Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 48 of 135
Found at i:17196781 original size:27 final size:27
Alignment explanation
Indices: 17196717--17196782 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
17196707 GTAGTTTATA
17196717 TATATATTTTTATAATTTATTAGATTCT
1 TATA-ATTTTTATAATTTATTAGATTCT
* * * * *
17196745 TATAAATTTTATGATTTTTTATATTTT
1 TATAATTTTTATAATTTATTAGATTCT
*
17196772 TATGATTTTTA
1 TATAATTTTTA
17196783 ATGGGAGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (27 bp):
TATAATTTTTATAATTTATTAGATTCT
Found at i:17203722 original size:16 final size:16
Alignment explanation
Indices: 17203701--17203750 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
17203691 AATTAAATTT
17203701 ATTAAAAAAATTTAAA
1 ATTAAAAAAATTTAAA
**
17203717 ATTAAAATGATTTAAA
1 ATTAAAAAAATTTAAA
*
17203733 TTTAAAAAAATTATAAA
1 ATTAAAAAAATT-TAAA
17203750 A
1 A
17203751 ATATATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 23 0.85
17 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTAAAAAAATTTAAA
Found at i:17212509 original size:14 final size:13
Alignment explanation
Indices: 17212477--17212511 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
17212467 ATTGAGGAAC
17212477 AAAATT-AAGTAA
1 AAAATTAAAGTAA
17212489 AAAATTAAAGTAA
1 AAAATTAAAGTAA
17212502 AAATATTAAA
1 AAA-ATTAAA
17212512 ATTCAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (13 bp):
AAAATTAAAGTAA
Found at i:17213294 original size:14 final size:14
Alignment explanation
Indices: 17213275--17213327 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
17213265 TAATAATATA
17213275 TAATAATTTTTAAT
1 TAATAATTTTTAAT
17213289 TAATAATTTATTTAAT
1 TAATAA-TT-TTTAAT
* *
17213305 ATTATAATTTTTATTT
1 -TAATAATTTTTA-AT
17213321 TAATAAT
1 TAATAAT
17213328 CATTTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.19
15 12 0.38
16 9 0.28
17 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATAATTTTTAAT
Found at i:17213749 original size:17 final size:16
Alignment explanation
Indices: 17213727--17213773 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 16
17213717 CGTGGCGGCG
17213727 CCTTAAAATGAAGTGGA
1 CCTTAAAATGAAG-GGA
17213744 CCTTAAAATGCAAGGGA
1 CCTTAAAATG-AAGGGA
17213761 CCTTAAAATGAAG
1 CCTTAAAATGAAG
17213774 AGCCTAACGC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.10
17 23 0.79
18 3 0.10
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (16 bp):
CCTTAAAATGAAGGGA
Found at i:17214480 original size:30 final size:30
Alignment explanation
Indices: 17214445--17214514 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
17214435 TTTTTGTTTG
*
17214445 TATTATATCTAACTTCAAATTTTGTATTCA
1 TATTATATCTAACTTCAAATTTTATATTCA
* ** **
17214475 TATTATATTTGGCTTCAAATTTTATATTTG
1 TATTATATCTAACTTCAAATTTTATATTCA
17214505 TATTATATCT
1 TATTATATCT
17214515 GAGTTCTAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (30 bp):
TATTATATCTAACTTCAAATTTTATATTCA
Found at i:17214827 original size:18 final size:18
Alignment explanation
Indices: 17214786--17214842 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
17214776 TATGCATGCG
* *
17214786 ACTGTTATGTGGCATATT
1 ACTGTTATGTAGTATATT
* *
17214804 ATTGTTATGTAGTATTTT
1 ACTGTTATGTAGTATATT
17214822 ACTGTTTATGTATGTATATT
1 ACTG-TTATGTA-GTATATT
17214842 A
1 A
17214843 TGTATGTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 17 0.55
19 7 0.23
20 7 0.23
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.53
Consensus pattern (18 bp):
ACTGTTATGTAGTATATT
Found at i:17214856 original size:28 final size:28
Alignment explanation
Indices: 17214815--17214885 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
17214805 TTGTTATGTA
* *
17214815 GTATTTTACTGTTTATGTATGTATATTAT
1 GTATGTTA-TGTTTATGTATGTATATTAC
* *
17214844 GTATGTTATGTTTGTTTATGTATATTAC
1 GTATGTTATGTTTATGTATGTATATTAC
17214872 GTATGTTATGTTTA
1 GTATGTTATGTTTA
17214886 ATGAATGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 30 0.81
29 7 0.19
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.58
Consensus pattern (28 bp):
GTATGTTATGTTTATGTATGTATATTAC
Found at i:17214878 original size:19 final size:18
Alignment explanation
Indices: 17214835--17214882 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
17214825 GTTTATGTAT
* * *
17214835 GTATATTATGTATGTTAT
1 GTATGTTATGTATATTAC
*
17214853 GTTTGTTTATGTATATTAC
1 GTATG-TTATGTATATTAC
17214872 GTATGTTATGT
1 GTATGTTATGT
17214883 TTAATGAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.23, C:0.02, G:0.19, T:0.56
Consensus pattern (18 bp):
GTATGTTATGTATATTAC
Found at i:17215722 original size:2 final size:2
Alignment explanation
Indices: 17215715--17215773 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
17215705 TCTTAAGTTT
17215715 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17215757 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
17215774 TTGTTTATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17220827 original size:2 final size:2
Alignment explanation
Indices: 17220820--17220852 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17220810 AAGAAGAGCC
17220820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17220853 CCAAAAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17221701 original size:24 final size:25
Alignment explanation
Indices: 17221655--17221701 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17221645 TCTCAAAAAA
* *
17221655 TTTCAAAATATTTATAAAATATTTT
1 TTTCAAAAAAATTATAAAATATTTT
*
17221680 TTTCAAAAAAATT-TAAATTATT
1 TTTCAAAAAAATTATAAAATATT
17221702 ACAAAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTCAAAAAAATTATAAAATATTTT
Found at i:17225326 original size:15 final size:15
Alignment explanation
Indices: 17225291--17225319 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17225281 TAGATAAATG
17225291 ATATACAAAAATCAA
1 ATATACAAAAATCAA
17225306 ATATACAAAAATCA
1 ATATACAAAAATCA
17225320 GAAATACGAA
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:0.66, C:0.14, G:0.00, T:0.21
Consensus pattern (15 bp):
ATATACAAAAATCAA
Found at i:17225489 original size:59 final size:59
Alignment explanation
Indices: 17225419--17225677 Score: 217
Period size: 58 Copynumber: 4.4 Consensus size: 59
17225409 TTTTGGATGC
* * *
17225419 TCGAGGGT-AAAATGGTAA-TTTTGGACACTCAGGGGGTAAAATGGTTATTTTTGGAAGGT
1 TCGA-GGTCAAAATGG-AATTTTTGGACATTCAGGGGGTAAAATGGTAATTTTTGGAAGTT
* * * * * * *
17225478 TCGAGGTTAAAAATAGAATTTTTAGATATTC-GAGGTTAAAATGGTAATTTTTAGAAGTT
1 TCGAGG-TCAAAATGGAATTTTTGGACATTCAGGGGGTAAAATGGTAATTTTTGGAAGTT
* * * ** *
17225537 TTGTGGTCAAAATGGAATTTTTGGACATTTA-GAAGTAAAATGGTAATTTTCGGAAGTT
1 TCGAGGTCAAAATGGAATTTTTGGACATTCAGGGGGTAAAATGGTAATTTTTGGAAGTT
* * ***
17225595 TCGAGGTCCAAAATGGAATTTTTAGACATT--TGGGGTAAAATGGTAATTTTCAAAAGTT
1 TCGAGGT-CAAAATGGAATTTTTGGACATTCAGGGGGTAAAATGGTAATTTTTGGAAGTT
* *
17225653 T-TAGGGTCAAAATGTAATTTTTGGA
1 TCGA-GGTCAAAATGGAATTTTTGGA
17225678 AAGTTTGGGG
Statistics
Matches: 161, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
57 17 0.11
58 74 0.46
59 55 0.34
60 15 0.09
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (59 bp):
TCGAGGTCAAAATGGAATTTTTGGACATTCAGGGGGTAAAATGGTAATTTTTGGAAGTT
Found at i:17225510 original size:29 final size:29
Alignment explanation
Indices: 17225477--17225532 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
17225467 TTTTGGAAGG
17225477 TTCGAGGTTAAAAATAG-AATTTTTAGATA
1 TTCGAGGTT-AAAATAGTAATTTTTAGATA
*
17225506 TTCGAGGTTAAAATGGTAATTTTTAGA
1 TTCGAGGTTAAAATAGTAATTTTTAGA
17225533 AGTTTTGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.39
Consensus pattern (29 bp):
TTCGAGGTTAAAATAGTAATTTTTAGATA
Found at i:17225555 original size:29 final size:29
Alignment explanation
Indices: 17225487--17225708 Score: 122
Period size: 29 Copynumber: 7.7 Consensus size: 29
17225477 TTCGAGGTTA
* * *
17225487 AAAATAGAATTTTTAG-A-TATTCGAGGTT
1 AAAATGGAATTTTTAGAAGT-TTTGAGGTC
*
17225515 AAAATGGTAATTTTTAGAAGTTTTGTGGTC
1 AAAATGG-AATTTTTAGAAGTTTTGAGGTC
* * *
17225545 AAAATGGAATTTTTGGACA-TTTAGAAGT-
1 AAAATGGAATTTTTAGA-AGTTTTGAGGTC
** *
17225573 AAAATGGTAATTTTCGGAAGTTTCGAGGTCC
1 AAAATGG-AATTTTTAGAAGTTTTGAGGT-C
*
17225604 AAAATGGAATTTTTAGACA--TTTGGGGT-
1 AAAATGGAATTTTTAGA-AGTTTTGAGGTC
* *
17225631 AAAATGGTAATTTTCAAAAGTTTT-AGGGTC
1 AAAATGG-AATTTTTAGAAGTTTTGA-GGTC
* * * *
17225661 AAAATGTAATTTTTGGAAAG-TTTGGGGGC
1 AAAATGGAATTTTTAG-AAGTTTTGAGGTC
*
17225690 AAAAATGTAATTTTT-GAAG
1 -AAAATGGAATTTTTAGAAG
17225709 ACTTCAAGGG
Statistics
Matches: 153, Mismatches: 24, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
27 8 0.05
28 25 0.16
29 65 0.42
30 46 0.30
31 9 0.06
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTAGAAGTTTTGAGGTC
Found at i:17225685 original size:58 final size:57
Alignment explanation
Indices: 17225451--17225687 Score: 224
Period size: 58 Copynumber: 4.1 Consensus size: 57
17225441 GGACACTCAG
* ** * * * * * * *
17225451 GGGGTAAAATGGTTATTTTTGGAAGGTTCGAGGTTAAAAATAGAATTTTTAGATATTC
1 GGGGTAAAATGGTAATTTTCAGAAGTTTTGAGG-TCAAAATGGAATTTTTGGACATTT
* * *
17225509 GAGGTTAAAATGGTAATTTTTAGAAGTTTTGTGGTCAAAATGGAATTTTTGGACATTT
1 G-GGGTAAAATGGTAATTTTCAGAAGTTTTGAGGTCAAAATGGAATTTTTGGACATTT
** * * *
17225567 AGAAGTAAAATGGTAATTTTCGGAAGTTTCGAGGTCCAAAATGGAATTTTTAGACATTT
1 -GGGGTAAAATGGTAATTTTCAGAAGTTTTGAGGT-CAAAATGGAATTTTTGGACATTT
* * *
17225626 GGGGTAAAATGGTAATTTTCAAAAGTTTT-AGGGTCAAAATGTAATTTTTGGAAAGTTT
1 GGGGTAAAATGGTAATTTTCAGAAGTTTTGA-GGTCAAAATGGAATTTTTGGACA-TTT
17225684 GGGG
1 GGGG
17225688 GCAAAAATGT
Statistics
Matches: 147, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
57 18 0.12
58 80 0.54
59 49 0.33
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTCAGAAGTTTTGAGGTCAAAATGGAATTTTTGGACATTT
Found at i:17227636 original size:6 final size:6
Alignment explanation
Indices: 17227618--17227726 Score: 88
Period size: 6 Copynumber: 19.2 Consensus size: 6
17227608 TTCTAAACCC
* * * *
17227618 AATTTA AAATTA AATTTA AA-ATA AATTGT- AGTTTA AA-TTA AATTTG
1 AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA
* * *
17227664 AATTTA AA-ATA AATTTA AA-TTA AACTT- AATATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
17227709 AATTTA AA-ATA AATTTA A
1 AATTTA AATTTA AATTTA A
17227727 TTAAAGATTG
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
5 26 0.32
6 53 0.66
7 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:17227642 original size:17 final size:17
Alignment explanation
Indices: 17227622--17227726 Score: 61
Period size: 17 Copynumber: 5.9 Consensus size: 17
17227612 AAACCCAATT
17227622 TAAAATTAAATTTAAAA
1 TAAAATTAAATTTAAAA
* * *
17227639 T-AAATTGTAGTTTAAAT
1 TAAAATT-AAATTTAAAA
* *
17227656 TAAATTTGAATTTAAAA
1 TAAAATTAAATTTAAAA
* *
17227673 TAAATTTAAATTAAACTTAA
1 TAAAATTAAATTTAA---AA
*
17227693 TATAAATTTAAATTTAAATT
1 TA-AAA-TTAAATTTAAA-A
17227713 TAAAA-TAAATTTAA
1 TAAAATTAAATTTAA
17227727 TTAAAGATTG
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
16 5 0.07
17 38 0.56
18 4 0.06
19 4 0.06
20 6 0.09
21 2 0.03
22 9 0.13
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAAATTAAATTTAAAA
Found at i:17227704 original size:45 final size:45
Alignment explanation
Indices: 17227618--17227731 Score: 151
Period size: 45 Copynumber: 2.5 Consensus size: 45
17227608 TTCTAAACCC
* * * * *
17227618 AATTTAAAATTAAATTTAAAATAAATTGTAGTTTAAATTAAATTTG
1 AATTTAAAA-TAAATTTAAATTAAACTGTAATATAAATTAAATTTA
17227664 AATTTAAAATAAATTTAAATTAAACT-TAATATAAATTTAAATTTA
1 AATTTAAAATAAATTTAAATTAAACTGTAATATAAA-TTAAATTTA
17227709 AATTTAAAATAAATTT-AATTAAA
1 AATTTAAAATAAATTTAAATTAAA
17227732 GATTGGGCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 14 0.23
45 39 0.63
46 9 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (45 bp):
AATTTAAAATAAATTTAAATTAAACTGTAATATAAATTAAATTTA
Found at i:17228305 original size:36 final size:36
Alignment explanation
Indices: 17228264--17228371 Score: 126
Period size: 36 Copynumber: 2.9 Consensus size: 36
17228254 AGATTAACTG
* *
17228264 ATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATCGA
1 ATGGTGATCTACCCCAGGCTCGGGGTAAGAGATCAA
* * *
17228300 ATGGTGATCTACCCTAGGTTCGGGGTAAAAGATCAA
1 ATGGTGATCTACCCCAGGCTCGGGGTAAGAGATCAA
* *
17228336 ATGACTGCAATCTACCCCAGGCTCAGGGTAAGAGAT
1 ATG-GTG--ATCTACCCCAGGCTCGGGGTAAGAGAT
17228372 TGATTGATGA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
36 34 0.58
37 2 0.03
39 23 0.39
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (36 bp):
