Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
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 54 of 171
Found at i:21839954 original size:31 final size:31
Alignment explanation
Indices: 21839916--21840026 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 31
21839906 GGGGGTTACA
21839916 ACTTCAATTTCAAGAGGATGACGTTGCTCTT
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTT
* ** * * *
21839947 ACTTCAATTTCGGAGATAAAGACTTGATATCCAACTCT
1 ACTTCAATTTC-AAGAGGATGAC--G-T-TGC-TCT-T
21839985 ACTTCAATTTCAAGAGGATGACGTTGCTCTT
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTT
21840016 ACTTCAATTTC
1 ACTTCAATTTC
21840027 GGAGATAAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
31 23 0.38
32 9 0.15
33 2 0.03
34 2 0.03
35 2 0.03
36 2 0.03
37 9 0.15
38 12 0.20
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (31 bp):
ACTTCAATTTCAAGAGGATGACGTTGCTCTT
Found at i:21840027 original size:69 final size:69
Alignment explanation
Indices: 21839916--21840073 Score: 300
Period size: 69 Copynumber: 2.3 Consensus size: 69
21839906 GGGGGTTACA
21839916 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAA
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAA
21839981 CTCT
66 CTCT
21839985 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAA
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAA
21840050 CTCT
66 CTCT
*
21840054 ACTTCAATTT-GAGAGGATGA
1 ACTTCAATTTCAAGAGGATGA
21840074 AGACGTGTTA
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
68 9 0.10
69 79 0.90
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (69 bp):
ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAA
CTCT
Found at i:21840111 original size:39 final size:39
Alignment explanation
Indices: 21840015--21840112 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 39
21840005 ACGTTGCTCT
* * *
21840015 TACTTCAATTTC-GGAGATAAAGACTTGATATCCAACTC
1 TACTTCAATTTCAGGGGATGAAGACGTGATATCCAACTC
* * *
21840053 TACTTCAATTTGAGAGGATGAAGACGTGTTATCC-ACTC
1 TACTTCAATTTCAGGGGATGAAGACGTGATATCCAACTC
21840091 TACTTCAATTTCAAGGGGATGA
1 TACTTCAATTTC-AGGGGATGA
21840113 CGTTGAGACC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 26 0.52
39 24 0.48
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (39 bp):
TACTTCAATTTCAGGGGATGAAGACGTGATATCCAACTC
Found at i:21852091 original size:58 final size:58
Alignment explanation
Indices: 21852023--21852449 Score: 467
Period size: 58 Copynumber: 7.3 Consensus size: 58
21852013 TATGGATACC
* * *
21852023 CGGGGCAAAATGGTAATTTT-GGTGTAATCGGGATTAAAATATGGAATTTTAAAAGCTT
1 CGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAA-ATGGAATTTTAAAAGCTT
* * * *
21852081 CGGGGTAAAATGGCAATTTTCGGTGAAATTGGGGTT-AGAATGGAATTTTAGAAGCTT
1 CGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* * ** *
21852138 TGAGGGTAAAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATAAAATTTT-AGAGCTT
1 CG-GGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* * * *
21852196 CAAGGGTAAAATGGTAATTTTTGGTGAAATCGGGG-TAAAAATAGAATTTTAAAAGTTT
1 C-GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* * * *
21852254 CGAGGGTAAAATGATAATTTTCGATGAAATCGAGGGTTAAAGACGGAATTTTAGAAA-CTT
1 CG-GGGTAAAATGGTAATTTTCGGTGAAATCG-GGGTTAAAAATGGAATTTTA-AAAGCTT
* *
21852314 CGAGGGTAAAAT-GTAATTTT-GGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
1 CG-GGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* * *
21852371 CGAGGGGTAAAATGGTAATTTTCAGTGAAATCGGGGTTAAAAACGGAA-TTTAAAA-ATT
1 C--GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
*
21852429 AAGGGGTAAAATGGTAATTTT
1 -CGGGGTAAAATGGTAATTTT
21852450 TGAAAGTTTT
Statistics
Matches: 315, Mismatches: 39, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
56 2 0.01
57 74 0.23
58 138 0.44
59 47 0.15
60 51 0.16
61 3 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (58 bp):
CGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
Found at i:21852114 original size:29 final size:29
Alignment explanation
Indices: 21852082--21852178 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
21852072 TAAAAGCTTC
21852082 GGGG-TAAAATGGCAATTTTCGGTGAAATT
1 GGGGTTAAAATGG-AATTTTCGGTGAAATT
* * ** **
21852111 GGGGTTAGAATGGAATTTTAGAAG-CTTT
1 GGGGTTAAAATGGAATTTTCGGTGAAATT
* *
21852139 GAGGG-TAAAATGGTAATTTTCAGTGAAATC
1 G-GGGTTAAAATGG-AATTTTCGGTGAAATT
21852169 GGGGTTAAAA
1 GGGGTTAAAA
21852179 ATAAAATTTT
Statistics
Matches: 49, Mismatches: 14, Indels: 9
0.68 0.19 0.12
Matches are distributed among these distances:
28 10 0.20
29 25 0.51
30 14 0.29
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (29 bp):
GGGGTTAAAATGGAATTTTCGGTGAAATT
Found at i:21852289 original size:30 final size:29
Alignment explanation
Indices: 21852139--21852352 Score: 87
Period size: 30 Copynumber: 7.3 Consensus size: 29
21852129 TAGAAGCTTT
* *
21852139 GAGGGTAAAATGGTAATTTTCAGTGAAATC
1 GAGGGTAAAATGATAATTTTGA-TGAAATC
* **
21852169 G-GGGTTAAAAAT-AAAATTTT-A-GAGCTTC
1 GAGGG-T-AAAATGATAATTTTGATGA-AATC
* * *
21852197 AAGGGTAAAATGGTAATTTTTGGTGAAATC
1 GAGGGTAAAATGATAA-TTTTGATGAAATC
*
21852227 G-GGGTAAAAAT-AGAATTTT-A--AAAGTTTC
1 GAGGGT-AAAATGATAATTTTGATGAAA---TC
21852255 GAGGGTAAAATGATAATTTTCGATGAAATC
1 GAGGGTAAAATGATAATTTT-GATGAAATC
* *
21852285 GAGGGTTAAA-GACGGAATTTT-A-GAAACTTC
1 GAGGGTAAAATGA--TAATTTTGATGAAA--TC
*
21852315 GAGGGTAAAATG-TAATTTTGGTGAAATC
1 GAGGGTAAAATGATAATTTTGATGAAATC
21852343 G-GGGTTAAAA
1 GAGGG-TAAAA
21852353 ACGGAATTTT
Statistics
Matches: 138, Mismatches: 20, Indels: 54
0.65 0.09 0.25
Matches are distributed among these distances:
25 3 0.02
27 10 0.07
28 35 0.25
29 31 0.22
30 41 0.30
31 15 0.11
33 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (29 bp):
GAGGGTAAAATGATAATTTTGATGAAATC
Found at i:21852421 original size:30 final size:30
Alignment explanation
Indices: 21852269--21852421 Score: 108
Period size: 30 Copynumber: 5.2 Consensus size: 30
21852259 GTAAAATGAT
* *
21852269 AATTTTCGATGAAATCGAGGGTTAAAGACGG
1 AATTTTAG-TGAAATCGAGGGTTAAAAACGG
* *
21852300 AATTTTA--GAAACTTCGAGGG-T-AAAATGT
1 AATTTTAGTGAAA--TCGAGGGTTAAAAACGG
*
21852328 AATTTTGGTGAAATCG-GGGTTAAAAACGG
1 AATTTTAGTGAAATCGAGGGTTAAAAACGG
* * *
21852357 AATTTTA--GAAGCTTCGAGGGGT-AAAATGG
1 AATTTTAGTGAA--ATCGAGGGTTAAAAACGG
21852386 TAATTTTCAGTGAAATCG-GGGTTAAAAACGG
1 -AATTTT-AGTGAAATCGAGGGTTAAAAACGG
21852417 AATTT
1 AATTT
21852422 AAAAATTAAG
Statistics
Matches: 94, Mismatches: 14, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
27 6 0.06
28 18 0.19
29 21 0.22
30 30 0.32
31 16 0.17
33 3 0.03
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (30 bp):
AATTTTAGTGAAATCGAGGGTTAAAAACGG
Found at i:21852474 original size:29 final size:30
Alignment explanation
Indices: 21852431--21852512 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
21852421 TAAAAATTAA
*
21852431 GGGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTT
21852460 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
21852490 AGGGTCAAAATATAATTTCTGGA
1 GGGGTCAAAATGTAATTT-TGGA
21852513 CAATTTAGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
29 14 0.30
30 29 0.62
31 4 0.09
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:21852851 original size:161 final size:161
Alignment explanation
Indices: 21852582--21852926 Score: 446
Period size: 161 Copynumber: 2.1 Consensus size: 161
21852572 GTATCCAGAG
* * *
21852582 GTCAAGGGACTAATTTGA-AAACCTTGAAAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTT
1 GTCAAAGGACTAATTT-ATAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTT
* * * *
21852646 AATTCAAGGACTAAATGAAAATAAATTAAAAATAGAAGGGACTAAATGTAGAAATAAGCCAAAA-
65 AATTCAAGGACTAAATGAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAC
* *
21852710 ATTGACACGTGGCAACCTCTGGTGCAGTCAAACA
130 A-TGACACGTGGCAACCT-TGGTACAATCAAACA
* *
21852744 GTCAAAGGACTAGTTTATAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAA-ATAAAGTT
1 GTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATA-AAAGTT
* * * * * *
21852808 GATT-TAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAC
65 AATTCAAGGACTAAATGAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAC
* *
21852872 ATGACACGTGGCAATCTTGGTATAATCAAACA
130 ATGACACGTGGCAACCTTGGTACAATCAAACA
*
21852904 GTCAAAGGACTAAATTATAAACC
1 GTCAAAGGACTAATTTATAAACC
21852927 AATTAAAATT
Statistics
Matches: 159, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
160 33 0.21
161 67 0.42
162 59 0.37
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (161 bp):
GTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTTA
ATTCAAGGACTAAATGAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAACA
TGACACGTGGCAACCTTGGTACAATCAAACA
Found at i:21853781 original size:34 final size:34
Alignment explanation
Indices: 21853733--21853797 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
21853723 ATTATTAATA
* **
21853733 CATTAATATTATTAATACTGACATTTATTATAAC
1 CATTAATATCATTAATAAAGACATTTATTATAAC
* *
21853767 CATTACTATCATTAATAAAGATATTTATTAT
1 CATTAATATCATTAATAAAGACATTTATTAT
21853798 GCATTTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (34 bp):
CATTAATATCATTAATAAAGACATTTATTATAAC
Found at i:21854254 original size:19 final size:20
Alignment explanation
Indices: 21854230--21854279 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
21854220 GTGGAGCTTG
21854230 GTGGTCAGCAGAT-GAGCTA
1 GTGGTCAGCAGATGGAGCTA
*
21854249 GTGGTCAGCAGATGGAGCTG
1 GTGGTCAGCAGATGGAGCTA
*
21854269 GTGGCCAGCAG
1 GTGGTCAGCAG
21854280 CAGTAGGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.22, C:0.18, G:0.42, T:0.18
Consensus pattern (20 bp):
GTGGTCAGCAGATGGAGCTA
Found at i:21854341 original size:14 final size:14
Alignment explanation
Indices: 21854324--21854350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21854314 ATTTGGACTA
21854324 TTGTAATTGGGCCT
1 TTGTAATTGGGCCT
21854338 TTGTAATTGGGCC
1 TTGTAATTGGGCC
21854351 CTGGGCCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (14 bp):
TTGTAATTGGGCCT
Found at i:21854414 original size:6 final size:6
Alignment explanation
Indices: 21854386--21854492 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
