Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3107
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: 64400
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:19461 original size:23 final size:24
Alignment explanation
Indices: 19410--19514 Score: 74
Period size: 23 Copynumber: 4.4 Consensus size: 24
19400 ATAGCTCGTA
*
19410 AGAGCTTACTAT-TTCAGCTC-AT
1 AGAGCTTACTGTATTCAGCTCAAT
* *
19432 TGTAGCTTACTG-ATTCATCTCGAA-
1 AG-AGCTTACTGTATTCAGCTC-AAT
* *
19456 AGAGCTTACCGTTTTCAGCTCAAT
1 AGAGCTTACTGTATTCAGCTCAAT
* *
19480 AGAGCTTACTGTTTATCTGCTCAAT
1 AGAGCTTACTGTAT-TCAGCTCAAT
*
19505 AAGAGTTTAC
1 -AGAGCTTAC
19515 CGACCATAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 25 0.38
24 21 0.32
25 10 0.15
26 8 0.12
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (24 bp):
AGAGCTTACTGTATTCAGCTCAAT
Found at i:19483 original size:24 final size:26
Alignment explanation
Indices: 19455--19516 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 26
19445 TTCATCTCGA
19455 AAGAGCTTACCGTTT-TCAGCTCAAT
1 AAGAGCTTACCGTTTATCAGCTCAAT
* *
19480 -AGAGCTTACTGTTTATCTGCTCAAT
1 AAGAGCTTACCGTTTATCAGCTCAAT
*
19505 AAGAGTTTACCG
1 AAGAGCTTACCG
19517 ACCATAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 13 0.42
25 9 0.29
26 9 0.29
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (26 bp):
AAGAGCTTACCGTTTATCAGCTCAAT
Found at i:29248 original size:28 final size:28
Alignment explanation
Indices: 29216--29272 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
29206 GTAGCCTAGG
*
29216 AATAGTATTCTCCATTCAGTTCTTTCTC
1 AATAGTATTCTCCATTCAATTCTTTCTC
29244 AATAGTATTCTCCATTCAATTCTTTCTC
1 AATAGTATTCTCCATTCAATTCTTTCTC
29272 A
1 A
29273 TTTCTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.46
Consensus pattern (28 bp):
AATAGTATTCTCCATTCAATTCTTTCTC
Found at i:33447 original size:16 final size:16
Alignment explanation
Indices: 33426--33458 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33416 ATGAACTTAG
*
33426 TATATGTTGATTTTCA
1 TATATGATGATTTTCA
33442 TATATGATGATTTTCA
1 TATATGATGATTTTCA
33458 T
1 T
33459 GTTGTTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (16 bp):
TATATGATGATTTTCA
Found at i:39512 original size:14 final size:14
Alignment explanation
Indices: 39493--39535 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
39483 TTGTTCATAT
39493 CGCTTGTTGATAAA
1 CGCTTGTTGATAAA
39507 CGCTTGTTGATAAA
1 CGCTTGTTGATAAA
39521 CGCTTGTTGATAAA
1 CGCTTGTTGATAAA
39535 C
1 C
39536 TGCAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (14 bp):
CGCTTGTTGATAAA
Found at i:40109 original size:16 final size:16
Alignment explanation
Indices: 40062--40109 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
40052 TGATTACAAC
*
40062 TCTATTCTATTACAGCT
1 TCTATTCTGTTACAG-T
*
40079 T-TATTCCGTTACAGT
1 TCTATTCTGTTACAGT
*
40094 TCTATTCTGTTCCAGT
1 TCTATTCTGTTACAGT
40110 GAACCAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 2 0.08
16 23 0.88
17 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (16 bp):
TCTATTCTGTTACAGT
Found at i:40664 original size:3 final size:3
Alignment explanation
Indices: 40656--40683 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40646 CCCTTTCCCC
40656 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40684 GAGATGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:41151 original size:36 final size:36
Alignment explanation
Indices: 41111--41183 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
41101 AGTAGAAAAG
41111 AAAAATTCACTAATATGGATTCTACTTGTGCGGCAT
1 AAAAATTCACTAATATGGATTCTACTTGTGCGGCAT
41147 AAAAATTCACTAATATGGATTCTACTTGTGCGGCAT
1 AAAAATTCACTAATATGGATTCTACTTGTGCGGCAT
41183 A
1 A
41184 GTTCGTACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (36 bp):
AAAAATTCACTAATATGGATTCTACTTGTGCGGCAT
Found at i:41922 original size:19 final size:19
Alignment explanation
Indices: 41881--41921 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
41871 AAATATAAAA
*
41881 ATATAAAAATAATTTTTAT
1 ATATAAAAATAATATTTAT
*
41900 ATATAATAA-AATATTTAT
1 ATATAAAAATAATATTTAT
41918 -TATA
1 ATATA
41922 TTTATTTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
19 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAAAAATAATATTTAT
Found at i:41977 original size:41 final size:39
Alignment explanation
Indices: 41893--41985 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 39
41883 ATAAAAATAA
* * * * *
41893 TTTTTATATATAATAAAATATTTATTATATTTATTTGTGT
1 TTTTTA-ATATAAGAAAACATTTATTATATTTAGTAGTAT
41933 TTTTTAATATAAGAAAACATTTATTATATTTAAAGTAGTAT
1 TTTTTAATATAAGAAAACATTTATTATATTT--AGTAGTAT
41974 TTTTTAATATAA
1 TTTTTAATATAA
41986 ATATTTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 23 0.50
40 6 0.13
41 17 0.37
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (39 bp):
TTTTTAATATAAGAAAACATTTATTATATTTAGTAGTAT
Found at i:42038 original size:21 final size:21
Alignment explanation
Indices: 42012--42055 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42002 TTTTAATGTG
42012 TTAGAAAACCTTTATTTTAAC
1 TTAGAAAACCTTTATTTTAAC
*
42033 TTAGAAAACTTTTATTTTAAC
1 TTAGAAAACCTTTATTTTAAC
42054 TT
1 TT
42056 TTTTTAGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (21 bp):
TTAGAAAACCTTTATTTTAAC
Found at i:42374 original size:15 final size:15
Alignment explanation
Indices: 42351--42380 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42341 TAATATAAAT
*
42351 TTAAGAACTAAAAAA