ATGGTGATCTACCCCAGGCTCGGGGTAAGAGATCAA
Found at i:17228820 original size:49 final size:49
Alignment explanation
Indices: 17228717--17230190 Score: 499
Period size: 49 Copynumber: 29.9 Consensus size: 49
17228707 CACGTTTTTA
* * * * * * ** *
17228717 AGGTACCGGGTTCGCCATTGCGACTTAAACCTTTCCCTTCAAATCTTCG
1 AGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTG
* * * * * *
17228766 TGGTACTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTTATGTCTCTG
1 AGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTG
* * * * *
17228815 AGGTACAAGG-TTCGCCGTTGCGACTTAAACCTTTCCC-TCTGTGTCTTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTC-ATGTCTTTG
* * * *
17228864 TGGTACTGGATCCGCCGTTGCGGCTTAGGTCTTT-CCTT--TGTGCTTCG
1 AGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGT-CTTTG
* * * *
17228911 TGGTACTAGA-TCTGCCGTTGCGGCTTAGATCTTTCCCTT-GTGTC-TTC
1 AGGTACTGGATTC-GCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTG
* * * * * *
17228958 ATGGTATTGGATCCGCCATTGCGACTTAGATTTTTCCCTTCATGTCTTTA
1 A-GGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTG
* ** * * *
17229008 AGGTACAAGG-TTCGCCACTGCGACTTAAACCTTTCCCTTGCA--TCTTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATCTTTCCCTT-CATGTCTTTG
* * * * * * * *
17229056 CGGTACTAGATCCTCCATTGTGGCTTAGATCTTTCCATTCATGTCTCTG
1 AGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTG
* * * * * * *
17229105 AGGTACAAGG-TTCGTCATTGCGACTTAAACCTTTCCCTTGCA--TCGTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATCTTTCCCTT-CATGTCTTTG
* * * *
17229153 CGGTACTGGATCCACCGTTGCGGCTTAGATATTTCCCTTCATGT-TTCTG
1 AGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTT-TG
* * * * * * *
17229202 AGGTACAAGG-TTCGCCGTTGCGACTTAAACCCTCCCCTT-TTGTATCTTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--TCTTTG
*
17229252 CA-GTACTGGATTCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTTG
1 -AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGTCTTTG
* * * * *
17229302 AGGTA-TAAGG-TTCGCCGTTGCGACTTAAACCCTTCCCTT-TTGTATCTTTG
1 AGGTACT--GGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--TCTTTG
* * * * * * *
17229352 CGGTACTGGATCCGTCATTGTGGTCTTAGATCTTTCCCATCATGTCTCTG
1 AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGTCTTTG
* * * *
17229402 AGGTA-TAAGG-TTCGTCGTTGCGACTTAAACCTTTCCCTT--TGCATCTTTG
1 AGGTACT--GGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--TCTTTG
* * * * * ** * * *
17229451 CGGTACTGGATCCGTCGTTGAGGTCTTAGATATTTTTCGTCATGTCTCTA
1 AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGTCTTTG
* * * * * * * **
17229501 AGGTACAAGG-TTCACCGTTACGACTTAAACCCTT-CCTTTTTGTATCTTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--TCTTTG
* * * * * *
17229551 CGGTACTGGATCCACCATTGCGGTCTTAGATCTTTCCCATCATGTCTCTG
1 AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGTCTTTG
* * *
17229601 AGGTA-TAAGG-TTCGTCGTTGCGACTTA-AACATTTCCCTT--TGCATCTTTG
1 AGGTACT--GGATTCGCCGTTGCGGCTTAGATC-TTTCCCTTCATG--TCTTTG
* * *
17229650 TGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTTG
1 AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGTCTTTG
* * ** * * * *
17229700 AGGTACAAGG-TTTGCCGTTGCAACTTAAACCCTTCCCTT-TTGTATCTTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--TCTTTG
* * * * * * *
17229750 TGGTATTGGATCCGCTGTTGCGGTCTTAGATCTTT-TCGTCATGTCTCTG
1 AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGTCTTTG
* * * *
17229799 AGGTA-TAAGG-TTCACCGTTGCGACTTAAACCTTTCCCATTGCA--TCTTTG
1 AGGTACT--GGATTCGCCGTTGCGGCTTAGATCTTTCCC-TT-CATGTCTTTG
* * * * * * *
17229848 TGGTACTGAATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATATTTTTG
1 AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGTCTTTG
* * * *
17229898 AGGTACAAGG-TTCGCCGTTGTGACTTA-AACTTTTCCCTT--TGCATCTTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATC-TTTCCCTTCATG--TCTTTG
* * * * * ** * *
17229947 CGATACTAGATCCACCGTTGCAATCTTAGATCTTTCCCGTCATGTCTCTG
1 AGGTACTGGATTCGCCGTTGC-GGCTTAGATCTTTCCCTTCATGTCTTTG
* ** * * * *
17229997 AGGTACAAGG-TTCGCCGTTGCAACTTAAACCCTTCCCTT-TTGTATCTTTG
1 AGGTAC-TGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--TCTTTG
* * * * * * *
17230047 CGGTACTGGATCCTCCGTTGCGATCTTAGATCTTTCTCGTCATGTCTCTG
1 AGGTACTGGATTCGCCGTTGCG-GCTTAGATCTTTCCCTTCATGTCTTTG
* * * * *
17230097 ATGTA-TAAGG-TTCGCCGTTGTGACTTAAACCTTTCCCTT--TGCATCTTTG
1 AGGTACT--GGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATG--TCTTTG
* * * *
17230146 CGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTTCCTTCATGT
1 AGGTACTGGATTCGCCGTTGCGG-CTTAGATCTTTCCCTTCATGT
17230191 TTCATGGTGC
Statistics
Matches: 1014, Mismatches: 305, Indels: 211
0.66 0.20 0.14
Matches are distributed among these distances:
46 4 0.00
47 48 0.05
48 138 0.14
49 409 0.40
50 320 0.32
51 76 0.07
52 19 0.02
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (49 bp):
AGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTG
Found at i:17229272 original size:50 final size:50
Alignment explanation
Indices: 17229212--17229362 Score: 141
Period size: 50 Copynumber: 3.0 Consensus size: 50
17229202 AGGTACAAGG
17229212 TTCGCCGTTGCGACTTAAACCCTCCCCTTTTGTATCTTTGCAGTACTGGA
1 TTCGCCGTTGCGACTTAAACCCTCCCCTTTTGTATCTTTGCAGTACTGGA
* * ** * **
17229262 TTCGCCGTTGCGGTCTTAGATCTTTCCCGTCATG--TCTTTG-AGGTA-TAAGG-
1 TTCGCCGTTGC-GACTTA-AACCCTCCCCTTTTGTATCTTTGCA-GTACT--GGA
* *
17229312 TTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGA
1 TTCGCCGTTGCGACTTAAACCCTCCCCTTTTGTATCTTTGCAGTACTGGA
17229362 T
1 T
17229363 CCGTCATTGT
Statistics
Matches: 75, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
48 8 0.11
49 9 0.12
50 41 0.55
51 8 0.11
52 9 0.12
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (50 bp):
TTCGCCGTTGCGACTTAAACCCTCCCCTTTTGTATCTTTGCAGTACTGGA
Found at i:17229494 original size:199 final size:198
Alignment explanation
Indices: 17228725--17230190 Score: 1693
Period size: 199 Copynumber: 7.4 Consensus size: 198
17228715 TAAGGTACCG
* *** * * * *
17228725 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTGGATTCACCGTTGTGG-
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGT
* * *
17228789 CTTAAATCTTTCCCTTTATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTC
66 CTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
** * * * * *
17228854 TGTGTCTTTGTGGTACTGGATCCGCCGTTGCGG-CTTAGGTC-TTTCC-T-TTGTGCTTCGTGGT
131 TGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGT-CTTTGAGGT
*
17228915 ACTA
195 ACAA
* * * * * *** * * *
17228919 -GATCTGCCGTTGCGGCTTAGATCTTTCCC-TTGTGTCTTCATGGTATTGGATCCGCCATTGC-G
1 GGTTC-GCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGG
* * * * **
17228981 ACTTAGATTTTTCCCTTCATGTCTTTAAGGTACAAGGTTCGCCACTGCGACTTAAACCTTTCCC-
65 TCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
* * * * * *
17229045 TTGCATCTTTGCGGTACTAGATCCTCCATTGTGG-CTTAGATC-TTTCCATTCATGTCTCTGAGG
130 TTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCC-GTCATGTCTTTGAGG
17229108 TACAA
194 TACAA
* * * *
17229113 GGTTCGTCATTGCGACTTAAACCTTTCCC-TTGCATCGTTGCGGTACTGGATCCACCGTTGCGG-
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGT
* * * *
17229176 CTTAGATATTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCCTCCCCTT
66 CTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCC-T
* * * *
17229241 TTGTATCTTTGCAGTACTGGATTCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTTGAGGT
130 TTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTTTGAGGT
*
17229306 ATAA
195 ACAA
* ** * *
17229310 GGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGTCATTGTGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCC-TTTGTATCTTTGCGGTACTGGATCCACCGTTGCGG
* * *
17229375 TCTTAGATCTTTCCCATCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
65 TCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
* * * * * *
17229440 TTGCATCTTTGCGGTACTGGATCCGTCGTTGAGGTCTTAGATATTTTTCGTCATGTCTCTAAGGT
130 TTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTTTGAGGT
17229505 ACAA
195 ACAA
* * * * *
17229509 GGTTCACCGTTACGACTTAAACCCTTCCTTTTTGTATCTTTGCGGTACTGGATCCACCATTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCC-CTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGG
* * * *
17229574 TCTTAGATCTTTCCCATCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACATTTCCCT
65 TCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
* *
17229639 TTGCATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTTGAGGT
130 TTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTTTGAGGT
17229704 ACAA
195 ACAA
* * * * * * *
17229708 GGTTTGCCGTTGCAACTTAAACCCTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCTGTTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCC-TTTGTATCTTTGCGGTACTGGATCCACCGTTGCGG
* * * * *
17229773 TCTTAGATCTTT-TCGTCATGTCTCTGAGGTATAAGGTTCACCGTTGCGACTTAAACCTTTCCCA
65 TCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
* * * *
17229837 TTGCATCTTTGTGGTACTGAATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATATTTTTGAGGT
130 TTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTTTGAGGT
17229902 ACAA
195 ACAA
* * * * * **
17229906 GGTTCGCCGTTGTGACTTAAACTTTTCCCTTTGCATCTTTGCGATACTAGATCCACCGTTGCAAT
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGT
* * *
17229971 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCAACTTAAACCCTTCCCTT
66 CTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCC-T
* * * * *
17230036 TTGTATCTTTGCGGTACTGGATCCTCCGTTGCGATCTTAGATC-TTTCTCGTCATGTCTCTGATG
130 TTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTC-CGTCATGTCTTTGAGG
*
17230100 TATAA
194 TACAA
* * *
17230105 GGTTCGCCGTTGTGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGT
* *
17230170 CTTAAATCTTTTCCTTCATGT
66 CTTAGATCTTTCCCTTCATGT
17230191 TTCATGGTGC
Statistics
Matches: 1082, Mismatches: 171, Indels: 33
0.84 0.13 0.03
Matches are distributed among these distances:
192 39 0.04
193 81 0.07
194 127 0.12
195 7 0.01
196 27 0.02
197 89 0.08
198 189 0.17
199 467 0.43
200 56 0.05
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (198 bp):
GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTTGCGGTACTGGATCCACCGTTGCGGT
CTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
TGCATCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTTCCGTCATGTCTTTGAGGTA
CAA
Found at i:17229498 original size:99 final size:99
Alignment explanation
Indices: 17228725--17230190 Score: 1675
Period size: 99 Copynumber: 14.9 Consensus size: 99
17228715 TAAGGTACCG
* *** * * * * *
17228725 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTGGATTCACCGTTGTGG-
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
* * *
17228789 CTTAAATCTTTCCCTTTATGTCTCTGAGGTACAA
66 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* ** *
17228823 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCTGTGTCTTTGTGGTACTGGATCCGCCGTTGCGG-
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
* * * *
17228887 CTTAGGTCTTT-CC-T-TTGTGCT-TCGTGGTACTA
66 CTTAGATCTTTCCCGTCATGT-CTCT-GAGGTACAA
* * * * *** * *
17228919 -GATCTGCCGTTGCGGCTTAGATCTTTCCCTTGTG--TCTTCATGGTATTGGATCCGCCATTGC-
1 GGTTC-GCCGTTGCGACTTAAACCTTTCCCTT-TGCATCTTTGCGGTACTGGATCCGCCGTTGCG
* * * * *
17228980 GACTTAGATTTTTCCCTTCATGTCTTTAAGGTACAA
64 GTCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
** * * * *
17229016 GGTTCGCCACTGCGACTTAAACCTTTCCC-TTGCATCTTTGCGGTACTAGATCCTCCATTGTGG-
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
**
17229079 CTTAGATCTTTCCATTCATGTCTCTGAGGTACAA
66 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * *
17229113 GGTTCGTCATTGCGACTTAAACCTTTCCC-TTGCATCGTTGCGGTACTGGATCCACCGTTGCGG-
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
* * *
17229176 CTTAGATATTTCCCTTCATGTTTCTGAGGTACAA
66 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * * *
17229210 GGTTCGCCGTTGCGACTTAAACCCTCCCCTTTTGTATCTTTGCAGTACTGGATTCGCCGTTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCC-TTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGG
* *
17229275 TCTTAGATCTTTCCCGTCATGTCTTTGAGGTATAA
65 TCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * * *
17229310 GGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGTCATTGTGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCC-TTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGG
* *
17229375 TCTTAGATCTTTCCCATCATGTCTCTGAGGTATAA
65 TCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * *
17229410 GGTTCGTCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGTCGTTGAGGT
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
* ** *
17229475 CTTAGATATTTTTCGTCATGTCTCTAAGGTACAA
66 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * * * * *
17229509 GGTTCACCGTTACGACTTAAACCCTTCCTTTTTGTATCTTTGCGGTACTGGATCCACCATTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCC-CTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGG
* *
17229574 TCTTAGATCTTTCCCATCATGTCTCTGAGGTATAA
65 TCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * *
17229609 GGTTCGTCGTTGCGACTTAAACATTTCCCTTTGCATCTTTGTGGTACTGGATCCGCCGTTGCGGT
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
*
17229674 CTTAGATCTTTCCCGTCATGTCTTTGAGGTACAA
66 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * * * * *
17229708 GGTTTGCCGTTGCAACTTAAACCCTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCTGTTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCC-TTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGG
* *
17229773 TCTTAGATCTTT-TCGTCATGTCTCTGAGGTATAA
65 TCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * *
17229807 GGTTCACCGTTGCGACTTAAACCTTTCCCATTGCATCTTTGTGGTACTGAATCCGCCGTTGCGGT
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
* * * *
17229872 CTTAGATCTTTTCCGTCATATTTTTGAGGTACAA
66 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * * * **
17229906 GGTTCGCCGTTGTGACTTAAACTTTTCCCTTTGCATCTTTGCGATACTAGATCCACCGTTGCAAT
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
17229971 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
66 CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
* * * * *
17230005 GGTTCGCCGTTGCAACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCTCCGTTGCGA
1 GGTTCGCCGTTGCGACTTAAACCTTTCCC-TTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGG
* * *
17230070 TCTTAGATCTTTCTCGTCATGTCTCTGATGTATAA
65 TCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
*
17230105 GGTTCGCCGTTGTGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
* * *
17230170 CTTAAATCTTTTCCTTCATGT
66 CTTAGATCTTTCCCGTCATGT
17230191 TTCATGGTGC
Statistics
Matches: 1167, Mismatches: 181, Indels: 39
0.84 0.13 0.03
Matches are distributed among these distances:
94 1 0.00
95 41 0.04
96 35 0.03
97 194 0.17
98 113 0.10
99 421 0.36
100 362 0.31
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (99 bp):
GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGCGGTACTGGATCCGCCGTTGCGGT
CTTAGATCTTTCCCGTCATGTCTCTGAGGTACAA
Found at i:17229925 original size:496 final size:492
Alignment explanation
Indices: 17228768--17230193 Score: 1800
Period size: 496 Copynumber: 2.9 Consensus size: 492
17228758 AATCTTCGTG
* * * * * * *
17228768 GTACTGGATTCACCGTTGTGG-CTTAAATCTTTCCCTTTATGTCTCTGAGGTACAAGGTTCGCCG
1 GTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCGCCG
* *
17228832 TTGCGACTTAAACCTTTCCCTCTGTGTCTTTGTGGTACTGGATCCGCCGTTGCGG-CTTAGGTC-
66 TTGCGACTTAAACCTTTCCCT-TGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCT
* * * * * * * *
17228895 TTTCCT-TTGTGCTTCGTGGTACTA-GATCTGCCGTTGCGGCTTAGATCTTTCCCTTGTG--TCT
130 TTTCCTCATGT-CTTTGAGGTACAAGGTTC-GCCGTTGCGACTTAAACCTTTCCCTT-TGCATCT
*** * * * * * *
17228956 TCATGGTATTGGATCCGCCATTGCGACTTAGATTTTTCCCTTCATGTCTTTAAGGTACAAGGTTC
192 TTGCGGTACTGGATCCGCCGTTGAGTCTTAGATTTTT-CCGTCATGTCTCTAAGGTACAAGGTTC
** * * * * *
17229021 GCCACTGCGACTTAAACCTTTCC-CTTGCATCTTTGCGGTACTAGATCCTCCATTGTGG-CTTAG
256 GCCGTTGCGACTTAAACCCTTCCTTTTGTATCTTTGCGGTACTGGATCCTCCATTGCGGTCTTAG
* *
17229084 ATCTTT-CCATTCATGTCTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCC-TTGCA
321 ATCTTTCCCA-TCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTGCA
* * *
17229147 TCGTTGCGGTACTGGATCCACCGTTGCGG-CTTAGATATTTCCCTTCATGTTTCTGAGGTACAAG
385 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACAAG
*
17229211 GTTCGCCGTTGCGACTTAAACCCTCCCCTTTTGTATCTTTGCA
450 GTTCGCCGTTGCAACTTAAACCCTCCCCTTTTGTATCTTTGCA
* *
17229254 GTACTGGATTCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTTGAGGTATAAGGTTCGCCG
1 GTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCGCCG
* * * * *
17229319 TTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGTCATTGTGGTCTTAGATC
66 TTGCGACTTAAACCTTTCCC--TTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATC
* * * *
17229384 TTTCCCATCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTGCATCTT
129 TTTTCC-TCATGTCTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTT
* *
17229449 TGCGGTACTGGATCCGTCGTTGAGGTCTTAGATATTTTTCGTCATGTCTCTAAGGTACAAGGTTC
193 TGCGGTACTGGATCCGCCGTTGA-GTCTTAGAT-TTTTCCGTCATGTCTCTAAGGTACAAGGTTC
* * *
17229514 ACCGTTACGACTTAAACCCTTCCTTTTTGTATCTTTGCGGTACTGGATCCACCATTGCGGTCTTA
256 GCCGTTGCGACTTAAACCCTTCC-TTTTGTATCTTTGCGGTACTGGATCCTCCATTGCGGTCTTA
*
17229579 GATCTTTCCCATCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACATTTCCCTTTGCA
320 GATCTTTCCCATCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTGCA
* *
17229644 TCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTT-TGAGGTACAA
385 TCTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGT-TTCTGAGGTACAA
* * **
17229708 GGTTTGCCGTTGCAACTTAAACCCTTCCCTTTTGTATCTTTGTG
449 GGTTCGCCGTTGCAACTTAAACCCTCCCCTTTTGTATCTTTGCA
* * * *
17229752 GTATTGGATCCGCTGTTGCGGTCTTAGATCTTT-TCGTCATGTCTCTGAGGTATAAGGTTCACCG
1 GTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCGCCG
* *
17229816 TTGCGACTTAAACCTTTCCCATTGCATCTTTGTGGTACTGAATCCGCCGTTGCGGTCTTAGATCT
66 TTGCGACTTAAACCTTTCCC-TTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCT
* * * *
17229881 TTTCCGTCATATTTTTGAGGTACAAGGTTCGCCGTTGTGACTTAAACTTTTCCCTTTGCATCTTT
130 TTTCC-TCATGTCTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTT
* * * * * *
17229946 GCGATACTAGATCCACCGTTGCAATCTTAGATCTTTCCCGTCATGTCTCTGAGGTACAAGGTTCG
194 GCGGTACTGGATCCGCCGTTG-AGTCTTAGAT-TTTTCCGTCATGTCTCTAAGGTACAAGGTTCG
* * *
17230011 CCGTTGCAACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCTCCGTTGCGATCTTAG
257 CCGTTGCGACTTAAACCCTT-CCTTTTGTATCTTTGCGGTACTGGATCCTCCATTGCGGTCTTAG
* * * * *
17230076 ATCTTTCTCGTCATGTCTCTGATGTATAAGGTTCGCCGTTGTGACTTAAACCTTTCCCTTTGCAT
321 ATCTTTCCCATCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTGCAT
* *
17230141 CTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTTCCTTCATGTTTC
386 CTTTGCGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTTTC
17230194 ATGGTGCTGA
Statistics
Matches: 810, Mismatches: 108, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
486 19 0.02
487 57 0.07
488 28 0.03
489 8 0.01
490 6 0.01
491 31 0.04
492 26 0.03
493 50 0.06
494 4 0.00
495 32 0.04
496 365 0.45
497 84 0.10
498 98 0.12
499 2 0.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (492 bp):
GTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCGCCG
TTGCGACTTAAACCTTTCCCTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTT
TTCCTCATGTCTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTGC
GGTACTGGATCCGCCGTTGAGTCTTAGATTTTTCCGTCATGTCTCTAAGGTACAAGGTTCGCCGT
TGCGACTTAAACCCTTCCTTTTGTATCTTTGCGGTACTGGATCCTCCATTGCGGTCTTAGATCTT
TCCCATCATGTCTCTGAGGTATAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTGCATCTTTG
CGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGC
CGTTGCAACTTAAACCCTCCCCTTTTGTATCTTTGCA
Found at i:17237613 original size:22 final size:22
Alignment explanation
Indices: 17237585--17237627 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17237575 TGATTGGGGC
*
17237585 AGCTGGTGGCAGTGCAAGTTGA
1 AGCTGGTGGCAGGGCAAGTTGA
*
17237607 AGCTGGTGGCAGGGGAAGTTG
1 AGCTGGTGGCAGGGCAAGTTG
17237628 CAAGGTGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.47, T:0.21
Consensus pattern (22 bp):
AGCTGGTGGCAGGGCAAGTTGA
Found at i:17241878 original size:12 final size:12
Alignment explanation
Indices: 17241840--17241879 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
17241830 TAAAAGAAAA
17241840 TAAAAATATATG
1 TAAAAATATATG
17241852 T--AAATATA-G
1 TAAAAATATATG
*
17241861 TAAAAATATATT
1 TAAAAATATATG
17241873 TAAAAAT
1 TAAAAAT
17241880 GCAACAGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
9 2 0.08
10 7 0.29
11 7 0.29
12 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (12 bp):
TAAAAATATATG
Found at i:17242787 original size:45 final size:44
Alignment explanation
Indices: 17242727--17243385 Score: 500
Period size: 45 Copynumber: 14.7 Consensus size: 44
17242717 GTGTGTGTGA
* * *
17242727 CTTCAATCTACCCCTCTGAATTAGGGGTATAAGATTAGATGGTGG
1 CTTCAATCTGCCCCTCTG-ATTAGGGGTAAAAGATTAGACGGTGG
* * * *
17242772 CTTTAATTTGCCCCTCTAGATTAAGGGTAAAAGATTAGACGGTGA
1 CTTCAATCTGCCCCTCT-GATTAGGGGTAAAAGATTAGACGGTGG
* *
17242817 CTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGACGGTGAG
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTG-G
* * * *
17242863 -TTCAATCTGCCCGTCTTGATTAGGGGTAAAAGATTGGATGTTGG
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
* * * * * ** *
17242907 CTTCAATTTGTCCCTCTTGACTAAGGGTAAAAGATTGGATAGTGA
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
* * * * * *
17242952 TTTCAATCTACCCCTCTTGACTAAGGGTAAAAAATTAGACGGTGA
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
* * * * *
17242997 CTTCAATCTG-TCC-CT--TTAGGTGTACAAGATTGGACAGTGG
1 CTTCAATCTGCCCCTCTGATTAGGGGTAAAAGATTAGACGGTGG
* * * * * *
17243037 CTTCAATCTACCTCTCTTGACTATGGGTAAAATATTGGACGGTGG
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
* * * * * *
17243082 CTTCAATCTGCCTCTCTTGACTAAGGGTAAAATATTGGACGGTAG
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
* * * * *
17243127 CTTCAATATGCCCCTCTTGACTAGGGGTAAAAGATTGGAAGATGG
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
* * * * * *
17243172 CTTCAATCTACCCCACTTAATTAAAGGGTAAAAGATTGGACGGTAG
1 CTTCAATCTGCCCCTC-TGATT-AGGGGTAAAAGATTAGACGGTGG
* * * * *
17243218 ATTCAATCTGCTCCTCTTGATTATGGGTAAAAAATTGGACGGTGG
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
* * *
17243263 CTTCAATCTGCCCCTTTTGATTAGGGGTAAAAGATTAGACAGTGA
1 CTTCAATCTGCCCC-TCTGATTAGGGGTAAAAGATTAGACGGTGG
* * * * * *
17243308 CTTCAATTTGCCTCTCTTGATTAGGGGTAAAATATTGGATGGTAG
1 CTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTAGACGGTGG
*
17243353 CTTCAATCTGCCCCTCTTGACTTAAGGGTAAAA
1 CTTCAATCTGCCCCTC-TGA-TTAGGGGTAAAA
17243386 TATTGGATGA
Statistics
Matches: 501, Mismatches: 100, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
40 26 0.05
41 1 0.00
42 2 0.00
43 2 0.00
44 4 0.01
45 416 0.83
46 50 0.10
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (44 bp):
CTTCAATCTGCCCCTCTGATTAGGGGTAAAAGATTAGACGGTGG
Found at i:17242831 original size:90 final size:89
Alignment explanation
Indices: 17242723--17243392 Score: 596
Period size: 90 Copynumber: 7.5 Consensus size: 89
17242713 AGTTGTGTGT
* * * * * *
17242723 GTGACTTCAATCTACCCCTCTGAATTAGGGGTATAAGATTAGATGGTGGCTTTAATTTGCCCCTC
1 GTGACTTCAATCTGCCCCTCTG-ATTAGGGGTAAAAGATTGGACGGTGGCTTCAATCTGCCCCTC
* * *
17242788 TAGATTAAGGGTAAAAGATTAGACG
65 TTGATTAGGGGTAAAAGATTGGACG
* *
17242813 GTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGACGGTGAG-TTCAATCTGCCCGT
1 GTGACTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTGGACGGTG-GCTTCAATCTGCCCCT
*
17242877 CTTGATTAGGGGTAAAAGATTGGATG
64 CTTGATTAGGGGTAAAAGATTGGACG
* * * * * * ** ** *
17242903 TTGGCTTCAATTTGTCCCTCTTGACTAAGGGTAAAAGATTGGATAGTGATTTCAATCTACCCCTC
1 GTGACTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTGGACGGTGGCTTCAATCTGCCCCTC
* * * *
17242968 TTGACTAAGGGTAAAAAATTAGACG
65 TTGATTAGGGGTAAAAGATTGGACG
* * * * * *
17242993 GTGACTTCAATCTG-TCC-CT--TTAGGTGTACAAGATTGGACAGTGGCTTCAATCTACCTCTCT
1 GTGACTTCAATCTGCCCCTCTGATTAGGGGTAAAAGATTGGACGGTGGCTTCAATCTGCCCCTCT
* * *
17243054 TGACTATGGGTAAAATATTGGACG
66 TGATTAGGGGTAAAAGATTGGACG
* * * * * * *
17243078 GTGGCTTCAATCTGCCTCTCTTGACTAAGGGTAAAATATTGGACGGTAGCTTCAATATGCCCCTC
1 GTGACTTCAATCTGCCCCTC-TGATTAGGGGTAAAAGATTGGACGGTGGCTTCAATCTGCCCCTC
* *
17243143 TTGACTAGGGGTAAAAGATTGGAAG
65 TTGATTAGGGGTAAAAGATTGGACG
* * * * * * * * *
17243168 ATGGCTTCAATCTACCCCACTTAATTAAAGGGTAAAAGATTGGACGGTAGATTCAATCTGCTCCT
1 GTGACTTCAATCTGCCCCTC-TGATT-AGGGGTAAAAGATTGGACGGTGGCTTCAATCTGCCCCT
* *
17243233 CTTGATTATGGGTAAAAAATTGGACG
64 CTTGATTAGGGGTAAAAGATTGGACG
* * * * * * *
17243259 GTGGCTTCAATCTGCCCCTTTTGATTAGGGGTAAAAGATTAGACAGTGACTTCAATTTGCCTCTC
1 GTGACTTCAATCTGCCCC-TCTGATTAGGGGTAAAAGATTGGACGGTGGCTTCAATCTGCCCCTC
* *
17243324 TTGATTAGGGGTAAAATATTGGATG
65 TTGATTAGGGGTAAAAGATTGGACG
* *
17243349 GT-AGCTTCAATCTGCCCCTCTTGACTTAAGGGTAAAATATTGGA
1 GTGA-CTTCAATCTGCCCCTC-TGA-TTAGGGGTAAAAGATTGGA