21854376 CATTTGGACT
* * *
21854386 TTTAAA TGTTAAA TTTAATA TTTTAA TTT-TA TTTAAA TTTAAA TTCAAA
1 TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
21854435 -TTAAA TTTAAA TATTTAA TTTAAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA T-TTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
21854483 --TAAA TTTAAA
1 TTTAAA TTTAAA
21854493 ATCAATTTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
4 4 0.05
5 12 0.15
6 45 0.55
7 21 0.26
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:21854450 original size:31 final size:31
Alignment explanation
Indices: 21854415--21854477 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
21854405 ATTTTAATTT
* *
21854415 TATTTAAATTT-AAATTCAAATTAAATTTAAA
1 TATTT-AATTTAAAATTCAAAATAAATCTAAA
*
21854446 TATTTAATTTAAAATTTAAAATAAATCTAAA
1 TATTTAATTTAAAATTCAAAATAAATCTAAA
21854477 T
1 T
21854478 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAATTTAAAATTCAAAATAAATCTAAA
Found at i:21854461 original size:37 final size:36
Alignment explanation
Indices: 21854411--21854484 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
21854401 TAATATTTTA
* *
21854411 ATTTTATTTAAATTTAAATTCAAAT-TAAATTTAAAT
1 ATTTAATTTAAATTTAAAAT-AAATCTAAATTTAAAT
21854447 ATTTAATTTAAAATTTAAAATAAATCTAAATTTAAAT
1 ATTTAATTT-AAATTTAAAATAAATCTAAATTTAAAT
21854484 A
1 A
21854485 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTAATTTAAATTTAAAATAAATCTAAATTTAAAT
Found at i:21854479 original size:17 final size:17
Alignment explanation
Indices: 21854416--21854492 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
21854406 TTTTAATTTT
*
21854416 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
*
21854434 A-TTAAATTTAAATATTTA
1 ATTTAAATTTAAA-A-TAA
21854452 ATTTAAAATTTAAAATAA
1 ATTT-AAATTTAAAATAA
*
21854470 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
21854486 ATTTAAA
1 ATTTAAA
21854493 ATCAATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 12 0.24
17 17 0.34
18 8 0.16
19 4 0.08
20 9 0.18
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:21856406 original size:35 final size:34
Alignment explanation
Indices: 21856367--21856477 Score: 104
Period size: 35 Copynumber: 3.2 Consensus size: 34
21856357 TGTATGGTGA
21856367 ATATATACATACCATATATATAAAGAATAAACTAT
1 ATATATACATACCATATATA-AAAGAATAAACTAT
* * *
21856402 ATATATACATA-TA-ATTTAAGGAAGATATAAGACGA-
1 ATATATACATACCATATATAA--AAGA-ATAA-ACTAT
* *
21856437 ATATACACATACCATGTATAAAA-AATAAACTAT
1 ATATATACATACCATATATAAAAGAATAAACTAT
21856470 ATATATAC
1 ATATATAC
21856478 TAACGAAGCA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
32 4 0.07
33 15 0.25
34 6 0.10
35 27 0.45
36 4 0.07
37 4 0.07
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (34 bp):
ATATATACATACCATATATAAAAGAATAAACTAT
Found at i:21861705 original size:22 final size:21
Alignment explanation
Indices: 21861669--21861736 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
21861659 TATATTGTTG
21861669 TTTTGGTGCTATTTTTTACTA
1 TTTTGGTGCTATTTTTTACTA
* * *
21861690 TTTTGGTCTCTATTTTTTGCTG
1 TTTTGGT-GCTATTTTTTACTA
*
21861712 TTTTGGT--T-TTTTTTACTG
1 TTTTGGTGCTATTTTTTACTA
21861730 TTTTGGT
1 TTTTGGT
21861737 TTTTTTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.38
19 1 0.02
21 7 0.17
22 18 0.43
ACGTcount: A:0.07, C:0.09, G:0.18, T:0.66
Consensus pattern (21 bp):
TTTTGGTGCTATTTTTTACTA
Found at i:21861725 original size:18 final size:18
Alignment explanation
Indices: 21861702--21861755 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
21861692 TTGGTCTCTA
*
21861702 TTTTTTGCTGTTTTGGTT
1 TTTTTTACTGTTTTGGTT
21861720 TTTTTTACTGTTTTGGTT
1 TTTTTTACTGTTTTGGTT
*
21861738 TTTTTTATTGTTTTGGTT
1 TTTTTTACTGTTTTGGTT
21861756 GTTGTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.04, C:0.04, G:0.19, T:0.74
Consensus pattern (18 bp):
TTTTTTACTGTTTTGGTT
Found at i:21861822 original size:12 final size:12
Alignment explanation
Indices: 21861791--21861844 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
21861781 ATTTTGATGC
21861791 TGTTATTTTT-T
1 TGTTATTTTTGT
21861802 TG-T-TTTTTGT
1 TGTTATTTTTGT
21861812 TGTTATTTTTGT
1 TGTTATTTTTGT
*
21861824 TGCTATTTTTGT
1 TGTTATTTTTGT
*
21861836 TGTTGTTTT
1 TGTTATTTT
21861845 GCTATTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 3 0.08
12 25 0.68
ACGTcount: A:0.06, C:0.02, G:0.17, T:0.76
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:21861898 original size:20 final size:21
Alignment explanation
Indices: 21861860--21861899 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21861850 TATTTTTACT
*
21861860 GTTGTTTTGATTGTCATTTTG
1 GTTGTTTTGAATGTCATTTTG
*
21861881 GTTG-TTTGAATGTTATTTT
1 GTTGTTTTGAATGTCATTTT
21861900 TATGCGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.12, C:0.03, G:0.23, T:0.62
Consensus pattern (21 bp):
GTTGTTTTGAATGTCATTTTG
Found at i:21863954 original size:18 final size:20
Alignment explanation
Indices: 21863931--21863967 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
21863921 TTATTCTGTC
21863931 TTTTTTTA-TTTTT-TTTTT
1 TTTTTTTAGTTTTTCTTTTT
21863949 TTTTTTTAGTTTTTCTTTT
1 TTTTTTTAGTTTTTCTTTT
21863968 AGTAATTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.05, C:0.03, G:0.03, T:0.89
Consensus pattern (20 bp):
TTTTTTTAGTTTTTCTTTTT
Found at i:21866681 original size:18 final size:18
Alignment explanation
Indices: 21866658--21866700 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21866648 GAAATTTTTT
21866658 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
21866676 TTAATTACAAATTTTAAA
1 TTAATTAAAAAATTTAAA
21866694 TTAATTA
1 TTAATTA
21866701 TAACTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:21869183 original size:2 final size:2
Alignment explanation
Indices: 21869176--21869215 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
21869166 TAATTCATGC
*
21869176 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21869216 AATTTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21879377 original size:6 final size:6
Alignment explanation
Indices: 21879366--21879394 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
21879356 TACATAATTA
21879366 ATTAAT ATTAAT ATTAAT ATTAAT ATTAA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAA
21879395 ATAAGAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:21880476 original size:29 final size:28
Alignment explanation
Indices: 21880422--21880861 Score: 332
Period size: 30 Copynumber: 15.1 Consensus size: 28
21880412 TGCATTTGAT
* *
21880422 CCCTAAACTTTACCAAAATTATATTTTAA
1 CCCTAAACTTT-CCAAAATCACATTTTAA
* *
21880451 CCCTAAACTTTCCTAATATCACATTTTGA
1 CCCTAAACTTTCC-AAAATCACATTTTAA
* * *
21880480 CCCCAAACTTTCCTAAAATTACATATTAA
1 CCCTAAACTTTCC-AAAATCACATTTTAA
* * * *
21880509 CCTTTAAACTTTTTCAAAATTACATTTTAG
1 CC-CTAAAC-TTTCCAAAATCACATTTTAA
* * *
21880539 CCCTAAAACTTTTCTAAAATCATATTTTGA
1 CCCT-AAAC-TTTCCAAAATCACATTTTAA
*
21880569 CCCTCAAACTTTTCCAAAATTACATTTTAA
1 CCCT-AAAC-TTTCCAAAATCACATTTTAA
* * *
21880599 CCCTTAAATTTTTTCAAAATCACATTTTTAC
1 CCC-TAAA-CTTTCCAAAATCACA-TTTTAA
*
21880630 CCCTAAACTTTTTCAAAAATCACATTTTAA
1 CCCTAAAC--TTTCCAAAATCACATTTTAA
* * *
21880660 ACCTAAACTTTCCAATAACCATATTTTAA
1 CCCTAAACTTTCCAA-AATCACATTTTAA
*
21880689 CCCTAAACTTCTCCAAAATCACATTTTGAT
1 CCCTAAACTT-TCCAAAATCACATTTT-AA
*
21880719 CCC-AAACTTTCCAAAAATCACATTTTGA
1 CCCTAAACTTTCC-AAAATCACATTTTAA
21880747 CCC-AAACTTTCCAATAA-C-CATTTTTAA
1 CCCTAAACTTTCCAA-AATCACA-TTTTAA
* * *
21880774 CCC-CAACTTCTCCAAAATTACAATTTAA
1 CCCTAAACTT-TCCAAAATCACATTTTAA
* * * *
21880802 CCTTAAACTTCCCAAAATTACATTTTTAC
1 CCCTAAACTTTCCAAAATCACA-TTTTAA
* * *
21880831 CCCTAAAATTTTTCAAAATTACATTTTAA
1 CCCT-AAACTTTCCAAAATCACATTTTAA
21880860 CC
1 CC
21880862 TCGAATTCTT
Statistics
Matches: 332, Mismatches: 58, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.01
27 18 0.05
28 48 0.14
29 118 0.36
30 121 0.36
31 25 0.08
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATCACATTTTAA
Found at i:21880498 original size:58 final size:57
Alignment explanation
Indices: 21880426--21880861 Score: 305
Period size: 58 Copynumber: 7.5 Consensus size: 57
21880416 TTTGATCCCT
* * * *
21880426 AAACTTTACC-AAAATTATATTTTAACCCTAAACTTTCCTAATATCACATTTTGACCCC
1 AAACTTT-CCTAAAATCACATTTTAACCCTAAACTTTCC-AAAATCACATTTTAACCCC
* * * * * * *
21880484 AAACTTTCCTAAAATTACATATTAACCTTTAAACTTTTTCAAAATTACATTTTAGCCCTA
1 AAACTTTCCTAAAATCACATTTTAACC-CTAAAC-TTTCCAAAATCACATTTTAACCC-C
* * * * *
21880544 AAACTTTTCTAAAATCATATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAACCCTT
1 AAACTTTCCTAAAATCACATTTTAACCCT-AAAC-TTTCCAAAATCACATTTTAACCC-C
** * * * *
21880604 AAA-TTTTTTCAAAATCACATTTTTACCCCTAAACTTTTTCAAAAATCACATTTTAAACCT
1 AAACTTTCCT-AAAATCACA-TTTTAACCCTAAAC--TTTCCAAAATCACATTTTAACCCC
* * * *
21880664 AAACTTTCC-AATAACCATATTTTAACCCTAAACTTCTCCAAAATCACATTTTGATCCC
1 AAACTTTCCTAA-AATCACATTTTAACCCTAAACTT-TCCAAAATCACATTTTAACCCC
* *
21880722 AAACTTTCCAAAAATCACATTTTGACCC-AAACTTTCCAATAA-C-CATTTTTAACCCC
1 AAACTTTCCTAAAATCACATTTTAACCCTAAACTTTCCAA-AATCACA-TTTTAACCCC
* * * * * *
21880778 -AACTTCTCC-AAAATTACAATTTAACCTTAAACTTCCCAAAATTACATTTTTACCCC
1 AAACTT-TCCTAAAATCACATTTTAACCCTAAACTTTCCAAAATCACATTTTAACCCC
* * *
21880834 TAAAATTT-TTCAAAATTACATTTTAACC
1 -AAACTTTCCT-AAAATCACATTTTAACC
21880862 TCGAATTCTT
Statistics
Matches: 307, Mismatches: 49, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
55 23 0.07
56 36 0.12
57 15 0.05
58 82 0.27
59 42 0.14
60 77 0.25
61 32 0.10
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (57 bp):
AAACTTTCCTAAAATCACATTTTAACCCTAAACTTTCCAAAATCACATTTTAACCCC
Found at i:21880520 original size:30 final size:30
Alignment explanation
Indices: 21880407--21880861 Score: 247
Period size: 29 Copynumber: 15.6 Consensus size: 30
21880397 GTTTTCCTTG
* * *
21880407 AAAATTGCATTTGATCCC-TAAACTTTACC-
1 AAAATTACATTTTAACCCTTAAACTTT-CCT
*
21880436 AAAATTATATTTTAACCC-TAAACTTTCCT
1 AAAATTACATTTTAACCCTTAAACTTTCCT
* * * *
21880465 AATATCACATTTTGACCC-CAAACTTTCCT
1 AAAATTACATTTTAACCCTTAAACTTTCCT
* * *
21880494 AAAATTACATATTAACCTTTAAACTTT-TT
