Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 112 of 185
Found at i:35027396 original size:50 final size:50
Alignment explanation
Indices: 35027337--35027448 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 50
35027327 AAGAAATCAG
* *
35027337 TCTTATTTCCTTGACTTTGCAATGAA-AATGATTGAAGCCACAACGACGAA
1 TCTTATTTCCTTGACGTTGCAACGAAGAA-GATTGAAGCCACAACGACGAA
* * * * * *
35027387 TCTTATTTCCCTGGCGTTGTAGCGAAGCAGATTGAAGCCACGACGACGAA
1 TCTTATTTCCTTGACGTTGCAACGAAGAAGATTGAAGCCACAACGACGAA
35027437 TCTTATCTTCCT
1 TCTTAT-TTCCT
35027449 GGCGTTAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
50 46 0.90
51 5 0.10
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (50 bp):
TCTTATTTCCTTGACGTTGCAACGAAGAAGATTGAAGCCACAACGACGAA
Found at i:35041639 original size:18 final size:16
Alignment explanation
Indices: 35041618--35041651 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
35041608 GTTTTGAAAT
35041618 TGAATAATTATTTGTAAA
1 TGAATAA-TATTT-TAAA
35041636 TGAATAATATTTTAAA
1 TGAATAATATTTTAAA
35041652 AACGAACGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
TGAATAATATTTTAAA
Found at i:35055749 original size:13 final size:13
Alignment explanation
Indices: 35055731--35055755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35055721 ACGTCTAAGT
35055731 TTAGCTAGCTGAG
1 TTAGCTAGCTGAG
35055744 TTAGCTAGCTGA
1 TTAGCTAGCTGA
35055756 TTTCGAATTC
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:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (13 bp):
TTAGCTAGCTGAG
Found at i:35058990 original size:17 final size:16
Alignment explanation
Indices: 35058968--35059007 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
35058958 TTTGCACACT
*
35058968 TTTTTTATATTCGAAAC
1 TTTTTTATACTCG-AAC
*
35058985 TTTTTTTTACTCGAAC
1 TTTTTTATACTCGAAC
35059001 TTTTTTA
1 TTTTTTA
35059008 CTTCTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTTTATACTCGAAC
Found at i:35059001 original size:16 final size:18
Alignment explanation
Indices: 35058965--35059006 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
35058955 TATTTTGCAC
*
35058965 ACTTTTTTTATATTCGAA
1 ACTTTTTTTATACTCGAA
35058983 ACTTTTTTT-TACTCG-A
1 ACTTTTTTTATACTCGAA
35058999 ACTTTTTT
1 ACTTTTTT
35059007 ACTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 9 0.39
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (18 bp):
ACTTTTTTTATACTCGAA
Found at i:35062360 original size:20 final size:18
Alignment explanation
Indices: 35062335--35062404 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 18
35062325 ACCATATTCT
*
35062335 ATTTTTAAATTTTAAAATTA
1 ATTTTTAAAATTT--AATTA
35062355 ATTTTTAGAAAATTTAATTA
1 ATTTTT--AAAATTTAATTA
*
35062375 ATTTTTAAAAAATTAACTTA
1 ATTTTT-AAAATTTAA-TTA
35062395 ATTTTTAAAA
1 ATTTTTAAAA
35062405 AATTAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.27
20 26 0.59
22 6 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (18 bp):
ATTTTTAAAATTTAATTA
Found at i:35062405 original size:20 final size:19
Alignment explanation
Indices: 35062350--35062417 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 19
35062340 TAAATTTTAA
*
35062350 AATTAATTTTTAGAAAATTT
1 AATTAATTTTTA-AAAAATT
35062370 AATTAATTTTTAAAAAATT
1 AATTAATTTTTAAAAAATT
35062389 AACTTAATTTTTAAAAAATT
1 AA-TTAATTTTTAAAAAATT
35062409 AAATTAATT
1 -AATTAATT
35062418 AGAAGTATCC
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 8 0.18
20 35 0.78
21 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (19 bp):
AATTAATTTTTAAAAAATT
Found at i:35062762 original size:7 final size:7
Alignment explanation
Indices: 35062726--35062777 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
35062716 ATTATTTCAT
*
35062726 TAAAAAG
1 TAAAAGG
*
35062733 TAAAAGA
1 TAAAAGG
*
35062740 AAAAAGAG
1 TAAAAG-G
35062748 -AAAA-G
1 TAAAAGG
35062753 TAAAAGG
1 TAAAAGG
35062760 TAAAAGG
1 TAAAAGG
35062767 TAAAAGG
1 TAAAAGG
35062774 TAAA
1 TAAA
35062778 TAAAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 1 0.03
6 4 0.11
7 33 0.87
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (7 bp):
TAAAAGG
Found at i:35072543 original size:23 final size:24
Alignment explanation
Indices: 35072507--35072557 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
35072497 AAAATGTTGG
**
35072507 AAATTGTTTTATTG-GATTTTATT
1 AAATTGTTCAATTGAGATTTTATT
*
35072530 AAATTGTTCAATTGATGATTTTGTT
1 AAATTGTTCAATTGA-GATTTTATT
35072555 AAA
1 AAA
35072558 AGAAATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 12 0.52
25 11 0.48
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (24 bp):
AAATTGTTCAATTGAGATTTTATT
Found at i:35079252 original size:17 final size:17
Alignment explanation
Indices: 35079230--35079262 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35079220 CCAAAATCGC
35079230 TATCTGGTCATCTCAAT
1 TATCTGGTCATCTCAAT
35079247 TATCTGGTCATCTCAA
1 TATCTGGTCATCTCAA
35079263 AGGTTGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (17 bp):
TATCTGGTCATCTCAAT
Found at i:35083325 original size:11 final size:11
Alignment explanation
Indices: 35083311--35083335 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35083301 ATTTTTCAAA
35083311 TTTTTAGAATT
1 TTTTTAGAATT
35083322 TTTTTAGAATT
1 TTTTTAGAATT
35083333 TTT
1 TTT
35083336 AAATAATTGT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTAGAATT
Found at i:35086881 original size:25 final size:26
Alignment explanation
Indices: 35086830--35086885 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
35086820 AAATTGGGAA
35086830 ATGGGTTGGGGTAGAAGGGGGGTGGG
1 ATGGGTTGGGGTAGAAGGGGGGTGGG
35086856 ATGGGTTGGGGTAGAA-GGGGGTGGG
1 ATGGGTTGGGGTAGAAGGGGGGTGGG
35086881 ATGGG
1 ATGGG
35086886 ATAGAAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.16, C:0.00, G:0.64, T:0.20
Consensus pattern (26 bp):
ATGGGTTGGGGTAGAAGGGGGGTGGG
Found at i:35086949 original size:30 final size:30
Alignment explanation
Indices: 35086891--35086949 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
35086881 ATGGGATAGA
*
35086891 AGTAAAAGTTTTGAGGGGAAAGTGAGAGGG
1 AGTAAAAGTTTTGAGGGGAAAGTAAGAGGG
35086921 AGTAAAAGTTTT-AGGGGAAAGTAAAGAGG
1 AGTAAAAGTTTTGAGGGGAAAGT-AAGAGG
35086950 TTTGGGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (30 bp):
AGTAAAAGTTTTGAGGGGAAAGTAAGAGGG
Found at i:35088600 original size:129 final size:129
Alignment explanation
Indices: 35088370--35088630 Score: 504
Period size: 129 Copynumber: 2.0 Consensus size: 129
35088360 CCTAAGACAC
*
35088370 TAAGGAGGATAGAGTGATGTTTGACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
1 TAAGGAGGATAGAGTGATGTTTCACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
35088435 TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
66 TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
35088499 TAAGGAGGATAGAGTGATGTTTCACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
1 TAAGGAGGATAGAGTGATGTTTCACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
*
35088564 TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAGATAGGAGGGCT
66 TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
35088628 TAA
1 TAA
35088631 AACTTGGTTC
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (129 bp):
TAAGGAGGATAGAGTGATGTTTCACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
Found at i:35089425 original size:43 final size:43
Alignment explanation
Indices: 35089377--35089463 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
35089367 ATCCCCCTAC
35089377 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
1 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
35089420 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
1 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
35089463 A
1 A
35089464 GTCTCAGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (43 bp):
AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
Found at i:35100513 original size:103 final size:103
Alignment explanation
Indices: 35100330--35100533 Score: 354
Period size: 103 Copynumber: 2.0 Consensus size: 103
35100320 CTAGTTTATG
*
35100330 GAATGGAGGAAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGGGTGTTATCTGAACTCCAG
1 GAATGGAGGAAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGAGTGTTATCTGAACTCCAG
* *
35100395 TTGGATGAAGTTGAATGGGTCCAGTCTCGATATGACTA
66 TTGGATGAAGCTGAATGGGTCCAATCTCGATATGACTA
* * *
35100433 GAATGGAGGCAGTATTACCCATTGAAGTTGGGATCCCTTCTCTACGAGTGTTATCTGAACTCTAG
1 GAATGGAGGAAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGAGTGTTATCTGAACTCCAG
35100498 TTGGATGAAGCTGAATGGGTCCAATCTCGATATGAC
66 TTGGATGAAGCTGAATGGGTCCAATCTCGATATGAC
35100534 CAGTTGAACC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (103 bp):
GAATGGAGGAAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGAGTGTTATCTGAACTCCAG
TTGGATGAAGCTGAATGGGTCCAATCTCGATATGACTA
Found at i:35102326 original size:44 final size:44
Alignment explanation
Indices: 35102277--35102476 Score: 119
Period size: 44 Copynumber: 4.5 Consensus size: 44
35102267 TGTCTTCCTG
*
35102277 AGCAGTAGTGGAGTAGGTTGAAGATAGCAGATCTTATCTCCCTA
1 AGCAGTAGTGGAGTAGATTGAAGATAGCAGATCTTATCTCCCTA
* * * * * *
35102321 AGCAGTAGTGCAGCAGATCGAAGA-CGACAAATCTTATCTTTCC-A
1 AGCAGTAGTGGAGTAGATTGAAGATAG-CAGATCTTATC-TCCCTA
* * * *
35102365 AG-A-TAGTGGGAAGAAGATTTAAGCCACTA--AG-CCTTGTCTCCCTGA
1 AGCAGTAGT-GG-AGTAGATTGAAG--A-TAGCAGATCTTATCTCCCT-A
* * * *
35102410 A-CAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTCCTTA
1 AGCAGTAGTGGAGTAGATTGAAGATAGCAGATCTTATCTCCCTA
* *
35102453 AGCAGTAGTGGAGCAGATCGAAGA
1 AGCAGTAGTGGAGTAGATTGAAGA
35102477 CGACAAATCT
Statistics
Matches: 114, Mismatches: 26, Indels: 32
0.66 0.15 0.19
Matches are distributed among these distances:
41 2 0.02
42 5 0.04
43 10 0.09
44 84 0.74
45 9 0.08
46 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.24
Consensus pattern (44 bp):
AGCAGTAGTGGAGTAGATTGAAGATAGCAGATCTTATCTCCCTA
Found at i:35102419 original size:132 final size:132
Alignment explanation
Indices: 35102176--35102565 Score: 663
Period size: 132 Copynumber: 3.0 Consensus size: 132
35102166 AAATTACAGG
* * *
35102176 TCTTGTCTCCCTAAGCAGTAGTGGAGAAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTG
1 TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
* *
35102241 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTTCCTGAGCAGTAGTGGAGTAGGTTGAAGATAGCA
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
35102306 GA
131 GA
* *
35102308 TCTTATCTCCCTAAGCAGTAGTGCAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
1 TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
* * *
35102373 GGAAGAAGATTTAAGCCACTAAGCCTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAGATAGCA
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
35102438 GA
131 GA
*
35102440 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
1 TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
* *
35102505 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGAT
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAT
35102566 TACAAATCCT
Statistics
Matches: 240, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 240 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
GA
