTCAAAATGAAATTTAAA
Found at i:15834 original size:8 final size:8
Alignment explanation
Indices: 15823--15857 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
15813 CCTTTCGGTA
*
15823 TTTCGACT
1 TTTCGGCT
*
15831 TTTCGGCA
1 TTTCGGCT
15839 TTTCGGCT
1 TTTCGGCT
15847 TTTCGGCT
1 TTTCGGCT
15855 TTT
1 TTT
15858 TCCGATCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.06, C:0.23, G:0.20, T:0.51
Consensus pattern (8 bp):
TTTCGGCT
Found at i:15834 original size:16 final size:16
Alignment explanation
Indices: 15815--15853 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
15805 ACTTTCAGCC
*
15815 TTTCGGTATTTCGACT
1 TTTCGGCATTTCGACT
*
15831 TTTCGGCATTTCGGCT
1 TTTCGGCATTTCGACT
15847 TTTCGGC
1 TTTCGGC
15854 TTTTTCCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.46
Consensus pattern (16 bp):
TTTCGGCATTTCGACT
Found at i:18193 original size:14 final size:14
Alignment explanation
Indices: 18174--18200 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18164 TTTTTTTACA
18174 TATATTTATATATG
1 TATATTTATATATG
18188 TATATTTATATAT
1 TATATTTATATAT
18201 ATGTTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TATATTTATATATG
Found at i:18195 original size:24 final size:24
Alignment explanation
Indices: 18168--18218 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
18158 AAATATTTTT
18168 TTTACATATAT-TTATATATGTATA
1 TTTACATATATGTT-TATATGTATA
* *
18192 TTTATATATATGTTTATATTTATA
1 TTTACATATATGTTTATATGTATA
18216 TTT
1 TTT
18219 CTTTTGGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTACATATATGTTTATATGTATA
Found at i:18213 original size:6 final size:6
Alignment explanation
Indices: 18174--18218 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
18164 TTTTTTTACA
* *
18174 TATATT TATATAT GTATATT TATATA TATGTT TATATT TATATT T
1 TATATT TATAT-T -TATATT TATATT TATATT TATATT TATATT T
18219 CTTTTGGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 26 0.79
7 2 0.06
8 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:21889 original size:18 final size:18
Alignment explanation
Indices: 21858--21897 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
21848 TCATATTTGA
*
21858 TTTT-TTTAAGATTAATT
1 TTTTATTTAAAATTAATT
21875 TTTTATTTAAAATTAATT
1 TTTTATTTAAAATTAATT
21893 TTTTA
1 TTTTA
21898 ATAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTATTTAAAATTAATT
Found at i:22037 original size:39 final size:41
Alignment explanation
Indices: 21963--22052 Score: 139
Period size: 39 Copynumber: 2.2 Consensus size: 41
21953 TTAAAAATAT
*
21963 TTATATTAAAAAATACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
*
22004 TTATATTAAAAAATAC-A-AATAAATATAGTAAATATTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
*
22043 TTGTATTAAA
1 TTATATTAAA
22053 TATAAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 29 0.63
40 1 0.02
41 16 0.35
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (41 bp):
TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
Found at i:22205 original size:29 final size:30
Alignment explanation
Indices: 22161--22220 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
22151 TTTAATATAA
22161 ATATAAATATATATAATTATTATT-TAACAT
1 ATATAAATATATATAA-TATTATTATAACAT
* *
22191 ATATAATTA-ATATAATATTTTTATAACAT
1 ATATAAATATATATAATATTATTATAACAT
22220 A
1 A
22221 ATATTTGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 13 0.48
30 8 0.30
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
ATATAAATATATATAATATTATTATAACAT
Found at i:29551 original size:18 final size:17
Alignment explanation
Indices: 29513--29555 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
29503 AGATGGATTT
*
29513 ACTAAA-TGTTTTTAGT
1 ACTAAATTGTTTTTAGG
29529 A-TAAATTGATTTTTAGG
1 ACTAAATTG-TTTTTAGG
29546 ACTAAATTGT
1 ACTAAATTGT
29556 GAAAAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 4 0.17
16 3 0.13
17 9 0.39
18 7 0.30
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (17 bp):
ACTAAATTGTTTTTAGG
Found at i:33327 original size:23 final size:23
Alignment explanation
Indices: 33301--33345 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
33291 TGGGTATGTG
33301 ATGAAGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
33324 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
33346 TTGAATTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Done.