Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 11 of 131
Found at i:3452274 original size:2 final size:2
Alignment explanation
Indices: 3452267--3452307 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3452257 ATGGGAGATA
3452267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3452308 AGCATGATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3453929 original size:25 final size:25
Alignment explanation
Indices: 3453901--3453972 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
3453891 TTTCATTCTT
*
3453901 ATTTTACCCTAGTAAAATTTTGACA
1 ATTTTACCCTAGTAAAATTTTAACA
* * *
3453926 ATTTTAGCCTTAGTAAAAATTTAACG
1 ATTTTA-CCCTAGTAAAATTTTAACA
* *
3453952 ATTTTGCCCGTGGTAAAATTT
1 ATTTTACCC-TAGTAAAATTT
3453973 CGAGAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTAACA
Found at i:3454143 original size:17 final size:18
Alignment explanation
Indices: 3454121--3454154 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3454111 CAAATGGATT
*
3454121 ATTTCCTTTTCC-TTTTC
1 ATTTCCATTTCCATTTTC
3454138 ATTTCCATTTCCATTTT
1 ATTTCCATTTCCATTTT
3454155 TGGAAACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTCCATTTCCATTTTC
Found at i:3456708 original size:64 final size:64
Alignment explanation
Indices: 3456605--3456731 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
3456595 GTAATTGTTC
3456605 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTT
1 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTT
* * * *
3456669 AAAAACATTGTCTTGACATCTATTTTCTAGATCTTGTAATCGAGAGTCGCCATAATGGATAGT
1 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGT
3456732 AATTTATGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (64 bp):
AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTT
Found at i:3459207 original size:49 final size:49
Alignment explanation
Indices: 3459151--3459284 Score: 144
Period size: 49 Copynumber: 2.7 Consensus size: 49
3459141 TAACCACATT
* * *
3459151 TATCTGGCAGTTTATTTGGAATTTCTAGTGGCTT-TTCCACATATATCTG
1 TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGTT-CACATATATCTG
* * *
3459200 TATCTGGCAGCTTGTCTGCAATTTTTAGTGGCTTGTTCATATATATCTG
1 TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGTTCACATATATCTG
* * * * * *
3459249 TATTTGGTAGCTTGTCTGCAATATCTGGTGGGTTGT
1 TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGT
3459285 CTACATTGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 70 0.97
50 2 0.03
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (49 bp):
TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGTTCACATATATCTG
Found at i:3465605 original size:26 final size:25
Alignment explanation
Indices: 3465531--3465606 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
3465521 TCTCATCCCT
* *
3465531 ATTTTTCCACCAGTAAAATTTTAACA
1 ATTTTTCC-CTAGTAAAATTTTGACA
* * *
3465557 ATTTTACCCTTGGTAAAATTTTGACG
1 ATTTTTCCC-TAGTAAAATTTTGACA
3465583 ATTTTTCCTCTAGTAAAATTTTGA
1 ATTTTTCC-CTAGTAAAATTTTGA
3465607 GAAAATATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.02
26 39 0.95
27 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (25 bp):
ATTTTTCCCTAGTAAAATTTTGACA
Found at i:3469974 original size:17 final size:17
Alignment explanation
Indices: 3469954--3469991 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3469944 TTCAATTAAT
3469954 TTAAATAAATAAATTTC
1 TTAAATAAATAAATTTC
* *
3469971 TTAATTAAATAATTTTC
1 TTAAATAAATAAATTTC
3469988 TTAA
1 TTAA
3469992 CTCAATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATAAATAAATTTC
Found at i:3486015 original size:27 final size:27
Alignment explanation
Indices: 3485985--3486091 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 27
3485975 AAATATCCCC
* *
3485985 GATGGGTAAAATAACCGAAATGCCGTT
1 GATGGGTAAAATGACCGAAATGCCCTT
*
3486012 GATGGGTAAAATGACCGTAATGCCCTT
1 GATGGGTAAAATGACCGAAATGCCCTT
* * *
3486039 G-TAGGGTAAAATGACCGTAATACCCCT
1 GAT-GGGTAAAATGACCGAAATGCCCTT
* *
3486066 -ATAGGGTAAAATGTCCGTAATGCCCT
1 GAT-GGGTAAAATGACCGAAATGCCCT
3486092 GGTGGGAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.01
27 69 0.99
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (27 bp):
GATGGGTAAAATGACCGAAATGCCCTT
Found at i:3486182 original size:24 final size:24
Alignment explanation
Indices: 3486149--3486207 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3486139 TATGTGGTTA
3486149 AATGACTGATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
* *
3486173 TATGACTGATTTGTTTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
3486197 AATGACTGATT
1 AATGACTGATT
3486208 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:3486309 original size:27 final size:27
Alignment explanation
Indices: 3486271--3486335 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
3486261 ATAGAGGAAG
3486271 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
3486296 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
3486324 TACTATTACTGG
1 TACTGTTACTGG
3486336 CAGCTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:3486341 original size:27 final size:27
Alignment explanation
Indices: 3486289--3486341 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
3486279 TGGTGGCTCT
* **
3486289 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
3486316 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
3486342 TGCTGCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:3486451 original size:32 final size:32
Alignment explanation
Indices: 3486410--3486542 Score: 108
Period size: 32 Copynumber: 4.2 Consensus size: 32
3486400 CATATTACCA
* *
3486410 TTACCGATGGCTGTGTGACGGTCATTTCACTG
1 TTACTGATGGCTGTGTGACGATCATTTCACTG
* * *
3486442 TTACTGATGGCTGTGTGCCTATCATATCACTG
1 TTACTGATGGCTGTGTGACGATCATTTCACTG
* * *
3486474 CTACTGATGGCTTTGT-ACCGATCATGTT-ACCG
1 TTACTGATGGCTGTGTGA-CGATCAT-TTCACTG
* ** * *
3486506 TTACTGATGGTTGTCCGTCGATCATATCACTG
1 TTACTGATGGCTGTGTGACGATCATTTCACTG
*
3486538 CTACT
1 TTACT
3486543 AATGACTTTG
Statistics
Matches: 77, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
31 1 0.01
32 75 0.97
33 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (32 bp):
TTACTGATGGCTGTGTGACGATCATTTCACTG
Found at i:3486483 original size:64 final size:64
Alignment explanation
Indices: 3486379--3486542 Score: 152
Period size: 64 Copynumber: 2.6 Consensus size: 64
3486369 GCTGCGATGC
* * *** * * *
3486379 TACTGATGGCTTTATGCCAATCATATTACCATTACCGATGGCTGTGTGA-CGGTCAT-TTCACTG
1 TACTGATGGCTGTATGCCAATCATATCACTGCTACTGATGGCTGTGT-ACCGATCATGTT-ACCG
3486442 T
64 T
* * *
3486443 TACTGATGGCTGTGTGCCTATCATATCACTGCTACTGATGGCTTTGTACCGATCATGTTACCGT
1 TACTGATGGCTGTATGCCAATCATATCACTGCTACTGATGGCTGTGTACCGATCATGTTACCGT
* ** * *
3486507 TACTGATGGTTGTCCGTCGATCATATCACTGCTACT
1 TACTGATGGCTGTATGCCAATCATATCACTGCTACT
3486543 AATGACTTTG
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 1 0.01
64 79 0.96
65 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (64 bp):
TACTGATGGCTGTATGCCAATCATATCACTGCTACTGATGGCTGTGTACCGATCATGTTACCGT
Found at i:3486555 original size:96 final size:96
Alignment explanation
Indices: 3486376--3486564 Score: 225
Period size: 96 Copynumber: 2.0 Consensus size: 96
3486366 TTTGCTGCGA
* ** * *
3486376 TGCTACTGATGGCTTTATGCCAATCATATTACCATTACCGATGGCTGTGTGACGGTCATTTCACT
1 TGCTACTGATGGCTTTATACCAATCATATTACCATTACCGATGGCTGTCCGACGATCATATCACT
* * * *
3486441 GTTACTGATGGCTGTGTGCCTATCATATCAC
66 GCTACTAATGACTGTGTGCCAATCATATCAC
* * * * * * *
3486472 TGCTACTGATGGCTTTGTACCGATCATGTTACCGTTACTGATGGTTGTCCGTCGATCATATCACT
1 TGCTACTGATGGCTTTATACCAATCATATTACCATTACCGATGGCTGTCCGACGATCATATCACT
*
3486537 GCTACTAATGACTTTGTGCCAATCATAT
66 GCTACTAATGACTGTGTGCCAATCATAT
3486565 TATTGTACTT
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (96 bp):
TGCTACTGATGGCTTTATACCAATCATATTACCATTACCGATGGCTGTCCGACGATCATATCACT
GCTACTAATGACTGTGTGCCAATCATATCAC
Found at i:3486832 original size:28 final size:28
Alignment explanation
Indices: 3486799--3486852 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3486789 CATACTGATA
*
3486799 CTGTATCGGGCTTAGGCCCACACTGTTT
1 CTGTATCGGGCTAAGGCCCACACTGTTT
*
3486827 CTGTATTGGGCTAAGGCCCACACTGT
1 CTGTATCGGGCTAAGGCCCACACTGT
3486853 ACTGTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.30
Consensus pattern (28 bp):
CTGTATCGGGCTAAGGCCCACACTGTTT
Found at i:3494493 original size:55 final size:56
Alignment explanation
Indices: 3494352--3494498 Score: 161
Period size: 55 Copynumber: 2.6 Consensus size: 56
3494342 TAATACTGAG
* * * *
3494352 TCTGGTGCCAGCCATTGACAGGCCAGTACCAAATTTTTTTTTTTAAAAAAAACACGTAC
1 TCTGGTGCCGGCCATTGACAGGCCAGCACCAAATTCTTTTTTCT---AAAAACACGTAC
* * * *
3494411 TCTAGTGCTGGCCATTGACATGCCAGCACCAAATTCTTTTTTCT-AAAACTCGTAC
1 TCTGGTGCCGGCCATTGACAGGCCAGCACCAAATTCTTTTTTCTAAAAACACGTAC
* * *
3494466 TTTGGTGCCGGCCATTAACAGGTCAGCACCAAA
1 TCTGGTGCCGGCCATTGACAGGCCAGCACCAAA
3494499 AAAATTTATT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
55 37 0.50
59 37 0.50
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (56 bp):
TCTGGTGCCGGCCATTGACAGGCCAGCACCAAATTCTTTTTTCTAAAAACACGTAC
Found at i:3494550 original size:54 final size:53
Alignment explanation
Indices: 3494475--3494766 Score: 374
Period size: 54 Copynumber: 5.4 Consensus size: 53
3494465 CTTTGGTGCC
* * *
3494475 GGCCATTAACAGGTCAGCACCAAAAAAATTTATTTTTTTTTGGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAATTTATTTTTTTTT-GTACTTGGTGGT
*
3494529 GGCCATTGATAGGCCAACACCAAAAAAATTTGATTTTTTTTTTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAATTT-A-TTTTTTTTTGTACTTGGTGGT
* *
3494584 GGTCATTGACAGGCCAACA-CAAAAAAA-TTAATTTTTTTTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAATTTATTTTTTTTTGTACTTGGTGGT
* * * * * *
3494635 GGCCATTGACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACAC-CAAAAAAATTTATTTTTTTTTGTACTTGGTGGT
* *
3494689 GGCCATTGACAGGCCAGCA-TAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAA-TTT-A-TTTTTTTTTGTACTTGGTGGT
3494744 GGCCATTGACAGGCCAACACCAA
1 GGCCATTGACAGGCCAACACCAA
3494767 TTTTTTTTTA
Statistics
Matches: 207, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
51 36 0.17
52 8 0.04
53 11 0.05
54 74 0.36
55 67 0.32
56 11 0.05
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (53 bp):
GGCCATTGACAGGCCAACACCAAAAAAATTTATTTTTTTTTGTACTTGGTGGT
Found at i:3494649 original size:160 final size:160
Alignment explanation
Indices: 3494475--3494763 Score: 465
Period size: 160 Copynumber: 1.8 Consensus size: 160
3494465 CTTTGGTGCC
* * * * *