17243393 TGAGGTGATG
Statistics
Matches: 473, Mismatches: 94, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
85 68 0.14
86 1 0.00
87 2 0.00
88 2 0.00
89 3 0.01
90 302 0.64
91 95 0.20
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (89 bp):
GTGACTTCAATCTGCCCCTCTGATTAGGGGTAAAAGATTGGACGGTGGCTTCAATCTGCCCCTCT
TGATTAGGGGTAAAAGATTGGACG
Found at i:17242915 original size:135 final size:134
Alignment explanation
Indices: 17242723--17243392 Score: 721
Period size: 135 Copynumber: 5.0 Consensus size: 134
17242713 AGTTGTGTGT
* * * * * *
17242723 GTGACTTCAATCTACCCCTC-TGAATTAGGGGTATAAGATTAGATGGTGGCTTTAATTTGCCCCT
1 GTGAGTTCAATCTGCCCCTCTTG-ATTAGGGGTAAAAGATTGGA-AGTGGCTTCAATTTGCCCCT
* * * *
17242787 CTAGATTAAGGGTAAAAGATTAGACGGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGAT
64 CTTGATTAAGGGTAAAAGATTGGACGGTGACTTCAATCTGCCCCTCTTGACTAAGGGTAAAAAAT
17242852 TGGACG
129 TGGACG
* * *
17242858 GTGAGTTCAATCTGCCCGTCTTGATTAGGGGTAAAAGATTGGATGTTGGCTTCAATTTGTCCCTC
1 GTGAGTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAG-TGGCTTCAATTTGCCCCTC
* ** * *
17242923 TTGACTAAGGGTAAAAGATTGGATAGTGATTTCAATCTACCCCTCTTGACTAAGGGTAAAAAATT
65 TTGATTAAGGGTAAAAGATTGGACGGTGACTTCAATCTGCCCCTCTTGACTAAGGGTAAAAAATT
*
17242988 AGACG
130 GGACG
* * * * * * *
17242993 GTGACTTCAATCTG-TCC-C-T--TTAGGTGTACAAGATTGGACAGTGGCTTCAATCTACCTCTC
1 GTGAGTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGA-AGTGGCTTCAATTTGCCCCTC
* * * * * *
17243053 TTGACTATGGGTAAAATATTGGACGGTGGCTTCAATCTGCCTCTCTTGACTAAGGGTAAAATATT
65 TTGATTAAGGGTAAAAGATTGGACGGTGACTTCAATCTGCCCCTCTTGACTAAGGGTAAAAAATT
17243118 GGACG
130 GGACG
* * * * *
17243123 GT-AGCTTCAATATGCCCCTCTTGACTAGGGGTAAAAGATTGGAAGATGGCTTCAATCTACCCCA
1 GTGAG-TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAG-TGGCTTCAATTTGCCCCT
* * * *
17243187 CTTAATTAAAGGGTAAAAGATTGGACGGTAGA-TTCAATCTGCTCCTCTTGATTATGGGTAAAAA
64 CTTGATT-AAGGGTAAAAGATTGGACGGT-GACTTCAATCTGCCCCTCTTGACTAAGGGTAAAAA
17243251 ATTGGACG
127 ATTGGACG
* * * *
17243259 GTG-GCTTCAATCTGCCCCTTTTGATTAGGGGTAAAAGATTAGACAGTGACTTCAATTTGCCTCT
1 GTGAG-TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGA-AGTGGCTTCAATTTGCCCCT
* * * *
17243323 CTTGATTAGGGGTAAAATATTGGATGGT-AGCTTCAATCTGCCCCTCTTGACTTAAGGGTAAAAT
64 CTTGATTAAGGGTAAAAGATTGGACGGTGA-CTTCAATCTGCCCCTCTTGAC-TAAGGGTAAAAA
17243387 ATTGGA
127 ATTGGA
17243393 TGAGGTGATG
Statistics
Matches: 445, Mismatches: 73, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
129 1 0.00
130 102 0.23
131 3 0.01
132 2 0.00
133 3 0.01
134 4 0.01
135 198 0.44
136 129 0.29
137 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (134 bp):
GTGAGTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAGTGGCTTCAATTTGCCCCTCT
TGATTAAGGGTAAAAGATTGGACGGTGACTTCAATCTGCCCCTCTTGACTAAGGGTAAAAAATTG
GACG
Found at i:17245923 original size:23 final size:22
Alignment explanation
Indices: 17245871--17245925 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17245861 TGTAAGGTGT
*
17245871 GAATA-AAAATGTTTGTCAAAA
1 GAATATAAAATATTTGTCAAAA
* *
17245892 GAATTTAAAATATTTGTCAAAT
1 GAATATAAAATATTTGTCAAAA
17245914 GAGATATAAAAT
1 GA-ATATAAAAT
17245926 GCATCGTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 4 0.14
22 16 0.57
23 8 0.29
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.33
Consensus pattern (22 bp):
GAATATAAAATATTTGTCAAAA
Found at i:17250241 original size:94 final size:94
Alignment explanation
Indices: 17250066--17250256 Score: 292
Period size: 94 Copynumber: 2.0 Consensus size: 94
17250056 TAGGACCGAA
* *
17250066 TTGAAACAACATGGAAATGTAGAAGGACTGGGGCAGCAAATACCCCTTTTTTCCAAAACACGCGG
1 TTGAAACAACATGCAAATGCAGAAGGACTGGGGCAGCAAATACCCCTTTTTTCCAAAACACGCGG
*
17250131 ATCCCAGTGAGATCCGATCGAGTTCGGAT
66 ATCCCAGTGACATCCGATCGAGTTCGGAT
* * *
17250160 TTGAAATAACATGCAAATGCGGAAGGACTGGGGTAGCAAATACCCCTTTTTTCCAAAACACGCGG
1 TTGAAACAACATGCAAATGCAGAAGGACTGGGGCAGCAAATACCCCTTTTTTCCAAAACACGCGG
* * * *
17250225 ATCCCAGTGACCTCCGATTGGGTTCGGGT
66 ATCCCAGTGACATCCGATCGAGTTCGGAT
17250254 TTG
1 TTG
17250257 GCATTGAAAC
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (94 bp):
TTGAAACAACATGCAAATGCAGAAGGACTGGGGCAGCAAATACCCCTTTTTTCCAAAACACGCGG
ATCCCAGTGACATCCGATCGAGTTCGGAT
Found at i:17251287 original size:16 final size:15
Alignment explanation
Indices: 17251256--17251289 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
17251246 AATTTAAAAT
17251256 TTTATTATTTTTTGG
1 TTTATTATTTTTTGG
*
17251271 TTTATTTTTTGTTTGG
1 TTTATTATTT-TTTGG
17251287 TTT
1 TTT
17251290 TAAATTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (15 bp):
TTTATTATTTTTTGG
Found at i:17255498 original size:26 final size:26
Alignment explanation
Indices: 17255468--17255517 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
17255458 GCTAGTTTCT
* *
17255468 AATAGAATTAGTTGATCAAATCAATA
1 AATAGAATCAATTGATCAAATCAATA
*
17255494 AATAGAATCAATTGTTCAAATCAA
1 AATAGAATCAATTGATCAAATCAA
17255518 CTATTACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (26 bp):
AATAGAATCAATTGATCAAATCAATA
Found at i:17255528 original size:13 final size:13
Alignment explanation
Indices: 17255512--17255536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17255502 CAATTGTTCA
17255512 AATCAACTATTAC
1 AATCAACTATTAC
17255525 AATCAACTATTA
1 AATCAACTATTA
17255537 ATTATCAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AATCAACTATTAC
Found at i:17264980 original size:18 final size:19
Alignment explanation
Indices: 17264958--17265000 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
17264948 GAGAGAAGAA
17264958 AGAAAGAAAGAA-A-GGAG
1 AGAAAGAAAGAAGATGGAG
*
17264975 AGGAAAAAAAGAAGATGGAG
1 A-GAAAGAAAGAAGATGGAG
17264995 AGAAAG
1 AGAAAG
17265001 GTAATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 10 0.48
19 5 0.24
20 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (19 bp):
AGAAAGAAAGAAGATGGAG
Found at i:17270351 original size:31 final size:31
Alignment explanation
Indices: 17270314--17270387 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
17270304 TTTATATTAC
*
17270314 TTACTTACTTACTACTACTAACAAAATAAAA
1 TTACTTACTAACTACTACTAACAAAATAAAA
17270345 TTACTTACTAACTACTACTAACAAAATAAAA
1 TTACTTACTAACTACTACTAACAAAATAAAA
*
17270376 GTACTTACTAAC
1 TTACTTACTAAC
17270388 AAACTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.31
Consensus pattern (31 bp):
TTACTTACTAACTACTACTAACAAAATAAAA
Found at i:17270478 original size:12 final size:12
Alignment explanation
Indices: 17270461--17270500 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
17270451 TTTACTTAAC
17270461 TAAATAAAAAAT
1 TAAATAAAAAAT
17270473 TAAATAAAAAA-
1 TAAATAAAAAAT
* *
17270484 TCAATTAAAAAT
1 TAAATAAAAAAT
17270496 TAAAT
1 TAAAT
17270501 TAAACAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:17276568 original size:80 final size:80
Alignment explanation
Indices: 17276435--17276594 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
17276425 AACACAGGGA
17276435 TTTAGAATTGAAGAGTTCTATTAATTCATTTTGGATATGGATATAGATATGGGGTCATCACGCAC
1 TTTAGAATTGAAGAGTTCTATTAATTCATTTTGGATATGGATATAGATATGGGGTCATCACGCAC
17276500 ATTCAGAACCAGTTC
66 ATTCAGAACCAGTTC
17276515 TTTAGAATTGAAGAGTTCTATTAATTCATTTTGGATATGGATATAGATATGGGGTCATCACGCAC
1 TTTAGAATTGAAGAGTTCTATTAATTCATTTTGGATATGGATATAGATATGGGGTCATCACGCAC
17276580 ATTCAGAACCAGTTC
66 ATTCAGAACCAGTTC
17276595 AGCAAAGGAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (80 bp):
TTTAGAATTGAAGAGTTCTATTAATTCATTTTGGATATGGATATAGATATGGGGTCATCACGCAC
ATTCAGAACCAGTTC
Found at i:17278602 original size:2 final size:2
Alignment explanation
Indices: 17278595--17278633 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17278585 ACATGACAAT
17278595 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
17278634 GAAAGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17279015 original size:35 final size:35
Alignment explanation
Indices: 17278957--17279032 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
17278947 CATATTTTTA
* *
17278957 ATAAAAATAATTAATTTACTTTTT-AATTTAATAT-
1 ATAAAAATAATTAACTTACTTTTTGAA-TAAATATG
* *
17278991 ATAAAAATTAATTTACTTATTTTTTGAATAAATATG
1 ATAAAAA-TAATTAACTTACTTTTTGAATAAATATG
17279027 ATAAAA
1 ATAAAA
17279033 TGCAATCCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 7 0.20
35 20 0.57
36 8 0.23
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (35 bp):
ATAAAAATAATTAACTTACTTTTTGAATAAATATG
Found at i:17279080 original size:7 final size:7
Alignment explanation
Indices: 17279068--17279093 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17279058 CTTTTTCTTT
17279068 TCCATTA
1 TCCATTA
17279075 TCCATTA
1 TCCATTA
17279082 TCCATTA
1 TCCATTA
17279089 TCCAT
1 TCCAT
17279094 AGATAGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (7 bp):
TCCATTA
Found at i:17290180 original size:24 final size:24
Alignment explanation
Indices: 17290130--17290176 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17290120 ATTTGAATTT
*
17290130 TTTACTTTATTTTTAGATATTTAA
1 TTTACTTTATTTTTAAATATTTAA
17290154 TTTA-TTTATTTTTTAAAT-TTTAA
1 TTTACTTTA-TTTTTAAATATTTAA
17290177 ATTTTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTACTTTATTTTTAAATATTTAA
Found at i:17302480 original size:39 final size:39
Alignment explanation
Indices: 17302436--17302538 Score: 136
Period size: 39 Copynumber: 2.6 Consensus size: 39
17302426 CATGTGTTGT
*
17302436 GGATTCTATGAAACTTGTGTGAGTAGCATTGAATGATGC
1 GGATTCTATGAAACTTGTGTGAGCAGCATTGAATGATGC
* * *
17302475 GGATTCTCTGAAGA-TCGTGTGAGCATCATTGAATGATGC
1 GGATTCTATGAA-ACTTGTGTGAGCAGCATTGAATGATGC
* *
17302514 GGATTCTTTGAAGCTTGTGTGAGCA
1 GGATTCTATGAAACTTGTGTGAGCA
17302539 ACATCAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 54 0.98
40 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (39 bp):
GGATTCTATGAAACTTGTGTGAGCAGCATTGAATGATGC
Found at i:17303268 original size:21 final size:23
Alignment explanation
Indices: 17303235--17303276 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
17303225 ACATTAATTT
*
17303235 TTTAGAGATTAAAAAA-ATAAGA
1 TTTAGAGAGTAAAAAATATAAGA
17303257 TTTA-AGAGTAAAAAATATAA
1 TTTAGAGAGTAAAAAATATAA
17303277 ATATCCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (23 bp):
TTTAGAGAGTAAAAAATATAAGA
Found at i:17306067 original size:41 final size:41
Alignment explanation
Indices: 17305907--17306107 Score: 217
Period size: 41 Copynumber: 4.9 Consensus size: 41
17305897 ACGTTTGGAT
* *
17305907 AGAAAACGCCGCAAAAGGT-AAAGCATTAGCGGCGCTTACG
1 AGAAAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGCTTACG
* ** *
17305947 GGAAAGCGTTGCTAAAGGTCAGAGCATTAGCGGCGCTTACG
1 AGAAAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGCTTACG
* * *
17305988 GGAAAGCTCCGCTAAAGGTCAAAGTATTAGCGGCGCTTACG
1 AGAAAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGCTTACG
* ** *
17306029 AGAAAGCGCCGCTAAAGGTCGAAGCATTAGCGATGCTTA-T
1 AGAAAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGCTTACG
* * * * *
17306069 AGAAAAGCACCGTTAAAAGTTAGAGCATTAGCGGCGCTT
1 AG-AAAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGCTT
17306108 TCTAATAAAC
Statistics
Matches: 133, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
40 16 0.12
41 117 0.88
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.18
Consensus pattern (41 bp):
AGAAAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGCTTACG
Found at i:17309899 original size:43 final size:42
Alignment explanation
Indices: 17309846--17310030 Score: 201
Period size: 43 Copynumber: 4.3 Consensus size: 42
17309836 AAATTCGAGT
*
17309846 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTT-TGGGAAAAGCGCCGCTAAAGACCATGTTC
** ** *
17309889 TTTATTGGCGTTTCTGGGAAAAGCGTTGTTAAAGACCATGTTC
1 TTTAGCGGCGTTT-TGGGAAAAGCGCCGCTAAAGACCATGTTC
*
17309932 TTTAGCGGCGTTTTTGAGG-TAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCG-TTTTG-GGAAAAGCGCCGCTAAAGACCATGTTC
* * * * *
17309975 TGTAACGACGTTTTTGGAAAAGCGCTGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTTGGGAAAAGCGCCGCTAAAGACCATGTTC
* *
17310017 TATAGCGGCATTTT
1 TTTAGCGGCGTTTT
17310031 CCCTTATAAA
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.02
42 36 0.31
43 75 0.64
44 5 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGTTTTGGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:17310046 original size:86 final size:85
Alignment explanation
Indices: 17309869--17310030 Score: 218
Period size: 85 Copynumber: 1.9 Consensus size: 85
17309859 GTGGGAAAAG
* ** * * * *