1 AAAATTACATTTTAACCCTTAAACTTTCCT
* * *
21880523 CAAAATTACATTTTAGCCCTAAAACTTTTCT
1 -AAAATTACATTTTAACCCTTAAACTTTCCT
* * * *
21880554 AAAATCATATTTTGACCCTCAAACTTTTCC-
1 AAAATTACATTTTAACCCTTAAAC-TTTCCT
**
21880584 AAAATTACATTTTAACCCTTAAA-TTTTTT
1 AAAATTACATTTTAACCCTTAAACTTTCCT
* * * * *
21880613 CAAAATCACATTTTTACCCCTAAACTTTTTCA
1 -AAAATTACATTTTAACCCTTAAAC-TTTCCT
* *
21880645 AAAATCACATTTTAAACC-TAAACTTTCC-
1 AAAATTACATTTTAACCCTTAAACTTTCCT
** *
21880673 AATAACCATATTTTAACCC-TAAACTTCTCC-
1 AA-AATTACATTTTAACCCTTAAACTT-TCCT
* * *
21880703 AAAATCACATTTTGATCCC--AAACTTTCCA
1 AAAATTACATTTT-AACCCTTAAACTTTCCT
* *
21880732 AAAATCACATTTTGACCC--AAACTTTCC-
1 AAAATTACATTTTAACCCTTAAACTTTCCT
* *
21880759 AATAA--CCATTTTTAACCC--CAACTTCTCC-
1 AA-AATTACA-TTTTAACCCTTAAACTT-TCCT
* *
21880787 AAAATTACAATTTAA-CCTTAAAC-TTCCC
1 AAAATTACATTTTAACCCTTAAACTTTCCT
* * * *
21880815 AAAATTACATTTTTACCCCTAAAATTT-TT
1 AAAATTACATTTTAACCCTTAAACTTTCCT
21880844 CAAAATTACATTTTAACC
1 -AAAATTACATTTTAACC
21880862 TCGAATTCTT
Statistics
Matches: 340, Mismatches: 62, Indels: 47
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.01
27 22 0.06
28 48 0.14
29 123 0.36
30 120 0.35
31 21 0.06
32 4 0.01
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTCCT
Found at i:21881965 original size:21 final size:21
Alignment explanation
Indices: 21881939--21881978 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
21881929 AGATTAGTGA
21881939 CGACTCTCATTTTTCAATTGG
1 CGACTCTCATTTTTCAATTGG
21881960 CGACTCTCATTTTTCAATT
1 CGACTCTCATTTTTCAATT
21881979 TAAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (21 bp):
CGACTCTCATTTTTCAATTGG
Found at i:21885026 original size:24 final size:24
Alignment explanation
Indices: 21884990--21885035 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
21884980 TTATTAAATA
*
21884990 TTAAAATAAAAAATATAAATATTT
1 TTAAAATAAAAAAAATAAATATTT
*
21885014 TTAAAA-AATAAAAAATTAATAT
1 TTAAAATAA-AAAAAATAAATAT
21885036 GGACGGGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAAATAAAAAAAATAAATATTT
Found at i:21885026 original size:31 final size:31
Alignment explanation
Indices: 21884962--21885026 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
21884952 AATTTTCAAT
* * *
21884962 AAATAAAAATTTATAAAATTATTAAATATTA
1 AAATAAAAATATATAAAATTATTAAAAAATA
*
21884993 AAATAAAAA-ATATAAATATTTTTAAAAAATA
1 AAATAAAAATATATAAA-ATTATTAAAAAATA
21885024 AAA
1 AAA
21885027 AATTAATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAATAAAAATATATAAAATTATTAAAAAATA
Found at i:21888235 original size:21 final size:21
Alignment explanation
Indices: 21888211--21888251 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21888201 TTTGAGGAAC
*
21888211 TTAATTAAAATTTTTAAAAGT
1 TTAATGAAAATTTTTAAAAGT
* *
21888232 TTAATGAGAATTTTTTAAAG
1 TTAATGAAAATTTTTAAAAG
21888252 AAATTGAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (21 bp):
TTAATGAAAATTTTTAAAAGT
Found at i:21889126 original size:12 final size:12
Alignment explanation
Indices: 21889109--21889136 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21889099 ACGTGAGGAA
21889109 TTGCTATATAAG
1 TTGCTATATAAG
21889121 TTGCTATATAAG
1 TTGCTATATAAG
21889133 TTGC
1 TTGC
21889137 AACTAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (12 bp):
TTGCTATATAAG
Found at i:21889736 original size:15 final size:15
Alignment explanation
Indices: 21889716--21889745 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21889706 GTTCAATGGA
*
21889716 ATTAACTATTTTCTT
1 ATTAACTATTATCTT
21889731 ATTAACTATTATCTT
1 ATTAACTATTATCTT
21889746 TTGTATCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAACTATTATCTT
Found at i:21896513 original size:10 final size:10
Alignment explanation
Indices: 21896467--21896570 Score: 58
Period size: 11 Copynumber: 10.4 Consensus size: 10
21896457 AAAAAATTGG
21896467 TTTTTATAAT
1 TTTTTATAAT
*
21896477 CTTTTTGT-AT
1 -TTTTTATAAT
*
21896487 ATTTT-TAAT
1 TTTTTATAAT
21896496 TTCGTTTATAAT
1 TT--TTTATAAT
21896508 TTTTTAT-A-
1 TTTTTATAAT
*
21896516 CTTTTATAAT
1 TTTTTATAAT
21896526 ATTTTGTA-AAT
1 -TTTT-TATAAT
**
21896537 TTAAT-TAAT
1 TTTTTATAAT
*
21896546 TTTTAATAAT
1 TTTTTATAAT
21896556 TTTTTCATAAT
1 TTTTT-ATAAT
21896567 TTTT
1 TTTT
21896571 ACAATTGCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
8 7 0.10
9 15 0.21
10 17 0.24
11 24 0.34
12 8 0.11
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:21896697 original size:19 final size:18
Alignment explanation
Indices: 21896651--21896721 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
21896641 TTTTTGCAAT
*
21896651 TTTTAATAGTTTTTATT-A
1 TTTTAATAATTTTT-TTAA
* *
21896669 TTATTTATAATTTTTTTCA
1 TT-TTAATAATTTTTTTAA
*
21896688 TTTATAATAAATTTTTTAA
1 TTT-TAATAATTTTTTTAA
21896707 TTTTAA-ATATTTTTT
1 TTTTAATA-ATTTTTT
21896722 CTACAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.02
18 14 0.33
19 28 0.65
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTTAATAATTTTTTTAA
Found at i:21897783 original size:20 final size:21
Alignment explanation
Indices: 21897745--21897783 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
21897735 ATTAGAAAAT
*
21897745 AAAACAGTTTGAATTTATTTA
1 AAAACAGTTTGAATATATTTA
*
21897766 AAAACA-TTTTAATATATT
1 AAAACAGTTTGAATATATT
21897784 AATATTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAACAGTTTGAATATATTTA
Found at i:21910988 original size:189 final size:192
Alignment explanation
Indices: 21910645--21910992 Score: 567
Period size: 189 Copynumber: 1.8 Consensus size: 192
21910635 ATTCTCTAAA
* * *
21910645 GCACCAAAATAAAACGTAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCTACAAAAAGCATTGC
1 GCACCAAAATAAAACGAAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCCACAAAAAGCAATGC
* * *
21910710 ACACAATGTGTTTGAGTAAATGCTCTCAAATATATTCTTTAAGTCAAGAATGAAGTGATTACATA
66 ACACAATGTATTTGAGTAAATGCTCTCAAATATATTCTTTAAGTCAAGAATAAAGTGATTACAAA
21910775 TGAAATGCGAAGGCTCTATTTATAGTTAAGCTCCCTCGAAAGAAGATAATTCTCATGAAAAT
131 TGAAATGCGAAGGCTCTATTTATAGTTAAGCTCCCTCGAAAGAAGATAATTCTCATGAAAAT
* * *
21910837 GCACCAAAATAAAATGAAAGCAAACTCAAAGCGAAAGAACT-AAAAAAGCCACAAAAAGTAATGC
1 GCACCAAAATAAAACGAAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCCACAAAAAGCAATGC
* *
21910901 ACACAATGTATTTGAGTAACTGCTCTC-AA-ATATTCTTTAATTCAAGAATAAAGTGATTACAAA
66 ACACAATGTATTTGAGTAAATGCTCTCAAATATATTCTTTAAGTCAAGAATAAAGTGATTACAAA
*
21910964 TGAAGTGCGAAGGCTCTATTTATAGTTAA
131 TGAAATGCGAAGGCTCTATTTATAGTTAA
21910993 ATTCACTCAG
Statistics
Matches: 144, Mismatches: 12, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
189 59 0.41
190 2 0.01
191 45 0.31
192 38 0.26
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (192 bp):
GCACCAAAATAAAACGAAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCCACAAAAAGCAATGC
ACACAATGTATTTGAGTAAATGCTCTCAAATATATTCTTTAAGTCAAGAATAAAGTGATTACAAA
TGAAATGCGAAGGCTCTATTTATAGTTAAGCTCCCTCGAAAGAAGATAATTCTCATGAAAAT
Found at i:21914216 original size:17 final size:18
Alignment explanation
Indices: 21914184--21914217 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21914174 ATTCAGTTCT
*
21914184 TTTTTCTTTTATATTTTG
1 TTTTTCTTCTATATTTTG
21914202 TTTTTCTTCTA-ATTTT
1 TTTTTCTTCTATATTTT
21914218 TATTTGCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTTCTTCTATATTTTG
Found at i:21919204 original size:34 final size:33
Alignment explanation
Indices: 21919130--21919204 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
21919120 AAAAGAAATG
21919130 AATTAACTATAAAAAATAATAAAAAATATTTATC
1 AATTAA-TATAAAAAATAATAAAAAATATTTATC
* * *
21919164 ATTTAATATAATAAATAATTAAAAATGATTATAT-
1 AATTAATATAAAAAATAATAAAAAAT-ATT-TATC
21919198 AATTAAT
1 AATTAAT
21919205 TAGAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 18 0.51
34 14 0.40
35 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (33 bp):
AATTAATATAAAAAATAATAAAAAATATTTATC
Found at i:21934632 original size:8 final size:9
Alignment explanation
Indices: 21934593--21934633 Score: 54
Period size: 8 Copynumber: 5.0 Consensus size: 9
21934583 TTTTAATTTG
21934593 TTTATATTA
1 TTTATATTA
21934602 TTTAT-TTA
1 TTTATATTA
21934610 TTTAT-TTA
1 TTTATATTA
21934618 TTT-TATT-
1 TTTATATTA
21934625 TTTATATTA
1 TTTATATTA
21934634 ACTTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 4 0.14
8 20 0.69
9 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATATTA
Found at i:21934632 original size:13 final size:13
Alignment explanation
Indices: 21934593--21934625 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
21934583 TTTTAATTTG
21934593 TTTATATTATTTA-
1 TTTAT-TTATTTAT
21934606 TTTATTTATTTAT
1 TTTATTTATTTAT
21934619 TTTATTT
1 TTTATTT
21934626 TTATATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:21934632 original size:21 final size:21
Alignment explanation
Indices: 21934583--21934632 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
21934573 TAAAAGTTAA
*
21934583 TTTTA-ATTTGTTTATATTAT
1 TTTTATATTTATTTATATTAT
*
21934603 TTATT-TATTTATTTATTTTAT
1 TT-TTATATTTATTTATATTAT
21934624 TTTTATATT
1 TTTTATATT
21934633 AACTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATATTTATTTATATTAT
Found at i:21935132 original size:139 final size:136
Alignment explanation
Indices: 21934925--21935322 Score: 565
Period size: 139 Copynumber: 2.9 Consensus size: 136
21934915 ATGGGCTATT
* * *
21934925 TAAA-AATAAATTATA-AAAATAATTAAATAATTTGAAT-AAAAT-AAAACAGAAAAAATAAATT
1 TAAATAATAAATTTTATAAAATAATTAAATAATTTGAATAAAAATAAAAAAAAAAAAAATAAATT
*
21934986 TAATTCTTTCAATTTGTTATGGATTTTTTACCTAAAATATATAAAATAAATACTAAAATTATAAT
66 TAATTCTTTCAATTTGTTATGG-TTTTTTACCTAAAATATATAAAATAAATACTAAAATTACAAT
21935051 TTAACAA
130 TTAACAA
*
21935058 TAAATAAT-AATATTTATAAAATAATTGAATAATTTGAATAAAAATAAAAATAAATAAAAAATAA
1 TAAATAATAAAT-TTTATAAAATAATTAAATAATTTGAATAAAAATAAAAA-AAA-AAAAAATAA
* * * * *
21935122 ATATAATTCTTTCAATTTATTATAGTTTTTT-CACTTAAATATATAAAATAAAATACTAAAATTG
63 ATTTAATTCTTTCAATTTGTTATGGTTTTTTAC-CTAAAATATATAAAAT-AAATACTAAAATTA
21935186 CAATTTAACAA
126 CAATTTAACAA
21935197 TAAATAATAAATTTTATAAAATAATTAAATAATTTGAATAAAAATAAAACAAAAAATAAAATAAA
