Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 5 of 322
Found at i:1134994 original size:32 final size:30
Alignment explanation
Indices: 1134938--1135003 Score: 71
Period size: 32 Copynumber: 2.1 Consensus size: 30
1134928 TTAATTAATT
* *
1134938 TTTTTAAAATTTTTGTGAGATTAATGAGAA
1 TTTTTAAAATTTTAGTGAGATTAATGAAAA
*
1134968 TTTTTAAATATTTTAAGTGA-ACTTAATTAAAA
1 TTTTTAAA-ATTTT-AGTGAGA-TTAATGAAAA
1135000 TTTT
1 TTTT
1135004 CATAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 8 0.27
31 6 0.20
32 16 0.53
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.50
Consensus pattern (30 bp):
TTTTTAAAATTTTAGTGAGATTAATGAAAA
Found at i:1138467 original size:25 final size:28
Alignment explanation
Indices: 1138432--1138482 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
1138422 TTGTTAAAAC
1138432 TCTTGTAAAAG-AAACTC-AAGAGAAAT
1 TCTTGTAAAAGAAAACTCAAAGAGAAAT
1138458 TCTTG-AAAAGAAAACTCAAAGAGAA
1 TCTTGTAAAAGAAAACTCAAAGAGAA
1138483 TTTATTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.22
26 11 0.48
27 7 0.30
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.20
Consensus pattern (28 bp):
TCTTGTAAAAGAAAACTCAAAGAGAAAT
Found at i:1138977 original size:15 final size:15
Alignment explanation
Indices: 1138957--1138986 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1138947 TATGAAGGCA
1138957 TCTCAACCCAGAAAT
1 TCTCAACCCAGAAAT
1138972 TCTCAACCCAGAAAT
1 TCTCAACCCAGAAAT
1138987 ACCAGGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (15 bp):
TCTCAACCCAGAAAT
Found at i:1147835 original size:41 final size:41
Alignment explanation
Indices: 1147761--1147847 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
1147751 ACCAGCTCTT
1147761 AGCCTGCTAGACCTATAGTCCGAAATATATCACCGACATTA
1 AGCCTGCTAGACCTATAGTCCGAAATATATCACCGACATTA
* * * * *
1147802 AGCCTGCTAGACGTA-AGGTCTGAATTATTTCACCGGCATTA
1 AGCCTGCTAGACCTATA-GTCCGAAATATATCACCGACATTA
1147843 AGCCT
1 AGCCT
1147848 ACTACGCACA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.03
41 39 0.98
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACCTATAGTCCGAAATATATCACCGACATTA
Found at i:1148488 original size:21 final size:21
Alignment explanation
Indices: 1148462--1148503 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1148452 TCATAAAATC
1148462 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
1148483 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
1148504 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:1152048 original size:15 final size:15
Alignment explanation
Indices: 1152030--1152076 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1152020 TAAAAGGAAT
**
1152030 AATAAAATACCACAA
1 AATAAAATAAAACAA
*
1152045 AATAAAATAAAATAA
1 AATAAAATAAAACAA
1152060 AATAAAATAAAA-AA
1 AATAAAATAAAACAA
1152074 AAT
1 AAT
1152077 GAGATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (15 bp):
AATAAAATAAAACAA
Found at i:1152051 original size:5 final size:5
Alignment explanation
Indices: 1152043--1152076 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1152033 AAAATACCAC
1152043 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1152077 GAGATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1155376 original size:20 final size:20
Alignment explanation
Indices: 1155330--1155378 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1155320 TATTTCTTGC
*
1155330 ATAAATATTTATATATATAT
1 ATAAATTTTTATATATATAT
* *
1155350 TTGAATTTTTATATATCA-AT
1 ATAAATTTTTATATAT-ATAT
1155370 ATAAATTTT
1 ATAAATTTT
1155379 CTCTTTGGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATTTTTATATATATAT
Found at i:1161044 original size:44 final size:45
Alignment explanation
Indices: 1160995--1161088 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
1160985 TATTACAACA
* * *
1160995 TCATTCTATTTAATCAAACACA-AGAA-TACTATTACAGTTCTATT
1 TCATTCCATTCAACCAAACA-ATAGAATTACTATTACAGTTCTATT
*
1161039 TCATTCCATTCAACCAAACAATTGAATTACTATTACAGTTCTATT
1 TCATTCCATTCAACCAAACAATAGAATTACTATTACAGTTCTATT
*
1161084 CCATT
1 TCATT
1161089 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 20 0.47
45 22 0.51
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.38
Consensus pattern (45 bp):
TCATTCCATTCAACCAAACAATAGAATTACTATTACAGTTCTATT
Found at i:1161091 original size:16 final size:16
Alignment explanation
Indices: 1161070--1161124 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1161060 TTGAATTACT
1161070 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
* *
1161086 ATTACAGCTCTATTCA
1 ATTACAGTTCTATTCC
1161102 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
1161118 ATTACAG
1 ATTACAG
1161125 CAAACCAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:1161367 original size:19 final size:19
Alignment explanation
Indices: 1161330--1161413 Score: 55
Period size: 20 Copynumber: 4.3 Consensus size: 19
1161320 AGATATTTTA
*
1161330 GTAAATACATATAAA-ATTG
1 GTAAATA-ATAGAAATATTG
1161349 GTAAATAATAGAAATATTG
1 GTAAATAATAGAAATATTG
* ** * *
1161368 ATAAAGTCTTAGATATTTTG
1 GTAAA-TAATAGAAATATTG
1161388 GTAAATTCAA-AGAAATATTG
1 GTAAA-T-AATAGAAATATTG
*
1161408 ATAAAT
1 GTAAAT
1161414 TTATATAAAC
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
18 6 0.12
19 16 0.33
20 27 0.55
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.35
Consensus pattern (19 bp):
GTAAATAATAGAAATATTG
Found at i:1161414 original size:20 final size:20
Alignment explanation
Indices: 1161358--1161414 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1161348 GGTAAATAAT
* **
1161358 AGAAATATTGATAAAGTCTT
1 AGAAATATTGATAAATTCAA
* * *
1161378 AGATATTTTGGTAAATTCAA
1 AGAAATATTGATAAATTCAA
1161398 AGAAATATTGATAAATT
1 AGAAATATTGATAAATT
1161415 TATATAAACT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.37
Consensus pattern (20 bp):
AGAAATATTGATAAATTCAA
Found at i:1161428 original size:40 final size:41
Alignment explanation
Indices: 1161338--1161433 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
1161328 TAGTAAATAC
*
1161338 ATATAAAATTGGTAAA-TAATAGAAATATTGATAAAGTCTT
1 ATATAAATTTGGTAAATTAATAGAAATATTGATAAAGTCTT
* *
1161378 AGAT-ATTTTGGTAAATTCAA-AGAAATATTGATAAA-T-TT
1 ATATAAATTTGGTAAATT-AATAGAAATATTGATAAAGTCTT
1161416 ATATAAACTTTGGTAAAT
1 ATATAAA-TTTGGTAAAT
1161434 AGTTAAAGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
38 5 0.11
39 11 0.23
40 29 0.62
41 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (41 bp):
ATATAAATTTGGTAAATTAATAGAAATATTGATAAAGTCTT
Found at i:1161548 original size:20 final size:20
Alignment explanation
Indices: 1161525--1161659 Score: 73
Period size: 20 Copynumber: 6.8 Consensus size: 20
1161515 AAAGCCTCAT
1161525 AAATATTAGTAAATC-TATAG
1 AAATATTAGTAAATCGT-TAG
*
1161545 AAAT-TTTGATAAATCGTTAG
1 AAATATTAG-TAAATCGTTAG
* * *
1161565 ATATATTGGTAAATTG-TA-
1 AAATATTAGTAAATCGTTAG
* * * *
1161583 AATATTTTGGAAAAGTCCTT-G
1 AA-ATATTAGTAAA-TCGTTAG
* *
1161604 AAAATATTAGAAAATTGTTAG
1 -AAATATTAGTAAATCGTTAG
*
1161625 ATATATTAGTAAATCGTTAG
1 AAATATTAGTAAATCGTTAG
* *
1161645 ATACATTAGTAAATC
1 AAATATTAGTAAATC
1161660 CTTAAATATT
Statistics
Matches: 89, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
18 1 0.01
19 14 0.16
20 57 0.64
21 15 0.17
22 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (20 bp):
AAATATTAGTAAATCGTTAG
Found at i:1161611 original size:80 final size:80
Alignment explanation
Indices: 1161525--1161680 Score: 192
Period size: 80 Copynumber: 1.9 Consensus size: 80
1161515 AAAGCCTCAT
* * * *
1161525 AAATATTAGTAAATCT-ATAGAAAT-TTTGATAAATCGTTAGATATATTGGTAAAT-TGTAAATA
1 AAATATTAGAAAAT-TGATAGAAATATTAG-TAAATCGTTAGATACATTAGTAAATCT-TAAATA
1161587 TTTTGGAAAAGTCCTTGA
63 TTTTGGAAAAGTCCTTGA
* *
1161605 AAATATTAGAAAATTGTTAGATATATTAGTAAATCGTTAGATACATTAGTAAATCCTTAAATATT
1 AAATATTAGAAAATTGATAGAAATATTAGTAAATCGTTAGATACATTAGTAAAT-CTTAAATATT
*
1161670 TTGGTAAAGTC
65 TTGGAAAAGTC
1161681 ATACAAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
79 1 0.02
80 42 0.65
81 21 0.32
82 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (80 bp):
AAATATTAGAAAATTGATAGAAATATTAGTAAATCGTTAGATACATTAGTAAATCTTAAATATTT
TGGAAAAGTCCTTGA
Found at i:1161676 original size:20 final size:20
Alignment explanation
Indices: 1161554--1161677 Score: 81
Period size: 20 Copynumber: 6.2 Consensus size: 20
1161544 GAAATTTTGA
*
1161554 TAAATCGTTAGATATATTGG
1 TAAATCGTTAAATATATTGG
* *
1161574 TAAATTG-TAAATATTTTGG
1 TAAATCGTTAAATATATTGG
* * *
1161593 AAAAGTCCTTGAAA-ATATTAG
1 TAAA-TCGTT-AAATATATTGG
* * * *
1161614 AAAATTGTTAGATATATTAG
1 TAAATCGTTAAATATATTGG
* * *
1161634 TAAATCGTTAGATACATTAG
1 TAAATCGTTAAATATATTGG
* *
1161654 TAAATCCTTAAATATTTTGG
1 TAAATCGTTAAATATATTGG
1161674 TAAA
1 TAAA
1161678 GTCATACAAA
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
19 15 0.19
20 53 0.65
21 10 0.12
22 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.39
Consensus pattern (20 bp):
TAAATCGTTAAATATATTGG
Found at i:1161677 original size:40 final size:40
Alignment explanation
Indices: 1161527--1161677 Score: 114
Period size: 40 Copynumber: 3.8 Consensus size: 40
1161517 AGCCTCATAA
*
1161527 ATATTAGTAAATCTATAGAA-ATTTTGATAAATCGTTAGAT
1 ATATTAGTAAATCTATA-AATATTTTGGTAAATCGTTAGAT
* * * * *
1161567 ATATTGGTAAAT-TGTAAATATTTTGGAAAAGTCCTT-GAAA
1 ATATTAGTAAATCTATAAATATTTTGGTAAA-TCGTTAG-AT
* * * * *
1161607 ATATTAGAAAAT-TGTTAGATATATTAGTAAATCGTTAGAT
1 ATATTAGTAAATCT-ATAAATATTTTGGTAAATCGTTAGAT
*
1161647 ACATTAGTAAATCCT-TAAATATTTTGGTAAA
1 ATATTAGTAAAT-CTATAAATATTTTGGTAAA
1161678 GTCATACAAA
Statistics
Matches: 84, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
38 2 0.02
39 13 0.15
40 55 0.65
41 13 0.15
42 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (40 bp):
ATATTAGTAAATCTATAAATATTTTGGTAAATCGTTAGAT
Found at i:1161803 original size:20 final size:20
Alignment explanation
Indices: 1161772--1161845 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
1161762 AAATTCTCAT
* *
1161772 AAATATTAGTAAATCAATAG
1 AAATTTTAGTAAATCATTAG
* * *
1161792 AAATTTTGGTAATTCGTTAG
1 AAATTTTAGTAAATCATTAG
* * * *
1161812 ATATTTTCGTAAAACATTAA
1 AAATTTTAGTAAATCATTAG
1161832 AAATTTTAGTAAAT
1 AAATTTTAGTAAAT
1161846 TGTTAGATGT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (20 bp):
AAATTTTAGTAAATCATTAG
Found at i:1161877 original size:40 final size:40
Alignment explanation
Indices: 1161748--1161882 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 40
1161738 TGGTTAAATC
* * * * * *
1161748 TTAAAAATTTTGTTAAATTC-TCATAAATATTAGTAAATCA
1 TTAAAAATTTTG-TAAATTCGTTAGATATTTTCGTAAAACA
* *
1161788 ATAGAAATTTTGGT-AATTCGTTAGATATTTTCGTAAAACA
1 TTAAAAATTTT-GTAAATTCGTTAGATATTTTCGTAAAACA
* * *
1161828 TTAAAAATTTTAGTAAATT-GTTAGATGTTTTGGTAAAACC
1 TTAAAAATTTT-GTAAATTCGTTAGATATTTTCGTAAAACA
*
1161868 TTAACAATTTTGTAA
1 TTAAAAATTTTGTAA
1161883 GGTGTGCCTC
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 9 0.12
40 63 0.82
41 5 0.06
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (40 bp):
TTAAAAATTTTGTAAATTCGTTAGATATTTTCGTAAAACA
Found at i:1162967 original size:25 final size:24
Alignment explanation
Indices: 1162916--1162968 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1162906 GTGTGCCTCG
* *
1162916 TATTTTTTCCCAATTAAACTGTGT
1 TATTTTTTCCCAATTAAACTCTAT
*
1162940 TATTTTTTCCCAATTAGACTCTAAT
1 TATTTTTTCCCAATTAAACTCT-AT
1162965 TATT
1 TATT
1162969 CCGGGGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (24 bp):
TATTTTTTCCCAATTAAACTCTAT
Found at i:1165015 original size:24 final size:25
Alignment explanation
Indices: 1164986--1165033 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1164976 CGTTGTATTT
* *
1164986 TTTTCCTAGTTAAACTCT-ATTATA
1 TTTTCCCAATTAAACTCTGATTATA
*
1165010 TTTTCCCAATTAGACTCTGATTAT
1 TTTTCCCAATTAAACTCTGATTAT
1165034 TCTAGGGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (25 bp):
TTTTCCCAATTAAACTCTGATTATA
Found at i:1167587 original size:20 final size:20
Alignment explanation
Indices: 1167529--1167587 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1167519 ATATATCGAT
*
1167529 AAATCCTTAGAAATATTT-GT
1 AAATCCTTAGAAAT-TTTGGC
* *
1167549 AAATCGTTAGATATTTTGGC
1 AAATCCTTAGAAATTTTGGC
*
1167569 AAATCCTTTGAAATTTTGG
1 AAATCCTTAGAAATTTTGG
