Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 41 of 141
Found at i:12382431 original size:67 final size:67
Alignment explanation
Indices: 12382307--12382433 Score: 200
Period size: 67 Copynumber: 1.9 Consensus size: 67
12382297 CGGGTCACAC
* * *
12382307 GGTGAGTTGAGCCTCGGATCACACGCTGAGGTATTTTTTAATTTCTGTTTTTCAAAAAATTACGA
1 GGTGAGTTGAGCCTCGGATCACACACTGAGGTATTTTTAAATTTCTATTTTTCAAAAAATTACGA
12382372 GA
66 GA
* *
12382374 GGTGAGTTGAGCCTCGGGTCACACACTGAGGTATTTTTGAAATTTCTATTTTTAAAAAAA
1 GGTGAGTTGAGCCTCGGATCACACACTGAGGTATTTTT-AAATTTCTATTTTTCAAAAAA
12382434 AAAAACTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 36 0.67
68 18 0.33
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (67 bp):
GGTGAGTTGAGCCTCGGATCACACACTGAGGTATTTTTAAATTTCTATTTTTCAAAAAATTACGA
GA
Found at i:12382683 original size:30 final size:30
Alignment explanation
Indices: 12382643--12382746 Score: 122
Period size: 29 Copynumber: 3.5 Consensus size: 30
12382633 TTTTTTACAC
* *
12382643 AATTGCATTTTGACCCCTAAATTTTTTTAA
1 AATTACATTTTGACCCCTAAATTTTCTTAA
* * *
12382673 AATTATATTTTGA-CCCTAAACTTTCTTGA
1 AATTACATTTTGACCCCTAAATTTTCTTAA
* *
12382702 AATTACATTTTGACCCTTAAATTTTC-CAA
1 AATTACATTTTGACCCCTAAATTTTCTTAA
*
12382731 AATTACACTTTGACCC
1 AATTACATTTTGACCC
12382747 TAGAGGTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
29 41 0.66
30 21 0.34
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (30 bp):
AATTACATTTTGACCCCTAAATTTTCTTAA
Found at i:12382690 original size:29 final size:28
Alignment explanation
Indices: 12382632--12382748 Score: 117
Period size: 29 Copynumber: 4.0 Consensus size: 28
12382622 CAAATTTCGT
*
12382632 ATTTTTTACACAATTGCATTTTGACCCCTAA
1 ATTTTTTA-A-AATTACATTTTGA-CCCTAA
*
12382663 ATTTTTTTAAAATTATATTTTGACCCTAA
1 A-TTTTTTAAAATTACATTTTGACCCTAA
* *
12382692 ACTTTCTTGAAATTACATTTTGACCCTTAA
1 A-TTTTTTAAAATTACATTTTGACCC-TAA
** *
12382722 ATTTTCCAAAATTACACTTTGACCCTA
1 ATTTTTTAAAATTACATTTTGACCCTA
12382749 GAGGTTTTGT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.03
29 47 0.64
30 15 0.21
31 2 0.03
32 7 0.10
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (28 bp):
ATTTTTTAAAATTACATTTTGACCCTAA
Found at i:12383099 original size:21 final size:21
Alignment explanation
Indices: 12383075--12383129 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
12383065 CAACCAAGAG
12383075 GCAAGAAAAAAGAAA-AAACAA
1 GCAAGAAAAAAGAAAGAAA-AA
*
12383096 GCAAGCAAAAAGAAAGAAAAA
1 GCAAGAAAAAAGAAAGAAAAA
12383117 G-AAGAAGAAAAGA
1 GCAAGAA-AAAAGA
12383130 GCAAAGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.13
21 23 0.77
22 3 0.10
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (21 bp):
GCAAGAAAAAAGAAAGAAAAA
Found at i:12383252 original size:4 final size:4
Alignment explanation
Indices: 12383243--12383323 Score: 78
Period size: 4 Copynumber: 20.0 Consensus size: 4
12383233 GGTTGATCGG
*
12383243 GAAA GAAA GAAA AAAGA GAAA GAAAA GAGAA GAAA GAAA GAAA GAAA G-AA
1 GAAA GAAA GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA
* *
12383293 GAAA G-AA G-AA GGAA GAAGA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA
12383324 AAATAAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
3 9 0.14
4 43 0.65
5 14 0.21
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:12383273 original size:7 final size:7
Alignment explanation
Indices: 12383243--12383348 Score: 63
Period size: 7 Copynumber: 15.0 Consensus size: 7
12383233 GGTTGATCGG
12383243 GAAAGAAA
1 GAAA-AAA
12383251 GAAAAAA
1 GAAAAAA
*
12383258 G-AGAAA
1 GAAAAAA
*
12383264 GAAAAGA
1 GAAAAAA
*
12383271 GAAGAAA
1 GAAAAAA
12383278 GAAAGAAA
1 GAAA-AAA
*
12383286 GAAAGAA
1 GAAAAAA
*
12383293 GAAAGAA
1 GAAAAAA
**
12383300 GAAGGAA
1 GAAAAAA
*
12383307 GAAGAAA
1 GAAAAAA
*
12383314 -AAGAAA
1 GAAAAAA
12383320 GAAAAAA
1 GAAAAAA
*
12383327 TAAAAAAA
1 -GAAAAAA
*
12383335 TAAAAAA
1 GAAAAAA
*
12383342 TAAAAAA
1 GAAAAAA
12383349 ATTAATTCAG
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
6 11 0.13
7 54 0.66
8 17 0.21
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (7 bp):
GAAAAAA
Found at i:12383334 original size:8 final size:8
Alignment explanation
Indices: 12383321--12383350 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
12383311 AAAAAGAAAG
12383321 AAAAAATA
1 AAAAAATA
12383329 AAAAAAT-
1 AAAAAATA
12383336 AAAAAATA
1 AAAAAATA
12383344 AAAAAAT
1 AAAAAAT
12383351 TAATTCAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:12383341 original size:15 final size:15
Alignment explanation
Indices: 12383321--12383350 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12383311 AAAAAGAAAG
12383321 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
12383336 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
12383351 TAATTCAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:12383558 original size:11 final size:11
Alignment explanation
Indices: 12383532--12383590 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
12383522 GCAGGCCGAA
12383532 AAAAAGAGAGGAG
1 AAAAA-AGA-GAG
12383545 AAAAAAGAGAG
1 AAAAAAGAGAG
*
12383556 AAAAAAAAGA-
1 AAAAAAGAGAG
*
12383566 AAGAAAAAAG-G
1 AA-AAAAGAGAG
12383577 AAAAAAGAGA-
1 AAAAAAGAGAG
12383587 AAAA
1 AAAA
12383591 GAGAAAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 12 0.29
11 21 0.51
12 3 0.07
13 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:12383561 original size:13 final size:13
Alignment explanation
Indices: 12383530--12383574 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
12383520 AGGCAGGCCG
12383530 AAAAAAAGAGAGGA
1 AAAAAAAGAGA-GA
*
12383544 GAAAAAAGAGAGA
1 AAAAAAAGAGAGA
*
12383557 AAAAAAAGAAAGA
1 AAAAAAAGAGAGA
12383570 AAAAA
1 AAAAA
12383575 GGAAAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAGA
Found at i:12383574 original size:15 final size:16
Alignment explanation
Indices: 12383543--12383601 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
12383533 AAAAGAGAGG
*
12383543 AGAAAA-AAGAGAGAAA
1 AGAAAAGAA-AGAAAAA
12383559 A-AAAAGAAAGAAAAA
1 AGAAAAGAAAGAAAAA
12383574 AGGAAAA-AAGAGAAAAA
1 A-GAAAAGAA-AGAAAAA
12383591 GAGAAAAGAAA
1 -AGAAAAGAAA
12383602 ATGTTTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
15 11 0.31
16 5 0.14
17 17 0.47
18 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAGAAAAA
Found at i:12383581 original size:8 final size:9
Alignment explanation
Indices: 12383542--12383597 Score: 59
Period size: 8 Copynumber: 6.8 Consensus size: 9
12383532 AAAAAGAGAG
12383542 GAGAAAAAA
1 GAGAAAAAA
*
12383551 GAGAGAAAA
1 GAGAAAAAA
*
12383560 -A-AAAGAA
1 GAGAAAAAA
12383567 -AGAAAAAA
1 GAGAAAAAA
12383575 G-GAAAAAA
1 GAGAAAAAA
12383583 GAG-AAAAA
1 GAGAAAAAA
12383591 GAGAAAA
1 GAGAAAA
12383598 GAAAATGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 5 0.13
8 22 0.56
9 12 0.31
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
GAGAAAAAA
Found at i:12383965 original size:20 final size:19
Alignment explanation
Indices: 12383925--12383966 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12383915 GAAAATATTC
*
12383925 AAAAAAATTCGTGTTTTTG
1 AAAAAAATTCGTGTTTCTG
12383944 AAAAAAATTTC-TGTGTTCTG
1 AAAAAAA-TTCGTGT-TTCTG
12383964 AAA
1 AAA
12383967 TCTTCGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (19 bp):
AAAAAAATTCGTGTTTCTG
Found at i:12384238 original size:37 final size:37
Alignment explanation
Indices: 12384196--12384313 Score: 114
Period size: 37 Copynumber: 3.1 Consensus size: 37
12384186 AAATAAAAAT
* *
12384196 AAAAAAGATTTCGTCTTTC-AAAATTCTCATGTTTTC
1 AAAAAAAATTTCGTCTTTCAAAAATTCTCGTGTTTTC
* * *
12384232 AAAAAAAAAAATTT-GTGTTTTCAAAAATTTTCGTATTTTC
1 ---AAAAAAAATTTCGT-CTTTCAAAAATTCTCGTGTTTTC
* * *
12384272 AAAAAAAAATTCGTGTTTCAAAAATCCTCGTGTTTTC
1 AAAAAAAATTTCGTCTTTCAAAAATTCTCGTGTTTTC
12384309 AAAAA
1 AAAAA
12384314 TTCTGGCGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
37 34 0.52
38 4 0.06
39 14 0.21
40 14 0.21
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (37 bp):
AAAAAAAATTTCGTCTTTCAAAAATTCTCGTGTTTTC
Found at i:12384347 original size:17 final size:18
Alignment explanation
Indices: 12384237--12384561 Score: 215
Period size: 17 Copynumber: 18.4 Consensus size: 18
12384227 TTTTCAAAAA
*
12384237 AAAAAATTT-GTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
12384254 AAAAATTTTCGTATTTTC
1 AAAAATTTTCGTGTTTTC
**
12384272 AAAAAAAAATTCGTG-TTTC
1 --AAAAATTTTCGTGTTTTC
**
12384291 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
12384309 AAAAATTCTGGCG-TTT-
1 AAAAATTTTCGTGTTTTC
12384325 AGAAAATTTTCGTGTTTTC
1 A-AAAATTTTCGTGTTTTC
* * *
12384344 AAAAA-TTCCG-GTGATCC
1 AAAAATTTTCGTGT-TTTC
*
12384361 AAAAATTTTTGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
12384379 TAAAAATTTCCATG-TTTC
1 -AAAAATTTTCGTGTTTTC
*
12384397 AAAAATTTTTGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
12384415 ACAAATTTCCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** * * *
12384433 AACGACTCTAGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
12384450 ACAAATTTTCGTGTTTTA
1 AAAAATTTTCGTGTTTTC
*
12384468 AAAAATTTTTGTGTTTTGC
1 AAAAATTTTCGTGTTTT-C
* *
12384487 AAAAATTCTCGTG-TTTA
1 AAAAATTTTCGTGTTTTC
* *
12384504 AAAAATTGTCGTG-TTTA
1 AAAAATTTTCGTGTTTTC
** *
12384521 AAAAAAATCCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
12384538 AAAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
12384555 AAAAATT
1 AAAAATT
12384562 CCATTAAAAA
Statistics
Matches: 235, Mismatches: 59, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
16 3 0.01
17 111 0.47
18 83 0.35
19 28 0.12
20 10 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:12384400 original size:36 final size:34
Alignment explanation
Indices: 12384250--12384563 Score: 240
Period size: 35 Copynumber: 8.9 Consensus size: 34
12384240 AAATTTGTGT
*
12384250 TTTCAAAAATTTTCGTATTTTCAAAAAAAAATT-CGTG
1 TTTCAAAAATTTTCGTGTTTTC----AAAAATTCCGTG
** * *
12384287 TTTCAAAAATCCTCGTGTTTTCAAAAATTCTGGCG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTC-CGTG