Found at i:35102487 original size:44 final size:44
Alignment explanation
Indices: 35102176--35102487 Score: 112
Period size: 44 Copynumber: 7.1 Consensus size: 44
35102166 AAATTACAGG
* * ** *
35102176 TCTTGTCTCCCTAAGCAGTAGTGGAGAAGATCAAAGACGGCAAA
1 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATTGAAGACGACAAA
* * * *
35102220 TCTTATCT--TTCCAAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAAG
1 TCTTGTCTCCTT--AAGCAGTAGT-GG-AGCAGATTGAAGACGA-CAAA
* * * * * *
35102264 CCTTGTCTTCC-TGAGCAGTAGTGGAGTAGGTTGAAGA-TAGCAGA
1 TCTTGTC-TCCTTAAGCAGTAGTGGAGCAGATTGAAGACGA-CAAA
* * * *
35102308 TCTTATCTCCCTAAGCAGTAGTGCAGCAGATCGAAGACGACAAA
1 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATTGAAGACGACAAA
* * * * *
35102352 TCTTATCT--TTCCAAG-A-TAGTGGGAAGAAGATTTAAG-CCACTAAG
1 TCTTGTCTCCTT--AAGCAGTAGT-GG-AGCAGATTGAAGACGAC-AAA
* * * * * * *
35102396 CCTTGTCTCCCTGAA-CAGCAGTGGAGTAGGTTGAAGA-TAGCAGA
1 TCTTGTCT-CCTTAAGCAGTAGTGGAGCAGATTGAAGACGA-CAAA
*
35102440 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATCGAAGACGACAAA
1 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATTGAAGACGACAAA
35102484 TCTT
1 TCTT
35102488 ATCTTTCCAA
Statistics
Matches: 189, Mismatches: 52, Indels: 54
0.64 0.18 0.18
Matches are distributed among these distances:
42 10 0.05
43 17 0.09
44 141 0.75
45 12 0.06
46 8 0.04
47 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATTGAAGACGACAAA
Found at i:35105730 original size:26 final size:26
Alignment explanation
Indices: 35105686--35105742 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
35105676 GCGACTCTCG
*
35105686 TTTCCTTTTTCAAAATCGATAT-CCAT
1 TTTCATTTTTCAAAATCGAT-TCCCAT
35105712 TTTCATTTTT-AAAAGTCGATTCCCAT
1 TTTCATTTTTCAAAA-TCGATTCCCAT
35105738 TTTCA
1 TTTCA
35105743 AACTTATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (26 bp):
TTTCATTTTTCAAAATCGATTCCCAT
Found at i:35110077 original size:15 final size:16
Alignment explanation
Indices: 35110059--35110091 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35110049 TCTCATATTT
*
35110059 TTCTTTA-TTTTTTTA
1 TTCTTTACTCTTTTTA
35110074 TTCTTTACTCTTTTTA
1 TTCTTTACTCTTTTTA
35110090 TT
1 TT
35110092 TCTCTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTACTCTTTTTA
Found at i:35116175 original size:6 final size:6
Alignment explanation
Indices: 35116164--35116214 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
35116154 TATAAAAATA
35116164 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
35116212 TTA
1 TTA
35116215 ATCAATAACC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:35120954 original size:15 final size:16
Alignment explanation
Indices: 35120924--35120955 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
35120914 CAAATAGGTT
35120924 TAGTGCATTATTTTTTA
1 TAGTGCATTA-TTTTTA
35120941 TAGTGCATTATTTTT
1 TAGTGCATTATTTTT
35120956 GAACGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (16 bp):
TAGTGCATTATTTTTA
Found at i:35125331 original size:41 final size:41
Alignment explanation
Indices: 35125176--35125321 Score: 217
Period size: 41 Copynumber: 3.6 Consensus size: 41
35125166 TGATTCAGTA
35125176 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
35125217 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* * *
35125258 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA--T
35125299 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
35125322 GTAACGTCTG
Statistics
Matches: 98, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 91 0.93
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:35132924 original size:41 final size:41
Alignment explanation
Indices: 35132769--35132914 Score: 217
Period size: 41 Copynumber: 3.6 Consensus size: 41
35132759 TGATTCAGTA
35132769 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
35132810 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* * *
35132851 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA--T
35132892 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
35132915 GTAACGTCTG
Statistics
Matches: 98, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 91 0.93
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:35136412 original size:16 final size:16
Alignment explanation
Indices: 35136391--35136442 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
35136381 TTTGGTTCGC
35136391 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
35136407 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
35136423 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
35136439 TGTA
1 TGTA
35136443 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:35136826 original size:14 final size:15
Alignment explanation
Indices: 35136777--35136828 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35136767 ATAAAATATA
35136777 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35136792 TATTAAATATATTAT
1 AATTAAATATATTAT
35136807 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
35136820 AATTTAATA
1 AATTAAATA
35136829 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35136830 original size:59 final size:58
Alignment explanation
Indices: 35136661--35136957 Score: 164
Period size: 59 Copynumber: 5.0 Consensus size: 58
35136651 ATCATATTTA
* * *
35136661 AACATAATTATTATTAGATATATTATAATTAAAATATA-GAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATG-ATTTAATAAAA-TATAAAT
* * * * *
35136720 AATCA-ATATTCTTATATGAATTTACTCA-AA-TAATAATATATGATACT-ATAAAATATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAA-AATATATGAT-TTAATAAAATATAAA-T
* * *
35136781 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAA-TATAAAT
* * * * * * * *
35136840 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAAGATAATTT
1 AACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATGAT-TTAATAAAATATAA-AT
* * *
35136901 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAA
35136958 ATAATTATAA
Statistics
Matches: 176, Mismatches: 38, Indels: 49
0.67 0.14 0.19
Matches are distributed among these distances:
57 10 0.06
58 11 0.06
59 53 0.30
60 34 0.19
61 46 0.26
62 13 0.07
63 9 0.05
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (58 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAAT
Found at i:35136876 original size:120 final size:121
Alignment explanation
Indices: 35136661--35136953 Score: 491
Period size: 120 Copynumber: 2.4 Consensus size: 121
35136651 ATCATATTTA
* *
35136661 AACATAATTATTATTAGATATATTATAATTAAAATATAGAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
35136726 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
*
35136781 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
35136846 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
* * *
35136902 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
35136954 TAAAATAATT
Statistics
Matches: 163, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 161 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
Found at i:35139806 original size:7 final size:7
Alignment explanation
Indices: 35139794--35139825 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
35139784 TAAAGATTCT
35139794 AAAAAAG
1 AAAAAAG
35139801 AAAAAAG
1 AAAAAAG
35139808 AAACAAAG
1 AAA-AAAG
35139816 AAAAAAG
1 AAAAAAG
35139823 AAA
1 AAA
35139826 TAGTAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:35139833 original size:16 final size:15
Alignment explanation
Indices: 35139797--35139825 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35139787 AGATTCTAAA
35139797 AAAGAAAAAAGAAAC
1 AAAGAAAAAAGAAAC
35139812 AAAGAAAAAAGAAA
1 AAAGAAAAAAGAAA
35139826 TAGTAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAC
Found at i:35140360 original size:13 final size:13
Alignment explanation
Indices: 35140342--35140366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35140332 AAGCGTGAAT
35140342 GGGGAGGGTAAAA
1 GGGGAGGGTAAAA
35140355 GGGGAGGGTAAA
1 GGGGAGGGTAAA
35140367 CTGAAGCGGC
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:0.36, C:0.00, G:0.56, T:0.08
Consensus pattern (13 bp):
GGGGAGGGTAAAA
Found at i:35149930 original size:20 final size:21
Alignment explanation
Indices: 35149905--35149952 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
35149895 GTTTCATTCA
*
35149905 AACCCTAGGTT-AAACATGCG
1 AACCCTAGATTCAAACATGCG
*
35149925 AACCCTAGATTCAAATATGCG
1 AACCCTAGATTCAAACATGCG
35149946 AACCCTA
1 AACCCTA
35149953 TATATGTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (21 bp):
AACCCTAGATTCAAACATGCG
Found at i:35150000 original size:22 final size:22
Alignment explanation
Indices: 35149975--35150017 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35149965 GTGAATTCTA
* *
35149975 TATATGTGTTATATGCAAACCC
1 TATATATGATATATGCAAACCC
35149997 TATATATGATATATGCAAACC
1 TATATATGATATATGCAAACC
35150018 ATTGTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
TATATATGATATATGCAAACCC
Found at i:35164855 original size:14 final size:14
Alignment explanation
Indices: 35164835--35164867 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
35164825 CATCATTTCG
35164835 CTATTATATTGCTA
1 CTATTATATTGCTA
*
35164849 TTATTATATTGCTA
1 CTATTATATTGCTA
35164863 CTATT
1 CTATT
35164868 TTGTTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (14 bp):
CTATTATATTGCTA
Found at i:35170590 original size:28 final size:28
Alignment explanation
Indices: 35170555--35170611 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
35170545 AATTTAAAAG
35170555 TAAAAAGAAATCTAAATAGGTAAATACA
1 TAAAAAGAAATCTAAATAGGTAAATACA
35170583 TAAAAAGAAATCTAAATAGGTAAATACA
1 TAAAAAGAAATCTAAATAGGTAAATACA
35170611 T
1 T
35170612 CTAATTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.23
Consensus pattern (28 bp):
TAAAAAGAAATCTAAATAGGTAAATACA
Found at i:35170607 original size:14 final size:14
Alignment explanation
Indices: 35170562--35170607 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
35170552 AAGTAAAAAG
35170562 AAATCTAAATAGGT
1 AAATCTAAATAGGT
*
35170576 AAATACATAAA-AAG-
1 AAAT-C-TAAATAGGT
35170590 AAATCTAAATAGGT
1 AAATCTAAATAGGT
35170604 AAAT
1 AAAT
35170608 ACATCTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 4 0.15
13 3 0.12
14 12 0.46
15 3 0.12
16 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.24
Consensus pattern (14 bp):
AAATCTAAATAGGT
Found at i:35176408 original size:27 final size:27
Alignment explanation
Indices: 35176378--35176448 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
35176368 GAGTTCACTA
* *
35176378 GGACAGTAAAAACAAAATAGTTTGCCG
1 GGACAGTAAACACAAAATAGTTCGCCG
* * **
35176405 GGACAATAAACACAAGATAGTTCGTTG
1 GGACAGTAAACACAAAATAGTTCGCCG
35176432 GGACAGTAAACACAAAA
1 GGACAGTAAACACAAAA
35176449 ATGTCTGCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (27 bp):
GGACAGTAAACACAAAATAGTTCGCCG
Found at i:35180636 original size:9 final size:9
Alignment explanation
Indices: 35180622--35180734 Score: 138
Period size: 9 Copynumber: 12.4 Consensus size: 9
35180612 TTTGGTTAAA
35180622 AATTACCCG
1 AATTACCCG
35180631 AATTACCCG
1 AATTACCCG
35180640 AATTACCCG
1 AATTACCCG
35180649 AATTACCCG
1 AATTACCCG
35180658 AATTACCCG
1 AATTACCCG
*
35180667 AATTACTCG
1 AATTACCCG
* *
35180676 AATTAACTG
