Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 12 of 444
Found at i:3571621 original size:47 final size:46
Alignment explanation
Indices: 3571557--3571666 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 46
3571547 GACATTGAGT
* *
3571557 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTT-ATC
* * *
3571604 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTATC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATC
3571650 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
3571667 CTTATCCCGG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
46 17 0.31
47 33 0.61
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (46 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATC
Found at i:3581076 original size:14 final size:14
Alignment explanation
Indices: 3581039--3581077 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
3581029 TTCAAGATTA
*
3581039 AAGTATCTTAAAAT
1 AAGTATTTTAAAAT
*
3581053 ATATTATTTTAAAAT
1 A-AGTATTTTAAAAT
3581068 AAGTATTTTA
1 AAGTATTTTA
3581078 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (14 bp):
AAGTATTTTAAAAT
Found at i:3581083 original size:18 final size:17
Alignment explanation
Indices: 3581049--3581093 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
3581039 AAGTATCTTA
*
3581049 AAATATATTATTTTAAAAT
1 AAATATTTTA-TTT-AAAT
*
3581068 AAGTATTTTATTTAAAT
1 AAATATTTTATTTAAAT
3581085 AAATATTTT
1 AAATATTTT
3581094 TGAAAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AAATATTTTATTTAAAT
Found at i:3589333 original size:42 final size:42
Alignment explanation
Indices: 3589274--3589357 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
3589264 ATATCATTGT
3589274 TGCCAAGCAAAATTGATGAAAACACTTGCATGTACATTCTTG
1 TGCCAAGCAAAATTGATGAAAACACTTGCATGTACATTCTTG
*
3589316 TGCCAAGCAAAATTGATGAAAACACTTGCTTGTACATTCTTG
1 TGCCAAGCAAAATTGATGAAAACACTTGCATGTACATTCTTG
3589358 GGAAAGTAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (42 bp):
TGCCAAGCAAAATTGATGAAAACACTTGCATGTACATTCTTG
Found at i:3619681 original size:16 final size:16
Alignment explanation
Indices: 3619660--3619693 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3619650 AAAAAAATCC
3619660 TTTTAGTTAATTTTTA
1 TTTTAGTTAATTTTTA
3619676 TTTTAGTTAATTTTTA
1 TTTTAGTTAATTTTTA
3619692 TT
1 TT
3619694 ATATAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTAGTTAATTTTTA
Found at i:3620974 original size:18 final size:18
Alignment explanation
Indices: 3620951--3620987 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3620941 AACCACGGGA
3620951 GTTAGATGAGATGACAAT
1 GTTAGATGAGATGACAAT
3620969 GTTAGATGAGATGACAAT
1 GTTAGATGAGATGACAAT
3620987 G
1 G
3620988 GTCTCTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (18 bp):
GTTAGATGAGATGACAAT
Found at i:3622193 original size:10 final size:10
Alignment explanation
Indices: 3622178--3622205 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3622168 ACCTTAAAAG
3622178 AAAGTTTTCA
1 AAAGTTTTCA
3622188 AAAGTTTTCA
1 AAAGTTTTCA
3622198 AAAGTTTT
1 AAAGTTTT
3622206 TAGCTATGGA
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:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (10 bp):
AAAGTTTTCA
Found at i:3626669 original size:10 final size:10
Alignment explanation
Indices: 3626650--3626708 Score: 93
Period size: 10 Copynumber: 5.9 Consensus size: 10
3626640 TTCAATTCTA
3626650 AAAGATAAAT
1 AAAGATAAAT
3626660 ACAA-ATAAAT
1 A-AAGATAAAT
3626670 AAAGATAAAT
1 AAAGATAAAT
3626680 AAAGATAAAT
1 AAAGATAAAT
*
3626690 AAGGATAAAT
1 AAAGATAAAT
3626700 AAAGATAAA
1 AAAGATAAA
3626709 AACTAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 2 0.04
10 41 0.91
11 2 0.04
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:3628688 original size:25 final size:23
Alignment explanation
Indices: 3628659--3628713 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 23
3628649 ATTAATATCA
*
3628659 AAAATAAAGTAATAAATAATAGGAT
1 AAAATAAAGTAATAAAAAATA--AT
3628684 AAAATAAAGTAATAAAAAATAAT
1 AAAATAAAGTAATAAAAAATAAT
3628707 AAAATAA
1 AAAATAA
3628714 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 9 0.31
25 20 0.69
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (23 bp):
AAAATAAAGTAATAAAAAATAAT
Found at i:3628707 original size:18 final size:18
Alignment explanation
Indices: 3628686--3628720 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3628676 AATAGGATAA
*
3628686 AATAAAGTAATAAAAAAT
1 AATAAAATAATAAAAAAT
3628704 AATAAAATAATAAAAAA
1 AATAAAATAATAAAAAA
3628721 ATTGGGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AATAAAATAATAAAAAAT
Found at i:3631644 original size:60 final size:60
Alignment explanation
Indices: 3631566--3631705 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 60
3631556 TAGTGTTAAC
* *
3631566 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
3631627 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
3631687 TGGGCCTTGCCCATATCAA
1 TGGGCCTAGCCCATATCAA
3631706 CACAGTTGGG
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
60 55 0.79
61 13 0.19
62 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:3631666 original size:28 final size:27
Alignment explanation
Indices: 3631565--3631666 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
3631555 TTAGTGTTAA
* *
3631565 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
3631593 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
3631625 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
3631653 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
3631667 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:3632068 original size:26 final size:27
Alignment explanation
Indices: 3632021--3632083 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
3632011 CAAAATTAAC
* * *
3632021 CCTAGGGGTATAACGGTCATTTT-ACA
1 CCTAGGGGTAAAACGATAATTTTCACA
*
3632047 CCTAGGGGTAAAACGATAATTTTCATA
1 CCTAGGGGTAAAACGATAATTTTCACA
*
3632074 CTTAGGGGTA
1 CCTAGGGGTA
3632084 GTTTAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
CCTAGGGGTAAAACGATAATTTTCACA
Found at i:3632869 original size:17 final size:17
Alignment explanation
Indices: 3632828--3632869 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3632818 AAGGAAATTA
*
3632828 AAAAAAGAAAAGATGAG
1 AAAAAAGAAAAGATAAG
*
3632845 ATAAAAGAAAAGA-AAG
1 AAAAAAGAAAAGATAAG
3632861 AAAAGAAGA
1 AAAA-AAGA
3632870 GTAGAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (17 bp):
AAAAAAGAAAAGATAAG
Found at i:3635732 original size:10 final size:10
Alignment explanation
Indices: 3635705--3635763 Score: 84
Period size: 10 Copynumber: 5.9 Consensus size: 10
3635695 TTCAATTCTA
3635705 AAAGATAAAT
1 AAAGATAAAT
3635715 ACAA-ATAAAT
1 A-AAGATAAAT
*
3635725 AAAGATAATT
1 AAAGATAAAT
3635735 AAAGATAAAT
1 AAAGATAAAT
*
3635745 AAGGATAAAT
1 AAAGATAAAT
3635755 AAAGATAAA
1 AAAGATAAA
3635764 AACTAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
9 2 0.05
10 39 0.91
11 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:3639949 original size:28 final size:28
Alignment explanation
Indices: 3639917--3639972 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3639907 GAAATGGCAG
3639917 ATAGCCATTGAAGAGCAAGACAGAGTTC
1 ATAGCCATTGAAGAGCAAGACAGAGTTC
3639945 ATAGCCATTGAAGAGCAAGACAGAGTTC
1 ATAGCCATTGAAGAGCAAGACAGAGTTC
3639973 TTTGCCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (28 bp):