1 TAAATAATAAATTTTATAAAATAATTAAATAATTTGAATAAAAATAAAA-AAAAAA-AAAATAAA
*
21935262 TTTAATTCTTTCAATTTGTTATGGGTTTTTTTACCTAAAATATATAAAATAAATATTAAAA
64 TTTAATTCTTTCAATTTGTTAT-GG-TTTTTTACCTAAAATATATAAAATAAATACTAAAA
21935323 CCCTAATTTA
Statistics
Matches: 234, Mismatches: 16, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
133 7 0.03
134 6 0.03
135 21 0.09
136 5 0.02
137 5 0.02
138 24 0.10
139 129 0.55
140 15 0.06
141 21 0.09
142 1 0.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.37
Consensus pattern (136 bp):
TAAATAATAAATTTTATAAAATAATTAAATAATTTGAATAAAAATAAAAAAAAAAAAAATAAATT
TAATTCTTTCAATTTGTTATGGTTTTTTACCTAAAATATATAAAATAAATACTAAAATTACAATT
TAACAA
Found at i:21938464 original size:2 final size:2
Alignment explanation
Indices: 21938457--21938504 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
21938447 TAAGTGAAGT
21938457 TA TA TA TA TA TA TA TA TA TA -A 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
21938498 TA TA TA T
1 TA TA TA T
21938505 TCAATTTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21938625 original size:16 final size:16
Alignment explanation
Indices: 21938606--21938639 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21938596 AAATAAATAA
*
21938606 TATTTTTCTAAAATTT
1 TATTTTTCAAAAATTT
*
21938622 TATTTTTGAAAAATTT
1 TATTTTTCAAAAATTT
21938638 TA
1 TA
21938640 AATTTTATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (16 bp):
TATTTTTCAAAAATTT
Found at i:21944793 original size:24 final size:23
Alignment explanation
Indices: 21944750--21944800 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
21944740 TTTCTAGAAG
*
21944750 ATTTAGTATTATTAGTATAATAT
1 ATTTAGTATTATTAGCATAATAT
* *
21944773 ATTTTGTATTTATTAGCATAATTT
1 ATTTAGTA-TTATTAGCATAATAT
21944797 ATTT
1 ATTT
21944801 GATCTACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (23 bp):
ATTTAGTATTATTAGCATAATAT
Found at i:21945302 original size:18 final size:19
Alignment explanation
Indices: 21945261--21945302 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
21945251 GATTTTGTAA
* *
21945261 ATAAAAGAGTTAATTAATT
1 ATAAAAGAGTGAATTAATC
21945280 A-AAAAGA-TGAATTAATC
1 ATAAAAGAGTGAATTAATC
21945297 ATAAAA
1 ATAAAA
21945303 AAATTAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
18 10 0.50
19 1 0.05
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (19 bp):
ATAAAAGAGTGAATTAATC
Found at i:21958420 original size:22 final size:22
Alignment explanation
Indices: 21958394--21958437 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21958384 AATTTAGAAC
21958394 CACTCAATAGCATAGGGAAAAA
1 CACTCAATAGCATAGGGAAAAA
*
21958416 CACTCAATAGTATAGGGAAAAA
1 CACTCAATAGCATAGGGAAAAA
21958438 TTGAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (22 bp):
CACTCAATAGCATAGGGAAAAA
Found at i:21966367 original size:12 final size:12
Alignment explanation
Indices: 21966350--21966431 Score: 58
Period size: 12 Copynumber: 6.9 Consensus size: 12
21966340 AGAGAAATAA
21966350 ACCACAACCACC
1 ACCACAACCACC
* *
21966362 ACCACAACAACG
1 ACCACAACCACC
21966374 ACCA-AACCACC
1 ACCACAACCACC
** *
21966385 ACCACTTCCATC
1 ACCACAACCACC
* * *
21966397 ACCACCACGACG
1 ACCACAACCACC
**
21966409 ACCACGGCCACC
1 ACCACAACCACC
*
21966421 ACCACCACCAC
1 ACCACAACCAC
21966432 TAAATTATTT
Statistics
Matches: 51, Mismatches: 18, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
11 9 0.18
12 42 0.82
ACGTcount: A:0.37, C:0.54, G:0.06, T:0.04
Consensus pattern (12 bp):
ACCACAACCACC
Found at i:21967957 original size:31 final size:30
Alignment explanation
Indices: 21967886--21967977 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 30
21967876 AAAATTTACC
* *
21967886 AACTTTTAAGTGGCCCCCAAAATTTATTTTTTT
1 AACTTTTAAGAGG--CCCAAAATTT-TTTTTTA
21967919 AACTTTTAAG-GGCCCAAAATTTTTTTTACTA
1 AACTTTTAAGAGGCCCAAAATTTTTTTT--TA
* * *
21967950 AACTTTTAAGAGACCTAAAAATTTTTTT
1 AACTTTTAAGAGGCCCAAAATTTTTTTT
21967978 CTCCAACTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.10
30 10 0.19
31 11 0.21
32 16 0.31
33 10 0.19
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (30 bp):
AACTTTTAAGAGGCCCAAAATTTTTTTTTA
Found at i:21971201 original size:6 final size:6
Alignment explanation
Indices: 21971190--21971232 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
21971180 ACAACCAGAG
* * * *
21971190 CTGGTT CTGGTT CCGGTT CTGGTG CTGCTT CGGGTT CTGGTT C
1 CTGGTT CTGGTT CTGGTT CTGGTT CTGGTT CTGGTT CTGGTT C
21971233 GGGCTCGACG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.23, G:0.35, T:0.42
Consensus pattern (6 bp):
CTGGTT
Found at i:21971990 original size:22 final size:22
Alignment explanation
Indices: 21971951--21971995 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
21971941 TATTGTATAC
*
21971951 TCATAAAAAATGGCTAAT-TAT
1 TCATAAAAAACGGCTAATGTAT
*
21971972 TCATAAAAAAACGGTTAATGTAT
1 TCAT-AAAAAACGGCTAATGTAT
21971995 T
1 T
21971996 TTTTCCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATAAAAAACGGCTAATGTAT
Found at i:21980257 original size:29 final size:30
Alignment explanation
Indices: 21980204--21980260 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
21980194 GAATTGGATC
21980204 AAATTAAAATTTCATATATAAAATTATAAA
1 AAATTAAAATTTCATATATAAAATTATAAA
* *
21980234 AAATTAAAA-TTCATGTATACAATTATA
1 AAATTAAAATTTCATATATAAAATTATA
21980261 CATTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATTAAAATTTCATATATAAAATTATAAA
Found at i:21984844 original size:56 final size:56
Alignment explanation
Indices: 21984782--21984889 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
21984772 TCCCCTTCTA
*
21984782 ATTATTTTTCCAAATTTTC-TTAGACTTTCTCTCTTTTCAAACACTCATTTTCTCTC
1 ATTATTTTTCCAAATTTTCTTTA-ACTTTCTCTCTTTTCAAACACACATTTTCTCTC
*
21984838 ATTATTTTTCCAGATTTTCTTTAACTTTCTCTCTTTTCAAACACACATTTTC
1 ATTATTTTTCCAAATTTTCTTTAACTTTCTCTCTTTTCAAACACACATTTTC
21984890 GCTTCACTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 46 0.94
57 3 0.06
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (56 bp):
ATTATTTTTCCAAATTTTCTTTAACTTTCTCTCTTTTCAAACACACATTTTCTCTC
Found at i:21987251 original size:23 final size:23
Alignment explanation
Indices: 21987225--21987345 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
21987215 ACACTAGCGC
21987225 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
21987248 GCTCTCTGTTTAACAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
21987271 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
21987296 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
21987319 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
21987342 GCTC
1 GCTC
21987346 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:21987288 original size:48 final size:46
Alignment explanation
Indices: 21987225--21987345 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
21987215 ACACTAGCGC
*
21987225 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAACACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAACACGTCGT-GT
* *
21987271 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAACACGTCGTGT
*
21987319 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
21987346 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAACACGTCGTGT
Found at i:21987374 original size:39 final size:39
Alignment explanation
Indices: 21987310--21987384 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
21987300 TCTGATTAGC
*
21987310 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
21987349 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
21987385 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:21987379 original size:23 final size:23
Alignment explanation
Indices: 21987344--21987437 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
21987334 CTTTGTGTGC
*
21987344 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
21987367 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
21987390 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
21987415 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
21987437 T
1 T
21987438 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:21988675 original size:17 final size:16
Alignment explanation
Indices: 21988653--21988699 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
21988643 AAAACTTTAG
21988653 ATTTTAAATCTTAATTT
1 ATTTTAAAT-TTAATTT
*
21988670 ATTTTAATTTTAAATTT
1 ATTTTAAATTT-AATTT
*
21988687 ATTATAAATTTAA
1 ATTTTAAATTTAA
21988700 GCTTATTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAAATTTAATTT
Found at i:21989790 original size:30 final size:30
Alignment explanation
Indices: 21989754--21989818 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
21989744 TCGTACTAAT
21989754 TAATTGAACTTATTAGATTTATAAACTTTA
1 TAATTGAACTTATTAGATTTATAAACTTTA
21989784 TAATTGAACTTATTAGATTTATAAACTTTA
1 TAATTGAACTTATTAGATTTATAAACTTTA
21989814 TAATT
1 TAATT
21989819 AATCATGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (30 bp):
TAATTGAACTTATTAGATTTATAAACTTTA
Found at i:21997250 original size:23 final size:23
Alignment explanation
Indices: 21997214--21997288 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
21997204 AAGTACTTAA
* *
21997214 CAGTAAGCATACACATTGCAATC
1 CAGTAGGCACACACATTGCAATC
21997237 CAGTAGGCACACACATTGCAATC
1 CAGTAGGCACACACATTGCAATC
*
21997260 CAGTAGGCACACACACTGCAAT-
1 CAGTAGGCACACACATTGCAATC
21997282 CAGTAGG
1 CAGTAGG
21997289 AGCACATAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 7 0.14
23 42 0.86
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (23 bp):
CAGTAGGCACACACATTGCAATC
Found at i:21997331 original size:23 final size:23
Alignment explanation
Indices: 21997305--21997353 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21997295 TAGCGCAAAT
* *
21997305 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
* *
21997328 CAGTAAGCACATGAATTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
21997351 CAG
1 CAG
21997354 AGCGCGCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.29, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:22000492 original size:23 final size:23
Alignment explanation
