Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_69 ID=scaffold_69-JGI_221_v2.0
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: 18098
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.29
Warning! 685 characters in sequence are not A, C, G, or T
Found at i:4595 original size:15 final size:13
Alignment explanation
Indices: 4577--4630 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 13
4567 AAAACAATTC
4577 AAAATCAAAATCAAA
1 AAAATCAAAAT--AA
*
4592 AAAATCGAAATAA
1 AAAATCAAAATAA
4605 AAAATC--AATAA
1 AAAATCAAAATAA
*
4616 AAAATGAAAA-AA
1 AAAATCAAAATAA
4628 AAA
1 AAA
4631 TGAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 10 0.29
12 5 0.14
13 10 0.29
15 10 0.29
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (13 bp):
AAAATCAAAATAA
Found at i:4608 original size:22 final size:20
Alignment explanation
Indices: 4583--4639 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 20
4573 ATTCAAAATC
4583 AAAATCAAAAAAATCGAAATAA
1 AAAATCAAAAAAAT-GAAA-AA
4605 AAAATCAATAAAAAATGAAAAA
1 AAAATC-A-AAAAAATGAAAAA
*
4627 AAAATGAAAAAAA
1 AAAATCAAAAAAA
4640 AACAAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 6 0.19
21 1 0.03
22 13 0.41
23 5 0.16
24 7 0.22
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAATCAAAAAAATGAAAAA
Found at i:4641 original size:11 final size:11
Alignment explanation
Indices: 4589--4660 Score: 76
Period size: 11 Copynumber: 6.5 Consensus size: 11
4579 AATCAAAATC
4589 AAAAAAATCGAA
1 AAAAAAAT-GAA
*
4601 ATAAAAAATCAA
1 A-AAAAAATGAA
*
4613 TAAAAAATGAA
1 AAAAAAATGAA
4624 AAAAAAATGAA
1 AAAAAAATGAA
*
4635 AAAAAAA-CAA
1 AAAAAAATGAA
4645 AAAAGAAA-GAA
1 AAAA-AAATGAA
4656 AAAAA
1 AAAAA
4661 GAAAAAATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
10 7 0.13
11 35 0.67
12 3 0.06
13 7 0.13
ACGTcount: A:0.81, C:0.04, G:0.07, T:0.08
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:4696 original size:7 final size:7
Alignment explanation
Indices: 4625--4700 Score: 50
Period size: 7 Copynumber: 10.6 Consensus size: 7
4615 AAAAATGAAA
4625 AAAAAATG
1 AAAAAA-G
4633 AAAAAA-
1 AAAAAAG
4639 AAACAAA-
1 AAA-AAAG
4646 AAAGAAAG
1 AAA-AAAG
4654 AAAAAAAG
1 -AAAAAAG
*
4662 AAAAAAT
1 AAAAAAG
* *
4669 CAAAATG
1 AAAAAAG
*
4676 -AAAATG
1 AAAAAAG
4682 ACAAAAAG
1 A-AAAAAG
4690 AAAAAAG
1 AAAAAAG
4697 AAAA
1 AAAA
4701 GGAAAGGACC
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
6 9 0.16
7 29 0.51
8 16 0.28
9 3 0.05
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:5623 original size:17 final size:18
Alignment explanation
Indices: 5596--5630 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5586 GCTTTAAGTC
*
5596 CAAAAATTAAAAATAAAT
1 CAAAAATTAAAAAAAAAT
5614 CAAAAA-TAAAAAAAAAT
1 CAAAAATTAAAAAAAAAT
5631 AGAGAGGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (18 bp):
CAAAAATTAAAAAAAAAT
Found at i:7251 original size:44 final size:44
Alignment explanation
Indices: 7116--7692 Score: 157
Period size: 44 Copynumber: 13.1 Consensus size: 44
7106 ATTACAGATA
* ** * * *
7116 TTGCCTTCCTGGATCAACAGCGAAGCAGATCGAAGATACCACCC
1 TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACTAGCC
* ** * * * * *
