Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1228
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: 133656
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
File 2 of 2
Found at i:125796 original size:284 final size:284
Alignment explanation
Indices: 125286--125845 Score: 949
Period size: 284 Copynumber: 2.0 Consensus size: 284
125276 TTAGGCACGG
125286 TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATTTTCTTTTGCATGGAAATCTTTTCT
1 TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATTTTCTTTTGCATGGAAATCTTTTCT
* * *
125351 TTGCCCCATTTTCCTTAATATCAAAATTCATCCCATAATTATGTCAAGCTTCGATTCACGCAAGA
66 TTACCCCATTTTCCTTAATATCAAAATTCATCCCATAACTATGACAAGCTTCGATTCACGCAAGA
*
125416 GGCTCCATGCTTTTCGAGATTGGGAGCTAAGAGCACATTCCCTTCATAAGGATACATGACATTGA
131 GGCTCCATGCTTTTCGAGATTGGGAGCTAAGAACACATTCCCTTCATAAGGATACATGACATTGA
* * *
125481 TGCTTTGGTTTCGCAAGAAAATGTTTTCTTTCCACCGTTTCTGATAGAAGTAAAGTTTGTCTCTT
196 TGCTTTGGTGTCGCAAGAAAAGGTTTTCTTTCCACCGTTTCTGATAGAAGTAAAGTTTGTCTCAT
125546 AAATAAGACAAACAAGCATGACTA
261 AAATAAGACAAACAAGCATGACTA
**
125570 TAAACACATTCTCCTCATTAGGATAAACGATATTCATGATTTTCTTTTGCATGGAAATCTTTTCT
1 TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATTTTCTTTTGCATGGAAATCTTTTCT
* * * * * *
125635 TTACGCTATTTTCCTTATTATCAAAATTCATCCCGTAACTATGACAAGCTTCGATTCTCGTAAGA
66 TTACCCCATTTTCCTTAATATCAAAATTCATCCCATAACTATGACAAGCTTCGATTCACGCAAGA
125700 GGCTCCATGCTTTTCGAGATTGGGAGCTAAGAACACATTCCCTTCATAAGGATACATGACATTGA
131 GGCTCCATGCTTTTCGAGATTGGGAGCTAAGAACACATTCCCTTCATAAGGATACATGACATTGA
* * *
125765 TGCTTTGGTGTCGCAAGAAAAGGTTTTCTTTCCACTGTTTTTTATAGAAGTAAAGTTTGTCTCAT
196 TGCTTTGGTGTCGCAAGAAAAGGTTTTCTTTCCACCGTTTCTGATAGAAGTAAAGTTTGTCTCAT
*
125830 AAATATGACAAACAAG
261 AAATAAGACAAACAAG
125846 AATTGTCATG
Statistics
Matches: 257, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
284 257 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (284 bp):
TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATTTTCTTTTGCATGGAAATCTTTTCT
TTACCCCATTTTCCTTAATATCAAAATTCATCCCATAACTATGACAAGCTTCGATTCACGCAAGA
GGCTCCATGCTTTTCGAGATTGGGAGCTAAGAACACATTCCCTTCATAAGGATACATGACATTGA
TGCTTTGGTGTCGCAAGAAAAGGTTTTCTTTCCACCGTTTCTGATAGAAGTAAAGTTTGTCTCAT
AAATAAGACAAACAAGCATGACTA
Found at i:126556 original size:284 final size:284
Alignment explanation
Indices: 126046--126602 Score: 891
Period size: 284 Copynumber: 2.0 Consensus size: 284
126036 TTAGGCACGG
* *
126046 TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATTTTCTTTTGCATGGAAATCTTTTCT
1 TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATATTCTTTTACATGGAAATCTTTTCT
* *
126111 TTGCCCCATTTTCCTTAATATCAAAATTCATCCCATAATTATGACAAGCTTCGATTCACGTAAGA
66 TTACCCCATTTTCCTTAATATCAAAATTCATCCCATAACTATGACAAGCTTCGATTCACGTAAGA
