Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 140 of 204
Found at i:42395766 original size:12 final size:12
Alignment explanation
Indices: 42395687--42395780 Score: 68
Period size: 12 Copynumber: 7.7 Consensus size: 12
42395677 CATTTCATAG
*
42395687 TTTTATTTTTTA
1 TTTTATTTTTAA
42395699 TTTCTCATTTTT-A
1 TTT-T-ATTTTTAA
* *
42395712 TCTTTATCTTTCA
1 T-TTTATTTTTAA
42395725 TTTTGA--TTTAA
1 TTTT-ATTTTTAA
**
42395736 TTTTAAATTTAA
1 TTTTATTTTTAA
42395748 TCTTTATTTTTAA
1 T-TTTATTTTTAA
*
42395761 TTTTATTGTTAA
1 TTTTATTTTTAA
42395773 TTTTATTT
1 TTTTATTT
42395781 ATTTTATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
10 1 0.01
11 8 0.12
12 34 0.50
13 17 0.25
14 8 0.12
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:42397776 original size:25 final size:24
Alignment explanation
Indices: 42397736--42397783 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
42397726 TTTCTTTAGT
*
42397736 TTTTATTTCTCTTTAGTTTTTTAA
1 TTTTATTTCTCTTTAGTATTTTAA
42397760 TTTTATTTCT-TAGTTAGTATTTTA
1 TTTTATTTCTCT--TTAGTATTTTA
42397784 CTTTCGCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 10 0.48
25 10 0.48
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (24 bp):
TTTTATTTCTCTTTAGTATTTTAA
Found at i:42398434 original size:17 final size:17
Alignment explanation
Indices: 42398412--42398447 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42398402 TTTTGAGCTT
42398412 AATGGCCTATTTATTGC
1 AATGGCCTATTTATTGC
42398429 AATGGCCTATTTATTGC
1 AATGGCCTATTTATTGC
42398446 AA
1 AA
42398448 ATTACCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (17 bp):
AATGGCCTATTTATTGC
Found at i:42399040 original size:36 final size:36
Alignment explanation
Indices: 42399000--42399075 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
42398990 ATTGAAAATG
42399000 CATGCAAACTATGATTCATGTTGACATTATGATGTA
1 CATGCAAACTATGATTCATGTTGACATTATGATGTA
42399036 CATGCAAACTATGATTCATGTTGACATTATGATGTA
1 CATGCAAACTATGATTCATGTTGACATTATGATGTA
42399072 CATG
1 CATG
42399076 TTGACATTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (36 bp):
CATGCAAACTATGATTCATGTTGACATTATGATGTA
Found at i:42399077 original size:20 final size:20
Alignment explanation
Indices: 42399016--42399084 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
42399006 AACTATGATT
42399016 CATGTTGACATTATGATGTA
1 CATGTTGACATTATGATGTA
* * *
42399036 CATG--CAAACTATGAT-T-
1 CATGTTGACATTATGATGTA
42399052 CATGTTGACATTATGATGTA
1 CATGTTGACATTATGATGTA
42399072 CATGTTGACATTA
1 CATGTTGACATTA
42399085 CTCTGGACGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 4 0.10
17 1 0.03
18 16 0.41
19 1 0.03
20 17 0.44
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
CATGTTGACATTATGATGTA
Found at i:42401363 original size:55 final size:55
Alignment explanation
Indices: 42401276--42401392 Score: 191
Period size: 55 Copynumber: 2.1 Consensus size: 55
42401266 TAGTATAAGA
*
42401276 ACTAAA-TCGCGTATAAGGTAAAAGTTGAATTATAGATTAAAAATTAATAAGGGG
1 ACTAAAGTCGCATATAAGGTAAAAGTTGAATTATAGATTAAAAATTAATAAGGGG
* * *
42401330 ACTAAAGTCGCATATAGGGTGAAAGTTGGATTATAGATTAAAAATTAATAAGGGG
1 ACTAAAGTCGCATATAAGGTAAAAGTTGAATTATAGATTAAAAATTAATAAGGGG
42401385 ACTAAAGT
1 ACTAAAGT
42401393 AATAATTATC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 6 0.10
55 52 0.90
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.27
Consensus pattern (55 bp):
ACTAAAGTCGCATATAAGGTAAAAGTTGAATTATAGATTAAAAATTAATAAGGGG
Found at i:42409234 original size:15 final size:14
Alignment explanation
Indices: 42409216--42409245 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
42409206 ATGCAAAATT
42409216 AGAAAGAAAAGAAAG
1 AGAAAGAAAA-AAAG
42409231 AGAAAGAAAAAAAG
1 AGAAAGAAAAAAAG
42409245 A
1 A
42409246 AAGAAGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAAAG
Found at i:42415462 original size:16 final size:16
Alignment explanation
Indices: 42415441--42415479 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
42415431 CTTCAACCCC
42415441 AACTTCTATTCTTCTG
1 AACTTCTATTCTTCTG
42415457 AACTTCTATTCTTCTG
1 AACTTCTATTCTTCTG
42415473 AACTTCT
1 AACTTCT
42415480 TCAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (16 bp):
AACTTCTATTCTTCTG
Found at i:42424843 original size:8 final size:8
Alignment explanation
Indices: 42424832--42424884 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
42424822 TATTTGCTTG
42424832 ATTCATTT
1 ATTCATTT
42424840 ATTCATTT
1 ATTCATTT
*
42424848 ACTCATTT
1 ATTCATTT
42424856 A--C--TT
1 ATTCATTT
42424860 ATTCATTT
1 ATTCATTT
*
42424868 ATCCATTAT
1 ATTCATT-T
42424877 ATTCATTT
1 ATTCATTT
42424885 TTACTCAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
4 3 0.08
6 2 0.05
8 25 0.68
9 7 0.19
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTCATTT
Found at i:42434947 original size:29 final size:26
Alignment explanation
Indices: 42434913--42434971 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 26
42434903 AGTACTGTTT
*
42434913 CTGGTGGCTCTGCCACACTCATACTGATA
1 CTGGTGCCTCTGCCACA-T-ATACTG-TA
*
42434942 CTGGTGCCTTTGCCACATATACTGTA
1 CTGGTGCCTCTGCCACATATACTGTA
42434968 CTGG
1 CTGG
42434972 CAGCTCTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 6 0.21
28 1 0.04
29 15 0.54
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.31
Consensus pattern (26 bp):
CTGGTGCCTCTGCCACATATACTGTA
Found at i:42435525 original size:19 final size:19
Alignment explanation
Indices: 42435501--42435544 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
42435491 TTCAAATAAG
42435501 TTTTCACAACAAACACTGT-
1 TTTTCACAACAAACAC-GTA
*
42435520 TTTTCATAACAAACACGTA
1 TTTTCACAACAAACACGTA
42435539 TTTTCA
1 TTTTCA
42435545 ACTTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (19 bp):
TTTTCACAACAAACACGTA
Found at i:42437174 original size:22 final size:22
Alignment explanation
Indices: 42437126--42437175 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
42437116 AATGGTAAGA
* * **
42437126 ATAAATTTTTATTTTTATTTTT
1 ATAATTTTTTAATTTTATAGTT
*
42437148 TTAATTTTTTAATTTTATAGTT
1 ATAATTTTTTAATTTTATAGTT
42437170 ATAATT
1 ATAATT
42437176 GAACTTAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
ATAATTTTTTAATTTTATAGTT
Found at i:42439773 original size:27 final size:27
Alignment explanation
Indices: 42439734--42439925 Score: 246
Period size: 27 Copynumber: 7.2 Consensus size: 27
42439724 GGTTGGGCCA
* *
42439734 TAAAATTACCGAAATACCCTTGAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
42439761 TAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
* *
42439788 TAAAATTATAGAAATACCCTC-AAAGG
1 TAAAATTATCGAAATACCCTCGAAGGG
42439814 TAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
* * *
42439841 TAAAATTACCAAAATACCCTCAAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
* *
42439868 TACAATTA-CTGAAATACCC-CAAAGGG
1 TAAAATTATC-GAAATACCCTCGAAGGG
* * *
42439894 TAAAATTATCAAAATACCCCCGATGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
42439921 TAAAA
1 TAAAA
42439926 CGACCGTAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
26 47 0.32
27 99 0.68
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (27 bp):
TAAAATTATCGAAATACCCTCGAAGGG
Found at i:42439867 original size:80 final size:80
Alignment explanation
Indices: 42439734--42439925 Score: 271
Period size: 80 Copynumber: 2.4 Consensus size: 80
42439724 GGTTGGGCCA
* * * * *
42439734 TAAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTA-TA
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTAAAATTACT-
42439798 GAAATACCCTCAAA-GG
65 GAAATACCC-CAAAGGG
*
42439814 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTACAATTACTG
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTAAAATTACTG
42439879 AAATACCCCAAAGGG
66 AAATACCCCAAAGGG
* * *
42439894 TAAAATTATCAAAATACCCCCGATGGGTAAAA
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAA
42439926 CGACCGTAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
79 4 0.04
80 96 0.95
81 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (80 bp):
TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTAAAATTACTG
AAATACCCCAAAGGG
Found at i:42439922 original size:53 final size:54
Alignment explanation
Indices: 42439734--42439925 Score: 248
Period size: 53 Copynumber: 3.6 Consensus size: 54
42439724 GGTTGGGCCA
* *
42439734 TAAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
* *
42439788 TAAAATTA-TAGAAATACCCTC-AAAGGTAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTACCA-AAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
* * *
42439841 TAAAATTACCAAAATACCCTCAAAGGGTACAATTA-CTGAAATACCC-CAAAGGG
1 TAAAATTACCAAAATACCCTCGAAGGGTAAAATTATC-GAAATACCCTCGAAGGG
* * *
42439894 TAAAATTATCAAAATACCCCCGATGGGTAAAA
1 TAAAATTACCAAAATACCCTCGAAGGGTAAAA
42439926 CGACCGTAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
53 83 0.69
54 38 0.31
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (54 bp):
TAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
Found at i:42439948 original size:80 final size:80
Alignment explanation
Indices: 42439734--42439953 Score: 212
Period size: 80 Copynumber: 2.8 Consensus size: 80
42439724 GGTTGGGCCA
* * ** ** * * * *
42439734 TAAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTATAG
1 TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCAAAGGGTAAAATTATAG
42439799 AAATACCCTCAAAGG
66 AAATACCCTCAAAGG
* * ** * *
