Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013776.1 Corchorus capsularis cultivar CVL-1 contig13797, whole genome shotgun sequence
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: 80321
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--43 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 A
1 A
44 AGATGCTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4133 original size:1 final size:1
Alignment explanation
Indices: 4129--4158 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
4119 TTTTTTCTTT
4129 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4159 CCCTTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9776 original size:94 final size:94
Alignment explanation
Indices: 9615--9802 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
9605 GACTAGATTG
* *
9615 AAATATTTAAAACTTAAATAATTAAAAAAAATCCAAAATTTACACCGCCGGTGTATCATATAATC
1 AAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAATTTACACCGCCAGTGTATCATATAATC
9680 ACCCTTTAATTAATTATAAAATGAGTAAA
66 ACCCTTTAATTAATTATAAAATGAGTAAA
9709 AAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAATTTACACCGCCAGTGTATCATATAATC
1 AAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAATTTACACCGCCAGTGTATCATATAATC
9774 ACCCTTTAATTAATTATAAAATGAGTAAA
66 ACCCTTTAATTAATTATAAAATGAGTAAA
9803 TCCTTTAATT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (94 bp):
AAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAATTTACACCGCCAGTGTATCATATAATC
ACCCTTTAATTAATTATAAAATGAGTAAA
Found at i:9816 original size:28 final size:28
Alignment explanation
Indices: 9776--9830 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
9766 ATATAATCAC
9776 CCTTTAATTAATTATAAAATGAGTAAAT
1 CCTTTAATTAATTATAAAATGAGTAAAT
9804 CCTTTAATTAATTATAAAATGAGTAAA
1 CCTTTAATTAATTATAAAATGAGTAAA
9831 AAATCTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (28 bp):
CCTTTAATTAATTATAAAATGAGTAAAT
Found at i:9907 original size:121 final size:122
Alignment explanation
Indices: 9682--9923 Score: 443
Period size: 121 Copynumber: 2.0 Consensus size: 122
9672 ATATAATCAC
9682 CCTTTAATTAATTATAAAATGAGTAAAAAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAA
1 CCTTTAATTAATTATAAAATGAGTAAAAAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAA
9747 TTTACACCGCCAGTGTATCATATAATCACCCTTTAATTAATTATAAAATGAGTAAAT
66 TTTACACCGCCAGTGTATCATATAATCACCCTTTAATTAATTATAAAATGAGTAAAT
* *
9804 CCTTTAATTAATTATAAAATGAGTAAAAAATCTTTAAAACTTAAATAATT-AAAAAAATCCAAAA
1 CCTTTAATTAATTATAAAATGAGTAAAAAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAA
9868 TTTACACCGCC-GATGTATCATATAATCACCCTTTAATTAATTATAAAATGAGTAAA
66 TTTACACCGCCAG-TGTATCATATAATCACCCTTTAATTAATTATAAAATGAGTAAA
9924 AAAAAATATT
Statistics
Matches: 117, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
120 1 0.01
121 67 0.57
122 49 0.42
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (122 bp):
CCTTTAATTAATTATAAAATGAGTAAAAAATATTTAAAACTTAAATAATTAAAAAAAACCCAAAA
TTTACACCGCCAGTGTATCATATAATCACCCTTTAATTAATTATAAAATGAGTAAAT
Found at i:12403 original size:13 final size:13
Alignment explanation
Indices: 12385--12409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12375 TTTAGTTTCG
12385 TTGAGTCAGTTTT
1 TTGAGTCAGTTTT
12398 TTGAGTCAGTTT
1 TTGAGTCAGTTT
12410 AGTTTGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (13 bp):
TTGAGTCAGTTTT
Found at i:20486 original size:25 final size:23
Alignment explanation
Indices: 20458--20511 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
20448 TTACTTCATA
20458 TATAATATTAAATCGGATTCTTTC
1 TATAATA-TAAATCGGATTCTTTC
*
20482 T-T-ATATAACTCGGATTCTTTC
1 TATAATATAAATCGGATTCTTTC
20503 T-T-ATATAAA
1 TATAATATAAA
20512 AAGTGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 23 0.82
22 3 0.11
23 1 0.04
24 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (23 bp):
TATAATATAAATCGGATTCTTTC
Found at i:20494 original size:21 final size:21
Alignment explanation
Indices: 20470--20510 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20460 TAATATTAAA
20470 TCGGATTCTTTCTTATATAAC
1 TCGGATTCTTTCTTATATAAC
20491 TCGGATTCTTTCTTATATAA
1 TCGGATTCTTTCTTATATAA
20511 AAAGTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (21 bp):
TCGGATTCTTTCTTATATAAC
Found at i:30635 original size:34 final size:34
Alignment explanation
Indices: 30587--30655 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
30577 ATTCAGTTTC
30587 CATGCAGCAACTAATTGTAAAAAGAAACATTAAA
1 CATGCAGCAACTAATTGTAAAAAGAAACATTAAA
* **
30621 CATGCAGCAGCTAATTGTCCAAAGAAACATTAAA
1 CATGCAGCAACTAATTGTAAAAAGAAACATTAAA
30655 C
1 C
30656 TAAAATAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.20
Consensus pattern (34 bp):
CATGCAGCAACTAATTGTAAAAAGAAACATTAAA
Found at i:32148 original size:24 final size:23
Alignment explanation
Indices: 32102--32148 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
32092 AATGTCAGAA
*
32102 GGAGAGAGCCAAATGCTGAGCAT
1 GGAGAGAGCCAAATGCTCAGCAT
32125 GGAGAAGAGCCAAATG-TCATGCAT
1 GGAG-AGAGCCAAATGCTCA-GCAT
32149 ACAGCAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.36, C:0.17, G:0.32, T:0.15
Consensus pattern (23 bp):
GGAGAGAGCCAAATGCTCAGCAT
