Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 104 of 332
Found at i:33621683 original size:22 final size:21
Alignment explanation
Indices: 33621601--33621683 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 21
33621591 AAAAAAATTC
33621601 AAAAAAAAA-TCGAAAAAAAAGAA
1 AAAAAAAAAGT-G-AAAAAAAG-A
33621624 AAAAAAAGAAGTGAGCAAAAAAG-
1 AAAAAAA-AAGTGA--AAAAAAGA
33621647 AAAAAAAAAGT-AAAAAAAGA
1 AAAAAAAAAGTGAAAAAAAGA
33621667 AGAAAAAAAAGTGAAAA
1 A-AAAAAAAAGTGAAAA
33621684 GTCTTGCGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
19 7 0.13
20 1 0.02
21 11 0.21
22 8 0.15
23 15 0.28
24 3 0.06
25 8 0.15
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAGTGAAAAAAAGA
Found at i:33622708 original size:6 final size:6
Alignment explanation
Indices: 33622688--33622789 Score: 62
Period size: 6 Copynumber: 16.5 Consensus size: 6
33622678 AAAGAAATTG
* ** * **
33622688 AAAG-A AAACAA AAAGAA AAAGAA ATTGCA AAAGAA AAAGAA ATCGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * * *
33622735 AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAGAGA
1 AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAGA-A
33622787 AAA
1 AAA
33622790 AAGAAATTGA
Statistics
Matches: 70, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
5 3 0.04
6 52 0.74
7 11 0.16
8 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:33622737 original size:18 final size:18
Alignment explanation
Indices: 33622688--33622784 Score: 70
Period size: 18 Copynumber: 5.3 Consensus size: 18
33622678 AAAGAAATTG
*
33622688 AAAGAAAAC-AAAAAGAA
1 AAAGAAATCGAAAAAGAA
* *
33622705 AAAGAAATTGCAAAAGAA
1 AAAGAAATCGAAAAAGAA
**
33622723 AAAGAAATCGAAAAAGTG
1 AAAGAAATCGAAAAAGAA
* ** *
33622741 AGAGAAAAAGAAAATGAAGA
1 AAAGAAATCGAAAAAG-A-A
*
33622761 AAAGAAAATTGAAAAAGAA
1 AAAG-AAATCGAAAAAGAA
33622780 AAAGA
1 AAAGA
33622785 GAAAAAAGAA
Statistics
Matches: 59, Mismatches: 17, Indels: 7
0.71 0.20 0.08
Matches are distributed among these distances:
17 7 0.12
18 34 0.58
19 5 0.08
20 4 0.07
21 9 0.15
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (18 bp):
AAAGAAATCGAAAAAGAA
Found at i:33622763 original size:15 final size:14
Alignment explanation
Indices: 33622742--33622795 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
33622732 GAAAAAGTGA
33622742 GAGAAAAAGAAAAT
1 GAGAAAAAGAAAAT
33622756 GA-AGAAAAGAAAAT
1 GAGA-AAAAGAAAAT
* *
33622770 -TGAAAAAGAAAAA
1 GAGAAAAAGAAAAT
33622783 GAGAAAAAAGAAA
1 GAG-AAAAAGAAA
33622796 TTGAAAGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 10 0.30
14 14 0.42
15 9 0.27
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (14 bp):
GAGAAAAAGAAAAT
Found at i:33622765 original size:14 final size:13
Alignment explanation
Indices: 33622745--33622801 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
33622735 AAAGTGAGAG
33622745 AAAAAGAAAATGA
1 AAAAAGAAAATGA
33622758 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
*
33622772 AAAAAGAAAAAGAGA
1 AAAAAG-AAAA-TGA
*
33622787 AAAAAGAAATTGA
1 AAAAAGAAAATGA
33622800 AA
1 AA
33622802 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 10 0.28
14 18 0.50
15 8 0.22
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:33622774 original size:27 final size:27
Alignment explanation
Indices: 33622744--33622801 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
33622734 AAAAGTGAGA
* *
33622744 GAAAAAGAAAATGA-AGAAAAGAAAATT
1 GAAAAAGAAAAAGAGAAAAAAG-AAATT
33622771 GAAAAAGAAAAAGAGAAAAAAGAAATT
1 GAAAAAGAAAAAGAGAAAAAAGAAATT
33622798 GAAA
1 GAAA
33622802 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAAAGAGAAAAAAGAAATT
Found at i:33622778 original size:13 final size:12
Alignment explanation
Indices: 33622674--33622781 Score: 57
Period size: 12 Copynumber: 9.0 Consensus size: 12
33622664 AGAAAGAGAT
*
33622674 TGAAAAAGAAAT
1 TGAAAAAGAAAA
33622686 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
33622696 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* **
33622707 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
33622720 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
33622730 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
33622744 -GAAAAAGAAAA
1 TGAAAAAGAAAA
33622755 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
33622769 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
33622782 AGAGAAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
10 10 0.14
11 10 0.14
12 26 0.35
13 14 0.19
14 12 0.16
15 2 0.03
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:33622835 original size:33 final size:33
Alignment explanation
Indices: 33622798--33622860 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33622788 AAAAGAAATT
33622798 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
33622831 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
33622861 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:33625477 original size:12 final size:12
Alignment explanation
Indices: 33625447--33625477 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33625437 AGAAATTCAG
*
33625447 AAAAAAATTCAA
1 AAAAAAAATCAA
33625459 AAAAAAAATCAA
1 AAAAAAAATCAA
33625471 AAAAAAA
1 AAAAAAA
33625478 GAAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:33625539 original size:22 final size:21
Alignment explanation
Indices: 33625471--33625539 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 21
33625461 AAAAAATCAA
33625471 AAAAAAAGAAAAAAAAGAAGTG
1 AAAAAAAGAAAAAAAA-AAGTG
33625493 AGCAAAAAAG-AAAAAAAAAGT-
1 A--AAAAAAGAAAAAAAAAAGTG
33625514 AAAAAAAGAAGAAAAAAAAGTG
1 AAAAAAAGAA-AAAAAAAAGTG
33625536 AAAA
1 AAAA
33625540 GTCTTGCGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.17
20 1 0.02
21 11 0.26
22 9 0.21
23 7 0.17
24 7 0.17
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAAGTG
Found at i:33626567 original size:6 final size:6
Alignment explanation
Indices: 33626547--33626652 Score: 70
Period size: 6 Copynumber: 17.2 Consensus size: 6
33626537 AAAGAAATTG
* ** * **
33626547 AAAG-A AAACAA AAAGAA AAAGAA ATTGCA AAAGAA AAAGAA ATCGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * * *
33626594 AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAGAAA
1 AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG-AA
33626646 AAAGAA A
1 AAAGAA A
33626653 TTGAAAGAGA
Statistics
Matches: 74, Mismatches: 22, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
5 3 0.04
6 54 0.73
7 13 0.18
8 4 0.05
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:33626637 original size:13 final size:12
Alignment explanation
Indices: 33626533--33626658 Score: 66
Period size: 12 Copynumber: 10.4 Consensus size: 12
33626523 GAGAAAGAAT
*
33626533 TGAAAAAGAAAT
1 TGAAAAAGAAAA
33626545 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
33626555 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* **
33626566 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
33626579 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
33626589 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
33626603 -GAAAAAGAAAA
1 TGAAAAAGAAAA
33626614 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
33626628 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
* *
33626641 AGAAAAAAGAAAT
1 TG-AAAAAGAAAA
33626654 TGAAA
1 TGAAA
33626659 GAGAGCTTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 26
0.69 0.10 0.20
Matches are distributed among these distances:
10 10 0.11
11 10 0.11
12 30 0.34
13 24 0.27
14 12 0.14
15 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.10
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:33626696 original size:33 final size:33
