Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 28 of 106
Found at i:11086464 original size:2 final size:2
Alignment explanation
Indices: 11086457--11086481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11086447 TTTTGCTTAA
11086457 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11086482 AAATTACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11087433 original size:38 final size:38
Alignment explanation
Indices: 11087373--11087568 Score: 250
Period size: 38 Copynumber: 5.2 Consensus size: 38
11087363 CAAAAAAGAA
* *
11087373 AAAAGGTTTCATTACCTCAGTTTTGAGGAGTTCATTTTT
1 AAAA-GTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* *
11087412 AAAAGTTTCGTTGTCTTAGTTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* **
11087450 AAAAGTCTCGTTGCCTCAACTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* **
11087488 AAAAGTTTTGTTGCCTCAGCCTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * * *
11087526 -AAAGTTTCATTGCCTCAATTTTGAGGAGTTTATTCTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
11087563 AAAAGT
1 AAAAGT
11087569 GTTATTACCT
Statistics
Matches: 136, Mismatches: 20, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
37 30 0.22
38 102 0.75
39 4 0.03
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (38 bp):
AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
Found at i:11087580 original size:38 final size:37
Alignment explanation
Indices: 11087373--11087598 Score: 220
Period size: 38 Copynumber: 5.9 Consensus size: 37
11087363 CAAAAAAGAA
* *
11087373 AAAAGGTTTCATTACCTCAGTTTTGAGGAGTTCATTTTT
1 AAAA-GTTT-ATTGCCTCAATTTTGAGGAGTTCATTTTT
* * * *
11087412 AAAAGTTTCGTTGTCTTAGTTTTGAGGAGTTCATTTTT
1 AAAAGTTT-ATTGCCTCAATTTTGAGGAGTTCATTTTT
** *
11087450 AAAAGTCTCGTTGCCTCAACTTTGAGGAGTTCATTTTT
1 AAAAGT-TTATTGCCTCAATTTTGAGGAGTTCATTTTT
* ***
11087488 AAAAGTTTTGTTGCCTCAGCCTTGAGGAGTTCATTTTT
1 AAAAG-TTTATTGCCTCAATTTTGAGGAGTTCATTTTT
* *
11087526 -AAAGTTTCATTGCCTCAATTTTGAGGAGTTTATTCTT
1 AAAAGTTT-ATTGCCTCAATTTTGAGGAGTTCATTTTT
* * *
11087563 AAAAGTGTTATTACCTCAATCTTGAGAAGTTCATTT
1 AAAAGT-TTATTGCCTCAATTTTGAGGAGTTCATTT
11087599 AAAAAAAAAA
Statistics
Matches: 159, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
36 3 0.02
37 27 0.17
38 121 0.76
39 8 0.05
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (37 bp):
AAAAGTTTATTGCCTCAATTTTGAGGAGTTCATTTTT
Found at i:11087580 original size:75 final size:75
Alignment explanation
Indices: 11087373--11087598 Score: 274
Period size: 75 Copynumber: 3.0 Consensus size: 75
11087363 CAAAAAAGAA
* * * * *
11087373 AAAAGGTTTCATTACCTCAGTTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGTCTTAGTTTTGAG
1 AAAA-GTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTAAAAGTTT-GTTGCCTCAGTCTTGAG
11087438 GAGTTCATTTTT
64 GAGTTCATTTTT
* * * *
11087450 AAAAGTCTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTTTTGTTGCCTCAGCCTTGAGG
1 AAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTAAAAG-TTTGTTGCCTCAGTCTTGAGG
11087515 AGTTCATTTTT
65 AGTTCATTTTT
* * * * * *
11087526 -AAAGTTTCATTGCCTCAATTTTGAGGAGTTTATTCTTAAAAGTGTTATTACCTCAATCTTGAGA
1 AAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTAAAAGT-TTGTTGCCTCAGTCTTGAGG
11087590 AGTTCATTT
65 AGTTCATTT
11087599 AAAAAAAAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
74 1 0.01
75 61 0.48
76 59 0.46
77 7 0.05
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (75 bp):
AAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTAAAAGTTTGTTGCCTCAGTCTTGAGGA
GTTCATTTTT
Found at i:11087797 original size:11 final size:11
Alignment explanation
Indices: 11087770--11087802 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11087760 AAAATAAACA
*
11087770 AAAAAAGA-AA
1 AAAAAAGAGAG
11087780 AAAAAAGAGAG
1 AAAAAAGAGAG
11087791 AAAAAAGAGAG
1 AAAAAAGAGAG
11087802 A
1 A
11087803 GAGGTACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:11087922 original size:2 final size:2
Alignment explanation
Indices: 11087915--11087942 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11087905 GAACGGTGGT
11087915 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11087943 AAGGATTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11089227 original size:14 final size:13
Alignment explanation
