Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 125 of 182
Found at i:39899459 original size:115 final size:115
Alignment explanation
Indices: 39899254--39899473 Score: 268
Period size: 115 Copynumber: 1.9 Consensus size: 115
39899244 CTCGGGGGTA
* * * ** *
39899254 AAATGGTAATTTTGATGAAATTGGGGTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATAGTA
1 AAATGGCAATTTTGATAAAATCGGGGTAAAAATGGAATTTTAAAAAGTTCGAGAGTAAAATAGTA
* **
39899319 ATTTTTGGTAAAATTGGGGTTAAAAT-GAAATTTTGGAAAATTCGAGAGTG
66 ATTTTTGGTAAAATAGGGGCAAAAATAG-AATTTTGGAAAATTCGAGAGTG
* *
39899369 AAATGGCAATTTTGGTAAAATCGGGGTTAAAATGGAATTTTAAAAAGTTCGAGAGTAAAAT-GAT
1 AAATGGCAATTTTGATAAAATCGGGGTAAAAATGGAATTTTAAAAAGTTCGAGAGTAAAATAG-T
*
39899433 AA-TTTTGG-AGAAATCAGGGGCAAAAATAGAATTTTGTAAAA
65 AATTTTTGGTA-AAAT-AGGGGCAAAAATAGAATTTTGGAAAA
39899474 CTTAAGGGTC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
113 1 0.01
114 11 0.12
115 76 0.85
116 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (115 bp):
AAATGGCAATTTTGATAAAATCGGGGTAAAAATGGAATTTTAAAAAGTTCGAGAGTAAAATAGTA
ATTTTTGGTAAAATAGGGGCAAAAATAGAATTTTGGAAAATTCGAGAGTG
Found at i:39900825 original size:17 final size:17
Alignment explanation
Indices: 39900781--39900835 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
39900771 TTAAACTTTT
39900781 TTTTAAATTT-AAAT--
1 TTTTAAATTTAAAATAA
*
39900795 TTTT-AATTCGAAAATAA
1 TTTTAAATT-TAAAATAA
39900812 TTTTAAATTTAAAATAA
1 TTTTAAATTTAAAATAA
*
39900829 ATTTAAA
1 TTTTAAA
39900836 CTCTAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 4 0.12
17 17 0.52
18 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTTAAATTTAAAATAA
Found at i:39900831 original size:18 final size:19
Alignment explanation
Indices: 39900790--39900832 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
39900780 TTTTTAAATT
*
39900790 TAAATTTTTAATTCGAAAA
1 TAAATTTTAAATTCGAAAA
*
39900809 T-AATTTTAAATT-TAAAA
1 TAAATTTTAAATTCGAAAA
39900826 TAAATTT
1 TAAATTT
39900833 AAACTCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 15 0.71
19 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATTTTAAATTCGAAAA
Found at i:39900843 original size:17 final size:16
Alignment explanation
Indices: 39900806--39900874 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 16
39900796 TTTAATTCGA
* *
39900806 AAATAATTTTAAATTT
1 AAATAAATTTAAACTT
39900822 AAAATAAATTTAAACTCT
1 -AAATAAATTTAAACT-T
**
39900840 AAATAAGCTTAAACTT
1 AAATAAATTTAAACTT
*
39900856 ACAATAAATTTAAAATT
1 A-AATAAATTTAAACTT
39900873 AA
1 AA
39900875 GATTGAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 3 0.07
17 39 0.91
18 1 0.02
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (16 bp):
AAATAAATTTAAACTT
Found at i:39902094 original size:16 final size:16
Alignment explanation
Indices: 39902073--39902105 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39902063 TTGGGTTGAG
*
39902073 AAAATTATTTAATTAA
1 AAAATTAATTAATTAA
39902089 AAAATTAATTAATTAA
1 AAAATTAATTAATTAA
39902105 A
1 A
39902106 TTTAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTAATTAATTAA
Found at i:39908518 original size:39 final size:40
Alignment explanation
Indices: 39908459--39908538 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
39908449 TATGCACTCA
*
39908459 ATGGACACCTTTTGAAGAGTCACAA-CCCTTTCAAATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
* * *
39908498 ATGGGCACCTATTGAAGAGTCACAATCCTTTTCATATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
39908538 A
1 A
39908539 CATACCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 23 0.64
40 13 0.36
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (40 bp):
ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
Found at i:39909805 original size:80 final size:79
Alignment explanation
Indices: 39909666--39909814 Score: 208
Period size: 80 Copynumber: 1.9 Consensus size: 79
39909656 GGCGCAAACC
* *
39909666 GTTGGTTAATCCAACTAGAGCTAAGCTCACTTTTGTAGTTTAACCGCTAGGCACTGGGTGCCAGG
1 GTTGGTTAATCCAACTAGAGCTAAGCTCACTTTCGTAGTTTAACCGCTAGGCACCGGGTGCCAGG
39909731 AATTGATGAGCTTT
66 AATTGATGAGCTTT
* ** * * * *
39909745 GTTGGTTAATCCAACTAGAGTTGGGCTTACTTATCGTGGTTTATCCGCTAGGCACCGGGTGCCAT
1 GTTGGTTAATCCAACTAGAGCTAAGCTCACTT-TCGTAGTTTAACCGCTAGGCACCGGGTGCCAG
39909810 GAATT
65 GAATT
39909815 AACGAAAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 28 0.47
80 32 0.53
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (79 bp):
GTTGGTTAATCCAACTAGAGCTAAGCTCACTTTCGTAGTTTAACCGCTAGGCACCGGGTGCCAGG
AATTGATGAGCTTT
Found at i:39913041 original size:118 final size:118
Alignment explanation
Indices: 39912833--39913066 Score: 468
Period size: 118 Copynumber: 2.0 Consensus size: 118
39912823 GGATTAACAA
39912833 CCCAACAAAACTCCCCTTGGGTTTTCGAATTATTGCTGAGCCATGTTTGACTTTTGAAGACAATG
1 CCCAACAAAACTCCCCTTGGGTTTTCGAATTATTGCTGAGCCATGTTTGACTTTTGAAGACAATG
39912898 GAAGATGGGTAATAAGATACATTCCCAAGGAAGTCAATTTTGAACAGCAGCTT
66 GAAGATGGGTAATAAGATACATTCCCAAGGAAGTCAATTTTGAACAGCAGCTT
39912951 CCCAACAAAACTCCCCTTGGGTTTTCGAATTATTGCTGAGCCATGTTTGACTTTTGAAGACAATG
1 CCCAACAAAACTCCCCTTGGGTTTTCGAATTATTGCTGAGCCATGTTTGACTTTTGAAGACAATG
39913016 GAAGATGGGTAATAAGATACATTCCCAAGGAAGTCAATTTTGAACAGCAGC
66 GAAGATGGGTAATAAGATACATTCCCAAGGAAGTCAATTTTGAACAGCAGC
39913067 GTAATCAGGA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (118 bp):
CCCAACAAAACTCCCCTTGGGTTTTCGAATTATTGCTGAGCCATGTTTGACTTTTGAAGACAATG
GAAGATGGGTAATAAGATACATTCCCAAGGAAGTCAATTTTGAACAGCAGCTT
Found at i:39914007 original size:25 final size:25
Alignment explanation
Indices: 39913970--39914020 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
39913960 GAGTGGGGTG
39913970 ATTATTTTGAATTAATATTAATATA
1 ATTATTTTGAATTAATATTAATATA
* *
39913995 ATTATTTTTAATTAATATTATTATA
1 ATTATTTTGAATTAATATTAATATA
39914020 A
1 A
39914021 AATTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTATTTTGAATTAATATTAATATA
Found at i:39930249 original size:11 final size:11
Alignment explanation
Indices: 39930233--39930259 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
39930223 GAGATCTTTA
39930233 TTTTTCTTTTC
1 TTTTTCTTTTC
39930244 TTTTTCTTTTC
1 TTTTTCTTTTC
39930255 TTTTT
1 TTTTT
39930260 GGGCTTGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:39930777 original size:51 final size:51
Alignment explanation
Indices: 39930714--39930978 Score: 141
Period size: 51 Copynumber: 5.3 Consensus size: 51
39930704 GAGGAAATTT
*
39930714 ATTTTTAAATAAAAATATGTTTTTTTTAGTTATTTTAAAAGAAAAGTTTAA
1 ATTTTTAAATAAAAATATGTTTTTTTTAATTATTTTAAAAGAAAAGTTTAA
** * * * ** * **
39930765 ATTTTTAAATAAAGTTTTG-ATTTTTTAACTATTTCGAAATAAAAGTTTGG
1 ATTTTTAAATAAAAATATGTTTTTTTTAATTATTTTAAAAGAAAAGTTTAA
* * * ** *
39930815 ATTTTTAAGT-AAAATA-ATTATTTTT--TT-TTAAAAAAGAAAA-TTTATT
1 ATTTTTAAATAAAAATATGTTTTTTTTAATTATTTTAAAAGAAAAGTTTA-A
* * * * * * *
39930861 TTTTTTAAAAAATAAAAATCTGTTTTTTAGTTA-ATTATAAAGAAAAAGTTTAA
1 ATTTTTAAATAA-AAATATGTTTTTTTTAATTATTTTA-AAAG-AAAAGTTTAA
* * * * * * * *
39930914 ATTTTTAAACAAAATTTTGATTTTTTAAACTATTTTAAAATAAAAGTTTGA
1 ATTTTTAAATAAAAATATGTTTTTTTTAATTATTTTAAAAGAAAAGTTTAA
*
39930965 ATTTTTAAGTAAAA
1 ATTTTTAAATAAAA
39930979 TAGTGATTTT
Statistics
Matches: 150, Mismatches: 52, Indels: 24
0.66 0.23 0.11
Matches are distributed among these distances:
45 3 0.02
46 16 0.11
47 2 0.01
48 4 0.03
49 14 0.09
50 32 0.21
51 40 0.27
52 18 0.12
53 17 0.11
54 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (51 bp):
ATTTTTAAATAAAAATATGTTTTTTTTAATTATTTTAAAAGAAAAGTTTAA
Found at i:39930818 original size:148 final size:145
Alignment explanation
Indices: 39930625--39931267 Score: 573
Period size: 150 Copynumber: 4.5 Consensus size: 145
39930615 TTATTTTGGG
* * * * *
39930625 AAAATTTTGGTTTTTGTCAAA-TAATTTCAAAAT-AAGGTTTTGATTTTTAAGAAAAATAGTAAT
1 AAAATTTTGATTTTT-TTAAACT-ATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAATAGTAAT
39930688 TTTCTTTAAAAAAGAGGAGGAAATTTATTTTTAAATAAAAATATGTTTTTTTTAGTTATTTTAAA
64 TTTCTTTAAAAAA-A-GA-GAAATTTATTTTTAAATAAAAATATG-TTTTTTTAGTTA-TTTAAA
*
39930753 AGAAAAGTTTAAATTTTTAAAT
124 AGAAAAGTTTAAATTTTTAAAC
* * * *
39930775 AAAGTTTTGA-TTTTTT-AACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAATTATTT
1 AAAATTTTGATTTTTTTAAACTATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAATAGTAATTT
* * * *
39930838 TTTTTTAAAAAAGA-AAATTTATTTTTTTTAAAAAATAAAAATCTG-TTTTTTAGTTAATTATAA
66 TCTTTAAAAAAAGAGAAATTTA---TTTTT---AAATAAAAATATGTTTTTTTAGTTATTTA-AA
39930901 AGAAAAAGTTTAAATTTTTAAAC
124 AG-AAAAGTTTAAATTTTTAAAC
* * *
39930924 AAAATTTTGA-TTTTTTAAACTATTTTAAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTT
1 AAAATTTTGATTTTTTTAAACTATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAATAGTAATTT
* * * *
39930988 TC-TTAAAAAAAGAGAAAGTTTATATTTAAA-AAAATATAAG-TTTTTTAATTA-TTATAAGAAA
66 TCTTTAAAAAAAGAGAAA-TTTATTTTTAAATAAAA-ATATGTTTTTTTAGTTATTTAAAAGAAA
*
39931049 ATTTTTAAATTTTTAAAC
129 A-GTTTAAATTTTTAAAC
* * *
39931067 AAAATTTTGATTTTTTTTAAAACTATTT-----T-GAAGTTTGGATTTTTAAGTAAAGTAGTGAT
1 AAAATTTTGA-TTTTTTT-AAACTATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAATAGTAAT
* * * *
39931126 TTTCATT--AAAAA-A-AACTATATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAA-A
64 TTTCTTTAAAAAAAGAGAAATTTATTTTT--AAATAAAAATATGTTTTTTTAGTTATTTAAAAGA
39931186 AAA--TT-AATTTTTAAAC
127 AAAGTTTAAATTTTTAAAC
** * * * * *
39931202 AAAATTTTGATTTATTTT-AACTATTTTGAAATAAAAATTTTGATTTTGAAGTAAAGTATTAATT
1 AAAATTTTGATTT-TTTTAAACTATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAATAGTAATT
39931266 TT
65 TT
39931268 GTTTTAATAA
Statistics
Matches: 418, Mismatches: 44, Indels: 73
0.78 0.08 0.14
Matches are distributed among these distances:
133 8 0.02
134 3 0.01
135 25 0.06
136 9 0.02
137 2 0.00
138 9 0.02
139 50 0.12
140 35 0.08
141 3 0.01
142 4 0.01
143 28 0.07
144 14 0.03
145 22 0.05
146 11 0.03
147 20 0.05
148 57 0.14
149 48 0.11
150 66 0.16
151 4 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (145 bp):
AAAATTTTGATTTTTTTAAACTATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAATAGTAATTT
TCTTTAAAAAAAGAGAAATTTATTTTTAAATAAAAATATGTTTTTTTAGTTATTTAAAAGAAAAG
TTTAAATTTTTAAAC
Found at i:39930878 original size:24 final size:23
Alignment explanation
Indices: 39930836--39930888 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
39930826 AAATAATTAT
* *
39930836 TTTTTTTTAAAAAAGAAAATTTA
1 TTTTTTTTAAAAAAAAAAATCTA
*
39930859 TTTTTTTTAAAAAATAAAAATCTG
1 TTTTTTTTAAAAAA-AAAAATCTA
39930883 TTTTTT
1 TTTTTT
39930889 AGTTAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTTTTTAAAAAAAAAAATCTA
Found at i:39930927 original size:20 final size:20
Alignment explanation
Indices: 39930904--39930943 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39930894 ATTATAAAGA
39930904 AAAAGTTTAAATTTTTAAAC
1 AAAAGTTTAAATTTTTAAAC
* * *
39930924 AAAATTTTGATTTTTTAAAC
1 AAAAGTTTAAATTTTTAAAC
39930944 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
AAAAGTTTAAATTTTTAAAC
Found at i:39930949 original size:31 final size:31
Alignment explanation
Indices: 39930914--39930972 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39930904 AAAAGTTTAA