7160 TTGCCTCCCTGGGTAG-CAGCGGAGCAGGAT-GAAAATAGC-AGATC
1 TTGCCTTCCTGTATTGACAGCGAAGCA-GATCGAAGACA-CTAG-CC
* *
7204 TTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACTAGCC
1 TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACTAGCC
** * * ** * * *
7248 TTGCC-TCACTGGGTTG-CAGCGGAGCAGGTTAAAGATAGTAGATC
1 TTGCCTTC-CTGTATTGACAGCGAAGCAGATCGAAGACACTAG-CC
* * * * *
7292 TTGTCTTCCTGCATTGACAGCGAAACAGATCAAAGACACCAGCC
1 TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACTAGCC
* ** * * ** * *
7336 TTGCCTCCCTGGGTT-ACAG-TAGAGCAGGTTAAAGATAGC-AGATC
1 TTGCCTTCCTGTATTGACAGCGA-AGCAGATCGAAGACA-CTAG-CC
* *
7380 TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCC
1 TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACTAGCC
* * * * * * **
7424 TTGCCTCCCTG-GTTG-CAGCGGAGCAGGTTGAAAACAGC-AGATA
1 TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACA-CTAG-CC
* * * * *
7467 TTGCCTTCCTGTACTGATAGTGAAGCAGATCGAAGATACTAGCA
1 TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACTAGCC
** * * * ** * *
7511 TTGCC-TCACTGGGTTG-CAGTGGAGCAGGTTAAAGATAGC-AGATC
1 TTGCCTTC-CTGTATTGACAGCGAAGCAGATCGAAGACA-CTAG-CC
* * * *
7555 TTGTCTTCTTAG-ATTGACAGCGAAGCAGATCGAAAACACCAGCC
1 TTGCCTTCCT-GTATTGACAGCGAAGCAGATCGAAGACACTAGCC
* * * * * * *
7599 TTGCCTCCCTCG-GTTG-CAGCGGAGCAGGT-TATAGATAGC-AGATC
1 TTGCCTTCCT-GTATTGACAGCGAAGCAGATCGA-AGACA-CTAG-CC
* * * *
7643 TTGCTTTCCTGTACTGACAGTGAAGCAGATCAAAGACACTAGCC
1 TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACTAGCC
7687 TTGCCT
1 TTGCCT
7693 CACTAGGTTA
Statistics
Matches: 377, Mismatches: 121, Indels: 70
0.66 0.21 0.12
Matches are distributed among these distances:
42 21 0.06
43 104 0.28
44 147 0.39
45 103 0.27
46 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.23
Consensus pattern (44 bp):
TTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACTAGCC
Found at i:7757 original size:351 final size:352
Alignment explanation
Indices: 7110--7853 Score: 994
Period size: 351 Copynumber: 2.1 Consensus size: 352
7100 TTAAAAATTA
* * * * * *
7110 CAGATATTGCCTTCCTGGATCAACAGCGAAGCAGATCGAAGATACCACCCTTGCCTCCCTGGGTA
1 CAGATATTGCCTTCCTGTATCGATAGTGAAGCAGATCGAAGATACCACCATTGCCTCACTGGGTA
* *
7175 GCAGCGGAGCAGGATGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGA
66 GCAGCGGAGCAGGATGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAAA
* * *
7240 CACTAGCCTTGCCTCACTGGGTTGCAGCGGAGCAGGTTAAAGATAGTAGATCTTGTCTTCCTGCA
131 CACCAGCCTTGCCTCACTCGGTTGCAGCGGAGCAGGTTAAAGATAGCAGATCTTGTCTTCCTGCA
* * * * *
7305 TTGACAGCGAAACAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTACAGTAGAGCAGGTTAAAG
196 CTGACAGCGAAACAGATCAAAGACACCAGCCTTGCCTCACTAGGTTACAGCAGAGCAAGTTAAAG
* * *
7370 ATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCCCT-
261 ATAGCAGATCTTGCCTTCCTGCACTAACAACGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTG
*
7434 GGTTGCAGCGGAGCAGGTTGAAAACAG
326 GGTTGCAGCGGAGCAGGTTGAAAACAC
* *
7461 CAGATATTGCCTTCCTGTA-CTGATAGTGAAGCAGATCGAAGATACTAGCATTGCCTCACTGGGT
1 CAGATATTGCCTTCCTGTATC-GATAGTGAAGCAGATCGAAGATACCACCATTGCCTCACTGGGT
* * * * * *
7525 TGCAGTGGAGCAGG-TTAAAGATAGCAGATCTTGTCTTCTTAG-ATTGACAGCGAAGCAGATCGA