ATAGCCATTGAAGAGCAAGACAGAGTTC
Found at i:3641268 original size:31 final size:31
Alignment explanation
Indices: 3641223--3641289 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3641213 TATCAATTTC
*
3641223 AGTCCCTAATATTATCAGG-TG-TTCTCAGTTT
1 AGTCCCTAACATTATC-GGATGTTTCT-AGTTT
*
3641254 AGTCTCTAACATTATCGGATGTTTCTAGTTT
1 AGTCCCTAACATTATCGGATGTTTCTAGTTT
3641285 AGTCC
1 AGTCC
3641290 TTTGAACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 2 0.06
31 25 0.81
32 4 0.13
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (31 bp):
AGTCCCTAACATTATCGGATGTTTCTAGTTT
Found at i:3641450 original size:28 final size:27
Alignment explanation
Indices: 3641419--3641497 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
3641409 AAATTTAAAA
*
3641419 AAAATTATTAAAAATTGAAAAAACTTA-T
1 AAAATTAATAAAAATT-AAAAAA-TTACT
*
3641447 AAAATTACAAAAAAATTAAAAAATTACT
1 AAAATTA-ATAAAAATTAAAAAATTACT
* * *
3641475 TAAATTACTAAAATTTTAAAAAA
1 AAAATTAATAAAA-ATTAAAAAA
3641498 AATTGTGGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 7 0.17
28 28 0.67
29 7 0.17
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.30
Consensus pattern (27 bp):
AAAATTAATAAAAATTAAAAAATTACT
Found at i:3641458 original size:19 final size:19
Alignment explanation
Indices: 3641397--3641473 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
3641387 TTTAAAAATG
*
3641397 AAAAAAGTACAAAAATTTA-A
1 AAAAAATTA-AAAAA-TTACA
*
3641417 AAAAAATTATTAAAAATT-GA
1 AAAAAATTA--AAAAATTACA
* *
3641437 AAAAACTTATAAAATTACA
1 AAAAAATTAAAAAATTACA
3641456 AAAAAATTAAAAAATTAC
1 AAAAAATTAAAAAATTAC
3641474 TTAAATTACT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
18 6 0.13
19 17 0.36
20 19 0.40
21 5 0.11
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAAATTAAAAAATTACA
Found at i:3641461 original size:11 final size:10
Alignment explanation
Indices: 3641397--3641469 Score: 51
Period size: 10 Copynumber: 7.4 Consensus size: 10
3641387 TTTAAAAATG
* *
3641397 AAAAAAGTAC
1 AAAAAATTAA
*
3641407 AAAAATTTAA
1 AAAAAATTAA
*
3641417 AAAAAATTAT
1 AAAAAATTAA
* *
3641427 TAAAAATTGA
1 AAAAAATTAA
*
3641437 AAAAACTT--
1 AAAAAATTAA
*
3641445 ATAAAATTACA
1 AAAAAATTA-A
3641456 AAAAAATTAA
1 AAAAAATTAA
3641466 AAAA
1 AAAA
3641470 TTACTTAAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
8 6 0.13
10 33 0.70
11 8 0.17
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:3641761 original size:17 final size:17
Alignment explanation
Indices: 3641739--3641771 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3641729 ATGTGATTTA
3641739 TAAAATTTCTAATATAT
1 TAAAATTTCTAATATAT
3641756 TAAAATTTCTAATATA
1 TAAAATTTCTAATATA
3641772 ATTTTTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATTTCTAATATAT
Found at i:3641968 original size:2 final size:2
Alignment explanation
Indices: 3641961--3641994 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3641951 AACTAAAATA
3641961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3641995 GAGACTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3642525 original size:22 final size:22
Alignment explanation
Indices: 3642499--3642550 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3642489 CCATAACAAT
* *
3642499 AAAATAGTAGCAATATAGTAAC
1 AAAATAGTAGCAAAATAATAAC
* *
3642521 GAAATTGTAGCAAAATAATAAC
1 AAAATAGTAGCAAAATAATAAC
3642543 AAAATAGT
1 AAAATAGT
3642551 TGATTCGGGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAATAAC
Found at i:3642536 original size:11 final size:11
Alignment explanation
Indices: 3642499--3642550 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
3642489 CCATAACAAT
3642499 AAAATAGTAGC
1 AAAATAGTAGC
* *
3642510 AATATAGTAAC
1 AAAATAGTAGC
* *
3642521 GAAATTGTAGC
1 AAAATAGTAGC
* *
3642532 AAAATAATAAC
1 AAAATAGTAGC
3642543 AAAATAGT
1 AAAATAGT
3642551 TGATTCGGGC
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (11 bp):
AAAATAGTAGC
Found at i:3656491 original size:6 final size:6
Alignment explanation
Indices: 3656480--3656523 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
3656470 TCATAACATT
3656480 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
3656524 AGAATGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:3656901 original size:20 final size:19
Alignment explanation
Indices: 3656868--3656909 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3656858 AGTAGTTTCA
3656868 TTTTTATAAGTTTTAAGTTT
1 TTTTTATAAGTTTTAA-TTT
* *
3656888 TTTTTTTAATTTTTAATTT
1 TTTTTATAAGTTTTAATTT
3656907 TTT
1 TTT
3656910 ATGATTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTATAAGTTTTAATTT
Found at i:3657423 original size:34 final size:34
Alignment explanation
Indices: 3657385--3657451 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
3657375 CTCTTCAATC
*
3657385 TTCAATTAGGGATAT-TCAATGCAATAGGGGCACA
1 TTCAATTAAGGAT-TCTCAATGCAATAGGGGCACA
*
3657419 TTCAATTAAGGATTCTCAATGCATTAGGGGCAC
1 TTCAATTAAGGATTCTCAATGCAATAGGGGCAC
3657452 CTTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (34 bp):
TTCAATTAAGGATTCTCAATGCAATAGGGGCACA
Found at i:3658471 original size:16 final size:17
Alignment explanation
Indices: 3658433--3658473 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3658423 ATTATCTAGA
3658433 AAATAAAAATTATTAAT
1 AAATAAAAATTATTAAT
*
3658450 ATATAAAAATT-TGT-AT
1 AAATAAAAATTAT-TAAT
3658466 AAATAAAA
1 AAATAAAA
3658474 TATTCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAATAAAAATTATTAAT
Found at i:3660777 original size:20 final size:18
Alignment explanation
Indices: 3660752--3660788 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
3660742 ATTGCTAAGT
3660752 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
3660772 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
3660789 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:3662636 original size:50 final size:50
Alignment explanation
Indices: 3662578--3662682 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
3662568 TTTTAATGTG
3662578 AGTA-TGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
1 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
*
3662627 GGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
1 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
3662677 AGTATT
1 AGTATT
3662683 AGTCGTGTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
49 3 0.06
50 50 0.94
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.40
Consensus pattern (50 bp):
AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
Found at i:3667240 original size:18 final size:18
Alignment explanation
Indices: 3667183--3667242 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
3667173 GACTGTCTAC
* *
3667183 TACTGAATAATTGACTGT
1 TACTGAATAAATGACTAT
*
3667201 TACAGAATAAATGACTGA-
1 TACTGAATAAATGACT-AT
*
3667219 TACTGAATAAATGAATAT
1 TACTGAATAAATGACTAT
3667237 TACTGA
1 TACTGA
3667243 TTAACCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 34 0.97
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (18 bp):
TACTGAATAAATGACTAT
Found at i:3675608 original size:18 final size:17
Alignment explanation
Indices: 3675577--3675610 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
3675567 CTAATACCAT
3675577 TATTATTTTATTATTAC
1 TATTATTTTATTATTAC
3675594 TATTATTTCTATTATTA
1 TATTATTT-TATTATTA