1 AATTACCCG
*
35180685 AATTAACCG
1 AATTACCCG
*
35180694 AATTAACCG
1 AATTACCCG
35180703 AATTA-CCG
1 AATTACCCG
*
35180711 AAAAATACCCG
1 --AATTACCCG
*
35180722 AATTACCTG
1 AATTACCCG
35180731 AATT
1 AATT
35180735 TTTTTATTTT
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
8 3 0.03
9 83 0.89
10 4 0.04
11 3 0.03
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:35182046 original size:34 final size:34
Alignment explanation
Indices: 35181993--35182080 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 34
35181983 TAGGTACCAT
* * * * * *
35181993 AGCACATCCCTCCAACACAATCAGACTGCACATC
1 AGCATATCCATCCCACACAACCAAACTGCACATA
** *
35182027 AGTGTATCCATCCCACACAACCAAATTGCACATA
1 AGCATATCCATCCCACACAACCAAACTGCACATA
35182061 AGCATATCCATCCCACACAA
1 AGCATATCCATCCCACACAA
35182081 GTAGATAGCA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.17
Consensus pattern (34 bp):
AGCATATCCATCCCACACAACCAAACTGCACATA
Found at i:35194269 original size:28 final size:28
Alignment explanation
Indices: 35194238--35194303 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
35194228 ACACAAAAAA
35194238 GCCCTTTTTTAAAAAATTACCGAAATGG
1 GCCCTTTTTTAAAAAATTACCGAAATGG
* * * * *
35194266 GCCCGTTATTTAAATATTTACTGGAATGG
1 GCCC-TTTTTTAAAAAATTACCGAAATGG
*
35194295 GCCATTTTT
1 GCCCTTTTT
35194304 CGGTAAATCA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (28 bp):
GCCCTTTTTTAAAAAATTACCGAAATGG
Found at i:35194656 original size:125 final size:126
Alignment explanation
Indices: 35194427--35194787 Score: 532
Period size: 125 Copynumber: 2.9 Consensus size: 126
35194417 GTCTTGGAAG
* *
35194427 AATTAATTTTGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTTTAGCAGGATGCTTTAT
1 AATT-ATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCTTTAT
* * *
35194491 GAGAAGAATTTGTTAAATCGCGCCCACATGGTCGCGCTTTTGCTACAGTAGGTCCT-GAAAA
65 GAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAA
* * *
35194552 AATTATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATT-T
1 AATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCT-TTAT
* * * * *
35194616 GAGAAGAATTTGTGAAATCGAGCCCTCGTGGACGCACTTTTGCTACAGTTGGTCCTGGAAGA
65 GAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAA
* * *
35194678 AATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATA-GCTTCTACCAGGATGCTTTATG
1 AATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCTTTATG
35194742 AGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACA
66 AGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACA
35194788 ATAGCATGTT
Statistics
Matches: 210, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
124 32 0.15
125 134 0.64
126 44 0.21
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (126 bp):
AATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCTTTATG
AGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAA
Found at i:35199113 original size:7 final size:7
Alignment explanation
Indices: 35199103--35199135 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
35199093 TTATATACAT
35199103 AATACTA
1 AATACTA
35199110 AATACTA
1 AATACTA
35199117 AATACTA
1 AATACTA
35199124 AATACTA
1 AATACTA
35199131 AATAC
1 AATAC
35199136 CAATCGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:35199342 original size:20 final size:20
Alignment explanation
Indices: 35199305--35199342 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35199295 TTTATTTTTA
*
35199305 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
35199325 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
35199343 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:35200386 original size:11 final size:11
Alignment explanation
Indices: 35200372--35200448 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
35200362 TTAAATATGG
35200372 ATTTGAGAGAA
1 ATTTGAGAGAA
*
35200383 ATTTG-GAAGGA
1 ATTTGAG-AGAA
35200394 ATTTGAGAGCAA
1 ATTTGAGAG-AA
35200406 A-TTGAGAGAAA
1 ATTTGAGAG-AA
35200417 ATTT-AGAGGAA
1 ATTTGAGA-GAA
35200428 A-TTGAGAGGAA
1 ATTTGAGA-GAA
35200439 ATTTGAGAGA
1 ATTTGAGAGA
35200449 GGATTAGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.05
11 41 0.73
12 12 0.21
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:35200416 original size:33 final size:33
Alignment explanation
Indices: 35200372--35200448 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
35200362 TTAAATATGG
* *
35200372 ATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAG-AGGAAATTGAGAGCAA
*
35200406 A-TTGAGAGAAAATTTAGAGGAAATTGAGAGGAA
1 ATTTGAGAG-AAATTTAGAGGAAATTGAGAGCAA
35200439 ATTTGAGAGA
1 ATTTGAGAGA
35200449 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAGGAAATTGAGAGCAA
Found at i:35200429 original size:22 final size:23
Alignment explanation
Indices: 35200393--35200447 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
35200383 ATTTGGAAGG
35200393 AATTTGAGAGCAAATTGAGAGAA
1 AATTTGAGAGCAAATTGAGAGAA
* *
35200416 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGAA
35200438 AATTTGAGAG
1 AATTTGAGAG
35200448 AGGATTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGAA
Found at i:35203199 original size:40 final size:39
Alignment explanation
Indices: 35203145--35203253 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 39
35203135 GTTTGGATAA
* * * **
35203145 AAAACACCGGTAAAAATCGAGCATTAGTGGCGCTTC-AGAG
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCAATTCTA-AG
*
35203185 AAAACGCCGCTAAAAAATGAGCATTAGCGGCAATTCTAAT
1 AAAACGCCGCT-AAAAATGAGCATTAGCGGCAATTCTAAG
*
35203225 AAAACGCCGCTAATAAT-ATGCATTAGCGG
1 AAAACGCCGCTAAAAATGA-GCATTAGCGG
35203254 TGTTTTTGGA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
38 1 0.02
39 15 0.25
40 36 0.61
41 7 0.12
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATGAGCATTAGCGGCAATTCTAAG
Found at i:35203535 original size:73 final size:73
Alignment explanation
Indices: 35203408--35203570 Score: 258
Period size: 73 Copynumber: 2.2 Consensus size: 73
35203398 TACAAAAGAT
* * * *
35203408 TGGCATTAGCGGCCCTTCTGTTAAACGCCGCAAAAAATTAAATCCAAACGCATCGTTTTGATTTG
1 TGGCATTAGCGGCGCTTCTGTAAAACGCCGCAAAAAATTAAATCAAAACACATCGTTTTGATTTG
35203473 AGATGTAG
66 AGATGTAG
35203481 TGGCATTAGCGGCGCTTCTGTAAAAGCGCCGCAAAAAGA-T-AATCAAAACACATCGTTTTGATT
1 TGGCATTAGCGGCGCTTCTGTAAAA-CGCCGCAAAAA-ATTAAATCAAAACACATCGTTTTGATT
35203544 TGAGATGTAG
64 TGAGATGTAG
35203554 TGGCATTAGCGGCGCTT
1 TGGCATTAGCGGCGCTT
35203571 TTTCGTAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
73 71 0.85
74 12 0.14
75 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (73 bp):
TGGCATTAGCGGCGCTTCTGTAAAACGCCGCAAAAAATTAAATCAAAACACATCGTTTTGATTTG
AGATGTAG
Found at i:35204146 original size:21 final size:22
Alignment explanation
Indices: 35204116--35204163 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
35204106 GGTGTTTGTG
35204116 GTTTACGGGTTTA-ATGTTTACA
1 GTTTACGGGTTTACA-GTTTACA
*
35204138 GTTTA-GGGTTTACAGTTTATA
1 GTTTACGGGTTTACAGTTTACA
35204159 GTTTA
1 GTTTA
35204164 TGATTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (22 bp):
GTTTACGGGTTTACAGTTTACA
Found at i:35204170 original size:21 final size:21
Alignment explanation
Indices: 35204131--35204170 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35204121 CGGGTTTAAT
*
35204131 GTTTACAGTTTAGGGTTTACA
1 GTTTACAGTTTAGGATTTACA
* *
35204152 GTTTATAGTTTATGATTTA
1 GTTTACAGTTTAGGATTTA
35204171 GGGTTTAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (21 bp):
GTTTACAGTTTAGGATTTACA
Found at i:35204790 original size:147 final size:145
Alignment explanation
Indices: 35204484--35205256 Score: 532
Period size: 147 Copynumber: 5.3 Consensus size: 145
35204474 TTTTTCAAAA
* * * *
35204484 TTTCCATGTTCTTAGTGGCGTTTTATGCAAAAACGCCACAAAATTGTCCTAATTATCG-GGGAAA
1 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATT-TCCTAATTGT-GTGGGAAA
* *
35204548 CGACAG-CGTTTC-ACGGTTATTTAGTGGCGCATACG-TATAAACGCCACAAACGGGTTAATTTA
64 CGAC-GTCGTTTCTACGGTTATTTAGTGGCGCA-A-GTTATAAACGCCGCAAATGGGTTAATTTA
* * * * *
35204610 ATCCCA-AAAAACGACATCGTA
126 GT--CAGGAAAACGTCGTCGTT
* * * * *
35204631 TTACTATATTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTACATAATTGTGTGGGAAAT
1 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTT-CCTAATTGTGTGGGAAAC
* * *
35204696 GACGTCGTTTCTGCGGTTATTTAGTGGCGCAAGATTATAAACGCCGCGAATGGGTTCATTTAGTC
65 GACGTCGTTTCTACGGTTATTTAGTGGCGCAAG-TTATAAACGCCGCAAATGGGTTAATTTAGTC
* *
35204761 ATGAATACGTCGTCGTT
129 AGGAAAACGTCGTCGTT
* * * *
35204778 TTTCCATGTTCTTAGTGGCGTTTTATACCAAAATGCCAGAATGTTGTCCTAATTGTTTGGGAAAC
1 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATT-TCCTAATTGTGTGGGAAAC
* * * * * ** **
35204843 GACTTCGTTTCCATGGTTAATTTAGTGGCGCTTACG-TGTAAACGCCGCAAA-GTTCTTCGTTTA
65 GACGTCGTTTCTACGGTT-ATTTAGTGGCGC--AAGTTATAAACGCCGCAAATG-GGTTAATTTA
* *
35204906 GTCATGGAAAATGTCGTCATT
126 GTCA-GGAAAACGTCGTCGTT
* * * * * * * * **
35204927 TTTCCATGTTGTGATTGGCATTTTATGCCTAAACGCCACAAT-TTTGACTAACTG-GCTGTTAAA
1 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTT-CCTAATTGTG-TGGGAAA
* * ** ** * *
35204990 AGATAG-CGTTTCTACTTTTAGTTT-GTGGCGCTTGTGTATAAACACCGCAAATGGGTAAATTTA
64 CGA-CGTCGTTTCTACGGTTA-TTTAGTGGCGCAAGT-TATAAACGCCGCAAATGGGTTAATTTA
* *
35205053 GTCAGGAATACGTCGTTGTT
126 GTCAGGAAAACGTCGTCGTT
* * ** * * * *
35205073 TTACTA-GTTAGTAGTGGCGTTTTATACCAAAACGCCAGAA-ATTTGTCGTAAGTGT-TTGGAAA
1 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATA-TT-TCCTAATTGTGTGGGAAA
* * ** * * ** *
35205135 CGACATCATTTCTGGGGTTATTTAGTGGCGCTTA-TGTAGAAACGCCGCAAATTTGTTAGTTTAG
64 CGACGTCGTTTCTACGGTTATTTAGTGGCGC-AAGT-TATAAACGCCGCAAATGGGTTAATTTAG
35205199 TCAAGGAAAACGTCGTCGTT
127 TC-AGGAAAACGTCGTCGTT
* * *
35205219 TTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCA
1 TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCA
35205257 AAATTAAGAC
Statistics
Matches: 483, Mismatches: 114, Indels: 58
0.74 0.17 0.09
Matches are distributed among these distances:
144 3 0.01
145 75 0.16
146 49 0.10
147 201 0.42
148 107 0.22
149 46 0.10
150 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (145 bp):
TTTCCATGTTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTCCTAATTGTGTGGGAAACG
ACGTCGTTTCTACGGTTATTTAGTGGCGCAAGTTATAAACGCCGCAAATGGGTTAATTTAGTCAG
GAAAACGTCGTCGTT
Found at i:35205255 original size:292 final size:295
Alignment explanation
Indices: 35204731--35205261 Score: 730
Period size: 292 Copynumber: 1.8 Consensus size: 295
35204721 GGCGCAAGAT
* * ** * * **
35204731 TATAAACGCCGCGAATGGGTTCATTTAGTCATGAATACGTCGTCGTTTTTCCATGTTCTTAGTGG
1 TATAAACACCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
* * * * *
35204796 CGTTTTATACCAAAATGCCAGAATGTTGTCCTAATTGTTTGGGAAACGACTTCGTTTCCATGGTT
66 CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTT
* * *
35204861 AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTCGTTTAGTCATGGAAAATGTCGTCAT
131 AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCAT
* * * * *
35204926 TTTTCCATGTTGTGATTGGCATTTTATGCCTAAACGCCACAATTTTGACTAACTGGCTGTTAAAA
196 TTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATTTTGACTAACTGGCTGTTAAAA
35204991 GATAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
261 GATAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