* *
126176 GGCTCAATGCTTTTCGAGATTGGGAGCTAAACACACATTCCCTTCATAAGGATACATGACATTGA
131 CGCTCAATGCTTTTCGAGATTGGGAGCTAAACACACATTCCCTTCATAAGCATACATGACATTGA
* * *
126241 TGCTTTGGTGTCGCAAGAAAAAGTTTTCTTTCCATCGTTTTTGATAGATGTAAAGTTTGTCTCTT
196 TGCTTTGGTGTCGCAAGAAAAAGTTTTCTTTCCACCGTTTTTCATAGAAGTAAAGTTTGTCTCTT
*
126306 AAATAAGACAAACAAGCATGACTA
261 AAATAAAACAAACAAGCATGACTA
*
126330 TAAACACATTCTCCTCATTAGGATAAACGATATTCACGATATTCTTTTACATGGAAATCTTTTCT
1 TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATATTCTTTTACATGGAAATCTTTTCT
** * ** *
126395 TTATGCTATTTTCCTTAATATCAAAATTCATCCTGTAACTATGACAAGCTTCGATTCTCGTAAGA
66 TTACCCCATTTTCCTTAATATCAAAATTCATCCCATAACTATGACAAGCTTCGATTCACGTAAGA
* *
126460 CGCTCCATGCTTTTCGAGATTGGGAGTTAAGA-ACACATTCCCTTCATAAGCATACATGACATTG
131 CGCTCAATGCTTTTCGAGATTGGGAGCTAA-ACACACATTCCCTTCATAAGCATACATGACATTG
* * * *
126524 ATGCTTTGGTTTTGCAAGAAAATGTTTTCTTTCCACCGTTTTTCATAGAAGTAATGTTTGTCTCT
195 ATGCTTTGGTGTCGCAAGAAAAAGTTTTCTTTCCACCGTTTTTCATAGAAGTAAAGTTTGTCTCT
126589 TAAATAAAACAAAC
260 TAAATAAAACAAAC
126603 GAGAATTGTC
Statistics
Matches: 249, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
284 248 1.00
285 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (284 bp):
TAAACACATTCTCCTCATTAGGATAAACGATATTCACAATATTCTTTTACATGGAAATCTTTTCT
TTACCCCATTTTCCTTAATATCAAAATTCATCCCATAACTATGACAAGCTTCGATTCACGTAAGA
CGCTCAATGCTTTTCGAGATTGGGAGCTAAACACACATTCCCTTCATAAGCATACATGACATTGA
TGCTTTGGTGTCGCAAGAAAAAGTTTTCTTTCCACCGTTTTTCATAGAAGTAAAGTTTGTCTCTT
AAATAAAACAAACAAGCATGACTA
Found at i:126836 original size:158 final size:156
Alignment explanation
Indices: 126661--127156 Score: 391
Period size: 158 Copynumber: 3.1 Consensus size: 156
126651 ACTTTGTCTT
*
126661 CTCA-TAGGAATACACGATATTGATTCTTTGGTTTCGTAGGAAAGGCTTTCTTCTCACAAATTTT
1 CTCATTAGG-ATAAACGATATTGATTCTTTGGTTTCGTAGGAAAGGCTTTCTT-TCACAAATTTT
* *
126725 TGTAAAGTCTGAGTTCGTGCCTCAAATGAGACAAACGAGGATTCTAGTCATGATCTTCATTTTTT
64 TATAAAGTCTGAGTTCGTGCCTCAAATGAGACAAAC-AGGATTCTAGTCATGATCTTCATTCTTT
* *
126790 TTGTGATTAGGGACTATAAACACATTCTC
128 TAGTGATTAGGCACTATAAACACATTCTC
* *** ** * * * * ***
126819 CTCATTAGGATAAACGATATTCACGATTTTCTTTTGCATGGAAA-TCTTTTCTTTCCGCTGTTTT
1 CTCATTAGGATAAACGATATTGATTCTTTGGTTTCGTA-GGAAAGGC-TTTCTTT-CACAAATTT
** * * * **
126883 TTATAGAAGTAAG-GTT--TGTCTCATAAAT-ACGACAAACAAGAAT-T-GTCATGCTAATCCCC
63 TTATA-AAGTCTGAGTTCGTGCCTC--AAATGA-GACAAACAGGATTCTAGTCATG---ATCTTC
* ** *
126942 ATTCTTTTCA-TGATTAGGCACCATAAAC-TTTGTCTT
121 ATTCTTTT-AGTGATTAGGCACTATAAACACAT-TCTC
* * * * *
126978 CTCATAAGGATACACGATATTGGTTCTTTGGTTTCGTAAGAAAGGCTTTCTTGTCACCAATTTTT
1 CTCATTAGGATAAACGATATTGATTCTTTGGTTTCGTAGGAAAGGCTTTCTT-TCACAAATTTTT
* * * * * * *
127043 TTAAAGTCTAAGCTCGTGCCTCAAATGAGACAAACAAGGATTCTACTAATGATTTTCATTCTTTC
