Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 107 of 120
Found at i:31323696 original size:71 final size:71
Alignment explanation
Indices: 31323572--31323754 Score: 260
Period size: 71 Copynumber: 2.6 Consensus size: 71
31323562 AGGCTATTAC
*
31323572 ACTAGTGCAGGAG-ACATCTACTGTCGGTTTACCCGACTAGCGCTAGGCACAAATATTTATCGAT
1 ACTAGTGCAGG-GCACATCTACTGTCGGTTTACCCAACTAGCGCTAGGCACAAATATTTATCGAT
*
31323636 TTATTTG
65 TTATTTA
* * * * *
31323643 ACTAGTGCAGGGCACATCTACTGTCGGTTTACCTAACTAGTGCTGGGCGCAAATTTTTATCGATT
1 ACTAGTGCAGGGCACATCTACTGTCGGTTTACCCAACTAGCGCTAGGCACAAATATTTATCGATT
31323708 TATTTA
66 TATTTA
* * *
31323714 ACTAGTGCAAGGCACATCTACTGCCGGTTTACCCGACTAGC
1 ACTAGTGCAGGGCACATCTACTGTCGGTTTACCCAACTAGC
31323755 ACTGAGCACA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
70 1 0.01
71 98 0.99
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (71 bp):
ACTAGTGCAGGGCACATCTACTGTCGGTTTACCCAACTAGCGCTAGGCACAAATATTTATCGATT
TATTTA
Found at i:31324625 original size:22 final size:21
Alignment explanation
Indices: 31324580--31324625 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
31324570 ATTGACATAT
*
31324580 TTTGAGTTGTTTTAAAGTGTA
1 TTTGAGTTGTTTTAAAATGTA
31324601 TTTGATGTTGTTTATAAAATG-A
1 TTTGA-GTTGTTT-TAAAATGTA
31324623 TTT
1 TTT
31324626 TAGGCTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 11 0.50
23 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTTGAGTTGTTTTAAAATGTA
Found at i:31326402 original size:15 final size:15
Alignment explanation
Indices: 31326382--31326415 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31326372 GGAGATAGCC
*
31326382 ATGATGATAAAGACG
1 ATGATGACAAAGACG
*
31326397 ATGATGACAAAGATG
1 ATGATGACAAAGACG
31326412 ATGA
1 ATGA
31326416 GAGGCATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.26, T:0.21
Consensus pattern (15 bp):
ATGATGACAAAGACG
Found at i:31328524 original size:19 final size:18
Alignment explanation
Indices: 31328519--31328564 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
31328509 ATATTTATTC
31328519 TTTTTATAAATTTTATATA
1 TTTTTA-AAATTTTATATA
*
31328538 TTTTTAAATAATTT-TA-A
1 TTTTTAAA-ATTTTATATA
31328555 TTTTTAAAAT
1 TTTTTAAAAT
31328565 GGTTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 9 0.38
18 4 0.17
19 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTAAAATTTTATATA
Found at i:31328803 original size:20 final size:20
Alignment explanation
Indices: 31328766--31328804 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31328756 GAGCACTGTA
*
31328766 GTGTTAACAGGAGCACAAAT
1 GTGTTAACAAGAGCACAAAT
* *
31328786 GTGTTATCAAGAGTACAAA
1 GTGTTAACAAGAGCACAAA
31328805 AAGTACTATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (20 bp):
GTGTTAACAAGAGCACAAAT
Found at i:31331852 original size:29 final size:28
Alignment explanation
Indices: 31331806--31331863 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
31331796 CTGAACATAT
31331806 TATGTTATAAAAATATTATATTAATTATA
1 TATGTTATAAAAATATTATA-TAATTATA
* *
31331835 TATGTTA-AATAATAATTATATATTTATA
1 TATGTTATAAAAAT-ATTATATAATTATA
31331863 T
1 T
31331864 TTATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TATGTTATAAAAATATTATATAATTATA
Found at i:31332061 original size:38 final size:38
Alignment explanation
Indices: 31331972--31332060 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
31331962 AAAAATTATA
* * *
31331972 TTTAATACAATAAAATATTTATTATATTTATTTGTGTT
1 TTTAATATAATAAAATATTTATTATATTTATTAGTATT
31332010 TTTAATATAATAAAATATTTATTATATTTATGGTAGTATTT
1 TTTAATATAATAAAATATTTATTATATTTAT--TAGTA-TT
31332051 TTTAATATAA
1 TTTAATATAA
31332061 ATACTATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 30 0.67
40 3 0.07
41 12 0.27
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (38 bp):
TTTAATATAATAAAATATTTATTATATTTATTAGTATT
Found at i:31333575 original size:5 final size:5
Alignment explanation
Indices: 31333565--31333593 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31333555 TATTAAATAT
31333565 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
31333594 TATATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:31334188 original size:21 final size:21
Alignment explanation
Indices: 31334162--31334204 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31334152 ACAACTCAAA
* *
31334162 ATTATTATTATTGTTGGTAAT
1 ATTATTACTATTGTTGATAAT
*
31334183 ATTATTACTGTTGTTGATAAT
1 ATTATTACTATTGTTGATAAT
31334204 A
1 A
31334205 ATAATATTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.53
Consensus pattern (21 bp):
ATTATTACTATTGTTGATAAT
Found at i:31334215 original size:21 final size:21
Alignment explanation
Indices: 31334167--31334215 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
31334157 TCAAAATTAT
* * * *
31334167 TATTATTGTTGGTAATATTAT
1 TATTGTTGTTGATAATAATAA
*
31334188 TACTGTTGTTGATAATAATAA
1 TATTGTTGTTGATAATAATAA
31334209 TATTGTT
1 TATTGTT
31334216 ATTAGTATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (21 bp):
TATTGTTGTTGATAATAATAA
Found at i:31346302 original size:11 final size:11
Alignment explanation
Indices: 31346284--31346316 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
31346274 GACAAAAAAA
31346284 TCTT-CTATTT
1 TCTTGCTATTT
31346294 TCTTGCTATTT
1 TCTTGCTATTT
*
31346305 TGTTGCTATTT
1 TCTTGCTATTT
31346316 T
1 T
31346317 TTTTGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.09, C:0.15, G:0.09, T:0.67
Consensus pattern (11 bp):
TCTTGCTATTT
Found at i:31347106 original size:61 final size:61
Alignment explanation
Indices: 31347041--31347170 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 61
31347031 AAAATTATGT
* * * * * * *
31347041 TAAAAATTTTAACGAATTT-ATCCTTTAATGTTTACAAAATTTATCATTTTAGTTC-TCATTC
1 TAAAAATTTCAACAAATTTGA-CCCTTAATATTTACAAAATTTATCAATTTA-TTCTTAACTC
* * *
31347102 TAAAAAATTCAATAAATTTGACCCTTAATATTTACAAAATTTTTCAATTTATTCTTAACTC
1 TAAAAATTTCAACAAATTTGACCCTTAATATTTACAAAATTTATCAATTTATTCTTAACTC
31347163 TAAAAATT
1 TAAAAATT
31347171 AAAATATATT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
60 3 0.05
61 52 0.93
62 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (61 bp):
TAAAAATTTCAACAAATTTGACCCTTAATATTTACAAAATTTATCAATTTATTCTTAACTC
Found at i:31347601 original size:23 final size:24
Alignment explanation
Indices: 31347575--31347628 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
31347565 AAAAAAAATC
**
31347575 TTAAAAATTA-CAGTAAAATATTT
1 TTAAAAATTATCAAAAAAATATTT
*
31347598 TTAAAAATTATTAAAAAAATATTT
1 TTAAAAATTATCAAAAAAATATTT
31347622 TTAAAAA
1 TTAAAAA
31347629 ATAAATTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
TTAAAAATTATCAAAAAAATATTT
Found at i:31347604 original size:24 final size:22
Alignment explanation
Indices: 31347556--31347630 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 22
31347546 ACCATAATTC
* *
31347556 TAAAAAAATAAAAAAA-A-TCT
1 TAAAAAATTAAAAAAATATTTT
*
31347576 T-AAAAATTACAGTAAAATATTTT
1 TAAAAAATTA-A-AAAAATATTTT
31347599 TAAAAATTATTAAAAAAATATTTT
1 TAAAAA--ATTAAAAAAATATTTT
31347623 TAAAAAAT
1 TAAAAAAT
31347631 AAATTTGCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
19 7 0.16
20 2 0.05
21 4 0.09
22 3 0.07
23 3 0.07
24 20 0.45
25 1 0.02
26 4 0.09
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (22 bp):
TAAAAAATTAAAAAAATATTTT
Found at i:31347630 original size:13 final size:13
Alignment explanation
Indices: 31347589--31347631 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
31347579 AAATTACAGT
31347589 AAAATATTTTT-A
1 AAAATATTTTTAA
* *
31347601 AAAAT-TATTAAA
1 AAAATATTTTTAA
31347613 AAAATATTTTTAA
1 AAAATATTTTTAA
31347626 AAAATA
1 AAAATA
31347632 AATTTGCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 3 0.12
12 11 0.44
13 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATATTTTTAA
Found at i:31354498 original size:18 final size:19
Alignment explanation
Indices: 31354459--31354498 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
31354449 TTCAACAATG
* *
31354459 ACAATATCTAAAATCTTGA
1 ACAATATCTAAAAACTTCA
31354478 ACAATA-CTAAAAACTTCA
1 ACAATATCTAAAAACTTCA
31354496 ACA
1 ACA
31354499 TGAGCCGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.25
Consensus pattern (19 bp):
ACAATATCTAAAAACTTCA
Found at i:31354986 original size:2 final size:2
Alignment explanation
Indices: 31354981--31355005 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31354971 TTAAAAAACA
31354981 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31355006 AATGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31355490 original size:145 final size:145
Alignment explanation
Indices: 31355303--31355581 Score: 395
Period size: 149 Copynumber: 1.9 Consensus size: 145
31355293 TTTATTTAAA
31355303 AAAAAAGAGAAAGTTTAGATTTTAAAACTAAAAATAATTTTTTAATCATTTTAAAGG-AAAGTTT