42439814 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTACAATTACT-
1 TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCAAAGGGTAAAATTA-TA
42439878 GAAATACCC-CAAAGGG
65 GAAATACCCTCAAA-GG
* ** *
42439894 TAAAATTATCAAAATACCCCCGATGGGTAAAACGACCGTAATAACC-CATTAGGGTAAAAT
1 TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCA-AAGGGTAAAAT
42439954 AACCATGATG
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
79 6 0.05
80 114 0.94
81 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (80 bp):
TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCAAAGGGTAAAATTATAG
AAATACCCTCAAAGG
Found at i:42440307 original size:16 final size:16
Alignment explanation
Indices: 42440286--42440316 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42440276 AATCAAGATT
42440286 TCAAGAATCAAGAAAA
1 TCAAGAATCAAGAAAA
*
42440302 TCAAGAATCAGGAAA
1 TCAAGAATCAAGAAA
42440317 TCTTGGTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (16 bp):
TCAAGAATCAAGAAAA
Found at i:42440318 original size:24 final size:24
Alignment explanation
Indices: 42440263--42440311 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
42440253 GATCTTGGTC
*
42440263 CAAGAATCAAGAAAATCAAGATTT
1 CAAGAATCAAGAAAATCAAGATAT
42440287 CAAGAATCAAGAAAATCAAGA-AT
1 CAAGAATCAAGAAAATCAAGATAT
42440310 CA
1 CA
42440312 GGAAATCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (24 bp):
CAAGAATCAAGAAAATCAAGATAT
Found at i:42447205 original size:16 final size:16
Alignment explanation
Indices: 42447184--42447223 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
42447174 CCTACTCCCT
42447184 CCCAATTTAAACCCAG
1 CCCAATTTAAACCCAG
*
42447200 CCCAATATAAACCCAG
1 CCCAATTTAAACCCAG
42447216 CCCAATTT
1 CCCAATTT
42447224 TTTCTTAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.38, G:0.05, T:0.20
Consensus pattern (16 bp):
CCCAATTTAAACCCAG
Found at i:42447706 original size:3 final size:3
Alignment explanation
Indices: 42447698--42447745 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
42447688 TGTGCTGTGA
42447698 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42447746 TCTCTTTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42448265 original size:8 final size:9
Alignment explanation
Indices: 42448230--42448280 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
42448220 AAAATTTTCA
*
42448230 GGTAATTCA
1 GGTAATTCG
*
42448239 GGTAAGTCG
1 GGTAATTCG
42448248 GGTAATTCG
1 GGTAATTCG
42448257 GGT-ATTCG
1 GGTAATTCG
42448265 GGTAATTCG
1 GGTAATTCG
42448274 GGTAATT
1 GGTAATT
42448281 TTAAACCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
8 8 0.21
9 30 0.79
ACGTcount: A:0.24, C:0.10, G:0.33, T:0.33
Consensus pattern (9 bp):
GGTAATTCG
Found at i:42448267 original size:17 final size:17
Alignment explanation
Indices: 42448230--42448277 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
42448220 AAAATTTTCA
*
42448230 GGTAATTCAGGTAAGTCG
1 GGTAATTCGGGT-AGTCG
*
42448248 GGTAATTCGGGTATTCG
1 GGTAATTCGGGTAGTCG
42448265 GGTAATTCGGGTA
1 GGTAATTCGGGTA
42448278 ATTTTAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.23, C:0.10, G:0.35, T:0.31
Consensus pattern (17 bp):
GGTAATTCGGGTAGTCG
Found at i:42448299 original size:35 final size:35
Alignment explanation
Indices: 42448260--42448330 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
42448250 TAATTCGGGT
*
42448260 ATTCGGGTAATTCGGGTAATTTTAAACCAAAAATG
1 ATTCGAGTAATTCGGGTAATTTTAAACCAAAAATG
42448295 ATTCGAGTAATTCGGGTAATTTTAAACCAAAAATG
1 ATTCGAGTAATTCGGGTAATTTTAAACCAAAAATG
42448330 A
1 A
42448331 ACAACACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (35 bp):
ATTCGAGTAATTCGGGTAATTTTAAACCAAAAATG
Found at i:42451666 original size:22 final size:21
Alignment explanation
Indices: 42451641--42451707 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
42451631 AACTTACAAA
42451641 TTAAAAAACCTTAAACCCTAAT
1 TTAAAAAACC-TAAACCCTAAT
** *
42451663 TTAAAATTCCCACAACCCTAAT
1 TTAAAAAACCTA-AACCCTAAT
* *
42451685 TTAATAAACCCTAAGCCCTAAT
1 TTAA-AAAACCTAAACCCTAAT
42451707 T
1 T
42451708 AGCAATTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.83
23 5 0.14
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.28
Consensus pattern (21 bp):
TTAAAAAACCTAAACCCTAAT
Found at i:42457706 original size:19 final size:18
Alignment explanation
Indices: 42457682--42457729 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
42457672 TTTGATATTG
*
42457682 TTAAATTTCTATAATTAGT
1 TTAAATTT-GATAATTAGT
**
42457701 TTAAATTTGATCTTTAGT
1 TTAAATTTGATAATTAGT
42457719 TTAAATTTGAT
1 TTAAATTTGAT
42457730 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.54
Consensus pattern (18 bp):
TTAAATTTGATAATTAGT
Found at i:42457719 original size:18 final size:18
Alignment explanation
Indices: 42457696--42457734 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
42457686 ATTTCTATAA
42457696 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
*
42457714 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTGATCT
42457732 TTA
1 TTA
42457735 AATTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:42458645 original size:12 final size:12
Alignment explanation
Indices: 42458621--42458653 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
42458611 CGTGATTCTT
42458621 TTATTTT-TACA
1 TTATTTTATACA
42458632 TTATTTTATACA
1 TTATTTTATACA
42458644 TTATTTTATA
1 TTATTTTATA
42458654 TCTTTATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTTTATACA
Found at i:42459224 original size:19 final size:18
Alignment explanation
Indices: 42459200--42459247 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
42459190 TCGTGATTGC
42459200 AAAATAAATTAAGCGAAAT
1 AAAATAAATTAAG-GAAAT
*
42459219 AAAATAAATT-AGTAAAT
1 AAAATAAATTAAGGAAAT
*
42459236 AAAATATATTAA
1 AAAATAAATTAA
42459248 AGCTTAGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 3 0.12
19 10 0.38
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAATAAATTAAGGAAAT
Found at i:42461759 original size:50 final size:49
Alignment explanation
Indices: 42461699--42461886 Score: 202
Period size: 50 Copynumber: 3.8 Consensus size: 49
42461689 GGGTAAAGAT
* *
42461699 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA-ATGAGAA
* * * *
42461749 GTCCCCTGTAAGACCATGTCTGGGACATGGTATGGGCACCGATATGAGAA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA-ATGAGAA
* * * *
42461799 CTCCCATGTAAAACCATATCTGGGATATGGCATTGGCAGTAC-AA-GA-AA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CGAATGAGAA
* *
42461847 CATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 -GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
42461887 GTTATTATCA
Statistics
Matches: 115, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
48 3 0.03
49 35 0.30
50 75 0.65
51 1 0.01
52 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (49 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAATGAGAA
Found at i:42465347 original size:19 final size:20
Alignment explanation
Indices: 42465325--42465368 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
42465315 TTGGGAAAGG
*
42465325 AAGAGTTTTATAGA-AAATA
1 AAGAGTTTTATAAAGAAATA
* *
42465344 AAGATTTTTCTAAAGAAATA
1 AAGAGTTTTATAAAGAAATA
42465364 AAGAG
1 AAGAG
42465369 AAAAGTGAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.52, C:0.02, G:0.16, T:0.30
Consensus pattern (20 bp):
AAGAGTTTTATAAAGAAATA
Found at i:42467969 original size:25 final size:24
Alignment explanation
Indices: 42467941--42468008 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 24
42467931 TTTTAAAACT
*
42467941 TATATGTAAAATATATTTATATGAA
1 TATAT-TAAAATATATTTACATGAA
* * *
42467966 TATAATTTAGATATATTTACATGTA
1 TAT-ATTAAAATATATTTACATGAA
*
42467991 TATA-TAATATATAATTTA
1 TATATTAAAATAT-ATTTA
42468009 TTTTTACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 6 0.17
24 6 0.17
25 21 0.60
26 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (24 bp):
TATATTAAAATATATTTACATGAA
Found at i:42468958 original size:8 final size:8
Alignment explanation
Indices: 42468947--42468980 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
42468937 TTTAATGAGA
42468947 TATTTTAT
1 TATTTTAT
42468955 TATTTTAT
1 TATTTTAT
42468963 TATTATTAT
1 TATT-TTAT
42468972 TATTTTAT
1 TATTTTAT
42468980 T
1 T
42468981 TAGTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTAT
Found at i:42468973 original size:17 final size:16
Alignment explanation
Indices: 42468947--42468980 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
42468937 TTTAATGAGA
42468947 TATTTTATTATTTTAT
1 TATTTTATTATTTTAT
42468963 TATTATTATTATTTTAT
1 TATT-TTATTATTTTAT
42468980 T
1 T
42468981 TAGTATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTATTATTTTAT
Found at i:42470775 original size:64 final size:64
Alignment explanation
Indices: 42470654--42470776 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
42470644 TTCCGATCAG
* * * * *
42470654 TATTGATCATGCATGTGTTGCAGACATACCGCAGCTCTTTGTGAATGTCTTGCTATATGATCGA
1 TATTGATCATGCATATGTTGCAGACATACCGCAGCTCTTTATGAACGTCTCGATATATGATCGA
*
42470718 TATTGATCCTGCATATGTTGCAGACATACCGCAGCTCTTTAT-AAGCGTCTCGATATATG
1 TATTGATCATGCATATGTTGCAGACATACCGCAGCTCTTTATGAA-CGTCTCGATATATG
42470777 GCTCTTCATG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 2 0.04
64 50 0.96
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (64 bp):
TATTGATCATGCATATGTTGCAGACATACCGCAGCTCTTTATGAACGTCTCGATATATGATCGA