65 AGCAGCGGAGCAGGATGAAA-ATAGCAGATCTTGCCTTCCT-GTACTGACAGCGAAGCAGATCGA
* *
7588 AAACACCAGCCTTGCCTCCCTCGGTTGCAGCGGAGCAGGTTATAGATAGCAGATCTTG-CTTTCC
128 AAACACCAGCCTTGCCTCACTCGGTTGCAGCGGAGCAGGTTAAAGATAGCAGATCTTGTC-TTCC
* * * *
7652 TGTACTGACAGTGAAGCAGATCAAAGACACTAGCCTTGCCTCACTAGGTTACAGCAGAGCAAGTT
192 TGCACTGACAGCGAAACAGATCAAAGACACCAGCCTTGCCTCACTAGGTTACAGCAGAGCAAGTT
* * * *
7717 GAAGATAGCAGATCTTGCCTTCCTGTACTAACAACGAAGCAGATCGAAGACACCAGCTTTGCCTC
257 AAAGATAGCAGATCTTGCCTTCCTGCACTAACAACGAAGCAGATCGAAGACACAAGCCTTGCCTC
* * *
7782 CTTGGGTTGTAGCGGAGTAGGTTGAAAACAC
322 CCTGGGTTGCAGCGGAGCAGGTTGAAAACAC
* * * * * *
7813 CAAATCTTACCTTCTTGTATCGGTAATGAAGCAGATCGAAG
1 CAGATATTGCCTTCCTGTATCGATAGTGAAGCAGATCGAAG
7854 CCAAAAATCC
Statistics
Matches: 340, Mismatches: 47, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
350 6 0.02
351 275 0.81
352 58 0.17
353 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (352 bp):
CAGATATTGCCTTCCTGTATCGATAGTGAAGCAGATCGAAGATACCACCATTGCCTCACTGGGTA
GCAGCGGAGCAGGATGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAAA
CACCAGCCTTGCCTCACTCGGTTGCAGCGGAGCAGGTTAAAGATAGCAGATCTTGTCTTCCTGCA
CTGACAGCGAAACAGATCAAAGACACCAGCCTTGCCTCACTAGGTTACAGCAGAGCAAGTTAAAG
ATAGCAGATCTTGCCTTCCTGCACTAACAACGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGTTGAAAACAC
Found at i:7826 original size:88 final size:87
Alignment explanation
Indices: 7087--7809 Score: 815
Period size: 88 Copynumber: 8.2 Consensus size: 87
7077 TCCATATACA
* * * * *
7087 GCAGTGGAGTAGGTTAAAAATTA-CAGATATTGCCTTCCTGGA-TCAACAGCGAAGCAGATCGAA
1 GCAGCGGAGCAGGTT-AAAA-TAGCAGATCTTGCCTTCCTGTACT-GACAGCGAAGCAGATCGAA
* * *
7150 GATACCACCCTTGCCTCCCTGGGTA
63 GACACCAGCCTTGCCTCCCTGGGTT
* *
7175 GCAGCGGAGCAGGATGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGA
1 GCAGCGGAGCAGG-TTAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* *
7240 CACTAGCCTTGCCTCACTGGGTT
65 CACCAGCCTTGCCTCCCTGGGTT
* * * * * *
7263 GCAGCGGAGCAGGTTAAAGATAGTAGATCTTGTCTTCCTGCATTGACAGCGAAACAGATCAAAGA
1 GCAGCGGAGCAGGTTAAA-ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
7328 CACCAGCCTTGCCTCCCTGGGTT
65 CACCAGCCTTGCCTCCCTGGGTT
* ** * *
7351 ACAGTAGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGA
1 GCAGCGGAGCAGGTTAAA-ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
*
7416 CACAAGCCTTGCCTCCCT-GGTT
65 CACCAGCCTTGCCTCCCTGGGTT
* * * *
7438 GCAGCGGAGCAGGTTGAAAACAGCAGATATTGCCTTCCTGTACTGATAGTGAAGCAGATCGAAGA
1 GCAGCGGAGCAGGTT-AAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* * * *
7503 TACTAGCATTGCCTCACTGGGTT
65 CACCAGCCTTGCCTCCCTGGGTT
* * * * *
7526 GCAGTGGAGCAGGTTAAAGATAGCAGATCTTGTCTTCTTAG-ATTGACAGCGAAGCAGATCGAAA
1 GCAGCGGAGCAGGTTAAA-ATAGCAGATCTTGCCTTCCT-GTACTGACAGCGAAGCAGATCGAAG
*
7590 ACACCAGCCTTGCCTCCCTCGGTT
64 ACACCAGCCTTGCCTCCCTGGGTT
* * * *
7614 GCAGCGGAGCAGGTTATAGATAGCAGATCTTGCTTTCCTGTACTGACAGTGAAGCAGATCAAAGA
1 GCAGCGGAGCAGGTTA-AAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* * *
7679 CACTAGCCTTGCCTCACTAGGTT
65 CACCAGCCTTGCCTCCCTGGGTT
* * * * * *
7702 ACAGCAGAGCAAGTTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAACGAAGCAGATCGAAGA
1 GCAGCGGAGCAGGTT-AAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* *
7767 CACCAGCTTTGCCTCCTTGGGTT
65 CACCAGCCTTGCCTCCCTGGGTT
* *
7790 GTAGCGGAGTAGGTTGAAAA
1 GCAGCGGAGCAGGTT-AAAA
7810 CACCAAATCT
Statistics
Matches: 536, Mismatches: 88, Indels: 22
0.83 0.14 0.03
Matches are distributed among these distances:
87 80 0.15
88 451 0.84
89 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (87 bp):
GCAGCGGAGCAGGTTAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC
ACCAGCCTTGCCTCCCTGGGTT
Found at i:8005 original size:44 final size:45
Alignment explanation
Indices: 7945--8032 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
7935 ATCGCATCAA
* * *
7945 GTCTTATCTCCTTGAAGTTGCAGCGGAGTGGACTGAGAA-AGCAG
1 GTCTTATCCCCCTGAAGTTGCAGCGGAGTAGACTGAGAATAGCAG
* *
7989 GTCTTATCCCCCTGAAGTTGCAGTGGGGTAGACTGAGAATAGCA
1 GTCTTATCCCCCTGAAGTTGCAGCGGAGTAGACTGAGAATAGCA
8033 AATCTTACGT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 34 0.89
45 4 0.11
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (45 bp):
GTCTTATCCCCCTGAAGTTGCAGCGGAGTAGACTGAGAATAGCAG
Found at i:8117 original size:50 final size:50
Alignment explanation
Indices: 8063--8422 Score: 238
Period size: 50 Copynumber: 7.2 Consensus size: 50
8053 GCAGTGGAAC
* * * * *
8063 AGATTGAAGCCACAATGGCAAATATTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACATTGCAGTTAAAA
* * * * ** ** *
8113 AGATT-AAACCTACAACAGCGAATCTTATTTCCCAGGCGGTGCAGTGGAAC
1 AGATTGAAGCC-ACAACGGCGAATCTTACTTCCCAGACATTGCAGTTAAAA
* * * * ** *
8163 AGTTTAAAGCCACAACGGTGAATCTTACTTCCCTGACATCCCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACATTGCAGTTAAAA
* * * ** * *
8213 AGATTGAAGCCACAACGGCAAATCTTACTTCTCAGGCGGTGCAGTGAAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACATTGCAGTTAAAA
* * **
8263 AGATTGAAGCTATAATAGCGAATCTTACTTTCCC-GACATTGCAGTTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGACATTGCAGTTAAAA
* * * * * * ** * ** *
8313 AGATTAAAGCTACAACAGCGAATATTATTTCCCAGGCGGTGTAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACATTGCAGTTAAAA
* * * * *
8363 AGTTTAAAGCCACAATGGCGAATCTTACTGCCCCGACATTGCAGTTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACATTGCAGTTAAAA
*
8413 TGATTGAAGC
1 AGATTGAAGC
8423 TACAGGCTAC
Statistics
Matches: 222, Mismatches: 84, Indels: 8
0.71 0.27 0.03
Matches are distributed among these distances:
49 9 0.04
50 205 0.92
51 8 0.04
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACATTGCAGTTAAAA
Found at i:8211 original size:100 final size:100
Alignment explanation
Indices: 8033--8426 Score: 484
Period size: 100 Copynumber: 3.9 Consensus size: 100
8023 GAGAATAGCA
* * * * *
8033 AATCTTACGTCCCAGGCGGTGCAGTGGAACAGATTGAAGCCACAATGGCAAATATTGCTTCCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGCGAATCTTACTTCCCCG
8098 ACATTGCAGTTAAAAAGATTAAACCTACAACAGCG
66 ACATTGCAGTTAAAAAGATTAAACCTACAACAGCG
* * * * *
8133 AATCTTATTTCCCAGGCGGTGCAGTGGAACAGTTTAAAGCCACAACGGTGAATCTTACTTCCCTG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGCGAATCTTACTTCCCCG
** * * * *
8198 ACATCCCAATTAAAAAGATTGAAGCC-ACAACGGCA
66 ACATTGCAGTTAAAAAGATT-AAACCTACAACAGCG
* * * * * * *