* *
35205026 TATAAACACCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTTGTTTTACTA-GTTAGTAGTGG
1 TATAAACACCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
* **
35205090 CGTTTTATACCAAAACGCCAGAAAT-TTGTCGTAAGTGTTT-GGAAACGACATCATTTCTGGGGT
66 CGTTTTATACCAAAACGCCAG-AATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGT
* * *
35205153 T-ATTTAGTGGCGCTTATGTAG-AAACGCCGCAAATTTGTTAGTTTAGTCAAGGAAAACGTCGTC
130 TAATTTAGTGGCGCTTACGT-GTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTC
* *
35205216 GTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATT
194 ATTTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATT
35205262 AAGACTGTCT
Statistics
Matches: 203, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
292 93 0.46
293 20 0.10
294 42 0.21
295 48 0.24
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (295 bp):
TATAAACACCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTT
AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCAT
TTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATTTTGACTAACTGGCTGTTAAAA
GATAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
Found at i:35205294 original size:147 final size:145
Alignment explanation
Indices: 35204700--35205329 Score: 347
Period size: 147 Copynumber: 4.3 Consensus size: 145
35204690 GGAAATGACG
** ** * * **
35204700 TCGTTTCTGCGGTTATTTAGTGGCGCAAGAT-TATAAACGCCGCGAATGGGTTCA-TTTAGTC-A
1 TCGTTTCTATGGTTATTTAGTGGCGC-TTATGTAGAAACGCCGCAAATTTGTT-AGTTTAGTCAA
* * * * * * * * *
35204762 TGAATACGTCGTCGTTTTTCCATGTTCTTAGTGGCGTTTTATACCAAAATGCCAGAATGTTGTCC
64 GGAAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAAT-TTG-AC
* *
35204827 TAAT-TG-T-TTGGGAAACGACT
127 T-GTCTGCTCTT---AAAAGACT
* * * * * *
35204847 TCGTTTCCATGGTTAATTTAGTGGCGCTTACGT-GTAAACGCCGCAAAGTTCTTCGTTTAGTCAT
1 TCGTTTCTATGGTT-ATTTAGTGGCGCTTATGTAG-AAACGCCGCAAATTTGTTAGTTTAGTCAA
* * * * * * * *
35204911 GGAAAATGTCGTCATTTTTCCATGTTGTGATTGGCATTTTATGCCTAAACGCCACAATTTTGACT
64 GGAAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCA-AAATTTGACT
** *
35204976 AACTGGCTGTTAAAAGA-T
128 GTCT-GCTCTTAAAAGACT
* * * * * ** * *
35204994 AGCGTTTCTACT-TTTAGTTT-GTGGCGCTTGTGTATAAACACCGCAAATGGGTAAATTTAGTC-
1 -TCGTTTCTA-TGGTTA-TTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCA
* * * * * *
35205056 AGGAATACGTCGTTGTTTTACTA-GTTA-GTAGTGGCGTTTTATACCAAAACGCCAGAAATTTGT
63 AGGAAAACGTCGTCGTTTTTCAATGTTATG-AGTGGCGTTTTATGCCAAAACGCCA-AAATTTGA
* * *
35205119 C-GTAAGTG-T-TTGGAAACGACA
126 CTGT--CTGCTCTT--AAAAGACT
* **
35205140 TCATTTCTGGGGTTATTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCAAGG
1 TCGTTTCTATGGTTATTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCAAGG
*
35205205 AAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATTAAGACTGT
66 AAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATT-TGACTGT
*
35205270 CTGCTACTTAAATGACT
130 CTGCT-CTTAAAAGACT
* * * * * * *
35205287 TCGTTTCTGTGGATATTTTGTGGCACTTGTTTATAAACGCCGC
1 TCGTTTCTATGGTTATTTAGTGGCGCTTATGTAGAAACGCCGC
35205330 TACCAGTGGG
Statistics
Matches: 359, Mismatches: 94, Indels: 60
0.70 0.18 0.12
Matches are distributed among these distances:
143 2 0.01
144 5 0.01
145 81 0.23
146 43 0.12
147 117 0.33
148 56 0.16
149 50 0.14
150 3 0.01
151 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (145 bp):
TCGTTTCTATGGTTATTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCAAGG
AAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATTTGACTGTC
TGCTCTTAAAAGACT
Found at i:35205309 original size:292 final size:294
Alignment explanation
Indices: 35204692--35205329 Score: 716
Period size: 292 Copynumber: 2.2 Consensus size: 294
35204682 ATTGTGTGGG
* * * ** * **
35204692 AAATGACGTCGTTTCTGCGGTTATTTAGTGGCGCAAGATTATAAACGCCGCGAATGGGTTCATTT
1 AAATGACTTCGTTTCTGTGGTTATTTTGTGGCGCTTG-TTATAAACGCCGCAAATGGGTAAATTT
* * ** *
35204757 AGTCATGAATACGTCGTCGTTTTTCCATGTTCTTAGTGGCGTTTTATACCAAAATGCCAGAATGT
65 AGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGGCGTTTTATACCAAAACGCCAGAATGT
* * * *
35204822 TGTCCTAATTGTTTGGGAAACGACTTCGTTTCCATGGTTAATTTAGTGGCGCTTACGTGTAAACG
130 TGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTTAATTTAGTGGCGCTTACGTGTAAACG
* * * * * *
35204887 CCGCAAAGTTCTTCGTTTAGTCATGGAAAATGTCGTCATTTTTCCATGTTGTGATTGGCATTTTA
195 CCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCATTTTTCAATGTTATGAGTGGCATTTTA
* * ** *
35204952 TGCCTAAACGCCACAATTTTGACTAACTGGCTGTT
260 TGCCAAAACGCCAAAATTAAGACTAACTGGCTCTT
* * * * * *
35204987 AAAAGA-TAGCGTTTCTACT-TTTAGTTTGTGGCGCTTGTGTATAAACACCGCAAATGGGTAAAT
1 AAATGACT-TCGTTTCT-GTGGTTATTTTGTGGCGCTTGT-TATAAACGCCGCAAATGGGTAAAT
* *
35205050 TTAGTCAGGAATACGTCGTTGTTTTACTA-GTTAGTAGTGGCGTTTTATACCAAAACGCCAGAAA
63 TTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGGCGTTTTATACCAAAACGCCAG-AA
* ** *
35205114 T-TTGTCGTAAGTGTTT-GGAAACGACATCATTTCTGGGGTT-ATTTAGTGGCGCTTATGTAG-A
127 TGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTTAATTTAGTGGCGCTTACGT-GTA
* * * *
35205175 AACGCCGCAAATTTGTTAGTTTAGTCAAGGAAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGT
191 AACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCATTTTTCAATGTTATGAGTGGCAT
**
35205240 TTTATGCCAAAACGCCAAAATTAAGACTGTCT-GCTACTT
256 TTTATGCCAAAACGCCAAAATTAAGACTAACTGGCT-CTT
* *
35205279 AAATGACTTCGTTTCTGTGGATATTTTGTGGCACTTGTTTATAAACGCCGC
1 AAATGACTTCGTTTCTGTGGTTATTTTGTGGCGCTTG-TTATAAACGCCGC
35205330 TACCAGTGGG
Statistics
Matches: 280, Mismatches: 54, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
291 4 0.01
292 138 0.49
293 22 0.08
294 43 0.15
295 73 0.26
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (294 bp):
AAATGACTTCGTTTCTGTGGTTATTTTGTGGCGCTTGTTATAAACGCCGCAAATGGGTAAATTTA
GTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGGCGTTTTATACCAAAACGCCAGAATGTT
GTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTTAATTTAGTGGCGCTTACGTGTAAACGC
CGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCATTTTTCAATGTTATGAGTGGCATTTTAT
GCCAAAACGCCAAAATTAAGACTAACTGGCTCTT
Found at i:35205798 original size:14 final size:14
Alignment explanation
Indices: 35205779--35205808 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35205769 TGTGGAATAT
*
35205779 TTCAGATTTTTTTA
1 TTCAGATTTTGTTA
35205793 TTCAGATTTTGTTA
1 TTCAGATTTTGTTA
35205807 TT
1 TT
35205809 TGGGTTTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (14 bp):
TTCAGATTTTGTTA
Found at i:35205824 original size:11 final size:11
Alignment explanation
Indices: 35205808--35205832 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35205798 ATTTTGTTAT
35205808 TTGGGTTTCTG
1 TTGGGTTTCTG
35205819 TTGGGTTTCTG
1 TTGGGTTTCTG
35205830 TTG
1 TTG
35205833 AATTTTGACT
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:0.00, C:0.08, G:0.36, T:0.56
Consensus pattern (11 bp):
TTGGGTTTCTG
Found at i:35206972 original size:69 final size:69
Alignment explanation
Indices: 35206899--35207040 Score: 239
Period size: 69 Copynumber: 2.1 Consensus size: 69
35206889 AAATTTTATT
* * *
35206899 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTTTAAATATTAAAACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
35206964 TTTC
66 TTTC
*
35206968 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAACACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
*
35207033 TTTT
66 TTTC
35207037 AATA
1 AATA
35207041 TATCACCCCA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (69 bp):
AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
TTTC
Found at i:35207161 original size:9 final size:9
Alignment explanation
Indices: 35207147--35207396 Score: 135
Period size: 9 Copynumber: 27.2 Consensus size: 9
35207137 ACTTACGTAA
35207147 TACATAACT
1 TACATAACT
35207156 TACATAATAACT
1 TAC---ATAACT
35207168 TACATAACT
1 TACATAACT
*
35207177 TATATAGAAACTT
1 TACAT---AAC-T
*
35207190 ATATATAAACT
1 -TACAT-AACT
*
35207201 TGCATAACT
1 TACATAACT
35207210 TACATAA--
1 TACATAACT
* * *
35207217 TATATAGCC
1 TACATAACT
*
35207226 TACATAAAT
1 TACATAACT
*
35207235 TGCATAACT
1 TACATAACT
*
35207244 CACATAA--
1 TACATAACT
*
35207251 TACACAACT
1 TACATAACT
35207260 TACATAACT
1 TACATAACT
*
35207269 TAAATAACT
1 TACATAACT
35207278 TACATAA--
1 TACATAACT
35207285 TACATAACT
1 TACATAACT
*
35207294 TACATTAATAT
1 TACA-TAA-CT
35207305 TAGACATAACT
1 T--ACATAACT
35207316 TACATAACT
1 TACATAACT
35207325 TAC--AACT
1 TACATAACT
35207332 TACATAACT
1 TACATAACT
*
35207341 TA-ATTACAT
1 TACATAAC-T
*
35207350 TATATACAACT
1 TACAT--AACT
*
35207361 TACATAACA
1 TACATAACT
35207370 TACATAA--
1 TACATAACT
*
35207377 TATATAACT
1 TACATAACT
35207386 TACATAACT
1 TACATAACT
35207395 TA
1 TA
35207397 TATATAAACT
Statistics
Matches: 188, Mismatches: 27, Indels: 52
0.70 0.10 0.19
Matches are distributed among these distances:
7 30 0.16
8 4 0.02
9 106 0.56
10 8 0.04
11 10 0.05
12 21 0.11
13 4 0.02
14 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:35207242 original size:34 final size:34
Alignment explanation
Indices: 35207136--35207338 Score: 148
Period size: 34 Copynumber: 5.8 Consensus size: 34
35207126 CTTATATATA
* *
35207136 AACTTACGTAATACATAACTTACATAATAACTTACAT
1 AACTTACATAATACATAACTTACAT-A-AA-TTGCAT
* *
35207173 AACTT--AT-ATAGA-AACTTATATATAAACTTGCAT
1 AACTTACATAATACATAAC-T-TACATAAA-TTGCAT
* * *
35207206 AACTTACATAATATATAGCCTACATAAATTGCAT
1 AACTTACATAATACATAACTTACATAAATTGCAT
* * * **
35207240 AACTCACATAATACACAACTTACATAACTTAAAT
1 AACTTACATAATACATAACTTACATAAATTGCAT
35207274 AACTTACATAATACATAACTTACATTAATATTAGACAT
1 AACTTACATAATACATAACTTACA-TAA-ATT-G-CAT
35207312 AACTTACATAACTTAC--AACTTACATAA
1 AACTTACATAA--TACATAACTTACATAA
35207339 CTTAATTACA
Statistics
Matches: 133, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
33 16 0.12
34 60 0.45
35 17 0.13
36 6 0.05
37 10 0.08
38 21 0.16
40 3 0.02
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (34 bp):
AACTTACATAATACATAACTTACATAAATTGCAT
Found at i:35207342 original size:25 final size:25
Alignment explanation
Indices: 35207197--35207342 Score: 53
Period size: 25 Copynumber: 6.0 Consensus size: 25
35207187 CTTATATATA
* *
35207197 AACTTGCATAACTTACATAA-TATAT
1 AACTTACATAACTTACATAACT-TAC
* * * * *
35207222 AGCCTACATAAATTGCATAACTCAC
1 AACTTACATAACTTACATAACTTAC
* * *
35207247 ATA-ATACACAACTTACATAACTTAAAT
1 A-ACTTACATAACTTACATAACTT--AC
35207274 AACTTACATAA--TACATAACTTAC
1 AACTTACATAACTTACATAACTTAC
35207297 -A-TTA-AT-A-TTAGACATAACTTAC
1 AACTTACATAACTT--ACATAACTTAC
35207319 ATAACTTAC--AACTTACATAACTTA
1 --AACTTACATAACTTACATAACTTA
35207343 ATTACATTAT
Statistics
Matches: 89, Mismatches: 17, Indels: 30
0.65 0.12 0.22
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 3 0.03
22 12 0.13
23 1 0.01
25 53 0.60
26 6 0.07
27 10 0.11
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAACTTAC
Found at i:35207373 original size:25 final size:25
Alignment explanation
Indices: 35207308--35207413 Score: 96
Period size: 25 Copynumber: 4.2 Consensus size: 25
35207298 TTAATATTAG
*
35207308 ACATAACTTACATAACT-TACAACTT
1 ACATAACATACATAA-TATACAACTT
*
35207333 ACATAACTTAATTACATTATATACAACTT
1 ACATAAC---A-TACATAATATACAACTT
*
35207362 ACATAACATACATAATATATAACTT
1 ACATAACATACATAATATACAACTT
*