1 AAAAAAGAGAAAGTTTAGATTTTAAAACTAAAAATAATTTTTTAATCA-TTTAAAGGAAAAGTTT
* *
31355367 AAA-TTTTTAAAACAAAA-TTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTTGATCTTTAA
65 AAATTTTTTAAAA-AAAAGTTTTAATCTTTTTCAACTATTTCAAAATAAAA-CTTTGATCTTTAA
31355430 GAAAAATGGTGGTTTTTT
128 GAAAAATGGTGGTTTTTT
* *
31355448 AAAAAAGAGAAAGTTTAGATTTTTAAAA-TAAAAATCTATTTTTTAGTCATTTAAAGGAAAAGTT
1 AAAAAAGAGAAAGTTTAGA-TTTTAAAACTAAAAAT-AATTTTTTAATCATTTAAAGGAAAAGTT
* * * *
31355512 TAAATTTTTTTTAAAAAAAAGTTTTAATCTTTTTCAACTATTTCTAAATAAAATTTTTATTTTTA
64 TAAA--TTTTTTAAAAAAAAGTTTTAATCTTTTTCAACTATTTCAAAATAAAACTTTGATCTTTA
31355577 AGAAA
127 AGAAA
31355582 GTAGTGATTT
Statistics
Matches: 119, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
145 34 0.29
146 29 0.24
148 18 0.15
149 38 0.32
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (145 bp):
AAAAAAGAGAAAGTTTAGATTTTAAAACTAAAAATAATTTTTTAATCATTTAAAGGAAAAGTTTA
AATTTTTTAAAAAAAAGTTTTAATCTTTTTCAACTATTTCAAAATAAAACTTTGATCTTTAAGAA
AAATGGTGGTTTTTT
Found at i:31355600 original size:145 final size:144
Alignment explanation
Indices: 31355304--31355628 Score: 380
Period size: 145 Copynumber: 2.3 Consensus size: 144
31355294 TTATTTAAAA
31355304 AAAAAGAGAAAGTTTAGA-TTTTAAAACTAAAAATAATTTTTTAATCATTTTAAAGGAAAGTTTA
1 AAAAAGAGAAAGTTTAGATTTTTAAAA-TAAAAATAATTTTTTAATCATTTTAAAGGAAAGTTTA
* *
31355368 AATTTTTAAAACAAAATTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTTGATCTTTAAGAA
65 AATTTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCAAAATAAAAGCTTTGATCTTTAAGAA
* *
31355433 AAATGGTGGTTTTTT
130 AAATAGTGATTTTTT
* *
31355448 AAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATCTATTTTTTAGTCA-TTTAAAGGAAAAGTT
1 -AAAAAGAGAAAGTTTAGATTTTTAAAATAAAAAT-AATTTTTTAATCATTTTAAAGG-AAAGTT
* * * *
31355512 TAAATTTTTTTTAAAA-AAAAGTTTTAATCTTTTTCAACTATTTCTAAATAAAA-TTTTTATTTT
63 TAAA---TTTTTAAAACAAAA-TTTTAATCTTTTTCAACTATTTCAAAATAAAAGCTTTGATCTT
*
31355575 TAAG-AAAGTAGTGATTTTTT
124 TAAGAAAAATAGTGATTTTTT
* * * *
31355595 -TAAAGA-AAA-TTTTGATTTTGAAAA-AAAAAAAATT
1 AAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATAATT
31355629 GGCCACCGTA
Statistics
Matches: 157, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
141 3 0.02
142 5 0.03
143 13 0.08
144 3 0.02
145 38 0.24
146 29 0.18
147 13 0.08
148 15 0.10
149 38 0.24
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (144 bp):
AAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATAATTTTTTAATCATTTTAAAGGAAAGTTTAA
ATTTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCAAAATAAAAGCTTTGATCTTTAAGAAA
AATAGTGATTTTTT
Found at i:31356943 original size:3 final size:3
Alignment explanation
Indices: 31356937--31356971 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31356927 TTAATCTTTA
31356937 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31356972 AGAATCGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31360564 original size:28 final size:28
Alignment explanation
Indices: 31360532--31360603 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
31360522 TTTAATAAGT
* *
31360532 TCGCACATTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* * *
31360560 TCGCACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
31360588 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
31360604 AATCTCATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:31362823 original size:24 final size:23
Alignment explanation
Indices: 31362771--31362842 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
31362761 CCTGTTAAGT
*
31362771 GCTCTTCGGAGCTACCCATTAATTA
1 GCTCTTCGGAGTTACCCATT-A-TA
31362796 -CTCTTCGGAGTTACCCATTATA
1 GCTCTTCGGAGTTACCCATTATA
*
31362818 GGCTCTTTGTGAGCTT-CCCATTATA
1 -GCTCTTCG-GAG-TTACCCATTATA
31362843 TTGCCTGGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 2 0.05
23 1 0.02
24 24 0.59
25 12 0.29
26 2 0.05
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (23 bp):
GCTCTTCGGAGTTACCCATTATA
Found at i:31366007 original size:12 final size:12
Alignment explanation
Indices: 31365986--31366015 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31365976 GGTTTTCTCA
31365986 AAATGAAAATGG
1 AAATGAAAATGG
*
31365998 AAATGGAAATGG
1 AAATGAAAATGG
31366010 AAATGA
1 AAATGA
31366016 GAATTGAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (12 bp):
AAATGAAAATGG
Found at i:31382939 original size:15 final size:16
Alignment explanation
Indices: 31382914--31382944 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
31382904 TATATCCTTT
31382914 ATAATTGATAAAATTA
1 ATAATTGATAAAATTA
31382930 ATAA-TGATAAAATTA
1 ATAATTGATAAAATTA
31382945 TATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATAATTGATAAAATTA
Found at i:31386029 original size:128 final size:126
Alignment explanation
Indices: 31385577--31386031 Score: 698
Period size: 126 Copynumber: 3.6 Consensus size: 126
31385567 TTTTTAAGAT
* ** * * * *
31385577 AACGCTTCTAGCATGATGTTTTATGAGAAGAATTTGTGAAATTGCGCCCTCGTGGACGTGCTTTT
1 AACGCTTCTAGCAGGATGCGTTATGAAAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTT
* *
31385642 GCTATAGTTGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAA
66 GCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAA
*
31385703 AACGCTTCTAGCAGGATGCGTTAT-AAGAAGAATTTGTGAAATCGCGCCCATGTGGACGCGCTTT
1 AACGCTTCTAGCAGGATGCGTTATGAA-AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTT
*
31385767 TGCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGATGTTTCTGAGCGAATAGTATAAAA
65 TGCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAA
* *
31385829 AACGCTTCTACCAGGATGCGTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTT
1 AACGCTTCTAGCAGGATGCGTTATGAAAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTT
** * *
31385894 GCTACAGTAGGTCCTGGAAAAAATAATGCCGAGTTGACATTTCTGAGCAAATAGTATAAAAAA
66 GCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTAT--AAAA
*
31385957 AACGCTTCCT-GCAGGATGCTTTATGAAAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTT
1 AACGCTT-CTAGCAGGATGCGTTATGAAAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTT
31386021 TGCTACAGTAG
65 TGCTACAGTAG
31386032 CATGTTCGGG
Statistics
Matches: 302, Mismatches: 22, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
125 1 0.00
126 225 0.75
127 1 0.00
128 73 0.24
129 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (126 bp):
AACGCTTCTAGCAGGATGCGTTATGAAAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTT
GCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAA
Found at i:31389090 original size:53 final size:53
Alignment explanation
Indices: 31389033--31389418 Score: 650
Period size: 53 Copynumber: 7.3 Consensus size: 53
31389023 TATTTTTTTC
* *
31389033 AATTATTAATTGATAATTGTATTGATGGTTAGTAAAATTATCAAATTATATCT
1 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCA
31389086 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTTAT-AAATTATATCA
1 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAA-TTATCAAATTATATCA
* * * *
31389139 AATTATTAATTGATCATTGTAGTAATGGTTAGTAAAATCATCAAATTATATCT
1 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCA
31389192 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATT-TACAAATTATATCA
1 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTAT-CAAATTATATCA
*
31389245 AATTATTAATTGATAATTGTAGTAATGGTTAGTAAAATTATCAAATTATATCA
1 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCA
*
31389298 AATTATTAATTGATAATTGTAGTAATGGTTAGTAAAATTATCAAATTATATCA
1 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCA
**
31389351 AATTATTAATTGATAATTGTATTAATATTTAGTAAAATTATCAAATTATATCA
1 AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCA
31389404 AATTATTAATTGATA
1 AATTATTAATTGATA
31389419 GTACCGGTCA
Statistics
Matches: 315, Mismatches: 14, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
52 4 0.01
53 306 0.97
54 5 0.02
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (53 bp):
AATTATTAATTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCA
Found at i:31389355 original size:18 final size:17
Alignment explanation
Indices: 31389332--31389409 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 17
31389322 ATGGTTAGTA
31389332 AAATTATCAAATTATATC
1 AAATTATCAAATT-TATC
* *
31389350 AAATTAT-TAATTGAT-
1 AAATTATCAAATTTATC
* * *
31389365 AATTGTATTAATATTTAGTA
1 AAAT-TATCAA-ATTTA-TC
31389385 AAATTATCAAATTATATC
1 AAATTATCAAATT-TATC
31389403 AAATTAT
1 AAATTAT
31389410 TAATTGATAG
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
15 3 0.07
16 5 0.11
17 5 0.11
18 22 0.48
19 8 0.17
20 3 0.07
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (17 bp):
AAATTATCAAATTTATC
Found at i:31389548 original size:21 final size:21
Alignment explanation
Indices: 31389515--31389696 Score: 91
Period size: 21 Copynumber: 8.2 Consensus size: 21
31389505 TCAAATTATA
* *
31389515 TTTAAGTTAAGGGTTAGGGTT
