Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 41 of 75
Found at i:13079499 original size:21 final size:21
Alignment explanation
Indices: 13079474--13079513 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13079464 GAAGATAAAG
*
13079474 TATATCGCTTGAAGAAAGCTT
1 TATATCGATTGAAGAAAGCTT
* *
13079495 TATATGGATTGAAGCAAGC
1 TATATCGATTGAAGAAAGC
13079514 CTCAAGAGCA
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:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TATATCGATTGAAGAAAGCTT
Found at i:13088649 original size:11 final size:11
Alignment explanation
Indices: 13088633--13088671 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
13088623 TAGCAATGCC
13088633 TATTTTAATCA
1 TATTTTAATCA
*
13088644 TATTTTAATTA
1 TATTTTAATCA
13088655 TATTTTAATCA
1 TATTTTAATCA
13088666 TATTTT
1 TATTTT
13088672 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTAATCA
Found at i:13096676 original size:22 final size:20
Alignment explanation
Indices: 13096642--13096682 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
13096632 AATTGTTGAT
*
13096642 AAATTGATGAATTAGGCTTG
1 AAATTGATGAATTAAGCTTG
13096662 AAATTGATAGAAATTAAGCTT
1 AAATTGAT-G-AATTAAGCTT
13096683 AGATTATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
AAATTGATGAATTAAGCTTG
Found at i:13098032 original size:43 final size:43
Alignment explanation
Indices: 13097984--13098296 Score: 430
Period size: 43 Copynumber: 7.3 Consensus size: 43
13097974 TTTTAGAAAT
* *
13097984 AAACGCCACTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
13098027 AAACGCCGCTATAGATCAGGACCTTTAGTGGTGCTTTTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
13098070 AAACGCTGCTATAGATCAGGACCTTTAGTGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* *
13098112 AAACGCCGCTATAGCTCAGGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
13098155 AAATGCCGCTATAGCTCAGGACCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * * *
13098198 AAACGCCGCTATAGATTAAGACCTTTAACGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * * *
13098241 AAACGACACTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
13098284 AAACGCCGCTATA
1 AAACGCCGCTATA
13098297 CGCTTTGATT
Statistics
Matches: 240, Mismatches: 29, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
42 37 0.15
43 203 0.85
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
Found at i:13106695 original size:9 final size:9
Alignment explanation
Indices: 13106681--13106719 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
13106671 TATAAAATTT
*
13106681 ATTATTCGA
1 ATTATTTGA
13106690 ATTATTTGA
1 ATTATTTGA
13106699 ATTATTTGA
1 ATTATTTGA
*
13106708 GTTATTTGA
1 ATTATTTGA
13106717 ATT
1 ATT
13106720 GCAATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (9 bp):
ATTATTTGA
Found at i:13109281 original size:15 final size:15
Alignment explanation
Indices: 13109247--13109275 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13109237 AAATTTATAA
13109247 GAAAAGAATAAAATC
1 GAAAAGAATAAAATC
13109262 GAAAAGAATAAAAT
1 GAAAAGAATAAAAT
13109276 TTAAAAAATA
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:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (15 bp):
GAAAAGAATAAAATC
Found at i:13109313 original size:14 final size:15
Alignment explanation
Indices: 13109294--13109324 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
13109284 TAATTGAGGA
13109294 TTGAAGATT-AAAAT
1 TTGAAGATTGAAAAT
13109308 TTGAAGATTGAAAAT
1 TTGAAGATTGAAAAT
13109323 TT
1 TT
13109325 AGGAAGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (15 bp):
TTGAAGATTGAAAAT
Found at i:13114935 original size:1 final size:1
Alignment explanation
Indices: 13114931--13114961 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
13114921 AGCCAATCAA
13114931 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13114962 GAGTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13116377 original size:18 final size:18
Alignment explanation
Indices: 13116340--13116373 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13116330 AATAAAGGGG
13116340 AAGAAGAAAAAGAAAATA
1 AAGAAGAAAAAGAAAATA
*
13116358 AAGAAGTAAAA-AAAAT
1 AAGAAGAAAAAGAAAAT
13116374 TAAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AAGAAGAAAAAGAAAATA
Found at i:13123695 original size:23 final size:24
Alignment explanation
Indices: 13123647--13123708 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
13123637 ACATATCTAA
13123647 AATAATATTAAATTTTGCTTCAAT
1 AATAATATTAAATTTTGCTTCAAT
* *
13123671 AATAATATTAACTTTT-TTTCAAT
1 AATAATATTAAATTTTGCTTCAAT
13123694 AATAATATTAAATTT
1 AATAATATTAAATTT
13123709 CTGATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (24 bp):
AATAATATTAAATTTTGCTTCAAT
Found at i:13127144 original size:14 final size:14
Alignment explanation
Indices: 13127125--13127151 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13127115 ACTATATTCC
13127125 CACTTTTACTGGTT
1 CACTTTTACTGGTT
13127139 CACTTTTACTGGT
1 CACTTTTACTGGT
13127152 CCATGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CACTTTTACTGGTT
Found at i:13129987 original size:64 final size:64
Alignment explanation
Indices: 13129878--13130018 Score: 237
Period size: 64 Copynumber: 2.2 Consensus size: 64
13129868 GACCAATGGC
*
13129878 ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATTTATTAATCCTAAACATATTATAT
1 ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATGTATTAATCCTAAACATATTATAT
* ** *
13129942 ACGCTCTATAATTGACACATGTGCACTGAAATGGGTTGATGTATTAATCCTAAACATATTATAT
1 ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATGTATTAATCCTAAACATATTATAT
13130006 ACGCTCTATAATT
1 ACGCTCTATAATT
13130019 AGTCAAATTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 72 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (64 bp):
ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATGTATTAATCCTAAACATATTATAT
Found at i:13135339 original size:23 final size:23
Alignment explanation
Indices: 13135309--13135352 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
13135299 GCCTGCTTTG
13135309 GTATGTATGCACTTTAGTCATAT
1 GTATGTATGCACTTTAGTCATAT
13135332 GTATGTATGCACTTTAGTCAT
1 GTATGTATGCACTTTAGTCAT
13135353 GGTAACTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (23 bp):
GTATGTATGCACTTTAGTCATAT
Found at i:13138558 original size:2 final size:2
Alignment explanation
Indices: 13138551--13138580 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13138541 AAGTGAAACC
13138551 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
13138581 ATGGTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13146659 original size:9 final size:9
Alignment explanation
Indices: 13146645--13146669 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
13146635 TTTCACATTA
13146645 TGTGAACTT
1 TGTGAACTT
13146654 TGTGAACTT
1 TGTGAACTT
13146663 TGTGAAC
1 TGTGAAC
13146670 ATGCTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (9 bp):
TGTGAACTT
Found at i:13160617 original size:5 final size:5
Alignment explanation
Indices: 13160607--13160656 Score: 84
Period size: 5 Copynumber: 10.0 Consensus size: 5
13160597 TTATTTTTAA
13160607 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT -TAATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT-ATT ATATT
13160657 TAGGCTAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 1 0.02
5 41 0.95
6 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:13160787 original size:37 final size:38
Alignment explanation
Indices: 13160712--13160787 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
13160702 ATAATATTAT
* *
13160712 AATTTTAGTATTAAAAATATATTAAATTATTTATATTTAG
1 AATTTTAG-ATTAAAAATATA-TAAATTATTAAAATTTAG
13160752 AATTTTA-ATTAAAACATATA-AAATTATTAAAATTTA
1 AATTTTAGATTAAAA-ATATATAAATTATTAAAATTTA
13160788 AGTTAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 14 0.42
38 7 0.21
39 5 0.15
40 7 0.21
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (38 bp):
AATTTTAGATTAAAAATATATAAATTATTAAAATTTAG
Found at i:13160919 original size:10 final size:10
Alignment explanation
Indices: 13160875--13160927 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
13160865 ATCAACTATT
13160875 TTTTATTCAA
1 TTTTATTCAA
**
13160885 TTTTAAACAAA
1 TTTTATTC-AA
*
13160896 TTATTTTGTCAA
1 TT-TTAT-TCAA
13160908 TTTTATTCAA
1 TTTTATTCAA
13160918 TTTTATTCAA
1 TTTTATTCAA
13160928 AACATTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 20 0.59
11 7 0.21
12 6 0.18
13 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (10 bp):
TTTTATTCAA
Found at i:13162797 original size:9 final size:9
Alignment explanation
Indices: 13162775--13162822 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
13162765 AACATATCAA
*
13162775 AAATTAACT
1 AAATTAACC
*
13162784 GAATTAACC
1 AAATTAACC
*
13162793 AAATTAATC
1 AAATTAACC
13162802 AAATTAACC
1 AAATTAACC
* *
13162811 GAATTAAAC
1 AAATTAACC
13162820 AAA
1 AAA
13162823 CAATCCTACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.25
Consensus pattern (9 bp):
AAATTAACC
Found at i:13162798 original size:18 final size:18
Alignment explanation