3675611 TTATGGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTTTATTATTAC
Found at i:3675620 original size:24 final size:24
Alignment explanation
Indices: 3675579--3675638 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
3675569 AATACCATTA
*
3675579 TTATT-TTATTATTACTATT-ATT
1 TTATTATTATTATGACTATTGATT
* *
3675601 TCTATTATTATTATGGCTATTGCTT
1 T-TATTATTATTATGACTATTGATT
*
3675626 TTATTATGATTAT
1 TTATTATTATTAT
3675639 ATTTTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 4 0.13
24 23 0.74
25 3 0.10
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.62
Consensus pattern (24 bp):
TTATTATTATTATGACTATTGATT
Found at i:3675703 original size:21 final size:22
Alignment explanation
Indices: 3675673--3675739 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
3675663 TATTATTTTA
3675673 TTATTAATTAATTTAACATTAT
1 TTATTAATTAATTTAACATTAT
* **
3675695 TTATT-ATT-ATTGTTATTTTA-
1 TTATTAATTAATT-TAACATTAT
*
3675715 TTATTAATTAATTTAGCATTAT
1 TTATTAATTAATTTAACATTAT
3675737 TTA
1 TTA
3675740 ATATTTCTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 8 0.24
21 15 0.44
22 11 0.32
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (22 bp):
TTATTAATTAATTTAACATTAT
Found at i:3675715 original size:42 final size:42
Alignment explanation
Indices: 3675665--3675744 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
3675655 TTTTTACTTA
*
3675665 TTATTTTATTATTAATTAATTTAACATTATTTATTATTATTG
1 TTATTTTATTATTAATTAATTTAACATTATTTAATATTATTG
*
3675707 TTATTTTATTATTAATTAATTTAGCATTATTTAATATT
1 TTATTTTATTATTAATTAATTTAACATTATTTAATATT
3675745 TCTTTATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (42 bp):
TTATTTTATTATTAATTAATTTAACATTATTTAATATTATTG
Found at i:3680464 original size:25 final size:24
Alignment explanation
Indices: 3680436--3680482 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3680426 TTTAAACGAG
*
3680436 ATTGAATTAGATTATAAATTTTACC
1 ATTGAATTAAATTA-AAATTTTACC
*
3680461 ATTGTATTAAATTAAAATTTTA
1 ATTGAATTAAATTAAAATTTTA
3680483 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
ATTGAATTAAATTAAAATTTTACC
Found at i:3680975 original size:6 final size:6
Alignment explanation
Indices: 3680966--3681000 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3680956 ATGTTGGAAT
*
3680966 TTTATA TTTATA TTTATT TTTAT- TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
3681001 AGAAGATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTATA
Found at i:3680992 original size:17 final size:18
Alignment explanation
Indices: 3680965--3680999 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3680955 GATGTTGGAA
3680965 TTTTATATTTATATTTAT
1 TTTTATATTTATATTTAT
3680983 TTTTAT-TTTATATTTAT
1 TTTTATATTTATATTTAT
3681000 AAGAAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATATTTATATTTAT
Found at i:3688340 original size:15 final size:15
Alignment explanation
Indices: 3688319--3688362 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3688309 TTTGTAAAAA
3688319 TAATATTTTAAATTT
1 TAATATTTTAAATTT
* **
3688334 TACTATTTTATCTTT
1 TAATATTTTAAATTT
3688349 TAATATTTTTAAAT
1 TAATA-TTTTAAAT
3688363 AAGTCTTAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATATTTTAAATTT
Found at i:3689959 original size:25 final size:25
Alignment explanation
Indices: 3689927--3689987 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
3689917 ACTTATCATA
**
3689927 TTTATTATTTATTACTATATTTAAT
1 TTTATTATTTATTAAAATATTTAAT
*
3689952 TTTATTATTAATTAAAATATTTAAT
1 TTTATTATTTATTAAAATATTTAAT
3689977 TATTATTATTT
1 T-TTATTATTT
3689988 TGTGTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 23 0.74
26 8 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATTATTTATTAAAATATTTAAT
Found at i:3691501 original size:16 final size:17
Alignment explanation
Indices: 3691470--3691508 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3691460 GAAACAATGT
3691470 CAAAC-ACCCATGAGCC
1 CAAACAACCCATGAGCC
*
3691486 GAAACAACCCAT-AGCC
1 CAAACAACCCATGAGCC
3691502 CAAACAA
1 CAAACAA
3691509 AAAATTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.46, C:0.38, G:0.10, T:0.05
Consensus pattern (17 bp):
CAAACAACCCATGAGCC
Found at i:3692158 original size:20 final size:19
Alignment explanation
Indices: 3692121--3692160 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3692111 ACGCTTGTAA
3692121 AATTATGGATTTAAAATAT
1 AATTATGGATTTAAAATAT
3692140 AATTATGTG-TTTAAAA-AT
1 AATTATG-GATTTAAAATAT
3692158 AAT
1 AAT
3692161 GTACAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 14 0.70
20 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
AATTATGGATTTAAAATAT
Found at i:3693565 original size:30 final size:28
Alignment explanation
Indices: 3693501--3693565 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 28
3693491 TAAATTAAGA
** *
3693501 ATTATTTTTTTAATTTCATGTATGATTT
1 ATTATTTTTTTAATTTCACATATAATTT
*
3693529 ATTTATTTTTTTATTGTTCACATATAATTAT
1 A-TTATTTTTTTAAT-TTCACATATAATT-T
3693560 ATTATT
1 ATTATT
3693566 GGGTTACCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 12 0.40
30 15 0.50
31 2 0.07
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (28 bp):
ATTATTTTTTTAATTTCACATATAATTT
Found at i:3697193 original size:31 final size:31
Alignment explanation
Indices: 3697155--3697228 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
3697145 ATTCCTTTAA
*
3697155 ATGTATATAATTGAA-TGAAAATTAAAATTTC
1 ATGTATATAATTGAACT-AAAATCAAAATTTC
* * *
3697186 ATGTATATATTTGAACTATAATCAAAGTTTC
1 ATGTATATAATTGAACTAAAATCAAAATTTC
*
3697217 ATGTGTATAATT
1 ATGTATATAATT
3697229 ATACCAAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (31 bp):
ATGTATATAATTGAACTAAAATCAAAATTTC
Found at i:3702256 original size:42 final size:42
Alignment explanation
Indices: 3702158--3702243 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
3702148 AAGCAAGTGG
3702158 TTGAGGAGATATTTGGCCAAAACAATTGGGAACTATGGTGAA
1 TTGAGGAGATATTTGGCCAAAACAATTGGGAACTATGGTGAA
3702200 TTGAGGAGATATTTGGCCAAAACAATTGGGAACTATGGTGAA
1 TTGAGGAGATATTTGGCCAAAACAATTGGGAACTATGGTGAA
3702242 TT
1 TT
3702244 ATTGAATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (42 bp):
TTGAGGAGATATTTGGCCAAAACAATTGGGAACTATGGTGAA
Found at i:3703035 original size:32 final size:32
Alignment explanation
Indices: 3702999--3703064 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
3702989 ATTATTTTTT
3702999 AATATTTAACTTCTCTATTTTTATAAAGTAAA
1 AATATTTAACTTCTCTATTTTTATAAAGTAAA
3703031 AATATTTAACTTCTCTATTTTTATAAAGTAAA
1 AATATTTAACTTCTCTATTTTTATAAAGTAAA
3703063 AA
1 AA
3703065 GAGTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (32 bp):
AATATTTAACTTCTCTATTTTTATAAAGTAAA
Found at i:3712686 original size:19 final size:19
Alignment explanation
Indices: 3712662--3712700 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3712652 ATTTTTAAAA
3712662 AATATTCT-TTATTATTTTT
1 AATATTCTATTA-TATTTTT
*
3712681 AATATTTTATTATATTTTT
1 AATATTCTATTATATTTTT
3712700 A
1 A
3712701 TTGTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
AATATTCTATTATATTTTT
Found at i:3712927 original size:18 final size:19
Alignment explanation
Indices: 3712904--3712950 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3712894 ATTTATCTAG
*
3712904 TTAAAATTAAATAAATTAT
1 TTAAAATTAAATAAATAAT
* *
3712923 TAAAAATT-TATAAATAAT
1 TTAAAATTAAATAAATAAT
3712941 TTAAAATTAA
1 TTAAAATTAA