17309869 CGCCGCTAAAGACCATGTTCTTTATTGGCGTTTCTGGGAAAAGCGTTGTTAAAGACCATGTTCTT
1 CGCCGCTAAAGACCATGTTCTGTAACGACGTTTCTGGGAAAAGCGCTGCTAAAGACCATGTTCTA
* *
17309934 TAGCGGCGTTTTTGAGGTAAG
66 TAGCGGCATTTTTGA-GTAAA
*
17309955 CGCCGCTAAAGACCATGTTCTGTAACGACGTTT-TTGGAAAAGCGCTGCTAAAGACCATGTTCTA
1 CGCCGCTAAAGACCATGTTCTGTAACGACGTTTCTGGGAAAAGCGCTGCTAAAGACCATGTTCTA
17310019 TAGCGGCATTTT
66 TAGCGGCATTTT
17310031 CCCTTATAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 38 0.57
86 29 0.43
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (85 bp):
CGCCGCTAAAGACCATGTTCTGTAACGACGTTTCTGGGAAAAGCGCTGCTAAAGACCATGTTCTA
TAGCGGCATTTTTGAGTAAA
Found at i:17310102 original size:12 final size:12
Alignment explanation
Indices: 17310085--17310109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17310075 ATTTTTATAA
17310085 GCGCCGCTAAAT
1 GCGCCGCTAAAT
17310097 GCGCCGCTAAAT
1 GCGCCGCTAAAT
17310109 G
1 G
17310110 TTTTAGCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.28, T:0.16
Consensus pattern (12 bp):
GCGCCGCTAAAT
Found at i:17311072 original size:24 final size:24
Alignment explanation
Indices: 17311045--17311094 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
17311035 AACATGAGCA
* *
17311045 AAGAACTATTAACGATCGACTTGC
1 AAGAACTATTAACAATCGACTAGC
17311069 AAGAACTATTAACAATCGACTAGC
1 AAGAACTATTAACAATCGACTAGC
17311093 AA
1 AA
17311095 AATTTAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (24 bp):
AAGAACTATTAACAATCGACTAGC
Found at i:17317318 original size:52 final size:53
Alignment explanation
Indices: 17317256--17317360 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 53
17317246 AACAATTTAA
17317256 TTTGTGGCTAGGATAAGAATATACCTGATACCCTAATCAA-CCAATAGGTTTG
1 TTTGTGGCTAGGATAAGAATATACCTGATACCCTAATCAACCCAATAGGTTTG
* * *
17317308 TTTGTGGCTAGGTTAGGAATATACTTGATACCCTAATCAACCCAATAGGTTTG
1 TTTGTGGCTAGGATAAGAATATACCTGATACCCTAATCAACCCAATAGGTTTG
17317361 ATCGTAATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 37 0.76
53 12 0.24
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (53 bp):
TTTGTGGCTAGGATAAGAATATACCTGATACCCTAATCAACCCAATAGGTTTG
Found at i:17320016 original size:2 final size:2
Alignment explanation
Indices: 17320011--17320048 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17320001 TTAAAACTTG
17320011 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17320049 GATGAGGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:17329171 original size:31 final size:31
Alignment explanation
Indices: 17329113--17329171 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17329103 TTTCAATAAG
*
17329113 TCATCATTGTCGAGAAACCTGGAATGGCGAC
1 TCATCATTGTCGAGAAACCAGGAATGGCGAC
* *
17329144 TCATCGTTGTCGAGCAACCAAGG-ATGGC
1 TCATCATTGTCGAGAAACC-AGGAATGGC
17329172 TTAATTGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.92
32 2 0.08
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (31 bp):
TCATCATTGTCGAGAAACCAGGAATGGCGAC
Found at i:17329632 original size:3 final size:3
Alignment explanation
Indices: 17329624--17329652 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17329614 TCACAAATTG
17329624 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17329653 CACTACTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17349704 original size:26 final size:26
Alignment explanation
Indices: 17349655--17349706 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17349645 TTATCCTTAA
* * * *
17349655 AATTTTTAATTAATTTATTTTAAAAT
1 AATTTTTAATGAATTAAATATAAAAT
17349681 AATTTTTAATGAATTAAATATAAAAT
1 AATTTTTAATGAATTAAATATAAAAT
17349707 TAAAATCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AATTTTTAATGAATTAAATATAAAAT
Found at i:17361485 original size:29 final size:28
Alignment explanation
Indices: 17361452--17361839 Score: 350
Period size: 29 Copynumber: 13.4 Consensus size: 28
17361442 GTCAAAAATG
* * *
17361452 ATTTTTAAAAATTTAAGGGTAAAATGGTA
1 ATTTTTGAAAGTTTAGGGGTAAAAT-GTA
* * *
17361481 ATTTTGGAAAAGTTTAAGGTTAAAATGGTA
1 ATTTTTG-AAAGTTTAGGGGTAAAAT-GTA
* *
17361511 ATTTTT-AGATGTTTAGGGATAAAATGGTA
1 ATTTTTGA-AAGTTTAGGGGTAAAAT-GTA
* ** * *
17361540 ATTTTTGGATA-TTCGGGGGTAAAATATG
1 ATTTTT-GAAAGTTTAGGGGTAAAATGTA
*
17361568 ATTTTTGAAAGTTTGAGGGATAAAAATGTA
1 ATTTTTGAAAGTTT-AGGGGT-AAAATGTA
* *
17361598 ATTTTTGGAAGTTTAAGGGTAAAAATGTA
1 ATTTTTGAAAGTTTAGGGGT-AAAATGTA
*
17361627 ATTTTTGAAAAGTTTCGGGGGTAAAATGGTA
1 ATTTTTG-AAAGTTT-AGGGGTAAAAT-GTA
17361658 ATTTTTGGAAAGTTT-GGGGTAAAATGTA
1 ATTTTT-GAAAGTTTAGGGGTAAAATGTA
17361686 ATTTTTGGAAAGTTTAGGGGTAAAATGTA
1 ATTTTT-GAAAGTTTAGGGGTAAAATGTA
* * *
17361715 ATTTTAGAAAATATAGGGGTAAAATGGTA
1 ATTTTTGAAAGTTTAGGGGTAAAAT-GTA
* *
17361744 ATTTTTAAAAGTTTAGGGGTAAAAATGTG
1 ATTTTTGAAAGTTTAGGGGT-AAAATGTA
* *
17361773 ATTTTTGGAAGTTCAGGGGTAAAATGTA
1 ATTTTTGAAAGTTTAGGGGTAAAATGTA
* * *
17361801 ATTTTTGAAAAGTTCAGGGTTAAAATGCA
1 ATTTTTG-AAAGTTTAGGGGTAAAATGTA
*
17361830 ATTTTGGAAA
1 ATTTTTGAAA
17361840 AGTTGAAATA
Statistics
Matches: 301, Mismatches: 43, Indels: 31
0.80 0.11 0.08
Matches are distributed among these distances:
27 3 0.01
28 62 0.21
29 154 0.51
30 60 0.20
31 21 0.07
32 1 0.00
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (28 bp):
ATTTTTGAAAGTTTAGGGGTAAAATGTA
Found at i:17363594 original size:6 final size:6
Alignment explanation
Indices: 17363577--17363657 Score: 53
Period size: 6 Copynumber: 13.7 Consensus size: 6
17363567 GACTTTTTAA
* ** *
17363577 TTAAATT TTAAAT TTAAAT TTAAA- ATAAAT TTAAACT CGAAA- ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT
* *
17363625 TTAAAT TTAAA- AT-AAT TTAAAAT TTAAAA TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAA
17363658 GTTCAATTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
4 2 0.03
5 9 0.16
6 33 0.57
7 14 0.24
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:17363595 original size:13 final size:13
Alignment explanation
Indices: 17363577--17363657 Score: 59
Period size: 13 Copynumber: 6.8 Consensus size: 13
17363567 GACTTTTTAA
*
17363577 TTAAATTTTAAAT
1 TTAAATTTAAAAT
17363590 TTAAATTTAAAA-
1 TTAAATTTAAAAT
*
17363602 -TAAATTTAAACT
1 TTAAATTTAAAAT
** *
17363614 CGAAA-AT-AAAT
1 TTAAATTTAAAAT
17363625 TTAAATTTAAAA-
1 TTAAATTTAAAAT
17363637 -T-AATTTAAAAT
1 TTAAATTTAAAAT
*
17363648 TTAAAATTAA
1 TTAAATTTAA
17363658 GTTCAATTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
10 9 0.17
11 17 0.33
12 3 0.06
13 23 0.44
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (13 bp):
TTAAATTTAAAAT
Found at i:17363605 original size:17 final size:17
Alignment explanation
Indices: 17363585--17363654 Score: 97
Period size: 17 Copynumber: 4.1 Consensus size: 17
17363575 AATTAAATTT
17363585 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
**
17363602 TAAATTTAAACTCGAAAA
1 TAAATTTAAA-TTTAAAA
17363620 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
17363637 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
17363654 T
1 T
17363655 TAAGTTCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
16 5 0.11
17 27 0.57
18 15 0.32
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:17376282 original size:168 final size:167
Alignment explanation
Indices: 17375997--17376497 Score: 714
Period size: 168 Copynumber: 3.0 Consensus size: 167
17375987 CATCAGAGAT
* *
17375997 TGAATATCCATGCAAGAGCCATATTGAAGATCAGAAGAGTGATGATCAAATGTGTCTAAAACCTG
1 TGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACCTG
* * * *
17376062 TCAAGGAAGAACCTAAAGATGATGTTTGTGATAAACCCTTGTATGGGACTCCTTCATGCAAGGAA
66 TCAAGGAAGAAGCTAAAGATGGTGTTTGTGATAAA-CCTTGTATGAGACTCCTCCATGCAAGGAA
* * *
17376127 ACTAAGAGGAAGAAATCACGATCACTATGTTCTAACAC
130 ACTAGGAGGAAGAAATCACGATCACAATGTTCTAAAAC
* * * *
17376165 TGAATATCTATGCAAGAGCTATATTGAAGATCATAAGAGTGATGATCAATTGTGTCTAAAACCTG
1 TGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACCTG
* *
17376230 TCAAGGAAGAAGCTAAAGATGGTTTTTATGATGAAACCTTGTATGAGACTCCTCCATGCAAGGAA
66 TCAAGGAAGAAGCTAAAGATGGTGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAA
* * * *
17376295 GCTAGGAGGAATAAATCACAATCACAATGTTCTAAAAT
130 ACTAGGAGGAAGAAATCACGATCACAATGTTCTAAAAC
* * * **
17376333 TGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGAAGATCAAGTGAGTCTAAAACCCA
1 TGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACCTG
* *
17376398 TCAAAGAAGAAGCTAAAGATGGTGTTTGTGATAAAACCTTCTATGAGACTCCTCCATGCAAGGAA
66 TCAAGGAAGAAGCTAAAGATGGTGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAA
* * *
17376463 ACTAGGAAGAAGAAACCGCGATCACAATGTTCTAA
130 ACTAGGAGGAAGAAATCACGATCACAATGTTCTAA
17376498 TCCTCGAAAG
Statistics
Matches: 296, Mismatches: 36, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
168 293 0.99
169 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (167 bp):
TGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACCTG
TCAAGGAAGAAGCTAAAGATGGTGTTTGTGATAAACCTTGTATGAGACTCCTCCATGCAAGGAAA
CTAGGAGGAAGAAATCACGATCACAATGTTCTAAAAC
Found at i:17380078 original size:24 final size:23
Alignment explanation
Indices: 17380035--17380085 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
17380025 AATATAAATA
17380035 AATATAATAAAAAATTTAAATCTT
1 AATATAATAAAAAA-TTAAATCTT
*
17380059 AATATCAATAGAAAAA-TAAATTTT
1 AATAT-AATA-AAAAATTAAATCTT
17380083 AAT
1 AAT
17380086 TTAGTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 15 0.62
25 4 0.17
26 5 0.21
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AATATAATAAAAAATTAAATCTT
Found at i:17381430 original size:7 final size:7
Alignment explanation
Indices: 17381418--17381442 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17381408 TTGAAGGATG
17381418 GTAATTT
1 GTAATTT
17381425 GTAATTT
1 GTAATTT
17381432 GTAATTT
1 GTAATTT
17381439 GTAA
1 GTAA
17381443 GCAACTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (7 bp):
GTAATTT
Found at i:17381768 original size:2 final size:2
Alignment explanation
Indices: 17381761--17381785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17381751 CATCAGCTGA
17381761 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17381786 AAACCTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17384921 original size:27 final size:26
Alignment explanation
Indices: 17384877--17384931 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
17384867 ATTCAACCAC
* *
17384877 AAAACAATGGCGGTTTTTTTCCTTTCA
1 AAAACAAAGGCGGGTTTTTT-CTTTCA
* *
17384904 AAAACAAAGGTGGGTTTTTTTTTTCA
1 AAAACAAAGGCGGGTTTTTTCTTTCA
17384930 AA
1 AA
17384932 GTTGTGTAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (26 bp):
AAAACAAAGGCGGGTTTTTTCTTTCA
Found at i:17385657 original size:12 final size:12
Alignment explanation
Indices: 17385636--17385757 Score: 60
Period size: 12 Copynumber: 10.4 Consensus size: 12
17385626 ATTTATAAAA
17385636 ATTTAATTTAAT
1 ATTTAATTTAAT
*
17385648 ATTTATTTTAAT
1 ATTTAATTTAAT
*
17385660 A-AT-ATTT--T
1 ATTTAATTTAAT
17385668 A-TTAATTTAAT
1 ATTTAATTTAAT
* * * *
17385679 ATTAAAATGATT
1 ATTTAATTTAAT
17385691 ATATTAATATTAA-
1 AT-TTAAT-TTAAT
17385704 ATTTAATTTAAT
1 ATTTAATTTAAT
* * * *
17385716 ATTAAAGTGATT
1 ATTTAATTTAAT
17385728 ATCTTAATATTAA-
1 AT-TTAAT-TTAAT
17385741 ATTTAATTTAAT
1 ATTTAATTTAAT
*
17385753 GTTTA
1 ATTTA
17385758 TCTTGCAGAT
Statistics
Matches: 79, Mismatches: 21, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 3 0.04
11 11 0.14
12 44 0.56
13 10 0.13
14 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (12 bp):
ATTTAATTTAAT
Found at i:17385691 original size:20 final size:18
Alignment explanation
Indices: 17385667--17385752 Score: 90
Period size: 20 Copynumber: 4.7 Consensus size: 18
17385657 AATAATATTT
17385667 TATTAATTTAATATTAAAA
1 TATTAATTTAATATT-AAA
17385686 TGATT-ATATTAATATTAAA
1 T-ATTAAT-TTAATATTAAA
17385705 T-TTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
17385722 GTGATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
17385742 T-TTAATTTAAT
1 TATTAATTTAAT
17385753 GTTTATCTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
17 20 0.34
18 5 0.08
19 10 0.17
20 24 0.41
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:17385714 original size:37 final size:37
Alignment explanation
Indices: 17385669--17385752 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
17385659 TAATATTTTA
17385669 TTAATTTAATATTAAAATGATTATATTAATATTAAAT
1 TTAATTTAATATTAAAATGATTATATTAATATTAAAT
* *
17385706 TTAATTTAATATTAAAGTGATTATCTTAATATTAAAT
1 TTAATTTAATATTAAAATGATTATATTAATATTAAAT
17385743 TTAATTTAAT
1 TTAATTTAAT
17385753 GTTTATCTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (37 bp):