35207387 ACATAAC-T-TAT-ATATA-AACTT
1 ACATAACATACATAATATACAACTT
35207408 ACATAA
1 ACATAA
35207414 TTTACTTAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
21 11 0.15
22 5 0.07
23 2 0.03
24 1 0.01
25 29 0.41
26 1 0.01
28 1 0.01
29 21 0.30
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (25 bp):
ACATAACATACATAATATACAACTT
Found at i:35207398 original size:16 final size:17
Alignment explanation
Indices: 35207256--35207396 Score: 94
Period size: 16 Copynumber: 7.9 Consensus size: 17
35207246 CATAATACAC
35207256 AACTTACATAACTTAAAT
1 AACTTACATAACTT-AAT
35207274 AACTTACATAA--TACAT
1 AACTTACATAACTTA-AT
*
35207290 AACTTACATTAATATTAGACAT
1 AACTTACA-TAA-CTT--A-AT
*
35207312 AACTTACATAACTT-AC
1 AACTTACATAACTTAAT
35207328 AACTTACATAACTTAAT
1 AACTTACATAACTTAAT
* *
35207345 TACATTATATACAACTTACAT
1 AAC-TTACAT--AACTTA-AT
*
35207366 AACATACATAA--TATAT
1 AACTTACATAACTTA-AT
35207382 AACTTACATAACTTA
1 AACTTACATAACTTA
35207397 TATATAAACT
Statistics
Matches: 99, Mismatches: 10, Indels: 28
0.72 0.07 0.20
Matches are distributed among these distances:
15 1 0.01
16 40 0.40
17 6 0.06
18 20 0.20
20 13 0.13
21 7 0.07
22 12 0.12
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.34
Consensus pattern (17 bp):
AACTTACATAACTTAAT
Found at i:35212938 original size:21 final size:21
Alignment explanation
Indices: 35212912--35212960 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
35212902 GAACTCCAAG
*
35212912 GCAGAGGCGGCAGCGAGGGAA
1 GCAGAGGCGGCAGCGAGAGAA
* *
35212933 GCAGAGGCTGCAGTGAGAGAA
1 GCAGAGGCGGCAGCGAGAGAA
35212954 GCAGAGG
1 GCAGAGG
35212961 TTCAAGCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.49, T:0.04
Consensus pattern (21 bp):
GCAGAGGCGGCAGCGAGAGAA
Found at i:35213198 original size:26 final size:26
Alignment explanation
Indices: 35213177--35213234 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
35213167 AAATTACATC
*
35213177 TTATTTATTT-ATATTTATATTATATA
1 TTATTCATTTAAT-TTTATATTATATA
*
35213203 TTATTCGTTTAATTTTATATTATATA
1 TTATTCATTTAATTTTATATTATATA
35213229 TTATTC
1 TTATTC
35213235 GGTTAGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (26 bp):
TTATTCATTTAATTTTATATTATATA
Found at i:35213389 original size:43 final size:43
Alignment explanation
Indices: 35213342--35213625 Score: 370
Period size: 43 Copynumber: 6.6 Consensus size: 43
35213332 TTATACCAAA
* * *
35213342 CGCCGCTAAAAGTTATGGCCTATAGCGGCGTTTGTGGGAAAAC
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* *
35213385 CGCCGCTAAAGGTCATGGCCTATAGCGACGTTTGTGGGAGAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
*
35213428 CGCCGCTAAAGGTCATGGCCTATAGCGGCATTTGTGGGAAAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* *
35213471 TGCCGCTAAAGGTCATGGCCTATAACGGCGTTTGTGGGAAAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* *
35213514 CGCCGCTAAAGATCATGGTCTATAGCGGCGTTTGTGGGAAAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* * *** * *
35213557 TGCCGCTAAAGATCATAATCTATAGCGGTGTTTGTGGGAGAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* * * **
35213600 CACTGCTAAAGATCATGTTCTATAGC
1 CGCCGCTAAAGGTCATGGCCTATAGC
35213626 AGTGTTTATT
Statistics
Matches: 216, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 216 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
Found at i:35220258 original size:19 final size:20
Alignment explanation
Indices: 35220214--35220279 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 20
35220204 TATAATTTTT
*
35220214 TTTTTAAAATATAAGTTTTGGAA
1 TTTTTAAAAT-TTA-TTTT-GAA
*
35220237 TTTTTATAA-TTATTTTGAA
1 TTTTTAAAATTTATTTTGAA
35220256 -TTTTAAAATTTATTTTGAA
1 TTTTTAAAATTTATTTTGAA
35220275 TTTTT
1 TTTTT
35220280 TTGTAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.18
19 13 0.34
20 8 0.21
21 2 0.05
23 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTTAAAATTTATTTTGAA
Found at i:35223178 original size:51 final size:50
Alignment explanation
Indices: 35223096--35223373 Score: 296
Period size: 51 Copynumber: 5.5 Consensus size: 50
35223086 GATGAACACG
35223096 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA-AAACT-ATGGTCACA
* * * *
35223147 TGTGTAGTACTAAT-TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
1 TGTGTAGTACT-ATGTGAAGGCTACTACGTGTATCGAAAA-CTATGGTCACA
* * * *
35223198 TGTGTAGTACTGTGTGAAGGTTACTACGTGAATCGGTAAA-TGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GAAAACT-ATGGTCACA
* * *
35223249 TGTGTAGTACTAAGTGAAGGCTACTATGTGTA-CTGAAAAGCTTTGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GAAAA-CTATGGTCACA
* * * *
35223300 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACT-TGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCG-AAAACTATGGTCACA
*
35223350 TATGTAGTACTATGTGAAGGCTAC
1 TGTGTAGTACTATGTGAAGGCTAC
35223374 ACTACACCAA
Statistics
Matches: 191, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
50 39 0.20
51 139 0.73
52 13 0.07
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAACTATGGTCACA
Found at i:35223272 original size:102 final size:102
Alignment explanation
Indices: 35223096--35223374 Score: 409
Period size: 102 Copynumber: 2.7 Consensus size: 102
35223086 GATGAACACG
* * *
35223096 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTACTAAG
35223161 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
66 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
* * *
35223198 TGTGTAGTACTGTGTGAAGGTTACTACGTGAATCGGTAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTACTAAG
* *
35223263 TGAAGGCTACTATGTGTACTGAAAAGCTTTGGTCACA
66 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
* * * * * *
35223300 TGTGTAGTACTATGTGAAGGCTACTACGTGAA-CCGTAAA-ACTTGATCACGTATGTAGTACTAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATA-ATGGTCACATGTGTAGTACTAA
35223363 GTGAAGGCTACA
65 GTGAAGGCTACA
35223375 CTACACCAAA
Statistics
Matches: 158, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
101 34 0.22
102 124 0.78
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTACTAAG
TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
Found at i:35223623 original size:41 final size:41
Alignment explanation
Indices: 35223566--35223790 Score: 342
Period size: 41 Copynumber: 5.5 Consensus size: 41
35223556 TGAACTTTCG
*
35223566 GGGCTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
*
35223607 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
* * * *
35223648 GGGATTTAGCGACGTTTTTGAAGAAGCGCCACTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
* *
35223689 GGGCTTTAGCAGCGTTTTTGAAGAAGTGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
* * *
35223730 GGGATTTAGCGGCGTTTTTTGGAGAAGCGCCGCTAATGCTTG
1 GGGCTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTTA
35223772 GGGCTTTAGCGGCGTTTTT
1 GGGCTTTAGCGGCGTTTTT
35223791 AGGGAAGCGT
Statistics
Matches: 164, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 127 0.77
42 37 0.23
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
Found at i:35224252 original size:21 final size:21
Alignment explanation
Indices: 35224218--35224259 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35224208 TCTAGTTTAA
* * *
35224218 GGGTTGTGATTTAGGGGTTAG
1 GGGTTATGAGTTAGAGGTTAG
35224239 GGGTTATGAGTTAGAGGTTAG
1 GGGTTATGAGTTAGAGGTTAG
35224260 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.36
Consensus pattern (21 bp):
GGGTTATGAGTTAGAGGTTAG
Found at i:35224270 original size:21 final size:21
Alignment explanation
Indices: 35224228--35224272 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35224218 GGGTTGTGAT
* * * *
35224228 TTAGGGGTTAGGGGTTATGAG
1 TTAGAGGTTAGAGATTAAGAG
35224249 TTAGAGGTTAGAGATTAAGAG
1 TTAGAGGTTAGAGATTAAGAG
35224270 TTA
1 TTA
35224273 TAGATTTAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (21 bp):
TTAGAGGTTAGAGATTAAGAG
Found at i:35228903 original size:20 final size:19
Alignment explanation
Indices: 35228859--35228905 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
35228849 ATTTAAAAAA
35228859 TAAAATAAAATATTTATCAT
1 TAAAAT-AAATATTTATCAT
*
35228879 AAAAATAAATA-TTATTCGAT
1 TAAAATAAATATTTA-TC-AT
35228899 TAAAATA
1 TAAAATA
35228906 TATTTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.13
19 7 0.30
20 13 0.57
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAATAAATATTTATCAT
Found at i:35229032 original size:43 final size:42
Alignment explanation
Indices: 35228964--35229236 Score: 127
Period size: 42 Copynumber: 6.7 Consensus size: 42
35228954 TAAAATTGCG
* * * * *
35228964 GCTAAAGATTATGGTCTTTAACGGCGTTTGTGGGAAAAGTGTC
1 GCTAAAGGTCATGGTCTTTAACGGCGTTAGTGGG-AAAGCGCC
* *
35229007 GTTAAAGGTCATGGTCTTTAGCGGCGTTAGTGGGAAAGCGCC
1 GCTAAAGGTCATGGTCTTTAACGGCGTTAGTGGGAAAGCGCC
* * * * * **** *
35229049 GCTAAAGGTCATAGTTTTTAAAGGTC-ATAAT-CTTTAGCGGC
1 GCTAAAGGTCATGGTCTTTAACGG-CGTTAGTGGGAAAGCGCC
* * * *
35229090 G-TTAAGGTCATGGTCTTT-A--GC---AG-CGAAAAGCACC
1 GCTAAAGGTCATGGTCTTTAACGGCGTTAGTGGGAAAGCGCC
* * * * * *
35229124 GTTAAAGTTCATGTTCTTTAGCGGCGTTTGTGGGAAAAACGCC
1 GCTAAAGGTCATGGTCTTTAACGGCGTTAGTGGG-AAAGCGCC
* * *
35229167 GCTAAAGGTCATGG-CTTTAGCGGCGTTTGTGGTAAAAGCGCC
1 GCTAAAGGTCATGGTCTTTAACGGCGTTAGTGG-GAAAGCGCC
* * * *
35229209 ACTAAAGGTTATGATCTTTAGCGGCGTT
1 GCTAAAGGTCATGGTCTTTAACGGCGTT
35229237 TTTTCCTGCG
Statistics
Matches: 171, Mismatches: 46, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
34 6 0.04
35 14 0.08
36 1 0.01
37 1 0.01
38 2 0.01
39 1 0.01
40 14 0.08
41 7 0.04
42 65 0.38
43 60 0.35
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (42 bp):
GCTAAAGGTCATGGTCTTTAACGGCGTTAGTGGGAAAGCGCC
Found at i:35229084 original size:16 final size:16
Alignment explanation
Indices: 35229051--35229084 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35229041 AAAGCGCCGC
* *
35229051 TAAAGGTCATAGTTTT
1 TAAAGGTCATAATCTT
35229067 TAAAGGTCATAATCTT
1 TAAAGGTCATAATCTT
35229083 TA
1 TA
35229085 GCGGCGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (16 bp):
TAAAGGTCATAATCTT
Found at i:35229195 original size:42 final size:43
Alignment explanation
Indices: 35229139--35229237 Score: 146
Period size: 42 Copynumber: 2.3 Consensus size: 43
35229129 AGTTCATGTT
*
35229139 CTTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATG-G
1 CTTTAGCGGCGTTTGTGGGAAAAACGCCACTAAAGGTCATGAG
* * * *
35229181 CTTTAGCGGCGTTTGTGGTAAAAGCGCCACTAAAGGTTATGAT
1 CTTTAGCGGCGTTTGTGGGAAAAACGCCACTAAAGGTCATGAG
35229224 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
35229238 TTTCCTGCGC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 37 0.73
43 14 0.27
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAACGCCACTAAAGGTCATGAG
Found at i:35236038 original size:51 final size:51
Alignment explanation
Indices: 35235982--35236227 Score: 266
Period size: 50 Copynumber: 4.9 Consensus size: 51
35235972 CCGAGAAGCT
* **
35235982 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGGTAAATG
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * * * *
35236033 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTA-CCG-AAAAGC
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAA-C
* *
35236083 TTTGGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAA-CCGTAAAAC
1 -TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * *
35236134 TTGATCACATATGTAGTATTATGTGAAGGCTACTACGTGAATC-GTAAAAC
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * * *
35236184 TTGATCATGTGTGTAGTGCTATATGAAGGCTACTACGTGTATCG
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG
35236228 AATGATAAAA
Statistics
Matches: 165, Mismatches: 25, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
49 3 0.02
50 83 0.50
51 75 0.45
52 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (51 bp):
TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
Found at i:35236093 original size:102 final size:102
Alignment explanation
Indices: 35235931--35236227 Score: 357
Period size: 102 Copynumber: 2.9 Consensus size: 102
35235921 TAAGGTATCG
* * * * *
35235931 ATGAACACTTGTGTAGTACTGTGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGT
* **
35235996 AGTACTGTGTGAAGGCTACTACGTGAATCGGTAAATG
66 AGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * *
35236033 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTATGT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGT
*
35236098 AGTACTATGTGAAGGCTACTACGTGAA-CCGTAAAAC
66 AGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * * * * * *
35236134 TTGATCACATATGTAGTATTATGTGAAGGCTACTACGTGAATCGTAAAA-C-TTGATCATGTGTG
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGTCACGTGTG
* * *
35236197 TAGTGCTATATGAAGGCTACTACGTGTATCG
65 TAGTACTATGTGAAGGCTACTACGTGAATCG
35236228 AATGATAAAA
Statistics
Matches: 166, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
100 35 0.21
101 44 0.27
102 87 0.52
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGT
AGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
Found at i:35236157 original size:50 final size:50
Alignment explanation
Indices: 35235942--35236222 Score: 260
Period size: 51 Copynumber: 5.6 Consensus size: 50
35235932 TGAACACTTG
* * * * * * * *
35235942 TGTAGTACTGTGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTG
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACATA
* * *** * *
35235993 TGTAGTACTGTGTGAAGGCTACTACGTGAATCGGTAAATGATGGTCACATG
1 TGTAGTACTATGTGAAGGCTACTACGTGAA-CCGTAAAACTTGATCACATA
* * * * *
35236044 TGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGTCACGTA
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGATCACATA
35236095 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
* * ** *
35236145 TGTAGTATTATGTGAAGGCTACTACGTGAATCGTAAAACTTGATCATGTG
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
* *
35236195 TGTAGTGCTATATGAAGGCTACTACGTG
1 TGTAGTACTATGTGAAGGCTACTACGTG
35236223 TATCGAATGA
Statistics
Matches: 194, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
49 3 0.02
50 81 0.42
51 101 0.52
52 8 0.04
53 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
Found at i:35237631 original size:26 final size:25
Alignment explanation
Indices: 35237599--35237785 Score: 132
Period size: 25 Copynumber: 7.5 Consensus size: 25
35237589 TACAATATGA
* * * *
35237599 CACAAGGGTTTTTCGTAAGATTAGC
1 CACAAAGGCTTTTCATAAGAATAGC
35237624 CACAAAGGCTTTTCATAAGAATAGC
1 CACAAAGGCTTTTCATAAGAATAGC
* *
35237649 CACAAAAGC-TTTC-TAGACAATACGC
1 CACAAAGGCTTTTCATA-AGAATA-GC
* * *
35237674 CACAAAGGCTTTCCATAAGATTAGT
1 CACAAAGGCTTTTCATAAGAATAGC
* *
35237699 CACAAAGGCTTTCCA-GAGAATA-C
1 CACAAAGGCTTTTCATAAGAATAGC
* * *
35237722 ACTACAAAGACTTTCCA-AACAATACGC
1 -C-ACAAAGGCTTTTCATAAGAATA-GC
* *
35237749 CACAAAGTCTTTTCATAAGATTAGC
1 CACAAAGGCTTTTCATAAGAATAGC
* *
35237774 CATAAAAGCTTT
1 CACAAAGGCTTT
35237786 CTAGATAATT
Statistics
Matches: 129, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
23 2 0.02
24 15 0.12
25 96 0.74
26 13 0.10
27 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (25 bp):
CACAAAGGCTTTTCATAAGAATAGC
Found at i:35237705 original size:75 final size:75
Alignment explanation
Indices: 35237582--35237786 Score: 218
Period size: 75 Copynumber: 2.7 Consensus size: 75
35237572 ATCATACAGT
* * * * * * * *
35237582 CTTTCCATACAATATGACACAAGGGTTTTTCGTAAGATTAGCCACAAAGGCTTTTCATAAGAATA
1 CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTCCA-AAGAATA
35237647 GC-C-ACAAA-A
65 -CACTACAAAGA
* * * *
35237656 GCTTTCTAGACAATACGCCACAAAGGCTTTCCATAAGATTAGTCACAAAGGCTTTCCAGAGAATA
1 -CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTCCAAAGAATA
35237721 CACTACAAAGA
65 CACTACAAAGA
* * * *
35237732 CTTTCCAAACAATACGCCACAAAGTCTTTTCATAAGATTAGCCATAAAAGCTTTC
1 CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTC
35237787 TAGATAATTC
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
73 1 0.01
74 7 0.06
75 100 0.92
76 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (75 bp):
CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTCCAAAGAATAC
ACTACAAAGA
Found at i:35237755 original size:50 final size:50
Alignment explanation
Indices: 35237623--35237760 Score: 161
Period size: 50 Copynumber: 2.8 Consensus size: 50
35237613 GTAAGATTAG
* * * *
35237623 CCACAAAGGCTTTTCATAAGAATAGCCACAAAAGCTTTCTAGACAATACG
1 CCACAAAGGCTTTCCATAAGAATAGCCACAAAGGCTTTCCAGACAATACA
* * *
35237673 CCACAAAGGCTTTCCATAAGATTAGTCACAAAGGCTTTCCAGAGAATACA
1 CCACAAAGGCTTTCCATAAGAATAGCCACAAAGGCTTTCCAGACAATACA
* * * *
35237723 CTACAAAGACTTTCCA-AACAATACGCCACAAAGTCTTT
1 CCACAAAGGCTTTCCATAAGAATA-GCCACAAAGGCTTT
35237761 TCATAAGATT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 5 0.07
50 69 0.93
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.22
Consensus pattern (50 bp):
CCACAAAGGCTTTCCATAAGAATAGCCACAAAGGCTTTCCAGACAATACA
Found at i:35241470 original size:69 final size:69
Alignment explanation
Indices: 35241359--35241496 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
35241349 AAGCTTTGGT
35241359 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGGTTTTTAGCAGCCTTTTTC
1 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGGTTTTTAGCAGCCTTTTTC
35241424 TGGC
66 TGGC
35241428 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGGTTTTTAGCAGCCTTTTTC
1 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGGTTTTTAGCAGCCTTTTTC
35241493 TGGC
66 TGGC
35241497 CCTATAGCGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (69 bp):
TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGGTTTTTAGCAGCCTTTTTC
TGGC
Found at i:35244240 original size:25 final size:25
Alignment explanation
Indices: 35244186--35244240 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
35244176 AGCACTCTCT
* *
35244186 CGAGCTATATAACAGAATGCTCATG
1 CGAGCCATATAACAGAATGCTCATC
* *
35244211 TGAGCCATATAACATGAA-GCTTATC
1 CGAGCCATATAACA-GAATGCTCATC
35244236 CGAGC
1 CGAGC
35244241 AATAATAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (25 bp):
CGAGCCATATAACAGAATGCTCATC
Found at i:35244388 original size:25 final size:24
Alignment explanation
Indices: 35244354--35244406 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
35244344 AAGTTCAAGT
35244354 GAGCCATATCAGGA-AGCTCACAAA
1 GAGCCATATCAGGACA-CTCACAAA
*
35244378 GAGCCTATATCAGGACACTCATAAA
1 GAGCC-ATATCAGGACACTCACAAA
35244403 GAGC
1 GAGC
35244407 TGCAGTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 20 0.77
26 1 0.04
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAGGACACTCACAAA
Found at i:35251587 original size:26 final size:24
Alignment explanation
Indices: 35251558--35251612 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
35251548 AGCAGCAGAC
*
35251558 GGATGGGAAGGAAAAAACTAAGTTAG
1 GGATGGG--GGAAAAAACTAAGTTAA
*
35251584 GGATTTGGGGAAAAAACTAAGTTAA
1 GGA-TGGGGGAAAAAACTAAGTTAA
35251609 GGAT
1 GGAT
35251613 TTAGGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 19 0.73
26 3 0.12
27 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.20
Consensus pattern (24 bp):
GGATGGGGGAAAAAACTAAGTTAA
Found at i:35251595 original size:25 final size:25
Alignment explanation
Indices: 35251567--35251622 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
35251557 CGGATGGGAA
* *
35251567 GGAAAAAACTAAGTTAGGGATTTGG
1 GGAAAAAACTAAGTTAAGGATTTAG
35251592 GGAAAAAACTAAGTTAAGGATTTAG
1 GGAAAAAACTAAGTTAAGGATTTAG
35251617 GGAAAA
1 GGAAAA
35251623 CGATTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.29, T:0.21
Consensus pattern (25 bp):
GGAAAAAACTAAGTTAAGGATTTAG
Found at i:35251830 original size:40 final size:41
Alignment explanation
Indices: 35251712--35251849 Score: 127
Period size: 41 Copynumber: 3.3 Consensus size: 41
35251702 TTTATAGGCG
* * *
35251712 AAACGCCGCTATTGCTTTACCTTTAGTGGCATTTGTGAGAA
1 AAACGCCGCTATTGCTTTACCTTTTGTGGCATTTATGACAA
* * * *
35251753 AAACGCCGCTATCGTTTTTAACCTTTT-TCAGCGTTTATG-CAA
1 AAACGCCGCTATTG-CTTT-ACCTTTTGT-GGCATTTATGACAA
* * **
35251795 AAATGCTGCTATTGCTTTACCTTTTGTGGCATTTATGGGAA
1 AAACGCCGCTATTGCTTTACCTTTTGTGGCATTTATGACAA
*
35251836 AAACACCGCTATTG
1 AAACGCCGCTATTG
35251850 TTGTTATACC
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
40 15 0.20
41 30 0.40
42 17 0.23
43 13 0.17
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (41 bp):
AAACGCCGCTATTGCTTTACCTTTTGTGGCATTTATGACAA
Found at i:35253303 original size:14 final size:15
Alignment explanation
Indices: 35253281--35253357 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
35253271 CAATCAAACA
35253281 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
35253295 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
35253310 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
35253330 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
35253344 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
35253358 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:35253322 original size:20 final size:20
Alignment explanation
Indices: 35253297--35253336 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35253287 AATATTTTCC
*
35253297 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
35253317 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
35253337 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:35253342 original size:34 final size:35
Alignment explanation
Indices: 35253285--35253351 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
35253275 CAAACACCAG
*
35253285 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
35253320 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
35253352 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:35254833 original size:21 final size:21
Alignment explanation
Indices: 35254801--35254840 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35254791 TTTGCTTCAT
*
35254801 CATTCTTGTCCTTGCTCAAGC
1 CATTCTTGTCCTTCCTCAAGC
35254822 CATT-TTGTTCCTTCCTCAA
1 CATTCTTG-TCCTTCCTCAA
35254841 CAGTGGAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.15, C:0.33, G:0.10, T:0.42
Consensus pattern (21 bp):
CATTCTTGTCCTTCCTCAAGC
Found at i:35255476 original size:18 final size:18
Alignment explanation
Indices: 35255419--35255477 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
35255409 AAATAAAAAA
* *
35255419 AATTCGGGTATTTTTCGGT
1 AATTCGGGTA-ATTTGGGT
* * *
35255438 AATTCGGTTAATTCGGTT
1 AATTCGGGTAATTTGGGT
35255456 AATTCGGGTAATTTGGGT
1 AATTCGGGTAATTTGGGT
35255474 AATT
1 AATT
35255478 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
18 23 0.72
19 9 0.28
