Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3516
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: 49713
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:9236 original size:119 final size:118
Alignment explanation
Indices: 9025--9374 Score: 549
Period size: 119 Copynumber: 2.9 Consensus size: 118
9015 AATTGAAGAC
* *
9025 AGCAGATCTAGA-CTTCAGACTTTTATGCTGAAGCAGATCCAAGATGATTTGGTTTTCTTGTGTT
1 AGCAGATCTA-ACCTTCAGA-TTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTT
* * * * *
9089 TACAAGGAACAAATTGAGGATATAGCAGATTTGACTCTCAGACGTTCTCAAATAT
64 TACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATAT
* *
9144 AGCAGATCTAACCTTCAGATGTTTATACTGAAACAGATCCAATATGATTTGGTATTCTTGTGTTT
1 AGCAGATCTAACCTTCAGAT-TTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
*
9209 ACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATGT
65 ACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATAT
9263 AGCAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
1 AGCAGATCTAACCTTCAGAT-TTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
* *
9328 ACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCT
65 ACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCT
9375 TAAACAAACT
Statistics
Matches: 214, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
118 2 0.01
119 212 0.99
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (118 bp):
AGCAGATCTAACCTTCAGATTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTA
CAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATAT
Found at i:9543 original size:321 final size:322
Alignment explanation
Indices: 9081--9709 Score: 992
Period size: 321 Copynumber: 2.0 Consensus size: 322
9071 ATTTGGTTTT
* * * *
9081 CTTGTGTTTACAAGGAACAAATTGAGGATATAGCAGATTTGACTCTCAGACGTTCTCAAATATAG
1 CTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATACAG
* * * *
9146 CAGATCTAACCTTCAGATGTTTATACTGAAACAGATCCAATATGATTTGGTATTCTTGTGTTTAC
66 CAGATCTAACCTTCAGATGTTTATACTGAAACAGATCCAAGATGATTTGGCATCCTTGTGCTTAC
9211 AAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATGTAGCAGATCTAACC
131 AAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATGTAGCAGATCTAACC
* * **
9276 TTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGAACAAAT
196 TTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAACAAAT
* *
9341 CGAGGACATTGCAGATATGACTCTCAAATGTTCT-TAAACAAACTCAAGAGGGTTTGGCATC
261 CGAGGACATAGCAGATATGACTCTCAAATGTTCTCAAAACAAACTCAAGAGGGTTTGGCATC
* * * *
9402 CTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGATTCTCAGATGTTCTCAGATACAG
1 CTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATACAG
*
9467 CAGATCTAACCTTCAGATGTTTATACT-AAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
66 CAGATCTAACCTTCAGATGTTTATACTGAAA-CAGATCCAAGATGATTTGGCATCCTTGTGCTTA
* *
9531 CAAGGGACAAATCGAGGACATAGCAGATTTGACTCTCAAAAGTTCTCAAATGTAGCAGATCTAAC
130 CAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATGTAGCAGATCTAAC
* * *
9596 CTTCAGATGTTTATCCTGAAGTAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAACAAA
195 CTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAACAAA
* * *
9661 TCGAGGACGTAGCAGATATGACTCTCGAATGTTCTCAAAACAGACTCAA
260 TCGAGGACATAGCAGATATGACTCTCAAATGTTCTCAAAACAAACTCAA
9710 ACAGATTGAA
Statistics
Matches: 279, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
320 3 0.01
321 265 0.95
322 11 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (322 bp):
CTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATACAG
CAGATCTAACCTTCAGATGTTTATACTGAAACAGATCCAAGATGATTTGGCATCCTTGTGCTTAC
AAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTCAAATGTAGCAGATCTAACC
TTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAACAAAT
CGAGGACATAGCAGATATGACTCTCAAATGTTCTCAAAACAAACTCAAGAGGGTTTGGCATC
Found at i:9566 original size:202 final size:202
Alignment explanation
Indices: 9191--9576 Score: 583
Period size: 202 Copynumber: 1.9 Consensus size: 202
9181 TCCAATATGA
* * *
9191 TTTGGTATTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCT
1 TTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCT
** * * *
9256 CAAATGTAGCAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCT
66 CAAATACAGCAGATCTAACCTTCAGATATTTATACTAAAGCAGATCCAAGATGATTTGGCATCCT
* * *
9321 TGTGTTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTTAAACAAACTC
131 TGTGCTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTTAAACAAACTC
9386 AAGAGGG
196 AAGAGGG
* * * * *
9393 TTTGGCATCCTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGATTCTCAGATGTTCT
1 TTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCT
* * *
9458 CAGATACAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATGGTTTGGCATCCT
66 CAAATACAGCAGATCTAACCTTCAGATATTTATACTAAAGCAGATCCAAGATGATTTGGCATCCT
* *
9523 TGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGACTCTCAAAAGTTCT
131 TGTGCTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCT
9577 CAAATGTAGC
Statistics
Matches: 163, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
202 163 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (202 bp):
TTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCT
CAAATACAGCAGATCTAACCTTCAGATATTTATACTAAAGCAGATCCAAGATGATTTGGCATCCT
TGTGCTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCAAAAGTTCTTAAACAAACTC
AAGAGGG
Found at i:9596 original size:119 final size:119
Alignment explanation
Indices: 9385--9703 Score: 487
Period size: 119 Copynumber: 2.7 Consensus size: 119
9375 TAAACAAACT
* *
9385 CAAGAGGGTTTGGCATCCTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGATTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGACTCTCA
* *
9450 GATGTTCTCAGATACAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATC
66 AATGTTCTCAAATACAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATC
9504 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGACTCTCA
* ** * * *
9569 AAAGTTCTCAAATGTAGCAGATCTAACCTTCAGATGTTTATCCTGAAGTAGATC
66 AATGTTCTCAAATACAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATC
* * * * * *
9623 CAAGATGATTTGGCATCCTTGTACTTACAAGGAACAAATCGAGGACGTAGCAGATATGACTCTCG
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGACTCTCA
9688 AATGTTCTCAAA-ACAG
66 AATGTTCTCAAATACAG
9704 ACTCAAACAG
Statistics
Matches: 181, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
118 2 0.01
119 179 0.99
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (119 bp):
CAAGATGGTTTGGCATCCTTGTGCTTACAAGGGACAAATCGAGGACATAGCAGATTTGACTCTCA
AATGTTCTCAAATACAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATC
Found at i:13615 original size:25 final size:26
Alignment explanation
Indices: 13578--13681 Score: 176
Period size: 25 Copynumber: 4.1 Consensus size: 26
13568 GTACAAATTA
*
13578 ATAATGGGTTAGGTAAATGTTTCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
*
13604 ATAAT-GGTTAGGTAAATATTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
13629 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
13655 ATAAT-GGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
13680 AT
1 AT
13682 GGGAATTTCA
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
25 45 0.61
26 29 0.39
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.37
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTCCATG
Found at i:13638 original size:51 final size:51
Alignment explanation
Indices: 13578--13681 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
13568 GTACAAATTA
*
13578 ATAATGGGTTAGGTAAATGTTTCATGATAATGGTTAGGTAAATATTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATATTCCATG
*
13629 ATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATATTCCATG
13680 AT
1 AT
13682 GGGAATTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.37
Consensus pattern (51 bp):
ATAATGGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATATTCCATG
Found at i:20623 original size:26 final size:26
Alignment explanation
Indices: 20594--20701 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
20584 TGGTACAAAT
* *
20594 TGATAATGGGTTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
20620 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20646 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20672 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20698 TGAT