Alignment explanation
Indices: 33626655--33626717 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33626645 AAAAGAAATT
33626655 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
33626688 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
33626718 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:33635555 original size:17 final size:18
Alignment explanation
Indices: 33635518--33635555 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
33635508 GATTGAGAGT
* *
33635518 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
33635536 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
33635553 GAA
1 GAA
33635556 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:33635568 original size:13 final size:12
Alignment explanation
Indices: 33635537--33635591 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
33635527 TGTGAAACAG
*
33635537 AAAAGAAATTGA
1 AAAAGAAGTTGA
33635549 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
33635561 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
33635573 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
33635585 AAAAGAA
1 AAAAGAA
33635592 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:33641808 original size:22 final size:22
Alignment explanation
Indices: 33641780--33641823 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33641770 TTTTGAACCA
33641780 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33641802 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33641824 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33642163 original size:13 final size:12
Alignment explanation
Indices: 33642131--33642162 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
33642121 AAAAGAGTTC
33642131 AAAAAAAATTGA
1 AAAAAAAATTGA
33642143 AAAAAAAATTGA
1 AAAAAAAATTGA
33642155 AAAAAAAA
1 AAAAAAAA
33642163 AAAAAATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:33644884 original size:23 final size:22
Alignment explanation
Indices: 33644832--33644884 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33644822 TCCACGTCTT
*
33644832 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33644854 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33644877 TTTCTTTT
1 TTTCTTTT
33644885 TCACTCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33646323 original size:11 final size:12
Alignment explanation
Indices: 33646307--33646423 Score: 57
Period size: 12 Copynumber: 9.6 Consensus size: 12
33646297 AAAGAAATTG
33646307 AAAGAAAAC-AA
1 AAAGAAAACGAA
33646318 AAAGAAAACG-A
1 AAAGAAAACGAA
33646329 AAA-AAAA-GAA
1 AAAGAAAACGAA
**
33646339 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
33646351 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
33646363 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
33646375 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
33646389 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
33646402 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
33646417 AAAGAAA
1 AAAGAAA
33646424 TTGAAAGAGA
Statistics
Matches: 82, Mismatches: 12, Indels: 21
0.71 0.10 0.18
Matches are distributed among these distances:
9 1 0.01
10 6 0.07
11 18 0.22
12 24 0.29
13 7 0.09
14 18 0.22
15 8 0.10
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:33646330 original size:21 final size:21
Alignment explanation
Indices: 33646295--33646335 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33646285 AAAGAGATTG
** *
33646295 AAAAAGAAATTGAAAGAAAAC
1 AAAAAGAAAACGAAAAAAAAC
33646316 AAAAAGAAAACGAAAAAAAA
1 AAAAAGAAAACGAAAAAAAA
33646336 GAAATTGCAA
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:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (21 bp):
AAAAAGAAAACGAAAAAAAAC
Found at i:33646331 original size:33 final size:33
Alignment explanation
Indices: 33646294--33646366 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
33646284 GAAAGAGATT
33646294 GAAAAAGAAATTGAAA-G-AAAACAAAAAGAAAAC
1 GAAAAAGAAA--GAAATGCAAAACAAAAAGAAAAC
* *
33646327 GAAAAA-AAAGAAATTGCAAAAGAAAAAGAAATC
1 GAAAAAGAAAGAAA-TGCAAAACAAAAAGAAAAC
33646360 GAAAAAG
1 GAAAAAG
33646367 TGAGAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
30 4 0.12
32 4 0.12
33 26 0.76
ACGTcount: A:0.71, C:0.05, G:0.16, T:0.07
Consensus pattern (33 bp):
GAAAAAGAAAGAAATGCAAAACAAAAAGAAAAC
Found at i:33646355 original size:6 final size:6
Alignment explanation
Indices: 33646307--33646411 Score: 50
Period size: 6 Copynumber: 16.7 Consensus size: 6
33646297 AAAGAAATTG
* * * *
33646307 AAAG-A AAACAA AAAGAA AACGAA AAAAAA GAAATTGCA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -AAA--GAA AAAGAA AAAGAA
** ** * * *
33646357 ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA
33646408 AAAG
1 AAAG
33646412 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 22, Indels: 13
0.67 0.21 0.12
Matches are distributed among these distances:
5 3 0.04
6 50 0.70
7 10 0.14
8 7 0.10
9 1 0.01
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:33646393 original size:14 final size:13
Alignment explanation
Indices: 33646372--33646409 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
33646362 AAAAGTGAGA
33646372 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
33646384 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
33646399 GAAAAAGAAAA
1 GAAAAAGAAAA
33646410 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:33646423 original size:21 final size:21
Alignment explanation
Indices: 33646373--33646423 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
33646363 AAAGTGAGAG
*
33646373 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
33646394 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
33646415 AAAAAGAAA
1 AAAAAGAAA
33646424 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:33646463 original size:33 final size:33
Alignment explanation
Indices: 33646426--33646488 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33646416 AAAAGAAATT
33646426 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
33646459 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
33646489 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:33648286 original size:20 final size:20
Alignment explanation
Indices: 33648263--33648316 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33648253 AGTTTTTCCC
*
33648263 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33648283 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33648303 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33648317 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33648298 original size:30 final size:30
Alignment explanation
Indices: 33648263--33648336 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33648253 AGTTTTTCCC
33648263 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33648293 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33648323 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33648337 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33648326 original size:20 final size:20
Alignment explanation
Indices: 33648263--33648327 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33648253 AGTTTTTCCC
* * * *
33648263 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33648283 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33648302 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33648323 AGCTC
1 AGCTC
33648328 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33653568 original size:13 final size:13
Alignment explanation
Indices: 33653550--33653578 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33653540 AATAGTTGTG
