Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2382
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, 580
Length: 968
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Found at i:419 original size:132 final size:132
Alignment explanation
Indices: 1--968 Score: 1391
Period size: 132 Copynumber: 7.4 Consensus size: 132
* * * * *
1 GGAGATAAGATCTACAATTTTCAACCTTCTCTGCTGCTGCTTAGAGAGACAAAGCTTTGTGGCTT
1 GGAGATAAGATATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTT
*
66 AAATCTGCTTCCCACTAACTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
66 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
131 AG
131 AG
* * * *
133 GGAGAGAAGATCA-ACAATC-TCAACCTACTCCACTGCTGCTCAGGGAGACAAGG-TTTGGTGGC
1 GGAGATAAGAT-ATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTT-GTGGC
* *
195 TTAAATCTGTTTCCCACTATCTTGGAAAGATAAGA--T---ATCTTTGATTTGCTCCACTACTGC
64 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGC
255 TTAG
129 TTAG
* * * * *
259 GGAGATAAGATATACAATCTTCAACCATCTCCACTACTTCTCAGAGAGACTAGGCTTTGTGGCTT
1 GGAGATAAGATATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTT
** *
324 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTTGATTTGCTCCACTACTGCTT
66 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
389 AG
131 AG
* * * * *
391 GGAGATAAGATATACAATCTTCAACCATCTCCACTACTTCTCAGAGAGACTAGGCTTTGTGGCTT
1 GGAGATAAGATATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTT
*
456 AAATCTGCATCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
66 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
521 AG
131 AG
* * *
523 GGAGATAAGATCA-ACAATC-TCAACCTACTCCGCTGCTGCTCAGCGAGACAAGGCTTGGTGGCT
1 GGAGATAAGAT-ATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCT
** *
586 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCT
65 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCT
651 TAG
130 TAG
* * *
654 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTCCTGCTCAGAGAGACAAGGCTTTTTGGCTT
1 GGAGATAAGATATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTT
* * *
719 AAATCTGCTTTCCACTATCTAGGAAAGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTT
66 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
784 AG
131 AG
* * *
786 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAGAGACAAGG-TTTCGTGGGT
1 GGAGATAAGATATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTT-GTGGCT
* *
850 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACAGCT
65 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCT
915 TAG
130 TAG
** * * *
918 AAAGATAAGTTCTACAATCTTTAACCTTCTCCGCTGCTGCTCAGAGAGACA
1 GGAGATAAGATATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACA
Statistics
Matches: 760, Mismatches: 62, Indels: 28
0.89 0.07 0.03
Matches are distributed among these distances:
125 1 0.00
126 43 0.06
127 67 0.09
128 3 0.00
129 2 0.00
130 3 0.00
131 186 0.24
132 454 0.60
133 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
GGAGATAAGATATACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTT
AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
AG
Found at i:529 original size:44 final size:44
Alignment explanation
Indices: 91--941 Score: 179
Period size: 44 Copynumber: 19.5 Consensus size: 44
81 TAACTTGGAA
* *
91 AGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * * *
135 AGAGAAGATCAACAATC-TCAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* * ***** * * *
178 AGACAAGGTTTGGTGGCTTAAATCTGTTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTACAATCTTTAATCTG-CT-CCACTACTGCTTAGG-G
* *
222 AGATAAGA--T---ATCTTTGATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * *
261 AGATAAGATATACAATCTTCAACCAT-CTCCACTACTTCTCAGAG
1 AGATAAGATTTACAATCTTTAATC-TGCTCCACTACTGCTTAGGG
* * **** * *
305 AGACTAGGCTTT-GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGA-TAAGATTTACAATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
349 AGATAAGATTTGTC-ATCTTTGATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATTT-ACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * *
393 AGATAAGATATACAATCTTCAACCAT-CTCCACTACTTCTCAGAG
1 AGATAAGATTTACAATCTTTAATC-TGCTCCACTACTGCTTAGGG
* * **** * *
437 AGACTAGGCTTT-GTGGCTTAAATCTGCATCCCACTA-T-CTT-GGAA
1 AGA-TAAGATTTACAATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* *
481 AGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
** * * * * * * *
525 AGATAAGATCAACAATC-TCAACCTACTCCGCTGCTGCTCAGCG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** ***** * *
