Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1362
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: 1919
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Found at i:150 original size:88 final size:89
Alignment explanation
Indices: 1--1916 Score: 2479
Period size: 88 Copynumber: 21.8 Consensus size: 89
* * * *
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCGGCATCGCTGTCAATACAGGAAGACAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
*
66 GATCTGCTT-TCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * *
89 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCGGCATCGCTGTCAATACAGGAAGACAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
*
154 GATCTGCTT-TCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * * * * *
177 CATCACAATCAAGAGAGGCAAGCTTTGTGTCTTCGACCTGCTTCACCGTCAATACAAGAAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
**
242 GATCTACTT-TCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * *
265 CATCACAACCGAGAGACGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAT
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
330 GATCT-TTTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * * **
353 CATCACATCCGAGGGAGGCAGGGCTTGTGTCTTCGATCTGATTCGCTGTCAATGCAGGAAGATAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
418 GAT-T-TTTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* ** * * * *
440 CATAACAACCGAGGTTGGCAAGGTTTGTGTCTTCGACCTGCTTCACCGTCAATACAAGAAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
**
505 GATCTACTT-TCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * *
528 CATCACAACCAAGAGAGGCAAGCTTTGTGTCTTCGACCTGCTTCACTGTCTATGCAGGAAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
* *
593 GATCTG-TTGTCCTCAACCACCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * *
616 TATCACAACCGAGGGAGGCAATGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
681 GATCTG-TTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * *
704 CATC-CTAATCGAGGGAGGCAAGGTTTGTGTCTTTGACCCGCTTCGCTGTCAATGCAGGAAGGCA
1 CATCAC-AACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCA
* **
768 AGATCT-ATTGTCTTCAACCAAATC
65 AGATCTGTTTGTCTTCAACCAGCTC
* * ** * * * * *
792 CATCATAACTGAGGGAGGCAAGGTCAGTGTCTTTGACATGCTTCCCTGACAATGAAGGAAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
857 GATCTG-TTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * *
880 CATC-CTAATCGAGGGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGGTGACAATACAGGAAGGCA
1 CATCAC-AACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCA
*
944 AGATCTG-TTGTCTTCAACCAGATC
65 AGATCTGTTTGTCTTCAACCAGCTC
* * * * * *
968 CATCAAAACCCAGGGAGGCAAGGTTTGTGTCTTCGATCTGATTCGCTGCCAATGCAGGAAGGGAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
*
1033 GATCTG-TTGTCTTCAACCAGTTC
66 GATCTGTTTGTCTTCAACCAGCTC
* ** * *
1056 CATCACAACCGAGGGAGGCAAGGTTTTTGTCTTCGAAATACTTCGCTGTCAATGCAGGAAGGTAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
*
1121 GATCTG-TTGTCTTCAACCCGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * *
1144 CATCACAACCGAGGGAGGCAAGGCTTGTGTCTTCGACCCGTTTCGCTGTCAATGTAGGTAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
1209 GATCT-TTTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * *
1232 CATCACAACCGAGGGAGGCAAGGCTTGTGTCTTCGACCCGTTTCGCTGTCAATGTAGGTAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
1297 GATCT-TTTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * *
1320 CATCACAACCGAGGGAGGCAAGGCTTGTGTCTTCGACCCGTTTCGCTGTCAATGTAGGTAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
1385 GATCT-TTTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * * *
1408 CATCACAACCGAGGGAGGCAAGGCTTGTGTCTTCGACCCGTTTCGCTGTCAATGTAGGTAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
1473 GATCT-TTTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * *
1496 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCCGTTTCGCTGTCAATGTAGGTAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
*
1561 GATCT-TTTGTCTTCAATCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * *
1584 CATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGTAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
1649 GATCTG-TTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * * *
1672 TATCACAACCGAGGGACGCAAGGTTTGTGTCTTCGATCTGCTACGCTGTCAATGCAGGAAGGCAA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
1737 GATCT-TTTGTCTTCAACCAGCTC
66 GATCTGTTTGTCTTCAACCAGCTC
* * *
1760 CATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGAT-AATGTAGGAAGGCC
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG-TCAATGCAGGAAGGCA
**
1824 AGATCT-ACTGTCTTCAACCAGCTC
65 AGATCTGTTTGTCTTCAACCAGCTC
* * *
1848 CAT----ATCGAGAGAGGCAAGGTTTGTGTCTTTC-ACCTGCTTTGCTGTCAATGCAGGAAGGCA
1 CATCACAACCGAGGGAGGCAAGGTTTGTGTC-TTCGACCTGCTTCGCTGTCAATGCAGGAAGGCA
1908 AGATCTGTT
65 AGATCTGTT
1917 GTC
Statistics
Matches: 1648, Mismatches: 163, Indels: 37
0.89 0.09 0.02
Matches are distributed among these distances:
83 1 0.00
84 53 0.03
85 3 0.00
87 78 0.05
88 1510 0.92
89 3 0.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (89 bp):
CATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAA
GATCTGTTTGTCTTCAACCAGCTC
Found at i:240 original size:44 final size:44
Alignment explanation
Indices: 16--595 Score: 133
Period size: 44 Copynumber: 13.2 Consensus size: 44
6 CAACCGAGGG
* * * * * *
16 AGGCAAGGTTTGTGTCTTCGACCGGCATCGCTGTCAATACAGGA
1 AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
* * * * * * * * * *
60 AGACAAGATCTGCTTTCTTCAACCAGCTCCATC-ACAA-CCGAGGG
1 AGGCAAGATTTG-TGTCTTCGACCAGCTTCACCGTCAATAC-AAGA
* * * * * *
104 AGGCAAGGTTTGTGTCTTCGACCGGCATCGCTGTCAATACAGGA
1 AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
* * * * * * *
148 AGACAAGATCTGCTTTCTTCAACCAGCTCCATC-ACAAT-CAAGA
1 AGGCAAGATTTG-TGTCTTCGACCAGCTTCACCGTCAATACAAGA
* *
191 GAGGCAAGCTTTGTGTCTTCGACCTGCTTCACCGTCAATACAAGA
1 -AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
** * * * * * * *
236 AGGCAAGATCTACTTTCTTCAACCAGCTCCATC-ACAA-CCGAGA
1 AGGCAAGAT-TTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
* * * * * * *
279 GACGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
* * * * * * *
324 AGGCATGATCTTTTGTCTTCAACCAGC-T--CCATCACATCCGAGGG
1 AGGCAAGAT-TTGTGTCTTCGACCAGCTTCACCGTCA-ATAC-AAGA
* ** * * * * * * *
368 AGGCAGGGCTTGTGTCTTCGATCTGATTCGCTGTCAATGCAGGA
1 AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
** * * * *** * * *
412 AGATAAGATTTTTGTCTTCAACCAGCTCCA-TAACAA-CCGAGGT
1 AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATAC-AAGA
* * *
455 TGGCAAGGTTTGTGTCTTCGACCTGCTTCACCGTCAATACAAGA
1 AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
** * * * * * *
499 AGGCAAGATCTACTTTCTTCAACCAGCTCCATC-ACAA-CCAAGA
1 AGGCAAGAT-TTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
* * * * * *
542 GAGGCAAGCTTTGTGTCTTCGACCTGCTTCACTGTCTATGCAGGA
1 -AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
587 AGGCAAGAT
1 AGGCAAGAT
596 CTGTTGTCCT
Statistics
Matches: 358, Mismatches: 153, Indels: 50
0.64 0.27 0.09
Matches are distributed among these distances:
42 5 0.01
43 114 0.32
44 148 0.41
45 87 0.24
46 4 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (44 bp):
AGGCAAGATTTGTGTCTTCGACCAGCTTCACCGTCAATACAAGA
Found at i:255 original size:45 final size:45
Alignment explanation
Indices: 118--263 Score: 109
Period size: 45 Copynumber: 3.3 Consensus size: 45
108 AAGGTTTGTG
* * * * * * *
118 TCTTCGACCGGCATCGCTGTCAATACAGGAAGACAAGATCTGCTT
1 TCTTCGACCAGCTTCACCGTCAATACAAGAAGGCAAGATCTACTT
* * * * * ** *
163 TCTTCAACCAGCTCCATC-ACAAT-CAAGAGAGGCAAGCT-TTGTG
1 TCTTCGACCAGCTTCACCGTCAATACAAGA-AGGCAAGATCTACTT
*
206 TCTTCGACCTGCTTCACCGTCAATACAAGAAGGCAAGATCTACTT
1 TCTTCGACCAGCTTCACCGTCAATACAAGAAGGCAAGATCTACTT
*
251 TCTTCAACCAGCT
1 TCTTCGACCAGCT
264 CCATCACAAC
Statistics
Matches: 72, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
43 20 0.28
44 23 0.32
45 29 0.40
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (45 bp):
TCTTCGACCAGCTTCACCGTCAATACAAGAAGGCAAGATCTACTT
Found at i:386 original size:43 final size:43
Alignment explanation