3712951 TTGTCGGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAATTAAATAAATAAT
Found at i:3715697 original size:24 final size:24
Alignment explanation
Indices: 3715665--3715712 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3715655 TATTGATATG
3715665 AATGATTTTGAATTTTTAAGATTA
1 AATGATTTTGAATTTTTAAGATTA
3715689 AATGATTTTGAATTTTTAAGATTA
1 AATGATTTTGAATTTTTAAGATTA
3715713 TATAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
AATGATTTTGAATTTTTAAGATTA
Found at i:3715720 original size:24 final size:24
Alignment explanation
Indices: 3715669--3715720 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3715659 GATATGAATG
*
3715669 ATTTTGAATTTTTAAGATTAAATG
1 ATTTTGAATTTTTAAGATTAAATA
*
3715693 ATTTTGAATTTTTAAGATTATATA
1 ATTTTGAATTTTTAAGATTAAATA
3715717 ATTT
1 ATTT
3715721 ATGTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTTGAATTTTTAAGATTAAATA
Found at i:3716006 original size:6 final size:6
Alignment explanation
Indices: 3715997--3716023 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3715987 TTAAAAATTA
3715997 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
3716024 TTCAGTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3723690 original size:10 final size:10
Alignment explanation
Indices: 3723671--3723701 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3723661 TCTTTTAATG
3723671 ATCC-AATTA
1 ATCCAAATTA
3723680 ATCCAAATTA
1 ATCCAAATTA
3723690 ATCCAAATTA
1 ATCCAAATTA
3723700 AT
1 AT
3723702 TTGATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (10 bp):
ATCCAAATTA
Found at i:3728169 original size:3 final size:3
Alignment explanation
Indices: 3728161--3728186 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3728151 ACGTCCCTTC
3728161 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
3728187 AGTTTCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3729647 original size:30 final size:30
Alignment explanation
Indices: 3729613--3729677 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
3729603 TACTAATATA
*
3729613 TAAAATATTATTATAATATATAACTATTA-C
1 TAAAATATTAATAT-ATATATAACTATTACC
*
3729643 TAAAAATATTAATATGTATATAACTATTACC
1 T-AAAATATTAATATATATATAACTATTACC
3729674 TAAA
1 TAAA
3729678 TTTTTAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAAATATTAATATATATATAACTATTACC
Found at i:3729649 original size:31 final size:31
Alignment explanation
Indices: 3729614--3729677 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
3729604 ACTAATATAT
*
3729614 AAAATATTATTATAATATATAACTATTA-CTA
1 AAAATATTAATAT-ATATATAACTATTACCTA
*
3729645 AAAATATTAATATGTATATAACTATTACCTA
1 AAAATATTAATATATATATAACTATTACCTA
3729676 AA
1 AA
3729678 TTTTTAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (31 bp):
AAAATATTAATATATATATAACTATTACCTA
Found at i:3731215 original size:2 final size:2
Alignment explanation
Indices: 3731208--3731232 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3731198 TAATATTTTA
3731208 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3731233 AATACTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3732347 original size:22 final size:22
Alignment explanation
Indices: 3732308--3732366 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
3732298 GTTTTAAGAA
*
3732308 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
3732329 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
3732351 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
3732367 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:3732383 original size:26 final size:24
Alignment explanation
Indices: 3732337--3732396 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
3732327 ATTTGTTTTA
*
3732337 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
3732361 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
3732387 TTTTTTATTT
1 ATATTTATTT
3732397 AATAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:3734336 original size:26 final size:24
Alignment explanation
Indices: 3734296--3734355 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
3734286 TTATTTTATT
* * *
3734296 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
3734320 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
3734346 AAATAAATAT
1 AAATAAATAT
3734356 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:3734360 original size:20 final size:20
Alignment explanation
Indices: 3734345--3734383 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3734335 TAAAAACATA
*
3734345 AAAATAAATATTAAAACAAAT
1 AAAAT-AATACTAAAACAAAT
3734366 AAAATAATACTAAAACAA
1 AAAATAATACTAAAACAA
3734384 TTCTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATACTAAAACAAAT
Found at i:3734370 original size:21 final size:19
Alignment explanation
Indices: 3734337--3734383 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3734327 AATATATTTA
* *
3734337 AAAACATAAAAATAAATATT
1 AAAACAAAAAAAT-AATACT
3734357 AAAACAAATAAAATAATACT
1 AAAACAAA-AAAATAATACT
3734377 AAAACAA
1 AAAACAA
3734384 TTCTTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAACAAAAAAATAATACT
Found at i:3736359 original size:29 final size:30
Alignment explanation
Indices: 3736305--3736364 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
3736295 AATTCATTTA
* *
3736305 CTGTTTAATAGTATAGGGACTAAA-TTGAT
1 CTGTTTAATAATAAAGGGACTAAATTTGAT
*
3736334 CTGTTTAATAATAAAGGGGGCT-AATTTGAT
1 CTGTTTAATAATAAA-GGGACTAAATTTGAT
3736364 C
1 C
3736365 AAGTCCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (30 bp):
CTGTTTAATAATAAAGGGACTAAATTTGAT
Found at i:3738735 original size:2 final size:2
Alignment explanation
Indices: 3738730--3738762 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3738720 CTTTGAGAGA
3738730 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 A
3738763 ATTTACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3738920 original size:22 final size:22
Alignment explanation
Indices: 3738889--3738930 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3738879 TGACATGAAC
*
3738889 AAATATTTTAAA-CTCGAAATTA
1 AAATAGTTTAAATCT-GAAATTA
3738911 AAATAGTTTAAATCTGAAAT
1 AAATAGTTTAAATCTGAAAT
3738931 GACTGACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATAGTTTAAATCTGAAATTA
Found at i:3742254 original size:3 final size:3
Alignment explanation
Indices: 3742246--3742292 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3742236 TTTACATTGT
3742246 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3742293 TTTACAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3750147 original size:6 final size:6
Alignment explanation
Indices: 3750110--3750143 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3750100 TTGTACCATT
* *
3750110 ATCAAC ATCAAC ATCAAC ATCACC ATCATC ATCA
1 ATCAAC ATCAAC ATCAAC ATCAAC ATCAAC ATCA
3750144 TCATATCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (6 bp):
ATCAAC
Found at i:3752199 original size:6 final size:6
Alignment explanation
Indices: 3752188--3752214 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3752178 GAGAAGGACT
3752188 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
3752215 ATGTATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:3754788 original size:33 final size:30
Alignment explanation
Indices: 3754728--3754797 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
3754718 CTAAGAAAAT
*