Found at i:32733 original size:57 final size:57
Alignment explanation
Indices: 32664--32777 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
32654 TAAGATAGTC
*
32664 TCTTCTATGTTCTAAGGAAAAGAAGATAAGATATATAGAATAGATTCCACACTTCAT
1 TCTTCTAAGTTCTAAGGAAAAGAAGATAAGATATATAGAATAGATTCCACACTTCAT
32721 TCTTCTAAGTTCTAAGGAAAAGAAGATAAGATATATAGAATAGATTCCACACTTCAT
1 TCTTCTAAGTTCTAAGGAAAAGAAGATAAGATATATAGAATAGATTCCACACTTCAT
32778 AATTAATTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (57 bp):
TCTTCTAAGTTCTAAGGAAAAGAAGATAAGATATATAGAATAGATTCCACACTTCAT
Found at i:34416 original size:62 final size:61
Alignment explanation
Indices: 34348--34471 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 61
34338 ATTTGGACAT
34348 AGAGATATAATTTTGCAAATTTCTTTCTTATCTTAAATTTTTTTTTGTATATTTACAAGTTA
1 AGAGATATAATTTTGCAAATTTCTTTCTTATCTT-AATTTTTTTTTGTATATTTACAAGTTA
34410 AGAGATATAATTTTGCAAATTTCTTTCTTATCTTAATTTTTTTTTGTATATTTACAAGTTA
1 AGAGATATAATTTTGCAAATTTCTTTCTTATCTTAATTTTTTTTTGTATATTTACAAGTTA
34471 A
1 A
34472 TCTTGTTCGA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 28 0.45
62 34 0.55
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (61 bp):
AGAGATATAATTTTGCAAATTTCTTTCTTATCTTAATTTTTTTTTGTATATTTACAAGTTA
Found at i:38112 original size:15 final size:15
Alignment explanation
Indices: 38092--38134 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38082 ATGATAACTT
38092 TTTTTTTCTTTTTGG
1 TTTTTTTCTTTTTGG
**
38107 TTTTTTT-TTTCACGG
1 TTTTTTTCTTT-TTGG
38122 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
38135 ATCAATTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
14 3 0.14
15 16 0.73
16 3 0.14
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTTTTGG
Found at i:38333 original size:30 final size:31
Alignment explanation
Indices: 38262--38334 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
38252 CGTCTGATTT
* *
38262 TATCCTGAATTGACACAACTTGAAAACGATA
1 TATCCTGAATTGACACAACATGAAAACAATA
* ** *
38293 TATTCTGAATTGACACAA-ATGGTAACAATG
1 TATCCTGAATTGACACAACATGAAAACAATA
38323 TATCCTGAATTG
1 TATCCTGAATTG
38335 CATTTTCGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (31 bp):
TATCCTGAATTGACACAACATGAAAACAATA
Found at i:38500 original size:32 final size:32
Alignment explanation
Indices: 38463--38546 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
38453 GCTGTTTTCG
*
38463 GGTTCGGGTTAAATTTGGGTCAGGTTGATTCA
1 GGTTCGGGTTAAATTTGGGTCAGGTTAATTCA
* * *
38495 GGTTCGGGTCAATTTTGGGTCAGGTTAATTCG
1 GGTTCGGGTTAAATTTGGGTCAGGTTAATTCA
38527 GGTTCGGGTTCAAA-TTGGGT
1 GGTTCGGGTT-AAATTTGGGT
38547 TTTGGCCAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 43 0.96
33 2 0.04
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.37
Consensus pattern (32 bp):
GGTTCGGGTTAAATTTGGGTCAGGTTAATTCA
Found at i:38536 original size:16 final size:16
Alignment explanation
Indices: 38459--38536 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
38449 TCGGGCTGTT
38459 TTCGGGTTCGGGTTAAA
1 TTCGGGTTCGGGTT-AA
* * *
38476 TTTGGG-TCAGGTTGA
1 TTCGGGTTCGGGTTAA
* *
38491 TTCAGGTTCGGGTCAA
1 TTCGGGTTCGGGTTAA
* *
38507 TTTTGGG-TCAGGTTAA
1 -TTCGGGTTCGGGTTAA
38523 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
38537 CAAATTGGGT
Statistics
Matches: 44, Mismatches: 14, Indels: 7
0.68 0.22 0.11
Matches are distributed among these distances:
15 10 0.23
16 25 0.57
17 9 0.20
ACGTcount: A:0.14, C:0.12, G:0.36, T:0.38
Consensus pattern (16 bp):
TTCGGGTTCGGGTTAA
Found at i:38766 original size:16 final size:16
Alignment explanation
Indices: 38747--38806 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
38737 GGGTTCGGGT
*
38747 TTTTTCGGGTTTCAAA
1 TTTTTCGGGTTTGAAA
**
38763 TTTTTCGGGTTCTGATT
1 TTTTTCGGGTT-TGAAA
* *
38780 TTTTTCGAGTTTGAAC
1 TTTTTCGGGTTTGAAA
38796 TTTTTCGGGTT
1 TTTTTCGGGTT
38807 CGGGTTTGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 24 0.67
17 12 0.33
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (16 bp):
TTTTTCGGGTTTGAAA
Found at i:38770 original size:32 final size:32
Alignment explanation
Indices: 38734--38813 Score: 106
Period size: 33 Copynumber: 2.5 Consensus size: 32
38724 TTTTTTCAGG
*
38734 TTCGGGTTCGGGTTTTTTCGGGTTTCAAATTT
1 TTCGGGTTCGGGTTTTTTCGAGTTTCAAATTT
** * *
38766 TTCGGGTTCTGATTTTTTTCGAGTTTGAACTTT
1 TTCGGGTTC-GGGTTTTTTCGAGTTTCAAATTT
38799 TTCGGGTTCGGGTTT
1 TTCGGGTTCGGGTTT
38814 GGATTCAGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 13 0.32
33 27 0.68
ACGTcount: A:0.09, C:0.12, G:0.28, T:0.51
Consensus pattern (32 bp):
TTCGGGTTCGGGTTTTTTCGAGTTTCAAATTT
Found at i:39194 original size:88 final size:90
Alignment explanation
Indices: 39032--39200 Score: 281
Period size: 88 Copynumber: 1.9 Consensus size: 90
39022 CTATAAAAAG
39032 TTATCTCTCATCTCCATTAATAAAGATAGATTAGTAATAATTCATATACTGTAGTTAAGTTATGA
1 TTATCTCTCATCTCCATTAATAAAGATAGATTAGTAATAATTCATATACTGTAGTTAAGTTATGA
39097 TTCACTAGCATTTTTTAAAAGTTAT
66 TTCACTAGCATTTTTTAAAAGTTAT
* *
39122 TTATCTCTCATCTCCA-TAATAAATATAGATTAGTAATCAATTCA-A-ACTGTATTTAAGTTATG
1 TTATCTCTCATCTCCATTAATAAAGATAGATTAGTAAT-AATTCATATACTGTAGTTAAGTTATG
*
39184 ATTCAGTAGCATTTTTT
65 ATTCACTAGCATTTTTT
