Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 138 of 213
Found at i:41158437 original size:30 final size:30
Alignment explanation
Indices: 41158365--41158437 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
41158355 CTGAATATAT
41158365 AATAAATATATTTTTTAATTTTTTAATTTTAA
1 AATAAAT-T-TTTTTTAATTTTTTAATTTTAA
** *
41158397 AATACTTTTTTTTTACTTTTTT-ATTTGTAA
1 AATAAATTTTTTTTAATTTTTTAATTT-TAA
41158427 AATAAATTTTT
1 AATAAATTTTT
41158438 GGTGTTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 4 0.11
30 25 0.71
31 1 0.03
32 5 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
AATAAATTTTTTTTAATTTTTTAATTTTAA
Found at i:41164275 original size:23 final size:23
Alignment explanation
Indices: 41164249--41164300 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
41164239 GGCACACGAG
41164249 GTGCCTAAAATACGACACATAAA
1 GTGCCTAAAATACGACACATAAA
** *
41164272 GTGCCCGATATACGACACATAAA
1 GTGCCTAAAATACGACACATAAA
*
41164295 ATGCCT
1 GTGCCT
41164301 GATCGGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (23 bp):
GTGCCTAAAATACGACACATAAA
Found at i:41164447 original size:27 final size:23
Alignment explanation
Indices: 41164408--41164466 Score: 57
Period size: 27 Copynumber: 2.4 Consensus size: 23
41164398 CAATTAAAAC
*
41164408 TCAATTCAGTCATAATTTCTCACATTT
1 TCAATTCAATCAT--TTTC-CAC-TTT
*
41164435 TCAATTGAATCATTTTCCACTTT
1 TCAATTCAATCATTTTCCACTTT
41164458 TCAA-TCAAT
1 TCAATTCAAT
41164467 TTTAAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.14
23 7 0.24
24 3 0.10
25 4 0.14
27 11 0.38
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (23 bp):
TCAATTCAATCATTTTCCACTTT
Found at i:41165439 original size:17 final size:16
Alignment explanation
Indices: 41165414--41165449 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41165404 AACCCTAGTT
* *
41165414 TTTCCCTTTTCTTTTC
1 TTTCCCCTTTCCTTTC
41165430 TTTCCCCTTTCCTTTC
1 TTTCCCCTTTCCTTTC
41165446 TTTC
1 TTTC
41165450 TTTTTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCCCCTTTCCTTTC
Found at i:41165507 original size:25 final size:23
Alignment explanation
Indices: 41165457--41165516 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
41165447 TTCTTTTTCG
41165457 TCTGTTCTCTATTTCTTTTTACCTA
1 TCTGTT-TCTATTTCTTTTTA-CTA
41165482 TTCTGTTTCTATTTCTCCTTTT-CTA
1 -TCTGTTTCTATTTCT--TTTTACTA
41165507 TCT-TTTCTAT
1 TCTGTTTCTAT
41165517 CTTTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.22
24 3 0.09
25 12 0.38
26 6 0.19
27 4 0.12
ACGTcount: A:0.10, C:0.23, G:0.03, T:0.63
Consensus pattern (23 bp):
TCTGTTTCTATTTCTTTTTACTA
Found at i:41165709 original size:22 final size:20
Alignment explanation
Indices: 41165684--41165723 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41165674 TTAAAATATA
41165684 ATAATATAATATAATATATTTT
1 ATAATA-AA-ATAATATATTTT
41165706 ATAATAAAATAATATATT
1 ATAATAAAATAATATATT
41165724 AATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATAAAATAATATATTTT
Found at i:41165717 original size:30 final size:28
Alignment explanation
Indices: 41165673--41165743 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 28
41165663 TTTTTGTTTA
*
41165673 TTTAAAATATAATAATATAATATAATATAT
1 TTTAAAATAAAATAATAT-AT-TAATATAT
*
41165703 TTTATAATAAAATAATATATTAATATAT
1 TTTAAAATAAAATAATATATTAATATAT
*
41165731 TTAAAACATAAAA
1 TTTAAA-ATAAAA
41165744 ATCTAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 12 0.33
29 8 0.22
30 16 0.44
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
TTTAAAATAAAATAATATATTAATATAT
Found at i:41165745 original size:30 final size:28
Alignment explanation
Indices: 41165671--41165752 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
41165661 TTTTTTTGTT
*
41165671 TATTTAAAATATAATAATATAATATAATA
1 TATTTAAAA-ATAAAAATATAATATAATA
* *
41165700 TATTTTATAAT-AAAATA-ATATATTAATA
1 TATTTAAAAATAAAAATATA-ATA-TAATA
*
41165728 TATTTAAAACATAAAAATCTAATAT
1 TATTTAAAA-ATAAAAATATAATAT
41165753 TTTTTTTCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
26 1 0.02
27 8 0.19
28 14 0.33
29 10 0.24
30 8 0.19
31 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TATTTAAAAATAAAAATATAATATAATA
Found at i:41167347 original size:33 final size:33
Alignment explanation
Indices: 41167310--41167417 Score: 137
Period size: 33 Copynumber: 3.3 Consensus size: 33
41167300 TGGCCCTGCC
*
41167310 ATGGTCTTCCATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
** * * * *
41167343 ATGGTCTTATCATCAG-AATGCCATAGCCTAGAT
1 ATGGTCTTA-CATTTGTAGTGCCATAACCCAGTT
41167376 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
41167409 ATGGTCTTA
1 ATGGTCTTA
41167418 TCATCAGAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
32 4 0.07
33 52 0.87
34 4 0.07
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (33 bp):
ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
Found at i:41167350 original size:66 final size:66
Alignment explanation
Indices: 41167309--41167452 Score: 229
Period size: 66 Copynumber: 2.2 Consensus size: 66
41167299 ATGGCCCTGC
*
41167309 CATGGTCTTCCATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAG
1 CATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAG
41167374 A
66 A
* *
41167375 TATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAG-CTCA
1 CATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCT-A
41167439 G-
65 GA
41167440 CTATGGTCTTACA
1 C-ATGGTCTTACA
41167453 CATGTATTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
65 2 0.03
66 70 0.97
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (66 bp):
CATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAG
A
Found at i:41167445 original size:33 final size:32
Alignment explanation
Indices: 41167328--41167450 Score: 113
Period size: 33 Copynumber: 3.7 Consensus size: 32
41167318 CCATTTGTAG
* *
41167328 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCAT-AGCCAGATATGGTCTTATCATCAGAA
** *
41167361 TGCCATAGCCTAGATATGGTCTTA-CATTTGTAG
1 TGCCATAGCC-AGATATGGTCTTATCATCAG-AA
* *
41167394 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCAT-AGCCAGATATGGTCTTATCATCAGAA
* *
41167427 TGTCATAGCTCAGCTATGGTCTTA
1 TGCCATAGC-CAGATATGGTCTTA
41167451 CACATGTATT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
32 9 0.12
33 56 0.78
34 7 0.10
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (32 bp):
TGCCATAGCCAGATATGGTCTTATCATCAGAA
Found at i:41172931 original size:46 final size:46
Alignment explanation
Indices: 41172880--41172973 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
41172870 ATCCGATTCG
* **
41172880 AAAAAAGGAAAAGGAAAAGAGAGAAAAAAATCAAAATCAAAATAAAA
1 AAAAAAGAAAAAATAAAA-AGAGAAAAAAATCAAAATCAAAATAAAA
** *
41172927 AAAAAAGAAAAAATAAAAAGAGAAATCAATCAAAGTCAAAATAAAA
1 AAAAAAGAAAAAATAAAAAGAGAAAAAAATCAAAATCAAAATAAAA
41172973 A
1 A
41172974 TATGAAAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
46 26 0.63
47 15 0.37
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.09
Consensus pattern (46 bp):
AAAAAAGAAAAAATAAAAAGAGAAAAAAATCAAAATCAAAATAAAA
Found at i:41173368 original size:7 final size:7
Alignment explanation
Indices: 41173356--41173388 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
41173346 AAAAGGAGTG
41173356 ATGAAAA
1 ATGAAAA
41173363 ATG-AAA
1 ATGAAAA
41173369 ATG-AAA
1 ATGAAAA
41173375 ATGAAAA
1 ATGAAAA
41173382 ATGAAAA
1 ATGAAAA
41173389 GTAAAATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:41174723 original size:87 final size:87
Alignment explanation
Indices: 41174615--41175207 Score: 954
Period size: 87 Copynumber: 6.8 Consensus size: 87
41174605 AGATCAGTGA
*
41174615 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
41174680 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * *
41174702 AGACCAAAAACAAAGCATTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
41174767 CTTCCTGCGTTAACAGCGAAGT
66 CTTCCTGCGTTAACAGCGAAGC
* *
41174789 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * * *
41174854 CTTCCTACGTTAATAGTGAAGT
66 CTTCCTGCGTTAACAGCGAAGC
* * * *
41174876 AGA-CAAAAAAAAAAGCCTTACCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
1 AGATC-AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
* * * *
41174940 CCTTCTTGCGTTAACACCAAAGT
65 CCTTCCTGCGTTAACAGCGAAGC
* *
41174963 AGATCAAAAACAAAGCCTTGTCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
41175028 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
*
41175050 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
41175115 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
41175137 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
41175202 CTTCCT
66 CTTCCT
41175208 AAGTACTAGC
Statistics
Matches: 467, Mismatches: 37, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
86 1 0.00
87 465 1.00
88 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:41175159 original size:43 final size:43
Alignment explanation
Indices: 41175023--41175159 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 43
41175013 GATAACAGAT
41175023 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
* * * * * * * * *
41175066 CTTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGT-TAAAGATAGCAGAT
1 CTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATCGAAA-ACA-AAG-C
41175110 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
41175153 CTTGCCT
1 CTTGCCT
41175160 CCATCAGTTG
Statistics
Matches: 67, Mismatches: 18, Indels: 18
0.65 0.17 0.17
Matches are distributed among these distances:
41 3 0.04
42 15 0.22
43 19 0.28
44 12 0.18
45 15 0.22
