Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 170 of 172
Found at i:55722158 original size:37 final size:37
Alignment explanation
Indices: 55722097--55722242 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
55722087 TACGTATGAT
* *
55722097 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55722132 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55722169 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55722206 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55722243 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:55722259 original size:46 final size:46
Alignment explanation
Indices: 55722206--55722474 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
55722196 TAAGTGTAGC
* **
55722206 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
55722252 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
55722298 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
55722350 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
55722396 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
55722448 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
55722475 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:55722325 original size:52 final size:52
Alignment explanation
Indices: 55722249--55722468 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
55722239 TAGCTAAAGC
* *
55722249 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
55722302 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
55722354 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
55722400 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
55722452 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
55722469 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:55722371 original size:98 final size:98
Alignment explanation
Indices: 55722206--55722474 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
55722196 TAAGTGTAGC
* * *
55722206 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
55722271 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
55722305 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
55722370 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
55722403 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
55722468 GATCAGA
66 GATCAGA
55722475 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:55746630 original size:24 final size:23
Alignment explanation
Indices: 55746578--55746631 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
55746568 ATGCTGAGGC
*
55746578 AATTTTAATATATTTATTCTTTA
1 AATTTTAATATATTTATTATTTA
55746601 AA-TTTAATTTATATTTA-TATTTA
1 AATTTTAA--TATATTTATTATTTA
55746624 AATTTTAA
1 AATTTTAA
55746632 GGAATCAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 13 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTTAATATATTTATTATTTA
Found at i:55752384 original size:60 final size:60
Alignment explanation
Indices: 55752318--55752437 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
55752308 TTTATCCTCC
55752318 AAAATTGTTTTATCTTGACGAATTTGTCCTACCTTCGATTCACTATCAAATTCAAAATCA
1 AAAATTGTTTTATCTTGACGAATTTGTCCTACCTTCGATTCACTATCAAATTCAAAATCA
55752378 AAAATTGTTTTATCTTGACGAATTTGTCCTACCTTCGATTCACTATCAAATTCAAAATCA
1 AAAATTGTTTTATCTTGACGAATTTGTCCTACCTTCGATTCACTATCAAATTCAAAATCA
55752438 GGGTATCCTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (60 bp):
AAAATTGTTTTATCTTGACGAATTTGTCCTACCTTCGATTCACTATCAAATTCAAAATCA
Found at i:55753082 original size:32 final size:32
Alignment explanation
Indices: 55753005--55753070 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
55752995 TTAAAAAAAC
55753005 TTAACTCATAAATTAGTATCTAAATTATACTT
1 TTAACTCATAAATTAGTATCTAAATTATACTT
55753037 TTAACTCATAAATTAGTATCTAAATTATACTT
1 TTAACTCATAAATTAGTATCTAAATTATACTT
55753069 TT
1 TT
55753071 TTTTCTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (32 bp):
TTAACTCATAAATTAGTATCTAAATTATACTT
Found at i:55754018 original size:60 final size:60
Alignment explanation
Indices: 55753952--55754088 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 60
55753942 AAAAAAATAC
55753952 AAAAAATAGAAATAAATTATAAGAA-TA-T-GAAATGATCTAAAAAAATATT-TA-ATTTTTTTT
1 AAAAAATAGAAA-AAATTATAA-AAGTATTAGAAAT--TCT-AAAAAATATTATATATTTTTTTT
* *
55754012 AAAAAAT-GATAAAAAATATAAAAGTATTAGAAATTGTAAAAAATATTATATATTTTTTTT
1 AAAAAATAGA-AAAAATTATAAAAGTATTAGAAATTCTAAAAAATATTATATATTTTTTTT
55754072 --AAAATAGAAAAAATTAT
1 AAAAAATAGAAAAAATTAT
55754089 TATATTTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
58 25 0.37
59 18 0.27
60 19 0.28
61 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.36
Consensus pattern (60 bp):
AAAAAATAGAAAAAATTATAAAAGTATTAGAAATTCTAAAAAATATTATATATTTTTTTT
Found at i:55759440 original size:52 final size:48
Alignment explanation
Indices: 55759421--55759623 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
55759411 TGACAAGTGG
* *
55759421 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55759467 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
55759519 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
55759565 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55759611 AAAGTGATAAGTG
1 AAAGTGATAAGTG
55759624 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:55759475 original size:98 final size:98
Alignment explanation
Indices: 55759355--55759623 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
55759345 TTTGAGTACT
*
55759355 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55759420 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
55759453 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55759518 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
55759551 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
55759616 GATAAGTG
65 GAAAAGTG
55759624 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:55759631 original size:37 final size:37
Alignment explanation
Indices: 55759587--55759732 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
55759577 GATAGCTTTA
*
55759587 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55759624 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
55759661 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
55759698 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55759733 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:55761063 original size:58 final size:58
Alignment explanation
Indices: 55760986--55761153 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 58
55760976 CATGTGAACA
55760986 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
55761045 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATA--
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
* * *
55761101 TGTG--A--T--TT-CGTGTAAGACCATAGTTGGGCTATGGCATCGGTATGTGATTTG
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
55761152 TG
1 TG
55761154 ATTACGTGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
49 38 0.37
50 2 0.02
51 2 0.02
52 1 0.01
54 1 0.01
56 4 0.04
58 51 0.49
59 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (58 bp):
TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:55761095 original size:28 final size:28
Alignment explanation
Indices: 55761005--55761095 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
55760995 GTGATTCCGT
55761005 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
55761033 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
55761062 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
55761091 GTAAG
1 GTAAG
55761096 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:55761118 original size:49 final size:49
Alignment explanation
Indices: 55761046--55761188 Score: 232
Period size: 49 Copynumber: 2.9 Consensus size: 49
55761036 AGTGATATGT
* *
55761046 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
55761095 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
55761144 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
55761189 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:55764399 original size:52 final size:48
Alignment explanation
Indices: 55764380--55764582 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
55764370 TGACAAGTGG
* *
55764380 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55764426 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
55764478 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
55764524 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55764570 AAAGTGATAAGTG
1 AAAGTGATAAGTG
55764583 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:55764434 original size:98 final size:98
Alignment explanation
Indices: 55764314--55764582 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
55764304 TTTGAGTACT
*
55764314 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55764379 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