* * *
39930914 ATTTTTAAACAAAATTTTGATTTTTTAAACT
1 ATTTTAAAACAAAAGTTTGAATTTTTAAACT
*
39930945 ATTTTAAAATAAAAGTTTGAATTTTTAA
1 ATTTTAAAACAAAAGTTTGAATTTTTAA
39930973 GTAAAATAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (31 bp):
ATTTTAAAACAAAAGTTTGAATTTTTAAACT
Found at i:39931055 original size:21 final size:21
Alignment explanation
Indices: 39931028--39931074 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
39931018 AAAATATAAG
* *
39931028 TTTTTTAATTATTATAAGAAAA
1 TTTTTAAATTATTA-AACAAAA
*
39931050 TTTTTAAATTTTTAAACAAAA
1 TTTTTAAATTATTAAACAAAA
39931071 TTTT
1 TTTT
39931075 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTTAAATTATTAAACAAAA
Found at i:39931697 original size:26 final size:25
Alignment explanation
Indices: 39931668--39931729 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
39931658 CACTTGCATA
*
39931668 ATTTTTTTTAT-TCTTATTTCATCTTT
1 ATTTTTTTTATATC-TATTT-ATATTT
*
39931694 ATTTATTTTCATATCTATTTATATTT
1 ATTT-TTTTTATATCTATTTATATTT
39931720 ATGTTTTTTT
1 AT-TTTTTTT
39931730 TACAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 15 0.50
27 13 0.43
28 2 0.07
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (25 bp):
ATTTTTTTTATATCTATTTATATTT
Found at i:39933256 original size:25 final size:26
Alignment explanation
Indices: 39933222--39933278 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
39933212 ACCCTTAACC
*
39933222 TTTAAAATAA-GAGTTAAATTATT-TT
1 TTTAAAATAATGA-TTAAAATATTATT
39933247 TTTAAAATAATGATTAAAATATTAATT
1 TTTAAAATAATGATTAAAATATT-ATT
39933274 TTTAA
1 TTTAA
39933279 TATTGTTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 19 0.68
26 2 0.07
27 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TTTAAAATAATGATTAAAATATTATT
Found at i:39934450 original size:16 final size:17
Alignment explanation
Indices: 39934429--39934461 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39934419 CCTTAAAGTC
39934429 CATAC-TAAAATCAAAA
1 CATACTTAAAATCAAAA
*
39934445 CATACTTAAAATTAAAA
1 CATACTTAAAATCAAAA
39934462 TGTCTGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
CATACTTAAAATCAAAA
Found at i:39934747 original size:42 final size:42
Alignment explanation
Indices: 39934700--39934783 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
39934690 AACCAATCAC
* *
39934700 ACCAATCAGGACTATAAGAGTCTATCTATCCAATCACACTGG
1 ACCAATCAGGACTACAAGAGTCTATCCATCCAATCACACTGG
39934742 ACCAATCAGGACTACAAGAGTCTATCCATCCAATCACACTGG
1 ACCAATCAGGACTACAAGAGTCTATCCATCCAATCACACTGG
39934784 TACATGATGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (42 bp):
ACCAATCAGGACTACAAGAGTCTATCCATCCAATCACACTGG
Found at i:39937772 original size:17 final size:17
Alignment explanation
Indices: 39937732--39937807 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 17
39937722 CCCAATGAGA
*
39937732 TAAATTTAGTTTT-AAAT
1 TAAATTTA-TTTTGAATT
*
39937749 TAGATTTATTTTGAATT
1 TAAATTTATTTTGAATT
*** **
39937766 TAAATTTGCATAAAATT
1 TAAATTTATTTTGAATT
* *
39937783 TAAACTTATTATGAATT
1 TAAATTTATTTTGAATT
39937800 TAAATTTA
1 TAAATTTA
39937808 AAATTAAATT
Statistics
Matches: 42, Mismatches: 16, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
16 4 0.10
17 38 0.90
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (17 bp):
TAAATTTATTTTGAATT
Found at i:39939764 original size:30 final size:31
Alignment explanation
Indices: 39939722--39939850 Score: 84
Period size: 30 Copynumber: 4.4 Consensus size: 31
39939712 TTGTGATCCT
* *
39939722 AAAC-TTCAAAAAAATTA-TATTTTA-ACCCC
1 AAACTTTCTAAAAAATTACCATTTTACA-CCC
39939751 AAAACTTT-T-AAAAATTACCATTTTACACCC
1 -AAACTTTCTAAAAAATTACCATTTTACACCC
39939781 AAACTTTCT--AAAATT-CCATTTTA-ACCC
1 AAACTTTCTAAAAAATTACCATTTTACACCC
* *
39939808 TAA-TTTC-ACCCAAAATTACCATTTTAC-CCC
1 AAACTTTCTA--AAAAATTACCATTTTACACCC
* *
39939838 GAACTTTCCAAAA
1 AAACTTTCTAAAA
39939851 TCCTATTTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 24
0.74 0.05 0.22
Matches are distributed among these distances:
26 4 0.05
27 6 0.07
28 8 0.10
29 27 0.33
30 29 0.35
31 7 0.09
32 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.01, T:0.33
Consensus pattern (31 bp):
AAACTTTCTAAAAAATTACCATTTTACACCC
Found at i:39939784 original size:29 final size:28
Alignment explanation
Indices: 39939731--39939922 Score: 117
Period size: 29 Copynumber: 6.7 Consensus size: 28
39939721 TAAACTTCAA
* *
39939731 AAAAATTA-TATTTTAACCCCAAAACTTTT
1 AAAAATTACCATTTTAA-CCC-AAACTTTC
39939760 AAAAATTACCATTTTACACCCAAACTTTC
1 AAAAATTACCATTTTA-ACCCAAACTTTC
* *
39939789 TAAAATT-CCATTTTAACCCTAA-TTTC
1 AAAAATTACCATTTTAACCCAAACTTTC
* *
39939815 ACCCAAAATTACCATTTTACCCCGAACTTTC
1 A---AAAATTACCATTTTAACCCAAACTTTC
* * *
39939846 CAAAA-T-CCTATTTTTAACCCTAATTTTAC
1 AAAAATTACC-A-TTTTAACCCAAACTTT-C
* ** *
39939875 CAAAATTATTATTTTACCCCCAAACTTTC
1 AAAAATTACCATTTTA-ACCCAAACTTTC
*
39939904 CAAAATT-CCATTTTTAACC
1 AAAAATTACCA-TTTTAACC
39939923 TCGAATTTTC
Statistics
Matches: 130, Mismatches: 19, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
26 6 0.05
27 8 0.06
28 28 0.22
29 51 0.39
30 32 0.25
31 5 0.04
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATTACCATTTTAACCCAAACTTTC
Found at i:39939878 original size:57 final size:57
Alignment explanation
Indices: 39939761--39939941 Score: 231
Period size: 58 Copynumber: 3.1 Consensus size: 57
39939751 AAAACTTTTA
* *
39939761 AAAATTACCATTTTACACCCAAACTTTCTAAAATTCCA-TTTTAACCCTAATTTCACCC
1 AAAATTACCATTTTAC-CCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTA-CC
*
39939819 AAAATTACCATTTTACCCCGAACTTTCCAAAA-TCCTATTTTTAACCCTAATTTTACC
1 AAAATTACCATTTTACCCCAAACTTTCCAAAATTCC-ATTTTTAACCCTAATTTTACC
** * *
39939876 AAAATTATTATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGAATTTTCCC
1 AAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACC-CTAATTTTACC
*
39939935 GAAATTA
1 AAAATTA
39939942 TATTTTTGCC
Statistics
Matches: 109, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
56 3 0.03
57 30 0.28
58 58 0.53
59 18 0.17
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACC
Found at i:39952607 original size:200 final size:199
Alignment explanation
Indices: 39952060--39952701 Score: 933
Period size: 202 Copynumber: 3.2 Consensus size: 199
39952050 AGACAGCGAA
* ** *
39952060 GCGGTCATCTTCCTGATGAGATACAGAGAAAGAATACCAACTCAACATTCAACATGAGCCAATCT
1 GCGGTCATCTTCCTGATAAGATACAGAG-AAGAATACCAACTCAACGCTCAACACGAG-CAATCT
* *
39952125 TCGTACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGATTAGCTTCCTG
64 TCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCTG
39952190 ATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAACA
129 ATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAACA
*
39952255 ACAGAG
194 ATAGAG
* *
39952261 GCGATCATCTTCCTGATGAGATATACAGAGAAGAATACCAACTCAACGCTCAACACGAGTCAATC
1 GCGGTCATCTTCCTGAT-A-AGATACAGAGAAGAATACCAACTCAACGCTCAACACGAG-CAATC
* *
39952326 TTCGTACCTAGTTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCT
63 TTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCT
* * *
39952391 GATGAGATATAGAGAAGTGGACCAAATTTTTCTTCCTAAGGAGATCCAGAGAAGCAAATTAAAAC
128 GATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAAC
39952456 AATAGAG
193 AATAGAG
* **
39952463 GCGGTCATCTTCCTGATAAGATACAGAGAAGAATGCCAACTCAACGCTCAATGCGAGCAAATCTT
1 GCGGTCATCTTCCTGATAAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGC-AATCTT
* * * * *
39952528 CGAACCCAGCTCCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGA
65 CGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCTGA
* * *
39952593 TGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAG
130 TGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAACA-
* **
39952658 ATGGTT
194 ATAGAG
* * * *
39952664 GCAGTCATCTTCCTGATGAGACACAGAGAAGAAAACCA
1 GCGGTCATCTTCCTGATAAGATACAGAGAAGAATACCA
39952702 GGTCAATGAA
Statistics
Matches: 396, Mismatches: 41, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
199 1 0.00
200 157 0.40
201 53 0.13
202 176 0.44
203 9 0.02
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (199 bp):
GCGGTCATCTTCCTGATAAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAATCTTC
GTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCTGAT
GAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAACAAT
AGAG
Found at i:39953068 original size:17 final size:17
Alignment explanation
Indices: 39953028--39953103 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
39953018 CCCAATGAGA
*
39953028 TAAATTTAGTTTT-AAAT
1 TAAATTTA-TTTTGAATT
*
39953045 TAGATTTATTTTGAATT
1 TAAATTTATTTTGAATT
*** **
39953062 TAAATTTGCATAAAATT
1 TAAATTTATTTTGAATT
*
39953079 TAAATTTATTATGAATT
1 TAAATTTATTTTGAATT
39953096 TAAATTTA
1 TAAATTTA
39953104 AAATTAAATT
Statistics
Matches: 44, Mismatches: 14, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
16 4 0.09
17 40 0.91
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (17 bp):
TAAATTTATTTTGAATT
Found at i:39955058 original size:30 final size:31
Alignment explanation
Indices: 39954996--39955058 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
39954986 AACTGTTCAG
39954996 AAATTATATTTATGATCCCAAAACTTCAAAA
1 AAATTATATTTATGATCCCAAAACTTCAAAA
*
39955027 AAATTATATTT-TGA-CCTCGAAACTTTCAAAA
1 AAATTATATTTATGATCC-CAAAAC-TTCAAAA
39955058 A
1 A
39955059 TTACCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 2 0.07
30 8 0.28
31 19 0.66
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (31 bp):
AAATTATATTTATGATCCCAAAACTTCAAAA
Found at i:39955068 original size:30 final size:29
Alignment explanation
Indices: 39955025--39955106 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
39955015 AAAACTTCAA
*
39955025 AAAAATTA-TATTTTGACCTCGAAACTTTC
1 AAAAATTACCATTTT-ACCTCGAAACTTTC
* *
39955054 AAAAATTACCATTTTACCCCTAAACTTTC
1 AAAAATTACCATTTTACCTCGAAACTTTC
*
39955083 CAAAATT-CCATTTTTAACCTCGAA
1 AAAAATTACCA-TTTT-ACCTCGAA
39955107 TTTTTTCGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.07
29 30 0.68
30 11 0.25
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAATTACCATTTTACCTCGAAACTTTC
Found at i:39956797 original size:15 final size:15
Alignment explanation
Indices: 39956777--39956805 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39956767 TTATATCTGA
39956777 AAAAACATAAAAGAC
1 AAAAACATAAAAGAC
39956792 AAAAACATAAAAGA
1 AAAAACATAAAAGA
39956806 TATAATAATG
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:0.76, C:0.10, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAACATAAAAGAC
Found at i:39960617 original size:18 final size:18
Alignment explanation
Indices: 39960596--39960634 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
39960586 AACAAACAGA
*
39960596 AAAGAAAACATGTTTAGC
1 AAAGAAAACATGTTTAAC
39960614 AAAGAAAACATGTTTAAC
1 AAAGAAAACATGTTTAAC
39960632 AAA
1 AAA
39960635 CAAGAGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (18 bp):
AAAGAAAACATGTTTAAC
Found at i:39960733 original size:24 final size:25
Alignment explanation
Indices: 39960686--39960739 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
39960676 TAGCAGAGAA