12384322 TTT-AGAAAATTTTCGTGTTTTCAAAAATTCCGGTG
1 TTTCA-AAAATTTTCGTGTTTTCAAAAATTCC-GTG
* * * *
12384357 ATCCAAAAATTTTTGTGTTTTCTAAAAATTTCCATG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAA-TTCCGTG
* *
12384393 TTTCAAAAATTTTTGTGTTTTCACAAATTTCCGTG
1 TTTCAAAAATTTTCGTGTTTTCA-AAAATTCCGTG
** * * * * *
12384428 TTTTCAACGACTCTAGTG-TTTCACAAATTTTCGTG
1 -TTTCAAAAATTTTCGTGTTTTCA-AAAATTCCGTG
* *
12384463 TTTTAAAAAATTTTTGTGTTTTGCAAAAATTCTCGTG
1 -TTTCAAAAATTTTCGTGTTTT-CAAAAATTC-CGTG
* * ** *
12384500 TTTAAAAAATTGTCGTGTTTAAAAAAAATCCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGTG
12384534 TTTCAAAAATTTTCGTG-TTTCAAAAATTCC
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCC
12384564 ATTAAAAAAA
Statistics
Matches: 224, Mismatches: 41, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
33 17 0.08
34 20 0.09
35 89 0.40
36 69 0.31
37 29 0.13
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (34 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGTG
Found at i:12384976 original size:17 final size:17
Alignment explanation
Indices: 12384954--12384987 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12384944 CGCTACAAGC
12384954 ATTTTAACATGAAAAAT
1 ATTTTAACATGAAAAAT
*
12384971 ATTTTAGCATGAAAAAT
1 ATTTTAACATGAAAAAT
12384988 TAAAGATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (17 bp):
ATTTTAACATGAAAAAT
Found at i:12393143 original size:44 final size:44
Alignment explanation
Indices: 12393095--12393179 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
12393085 GTAGGTCAAA
*
12393095 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAC
* *
12393139 TAATATTAAAATAATCTACATTAATCAAAGTTTAAGTGGGA
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGA
12393180 GAAAAAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAC
Found at i:12394995 original size:17 final size:17
Alignment explanation
Indices: 12394975--12395033 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
12394965 TATGTGCTGA
12394975 TTGGCGAAATCTATGTT
1 TTGGCGAAATCTATGTT
* * *
12394992 TTGGTGAGATTTATGTT
1 TTGGCGAAATCTATGTT
* *
12395009 TTGGCGAGATCTATGAT
1 TTGGCGAAATCTATGTT
*
12395026 TTGACGAA
1 TTGGCGAA
12395034 TTCTTCTGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (17 bp):
TTGGCGAAATCTATGTT
Found at i:12396682 original size:15 final size:15
Alignment explanation
Indices: 12396662--12396696 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12396652 AAAACAACAA
12396662 AATAAAAATACTAAT
1 AATAAAAATACTAAT
*
12396677 AATAAAAATAGTAAT
1 AATAAAAATACTAAT
12396692 AATAA
1 AATAA
12396697 TTATAATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAAAAATACTAAT
Found at i:12396747 original size:22 final size:21
Alignment explanation
Indices: 12396722--12396764 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12396712 TGAAGTTCAC
*
12396722 AAATAAAAAGGAAAATAAAACA
1 AAAT-AAAAGCAAAATAAAACA
*
12396744 AAATAAAAGCAAAATTAAACA
1 AAATAAAAGCAAAATAAAACA
12396765 TAAAAATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (21 bp):
AAATAAAAGCAAAATAAAACA
Found at i:12396793 original size:9 final size:9
Alignment explanation
Indices: 12396780--12396841 Score: 81
Period size: 9 Copynumber: 6.9 Consensus size: 9
12396770 ATCACGATGA
*
12396780 AATAATAAA
1 AATAATAAT
*
12396789 AATAA-AAG
1 AATAATAAT
*
12396797 AGTAAATAAT
1 AATA-ATAAT
12396807 AATAATAAT
1 AATAATAAT
12396816 AATAATAAT
1 AATAATAAT
12396825 AATAATAAT
1 AATAATAAT
12396834 AATAATAA
1 AATAATAA
12396842 ACAACACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
8 5 0.11
9 37 0.79
10 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (9 bp):
AATAATAAT
Found at i:12396794 original size:6 final size:6
Alignment explanation
Indices: 12396780--12396841 Score: 81
Period size: 6 Copynumber: 10.3 Consensus size: 6
12396770 ATCACGATGA
* * *
12396780 AATAAT AAAAAT AA-AAG AGTAAAT AATAAT AATAAT AATAAT AATAAT
1 AATAAT AATAAT AATAAT AATA-AT AATAAT AATAAT AATAAT AATAAT
12396828 AATAAT AATAAT AA
1 AATAAT AATAAT AA
12396842 ACAACACAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 3 0.06
6 42 0.86
7 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (6 bp):
AATAAT
Found at i:12396809 original size:3 final size:3
Alignment explanation
Indices: 12396801--12396841 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12396791 TAAAAGAGTA
12396801 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12396842 ACAACACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12398677 original size:44 final size:44
Alignment explanation
Indices: 12398508--12398679 Score: 157
Period size: 44 Copynumber: 3.9 Consensus size: 44
12398498 GATTCGCTGT
* ** * * * * *
12398508 CTTCAGTCTGCTCTGCTGCAACTTCAGGGGGATAGGACTCGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAA
* * ** *
12398553 CTTCAGTCTGCTCCATTGCAACTTCAGGGAGATAAGGCTGGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAA
* * *
12398597 CTTCGATCTGCCCCACTGCAACTTCAAGGG-GATAAGATTAGTGA
1 CTTCAATCTGCTCCACTGCAACTTC-AGGGAGATAAGATTAGTAA
* *
12398641 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
12398680 TGCCATAATG
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
43 4 0.04
44 63 0.60
45 38 0.36
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAA
Found at i:12399937 original size:51 final size:51
Alignment explanation
Indices: 12399861--12399959 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
12399851 CCTTTCTTTT
*
12399861 TTTTTTTAGAATTCAAAGCGCCCTTTACGGGTTTTCACCTTGGTCTCTCCA
1 TTTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTTGGTCTCTCCA
* *
12399912 TTTTTTTAGGACTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTCTCT
1 TTTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTTGGTCTCT
12399960 TCTGGTGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.41
Consensus pattern (51 bp):
TTTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTTGGTCTCTCCA
Found at i:12406955 original size:24 final size:24
Alignment explanation
Indices: 12406908--12406955 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12406898 GAATCTTAGC
* *
12406908 TAGCTGCTCTTGCATTTGCATTTG
1 TAGCTGCTCTTGCATCTCCATTTG
* *
12406932 TAGCTGGTCTTGCATCTCCTTTTG
1 TAGCTGCTCTTGCATCTCCATTTG
12406956 AAGTTGTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (24 bp):
TAGCTGCTCTTGCATCTCCATTTG
Found at i:12407122 original size:19 final size:20
Alignment explanation
Indices: 12407098--12407144 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
12407088 TGGTGGACTT
* *
12407098 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
12407117 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
12407137 -AATGCAAA
1 TAATGCAAA
12407145 AAAGACGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:12411245 original size:41 final size:41
Alignment explanation
Indices: 12411195--12411351 Score: 219
Period size: 41 Copynumber: 3.8 Consensus size: 41
12411185 TTAATTTAAA
*
12411195 CAGATTCACCGGCACTTAGCCTGTTAGGCTTA-AAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAA-CCTGATT
*
12411237 CAGATCACCGGCACTTAGCCTTCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
12411278 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGAGT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
** *
12411319 CAG-TACACCGGCTTTTAGCCTGCTAGACTTATA
1 CAGAT-CACCGGCACTTAGCCTGCTAGGCTTATA
12411352 GTCCGAAATG
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
40 1 0.01
41 99 0.93
42 6 0.06
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:12412167 original size:78 final size:78
Alignment explanation
Indices: 12412046--12412556 Score: 891
Period size: 78 Copynumber: 6.6 Consensus size: 78
12412036 ACATTCAACA
* * **
12412046 TTAACTAAATTCAA-AACTTATTCATGTACATACACGTATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
*
12412110 AACATACTTACTT
66 AACATACATACTT
*
12412123 TTAACTAAATTCAAGAATTTATTCATGTATATACATATACATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
12412188 AACATACATACTT
66 AACATACATACTT
*
12412201 TTAACTAAATTCAAGAATTTATTCATGTACATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
*
12412266 AACATGCATACTT
66 AACATACATACTT
*
12412279 TTAACTAAATTCAAGAATTTATTCGTGTATATACATATATATCCG-ACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
12412343 AACATACATACTT
66 AACATACATACTT
12412356 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
12412421 AACATACATACTT
66 AACATACATACTT
12412434 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
12412499 AACATACATACTT
66 AACATACATACTT
** *
12412512 TTAACTAAATTCAAGAACATATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATA-TATCC
12412557 ACTATTAGTT
Statistics
Matches: 415, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
77 89 0.21
78 321 0.77
79 5 0.01
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (78 bp):
TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:12412365 original size:233 final size:234
Alignment explanation
Indices: 12412046--12412556 Score: 900
Period size: 233 Copynumber: 2.2 Consensus size: 234
12412036 ACATTCAACA
* **
12412046 TTAACTAAATTCAA-AACTTATTCATGTACATACACGTATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
*
12412110 AACATACTTACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATACATCCGAACTTTA
66 AACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATACATCCGAACTTTA
12412175 TATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTACATACATATA
131 TATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTACATACATATA
*
12412240 TATCCGAACTTTATATATATAAATATAACATGCATACTT
196 TATCCGAACTTTATATATATAAATATAACATACATACTT
* *
12412279 TTAACTAAATTCAAGAATTTATTCGTGTATATACATATATATCCG-ACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
*
12412343 AACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTA
66 AACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATACATCCGAACTTTA
*
