Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 15 of 182
Found at i:6133495 original size:23 final size:23
Alignment explanation
Indices: 6133469--6133523 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
6133459 GAACATTAAC
6133469 GTGCTTACTGTTCAACACTGTGT
1 GTGCTTACTGTTCAACACTGTGT
* *
6133492 GTGCTCACTGTTCAGCACTGTGT
1 GTGCTTACTGTTCAACACTGTGT
6133515 GTGCTTACT
1 GTGCTTACT
6133524 AATTCGCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (23 bp):
GTGCTTACTGTTCAACACTGTGT
Found at i:6133616 original size:23 final size:23
Alignment explanation
Indices: 6133484--6133616 Score: 135
Period size: 23 Copynumber: 5.8 Consensus size: 23
6133474 TACTGTTCAA
* *
6133484 CACTGTGTGTGCTCACTG-TTCAG
1 CACTGTGTGTGCTTACTGATT-TG
* *
6133507 CACTGTGTGTGCTTACTAATTCG
1 CACTGTGTGTGCTTACTGATTTG
***
6133530 CACTAAATGTGCTTACTGATTTG
1 CACTGTGTGTGCTTACTGATTTG
*
6133553 CACTGTGTGTGCTTA-TTACTTTG
1 CACTGTGTGTGCTTACTGA-TTTG
* *
6133576 CACTGCGTGTGCCTACTGATTTG
1 CACTGTGTGTGCTTACTGATTTG
*
6133599 CACTGTGTGTGGTTACTG
1 CACTGTGTGTGCTTACTG
6133617 TTTCCCCAGC
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
22 2 0.02
23 83 0.93
24 4 0.04
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (23 bp):
CACTGTGTGTGCTTACTGATTTG
Found at i:6145261 original size:31 final size:31
Alignment explanation
Indices: 6145223--6145287 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
6145213 TTTGTTGATG
6145223 TATTGTTTTCAAAAATTTAATATCATCTTTA
1 TATTGTTTTCAAAAATTTAATATCATCTTTA
*
6145254 TATTGTTTTCAAAAATTTAATGTCATCTTTA
1 TATTGTTTTCAAAAATTTAATATCATCTTTA
6145285 TAT
1 TAT
6145288 GTTGTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (31 bp):
TATTGTTTTCAAAAATTTAATATCATCTTTA
Found at i:6149235 original size:18 final size:18
Alignment explanation
Indices: 6149208--6149243 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6149198 GTTAAAATTT
* *
6149208 TATTTTAATAATTTTATA
1 TATTTCAATAATATTATA
6149226 TATTTCAATAATATTATA
1 TATTTCAATAATATTATA
6149244 CAAATGTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTCAATAATATTATA
Found at i:6155717 original size:18 final size:17
Alignment explanation
Indices: 6155689--6155728 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
6155679 CATCACTAGC
6155689 AACTTGCATG-ATGCAA
1 AACTTGCATGAATGCAA
6155705 ATACTTGGCATGAATGCAA
1 A-ACTT-GCATGAATGCAA
6155724 AACTT
1 AACTT
6155729 TACACATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 4 0.19
18 9 0.43
19 7 0.33
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (17 bp):
AACTTGCATGAATGCAA
Found at i:6157367 original size:5 final size:5
Alignment explanation
Indices: 6157359--6157400 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
6157349 TTTTAAATTT
6157359 TTAAA TTAAA TTAAA TTAAA TTAAA --AAA TTTTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA --TTAAA TTAAA TT
6157401 GAATCGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.09
5 27 0.82
7 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:6157374 original size:30 final size:30
Alignment explanation
Indices: 6157339--6157422 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
6157329 ATTTTAATAG
* ** *
6157339 TTAAATTTAATTTTAAATTTTTAAATTAAA
1 TTAAATTAAATTAAAAAATTTTAAATTAAA
6157369 TTAAATTAAATTAAAAAATTTTAAATTAAA
1 TTAAATTAAATTAAAAAATTTTAAATTAAA
* ** *
6157399 TTGAATCGAATTAATAAATTTTAA
1 TTAAATTAAATTAAAAAATTTTAA
6157423 TATTTATATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (30 bp):
TTAAATTAAATTAAAAAATTTTAAATTAAA
Found at i:6163153 original size:16 final size:16
Alignment explanation
Indices: 6163134--6163178 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
6163124 TATTATTAAT
6163134 AATTTAAAATTTTATA
1 AATTTAAAATTTTATA
*
6163150 AATTATAAAATATT-TA
1 AATT-TAAAATTTTATA
6163166 AA-TTAAAATTTTA
1 AATTTAAAATTTTA
6163179 GCATTCCGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 8 0.32
15 1 0.04
16 8 0.32
17 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAAAATTTTATA
Found at i:6176131 original size:16 final size:18
Alignment explanation
Indices: 6176095--6176132 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6176085 GAAACATTTA
*
6176095 TTTTAATGTTTTCAGTAT
1 TTTTAATGTATTCAGTAT
6176113 TTTTAATGTATT-A-TAT
1 TTTTAATGTATTCAGTAT
6176129 TTTT
1 TTTT
6176133 TAATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.66
Consensus pattern (18 bp):
TTTTAATGTATTCAGTAT
Found at i:6176908 original size:25 final size:26
Alignment explanation
Indices: 6176859--6176909 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
6176849 AATAAATAAA
* *
6176859 TTTTATATAGTATTTTTGAAATTATT
1 TTTTATATACTACTTTTGAAATTATT
*
6176885 TTTTATATACTACTTTT-AAGTTATT
1 TTTTATATACTACTTTTGAAATTATT
6176910 ACTATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTATATACTACTTTTGAAATTATT
Found at i:6177419 original size:19 final size:18
Alignment explanation
Indices: 6177395--6177459 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
6177385 TACAGGTTAT
6177395 AAAAATTAAATTATAACAA
1 AAAAATTAAATTATAA-AA
***
6177414 AAAAATTTTGTTATAAATA
1 AAAAATTAAATTATAAA-A
*
6177433 AAAAA-TAAATTATATTAA
1 AAAAATTAAATTATA-AAA
6177451 AAAAATTAA
1 AAAAATTAA
6177460 CGTTACAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 13 0.36
19 23 0.64
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATTAAATTATAAAA
Found at i:6177648 original size:20 final size:19
Alignment explanation
Indices: 6177622--6177666 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
6177612 AATCTTTATA
*
6177622 AATTTTTATAGTAATTAAT
1 AATTTTTATAATAATTAAT
6177641 ATATTTTTATAATAATTAAT
1 A-ATTTTTATAATAATTAAT
6177661 AATTTT
1 AATTTT
6177667 AATTTAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTTTATAATAATTAAT
Found at i:6178548 original size:21 final size:21
Alignment explanation
Indices: 6178470--6178552 Score: 55
Period size: 21 Copynumber: 3.8 Consensus size: 21
6178460 ATCTAAAAAA
*
6178470 TGAT-ATTAGATTAATTAAAT
1 TGATGATTAAATTAATTAAAT
6178490 AGTGAATAGATATAAATTAATTAAAT
1 --TG-AT-GAT-TAAATTAATTAAAT
* **
6178516 CGA-GTAAAAAATTAATTAAAT
1 TGATG-ATTAAATTAATTAAAT
6178537 TGATGATTAAA-TAATT
1 TGATGATTAAATTAATT
6178553 TTTTATAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
20 5 0.10
21 20 0.42
22 4 0.08
23 3 0.06
24 1 0.02
25 2 0.04
26 13 0.27
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.37
Consensus pattern (21 bp):
TGATGATTAAATTAATTAAAT
Found at i:6183352 original size:18 final size:17
Alignment explanation
Indices: 6183329--6183362 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6183319 AATGTCCATT
6183329 AATACACAAAAATAATTC
1 AATACA-AAAAATAATTC
*
6183347 AATACAAACAATAATT
1 AATACAAAAAATAATT
6183363 TCAAAGTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
AATACAAAAAATAATTC
Found at i:6188970 original size:6 final size:6
Alignment explanation
Indices: 6188959--6189010 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
6188949 TCTCACCCTC
* * *
6188959 CCCAAT CCCAAT CCCAAT CCCAAT CCCAAC CCCAAC CCCAAC CCCAAT
1 CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT
6189007 CCCA
1 CCCA
6189011 TGCTTTCACC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.33, C:0.58, G:0.00, T:0.10
Consensus pattern (6 bp):
CCCAAT
Found at i:6199607 original size:17 final size:17
Alignment explanation
Indices: 6199585--6199619 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6199575 CAAAAGAAAA
6199585 TCCCTGGGTATTTAATT
1 TCCCTGGGTATTTAATT
6199602 TCCCTGGGTATTTAATT
1 TCCCTGGGTATTTAATT
6199619 T
1 T
6199620 TAATGATGAA
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:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (17 bp):
TCCCTGGGTATTTAATT
Found at i:6200605 original size:23 final size:23
Alignment explanation
Indices: 6200579--6200725 Score: 170
Period size: 23 Copynumber: 6.3 Consensus size: 23
6200569 AGTACTGGGC
6200579 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
6200602 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
6200625 ATCGGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
6200648 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
6200672 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
6200696 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
6200719 ATCAGAG
1 AACAGAG
6200726 CGCGCGCTAG
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.01
23 87 0.82
24 2 0.02
25 15 0.14
26 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:6200638 original size:46 final size:46
Alignment explanation
Indices: 6200581--6200725 Score: 202