*
39960686 AAGAAGAGAAAAGGAAATTGGGAAG
1 AAGAAGAAAAAAGGAAATTGGGAAG
39960711 AAGAAGAAAAAA-GAGAATT-GGAAG
1 AAGAAGAAAAAAGGA-AATTGGGAAG
39960735 AAGAA
1 AAGAA
39960740 AGGTCATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.07
Consensus pattern (25 bp):
AAGAAGAAAAAAGGAAATTGGGAAG
Found at i:39962540 original size:21 final size:20
Alignment explanation
Indices: 39962503--39962542 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39962493 CATGTGTACA
*
39962503 TTATGTTAATATAATATTAT
1 TTATCTTAATATAATATTAT
*
39962523 TTATCTTATATATCATATTA
1 TTATCTTA-ATATAATATTA
39962543 ATAAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATCTTAATATAATATTAT
Found at i:39964022 original size:19 final size:19
Alignment explanation
Indices: 39963987--39964040 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
39963977 ACTCAAAATC
*
39963987 ATAAAAATTTAAAAAATCAAA
1 ATAAAAAGTT-AAAAAT-AAA
*
39964008 ATTAAAA-TTAAAAATAAA
1 ATAAAAAGTTAAAAATAAA
39964026 ATAAAAAGTTAAAAA
1 ATAAAAAGTTAAAAA
39964041 CAATTAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 9 0.30
19 13 0.43
20 2 0.07
21 6 0.20
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAAAAAGTTAAAAATAAA
Found at i:39966549 original size:28 final size:29
Alignment explanation
Indices: 39966503--39966562 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
39966493 AAAAAGAGTT
**
39966503 AAATCGTTTTTAATGAAAATA-ATAACTAA
1 AAATCGTTTTTAAACAAAA-ACATAACTAA
39966532 AAAT-GTTTTTAAACAAAAACGATAACTAA
1 AAATCGTTTTTAAACAAAAAC-ATAACTAA
39966561 AA
1 AA
39966563 TATTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
29 14 0.52
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATCGTTTTTAAACAAAAACATAACTAA
Found at i:39966881 original size:30 final size:30
Alignment explanation
Indices: 39966819--39966885 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
39966809 AAAAAATCAT
* *
39966819 TTTAATTTTTTTAAAAAAATTGATGGTCAAA
1 TTTAA-TTTTTTAAAAAAATTGAAGGTAAAA
*
39966850 TTTAATTTTTTAAAGAAATT-AAGGTAAAA
1 TTTAATTTTTTAAAAAAATTGAAGGTAAAA
*
39966879 ATTAATT
1 TTTAATT
39966886 GAAAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.41
30 14 0.44
31 5 0.16
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (30 bp):
TTTAATTTTTTAAAAAAATTGAAGGTAAAA
Found at i:39967979 original size:23 final size:23
Alignment explanation
Indices: 39967953--39967996 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
39967943 TAACAAACAT
* *
39967953 TCAAATTCATTTAAAACATTCTC
1 TCAAAATCATATAAAACATTCTC
*
39967976 TCAAAATCATATAAATCATTC
1 TCAAAATCATATAAAACATTC
39967997 AATAAACATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (23 bp):
TCAAAATCATATAAAACATTCTC
Found at i:39968847 original size:79 final size:79
Alignment explanation
Indices: 39968705--39968924 Score: 244
Period size: 79 Copynumber: 2.8 Consensus size: 79
39968695 AACAGTTATG
* * * * * * * ** **
39968705 GCACCCAGTGCCTAGCGGATAAAACGCAATTGTGAGCCTAGATCTAGTTGGATT-AACCAACAAT
1 GCACCCAGTGCTTAGCGGATAAACCGCAAATGTAAACCCAGCTCTAGTCAG-TTAAACTGACAAT
**
39968769 ATTTGTCAAATCTTA
65 ATCCGTCAAATCTTA
* * * *
39968784 GCACCTAGTGCTTAGCGGGTAAACCGCAAATGTAAACCCAGCTCTAGTCAGTTAAATTGACAATG
1 GCACCCAGTGCTTAGCGGATAAACCGCAAATGTAAACCCAGCTCTAGTCAGTTAAACTGACAATA
*
39968849 TCCGTCAAATCTTG
66 TCCGTCAAATCTTA
* *
39968863 GCACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACTGACA
1 GCACCCAGTGCTTAGCGGATAAACCGCAAATGTAAACCCAGCTCTAGTCAGTTAAACTGACA
39968925 TTGTAAGTTA
Statistics
Matches: 117, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
78 2 0.02
79 115 0.98
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (79 bp):
GCACCCAGTGCTTAGCGGATAAACCGCAAATGTAAACCCAGCTCTAGTCAGTTAAACTGACAATA
TCCGTCAAATCTTA
Found at i:39971617 original size:39 final size:40
Alignment explanation
Indices: 39971562--39971639 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 40
39971552 TATGCACTCA
* * *
39971562 ATGGACACCTTTTGAAGAGTTACAACCTTTTTCAAATTGT
1 ATGGACACCTATTGAAGAGTCACAACCCTTTTCAAATTGT
* *
39971602 ATGGAC-CCTATTGAAGGGTCACAACCCTTTTCATATTG
1 ATGGACACCTATTGAAGAGTCACAACCCTTTTCAAATTG
39971640 GACATACCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 27 0.82
40 6 0.18
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (40 bp):
ATGGACACCTATTGAAGAGTCACAACCCTTTTCAAATTGT
Found at i:39976367 original size:40 final size:40
Alignment explanation
Indices: 39976312--39976392 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
39976302 TATGCACTCA
* *
39976312 ATGGACACCTTTTGAAGAGTCACAACCTTTTTCAAATTGG
1 ATGGACACCTATTGAAGAGTCACAACCCTTTTCAAATTGG
* *
39976352 ATGGACACCTATTGAAGGGTCACAACCCTTTTCATATTGG
1 ATGGACACCTATTGAAGAGTCACAACCCTTTTCAAATTGG
39976392 A
1 A
39976393 CATACCTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (40 bp):
ATGGACACCTATTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:39983320 original size:14 final size:13
Alignment explanation
Indices: 39983297--39983335 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
39983287 ACCCAAATTC
*
39983297 ATTTTTATTTTTA
1 ATTTTTATTTTCA
39983310 ATTTTTAATTTTCA
1 ATTTTT-ATTTTCA
39983324 A-TTTTATTTTCA
1 ATTTTTATTTTCA
39983336 GTTGAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 7 0.29
13 10 0.42
14 7 0.29
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTATTTTCA
Found at i:39989208 original size:19 final size:20
Alignment explanation
Indices: 39989184--39989221 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39989174 ACAACATATA
39989184 TCAATAAA-TTTATAAAATT
1 TCAATAAAGTTTATAAAATT
*
39989203 TCAATAAAGTTTCTAAAAT
1 TCAATAAAGTTTATAAAAT
39989222 AAAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (20 bp):
TCAATAAAGTTTATAAAATT
Found at i:39997333 original size:5 final size:6
Alignment explanation
Indices: 39997312--39997363 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
39997302 TGGTTTTCCC
* *
39997312 AAAATG AAAAAG AAAAAT- AAAATG AAAATG AAAAAG AAAAATG AGAAATG
1 AAAATG AAAATG -AAAATG AAAATG AAAATG AAAATG -AAAATG A-AAATG
39997362 AA
1 AA
39997364 TTCATTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 5 0.13
6 18 0.47
7 15 0.39
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:39997335 original size:18 final size:18
Alignment explanation
Indices: 39997312--39997351 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39997302 TGGTTTTCCC
*
39997312 AAAATGAAAAAGAAAAAT
1 AAAATGAAAAAGAAAAAG
*
39997330 AAAATGAAAATGAAAAAG
1 AAAATGAAAAAGAAAAAG
39997348 AAAA
1 AAAA
39997352 ATGAGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAATGAAAAAGAAAAAG
Found at i:39997340 original size:24 final size:26
Alignment explanation
Indices: 39997313--39997363 Score: 88
Period size: 24 Copynumber: 2.0 Consensus size: 26
39997303 GGTTTTCCCA
39997313 AAATGAAAAAGAAAAAT-A-AAATGA
1 AAATGAAAAAGAAAAATGAGAAATGA
39997337 AAATGAAAAAGAAAAATGAGAAATGA
1 AAATGAAAAAGAAAAATGAGAAATGA
39997363 A
1 A
39997364 TTCATTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 17 0.68
25 1 0.04
26 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.12
Consensus pattern (26 bp):
AAATGAAAAAGAAAAATGAGAAATGA
Found at i:39997346 original size:13 final size:13
Alignment explanation
Indices: 39997312--39997355 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
39997302 TGGTTTTCCC
39997312 AAAATGAAAAAGA
1 AAAATGAAAAAGA
*
39997325 AAAAT-AAAATG-
1 AAAATGAAAAAGA
39997336 AAAATGAAAAAGA
1 AAAATGAAAAAGA
39997349 AAAATGA
1 AAAATGA
39997356 GAAATGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 10 0.37
13 12 0.44
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (13 bp):
AAAATGAAAAAGA
Found at i:39999576 original size:41 final size:41
Alignment explanation
Indices: 39999518--39999629 Score: 161
Period size: 41 Copynumber: 2.7 Consensus size: 41
39999508 TGTATAAATG
* *
39999518 GAAGACTCATGTTTCGAAATAAGAATGAGATTATGAATAAA
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAAA
* * * *
39999559 GAAGACTCACGTCTCGAAATGAGAATGAGATTTTGATTAAG
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAAA
*
39999600 GAAGACTCATGTCTCGAGATGAGAATGAGA
1 GAAGACTCATGTCTCGAAATGAGAATGAGA
39999630 ATATTGTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (41 bp):
GAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAAA
Found at i:39999672 original size:82 final size:82
Alignment explanation
Indices: 39999517--39999673 Score: 183
Period size: 82 Copynumber: 1.9 Consensus size: 82
39999507 TTGTATAAAT
* * *
39999517 GGAAGACTCATGTTTCGAAATAAGAATGAGATTATGAATAAAGAAGACTCACGTCTCGAAATGAG
1 GGAAGACTCATGTCTCGAAATAAGAATGAGAATATGAATAAAGAAGACTCACGACTCGAAATGAG
*
39999582 AATGAGATTTTGATTAA
66 AATAAGATTTTGATTAA
* * * * * *
39999599 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATTG-TTAAAGGAAGACTTATGACTCGATA-G
1 GGAAGACTCATGTCTCGAAATAAGAATGAGAATA-TGAATAAA-GAAGACTCACGACTCGAAATG
*
39999662 AGCATAAGATTT
64 AGAATAAGATTT
39999674 GTTTGAAGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 45 0.73
83 17 0.27
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (82 bp):
GGAAGACTCATGTCTCGAAATAAGAATGAGAATATGAATAAAGAAGACTCACGACTCGAAATGAG
AATAAGATTTTGATTAA
Found at i:40000223 original size:21 final size:21
Alignment explanation
Indices: 40000199--40000251 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
40000189 GAAATGAGTT
40000199 GTATCGGTAGTTAAAATTCAA
1 GTATCGGTAGTTAAAATTCAA
*
40000220 GTATTGGTAGTTAAAATTCAA
1 GTATCGGTAGTTAAAATTCAA
* *
40000241 GTTTCAGTAGT
1 GTATCGGTAGT
40000252 ACAAGCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (21 bp):
GTATCGGTAGTTAAAATTCAA
Found at i:40003911 original size:41 final size:41
Alignment explanation
Indices: 40003820--40003982 Score: 195
Period size: 41 Copynumber: 3.9 Consensus size: 41
40003810 GGTGTATAAA
* * *
40003820 AAGGAAGACTCATGTCTCGAGTTGAGCATAAGAAATTAT--AT
1 AAGGAAGACTCATGTCTCGAGATGAG-A-ATGAGATTATGAAT
40003861 AAATGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * * *
40003904 AAGGAAGACTCATGTCTCAAAATGAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* *
40003945 AAGGAAGACTCATGTCTCGAGAGGAGAATGAGAATATG
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATG
40003983 GTTAAAAGAA
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
41 76 0.72
42 5 0.05
43 25 0.24
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:40011029 original size:41 final size:41
Alignment explanation
Indices: 40010963--40011074 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 41
40010953 TTGTATAAAT
* ** *
40010963 GGAAGACTCATGTGTTGAGATGAGAATGAGATTCTAAATAA
1 GGAAGACTCATGTCTCAAGACGAGAATGAGATTCTAAATAA
* * * *
40011004 GGGAA-ACTCATGTCTCGAA-ACGAGAATGAAATTTTGATTAA
1 -GGAAGACTCATGTCTC-AAGACGAGAATGAGATTCTAAATAA
*
40011045 GGAAGACTCATGTCTCAAGAGGAGAATGAG
1 GGAAGACTCATGTCTCAAGACGAGAATGAG
40011075 GATATGGTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
40 6 0.11
41 46 0.81
42 5 0.09
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (41 bp):
GGAAGACTCATGTCTCAAGACGAGAATGAGATTCTAAATAA
Found at i:40017642 original size:41 final size:41
Alignment explanation