33653550 TGTTATTTAATTA
1 TGTTATTTAATTA
33653563 TGTTATTTAATTA
1 TGTTATTTAATTA
33653576 TGT
1 TGT
33653579 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:33655574 original size:30 final size:30
Alignment explanation
Indices: 33655540--33655636 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
33655530 TAAACTAAAA
33655540 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33655570 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
33655600 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
33655629 ATGAGCTA
1 -TGAGCTA
33655637 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33659621 original size:30 final size:31
Alignment explanation
Indices: 33659587--33659683 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
33659577 AGCTCACTCC
*
33659587 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
33659617 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
33659647 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
33659677 TAGCTCA
1 TAGCTCA
33659684 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:33660772 original size:4 final size:4
Alignment explanation
Indices: 33660763--33660790 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33660753 TTAAACTAAG
33660763 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
33660791 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:33662421 original size:10 final size:10
Alignment explanation
Indices: 33662408--33662453 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
33662398 AGCTCACTTG
33662408 AGCTCGTTTT
1 AGCTCGTTTT
*
33662418 AGCTCGTTTG
1 AGCTCGTTTT
*
33662428 AGCTCGAATTT
1 AGCTCG-TTTT
*
33662439 AGCTCGTTTC
1 AGCTCGTTTT
33662449 AGCTC
1 AGCTC
33662454 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:33662441 original size:21 final size:20
Alignment explanation
Indices: 33662405--33662453 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
33662395 ATCAGCTCAC
*
33662405 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
33662425 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
33662446 TTCAGCTC
1 TTGAGCTC
33662454 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:33662693 original size:13 final size:13
Alignment explanation
Indices: 33662675--33662703 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33662665 AATAGTTGTG
33662675 TGTTATTTAATTA
1 TGTTATTTAATTA
33662688 TGTTATTTAATTA
1 TGTTATTTAATTA
33662701 TGT
1 TGT
33662704 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:33665151 original size:68 final size:67
Alignment explanation
Indices: 33665079--33665228 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
33665069 CATCATGTGT
* * * *
33665079 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
33665141 ATGTAG
62 ATGTAG
** * *
33665147 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
33665212 AG
66 AG
33665214 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
33665229 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:33665184 original size:64 final size:64
Alignment explanation
Indices: 33665103--33665285 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
33665093 AGACATTATG
* *
33665103 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
33665167 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
33665232 AA
63 AA
* * * *
33665234 ACTG--GCTA-GTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
33665286 CGAACTATAT
Statistics
Matches: 97, Mismatches: 17, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
61 1 0.01
62 19 0.20
63 1 0.01
64 24 0.25
65 13 0.13
66 6 0.06
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:33667908 original size:15 final size:14
Alignment explanation
Indices: 33667890--33667935 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
33667880 AAACAAAGAA
33667890 AAGAAAAAGCAAAAG
1 AAGAAAAAG-AAAAG
33667905 AAGAAAAAGAAAACG
1 AAGAAAAAGAAAA-G
*
33667920 AAATAAAAAGAAAAG
1 -AAGAAAAAGAAAAG
33667935 A
1 A
33667936 GCGGCAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 12 0.43
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.02
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:33668071 original size:30 final size:30
Alignment explanation
Indices: 33668015--33668091 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
33668005 TTTGGAAAAC
*
33668015 AAAAAG-GAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAG-AATGAAAAAGAAAATGAGAGTG
***
33668045 AAAAAGAGAATGAAAAAGAGTTTGAGAGTG
1 AAAAAGAGAATGAAAAAGAAAATGAGAGTG
*
33668075 GAAAAGA-AGATGAAAAA
1 AAAAAGAGA-ATGAAAAA
33668092 AAATTGAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 38 0.95
31 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (30 bp):
AAAAAGAGAATGAAAAAGAAAATGAGAGTG
Found at i:33670879 original size:39 final size:39
Alignment explanation
Indices: 33670836--33670961 Score: 180
Period size: 39 Copynumber: 3.2 Consensus size: 39
33670826 CCGGTAATTT
* * * *
33670836 GCCTGCTAAGTATAAACCCGAACTTAACACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAATTTATCACCGGCACGAG
* *
33670875 GCCTGCTAGGTATAAACCTGAATTTATCACTGGTACGAG
1 GCCTGCTAGGTATAAACCTGAATTTATCACCGGCACGAG
* *
33670914 GCCTACTAGGTATAAACCTAAATTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAATTTATCACCGGCACGAG
33670953 GCCTGCTAG
1 GCCTGCTAG
33670962 ACATTAAGTC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTGAATTTATCACCGGCACGAG
Found at i:33674210 original size:12 final size:13
Alignment explanation
Indices: 33674193--33674225 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
33674183 AATGTGAAAC
33674193 AGAAAGAAATTGA
1 AGAAAGAAATTGA
*
33674206 A-AAAGAAGTTGA
1 AGAAAGAAATTGA
33674218 AGAAAGAA
1 AGAAAGAA
33674226 GAAAAATGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (13 bp):
AGAAAGAAATTGA
Found at i:33674237 original size:22 final size:22
Alignment explanation
Indices: 33674204--33674256 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
33674194 GAAAGAAATT
33674204 GAAAAAGAAGTT-GAAGAAAGAA
1 GAAAAAGAAGTTAGAA-AAAGAA
33674226 GAAAAATG-AGTTAGAAAAAGAA
1 GAAAAA-GAAGTTAGAAAAAGAA
33674248 -ACAAAAGAA
1 GA-AAAAGAA
33674257 AAAGACGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
21 2 0.07
22 21 0.78
23 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (22 bp):
GAAAAAGAAGTTAGAAAAAGAA
Found at i:33680290 original size:19 final size:19
Alignment explanation
Indices: 33680266--33680305 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33680256 AGCTCCCATG
33680266 TAGCTCCACA-CCAGCTCAT
1 TAGCT-CACATCCAGCTCAT
*
33680285 TAGCTCAGATCCAGCTCAT
1 TAGCTCACATCCAGCTCAT
33680304 TA
1 TA
33680306 TTAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.25
Consensus pattern (19 bp):
TAGCTCACATCCAGCTCAT
Found at i:33681550 original size:21 final size:21
Alignment explanation
Indices: 33681524--33681586 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
33681514 TTGGTATTTG
33681524 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
33681545 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
33681566 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
33681587 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:33682910 original size:30 final size:30
Alignment explanation
Indices: 33682874--33682961 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
33682864 GTATCACATA
*
33682874 TTCAGCTCACGAGCTAAACCTTAGCTCAGC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
33682904 TTCAGCTTAGGAGTTTAATCTCAACTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
33682934 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