3494475 GGCCATTAACAGGTCAGCAC-CAAAAAAATTTATTTTTTTTTGGTACTTGGTGGTGGCCATTGAT
1 GGCCATTAACAGGTCAGCACAAAAAAAAATTGATTTATTTCT-GTACTTGGTGGTGGCCATTGAC
*
3494539 AGGCCAACACCAAAAAAA-TTTGATTTTTTTTTTGTACTTGGTGGTGGTCATTGACAGGCCAACA
65 AGGCCAACA-CAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACA
3494603 CAAAAAAATTAATTTTTTTTGTACTTGGTGGT
129 CAAAAAAATTAATTTTTTTTGTACTTGGTGGT
*
3494635 GGCCATTGACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGTGGCCATTGACA
1 GGCCATTAACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGTGGCCATTGACA
* *
3494700 GGCCAGCATAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACAC
66 GGCCAACACAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACAC
3494764 CAATTTTTTT
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
159 7 0.06
160 94 0.80
161 17 0.14
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (160 bp):
GGCCATTAACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGTGGCCATTGACA
GGCCAACACAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACACA
AAAAAATTAATTTTTTTTGTACTTGGTGGT
Found at i:3495957 original size:20 final size:21
Alignment explanation
Indices: 3495929--3495976 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
3495919 ATATTGTACA
*
3495929 TTAAATATG-GTAAAAAAATT
1 TTAATTATGAGTAAAAAAATT
* *
3495949 TTAATTATGATTTAAAAAATT
1 TTAATTATGAGTAAAAAAATT
3495970 TT-ATTAT
1 TTAATTAT
3495977 TGTGATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (21 bp):
TTAATTATGAGTAAAAAAATT
Found at i:3498736 original size:104 final size:105
Alignment explanation
Indices: 3498525--3498751 Score: 244
Period size: 104 Copynumber: 2.2 Consensus size: 105
3498515 ACAGAGAGTT
* * *
3498525 ACACGGCCTGGGCACACGCCCATGTCGTCTGCCCATGTGGTTCTAAATCATAAATTGTGAGTTAC
1 ACACGGCCTGGGCACACGCCCATGTCGTCTGCCCATGCGGTTCTAAAGCATAAATAGTGAGTTAC
* * * *** *
3498590 AAGGCCTGGGCACACGCCCATATCCTTGCCCGTGTGGCTC
66 AAGGCCTGGACACAAGCCCATACCCTTGCAAATATGGCTC
* * * *
3498630 ACACGGCCTGGACACACGCTCATGT--TCTTGCCCGTGCGGTTCTAAAGCTTAAATAGTGAGTTA
1 ACACGGCCTGGGCACACGCCCATGTCGTC-TGCCCATGCGGTTCTAAAGCATAAATAGTGAGTTA
* * * *
3498693 CACGGCTTGGACACAAGCTCATACCCTTAG-AAATATGGTTC
65 CAAGGCCTGGACACAAGCCCATACCCTT-GCAAATATGGCTC
*
3498734 ACATGGCCTGGGCACACG
1 ACACGGCCTGGGCACACG
3498752 TCTATGTCCT
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
103 2 0.02
104 74 0.74
105 24 0.24
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (105 bp):
ACACGGCCTGGGCACACGCCCATGTCGTCTGCCCATGCGGTTCTAAAGCATAAATAGTGAGTTAC
AAGGCCTGGACACAAGCCCATACCCTTGCAAATATGGCTC
Found at i:3500681 original size:15 final size:17
Alignment explanation
Indices: 3500649--3500682 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3500639 TTTTTGCTAG
3500649 AATAATATTAACTTAAA
1 AATAATATTAACTTAAA
3500666 AATAATA-TAA-TTAAA
1 AATAATATTAACTTAAA
3500681 AA
1 AA
3500683 AATTAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATATTAACTTAAA
Found at i:3509859 original size:41 final size:41
Alignment explanation
Indices: 3509814--3509999 Score: 309
Period size: 41 Copynumber: 4.5 Consensus size: 41
3509804 GACTTTAAGT
3509814 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
3509855 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
3509896 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* * * * *
3509937 CTAGCAAGCTATGTGTCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* *
3509978 CTAGCAGGCTAAGTGCGGGTGA
1 CTAGCAGGCTATGTGCCGGTGA
3510000 ATACGCTAAT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 136 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
Found at i:3512941 original size:20 final size:20
Alignment explanation
Indices: 3512884--3512959 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
3512874 AATAAAGAGG
*
3512884 AAAGAAA-AAGAATCGAAAAAT
1 AAAGAAAGAAGAA--GAAAAAA
3512905 AAAGAAAAGAA-AAGAAAAAA
1 AAAG-AAAGAAGAAGAAAAAA
*
3512925 AAAGAAAGAAGAGGAAAAAA
1 AAAGAAAGAAGAAGAAAAAA
*
3512945 ATAG-AAGAAGAAGAA
1 AAAGAAAGAAGAAGAA
3512960 CTAATGTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 16 0.33
20 21 0.44
21 4 0.08
22 5 0.10
23 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAGAAAGAAGAAGAAAAAA
Found at i:3521423 original size:43 final size:43
Alignment explanation
Indices: 3521391--3521588 Score: 220
Period size: 42 Copynumber: 4.7 Consensus size: 43
3521381 GTTACTATAA
* * *
3521391 AACATGACCTTTAGCGGCGCTTTTCCCAAAAACACAACTAAAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
* * *
3521434 AACATGACCTTTAGCGGCGC-TTTCCCACAAATGCCGCTATAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
** ** * *
3521476 AACATGATGTTTAGATGCGCTTTCCCCACAAA-GCCATTAAAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
* * *
3521518 AACATGACCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
** *
3521561 AACATGACCTTTAATGGCGCTTTCCCCA
1 AACATGACCTTTAGCGGCGCTTTTCCCA
3521589 GAAGCACCGC
Statistics
Matches: 126, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 65 0.52
43 61 0.48
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
Found at i:3521545 original size:85 final size:84
Alignment explanation
Indices: 3521391--3521588 Score: 247
Period size: 85 Copynumber: 2.3 Consensus size: 84
3521381 GTTACTATAA
** * * * *
3521391 AACATGACCTTTAGCGGCGCTTTTCCCA-AAAACACAACTAAAGAACATGACCTTTAGCGGCGCT
1 AACATGACCTTTAATGGCGCTTTCCCCACAAAGC-C-ATTAAAGAACATGACCTTTAGCGACGCT
** *
3521455 TTCCCACAAATGCCGCTATAG
64 TTCCCACAAACACCGCTAAAG
**
3521476 AACATGATGTTTAGAT-GCGCTTTCCCCACAAAGCCATTAAAGAACATGACCTTTAGCGACGCTT
1 AACATGACCTTTA-ATGGCGCTTTCCCCACAAAGCCATTAAAGAACATGACCTTTAGCGACGC-T
3521540 TTCCCACAAACACCGCTAAAG
64 TTCCCACAAACACCGCTAAAG
3521561 AACATGACCTTTAATGGCGCTTTCCCCA
1 AACATGACCTTTAATGGCGCTTTCCCCA
3521589 GAAGCACCGC
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
84 27 0.28
85 65 0.68
86 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (84 bp):
AACATGACCTTTAATGGCGCTTTCCCCACAAAGCCATTAAAGAACATGACCTTTAGCGACGCTTT
CCCACAAACACCGCTAAAG
Found at i:3521597 original size:43 final size:43
Alignment explanation
Indices: 3521391--3521602 Score: 230
Period size: 43 Copynumber: 5.0 Consensus size: 43
3521381 GTTACTATAA
* * **
3521391 AACATGACCTTTAGCGGCGCTTTTCCCAAAAACACAACTAAAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
** *
3521434 AACATGACCTTTAGCGGCGCTTT-CCCACAAATGCCGCTATAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
** ** * **
3521476 AACATGATGTTTAGATGCGCTTTCCCCACAAA-GCCATTAAAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
* *
3521518 AACATGACCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
** * *
3521561 AACATGACCTTTAATGGCGCTTTCCCCAGAAGCACCGCTAAA
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAA
3521603 AGTCATGTTC
Statistics
Matches: 139, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
42 65 0.47
43 74 0.53
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
Found at i:3527557 original size:27 final size:27
Alignment explanation
Indices: 3527527--3527618 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
3527517 CAAAGTTTTG
3527527 TGTAAGTTATGATATGATATATATTTA
1 TGTAAGTTATGATATGATATATATTTA
* * * ** *
3527554 TGTAAGCTATGTAAATTATGCA-AGTTA
1 TGTAAGTTATG-ATATGATATATATTTA
*
3527581 TGTAAGTTATGATATGATATATATTAA
1 TGTAAGTTATGATATGATATATATTTA
3527608 TGTAAGTTATG
1 TGTAAGTTATG
3527619 TAAGTTATGA
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
26 6 0.12
27 38 0.76
28 6 0.12
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.43
Consensus pattern (27 bp):
TGTAAGTTATGATATGATATATATTTA
Found at i:3527564 original size:9 final size:9
Alignment explanation
Indices: 3527551--3527627 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 9
3527541 TGATATATAT
3527551 TTATGTAAG
1 TTATGTAAG
* *
3527560 CTATGTAAA
1 TTATGTAAG
*
3527569 TTATGCAAG
1 TTATGTAAG
3527578 TTATGTAAG
1 TTATGTAAG
*
3527587 TTATGATATG
1 TTATG-TAAG
* *
3527597 ATATAT-A-
1 TTATGTAAG
3527604 TTAATGTAAG
1 TT-ATGTAAG
3527614 TTATGTAAG
1 TTATGTAAG
3527623 TTATG
1 TTATG
3527628 ATTATCATCT
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
7 1 0.02
8 3 0.06
9 40 0.77
10 8 0.15
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3527656 original size:13 final size:13
Alignment explanation
Indices: 3527638--3527662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3527628 ATTATCATCT
3527638 TTAAATTTTAACA
1 TTAAATTTTAACA
3527651 TTAAATTTTAAC
1 TTAAATTTTAAC
3527663 CCTTTAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTTTAACA
Found at i:3529946 original size:22 final size:22
Alignment explanation
Indices: 3529903--3529946 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3529893 AACATATAAT
*
3529903 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
3529925 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
3529947 CAACAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:3537935 original size:2 final size:2
Alignment explanation
Indices: 3537928--3537952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3537918 TTGTTTTGGT
3537928 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3537953 TGGTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3545452 original size:26 final size:27
Alignment explanation
Indices: 3545388--3545459 Score: 103
Period size: 26 Copynumber: 2.7 Consensus size: 27
3545378 TTTTCTCGGG
*
3545388 ATTTTACTAGGGGTAAAATCATCAAAA
1 ATTTTACTAAGGGTAAAATCATCAAAA
*
3545415 ATTTTA-TCAAGGGTAAAATCGTC-AAA
1 ATTTTACT-AAGGGTAAAATCATCAAAA
3545441 ATTTTACTAAGGGTAAAAT
1 ATTTTACTAAGGGTAAAAT
3545460 AGTGATGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (27 bp):
ATTTTACTAAGGGTAAAATCATCAAAA
Found at i:3559859 original size:43 final size:43
Alignment explanation
Indices: 3559796--3559933 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 43
3559786 GCGCCGTAAA
* * *
3559796 AAACGCCGCTATAGAGCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
3559839 AAACGCCGCTAAAGAACATGACCTTTAACGGCTCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
3559882 AAACGCTGCTAAAGAACATGACCTTTAGCGGTGC---TCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
3559922 AAACGCCACTAA
1 AAACGCCGCTAA
3559934 TTTTAGTAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
40 15 0.18
43 67 0.82
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:3561419 original size:33 final size:35
Alignment explanation
Indices: 3561382--3561447 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
3561372 CAGTAAAATA
*