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.44
Consensus pattern (18 bp):
AATTCGGGTAATTTGGGT
Found at i:35255478 original size:9 final size:9
Alignment explanation
Indices: 35255435--35255477 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
35255425 GGTATTTTTC
35255435 GGTAATTCG
1 GGTAATTCG
*
35255444 GTTAATTCG
1 GGTAATTCG
*
35255453 GTTAATTCG
1 GGTAATTCG
*
35255462 GGTAATTTG
1 GGTAATTCG
35255471 GGTAATT
1 GGTAATT
35255478 TTTAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (9 bp):
GGTAATTCG
Found at i:35255654 original size:12 final size:12
Alignment explanation
Indices: 35255637--35255661 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35255627 AGTAATTTCG
35255637 GGTCGGTTAACC
1 GGTCGGTTAACC
35255649 GGTCGGTTAACC
1 GGTCGGTTAACC
35255661 G
1 G
35255662 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:35259983 original size:10 final size:10
Alignment explanation
Indices: 35259975--35260147 Score: 94
Period size: 10 Copynumber: 17.0 Consensus size: 10
35259965 AGAGGGAAAG
35259975 AAGAAGAAAGA
1 AAGAAG-AAGA
35259986 AAGAA-AAGGA
1 AAGAAGAA-GA
* *
35259996 AAGGAGAGGA
1 AAGAAGAAGA
*
35260006 AAGAAAAAG-
1 AAGAAGAAGA
35260015 AAGAA-AAGGA
1 AAGAAGAA-GA
*
35260025 AAGGAA-AGGA
1 AA-GAAGAAGA
*
35260035 AAGGAGAAGAA
1 AAGAAGAAG-A
35260046 GAAGAAGAAGA
1 -AAGAAGAAGA
35260057 AA-AATGAAAGA
1 AAGAA-G-AAGA
35260068 AA-AAGAAGGA
1 AAGAAGAA-GA
35260078 AAGAA-AAGGA
1 AAGAAGAA-GA
*
35260088 AAGGAGAAGA
1 AAGAAGAAGA
35260098 AA-AAGAAGA
1 AAGAAGAAGA
*
35260107 AAAAAGAAAGA
1 AAGAAG-AAGA
35260118 AA-AAGAAGGA
1 AAGAAGAA-GA
*
35260128 AAGAAAAAGA
1 AAGAAGAAGA
*
35260138 AAGGAGAAGA
1 AAGAAGAAGA
35260148 GAAAAAAAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 35
0.73 0.08 0.19
Matches are distributed among these distances:
8 2 0.02
9 24 0.18
10 63 0.48
11 34 0.26
12 8 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (10 bp):
AAGAAGAAGA
Found at i:35259996 original size:24 final size:24
Alignment explanation
Indices: 35259969--35260205 Score: 149
Period size: 24 Copynumber: 10.0 Consensus size: 24
35259959 GAGAAGAGAG
35259969 GGAAAGAAGAAGAAAGAAAGAAAA
1 GGAAAGAAGAAGAAAGAAAGAAAA
*
35259993 GGAAAG--G-AG-AGGAAAGAAAA
1 GGAAAGAAGAAGAAAGAAAGAAAA
* *
35260013 AG-AAGAA-AAGGAAAGGAAAGGAAA
1 GGAAAGAAGAA-GAAA-GAAAGAAAA
35260037 GGAGAAGAAGAAG-AAG-AAGAAAAA
1 GGA-AAGAAGAAGAAAGAAAG-AAAA
* * *
35260061 TGAAAGAAAAAGAAGGAAAGAAAA
1 GGAAAGAAGAAGAAAGAAAGAAAA
* *
35260085 GGAAAGGAGAAGAAAAAGAAGAAAAA
1 GGAAAGAAGAAGAAAGA-AAG-AAAA
* * *
35260111 AGAAAGAAAAAGAAGGAAAGAAAA
1 GGAAAGAAGAAGAAAGAAAGAAAA
* *
35260135 AGAAAGGAGAAGAGAA-AAA-AAAA
1 GGAAAGAAGAAGA-AAGAAAGAAAA
* *
35260158 GGAAAGGAGAAGAGAA-AAAAAAAA
1 GGAAAGAAGAAGA-AAGAAAGAAAA
*
35260182 GGGAAGGAAGGAA-AAA-AAAGAAAA
1 -GGAAAGAA-GAAGAAAGAAAGAAAA
35260206 AAATAATTTT
Statistics
Matches: 169, Mismatches: 26, Indels: 36
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.02
20 11 0.07
21 3 0.02
22 2 0.01
23 34 0.20
24 70 0.41
25 19 0.11
26 25 0.15
27 2 0.01
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.00
Consensus pattern (24 bp):
GGAAAGAAGAAGAAAGAAAGAAAA
Found at i:35259998 original size:5 final size:5
Alignment explanation
Indices: 35259980--35260039 Score: 61
Period size: 5 Copynumber: 12.4 Consensus size: 5
35259970 GAAAGAAGAA
* * * * *
35259980 GAAA- GAAAG AAAAG GAAAG GAGAG GAAAG AAAAA G-AAG AAAAG GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
35260028 GAAAG GAAAG GA
1 GAAAG GAAAG GA
35260040 GAAGAAGAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
4 6 0.14
5 38 0.86
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:35260020 original size:29 final size:29
Alignment explanation
Indices: 35259975--35260109 Score: 148
Period size: 29 Copynumber: 4.6 Consensus size: 29
35259965 AGAGGGAAAG
*
35259975 AAGAAGAAAGAAAGAAAAGGAAAGGAGAGGA
1 AAGAA-AAAG-AAGAAAAGGAAAGGAAAGGA
35260006 AAGAAAAAGAAGAAAAGGAAAGGAAAGGA
1 AAGAAAAAGAAGAAAAGGAAAGGAAAGGA
* * * *
35260035 AAGGAGAAGAAGAAGAA-G-AAGAAAAATGA
1 AAGAAAAAGAAGAA-AAGGAAAG-GAAAGGA
* *
35260064 AAGAAAAAGAAGGAAAGAAAAGGAAAGGA
1 AAGAAAAAGAAGAAAAGGAAAGGAAAGGA
35260093 GAAGAAAAAGAAGAAAA
1 -AAGAAAAAGAAGAAAA
35260110 AAGAAAGAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
28 5 0.06
29 53 0.61
30 24 0.28
31 5 0.06
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (29 bp):
AAGAAAAAGAAGAAAAGGAAAGGAAAGGA
Found at i:35260050 original size:6 final size:6
Alignment explanation
Indices: 35260039--35260138 Score: 50
Period size: 6 Copynumber: 17.2 Consensus size: 6
35260029 AAAGGAAAGG
* * * *
35260039 AGAAGA AGAAGA AGAAGA AAAATGAA AGAAAA AGAAGG A-AAGA A-AAGG
1 AGAAGA AGAAGA AGAAGA AGAA-G-A AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
35260087 A-AAGG AGAAGA AAAAGA AGAA-A A-AAGAA AGAAAA AGAAGG A-AAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAG-A AGAAGA AGAAGA AGAAGA
*
35260132 AAAAGA A
1 AGAAGA A
35260139 AGGAGAAGAG
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.03
5 19 0.26
6 45 0.62
7 3 0.04
8 4 0.05
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (6 bp):
AGAAGA
Found at i:35260104 original size:50 final size:51
Alignment explanation
Indices: 35260011--35260152 Score: 216
Period size: 50 Copynumber: 2.8 Consensus size: 51
35260001 GAGGAAAGAA
* * *
35260011 AAAGAAGAA-AAGGAAAGGAAAGGAAAGGAGAAGAAGAAGAAGAAGAAAAATG
1 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAG-AGAA-AAGAAGAAAAAAG
35260063 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA-AAAAGAAGAAAAAAG
1 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAGAAGAAAAAAG
*
35260113 AAAGAAAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAA
1 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
35260153 AAAAAGGAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
50 46 0.55
51 6 0.07
52 9 0.11
53 23 0.27
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.01
Consensus pattern (51 bp):
AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAGAAGAAAAAAG
Found at i:35260174 original size:41 final size:40
Alignment explanation
Indices: 35260053--35260176 Score: 118
Period size: 36 Copynumber: 3.2 Consensus size: 40
35260043 GAAGAAGAAG
* * *
35260053 AAGAAAAATGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG-
1 AAGAAAAA-GAAAGGAAAAG-AGAAAAAAAAAGGAAAGGAGA
* *
35260094 AAGAAAAAG-AA-GAAAAAAGAAAGAAAAA-G-AA-G-GA
1 AAGAAAAAGAAAGGAAAAGAGAAAAAAAAAGGAAAGGAGA
*
35260128 AAGAAAAAGAAAGGAGAAGAGAAAAAAAAAGGAAAGGAGA
1 AAGAAAAAGAAAGGAAAAGAGAAAAAAAAAGGAAAGGAGA
35260168 AGAGAAAAA
1 A-AGAAAAA
35260177 AAAAAGGGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
33 1 0.01
34 10 0.15
35 4 0.06
36 15 0.22
37 9 0.13
38 6 0.09
39 3 0.04
40 4 0.06
41 15 0.22
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (40 bp):
AAGAAAAAGAAAGGAAAAGAGAAAAAAAAAGGAAAGGAGA
Found at i:35260187 original size:18 final size:19
Alignment explanation
Indices: 35260131--35260201 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 19
35260121 AGAAGGAAAG
*
35260131 AAAAAGAAAGGAGAAGAGAAA
1 AAAAAAAAAGGAGAAGAG--A
35260152 AAAAAAGGAAAGGAGAAGAGA
1 AAAAAA--AAAGGAGAAGAGA
35260173 AAAAAAAAAGG-GAAG-GA
1 AAAAAAAAAGGAGAAGAGA
35260190 AGGAAAAAAAAG
1 A--AAAAAAAAG
35260202 AAAAAAATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 14 0.31
21 12 0.27
23 12 0.27
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGGAGAAGAGA
Found at i:35260907 original size:7 final size:8
Alignment explanation
Indices: 35260886--35260932 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
35260876 TGAAATAATG
35260886 TAAAATTA
1 TAAAATTA
35260894 TAAAATTA
1 TAAAATTA
35260902 -AAAATTA
1 TAAAATTA
*
35260909 TAATATTTTA
1 TAA-A-ATTA
*
35260919 TAAAATAA
1 TAAAATTA
35260927 TAAAAT
1 TAAAAT
35260933 GCGGAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.21
8 18 0.55
9 2 0.06
10 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAAAATTA
Found at i:35261153 original size:319 final size:311
Alignment explanation
Indices: 35260539--35261307 Score: 1313
Period size: 319 Copynumber: 2.4 Consensus size: 311
35260529 AATTGTATAT
* * * **
35260539 TTAATAAATTTCAAACATAATGCACTGAAGTAATGTAAAATGATAAAATTAAAAATTACGATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
* * *
35260604 TTTTAAAATAATAAAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
66 TTATAAAATAATAAAATGCGGA-GAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAA
*
35260669 ACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATA
130 ACTTTTTTAAAAATTCAGAAATAATAAATACAAATATTTCAAACAAAATGCACTGAAATAATATA
*
35260734 AAATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGGGAAAATAATACGAGCAAAGGG
195 AAATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGAGAAAATAATACGAGCAAAGGG
35260799 CAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
260 CAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
35260851 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
*
35260916 TTATAAAATAATAAAATGCGGAGAAAAAATACGAACAAATGGCTGAAGTAAGAGTGTATTACAAA
66 TTATAAAATAATAAAATGCGGAGAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAAA
35260981 CTTTTTTAAAAATTCAGAAATAATAAATACAAATATTTCAAACAAAATGCACTGGAATAATATAA
131 CTTTTTTAAAAATTCAGAAATAATAAATACAAATATTTCAAACAAAATGCACT-G---AA-AT--
* *
35261046 AATAATAAAATACGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGAGAAAATAATACGAG
189 AAT-ATAAAATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGAGAAAATAATACGAG
35261111 CAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
253 CAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
*
35261170 TTAATAAATTTCAAACATTATGCACTAAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
*
35261235 TTCTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAA
66 TTATAAAATAATAAAATGCGGAG-AAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAA
35261300 ACTTTTTT
130 ACTTTTTT
35261308 TCAACTTGCA
Statistics
Matches: 432, Mismatches: 16, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
311 92 0.21
312 82 0.19
315 2 0.00
316 2 0.00
318 3 0.01
319 203 0.47
320 48 0.11
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (311 bp):
TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
TTATAAAATAATAAAATGCGGAGAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAAA
CTTTTTTAAAAATTCAGAAATAATAAATACAAATATTTCAAACAAAATGCACTGAAATAATATAA
AATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGAGAAAATAATACGAGCAAAGGGC
AGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
Found at i:35261218 original size:162 final size:161
Alignment explanation
Indices: 35260730--35261236 Score: 551
Period size: 162 Copynumber: 3.2 Consensus size: 161
35260720 ACTGAAATAA
* *
35260730 TATAAAATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGGGAAAATAATACGAGCAA
1 TATAAAAT-AGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGAGAAAATAATACGAGCAA
35260795 AGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAATTAATAAAT
65 AGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAATTAATAAAT
35260860 TTCAAACATTATGCACTGAAATAATGTAAAAT
130 TTCAAACATTATGCACTGAAATAATGTAAAAT
* * *
35260892 TATAAAATTA-AAAATTATAATA-TTTTA-T-AAAATAAT-AAAATGCGGAGAAAA-AATACGAA