Indices: 11089202--11089236 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
11089192 TTAATTACTC
11089202 AATAAAAATAATA
1 AATAAAAATAATA
11089215 AATAAATAATAATA
1 AATAAA-AATAATA
*
11089229 GATAAAAA
1 AATAAAAA
11089237 AATGATGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAAAAATAATA
Found at i:11089339 original size:19 final size:19
Alignment explanation
Indices: 11089315--11089355 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11089305 ACATGACATT
11089315 AAATAAATAGAAAAATAA-A
1 AAATAAATA-AAAAATAATA
*
11089334 AAATAAATAAATAATAATA
1 AAATAAATAAAAAATAATA
11089353 AAA
1 AAA
11089356 ATCTAAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAAATAAAAAATAATA
Found at i:11089496 original size:27 final size:27
Alignment explanation
Indices: 11089446--11089532 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 27
11089436 AGTAACTTAG
*
11089446 AATAAAAAATGTAAGATATAAAAAAATAAT
1 AATAAAAAA--TAAAATA-AAAAAAATAAT
* * * * *
11089476 AATTAGAAATAAAATAGAAAATATGAT
1 AATAAAAAATAAAATAAAAAAAATAAT
*
11089503 AATAAAAAATATAATAAAATGAAAATAAT
1 AATAAAAAATAAAATAAAA--AAAATAAT
11089532 A
1 A
11089533 GTTAAATAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
27 23 0.53
28 6 0.14
29 7 0.16
30 7 0.16
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (27 bp):
AATAAAAAATAAAATAAAAAAAATAAT
Found at i:11089516 original size:12 final size:13
Alignment explanation
Indices: 11089466--11089521 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
11089456 GTAAGATATA
11089466 AAAAAATAATAAT
1 AAAAAATAATAAT
* *
11089479 TAGAAATAA-AAT
1 AAAAAATAATAAT
*
11089491 AGAAAATATGATAAT
1 A-AAAA-ATAATAAT
11089506 AAAAAAT-ATAAT
1 AAAAAATAATAAT
11089518 AAAA
1 AAAA
11089522 TGAAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 12 0.34
13 12 0.34
14 7 0.20
15 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:11099062 original size:45 final size:45
Alignment explanation
Indices: 11099011--11099100 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
11099001 GTCACTTTCT
11099011 CTTTGCGGTAGATATATCAAATTATTGTATTCATAACCTTTTACA
1 CTTTGCGGTAGATATATCAAATTATTGTATTCATAACCTTTTACA
11099056 CTTTGCGGTAGATATATCAAATTATTGTATTCATAACCTTTTACA
1 CTTTGCGGTAGATATATCAAATTATTGTATTCATAACCTTTTACA
11099101 AGTCAGTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (45 bp):
CTTTGCGGTAGATATATCAAATTATTGTATTCATAACCTTTTACA
Found at i:11099727 original size:29 final size:28
Alignment explanation
Indices: 11099694--11099761 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
11099684 AAATGTTTAC
11099694 ATTTTTATTCTTTTA-TTACATTAAATAAA
1 ATTTTTATT-TTTTATTTACATTAAAT-AA
*
11099723 ATTTTTATATTTTTATTTTATATTAAATAA
1 ATTTTTAT-TTTTTA-TTTACATTAAATAA
*
11099753 TTTTTTATT
1 ATTTTTATT
11099762 ATTAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 14 0.41
30 10 0.29
31 10 0.29
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTTTTATTTTTTATTTACATTAAATAA
Found at i:11099760 original size:17 final size:17
Alignment explanation
Indices: 11099738--11099771 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11099728 TATATTTTTA
11099738 TTTTA-TATTAAATAATT
1 TTTTATTATT-AATAATT
11099755 TTTTATTATTAATAATT
1 TTTTATTATTAATAATT
11099772 AATTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATTATTAATAATT
Found at i:11099863 original size:30 final size:31
Alignment explanation
Indices: 11099820--11099885 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
11099810 TACGTGATAT
* * **
11099820 TAATATGATATATTAATATGTTATAAT-AAA
1 TAATATAACATATTAATATAATATAATAAAA
*
11099850 TAATATAACATATTGATATAATATAATAAAA
1 TAATATAACATATTAATATAATATAATAAAA
11099881 TAATA
1 TAATA
11099886 ATATAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (31 bp):
TAATATAACATATTAATATAATATAATAAAA
Found at i:11099878 original size:21 final size:20
Alignment explanation
Indices: 11099854--11099915 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
11099844 AATAAATAAT
11099854 ATAACATATTGATATAATATA
1 ATAA-ATATTGATATAATATA
11099875 ATAAA-A-T-A-ATAATATA
1 ATAAATATTGATATAATATA
* *
11099891 ATAAAATATTGATATGATATG
1 AT-AAATATTGATATAATATA
11099912 ATAA
1 ATAA
11099916 TATAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
16 10 0.29
17 4 0.12
18 2 0.06
19 2 0.06
20 4 0.12
21 12 0.35