55764412 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55764477 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
55764510 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
55764575 GATAAGTG
65 GAAAAGTG
55764583 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:55764590 original size:37 final size:37
Alignment explanation
Indices: 55764546--55764691 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
55764536 GATAGCTTTA
*
55764546 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55764583 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
55764620 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
55764657 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55764692 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:55767340 original size:6 final size:6
Alignment explanation
Indices: 55767331--55767355 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55767321 TTTATTTTAT
55767331 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
55767356 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:55782683 original size:15 final size:16
Alignment explanation
Indices: 55782665--55782703 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
55782655 TTTGTTTGGA
55782665 TTTTTTAAT-TTTCAG
1 TTTTTTAATATTTCAG
* *
55782680 TTTTTTCATATTTGAG
1 TTTTTTAATATTTCAG
55782696 TTTTTTAA
1 TTTTTTAA
55782704 GTTTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.67
Consensus pattern (16 bp):
TTTTTTAATATTTCAG
Found at i:55782769 original size:13 final size:13
Alignment explanation
Indices: 55782751--55782775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55782741 TGTAATAAGA
55782751 ATAAAAATTTTAT
1 ATAAAAATTTTAT
55782764 ATAAAAATTTTA
1 ATAAAAATTTTA
55782776 ATTTTAATAG
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAAATTTTAT
Found at i:55784950 original size:39 final size:40
Alignment explanation
Indices: 55784905--55785089 Score: 187
Period size: 40 Copynumber: 4.7 Consensus size: 40
55784895 GCTCCTCGTT
* *
55784905 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
* ** *
55784945 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
* * *
55784984 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
* * * * * *
55785024 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCA-CA
*
55785065 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
55785090 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 38 0.31
40 75 0.61
41 9 0.07
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
Found at i:55785005 original size:40 final size:39
Alignment explanation
Indices: 55784872--55785089 Score: 174
Period size: 40 Copynumber: 5.5 Consensus size: 39
55784862 AAATCACGTA
* * **
55784872 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * *
55784911 CCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
55784950 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
55784990 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
55785030 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
55785070 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
55785090 CAGCATTCAA
Statistics
Matches: 145, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.01
39 49 0.34
40 86 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:55790790 original size:12 final size:12
Alignment explanation
Indices: 55790775--55790805 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
55790765 AATAATTAAA
55790775 TAAATTCGAAAT
1 TAAATTCGAAAT
55790787 TAAATTCGAAAT
1 TAAATTCGAAAT
55790799 TAAATTC
1 TAAATTC
55790806 AGATTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (12 bp):
TAAATTCGAAAT
Found at i:55792038 original size:50 final size:49
Alignment explanation
Indices: 55791984--55792097 Score: 119
Period size: 47 Copynumber: 2.3 Consensus size: 49
55791974 CCTATGCATA
55791984 TGGGAGTAGGTCATTTATTATCACTTTCCGTAAGCCCCCTCCCATGTGTC
1 TGGGAGTAGGTCATTTATTATCACTTTCCGTAAGCCCCC-CCCATGTGTC
* * * * *
55792034 TGGGAGCAAGG---TTT-TTATTACTTTTCGTGAGCCTCCCCCATGTGTC
1 TGGGAG-TAGGTCATTTATTATCACTTTCCGTAAGCCCCCCCCATGTGTC
*
55792080 TAGGAGTAGGGTCATTTA
1 TGGGAGTA-GGTCATTTA
55792098 AATACCTTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
45 1 0.02
46 17 0.33
47 18 0.35
48 3 0.06
49 3 0.06
50 6 0.12
51 3 0.06
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (49 bp):
TGGGAGTAGGTCATTTATTATCACTTTCCGTAAGCCCCCCCCATGTGTC
Found at i:55792181 original size:50 final size:50
Alignment explanation
Indices: 55792121--55792285 Score: 156
Period size: 50 Copynumber: 3.3 Consensus size: 50
55792111 AGTCTCCCCA
* * * *
55792121 CATGCTTCTAGGAGTAGGGCCTTAATTACCACCTTCCGTAAGCCTCTTCC
1 CATGCGTCTAGGAGCAAGGCCTTAATTACCACCTTCCGTAAGCCTCCTCC
* * *
55792171 CATGCGTCTAGGAGCAATGCCTTTATTACCACCTTCTGTAAGCCTCCTCC
1 CATGCGTCTAGGAGCAAGGCCTTAATTACCACCTTCCGTAAGCCTCCTCC
* * * * ** *
55792221 TATGCGTCTAGAAGCAGAGTCATT--TTAATACCTTTCGTAAGCCTCC-CC
1 CATGCGTCTAGGAGCA-AGGCCTTAATTACCACCTTCCGTAAGCCTCCTCC
*
55792269 CTATGCATCTAGGAGCA
1 C-ATGCGTCTAGGAGCA
55792286 GGACATTTTT
Statistics
Matches: 94, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
48 2 0.02
49 31 0.33
50 57 0.61
51 4 0.04
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (50 bp):
CATGCGTCTAGGAGCAAGGCCTTAATTACCACCTTCCGTAAGCCTCCTCC
Found at i:55795398 original size:50 final size:50
Alignment explanation
Indices: 55795323--55795499 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
55795313 CCACGGCAAC
* *
55795323 AAGTGATAAATGATAGCTTTGGCTACACTTATCTAATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
* *
55795373 AAGTGATAAGT-AGTAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGA-TAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
* * *
55795423 AAGTGATAAGTGATATCTTCGGCTACACCTATCTAATCAGGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
* *
55795473 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
55795500 CTGATCAGTG
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.01
50 87 0.78
51 24 0.21
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
Found at i:55795513 original size:31 final size:31
Alignment explanation
Indices: 55795475--55795584 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
55795465 ACAAATGACA
55795475 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
55795506 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
55795537 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
55795568 AGTGAAAAATGGTAGCT
1 AGTGAAAAGTGGTAGCT
55795585 GTTACAACCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:55795822 original size:50 final size:50
Alignment explanation
Indices: 55795764--55795864 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
55795754 TTACCATTCA
*
55795764 ATCAACACTTTGACACTTGTATAAGCATCAAACAGCAACATTGTTAGTAT
1 ATCAACACTTTGACACTTGTATAAGCACCAAACAGCAACATTGTTAGTAT
55795814 ATCAACACTTTGACACTTGTATAAGCACCAAACAGCAACATTGTTAGTAT
1 ATCAACACTTTGACACTTGTATAAGCACCAAACAGCAACATTGTTAGTAT
55795864 A
1 A
55795865 CTTGCACATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.29
Consensus pattern (50 bp):
ATCAACACTTTGACACTTGTATAAGCACCAAACAGCAACATTGTTAGTAT
Found at i:55796351 original size:46 final size:46
Alignment explanation
Indices: 55796291--55796564 Score: 433
Period size: 46 Copynumber: 6.0 Consensus size: 46
55796281 TTTGACATGA
* * * * * *
55796291 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
55796337 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
55796383 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
55796429 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
55796475 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
55796521 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
55796565 AGAGCACACT
Statistics
Matches: 215, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 4 0.02
46 211 0.98
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:55799044 original size:42 final size:42
Alignment explanation
Indices: 55798968--55799072 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
55798958 ATTTTTCTTG
* *
55798968 ATAGCTGGGCTATGGCATCGATATATGAATATGTGTAAGACC
1 ATAGTTGGGCTATGGCATCGATATATGAAGATGTGTAAGACC
*
55799010 ATAGTTGGGCTATGGCATC-ATTATGTGAAGATGTGTAAGACC
1 ATAGTTGGGCTATGGCATCGA-TATATGAAGATGTGTAAGACC
***
55799052 ATAGTTGAAATATGGCATCGA
1 ATAGTTGGGCTATGGCATCGA
55799073 GAAAATGAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.02
42 53 0.96
43 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (42 bp):
ATAGTTGGGCTATGGCATCGATATATGAAGATGTGTAAGACC
Found at i:55801134 original size:21 final size:21
Alignment explanation
Indices: 55801108--55801151 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
55801098 GTCGAGAGGG
55801108 AAAGAAAATGCGAGAGCCGAC