1167588 TTCAACTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
AAATCCTTAGAAATTTTGGC
Found at i:1167618 original size:20 final size:20
Alignment explanation
Indices: 1167595--1167670 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 20
1167585 TGGTTCAACT
*
1167595 TTAGAAATATTGGCAATTTA
1 TTAGAAATATTGGCAAATTA
* * * * *
1167615 TTAGATACATTGGTAAGTTC
1 TTAGAAATATTGGCAAATTA
* *
1167635 TTAGAAAT-TTGGTAAATTG
1 TTAGAAATATTGGCAAATTA
* *
1167654 TTAGATATTTTGGCAAA
1 TTAGAAATATTGGCAAA
1167671 ATCATAGAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 16 0.36
20 28 0.64
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
TTAGAAATATTGGCAAATTA
Found at i:1167648 original size:19 final size:19
Alignment explanation
Indices: 1167624--1167685 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1167614 ATTAGATACA
*
1167624 TTGGTAAGTTCTTAGAAAT
1 TTGGTAAATTCTTAGAAAT
* *
1167643 TTGGTAAATTGTTAGATATT
1 TTGGTAAATTCTTAGA-AAT
* * *
1167663 TTGGCAAAATCATAGAAAT
1 TTGGTAAATTCTTAGAAAT
1167682 TTGG
1 TTGG
1167686 GTAATTGTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (19 bp):
TTGGTAAATTCTTAGAAAT
Found at i:1167848 original size:20 final size:20
Alignment explanation
Indices: 1167781--1167855 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
1167771 TGGCAAATTG
* *
1167781 TTAGATGTATTGGT-TAGTTC
1 TTAGATATATTGGTATA-TCC
* * * *
1167801 TTAGAAATATTAGTAAATCG
1 TTAGATATATTGGTATATCC
*
1167821 TTAAATATATTGGTATATCC
1 TTAGATATATTGGTATATCC
*
1167841 TTAGATATTTTGGTA
1 TTAGATATATTGGTA
1167856 AAGCTGTTTA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 40 0.98
21 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.45
Consensus pattern (20 bp):
TTAGATATATTGGTATATCC
Found at i:1167857 original size:40 final size:40
Alignment explanation
Indices: 1167762--1167857 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 40
1167752 GAAAAATACA
* * * * * *
1167762 TAGAAAATTTGGCAAATTGTTAGATGTATTGGTTAGTTCT
1 TAGAAATTTTGGTAAATCGTTAAATATATTGGTTAGTCCT
* *
1167802 TAGAAATATTAGTAAATCGTTAAATATATTGGTATA-TCCT
1 TAGAAATTTTGGTAAATCGTTAAATATATTGGT-TAGTCCT
*
1167842 TAGATATTTTGGTAAA
1 TAGAAATTTTGGTAAA
1167858 GCTGTTTATT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
40 42 0.95
41 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (40 bp):
TAGAAATTTTGGTAAATCGTTAAATATATTGGTTAGTCCT
Found at i:1168514 original size:22 final size:22
Alignment explanation
Indices: 1168474--1168529 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1168464 AATAAAATTG
*
1168474 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
1168494 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
1168516 TATTAATAATTTAT
1 AAATAATAAATTAT
1168530 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:1175536 original size:10 final size:10
Alignment explanation
Indices: 1175501--1175600 Score: 66
Period size: 10 Copynumber: 10.1 Consensus size: 10
1175491 AAATAAATTC
1175501 TATAAAAACAT
1 TATAAAAAC-T
1175512 T-TAAAAA-T
1 TATAAAAACT
*
1175520 TCTTAAAAACT
1 T-ATAAAAACT
*
1175531 TATAAAAAAT
1 TATAAAAACT
* *
1175541 CATAAAAA-A
1 TATAAAAACT
*
1175550 TATTAAAA-T
1 TATAAAAACT
*
1175559 TGATATAAACT
1 T-ATAAAAACT
1175570 TATAAAAAC-
1 TATAAAAACT
*
1175579 TATAAAAAAAT
1 TAT-AAAAACT
1175590 TATAAAAACT
1 TATAAAAACT
1175600 T
1 T
1175601 GAACCAGACT
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
8 2 0.03
9 10 0.14
10 50 0.71
11 8 0.11
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (10 bp):
TATAAAAACT
Found at i:1175547 original size:19 final size:19
Alignment explanation
Indices: 1175525--1175577 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
1175515 AAAATTCTTA
1175525 AAAACTTATAAAAAATCAT
1 AAAACTTATAAAAAATCAT
** * * *
1175544 AAAAAATATTAAAATTGAT
1 AAAACTTATAAAAAATCAT
1175563 ATAAACTTATAAAAA
1 A-AAACTTATAAAAA
1175578 CTATAAAAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAACTTATAAAAAATCAT
Found at i:1175558 original size:39 final size:38
Alignment explanation
Indices: 1175501--1175591 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 38
1175491 AAATAAATTC
*
1175501 TATAAAAACAT-TTAAAAATTCTTAAAAACTTATAAAAAA
1 TATAAAAA-ATATT-AAAATTCATAAAAACTTATAAAAAA
* * *
1175540 TCATAAAAAATATTAAAATTGATATAAACTTATAAAAAC
1 T-ATAAAAAATATTAAAATTCATAAAAACTTATAAAAAA
1175579 TATAAAAAA-ATTA
1 TATAAAAAATATTA
1175592 TAAAAACTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 4 0.09
38 8 0.17
39 25 0.54
40 9 0.20
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.31
Consensus pattern (38 bp):
TATAAAAAATATTAAAATTCATAAAAACTTATAAAAAA
Found at i:1176288 original size:27 final size:26
Alignment explanation
Indices: 1176249--1176325 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 26
1176239 TTTTTATAGT
1176249 TTTTATAATTTTTTTTATCAATTTTAATA
1 TTTT-TAA-TTTTTTTAT-AATTTTAATA
*
1176278 TTTTTAA-TTTTTAATAATTTTAATA
1 TTTTTAATTTTTTTATAATTTTAATA
* *
1176303 TATTTTTATTATTTTATAATTTT
1 T-TTTTAATTTTTTTATAATTTT
1176326 TTATGATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 11 0.26
26 12 0.29
27 12 0.29
28 3 0.07
29 4 0.10
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTAATTTTTTTATAATTTTAATA
Found at i:1176297 original size:10 final size:9
Alignment explanation
Indices: 1176239--1176336 Score: 60
Period size: 10 Copynumber: 10.6 Consensus size: 9
1176229 TTTTTTTATG
*
1176239 TTTTTATAG
1 TTTTTATAA
1176248 TTTTTATAA
1 TTTTTATAA
1176257 TTTTTTTTATCAA
1 ---TTTTTAT-AA
*
1176270 TTTTAAT-A
1 TTTTTATAA
1176278 -TTTT-TAA
1 TTTTTATAA
1176285 TTTTTAATAA
1 TTTTT-ATAA
*
1176295 TTTTAATATA
1 TTTTTATA-A
*
1176305 TTTTTATTA
1 TTTTTATAA
1176314 -TTTTATAA
1 TTTTTATAA
*
1176322 TTTTTTATGA
1 -TTTTTATAA
1176332 TTTTT
1 TTTTT
1176337 TTCTGATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
6 1 0.01
7 4 0.06
8 12 0.17
9 17 0.24
10 27 0.39
12 7 0.10
13 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1176334 original size:27 final size:26
Alignment explanation
Indices: 1176259--1176336 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
1176249 TTTTATAATT
*
1176259 TTTTTTATCAA-TTTTAATATTTTTAA
1 TTTTTTAT-AATTTTTTATATTTTTAA
* *
1176285 TTTTTAATAATTTTAATATATTTTT-A
1 TTTTTTATAATTTT-TTATATTTTTAA
1176311 TTATTTTATAATTTTTTATGATTTTT
1 TT-TTTTATAATTTTTTAT-ATTTTT
1176337 TTCTGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
25 2 0.05
26 16 0.37
27 25 0.58
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (26 bp):
TTTTTTATAATTTTTTATATTTTTAA
Found at i:1176336 original size:19 final size:19
Alignment explanation
Indices: 1176230--1176336 Score: 57
Period size: 18 Copynumber: 5.8 Consensus size: 19
1176220 TTTGCTAGAT
*
1176230 TTTTTTATG-TTTTTATAG
1 TTTTTTATGATTTTTATAA
**
1176248 TTTTTATAATTTTTTTTATCAA
1 TTTTT-T-ATGATTTTTAT-AA
*
1176270 -TTTTAAT-A-TTTT-TAA
1 TTTTTTATGATTTTTATAA
* * *
1176285 TTTTTAATAATTTTAAT-A
1 TTTTTTATGATTTTTATAA
*
1176303 TATTTTTATTA-TTTTATAA
1 T-TTTTTATGATTTTTATAA
1176322 TTTTTTATGATTTTT
1 TTTTTTATGATTTTT
1176337 TTCTGATTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
15 2 0.03
16 8 0.12
17 5 0.07
18 23 0.33
19 17 0.25
20 2 0.03
21 11 0.16
22 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTATGATTTTTATAA
Found at i:1192236 original size:51 final size:50
Alignment explanation
Indices: 1192129--1192236 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 50
1192119 TGAAAAATAA
* * *
1192129 AATACTAGGAAGACTAATTTTATATATAACCCTAATTTGTATAAAACATCC
1 AATA-TAGGAAGACTAATTTTATATATAACCATAATTTATATAAAACAGCC
* * * * * *
1192180 TATATAGGAAGAGTTAGTTTTGTATATAAGCATAATTTATATAAACCAGCC
1 AATATAGGAAGA-CTAATTTTATATATAACCATAATTTATATAAAACAGCC
1192231 AATATA
1 AATATA
1192237 TAGAAAGTGA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
50 8 0.17
51 38 0.83
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (50 bp):
AATATAGGAAGACTAATTTTATATATAACCATAATTTATATAAAACAGCC
Found at i:1204450 original size:33 final size:33
Alignment explanation
Indices: 1204395--1204508 Score: 90
Period size: 33 Copynumber: 3.5 Consensus size: 33
1204385 TAGTCCAACT
* * *
1204395 ATGGTCTTACACATGCATTACCATGACCCTGTC
1 ATGGTCTTACACATGCAGTACCATAACCCAGTC
** * *
1204428 ATGGTCTTACATTTGTAGTACCATAACCCAGTT
1 ATGGTCTTACACATGCAGTACCATAACCCAGTC
* * *
1204461 ATGGTCTTATCATCA-GAATGT--CATAGCCCAGTT
1 ATGGTCTTA-CA-CATGCA-GTACCATAACCCAGTC
1204494 ATGGTCTTACACATG
1 ATGGTCTTACACATG
1204509 TATATATACT
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
31 2 0.03
32 3 0.05
33 55 0.83
34 4 0.06
35 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (33 bp):
ATGGTCTTACACATGCAGTACCATAACCCAGTC
Found at i:1210087 original size:28 final size:31
Alignment explanation
Indices: 1210051--1210120 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 31
1210041 TATTTAATTT
*
1210051 TTAAAAGTTTAATGACT-AAAT-AAA-AAAA
1 TTAATAGTTTAATGACTAAAATGAAATAAAA
* * * *
1210079 TTAATAGTTGAGTGATTAAAATGAAATGAAA
1 TTAATAGTTTAATGACTAAAATGAAATAAAA
1210110 TTAATAGTTTA
1 TTAATAGTTTA
1210121 GTGTTGGGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 13 0.39
29 4 0.12
30 3 0.09
31 13 0.39
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.34
Consensus pattern (31 bp):
TTAATAGTTTAATGACTAAAATGAAATAAAA
Found at i:1211227 original size:23 final size:24
Alignment explanation
Indices: 1211174--1211227 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1211164 ATAAATTTAG
* *
1211174 TTTTTAAATAATATTTTTAATATA
1 TTTTTAAATAATACTTATAATATA
*
1211198 TTATTAAA-AATACTTATAATA-A
1 TTTTTAAATAATACTTATAATATA
1211220 TGTTTTAA
1 T-TTTTAA
1211228 TAACAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.64
24 7 0.28
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTTAAATAATACTTATAATATA
Found at i:1216692 original size:65 final size:65
Alignment explanation
Indices: 1216585--1216723 Score: 154
Period size: 65 Copynumber: 2.1 Consensus size: 65
1216575 ACTGGTGAAT
* * * * *
1216585 AAGCAAGAAGCGAAAACCAGTAGAAGGCAGGGAAGCAGCAGTGGGGACAATGGCGAAGAAA-CAA
1 AAGCAAGAAGCAAAAACCAGCAAAAGGCAGAGAAGCAACAGTGGGGACAATGGCGAA-AAACCAA
1216649 G
65 G
* * * * * *
1216650 AAGCAATAAGCAAAAAGCAGCAAAAGGCAGAGAAGTAACAGTGGTGATAGTGGCGAAAAACCAAG
1 AAGCAAGAAGCAAAAACCAGCAAAAGGCAGAGAAGCAACAGTGGGGACAATGGCGAAAAACCAAG
*
1216715 AAGTAAGAA
1 AAGCAAGAA
1216724 AAATTTTAGG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
64 3 0.05
65 57 0.95
ACGTcount: A:0.48, C:0.14, G:0.31, T:0.07
Consensus pattern (65 bp):
AAGCAAGAAGCAAAAACCAGCAAAAGGCAGAGAAGCAACAGTGGGGACAATGGCGAAAAACCAAG
Found at i:1227898 original size:43 final size:42
Alignment explanation
Indices: 1227807--1228011 Score: 293
Period size: 43 Copynumber: 4.8 Consensus size: 42
1227797 CAAACAAAAA
* * *
1227807 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTCCTACG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
* *
1227849 TGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTCTAAG
*
1227892 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
* * *
1227934 CGTCGCTAAAGAACATGGTCTTTAGCGGAGTCTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGT-TTTTTTCTAAG
* *
1227977 CGCCGCTAAAGAACATGTTCTTTACCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
1228012 ATACAAAAAC
Statistics
Matches: 146, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
42 70 0.48
43 76 0.52
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:1227943 original size:85 final size:85
Alignment explanation
Indices: 1227807--1228011 Score: 302
Period size: 85 Copynumber: 2.4 Consensus size: 85
1227797 CAAACAAAAA
* * * * *
1227807 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTCCTACGTGCCTCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTT
* *
1227872 AGCGGCGTTTTTTTTCTAAG
66 AGCGGAGTCTTTTTTCTAAG
* * *
1227892 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCGTCGCTAAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTT
1227957 AGCGGAGTCTTTTTTCTAAG
66 AGCGGAGTCTTTTTTCTAAG
* *
1227977 CGCCGCTAAAGAACATGTTCTTTACCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
1228012 ATACAAAAAC
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 107 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (85 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTT
AGCGGAGTCTTTTTTCTAAG
Found at i:1228396 original size:21 final size:21
Alignment explanation
Indices: 1228328--1228398 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1228318 TTTTGCTCTG
*
1228328 CTCTGCTTCTCTCGCTGT-AGC
1 CTCTGCTTCCCTCGCT-TCAGC
* *
1228349 CTCCGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTTCAGC
* *
1228370 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTTCAGC
1228391 CTCTGCTT
1 CTCTGCTT
1228399 TAAGTTGTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.03, C:0.46, G:0.18, T:0.32
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTTCAGC
Found at i:1231087 original size:9 final size:9
Alignment explanation
Indices: 1231072--1231528 Score: 341
Period size: 9 Copynumber: 49.9 Consensus size: 9
1231062 TTTTTATGTA
1231072 TTATGTAAG
1 TTATGTAAG
*
1231081 CTATGTAAG
1 TTATGTAAG
* *
1231090 TTATTTAAT
1 TTATGTAAG
1231099 TTATGTAAG
1 TTATGTAAG
* *
1231108 ATATGTAGG
1 TTATGTAAG
*
1231117 TTAT-TTAG
1 TTATGTAAG
1231125 TTTATGTAAG
1 -TTATGTAAG
* *
1231135 TTATTTAAT
1 TTATGTAAG
*
1231144 TTATGCAAG
1 TTATGTAAG
1231153 TTTATGTAAG
1 -TTATGTAAG
1231163 TTATGTAAG
1 TTATGTAAG
* * * *
1231172 TCCACGGAAT
1 T-TATGTAAG
1231182 TTATGTCAA-
1 TTATGT-AAG
*
1231191 TTATTTAAG
1 TTATGTAAG
* *
1231200 TTATTTAAT
1 TTATGTAAG
1231209 TTATGTAAG
1 TTATGTAAG
1231218 TTATGTAAG
1 TTATGTAAG
*
1231227 TTAT-TTAG
1 TTATGTAAG
1231235 TTTATGTAAG
1 -TTATGTAAG
* *
1231245 TTATTTAAT
1 TTATGTAAG
*
1231254 TTATGCAAG
1 TTATGTAAG
1231263 TTTATGTAAG
1 -TTATGTAAG
1231273 TTATGTAAG
1 TTATGTAAG
* * * *
1231282 TCCACGGAAT
1 T-TATGTAAG
1231292 TTATGTCAA-
1 TTATGT-AAG
*
1231301 TTATTTAAG
1 TTATGTAAG
* *
1231310 TTATTTAAT
1 TTATGTAAG
1231319 TTATGTAAG
1 TTATGTAAG
1231328 TTTATGTAAG
1 -TTATGTAAG
*
1231338 TTTTGTAAG
1 TTATGTAAG
* *
1231347 TTATTTAAT
1 TTATGTAAG
1231356 TTATGTAAG
1 TTATGTAAG
1231365 TTATGTAAG
1 TTATGTAAG
*
1231374 TTAT-TTAG
1 TTATGTAAG
1231382 TTTATGTAAG
1 -TTATGTAAG
* *
1231392 TTATTTAAT
1 TTATGTAAG
*
1231401 TTATGCAAG
1 TTATGTAAG
1231410 TTTATGTAAG
1 -TTATGTAAG
1231420 TTATGTAAG
1 TTATGTAAG
* * * *
1231429 TCCACGGAAT
1 T-TATGTAAG
1231439 TTATGTCAA-
1 TTATGT-AAG
*
1231448 TTATTTAAG
1 TTATGTAAG
* *
1231457 TTATTTAAT
1 TTATGTAAG
1231466 TTATGTAAG
1 TTATGTAAG
*
1231475 TTATGTAAA
1 TTATGTAAG
* *
1231484 TTATTTAAT
1 TTATGTAAG
*
1231493 TTATGCAAG
1 TTATGTAAG
1231502 TTTATGTAAG
1 -TTATGTAAG
1231512 TTATGTAAG
1 TTATGTAAG
1231521 TTATGTAA
1 TTATGTAA
1231529 CTTAATACAC
Statistics
Matches: 348, Mismatches: 80, Indels: 40
0.74 0.17 0.09
Matches are distributed among these distances:
8 14 0.04
9 263 0.76
10 71 0.20
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1231216 original size:110 final size:109
Alignment explanation
Indices: 1231086--1231377 Score: 483
Period size: 110 Copynumber: 2.7 Consensus size: 109
1231076 GTAAGCTATG
*
1231086 TAAGTTATTTAATTTATGTAAGATATGTAGGTTATTTAGTTTATGTAAGTTATTTAATTTATGCA
1 TAAGTTATTTAATTTATGTAAG-TATGTAAGTTATTTAGTTTATGTAAGTTATTTAATTTATGCA
1231151 AGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATT
65 AGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATT
1231196 TAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAGTTTATGTAAGTTATTTAATTTATGCA
1 TAAGTTATTTAATTTATGTAAG-TATGTAAGTTATTTAGTTTATGTAAGTTATTTAATTTATGCA
1231261 AGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATT
65 AGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATT
* *
1231306 TAAGTTATTTAATTTATGTAAGT-T-TATG-TA---AGTTT-TGTAAGTTATTTAATTTATGTAA
1 TAAGTTATTTAATTTATGTAAGTATGTAAGTTATTTAGTTTATGTAAGTTATTTAATTTATGCAA
1231364 G-TTATGTAAGTTAT
66 GTTTATGTAAGTTAT
1231378 TTAGTTTATG
Statistics
Matches: 178, Mismatches: 4, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
101 13 0.07
102 23 0.13
103 5 0.03
106 2 0.01
107 3 0.02
108 1 0.01
109 1 0.01
110 130 0.73
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (109 bp):
TAAGTTATTTAATTTATGTAAGTATGTAAGTTATTTAGTTTATGTAAGTTATTTAATTTATGCAA
GTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATT
Found at i:1231347 original size:147 final size:146
Alignment explanation
Indices: 1231182--1231524 Score: 607
Period size: 147 Copynumber: 2.3 Consensus size: 146
1231172 TCCACGGAAT
*
1231182 TTATGTCAATTATTTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAGTTTATGTAAGTT
1 TTATGTAAATTATTTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAGTTTATGTAAGTT
1231247 ATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATTTAAGTT
66 ATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATTTAAGTT
1231312 ATTTAATTTATGTAAG
131 ATTTAATTTATGTAAG
*
1231328 TTTATGTAAGTT-TTGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAGTTTATGTAAG
1 -TTATGTAAATTATT-TAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAGTTTATGTAAG
1231392 TTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATTTAAG
64 TTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATTTAAG
1231457 TTATTTAATTTATGTAAG
129 TTATTTAATTTATGTAAG
* **
1231475 TTATGTAAATTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTTAT
1 TTATGTAAATTATTTAAGTTATTTAA-TTTATGTAAGTTATGTAAGTTAT
1231525 GTAACTTAAT
Statistics
Matches: 187, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
146 21 0.11
147 166 0.89
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (146 bp):
TTATGTAAATTATTTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAGTTTATGTAAGTT
ATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATTTAAGTT
ATTTAATTTATGTAAG
Found at i:1231420 original size:110 final size:108
Alignment explanation
Indices: 1231090--1231528 Score: 382
Period size: 110 Copynumber: 3.9 Consensus size: 108
1231080 GCTATGTAAG
* * * * *
1231090 TTATTTAATTTATGTAAGATATGTAGGTTATTTAGTTTATGTAAGTTATTTAATTTATGCAAGTT
1 TTATGTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAATTTATGCAAGTT
** * * *
1231155 TATGTAAGTTATGTAAGTCCACGGAATTTATGTCAA-TTATTTAAG
66 TATGTAAGTTATGTAA-TTTATGCAA-TTATGT-AAGTTATTTAAT
* * *
1231200 TTATTTAATTTATGTAAGTTATGTAAGTTATTTAGTTTATGTAAGTTATTTAATTTATGCAAGTT
1 TTATGTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAATTTATGCAAGTT
*
1231265 TATGTAAGTTATGTAAGTCCACGGAATTTATGTCAATTATTTAAGTTATTTAAT
66 TATGTAAGTTA--T--GT------AATTTATG-CAATTATGTAAGTTATTTAAT
* * **
1231319 TTATGTAAGTTTATGTAAGTTTTGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTAT-TTAGT
1 TTATGTAA-TTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAATTTATGCAAGT
* *
1231383 TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGT
65 TTATGTAAGTTATGTAATTTATGCAA--TTATGTAAGTTATTTAA-T
** * * * * **
1231430 CCACGGAATTTATGTCAA-TTATTTAAGTTATTTAATTTATGTAAGTTATGTAAATTATTTAA-T
1 TTATGTAATTTATGT-AAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAATTTATGCAAGT
* * *
1231493 TTATGCAAGTTTATGTAAGTTATGTAAGTTATGTAA
65 TTATGTAAG-TTATGTAATTTATGCAA-TTATGTAA
1231529 CTTAATACAC
Statistics
Matches: 279, Mismatches: 31, Indels: 38
0.80 0.09 0.11
Matches are distributed among these distances:
108 3 0.01
109 8 0.03
110 150 0.54
111 23 0.08
112 1 0.00
114 2 0.01
115 1 0.00
117 1 0.00
118 2 0.01
119 38 0.14
120 50 0.18
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (108 bp):
TTATGTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAATTTATGCAAGTT
TATGTAAGTTATGTAATTTATGCAATTATGTAAGTTATTTAAT
Found at i:1231612 original size:16 final size:16
Alignment explanation
Indices: 1231587--1231624 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1231577 GAGAACGAAG
*
1231587 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
1231602 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
1231618 TAAATTT
1 TAAATTT
1231625 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:1231639 original size:13 final size:13
Alignment explanation
Indices: 1231621--1231653 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1231611 ATACAAATAA
1231621 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1231634 ATTTAGAAAACTT
1 ATTTAGAAAACTT
*
1231647 ATATAGA
1 ATTTAGA
1231654 TATTAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1233824 original size:191 final size:191
Alignment explanation
Indices: 1233530--1233878 Score: 554
Period size: 191 Copynumber: 1.8 Consensus size: 191
1233520 ATTTGTGCGA
* * * *
1233530 GCATTAGAGAAAGAAAAAATCAAACAGAAAAATGAATAGCCATATACGTATTCAACGAATAAATT
1 GCATTACAGAAAGAAAAAATCAAACAGAAAAATGAATAGCCATATACGGAGTCAACGAAGAAATT
*
1233595 AGGGATTTGGAAAGATTTTTACCAGTCAGCCCAGACGAGAAGCAATATTCGATCGAAAAGAGGGG
66 AGGGATTTGGAAAGATTTTTACCAGTCAGCCCAGACGAGAAGCAATATTCGACCGAAAAGAGGGG
* ** *
1233660 AAATCGTCGTTGAAGGGGTGAATGGTCTCTGGAATTTAAAGAGAAAGGAAAAACAAAGCCG
131 AAATCGCCGTTGAAAAGGTGAAAGGTCTCTGGAATTTAAAGAGAAAGGAAAAACAAAGCCG
* * *
1233721 GCATTACAGAAAGAAAAAATCGAACATAAAAATGAATAGCCATATACGGAGTCAACGGAGAAATT
1 GCATTACAGAAAGAAAAAATCAAACAGAAAAATGAATAGCCATATACGGAGTCAACGAAGAAATT
* * * *
1233786 AGGGATTTGGAAAGTTTTTTACCAGTCAGCCCAGACGAGAATCGATATTCGACCGAGAAGAGGGG
66 AGGGATTTGGAAAGATTTTTACCAGTCAGCCCAGACGAGAAGCAATATTCGACCGAAAAGAGGGG
1233851 AAATCGCCGTTGAAAAGGTGAAAGGTCT
131 AAATCGCCGTTGAAAAGGTGAAAGGTCT
1233879 AGGGATTTAC
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
191 142 1.00
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.20
Consensus pattern (191 bp):
GCATTACAGAAAGAAAAAATCAAACAGAAAAATGAATAGCCATATACGGAGTCAACGAAGAAATT
AGGGATTTGGAAAGATTTTTACCAGTCAGCCCAGACGAGAAGCAATATTCGACCGAAAAGAGGGG
AAATCGCCGTTGAAAAGGTGAAAGGTCTCTGGAATTTAAAGAGAAAGGAAAAACAAAGCCG
Found at i:1234413 original size:22 final size:23
Alignment explanation
Indices: 1234388--1234444 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1234378 CTTTAACCAA
*
1234388 AAACCTTAAACCAC-TT-ACTCTG
1 AAACCTTAAACC-CTTTAACACTG
* *
1234410 AAACCCTAAACCCTTTAACACTT
1 AAACCTTAAACCCTTTAACACTG
1234433 AAACCTTAAACC
1 AAACCTTAAACC
1234445 TTAGCCCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 13 0.45
23 15 0.52
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.25
Consensus pattern (23 bp):
AAACCTTAAACCCTTTAACACTG
Found at i:1234565 original size:21 final size:21
Alignment explanation
Indices: 1234541--1234584 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1234531 AACCCCTATC
* *
1234541 CCTTAATCTCCAACC-TCTAAA
1 CCTTAAACTCAAACCAT-TAAA
1234562 CCTTAAACTCAAACCATTAAA
1 CCTTAAACTCAAACCATTAAA
1234583 CC
1 CC
1234585 AAGTACCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
CCTTAAACTCAAACCATTAAA
Found at i:1234745 original size:15 final size:15
Alignment explanation
Indices: 1234725--1234753 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1234715 CCATAATCTT
1234725 TAAACCCTAAACCTG
1 TAAACCCTAAACCTG
1234740 TAAACCCTAAACCT
1 TAAACCCTAAACCT
1234754 TGACTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.34, G:0.03, T:0.21
Consensus pattern (15 bp):
TAAACCCTAAACCTG
Found at i:1234801 original size:21 final size:21
Alignment explanation
Indices: 1234777--1234846 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
1234767 ATAAACTATA
*
1234777 AACCCTAAACCCCTAACCCTT
1 AACCATAAACCCCTAACCCTT
* *
1234798 AACCATTAACCCGTAACACC-T
1 AACCATAAACCCCTAAC-CCTT
1234819 ATA-CATTAAACCCC-AACCCTT
1 A-ACCA-TAAACCCCTAACCCTT
1234840 AAACCAT
1 -AACCAT
1234847 GGCCCGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.05
21 24 0.63
22 12 0.32
ACGTcount: A:0.39, C:0.40, G:0.01, T:0.20
Consensus pattern (21 bp):
AACCATAAACCCCTAACCCTT
Found at i:1235475 original size:114 final size:114
Alignment explanation
Indices: 1235257--1236239 Score: 1319
Period size: 114 Copynumber: 8.6 Consensus size: 114
1235247 GTTTTGGTTT
* * * * *
1235257 AAAACGATGTGTTTTGGTTAAGATTTATTCGCAGCGCTTTGTATAATGCGCCGCTAATGATGTAC
1 AAAACGATGCGTTTTGGTTAAGATTT-TTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGC
* * ** **
1235322 TTTAGCGGCGTTT-TAC-TATAGTTCCACTAATTCTAAAATACCTCAACAA
65 TTTAGCGGCATTTATCCTTA-AGCGCCACTAATTCTAAAATACCTCAACCC
* * * ** * *
1235371 AAAATGACGCGTTTTGGTTAAGATTTATTGCGGCGCTTTCAATAATGTGCCGCTAATGGTGTTCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* *
1235436 TTAGCGGCATTTATCCTTAAGCGCGACTAAATCTAAAATACCTCAACCC
66 TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * *
1235485 AAAACGATGCG-TTTGGTTAAGATTTTTTGCGGCGCTTTGAATAATGCACCGCTAGTGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* *