12412408 TATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATA
131 TATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTACATACATATA
12412473 TATCCGAACTTTATATATATAAATATAACATACATACTT
196 TATCCGAACTTTATATATATAAATATAACATACATACTT
* *
12412512 TTAACTAAATTCAAGAACATATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
12412557 ACTATTAGTT
Statistics
Matches: 263, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
233 233 0.89
234 30 0.11
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (234 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATACATCCGAACTTTA
TATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTACATACATATA
TATCCGAACTTTATATATATAAATATAACATACATACTT
Found at i:12416273 original size:291 final size:291
Alignment explanation
Indices: 12415749--12416625 Score: 1745
Period size: 291 Copynumber: 3.0 Consensus size: 291
12415739 AATGATATGA
12415749 ATCTGACTATGGATCTGGGTATGTGGCTAACATGAAGAAGTTTTGTCTGAATGGTCATATGGGTG
1 ATCTGACTATGGATCTGGGTATGTGGCTAACATGAAGAAGTTTTGTCTGAATGGTCATATGGGTG
12415814 TATTGTATACGCCAAAGAATAGTAAACTGACATATCGGCTGTCTGTGAATGGTACTCATCATTTG
66 TATTGTATACGCCAAAGAATAGTAAACTGACATATCGGCTGTCTGTGAATGGTACTCATCATTTG
12415879 GCGAATTGTGTAATTATGTGTGACACACAGTCGTGTGTTAAATTGTATATCACAACAAGTCACTA
131 GCGAATTGTGTAATTATGTGTGACACACAGTCGTGTGTTAAATTGTATATCACAACAAGTCACTA
12415944 AATGTATATGTAACACCCCTTACCCGTATTCGACACCGAAATAGGGTATGAGGCATTACCGGAGT
196 AATGTATATGTAACACCCCTTACCCGTATTCGACACCGAAATAGGGTATGAGGCATTACCGGAGT
12416009 TTACTAATTAATTTTCAGACACTCCATTTTT
261 TTACTAATTAATTTTCAGACACTCCATTTTT
12416040 ATCTGACTATGGATCTGGGTATGTGGCTAACATGAAGAAGTTTTGTCTGAATGGTCATATGGGTG
1 ATCTGACTATGGATCTGGGTATGTGGCTAACATGAAGAAGTTTTGTCTGAATGGTCATATGGGTG
12416105 TATTGTATACGCCAAAGAATAGTAAACTGACATATCGGCTGTCTGTGAATGGTACTCATCATTTG
66 TATTGTATACGCCAAAGAATAGTAAACTGACATATCGGCTGTCTGTGAATGGTACTCATCATTTG
12416170 GCGAATTGTGTAATTATGTGTGACACACAGTCGTGTGTTAAATTGTATATCACAACAAGTCACTA
131 GCGAATTGTGTAATTATGTGTGACACACAGTCGTGTGTTAAATTGTATATCACAACAAGTCACTA
12416235 AATGTATATGTAACACCCCTTACCCGTATTCGACACCGAAATAGGGTATGAGGCATTACCGGAGT
196 AATGTATATGTAACACCCCTTACCCGTATTCGACACCGAAATAGGGTATGAGGCATTACCGGAGT
12416300 TTACTAATTAATTTTCAGACACTCCATTTTT
261 TTACTAATTAATTTTCAGACACTCCATTTTT
12416331 ATCTGACTATGGATCTGGGTATGTGGCTAACATGAAGAAGTTTTGTCTGAATGGTCATATGGGTG
1 ATCTGACTATGGATCTGGGTATGTGGCTAACATGAAGAAGTTTTGTCTGAATGGTCATATGGGTG
12416396 TATTGTATACGCCAAAGAATAGTAAACTGACATATCGGCTGTCTGTGAATGGTACTCATCATTTG
66 TATTGTATACGCCAAAGAATAGTAAACTGACATATCGGCTGTCTGTGAATGGTACTCATCATTTG
12416461 GCGAATTGTGTAATTATGTGTGACACACAGTCGTGTGTTAAATTGTATATCACAACAAGTCACTA
131 GCGAATTGTGTAATTATGTGTGACACACAGTCGTGTGTTAAATTGTATATCACAACAAGTCACTA
12416526 AATGTATATGTAACACCCCTTACCCGTATTCGACACCGAAATAGGGTATGAGGCATTACCGGAGT
196 AATGTATATGTAACACCCCTTACCCGTATTCGACACCGAAATAGGGTATGAGGCATTACCGGAGT
*
12416591 TTACTAATTAATTTTCAGACATTCCATTTTT
261 TTACTAATTAATTTTCAGACACTCCATTTTT
12416622 ATCT
1 ATCT
12416626 AACATTCATA
Statistics
Matches: 585, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
291 585 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (291 bp):
ATCTGACTATGGATCTGGGTATGTGGCTAACATGAAGAAGTTTTGTCTGAATGGTCATATGGGTG
TATTGTATACGCCAAAGAATAGTAAACTGACATATCGGCTGTCTGTGAATGGTACTCATCATTTG
GCGAATTGTGTAATTATGTGTGACACACAGTCGTGTGTTAAATTGTATATCACAACAAGTCACTA
AATGTATATGTAACACCCCTTACCCGTATTCGACACCGAAATAGGGTATGAGGCATTACCGGAGT
TTACTAATTAATTTTCAGACACTCCATTTTT
Found at i:12417887 original size:24 final size:24
Alignment explanation
Indices: 12417855--12417901 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12417845 CTAAATTTAT
*
12417855 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
12417879 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
12417902 ATTTCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:12426091 original size:19 final size:19
Alignment explanation
Indices: 12426063--12426102 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12426053 AATAAAATAT
* *
12426063 TATTTAAATTATTTTAAAA
1 TATTTAAATTACTCTAAAA
*
12426082 TATTTTAATTACTCTAAAA
1 TATTTAAATTACTCTAAAA
12426101 TA
1 TA
12426103 GAGTTTTAAC
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:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAAATTACTCTAAAA
Found at i:12428780 original size:15 final size:15
Alignment explanation
Indices: 12428760--12428789 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12428750 ATTCCAACCC
*
12428760 AAATTAAATATATTT
1 AAATTAAACATATTT
12428775 AAATTAAACATATTT
1 AAATTAAACATATTT
12428790 TGGACACTTC
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTAAACATATTT
Found at i:12434012 original size:29 final size:30
Alignment explanation
Indices: 12433948--12434015 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
12433938 TATATATTTT
*
12433948 TAATATTTATAATTTTGAAAAGATTAAATTA
1 TAAT-TTTATAATTTTGAAAAGATTAAAGTA
* * * *
12433979 AAATTTTATTATTTT-TAAAGATTAAGGTA
1 TAATTTTATAATTTTGAAAAGATTAAAGTA
12434008 TAATTTTA
1 TAATTTTA
12434016 CAATATACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 18 0.58
30 10 0.32
31 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (30 bp):
TAATTTTATAATTTTGAAAAGATTAAAGTA
Found at i:12440084 original size:5 final size:5
Alignment explanation
Indices: 12440074--12440100 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12440064 CTAACCATTA
12440074 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
12440101 AATTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:12444229 original size:17 final size:17
Alignment explanation
Indices: 12444204--12444237 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12444194 TCCTTTCTCC
12444204 CTTTCTTTTC-TTTTTT
1 CTTTCTTTTCGTTTTTT
12444220 CTTTCTTTTTCGTTTTTT
1 CTTTC-TTTTCGTTTTTT
12444238 TATTTCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
CTTTCTTTTCGTTTTTT
Found at i:12451484 original size:18 final size:19
Alignment explanation
Indices: 12451461--12451503 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12451451 TTAATATTAC
*
12451461 ACATTTCAAT-TTCACATT
1 ACATTTCAATGTCCACATT
12451479 ACATTTCAATGTCCACATT
1 ACATTTCAATGTCCACATT
*
12451498 ATATTT
1 ACATTT
12451504 TTCTTATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (19 bp):
ACATTTCAATGTCCACATT
Found at i:12454673 original size:22 final size:22
Alignment explanation
Indices: 12454645--12454688 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12454635 TGAAAAAGGA
12454645 ATGGAGGAAGATTGTTATTATT
1 ATGGAGGAAGATTGTTATTATT
12454667 ATGGAGGAAGATTGTTATTATT
1 ATGGAGGAAGATTGTTATTATT
12454689 TTATAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (22 bp):
ATGGAGGAAGATTGTTATTATT
Found at i:12460721 original size:17 final size:17
Alignment explanation
Indices: 12460699--12460735 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
12460689 TTCTGTGGCT
12460699 TTCGTTCATCTTTCGAG
1 TTCGTTCATCTTTCGAG
12460716 TTCGTTCATCTTTCGAG
1 TTCGTTCATCTTTCGAG
12460733 TTC
1 TTC
12460736 ATTCTTCCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.16, T:0.49
Consensus pattern (17 bp):
TTCGTTCATCTTTCGAG
Found at i:12469618 original size:4 final size:4
Alignment explanation
Indices: 12469597--12469646 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
12469587 TATATATATA
* * * *
12469597 TATG TGTG TGTG TGTG TATG TATG AATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12469645 TA
1 TA
12469647 CAAGTAATCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:12475785 original size:13 final size:13
Alignment explanation
Indices: 12475767--12475799 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12475757 AAGCTAAAGC
12475767 TTATAATAAGTTA
1 TTATAATAAGTTA
12475780 TTATAATAAGTTA
1 TTATAATAAGTTA
*
12475793 TTGTAAT
1 TTATAAT
12475800 TGATTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (13 bp):
TTATAATAAGTTA
Found at i:12475831 original size:20 final size:21
Alignment explanation
Indices: 12475793--12475833 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12475783 TAATAAGTTA
12475793 TTGTAATTGATTTAAGTTTTTT
1 TTGTAATT-ATTTAAGTTTTTT
*
12475815 TTGTAATT-TTTATGTTTTT
1 TTGTAATTATTTAAGTTTTT
12475834 AAGTCCCCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (21 bp):
TTGTAATTATTTAAGTTTTTT
Found at i:12487572 original size:35 final size:35
Alignment explanation
Indices: 12487523--12487592 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
12487513 ACATGCAAAG
12487523 AGAAAGCTTAAATAAAATCTCTTCTCCCCTCCTAT
1 AGAAAGCTTAAATAAAATCTCTTCTCCCCTCCTAT
*
12487558 AGAAAGCTTGAATAAAATCTCTTCTCCCCTCCTAT
1 AGAAAGCTTAAATAAAATCTCTTCTCCCCTCCTAT
12487593 GGTGATATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (35 bp):
AGAAAGCTTAAATAAAATCTCTTCTCCCCTCCTAT
Found at i:12493501 original size:43 final size:44
Alignment explanation
Indices: 12493421--12493506 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 44
12493411 TGCGATTCAT
12493421 GGTAAAATGACCGAAATAACCTCGAAGGATAAAATGATCGAAAG
1 GGTAAAATGACCGAAATAACCTCGAAGGATAAAATGATCGAAAG
* * *
12493465 GGTAAAATGACTGAAAT-ATCTCGAAGGGTAAAATGATCGAAA
1 GGTAAAATGACCGAAATAACCTCGAAGGATAAAATGATCGAAA
12493507 TACCCCGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 23 0.59
44 16 0.41
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.19
Consensus pattern (44 bp):
GGTAAAATGACCGAAATAACCTCGAAGGATAAAATGATCGAAAG
Found at i:12493586 original size:53 final size:53
Alignment explanation
Indices: 12493462--12493698 Score: 277
Period size: 53 Copynumber: 4.5 Consensus size: 53
12493452 AAATGATCGA
*
12493462 AAGGGTAAAATGACTGAAATA-TCTCGAAGGGTAAAATGA-TCGAAATACCCCG
1 AAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACT-GAAATACCCCG
* * *
12493514 AAGGGTAAAATGACTGAAATACCC-CGAAAGGTAAAATGACTGAAATGCCCTTG
1 AAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACTGAAATACCC-CG
* * *
12493567 AAGGGTGAAATAACTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCG
1 AAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCG
* * *