Found at i:42475110 original size:19 final size:18
Alignment explanation
Indices: 42475080--42475129 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
42475070 TATGGGGTCA
*
42475080 GATCCATTTTTTGCCACC
1 GATCCATTTTTTTCCACC
42475098 GATCCATTTTTTTCCACC
1 GATCCATTTTTTTCCACC
42475116 GATCCAATTTTTTT
1 GATCC-ATTTTTTT
42475130 AGGAAGGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 22 0.73
19 8 0.27
ACGTcount: A:0.18, C:0.28, G:0.08, T:0.46
Consensus pattern (18 bp):
GATCCATTTTTTTCCACC
Found at i:42476582 original size:28 final size:28
Alignment explanation
Indices: 42476539--42476595 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
42476529 CCTTTCTCTG
*
42476539 GTTAGCACTTACTGATCTGTTAGTATTT
1 GTTAGCACTTAATGATCTGTTAGTATTT
42476567 GTTAGCACTTAATGATCTGTTAGTATTT
1 GTTAGCACTTAATGATCTGTTAGTATTT
42476595 G
1 G
42476596 ATGCTAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (28 bp):
GTTAGCACTTAATGATCTGTTAGTATTT
Found at i:42477105 original size:20 final size:20
Alignment explanation
Indices: 42477068--42477108 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42477058 GCAGTGCACT
* * *
42477068 TAAAAATTATTTATTTTTTA
1 TAAAAATTAATCAATTTTTA
42477088 TAAAAATTAATCAATTTTTA
1 TAAAAATTAATCAATTTTTA
42477108 T
1 T
42477109 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAAATTAATCAATTTTTA
Found at i:42479184 original size:35 final size:37
Alignment explanation
Indices: 42479136--42479206 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 37
42479126 ATTTGTTAGA
42479136 TATTGATTATGTTTTAACCTTGTTGGATATT-AAATT
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAAATT
**
42479172 TATT-ATTATGTTTTAAGTTTGTTGGATATTGAAAT
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAAAT
42479207 GATTGACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 24 0.75
36 8 0.25
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (37 bp):
TATTGATTATGTTTTAACCTTGTTGGATATTGAAATT
Found at i:42480581 original size:34 final size:35
Alignment explanation
Indices: 42480515--42480581 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
42480505 CAAACATCAG
* * *
42480515 AAAATATTTTCCAGTAAATCATTTTATAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
*
42480550 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
42480582 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
Found at i:42481986 original size:3 final size:3
Alignment explanation
Indices: 42481978--42482013 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
42481968 GTATTGTTTA
*
42481978 ATT ATT ATT ATT ATT TTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42482014 GGCAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:42490599 original size:30 final size:30
Alignment explanation
Indices: 42490563--42490624 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
42490553 ACTTATTTTA
42490563 TTGTTAATTTTGCTATTATTTTAAAGACAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
* * *
42490593 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
42490623 TT
1 TT
42490625 ACTTATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGCTATTATTTTAAAGACAT
Found at i:42502597 original size:63 final size:63
Alignment explanation
Indices: 42502530--42502698 Score: 191
Period size: 63 Copynumber: 2.7 Consensus size: 63
42502520 ACACACCCAA
* * * *
42502530 GTCTCTGGCCTGTGTGACTCTAATTC-CAAAATAGTGAGTTACACGACTTGGACACACTCTTGT
1 GTCTCTGGCCTGTGTGACTCTAATTCAC-AAACAGTGAGTTACACGACCTAGACACACACTTGT
* * * *
42502593 GTCTCTGGCCCGTGTGACCCTAATTTACAAACAGTGAGTTACACGGCCTAGACACACACTTGT
1 GTCTCTGGCCTGTGTGACTCTAATTCACAAACAGTGAGTTACACGACCTAGACACACACTTGT
* * *
42502656 GCCTCTAGCCTGTGTGACTCT-ATCTGCA-AAACAATGAGTTACA
1 GTCTCTGGCCTGTGTGACTCTAAT-T-CACAAACAGTGAGTTACA
42502699 TGGTCTACCA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
62 2 0.02
63 85 0.96
64 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (63 bp):
GTCTCTGGCCTGTGTGACTCTAATTCACAAACAGTGAGTTACACGACCTAGACACACACTTGT
Found at i:42503712 original size:10 final size:9
Alignment explanation
Indices: 42503694--42503747 Score: 63
Period size: 10 Copynumber: 5.7 Consensus size: 9
42503684 GAAAGTTGTT
42503694 TAAAAATTA
1 TAAAAATTA
42503703 TAATAAATTA
1 TAA-AAATTA
42503713 TAAATAATTA
1 TAAA-AATTA
* *
42503723 TTAAAATTT
1 TAAAAATTA
42503732 TAAAAATTAA
1 TAAAAATT-A
42503742 TAAAAA
1 TAAAAA
42503748 GTATTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
9 15 0.39
10 23 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAAAATTA
Found at i:42503739 original size:18 final size:18
Alignment explanation
Indices: 42503692--42503746 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
42503682 TAGAAAGTTG
*
42503692 TTTAAAAATTATAATAAAT
1 TTTAAAAATTATTA-AAAT
*
42503711 TATAAATAATTATTAAAAT
1 TTTAAA-AATTATTAAAAT
*
42503730 TTTAAAAATTAATAAAA
1 TTTAAAAATTATTAAAA
42503747 AGTATTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 10 0.32
19 14 0.45
20 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAAATTATTAAAAT
Found at i:42503752 original size:28 final size:29
Alignment explanation
Indices: 42503696--42503753 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
42503686 AAGTTGTTTA
*
42503696 AAAATTATAATAAATTATAAATAATTATT
1 AAAATTATAATAAATTATAAATAAGTATT
*
42503725 AAAATTTTAA-AAATTAATAAA-AAGTATT
1 AAAATTATAATAAATT-ATAAATAAGTATT
42503753 A
1 A
42503754 TAAAAGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTATAATAAATTATAAATAAGTATT
Found at i:42509462 original size:13 final size:13
Alignment explanation
Indices: 42509444--42509469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42509434 TCGTGTTCTA
42509444 AAAACCATTTGTT
1 AAAACCATTTGTT
42509457 AAAACCATTTGTT
1 AAAACCATTTGTT
42509470 TACGTAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:42516553 original size:13 final size:13
Alignment explanation
Indices: 42516535--42516560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42516525 CGTGTTTTCA
42516535 AAAACCATTTGTT
1 AAAACCATTTGTT
42516548 AAAACCATTTGTT
1 AAAACCATTTGTT
42516561 TGCGTAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:42516904 original size:23 final size:23
Alignment explanation
Indices: 42516878--42516931 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
42516868 TCATCTTCTA
42516878 CACACCATCTCCGACCATCCCAT
1 CACACCATCTCCGACCATCCCAT
42516901 CACACCATCTCCGACCATCCCAT
1 CACACCATCTCCGACCATCCCAT
42516924 CACACCAT
1 CACACCAT
42516932 GTGGGGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.52, G:0.04, T:0.17
Consensus pattern (23 bp):
CACACCATCTCCGACCATCCCAT
Found at i:42520972 original size:25 final size:23
Alignment explanation
Indices: 42520933--42520988 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
42520923 AAGATTAGAA
*
42520933 AAAAATTATAAATAATAA-TAAAT
1 AAAAATTTTAAATAA-AATTAAAT
*
42520956 AATAAATTTTAGAATAAAATTTAAT
1 AA-AAATTTTA-AATAAAATTAAAT
42520981 AAAAATTT
1 AAAAATTT
42520989 AAAAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 15 0.54
25 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAATTTTAAATAAAATTAAAT
Found at i:42521001 original size:18 final size:18
Alignment explanation
Indices: 42520970--42521005 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42520960 AATTTTAGAA
*
42520970 TAAAATTTAATAAAAATT
1 TAAAAATTAATAAAAATT
*
42520988 TAAAAATTATTAAAAATT
1 TAAAAATTAATAAAAATT
42521006 ATAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAATTAATAAAAATT
Found at i:42521310 original size:9 final size:9
Alignment explanation
Indices: 42521273--42521331 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
42521263 ACTTGATAAA
42521273 ATTTTATA-
1 ATTTTATAT
*
42521281 ATTTTTTTAT
1 A-TTTTATAT
42521291 ATTTCTATAT
1 ATTT-TATAT
42521301 ATTTTATAT
1 ATTTTATAT
*
42521310 ATTTT-TACG
1 ATTTTATA-T
42521319 ATTTT-TAT
1 ATTTTATAT
42521327 ATTTT
1 ATTTT
42521332 TTCTAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 8 0.19
9 26 0.60
10 9 0.21
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTATAT
Found at i:42521322 original size:28 final size:27
Alignment explanation
Indices: 42521273--42521343 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
42521263 ACTTGATAAA
* *
42521273 ATTTTATAATTTTTTTATATTTCTATAT
1 ATTTTAT-ATATTTTTAGATTTCTATAT
*
42521301 ATTTTATATATTTTTACGATTTTTATAT
1 ATTTTATATATTTTTA-GATTTCTATAT
* *
42521329 TTTTTCTA-ATTTTTA
1 ATTTTATATATTTTTA
42521344 ATAAATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (27 bp):
ATTTTATATATTTTTAGATTTCTATAT
Found at i:42521524 original size:90 final size:88
Alignment explanation
Indices: 42521430--42521656 Score: 280
Period size: 91 Copynumber: 2.6 Consensus size: 88
42521420 AATTTTTAAT
* *
42521430 AAAAGTAGGGGCTTAATGGCTTTTTTTTTAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAG
1 AAAAGTAGGGGCTTAATTG-TTTTTTTTTAAAAAGTTTGAGGG-CTTTTTGATACATTTTGAAAG
** *
42521495 TTCAAGTACCCAATTAAGTGCAAAA
64 TTCAAGTACCCAAACAAGTACAAAA
*** *
42521520 AAAAGTAGGGGCTTAATTGTTTTTTAAGAAAAAAAGTTTGAGGGCTTTTTTTATACATTTTGAAA
1 AAAAGTAGGGGCTTAATTGTTTTTT--TTTAAAAAGTTTGAGGGC-TTTTTGATACATTTTGAAA
*
42521585 GTTCAAGTACCCAAACGAGTACAAAA
63 GTTCAAGTACCCAAACAAGTACAAAA
* *
42521611 AAAA--A-AGGCTTAATTGTTTTTTTTTAAAGAGTTTGAGGGCTTTTTG
1 AAAAGTAGGGGCTTAATTGTTTTTTTTTAAAAAGTTTGAGGGCTTTTTG
42521657 CACCATTAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
85 5 0.04
86 14 0.12
88 16 0.14