Indices: 40017530--40017716 Score: 196
Period size: 41 Copynumber: 4.5 Consensus size: 41
40017520 GGTGTATAAA
* * * * * *
40017530 AAGGAAGACTCATGTCTCGGGTTAAGCATGAGA-AATTGTATA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTA-TG-ATT
*
40017572 AATGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
* * * *
40017614 AAGGAAGACTCATGTCTCAAAATAAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
* *
40017655 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
* *
40017696 AAGGGAAGACTTATGACTCGA
1 AA-GGAAGACTCATGTCTCGA
40017717 TAGAGCATAA
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
41 71 0.58
42 21 0.17
43 29 0.24
44 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
Found at i:40017680 original size:82 final size:84
Alignment explanation
Indices: 40017530--40017706 Score: 232
Period size: 82 Copynumber: 2.1 Consensus size: 84
40017520 GGTGTATAAA
**** *
40017530 AAGGAAGACTCATGTCTCGGGTTAAGCATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAGA
1 AAGGAAGACTCATGTCTCAAAATAAGAATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAGA
*
40017595 TGAGAATGAGATTATGAAT
66 TGAGAATGAGAATATGAAT
** *
40017614 AAGGAAGACTCATGTCTCAAAATAAGAATGAGATTTTG-ATTAA-GGAAGACTCATGTCTCGAGA
1 AAGGAAGACTCATGTCTCAAAATAAGAATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAGA
**
40017677 TGAGAATGAGAATATGGTT
66 TGAGAATGAGAATATGAAT
40017696 AAGGGAAGACT
1 AA-GGAAGACT
40017707 TATGACTCGA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 38 0.47
83 12 0.15
84 31 0.38
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.25
Consensus pattern (84 bp):
AAGGAAGACTCATGTCTCAAAATAAGAATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAGA
TGAGAATGAGAATATGAAT
Found at i:40018858 original size:18 final size:18
Alignment explanation
Indices: 40018832--40018866 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40018822 AACAATATGA
40018832 AGGTCAAGGTCAAGATGG
1 AGGTCAAGGTCAAGATGG
* *
40018850 AGGTGAAGGTGAAGATG
1 AGGTCAAGGTCAAGATG
40018867 AAGATGAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.43, T:0.17
Consensus pattern (18 bp):
AGGTCAAGGTCAAGATGG
Found at i:40018874 original size:18 final size:18
Alignment explanation
Indices: 40018837--40018875 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40018827 TATGAAGGTC
* *
40018837 AAGGTCAAGATGGAGGTG
1 AAGGTCAAGATGAAGATG
*
40018855 AAGGTGAAGATGAAGATG
1 AAGGTCAAGATGAAGATG
40018873 AAG
1 AAG
40018876 AAGATGAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.41, T:0.15
Consensus pattern (18 bp):
AAGGTCAAGATGAAGATG
Found at i:40020534 original size:49 final size:49
Alignment explanation
Indices: 40020457--40020563 Score: 135
Period size: 49 Copynumber: 2.2 Consensus size: 49
40020447 GTCGCATTGC
* * *
40020457 AACTTGGGCTCCTAGTTCATAGTGGTTATATGGTCACGGGTTAAAGTAT
1 AACTAGGGCTCCTAGTTCATAGTGGTTATATAGTCACGAGTTAAAGTAT
* *
40020506 AACTAGGGCT-CTCAGTTGATAGTGGTTATATAGTCACGAGTTCAAGTAT
1 AACTAGGGCTCCT-AGTTCATAGTGGTTATATAGTCACGAGTTAAAGTAT
* *
40020555 GACTCGGGC
1 AACTAGGGC
40020564 CTCCAATTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 2 0.04
49 48 0.96
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (49 bp):
AACTAGGGCTCCTAGTTCATAGTGGTTATATAGTCACGAGTTAAAGTAT
Found at i:40023079 original size:3 final size:3
Alignment explanation
Indices: 40023071--40023097 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40023061 AGGGCCCAAT
40023071 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
40023098 GGGTTTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40023708 original size:50 final size:48
Alignment explanation
Indices: 40023643--40023845 Score: 133
Period size: 50 Copynumber: 4.1 Consensus size: 48
40023633 AGAAAAAAAG
*
40023643 AAAAAGTTTATATTTTTAAAAATAAAATTATGTTTTTTAGTTATTATAAA
1 AAAAAGTTTAAATTTTT--AAATAAAATTATGTTTTTTAGTTATTATAAA
* * ** *
40023693 AAAAAGTTTAAATTTTTAAACAAAATTTTGAATTTTTTAAACTATTTTGAAA
1 AAAAAGTTTAAATTTTTAAATAAAATTATG--TTTTTT-AGTTATTAT-AAA
* * * * * *
40023745 TAAAAGTTTAAATTTTTAAGT-AAAGTAGTGATTTTTA-TTA-AAAAAGA
1 AAAAAGTTTAAATTTTTAAATAAAATTA-TGTTTTTTAGTTATTATAA-A
* * * * * *
40023792 AAGAAAGTTTATATTTTAAAAATAAAAATATATTTTTTTGTTATTTTAAA
1 AA-AAAGTTTAAATTTT-TAAATAAAATTATGTTTTTTAGTTATTATAAA
40023842 AAAA
1 AAAA
40023846 TTAATTTTTA
Statistics
Matches: 115, Mismatches: 27, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
46 2 0.02
47 2 0.02
48 26 0.23
49 12 0.10
50 38 0.33
51 12 0.10
52 23 0.20
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (48 bp):
AAAAAGTTTAAATTTTTAAATAAAATTATGTTTTTTAGTTATTATAAA
Found at i:40023717 original size:21 final size:21
Alignment explanation
Indices: 40023689--40023734 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
40023679 TTAGTTATTA
*
40023689 TAAAAAAAAGTTT-AAATTTT
1 TAAACAAAAGTTTGAAATTTT
* *
40023709 TAAACAAAATTTTGAATTTTT
1 TAAACAAAAGTTTGAAATTTT
40023730 TAAAC
1 TAAAC
40023735 TATTTTGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (21 bp):
TAAACAAAAGTTTGAAATTTT
Found at i:40023938 original size:145 final size:149
Alignment explanation
Indices: 40023636--40023924 Score: 394
Period size: 145 Copynumber: 2.0 Consensus size: 149
40023626 AAAAAAGAGA
* *
40023636 AAAAAAG-AA-AAAGTTTATATTTTTAAAAATAAAATTATGTTTTTTAGTTATTATAAAAAAAAG
1 AAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTATAAAAAAAAG
* *
40023699 TTTAAATTTTTAAACAAAATTTTGAATTTTTTAAACTATTTTGAAATAAAAGTTTAAATTTTTAA
66 -TTAAATTTTTAAACAAAATTTTGAATTTTTTAAACTATTTCGAAATAAAAGTTTAAATTTTGAA
*
40023764 GTAAAGTAGTGATTTTTATT
130 ATAAAGTAGTGATTTTTATT
* *
40023784 AAAAAAGAAAGAAAGTTTATA-TTTTAAAAATAAAAATATATTTTTTTGTTATT-TTAAAAAAA-
1 AAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTATAAAAAAAAG
* * * * **
40023846 TT-AATTTTTAAACACAGTTTTG-ATTTATTTTAACTATTTCGAAATGAAAGTTTTGATTTTGAA
66 TTAAATTTTTAAACAAAATTTTGAATTT-TTTAAACTATTTCGAAATAAAAGTTTAAATTTTGAA
40023909 ATAAAGTAGTGATTTT
130 ATAAAGTAGTGATTTT
40023925 ATTTTAATTA
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
144 4 0.03
145 63 0.50
146 2 0.02
148 15 0.12
149 31 0.25
150 10 0.08
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (149 bp):
AAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTATAAAAAAAAG
TTAAATTTTTAAACAAAATTTTGAATTTTTTAAACTATTTCGAAATAAAAGTTTAAATTTTGAAA
TAAAGTAGTGATTTTTATT
Found at i:40024538 original size:10 final size:9
Alignment explanation
Indices: 40024485--40024544 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 9
40024475 CTTGTATAAT
40024485 TTTTATTTA
1 TTTTATTTA
40024494 TTCTTATTTCA
1 TT-TTATTT-A
40024505 TCTTTATTTA
1 T-TTTATTTA
40024515 TTTTCATATCTA
1 TTTT-AT-T-TA
40024527 TTTATATTTA
1 TTT-TATTTA
40024537 TTTT-TTTA
1 TTTTATTTA
40024545 CACATGCCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
8 4 0.09
9 6 0.14
10 15 0.34
11 10 0.23
12 8 0.18
13 1 0.02
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTATTTA
Found at i:40026028 original size:24 final size:25
Alignment explanation
Indices: 40025996--40026043 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
40025986 TCTTTAATAT
* *
40025996 TTATATTTTTTA-TCAATTTGACCA
1 TTATATTTTTAATTAAATTTGACCA
*
40026020 TTATTTTTTTAATTAAATTTGACC
1 TTATATTTTTAATTAAATTTGACC
40026044 CTTAATCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATATTTTTAATTAAATTTGACCA
Found at i:40026061 original size:25 final size:25
Alignment explanation
Indices: 40026010--40026061 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
40026000 ATTTTTTATC
* * * *
40026010 AATTTGACCATTATTTTTTTAATTA
1 AATTTGACCATTAATCTTTAAAATA
*
40026035 AATTTGACCCTTAATCTTTAAAATA
1 AATTTGACCATTAATCTTTAAAATA
40026060 AA
1 AA
40026062 AATCAAATCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (25 bp):
AATTTGACCATTAATCTTTAAAATA
Found at i:40026327 original size:17 final size:16
Alignment explanation
Indices: 40026293--40026324 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40026283 AACAAATAAT
40026293 TAAAAAATTATAAAAA
1 TAAAAAATTATAAAAA
*
40026309 TAAAAAATTTTAAAAA
1 TAAAAAATTATAAAAA
40026325 ATACAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAAATTATAAAAA
Found at i:40035933 original size:18 final size:18
Alignment explanation
Indices: 40035901--40035935 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40035891 AACTAGCAAA
* *
40035901 AAAAAAGAGAGAAGAAAG
1 AAAAAAGAAAAAAGAAAG
40035919 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
40035936 AGAAGGGGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAGAAAG
Found at i:40037079 original size:99 final size:100
Alignment explanation
Indices: 40036897--40037173 Score: 271
Period size: 101 Copynumber: 2.8 Consensus size: 100
40036887 AAGGGTGGAG
* * * *
40036897 TAAAACAAGTAACAAATCTCAACCTCCACTGAAGTTGCAGTGGAATGGAGTGAAG---CCAAAAC
1 TAAAACAAGTAACAGATCTCAATCTCC-CTGAAGTTGCAGTGGAATGAAGTGAAGTTACC-ACAC
* * *
40036959 CTTAAATCCTAT-ATCCTTAAAGTTATAGTGGATCA-GAT
64 C--AAATCCTATCTTCCTTAAAGTTACAGT-GAACAGGAT
* * **
40036997 TAAAACAAGTAACAGACCTCAATCTCCTTGAAGTTGCAGTGGAATGAAGCAAAGTTACCACACCA
1 TAAAACAAGTAACAGATCTCAATCTCCCTGAAGTTGCAGTGGAATGAAGTGAAGTTACCACACCA
*
40037062 AATCCTATCTTCC-TAAAGTTACAGTGAAGAGGAT
66 AATCCTATCTTCCTTAAAGTTACAGTGAACAGGAT
*** * *
40037096 TAAAACTATAGTAGTGGATCTCAATCTCCCTAAAGTTGTAGTGGAATGAAGTGAAGTTA-CATCA
1 TAAAAC-A-AGTAACAGATCTCAATCTCCCTGAAGTTGCAGTGGAATGAAGTGAAGTTACCA-CA
*
40037160 CCAAATCCAATCTT
63 CCAAATCCTATCTT
40037174 TTACCCCTAA
Statistics
Matches: 147, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
98 3 0.02
99 52 0.35
100 30 0.20
101 60 0.41
102 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (100 bp):
TAAAACAAGTAACAGATCTCAATCTCCCTGAAGTTGCAGTGGAATGAAGTGAAGTTACCACACCA
AATCCTATCTTCCTTAAAGTTACAGTGAACAGGAT
Found at i:40037238 original size:47 final size:47
Alignment explanation
Indices: 40037157--40037319 Score: 154
Period size: 47 Copynumber: 3.5 Consensus size: 47
40037147 TGAAGTTACA
* * ** *
40037157 TCACCAAATCCAATCTTTTACCCCTAATTTAGAGGAGAAGATTGAAG
1 TCACCACATCCAATCTTTTATCCCTAATCCAGAGGGGAAGATTGAAG
** * * *
40037204 TCATTATATCTAATCTTTTATCCCTAATCCAGAGGGGCAA-ATTAAAG
1 TCACCACATCCAATCTTTTATCCCTAATCCAGAGGGG-AAGATTGAAG
** *
40037251 TCACCACATCCAATCTTTT-TCTTTAATCCAGAGGGGTAGATTGAAG
1 TCACCACATCCAATCTTTTATCCCTAATCCAGAGGGGAAGATTGAAG
*
40037297 TCA-C-CATCAAATCTTTTACTCCC
1 TCACCACATCCAATCTTTTA-TCCC
40037320 ATCCAGTCTT
Statistics
Matches: 92, Mismatches: 20, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
44 12 0.13
45 2 0.02
46 26 0.28
47 50 0.54
48 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (47 bp):
TCACCACATCCAATCTTTTATCCCTAATCCAGAGGGGAAGATTGAAG
Found at i:40037325 original size:44 final size:46
Alignment explanation
Indices: 40037215--40037325 Score: 111
Period size: 46 Copynumber: 2.4 Consensus size: 46
40037205 CATTATATCT
*
40037215 AATCTTTTA-TCCCTAATCCAGAGGGGCAAATTAAAGTCACCACATCC
1 AATCTTTTACTCCC--ATCCAGAGGGGCAAATTAAAGTCACCACATCA
* *** * * *
40037262 AATCTTTTTCTTTAATCCAGAGGGGTAGATTGAAGTCA-C-CATCA
1 AATCTTTTACTCCCATCCAGAGGGGCAAATTAAAGTCACCACATCA
40037306 AATCTTTTACTCCCATCCAG
1 AATCTTTTACTCCCATCCAG
