Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold719
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: 8743
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:987 original size:44 final size:44
Alignment explanation
Indices: 894--1249 Score: 212
Period size: 44 Copynumber: 8.2 Consensus size: 44
884 TAATGTGATA
* * *
894 TGCTCTACTGCAACTTCAGAGAGATAAGATCTAT-TACTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCTACTTCAATC
* * * * *
938 CGCTCCACTACAAATTCAGGGAGATAGGATTATCGACTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTATCTACTTCAATC
* * * *
982 TGCTCCACTGGAACCTCAGGGAGATAAGATT-TGCTTCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTAT-CTACTTCAATC
** * * * *
1026 TGCTCCACTGTGACTTCAGGGGGATAAGACTTGTTTTC-TCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCTACTTCAATC
* * * * *
1070 TGCTCCGCTGCAACTTCAGGGAGATAAGACTTGTTTTC-TCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCTACTTCAATC
* * * * * * * *
1114 TGCTCCGCTGCAACTTCAAGAAGATAA-A--ACCCAATGCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTATCTACTTCAATC
* ** * *
1155 TGCTCCACTACTGCTT-AGGGAGATAAGATCTAT-T-TTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCTACTTCAATC
* * * **
1197 CGCTCCACTGCAACTTCAGGGAGATAGGATTGAT-TTCTTCTGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATT-ATCTACTTCAATC
1241 TGCTCCACT
1 TGCTCCACT
1250 ACTGCTTAGG
Statistics
Matches: 239, Mismatches: 61, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
40 8 0.03
41 16 0.07
42 17 0.07
43 20 0.08
44 172 0.72
45 5 0.02
46 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGATTATCTACTTCAATC
Found at i:1431 original size:44 final size:43
Alignment explanation
Indices: 1383--1607 Score: 126
Period size: 44 Copynumber: 5.2 Consensus size: 43
1373 GTGCTTAGGA
1383 AGGCAAGATCTGCTATCTTTAATCAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGCTAT-TTTAATCAGCTCCACTGCAACCGATGG
* * * * * * * *
1427 AGGCAAG-TCT-TTGTTTTCGATCTGCTTCGCCGTTAACAC-A-GG
1 AGGCAAGATCTGCTATTTT-AATCAGCTCCACTG-CAAC-CGATGG
*
1469 AAGGCAAGATCTGCTATTTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGATCTGCTA-TTTTAATCAGCTCCACTGCAACCGATGG
* ** * * *
1514 AGGCAAGACTTTG-T-TTTCGAT-ATGCTTCGCTGTTAA-CGCA-GG
1 AGGCAAGA-TCTGCTATTTTAATCA-GCTCCACTG-CAACCG-ATGG
* *
1556 AAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAATCGATGG
1 -AGGCAAGATCTGCTAT-TTTAATCAGCTCCACTGCAACCGATGG
1601 AGGCAAG
1 AGGCAAG
1608 CCTTTGTTTT
Statistics
Matches: 130, Mismatches: 31, Indels: 40
0.65 0.15 0.20
Matches are distributed among these distances:
41 4 0.03
42 31 0.24
43 27 0.21
44 35 0.27
45 28 0.22
46 5 0.04
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (43 bp):
AGGCAAGATCTGCTATTTTAATCAGCTCCACTGCAACCGATGG
Found at i:1501 original size:87 final size:87
Alignment explanation
Indices: 1379--1694 Score: 515
Period size: 87 Copynumber: 3.6 Consensus size: 87
1369 GCTAGTGCTT
* *
1379 AGGAAGGCAAGATCTGCTATCTTTAATCAGCTCCACTGCAACCGATGGAGGCAAGTCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
* *
1444 CGATCTGCTTCGCCGTTAACAC
66 CGATCTGCTTCGCTGTTAACGC
*
1466 AGGAAGGCAAGATCTGCTATTTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
*
1531 CGATATGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* *
1553 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAATCGATGGAGGCAAGCCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
* *
1618 CGGTCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAACGC
* * *
1640 AGGAAGGTAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAG
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