12493620 AAGGGTACAATGA-TCAAAATACCCTCGAAGGGTCAAATGACTGAAATACCCAC-
1 AAGGGTAAAATGACT-GAAATACCCTCGAAGGGTAAAATGACTGAAATACCC-CG
* **
12493673 ATAGGGTTAAATGACTGTTATACCCT
1 A-AGGGTAAAATGACTGAAATACCCT
12493699 TAGAGATGAA
Statistics
Matches: 156, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
52 44 0.28
53 70 0.45
54 41 0.26
55 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (53 bp):
AAGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCG
Found at i:12493670 original size:27 final size:27
Alignment explanation
Indices: 12493462--12493698 Score: 272
Period size: 26 Copynumber: 8.9 Consensus size: 27
12493452 AAATGATCGA
*
12493462 AAGGGTAAAATGACTGAAATA-TCTCG
1 AAGGGTAAAATGACTGAAATACCCTCG
12493488 AAGGGTAAAATGA-TCGAAATACCC-CG
1 AAGGGTAAAATGACT-GAAATACCCTCG
12493514 AAGGGTAAAATGACTGAAATACCC-CG
1 AAGGGTAAAATGACTGAAATACCCTCG
* * *
12493540 AAAGGTAAAATGACTGAAATGCCCTTG
1 AAGGGTAAAATGACTGAAATACCCTCG
* *
12493567 AAGGGTGAAATAACTGAAATACCCTCG
1 AAGGGTAAAATGACTGAAATACCCTCG
*
12493594 AAGGGTAAAATGACCGAAATACCC-CG
1 AAGGGTAAAATGACTGAAATACCCTCG
* *
12493620 AAGGGTACAATGA-TCAAAATACCCTCG
1 AAGGGTAAAATGACT-GAAATACCCTCG
* *
12493647 AAGGGTCAAATGACTGAAATACCCAC-
1 AAGGGTAAAATGACTGAAATACCCTCG
* **
12493673 ATAGGGTTAAATGACTGTTATACCCT
1 A-AGGGTAAAATGACTGAAATACCCT
12493699 TAGAGATGAA
Statistics
Matches: 180, Mismatches: 23, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
25 1 0.01
26 90 0.50
27 88 0.49
28 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (27 bp):
AAGGGTAAAATGACTGAAATACCCTCG
Found at i:12493697 original size:80 final size:79
Alignment explanation
Indices: 12493459--12493689 Score: 272
Period size: 80 Copynumber: 2.9 Consensus size: 79
12493449 ATAAAATGAT
* *
12493459 CGAAAGGGTAAAATGACTGAAATA-TCTCGAAGGGTAAAATGA-TCGAAATACCCCGAAGGGTAA
1 CGAAA-GGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACT-GAAATACCCCGAAGGGTAA
12493522 AATGACTGAAATACCC
64 AATGACTGAAATACCC
* * * * *
12493538 CGAAAGGTAAAATGACTGAAATGCCCTTGAAGGGTGAAATAACTGAAATACCCTCGAAGGGTAAA
1 CGAAAGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACTGAAATACCC-CGAAGGGTAAA
*
12493603 ATGACCGAAATACCC
65 ATGACTGAAATACCC
* * * *
12493618 CGAAGGGTACAATGA-TCAAAATACCCTCGAAGGGTCAAATGACTGAAATACCCAC-ATAGGGTT
1 CGAAAGGTAAAATGACT-AAAATACCCTCGAAGGGTAAAATGACTGAAATACCC-CGA-AGGGTA
12493681 AAATGACTG
63 AAATGACTG
12493690 TTATACCCTT
Statistics
Matches: 131, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
78 17 0.13
79 30 0.23
80 84 0.64
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (79 bp):
CGAAAGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCGAAGGGTAAAA
TGACTGAAATACCC
Found at i:12493916 original size:26 final size:26
Alignment explanation
Indices: 12493881--12493931 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12493871 GCCACATATA
*
12493881 CTATTACTGGCAGCTTCGCTGTGATT
1 CTATTACTGGCAGCTTCGATGTGATT
*
12493907 CTATTACTGGCAGCTTTGATGTGAT
1 CTATTACTGGCAGCTTCGATGTGAT
12493932 ATTGGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.39
Consensus pattern (26 bp):
CTATTACTGGCAGCTTCGATGTGATT
Found at i:12494099 original size:33 final size:32
Alignment explanation
Indices: 12494029--12494121 Score: 113
Period size: 33 Copynumber: 3.0 Consensus size: 32
12494019 TACATTATTG
12494029 CACTGTACTGGTTACTGTATTGGGCTAAGG--C
1 CACTGTACT-GTTACTGTATTGGGCTAAGGCCC
*
12494060 C-C-GTACTGTTACTGTTTTGGGCTAAGGCCC
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCC
* *
12494090 ACACTGTACTGTTACTGTATAGGGCTTAGGCC
1 -CACTGTACTGTTACTGTATTGGGCTAAGGCC
12494122 TAGACTAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 19 0.36
29 5 0.09
30 2 0.04
31 2 0.04
32 1 0.02
33 24 0.45
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (32 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCCC
Found at i:12503112 original size:61 final size:61
Alignment explanation
Indices: 12502941--12503123 Score: 169
Period size: 61 Copynumber: 3.0 Consensus size: 61
12502931 TTTGAAGGGG
* *
12502941 AAGTAAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAACCATATATTTTAATTA
1 AAGTAAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATCATATATTTTGATTA
* * * * * * * * * *
12503002 AAATATATTTA-ATAATAATTATTTCA-AATT-A-TATTTTA-TAGTATCATATATTATGATTT
1 AAGTAAATTCATATAA-AAATA-TTGATTATTAAGAATTTTATTA-AATCATATATTTTGATTA
* * *
12503061 TAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTGATTA
1 AAGTAAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATCATATATTTTGATTA
12503122 AA
1 AA
12503124 ATATATTTAA
Statistics
Matches: 88, Mismatches: 26, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
58 5 0.06
59 32 0.36
60 10 0.11
61 36 0.41
62 5 0.06
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (61 bp):
AAGTAAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATCATATATTTTGATTA
Found at i:12503123 original size:18 final size:17
Alignment explanation
Indices: 12503095--12503129 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12503085 ATTATTAAGA
*
12503095 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12503112 ATTTTGATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12503130 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12503383 original size:16 final size:16
Alignment explanation
Indices: 12503362--12503397 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12503352 TTGAATTGCT
*
12503362 ATTACGCATCTATTTC
1 ATTACGCATCTATTCC
*
12503378 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
12503394 ATTA
1 ATTA
12503398 GAGCAAACCG
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:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:12503820 original size:6 final size:6
Alignment explanation
Indices: 12503809--12503849 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
12503799 TACCTCACTT
12503809 CAACAC CAACAC CAACAC CAACAC CAACAC CAACAC CAACA
1 CAACAC CAACAC CAACAC CAACAC CAACAC CAACAC CAACA
12503850 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (6 bp):
CAACAC
Found at i:12510024 original size:18 final size:18
Alignment explanation
Indices: 12510001--12510037 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12509991 TTGTGCTCTT
12510001 TTTTAAAAGTAAAATACA
1 TTTTAAAAGTAAAATACA
12510019 TTTTAAAAGTAAAATACA
1 TTTTAAAAGTAAAATACA
12510037 T
1 T
12510038 AGGTAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
TTTTAAAAGTAAAATACA
Found at i:12511377 original size:10 final size:9
Alignment explanation
Indices: 12511362--12511387 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12511352 CTTTATATTC
12511362 TTTTTTTTG
1 TTTTTTTTG
12511371 TTTTTTTTG
1 TTTTTTTTG
12511380 TTTTTTTT
1 TTTTTTTT
12511388 ATGGTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:12513578 original size:20 final size:19
Alignment explanation
Indices: 12513548--12513588 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
12513538 TGCCCGGGCT
12513548 AAAAGCCCAAAACTAAACAAC
1 AAAAGCCCAAAAC-AAA-AAC
12513569 AAAA-CCCAAAACAAAAAC
1 AAAAGCCCAAAACAAAAAC
12513587 AA
1 AA
12513589 GCCCAGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 3 0.15
20 8 0.40
21 4 0.20
ACGTcount: A:0.68, C:0.27, G:0.02, T:0.02
Consensus pattern (19 bp):
AAAAGCCCAAAACAAAAAC
Found at i:12513940 original size:13 final size:15
Alignment explanation
Indices: 12513924--12513956 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
12513914 TTCTGTTTTC
12513924 TTTTTATTT-TT-AT
1 TTTTTATTTATTCAT
12513937 TTTTTATTTATTCAT
1 TTTTTATTTATTCAT
12513952 TTTTT
1 TTTTT
12513957 TACAAATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTATTCAT
Found at i:12518540 original size:19 final size:19
Alignment explanation
Indices: 12518516--12518553 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12518506 TACACTTTTA
*
12518516 ATTATG-CATCAATTTTAAT
1 ATTATGTCAT-AACTTTAAT
12518535 ATTATGTCATAACTTTAAT
1 ATTATGTCATAACTTTAAT
12518554 TACCTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (19 bp):
ATTATGTCATAACTTTAAT
Found at i:12518850 original size:21 final size:21
Alignment explanation
Indices: 12518797--12518883 Score: 88
Period size: 20 Copynumber: 4.1 Consensus size: 21
12518787 CCTGATCAGT
*
12518797 ATACGACACA-TAAGTGCCTG
1 ATACGACACACGAAGTGCCTG
* *
12518817 AAACGAC-CACGAGGTGCCTG
1 ATACGACACACGAAGTGCCTG
*
12518837 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAAGTGCCTG
**
12518858 AAATACGACACATAAAGTGCCTG
1 --ATACGACACACGAAGTGCCTG
12518881 ATA
1 ATA
12518884 TACAACACAT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 20 0.36
21 16 0.29
23 18 0.32
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (21 bp):
ATACGACACACGAAGTGCCTG
Found at i:12518867 original size:23 final size:22
Alignment explanation
Indices: 12518797--12518904 Score: 98
Period size: 23 Copynumber: 5.0 Consensus size: 22
12518787 CCTGATCAGT
*
12518797 ATACGACACA-TAAGTGCCTGA
1 ATACGACACACGAAGTGCCTGA
*
12518818 A-ACGAC-CACGAGGTGCCTG-
1 ATACGACACACGAAGTGCCTGA
*
12518837 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAAGTGCCTG-A
**
12518860 ATACGACACATAAAGTGCCTGA
1 ATACGACACACGAAGTGCCTGA
* **
12518882 TATACAACACATAAAGTGCCTGA
1 -ATACGACACACGAAGTGCCTGA
12518905 TCGGCAAAGC
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.04
20 18 0.24
21 14 0.19
22 1 0.01
23 39 0.52
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (22 bp):
ATACGACACACGAAGTGCCTGA
Found at i:12523166 original size:19 final size:19
Alignment explanation
Indices: 12523142--12523178 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12523132 TGATTGGTGT
12523142 TTGTGGTGGTCGGTCGATG
1 TTGTGGTGGTCGGTCGATG
12523161 TTGTGGTGGTCGGTCGAT
1 TTGTGGTGGTCGGTCGAT
12523179 TGGTGTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.11, G:0.46, T:0.38
Consensus pattern (19 bp):
TTGTGGTGGTCGGTCGATG
Found at i:12524991 original size:41 final size:41
Alignment explanation
Indices: 12524934--12525042 Score: 191
Period size: 41 Copynumber: 2.7 Consensus size: 41
