Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 12 of 168
Found at i:3384768 original size:13 final size:13
Alignment explanation
Indices: 3384750--3384774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3384740 TAAAAGAGTT
3384750 ATTAATTAAAAAG
1 ATTAATTAAAAAG
3384763 ATTAATTAAAAA
1 ATTAATTAAAAA
3384775 TTAAAAAAAA
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:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:3389554 original size:97 final size:100
Alignment explanation
Indices: 3389351--3389704 Score: 283
Period size: 97 Copynumber: 3.5 Consensus size: 100
3389341 AAACAGATTC
* * *
3389351 CATTGATTCATAAAGGGGTGTGATTG-GACCAAAGGTAAGAATAGTACCATTCGGTTCATTGCCA
1 CATTGATTCATAAAGGGGTGTGTTTGAG-CCAAAGGCAAGAATAGTACCA-TC-GTTCATTGCAA
* * *
3389415 ATGTGAACTCCATTATGAATCCACCATTACAAGGATTT
63 ATGTGAACTCCATTATAAATCCACCATAACAAGCATTT
3389453 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTA-C-T-GTTCATTG-AATAT
1 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTACCATCGTTCATTGCAA-AT
* *
3389514 GTGGACTCCATT-TCAAATCCACCATAACGAGCATTT
65 GTGAACTCCATTAT-AAATCCACCATAACAAGCATTT
* * * * * *
3389550 CATTGATTCAGAAA-GGG-GTGTTTGAGCCAAAGGTAATAATATTACCGATTGGTTTCATTATCA
1 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTACC-A-TCG-TTCATT-GCA
* * ** * ** *
3389613 AATGGTGGACCCCATTACGAATCCACCATTATGAGCACTT
62 AAT-GTGAACTCCATTATAAATCCACCATAACAAGCATTT
* * * * * * **
3389653 GATTTGATTTACAAAGGAGTGTGTTTGAGCCAAGGGTAAGAACGGTACCATC
1 CA-TTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTACCATC
3389705 ACATGCATTC
Statistics
Matches: 207, Mismatches: 29, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
95 24 0.12
96 6 0.03
97 52 0.25
99 2 0.01
100 1 0.00
101 7 0.03
102 44 0.21
103 33 0.16
104 11 0.05
105 3 0.01
106 24 0.12
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (100 bp):
CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTACCATCGTTCATTGCAAATG
TGAACTCCATTATAAATCCACCATAACAAGCATTT
Found at i:3394433 original size:3 final size:3
Alignment explanation
Indices: 3394425--3394449 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3394415 GAAATCTTTC
3394425 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3394450 AGAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3395792 original size:13 final size:13
Alignment explanation
Indices: 3395774--3395799 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3395764 AGTGTTTCCC
3395774 AAAACCATTTGTT
1 AAAACCATTTGTT
3395787 AAAACCATTTGTT
1 AAAACCATTTGTT
3395800 TGCGTAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:3396156 original size:13 final size:14
Alignment explanation
Indices: 3396134--3396167 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3396124 ATGCACATAT
3396134 CAGAATCAAATAAA
1 CAGAATCAAATAAA
*
3396148 CAGAA-CAAATATA
1 CAGAATCAAATAAA
3396161 CAGAATC
1 CAGAATC
3396168 TTACCCCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.15
Consensus pattern (14 bp):
CAGAATCAAATAAA
Found at i:3407268 original size:29 final size:30
Alignment explanation
Indices: 3407236--3407301 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
3407226 TAGGGAGTGT
* * * *
3407236 ATCAAATTAGTTCCTCTATTATTAAATAG-
1 ATCAAATTAGTCCCTATACTATTAAAAAGA
*
3407265 ATCAATTTAGTCCCTATACTATTAAAAAGA
1 ATCAAATTAGTCCCTATACTATTAAAAAGA
3407295 ATCAAAT
1 ATCAAAT
3407302 AAATCCAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (30 bp):
ATCAAATTAGTCCCTATACTATTAAAAAGA
Found at i:3408398 original size:20 final size:20
Alignment explanation
Indices: 3408358--3408398 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3408348 CTAAAATTCA
* *
3408358 TTTAATAAAATATATTTAAT
1 TTTAATAAAATATAATAAAT
*
3408378 TTTAATAAAATTTAATAAAT
1 TTTAATAAAATATAATAAAT
3408398 T
1 T
3408399 GTTATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAATAAAATATAATAAAT
Found at i:3413922 original size:25 final size:25
Alignment explanation
Indices: 3413894--3413942 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3413884 GGGTGTTTGA
3413894 TTTTATTTACTTATTTATTATTTAG
1 TTTTATTTACTTATTTATTATTTAG
* * * *
3413919 TTTTTTTTATTTTTTTATTTTTTA
1 TTTTATTTACTTATTTATTATTTA
3413943 CTTAAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (25 bp):
TTTTATTTACTTATTTATTATTTAG
Found at i:3415037 original size:11 final size:10
Alignment explanation
Indices: 3415020--3415044 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3415010 ATTATTATAA
3415020 GTTTTTTTTT
1 GTTTTTTTTT
3415030 GTTTTTTTTT
1 GTTTTTTTTT
3415040 GTTTT
1 GTTTT
3415045 ATATATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
GTTTTTTTTT
Found at i:3416062 original size:16 final size:16
Alignment explanation
Indices: 3416041--3416108 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
3416031 TTTGGTTCGC
*
3416041 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
3416057 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3416073 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3416089 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3416105 TGTA
1 TGTA
3416109 ATAGCAAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3416365 original size:18 final size:17
Alignment explanation
Indices: 3416344--3416378 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3416334 TTATTATTAA
*
3416344 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3416362 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3416379 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3416432 original size:157 final size:160
Alignment explanation
Indices: 3416238--3416548 Score: 547
Period size: 160 Copynumber: 2.0 Consensus size: 160
3416228 CCCTTAGCAT
*
3416238 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAA-TA-A-TATTATTAT
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGAAGATTATTATTAT
* * *
3416300 CAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
66 CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAAAACATTTTAATTAAAATATA
3416365 TAATTTAATAAAATTCTTAATAATTACCAG
131 TAATTTAATAAAATTCTTAATAATTACCAG
*
3416395 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGAAGATTATTATTAT
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGAAGATTATTATTAT
*
3416460 CAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAAAACATTTTAATTAAAATATA
66 CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAAAACATTTTAATTAAAATATA
3416525 TAATTTAATAAAATTCTTAATAAT
131 TAATTTAATAAAATTCTTAATAAT
3416549 CAATATTCTT
Statistics
Matches: 145, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
157 49 0.34
158 1 0.01
159 1 0.01
160 94 0.65
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (160 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGAAGATTATTATTAT
CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAAAACATTTTAATTAAAATATA
TAATTTAATAAAATTCTTAATAATTACCAG
Found at i:3416656 original size:59 final size:57
Alignment explanation
Indices: 3416484--3416659 Score: 158
Period size: 59 Copynumber: 3.0 Consensus size: 57
3416474 TTAATCATAT
* *
3416484 TTTAACATAATTATTATTAAAAACATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTA
* ** * ** * * * *
3416541 TTAATAATCA-ATATTCTTATATAAATTTACTAAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTAT-TAAAAATATTTTAATTAAAATATATAAT-TTAATAAAAT-T-A
3416604 TTTAACATAATTATTATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATT
1 TTTAACATAATTATTATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATT
3416660 CTTAATAATC
Statistics
Matches: 87, Mismatches: 22, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
57 2 0.02
58 2 0.02
59 31 0.36
60 18 0.21
61 30 0.34
62 2 0.02
63 2 0.02
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (57 bp):
TTTAACATAATTATTATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTA
Found at i:3421448 original size:47 final size:47
Alignment explanation
Indices: 3421394--3421488 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
3421384 TAAGTGAAAC
* *
3421394 TAAGCTTCGGGCTAACGAGTTCGAACATATTTGGGTTCGTTGTAAAA
1 TAAGCTTCGGGCTAACGAGTTCGAACATATTCGAGTTCGTTGTAAAA
*
3421441 TAAGCTTCGGGCTAACGAGTTCGAACATATTCGAGTTTGTTGTAAAA
1 TAAGCTTCGGGCTAACGAGTTCGAACATATTCGAGTTCGTTGTAAAA
3421488 T
1 T
3421489 GGATGGTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (47 bp):
TAAGCTTCGGGCTAACGAGTTCGAACATATTCGAGTTCGTTGTAAAA
Found at i:3423112 original size:34 final size:32
Alignment explanation
Indices: 3423074--3423178 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 32
3423064 AGTACACTAT
*
3423074 ATGCTCAAGTGAGCCATTCCAACCAGCACACCAA
1 ATGCTCAA--GAGCCAATCCAACCAGCACACCAA
*
3423108 ATGCTCGCAAGAGCCAATCCATCCAGCACACCAA
1 ATGCT--CAAGAGCCAATCCAACCAGCACACCAA
* ** *
3423142 ATGCTCGTAAGAGCAAATCCATTCAGCATACCAA
1 ATGCTC--AAGAGCCAATCCAACCAGCACACCAA
3423176 ATG
1 ATG
3423179 ATTTATTCTG
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
32 1 0.02
34 58 0.94
36 3 0.05
ACGTcount: A:0.36, C:0.32, G:0.15, T:0.16
Consensus pattern (32 bp):
ATGCTCAAGAGCCAATCCAACCAGCACACCAA
Found at i:3434463 original size:15 final size:15
Alignment explanation
Indices: 3434443--3434475 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3434433 TAAAGATTAA
3434443 ATTTCAAATTTAAGC