1 TTTAGGTTTAGGGTTAGGGTT
*
31389536 TTTAGGTTTAGGGTTTAGGATTT
1 TTTAGGTTTAGGG-TTAGG-GTT
* *
31389559 TTTA-GTTAAAGGTTTAGGAG-T
1 TTTAGGTT-TAGGGTTAGG-GTT
*
31389580 TTTAGGTTTAAGGTTAGGGTTT
1 TTTAGGTTTAGGGTTAGGG-TT
**
31389602 TTTA-GTTTATGATTTAGGGTT
1 TTTAGGTTTA-GGGTTAGGGTT
* * *
31389623 TTTAAGTTAAGGGTTTAAAGTTTAGGGT
1 TTTAGGTTTAGGG-TT--AG----GGTT
* * *
31389651 TTAAGATTTAGGGTTTGGGTT
1 TTTAGGTTTAGGGTTAGGGTT
*
31389672 TTTAGGTTTAGGGTTAGTGTT
1 TTTAGGTTTAGGGTTAGGGTT
31389693 TTTA
1 TTTA
31389697 ATTTAAAGGC
Statistics
Matches: 120, Mismatches: 26, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
20 1 0.01
21 59 0.49
22 34 0.28
23 9 0.08
24 2 0.02
25 1 0.01
27 2 0.02
28 12 0.10
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (21 bp):
TTTAGGTTTAGGGTTAGGGTT
Found at i:31389559 original size:22 final size:21
Alignment explanation
Indices: 31389519--31389639 Score: 86
Period size: 22 Copynumber: 5.6 Consensus size: 21
31389509 ATTATATTTA
*
31389519 AGTTAAGGG-TTAGGGTTTTT
1 AGTTAAGGGTTTAGGATTTTT
*
31389539 AGGTTTAGGGTTTAGGATTTTTT
1 A-GTTAAGGGTTTAGGA-TTTTT
* *
31389562 AGTTAAAGGTTTAGGAGTTTT
1 AGTTAAGGGTTTAGGATTTTT
*
31389583 AGGTTTAA-GG-TTAGGGTTTTTT
1 A-G-TTAAGGGTTTA-GGATTTTT
* * * *
31389605 AGTTTATGATTTAGGGTTTTT
1 AGTTAAGGGTTTAGGATTTTT
31389626 AAGTTAAGGGTTTA
1 -AGTTAAGGGTTTA
31389640 AAGTTTAGGG
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.05
21 24 0.30
22 41 0.52
23 10 0.13
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
AGTTAAGGGTTTAGGATTTTT
Found at i:31389597 original size:43 final size:43
Alignment explanation
Indices: 31389519--31389639 Score: 122
Period size: 43 Copynumber: 2.8 Consensus size: 43
31389509 ATTATATTTA
*
31389519 AGTTAAGGGTTAGGGTTTTTAGGTTTAGGGTTTAGGATTTTTT
1 AGTTAAGGGTTAGGGTTTTTAGGTTTAAGGTTTAGGATTTTTT
* *
31389562 AGTTAAAGGTTTAGGAG-TTTTAGGTTTAAGG-TTAGGGTTTTTT
1 AGTT-AAGGGTTAGG-GTTTTTAGGTTTAAGGTTTAGGATTTTTT
* ** *
31389605 AGTTTATGATTTAGGGTTTTTAAG-TTAAGGGTTTA
1 AG-TTAAGGGTTAGGGTTTTTAGGTTTAA-GGTTTA
31389640 AAGTTTAGGG
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
42 5 0.08
43 33 0.50
44 27 0.41
45 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (43 bp):
AGTTAAGGGTTAGGGTTTTTAGGTTTAAGGTTTAGGATTTTTT
Found at i:31389601 original size:65 final size:63
Alignment explanation
Indices: 31389521--31389666 Score: 168
Period size: 65 Copynumber: 2.2 Consensus size: 63
31389511 TATATTTAAG
* * *
31389521 TTAAGGGTTAGGGTTTTTAGGTTTAGGGTTTAGGATTTTTTAGTTAAAGGTTTAGGAGTTTTA-G
1 TTAA-GGTTAGGGTTTTTA-GTTTAGGATTTAGGATTTTTAAGTTAAAGGTTTA-AAG-TTTAGG
31389585 GT
62 GT
* * *
31389587 TTAAGGTTAGGGTTTTTTAGTTTATGATTTAGGGTTTTTAAGTTAAGGGTTTAAAGTTTAGGGT
1 TTAAGGTTAGGG-TTTTTAGTTTAGGATTTAGGATTTTTAAGTTAAAGGTTTAAAGTTTAGGGT
*
31389651 TTAAGATTTAGGGTTT
1 TTAAG-GTTAGGGTTT
31389667 GGGTTTTTAG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
63 4 0.06
64 13 0.19
65 43 0.61
66 10 0.14
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (63 bp):
TTAAGGTTAGGGTTTTTAGTTTAGGATTTAGGATTTTTAAGTTAAAGGTTTAAAGTTTAGGGT
Found at i:31389649 original size:14 final size:13
Alignment explanation
Indices: 31389623--31389666 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
31389613 ATTTAGGGTT
*
31389623 TTTAAGTTAAGGG
1 TTTAAGTTTAGGG
31389636 TTTAAAGTTTAGGG
1 TTT-AAGTTTAGGG
31389650 TTTAAGATTTAGGG
1 TTTAAG-TTTAGGG
31389664 TTT
1 TTT
31389667 GGGTTTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (13 bp):
TTTAAGTTTAGGG
Found at i:31389753 original size:22 final size:21
Alignment explanation
Indices: 31389719--31389862 Score: 74
Period size: 22 Copynumber: 6.6 Consensus size: 21
31389709 TGGTTTCAAA
*
31389719 AGTTTAGGATTTAAGGTTTTTT
1 AGTTAAGG-TTTAAGGTTTTTT
* *
31389741 AGTTAAAGGTTTATGGTTTTTA
1 AGTT-AAGGTTTAAGGTTTTTT
* * **
31389763 AGTTTAAAGTTTAGGGTTTTAG
1 AG-TTAAGGTTTAAGGTTTTTT
* * * **
31389785 GGTTTAGAGTTTATGG-TTTCA
1 AGTTAAG-GTTTAAGGTTTTTT
* *
31389806 AGTTAAAAGTTTAAGGTTTTTA
1 AGTT-AAGGTTTAAGGTTTTTT
*
31389828 AGTTAAGAGTTTAGGGTTTTTT
1 AGTTAAG-GTTTAAGGTTTTTT
* *
31389850 AATTAAGGGTTAA
1 AGTTAAGGTTTAA
31389863 AGATTTTAAG
Statistics
Matches: 92, Mismatches: 24, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
21 22 0.24
22 65 0.71
23 5 0.05
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.47
Consensus pattern (21 bp):
AGTTAAGGTTTAAGGTTTTTT
Found at i:31389837 original size:43 final size:43
Alignment explanation
Indices: 31389728--31389846 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 43
31389718 AAGTTTAGGA
* * *
31389728 TTTAAGGTTTTTTAGTTAA-AGGTTTATGGTTTTTAAGTTTAAAG
1 TTTAAGGTTTTTAAGTTAAGA-GTTTATGG-TTTCAAGTTAAAAG
* * *
31389772 TTT-AGGGTTTTAGGGTTTAGAGTTTATGGTTTCAAGTTAAAAG
1 TTTAAGGTTTTTA-AGTTAAGAGTTTATGGTTTCAAGTTAAAAG
*
31389815 TTTAAGGTTTTTAAGTTAAGAGTTTAGGGTTT
1 TTTAAGGTTTTTAAGTTAAGAGTTTATGGTTT
31389847 TTTAATTAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
43 38 0.61
44 23 0.37
45 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (43 bp):
TTTAAGGTTTTTAAGTTAAGAGTTTATGGTTTCAAGTTAAAAG
Found at i:31389874 original size:65 final size:65
Alignment explanation
Indices: 31389736--31389874 Score: 145
Period size: 65 Copynumber: 2.1 Consensus size: 65
31389726 GATTTAAGGT
* * * ** * * * *
31389736 TTTTTAGTTAAAGGTTTATGGTTTTTAAGTTTAAAGTTTAGGGTTTTAGGGTTTAGAGTTTATGG
1 TTTTAAGTTAAAAGTTTAAGGTTTTTAAGTTTAAAGTTTAGGGTTTTAGAATTAAGAGTTAAAGA
* ** *
31389801 TTTCAAGTTAAAAGTTTAAGGTTTTTAAG-TTAAGAGTTTAGGGTTTTTTAATTAAGGGTTAAAG
1 TTTTAAGTTAAAAGTTTAAGGTTTTTAAGTTTAA-AGTTTAGGGTTTTAGAATTAAGAGTTAAAG
31389865 A
65 A
31389866 TTTTAAGTT
1 TTTTAAGTT
31389875 TAGGGTTAGT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
64 4 0.07
65 55 0.93
ACGTcount: A:0.28, C:0.01, G:0.23, T:0.48
Consensus pattern (65 bp):
TTTTAAGTTAAAAGTTTAAGGTTTTTAAGTTTAAAGTTTAGGGTTTTAGAATTAAGAGTTAAAGA
Found at i:31389910 original size:20 final size:20
Alignment explanation
Indices: 31389846--31389912 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
31389836 GTTTAGGGTT
*
31389846 TTTTAA-TTAAGGGTTAAAGA
1 TTTTAATTTAAGGGTT-AGGA
*
31389866 TTTTAAGTTT-AGGGTTAGTGT
1 TTTTAA-TTTAAGGGTTAG-GA
*
31389887 TTTTAATTTAAAGGTTAGGA
1 TTTTAATTTAAGGGTTAGGA
31389907 TTTTAA
1 TTTTAA
31389913 AGGTTTAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 17 0.44
21 20 0.51
22 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (20 bp):
TTTTAATTTAAGGGTTAGGA
Found at i:31389971 original size:23 final size:21
Alignment explanation
Indices: 31389736--31389977 Score: 72
Period size: 22 Copynumber: 11.1 Consensus size: 21
31389726 GATTTAAGGT
31389736 TTTTTAGTTAAAGGTTTATGG-
1 TTTTTAGTTAAAGGTTTA-GGA
31389757 TTTTTAAGTTTAAA-GTTTAGG-
1 TTTTT-AG-TTAAAGGTTTAGGA
* *
31389778 GTTTTAGGGTT-TAGAGTTTATGG-
1 TTTTTA--GTTAAAG-GTTTA-GGA
** *
31389801 TTTCAAGTTAAAAGTTTAAGG-
1 TTTTTAGTTAAAGGTTT-AGGA
*
31389822 TTTTTAAGTT-AAGAGTTTAGGGT
1 TTTTT-AGTTAAAG-GTTTA-GGA
* * * *
31389845 TTTTTAATTAAGGGTTAAAGA
1 TTTTTAGTTAAAGGTTTAGGA
* * *
31389866 TTTTAAGTT-TAGGGTTAGTG-
1 TTTTTAGTTAAAGGTTTAG-GA
*
31389886 TTTTTAATTTAAAGG-TTAGGA
1 TTTTT-AGTTAAAGGTTTAGGA
* * * *
31389907 TTTTAAAGGTTTAAGATTTAGGG
1 TTTT-TA-GTTAAAGGTTTAGGA
*
31389930 TTTTTTAGTTAAAGGTTTATGA
1 TTTT-TAGTTAAAGGTTTAGGA
*
31389952 TTTTTAGGTTTAAGGTTTTAGGA
1 TTTTTA-GTTAAAGG-TTTAGGA
31389975 TTT
1 TTT
31389978 AGGTTTTTAG
Statistics
Matches: 160, Mismatches: 38, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
20 11 0.07
21 51 0.32
22 62 0.39
23 36 0.22
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (21 bp):
TTTTTAGTTAAAGGTTTAGGA
Found at i:31389972 original size:14 final size:14
Alignment explanation
Indices: 31389942--31389990 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
31389932 TTTTAGTTAA
*
31389942 AGGTTTATGATTTTT
1 AGGTTTA-GGTTTTT
31389957 AGGTTTAAGG-TTTT
1 AGGTTT-AGGTTTTT
31389971 AGGATTTAGGTTTTT
1 AGG-TTTAGGTTTTT
31389986 AGGTT
1 AGGTT
31389991 AAGAGGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 12 0.40
15 17 0.57
16 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (14 bp):
AGGTTTAGGTTTTT
Found at i:31390092 original size:22 final size:22
Alignment explanation
Indices: 31389960--31390280 Score: 118
Period size: 22 Copynumber: 14.0 Consensus size: 22
31389950 GATTTTTAGG
*
31389960 TTTAAGGTTTTAGGATTTA-GGTT
1 TTTAA-GTTTAAGG-TTTAGGGTT
* * *
31389983 TTT-AGGTTAAGAGGTTAAGGTT
1 TTTAAGTTTAAG-GTTTAGGGTT
* * *
31390005 TTTTAGTTTATGCTTTAGGGTT
1 TTTAAGTTTAAGGTTTAGGGTT
* * *
31390027 TTT-AGGTTAAGAATTTAAGGTT
1 TTTAAGTTTAAG-GTTTAGGGTT
* *
31390049 TTT-AGGTTAAGGTTTTATGGTT
1 TTTAAGTTTAAGG-TTTAGGGTT
31390071 TTTAAGTTTAAGGTTTAGGGTTTAT
1 TTTAAGTTTAAGGTTTAGGG--T-T
* *
31390096 AGTTTTAGGTTAAGAGTTTAGGGTT
1 --TTTAAGTTTAAG-GTTTAGGGTT
* * *
31390121 TTTTAA-TTTATGGTTTAAGATT