46 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (43 bp):
CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
Found at i:41178310 original size:43 final size:42
Alignment explanation
Indices: 41178184--41178386 Score: 123
Period size: 42 Copynumber: 5.1 Consensus size: 42
41178174 TAAAATGGTA
*
41178184 AAAAAATTATTACATAAATACAAAGTTGACTATTTAAATTGC
1 AAAAAATTATTACATTAATACAAAGTTGACTATTTAAATTGC
* * * * * ** *
41178226 AAAAAA--A-AAAACTCATA-AGA-TTGA-TAAATAAAATGAC
1 AAAAAATTATTACATTAATACAAAGTTGACTATTTAAATTG-C
41178263 AAAAAATTCATTACATTAATACAAAGTTGACTATTTAAATTGC
1 AAAAAATT-ATTACATTAATACAAAGTTGACTATTTAAATTGC
* * * * *
41178306 AAAAAA--A--AC---CATA-AAA-TTGA-TAAATAAAATGGA
1 AAAAAATTATTACATTAATACAAAGTTGACT-ATTTAAATTGC
* *
41178339 AAAAAATTATTACATAAATACAAAGTTGACTATTAAAATTGC
1 AAAAAATTATTACATTAATACAAAGTTGACTATTTAAATTGC
41178381 AAAAAA
1 AAAAAA
41178387 ACCCATAAAA
Statistics
Matches: 116, Mismatches: 26, Indels: 38
0.64 0.14 0.21
Matches are distributed among these distances:
32 1 0.01
33 17 0.15
34 3 0.03
35 4 0.03
36 8 0.07
37 13 0.11
38 4 0.03
39 5 0.04
40 6 0.05
41 9 0.08
42 26 0.22
43 12 0.10
44 8 0.07
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (42 bp):
AAAAAATTATTACATTAATACAAAGTTGACTATTTAAATTGC
Found at i:41178361 original size:75 final size:76
Alignment explanation
Indices: 41178165--41178512 Score: 504
Period size: 75 Copynumber: 4.5 Consensus size: 76
41178155 TGGTGTCAAC
*
41178165 ATTGATAATTAAAATGGTAAAAAAATTATTACATAAATACAAAGTTGACTATTTAAATTGCAAAA
1 ATTGATAAATAAAATGG-AAAAAAATTATTACATAAATACAAAGTTGACTATTTAAATTGC--AA
*
41178230 AAAAAAACTCATAAG
63 AAAAAAAC-CATAAA
*
41178245 ATTGATAAATAAAAT-GACAAAAAATTCATTACATTAATACAAAGTTGACTATTTAAATTGC-AA
1 ATTGATAAATAAAATGGA-AAAAAATT-ATTACATAAATACAAAGTTGACTATTTAAATTGCAAA
41178308 AAAAAACCATAAA
64 AAAAAACCATAAA
*
41178321 ATTGATAAATAAAATGGAAAAAAATTATTACATAAATACAAAGTTGACTATTAAAATTGC-AAAA
1 ATTGATAAATAAAATGGAAAAAAATTATTACATAAATACAAAGTTGACTATTTAAATTGCAAAAA
*
41178385 AAACCCATAAA
66 AAAACCATAAA
* * **
41178396 ATTGATAAATAAAATGGCAACAAATTCATTACATAAATATGAAGTTGACTATTTAAATTGCAAAA
1 ATTGATAAATAAAATGGAAAAAAATT-ATTACATAAATACAAAGTTGACTATTTAAATTGCAAAA
41178461 AAAAATCCATAAA
65 AAAAA-CCATAAA
*
41178474 ATTGATAAATAAAATGGAAAAAAATCCATTACATAAATA
1 ATTGATAAATAAAATGGAAAAAAAT-TATTACATAAATA
41178513 TGAAGTTATT
Statistics
Matches: 246, Mismatches: 15, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
75 70 0.28
76 59 0.24
77 18 0.07
78 43 0.17
79 9 0.04
80 47 0.19
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.27
Consensus pattern (76 bp):
ATTGATAAATAAAATGGAAAAAAATTATTACATAAATACAAAGTTGACTATTTAAATTGCAAAAA
AAAACCATAAA
Found at i:41178448 original size:151 final size:154
Alignment explanation
Indices: 41178165--41178512 Score: 540
Period size: 151 Copynumber: 2.2 Consensus size: 154
41178155 TGGTGTCAAC
* *
41178165 ATTGATAATTAAAATGGTAAAAAAATTATTACATAAATACAAAGTTGACTATTTAAATTGCAAAA
1 ATTGATAAATAAAATGG-AAAAAAATTATTACATAAATACAAAGTTGACTATTAAAATTGC---A
* * *
41178230 AAAAAAACTCATAAGATTGATAAATAAAATGACAAAAAATTCATTACATTAATACAAAGTTGACT
62 AAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAATACAAAGTTGACT
41178295 ATTTAAATTGC-AAAAAAAA-CCATAAA
127 ATTTAAATTGCAAAAAAAAATCCATAAA
41178321 ATTGATAAATAAAATGGAAAAAAATTATTACATAAATACAAAGTTGACTATTAAAATTGC-AAAA
1 ATTGATAAATAAAATGGAAAAAAATTATTACATAAATACAAAGTTGACTATTAAAATTGCAAAAA
* * **
41178385 AAACCCATAAAATTGATAAATAAAATGGCAACAAATTCATTACATAAATATGAAGTTGACTATTT
66 AAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAATACAAAGTTGACTATTT
41178450 AAATTGCAAAAAAAAATCCATAAA
131 AAATTGCAAAAAAAAATCCATAAA
*
41178474 ATTGATAAATAAAATGGAAAAAAATCCATTACATAAATA
1 ATTGATAAATAAAATGGAAAAAAAT-TATTACATAAATA
41178513 TGAAGTTATT
Statistics
Matches: 179, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
151 69 0.39
152 8 0.04
153 32 0.18
154 12 0.07
155 42 0.23
156 16 0.09
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.27
Consensus pattern (154 bp):
ATTGATAAATAAAATGGAAAAAAATTATTACATAAATACAAAGTTGACTATTAAAATTGCAAAAA
AAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAATACAAAGTTGACTATTT
AAATTGCAAAAAAAAATCCATAAA
Found at i:41178795 original size:33 final size:33
Alignment explanation
Indices: 41178702--41178849 Score: 111
Period size: 33 Copynumber: 4.5 Consensus size: 33
41178692 AACTTGAGCT
* * *
41178702 GGGAGGAGTGGAGTACGACAATGGATACGGGCC
1 GGGAAGAGTGGAGTACGGCAGTGGATACGGGCC
* * * *
41178735 AGGATGAGTGGAGTACAGCGGTGGATACGGGCC
1 GGGAAGAGTGGAGTACGGCAGTGGATACGGGCC
* * *
41178768 GGGAAGAGTGGAGTACGGTAGTAGATACGAGCC
1 GGGAAGAGTGGAGTACGGCAGTGGATACGGGCC
* * * *
41178801 -GAAAGGAGCGGAGTACTG-AGGTGGATACGAGCC
1 GGGAA-GAGTGGAGTACGGCA-GTGGATACGGGCC
* * *
41178834 AGGATGACTGGAGTAC
1 GGGAAGAGTGGAGTAC
41178850 TGAGGTGGTA
Statistics
Matches: 91, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
32 4 0.04
33 85 0.93
34 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.43, T:0.14
Consensus pattern (33 bp):
GGGAAGAGTGGAGTACGGCAGTGGATACGGGCC
Found at i:41178850 original size:33 final size:33
Alignment explanation
Indices: 41178723--41178857 Score: 116
Period size: 33 Copynumber: 4.1 Consensus size: 33
41178713 AGTACGACAA
* * * *
41178723 TGGATACGGGCCAGGATGAGTGGAGTACAGCGG
1 TGGATACGAGCCAGGATGACTGGAGTACTGAGG
* * * * *
41178756 TGGATACGGGCCGGGAAGAGTGGAGTACGGTA-G
1 TGGATACGAGCCAGGATGACTGGAGTACTG-AGG
*
41178789 TAGATACGAGCCGAAAGGA-G-C-GGAGTACTGAGG
1 TGGATACGAGCC---AGGATGACTGGAGTACTGAGG
41178822 TGGATACGAGCCAGGATGACTGGAGTACTGAGG
1 TGGATACGAGCCAGGATGACTGGAGTACTGAGG
41178855 TGG
1 TGG
41178858 TAGTGGGCTG
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
30 4 0.05
31 1 0.01
32 2 0.02
33 73 0.87
35 1 0.01
36 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.44, T:0.16
Consensus pattern (33 bp):
TGGATACGAGCCAGGATGACTGGAGTACTGAGG
Found at i:41181087 original size:77 final size:77
Alignment explanation
Indices: 41180968--41181119 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 77
41180958 TACTAACAAA
41180968 ATAACTATAAAATTATTATTTTTAAAATACATTACTAAAAAATCACAAAAA-CATA-ACTAAACA
1 ATAACTATAAAATTATTATTTTTAAAATACATTACTAAAAAATCACAAAAACCATATACTAAACA
41181031 CTAAAAATTTAT
66 CTAAAAATTTAT
* * *
41181043 ATAACTATAAATTTAATTTTTTTTAAAATTACATTACTAAAAAATCACAAAAACCCTATACTAAA
1 ATAACTATAAAATT-ATTATTTTTAAAA-TACATTACTAAAAAATCACAAAAACCATATACTAAA
*
41181108 CACTAACAATTT
64 CACTAAAAATTT
41181120 GTAACCTAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
75 13 0.19
76 12 0.17
77 24 0.35
78 3 0.04
79 17 0.25
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (77 bp):
ATAACTATAAAATTATTATTTTTAAAATACATTACTAAAAAATCACAAAAACCATATACTAAACA
CTAAAAATTTAT
Found at i:41181140 original size:67 final size:67
Alignment explanation
Indices: 41181105--41181284 Score: 328
Period size: 67 Copynumber: 2.7 Consensus size: 67
41181095 ACCCTATACT
41181105 AAACACTAACAATTTGTAACCTAATCCCACAAATTACTAACAAAATAAATAACTATAACAAAACA
1 AAACACTAACAATTTGTAACCTAATCCCACAAATTACTAACAAAATAAATAACTATAACAAAACA
41181170 CA
66 CA
41181172 AAACACTAACAATTTGTAACCTAATCCCACAAATTACTAACAAAATAAATAACTATAACAAAACA
1 AAACACTAACAATTTGTAACCTAATCCCACAAATTACTAACAAAATAAATAACTATAACAAAACA
41181237 CA
66 CA
* *
41181239 AAACACTAACAATTTGTAACCTAAT--CATAAACTACTAACAAAATAA
1 AAACACTAACAATTTGTAACCTAATCCCACAAATTACTAACAAAATAA
41181285 CTATAATTTT
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
65 19 0.17
67 92 0.83
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.22
Consensus pattern (67 bp):
AAACACTAACAATTTGTAACCTAATCCCACAAATTACTAACAAAATAAATAACTATAACAAAACA
CA
Found at i:41181144 original size:31 final size:31
Alignment explanation
Indices: 41181109--41181214 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
41181099 TATACTAAAC
41181109 ACTAACAATTTGTAACCTAATCCCACAAATT
1 ACTAACAATTTGTAACCTAATCCCACAAATT
*** * * **
41181140 ACTAACAAAATAAATAA-CTATAACAAAACACAAAAC
1 ACTAAC--AATTTGTAACCTA-ATC---CCACAAATT
41181176 ACTAACAATTTGTAACCTAATCCCACAAATT
1 ACTAACAATTTGTAACCTAATCCCACAAATT
41181207 ACTAACAA
1 ACTAACAA
41181215 AATAAATAAC
Statistics
Matches: 54, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
31 20 0.37
32 3 0.06
33 8 0.15
34 8 0.15
35 3 0.06
36 12 0.22
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (31 bp):
ACTAACAATTTGTAACCTAATCCCACAAATT
Found at i:41181173 original size:36 final size:36
Alignment explanation
Indices: 41181140--41181250 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
41181130 CCCACAAATT
41181140 ACTAACAAAATAAATAACTATAACAAAACACAAAAC
1 ACTAACAAAATAAATAACTATAACAAAACACAAAAC
*** * * **
41181176 ACTAAC--AATTTGTAACCTA-ATC---CCACAAATT
1 ACTAACAAAATAAATAA-CTATAACAAAACACAAAAC
41181207 ACTAACAAAATAAATAACTATAACAAAACACAAAAC
1 ACTAACAAAATAAATAACTATAACAAAACACAAAAC
41181243 ACTAACAA
1 ACTAACAA
41181251 TTTGTAACCT
Statistics
Matches: 54, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
31 12 0.22
32 3 0.06
33 8 0.15
34 8 0.15
35 3 0.06
36 20 0.37
ACGTcount: A:0.59, C:0.22, G:0.01, T:0.18
Consensus pattern (36 bp):
ACTAACAAAATAAATAACTATAACAAAACACAAAAC
Found at i:41181481 original size:60 final size:60
Alignment explanation
Indices: 41181412--41181530 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
41181402 ATACTAAACT
*
41181412 AAACACAACAATTTATAACATAATCCTAAATGACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATGACTAACAAATTAATTTTAAAATAATTAC
*
41181472 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATGACTAACAAATTAATTTTAAAATAATTA
41181531 TAAAAAAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATGACTAACAAATTAATTTTAAAATAATTAC