Indices: 22000462--22000513 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
22000452 AAATCAGTAG
* * *
22000462 GCACACGAGGTGTGAGACAATAA
1 GCACACGAAGTGCGAAACAATAA
*
22000485 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAATAA
22000508 GCACAC
1 GCACAC
22000514 AAAAATGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.27, T:0.10
Consensus pattern (23 bp):
GCACACGAAGTGCGAAACAATAA
Found at i:22011901 original size:34 final size:35
Alignment explanation
Indices: 22011857--22011969 Score: 102
Period size: 34 Copynumber: 3.5 Consensus size: 35
22011847 TATTTATAAA
22011857 TTAAAAATAAA-TATATCGTAACACACTGAAACAC
1 TTAAAAATAAATTATATCGTAACACACTGAAACAC
* ***
22011891 TTAAATATAAATTATAT--T-ATTTA-T--AA-A-
1 TTAAAAATAAATTATATCGTAACACACTGAAACAC
22011918 TTAAAAAATAAA-TATATCGTAACACACTGAAACAC
1 TT-AAAAATAAATTATATCGTAACACACTGAAACAC
*
22011953 TTAAATATAAATTATAT
1 TTAAAAATAAATTATAT
22011970 TATTTACTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 21
0.66 0.10 0.24
Matches are distributed among these distances:
27 7 0.12
28 9 0.15
29 3 0.05
30 2 0.03
31 2 0.03
32 2 0.03
33 3 0.05
34 19 0.32
35 12 0.20
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (35 bp):
TTAAAAATAAATTATATCGTAACACACTGAAACAC
Found at i:22011910 original size:61 final size:62
Alignment explanation
Indices: 22011835--22011975 Score: 275
Period size: 62 Copynumber: 2.3 Consensus size: 62
22011825 TTAGTAGAAT
22011835 TATAAATTATATTATTTATAAATT-AAAAATAAATATATCGTAACACACTGAAACACTTAAA
1 TATAAATTATATTATTTATAAATTAAAAAATAAATATATCGTAACACACTGAAACACTTAAA
22011896 TATAAATTATATTATTTATAAATTAAAAAATAAATATATCGTAACACACTGAAACACTTAAA
1 TATAAATTATATTATTTATAAATTAAAAAATAAATATATCGTAACACACTGAAACACTTAAA
22011958 TATAAATTATATTATTTA
1 TATAAATTATATTATTTA
22011976 CTTTTTTGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
61 24 0.30
62 55 0.70
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.37
Consensus pattern (62 bp):
TATAAATTATATTATTTATAAATTAAAAAATAAATATATCGTAACACACTGAAACACTTAAA
Found at i:22012077 original size:13 final size:13
Alignment explanation
Indices: 22012055--22012096 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
22012045 TTAAATCAAG
22012055 TTTTTCAAAAGTAC
1 TTTTT-AAAAGTAC
*
22012069 TTTTTAAAATTAC
1 TTTTTAAAAGTAC
22012082 TTTTTAAAAGTAC
1 TTTTTAAAAGTAC
22012095 TT
1 TT
22012097 CTCAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.50
Consensus pattern (13 bp):
TTTTTAAAAGTAC
Found at i:22012103 original size:13 final size:13
Alignment explanation
Indices: 22012056--22012103 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
22012046 TAAATCAAGT
22012056 TTTTCAAAAGTAC
1 TTTTCAAAAGTAC
* *
22012069 TTTTTAAAATTAC
1 TTTTCAAAAGTAC
*
22012082 TTTTTAAAAGTAC
1 TTTTCAAAAGTAC
*
22012095 TTCTCAAAA
1 TTTTCAAAA
22012104 CTAATGCTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:22012305 original size:2 final size:2
Alignment explanation
Indices: 22012295--22012356 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
22012285 GTGAACACAC
*
22012295 CT CT TT 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 CT CT
22012337 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
22012357 ATATATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:22012361 original size:2 final size:2
Alignment explanation
Indices: 22012356--22012388 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22012346 TCTCTCTCTC
22012356 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
22012389 TTGTAACAAA
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:22019288 original size:20 final size:20
Alignment explanation
Indices: 22019263--22019305 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
22019253 CCTGAATTTT
22019263 AAAATTTAAAAA-ATAAAATA
1 AAAATTTAAAAATA-AAAATA
*
22019283 AAAATTTGAAAATAAAAATA
1 AAAATTTAAAAATAAAAATA
22019303 AAA
1 AAA
22019306 GAAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATTTAAAAATAAAAATA
Found at i:22023129 original size:6 final size:6
Alignment explanation
Indices: 22023083--22023111 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22023073 TAACGAAGGT
22023083 ATAGGA ATAGGA ATAGGA ATAGGA ATAGG
1 ATAGGA ATAGGA ATAGGA ATAGGA ATAGG
22023112 GGTGTTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (6 bp):
ATAGGA
Found at i:22032514 original size:3 final size:3
Alignment explanation
Indices: 22032506--22032620 Score: 115
Period size: 3 Copynumber: 38.7 Consensus size: 3
22032496 TCCAATTGCA
* *
22032506 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAC AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
22032553 AAT AAC AAT AAC AAT AAC AAC AAT AAC AAT AAC AAT AAC AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
22032601 AAC AAT AAT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
22032621 AACATTCCAC
Statistics
Matches: 89, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
2 2 0.02
3 87 0.98
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (3 bp):
AAT
Found at i:22032532 original size:17 final size:17
Alignment explanation
Indices: 22032510--22032544 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22032500 ATTGCAAATA
22032510 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
22032527 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
22032544 A
1 A
22032545 ACAATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:22044774 original size:29 final size:29
Alignment explanation
Indices: 22044745--22044801 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
22044735 TTTTTCTATA
*
22044745 AATTTTATAT-TTT-TAATAAAATTTAAAT
1 AATTTTATATGTTTCTAA-AAAATATAAAT
*
22044773 AATTTTTTATGTTTCTAAAAAATATAAAT
1 AATTTTATATGTTTCTAAAAAATATAAAT
22044802 TATATCACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.36
29 13 0.52
30 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
AATTTTATATGTTTCTAAAAAATATAAAT
Found at i:22050007 original size:18 final size:18
Alignment explanation
Indices: 22049984--22050018 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22049974 TGAGGGGAAA
*
22049984 GGGAGGGAGACAAAGAAC
1 GGGAGGGAGAAAAAGAAC
22050002 GGGAGGGAGAAAAAGAA
1 GGGAGGGAGAAAAAGAA
22050019 GTGCTGCTCA
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:0.49, C:0.06, G:0.46, T:0.00
Consensus pattern (18 bp):
GGGAGGGAGAAAAAGAAC
Found at i:22051201 original size:19 final size:19
Alignment explanation
Indices: 22051179--22051236 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
22051169 GTGTATAAAA
22051179 AATATATATATATATATAT
1 AATATATATATATATATAT
*
22051198 AATATATATATATATATAA
1 AATATATATATATATATAT
* *
22051217 AAT-TAGA-AAATATATAT
1 AATATATATATATATATAT
22051234 AAT
1 AAT
22051237 CTAAAAAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 11 0.31
18 3 0.09
19 21 0.60
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AATATATATATATATATAT
Found at i:22051202 original size:17 final size:17
Alignment explanation
Indices: 22051182--22051216 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22051172 TATAAAAAAT
22051182 ATATATATATATATATA
1 ATATATATATATATATA
22051199 ATATATATATATATATA
1 ATATATATATATATATA
22051216 A
1 A
22051217 AATTAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:22051234 original size:2 final size:2
Alignment explanation
Indices: 22051180--22051215 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
22051170 TGTATAAAAA
22051180 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22051216 AAATTAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22053893 original size:19 final size:18
Alignment explanation
Indices: 22053858--22053930 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 18
22053848 CTACTGAGTT
22053858 AGTTT-TTTTTATAAAATTA
1 AGTTTATTTTT-T-AAATTA
22053877 AGTTTATTTCTTTAAATTA
1 AGTTTATTT-TTTAAATTA
* *
22053896 AGAGTTATTTTTTAATTTA
1 AG-TTTATTTTTTAAATTA
22053915 ATGTATTATTTATTTA
1 A-GT-TTATTT-TTTA
22053931 TTTTGTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 22 0.49
20 17 0.38
21 6 0.13
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (18 bp):
AGTTTATTTTTTAAATTA
Found at i:22054938 original size:8 final size:8
Alignment explanation
Indices: 22054911--22054962 Score: 50
Period size: 8 Copynumber: 6.0 Consensus size: 8
22054901 TTTAAATTTT
22054911 TTTTTAAA
1 TTTTTAAA
* *
22054919 TTTTCAAC
1 TTTTTAAA
22054927 TTTTTAAA
1 TTTTTAAA
22054935 TTTTTTATAA
1 -TTTTTA-AA
22054945 TTCTTTAGAA
1 TT-TTTA-AA
22054955 TTTTTAAA
1 TTTTTAAA
22054963 AATTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 14 0.39
9 12 0.33
10 10 0.28
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (8 bp):
TTTTTAAA
Found at i:22058842 original size:22 final size:22
Alignment explanation
Indices: 22058817--22058876 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
22058807 TTATATTACT
22058817 AATAATATATTAAAATATAAAA
1 AATAATATATTAAAATATAAAA
* *
22058839 AATAATATA-TAATATAT-TAA
1 AATAATATATTAAAATATAAAA
22058859 AATAA-AGT-TTAAAATATA
1 AATAATA-TATTAAAATATA
22058877 TTTTTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
21 7 0.22
22 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AATAATATATTAAAATATAAAA
Found at i:22059003 original size:25 final size:23
Alignment explanation
Indices: 22058975--22059021 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
22058965 AATTGCAAGA
22058975 AATTAAATACTTTTTAGAATTTTAG
1 AATTAAATA--TTTTAGAATTTTAG
* *
22059000 AATTATATATTTTATAATTTTA
1 AATTAAATATTTTAGAATTTTA
22059022 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
AATTAAATATTTTAGAATTTTAG
Found at i:22059765 original size:16 final size:16
Alignment explanation
Indices: 22059744--22059776 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
22059734 TCTCAGTATG
22059744 TAGGAGTGTTCAAATT
1 TAGGAGTGTTCAAATT
22059760 TAGGAGTGTTCAAATT
1 TAGGAGTGTTCAAATT
22059776 T
1 T
22059777 TAGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (16 bp):
TAGGAGTGTTCAAATT
Found at i:22059803 original size:13 final size:13
Alignment explanation
Indices: 22059785--22059809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22059775 TTTAGTTAAA