8233 AATCTTACTTCTCAGGCGGTGCAGTGAAACAGATTGAAGCTATAATAGCGAATCTTACTTTCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGCGAATCTTACTTCCCCG
*
8298 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
66 ACATTGCAGTTAAAAAGATTAAACCTACAACAGCG
* * * * *
8333 AATATTATTTCCCAGGCGGTGTAGTGGAACAGTTTAAAGCCACAATGGCGAATCTTACTGCCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGCGAATCTTACTTCCCCG
* * *
8398 ACATTGCAGTTAAAATGATTGAAGCTACA
66 ACATTGCAGTTAAAAAGATTAAACCTACA
8427 GGCTACGTAT
Statistics
Matches: 243, Mismatches: 49, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
99 3 0.01
100 236 0.97
101 4 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (100 bp):
AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGCGAATCTTACTTCCCCG
ACATTGCAGTTAAAAAGATTAAACCTACAACAGCG
Found at i:8345 original size:150 final size:150
Alignment explanation
Indices: 8063--8345 Score: 316
Period size: 150 Copynumber: 1.9 Consensus size: 150
8053 GCAGTGGAAC
* * * * *
8063 AGATTGAAGCCACAATGGCAAATATTGCTTCCCCGACATTGCAGTTAAAAAGATTAAACCTACAA
1 AGATTGAAGCCACAACGGCAAATATTACTTCCCAGACAGTGCAGTGAAAAAGATTAAACCTACAA
* * * * * * * *
8128 CAGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACAGTTTAAAGCCACAACGGTGAATCTTACTT
66 CAGCGAATCTTATTTCCCAGACAGTGCAGTGAAAAAGATTAAAGCCACAACAGCGAATATTACTT
8193 CCCTGACATCCCAATTAAAA
131 CCCTGACATCCCAATTAAAA
* * * * * * * *
8213 AGATTGAAGCCACAACGGCAAATCTTACTTCTCAGGCGGTGCAGTGAAACAGATTGAAGCTATAA
1 AGATTGAAGCCACAACGGCAAATATTACTTCCCAGACAGTGCAGTGAAAAAGATTAAACCTACAA
* * * * *
8278 TAGCGAATCTTACTTTCCC-GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATATTATT
66 CAGCGAATCTTA-TTTCCCAGACAGTGCAGTGAAAAAGATTAAAGCCACAACAGCGAATATTACT
8342 TCCC
130 TCCC
8346 AGGCGGTGTA
Statistics
Matches: 106, Mismatches: 26, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
150 100 0.94
151 6 0.06
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (150 bp):
AGATTGAAGCCACAACGGCAAATATTACTTCCCAGACAGTGCAGTGAAAAAGATTAAACCTACAA
CAGCGAATCTTATTTCCCAGACAGTGCAGTGAAAAAGATTAAAGCCACAACAGCGAATATTACTT
CCCTGACATCCCAATTAAAA
Found at i:8373 original size:200 final size:200
Alignment explanation
Indices: 8030--8422 Score: 597
Period size: 200 Copynumber: 2.0 Consensus size: 200
8020 ACTGAGAATA
* * *
8030 GCAAATCTTACGTCCCAGGCGGTGCAGTGGAACAGATTGAAGCCACAATGGCAAATATTGCTTCC
1 GCAAATCTTACGTCCCAGGCGGTGCAGTGAAACAGATTGAAGCCACAATAGCAAATATTACTTCC
*
8095 CCGACATTGCAGTTAAAAAGATTAAACCTACAACAGCGAATCTTATTTCCCAGGCGGTGCAGTGG
66 CCGACATTGCAGTTAAAAAGATTAAACCTACAACAGCGAATATTATTTCCCAGGCGGTGCAGTGG
* * *
8160 AACAGTTTAAAGCCACAACGGTGAATCTTACTTCCCTGACATCCCAATTAAAAAGATTGAAGCCA
131 AACAGTTTAAAGCCACAACGGCGAATCTTACTGCCCCGACATCCCAATTAAAAAGATTGAAGCCA
8225 CAACG
196 CAACG
* * * * * * *
8230 GCAAATCTTACTTCTCAGGCGGTGCAGTGAAACAGATTGAAGCTATAATAGCGAATCTTACTTTC
1 GCAAATCTTACGTCCCAGGCGGTGCAGTGAAACAGATTGAAGCCACAATAGCAAATATTACTTCC
* *
8295 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATATTATTTCCCAGGCGGTGTAGTGG
66 CCGACATTGCAGTTAAAAAGATTAAACCTACAACAGCGAATATTATTTCCCAGGCGGTGCAGTGG
* ** * *
8360 AACAGTTTAAAGCCACAATGGCGAATCTTACTGCCCCGACATTGCAGTTAAAATGATTGAAGC
131 AACAGTTTAAAGCCACAACGGCGAATCTTACTGCCCCGACATCCCAATTAAAAAGATTGAAGC
8423 TACAGGCTAC