Found at i:41182885 original size:51 final size:52
Alignment explanation
Indices: 41182790--41182887 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 52
41182780 TATAAATATA
* * * *
41182790 CGTTCATAACAATTTGTATCAATTGTTCATAATTATTATAATAATTAATTTG
1 CGTTCATAACAACTCGTATCAATTGTTCATAATAAATATAATAATTAATTTG
* *
41182842 CGTTGATAACAACTCGTATCTA-TGTTCATAAATAAATAT-ATAATTA
1 CGTTCATAACAACTCGTATCAATTGTTCAT-AATAAATATAATAATTA
41182888 TATTAAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
51 14 0.36
52 25 0.64
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (52 bp):
CGTTCATAACAACTCGTATCAATTGTTCATAATAAATATAATAATTAATTTG
Found at i:41182968 original size:23 final size:23
Alignment explanation
Indices: 41182942--41182997 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
41182932 TGAATTAATT
41182942 TTAATTTTAAT-TTAAAAAGAAAG
1 TTAATTTTAATCTTAAAAA-AAAG
* *
41182965 TTAA-TTTAATCTTCAAAATAAG
1 TTAATTTTAATCTTAAAAAAAAG
41182987 TTAAATTTTAA
1 TT-AATTTTAA
41182998 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.39
23 12 0.43
24 5 0.18
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (23 bp):
TTAATTTTAATCTTAAAAAAAAG
Found at i:41183050 original size:18 final size:18
Alignment explanation
Indices: 41183001--41183051 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
41182991 ATTTTAAATA
41183001 ATTAAAAATAA-AATATT
1 ATTAAAAATAATAATATT
* * *
41183018 ATCTTATAAT-TTAATATT
1 AT-TAAAAATAATAATATT
41183036 ATTAAAAATAATAATA
1 ATTAAAAATAATAATA
41183052 GTGAATATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAAAAATAATAATATT
Found at i:41185523 original size:10 final size:10
Alignment explanation
Indices: 41185491--41185546 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
41185481 TAATATATAA
41185491 TTATAAAAAT
1 TTATAAAAAT
* *
41185501 TTTTAAGAA-
1 TTATAAAAAT
41185510 TTATAAAAAT
1 TTATAAAAAT
41185520 TTATCAAAAA-
1 TTAT-AAAAAT
* *
41185530 GTATTAAAAT
1 TTATAAAAAT
41185540 TTATAAA
1 TTATAAA
41185547 TAAAAGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
9 11 0.31
10 19 0.54
11 5 0.14
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:41187880 original size:11 final size:11
Alignment explanation
Indices: 41187864--41187888 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41187854 GTAGTGCCGT
41187864 TTTTATTTTTA
1 TTTTATTTTTA
41187875 TTTTATTTTTA
1 TTTTATTTTTA
41187886 TTT
1 TTT
41187889 ACATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:41189953 original size:5 final size:6
Alignment explanation
Indices: 41189936--41189961 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41189926 AAATTTCTAC
41189936 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
41189962 GAATTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:41193843 original size:6 final size:6
Alignment explanation
Indices: 41193832--41193902 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
41193822 AATAAACTAC
* * * *
41193832 GAAAGA GAAAGA GAAAGA GAAAGA GAGAGA GAGAGA GAGAGA GAGAGA
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA
* *
41193880 GAGAGA GGAGAGA GAAA-A GAAAG
1 GAAAGA -GAAAGA GAAAGA GAAAG
41193903 CCCAAAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.08
6 50 0.82
7 6 0.10
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:41193860 original size:2 final size:2
Alignment explanation
Indices: 41193835--41193894 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
41193825 AAACTACGAA
* * *
41193835 AG AG AA AG AG AA AG AG AA 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
41193877 AG AG AG AG AG -G AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
41193895 AAAGAAAGCC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41201776 original size:18 final size:18
Alignment explanation
Indices: 41201753--41201789 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41201743 ATCCCAACAT
*
41201753 ATAAATATGAACGATAAA
1 ATAAATATAAACGATAAA
*
41201771 ATAAATATAAAGGATAAA
1 ATAAATATAAACGATAAA
41201789 A
1 A
41201790 AATACATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.22
Consensus pattern (18 bp):
ATAAATATAAACGATAAA
Found at i:41202911 original size:3 final size:3
Alignment explanation
Indices: 41202903--41202930 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41202893 GTTGACAATA
41202903 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41202931 TGAATAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41212716 original size:8 final size:8
Alignment explanation
Indices: 41212705--41212736 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
41212695 ACCTAAAAAT
41212705 ATACCCAA
1 ATACCCAA
41212713 ATACCCAA
1 ATACCCAA
41212721 ATACCCAA
1 ATACCCAA
*
41212729 ATCCCCAA
1 ATACCCAA
41212737 TAAGTCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12
Consensus pattern (8 bp):
ATACCCAA
Found at i:41218452 original size:6 final size:6
Alignment explanation
Indices: 41218441--41218486 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
41218431 TAAAAAGAAT
** *
41218441 TAAAAA TAAAAA TAAAAA TAAACG T-AAAA TAAATA -AAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
41218487 AAATAAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
5 7 0.22
6 25 0.78
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:41218489 original size:11 final size:11
Alignment explanation
Indices: 41218442--41218489 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
41218432 AAAAAGAATT
41218442 AAAAATAAAAA
1 AAAAATAAAAA
**
41218453 TAAAAATAAACG
1 -AAAAATAAAAA
* *
41218465 TAAAATAAATA
1 AAAAATAAAAA
41218476 AAAAATAAAAA
1 AAAAATAAAAA
41218487 AAA
1 AAA
41218490 TAAACTTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:41218490 original size:16 final size:16
Alignment explanation
Indices: 41218424--41218493 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
41218414 TAAGGCTAAG
*
41218424 AAAATAATAAAAAGAAT
1 AAAA-AATAAAAAAAAT
*
41218441 TAAAAATAAAAATAAA-
1 AAAAAATAAAAA-AAAT
* *
41218457 AATAAACGTAAAATAAAT
1 AA-AAA-ATAAAAAAAAT
41218475 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
41218491 AAA
1 AAA
41218494 CTTAATGGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
16 21 0.50
17 14 0.33
18 7 0.17
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:41219969 original size:16 final size:15
Alignment explanation
Indices: 41219948--41219979 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
41219938 GCAAACTAAG
41219948 AAATAATAATGAAGAA
1 AAATAATAAT-AAGAA
41219964 AAATAATAATAAGAA
1 AAATAATAATAAGAA
41219979 A
1 A
41219980 TAAAGTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (15 bp):
AAATAATAATAAGAA
Found at i:41219970 original size:13 final size:14
Alignment explanation
Indices: 41219945--41219982 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
41219935 CATGCAAACT
41219945 AAGAAATAATAATG
1 AAGAAATAATAATG
41219959 AAGAAAAATAATAAT-
1 AAG--AAATAATAATG
41219974 AAGAAATAA
1 AAGAAATAA
41219983 AGTGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 3 0.14
16 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (14 bp):
AAGAAATAATAATG
Found at i:41230376 original size:20 final size:20
Alignment explanation
Indices: 41230330--41230376 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41230320 TAGTAAAGTT
*
41230330 ATAAAATTAATTTTAGAATA
1 ATAAAATTAATTTTAAAATA
*
41230350 ATTAAATTAA-TTTAAAATAA
1 ATAAAATTAATTTTAAAAT-A
41230370 ATAAAAT
1 ATAAAAT
41230377 AAAACAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAAAATTAATTTTAAAATA
Found at i:41240177 original size:27 final size:27
Alignment explanation
Indices: 41240139--41240194 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
41240129 TCGAATCACC
41240139 TTACAATTCAATTGTTTTAATAAAACG
1 TTACAATTCAATTGTTTTAATAAAACG
41240166 TTACAATTCAATTGTTTTAATAAAACG
1 TTACAATTCAATTGTTTTAATAAAACG
41240193 TT
1 TT
41240195 TCGATTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (27 bp):
TTACAATTCAATTGTTTTAATAAAACG
Found at i:41244034 original size:85 final size:85
Alignment explanation
Indices: 41243891--41244141 Score: 324
Period size: 85 Copynumber: 3.0 Consensus size: 85
41243881 ACCATCGCTG
* *
41243891 ATTTGCAGTTATTGCCACTTGTTGTAGGTGCACAACATATTTGTAAATTAAATGAACTGCCACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAAATTAAATGAACTGCCACTT
*
41243956 GGTTTGTGATCGAACTGCAT
66 GGTTTGTGATCGAACCGCAT
* * * * *
41243976 ATTTGCAATTAGTGCCACTTGTTGTGGGTGCACAACAAATTTGTAAATTAAACGAACTGCTACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAAATTAAATGAACTGCCACTT
** *
41244041 GGTTCATGATCGAACCGTAT
66 GGTTTGTGATCGAACCGCAT
*** ** * *
41244061 ATTTTTTGTTACTATCACTTGTTATGGGTGCACAACATATTTG-AAGATTAAATGAACTGTCACT
1 ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAA-ATTAAATGAACTGCCACT
41244125 TGGTTTGTGATCGAACC
65 TGGTTTGTGATCGAACC
41244142 ACACTGTTTG
Statistics
Matches: 141, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
84 2 0.01
85 139 0.99
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (85 bp):
ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAAATTAAATGAACTGCCACTT
GGTTTGTGATCGAACCGCAT
Found at i:41247537 original size:12 final size:12
Alignment explanation
Indices: 41247503--41247540 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41247493 ATTTTTAATT
41247503 AAGTAAATGTTAA
1 AAGTAAA-GTTAA
*
41247516 AA-TTAAGTTAA
1 AAGTAAAGTTAA
41247527 AAGTAAAGTTAA
1 AAGTAAAGTTAA
41247539 AA
1 AA
41247541 TATAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 7 0.32
12 13 0.59