22059785 ATCGAATTAATTG
1 ATCGAATTAATTG
22059798 ATCGAATTAATT
1 ATCGAATTAATT
22059810 TAATTCGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
ATCGAATTAATTG
Found at i:22067798 original size:15 final size:16
Alignment explanation
Indices: 22067771--22067800 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22067761 TTAAAGATTA
22067771 AATTTATTTTGAATTT
1 AATTTATTTTGAATTT
22067787 AATTTA-TTTGAATT
1 AATTTATTTTGAATT
22067801 CATAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (16 bp):
AATTTATTTTGAATTT
Found at i:22068546 original size:12 final size:12
Alignment explanation
Indices: 22068531--22068565 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
22068521 TTTAAATATC
22068531 ATTAATAATAAT
1 ATTAATAATAAT
*
22068543 ATTAGTAATAAT
1 ATTAATAATAAT
*
22068555 AATAATAATAA
1 ATTAATAATAA
22068566 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:22068578 original size:19 final size:20
Alignment explanation
Indices: 22068554--22068592 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
22068544 TTAGTAATAA
22068554 TAATAATAATAAAT-TTTTT
1 TAATAATAATAAATGTTTTT
22068573 TAATAATAATAAATGTTTTT
1 TAATAATAATAAATGTTTTT
22068593 GGTAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TAATAATAATAAATGTTTTT
Found at i:22069580 original size:29 final size:29
Alignment explanation
Indices: 22069540--22069737 Score: 113
Period size: 29 Copynumber: 6.8 Consensus size: 29
22069530 TCTAGTCCCC
*
22069540 AAACTTTCCAAAATTCTATTTTAGACACCA
1 AAACTTTCCAAAATTCCATTTT-GACACCA
* *
22069570 AAAC-TTCCAAAAATTACCATTTT-ACCCCT
1 AAACTTTCC-AAAATT-CCATTTTGACACCA
***
22069599 AAACTTTCCAAAATTCCATTTTTGACATTG
1 AAACTTTCCAAAATTCCA-TTTTGACACCA
* * *
22069629 AAAC-TTCCAAAAATTACCGTTTT-ACCCCT
1 AAACTTTCC-AAAATT-CCATTTTGACACCA
* *
22069658 AAACTTTCCAAAATCCCATTTTTA-ACCTCA
1 AAACTTTCCAAAATTCCATTTTGACA-C-CA
* * * *
22069688 AAAC-TTCAAAAATTATCATTTT-ACCCCT
1 AAACTTTCCAAAATT-CCATTTTGACACCA
* *
22069716 AAACTTTCCAAATTTTCATTTT
1 AAACTTTCCAAAATTCCATTTT
22069738 TGACCCCGAT
Statistics
Matches: 131, Mismatches: 23, Indels: 30
0.71 0.12 0.16
Matches are distributed among these distances:
28 21 0.16
29 57 0.44
30 45 0.34
31 8 0.06
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTGACACCA
Found at i:22069633 original size:59 final size:59
Alignment explanation
Indices: 22069536--22069741 Score: 290
Period size: 59 Copynumber: 3.5 Consensus size: 59
22069526 GCTCTCTAGT
* * *
22069536 CCCC-AAACTTTCCAAAATTCTATTTTAGACACCAAAACTTCCAAAAATTACCATTTTA
1 CCCCTAAACTTTCCAAAATTCCATTTTTGACATCAAAACTTCCAAAAATTACCATTTTA
** *
22069594 CCCCTAAACTTTCCAAAATTCCATTTTTGACATTGAAACTTCCAAAAATTACCGTTTTA
1 CCCCTAAACTTTCCAAAATTCCATTTTTGACATCAAAACTTCCAAAAATTACCATTTTA
* * * *
22069653 CCCCTAAACTTTCCAAAATCCCATTTTTAACCTCAAAACTT-CAAAAATTATCATTTTA
1 CCCCTAAACTTTCCAAAATTCCATTTTTGACATCAAAACTTCCAAAAATTACCATTTTA
* *
22069711 CCCCTAAACTTTCCAAATTTTCATTTTTGAC
1 CCCCTAAACTTTCCAAAATTCCATTTTTGAC
22069742 CCCGATTTCA
Statistics
Matches: 130, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
58 46 0.35
59 84 0.65
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.35
Consensus pattern (59 bp):
CCCCTAAACTTTCCAAAATTCCATTTTTGACATCAAAACTTCCAAAAATTACCATTTTA
Found at i:22069758 original size:58 final size:58
Alignment explanation
Indices: 22069579--22070004 Score: 359
Period size: 59 Copynumber: 7.3 Consensus size: 58
22069569 AAAACTTCCA
* *** * *
22069579 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACATTGAAACTTC-CA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTGACCCCG--ATTTCACC
* * ** *
22069638 AAAATTACCGTTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCAAAACTTCA--
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTGACC-C-CGATTTCACC
* * **
22069696 AAAATTATCATTTTACCCCTAAACTTTCCAAATTTTCATTTTTGACCCCGATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACC
* * * * * * **
22069754 AAAATTATCA-TTTACCCCCATA-TTTTCAAAATACTATTTTTGACCCTTATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACC
* * * * * * *
22069810 CAAATTGCCATTTTA-CCCTCGAACCTTCCAAAATTCCATTTTTAACCTCGATTTCACCC
1 AAAATTACCATTTTACCCCT-AAACTTTCCAAAATCCCATTTTTGACCCCGATTTCA-CC
*
22069869 AAAAATTACCATTTT-CCCCTGAACTTTCCAAAATCCCATTTTT-ACCCTCGATTTCACC
1 -AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTGACCC-CGATTTCACC
** * *
22069927 AAAAATTAGTATTTTA-CCCTCGAACCTTCCAAAATCCCATTTTTGACCCCGATTTCACC
1 -AAAATTACCATTTTACCCCT-AAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACC
22069986 AAAAATTA-CATTTTTACCC
1 -AAAATTACCA-TTTTACCC
22070005 TTGGAAGTCA
Statistics
Matches: 302, Mismatches: 48, Indels: 33
0.79 0.13 0.09
Matches are distributed among these distances:
56 42 0.14
57 16 0.05
58 98 0.32
59 124 0.41
60 22 0.07
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTGACCCCGATTTCACC
Found at i:22069844 original size:29 final size:29
Alignment explanation
Indices: 22069811--22069969 Score: 96
Period size: 29 Copynumber: 5.4 Consensus size: 29
22069801 TATTTCACCC
*
22069811 AAATTGCCATTTTACCCTCGAACCTTCCA
1 AAATTCCCATTTTACCCTCGAACCTTCCA
* ** **
22069840 AAATT-CCATTTTTAACCTCGATTTCACCCAA
1 AAATTCCCA-TTTTACCCTCGA-ACCTTCC-A
* * *
22069871 AAATTACCATTTTCCCCT-GAACTTTCCA
1 AAATTCCCATTTTACCCTCGAACCTTCCA
*
22069899 AAA-TCCCATTTTTACCCTCG-A-TTTCACCAA
1 AAATTCCCA-TTTTACCCTCGAACCTT--CC-A
***
22069929 AAATTAGTATTTTACCCTCGAACCTTCCA
1 AAATTCCCATTTTACCCTCGAACCTTCCA
22069958 AAA-TCCCATTTT
1 AAATTCCCATTTT
22069970 TGACCCCGAT
Statistics
Matches: 97, Mismatches: 21, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
27 7 0.07
28 22 0.23
29 25 0.26
30 22 0.23
31 16 0.16
32 5 0.05
ACGTcount: A:0.30, C:0.31, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATTCCCATTTTACCCTCGAACCTTCCA
Found at i:22070027 original size:59 final size:56
Alignment explanation
Indices: 22069635--22070005 Score: 238
Period size: 58 Copynumber: 6.4 Consensus size: 56
22069625 ATTGAAACTT
** * * *** *
22069635 CCAAAAATTACCGTTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTC-AAAACT
1 CCAAAAATTACATTTTTA-CCCTGAAC-TTCCAAAATCCCATTTTT-ACCCCGATTTCA
* * * **
22069693 TCAAAAATTATCA-TTTTACCCCTAAACTTTCCAAATTTTCATTTTTGACCCCGATTTCA
1 CCAAAAATTA-CATTTTTA-CCCTGAAC-TTCCAAAATCCCATTTTT-ACCCCGATTTCA
** * * * * **
22069752 CC-AAAATTATCA--TTTACCCCCATATTTTCAAAATACTATTTTTGACCCTTATTTCA
1 CCAAAAATTA-CATTTTTACCCTGA-ACTTCCAAAATCCCATTTTT-ACCCCGATTTCA
* * * *
22069808 CC-CAAATTGCCA-TTTTACCCTCGAACCTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATT-ACATTTTTACCCT-GAA-CTTCCAAAATCCCATTTTT-ACCCCGATTTCA
*
22069866 CCCAAAAATTACCA-TTTTCCCCTGAACTTTCCAAAATCCCATTTTTACCCTCGATTTCA
1 -CCAAAAATTA-CATTTTTACCCTGAAC-TTCCAAAATCCCATTTTTACCC-CGATTTCA
*
22069925 CCAAAAATTA-GTATTTTACCCTCGAACCTTCCAAAATCCCATTTTTGACCCCGATTTCA
1 CCAAAAATTACAT-TTTTACCCT-GAA-CTTCCAAAATCCCATTTTT-ACCCCGATTTCA
22069984 CCAAAAATTACATTTTTACCCT
1 CCAAAAATTACATTTTTACCCT
22070006 TGGAAGTCAA
Statistics
Matches: 253, Mismatches: 42, Indels: 35
0.77 0.13 0.11
Matches are distributed among these distances:
56 37 0.15
57 13 0.05
58 100 0.40
59 82 0.32
60 21 0.08
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.36
Consensus pattern (56 bp):
CCAAAAATTACATTTTTACCCTGAACTTCCAAAATCCCATTTTTACCCCGATTTCA
Found at i:22082620 original size:54 final size:54
Alignment explanation
Indices: 22082523--22082930 Score: 313
Period size: 54 Copynumber: 7.3 Consensus size: 54
22082513 GAAAAAAAAA
* * ** **
22082523 ATTAGATAAAAAAAATTTTTAGTGTTGGCCATGCAATGATCGACACCAGTATTTTTT
1 ATTAGATAAAAAAAA--TTTGGTGTTGGCCATGCATTGGCCGACACCA-CCTTTTTT
* *
22082580 ATTAGAT-AAAAAAATTTGGTGTTGGCCAATGC-TTGGTCGACACTACCTTTTTT
1 ATTAGATAAAAAAAATTTGGTGTTGGCC-ATGCATTGGCCGACACCACCTTTTTT
* **
22082633 ATCAGATAAAAAAAAATTTGGTGTTAACCATGCATTGGCCGACACCACCTTTTTT
1 ATTAGAT-AAAAAAAATTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTT
* * ** * *
22082688 ATCAGATAAAAAAAATTTGGTGTTAGTTATGCATTGACCGACATCA-CTTTTTT
1 ATTAGATAAAAAAAATTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTT
** * *
22082741 ATTAGATAATAAATATTTTTTTGGTGTTGGCCATGCATTGACCGACACAACCTTTTTT
1 ATTAGATAA-AAA-A--AATTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTT
* * * **
22082799 ATCT-GATAAAAAAATATTTTTTTGTGTTGGTCATGCATTGGTCGACACCAATATTTTTT
1 AT-TAGATAAAAAAA-A---TTTGGTGTTGGCCATGCATTGGCCGACACC-ACCTTTTTT
* * * *
22082858 ATCAGATAAAAAATATTTTTTTTGGTGTTGGCCAATGC-TTGGCCGACACCATCTTATTT
1 ATTAGATAAAAAA-A----ATTTGGTGTTGGCC-ATGCATTGGCCGACACCACCTTTTTT
*
22082917 ATTTGATAAAAAAA
1 ATTAGATAAAAAAA
22082931 TAAATTTATT
Statistics
Matches: 288, Mismatches: 42, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
53 27 0.09
54 63 0.22
55 49 0.17
56 8 0.03
57 36 0.12
58 40 0.14
59 37 0.13
60 23 0.08
61 4 0.01
63 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (54 bp):
ATTAGATAAAAAAAATTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTT
Found at i:22082648 original size:57 final size:57
Alignment explanation
Indices: 22082587--22082937 Score: 252
Period size: 55 Copynumber: 6.2 Consensus size: 57
22082577 TTTATTAGAT
* *
22082587 AAAAAAATTTGGTGTTGGCCAATGC-TTGGTCGACACTACCTTTTTTATCAGAT--AA
1 AAAAAAATTTGGTGTTGGCC-ATGCATTGGCCGACACAACCTTTTTTATCAGATAAAA
** *
22082642 AAAAAAATTTGGTGTTAACCATGCATTGGCCGACACCACCTTTTTTATCAGAT---A
1 AAAAAAATTTGGTGTTGGCCATGCATTGGCCGACACAACCTTTTTTATCAGATAAAA
* ** * *
22082696 AAAAAAATTTGGTGTTAGTTATGCATTGACCGACATC-A-CTTTTTTATTAGATAATAA
1 AAAAAAATTTGGTGTTGGCCATGCATTGGCCGACA-CAACCTTTTTTATCAGATAA-AA
* **** * *
22082753 ATATTTTTTTGGTGTTGGCCATGCATTGACCGACACAACCTTTTTTATCTGATAAAA
1 AAAAAAATTTGGTGTTGGCCATGCATTGGCCGACACAACCTTTTTTATCAGATAAAA
*** * * * **
22082810 AAATATTTTTTTGTGTTGGTCATGCATTGGTCGACACCAATATTTTTTATCAGATAAAA
1 AAA-AAAATTTGGTGTTGGCCATGCATTGGCCGACA-CAACCTTTTTTATCAGATAAAA
**** * * * **
22082869 AATATTTTTTTTGGTGTTGGCCAATGC-TTGGCCGACACCATCTTATTTATTTGATAAAA
1 AA-A-AAAATTTGGTGTTGGCC-ATGCATTGGCCGACACAACCTTTTTTATCAGATAAAA
*
22082928 AAATAAATTT
1 AAAAAAATTT
22082938 ATTTGCTTCT
Statistics
Matches: 244, Mismatches: 40, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
53 13 0.05