Indices: 251--386 Score: 105
Period size: 43 Copynumber: 3.1 Consensus size: 43
241 AGATCTACTT
* * * * *
251 TCTTCAACCAGCTCCATCACAACCGAGAGACGCAAGGTTTGTG
1 TCTTCAACCAGCTCCATCACATCCGAGGGAGGCAGGGCTTGTG
* * * * * ** *
294 TCTTCGACCTGCTTCGCTGTCA-ATGC-AGGAAGGCATGATCTTTTG
1 TCTTCAACCAGC-TC-C-ATCACATCCGAGGGAGGCA-GGGCTTGTG
339 TCTTCAACCAGCTCCATCACATCCGAGGGAGGCAGGGCTTGTG
1 TCTTCAACCAGCTCCATCACATCCGAGGGAGGCAGGGCTTGTG
382 TCTTC
1 TCTTC
387 GATCTGATTC
Statistics
Matches: 66, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
42 3 0.05
43 25 0.38
44 18 0.27
45 17 0.26
46 3 0.05
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (43 bp):
TCTTCAACCAGCTCCATCACATCCGAGGGAGGCAGGGCTTGTG
Found at i:1001 original size:43 final size:44
Alignment explanation
Indices: 670--1769 Score: 172
Period size: 44 Copynumber: 25.0 Consensus size: 44
660 GCTGTCAATG
* *
670 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC-CTAATC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCAC-AACC
* * * * ** * * ** **
714 GAGGGAGGCAAGGTTTG-TGTCTTTGACCCGCTTCGC-TGTCAATG
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAG-ATC-CATCACAACC
* * * *
758 CAGGAAGGCAAGATCTATTGTCTTCAACCAAATCCATCATAACT
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * ** * * * **
802 GAGGGAGGCAAGGTCAG-TGTCTTTGA-CATGCTTCCCTGACAATG
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCA-G-ATCCATCACAACC
* * *
846 AAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC-CTAATC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCAC-AACC
* * * * ** * * ** * **
890 GAGGGAGGCAAGGTTTG-TGTCTTTGACCTGCTTCGGTGACAATA
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAG-ATCCATCACAACC
*
934 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCAAAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * **
978 CAGGGAGGCAAGGTTTG-TGTCTTCGATCTGATTCGC-TGC-CAATG
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGA-TC-CAT-CACAACC
* *
1022 CAGGAAGGGAAGATCTGTTGTCTTCAACCAGTTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * ** ** ** **
1066 GAGGGAGGCAAGGT-TTTTGTCTTCGAAATACTTCGC-TGTCAATG
1 CAGGAAGGCAAGATCTGTTGTCTTC-AACCAGATC-CATCACAACC
* * *
1110 CAGGAAGGTAAGATCTGTTGTCTTCAACCCGCTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * ** **
1154 GAGGGAGGCAAG-GCT-TGTGTCTTCGACCCGTTTCGC-TGTCAATG
1 CAGGAAGGCAAGATCTGT-TGTCTTCAACCAG-ATC-CATCACAACC
* * * *
1198 TAGGTAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * ** **
1242 GAGGGAGGCAAG-GCT-TGTGTCTTCGACCCGTTTCGC-TGTCAATG
1 CAGGAAGGCAAGATCTGT-TGTCTTCAACCAG-ATC-CATCACAACC
* * * *
1286 TAGGTAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * ** **
1330 GAGGGAGGCAAG-GCT-TGTGTCTTCGACCCGTTTCGC-TGTCAATG
1 CAGGAAGGCAAGATCTGT-TGTCTTCAACCAG-ATC-CATCACAACC
* * * *
1374 TAGGTAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * ** **
1418 GAGGGAGGCAAG-GCT-TGTGTCTTCGACCCGTTTCGC-TGTCAATG
1 CAGGAAGGCAAGATCTGT-TGTCTTCAACCAG-ATC-CATCACAACC
* * * *
1462 TAGGTAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * * ** **
1506 GAGGGAGGCAAGGTTTG-TGTCTTCGACCCGTTTCGC-TGTCAATG
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAG-ATC-CATCACAACC
* * * * *
1550 TAGGTAGGCAAGATCTTTTGTCTTCAATCAGCTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * * ** **
1594 GA-GAGAGGCAAGGTTTG-TGTCTTCGACCTGCTTCACTGTCAATG
1 CAGGA-AGGCAAGATCTGTTGTCTTCAACCAGATCCA-TCACAACC
* * *
1638 CAGGTAGGCAAGATCTGTTGTCTTCAACCAGCTCTATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
* * * * * * * * * ** **
1682 GAGGGACGCAAGGTTTG-TGTCTTCGATCTGCTACGC-TGTCAATG
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGAT-C-CATCACAACC
* *
1726 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACC
1 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
1770 GAGAGAGGCA
Statistics
Matches: 721, Mismatches: 276, Indels: 118
0.65 0.25 0.11
Matches are distributed among these distances:
42 6 0.01
43 149 0.21
44 414 0.57
45 146 0.20
46 6 0.01
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGTTGTCTTCAACCAGATCCATCACAACC
Done.