3561382 TTTTCCGTAAAATGATTT-CT-GAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3561415 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3561448 CTGATGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 17 0.59
34 2 0.07
35 10 0.34
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3561421 original size:19 final size:20
Alignment explanation
Indices: 3561397--3561435 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3561387 CGTAAAATGA
*
3561397 TTTCTG-AAAATGTTTTACT
1 TTTCTGTAAAATGATTTACT
3561416 TTTCTGTAAAATGATTTACT
1 TTTCTGTAAAATGATTTACT
3561436 GGAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTCTGTAAAATGATTTACT
Found at i:3561559 original size:20 final size:20
Alignment explanation
Indices: 3561534--3561572 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3561524 GTTTTTACAT
3561534 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
3561554 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
3561573 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:3564002 original size:130 final size:131
Alignment explanation
Indices: 3563769--3564031 Score: 492
Period size: 130 Copynumber: 2.0 Consensus size: 131
3563759 NNNNNNNNCA
3563769 AGACGATTTTGAGTGATTTGCTCAGTTGAAACTTTGTTCACAACACAATATGACAAGTCAACATG
1 AGACGATTTTGAGTGATTTGCTCAGTTGAAACTTTGTTCACAACACAATATGACAAGTCAACATG
3563834 TATTGTTTTGCTTAGTGATAAATAATATGTTTTTTTTAAGTAACATCAAGGAAT-GCATGATTTC
66 TATTGTTTTGCTTAGTGATAAATAATATGTTTTTTTTAAGTAACATCAAGGAATAGCATGATTTC
3563898 T
131 T
**
3563899 AGACGATTTTGAGTGATTTGCTCAGTTGAAACTTTGTTTTCAACACAATATGACAAGTCAACATG
1 AGACGATTTTGAGTGATTTGCTCAGTTGAAACTTTGTTCACAACACAATATGACAAGTCAACATG
3563964 TATTGTTTTGCTTAGTGATAAATAATATGTTTTTTTTAAGTAACATCAAGGAATGAGCATGATTT
66 TATTGTTTTGCTTAGTGATAAATAATATGTTTTTTTTAAGTAACATCAAGGAAT-AGCATGATTT
3564029 CT
130 CT
3564031 A
1 A
3564032 TATGCTAATG
Statistics
Matches: 129, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
130 117 0.91
132 12 0.09
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (131 bp):
AGACGATTTTGAGTGATTTGCTCAGTTGAAACTTTGTTCACAACACAATATGACAAGTCAACATG
TATTGTTTTGCTTAGTGATAAATAATATGTTTTTTTTAAGTAACATCAAGGAATAGCATGATTTC
T
Found at i:3565378 original size:11 final size:11
Alignment explanation
Indices: 3565362--3565387 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3565352 AACCATCTGT
3565362 ATATAACCAAA
1 ATATAACCAAA
3565373 ATATAACCAAA
1 ATATAACCAAA
3565384 ATAT
1 ATAT
3565388 CATCCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Found at i:3565658 original size:25 final size:25
Alignment explanation
Indices: 3565630--3565679 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3565620 AGAAGAGAAG
*
3565630 ATGAAGATCAGAAGAAGAAAAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
* *
3565655 ATGAAGAACGGAAGAAGAAGAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
3565680 GCCTTACCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.32, T:0.06
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGAAAAAGGA
Found at i:3571957 original size:77 final size:76
Alignment explanation
Indices: 3571797--3572200 Score: 450
Period size: 77 Copynumber: 5.2 Consensus size: 76
3571787 GAAATTAGCA
* * * ** *
3571797 AACTGTTAGAATATCGAAGGTTGCGATCTTAAATCAACGAACCGTAAAAATTATAGAAGCGAAAT
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACAGCCGCGATAT
*
3571862 TAAATCAAGTG
66 TAAATCAAGCG
* * * *
3571873 AACTGTTAAAATATCGAAGGTTGCGATCTTAAGTCGAACGAACCGTAAAAATGACAGCTGCGATA
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AACGAACCGTAAAAATGACAGCCGCGATA
**
3571938 TTAAATCAATTG
65 TTAAATCAAGCG
* * * ** * *
3571950 AATTGTTAAAATATTGAAGGTCGCGATCTTAAATCGAGTGAACCGTAAAAATGACAGCCACAATA
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AACGAACCGTAAAAATGACAGCCGCGATA
* *
3572015 TTAAATCGAGCA
65 TTAAATCAAGCG
* * * * * * * *
3572027 AACTATTAGAATATCAAAGGTCGCAATCTTAAATTAAGTGGACCGTAAAAATGACAGTCGCAATA
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAA-CGAACCGTAAAAATGACAGCCGCGATA
3572092 TTAAATCAAGCG
65 TTAAATCAAGCG
* *
3572104 AACTGTTAGAATATCGAAGGTCGCGATCTTAAAATCAAGCGAACTGTAAAAATGACAACCGCTG-
1 AACTGTTAGAATATCGAAGGTCGCGATCTT-AAATCAA-CGAACCGTAAAAATGACAGCCGC-GA
*
3572168 TATTAAATCAAGAG
63 TATTAAATCAAGCG
3572182 AACTGTTAGAATATCGAAG
1 AACTGTTAGAATATCGAAG
3572201 ATCATGATAG
Statistics
Matches: 279, Mismatches: 45, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
76 34 0.12
77 188 0.67
78 57 0.20
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (76 bp):
AACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACAGCCGCGATAT
TAAATCAAGCG
Found at i:3572001 original size:40 final size:39
Alignment explanation
Indices: 3571806--3572001 Score: 127
Period size: 40 Copynumber: 5.1 Consensus size: 39
3571796 AAACTGTTAG
*
3571806 AATATCGAAGGTTGCGATCTTAAATC-AACGAACCGTAAA
1 AATATCGAAGG-TGCGATCTTAAATCAAATGAACCGTAAA
* ** * * *
3571845 AATTATAGAA---GCGAAATTAAATCAAGTGAACTGTTAA
1 AA-TATCGAAGGTGCGATCTTAAATCAAATGAACCGTAAA
* * *
3571882 AATATCGAAGGTTGCGATCTTAAGTCGAACGAACCGT-AA
1 AATATCGAAGG-TGCGATCTTAAATCAAATGAACCGTAAA
* * * ** *
3571921 AA-AT-GACAGCTGCGATATTAAATCAATTGAATTGTTAA
1 AATATCGA-AGGTGCGATCTTAAATCAAATGAACCGTAAA
* * *
3571959 AATATTGAAGGTCGCGATCTTAAATCGAGTGAACCGTAAA
1 AATATCGAAGGT-GCGATCTTAAATCAAATGAACCGTAAA
3571999 AAT
1 AAT
3572002 GACAGCCACA
Statistics
Matches: 116, Mismatches: 30, Indels: 21
0.69 0.18 0.13
Matches are distributed among these distances:
36 17 0.15
37 31 0.27
38 8 0.07
39 11 0.09
40 49 0.42
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (39 bp):
AATATCGAAGGTGCGATCTTAAATCAAATGAACCGTAAA
Found at i:3580897 original size:2 final size:2
Alignment explanation
Indices: 3580890--3580927 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3580880 TCACATTGTT
* *
3580890 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3580928 ATGTTGTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3582964 original size:16 final size:16
Alignment explanation
Indices: 3582943--3582975 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3582933 CGTTTGGTTC
3582943 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
*
3582959 GCTGTAATGGAATAGA
1 GCTGTAATAGAATAGA
3582975 G
1 G
3582976 GCATAATAGT
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:0.39, C:0.06, G:0.30, T:0.24
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:3583176 original size:21 final size:21
Alignment explanation
Indices: 3583152--3583215 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 21
3583142 AGAGAATCAG
3583152 AGGCGGCAACGAGAGAAGTAC
1 AGGCGGCAACGAGAGAAGTAC
3583173 AGGCTGGCGGCAACGAGAGAAGTAC
1 A----GGCGGCAACGAGAGAAGTAC
* * *
3583198 AAGCTGCAGCGAGAGAAG
1 AGGCGGCAACGAGAGAAG
3583216 CAGAGGCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 15 0.42
25 21 0.58
ACGTcount: A:0.36, C:0.19, G:0.39, T:0.06
Consensus pattern (21 bp):
AGGCGGCAACGAGAGAAGTAC
Found at i:3583187 original size:25 final size:25
Alignment explanation
Indices: 3583153--3583203 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3583143 GAGAATCAGA
*
3583153 GGCGGCAACGAGAGAAGTACAGGCT
1 GGCGGCAACGAGAGAAGTACAAGCT
3583178 GGCGGCAACGAGAGAAGTACAAGCT
1 GGCGGCAACGAGAGAAGTACAAGCT
3583203 G
1 G
3583204 CAGCGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.39, T:0.08
Consensus pattern (25 bp):
GGCGGCAACGAGAGAAGTACAAGCT
Found at i:3583229 original size:21 final size:21
Alignment explanation
Indices: 3583205--3583262 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
3583195 TACAAGCTGC
*
3583205 AGCGAGAGAAGCAGAGGCTAA
1 AGCGAGGGAAGCAGAGGCTAA
**
3583226 AGCGAGGGAAGCAGAGGCTGC
1 AGCGAGGGAAGCAGAGGCTAA
3583247 AGCGAGGGAAGCAGAG
1 AGCGAGGGAAGCAGAG
3583263 CAGCGTCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.45, T:0.03
Consensus pattern (21 bp):
AGCGAGGGAAGCAGAGGCTAA
Found at i:3583658 original size:43 final size:42
Alignment explanation
Indices: 3583608--3583860 Score: 231
Period size: 43 Copynumber: 5.9 Consensus size: 42
3583598 TAAAGGTGTT
*
3583608 GGTCTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAG
1 GGTCTTTAGCGGCGTTTTTGG-CAAAGCGCCGCTAAAGATAAG
* * * * *
3583651 GGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAT
1 GGTCTTTAGCGGCGTTTTTGG-CAAAGCGCCGCTAAAGATAAG
* * * * *
3583694 AGTCTTTAGTGGTGTTTTTGGGAGAAGCGCTGCTAAAGATAAG
1 GGTCTTTAGCGGCGTTTTTGGCA-AAGCGCCGCTAAAGATAAG
*** *
3583737 GGTCTTTAGCGGCGTTTGAAAG-AGAAGCGCCGCTAAAGATTAG
1 GGTCTTTAGCGGCGTTT-TTGGCA-AAGCGCCGCTAAAGATAAG
* *
3583780 GGTCTTTAGCGGCGTTTGT-GCAAGATGCGCCGCTAAAGATCAG
1 GGTCTTTAGCGGCGTTTTTGGCAA-A-GCGCCGCTAAAGATAAG
* ** *
3583823 GGTCTTTAGCGGTGTTTTTTTCTAAAACGCCGCTAAAG
1 GGTCTTTAGCGGCGTTTTTGGC-AAAGCGCCGCTAAAG
3583861 TTAGCGGCGC
Statistics
Matches: 172, Mismatches: 31, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
41 2 0.01
42 3 0.02
43 162 0.94
44 3 0.02
45 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (42 bp):
GGTCTTTAGCGGCGTTTTTGGCAAAGCGCCGCTAAAGATAAG
Found at i:3583714 original size:86 final size:84
Alignment explanation
Indices: 3583570--3583840 Score: 296
Period size: 86 Copynumber: 3.2 Consensus size: 84
3583560 ATCTGCCAAA
* * * **
3583570 TTTAGTGGCGTTTTTTAAAAAA-CGCCACTAAAGGTGTTGGTCTTTAGTGGCGTTTTTGGTCAAA
1 TTTAGCGGCG-TTTTGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGG-CAAA
3583634 GCGCCGCTAAAGATAAGGGTC
64 GCGCCGCTAAAGATAAGGGTC
* * * *
3583655 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATAGTCTTTAGTGGTGTTTTTGGGAGAA
1 TTTAGCGGCGTTT-TGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGGCA-AA
*
3583720 GCGCTGCTAAAGATAAGGGTC
64 GCGCCGCTAAAGATAAGGGTC
* * * * *
3583741 TTTAGCGGCG-TTTGAAAGAGAAGCGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTTGT-GCAAG
1 TTTAGCGGCGTTTTGAAA-A-AAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGGCAA-
*
3583804 ATGCGCCGCTAAAGATCAGGGTC
63 A-GCGCCGCTAAAGATAAGGGTC
*
3583827 TTTAGCGGTGTTTT
1 TTTAGCGGCGTTTT
3583841 TTTCTAAAAC
Statistics
Matches: 156, Mismatches: 22, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
84 8 0.05
85 22 0.14
86 123 0.79
87 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (84 bp):
TTTAGCGGCGTTTTGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGTGGCGTTTTTGGCAAAGC
GCCGCTAAAGATAAGGGTC
Found at i:3590486 original size:13 final size:13
Alignment explanation
Indices: 3590468--3590492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3590458 GTGATTTTTG
3590468 TAAATTTTGAATT
1 TAAATTTTGAATT
3590481 TAAATTTTGAAT
1 TAAATTTTGAAT