1 T-TTAAGTTTAAGGTTTAGGGTT
* *
31390143 TTTAAG-TTAAGAGTTTCGGTTT
1 TTTAAGTTTAAG-GTTTAGGGTT
* * * *
31390165 TTTTAGTTAAAAG-TTAGGGGT
1 TTTAAGTTTAAGGTTTAGGGTT
* * *
31390186 TTTAGGTTTAGGGTTAATATTAGTGTT
1 TTTAAGTTTAAGG----T-TTAGGGTT
*
31390213 TTTAA-TTTAAGGGTTAGGGTT
1 TTTAAGTTTAAGGTTTAGGGTT
* * **
31390234 TTAAGAGTTTAGGGTTTATAGTT
1 TTTA-AGTTTAAGGTTTAGGGTT
*
31390257 TTTAGGTTTAAGGGTTTAGGGTT
1 TTTAAGTTTAA-GGTTTAGGGTT
31390280 T
1 T
31390281 ATATTTTTAG
Statistics
Matches: 219, Mismatches: 54, Indels: 50
0.68 0.17 0.15
Matches are distributed among these distances:
21 45 0.21
22 83 0.38
23 50 0.23
24 4 0.02
25 2 0.01
26 7 0.03
27 20 0.09
28 8 0.04
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.50
Consensus pattern (22 bp):
TTTAAGTTTAAGGTTTAGGGTT
Found at i:31390105 original size:21 final size:20
Alignment explanation
Indices: 31390071--31390115 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
31390061 TTTTATGGTT
* *
31390071 TTTAAGTTTAAGGTTTAGGG
1 TTTAAGTTTAAGGTTAAGAG
*
31390091 TTTATAGTTTTAGGTTAAGAG
1 TTTA-AGTTTAAGGTTAAGAG
31390112 TTTA
1 TTTA
31390116 GGGTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (20 bp):
TTTAAGTTTAAGGTTAAGAG
Found at i:31390123 original size:116 final size:117
Alignment explanation
Indices: 31389917--31390175 Score: 314
Period size: 116 Copynumber: 2.2 Consensus size: 117
31389907 TTTTAAAGGT
* * *
31389917 TTAAG-ATTTAGGGTTTTTTAGTTAAAGGTTTATGATTTTTAGGTTTAAGGTTTTAGGATTTAGG
1 TTAAGAATTTAAGGTTTTTTAGTTAAAGGTTTATGATTTTTAAGTTTAAGGTTTTAGGATTTAAG
* * * *
31389981 TTTTTAGGTTAAGAGGTTAAGGTTTTTTAGTTTATGCTTTAGGGTTTTTAGG
66 TTTTTAGGTTAAGAGGTTAAGGTTTTTTAATTTATGCTTTAAGATTTTTAAG
* *
31390033 TTAAGAATTTAAGG-TTTTTAGGTT-AAGGTTTTATGGTTTTTAAGTTTAAGG-TTTAGGGTTTA
1 TTAAGAATTTAAGGTTTTTTA-GTTAAAGG-TTTATGATTTTTAAGTTTAAGGTTTTAGGATTTA
* * *
31390095 TAG-TTTTAGGTTAAGAGTTTAGGGTTTTTTAATTTATGGTTTAAGATTTTTAAG
64 -AGTTTTTAGGTTAAGAGGTTAAGGTTTTTTAATTTATGCTTTAAGATTTTTAAG
* *
31390149 TTAAGAGTTT-CGGTTTTTTTAGTTAAA
1 TTAAGAATTTAAGG-TTTTTTAGTTAAA
31390176 AGTTAGGGGT
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
115 2 0.02
116 81 0.66
117 39 0.32
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.51
Consensus pattern (117 bp):
TTAAGAATTTAAGGTTTTTTAGTTAAAGGTTTATGATTTTTAAGTTTAAGGTTTTAGGATTTAAG
TTTTTAGGTTAAGAGGTTAAGGTTTTTTAATTTATGCTTTAAGATTTTTAAG
Found at i:31390130 original size:28 final size:30
Alignment explanation
Indices: 31390076--31390140 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
31390066 TGGTTTTTAA
*
31390076 GTTTAAG-GTTTAGGGTTTATAGTTTTA-G
1 GTTTAAGAGTTTAGGGTTTATAGATTTATG
*
31390104 G-TTAAGAGTTTAGGGTTTTTTA-ATTTATG
1 GTTTAAGAGTTTAGGG-TTTATAGATTTATG
31390133 GTTTAAGA
1 GTTTAAGA
31390141 TTTTTAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 5 0.16
28 13 0.42
29 7 0.23
30 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (30 bp):
GTTTAAGAGTTTAGGGTTTATAGATTTATG
Found at i:31390236 original size:15 final size:16
Alignment explanation
Indices: 31390218--31390250 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31390208 GTGTTTTTAA
31390218 TTTAAG-GGTTAGGGT
1 TTTAAGAGGTTAGGGT
*
31390233 TTTAAGAGTTTAGGGT
1 TTTAAGAGGTTAGGGT
31390249 TT
1 TT
31390251 ATAGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (16 bp):
TTTAAGAGGTTAGGGT
Found at i:31390247 original size:16 final size:15
Alignment explanation
Indices: 31390226--31390281 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
31390216 AATTTAAGGG
31390226 TTAGGGTTTTAAGAGT
1 TTAGGG-TTTAAGAGT
**
31390242 TTAGGGTTTATAGTTT
1 TTAGGGTTTA-AGAGT
*
31390258 TTA-GGTTTAAGGGT
1 TTAGGGTTTAAGAGT
31390272 TTAGGGTTTA
1 TTAGGGTTTA
31390282 TATTTTTAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 6 0.18
15 16 0.47
16 12 0.35
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (15 bp):
TTAGGGTTTAAGAGT
Found at i:31390257 original size:23 final size:23
Alignment explanation
Indices: 31390218--31390274 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
31390208 GTGTTTTTAA
**
31390218 TTTAAGGG-TTAGGGTTTTAAGAG
1 TTTAAGGGTTTATAGTTTTAAG-G
*
31390241 TTT-AGGGTTTATAGTTTTTAGG
1 TTTAAGGGTTTATAGTTTTAAGG
31390263 TTTAAGGGTTTA
1 TTTAAGGGTTTA
31390275 GGGTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (23 bp):
TTTAAGGGTTTATAGTTTTAAGG
Found at i:31390267 original size:30 final size:29
Alignment explanation
Indices: 31390233--31390293 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
31390223 GGGTTAGGGT
31390233 TTTAAGAGTTTAGGGTTTATAGTTTTTAGG
1 TTTAAGAGTTTAGGGTTTATA-TTTTTAGG
*
31390263 TTTAAGGGTTTAGGGTTTATATTTTTAGG
1 TTTAAGAGTTTAGGGTTTATATTTTTAGG
31390292 TT
1 TT
31390294 AAGGAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.52
Consensus pattern (29 bp):
TTTAAGAGTTTAGGGTTTATATTTTTAGG
Found at i:31390289 original size:15 final size:16
Alignment explanation
Indices: 31390241--31390291 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
31390231 GTTTTAAGAG
31390241 TTTAGGGTTTATAGTT
1 TTTAGGGTTTATAGTT
**
31390257 TTTA-GGTTTA-AGGG
1 TTTAGGGTTTATAGTT
31390271 TTTAGGGTTTATA-TT
1 TTTAGGGTTTATAGTT
31390286 TTTAGG
1 TTTAGG
31390292 TTAAGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.21
15 18 0.62
16 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (16 bp):
TTTAGGGTTTATAGTT
Found at i:31395711 original size:12 final size:12
Alignment explanation
Indices: 31395694--31395732 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
31395684 AACTACGAGT
31395694 GCATCATAAAAG
1 GCATCATAAAAG
*
31395706 GCATCATAAAAT
1 GCATCATAAAAG
31395718 GCATCATAAAAG
1 GCATCATAAAAG
31395730 GCA
1 GCA
31395733 GTTTCAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
GCATCATAAAAG
Found at i:31407474 original size:15 final size:15
Alignment explanation
Indices: 31407456--31407485 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31407446 AAACTCTATT
31407456 ATATTAAGATAATTA
1 ATATTAAGATAATTA
*
31407471 ATATTGAGATAATTA
1 ATATTAAGATAATTA
31407486 TTAAGGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:31418489 original size:7 final size:7
Alignment explanation
Indices: 31418477--31418501 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31418467 TATTTTCTTG
31418477 TTTGAAC
1 TTTGAAC
31418484 TTTGAAC
1 TTTGAAC
31418491 TTTGAAC
1 TTTGAAC
31418498 TTTG
1 TTTG
31418502 CAAATGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (7 bp):
TTTGAAC
Found at i:31419279 original size:2 final size:2
Alignment explanation
Indices: 31419272--31419296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31419262 CTACTGCTTT
31419272 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
31419297 TTTTCTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31419343 original size:1 final size:1
Alignment explanation
Indices: 31419337--31419374 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
31419327 GCTTTCCCTC
31419337 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31419375 AAATTTAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31426428 original size:16 final size:16
Alignment explanation
Indices: 31426404--31426447 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
31426394 GATCAATTTT
* *
31426404 TTTATTTTTAATTTAA
1 TTTAATTTTAACTTAA
*
31426420 TTTAATTTTTACTTAA
1 TTTAATTTTAACTTAA
31426436 TGTTAATTTTAA
1 T-TTAATTTTAA
31426448 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTAATTTTAACTTAA
Found at i:31428924 original size:23 final size:23
Alignment explanation
Indices: 31428888--31428931 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31428878 TGGTTATGTC
31428888 AATGCAGTATTTTCAAAAAACAT
1 AATGCAGTATTTTCAAAAAACAT
*
31428911 AATGCAG-ATGTTTCAGAAAAC
1 AATGCAGTAT-TTTCAAAAAAC
31428932 TTCCTACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (23 bp):
AATGCAGTATTTTCAAAAAACAT
Found at i:31429622 original size:29 final size:29
Alignment explanation
Indices: 31429580--31429652 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
31429570 AAATGGACTT
* ***
31429580 ACACGCCCGTGTGGTCCACACAGCTTGGC
1 ACACGCCCGTGTGGCCCACACAGCTCACC
31429609 ACACGCCCGTGTGGCCCACACAGCTCACC
1 ACACGCCCGTGTGGCCCACACAGCTCACC
*
31429638 ACACGCCCATGTGGC
1 ACACGCCCGTGTGGC
31429653 ATCAGTAGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.42, G:0.25, T:0.14
Consensus pattern (29 bp):
ACACGCCCGTGTGGCCCACACAGCTCACC
Found at i:31436892 original size:61 final size:59
Alignment explanation
Indices: 31436796--31436971 Score: 185
Period size: 61 Copynumber: 2.9 Consensus size: 59
31436786 ATTGCGAGGT
* * *
31436796 CAATGGTGTTTGGTTGATTTGGGCATCATAGAAATGGCTTTGTGTAGTAGGCTGCTG-GAC
1 CAATGGTGCTTGGTTGATATGGGCATCATAGAAATGG-TTTGTGTAGTAGGCTGCCGAG-C
* * *
31436856 ATAATGGTGCTTGGTTGATATGGGCATCATAGAAATGGTTTCTTGGTTAATAGGCTGCCGAGC
1 -CAATGGTGCTTGGTTGATATGGGCATCATAGAAATGGTTT-GT-G-TAGTAGGCTGCCGAGC