1 AAAGAAAATGCGAGAGCCGAC
55801129 AAAGAAAATGCGAGAGCCGAC
1 AAAGAAAATGCGAGAGCCGAC
55801150 AA
1 AA
55801152 CGAGTAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.18, G:0.27, T:0.05
Consensus pattern (21 bp):
AAAGAAAATGCGAGAGCCGAC
Found at i:55819350 original size:21 final size:21
Alignment explanation
Indices: 55819311--55819355 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55819301 ATTTAATTAA
*
55819311 TTTTTAATATTTTAAAATATT
1 TTTTTAATATTTTAAAATAAT
*
55819332 TTTTTATATATTTT-TAATAAT
1 TTTTTA-ATATTTTAAAATAAT
55819353 TTT
1 TTT
55819356 AATGATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTAATATTTTAAAATAAT
Found at i:55819367 original size:10 final size:9
Alignment explanation
Indices: 55819310--55819378 Score: 59
Period size: 9 Copynumber: 7.2 Consensus size: 9
55819300 CATTTAATTA
55819310 ATTTTTAAT
1 ATTTTTAAT
*
55819319 ATTTTAAAAT
1 ATTTT-TAAT
55819329 ATTTTTTTATAT
1 A--TTTTTA-AT
55819341 ATTTTTAAT
1 ATTTTTAAT
*
55819350 AATTTTAAT
1 ATTTTTAAT
55819359 GATTTTTAA-
1 -ATTTTTAAT
*
55819368 ATTTTAAAT
1 ATTTTTAAT
55819377 AT
1 AT
55819379 AATTTTTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
8 7 0.14
9 17 0.35
10 17 0.35
11 1 0.02
12 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:55824615 original size:25 final size:24
Alignment explanation
Indices: 55824587--55824633 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
55824577 TTACATATAT
55824587 TTTTATAATTTAAATTTTATTTACC
1 TTTTATAATTTAAATTTT-TTTACC
* * *
55824612 TTTTTTAGTTTAGATTTTTTTA
1 TTTTATAATTTAAATTTTTTTA
55824634 ATTTTTTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTATAATTTAAATTTTTTTACC
Found at i:55829556 original size:20 final size:20
Alignment explanation
Indices: 55829531--55829580 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
55829521 TGGCTTAAAA
55829531 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
55829551 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
55829568 GTGGTAGTGGATT
1 TTGGTAGTGGATT
55829581 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:55834195 original size:20 final size:20
Alignment explanation
Indices: 55834170--55834219 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
55834160 TGGCTTAAAA
55834170 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
55834190 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
55834207 GTGGTAGTGGATT
1 TTGGTAGTGGATT
55834220 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:55842123 original size:19 final size:20
Alignment explanation
Indices: 55842095--55842167 Score: 80
Period size: 19 Copynumber: 3.6 Consensus size: 20
55842085 CTCATTTTGG
55842095 GAAG-AAAGAAGGAGAAGAA
1 GAAGAAAAGAAGGAGAAGAA
*
55842114 -AAGAAAAGAAAGA-AGAGAA
1 GAAGAAAAGAAGGAGA-AGAA
55842133 GAAGAAAAGAAGAGAGGAAGAA
1 GAAGAAAAGAAG-GA-GAAGAA
55842155 GAAGGAAAAGAAG
1 GAA-GAAAAGAAG
55842168 AAGCAGGCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
18 4 0.09
19 12 0.27
20 10 0.22
21 2 0.04
22 7 0.16
23 10 0.22
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
GAAGAAAAGAAGGAGAAGAA
Found at i:55842126 original size:23 final size:21
Alignment explanation
Indices: 55842100--55842170 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 21
55842090 TTTGGGAAGA
55842100 AAGAAGGAGAAGAAAAGAAAAG
1 AAGAAGGAGAAG-AAAGAAAAG
55842122 AAAGAA-GAGAAG-AAGAAAAG
1 -AAGAAGGAGAAGAAAGAAAAG
*
55842142 AAGAGAGGAAGAAGAAGGAAAAG
1 AAGA-AGG-AGAAGAAAGAAAAG
55842165 AAGAAG
1 AAGAAG
55842171 CAGGCAGCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 4 0.09
20 9 0.21
21 1 0.02
22 13 0.30
23 16 0.37
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAGAAGGAGAAGAAAGAAAAG
Found at i:55842129 original size:3 final size:3
Alignment explanation
Indices: 55842095--55842170 Score: 65
Period size: 3 Copynumber: 26.3 Consensus size: 3
55842085 CTCATTTTGG
*
55842095 GAA GAAA GAA GGA GAA GAA -AA GAA -AA GAAA GAA G-A GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA
*
55842139 -AA GAA G-A GAG GAA GAA GAA GGAA -AA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA G
55842171 CAGGCAGCAT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
2 12 0.20
3 39 0.65
4 9 0.15
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55842686 original size:17 final size:16
Alignment explanation
Indices: 55842663--55842705 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
55842653 TATCTTAATG
55842663 AAAAAATAAAATACGA
1 AAAAAATAAAATACGA
*
55842679 AAAGAAATAAAATATGA
1 AAA-AAATAAAATACGA
55842696 AAAAAATAAA
1 AAAAAATAAA
55842706 TTTTTTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAATACGA
Found at i:55843104 original size:138 final size:137
Alignment explanation
Indices: 55842742--55843355 Score: 642
Period size: 138 Copynumber: 4.5 Consensus size: 137
55842732 GTTTTTTTAT
* * * *
55842742 TAAAATAATATAAAAATAAAATACGGAAATAGTATATTTTAAAAAATAATATCCAAAAATTTTAA
1 TAAAATAATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTTAA
* * * * *
55842807 AAATACAAATAAA-GTGACAAAATTAGGGTTATTT-------ACTAAAATTATACATTTGAAACA
66 AAATACAAACAAATG-GCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATACATTTGAAACA
55842864 TTATGTAC
130 TTATGTAC
** * * * *
55842872 TAAAATAATATTAAAATAAAATAGGAAAATAATATATTTT-AAAAA-AAAGTTTAAAAATTTTAA
1 TAAAATAATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTTAA
* *
55842935 AAATACAAACAAAGGGCCAAAATCAGGGTTATTTAAAAAACACTAAAATAATACATTTGAAACAT
66 AAATACAAACAAATGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATACATTTGAAACAT
55843000 TATGTAC
131 TATGTAC
55843007 TAAAATAAGATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAAT-TAAAAATTTT
1 TAAAAT-A-ATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTT
*
55843071 AAAAATACAAACAAATGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATATATTTGAAAC
64 AAAAATACAAACAAATGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATACATTTGAAAC
55843136 ATTATGTAC
129 ATTATGTAC
* * * *
55843145 --------T---AAAATAAAATACGAAAATAATATATTTTAAAAAATAAAGTCTGAAAATTTAAA
1 TAAAATAATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTTAA
* * *
55843199 AAATACAAACAAATAGCCAAAATCAGAGTTATTTACTAAATTAATATAAAAAAATTTAAAATAAT
66 AAATACAAACAAATGGCCAAAATCAGAG-----T--T--ATT--TA-AAAAACA-CTAAAATAAT
55843264 ACATTTGAAACATTATGTAC
118 ACATTTGAAACATTATGTAC
** *
55843284 TAAAATAATATAAAAAAAATAAAATATAAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTT
1 TAAAAT-A-AT-AAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTT
*
55843349 CAAAAAT
63 TAAAAAT
55843356 TTTAAAAATA
Statistics
Matches: 409, Mismatches: 35, Indels: 57
0.82 0.07 0.11
Matches are distributed among these distances:
125 38 0.09
126 37 0.09
128 44 0.11
129 6 0.01
130 36 0.09
131 1 0.00
133 1 0.00
135 39 0.10
136 1 0.00
137 31 0.08
138 92 0.22
139 32 0.08
149 1 0.00
153 50 0.12
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (137 bp):
TAAAATAATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTTAA
AAATACAAACAAATGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATACATTTGAAACAT
TATGTAC
Found at i:55843575 original size:15 final size:16
Alignment explanation
Indices: 55843544--55843601 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
55843534 ACCGAGTGTA
**
55843544 TTAAATATATTATATT
1 TTAAATATAAAATATT
55843560 TTAAATA-AAAATATT
1 TTAAATATAAAATATT
** *
55843575 TTACTTATTAAATATT
1 TTAAATATAAAATATT
55843591 TTAAATTATAA
1 TTAAA-TATAA
55843602 TAAAAATATT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
15 11 0.34
16 17 0.53
17 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATATAAAATATT
Found at i:55843586 original size:38 final size:38
Alignment explanation
Indices: 55843542--55843638 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 38
55843532 ATACCGAGTG
55843542 TATTAAATATATTATATTTTAAATAAAAATATTT-TACT
1 TATTAAATATATTATATTTT-AATAAAAATATTTGTACT
* * * *
55843580 TATTAAATATTTTAAATTATAATAAAAATATTTGTATT
1 TATTAAATATATTATATTTTAATAAAAATATTTGTACT
*
55843618 TGAGTTGAATATATT-TATTTT
1 T-A-TTAAATATATTATATTTT
55843639 TTTAATGTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
37 13 0.27
38 21 0.44
39 5 0.10
40 9 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (38 bp):
TATTAAATATATTATATTTTAATAAAAATATTTGTACT
Found at i:55849701 original size:17 final size:16
Alignment explanation
Indices: 55849673--55849714 Score: 75
Period size: 17 Copynumber: 2.6 Consensus size: 16
55849663 CCCCAAAAAA
55849673 TTATTTTTTTCATATT
1 TTATTTTTTTCATATT
55849689 TTATTTCTTTTCATATT
1 TTATTT-TTTTCATATT
55849706 TTATTTTTT
1 TTATTTTTT
55849715 CGTTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTTTTCATATT
Found at i:55849744 original size:16 final size:16
Alignment explanation
Indices: 55849673--55849755 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 16