1 ATTTCAAATTTAAGC
3434458 ATTTCAAATTTAAGC
1 ATTTCAAATTTAAGC
3434473 ATT
1 ATT
3434476 ATATAGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (15 bp):
ATTTCAAATTTAAGC
Found at i:3436837 original size:18 final size:18
Alignment explanation
Indices: 3436814--3436861 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3436804 AATTGAAATA
3436814 AATAATAATAATATCAA-T
1 AATAATAATAATAT-AATT
* *
3436832 AATAATAACAATGTAATT
1 AATAATAATAATATAATT
*
3436850 AATAATGATAAT
1 AATAATAATAAT
3436862 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (18 bp):
AATAATAATAATATAATT
Found at i:3440651 original size:2 final size:2
Alignment explanation
Indices: 3440624--3440682 Score: 82
Period size: 2 Copynumber: 27.5 Consensus size: 2
3440614 CTATTGCTTC
3440624 AT AT CAT AT CAT AT CAT AT CAT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT -AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
3440668 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
3440683 ACACGATACA
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 45 0.85
3 8 0.15
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3441592 original size:22 final size:21
Alignment explanation
Indices: 3441567--3441619 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
3441557 AAAATATTTA
*
3441567 ATTTTTTTTAATAAAGCCAAAC
1 ATTTTTTTTAACAAA-CCAAAC
* * *
3441589 ATTTTAATTTAACAAACCATAT
1 ATTTT-TTTTAACAAACCAAAC
3441611 ATTTTTTTT
1 ATTTTTTTT
3441620 CACATCAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTTTTTAACAAACCAAAC
Found at i:3443937 original size:22 final size:22
Alignment explanation
Indices: 3443911--3443952 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3443901 ATTATATAAA
3443911 ATGATATAA-ATAAATAAATGAC
1 ATGATATAATA-AAATAAATGAC
3443933 ATGATATAATAAAATAAATG
1 ATGATATAATAAAATAAATG
3443953 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (22 bp):
ATGATATAATAAAATAAATGAC
Found at i:3444806 original size:22 final size:22
Alignment explanation
Indices: 3444775--3444817 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3444765 GCGCAAAAGT
3444775 AAAAAAAAGCGGTAAGATTCGC
1 AAAAAAAAGCGGTAAGATTCGC
*
3444797 AAAAAGAAGCGGTAAGATTCG
1 AAAAAAAAGCGGTAAGATTCG
3444818 ACTTTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.14
Consensus pattern (22 bp):
AAAAAAAAGCGGTAAGATTCGC
Found at i:3445527 original size:44 final size:44
Alignment explanation
Indices: 3445486--3445888 Score: 190
Period size: 44 Copynumber: 9.0 Consensus size: 44
3445476 CTGGGAGAAG
*
3445486 AGACTTGTAGCTTTGATCTACTCCGCTGCAACTTCAAGGAGATA
1 AGACTTGTAGCTTTGATCTACTCCACTGCAACTTCAAGGAGATA
* * * * * * *
3445530 AGAATTGGTAACTTTAACCTTCTCCACTGTAACTTCAGGGAGATA
1 AGACTT-GTAGCTTTGATCTACTCCACTGCAACTTCAAGGAGATA
* * * * * *
3445575 AGGCTTGT-GTATTTTTATCCTGCTCCACTGCAACTTTAGGGAGATA
1 AGACTTGTAG--CTTTGAT-CTACTCCACTGCAACTTCAAGGAGATA
* * * * * *
3445621 AGGA-TTGTGGCTTCGATCTGCTCCAATGTAATTTCAAGGAGA-A
1 A-GACTTGTAGCTTTGATCTACTCCACTGCAACTTCAAGGAGATA
* ** *
3445664 GAGATTTGTAGCTTTGATCTACTCTTCTGCAACTTTAAGGAGATA
1 -AGACTTGTAGCTTTGATCTACTCCACTGCAACTTCAAGGAGATA
* * * * * *
3445709 AGAATTGGTA-ATTTCAACCTGCTCCACTGCAACTTCAGGGAGATA
1 AGACTT-GTAGCTTT-GATCTACTCCACTGCAACTTCAAGGAGATA
* * * * * * * * *
3445754 AGGA-TTGT-GGTTTCAATCTGCTCTAATGTAATTTTAGGGAGA-A
1 A-GACTTGTAGCTTT-GATCTACTCCACTGCAACTTCAAGGAGATA
* * * * *
3445797 GAAATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATA
1 -AGACTTGTAGCTTTGATCTACTCCACTGCAACTTCAAGGAGATA
* * ** * * *
3445842 AGAATTGGTAACTTCAACCTACTCCACTGTAACTTCAGGGAGATA
1 AGACTT-GTAGCTTTGATCTACTCCACTGCAACTTCAAGGAGATA
3445887 AG
1 AG
3445889 GTTTGCAACT
Statistics
Matches: 270, Mismatches: 71, Indels: 35
0.72 0.19 0.09
Matches are distributed among these distances:
43 5 0.02
44 122 0.45
45 110 0.41
46 31 0.11
47 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (44 bp):
AGACTTGTAGCTTTGATCTACTCCACTGCAACTTCAAGGAGATA
Found at i:3445616 original size:46 final size:46
Alignment explanation
Indices: 3445506--3446029 Score: 222
Period size: 45 Copynumber: 11.6 Consensus size: 46
3445496 CTTTGATCTA
* * * *
3445506 CTCCGCTGCAACTTCAAGGAGATAAGAATTG-GTAACTTTAACCTT
1 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGTAACTTTAACCTG
* * ** *
3445551 CTCCACTGTAACTTCAGGGAGATAAGGCTTGTGTATTTTTATCCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGTAACTTTAACCTG
* * ** *
3445597 CTCCACTGCAACTTTAGGGAGATAAGGATTGTG--GCTTCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGTAACTTTAACCTG
* * * * * * * *
3445641 CTCCAATGTAATTTCAAGGAG--AAGAGATT-TGTAGCTTTGATCTA
1 CTCCACTGCAACTTCAGGGAGATAAG-GATTGTGTAACTTTAACCTG
** * * *
3445685 CTCTTCTGCAACTTTAAGGAGATAAGAATTG-GTAA-TTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGTAACTTT-AACCTG
* *
3445730 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGGT---TTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGATTGT-GTAACTTTAACCTG
* * * * * * * ** * *
3445774 CTCTAATGTAATTTTAGGGAG--AAGAAATT-TGTAGCTTCGATCTA
1 CTCCACTGCAACTTCAGGGAGATAAG-GATTGTGTAACTTTAACCTG
* * * * * *
3445818 CTCCGCTGCAACTTTAAGGAGATAAGAATTG-GTAACTTCAACCTA
1 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGTAACTTTAACCTG
* * * * * *
3445863 CTCCACTGTAACTTCAGGGAGATAAGGTTTGCAACTTGTAGCTTCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGGATTG-----TGTAACTTTAACCTG
* * * * * * **
3445914 TTCCGCTGCAACTTCAGGGAAATAA-GATTCG-CTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGATT-GTGTAACTTTAACCTG
* * * * * *
3445959 CTCAACTACAACATCAGGGAGATAA-GACT-AGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGTAACTTTAACCTG
*
3446003 CTCCACTGCAACTTTAGGGAGATAAGG
1 CTCCACTGCAACTTCAGGGAGATAAGG
3446030 TTTGCTATGA
Statistics
Matches: 361, Mismatches: 92, Indels: 52
0.71 0.18 0.10
Matches are distributed among these distances:
41 2 0.01
42 9 0.02
43 7 0.02
44 122 0.34
45 136 0.38
46 46 0.13
47 2 0.01
50 3 0.01
51 34 0.09
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (46 bp):
CTCCACTGCAACTTCAGGGAGATAAGGATTGTGTAACTTTAACCTG
Found at i:3445749 original size:133 final size:133
Alignment explanation
Indices: 3445593--3445889 Score: 477
Period size: 133 Copynumber: 2.2 Consensus size: 133
3445583 GTATTTTTAT
* *
3445593 CCTGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAA
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGGATTGTGGCTTCAATCTGCTCCAATGTAATTTCAA
* * ** *
3445658 GGAGAAGAGATTTGTAGCTTTGATCTACTCTTCTGCAACTTTAAGGAGATAAGAATTGGTAATTT
66 GGAGAAGAAATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTGGTAACTT
3445723 CAA
131 CAA
* * * *
3445726 CCTGCTCCACTGCAACTTCAGGGAGATAAGGATTGTGGTTTCAATCTGCTCTAATGTAATTTTAG
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGGATTGTGGCTTCAATCTGCTCCAATGTAATTTCAA
3445791 GGAGAAGAAATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTGGTAACTT
66 GGAGAAGAAATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTGGTAACTT
3445856 CAA
131 CAA
* *
3445859 CCTACTCCACTGTAACTTCAGGGAGATAAGG
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGG
3445890 TTTGCAACTT
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
133 151 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (133 bp):
CCTGCTCCACTGCAACTTCAGGGAGATAAGGATTGTGGCTTCAATCTGCTCCAATGTAATTTCAA
GGAGAAGAAATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTGGTAACTT
CAA
Found at i:3445976 original size:96 final size:96
Alignment explanation
Indices: 3445802--3445984 Score: 224
Period size: 96 Copynumber: 1.9 Consensus size: 96
3445792 GAGAAGAAAT
* * * * *
3445802 TTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTGGTAACTTCAACCTACTCC
1 TTGTAGCTTCAATCTACTCCGCTGCAACTTCAAGGAAATAAGAATTGCTAACTTCAACCTACTCA
** *
3445867 ACTGTAACTTCAGGGAGATAAGGTTTGCAAC
66 ACTACAACATCAGGGAGATAAGGTTTGCAAC
* * * ** *
3445898 TTGTAGCTTCAATCTATTCCGCTGCAACTTCAGGGAAATAAG-ATTCGCTATCTTCAGTCTGCTC
1 TTGTAGCTTCAATCTACTCCGCTGCAACTTCAAGGAAATAAGAATT-GCTAACTTCAACCTACTC
3445962 AACTACAACATCAGGGAGATAAG
65 AACTACAACATCAGGGAGATAAG
3445985 ACTAGTAACT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 3 0.04
96 69 0.96
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (96 bp):
TTGTAGCTTCAATCTACTCCGCTGCAACTTCAAGGAAATAAGAATTGCTAACTTCAACCTACTCA
ACTACAACATCAGGGAGATAAGGTTTGCAAC
Found at i:3446022 original size:44 final size:45
Alignment explanation
Indices: 3445919--3446028 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 45
3445909 ATCTATTCCG
* * * * **
3445919 CTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCAA
1 CTGCAACTTCAGGGAGATAAGACTAGCTAACTTCAACCTGCTCAA
* * *
3445964 CTACAACATCAGGGAGATAAGACTAG-TAACTTCAACCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGACTAGCTAACTTCAACCTGCTCAA
*
3446008 CTGCAACTTTAGGGAGATAAG
1 CTGCAACTTCAGGGAGATAAG
3446029 GTTTGCTATG
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
44 32 0.60
45 21 0.40
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (45 bp):
CTGCAACTTCAGGGAGATAAGACTAGCTAACTTCAACCTGCTCAA
Found at i:3452504 original size:53 final size:53
Alignment explanation
Indices: 3452437--3452547 Score: 159
Period size: 53 Copynumber: 2.1 Consensus size: 53
3452427 AAAATGAGGA
* *
3452437 CACACGGCCGTGTCCTAACCCATGTCCGTGCCCGCGTAACTCTCTGACTTGGT