13 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (12 bp):
AAGTAAAGTTAA
Found at i:41248699 original size:4 final size:4
Alignment explanation
Indices: 41248690--41248789 Score: 173
Period size: 4 Copynumber: 25.0 Consensus size: 4
41248680 TTTATTATAG
41248690 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
41248738 TATA TGTA TGTA TGTA TGTA TGTA GGTA TGTA CGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
41248786 TGTA
1 TGTA
41248790 AATATGTAAC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 90 1.00
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:41250411 original size:25 final size:24
Alignment explanation
Indices: 41250351--41250413 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
41250341 GTACATCTAT
41250351 GCTCATACGAGCTATAAACGGTAA
1 GCTCATACGAGCTATAAACGGTAA
* ** *
41250375 GCTCTTTTGAGCTGA-ATAATGGTAA
1 GCTCATACGAGCT-ATA-AACGGTAA
41250400 GCTCATACGAGCTA
1 GCTCATACGAGCTA
41250414 AGAGCCGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (24 bp):
GCTCATACGAGCTATAAACGGTAA
Found at i:41258061 original size:25 final size:26
Alignment explanation
Indices: 41258019--41258072 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
41258009 TTCTCCTAAA
*
41258019 TTTCAATTTTATTTAATTATTTAAT-T
1 TTTCAATTTTATTGAATTA-TTAATAT
41258045 TTTCAA-TTTATTGAATTATTAATAT
1 TTTCAATTTTATTGAATTATTAATAT
41258070 TTT
1 TTT
41258073 ATACTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAATAT
Found at i:41260271 original size:14 final size:14
Alignment explanation
Indices: 41260254--41260299 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
41260244 TGCTCGTGAA
*
41260254 AAAATAAAAGAAAG
1 AAAAGAAAAGAAAG
41260268 AAAAGAAAAGAAA-
1 AAAAGAAAAGAAAG
*
41260281 AAGAGAAAA-AAAG
1 AAAAGAAAAGAAAG
*
41260294 AGAAGA
1 AAAAGA
41260300 GCTTATGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 3 0.11
13 12 0.44
14 12 0.44
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:41263139 original size:10 final size:10
Alignment explanation
Indices: 41263116--41263163 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
41263106 GAATCTGTCG
*
41263116 AAAATAAATT
1 AAAATTAATT
*
41263126 AAAATTAATC
1 AAAATTAATT
*
41263136 AAAATTTATTAT
1 AAAA-TTAAT-T
41263148 AAAATTAATT
1 AAAATTAATT
41263158 AAAATT
1 AAAATT
41263164 CAACACGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 19 0.61
11 8 0.26
12 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTAATT
Found at i:41264007 original size:11 final size:11
Alignment explanation
Indices: 41263993--41264065 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 11
41263983 TAAATTTATC
41263993 ATATTTTTAAA
1 ATATTTTTAAA
41264004 ATATTTTT-AA
1 ATATTTTTAAA
*
41264014 A-A-TTTT-CA
1 ATATTTTTAAA
*
41264022 AT-TTCTTAAA
1 ATATTTTTAAA
*
41264032 ATATTTTTTAA
1 ATATTTTTAAA
*
41264043 TTATTTTTTAAA
1 ATA-TTTTTAAA
41264055 ATATATTTTAA
1 ATAT-TTTTAA
41264066 TATTTAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
8 6 0.12
9 4 0.08
10 6 0.12
11 17 0.35
12 15 0.31
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:41264042 original size:12 final size:12
Alignment explanation
Indices: 41264022--41264065 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
41264012 AAAATTTTCA
*
41264022 ATTTCTTAAAAT
1 ATTTTTTAAAAT
*
41264034 ATTTTTT-AATT
1 ATTTTTTAAAAT
41264045 ATTTTTTAAAAT
1 ATTTTTTAAAAT
*
41264057 ATATTTTAA
1 ATTTTTTAA
41264066 TATTTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTTAAAAT
Found at i:41264053 original size:23 final size:22
Alignment explanation
Indices: 41264022--41264070 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
41264012 AAAATTTTCA
*
41264022 ATTTCTTAAAATATTTTTTAATT
1 ATTTCTTAAAATATATTTTAA-T
*
41264045 ATTTTTTAAAATATATTTTAAT
1 ATTTCTTAAAATATATTTTAAT
41264067 ATTT
1 ATTT
41264071 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTCTTAAAATATATTTTAAT
Found at i:41265646 original size:16 final size:16
Alignment explanation
Indices: 41265622--41265675 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
41265612 CAAATCGAGT
*
41265622 TATTCAAATTATTTTA
1 TATTTAAATTATTTTA
**
41265638 TATTTAAATTATTAAA
1 TATTTAAATTATTTTA
41265654 TATATTAAATTATTTTA
1 TAT-TTAAATTATTTTA
41265671 TATTT
1 TATTT
41265676 TTAATAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTAAATTATTTTA
Found at i:41265673 original size:17 final size:17
Alignment explanation
Indices: 41265622--41265673 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
41265612 CAAATCGAGT
41265622 TATTCAAATTATTTTATA
1 TATT-AAATTATTTTATA
**
41265640 T-TTAAATTATTAAATA
1 TATTAAATTATTTTATA
41265656 TATTAAATTATTTTATA
1 TATTAAATTATTTTATA
41265673 T
1 T
41265674 TTTTAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 12 0.41
17 16 0.55
18 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAAATTATTTTATA
Found at i:41265733 original size:20 final size:20
Alignment explanation
Indices: 41265708--41265745 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41265698 TGAATAAAAT
41265708 TTATTATTGTAATGCATGGA
1 TTATTATTGTAATGCATGGA
41265728 TTATTATTGTAATGCATG
1 TTATTATTGTAATGCATG
41265746 AATAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (20 bp):
TTATTATTGTAATGCATGGA
Found at i:41269274 original size:21 final size:21
Alignment explanation
Indices: 41269249--41269303 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
41269239 TAACTTCATT
41269249 TATTTTAATAAAAAACATT-AA
1 TATTTTAATAAAAAA-ATTGAA
* * *
41269270 TATTTTTATATAAAATTTGAA
1 TATTTTAATAAAAAAATTGAA
*
41269291 CATTTTAATAAAA
1 TATTTTAATAAAA
41269304 TAATATCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTTTAATAAAAAAATTGAA
Found at i:41281038 original size:9 final size:9
Alignment explanation
Indices: 41281024--41281054 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
41281014 GATAAAGTAA
41281024 AATTAAATT
1 AATTAAATT
41281033 AATTAAATT
1 AATTAAATT
41281042 AATTAAAATT
1 AATT-AAATT
41281052 AAT
1 AAT
41281055 GTTATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:41290401 original size:41 final size:41
Alignment explanation
Indices: 41290346--41290463 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 41
41290336 TACTAAAGTA
* *
41290346 CACCAGCATGAAGCCTGTTAGACAATAAGTCTGAAGTAATT
1 CACCAGCATCAAGCCTGTTAGACAATAAGTCTGAAATAATT
* * *
41290387 CACCGGCATCAAGCCTGCTAGACATTAAGTCTGAAATAATT
1 CACCAGCATCAAGCCTGTTAGACAATAAGTCTGAAATAATT
* * *
41290428 CACCAGCATCAAGCCTGTTAGGCACTAAGCCTGAAA
1 CACCAGCATCAAGCCTGTTAGACAATAAGTCTGAAA
41290464 ACCAATTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (41 bp):
CACCAGCATCAAGCCTGTTAGACAATAAGTCTGAAATAATT
Found at i:41291819 original size:13 final size:13
Alignment explanation
Indices: 41291801--41291826 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41291791 TCAAACTATC
41291801 AAATTTTCACACA
1 AAATTTTCACACA
41291814 AAATTTTCACACA
1 AAATTTTCACACA
41291827 TATAACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTTCACACA
Found at i:41292821 original size:32 final size:32
Alignment explanation
Indices: 41292780--41292877 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 32
41292770 AAGAAAGGGA
41292780 AAAAAAAGAATGATAGTGGATGCATACAAATT
1 AAAAAAAGAATGATAGTGGATGCATACAAATT
* * ***
41292812 AAAAAAAGAA--A-A--GAAAG-A-A-AAGGG
1 AAAAAAAGAATGATAGTGGATGCATACAAATT
41292836 AAAAAAAGAATGATAGTGGATGCATACAAATT
1 AAAAAAAGAATGATAGTGGATGCATACAAATT
41292868 AAAAAAAGAA
1 AAAAAAAGAA
41292878 AAGAAAGAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
24 12 0.25
25 1 0.02
26 2 0.04
27 4 0.08
29 4 0.08
30 2 0.04
31 1 0.02
32 22 0.46
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.14
Consensus pattern (32 bp):
AAAAAAAGAATGATAGTGGATGCATACAAATT
Found at i:41292850 original size:56 final size:57
Alignment explanation
Indices: 41292769--41292888 Score: 226
Period size: 56 Copynumber: 2.1 Consensus size: 57
41292759 ATTTATAATA
41292769 AAAG-AAAGGGAAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
1 AAAGAAAAGGGAAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
41292825 AAAGAAAAGGG-AAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
1 AAAGAAAAGGGAAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
41292881 AAAGAAAA
1 AAAGAAAA
41292889 AAGAAAGAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 57 0.90
57 6 0.10
ACGTcount: A:0.64, C:0.03, G:0.21, T:0.12
Consensus pattern (57 bp):
AAAGAAAAGGGAAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
Found at i:41292895 original size:15 final size:16
Alignment explanation
Indices: 41292869--41292903 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41292859 ATACAAATTA
41292869 AAAAAAGAAAAGAAAG
1 AAAAAAGAAAAGAAAG
*
41292885 AAAAAAG-AAAGAAAT
1 AAAAAAGAAAAGAAAG
41292900 AAAA
1 AAAA
41292904 TGAGAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAG
Found at i:41293354 original size:12 final size:12
Alignment explanation
Indices: 41293337--41293362 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41293327 GTGTGAAAAT
41293337 TGAAATTTTATG
1 TGAAATTTTATG
41293349 TGAAATTTTATG
1 TGAAATTTTATG
41293361 TG
1 TG
41293363 TAATATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (12 bp):
TGAAATTTTATG
Found at i:41300966 original size:37 final size:37
Alignment explanation
Indices: 41300916--41300994 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
41300906 TTATTACGAA
* *
41300916 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
41300953 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
41300990 GTCTT