1235549 TTAGCGGCATTTATCCATAAGCGCCACTAATTCTAATATACCTCAACCC
66 TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * *
1235598 AAAACGATGCGTTTCGGTTAAGATTTTTTGCGGCGCTTTGTATGATGCACCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * * * *
1235663 TTAGCGGCGTTTTTACTTAAGCGCCACTAATTCTAAAGTACATCAACCC
66 TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * * * * *
1235712 AGAACGATGTGTTTTGGTTAAGATTTTTTCCGGCGCTTTGTATGATGCGCCGCTAATGGTCTACT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * *
1235777 TTAGCGGCGTTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC
66 TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * ** *
1235826 AGAACGATGCGTTTTGGTTATGATTTTTTGCGGCGCTCAGTATAATGCGTCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* *
1235891 TTAGCGGCATTTATCCATAAGCGCCACTAATTCTAATATACCTCAACCC
66 TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* ** * *
1235940 AAAACGATGCGTTTCGGTTAAGATTTTTTGCGGCAATTTGTATGATGCGCCGCGAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* *
1236005 TTAGCGGCATTTATCCATAAGCGCCACTAATTCTAATATACCTCAACCC
66 TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* ** * *
1236054 AAAACGATGCGTTTCGGTTAAGATTTTTTGCGGCAATTTGTATGATGCGCCGCGAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
*
1236119 TTAGCGGCGTTT-TGCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
66 TTAGCGGCATTTAT-CCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
* * *
1236168 AGAACGATGTGTTTTGGTTAAGA-TTTTTGCGGCGCTTTATATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
1236232 TTAGCGGC
66 TTAGCGGC
1236240 GTTTGTCGAA
Statistics
Matches: 779, Mismatches: 86, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
113 190 0.24
114 587 0.75
115 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (114 bp):
AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
TTAGCGGCATTTATCCTTAAGCGCCACTAATTCTAAAATACCTCAACCC
Found at i:1240838 original size:31 final size:31
Alignment explanation
Indices: 1240796--1241351 Score: 297
Period size: 31 Copynumber: 18.1 Consensus size: 31
1240786 CAACGATATA
* * *
1240796 TATATTCATATACGAACCAAATTTGGCAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
* *
1240827 TATATCTATATACAAATC-AATTCGGCAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
* *
1240857 TATAACCATATACGAATCAAGTTCGGCAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
* * *
1240888 TATAAT-CATATACAAATTAAATTCAGCAATG
1 TAT-ATCCATATACGAATCAAATTCGGCAATG
* *
1240919 TATAACCATATATGAATC-AATTCGGCAACT-
1 TATATCCATATACGAATCAAATTCGGCAA-TG
* **
1240949 TATATCCATATAC-AATTCAATTTCAACAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * * * *
1240980 TATAACCATGTACAAATTAATTTCAGCAATA
1 TATATCCATATACGAATCAAATTCGGCAATG
*
1241011 TATAAT-CATATACAAATC-AATTCGGCAACT-
1 TAT-ATCCATATACGAATCAAATTCGGCAA-TG
* **
1241041 TATATCCATATAC-AATTCAATTTCAACAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * * * *
1241072 TATAACCATGTACAAATTAATTTCAGCAATA
1 TATATCCATATACGAATCAAATTCGGCAATG
*
1241103 TATAAT-CATATACAAATC-AATTCGGCAACT-
1 TAT-ATCCATATACGAATCAAATTCGGCAA-TG
* **
1241133 TATATCCATATAC-AATTCAATTTCAACAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * * * *
1241164 TATAACCATGTACAAATTAATTTCAGCAATA
1 TATATCCATATACGAATCAAATTCGGCAATG
*
1241195 TATAAT-CATATACAAATC-AATTCGGCAACT-
1 TAT-ATCCATATACGAATCAAATTCGGCAA-TG
* **
1241225 TATATCCATATAC-AATTCAATTTCAACAATG
1 TATATCCATATACGAA-TCAAATTCGGCAATG
* * * * *
1241256 TATAACCATATACAAATTAATTTCAGCAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
* * *
1241287 TACAAT-CATATACAAATC-AATTTGGCAACT-
1 TA-TATCCATATACGAATCAAATTCGGCAA-TG
* * * * *
1241317 TATATCCATATGCAAATCAATTTTGACAATG
1 TATATCCATATACGAATCAAATTCGGCAATG
1241348 TATA
1 TATA
1241352 ACTATAAACA
Statistics
Matches: 415, Mismatches: 76, Indels: 68
0.74 0.14 0.12
Matches are distributed among these distances:
29 16 0.04
30 134 0.32
31 252 0.61
32 13 0.03
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (31 bp):
TATATCCATATACGAATCAAATTCGGCAATG
Found at i:1240958 original size:92 final size:92
Alignment explanation
Indices: 1240821--1241383 Score: 839
Period size: 92 Copynumber: 6.1 Consensus size: 92
1240811 ACCAAATTTG
* * * **
1240821 GCAATGTAT-ATCTATATACAAATCAATTCGGCAA-TGTATAACCATATACGAA-TCAAGTTCGG
1 GCAATATATAATC-ATATACAAATCAATTCGGCAACT-TATATCCATATAC-AATTCAATTTCAA
* *
1240883 CAATGTATAATCATATACAAATTAAATTCA
63 CAATGTATAACCATATACAAATTAATTTCA
* * **
1240913 GCAATGTATAACCATATATGAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
1 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
*
1240978 TGTATAACCATGTACAAATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
1241005 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
1 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
*
1241070 TGTATAACCATGTACAAATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
1241097 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
1 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
*
1241162 TGTATAACCATGTACAAATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
1241189 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
1 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
1241254 TGTATAACCATATACAAATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
* * * * * **
1241281 GCAATGTACAATCATATACAAATCAATTTGGCAACTTATATCCATATGCAAATCAATTTTGACAA
1 GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
* *
1241346 TGTATAACTATAAAC-AATTCGAA-TTCA
66 TGTATAACCATATACAAATT--AATTTCA
1241373 GCAATATATAA
1 GCAATATATAA
1241384 AACAATCAAA
Statistics
Matches: 440, Mismatches: 26, Indels: 10
0.92 0.05 0.02
Matches are distributed among these distances:
91 6 0.01
92 429 0.98
93 5 0.01
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (92 bp):
GCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
TGTATAACCATATACAAATTAATTTCA
Found at i:1241386 original size:26 final size:25
Alignment explanation
Indices: 1241357--1241407 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1241347 GTATAACTAT
*
1241357 AAACAATTCGAATTCAGCAATATATA
1 AAACAA-TCAAATTCAGCAATATATA
*
1241383 AAACAATCAAATTCAGCAATGTATA
1 AAACAATCAAATTCAGCAATATATA
1241408 TCTATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (25 bp):
AAACAATCAAATTCAGCAATATATA
Found at i:1245847 original size:44 final size:44
Alignment explanation
Indices: 1245784--1246089 Score: 156
Period size: 44 Copynumber: 6.7 Consensus size: 44
1245774 CTTACCATAG
*
1245784 CAAATCTTATATCCTTGAAGTTGCAGTGGAGCAAGATAAAACTA
1 CAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATAAAACTA
* * * **
1245828 CAAATCCTATATCCCTGAAGTCGCAGTGGATC-AGATTAAAGTTA
1 CAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-TAAAACTA
* * * *
1245872 CAATTCATATA-CTCCTGAAGTTGCAGTAGG-TCGAA-ATGAAACTA
1 CAAATCTTATATC-CCTGAAGTTGCAGT-GGAGC-AAGATAAAACTA
* * * * * *
1245916 TGAGGGTGAATCTTATCTCCCTGAAGTTACAGTAGAGCAAGATGAAGCTA
1 -CA-----AATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATAAAACTA
* * * * *
1245966 CAAATATTATACCCCTAAAGTTGCAGTGGGTTGGAATGA-AACTATGA-TA
1 CAAATCTTATATCCCTGAAGTTGCAGT-GG-AGCAA-GATAA--A--ACTA
* * * * *
1246015 GCAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAAGATGAAGCTA
1 -CAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATAAAACTA
* *
1246060 CAAATCCTATATCCCTAAAGTTGCAGTGGA
1 CAAATCTTATATCCCTGAAGTTGCAGTGGA
1246090 TTAGATTGAA
Statistics
Matches: 196, Mismatches: 42, Indels: 48
0.69 0.15 0.17
Matches are distributed among these distances:
43 4 0.02
44 110 0.56
45 7 0.04
46 6 0.03
47 4 0.02
48 5 0.03
49 7 0.04
50 52 0.27
51 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (44 bp):
CAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATAAAACTA
Found at i:1246055 original size:50 final size:50
Alignment explanation
Indices: 1245889--1246055 Score: 120
Period size: 50 Copynumber: 3.5 Consensus size: 50
1245879 TATACTCCTG
** ** *
1245889 AAGTTGCAGTAG-GTCGAA-ATGAAACTATGAGGGTGAATCTTATCTCCCTG
1 AAGTTGCAGTAGAG-C-AAGATGAAACTATGATAGCAAATCTTATCTCCCTA
* * *
1245939 AAGTTACAGTAGAGCAAGATG--A--A-GCTA-CAAATATTATAC-CCCTA
1 AAGTTGCAGTAGAGCAAGATGAAACTATGATAGCAAATCTTAT-CTCCCTA
* ***
1245983 AAGTTGCAGT-GGGTTGGAATGAAACTATGATAGCAAATCTTATCTCCCTA
1 AAGTTGCAGTAGAGCAAG-ATGAAACTATGATAGCAAATCTTATCTCCCTA
1246033 AAGTTGCAGTAGAGCAAGATGAA
1 AAGTTGCAGTAGAGCAAGATGAA
1246056 GCTACAAATC
Statistics
Matches: 86, Mismatches: 19, Indels: 24
0.67 0.15 0.19
Matches are distributed among these distances:
43 3 0.03
44 23 0.27
45 2 0.02
46 2 0.02
48 2 0.02
49 6 0.07
50 44 0.51
51 4 0.05
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (50 bp):
AAGTTGCAGTAGAGCAAGATGAAACTATGATAGCAAATCTTATCTCCCTA
Found at i:1246087 original size:94 final size:94
Alignment explanation
Indices: 1245879--1246088 Score: 294
Period size: 94 Copynumber: 2.2 Consensus size: 94
1245869 TTACAATTCA
* * * * ** *
1245879 TATACTCCTGAAGTTGCAGTAGGTCGAAATGAAACTATGAGGGTGAATCTTATCTCCCTGAAGTT
1 TATACCCCTAAAGTTGCAGTGGGTCGAAATGAAACTATGAGAGCAAATCTTATCTCCCTAAAGTT
*
1245944 ACAGTAGAGCAAGATGAAGCTACAAATAT
66 ACAGTAGAGCAAGATGAAGCTACAAATAC
* * *
1245973 TATACCCCTAAAGTTGCAGTGGGTTGGAATGAAACTATGATAGCAAATCTTATCTCCCTAAAGTT
1 TATACCCCTAAAGTTGCAGTGGGTCGAAATGAAACTATGAGAGCAAATCTTATCTCCCTAAAGTT
* *
1246038 GCAGTAGAGCAAGATGAAGCTACAAATCC
66 ACAGTAGAGCAAGATGAAGCTACAAATAC
*
1246067 TATATCCCTAAAGTTGCAGTGG
1 TATACCCCTAAAGTTGCAGTGG
1246089 ATTAGATTGA
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 102 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (94 bp):
TATACCCCTAAAGTTGCAGTGGGTCGAAATGAAACTATGAGAGCAAATCTTATCTCCCTAAAGTT
ACAGTAGAGCAAGATGAAGCTACAAATAC
Found at i:1246100 original size:44 final size:44
Alignment explanation
Indices: 1245958--1246566 Score: 212
Period size: 44 Copynumber: 13.1 Consensus size: 44
1245948 TAGAGCAAGA
* * * *
1245958 TGAAGCTACAAATATTATACCCCTAAAGTTGCAGTGGGTTGGAA
1 TGAAGCTACAAATCTTATACCCCTAAAGTTGCAGTGGATTAGAT
* * **
1246002 TGAAACTATGATAGCAAATCTTAT-CTCCCTAAAGTTGCAGTAGAGCAAGA-
1 TG--A--A-GCTA-CAAATCTTATAC-CCCTAAAGTTGCAGTGGA-TTAGAT
* *
1246052 TGAAGCTACAAATCCTATATCCCTAAAGTTGCAGTGGATTAGAT
1 TGAAGCTACAAATCTTATACCCCTAAAGTTGCAGTGGATTAGAT
* * * ** *
1246096 TGAAGCTACAATTTTTATACCCCTGAAGTTGTAACGAGTCAAAGTA-AT
1 TGAAGCTACAAATCTTATACCCCTAAAGTTG---C-AGT-GGATTAGAT
** * * *
1246144 TCTA-CTATAGTGAATCTTAT-CTCCCTGAAGTTGCAGTGGACTAGAT
1 TGAAGCTACA---AATCTTATAC-CCCTAAAGTTGCAGTGGATTAGAT
* * * *
1246190 TGAAGCTACAAATCTTATACCCCTGAAGTTGTAGTGGGTTGGAT
1 TGAAGCTACAAATCTTATACCCCTAAAGTTGCAGTGGATTAGAT
* * * *
1246234 TGAAAATACAACAAATCCTATACCCCTAAAGTTGCAGTGAGACGTACTAAAT
1 TG--AA-GCTACAAATCTTATACCCCTAAAGTTGCAGTG-GA--T--TAGAT
* * * * *
1246286 CT--ACCATAGCGAATTTTAT-CTCCCTAAAATTGCAGTGGAGTAGAT
1 -TGAAGC-TA-CAAATCTTATAC-CCCTAAAGTTGCAGTGGATTAGAT
* * * *
1246331 TGAAGCTACAAATCCTATACCCCTAAAGTTACAGTGGCTCAGAT
1 TGAAGCTACAAATCTTATACCCCTAAAGTTGCAGTGGATTAGAT
* * * ** *
1246375 TGGATCTACCATAGCGAATCTTAT-CTCCCTAAAATTGCAGTGGAGCAAAT
1 T-GA---AGC-TA-CAAATCTTATAC-CCCTAAAGTTGCAGTGGATTAGAT
* * * *
1246425 TGAAACTACAAATCTTATACCCCTGAAGTTGCAGTGGGTAAGAT
1 TGAAGCTACAAATCTTATACCCCTAAAGTTGCAGTGGATTAGAT
** * * * * *
1246469 TGATTCTACTATACCGAATCTTAT-CTCCTTGAATTTACAGTGGAGTAGAT
1 TGAAGCTAC---A---AATCTTATAC-CCCTAAAGTTGCAGTGGATTAGAT
* * * * * *
1246519 TGAAGCTAGAAATCATATACCTCTGAAGTTGTAGTGGATTGGAT
1 TGAAGCTACAAATCTTATACCCCTAAAGTTGCAGTGGATTAGAT
1246563 TGAA
1 TGAA
1246567 ACTATAACAA
Statistics
Matches: 416, Mismatches: 96, Indels: 106
0.67 0.16 0.17
Matches are distributed among these distances:
43 3 0.01
44 174 0.42
45 20 0.05
46 15 0.04
47 39 0.09
48 13 0.03
49 19 0.05
50 127 0.31
51 2 0.00
52 3 0.01
53 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (44 bp):
TGAAGCTACAAATCTTATACCCCTAAAGTTGCAGTGGATTAGAT
Found at i:1246321 original size:141 final size:138
Alignment explanation
Indices: 1246012--1246376 Score: 399
Period size: 141 Copynumber: 2.6 Consensus size: 138
1246002 TGAAACTATG
* * * *
1246012 ATAGCAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAAGA-TGAAGCTACAAATCCTATATCCCT
1 ATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGA-CTAGATTGAAGCTACAAATCCTATACCCCT