Period size: 46 Copynumber: 3.1 Consensus size: 46
6200571 TACTGGGCAA
* *
6200581 CAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
* * *
6200627 CGGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
*
6200673 AACAGAGAGCACGA-GACGTGCTAAACAGAGAGCACACACAGTGCTAAT
1 --CAGAGAGCAC-ACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
6200721 CAGAG
1 CAGAG
6200726 CGCGCGCTAG
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
46 46 0.53
48 40 0.46
49 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.26, T:0.11
Consensus pattern (46 bp):
CAGAGAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
Found at i:6212064 original size:16 final size:16
Alignment explanation
Indices: 6212043--6212078 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6212033 ACCAAAAGAA
*
6212043 TATAAAATATTAAAAT
1 TATAAAATAATAAAAT
*
6212059 TATAAAATAATATAAT
1 TATAAAATAATAAAAT
6212075 TATA
1 TATA
6212079 TTCAATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAAAATAATAAAAT
Found at i:6219870 original size:27 final size:29
Alignment explanation
Indices: 6219835--6219892 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
6219825 ATAAAATTAC
6219835 AATTTGATTT-TT-TTTAAAAATAATAAA
1 AATTTGATTTATTCTTTAAAAATAATAAA
*
6219862 AATTTGATTTAATTCTTTAAAAATTATAAA
1 AATTTGATTT-ATTCTTTAAAAATAATAAA
6219892 A
1 A
6219893 TATAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.37
29 2 0.07
30 15 0.56
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (29 bp):
AATTTGATTTATTCTTTAAAAATAATAAA
Found at i:6227046 original size:19 final size:19
Alignment explanation
Indices: 6227016--6227066 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
6227006 TACGTTGAAG
*
6227016 ATTATTTAAAAAGTATTAAGA
1 ATTA-TTAAAAAATATTAA-A
*
6227037 ATTATAAAAAAATATTAAA
1 ATTATTAAAAAATATTAAA
6227056 ATTATTAAAAA
1 ATTATTAAAAA
6227067 CAATGTCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 11 0.41
20 12 0.44
21 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
ATTATTAAAAAATATTAAA
Found at i:6227046 original size:20 final size:19
Alignment explanation
Indices: 6227023--6227066 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6227013 AAGATTATTT
*
6227023 AAAAAGTATTAAGAATTATA
1 AAAAAATATTAA-AATTATA
*
6227043 AAAAAATATTAAAATTATT
1 AAAAAATATTAAAATTATA
6227062 AAAAA
1 AAAAA
6227067 CAATGTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAAATATTAAAATTATA
Found at i:6227066 original size:10 final size:10
Alignment explanation
Indices: 6227016--6227066 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
6227006 TACGTTGAAG
6227016 ATTATTTAAAA
1 ATTA-TTAAAA
* *
6227027 AGTATTAAGA
1 ATTATTAAAA
*
6227037 ATTATAAAAA
1 ATTATTAAAA
*
6227047 AATATT-AAA
1 ATTATTAAAA
6227056 ATTATTAAAA
1 ATTATTAAAA
6227066 A
1 A
6227067 CAATGTCAGA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
9 8 0.26
10 20 0.65
11 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (10 bp):
ATTATTAAAA
Found at i:6228705 original size:17 final size:18
Alignment explanation
Indices: 6228669--6228707 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6228659 ATTTTTTAAA
*
6228669 TAATTTTATTATAATTTT
1 TAATTGTATTATAATTTT
*
6228687 TAATTGTATT-TATTTTT
1 TAATTGTATTATAATTTT
6228704 TAAT
1 TAAT
6228708 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TAATTGTATTATAATTTT
Found at i:6229114 original size:25 final size:27
Alignment explanation
Indices: 6229054--6229114 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
6229044 AGTCTAATTT
*
6229054 AATATTAATT-TAATTAAAAATTATTAA
1 AATA-TAATTATAATTAAAAATTATAAA
6229081 AATAT--TTATAATTAAAAA-TA-AAA
1 AATATAATTATAATTAAAAATTATAAA
6229104 AATATAATTAT
1 AATATAATTAT
6229115 TGTTACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
23 7 0.23
24 4 0.13
25 14 0.47
26 1 0.03
27 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATAATTATAATTAAAAATTATAAA
Found at i:6233842 original size:42 final size:41
Alignment explanation
Indices: 6233717--6233982 Score: 232
Period size: 42 Copynumber: 6.4 Consensus size: 41
6233707 CGTTTGGAAA
* * * *
6233717 CAAAGCGCCGCAAAAGGTAAAG-CATTAGCGGGGCTTTTCC
1 CAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTCC
* * * * * *
6233757 TAATGCGCCGCTAAAGGTAAAG-CATTAGCGGCACTTTTTC
1 CAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTCC
** *
6233797 CACAAGCGCCGCTAAAGGTTGGGTCATTAACGGCGCTTTTCC
1 CA-AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTCC
* * * *
6233839 CACAAGCGCCGCTAAAAGTCGGGTCATTAGCGGCGATTTCCC
1 CA-AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTCC
* * * *
6233881 CAAAGTGCCGCTAAAGGTCTGGTCATTAGCGACGCTTATAT-A
1 CAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTT-T-TCC
* * * *
6233923 AAAAGCGTCGCTGAAGGTCAGGTCATTAGCGGCGCTTTTCT
1 CAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTCC
*
6233964 AATAAGCGCCGCTAAAGGT
1 CA-AAGCGCCGCTAAAGGT
6233983 GCGCATTTGC
Statistics
Matches: 185, Mismatches: 35, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
40 36 0.19
41 49 0.26
42 100 0.54
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (41 bp):
CAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTCC
Found at i:6235438 original size:43 final size:43
Alignment explanation
Indices: 6235319--6235440 Score: 181
Period size: 43 Copynumber: 2.8 Consensus size: 43
6235309 CTATTCCCGC
** * *
6235319 AAGCGCCGCTAAAGAATATGGTATTTAGCGGCGCTTGCGGGAA
1 AAGCGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTTGCGGGAA
* * *
6235362 TAGCGTCGCTAAAGAGCATGGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTTGCGGGAA
6235405 AAGCGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTT
6235441 TTTTCTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTTGCGGGAA
Found at i:6236988 original size:7 final size:7
Alignment explanation
Indices: 6236976--6237010 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
6236966 TATACTCTTA
6236976 GAAAAGG
1 GAAAAGG
6236983 GAAAAGG
1 GAAAAGG
6236990 GAAAAGG
1 GAAAAGG
6236997 GAAAAGG
1 GAAAAGG
6237004 GAAAAGG
1 GAAAAGG
6237011 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GAAAAGG
Found at i:6242628 original size:9 final size:9
Alignment explanation
Indices: 6242616--6242642 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6242606 TGAGGTTCCT
6242616 GAGAAGCAG
1 GAGAAGCAG
6242625 GAGAAGCAG
1 GAGAAGCAG
6242634 GAGAAGCAG
1 GAGAAGCAG
6242643 ATGAGGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.44, T:0.00
Consensus pattern (9 bp):
GAGAAGCAG
Found at i:6247112 original size:955 final size:939
Alignment explanation
Indices: 6245256--6247126 Score: 2358
Period size: 955 Copynumber: 2.0 Consensus size: 939
6245246 TGGCTGAATA
6245256 ACTAGATAGATCCACTTTTGACTCAAATCCTGTTGTCTTTGCTAATCAATTTTGTACTAGCTTCA
1 ACTAGATAGATCCACTTTTGACTCAAATCCTGTTGTCTTTGCTAATCAATTTTGTACTAGCTTCA
* *
6245321 AATTTCAGAAGTTAAAATATGTTTAAGTTACAGTTAAACTAAATTACCATAGAAATTATGTCAGC
66 AATTTC--AAG---AAATATGTTCAAGTTACAGTTAAACTAAATTACCACAGAAATTATGTCAGC
6245386 TGACGATCAGCACATGACGTTACCTAAATGATGCAACCATCAATAGATTCTCTTAGACCATATCG
126 TGACGATCAGCACATGACGTTACCTAAATGATGCAACCATCAATAGATTCTCTTAGACCATATCG
* * *
6245451 AACAAATTAAGATTACCTATATTCAGCACACGCCACTTGCCGACATAAATAACAAGATTAATAGA
191 AACAAATTAAGATAACCTATATTCAGCACACGCCACTAGCCAACATAAATAACAAGATTAATAGA
** * * * *
6245516 TTTGAGTGTTTTTGACGTGACATGAAACGTAAAATCAAGAACCGTTACTCATGTGTCCAAATTCA
256 TACGAGTGTTTTTGACGTAACATAAAACGTAAAAGCAAGAACCGTTACTCATGTGCCCAAATTCA
* * * *
6245581 TCTGTATAAAAACCGACAGATCTTACTCCATGTTAGTATATGAGCAACAGGACGCGTGCTAGTGT
321 TCCGTATAAAAACCGACAGATCTTAATCCATGTTAGTATATGAGCAACAGGACACGTGCTAGGGT
* * * *
6245646 TTGAACAAGATTTGCAATGAGCCGACAAACATGCAATCTAAGAATTTCCAACTTTATTTGTCTAA
386 TTGAACAAGACTCGCAATGAGCCAACAAACATGCAATCTAAGAATTTCCAAATTTATTTGTCTAA
* ** * *
6245711 AACTAACAGATCTTAGTAGATATTAACCACTTGAGCGGCAGAAAACATGCTATTATTTGCACTTG
451 AACCAACAGATCTTAGTAGATATTAACCACTCAAGCAGCAGAAAACATGCTAGTATTTGCACTTG
* * * *
6245776 ATAACAACTCATATTCGGCTAATCAGCATGTAATCCTACTTTATCCTCATGACCTACCAACTTCT
516 ATAACAACTCATATTCGGCTAATCAGAATGCAATCCTACTTTATCCTCATGACCCACAAACTTCT
* * * *
6245841 ACCAATTATATTACCGGTTTCGAGCAAAAGGCAAAACAAATCCACGCTTGTAAAAAGCATTTAAT
581 ACCAACTATATTACCGGTTACGAGCAAAAGGCAAAACAAATCCACGCATGTAAAAAGCATCTAAT
* * * * * **
6245906 GCAAAACATACCCTAGCTTGGGAAGAAGAGTCTTCAGGAATTCCCTGGTGTCAAAAAGTATATAA
646 GCAAAACATACCCTAACATAGGAAGAACAGCCTTCAAAAATTCCCTGGTGTCAAAAAGTATATAA
*
6245971 CCACAAAAATCAGTCAGTAACAACAAGTATGCAATAGTAAATTTCAGACAATTTGATAAATACAG
711 CCACAAAAATCAGTCAGT-A-AACAAGTATGCAATAATAAATTTCAGACAATTTGATAAATACAG