Indices: 13162785--13162822 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13162775 AAATTAACTG
13162785 AATTAACCAAATTAATCA
1 AATTAACCAAATTAATCA
* *
13162803 AATTAACCGAATTAAACA
1 AATTAACCAAATTAATCA
13162821 AA
1 AA
13162823 CAATCCTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTAACCAAATTAATCA
Found at i:13162869 original size:45 final size:45
Alignment explanation
Indices: 13162818--13162905 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
13162808 ACCGAATTAA
*
13162818 ACAAACAATCCTACCGTAATACCTACATTAAATGCACATAATTCT
1 ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATTCT
*
13162863 ACAAACAATCCTATCATAATACCTACATTAAATGCACATAATT
1 ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATT
13162906 AATTTACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.27
Consensus pattern (45 bp):
ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATTCT
Found at i:13180209 original size:49 final size:44
Alignment explanation
Indices: 13180150--13180241 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
13180140 GGTGTATCGA
*
13180150 TACCGAAAAATAATTTTAAAATTAAAATTAAATTTTTATTATTTATTTG
1 TACCAAAAAATAATTTT-AAA-T-AAATT--ATTTTTATTATTTATTTG
*
13180199 TACCAAAAAATAATTTTAAATATATTATTTTTATTATTTATTT
1 TACCAAAAAATAATTTTAAATAAATTATTTTTATTATTTATTT
13180242 TGGATTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
44 17 0.41
46 4 0.10
47 1 0.02
48 3 0.07
49 16 0.39
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (44 bp):
TACCAAAAAATAATTTTAAATAAATTATTTTTATTATTTATTTG
Found at i:13192262 original size:13 final size:13
Alignment explanation
Indices: 13192229--13192263 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
13192219 TATTTAAATG
* *
13192229 TTATTATCATTTA
1 TTATTATTATTAA
13192242 TTATTATTATTAA
1 TTATTATTATTAA
13192255 TTATTATTA
1 TTATTATTA
13192264 GTTTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:13192446 original size:35 final size:33
Alignment explanation
Indices: 13192373--13192453 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 33
13192363 TATACCCATG
* * * *
13192373 TATAT-TTTTATATATGCGTACACATATATGTT
1 TATATATTTTATTTATGCATACACATACATGTC
*
13192405 TCTATATTTTATTTATGCATACCTACATACATGTC
1 TATATATTTTATTTATGCATA-C-ACATACATGTC
*
13192440 TATATATTTCATTT
1 TATATATTTTATTT
13192454 TCATAATGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 4 0.10
33 13 0.33
34 1 0.03
35 21 0.54
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.51
Consensus pattern (33 bp):
TATATATTTTATTTATGCATACACATACATGTC
Found at i:13192531 original size:33 final size:34
Alignment explanation
Indices: 13192471--13192535 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
13192461 GTGTATATAT
13192471 ATATATATATTCTTATATATTCCTTATATTTTCA
1 ATATATATATTCTTATATATTCCTTATATTTTCA
* * *
13192505 ATATATATTTTGTT-TATATTCTTTATATTTT
1 ATATATATATTCTTATATATTCCTTATATTTT
13192536 ACGATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (34 bp):
ATATATATATTCTTATATATTCCTTATATTTTCA
Found at i:13206426 original size:45 final size:45
Alignment explanation
Indices: 13206358--13206680 Score: 454
Period size: 45 Copynumber: 7.2 Consensus size: 45
13206348 CTCAGAGAAC
* * * *
13206358 AGATCGAATATAGCAGATATTGTCTTCCTGAATTGGCAGGGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
13206403 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
13206448 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * *
13206493 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGACAACAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
13206538 AGATCAAAGATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGGAGT
1 AGATCGAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGT
*
13206583 AGATCGAAGATAGCA-AGTCTTGTCTTTCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
13206628 AGA-CTGAAGATAACAGATCTTGTCTTCCTGTACTAGCAGCGAAGC
1 AGATC-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
13206673 AGATCGAA
1 AGATCGAA
13206681 AAACAACAAG
Statistics
Matches: 252, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
44 2 0.01
45 248 0.98
46 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (45 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:13206739 original size:135 final size:135
Alignment explanation
Indices: 13206438--13206741 Score: 312
Period size: 135 Copynumber: 2.3 Consensus size: 135
13206428 TCCTATATTG
* * * * *
13206438 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGA
1 GCAGCGGAGTAGATCCAAAACAGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGA
* * * * * * * *
13206503 TAGCAGATCTTGTCTTCCTGTATTGACAACAAAGTAGATCAAAGATAGCAAGTCTTGTCTTCCTG
66 TAACAGATCTTGTCTTCCTGTATAGACAACAAAGCAGATCAAAAACAACAAGTCTTATCTCCCTG
* *
13206568 TATTG
131 TAGTC
* * * * * *
13206573 GCAGCGGAGTAGATCGAAGATAGCAAGTCTTGTCTTTCTGTATTGGCAGCGAAGTAGA-CTGAAG
1 GCAGCGGAGTAGATCCAAAACAGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC-GAAG
* *
13206637 ATAACAGATCTTGTCTTCCTGTACTAG-CAGCGAAGCAGATCGAAAAACAACAAGTCTTATCTCC
65 ATAACAGATCTTGTCTTCCTGTA-TAGACAACAAAGCAGATC-AAAAACAACAAGTCTTATCTCC
13206701 CTG-ACGTC
128 CTGTA-GTC
*
13206709 GCAGTGGAGTAGA-CCAAAACCA-CAAATCTTGTC
1 GCAGCGGAGTAGATCCAAAA-CAGCAAATCTTGTC
13206742 CCCCTGAAAT
Statistics
Matches: 142, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
134 1 0.01
135 105 0.74
136 36 0.25
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (135 bp):
GCAGCGGAGTAGATCCAAAACAGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGA
TAACAGATCTTGTCTTCCTGTATAGACAACAAAGCAGATCAAAAACAACAAGTCTTATCTCCCTG
TAGTC
Found at i:13208599 original size:39 final size:39
Alignment explanation
Indices: 13208513--13208600 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
13208503 AAAAAACGTT
* **
13208513 GCTAAAGATCGAGCATTAGCGGCGGTTTTAAAAAAATGCC
1 GCTAAAAAT-GAGCATTAGCGGCGGTTTTAAAAAAACACC
* *
13208553 GCTAAAAATGAGCATTAGCGGCGTTTTGTAAAAAAGCACC
1 GCTAAAAATGAGCATTAGCGGCGGTTT-TAAAAAAACACC
*
13208593 GCAAAAAA
1 GCTAAAAA
13208601 CCTAAGCCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 17 0.41
40 24 0.59
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (39 bp):
GCTAAAAATGAGCATTAGCGGCGGTTTTAAAAAAACACC
Found at i:13208600 original size:40 final size:39
Alignment explanation
Indices: 13208523--13208600 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
13208513 GCTAAAGATC
** *
13208523 GAGCATTAGCGGCGGTTTTAAAAAAATGCCGCTAAAAAT
1 GAGCATTAGCGGCGGTTTTAAAAAAACACCGCAAAAAAT
* *
13208562 GAGCATTAGCGGCGTTTTGTAAAAAAGCACCGCAAAAAA
1 GAGCATTAGCGGCGGTTT-TAAAAAAACACCGCAAAAAA
13208601 CCTAAGCCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (39 bp):
GAGCATTAGCGGCGGTTTTAAAAAAACACCGCAAAAAAT
Found at i:13208934 original size:14 final size:15
Alignment explanation
Indices: 13208906--13208938 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
13208896 AAGGTTTATA
13208906 GATTATGGAATTAGG
1 GATTATGGAATTAGG
13208921 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
13208935 GATT
1 GATT
13208939 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:13209014 original size:21 final size:21
Alignment explanation
Indices: 13208962--13209015 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
13208952 TGTGATTTAA
* * *
13208962 GGTTTATAGGTTAGGGGTTAG
1 GGTTTAGAGGTTAAGAGTTAG
*
13208983 GGGTTAGAGGTTAAGAGTTAG
1 GGTTTAGAGGTTAAGAGTTAG
13209004 GGATTTA-AGGTT
1 GG-TTTAGAGGTT
13209016 TATGGATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (21 bp):
GGTTTAGAGGTTAAGAGTTAG
Found at i:13209130 original size:7 final size:7
Alignment explanation
Indices: 13209085--13209139 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
13209075 TATTAAATAA
13209085 GGTTTAGG
1 GGTTTA-G
*
13209093 GGTTAAG
1 GGTTTAG
13209100 GG-TTAG
1 GGTTTAG
13209106 GGATTT-G
1 GG-TTTAG
13209113 GG-TTAG
1 GGTTTAG
*
13209119 CGTTTAG
1 GGTTTAG
13209126 GGTTTAG
1 GGTTTAG
13209133 GGTTTAG
1 GGTTTAG
13209140 ATTAATTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
5 2 0.05
6 7 0.18
7 23 0.59
8 7 0.18
ACGTcount: A:0.16, C:0.02, G:0.44, T:0.38
Consensus pattern (7 bp):
GGTTTAG
Found at i:13209137 original size:14 final size:13
Alignment explanation
Indices: 13209092--13209139 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
13209082 TAAGGTTTAG
*
13209092 GGGTTAAGGGTTA
1 GGGTTTAGGGTTA
13209105 GGGATTT-GGGTTA
1 GGG-TTTAGGGTTA
*
13209118 GCGTTTAGGGTTTA
1 GGGTTTAGGG-TTA
13209132 GGGTTTAG
1 GGGTTTAG
13209140 ATTAATTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.10
13 14 0.48
14 12 0.41
ACGTcount: A:0.17, C:0.02, G:0.44, T:0.38
Consensus pattern (13 bp):
GGGTTTAGGGTTA
Found at i:13210732 original size:6 final size:6
Alignment explanation
Indices: 13210716--13210748 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
13210706 TGTGGTTTGA
13210716 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
13210749 TTTGAGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:13210991 original size:24 final size:24
Alignment explanation
Indices: 13210964--13211016 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
13210954 TGTAGAATAA