39201 TAAGACTAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
88 32 0.43
89 21 0.28
90 22 0.29
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (90 bp):
TTATCTCTCATCTCCATTAATAAAGATAGATTAGTAATAATTCATATACTGTAGTTAAGTTATGA
TTCACTAGCATTTTTTAAAAGTTAT
Found at i:42181 original size:110 final size:109
Alignment explanation
Indices: 41967--42195 Score: 246
Period size: 110 Copynumber: 2.1 Consensus size: 109
41957 AGATGAGCAT
* * * * **
41967 AGCGGGTCGCGGCCCACCATGGTCCGGGTCGCGCGCGACCCGCGATCGCGCCCGACCTTGACCAT
1 AGCGGGTCGCGGCCCACCACGGTCCGGATCGCACGCGACACGCGATCGCGCCCGACCCGGACCAT
* * * *
42032 GGCAGGCCGCGATCCGGGCGCGACCCGCCATGAATCGGGTCGCG
66 GGCAGGCCGCGACCCGCGCGCAACCCGCCATGAACCGGGTCGCG
* * * *
42076 ACGCGGGTCGCGGCCCATCACGGTCCGGATCGCATGCGATCACG-GGTCGCGCGCGACCCGGACC
1 A-GCGGGTCGCGGCCCACCACGGTCCGGATCGCACGCGA-CACGCGATCGCGCCCGACCCGGACC
** * *
42140 ATGGTGGGCCGCGACCCGCGCGCAACCCAGCCGTG-GCCGGGTCGCG
64 ATGGCAGGCCGCGACCCGCGCGCAACCC-GCCATGAACCGGGTCGCG
*
42186 ATCGGGTCGC
1 AGCGGGTCGC
42196 AACCCGTGTT
Statistics
Matches: 98, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
109 9 0.09
110 81 0.83
111 8 0.08
ACGTcount: A:0.13, C:0.39, G:0.38, T:0.11
Consensus pattern (109 bp):
AGCGGGTCGCGGCCCACCACGGTCCGGATCGCACGCGACACGCGATCGCGCCCGACCCGGACCAT
GGCAGGCCGCGACCCGCGCGCAACCCGCCATGAACCGGGTCGCG
Found at i:43169 original size:18 final size:17
Alignment explanation
Indices: 43143--43176 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43133 TTTTCCCGTC
43143 GATTATTTTTTGAAAAA
1 GATTATTTTTTGAAAAA
43160 GATTATTTTTTGAAAAA
1 GATTATTTTTTGAAAAA
43177 TCTGTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GATTATTTTTTGAAAAA
Found at i:44323 original size:114 final size:114
Alignment explanation
Indices: 43859--44337 Score: 545
Period size: 114 Copynumber: 4.2 Consensus size: 114
43849 AAACGCATTT
* * *
43859 AATTGGGGGCGTTTCAAG-ATAAAAATGCCGCAATATATAATCTTTTCCTATGAA-TACGAATTT
1 AATTGGGGGCGTTTC-AGTATAAAAACGCCGCCATATATAATCTTTTCCTA-GAATTACAAATTT
* * * * * *
43922 GGGGAAAATAAATACTAAAAATTAGCT-ACGTTTTTTTCATAAAAGCTCCACT
64 GGTGAAAATAAAGACT-AAAATTAG-TGGCGTTTTTCTCATAAAAGCGCCACA
* * * * * * * * *
43974 AATTAGTGGCGTTTTAGGT-TAAAAACACCACCATATATAATCTTTTCCTACAAATATAAATCTG
1 AATTGGGGGCGTTTCA-GTATAAAAACGCCGCCATATATAATCTTTTCCTAGAATTACAAATTTG
* *
44038 ATGAAAATAAAGACTAAAATTAGCGGCGTTTTTCTCATAAAAGCGCCACA
65 GTGAAAATAAAGACTAAAATTAGTGGCGTTTTTCTCATAAAAGCGCCACA
** * * * *
44088 AATTTTGGGCGTTTCAGTATAAAAACGCTGTCATATATAATATTTTCCTAAAATTACAAATTTGG
1 AATTGGGGGCGTTTCAGTATAAAAACGCCGCCATATATAATCTTTTCCTAGAATTACAAATTTGG
*
44153 TGAAAATAAAGACTAAAATTAGTGGCGTTTTTCTCATAAAAACGCCACA
66 TGAAAATAAAGACTAAAATTAGTGGCGTTTTTCTCATAAAAGCGCCACA
*
44202 AATTGGGGGCGTTTCAGTATAAAAACGCCGCCATATATAATCTTTTCCTAGAATTACAAATTTAG
1 AATTGGGGGCGTTTCAGTATAAAAACGCCGCCATATATAATCTTTTCCTAGAATTACAAATTTGG
* * * * *
44267 TTAAAATGAAGAATAAAATTAGTGGCGCTTTTCTCATAAAATCGCCAC-
66 TGAAAATAAAGACTAAAATTAGTGGCGTTTTTCTCATAAAAGCGCCACA
* * *
44315 TATATGGGGGCATTTCAGGATAA
1 AAT-TGGGGGCGTTTCAGTATAA
44338 TCTTTTCCTG
Statistics
Matches: 308, Mismatches: 50, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
113 4 0.01
114 245 0.80
115 59 0.19
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (114 bp):
AATTGGGGGCGTTTCAGTATAAAAACGCCGCCATATATAATCTTTTCCTAGAATTACAAATTTGG
TGAAAATAAAGACTAAAATTAGTGGCGTTTTTCTCATAAAAGCGCCACA
Found at i:44404 original size:96 final size:94
Alignment explanation
Indices: 44238--44432 Score: 234
Period size: 96 Copynumber: 2.0 Consensus size: 94
44228 GCCGCCATAT
* * * * *
44238 ATAATCTTTTCCTAGAATTACAAATTTAGTTAAAATGAAGAATAAAATTAGTGGCGCTTTTCTCA
1 ATAATCTTTTCCTAGAAATACAAATTTAGTAAAAATGAAAAATAAAACTAGTAGCGCTTTTCTCA
*
44303 TAAAATCGCCACTATATGGGGGCATTTCAGG
66 -AAAAT-ACCACTATATGGGGGCATTTCAGG
* *
44334 ATAATCTTTTCCT-GAAAATACAAATTTTGTAAAAAT-AAAAACTAAAACTAGTAGCGTTTCTTT
1 ATAATCTTTTCCTAG-AAATACAAATTTAGTAAAAATGAAAAA-TAAAACTAGTAGCG-CT-TTT
*
44397 CTC-AAAATACCACTATATGGGGGCGTTTCAGG
62 CTCAAAAATACCACTATATGGGGGCATTTCAGG
44429 ATAA
1 ATAA
44433 AAAAAGGCAC
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
95 31 0.36
96 48 0.56
97 1 0.01
98 6 0.07
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (94 bp):
ATAATCTTTTCCTAGAAATACAAATTTAGTAAAAATGAAAAATAAAACTAGTAGCGCTTTTCTCA
AAAATACCACTATATGGGGGCATTTCAGG
Found at i:48815 original size:17 final size:17
Alignment explanation
Indices: 48793--48831 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
48783 GCAACTTCCT
48793 AAATGCAATTTTCTCCC
1 AAATGCAATTTTCTCCC
* *
48810 AAATGCAGTTTTCTCCT
1 AAATGCAATTTTCTCCC
48827 AAATG
1 AAATG
48832 TAAAAGGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (17 bp):
AAATGCAATTTTCTCCC
Found at i:49113 original size:26 final size:27
Alignment explanation
Indices: 49084--49151 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 27
49074 GGGTGTGCTC
49084 AAATGACCAAAATGCCTCC-GATGCGA
1 AAATGACCAAAATGCCTCCTGATGCGA
* * *
49110 AAATGACCAAATTG-CTCCTGGTGTGA
1 AAATGACCAAAATGCCTCCTGATGCGA
49136 AAATGACCAAAATGCC
1 AAATGACCAAAATGCC
49152 CCCAGTGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 4 0.11
26 31 0.86