* * * ** * * * *
1246076 AAAGTTGCAGTGGATTAGATTGAAGCTACAATTTTTATACCCCTGAAGTTGTAACGAGTCAAAGT
65 AAAGTTGCAGTGGATTAGATTGAAACAACAAATCCTATACCCCTAAAGTTGCAACGAGACAAACT
* *
1246141 AATTCTACT
130 AAATCTACC
* * * *
1246150 ATAGTGAATCTTATCTCCCTGAAGTTGCAGTGGACTAGATTGAAGCTACAAATCTTATACCCCTG
1 ATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGACTAGATTGAAGCTACAAATCCTATACCCCTA
* * * ** **
1246215 AAGTTGTAGTGGGTTGGATTGAAAATACAACAAATCCTATACCCCTAAAGTTGCAGTGAGACGTA
66 AAGTTGCAGTGGATTAGATTG--AA-ACAACAAATCCTATACCCCTAAAGTTGCAACGAGACAAA
1246280 CTAAATCTACC
128 CTAAATCTACC
* * *
1246291 ATAGCGAATTTTATCTCCCTAAAATTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCCCTA
1 ATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGACTAGATTGAAGCTACAAATCCTATACCCCTA
* * *
1246356 AAGTTACAGTGGCTCAGATTG
66 AAGTTGCAGTGGATTAGATTG
1246377 GATCTACCAT
Statistics
Matches: 185, Mismatches: 38, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
137 4 0.02
138 70 0.38
140 2 0.01
141 109 0.59
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (138 bp):
ATAGCGAATCTTATCTCCCTAAAGTTGCAGTGGACTAGATTGAAGCTACAAATCCTATACCCCTA
AAGTTGCAGTGGATTAGATTGAAACAACAAATCCTATACCCCTAAAGTTGCAACGAGACAAACTA
AATCTACC
Found at i:1246354 original size:94 final size:93
Alignment explanation
Indices: 1246244--1246555 Score: 356
Period size: 94 Copynumber: 3.3 Consensus size: 93
1246234 TGAAAATACA
* * *
1246244 ACAAATCCTATACCCCTAAAGTTGCAGTGAG-ACGTACTAAATCTACCATAGCGAATTTTATCTC
1 ACAAATCCTATACCCCTAAAGTTGCAGTG-GCACG-ATTGAATCTACCATAGCGAATCTTATCTC
1246308 CCTAAAATTGCAGTGGAGTAGATTGAAGCT
64 CCTAAAATTGCAGTGGAGTAGATTGAAGCT
* * *
1246338 ACAAATCCTATACCCCTAAAGTTACAGTGGCTCAGATTGGATCTACCATAGCGAATCTTATCTCC
1 ACAAATCCTATACCCCTAAAGTTGCAGTGGCAC-GATTGAATCTACCATAGCGAATCTTATCTCC
* * *
1246403 CTAAAATTGCAGTGGAGCAAATTGAAACT
65 CTAAAATTGCAGTGGAGTAGATTGAAGCT
* * * * * * *
1246432 ACAAATCTTATACCCCTGAAGTTGCAGTGGGTAAGATTGATTCTACTATACCGAATCTTATCTCC
1 ACAAATCCTATACCCCTAAAGTTGCAGT-GGCACGATTGAATCTACCATAGCGAATCTTATCTCC
* * * *
1246497 TTGAATTTACAGTGGAGTAGATTGAAGCT
65 CTAAAATTGCAGTGGAGTAGATTGAAGCT
* * * * *
1246526 AGAAATCATATACCTCTGAAGTTGTAGTGG
1 ACAAATCCTATACCCCTAAAGTTGCAGTGG
1246556 ATTGGATTGA
Statistics
Matches: 185, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
93 3 0.02
94 179 0.97
95 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (93 bp):
ACAAATCCTATACCCCTAAAGTTGCAGTGGCACGATTGAATCTACCATAGCGAATCTTATCTCCC
TAAAATTGCAGTGGAGTAGATTGAAGCT
Found at i:1246583 original size:94 final size:93
Alignment explanation
Indices: 1246295--1246609 Score: 299
Period size: 94 Copynumber: 3.4 Consensus size: 93
1246285 TCTACCATAG
* * * * *
1246295 CGAATTTTATCTCCCTAAAATTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCCCTAAAGT
1 CGAATCTTATCTCCTTGAAATTGCAGTGGAGTAGATTGAAGCTACAAATCATATACCCCTGAAGT
* * * * ** *
1246360 TACAGTGGCTCAGATTGGATCTACCATA
66 TGCAGTGGATAAGATTGAATCTATAACA
* * * * * *
1246388 GCGAATCTTATCTCCCTAAAATTGCAGTGGAGCAAATTGAAACTACAAATCTTATACCCCTGAAG
1 -CGAATCTTATCTCCTTGAAATTGCAGTGGAGTAGATTGAAGCTACAAATCATATACCCCTGAAG
* *
1246453 TTGCAGTGGGTAAGATTGATTCTACTATAC-
65 TTGCAGTGGATAAGATTGAATCTA-TA-ACA
* * * *
1246483 CGAATCTTATCTCCTTGAATTTACAGTGGAGTAGATTGAAGCTAGAAATCATATACCTCTGAAGT
1 CGAATCTTATCTCCTTGAAATTGCAGTGGAGTAGATTGAAGCTACAAATCATATACCCCTGAAGT
* ** *
1246548 TGTAGTGGATTGGATTGAAACTATAACAA
66 TGCAGTGGATAAGATTGAATCTATAAC-A
* * * *
1246577 CAAATCTTATCTCTTTGAAGTTGCAATGGAGTA
1 CGAATCTTATCTCCTTGAAATTGCAGTGGAGTA
1246610 AGATGAAACT
Statistics
Matches: 182, Mismatches: 35, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
92 2 0.01
93 2 0.01
94 177 0.97
96 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (93 bp):
CGAATCTTATCTCCTTGAAATTGCAGTGGAGTAGATTGAAGCTACAAATCATATACCCCTGAAGT
TGCAGTGGATAAGATTGAATCTATAACA
Found at i:1246585 original size:188 final size:188
Alignment explanation
Indices: 1246244--1246589 Score: 406
Period size: 188 Copynumber: 1.8 Consensus size: 188
1246234 TGAAAATACA
* * *
1246244 ACAAATCCTATACCCCTAAAGTTGCAGTGAGACGTACTAAATCTACCATAGCGAATTTTATCTCC
1 ACAAATCCTATACCCCTAAAGTTGCAGTGAGAAGTACTAAATCTACCATACCGAATCTTATCTCC
* * *
1246309 CTAAAATTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCCCTAAAGTTACAGTGGCTCAGA
66 CTAAAATTACAGTGGAGTAGATTGAAGCTACAAATCATATACCCCTAAAGTTACAGTGGATCAGA
* * * * * *
1246374 TTGGATCTACCATAGCGAATCTTATCTCCCTAAAATTGCAGTGGAGCAAATTGAAACT
131 TTGAAACTACAACAACAAATCTTATCTCCCTAAAATTGCAGTGGAGCAAATTGAAACT
* * * * * * *
1246432 ACAAATCTTATACCCCTGAAGTTGCAGTGGGTAAG-ATTGATTCTACTATACCGAATCTTATCTC
1 ACAAATCCTATACCCCTAAAGTTGCAGTGAG-AAGTACTAAATCTACCATACCGAATCTTATCTC
* * * * * * ** **
1246496 CTTGAATTTACAGTGGAGTAGATTGAAGCTAGAAATCATATACCTCTGAAGTTGTAGTGGATTGG
65 CCTAAAATTACAGTGGAGTAGATTGAAGCTACAAATCATATACCCCTAAAGTTACAGTGGATCAG
*
1246561 ATTGAAACTATAACAACAAATCTTATCTC
130 ATTGAAACTACAACAACAAATCTTATCTC
1246590 TTTGAAGTTG
Statistics
Matches: 127, Mismatches: 30, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
188 125 0.98
189 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (188 bp):
ACAAATCCTATACCCCTAAAGTTGCAGTGAGAAGTACTAAATCTACCATACCGAATCTTATCTCC
CTAAAATTACAGTGGAGTAGATTGAAGCTACAAATCATATACCCCTAAAGTTACAGTGGATCAGA
TTGAAACTACAACAACAAATCTTATCTCCCTAAAATTGCAGTGGAGCAAATTGAAACT
Found at i:1247758 original size:21 final size:22
Alignment explanation
Indices: 1247728--1247780 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1247718 TTTTTACCCT
1247728 TTTTTAATTTCATCCTA-TTTCC
1 TTTTT-ATTTCATCCTATTTTCC
* *
1247750 TTTTTATTTTATTCTATTTTTCC
1 TTTTTATTTCATCCTA-TTTTCC
1247773 TTTTTATT
1 TTTTTATT
1247781 ATATTCTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 9 0.33
22 5 0.19
23 13 0.48
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTATTTCATCCTATTTTCC
Found at i:1248339 original size:11 final size:11
Alignment explanation
Indices: 1248318--1248385 Score: 66
Period size: 11 Copynumber: 6.0 Consensus size: 11
1248308 AACTAATCCT
1248318 CTCTCAAATTTC
1 CTCT-AAATTTC
1248330 CTCTAAATTTC
1 CTCTAAATTTC
*
1248341 CTGTAAATTTC
1 CTCTAAATTTC
* *
1248352 CTCTCAATTTA
1 CTCTAAATTTC
1248363 CTCTCAAA-TTC
1 CTCT-AAATTTC
*
1248374 CTTCCAAATTTC
1 C-TCTAAATTTC
1248386 TCTCAAATCC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 35 0.76
12 11 0.24
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.43
Consensus pattern (11 bp):
CTCTAAATTTC
Found at i:1248374 original size:22 final size:22
Alignment explanation
Indices: 1248317--1248393 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
1248307 AAACTAATCC
*
1248317 TCTCTCAAATTTCCTCTAAATT
1 TCTCTCAAATTTCCTCTCAATT
*
1248339 TC-CTGTAAATTTCCTCTCAATT
1 TCTCT-CAAATTTCCTCTCAATT
1248361 TACTCTCAAA-TTCCT-TCCAAATT
1 T-CTCTCAAATTTCCTCT-C-AATT
1248384 TCTCTCAAAT
1 TCTCTCAAAT
1248394 CCATATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.07
22 32 0.70
23 9 0.20
24 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.01, T:0.43
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:1248375 original size:33 final size:32
Alignment explanation
Indices: 1248317--1248391 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 32
1248307 AAACTAATCC
*
1248317 TCTCTCAAATTTCCTCTAAATTTCCTGT-AAATT
1 TCTCTC-AATTTACTCTAAATTTCCT-TCAAATT
1248350 TCCTCTCAATTTACTCTCAAA-TTCCTTCCAAATT
1 T-CTCTCAATTTACTCT-AAATTTCCTT-CAAATT
1248384 TCTCTCAA
1 TCTCTCAA
1248392 ATCCATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
32 1 0.03
33 22 0.59
34 14 0.38
ACGTcount: A:0.27, C:0.29, G:0.01, T:0.43
Consensus pattern (32 bp):
TCTCTCAATTTACTCTAAATTTCCTTCAAATT
Found at i:1248392 original size:11 final size:11
Alignment explanation
Indices: 1248317--1248393 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
1248307 AAACTAATCC
1248317 TCTCTCAAATT
1 TCTCTCAAATT
1248328 TC-CTCTAAATT
1 TCTCTC-AAATT
*
1248339 TC-CTGTAAATT
1 TCTCT-CAAATT
1248350 TCCTCTC-AATT
1 T-CTCTCAAATT
1248361 TACTCTCAAATT
1 T-CTCTCAAATT
*
1248373 CCT-TCCAAATT
1 TCTCT-CAAATT
1248384 TCTCTCAAAT
1 TCTCTCAAAT
1248394 CCATATTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 4 0.07
11 42 0.78
12 6 0.11
13 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.01, T:0.43
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:1249637 original size:7 final size:7
Alignment explanation
Indices: 1249625--1249657 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1249615 TAGTCGATTG
1249625 GTATTTA
1 GTATTTA
1249632 GTATTTA
1 GTATTTA
1249639 GTATTTA
1 GTATTTA
1249646 GTATTTA
1 GTATTTA
1249653 GTATT
1 GTATT
1249658 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:1250335 original size:18 final size:18
Alignment explanation
Indices: 1250308--1250347 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1250298 CAGGTGCGTT
* *
1250308 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATCTA
1250326 TCCTAACCCTTATATCTA
1 TCCTAACCCTTATATCTA
1250344 TCCT
1 TCCT
1250348 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.05, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATCTA
Found at i:1250812 original size:25 final size:25
Alignment explanation
Indices: 1250779--1250925 Score: 180
Period size: 25 Copynumber: 6.1 Consensus size: 25
1250769 TTTGATATTT
1250779 TTTGATGTAATAAAATAGAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
1250804 TTTGATGTAATAAAATAGAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
* *
1250829 TTTGATGTAATAAAATAGAAATTTT
1 TTTGATGTAATAAAATAGAAGTTTA
** *
1250854 TTTGA-GT--T-ATTTTG-A-TATTA
1 TTTGATGTAATAAAATAGAAGT-TTA
*
1250874 TTTGATGTAATATAATAGAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
*
1250899 TTTGATGTAATAAAATATAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
1250924 TT
1 TT
1250926 CTCCAACGCC
Statistics
Matches: 103, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.01
20 8 0.08
21 5 0.05
22 1 0.01
23 1 0.01
24 4 0.04
25 82 0.80
26 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (25 bp):
TTTGATGTAATAAAATAGAAGTTTA
Found at i:1252660 original size:125 final size:121
Alignment explanation
Indices: 1252435--1252785 Score: 394
Period size: 125 Copynumber: 2.9 Consensus size: 121
1252425 CAAACATGCT
* * *
1252435 ACTGTAGCAAAAGCGCGTCCACG-TGGGCGCGATTTCACAAATTCTTCTCGTAAAGCATCCTGGT
1 ACTGTAGCAAAAGCGTGTCCACGAT--G-GCGATTTAACAAATTCTTCTC-AAAAGCATCCTGGT
* *
1252499 AGAAGCGATTTTATACAATTTGCTCAGAAACATCAACTCGAAATTATTTTTTCCAAGACCA
62 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTT-CAAGACCA
* * * * *
1252560 ACTGTAGCAAAAGCGTGTCCACGATGGCATGATTTTAGACATTCTTCTCAAATAGCATCCTGCTT
1 ACTGTAGCAAAAGCGTGTCCACGATGGC--GATTTAACAAATTCTTCTCAAA-AGCATCCTGGTA
* * *
1252625 GAAGC-ATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTTCAGGACCT
63 GAAGCGA-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAAGACCA
* * *
1252684 ACTATAGCAAAAGCGCTG-----GA-CGCGATTTAACAAATTCTTCTCATAAAGCATCCTGGTAA
1 ACTGTAGCAAAAGCG-TGTCCACGATGGCGATTTAACAAATTCTTCTCA-AAAGCATCCTGGTAG
*
1252743 AAGCGATTTTATACTATTTTCTCAGAAACGTCAACTCGAAATT
64 AAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATT
1252786 CTTTCTTACA
Statistics
Matches: 196, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
117 66 0.34
118 3 0.02
119 2 0.01
120 2 0.01
123 2 0.01
124 24 0.12
125 96 0.49
126 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (121 bp):
ACTGTAGCAAAAGCGTGTCCACGATGGCGATTTAACAAATTCTTCTCAAAAGCATCCTGGTAGAA
GCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAAGACCA
Found at i:1255793 original size:25 final size:25
Alignment explanation
Indices: 1255759--1255811 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1255749 GTTTTGATTT
1255759 TGTCCACAATAAAGAGTGTAAAAAA
1 TGTCCACAATAAAGAGTGTAAAAAA
1255784 TGTCCACAATAAAGAGTGTAAAAAA
1 TGTCCACAATAAAGAGTGTAAAAAA
1255809 TGT
1 TGT
1255812 GTGATGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (25 bp):
TGTCCACAATAAAGAGTGTAAAAAA
Found at i:1258612 original size:43 final size:43
Alignment explanation
Indices: 1258571--1259039 Score: 566
Period size: 43 Copynumber: 10.9 Consensus size: 43
1258561 AAGCGCCGCA
* * * *
1258571 ATAGACTATGGTCTTTAGCGGCGCTTACACAAAACACGCCGCT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* * *