6246036 ATACAAGATTATAAAATTCCTTAGTCAGGTACTAGATTTTTCCATTATGATCTAAAACATTAAGC
774 ATACAAGATTATAAAATTCCTTAGTCAGGTACTAGATTTTTCCATTATGATCTAAAACATTAAGC
* *
6246101 AGCAGAAGTCAGATAAAATGTTGACAAGGTGGCTACATTTGAAACTTTTACAATTAGTACAACTA
839 AACAAAAGTCAGATAAAATGTTGACAAGGTGGCTACATTTGAAACTTTTACAATTAGTACAACTA
6246166 TGTTCATTGCCTTGAAACTCATTGATATAAAAGAGT
904 TGTTCATTGCCTTGAAACTCATTGATATAAAAGAGT
* * * * *
6246202 ACTA-ATAGATCCACTTTTGACTCAAATCCTGTTGTGTTTGCTGATTAGTTTTGTATTAGCTTC-
1 ACTAGATAGATCCACTTTTGACTCAAATCCTGTTGTCTTTGCTAATCAATTTTGTACTAGCTTCA
* *
6246265 AATATTC-AG-AA-CT-TTCAAGTTACAGTTAAACTAAATTACCACAGAAATTATGTCAGCTTAC
66 AAT-TTCAAGAAATATGTTCAAGTTACAGTTAAACTAAATTACCACAGAAATTATGTCAGCTGAC
* * *
6246326 GATCGGCACATGACGTTACCTAAATGATGCAATCATCAATAGATTCTCTTTGACCATATCGAACA
130 GATCAGCACATGACGTTACCTAAATGATGCAACCATCAATAGATTCTCTTAGACCATATCGAACA
* * * *
6246391 AATTAAGGTAACCTATATTCAGCACATGCCACTAGCCAACATAAATAACTAGATTACTAGA-ACG
195 AATTAAGATAACCTATATTCAGCACACGCCACTAGCCAACATAAATAACAAGATTAATAGATACG
* * *
6246455 AGTGTTCTTGACATGACTTAATCATAATATAAAAGGTAAAAGCAAGAAGCGTTACTCATG-GACC
260 AGTGTT-TT----TGACGTAA-C-----ATAAAACGTAAAAGCAAGAACCGTTACTCATGTG-CC
* *
6246519 CAAATTTATCCGTA-CAAAACCGACAGATCTTAATCCATGTTAGTATATGAGCAACAGGACACGT
313 CAAATTCATCCGTATAAAAACCGACAGATCTTAATCCATGTTAGTATATGAGCAACAGGACACGT
* * *
6246583 GC-CGGGCATTTGAACAAGACTCGCGATGAGCCAACAAACATGCAATCTAAG-GTTCTCCAAATT
378 GCTAGGG--TTTGAACAAGACTCGCAATGAGCCAACAAACATGCAATCTAAGAATT-TCCAAATT
*
6246646 TATTTGTCTAAAAACCAACAGATCTTGGTAGATATTAACCACTCAAGCAGCAGAAAACATGCTAG
440 TATTTGTCT-AAAACCAACAGATCTTAGTAGATATTAACCACTCAAGCAGCAGAAAACATGCTAG
** *
6246711 TATTTGAACAATGCACTTGATTAA-AGA-TCATATTCTTCTAATCAGAATGCAATCCTATTTTAT
504 TA-TT------TGCACTTGA-TAACA-ACTCATATTCGGCTAATCAGAATGCAATCCTACTTTAT
* * * * *
6246774 CCTCAAATCATGACCCACAAACTTGTACCAACTGTGTTACCGGTTACTAGCAAAAGGCAAAACCG
560 -C-C---TCATGACCCACAAACTTCTACCAACTATATTACCGGTTACGAGCAAAAGGCAAAA-CA
** ** * *
6246839 CGT-TGCGCATGT-CAAATCATCTAA-GCAAAACATACCCTAACATAGGAAGAACAGCCTTCAAA
619 AATCCACGCATGTAAAAAGCATCTAATGCAAAACATACCCTAACATAGGAAGAACAGCCTTCAAA
* * * * * * * *
6246901 AATTCCTTGGTGTCAAAAAAGTATATGACCTCCAGAGTCGGTTAGT-AACAAGTATGCAATAATA
684 AATTCCCTGGTGTC-AAAAAGTATATAACCACAAAAATCAGTCAGTAAACAAGTATGCAATAATA
* * * * * *
6246965 GATTTCGGACGATTTGATAAGTACAGATAGC-AGATTATAAGATTCCTTAGTCAGGTACTGGATT
748 AATTTCAGACAATTTGATAAATACAGATA-CAAGATTATAAAATTCCTTAGTCAGGTACTAGATT
*
6247029 TTTCCATTATGATCTAAAACATTAAGCAACAAAATTCAGATAAAATGTTGACAAGGTGGCTACAT
812 TTTCCATTATGATCTAAAACATTAAGCAACAAAAGTCAGATAAAATGTTGACAAGGTGGCTACAT
* * *
6247094 TTG-AACATTTTGCAATTAGTAGAATTATGTTCA
877 TTGAAAC-TTTTACAATTAGTACAACTATGTTCA
6247127 GTGTTTTTGT
Statistics
Matches: 793, Mismatches: 97, Indels: 61
0.83 0.10 0.06
Matches are distributed among these distances:
935 7 0.01
936 163 0.21
937 1 0.00
938 2 0.00
940 6 0.01
941 1 0.00
942 2 0.00
944 5 0.01
945 109 0.14
946 100 0.13
947 51 0.06
948 2 0.00
954 44 0.06
955 166 0.21
956 2 0.00
957 44 0.06
958 33 0.04
959 53 0.07
960 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (939 bp):
ACTAGATAGATCCACTTTTGACTCAAATCCTGTTGTCTTTGCTAATCAATTTTGTACTAGCTTCA
AATTTCAAGAAATATGTTCAAGTTACAGTTAAACTAAATTACCACAGAAATTATGTCAGCTGACG
ATCAGCACATGACGTTACCTAAATGATGCAACCATCAATAGATTCTCTTAGACCATATCGAACAA
ATTAAGATAACCTATATTCAGCACACGCCACTAGCCAACATAAATAACAAGATTAATAGATACGA
GTGTTTTTGACGTAACATAAAACGTAAAAGCAAGAACCGTTACTCATGTGCCCAAATTCATCCGT
ATAAAAACCGACAGATCTTAATCCATGTTAGTATATGAGCAACAGGACACGTGCTAGGGTTTGAA
CAAGACTCGCAATGAGCCAACAAACATGCAATCTAAGAATTTCCAAATTTATTTGTCTAAAACCA
ACAGATCTTAGTAGATATTAACCACTCAAGCAGCAGAAAACATGCTAGTATTTGCACTTGATAAC
AACTCATATTCGGCTAATCAGAATGCAATCCTACTTTATCCTCATGACCCACAAACTTCTACCAA
CTATATTACCGGTTACGAGCAAAAGGCAAAACAAATCCACGCATGTAAAAAGCATCTAATGCAAA
ACATACCCTAACATAGGAAGAACAGCCTTCAAAAATTCCCTGGTGTCAAAAAGTATATAACCACA
AAAATCAGTCAGTAAACAAGTATGCAATAATAAATTTCAGACAATTTGATAAATACAGATACAAG
ATTATAAAATTCCTTAGTCAGGTACTAGATTTTTCCATTATGATCTAAAACATTAAGCAACAAAA
GTCAGATAAAATGTTGACAAGGTGGCTACATTTGAAACTTTTACAATTAGTACAACTATGTTCAT
TGCCTTGAAACTCATTGATATAAAAGAGT
Found at i:6248721 original size:32 final size:32
Alignment explanation
Indices: 6248669--6248731 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
6248659 TTATAAACTT
* * *
6248669 ATAAATTGATTACTTGAATTTAATCACTCATG
1 ATAAATTAATTAATTGAATTTAATAACTCATG
* *
6248701 ATAAATTAATTAATTTAATTTGATAACTCAT
1 ATAAATTAATTAATTGAATTTAATAACTCAT
6248732 ACTAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCATG
Found at i:6255376 original size:30 final size:29
Alignment explanation
Indices: 6255340--6255401 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
6255330 GGATAAAAGG
* *
6255340 AAAGTAAAAGTTTT-AGCGGAAAAGTGAAAA
1 AAAGTAAAAATTTTGAG-AGAAAAGT-AAAA
6255370 AAAGTAAAAATTTTGAGAGAAAAGTAAAA
1 AAAGTAAAAATTTTGAGAGAAAAGTAAAA
6255399 AAA
1 AAA
6255402 CTCGAAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.24
30 20 0.69
31 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (29 bp):
AAAGTAAAAATTTTGAGAGAAAAGTAAAA
Found at i:6255528 original size:18 final size:18
Alignment explanation
Indices: 6255497--6255544 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
6255487 AAAATTTAAA
6255497 AAATAATTCGAATTAATTC
1 AAATAATTC-AATTAATTC
*
6255516 AAATAATTCAATTCATTC
1 AAATAATTCAATTAATTC
**
6255534 ATTTAATTCAA
1 AAATAATTCAA
6255545 AATTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATAATTCAATTAATTC
Found at i:6271848 original size:10 final size:11
Alignment explanation
Indices: 6271828--6271860 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6271818 GAATTTGTAT
6271828 ATAACAAATTA
1 ATAACAAATTA
6271839 ATAA-AAATTA
1 ATAACAAATTA
*
6271849 ATAATAAATTA
1 ATAACAAATTA
6271860 A
1 A
6271861 AATATAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAACAAATTA
Found at i:6271864 original size:10 final size:11
Alignment explanation
Indices: 6271828--6271864 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
6271818 GAATTTGTAT
*
6271828 ATAACAAATTA
1 ATAATAAATTA
6271839 ATAA-AAATTA
1 ATAATAAATTA
6271849 ATAATAAATTA
1 ATAATAAATTA
6271860 A-AATA
1 ATAATA
6271865 TAAGTAGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATAAATTA
Found at i:6279939 original size:25 final size:25
Alignment explanation
Indices: 6279908--6279963 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
6279898 GTTCCAATCC
*
6279908 TTTTTTTCCTTACAAAACTTGCTTT
1 TTTTTTTCCTTACAAAACATGCTTT
6279933 TGTTTTTTCCTTACAAAACATGCTTT
1 T-TTTTTTCCTTACAAAACATGCTTT
6279959 TTTTT
1 TTTTT
6279964 GTACCCTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.20, C:0.18, G:0.05, T:0.57
Consensus pattern (25 bp):
TTTTTTTCCTTACAAAACATGCTTT
Found at i:6283408 original size:23 final size:24
Alignment explanation
Indices: 6283341--6283408 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 24
6283331 TGAAATTTAA
* * *
6283341 TAATTTTATCTATTCAAAAAAATT
1 TAATTTTATTTATTCAAAATAAGT
** *
6283365 TAATAAT-TTTATTCAACATAAGT
1 TAATTTTATTTATTCAAAATAAGT
6283388 TAATTTTATTTATT-AAAATAA
1 TAATTTTATTTATTCAAAATAA
6283409 AATATAAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
23 23 0.68
24 11 0.32
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (24 bp):
TAATTTTATTTATTCAAAATAAGT
Found at i:6284209 original size:18 final size:18
Alignment explanation
Indices: 6284186--6284220 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6284176 CCAGCACTTT
*
6284186 CAACAACAACATCAGCAG
1 CAACAACAACAACAGCAG
6284204 CAACAACAACAACAGCA
1 CAACAACAACAACAGCA
6284221 TCAGCAACAG
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:0.54, C:0.34, G:0.09, T:0.03
Consensus pattern (18 bp):
CAACAACAACAACAGCAG
Found at i:6298469 original size:25 final size:25
Alignment explanation
Indices: 6298438--6298489 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
6298428 AGTTTGACTC
*
6298438 AAACAAATAAACAGAGTTTAATTGA
1 AAACAAATAAACAAAGTTTAATTGA
6298463 AAACAAATAAACAAAGTTTAATTGA
1 AAACAAATAAACAAAGTTTAATTGA
6298488 AA
1 AA
6298490 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.23
Consensus pattern (25 bp):
AAACAAATAAACAAAGTTTAATTGA
Found at i:6300349 original size:25 final size:25
Alignment explanation
Indices: 6300321--6300368 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6300311 TGACTCAAAT
* * *
6300321 AAATAAATAGAGTTTAATTGAAAAC
1 AAATAAACAAAGTTTAACTGAAAAC
6300346 AAATAAACAAAGTTTAACTGAAA
1 AAATAAACAAAGTTTAACTGAAA
6300369 GATTATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.25
Consensus pattern (25 bp):