27 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATGCCTCCTGATGCGA
Found at i:49159 original size:26 final size:25
Alignment explanation
Indices: 49084--49163 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 25
49074 GGGTGTGCTC
* *
49084 AAATGACCAAAATGCCTCCGATGCGA
1 AAATGACCAAAATGCCCCCG-TGTGA
* **
49110 AAATGACCAAATTGCTCCTGGTGTGA
1 AAATGACCAAAATGC-CCCCGTGTGA
49136 AAATGACCAAAATGCCCCCAGTGTGA
1 AAATGACCAAAATGCCCCC-GTGTGA
49162 AA
1 AA
49164 TTTAGAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 2 0.05
26 40 0.91
27 2 0.05
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (25 bp):
AAATGACCAAAATGCCCCCGTGTGA
Found at i:49297 original size:29 final size:29
Alignment explanation
Indices: 49240--49296 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
49230 ACAAAGTTAT
*
49240 CAATCCAAAGACAATTTTTTACCAAAAAA
1 CAATCCAAAGACAATATTTTACCAAAAAA
49269 CAATCCAAAGACAA-ATTTTACCAAAAAA
1 CAATCCAAAGACAATATTTTACCAAAAAA
49297 AAAAAAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.21
Consensus pattern (29 bp):
CAATCCAAAGACAATATTTTACCAAAAAA
Found at i:52423 original size:3 final size:3
Alignment explanation
Indices: 52415--52450 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
52405 ATCTAGGATA
52415 TAT TAT TA- TAT TAT TA- TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52451 CGATCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.20
3 24 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:52426 original size:8 final size:8
Alignment explanation
Indices: 52413--52447 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
52403 ACATCTAGGA
52413 TATATTAT
1 TATATTAT
52421 TATATTAT
1 TATATTAT
52429 TATATTAT
1 TATATTAT
52437 TATATTAT
1 TATATTAT
52445 TAT
1 TAT
52448 TATCGATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATATTAT
Found at i:52999 original size:90 final size:90
Alignment explanation
Indices: 52896--53080 Score: 334
Period size: 90 Copynumber: 2.1 Consensus size: 90
52886 GAGGGGTTGT
* *
52896 TGTGGTTTCAGGGTTAGGGGGAGGTGGAGGGGAAAAGGTTGTGACCATAGGGGGAGGTGTGGTTG
1 TGTGGTTTCAGGGTTAGGGGGAGGTGGAGGGGAAAAGGTTGTGACCATAGGGGGAGGTGTGATTA
52961 TGGCATCAGGAGGTGAGGAAGGTGG
66 TGGCATCAGGAGGTGAGGAAGGTGG
* *
52986 TGTGGTTTCAGGGTTAGGGGGAGGTGGAGGGGAAAAGGTTGTGGCCATAGGGGGAGGTGTTATTA
1 TGTGGTTTCAGGGTTAGGGGGAGGTGGAGGGGAAAAGGTTGTGACCATAGGGGGAGGTGTGATTA
53051 TGGCATCAGGAGGTGAGGAAGGTGG
66 TGGCATCAGGAGGTGAGGAAGGTGG
53076 TGTGG
1 TGTGG
53081 CTTTAGGTTC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.20, C:0.05, G:0.51, T:0.23
Consensus pattern (90 bp):
TGTGGTTTCAGGGTTAGGGGGAGGTGGAGGGGAAAAGGTTGTGACCATAGGGGGAGGTGTGATTA
TGGCATCAGGAGGTGAGGAAGGTGG
Found at i:54794 original size:30 final size:27
Alignment explanation
Indices: 54721--54796 Score: 71
Period size: 30 Copynumber: 2.6 Consensus size: 27
54711 TATAGGAGGA
54721 GGTGGAGGGGGAGGGGTGGTTGTGGTT
1 GGTGGAGGGGGAGGGGTGGTTGTGGTT
** *
54748 GGTGGGAGAGGTGGAGGGGTTTTTATTGGTGAT
1 GGT-GGAG-GG-GGAGGGGTGGTT-GTGGT--T
54781 GGTGGAGGGGGAGGGG
1 GGTGGAGGGGGAGGGG
54797 GAGGGAAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 3 0.08
28 4 0.10
29 2 0.05
30 17 0.43
31 6 0.15
32 4 0.10
33 4 0.10
ACGTcount: A:0.12, C:0.00, G:0.63, T:0.25
Consensus pattern (27 bp):
GGTGGAGGGGGAGGGGTGGTTGTGGTT
Found at i:54857 original size:24 final size:24
Alignment explanation
Indices: 54830--54901 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
54820 GGGGGGGGGA
54830 GGTGGAAGGGTTGTTATTGGTGAT
1 GGTGGAAGGGTTGTTATTGGTGAT
*
54854 GGT-GAA--GTTG-GA--GGTGGA-
1 GGTGGAAGGGTTGTTATTGGT-GAT
*
54872 GGTGGAGGGGTTGTTATTGGTGAT
1 GGTGGAAGGGTTGTTATTGGTGAT
54896 GGTGGA
1 GGTGGA
54902 GTTGGAGGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
18 6 0.16
19 4 0.11
20 1 0.03
21 8 0.22
22 1 0.03
23 5 0.14
24 12 0.32
ACGTcount: A:0.17, C:0.00, G:0.51, T:0.32
Consensus pattern (24 bp):
GGTGGAAGGGTTGTTATTGGTGAT
Found at i:54886 original size:42 final size:42
Alignment explanation
Indices: 54824--54921 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
54814 GGGGGGGGGG
*
54824 GGGGGAGGTGGAAGGGTTGTTATTGGTGATGGTGAAGTTGGA
1 GGGGGAGGTGGAGGGGTTGTTATTGGTGATGGTGAAGTTGGA
* *
54866 GGTGGAGGTGGAGGGGTTGTTATTGGTGATGGTGGAGTTGGA
1 GGGGGAGGTGGAGGGGTTGTTATTGGTGATGGTGAAGTTGGA
*
54908 GGGGGAGTTGGAGG
1 GGGGGAGGTGGAGG
54922 TGGTGGTGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.16, C:0.00, G:0.56, T:0.28
Consensus pattern (42 bp):
GGGGGAGGTGGAGGGGTTGTTATTGGTGATGGTGAAGTTGGA
Found at i:54900 original size:30 final size:30
Alignment explanation
Indices: 54866--54966 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 30
54856 TGAAGTTGGA
54866 GGTGGAGGTGGAGGGGTTGTTATTGGTGAT
1 GGTGGAGGTGGAGGGGTTGTTATTGGTGAT
* ** *** *
54896 GGTGGAGTTGGAGGGGGAGTTGGAGGTGGT
1 GGTGGAGGTGGAGGGGTTGTTATTGGTGAT
*
54926 GGTGGTGGTGGAGGGGTTGTTATTGGTGAT
1 GGTGGAGGTGGAGGGGTTGTTATTGGTGAT
*
54956 GGAGGAGGTGG
1 GGTGGAGGTGG
54967 CGGCGGGGGA
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.13, C:0.00, G:0.58, T:0.29
Consensus pattern (30 bp):
GGTGGAGGTGGAGGGGTTGTTATTGGTGAT
Found at i:54935 original size:42 final size:42
Alignment explanation