12524924 TTTAACATAT
*
12524934 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
12524975 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
12525016 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
12525043 AAGTCCGAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:12526886 original size:13 final size:13
Alignment explanation
Indices: 12526868--12526892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12526858 ACAAACGATA
12526868 AAATTTTCACACG
1 AAATTTTCACACG
12526881 AAATTTTCACAC
1 AAATTTTCACAC
12526893 AAGTAAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:12528748 original size:32 final size:32
Alignment explanation
Indices: 12528703--12528766 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
12528693 TATTCTCATG
*
12528703 GATTTTGCTTTAGATCCGCTGTTAATATGTTT
1 GATTTTGCATTAGATCCGCTGTTAATATGTTT
12528735 GATTTTGCATTAGATCCGCTGTTAATATGTTT
1 GATTTTGCATTAGATCCGCTGTTAATATGTTT
12528767 TTCTTCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.48
Consensus pattern (32 bp):
GATTTTGCATTAGATCCGCTGTTAATATGTTT
Found at i:12533539 original size:22 final size:23
Alignment explanation
Indices: 12533512--12533562 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
12533502 CTCTCCTATT
* *
12533512 AATATAAATA-ATATTTTAGATG
1 AATATAAATAGATATATAAGATG
12533534 AATAT-AATAGATATATAAGATG
1 AATATAAATAGATATATAAGATG
12533556 AAT-TAAA
1 AATATAAA
12533563 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (23 bp):
AATATAAATAGATATATAAGATG
Found at i:12533627 original size:15 final size:16
Alignment explanation
Indices: 12533604--12533645 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
12533594 TAAATTTAAT
12533604 AATTAAATTAT-TAAAA
1 AATT-AATTATATAAAA
*
12533620 TATTAATTATATAAAA
1 AATTAATTATATAAAA
12533636 AATTAGATTA
1 AATTA-ATTA
12533646 GTTTTACGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 12 0.55
17 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AATTAATTATATAAAA
Found at i:12538544 original size:19 final size:19
Alignment explanation
Indices: 12538522--12538584 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
12538512 AAATTTGGAG
12538522 TTTTTATAAA-TATTTTGAA
1 TTTTTA-AAATTATTTTGAA
* *
12538541 TTTTAAAAATTATTTTAAAA
1 TTTTTAAAATTATTTT-GAA
*
12538561 TTTTGAAAATTATTTTGAA
1 TTTTTAAAATTATTTTGAA
12538580 TTTTT
1 TTTTT
12538585 TTTATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.08
19 17 0.46
20 17 0.46
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTTAAAATTATTTTGAA
Found at i:12538584 original size:20 final size:19
Alignment explanation
Indices: 12538523--12538583 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 19
12538513 AATTTGGAGT
*
12538523 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
*
12538541 TTTTAAAAATTATTTTAAAA
1 TTTTAAAAATTATTTT-GAA
*
12538561 TTTTGAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
12538580 TTTT
1 TTTT
12538584 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 8 0.22
19 12 0.32
20 17 0.46
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:12544942 original size:18 final size:18
Alignment explanation
Indices: 12544919--12544956 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12544909 TAGTAGTGGC
12544919 GTTTATGAGAAAAACGCT
1 GTTTATGAGAAAAACGCT
*
12544937 GTTTATGATAAAAACGCT
1 GTTTATGAGAAAAACGCT
12544955 GT
1 GT
12544957 AAAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (18 bp):
GTTTATGAGAAAAACGCT
Found at i:12545303 original size:12 final size:12
Alignment explanation
Indices: 12545286--12545311 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12545276 CGCCATCGAC
12545286 TTCGAAATGGAT
1 TTCGAAATGGAT
12545298 TTCGAAATGGAT
1 TTCGAAATGGAT
12545310 TT
1 TT
12545312 GGGTAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (12 bp):
TTCGAAATGGAT
Found at i:12554147 original size:43 final size:42
Alignment explanation
Indices: 12554053--12554290 Score: 207
Period size: 43 Copynumber: 5.6 Consensus size: 42
12554043 ATCCGTTACT
* * * **
12554053 CGGTGGATTCAGCACTTAGGAACCACTTTA-AATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTTACAA-TCAAAGATA
* *
12554095 CAG-GGAATCAGCACATAGCAACCCCTTTCACAATCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAAGATA
* * **
12554137 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTACAATCAAAGATA
* * * *
12554180 C-GAGGAATCAGCACATAGCATCCCCTTTCACAATCAAATATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAAGATA
* * * * *
12554222 CGGTGGAATCAACACTTAGAAACCACATTTAGAATCAATA-ATT
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTACAATCAA-AGATA
12554265 CGG-GGAATCAGCACTTAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCCCT
12554291 CGGGGAATCT
Statistics
Matches: 156, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
41 28 0.18
42 58 0.37
43 60 0.38
44 10 0.06
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (42 bp):
CGGTGGAATCAGCACTTAGCAACCCCTTTACAATCAAAGATA
Found at i:12554195 original size:85 final size:85
Alignment explanation
Indices: 12554053--12554290 Score: 320
Period size: 85 Copynumber: 2.8 Consensus size: 85
12554043 ATCCGTTACT
* *
12554053 CGGTGGATTCAGCACTTAGGAACCA-CTTTAAATTCAGTGATAC-AGGGAATCAGCACATAGCAA
1 CGGTGGAATCAGCACTTAGAAACCACCTTTAAATTCAGTGATACGA-GGAATCAGCACATAGCAA
12554116 CCCCTTTCACAATCAAAGATA
65 CCCCTTTCACAATCAAAGATA
* * *
12554137 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGAGGAATCAGCACATAGCATC
1 CGGTGGAATCAGCACTTAGAAACCACCTTTAAATTCAGTGATACGAGGAATCAGCACATAGCAAC
*
12554202 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAAGATA
* * * * * * *
12554222 CGGTGGAATCAACACTTAGAAACCACATTTAGAA-TCAATAATTCGGGGAATCAGCACTTAGCAA
1 CGGTGGAATCAGCACTTAGAAACCACCTTTA-AATTCAGTGATACGAGGAATCAGCACATAGCAA
12554286 CCCCT
65 CCCCT
12554291 CGGGGAATCT
Statistics
Matches: 136, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
84 23 0.17
85 111 0.82
86 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGAAACCACCTTTAAATTCAGTGATACGAGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:12554293 original size:26 final size:26
Alignment explanation
Indices: 12554264--12554316 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
12554254 AATCAATAAT
12554264 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
* *
12554290 TCGGGGAATCTGCACTTAGCGACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
12554316 T
1 T
12554317 TTTTATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (26 bp):
TCGGGGAATCAGCACTTAGCAACCCC
Found at i:12556752 original size:21 final size:21
Alignment explanation
Indices: 12556723--12556772 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
12556713 CTACGACTTA
* * * *
12556723 AAGCGGAGGTAGCAGCGAGGG
1 AAGCAGAGGCAGCAACGAAGG
12556744 AAGCAGAGGCAGCAACGAAGG
1 AAGCAGAGGCAGCAACGAAGG
*
12556765 AAGTAGAG
1 AAGCAGAG
12556773 CAAAGCAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAAGG
Found at i:12557245 original size:43 final size:42
Alignment explanation
Indices: 12557143--12557271 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
12557133 AGAACATGAG
* *
12557143 CTTTAGCGGCATTTTTGGGAAAAGTGCCGCTAAAGGTCCATGTT
1 CTTTAGCGGCATTTGTGGGAAAA-CGCCGCTAAAGGT-CATGTT
* * *
12557187 CTGTAGCAGCGTTTGTGGGGAAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCATTTGT-GGGAAAACGCCGCTAAAGGTCATGTT
* *
12557230 GTTTAGCGGCATTTGTGGGAAAGCGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCATTTGTGGGAAAACGCCGCTAAAGGTCATGTT
12557272 TTGTAGTGGC
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 25 0.34
43 18 0.24
44 24 0.32
45 7 0.09
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (42 bp):
CTTTAGCGGCATTTGTGGGAAAACGCCGCTAAAGGTCATGTT
Found at i:12557260 original size:42 final size:42
Alignment explanation
Indices: 12557143--12557271 Score: 168
Period size: 44 Copynumber: 3.0 Consensus size: 42
12557133 AGAACATGAG
* *
12557143 CTTTAGCGGCATTTTTGGGAAAAGTGCCGCTAAAGGTCCATGTT
1 CTTTAGCGGCATTTGTGGG-AAAGCGCCGCTAAAGGT-CATGTT
* * * *
12557187 CTGTAGCAGCGTTTGTGGGGAAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCATTTGT-GGGAAAGCGCCGCTAAAGGTCATGTT
*
12557230 GTTTAGCGGCATTTGTGGGAAAGCGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCATTTGTGGGAAAGCGCCGCTAAAGGTCATGTT
12557272 TTGTAGTGGC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 25 0.34
43 18 0.25
44 27 0.37
45 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (42 bp):
CTTTAGCGGCATTTGTGGGAAAGCGCCGCTAAAGGTCATGTT
Found at i:12567994 original size:11 final size:12
Alignment explanation
Indices: 12567957--12567991 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
12567947 ATGTTATAAT
12567957 ATTAATATTTTA
1 ATTAATATTTTA
12567969 ATTAA-ATTTTA
1 ATTAATATTTTA
12567980 ATTAATATTTTA
1 ATTAATATTTTA
12567992 TTATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTAATATTTTA
Found at i:12568108 original size:11 final size:11
Alignment explanation
Indices: 12568092--12568118 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12568082 AATCTCACTT
12568092 TTTCTCTCAAA
1 TTTCTCTCAAA
12568103 TTTCTCTCAAA
1 TTTCTCTCAAA
12568114 TTTCT
1 TTTCT
12568119 ATAGCCACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:12596818 original size:81 final size:81
Alignment explanation
Indices: 12596705--12596875 Score: 204
Period size: 81 Copynumber: 2.1 Consensus size: 81
12596695 AGGTATAACA
* * *
12596705 GTCATTTTACCCTATGAGGGTATTTCGATCATTCTA-CCTTATGGGGGTATTTTAG-TCATTTTA
1 GTCATTTTACCCTATGAAGGTATTTCGATCATTCTATCC-TATGGGAGTA-TTTAGATCAATTTA
12596768 ACCTATAGGGGTATTTCG
64 ACCTATAGGGGTATTTCG
* * * *
12596786 GTCATTTTACCCTATGAATGTATTTC-AGTCATTTTATCCTATGGGAGTATTTCGATCAATTTAC
1 GTCATTTTACCCTATGAAGGTATTTCGA-TCATTCTATCCTATGGGAGTATTTAGATCAATTTAA
* *
12596850 CCTATGGGGGTATTTTG
65 CCTATAGGGGTATTTCG
*
12596867 GTAATTTTA
1 GTCATTTTA
12596876 TTGACCTCTC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 5 0.06
81 70 0.91
82 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.43