AAATAAACAAAGTTTAACTGAAAAC
Found at i:6304619 original size:4 final size:4
Alignment explanation
Indices: 6304610--6304634 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6304600 GAGAAAATGG
6304610 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
6304635 GGGGACAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:6306283 original size:2 final size:2
Alignment explanation
Indices: 6306276--6306301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6306266 AAAAATACAA
6306276 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6306302 TTAAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6308851 original size:15 final size:15
Alignment explanation
Indices: 6308831--6308860 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6308821 AAGTCCTAAG
*
6308831 AAAATAGAACTAGAA
1 AAAATAGAAATAGAA
6308846 AAAATAGAAATAGAA
1 AAAATAGAAATAGAA
6308861 TTTTTAGGAT
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:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAATAGAAATAGAA
Found at i:6312143 original size:20 final size:21
Alignment explanation
Indices: 6312115--6312153 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
6312105 CGTAATTTGT
*
6312115 TCATATAAT-TATTTTTAGTA
1 TCATATAATAAATTTTTAGTA
*
6312135 TCATCTAATAAATTTTTAG
1 TCATATAATAAATTTTTAG
6312154 ATTTGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (21 bp):
TCATATAATAAATTTTTAGTA
Found at i:6315687 original size:18 final size:18
Alignment explanation
Indices: 6315664--6315704 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
6315654 TACCATTTAT
6315664 TTATTTAGTATACTAAAA
1 TTATTTAGTATACTAAAA
6315682 TTATTTAGTATACTAAAA
1 TTATTTAGTATACTAAAA
6315700 TTATT
1 TTATT
6315705 AATTCCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TTATTTAGTATACTAAAA
Found at i:6317627 original size:30 final size:31
Alignment explanation
Indices: 6317593--6317652 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
6317583 AAAATTAGTA
6317593 TAAAAT-ATT-AAAAAATCAATTAAGACCTTT
1 TAAAATAATTAAAAAAATCAATTAAG-CCTTT
6317623 TAAAATAATTAAAAAAATCAATTAAGCCTT
1 TAAAATAATTAAAAAAATCAATTAAGCCTT
6317653 CCATGTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 6 0.21
31 7 0.25
32 15 0.54
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (31 bp):
TAAAATAATTAAAAAAATCAATTAAGCCTTT
Found at i:6329254 original size:26 final size:26
Alignment explanation
Indices: 6329225--6329276 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
6329215 AATCTCAAAA
6329225 CAAAATGTAAAATTAAGAGTGAGTGT
1 CAAAATGTAAAATTAAGAGTGAGTGT
*
6329251 CAAAATGTAAAATTAGGAGTGAGTGT
1 CAAAATGTAAAATTAAGAGTGAGTGT
6329277 TAGATCGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.27
Consensus pattern (26 bp):
CAAAATGTAAAATTAAGAGTGAGTGT
Found at i:6329730 original size:20 final size:19
Alignment explanation
Indices: 6329687--6329738 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
6329677 AAAAATATAA
*
6329687 ATTTTGAAATTTTATAAAT
1 ATTTTGAATTTTTATAAAT
6329706 ATTTTGAATTTTTGA-AAATT
1 ATTTTGAATTTTT-ATAAA-T
6329726 ATTTTGAATTTTT
1 ATTTTGAATTTTT
6329739 TTTGTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTTATAAAT
Found at i:6335122 original size:46 final size:46
Alignment explanation
Indices: 6335065--6335163 Score: 162
Period size: 46 Copynumber: 2.2 Consensus size: 46
6335055 TTAAATTCTA
*
6335065 TTTTTGTAATTTAAATATATTGCTTTAAATTGATTTATTCTTTAAT
1 TTTTTGTAATTTAAATATATTGCTTTAAATTGATTTATTCTCTAAT
* *
6335111 TTTTTTTAATTTAAATATATTGTTTTAAATTGATTTATTCTCTAAT
1 TTTTTGTAATTTAAATATATTGCTTTAAATTGATTTATTCTCTAAT
*
6335157 TATTTGT
1 TTTTTGT
6335164 GTAAGTTCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (46 bp):
TTTTTGTAATTTAAATATATTGCTTTAAATTGATTTATTCTCTAAT
Found at i:6342251 original size:20 final size:18
Alignment explanation
Indices: 6342214--6342259 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
6342204 TTATTATTTT
6342214 AAATATATAAAATTAAGA
1 AAATATATAAAATTAAGA
*
6342232 AAATATATACAATTAA-A
1 AAATATATAAAATTAAGA
*
6342249 AGATATA-AAAA
1 AAATATATAAAA
6342260 GTCTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 3 0.12
17 7 0.28
18 15 0.60
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
AAATATATAAAATTAAGA
Found at i:6342336 original size:25 final size:25
Alignment explanation
Indices: 6342304--6342356 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
6342294 ATAAAAAGCA
6342304 CGTCTAATATGGATAAATGATTGTT
1 CGTCTAATATGGATAAATGATTGTT
6342329 CGTCTAATATGGATAAATGATTGTT
1 CGTCTAATATGGATAAATGATTGTT
6342354 CGT
1 CGT
6342357 GTATTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (25 bp):
CGTCTAATATGGATAAATGATTGTT
Found at i:6347381 original size:2 final size:2
Alignment explanation
Indices: 6347376--6347400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6347366 TTTTTCTCCT
6347376 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
6347401 TGTTATCTAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6354109 original size:135 final size:135
Alignment explanation
Indices: 6353861--6354489 Score: 914
Period size: 135 Copynumber: 4.6 Consensus size: 135
6353851 AAATTAATTT
** * * *
6353861 AATTAAAAAATTAATAGGGCCCAACCAAGCTCGAACCTGTGACCTTTTGATCTGCAGTCAAATGC
1 AATTAAAAAA-TAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGC
*
6353926 TCTACCACTGAGCTATGGACCCTTAATGCTGTGTAAAATGAACTATAATAATAGATGATTTAGTA
65 TCTACCACTGAGCTATGGACCCTTGATGCTGTGTAAAATGAACTATAATAATAGATGATTTAGTA
6353991 ATATAA
130 ATATAA
* *
6353997 AATTAAAAAATAATAGGGCCCAACCGGGTTCGTACCAGTGACCTCTTGATCTGCAGTCAAATGCT
1 AATTAAAAAATAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCT
* * * *
6354062 CTACAACTGAGCTATGGACCCTTGATGCTGTGTAAAATGACCCATAATAATAGATGATTTAGTTA
66 CTACCACTGAGCTATGGACCCTTGATGCTGTGTAAAATGAACTATAATAATAGATGATTTAGTAA
6354127 TATAA
131 TATAA
*
6354132 AATTAAAAAATAATAGAGCCCAA-------CGAACCGGTGACCTCTTGATCTGCAGTCAAATGCT
1 AATTAAAAAATAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCT
* *
6354190 CTACAACTGAGCTATGGACCCTTGATGCTGTGTAAAATGAACTATAATAATAGATGATTTAGTTA
66 CTACCACTGAGCTATGGACCCTTGATGCTGTGTAAAATGAACTATAATAATAGATGATTTAGTAA
6354255 TATAA
131 TATAA
6354260 AATTAAAAAATAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCT
1 AATTAAAAAATAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCT
* * * * *
6354325 CTACCACTGAGCTATGGACCCTTGATGCTGTG-CAAGTGAAATATAATAATAAATGATGTTTAAT
66 CTACCACTGAGCTATGGACCCTTGATGCTGTGTAAAATGAACTATAATAATAGATGA--TTTAGT
*
6354389 AAAATTAAA
129 AATA-T-AA
6354398 CATTTAGTTAAAAAATAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAA
1 -A---A-TTAAAAAATAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAA
*
6354463 ATGCTCTACCACTGAGCTATAGACCCT
61 ATGCTCTACCACTGAGCTATGGACCCT
6354490 AGATAACGAT
Statistics
Matches: 451, Mismatches: 26, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
128 123 0.27
134 20 0.04
135 202 0.45
136 17 0.04
137 1 0.00
138 2 0.00
139 1 0.00
142 1 0.00
143 84 0.19
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (135 bp):
AATTAAAAAATAATAGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCT
CTACCACTGAGCTATGGACCCTTGATGCTGTGTAAAATGAACTATAATAATAGATGATTTAGTAA
TATAA
Found at i:6354336 original size:263 final size:269
Alignment explanation
Indices: 6353830--6354489 Score: 895
Period size: 263 Copynumber: 2.4 Consensus size: 269
6353820 AATAAAATAA
** * *
6353830 AATAATAAATGATGTTTAATAAAATT-AATTTAATTAAAAAATTAATAGGGCCCAACCAAGCTCG
1 AATAATAAATGA-GTTTAATAAAATTAAACATAGTTAAAAAA-TAATAGAG--C--CCAAG--CG
* *
6353894 AACCTGTGACCTTTTGATCTGCAGTCAAATGCTCTACCACTGAGCTATGGACCCTTAATGCTGTG
58 AACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTATGGACCCTTAATGCTGTG
6353959 TAAAATGAACTATAATAATAGATGATTTAGTAATATAAAATTAAAAAATAATAGGGCCCAACCGG
123 TAAAATGAACTATAATAATAGATGATTTAGTAATATAAAATTAAAAAATAATAGGGCCCAACCGG
*
6354024 GTTCGTACCAGTGACCTCTTGATCTGCAGTCAAATGCTCTACAACTGAGCTATGGACCCTTGATG
188 GTTCGAACCAGTGACCTCTTGATCTGCAGTCAAATGCTCTACAACTGAGCTATGGACCCTTGATG
**
6354089 CTGTGTAAAATGACCCAT
253 CTGTG-AAAATGAAACAT
* * * *
6354107 AATAATAGATGA-TTTAGTTATA-T-AA-A-A-TTAAAAAATAATAGAGCCCAA-CGAACCGGTG
1 AATAATAAATGAGTTTAATAAAATTAAACATAGTTAAAAAATAATAGAGCCCAAGCGAACCGGTG
* *
6354165 ACCTCTTGATCTGCAGTCAAATGCTCTACAACTGAGCTATGGACCCTTGATGCTGTGTAAAATGA
66 ACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTATGGACCCTTAATGCTGTGTAAAATGA
*
6354230 ACTATAATAATAGATGATTTAGTTATATAAAATTAAAAAATAATAGGGCCCAACCGGGTTCGAAC
131 ACTATAATAATAGATGATTTAGTAATATAAAATTAAAAAATAATAGGGCCCAACCGGGTTCGAAC
* * *