1 CACACGGCCATGTCCTAACCCATGTCCATGCCCGCGTAACTCTCTGACTTGGT
* * * *
3452490 CACACGGTCATGTCCTAGCCCATGTCCATGCCCGTGTAACTCTTTGACTTGGT
1 CACACGGCCATGTCCTAACCCATGTCCATGCCCGCGTAACTCTCTGACTTGGT
*
3452543 TACAC
1 CACAC
3452548 AACCAAGTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (53 bp):
CACACGGCCATGTCCTAACCCATGTCCATGCCCGCGTAACTCTCTGACTTGGT
Found at i:3453216 original size:9 final size:9
Alignment explanation
Indices: 3453202--3453232 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3453192 GTTAAACGAA
3453202 TCGAGTTAT
1 TCGAGTTAT
*
3453211 TCGAGTTAA
1 TCGAGTTAT
3453220 TCGAGTTAT
1 TCGAGTTAT
3453229 TCGA
1 TCGA
3453233 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:3453302 original size:9 final size:9
Alignment explanation
Indices: 3453285--3453321 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3453275 TGAGTTTTCG
3453285 AATTCGAAT
1 AATTCGAAT
*
3453294 AACTCGAAT
1 AATTCGAAT
3453303 AATTCGAAT
1 AATTCGAAT
3453312 AATTCGAAT
1 AATTCGAAT
3453321 A
1 A
3453322 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3454368 original size:52 final size:52
Alignment explanation
Indices: 3454307--3454412 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
3454297 AAACACAAAG
3454307 TAAGCATTTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACCTTGCCAA
1 TAAGCATTTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACCTTGCCAA
3454359 TAAGCATTTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACCTTGCCAA
1 TAAGCATTTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACCTTGCCAA
3454411 TA
1 TA
3454413 TAATATATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (52 bp):
TAAGCATTTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACCTTGCCAA
Found at i:3454640 original size:29 final size:31
Alignment explanation
Indices: 3454605--3454682 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
3454595 GTTGACAGAT
3454605 CCTTTTTCATAATTTGATAACCGAAG-T-TAC
1 CCTTTTTCATAATTTGATAACCGAAGCTCT-C
* * * *
3454635 CC-TTTTAATAATTCGACAGCCGAAGCTCTC
1 CCTTTTTCATAATTTGATAACCGAAGCTCTC
*
3454665 CCTTTTTCATTATTTGAT
1 CCTTTTTCATAATTTGAT
3454683 GGTCATTACC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
29 19 0.51
30 6 0.16
31 12 0.32
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (31 bp):
CCTTTTTCATAATTTGATAACCGAAGCTCTC
Found at i:3454755 original size:30 final size:30
Alignment explanation
Indices: 3454603--3454812 Score: 153
Period size: 30 Copynumber: 7.0 Consensus size: 30
3454593 TGGTTGACAG
* * **
3454603 ATCCTTTTTCATAATTTGATAACCGAAGTT
1 ATCCCTTTTCATAATTTGATAGCCGAAGCC
* * *
3454633 A-CCCTTTTAATAATTCGACAGCCGAAGCTC
1 ATCCCTTTTCATAATTTGATAGCCGAAGC-C
* * *
3454663 -TCCCTTTTTCATTATTTGATGGTC-ATTA-CC
1 ATCCC-TTTTCATAATTTGATAGCCGA--AGCC
** * * *
3454693 ATCCCTTTTCATTGTTCGATAGTCGTCA-CC
1 ATCCCTTTTCATAATTTGATAGCCG-AAGCC
3454723 ATCCCTTTTCATAATTTGATAGCCGAAGCC
1 ATCCCTTTTCATAATTTGATAGCCGAAGCC
* *
3454753 ATCTCTTTTCATAGA-TTGATAGTCGAAGCC
1 ATCCCTTTTCATA-ATTTGATAGCCGAAGCC
* *
3454783 ATCCCTTTTCATAGTATGATAGCCGAAGCC
1 ATCCCTTTTCATAATTTGATAGCCGAAGCC
3454813 GAAGCCGAAG
Statistics
Matches: 141, Mismatches: 28, Indels: 22
0.74 0.15 0.12
Matches are distributed among these distances:
29 22 0.16
30 99 0.70
31 19 0.13
32 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATAGCCGAAGCC
Found at i:3457130 original size:25 final size:25
Alignment explanation
Indices: 3457091--3457138 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3457081 TTTTAGAGAG
*
3457091 AAAATTCTCTGAAGAAATTATTTCAA
1 AAAATTCTCTAAAGAAATT-TTTCAA
*
3457117 AAAATT-TCTAAAGATATTTTTC
1 AAAATTCTCTAAAGAAATTTTTC
3457139 TTATTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 10 0.50
26 6 0.30
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (25 bp):
AAAATTCTCTAAAGAAATTTTTCAA
Found at i:3463679 original size:14 final size:14
Alignment explanation
Indices: 3463660--3463687 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3463650 AAGGAGGGGG
3463660 AAAATCAGTGTAAA
1 AAAATCAGTGTAAA
3463674 AAAATCAGTGTAAA
1 AAAATCAGTGTAAA
3463688 GAGGACGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAAATCAGTGTAAA
Found at i:3464424 original size:25 final size:25
Alignment explanation
Indices: 3464396--3464461 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
3464386 TCAAGTTGTT
*
3464396 TTATATAATAATTATTTTAAAATC-A
1 TTATATACTAATTATTTT-AAATCAA
* *
3464421 TTATATACTATTTACTTTAAATCAA
1 TTATATACTAATTATTTTAAATCAA
3464446 TT-TATACTAATTATTT
1 TTATATACTAATTATTT
3464462 AAAGCTCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 17 0.49
25 18 0.51
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATATACTAATTATTTTAAATCAA
Found at i:3464472 original size:24 final size:23
Alignment explanation
Indices: 3464399--3464464 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
3464389 AGTTGTTTTA
* *
3464399 TATAATAATTATTTTAAAATCATT
1 TATACTAATTACTTT-AAATCATT
*
3464423 ATATACTATTTACTTTAAATCAATT
1 -TATACTAATTACTTTAAATC-ATT
3464448 TATACTAATTA-TTTAAA
1 TATACTAATTACTTTAAA
3464465 GCTCATTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.17
24 15 0.42
25 15 0.42
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (23 bp):
TATACTAATTACTTTAAATCATT
Found at i:3464530 original size:23 final size:23
Alignment explanation
Indices: 3464455--3464531 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
3464445 ATTTATACTA
3464455 ATTATTTAAAGCTCA-TTTTCATAT
1 ATTATTTAAA--TCATTTTTCATAT
* ** * * *
3464479 AATATTTATTTAATTTTTTA-AC
1 ATTATTTAAATCATTTTTCATAT
3464501 ATCTATTTAAATCATTTTTCATAT
1 AT-TATTTAAATCATTTTTCATAT
3464525 ATTATTT
1 ATTATTT
3464532 TAGATTCTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 7
0.67 0.21 0.12
Matches are distributed among these distances:
22 4 0.11
23 24 0.63
24 10 0.26
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.56
Consensus pattern (23 bp):
ATTATTTAAATCATTTTTCATAT
Found at i:3464914 original size:3 final size:3
Alignment explanation
Indices: 3464906--3464961 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
3464896 ATGATGTGGA
3464906 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3464954 ATT ATT AT
1 ATT ATT AT
3464962 GTGTATTGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3475240 original size:27 final size:26
Alignment explanation
Indices: 3475210--3475581 Score: 203
Period size: 27 Copynumber: 13.8 Consensus size: 26
3475200 ACCTTCGAAA
*
3475210 GGTAAAATGAATGAAATACCCTATATG
1 GGTAAAATGACTGAAATACCCTATA-G
* *
3475237 GGTAAAATAACTGAAATGCCCCTATAG
1 GGTAAAATGACTGAAAT-ACCCTATAG
* * **
3475264 GATAAAATGACCGAAATACCCCCGTAG
1 GGTAAAATGACTGAAATA-CCCTATAG
* *
3475291 GGTAGAAT-ACTGAAATACCCTTATAT
1 GGTAAAATGACTGAAATACCC-TATAG
* *
3475317 GGTAAAATGA-TCGTAATACCCCTGTAG
1 GGTAAAATGACT-GAAATA-CCCTATAG
* * * *
3475344 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACTGAAAT-ACCCTATAG
* *
3475371 GGTAAAATGACTGTAATGCCCCTATAG
1 GGTAAAATGACTGAAAT-ACCCTATAG
* *
3475398 GGTAAAATGAC-CATAATACCCCAGTAG
1 GGTAAAATGACTGA-AATACCCTA-TAG
* * * * *
3475425 GGTAAAATAACCGTAATGCCCCTGTAG
1 GGTAAAATGACTGAAAT-ACCCTATAG
* * * *
3475452 GGTAAAATGATTGTAATACACCTGTAA
1 GGTAAAATGACTGAAATAC-CCTATAG
* * * *
3475479 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACTGAAAT-ACCCTATAG
* * *
3475506 GATAAAAT-AATGGTAATACCCTTATAG
1 GGTAAAATGACT-GAAATACCC-TATAG
* * * *
3475533 GATAAAATGACCGTAATACCCTTGTAG
1 GGTAAAATGACTGAAATACCC-TATAG
* *
3475560 GGTAAAATGACCGTAATACCCT
1 GGTAAAATGACTGAAATACCCT
3475582 CGAGGTCAAA
Statistics
Matches: 277, Mismatches: 51, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
25 3 0.01
26 28 0.10
27 231 0.83
28 15 0.05
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (26 bp):
GGTAAAATGACTGAAATACCCTATAG
Found at i:3475419 original size:81 final size:81
Alignment explanation
Indices: 3475210--3475580 Score: 395
Period size: 81 Copynumber: 4.6 Consensus size: 81
3475200 ACCTTCGAAA
* * * * * * * *
3475210 GGTAAAATGAATGAAATA-CCCTATATGGGTAAAATAACTGAAATGCCCCTATAGGATAAAATGA
1 GGTAAAATGACTGTAATACCCCTATA-GGGTAAAATGACCGTAATACCCCTGTAGGATAAAATAA
* *
3475274 CCGAAATACCCCCGTAG
65 CCGTAATACCCCTGTAG
* * * * * * *
3475291 GGTAGAAT-ACTGAAATACCCTTATATGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGAC
1 GGTAAAATGACTGTAATACCCCTATAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATAAC
*
3475355 CGTAATGCCCCTGTAG
66 CGTAATACCCCTGTAG
* * * *
3475371 GGTAAAATGACTGTAATGCCCCTATAGGGTAAAATGACCATAATACCCCAGTAGGGTAAAATAAC
1 GGTAAAATGACTGTAATACCCCTATAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATAAC
*
3475436 CGTAATGCCCCTGTAG
66 CGTAATACCCCTGTAG
* * * * * *
3475452 GGTAAAATGATTGTAATACACCTGTAAGGTAAAATGACCGTAATGCCCCTGTAGGATAAAATAAT
1 GGTAAAATGACTGTAATACCCCTATAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATAAC
* * *
3475517 GGTAATACCCTTATAG
66 CGTAATACCCCTGTAG
* * * *
3475533 GATAAAATGACCGTAATACCCTTGTAGGGTAAAATGACCGTAATACCC
1 GGTAAAATGACTGTAATACCCCTATAGGGTAAAATGACCGTAATACCC
3475581 TCGAGGTCAA
Statistics
Matches: 244, Mismatches: 44, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
80 59 0.24
81 185 0.76
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (81 bp):
GGTAAAATGACTGTAATACCCCTATAGGGTAAAATGACCGTAATACCCCTGTAGGATAAAATAAC