1258614 ATAGACCATAGTCTTTCGCGGCGC-TATACAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* * * *
1258656 ATAGATCATGGTCTTTTAGCAGCG-TTTGTACATAAAACGCCACT
1 ATAGACCATGGTC-TTTAGCGGCGCTTAG-ACAAAAAACGCCACT
* * *
1258700 ATAAACCATGGTCTTTAGCGGCGCTTGGACAAAAAGCGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* * * *
1258743 ATAGACCGTGTTCTTTAGCGGCGATTGGACAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* * *
1258786 ATAGACCCTGGTCTTTAGCGGCGCTTGGA-AAAAAAAGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* * *
1258828 ATAGGCCATTGTCTTTAGCGGCGTTTAGACAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* *
1258871 ATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCTCT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
*
1258914 ATATACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* * * *
1258957 ATAGACCATGGTCTTTAGCGGCGCGTATACGAAAAATGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
* * * * **
1259000 ATAGGCCGTGTTCTTTAGCGGTGCTTACCCAAAAAACGCC
1 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCC
1259040 GCTAATTTTG
Statistics
Matches: 365, Mismatches: 56, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
42 62 0.17
43 275 0.75
44 28 0.08
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (43 bp):
ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACT
Found at i:1258959 original size:214 final size:215
Alignment explanation
Indices: 1258579--1259035 Score: 587
Period size: 214 Copynumber: 2.1 Consensus size: 215
1258569 CAATAGACTA
* * * * *
1258579 TGGTCTTTAGCGGCGCTTACACAAAACACGCCGCTATAGACCATAGTCTTTCGCGGCGCTATACA
1 TGGTCTTTAGCGGCGCTTACACAAAAAAAGCCACTATAGACCATAGTCTTTAGCGGCGCTAGACA
* * *
1258644 AAAAACGCCACTATAGATCATGGTCTTTTAGCAGCGTTTGTACATAAAACGCCACTATAAACCAT
66 AAAAACGCCACTATAGACCATGGTCTTTTAGCAGCGTTAGTACAAAAAACGCCACTATAAACCAT
* * * * * *
1258709 GGTCTTTAGCGGCGCTTGGACAAAAAGCGCCACTATAGACCGTGTTCTTTAGCGGCGATTGGACA
131 GGTCTTTAGCGGCGCTTAGACAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGAGTAGACA
1258774 AAAAACGCCACTATAGACCC
196 AAAAACGCCACTATAGACCC
** * * *
1258794 TGGTCTTTAGCGGCGCTTGGA-AAAAAAAGCCACTATAGGCCATTGTCTTTAGCGGCGTTTAGAC
1 TGGTCTTTAGCGGCGCTTACACAAAAAAAGCCACTATAGACCATAGTCTTTAGCGGCG-CTAGAC
* * * *
1258858 AAAAAACGCCACTATAGACCATGGTC-TTTAGCGGCGCTTAG-CCAAAAAACGCCTCTATATACC
65 AAAAAACGCCACTATAGACCATGGTCTTTTAGCAGCG-TTAGTACAAAAAACGCCACTATAAACC
* *
1258921 ATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGCGTATA
129 ATGGTCTTTAGCGGCGCTTAGACAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGAGTAGA
* * * *
1258986 CGAAAAATGCCACTATAGGCCG
194 CAAAAAACGCCACTATAGACCC
* * *
1259008 TGTTCTTTAGCGGTGCTTACCCAAAAAA
1 TGGTCTTTAGCGGCGCTTACACAAAAAA
1259036 CGCCGCTAAT
Statistics
Matches: 205, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
214 148 0.72
215 57 0.28
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (215 bp):
TGGTCTTTAGCGGCGCTTACACAAAAAAAGCCACTATAGACCATAGTCTTTAGCGGCGCTAGACA
AAAAACGCCACTATAGACCATGGTCTTTTAGCAGCGTTAGTACAAAAAACGCCACTATAAACCAT
GGTCTTTAGCGGCGCTTAGACAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGAGTAGACA
AAAAACGCCACTATAGACCC
Found at i:1259398 original size:21 final size:21
Alignment explanation
Indices: 1259344--1259413 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
1259334 TTTACGCTGT
*
1259344 TCTGCTTCCCTCGTTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
***
1259365 TCCAATTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
* * *
1259386 TCTGCTTCTCTCGCTGCTGCA
1 TCTGCTTCCCTCGCTGCAGCC
1259407 TCTGCTT
1 TCTGCTT
1259414 TAAGCTGCTG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.07, C:0.41, G:0.17, T:0.34
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCC
Found at i:1260558 original size:5 final size:5
Alignment explanation
Indices: 1260548--1260572 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1260538 TTTGTTATTG
1260548 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
1260573 AAAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:1260756 original size:20 final size:19
Alignment explanation
Indices: 1260703--1260757 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1260693 ATGATCTATC
1260703 TATATATATAT-ATATAGA
1 TATATATATATAATATAGA
* * *
1260721 TAGATCATAAAAAATATAGA
1 TATAT-ATATATAATATAGA
1260741 TATTATATATATAATAT
1 TA-TATATATATAATAT
1260758 CTATATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 18 0.64
21 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (19 bp):
TATATATATATAATATAGA
Found at i:1260811 original size:2 final size:2
Alignment explanation
Indices: 1260664--1260794 Score: 51
Period size: 2 Copynumber: 67.5 Consensus size: 2
1260654 ATGCGTTTTC
* * * * *
1260664 AT AT -T AT AT AT AT A- AT AT CT AT AT -T TT TT AT GAT CT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
* * * * *
1260704 AT AT AT AT AT AT AT AG AT AG AT CAT A- AA AA AT AT AG AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
* * * * *
1260745 AT AT AT AT A- AT AT CT AT AT -T TT TT AT GAT CT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
1260786 AT AT AT AT A
1 AT AT AT AT A
1260795 CACGTACCCT
Statistics
Matches: 98, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
1 7 0.07
2 85 0.87
3 6 0.06
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1260925 original size:13 final size:13
Alignment explanation
Indices: 1260907--1260932 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1260897 TTTTTAAAAC
1260907 ATGTATTTTATAT
1 ATGTATTTTATAT
1260920 ATGTATTTTATAT
1 ATGTATTTTATAT
1260933 TTTATGATTC
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATGTATTTTATAT
Found at i:1261278 original size:16 final size:16
Alignment explanation
Indices: 1261256--1261294 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1261246 ATAACGTATA
*
1261256 CATATATATATACTTT
1 CATATATACATACTTT
* *
1261272 TATATATACATGCTTT
1 CATATATACATACTTT
1261288 CATATAT
1 CATATAT
1261295 CTCCATAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (16 bp):
CATATATACATACTTT
Found at i:1262185 original size:21 final size:21
Alignment explanation
Indices: 1262142--1262187 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1262132 TTGAATCTCA
* **
1262142 GCTTCTCTCGCTGCTGCCTCT
1 GCTTCTCTCGCTGCCGCAACT
*
1262163 GCTTCTCTCGTTGCCGCAACT
1 GCTTCTCTCGCTGCCGCAACT
1262184 GCTT
1 GCTT
1262188 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.39, G:0.20, T:0.37
Consensus pattern (21 bp):
GCTTCTCTCGCTGCCGCAACT
Found at i:1267760 original size:25 final size:25
Alignment explanation
Indices: 1267732--1267836 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
1267722 GTTACATAAT
*
1267732 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
*
1267757 TTATGAACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
* *
1267783 TCATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* * *
1267808 TTGTGTATTATGTAACTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
1267833 TTAT
1 TTAT
1267837 CAAAGTAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
23 1 0.02
24 2 0.03
25 41 0.64
26 17 0.27
27 2 0.03
28 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:1267827 original size:9 final size:9
Alignment explanation
Indices: 1267743--1268096 Score: 254
Period size: 9 Copynumber: 41.3 Consensus size: 9
1267733 TATGTATTAA
*
1267743 GTAAATTAT
1 GTAAGTTAT
1267752 GTAAGTTAT
1 GTAAGTTAT
1267761 G-AACGTGTA-
1 GTAA-GT-TAT
1267770 -TAAGTTAT
1 GTAAGTTAT
*
1267778 GTAAGTCAT
1 GTAAGTTAT
*
1267787 GT-A-TTAA
1 GTAAGTTAT
*
1267794 GTAAGCTAT
1 GTAAGTTAT
*
1267803 GTAAGTTGT
1 GTAAGTTAT
1267812 GT-A-TTAT
1 GTAAGTTAT
*
1267819 GTAACTTAT
1 GTAAGTTAT
1267828 GTAAGTTAT
1 GTAAGTTAT
** *
1267837 CAAAGTAAT
1 GTAAGTTAT
*
1267846 GTATGTTAT
1 GTAAGTTAT
1267855 GTAAG-T-T
1 GTAAGTTAT
1267862 GTAAGTTAT
1 GTAAGTTAT
1267871 GT-A-TTAT
1 GTAAGTTAT
1267878 GT-AGCTTAT
1 GTAAG-TTAT
1267887 GTAAGTTA-
1 GTAAGTTAT
** *
1267895 CCAAATTAAT
1 GTAAGTT-AT
*
1267905 GTATGTTAT
1 GTAAGTTAT
1267914 GTAAG-T-T
1 GTAAGTTAT
1267921 GTAAGTTAT
1 GTAAGTTAT
1267930 GT-A-TTAT
1 GTAAGTTAT
*
1267937 GTAACTTAT
1 GTAAGTTAT
1267946 GTAAGTTAT
1 GTAAGTTAT
* *
1267955 -CAAATTAAT
1 GTAAGTT-AT
*
1267964 GTATGTTAT
1 GTAAGTTAT
1267973 GTAAG-T-T
1 GTAAGTTAT
1267980 GTAAGTTAT
1 GTAAGTTAT
*
1267989 -TATGTATTAT
1 GTAAG--TTAT
1267999 GTAAGTTAT
1 GTAAGTTAT
1268008 GTAAGTTAT
1 GTAAGTTAT
1268017 GTAAGTTAT
1 GTAAGTTAT
1268026 GT-A-TTAT
1 GTAAGTTAT
*
1268033 GTAGGTTAT
1 GTAAGTTAT
*
1268042 GTAAGTTGT
1 GTAAGTTAT
*
1268051 GTAAGATAT
1 GTAAGTTAT
*
1268060 TTAAGTTAT
1 GTAAGTTAT
*
1268069 GTAAGTTTT
1 GTAAGTTAT
1268078 GT-A-TTAT
1 GTAAGTTAT
1268085 GTAAGTTAT
1 GTAAGTTAT
1268094 GTA
1 GTA
1268097 TGCTATGTAT
Statistics
Matches: 269, Mismatches: 45, Indels: 62
0.72 0.12 0.16
Matches are distributed among these distances:
7 53 0.20
8 31 0.12
9 168 0.62
10 14 0.05
11 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:1267849 original size:59 final size:58
Alignment explanation
Indices: 1267770--1268053 Score: 329
Period size: 59 Copynumber: 4.8 Consensus size: 58
1267760 TGAACGTGTA
** * * *
1267770 TAAGTTATGTAAGTCATGTA-TTAAGTAAGCTATGTAAGTTGTGTATTATGTAACTTATG
1 TAAGTTATCAAAGTAATGTAGTTATGTAAG-T-TGTAAGTTATGTATTATGTAACTTATG
*
1267829 TAAGTTATCAAAGTAATGTATGTTATGTAAGTTGTAAGTTATGTATTATGTAGCTTATG
1 TAAGTTATCAAAGTAATGTA-GTTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
* *
1267888 TAAGTTACCAAATTAATGTATGTTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
1 TAAGTTATCAAAGTAATGTA-GTTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
* *
1267947 TAAGTTATCAAATTAATGTATGTTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTATG
1 TAAGTTATCAAAGTAATGTA-GTTATGTAAGTTGTAAG---TTATGTATTATGTAACTTATG
** * * *
1268009 TAAGTTATGTAAGTTATGTA-TTATGTAGGTTATGTAAGTTGTGTA
1 TAAGTTATCAAAGTAATGTAGTTATGTAAG-T-TGTAAGTTATGTA
1268054 AGATATTTAA
Statistics
Matches: 201, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
59 141 0.70
60 9 0.04
61 9 0.04
62 42 0.21
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (58 bp):
TAAGTTATCAAAGTAATGTAGTTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
Found at i:1267993 original size:19 final size:19
Alignment explanation
Indices: 1267969--1268025 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1267959 TTAATGTATG
1267969 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
1267988 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
*
1268007 TGTAAGT--TATGTAAGTTA
1 T-TATGTAGTATGTAAGTTA
1268025 T
1 T
1268026 GTATTATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 14 0.41
19 16 0.47
20 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:1268054 original size:34 final size:34
Alignment explanation
Indices: 1267770--1268239 Score: 218
Period size: 34 Copynumber: 13.9 Consensus size: 34
1267760 TGAACGTGTA
* * *
1267770 TAAGTTATGTAAGTCATGTATTAAGTAAGCTATG
1 TAAGTTATGTAAGTTATGTATTATGTAAGTTATG
* *
1267804 TAAGTTGTGT-A-TTATGTAACTTATGTAAGTTATC
1 TAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATG
* * * *
1267838 AAAGTAATGTATGTTATGTAAGT-TGTAAGTTATG
1 TAAGTTATGTAAGTTATGT-ATTATGTAAGTTATG
** *
1267872 T-A-TTATGT-AGCTTATGTAAGTTA-CCAAATTAATG
1 TAAGTTATGTAAG-TTATGT-A-TTATGTAAGTT-ATG
*
1267906 TATGTTATGTAAG-T-TGTAAGTTATGT-A-TTATG
1 TAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATG
* ** *
1267938 TAACTTATGTAAGTTATCAAATTAATGTATGTTATG
1 TAAGTTATGTAAGTTAT-GTATT-ATGTAAGTTATG
1267974 TAAG-T-TGTAAGTTATTATGTATTATGTAAGTTATG
1 TAAGTTATGTAAG---TTATGTATTATGTAAGTTATG
*
1268009 TAAGTTATGTAAGTTATGTATTATGTAGGTTATG
1 TAAGTTATGTAAGTTATGTATTATGTAAGTTATG
* * * *
1268043 TAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTG
1 TAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATG
1268079 T-A-TTATGTAAGTTATGTATGCTATGT-A-TTATG
1 TAAGTTATGTAAGTTATGTAT--TATGTAAGTTATG
* * * * *
1268111 TGAGTTTATATAA--AAT-TTTTATATAAGTTATG
1 TAAG-TTATGTAAGTTATGTATTATGTAAGTTATG
* ** *
1268143 T-A-TTATGCAAG----GTAACATATAAGTTTATG
1 TAAGTTATGTAAGTTATGTATTATGTAAG-TTATG
*
1268172 TAAGTTATGAATGTAAGTTATGTATTATGTAAGTTATT
1 TAAG-T-T--ATGTAAGTTATGTATTATGTAAGTTATG
* * * *
1268210 TAAATTATTTAAGTTGTGTATTAAGTAAGT