3754728 ATATATATATATATAAATAATAGTATTAGAA
1 ATATATATATATATAAATAATAATATTA-AA
* *
3754759 ATCATATAGTATATATAACTGATAATATTAAA
1 AT-ATATA-TATATATAAATAATAATATTAAA
3754791 ATATATA
1 ATATATA
3754798 CATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 18 0.53
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATATATATATATATAAATAATAATATTAAA
Found at i:3754979 original size:15 final size:16
Alignment explanation
Indices: 3754945--3754976 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3754935 AGGTAAATAT
3754945 AATAAAATGATATTAA
1 AATAAAATGATATTAA
3754961 AATAAAA-G-TATTAA
1 AATAAAATGATATTAA
3754975 AA
1 AA
3754977 ATAGTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AATAAAATGATATTAA
Found at i:3755022 original size:3 final size:3
Alignment explanation
Indices: 3755014--3755064 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3755004 ACAAGGATAT
3755014 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3755062 ATA
1 ATA
3755065 TTGAAACACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3755182 original size:3 final size:3
Alignment explanation
Indices: 3755168--3755252 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
3755158 AATGTATTTC
* *
3755168 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3755216 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3755253 TTGAAATGCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3755854 original size:12 final size:12
Alignment explanation
Indices: 3755837--3755891 Score: 110
Period size: 12 Copynumber: 4.6 Consensus size: 12
3755827 AGGTAATTTT
3755837 TTTTTTTGTATA
1 TTTTTTTGTATA
3755849 TTTTTTTGTATA
1 TTTTTTTGTATA
3755861 TTTTTTTGTATA
1 TTTTTTTGTATA
3755873 TTTTTTTGTATA
1 TTTTTTTGTATA
3755885 TTTTTTT
1 TTTTTTT
3755892 ATGTTTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTGTATA
Found at i:3756317 original size:35 final size:35
Alignment explanation
Indices: 3756259--3756375 Score: 191
Period size: 35 Copynumber: 3.4 Consensus size: 35
3756249 GCAGGTGCGG
* * *
3756259 TGGGAGTGTGTGA-TGGTGTTGGTGGCAGACAGCA
1 TGGGAGAGTGGGAGTGGTGCTGGTGGCAGACAGCA
*
3756293 TGGGAGAATGGGAGTGGTGCTGGTGGCAGACAGCA
1 TGGGAGAGTGGGAGTGGTGCTGGTGGCAGACAGCA
3756328 TGGGAGAGTGGGAGTGGTGCTGGTGGCAGACAGCA
1 TGGGAGAGTGGGAGTGGTGCTGGTGGCAGACAGCA
3756363 TGGGAGAGTGGGA
1 TGGGAGAGTGGGA
3756376 AGAGGCAAGT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
34 10 0.13
35 67 0.87
ACGTcount: A:0.21, C:0.09, G:0.50, T:0.20
Consensus pattern (35 bp):
TGGGAGAGTGGGAGTGGTGCTGGTGGCAGACAGCA
Found at i:3762184 original size:135 final size:135
Alignment explanation
Indices: 3761935--3762184 Score: 286
Period size: 135 Copynumber: 1.9 Consensus size: 135
3761925 AATTGAAAAT
* * *
3761935 AAAGCCTCGAGATCAGGTGGTTGAAAGAACCCATTCCTCGGTGGCTCTCTCTTCATATAAACCGC
1 AAAGCCTCGAGATCAGGTGGATGAAAGAACCCATTCCTCGGAGACTCTCTCTTCATATAAACCGC
* * * ***
3762000 TTGTTTCTTCTTAGGCGCCGGCGGACATAGCGGAGGGGGCGCCTTTTGTGTCTGCCGCATCGATG
66 TTGTTTCTTCTTAGGCGCCGGCGGACACAGCGGAGGAGCCGCAGCTTGTGTCTGCCGCATCGATG
3762065 TAAAC
131 TAAAC
* * ** * * *
3762070 AAAGCCTCGAGATCGGGTGGATGAAAGAACTCATTGTTCGGAGACTTTCTCTTTATATGAACCGC
1 AAAGCCTCGAGATCAGGTGGATGAAAGAACCCATTCCTCGGAGACTCTCTCTTCATATAAACCGC
* * * * * *
3762135 TTGTTTTTTCTTCGGTGCC-GCTGGACACGGGGGAGGAGCCGTAGCTTGTG
66 TTGTTTCTTCTTAGGCGCCGGC-GGACACAGCGGAGGAGCCGCAGCTTGTG
3762185 AGTGCCGCCT
Statistics
Matches: 92, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
134 2 0.02
135 90 0.98
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (135 bp):
AAAGCCTCGAGATCAGGTGGATGAAAGAACCCATTCCTCGGAGACTCTCTCTTCATATAAACCGC
TTGTTTCTTCTTAGGCGCCGGCGGACACAGCGGAGGAGCCGCAGCTTGTGTCTGCCGCATCGATG
TAAAC
Found at i:3770958 original size:325 final size:325
Alignment explanation
Indices: 3770368--3771021 Score: 1263
Period size: 325 Copynumber: 2.0 Consensus size: 325
3770358 GGGACTCTGG
*
3770368 TCTTTAGGCCGAACCTATATACGATGAGACTTGAATTGGTTTTCTCTTTTTGTAAATGAAGACAT
1 TCTTTAGGCCGAACCTATATACGATGAGACTTGAATTGGTTTTCTCTTTTTGTAAATGAAGACAC
3770433 TTCTGCAGAAAGCAACAACGGAGATTTTTATTTGTTTTTTCATTTTTTTGATATTTGTAAGTACT
66 TTCTGCAGAAAGCAACAACGGAGATTTTTATTTGTTTTTTCATTTTTTTGATATTTGTAAGTACT
*
3770498 TATAGCTTTAAAAGAAAATATATTAATGAACTTCATTGCATTTGAATATGAGAATAAGAGGATAA
131 TATAGCTTTAAAAGAAAATACATTAATGAACTTCATTGCATTTGAATATGAGAATAAGAGGATAA
3770563 TGATGTCAGGATTTGAAACTCAGATGGTCAGACCTACTTAACATTACCTCGTATGGCCAATACAA
196 TGATGTCAGGATTTGAAACTCAGATGGTCAGACCTACTTAACATTACCTCGTATGGCCAATACAA
*
3770628 CAAGAAACTCAAGACGGTCGGACCTACTTAACATTCACCTAAACCGCTAGCTTCGATCTAATACA
261 CAAGAAACTCAAGAAGGTCGGACCTACTTAACATTCACCTAAACCGCTAGCTTCGATCTAATACA
3770693 TCTTTAGGCCGAACCTATATACGATGAGACTTGAATTGGTTTTCTCTTTTTGTAAATGAAGACAC
1 TCTTTAGGCCGAACCTATATACGATGAGACTTGAATTGGTTTTCTCTTTTTGTAAATGAAGACAC
3770758 TTCTGCAGAAAGCAACAACGGAGATTTTTATTTGTTTTTTCATTTTTTTGATATTTGTAAGTACT
66 TTCTGCAGAAAGCAACAACGGAGATTTTTATTTGTTTTTTCATTTTTTTGATATTTGTAAGTACT
3770823 TATAGCTTTAAAAGAAAATACATTAATGAACTTCATTGCATTTGAATATGAGAATAAGAGGATAA
131 TATAGCTTTAAAAGAAAATACATTAATGAACTTCATTGCATTTGAATATGAGAATAAGAGGATAA
* *
3770888 TGATGTCGGGATTTGAAACTCAGATGGTCAGACCTACTTAACATTACCTCGTCTGGCCAATACAA
196 TGATGTCAGGATTTGAAACTCAGATGGTCAGACCTACTTAACATTACCTCGTATGGCCAATACAA
3770953 CAAGAAACTCAAGAAGGTCGGACCTACTTAACATTCACCTAAACCGCTAGCTTCGATCTAATACA
261 CAAGAAACTCAAGAAGGTCGGACCTACTTAACATTCACCTAAACCGCTAGCTTCGATCTAATACA
3771018 TCTT
1 TCTT
3771022 ACCACCGGCT
Statistics
Matches: 324, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
325 324 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (325 bp):
TCTTTAGGCCGAACCTATATACGATGAGACTTGAATTGGTTTTCTCTTTTTGTAAATGAAGACAC
TTCTGCAGAAAGCAACAACGGAGATTTTTATTTGTTTTTTCATTTTTTTGATATTTGTAAGTACT
TATAGCTTTAAAAGAAAATACATTAATGAACTTCATTGCATTTGAATATGAGAATAAGAGGATAA
TGATGTCAGGATTTGAAACTCAGATGGTCAGACCTACTTAACATTACCTCGTATGGCCAATACAA
CAAGAAACTCAAGAAGGTCGGACCTACTTAACATTCACCTAAACCGCTAGCTTCGATCTAATACA
Found at i:3771387 original size:176 final size:177
Alignment explanation
Indices: 3771089--3771442 Score: 656
Period size: 176 Copynumber: 2.0 Consensus size: 177
3771079 TTTTCGATAA
3771089 ATACCAGTAAGCAGCCCCTGGTTTCTTATTTATGTAACCTGTTGGGAAAATGCAGCAAACAGATC
1 ATACCAGTAAGCAGCCCCTGGTTTCTTATTTATGTAACCTGTTGGGAAAATGCAGCAAACAGATC
* * *
3771154 ATCAATATCAATTTTTCATATCGATTGCGTGCACGGTAATCCATGTTTTCATGCATCTTTATGTC
66 ATCAATATCAATTTTTCATATCAATTGCATGCACAGTAATCCATGTTTTCATGCATCTTTATGTC
3771219 TAAATGTGTCAT-CATGCAAGAGACTGTGAGAGGGGAGATGTTTTCC
131 TAAATGTGTCATGCATGCAAGAGACTGTGAGAGGGGAGATGTTTTCC
*
3771265 ATACCAGTAAGCAGCCTCTGGTTTCTTATTTATGTAACCTGTTGGGAAAATGCAGCAAACAGATC
1 ATACCAGTAAGCAGCCCCTGGTTTCTTATTTATGTAACCTGTTGGGAAAATGCAGCAAACAGATC
*
3771330 ATCAATATCAATTTTTCATATCAATTGCATGCACAGTAATCCATGTTTTCGTGCATCTTTATGTC
66 ATCAATATCAATTTTTCATATCAATTGCATGCACAGTAATCCATGTTTTCATGCATCTTTATGTC
3771395 TAAATGTGTCATGCATGCAAGAGACTGTGAGAGGGGAGATGTTTTCC
131 TAAATGTGTCATGCATGCAAGAGACTGTGAGAGGGGAGATGTTTTCC
3771442 A
1 A
3771443 CACCTTGTCT
Statistics
Matches: 172, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
176 137 0.80
177 35 0.20
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (177 bp):
ATACCAGTAAGCAGCCCCTGGTTTCTTATTTATGTAACCTGTTGGGAAAATGCAGCAAACAGATC
ATCAATATCAATTTTTCATATCAATTGCATGCACAGTAATCCATGTTTTCATGCATCTTTATGTC
TAAATGTGTCATGCATGCAAGAGACTGTGAGAGGGGAGATGTTTTCC
Found at i:3783348 original size:28 final size:28