1 GTCTT
41300995 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:41301191 original size:47 final size:47
Alignment explanation
Indices: 41301113--41301555 Score: 724
Period size: 47 Copynumber: 9.4 Consensus size: 47
41301103 CCCTTCGGGA
* * * * * * *
41301113 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41301160 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41301207 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41301254 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41301301 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41301348 CTTATCCACATATATATACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTAT-CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41301396 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41301443 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41301490 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41301537 CTTATCACATATATACACT
1 CTTATCACATATATACACT
41301556 GTCTTGGCTG
Statistics
Matches: 374, Mismatches: 21, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
47 329 0.88
48 45 0.12
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41301432 original size:189 final size:188
Alignment explanation
Indices: 41301113--41301555 Score: 733
Period size: 189 Copynumber: 2.4 Consensus size: 188
41301103 CCCTTCGGGA
** * * * * * * * *
41301113 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
41301178 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
* * *
41301243 GGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 GGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41301301 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCCACATATATATA
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-CACATATATACA
*
41301366 CTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
65 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
41301431 CGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
130 CGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
41301490 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
41301555 T
66 T
41301556 GTCTTGGCTG
Statistics
Matches: 236, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
188 54 0.23
189 182 0.77
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41305306 original size:25 final size:25
Alignment explanation
Indices: 41305277--41305324 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
41305267 CTATTATTTT
41305277 TTTTCTTTT-TGTTTTATTAGTATAA
1 TTTTCTTTTCT-TTTTATTAGTATAA
*
41305302 TTTTCTTTTCTTTTTATTTGTAT
1 TTTTCTTTTCTTTTTATTAGTAT
41305325 TTTCATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (25 bp):
TTTTCTTTTCTTTTTATTAGTATAA
Found at i:41305877 original size:19 final size:19
Alignment explanation
Indices: 41305853--41305894 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
41305843 AACAAAAGAT
41305853 CGTGTTCTAACTTACGGGA
1 CGTGTTCTAACTTACGGGA
41305872 CGTGTTCTAACTTACGGGA
1 CGTGTTCTAACTTACGGGA
41305891 CGTG
1 CGTG
41305895 ATCTCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (19 bp):
CGTGTTCTAACTTACGGGA
Found at i:41312917 original size:230 final size:231
Alignment explanation
Indices: 41312504--41312944 Score: 627
Period size: 230 Copynumber: 1.9 Consensus size: 231
41312494 TAGACCCTCG
* * *
41312504 ATTAGAGATTTTTGACGGATGAGTGAACACCACTCACCGTTATTGTAGGATTACTCTTGTAAGAT
1 ATTAGAGA-TTTTGACGAATGAGTGAACACCAATCACCCTTATTGTAGGATTACTCTTGTAAGAT
* * *
41312569 AGTTCGACTGAACCTTCCCTCATCAGGTAGTTTGAATGGATACTTCTAGAGGTAGATAGTCCCTG
65 AGTTCAACTGAACCTTCCCTCATAAGGTAGTTTGAATGGATACTTCTAGAGGTAGATAATCCCTG
*
41312634 ACGAACTATCTAACCCCTAGATTGTATAAGGTATACTTTTCATTTATAAGAAAATCCTTAATGGA
130 ACGAACTATCTAACCCCTAGATTGTATAAGGTATACTTCTCATTTATAAGAAAATCCTTAATGGA
*
41312699 TTTTACAACACTAGATATTTGACGTATTAGGCCTTCA
195 TTTCACAACACTAGATATTTGACGTATTAGGCCTTCA
*
41312736 ATTAGAGA-TTTGACGAATG-GATGAACACCAATCACCCTTATTGTTGGATTACTCTTGTAAGAT
1 ATTAGAGATTTTGACGAATGAG-TGAACACCAATCACCCTTATTGTAGGATTACTCTTGTAAGAT
* * * * * *
41312799 ATTTCAACTGAACCTT-CTTCCATAAGGTAGTTTGAATTGATATTTCTAGAGGTGGATAATCCTT
65 AGTTCAACTGAACCTTCCCT-CATAAGGTAGTTTGAATGGATACTTCTAGAGGTAGATAATCCCT
* * * ** * * *
41312863 GGCGAACTATCTCATCTTTAGATTGTATAAGGTGTACTTCTCATTTATAAGAAAATCCTTACTGT
129 GACGAACTATCTAACCCCTAGATTGTATAAGGTATACTTCTCATTTATAAGAAAATCCTTAATGG
41312928 ATTTCACAACACTAGAT
194 ATTTCACAACACTAGAT
41312945 GCTCCAAATA
Statistics
Matches: 184, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
229 3 0.02
230 173 0.94
232 8 0.04
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (231 bp):
ATTAGAGATTTTGACGAATGAGTGAACACCAATCACCCTTATTGTAGGATTACTCTTGTAAGATA
GTTCAACTGAACCTTCCCTCATAAGGTAGTTTGAATGGATACTTCTAGAGGTAGATAATCCCTGA
CGAACTATCTAACCCCTAGATTGTATAAGGTATACTTCTCATTTATAAGAAAATCCTTAATGGAT
TTCACAACACTAGATATTTGACGTATTAGGCCTTCA
Found at i:41314286 original size:27 final size:27
Alignment explanation
Indices: 41314250--41314306 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
41314240 AAATATATAT
41314250 ATATGGCAAACTCTAAAGGAATGGAAC
1 ATATGGCAAACTCTAAAGGAATGGAAC
* *
41314277 ATATGGCAAACTTTGAAGGAATGGAAC
1 ATATGGCAAACTCTAAAGGAATGGAAC
41314304 ATA
1 ATA
41314307 ATGGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (27 bp):
ATATGGCAAACTCTAAAGGAATGGAAC
Found at i:41319258 original size:47 final size:47
Alignment explanation
Indices: 41319204--41319297 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
41319194 GAAAAGGGAC
41319204 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
1 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
41319251 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
1 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
41319298 AAGATGGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (47 bp):
TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
Found at i:41324968 original size:35 final size:35
Alignment explanation
Indices: 41324817--41324977 Score: 107
Period size: 35 Copynumber: 4.6 Consensus size: 35
41324807 TAACCATTTT
* * * *
41324817 CATGGTGTTACTATGTAAAGCCTATATA-T-TTTC
1 CATGGTGTCACTCTGTAGAGCTTATATACTGTTTC
** *
41324850 CATGGTGTCACTCCCTAGAGCCTT-TATACCGTTTC
1 CATGGTGTCACTCTGTAGAG-CTTATATACTGTTTC
* * * ** *
41324885 CATGAT-TACACTCTAG-AAAGCTTGTAGATAACAATTTT
1 CATGGTGT-CACTCT-GTAGAGC-T-TATAT-ACTGTTTC
41324923 CATGGTGTCACTCTGTAGAGCTTATATACTGTTTC
1 CATGGTGTCACTCTGTAGAGCTTATATACTGTTTC
*
41324958 CATGGTGTCACTCCGTAGAG
1 CATGGTGTCACTCTGTAGAG
41324978 GCAATGGATA
Statistics
Matches: 95, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
33 19 0.20
34 4 0.04
35 42 0.44
36 5 0.05
37 4 0.04
38 20 0.21
39 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (35 bp):
CATGGTGTCACTCTGTAGAGCTTATATACTGTTTC
Found at i:41327797 original size:28 final size:27
Alignment explanation
Indices: 41327735--41327897 Score: 254
Period size: 28 Copynumber: 5.9 Consensus size: 27
41327725 TTATTAAGTC
* * *
41327735 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
41327762 CGCACACTTAGCGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
41327790 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
41327817 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
41327845 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
41327873 CGCACACTTAGTGCTACATAGTCAA
1 CGCACACTTAGTGCTACATAGTCAA
41327898 TTCAATTCGC
Statistics
Matches: 129, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 49 0.38
28 80 0.62
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.25
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:41327819 original size:55 final size:55
Alignment explanation
Indices: 41327735--41327919 Score: 262
Period size: 55 Copynumber: 3.3 Consensus size: 55
41327725 TTATTAAGTC
* * * * *
41327735 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGCGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCATACT
*
41327790 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCATACT
*
41327845 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAATTCAATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTC-A-T--ACT
41327905 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41327920 GCACAATTTA
Statistics
Matches: 117, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
55 72 0.62
56 27 0.23
57 1 0.01
60 17 0.15
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCATACT
Found at i:41327874 original size:83 final size:82
Alignment explanation
Indices: 41327735--41327897 Score: 263
Period size: 83 Copynumber: 2.0 Consensus size: 82
41327725 TTATTAAGTC
* *
41327735 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGCGCTACATAATCATACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGCGCTACATAATCAAACTCGCACACTTA
41327800 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
* * * *
41327817 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTCAGTGCTACATAATC-AACTCGCACACTTAGCGCTACATAATCAAACTCGCACACTT
41327882 AGTGCTACATAGTCAA
65 AGTGCTACATAGTCAA
41327898 TTCAATTCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
82 20 0.27
83 54 0.73
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.25
Consensus pattern (82 bp):
CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGCGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:41338103 original size:81 final size:81
Alignment explanation
Indices: 41338002--41338158 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 81
41337992 AAAATTACCG
* * *
41338002 AAATACCCTCGAAGGGTAAAATTACT-AGAACACCCTCGAAGGGTAAAATGATCGAAACACCCCT