CGTAATACCCCTGTAG
Found at i:3475581 original size:54 final size:53
Alignment explanation
Indices: 3475209--3475581 Score: 340
Period size: 54 Copynumber: 6.9 Consensus size: 53
3475199 TACCTTCGAA
** * * * * * * *
3475209 AGGTAAAATGAATGAAATA-CCCTATATGGGTAAAATAACTGAAATGCCCCTAT
1 AGGTAAAATGACCGTAATACCCCTGTA-GGGTAAAATGACCGTAATACCCTTAT
* * * * *
3475262 AGGATAAAATGACCGAAATACCCCCGTAGGGTAGAAT-ACTGAAATACCCTTAT
1 AGG-TAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTAT
* * * *
3475315 ATGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTGT
1 A-GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTAT
* * * * *
3475369 AGGGTAAAATGACTGTAATGCCCCTATAGGGTAAAATGACCATAATACCC-CAGT
1 A-GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTA-T
* * **
3475423 AGGGTAAAATAACCGTAATGCCCCTGTAGGGTAAAATGATTGTAATACACCTGTA-
1 A-GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATAC-CCT-TAT
* * * **
3475478 AGGTAAAATGACCGTAATGCCCCTGTAGGATAAAATAATGGTAATACCCTTAT
1 AGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTAT
*
3475531 AGGATAAAATGACCGTAATACCCTTGTAGGGTAAAATGACCGTAATACCCT
1 AGG-TAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCT
3475582 CGAGGTCAAA
Statistics
Matches: 268, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.01
53 53 0.20
54 204 0.76
55 8 0.03
57 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (53 bp):
AGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTAT
Found at i:3475824 original size:26 final size:25
Alignment explanation
Indices: 3475787--3475839 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
3475777 TTGGCCACAT
*
3475787 ATACTATACTGGCAGCTTTGTTGCG
1 ATACTATACTGGCAGCTTTGCTGCG
*
3475812 ATACTACTGCTGGCAGCTTTGCTGCG
1 ATACTA-TACTGGCAGCTTTGCTGCG
3475838 AT
1 AT
3475840 GCCACTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.34
Consensus pattern (25 bp):
ATACTATACTGGCAGCTTTGCTGCG
Found at i:3475846 original size:26 final size:26
Alignment explanation
Indices: 3475795--3475846 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3475785 ATATACTATA
* *
3475795 CTGGCAGCTTTGTTGCGATACTACTG
1 CTGGCAGCTTTGCTGCGATACCACTG
*
3475821 CTGGCAGCTTTGCTGCGATGCCACTG
1 CTGGCAGCTTTGCTGCGATACCACTG
3475847 ATGGATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.13, C:0.27, G:0.29, T:0.31
Consensus pattern (26 bp):
CTGGCAGCTTTGCTGCGATACCACTG
Found at i:3475888 original size:32 final size:32
Alignment explanation
Indices: 3475843--3476045 Score: 280
Period size: 32 Copynumber: 6.3 Consensus size: 32
3475833 CTGCGATGCC
* * *
3475843 ACTGATGGATTTGTGCCAATCATATTACCATT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
*
3475875 ACTGATGGCTTTGTGCCAATCATATTACCGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
* * *
3475907 ATTGATGGCTTTGTTCCGATCATATTACTGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
* *
3475939 ACTGATGGCTTTATGCCGATCATATTATCGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
* * *
3475971 ATTGATGGCTTTGTACCGATCATATTACCATT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
* *
3476003 ACTAATGGCTTTGTACCGATCATATTACCGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
3476035 ACTGATGGCTT
1 ACTGATGGCTT
3476046 GTAGCCATTC
Statistics
Matches: 151, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 151 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (32 bp):
ACTGATGGCTTTGTGCCGATCATATTACCGTT
Found at i:3476072 original size:22 final size:21
Alignment explanation
Indices: 3476042--3476098 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
3476032 GTTACTGATG
3476042 GCTTGTAGCCATTCTGTTTATA
1 GCTT-TAGCCATTCTGTTTATA
* * *
3476064 GCTTATAGCTATCCTGTTTATG
1 GCTT-TAGCCATTCTGTTTATA
3476086 GCTGTTAGCCATT
1 GCT-TTAGCCATT
3476099 TTGACTACTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (21 bp):
GCTTTAGCCATTCTGTTTATA
Found at i:3480463 original size:25 final size:25
Alignment explanation
Indices: 3480435--3480491 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
3480425 TCTCAACATT
*
3480435 TATAATTTTTTTGTCAATTTAAAAGTA
1 TATAA-TTCTTTG-CAATTTAAAAGTA
*
3480462 TATAATTCTTTGCCATTTAAAAGTA
1 TATAATTCTTTGCAATTTAAAAGTA
*
3480487 CATAA
1 TATAA
3480492 AATCTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 16 0.59
26 6 0.22
27 5 0.19
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (25 bp):
TATAATTCTTTGCAATTTAAAAGTA
Found at i:3480505 original size:26 final size:25
Alignment explanation
Indices: 3480450--3480505 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
3480440 TTTTTTTGTC
* * *
3480450 AATTTAAAAGTATATAATTCTTTGC
1 AATTTAAAAGTACATAAATCTTTGA
* *
3480475 CATTTAAAAGTACATAAAATCTTTTA
1 AATTTAAAAGTACAT-AAATCTTTGA
3480501 AATTT
1 AATTT
3480506 TTTTTATGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (25 bp):
AATTTAAAAGTACATAAATCTTTGA
Found at i:3480746 original size:23 final size:24
Alignment explanation
Indices: 3480705--3480750 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3480695 GGTTGACTTG
3480705 CAAACCAATACAAACTAGTTGAAC
1 CAAACCAATACAAACTAGTTGAAC
* *
3480729 CAAACTAA-ACAAATTAGTTGAA
1 CAAACCAATACAAACTAGTTGAA
3480751 TCAATTTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.52, C:0.20, G:0.09, T:0.20
Consensus pattern (24 bp):
CAAACCAATACAAACTAGTTGAAC
Found at i:3481083 original size:26 final size:27
Alignment explanation
Indices: 3481025--3481088 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
3481015 TTCAATTTTC
*
3481025 AATTTT-ATATAAAAATTATAAATTTAA
1 AATTTTAAAATAAAAA-TATAAATTTAA
*
3481052 AATTTTAAAATAAAAA-ATAAATTTTA
1 AATTTTAAAATAAAAATATAAATTTAA
*
3481078 ATTTTTAAAAT
1 AATTTTAAAAT
3481089 TATGTACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.58
27 6 0.18
28 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTTTAAAATAAAAATATAAATTTAA
Found at i:3486786 original size:6 final size:6
Alignment explanation
Indices: 3486762--3486805 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3486752 TGCCTTCTTC
* * *
3486762 TCCCCTT TCCCCT TTCCCT TCCCCT TCCCTT TTCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
3486806 GGATTGCAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TCCCCT
Found at i:3486789 original size:18 final size:18
Alignment explanation
Indices: 3486762--3486805 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
3486752 TGCCTTCTTC
3486762 TCCCCTTTCCCCTTTCCCT
1 TCCCC-TTCCCCTTTCCCT
*
3486781 TCCCCTTCCCTTTTCCCT
1 TCCCCTTCCCCTTTCCCT
3486799 TCCCCTT
1 TCCCCTT
3486806 GGATTGCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCCCTTCCCCTTTCCCT
Found at i:3486882 original size:25 final size:25
Alignment explanation
Indices: 3486848--3486897 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3486838 CAGGTAAGGC
3486848 TCCTTCTTCTTCTTCCGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* *
3486873 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
3486898 CTTCTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.04, C:0.32, G:0.04, T:0.60
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:3487101 original size:11 final size:11
Alignment explanation
Indices: 3487085--3487110 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3487075 TTGCTGGATG
3487085 ATATTTTGGTT
1 ATATTTTGGTT
3487096 ATATTTTGGTT
1 ATATTTTGGTT
3487107 ATAT
1 ATAT
3487111 ACAGATGGTT
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:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:3489791 original size:33 final size:33
Alignment explanation
Indices: 3489754--3489820 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
3489744 ATGAAGAAGT
*
3489754 AAAATAAAATCGGTATAATCTACAAATATATGA
1 AAAATAAAATCGGTATAATCTACAAATAGATGA
3489787 AAAATAAAATCGGTATAATCTACAAATAGATGA
1 AAAATAAAATCGGTATAATCTACAAATAGATGA
3489820 A
1 A
3489821 CATTTGGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAATAAAATCGGTATAATCTACAAATAGATGA
Found at i:3489955 original size:22 final size:20
Alignment explanation
Indices: 3489912--3489950 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3489902 TAATTTAAAA
*
3489912 TATAAAAATTTATTACTATG
1 TATAAAAATTTATTAATATG
*
3489932 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
3489951 ATGTAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:3490012 original size:32 final size:32
Alignment explanation
Indices: 3489971--3490057 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
3489961 AACTTTTCCG
** *
3489971 GAAAATATTTTCAAGAAATCTGTCAAACAGCA
1 GAAAATATTTTCAAGAAATCAATCAAACACCA
*
3490003 GAAAATATTTTACACAG-ATTCAATCAAACACCA
1 GAAAATATTTT-CA-AGAAATCAATCAAACACCA
*
3490036 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTCAAG-AAATCA
3490058 TTTTACAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.04
32 12 0.27
33 29 0.64
34 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAAGAAATCAATCAAACACCA
Found at i:3490055 original size:14 final size:15
Alignment explanation
Indices: 3490033--3490109 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3490023 CAATCAAACA
3490033 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
3490047 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
3490062 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