Alignment explanation
Indices: 3783308--3783361 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3783298 TACAGTTTGG
3783308 TACATGTACTTTTTTGGGTCCATTTTCA
1 TACATGTACTTTTTTGGGTCCATTTTCA
3783336 TACATGTACTTTTTTGGGTCCATTTT
1 TACATGTACTTTTTTGGGTCCATTTT
3783362 GATAGATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.52
Consensus pattern (28 bp):
TACATGTACTTTTTTGGGTCCATTTTCA
Found at i:3788493 original size:13 final size:14
Alignment explanation
Indices: 3788477--3788508 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3788467 CTTTTTCGGA
3788477 TTTATTTTAT-TTT
1 TTTATTTTATATTT
3788490 TTTATTTTATATTT
1 TTTATTTTATATTT
3788504 TTTAT
1 TTTAT
3788509 CGGGATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATATTT
Found at i:3789368 original size:12 final size:12
Alignment explanation
Indices: 3789351--3789379 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3789341 CACATCAACA
3789351 TTTAATTAATTT
1 TTTAATTAATTT
3789363 TTTAATTAATTT
1 TTTAATTAATTT
3789375 TTTAA
1 TTTAA
3789380 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTAATTAATTT
Found at i:3789390 original size:9 final size:9
Alignment explanation
Indices: 3789373--3789416 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
3789363 TTTAATTAAT
*
3789373 TTTTTAAAA
1 TTTTAAAAA
3789382 TTTTAAAAA
1 TTTTAAAAA
** *
3789391 CATTAACAA
1 TTTTAAAAA
3789400 TTTTAAAAA
1 TTTTAAAAA
3789409 TTTTAAAA
1 TTTTAAAA
3789417 GTTAATTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:3789414 original size:18 final size:17
Alignment explanation
Indices: 3789374--3789416 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
3789364 TTAATTAATT
3789374 TTTTAAAATTTTAAAAA
1 TTTTAAAATTTTAAAAA
**
3789391 CATTAACAATTTTAAAAA
1 TTTTAA-AATTTTAAAAA
3789409 TTTTAAAA
1 TTTTAAAA
3789417 GTTAATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAATTTTAAAAA
Found at i:3791043 original size:17 final size:16
Alignment explanation
Indices: 3791023--3791061 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
3791013 AAAAAATCAA
*
3791023 ATAAAATAATAAATTTT
1 ATAAAA-AATAAAATTT
3791040 ATAATAAAATAAAATTT
1 ATAA-AAAATAAAATTT
3791057 ATAAA
1 ATAAA
3791062 CAACACCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.85
18 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAAAATAAAATTT
Found at i:3795901 original size:3 final size:3
Alignment explanation
Indices: 3795893--3795927 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3795883 TTGTTCCTAC
3795893 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3795928 GTCTTGAAAG
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):
TAT
Found at i:3797939 original size:96 final size:94
Alignment explanation
Indices: 3797824--3798035 Score: 221
Period size: 96 Copynumber: 2.2 Consensus size: 94
3797814 AGTTTAGTTT
* * * * * *
3797824 AAAAGGTGATATTCATATAAATTCGGATTTAGTC-AAGCTGTTATATTTGTGTAAATCTGGG-TT
1 AAAAAGTGATATTCGTATAAATTCGGATTAAGTCGAA-CTGCTAAATTTGTATAAAT-TGGGATT
* * *
3797887 TAGTGTAGTTCATTTATATATATATATTTCTAA
64 TAGTCTAGTTCATTCATATA-ACATATTT-TAA
* *
3797920 AAAAAGTGATATTCGTATAAATTTGGATTAAGTCGAATTGCTAAATTTGTATAAATTGGGATTTA
1 AAAAAGTGATATTCGTATAAATTCGGATTAAGTCGAACTGCTAAATTTGTATAAATTGGGATTTA
** * *
3797985 GTCTAGTTGGTTCATATAACCTCTTTTAA
66 GTCTAGTTCATTCATATAACATATTTTAA
* *
3798014 AATAAGTGATATTCGTTTAAAT
1 AAAAAGTGATATTCGTATAAAT
3798036 CTGGGTTTAA
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
94 23 0.24
95 9 0.09
96 63 0.65
97 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.42
Consensus pattern (94 bp):
AAAAAGTGATATTCGTATAAATTCGGATTAAGTCGAACTGCTAAATTTGTATAAATTGGGATTTA
GTCTAGTTCATTCATATAACATATTTTAA
Found at i:3803746 original size:20 final size:20
Alignment explanation
Indices: 3803717--3803754 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3803707 ACAGTTGGAT
*
3803717 TTAAATTTAAAATTAAAAAA
1 TTAAAATTAAAATTAAAAAA
3803737 TTAAAATTAAAATTAAAA
1 TTAAAATTAAAATTAAAA
3803755 TTTATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAAATTAAAATTAAAAAA
Found at i:3803748 original size:12 final size:12
Alignment explanation
Indices: 3803717--3803756 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3803707 ACAGTTGGAT
*
3803717 TTAAATTTAAAA
1 TTAAAATTAAAA
3803729 TTAAAAAATTAAAA
1 TT--AAAATTAAAA
3803743 TTAAAATTAAAA
1 TTAAAATTAAAA
3803755 TT
1 TT
3803757 TATGAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 14 0.56
14 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAATTAAAA
Found at i:3811136 original size:2 final size:2
Alignment explanation
Indices: 3811129--3811159 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3811119 GATGATACTT
3811129 TA TA TA 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 TA TA TA T
3811160 TTTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3813048 original size:19 final size:18
Alignment explanation
Indices: 3813026--3813108 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 18
3813016 ATTATGAAAA
3813026 ATAAAAATCAATAAAATTT
1 ATAAAAAT-AATAAAATTT
* *
3813045 ATAAAAATTATTAAATTT
1 ATAAAAATAATAAAATTT
*
3813063 AATAAAAAGGAATTAAAATTT
1 -ATAAAAA-TAA-TAAAATTT
*
3813084 ATTAACAATTAA-AAAA-TT
1 A-TAA-AAATAATAAAATTT
3813102 ATAAAAA
1 ATAAAAA
3813109 ATTTAAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.04
17 3 0.06
18 11 0.22
19 19 0.37
20 2 0.04
21 12 0.24
22 2 0.04
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAAAAATAATAAAATTT
Found at i:3813060 original size:18 final size:18
Alignment explanation
Indices: 3813039--3813124 Score: 59
Period size: 17 Copynumber: 4.7 Consensus size: 18
3813029 AAAATCAATA
3813039 AAATTTATAAAAATTATT
1 AAATTTATAAAAATTATT
**
3813057 AAATTTAATAAAAAGGAATT
1 AAATTT-ATAAAAA-TTATT
* *
3813077 AAAATTTATTAACAATTA-A
1 -AAATTTA-TAAAAATTATT
* *
3813096 AAAATTATAAAAAAT-TT
1 AAATTTATAAAAATTATT
*
3813113 AAAATTATAAAA
1 AAATTTATAAAA
3813125 TTTTATAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
17 18 0.34
18 12 0.23
19 7 0.13
20 5 0.09
21 11 0.21
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (18 bp):
AAATTTATAAAAATTATT
Found at i:3813125 original size:25 final size:26
Alignment explanation
Indices: 3813085--3813135 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
3813075 TTAAAATTTA
3813085 TTAACAATTAAAAAATTATAAAAAAT
1 TTAACAATTAAAAAATTATAAAAAAT
* * *
3813111 TTAA-AATTATAAAATTTTATAAAAT
1 TTAACAATTAAAAAATTATAAAAAAT
3813136 AGTAAGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TTAACAATTAAAAAATTATAAAAAAT
Found at i:3813161 original size:28 final size:26
Alignment explanation
Indices: 3813095--3813189 Score: 86
Period size: 26 Copynumber: 3.5 Consensus size: 26
3813085 TTAACAATTA
* *
3813095 AAAAATTATAAAAAATTTAAAATT-AT
1 AAAAATT-TATAAAATATAAAATTCAT
*
3813121 AAAATTTTATAAAATAGTAAGAAATTCAT
1 AAAAATTTATAAAATA-T-A-AAATTCAT
*
3813150 AAAAATTT-TAAAATATAAAATTCTT
1 AAAAATTTATAAAATATAAAATTCAT
*
3813175 AAAAAAATTATAAAA
1 -AAAAATTTATAAAA
3813190 ATTATTGTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
25 14 0.25
26 15 0.26
27 7 0.12
28 12 0.21
29 9 0.16
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAAATTTATAAAATATAAAATTCAT
Found at i:3813189 original size:9 final size:9
Alignment explanation
Indices: 3813012--3813194 Score: 78
Period size: 10 Copynumber: 20.0 Consensus size: 9