55849663 CCCCAAAAAA
*
55849673 TTATTTTTTTCATATT
1 TTATTTTTTTAATATT
*
55849689 TTATTTCTTTTCATATT
1 TTATTT-TTTTAATATT
*** **
55849706 TTATTTTTTCGTTAAG
1 TTATTTTTTTAATATT
*
55849722 ATA-TTTTTTAATATT
1 TTATTTTTTTAATATT
*
55849737 TTATTTTTTATACTATT
1 TTATTTTTT-TAATATT
55849754 TT
1 TT
55849756 TGTAAAATAG
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
15 9 0.18
16 18 0.35
17 24 0.47
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (16 bp):
TTATTTTTTTAATATT
Found at i:55850242 original size:3 final size:3
Alignment explanation
Indices: 55850222--55850288 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
55850212 GTGCTTCTCT
* * *
55850222 TTC TTC TCC TTC TCC TTC TTC TT- TTC CT- TTC TTC -TC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC
55850265 TT- TTC TTC TTC TTC TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC -TTC TTC
55850289 CCAAAATGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 7 0.13
3 39 0.75
4 6 0.12
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:55850473 original size:21 final size:20
Alignment explanation
Indices: 55850447--55850486 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
55850437 CCGCTCTGTC
*
55850447 TGCTTCAGTTTCTTTTTTTTT
1 TGCTTCAGCTT-TTTTTTTTT
55850468 TGCTTCAGCTTTTTTTTTT
1 TGCTTCAGCTTTTTTTTTT
55850487 CAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.05, C:0.15, G:0.10, T:0.70
Consensus pattern (20 bp):
TGCTTCAGCTTTTTTTTTTT
Found at i:55851023 original size:238 final size:237
Alignment explanation
Indices: 55850613--55851185 Score: 745
Period size: 238 Copynumber: 2.4 Consensus size: 237
55850603 TATTATTCAA
* * *
55850613 ATTCTTCATCTAGGAGAAGAAAGAGTCTCGATAGGTCCAGTTCTA-TAGTAAACACTGCTGCAGC
1 ATTCTTCTTCTAGGAGAAG-AA-AGTCTTGATAGGTCCAGTTCTATTAGT-AAGACTGCTGCAGC
** *
55850677 TGTAGTGGTTGAGATGGATGAAATGAAATCAGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTTT
63 TGTAGTGGTTGAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTTG
** * * *
55850742 ATTATGTCAAAGGACCTAAGCTTGATGTACTAGATATTGATTCTAACTCCAATTCTTTGAGGGGT
128 ATTACATCAAAGGACCTAAGCTCGATGTACTAGATAGTGATTCTAACTCCAATTCTTTGAGGGAT
* *
55850807 GAATCACTTCCCGGAGATCAAACTCAAACAAGGGATTATTATTTTG
193 GAATCACTGCCCGGAGAGCAAACTCAAACAA-GGATTATTATTTTG
* * ** * *
55850853 ATTCTTCTTCTAGGATAAGAAAGTCTTGATAGGTCCAGTTCTATTGGTAAGTTTACTGCAGCTAT
1 ATTCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGTAAGACTGCTGCAGCTGT
* * * * * *
55850918 AGTAGG-TCAGCTGGATGAAAGGAAATTGGTTTCTAATGCAAAGGTCTTTCCTGCGACTGTTGAT
66 AGT-GGTTGAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTTGAT
* * * * *
55850982 TACATCAATGGATCTAAGCTCGGTGTTCTAGATGGTGATTCTAACTCCAATTCTTTGAGGGATGA
130 TACATCAAAGGACCTAAGCTCGATGTACTAGATAGTGATTCTAACTCCAATTCTTTGAGGGATGA
* * * * *
55851047 ATCACTGCCTGGAGGGCTAACTCAGATAAGGATTATTATTTTG
195 ATCACTGCCCGGAGAGCAAACTCAAACAAGGATTATTATTTTG
* * *
55851090 AATCTTCTTCTAGGAGAAGAAAGTCTTGATATGTCCAGTTCTATTAGTAAGACTGTTGCAGCTGT
1 ATTCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGTAAGACTGCTGCAGCTGT
55851155 AGTGGTTGAGATGGATGAAATGAAATTGGTT
66 AGTGGTTGAGATGGATGAAATGAAATTGGTT
55851186 AAAGTTGATT
Statistics
Matches: 283, Mismatches: 47, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
236 2 0.01
237 95 0.34
238 162 0.57
239 7 0.02
240 17 0.06
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (237 bp):
ATTCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGTAAGACTGCTGCAGCTGT
AGTGGTTGAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTTGATT
ACATCAAAGGACCTAAGCTCGATGTACTAGATAGTGATTCTAACTCCAATTCTTTGAGGGATGAA
TCACTGCCCGGAGAGCAAACTCAAACAAGGATTATTATTTTG
Found at i:55851383 original size:209 final size:208
Alignment explanation
Indices: 55851018--55851394 Score: 537
Period size: 209 Copynumber: 1.8 Consensus size: 208
55851008 TCTAGATGGT
* *
55851018 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGGAGGGCTAACTCAGATAAGGATTAT
1 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGGCTAACTCAGACAAGGATTAT
* * * **
55851083 TATTTTGAATCTTCTTCTAGGAGAAGAAAGTCTTGATATGTCCAGTTCTATTAGTAAGACTGTTG
66 TATTCTGAATCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGGAAGACTGCGG
* **
55851148 CAGCTGTAGTGGTTGAGATGGATGAAATGAAATTGGTTAAAGTTGATTACGTTCATGGACCTTGG
131 CAGCTATAGTGGTTGAGACCGATGAAATGAAATTGGTTAAAGTTGATTACGTTCATGGACCTTGG
55851213 TGTGCCGGATAGG
196 TGTGCCGGATAGG
* * * *
55851226 GATTCTAACTCCCATTCTTTGAGGGATGAATCACTTCCTGAAGGGTCTGA-TCAGACGA-GATTA
1 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGG-CTAACTCAGACAAGGATTA
*
55851289 TTATTCT-AATTCTTCTTCTAGGAGAAGAAAGAGTCTCT-ATAGGTCCGGTTCTATTAGGAAGAC
65 TTATTCTGAA-TCTTCTTCTAGGAGAAG-AA-AGTCT-TGATAGGTCCAGTTCTATTAGGAAGAC
*
55851352 TGCGGCATCTATAGTGGTTGAGACCGATGAAATGAAATTGGTT
126 TGCGGCAGCTATAGTGGTTGAGACCGATGAAATGAAATTGGTT
55851395 TCTAGTGTTT
Statistics
Matches: 148, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
206 2 0.01
207 28 0.19
208 50 0.34
209 67 0.45
210 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (208 bp):
GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGGCTAACTCAGACAAGGATTAT
TATTCTGAATCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGGAAGACTGCGG
CAGCTATAGTGGTTGAGACCGATGAAATGAAATTGGTTAAAGTTGATTACGTTCATGGACCTTGG
TGTGCCGGATAGG
Found at i:55856362 original size:10 final size:10
Alignment explanation
Indices: 55856349--55856382 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
55856339 TTTTGAGAAA
55856349 TTTAATTTTT
1 TTTAATTTTT
*
55856359 TTTAATGTTCT
1 TTTAAT-TTTT
55856370 TTTAATTTTT
1 TTTAATTTTT
55856380 TTT
1 TTT
55856383 CATTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:55859655 original size:25 final size:24
Alignment explanation
Indices: 55859601--55859655 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
55859591 CCTTAAAAGA
**
55859601 AAAAAAAAATGGTCCCTAAGATGG
1 AAAAAAAAATGGTCCAAAAGATGG
*
55859625 AGAAAAAAAATGGTCCAAAAGGTGTG
1 A-AAAAAAAATGGTCCAAAAGATG-G
55859651 AAAAA
1 AAAAA
55859656 CTTCATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 23 0.88
26 2 0.08
ACGTcount: A:0.55, C:0.09, G:0.22, T:0.15
Consensus pattern (24 bp):
AAAAAAAAATGGTCCAAAAGATGG
Found at i:55860121 original size:23 final size:23
Alignment explanation
Indices: 55860076--55860131 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
55860066 AATGCAACAA
* * * *
55860076 GAGACCAGAAGCAGTTCAGCATG
1 GAGACCAGCACCAGCTCAACATG
55860099 GAGACCAGCACCAGCTCAACATG
1 GAGACCAGCACCAGCTCAACATG
* *
55860122 AAGATCAGCA
1 GAGACCAGCA
55860132 TTGGAGTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.25, T:0.11
Consensus pattern (23 bp):
GAGACCAGCACCAGCTCAACATG
Found at i:55862871 original size:19 final size:20
Alignment explanation
Indices: 55862843--55862881 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
55862833 TCTCATTTTT
55862843 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
55862862 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
55862882 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:55862899 original size:25 final size:23
Alignment explanation
Indices: 55862862--55862907 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
55862852 TTTGTTTTAA
*
55862862 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
55862885 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
55862908 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:55863115 original size:23 final size:20
Alignment explanation
Indices: 55863080--55863125 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 20
55863070 TATGTCCATC
55863080 TTTTAAACATTGTACATATATA
1 TTTTAAACATTGTACA-AT-TA
*
55863102 TTTTATAATATTGTACAATTA
1 TTTTA-AACATTGTACAATTA
55863123 TTT
1 TTT
55863126 AATTACGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 7 0.32
23 10 0.45
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTAAACATTGTACAATTA
Found at i:55865468 original size:13 final size:13
Alignment explanation
Indices: 55865450--55865474 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55865440 TTTCGAGTGT
55865450 TTTTTATTTTTTA
1 TTTTTATTTTTTA
55865463 TTTTTATTTTTT
1 TTTTTATTTTTT
55865475 TGAGACGTTT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:55865485 original size:33 final size:35
Alignment explanation
Indices: 55865431--55865509 Score: 83
Period size: 38 Copynumber: 2.2 Consensus size: 35
55865421 AAGGTGACCC
*
55865431 TTTTATTATTTTCGAGTGTTTT-T-TATT-TTTTAT
1 TTTTATT-TTTTCGAGCGTTTTATATATTGTTTTAT
*
55865464 TTTTATTTTTTTGAGACGTTTTACTACTATTGTTTTAT
1 TTTTATTTTTTCGAG-CGTTTTA-TA-TATTGTTTTAT
55865502 TTTTATTT
1 TTTTATTT
55865510 ACATATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 7 0.18
33 12 0.32
35 1 0.03
37 4 0.11
38 14 0.37
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (35 bp):
TTTTATTTTTTCGAGCGTTTTATATATTGTTTTAT
Found at i:55866114 original size:3 final size:3