89 7 0.06
90 19 0.16
91 57 0.48
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (88 bp):
AAAAGTAGGGGCTTAATTGTTTTTTTTTAAAAAGTTTGAGGGCTTTTTGATACATTTTGAAAGTT
CAAGTACCCAAACAAGTACAAAA
Found at i:42533896 original size:17 final size:19
Alignment explanation
Indices: 42533874--42533936 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
42533864 TATGGAAACA
42533874 TAATCTT-CA-AGGATATG
1 TAATCTTACATAGGATATG
* *
42533891 TAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
* *
42533910 TAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
*
42533929 CAATCTTA
1 TAATCTTA
42533937 GAAGATATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.17
18 1 0.02
19 33 0.80
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (19 bp):
TAATCTTACATAGGATATG
Found at i:42533909 original size:19 final size:19
Alignment explanation
Indices: 42533885--42533961 Score: 100
Period size: 19 Copynumber: 3.8 Consensus size: 19
42533875 AATCTTCAAG
42533885 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
42533904 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
42533923 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTT---AGATAT
*
42533945 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
42533962 GATTTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
19 31 0.61
20 3 0.06
22 8 0.16
23 9 0.18
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:42533934 original size:38 final size:40
Alignment explanation
Indices: 42533885--42533961 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 40
42533875 AATCTTCAAG
*
42533885 GATATGTAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
42533923 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
42533962 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.36
41 8 0.24
42 13 0.39
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:42534392 original size:2 final size:2
Alignment explanation
Indices: 42534381--42534414 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
42534371 ACACATGCAC
42534381 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42534415 ATTCAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42534464 original size:17 final size:17
Alignment explanation
Indices: 42534442--42534476 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42534432 TTTATATACA
* *
42534442 TATATATATTTACATTT
1 TATATACATATACATTT
42534459 TATATACATATACATTT
1 TATATACATATACATTT
42534476 T
1 T
42534477 TTATTTCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATACATATACATTT
Found at i:42534674 original size:30 final size:31
Alignment explanation
Indices: 42534640--42534697 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
42534630 TATTTGTTTT
*
42534640 TATATATATGTA-ATTATCTTTTTTATAATC
1 TATATATATGTAGATAATCTTTTTTATAATC
*
42534670 TATATATATGTAGATAATTTTTTTTATA
1 TATATATATGTAGATAATCTTTTTTATA
42534698 TATGTACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (31 bp):
TATATATATGTAGATAATCTTTTTTATAATC
Found at i:42536464 original size:8 final size:8
Alignment explanation
Indices: 42536451--42536475 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42536441 GTTTTTTTAA
42536451 ATTAAAAT
1 ATTAAAAT
42536459 ATTAAAAT
1 ATTAAAAT
42536467 ATTAAAAT
1 ATTAAAAT
42536475 A
1 A
42536476 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTAAAAT
Found at i:42538591 original size:9 final size:9
Alignment explanation
Indices: 42538577--42538602 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42538567 GGATTAAATT
42538577 GTAAAAGTA
1 GTAAAAGTA
42538586 GTAAAAGTA
1 GTAAAAGTA
42538595 GTAAAAGT
1 GTAAAAGT
42538603 TAATCACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GTAAAAGTA
Found at i:42541190 original size:2 final size:2
Alignment explanation
Indices: 42541185--42541218 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42541175 TATTATATAC
42541185 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42541219 ACACTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42547604 original size:35 final size:35
Alignment explanation
Indices: 42547565--42547631 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
42547555 GTAAGAGAAA
*
42547565 TATATCGTATGTATCACTATATATAGTAAATGCGT
1 TATATCGTACGTATCACTATATATAGTAAATGCGT
*
42547600 TATATCGTACGTATCACTATATGTAGTAAATG
1 TATATCGTACGTATCACTATATATAGTAAATG
42547632 TGTTTTCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (35 bp):
TATATCGTACGTATCACTATATATAGTAAATGCGT
Found at i:42563093 original size:218 final size:219
Alignment explanation
Indices: 42562715--42563157 Score: 608
Period size: 218 Copynumber: 2.0 Consensus size: 219
42562705 CATGCTACGA
* * *
42562715 TTAAAAGAAGGTAGCTTAGCATGTATAATGAAGGTAAGTAGAGCTGATTATGGGACACGCTTGAT
1 TTAAAAGAAAGTAGCTTAGCATGTATAATAAAGGTAACTAGAGCTGATTATGGGACACGCTTGAT
* *** *
42562780 CCATGCAAGGTATTTAGATTAATTTTTTAAGTTTGAGTCCGATTTGATTTGAAAAATGGATTTAA
66 CCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTCCGACCCGATCTGAAAAATGGATTTAA
* * *
42562845 TTTTTCGTTTACGTTTGGTCCAATTTAAGAAAGGTAAATTC-GGCCCAACCCGGTCCA-TCCATA
131 TTTTTCGTTTACGTTCGATCCAATTTAAGAAAGGTAAATCCGGGCCCAACCCGGTCCACT-CATA
42562908 TTTAATTTTTTAGATTCA-TTTTTAT
195 TTTAATTTTTTAGATT-AGTTTTTAT
* * *
42562933 TTAAAAGAAAGTAGCTTAGCATGTATAATAAAGGTAACTAGAGGTGATTATGGGCCGA-GTTTGA
1 TTAAAAGAAAGTAGCTTAGCATGTATAATAAAGGTAACTAGAGCTGATTATGGGAC-ACGCTTGA
* * * * *
42562997 TTCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTTCTACCCGATCCT-AGAAATGGGTTT
65 TCCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTCCGACCCGAT-CTGAAAAATGGATTT
* * *
42563061 AATTTTTTGTTTACGTTCGATCCTATTTAAGAAAGGTAAATCCGGGCCCAACCTGGTCCACTCAT
129 AATTTTTCGTTTACGTTCGATCCAATTTAAGAAAGGTAAATCCGGGCCCAACCCGGTCCACTCAT
*
42563126 ATTTGATTTTTTAGATTAGTTTTTAT
194 ATTTAATTTTTTAGATTAGTTTTTAT
42563152 TTAAAA
1 TTAAAA
42563158 ATCATTTAAA
Statistics
Matches: 197, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
218 147 0.75
219 49 0.25
220 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (219 bp):
TTAAAAGAAAGTAGCTTAGCATGTATAATAAAGGTAACTAGAGCTGATTATGGGACACGCTTGAT
CCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTCCGACCCGATCTGAAAAATGGATTTAA
TTTTTCGTTTACGTTCGATCCAATTTAAGAAAGGTAAATCCGGGCCCAACCCGGTCCACTCATAT
TTAATTTTTTAGATTAGTTTTTAT
Found at i:42564957 original size:2 final size:2
Alignment explanation
Indices: 42564950--42564975 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42564940 GCTAACCAAG
42564950 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42564976 TATCATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42571026 original size:13 final size:14
Alignment explanation
Indices: 42570997--42571029 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
42570987 TATGATTAGT
*
42570997 GTTAATTAGGCTTA
1 GTTAATTAAGCTTA
42571011 GTTAATTAAG-TTA
1 GTTAATTAAGCTTA
42571024 GTTAAT
1 GTTAAT
42571030 ATTAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (14 bp):
GTTAATTAAGCTTA
Found at i:42573256 original size:3 final size:3
Alignment explanation
Indices: 42573248--42573305 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
42573238 ATAATCAAAT
* *
42573248 ATA ATA ATA ATA ACA ATA ATAA ATA GTA A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
42573293 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
42573306 AGTGATTAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:42574501 original size:44 final size:44
Alignment explanation
Indices: 42574453--42574714 Score: 364
Period size: 44 Copynumber: 6.0 Consensus size: 44
42574443 AGACAAGATC
* * * *
42574453 TACAATCTTCAATCTATTACACTGCTGTTCAGAGAGATAGGACA
1 TACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT
* *
42574497 TACAATCTTCCACCTATTCCACTGCTGTTCAGGGAGCTAGGACT
1 TACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT
* * * *
42574541 TACAATCTTCCACCTATTCCACTACTGTTTAGGGAGCTAGGACT
1 TACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT
* *
42574585 TACAATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACT
1 TACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT
*
42574629 TGCAATCTTCAACCTATTCCACTGCTGGTT-AGGGAGATAGGACT
1 TACAATCTTCAACCTATTCCACTGCT-GTTCAGGGAGATAGGACT
* * *
42574673 TGCAATCTTCAACCTATTCCACTGCCGTCCAGGGAGATAGGA
1 TACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGA
42574715 ATAGTGGCTT
Statistics
Matches: 199, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 2 0.01
44 195 0.98
45 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (44 bp):
TACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT
Found at i:42574755 original size:132 final size:132
Alignment explanation
Indices: 42574481--42574744 Score: 282
Period size: 132 Copynumber: 2.0 Consensus size: 132
42574471 ACACTGCTGT
* * * * *
42574481 TCAGAGAGATAGGACATACAATCTTCCACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAA
1 TCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTACAA
* * ** * * * ** *
42574546 TCTTCCACCTATTCCACTACTGTTTAGGGAGCTAGGACTTACAATCTTCCACCTATTCCACTGCT
66 TCTTCAACCTATTCCACTACCGTCCAGGGAGATAGGACATACAAGCTTAAACCTATTCCACTACT
**
42574611 GG
131 AC
*
42574613 TCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTT-AGGGAGATAGGACTTGCA
1 TCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCT-GTTCAGGGAGATAGGACTTACA
* *** *
42574677 ATCTTCAACCTATTCCACTGCCGTCCAGGGAGATAGGA-ATAGTGGCTTAAATCTACTTCC-CTA
