Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold290
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: 28402
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:6943 original size:38 final size:38
Alignment explanation
Indices: 6870--7035 Score: 262
Period size: 38 Copynumber: 4.3 Consensus size: 38
6860 TCCAATTACT
* *
6870 AGCATAAAGCCTG-GGGAACTATAAACCCGAATATAATACC
1 AGCATTAAGCCTGCGGG-ACT-T-AACCCGGATATAATACC
6910 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
*
6948 AGCATTAAGCCTGCGGGATTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
*
6986 AGCATTAAGCCTGCAGGACTTAACCCGGATATAATACC
1 AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
7024 AGCATTAAGCCT
1 AGCATTAAGCCT
7036 ATTTAATCAT
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
38 101 0.84
39 1 0.01
40 15 0.12
41 3 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (38 bp):
AGCATTAAGCCTGCGGGACTTAACCCGGATATAATACC
Found at i:10414 original size:27 final size:26
Alignment explanation
Indices: 10351--10462 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
10341 AGCATGGCTG
* *
10351 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
10377 CCAAAAGCAGATAATCGTGGCAGAGCCA
1 CCAGAA-CAGATAAT-GTGGCAGAGCCA
* *
10405 CTAGAACAGATATATGTGGCAAAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
10432 CCCGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
10459 CCAG
1 CCAG
10463 GACGTTTCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 6 0.08
27 49 0.69
28 16 0.23
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:11768 original size:377 final size:377
Alignment explanation
Indices: 11074--11828 Score: 1510
Period size: 377 Copynumber: 2.0 Consensus size: 377
11064 CCTTAGGCAC
11074 TAGCGAACCTACCTTTGCCGAAGTTAACGACTAGGTTTAGATCCAGTTGTTCCACTTGTCCAAGC
1 TAGCGAACCTACCTTTGCCGAAGTTAACGACTAGGTTTAGATCCAGTTGTTCCACTTGTCCAAGC
11139 CCTTGATCAGAAGCTTCTAGATCACAGTATTATCAAAATAAAATAGTTATCATAACCCTTAGGGC
66 CCTTGATCAGAAGCTTCTAGATCACAGTATTATCAAAATAAAATAGTTATCATAACCCTTAGGGC
11204 TTCAAGCCCAAATCGACAGCCTCCCTAGCCTTTAGAGGTTTCGGCTTCTTCTAAAACCTGAAATA
131 TTCAAGCCCAAATCGACAGCCTCCCTAGCCTTTAGAGGTTTCGGCTTCTTCTAAAACCTGAAATA
11269 AAGAATAGGTTCAAAGACTTACCACCGGTTCCTTCGATCAATGATTCCAATTAATTCCTACTCGA
196 AAGAATAGGTTCAAAGACTTACCACCGGTTCCTTCGATCAATGATTCCAATTAATTCCTACTCGA
11334 TTCTGATGCAGATCTACCCCTTAAATGATAACAAAATTCGAGCCTTTAGTGATCTTAAAATTCAG
261 TTCTGATGCAGATCTACCCCTTAAATGATAACAAAATTCGAGCCTTTAGTGATCTTAAAATTCAG
11399 CTATGTCCCTATGGCTATGCGTTTTCAGCTTTTTGTAATAGTGGAGAAAAGA
326 CTATGTCCCTATGGCTATGCGTTTTCAGCTTTTTGTAATAGTGGAGAAAAGA
11451 TAGCGAACCTACCTTTGCCGAAGTTAACGACTAGGTTTAGATCCAGTTGTTCCACTTGTCCAAGC
1 TAGCGAACCTACCTTTGCCGAAGTTAACGACTAGGTTTAGATCCAGTTGTTCCACTTGTCCAAGC
11516 CCTTGATCAGAAGCTTCTAGATCACAGTATTATCAAAATAAAATAGTTATCATAACCCTTAGGGC
66 CCTTGATCAGAAGCTTCTAGATCACAGTATTATCAAAATAAAATAGTTATCATAACCCTTAGGGC
11581 TTCAAGCCCAAATCGACAGCCTCCCTAGCCTTTAGAGGTTTCGGCTTCTTCTAAAACCTGAAATA
131 TTCAAGCCCAAATCGACAGCCTCCCTAGCCTTTAGAGGTTTCGGCTTCTTCTAAAACCTGAAATA
11646 AAGAATAGGTTCAAAGACTTACCACCGGTTCCTTCGATCAATGATTCCAATTAATTCCTACTCGA
196 AAGAATAGGTTCAAAGACTTACCACCGGTTCCTTCGATCAATGATTCCAATTAATTCCTACTCGA