Alignment explanation
Indices: 55866106--55866165 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
55866096 TTAATTTTAA
* * * * *
55866106 TAT TAT TAT TGT TAT TAT TAG TAT TAT TGT TAA TAT TAT TTT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
55866153 CAT TAT TAC TAT T
1 TAT TAT TAT TAT T
55866166 TTTCATTTTT
Statistics
Matches: 42, Mismatches: 14, Indels: 2
0.72 0.24 0.03
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55866345 original size:3 final size:3
Alignment explanation
Indices: 55866337--55866513 Score: 123
Period size: 3 Copynumber: 58.3 Consensus size: 3
55866327 CACATTCATT
* * *
55866337 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTC TTT TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
55866383 TTA TTTA TTA TTA TTA TTC TTT TTA TTA ATA TTA TTA TTTA CTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * *
55866430 TTA TGT- TTA CTT- TTA -TA CTA -TA GTTA -TA CTT- TCTC TTA TGA
1 TTA T-TA TTA -TTA TTA TTA TTA TTA -TTA TTA -TTA T-TA TTA TTA
* * *
55866471 TCA TCA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55866514 ACTTTCTTTT
Statistics
Matches: 142, Mismatches: 18, Indels: 28
0.76 0.10 0.15
Matches are distributed among these distances:
2 10 0.07
3 116 0.82
4 16 0.11
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:55866382 original size:34 final size:34
Alignment explanation
Indices: 55866330--55866433 Score: 181
Period size: 34 Copynumber: 3.1 Consensus size: 34
55866320 TTACTGTCAC
* *
55866330 ATTCATTTTATTATTATTATTATTTATTATTATT
1 ATTCTTTTTATTAATATTATTATTTATTATTATT
55866364 ATTCTTTTTATTAATATTATTATTTATTATTATT
1 ATTCTTTTTATTAATATTATTATTTATTATTATT
*
55866398 ATTCTTTTTATTAATATTATTATTTACTATTATT
1 ATTCTTTTTATTAATATTATTATTTATTATTATT
55866432 AT
1 AT
55866434 GTTTACTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (34 bp):
ATTCTTTTTATTAATATTATTATTTATTATTATT
Found at i:55869160 original size:20 final size:21
Alignment explanation
Indices: 55869124--55869162 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
55869114 CACTCAACTT
55869124 TTAAAACTTATGTAATAGTCA
1 TTAAAACTTATGTAATAGTCA
55869145 TTAAAA-TTATCG-AATAGT
1 TTAAAACTTAT-GTAATAGT
55869163 TACATTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (21 bp):
TTAAAACTTATGTAATAGTCA
Found at i:55881448 original size:6 final size:6
Alignment explanation
Indices: 55881437--55881473 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
55881427 AAACCCAGCC
55881437 GTCGAG GTCGAG GTCGAG GTCGAG GTCGAG GTCGAG G
1 GTCGAG GTCGAG GTCGAG GTCGAG GTCGAG GTCGAG G
55881474 GTTTTACAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.51, T:0.16
Consensus pattern (6 bp):
GTCGAG
Found at i:55885184 original size:9 final size:9
Alignment explanation
Indices: 55885170--55885200 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
55885160 TCTTTTCAGC
55885170 AAAAAAATA
1 AAAAAAATA
55885179 AAAAAAATA
1 AAAAAAATA
55885188 AAAAAAATA
1 AAAAAAATA
55885197 AAAA
1 AAAA
55885201 GCTAGAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:55888386 original size:43 final size:43
Alignment explanation
Indices: 55888337--55888425 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
55888327 AATGTGAAGA
*
55888337 GTTAAATTTATTAAATTATTTAGAATTAAGATTTGGCTATTTG
1 GTTAAATTTATTAAATTATTTAGAATCAAGATTTGGCTATTTG
55888380 GTTAAATTTATTAAATTATTTAGAATCAAGATTTGGCTATTTG
1 GTTAAATTTATTAAATTATTTAGAATCAAGATTTGGCTATTTG
55888423 GTT
1 GTT
55888426 TCTAAGCAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (43 bp):
GTTAAATTTATTAAATTATTTAGAATCAAGATTTGGCTATTTG
Found at i:55889698 original size:22 final size:22
Alignment explanation
Indices: 55889670--55889713 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55889660 TAATACATTA
55889670 AAAATAAAAATTAATTAATAAG
1 AAAATAAAAATTAATTAATAAG
* *
55889692 AAAATAATAATTTATTAATAAG
1 AAAATAAAAATTAATTAATAAG
55889714 GTAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
AAAATAAAAATTAATTAATAAG
Found at i:55889792 original size:29 final size:30
Alignment explanation
Indices: 55889760--55889823 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
55889750 TTTTCTTCAA
*
55889760 CCAACCATGAA-AAGTCCTTTTTTGATCAC
1 CCAACCATGAATAACTCCTTTTTTGATCAC
* *
55889789 CCAACCATTAATAACTCCTTTTTTTATCAC
1 CCAACCATGAATAACTCCTTTTTTGATCAC
*
55889819 TCAAC
1 CCAAC
55889824 TATTCAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (30 bp):
CCAACCATGAATAACTCCTTTTTTGATCAC
Found at i:55900568 original size:16 final size:13
Alignment explanation
Indices: 55900534--55900558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55900524 TCTAATCATA
55900534 TAATAATTTATAT
1 TAATAATTTATAT
55900547 TAATAATTTATA
1 TAATAATTTATA
55900559 ATTTTAATAA
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:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAATTTATAT
Found at i:55900608 original size:13 final size:14
Alignment explanation
Indices: 55900590--55900631 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
55900580 TTTCAATTTT
55900590 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
55900603 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
55900618 ATTTTAAATAATAT
1 ATTTT-AATAATAT
55900632 TCTTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:55900616 original size:16 final size:16
Alignment explanation
Indices: 55900594--55900630 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
55900584 AATTTTATTT
55900594 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
55900611 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
55900626 TAATA
1 TAATA
55900631 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:55900684 original size:15 final size:15
Alignment explanation
Indices: 55900664--55900720 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
55900654 CTTCAATATT
55900664 AATATTTTAATAATA
1 AATATTTTAATAATA
*
55900679 AATATTTATTAAAATTATA
1 AATA-TT-TT--AATAATA
*
55900698 AATATATTAATAATA
1 AATATTTTAATAATA
*
55900713 AATGTTTT
1 AATATTTT
55900721 GTAGTGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:55904138 original size:19 final size:20
Alignment explanation
Indices: 55904107--55904160 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
55904097 AAAAATATAA
55904107 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTG-AATTTTTGA-AAATT
55904127 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
55904147 ATTTTG-ATTTTTGA
1 ATTTTGAATTTTTGA
55904161 TTTGTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:55905949 original size:24 final size:24
Alignment explanation
Indices: 55905917--55905965 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
55905907 AAAAAACCGA
55905917 CAGAACAGTAGCTTCCATTACTCC
1 CAGAACAGTAGCTTCCATTACTCC
55905941 CAGAACAGTAGCTTCCATTACTCC
1 CAGAACAGTAGCTTCCATTACTCC
55905965 C
1 C
55905966 TAATAGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.24
Consensus pattern (24 bp):
CAGAACAGTAGCTTCCATTACTCC
Found at i:55907130 original size:20 final size:20
Alignment explanation
Indices: 55907105--55907144 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
55907095 ACCCAGTAAG
*
55907105 TTAGGGTACAATCCTCCCGT
1 TTAGGGCACAATCCTCCCGT
55907125 TTAGGGCACAATCCTCCCGT
1 TTAGGGCACAATCCTCCCGT
55907145 GGATCCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.28
Consensus pattern (20 bp):
TTAGGGCACAATCCTCCCGT
Found at i:55907400 original size:3 final size:3
Alignment explanation
Indices: 55907392--55907523 Score: 69
Period size: 3 Copynumber: 44.0 Consensus size: 3
55907382 TAGTGCCATT
* * * * * * *
55907392 ATA ATA ATA AAA ATA AAA ATA ATA AAA ATA ACA AT- ATG TTA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
55907439 ATA ATAA ATAA ATA TTG GTA ATA A-A TATA TATA A-A ATA ATA GTA A-A
1 ATA AT-A AT-A ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA
55907485 AGTA ATA A-A ATAA ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 A-TA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
55907524 CTCTCCCCCT
Statistics
Matches: 100, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
2 11 0.11
3 72 0.72
4 17 0.17
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:55907505 original size:29 final size:31
Alignment explanation
Indices: 55907456--55907521 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
55907446 ATAAATATTG
* *
55907456 GTAATAAATATATATAAAATAATAGTAA-AA
1 GTAATAAATATAAATAAAATAATAATAATAA
55907486 GTAATAAA-ATAAATAAAATAATAATAATAA
1 GTAATAAATATAAATAAAATAATAATAATAA
55907516 -TAATAA
1 GTAATAA
55907522 TACTCTCCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (31 bp):
GTAATAAATATAAATAAAATAATAATAATAA
Found at i:55907913 original size:30 final size:30
Alignment explanation
Indices: 55907877--55907957 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