65 ATCTTCAACCTATTCCACTACCGTCCAGGGAGATAGGACATACAAGCTTAAACCTA-TTCCACTA
42574740 CTAC
129 CTAC
42574744 T
1 T
42574745 TGGGGTAGAT
Statistics
Matches: 107, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
131 14 0.13
132 90 0.84
133 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (132 bp):
TCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTACAA
TCTTCAACCTATTCCACTACCGTCCAGGGAGATAGGACATACAAGCTTAAACCTATTCCACTACT
AC
Found at i:42574928 original size:89 final size:88
Alignment explanation
Indices: 42574799--42574992 Score: 210
Period size: 88 Copynumber: 2.2 Consensus size: 88
42574789 TTAGGGAGAT
* * ** * *
42574799 AAGATCTGTAATTTTCAACCTACTCCACTACTGCTTAGGGAGATAAGGCTTACAATCTTCGATCT
1 AAGATCTGTTATTTTCAACCTACTCCACTACTACCCAGGGAGACAAGGCTGAC-ATCTTCGATCT
* * *
42574864 GCTTCACCGTCAGTACAGGGAGGC
65 GCTTCACCGTCAATACAAGAAGGC
* * * * *
42574888 AAGATCTGTTATTTTCAACCTGCTCCGCTA-TAACCCAGGGAGGCAAGGCTGGCGTCTTCGATCT
1 AAGATCTGTTATTTTCAACCTACTCCACTACT-ACCCAGGGAGACAAGGCTGACATCTTCGATCT
* *
42574952 GCTTCACTGTCAATGCAAGAAGGC
65 GCTTCACCGTCAATACAAGAAGGC
*
42574976 AAGATCTGTTATCTTCA
1 AAGATCTGTTATTTTCA
42574993 CTGATCTGTT
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
88 46 0.53
89 41 0.47
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (88 bp):
AAGATCTGTTATTTTCAACCTACTCCACTACTACCCAGGGAGACAAGGCTGACATCTTCGATCTG
CTTCACCGTCAATACAAGAAGGC
Found at i:42578698 original size:11 final size:11
Alignment explanation
Indices: 42578672--42578705 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
42578662 CGAAATAGGG
*
42578672 GAAAGGAAAGAA
1 GAAAAGAAA-AA
42578684 GAAAAGAAAAA
1 GAAAAGAAAAA
42578695 GAAAAGAAAAA
1 GAAAAGAAAAA
42578706 ACTAGGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:42583195 original size:25 final size:25
Alignment explanation
Indices: 42583161--42583214 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
42583151 ATGAAAGGAA
42583161 TGTACCAACGTATTACAGATCAAGT
1 TGTACCAACGTATTACAGATCAAGT
42583186 TGTACCAACGTATTACAGATCAAGT
1 TGTACCAACGTATTACAGATCAAGT
42583211 TGTA
1 TGTA
42583215 GTCAAGCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (25 bp):
TGTACCAACGTATTACAGATCAAGT
Found at i:42584433 original size:46 final size:45
Alignment explanation
Indices: 42584337--42584438 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
42584327 TTTTCATAAC
*** *
42584337 ATATGATTCAATACTAAAATCATTCCAAACTAACATGGTAAGCAAT
1 ATATGA-TCAATACTAAAATCATTCCAAACTAACATAACAAGCAAA
* ** *
42584383 ATATGACTCAATACTAAAATCATTCCCAACTAGTATAACAAGTAAA
1 ATATGA-TCAATACTAAAATCATTCCAAACTAACATAACAAGCAAA
42584429 ATATGATCAA
1 ATATGATCAA
42584439 AATTGAAACA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 4 0.09
46 43 0.91
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (45 bp):
ATATGATCAATACTAAAATCATTCCAAACTAACATAACAAGCAAA
Found at i:42587599 original size:84 final size:84
Alignment explanation
Indices: 42587444--42587948 Score: 803
Period size: 84 Copynumber: 6.0 Consensus size: 84
42587434 CGCAAAAAAT
* * * *
42587444 AAAACACAACGGCATCGTTTAGTGGCCTTTGGTGGCCTTACTGGCGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
*
42587509 AATGGTCTGCGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
* *
42587528 AAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
*
42587593 AATGGTCTATGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
*
42587612 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCACCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
42587677 AATGGTCTGTGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
* * *
42587696 AAAATACAACGGCGTCGTTTAGTGGCCTTTGGTGGCCTTAGTGGCGTTTTTTGTCTAGCGCGGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
42587761 AATGGTCTGTGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
* * * *
42587780 AAAATACAACGGCGTCGTTTAGTGGCCTCCGGTGGCCTTAGTGGCATTTTTAGTCTAGCGTCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
42587845 AATGGTCTGTGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
* * * * * *
42587864 AAAATACAACGGCGTCGTTTAGTGGCCTTCAGTAGCCTTAGGGGCATATTTGGTCGAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
*
42587929 AATGGTATGTGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
42587948 A
1 A
42587949 GCATTTTTAA
Statistics
Matches: 390, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 390 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (84 bp):
AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
AATGGTCTGTGTTTTTAGC
Found at i:42588082 original size:84 final size:84
Alignment explanation
Indices: 42587977--42588142 Score: 289
Period size: 84 Copynumber: 2.0 Consensus size: 84
42587967 CGCAAAAAAT
* *
42587977 AAAATACAACGGCATTGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCATTGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCACT
42588042 AATGGTCTATGTTTTTAGC
66 AATGGTCTATGTTTTTAGC
42588061 AAAATACAACGGC-TTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCAC
1 AAAATACAACGGCATT-GTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCAC
*
42588125 TAATGGTCTGTGTTTTTA
65 TAATGGTCTATGTTTTTA
42588143 ACGGCGTTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 2 0.03
84 76 0.97
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (84 bp):
AAAATACAACGGCATTGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCACT
AATGGTCTATGTTTTTAGC
Found at i:42588115 original size:197 final size:198
Alignment explanation
Indices: 42587780--42588308 Score: 853
Period size: 197 Copynumber: 2.7 Consensus size: 198
42587770 TGTTTTTAGC
* * * *
42587780 AAAATACAACGGCGTCGTTTAGTGGCCTCCGGTGGCCTTAGTGGCATTTTTAGTCTAGCGTCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* * *
42587845 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCAGTAGCCTTAGGGGCA
66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCA
* * * *
42587910 TATTTGGTCGAGCGCCGCTAATGGTATGTGTTTTTAGCAGCATTTTTA-AAAAAACGCCGCAAAA
131 TTTTTGGTCGAGCGCCACTAATGGTATGTGTTTTTAACAGCATTTTCATAAAAAACGCCGCAAAA
42587974 AAT
196 AAT
* *
42587977 AAAATACAACGGCATTGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* *
42588042 AATGGTCTATGTTTTTAGCAAAATACAACGGCTTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCA
66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCA
* * * *
42588107 TTTTTGGTCTAGCGCCACTAATGGTCTGTGTTTTTAACGGCGTTTTCATAAAAAACGCCGCAAAA
131 TTTTTGGTCGAGCGCCACTAATGGTATGTGTTTTTAACAGCATTTTCATAAAAAACGCCGCAAAA
42588172 AAT
196 AAT
* *
42588175 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGCCCTTAGTGGCGTTTTTGGTCTAACGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
*
42588240 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG
66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCA
42588305 TTTT
131 TTTT
42588309 NNNNNNNNNN
Statistics
Matches: 305, Mismatches: 26, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
197 159 0.52
198 146 0.48
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (198 bp):
AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCA
TTTTTGGTCGAGCGCCACTAATGGTATGTGTTTTTAACAGCATTTTCATAAAAAACGCCGCAAAA
AAT
Found at i:42590699 original size:21 final size:21
Alignment explanation
Indices: 42590674--42590720 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42590664 TGGTCGAGAT
* *
42590674 TTAAGGTTTAGGGGTTAGGGG
1 TTAAGGGTTAGAGGTTAGGGG
* *
42590695 TTAAGGGTTAGATGTTAGTGG
1 TTAAGGGTTAGAGGTTAGGGG
42590716 TTAAG
1 TTAAG
42590721 ACTTAGGGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.36
Consensus pattern (21 bp):
TTAAGGGTTAGAGGTTAGGGG
Found at i:42590726 original size:21 final size:21
Alignment explanation
Indices: 42590687--42590726 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42590677 AGGTTTAGGG
**
42590687 GTTAGGGGTTAAGGGTTAGAT
1 GTTAGGGGTTAAGACTTAGAT
*
42590708 GTTAGTGGTTAAGACTTAG
1 GTTAGGGGTTAAGACTTAG
42590727 GGATTTTGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.38, T:0.35
Consensus pattern (21 bp):
GTTAGGGGTTAAGACTTAGAT
Found at i:42595773 original size:21 final size:21
Alignment explanation
Indices: 42595747--42595817 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
42595737 CTACAACTTA
*
42595747 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
42595768 AAGCAGCA-GCTACAGCGAGGG
1 AAGCAG-AGGCTGCAGCGAGGG
*
42595789 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
42595810 AAGCAGAG
1 AAGCAGAG
42595818 CAGAGCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.44, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:42599439 original size:33 final size:34
Alignment explanation
Indices: 42599388--42599456 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
42599378 ATATATTATG
*
42599388 TAATATATATGATATAAAAAATAAATATAATAATT
1 TAATATAAATGATATAAAAAATAAAT-TAATAATT
* *
42599423 TAATATAAAT-AT-TAAAAAATATATTAATTATT
1 TAATATAAATGATATAAAAAATAAATTAATAATT
42599455 TA
1 TA
42599457 TGTTTAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 9 0.29
33 11 0.35
34 2 0.06
35 9 0.29
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (34 bp):
TAATATAAATGATATAAAAAATAAATTAATAATT
Found at i:42599456 original size:32 final size:35
Alignment explanation
Indices: 42599376--42599456 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
42599366 GTTATTTTTT
* *
42599376 ATATATATTATGTAATATATATGATATAAAAAATAA
1 ATATA-ATTATTTAATATAAATGATATAAAAAATAA
* *
42599412 ATATAATAATTTAATATAAAT-AT-TAAAAAATAT