13210964 GAAATATCTAAAACTATTTATTTT
1 GAAATATCTAAAACTATTTATTTT
*
13210988 GAAATATCTGAAACTATTTATTTT
1 GAAATATCTAAAACTATTTATTTT
13211012 GAAAT
1 GAAAT
13211017 GTTCTGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (24 bp):
GAAATATCTAAAACTATTTATTTT
Found at i:13213371 original size:31 final size:31
Alignment explanation
Indices: 13213336--13213405 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
13213326 CAGCATAACT
13213336 TATTGCTGAAGTTATACAGCCACGTTGTTTG
1 TATTGCTGAAGTTATACAGCCACGTTGTTTG
13213367 TATTGCTGAAGTTATACAGCCACGTTGTTTG
1 TATTGCTGAAGTTATACAGCCACGTTGTTTG
*
13213398 CA-TGCTGA
1 TATTGCTGA
13213406 TTACCAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (31 bp):
TATTGCTGAAGTTATACAGCCACGTTGTTTG
Found at i:13213937 original size:18 final size:18
Alignment explanation
Indices: 13213914--13213973 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
13213904 ATGTAATTCT
13213914 AATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
* * **
13213932 AATGTAA-AC-AATTTTCT
1 AATGTAATTCTAA-TATAG
*
13213949 TATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
13213967 AATGTAA
1 AATGTAA
13213974 CTTGTTTTAA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 2 0.07
17 9 0.31
18 16 0.55
19 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (18 bp):
AATGTAATTCTAATATAG
Found at i:13214268 original size:43 final size:42
Alignment explanation
Indices: 13214160--13214291 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 42
13214150 TAATTTGTTT
* * * *
13214160 TAAAAGTCATG-TTTTTAGCGGCGTTTGTGAAAAAGCGTCGC
1 TAAAGGTCATGCTCTTTAGCGGCGTTTGTGTAAAAGCGCCGC
* ** *
13214201 TAAAGGTCATTCTCCATAGTGGCGTTTGTGGTAAAAGCGCCGC
1 TAAAGGTCATGCTCTTTAGCGGCGTTTGT-GTAAAAGCGCCGC
* * * *
13214244 TAAAGGTCCTAGC-CTTTAGCGGCGTTTTTATAAAAGTGCCGC
1 TAAAGGTCAT-GCTCTTTAGCGGCGTTTGTGTAAAAGCGCCGC
13214286 TAAAGG
1 TAAAGG
13214292 CCAAAAAAAC
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
41 9 0.12
42 30 0.42
43 32 0.44
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
TAAAGGTCATGCTCTTTAGCGGCGTTTGTGTAAAAGCGCCGC
Found at i:13214388 original size:13 final size:13
Alignment explanation
Indices: 13214333--13214392 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
13214323 GTGTAGTGCT
13214333 TATATTTTCAATA
1 TATATTTTCAATA
**
13214346 TATATCTTGTTTATA
1 TATAT-TT-TCAATA
* *
13214361 TATATATTC-CT-
1 TATATTTTCAATA
13214372 TATATTTTCAATA
1 TATATTTTCAATA
13214385 TATATTTT
1 TATATTTT
13214393 GTTTATATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
11 8 0.22
12 2 0.06
13 14 0.39
14 3 0.08
15 9 0.25
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (13 bp):
TATATTTTCAATA
Found at i:13214409 original size:24 final size:23
Alignment explanation
Indices: 13214355--13214409 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
13214345 ATATATCTTG
13214355 TTTATATATATATTCCTTATATT
1 TTTATATATATATTCCTTATATT
* * **
13214378 TTCAATATATATTTTGTTTATATT
1 TT-TATATATATATTCCTTATATT
13214402 CTTTATAT
1 -TTTATAT
13214410 TTTACGATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 21 0.84
25 2 0.08
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTATATATATATTCCTTATATT
Found at i:13219474 original size:21 final size:21
Alignment explanation
Indices: 13219449--13219490 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13219439 TTACTGGACA
*
13219449 TTTTATTTATATATTTTTTAT
1 TTTTATATATATATTTTTTAT
*
13219470 TTTTATATATATGTTTTTTAT
1 TTTTATATATATATTTTTTAT
13219491 ATTATGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATATATATATTTTTTAT
Found at i:13219496 original size:14 final size:14
Alignment explanation
Indices: 13219469--13219507 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
13219459 ATATTTTTTA
*
13219469 TTTTTATATATATGT
1 TTTTTATAT-TATGG
13219484 TTTTTATATTATGG
1 TTTTTATATTATGG
*
13219498 TTTTAATATT
1 TTTTTATATT
13219508 TGGGCTCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (14 bp):
TTTTTATATTATGG
Found at i:13219829 original size:17 final size:18
Alignment explanation
Indices: 13219803--13219836 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13219793 AAATTTGAGA
13219803 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
13219820 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
13219837 AGAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:13230233 original size:75 final size:75
Alignment explanation
Indices: 13230141--13230291 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
13230131 TCTGGAACTA
* * *
13230141 ACTCAAGCAAACCGCACAACCATGCATAAATATAATATGTCTCTTATAATACTAAGCCTCAACCA
1 ACTCAAACAAACCGCACAACCATGCATAAATATAATATGTCTCGTATAATACTAAACCTCAACCA
13230206 AAATATGCAT
66 AAATATGCAT
* *
13230216 ACTCAAACAAACTGCACAACCATGCATAAATATAATATGTCTGGTATAATACTAAACCTCAACCA
1 ACTCAAACAAACCGCACAACCATGCATAAATATAATATGTCTCGTATAATACTAAACCTCAACCA
*
13230281 GAATATGCAT
66 AAATATGCAT
13230291 A
1 A
13230292 ATTATTCACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (75 bp):
ACTCAAACAAACCGCACAACCATGCATAAATATAATATGTCTCGTATAATACTAAACCTCAACCA
AAATATGCAT
Found at i:13230746 original size:31 final size:31
Alignment explanation
Indices: 13230711--13230786 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
13230701 CTCCTCGAAT
13230711 GCATATAACCGAATATTGATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
* *
13230742 GCATATAACCGAGTATTTATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
* *
13230773 GAATATACCCGAAT
1 GCATATAACCGAAT
13230787 GTATGTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (31 bp):
GCATATAACCGAATATTGATATACATCAAGA
Found at i:13232256 original size:18 final size:18
Alignment explanation
Indices: 13232233--13232268 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13232223 TTAGTCTCTC
13232233 AAAATTTTAATTTCGCAA
1 AAAATTTTAATTTCGCAA
13232251 AAAATTTTAATTTCGCAA
1 AAAATTTTAATTTCGCAA
13232269 TTTAGCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
AAAATTTTAATTTCGCAA
Found at i:13236389 original size:19 final size:19
Alignment explanation
Indices: 13236346--13236390 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
13236336 AGCCAGGCCT
* *
13236346 CCTCCTCGCGCATGTTGCG
1 CCTCCGCGCGCATGTAGCG
13236365 --TCCGCGCGCATGTAGCG
1 CCTCCGCGCGCATGTAGCG
13236382 CCTCCGCGC
1 CCTCCGCGC
13236391 CAAATCCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.68
19 7 0.32
ACGTcount: A:0.07, C:0.44, G:0.29, T:0.20
Consensus pattern (19 bp):
CCTCCGCGCGCATGTAGCG
Found at i:13237750 original size:39 final size:41
Alignment explanation
Indices: 13237609--13237761 Score: 138
Period size: 40 Copynumber: 3.8 Consensus size: 41
13237599 AGCGGCACTT
* * * *
13237609 TTAGCGGCG-TTTGGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTT-TACAAAAAGCACCGCTAAAAATCAAGCA
* *
13237650 TTAGCGGCGCTTTTACAAAAA-CACCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTTTACAAAAAGCACCGCTAAAAATCAAGCA
* ** *
13237690 TTAGCGACGCATTTT--GGAAAGCGCCGCTAAAAAT-AAGCA
1 TTAGCGGCGC-TTTTACAAAAAGCACCGCTAAAAATCAAGCA
* *
13237729 TTAGCGGCG-TTTTTCAAAAAGCACCGCAAAAAA
1 TTAGCGGCGCTTTTACAAAAAGCACCGCTAAAAA
13237762 CCTAAGCCCA
Statistics
Matches: 91, Mismatches: 16, Indels: 12
0.76 0.13 0.10
Matches are distributed among these distances:
37 4 0.04
39 29 0.32
40 35 0.38
41 20 0.22
42 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTTACAAAAAGCACCGCTAAAAATCAAGCA
Found at i:13237777 original size:79 final size:80
Alignment explanation
Indices: 13237631--13237778 Score: 176
Period size: 79 Copynumber: 1.9 Consensus size: 80
13237621 GGACAAAAAA
* * * * ** *
13237631 CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAACACCGCTAAAGATCGAGCATTAGCG
1 CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAACACCGCAAAAAACCAAGCACCAACG
13237696 ACGCATTTTGGAAAG
66 ACGCATTTTGGAAAG
* *
13237711 CGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTTTCAAAAAGCACCGCAAAAAACCTAAGC-CCAA
1 CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAA-CACCGCAAAAAACC-AAGCACCAA
13237773 CGACGC
64 CGACGC
13237779 CGTTTTCAGC
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
78 10 0.18
79 32 0.56
80 15 0.26
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (80 bp):
CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAACACCGCAAAAAACCAAGCACCAACG
ACGCATTTTGGAAAG
Found at i:13237872 original size:41 final size:41
Alignment explanation
Indices: 13237810--13238037 Score: 307
Period size: 41 Copynumber: 5.6 Consensus size: 41
13237800 CTATAGTGGT
** * *
13237810 GTTTTTGAAAAAGCGTTGCTAATGCTCCTACCTTTAGCAGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
* * *
13237851 GTTTTTGAACAAGCGCAGCTAATGCTCGTACCGTTAGCAGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
*
13237892 GTTTTTGAACAAGCGCAG-TGAATGCTCGTACCTTTAGCGGC
1 GTTTTTGAAAAAGCGCAGCT-AATGCTCGTACCTTTAGCGGC
* *
13237933 GTTTTTGAAAAGGCGCCGCTAATGCTCGTACCTTTAGCGGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
* * *
13237974 GTTTTTGAAGAAGCGCCGCTAATGCTTGTACCTTTAGCGGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
13238015 GTTTTTGAAAAAGCGTC-GCTAAT