3590493 ATTTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TAAATTTTGAATT
Found at i:3590561 original size:24 final size:24
Alignment explanation
Indices: 3590493--3590563 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
3590483 AATTTTGAAT
* *
3590493 ATTTATATT-ATTAATAAACATTTT
1 ATTTAAATTAATTAATAAA-ATTTA
*
3590517 ATTTAAATTAATATCATAAAATTTA
1 ATTTAAATTAAT-TAATAAAATTTA
* *
3590542 ATTTAATTTAATTAAGAAAATT
1 ATTTAAATTAATTAATAAAATT
3590564 ACGAAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 16 0.41
25 17 0.44
26 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (24 bp):
ATTTAAATTAATTAATAAAATTTA
Found at i:3593583 original size:22 final size:22
Alignment explanation
Indices: 3593552--3593618 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
3593542 TGCACTAATG
3593552 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* * *
3593574 TATAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
3593596 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
3593618 A
1 A
3593619 TAATCAGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:3600894 original size:27 final size:27
Alignment explanation
Indices: 3600856--3601054 Score: 211
Period size: 27 Copynumber: 7.4 Consensus size: 27
3600846 ACCAAAAAAT
*
3600856 AGGGTAAAATGATCGAAATACCCCCAA
1 AGGGTAAAATGACCGAAATACCCCCAA
** *
3600883 AGGGTAAAATGACAAAAATACCCCCAG
1 AGGGTAAAATGACCGAAATACCCCCAA
* *
3600910 AGGGTAAAATGACCGAAATACCCCTAT
1 AGGGTAAAATGACCGAAATACCCCCAA
* *
3600937 AGGGTAAAACGACCGAAATATCCCCAGA
1 AGGGTAAAATGACCGAAATACCCCCA-A
* ** *
3600965 A-GGTAAAATGACCGAAATAACCTTAG
1 AGGGTAAAATGACCGAAATACCCCCAA
** *
3600991 ATTGTAAAGTGACCGAAATACCCCCAA
1 AGGGTAAAATGACCGAAATACCCCCAA
** * *
3601018 AGGGTAAGTTGACCGAAATACCCTCAT
1 AGGGTAAAATGACCGAAATACCCCCAA
3601045 AGGGTAAAAT
1 AGGGTAAAAT
3601055 AACTGTTATA
Statistics
Matches: 139, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
26 1 0.01
27 137 0.99
28 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.17
Consensus pattern (27 bp):
AGGGTAAAATGACCGAAATACCCCCAA
Found at i:3602287 original size:27 final size:27
Alignment explanation
Indices: 3602246--3602338 Score: 134
Period size: 27 Copynumber: 3.4 Consensus size: 27
3602236 TACATTTAGT
*
3602246 GGTAAAATAACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
* *
3602273 GGTATAATGATTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
*
3602300 GGTAAAATGACCGAAATACCCCCACT-G
1 GGTAAAATGACTGAAATACCCCCA-TAG
3602327 GGTAAAATGACT
1 GGTAAAATGACT
3602339 ATTATACCCC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCCATAG
Found at i:3605789 original size:3 final size:3
Alignment explanation
Indices: 3605781--3605817 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3605771 NNNNNNNNNN
3605781 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3605818 GAAACATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3606565 original size:18 final size:17
Alignment explanation
Indices: 3606540--3606584 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3606530 AGCCTCCTTC
* *
3606540 GAAAAAATAGAATAATA
1 GAAAAAATAAAATAAGA
3606557 GATAAAAATGAAAATAAGA
1 GA-AAAAAT-AAAATAAGA
3606576 GAAAAAATA
1 GAAAAAATA
3606585 CAATTCGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 9 0.38
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (17 bp):
GAAAAAATAAAATAAGA
Found at i:3607008 original size:24 final size:24
Alignment explanation
Indices: 3606981--3607041 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
3606971 GGGGGAGTTG
*
3606981 AGGAGAAATCAGTGGAGGGATTCA
1 AGGAGAAATCAGTGGAGAGATTCA
** * **
3607005 AGGAGGGATAAGTGGAGAGATTTT
1 AGGAGAAATCAGTGGAGAGATTCA
3607029 AGGAGAAAATCAG
1 AGGAG-AAATCAG
3607042 GGGATGTGAG
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.39, C:0.05, G:0.38, T:0.18
Consensus pattern (24 bp):
AGGAGAAATCAGTGGAGAGATTCA
Found at i:3609708 original size:19 final size:18
Alignment explanation
Indices: 3609684--3609726 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3609674 TGGGCTTCAT
3609684 TGGGCCAAAATGGGCTATG
1 TGGGCCAAAATGGGCT-TG
*
3609703 TGGGCC-TAATGGGCTTG
1 TGGGCCAAAATGGGCTTG
*
3609720 TGAGCCA
1 TGGGCCA
3609727 TACGAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (18 bp):
TGGGCCAAAATGGGCTTG
Found at i:3610108 original size:27 final size:27
Alignment explanation
Indices: 3610077--3610253 Score: 135
Period size: 27 Copynumber: 6.6 Consensus size: 27
3610067 CCAATATTTA
* *
3610077 TAAAATAACTGTAATAACCTTATAGGG
1 TAAAATAACCGTAATAACCCTATAGGG
*
3610104 TAAAATAACCGTAATACCCCTATAGGG
1 TAAAATAACCGTAATAACCCTATAGGG
* * * *
3610131 TAAAATCACC-AAAAAACCCCCATAGGG
1 TAAAATAACCGTAATAA-CCCTATAGGG
* * * *
3610158 TAAAATGACCGTGAT-GCCTCTGTAGGG
1 TAAAATAACCGTAATAACC-CTATAGGG
3610185 TAAAATAACCGTAAT-ACCCTCATAGGG
1 TAAAATAACCGTAATAACCCT-ATAGGG
* * * * * * *
3610212 TTAAATGATCGAAATACCCCTGTAAGG
1 TAAAATAACCGTAATAACCCTATAGGG
*
3610239 TAAAATGACCGTAAT
1 TAAAATAACCGTAAT
3610254 GCCTCTGGAG
Statistics
Matches: 116, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
26 7 0.06
27 104 0.90
28 5 0.04
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (27 bp):
TAAAATAACCGTAATAACCCTATAGGG
Found at i:3610135 original size:54 final size:54
Alignment explanation
Indices: 3610077--3610253 Score: 185
Period size: 54 Copynumber: 3.3 Consensus size: 54
3610067 CCAATATTTA
* * * *
3610077 TAAAATAACTGTAATAACCTTATAGGGTAAAATAACCGTAATACCCCTATAGGG
1 TAAAATAACCGTAATAACCTCATAGGGTAAAATGACCGTAATACCCCTGTAGGG
* * * * * * *
3610131 TAAAATCACC-AAAAAACCCCCATAGGGTAAAATGACCGTGATGCCTCTGTAGGG
1 TAAAATAACCGTAATAA-CCTCATAGGGTAAAATGACCGTAATACCCCTGTAGGG
* * * * *
3610185 TAAAATAACCGTAATACCCTCATAGGGTTAAATGATCGAAATACCCCTGTAAGG
1 TAAAATAACCGTAATAACCTCATAGGGTAAAATGACCGTAATACCCCTGTAGGG
*
3610239 TAAAATGACCGTAAT
1 TAAAATAACCGTAAT
3610254 GCCTCTGGAG
Statistics
Matches: 97, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
53 4 0.04
54 90 0.93
55 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (54 bp):
TAAAATAACCGTAATAACCTCATAGGGTAAAATGACCGTAATACCCCTGTAGGG
Found at i:3610212 original size:81 final size:81
Alignment explanation
Indices: 3610099--3610269 Score: 236
Period size: 81 Copynumber: 2.1 Consensus size: 81
3610089 AATAACCTTA
*
3610099 TAGGGTAAAATAACCGTAATACCCCTATAGGGTAAAATCACCAAAAAACCCCCATAGGGTAAAAT
1 TAGGGTAAAATAACCGTAATACCCCTATAGGGTAAAATCACCAAAAAACCCCCATAAGGTAAAAT
*
3610164 GACCGTGATGCCTCTG
66 GACCGTAATGCCTCTG
* * * * * **
3610180 TAGGGTAAAATAACCGTAATA-CCCTCATAGGGTTAAATGATCGAAATACCCCTGTAAGGTAAAA
1 TAGGGTAAAATAACCGTAATACCCCT-ATAGGGTAAAATCACCAAAAAACCCCCATAAGGTAAAA
3610244 TGACCGTAATGCCTCTG
65 TGACCGTAATGCCTCTG
*
3610261 GAGGGTAAA
1 TAGGGTAAA
3610270 TGACTATTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 4 0.05
81 75 0.95
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (81 bp):
TAGGGTAAAATAACCGTAATACCCCTATAGGGTAAAATCACCAAAAAACCCCCATAAGGTAAAAT
GACCGTAATGCCTCTG
Found at i:3610267 original size:27 final size:27
Alignment explanation
Indices: 3610099--3610273 Score: 120
Period size: 27 Copynumber: 6.5 Consensus size: 27
3610089 AATAACCTTA
* * * *
3610099 TAGGGTAAAATAACCGTAATACCCCTA
1 TAGGGTAAAATGACCGTAATGCCTCTG
* ** ** * **
3610126 TAGGGTAAAATCACCAAAAAACCCCCA
1 TAGGGTAAAATGACCGTAATGCCTCTG
*
3610153 TAGGGTAAAATGACCGTGATGCCTCTG
1 TAGGGTAAAATGACCGTAATGCCTCTG
* * *
3610180 TAGGGTAAAATAACCGTAATACC-CTCA
1 TAGGGTAAAATGACCGTAATGCCTCT-G
* * * * *
3610207 TAGGGTTAAATGATCGAAATACCCCTG
1 TAGGGTAAAATGACCGTAATGCCTCTG
*
3610234 TAAGGTAAAATGACCGTAATGCCTCTG
1 TAGGGTAAAATGACCGTAATGCCTCTG
*
3610261 GAGGGT-AAATGAC
1 TAGGGTAAAATGAC
3610274 TATTTTACCT
Statistics
Matches: 115, Mismatches: 31, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
26 9 0.08
27 104 0.90
28 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (27 bp):
TAGGGTAAAATGACCGTAATGCCTCTG
Found at i:3611996 original size:27 final size:26
Alignment explanation
Indices: 3611668--3612001 Score: 258
Period size: 27 Copynumber: 12.4 Consensus size: 26
3611658 CCAAAAATAG
*
3611668 GGTAAAATGACCGAAATACCCCCATAA
1 GGTAAAATGATCGAAATACCCCCAT-A
* *
3611695 GGTAACATGATCGAAATACCCCCAGA
1 GGTAAAATGATCGAAATACCCCCATA
* *
3611721 GAGTAAAATGATCAAAATACCGCCATA
1 G-GTAAAATGATCGAAATACCCCCATA
* * * *
3611748 GGGTAAAATAACCTAAATACCCTCATA
1 -GGTAAAATGATCGAAATACCCCCATA
* *
3611775 GGGTAAAA-CAACAGAAATACCCCCATA
1 -GGTAAAATGATC-GAAATACCCCCATA
*
3611802 GGATAAAACGA-CTGAAATACCCCCATA
1 GG-TAAAATGATC-GAAATACCCCCATA
* *
3611829 GGGTAAAACGATCGAAATAACCCCATA
1 -GGTAAAATGATCGAAATACCCCCATA
* * *
3611856 GGCTAAAACGACCGAAATACCCCCAAAA
1 GG-TAAAATGATCGAAATACCCCC-ATA
* * * * *
3611884 GATAAAATGACCAAAATACCTCCAATG
1 GGTAAAATGATCGAAATACC-CCCATA
**
3611911 GGTAAAATGATCGAAATACCCCTGTA
1 GGTAAAATGATCGAAATACCCCCATA
* * *
3611937 GGGTAAATTGATCGAAATACACTCATAA
1 -GGTAAAATGATCGAAATACCCCCAT-A
* *
3611965 GGTAAAATAATCAAAATACCCCCATA
1 GGTAAAATGATCGAAATACCCCCATA
*
3611991 GTGTAACATGA
1 G-GTAAAATGA
3612002 CTGTTATACT
Statistics
Matches: 248, Mismatches: 46, Indels: 26
0.77 0.14 0.08
Matches are distributed among these distances:
26 13 0.05
27 224 0.90
28 11 0.04
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (26 bp):
GGTAAAATGATCGAAATACCCCCATA
Found at i:3613593 original size:14 final size:14
Alignment explanation
Indices: 3613570--3613601 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3613560 AAAATCTTTG
3613570 TGAT-ACTCTGATT
1 TGATCACTCTGATT
3613583 TGATCACTCTGATT
1 TGATCACTCTGATT
3613597 TGATC
1 TGATC
3613602 TGTTCTGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.44
Consensus pattern (14 bp):
TGATCACTCTGATT
Found at i:3616203 original size:3 final size:3
Alignment explanation
Indices: 3616195--3616229 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3616185 NNNNNNNNNN
3616195 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3616230 CAATTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3616829 original size:149 final size:150
Alignment explanation
Indices: 3616549--3616838 Score: 413
Period size: 150 Copynumber: 1.9 Consensus size: 150
3616539 AAAAGTTTTC
** *
3616549 ATTTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATTTGTCTTTTGTCATATTAAAGG
1 ATTTTTTAAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATTTGTCTTTTGTCATATTAAAGG
*
3616614 AAAAGTTTAAAATTAAAAAAAAAACGTTTTAATCTTTTTCAACTATTTCGAAACAAAGTTTTGAT
66 AAAAGTTTAAAATTAAAAAAAAAACGTTTTAATCTTTTTCAACTATTTCGAAACAAAATTTTGAT
3616679 TTTTAAGAAAAAATAGTTAT