1 TATAAAA-TAGAAAA-TAAAATATTTTTATTGAAAGTAATAAAAAT-C-GAGAAAATAATACGAG
* * * * * * * * * * * *
35260951 CAAATGGC-TGAAGTAAGAG----TGTATTACA--AACTT-TTTTAAAAATTCAGA-AATAATAA
62 CAAAGGGCAGGGA-TAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAA-ACACACTA-AATTA
** * *
35261007 ATACAAATATTTCAAACAAAATGCACTGGAATAATATAAAAT
124 AT---AA-ATTTCAAACATTATGCACTGAAATAATGTAAAAT
*
35261049 AATAAAATACGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGAGAAAATAATACGAGCAA
1 TATAAAATA-GAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGAGAAAATAATACGAGCAA
35261114 AGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAATTAATAAAT
65 AGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAATTAATAAAT
*
35261179 TTCAAACATTATGCACTAAAATAATGTAAAAT
130 TTCAAACATTATGCACTGAAATAATGTAAAAT
*
35261211 TATAAAATTA-AAAATTATAATATTTT
1 TATAAAA-TAGAAAA-TAAAATATTTT
35261237 CTAAAATAAT
Statistics
Matches: 272, Mismatches: 44, Indels: 58
0.73 0.12 0.16
Matches are distributed among these distances:
152 9 0.03
153 13 0.05
155 7 0.03
156 4 0.01
157 42 0.15
158 16 0.06
159 34 0.12
160 34 0.12
161 20 0.07
162 59 0.22
163 5 0.02
164 7 0.03
166 13 0.05
167 9 0.03
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.29
Consensus pattern (161 bp):
TATAAAATAGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGAGAAAATAATACGAGCAAA
GGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAATTAATAAATT
TCAAACATTATGCACTGAAATAATGTAAAAT
Found at i:35266408 original size:3 final size:3
Alignment explanation
Indices: 35266400--35266458 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
35266390 TAATACTAAG
35266400 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
35266448 AAC AAC AAC AA
1 AAC AAC AAC AA
35266459 TAATAATAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:35266463 original size:3 final size:3
Alignment explanation
Indices: 35266457--35266481 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35266447 CAACAACAAC
35266457 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
35266482 CTAGCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35266770 original size:27 final size:27
Alignment explanation
Indices: 35266725--35266814 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
35266715 GAGTAGTCCT
* *
35266725 GCCAATCAGTATGGAACCATTGGTGCT
1 GCCAATCAGTATGGCACCATTGGTGCC
*
35266752 GCCAACCTCA-T-TGGCACCATCGGTGCC
1 GCCAA--TCAGTATGGCACCATTGGTGCC
*
35266779 GCCAATCAGTATGGCACCTTTGGTGCC
1 GCCAATCAGTATGGCACCATTGGTGCC
35266806 GCCAATCAG
1 GCCAATCAG
35266815 AAACCCTCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 46 0.85
28 1 0.02
29 3 0.06
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (27 bp):
GCCAATCAGTATGGCACCATTGGTGCC
Found at i:35269914 original size:46 final size:45
Alignment explanation
Indices: 35269805--35270252 Score: 450
Period size: 46 Copynumber: 9.6 Consensus size: 45
35269795 CTTACATATG
* *
35269805 ATCACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCT
* *
35269848 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA-GCT
*
35269894 AACACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-AG--
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCT
*
35269932 --CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCT
* * * *
35269976 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG-CTAAGCT
*
35270022 ATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCT
1 ATCACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAG-CTAAGCT
35270074 ATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCT
1 ATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCT-AAGCT
* *
35270126 ATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG-CTAAGCT
*
35270172 ATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCT-AAGCT
* *
35270224 ACCACTTATCGCTTTGTCACTTGATCAGA
1 ATCACTTATCACTTTGTCACTTGATCAGA
35270253 AGTACTCAAA
Statistics
Matches: 352, Mismatches: 23, Indels: 57
0.81 0.05 0.13
Matches are distributed among these distances:
36 29 0.08
38 3 0.01
40 2 0.01
41 1 0.00
42 3 0.01
43 11 0.03
44 7 0.02
45 21 0.06
46 138 0.39
47 2 0.01
48 1 0.00
49 1 0.00
50 2 0.01
51 5 0.01
52 126 0.36
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (45 bp):
ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCT
Found at i:35269937 original size:36 final size:36
Alignment explanation
Indices: 35269896--35270014 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
35269886 CTAAGGCTAA
35269896 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
35269932 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
*
35269974 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
35270014 C
1 C
35270015 CGAAGCTATC
Statistics
Matches: 70, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
36 30 0.43
38 3 0.04
40 3 0.04
42 3 0.04
44 3 0.04
46 28 0.40
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:35269957 original size:82 final size:82
Alignment explanation
Indices: 35269850--35270014 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
35269840 GCTAGGCTAC
*
35269850 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
35269915 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* * *
35269932 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
35269997 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
35270014 C
1 C
35270015 CGAAGCTATC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
TGATCAGATAAGTATAG
Found at i:35270051 original size:52 final size:52
Alignment explanation
Indices: 35269978--35270246 Score: 370
Period size: 52 Copynumber: 5.2 Consensus size: 52
35269968 CTAAAGCTAC
* * *
35269978 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
35270031 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
35270083 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
35270135 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
35270181 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
35270233 CGCTTTGTCACTTG
1 CACTTT-TCACTTG
35270247 ATCAGAAGTA
Statistics
Matches: 192, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
46 42 0.22
52 135 0.70
53 15 0.08
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:35270143 original size:98 final size:98
Alignment explanation
Indices: 35269932--35270252 Score: 438
Period size: 98 Copynumber: 3.3 Consensus size: 98
35269922 ATAAGTATAG
* ** *
35269932 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC--T----TT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
* * *
35269991 GTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
35270024 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
35270089 CCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
60 CCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
35270128 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
* *
35270193 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
*
35270226 CACTTATCGCTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
35270253 AGTACTCAAA
Statistics
Matches: 205, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
92 10 0.05
95 1 0.00
98 150 0.73
100 1 0.00
101 1 0.00
104 42 0.20
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
Found at i:35270211 original size:150 final size:150
Alignment explanation
Indices: 35269946--35270238 Score: 505
Period size: 150 Copynumber: 2.0 Consensus size: 150
35269936 TATCACTTTT
*
35269946 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAGTA
1 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
* * *
35270011 TAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 TAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAC
35270076 CACTTATCACTTTCCACTTG
131 CACTTATCACTTTCCACTTG
* *
35270096 TCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTA
1 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
* *
35270161 TAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 TAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAC
*
35270226 CACTTATCGCTTT
131 CACTTATCACTTT
35270239 GTCACTTGAT
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
150 134 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (150 bp):
TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
TAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAC
CACTTATCACTTTCCACTTG
Found at i:35283375 original size:42 final size:42
Alignment explanation
Indices: 35283316--35283414 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
35283306 CAGTAGCTTC
* *
35283316 ACACGGCCTAGCACATGGTCATGTAAGGCCATTTCGAAGGGT
1 ACACGGCCTGGCACATGGGCATGTAAGGCCATTTCGAAGGGT
*
35283358 ACACGGCCTGGCACATGGGCCTGTAAGGCCATTTCGAAGGGT
1 ACACGGCCTGGCACATGGGCATGTAAGGCCATTTCGAAGGGT
**
35283400 ACACATCCTGGCACA
1 ACACGGCCTGGCACA
35283415 CGAGCGTGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.19
Consensus pattern (42 bp):
ACACGGCCTGGCACATGGGCATGTAAGGCCATTTCGAAGGGT
Found at i:35284327 original size:39 final size:39
Alignment explanation
Indices: 35284217--35284328 Score: 154
Period size: 38 Copynumber: 2.9 Consensus size: 39
35284207 TTAGTTTGAT
*
35284217 TATTTAATTATGTCATAATTTGAACATCATTAATATGAG
1 TATTTAATTATGTCATAATTTGAACATCATTAATAAGAG
* * *
35284256 T-TTTAATTATGTCATAATCTAAATATCATTAATAAGAG
1 TATTTAATTATGTCATAATTTGAACATCATTAATAAGAG
* * *
35284294 TATTTAATTATGTCATAGTTTGGACATCTTTAATA
1 TATTTAATTATGTCATAATTTGAACATCATTAATA
35284329 CATGTTTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
38 34 0.55
39 28 0.45
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.45
Consensus pattern (39 bp):
TATTTAATTATGTCATAATTTGAACATCATTAATAAGAG
Found at i:35284339 original size:39 final size:38
Alignment explanation
Indices: 35284219--35284339 Score: 127
Period size: 39 Copynumber: 3.1 Consensus size: 38
35284209 AGTTTGATTA
*
35284219 TTTAATTATGTCATAATTTGAACATCATTAAT-ATGAGT
1 TTTAATTATGTCATAATTTGAACATCATTAATAATG-TT
* * * * *
35284257 TTTAATTATGTCATAATCTAAATATCATTAATAAGAGTA
1 TTTAATTATGTCATAATTTGAACATCATTAATAA-TGTT
* * *
35284296 TTTAATTATGTCATAGTTTGGACATCTTTAATACATGTT
1 TTTAATTATGTCATAATTTGAACATCATTAATA-ATGTT
35284335 TTTAA
1 TTTAA
35284340 GTGTGTTTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
38 29 0.44
39 35 0.53
40 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (38 bp):
TTTAATTATGTCATAATTTGAACATCATTAATAATGTT
Found at i:35288506 original size:27 final size:27
Alignment explanation
Indices: 35288476--35288527 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
35288466 TTAAAAAAAA
35288476 ATAT-TATCTATAAAAA-AAATATTTAAG
1 ATATCTAT-TATAAAAATAAAT-TTTAAG
*
35288503 ATATCTATTTTAAAAATAAATTTTA
1 ATATCTATTATAAAAATAAATTTTA
35288528 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATCTATTATAAAAATAAATTTTAAG
Found at i:35290355 original size:20 final size:18
Alignment explanation
Indices: 35290308--35290356 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
35290298 CAAGATAAAC
35290308 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
35290325 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
35290345 ATTAAATTAATA
1 ATTAAATTAATA
35290357 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Done.