Indices: 54824--54935 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
54814 GGGGGGGGGG
* * *
54824 GGGGGAGGTGGAAGGGTTGTTATTGGTGATGGTGAAGTTGGA
1 GGGGGAGGTGGAGGGGTTGGTAGTGGTGATGGTGAAGTTGGA
* * * *
54866 GGTGGAGGTGGAGGGGTTGTTATTGGTGATGGTGGAGTTGGA
1 GGGGGAGGTGGAGGGGTTGGTAGTGGTGATGGTGAAGTTGGA
* *
54908 GGGGGAGTTGGAGGTGG-TGGTGGTGGTG
1 GGGGGAGGTGGAGG-GGTTGGTAGTGGTG
54936 GAGGGGTTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 59 0.97
43 2 0.03
ACGTcount: A:0.14, C:0.00, G:0.57, T:0.29
Consensus pattern (42 bp):
GGGGGAGGTGGAGGGGTTGGTAGTGGTGATGGTGAAGTTGGA
Found at i:55957 original size:3 final size:3
Alignment explanation
Indices: 55951--55995 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
55941 TTTGCTACTT
55951 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
55996 TCAATACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56306 original size:28 final size:28
Alignment explanation
Indices: 56263--56325 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
56253 ATTATTATTG
* *
56263 TTATCATTGTTGCTATATATCATCATCA
1 TTATCATTATTACTATATATCATCATCA
*
56291 TTATCATTATTACTATATATTATCATCA
1 TTATCATTATTACTATATATCATCATCA
*
56319 TCATCAT
1 TTATCAT
56326 CATGTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.48
Consensus pattern (28 bp):
TTATCATTATTACTATATATCATCATCA
Found at i:64560 original size:27 final size:26
Alignment explanation
Indices: 64506--64633 Score: 156
Period size: 27 Copynumber: 4.8 Consensus size: 26
64496 ATCGATAATT
64506 AGTAAAAAGAGTAAGAAACA-A-TATTC
1 AGTAAAAAGAGTAAGAAA-AGAGTA-TC
64532 AGTAAAAAGAGTAAGAAAAGAGTCATC
1 AGTAAAAAGAGTAAGAAAAGAGT-ATC
64559 AGTAAAAAGAGTAAGAAAAGAGTCATC
1 AGTAAAAAGAGTAAGAAAAGAGT-ATC
* *
64586 AGTAAAAAGAATAGGAAACA-A-TATCC
1 AGTAAAAAGAGTAAGAAA-AGAGTAT-C
64612 AGTAAAAAGAGTAAGAAAAGAG
1 AGTAAAAAGAGTAAGAAAAGAG
64634 CAATAATAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.04
26 38 0.42
27 47 0.52
28 2 0.02
ACGTcount: A:0.58, C:0.07, G:0.20, T:0.15
Consensus pattern (26 bp):
AGTAAAAAGAGTAAGAAAAGAGTATC
Found at i:64564 original size:53 final size:53
Alignment explanation
Indices: 64506--64633 Score: 158
Period size: 53 Copynumber: 2.4 Consensus size: 53
64496 ATCGATAATT
*
64506 AGTAAAAAGAGTAAGAAACA-A-T-ATTCAGTAAAAAGAGTAAGAAA-AGAGTCAT-C
1 AGTAAAAAGAGTAAGAAA-AGAGTCA-TCAGTAAAAAGAATAAGAAACA-A-T-ATCC
*
64559 AGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAATAGGAAACAATATCC
1 AGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAATAAGAAACAATATCC
64612 AGTAAAAAGAGTAAGAAAAGAG
1 AGTAAAAAGAGTAAGAAAAGAG
64634 CAATAATAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
52 3 0.04
53 43 0.63
54 20 0.29
55 2 0.03
ACGTcount: A:0.58, C:0.07, G:0.20, T:0.15
Consensus pattern (53 bp):
AGTAAAAAGAGTAAGAAAAGAGTCATCAGTAAAAAGAATAAGAAACAATATCC
Found at i:64568 original size:16 final size:16
Alignment explanation
Indices: 64547--64595 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
64537 AAAGAGTAAG
64547 AAAAGAGTCATCAGTA
1 AAAAGAGTCATCAGTA
64563 AAAAGAGT-A--AG--
1 AAAAGAGTCATCAGTA
64574 AAAAGAGTCATCAGTA
1 AAAAGAGTCATCAGTA
64590 AAAAGA
1 AAAAGA
64596 ATAGGAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 8 0.29
12 1 0.04
13 2 0.07
14 2 0.07
15 1 0.04
16 14 0.50
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.14
Consensus pattern (16 bp):
AAAAGAGTCATCAGTA
Found at i:64754 original size:7 final size:7
Alignment explanation
Indices: 64744--64825 Score: 53
Period size: 7 Copynumber: 11.9 Consensus size: 7
64734 AATGGTAATC
64744 AGTAAAG
1 AGTAAAG
64751 AGTAAAG
1 AGTAAAG
**
64758 AGTAATC
1 AGTAAAG
64765 AGTAAAG
1 AGTAAAG
**
64772 AAAAAATG
1 AGTAAA-G
64780 -GTAAAG
1 AGTAAAG
*
64786 AGTAAAA
1 AGTAAAG
**
64793 AGTAATC
1 AGTAAAG
64800 AGTAAAG
1 AGTAAAG
64807 AG-AAATG
1 AGTAAA-G
*
64814 A-TAATG
1 AGTAAAG
64820 AGTAAA
1 AGTAAA
64826 AGAGAATTCA
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
6 6 0.11
7 48 0.87
8 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:64763 original size:21 final size:20
Alignment explanation
Indices: 64738--64831 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 20
64728 AAAAATAATG
64738 GTAATCAGTAAAGAGTAAAGA
1 GTAATCAGTAAAGAG-AAAGA
64759 GTAATCAGT-AA-AGAAA-A
1 GTAATCAGTAAAGAGAAAGA
* *
64776 --AAT-GGTAAAGAGTAAAAA
1 GTAATCAGTAAAGAG-AAAGA
64794 GTAATCAGTAAAGAGAAATGA
1 GTAATCAGTAAAGAGAAA-GA
*
64815 -TAATGAGTAAAAGAGAA
1 GTAATCAGT-AAAGAGAA
64832 TTCAACAAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.03
15 5 0.08
16 2 0.03
17 4 0.07
18 4 0.07
19 2 0.03
20 15 0.25
21 26 0.43
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.18
Consensus pattern (20 bp):
GTAATCAGTAAAGAGAAAGA
Found at i:64784 original size:35 final size:34
Alignment explanation
Indices: 64745--64864 Score: 152
Period size: 35 Copynumber: 3.5 Consensus size: 34
64735 ATGGTAATCA
64745 GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAG-AAAAATG
* *
64780 GTAAAGAGTAAAAAGTAATCAGTAAAGAGAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
* * **
64814 ATAATGAGTAAAAGAG-AATTCAACAAAGAAAAATG
1 GTAAAGAGT-AAAGAGTAA-TCAGTAAAGAAAAATG
64849 GTAAAGAGTAAAGAGT
1 GTAAAGAGTAAAGAGT