1 GTTTTTGAAAAAGCG-CAGCTAAT
13238038 AATAAAATCT
Statistics
Matches: 170, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 167 0.98
42 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (41 bp):
GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
Found at i:13239112 original size:7 final size:7
Alignment explanation
Indices: 13239100--13239155 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
13239090 TCTTGAGTTC
13239100 AGGGTTT
1 AGGGTTT
13239107 AGGGTTT
1 AGGGTTT
13239114 A-GGTTT
1 AGGGTTT
*
13239120 AGGGCTT
1 AGGGTTT
*
13239127 AGGGATT
1 AGGGTTT
13239134 -GGAGTTT
1 AGG-GTTT
*
13239141 AAGGTTT
1 AGGGTTT
*
13239148 AGAGTTT
1 AGGGTTT
13239155 A
1 A
13239156 TATTTTAGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 8 0.20
7 31 0.77
8 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.38, T:0.39
Consensus pattern (7 bp):
AGGGTTT
Found at i:13240046 original size:164 final size:163
Alignment explanation
Indices: 13239774--13240115 Score: 614
Period size: 164 Copynumber: 2.1 Consensus size: 163
13239764 TAACAGATTT
13239774 AAAATGAAATAATTTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGT
1 AAAATGAAATAA-TTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGT
*
13239839 TTTTATAAAAAACGCGACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
65 TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
* *
13239904 ATTTTTAGCATAGAAAAACGGT-GTCGTTTTGTAC
130 ATTTTTAGCATAGAAAAAC-ATCGTCATTTTGTAC
*
13239938 AAAAATGAAATAATTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGGCGT
1 -AAAATGAAATAATTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGT
13240003 TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
65 TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
13240068 ATTTTTAGCATAGAAAAACATCGTCATTTTGTAC
130 ATTTTTAGCATAGAAAAACATCGTCATTTTGTAC
13240102 AAAATGAAATAATT
1 AAAATGAAATAATT
13240116 AAAAACGCCG
Statistics
Matches: 172, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
163 15 0.09
164 145 0.84
165 12 0.07
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (163 bp):
AAAATGAAATAATTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGTT
TTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAGA
TTTTTAGCATAGAAAAACATCGTCATTTTGTAC
Found at i:13253696 original size:6 final size:6
Alignment explanation
Indices: 13253687--13253802 Score: 53
Period size: 6 Copynumber: 19.8 Consensus size: 6
13253677 AAGAAAAAGA
* * * *
13253687 AAAATC AAAATC AAAGTT AAAATG AAAATG AAAA-- AAAATC AAAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC -AAAATC
* * * ** * *
13253734 AAAATT AAAA-A AAAAAC AAAAAG AAGAA-- AGAATC AAAATC AAGATC
1 AAAATC AAAATC AAAATC AAAATC AA-AATC AAAATC AAAATC AAAATC
* * *
13253780 AAAATG AAAATG AAAATG AAAAT
1 AAAATC AAAATC AAAATC AAAAT
13253803 GAGAAAAAGA
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
4 6 0.07
5 5 0.06
6 71 0.79
7 8 0.09
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:13253755 original size:34 final size:35
Alignment explanation
Indices: 13253686--13253772 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 35
13253676 GAAGAAAAAG
* * **
13253686 AAAAATC-AAAATCAAAGTTAAAATGAAAATGAAA
1 AAAAATCAAAAATCAAAATTAAAATAAAAAACAAA
13253720 AAAAATCAAAAATCAAAATTAAAA-AAAAAACAAA
1 AAAAATCAAAAATCAAAATTAAAATAAAAAACAAA
* *
13253754 AAGAA-GAAAGAATCAAAAT
1 AAAAATCAAA-AATCAAAAT
13253773 CAAGATCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 3 0.07
34 27 0.60
35 15 0.33
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (35 bp):
AAAAATCAAAAATCAAAATTAAAATAAAAAACAAA
Found at i:13253814 original size:20 final size:21
Alignment explanation
Indices: 13253785--13253835 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 21
13253775 AGATCAAAAT
*
13253785 GAAAATGAAAATGAA-AATGA
1 GAAAAAGAAAATGAAGAATGA
13253805 GAAAAAG-AAA-GAAGAATGA
1 GAAAAAGAAAATGAAGAATGA
13253824 -AAAAAGAGAAAT
1 GAAAAAGA-AAAT
13253836 CTAGATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.35
19 8 0.31
20 9 0.35
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.10
Consensus pattern (21 bp):
GAAAAAGAAAATGAAGAATGA
Found at i:13255616 original size:43 final size:43
Alignment explanation
Indices: 13255566--13255703 Score: 104
Period size: 43 Copynumber: 3.2 Consensus size: 43
13255556 AGATAGCAGA
13255566 TCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAG
1 TCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAG
** ** * * * * * *
13255609 TCTTGCC-TCCAT-CGGTT-GTAGTGGAGCTGGT-TAAAGATAGCAG
1 TCTTGCCTTCC-TGC-GTTAACAACGAAGCAGATCGAAA-ACA-AAG
13255652 ATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAG
1 -TCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAG
*
13255696 CCTTGCCT
1 TCTTGCCT
13255704 CCATCAGTTG
Statistics
Matches: 65, Mismatches: 21, Indels: 18
0.62 0.20 0.17
Matches are distributed among these distances:
41 3 0.05
42 13 0.20
43 20 0.31
44 13 0.20
45 13 0.20
46 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (43 bp):
TCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAG
Found at i:13255653 original size:87 final size:87
Alignment explanation
Indices: 13255507--13255784 Score: 470
Period size: 87 Copynumber: 3.2 Consensus size: 87
13255497 AGATCAGTGA
* *
13255507 AGATCGAAAACAATGTCTTGCCTCCATCTGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
13255572 CTTCCTGCGTTAACAACGAAGC
66 CTTCCTGCGTTAACAACGAAGC
*
13255594 AGATCGAAAACAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
13255659 CTTCCTGCGTTAACAACGAAGC
66 CTTCCTGCGTTAACAACGAAGC
* *
13255681 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGC
1 AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
13255745 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAACGAAGC
* *
13255767 ATATCGAAATC-AAGTCTT
1 AGATCGAAAACAAAGTCTT
13255785 ATCTCCCTGA
Statistics
Matches: 182, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
85 6 0.03
86 42 0.23
87 134 0.74
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (87 bp):
AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAACGAAGC
Found at i:13256223 original size:40 final size:40
Alignment explanation
Indices: 13256168--13256386 Score: 219
Period size: 40 Copynumber: 5.3 Consensus size: 40
13256158 NNNNNNNNNN
13256168 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
13256208 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
* * *
13256248 AGTGGAGCAGA-CAGAAGAAATCAAGTCCTATCTTCCTAAGCAGT
1 AGTGGAGCAGATC----G-CATCAAGTCTTATCTCCCTAAGCAGT
* * * *
13256292 AGTGGAGTAGGA-CAAAGCTTGC-AGATTTTATCTCCCTAAGTAGT
1 AGTGGAGCA-GATC---GCAT-CAAG-TCTTATCTCCCTAAGCAGT
* * * *
13256336 AATAGAGCAAATCACATCAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
13256376 AGTGGAGCAGA
1 AGTGGAGCAGA
13256387 CAGAACTAAT
Statistics
Matches: 147, Mismatches: 22, Indels: 20
0.78 0.12 0.11
Matches are distributed among these distances:
39 1 0.01
40 77 0.52
41 4 0.03
43 5 0.03
44 57 0.39
45 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (40 bp):
AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
Found at i:13258072 original size:12 final size:12
Alignment explanation
Indices: 13258055--13258106 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
13258045 TAGCAATTTC
13258055 ATTATTTAGT-TT
1 ATTA-TTAGTATT
*
13258067 ATTATTATTATT
1 ATTATTAGTATT
*
13258079 ATTATTAGTGTT
1 ATTATTAGTATT
* *
13258091 ATTATCATTATT
1 ATTATTAGTATT
13258103 ATTA
1 ATTA
13258107 CTATTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 4 0.12
12 29 0.88
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (12 bp):
ATTATTAGTATT
Found at i:13258073 original size:3 final size:3
Alignment explanation
Indices: 13258065--13258115 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
13258055 ATTATTTAGT
* * * *
13258065 TTA TTA TTA TTA TTA TTA TTA GTG TTA TTA TCA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13258113 TTA
1 TTA
13258116 ACAATTTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:13259033 original size:113 final size:109
Alignment explanation
Indices: 13258750--13259061 Score: 421
Period size: 108 Copynumber: 2.8 Consensus size: 109
13258740 TTTTTAATTG
* *
13258750 AGGCAATATTTAGCGTTTGGAAATTCAGAGAAAACGT-CCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGAAATTC-GAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * * *
13258814 TCGTTCAACAAAATAGCTAAATGTCC-TTTCAAAATTTTAAAATA
65 TCGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATA
* * * *
13258858 AGGCAATGTTTTGCGGTTGGAAATTCGAGGAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
13258923 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAAAAATTTCGAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTT---AAAAATTTCAAAATA
*
13258970 AGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * *
13259035 TCATTTAACCAAATAGCCAAATATCCT
65 TCGTTCAACCAAATAGCTAAATATCCT
13259062 CTTGAATTTC
Statistics
Matches: 177, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
107 8 0.05
108 72 0.41
109 3 0.02
112 28 0.16
113 66 0.37
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATA
Found at i:13263418 original size:86 final size:86
Alignment explanation
Indices: 13263125--13263422 Score: 345
Period size: 86 Copynumber: 3.5 Consensus size: 86
13263115 ATGATATGTT
* * * * * * *
13263125 TTTAGCGGCATTT-TGGCAAGAAGCACCGCTAAAGGT-TTGTTCTATAGCGGCGTTTTTGAGAAA
1 TTTAGCGGCGTTTGTGACAA-AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAG-GA
* *
13263188 AAACGCTGCTAAAGGTCAC-GTTC
64 AAACGCCGCTAAAGGTC-CTGGTC
* * *
13263211 TTTAGCGGCGTTTGTAACAAAAGCGCCGCTAAAGGCCATAGTCTATAGCGGCGTTTGTG-GGAAA
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAGGAAA
*
13263275 AGCGCCGCTAAAGG-CCATGGTA
66 A-CGCCGCTAAAGGTCC-TGGTC
* * *
13263297 TATAGCGGTGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGTGGCGTTTGTGAGGAAA
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAGGAAA
13263362 ACGCCGCTAAAGGTCCTGGTC
66 ACGCCGCTAAAGGTCCTGGTC
** *
13263383 TTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCATG
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
13263423 ACCTTTAGCG
Statistics
Matches: 180, Mismatches: 25, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
84 1 0.01
85 5 0.03
86 144 0.80
87 30 0.17
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAGGAAA
ACGCCGCTAAAGGTCCTGGTC
Found at i:13263433 original size:43 final size:43
Alignment explanation
Indices: 13263127--13263422 Score: 310
Period size: 43 Copynumber: 6.9 Consensus size: 43
13263117 GATATGTTTT
* * * * *
13263127 TAGCGGCATTT-TGGCAAGAAGCACCGCTAAAGGT-TTGTTCTA
1 TAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGGTCATGGTCTA
* * * * * * *
13263169 TAGCGGCGTTTTTGAGAAAAAACGCTGCTAAAGGTCACGTTCTT
1 TAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
*** * *
13263213 TAGCGGCGTTTGTAACAAAAGCGCCGCTAAAGGCCATAGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
13263256 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTATA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* **
13263299 TAGCGGTGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
13263342 TAGTGGCGTTTGTGAGGAAAA-CGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
*
13263385 TAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCATG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATG
13263423 ACCTTTAGCG
Statistics
Matches: 211, Mismatches: 38, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
42 16 0.08
43 171 0.81
44 24 0.11
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:13278237 original size:14 final size:14
Alignment explanation
Indices: 13278216--13278249 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
13278206 AATATAAAAT
13278216 TAAA-TTGAAGAAA
1 TAAAGTTGAAGAAA
13278229 TAAAGTTGAAGAAA
1 TAAAGTTGAAGAAA
13278243 TAAAGTT
1 TAAAGTT
13278250 AGCCTCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (14 bp):
TAAAGTTGAAGAAA
Found at i:13278807 original size:41 final size:40
Alignment explanation
Indices: 13278762--13278857 Score: 120
Period size: 41 Copynumber: 2.4 Consensus size: 40
13278752 AATTTAACCG
* * * *
13278762 ATGAGACACTGGGTGTTAATTTATTACTTTGAATTTATTCA
1 ATGAGACACTGGGTGTCAATTTAGTACTTCGAA-TTATCCA
* *
13278803 ATGAGATACTGGGTGTCAATTTAGTACTTCGAATTATCCG
1 ATGAGACACTGGGTGTCAATTTAGTACTTCGAATTATCCA
*
13278843 ATGAGGCACTGGGTG
1 ATGAGACACTGGGTG
13278858 CCAAATTGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 18 0.38
41 29 0.62
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTTAGTACTTCGAATTATCCA
Found at i:13282862 original size:41 final size:41
Alignment explanation
Indices: 13282800--13282907 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 41
13282790 AATTGCTAAT
* *
13282800 TTACTTCGG-TTTATCCAATGAGACACTGGGTGTCAATTTA
1 TTACTTCGGATTTATCCGATGAGACACTGAGTGTCAATTTA
*
13282840 TTACTTCGGATTTATTCGATGAGACACTGAGTGTCAATTTA
1 TTACTTCGGATTTATCCGATGAGACACTGAGTGTCAATTTA
* * *
13282881 CTACTTC-GAATTATCCGATGAGGCACT
1 TTACTTCGGATTTATCCGATGAGACACT
13282908 ATGTGCCAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 26 0.43
41 34 0.57
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (41 bp):
TTACTTCGGATTTATCCGATGAGACACTGAGTGTCAATTTA
Found at i:13284615 original size:40 final size:39
Alignment explanation
Indices: 13284561--13284696 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
13284551 ACCAGTTTGG
* *
13284561 CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTTA
1 CACCCAGTGCCTCATCGGATAATACGAAGTA-TAAATTGA
* * * * *
13284601 CACCAAGTGTCTCATCTGTTAA-ACTGAAGTA-AAATTGG
1 CACCCAGTGCCTCATCGGATAATAC-GAAGTATAAATTGA
* * *
13284639 CACTCAGTGCCTCATCGAATAAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGAT-AATACGAAGT-ATAAATTGA
*
13284680 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
13284697 ACTCGAAGTT
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
38 19 0.26
39 8 0.11
40 26 0.35
41 21 0.28
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATACGAAGTATAAATTGA
Found at i:13286915 original size:12 final size:12
Alignment explanation
Indices: 13286892--13286929 Score: 67
Period size: 12 Copynumber: 3.1 Consensus size: 12
13286882 GCCGAGCCAC
13286892 ACACCTGTGTGCT
1 ACACC-GTGTGCT
13286905 ACACCGTGTGCT
1 ACACCGTGTGCT
13286917 ACACCGTGTGCT
1 ACACCGTGTGCT
13286929 A
1 A
13286930 GCTGTGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26
Consensus pattern (12 bp):
ACACCGTGTGCT
Found at i:13287929 original size:40 final size:38
Alignment explanation
Indices: 13287885--13288025 Score: 149
Period size: 40 Copynumber: 3.6 Consensus size: 38
13287875 ACACACCAAT
* *
13287885 TTGACACTTAGTGCCTCATCAGATAATTCGAAGTAGTAAA
1 TTGACACTCAGTGCCTCATC-GATAAATCGAAGTA-TAAA
* * *
13287925 TTGACACCCAGTGTCTCATCGGATAAACCGAAGTA-AAA
1 TTGACACTCAGTGCCTCATC-GATAAATCGAAGTATAAA
*
13287963 TTGGCACTCAGTGCCTCATCGAATAAATCTGAAGTAATAAA
1 TTGACACTCAGTGCCTCATCG-ATAAATC-GAAGT-ATAAA
* *
13288004 TTGACACCCAGTGTCTCATCGA
1 TTGACACTCAGTGCCTCATCGA
13288026 CTCAAAGTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
37 1 0.01
38 26 0.31
39 5 0.06
40 31 0.37
41 21 0.25
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (38 bp):
TTGACACTCAGTGCCTCATCGATAAATCGAAGTATAAA
Found at i:13288022 original size:41 final size:40
Alignment explanation
Indices: 13287913--13288025 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 40
13287903 TCAGATAATT
* *
13287913 CGAAGTAGTAAATTGACACCCAGTGTCTCATCGGATAAAC
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAAC
* * *
13287953 CGAAGT-A-AAATTGGCACTCAGTGCCTCATCGAATAAATC
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAA-C
*
13287992 TGAAGTAATAAATTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGA
13288026 CTCAAAGTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 26 0.43
39 6 0.10
40 7 0.11
41 22 0.36
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAAC
Found at i:13288886 original size:4 final size:4
Alignment explanation
Indices: 13288877--13288933 Score: 55
Period size: 4 Copynumber: 13.8 Consensus size: 4
13288867 CCTTTTTCTT
13288877 TTTC TTTC TTTC TTTC -TTC TTTC TGTTTC ATTT- TTATC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC --TTTC -TTTC TT-TC TTTC TTTC
*
13288923 TTTA TTTC TTT
1 TTTC TTTC TTT
13288934 TTATTACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
3 5 0.11
4 31 0.69
5 5 0.11
6 4 0.09
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:13288990 original size:18 final size:18
Alignment explanation
Indices: 13288967--13289003 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13288957 CTATTATGTT
*
13288967 TTATTATACATTAATATA
1 TTATTATACAATAATATA
*
13288985 TTATTATATAATAATATA
1 TTATTATACAATAATATA
13289003 T
1 T
13289004 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTATACAATAATATA
Found at i:13288994 original size:2 final size:2
Alignment explanation
Indices: 13288980--13289028 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
13288970 TTATACATTA
13288980 AT AT AT -T AT -T AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13289018 AT AT AT AT AT A
1 AT AT AT AT AT A
13289029 CTCACAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13294200 original size:47 final size:47
Alignment explanation
Indices: 13294046--13294198 Score: 243
Period size: 47 Copynumber: 3.3 Consensus size: 47
13294036 GTCACAGTAA
13294046 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
* *
13294093 TGCAAATAAACTACTAATAATCAAAATTGTGGATAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
* * * *
13294140 TACAGATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
*
13294187 TGTAAATAAACT
1 TGCAAATAAACT
13294199 GCTAAAAACT
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (47 bp):
TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
Found at i:13299229 original size:22 final size:24
Alignment explanation
Indices: 13299187--13299230 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
13299177 TAACTAAGCT
13299187 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
13299211 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
13299231 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:13299628 original size:15 final size:15