1 TAAGTTATGTAAGTTATGTATTATGTAAGT
1268240 CATGCAGGCT
Statistics
Matches: 333, Mismatches: 58, Indels: 90
0.69 0.12 0.19
Matches are distributed among these distances:
28 8 0.02
29 12 0.04
30 5 0.02
31 3 0.01
32 47 0.14
33 19 0.06
34 137 0.41
35 33 0.10
36 40 0.12
37 13 0.04
38 7 0.02
39 9 0.03
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (34 bp):
TAAGTTATGTAAGTTATGTATTATGTAAGTTATG
Found at i:1268054 original size:43 final size:43
Alignment explanation
Indices: 1267743--1268229 Score: 231
Period size: 43 Copynumber: 11.5 Consensus size: 43
1267733 TATGTATTAA
* * *
1267743 GTAAATTATGTAAGTTATG-AACGTGTAT-AAGTTATGTAAGTCAT
1 GTAAGTTATGTAAGTTATGTAA-GT-TATGTA-TTATGTAAGTTAT
* * * *
1267787 GT-A-TTAAGTAAGCTATGTAAGTTGTGTATTATGTAACTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
** * * *
1267828 GTAAGTTATCAAAGTAATGTATGTTATGTAAGT-TGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGT-ATTATGTAAGTTAT
*** *
1267871 GT-A-TTATGT-AGCTTATGTAAGTTACCAAATTAATGTATGTTAT
1 GTAAGTTATGTAAG-TTATGTAAGTTA-TGTATT-ATGTAAGTTAT
1267914 GTAAG-T-TGTAAGTTATGT-A-TTATGTAACTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
* * * *
1267955 -CAAATTAATGTATGTTATGTAAGTTGTAAGTTATTATGT-A-TTAT
1 GTAAGTT-ATGTAAGTTATGTAAG-T-TATG-TATTATGTAAGTTAT
*
1267999 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAGGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
* * *
1268042 GTAAGTTGTGTAAGATATTTAAGTTATGTA--A-GT---TT-T
1 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
* * *
1268078 GT-A-TTATGTAAGTTATGTATGCTATGTATTATGTGAGTTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAG-TTAT
* * * * * *
1268120 ATAA--AAT-T--TTTATATAAGTTATGTATTATGCAAGGTAACAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAA-GT--TAT
*
1268161 ATAAGTTTATGTAAGTTATGAATGTAAGTTATGTATTATGTAAGTTAT
1 GTAAG-TTATGTAAG-T-T--ATGTAAGTTATGTATTATGTAAGTTAT
* * * *
1268209 TTAAATTATTTAAGTTGTGTA
1 GTAAGTTATGTAAGTTATGTA
1268230 TTAAGTAAGT
Statistics
Matches: 333, Mismatches: 63, Indels: 95
0.68 0.13 0.19
Matches are distributed among these distances:
34 20 0.06
35 1 0.00
36 4 0.01
37 4 0.01
39 20 0.06
40 7 0.02
41 64 0.19
42 27 0.08
43 99 0.30
44 30 0.09
45 7 0.02
46 8 0.02
47 12 0.04
48 7 0.02
49 1 0.00
50 2 0.01
51 20 0.06
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (43 bp):
GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
Found at i:1268116 original size:25 final size:25
Alignment explanation
Indices: 1267800--1268097 Score: 116
Period size: 25 Copynumber: 12.0 Consensus size: 25
1267790 TTAAGTAAGC
*
1267800 TATGTAAGTTGTGT-A-TTATGTAACT
1 TATGTAAGTTATGTAAGTTATGT-A-T
** *
1267825 TATGTAAGTTATCAAAGTAATGTATGT
1 TATGTAAGTTATGTAAGTTATGTA--T
1267852 TATGTAAG-T-TGTAAGTTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
***
1267875 TATGT-AGCTTATGTAAGTTACCAAAT
1 TATGTAAG-TTATGTAAGTTA-TGTAT
*
1267901 TAATGTATGTTATGTAAG-T-TGTAAGT
1 T-ATGTAAGTTATGTAAGTTATGT-A-T
*
1267927 TATGT-A-TTATGTAACTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
* * * *
1267952 TAT-CAAATTAATGTATGTTATGTAAG
1 TATGTAAGTT-ATGTAAGTTATGT-AT
1267978 T-TGTAAG---T-T-A-TTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
1267996 TATGTAAGTTATGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
*
1268023 TATGT-A-TTATGTAGGTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
* * *
1268048 TGTGTAAGATATTTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
*
1268075 TTTGT-A-TTATGTAAGTTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
1268098 GCTATGTATT
Statistics
Matches: 212, Mismatches: 33, Indels: 58
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.01
19 12 0.06
21 1 0.00
22 4 0.02
23 16 0.08
24 4 0.02
25 88 0.42
26 18 0.08
27 66 0.31
28 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (25 bp):
TATGTAAGTTATGTAAGTTATGTAT
Found at i:1268187 original size:13 final size:15
Alignment explanation
Indices: 1268168--1268208 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
1268158 CATATAAGTT
1268168 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
1268182 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
1268196 TTATGTAAGTTAT
1 -TATGTAAGTTAT
1268209 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:1268319 original size:19 final size:20
Alignment explanation
Indices: 1268297--1268343 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1268287 TTTTTCAAAT
* *
1268297 ATATATAAAATTTTA-ATAA
1 ATATATAAAACTGTATATAA
1268316 ATATATTAAAACTGTATATAA
1 ATATA-TAAAACTGTATATAA
1268337 ATATATA
1 ATATATA
1268344 TATCAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATATAAAACTGTATATAA
Found at i:1268319 original size:21 final size:22
Alignment explanation
Indices: 1268293--1268345 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1268283 TAAATTTTTC
* *
1268293 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAACTGTATAT
1268314 AAATATAT-TAAAACTGTATAT
1 AAATATATATAAAACTGTATAT
1268335 AAATATATATA
1 AAATATATATA
1268346 TCAAAGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATATAAAACTGTATAT
Found at i:1271210 original size:27 final size:27
Alignment explanation
Indices: 1271162--1271213 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1271152 TCTTACATTT
* *
1271162 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
**
1271189 AAATAAATAATTACTTACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
1271214 TTTGTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:1271640 original size:17 final size:18
Alignment explanation
Indices: 1271606--1271646 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1271596 ACCCCGGCCA
*
1271606 AACCCCTAAAACCTCTCT
1 AACCCTTAAAACCTCTCT
*
1271624 AACCCTTAAATCC-CTCT
1 AACCCTTAAAACCTCTCT
1271641 AACCCT
1 AACCCT
1271647 AATTAACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (18 bp):
AACCCTTAAAACCTCTCT
Found at i:1273079 original size:14 final size:14
Alignment explanation
Indices: 1273060--1273127 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
1273050 ATGACCGTTG
1273060 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
1273074 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
1273089 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
1273102 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
1273115 AAACCTTAAATCT
1 AAACCCTAAATCT
1273128 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:1273083 original size:15 final size:15
Alignment explanation
Indices: 1273063--1273100 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1273053 ACCGTTGAAA
1273063 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
1273078 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
1273093 CCCTAAAT
1 CCCTAAAT
1273101 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:1273639 original size:41 final size:40
Alignment explanation
Indices: 1273575--1273813 Score: 194
Period size: 41 Copynumber: 5.8 Consensus size: 40
1273565 TTTTGTTACT
1273575 ATTAGCGGCGCTTAGA-AACAAACGCCGCTAAAGGCAGGAGA
1 ATTAGCGGCGCTTAGATAA-AAACGCCGCTAAAGGCA-GAGA
* * * * * * *
1273616 ATTAGTGGCGCTCAGATAAAAACGTCACTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAG-GCAGAGA
** * *
1273657 ATTAGCGGTTCTTAGACAAAAACGCCGCTAAAGGCCAGAGG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-CAGAGA
* * * * * *
1273698 ATTAGTGGCGCTGAGATAAAAACGCCACTAAAGCTCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAG-GCAGAGA
* * * *
1273739 CTTAGCGGCGCTTAGACAAAAATGTCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-CAGAGA
* *
1273780 TTTAGCGGCGCTCATG-TAAAAACGCCGCTAAAGG
1 ATTAGCGGCGCTTA-GATAAAAACGCCGCTAAAGG
1273814 TTTAAAAATC
Statistics
Matches: 151, Mismatches: 41, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
41 147 0.97
42 4 0.03
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCAGAGA
Found at i:1273715 original size:82 final size:82
Alignment explanation
Indices: 1273575--1273812 Score: 313
Period size: 82 Copynumber: 2.9 Consensus size: 82
1273565 TTTTGTTACT
*
1273575 ATTAGCGGCGCTTAGA-AACAAACGCCGCTAAAGG-CAGGAGAATTAGTGGCGCTCAGATAAAAA
1 ATTAGCGGCGCTTAGACAA-AAACGCCGCTAAAGGCCA-GAGGATTAGTGGCGCTCAGATAAAAA
*
1273638 CGTCACTAAAGATCCGAGC
64 CGCCACTAAAGATCCGAGC
** *
1273657 ATTAGCGGTTCTTAGACAAAAACGCCGCTAAAGGCCAGAGGATTAGTGGCGCTGAGATAAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAGGATTAGTGGCGCTCAGATAAAAACG
*
1273722 CCACTAAAGCTCCGAGC
66 CCACTAAAGATCCGAGC
* * * *
1273739 CTTAGCGGCGCTTAGACAAAAATGTCGCTAAAGGCCAGA-GATTTAGCGGCGCTCATG-TAAAAA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAGGA-TTAGTGGCGCTCA-GATAAAAA
*
1273802 CGCCGCTAAAG
64 CGCCACTAAAG
1273813 GTTTAAAAAT
Statistics
Matches: 138, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
81 2 0.01
82 131 0.95
83 5 0.04
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (82 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCCAGAGGATTAGTGGCGCTCAGATAAAAACG
CCACTAAAGATCCGAGC
Found at i:1275114 original size:22 final size:22
Alignment explanation
Indices: 1275049--1275116 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
1275039 ATTTGGAAAT
*
1275049 CAACAATTCAATATTTTATATG
1 CAACAATTCAATAATTTATATG
* *
1275071 CAGAAAATT-AATAA---AAAT-
1 CA-ACAATTCAATAATTTATATG
1275089 CAACAATTCAATAATTTATATG
1 CAACAATTCAATAATTTATATG
1275111 CAACAA
1 CAACAA
1275117 AGTAGTCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
17 5 0.14
18 7 0.20
19 3 0.09
21 3 0.09
22 12 0.34
23 5 0.14
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (22 bp):
CAACAATTCAATAATTTATATG
Found at i:1276483 original size:21 final size:21
Alignment explanation
Indices: 1276457--1276514 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1276447 AAAACTGAGA
1276457 AATTTTTTAATAAATATTTT-
1 AATTTTTTAATAAATATTTTG
**
1276477 AATTTTTTGAAT-GCTATTTTG
1 AATTTTTT-AATAAATATTTTG
*
1276498 AAATTTTTAATAAATAT
1 AATTTTTTAATAAATAT
1276515 AATGGATACC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
AATTTTTTAATAAATATTTTG
Found at i:1283688 original size:21 final size:21
Alignment explanation
Indices: 1283662--1283702 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1283652 ATCTGCTCAA
*
1283662 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
1283683 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
1283703 TTGCTCGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:1288433 original size:26 final size:24
Alignment explanation
Indices: 1288388--1288435 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1288378 TATAATTAAT
*
1288388 TATTTAAACACATTTAATATTTTA
1 TATTTAAAAACATTTAATATTTTA
1288412 TATTTAATAAACATCTTAATATTT
1 TATTTAA-AAACAT-TTAATATTT
1288436 AAGATTGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTAAAAACATTTAATATTTTA
Found at i:1288808 original size:128 final size:131
Alignment explanation
Indices: 1288631--1288903 Score: 399
Period size: 128 Copynumber: 2.0 Consensus size: 131
1288621 TTGCTTCGTG
* *
1288631 TTGGACAGTATGGCTAGCTTGAAACGAGAAGGTGTTTGAAAGGTCGGTGGCTACAATTGATTCTT
1 TTGGACAATATGGCTAGCTTGAAACGAGAAGGTGTTTAAAAGGTCGGTGGCTACAATTGATTCTT
*
1288696 TAATCTTTC-AA-AG-TTGATGTGGGCTAGATCGGTACATGATGATTGTATATTTTCGGAGGTTG
66 TAATCTTTCAAAGAGATTGATGTGGGCTAGATCGGTACATGATGATTCTATATTTTCGGAGGTTG
1288758 A
131 A
*
1288759 TTGGACAATATGGCTAGCTTGAAACGAGAAGGTGTTTAAAAGGTCGGTGGCTGCAATTGATTCTT
1 TTGGACAATATGGCTAGCTTGAAACGAGAAGGTGTTTAAAAGGTCGGTGGCTACAATTGATTCTT
1288824 TAATCTTTCAATAAAAAATGAGATCATTGATGTGGGCTAGATCGGTACATGATGATTCTATATTT
66 TAATCTTTC------AAA-GAG---ATTGATGTGGGCTAGATCGGTACATGATGATTCTATATTT
1288889 TCGGAGGTTGA
121 TCGGAGGTTGA
1288900 TTGG
1 TTGG
1288904 CGGGGATGGC
Statistics
Matches: 128, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
128 71 0.55
135 2 0.02
137 2 0.02
141 53 0.41
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (131 bp):
TTGGACAATATGGCTAGCTTGAAACGAGAAGGTGTTTAAAAGGTCGGTGGCTACAATTGATTCTT
TAATCTTTCAAAGAGATTGATGTGGGCTAGATCGGTACATGATGATTCTATATTTTCGGAGGTTG
A
Found at i:1289570 original size:11 final size:11
Alignment explanation
Indices: 1289554--1289596 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1289544 TAGAATATAT
1289554 CCCATACCTTG
1 CCCATACCTTG
*
1289565 CCCATACCTTT