3490082 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
3490096 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
3490110 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:3490074 original size:20 final size:20
Alignment explanation
Indices: 3490049--3490088 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3490039 AATATTTTCC
*
3490049 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3490069 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3490089 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3490094 original size:34 final size:35
Alignment explanation
Indices: 3490037--3490103 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3490027 CAAACACCAG
*
3490037 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3490072 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3490104 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3490110 original size:14 final size:14
Alignment explanation
Indices: 3490072--3490111 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3490062 ACAGAAAAGT
*
3490072 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
3490086 AAATCATTTTACGG
1 AAAACATTTTACAG
3490100 AAAACATTTTAC
1 AAAACATTTTAC
3490112 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:3496604 original size:18 final size:18
Alignment explanation
Indices: 3496581--3496625 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3496571 ATCCCAATGA
3496581 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
3496599 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
3496617 TCACCACCA
1 TCGCCACCA
3496626 ACCATGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:3497408 original size:3 final size:3
Alignment explanation
Indices: 3497400--3497434 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3497390 ATAACATCTT
3497400 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3497435 TAATAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3497535 original size:12 final size:10
Alignment explanation
Indices: 3497498--3497530 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
3497488 AGTAAAACAA
3497498 AAAATATTAC
1 AAAATATTAC
3497508 AAAATA-TAC
1 AAAATATTAC
3497517 AAAATATTAC
1 AAAATATTAC
3497527 AAAA
1 AAAA
3497531 AATATCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATATTAC
Found at i:3497576 original size:10 final size:11
Alignment explanation
Indices: 3497535--3497575 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
3497525 ACAAAAAATA
3497535 TCTTCTTTTTC
1 TCTTCTTTTTC
*
3497546 TCCTCTTTTTC
1 TCTTCTTTTTC
3497557 TC-TCTTTTTC
1 TCTTCTTTTTC
3497567 TCTTCTTTT
1 TCTTCTTTT
3497576 CAGCAACAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TCTTCTTTTTC
Found at i:3497689 original size:27 final size:27
Alignment explanation
Indices: 3497658--3497722 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
3497648 AATACGAGTA
3497658 GTGCCGCCAATGG-TATTGGCACCATTG
1 GTGCCGCCAATGGCT-TTGGCACCATTG
*
3497685 GTGCCGCCAATGGCTTTGGCACCTTTG
1 GTGCCGCCAATGGCTTTGGCACCATTG
3497712 GTGCCGCCAAT
1 GTGCCGCCAAT
3497723 CCCATTGGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
GTGCCGCCAATGGCTTTGGCACCATTG
Found at i:3497730 original size:27 final size:27
Alignment explanation
Indices: 3497658--3497731 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
3497648 AATACGAGTA
*
3497658 GTGCCGCCAATGGTATTGGCACCATTG
1 GTGCCGCCAATGGCATTGGCACCATTG
* *
3497685 GTGCCGCCAATGGCTTTGGCACCTTTG
1 GTGCCGCCAATGGCATTGGCACCATTG
**
3497712 GTGCCGCCAATCCCATTGGC
1 GTGCCGCCAATGGCATTGGC
3497732 GTGACCAAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (27 bp):
GTGCCGCCAATGGCATTGGCACCATTG
Found at i:3497811 original size:22 final size:22
Alignment explanation
Indices: 3497786--3497829 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3497776 TTTTTTTGAT
**
3497786 TATATTTTGGTAAATAAAAAAA
1 TATATTTTAATAAATAAAAAAA
3497808 TATATTTTAATAAATAAAAAAA
1 TATATTTTAATAAATAAAAAAA
3497830 GTTATAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
TATATTTTAATAAATAAAAAAA
Found at i:3499455 original size:42 final size:43
Alignment explanation
Indices: 3499403--3499488 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
3499393 TTTCATAAAA
3499403 TTTAAAATTTTAACTGTTTAAATATTAAGGATAA-ATAATATT
1 TTTAAAATTTTAACTGTTTAAATATTAAGGATAATATAATATT
* * * * * *
3499445 TTTAATATTTTGATTGTTTTAATTTTAAGGATAATATATTATT
1 TTTAAAATTTTAACTGTTTAAATATTAAGGATAATATAATATT
3499488 T
1 T
3499489 ATCCTTTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 29 0.78
43 8 0.22
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.52
Consensus pattern (43 bp):
TTTAAAATTTTAACTGTTTAAATATTAAGGATAATATAATATT
Found at i:3500097 original size:14 final size:14
Alignment explanation
Indices: 3500078--3500110 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3500068 CCGAATCCCC
*
3500078 TAAACCTTAAGCCT
1 TAAACCTTAAGACT
3500092 TAAACCTTAAGACT
1 TAAACCTTAAGACT
3500106 TAAAC
1 TAAAC
3500111 TTGAATCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (14 bp):
TAAACCTTAAGACT
Found at i:3501074 original size:22 final size:22
Alignment explanation
Indices: 3501048--3501107 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
3501038 TAAAACATTG
*
3501048 TGAAAATTTATAAATTATTTTT
1 TGAAAATTTATAAATTATGTTT
*
3501070 TG-AAA-TTATAAAAATATGTTT
1 TGAAAATTTAT-AAATTATGTTT
3501091 T-AAAATTT-T-AATTATGT
1 TGAAAATTTATAAATTATGT
3501108 AAAACAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 7 0.22
20 4 0.12
21 17 0.53
22 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TGAAAATTTATAAATTATGTTT
Found at i:3504135 original size:96 final size:96
Alignment explanation
Indices: 3503958--3504152 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 96
3503948 CCATATTTTC
** * ** *
3503958 TGGTACACAAACTCCATGGTGATCACTATCCACATGATCACCGACTCTCCCCGCTAGTGGGATCA
1 TGGTACACAAACTCCATGGTGATCACTATCCACACAATCACCAACTCTCCCAACTAGTGAGATCA
*
3504023 ACGGATCATGGCTTAATGGTAGAATAGGATA
66 ACGGATAATGGCTTAATGGTAGAATAGGATA
* * *
3504054 TGGTACACAAGCTCCATGGTGATCACTA-CCAGCACAATCACCAACTC-CCACAATTGGTGAGAT
1 TGGTACACAAACTCCATGGTGATCACTATCCA-CACAATCACCAACTCTCC-CAACTAGTGAGAT
* * *
3504117 CAAGGGATAATGGTTTAATGGTAGAATATGATA
64 CAACGGATAATGGCTTAATGGTAGAATAGGATA
3504150 TGG
1 TGG
3504153 GAGCTGCATC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
95 5 0.06
96 79 0.94
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (96 bp):
TGGTACACAAACTCCATGGTGATCACTATCCACACAATCACCAACTCTCCCAACTAGTGAGATCA
ACGGATAATGGCTTAATGGTAGAATAGGATA
Found at i:3505189 original size:42 final size:42
Alignment explanation
Indices: 3505143--3505227 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
3505133 AATATCATTT
* * *
3505143 ATCCTTTCA-TAAAATTTTAAAATTTTAACTGTTTTAATTTTA
1 ATCC-TTCACTAAAATTTTAAAACTTTAACTATTTTAATATTA
3505185 ATCCTTCACTAAAATTTTAAAACTTTAACTATTTTAATATTA
1 ATCCTTCACTAAAATTTTAAAACTTTAACTATTTTAATATTA
3505227 A
1 A
3505228 AGATAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (42 bp):
ATCCTTCACTAAAATTTTAAAACTTTAACTATTTTAATATTA
Found at i:3505408 original size:32 final size:32
Alignment explanation
Indices: 3505372--3505434 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
3505362 GGATAAAATA
*
3505372 TTATTTATCATTTCATCAAATTTTAAAAATTG
1 TTATTTATCATTTCATAAAATTTTAAAAATTG
* * *
3505404 TTATTTCTCTTTTCATAAAATTTTCAAAATT
1 TTATTTATCATTTCATAAAATTTTAAAAATT
3505435 TAACTGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (32 bp):
TTATTTATCATTTCATAAAATTTTAAAAATTG
Found at i:3505812 original size:14 final size:14
Alignment explanation
Indices: 3505795--3505845 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3505785 CTAAGCTCTA
3505795 AACTCTAAATCTTG
1 AACTCTAAATCTTG
*
3505809 AACTTTAAAT-TATG
1 AACTCTAAATCT-TG
*
3505823 AACCCTAAATCTT-
1 AACTCTAAATCTTG
3505836 AAGCTCTAAA
1 AA-CTCTAAA
3505846 CCTAAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 26 0.87
15 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (14 bp):
AACTCTAAATCTTG
Found at i:3505872 original size:21 final size:21
Alignment explanation
Indices: 3505846--3505888 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3505836 AAGCTCTAAA
3505846 CCTAAACCCTAAACCCTACAC
1 CCTAAACCCTAAACCCTACAC
*
3505867 CCTAAACCCTACACCCTACAC
1 CCTAAACCCTAAACCCTACAC
3505888 C
1 C
3505889 TTACACCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.51, G:0.00, T:0.14
Consensus pattern (21 bp):
CCTAAACCCTAAACCCTACAC
Found at i:3505875 original size:7 final size:7
Alignment explanation
Indices: 3505841--3505977 Score: 66
Period size: 7 Copynumber: 20.0 Consensus size: 7
3505831 ATCTTAAGCT
3505841 CTAAA-C
1 CTAAACC
3505847 CTAAACC
1 CTAAACC
3505854 CTAAACC
1 CTAAACC
*
3505861 CTACACC
1 CTAAACC
3505868 CTAAACC
1 CTAAACC
*
3505875 CTACACC
1 CTAAACC
*
3505882 CTACACC
1 CTAAACC
* *
3505889 TTACACC
1 CTAAACC
* *
3505896 TTCAA-C
1 CTAAACC
* *
3505902 CTCAACT
1 CTAAACC
* *
3505909 CGAACCTC
1 CTAAAC-C
3505917 CTAAACC
1 CTAAACC
* *
3505924 TTAAACA
1 CTAAACC
3505931 CTAAA-C
1 CTAAACC
*
3505937 CTACACC
1 CTAAACC
*
3505944 CTAAGCC
1 CTAAACC
* *
3505951 CTCAA-G
1 CTAAACC
*
3505957 CTTAACC
1 CTAAACC
3505964 CTAAACC
1 CTAAACC
*
3505971 TTAAACC
1 CTAAACC