TTAATTTAATATTAAAATGATTATATTAATATTAAAT
Found at i:17386990 original size:20 final size:19
Alignment explanation
Indices: 17386949--17386994 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
17386939 AATTATATTG
17386949 AATA-TTGAATATGATAAA
1 AATATTTGAATATGATAAA
* *
17386967 AATATTTGAATTATTATAAT
1 AATATTTGAA-TATGATAAA
17386987 AATATTTG
1 AATATTTG
17386995 TATGGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 5 0.21
20 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (19 bp):
AATATTTGAATATGATAAA
Found at i:17392713 original size:14 final size:15
Alignment explanation
Indices: 17392677--17392714 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
17392667 TGTTATATAG
17392677 AATTATATTACATAT
1 AATTATATTACATAT
* *
17392692 TATAATATT-CATAT
1 AATTATATTACATAT
17392706 AATTATATT
1 AATTATATT
17392715 GGAATATAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTATATTACATAT
Found at i:17402112 original size:34 final size:32
Alignment explanation
Indices: 17402069--17402141 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
17402059 ATTAATTGTT
* *
17402069 TATTTAAAATTAACATGTAATATATTTTTAAGT-C
1 TATTTAAAATTAAAAT-TAA-A-ATTTTTAAATAC
17402103 TATTTAAAATTAAAATTAAAATTTTTAAATAC
1 TATTTAAAATTAAAATTAAAATTTTTAAATAC
17402135 TATTTAA
1 TATTTAA
17402142 TTGTCTCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 9 0.25
32 9 0.25
33 3 0.08
34 15 0.42
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (32 bp):
TATTTAAAATTAAAATTAAAATTTTTAAATAC
Found at i:17402721 original size:11 final size:11
Alignment explanation
Indices: 17402703--17402736 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17402693 TAATTAAAAT
17402703 AATTTCATTTC
1 AATTTCATTTC
* *
17402714 ATTTTCATTAC
1 AATTTCATTTC
17402725 AATTTCATTTC
1 AATTTCATTTC
17402736 A
1 A
17402737 GATAATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTCATTTC
Found at i:17403146 original size:3 final size:3
Alignment explanation
Indices: 17403138--17403177 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
17403128 TACTATTCAT
17403138 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17403178 CATCATCATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17403284 original size:13 final size:13
Alignment explanation
Indices: 17403268--17403292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17403258 ATGTCCTTTA
17403268 AAAATTAAAAATT
1 AAAATTAAAAATT
17403281 AAAATTAAAAAT
1 AAAATTAAAAAT
17403293 GCTAATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:17406458 original size:59 final size:60
Alignment explanation
Indices: 17406351--17406738 Score: 494
Period size: 59 Copynumber: 6.6 Consensus size: 60
17406341 TTGGACACCC
* * * *
17406351 GGGGCAAAATGGTAA-TTATGGT-AAAGTCGAGGTTAAAAAATAGAATTTTTA-AGAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTT-AAAAATAGAATTTTTAGAAAGTTCG
* * *
17406410 AGGGTAAAACT-GTAATTTTTGGTGAAATCGGGGTTAAAAATAGTA-TTTTAGAAAGTTTG
1 GGGGTAAAA-TGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTTCG
* * **
17406469 GGGGTAAAATGGTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAA-TTTT-GGAAGTTTA
1 GGGGTAAAATGGTAATTTTT-GGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTTCG
17406528 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATAGAA-TTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTTCG
* * * *
17406586 GGGGTAAAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAA-TTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTTCG
*
17406645 GGGGT-AAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTTAGAAAGTTCG
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTTCG
17406704 GGGGTAAAATGGTAATTTTTGGGTGAAATCGGGGT
1 GGGGTAAAATGGTAATTTTT-GGTGAAATCGGGGT
17406739 CAGAATGTAT
Statistics
Matches: 295, Mismatches: 23, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
57 13 0.04
58 68 0.23
59 147 0.50
60 64 0.22
61 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (60 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTTCG
Found at i:17406621 original size:176 final size:177
Alignment explanation
Indices: 17406351--17406738 Score: 527
Period size: 176 Copynumber: 2.2 Consensus size: 177
17406341 TTGGACACCC
* * * *
17406351 GGGGCAAAATGGTAA-TTATGGT-AAAGTCGAGGTTAAAAAATAGAATTTTTAAGAGTTCGAGGG
1 GGGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTT-AAAAATAGAATTTTTAAAAGTTCGAGGG
* * *
17406414 TAAAACTGTAATTTTTGGTGAAATCGGGGTTAAAAATAGTATTTTAGAAAGTTTGGGGGTAAAAT
64 TAAAACTGTAATTTTTGATGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCGGGGGT-AAAT
* *
17406479 GGTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTT-GGAAGTTTA
128 GGTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCA
*
17406528 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATAGAA-TTTTAGAAAGTTCGGGGGT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTA-AAAGTTCGAGGGT
* * *
17406591 AAAA-TGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAATG
65 AAAACT-GTAATTTTTGATGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCGGGGGTAAATG
* * * *
17406655 GTAATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCG
129 GTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCA
17406704 GGGGTAAAATGGTAATTTTTGGGTGAAATCGGGGT
1 GGGGTAAAATGGTAATTTTT-GGTGAAATCGGGGT
17406739 CAGAATGTAT
Statistics
Matches: 188, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
175 47 0.25
176 97 0.52
177 28 0.15
178 13 0.07
179 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (177 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAAAAGTTCGAGGGTA
AAACTGTAATTTTTGATGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCGGGGGTAAATGGT
AATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCA
Found at i:17407483 original size:12 final size:12
Alignment explanation
Indices: 17407466--17407499 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
17407456 CAAGGTAGTA
17407466 TTTCTTCTCTTT
1 TTTCTTCTCTTT
17407478 TTTCTTCT-TTT
1 TTTCTTCTCTTT
17407489 TTTCTT-TCTTT
1 TTTCTTCTCTTT
17407500 ATTGTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 12 0.57
12 8 0.38
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTCTCTTT
Found at i:17407491 original size:11 final size:11
Alignment explanation
Indices: 17407466--17407499 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
17407456 CAAGGTAGTA
17407466 TTTCTTCTCTTT
1 TTTCTTCT-TTT
17407478 TTTCTTCTTTT
1 TTTCTTCTTTT
17407489 TTTCTTTCTTT
1 TTTC-TTCTTT
17407500 ATTGTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTCTTTT
Found at i:17407763 original size:3 final size:3
Alignment explanation
Indices: 17407757--17407781 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17407747 TTATCTTCTT
17407757 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
17407782 ATTTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17407821 original size:19 final size:19
Alignment explanation
Indices: 17407799--17407842 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17407789 ATAAAACCCT
* *
17407799 TTATTAATTATTATTAATA
1 TTATTAATTACTACTAATA
* *
17407818 TTATTTATTACTGCTAATA
1 TTATTAATTACTACTAATA
17407837 TTATTA
1 TTATTA
17407843 GTGTCATTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (19 bp):
TTATTAATTACTACTAATA
Found at i:17407825 original size:16 final size:18
Alignment explanation
Indices: 17407800--17407841 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
17407790 TAAAACCCTT
*
17407800 TATTAATTATTA-T-TAA
1 TATTATTTATTACTCTAA
17407816 TATTATTTATTACTGCTAA
1 TATTATTTATTACT-CTAA
17407835 TATTATT
1 TATTATT
17407842 AGTGTCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 11 0.50
17 1 0.05
19 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTATTTATTACTCTAA
Found at i:17408601 original size:26 final size:26
Alignment explanation
Indices: 17408565--17408614 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
17408555 TGCCCCTCTT
17408565 TGCTTGTTGTTGTGTAACAGGAACGA
1 TGCTTGTTGTTGTGTAACAGGAACGA
17408591 TGCTTGTTGTTGTGTAACAGGAAC
1 TGCTTGTTGTTGTGTAACAGGAAC
17408615 AAAGCAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (26 bp):
TGCTTGTTGTTGTGTAACAGGAACGA
Found at i:17408860 original size:38 final size:37
Alignment explanation
Indices: 17408818--17409609 Score: 254
Period size: 38 Copynumber: 21.2 Consensus size: 37
17408808 CTCTTATTCG
17408818 ATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCA
1 ATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCA
* * * *
17408856 ATTTCAAGTGGGTAGCAA-A--TGATGT-TGCTCT-TACTTCA
1 ATTTC-AG-AGATA--AAGACTTG-T-TATCCACTCTACTTCA
* * *
17408894 ATTTTCAGAGATGACGACTTGTTGTCCAACTCTACTTCA
1 A-TTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCA
* ** *
17408933 ATTTCAAGAAGAT-AGGAAATG--A-CCTTGCTCTTACTTCA
1 ATTTC-AG-AGATAAAGACTTGTTATCC--ACTC-TACTTCA
*
17408971 ATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCA
1 ATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCA
*
17409009 ATTTCAAGAGGATGGGAAAAGATCTTG-----CTCT-TACTTCA
1 ATTTC-AGA-GAT----AAAGA-CTTGTTATCCACTCTACTTCA
* * *
17409047 ATTTTCAGAGATGACGACTTGTTGTCCAACTCTACTTCA
1 A-TTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCA
* *** **
17409086 ATTTCAAGAGGAT-AGGAAAAG--ATCTTGCTCTTACTTCA
1 ATTTC-AGA-GATAAAGACTTGTTATC-CACTC-TACTTCA
*
17409124 ATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCA
1 ATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCA
* *** **
17409162 ATTTCAAGAGGAT-AGGAAAAG--ATCTTGCTCTTACTTCA
1 ATTTC-AGA-GATAAAGACTTGTTATC-CACTC-TACTTCA
17409200 ATTTCAGAGATAAAGACTTGTTATCTCACTCTACTTCA
1 ATTTCAGAGATAAAGACTTGTTATC-CACTCTACTTCA
* * *
17409238 ATTTCAAGAGGATAGGAA-ACGATG-T-TGCTCT-TACTTCA
1 ATTTC-AGA-GATA--AAGAC-TTGTTATCCACTCTACTTCA
*
17409276 ATTTCAGAGATAATGACTTGTTATCCCACTCTACTTCA
1 ATTTCAGAGATAAAGACTTGTTAT-CCACTCTACTTCA
* * *
17409314 ATTTCAAGAGGATAGGAA-ACGATG-T-TGCTCT-TACTTCA
1 ATTTC-AGA-GATA--AAGAC-TTGTTATCCACTCTACTTCA
*
17409352 ATTTCAGAGATAATGACTTGTTATCCAGCTCTACTTCA
1 ATTTCAGAGATAAAGACTTGTTATCCA-CTCTACTTCA
** * * *
17409390 ATTTCA-AGAGGATGAC--G-T-TGCTCT-TACTTCA
1 ATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCA
* *
17409421 ATTTCAGAGATAAAGACGTGTTATCCAACTTTACTTCA
1 ATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCA
* * ** ** *
17409459 ATTTCAAGCGGATAGGAAAAAAT-TT-GGCTC-CTACTTCA
1 ATTTC-AG-AGATA--AAGACTTGTTATCCACTCTACTTCA
*
17409497 ATTTCGGAGATAAAGACTTGTTATCCACTCTACTTCA
1 ATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCA
* *
17409534 ATTTTAAGAGGAT--AGACGTTGCT-T----T-TACTTCA
1 A-TTTCAGA-GATAAAGAC-TTGTTATCCACTCTACTTCA
* * *
17409566 ATTTCAGAGATAAAGACGTGTTATCCAACTTTACTCCA
1 ATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCA
17409604 ATTTCA
1 ATTTCA
17409610 AGCGGACAGA
Statistics
Matches: 557, Mismatches: 100, Indels: 194
0.65 0.12 0.23
Matches are distributed among these distances:
30 3 0.01
31 22 0.04
32 26 0.05
33 6 0.01
34 12 0.02
35 11 0.02
36 33 0.06
37 80 0.14
38 206 0.37
39 89 0.16
40 37 0.07
41 10 0.02
42 13 0.02
44 5 0.01
45 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (37 bp):
ATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCA
Found at i:17409017 original size:76 final size:76
Alignment explanation
Indices: 17408802--17409629 Score: 1114
Period size: 76 Copynumber: 11.1 Consensus size: 76
17408792 TCGAGGCTTT
* *
17408802 ATCTTGCTCTTA-TTCGATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGTG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
* * *
17408866 GGTAGCAAATG
66 GATAGGAAAAG
* * * *
17408877 ATGTTGCTCTTACTTCAATTTTCAGAGATGACGACTTGTTGTCCAACTCTACTTCAATTTCAAGA
1 ATCTTGCTCTTACTTCAA-TTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
* *
17408942 AGATAGGAAATG
65 GGATAGGAAAAG
* *
17408954 ACCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
17409019 GATGGGAAAAG
66 GATAGGAAAAG
* * *
17409030 ATCTTGCTCTTACTTCAATTTTCAGAGATGACGACTTGTTGTCCAACTCTACTTCAATTTCAAGA
1 ATCTTGCTCTTACTTCAA-TTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
17409095 GGATAGGAAAAG
65 GGATAGGAAAAG
*
17409107 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
17409172 GATAGGAAAAG
66 GATAGGAAAAG
17409183 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCTC-ACTCTACTTCAATTTCAAGA
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATC-CAACTCTACTTCAATTTCAAGA
*
17409247 GGATAGGAAACG
65 GGATAGGAAAAG
* * *