Consensus pattern (81 bp):
GTCATTTTACCCTATGAAGGTATTTCGATCATTCTATCCTATGGGAGTATTTAGATCAATTTAAC
CTATAGGGGTATTTCG
Found at i:12596874 original size:54 final size:53
Alignment explanation
Indices: 12596704--12596876 Score: 204
Period size: 54 Copynumber: 3.2 Consensus size: 53
12596694 GAGGTATAAC
* *
12596704 AGTCATTTTACCCTATGAGGGTATTTCGATC-ATTCTACCTTATGGGGGTATTTT
1 AGTCATTTTATCCTATG-GGGTATTTCGATCAATT-TACCCTATGGGGGTATTTT
* * * *** *
12596758 AGTCATTTTAACCTATAGGGGTATTTCGGTCATTTTACCCTATGAATGTATTTC
1 AGTCATTTTATCCTAT-GGGGTATTTCGATCAATTTACCCTATGGGGGTATTTT
12596812 AGTCATTTTATCCTATGGGAGTATTTCGATCAATTTACCCTATGGGGGTATTTT
1 AGTCATTTTATCCTATGGG-GTATTTCGATCAATTTACCCTATGGGGGTATTTT
* *
12596866 GGTAATTTTAT
1 AGTCATTTTAT
12596877 TGACCTCTCG
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 3 0.03
54 93 0.94
55 3 0.03
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (53 bp):
AGTCATTTTATCCTATGGGGTATTTCGATCAATTTACCCTATGGGGGTATTTT
Found at i:12596875 original size:27 final size:27
Alignment explanation
Indices: 12596705--12596875 Score: 180
Period size: 27 Copynumber: 6.3 Consensus size: 27
12596695 AGGTATAACA
*
12596705 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * **
12596732 ATCATTCTACCTTATGGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
12596759 GTCATTTTAACCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*** *
12596786 GTCATTTTACCCTATGAATGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
12596813 GTCATTTTATCCTATGGGAGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
12596840 ATCAATTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
12596867 GTAATTTTA
1 GTCATTTTA
12596876 TTGACCTCTC
Statistics
Matches: 112, Mismatches: 32, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 112 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:12599969 original size:6 final size:6
Alignment explanation
Indices: 12599960--12600041 Score: 112
Period size: 6 Copynumber: 13.7 Consensus size: 6
12599950 AGTCTAAGAA
* *
12599960 AAAAAT AAAACT AAAAGA- AAAAAT AAAAAT GAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
12600008 AAAAAT AAAAAT AAAAGT AAAAGT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
12600042 CCAAAATCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
5 1 0.01
6 67 0.99
ACGTcount: A:0.79, C:0.01, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:12601766 original size:6 final size:6
Alignment explanation
Indices: 12601740--12601864 Score: 52
Period size: 6 Copynumber: 21.7 Consensus size: 6
12601730 CAGAACAACG
* * *
12601740 ATAATA ATGAA-A ATGAA-A ATAATA ATAAGA ATCATA AGAATA ATAATA
1 ATAATA AT-AATA AT-AATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * ** *
12601788 A-AATTA ATGATA ATAA-A CTAAGA ATAATA A-AATA A-AGGA AAAATA
1 ATAA-TA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* *
12601833 A-AA-A ATAATA A-AAGTA TTAATA ATAAAA ATAA
1 ATAATA ATAATA ATAA-TA ATAATA ATAATA ATAA
12601865 ATATGAAATA
Statistics
Matches: 91, Mismatches: 18, Indels: 20
0.71 0.14 0.16
Matches are distributed among these distances:
4 2 0.02
5 22 0.24
6 62 0.68
7 5 0.05
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (6 bp):
ATAATA
Found at i:12601800 original size:18 final size:17
Alignment explanation
Indices: 12601739--12601803 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
12601729 TCAGAACAAC
*
12601739 GATAATAATGAAAATGAA
1 GATAATAAT-AAAATTAA
*
12601757 AATAATAATAAGAATCATAA
1 GATAATAATAA-AAT--TAA
12601777 GAATAATAATAAAATTAA
1 G-ATAATAATAAAATTAA
12601795 TGATAATAA
1 -GATAATAA
12601804 ACTAAGAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.05
18 21 0.54
19 1 0.03
20 5 0.13
21 10 0.26
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (17 bp):
GATAATAATAAAATTAA
Found at i:12601842 original size:29 final size:29
Alignment explanation
Indices: 12601778--12601843 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
12601768 GAATCATAAG
* * * *
12601778 AATAATAATAAAATTAATGATAATAAACT
1 AATAATAATAAAATAAAGGAAAATAAACA
*
12601807 AAGAATAATAAAATAAAGGAAAAATAAA-A
1 AATAATAATAAAATAAAGG-AAAATAAACA
12601836 AATAATAA
1 AATAATAA
12601844 AAGTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (29 bp):
AATAATAATAAAATAAAGGAAAATAAACA
Found at i:12612306 original size:14 final size:14
Alignment explanation
Indices: 12612286--12612314 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12612276 TGGTATCTAG
12612286 ATTTTTTT-AAAAT
1 ATTTTTTTAAAAAT
12612299 ATTTTTTTAAAAAT
1 ATTTTTTTAAAAAT
12612313 AT
1 AT
12612315 GTATTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTTTTAAAAAT
Found at i:12613258 original size:107 final size:107
Alignment explanation
Indices: 12613072--12613275 Score: 327
Period size: 107 Copynumber: 1.9 Consensus size: 107
12613062 CCATACTTTG
* * * * *
12613072 AAGTTTTAAGAGGATATTTGGCTATTTAGTTGAACGAGAAATCGAAAACTAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAAACCAGCACGTTAGAGCAC
* *
12613137 GTTTTCTCGATTTTCCAAACGCGAAATATTGCTTTACTTTAA
66 GTTTTCTCGATTTTCCAAAAGCAAAATATTGCTTTACTTTAA
* *
12613179 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAATGAGAAATCGAAACCCAGCACGTTAGAGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAAACCAGCACGTTAGAGCAC
12613244 GTTTTCTCGATTTTCCAAAAGCAAAATATTGC
66 GTTTTCTCGATTTTCCAAAAGCAAAATATTGC
12613276 CTCGTTTTGA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 88 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (107 bp):
AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAAACCAGCACGTTAGAGCAC
GTTTTCTCGATTTTCCAAAAGCAAAATATTGCTTTACTTTAA
Found at i:12613991 original size:15 final size:15
Alignment explanation
Indices: 12613964--12613998 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12613954 AAATATTTTA
12613964 ATAT-AGATAATAAT
1 ATATAAGATAATAAT
*
12613978 ATATAAGATGATAAT
1 ATATAAGATAATAAT
12613993 ATATAA
1 ATATAA
12613999 ATTTAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (15 bp):
ATATAAGATAATAAT
Found at i:12615724 original size:40 final size:40
Alignment explanation
Indices: 12615680--12615808 Score: 129
Period size: 40 Copynumber: 3.1 Consensus size: 40
12615670 TTGCTCTACT
12615680 ACTGCTTAGGGAGATAAGATCTATGGTTTTAATCCGCTCC
1 ACTGCTTAGGGAGATAAGATCTATGGTTTTAATCCGCTCC
* * * * *
12615720 ACTGCAACTTCAGGGAGATAGGA-CTTGATGTGATCTACTCCACT--
1 ACTG---CTT-AGGGAGATAAGATC-T-ATG-GTTTTAATCCGCTCC
12615764 ACTGCTTAGGGAGATAAGATCTATGGTTTTAATCCGCTCC
1 ACTGCTTAGGGAGATAAGATCTATGGTTTTAATCCGCTCC
12615804 ACTGC
1 ACTGC
12615809 AACTTCAGGG
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
38 9 0.13
39 3 0.04
40 21 0.30
41 4 0.06
43 4 0.06
44 16 0.23
45 3 0.04
46 9 0.13
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (40 bp):
ACTGCTTAGGGAGATAAGATCTATGGTTTTAATCCGCTCC
Found at i:12615735 original size:84 final size:84
Alignment explanation
Indices: 12615647--12615868 Score: 390
Period size: 84 Copynumber: 2.6 Consensus size: 84
12615637 ACCACTGCTT
* * * * * *
12615647 AGGGAGATAAGACTTGGTGCGATTTGCTCTACTACTGCTTAGGGAGATAAGATCTATGGTTTTAA
1 AGGGAGATAGGACTTGATGTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAA
12615712 TCCGCTCCACTGCAACTTC
66 TCCGCTCCACTGCAACTTC
12615731 AGGGAGATAGGACTTGATGTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAA
1 AGGGAGATAGGACTTGATGTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAA
12615796 TCCGCTCCACTGCAACTTC
66 TCCGCTCCACTGCAACTTC
12615815 AGGGAGATAGGACTTGATGTGATCTACTCCACTACTGCTTAGGGAGATAAGATC
1 AGGGAGATAGGACTTGATGTGATCTACTCCACTACTGCTTAGGGAGATAAGATC
12615869 CGTAATCTTC
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 132 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (84 bp):
AGGGAGATAGGACTTGATGTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAA
TCCGCTCCACTGCAACTTC
Found at i:12615739 original size:44 final size:44
Alignment explanation
Indices: 12615687--12615823 Score: 165
Period size: 44 Copynumber: 3.2 Consensus size: 44
12615677 ACTACTGCTT
12615687 AGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTC
1 AGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTC
* * * * ** * **
12615731 AGGGAGATAGGA-CT-T-GATGTGATCTACTCCACTACTGCTT-
1 AGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTC
12615771 AGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTC
1 AGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTC
12615815 AGGGAGATA
1 AGGGAGATA
12615824 GGACTTGATG
Statistics
Matches: 71, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
40 11 0.15
41 19 0.27
42 2 0.03
43 19 0.27
44 20 0.28
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
AGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTC
Found at i:12615819 original size:128 final size:125
Alignment explanation
Indices: 12615575--12615823 Score: 270
Period size: 128 Copynumber: 1.9 Consensus size: 125
12615565 ATGAGATTTG
* * *
12615575 TGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTTCGTCTGCTCCACC
1 TGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGG---TATGTCGTCTACTCCACC
* ** * **
12615640 ACTGCTTAGGGAGATAAGACTTGGTGCGATTTGCTCTACTACTGCTTAGGGAGATAAGATCTA
63 ACTGCTTAGGGAGATAAGACTTGGTGCAATCCGCTCCACTACAACTTAGGGAGATAAGATCTA
* *
12615703 TGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTT-G-ATGT-GATCTACTCCACTA
1 TGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGA-TTGGTATGTCG-TCTACTCCACCA
** *
12615765 CTGCTTAGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
64 CTGCTTAGGGAGATAAGA-CT-TGG-TGCAATCCGCTCCACTACAACTT-AGGGAGATA
12615824 GGACTTGATG
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
123 1 0.01
124 30 0.30
125 2 0.02
126 3 0.03
127 14 0.14
128 49 0.49
129 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (125 bp):
TGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTATGTCGTCTACTCCACCACT
GCTTAGGGAGATAAGACTTGGTGCAATCCGCTCCACTACAACTTAGGGAGATAAGATCTA
Found at i:12615852 original size:44 final size:44