64865 GAAATAAAGA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
34 21 0.29
35 51 0.71
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (34 bp):
GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
Found at i:64948 original size:22 final size:21
Alignment explanation
Indices: 64935--65164 Score: 220
Period size: 22 Copynumber: 10.9 Consensus size: 21
64925 AAGGTAAAAT
64935 AGTAAAAAGTAAAAGGTAATC
1 AGTAAAAAGTAAAAGGTAATC
** *
64956 AGTAAAGGGTAAAATGGTAATT
1 AGTAAAAAGTAAAA-GGTAATC
*
64978 AGGAAAAAGTAAAATGGTAATC
1 AGTAAAAAGTAAAA-GGTAATC
65000 AGTAAAAAGTAAAAGAGTAATC
1 AGTAAAAAGTAAAAG-GTAATC
* *
65022 AGTAAAAAGTGATAA--TGATC
1 AGTAAAAAGT-AAAAGGTAATC
* * * *
65042 AGTAAGAAG-CAATGGTAATT
1 AGTAAAAAGTAAAAGGTAATC
*
65062 AGTAAAAAGTAAAATAGTAATC
1 AGTAAAAAGTAAAA-GGTAATC
65084 AGTAAAAAGTAAAAAGGTAATC
1 AGTAAAAAGT-AAAAGGTAATC
*
65106 AGT-AAGAGTAAAAGGTAATC
1 AGTAAAAAGTAAAAGGTAATC
* *
65126 AGT-AAGACTAAAAGAGTAATC
1 AGTAAAAAGTAAAAG-GTAATC
65147 AGT-AAAAGTAAAATGGTA
1 AGTAAAAAGTAAAA-GGTA
65165 GAAAATAAAG
Statistics
Matches: 173, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.01
20 47 0.27
21 40 0.23
22 78 0.45
23 7 0.04
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTAAAAAGTAAAAGGTAATC
Found at i:65072 original size:7 final size:7
Alignment explanation
Indices: 65062--65303 Score: 73
Period size: 7 Copynumber: 34.0 Consensus size: 7
65052 AATGGTAATT
65062 AGTAAAA
1 AGTAAAA
65069 AGTAAAA
1 AGTAAAA
**
65076 TAGTAATC
1 -AGTAAAA
65084 AGTAAAA
1 AGTAAAA
65091 AGTAAAA
1 AGTAAAA
**
65098 AGGTAATC
1 A-GTAAAA
*
65106 AGT-AAG
1 AGTAAAA
65112 AGTAAAA
1 AGTAAAA
* **
65119 GGTAATC
1 AGTAAAA
*
65126 AGT-AAG
1 AGTAAAA
*
65132 ACTAAAA
1 AGTAAAA
**
65139 GAGTAATC
1 -AGTAAAA
65147 AGT-AAA
1 AGTAAAA
65153 AGTAAAA
1 AGTAAAA
*
65160 TGGTAGAAA
1 -AGTA-AAA
*
65169 A-TAAAG
1 AGTAAAA
**
65175 AGTAATT
1 AGTAAAA
65182 AGTAAAGA
1 AGTAAA-A
65190 A--AAAA
1 AGTAAAA
* *
65195 TGGTAAAG
1 -AGTAAAA
65203 AGTAAAA
1 AGTAAAA
**
65210 GAGTAATT
1 -AGTAAAA
*
65218 AGTAAAG
1 AGTAAAA
65225 AGTAAAA
1 AGTAAAA
*
65232 TGGTAAAA
1 -AGTAAAA
*
65240 AGTAAAG
1 AGTAAAA
**
65247 AGTAATC
1 AGTAAAA
65254 AGTAAAA
1 AGTAAAA
65261 AGTAAAA
1 AGTAAAA
*
65268 TGGTAAAA
1 -AGTAAAA
* *
65276 AGTGAAG
1 AGTAAAA
**
65283 AGTAATC
1 AGTAAAA
65290 AGTAAAA
1 AGTAAAA
*
65297 GGTAAAA
1 AGTAAAA
65304 TGGTAAAGAG
Statistics
Matches: 164, Mismatches: 55, Indels: 32
0.65 0.22 0.13
Matches are distributed among these distances:
5 1 0.01
6 17 0.10
7 105 0.64
8 38 0.23
9 3 0.02
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:65103 original size:15 final size:15
Alignment explanation
Indices: 65061--65099 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
65051 CAATGGTAAT
65061 TAGTAAAAAGTAAAA
1 TAGTAAAAAGTAAAA
**
65076 TAGTAATCAGTAAAA
1 TAGTAAAAAGTAAAA
65091 -AGTAAAAAG
1 TAGTAAAAAG
65100 GTAATCAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (15 bp):
TAGTAAAAAGTAAAA
Found at i:65154 original size:84 final size:84
Alignment explanation
Indices: 64935--65160 Score: 253
Period size: 84 Copynumber: 2.7 Consensus size: 84
64925 AAGGTAAAAT
** * *
64935 AGTAAAAAGTAAAAGGTAATCAGTAAAGGGTAAAATGGTAATTAGGAAAAAGTAAAATGGTAATC
1 AGTAAAAAGTAAAAGGTAATCAGT-AAGAATAAAA-GGTAATTA-GTAAAAGTAAAATAGTAATC
65000 AGTAAAAAGTAAAAGAGTAATC
63 AGTAAAAAGTAAAAGAGTAATC
* * ** *
65022 AGTAAAAAGTGATAA--TGATCAGTAAGAAGCAATGGTAATTAGTAAAAAGTAAAATAGTAATCA
1 AGTAAAAAGT-AAAAGGTAATCAGTAAGAATAAAAGGTAATTAGT-AAAAGTAAAATAGTAATCA
65085 GTAAAAAGTAAAA-AGGTAATC
64 GTAAAAAGTAAAAGA-GTAATC
* * *
65106 AGT-AAGAGTAAAAGGTAATCAGTAAGACTAAAAGAGTAATCAGTAAAAGTAAAAT
1 AGTAAAAAGTAAAAGGTAATCAGTAAGAATAAAAG-GTAATTAGTAAAAGTAAAAT
65161 GGTAGAAAAT
Statistics
Matches: 116, Mismatches: 17, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
82 3 0.03
83 7 0.06
84 73 0.63
85 13 0.11
86 7 0.06
87 10 0.09
88 3 0.03
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.21
Consensus pattern (84 bp):
AGTAAAAAGTAAAAGGTAATCAGTAAGAATAAAAGGTAATTAGTAAAAGTAAAATAGTAATCAGT
AAAAAGTAAAAGAGTAATC
Found at i:65218 original size:36 final size:35
Alignment explanation
Indices: 65136--65331 Score: 220
Period size: 36 Copynumber: 5.5 Consensus size: 35
65126 AGTAAGACTA
*
65136 AAAGAGTAATCAGTAAA-AGTAAAATGGTAGAA-AAT
1 AAAGAGTAATCAGTAAAGA-TAAAATGGTA-AAGAGT
* *
65171 AAAGAGTAATTAGTAAAGAAAAAATGGTAAAGAGT
1 AAAGAGTAATCAGTAAAGATAAAATGGTAAAGAGT
* *
65206 AAAAGAGTAATTAGTAAAGAGTAAAATGGTAAAAAGT
1 -AAAGAGTAATCAGTAAAGA-TAAAATGGTAAAGAGT
* *
65243 AAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAGT
1 AAAGAGTAATCAGTAAAGA-TAAAATGGTAAAGAGT
* * *
65279 GAAGAGTAATCAGTAAAAGGTAAAATGGTAAAGAGA
1 AAAGAGTAATCAGT-AAAGATAAAATGGTAAAGAGT
65315 AAAGAGTAA--AGTAAAGA
1 AAAGAGTAATCAGTAAAGA
65332 GTAATCAGTA
Statistics
Matches: 142, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
33 4 0.03
34 5 0.04
35 27 0.19
36 89 0.63
37 17 0.12
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (35 bp):
AAAGAGTAATCAGTAAAGATAAAATGGTAAAGAGT
Found at i:65222 original size:22 final size:22
Alignment explanation
Indices: 65197--65251 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