* * *
31436919 CAATGGTGCTTGGTTAAAATGGGCA-CTATACAAATGGTTCTGTGTAGTAGGCT
1 CAATGGTGCTTGGTTGATATGGGCATC-ATAGAAATGGTT-TGTGTAGTAGGCT
31436972 TCACTAAGCA
Statistics
Matches: 97, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
60 11 0.11
61 37 0.38
62 35 0.36
63 13 0.13
64 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.34
Consensus pattern (59 bp):
CAATGGTGCTTGGTTGATATGGGCATCATAGAAATGGTTTGTGTAGTAGGCTGCCGAGC
Found at i:31444003 original size:24 final size:24
Alignment explanation
Indices: 31443949--31443997 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
31443939 AGATATGTCA
* *
31443949 TCATTGTTTATAATTTTAATTTTT
1 TCATTTTTTATAAATTTAATTTTT
31443973 TCATTTTTTATAAATTTAATTTTT
1 TCATTTTTTATAAATTTAATTTTT
31443997 T
1 T
31443998 TCTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
TCATTTTTTATAAATTTAATTTTT
Found at i:31446802 original size:29 final size:29
Alignment explanation
Indices: 31446741--31446805 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
31446731 GTTTAATGTT
* ** *
31446741 CAATTCTATACATGAAATTTGATTTTCTG
1 CAATTCTATACATGAAACTTGATTTGATC
*
31446770 CAATTTTATACATGAAACTTGATTTGATC
1 CAATTCTATACATGAAACTTGATTTGATC
31446799 CAATTCT
1 CAATTCT
31446806 CACAAATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
CAATTCTATACATGAAACTTGATTTGATC
Found at i:31447596 original size:14 final size:14
Alignment explanation
Indices: 31447577--31447607 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31447567 TGAATTGTTT
*
31447577 TAATCTAAATTTAC
1 TAATCTAAATTAAC
31447591 TAATCTAAATTAAC
1 TAATCTAAATTAAC
31447605 TAA
1 TAA
31447608 GAACGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:31451530 original size:6 final size:6
Alignment explanation
Indices: 31451519--31451559 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
31451509 TTATCTATAT
* *
31451519 TTTTTG TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
31451560 TATAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:31451561 original size:19 final size:19
Alignment explanation
Indices: 31451516--31451562 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
31451506 TGGTTATCTA
* *
31451516 TATTTTTTGTTTTTGTTTT
1 TATTTTTTATTTTTATTTT
31451535 TA-TTTTTATTTTTATTTT
1 TATTTTTTATTTTTATTTT
31451553 TATTTTTTAT
1 TATTTTTTAT
31451563 AATTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (19 bp):
TATTTTTTATTTTTATTTT
Found at i:31451698 original size:7 final size:7
Alignment explanation
Indices: 31451686--31451716 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
31451676 CATAATAAGT
31451686 TTTTATA
1 TTTTATA
31451693 TTTTATA
1 TTTTATA
31451700 TTTTATA
1 TTTTATA
31451707 TTTTATA
1 TTTTATA
31451714 TTT
1 TTT
31451717 AATTGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTATA
Found at i:31464427 original size:15 final size:15
Alignment explanation
Indices: 31464407--31464444 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
31464397 ACAGAGATTA
31464407 TTTTCTCTCCAAAAT
1 TTTTCTCTCCAAAAT
31464422 TTTTCTCTCCAAAAT
1 TTTTCTCTCCAAAAT
*
31464437 TCTTCTCT
1 TTTTCTCT
31464445 TTTCCTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTCTCTCCAAAAT
Found at i:31465334 original size:16 final size:18
Alignment explanation
Indices: 31465299--31465337 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
31465289 AACATCATTT
31465299 TTTTTGAAAAAACGGAAA
1 TTTTTGAAAAAACGGAAA
*
31465317 TTTTTG-AAACAC-GAAA
1 TTTTTGAAAAAACGGAAA
31465333 TTTTT
1 TTTTT
31465338 TTGAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTTTGAAAAAACGGAAA
Found at i:31465345 original size:19 final size:19
Alignment explanation
Indices: 31465297--31465352 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
31465287 ATAACATCAT
*
31465297 TTTTTTTGAAAAAACGGAAA
1 TTTTTTTGAAAACAC-GAAA
31465317 --TTTTTG-AAACACGAAA
1 TTTTTTTGAAAACACGAAA
*
31465333 TTTTTTTGAAAACAAGAAA
1 TTTTTTTGAAAACACGAAA
31465352 T
1 T
31465353 ATTTGATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 4 0.13
17 5 0.16
18 12 0.39
19 10 0.32
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (19 bp):
TTTTTTTGAAAACACGAAA
Found at i:31466138 original size:15 final size:16
Alignment explanation
Indices: 31466110--31466147 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
31466100 CAGAATGTAG
*
31466110 TTTTT-TTTCTCTTTT
1 TTTTTCTTTCTCTTTC
31466125 TTTTTCTTTC-CTTTC
1 TTTTTCTTTCTCTTTC
31466140 TTTTTCTT
1 TTTTTCTT
31466148 CTTCTCCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTCTCTTTC
Found at i:31466157 original size:20 final size:18
Alignment explanation
Indices: 31466122--31466172 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
31466112 TTTTTTCTCT
*
31466122 TTTTTTTTCTTTCCTTTC
1 TTTTTCTTCTTTCCTTTC
31466140 TTTTTCTTCTTCTCCCTTTC
1 TTTTTCTTCTT-T-CCTTTC
* *
31466160 TTCTTCCTCTTTC
1 TTTTTCTTCTTTC
31466173 GGCCCTACCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.39
19 2 0.07
20 15 0.54
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTCTTCTTTCCTTTC
Found at i:31466284 original size:15 final size:15
Alignment explanation
Indices: 31466262--31466321 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
31466252 CTTTCTCTTC
31466262 TCTCTTTCTTTATCT
1 TCTCTTTCTTTATCT
* *
31466277 TTTCTTTCTTTTTCT
1 TCTCTTTCTTTATCT
*
31466292 TCT-TTTCTTTCTTCT
1 TCTCTTTCTTT-ATCT
31466307 T-TCTTT-TTT-TCT
1 TCTCTTTCTTTATCT
31466319 TCT
1 TCT
31466322 TTCTTCCTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.10
13 1 0.03
14 11 0.28
15 23 0.59
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (15 bp):
TCTCTTTCTTTATCT
Found at i:31466291 original size:29 final size:29
Alignment explanation
Indices: 31466242--31466326 Score: 74
Period size: 28 Copynumber: 3.0 Consensus size: 29
31466232 TCACCGATGC
* *
31466242 TTATCCTTTCCTTTC-TCTTCTCTCTTTCT
1 TTAT-CTTTTCTTTCTTTTTCTCTCTTTCT
31466271 TTATCTTTTCTTTCTTTTTCT-TCTTT-T
1 TTATCTTTTCTTTCTTTTTCTCTCTTTCT
*
31466298 CTT-TC--TTCTTTCTTTTTTTCTTCTTTCT
1 -TTATCTTTTCTTTCTTTTTCTC-TCTTTCT
31466326 T
1 T
31466327 CCTCCTCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
25 13 0.27
27 9 0.19
28 17 0.35
29 9 0.19
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (29 bp):
TTATCTTTTCTTTCTTTTTCTCTCTTTCT
Found at i:31466297 original size:18 final size:18
Alignment explanation
Indices: 31466274--31466323 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
31466264 TCTTTCTTTA
31466274 TCTTTTCTTTCTTTTTCT
1 TCTTTTCTTTCTTTTTCT
31466292 TCTTTTCTTTCTTCTTTCT
1 TCTTTTCTTTCTT-TTTCT
*
31466311 TTTTTTC-TTCTTT
1 TCTTTTCTTTCTTT
31466324 CTTCCTCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 1 0.03
18 18 0.60
19 11 0.37
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TCTTTTCTTTCTTTTTCT
Found at i:31466322 original size:15 final size:15
Alignment explanation
Indices: 31466277--31466326 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
31466267 TTCTTTATCT
*
31466277 TTTCTTTCTTT-TTC
1 TTTCTTTTTTTCTTC
31466291 -TTCTTTTCTTTCTTC
1 TTTCTTTT-TTTCTTC
31466306 TTTCTTTTTTTCTTC
1 TTTCTTTTTTTCTTC
31466321 TTTCTT
1 TTTCTT
31466327 CCTCCTCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 6 0.19
14 3 0.09
15 16 0.50
16 7 0.22
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTTTCTTC
Found at i:31467771 original size:6 final size:6
Alignment explanation
Indices: 31467761--31467807 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
31467751 TTCCCACTCA
* * *
31467761 TAATAA TAATAC TAATAA TAATAC TAATAC TAATAC TAATAT TAATA
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATA
31467808 GTTACCTCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (6 bp):
TAATAC
Found at i:31467778 original size:12 final size:12
Alignment explanation
Indices: 31467761--31467807 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
31467751 TTCCCACTCA
31467761 TAATAATAATAC
1 TAATAATAATAC
31467773 TAATAATAATAC
1 TAATAATAATAC
*
31467785 TAATACTAATAC
1 TAATAATAATAC
*
31467797 TAATATTAATA
1 TAATAATAATA
31467808 GTTACCTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:31468525 original size:17 final size:17
Alignment explanation
Indices: 31468505--31468539 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31468495 TTTCCTATTC
*
31468505 TGTTTATTTTCTTCTTT
1 TGTTTATTTTATTCTTT
*
31468522 TGTTTCTTTTATTCTTT
1 TGTTTATTTTATTCTTT
31468539 T
1 T
31468540 AAATTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (17 bp):
TGTTTATTTTATTCTTT
Found at i:31468588 original size:16 final size:17
Alignment explanation
Indices: 31468560--31468591 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31468550 TTGTTTATTA
31468560 TTTAATAAATATAATAC
1 TTTAATAAATATAATAC
31468577 TTTAAT-AATATAATA
1 TTTAATAAATATAATA