131 TTTTAAGAAAAAATAGTTAT
* *
3616699 ATTTTTTAAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATTTGTTTTTTAGTCATTTTAAAG
1 ATTTTTTAAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATTTGTCTTTT-GTCATATTAAAG
** ** ** * ** *
3616764 GAAAA-TTTAATTTTTTAAAACCAA-TTTTTGGTCTTTTTCAACTATTTCGAAATAAAATTTTGA
65 GAAAAGTTTAAAATTAAAAAAAAAACGTTTTAATCTTTTTCAACTATTTCGAAACAAAATTTTGA
3616827 TTTTTAAGAAAA
130 TTTTTAAGAAAA
3616839 GTAGTGACTT
Statistics
Matches: 123, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
149 46 0.37
150 61 0.50
151 16 0.13
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (150 bp):
ATTTTTTAAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATTTGTCTTTTGTCATATTAAAGG
AAAAGTTTAAAATTAAAAAAAAAACGTTTTAATCTTTTTCAACTATTTCGAAACAAAATTTTGAT
TTTTAAGAAAAAATAGTTAT
Found at i:3617775 original size:27 final size:27
Alignment explanation
Indices: 3617742--3617830 Score: 160
Period size: 27 Copynumber: 3.3 Consensus size: 27
3617732 TAAGTAGGTG
*
3617742 TTACATTTTAATGAAACCATAATGTTT
1 TTACATTTTAATGAAACCATAAGGTTT
3617769 TTACATTTTAATGAAACCATAAGGTTT
1 TTACATTTTAATGAAACCATAAGGTTT
*
3617796 TTACATTTTAAGGAAACCATAAGGTTT
1 TTACATTTTAATGAAACCATAAGGTTT
3617823 TTACATTT
1 TTACATTT
3617831 GAATTTAGGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (27 bp):
TTACATTTTAATGAAACCATAAGGTTT
Found at i:3619712 original size:15 final size:17
Alignment explanation
Indices: 3619669--3619706 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3619659 GAATGGATTA
* *
3619669 TTATATTGAACGAACTG
1 TTATATTGTATGAACTG
3619686 TTATATTGTATGAACTG
1 TTATATTGTATGAACTG
3619703 TTAT
1 TTAT
3619707 TTTATGCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (17 bp):
TTATATTGTATGAACTG
Found at i:3619717 original size:17 final size:17
Alignment explanation
Indices: 3619679--3619739 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
3619669 TTATATTGAA
3619679 CGAACTGTTATATTGTAT-
1 CGAACTGTTAT-TT-TATG
3619697 -GAACTGTTATTTTATG
1 CGAACTGTTATTTTATG
* *
3619713 CGAACTGCCTATTCTATG
1 CGAACTG-TTATTTTATG
*
3619731 TGAACTGTT
1 CGAACTGTT
3619740 TAATTTGAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
15 3 0.08
16 2 0.06
17 17 0.47
18 14 0.39
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (17 bp):
CGAACTGTTATTTTATG
Found at i:3635957 original size:50 final size:50
Alignment explanation
Indices: 3635846--3636142 Score: 186
Period size: 50 Copynumber: 5.8 Consensus size: 50
3635836 ATTTGGGTAA
* * * *
3635846 AGAGATCCCATGTAAGACCATGTTTGGGACATGATATTGGCATCATTAAAGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTATTGGCA-C---CAAG--ATG
* *
3635902 AGAGGTTCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCAAGATG
** * * * * *
3635952 AGAGGTCCCCCGTAAGACCATGTCTGAGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCAAGATG
** * * * * * * *
3636002 AGAACTCCCATGTAAGACCGTATCTGGGATATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCAAGATG
*** * * * ** *
3636052 AGAACACCCATGTAAGACCATATCTGAGATATGGCT-TTGGCA-GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG-TATTGGCACCAAGATG
* ** *
3636101 AAACATCTCATGTAAGACCATGTCTGGGACATGGCT-TTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG-TATTGGCA
3636143 TGTTATTATC
Statistics
Matches: 201, Mismatches: 39, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
49 38 0.19
50 122 0.61
52 3 0.01
55 1 0.00
56 37 0.18
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCAAGATG
Found at i:3649946 original size:18 final size:18
Alignment explanation
Indices: 3649899--3649960 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
3649889 TATATCTATT
*
3649899 TCTGAATATGAATATGTA
1 TCTGATTATGAATATGTA
* * * *
3649917 TCTCATTTTGAATCTGTG
1 TCTGATTATGAATATGTA
*
3649935 TCTGATTATGAAATATGCA
1 TCTGATTATG-AATATGTA
3649954 TCTGATT
1 TCTGATT
3649961 CTGTATGTGA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
18 21 0.64
19 12 0.36
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (18 bp):
TCTGATTATGAATATGTA
Found at i:3651739 original size:50 final size:50
Alignment explanation
Indices: 3651634--3651740 Score: 117
Period size: 50 Copynumber: 2.1 Consensus size: 50
3651624 TTATTGAGGT
* * *
3651634 TATGAGAGGTCCCACATAAGACCATGTCTGGGACATGGCGGTGGTACTGA
1 TATGAGAGGTCCCACATAAAACCATGTCTGGGACATGGCGGTGGCACCGA
* * * ** *
3651684 GATGAGAGGTCCCCCGTAAAACTGTGTCTGGGACATGGC-ATGGGCACCGA
1 TATGAGAGGTCCCACATAAAACCATGTCTGGGACATGGCGGT-GGCACCGA
3651734 TATGAGA
1 TATGAGA
3651741 ACTCTCATGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
49 1 0.02
50 45 0.98
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.21
Consensus pattern (50 bp):
TATGAGAGGTCCCACATAAAACCATGTCTGGGACATGGCGGTGGCACCGA
Found at i:3659322 original size:21 final size:21
Alignment explanation
Indices: 3659304--3659354 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3659294 TACTAATATT
*
3659304 AACACTAATAATGATAATAAA
1 AACAATAATAATGATAATAAA
3659325 AACAATAATAAT-ATGAATAATA
1 AACAATAATAATGAT-AATAA-A
*
3659347 ACCAATAA
1 AACAATAA
3659355 AAAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.62
22 8 0.31
ACGTcount: A:0.63, C:0.10, G:0.04, T:0.24
Consensus pattern (21 bp):
AACAATAATAATGATAATAAA
Found at i:3659659 original size:12 final size:12
Alignment explanation
Indices: 3659642--3659671 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3659632 GACTCATGGA
3659642 GAAAGGAGATGT
1 GAAAGGAGATGT
*
3659654 GAAAGGTGATGT
1 GAAAGGAGATGT
3659666 GAAAGG
1 GAAAGG
3659672 GAGACAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (12 bp):
GAAAGGAGATGT
Found at i:3670133 original size:61 final size:61
Alignment explanation
Indices: 3670038--3670158 Score: 215
Period size: 61 Copynumber: 2.0 Consensus size: 61
3670028 TCTTAATCTT
* *
3670038 CAAGCCTCCATGGTTGGTTTCATGTGAAAGAATACTCTTGAATTAGAATTTGATGTGATAA
1 CAAGCCTCCACGGTTGGTTTCATGTGAAAGAATACTCTTGAATTAAAATTTGATGTGATAA
*
3670099 CAAGCCTCCACGGTTGGTTTCATGTGATAGAATACTCTTGAATTAAAATTTGATGTGATA
1 CAAGCCTCCACGGTTGGTTTCATGTGAAAGAATACTCTTGAATTAAAATTTGATGTGATA
3670159 TCTCACATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.35
Consensus pattern (61 bp):
CAAGCCTCCACGGTTGGTTTCATGTGAAAGAATACTCTTGAATTAAAATTTGATGTGATAA
Found at i:3672379 original size:24 final size:24
Alignment explanation
Indices: 3672334--3672381 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3672324 TTTTATTTAT
**
3672334 ATAAAACTATAATTTGGACTAATA
1 ATAAAACTATAATTTACACTAATA
* *
3672358 ATAAAGCTATAATTTACTCTAATA
1 ATAAAACTATAATTTACACTAATA
3672382 TGATCTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (24 bp):
ATAAAACTATAATTTACACTAATA
Found at i:3682063 original size:19 final size:19
Alignment explanation
Indices: 3682041--3682085 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3682031 AAGCACATAG
* * *
3682041 TGGCATATGAGGTGCATCC
1 TGGCACATGAAGTGCACCC
3682060 TGGCACATGAAGTGCACCC
1 TGGCACATGAAGTGCACCC
3682079 TGGCACA
1 TGGCACA
3682086 CAAAACGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (19 bp):
TGGCACATGAAGTGCACCC
Found at i:3682120 original size:19 final size:19
Alignment explanation
Indices: 3682107--3682152 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3682097 TTGGCGCACG
3682107 AAGTGCATCCTGGCACACA
1 AAGTGCATCCTGGCACACA
* * **
3682126 AGGTGCATCCAGGTGCACA
1 AAGTGCATCCTGGCACACA
3682145 AAGTGCAT
1 AAGTGCAT
3682153 AATCTCATAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (19 bp):
AAGTGCATCCTGGCACACA
Found at i:3688655 original size:22 final size:21
Alignment explanation
Indices: 3688627--3688672 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
3688617 ATTAAATAAG
3688627 TTTTAGT-TTATGTATCTTATTT
1 TTTTAGTGTT-TGTATC-TATTT
*
3688649 TTTTAGTGTTTTTATCTATTT
1 TTTTAGTGTTTGTATCTATTT
3688670 TTT
1 TTT
3688673 AATCTACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 12 0.55
23 2 0.09
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTTAGTGTTTGTATCTATTT
Found at i:3694825 original size:18 final size:18
Alignment explanation
Indices: 3694802--3694837 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3694792 TGTGTACAAG
*
3694802 GAAGCTTTATTTAACACA
1 GAAGCTCTATTTAACACA
3694820 GAAGCTCTATTTAACACA
1 GAAGCTCTATTTAACACA
3694838 AACGAACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (18 bp):
GAAGCTCTATTTAACACA
Found at i:3703624 original size:20 final size:21
Alignment explanation
Indices: 3703596--3703634 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3703586 AAGTATTTTT
3703596 ATTATTTTTTAATATTTTACA
1 ATTATTTTTTAATATTTTACA
3703617 ATTA-TTTTTAATATTTTA
1 ATTATTTTTTAATATTTTA
3703635 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTTTTTAATATTTTACA
Found at i:3703640 original size:21 final size:21
Alignment explanation
Indices: 3703596--3703640 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
3703586 AAGTATTTTT
*
3703596 ATTATTTTTTAATATTTTACA
1 ATTATTTTTTAATATTTTAAA
3703617 ATTA-TTTTTAATATTTTATAA
1 ATTATTTTTTAATATTTTA-AA
3703638 ATT
1 ATT
3703641 TTATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTTTTTAATATTTTAAA
Found at i:3710699 original size:27 final size:27
Alignment explanation
Indices: 3710660--3711315 Score: 531
Period size: 27 Copynumber: 24.4 Consensus size: 27
3710650 GTAATGGGAC
*
3710660 TAAAATGACCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
*
3710687 TAAAATGATCGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* *
3710714 TAAAATGATTGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* * **
3710741 TAAAATG-GCTGAAATACCGCTAAAGGG
1 TAAAATGATC-GAAATACCCCCGAAGGG
* * **
3710768 TAAAATGATCGAAATATCGCTAAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
3710795 TAAAATGATCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* * * *
3710822 TAAAATGACCAAAATACTCGCGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* * * ** *
3710849 TATAATTATCGAAATGCCCTTGAAGGA
1 TAAAATGATCGAAATACCCCCGAAGGG
* ***
3710876 TAAAATGATCGAAATATCCTTAAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* *
3710903 TAAAATGATCTAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
*
3710930 TAAAATGATCGAAATA-CCCTGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* * * *
3710956 TAAATTGATCGAAAGACCCCCGAAAGA
1 TAAAATGATCGAAATACCCCCGAAGGG
* *
3710983 TAAAATTACCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* * * ***
3711010 TAAACT-ATCAAAATAACCTTAAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* * *
3711036 T-AAATGA-CTAAAATACCCTCAAAGGG
1 TAAAATGATC-GAAATACCCCCGAAGGG