6354295 CGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTATGGACCCTTGATGCTGTGCAA
196 CAGTGACCTCTTGATCTGCAGTCAAATGCTCTACAACTGAGCTATGGACCCTTGATGCTGTGAAA
* *
6354360 GTGAAATAT
261 ATGAAACAT
*
6354369 AATAATAAATGATGTTTAATAAAATTAAACATTTAGTTAAAAAATAATAGGGCCCAACCGGGTTC
1 AATAATAAATGA-GTTTAATAAAATTAAACA--TAGTTAAAAAATAATAGAGCCCAA----G--C
*
6354434 GAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTATAGACCCT
57 GAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTATGGACCCT
6354490 AGATAACGAT
Statistics
Matches: 341, Mismatches: 26, Indels: 31
0.86 0.07 0.08
Matches are distributed among these distances:
262 18 0.05
263 194 0.57
264 7 0.02
265 1 0.00
266 6 0.02
267 1 0.00
268 1 0.00
270 8 0.02
271 28 0.08
272 1 0.00
274 3 0.01
275 7 0.02
277 11 0.03
278 55 0.16
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (269 bp):
AATAATAAATGAGTTTAATAAAATTAAACATAGTTAAAAAATAATAGAGCCCAAGCGAACCGGTG
ACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTATGGACCCTTAATGCTGTGTAAAATGA
ACTATAATAATAGATGATTTAGTAATATAAAATTAAAAAATAATAGGGCCCAACCGGGTTCGAAC
CAGTGACCTCTTGATCTGCAGTCAAATGCTCTACAACTGAGCTATGGACCCTTGATGCTGTGAAA
ATGAAACAT
Found at i:6370760 original size:21 final size:22
Alignment explanation
Indices: 6370719--6370768 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
6370709 TACTAAAATG
6370719 AAAATTTTTAATTTAAATTTTTT
1 AAAA-TTTTAATTTAAATTTTTT
6370742 AAAATTTTAATTT-AATTTTTT
1 AAAATTTTAATTTAAATTTTTT
6370763 AAAATT
1 AAAATT
6370769 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 14 0.52
22 9 0.33
23 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAAATTTTAATTTAAATTTTTT
Found at i:6370782 original size:15 final size:16
Alignment explanation
Indices: 6370764--6370797 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6370754 TAATTTTTTA
6370764 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
6370779 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
6370795 AAA
1 AAA
6370798 ATTCTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:6370987 original size:26 final size:25
Alignment explanation
Indices: 6370958--6371013 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
6370948 CAAAAGTATA
*
6370958 TTTACAAAAAAGTATTGTATAAAAAT
1 TTTACAAAAAAGTATTATAT-AAAAT
* *
6370984 TTTAATAAAAAAGTATTATGTAAAAT
1 TTT-ACAAAAAAGTATTATATAAAAT
6371010 TTTA
1 TTTA
6371014 ATAACCTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 11 0.42
27 14 0.54
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (25 bp):
TTTACAAAAAAGTATTATATAAAAT
Found at i:6371014 original size:26 final size:27
Alignment explanation
Indices: 6370963--6371017 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
6370953 GTATATTTAC
*
6370963 AAAAAAGTATTGTATAAAAATTTTAAT
1 AAAAAAGTATTATATAAAAATTTTAAT
*
6370990 AAAAAAGTATTATGT-AAAATTTTAAT
1 AAAAAAGTATTATATAAAAATTTTAAT
6371016 AA
1 AA
6371018 CCTCACGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.36
Consensus pattern (27 bp):
AAAAAAGTATTATATAAAAATTTTAAT
Found at i:6385425 original size:17 final size:18
Alignment explanation
Indices: 6385380--6385425 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
6385370 CACCACATGC
6385380 TTGATGTTGATTTCGGTTT
1 TTGATGTT-ATTTCGGTTT
* *
6385399 TTTATTTTATTT-GGTTT
1 TTGATGTTATTTCGGTTT
6385416 TTGATGTTAT
1 TTGATGTTAT
6385426 AATTAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 13 0.57
18 4 0.17
19 6 0.26
ACGTcount: A:0.13, C:0.02, G:0.20, T:0.65
Consensus pattern (18 bp):
TTGATGTTATTTCGGTTT
Found at i:6387067 original size:21 final size:21
Alignment explanation
Indices: 6387043--6387085 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6387033 AAAGAGAATG
6387043 AAAA-ATAAAGAAAAAAATTAA
1 AAAACATAAA-AAAAAAATTAA
*
6387064 AAAACATAAAAGAAAAATTAA
1 AAAACATAAAAAAAAAATTAA
6387085 A
1 A
6387086 TTGCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAACATAAAAAAAAAATTAA
Found at i:6399757 original size:2 final size:2
Alignment explanation
Indices: 6399752--6399782 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6399742 AGCGTGTGTT
6399752 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6399783 AGTAAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6416028 original size:19 final size:20
Alignment explanation
Indices: 6415985--6416031 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
6415975 TTCGTATTAT
6415985 ATTATTTATGATATCATTGTA
1 ATTATTTATGATAT-ATTGTA
6416006 ATTATTTAATGATAT-TT-TA
1 ATTATTT-ATGATATATTGTA
6416025 ATTATTT
1 ATTATTT
6416032 TTCATGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 7 0.28
22 7 0.28
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTATTTATGATATATTGTA
Found at i:6429458 original size:34 final size:34
Alignment explanation
Indices: 6429414--6429482 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
6429404 TCTTTCAACA
* *
6429414 AAAATACAAAATAATTT-TCAAAATTTTAAATTTT
1 AAAATACAAAAT-ATTTATCAAAATTTCAAAATTT
*
6429448 AAAATTCAAAATATTTATCAAAATTTCAAAATTT
1 AAAATACAAAATATTTATCAAAATTTCAAAATTT
6429482 A
1 A
6429483 TATATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATACAAAATATTTATCAAAATTTCAAAATTT
Found at i:6433684 original size:18 final size:18
Alignment explanation
Indices: 6433650--6433685 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6433640 GAGACGGTGA
*
6433650 CCTTTAGTTTCTGCCTCT
1 CCTTTAGTTCCTGCCTCT
*
6433668 CCTTTAGTTCCTTCCTCT
1 CCTTTAGTTCCTGCCTCT
6433686 TTTTTGCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.36, G:0.08, T:0.50
Consensus pattern (18 bp):
CCTTTAGTTCCTGCCTCT
Found at i:6437710 original size:12 final size:12
Alignment explanation
Indices: 6437689--6437721 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
6437679 TAGGTGGTTC
6437689 TTTC-TTTTTCT
1 TTTCTTTTTTCT
6437700 TTTCTTTTTTCT
1 TTTCTTTTTTCT
6437712 TTT-TTTTTTC
1 TTTCTTTTTTC
6437722 CTTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:6442875 original size:18 final size:18
Alignment explanation
Indices: 6442852--6442886 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6442842 TCAAAAAAAA
6442852 AAAAAAAAGCCTCCAAAT
1 AAAAAAAAGCCTCCAAAT
*
6442870 AAAAAAAATCCTCCAAA
1 AAAAAAAAGCCTCCAAA
6442887 CTCTTTTTTT
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:0.63, C:0.23, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAAAAAAGCCTCCAAAT
Found at i:6442928 original size:2 final size:2
Alignment explanation
Indices: 6442921--6442968 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6442911 AAAACAAACA
6442921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6442963 AT AT AT
1 AT AT AT
6442969 GCTTGTTGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6450503 original size:28 final size:28
Alignment explanation
Indices: 6450447--6450503 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
6450437 CATATCCAAA
*
6450447 TTTATTTTAATCTAAATTTTAATATATT
1 TTTATTTTAATCTAAATTTTAACATATT
*
6450475 TTTATTATTAAT-TCAATTTGTAACA-ATT
1 TTTATT-TTAATCTAAATTT-TAACATATT
6450503 T
1 T
6450504 CATTTCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTATTTTAATCTAAATTTTAACATATT
Found at i:6454114 original size:17 final size:18
Alignment explanation
Indices: 6454078--6454118 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6454068 ATTTCACGTA
6454078 TTTTTATGAACTTTATAT
1 TTTTTATGAACTTTATAT
* *
6454096 TTTTTTTGAATTTTA-AT
1 TTTTTATGAACTTTATAT
6454113 TTTTTA
1 TTTTTA
6454119 ATATTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTATGAACTTTATAT
Found at i:6454541 original size:17 final size:18
Alignment explanation
Indices: 6454508--6454542 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6454498 TAAAGTGAAT
*
6454508 AATCAAATTTAATAAAAA
1 AATCAAATTTAACAAAAA
6454526 AATCAAA-TTAACAAAAA
1 AATCAAATTTAACAAAAA
6454543 GAACATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
AATCAAATTTAACAAAAA
Found at i:6456520 original size:30 final size:29
Alignment explanation
Indices: 6456454--6456528 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
6456444 AATAATTGTT
* * *
6456454 TTTTATAATTTTTAAAAAATTAAATTAAA
1 TTTTATTATTTTTAAAAAATCAAAATAAA
**
6456483 TTATTATTATTTTTAAGGAATCAAAATATAA
1 TT-TTATTATTTTTAAAAAATCAAAATA-AA
*
6456514 TTTTATTATTATTAA
1 TTTTATTATTTTTAA
6456529 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.05
30 32 0.84
31 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTTATTATTTTTAAAAAATCAAAATAAA
Found at i:6458698 original size:32 final size:32
Alignment explanation
Indices: 6458636--6458698 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
6458626 GACTGTCATT