1695 GCTTGATGTG
Statistics
Matches: 213, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 213 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
CGATCTGCTTCGCTGTTAACGC
Found at i:1777 original size:44 final size:43
Alignment explanation
Indices: 1705--2263 Score: 233
Period size: 44 Copynumber: 12.8 Consensus size: 43
1695 GCTTGATGTG
* * * *
1705 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATGATTTCA
* * * ** *
1749 ATCCGCTCCACTGCAAATTCAGGGAGATAGGATTATCGGCTACA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-GATTTCA
* * **
1793 ATATGCTCCACTGTAAAC-TCAGGGAGATAAGATTCACCATCTTCA
1 ATCTGCTCCACTG-CAACTTCAGGGAGATAAGATT-ATGAT-TTCA
* * * * *
1838 GTCTGCCCCACTGCAACTTCA-GGAGGATAAGACT-TGCTTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGA-GATAAGATTATG-AT-TTCA
* * * * ** * *
1882 GTCTGCTCCGCTGTAACCTCAGGGAGATAAGA-CCTGATGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGATTTCA
* * * * *
1923 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATGATTTCA
* * * ** *
1967 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACCGGCTACA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTA-TGATTTCA
**
2011 ATCTGCTCCACTGCAAAC-TCAGGGAGATAAGATTCAACATCTTCA
1 ATCTGCTCCACTGC-AACTTCAGGGAGATAAGATT-ATGAT-TTCA
* * * * * *
2056 GTCTGCCCCACTGCAACTTCAGGGGGATAAGACT-TGCTTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATG-AT-TTCA
* * * * * * ** * *
2100 GTCCGCTCCGCTGCAACCTCAAGGTGATAAGA-CCTGATGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGATTTCA
* ** * * *
2141 ATCTACTTTACTGTAAAC-TCAGAGAGATAAGATCTATTATTTCA
1 ATCTGCTCCACTG-CAACTTCAGGGAGATAAGAT-TATGATTTCA
* * * * *
2185 ATCCGTTCCACTGCAACTTCAAGGAGATAGGATTATCG-TCTACA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-GAT-TTCA
*
2229 ATCTGCTCCACTGCAA-TCTCAGGGAAAGTAAGATT
1 ATCTGCTCCACTGCAACT-TCAGGGAGA-TAAGATT
2264 CGCCGTTGTG
Statistics
Matches: 374, Mismatches: 113, Indels: 55
0.69 0.21 0.10
Matches are distributed among these distances:
41 45 0.12
42 5 0.01
43 23 0.06
44 232 0.62
45 69 0.18
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGATTTCA
Found at i:2076 original size:218 final size:218
Alignment explanation
Indices: 1698--2264 Score: 947
Period size: 218 Copynumber: 2.6 Consensus size: 218
1688 AGGCAAGGCT
1698 TGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCAATCCGCTCCACTGC
1 TGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCAATCCGCTCCACTGC
* * *
1763 AAATTCAGGGAGATAGGATTATCGGCTACAATATGCTCCACTGTAAACTCAGGGAGATAAGATTC
66 AACTTCAGGGAGATAGGATTATCGGCTACAATCTGCTCCACTGCAAACTCAGGGAGATAAGATTC
* *
1828 ACCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTCTTCGGTCTGCTCCGC
131 AACATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTCTTCGGTCCGCTCCGC
* *
1893 TGTAACCTCAGGGAGATAAGACC
196 TGCAACCTCAAGGAGATAAGACC
*
1916 TGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCGATCCGCTCCACTGC
1 TGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCAATCCGCTCCACTGC
*
1981 AACTTCAGGGAGATAGGATTACCGGCTACAATCTGCTCCACTGCAAACTCAGGGAGATAAGATTC
66 AACTTCAGGGAGATAGGATTATCGGCTACAATCTGCTCCACTGCAAACTCAGGGAGATAAGATTC
*
2046 AACATCTTCAGTCTGCCCCACTGCAACTTCAGGGGGATAAGACTTGCTTCTTCGGTCCGCTCCGC
131 AACATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTCTTCGGTCCGCTCCGC
*
2111 TGCAACCTCAAGGTGATAAGACC
196 TGCAACCTCAAGGAGATAAGACC
* * *
2134 TGATGTGATCTACTTTACTGTAAAC-TCAGAGAGATAAGATCTATTATTTCAATCCGTTCCACTG
1 TGATGTGATCTACTCTACTG-CAACTTCAGAGAGATAAGATCTATTATTTCAATCCGCTCCACTG
* * * *
2198 CAACTTCAAGGAGATAGGATTATCGTCTACAATCTGCTCCACTGCAATCTCAGGGAAAGTAAGAT