1 AAATACCCTCAAAGGATAAAATGACTGA-AACACCCTCGAAGGGTAAAATGATCGAAACACCCCT
41338066 AAAGGGTAAAATTATTT
65 AAAGGGTAAAATTATTT
* * * *
41338083 AAATACCCTCAAAGGATAAAATGACTGAAATACCCTCGATGGGTAAAATGATCGTAACACCCCTT
1 AAATACCCTCAAAGGATAAAATGACTGAAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
*
41338148 TAGGGTAAAAT
66 AAGGGTAAAAT
41338159 GACTGTAATG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 66 0.99
82 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (81 bp):
AAATACCCTCAAAGGATAAAATGACTGAAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
AAGGGTAAAATTATTT
Found at i:41338133 original size:27 final size:27
Alignment explanation
Indices: 41337963--41338131 Score: 182
Period size: 27 Copynumber: 6.3 Consensus size: 27
41337953 CGAAAAGGTT
*
41337963 GTAAAATTACTGAAATACCCTCGAAGA
1 GTAAAATTACTGAAATACCCTCGAAGG
*
41337990 GTAAAATTACCGAAATACCCTCGAAGG
1 GTAAAATTACTGAAATACCCTCGAAGG
*
41338017 GTAAAATTACT-AGAACACCCTCGAAGG
1 GTAAAATTACTGA-AATACCCTCGAAGG
* * *
41338044 GTAAAATGA-TCGAAACACCC-CTAAAGG
1 GTAAAATTACT-GAAATACCCTC-GAAGG
* * *
41338071 GTAAAATTATTTAAATACCCTCAAAGG
1 GTAAAATTACTGAAATACCCTCGAAGG
* * *
41338098 ATAAAATGACTGAAATACCCTCGATGG
1 GTAAAATTACTGAAATACCCTCGAAGG
41338125 GTAAAAT
1 GTAAAAT
41338132 GATCGTAACA
Statistics
Matches: 120, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.03
27 114 0.95
28 3 0.03
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
GTAAAATTACTGAAATACCCTCGAAGG
Found at i:41338184 original size:81 final size:81
Alignment explanation
Indices: 41338002--41338187 Score: 225
Period size: 81 Copynumber: 2.3 Consensus size: 81
41337992 AAAATTACCG
* *
41338002 AAATACCCTCGAAGGGTAAAATTACTAGAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
1 AAATACCCTCAAAGGGTAAAATGACTAGAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
* *
41338067 AAGGGTAAAATTATTT
66 AAGGGTAAAATGATGT
* * * *
41338083 AAATACCCTCAAAGGATAAAATGACT-GAAATACCCTCGATGGGTAAAATGATCGTAACACCCCT
1 AAATACCCTCAAAGGGTAAAATGACTAG-AACACCCTCGAAGGGTAAAATGATCGAAACACCCCT
**
41338147 TTAGGGTAAAATGACTGT
65 AAAGGGTAAAATGA-TGT
*
41338165 -AATGCCCT-AATAGGGTAAAATGA
1 AAATACCCTCAA-AGGGTAAAATGA
41338188 TTGATTTGCC
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.03
81 85 0.94
82 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (81 bp):
AAATACCCTCAAAGGGTAAAATGACTAGAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
AAGGGTAAAATGATGT
Found at i:41338214 original size:24 final size:24
Alignment explanation
Indices: 41338182--41338259 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
41338172 TAATAGGGTA
41338182 AAATGATTGATTTGCCTATGATGT
1 AAATGATTGATTTGCCTATGATGT
* *
41338206 AAATGATTGATTTATCCGA-GATGT
1 AAATGATTGATTT-GCCTATGATGT
* * * * *
41338230 AAATGACTAATTTGTCTGTGATTT
1 AAATGATTGATTTGCCTATGATGT
41338254 AAATGA
1 AAATGA
41338260 ATAATTTCTC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.02
24 39 0.91
25 3 0.07
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (24 bp):
AAATGATTGATTTGCCTATGATGT
Found at i:41338393 original size:27 final size:27
Alignment explanation
Indices: 41338353--41338418 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
41338343 ATGAAGGAAG
*
41338353 TACTG-TACTGGTGGCTTTGCCACA-A
1 TACTGTTACTGGTGGCTTGGCCACATA
*
41338378 TCACTGTTACTTGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
41338406 TACTGTTACTGGT
1 TACTGTTACTGGT
41338419 AGATTTCCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 28 0.80
28 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:41338515 original size:32 final size:32
Alignment explanation
Indices: 41338464--41338650 Score: 230
Period size: 32 Copynumber: 5.8 Consensus size: 32
41338454 GCGATGCTAT
* * * * *
41338464 TGATGACTTTGTGCTGATCATATTACCATTAT
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* *
41338496 TGATGGCTGTGTGTCGATCATATTACCATTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* * *
41338528 TGATGGCTGTATGACGATCATATTACTACTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* * *
41338560 TGATGGCTTTGTGTCGATCATACTACTATTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
*
41338592 TGATGGCTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* *
41338624 TGATGGCTTTGTGCCAATCATATTACT
1 TGATGGCTGTGTGCCGATCATATTACT
41338651 GTACTTATTG
Statistics
Matches: 135, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 135 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (32 bp):
TGATGGCTGTGTGCCGATCATATTACTATTAC
Found at i:41338628 original size:96 final size:96
Alignment explanation
Indices: 41338464--41338650 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
41338454 GCGATGCTAT
* * * *
41338464 TGATGACTTTGTGCTGATCATATTACCATTATTGATGGCTGTGTGTCGATCATATTACCATTACT
1 TGATGACTTTGTGCTGATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACCACTACT
*
41338529 GATGGCTGTATGACGATCATATTACTACTAC
66 GATGGCTGTATGACAATCATATTACTACTAC
* * *
41338560 TGATGGCTTTGTG-TCGATCATACTACTATTACTGATGGCTGTGTGCCGATCATATTACTACTAC
1 TGATGACTTTGTGCT-GATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACCACTAC
* * *
41338624 TGATGGCTTTGTGCCAATCATATTACT
65 TGATGGCTGTATGACAATCATATTACT
41338651 GTACTTATTG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 78 0.99
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (96 bp):
TGATGACTTTGTGCTGATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACCACTACT
GATGGCTGTATGACAATCATATTACTACTAC
Found at i:41343833 original size:40 final size:40
Alignment explanation
Indices: 41343768--41343910 Score: 157
Period size: 40 Copynumber: 3.6 Consensus size: 40
41343758 AACTAATGAA
* *
41343768 TGAAAGCACATACGTG-CCCTGTTTGTATTTCGATACCTC
1 TGAATGCACATACGTGCCCCTGTTTGTATTTCGATACCCC
* * *
41343807 TGAATGCACATATGTGCCCCTATTTGTACTTT-GGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTA-TTTCGATACCCC
* *
41343847 TGAATGCACATACGTTCCCCTGTTTGTATTTCAATACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTATTTCGATACCCC
* * **
41343887 TGGACGCTGATACGTG-CCCTGTTT
1 TGAATGCACATACGTGCCCCTGTTT
41343911 ATACTTTGGT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 25 0.29
40 58 0.67
41 3 0.03
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.34
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTGTATTTCGATACCCC
Found at i:41343928 original size:79 final size:79
Alignment explanation
Indices: 41343768--41343930 Score: 202
Period size: 79 Copynumber: 2.1 Consensus size: 79
41343758 AACTAATGAA
* * * * * * *
41343768 TGAAAGCACATACGTGCCCTGTTTGTATTTCGATACCTCTGAATGCACATATGTGCCCCTATTTG
1 TGAATGCACATACGTCCCCTGTTTGTATTTCAATACCCCTGAACGCACATACGTGCCCCTATTTA
*
41343833 TACTTTGGTACCCC
66 TACTTTGGTAACCC
* ** *
41343847 TGAATGCACATACGTTCCCCTGTTTGTATTTCAATACCCCTGGACGCTGATACGTG-CCCTGTTT
1 TGAATGCACATACG-TCCCCTGTTTGTATTTCAATACCCCTGAACGCACATACGTGCCCCTATTT
41343911 ATACTTTGGTAACCC
65 ATACTTTGGTAACCC
41343926 TGAAT
1 TGAAT
41343931 CAAATAGTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 38 0.54
80 33 0.46
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (79 bp):
TGAATGCACATACGTCCCCTGTTTGTATTTCAATACCCCTGAACGCACATACGTGCCCCTATTTA
TACTTTGGTAACCC
Found at i:41344613 original size:30 final size:27
Alignment explanation
Indices: 41344560--41344615 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
41344550 CTTTTAGGTT
*
41344560 CACACAGGCTGGCACACGGTCGTGTGA
1 CACACAGGCTGGCACACGATCGTGTGA
41344587 CACACAAGGCCTGGCGACACGATCGTGTG
1 CACAC-AGG-CTGGC-ACACGATCGTGTG
41344616 TCATTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 3 0.12
29 5 0.20
30 12 0.48
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.14
Consensus pattern (27 bp):
CACACAGGCTGGCACACGATCGTGTGA
Found at i:41347026 original size:70 final size:70
Alignment explanation
Indices: 41346950--41347099 Score: 246
Period size: 70 Copynumber: 2.1 Consensus size: 70
41346940 ACCATAGCGA
*
41346950 GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGTAGTGTTTATATGTAAGATAT
1 GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGATAT
41347015 AGCTG
66 AGCTG
* * * *
41347020 GGCTATGCCATTTATTCAAACGTAAGACCATGGTTGGACTATGGCAGTGTTTATATGTAATATAT
1 GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGATAT
*
41347085 AGTTG
66 AGCTG
41347090 GGCTATGGCA
1 GGCTATGGCA
41347100 TTCTGATAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (70 bp):
GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGATAT
AGCTG
Found at i:41347406 original size:20 final size:21
Alignment explanation
Indices: 41347369--41347408 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41347359 GACTAAATCA
* *
41347369 GAAACATAGAGAATTTTTCAG
1 GAAACAAAGAGAAATTTTCAG
41347390 GAAACAAAGA-AAATTTTCA
1 GAAACAAAGAGAAATTTTCA
41347409 ACACTGCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (21 bp):
GAAACAAAGAGAAATTTTCAG
Found at i:41348885 original size:25 final size:25
Alignment explanation
Indices: 41348823--41348878 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
41348813 TGCTAACTCA
* *
41348823 AGCTATAGATCGGTATGCTCTCACG
1 AGCTATACATCAGTATGCTCTCACG
41348848 AGCTATACATCAGTATGCT-TACACG
1 AGCTATACATCAGTATGCTCT-CACG
41348873 AGCTAT
1 AGCTAT
41348879 GGGTCAGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCTATACATCAGTATGCTCTCACG
Found at i:41349264 original size:40 final size:40
Alignment explanation
Indices: 41349220--41349301 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
41349210 CCCCGATCTA
* * *
41349220 AAGTCACACGAGATCTGTCTTGATCTATACGGATAAATTT
1 AAGTCACACGAGATCTATCTTGATATATACGGATAAACTT