40037326 TCTTTTACCA
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
44 20 0.39
45 1 0.02
46 21 0.41
47 8 0.16
48 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (46 bp):
AATCTTTTACTCCCATCCAGAGGGGCAAATTAAAGTCACCACATCA
Found at i:40037368 original size:45 final size:45
Alignment explanation
Indices: 40037318--40037901 Score: 411
Period size: 45 Copynumber: 12.9 Consensus size: 45
40037308 TCTTTTACTC
* * * *
40037318 CCATCCAGTCTTTTACCACTAATCCATAGGGGCAGATTAAAGCAA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
* * ** *
40037363 CCATCCAGTCTTTTACCCCTAATCCAGAGTGATAGATTAAAGCAA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
* **
40037408 CCATCCAGTCTTTTACCCCTTTTACCCTTAATCTAGAGGGGCAGATTAAAGTTA
1 CCATCCAGTCTTTTA---C-----CCC-TAATCTAGAGGGGCAGATTGAAGCAA
* * * * *
40037462 CTATCCAATCTTTTACCCCTAATTTAGAGGGACAGATTAAAGTC-A
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAG-CAA
* * *
40037507 CCATCTAGTCTTTTACCCCTAAT-TAAGAGGGGAAGATTGAAGCCA
1 CCATCCAGTCTTTTACCCCTAATCT-AGAGGGGCAGATTGAAGCAA
* * * ** **
40037552 CCATCTAGTCCTCTAATCC-AAAGTA-A---G-AGATTGAAGCAA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
** * * * * *
40037591 CCATCCAG---TTTAAACCTCATCCAAAGGGGCAGACTGAAGCCA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
* * *
40037633 CCATCCAGTCTTTTACCCTTAATCTAGAGGGGTAGATTAAAGCAA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
* * * * *
40037678 GCATCCAATATTTTACCCCTGATCTAGAGGGGCAGATTGAAGCCA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
* *
40037723 CCATCCAGTCTTTTACCCCTAATCTAGAGAGGCAGATTGAAGCCA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
* * * * *
40037768 CCATCTAGTCTTTTACCCTTAATCTAGAGGGACAGTTTGAAGCTA
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
* * * * * *
40037813 TCATTCAGTCTTTTACCCTTAATGTAGAGGGGTAGATTAAAGTC-A
1 CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAG-CAA
* * **
40037858 CCAAATCCAATCTTTTACCCTTAAATCTA-AAAGGCAGATTGAAG
1 CC--ATCCAGTCTTTTACCCCT-AATCTAGAGGGGCAGATTGAAG
40037902 TTACAACATC
Statistics
Matches: 431, Mismatches: 82, Indels: 50
0.77 0.15 0.09
Matches are distributed among these distances:
36 6 0.01
37 2 0.00
38 1 0.00
39 18 0.04
40 1 0.00
41 1 0.00
42 18 0.04
43 1 0.00
44 5 0.01
45 304 0.71
46 4 0.01
47 27 0.06
48 6 0.01
51 1 0.00
53 3 0.01
54 33 0.08
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (45 bp):
CCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCAA
Found at i:40037454 original size:54 final size:54
Alignment explanation
Indices: 40037372--40037481 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 54
40037362 ACCATCCAGT
* * *
40037372 CTTTTACCCCTAATCCAGAGTGATAGATTAAAGCAACCATCCAGTCTTTTACCC
1 CTTTTACCCCTAATCCAGAGGGACAGATTAAAGCAACCATCCAATCTTTTACCC
* * * ** *
40037426 CTTTTACCCTTAATCTAGAGGGGCAGATTAAAGTTACTATCCAATCTTTTACCC
1 CTTTTACCCCTAATCCAGAGGGACAGATTAAAGCAACCATCCAATCTTTTACCC
40037480 CT
1 CT
40037482 AATTTAGAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (54 bp):
CTTTTACCCCTAATCCAGAGGGACAGATTAAAGCAACCATCCAATCTTTTACCC
Found at i:40037499 original size:99 final size:99
Alignment explanation
Indices: 40037327--40037526 Score: 269
Period size: 99 Copynumber: 2.0 Consensus size: 99
40037317 CCCATCCAGT
* *
40037327 CTTTTACCACTAATCCATAGGGGCAGATTAAAGCAACCATCCAGTCTTTTACCCCTAATCCAGAG
1 CTTTTACCACTAATCCAGAGGGGCAGATTAAAGCAACCATCCAATCTTTTACCCCTAATCCAGAG
* *
40037392 TGATAGATTAAAG-CAACCATCCAGTCTTTTACCC
66 GGACAGATTAAAGTC-ACCATCCAGTCTTTTACCC
* ** * **
40037426 CTTTTACC-CTTAATCTAGAGGGGCAGATTAAAGTTACTATCCAATCTTTTACCCCTAATTTAGA
1 CTTTTACCAC-TAATCCAGAGGGGCAGATTAAAGCAACCATCCAATCTTTTACCCCTAATCCAGA
*
40037490 GGGACAGATTAAAGTCACCATCTAGTCTTTTACCC
65 GGGACAGATTAAAGTCACCATCCAGTCTTTTACCC
40037525 CT
1 CT
40037527 AATTAAGAGG
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
98 1 0.01
99 86 0.98
100 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (99 bp):
CTTTTACCACTAATCCAGAGGGGCAGATTAAAGCAACCATCCAATCTTTTACCCCTAATCCAGAG
GGACAGATTAAAGTCACCATCCAGTCTTTTACCC
Found at i:40039393 original size:22 final size:21
Alignment explanation
Indices: 40039368--40039416 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
40039358 TTATTTTTAC
*
40039368 TTTATATCTAATTTTATTTATT
1 TTTATAGCT-ATTTTATTTATT
*
40039390 TTTATAGGTATTTTATTTATT
1 TTTATAGCTATTTTATTTATT
40039411 TGTTAT
1 T-TTAT
40039417 TAGTTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTATAGCTATTTTATTTATT
Found at i:40042189 original size:894 final size:894
Alignment explanation
Indices: 40040253--40043835 Score: 5934
Period size: 894 Copynumber: 4.0 Consensus size: 894
40040243 TTCCTCATGC
* * * *
40040253 GTAACCAACTCCCGAACTTATTTTATGGTTTCAAAGACTAAAATTTTTGTTTGGAGGATTTTAAA
1 GTAACCGACTCCCGAACTTGTTTTATGATTTCAAAGACTAAAATTTTTGTTTGGAGGATTTGAAA
* * * *
40040318 ATTTACAAAGAGATCTAATCACACCTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTCT
66 ATTTACGAAGTGATCCAATCACACCTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTCC
* ** * *
40040383 AAAATATAAGTCGAGA------TTTAAAAAAAAAAGATTTTGAAACTAATCAACCACACAACAGA
131 AAAATATAAATCGAGACTTTTTTTTCCAAAAAAATGATTTCGAAACTAATCAACCACACAACAGA
* *
40040442 GCACTCCCAAATCCTACATACGAAGAAAAATCATATCAATCAACAACCAAAAGTTAAACTAATAA
196 GCACTCCCAAATCCTACATACGAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATAA
* * * *
40040507 TCAACTTCGGA-ACTTCCTCTTTACCTAAAATAGACCCCAAAACCTACATTCGAGTACTTACCCC
261 TCAACTTC-GATACTTCCCCTTTACCAAAAATAGACCCCAAAACTTACATTCGAGTACTTACCCT
** * * * ***
40040571 CCAAAAAAAGCCATTTAAAGCATTTAATTTGCTGGGAATTTGTCTAACATCACACATTCCTCTGT
325 GAAAAAAAAGCCATTCAAAGCACTTAATTTGCTAGGAATTTGTCTAACATCACACATTCCTCCCC
* * *
40040636 TATTAGAAAGCAAAACCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTACCAAT
390 TATTAGAAAGAAAAATCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAAT
* *
40040701 ACAACTAAAACCTTTACCACCGAAACAAAACAATAATACTTACATCGAATTACTTACGTTCAAAA
455 ACAACTAAAACCTTTACCATCGAAACAAAACAATAATACTTACATTGAATTACTTACGTTCAAAA
* * *
40040766 CTAATAATGCAACAAAACGCTCGTATGAATGATGAACAAAGAATCGATAGCAAGATGGGCAAGCA
520 CTAATAATGCAACAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGCA
40040831 AAGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAATGTGAC
585 AAGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAATGTGAC
*
40040896 AAGAGGGGGAGTAGT-GACGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATTTTTTTAAA
650 AAGAGGGGGAGTAGTGGACGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATTTTTTT-TA
* * *
40040960 AATAATAAGAATTAAAATCAGGATGTTCTAATAATATCCTAACTTACTAGATATTTTTT-TTAGA
714 AATAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTAGAT-TTTTTTGTTAGA
* * * *
40041024 ATTCATATTGAACTCAAACTCTAATAAATAGCAGAAAATAAAAAAATATTTCACATTTGCGCATA
778 ATTCATATTGAACTCAAATTCTAACAAATAGTAGGAAAT-AAAAAATATTTCACATTTGCGCATA
*
40041089 ATGGGATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
842 ACGGGATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
* ** * *
40041142 ATAATTGACTCCCGAACTTGTTTTATGGTTTCAAAGACTAAAATTTTTGTTTGGAGGATTTTAAA
1 GTAACCGACTCCCGAACTTGTTTTATGATTTCAAAGACTAAAATTTTTGTTTGGAGGATTTGAAA
* * * * *
40041207 ATTTAC-AAGGTGATCTAATTACACTTATTTTTAAAAGATTGGTGGCGACTCAATTTTTATTTTC
66 ATTTACGAA-GTGATCCAATCACACCTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTC
* * * *
40041271 TAAAATATAAATCGAGACTTTTTTTTTCAAAAAAATGATTTTGAAACTAATCAACCACACAACAA
130 CAAAATATAAATCGAGACTTTTTTTTCCAAAAAAATGATTTCGAAACTAATCAACCACACAACAG
*
40041336 AGCACT-CCAAATCCTACATACAAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATA
195 AGCACTCCCAAATCCTACATACGAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATA
*
40041400 ATCAACTTCGGTACTTCCTCC-TTACCAAAAATAGACCCCAAAACTTACATTCGAGTACTTACCC
260 ATCAACTTCGATACTTCC-CCTTTACCAAAAATAGACCCCAAAACTTACATTCGAGTACTTACCC
*
40041464 TGAAAAAAAAGCTATTCAAAGCACTTAATTTGCTAGGAATTTGTCTAACATCACACATTCCTCCC
324 TGAAAAAAAAGCCATTCAAAGCACTTAATTTGCTAGGAATTTGTCTAACATCACACATTCCTCCC
40041529 CTATTAGAAAGAAAAATCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAA
389 CTATTAGAAAGAAAAATCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAA
40041594 TACAACTAAAACCTTTACCATCGAAACAAAACAATAATACTTACATTGAATTACTTACGTTCAAA
454 TACAACTAAAACCTTTACCATCGAAACAAAACAATAATACTTACATTGAATTACTTACGTTCAAA
40041659 ACTAATAATGCAACAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGC
519 ACTAATAATGCAACAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGC
40041724 AAAGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAATGTGA
584 AAAGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAATGTGA
*
40041789 CAAGAGGGGGAGTAGTGGGCGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATTTTTTTTA
649 CAAGAGGGGGAGTAGTGGACGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATTTTTTTTA
40041854 AATAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTAGATTTTTTTGTTAGAA
714 AATAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTAGATTTTTTTGTTAGAA
40041919 TTCATATTGAACTCAAATTCTAACAAATAGTAGGAAATAAAAAATATTTCACATTTGCGCATAAC
779 TTCATATTGAACTCAAATTCTAACAAATAGTAGGAAATAAAAAATATTTCACATTTGCGCATAAC
40041984 GGGATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
844 GGGATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
* * *
40042035 GTAACCGACTCCTGAACTTGTTTTATGATTTCAAAGATTAAAATTTTTGTTTGGAGGATTTGAAG
1 GTAACCGACTCCCGAACTTGTTTTATGATTTCAAAGACTAAAATTTTTGTTTGGAGGATTTGAAA
* * *
40042100 ATTTATGAATTGATCCAATCACACTTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTCC
66 ATTTACGAAGTGATCCAATCACACCTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTCC
* * *
40042165 AAAATATAAATTGAGACTTTTTTTTTCCAAAAAAATGGTTTCGAAACTAATCAACCACTCAACAG
131 AAAATATAAATCGAGAC-TTTTTTTTCCAAAAAAATGATTTCGAAACTAATCAACCACACAACAG
*
40042230 AGCACTCCCAAATCCTATATACGAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATA
195 AGCACTCCCAAATCCTACATACGAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATA
* * *
40042295 ATCAACTTCGATACTTCCCCTTTACCAAAAATAGACTCTAAAATTTACATTCGAGTACTTACCCT
260 ATCAACTTCGATACTTCCCCTTTACCAAAAATAGACCCCAAAACTTACATTCGAGTACTTACCCT
*
40042360 G-AAAAAAAGCTATTCAAAGCACTTAATTTGCTAGGAATTTGTCTAACATCACACATTCCTCCCC
325 GAAAAAAAAGCCATTCAAAGCACTTAATTTGCTAGGAATTTGTCTAACATCACACATTCCTCCCC
40042424 TATTAGAAAGAAAAATCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAAT
390 TATTAGAAAGAAAAATCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAAT
*
40042489 ACAACTAAAACCTTTACCATCGACACAAAACAATAATACTTACATTGAATTACTTACGTTCAAAA
455 ACAACTAAAACCTTTACCATCGAAACAAAACAATAATACTTACATTGAATTACTTACGTTCAAAA
40042554 CTAATAATGCAACAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGCA
520 CTAATAATGCAACAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGCA
40042619 AAGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAATGTGAC
585 AAGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAATGTGAC
*
40042684 AAGAGGGGGAGTAGTGGGCGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATTTTTTTTAA
650 AAGAGGGGGAGTAGTGGACGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATTTTTTTTAA
40042749 ATAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTAGATTTTTTTGTTAGAAT
715 ATAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTAGATTTTTTTGTTAGAAT
40042814 TCATATTGAACTCAAATTCTAACAAATAGTAGGAAATAAAAAATATTTCACATTTGCGCATAACG
780 TCATATTGAACTCAAATTCTAACAAATAGTAGGAAATAAAAAATATTTCACATTTGCGCATAACG
40042879 GGATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
845 GGATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
* * *
40042929 GTAACCGACTCCTGAACTTGTTTTATGATTTCAAAGATTAAAATTTTTGTTTGGAGGATTTGAAG
1 GTAACCGACTCCCGAACTTGTTTTATGATTTCAAAGACTAAAATTTTTGTTTGGAGGATTTGAAA
*
40042994 ATTTACGAATTGATCCAATCACACCTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTCC
66 ATTTACGAAGTGATCCAATCACACCTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTCC
* * *
40043059 AAAATATAAATTGAGACTTTTTTTTTCCAAAAAAATGGTTTCGAAACTAATCAACCACTCAACAG
131 AAAATATAAATCGAGAC-TTTTTTTTCCAAAAAAATGATTTCGAAACTAATCAACCACACAACAG
40043124 AGCACTCCCAAATCCTACATACGAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATA
195 AGCACTCCCAAATCCTACATACGAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATA
* * * *
40043189 ATCAACTTCGATACTTCCCCTTTACCAAAAATAGACTCTAAAATTTACATTTGAGTACTTACCCT
260 ATCAACTTCGATACTTCCCCTTTACCAAAAATAGACCCCAAAACTTACATTCGAGTACTTACCCT
*
40043254 -AAAAAAAAGCCATTCAAAGCACTTAATTTGCTGGGAATTTGTCTAACATCACACATTCCTCCCC
325 GAAAAAAAAGCCATTCAAAGCACTTAATTTGCTAGGAATTTGTCTAACATCACACATTCCTCCCC
*
40043318 TATTAGAAAGAAAAATCATTAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAAT
390 TATTAGAAAGAAAAATCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAAT
*
40043383 ACAGCTAAAACCTTTACCATCGAAACAAAACAATAATACTTACATTGAATTACTTACGTTCAAAA
455 ACAACTAAAACCTTTACCATCGAAACAAAACAATAATACTTACATTGAATTACTTACGTTCAAAA
* *
40043448 CTAAAAATGCAAGAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGCA
520 CTAATAATGCAACAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGCA
*
40043513 AAGAACAATGAAAAATCAGGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAAAGAAAA
585 AAGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAA-G-----GAAAAAGAAAA
** * * * *
40043578 TGTGACAAGATAGGGAGTAATGGACATTTTGAGAAGGAGAGAAATTAGGGGAATTTTACAATTCT
644 TGTGACAAGAGGGGGAGTAGTGGACGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATT-T
*
40043643 TTTTTAGAATAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTATATTTTTTT
708 TTTTTA-AATAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTAGA--TTTTT
*
40043708 TTGTTAGAATTCATATTGAACTCAACTTCTAACAAATAGTAGGAAATAAAAAATATTTCACATTT
770 TTGTTAGAATTCATATTGAACTCAAATTCTAACAAATAGTAGGAAATAAAAAATATTTCACATTT
* * * * *
40043773 GAGCATAACAGGATTCAAACACAAGCCCTAGGGGTAAGTTGAAGCGTTACCATTAAACCA
835 GCGCATAACGGGATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
40043833 GTA
1 GTA
40043836 GGGTCATCCT
Statistics
Matches: 2564, Mismatches: 104, Indels: 37
0.95 0.04 0.01
Matches are distributed among these distances:
888 2 0.00
889 132 0.05
893 212 0.08
894 1761 0.69
895 206 0.08
900 67 0.03
901 7 0.00
902 50 0.02
904 127 0.05
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (894 bp):
GTAACCGACTCCCGAACTTGTTTTATGATTTCAAAGACTAAAATTTTTGTTTGGAGGATTTGAAA
ATTTACGAAGTGATCCAATCACACCTATTTTTAAAAGATTGGTGGCGACTCCATTTTCATTTTCC
AAAATATAAATCGAGACTTTTTTTTCCAAAAAAATGATTTCGAAACTAATCAACCACACAACAGA
GCACTCCCAAATCCTACATACGAAGAAAAATCATATCAATCAACAACCACAAGTTAATCTAATAA
TCAACTTCGATACTTCCCCTTTACCAAAAATAGACCCCAAAACTTACATTCGAGTACTTACCCTG
AAAAAAAAGCCATTCAAAGCACTTAATTTGCTAGGAATTTGTCTAACATCACACATTCCTCCCCT
ATTAGAAAGAAAAATCATCAATCTCGAAATCCATAACGTACTGAAATGTAAACTAAGTATCAATA
CAACTAAAACCTTTACCATCGAAACAAAACAATAATACTTACATTGAATTACTTACGTTCAAAAC
TAATAATGCAACAACACACTCGTATGAATGATGGACAAAGAATCGATAGCAAGATGGGCAAGCAA
AGAACAATGAAAAATCAAGAAGAAAAGAAGCAAGAAGGAAGGAAAAGGAAAAAGAAAATGTGACA
AGAGGGGGAGTAGTGGACGTTTTGGGAAGGAGAGAAATTAGGAGAATTTTACAATTTTTTTTAAA
TAATAAGAATTAAAATCAAGATATTCTAATAATATCCTAACTCACTAGATTTTTTTGTTAGAATT
CATATTGAACTCAAATTCTAACAAATAGTAGGAAATAAAAAATATTTCACATTTGCGCATAACGG
GATTCAAACACAAGCCCTAGGGGCAAGTTGAAGCCTTACCATTGAACCA
Found at i:40048448 original size:17 final size:17
Alignment explanation
Indices: 40048428--40048467 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
40048418 TAGATGCAGC
*
40048428 GACAATAAAAATCCAGT
1 GACAATAAAAATCCAGG
*
40048445 GACAATAAAAATGCAGG
1 GACAATAAAAATCCAGG
40048462 GACAAT
1 GACAAT
40048468 TATACTACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (17 bp):
GACAATAAAAATCCAGG
Found at i:40058537 original size:24 final size:24
Alignment explanation
Indices: 40058499--40058708 Score: 168
Period size: 24 Copynumber: 8.7 Consensus size: 24
40058489 GTTTAGTGCA
40058499 TTTACGCTCGCCAGCTAATGTACG
1 TTTACGCTCGCCAGCTAATGTACG
* *
40058523 TTTACGCTTGTCAGCTAATGTACG
1 TTTACGCTCGCCAGCTAATGTACG
* * *
40058547 TTTATGCTCTCCAGCTAATGTACA
1 TTTACGCTCGCCAGCTAATGTACG
*
40058571 TTTACGCTCGTCAGCTAATGTACG
1 TTTACGCTCGCCAGCTAATGTACG
* * * * * **
40058595 TTTACACTAGACAACTAATATGTG
1 TTTACGCTCGCCAGCTAATGTACG
* * *
40058619 TTTACGCTCACCAGCAAATGCACG
1 TTTACGCTCGCCAGCTAATGTACG
* ** * * *
40058643 TTTACACTCGTTAACTAATTTACA
1 TTTACGCTCGCCAGCTAATGTACG
* * *
40058667 TTTATGCTCACCAGTTAATGTATACG
1 TTTACGCTCGCCAGCTAATG--TACG
*
40058693 TTTACGCTCTCCAGCT
1 TTTACGCTCGCCAGCT
40058709 GATAGCATTA
Statistics
Matches: 135, Mismatches: 49, Indels: 2
0.73 0.26 0.01
Matches are distributed among these distances:
24 119 0.88
26 16 0.12
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTAATGTACG
Found at i:40058622 original size:72 final size:72
Alignment explanation
Indices: 40058497--40058653 Score: 188
Period size: 72 Copynumber: 2.2 Consensus size: 72
40058487 AAGTTTAGTG
* * * * * * * *
40058497 CATTTACGCTCGCCAGCTAATGTACGTTTACGCTTGTCAGCTAATGTACGTTTATGCTCTCCAGC
1 CATTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACGCTCACCAGC
* *
40058562 TAATGTA
66 AAATGCA
**
40058569 CATTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATGTGTTTACGCTCACCAGC
1 CATTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACGCTCACCAGC
40058634 AAATGCA
66 AAATGCA
* *
40058641 CGTTTACACTCGT
1 CATTTACGCTCGT
40058654 TAACTAATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (72 bp):
CATTTACGCTCGTCAGCTAATGTACGTTTACACTAGACAACTAATATACGTTTACGCTCACCAGC
AAATGCA
Found at i:40059148 original size:26 final size:26
Alignment explanation
Indices: 40059119--40059168 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
40059109 AAGAATGCCG
40059119 CTGCATGAACATGTCCAA-AATTGTCA
1 CTGCATGAACATGT-CAAGAATTGTCA
*
40059145 CTGCATGAACGTGTCAAGAATTGT
1 CTGCATGAACATGTCAAGAATTGT
40059169 GCCCAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (26 bp):
CTGCATGAACATGTCAAGAATTGTCA
Found at i:40059982 original size:16 final size:16
Alignment explanation
Indices: 40059961--40059991 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40059951 TTGTGGATCC
40059961 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
40059977 CATTTTATCTTTATT
1 CATTTTACCTTTATT
40059992 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:40062397 original size:69 final size:69
Alignment explanation
Indices: 40062316--40062450 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 69
40062306 TTAATTGTCA
*
40062316 CTGCATTTGCGTTATCATTGCATTTCCATTTGTTAATGCATTGAGGAAAATACAGACTTTAAGTT
1 CTGCATTTGCGTTATCATTGCATTTCCATTTGTCAATGCATTGAGGAAAATACAGACTTTAAGTT
40062381 TGAG
66 TGAG
* * * *
40062385 CTGCATTTGCGTTATCATTGCGTTTCCATTTGTCAATGTATTGAGGACAATGCAGACTTTAAGTT
1 CTGCATTTGCGTTATCATTGCATTTCCATTTGTCAATGCATTGAGGAAAATACAGACTTTAAGTT
40062450 T
66 T
40062451 TAGGGGAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (69 bp):
CTGCATTTGCGTTATCATTGCATTTCCATTTGTCAATGCATTGAGGAAAATACAGACTTTAAGTT
TGAG
Found at i:40062995 original size:16 final size:16
Alignment explanation
Indices: 40062958--40062991 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40062948 TCAGTCATAT
40062958 AAAA-AATAGAAGAAG
1 AAAAGAATAGAAGAAG
40062973 AAAAGAATAGAA-AAG
1 AAAAGAATAGAAGAAG
40062988 AAAA
1 AAAA
40062992 AGAAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AAAAGAATAGAAGAAG
Found at i:40063623 original size:37 final size:37
Alignment explanation
Indices: 40063549--40063636 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 37
40063539 CAAATTTGCG
* * *
40063549 CCCAAAACTGTCGCCACATGAGCACTTCCAGATTGCA
1 CCCAAAACTGTCACCACATGAACACTTCCAGAATGCA
* * **
40063586 CCCAAAACTGTCACCACATGAATATTTCTGGAATGCA
1 CCCAAAACTGTCACCACATGAACACTTCCAGAATGCA
* *
40063623 CCTAAGACTGTCAC
1 CCCAAAACTGTCAC
40063637 TGCATAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.22
Consensus pattern (37 bp):
CCCAAAACTGTCACCACATGAACACTTCCAGAATGCA
Found at i:40063711 original size:37 final size:37
Alignment explanation
Indices: 40063631--40063711 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
40063621 CACCTAAGAC
* * *
40063631 TGTCACTGCATAAATATTCTTCAATTGCATCCAGGAC
1 TGTCGCTGCATAAATATTCTTCAATTGCACCCAGGAA
* *
40063668 TATCGCTGCATAAGTATTCTTCAATTGCACCCAGGAA
1 TGTCGCTGCATAAATATTCTTCAATTGCACCCAGGAA
40063705 TGTCGCT
1 TGTCGCT
40063712 ACATGAACGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (37 bp):
TGTCGCTGCATAAATATTCTTCAATTGCACCCAGGAA
Found at i:40064801 original size:24 final size:24
Alignment explanation
Indices: 40064772--40064872 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
40064762 ACGCGATCAC
40064772 CAGCTAATGTACGTTTACGCTCGT
1 CAGCTAATGTACGTTTACGCTCGT
* * * ** *
40064796 CGGCTAAAGTATGTTTACAATTGT
1 CAGCTAATGTACGTTTACGCTCGT
* ** *
40064820 CAACTTCTGCACGTTTACGCTCGT
1 CAGCTAATGTACGTTTACGCTCGT
** *
40064844 CAGCTTCTGTACATTTACGCTCGT
1 CAGCTAATGTACGTTTACGCTCGT
40064868 CAGCT
1 CAGCT
40064873 TTTCAGATAT
Statistics
Matches: 58, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (24 bp):
CAGCTAATGTACGTTTACGCTCGT
Found at i:40070691 original size:48 final size:48
Alignment explanation
Indices: 40070623--40070793 Score: 184
Period size: 48 Copynumber: 3.6 Consensus size: 48
40070613 TACGCTTGCT
* * *
40070623 AGCTAATGTACGTTTACGCTCATCAACTAATATACGTTTACT-CTCGCC
1 AGCTAATATACGTTTACGCTCGTCAGCTAATATACGTTTA-TGCTCGCC
* * * *
40070671 AGTTAATATACATTTACGCTCGTCAGCTAATGTATGTTTATGCTCGCC
1 AGCTAATATACGTTTACGCTCGTCAGCTAATATACGTTTATGCTCGCC
* ** * *
40070719 AGCTAATATACGTTTATGCTCGTCAGCTAACGTACATTTATGCTCGTC
1 AGCTAATATACGTTTACGCTCGTCAGCTAATATACGTTTATGCTCGCC
** *
40070767 AGCTTCTGTACGTTTA-GCTCGTCAGCT
1 AGCTAATATACGTTTACGCTCGTCAGCT
40070794 TTTTCAGATA
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
47 12 0.11
48 93 0.89
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (48 bp):
AGCTAATATACGTTTACGCTCGTCAGCTAATATACGTTTATGCTCGCC
Found at i:40070726 original size:72 final size:71
Alignment explanation
Indices: 40070609--40070793 Score: 212
Period size: 72 Copynumber: 2.6 Consensus size: 71
40070599 AAGCTCAATT
* * *
40070609 CATTTACGCTTG-CTAGCTAATGTACGTTTACGCTCATCAACTAATATACGTTTACT-CTCGCCA
1 CATTTACGCTCGTC-AGCTAATGTACGTTTA-GCTCGTCAGCTAATATACGTTTA-TGCTCGCCA
* *
40070672 GTTAATATA
63 GCTAACATA
* * *
40070681 CATTTACGCTCGTCAGCTAATGTATGTTTATGCTCGCCAGCTAATATACGTTTATGCTCGTCAGC