3813002 ACACGTGGAA
3813012 AAAAATTAT
1 AAAAATTAT
*
3813021 GAAAA--AT
1 AAAAATTAT
*
3813028 AAAAATCAAT
1 AAAAAT-TAT
*
3813038 AAAATTTAT
1 AAAAATTAT
3813047 AAAAATTAT
1 AAAAATTAT
* *
3813056 TAAATTTAAT
1 AAAAATT-AT
**
3813066 AAAAAGGAATT
1 AAAAA-TTA-T
*
3813077 AAAATTTATT
1 AAAAATTA-T
*
3813087 AACAATTA-
1 AAAAATTAT
3813095 AAAAATTAT
1 AAAAATTAT
3813104 AAAAAATT-T
1 -AAAAATTAT
3813113 -AAAATTAT
1 AAAAATTAT
*
3813121 -AAAATTTT
1 AAAAATTAT
3813129 ATAAAA-TAGT
1 A-AAAATTA-T
3813139 AAGAAATTCAT
1 AA-AAATT-AT
3813150 AAAAATT-T
1 AAAAATTAT
*
3813158 TAAAA-TAT
1 AAAAATTAT
* *
3813166 AAAATTCTTAA
1 AAAA--ATTAT
3813177 AAAAATTAT
1 AAAAATTAT
3813186 AAAAATTAT
1 AAAAATTAT
3813195 TGTACCAAAG
Statistics
Matches: 130, Mismatches: 25, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
7 13 0.10
8 24 0.18
9 34 0.26
10 43 0.33
11 15 0.12
12 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3813432 original size:20 final size:18
Alignment explanation
Indices: 3813409--3813471 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
3813399 AATTTTAAAT
3813409 ATTTTTATATTTTTATTAG
1 ATTTTTATATTTTTATT-G
* *
3813428 AATTTAATAATTTTTATTG
1 ATTTTTAT-ATTTTTATTG
* *
3813447 TTTTTTAT-TTTTTATAG
1 ATTTTTATATTTTTATTG
*
3813464 TTTTTTAT
1 ATTTTTAT
3813472 CACATATCAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
17 16 0.43
19 12 0.32
20 9 0.24
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (18 bp):
ATTTTTATATTTTTATTG
Found at i:3813460 original size:17 final size:17
Alignment explanation
Indices: 3813438--3813471 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3813428 AATTTAATAA
*
3813438 TTTTTATTGTTTTTTAT
1 TTTTTATAGTTTTTTAT
3813455 TTTTTATAGTTTTTTAT
1 TTTTTATAGTTTTTTAT
3813472 CACATATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTATAGTTTTTTAT
Found at i:3815717 original size:30 final size:30
Alignment explanation
Indices: 3815659--3815718 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3815649 TTCCCGAGCC
* *
3815659 TAGGGGCAAAAGTGTAATTATGTAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
3815689 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
3815719 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:3822131 original size:13 final size:13
Alignment explanation
Indices: 3822113--3822137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3822103 GATTGTTATA
3822113 ACTAAATTGCATG
1 ACTAAATTGCATG
3822126 ACTAAATTGCAT
1 ACTAAATTGCAT
3822138 TAATTTAGTT
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:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
ACTAAATTGCATG
Found at i:3823028 original size:38 final size:39
Alignment explanation
Indices: 3822978--3823189 Score: 192
Period size: 46 Copynumber: 4.9 Consensus size: 39
3822968 CTGATATGAA
*
3822978 ATGTGTAAGACCATTGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
3823017 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
3823055 ATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAG
1 --AT-----GTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----T--G
* *
3823108 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCGTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
3823147 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
3823190 ATGACAGAAA
Statistics
Matches: 146, Mismatches: 5, Indels: 37
0.78 0.03 0.20
Matches are distributed among these distances:
38 37 0.25
39 1 0.01
41 5 0.03
44 1 0.01
46 98 0.67
51 3 0.02
53 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (39 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:3823085 original size:46 final size:46
Alignment explanation
Indices: 3823017--3823233 Score: 292
Period size: 46 Copynumber: 4.7 Consensus size: 46
3823007 TGGCAACCTG
*
3823017 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* * *
3823063 CGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* *
3823109 TGTGTAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* ** *
3823155 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAA
* * * *
3823201 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
3823234 TCACGTCAAA
Statistics
Matches: 153, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 152 0.99
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.21
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:3823340 original size:13 final size:13
Alignment explanation
Indices: 3823322--3823351 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3823312 TCAGATGACG
3823322 AATGGTTATATGA
1 AATGGTTATATGA
*
3823335 AATGGTTGTATGA
1 AATGGTTATATGA
3823348 AATG
1 AATG
3823352 TTTACAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (13 bp):
AATGGTTATATGA
Found at i:3823539 original size:23 final size:25
Alignment explanation
Indices: 3823494--3823540 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3823484 AATAAATATA
*
3823494 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
3823519 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
3823541 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:3825962 original size:19 final size:20
Alignment explanation
Indices: 3825916--3825962 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3825906 TATATATCAC
3825916 ATCAATAAATAATTTAAAAATT
1 ATCAA-AAATAATTTAAAAA-T
*
3825938 AT-AAAAATATTTTAAAAA-
1 ATCAAAAATAATTTAAAAAT
3825956 ATCAAAA
1 ATCAAAA
3825963 TTTTCCCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.09
19 4 0.17
20 13 0.57
21 2 0.09
22 2 0.09
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
ATCAAAAATAATTTAAAAAT
Found at i:3827493 original size:17 final size:16
Alignment explanation
Indices: 3827467--3827504 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3827457 CATGTCTTTA
*
3827467 ATATAAAAAATACATAT
1 ATATATAAAATA-ATAT
3827484 ATATATAAAATAATAT
1 ATATATAAAATAATAT
3827500 A-ATAT
1 ATATAT
3827505 TGAAACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATAAAATAATAT
Found at i:3828243 original size:9 final size:8
Alignment explanation
Indices: 3828222--3828251 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3828212 AATCTGATTT
3828222 TTTTTATA
1 TTTTTATA
3828230 TTTTTATA
1 TTTTTATA
3828238 TGTTTTATA
1 T-TTTTATA
3828247 TTTTT
1 TTTTT
3828252 GCACTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (8 bp):
TTTTTATA
Found at i:3840648 original size:23 final size:23
Alignment explanation
Indices: 3840605--3840649 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3840595 TAACGATTTA
* *
3840605 ATATTTTATTTAATAGCTATTCT
1 ATATTTTATTTAACAGATATTCT
*
3840628 ATATTTTATTTAACATATATTC
1 ATATTTTATTTAACAGATATTC
3840650 CCATCAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTTTATTTAACAGATATTCT
Found at i:3842893 original size:18 final size:19
Alignment explanation
Indices: 3842867--3842905 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3842857 AATATGTTCT
*
3842867 AAATTACATAATA-TATAA
1 AAATAACATAATATTATAA
3842885 AAATAACATAATATTATAA
1 AAATAACATAATATTATAA
3842904 AA
1 AA
3842906 TATTATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAACATAATATTATAA
Found at i:3843251 original size:31 final size:30
Alignment explanation
Indices: 3843215--3843290 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 30
3843205 ATATCAAAAT
3843215 TATATATAAATTTTGATTTAATGTATAT-TG