55907867 CATGGTGGCA
*
55907877 AGTAGGGTAATGGAGTTAGTGGGGT-AGCTT
1 AGTAGGGTGATGGAGTTAGTGGGGTGA-CTT
*
55907907 AGTAGGGTGATAGAGTTAGTGGGGTGACTT
1 AGTAGGGTGATGGAGTTAGTGGGGTGACTT
*
55907937 AGT-GGGTGATGAAGTTAGTGG
1 AGTAGGGTGATGGAGTTAGTGG
55907958 TCAGTTTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 16 0.35
30 29 0.63
31 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.44, T:0.30
Consensus pattern (30 bp):
AGTAGGGTGATGGAGTTAGTGGGGTGACTT
Found at i:55910480 original size:34 final size:35
Alignment explanation
Indices: 55910435--55910504 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
55910425 TATGTTTGAA
* *
55910435 TTTTATCATTAAAATTTATCA-TCAATTTTAATTT
1 TTTTATCATTAAAATTTACCATTCAATTTCAATTT
*
55910469 TTTTATTATTAAAATTTACCATTCAATTTCAATTT
1 TTTTATCATTAAAATTTACCATTCAATTTCAATTT
55910504 T
1 T
55910505 GATAATTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 19 0.59
35 13 0.41
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTTATCATTAAAATTTACCATTCAATTTCAATTT
Found at i:55911995 original size:37 final size:37
Alignment explanation
Indices: 55911938--55912043 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
55911928 TATGATCACT
*
55911938 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
55911973 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
*
55912010 TATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
55912044 GAAGCTATCA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 6 0.09
36 4 0.06
37 54 0.84
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:55912085 original size:52 final size:52
Alignment explanation
Indices: 55912006--55912170 Score: 243
Period size: 46 Copynumber: 3.2 Consensus size: 52
55911996 TAAGTGTAGC
* *
55912006 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
55912059 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
55912111 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
55912157 CACTTTGTCACTTG
1 CACTTT-TCACTTG
55912171 ATCAGAAGTA
Statistics
Matches: 101, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
46 44 0.44
49 1 0.01
50 1 0.01
52 43 0.43
53 12 0.12
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:55920428 original size:3 final size:3
Alignment explanation
Indices: 55920420--55920532 Score: 74
Period size: 3 Copynumber: 37.7 Consensus size: 3
55920410 GAGGGGAGAG
*
55920420 TAT TAT TAT TAT TAT TAT T-T TAT TACT T-T TAC TAT TAT T-T TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * * *
55920462 TAT ATATT TAT TAT CAT TATT TATT TAT TAT TAT TAG TAA CA- TAT TGT
1 TAT -TA-T TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* *
55920510 TAT TTT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
55920533 CTATAATGGC
Statistics
Matches: 87, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
2 9 0.10
3 64 0.74
4 13 0.15
5 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:55920444 original size:17 final size:18
Alignment explanation
Indices: 55920420--55920497 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 18
55920410 GAGGGGAGAG
55920420 TATTATTATTATTA-TTAT
1 TATTATTATT-TTATTTAT
*
55920438 T-TTATTACTTTTA-CTAT
1 TATTATTA-TTTTATTTAT
*
55920455 TATT-TTATATATATTTAT
1 TATTATTAT-TTTATTTAT
*
55920473 TATCATTA-TTTATTTAT
1 TATTATTATTTTATTTAT
55920490 TATTATTA
1 TATTATTA
55920498 GTAACATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.02
17 34 0.69
18 11 0.22
19 3 0.06
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTTTATTTAT
Found at i:55922814 original size:79 final size:78
Alignment explanation
Indices: 55922683--55922901 Score: 303
Period size: 79 Copynumber: 2.8 Consensus size: 78
55922673 GTTACATCTT
* * * * *
55922683 ATGTAACTGTAGTGAATCAGGATTAGCTGTTCAGGTCAAATCCTATCCACCTTAAGTTATCATAA
1 ATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATAA
55922748 GGAATCATATATC
66 GGAATCATATATC
* * *
55922761 GTGTAACCGTAGCGAATCAGGATTACCATTTTCAGATCAAATCCTATCCACCTTAGGTTACCATA
1 ATGTAACCGTAGCGAATCAGGATTACC-TTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATA
*
55922826 ATGAATCATATATC
65 AGGAATCATATATC
* * * *
55922840 ATGTAACCGTAACGAATAAGGATTACCCTTTTCAGGTCAAATTCTATCCGCCTTAAGTTACC
1 ATGTAACCGTAGCGAATCAGGATTA-CCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACC
55922902 GTAGTGAATC
Statistics
Matches: 123, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
78 23 0.19
79 98 0.80
80 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (78 bp):
ATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATAA
GGAATCATATATC
Found at i:55922941 original size:40 final size:40
Alignment explanation
Indices: 55922877--55923014 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 40
55922867 CTTTTCAGGT
* * * * *
55922877 CAAATTCTATCCGCCTTAAGTTACCGTAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* *
55922917 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* ** ** *
55922957 CAAATCCTATCCACTTTGAGGTATTATAGTGAATTAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* *
55922997 CGAATCCTATCCATTTTA
1 CAAATCCTATCCACTTTA
55923015 TATTCTCGAG
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
Found at i:55923450 original size:90 final size:91
Alignment explanation
Indices: 55923345--55923525 Score: 337
Period size: 90 Copynumber: 2.0 Consensus size: 91
55923335 ACCCGATCTT
55923345 AAATTAATAATTTCATTCAATTTATTAATTTAGATAATAAAACAATTCATTCCCTTCAATTTGGT
1 AAATTAATAATTTCATTCAATTTATTAATTTAGATAATAAAACAATTCATTCCCTTCAATTTGGT
55923410 CA-TTTTTGACATTTTTACAAAATTG
66 CATTTTTTGACATTTTTACAAAATTG
55923435 AAATTAATAATTTCATTCAATTTATTAATTTAGATAATAAAACAATTCATTCCCTTCAATTTGGT
1 AAATTAATAATTTCATTCAATTTATTAATTTAGATAATAAAACAATTCATTCCCTTCAATTTGGT
*
55923500 CATTTTTTTTACATTTTTACAAAATT
66 CA-TTTTTTGACATTTTTACAAAATT
55923526 ACCCCCTAAA
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
90 67 0.76
92 21 0.24
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (91 bp):
AAATTAATAATTTCATTCAATTTATTAATTTAGATAATAAAACAATTCATTCCCTTCAATTTGGT
CATTTTTTGACATTTTTACAAAATTG
Found at i:55925816 original size:10 final size:10
Alignment explanation
Indices: 55925801--55925825 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55925791 AAATTCTAAT
55925801 TTTTTATATA
1 TTTTTATATA
55925811 TTTTTATATA
1 TTTTTATATA
55925821 TTTTT
1 TTTTT
55925826 GGAATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATATA
Found at i:55936473 original size:21 final size:20
Alignment explanation
Indices: 55936447--55936486 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
55936437 TAATAGGCAC
55936447 AATTAATCTCTATAT-TTTTAG
1 AATTAAT-T-TATATGTTTTAG
55936468 AATTAATTTATATGTTTTA
1 AATTAATTTATATGTTTTA
55936487 ATTTAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTAATTTATATGTTTTAG
Found at i:55944714 original size:24 final size:23
Alignment explanation
Indices: 55944687--55944732 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55944677 ATAATTAAAT
* *
55944687 TAATTAATTTTAAATAAATTTATG
1 TAATTAA-TGTAAATAAAATTATG
55944711 TAATTAATGTAAATAAAATTAT
1 TAATTAATGTAAATAAAATTAT
55944733 TAAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TAATTAATGTAAATAAAATTATG
Found at i:55944715 original size:20 final size:20
Alignment explanation
Indices: 55944670--55944706 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
55944660 GAGAATTGAT
*
55944670 TTAATTTATAATTAAATTAA
1 TTAATTTATAAATAAATTAA
55944690 TTAATTT-TAAATAAATT
1 TTAATTTATAAATAAATT
55944707 TATGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTTATAAATAAATTAA
Found at i:55945759 original size:21 final size:21
Alignment explanation
Indices: 55945733--55945775 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
55945723 GAGGTGACGG
55945733 AGTACTGCTTTTTTCACTTTT
1 AGTACTGCTTTTTTCACTTTT
55945754 AGTACTGCTTTTTTCACTTTT
1 AGTACTGCTTTTTTCACTTTT
55945775 A
1 A
55945776 CATCTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (21 bp):
AGTACTGCTTTTTTCACTTTT
Found at i:55947264 original size:24 final size:24
Alignment explanation
Indices: 55947232--55947284 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
55947222 AACAGCCCAA
55947232 TTGTTGACCTTCGATTTCATTATT
1 TTGTTGACCTTCGATTTCATTATT
55947256 TTGTTGACCTTCGATTTCATTATT
1 TTGTTGACCTTCGATTTCATTATT
55947280 TTGTT
1 TTGTT
55947285 CTGAAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (24 bp):
TTGTTGACCTTCGATTTCATTATT
Found at i:55950742 original size:5 final size:5
Alignment explanation
Indices: 55950732--55950756 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55950722 AATAATTAAG
55950732 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
55950757 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:55950826 original size:31 final size:30
Alignment explanation
Indices: 55950791--55950851 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