3505978 ATATTAATCT
Statistics
Matches: 98, Mismatches: 28, Indels: 9
0.73 0.21 0.07
Matches are distributed among these distances:
6 18 0.18
7 76 0.78
8 4 0.04
ACGTcount: A:0.36, C:0.42, G:0.02, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:3523744 original size:11 final size:12
Alignment explanation
Indices: 3523713--3523742 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3523703 TCATTCTTTT
3523713 AAAAAAAA-TTC
1 AAAAAAAACTTC
3523724 AAAAAAAACTTC
1 AAAAAAAACTTC
3523736 AAAAAAA
1 AAAAAAA
3523743 CTCTCCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAAACTTC
Found at i:3524419 original size:15 final size:15
Alignment explanation
Indices: 3524399--3524429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3524389 AAGGTTTCTA
3524399 ACTGTAATTTGGGCC
1 ACTGTAATTTGGGCC
*
3524414 ACTGTAGTTTGGGCC
1 ACTGTAATTTGGGCC
3524429 A
1 A
3524430 TTGTTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (15 bp):
ACTGTAATTTGGGCC
Found at i:3524876 original size:44 final size:44
Alignment explanation
Indices: 3524822--3524934 Score: 156
Period size: 44 Copynumber: 2.6 Consensus size: 44
3524812 GATCTACTCT
* * *
3524822 ACTGCAACTTCAGAGAGATAAGATCTGTA-ATTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGAT-TATAGACTTTAATCCGCTCC
* *
3524866 ACTGCAACTTCAGGGAGATAGGATTATAGACTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTATAGACTTTAATCCGCTCC
*
3524910 ACTGCAAATTCAGGGAGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
3524935 TATATCTTCG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 3 0.05
44 58 0.95
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTATAGACTTTAATCCGCTCC
Found at i:3525088 original size:88 final size:88
Alignment explanation
Indices: 3524939--3525527 Score: 718
Period size: 88 Copynumber: 6.7 Consensus size: 88
3524929 AAGATTTATA
* * * * * * *
3524939 TCTTCGATCTACTTCATGCCGATACATTAAGACAAAATCTTATACCCTTGATCTACTTCATGCCA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
*
3525004 ATACATGAAGACAAGATCTATTT
66 ATACATGAAGACAAGATCTGTTT
* *
3525027 TCTTCGATCTACTTTACACCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
*
3525092 ATACATGAAGACAAGATCCGTTT
66 ATACATGAAGACAAGATCTGTTT
*
3525115 TCTTCTATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
**
3525180 ATACATGAAGACAAGATCCCTTT
66 ATACATGAAGACAAGATCTGTTT
* *
3525203 TCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTTCTACCTTTGATCTACTTCATGTCG
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
3525268 ATACATGAAGACAAGAT-TCGTTT
66 ATACATGAAGACAAGATCT-GTTT
* * *
3525291 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTACCTTTGATCTACTTCACGCCA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
*
3525356 ATACATGAAGACAAGATCTGCTT
66 ATACATGAAGACAAGATCTGTTT
* * * * * * ** * *
3525379 TCTTTGATCTACTTCGCCCTCAGT--ATGGAAAGACAAGATCTGCTATCTTCAATCCACTTCGCT
1 TCTTCGATCTACTTCACGC-CAATACAT-G-AAGACAAGATCTTCTACCTTTGATCTACTTC-AT
* * * * * * *
3525442 ACCAATATA-GAAAGATAGGATTTGCTT
62 GCCGATACATG-AAGACAAGATCTGTTT
* * ** *
3525469 TCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTTAATCTACTTC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTC
3525528 GCCACCAATA
Statistics
Matches: 443, Mismatches: 49, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
87 2 0.00
88 340 0.77
89 62 0.14
90 37 0.08
91 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (88 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
ATACATGAAGACAAGATCTGTTT
Found at i:3525501 original size:44 final size:44
Alignment explanation
Indices: 3524939--3525766 Score: 612
Period size: 44 Copynumber: 18.9 Consensus size: 44
3524929 AAGATTTATA
* * * * ** *
3524939 TCTTCGATCTACTTCATGCCGATACATTAAGACAAAATCTTATAC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT-T
* * **
3524984 CCTT-GATCTACTTCATGCCAATACATGAAGACAAGATCTATTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *
3525027 TCTTCGATCTACTTTACACCAATACATGAAGACAAGATCTTCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * * *
3525071 CCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCCGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *
3525115 TCTTCTATCTACTTCACGCCAATACATGAAGACAAGATCTTCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *
3525159 CCTTTGATCTACTTCATGCCGATACATGAAGACAAGATC-CCTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-TT
* * *
3525203 TCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTTCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * * *
3525247 CCTTTGATCTACTTCATGTCGATACATGAAGACAAGAT-TCGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT-GCTT
*
3525291 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
3525335 CCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *
3525379 TCTTTGATCTACTTCGCCCTCAGT--ATGGAAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGC-CAATACAT-G-AAGACAAGATCTGCTT
* * * * * * * *
3525424 TCTTCAATCCACTTCGCTACCAATATA-GAAAGATAGGATTTGCTT
1 TCTTCGATCTACTTCAC-GCCAATACATG-AAGACAAGATCTGCTT
*
3525469 TCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
** * * ***
3525513 TCTTTAATCTACTTCGCCACCAATATGGGAAGACAAGA--T-C--
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
* * * * * * * *
3525553 -C-T-GAATCCACTTC-CTACCAATATAAGAAAATAGGATCTGCTA
1 TCTTCG-ATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTT
3525595 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *** * * *
3525639 TCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAAATCTGC-A
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
* * * * * * * *
3525683 CCTTCGATCCACTTC-CTACCAATATAGGAAAAC-AGAACTTGCTA
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATC-TGCTT
*
3525727 TCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
3525767 ACTATTTTCA
Statistics
Matches: 618, Mismatches: 135, Indels: 61
0.76 0.17 0.07
Matches are distributed among these distances:
36 1 0.00
37 15 0.02
38 9 0.01
39 2 0.00
40 1 0.00
42 5 0.01
43 24 0.04
44 448 0.72
45 111 0.18
46 1 0.00
47 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:3525634 original size:126 final size:126
Alignment explanation
Indices: 3525326--3525766 Score: 548
Period size: 126 Copynumber: 3.4 Consensus size: 126
3525316 ATGAAGACAA
* *
3525326 GATCTGCTACCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
1 GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
* *
3525391 TTCGCC-CTCAGTATGGAAAGACAAGATCTGCTATCTTCAATCCACTTCGCTACCAATAT-AGAA
66 TTCGCCAC-CAGTATGGGAAGACAAGA--T-C---C-TGAATCCACTTC-CTACCAATATAAGAA
3525454 AGATAG
122 A-ATAG
* * * *
3525460 GATTTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTTAATCTAC
1 GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
*
3525525 TTCGCCACCAATATGGGAAGACAAGATCCTGAATCCACTTCCTACCAATATAAGAAAATAG
66 TTCGCCACCAGTATGGGAAGACAAGATCCTGAATCCACTTCCTACCAATATAAGAAAATAG
*
3525586 GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
* * *
3525651 TTCGCCACCAGTATGGGAAGATAAAAT-CTGCACCTTCGATCCACTTCCTACCAATATAGGAAAA
66 TTCGCCACCAGTATGGGAAGACAAGATCCTG-A------ATCCACTTCCTACCAATATAAGAAAA
*
3525715 CA-
124 TAG
* *
3525717 GAACTTGCTATCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCT
1 GATC-TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
3525767 ACTATTTTCA
Statistics
Matches: 276, Mismatches: 21, Indels: 22
0.87 0.07 0.07
Matches are distributed among these distances:
125 3 0.01
126 99 0.36
127 16 0.06
128 1 0.00
131 4 0.01
132 71 0.26
134 81 0.29
135 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (126 bp):
GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
TTCGCCACCAGTATGGGAAGACAAGATCCTGAATCCACTTCCTACCAATATAAGAAAATAG
Found at i:3526718 original size:26 final size:26
Alignment explanation
Indices: 3526683--3526732 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3526673 GTGTCTTGAA
3526683 AAGAAAAAAGATATT-CAAGAACAATG
1 AAGAAAAAAG-TATTACAAGAACAATG
*
3526709 AAGAATAAAGTATTACAAGAACAA
1 AAGAAAAAAGTATTACAAGAACAA
3526733 ACAAAAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.62, C:0.08, G:0.14, T:0.16
Consensus pattern (26 bp):
AAGAAAAAAGTATTACAAGAACAATG
Found at i:3538939 original size:15 final size:15
Alignment explanation
Indices: 3538919--3538949 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3538909 AGGGTTTCTG
3538919 ACTGTAATTTGGGCC
1 ACTGTAATTTGGGCC
*
3538934 ACTGTAGTTTGGGCC
1 ACTGTAATTTGGGCC
3538949 A
1 A
3538950 TTGTTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (15 bp):
ACTGTAATTTGGGCC
Found at i:3544383 original size:31 final size:31
Alignment explanation
Indices: 3544348--3544410 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3544338 TCGTAGAGGT
3544348 AGACATATATCTAGTAAAGGAGAGATATTCA
1 AGACATATATCTAGTAAAGGAGAGATATTCA
3544379 AGACATATATCTAGTAAAGGAGAGATATTCA
1 AGACATATATCTAGTAAAGGAGAGATATTCA
3544410 A
1 A
3544411 TCATTCGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (31 bp):
AGACATATATCTAGTAAAGGAGAGATATTCA
Found at i:3548379 original size:20 final size:20
Alignment explanation
Indices: 3548354--3548423 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
3548344 CGTTTTAAGG
3548354 TTTAGGGTTAGGGTTCATGA
1 TTTAGGGTTAGGGTTCATGA
* * *
3548374 TTTAGGTTTGGAGGTT-ATGG
1 TTTAGGGTTAG-GGTTCATGA
* *