33682962 TTTTAGTTTA
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:33686205 original size:13 final size:13
Alignment explanation
Indices: 33686187--33686257 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
33686177 TACAAGTTTG
*
33686187 AAAAAAAACCGAA
1 AAAAAAAATCGAA
*
33686200 AAAAAAATTTCGAA
1 AAAAAAA-ATCGAA
* *
33686214 AAAAAAATTTGAA
1 AAAAAAAATCGAA
33686227 AAAAAAAATTC--A
1 AAAAAAAA-TCGAA
* *
33686239 ATAAAAAATTGAA
1 AAAAAAAATCGAA
33686252 AAAAAA
1 AAAAAA
33686258 TGATTTATGC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 1 0.02
12 8 0.17
13 25 0.54
14 12 0.26
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:33686221 original size:14 final size:14
Alignment explanation
Indices: 33686196--33686257 Score: 78
Period size: 13 Copynumber: 4.7 Consensus size: 14
33686186 GAAAAAAAAC
33686196 CGAAAAAAAAATTT
1 CGAAAAAAAAATTT
33686210 CGAAAAAAAAATTT
1 CGAAAAAAAAATTT
*
33686224 -GAAAAAAAAAATT
1 CGAAAAAAAAATTT
*
33686237 C-AATAAAAAA-TT
1 CGAAAAAAAAATTT
33686249 -GAAAAAAAA
1 CGAAAAAAAA
33686258 TGATTTATGC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
12 9 0.21
13 20 0.47
14 14 0.33
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.18
Consensus pattern (14 bp):
CGAAAAAAAAATTT
Found at i:33687181 original size:5 final size:5
Alignment explanation
Indices: 33687171--33687227 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33687161 AAGAGAAAAC
*
33687171 AAAGA AAAGA AAAGA AAAGGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAGA AAA-G-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
33687218 AAAGA AAAGA
1 AAAGA AAAGA
33687228 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:33687194 original size:21 final size:20
Alignment explanation
Indices: 33687170--33687227 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
33687160 AAAGAGAAAA
*
33687170 CAAAGAAAAGAAAAGAAAAGG
1 CAAA-AAAAGAAAAGAAAACG
*
33687191 CAAAAGAAGAAAAAGAAAACG
1 CAAAAAAAG-AAAAGAAAACG
*
33687212 AAATAAAAAGAAAAGA
1 CAA-AAAAAGAAAAGA
33687228 GAGGCAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 22 0.71
22 5 0.16
ACGTcount: A:0.74, C:0.05, G:0.19, T:0.02
Consensus pattern (20 bp):
CAAAAAAAGAAAAGAAAACG
Found at i:33690060 original size:30 final size:30
Alignment explanation
Indices: 33690026--33690122 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
33690016 TAAACTAAAA
*
33690026 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
33690056 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* *
33690086 TGAGCTAAGGTTTAGCTCGTAAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
33690116 TGAGCTA
1 TGAGCTA
33690123 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:33691579 original size:11 final size:10
Alignment explanation
Indices: 33691554--33691614 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
33691544 ACCAATAAAA
33691554 TAAA-TGAGC
1 TAAATTGAGC
*
33691563 TGAATTGTAGC
1 TAAATTG-AGC
33691574 TAAATTGAGC
1 TAAATTGAGC
**
33691584 TCGATTGAGC
1 TAAATTGAGC
33691594 TGAAA-TGAGC
1 T-AAATTGAGC
*
33691604 TCAATTGAGC
1 TAAATTGAGC
33691614 T
1 T
33691615 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:33691615 original size:20 final size:20
Alignment explanation
Indices: 33691555--33691615 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
33691545 CCAATAAAAT
*
33691555 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
33691575 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
33691596 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
33691616 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:33693776 original size:12 final size:12
Alignment explanation
Indices: 33693745--33693769 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33693735 CTTTTCAATC
33693745 TCATTTTCTTTT
1 TCATTTTCTTTT
33693757 TCATTTTCTTTT
1 TCATTTTCTTTT
33693769 T
1 T
33693770 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:33693863 original size:21 final size:20
Alignment explanation
Indices: 33693837--33693893 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
33693827 CTCTTGCCTC
*
33693837 TCTTTTCTTTTTATTTCATTT
1 TCTTTTCTTTTT-TTGCATTT
* *
33693858 TCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTTTTTTTGCATTT
33693879 TCTTTT-TTTTCTTTG
1 TCTTTTCTTTT-TTTG
33693894 TTTTCTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.10
20 8 0.27
21 10 0.33
22 9 0.30
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (20 bp):
TCTTTTCTTTTTTTGCATTT
Found at i:33693877 original size:15 final size:14
Alignment explanation
Indices: 33693837--33693892 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 14
33693827 CTCTTGCCTC
*
33693837 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
33693852 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
33693867 TCTTTTGCTTTTTCTT
1 TCTTTT-CTTTTTC-T
*
33693883 TTTTTTCTTT
1 TCTTTTCTTT
33693893 GTTTTCTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 4 0.11
15 16 0.44
16 16 0.44
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:33696420 original size:30 final size:30
Alignment explanation
Indices: 33696386--33696482 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
33696376 TAAACTAAAA
*
33696386 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * *
33696416 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* *
33696446 TGAGCTAAGGTTTAGCTCGTAAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
33696476 TGAGCTA
1 TGAGCTA
33696483 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
29 2 0.04
30 44 0.83
31 7 0.13
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:33699626 original size:12 final size:12
Alignment explanation
Indices: 33699603--33699650 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
33699593 GATCGTATCA
*
33699603 CATTCTCTTTTT
1 CATTCTCATTTT
*
33699615 CAATCTCATTTT
1 CATTCTCATTTT
*
33699627 CATTTTCATTTT
1 CATTCTCATTTT
*
33699639 CATTTTCATTTT
1 CATTCTCATTTT
33699651 GTTTTTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (12 bp):
CATTCTCATTTT
Found at i:33699631 original size:6 final size:6
Alignment explanation
Indices: 33699620--33699650 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
33699610 TTTTTCAATC
33699620 TCATTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
33699651 GTTTTTGTTT
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:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:33699632 original size:18 final size:18
Alignment explanation
Indices: 33699611--33699650 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
33699601 CACATTCTCT
33699611 TTTTCAATCTCATTTTCA
1 TTTTCAATCTCATTTTCA
* *
33699629 TTTTCATTTTCATTTTCA
1 TTTTCAATCTCATTTTCA
33699647 TTTT
1 TTTT
33699651 GTTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTCAATCTCATTTTCA
Found at i:33699751 original size:16 final size:14
Alignment explanation
Indices: 33699730--33699793 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 14
33699720 CTTTTGCCTC
33699730 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
33699745 TCGTTTTCTTTTTGT
1 TC-TTTTCTTTTTTT
33699760 TCTTTTGCTTTTTCTT
1 TCTTTT-CTTTTT-TT
*
33699776 TCCTTTTCTTTGTTT
1 T-CTTTTCTTTTTTT
33699791 TCT
1 TCT
33699794 CATTACAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 6 0.14
15 14 0.33
16 17 0.40
17 5 0.12
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:33700046 original size:30 final size:30
Alignment explanation
Indices: 33700012--33700108 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33700002 AGCTCACTCC
33700012 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