Statistics
Matches: 172, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
200 172 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (200 bp):
GCAAATCTTACGTCCCAGGCGGTGCAGTGAAACAGATTGAAGCCACAATAGCAAATATTACTTCC
CCGACATTGCAGTTAAAAAGATTAAACCTACAACAGCGAATATTATTTCCCAGGCGGTGCAGTGG
AACAGTTTAAAGCCACAACGGCGAATCTTACTGCCCCGACATCCCAATTAAAAAGATTGAAGCCA
CAACG
Found at i:10079 original size:13 final size:14
Alignment explanation
Indices: 10063--10095 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
10053 TGATATTTTA
*
10063 TTTTATTTTGT-TT
1 TTTTATTTTCTCTT
10076 TTTTATTTTCTCTT
1 TTTTATTTTCTCTT
10090 TTTTAT
1 TTTTAT
10096 ATTACTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTATTTTCTCTT
Found at i:12597 original size:22 final size:22
Alignment explanation
Indices: 12569--12617 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
12559 AGTGGTCTCA
12569 GGTGCTAGAGAGATACGTCCCC
1 GGTGCTAGAGAGATACGTCCCC
12591 GGTGCTAGAGAGATACGTCCCC
1 GGTGCTAGAGAGATACGTCCCC
12613 GGTGC
1 GGTGC
12618 CATCACAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (22 bp):
GGTGCTAGAGAGATACGTCCCC
Found at i:14267 original size:116 final size:116
Alignment explanation
Indices: 14063--14287 Score: 414
Period size: 116 Copynumber: 1.9 Consensus size: 116
14053 AAATTGTATT
14063 AAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
1 AAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
* *
14128 ACCAGTCAAAATATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATC
66 ACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAATTATC
* *
14179 AAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGTTAGT
1 AAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
14244 ACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAA
66 ACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAA
14288 CATTGTTAAC
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (116 bp):
AAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
ACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAATTATC
Found at i:14319 original size:23 final size:23
Alignment explanation
Indices: 14293--14576 Score: 167
Period size: 23 Copynumber: 10.8 Consensus size: 23
14283 TGTAACATTG
* *
14293 TTAACTTAGTTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
14316 TTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
14339 TTAAATTAGGTTAGGGTTAAGGTTTGTAA
1 TTAAATTAGGTTAGGG-T----TTT-TAA
14368 TTAATTTAAGTTAAGGGTTAGGGTTTTTAA
1 TT-A---AA-TT-A-GGTTAGGGTTTTTAA
14398 TTAAATTAAGTTAGGGTTAGGGTTTTTAA
1 TT--A--AA-TTA-GGTTAGGGTTTTTAA
*
14427 TTAAATTAGGTTAGGGCTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
14450 TTAAATTAGGTTAAGGTTAGGGTTTTTAA
1 TT-AA--A--TT-AGGTTAGGGTTTTTAA
* *
14479 GTT-AA-GAGTTTAGGGTTTTTAA
1 -TTAAATTAGGTTAGGGTTTTTAA
14501 TTAAATTAGGTTAAGGTTAGGCTTTTTAA
1 TTAAATTAGGTT-A-G---GG-TTTTTAA
14530 TTAAATTAGGTTAGGGTTAGGGTTTTTAA
1 TT-AA--A--TTA-GGTTAGGGTTTTTAA
14559 TTAAATTAGGTTAGGGTT
1 TTAAATTAGGTTAGGGTT
14577 AGGGTTTTTA
Statistics
Matches: 218, Mismatches: 8, Indels: 70
0.74 0.03 0.24
Matches are distributed among these distances:
21 2 0.01
22 17 0.08
23 67 0.31
24 10 0.05