65 ATAAAGTCTGAGTTCGTGCCTCAAATGAGACAAAC-AGGATTCTAGTCATGATCTTCATTCTTTT
*
127108 AGTGATTACGCACTATAAACACATTCTC
129 AGTGATTAGGCACTATAAACACATTCTC
127136 CTCATTAGGATAAACGATATT
1 CTCATTAGGATAAACGATATT
127157 CACGATTTTC
Statistics
Matches: 247, Mismatches: 67, Indels: 48
0.68 0.19 0.13
Matches are distributed among these distances:
156 6 0.02
157 11 0.04
158 112 0.45
159 103 0.42
160 11 0.04
161 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (156 bp):
CTCATTAGGATAAACGATATTGATTCTTTGGTTTCGTAGGAAAGGCTTTCTTTCACAAATTTTTA
TAAAGTCTGAGTTCGTGCCTCAAATGAGACAAACAGGATTCTAGTCATGATCTTCATTCTTTTAG
TGATTAGGCACTATAAACACATTCTC
Found at i:127042 original size:159 final size:155
Alignment explanation
Indices: 126549--127043 Score: 393
Period size: 159 Copynumber: 3.1 Consensus size: 155
126539 AAGAAAATGT
* * * * *
126549 TTTCTTTCCACC-GTTTTTCATAGAAGTAATGTTTGTCTCTTAAATAAAACAAACGAGAATTGTC
1 TTTCTTT-CACCAATTTTTTATAGAAGTAAGGTTTGTCTC-TAAAT-AGACAAACAAGAATTGTC
*
126613 ATGCTAATCCCCATTCTTTTCATGATTAGGCACCACAAACTTTGTCTTCTCATAGGAATACACGA
63 ATGCTAATCCCCATTCTTTTCATGATTAGGCACCATAAACTTTGTCTTCTCATAGG-ATACACGA
*
126678 TATTGATTCTTTGGTTTCGTAGGAAAGGC
127 TATTGGTTCTTTGGTTTCGTAGGAAAGGC
* * ** * * *
126707 TTTCTTCTCA-CAAATTTTTGTA-AAGTCTGAGTTCGTGC-CTCAAATGAGACAAACGAGGATTC
1 TTTCTT-TCACCAATTTTTTATAGAAGTAAG-GTTTGT-CTCT-AAAT-AGACAAAC-AAGAAT-
** * ** * * ** *
126769 TAGTCATG---ATCTTCATTTTTTTTGTGATTAGGGACTATAAACACAT-TCTCCTCATTAGGAT
59 T-GTCATGCTAATCCCCATTCTTTTCATGATTAGGCACCATAAAC-TTTGTCTTCTCA-TAGGAT
* * * * * * *
126830 AAACGATATTCACGAT-TTT-CTTTTGCATGGAAA-TC
121 ACACGATATT--GGTTCTTTGGTTTCGTA-GGAAAGGC
**
126865 TTTTCTTTC-CGCTGTTTTTTATAGAAGTAAGGTTTGTCTCATAAATACGACAAACAAGAATTGT
1 -TTTCTTTCAC-CAATTTTTTATAGAAGTAAGGTTTGTCTC-TAAATA-GACAAACAAGAATTGT
126929 CATGCTAATCCCCATTCTTTTCATGATTAGGCACCATAAACTTTGTCTTCTCATAAGGATACACG
62 CATGCTAATCCCCATTCTTTTCATGATTAGGCACCATAAACTTTGTCTTCTCAT-AGGATACACG
*
126994 ATATTGGTTCTTTGGTTTCGTAAGAAAGGC
126 ATATTGGTTCTTTGGTTTCGTAGGAAAGGC
127024 TTTCTTGTCACCAATTTTTT
1 TTTCTT-TCACCAATTTTTT
127044 TAAAGTCTAA
Statistics
Matches: 246, Mismatches: 61, Indels: 59
0.67 0.17 0.16
Matches are distributed among these distances:
156 6 0.02
157 9 0.04
158 104 0.42
159 112 0.46
160 9 0.04
161 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (155 bp):
TTTCTTTCACCAATTTTTTATAGAAGTAAGGTTTGTCTCTAAATAGACAAACAAGAATTGTCATG
CTAATCCCCATTCTTTTCATGATTAGGCACCATAAACTTTGTCTTCTCATAGGATACACGATATT
GGTTCTTTGGTTTCGTAGGAAAGGC
Found at i:127066 original size:317 final size:317
Alignment explanation
Indices: 126533--127185 Score: 1038
Period size: 317 Copynumber: 2.1 Consensus size: 317
126523 GATGCTTTGG
* * * * *
126533 TTTTGCAAGAAAATGTTTTCTTTCCACCGTTTTTCATAGAAGTAATGTTTGTCTCTTAAATAAAA