33700042 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
33700072 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
33700102 TAGCTCA
1 TAGCTCA
33700109 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:33703918 original size:23 final size:24
Alignment explanation
Indices: 33703892--33703937 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33703882 TTTCTTTTGT
33703892 TTCTTT-TTCTAAC-TCATTTTCAC
1 TTCTTTCTTC-AACTTCATTTTCAC
*
33703915 TTCTTTCTTCAACTTCTTTTTCA
1 TTCTTTCTTCAACTTCATTTTCA
33703938 AATTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTTCAACTTCATTTTCAC
Found at i:33703947 original size:13 final size:12
Alignment explanation
Indices: 33703892--33703938 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
33703882 TTTCTTTTGT
33703892 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
*
33703905 -TCATTTTC-AC
1 TTCTTTTTCAAC
33703915 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
33703928 TTCTTTTTCAA
1 TTCTTTTTCAA
33703939 ATTTCTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
10 2 0.07
11 4 0.14
12 15 0.52
13 8 0.28
ACGTcount: A:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:33703954 original size:18 final size:18
Alignment explanation
Indices: 33703928--33703966 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33703918 TTTCTTCAAC
* *
33703928 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
33703946 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
33703964 TTC
1 TTC
33703967 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:33708755 original size:19 final size:19
Alignment explanation
Indices: 33708731--33708770 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33708721 AGCTCCCATG
33708731 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
33708750 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
33708769 TA
1 TA
33708771 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:33711897 original size:23 final size:22
Alignment explanation
Indices: 33711845--33711897 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33711835 TCCACGTCTT
*
33711845 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33711867 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33711890 TTTCTTTT
1 TTTCTTTT
33711898 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33714787 original size:14 final size:14
Alignment explanation
Indices: 33714765--33714812 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
33714755 ACCTAAATCG
* *
33714765 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
33714779 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
33714793 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
33714807 ACCATT
1 ACCATT
33714813 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:33715220 original size:135 final size:135
Alignment explanation
Indices: 33714973--33715243 Score: 515
Period size: 135 Copynumber: 2.0 Consensus size: 135
33714963 AGATCTAATG
*
33714973 ATAGAGGAATTCGCGCGGACCAAGATCGAGTTGTCAAGTCACGGGAAACTCCTACGAAAGCTCTA
1 ATAGAGGAATTCACGCGGACCAAGATCGAGTTGTCAAGTCACGGGAAACTCCTACGAAAGCTCTA
* *
33715038 AACGAATAGATCTAAAATCGAAAACAAAGATTAAGATTAAACTGAATCAGATTTGAATTTAAAAT
66 AACGAATAGATCTAAAATCAAAAACAAAGATTAAGATTAAACCGAATCAGATTTGAATTTAAAAT
33715103 TCCCA
131 TCCCA
33715108 ATAGAGGAATTCACGCGGACCAAGATCGAGTTGTCAAGTCACGGGAAACTCCTACGAAAGCTCTA
1 ATAGAGGAATTCACGCGGACCAAGATCGAGTTGTCAAGTCACGGGAAACTCCTACGAAAGCTCTA
33715173 AACGAATAGATCTAAAATCAAAAACAAAGATTAAGATTAAACCGAATCAGATTTGAATTTAAAAT
66 AACGAATAGATCTAAAATCAAAAACAAAGATTAAGATTAAACCGAATCAGATTTGAATTTAAAAT
33715238 TCCCA
131 TCCCA
33715243 A
1 A
33715244 ATTCAATTAA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
135 133 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (135 bp):
ATAGAGGAATTCACGCGGACCAAGATCGAGTTGTCAAGTCACGGGAAACTCCTACGAAAGCTCTA
AACGAATAGATCTAAAATCAAAAACAAAGATTAAGATTAAACCGAATCAGATTTGAATTTAAAAT
TCCCA
Found at i:33719957 original size:27 final size:27
Alignment explanation
Indices: 33719917--33720000 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
33719907 GTCGTTAAGA
*
33719917 CCCCGGTTTATAAAATTATTGAAATAC
1 CCCCGGTTTGTAAAATTATTGAAATAC
* *
33719944 CCCCAGTTTGTAAAATTACTGAAATAC
1 CCCCGGTTTGTAAAATTATTGAAATAC
* * * *
33719971 CTCCGGATTGTGAAATTATCGAAATAC
1 CCCCGGTTTGTAAAATTATTGAAATAC
33719998 CCC
1 CCC
33720001 TAATTTATGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (27 bp):
CCCCGGTTTGTAAAATTATTGAAATAC
Found at i:33730709 original size:13 final size:13
Alignment explanation
Indices: 33730691--33730725 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
33730681 CTACTAACCT
33730691 ACATAATTAAATA
1 ACATAATTAAATA
33730704 ACATAATTAAATA
1 ACATAATTAAATA
*
33730717 AAATAATTA
1 ACATAATTA
33730726 TTCATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:33730992 original size:19 final size:21
Alignment explanation
Indices: 33730939--33730993 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
33730929 AAGGAGAAAT
* *
33730939 GAGCTGAAATGAGCTAAATTC
1 GAGCTCAAGTGAGCTAAATTC
*
33730960 GAGCTCAAGCGAGCTAAA-TC
1 GAGCTCAAGTGAGCTAAATTC
33730980 GAG-TCAAGTGAGCT
1 GAGCTCAAGTGAGCT
33730994 GATTGAAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 10 0.33
20 5 0.17
21 15 0.50
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (21 bp):
GAGCTCAAGTGAGCTAAATTC
Found at i:33731544 original size:32 final size:32
Alignment explanation
Indices: 33731508--33731574 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
33731498 GTATATGAGA
*
33731508 TCTGTCACT-GTATTGGGCTTAGGCTCACTTG-T
1 TCTGTCACTGGT-TTGGG-TTAGGCCCACTTGAT
* *
33731540 TCTGTTATTGGTTTGGGTTAGGCCCACTTGAT
1 TCTGTCACTGGTTTGGGTTAGGCCCACTTGAT
33731572 TCT
1 TCT
33731575 ATTATGGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 12 0.40
32 16 0.53
33 2 0.07
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.43
Consensus pattern (32 bp):
TCTGTCACTGGTTTGGGTTAGGCCCACTTGAT
Found at i:33733766 original size:22 final size:22
Alignment explanation
Indices: 33733738--33733781 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33733728 TTTTGAACCA
33733738 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33733760 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33733782 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33736387 original size:20 final size:20
Alignment explanation
Indices: 33736362--33736404 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
33736352 AAAAGAAAAG
33736362 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
33736382 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
33736402 AAA
1 AAA
33736405 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:33740247 original size:22 final size:22
Alignment explanation
Indices: 33740219--33740262 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33740209 TTTTGAACCA
33740219 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33740241 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33740263 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33740768 original size:16 final size:16
Alignment explanation
Indices: 33740747--33740781 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33740737 ATAATATACT
33740747 TTACATGAATTACATG
1 TTACATGAATTACATG
* *
33740763 TTACATGGATTATATG
1 TTACATGAATTACATG
33740779 TTA
1 TTA
33740782 TAAGAGTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (16 bp):
TTACATGAATTACATG
Found at i:33746203 original size:30 final size:30
Alignment explanation
Indices: 33746118--33746214 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33746108 TAAACTAAAA
* *