1 TGAT
20702 GGGAATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27760 original size:32 final size:35
Alignment explanation
Indices: 27703--27788 Score: 90
Period size: 38 Copynumber: 2.5 Consensus size: 35
27693 CAACACATCA
* *
27703 TTTTCATTTGTTAAC-CTTTTAGGATA-A-CAACC
1 TTTTCATTTGATATCTCTTTTAGGATATATCAACC
27735 TTTTCATTTGATATCTCTTTT-GGATATATTTTTCAACC
1 TTTTCATTTGATATCTCTTTTAGGATATA----TCAACC
27773 TTTTCATTTGATATCT
1 TTTTCATTTGATATCT
27789 ATTTCAGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 18 0.40
33 6 0.13
38 21 0.47
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.52
Consensus pattern (35 bp):
TTTTCATTTGATATCTCTTTTAGGATATATCAACC
Found at i:27799 original size:38 final size:40
Alignment explanation
Indices: 27730--27819 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 40
27720 TTTAGGATAA
* ** *
27730 CAACCTTTTCATTTGATATCTCTTTTGGATA-TA-TTTTT
1 CAACCTTTTCATTTGATATCTATTTCAGATATTACCTTTT
27768 CAACCTTTTCATTTGATATCTATTTCAGATATTTACCTTTT
1 CAACCTTTTCATTTGATATCTATTTCAGATA-TTACCTTTT
27809 CAACCTTTTCA
1 CAACCTTTTCA
27820 AGAATTTGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 28 0.62
40 2 0.04
41 15 0.33
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (40 bp):
CAACCTTTTCATTTGATATCTATTTCAGATATTACCTTTT
Found at i:34313 original size:18 final size:19
Alignment explanation
Indices: 34276--34313 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34266 GAGTAATTAT
*
34276 TTAAAATATACATATATAA
1 TTAAAATACACATATATAA
*
34295 TTAAAATACA-ATATTTAA
1 TTAAAATACACATATATAA
34313 T
1 T
34314 AATGCATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAATACACATATATAA
Found at i:36385 original size:87 final size:85
Alignment explanation
Indices: 36294--36566 Score: 227
Period size: 87 Copynumber: 3.1 Consensus size: 85
36284 TGAAAGCCAA
* *
36294 ATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATTATCTGGGATCTGCTTC
1 ATCTGCTATG-CTTCGATTTGTTCCTTGTAAACACAAGGACGCCAAATTATCTTGGATCTGCTTC
36359 AGTATAAACATCTGAAGGTTAG
65 AGTA-AAACATCTGAAGGTTAG
* * * * * *
36381 ATCTGCTATG--T-G-TCTGCTCTCC--GTCGAATA-TAGAGACGTCAGATCTGTTATCTTGGAT
1 ATCTGCTATGCTTCGATTTG-T-TCCTTGT-AAACACAAG-GACGCCA-A---ATTATCTTGGAT
* * *
36439 CTGCTTTGATGTGAAAACATCTGAAAGTCAG
58 CTGC-TTCA-GT-AAAACATCTGAAGGTTAG
* * * *
36470 ATCTGCTATGCTTTCGATTTGCTCCTTGTAAACACAAGAACGCCAAATCATCTTGGATCTACTTC
1 ATCTGCTATGC-TTCGATTTGTTCCTTGTAAACACAAGGACGCCAAATTATCTTGGATCTGCTTC
36535 AGTAAAAACATCTGAAGGTTAG
65 AGT-AAAACATCTGAAGGTTAG
36557 ATCTGCTATG
1 ATCTGCTATG
36567 TATCTGCTCT
Statistics
Matches: 142, Mismatches: 25, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
82 7 0.05
83 10 0.07
84 5 0.04
87 52 0.37
88 6 0.04
89 40 0.28
90 1 0.01
92 5 0.04
93 9 0.06
94 7 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (85 bp):
ATCTGCTATGCTTCGATTTGTTCCTTGTAAACACAAGGACGCCAAATTATCTTGGATCTGCTTCA
GTAAAACATCTGAAGGTTAG
Found at i:44213 original size:119 final size:120
Alignment explanation
Indices: 44031--44253 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
44021 TCCTCGTTCA
*
44031 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
44096 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
44151 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
44213 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
44254 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:44253 original size:40 final size:40
Alignment explanation
Indices: 44029--44253 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
44019 GCTCCTCGTT
* *
44029 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
44069 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
44109 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
44149 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
44188 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
44229 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
44254 CATCATTCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 119 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Done.