* *
6458636 ATAATTATTTTTTATCCAAAAACTTGAGGTTC
1 ATAATTATTTTTTATCCAAAAACATAAGGTTC
* *
6458668 ATAATTATTTTTTATCCAAACAGATAAGGTT
1 ATAATTATTTTTTATCCAAAAACATAAGGTT
6458699 AGGTTAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (32 bp):
ATAATTATTTTTTATCCAAAAACATAAGGTTC
Found at i:6459518 original size:16 final size:16
Alignment explanation
Indices: 6459499--6459529 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6459489 GATACAAATT
*
6459499 TAAAAACTAAAAAAAA
1 TAAAAAATAAAAAAAA
6459515 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
6459530 GTTACAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
TAAAAAATAAAAAAAA
Found at i:6478014 original size:16 final size:17
Alignment explanation
Indices: 6477993--6478028 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
6477983 GGTTGAGCAA
*
6477993 AAAAACCGATC-AAACC
1 AAAAACCAATCTAAACC
6478009 AAAAACCAATCTAAACC
1 AAAAACCAATCTAAACC
6478026 AAA
1 AAA
6478029 GTATTTGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.61, C:0.28, G:0.03, T:0.08
Consensus pattern (17 bp):
AAAAACCAATCTAAACC
Found at i:6484870 original size:14 final size:15
Alignment explanation
Indices: 6484852--6484893 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
6484842 TTAAAATTAA
6484852 AAATTTAGTTTTTAT
1 AAATTTAGTTTTTAT
*
6484867 AATTTTA--TTTTAT
1 AAATTTAGTTTTTAT
6484880 GAAATTTAGTTTTT
1 -AAATTTAGTTTTT
6484894 TTTTTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 6 0.27
14 6 0.27
15 6 0.27
16 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
AAATTTAGTTTTTAT
Found at i:6485876 original size:17 final size:17
Alignment explanation
Indices: 6485841--6485894 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
6485831 AGTGTTTTTT
* *
6485841 AAAAATATTTTTGACATA
1 AAAAATAATTTT-AAATA
*
6485859 AAAAATACTTTTAAATAA
1 AAAAATAATTTTAAAT-A
*
6485877 AAAAATAATGTTAAATA
1 AAAAATAATTTTAAATA
6485894 A
1 A
6485895 GTAACTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 5 0.16
18 26 0.84
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAAATAATTTTAAATA
Found at i:6491653 original size:7 final size:7
Alignment explanation
Indices: 6491638--6491668 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
6491628 ACAAACATGT
*
6491638 AAAACAA
1 AAAAGAA
6491645 AAAAGAA
1 AAAAGAA
6491652 AAAAGAA
1 AAAAGAA
6491659 AAAAGAA
1 AAAAGAA
6491666 AAA
1 AAA
6491669 TATATTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:6494961 original size:31 final size:31
Alignment explanation
Indices: 6494926--6494991 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
6494916 TTTTTAACTA
6494926 AATTT-ATCCATCA-ACCATTTAAAAAAAGTTG
1 AATTTGATCC-TCATACC-TTTAAAAAAAGTTG
* * *
6494957 AATTTGATCCTTATTCCTTTAAAAAGAGTTG
1 AATTTGATCCTCATACCTTTAAAAAAAGTTG
6494988 AATT
1 AATT
6494992 ATTTTTTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (31 bp):
AATTTGATCCTCATACCTTTAAAAAAAGTTG
Found at i:6497083 original size:40 final size:38
Alignment explanation
Indices: 6497015--6497149 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
6497005 ACCAGAATGG
* *
6497015 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
6497055 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
6497092 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
6497133 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
6497150 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:6497147 original size:41 final size:38
Alignment explanation
Indices: 6497047--6497150 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
6497037 TTCGAAGCAA
* *
6497047 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
6497084 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
6497122 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
6497151 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:6497968 original size:24 final size:23
Alignment explanation
Indices: 6497943--6497993 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 23
6497933 TAGCTCTCTG
6497943 TTCTTTCTTCTTTTATTTCTTTTGT
1 TTCTTTCTT-TTTTA-TTCTTTTGT
*
6497968 TTCTTTCTTTTTTATTCTTTTAT
1 TTCTTTCTTTTTTATTCTTTTGT
6497991 TTC
1 TTC
6497994 ATATACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 5 0.20
25 9 0.36
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (23 bp):
TTCTTTCTTTTTTATTCTTTTGT
Found at i:6498049 original size:11 final size:12
Alignment explanation
Indices: 6498016--6498074 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
6498006 ATATTAGTTA
6498016 ATAATAATAA-T
1 ATAATAATAATT
*
6498027 ATAATACTAATT
1 ATAATAATAATT
6498039 A-AATAATAATTT
1 ATAATAATAA-TT
* *
6498051 ATATTATTATATT
1 ATAATAATA-ATT
*
6498064 ATAATATTAAT
1 ATAATAATAAT
6498075 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 16 0.41
12 7 0.18
13 15 0.38
14 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:6499175 original size:22 final size:20
Alignment explanation
Indices: 6499149--6499200 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
6499139 GCAACAGTAG
6499149 GCACACAAAGTGCTAATCAGAA
1 GCACACAAAGTGCTAA-CAG-A
*
6499171 GCACACACAGTGCTGAACAGA
1 GCACACAAAGTGCT-AACAGA
*
6499192 GGACACAAA
1 GCACACAAA
6499201 ACGTGCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.10
Consensus pattern (20 bp):
GCACACAAAGTGCTAACAGA
Found at i:6499207 original size:45 final size:46
Alignment explanation
Indices: 6499119--6499209 Score: 109
Period size: 45 Copynumber: 2.0 Consensus size: 46
6499109 AAGTACTTAA
*
6499119 CAGAAGCACATAAGTGCTGGGCAACAGTAGGCACACAAAGTGCTAAT
1 CAGAAGCACACAAGTGCT-GGCAACAGTAGGCACACAAAGTGCTAAT
6499166 CAGAAGCACACACAGTGCT-G-AACAG-AGG-ACACAAAACGTGCTAA
1 CAGAAGCACACA-AGTGCTGGCAACAGTAGGCACAC-AAA-GTGCTAA
6499210 ACAGTAGGCG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
43 4 0.10
44 6 0.15
45 12 0.30
46 1 0.03
47 11 0.28
48 6 0.15
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (46 bp):
CAGAAGCACACAAGTGCTGGCAACAGTAGGCACACAAAGTGCTAAT
Found at i:6499327 original size:24 final size:26
Alignment explanation
Indices: 6499281--6499328 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
6499271 TCTACATGGG
6499281 CATAATCTCACATATTCATCATTTCT
1 CATAATCTCACATATTCATCATTTCT
* *
6499307 CATAATTTCATATA-TCA-CATTT
1 CATAATCTCACATATTCATCATTT
6499329 ACATTTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 3 0.15
26 12 0.60
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (26 bp):
CATAATCTCACATATTCATCATTTCT
Found at i:6512933 original size:130 final size:129
Alignment explanation
Indices: 6512692--6512936 Score: 330
Period size: 130 Copynumber: 1.9 Consensus size: 129
6512682 TGGAGAATCT
* * * * * * * *
6512692 TAATTTGATTGCGTAAGTTTGAGGCAACCTGAATCGAGTGGTTGATAAATTACTAAAAGAGTGAT
1 TAATTTGATTGCGTAAATTTGAAGCAACCTCAAACAAGTGATGGATAAATTACTAAAAGAGTGAC
* *
6512757 TACGTGTTCATACCAAATTTTAAGAGAATTTGAACACTTTTCCAATTAAATTAACCTATAATTA
66 TACGTGTTCATACCAAATATTAAGAGAATTTGAACAATTTTCCAATTAAATTAACCTATAATTA
6512821 TAATTTGATTGCGTAAATTTGAAGCAA-CTCCAAACAAGTGATGGATAAATTTACTAAAAGAGTG
1 TAATTTGATTGCGTAAATTTGAAGCAACCT-CAAACAAGTGATGGATAAA-TTACTAAAAGAGTG
** * * *
6512885 ACTACGTGTTCATATTAAATATTAAGAGGATTTGAATAATTTTTCAATTAAA
64 ACTACGTGTTCATACCAAATATTAAGAGAATTTGAACAATTTTCCAATTAAA
6512937 AATTTTCAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
128 2 0.02
129 39 0.39
130 58 0.59
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (129 bp):
TAATTTGATTGCGTAAATTTGAAGCAACCTCAAACAAGTGATGGATAAATTACTAAAAGAGTGAC
TACGTGTTCATACCAAATATTAAGAGAATTTGAACAATTTTCCAATTAAATTAACCTATAATTA
Found at i:6514276 original size:16 final size:16
Alignment explanation
Indices: 6514239--6514280 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
6514229 TTAGGGTTTA
* *
6514239 AAATTTTTAATTAATT
1 AAATATTTATTTAATT
6514255 -AA-ATTTATTTAATT
1 AAATATTTATTTAATT
6514269 AAATATTTATTT
1 AAATATTTATTT
6514281 TCATTCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.45
15 4 0.18
16 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTATTTAATT
Found at i:6527400 original size:16 final size:15
Alignment explanation
Indices: 6527381--6527419 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6527371 ACACTCTTAT
6527381 TTTTTACTTCTTTTAA
1 TTTTT-CTTCTTTTAA
*
6527397 TTTTGTTTTCTTTTAA
1 TTTT-TCTTCTTTTAA
6527413 TTTTTCT
1 TTTTTCT
6527420 CAGATCACGC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 17 0.85
17 1 0.05
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTCTTCTTTTAA
Found at i:6529695 original size:23 final size:23
Alignment explanation