** *
3711062 TAAAATGATCGAAATACCCTTGAAAGG
1 TAAAATGATCGAAATACCCCCGAAGGG
3711089 TAAAATGA-CTGAAATA-CCCCGAAGGG
1 TAAAATGATC-GAAATACCCCCGAAGGG
*
3711115 TAAAATGATCGAAATACCCCCGAAGGA
1 TAAAATGATCGAAATACCCCCGAAGGG
* * *
3711142 TAAAATTACCGAAATACCCCCGAAGGA
1 TAAAATGATCGAAATACCCCCGAAGGG
* * **
3711169 TAAAATTACCGAAATACCCCTAAAGGG
1 TAAAATGATCGAAATACCCCCGAAGGG
* * ***
3711196 TAAAATTATCAAAAT-CTCCTTAAAGGG
1 TAAAATGATCGAAATAC-CCCCGAAGGG
* *
3711223 TAAAATTA-CTAAAATACCCCCGAAGGGG
1 TAAAATGATC-GAAATACCCCCGAA-GGG
* * * * *
3711251 TAAAATTACCGACATA-TCTCGTAAGGG
1 TAAAATGATCGAAATACCCCCG-AAGGG
* * *
3711278 TAAAATTACCGAAATACCCCCTATAGGG
1 TAAAATGATCGAAATACCCCCGA-AGGG
*
3711306 TGAAATGATC
1 TAAAATGATC
3711316 TTTATACCCC
Statistics
Matches: 519, Mismatches: 92, Indels: 35
0.80 0.14 0.05
Matches are distributed among these distances:
25 4 0.01
26 78 0.15
27 403 0.78
28 33 0.06
29 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCCCGAAGGG
Found at i:3711730 original size:28 final size:28
Alignment explanation
Indices: 3711690--3711768 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
3711680 TAATGTTACT
*
3711690 GTATTTGGTTAAGGCCCACACTGATACC
1 GTATTGGGTTAAGGCCCACACTGATACC
* * * *
3711718 GTATTGGGTTAAGTCCCACAGTGCTACT
1 GTATTGGGTTAAGGCCCACACTGATACC
* * *
3711746 GAATTGGGCTAAGGCCCTCACTG
1 GTATTGGGTTAAGGCCCACACTG
3711769 TACTGTCACT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (28 bp):
GTATTGGGTTAAGGCCCACACTGATACC
Found at i:3718792 original size:27 final size:26
Alignment explanation
Indices: 3718752--3719269 Score: 365
Period size: 27 Copynumber: 19.3 Consensus size: 26
3718742 GTATTGGGCC
* *
3718752 TAAAATGTCTGAAATACCTCCGAAGGG
1 TAAAATGACCGAAATACC-CCGAAGGG
*
3718779 TAAAATGACCGAAATACCCTCGAAGAG
1 TAAAATGACCGAAATACCC-CGAAGGG
* * * * *
3718806 TAAAATTACCAAAATGCCCTTGAAAGG
1 TAAAATGACCGAAATACCC-CGAAGGG
* * *
3718833 TAAAATGATCGAAATACACTCGAAAGG
1 TAAAATGACCGAAATAC-CCCGAAGGG
* *
3718860 TAAAATGATCGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCC-CGAAGGG
*
3718887 TAAAATGACCGAAATACCCTCGAAAGG
1 TAAAATGACCGAAATACCC-CGAAGGG
**
3718914 TAAAATGACCGAAATACCTTGAAGGG
1 TAAAATGACCGAAATACCCCGAAGGG
* *
3718940 TAAAGTGACCGAAATACCGTCGAAGGG
1 TAAAATGACCGAAATACC-CCGAAGGG
**** *
3718967 TAAAATGACCGAAATATCTTTAAAAGG
1 TAAAATGACCGAAATA-CCCCGAAGGG
* * * *
3718994 TAAAATTACCAAAATACACTCGAAGGT
1 TAAAATGACCGAAATAC-CCCGAAGGG
*
3719021 TAAAATGACCAAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCC-CGAAGGG
* *
3719048 TAAAATGACTGAAATA-CTCGAAGGG
1 TAAAATGACCGAAATACCCCGAAGGG
* * **
3719073 TAAAATGACCAAAATACCCCTAAAATG
1 TAAAATGACCGAAATACCCC-GAAGGG
* * *
3719100 TAAAATTACCAAAATACCCCTGAATGG
1 TAAAATGACCGAAATACCCC-GAAGGG
* **
3719127 TAAAATTA-CGAAAATATCCCTAAAGGG
1 TAAAATGACCG-AAATA-CCCCGAAGGG
* * * * *
3719154 TAAAATTATCAAAATATCTCTGAAGGG
1 TAAAATGACCGAAATA-CCCCGAAGGG
* * *
3719181 TAAAATTACCAAAATACCCTTGAAGGG
1 TAAAATGACCGAAATACCC-CGAAGGG
* ** *
3719208 TAAAATTACCGAAATACCCTTTAAGGA
1 TAAAATGACCGAAATACCC-CGAAGGG
* *
3719235 TAAAATTACCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCGA-AGGG
*
3719262 TGAAATGA
1 TAAAATGA
3719270 TCTTTATACC
Statistics
Matches: 406, Mismatches: 71, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
25 21 0.05
26 33 0.08
27 346 0.85
28 6 0.01
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (26 bp):
TAAAATGACCGAAATACCCCGAAGGG
Found at i:3718840 original size:54 final size:53
Alignment explanation
Indices: 3718777--3719253 Score: 419
Period size: 54 Copynumber: 8.9 Consensus size: 53
3718767 ACCTCCGAAG
* *
3718777 GGTAAAATGACCGAAATACCCTCGAAGAGTAAAATTACCAAAATGCCCTTGAAA
1 GGTAAAATGACCGAAATACCCTCGAAG-GTAAAATGACCAAAATACCCTTGAAA
* * * * * **
3718831 GGTAAAATGATCGAAATACACTCGAAAGGTAAAATGATCGAAATACCCTCGATG
1 GGTAAAATGACCGAAATACCCTCG-AAGGTAAAATGACCAAAATACCCTTGAAA
* *
3718885 GGTAAAATGACCGAAATACCCTCGAAAGGTAAAATGACCGAAATA-CCTTGAAG
1 GGTAAAATGACCGAAATACCCTCG-AAGGTAAAATGACCAAAATACCCTTGAAA
* * * * * *
3718938 GGTAAAGTGACCGAAATACCGTCGAAGGGTAAAATGACCGAAATATCTTTAAAA
1 GGTAAAATGACCGAAATACCCTCGAA-GGTAAAATGACCAAAATACCCTTGAAA
* * * * *
3718992 GGTAAAATTACCAAAATACACTCGAAGGTTAAAATGACCAAAATACCCTCGAAG
1 GGTAAAATGACCGAAATACCCTCGAAGG-TAAAATGACCAAAATACCCTTGAAA
* * *
3719046 GGTAAAATGACTGAAATA--CTCGAAGGGTAAAATGACCAAAATACCCCTAAAA
1 GGTAAAATGACCGAAATACCCTCGAA-GGTAAAATGACCAAAATACCCTTGAAA
* * * * *
3719098 TGTAAAATTACCAAAATACCC-CTGAATGGTAAAATTACGAAAATATCCC-T-AAA
1 GGTAAAATGACCGAAATACCCTC-GAA-GGTAAAATGACCAAAATA-CCCTTGAAA
* * * * * *
3719151 GGGTAAAATTATCAAAATA-TCTCTGAAGGGTAAAATTACCAAAATACCCTTGAAG
1 -GGTAAAATGACCGAAATACCCTC-GAA-GGTAAAATGACCAAAATACCCTTGAAA
* ** * *
3719206 GGTAAAATTACCGAAATACCCTTTAAGGATAAAATTACCGAAATACCC
1 GGTAAAATGACCGAAATACCCTCGAAGG-TAAAATGACCAAAATACCC
3719254 CCATAGGGTG
Statistics
Matches: 352, Mismatches: 56, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
52 43 0.12
53 60 0.17
54 239 0.68
55 10 0.03
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.21
Consensus pattern (53 bp):
GGTAAAATGACCGAAATACCCTCGAAGGTAAAATGACCAAAATACCCTTGAAA
Found at i:3718890 original size:81 final size:80
Alignment explanation
Indices: 3718752--3719252 Score: 460
Period size: 81 Copynumber: 6.2 Consensus size: 80
3718742 GTATTGGGCC
* * * * * * *
3718752 TAAAATGTCTGAAATACCTCCGAAGGGTAAAATGACCGAAATACCCTCGAAGAGTAAAATTACCA
1 TAAAATGACCGAAATACCT-CGAAAGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCG
*
3718817 AAATGCCCTTGAAAGG
65 AAATACCCTTGAAAGG
* * * *
3718833 TAAAATGATCGAAATACACTCGAAAGGTAAAATGATCGAAATACCCTCGATGGGTAAAATGACCG
1 TAAAATGACCGAAATAC-CTCGAAAGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCG
*
3718898 AAATACCCTCGAAAGG
65 AAATACCCTTGAAAGG
* * * * *
3718914 TAAAATGACCGAAATACCTTGAAGGGTAAAGTGACCGAAATACCGTCGAAGGGTAAAATGACCGA
1 TAAAATGACCGAAATACCTCGAAAGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCGA
* * *
3718979 AATATCTTTAAAAGG
66 AATACCCTTGAAAGG
* * *
3718994 TAAAATTACCAAAATACACTCG-AAGGTTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACT
1 TAAAATGACCGAAATAC-CTCGAAAGG-TAAAATGACCAAAATACCCTCGAAGGGTAAAATGACC
* *
3719058 GAAATA--CTCGAAGGG
64 GAAATACCCTTGAAAGG
* * * * * * *
3719073 TAAAATGACCAAAATACCCCTAAAATGTAAAATTACCAAAATACCC-CTGAATGGTAAAATTA-C
1 TAAAATGACCGAAATACCTC-GAAAGGTAAAATGACCAAAATACCCTC-GAAGGGTAAAATGACC
3719136 GAAAATATCCC-T-AAAGGG
64 G-AAATA-CCCTTGAAA-GG
* * * * * * * *
3719154 TAAAATTATCAAAATATCTCTGAAGGGTAAAATTACCAAAATACCCTTGAAGGGTAAAATTACCG
1 TAAAATGACCGAAATACCTC-GAAAGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCG
*
3719219 AAATACCCTT-TAAGG
65 AAATACCCTTGAAAGG
*
3719234 ATAAAATTACCGAAATACC
1 -TAAAATGACCGAAATACC
3719253 CCCATAGGGT
Statistics
Matches: 348, Mismatches: 57, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
78 4 0.01
79 56 0.16
80 81 0.23
81 202 0.58
82 5 0.01
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.21
Consensus pattern (80 bp):
TAAAATGACCGAAATACCTCGAAAGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCGA
AATACCCTTGAAAGG
Found at i:3719630 original size:28 final size:28
Alignment explanation
Indices: 3719593--3719646 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3719583 ACTGTAATGT
* *
3719593 TACTGTATTGGGTTAAGGCCCACACTAC
1 TACTGAATTGGGCTAAGGCCCACACTAC
*
3719621 TACTGAATTGGGCTAAGGCCCTCACT
1 TACTGAATTGGGCTAAGGCCCACACT
3719647 GTACTGTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (28 bp):
TACTGAATTGGGCTAAGGCCCACACTAC
Found at i:3723007 original size:20 final size:21
Alignment explanation
Indices: 3722971--3723009 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3722961 TTGGTATCAT
3722971 TTTTAAGAAAGGTATCGATTA
1 TTTTAAGAAAGGTATCGATTA
*
3722992 TTTTCAGAAA-GTATCGAT
1 TTTTAAGAAAGGTATCGAT
3723010 ACCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (21 bp):
TTTTAAGAAAGGTATCGATTA
Found at i:3723218 original size:20 final size:21
Alignment explanation
Indices: 3723195--3723242 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3723185 AATGATTTTA
3723195 ACTTGATTG-AAATCATTGTC
1 ACTTGATTGAAAATCATTGTC
*
3723215 ACTTGGA--GAAAATCATTTTC
1 ACTT-GATTGAAAATCATTGTC
3723235 ACTTGATT
1 ACTTGATT
3723243 TTAAAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
19 3 0.13
20 18 0.78
21 2 0.09
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
ACTTGATTGAAAATCATTGTC
Found at i:3725104 original size:41 final size:40
Alignment explanation
Indices: 3725000--3725362 Score: 334
Period size: 41 Copynumber: 8.7 Consensus size: 40
3724990 TCTCTAAATG
* * *
3725000 TAAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATGA
1 TAAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * *
3725040 AAAAGGGTTGCT-A-TGCGTCGATTCCCCATATCATTGATTA
1 TAAGGGGTTGCTAAGTGC-T-GATTCCCCGTATCATTGATTA
* *
3725080 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGTCCTTGATTGTA
1 TAAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TA
* * * *
3725124 AAAGGGGTTGTTATGTACTGATTCCCCGTATCATTGATTA
1 TAAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * *
3725164 TAAGGTGGTTGCTAAGTGCTGATTCCATCGTGTCCTTGATTGTA
1 TAAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TA
* * * *
3725208 AAAGGGGTTGTTATGTGCTAATTCCCCGTATCATTGATTA
1 TAAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * * *
3725248 TAAGGTGGTTGATAAGTGCTGATTCCACTGTATCCTTGATTG
1 TAAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTA
* * *
3725290 TGAAAGGGGTTGCTATGTGCTGATTCCCCGTATTATTAATTA
1 T--AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
3725332 TAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 TAAGG-GGTTGCTAAGTGCTGATTCC-CCGT
3725363 GTAACAGTTA
Statistics
Matches: 259, Mismatches: 46, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
38 3 0.01
39 1 0.00
40 47 0.18
41 68 0.26
42 67 0.26
43 57 0.22
44 16 0.06
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (40 bp):
TAAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
Found at i:3725156 original size:84 final size:84
Alignment explanation
Indices: 3725000--3725364 Score: 524
Period size: 84 Copynumber: 4.4 Consensus size: 84
3724990 TCTCTAAATG
* ** * * *
3725000 TAAGG-GGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-TG-AAAAAGGGTTGCTATGCG-TCG
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGTCCTTGATTGTAAAAGGGGTTGCTATGTGCT-G
*
3725060 ATTCCCCATATCATTGATTA
65 ATTCCCCGTATCATTGATTA
* *