Alignment explanation
Indices: 13299608--13299636 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13299598 TTCTTTCCTG
13299608 TTTTTCTTTTGTTTC
1 TTTTTCTTTTGTTTC
13299623 TTTTTCTTTTGTTT
1 TTTTTCTTTTGTTT
13299637 TACTTACTTA
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:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTGTTTC
Found at i:13300306 original size:6 final size:6
Alignment explanation
Indices: 13300295--13300321 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13300285 TAAATAAATA
13300295 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
13300322 TTTATGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:13311665 original size:28 final size:28
Alignment explanation
Indices: 13311628--13311697 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
13311618 AAATAAAAAA
*
13311628 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATA-ATTTTTTTTAT
*
13311656 TTACTAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
13311684 TTACCAAAATATAT
1 TTACCAAAATATAT
13311698 CAAAAAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 34 0.89
29 4 0.11
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:13311713 original size:8 final size:8
Alignment explanation
Indices: 13311698--13311743 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
13311688 CAAAATATAT
13311698 CAAAAAAA
1 CAAAAAAA
13311706 CCAAAAAAA
1 -CAAAAAAA
13311715 CAAAAAAA
1 CAAAAAAA
13311723 -ATAAAAAA
1 CA-AAAAAA
13311731 CAGAAAAAA
1 CA-AAAAAA
13311740 -AAAA
1 CAAAA
13311744 CTGGACTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 4 0.12
8 15 0.44
9 15 0.44
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (8 bp):
CAAAAAAA
Found at i:13311728 original size:16 final size:17
Alignment explanation
Indices: 13311709--13311740 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13311699 AAAAAAACCA
13311709 AAAAAACA-AAAAAAAT
1 AAAAAACAGAAAAAAAT
13311725 AAAAAACAGAAAAAAA
1 AAAAAACAGAAAAAAA
13311741 AAACTGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAACAGAAAAAAAT
Found at i:13311811 original size:27 final size:27
Alignment explanation
Indices: 13311771--13311849 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
13311761 TTCCCTGGGT
*
13311771 CAAGGGAACACTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
*
13311798 GAAGGGAACCCTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
**
13311825 CAAGGGTTCCCTGTTGGCGGCACCA
1 CAAGGGAACCCTGTTGGCGGCACCA
13311850 CTCGTGTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.32, T:0.14
Consensus pattern (27 bp):
CAAGGGAACCCTGTTGGCGGCACCAAA
Found at i:13318115 original size:27 final size:28
Alignment explanation
Indices: 13318077--13318145 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
13318067 TCTGTTTTTT
13318077 TATATATTTTGGTAAATAAAAAAAT-TA
1 TATATATTTTGGTAAATAAAAAAATGTA
*
13318104 TATATTTTTTGGTAAATAAAAAAATGTA
1 TATATATTTTGGTAAATAAAAAAATGTA
*
13318132 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
13318146 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 34 0.89
28 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.42
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAATGTA
Found at i:13318669 original size:29 final size:30
Alignment explanation
Indices: 13318627--13318694 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
13318617 NNNNNNNNNN
*
13318627 TTAAAATATATTTTTTAATTTTTT-TAATT
1 TTAAAATATATTTTTTAATTTTTTAAAATT
13318656 TTAAAATACT-TTTTTTAATTTTTTAAAAATT
1 TTAAAATA-TATTTTTTAATTTTTT-AAAATT
13318687 TTAAAATA
1 TTAAAATA
13318695 AAAATGGGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 22 0.63
30 1 0.03
31 12 0.34
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
TTAAAATATATTTTTTAATTTTTTAAAATT
Found at i:13318688 original size:20 final size:18
Alignment explanation
Indices: 13318643--13318688 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
13318633 TATATTTTTT
13318643 AATTTTTTTAATTTTAAA
1 AATTTTTTTAATTTTAAA
13318661 ATACTTTTTTTAATTTTTTAAA
1 A-A-TTTTTTTAA--TTTTAAA
13318683 AATTTT
1 AATTTT
13318689 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.04
19 1 0.04
20 13 0.54
21 1 0.04
22 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTTTTTAATTTTAAA
Found at i:13320210 original size:17 final size:16
Alignment explanation
Indices: 13320177--13320217 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
13320167 AAAATGACCC
*
13320177 AAAAATAAATAATTAT
1 AAAAATAAATAAGTAT
*
13320193 AAAAATAACTCAAGTAT
1 AAAAATAAAT-AAGTAT
13320210 AAAAATAA
1 AAAAATAA
13320218 TTATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATAAATAAGTAT
Found at i:13320376 original size:90 final size:91
Alignment explanation
Indices: 13320276--13320445 Score: 216
Period size: 90 Copynumber: 1.9 Consensus size: 91
13320266 GGCAGGTATA
* * * * *** *
13320276 ACCTTAATTTTTGACCAAATTATTACCTTATAATTGTGTCAAGTTTAAAATTTTTAATTTTTTGG
1 ACCTTAATTTTTGACCAAATAATCACCTAATAATTGTGTCAAGCTTAAAAAAATTAAATTTTTGG
13320341 GTT-GGGGGACTTAACGGCCGACACC
66 GTTGGGGGGACTTAACGGCCGACACC
* * * * *
13320366 ACCTTGATTTTTGACCCAATAATCATCTAATGATTGTGTCAGGCTTAAAAAAATTAAATTTTTGG
1 ACCTTAATTTTTGACCAAATAATCACCTAATAATTGTGTCAAGCTTAAAAAAATTAAATTTTTGG
13320431 GTTGGGGGGACTTAA
66 GTTGGGGGGACTTAA
13320446 GGCTATTAGA
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
90 55 0.83
91 11 0.17
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (91 bp):
ACCTTAATTTTTGACCAAATAATCACCTAATAATTGTGTCAAGCTTAAAAAAATTAAATTTTTGG
GTTGGGGGGACTTAACGGCCGACACC
Found at i:13322742 original size:42 final size:42
Alignment explanation
Indices: 13322655--13322809 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 42
13322645 TTGTGTTTAC
* * * * * * *
13322655 TTTCTGTTTAGCTCTCACGAACTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
*
13322697 TTTCCGTTCAGCT-TTATTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTA-TGAGCTTCTGTTTAACCCTTATGGG
* * * *
13322739 TTTCTGTTCAACTCTTACGAGCTTCCGTTCAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* *
13322781 TTTCTGTTTAGCTCTCATGAGCTTCTGTT
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTT
13322810 CAGCCTTTGA
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 2 0.02
42 88 0.95
43 3 0.03
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
Found at i:13322807 original size:63 final size:63
Alignment explanation
Indices: 13322655--13322811 Score: 163
Period size: 63 Copynumber: 2.5 Consensus size: 63
13322645 TTGTGTTTAC
* * * * * * *
13322655 TTTCTGTTTAGCTCTCACGAACTTCTGTTTAACTCATATGAGTTTCCGTTCAGCTTTATTGAG
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAACTCATACGAGCTTCCGTTCACCCTTATTGAG
* * * * * * * *
13322718 CTTCTGTTTAACCCTTATGGGTTTCTGTTCAACTCTTACGAGCTTCCGTTCAACCCTTA-TGGG
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAACTCATACGAGCTTCCGTTC-ACCCTTATTGAG
13322781 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCA
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCA
13322812 GCCTTTGAGC
Statistics
Matches: 72, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
63 67 0.93
64 5 0.07
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (63 bp):
TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAACTCATACGAGCTTCCGTTCACCCTTATTGAG
Found at i:13322808 original size:21 final size:21
Alignment explanation
Indices: 13322676--13322826 Score: 110
Period size: 21 Copynumber: 7.3 Consensus size: 21
13322666 CTCTCACGAA
* *
13322676 CTTCTGTTTAACTCATATGAG
1 CTTCTGTTCAACTCTTATGAG
* * *
13322697 TTTCCGTTCAGCT-TTATTGAG
1 CTTCTGTTCAACTCTTA-TGAG
* * *
13322718 CTTCTGTTTAACCCTTATGGG
1 CTTCTGTTCAACTCTTATGAG
* *
13322739 TTTCTGTTCAACTCTTACGAG
1 CTTCTGTTCAACTCTTATGAG
* * *
13322760 CTTCCGTTCAACCCTTATGGG
1 CTTCTGTTCAACTCTTATGAG
* * * *
13322781 TTTCTGTTTAGCTCTCATGAG
1 CTTCTGTTCAACTCTTATGAG
*
13322802 CTTCTGTTCAGC-CTT-TGAG
1 CTTCTGTTCAACTCTTATGAG
13322821 CTTCTG
1 CTTCTG
13322827 ATAACGATAT
Statistics
Matches: 97, Mismatches: 31, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
19 10 0.10
20 4 0.04
21 80 0.82
22 3 0.03
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (21 bp):
CTTCTGTTCAACTCTTATGAG
Found at i:13329565 original size:335 final size:334
Alignment explanation
Indices: 13328955--13329625 Score: 1281
Period size: 335 Copynumber: 2.0 Consensus size: 334
13328945 AGGACTAAAT
13328955 TAGAAAAGGTGCAAAACTTGCTAATTAAAAGAAATAGTGATTAAATAACCTAAATGGTAAATAAT
1 TAGAAAAGGTGCAAAACTTGCTAATTAAAAGAAATAGTGATTAAATAACCTAAATGGTAAATAAT
13329020 GGAAGATTTAAAGAGTAATTAAGCCTAAATGAATTGGCTGAGGCGGCATAAGCACAAAAAAAAAT
66 GGAAGATTTAAAGAGTAATTAAGCCTAAATGAATTGGCTGAGGCGGCATAAGCACAAAAAAAAAT
13329085 GCTAAAATGATGTGATTAAAAGGAAAAAATGGAAATAAATGAAATTAAAATATCAAATTGAAAAG
131 GCTAAAATGATGTGATTAAAAGGAAAAAATGGAAATAAATGAAATTAAAATATCAAATTGAAAAG
**
13329150 CCTAAAAGTTTCTAGAAATTTCTTCATCAATTTTCTGTTCAAAAATAGCATTGAAGAGCTCTCAA
196 CCTAAAAGTTTCTAGAAATTTCTTCATCAATTTTCTGTTCAAAAATAGCATTGAAGAGAGCTC-A
13329215 GGCTAGTTTTCATATTTTAGCTTCATATCAAGAGCCCGTAGATACTCATGAAAAAGGAAAATTAG