33746118 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
33746148 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
33746178 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
33746207 ATGAGCTA
1 -TGAGCTA
33746215 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:33752939 original size:33 final size:33
Alignment explanation
Indices: 33752901--33752963 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33752891 GATTACTCAC
33752901 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
33752934 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
33752964 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:33752990 original size:21 final size:21
Alignment explanation
Indices: 33752961--33753016 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
33752951 CAAGCTCTCT
*
33752961 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
33752982 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
33753003 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
33753017 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:33753009 original size:14 final size:14
Alignment explanation
Indices: 33752960--33753016 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
33752950 TCAAGCTCTC
33752960 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
33752973 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
33752987 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
33753001 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
33753015 TT
1 TT
33753017 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:33753045 original size:17 final size:17
Alignment explanation
Indices: 33753025--33753081 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
33753015 TTCTCTCACT
33753025 TTTTCGATTTCTTTTTC
1 TTTTCGATTTCTTTTTC
*
33753042 TTTTGCAATTTC-TTTTC
1 TTTT-CGATTTCTTTTTC
* *
33753059 TTTTTCGTTTTCTTTTTG
1 -TTTTCGATTTCTTTTTC
33753077 TTTTC
1 TTTTC
33753082 TTTCAATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (17 bp):
TTTTCGATTTCTTTTTC
Found at i:33753075 original size:18 final size:18
Alignment explanation
Indices: 33752978--33753115 Score: 79
Period size: 18 Copynumber: 7.7 Consensus size: 18
33752968 TCTTTTTTCG
33752978 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
33752997 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
33753017 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
33753035 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
33753053 C-TTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
33753070 CTTTTT-GTTTTC--TTT
1 CTTTTTCTTTTTCATTTT
** * *
33753085 CAATTTCTTTTTCAATCT
1 CTTTTTCTTTTTCATTTT
*
33753103 CTTTTTCCTTTTC
1 CTTTTTCTTTTTC
33753116 TCGCTCAATG
Statistics
Matches: 89, Mismatches: 22, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
15 7 0.08
16 5 0.06
17 20 0.22
18 38 0.43
19 3 0.03
20 8 0.09
21 8 0.09
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:33753097 original size:6 final size:6
Alignment explanation
Indices: 33752978--33753084 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
33752968 TCTTTTTTCG
* * * **
33752978 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
33753029 CGATTT CTTTTT CTTTTG CAATTT C-TTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33753076 -GTTTT CTTT
1 CTTTTT CTTT
33753085 CAATTTCTTT
Statistics
Matches: 73, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
5 8 0.11
6 53 0.73
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:33754105 original size:20 final size:21
Alignment explanation
Indices: 33754080--33754119 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
33754070 CTTTTCACTT
*
33754080 TTTTTTTGTTC-CTTTTTTTC
1 TTTTTTTGCTCACTTTTTTTC
33754100 TTTTTTTGCTCACTTTTTTT
1 TTTTTTTGCTCACTTTTTTT
33754120 TTTGAATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTTTGCTCACTTTTTTTC
Found at i:33756550 original size:42 final size:43
Alignment explanation
Indices: 33756448--33756612 Score: 140
Period size: 42 Copynumber: 3.8 Consensus size: 43
33756438 CAATGTCAAC
* * * *
33756448 GTCCTAGACATGGTCTTACATATAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACACAAAATCAAATATCGATGCCAAT
* *
33756491 ATCCCAGATA-GGCTCTTACACAAAATCAAATA-CGATGCCAAT
1 GTCCCAGACATGG-TCTTACACAAAATCAAATATCGATGCCAAT
* ** *
33756533 GTCCCAGACATGGTCTTACATGTAATTCTCAAAT-T-GATGCCAAC
1 GTCCCAGACATGGTCTTACA--CAA-AATCAAATATCGATGCCAAT
* * * *
33756577 GTCCTAGACGTGCTCTTACACAAAATCACATATCGA
1 GTCCCAGACATGGTCTTACACAAAATCAAATATCGA
33756613 AATCCTATGT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
41 5 0.05
42 29 0.31
43 28 0.29
44 27 0.28
45 6 0.06
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACAAAATCAAATATCGATGCCAAT
Found at i:33761020 original size:23 final size:22
Alignment explanation
Indices: 33760969--33761031 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 22
33760959 CCTCGTCTTT
*
33760969 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
33760991 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
33761014 TTCTTTTCAATTTCTTTT
1 TTCTTTTC--TTTCTTTT
33761032 CTTTTCACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
21 2 0.06
22 5 0.15
23 15 0.44
24 11 0.32
25 1 0.03
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33761033 original size:16 final size:17
Alignment explanation
Indices: 33761014--33761049 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
33761004 TTTCTTCAAC
*
33761014 TTCTTTTCA-ATTTCTT
1 TTCTTTTCACATTCCTT
33761030 TTCTTTTCACATTCCTT
1 TTCTTTTCACATTCCTT
33761047 TTC
1 TTC
33761050 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCTTTTCACATTCCTT
Found at i:33766895 original size:12 final size:12
Alignment explanation
Indices: 33766878--33766928 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 12
33766868 ATAGGTACGT
33766878 AAAAAAATTGAAA
1 AAAAAAATTG-AA
33766891 AAAAAAATTTTTTGAA
1 AAAAAAA----TTGAA
33766907 AAAAAAATTGAA
1 AAAAAAATTGAA
33766919 AAAAAAATTG
1 AAAAAAATTG
33766929 CATACGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 15 0.44
13 7 0.21
16 9 0.26
17 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:33769172 original size:17 final size:17
Alignment explanation
Indices: 33769127--33769174 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
33769117 AGAAAAGAGC
* *
33769127 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
33769144 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
33769161 GAAAATTCAAAAAA
1 GAAAATTCAAAAAA
33769175 GAGAATGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.08
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:33776472 original size:13 final size:13
Alignment explanation
Indices: 33776425--33776474 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
33776415 ATAGGTACGT
*
33776425 AAAAAACTGAAAA
1 AAAAAATTGAAAA
33776438 AAAAAATTTTTG-AAA
1 AAAAAA---TTGAAAA
33776453 AAAAAATTGAAAA
1 AAAAAATTGAAAA
33776466 AAAAAATTG
1 AAAAAATTG
33776475 CATACGGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 18 0.56
15 9 0.28
16 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (13 bp):
AAAAAATTGAAAA
Found at i:33778719 original size:4 final size:4
Alignment explanation
Indices: 33778710--33778735 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33778700 TCTTGGACTG
33778710 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
33778736 AATAAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:33780134 original size:23 final size:22
Alignment explanation
Indices: 33780082--33780142 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
33780072 CCTTTCCACG
* *
33780082 TCTTTTTC-TTTTGTTTCTTTT