17409259 ATGTTGCTCTTACTTCAATTTCAGAGATAATGACTTGTTATCCCACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
17409324 GATAGGAAACG
66 GATAGGAAAAG
* * *
17409335 ATGTTGCTCTTACTTCAATTTCAGAGATAATGACTTGTTATCCAGCTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
17409400 GAT--G--ACG
66 GATAGGAAAAG
* * *
17409407 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
17409469 GATAGGAAAAA
66 GATAGGAAAAG
* * *
17409480 AT-TTGGCTCCTACTTCAATTTCGGAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTTAAGA
1 ATCTT-GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
*
17409543 GGATA-G--ACG
65 GGATAGGAAAAG
* * * * *
17409552 ---TTGCTTTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTCCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
* * *
17409614 GACAGAAAAAA
66 GATAGGAAAAG
17409625 ATCTT
1 ATCTT
17409630 ACTGTGGTCT
Statistics
Matches: 679, Mismatches: 55, Indels: 37
0.88 0.07 0.05
Matches are distributed among these distances:
69 94 0.14
70 22 0.03
71 1 0.00
72 4 0.01
73 2 0.00
74 2 0.00
75 36 0.05
76 377 0.56
77 141 0.21
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
GATAGGAAAAG
Found at i:17409100 original size:153 final size:152
Alignment explanation
Indices: 17408804--17409629 Score: 1101
Period size: 153 Copynumber: 5.5 Consensus size: 152
17408794 GAGGCTTTAT
* * *
17408804 CTTGCTCTTA-TTCGATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGTGGG
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
* * * * * *
17408868 TAGCAAATGATGTTGCTCTTACTTCAATTTTCAGAGATGACGACTTGTTGTCCAACTCTACTTCA
66 TAGGAAAAGATCTTGCTCTTACTTCAA-TTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCA
*
17408933 ATTTCAAGAAGATAGGAAATGAC
130 ATTTCAAGAGGATAGGAAATGAC
*
17408956 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGA
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
* * * *
17409021 TGGGAAAAGATCTTGCTCTTACTTCAATTTTCAGAGATGACGACTTGTTGTCCAACTCTACTTCA
66 TAGGAAAAGATCTTGCTCTTACTTCAA-TTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCA
* *
17409086 ATTTCAAGAGGATAGGAAAAGAT
130 ATTTCAAGAGGATAGGAAATGAC
*
17409109 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGA
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
17409174 TAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCTC-ACTCTACTTCA
66 TAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATC-CAACTCTACTTCA
* *
17409238 ATTTCAAGAGGATAGGAAACGAT
130 ATTTCAAGAGGATAGGAAATGAC
* * *
17409261 GTTGCTCTTACTTCAATTTCAGAGATAATGACTTGTTATCCCACTCTACTTCAATTTCAAGAGGA
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
* * * *
17409326 TAGGAAACGATGTTGCTCTTACTTCAATTTCAGAGATAATGACTTGTTATCCAGCTCTACTTCAA
66 TAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAA
17409391 TTTC-A-A-G--AGG--ATGAC
131 TTTCAAGAGGATAGGAAATGAC
* * * *
17409406 GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGCGGA
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
* * *
17409471 TAGGAAAAAAT-TTGGCTCCTACTTCAATTTCGGAGATAAAGACTTGTTATCC-ACTCTACTTCA
66 TAGGAAAAGATCTT-GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCA
*
17409534 ATTTTAAGAGGAT-----A-GAC
130 ATTTCAAGAGGATAGGAAATGAC
* * * * * *
17409551 GTTGCTTTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTCCAATTTCAAGCGGA
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
* * *
17409616 CAGAAAAAAATCTT
66 TAGGAAAAGATCTT
17409630 ACTGTGGTCT
Statistics
Matches: 622, Mismatches: 42, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
144 16 0.03
145 183 0.29
146 4 0.01
147 4 0.01
149 1 0.00
150 1 0.00
151 2 0.00
152 188 0.30
153 223 0.36
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (152 bp):
CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
TAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAA
TTTCAAGAGGATAGGAAATGAC
Found at i:17421669 original size:59 final size:60
Alignment explanation
Indices: 17421560--17421949 Score: 498
Period size: 59 Copynumber: 6.6 Consensus size: 60
17421550 TTTGGACACC
* * * *
17421560 CGGGGGCAAAATGGTAA-TTATGGT-AAAGTCGAGGTTAAAAAATAGAATTTTTA-AGAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTT-AAAAATAGAATTTTTAGAAAGTT
* *
17421619 CGAGGGTAAAACT-GTAATTTTTGGTGAAATCGGGGTTAAAAATAGTA-TTTTAGAAAGTT
1 CGGGGGTAAAA-TGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTT
* * *
17421678 TGGGGGTAAAATGGTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAA-TTTT-GGAAGTT
1 CGGGGGTAAAATGGTAATTTTT-GGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTT
**
17421737 TAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATAGAA-TTTTAGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTT
* * * *
17421795 CGGGGGTAAAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAA-TTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTT
*
17421854 CGGGGGT-AAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTTAGAAAGTT
1 CGGGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTT
17421913 CGGGGGTAAAATGGTAATTTTTGGGTGAAATCGGGGT
1 CGGGGGTAAAATGGTAATTTTT-GGTGAAATCGGGGT
17421950 CAGAATGTAT
Statistics
Matches: 297, Mismatches: 23, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
57 13 0.04
58 68 0.23
59 149 0.50
60 64 0.22
61 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (60 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAGAAAGTT
Found at i:17421832 original size:176 final size:177
Alignment explanation
Indices: 17421562--17421949 Score: 527
Period size: 176 Copynumber: 2.2 Consensus size: 177
17421552 TGGACACCCG
* * * *
17421562 GGGGCAAAATGGTAA-TTATGGT-AAAGTCGAGGTTAAAAAATAGAATTTTTAAGAGTTCGAGGG
1 GGGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTT-AAAAATAGAATTTTTAAAAGTTCGAGGG
* * *
17421625 TAAAACTGTAATTTTTGGTGAAATCGGGGTTAAAAATAGTATTTTAGAAAGTTTGGGGGTAAAAT
64 TAAAACTGTAATTTTTGATGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCGGGGGT-AAAT
* *
17421690 GGTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTT-GGAAGTTTA
128 GGTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCA
*
17421739 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATAGAA-TTTTAGAAAGTTCGGGGGT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTA-AAAGTTCGAGGGT
* * *
17421802 AAAA-TGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAATG
65 AAAACT-GTAATTTTTGATGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCGGGGGTAAATG
* * * *
17421866 GTAATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCG
129 GTAATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCA
17421915 GGGGTAAAATGGTAATTTTTGGGTGAAATCGGGGT
1 GGGGTAAAATGGTAATTTTT-GGTGAAATCGGGGT
17421950 CAGAATGTAT
Statistics
Matches: 188, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
175 47 0.25
176 97 0.52
177 28 0.15
178 13 0.07
179 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (177 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTAAAAGTTCGAGGGTA
AAACTGTAATTTTTGATGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCGGGGGTAAATGGT
AATTTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTCA
Found at i:17422692 original size:12 final size:11
Alignment explanation
Indices: 17422675--17422720 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
17422665 CAAGGTAGTA
17422675 TTTCTTCTCTTT
1 TTTCTTCT-TTT
17422687 TTTCTTCTTTT
1 TTTCTTCTTTT
*
17422698 TTGTTTTCTTTT
1 TT-TCTTCTTTT
17422710 TTTCTTTCTTT
1 TTTC-TTCTTT
17422721 ATTGTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 6 0.20
12 24 0.80
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTCTTCTTTT
Found at i:17422714 original size:23 final size:25
Alignment explanation
Indices: 17422679--17422726 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
17422669 GTAGTATTTC
*
17422679 TTCTCTTTTTTC-TTCTTTTTTGTT
1 TTCTCTTTTTTCTTTCTTTATTGTT
17422703 TTCT-TTTTTTCTTTCTTTATTGTT
1 TTCTCTTTTTTCTTTCTTTATTGTT
17422727 AAAACAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (25 bp):
TTCTCTTTTTTCTTTCTTTATTGTT
Found at i:17423000 original size:16 final size:16
Alignment explanation
Indices: 17422981--17423018 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
17422971 TCTTCTTTTA
17422981 TTATTATTATTAATAT
1 TTATTATTATTAATAT
17422997 TTATTATTATTAATAT
1 TTATTATTATTAATAT
17423013 TATATT
1 T-TATT
17423019 TAATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATTATTAATAT
Found at i:17423055 original size:19 final size:19
Alignment explanation
Indices: 17422978--17423076 Score: 57
Period size: 19 Copynumber: 5.3 Consensus size: 19
17422968 TTATCTTCTT
17422978 TTATT-ATTATTATTAATA
1 TTATTAATTATTATTAATA
17422996 -T-TT-ATTATTATTAATA
1 TTATTAATTATTATTAATA
* * *
17423012 TTA-TATTTAATA-TAAAA
1 TTATTAATTATTATTAATA
17423029 CCCTTTATTAATTATTATTAATA
1 ----TTATTAATTATTATTAATA
* * **
17423052 TTATTTATTACTGCTAATA
1 TTATTAATTATTATTAATA
17423071 TTATTA
1 TTATTA
17423077 GTGTCATTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
16 15 0.25
17 7 0.11
18 5 0.08
19 20 0.33
21 3 0.05
22 7 0.11
23 4 0.07
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (19 bp):
TTATTAATTATTATTAATA
Found at i:17423059 original size:16 final size:18
Alignment explanation
Indices: 17423034--17423075 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
17423024 TAAAACCCTT
*
17423034 TATTAATTATTA-T-TAA
1 TATTATTTATTACTCTAA
17423050 TATTATTTATTACTGCTAA
1 TATTATTTATTACT-CTAA
17423069 TATTATT
1 TATTATT
17423076 AGTGTCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 11 0.50
17 1 0.05
19 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTATTTATTACTCTAA
Found at i:17423764 original size:17 final size:17
Alignment explanation
Indices: 17423742--17423809 Score: 77
Period size: 16 Copynumber: 4.1 Consensus size: 17
17423732 TTAATTTATT
* *
17423742 AATTTAATATCATTTTA
1 AATTTAATATAAATTTA
17423759 AATTTAAT-TAAATTTA
1 AATTTAATATAAATTTA
* *
17423775 AATTTAAGATAAGTTTA
1 AATTTAATATAAATTTA
*
17423792 AATTTAA-ATAAAATTA
1 AATTTAATATAAATTTA
17423808 AA
1 AA
17423810 AATTAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 22 0.50
17 22 0.50
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (17 bp):
AATTTAATATAAATTTA
Found at i:17429453 original size:3 final size:3
Alignment explanation
Indices: 17429447--17429516 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
17429437 TTATAAAACA
17429447 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17429494 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
17429517 AGCTGACACA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17434488 original size:21 final size:22
Alignment explanation
Indices: 17434462--17434512 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
17434452 AAGTAATAAA
17434462 AATAAAAATTAT-AAAAATTAT
1 AATAAAAATTATAAAAAATTAT
17434483 AATAAAAA-TATAAAAAATTAT
1 AATAAAAATTATAAAAAATTAT
17434504 --TAAAAATTA
1 AATAAAAATTA
17434513 GAATTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.21
20 5 0.18
21 17 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAAAAATTATAAAAAATTAT
Found at i:17434507 original size:11 final size:10
Alignment explanation
Indices: 17434465--17434512 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
17434455 TAATAAAAAT
17434465 AAAAATTAT-
1 AAAAATTATA
17434474 AAAAATTATA
1 AAAAATTATA
*
17434484 ATAAAAATATA
1 A-AAAATTATA
*
17434495 AAAAATTATT
1 AAAAATTATA
17434505 AAAAATTA
1 AAAAATTA
17434513 GAATTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 9 0.26
10 16 0.47
11 9 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:17434537 original size:29 final size:29
Alignment explanation
Indices: 17434495--17434557 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
17434485 TAAAAATATA
* *
17434495 AAAAATTATTAAAAATTAG-AATTTTTTAT
1 AAAAATCATAAAAAATT-GTAATTTTTTAT
17434524 AAAAATCATAAAAAATTGTAATTTTTTAT
1 AAAAATCATAAAAAATTGTAATTTTTTAT
17434553 AAAAA
1 AAAAA
17434558 ATTGTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAAATCATAAAAAATTGTAATTTTTTAT
Found at i:17434556 original size:20 final size:20
Alignment explanation
Indices: 17434531--17434580 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
17434521 TATAAAAATC
17434531 ATAAAAAATTGTAATTTTTT
1 ATAAAAAATTGTAATTTTTT
17434551 ATAAAAAATTGTAATTTTTT
1 ATAAAAAATTGTAATTTTTT
17434571 ATAAAAAATT
1 ATAAAAAATT
17434581 ATAAAATGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
ATAAAAAATTGTAATTTTTT
Found at i:17434847 original size:10 final size:10
Alignment explanation
Indices: 17434805--17434907 Score: 71
Period size: 10 Copynumber: 10.9 Consensus size: 10