1 ATATAATTATTTAATATAAATGATATAAAAAATAA
42599445 AT-TAATTATTTA
1 ATATAATTATTTA
42599457 TGTTTAAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 9 0.22
33 11 0.28
34 2 0.05
35 13 0.32
36 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (35 bp):
ATATAATTATTTAATATAAATGATATAAAAAATAA
Found at i:42600252 original size:17 final size:17
Alignment explanation
Indices: 42600205--42600254 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
42600195 AAAAAAATTA
*
42600205 AATTATAATATTCAAAG
1 AATTATAATATTTAAAG
*
42600222 AATACATAA-ATTTAAAG
1 AAT-TATAATATTTAAAG
*
42600239 AATTATAATCTTTAAA
1 AATTATAATATTTAAA
42600255 ATTTTACTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (17 bp):
AATTATAATATTTAAAG
Found at i:42600502 original size:22 final size:22
Alignment explanation
Indices: 42600477--42600523 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
42600467 AATTTTAATA
42600477 TTCAATTTAGTACTTGAA-TTTT
1 TTCAATTTAGTACTT-AAGTTTT
42600499 TTCAATTTAGTACTTAAGTTTT
1 TTCAATTTAGTACTTAAGTTTT
42600521 TTC
1 TTC
42600524 TTTGTCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (22 bp):
TTCAATTTAGTACTTAAGTTTT
Found at i:42602745 original size:10 final size:11
Alignment explanation
Indices: 42602719--42602744 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42602709 AATAAGATTG
42602719 AAAAATAATTT
1 AAAAATAATTT
42602730 AAAAATAATTT
1 AAAAATAATTT
42602741 AAAA
1 AAAA
42602745 TTAGGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATAATTT
Found at i:42608388 original size:25 final size:26
Alignment explanation
Indices: 42608359--42608411 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
42608349 AAATTGTAAA
42608359 CTAGAAAAATATC-TCTAGA-AATTTT
1 CTAGAAAAATATCTTC-AGAGAATTTT
* *
42608384 CTAGAATAATTTCTTCAGAGAATTTT
1 CTAGAAAAATATCTTCAGAGAATTTT
42608410 CT
1 CT
42608412 CTCTACAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (26 bp):
CTAGAAAAATATCTTCAGAGAATTTT
Found at i:42614100 original size:3 final size:3
Alignment explanation
Indices: 42614092--42614188 Score: 81
Period size: 3 Copynumber: 30.3 Consensus size: 3
42614082 AAGTGAAAAT
42614092 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGGTA AGTA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA A-TA ATA ATA AT-A
* * *
42614141 ATGCA ATA ATA ATA ATA A-A ACTA ATTA GT- TTA CTA ATA ATA ATA ATA
1 AT--A ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA ATA ATA ATA ATA
42614188 A
1 A
42614189 CAAGAACGGG
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
2 3 0.04
3 61 0.75
4 11 0.14
5 6 0.07
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:42616263 original size:132 final size:132
Alignment explanation
Indices: 42616109--42616400 Score: 476
Period size: 132 Copynumber: 2.2 Consensus size: 132
42616099 GGAAGATAAA
*
42616109 ATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTAATGGCTTAAATCTGCTT
1 ATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGATAGGACTAATGGCTTAAATCTGCTT
*
42616174 CCCTACTACCTTGAAAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACA
66 CCCTACTACCTTGAAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACA
42616239 GG
131 GG
* * *
42616241 ATCTACAATCTTTAACCTACTCCACTGCTGCTCGGGGAGATAGGATTAGTGGCTTAAATCTGCTT
1 ATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGATAGGACTAATGGCTTAAATCTGCTT
* ** ** *
42616306 CCTTACTACCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTTTACTACTGCTTAGGGTGACA
66 CCCTACTACCTTGAAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACA
42616371 GG
131 GG
*
42616373 ATCTACAATCTTTAACCTACTCTACTGC
1 ATCTACAATCTTTAACCTACTCCACTGC
42616401 AAACTCAGGA
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
132 148 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (132 bp):
ATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGATAGGACTAATGGCTTAAATCTGCTT
CCCTACTACCTTGAAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACA
GG
Found at i:42616519 original size:89 final size:89
Alignment explanation
Indices: 42616396--42616829 Score: 541
Period size: 89 Copynumber: 4.9 Consensus size: 89
42616386 AACCTACTCT
* *
42616396 ACTGCAAACTCA-GGAGGC-AAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACA
1 ACTGCAAACTCAGGGAGGCGAA-GCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACA
* * *
42616459 AGATCTGTTATTTTTAGTCTGCTCC
65 AGATCTGCTATCTTCAGTCTGCTCC
* ** *
42616484 ATTGCAAACTCAGGGAGGCGAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAACACAAGAAGACAA
1 ACTGCAAACTCAGGGAGGCGAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACAA
* *
42616549 GATCTGCTATATTCAGTCTGCTCT
66 GATCTGCTATCTTCAGTCTGCTCC
* * * * * * * *
42616573 AAT-CTAAACTTAGAGAGGCGAGGCTGGTGTCTTCGATCTACTTCGCTACCAGTACAAGAAGATA
1 ACTGC-AAACTCAGGGAGGCGAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACA
*
42616637 AGATCTGCTATCTTCAGTCTGTTCC
65 AGATCTGCTATCTTCAGTCTGCTCC
* * *
42616662 ACTGCAAACTCAGGGAGGCGATGCTGGTGTCTTCGATCTGTTTCGCTGCCAGTACAGGAGGACAA
1 ACTGCAAACTCAGGGAGGCGAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACAA
* * *
42616727 GATCTGGTATCTTTAGTCTGCTCT
66 GATCTGCTATCTTCAGTCTGCTCC
* * * * * *
42616751 GCTGCAAACTCAGGGAGGCGACGCTGGTGTCTTCGATCTGCTTTGCTGCCGGTTCAGAAAGACAA
1 ACTGCAAACTCAGGGAGGCGAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACAA
42616816 GATCTGCTATCTTC
66 GATCTGCTATCTTC
42616830 TTTAATCCAT
Statistics
Matches: 296, Mismatches: 46, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
88 12 0.04
89 281 0.95
90 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (89 bp):
ACTGCAAACTCAGGGAGGCGAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACAA
GATCTGCTATCTTCAGTCTGCTCC
Found at i:42616791 original size:44 final size:43
Alignment explanation
Indices: 42616663--42616799 Score: 120
Period size: 44 Copynumber: 3.1 Consensus size: 43
42616653 GTCTGTTCCA
42616663 CTGCAAACTCAGGGAGGCGATGCTGGTGTCTTCGATCTG-TTTCG
1 CTGCAAACTCAGGGAGGCGA-GCTGGTGTCTTCGATCTGCTTT-G
* * * * * *
42616707 CTGC-CAGTACA-GGAGGACAAGATCTGGTATCTT-TAGTCTGCTCTG
1 CTGCAAACT-CAGGGAGG-C--GAGCTGGTGTCTTCGA-TCTGCTTTG
42616752 CTGCAAACTCAGGGAGGCGACGCTGGTGTCTTCGATCTGCTTTG
1 CTGCAAACTCAGGGAGGCGA-GCTGGTGTCTTCGATCTGCTTTG
42616796 CTGC
1 CTGC
42616800 CGGTTCAGAA
Statistics
Matches: 71, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
43 9 0.13
44 29 0.41
45 22 0.31
46 11 0.15
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (43 bp):
CTGCAAACTCAGGGAGGCGAGCTGGTGTCTTCGATCTGCTTTG
Found at i:42621268 original size:30 final size:29
Alignment explanation
Indices: 42621177--42621305 Score: 143
Period size: 29 Copynumber: 4.4 Consensus size: 29
42621167 CAAAAAATAT
*** * *
42621177 AAATTACATTTTGGCCCCAAAACTTTTCT
1 AAATTACATTTCAACCCCTAAACTTTTCA
*
42621206 AAATTACATTTCAACCCTTAAACTTTTCA
1 AAATTACATTTCAACCCCTAAACTTTTCA
42621235 AAATTACATTTCAACCCCTAAACTTTCTCA
1 AAATTACATTTCAACCCCTAAACTTT-TCA
* * *
42621265 AAATTTCACTTCGACCCCTAAA-TTTTCTA
1 AAATTACATTTCAACCCCTAAACTTTTC-A
42621294 GAAATTACATTT
1 -AAATTACATTT
42621306 TGGCCCTATA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
28 2 0.02
29 52 0.61
30 31 0.36
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AAATTACATTTCAACCCCTAAACTTTTCA
Found at i:42621319 original size:29 final size:29
Alignment explanation
Indices: 42621177--42621335 Score: 78
Period size: 29 Copynumber: 5.4 Consensus size: 29
42621167 CAAAAAATAT
*
42621177 AAATTACATTTTGGCCCCAAAACTTTT-CT-
1 AAATTACATTTTGG-CCCTAAA-TTTTCCTA
***
42621206 AAATTACATTTCAACCCTTAAACTTTT-C-A
1 AAATTACATTTTGGCCC-TAAA-TTTTCCTA
*** *
42621235 AAATTACATTTCAACCCCTAAACTTT-CTCA
1 AAATTACATTT-TGGCCCTAAATTTTCCT-A
* * * *
42621265 AAATTTCACTTCGACCCCTAAATTTT-CTA
1 AAATTACATTTTG-GCCCTAAATTTTCCTA
*
42621294 GAAATTACATTTTGGCCCTATATTTTCCTA
1 -AAATTACATTTTGGCCCTAAATTTTCCTA
*
42621324 AAATTATATTTT
1 AAATTACATTTT
42621336 TACCCCAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
28 7 0.07
29 57 0.55
30 40 0.38
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTGGCCCTAAATTTTCCTA
Found at i:42621919 original size:10 final size:10
Alignment explanation
Indices: 42621898--42621958 Score: 79
Period size: 11 Copynumber: 5.9 Consensus size: 10
42621888 AGAAGAAGGA
42621898 AAAAAAGAAAG
1 AAAAAAG-AAG
42621909 AAAAAAGAAG
1 AAAAAAGAAG
42621919 -AAAAAGAGAG
1 AAAAAAGA-AG
42621929 AAAAAAGAAG
1 AAAAAAGAAG
*
42621939 AAGAAAAAAAG
1 AA-AAAAGAAG
42621950 AAAAAAGAA
1 AAAAAAGAA
42621959 TTTTTTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 7 0.16
10 15 0.33
11 23 0.51
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:42621924 original size:20 final size:20
Alignment explanation
Indices: 42621886--42621958 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
42621876 GGGGAGACCC
* *
42621886 AAAGAAGAAGGAA-AAAAAG
1 AAAGAAAAAAGAAGAAAAAG
42621905 AAAGAAAAAAGAAGAAAAAG
1 AAAGAAAAAAGAAGAAAAAG
* *
42621925 AGAGAAAAAAGAAGAAGAAAA
1 AAAGAAAAAAGAAGAA-AAAG
42621946 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
42621959 TTTTTTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.23
20 21 0.45
21 15 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAGAAGAAAAAG
Found at i:42622282 original size:16 final size:15
Alignment explanation
Indices: 42622247--42622275 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42622237 CCAGCAGGCC
42622247 AAAAAAGAGAAAAAG
1 AAAAAAGAGAAAAAG