65187 AGAAAAAATG
**
65197 GTAAAGAGTAAAA-GAGTAATTA
1 GTAAAGAGTAAAATG-GTAAAAA
65219 GTAAAGAGTAAAATGGTAAAAA
1 GTAAAGAGTAAAATGGTAAAAA
65241 GTAAAGAGTAA
1 GTAAAGAGTAA
65252 TCAGTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAAAAA
Found at i:65247 original size:72 final size:71
Alignment explanation
Indices: 65129--65331 Score: 263
Period size: 72 Copynumber: 2.8 Consensus size: 71
65119 GGTAATCAGT
*
65129 AAGACTAAAAGAGTAATCAGTAAAAGTAAAATGGTAGAAAA-TAAAGAGTAATTAGTAAAGAA-A
1 AAGAGTAAAAGAGTAATCAGTAAAAGTAAAATGGTA-AAAAGTAAAGAGTAA-TAGTAAAGAAGA
65192 AAATGGTA
64 AAATGGTA
*
65200 AAGAGTAAAAGAGTAATTAGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAA-AAGT
1 AAGAGTAAAAGAGTAATCAGTAAA-AGTAAAATGGTAAAAAGTAAAGAGTAAT-AGTAAAGAAG-
65264 AAAATGGTA
63 AAAATGGTA
* * * *
65273 AAAAGT-GAAGAGTAATCAGTAAAAGGTAAAATGGTAAAGAGAAAAGAGTAA-AGTAAAGA
1 AAGAGTAAAAGAGTAATCAGTAAAA-GTAAAATGGTAAAAAGTAAAGAGTAATAGTAAAGA
65332 GTAATCAGTA
Statistics
Matches: 118, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
70 6 0.05
71 31 0.26
72 67 0.57
73 14 0.12
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (71 bp):
AAGAGTAAAAGAGTAATCAGTAAAAGTAAAATGGTAAAAAGTAAAGAGTAATAGTAAAGAAGAAA
ATGGTA
Found at i:65332 original size:12 final size:12
Alignment explanation
Indices: 65315--65374 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
65305 GGTAAAGAGA
65315 AAAGAGTAAAGT
1 AAAGAGTAAAGT
65327 AAAGAGTAATCAGT
1 AAAGAGTAA--AGT
*
65341 AAAGA-AAAATGGT
1 AAAGAGTAAA--GT
*
65354 AAAGAGTAAAGA
1 AAAGAGTAAAGT
65366 AAAGAGTAA
1 AAAGAGTAA
65375 TCAGCAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.03
12 19 0.47
13 9 0.22
14 11 0.28
ACGTcount: A:0.60, C:0.02, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAGAGTAAAGT
Found at i:65333 original size:48 final size:46
Alignment explanation
Indices: 65274--65365 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
65264 AAAATGGTAA
* *
65274 AAAGTGAAGAGTAATCAGTAAAAGGTAAAATGGTAAAGAGAAAAGAGT
1 AAAGTAAAGAGTAATCAGT-AAA-GAAAAATGGTAAAGAGAAAAGAGT
*
65322 AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGA
1 AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGAAAAGA
65366 AAAGAGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 20 0.49
47 3 0.07
48 18 0.44
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.16
Consensus pattern (46 bp):
AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGAAAAGAGT
Found at i:65334 original size:7 final size:7
Alignment explanation
Indices: 65170--65451 Score: 85
Period size: 7 Copynumber: 40.9 Consensus size: 7
65160 TGGTAGAAAA
65170 TAAAGAG
1 TAAAGAG
**
65177 TAATTAG
1 TAAAGAG
*
65184 TAAAGAA
1 TAAAGAG
*
65191 AAAATG-G
1 TAAA-GAG
65198 TAAAGAG
1 TAAAGAG
65205 TAAAAGAG
1 T-AAAGAG
**
65213 TAATTAG
1 TAAAGAG
65220 TAAAGAG
1 TAAAGAG
65227 TAAA-ATGG
1 TAAAGA--G
*
65235 TAAAAAG
1 TAAAGAG
65242 TAAAGAG
1 TAAAGAG
**
65249 TAATCAG
1 TAAAGAG
*
65256 TAAAAAG
1 TAAAGAG
65263 TAAA-ATGG
1 TAAAGA--G
*
65271 TAAAAAG
1 TAAAGAG
*
65278 TGAAGAG
1 TAAAGAG
**
65285 TAATCAG
1 TAAAGAG
65292 TAAA-AGG
1 TAAAGA-G
65299 TAAA-ATGG
1 TAAAGA--G
65307 TAAAGAG
1 TAAAGAG
*
65314 AAAAGAG
1 TAAAGAG
65321 T-AA-AG
1 TAAAGAG
65326 TAAAGAG
1 TAAAGAG
**
65333 TAATCAG
1 TAAAGAG
65340 TAAAGA-
1 TAAAGAG
*
65346 AAAATG-G
1 TAAA-GAG
65353 TAAAGAG
1 TAAAGAG
65360 TAAAGA-
1 TAAAGAG
65366 -AAAGAG
1 TAAAGAG
**
65372 TAATCAG
1 TAAAGAG
*
65379 CAAAGA-
1 TAAAGAG
*
65385 -AAACAG
1 TAAAGAG
65391 TAAAGAG
1 TAAAGAG
*
65398 TGAAGAG
1 TAAAGAG
65405 --AAGTCAG
1 TAAAG--AG
65412 TAAAGA-
1 TAAAGAG
*
65418 AAAATG-G
1 TAAA-GAG
*
65425 TAAAAAG
1 TAAAGAG
65432 TAAAGAG
1 TAAAGAG
**
65439 TAATCAG
1 TAAAGAG
65446 TAAAGA
1 TAAAGA
65452 AGAATGGTAA
Statistics
Matches: 200, Mismatches: 47, Indels: 56
0.66 0.16 0.18
Matches are distributed among these distances:
5 15 0.08
6 15 0.08
7 140 0.70
8 24 0.12
9 6 0.03
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (7 bp):
TAAAGAG
Found at i:65341 original size:19 final size:19
Alignment explanation
Indices: 65319--65393 Score: 80
Period size: 19 Copynumber: 3.9 Consensus size: 19
65309 AAGAGAAAAG
*
65319 AGTAAAGTAAAGAGTAATC
1 AGTAAAGAAAAGAGTAATC
**
65338 AGTAAAGAAAA-ATGGTAAAG
1 AGTAAAGAAAAGA--GTAATC
65358 AGTAAAGAAAAGAGTAATC
1 AGTAAAGAAAAGAGTAATC
* *
65377 AGCAAAGAAAACAGTAA
1 AGTAAAGAAAAGAGTAA
65394 AGAGTGAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.02
19 29 0.63
20 15 0.33
21 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (19 bp):
AGTAAAGAAAAGAGTAATC
Found at i:65362 original size:34 final size:34
Alignment explanation
Indices: 65324--65519 Score: 211
Period size: 34 Copynumber: 5.6 Consensus size: 34
65314 AAAAGAGTAA
65324 AGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAG
*
65358 AGTAAAGAAAAGAGTAATCAGCAAAGAAAACA--GTAAAG
1 AGT-----AAAGAGTAATCAGTAAAGAAAA-ATGGTAAAG
* *
65396 AGTGAAGAG-AAGTCAGTAAAGAAAAATGGTAAAA
1 AGTAAAGAGTAA-TCAGTAAAGAAAAATGGTAAAG
* *
65430 AGTAAAGAGTAATCAGTAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAG
* *
65464 AATAAAGAATAATCAGTAAAGAAAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAG-AAAAATGGTAAAG
65499 AGTAAA-ATGTTAATCAGTAAA