1 TTAAAAACTAAAAAA
42366 TTAAAAACTAAAAAA
1 TTAAAAACTAAAAAA
42381 AAAACCACGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (15 bp):
TTAAAAACTAAAAAA
Found at i:44201 original size:17 final size:18
Alignment explanation
Indices: 44169--44203 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44159 TATGAAAAAC
44169 TAAATAAAACAAACAAAT
1 TAAATAAAACAAACAAAT
*
44187 TAAATTAAA-AAACAAAT
1 TAAATAAAACAAACAAAT
44204 AACTAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAATAAAACAAACAAAT
Found at i:46013 original size:18 final size:17
Alignment explanation
Indices: 45990--46023 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45980 GGATGATAAA
45990 ATTAAATAAAACAAACAG
1 ATTAAATAAAA-AAACAG
*
46008 ATTAAATTAAAAAACA
1 ATTAAATAAAAAAACA
46024 AATAACTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.21
Consensus pattern (17 bp):
ATTAAATAAAAAAACAG
Found at i:48006 original size:21 final size:21
Alignment explanation
Indices: 47982--48023 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
47972 ATACTTAATA
47982 GATAACTTCTTTTTTATTTAG
1 GATAACTTCTTTTTTATTTAG
48003 GATAACTTCTTTTTTATTTAG
1 GATAACTTCTTTTTTATTTAG
48024 CTTAGGCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
GATAACTTCTTTTTTATTTAG
Found at i:52767 original size:3 final size:3
Alignment explanation
Indices: 52753--52791 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
52743 ATGGAAGATT
* *
52753 TTA TTAA TTA TTA TTG TTA ATA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
52792 TGATTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:53195 original size:17 final size:17
Alignment explanation
Indices: 53173--53207 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53163 TAAATAGAAT
53173 AAAAAGAA-AGTAAAAGA
1 AAAAAGAACAG-AAAAGA
53190 AAAAAGAACAGAAAAGA
1 AAAAAGAACAGAAAAGA
53207 A
1 A
53208 GCAGAGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAAGAACAGAAAAGA
Found at i:53651 original size:17 final size:18
Alignment explanation
Indices: 53631--53664 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53621 TAAAAGAGTT
*
53631 AATTA-GGATTAAATTGG
1 AATTAGGGAATAAATTGG
53648 AATTAGGGAATAAATTG
1 AATTAGGGAATAAATTG
53665 AATAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (18 bp):
AATTAGGGAATAAATTGG
Found at i:53894 original size:13 final size:13
Alignment explanation
Indices: 53876--53901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53866 TCATGGGACA
53876 TCTAAGATAAGGT
1 TCTAAGATAAGGT
53889 TCTAAGATAAGGT
1 TCTAAGATAAGGT
53902 AAGTAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
TCTAAGATAAGGT
Found at i:56306 original size:79 final size:81
Alignment explanation
Indices: 56170--56354 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
56160 TTGAATGATG
* *
56170 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
56234 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
56249 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
56311 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
56329 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56355 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:56368 original size:40 final size:40
Alignment explanation
Indices: 56171--56354 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
56161 TGAATGATGT
* * * *
56171 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
56211 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
56251 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
56289 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
56330 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
56355 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:56376 original size:79 final size:79
Alignment explanation
Indices: 56223--56387 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
56213 GGACTAAGAT
* * **
56223 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
56288 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
56302 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
56365 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
56381 CCGAAGG
1 CCGAAGG
56388 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:64177 original size:40 final size:39
Alignment explanation
Indices: 64093--64265 Score: 188
Period size: 40 Copynumber: 4.4 Consensus size: 39
64083 TTGAATGATG
* * * *
64093 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
64133 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
64173 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
64212 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
64253 -CCGGGCTATGTCC
1 TCCGGGCTAAGTCC
64266 CGAGAGCATT
Statistics
Matches: 113, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
39 37 0.33
40 66 0.58
41 10 0.09
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:64229 original size:79 final size:80
Alignment explanation
Indices: 64093--64268 Score: 207
Period size: 79 Copynumber: 2.2 Consensus size: 80
64083 TTGAATGATG
* *
64093 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
64158 GTGCGAGATACTAAT
66 GTGCGAGATACTAAT
* * * **
64173 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
64235 TTGTGCGAGTTACT-AT
64 TTGTGCGAGATACTAAT
* *
64251 AACCGGGCTATGTCCCGA
1 -TCCGGGCTAAGTCCCGA
64269 GAGCATTTGA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.04
79 56 0.68
80 23 0.28
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTAAT
Done.