Alignment explanation
Indices: 12615720--12615852 Score: 145
Period size: 44 Copynumber: 3.1 Consensus size: 44
12615710 AATCCGCTCC
12615720 ACTGCAACTTCAGGGAGATAGGACTTGATGTGATCTACTCCACT
1 ACTGCAACTTCAGGGAGATAGGACTTGATGTGATCTACTCCACT
* * * * *
12615764 ACTG---CTT-AGGGAGATAAGA-TCT-ATG-GTTTTAATCCGCT
1 ACTGCAACTTCAGGGAGATAGGACT-TGATGTGATCTACTCCACT
12615802 CCACTGCAACTTCAGGGAGATAGGACTTGATGTGATCTACTCCACT
1 --ACTGCAACTTCAGGGAGATAGGACTTGATGTGATCTACTCCACT
12615848 ACTGC
1 ACTGC
12615853 TTAGGGAGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
38 9 0.13
39 4 0.06
40 16 0.23
41 3 0.04
43 3 0.04
44 21 0.30
45 4 0.06
46 9 0.13
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAGGACTTGATGTGATCTACTCCACT
Found at i:12616062 original size:88 final size:87
Alignment explanation
Indices: 12615962--12616181 Score: 341
Period size: 88 Copynumber: 2.5 Consensus size: 87
12615952 AAATCTGCCA
* * * * *
12615962 TCTTCGACCTGCTCTGTTGTTGATGCAGGAGGGCAATATCTGTTGTCTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCT-TGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
12616027 ACCCGAGAGAGGCAAGGTTTGTG
65 AACCGAGAGAGGCAAGGTTTGTG
12616050 TCTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTT-GCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
12616115 AACCGAGAGAGGTAAGGTTTGTG
65 AACCGAGAGAGGCAAGGTTTGTG
*
12616138 TCTTCGATCTGCTTTGCTGTTAATGCAGGAAGGCAAGAGCTGTT
1 TCTTCGATCTGC-TTGCTGTTAATGCAGGAAGGCAAGATCTGTT
12616182 AATGCAGGAA
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
87 1 0.01
88 119 0.98
89 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (87 bp):
TCTTCGATCTGCTTGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACA
ACCGAGAGAGGCAAGGTTTGTG
Found at i:12616084 original size:44 final size:43
Alignment explanation
Indices: 12616036--12616174 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 43
12616026 CACCCGAGAG
12616036 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTT-GCTGTTAATGCAGGA
* * * * * * * *
12616080 AGGCAAGATCTGTTGTCTTCAACCAGC-T-CTGCTACA-ACCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTGCTGTTA-ATGCAG-GA
*
12616123 GAGGTAAGGTTTGTGTCTTCGATCTGCTTTGCTGTTAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGC-TTGCTGTTAATGCAGGA
12616168 AGGCAAG
1 AGGCAAG
12616175 AGCTGTTAAT
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 7 0.10
43 14 0.20
44 26 0.38
45 15 0.22
46 7 0.10
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTGCTGTTAATGCAGGA
Found at i:12616142 original size:43 final size:43
Alignment explanation
Indices: 12616005--12616142 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 43
12615995 CAATATCTGT
*
12616005 TGTCTTCAACCAGCTCTGCTACACCCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
* * * ** * * *
12616048 TGTCTTCGATCTGCT-TCGCTGTTAA-TGCAG-GAAGGCAAGATCTG
1 TGTCTTCAACCAGCTCT-GCT-ACAACCG-AGAG-AGGCAAGGTTTG
*
12616092 TTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGTAAGGTTTG
1 -TGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
12616136 TGTCTTC
1 TGTCTTC
12616143 GATCTGCTTT
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 1 0.01
43 24 0.35
44 26 0.38
45 17 0.25
46 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
Found at i:12616183 original size:23 final size:23
Alignment explanation
Indices: 12616153--12616205 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
12616143 GATCTGCTTT
12616153 GCTGTTAATGCAGGAAGGCAAGA
1 GCTGTTAATGCAGGAAGGCAAGA
12616176 GCTGTTAATGCAGGAAGGCAAGA
1 GCTGTTAATGCAGGAAGGCAAGA
*
12616199 TCTGTTA
1 GCTGTTA
12616206 TCTTTAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.23
Consensus pattern (23 bp):
GCTGTTAATGCAGGAAGGCAAGA
Found at i:12616335 original size:45 final size:45
Alignment explanation
Indices: 12616191--12616503 Score: 140
Period size: 44 Copynumber: 7.2 Consensus size: 45
12616181 TAATGCAGGA
* * *
12616191 AGGCAA-GATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGGATTTGTTATCTTTAACTAGCTCCACTGTAACCGATGG
* * ** * *
12616235 AGGCAAGGTTTTCTT-T-TCGATCT-GCTCCACTATTAACAC-A-GG
1 AGGCAAGGATTTGTTATCTTTAACTAGCTCCACT-GTAAC-CGATGG
*
12616277 AAGGCAA-GATTTGTTATCTTTAACTAGCTCTACTGTAACCGATGG
1 -AGGCAAGGATTTGTTATCTTTAACTAGCTCCACTGTAACCGATGG
* ** * * * * *
12616322 AGGCAAGGCTTTGTT-T-TCGATCT-GCTTCGCTGTTAA-TGCATGA
1 AGGCAAGGATTTGTTATCTTTAACTAGCTCCACTG-TAACCG-ATGG
* * * * *
12616365 AGGCAA-GATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGG
1 AGGCAAGGATTTGTTATCTTTAACTAGCTCCACTGTAACCGATGG
* * ** *
12616409 AGGCAAGGTTTTCTT-T-TCGATCT-GCTCCACTGTTAA-CGCA-GG
1 AGGCAAGGATTTGTTATCTTTAACTAGCTCCACTG-TAACCG-ATGG
* * * *
12616451 AAGGCAA-GATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGGATTTGTTATCTTTAACTAGCTCCACTGTAACCGATGG
12616496 AGGCAAGG
1 AGGCAAGG
12616504 CTTTCTTTTC
Statistics
Matches: 186, Mismatches: 57, Indels: 51
0.63 0.19 0.17
Matches are distributed among these distances:
42 45 0.24
43 44 0.24
44 50 0.27
45 47 0.25
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (45 bp):
AGGCAAGGATTTGTTATCTTTAACTAGCTCCACTGTAACCGATGG
Found at i:12616339 original size:87 final size:87
Alignment explanation
Indices: 12616177--12616516 Score: 527
Period size: 87 Copynumber: 3.9 Consensus size: 87
12616167 AAGGCAAGAG
* *
12616177 CTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
1 CTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
*
12616242 GTTTTCTTTTCGATCTGCTCCA
66 GCTTTCTTTTCGATCTGCTCCA
* * * * * * *
12616264 CTATTAACACAGGAAGGCAAGATTTGTTATCTTTAACTAGCTCTACTGTAACCGATGGAGGCAAG
1 CTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
* * *
12616329 GCTTTGTTTTCGATCTGCTTCG
66 GCTTTCTTTTCGATCTGCTCCA
* * *
12616351 CTGTTAATGCATGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAG
1 CTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
*
12616416 GTTTTCTTTTCGATCTGCTCCA
66 GCTTTCTTTTCGATCTGCTCCA
12616438 CTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
1 CTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
12616503 GCTTTCTTTTCGAT
66 GCTTTCTTTTCGAT
12616517 TTTTCACTGA
Statistics
Matches: 224, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 224 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (87 bp):
CTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAG
GCTTTCTTTTCGATCTGCTCCA
Found at i:12616471 original size:174 final size:174
Alignment explanation
Indices: 12616176--12616516 Score: 583
Period size: 174 Copynumber: 2.0 Consensus size: 174
12616166 GAAGGCAAGA
*
12616176 GCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
1 GCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
* * *
12616241 GGTTTTCTTTTCGATCTGCTCCACTATTAACACAGGAAGGCAAGATTTGTTATCTTTAACTAGCT
66 GGTTTTCTTTTCGATCTGCTCCACTATTAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCT
* * *
12616306 CTACTGTAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTC
131 CCACTGCAACCGATGGAGGCAAGGCTTTCTTTTCGATCTGCTTC
* *
12616350 GCTGTTAATGCATGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAA
1 GCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
* *
12616415 GGTTTTCTTTTCGATCTGCTCCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCT
66 GGTTTTCTTTTCGATCTGCTCCACTATTAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCT
12616480 CCACTGCAACCGATGGAGGCAAGGCTTTCTTTTCGAT
131 CCACTGCAACCGATGGAGGCAAGGCTTTCTTTTCGAT
12616517 TTTTCACTGA
Statistics
Matches: 156, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
174 156 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (174 bp):
GCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
GGTTTTCTTTTCGATCTGCTCCACTATTAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCT
CCACTGCAACCGATGGAGGCAAGGCTTTCTTTTCGATCTGCTTC
Found at i:12622736 original size:15 final size:15
Alignment explanation
Indices: 12622709--12622743 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12622699 AAATATTTTA
12622709 ATAT-AGATAATAAT
1 ATATAAGATAATAAT
*
12622723 ATATAAGATGATAAT
1 ATATAAGATAATAAT
12622738 ATATAA
1 ATATAA
12622744 ATTTAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (15 bp):
ATATAAGATAATAAT
Found at i:12633500 original size:12 final size:12
Alignment explanation
Indices: 12633483--12633509 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12633473 GAATATGTGG
12633483 CAAAGAACAACT
1 CAAAGAACAACT
12633495 CAAAGAACAACT
1 CAAAGAACAACT
12633507 CAA
1 CAA
12633510 CTGCTATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.26, G:0.07, T:0.07
Consensus pattern (12 bp):
CAAAGAACAACT
Found at i:12646023 original size:50 final size:49
Alignment explanation
Indices: 12645945--12646132 Score: 198
Period size: 50 Copynumber: 3.8 Consensus size: 49
12645935 TATACAGTCT
* *
12645945 TTCCAAATAATACGCCACAAAAGTTTTTCATAAGATTAGTCATAAAGGCA
1 TTCCAAATAATACGCCACAAAGGCTTTTCATAAGATTAG-CATAAAGGCA
* * *
12645995 TTCCAAATAATACACCACAAAGGCTTTTCATAAGATTAGCCTCAAAGGCT
1 TTCCAAATAATACGCCACAAAGGCTTTTCATAAGATTAGCAT-AAAGGCA
** * * * *
12646045 TTTTACATAATACGCCACAAAGGCTTTTCATAATATTAGCCACAATGG-A
1 TTCCAAATAATACGCCACAAAGGCTTTTCATAAGATTAG-CATAAAGGCA
** * *
12646094 TTTTTAGATAATACGCCACAAAGGCTTTCCATAAGATTA
1 -TTCCAAATAATACGCCACAAAGGCTTTTCATAAGATTA
12646133 TCCCCAAAGG
Statistics
Matches: 118, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.02
50 115 0.97
51 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (49 bp):
TTCCAAATAATACGCCACAAAGGCTTTTCATAAGATTAGCATAAAGGCA
Found at i:12646040 original size:25 final size:25
Alignment explanation
Indices: 12645958--12646149 Score: 128
Period size: 25 Copynumber: 7.7 Consensus size: 25
12645948 CAAATAATAC
* *
12645958 GCCACAAAAGTTTTTCATAAGATTA
1 GCCACAAAGGCTTTTCATAAGATTA
* * * * * *
12645983 GTCATAAAGGCATTCCA-AATAATA
1 GCCACAAAGGCTTTTCATAAGATTA
*
12646007 CACCACAAAGGCTTTTCATAAGATTA
1 -GCCACAAAGGCTTTTCATAAGATTA
*
12646033 GCCTCAAAGGCTTTTTACAT-A-A-TA
1 GCCACAAAGGC-TTTT-CATAAGATTA
*
12646057 CGCCACAAAGGCTTTTCATAATATTA