1 AGTAAAGA-G-TAATCAGTAAA
65520 AGGTAATGGC
Statistics
Matches: 137, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
32 3 0.02
33 17 0.12
34 57 0.42
35 18 0.13
36 11 0.08
38 9 0.07
39 21 0.15
40 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.21, T:0.17
Consensus pattern (34 bp):
AGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAG
Found at i:65369 original size:72 final size:72
Alignment explanation
Indices: 65312--65504 Score: 188
Period size: 72 Copynumber: 2.8 Consensus size: 72
65302 AATGGTAAAG
* *
65312 AGAAAAGAGT-AA-AGTAAAGAGTAA-TCAGTAAAGAAAAATGGTAAAGAGTAAAGAAAAGAGTA
1 AGAAAACAGTAAAGAGTAAAGAG-AAGTCAGTAAAGAAAAATGGTAAAAAGTAAAGAAAAGAGTA
*
65374 ATCAGCAA
65 ATCAGAAA
*
65382 AGAAAACAGTAAAGAGTGAAGAGAAGTCAGTAAAGAAAAATGGTAAAAAGT-----AAAGAGTAA
1 AGAAAACAGTAAAGAGTAAAGAGAAGTCAGTAAAGAAAAATGGTAAAAAGTAAAGAAAAGAGTAA
*
65442 TCAGTAA
66 TCAGAAA
** * * * *
65449 AGAAGAATGGTAAAAAATAAAGA-ATAATCAGTAAAGAAAAAATGGTAAAGAGTAAA
1 AGAA-AACAGTAAAGAGTAAAGAGA-AGTCAGTAAAG-AAAAATGGTAAAAAGTAAA
65505 ATGTTAATCA
Statistics
Matches: 103, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
67 20 0.19
68 23 0.22
69 15 0.15
70 9 0.09
71 4 0.04
72 32 0.31
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (72 bp):
AGAAAACAGTAAAGAGTAAAGAGAAGTCAGTAAAGAAAAATGGTAAAAAGTAAAGAAAAGAGTAA
TCAGAAA
Found at i:65403 original size:19 final size:19
Alignment explanation
Indices: 65315--65417 Score: 73
Period size: 19 Copynumber: 5.3 Consensus size: 19
65305 GGTAAAGAGA
* *
65315 AAAGAGTAAAGTAAAGAGT
1 AAAGAGTAAAGAAAACAGT
**
65334 AATCAGTAAAGAAAA-ATGGT
1 AAAGAGTAAAGAAAACA--GT
*
65354 AAAGAGTAAAGAAAAGAGT
1 AAAGAGTAAAGAAAACAGT
** *
65373 AATCAGCAAAGAAAACAGT
1 AAAGAGTAAAGAAAACAGT
**
65392 AAAGAGTGAAGAGAAGTCAGT
1 AAAGAGT-AA-AGAAAACAGT
65413 AAAGA
1 AAAGA
65418 AAAATGGTAA
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
18 1 0.02
19 33 0.51
20 17 0.26
21 14 0.22
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (19 bp):
AAAGAGTAAAGAAAACAGT
Found at i:65603 original size:21 final size:21
Alignment explanation
Indices: 65543--65609 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
65533 CGGTAAAGAA
*
65543 TAAAATGGTAACTAGTAATCAG
1 TAAAATAGTAA-TAGTAATCAG
65565 TACAAA-A-TAA-AGAATAATCAG
1 TA-AAATAGTAATAG--TAATCAG
65586 TAAAATAGTAATAGTAATCAG
1 TAAAATAGTAATAGTAATCAG
65607 TAA
1 TAA
65610 TTCAGTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 23 0.61
22 5 0.13
23 5 0.13
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.25
Consensus pattern (21 bp):
TAAAATAGTAATAGTAATCAG
Found at i:68576 original size:52 final size:50
Alignment explanation
Indices: 68509--68605 Score: 122
Period size: 52 Copynumber: 1.9 Consensus size: 50
68499 AGTCAAATTA
* *
68509 TCATAAATTCGAGATCCAGTCATCAAAGACCCTCGAATCAAATCAAACTCCC
1 TCATAAATTCAAGATCAAGTCAT--AAGACCCTCGAATCAAATCAAACTCCC
* ** *
68561 TCATCAATTCAAGATCAAGTCATTTGACCCTTGAATCAAATCAAA
1 TCATAAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAA
68606 TCAAACTCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 19 0.49
52 20 0.51
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (50 bp):
TCATAAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAACTCCC
Found at i:71562 original size:50 final size:51
Alignment explanation
Indices: 71474--71570 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 51
71464 AGTCAAATTA
*
71474 TCATCAATTCGAGATCAAGTCATCAAAGACCCTCGAATCAAATCAAACTCCC
1 TCATCAATTCAAGATCAAGTCAT-AAAGACCCTCGAATCAAATCAAACTCCC
** *
71526 TCATCAATTCAAGATCAAGTCAT-TTGACCCTTGAATCAAATCAAA
1 TCATCAATTCAAGATCAAGTCATAAAGACCCTCGAATCAAATCAAA
71571 TCAAACTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 19 0.46
52 22 0.54
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (51 bp):
TCATCAATTCAAGATCAAGTCATAAAGACCCTCGAATCAAATCAAACTCCC
Found at i:71563 original size:45 final size:43
Alignment explanation
Indices: 71438--71568 Score: 118
Period size: 52 Copynumber: 2.8 Consensus size: 43
71428 TTTGTGTTCG
* * *
71438 TTCAAGATCAAGTCATTCGACCCTTGAGTCAAATTATCATCAA
1 TTCAAGATCAAGTCATTAGACCCTTGAATCAAATCATCATCAA
* * *
71481 TTCGAGATCAAGTCATCAAAGACCCTCGAATCAAATCAAACTCCCTCATCAA
1 TTCAAGATCAAGTCAT--TAGACCCTTGAATCAAATC--A-----TCATCAA
*
71533 TTCAAGATCAAGTCATTTGACCCTTGAATCAAATCA
1 TTCAAGATCAAGTCATTAGACCCTTGAATCAAATCA
71569 AATCAAACTC
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
43 15 0.22
45 14 0.20
47 1 0.01
48 1 0.01
50 16 0.23
52 22 0.32
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.27
Consensus pattern (43 bp):
TTCAAGATCAAGTCATTAGACCCTTGAATCAAATCATCATCAA
Found at i:80223 original size:2 final size:2
Alignment explanation
Indices: 80216--80317 Score: 195
Period size: 2 Copynumber: 51.0 Consensus size: 2
80206 ATTTCTTTGT
80216 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
80258 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG NG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
80300 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
80318 GAAG
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.49, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.