3725080 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGTCCTTGATTGTAAAAGGGGTTGTTATGTACTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGTCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
3725145 TTCCCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
* * *
3725164 TAAGGTGGTTGCTAAGTGCTGATTCCATCGTGTCCTTGATTGTAAAAGGGGTTGTTATGTGCTAA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGTCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
3725229 TTCCCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
* * * *
3725248 TAAGGTGGTTGATAAGTGCTGATTCCACTGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGTCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
* *
3725313 TTCCCCGTATTATTAATTA
66 TTCCCCGTATCATTGATTA
3725332 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGT
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGT
3725365 AACAGTTAAT
Statistics
Matches: 256, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
80 5 0.02
81 19 0.07
82 9 0.04
83 2 0.01
84 220 0.86
85 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (84 bp):
TAAGGTGGTTGCTAAGTGCTGATTCCACCGTGTCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
TTCCCCGTATCATTGATTA
Found at i:3734812 original size:20 final size:19
Alignment explanation
Indices: 3734749--3734838 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 19
3734739 TCCTAGGTCA
*
3734749 ATTTTGACTTGTTTGAAAATC
1 ATTTTCACTTG-TT-AAAATC
* * *
3734770 ATTTTGA-TGTGTTGAAATG
1 ATTTTCACT-TGTTAAAATC
*
3734789 ATTTTAACTTGATTAAAATC
1 ATTTTCACTTG-TTAAAATC
*
3734809 ATTTTCACTTGGTTAAAATA
1 ATTTTCACTT-GTTAAAATC
3734829 ATTTTCACTT
1 ATTTTCACTT
3734839 ACTTTTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
19 12 0.21
20 36 0.62
21 10 0.17
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (19 bp):
ATTTTCACTTGTTAAAATC
Found at i:3734833 original size:40 final size:40
Alignment explanation
Indices: 3734748--3734838 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 40
3734738 GTCCTAGGTC
* * * *
3734748 AATTTTGACTTGTTTGAAAATCATTTTGATGTGTTGAAAT
1 AATTTTAACTTGATTGAAAATCATTTTCATGTGTTAAAAT
*
3734788 GATTTTAACTTGATT-AAAATCATTTTCACT-TGGTTAAAAT
1 AATTTTAACTTGATTGAAAATCATTTTCA-TGT-GTTAAAAT
*
3734828 AATTTTCACTT
1 AATTTTAACTT
3734839 ACTTTTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
39 13 0.31
40 29 0.69
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (40 bp):
AATTTTAACTTGATTGAAAATCATTTTCATGTGTTAAAAT
Found at i:3735557 original size:44 final size:42
Alignment explanation
Indices: 3735507--3735605 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
3735497 TCGCACAGGG
* * * *
3735507 ACATGGTTGTGTGGACAAATCGTGTAC-AATTCAAAGTTTGGGTC
1 ACATGGTTGTGTCG-CAAACCGTGTACAAATT-AAA-TTAGAGTC
* * *
3735551 ACATGGTCGTGTCGCAGACCGTGTGCAAATTAAATTAGAGTC
1 ACATGGTTGTGTCGCAAACCGTGTACAAATTAAATTAGAGTC
3735593 ACATGGTTGTGTC
1 ACATGGTTGTGTC
3735606 ACAGACTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
42 18 0.39
43 12 0.26
44 16 0.35
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (42 bp):
ACATGGTTGTGTCGCAAACCGTGTACAAATTAAATTAGAGTC
Found at i:3737019 original size:45 final size:45
Alignment explanation
Indices: 3736970--3737109 Score: 199
Period size: 45 Copynumber: 3.1 Consensus size: 45
3736960 CAGTCTTAAA
* * * *
3736970 CGTTTGAATCCTGATGCCATAACATCTTTTAGCTATGGTCTTACT
1 CGTTTGAATCGTGATGCTAGAACATCTTTCAGCTATGGTCTTACT
*
3737015 CGTTTGAATCGTGATGCTAGAACATCTTTCAGCTATTGTCTTACT
1 CGTTTGAATCGTGATGCTAGAACATCTTTCAGCTATGGTCTTACT
* * *
3737060 CGTTTGAATCGTGGTGCTAGAGCGTCTTTCAGCTATGGTCTTACT
1 CGTTTGAATCGTGATGCTAGAACATCTTTCAGCTATGGTCTTACT
*
3737105 AGTTT
1 CGTTT
3737110 TTCAACCAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 85 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (45 bp):
CGTTTGAATCGTGATGCTAGAACATCTTTCAGCTATGGTCTTACT
Found at i:3741855 original size:45 final size:45
Alignment explanation
Indices: 3741747--3741903 Score: 156
Period size: 45 Copynumber: 3.5 Consensus size: 45
3741737 CCAAGACATG
* * * *
3741747 ACGTCTTTCAACTATGGTCTTATTCACTTTCTG--TCATGTTACCATA
1 ACGTCTTTCAACTATGGTC-T-TCCACATT-TGAATCGTGATACCATA
** *
3741793 GTGTCTTTCAACCATGGTCTTCCACATTTGAATCGTGATACCATA
1 ACGTCTTTCAACTATGGTCTTCCACATTTGAATCGTGATACCATA
** * * *
3741838 ACGTCTTTCAGTTATGGTCTTCCTCATTTGAGTCGTGATGCCATA
1 ACGTCTTTCAACTATGGTCTTCCACATTTGAATCGTGATACCATA
*
3741883 GCGTCTTTCAACTATGGTCTT
1 ACGTCTTTCAACTATGGTCTT
3741904 ACTTATTTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
43 2 0.02
44 6 0.07
45 67 0.74
46 16 0.18
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (45 bp):
ACGTCTTTCAACTATGGTCTTCCACATTTGAATCGTGATACCATA
Found at i:3753119 original size:36 final size:36
Alignment explanation
Indices: 3753079--3753171 Score: 116
Period size: 35 Copynumber: 2.6 Consensus size: 36
3753069 GTATGTCGTC
*
3753079 AATCCAACAAAAACACACCAAATGCTCATAAGAGCT
1 AATCCAACAGAAACACACCAAATGCTCATAAGAGCT
** *
3753115 AATCCTTCCGAAACACACC-AATGCTCATAAGAGCT
1 AATCCAACAGAAACACACCAAATGCTCATAAGAGCT
* * *
3753150 AGTCCAACTGAAATACACCAAA
1 AATCCAACAGAAACACACCAAA
3753172 CAGAGAGTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 30 0.64
36 17 0.36
ACGTcount: A:0.45, C:0.29, G:0.10, T:0.16
Consensus pattern (36 bp):
AATCCAACAGAAACACACCAAATGCTCATAAGAGCT
Found at i:3770189 original size:12 final size:12
Alignment explanation
Indices: 3770172--3770215 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
3770162 AGGTAATTGG
3770172 TCAGGAAACACA
1 TCAGGAAACACA
3770184 TCAGGAAACACA
1 TCAGGAAACACA
* *
3770196 TTAGAAAACACA
1 TCAGGAAACACA
3770208 TCAGGAAA
1 TCAGGAAA
3770216 GTCTTTCACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.52, C:0.20, G:0.16, T:0.11
Consensus pattern (12 bp):
TCAGGAAACACA
Found at i:3774323 original size:39 final size:40
Alignment explanation
Indices: 3774253--3774395 Score: 146
Period size: 40 Copynumber: 3.6 Consensus size: 40
3774243 ACGGTTTTAC
* * * ** *
3774253 AAGTTGTGTACCAGCAAAGCTCTTCCCTGAGC-TAAGGAT
1 AAGTTGTGTATCAACAAAGCTCCTCTGTGAGCTTATGGAT
* * * *
3774292 AAGTTGTGTATCAGCATAGCTCCTCTGTGAGCTTTTGGAC
1 AAGTTGTGTATCAACAAAGCTCCTCTGTGAGCTTATGGAT
* *
3774332 AAGTTGTGTATCAACGAAGCTCAC-CTGCGAGCTTATGGAT
1 AAGTTGTGTATCAACAAAGCTC-CTCTGTGAGCTTATGGAT
*
3774372 AAGCTGTGTATCAACAAAGCTCCT
1 AAGTTGTGTATCAACAAAGCTCCT
3774396 TGTCGAAACC
Statistics
Matches: 85, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 28 0.33
40 56 0.66
41 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (40 bp):
AAGTTGTGTATCAACAAAGCTCCTCTGTGAGCTTATGGAT
Found at i:3777013 original size:44 final size:44
Alignment explanation
Indices: 3776910--3777070 Score: 142
Period size: 44 Copynumber: 3.6 Consensus size: 44
3776900 TTTTAGTCTG
* * * * * * * *
3776910 CTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAATCTG
1 CTCCACTACAACTTCAGAGAGATAAGATTAG-TAACTTCAACCTA
* ** * *
3776955 CTCCACTGCAACTTCAGAGAGATAAGATTAGTGGCTTTAATCTA
1 CTCCACTACAACTTCAGAGAGATAAGATTAGTAACTTCAACCTA
** * * *
3776999 CTGTACTACAACTTCAGATAGATAAGACTAGTAACTTCAACCTG
1 CTCCACTACAACTTCAGAGAGATAAGATTAGTAACTTCAACCTA
*
3777043 CTCCACTGCAACTTCAGAGAGATAAGAT
1 CTCCACTACAACTTCAGAGAGATAAGAT
3777071 CTGTTATTTA
Statistics
Matches: 93, Mismatches: 23, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
44 65 0.70
45 28 0.30
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (44 bp):
CTCCACTACAACTTCAGAGAGATAAGATTAGTAACTTCAACCTA
Found at i:3777237 original size:136 final size:137
Alignment explanation
Indices: 3777088--3777397 Score: 415
Period size: 136 Copynumber: 2.3 Consensus size: 137
3777078 TTATAGCTTA
* * **
3777088 AATCTGTTGCACTGCAACTTCAAGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAAA
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTTCAAA
* * * * *
3777153 GAGATAAGATATGTTATTTATAGCTTTAATTTTTTCCACTGCAACTTTAGGG-AATAAGATTCTC
66 GAGATAAGATATGTAAGTTATAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGATTCGC
3777217 TATCATC
131 TATCATC
* * *
3777224 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTTCAGA
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTTCAAA
* * *
3777289 GAGATAGGATCTGTAAGTTCTAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGATTCGC
66 GAGATAAGATATGTAAGTTATAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGATTCGC
*
3777354 TATCTTC
131 TATCATC
* * * ***
3777361 AGTCTACTCCACTACAACTTTTGGGAGATAAGACTTG
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTG
3777398 TAACTTCAAC
Statistics
Matches: 153, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
136 103 0.67
137 50 0.33
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (137 bp):
AATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTTCAAA
GAGATAAGATATGTAAGTTATAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGATTCGC
TATCATC
Found at i:3777282 original size:41 final size:44
Alignment explanation
Indices: 3777187--3777480 Score: 152
Period size: 44 Copynumber: 6.6 Consensus size: 44
3777177 TTTAATTTTT
3777187 TCCACTGCAACTTTAGGGA-ATAAGATTCTCTATCATCAATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGA-TCTCTATCATCAATCTGC
*
3777231 TCCACTGCAACTTTAGGGAGATAAGA-CT-TGAT-AT-GATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATCTCT-ATCATCAATCTGC
* * * * * * * *
3777272 TCTACTGCAACTTCAGAGAGATAGGATCTGTAAGTTCTAGCTTTAATTTGT
1 TCCACTGCAACTTTAGGGAGATAAGATCTCT-A--TC-A---TCAATCTGC
* * * * * *
3777323 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTAC
1 TCCACTGCAACTTTAGGGAGATAAGA-TCTCTATCATCAATCTGC
* * * * * *
3777368 TCCACTACAACTTTTGGGAGATAAGA-CTTGTAACTTCAACCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATC-TCTATCATCAATCTGC
* * ** * * * *
3777412 TCCACTACAACTTCAGGGAGATAAGGAT-AGTAACTTAAACCTGC
1 TCCACTGCAACTTTAGGGAGATAA-GATCTCTATCATCAATCTGC
* *
3777456 TCCACTGCAACTTCAGAGAGATAAG
1 TCCACTGCAACTTTAGGGAGATAAG
3777481 GTTTGATATG
Statistics
Matches: 197, Mismatches: 37, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
41 28 0.14
42 5 0.03
43 8 0.04
44 87 0.44
45 35 0.18
47 1 0.01
49 2 0.01
50 1 0.01
51 27 0.14
52 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (44 bp):
TCCACTGCAACTTTAGGGAGATAAGATCTCTATCATCAATCTGC
Found at i:3777420 original size:44 final size:44
Alignment explanation
Indices: 3777367--3777481 Score: 160
Period size: 44 Copynumber: 2.6 Consensus size: 44
3777357 CTTCAGTCTA
** * *
3777367 CTCCACTACAACTTTTGGGAGATAA-GACTTGTAACTTCAACCTG
1 CTCCACTACAACTTCAGGGAGATAAGGA-TAGTAACTTAAACCTG
3777411 CTCCACTACAACTTCAGGGAGATAAGGATAGTAACTTAAACCTG
1 CTCCACTACAACTTCAGGGAGATAAGGATAGTAACTTAAACCTG