1 TCTTTTTCATTTTCTTTCTTCT
**
33780103 TCTAATTCATTTTCTCTTCTTCT
1 TCTTTTTCATTTTCT-TTCTTCT
*
33780126 TCTTTTTCAATTTCTTT
1 TCTTTTTCATTTTCTTT
33780143 TTTTTCACTC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 6 0.19
22 7 0.23
23 18 0.58
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.70
Consensus pattern (22 bp):
TCTTTTTCATTTTCTTTCTTCT
Found at i:33782468 original size:11 final size:11
Alignment explanation
Indices: 33782446--33782478 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
33782436 TTAAACTAAG
33782446 TAAATAAATAAA
1 TAAAT-AATAAA
33782458 TAAATAATAAA
1 TAAATAATAAA
33782469 TAAA-AATAAA
1 TAAATAATAAA
33782479 ACTTTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.29
11 10 0.48
12 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:33784335 original size:30 final size:30
Alignment explanation
Indices: 33784301--33784397 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33784291 AGCTCACTCC
33784301 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
33784331 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
33784361 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33784391 TAGCTCA
1 TAGCTCA
33784398 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33792545 original size:18 final size:20
Alignment explanation
Indices: 33792524--33792561 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33792514 TTCACTTTCA
33792524 TTTT-TTTATTT-TTCTCTC
1 TTTTCTTTATTTCTTCTCTC
*
33792542 TTTTCTTTGTTTCTTCTCTC
1 TTTTCTTTATTTCTTCTCTC
33792562 GATTTCACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTCTTTATTTCTTCTCTC
Found at i:33793599 original size:16 final size:15
Alignment explanation
Indices: 33793566--33793599 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
33793556 TTTTTTTTCT
*
33793566 CTTCGATTTTTTTAA
1 CTTCGATTTTTTAAA
33793581 CTTCGATTTTTTAACA
1 CTTCGATTTTTTAA-A
33793597 CTT
1 CTT
33793600 TTTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.56
Consensus pattern (15 bp):
CTTCGATTTTTTAAA
Found at i:33793625 original size:9 final size:10
Alignment explanation
Indices: 33793597--33793650 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
33793587 TTTTTTAACA
*
33793597 CTTTTTTTTG
1 CTTTTTTTTC
*
33793607 CTTTTTTTTT
1 CTTTTTTTTC
33793617 CTTTTTTTTC
1 CTTTTTTTTC
33793627 CTTTTATACTTCTC
1 CTTTT-T--TT-TC
33793641 CTTTTTTTTC
1 CTTTTTTTTC
33793651 AATTACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 25 0.66
11 3 0.08
13 3 0.08
14 7 0.18
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.76
Consensus pattern (10 bp):
CTTTTTTTTC
Found at i:33793701 original size:9 final size:9
Alignment explanation
Indices: 33793687--33793713 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
33793677 TTTGTTACAA
33793687 AAAAATAAT
1 AAAAATAAT
33793696 AAAAATAAT
1 AAAAATAAT
33793705 AAAAATAAT
1 AAAAATAAT
33793714 TTTTTTGAAT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATAAT
Found at i:33799182 original size:38 final size:38
Alignment explanation
Indices: 33799121--33799224 Score: 111
Period size: 38 Copynumber: 2.7 Consensus size: 38
33799111 TAAAGACCCG
* ** * *
33799121 CAGGCCTCGTGCTGGTAAAATATCCGGGTTAAATCTCA
1 CAGGCCTAGTGCTGGTATTATATCCGGGATAAATCCCA
* * *
33799159 TAGGCTTCA-TTCTGGTATTATATCCGGGATAAATCCCA
1 CAGGCCT-AGTGCTGGTATTATATCCGGGATAAATCCCA
*
33799197 CAGGCCTAGTGCTGGTATTATATTCGGG
1 CAGGCCTAGTGCTGGTATTATATCCGGG
33799225 CCTTCGTGCC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 1 0.02
38 51 0.98
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (38 bp):
CAGGCCTAGTGCTGGTATTATATCCGGGATAAATCCCA
Found at i:33799336 original size:43 final size:43
Alignment explanation
Indices: 33799217--33799327 Score: 197
Period size: 42 Copynumber: 2.6 Consensus size: 43
33799207 GCTGGTATTA
*
33799217 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGATGATGTG
33799260 TATTC-GGCCTTCGTGCCTAGCAGGCTTCGTGCCGATGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGATGATGTG
*
33799302 TATTCGGGCCTTTGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
33799328 GTAATGCCGG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
42 41 0.63
43 24 0.37
ACGTcount: A:0.11, C:0.26, G:0.32, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGATGATGTG
Found at i:33799723 original size:45 final size:45
Alignment explanation
Indices: 33799659--33799779 Score: 208
Period size: 45 Copynumber: 2.7 Consensus size: 45
33799649 TTGATTTTAT
33799659 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
1 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
33799704 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
1 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
* *
33799749 TATTCGGG-CTTTCGAGCCTAGCAGGCTATAA
1 TATTCGGGCCTTT-GAGCTTAGCAGACTATAA
33799780 AGCTGGTGAA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
44 4 0.05
45 69 0.95
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
Found at i:33800633 original size:13 final size:13
Alignment explanation
Indices: 33800615--33800639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33800605 ATGTGCCTGA
33800615 AAGCAATTTAATG
1 AAGCAATTTAATG
33800628 AAGCAATTTAAT
1 AAGCAATTTAAT
33800640 TCATGTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (13 bp):
AAGCAATTTAATG
Found at i:33804112 original size:21 final size:21
Alignment explanation
Indices: 33804068--33804130 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
33804058 TTTGAACCAT
* * *
33804068 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
*
33804090 TACCATTTCATACGAATTCCA
1 TACCATTTCATACCAATTCCA
*
33804111 TACCATTTCGTACCAATTCC
1 TACCATTTCATACCAATTCC
33804131 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 24 0.69
22 11 0.31
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:33804542 original size:13 final size:13
Alignment explanation
Indices: 33804524--33804548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33804514 TGGCCATCAT
33804524 GGTGTGAACACAA
1 GGTGTGAACACAA
33804537 GGTGTGAACACA
1 GGTGTGAACACA
33804549 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:33805111 original size:30 final size:29
Alignment explanation
Indices: 33805027--33805122 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
33805017 TAAACTAAAA
* * *
33805027 TGAGCTAAGCTTTACTTGTGAGCTAAAGT
1 TGAGCTAAGATTTACTCGTGAGCTGAAGT
* * * *
33805056 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATT-TACTCGTGAGCTGAAGT
*
33805086 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTA-CTCGTGAGCTGAAGT
33805115 ATGAGCTA
1 -TGAGCTA
33805123 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
29 12 0.23
30 40 0.77
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (29 bp):
TGAGCTAAGATTTACTCGTGAGCTGAAGT
Found at i:33807092 original size:28 final size:27
Alignment explanation
Indices: 33807044--33807189 Score: 159
Period size: 28 Copynumber: 5.2 Consensus size: 27
33807034 AAGTCTACAT
*
33807044 ACATGCATATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCA-TAGGCCCAATC
* *
33807072 TCATTCATATAGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCA-TAGGCCC-AATC
* *
33807101 ACATTCATATGGCCCATCGACCCCAATC
1 ACATTCATATGGCCCATAG-GCCCAATC
*
33807129 ACATTCATATGGCCCATCGGCCCAATC
1 ACATTCATATGGCCCATAGGCCCAATC
* *
33807156 AC-TATCATATGGCTCGTCAGGCCCAATC
1 ACAT-TCATATGGCCCAT-AGGCCCAATC
33807184 ACATTC
1 ACATTC
33807190 GTAGTCATGC
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 20 0.20
28 58 0.57
29 22 0.22
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (27 bp):
ACATTCATATGGCCCATAGGCCCAATC
Found at i:33807181 original size:55 final size:57