55950781 GAAACAGAAT
*
55950791 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
55950822 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
55950852 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:55952597 original size:39 final size:41
Alignment explanation
Indices: 55952465--55952615 Score: 236
Period size: 41 Copynumber: 3.8 Consensus size: 41
55952455 GCAGTGCTTA
*
55952465 TTAGCGGCGTTTTTGAGAAAGTGCCGCTAATGCTCGTGCCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGTGCCT
*
55952506 TTAGCGGCGTTTTTGAGAAAGCGCCACTAATGCTCGTGCCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGTGCCT
*
55952547 TTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCT-G-GCCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGTGCCT
* *
55952586 TTAGCGGCGTTTTTCA-AAAACGCCGCTAAT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAAT
55952616 AATAAAAGCT
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
38 13 0.12
39 19 0.18
40 1 0.01
41 71 0.68
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGTGCCT
Found at i:55962757 original size:18 final size:18
Alignment explanation
Indices: 55962730--55962822 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 18
55962720 TACGACCGTT
* *
55962730 TACGGTACTATTTACGTA
1 TACGGCACTATTCACGTA
* *
55962748 TACGACACTATTTACGTA
1 TACGGCACTATTCACGTA
*
55962766 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
*
55962784 TATGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
55962802 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
55962820 TAC
1 TAC
55962823 AGTAGTTGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:55962777 original size:36 final size:36
Alignment explanation
Indices: 55962730--55962822 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
55962720 TACGACCGTT
* *
55962730 TACGGTACTATTTACGTATACGACACTATTTACGTA
1 TACGGTACTATTCACGTATACGACACTATTCACGTA
* *
55962766 TACGGTACTATTCACGTATATGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGACACTATTCACGTA
*
55962802 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
55962823 AGTAGTTGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGACACTATTCACGTA
Found at i:55971508 original size:31 final size:28
Alignment explanation
Indices: 55971465--55971523 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
55971455 TGATGAAGAA
55971465 TTTTCATCAAATCAACCCTTAAATAAGAATT
1 TTTTCATCAAAT---CCCTTAAATAAGAATT
*
55971496 TTTTTATCAAATCCCTTAAATAAGAATT
1 TTTTCATCAAATCCCTTAAATAAGAATT
55971524 AAATGACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 16 0.59
31 11 0.41
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (28 bp):
TTTTCATCAAATCCCTTAAATAAGAATT
Found at i:55977565 original size:17 final size:16
Alignment explanation
Indices: 55977539--55977571 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
55977529 TAAATCCCAG
55977539 ATTTTGATACCCATAT
1 ATTTTGATACCCATAT
55977555 ATTTCTGATACCCATAT
1 ATTT-TGATACCCATAT
55977572 CTTTGACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTTGATACCCATAT
Found at i:55983153 original size:39 final size:39
Alignment explanation
Indices: 55983100--55983205 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 39
55983090 ATATAGATTT
* *
55983100 TTTTTTAACTTAAAGTTTAAAGTTTT-GAAAGG-ATTATTA
1 TTTTTAAATTTAAAGTTTAAA-TTTTAG-AAGGAATTATTA
* *
55983139 TTTTTAAATTTAAAGTTTAAATTTTAGATGGAATTGTTA
1 TTTTTAAATTTAAAGTTTAAATTTTAGAAGGAATTATTA
* *
55983178 TTTTTAAATTTAAATTTTAAACTTTAGA
1 TTTTTAAATTTAAAGTTTAAATTTTAGA
55983206 TAATACTTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
38 7 0.12
39 52 0.88
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (39 bp):
TTTTTAAATTTAAAGTTTAAATTTTAGAAGGAATTATTA
Found at i:55989486 original size:6 final size:6
Alignment explanation
Indices: 55989475--55989523 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
55989465 TACTCCATGC
*
55989475 TTTATT TTTATT TTTATT TTTATT TTTGATCT ATT-TT TTTAGTT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTT-AT-T TTTATT TTTA-TT TTTAT
55989524 AATTTCTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 3 0.08
6 23 0.62
7 8 0.22
8 3 0.08
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:55991404 original size:115 final size:116
Alignment explanation
Indices: 55991200--55991431 Score: 412
Period size: 115 Copynumber: 2.0 Consensus size: 116
55991190 GGACAATTAA
* *
55991200 ACAAACTTATTTATTCTTTCAAATGCACTCACAAAAATCTCGTTCCACAATAAGCAAATAAATGC
1 ACAAACTTATTTATTCTTTCAAATGCACTCACAAAAA-CTCATTCCACAATAAACAAATAAATGC
*
55991265 TCTCAATCCCCTATACAAAACCTATATAACTCTCTTAATATATAAGAGTTTT
65 TCTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
*
55991317 ACAAACTTATTTATTCTTTCAAATGCACTCACAAAAA-TCATTCCACAATAAACAAATAAGTGCT
1 ACAAACTTATTTATTCTTTCAAATGCACTCACAAAAACTCATTCCACAATAAACAAATAAATGCT
55991381 CTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
66 CTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
55991432 TGAGACTTCC
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
115 74 0.67
117 37 0.33
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (116 bp):
ACAAACTTATTTATTCTTTCAAATGCACTCACAAAAACTCATTCCACAATAAACAAATAAATGCT
CTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
Found at i:55996209 original size:34 final size:34
Alignment explanation
Indices: 55996166--55996234 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
55996156 TACGTTTTGA
55996166 AAGTTTAGAGGATTAGATCAACACCAGAAATCAC
1 AAGTTTAGAGGATTAGATCAACACCAGAAATCAC
55996200 AAGTTTAGAGGATTAGATCAACACCAGAAATCAC
1 AAGTTTAGAGGATTAGATCAACACCAGAAATCAC
55996234 A
1 A
55996235 CTCTCCAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.20
Consensus pattern (34 bp):
AAGTTTAGAGGATTAGATCAACACCAGAAATCAC
Found at i:56000771 original size:43 final size:43
Alignment explanation
Indices: 56000684--56000807 Score: 117
Period size: 43 Copynumber: 2.9 Consensus size: 43
56000674 GGCTTGTACA
* * * * * *
56000684 ATGCCAACGTCCCAGACGTGGTCTTACATGCAATCAC-AGATCG
1 ATGCCAAAGTCCCAAAAGTGGTCTTACACGAAAACACAAG-TCG
** * *
56000727 ATGCCACTGTCCTAAATAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAAGTCCCAAA-AGTGGTCTTACACGAAAACACAAGTCG
*
56000770 ATGCCAAAGTCCCAAACGTGGTCTTACACGAAAACACA
1 ATGCCAAAGTCCCAAAAGTGGTCTTACACGAAAACACA
56000808 TATCGGAAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
42 1 0.02
43 61 0.94
44 3 0.05
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (43 bp):
ATGCCAAAGTCCCAAAAGTGGTCTTACACGAAAACACAAGTCG
Found at i:56006956 original size:21 final size:21
Alignment explanation
Indices: 56006927--56006975 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
56006917 AATAGAAGTT
* *
56006927 GTGAGTGACAGGAAATTGACA
1 GTGAATGACAGGAAACTGACA
*
56006948 GTGAATGACAGGGAACTGACA
1 GTGAATGACAGGAAACTGACA
56006969 -TGAATGA
1 GTGAATGA
56006976 TTTTATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.39, C:0.10, G:0.33, T:0.18
Consensus pattern (21 bp):
GTGAATGACAGGAAACTGACA
Found at i:56010800 original size:21 final size:22
Alignment explanation
Indices: 56010773--56010821 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
56010763 TTTGGATTAG
56010773 TATTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTGTAAT
56010795 T-TTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTGTAAT
56010816 TATTTT
1 TATTTT
56010822 ATAATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (22 bp):
TATTTTGTATGAATATTGTAAT
Found at i:56010881 original size:60 final size:60
Alignment explanation
Indices: 56010809--56010930 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 60
56010799 TGTATGAATA
* * * *
56010809 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
56010869 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
56010929 TT
1 TT
56010931 AGTTTAGTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
Found at i:56011084 original size:15 final size:16
Alignment explanation
Indices: 56011044--56011082 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
56011034 TTAACTCATT
56011044 TAATTTTTATATAATG
1 TAATTTTTATATAATG
56011060 TAATTTTTATATAATG
1 TAATTTTTATATAATG
56011076 TAATTTT
1 TAATTTT
56011083 ATTTGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TAATTTTTATATAATG
Found at i:56012722 original size:6 final size:6
Alignment explanation
Indices: 56012713--56012765 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
56012703 ACCAGAGCAA
* **
56012713 GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG GAGCCA GAGCTA GAGCCG
1 GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG GAGCCG
56012761 GAGCC
1 GAGCC
56012766 AGAGGCAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.21, C:0.32, G:0.45, T:0.02
Consensus pattern (6 bp):
GAGCCG
Found at i:56012734 original size:18 final size:18
Alignment explanation