54 37 0.15
55 45 0.18
56 1 0.00
57 37 0.15
58 42 0.17
59 40 0.16
60 25 0.10
61 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (57 bp):
AAAAAAATTTGGTGTTGGCCATGCATTGGCCGACACAACCTTTTTTATCAGATAAAA
Found at i:22082676 original size:55 final size:55
Alignment explanation
Indices: 22082526--22082817 Score: 254
Period size: 55 Copynumber: 5.3 Consensus size: 55
22082516 AAAAAAAATT
* * * * * * ** *
22082526 AGATAAAAAAAATTTTTAGTGTTGGCCATGCAATGATCGACACCAGTATTTTTTATT
1 AGATAAAAAAAA-ATTTGGTGTTAGCCATGCATTGACCGACACTA-CCTTTTTTATC
* **
22082583 AGAT--AAAAAAATTTGGTGTTGGCCAATGC-TTGGTCGACACTACCTTTTTTATC
1 AGATAAAAAAAAATTTGGTGTTAGCC-ATGCATTGACCGACACTACCTTTTTTATC
* * *
22082636 AGATAAAAAAAAATTTGGTGTTAACCATGCATTGGCCGACACCACCTTTTTTATC
1 AGATAAAAAAAAATTTGGTGTTAGCCATGCATTGACCGACACTACCTTTTTTATC
** *
22082691 AGAT-AAAAAAAATTTGGTGTTAGTTATGCATTGACCGACA-T-CACTTTTTTATT
1 AGATAAAAAAAAATTTGGTGTTAGCCATGCATTGACCGACACTAC-CTTTTTTATC
*** * *
22082744 AGATAATAAATATTTTTTTGGTGTTGGCCATGCATTGACCGACACAACCTTTTTTATC
1 AGATAA-AAA-A-AAATTTGGTGTTAGCCATGCATTGACCGACACTACCTTTTTTATC
* *
22082802 TGATAAAAAAATATTT
1 AGATAAAAAAAAATTT
22082818 TTTTGTGTTG
Statistics
Matches: 195, Mismatches: 29, Indels: 24
0.79 0.12 0.10
Matches are distributed among these distances:
52 1 0.01
53 25 0.13
54 59 0.30
55 61 0.31
56 2 0.01
57 32 0.16
58 14 0.07
59 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (55 bp):
AGATAAAAAAAAATTTGGTGTTAGCCATGCATTGACCGACACTACCTTTTTTATC
Found at i:22083833 original size:30 final size:30
Alignment explanation
Indices: 22083798--22083875 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
22083788 ATTAAAAAAT
* *
22083798 TTTAAAATATAAATGAAATTAGAAATTAAA
1 TTTAAAATATAAACGAAATTACAAATTAAA
22083828 TTTAAAATATAAACGAAATTACAAATTAAA
1 TTTAAAATATAAACGAAATTACAAATTAAA
*
22083858 TTTAAAAAATAAACGAAA
1 TTTAAAATATAAACGAAA
22083876 AAAATCAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (30 bp):
TTTAAAATATAAACGAAATTACAAATTAAA
Found at i:22084761 original size:21 final size:21
Alignment explanation
Indices: 22084695--22084761 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
22084685 TTTTCATGGC
*
22084695 TAAAAAAATATTTCGAAAATG
1 TAAAAAAATATTTCCAAAATG
* ** **
22084716 TAAAATATAAGATTTTTAATTTG
1 TAAAA-A-AATATTTCCAAAATG
22084739 TAAAAAAATATTTCCAAAATG
1 TAAAAAAATATTTCCAAAATG
22084760 TA
1 TA
22084762 TTTTTTAATA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
21 17 0.50
22 2 0.06
23 15 0.44
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.36
Consensus pattern (21 bp):
TAAAAAAATATTTCCAAAATG
Found at i:22084856 original size:19 final size:19
Alignment explanation
Indices: 22084832--22084874 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
22084822 AAATAATTTT
*
22084832 AAAAAAATTCGAAAA-GCTA
1 AAAAAAATTCAAAAATG-TA
*
22084851 AAAAAATTTCAAAAATGTA
1 AAAAAAATTCAAAAATGTA
22084870 AAAAA
1 AAAAA
22084875 TATATGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAAAAATTCAAAAATGTA
Found at i:22084955 original size:21 final size:20
Alignment explanation
Indices: 22084912--22084960 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
22084902 TTATTTCTGC
*
22084912 AAAAAA-TTCGAAAATATAA
1 AAAAAATTTCGAAAATAAAA
*
22084931 AAAACATTTCGAAAATAGAAA
1 AAAAAATTTCGAAAATA-AAA
22084952 AAAAAATTT
1 AAAAAATTT
22084961 AAAAATTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.20
20 10 0.40
21 10 0.40
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.22
Consensus pattern (20 bp):
AAAAAATTTCGAAAATAAAA
Found at i:22086137 original size:22 final size:22
Alignment explanation
Indices: 22086109--22086157 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
22086099 GTAGTCGAAA
*
22086109 GGTGGTGGTGAGCTAGAATTTG
1 GGTGGTGGTGAGCTAAAATTTG
22086131 GGTGGTGGTGAGCTAAAATTTG
1 GGTGGTGGTGAGCTAAAATTTG
22086153 GGTGG
1 GGTGG
22086158 CCCAATGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.04, G:0.47, T:0.31
Consensus pattern (22 bp):
GGTGGTGGTGAGCTAAAATTTG
Found at i:22086338 original size:94 final size:95
Alignment explanation
Indices: 22086225--22086407 Score: 323
Period size: 94 Copynumber: 1.9 Consensus size: 95
22086215 TTAAGAGTAT
* *
22086225 TTTGGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAAT-
1 TTTGATAAATAATACATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAATC
22086289 TTTTTTATTTAAATAATTTTAAAATTTGAA
66 TTTTTTATTTAAATAATTTTAAAATTTGAA
* *
22086319 TTTGATAAATAATGCATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATC
1 TTTGATAAATAATACATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAATC
22086384 TTTTTTATTTAAATAATTTTAAAA
66 TTTTTTATTTAAATAATTTTAAAA
22086408 GTGATTTTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
94 60 0.71
95 24 0.29
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (95 bp):
TTTGATAAATAATACATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATAATC
TTTTTTATTTAAATAATTTTAAAATTTGAA
Found at i:22086476 original size:18 final size:20
Alignment explanation
Indices: 22086453--22086506 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
22086443 CAACTTCATT
22086453 TAATTTTAATTTCAAA-T-G
1 TAATTTTAATTTCAAACTAG
22086471 TAATTTTAATTT-AAACTAG
1 TAATTTTAATTTCAAACTAG
*
22086490 -AATTTTAAATTCAAACT
1 TAATTTTAATTTCAAACT
22086507 TGTATAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.09
18 23 0.72
19 6 0.19
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (20 bp):
TAATTTTAATTTCAAACTAG
Found at i:22088510 original size:25 final size:23
Alignment explanation
Indices: 22088458--22088544 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
22088448 ACCTTAGCGC
* *
22088458 GCTCTCTGTTTAGCACATCT-CGT
1 GCTCTCTGTTTAGCAC-TGTGTGT
*
22088481 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
*
22088506 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
22088529 GCTCTCCGTTTAGCAC
1 GCTCTCTGTTTAGCAC
22088545 GTTTGTACTC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 35 0.64
24 4 0.07
25 16 0.29
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:22088560 original size:22 final size:23
Alignment explanation
Indices: 22088492--22088560 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
22088482 CTCTCTGTTA
* *
22088492 TTAGCAC-TGTGTGTGCTCTCTGT
1 TTAGCACGT-TGTGTACTCTCCGT
* *
22088515 TTAGCACTTTGTGTGCTCTCCGT
1 TTAGCACGTTGTGTACTCTCCGT
*
22088538 TTAGCACGTT-TGTACTCTTCGT
1 TTAGCACGTTGTGTACTCTCCGT
22088560 T
1 T
22088561 CATTTGTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
22 11 0.27
23 29 0.71
24 1 0.02
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (23 bp):
TTAGCACGTTGTGTACTCTCCGT
Found at i:22091520 original size:26 final size:25
Alignment explanation
Indices: 22091491--22091540 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
22091481 TTTTTTTCGT
22091491 TTATTTCTTAACATTAATTTTAATTG
1 TTATTTCTTAACA-TAATTTTAATTG
* * *
22091517 TTATTTTTTAATATATTTTTAATT
1 TTATTTCTTAACATAATTTTAATT
22091541 TGTCGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (25 bp):
TTATTTCTTAACATAATTTTAATTG
Found at i:22092527 original size:62 final size:61
Alignment explanation
Indices: 22092343--22092527 Score: 180
Period size: 63 Copynumber: 3.0 Consensus size: 61
22092333 GAGGGAAAGT
* * * * *
22092343 TGGTGTCGGCCAATGCATGGCAAACATAAAAAGAAATTTGGTTTTTTTATCAGATAAATAA-AG
1 TGGTGTC-GCCAATGAATGACCAACATAAAAA-AAATTT-GTTTTTTTATCAGATAAAAAATAC
* * * * *
22092406 TGGTGTCGACCAA-GCATTGTCCAACACCAAAAAAAA--TATTTTTTTATCTGATAAAAAAATAC
1 TGGTGTCG-CCAATG-AATGACCAACA-TAAAAAAAATTTGTTTTTTTATCAGAT-AAAAAATAC
22092468 TGGTGTCAGCCAATGAATGACCAACATAAAAAAAATTTGTTTTTTTATCAGATAAAAAAT
1 TGGTGTC-GCCAATGAATGACCAACATAAAAAAAATTTGTTTTTTTATCAGATAAAAAAT
22092528 GTGATGTCTG
Statistics
Matches: 99, Mismatches: 14, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
60 13 0.13
61 14 0.14
62 30 0.30
63 37 0.37
64 5 0.05
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (61 bp):
TGGTGTCGCCAATGAATGACCAACATAAAAAAAATTTGTTTTTTTATCAGATAAAAAATAC
Found at i:22092541 original size:61 final size:59
Alignment explanation
Indices: 22092346--22092592 Score: 180
Period size: 61 Copynumber: 4.0 Consensus size: 59
22092336 GGAAAGTTGG
* * *
22092346 TGTCGGCCAATGC-ATGGCAAACATAAAAAGAAATTTGGTTTTTTTATCAGATAAATAAA-GTGG
1 TGTC-GCCAA-GCAATGGCCAACACAAAAA-AAA-TT-GTTTTTTTATCAGATAAA-AAATGTGA
* * * * * *
22092409 TGTCGACCAAGCATTGTCCAACACCAAAAAAAA-TATTTTTTTATCTGATAAAAAAATACTGG
1 TGTCG-CCAAGCAATGGCCAACA-CAAAAAAAATTGTTTTTTTATCAGAT-AAAAAAT-GTGA
* *
22092471 TGTCAGCCAATG-AATGACCAACATAAAAAAAATTTGTTTTTTTATCAGATAAAAAATGTGA
1 TGTC-GCCAA-GCAATGGCCAACACAAAAAAAA-TTGTTTTTTTATCAGATAAAAAATGTGA
* * ** * *
22092532 TGTCTGCCAAGCATTGGCCAACACAAAATAAATT-ACTTTTTATTAGATAAAAAAGGTGA
1 TGTC-GCCAAGCAATGGCCAACACAAAAAAAATTGTTTTTTTATCAGATAAAAAATGTGA
22092591 TG
1 TG
22092593 CCGGTCAATG
Statistics
Matches: 150, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
59 23 0.15
60 19 0.13
61 39 0.26
62 30 0.20
63 34 0.23
64 5 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (59 bp):
TGTCGCCAAGCAATGGCCAACACAAAAAAAATTGTTTTTTTATCAGATAAAAAATGTGA
Found at i:22092572 original size:123 final size:124
Alignment explanation
Indices: 22092343--22092585 Score: 327
Period size: 123 Copynumber: 2.0 Consensus size: 124
22092333 GAGGGAAAGT
* * *
22092343 TGGTGTCGGCCAATGCATGGCAAACATAAAAAGAAATTTGGTTTTTTTATCAGATAAATAAAGTG
1 TGGTGTCAGCCAATGAATGACAAACATAAAAAGAAATTTGGTTTTTTTATCAGATAAATAAAGTG
* * *
22092408 GTGTCGACCAAGCATTGTCCAACACCAAAAAAAATATTTTTTTATCT-GATAAAAAAATAC
66 ATGTCGACCAAGCATTGGCCAACACCAAAAAAAATA-CTTTTTAT-TAGATAAAAAAATAC
*
22092468 TGGTGTCAGCCAATGAATGACCAACATAAAAA-AAATTT-GTTTTTTTATCAGATAAA-AAATGT
1 TGGTGTCAGCCAATGAATGACAAACATAAAAAGAAATTTGGTTTTTTTATCAGATAAATAAA-GT
*
22092530 GATGTCTG-CCAAGCATTGGCCAACA-CAAAATAAATTACTTTTTATTAGATAAAAAA
65 GATGTC-GACCAAGCATTGGCCAACACCAAAA-AAAATACTTTTTATTAGATAAAAAA
22092586 GGTGATGCCG
Statistics
Matches: 106, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
121 1 0.01
122 24 0.23
123 46 0.43
124 7 0.07
125 28 0.26
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (124 bp):