3548394 TTTAGGGGTTAGTGTTCAAGA
1 TTTA-GGGTTAGGGTTCATGA
*
3548415 GTTAGGGTT
1 TTTAGGGTT
3548424 TAGAATTTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.19, C:0.03, G:0.37, T:0.41
Consensus pattern (20 bp):
TTTAGGGTTAGGGTTCATGA
Found at i:3548437 original size:41 final size:39
Alignment explanation
Indices: 3548351--3548437 Score: 93
Period size: 41 Copynumber: 2.2 Consensus size: 39
3548341 TTGCGTTTTA
* * * *
3548351 AGGTTTAGGGTTAGGGTTCATGATTTAGGTTTGGAGGTT
1 AGGTTTAGGGTTAGGGTTCAAGAGTTAGGTTTAGAAGTT
* *
3548390 ATGGTTTAGGGGTTAGTGTTCAAGAGTTAGGGTTTAGAATTT
1 A-GGTTTA-GGGTTAGGGTTCAAGAGTTA-GGTTTAGAAGTT
3548432 AGGTTT
1 AGGTTT
3548438 CATGTTTAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 1 0.03
40 6 0.15
41 22 0.56
42 10 0.26
ACGTcount: A:0.21, C:0.02, G:0.36, T:0.41
Consensus pattern (39 bp):
AGGTTTAGGGTTAGGGTTCAAGAGTTAGGTTTAGAAGTT
Found at i:3548508 original size:7 final size:7
Alignment explanation
Indices: 3548498--3548523 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3548488 AGGTTTAGGG
3548498 TTTAGAA
1 TTTAGAA
3548505 TTTAGAA
1 TTTAGAA
3548512 TTTAGAA
1 TTTAGAA
3548519 TTTAG
1 TTTAG
3548524 GTGTCAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (7 bp):
TTTAGAA
Found at i:3548508 original size:14 final size:14
Alignment explanation
Indices: 3548491--3548524 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3548481 TGGTTCAAGG
*
3548491 TTTAGGGTTTAGAA
1 TTTAGGATTTAGAA
*
3548505 TTTAGAATTTAGAA
1 TTTAGGATTTAGAA
3548519 TTTAGG
1 TTTAGG
3548525 TGTCAATGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TTTAGGATTTAGAA
Found at i:3548564 original size:13 final size:14
Alignment explanation
Indices: 3548519--3548565 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3548509 GAATTTAGAA
3548519 TTTAGGTGTCAATG
1 TTTAGGTGTCAATG
* *
3548533 TTTTGAGT-TCAAGG
1 TTTAG-GTGTCAATG
3548547 TTTAGGTGTC-ATG
1 TTTAGGTGTCAATG
3548560 TTTAGG
1 TTTAGG
3548566 GTTCAGGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 10 0.37
14 15 0.56
15 2 0.07
ACGTcount: A:0.19, C:0.06, G:0.30, T:0.45
Consensus pattern (14 bp):
TTTAGGTGTCAATG
Found at i:3548569 original size:27 final size:28
Alignment explanation
Indices: 3548519--3548576 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
3548509 GAATTTAGAA
*
3548519 TTTAGGTGTCAATGTTTTGAGTTCAAGG
1 TTTAGGTGTCAATGTTTAGAGTTCAAGG
* *
3548547 TTTAGGTGTC-ATGTTTAGGGTTCAGGG
1 TTTAGGTGTCAATGTTTAGAGTTCAAGG
3548574 TTT
1 TTT
3548577 GCATTTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.17, C:0.07, G:0.31, T:0.45
Consensus pattern (28 bp):
TTTAGGTGTCAATGTTTAGAGTTCAAGG
Found at i:3548631 original size:7 final size:7
Alignment explanation
Indices: 3548594--3548674 Score: 51
Period size: 7 Copynumber: 11.1 Consensus size: 7
3548584 GTGTTTCGAG
*
3548594 TTTAGGG
1 TTTAGGT
*
3548601 TTTAGGG
1 TTTAGGT
*
3548608 TTTAGGA
1 TTTAGGT
3548615 TTTAGAGT
1 TTTAG-GT
3548623 TTTAGGT
1 TTTAGGT
3548630 TTATA-GT
1 TT-TAGGT
3548637 TTT-GAGT
1 TTTAG-GT
3548644 TTT-GAGT
1 TTTAG-GT
*
3548651 TTTGAGTT
1 TTT-AGGT
3548659 TTTAGGT
1 TTTAGGT
3548666 TTTGAGGT
1 TTT-AGGT
3548674 T
1 T
3548675 AGGGTTGGGG
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
6 1 0.02
7 44 0.70
8 17 0.27
9 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (7 bp):
TTTAGGT
Found at i:3548674 original size:8 final size:7
Alignment explanation
Indices: 3548634--3548671 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
3548624 TTAGGTTTAT
3548634 AGTTTTG
1 AGTTTTG
3548641 AGTTTTG
1 AGTTTTG
3548648 AGTTTTG
1 AGTTTTG
*
3548655 AGTTTTT
1 AGTTTTG
3548662 AGGTTTTG
1 A-GTTTTG
3548670 AG
1 AG
3548672 GTTAGGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (7 bp):
AGTTTTG
Found at i:3548779 original size:28 final size:28
Alignment explanation
Indices: 3548748--3548807 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3548738 CGGGTTTCGA
* * *
3548748 ATTTCGAGTTTTGAGTTTATGGTTTATG
1 ATTTCGAGTTTAGAGTTTAAGGTTTAGG
** *
3548776 ATTTTTAGTTTAGTGTTTAAGGTTTAGG
1 ATTTCGAGTTTAGAGTTTAAGGTTTAGG
3548804 ATTT
1 ATTT
3548808 TGGGCTTCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.02, G:0.23, T:0.55
Consensus pattern (28 bp):
ATTTCGAGTTTAGAGTTTAAGGTTTAGG
Found at i:3548924 original size:28 final size:27
Alignment explanation
Indices: 3548892--3548991 Score: 87
Period size: 28 Copynumber: 3.6 Consensus size: 27
3548882 TTAGGGTTTG
*
3548892 GGGTTTATGGTTTATGGTTTAATATTTT
1 GGGTTTAGGGTTTAT-GTTTAATATTTT
* **
3548920 GGGTTTATGGTTTCAAT-TTTAAGGTTTT
1 GGGTTTAGGGTTT--ATGTTTAATATTTT
*
3548948 GGGTTTAGGGTCTCATG-TTACATATTTT
1 GGGTTTAGGGT-TTATGTTTA-ATATTTT
*
3548976 GGATTTAGGGTTTATG
1 GGGTTTAGGGTTTATG
3548992 GGTTTGGGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
27 9 0.15
28 47 0.80
29 1 0.02
30 2 0.03
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (27 bp):
GGGTTTAGGGTTTATGTTTAATATTTT
Found at i:3548945 original size:21 final size:21
Alignment explanation
Indices: 3548895--3548954 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3548885 GGGTTTGGGG
*
3548895 TTTATGGTTTATGGTTTAATA
1 TTTAAGGTTTATGGTTTAATA
**
3548916 TTTTGGGTTTATGGTTTCAAT-
1 TTTAAGGTTTATGGTTT-AATA
3548937 TTTAAGGTTT-TGGGTTTA
1 TTTAAGGTTTAT-GGTTTA
3548955 GGGTCTCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 2 0.06
21 28 0.85
22 3 0.09
ACGTcount: A:0.18, C:0.02, G:0.23, T:0.57
Consensus pattern (21 bp):
TTTAAGGTTTATGGTTTAATA
Found at i:3548946 original size:56 final size:56
Alignment explanation
Indices: 3548880--3548988 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
3548870 TGGTTTAAGG
* * * * *
3548880 TTTTAGGGTTTGGGGTTTATGGT-TTATGGTTTA-ATATTTTGGGTTTATGGTTTCAA
1 TTTTAAGGTTTGGGGTTTAGGGTCTCAT-G-TTACATATTTTGGATTTAGGGTTTCAA
*
3548936 TTTTAAGGTTTTGGGTTTAGGGTCTCATGTTACATATTTTGGATTTAGGGTTT
1 TTTTAAGGTTTGGGGTTTAGGGTCTCATGTTACATATTTTGGATTTAGGGTTT
3548989 ATGGGTTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 3 0.07
56 39 0.87
57 3 0.07
ACGTcount: A:0.17, C:0.04, G:0.28, T:0.52
Consensus pattern (56 bp):
TTTTAAGGTTTGGGGTTTAGGGTCTCATGTTACATATTTTGGATTTAGGGTTTCAA
Found at i:3549026 original size:188 final size:187
Alignment explanation
Indices: 3548832--3549233 Score: 621
Period size: 188 Copynumber: 2.1 Consensus size: 187
3548822 TGAGTTTTGT
* * *
3548832 GTTTTGAGTTTCGGGTTTCA-AGTTTAT-AT-TTAGAGGTTTGGTTTAAGGTTTTAGGGTTTGGG
1 GTTTTGAGTTTCGAGTTT-AGAGTTTATGATGTTAGA--ATT-GTGTAAGGTTTTAGGGTTTGGG
*
3548894 GTTTATGGTTTATGGTTTAATATTTTGGGTTTATGGTTTCAATTTTAAGGTTTTGGGTTTAGGGT
62 GTTTATGGTTTATGGTTTAATATTTTGGGTTTATGGTTTCAATTTTAAGGTTTTGGATTTAGGGT
3548959 CTCATGTTACATATTTTGGATTTAGGGTTTATGGGTTTGGGTTTAAGGATTCATGTTTCTA
127 CTCATGTTACATATTTTGGATTTAGGGTTTATGGGTTTGGGTTTAAGGATTCATGTTTCTA
* * * * *
3549020 GTTTTGATTTTTGAGTTTAGGGTTTATGGTTGTTAGAATTGTGTAAGGTTTTGGGGTTTGGGGTT
1 GTTTTGAGTTTCGAGTTTAGAGTTTAT-GATGTTAGAATTGTGTAAGGTTTTAGGGTTTGGGGTT
3549085 TATGGTTTATGGTTTAATATTTTGGGTTTATGGTTTCAATTTTAAGGTTTTGGATTTAGGGTCTC
65 TATGGTTTATGGTTTAATATTTTGGGTTTATGGTTTCAATTTTAAGGTTTTGGATTTAGGGTCTC
*
3549150 ATGTTTCATATTTTGGATTTAGGGTTTATGGGTTTGGGTTTAAGGATTCATGTTTCTA
130 ATGTTACATATTTTGGATTTAGGGTTTATGGGTTTGGGTTTAAGGATTCATGTTTCTA
* * *
3549208 GTTTTGATTTTTGAGTTTAGGGTTTA
1 GTTTTGAGTTTCGAGTTTAGAGTTTA
3549234 GGGTTTATAG
Statistics
Matches: 200, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
187 1 0.00
188 191 0.95
189 2 0.01
190 1 0.00
191 5 0.03
ACGTcount: A:0.17, C:0.03, G:0.28, T:0.51
Consensus pattern (187 bp):
GTTTTGAGTTTCGAGTTTAGAGTTTATGATGTTAGAATTGTGTAAGGTTTTAGGGTTTGGGGTTT
ATGGTTTATGGTTTAATATTTTGGGTTTATGGTTTCAATTTTAAGGTTTTGGATTTAGGGTCTCA
TGTTACATATTTTGGATTTAGGGTTTATGGGTTTGGGTTTAAGGATTCATGTTTCTA
Found at i:3549118 original size:28 final size:27
Alignment explanation
Indices: 3549083--3549179 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 27
3549073 GGGTTTGGGG
* *
3549083 TTTATGGTTTATGGTTTAATATTTTGGG
1 TTTAGGGTTTAT-GTTTAATATTTTGGA
* **
3549111 TTTATGGTTTCAAT-TTTAAGGTTTTGGA
1 TTTAGGGTTT--ATGTTTAATATTTTGGA
* *
3549139 TTTAGGGTCTCATGTTTCATATTTTGGA
1 TTTAGGGT-TTATGTTTAATATTTTGGA
3549167 TTTAGGGTTTATG
1 TTTAGGGTTTATG
3549180 GGTTTGGGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
27 6 0.11
28 47 0.84
29 1 0.02
30 2 0.04
ACGTcount: A:0.19, C:0.04, G:0.24, T:0.54
Consensus pattern (27 bp):
TTTAGGGTTTATGTTTAATATTTTGGA
Found at i:3549133 original size:21 final size:21
Alignment explanation
Indices: 3549083--3549142 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3549073 GGGTTTGGGG
*
3549083 TTTATGGTTTATGGTTTAATA
1 TTTAAGGTTTATGGTTTAATA
**
3549104 TTTTGGGTTTATGGTTTCAAT-
1 TTTAAGGTTTATGGTTT-AATA
3549125 TTTAAGGTTT-TGGATTTA
1 TTTAAGGTTTATGG-TTTA
3549143 GGGTCTCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 4 0.12
21 26 0.79
22 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.57
Consensus pattern (21 bp):
TTTAAGGTTTATGGTTTAATA
Found at i:3550095 original size:29 final size:29
Alignment explanation
Indices: 3550039--3550097 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3550029 TATTTTATTC
** ***
3550039 ATGTATTTTATCTTAATTTTTTTCACAGA
1 ATGTATTTTATCTTAATTGGTAAAACAGA
3550068 ATGTATTTTATCTTAATTGGTAAAACAGA
1 ATGTATTTTATCTTAATTGGTAAAACAGA