1 CATTTACGCTCGTCAGCTAATGTACGTTTA-GCTCGTCAGCTAATATACGTTTATGCTCGCCAGC
*
40070746 TAACGTA
65 TAACATA
* **
40070753 CATTTATGCTCGTCAGCTTCTGTACGTTTAGCTCGTCAGCT
1 CATTTACGCTCGTCAGCTAATGTACGTTTAGCTCGTCAGCT
40070794 TTTTCAGATA
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
71 11 0.11
72 84 0.88
73 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (71 bp):
CATTTACGCTCGTCAGCTAATGTACGTTTAGCTCGTCAGCTAATATACGTTTATGCTCGCCAGCT
AACATA
Found at i:40070758 original size:24 final size:24
Alignment explanation
Indices: 40070623--40070793 Score: 132
Period size: 24 Copynumber: 7.2 Consensus size: 24
40070613 TACGCTTGCT
* * *
40070623 AGCTAATGTACGTTTACGCTCATC
1 AGCTAACGTACGTTTATGCTCGTC
* ** *
40070647 AACTAATATACGTTTACT-CTCGCC
1 AGCTAACGTACGTTTA-TGCTCGTC
* ** * *
40070671 AGTTAATATACATTTACGCTCGTC
1 AGCTAACGTACGTTTATGCTCGTC
* * *
40070695 AGCTAATGTATGTTTATGCTCGCC
1 AGCTAACGTACGTTTATGCTCGTC
**
40070719 AGCTAATATACGTTTATGCTCGTC
1 AGCTAACGTACGTTTATGCTCGTC
*
40070743 AGCTAACGTACATTTATGCTCGTC
1 AGCTAACGTACGTTTATGCTCGTC
*
40070767 AGCT-TCTGTACGTTTA-GCTCGTC
1 AGCTAAC-GTACGTTTATGCTCGTC
40070790 AGCT
1 AGCT
40070794 TTTTCAGATA
Statistics
Matches: 120, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
23 12 0.10
24 108 0.90
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (24 bp):
AGCTAACGTACGTTTATGCTCGTC
Found at i:40071560 original size:11 final size:11
Alignment explanation
Indices: 40071529--40071561 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
40071519 GATTTTCTAC
40071529 CATTTCCTTTA
1 CATTTCCTTTA
40071540 -ATTTCCTTTA
1 CATTTCCTTTA
*
40071550 CATTTCTTTTA
1 CATTTCCTTTA
40071561 C
1 C
40071562 TTATTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (11 bp):
CATTTCCTTTA
Found at i:40075372 original size:20 final size:21
Alignment explanation
Indices: 40075334--40075375 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
40075324 CTATTCTCTT
40075334 CACCTAAACACTCTCAAATCA
1 CACCTAAACACTCTCAAATCA
* *
40075355 CACCTAAA-TCTCTTAAATCA
1 CACCTAAACACTCTCAAATCA
40075375 C
1 C
40075376 TCACCCCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (21 bp):
CACCTAAACACTCTCAAATCA
Found at i:40095005 original size:15 final size:16
Alignment explanation
Indices: 40094985--40095017 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40094975 ATTAAAAAAA
40094985 TTAATTTGATGT-TTT
1 TTAATTTGATGTATTT
*
40095000 TTAATTTTATGTATTT
1 TTAATTTGATGTATTT
40095016 TT
1 TT
40095018 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (16 bp):
TTAATTTGATGTATTT
Found at i:40095168 original size:19 final size:20
Alignment explanation
Indices: 40095131--40095171 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
40095121 ATAATAAAAA
*
40095131 AAATAAGCAAAAGTTCAAGT
1 AAATAAGCAAAAGTCCAAGT
*
40095151 AAATAA-CATAAGTCCAAGT
1 AAATAAGCAAAAGTCCAAGT
40095170 AA
1 AA
40095172 CAACAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (20 bp):
AAATAAGCAAAAGTCCAAGT
Found at i:40095590 original size:58 final size:58
Alignment explanation
Indices: 40095505--40095623 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 58
40095495 AAAGAAGTTT
* *
40095505 TTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGATTATAAATATTTGGATTTAA
1 TTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGATTAAAAATATTTGGATTTAA
* * * * * *
40095563 TTTATTAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTAA
1 TTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGATTAAAAATATTTGGATTTAA
40095621 TTT
1 TTT
40095624 GTTGATGGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (58 bp):
TTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGATTAAAAATATTTGGATTTAA
Found at i:40095637 original size:58 final size:58
Alignment explanation
Indices: 40095528--40095638 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
40095518 TTTAGGAATA
* **
40095528 AAATTATATTTGGGATTATAAATATTTGGATTTAATTTATTAGTGTTTTTTAATAATG
1 AAATTATATTTGGGATTAAAAATATTTGGATTTAATTTATTAGTGGGTTTTAATAATG
* * *
40095586 AAATTATATTTGGGTTTAAAAATATTTGGGTTTAATTTGTT-GATGGGTTTTAA
1 AAATTATATTTGGGATTAAAAATATTTGGATTTAATTTATTAG-TGGGTTTTAA
40095639 ATATTAGGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 1 0.02
58 45 0.98
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.50
Consensus pattern (58 bp):
AAATTATATTTGGGATTAAAAATATTTGGATTTAATTTATTAGTGGGTTTTAATAATG
Found at i:40096933 original size:33 final size:33
Alignment explanation
Indices: 40096891--40096957 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
40096881 CGTGTCAGAA
40096891 AAACTCTCTAGTGCCGCCACTTAGAATCTATCC
1 AAACTCTCTAGTGCCGCCACTTAGAATCTATCC
40096924 AAACTCTCTAGTGCCGCCACTTAGAATCTATCC
1 AAACTCTCTAGTGCCGCCACTTAGAATCTATCC
40096957 A
1 A
40096958 CTTAACTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.27
Consensus pattern (33 bp):
AAACTCTCTAGTGCCGCCACTTAGAATCTATCC
Found at i:40103036 original size:15 final size:16
Alignment explanation
Indices: 40103006--40103044 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
40102996 TAATAAAAAT
40103006 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
40103023 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
40103038 ATAATTT
1 ATAATTT
40103045 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:40104000 original size:20 final size:22
Alignment explanation
Indices: 40103966--40104005 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
40103956 TTTTAAAATT
40103966 ATTTTTTATTGTTATAAAATGA
1 ATTTTTTATTGTTATAAAATGA
40103988 ATTTTTT-TT-TTATAAAAT
1 ATTTTTTATTGTTATAAAAT
40104006 TATTAAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTTTTATTGTTATAAAATGA
Found at i:40104816 original size:27 final size:28
Alignment explanation
Indices: 40104771--40104823 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
40104761 ATGATGATAG
40104771 TTTTATAAAAATAAAAAAATAATTTTCA
1 TTTTATAAAAATAAAAAAATAATTTTCA
40104799 TTTTATAAAAAT-AAAAAATAATTTT
1 TTTTATAAAAATAAAAAAATAATTTT
40104824 AATAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTTATAAAAATAAAAAAATAATTTTCA
Found at i:40106920 original size:2 final size:2
Alignment explanation
Indices: 40106913--40106955 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
40106903 ACCACTAACT
40106913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40106954 TA
1 TA
40106956 ACAACCTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40110080 original size:21 final size:19
Alignment explanation
Indices: 40110056--40110096 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
40110046 TGTTGAATGT
40110056 TGATAAACTTGAATTTTAGCA
1 TGATAAA-TTGAATTTT-GCA
*
40110077 TGATTAATTGAATTTTGCA
1 TGATAAATTGAATTTTGCA
40110096 T
1 T
40110097 ACTTGTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (19 bp):
TGATAAATTGAATTTTGCA
Found at i:40113378 original size:2 final size:2
Alignment explanation
Indices: 40113373--40113398 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40113363 TAAAAAAAAA
40113373 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
40113399 CATTTTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40123737 original size:23 final size:22
Alignment explanation
Indices: 40123669--40123744 Score: 91
Period size: 22 Copynumber: 3.4 Consensus size: 22
40123659 AATAAAATAG
40123669 TTGAGAGAATAAATGAATAGGA
1 TTGAGAGAATAAATGAATAGGA
* *
40123691 TGGAGAGAATAAATGAATATGA
1 TTGAGAGAATAAATGAATAGGA
*
40123713 TTGAGAGAATTGAGA-GAATAGGA
1 TTGAGAGAA-T-AAATGAATAGGA
*
40123736 TTGAAAGAA
1 TTGAGAGAA
40123745 AAAAAACTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 28 0.61
23 16 0.35
24 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (22 bp):
TTGAGAGAATAAATGAATAGGA
Found at i:40125415 original size:12 final size:12
Alignment explanation
Indices: 40125400--40125424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40125390 GCTCTCTAGC
40125400 TTTCCCTTCCAT
1 TTTCCCTTCCAT
40125412 TTTCCCTTCCAT
1 TTTCCCTTCCAT
40125424 T
1 T
40125425 CTCTTTCCGA
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:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTCCCTTCCAT
Found at i:40127034 original size:414 final size:416
Alignment explanation
Indices: 40126262--40127092 Score: 1522
Period size: 414 Copynumber: 2.0 Consensus size: 416
40126252 TAATTAAGTA
*
40126262 ATTAAAGCAATTACCTAACACATTTATGTCATATTGATTAAAACTTAGAAACCGTGAATTGAAAT
1 ATTAAAGCAATTACCTAACACATTTATGTCATATTGATTAAAACTTAAAAACCGTGAATTGAAAT
*
40126327 TTAATTTAATTTTTATTTTTAACTTTGATTAATTTTAGTTAAGTTTGATACTCTTCCAAATTACT
66 TTAATTTAATTTTTATTTTTAACTTTGATTAATTTTAGTTAAGTTTGATACTCTTCCAAATTAAT
*
40126392 ATTTTTTTCTTAAGATTAAATATTTCATAAATACTTTTCCTAGCACAATCCCTGTGGGTACGATA
131 ATTTTTTTCTTAAGATTAAATATTTCATAAATACTTTTCCTAGCACAATACCTGTGGGTACGATA
* * *
40126457 CTAGGCATTTACTTGTTACTTTATTACTTGAATACGATTTTGTACACTTGCACATTTTCATCTTT
196 CTAGACATTTACTTGTTACTTTATTACTTAAATACAATTTTGTACACTTGCACATTTTCATCTTT
*
40126522 CCAACAACTACTAGTCACCACCGACCACCGTAACCCAACGCAGTGGTGCACCTTCCCATCCTATC
261 CCAACAACTACTAGTCACCACCGACCACCGTAACCCAACGCAATGGTGCACCTTCCCATCCTATC
*
40126587 ACTTCACTCACCACCGTCCGATATTTCAAGGCTCAAGCAGCTTGCACTCTTCTAGGTTCTCTGTT
326 ACTTCACTCACCACCGTCCAATATTTCAAGGCTCAAGCAGCTTGCACTCTTCTAGGTTCTCTGTT
40126652 GTCGTCACTATCGTCATTTCTAGAAC
391 GTCGTCACTATCGTCATTTCTAGAAC
*
40126678 ATTAAAGCAATTACCTAACACATTTATGTCATATTGATTAAAACTTAAAAATCGTGAATTGAAAT
1 ATTAAAGCAATTACCTAACACATTTATGTCATATTGATTAAAACTTAAAAACCGTGAATTGAAAT
40126743 TTAATTTAATTTTTATTTTTAACTTTGATTAATTTTAGTTAAGTTTGATACTCTTCCAAATTAAT
66 TTAATTTAATTTTTATTTTTAACTTTGATTAATTTTAGTTAAGTTTGATACTCTTCCAAATTAAT
*
40126808 A-TTTTTT-TTAAGATTAAATATTTCATAAATACTTTTCCTAGCACAATATCTGTGGGTACGATA
131 ATTTTTTTCTTAAGATTAAATATTTCATAAATACTTTTCCTAGCACAATACCTGTGGGTACGATA
* * *
40126871 CTAGACATTTATTTGTTACTTTATTATTTAAATACAATTTTGTATACTTGCACATTTTCATCTTT
196 CTAGACATTTACTTGTTACTTTATTACTTAAATACAATTTTGTACACTTGCACATTTTCATCTTT
*
40126936 CCAACAACTACTAGTCACCACTGACCACCGTAACCCAACGCAATGGTGCACCTTCCCATCCTATC
261 CCAACAACTACTAGTCACCACCGACCACCGTAACCCAACGCAATGGTGCACCTTCCCATCCTATC
40127001 ACTTCACTCACCACCGTCCAATATTTCAAGGCTCAAGCAGCTTGCACTCTTCTAGGTTCTCTGTT
326 ACTTCACTCACCACCGTCCAATATTTCAAGGCTCAAGCAGCTTGCACTCTTCTAGGTTCTCTGTT
40127066 GTCGTCACTATCGTCATTTCTAGAAC
391 GTCGTCACTATCGTCATTTCTAGAAC
40127092 A
1 A
40127093 CCATAAAAAA
Statistics
Matches: 401, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
414 267 0.67
415 6 0.01
416 128 0.32
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (416 bp):
ATTAAAGCAATTACCTAACACATTTATGTCATATTGATTAAAACTTAAAAACCGTGAATTGAAAT
TTAATTTAATTTTTATTTTTAACTTTGATTAATTTTAGTTAAGTTTGATACTCTTCCAAATTAAT
ATTTTTTTCTTAAGATTAAATATTTCATAAATACTTTTCCTAGCACAATACCTGTGGGTACGATA
CTAGACATTTACTTGTTACTTTATTACTTAAATACAATTTTGTACACTTGCACATTTTCATCTTT
CCAACAACTACTAGTCACCACCGACCACCGTAACCCAACGCAATGGTGCACCTTCCCATCCTATC
ACTTCACTCACCACCGTCCAATATTTCAAGGCTCAAGCAGCTTGCACTCTTCTAGGTTCTCTGTT
GTCGTCACTATCGTCATTTCTAGAAC
Found at i:40134367 original size:40 final size:40
Alignment explanation
Indices: 40134312--40134401 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