17434795 ACTTTGTAAA
17434805 ATTTTATAATT
1 ATTTTATAA-T
17434816 ATTTT-T-AT
1 ATTTTATAAT
*
17434824 -TTTTCTATAT
1 ATTTTATA-AT
17434834 ATTTTATAAT
1 ATTTTATAAT
17434844 ATTTTATAAT
1 ATTTTATAAT
17434854 A-TTTATAA-
1 ATTTTATAAT
17434862 ATTTTAT--T
1 ATTTTATAAT
*
17434870 -TTTTATAGT
1 ATTTTATAAT
* *
17434879 TTTTTATTAAA
1 ATTTTA-TAAT
*
17434890 ATTTAATAAT
1 ATTTTATAAT
17434900 -TTTTATAA
1 ATTTTATAA
17434908 CTTTTATTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
7 10 0.13
8 3 0.04
9 21 0.28
10 24 0.32
11 17 0.23
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:17434860 original size:28 final size:29
Alignment explanation
Indices: 17434803--17434868 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
17434793 CGACTTTGTA
* *
17434803 AAATTTTATAATTATTTTTATTTTTCTAT
1 AAATTTTATAATTATTTTTAATATTCTAT
*
17434832 ATATTTTATAA-TATTTTATAATATT-TAT
1 AAATTTTATAATTATTTT-TAATATTCTAT
17434860 AAATTTTAT
1 AAATTTTAT
17434869 TTTTTATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
AAATTTTATAATTATTTTTAATATTCTAT
Found at i:17434884 original size:45 final size:45
Alignment explanation
Indices: 17434818--17434926 Score: 141
Period size: 46 Copynumber: 2.4 Consensus size: 45
17434808 TTATAATTAT
* * *
17434818 TTTTATTTTTCTATATATTTTA-TAATATTTTATAATATTTATAAA
1 TTTTATTTTT-TATATTTTTTATTAAAATTTAATAATATTTATAAA
* *
17434863 TTTTATTTTTTATAGTTTTTTATTAAAATTTAATAATTTTTATAAC
1 TTTTATTTTTTATA-TTTTTTATTAAAATTTAATAATATTTATAAA
17434909 TTTTATTTTTT-TATTTTT
1 TTTTATTTTTTATATTTTT
17434927 GTGGTTGTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
44 9 0.16
45 18 0.32
46 30 0.53
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (45 bp):
TTTTATTTTTTATATTTTTTATTAAAATTTAATAATATTTATAAA
Found at i:17434912 original size:10 final size:9
Alignment explanation
Indices: 17434806--17434914 Score: 62
Period size: 9 Copynumber: 11.7 Consensus size: 9
17434796 CTTTGTAAAA
17434806 TTTTATAAT
1 TTTTATAAT
*
17434815 TATTT-TTAT
1 T-TTTATAAT
*
17434824 TTTTCTATAT
1 TTTTATA-AT
17434834 ATTTTATAAT
1 -TTTTATAAT
17434844 ATTTTATAAT
1 -TTTTATAAT
* *
17434854 ATTTATAAA
1 TTTTATAAT
17434863 TTTTAT--T
1 TTTTATAAT
*
17434870 TTTTATAGTT
1 TTTTATA-AT
*
17434880 TTTTATTAAAA
1 TTTTA-T-AAT
*
17434891 TTTAATAAT
1 TTTTATAAT
*
17434900 TTTTATAAC
1 TTTTATAAT
17434909 TTTTAT
1 TTTTAT
17434915 TTTTTTATTT
Statistics
Matches: 78, Mismatches: 13, Indels: 18
0.72 0.12 0.17
Matches are distributed among these distances:
7 6 0.08
8 3 0.04
9 33 0.42
10 24 0.31
11 11 0.14
12 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:17437186 original size:121 final size:116
Alignment explanation
Indices: 17436972--17437321 Score: 456
Period size: 121 Copynumber: 3.0 Consensus size: 116
17436962 TTAGGATTTG
17436972 TTTGTTTCTTTTATTTTTTATTTTTAAATTATTTAAAATATGTTTCTAACAAATTAAGGAATTAA
1 TTTGTTTC-TTTA-TTTTT-TTTTTAAATTATTTAAAATATGTTTCTAACAAATTAAGGAATTAA
17437037 TTTTTAATAGGTTTAAAGCAACAGTTTTGACAATTTCTAGAGAATGGTTCAAGGGA
63 TTTTTAATAGGTTTAAAGCAACAGTTTTGACAATTTCTA-A-AATGGTTCAAGGGA
*
17437093 TTTGTTTCTTTCATTTTTTGTCTTTAAATTATTTAAAATATGTTTCTAACAAATTAAGGAGTTAA
1 TTTGTTTCTTT-ATTTTTT-T-TTTAAATTATTTAAAATATGTTTCTAACAAATTAAGGAATTAA
17437158 TTTTTAATAGGTTTAAAGCAACAGTTTTGACAATTTCT----TGGTTCAAGGGA
63 TTTTTAATAGGTTTAAAGCAACAGTTTTGACAATTTCTAAAATGGTTCAAGGGA
* *
17437208 --------TTTA-TTTCTTTTTAAATTATTTAATATATGTTTCTAACAAATTAAGGAATTAATTT
1 TTTGTTTCTTTATTTTTTTTTTAAATTATTTAAAATATGTTTCTAACAAATTAAGGAATTAATTT
* * *
17437264 TTAATAGGTTTAAAAGCAATAGCTTTGACAATTTCTAAAAATTGGTTCAATGGA
66 TTAATAGGTTT-AAAGCAACAGTTTTGACAATTTCT-AAAA-TGGTTCAAGGGA
17437318 TTTG
1 TTTG
17437322 AAATTTTTCT
Statistics
Matches: 208, Mismatches: 7, Indels: 35
0.83 0.03 0.14
Matches are distributed among these distances:
103 55 0.26
104 23 0.11
105 4 0.02
106 1 0.00
107 3 0.01
110 11 0.05
115 12 0.06
119 1 0.00
120 9 0.04
121 89 0.43
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (116 bp):
TTTGTTTCTTTATTTTTTTTTTAAATTATTTAAAATATGTTTCTAACAAATTAAGGAATTAATTT
TTAATAGGTTTAAAGCAACAGTTTTGACAATTTCTAAAATGGTTCAAGGGA
Found at i:17443498 original size:4 final size:4
Alignment explanation
Indices: 17443479--17443542 Score: 51
Period size: 4 Copynumber: 16.2 Consensus size: 4
17443469 CCAACGTGAG
* * * * *
17443479 AAGA AGGA AA-A AAGA AAGA AAAA AAAA AAGA AAGA TAGA AAGG AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
*
17443525 AAGG AAGA AAGA GAAGA A
1 AAGA AAGA AAGA -AAGA A
17443543 GATAATGTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
3 6 0.12
4 39 0.80
5 4 0.08
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:17443707 original size:18 final size:18
Alignment explanation
Indices: 17443684--17443718 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17443674 GGAAGAAATG
17443684 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
17443702 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
17443719 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:17443812 original size:23 final size:23
Alignment explanation
Indices: 17443738--17443815 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
17443728 TTTAAAATAT
*
17443738 TTTAATTTGTTAGTTAATTTGATCA
1 TTTAATTT-TTA-TTAATTTGATTA
* * *
17443763 TTTTAAGTTTT-TTATTTTGTTTAA
1 -TTTAATTTTTATTAATTTGATT-A
17443787 TTTAATTTTTAATTAATTTG-TTA
1 TTTAATTTTT-ATTAATTTGATTA
17443810 TTTAAT
1 TTTAAT
17443816 GTTGTTATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
23 24 0.56
24 3 0.07
25 9 0.21
26 7 0.16
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.64
Consensus pattern (23 bp):
TTTAATTTTTATTAATTTGATTA
Found at i:17444672 original size:15 final size:15
Alignment explanation
Indices: 17444652--17444698 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
17444642 AACCTAGCTA
17444652 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
17444667 ATTAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
17444682 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
17444698 A
1 A
17444699 ATATCCTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:17444696 original size:16 final size:16
Alignment explanation
Indices: 17444650--17444700 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
17444640 TAAACCTAGC
17444650 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
17444666 T-ATTAATATA-AAAAA
1 TAATTAAT-TACCAAAA
17444681 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
17444697 TAAT
1 TAAT
17444701 ATCCTCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:17448181 original size:24 final size:24
Alignment explanation
Indices: 17448154--17448206 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
17448144 TAGCCCATAA
* *
17448154 GAGCTCAAAATGGTTAGCTCTTAC
1 GAGCCCAAAATGATTAGCTCTTAC
*
17448178 GAGCCCAGAATGATTAGCTCTTAC
1 GAGCCCAAAATGATTAGCTCTTAC
*
17448202 AAGCC
1 GAGCC
17448207 TAGAATCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
GAGCCCAAAATGATTAGCTCTTAC
Found at i:17448211 original size:24 final size:24
Alignment explanation
Indices: 17448162--17448212 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
17448152 AAGAGCTCAA
* *
17448162 AATGGTTAGCTCTTACGAGCCCAG
1 AATGATTAGCTCTTACAAGCCCAG
*
17448186 AATGATTAGCTCTTACAAGCCTAG
1 AATGATTAGCTCTTACAAGCCCAG
17448210 AAT
1 AAT
17448213 CAGAATAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (24 bp):
AATGATTAGCTCTTACAAGCCCAG
Found at i:17448242 original size:27 final size:27
Alignment explanation
Indices: 17448210--17448273 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
17448200 ACAAGCCTAG
*
17448210 AATCAGAATAACACTTTTTTGAGCCAA
1 AATCAGAATAACACTCTTTTGAGCCAA
*
17448237 AATCAGAATAACGCTCTTTTGAGCCAA
1 AATCAGAATAACACTCTTTTGAGCCAA
*
17448264 AATCAAAATA
1 AATCAGAATA
17448274 CTCATCAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (27 bp):
AATCAGAATAACACTCTTTTGAGCCAA
Found at i:17452682 original size:4 final size:4
Alignment explanation
Indices: 17452673--17452740 Score: 75
Period size: 4 Copynumber: 17.0 Consensus size: 4
17452663 TTTCTCCTTC
* * * * *
17452673 TTCT TTCT TTCCT CTCC TTC- TTCC TTCC TTCC TTCT TTCT TTCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
17452721 TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT
17452741 CGTTTATTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.05
4 52 0.90
5 3 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTCT
Found at i:17452690 original size:20 final size:20
Alignment explanation
Indices: 17452665--17452723 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
17452655 ACACTACCTT
17452665 TCTCCTTCTTCTTTCTTTCC
1 TCTCCTTCTTCTTTCTTTCC
* *
17452685 TCTCCTTCTTCCTTCCTTCC
1 TCTCCTTCTTCTTTCTTTCC
*
17452705 T-TCTTTCTTTCTTTCTTTC
1 TCTCCTTC-TTCTTTCTTTC
17452724 TTTCTTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTCCTTCTTCTTTCTTTCC
Found at i:17452851 original size:19 final size:19
Alignment explanation
Indices: 17452827--17452865 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17452817 TTTACAATCA
* *
17452827 AAATAAAATCAACATACAC
1 AAATAAAATAAACACACAC
17452846 AAATAAAATAAACACACAC
1 AAATAAAATAAACACACAC
17452865 A
1 A
17452866 CGGCATAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.13
Consensus pattern (19 bp):
AAATAAAATAAACACACAC
Found at i:17455195 original size:104 final size:104
Alignment explanation
Indices: 17455021--17455213 Score: 262
Period size: 104 Copynumber: 1.9 Consensus size: 104
17455011 ATACATTGGA
* * **
17455021 CCTTTTGACGCGAAATGAAATGACACCCAAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCT
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCT
* *
17455086 CAATTTTTTTCTTCTCTCTTTTTTTTAGAATGCGTTAGC
66 CAATTTATTTATTCTCTCTTTTTTTTAGAATGCGTTAGC
* * * *
17455125 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCTACCCCGGTTACTCAGTCTAACACATTC-
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCT
* *
17455189 CGAATTTATTTATTTTTTCTTTTTT
66 C-AATTTATTTATTCTCTCTTTTTT
17455214 ATTCGGGTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
103 1 0.01
104 75 0.99
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (104 bp):
CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCT
CAATTTATTTATTCTCTCTTTTTTTTAGAATGCGTTAGC
Found at i:17456010 original size:8 final size:8
Alignment explanation
Indices: 17455964--17456013 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
17455954 TTCCTGGACA
17455964 AAAATAAAT
1 AAAA-AAAT
*
17455973 AAATAAAT
1 AAAAAAAT
17455981 AAAATAAGAT
1 AAAA-AA-AT
*
17455991 AGAAAAAT
1 AAAAAAAT
17455999 AAAAAAAT
1 AAAAAAAT
17456007 AAAAAAA
1 AAAAAAA
17456014 ATAATTGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 23 0.66
9 7 0.20
10 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:17458629 original size:16 final size:16
Alignment explanation
Indices: 17458588--17458629 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
17458578 GAAACGGAAT
17458588 TAAAAATAAAAGAAAG
1 TAAAAATAAAAGAAAG
* *
17458604 TATAATTAAAAGAAA-
1 TAAAAATAAAAGAAAG
17458619 TAGAAAATAAA
1 TA-AAAATAAA
17458630 GAAGTTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAAGAAAG
Found at i:17459449 original size:19 final size:19
Alignment explanation
Indices: 17459425--17459467 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17459415 AAATATAAAT
17459425 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
17459444 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
17459463 TAAAT
1 TAAAT
17459468 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:17460512 original size:9 final size:9
Alignment explanation
Indices: 17460454--17460512 Score: 64
Period size: 9 Copynumber: 6.2 Consensus size: 9
17460444 AATTAAAAAA
17460454 TTATAAATTT
1 TTAT-AATTT
*
17460464 TTATAAGTT
1 TTATAATTT
17460473 TTATAATTTT
1 TTATAA-TTT
*
17460483 TTAATAATGT
1 TT-ATAATTT
*
17460493 TAATAATTT
1 TTATAATTT
17460502 TTATAATTT
1 TTATAATTT
17460511 TT
1 TT
17460513 TACTTTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
9 26 0.63
10 11 0.27
11 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TTATAATTT
Found at i:17465684 original size:17 final size:17
Alignment explanation
Indices: 17465662--17465696 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17465652 AATAGGGAAA
17465662 GTAATCTTAA-AAGATTT
1 GTAATC-TAATAAGATTT
17465679 GTAATCTAATAAGATTT
1 GTAATCTAATAAGATTT
17465696 G
1 G
17465697 GTTTTGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (17 bp):
GTAATCTAATAAGATTT
Done.