Indices: 56012707--56012769 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
56012697 TCATGCACCA
*
56012707 GAGCAAGAGCCGGAGCCG
1 GAGCCAGAGCCGGAGCCG
*
56012725 GAGCCGGAGCCGGAGCCG
1 GAGCCAGAGCCGGAGCCG
**
56012743 GAGCCAGAGCTAGAGCCG
1 GAGCCAGAGCCGGAGCCG
56012761 GAGCCAGAG
1 GAGCCAGAG
56012770 GCAGAGACGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.25, C:0.29, G:0.44, T:0.02
Consensus pattern (18 bp):
GAGCCAGAGCCGGAGCCG
Found at i:56012775 original size:18 final size:18
Alignment explanation
Indices: 56012719--56012780 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
56012709 GCAAGAGCCG
* * *
56012719 GAGCCGGAGCCGGAGCCG
1 GAGCCGGAGCCAGAGGCA
56012737 GAGCCGGAGCCAGA-GCTA
1 GAGCCGGAGCCAGAGGC-A
56012755 GAGCCGGAGCCAGAGGCA
1 GAGCCGGAGCCAGAGGCA
*
56012773 GAGACGGA
1 GAGCCGGA
56012781 ACTACATTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 1 0.03
18 35 0.92
19 2 0.05
ACGTcount: A:0.26, C:0.27, G:0.45, T:0.02
Consensus pattern (18 bp):
GAGCCGGAGCCAGAGGCA
Found at i:56016363 original size:27 final size:27
Alignment explanation
Indices: 56016319--56016389 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
56016309 AAGACCATTA
*
56016319 GCGCCTCTCA-ATATGGCACAACTAATG
1 GCGCCTCTCAGATA-GGCACAACCAATG
* * *
56016346 GCGCCTGTCAGATAGGCACCACCATTG
1 GCGCCTCTCAGATAGGCACAACCAATG
*
56016373 GCGCCTCTGAGATAGGC
1 GCGCCTCTCAGATAGGC
56016390 GCCACTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (27 bp):
GCGCCTCTCAGATAGGCACAACCAATG
Found at i:56021257 original size:18 final size:19
Alignment explanation
Indices: 56021230--56021266 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
56021220 GAATTCTACC
56021230 ATTTAAAAATA-AAATAAA
1 ATTTAAAAATACAAATAAA
*
56021248 ATTTATAAATACAAATAAA
1 ATTTAAAAATACAAATAAA
56021267 TAATTGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTTAAAAATACAAATAAA
Found at i:56027020 original size:34 final size:34
Alignment explanation
Indices: 56026977--56027048 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
56026967 GATGAATTAC
56026977 CTTTTAAAATTGTAGAGGGAGAAGATTTCAAATA
1 CTTTTAAAATTGTAGAGGGAGAAGATTTCAAATA
*
56027011 CTTTTAAAATTGTAGAGGGAGAAGGTTTCAAATA
1 CTTTTAAAATTGTAGAGGGAGAAGATTTCAAATA
56027045 CTTT
1 CTTT
56027049 CTTTCTATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.35
Consensus pattern (34 bp):
CTTTTAAAATTGTAGAGGGAGAAGATTTCAAATA
Found at i:56037482 original size:15 final size:15
Alignment explanation
Indices: 56037435--56037487 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
56037425 CTTATATAGT
56037435 TTAATTAAAT-TTAA
1 TTAATTAAATCTTAA
*
56037449 TTAATT--ATCCTTTAT
1 TTAATTAAAT-C-TTAA
56037464 TTAATTAAATCTTAA
1 TTAATTAAATCTTAA
56037479 TTAATTAAA
1 TTAATTAAA
56037488 AGTTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.06
14 6 0.19
15 21 0.66
16 1 0.03
17 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATTAAATCTTAA
Found at i:56041681 original size:14 final size:14
Alignment explanation
Indices: 56041662--56041691 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56041652 TCTAAGCGTC
56041662 ATTCCTATACTCCA
1 ATTCCTATACTCCA
*
56041676 ATTCCTCTACTCCA
1 ATTCCTATACTCCA
56041690 AT
1 AT
56041692 GAAGCAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTCCTATACTCCA
Found at i:56046844 original size:15 final size:15
Alignment explanation
Indices: 56046824--56046901 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
56046814 TTTATGGAAA
56046824 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
56046839 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
56046853 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
56046869 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
56046883 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
56046899 ATC
1 ATC
56046902 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:56046852 original size:30 final size:30
Alignment explanation
Indices: 56046817--56046901 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
56046807 ATCCATATTT
*
56046817 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
56046847 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
56046877 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
56046902 GAGATATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:56051517 original size:30 final size:30
Alignment explanation
Indices: 56051482--56052325 Score: 1652
Period size: 30 Copynumber: 28.1 Consensus size: 30
56051472 TCCATATTTA
* *
56051482 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051512 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051542 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051572 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051602 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051632 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051662 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051692 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051722 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051752 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051782 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051812 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051842 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051872 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051902 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051932 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051962 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56051992 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052022 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052052 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052082 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052112 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052142 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052172 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052202 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052232 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
56052262 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
56052292 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
56052323 TGG
1 TGG
56052326 CATAATAAAA
Statistics
Matches: 810, Mismatches: 3, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
30 802 0.99
31 8 0.01
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:56056305 original size:14 final size:15
Alignment explanation
Indices: 56056283--56056312 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
56056273 CATTTTCGGA
56056283 TAAAGTTTTTTTATT
1 TAAAGTTTTTTTATT
56056298 TAAA-TTTTTTTATT
1 TAAAGTTTTTTTATT
56056312 T
1 T
56056313 TTTTAAGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TAAAGTTTTTTTATT
Found at i:56059536 original size:87 final size:87
Alignment explanation
Indices: 56059387--56059697 Score: 471
Period size: 87 Copynumber: 3.6 Consensus size: 87
56059377 NNNNNNNNNN
* *
56059387 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
*
56059452 CCGATGGAGGCAAGGCTTTATT
66 CCGATGGAGGCAAGGCTTTGTT
* * * * * * **
56059474 TTCGATCGGCTCCACTGTTAACGCAGGAAGGTAAGATTTGTTATCTTTAACCAGCTGGACTGCAA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
56059539 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
**
56059561 TTCGATCTGCTTCGGTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
*
56059626 CCGATGGAGGCAAAGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
56059648 TTCGATCTTCTTCACTGTTAATGCAGGAAGGCAAGATCTGCTT-TCTTTGA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTG-TTATCTTTGA
56059698 TCTATTCTCT
Statistics
Matches: 198, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
87 196 0.99
88 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (87 bp):
TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:56060303 original size:108 final size:108
Alignment explanation
Indices: 56060114--56060309 Score: 329
Period size: 108 Copynumber: 1.8 Consensus size: 108
56060104 GAAAAATGCT
*
56060114 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAAATTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
56060179 CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGAATAAGA
66 CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGAATAAGA
* * * **
56060222 TGAAAAAGATTATCACAATGGATAAGATGAAAATTTGTTGAGAGCAAAGCTCTAAATGAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAAATTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
*
56060287 TAATCAAGATAGCAAATTTTGCT
66 CAATCAAGATAGCAAATTTTGCT
56060310 AGAATACAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 81 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAAAATGAAAATTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGAATAAGA
Done.