3550097 A
1 A
3550098 AAGGTTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.47
Consensus pattern (29 bp):
ATGTATTTTATCTTAATTGGTAAAACAGA
Found at i:3550465 original size:18 final size:22
Alignment explanation
Indices: 3550429--3550471 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 22
3550419 CTTTAAAATG
3550429 AAAAATAATAATAACAATTT-A
1 AAAAATAATAATAACAATTTCA
3550450 AAAAAT-ATAA-AA-AATTTCA
1 AAAAATAATAATAACAATTTCA
3550469 AAA
1 AAA
3550472 TTCAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 4 0.19
21 6 0.29
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAATAATAATAACAATTTCA
Found at i:3556090 original size:2 final size:2
Alignment explanation
Indices: 3556071--3556110 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3556061 ATCTTACCTC
* *
3556071 AT AT AT CT AT AT CT -T 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
3556111 AGTACGAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3556623 original size:27 final size:28
Alignment explanation
Indices: 3556587--3556643 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
3556577 ACCAAAATGT
3556587 TATAACTTTTTTTATTTACCAAAAAATA
1 TATAACTTTTTTTATTTACCAAAAAATA
*
3556615 TATAA-TTTTTTTATTTATCAAAAAATA
1 TATAACTTTTTTTATTTACCAAAAAATA
3556642 TA
1 TA
3556644 AAAAAACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
TATAACTTTTTTTATTTACCAAAAAATA
Found at i:3556828 original size:18 final size:18
Alignment explanation
Indices: 3556805--3556877 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
3556795 GAAGGAGAGG
3556805 GGAAGAAGAAGAAAGAAA
1 GGAAGAAGAAGAAAGAAA
*
3556823 GGAAGAAGGAA-AAGGAAA
1 GGAAGAA-GAAGAAAGAAA
3556841 GG-AG-AG--GAAAGAAA
1 GGAAGAAGAAGAAAGAAA
*
3556855 -GAAAAAGAAGGAAAGAAAA
1 GGAAGAAGAA-GAAAG-AAA
3556874 GGAA
1 GGAA
3556878 AGGGGAGGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
13 1 0.02
14 7 0.16
15 3 0.07
16 1 0.02
17 2 0.05
18 20 0.47
19 6 0.14
20 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (18 bp):
GGAAGAAGAAGAAAGAAA
Found at i:3556829 original size:12 final size:13
Alignment explanation
Indices: 3556812--3556877 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
3556802 AGGGGAAGAA
3556812 GAAGAAAG-AAAG
1 GAAGAAAGAAAAG
*
3556824 GAAGAAGGAAAA-
1 GAAGAAAGAAAAG
* *
3556836 G--GAAAGGAGAG
1 GAAGAAAGAAAAG
*
3556847 GAAAGAAAGAAAAA
1 G-AAGAAAGAAAAG
3556861 GAAGGAAAGAAAAG
1 GAA-GAAAGAAAAG
3556875 GAA
1 GAA
3556878 AGGGGAGGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
10 6 0.15
11 1 0.03
12 8 0.20
13 5 0.12
14 20 0.50
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
GAAGAAAGAAAAG
Found at i:3556832 original size:32 final size:32
Alignment explanation
Indices: 3556791--3556855 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3556781 GTTGGTGGGG
* * *
3556791 GGAAGAAGGAGAGGGGAAGAAGAAGAAAGAAA
1 GGAAGAAGGAAAAGGAAAGAAGAAGAAAGAAA
* *
3556823 GGAAGAAGGAAAAGGAAAGGAGAGGAAAGAAA
1 GGAAGAAGGAAAAGGAAAGAAGAAGAAAGAAA
3556855 G
1 G
3556856 AAAAAGAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (32 bp):
GGAAGAAGGAAAAGGAAAGAAGAAGAAAGAAA
Found at i:3556850 original size:10 final size:10
Alignment explanation
Indices: 3556815--3556919 Score: 60
Period size: 10 Copynumber: 10.7 Consensus size: 10
3556805 GGAAGAAGAA
3556815 GAAA-GAAAG
1 GAAAGGAAAG
3556824 GAAGAAGGAAAAG
1 G-A-AAGG-AAAG
*
3556837 GAAAGGAGAG
1 GAAAGGAAAG
3556847 GAAA-GAAAG
1 GAAAGGAAAG
* *
3556856 AAAAAG-AAG
1 GAAAGGAAAG
*
3556865 GAAAGAAAAG
1 GAAAGGAAAG
**
3556875 GAAAGGGGAG
1 GAAAGGAAAG
3556885 GAAA-GAAA-
1 GAAAGGAAAG
*
3556893 GAAA-AATAAG
1 GAAAGGA-AAG
*
3556903 GAAAGAAAAG
1 GAAAGGAAAG
3556913 GAAAGGA
1 GAAAGGA
3556920 GAAGATAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
8 5 0.07
9 18 0.24
10 36 0.49
11 8 0.11
12 2 0.03
13 5 0.07
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (10 bp):
GAAAGGAAAG
Found at i:3556851 original size:28 final size:28
Alignment explanation
Indices: 3556810--3556880 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
3556800 AGAGGGGAAG
* *
3556810 AAGAAGAAAGAAAGGAAGAAGGAA-AAGGA
1 AAGAA-AAGGAAAGGAAGAA-AAAGAAGGA
* * *
3556839 AAGGAGAGGAAAGAAAGAAAAAGAAGGA
1 AAGAAAAGGAAAGGAAGAAAAAGAAGGA
3556867 AAGAAAAGGAAAGG
1 AAGAAAAGGAAAGG
3556881 GGAGGAAAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
27 2 0.06
28 27 0.82
29 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (28 bp):
AAGAAAAGGAAAGGAAGAAAAAGAAGGA
Found at i:3556873 original size:38 final size:38
Alignment explanation
Indices: 3556813--3556921 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 38
3556803 GGGGAAGAAG
* *
3556813 AAGAAAG-AAAGGAA-GAAGGAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
3556849 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
3556887 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGA
3556922 AGATAAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 7 0.11
37 6 0.09
38 53 0.80
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:3557691 original size:19 final size:19
Alignment explanation
Indices: 3557663--3557701 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3557653 ATATATTGGT
*
3557663 TTTTTTTAATATTTTATTA
1 TTTTTGTAATATTTTATTA
*
3557682 TTTTTGTAATGTTTTATTA
1 TTTTTGTAATATTTTATTA
3557701 T
1 T
3557702 GGGTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTTGTAATATTTTATTA
Found at i:3557766 original size:27 final size:26
Alignment explanation
Indices: 3557736--3557805 Score: 106
Period size: 27 Copynumber: 2.7 Consensus size: 26
3557726 AAATAAAAAA
3557736 TTACCAAAATATTATAACTTTTTTTAT
1 TTACCAAAATATTATAA-TTTTTTTAT
*
3557763 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATAT-TATAATTTTTTTAT
3557790 TTACCAAAATA-TATAA
1 TTACCAAAATATTATAA
3557806 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 5 0.12
27 30 0.75
28 5 0.12
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (26 bp):
TTACCAAAATATTATAATTTTTTTAT
Found at i:3557823 original size:14 final size:15
Alignment explanation
Indices: 3557804--3557840 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3557794 CAAAATATAT
3557804 AAAAAAAT-AAAAAC
1 AAAAAAATAAAAAAC
3557818 AAAAAAATAAAAAAC
1 AAAAAAATAAAAAAC
3557833 AGAAAAAA
1 A-AAAAAA
3557841 AACACACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 7 0.33
16 6 0.29
ACGTcount: A:0.86, C:0.05, G:0.03, T:0.05
Consensus pattern (15 bp):
AAAAAAATAAAAAAC
Found at i:3560540 original size:17 final size:17
Alignment explanation
Indices: 3560518--3560554 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3560508 ATGGGGTAAG
3560518 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
3560535 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
3560552 ATG
1 ATG
3560555 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:3561164 original size:25 final size:25
Alignment explanation
Indices: 3561130--3561181 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3561120 CCCAGCCAGA
3561130 TCCGAAACAATCTGGATTTGTCGGT
1 TCCGAAACAATCTGGATTTGTCGGT
3561155 TCCGAAACAATCTGGATTTGTCGGT
1 TCCGAAACAATCTGGATTTGTCGGT
3561180 TC
1 TC
3561182 AGATAGCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (25 bp):
TCCGAAACAATCTGGATTTGTCGGT
Found at i:3561586 original size:15 final size:14
Alignment explanation
Indices: 3561546--3561574 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3561536 TTCTTGTATC
3561546 AATTTAATTATTCT
1 AATTTAATTATTCT
3561560 AATTTAATTATTCT
1 AATTTAATTATTCT
3561574 A
1 A
3561575 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:3565339 original size:27 final size:27
Alignment explanation
Indices: 3565305--3565361 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
3565295 GTCAATTGCT
* *
3565305 ATCCGTGTTGCAATTGGAAGGCGTATC
1 ATCCGTGTTGCAATTGGAAGACCTATC
3565332 ATCCGTGTTGCAATTGGAAGACCTATC
1 ATCCGTGTTGCAATTGGAAGACCTATC
3565359 ATC
1 ATC
3565362 ATCAACTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (27 bp):
ATCCGTGTTGCAATTGGAAGACCTATC
Found at i:3569634 original size:6 final size:6
Alignment explanation
Indices: 3569623--3569657 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3569613 CTGTACTAAA
3569623 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTT
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTT
3569658 GGTCGGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
ATCTTC
Found at i:3572627 original size:18 final size:18
Alignment explanation
Indices: 3572580--3572629 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3572570 CGAAATACTT
*
3572580 ATTCGAGTTGACTAGAATA
1 ATTCGA-TTAACTAGAATA
* * *
3572599 ATTTGAATAACTTGAATA
1 ATTCGATTAACTAGAATA
3572617 ATTCGATTAACTA
1 ATTCGATTAACTA
3572630 AAAATTTGAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (18 bp):
ATTCGATTAACTAGAATA
Found at i:3578757 original size:27 final size:27
Alignment explanation
Indices: 3578719--3578772 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3578709 ATACTGTTAC
3578719 ATATTGACGTGTCTCAAAGTGAAATTT
1 ATATTGACGTGTCTCAAAGTGAAATTT
3578746 ATATTGACGTGTCTCAAAGTGAAATTT
1 ATATTGACGTGTCTCAAAGTGAAATTT
3578773 GACTATCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (27 bp):
ATATTGACGTGTCTCAAAGTGAAATTT
Done.