31468592 TAATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAATAAATATAATAC
Found at i:31468612 original size:25 final size:25
Alignment explanation
Indices: 31468556--31468617 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
31468546 TGTTTTGTTT
*
31468556 ATTATTTAATAAATATAATACTTTA
1 ATTATATAATAAATATAATACTTTA
* *
31468581 ATAATATAATATAATATAATA-TTTT
1 ATTATATAATA-AATATAATACTTTA
*
31468606 CTTATATAATAA
1 ATTATATAATAA
31468618 GTAATTACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 21 0.68
26 9 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATATAATAAATATAATACTTTA
Found at i:31468773 original size:14 final size:14
Alignment explanation
Indices: 31468714--31468764 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
31468704 ATTTTATAAT
31468714 ATAATAATAATTATA
1 ATAATAATAATT-TA
* *
31468729 ATGATTTAACAATTTA
1 AT-A-ATAATAATTTA
31468745 ATAATAATAATTTA
1 ATAATAATAATTTA
31468759 ATAATA
1 ATAATA
31468765 TTTTTTTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 15 0.50
15 3 0.10
16 5 0.17
17 7 0.23
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:31470227 original size:17 final size:17
Alignment explanation
Indices: 31470205--31470237 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31470195 TATTTAATTC
31470205 TTTTAATAT-ATTATATA
1 TTTTAA-ATCATTATATA
31470222 TTTTAAATCATTATAT
1 TTTTAAATCATTATAT
31470238 GTATAAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAATCATTATATA
Found at i:31470462 original size:19 final size:19
Alignment explanation
Indices: 31470438--31470482 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
31470428 ACATACATAC
31470438 TTATATATA-TATATATATT
1 TTATATATACT-TATATATT
*
31470457 TTATATGTACTTATATATT
1 TTATATATACTTATATATT
31470476 TTCATAT
1 TT-ATAT
31470483 TTTATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATATATACTTATATATT
Found at i:31483151 original size:44 final size:43
Alignment explanation
Indices: 31483045--31483518 Score: 274
Period size: 44 Copynumber: 10.9 Consensus size: 43
31483035 AATATTAGAG
* *
31483045 ATCTTATCTCCCTG-AGATTACAGTGGAGCAGATCGTA--TCAA
1 ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGCACAA
* * *
31483086 GTCTTATCTCCCTG-AGATTACAGAGGAGCAGATCGGAGCCACAA
1 ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAG-CACAA
* * * **
31483130 ACCTTATCTCCCTGAAGTTACAGTGG-GCAGGTTGAATATACAA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAA-GCACAA
* * * * * * *
31483173 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTTAG
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCA---CAA
* * *
31483219 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAG-CACAA
* * *
31483263 ATCTTATCTTCCT-AAGTTTACAGCGGAGCAGATCGAAG-ACACT
1 ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGCACA-A
* * ** **
31483306 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATA-AA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCACAA
* * * * * *
31483348 GGATCTTATCTCTCTGAATTTATAGTAGAGTAGATC---GCATCAG
1 --ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCA-CAA
* * * * *
31483391 GTCTTATCTCCCTGATA-TTACAATGGAGCAGACCGAAGGATTTCAG
1 ATCTTATCTCCCTGA-AGTTACAGTGGAGCAGATCGAAGCA---CAA
* * *
31483437 ATCTTATCTCCCTGAGGTTACAGTGGAACAGATTGAAGC-CAGA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCACA-A
*
31483480 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAG
1 -ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAG
31483519 GACACTATCC
Statistics
Matches: 330, Mismatches: 75, Indels: 53
0.72 0.16 0.12
Matches are distributed among these distances:
41 60 0.18
42 5 0.02
43 67 0.20
44 125 0.38
45 2 0.01
46 70 0.21
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCACAA
Found at i:31483194 original size:87 final size:87
Alignment explanation
Indices: 31483047--31483513 Score: 275
Period size: 87 Copynumber: 5.4 Consensus size: 87
31483037 TATTAGAGAT
*
31483047 CTTATCTCCCTG-AGATTACAGTGGAGCAGATCG--TAT-CAAGTCTTATCTCCCTGAGATTACA
1 CTTATCTCCCTGAAG-TTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGAGATTACA
*
31483108 GAGGAGCAGATCGGAGCCACAAAC
65 GAGGAGCAGATCGAAG-CACAAAC
* *
31483132 CTTATCTCCCTGAAGTTACAGTGG-GCAGGTTGAATATACAAGTCTTATCTCCCTGAGGTTACAG
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGAGATTACAG
* * * * * * *
31483196 TGGAGTAGACCGAAGAATTTTAGAT
66 AGGAGCAGATCGAAGCA---CAAAC
* *** * * * * *
31483221 CTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTTCCTAAGTTTACAG
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGAGATTACAG
* * *
31483286 CGGAGCAGATCGAAGACACTATC
66 AGGAGCAGATCGAAG-CACAAAC
* * *
31483309 C-TATCTCCCTGAAGTTACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGA-ATTTA
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAA-G-TCTTATCTCCCTGAGA-TTA
* * ***
31483370 TAGTA-GAGTAGATC---GCATCAGGT
63 CAG-AGGAGCAGATCGAAGCA-CAAAC
* ** * * *
31483393 CTTATCTCCCTGATA-TTACAATGGAGCAGACCGAAGGATTTC-AGATCTTATCTCCCTGAGGTT
1 CTTATCTCCCTGA-AGTTACAGTGGAGCAGATTGAA-TA-TACAAG-TCTTATCTCCCTGAGATT
* * * *
31483456 ACAGTGGAACAGATTGAAGC-CAGAGAT
62 ACAGAGGAGCAGATCGAAGCACA-A-AC
*
31483483 CTTATCTCCCTG-AGATTACAGCGGAGCAGAT
1 CTTATCTCCCTGAAG-TTACAGTGGAGCAGAT
31483514 CGAAGGACAC
Statistics
Matches: 288, Mismatches: 65, Indels: 53
0.71 0.16 0.13
Matches are distributed among these distances:
83 2 0.01
84 9 0.03
85 47 0.16
86 12 0.04
87 115 0.40
88 6 0.02
89 25 0.09
90 71 0.25
91 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (87 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGAGATTACAG
AGGAGCAGATCGAAGCACAAAC
Found at i:31483284 original size:133 final size:133
Alignment explanation
Indices: 31483087--31483333 Score: 327
Period size: 133 Copynumber: 1.9 Consensus size: 133
31483077 TCGTATCAAG
*
31483087 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGGAGCCACAAACCTTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACA
* * * * * * *
31483152 GTGG-GCAGGTTGAATATACAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTT
66 GCGGAGCAGATCGAAGACACAA-TCCTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTT
31483216 TAGA
130 TAGA
* * * * * *
31483220 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTTCCT-AAGTTTAC
1 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAG-TTAC
*
31483284 AGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAG
65 AGCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTACAGTGGAG
31483334 CGGATTAAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
132 3 0.03
133 82 0.85
134 12 0.12
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (133 bp):
TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACA
GCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTT
AGA
Found at i:31485244 original size:44 final size:41
Alignment explanation
Indices: 31485189--31485301 Score: 127
Period size: 41 Copynumber: 2.7 Consensus size: 41
31485179 GACACTATCC
*
31485189 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGA-TAAAAT-AAGG-TCT
* ** * * *
31485233 TATCTCTCTGAAGTTACAGCAGAGTAGATCATATCAGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATAAAATAAGGTCT
*
31485274 TATCTCCCTGAGGTTACAGTGGAGTAGA
1 TATCTCCCTGAAGTTACAGTGGAGTAGA
31485302 CCGAAGAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 27 0.47
42 3 0.05
43 4 0.07
44 24 0.41
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (41 bp):
TATCTCCCTGAAGTTACAGTGGAGTAGATAAAATAAGGTCT
Found at i:31486427 original size:3 final size:3
Alignment explanation
Indices: 31486419--31486449 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
31486409 ACTGTTTCTA
*
31486419 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31486450 CTACATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:31491895 original size:28 final size:28
Alignment explanation
Indices: 31491860--31491934 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
31491850 AAATTAGGGC
* *
31491860 TAAATTAGGTTATGGTTTTAAATTAAAT
1 TAAATTAGGTTAGGGTTTTAAATCAAAT
*
31491888 TAAATTAGGTTAGGGTTTTTAATCAAAT
1 TAAATTAGGTTAGGGTTTTAAATCAAAT
**
31491916 TAGGTTAGGTTAGGGTTTT
1 TAAATTAGGTTAGGGTTTT
31491935 CATGTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (28 bp):
TAAATTAGGTTAGGGTTTTAAATCAAAT
Found at i:31498084 original size:30 final size:29
Alignment explanation
Indices: 31498040--31498141 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 29
31498030 GGTCAATCTA
*
31498040 TAATTTTAAGAAAGTTTAGAGTTTAAAAATG
1 TAATTTTAA-AAAGTTTAGAGGTT-AAAATG
* * * * *
31498071 AAATTTTGAAAAGTTGAGGGGTCAAAATG
1 TAATTTTAAAAAGTTTAGAGGTTAAAATG
31498100 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
1 TAATTTTA-AAAAGTTTAGAGGTTAAAATG
31498130 TAATTTTAAAAA
1 TAATTTTAAAAA
31498142 AATAAAATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
29 16 0.27
30 36 0.61
31 7 0.12