Indices: 6529658--6529713 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
6529648 GGATGTCACT
* * *
6529658 TTGCACCG-AAGTGCCGCTGCCGC
1 TTGCACCGTAA-TGCCACTCCCAC
*
6529681 TTGCATCGTAATGCCACTCCCAC
1 TTGCACCGTAATGCCACTCCCAC
6529704 TTGCACCGTA
1 TTGCACCGTA
6529714 GTGTCACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.18, C:0.38, G:0.21, T:0.23
Consensus pattern (23 bp):
TTGCACCGTAATGCCACTCCCAC
Found at i:6535783 original size:41 final size:41
Alignment explanation
Indices: 6535730--6535812 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
6535720 CCCTTTTTTT
6535730 AAATTGTTGTGCAATTAAAAACAAGAGAGAAATCACATTAA
1 AAATTGTTGTGCAATTAAAAACAAGAGAGAAATCACATTAA
6535771 AAATTGTTGTGCAATTAAAAACAAGAGAGAAATCACATTAA
1 AAATTGTTGTGCAATTAAAAACAAGAGAGAAATCACATTAA
6535812 A
1 A
6535813 TTTACTCGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (41 bp):
AAATTGTTGTGCAATTAAAAACAAGAGAGAAATCACATTAA
Found at i:6543993 original size:2 final size:2
Alignment explanation
Indices: 6543986--6544012 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6543976 TTGCTAATAA
6543986 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6544013 AAAAAGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6556470 original size:23 final size:23
Alignment explanation
Indices: 6556414--6556529 Score: 151
Period size: 23 Copynumber: 5.0 Consensus size: 23
6556404 TCATTAATAT
* *
6556414 TGTTCGTAAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
6556438 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
6556461 TGTTCGTGAACGTGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
* *
6556484 TGCTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAA
*
6556507 TGTTCGTGAATATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
6556530 CTTAAATGAA
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
23 61 0.77
24 18 0.23
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:6556540 original size:46 final size:45
Alignment explanation
Indices: 6556414--6556547 Score: 126
Period size: 46 Copynumber: 2.9 Consensus size: 45
6556404 TCATTAATAT
* * * * * *
6556414 TGTTCGTAAACATGTTCAATTATATGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTA-AT-CTAATGAACATGTTTGATTAA
* **
6556461 TGTTCGTGAACGTGTTCGATTAATGCTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAAT-CTAATGAACATGTTTGATTAA
*
6556507 TGTTCGTGAATATGTTCGATTAA-CTTAAATGAACATGTTTG
1 TGTTCGTGAACATGTTCGATTAATC-T-AATGAACATGTTTG
6556548 TGAACATTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 53 0.72
47 19 0.26
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (45 bp):
TGTTCGTGAACATGTTCGATTAATCTAATGAACATGTTTGATTAA
Found at i:6560437 original size:20 final size:18
Alignment explanation
Indices: 6560408--6560448 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
6560398 TTTTGAGCAA
*
6560408 TTTAATTTTTTTTATGTTCT
1 TTTAACTTTTTTT-T-TTCT
6560428 TTTAACTTTTTTTTTTCT
1 TTTAACTTTTTTTTTTCT
6560446 TTT
1 TTT
6560449 GCTCCTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTAACTTTTTTTTTTCT
Found at i:6569895 original size:3 final size:3
Alignment explanation
Indices: 6569887--6569918 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6569877 AATTAATATT
6569887 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
6569919 TTTCTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:6578380 original size:4 final size:4
Alignment explanation
Indices: 6578371--6578410 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
6578361 TGTCTCCCTG
6578371 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
6578411 CATCTCGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:6583724 original size:2 final size:2
Alignment explanation
Indices: 6583717--6583754 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6583707 TATACAGACA
6583717 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
6583755 TGAGAATAAA
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:6585062 original size:17 final size:17
Alignment explanation
Indices: 6585040--6585078 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6585030 AGATTTTATA
6585040 TATATATTCTGAATTTT
1 TATATATTCTGAATTTT
* **
6585057 TATATATTTTTCATTTT
1 TATATATTCTGAATTTT
6585074 TATAT
1 TATAT
6585079 TTTTTTGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (17 bp):
TATATATTCTGAATTTT
Found at i:6585084 original size:17 final size:17
Alignment explanation
Indices: 6585052--6585083 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6585042 TATATTCTGA
6585052 ATTTTTATATATTTTTC
1 ATTTTTATATATTTTTC
6585069 ATTTTTATAT-TTTTT
1 ATTTTTATATATTTTT
6585084 TGTGTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTATATATTTTTC
Found at i:6586823 original size:59 final size:58
Alignment explanation
Indices: 6586677--6586823 Score: 154
Period size: 58 Copynumber: 2.5 Consensus size: 58
6586667 CGACACCCAA
* * * * * * * * *
6586677 AAATACGAAAAAAATATTTTTTGGGTGTTTGCCAAGCCATGATCGATATCTCTTTTTC
1 AAATACCAAAAAAATATTTTTTGGATGTCTACCAAACCATGACCGAAACCCCTTTTTC
*
6586735 AAATACCAAAAAAA-ATATTTTT-GAGTGTCTACTAAACCATGACCGAAACCCCTTTTTTC
1 AAATACCAAAAAAATAT-TTTTTGGA-TGTCTACCAAACCATGACCGAAACCCC-TTTTTC
*
6586794 AGATACCAAAAAAATATTTTTTGGATGTCT
1 AAATACCAAAAAAATATTTTTTGGATGTCT
6586824 GTCAACCCAT
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
57 3 0.04
58 37 0.51
59 29 0.40
60 4 0.05
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (58 bp):
AAATACCAAAAAAATATTTTTTGGATGTCTACCAAACCATGACCGAAACCCCTTTTTC
Found at i:6590240 original size:2 final size:2
Alignment explanation
Indices: 6590233--6590274 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6590223 ACGACATTAA
6590233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6590275 TAAGAATCGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6592717 original size:34 final size:34
Alignment explanation
Indices: 6592642--6592717 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
6592632 CATAAATTAA
* *
6592642 ACCCAAATATTTTTAATTTTTTACCTTTTATCTT
1 ACCCAAATATTTTTAATTTTCTACCTTTTACCTT
** *
6592676 ATTCAAATATTTTTAATTTTCTACTTTTTACCTT
1 ACCCAAATATTTTTAATTTTCTACCTTTTACCTT
6592710 ACCCAAAT
1 ACCCAAAT
6592718 GTTGTTTACT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (34 bp):
ACCCAAATATTTTTAATTTTCTACCTTTTACCTT
Found at i:6600506 original size:31 final size:31
Alignment explanation
Indices: 6600470--6600529 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
6600460 TTTTTGGTCC
6600470 AATTTGATA-CTCAAACTTGACACTTTTTTCT
1 AATTTGATATCT-AAACTTGACACTTTTTTCT
*
6600501 AATTTGGTATCTAAACTTGACACTTTTTT
1 AATTTGATATCTAAACTTGACACTTTTTT
6600530 TTAAGTTGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (31 bp):
AATTTGATATCTAAACTTGACACTTTTTTCT
Found at i:6600578 original size:90 final size:91
Alignment explanation
Indices: 6600426--6600596 Score: 213
Period size: 90 Copynumber: 1.9 Consensus size: 91
6600416 ATACTTGAAT
* * * *
6600426 TTGACAATTTTTATTAATTTGGTACCTAAACTTTTTTTTGGTCCAATTTGATACTCAAACTTGAC
1 TTGACAATTTTTATTAAGTTGGCACCTAAACTTTTTTTGGGTCCAATTAGATACTCAAACTTGAC
*
6600491 ACTTTTTTCTAATTTGGTATCTAAAC
66 ACTTTTTCCTAATTTGGTATCTAAAC
* * * *
6600517 TTGACACTTTTTTTTAAGTTGGCACTTAAA-TTTTTTTGGGTCCAATTCAGTATA-T-GAACTTG
1 TTGACAATTTTTATTAAGTTGGCACCTAAACTTTTTTTGGGTCCAATT-AG-ATACTCAAACTTG
*
6600579 ACTCTTTTTCCTAATTTG
64 ACACTTTTTCCTAATTTG
6600597 ATACCTAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
90 38 0.56
91 27 0.40
92 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (91 bp):
TTGACAATTTTTATTAAGTTGGCACCTAAACTTTTTTTGGGTCCAATTAGATACTCAAACTTGAC
ACTTTTTCCTAATTTGGTATCTAAAC
Found at i:6612527 original size:18 final size:18
Alignment explanation
Indices: 6612504--6612541 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6612494 TTGAATTTTT
* *
6612504 TTTAAATTAAAAGTTAAA
1 TTTAAATAAAAAATTAAA
6612522 TTTAAATAAAAAATTAAA
1 TTTAAATAAAAAATTAAA
6612540 TT
1 TT
6612542 AAAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TTTAAATAAAAAATTAAA
Found at i:6612801 original size:28 final size:27
Alignment explanation
Indices: 6612761--6612814 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
6612751 TAATTGATAT
*
6612761 AGATATAACTTATATTTTGATTAAAAAA
1 AGATATAACTTATA-TTTAATTAAAAAA
6612789 AGATATAACTTATATTTAATTAAAAA
1 AGATATAACTTATATTTAATTAAAAA
6612815 TTCGATTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (27 bp):
AGATATAACTTATATTTAATTAAAAAA
Found at i:6624658 original size:39 final size:40
Alignment explanation
Indices: 6624609--6624705 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 40