40134302 GATGATCAAA
40134312 AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
1 AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
* **
40134352 AAATGATATTTGACTAATAATTTGAAATTGTAATTTTATT
1 AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
*
40134392 AAATAATATT
1 AAATGATATT
40134402 GGGATAATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (40 bp):
AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
Found at i:40141787 original size:24 final size:23
Alignment explanation
Indices: 40141738--40141787 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
40141728 AGTTATCACG
* *
40141738 TTTTTCTGTTTTTTTGACACATT
1 TTTTTCTGCTTTTTTGACACACT
* *
40141761 TTTTCTCTGCTTTTTTGATACGCT
1 TTTT-TCTGCTTTTTTGACACACT
40141785 TTT
1 TTT
40141788 CTTATGCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.64
Consensus pattern (23 bp):
TTTTTCTGCTTTTTTGACACACT
Found at i:40144160 original size:14 final size:14
Alignment explanation
Indices: 40144141--40144173 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40144131 CAAAACAATT
*
40144141 ACATCATTTTCAAG
1 ACATCATTTTAAAG
40144155 ACATCATTTTAAAG
1 ACATCATTTTAAAG
40144169 -CATCA
1 ACATCA
40144174 AATGTACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (14 bp):
ACATCATTTTAAAG
Found at i:40144912 original size:142 final size:142
Alignment explanation
Indices: 40144656--40144937 Score: 413
Period size: 142 Copynumber: 2.0 Consensus size: 142
40144646 ATGTAATGCT
** * * * *
40144656 CACACGAGCTATGAAATGGGCCTGCTCACACGAGTTGTGGGTTGAGATGTTAGGCTACACGATGC
1 CACACGAGCTATGAAATGGGCCTGCTCACACGAACTCTGAGTCGAGATGTTAGGCTACACCATGC
* * *
40144721 TACTCACACAAGCTGTGGATAATCCGCAATAAATGTCAACTCTTAGCCATCGGTAGAACATCTAA
66 TACTCACACAAGCTGTGGAGAATCCACAATAAATGTCAACTCTCAGCCATCGGTAGAACATCTAA
40144786 GACCAGCACCCA
131 GACCAGCACCCA
*
40144798 CACACGAGCTATGAAATGGGCCTGCTCACATGAACTCTGAGTCGAGATGTTAGGCTACACCATGC
1 CACACGAGCTATGAAATGGGCCTGCTCACACGAACTCTGAGTCGAGATGTTAGGCTACACCATGC
* * * * *
40144863 TGCTGACACGAGTTGTGGAGAATCCACAATAAATGTCGAA-TCTCAGCCATCGGTAGGACATCTA
66 TACTCACACAAGCTGTGGAGAATCCACAATAAATGTC-AACTCTCAGCCATCGGTAGAACATCTA
40144927 AGACCAGCACC
130 AGACCAGCACC
40144938 AATATAACCT
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
142 122 0.98
143 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (142 bp):
CACACGAGCTATGAAATGGGCCTGCTCACACGAACTCTGAGTCGAGATGTTAGGCTACACCATGC
TACTCACACAAGCTGTGGAGAATCCACAATAAATGTCAACTCTCAGCCATCGGTAGAACATCTAA
GACCAGCACCCA
Found at i:40145994 original size:24 final size:25
Alignment explanation
Indices: 40145967--40146017 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
40145957 TTCCAAGAAT
*
40145967 TTAGGTCATACGAGCCCAAATA-AG
1 TTAGCTCATACGAGCCCAAATAGAG
** *
40145991 TTAGCTCATTTGAGCCCAGATAGAG
1 TTAGCTCATACGAGCCCAAATAGAG
40146016 TT
1 TT
40146018 TAACCAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (25 bp):
TTAGCTCATACGAGCCCAAATAGAG
Found at i:40147678 original size:15 final size:15
Alignment explanation
Indices: 40147654--40147695 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
40147644 TTAATTCAAT
40147654 AATT-AAAATTCCTC
1 AATTCAAAATTCCTC
40147668 AATTCAAAATTCCTC
1 AATTCAAAATTCCTC
40147683 AATTCAAAATTCC
1 AATTCAAAATTCC
40147696 ATATAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTCAAAATTCCTC
Found at i:40154141 original size:18 final size:21
Alignment explanation
Indices: 40154095--40154141 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 21
40154085 GGAGAAGCCT
40154095 GAGGAGAAGAAGGAAATTGAA
1 GAGGAGAAGAAGGAAATTGAA
40154116 GA--AG-AGAAGG-AA-T-AA
1 GAGGAGAAGAAGGAAATTGAA
40154131 GAGGAGAAGAA
1 GAGGAGAAGAA
40154142 TGAAGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
15 4 0.17
16 1 0.04
17 4 0.17
18 10 0.43
19 2 0.09
21 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.06
Consensus pattern (21 bp):
GAGGAGAAGAAGGAAATTGAA
Found at i:40156654 original size:19 final size:19
Alignment explanation
Indices: 40156632--40156676 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40156622 TTATATTAGG
40156632 ATTTAATATTT-AAGATATT
1 ATTTAATATTTAAAGATA-T
* *
40156651 ATTTATTATTTAAAGTTAT
1 ATTTAATATTTAAAGATAT
40156670 ATTTAAT
1 ATTTAAT
40156677 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTAATATTTAAAGATAT
Found at i:40157497 original size:15 final size:16
Alignment explanation
Indices: 40157479--40157508 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40157469 CTTCCCTATT
40157479 TTCTATTT-CTTTTAA
1 TTCTATTTACTTTTAA
40157494 TTCTATTTACTTTTA
1 TTCTATTTACTTTTA
40157509 TTTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTATTTACTTTTAA
Found at i:40157513 original size:22 final size:21
Alignment explanation
Indices: 40157478--40157534 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
40157468 ACTTCCCTAT
40157478 TTTCTATTT-CTTTTAATTCTA
1 TTTCT-TTTACTTTTAATTCTA
* * *
40157499 TTTACTTTTATTTTTAATTTTG
1 TTT-CTTTTACTTTTAATTCTA
40157521 TTTCTTTTACTTTT
1 TTTCTTTTACTTTT
40157535 CCTTAGATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTCTTTTACTTTTAATTCTA
Found at i:40160270 original size:6 final size:6
Alignment explanation
Indices: 40160259--40160284 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40160249 GGCAACCCAA
40160259 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
40160285 TTCTATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:40161866 original size:19 final size:18
Alignment explanation
Indices: 40161844--40161888 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
40161834 TTATATTAGG
40161844 ATTTAATATTTAAGATATT
1 ATTTAATATTTAA-ATATT
* *
40161863 ATTTATTATTTAAATTTT
1 ATTTAATATTTAAATATT
40161881 ATATTAAT
1 AT-TTAAT
40161889 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTAATATTTAAATATT
Found at i:40162649 original size:15 final size:16
Alignment explanation
Indices: 40162629--40162658 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40162619 CTTCCCTATT
40162629 TTCTATTT-CTTTTAA
1 TTCTATTTACTTTTAA
40162644 TTCTATTTACTTTTA
1 TTCTATTTACTTTTA
40162659 TTTTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTATTTACTTTTAA
Found at i:40164720 original size:29 final size:29
Alignment explanation
Indices: 40164661--40164720 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
40164651 AAATAATAGG
** *
40164661 ATTTTTTAACTCGACTCAATTTGACTCAA
1 ATTTTTTAACTCGACTCAATTCAAATCAA
* * *
40164690 ATTTTTTTATTCGACTCAATTCAAATTAA
1 ATTTTTTAACTCGACTCAATTCAAATCAA
40164719 AT
1 AT
40164721 CGATTCAACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTTTTAACTCGACTCAATTCAAATCAA
Found at i:40166674 original size:23 final size:23
Alignment explanation
Indices: 40165988--40166666 Score: 871
Period size: 23 Copynumber: 29.3 Consensus size: 23
40165978 CTTATATCTA
40165988 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
40166011 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
40166034 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
40166057 TGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
40166080 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
40166103 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
40166126 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
40166149 TGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
40166172 TGCTTAAATATTAATATTATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
40166195 TGCTAAAATATTAATTTGA-TTG
1 TGCTTAAATATTAATGTGATTTG
40166217 TGCTTAAATATTAATATGATGTGATTTG
1 TGCTTAAATA-T--TA--ATGTGATTTG
* *
40166245 TGTTTAAATATTAATCTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
40166268 TG-TTCAAATATTAATGTGATTTA
1 TGCTT-AAATATTAATGTGATTTG
40166291 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
40166314 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
40166337 TGCTAAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
40166360 TGCTTAAATATTTATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
40166383 TGTTTAAATATTAATCTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
40166406 TG-TTCAAATATTAATGTGATTTA
1 TGCTT-AAATATTAATGTGATTTG
* *
40166429 TGCTTAAATATTAATTTGACTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
40166452 TGCTCAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
40166475 TCCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
40166498 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
40166521 TACTCAAATATTAATGTTATTTG
1 TGCTTAAATATTAATGTGATTTG
*
40166544 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
40166567 TGCTCAGATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
40166590 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
40166613 TTCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
40166636 TGATTAAATATTTAA-GTGATTTG
1 TGCTTAAATA-TTAATGTGATTTG
40166659 TGCTTAAA
1 TGCTTAAA
40166667 GAATTAAGAT
Statistics
Matches: 565, Mismatches: 80, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
22 16 0.03
23 519 0.92
24 8 0.01
25 4 0.01
27 6 0.01
28 12 0.02
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:40166786 original size:36 final size:36
Alignment explanation
Indices: 40166746--40166857 Score: 172
Period size: 36 Copynumber: 3.1 Consensus size: 36
40166736 TGTGAACGTG
*
40166746 AATATATGAGTATGTTCTTCATGCTATGTGACAGAA
1 AATATATGAGTATGTTCTTCATGCCATGTGACAGAA
* * *
40166782 AATATGTGGGTATGTTCTTCATGCCATGTGACTGAA
1 AATATATGAGTATGTTCTTCATGCCATGTGACAGAA
40166818 AATATAT-AGGTATGTTCTTCATGCCATGTGACAGAA
1 AATATATGA-GTATGTTCTTCATGCCATGTGACAGAA
40166854 AATA
1 AATA
40166858 GTGTGATAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (36 bp):
AATATATGAGTATGTTCTTCATGCCATGTGACAGAA
Found at i:40171228 original size:15 final size:16
Alignment explanation
Indices: 40171210--40171239 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40171200 ATATATTTTG
40171210 AAAT-TAAAAAATATT
1 AAATCTAAAAAATATT
40171225 AAATCTAAAAAATAT
1 AAATCTAAAAAATAT
40171240 AATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATCTAAAAAATATT
Found at i:40171254 original size:19 final size:19
Alignment explanation
Indices: 40171230--40171277 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
40171220 ATATTAAATC
*
40171230 TAAAAAATATAATTTTTAA
1 TAAAAAATATAATTTTAAA
40171249 TAAAAAAT-T-ATTTTAAA
1 TAAAAAATATAATTTTAAA
* *
40171266 GATAAAATATAA
1 TAAAAAATATAA
40171278 AATTCAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAAAAATATAATTTTAAA
Found at i:40171605 original size:11 final size:11
Alignment explanation
Indices: 40171537--40171605 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
40171527 CCACGTCAAC
*
40171537 AAATGATTTTA
1 AAATTATTTTA
*
40171548 AAATTAATTTA
1 AAATTATTTTA
40171559 AAATTAATTTTTA
1 AAATT-A-TTTTA
40171572 AAA-TA---TA
1 AAATTATTTTA
40171579 AAATTA--TTA
1 AAATTATTTTA
40171588 AAATTATTTTA
1 AAATTATTTTA
40171599 AAATTAT
1 AAATTAT
40171606 AATCATTATC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 8 0.16
11 25 0.51
12 2 0.04
13 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (11 bp):
AAATTATTTTA
Done.