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.35
Consensus pattern (29 bp):
TAATTTTAAAAAGTTTAGAGGTTAAAATG
Found at i:31498129 original size:59 final size:60
Alignment explanation
Indices: 31498006--31498141 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
31497996 TTTAGGTGTC
* * ** *
31498006 AAATGAAAATTTTG-GAAGTTTAGGGGTCAATCTATAATTTTAAGAAAGTTTAGAGTTTAA
1 AAATG-AAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAGAAAGTTTAGAGGTTAA
*
31498066 AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATGTAATTTT-AGAAAAGTTTAGAGGTT-A
1 AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAG-AAAGTTTAGAGGTTAA
* *
31498125 AAATGTAATTTTAAAAA
1 AAATGAAATTTTGAAAA
31498142 AATAAAATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
59 26 0.39
60 40 0.61
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (60 bp):
AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAGAAAGTTTAGAGGTTAA
Found at i:31498641 original size:2 final size:2
Alignment explanation
Indices: 31498634--31498658 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31498624 CAACATATTA
31498634 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31498659 AAAATCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31501918 original size:18 final size:18
Alignment explanation
Indices: 31501891--31501943 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
31501881 TGCATGCATC
* *
31501891 ATGCATGCTCTTTGTTTG
1 ATGCATGCTCCTTGTTTA
* *
31501909 ATGCACGCTCCGTGTTTA
1 ATGCATGCTCCTTGTTTA
31501927 ATGCATGCTCCTTGTTT
1 ATGCATGCTCCTTGTTT
31501944 CTTACAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (18 bp):
ATGCATGCTCCTTGTTTA
Found at i:31506596 original size:16 final size:16
Alignment explanation
Indices: 31506565--31506603 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31506555 TGTTGTTTAG
*
31506565 TAGAATAACTCATGTT
1 TAGAACAACTCATGTT
* *
31506581 TGGAACAACTCGTGTT
1 TAGAACAACTCATGTT
31506597 TAGAACA
1 TAGAACA
31506604 CTCTTTGTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (16 bp):
TAGAACAACTCATGTT
Found at i:31508880 original size:30 final size:30
Alignment explanation
Indices: 31508846--31508904 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
31508836 AAAATGTAAT
*
31508846 ATTAGTAATCATATTGTAACTTTTAAAAAC
1 ATTAGTAATCATATTGTAAATTTTAAAAAC
* *
31508876 ATTAGTGATCATATTGTAAATTTTTAAAA
1 ATTAGTAATCATATTGTAAATTTTAAAAA
31508905 TTTGGTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (30 bp):
ATTAGTAATCATATTGTAAATTTTAAAAAC
Found at i:31517193 original size:19 final size:21
Alignment explanation
Indices: 31517169--31517209 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
31517159 AGAGAACACG
31517169 CACATGC-ACAACAT-GAAAA
1 CACATGCAACAACATAGAAAA
*
31517188 CACATGCAACCACATAGAAAA
1 CACATGCAACAACATAGAAAA
31517209 C
1 C
31517210 CTTTCCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.51, C:0.29, G:0.10, T:0.10
Consensus pattern (21 bp):
CACATGCAACAACATAGAAAA
Found at i:31522582 original size:23 final size:23
Alignment explanation
Indices: 31522538--31522582 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31522528 TTTTAAAAAA
* *
31522538 ATATGTTTTTTAATTGATATTTT
1 ATATATTTTTTAATTGAAATTTT
31522561 ATATATTTTTATAATT-AAATTT
1 ATATATTTTT-TAATTGAAATTT
31522583 ACATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
ATATATTTTTTAATTGAAATTTT
Found at i:31523971 original size:11 final size:11
Alignment explanation
Indices: 31523955--31524009 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
31523945 ATAATTATAC
31523955 AAAATTATTTA
1 AAAATTATTTA
31523966 AAAATTA--TA
1 AAAATTATTTA
31523975 AAAA-TATATT-
1 AAAATTAT-TTA
*
31523985 AACATTATTTA
1 AAAATTATTTA
31523996 AAAATTA-TTA
1 AAAATTATTTA
31524006 AAAA
1 AAAA
31524010 AGAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 12 0.32
11 17 0.46
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATTATTTA
Found at i:31523971 original size:21 final size:21
Alignment explanation
Indices: 31523941--31523984 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31523931 CCGCTGGTTT
*
31523941 TTTAATAATTATACAAAAT-TA
1 TTTAAAAATTATA-AAAATATA
31523962 TTTAAAAATTATAAAAATATA
1 TTTAAAAATTATAAAAATATA
31523983 TT
1 TT
31523985 AACATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAAAATTATAAAAATATA
Found at i:31524010 original size:11 final size:10
Alignment explanation
Indices: 31523942--31524009 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
31523932 CGCTGGTTTT
*
31523942 TTAATAATTA
1 TTAAAAATTA
31523952 -TACAAAATTA
1 TTA-AAAATTA
31523962 TTTAAAAATTA
1 -TTAAAAATTA
31523973 -TAAAAATATA
1 TTAAAAAT-TA
*
31523983 TT-AACATTA
1 TTAAAAATTA
31523992 TTTAAAAATTA
1 -TTAAAAATTA
31524003 TTAAAAA
1 TTAAAAA
31524010 AGAATATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
9 11 0.23
10 21 0.44
11 14 0.29
12 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:31524184 original size:20 final size:20
Alignment explanation
Indices: 31524159--31524200 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31524149 TATCTATTTG
*
31524159 AATTAT-AAGAAATTGTAAAA
1 AATTATCAAG-AATTATAAAA
31524179 AATTATCAAGAATTATAAAA
1 AATTATCAAGAATTATAAAA
31524199 AA
1 AA
31524201 AAAAAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (20 bp):
AATTATCAAGAATTATAAAA
Found at i:31525871 original size:29 final size:29
Alignment explanation
Indices: 31525837--31525895 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
31525827 TTCTTGTAAC
31525837 ATAGTTTTTCTATGTTTTCCATTTGTTAA
1 ATAGTTTTTCTATGTTTTCCATTTGTTAA
31525866 ATAGTTTTTCTATGTTTTCCATTTGTTAA
1 ATAGTTTTTCTATGTTTTCCATTTGTTAA
31525895 A
1 A
31525896 ACTGGTCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.58
Consensus pattern (29 bp):
ATAGTTTTTCTATGTTTTCCATTTGTTAA
Found at i:31530453 original size:13 final size:13
Alignment explanation
Indices: 31530435--31530513 Score: 68
Period size: 13 Copynumber: 5.6 Consensus size: 13
31530425 AAGTAATCGT
31530435 AAATGGGAATGGG
1 AAATGGGAATGGG
*
31530448 AAATGGGAATGAG
1 AAATGGGAATGGG
*
31530461 AAATGGGAGGAGGGG
1 AAATGGGA--ATGGG
* *
31530476 AATCGATGGAAGAGGGG
1 AA---ATGGGA-ATGGG
31530493 AAATGGGAATGGG
1 AAATGGGAATGGG
31530506 AAATGGGA
1 AAATGGGA
31530514 GGAGGGCACG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
13 32 0.58
14 5 0.09
15 5 0.09
17 8 0.15
18 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.47, T:0.13
Consensus pattern (13 bp):
AAATGGGAATGGG
Found at i:31530545 original size:43 final size:43
Alignment explanation
Indices: 31530445--31530580 Score: 218
Period size: 43 Copynumber: 3.1 Consensus size: 43
31530435 AAATGGGAAT
* * *
31530445 GGGAAATGGGAATGAGAAATGGGAGGAGGGGAATCGATGGAAGAG
1 GGGAAATGGGAATGGGAAATGGGAGGA-GGGCA-CGGTGGAAGAG
*
31530490 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTCGAAGAG
1 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
31530533 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
1 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
31530576 GGGAA
1 GGGAA
31530581 TCGATGGAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
43 56 0.65
44 4 0.05
45 26 0.30
ACGTcount: A:0.35, C:0.04, G:0.51, T:0.10
Consensus pattern (43 bp):
GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
Found at i:31530694 original size:24 final size:24
Alignment explanation
Indices: 31530640--31530695 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
31530630 ATTTTAAAAA
*
31530640 TAAAAAAATATATGTAATGTATTT
1 TAAAAATATATATGTAATGTATTT
*
31530664 TAAAAATATATATGTAGTGTATTT
1 TAAAAATATATATGTAATGTATTT
31530688 TAAAAATA
1 TAAAAATA
31530696 AAAAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (24 bp):
TAAAAATATATATGTAATGTATTT
Found at i:31530703 original size:29 final size:29
Alignment explanation
Indices: 31530626--31530836 Score: 297
Period size: 29 Copynumber: 7.2 Consensus size: 29
31530616 CATTGTATTT
31530626 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAAT-AAAAAATATATGTA
*
31530656 ATGTATTTTAAAAAT-----ATATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
31530680 GTGTATTTTAAAAATAAAAAATATATATATGTA
1 GTGTATTTTAAAAAT--AAAA-A-ATATATGTA
*
31530713 GTGTATTTTTAAAATAAAAAATATATGTAA
1 GTGTATTTTAAAAATAAAAAATATATGT-A
31530743 GTGTATTTTAAAAATAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
*
31530772 CTGTATTTTAAAAATAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
31530801 GTGTATTTTAAAAATAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
*
31530830 CTGTATT
1 GTGTATT
31530837 CGGTTTATTC
Statistics
Matches: 164, Mismatches: 7, Indels: 21
0.85 0.04 0.11
Matches are distributed among these distances:
24 23 0.14
29 71 0.43
30 43 0.26
31 4 0.02
33 23 0.14
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (29 bp):
GTGTATTTTAAAAATAAAAAATATATGTA