6624599 TTTAATTAGT
* *
6624609 TTTTTAAAATT-TCAAAA-ATTCAAAAAA-ATCATAAAATTA
1 TTTTTAAAATTAT-AAAATATT-AAAAAATATCAAAAAAATA
6624648 TTTTTAAAATTATAAAATTATTAAAAAATATCAAAAAAATA
1 TTTTTAAAATTATAAAA-TATTAAAAAATATCAAAAAAATA
6624689 TTTTTAAAA-TA-AAAATA
1 TTTTTAAAATTATAAAATA
6624706 ATAATTAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
38 2 0.04
39 19 0.37
40 9 0.17
41 22 0.42
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (40 bp):
TTTTTAAAATTATAAAATATTAAAAAATATCAAAAAAATA
Found at i:6628049 original size:18 final size:18
Alignment explanation
Indices: 6628026--6628060 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6628016 CCATAGCCAC
6628026 CTTCAC-CAATCACATTCT
1 CTTCACACAATC-CATTCT
6628044 CTTCACACAATCCATTC
1 CTTCACACAATCCATTC
6628061 GTAGCTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (18 bp):
CTTCACACAATCCATTCT
Found at i:6635917 original size:17 final size:18
Alignment explanation
Indices: 6635880--6635917 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
6635870 GGAAACTAAT
*
6635880 AAATAGGAACGAACAAGA
1 AAATAGGAACGAACAAAA
*
6635898 AAATA-GAAGGAACAAAA
1 AAATAGGAACGAACAAAA
6635915 AAA
1 AAA
6635918 GTCCCGATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.08, G:0.18, T:0.05
Consensus pattern (18 bp):
AAATAGGAACGAACAAAA
Found at i:6638437 original size:18 final size:17
Alignment explanation
Indices: 6638414--6638451 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
6638404 TTAATATTTA
*
6638414 TATTATAATTTTAAATGT
1 TATTATAAATTTAAAT-T
6638432 TATTATAAATTTAAATT
1 TATTATAAATTTAAATT
6638449 TAT
1 TAT
6638452 GTGATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTATAAATTTAAATT
Found at i:6638691 original size:21 final size:19
Alignment explanation
Indices: 6638652--6638691 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
6638642 AAGGACGAGT
*
6638652 AAAATTCAATTTGATTAAA
1 AAAATTCAATTTGAATAAA
6638671 AAAATTCGAATTTTGAATAAA
1 AAAATTC-AA-TTTGAATAAA
6638692 TCGAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (19 bp):
AAAATTCAATTTGAATAAA
Found at i:6640693 original size:261 final size:261
Alignment explanation
Indices: 6640229--6640746 Score: 1011
Period size: 261 Copynumber: 2.0 Consensus size: 261
6640219 GAACGCTAAT
6640229 AACCGATTGTTTTTTAATGATTCAGGAAATCGAGAATTTCATACACCAGAGAATTTTTGCTGTCA
1 AACCGATTGTTTTTTAATGATTCAGGAAATCGAGAATTTCATACACCAGAGAATTTTTGCTGTCA
6640294 CTGAGTGAACTGGATATCTGCAAAAAGTTACCCGCGGGTTTCGATCAATCAATTTTGAGGTGAGA
66 CTGAGTGAACTGGATATCTGCAAAAAGTTACCCGCGGGTTTCGATCAATCAATTTTGAGGTGAGA
6640359 TTATTTTTTATGGTCATTGAGTTTTTACTTAGTAAAATTATGAAGAAGGCAAACTTAGATCTTTT
131 TTATTTTTTATGGTCATTGAGTTTTTACTTAGTAAAATTATGAAGAAGGCAAACTTAGATCTTTT
6640424 TGTTATTCATTGATATGTGGTTGGAG-ATATGAATTTGAGGATACATCACAAGATCGGCAAAGTT
196 TGTTATTCATTGATATGTGGTTGGAGCA-ATGAATTTGAGGATACATCACAAGATCGGCAAAGTT
6640488 AA
260 AA
6640490 AACCGATTGTTTTTTAATGATTCAGGAAATCGAGAATTTCATACACCAGAGAATTTTTGCTGTCA
1 AACCGATTGTTTTTTAATGATTCAGGAAATCGAGAATTTCATACACCAGAGAATTTTTGCTGTCA
*
6640555 CTGAGTGAACTGGATATCTGCAAAAAGTTACTCGCGGGTTTCGATCAATCAATTTTGAGGTGAGA
66 CTGAGTGAACTGGATATCTGCAAAAAGTTACCCGCGGGTTTCGATCAATCAATTTTGAGGTGAGA
6640620 TTATTTTTTATGGTCATTGAGTTTTTACTTAGTAAAATTATGAAGAAGGCAAACTTAGATCTTTT
131 TTATTTTTTATGGTCATTGAGTTTTTACTTAGTAAAATTATGAAGAAGGCAAACTTAGATCTTTT
6640685 TGTTATTCATTGATATGTGGTTGGAGCAATGAATTTGAGGATACATCACAAGATCGGCAAAG
196 TGTTATTCATTGATATGTGGTTGGAGCAATGAATTTGAGGATACATCACAAGATCGGCAAAG
6640747 AATTCCTGGC
Statistics
Matches: 255, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
261 254 1.00
262 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (261 bp):
AACCGATTGTTTTTTAATGATTCAGGAAATCGAGAATTTCATACACCAGAGAATTTTTGCTGTCA
CTGAGTGAACTGGATATCTGCAAAAAGTTACCCGCGGGTTTCGATCAATCAATTTTGAGGTGAGA
TTATTTTTTATGGTCATTGAGTTTTTACTTAGTAAAATTATGAAGAAGGCAAACTTAGATCTTTT
TGTTATTCATTGATATGTGGTTGGAGCAATGAATTTGAGGATACATCACAAGATCGGCAAAGTTA
A
Found at i:6648458 original size:6 final size:6
Alignment explanation
Indices: 6648447--6648497 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
6648437 TGATCAAAAT
* * *
6648447 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAA TAAAAG TGAAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
6648495 TGA
1 TGA
6648498 TATGAATTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (6 bp):
TGAAAG
Found at i:6650151 original size:28 final size:29
Alignment explanation
Indices: 6650110--6650168 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
6650100 TTTAAAAAAA
*
6650110 TTTAATAATATTAATAATTAAAT-CTAAAT
1 TTTAATAATATTAA-AATAAAATACTAAAT
* *
6650139 TTTAA-AATTTTAAAATAAAATATTAAAT
1 TTTAATAATATTAAAATAAAATACTAAAT
6650167 TT
1 TT
6650169 CAAAGTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 7 0.27
28 14 0.54
29 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTAATAATATTAAAATAAAATACTAAAT
Found at i:6668127 original size:6 final size:6
Alignment explanation
Indices: 6668118--6668148 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
6668108 TTTGTCTTTG
6668118 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA T
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA T
6668149 GTTGTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:6668700 original size:55 final size:57
Alignment explanation
Indices: 6668618--6668732 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 57
6668608 CAAAAATTCA
* * *
6668618 AAAAAATTATTTTTTTATTCGTGTTTTTTTATGCCGGCCATTAGAT-GACAAACACCC
1 AAAAAATTATTTTTTTATTCGTATTTTTTGATGCCAGCCATTAGATGGA-AAACACCC
* * *
6668675 AAAAAA-TA-TTTTTTATTCGTATTTTTTGATGTCAGTCATTAGTTGGAAAACACCC
1 AAAAAATTATTTTTTTATTCGTATTTTTTGATGCCAGCCATTAGATGGAAAACACCC
6668730 AAA
1 AAA
6668733 TTTTTTTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
55 41 0.80
56 4 0.08
57 6 0.12
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (57 bp):
AAAAAATTATTTTTTTATTCGTATTTTTTGATGCCAGCCATTAGATGGAAAACACCC
Found at i:6670044 original size:17 final size:17
Alignment explanation
Indices: 6669998--6670044 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
6669988 TTTAAAGTTA
*
6669998 TATTTTGTTT-AGTATT
1 TATTTTGTTTAATTATT
*
6670014 TATTATT-TTAAATTATT
1 TATT-TTGTTTAATTATT
6670031 TATTTTGTTTAATT
1 TATTTTGTTTAATT
6670045 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TATTTTGTTTAATTATT
Found at i:6670192 original size:5 final size:5
Alignment explanation
Indices: 6670182--6670206 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6670172 AGAAATTTTG
6670182 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
6670207 TTTTGTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:6670468 original size:142 final size:147
Alignment explanation
Indices: 6670302--6670611 Score: 459
Period size: 155 Copynumber: 2.1 Consensus size: 147
6670292 TTTACCAAAA
*
6670302 TGGTATAAAATAAATATTTATATATTAAATTGATATATCCACCACATTTTCGTAATTAAT-G-GT
1 TGGTAAAAAATAAATATTTATATATTAAATTGATATATCCACCACATTTTCGTAATTAATGGTGT
* *
6670365 GT-G-TGG-ATATAAATATTTATTTTGTACCATTTTAGTAAATAACCCATTTTGGTATTTAATTA
66 GTGGTTGGTATATAAATAATTATTTTGTACCATTTTAGTAAATAACCCATTTTGATATTTAATTA
6670427 TTATTTTTGTATTATAT
131 TTATTTTTGTATTATAT
* * *
6670444 TGGTACAAAATAAATATTTATATATTAAATTGGTATATCCACCACATTTTTGTAATTAATGGTGT
1 TGGTAAAAAATAAATATTTATATATTAAATTGATATATCCACCACATTTTCGTAATTAATGGTGT
6670509 GTGGATACCATTTTGGTATATAAATAATTATTTTGTACCATTTTAGTAAATAACCCATTTTGATA
66 GTGG--------TTGGTATATAAATAATTATTTTGTACCATTTTAGTAAATAACCCATTTTGATA
6670574 TTTAATTATTATTTTTGTATTATAT
123 TTTAATTATTATTTTTGTATTATAT
6670599 TGGTAAAAAATAA
1 TGGTAAAAAATAA
6670612 TAAAAATTGT
Statistics
Matches: 149, Mismatches: 6, Indels: 13
0.89 0.04 0.08
Matches are distributed among these distances:
142 57 0.38
143 1 0.01
144 4 0.03
145 1 0.01
154 3 0.02
155 83 0.56
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (147 bp):
TGGTAAAAAATAAATATTTATATATTAAATTGATATATCCACCACATTTTCGTAATTAATGGTGT
GTGGTTGGTATATAAATAATTATTTTGTACCATTTTAGTAAATAACCCATTTTGATATTTAATTA
TTATTTTTGTATTATAT
Found at i:6687196 original size:16 final size:15
Alignment explanation
Indices: 6687175--6687225 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
6687165 GCTCAAAGGG
6687175 TTTTCCTTGTCCTTTA
1 TTTTCC-TGTCCTTTA
* *
6687191 TTTTCCCGTTCCTTCA
1 TTTTCCTG-TCCTTTA
6687207 TTTT-CT-TCCTTTA
1 TTTTCCTGTCCTTTA
6687220 TTTTCC
1 TTTTCC
6687226 ATGATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 10 0.34
14 1 0.03
15 2 0.07
16 16 0.55
ACGTcount: A:0.06, C:0.29, G:0.04, T:0.61
Consensus pattern (15 bp):
TTTTCCTGTCCTTTA
Done.