11711 TTCTGATGCAGATCTACCCCTTAAATGATAACAAAATTCGAGCCTTTAGTGATCTTAAAATTCAG
261 TTCTGATGCAGATCTACCCCTTAAATGATAACAAAATTCGAGCCTTTAGTGATCTTAAAATTCAG
11776 CTATGTCCCTATGGCTATGCGTTTTCAGCTTTTTGTAATAGTGGAGAAAAGA
326 CTATGTCCCTATGGCTATGCGTTTTCAGCTTTTTGTAATAGTGGAGAAAAGA
11828 T
1 T
11829 GAGGATTTGT
Statistics
Matches: 378, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
377 378 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (377 bp):
TAGCGAACCTACCTTTGCCGAAGTTAACGACTAGGTTTAGATCCAGTTGTTCCACTTGTCCAAGC
CCTTGATCAGAAGCTTCTAGATCACAGTATTATCAAAATAAAATAGTTATCATAACCCTTAGGGC
TTCAAGCCCAAATCGACAGCCTCCCTAGCCTTTAGAGGTTTCGGCTTCTTCTAAAACCTGAAATA
AAGAATAGGTTCAAAGACTTACCACCGGTTCCTTCGATCAATGATTCCAATTAATTCCTACTCGA
TTCTGATGCAGATCTACCCCTTAAATGATAACAAAATTCGAGCCTTTAGTGATCTTAAAATTCAG
CTATGTCCCTATGGCTATGCGTTTTCAGCTTTTTGTAATAGTGGAGAAAAGA
Found at i:12108 original size:39 final size:36
Alignment explanation
Indices: 12055--12138 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 36
12045 TATAGAGCAA
*
12055 AAAAGAAAAAGAAGAGGAAAA-AGTAGATGGAGAGAAGAAG
1 AAAAG-AAAAGAAGAAGAAAAGAG--GATGGA-AGAAG-AG
12095 AAAAGAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
1 AAAAGAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
*
12131 AGAAGAAA
1 AAAAGAAA
12139 CGATGAAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 9 0.22
37 5 0.12
38 6 0.15
39 14 0.34
40 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (36 bp):
AAAAGAAAAGAAGAAGAAAAGAGGATGGAAGAAGAG
Found at i:17643 original size:18 final size:19
Alignment explanation
Indices: 17619--17661 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17609 ATATAAAGAT
17619 ATATAAGTAAA-AT-AAATA
1 ATATAAG-AAATATCAAATA
*
17637 TTATAAGAAATATCAAATA
1 ATATAAGAAATATCAAATA
17656 ATATAA
1 ATATAA
17662 CATAGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 10 0.48
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
ATATAAGAAATATCAAATA
Found at i:21300 original size:18 final size:16
Alignment explanation
Indices: 21276--21318 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
21266 AATGTTAAGA
*
21276 ATTTTTTATTAAATTT
1 ATTTTTTATTAAAGTT
21292 AAGTTTTTTA-TAAAGTT
1 -A-TTTTTTATTAAAGTT
21309 ATTTTTTATT
1 ATTTTTTATT
21319 GTATGACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 7 0.30
16 2 0.09
17 7 0.30
18 7 0.30
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (16 bp):
ATTTTTTATTAAAGTT
Found at i:22944 original size:16 final size:16
Alignment explanation
Indices: 22911--22944 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22901 GACAACTGTT
* *
22911 AACATTAATGGGAGAC
1 AACATTAATGGAAAAC
22927 AACATTAATGGAAAAC
1 AACATTAATGGAAAAC
22943 AA
1 AA
22945 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGAAAAC
Found at i:25764 original size:21 final size:21
Alignment explanation
Indices: 25738--25778 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25728 AGACGAGCAA
* *
25738 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
25759 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
25779 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Done.