* *
3777455 CTCCACTGCAACTTCAGAGAGATAAGG
1 CTCCACTACAACTTCAGGGAGATAAGG
3777482 TTTGATATGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 62 0.97
45 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (44 bp):
CTCCACTACAACTTCAGGGAGATAAGGATAGTAACTTAAACCTG
Found at i:3778394 original size:16 final size:14
Alignment explanation
Indices: 3778371--3778413 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
3778361 CCTCTCCTAT
3778371 TTCTTTTTCTTATTC
1 TTCTTTTTCTT-TTC
3778386 TTCCTTTTTCTTTTC
1 TT-CTTTTTCTTTTC
*
3778401 TTTTTTTTCTTTT
1 TTCTTTTTCTTTT
3778414 TTAAAAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.38
15 7 0.27
16 9 0.35
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:3778414 original size:21 final size:21
Alignment explanation
Indices: 3778365--3778415 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 21
3778355 CATTGTCCTC
*
3778365 TCCTATTTCTTTTTCTTATTCT
1 TCCT-TTTTTTTTTCTTATTCT
* *
3778387 TCCTTTTTCTTTTCTT-TTTT
1 TCCTTTTTTTTTTCTTATTCT
*
3778407 TTCTTTTTT
1 TCCTTTTTT
3778416 AAAAGTGACG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
TCCTTTTTTTTTTCTTATTCT
Found at i:3784418 original size:20 final size:20
Alignment explanation
Indices: 3784393--3784432 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3784383 TTGTTATTAA
3784393 TATTTTGAACTTTTAAAATT
1 TATTTTGAACTTTTAAAATT
* *
3784413 TATTTTGAATTTTTATAATT
1 TATTTTGAACTTTTAAAATT
3784433 ACTAATTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (20 bp):
TATTTTGAACTTTTAAAATT
Found at i:3818988 original size:33 final size:33
Alignment explanation
Indices: 3818941--3819008 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3818931 CCTCTATTTT
3818941 GGTTCTGGTTACCCATGTAATACACAAATTCTA
1 GGTTCTGGTTACCCATGTAATACACAAATTCTA
*
3818974 GGTTTTGGTTACCCATGTAATACACAAATTCTA
1 GGTTCTGGTTACCCATGTAATACACAAATTCTA
3819007 GG
1 GG
3819009 CTCGATTGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (33 bp):
GGTTCTGGTTACCCATGTAATACACAAATTCTA
Found at i:3822120 original size:10 final size:10
Alignment explanation
Indices: 3822105--3822132 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3822095 TTGAACATAA
3822105 AAAAGAAAGG
1 AAAAGAAAGG
3822115 AAAAGAAAGG
1 AAAAGAAAGG
3822125 AAAAGAAA
1 AAAAGAAA
3822133 ACATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGG
Found at i:3822129 original size:6 final size:5
Alignment explanation
Indices: 3822105--3822155 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
3822095 TTGAACATAA
* * * * *
3822105 AAAAG AAAGG AAAAG AAAGG AAAAG AAAAC ATAA- AAAAG AAAGG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
3822154 AA
1 AA
3822156 CCGAAATCAG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
4 3 0.08
5 33 0.92
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:3822706 original size:20 final size:21
Alignment explanation
Indices: 3822666--3822724 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
3822656 CATTTGAAAC
*
3822666 TTTATTTGTTGATTTGGTTTA
1 TTTATTTTTTGATTTGGTTTA
**
3822687 -TTATTTTTTGATTTTTTTTA
1 TTTATTTTTTGATTTGGTTTA
*
3822707 TTTACTTATTTGATTTGG
1 TTTA-TTTTTTGATTTGG
3822725 GCCGAGCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 17 0.57
21 3 0.10
22 10 0.33
ACGTcount: A:0.15, C:0.02, G:0.14, T:0.69
Consensus pattern (21 bp):
TTTATTTTTTGATTTGGTTTA
Found at i:3823088 original size:44 final size:44
Alignment explanation
Indices: 3823021--3823138 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
3823011 AATGCGATCT
* * * *
3823021 ACTCCGCTGTAA-CTTCAGAGAGATAAGATT-CTTTGTTTTAATCC
1 ACTCCGCTGTAATC-TCAGGGAGATAAGATTAC-TAGCTTCAATCC
* * * *
3823065 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 ACTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCC
* *
3823109 ACGCCGCTGTAATCTCAAGGAGATAAGATT
1 ACTCCGCTGTAATCTCAGGGAGATAAGATT
3823139 TCTGGCTTGA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 57 0.97
45 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
ACTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCC
Found at i:3841319 original size:45 final size:44
Alignment explanation
Indices: 3841240--3841327 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
3841230 TATACGCCTA
* *
3841240 AAATGTGTAAGACCATAGCTGAAAGATGTCATGGCATCATGATAG
1 AAATGAGTAAGACCATAGCTGAAAGATCTCATGGCATCA-GATAG
3841285 AAATGAGTAAGACCATAGCT-AGAAGA-CTCTATGGCATCAGATA
1 AAATGAGTAAGACCATAGCTGA-AAGATCTC-ATGGCATCAGATA
3841328 AATGTGCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 7 0.18
45 32 0.82
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (44 bp):
AAATGAGTAAGACCATAGCTGAAAGATCTCATGGCATCAGATAG
Found at i:3842704 original size:138 final size:138
Alignment explanation
Indices: 3842431--3842714 Score: 439
Period size: 138 Copynumber: 2.1 Consensus size: 138
3842421 GAGAACATAT
* *
3842431 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTTTATATATTTTACCAATTTTTTT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAATTTTATT
* * * *
3842496 AATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAGTTAATATTCTTT
66 AATATAAACAGTTATATTAAATAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
3842561 TCGAAAGA
131 TCGAAAGA
*
3842569 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAA-TTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAC-CAATTTTAT
* *
3842633 TAATATAAACAGTTATATTAAATAATTTCAGTCAAAATATAAAAGATATGAAAATT-AT-TTGTT
65 TAATATAAACAGTTATATTAAATAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTT
3842696 TTCCCGAAAGA
130 TT--CGAAAGA
3842707 ATATAATT
1 ATATAATT
3842715 CATTTTTCTA
Statistics
Matches: 134, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
136 6 0.04
137 2 0.01
138 124 0.93
139 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.42
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAATTTTATT
AATATAAACAGTTATATTAAATAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
TCGAAAGA
Found at i:3849333 original size:23 final size:23
Alignment explanation
Indices: 3849307--3849353 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3849297 TATTTCGTCA
3849307 TAGATTCTATTATGGTAAAGTTG
1 TAGATTCTATTATGGTAAAGTTG
3849330 TAGATTCTATTATGGTAAAGTTG
1 TAGATTCTATTATGGTAAAGTTG
3849353 T
1 T
3849354 TACAACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (23 bp):
TAGATTCTATTATGGTAAAGTTG
Found at i:3849423 original size:13 final size:13
Alignment explanation
Indices: 3849405--3849446 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
3849395 TAATTAAGAG
3849405 TTAAATTAATTTA
1 TTAAATTAATTTA
3849418 TTAAATTAATTTA
1 TTAAATTAATTTA
*
3849431 TTAAATAATATTTA
1 TTAAATTA-ATTTA
3849445 TT
1 TT
3849447 TTGAGAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 20 0.74
14 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATTAATTTA
Found at i:3853868 original size:37 final size:37
Alignment explanation
Indices: 3853825--3853938 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
3853815 CCACTGGATA
3853825 ATGCCATATAGTCGAGTCTGGCGGACCTCCTTAGATC
1 ATGCCATATAGTCGAGTCTGGCGGACCTCCTTAGATC
*
3853862 ATGCCATATAGTCGAGTCTGGTGGACCTCCTTAGATC
1 ATGCCATATAGTCGAGTCTGGCGGACCTCCTTAGATC
* * *
3853899 ATGCCATATAGGCGAGTCTCGCGGACCTCCTTGGATC
1 ATGCCATATAGTCGAGTCTGGCGGACCTCCTTAGATC
3853936 ATG
1 ATG
3853939 ACAGGTAGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.27
Consensus pattern (37 bp):
ATGCCATATAGTCGAGTCTGGCGGACCTCCTTAGATC
Found at i:3853971 original size:74 final size:74
Alignment explanation
Indices: 3853825--3853976 Score: 171
Period size: 74 Copynumber: 2.1 Consensus size: 74
3853815 CCACTGGATA
* * * * * *** *
3853825 ATGCCATATAGTCGAGTCTGGCGGACCTCCTTAGATCATGCCATATAGTCGAGTCTGGTGGACCT
1 ATGCCATATAGGCGAGTCTCGCGGACCTCCTTAGATCATGACAGATAGTCGAATCTGGCAAACCA
*
3853890 CCTTAGATC
66 CCCTAGATC
* * *
3853899 ATGCCATATAGGCGAGTCTCGCGGACCTCCTTGGATCATGACAGGTAGGT-GAATCTGGCAAATC
1 ATGCCATATAGGCGAGTCTCGCGGACCTCCTTAGATCATGACAGATA-GTCGAATCTGGCAAACC
3853963 ACCCTAGATC
65 ACCCTAGATC
3853973 ATGC
1 ATGC
3853977 AATGGCCATG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
74 62 0.97
75 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.26
Consensus pattern (74 bp):
ATGCCATATAGGCGAGTCTCGCGGACCTCCTTAGATCATGACAGATAGTCGAATCTGGCAAACCA
CCCTAGATC
Found at i:3861449 original size:23 final size:22
Alignment explanation
Indices: 3861406--3861449 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
3861396 TTCTAAGTCG
3861406 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
3861429 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
3861450 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:3861559 original size:45 final size:45
Alignment explanation
Indices: 3861495--3861587 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
3861485 ACAGATACTT
* *
3861495 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
* *
3861540 GGTGGAATCAGCAGATAGCAACCACCTTACTAATCAATGATGTTC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
3861585 GGT
1 GGT
3861588 TCACATAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:3874578 original size:49 final size:49
Alignment explanation
Indices: 3874520--3874845 Score: 202
Period size: 49 Copynumber: 6.5 Consensus size: 49
3874510 CAGGCCAAAG
*
3874520 CCATGTCCCAAACATGGTCTTACATGGGATGTTTCCTGTACTGCCAATT
1 CCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTACTGCCAATT
* * * * * *
3874569 CCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATAT-CGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC--TGCCAATT
* * *
3874619 CCATGTCCCAGACATGGTCTTAC-GGGGACCTCTTAT-CTCG-A-TGCCAACGT
1 CCATGTCCCAGACATGGTCTTACATGGGA--TGTT-TCCT-GTACTGCCAA-TT
* * ** * * *
3874669 -CATGTCCCAGACATGGTCTTACGTGGGACCTCTCACAACCTTAATAATGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGA--TGT---TTCC-T-GTACTGCCAATT
*
3874724 CCATGTCCCAGACATGGCCTTACATGGGATGTTTCCTGTACTGCCAATT
1 CCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTACTGCCAATT
* * * * * *
3874773 CCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATAT-CGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC--TGCCAATT
*
3874823 CCATGTCCCAGACATTGTCTTAC
1 CCATGTCCCAGACATGGTCTTAC
3874846 GGGGGACCTC
Statistics
Matches: 214, Mismatches: 42, Indels: 41
0.72 0.14 0.14
Matches are distributed among these distances:
48 8 0.04
49 100 0.47
50 63 0.29
51 3 0.01
52 3 0.01
53 1 0.00
54 3 0.01
55 1 0.00
56 32 0.15
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTACTGCCAATT
Done.