568 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTACAATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
612 AGATAAGATTTGTC-GTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTT-ACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
656 AGATAAGATCTACAATCTTCAACCTTCTCCGCTCCTGCTCAGAG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* * **** * *
700 AGACAAGGCTTT-TTGGCTTAAATCTGCTTTCCACTA-T-C-TAGGAA
1 AGATAA-GATTTACAATCTTTAATCTGC--TCCACTACTGCTTAGG-G
*
744 AGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
788 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAG
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * *
832 AGACAAGGTTT-C-GTGGGTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTACAAT--CTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * * * **
876 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACAGCTTAGAA
1 AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
920 AGATAAG-TTCTACAATCTTTAA
1 AGATAAGATT-TACAATCTTTAA
942 CCTTCTCCGC
Statistics
Matches: 547, Mismatches: 198, Indels: 124
0.63 0.23 0.14
Matches are distributed among these distances:
37 6 0.01
38 2 0.00
39 18 0.03
40 2 0.00
41 1 0.00
42 33 0.06
43 92 0.17
44 324 0.59
45 38 0.07
46 31 0.06
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTACAATCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:855 original size:395 final size:389
Alignment explanation
Indices: 1--968 Score: 1468
Period size: 395 Copynumber: 2.5 Consensus size: 389
* * * *
1 GGAGATAAGATCTACAATTTTCAACCTTCTCTGCTGCTGCTTAGAGAGACAAAGCTTTGTGGCTT
1 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAGAGAC-AAGGTTTGTGGCTT
*
66 AAATCTGCTTCCCACTAACTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
65 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
* * * *
131 AGGGAGAGAAGATCAACAATCTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCT
130 AGGGAGATAAGATCAACAATCTCAACCTACTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCT
* *
196 TAAATCTGTTTCCCACTATCTTGGAAAGATAAGATATCTTTGATTTGCTCCACTACTGCTTAGGG
195 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATATCTTTGATCTGCTCCACTACTGCTTAGGG
* *
261 AGATAAGATATACAATCTTCAACCATCTCCACTACTTCTCAGAGAGACTAGGCTTTGTGGCTTAA
260 AGATAAGATATACAATCTTCAACCATCTCCACTACTGCTCAGAGAGACAAGGCTTTGTGGCTTAA
* ** * *
326 ATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTTGATTTGCTCCACTACTGCTTAG
325 ATCTGCTTCCCACTATCTAGGAAAGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAG
* * * * * * *
391 GGAGATAAGATATACAATCTTCAACCATCTCCACTACTTCTCAGAGAGACTAGGCTTTGTGGCTT
1 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAGAGACAAGG-TTTGTGGCTT
*
456 AAATCTGCATCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
65 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
*
521 AGGGAGATAAGATCAACAATCTCAACCTACTCCGCTGCTGCTCAGCGAGACAAGGCTTGGTGGCT
130 AGGGAGATAAGATCAACAATCTCAACCTACTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCT
*
586 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCT
195 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGA----T-ATCTTTGATCTGCTCCACTACTGCT
* * * * *
651 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTCCTGCTCAGAGAGACAAGGCTTTTTGG
255 TAGGGAGATAAGATATACAATCTTCAACCATCTCCACTACTGCTCAGAGAGACAAGGCTTTGTGG
*
716 CTTAAATCTGCTTTCCACTATCTAGGAAAGATAAGATTTACCATCTTTAATCTGCTCCACTACTG
320 CTTAAATCTGCTTCCCACTATCTAGGAAAGATAAGATTTACCATCTTTAATCTGCTCCACTACTG
781 CTTAG
385 CTTAG
*
786 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAGAGACAAGGTTTCGTGGGTT
1 GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAGAGACAAGGTTT-GTGGCTT
* *
851 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACAGCTT
65 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTT
** * * * *
916 AGAAAGATAAGTTCTACAATCTTTAACCTTCTCCGCTGCTGCTCAGAGAGACA
130 AGGGAGATAAGATCAACAATC-TCAACCTACTCCGCTGCTGCTCAGAGAGACA
Statistics
Matches: 520, Mismatches: 50, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
389 2 0.00
390 209 0.40
394 4 0.01
395 277 0.53
396 28 0.05
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (389 bp):
GGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGAGAGACAAGGTTTGTGGCTTA
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCAACAATCTCAACCTACTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTT
AAATCTGCTTCCCACTATCTTGGAAAGATAAGATATCTTTGATCTGCTCCACTACTGCTTAGGGA
GATAAGATATACAATCTTCAACCATCTCCACTACTGCTCAGAGAGACAAGGCTTTGTGGCTTAAA
TCTGCTTCCCACTATCTAGGAAAGATAAGATTTACCATCTTTAATCTGCTCCACTACTGCTTAG
Done.