42622262 AAAAAA-AGAAAAAG
1 AAAAAAGAGAAAAAG
42622276 GGAAAAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGAAAAAG
Found at i:42622589 original size:20 final size:20
Alignment explanation
Indices: 42622567--42622603 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
42622557 AAAATATTCA
42622567 AAAATCCTCGT-TTTTAAAG
1 AAAATCCTCGTGTTTTAAAG
*
42622586 AAAATTCTCGTGTTTTAA
1 AAAATCCTCGTGTTTTAA
42622604 TAGGATCACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
AAAATCCTCGTGTTTTAAAG
Found at i:42622819 original size:18 final size:18
Alignment explanation
Indices: 42622767--42623005 Score: 177
Period size: 18 Copynumber: 13.3 Consensus size: 18
42622757 GAGTTTTCAG
*
42622767 AAAAATTTTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
42622784 AAAAATTTTTTGTATTTTC
1 AAAAA-TTTTCGTGTTTTC
* *
42622803 AAAAATTTCCGTGTTTTT
1 AAAAATTTTCGTGTTTTC
*
42622821 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
**
42622839 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
42622857 -AAAA-TTTCG-GTATTTA
1 AAAAATTTTCGTGT-TTTC
42622873 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* ** *
42622891 AGAAATTCCCGTGTTTTAA
1 AAAAATTTTCGTGTTTT-C
**
42622910 AACAAAACTTCTGTGTTTTC
1 AA-AAATTTTC-GTGTTTTC
*
42622930 -AAAATTTTCGTGTTTTT
1 AAAAATTTTCGTGTTTTC
* *
42622947 AAGAATTTTCGTG-TCTC
1 AAAAATTTTCGTGTTTTC
* *
42622964 TAAAATTCTCGTGTTCTT-
1 AAAAATTTTCGTGTT-TTC
*
42622982 AAGAATTTTTCGTGTTTTC
1 AA-AAATTTTCGTGTTTTC
42623001 AAAAA
1 AAAAA
42623006 AAATAATTGT
Statistics
Matches: 169, Mismatches: 39, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
15 2 0.01
16 6 0.04
17 32 0.19
18 91 0.54
19 27 0.16
20 4 0.02
21 7 0.04
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:42632993 original size:50 final size:50
Alignment explanation
Indices: 42632936--42633035 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
42632926 TGGATTTGTT
42632936 CTTGACGGGGATATTCCATACAAAAGAGGAAAAGATCAAGTGCTCCTGAG
1 CTTGACGGGGATATTCCATACAAAAGAGGAAAAGATCAAGTGCTCCTGAG
* * *
42632986 CTTGACGGGGATATTCTATACAAAAGGGGAAAAGATCAAGTGCTCTTGAG
1 CTTGACGGGGATATTCCATACAAAAGAGGAAAAGATCAAGTGCTCCTGAG
42633036 GTGCGTGGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (50 bp):
CTTGACGGGGATATTCCATACAAAAGAGGAAAAGATCAAGTGCTCCTGAG
Found at i:42634163 original size:19 final size:17
Alignment explanation
Indices: 42634132--42634221 Score: 99
Period size: 18 Copynumber: 4.9 Consensus size: 17
42634122 ATTATAGCCT
* *
42634132 AAAAAAAGAAAAAAAAT
1 AAAAAAAAAAAAAAAAC
42634149 AAAAAAACAACAAAAAAAC
1 AAAAAAA-AA-AAAAAAAC
42634168 AAAAAACAAAAAAAAAAC
1 AAAAAA-AAAAAAAAAAC
*
42634186 AAAAAAACAAAAAAAAGC
1 AAAAAAA-AAAAAAAAAC
42634204 AAAAAAGTAAAAAAAAAA
1 AAAAAA--AAAAAAAAAA
42634222 GAAGAAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
17 8 0.13
18 30 0.48
19 23 0.37
20 2 0.03
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAC
Found at i:42634163 original size:26 final size:25
Alignment explanation
Indices: 42634134--42634230 Score: 88
Period size: 26 Copynumber: 3.8 Consensus size: 25
42634124 TATAGCCTAA
* *
42634134 AAAAAGAAAAAAAATAAAAAAACAAC
1 AAAAA-AAAAAAAACAAAAAAAAAAC
42634160 AAAAAAACAAAAAACAAAAAAAAAAC
1 AAAAAAA-AAAAAACAAAAAAAAAAC
* **
42634186 AAAAAAACAAAAAA-AAGCAAAAAAGT
1 AAAAAAA-AAAAAACAA-AAAAAAAAC
* *
42634212 AAAAAAAAAAGAAGAAAAA
1 AAAAAAAAAAAAACAAAAA
42634231 TCAAGATGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
25 11 0.18
26 50 0.82
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAAAACAAAAAAAAAAC
Found at i:42634182 original size:37 final size:35
Alignment explanation
Indices: 42634133--42634230 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 35
42634123 TTATAGCCTA
* *
42634133 AAAAAAGAAAAAAAATAAAAAAACAACAAAAAAACA
1 AAAAAAAAAAAAAAACAAAAAAACAA-AAAAAAACA
*
42634169 AAAAACAAAAAAAAAACAAAAAAACAAAAAAAAGCA
1 AAAAA-AAAAAAAAAACAAAAAAACAAAAAAAAACA
*
42634205 AAAAAGTAAAAAAAAAAGAAGAAAAA
1 AAAAA--AAAAAAAAAACAA-AAAAA
42634231 TCAAGATGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 18 0.33
37 31 0.57
38 5 0.09
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (35 bp):
AAAAAAAAAAAAAAACAAAAAAACAAAAAAAAACA
Found at i:42634230 original size:1 final size:1
Alignment explanation
Indices: 42634132--42634221 Score: 72
Period size: 1 Copynumber: 90.0 Consensus size: 1
42634122 ATTATAGCCT
* * * * * * * *
42634132 AAAAAAAGAAAAAAAATAAAAAAACAACAAAAAAACAAAAAACAAAAAAAAAACAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** **
42634197 AAAAAGCAAAAAAGTAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
42634222 GAAGAAAAAT
Statistics
Matches: 67, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:42635364 original size:73 final size:73
Alignment explanation
Indices: 42635246--42635747 Score: 674
Period size: 75 Copynumber: 6.8 Consensus size: 73
42635236 NNNNNNNNNT
*
42635246 GTATTTTAAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
42635310 ATCCTGAG
66 ATCCTGAG
42635318 GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-
42635383 GCA-CGCTGAG
65 -CATC-CTGAG
*
42635393 GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
42635458 ATCCTGAG
66 ATCCTGAG
*
42635466 GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTC
1 GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-
42635531 GCA-CGCTGAG
65 -CATC-CTGAG
* * *
42635541 GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGAGTC
1 GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
42635606 AT-GTCGAG
66 ATCCT-GAG
* * * **
42635614 GTATTTTTCAATTTTTGGTTTTCACAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTAG
1 GTA-TTTTCAATTTCT-GTTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
42635679 GTCATATGCC-GAG
63 GTC--AT-CCTGAG
* ** * *
42635692 GTATTCTTCAATTTCTATTTTTCAAAGCTCAACTCATAATT-TGAGAAGTGAGTTGA
1 GTATT-TTCAATTTCTGTTTTTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGA
42635748 ATTTTGGATC
Statistics
Matches: 385, Mismatches: 26, Indels: 34
0.87 0.06 0.08
Matches are distributed among these distances:
72 16 0.04
73 124 0.32
74 13 0.03
75 142 0.37
76 64 0.17
77 9 0.02
78 17 0.04
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (73 bp):
GTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ATCCTGAG
Found at i:42635530 original size:148 final size:148
Alignment explanation
Indices: 42635246--42635747 Score: 751
Period size: 148 Copynumber: 3.4 Consensus size: 148
42635236 NNNNNNNNNT
42635246 GTATTTTAAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
42635310 ATCCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
66 ATCCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGC
42635375 CTCGGGTCGCACGCTGAG
131 CTCGGGTCGCACGCTGAG
42635393 GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
42635458 ATCCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGC
66 ATCCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGC
42635523 CTCGGGTCGCACGCTGAG
131 CTCGGGTCGCACGCTGAG
* *
42635541 GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGAGTC
1 GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* * *
42635606 AT-GTCGAGGTATTTTTCAATTTTTGGTTTTCACAAAAATCAACTCATATTGC-AAGAGGTGAGT
66 ATCCT-GAGGTA-TTTTCAATTTCT-GTTTT-TCAAAAATCAACTCATATTGCGAA-AGGTGAGT
** ** * *
42635669 TGAGCCTTAGGTCATATGCCGAG
126 TGAGCCTCGGGTCGCACGCTGAG
* * ** * *
42635692 GTATTCTTCAATTTCTATTTTTCAAAGCTCAACTCATAATT-TGAGAAGTGAGTTGA
1 GTATT-TTAAATTTCTGTTTTTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGA
42635748 ATTTTGGATC
Statistics
Matches: 329, Mismatches: 18, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
147 17 0.05
148 201 0.61
149 11 0.03
150 7 0.02
151 50 0.15
152 40 0.12
153 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (148 bp):
GTATTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ATCCTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGC
CTCGGGTCGCACGCTGAG
Found at i:42636158 original size:30 final size:28
Alignment explanation
Indices: 42636086--42636195 Score: 105
Period size: 29 Copynumber: 3.8 Consensus size: 28
42636076 TTTGGCCCCA
*
42636086 AAACTTTTCTAAATTACATTTCAAACCCT
1 AAACTTTTCAAAATTACATTTC-AACCCT
* *
42636115 GAACTTTTCAAAATTACATTTCAACTCTT
1 AAACTTTTCAAAATTACATTTCAAC-CCT
* * *
42636144 AAACTTTCTCAAAATTTCACTTCGACCCCT
1 AAACTTT-TCAAAATTACATTTC-AACCCT
42636174 AAA-TTTTCTAGAAATTACATTT
1 AAACTTTTC-A-AAATTACATTT
42636196 TGGCCCTATA
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
28 5 0.08
29 32 0.48
30 27 0.41
31 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (28 bp):
AAACTTTTCAAAATTACATTTCAACCCT
Found at i:42636209 original size:29 final size:29
Alignment explanation
Indices: 42636170--42636225 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
42636160 TCACTTCGAC
42636170 CCCTAAA-TTTTCTAGAAATTACATTTTGG
1 CCCTAAATTTTTCTA-AAATTACATTTTGG
* *
42636199 CCCTATATTTTTCTAAAATTATATTTT
1 CCCTAAATTTTTCTAAAATTACATTTT
42636226 TACCCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.48
Consensus pattern (29 bp):
CCCTAAATTTTTCTAAAATTACATTTTGG
Found at i:42636788 original size:11 final size:11
Alignment explanation
Indices: 42636772--42636833 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
42636762 AGAAGAAGGA
42636772 AAAAAAGAAAG
1 AAAAAAGAAAG
42636783 AAAAAAG-AAG
1 AAAAAAGAAAG
*
42636793 -AAAAAGAGAG
1 AAAAAAGAAAG
42636803 AAAAAAG-AAG
1 AAAAAAGAAAG
*
42636813 AAGGAAA-AAAG