260 GGCTAGTTTTCATATTTTAGCTTCATATCAAGAGCCCGTAGATACTCATGAAAAAGGAAAATTAG
13329280 CAGAATAGTC
325 CAGAATAGTC
13329290 TAGAAAAGGTGCAAAACTTGCTAATTAAAAGAAATAGTGATTAAATAACCTAAATGGTAAATAAT
1 TAGAAAAGGTGCAAAACTTGCTAATTAAAAGAAATAGTGATTAAATAACCTAAATGGTAAATAAT
13329355 GGAAGATTTAAAGAGTAATTAAGCCTAAATGAATTGGCTGAGGCGGCATAAGCACAAAAAAAAAT
66 GGAAGATTTAAAGAGTAATTAAGCCTAAATGAATTGGCTGAGGCGGCATAAGCACAAAAAAAAAT
13329420 GCTAAAATGATGTGATTAAAAGGAAAAAATGGAAATAAATGAAATTAAAATATCAAATTGAAAAG
131 GCTAAAATGATGTGATTAAAAGGAAAAAATGGAAATAAATGAAATTAAAATATCAAATTGAAAAG
13329485 CCTAAAAGTTTCTAGAAATTTCTTCATCAATTTTCTGTTCAAAAATAGCATTGAAGGAAGAGCTC
196 CCTAAAAGTTTCTAGAAATTTCTTCATCAATTTTCTGTTCAAAAATAGCATTGAA-G-AGAGCTC
*
13329550 -TGCTAGTTTTCATATTTTAGCTTCATATCAAGAGCCCGTAGATACTCATGAAAAAGGAAAATTA
259 AGGCTAGTTTTCATATTTTAGCTTCATATCAAGAGCCCGTAGATACTCATGAAAAAGGAAAATTA
13329614 GCAGAATAGTC
324 GCAGAATAGTC
13329625 T
1 T
13329626 CTGAACTCCT
Statistics
Matches: 331, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
335 325 0.98
336 1 0.00
337 5 0.02
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (334 bp):
TAGAAAAGGTGCAAAACTTGCTAATTAAAAGAAATAGTGATTAAATAACCTAAATGGTAAATAAT
GGAAGATTTAAAGAGTAATTAAGCCTAAATGAATTGGCTGAGGCGGCATAAGCACAAAAAAAAAT
GCTAAAATGATGTGATTAAAAGGAAAAAATGGAAATAAATGAAATTAAAATATCAAATTGAAAAG
CCTAAAAGTTTCTAGAAATTTCTTCATCAATTTTCTGTTCAAAAATAGCATTGAAGAGAGCTCAG
GCTAGTTTTCATATTTTAGCTTCATATCAAGAGCCCGTAGATACTCATGAAAAAGGAAAATTAGC
AGAATAGTC
Found at i:13330014 original size:42 final size:42
Alignment explanation
Indices: 13329908--13330064 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 42
13329898 TCGTGTTTAC
* * * * * *
13329908 TTTCCATTTATCTCTCACGAGCTTCTGTTTAACTCATATGAA
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAG
* * * * * *
13329950 TTTCCGTTCAACTCT-ATTGAGCTTCTGTTTAACCTTTATGGG
1 TTTCCGTTTAGCTCTCA-CGAGCTTCTGTTCAACCCTTATGAG
* * *
13329992 TTTCCGTTTAGTTCTTACGAGCTTCCGTTCAACCCTTATGAG
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAG
* *
13330034 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCA
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTCA
13330065 GCCTTCGGGC
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
41 1 0.01
42 89 0.98
43 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAG
Found at i:13332512 original size:47 final size:47
Alignment explanation
Indices: 13332455--13332607 Score: 252
Period size: 47 Copynumber: 3.2 Consensus size: 47
13332445 AAATGTTTTA
13332455 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
1 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
* * *
13332502 AATAATTAAATTATTAAGATATTATATAGTGTAAAATAAAATAATTT
1 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
*
13332549 AATAAATAAATTGTTAAGTTATTATATAGTGTAAAGTAAAATAATTT
1 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
*
13332596 AAATAAAAAAAT
1 -AATAAATAAAT
13332608 ATACATTATT
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
47 87 0.90
48 10 0.10
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.39
Consensus pattern (47 bp):
AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
Found at i:13332638 original size:94 final size:94
Alignment explanation
Indices: 13332437--13332609 Score: 269
Period size: 94 Copynumber: 1.8 Consensus size: 94
13332427 TCATGATTAT
**
13332437 TGTAAAAT-AAATGTTTTAAATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATT
1 TGTAAAATAAAATAATTT-AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATT
* *
13332501 TAATAATTAAATTATTAAGATATTATATAG
65 TAATAATAAAAATATTAAGATATTATATAG
*
13332531 TGTAAAATAAAATAATTTAATAAATAAATTGTTAAGTTATTATATAGTGTAAAGTAAAATAATTT
1 TGTAAAATAAAATAATTTAATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
13332596 AAATAA-AAAAATAT
66 -AATAATAAAAATAT
13332610 ACATTATTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
94 60 0.83
95 12 0.17
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (94 bp):
TGTAAAATAAAATAATTTAATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
AATAATAAAAATATTAAGATATTATATAG
Found at i:13332692 original size:24 final size:23
Alignment explanation
Indices: 13332660--13332721 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 23
13332650 TTATATACAG
13332660 TAAAGTAAATAAATTATTCAATTA
1 TAAAGTAAATAAATTATTC-ATTA
*
13332684 TAAAGTAAATAAATTATTCATTT
1 TAAAGTAAATAAATTATTCATTA
13332707 TAAAGATTAAATAAA
1 TAAAG--TAAATAAA
13332722 AAACTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 8 0.23
24 19 0.54
25 8 0.23
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (23 bp):
TAAAGTAAATAAATTATTCATTA
Found at i:13334759 original size:21 final size:22
Alignment explanation
Indices: 13334718--13334759 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13334708 AAAACTAATT
*
13334718 TACGAAAATATTTATAATTTATA
1 TACGAAAATA-TTAAAATTTATA
13334741 TACGAAAATA-TAAAATTTA
1 TACGAAAATATTAAAATTTA
13334760 ACCAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
TACGAAAATATTAAAATTTATA
Found at i:13335740 original size:30 final size:30
Alignment explanation
Indices: 13335699--13335761 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
13335689 ACTTATTTTA
13335699 TTGTAAATTTTGTTATTATTTTAAAGACAT
1 TTGTAAATTTTGTTATTATTTTAAAGACAT
* *
13335729 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTAAATTTTGTTATTATTTTAAAGACAT
13335759 TTG
1 TTG
13335762 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTAAATTTTGTTATTATTTTAAAGACAT
Found at i:13339938 original size:27 final size:27
Alignment explanation
Indices: 13339898--13339953 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
13339888 ATCACTAACT
* *
13339898 AATACTAATGTAATATTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
13339925 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
13339952 AA
1 AA
13339954 AAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:13340472 original size:5 final size:5
Alignment explanation
Indices: 13340464--13340489 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13340454 GATGGAAGGG
13340464 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
13340490 GAGGGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:13342418 original size:44 final size:44
Alignment explanation
Indices: 13342355--13342443 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
13342345 GAGGAAATAC
*
13342355 TATTGGGACTTGGGAGGAGTTTTAAAGAGAGTTAAATAAGTAGT
1 TATTGGGACTTGGGAGGAGTTTTAAAGAGAGTTAAATAACTAGT
13342399 TATTGGGACTTGGGAGGAGTTTTAAAGAGAGTTAAATAACTAGT
1 TATTGGGACTTGGGAGGAGTTTTAAAGAGAGTTAAATAACTAGT
13342443 T
1 T
13342444 TTATTAGCAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (44 bp):
TATTGGGACTTGGGAGGAGTTTTAAAGAGAGTTAAATAACTAGT
Found at i:13349752 original size:24 final size:27
Alignment explanation
Indices: 13349707--13349813 Score: 75
Period size: 27 Copynumber: 4.0 Consensus size: 27
13349697 CAAAAAATAG
*
13349707 AAATAATATATATATAATAATATATAA
1 AAATAATATATATATAAGAATATATAA
13349734 AAATAATATAT-T-T-AGAATATATAAA
1 AAATAATATATATATAAGAATATAT-AA
* * *
13349759 TAAATAAAATAGATATAA-TATATA-AA
1 -AAATAATATATATATAAGAATATATAA
*
13349785 TAAATTGAATATA-ATATTA-AATATATAA
1 -AAA-T-AATATATATATAAGAATATATAA
13349813 A
1 A
13349814 TAAATTAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
24 8 0.12
25 3 0.05
26 16 0.25
27 24 0.37
28 13 0.20
29 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AAATAATATATATATAAGAATATATAA
Found at i:13349798 original size:22 final size:22
Alignment explanation
Indices: 13349680--13349807 Score: 74
Period size: 22 Copynumber: 6.0 Consensus size: 22
13349670 ACTTTTTTGT
* *
13349680 ATTGAATATAATGTATACAAAAA
1 ATTGAATATAATATATA-AATAA
* *
13349703 ATAGAA-ATAATATATATAT-A
1 ATTGAATATAATATATAAATAA
* *
13349723 A-T-AATAT-ATAAAAATAATATA
1 ATTGAATATAATATATA-AATA-A
* *
13349744 TTTAGAATAT-ATAAATAAATAA
1 ATT-GAATATAATATATAAATAA
*
13349766 AAT-AGATATAATATATAAATAA
1 ATTGA-ATATAATATATAAATAA
13349788 ATTGAATATAATAT-TAAATA
1 ATTGAATATAATATATAAATA
13349808 TATAAATAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
18 7 0.09
19 4 0.05
20 3 0.04
21 12 0.15
22 34 0.42
23 10 0.12
24 11 0.14
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (22 bp):
ATTGAATATAATATATAAATAA
Found at i:13349810 original size:55 final size:53
Alignment explanation
Indices: 13349707--13349818 Score: 140
Period size: 53 Copynumber: 2.1 Consensus size: 53
13349697 CAAAAAATAG
* *
13349707 AAATAATATATATATAATAATATATAAAAATAATATATTTAGAATATATAAAT
1 AAATAAAATAGATATAATAATATATAAAAATAATATATTTAGAATATATAAAT
13349760 AAATAAAATAGATATAAT-ATATA-AATAAATTGAATATAATATTA-AATATATAAAT
1 AAATAAAATAGATATAATAATATATAA-AAA-T-AATAT-AT-TTAGAATATATAAAT
13349815 AAAT
1 AAAT
13349819 TAAACCAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
51 2 0.04
52 8 0.15
53 17 0.33
54 5 0.10
55 17 0.33
56 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (53 bp):
AAATAAAATAGATATAATAATATATAAAAATAATATATTTAGAATATATAAAT
Found at i:13349820 original size:17 final size:17
Alignment explanation
Indices: 13349749--13349822 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 17