65 CAACTTCAGGGAGATAGGATTATCGGCTACAATCTGCTCCACTGCAAACTCAGGGAGA-TAAGAT
2263 TC
129 TC
2265 GCCGTTGTGG
Statistics
Matches: 327, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
218 316 0.97
219 11 0.03
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (218 bp):
TGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCAATCCGCTCCACTGC
AACTTCAGGGAGATAGGATTATCGGCTACAATCTGCTCCACTGCAAACTCAGGGAGATAAGATTC
AACATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTCTTCGGTCCGCTCCGC
TGCAACCTCAAGGAGATAAGACC
Found at i:2424 original size:100 final size:100
Alignment explanation
Indices: 2251--2431 Score: 263
Period size: 100 Copynumber: 1.8 Consensus size: 100
2241 GCAATCTCAG
* * ** * *
2251 GGAAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTACAATGTCAGGGAAATAAGATTCG
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTACAAAATCAGGGAAACAAGATTCA
2316 CCGTCGTAGATTTAATTTGTTTCACTATATTTCCA
66 CCGTCGTAGATTTAATTTGTTTCACTATATTTCCA
* * * *
2351 GGAAAGTAAGATTTGCCGTTGTGGCTTCGATCTTTTAAATTGCAAAATCAGGGAAGCAAGATTCA
1 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTACAAAATCAGGGAAACAAGATTCA
*
2416 CCGTCGTAGCTTTAAT
66 CCGTCGTAGATTTAAT
2432 CTGCTCCACT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 70 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (100 bp):
GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTACAAAATCAGGGAAACAAGATTCA
CCGTCGTAGATTTAATTTGTTTCACTATATTTCCA
Found at i:2452 original size:100 final size:99
Alignment explanation
Indices: 2228--2444 Score: 254
Period size: 100 Copynumber: 2.2 Consensus size: 99
2218 TATCGTCTAC
* *
2228 AATCTGCTCCACTGCAATCTCAGGGAAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTA
1 AATCTGCTCCACTGCAATC-CA-GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTA
** * *
2293 CAATGTCAGGGAAATAAGATTCGCCGTCGTAGATTT
64 CAAAATCAGGGAAACAAGATTCACCGTCGTAGATTT
* * * ** * * * *
2329 AATTTGTTTCACTATATTTCCAGGAAAGTAAGATTTGCCGTTGTGGCTTCGATCTTTTAAATTGC
1 AATCTGCTCCACTGCA-ATCCAGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTAC
* *
2394 AAAATCAGGGAAGCAAGATTCACCGTCGTAGCTTT
65 AAAATCAGGGAAACAAGATTCACCGTCGTAGATTT
2429 AATCTGCTCCACTGCA
1 AATCTGCTCCACTGCA
2445 CTGCCAGGCA
Statistics
Matches: 93, Mismatches: 22, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
100 78 0.84
101 13 0.14
102 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (99 bp):
AATCTGCTCCACTGCAATCCAGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTACA
AAATCAGGGAAACAAGATTCACCGTCGTAGATTT
Found at i:3618 original size:7 final size:7
Alignment explanation
Indices: 3599--3665 Score: 81
Period size: 7 Copynumber: 10.0 Consensus size: 7
3589 TTAGCCTCTC
3599 CATTTTT
1 CATTTTT
3606 -ATTTTTT
1 CA-TTTTT
3613 CA-TTTT
1 CATTTTT
3619 --TTTTT
1 CATTTTT
3624 CATTTTT
1 CATTTTT
3631 CATTTTT
1 CATTTTT
3638 CATTTTAT
1 CATTTT-T
3646 CATTTTT
1 CATTTTT
3653 CA-TTTT
1 CATTTTT
3659 CATTTTT
1 CATTTTT
3666 TTGACTCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.08
6 11 0.21
7 30 0.57
8 8 0.15
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:3667 original size:15 final size:15
Alignment explanation
Indices: 3617--3667 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3607 TTTTTTCATT
3617 TTTTTTTCATTTTTCA
1 TTTTTTTCA-TTTTCA
3633 --TTTTTCATTTT-A
1 TTTTTTTCATTTTCA
*
3645 TCATTTTTCATTTTCA
1 T-TTTTTTCATTTTCA
3661 TTTTTTT
1 TTTTTTT
3668 GACTCAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
12 1 0.03
13 4 0.13
14 7 0.23
15 16 0.53
16 2 0.07
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTTTCATTTTCA
Done.