25 3 0.01
26 3 0.01
27 1 0.00
28 10 0.05
29 57 0.26
30 19 0.09
31 5 0.02
32 1 0.00
33 3 0.01
34 6 0.03
35 6 0.03
36 8 0.04
ACGTcount: A:0.30, C:0.01, G:0.24, T:0.45
Consensus pattern (23 bp):
TTAAATTAGGTTAGGGTTTTTAA
Found at i:14363 original size:29 final size:29
Alignment explanation
Indices: 14303--14611 Score: 286
Period size: 29 Copynumber: 11.2 Consensus size: 29
14293 TTAACTTAGT
14303 TTAGGGTTTTTAATT-AA--A--TTA-GG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
14326 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* * * *
14355 TTAAGGTTTGTAATTAATTTAAGTTAAGGG
1 TTAGGGTTTTTAATTAAATTAGGTT-AGGG
*
14385 TTAGGGTTTTTAATTAAATTAAGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
14414 TTAGGGTTTTTAATT-AA--A--TTA-GG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
14437 TTAGGGCTTTTAATTAAATTAGGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
14466 TTAGGGTTTTTAAGTT-AA-GAGTTTAGGG
1 TTAGGGTTTTTAA-TTAAATTAGGTTAGGG
* *
14494 TT----TTTAATTAAATT--A-G--GTTAAGG
1 TTAGGGTTT--TT-AATTAAATTAGGTTAGGG
*
14517 TTAGGCTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
14546 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
*
14575 TTAGGGTTTTTAATTAATTTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
14604 TTTAGGGT
1 -TTAGGGT
14612 AAAATTAGGT
Statistics
Matches: 241, Mismatches: 18, Indels: 47
0.79 0.06 0.15
Matches are distributed among these distances:
23 38 0.16
24 14 0.06
25 4 0.02
26 8 0.03
27 5 0.02
28 17 0.07
29 120 0.50
30 35 0.15
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:14440 original size:52 final size:52
Alignment explanation
Indices: 14303--14606 Score: 378
Period size: 52 Copynumber: 5.6 Consensus size: 52
14293 TTAACTTAGT
14303 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
* * *
14355 TTAAGGTTTGTAATTAATTTAAGTTAAGGGTTAGGGTTTTTAATTAAATTAAGTTAGGG
1 TT-AGGGTT-T--TTAA-TTAAATT-A-GGTTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
14414 TTAGGGTTTTTAATTAAATTAGGTTAGGGCTTTTAATTAAATTAGGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
* * *
14466 TTAGGGTTTTTAAGTT-AA-GAGTTTAGGGTTTTTAATTAAATTAGGTTAAGG
1 TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
*
14517 TTAGGCTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGG
*
14575 TTAGGGTTTTTAATTAATTTAGGTTAGGGTTT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
14607 AGGGTAAAAT
Statistics
Matches: 219, Mismatches: 17, Indels: 32
0.82 0.06 0.12
Matches are distributed among these distances:
50 2 0.01
51 42 0.19
52 57 0.26
53 11 0.05
54 8 0.04
55 4 0.02
56 4 0.02
57 10 0.05
58 49 0.22
59 32 0.15
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.46
Consensus pattern (52 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:14493 original size:22 final size:20
Alignment explanation
Indices: 14459--14504 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
14449 ATTAAATTAG
14459 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGTTTTTAA
14479 GTTAAGAGTTTAGGGTTTTTAA
1 GTTAAG-G-TTAGGGTTTTTAA
14501 -TTAA
1 GTTAA
14505 ATTAGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
22 13 0.54