1 AA-AAAAGAAAG
42636824 AAAAAAGAAA
1 AAAAAAGAAA
42636834 TTTTTTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 6 0.14
10 12 0.29
11 24 0.57
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:42636791 original size:7 final size:7
Alignment explanation
Indices: 42636779--42636833 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
42636769 GGAAAAAAAG
42636779 AAAGAAA
1 AAAGAAA
*
42636786 AAAGAAG
1 AAAGAAA
*
42636793 AAA-AAG
1 AAAGAAA
*
42636799 AGAGAAA
1 AAAGAAA
*
42636806 AAAGAAG
1 AAAGAAA
*
42636813 AAGGAAA
1 AAAGAAA
42636820 AAAGAAA
1 AAAGAAA
42636827 AAAGAAA
1 AAAGAAA
42636834 TTTTTTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 5 0.13
7 34 0.87
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:42636956 original size:22 final size:23
Alignment explanation
Indices: 42636917--42636966 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
42636907 CCAACAGTAG
42636917 CAAAGAGCAGCCCAAAAAAAAAC
1 CAAAGAGCAGCCCAAAAAAAAAC
* *
42636940 CAAAGAGCAG-CCAAAAAATAAT
1 CAAAGAGCAGCCCAAAAAAAAAC
42636962 CAAAG
1 CAAAG
42636967 CAGAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.60, C:0.22, G:0.14, T:0.04
Consensus pattern (23 bp):
CAAAGAGCAGCCCAAAAAAAAAC
Found at i:42637623 original size:18 final size:17
Alignment explanation
Indices: 42637591--42637882 Score: 157
Period size: 18 Copynumber: 16.3 Consensus size: 17
42637581 CATTTTAAAA
42637591 AAAAATTTGCCGT-TTTTC
1 AAAAATTT--CGTGTTTTC
* *
42637609 AAAAATTTCGAG-TTTA
1 AAAAATTTCGTGTTTTC
** *
42637625 AAAAAAATCGAGTTTTC
1 AAAAATTTCGTGTTTTC
*
42637642 AGAAAAATTTTCATG-TTTC
1 --AAAAA-TTTCGTGTTTTC
*
42637661 AAAAATTTTCTGTATTTTC
1 AAAAA-TTTC-GTGTTTTC
42637680 AAAAATTTACGTGTTTTC
1 AAAAATTT-CGTGTTTTC
42637698 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
*
42637716 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
*
42637734 -AAAATTTCG-GTATTTA
1 AAAAATTTCGTGT-TTTC
42637750 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
* * **
42637768 AGAAATTCCCGTGTTTAAAAA
1 AAAAATT-TCGTGTTT---TC
*
42637789 AAAAACTTCTGTGTTTTC
1 AAAAATTTC-GTGTTTTC
* *
42637807 AAAATTTTCGTGTTTTT
1 AAAAATTTCGTGTTTTC
* *
42637824 AAGAATTTTCGTG-TCTC
1 AA-AAATTTCGTGTTTTC
*
42637841 TAAAATTCTCGTGTTCTT-
1 AAAAATT-TCGTGTT-TTC
*
42637859 AAGAATTTTTCGTGTTTTC
1 AA-AA-ATTTCGTGTTTTC
42637878 AAAAA
1 AAAAA
42637883 AAATAATTGT
Statistics
Matches: 213, Mismatches: 36, Indels: 51
0.71 0.12 0.17
Matches are distributed among these distances:
15 2 0.01
16 25 0.12
17 41 0.19
18 93 0.44
19 35 0.16
20 6 0.03
21 11 0.05
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:42637819 original size:17 final size:17
Alignment explanation
Indices: 42637799--42637881 Score: 80
Period size: 17 Copynumber: 4.7 Consensus size: 17
42637789 AAAAACTTCT
42637799 GTGTTTTCAAAATTTTC
1 GTGTTTTCAAAATTTTC
*
42637816 GTGTTTTTAAGAATTTTC
1 GTGTTTTCAA-AATTTTC
* *
42637834 GTG-TCTCTAAAATTCTC
1 GTGTTTTC-AAAATTTTC
42637851 GTGTTCTT-AAGAATTTTTC
1 GTGTT-TTCAA-AA-TTTTC
42637870 GTGTTTTCAAAA
1 GTGTTTTCAAAA
42637882 AAAATAATTG
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
17 22 0.42
18 19 0.36
19 12 0.23
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (17 bp):
GTGTTTTCAAAATTTTC
Found at i:42639757 original size:21 final size:21
Alignment explanation
Indices: 42639733--42639778 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
42639723 TAAAAACGGT
42639733 ATAAATGGGTAAATAATAATA
1 ATAAATGGGTAAATAATAATA
*
42639754 AT-AA--GGTAAGTAATAATA
1 ATAAATGGGTAAATAATAATA
42639772 ATAAATG
1 ATAAATG
42639779 CAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 15 0.71
19 2 0.10
20 2 0.10
21 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (21 bp):
ATAAATGGGTAAATAATAATA
Found at i:42639761 original size:18 final size:18
Alignment explanation
Indices: 42639740--42639775 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42639730 GGTATAAATG
42639740 GGTAAATAATAATAATAA
1 GGTAAATAATAATAATAA
*
42639758 GGTAAGTAATAATAATAA
1 GGTAAATAATAATAATAA
42639776 ATGCAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (18 bp):
GGTAAATAATAATAATAA
Found at i:42639785 original size:18 final size:17
Alignment explanation
Indices: 42639744--42639790 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
42639734 TAAATGGGTA
*
42639744 AATAATAATAATAAGGT
1 AATAATAATAATAAGGC
*
42639761 AAGTAATAATAATAAATGC
1 AA-TAATAATAAT-AAGGC
42639780 AATAATAATAA
1 AATAATAATAA
42639791 CAATAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.08
18 19 0.73
19 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.28
Consensus pattern (17 bp):
AATAATAATAATAAGGC
Found at i:42649780 original size:29 final size:28
Alignment explanation
Indices: 42649715--42649843 Score: 87
Period size: 29 Copynumber: 4.8 Consensus size: 28
42649705 GTTATTTATT
* *
42649715 TATTTATTTATTTAATATTTATATAAAA
1 TATTTATTTATTTAATATTTTTTTAAAA
* *
42649743 T-TTAAATTTATTTTATATTTTTTTGAAAA
1 TATT-TATTTATTTAATATTTTTTT-AAAA
* * *
42649772 TATTTATTTGTTTGATATATTTTT--AA
1 TATTTATTTATTTAATATTTTTTTAAAA
*
42649798 T-TTTA-TTA-TT-ATA--TTTTAAAAA
1 TATTTATTTATTTAATATTTTTTTAAAA
*
42649820 TATTTATGTATTTACATATTTTTT
1 TATTTATTTATTTA-ATATTTTTT
42649844 AATTTTTTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 23
0.70 0.10 0.21
Matches are distributed among these distances:
20 4 0.05
22 6 0.08
23 6 0.08
24 4 0.05
25 6 0.08
26 3 0.04
27 5 0.06
28 17 0.22
29 25 0.32
30 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (28 bp):
TATTTATTTATTTAATATTTTTTTAAAA
Found at i:42649843 original size:48 final size:45
Alignment explanation
Indices: 42649752--42649849 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 45
42649742 ATTTAAATTT
* * * *
42649752 ATTTTATATTTTTTTGAAAATATTTATTTGTTTGATATATTTTTA
1 ATTTTATATTTTTTTAAAAATATTTATGTATTTCATATATTTTTA
42649797 ATTTTATTATTATATTTTAAAAATATTTATGTATTTACATAT-TTTTTA
1 ATTTTA-TATT-T-TTTTAAAAATATTTATGTATTT-CATATATTTTTA
42649845 ATTTT
1 ATTTT
42649850 TTTAGAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
45 6 0.13
46 4 0.09
47 1 0.02
48 30 0.67
49 4 0.09
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (45 bp):
ATTTTATATTTTTTTAAAAATATTTATGTATTTCATATATTTTTA
Found at i:42650218 original size:19 final size:18
Alignment explanation
Indices: 42650196--42650238 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
42650186 AAAATACAAA
*
42650196 AAAAATCAAAATAATTTTT
1 AAAAATAAAAAT-ATTTTT
*
42650215 AAAATTAAAAATATTTTT
1 AAAAATAAAAATATTTTT
42650233 AAAAAT
1 AAAAAT
42650239 TCTAAAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATAAAAATATTTTT
Found at i:42650239 original size:19 final size:19
Alignment explanation
Indices: 42650203--42650281 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 19
42650193 AAAAAAAATC
42650203 AAAATAATTTTT-AAAATTA
1 AAAAT-ATTTTTAAAAATTA
42650222 AAAATATTTTTAAAAATTCTA
1 AAAATATTTTTAAAAA-T-TA
*
42650243 AAACTTATCTTTTAAAAAAATTA
1 AAA-ATAT-TTTT--AAAAATTA
* *
42650266 TAAATTTTTTTAAAAA
1 AAAATATTTTTAAAAA
42650282 ATATAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
18 6 0.12
19 14 0.29
20 1 0.02
21 9 0.18
22 5 0.10
23 8 0.16
24 1 0.02
25 5 0.10
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATATTTTTAAAAATTA
Found at i:42650379 original size:35 final size:35
Alignment explanation
Indices: 42650343--42650419 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
42650333 TTTGGGAACT
42650343 AAATAATTTAATTAATGATTTAAGTTTATCATACTA
1 AAAT-ATTTAATTAATGATTTAAGTTTATCATACTA
42650379 AAATATTTAATTAATGATTTAAGTTTATCATACTA
1 AAATATTTAATTAATGATTTAAGTTTATCATACTA
42650414 AAATAT
1 AAATAT
42650420 CTTTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 37 0.90
36 4 0.10
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (35 bp):
AAATATTTAATTAATGATTTAAGTTTATCATACTA
Found at i:42650865 original size:126 final size:123
Alignment explanation
Indices: 42650640--42650892 Score: 375
Period size: 126 Copynumber: 2.0 Consensus size: 123
42650630 AATGCTCACC
*
42650640 CCTAATTATACTGATTCTTTTAACTACCACTTTATCTTGTTGTTTGTAATTTTAACGAGAGTGAC
1 CCTAATTATACTAATTCTTTTAACTACCACTTTATCTTGTTGTTTGTAATTTTAACGAGAGTGAC
* *
42650705 CAAAATGACCGAACTATGTAACGTGAGTGCTTAAATTACAAACTTTTTTTTATTTTAGGTG
66 CAAAATGACCGAACTATATAACGTGAGTGCTTAAATTACAAA---TTTTTTATTTTAAGTG
**
42650766 CCTAATTATA-TCAATTCTTTTAACTGTCACTTTATCTTGTTGTTTGTAATTTTAACGAGAGTGA
1 CCTAATTATACT-AATTCTTTTAACTACCACTTTATCTTGTTGTTTGTAATTTTAACGAGAGTGA
* * *
42650830 -CAACAATTATCGAACTATATAACGTTAGTGCTTAAATTACAAATTTTTTATTTTAAGTG
65 CCAA-AATGACCGAACTATATAACGTGAGTGCTTAAATTACAAATTTTTTATTTTAAGTG
42650889 CCTA
1 CCTA
42650893 TAATAAAAAA
Statistics
Matches: 117, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
123 19 0.16
125 4 0.03
126 94 0.80
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (123 bp):
CCTAATTATACTAATTCTTTTAACTACCACTTTATCTTGTTGTTTGTAATTTTAACGAGAGTGAC
CAAAATGACCGAACTATATAACGTGAGTGCTTAAATTACAAATTTTTTATTTTAAGTG
Found at i:42654902 original size:24 final size:24
Alignment explanation
Indices: 42654852--42654902 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42654842 TATAACATTT
**
42654852 AAAAATTCCTAAAATTTATGGATA
1 AAAAATTCCTAAAATTTATAAATA
42654876 AAAAATTCCTAAAATTTA-AAATA
1 AAAAATTCCTAAAATTTATAAATA
42654899 AAAA
1 AAAA
42654903 TAAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAATTCCTAAAATTTATAAATA
Done.