Found at i:31530820 original size:88 final size:85
Alignment explanation
Indices: 31530626--31530836 Score: 302
Period size: 88 Copynumber: 2.4 Consensus size: 85
31530616 CATTGTATTT
*
31530626 GTGTATTTTAAAAATAAAAAAATATATGTAATGTATTTTAAAAATATATATGTAGTGTATTTTAA
1 GTGTATTTTAAAAAT-AAAAAATATATGTAATGTATTTTAAAAATATATATGTACTGTATTTTAA
31530691 AAATAAAAAATATATATATGTA
65 AAAT-AAAAATATATATATGTA
*
31530713 GTGTATTTTTAAAATAAAAAATATATGTAAGTGTATTTTAAAAATAAAAAATATATGTACTGTAT
1 GTGTATTTTAAAAATAAAAAATATATGTAA-TGTATTTTAAAAAT-----ATATATGTACTGTAT
31530778 TTTAAAAAT-AAAA-A-ATATATGTA
60 TTTAAAAATAAAAATATATATATGTA
*
31530801 GTGTATTTTAAAAATAAAAAATATATGTACTGTATT
1 GTGTATTTTAAAAATAAAAAATATATGTAATGTATT
31530837 CGGTTTATTC
Statistics
Matches: 114, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
86 15 0.13
87 34 0.30
88 37 0.32
89 1 0.01
90 4 0.04
92 23 0.20
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (85 bp):
GTGTATTTTAAAAATAAAAAATATATGTAATGTATTTTAAAAATATATATGTACTGTATTTTAAA
AATAAAAATATATATATGTA
Found at i:31531735 original size:21 final size:21
Alignment explanation
Indices: 31531711--31531763 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
31531701 CATTGTTTCT
*
31531711 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
31531732 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
31531753 AATCTCACCGC
1 AATCTCACCGC
31531764 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:31536583 original size:19 final size:19
Alignment explanation
Indices: 31536552--31536598 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
31536542 TATTTTTTAA
31536552 TTTAAATATTTT-AAATACTT
1 TTTAAA-ATTTTAAAATA-TT
*
31536572 TTTTAAATTTTAAAATATT
1 TTTAAAATTTTAAAATATT
31536591 TTTAAAAT
1 TTTAAAAT
31536599 ACTTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATTTTAAAATATT
Found at i:31536593 original size:11 final size:11
Alignment explanation
Indices: 31536579--31536636 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
31536569 CTTTTTTAAA
31536579 TTTTAAAATAT
1 TTTTAAAATAT
31536590 TTTTAAAATACT
1 TTTTAAAATA-T
* *
31536602 TTTT---TTAA
1 TTTTAAAATAT
31536610 TTTTAAAATAT
1 TTTTAAAATAT
31536621 TTTTAAAATACT
1 TTTTAAAATA-T
31536633 TTTT
1 TTTT
31536637 TTAATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 4 0.11
9 2 0.05
11 22 0.58
12 10 0.26
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:31536637 original size:32 final size:31
Alignment explanation
Indices: 31536544--31536651 Score: 170
Period size: 31 Copynumber: 3.6 Consensus size: 31
31536534 ATAATAAATA
31536544 TTTTTTAA-TTT-AAATA-TTTT-AAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
*
31536571 TTTTTAAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
31536602 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
31536633 TTTTTTAATTTTTAAAATA
1 TTTTTTAA-TTTTAAAATA
31536652 AATTTTTGGT
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
27 7 0.09
28 3 0.04
29 5 0.07
30 4 0.05
31 45 0.61
32 10 0.14
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:31536657 original size:21 final size:21
Alignment explanation
Indices: 31536619--31536658 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31536609 ATTTTAAAAT
**
31536619 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
31536640 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
31536659 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:31536665 original size:22 final size:21
Alignment explanation
Indices: 31536618--31536676 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
31536608 AATTTTAAAA
* *
31536618 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
31536638 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
31536661 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
31536677 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:31541728 original size:20 final size:19
Alignment explanation
Indices: 31541658--31541727 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
31541648 AAATATAAAA
31541658 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTA-AAATTAT
*
31541678 TTTGAA-TGTTAAAATTTAT
1 TTTGAATTTTTAAAA-TTAT
31541697 TTTGAATTTTTGAAAATTAT
1 TTTGAATTTTT-AAAATTAT
31541717 TTTGAATTTTT
1 TTTGAATTTTT
31541728 GTTGAGAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 11 0.25
20 22 0.50
21 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TTTGAATTTTTAAAATTAT
Found at i:31552582 original size:2 final size:2
Alignment explanation
Indices: 31552575--31552638 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
31552565 CACTATTTGG
31552575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
31552617 TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
31552639 AAATTGTTGC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31553593 original size:2 final size:2
Alignment explanation
Indices: 31553588--31553619 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31553578 ACACACACAC
31553588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31553620 CTATTTGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31555177 original size:30 final size:30
Alignment explanation
Indices: 31555143--31555199 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
31555133 GTTCCTTGAT
31555143 TATTGTTTTCATGGCTTGCTTATGTTGGAA
1 TATTGTTTTCATGGCTTGCTTATGTTGGAA
31555173 TATTGTTTTCATGGCTTGCTTATGTTG
1 TATTGTTTTCATGGCTTGCTTATGTTG
31555200 CACTGACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.53
Consensus pattern (30 bp):
TATTGTTTTCATGGCTTGCTTATGTTGGAA
Found at i:31561361 original size:17 final size:18
Alignment explanation
Indices: 31561329--31561366 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31561319 TTTCTAATTC
31561329 AATAAAAATAATTTACCA
1 AATAAAAATAATTTACCA
*
31561347 AATAAAAGTAA-TTACCA
1 AATAAAAATAATTTACCA
31561364 AAT
1 AAT
31561367 GTTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAAAAATAATTTACCA
Found at i:31561412 original size:2 final size:2
Alignment explanation
Indices: 31561407--31561434 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31561397 TATTCCCTTA
31561407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31561435 CAATTAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31561598 original size:30 final size:29
Alignment explanation
Indices: 31561564--31561623 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
31561554 TTAAAGTTTG
* *
31561564 AATTACAATTATAAGT-AATACATTTCAAAT
1 AATTACAATCATAA-TAAAT-CATTACAAAT
*
31561594 AATTATAATCATAATAAATCATTACAAAT
1 AATTACAATCATAATAAATCATTACAAAT
31561623 A
1 A
31561624 CACAACACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (29 bp):
AATTACAATCATAATAAATCATTACAAAT
Found at i:31566153 original size:34 final size:34
Alignment explanation
Indices: 31566098--31566166 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 34
31566088 CTAATTATTG
31566098 TAATTCACTAAAAAAAATATATTTTTGTCACCAAA
1 TAATTCACTAAAAAAAATATATTTTTGTCA-CAAA
*
31566133 TAATTCACT-AAAAAATTATATTTTTGTCACAAA
1 TAATTCACTAAAAAAAATATATTTTTGTCACAAA
31566166 T
1 T
31566167 TATAAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 5 0.15
34 19 0.58
35 9 0.27
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (34 bp):
TAATTCACTAAAAAAAATATATTTTTGTCACAAA
Found at i:31578833 original size:24 final size:24
Alignment explanation
Indices: 31578806--31578897 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
31578796 TTGTCGATAT
*
31578806 TGGCTCGCATGAGATTCCCGTTTA
1 TGGCTCGCATGAGCTTCCCGTTTA
* *
31578830 TGGCTCGTATGAGCTTCCCGATTA
1 TGGCTCGCATGAGCTTCCCGTTTA
* ** * *
31578854 TGTCTCTTATGAGTTTCTCGTTATA
1 TGGCTCGCATGAGCTTCCCGTT-TA
* *
31578879 TGACTCACATGAGCTTCCC
1 TGGCTCGCATGAGCTTCCC
31578898 ATTATATGAC
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
24 38 0.70
25 16 0.30
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (24 bp):
TGGCTCGCATGAGCTTCCCGTTTA
Found at i:31578918 original size:25 final size:25
Alignment explanation
Indices: 31578874--31578921 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31578864 GAGTTTCTCG
**
31578874 TTATATGACTCACATGAGCTTCCCA
1 TTATATGACTCACAAAAGCTTCCCA
*
31578899 TTATATGACTCAGAAAAGCTTCC
1 TTATATGACTCACAAAAGCTTCC
31578922 TATTTACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (25 bp):
TTATATGACTCACAAAAGCTTCCCA
Found at i:31584078 original size:28 final size:28
Alignment explanation
Indices: 31584047--31584101 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
31584037 ATCAAATGTC
*
31584047 AATTTCGTAATTCAATCATACAAAAGTT
1 AATTTCATAATTCAATCATACAAAAGTT
*
31584075 AATTTCATAATTCAATCATGCAAAAGT
1 AATTTCATAATTCAATCATACAAAAGT
31584102 GAAGTGGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.35
Consensus pattern (28 bp):
AATTTCATAATTCAATCATACAAAAGTT
Done.