1 -GCCACAAAGGCTTTTCATAAGATTA
* *
12646083 GCCACAATGGATTTT--T-AGATAATA
1 GCCACAAAGGCTTTTCATAAGAT--TA
*
12646107 CGCCACAAAGGCTTTCCATAAGATTA
1 -GCCACAAAGGCTTTTCATAAGATTA
* *
12646133 TCCCCAAAGGCTTTTCA
1 GCCACAAAGGCTTTTCA
12646150 GGTAATTCAT
Statistics
Matches: 126, Mismatches: 27, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
22 3 0.02
23 4 0.03
24 14 0.11
25 83 0.66
26 14 0.11
27 4 0.03
28 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (25 bp):
GCCACAAAGGCTTTTCATAAGATTA
Found at i:12646127 original size:100 final size:100
Alignment explanation
Indices: 12645951--12646147 Score: 261
Period size: 100 Copynumber: 2.0 Consensus size: 100
12645941 GTCTTTCCAA
* * *
12645951 ATAATACGCCACAAAAGTTTTTCATAAGATTAGTCATAAAGGCATTCCAAATAATACACCACAAA
1 ATAATACGCCACAAAAGCTTTTCATAAGATTAGCCACAAAGGCATTCCAAATAATACACCACAAA
* *
12646016 GGCTTTTCATAAGATTAGCCTCAAAGGCTTTTTAC
66 GGCTTTCCATAAGATTAGCCCCAAAGGCTTTTTAC
* * * ** * *
12646051 ATAATACGCCACAAAGGCTTTTCATAATATTAGCCACAATGG-ATTTTTAGATAATACGCCACAA
1 ATAATACGCCACAAAAGCTTTTCATAAGATTAGCCACAAAGGCA-TTCCAAATAATACACCACAA
*
12646115 AGGCTTTCCATAAGATTATCCCCAAAGGCTTTT
65 AGGCTTTCCATAAGATTAGCCCCAAAGGCTTTT
12646148 CAGGTAATTC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 1 0.01
100 82 0.99
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (100 bp):
ATAATACGCCACAAAAGCTTTTCATAAGATTAGCCACAAAGGCATTCCAAATAATACACCACAAA
GGCTTTCCATAAGATTAGCCCCAAAGGCTTTTTAC
Found at i:12654914 original size:30 final size:28
Alignment explanation
Indices: 12654878--12654942 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
12654868 AATTAATAAA
12654878 TATAAAA-TTGTATTTTAATTCTCTTAAAAT
1 TATAAAATTTG-A-TTTAA-TCTCTTAAAAT
*
12654908 TATAAAAATTTGATTTAATCTTTTAAAAT
1 TAT-AAAATTTGATTTAATCTCTTAAAAT
12654937 TATAAA
1 TATAAA
12654943 GATATAGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 8 0.25
31 5 0.16
32 3 0.09
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (28 bp):
TATAAAATTTGATTTAATCTCTTAAAAT
Found at i:12656481 original size:17 final size:19
Alignment explanation
Indices: 12656433--12656482 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
12656423 CATGACTTTA
*
12656433 AGAAAATTAGAATTAGATTG
1 AGAAAATTA-ATTTAGATTG
12656453 AGAAAATT-ATTTA-ATTG
1 AGAAAATTAATTTAGATTG
12656470 A-AAAATTAATTTA
1 AGAAAATTAATTTA
12656483 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.21
17 10 0.36
18 4 0.14
20 8 0.29
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (19 bp):
AGAAAATTAATTTAGATTG
Found at i:12658282 original size:18 final size:18
Alignment explanation
Indices: 12658259--12658295 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12658249 TATAGTTTGA
12658259 TATTCGAATTATTTGAAT
1 TATTCGAATTATTTGAAT
*
12658277 TATTCGAGTTATTTGAAT
1 TATTCGAATTATTTGAAT
12658295 T
1 T
12658296 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTCGAATTATTTGAAT
Found at i:12658298 original size:15 final size:16
Alignment explanation
Indices: 12658254--12658299 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
12658244 AATATTATAG
12658254 TTTGATATTCGAATTA
1 TTTGATATTCGAATTA
*
12658270 TTTGAATTATTCGAGTTA
1 TTTG-A-TATTCGAATTA
12658288 TTTGA-ATTCGAA
1 TTTGATATTCGAA
12658300 AACTCAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 4 0.15
17 2 0.08
18 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (16 bp):
TTTGATATTCGAATTA
Found at i:12662763 original size:24 final size:23
Alignment explanation
Indices: 12662719--12662768 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
12662709 TGTTATGGTT
12662719 AAAATTAAATTTATAATATTTATA
1 AAAATTAAATTTATAATATTT-TA
12662743 AAAATTAATTATTT-TAA-ATTTTA
1 AAAATTAA--ATTTATAATATTTTA
12662766 AAA
1 AAA
12662769 CACTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.21
24 12 0.50
25 3 0.12
26 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATTAAATTTATAATATTTTA
Found at i:12662867 original size:27 final size:27
Alignment explanation
Indices: 12662826--12662877 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12662816 CGTATACTTT
* *
12662826 AACTCCATTAAATACATTTTTTAAAAA
1 AACTCCACTAAATACATTATTTAAAAA
*
12662853 AACTCCACTAGATACATTATTTAAA
1 AACTCCACTAAATACATTATTTAAA
12662878 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (27 bp):
AACTCCACTAAATACATTATTTAAAAA
Found at i:12663672 original size:24 final size:23
Alignment explanation
Indices: 12663644--12663688 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12663634 TGTATTTTAT
12663644 TTTATATATATAAATATTTGTTTC
1 TTTATATATATAAAT-TTTGTTTC
* *
12663668 TTTATATTTATATATTTTGTT
1 TTTATATATATAAATTTTGTT
12663689 CGCTAACGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTATATATATAAATTTTGTTTC
Found at i:12664763 original size:17 final size:16
Alignment explanation
Indices: 12664723--12664754 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12664713 CACCAAGGTG
12664723 AAAAATATTTTTTTTCC
1 AAAAATATTTTTTTT-C
12664740 AAAAATATTTTTTTT
1 AAAAATATTTTTTTT
12664755 AATTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
AAAAATATTTTTTTTC
Found at i:12664887 original size:86 final size:87
Alignment explanation
Indices: 12664787--12665046 Score: 319
Period size: 86 Copynumber: 3.0 Consensus size: 87
12664777 ATTTTTTCTG
* * * *
12664787 CCGTTCAACAGATTTTTTTCCTCTATTTTA-TTTATTTCTAAACGGGAGATTAAAGGTAAATAAA
1 CCGTTCAAC-GATTTTATTCCTATATTTTATTTTATTTCCAAACGGGAAATTAAAGGTAAATAAA
12664851 ATCTATTTCGGGATTGATTCCCT
65 ATCTATTTCGGGATTGATTCCCT
* *
12664874 CCGTTCAACGATTTTATT-CTATTTTTTATTTTATTTCCAAACTGGAAATTAAAGGTAAATAAAA
1 CCGTTCAACGATTTTATTCCTATATTTTATTTTATTTCCAAACGGGAAATTAAAGGTAAATAAAA
*
12664938 TTTATTTCGGGATTGATTCCCT
66 TCTATTTCGGGATTGATTCCCT
* * * **
12664960 CCGTTCAACGATTTTATTCC-AAATTTTTATTTTATTTCCAAAAATGAGAAATTAAAATTAAATA
1 CCGTTCAACGATTTTATTCCTATA-TTTTATTTTATTTCC--AAACGGGAAATTAAAGGTAAATA
* * *
12665024 AAATTTTGTTTCGGGATTTATTC
63 AAA-TCTATTTCGGGATTGATTC
12665047 TCGTAGTTTA
Statistics
Matches: 151, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
85 8 0.05
86 80 0.53
87 25 0.17
89 21 0.14
90 17 0.11
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (87 bp):
CCGTTCAACGATTTTATTCCTATATTTTATTTTATTTCCAAACGGGAAATTAAAGGTAAATAAAA
TCTATTTCGGGATTGATTCCCT
Found at i:12665141 original size:84 final size:86
Alignment explanation
Indices: 12665009--12665236 Score: 246
Period size: 84 Copynumber: 2.7 Consensus size: 86
12664999 AAAAATGAGA
* * *
12665009 AATTAAAATTAAATAAAATTTTGTTTCGGGATTTATTCTCGTAGTTTAACAAGATTTTATTTGAT
1 AATTAAAATTAAATAAAATTATGTTTCGGGATTTATTCACGCAGTTTAACAAGATTTTATTTGAT
*
12665074 TTTGTTTTGTTTCTAAATTAG
66 TTTATTTTGTTTCTAAATTAG
12665095 AATT-AAATTAAATAAAA-TATG-TTCTGGGATTTATTCACGCCA-TTTAACAAGATTTTATTTG
1 AATTAAAATTAAATAAAATTATGTTTC-GGGATTTATTCACG-CAGTTTAACAAGATTTTATTTG
*
12665156 ATTTTATTTTGTTT-TCAAA-TAA
64 ATTTTATTTTGTTTCT-AAATTAG
* * *
12665178 AGATGT--AATCAAAT--AATTATGTTTCGGGATTTATTTC-CGCCGTTTAA-TAGATTTTATTT
1 A-AT-TAAAATTAAATAAAATTATGTTTCGGGATTTA-TTCACGCAGTTTAACAAGATTTTATTT
12665237 TGATATAATT
Statistics
Matches: 125, Mismatches: 8, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
82 14 0.11
83 26 0.21
84 66 0.53
85 15 0.12
86 4 0.03
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (86 bp):
AATTAAAATTAAATAAAATTATGTTTCGGGATTTATTCACGCAGTTTAACAAGATTTTATTTGAT
TTTATTTTGTTTCTAAATTAG
Found at i:12669369 original size:3 final size:3
Alignment explanation
Indices: 12669361--12669387 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12669351 GTGAAAATAA
12669361 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
12669388 GTGGTGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:12670453 original size:146 final size:144
Alignment explanation
Indices: 12670134--12670567 Score: 751
Period size: 146 Copynumber: 3.0 Consensus size: 144
12670124 GCTCAAAAAC
* * *
12670134 ACAATTTACCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTCCGTGTCTAAT
1 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
12670199 AGAAATTGCACTGTTTTTATATTCTATCACTGGTTAATAGAAAACTTAGATTCCAACAAATTCCA
66 AGAAATTGCACTGTTTTTATATTCTATCACTGGTTAATAGAAAACTTAGATTCCAACAAATTCCA
12670264 GACATGCAAAGAAT
131 GACATGCAAAGAAT
* *
12670278 ACAATTTCCCATTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGAACAAAATTTCATGTCTAAT
1 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
*
12670343 AGAAATTGCAGTGTTTTTATATTCTATCACCCTGGTTAATAGAAAACTTAGATTCCAACAAATTC
66 AGAAATTGCACTGTTTTTATATTCTATCA--CTGGTTAATAGAAAACTTAGATTCCAACAAATTC
12670408 CAGACATGCAAAGAAT
129 CAGACATGCAAAGAAT
12670424 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
1 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
* * *
12670489 AGAAATTGCATTGTTTTTATATTCTATCACTGGTTAATAGACAATTTAGATTCCAACAAATTCCA
66 AGAAATTGCACTGTTTTTATATTCTATCACTGGTTAATAGAAAACTTAGATTCCAACAAATT-C-
12670554 CAGACATGCAAAGA
129 CAGACATGCAAAGA
12670568 GTAGAGATTC
Statistics
Matches: 275, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
144 119 0.43
145 1 0.00
146 155 0.56
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (144 bp):
ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
AGAAATTGCACTGTTTTTATATTCTATCACTGGTTAATAGAAAACTTAGATTCCAACAAATTCCA
GACATGCAAAGAAT
Found at i:12704468 original size:44 final size:45
Alignment explanation
Indices: 12704410--12704531 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 45
12704400 GATCGCATCT
* *
12704410 AGTCTTATCTTCCTGAAGTTGCAGTGAAGCAGACT-AA-TTGAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATG-GCA
* *
12704454 AGTCTTATCCTCCTGAAGTTGCAGCGAGGCAGACTGAAGATGGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCA
* * * *
12704499 AATCTTAT-CTCATTGAAGTTGTAGTGAAACAGA
1 AGTCTTATCCTC-CTGAAGTTGCAGTGAAGCAGA
12704532 TTAAAGCCGA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
44 35 0.54
45 28 0.43
46 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (45 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCA
Done.