1 TATATATAAATTTTGATTT-ATGTATATATG
* *
3843245 TCATATATGAA-TTT--TTTATTTATATATG
1 T-ATATATAAATTTTGATTTATGTATATATG
3843273 T-TATATAAATTTTGATTT
1 TATATATAAATTTTGATTT
3843291 TATATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
26 7 0.18
27 10 0.26
28 6 0.16
29 3 0.08
30 4 0.11
31 8 0.21
ACGTcount: A:0.34, C:0.01, G:0.08, T:0.57
Consensus pattern (30 bp):
TATATATAAATTTTGATTTATGTATATATG
Found at i:3852889 original size:21 final size:21
Alignment explanation
Indices: 3852851--3852890 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3852841 GGTGTTCATG
*
3852851 GGCCGGGTTCTGGTCGGGCCT
1 GGCCGGGTTCTAGTCGGGCCT
3852872 GGCCGGGTTC-AGTCCGGGC
1 GGCCGGGTTCTAGT-CGGGC
3852891 TCAACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.03, C:0.30, G:0.47, T:0.20
Consensus pattern (21 bp):
GGCCGGGTTCTAGTCGGGCCT
Found at i:3853039 original size:13 final size:12
Alignment explanation
Indices: 3853017--3853050 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
3853007 GGCCCGCCCG
3853017 TATTAATTTTTTA
1 TATT-ATTTTTTA
3853030 TATTA-TTTTTA
1 TATTATTTTTTA
3853041 TATTATTTTT
1 TATTATTTTT
3853051 AAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 5 0.25
13 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:3853056 original size:13 final size:11
Alignment explanation
Indices: 3853024--3853051 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3853014 CCGTATTAAT
3853024 TTTTTATATTA
1 TTTTTATATTA
3853035 TTTTTATATTA
1 TTTTTATATTA
3853046 TTTTTA
1 TTTTTA
3853052 AATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:3861682 original size:27 final size:27
Alignment explanation
Indices: 3861651--3861713 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
3861641 AGATATTTTG
*
3861651 ATATTTTATAATT-ATTTATTTAGAT-AA
1 ATATTTTATAATTAATAT-TTTA-ATAAA
3861678 ATATTATT-TAATTAATATTTTAATAAA
1 ATATT-TTATAATTAATATTTTAATAAA
3861705 ATATTTTAT
1 ATATTTTAT
3861714 TAGTATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
26 4 0.13
27 22 0.71
28 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATATTTTATAATTAATATTTTAATAAA
Found at i:3861722 original size:11 final size:11
Alignment explanation
Indices: 3861706--3861730 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3861696 TTTAATAAAA
3861706 TATTTTATTAG
1 TATTTTATTAG
3861717 TATTTTATTAG
1 TATTTTATTAG
3861728 TAT
1 TAT
3861731 ATAAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTTATTAG
Found at i:3866299 original size:46 final size:45
Alignment explanation
Indices: 3866232--3866367 Score: 182
Period size: 46 Copynumber: 3.0 Consensus size: 45
3866222 AGTGTGCTAT
*
3866232 CTGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATA-GAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
*
3866278 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
1 CTGATA-GAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
* * * * *
3866324 ATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATAG-AAATGTGTAAGACCATGGTTGAAAGATACTATGGCA
3866368 TCATGTCAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 79 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (45 bp):
CTGATAGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
Found at i:3871083 original size:43 final size:41
Alignment explanation
Indices: 3871035--3871258 Score: 267
Period size: 40 Copynumber: 5.5 Consensus size: 41
3871025 TCGGATGATG
3871035 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC--GTAGTTACTATA
*
3871078 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC--GTAGTTACTATA
* * * *
3871121 CCCGGGCTAAGTTCCGAAGGCATTTGT-CCTAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGTAGTTACTATA
* ** *
3871161 TCCGGGCTAAGTCTCGAAGGCATTCATGC-TAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGTAGTTACTATA
* *
3871201 TCCGGGCTAAGCCCCGAAGGCATTTGTGCGT-GTTGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGTAGTTACTATA
* *
3871241 TCC-GGCTAAATCCTGAAG
1 TCCGGGCTAAGTCCCGAAG
3871259 ACACTTGGGT
Statistics
Matches: 159, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 12 0.08
40 77 0.48
41 2 0.01
42 1 0.01
43 67 0.42
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.27
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGTAGTTACTATA
Found at i:3874359 original size:2 final size:2
Alignment explanation
Indices: 3874354--3874386 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3874344 ATATATATAT
3874354 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3874387 AAACTCCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3875582 original size:18 final size:18
Alignment explanation
Indices: 3875554--3875595 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
3875544 GGTAAGAAAG
3875554 AGATAGAGTCAATTCCTAT
1 AGAT-GAGTCAATTCCTAT
3875573 AGATGAGTCAATTCCTAT
1 AGATGAGTCAATTCCTAT
3875591 AGATG
1 AGATG
3875596 GGGTTATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (18 bp):
AGATGAGTCAATTCCTAT
Found at i:3878805 original size:21 final size:21
Alignment explanation
Indices: 3878779--3878819 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3878769 ATCTGCTCAA
* *
3878779 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3878800 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3878820 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3882905 original size:51 final size:51
Alignment explanation
Indices: 3882816--3882921 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 51
3882806 TGTTGATAGA
**
3882816 AAATATTACGGGTTAAATATGTTAAATCATGATTAAATT-G-ACGAAATGTGT
1 AAATATTACGGGTTAAATATGTTAAATCATGACCAAATTAGTA-G-AATGTGT
* * *
3882867 AAATGTTATGGGTTAAATTTGTTAAATCAAT-ACCAAATTAGTAGAATGTGT
1 AAATATTACGGGTTAAATATGTTAAATC-ATGACCAAATTAGTAGAATGTGT
3882918 AAAT
1 AAAT
3882922 TTTGAGGGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
51 42 0.89
52 4 0.09
53 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (51 bp):
AAATATTACGGGTTAAATATGTTAAATCATGACCAAATTAGTAGAATGTGT
Found at i:3887304 original size:22 final size:21
Alignment explanation
Indices: 3887272--3887318 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
3887262 AACTTTCAAA
* *
3887272 TTTAGGATCTTGGGTTTAGTGG
1 TTTAGGATCTTAGATTTA-TGG
*
3887294 TTTAGGGTCTTAGATTTATGG
1 TTTAGGATCTTAGATTTATGG
3887315 TTTA
1 TTTA
3887319 TAATTTTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.17, C:0.04, G:0.30, T:0.49
Consensus pattern (21 bp):
TTTAGGATCTTAGATTTATGG
Found at i:3887533 original size:17 final size:18
Alignment explanation
Indices: 3887491--3887530 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
3887481 ATACTAGTTT
3887491 TTTTTATTTCTTATATTA
1 TTTTTATTTCTTATATTA
3887509 TTTTTATTTC-TATTATTA
1 TTTTTATTTCTTA-TATTA
3887527 TTTT
1 TTTT
3887531 ATTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTATTTCTTATATTA
Found at i:3887540 original size:12 final size:11
Alignment explanation
Indices: 3887488--3887540 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
3887478 AGAATACTAG
3887488 TTTT-TTTTAT
1 TTTTATTTTAT
*
3887498 TTCTTATATTAT
1 TT-TTATTTTAT
3887510 TTTTATTTCTAT
1 TTTTATTT-TAT
*
3887522 TATTATTTTAT
1 TTTTATTTTAT
3887533 TATTTATT
1 T-TTTATT
3887541 GTCTATTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 2 0.06
11 11 0.31
12 22 0.63
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTTAT
Done.