** *
41349260 AAGTCGTACGAGGTCTATCTTGATATATACGGATAAACTT
1 AAGTCACACGAGATCTATCTTGATATATACGGATAAACTT
41349300 AA
1 AA
41349302 CTCAGTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (40 bp):
AAGTCACACGAGATCTATCTTGATATATACGGATAAACTT
Found at i:41351639 original size:40 final size:40
Alignment explanation
Indices: 41351565--41351676 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 40
41351555 CAACATTGAA
* * * *
41351565 GGGTACCAAAGTACAAAC-GGGGCATGTATGTGCATTTTG
1 GGGTACCGAACTACAAACAGGGGCACGTATGTGCATTTAG
* * *
41351604 GGGTACTGAACTGCAAACAGGGGCACGTATTTGCATTTAG
1 GGGTACCGAACTACAAACAGGGGCACGTATGTGCATTTAG
* * *
41351644 GGGTACCGAAGTACAAACAAGGGCACATATGTG
1 GGGTACCGAACTACAAACAGGGGCACGTATGTG
41351677 TATTCATACA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
39 14 0.24
40 45 0.76
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (40 bp):
GGGTACCGAACTACAAACAGGGGCACGTATGTGCATTTAG
Found at i:41351979 original size:26 final size:26
Alignment explanation
Indices: 41351890--41351990 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
41351880 TGAAAAGGTT
* *
41351890 GTAAAATTACTGAAATAGCCTCAAAG
1 GTAAAATTACTGAAATACCCTCGAAG
* *
41351916 AGTAAAATTACCGAAAGACCCTCGAATG
1 -GTAAAATTACTGAAATACCCTCGAA-G
* *
41351944 GTAATATTACTGAAATACCCTTGAAG
1 GTAAAATTACTGAAATACCCTCGAAG
41351970 GTAAAATTACT-AGAATACCCT
1 GTAAAATTACTGA-AATACCCT
41351991 AAAAAAATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.02
26 19 0.30
27 42 0.67
28 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (26 bp):
GTAAAATTACTGAAATACCCTCGAAG
Found at i:41352065 original size:27 final size:26
Alignment explanation
Indices: 41352007--41352127 Score: 127
Period size: 27 Copynumber: 4.5 Consensus size: 26
41351997 ATACCCTCAA
* *
41352007 AGGGTAAAATGGA-CGAAATACCCTCGT
1 AGGGTAAAAT-GACCGTAATGCCCT-GT
* * *
41352034 TGGGTAAAATGACCGCAACGCCTCTGT
1 AGGGTAAAATGACCGTAATGCC-CTGT
41352061 AGGGTAAAATGACCGTAATGACCCTGT
1 AGGGTAAAATGACCGTAATG-CCCTGT
*
41352088 AGGGTAAAATGACAGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATG-CCCTGT
*
41352115 AGGATAAAATGAC
1 AGGGTAAAATGAC
41352128 TATTTTACCT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.02
27 75 0.93
28 4 0.05
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (26 bp):
AGGGTAAAATGACCGTAATGCCCTGT
Found at i:41352093 original size:54 final size:54
Alignment explanation
Indices: 41352007--41352127 Score: 147
Period size: 54 Copynumber: 2.2 Consensus size: 54
41351997 ATACCCTCAA
* * *
41352007 AGGGTAAAATGGA-CGAAATACCCTCGTTGGGTAAAATGACCGCAACGCCTCTGT
1 AGGGTAAAAT-GACCGAAATACCCTCGTAGGGTAAAATGACAGCAACGCCCCTGT
* * *
41352061 AGGGTAAAATGACCGTAATGACCCT-GTAGGGTAAAATGACAGTAATGCCCCTGT
1 AGGGTAAAATGACCGAAAT-ACCCTCGTAGGGTAAAATGACAGCAACGCCCCTGT
*
41352115 AGGATAAAATGAC
1 AGGGTAAAATGAC
41352128 TATTTTACCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.03
54 51 0.88
55 5 0.09
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (54 bp):
AGGGTAAAATGACCGAAATACCCTCGTAGGGTAAAATGACAGCAACGCCCCTGT
Found at i:41352279 original size:24 final size:24
Alignment explanation
Indices: 41352145--41352266 Score: 154
Period size: 24 Copynumber: 5.1 Consensus size: 24
41352135 CCTCTCAGAG
* *
41352145 TTAAATGATTGATTTGCCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * * *
41352169 GTAAATGATTGATTTGTCCGAGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * *
41352193 GTAAATGACTAATTTGTCTATGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
41352217 TTAAATGACTGATTTGTGTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
41352241 TTAAATGACTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
41352265 TT
1 TT
41352267 GTATGATTGA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.44
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTGAT
Found at i:41352403 original size:27 final size:26
Alignment explanation
Indices: 41352342--41352406 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
41352332 ATGGGGGAAG
* *
41352342 TACTG-TACTGGTGGCTTTGCCATAA
1 TACTGTTACTGGTGGCTTGGCCACAA
*
41352367 TCACTATTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACA-A
41352395 TACTGTTACTGG
1 TACTGTTACTGG
41352407 CAGCTTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 3 0.09
27 27 0.82
28 2 0.06
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (26 bp):
TACTGTTACTGGTGGCTTGGCCACAA
Found at i:41352607 original size:32 final size:32
Alignment explanation
Indices: 41352455--41352607 Score: 143
Period size: 32 Copynumber: 4.8 Consensus size: 32
41352445 AATGCTATTA
* * *
41352455 ATGGCTTTGTGCTGATCATATTACCATTACTG
1 ATGGCTTTGTGCCGATCATATTACTACTACTG
41352487 ATGG-TTGTGTGCCGATCATATTACTACTACTG
1 ATGGCTT-TGTGCCGATCATATTACTACTACTG
*
41352519 ATGGCTTTGTGCCGGCTACACTATTA-T--TACTG
1 ATGGCTTTGTGCC-GAT-CA-TATTACTACTACTG
* * * * *
41352551 ATGGCTGTGTGTCGGTCATCTTACTACTACTA
1 ATGGCTTTGTGCCGATCATATTACTACTACTG
* *
41352583 ATGGCTTTGTGCCAATCGTATTACT
1 ATGGCTTTGTGCCGATCATATTACT
41352608 GTACTTATGG
Statistics
Matches: 98, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
29 4 0.04
30 3 0.03
31 4 0.04
32 75 0.77
33 4 0.04
34 3 0.03
35 5 0.05
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (32 bp):
ATGGCTTTGTGCCGATCATATTACTACTACTG
Found at i:41353882 original size:51 final size:51
Alignment explanation
Indices: 41353788--41353886 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
41353778 ATGAACTCAT
* *
41353788 GTTTAATGTCCTGGCGGACTCCATAAGTTGCCATAACCTAACTATGGTAAG
1 GTTTAATGTCCTAGCGGACTCCATAAGTTGCCATAACCAAACTATGGTAAG
* ** ** *
41353839 GTTTAATGTCCTATCGGACTCCATGTGTTGTTATAGCCAAACTATGGT
1 GTTTAATGTCCTAGCGGACTCCATAAGTTGCCATAACCAAACTATGGT
41353887 CACCGTTGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (51 bp):
GTTTAATGTCCTAGCGGACTCCATAAGTTGCCATAACCAAACTATGGTAAG
Found at i:41356982 original size:50 final size:49
Alignment explanation
Indices: 41356858--41356987 Score: 174
Period size: 49 Copynumber: 2.6 Consensus size: 49
41356848 GATAATAACA
* *
41356858 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATAC
* *
41356907 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATAT-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATATAC
*
41356955 GGTGCCCATGCCATGTCCCAGACATGGTCTTAC
1 --TGCCAATGCCATGTCCCAGACATGGTCTTAC
41356988 GGTGTGACAG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 4 0.06
49 39 0.55
50 28 0.39
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATAC
Found at i:41358730 original size:40 final size:40
Alignment explanation
Indices: 41358633--41358858 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
41358623 TTGAATGATG
* * * * *
41358633 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * * *
41358673 TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
41358713 TTCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
41358753 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
41358793 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
41358834 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
41358859 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 152 0.93
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41370534 original size:29 final size:29
Alignment explanation
Indices: 41370457--41370598 Score: 115
Period size: 30 Copynumber: 4.9 Consensus size: 29
41370447 TGGTATCCAC
*
41370457 CACCAGTACATAGTACATGGAAAC-ATAG
1 CACCAGTACATAGTACATGGAAACTATAA
* * * *
41370485 CACCAGCACAGAGTGCCTGGAAACTATAA
1 CACCAGTACATAGTACATGGAAACTATAA
* * * *
41370514 CACCGGTACATAGTTCTTGGAAACTGTAA
1 CACCAGTACATAGTACATGGAAACTATAA
* * **
41370543 TCACCGGTACATAGTACCTAAAAACTATAA
1 -CACCAGTACATAGTACATGGAAACTATAA
* * *
41370573 TCACCAGTGCATAGTACCTAGAAACT
1 -CACCAGTACATAGTACATGGAAACT
41370599 GAAACCACTG
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
28 20 0.22
29 26 0.28
30 47 0.51
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (29 bp):
CACCAGTACATAGTACATGGAAACTATAA
Found at i:41370550 original size:30 final size:29
Alignment explanation
Indices: 41370457--41370557 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 29
41370447 TGGTATCCAC
* * * *
41370457 CACCAGTACATAGTACATGGAAAC-ATAG
1 CACCGGTACATAGTTCTTGGAAACTATAA
* * * * *
41370485 CACCAGCACAGAGTGCCTGGAAACTATAA
1 CACCGGTACATAGTTCTTGGAAACTATAA
*
41370514 CACCGGTACATAGTTCTTGGAAACTGTAA
1 CACCGGTACATAGTTCTTGGAAACTATAA
41370543 TCACCGGTACATAGT
1 -CACCGGTACATAGT
41370558 ACCTAAAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 20 0.33
29 26 0.43
30 14 0.23
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (29 bp):
CACCGGTACATAGTTCTTGGAAACTATAA
Found at i:41370568 original size:30 final size:30
Alignment explanation
Indices: 41370504--41370598 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 30
41370494 AGAGTGCCTG
* * *
41370504 GAAACTATAA-CACCGGTACATAGTTCTTG
1 GAAACTATAATCACCGGTACATAGTACCTA
*
41370533 GAAACTGTAATCACCGGTACATAGTACCTA
1 GAAACTATAATCACCGGTACATAGTACCTA
* * *
41370563 AAAACTATAATCACCAGTGCATAGTACCTA
1 GAAACTATAATCACCGGTACATAGTACCTA
41370593 GAAACT
1 GAAACT
41370599 GAAACCACTG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
29 9 0.16
30 47 0.84
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (30 bp):
GAAACTATAATCACCGGTACATAGTACCTA
Found at i:41374092 original size:18 final size:19
Alignment explanation
Indices: 41374057--41374092 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41374047 ATTTTAGGGT
*
41374057 TTTCATTCTTAGGTTTTTC
1 TTTCATTCTTAAGTTTTTC
41374076 TTTCATTC-TAAGTTTTT