1 CCCATACCTTG
*
1289576 CCCATACC-TA
1 CCCATACCTTG
1289586 CCCATACCTTG
1 CCCATACCTTG
1289597 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:1289581 original size:22 final size:21
Alignment explanation
Indices: 1289553--1289595 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1289543 TTAGAATATA
*
1289553 TCCCATACCTTGCCCATACCTT
1 TCCCATACC-TACCCATACCTT
1289575 TCCCATACCTACCCATACCTT
1 TCCCATACCTACCCATACCTT
1289596 GGAAAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.21, C:0.47, G:0.02, T:0.30
Consensus pattern (21 bp):
TCCCATACCTACCCATACCTT
Found at i:1291859 original size:25 final size:24
Alignment explanation
Indices: 1291816--1291864 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1291806 TGTCAACAAT
* *
1291816 AATTTTTTATTTTATATATTTTTA
1 AATTTATTATTTTATATATATTTA
1291840 AATTTATTATTTTTATATATATTTA
1 AATTTATTA-TTTTATATATATTTA
1291865 TTGAATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
AATTTATTATTTTATATATATTTA
Found at i:1291862 original size:15 final size:15
Alignment explanation
Indices: 1291819--1291862 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1291809 CAACAATAAT
1291819 TTTTTAT-TTTATATA
1 TTTTTATATTTAT-TA
*
1291834 TTTTTAAATTTATTA
1 TTTTTATATTTATTA
*
1291849 TTTTTATATATATT
1 TTTTTATATTTATT
1291863 TATTGAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTATATTTATTA
Found at i:1292355 original size:275 final size:275
Alignment explanation
Indices: 1291864--1292414 Score: 1093
Period size: 275 Copynumber: 2.0 Consensus size: 275
1291854 ATATATATTT
1291864 ATTGAATTGTTTAGATTTAGAATCAAATTGAGAACACTTGTAAATTTTGAGGTTAATTTTTTAAA
1 ATTGAATTGTTTAGATTTAGAATCAAATTGAGAACACTTGTAAATTTTGAGGTTAATTTTTTAAA
1291929 ATCATGACTAAATTGATATAATATGTAAAAGTTGTGGGCTAAATAACTGAACTATATAATGTAGG
66 ATCATGACTAAATTGATATAATATGTAAAAGTTGTGGGCTAAATAACTGAACTATATAATGTAGG
1291994 TGCTGAAATTGTAAACTTTTTAGCTTGGGTGCCTAAAATAAAAATTTTTGATAGTTGGGTGATTA
131 TGCTGAAATTGTAAACTTTTTAGCTTGGGTGCCTAAAATAAAAATTTTTGATAGTTGGGTGATTA
*
1292059 TGTATGCAGTTTACCCATATTATTATCAATAATATATAAATAACTTTAAAATATAACCCCTGAAT
196 TGTATGCAGTTTACCCATATTATTATCAATAATATATAAATAACTTTAAAATATAAACCCTGAAT
1292124 TTTTTTAAATGAAAA
261 TTTTTTAAATGAAAA
1292139 ATTGAATTGTTTAGATTTAGAATCAAATTGAGAACACTTGTAAATTTTGAGGTTAATTTTTTAAA
1 ATTGAATTGTTTAGATTTAGAATCAAATTGAGAACACTTGTAAATTTTGAGGTTAATTTTTTAAA
1292204 ATCATGACTAAATTGATATAATATGTAAAAGTTGTGGGCTAAATAACTGAACTATATAATGTAGG
66 ATCATGACTAAATTGATATAATATGTAAAAGTTGTGGGCTAAATAACTGAACTATATAATGTAGG
1292269 TGCTGAAATTGTAAACTTTTTAGCTTGGGTGCCTAAAATAAAAATTTTTGATAGTTGGGTGATTA
131 TGCTGAAATTGTAAACTTTTTAGCTTGGGTGCCTAAAATAAAAATTTTTGATAGTTGGGTGATTA
1292334 TGTATGCAGTTTACCCATATTATTATCAATAATATATAAATAACTTTAAAATATAAACCCTGAAT
196 TGTATGCAGTTTACCCATATTATTATCAATAATATATAAATAACTTTAAAATATAAACCCTGAAT
1292399 TTTTTTAAATGAAAA
261 TTTTTTAAATGAAAA
1292414 A
1 A
1292415 ACTTTAAAGA
Statistics
Matches: 275, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
275 275 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (275 bp):
ATTGAATTGTTTAGATTTAGAATCAAATTGAGAACACTTGTAAATTTTGAGGTTAATTTTTTAAA
ATCATGACTAAATTGATATAATATGTAAAAGTTGTGGGCTAAATAACTGAACTATATAATGTAGG
TGCTGAAATTGTAAACTTTTTAGCTTGGGTGCCTAAAATAAAAATTTTTGATAGTTGGGTGATTA
TGTATGCAGTTTACCCATATTATTATCAATAATATATAAATAACTTTAAAATATAAACCCTGAAT
TTTTTTAAATGAAAA
Found at i:1307343 original size:132 final size:133
Alignment explanation
Indices: 1307099--1307720 Score: 875
Period size: 132 Copynumber: 4.7 Consensus size: 133
1307089 TGAAGTCATT
* * * *
1307099 AAAGCAGATCTTCTCTTCATGTATTGGCATGAAGTAGATCGAGGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* *
1307164 TATTGGTAGAAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
1307228 AAG
131 AAG
* * * * * *
1307231 AAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTGGATCAAAGAT-GCAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* *** ***
1307295 TATTGGTGGCGAAGTGGATCGAAGAAAGCAGATCTTGTC-TCATGTATTGG-CATGAAGTAGATC
66 TATTGGTAG-GAAGTGGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
1307358 GAAG
130 GAAG
* *
1307362 -ATGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* *
1307426 TATTGGTAGGAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCCATATCGGTGGCGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
*
1307490 CAG
131 AAG
*
1307493 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* * * * *
1307558 TATTGATAGGAAGTGGATCCAAGATA-CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCG
66 TATTGGTAGGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
1307622 AAG
131 AAG
**
1307625 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGCCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
*
1307690 TATTGGTAGGAAGTGGATTGAA-AAA-CAGATC
66 TATTGGTAGGAAGTGGATCGAAGAAAGCAGATC
1307721 CTATCTCCCT
Statistics
Matches: 428, Mismatches: 55, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
129 13 0.03
130 61 0.14
131 80 0.19
132 261 0.61
133 13 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (133 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
AAG
Found at i:1307573 original size:262 final size:264
Alignment explanation
Indices: 1307099--1307707 Score: 913
Period size: 262 Copynumber: 2.3 Consensus size: 264
1307089 TGAAGTCATT
* * *
1307099 AAAGCAGATCTTCTCTTCATGTATTGGCATGAAGTAGATCG-AGGATAGCAGGTCCTATCTTCCT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGG-TAGCAGATCCTATCTTCCT
* *
1307163 ATATTGGTAGAAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
65 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATCGGTGGCGAAGTAGATCG
* * *
1307228 AAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTGGATCAAAGATGCAGATCTTGTCTTCC
130 AAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATGCAGATCCTATCTTCC
* * * ** *
1307293 CATATTGGTGGCGAAGTGGATCGAAGAAAGCAGATCTTGTC-TCATGTATTGG-CATGAAGTAGA
195 CATATTGATAGCGAAGTGGATCCAAGAAA-CAGATCTTGTCTTCACATACTGGTCATGAAGTAGA
1307356 TCGAAG
259 TCGAAG
*
1307362 -ATGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
*
1307426 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATCGGTGGCGAAGTAGATCGC
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATCGGTGGCGAAGTAGATCGA
* * *
1307491 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
131 AGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAT-GCAGATCCTATCTTCC
* * * **
1307556 TATATTGATAG-GAAGTGGATCCAAGATACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGAT
195 CATATTGATAGCGAAGTGGATCCAAGAAACAGATCTTGTCTTCACATACTGGTCATGAAGTAGAT
1307620 CGAAG
260 CGAAG
* **
1307625 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGCCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
1307690 TATTGGTAGGAAGTGGAT
66 TATTGGTAGGAAGTGGAT
1307708 TGAAAAACAG
Statistics
Matches: 313, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
261 11 0.04
262 185 0.59
263 39 0.12
264 78 0.25
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (264 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATCGGTGGCGAAGTAGATCGA
AGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATGCAGATCCTATCTTCCC
ATATTGATAGCGAAGTGGATCCAAGAAACAGATCTTGTCTTCACATACTGGTCATGAAGTAGATC
GAAG
Found at i:1307703 original size:44 final size:45
Alignment explanation
Indices: 1307101--1307703 Score: 563
Period size: 44 Copynumber: 13.8 Consensus size: 45
1307091 AAGTCATTAA
* * * * *
1307101 AGCAGATCTTCTCTTCATGTATTGGCA-TGAAGTAGATCGAGGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * * *
1307145 AGCAGGTCCTATCTTCCTATATTGGTAG-AAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * *
1307189 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * * * *
1307233 AGCAAATCTTGTCTTCATGTATTGG-CGTGAAGTGGATCAAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * * *
1307277 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTGGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * *
1307321 AGCAGATCTTGTC-TCATGTATTGGCA-TGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * *
1307364 -GCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * *
1307407 AGCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * * * *
1307451 -GCAGATCTTGTCTTCCCATATCGGTGGCGAAGTAGATCGCAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * *
1307495 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * * * *
1307539 AGCAGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * * *
1307583 A-CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* * *
1307627 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
* *
1307671 AGCAGATCCTGCCTTCCTATATTGGTAG-GAAGT
1 AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGT
1307704 GGATTGAAAA
Statistics
Matches: 447, Mismatches: 97, Indels: 30
0.78 0.17 0.05
Matches are distributed among these distances:
42 12 0.03
43 124 0.28
44 237 0.53
45 74 0.17
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT
Found at i:1309309 original size:22 final size:22
Alignment explanation
Indices: 1309284--1309340 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
1309274 TTAACACTAT
1309284 TTTTGTATATTTTTAA-ACTGTC
1 TTTT-TATATTTTTAAGACTGTC
*
1309306 TTTTT-TATTATTTAAGACTTTC
1 TTTTTATATT-TTTAAGACTGTC
1309328 TTTTATATATTTT
1 TTTT-TATATTTT
1309341 ATTTTAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTTATATTTTTAAGACTGTC
Found at i:1309338 original size:21 final size:20
Alignment explanation
Indices: 1309289--1309339 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1309279 ACTATTTTTG
*
1309289 TATATTTTTAAACTGTCTTT
1 TATATATTTAAACTGTCTTT
* *
1309309 TTTATTATTTAAGACTTTCTTT
1 TATA-TATTTAA-ACTGTCTTT
1309331 TATATATTT
1 TATATATTT
1309340 TATTTTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 11 0.44
22 11 0.44
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (20 bp):
TATATATTTAAACTGTCTTT
Found at i:1314338 original size:14 final size:14
Alignment explanation
Indices: 1314319--1314346 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1314309 AATAATGCAC
1314319 TCATTATTTAATTA
1 TCATTATTTAATTA
1314333 TCATTATTTAATTA
1 TCATTATTTAATTA
1314347 GATCAACAGA
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:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TCATTATTTAATTA
Found at i:1317273 original size:72 final size:72
Alignment explanation
Indices: 1317126--1317273 Score: 190
Period size: 72 Copynumber: 2.1 Consensus size: 72
1317116 GAGGAAAAGT
* *
1317126 ACCATTTAATTGATTTTCTGAAACATCAAATAACTTCAAAGATGACAGCTCCCCTAGAGACCATG
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGATGAAAGCTCCCCTAGAGACCATG
**
1317191 GAATTTG
66 GAATGGG
* * ** **
1317198 ACCATTTAATTGATTTTCTGAAATATCAAAGAATTTCAAAGATGATAAG-TCCCCTATCGATGAT
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGATGA-AAGCTCCCCTAGAGACCAT
1317262 GGAATGGG
65 GGAATGGG
1317270 ACCA
1 ACCA
1317274 GAAATTTTGT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 63 0.97
73 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAAGAACTTCAAAGATGAAAGCTCCCCTAGAGACCATG
GAATGGG
Found at i:1323902 original size:20 final size:20
Alignment explanation
Indices: 1323877--1323915 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1323867 TCGTCCGTTA
1323877 TATTTCCTATTAGGTGATTC
1 TATTTCCTATTAGGTGATTC
1323897 TATTTCCTATTAGGTGATT
1 TATTTCCTATTAGGTGATT
1323916 TCTTGATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (20 bp):
TATTTCCTATTAGGTGATTC
Found at i:1333658 original size:13 final size:14
Alignment explanation
Indices: 1333618--1333660 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
1333608 ACTAATGACA
1333618 AATTAAACCATTAT
1 AATTAAACCATTAT
1333632 AATTAAACCATTAT
1 AATTAAACCATTAT
1333646 AATTAAA-CATTAT
1 AATTAAACCATTAT
1333659 AA
1 AA
1333661 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:1335480 original size:27 final size:27
Alignment explanation
Indices: 1335450--1335507 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1335440 GTTTTGTAAG
* *
1335450 TTATAAAAGTTATGGTATGATATATAT
1 TTATAAAAGTTATGATATAATATATAT
**
1335477 TTATGTAAGTTATGATATAATATATAT
1 TTATAAAAGTTATGATATAATATATAT
1335504 TTAT
1 TTAT
1335508 GTATTATGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (27 bp):
TTATAAAAGTTATGATATAATATATAT
Done.