Alignment explanation
Indices: 33807044--33807189 Score: 167
Period size: 57 Copynumber: 2.6 Consensus size: 57
33807034 AAGTCTACAT
* *
33807044 ACATGCATATGGCCCA-CTAGGCCCAATCTCATTCATATAGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATC-AGGCCCAATCACATTCATATAGCCCATTAGGCCCAAATC
* * *
33807101 ACATTCATATGGCCCATC-GACCCCAATCACATTCATATGGCCCA-TCGGCCC-AATC
1 ACATTCATATGGCCCATCAG-GCCCAATCACATTCATATAGCCCATTAGGCCCAAATC
* *
33807156 AC-TATCATATGGCTCGTCAGGCCCAATCACATTC
1 ACAT-TCATATGGCCCATCAGGCCCAATCACATTC
33807190 GTAGTCATGC
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
54 1 0.01
55 31 0.40
56 8 0.10
57 36 0.47
58 1 0.01
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (57 bp):
ACATTCATATGGCCCATCAGGCCCAATCACATTCATATAGCCCATTAGGCCCAAATC
Found at i:33809316 original size:26 final size:26
Alignment explanation
Indices: 33809287--33809394 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
33809277 TGGTACAAAT
33809287 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
33809313 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
33809339 TGATAATGGGTTAGGTAAAAGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
33809365 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
33809391 TGAT
1 TGAT
33809395 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:33813506 original size:30 final size:31
Alignment explanation
Indices: 33813435--33813517 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 31
33813425 CTTTTGTTTC
* *
33813435 AATTTCTTTTTC-ATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTTC-TCTTTTTCAATCTCA
*
33813466 AAATTC-TTTTCTTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCTTTCTCTTTTTCAATCTCA
*
33813495 ATTTTCTTTTTCATTT-TCTTTTT
1 AATTTCTTTTTC-TTTCTCTTTTT
33813518 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 4 0.09
30 30 0.68
31 10 0.23
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (31 bp):
AATTTCTTTTTCTTTCTCTTTTTCAATCTCA
Found at i:33813517 original size:18 final size:18
Alignment explanation
Indices: 33813472--33813523 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
33813462 CTCAAAATTC
*
33813472 TTTTCTTTCTCTTTTTCA
1 TTTTCTTTTTCTTTTTCA
* * *
33813490 ATCTCATTTTCTTTTTCA
1 TTTTCTTTTTCTTTTTCA
33813508 TTTTCTTTTTGCTTTT
1 TTTTCTTTTT-CTTTT
33813524 CAAAGGCTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTTCA
Found at i:33813524 original size:12 final size:12
Alignment explanation
Indices: 33813493--33813517 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33813483 TTTTTCAATC
33813493 TCATTTTCTTTT
1 TCATTTTCTTTT
33813505 TCATTTTCTTTT
1 TCATTTTCTTTT
33813517 T
1 T
33813518 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:33813596 original size:5 final size:5
Alignment explanation
Indices: 33813586--33813642 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33813576 CTCTTGCCTC
*
33813586 TCTTT TCTTT T-TATT TCTTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
33813633 TCTTT TCTTT
1 TCTTT TCTTT
33813643 GTTTTATCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:33813606 original size:15 final size:14
Alignment explanation
Indices: 33813586--33813653 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 14
33813576 CTCTTGCCTC
33813586 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
33813601 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
33813616 TCTTTTGCTTTTTCTTT
1 TCTTTT-C-TTTT-TTT
33813633 TCTTTTCTTTGTTTT
1 TCTTTTCTTT-TTTT
33813648 ATCTTT
1 -TCTTT
33813654 ACAAGAATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.09
15 12 0.27
16 21 0.47
17 8 0.18
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:33813618 original size:25 final size:25
Alignment explanation
Indices: 33813590--33813638 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
33813580 TGCCTCTCTT
33813590 TTCTTTT-TATTTCTTTTTCTTTTTC
1 TTCTTTTCTATTTC-TTTTCTTTTTC
*
33813615 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTATTTCTTTTCTTTT
33813639 CTTTGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 9 0.43
27 5 0.24
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTATTTCTTTTCTTTTTC
Found at i:33813643 original size:21 final size:21
Alignment explanation
Indices: 33813586--33813653 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
33813576 CTCTTGCCTC
*
33813586 TCTTTTCTTTT-TATTTCTTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
33813607 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
33813628 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
33813648 ATCTTT
1 -TCTTT
33813654 ACAAGAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 7 0.17
21 28 0.70
22 5 0.12
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:33815699 original size:46 final size:46
Alignment explanation
Indices: 33815649--33815803 Score: 156
Period size: 46 Copynumber: 3.3 Consensus size: 46
33815639 TGGTTGAGCA
33815649 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
33815695 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
33815740 CATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
33815788 CCCGAGCTCGTTGAGT
1 TCCGAACTCGTTGAGT
33815804 GATACGAGTC
Statistics
Matches: 86, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.05
45 3 0.03
46 42 0.49
47 27 0.31
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:33824651 original size:46 final size:46
Alignment explanation
Indices: 33824601--33824760 Score: 193
Period size: 46 Copynumber: 3.5 Consensus size: 46
33824591 TGGTTGAGCA
*
33824601 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * * *
33824647 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-GCGA-ACG
33824692 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
33824738 CCCGAGCTCGTTGAGTTG-GTCCG
1 TCCGAACTCGTTGAGTTGAGTCCG
33824761 CGCACAACCC
Statistics
Matches: 94, Mismatches: 15, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
43 3 0.03
44 2 0.02
45 36 0.38
46 48 0.51
47 2 0.02
48 3 0.03
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:33824780 original size:91 final size:91
Alignment explanation
Indices: 33824598--33824765 Score: 248
Period size: 91 Copynumber: 1.9 Consensus size: 91
33824588 GGATGGTTGA
* *
33824598 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
** ***
33824663 TGAGTCCGAGTTCGTGAGATAACTAG
66 TGAGTCCGAGCACCCCAGATAACTAG
*
33824689 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
33824754 TG-GTCCGCGCAC
66 TGAGTCCGAGCAC
33824766 AACCCAATTC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 7 0.10
91 64 0.90
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGCACCCCAGATAACTAG
Found at i:33833015 original size:17 final size:18
Alignment explanation
Indices: 33832968--33833018 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
33832958 TTTCAATCTC
33832968 ATCACTCAT-TTCTTTTGA
1 ATCACTCATCTT-TTTTGA
**
33832986 ATCACTC-TCTCTTTTTTT
1 ATCACTCATCT-TTTTTGA
33833004 ATCACTCATCTTTTT
1 ATCACTCATCTTTTT
33833019 GTTTTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 1 0.04
18 23 0.82
19 4 0.14
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (18 bp):
ATCACTCATCTTTTTTGA
Found at i:33833611 original size:20 final size:20
Alignment explanation
Indices: 33833567--33833611 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
33833557 CTCGTTTCCT
*
33833567 GCTCACTCGAGCTCAAGTCA
1 GCTCACTCAAGCTCAAGTCA
* *
33833587 ACTCACTCAAGCTCAATTCA
1 GCTCACTCAAGCTCAAGTCA
33833607 GCTCA
1 GCTCA
33833612 ATCTTAACCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.36, G:0.13, T:0.22
Consensus pattern (20 bp):
GCTCACTCAAGCTCAAGTCA
Done.