13349739 ATATATTTAG
*
13349749 AATATATAAATAAATAA
1 AATATATAAATAAATTA
* *
13349766 AATAGATATAATATA-TA
1 AATATATA-AATAAATTA
*
13349783 AATAAATTGAATATAATATTA
1 AATATA-T-AA-ATAA-ATTA
13349804 AATATATAAATAAATTA
1 AATATATAAATAAATTA
13349821 AA
1 AA
13349823 CCAAAAGAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
17 19 0.42
18 11 0.24
19 6 0.13
20 2 0.04
21 7 0.16
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AATATATAAATAAATTA
Found at i:13353918 original size:13 final size:14
Alignment explanation
Indices: 13353902--13353930 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13353892 CTTTTAGCTT
13353902 TTACTTTAA-TTCA
1 TTACTTTAATTTCA
13353915 TTACTTTAATTTCA
1 TTACTTTAATTTCA
13353929 TT
1 TT
13353931 TATCCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (14 bp):
TTACTTTAATTTCA
Found at i:13360539 original size:18 final size:18
Alignment explanation
Indices: 13360453--13360540 Score: 72
Period size: 18 Copynumber: 4.7 Consensus size: 18
13360443 TACCCTTTTC
13360453 TTTA-TTTTATTTTATTAT
1 TTTATTTTTATTTT-TTAT
* *
13360471 TTTATTATTATTTGTTAT
1 TTTATTTTTATTTTTTAT
* * *
13360489 ATTATTTATATATATTTGAT
1 TTTATTT-T-TATTTTTTAT
13360509 TTGT-TTCTTTATTTTTTAT
1 TT-TATT-TTTATTTTTTAT
13360528 TTTATTTTTATTT
1 TTTATTTTTATTT
13360541 ATGCTTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
18 21 0.39
19 20 0.37
20 11 0.20
21 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTATTTTTATTTTTTAT
Found at i:13360540 original size:11 final size:11
Alignment explanation
Indices: 13360453--13360540 Score: 54
Period size: 13 Copynumber: 7.2 Consensus size: 11
13360443 TACCCTTTTC
13360453 TTTA-TTTTAT
1 TTTATTTTTAT
13360463 TTTATTATTTTAT
1 TTTA-T-TTTTAT
13360476 TATTATTTGTTAT
1 T-TTATTT-TTAT
*
13360489 ATTATTTATATAT
1 TTTATTT-T-TAT
13360502 ATTTGATTTGTT-T
1 -TTT-ATTT-TTAT
13360515 CTTTATTTTTTAT
1 -TTTA-TTTTTAT
13360528 TTTATTTTTAT
1 TTTATTTTTAT
13360539 TT
1 TT
13360541 ATGCTTAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
10 4 0.06
11 9 0.14
12 16 0.25
13 23 0.37
14 6 0.10
15 5 0.08
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:13360604 original size:12 final size:12
Alignment explanation
Indices: 13360569--13360609 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
13360559 TATTTTAATT
13360569 CTATTATTTTTA
1 CTATTATTTTTA
*
13360581 GTATT-TTTTTA
1 CTATTATTTTTA
*
13360592 CTATTATTCTTA
1 CTATTATTTTTA
13360604 CTATTA
1 CTATTA
13360610 CCTTTCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (12 bp):
CTATTATTTTTA
Found at i:13360677 original size:6 final size:6
Alignment explanation
Indices: 13360644--13360708 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
13360634 AGTTTATTTC
* * * * *
13360644 TTTTCT TTTTCT TTTTA- TTTTAG CTTTAT TTTTAT TTTTGT TTTTAGT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T
13360692 TGCTTTAT TTTTAT TTT
1 T--TTTAT TTTTAT TTT
13360709 CTTAGACTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 5 0.10
6 36 0.73
7 2 0.04
8 2 0.04
9 4 0.08
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:13361679 original size:21 final size:21
Alignment explanation
Indices: 13361655--13361698 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
13361645 TCCTGAATTA
13361655 TTTAAATTCATGTTTCTATAC
1 TTTAAATTCATGTTTCTATAC
13361676 TTTAAATTCATGTTTCTATAC
1 TTTAAATTCATGTTTCTATAC
13361697 TT
1 TT
13361699 AGGAGAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAAATTCATGTTTCTATAC
Found at i:13364106 original size:19 final size:19
Alignment explanation
Indices: 13364084--13364161 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
13364074 TAATTAAAGG
**
13364084 ATAAATTATATTTAAAGCA
1 ATAAATTATATTTAAAATA
* *
13364103 ATAAATTTAAATTAAAAATA
1 ATAAA-TTATATTTAAAATA
13364123 ATAAATTATATTTAAAATA
1 ATAAATTATATTTAAAATA
*
13364142 ATAAATT-TCAATTAAAATA
1 ATAAATTAT-ATTTAAAATA
13364161 A
1 A
13364162 AATAATTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 1 0.02
19 34 0.68
20 15 0.30
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (19 bp):
ATAAATTATATTTAAAATA
Found at i:13364127 original size:20 final size:20
Alignment explanation
Indices: 13364102--13364182 Score: 96
Period size: 19 Copynumber: 4.2 Consensus size: 20
13364092 TATTTAAAGC
13364102 AATAAATTTAAATTAAAAAT
1 AATAAATTTAAATTAAAAAT
* *
13364122 AATAAA-TTATATTTAAAAT
1 AATAAATTTAAATTAAAAAT
*
13364141 AATAAATTTCAATT-AAAAT
1 AATAAATTTAAATTAAAAAT
*
13364160 AAAATAATTTAAA-TAAAAAT
1 AATA-AATTTAAATTAAAAAT
13364180 AAT
1 AAT
13364183 TAAGTATAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 26 0.51
20 25 0.49
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAAATTTAAATTAAAAAT
Found at i:13364127 original size:39 final size:39
Alignment explanation
Indices: 13364084--13364238 Score: 132
Period size: 39 Copynumber: 4.2 Consensus size: 39
13364074 TAATTAAAGG
13364084 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
1 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
** *
13364123 ATAAATTATATTTAAAATAATAAATTTCAATT-AAAAT-
1 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
* **
13364160 A-AAA-TA-ATTTAAA-TAA-AAA--T-AATTAAGTATA
1 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
* * *
13364191 GGATAAATCATATTTAAAGCAATAAATTTAAACTAGAAATA
1 --ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
*
13364232 ATTAATT
1 ATAAATT
13364239 GAATGATAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
29 4 0.04
30 4 0.04
32 3 0.03
33 4 0.04
34 10 0.11
35 3 0.03
36 10 0.11
37 3 0.03
38 8 0.09
39 34 0.37
40 1 0.01
41 7 0.08
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (39 bp):
ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
Found at i:13364168 original size:14 final size:15
Alignment explanation
Indices: 13364151--13364185 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
13364141 AATAAATTTC
13364151 AATTAAAAT-AAAAT
1 AATTAAAATAAAAAT
*
13364165 AATTTAAATAAAAAT
1 AATTAAAATAAAAAT
13364180 AATTAA
1 AATTAA
13364186 GTATAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTAAAATAAAAAT
Found at i:13364808 original size:16 final size:16
Alignment explanation
Indices: 13364777--13364811 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
13364767 TTTTAGGTCA
13364777 TTTAGGTGATTGTTTT
1 TTTAGGTGATTGTTTT
13364793 TTTA-GTGATTGTTTT
1 TTTAGGTGATTGTTTT
13364808 TTTA
1 TTTA
13364812 ACATGGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.66
Consensus pattern (16 bp):
TTTAGGTGATTGTTTT
Found at i:13375226 original size:27 final size:27
Alignment explanation
Indices: 13375188--13375239 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
13375178 TATTAAAGTT
*
13375188 ATTGAAGGGAGGTCAACTCCATCAAAA
1 ATTGAAGGGAGGTCAACTACATCAAAA
13375215 ATTGAAGGGAGGTCAACTACATCAA
1 ATTGAAGGGAGGTCAACTACATCAA
13375240 GAGAAACCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (27 bp):
ATTGAAGGGAGGTCAACTACATCAAAA
Found at i:13375878 original size:18 final size:18
Alignment explanation
Indices: 13375857--13375906 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
13375847 ATTAATATTT
13375857 AAAAAATTAAAAATATAA
1 AAAAAATTAAAAATATAA
* ** *
13375875 AAAAAATTTAATTTTTAA
1 AAAAAATTAAAAATATAA
*
13375893 AAAAAAATAAAAAT
1 AAAAAATTAAAAAT
13375907 TATTAAAAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATTAAAAATATAA
Found at i:13381149 original size:3 final size:3
Alignment explanation
Indices: 13381127--13381199 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
13381117 ATATAATGAG
* *
13381127 AAT AAC AAT GAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
13381173 AAT AAT AAT AATT GGT AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT AAT AAT AAT AA
13381200 CAACATCAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 56 0.93
4 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13386776 original size:16 final size:16
Alignment explanation
Indices: 13386757--13386788 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13386747 AAAATAACCC
13386757 AAATTTAAAACGATTT
1 AAATTTAAAACGATTT
*
13386773 AAATTTAAAATGATTT
1 AAATTTAAAACGATTT
13386789 GGATAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
AAATTTAAAACGATTT
Found at i:13395585 original size:27 final size:31
Alignment explanation
Indices: 13395542--13395605 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 31
13395532 TTTTTTTATG
* *
13395542 AAAAA-TATTCTTTAAAAT-T-CAAAAAA-T
1 AAAAATTATTCTTAAAAATATAAAAAAAATT
13395569 AAAAATTATT-TTAAAAATATAAAAAAAATT
1 AAAAATTATTCTTAAAAATATAAAAAAAATT
13395599 AAAAATT
1 AAAAATT
13395606 CAATGTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 12 0.39
28 5 0.16
29 6 0.19
30 8 0.26
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAAATTATTCTTAAAAATATAAAAAAAATT
Found at i:13402792 original size:3 final size:3
Alignment explanation
Indices: 13402784--13402809 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13402774 ATGCTAGTAA
13402784 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
13402810 AGCCAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Done.