TGGTGTCAGCCAATGAATGACAAACATAAAAAGAAATTTGGTTTTTTTATCAGATAAATAAAGTG
ATGTCGACCAAGCATTGGCCAACACCAAAAAAAATACTTTTTATTAGATAAAAAAATAC
Found at i:22092613 original size:59 final size:60
Alignment explanation
Indices: 22092386--22092626 Score: 145
Period size: 59 Copynumber: 4.0 Consensus size: 60
22092376 AAATTTGGTT
* * * * *
22092386 TTTTTATCAGATAAATAAA-GTGGTGTCGACCAAGCATT-GTCCAACACCAAAAAAAA-TATT
1 TTTTTATCAGATAAA-AAAGGTGATGCCGGCCAAGCATTAG-CCAACACTAAAAAAAATTA-C
* ** * * * * * **
22092446 TTTTTATCTGATAAAAAAATACTGGTGTCAGCCAATGAATGA-CCAACA-TAAAAAAAATTTGTT
1 TTTTTATCAGAT-AAAAAA-GGTGATGCCGGCCAA-GCATTAGCCAACACTAAAAAAAA-TT-AC
* * * * *
22092509 TTTTTATCAGATAAAAAATGTGATGTCTGCCAAGCATTGGCCAACAC-AAAATAAATTAC
1 TTTTTATCAGATAAAAAAGGTGATGCCGGCCAAGCATTAGCCAACACTAAAAAAAATTAC
* * *
22092568 TTTTTATTAGATAAAAAAGGTGATGCCGGTCAATGCA-TAGTCAACACTAAAAAAAATTA
1 TTTTTATCAGATAAAAAAGGTGATGCCGGCCAA-GCATTAGCCAACACTAAAAAAAATTA
22092627 TCTGATAAAA
Statistics
Matches: 142, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
59 36 0.25
60 32 0.23
61 35 0.25
62 23 0.16
63 16 0.11
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (60 bp):
TTTTTATCAGATAAAAAAGGTGATGCCGGCCAAGCATTAGCCAACACTAAAAAAAATTAC
Found at i:22092714 original size:57 final size:56
Alignment explanation
Indices: 22092624--22092947 Score: 267
Period size: 57 Copynumber: 5.9 Consensus size: 56
22092614 CTAAAAAAAA
* *** *
22092624 TTATCTGAT-AAAAA-AGTGGTGTCGAAAAATGCATGGCCGACACCAAAATTTTTT
1 TTATCTGATAAAAAATACTGGTGTCGGTCAATGCATGGCCAACACCAAAATTTTTT
* ***
22092678 TTATCTGATAAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTCAAAA---AAA
1 TTATCTGAT-AAAAAATACTGGTGTCGGTCAATGCATGGCCAACAC-CAAAATTTTTT
* *** *
22092733 TTATCTGAT-AAAAA-AGTGGTGTCGAAAAATGCATGGCCGACACCAAAATTTTTT
1 TTATCTGATAAAAAATACTGGTGTCGGTCAATGCATGGCCAACACCAAAATTTTTT
* ***
22092787 TTATCTGATAAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTCAAAA---AAA
1 TTATCTGAT-AAAAAATACTGGTGTCGGTCAATGCATGGCCAACAC-CAAAATTTTTT
* * *
22092842 TTATCTGATAAAAAA-AGTGGTGTCGATCAA-GCATTGGCCAACACCAATATTTTTTT
1 TTATCTGATAAAAAATACTGGTGTCGGTCAATGCA-TGGCCAACACCAA-AATTTTTT
* * * * * *
22092898 TTATTTGATAAAAAATATTGGTGTCAGCCAATGCATGACCAACACTAAAA
1 TTATCTGATAAAAAATACTGGTGTCGGTCAATGCATGGCCAACACCAAAA
22092948 AAAATTTATC
Statistics
Matches: 210, Mismatches: 42, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
51 5 0.02
52 29 0.14
53 28 0.13
54 24 0.11
55 18 0.09
56 25 0.12
57 68 0.32
58 13 0.06
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (56 bp):
TTATCTGATAAAAAATACTGGTGTCGGTCAATGCATGGCCAACACCAAAATTTTTT
Found at i:22092886 original size:110 final size:110
Alignment explanation
Indices: 22092389--22093009 Score: 609
Period size: 109 Copynumber: 5.5 Consensus size: 110
22092379 TTTGGTTTTT
* * * *
22092389 TTATCAGATAAATAAAGTGGTGTCGACCAAGCATTGTCCAACACCAAAAAAAATATTTTTTTATC
1 TTATCTGATAAAAAAAGTGGTGTCGAACAAGCATTGGCCAACACC----AAAAT-TTTTTTTATC
* * *
22092454 TGATAAAAAAATACTGGTGTCAGCCAATGAATGACCAACA-TAAAAAAAA
61 TGATAAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTAAAAAAAA
* * * *
22092503 TTTGTTTTTTTATCAGATAAAAAATGTGATGTCTG-CCAAGCATTGGCCAACA-CAAAATAAATT
1 ---------TTATCTGATAAAAAAAGTGGTGTC-GAACAAGCATTGGCCAACACCAAAAT---TT
** * * *
22092566 ACTTTTTAT-TAGAT-AAAAAA-GGTGATGCCGGTCAATGCAT-AGTCAACACTAAAAAAAA
53 --TTTTTATCT-GATAAAAAAATACTGGTGTCGGTCAATGCATGA-CCAACACTAAAAAAAA
* *
22092624 TTATCTGAT-AAAAAAGTGGTGTCGAAAAATGCA-TGGCCGACACCAAAATTTTTTTTATCTGAT
1 TTATCTGATAAAAAAAGTGGTGTCGAACAA-GCATTGGCCAACACCAAAATTTTTTTTATCTGAT
*
22092687 AAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTCAAAAAAA
65 AAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTAAAAAAAA
* *
22092733 TTATCTGAT-AAAAAAGTGGTGTCGAAAAATGCA-TGGCCGACACCAAAATTTTTTTTATCTGAT
1 TTATCTGATAAAAAAAGTGGTGTCGAACAA-GCATTGGCCAACACCAAAATTTTTTTTATCTGAT
*
22092796 AAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTCAAAAAAA
65 AAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTAAAAAAAA
* * *
22092842 TTATCTGATAAAAAAAGTGGTGTCGATCAAGCATTGGCCAACACCAATATTTTTTTTTATTTGAT
1 TTATCTGATAAAAAAAGTGGTGTCGAACAAGCATTGGCCAACACCAA-AATTTTTTTTATCTGAT
* * *
22092907 -AAAAAATATTGGTGTCAGCCAATGCATGACCAACACTAAAAAAAA
65 AAAAAAATACTGGTGTCGGTCAATGCATGACCAACACTAAAAAAAA
* * * * * * *
22092952 TTTATCTAACAAAAAAGGTGGTGTCGATCAAGCATTGGCTAACACTAAATTTTTTTTT
1 -TTATCTGATAAAAAAAGTGGTGTCGAACAAGCATTGGCCAACACCAAAATTTTTTTT
22093010 CAAAATCTCG
Statistics
Matches: 441, Mismatches: 38, Indels: 51
0.83 0.07 0.10
Matches are distributed among these distances:
107 10 0.02
108 7 0.02
109 153 0.35
110 83 0.19
111 79 0.18
112 17 0.04
118 5 0.01
119 1 0.00
120 21 0.05
121 16 0.04
122 11 0.02
123 37 0.08
124 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (110 bp):
TTATCTGATAAAAAAAGTGGTGTCGAACAAGCATTGGCCAACACCAAAATTTTTTTTATCTGATA
AAAAAATACTGGTGTCGGTCAATGCATGACCAACACTAAAAAAAA
Found at i:22093925 original size:39 final size:41
Alignment explanation
Indices: 22093851--22093932 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 41
22093841 ATACATTAAA
* * * *
22093851 TTTATTTATATTAAAAATACCATCATAAATATAATAAATAT
1 TTTATTTATATTAAAAAAAACATAATAAATATAATAAACAT
22093892 TTTA-TTATATTAAAAAAAACA-AATAAATATAATAAACAT
1 TTTATTTATATTAAAAAAAACATAATAAATATAATAAACAT
22093931 TT
1 TT
22093933 GAGTGTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 18 0.49
40 15 0.41
41 4 0.11
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (41 bp):
TTTATTTATATTAAAAAAAACATAATAAATATAATAAACAT
Found at i:22100043 original size:27 final size:27
Alignment explanation
Indices: 22099982--22100036 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
22099972 CAAAAAAAAA
22099982 AAGCAATTAAGCTATTATATTTTTTTT
1 AAGCAATTAAGCTATTATATTTTTTTT
22100009 AAGCAATTAAGCTATTATATTTTTTTT
1 AAGCAATTAAGCTATTATATTTTTTTT
22100036 A
1 A
22100037 CTCAATTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (27 bp):
AAGCAATTAAGCTATTATATTTTTTTT
Found at i:22100129 original size:10 final size:9
Alignment explanation
Indices: 22100115--22100205 Score: 62
Period size: 10 Copynumber: 10.0 Consensus size: 9
22100105 TTGCTCTTAT
22100115 TAAAAATTA
1 TAAAAATTA
22100124 TAAAAAATTA
1 T-AAAAATTA
22100134 TAAAAATTA
1 TAAAAATTA
* *
22100143 TTAAATTTA
1 TAAAAATTA
*
22100152 GAAAAATTA
1 TAAAAATTA
**
22100161 TTAAATTTTAA
1 -TAAAAATT-A
*
22100172 TAAAAATAA
1 TAAAAATTA
22100181 T-AAAA-T-
1 TAAAAATTA
*
22100187 TAAAATTTA
1 TAAAAATTA
22100196 TTAAAAATTA
1 -TAAAAATTA
22100206 GAATTTTGTT
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
6 1 0.02
7 3 0.05
8 5 0.08
9 24 0.39
10 27 0.44
11 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (9 bp):
TAAAAATTA
Found at i:22100139 original size:19 final size:19
Alignment explanation
Indices: 22100115--22100277 Score: 73
Period size: 19 Copynumber: 8.3 Consensus size: 19
22100105 TTGCTCTTAT
*
22100115 TAAAAATTATAAAAAATTA
1 TAAAAATTATAAAAATTTA
*
22100134 TAAAAATTAT-TAAATTTA
1 TAAAAATTATAAAAATTTA
* * *
22100152 GAAAAATTATTAAATTTTAA
1 TAAAAATTATAAAAATTT-A
*
22100172 TAAAAATAATAAAATTAAAATTTA
1 TAAAAAT--T---ATAAAAATTTA
* ***
22100196 TTAAAAATTAGAATTTTGTTTA
1 -TAAAAATTATAA--AAATTTA
**
22100218 TAAAAATCGTAAAAA--TA
1 TAAAAATTATAAAAATTTA
* *
22100235 -AAAAATTGTAAAATTTTA
1 TAAAAATTATAAAAATTTA
*
22100253 TAAAAATCATAAAAAATTTA
1 TAAAAATTAT-AAAAATTTA
22100273 TAAAA
1 TAAAA
22100278 TGCATAAAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 27
0.68 0.15 0.17
Matches are distributed among these distances:
16 12 0.11
17 2 0.02
18 17 0.16
19 22 0.21
20 22 0.21
21 9 0.08
22 5 0.05
23 1 0.01
24 1 0.01
25 16 0.15
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (19 bp):
TAAAAATTATAAAAATTTA
Found at i:22100156 original size:18 final size:18
Alignment explanation
Indices: 22100116--22100168 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
22100106 TGCTCTTATT
* * *
22100116 AAAAATTATAAAAAATTAT
1 AAAAATTAT-TAAATTTAG
22100135 AAAAATTATTAAATTTAG
1 AAAAATTATTAAATTTAG
22100153 AAAAATTATTAAATTT
1 AAAAATTATTAAATTT
22100169 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAAATTATTAAATTTAG
Found at i:22100267 original size:20 final size:20
Alignment explanation
Indices: 22100244--22100288 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
22100234 AAAAAATTGT
*
22100244 AAAATTTTATAAAAAT-CATA
1 AAAAATTTAT-AAAATGCATA
22100264 AAAAATTTATAAAATGCATA
1 AAAAATTTATAAAATGCATA
22100284 AAAAA
1 AAAAA
22100289 ATCCCTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATTTATAAAATGCATA
Found at i:22100422 original size:10 final size:9
Alignment explanation
Indices: 22100390--22100432 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
22100380 AACATGTGAC
22100390 TAAAAATAA
1 TAAAAATAA
*
22100399 TAAAAAAAA
1 TAAAAATAA
*
22100408 CAAAAATCAA
1 TAAAAAT-AA
*
22100418 TAAAAATTA
1 TAAAAATAA
22100427 TAAAAA
1 TAAAAA
22100433 ATTATAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (9 bp):
TAAAAATAA
Found at i:22100565 original size:9 final size:9
Alignment explanation
Indices: 22100504--22100686 Score: 87
Period size: 9 Copynumber: 20.6 Consensus size: 9
22100494 TAACATTTCG
22100504 TATAATTTCT
1 TATAATTT-T
*
22100514 TACAA-TTT
1 TATAATTTT
*
22100522 TATAAATTT
1 TATAATTTT
22100531 TATAATTTT
1 TATAATTTT
* *
22100540 T-T-ATGTC
1 TATAATTTT
22100547 TAT-ATATTT
1 TATAAT-TTT
22100556 TATAATTTT
1 TATAATTTT
**
22100565 TACGATTTT
1 TATAATTTT
**
22100574 TACGATTTT
1 TATAATTTT
22100583 T-TAATTTT
1 TATAATTTT
22100591 TAATAATTTT
1 T-ATAATTTT
*
22100601 TA-AATATT
1 TATAATTTT
*
22100609 TA-ATTTTT
1 TATAATTTT
*
22100617 TATTAAAATTT
1 TA-T-AATTTT
* *
22100628 AATAATATT
1 TATAATTTT
22100637 TATAACTTTT
1 TATAA-TTTT
*
22100647 TATTGATTTT
1 TA-TAATTTT
* *
22100657 AAT-TTTTT
1 TATAATTTT
22100665 TAT-ATTTT
1 TATAATTTT
22100673 TATAATTTT
1 TATAATTTT
*
22100682 AATAA
1 TATAA
22100687 AAGCAGAGGC
Statistics
Matches: 134, Mismatches: 27, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
7 4 0.03
8 41 0.31
9 57 0.43
10 25 0.19
11 7 0.05
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (9 bp):
TATAATTTT
Done.