1 TTTCATTCTTAAGTTTTT
41374093 ACTTAGGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.64
Consensus pattern (19 bp):
TTTCATTCTTAAGTTTTTC
Found at i:41402239 original size:13 final size:12
Alignment explanation
Indices: 41402214--41402251 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
41402204 AATGAATGAG
*
41402214 TTTTTCTTACTT
1 TTTTTCTTTCTT
41402226 TTTTTACTTTCTT
1 TTTTT-CTTTCTT
41402239 TTTTTCTTT-TT
1 TTTTTCTTTCTT
41402250 TT
1 TT
41402252 CAATATGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 9 0.38
13 11 0.46
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:41406755 original size:49 final size:50
Alignment explanation
Indices: 41406605--41406794 Score: 168
Period size: 49 Copynumber: 3.8 Consensus size: 50
41406595 GAATATAACA
* * * ** * * * *
41406605 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * * * **
41406654 TGCCAAAGTCATATCCCTGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * *
41406704 TGCCCATGCCATGTCCTAGACATGGTCTTACA-GGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
41406753 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41406795 TTACCCAAAT
Statistics
Matches: 111, Mismatches: 28, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
49 77 0.69
50 34 0.31
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:41410398 original size:26 final size:26
Alignment explanation
Indices: 41410369--41410423 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
41410359 TTACTTTTTT
*
41410369 TTTCATATAAGCATTTCATCTAAACA
1 TTTCATATAACCATTTCATCTAAACA
* * * *
41410395 TTTCATCTTACCATTTCATTTACACA
1 TTTCATATAACCATTTCATCTAAACA
41410421 TTT
1 TTT
41410424 AACTCATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTCATATAACCATTTCATCTAAACA
Found at i:41413144 original size:57 final size:58
Alignment explanation
Indices: 41413080--41413194 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 58
41413070 CATTTCCAAG
* * * * *
41413080 TCATTTTCATTTTGGAGAAAACCACATTCATTTTCAAATGATT-TCATTTCTCTATTT
1 TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCTCATTTCTCCATTT
* *
41413137 TCATTTTCATTTAGGAGAAAACCATAATAATTTCCAAATGTTTCTCATTTCTCCATTT
1 TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCTCATTTCTCCATTT
41413195 CTATTTATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 37 0.74
58 13 0.26
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (58 bp):
TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCTCATTTCTCCATTT
Found at i:41418144 original size:27 final size:27
Alignment explanation
Indices: 41418114--41418165 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
41418104 TATGGAGCCA
*
41418114 TTCCTTTACAGTTTACCATACATATCT
1 TTCCTTTACAGTTCACCATACATATCT
* *
41418141 TTCCTTTAGAGTTCGCCATACATAT
1 TTCCTTTACAGTTCACCATACATAT
41418166 TATTCTTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (27 bp):
TTCCTTTACAGTTCACCATACATATCT
Found at i:41418207 original size:27 final size:26
Alignment explanation
Indices: 41418123--41418207 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
41418113 ATTCCTTTAC
* *
41418123 AGTTTACCATACATATCTTTCCTTTAG
1 AGTTTACCATACATA-CTATCCTTCAG
** * * *
41418150 AGTTCGCCATACATATTATTCTTCCAA
1 AGTTTACCATACATACTATCCTT-CAG
*
41418177 AGTTTACCATATATACCTATCCTTCAG
1 AGTTTACCATACATA-CTATCCTTCAG
41418204 AGTT
1 AGTT
41418208 CTCCGGGAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
26 5 0.12
27 32 0.74
28 6 0.14
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (26 bp):
AGTTTACCATACATACTATCCTTCAG
Found at i:41418345 original size:27 final size:27
Alignment explanation
Indices: 41418300--41418362 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
41418290 ATATACCAAG
* *
41418300 AAGGCATTCGTTTTTATAGATTGCCACA
1 AAGGC-TTCATTTTCATAGATTGCCACA
41418328 AAGGCTTCATTTTCATAGATTGCCACA
1 AAGGCTTCATTTTCATAGATTGCCACA
*
41418355 AAGACTTC
1 AAGGCTTC
41418363 TTGTAACACC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (27 bp):
AAGGCTTCATTTTCATAGATTGCCACA
Found at i:41419814 original size:30 final size:30
Alignment explanation
Indices: 41419778--41419993 Score: 156
Period size: 30 Copynumber: 7.2 Consensus size: 30
41419768 CTATTACCAC
* *
41419778 CCCTTTTCATAGTTCGATAGTCGAAGCTGT
1 CCCTTTTCATAATTCGATAGTCGAAGCTAT
* * * * *
41419808 CCCTTTTCATATTTTGATCGCCGAAGCCAT
1 CCCTTTTCATAATTCGATAGTCGAAGCTAT
* ** * * *
41419838 CCCTTCTCATTGTT-GATGGTCGTCA-CCAT
1 CCCTTTTCATAATTCGATAGTCG-AAGCTAT
** * * *
41419867 CCCTTTTCATTGTT-GATGGTCGTCA-TTAT
1 CCCTTTTCATAATTCGATAGTCG-AAGCTAT
41419896 CCCTTTTCATAATTCGATAG-CTGAAGCCCTAT
1 CCCTTTTCATAATTCGATAGTC-GAAG--CTAT
*
41419928 CCCTTTTCATAATTCGATAG-CTGAAGCCAT
1 CCCTTTTCATAATTCGATAGTC-GAAGCTAT
*
41419958 CCCTTTTCATAATTTGATAGTCGAAGCTAT
1 CCCTTTTCATAATTCGATAGTCGAAGCTAT
41419988 CCCTTT
1 CCCTTT
41419994 CCATTGGTCA
Statistics
Matches: 156, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
29 50 0.32
30 76 0.49
31 1 0.01
32 29 0.19
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (30 bp):
CCCTTTTCATAATTCGATAGTCGAAGCTAT
Found at i:41419866 original size:29 final size:29
Alignment explanation
Indices: 41419834--41419905 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
41419824 ATCGCCGAAG
*
41419834 CCATCCCTTCTCATTGTTGATGGTCGTCA
1 CCATCCCTTTTCATTGTTGATGGTCGTCA
41419863 CCATCCCTTTTCATTGTTGATGGTCGTCA
1 CCATCCCTTTTCATTGTTGATGGTCGTCA
**
41419892 TTATCCCTTTTCAT
1 CCATCCCTTTTCAT
41419906 AATTCGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (29 bp):
CCATCCCTTTTCATTGTTGATGGTCGTCA
Found at i:41421308 original size:53 final size:54
Alignment explanation
Indices: 41421231--41421336 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 54
41421221 ACCCCCTTAG
* * * *
41421231 TTCTTTCCAATATGATGCCCTAACCCACAAATTATGGTCTTACATGATATGGTA
1 TTCTTTCCAATATGATACCATAACCCACAAATTATGGTATTACACGATATGGTA
* *
41421285 TTCTTTCC-ATATGATACCATAACCCACTAGTTATGGTATTACACGATATGGT
1 TTCTTTCCAATATGATACCATAACCCACAAATTATGGTATTACACGATATGGT
41421337 GCCATGGACT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 38 0.83
54 8 0.17
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (54 bp):
TTCTTTCCAATATGATACCATAACCCACAAATTATGGTATTACACGATATGGTA
Found at i:41424071 original size:26 final size:26
Alignment explanation
Indices: 41424042--41424097 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
41424032 CATTTCGACC
41424042 CACAGCCCATGTGAGCAAG-CCCATTT
1 CACAGCCCATGTGAG-AAGACCCATTT
* * *
41424068 CACAGCTCGTGTGAGTAGACCCATTT
1 CACAGCCCATGTGAGAAGACCCATTT
41424094 CACA
1 CACA
41424098 ACTCGGGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.21
Consensus pattern (26 bp):
CACAGCCCATGTGAGAAGACCCATTT
Found at i:41429687 original size:39 final size:40
Alignment explanation
Indices: 41429592--41429814 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
41429582 TTGAATGATG
*
41429592 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
41429630 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
41429671 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
41429710 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
41429749 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
41429788 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41429815 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41429778 original size:79 final size:81
Alignment explanation
Indices: 41429592--41429814 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
41429582 TTGAATGATG
* * *
41429592 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
41429654 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
41429671 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
41429732 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
41429749 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
41429813 TG
66 TG
41429815 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:41429836 original size:79 final size:79
Alignment explanation
Indices: 41429592--41429847 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
41429582 TTGAATGATG
* * * *
41429592 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
41429653 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
41429671 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
41429735 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
41429749 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
41429812 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
41429829 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41429848 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:41431816 original size:30 final size:30
Alignment explanation
Indices: 41431757--41431818 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
41431747 TACTCCTTTG
*
41431757 GTCTTTTTCAATTTCAAAAATGAAAAAAAATA
1 GTCTTTTTCAA--TCAAAAATCAAAAAAAATA
41431789 GTCTTTTTCAA-CAAAAATCACAAAAAAATA
1 GTCTTTTTCAATCAAAAATCA-AAAAAAATA
41431819 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.29
30 9 0.32
32 11 0.39
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.31
Consensus pattern (30 bp):
GTCTTTTTCAATCAAAAATCAAAAAAAATA
Found at i:41431860 original size:19 final size:20
Alignment explanation
Indices: 41431816--41431861 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
41431806 TCACAAAAAA
* *
41431816 ATAATAATTTAAAATGATTT
1 ATAAAAATTCAAAATGATTT
41431836 -TCAAAAATTCAAAAT-ATTT
1 AT-AAAAATTCAAAATGATTT
41431855 ATAAAAA
1 ATAAAAA
41431862 AAAGTCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAAAATTCAAAATGATTT
Done.