1 TTTTGCATGGAAATCTTTTCTTTCCACCGTTTTTCATAGAAGTAAGGTTTGTCTCATAAATAAAA
*
126598 CAAACGAGAATTGTCATGCTAATCCCCATTCTTTTCATGATTAGGCACCACAAACTTTGTCTTCT
66 CAAACAAGAATTGTCATGCTAATCCCCATTCTTTTCATGATTAGGCACCACAAACTTTGTCTTCT
*
126663 CATAGGAATACACGATATTGATTCTTTGGTTTCGTAGGAAAGGCTTTCTTCTCACAAATTTTTGT
131 CATAGGAATACACGATATTGATTCTTTGGTTTCGTAAGAAAGGCTTTCTTCTCACAAATTTTTGT
* * * * * * **
126728 AAAGTCTGAGTTCGTGCCTCAAATGAGACAAACGAGGATTCTAGTCATGATCTTCATTTTTTTTG
196 AAAGTCTAAGCTCGTGCCTCAAATGAGACAAACAAGGATTCTACTAATGATCTTCATTCTTTCAG
* *
126793 TGATTAGGGACTATAAACACATTCTCCTCATTAGGATAAACGATATTCACGATTTTC
261 TGATTACGCACTATAAACACATTCTCCTCATTAGGATAAACGATATTCACGATTTTC
* * * **
126850 TTTTGCATGGAAATCTTTTCTTTCCGCTGTTTTTTATAGAAGTAAGGTTTGTCTCATAAATACGA
1 TTTTGCATGGAAATCTTTTCTTTCCACCGTTTTTCATAGAAGTAAGGTTTGTCTCATAAATAAAA
*
126915 CAAACAAGAATTGTCATGCTAATCCCCATTCTTTTCATGATTAGGCACCATAAACTTTGTCTTCT
66 CAAACAAGAATTGTCATGCTAATCCCCATTCTTTTCATGATTAGGCACCACAAACTTTGTCTTCT
* * * *
126980 CATAAGG-ATACACGATATTGGTTCTTTGGTTTCGTAAGAAAGGCTTTCTTGTCACCAATTTTTT
131 CAT-AGGAATACACGATATTGATTCTTTGGTTTCGTAAGAAAGGCTTTCTTCTCACAAATTTTTG
*
127044 TAAAGTCTAAGCTCGTGCCTCAAATGAGACAAACAAGGATTCTACTAATGATTTTCATTCTTTCA
195 TAAAGTCTAAGCTCGTGCCTCAAATGAGACAAACAAGGATTCTACTAATGATCTTCATTCTTTCA
127109 GTGATTACGCACTATAAACACATTCTCCTCATTAGGATAAACGATATTCACGATTTTC
260 GTGATTACGCACTATAAACACATTCTCCTCATTAGGATAAACGATATTCACGATTTTC
127167 TTTTGCATGGAAATCTTTT
1 TTTTGCATGGAAATCTTTT
127186 TTGGGCCATA
Statistics
Matches: 307, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
317 304 0.99
318 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (317 bp):
TTTTGCATGGAAATCTTTTCTTTCCACCGTTTTTCATAGAAGTAAGGTTTGTCTCATAAATAAAA
CAAACAAGAATTGTCATGCTAATCCCCATTCTTTTCATGATTAGGCACCACAAACTTTGTCTTCT
CATAGGAATACACGATATTGATTCTTTGGTTTCGTAAGAAAGGCTTTCTTCTCACAAATTTTTGT
AAAGTCTAAGCTCGTGCCTCAAATGAGACAAACAAGGATTCTACTAATGATCTTCATTCTTTCAG
TGATTACGCACTATAAACACATTCTCCTCATTAGGATAAACGATATTCACGATTTTC
Found at i:127718 original size:13 final size:13
Alignment explanation
Indices: 127700--127725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127690 TACACAAAGT
127700 ATGTATCGATACA
1 ATGTATCGATACA
127713 ATGTATCGATACA
1 ATGTATCGATACA
127726 CAAAAAAAAT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:133600 original size:13 final size:13
Alignment explanation
Indices: 133582--133615 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
133572 AATCCCCCTC
133582 TATCGATA-CAGTG
1 TATCGATACCA-TG
133595 TATCGATACCATG
1 TATCGATACCATG
133608 TATCGATA
1 TATCGATA
133616 TAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 18 0.90
14 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (13 bp):
TATCGATACCATG
Done.