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTAA
Found at i:14533 original size:80 final size:73
Alignment explanation
Indices: 14414--14562 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 73
14404 TAAGTTAGGG
14414 TTAGGGTTTTTAATTAAATTAGGTTAGGGCTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGCTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAA
14479 GTTAAGAGT
66 -TTAAGAGT
*
14488 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGCTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTT-A-G---GGC-TTTTAATTAAATTAGGTTAAGGTTAGGGT
14553 TTTTAATTAA
60 TTTTAATTAA
14563 ATTAGGTTAG
Statistics
Matches: 68, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
74 25 0.37
75 1 0.01
76 1 0.01
79 7 0.10
80 34 0.50
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (73 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGCTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAA
TTAAGAGT
Found at i:14656 original size:25 final size:25
Alignment explanation
Indices: 14628--14765 Score: 137
Period size: 25 Copynumber: 5.7 Consensus size: 25
14618 AGGTTAAGGT
14628 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
14653 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * *** *
14676 --AAATAAC-TCGAAAT-TTTTTTTA
1 TTTTATTACATC-AAATAAACTTCTA
14698 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
14723 TTTCATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
14748 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
14766 TATCAAAATA
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
20 2 0.02
21 9 0.10
22 2 0.02
23 2 0.02
24 12 0.13
25 63 0.70
ACGTcount: A:0.41, C:0.14, G:0.01, T:0.43
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:15265 original size:18 final size:18
Alignment explanation
Indices: 15242--15276 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15232 CAGAAAAGGA
*
15242 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
15260 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
15277 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:15941 original size:7 final size:7
Alignment explanation
Indices: 15931--15962 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
15921 TTATATACAT
15931 AATACTA
1 AATACTA
15938 AATACTA
1 AATACTA
15945 AATACTA
1 AATACTA
15952 AATACTA
1 AATACTA
15959 AATA
1 AATA
15963 TCAATCGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:17166 original size:22 final size:22
Alignment explanation
Indices: 17141--17195 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
17131 AATATGGATT
17141 TGAGAGAATTTTGGAAGGAAAG
1 TGAGAGAATTTTGGAAGGAAAG
*
17163 TGAGAGAATTTTGGAAGGAAAT
1 TGAGAGAATTTTGGAAGGAAAG
17185 TGAGAGGAATT
1 TGAGA-GAATT
17196 GAGAGGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (22 bp):
TGAGAGAATTTTGGAAGGAAAG
Found at i:17212 original size:12 final size:11
Alignment explanation
Indices: 17178--17212 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
17168 GAATTTTGGA
17178 AGGAAATTGAG
1 AGGAAATTGAG
17189 AGG-AATTGAG
1 AGGAAATTGAG
17199 AGGAAATATGAG
1 AGGAAAT-TGAG
17211 AG
1 AG
17213 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Done.