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (20 bp):
ATAAATATTGATATAATATA
Found at i:11099888 original size:16 final size:16
Alignment explanation
Indices: 11099867--11099935 Score: 66
Period size: 16 Copynumber: 4.0 Consensus size: 16
11099857 ACATATTGAT
11099867 ATAATATAATAAAATA
1 ATAATATAATAAAATA
11099883 ATAATATAATAAAATA
1 ATAATATAATAAAATA
* *
11099899 TTGATATGATATGATAATATA
1 ---ATA--ATATAATAAAATA
*
11099920 ATAATATGATAAAATA
1 ATAATATAATAAAATA
11099936 GTATCATAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 28 0.62
18 3 0.07
19 3 0.07
21 11 0.24
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATAATATAATAAAATA
Found at i:11099921 original size:37 final size:37
Alignment explanation
Indices: 11099841--11099935 Score: 129
Period size: 37 Copynumber: 2.5 Consensus size: 37
11099831 ATTAATATGT
11099841 TATAATAA-ATAATATAACATATTGATATAATATAATAA
1 TATAATAATATAATA-AA-ATATTGATATAATATAATAA
* * *
11099879 AATAATAATATAATAAAATATTGATATGATATGATAA
1 TATAATAATATAATAAAATATTGATATAATATAATAA
*
11099916 TATAATAATATGATAAAATA
1 TATAATAATATAATAAAATA
11099936 GTATCATAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
37 36 0.71
38 9 0.18
39 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (37 bp):
TATAATAATATAATAAAATATTGATATAATATAATAA
Found at i:11100431 original size:3 final size:3
Alignment explanation
Indices: 11100423--11100476 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
11100413 GGTGATAATC
* *
11100423 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAAG AAG ATG AGG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG
11100468 AAG AAG AAG
1 AAG AAG AAG
11100477 TAAAGGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:11101141 original size:15 final size:15
Alignment explanation
Indices: 11101117--11101151 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11101107 ATTTATTATG
11101117 ATTA-TTTATTTTTA
1 ATTATTTTATTTTTA
11101131 ATTATTTTATTTTTA
1 ATTATTTTATTTTTA
*
11101146 AATATT
1 ATTATT
11101152 AATAATATAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTATTTTATTTTTA
Found at i:11101323 original size:18 final size:19
Alignment explanation
Indices: 11101276--11101333 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
11101266 TTATCTTTTA
11101276 AATATTAATAGTTGATTATTT
1 AATATTAATA-TT-ATTATTT
11101297 AAGTATTAATATT-TTATTT
1 AA-TATTAATATTATTATTT
* *
11101316 TATATTAATATTAATATT
1 AATATTAATATTATTATT
11101334 ATAAAATANN
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 10 0.30
19 11 0.33
21 4 0.12
22 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
AATATTAATATTATTATTT
Found at i:11101569 original size:17 final size:16
Alignment explanation
Indices: 11101547--11101582 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
11101537 TTATCATTAA
11101547 TTAAAATATTAATTATT
1 TTAAAATATTAATT-TT
11101564 TTAAAATATTAATTTT
1 TTAAAATATTAATTTT
11101580 TTA
1 TTA
11101583 TTTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAAATATTAATTTT
Found at i:11103676 original size:28 final size:30
Alignment explanation
Indices: 11103622--11103681 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
11103612 ACTATTTCAC
*
11103622 TTTATGCAAAAAAGCCCTTATTCTTTT-AT
1 TTTATCCAAAAAAGCCCTTATTCTTTTGAT
**
11103651 TTTATCCAAAAAAGCTTTTATT-TTTTGAT
1 TTTATCCAAAAAAGCCCTTATTCTTTTGAT
11103680 TT
1 TT
11103682 GTACTCACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (30 bp):
TTTATCCAAAAAAGCCCTTATTCTTTTGAT
Found at i:11122353 original size:18 final size:17
Alignment explanation
Indices: 11122327--11122366 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
11122317 AAAGAAAGTA
* *
11122327 AGAAAAGAATTAGGGAG
1 AGAAGAGAATTAGAGAG
11122344 TAGAAGAGAATTAGAGAG
1 -AGAAGAGAATTAGAGAG
11122362 AGAAG
1 AGAAG
11122367 CTCTCTCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.12
Consensus pattern (17 bp):
AGAAGAGAATTAGAGAG
Found at i:11122583 original size:14 final size:14
Alignment explanation
Indices: 11122564--11122609 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
11122554 GTTTTCGAGT
*
11122564 AAAAGGTAAAAGAG
1 AAAAGGTACAAGAG
* *
11122578 AAAAGGTACACGTG
1 AAAAGGTACAAGAG
*
11122592 AAAAGATACAAGAG
1 AAAAGGTACAAGAG
11122606 AAAA
1 AAAA
11122610 AGTCGTACGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.24, T:0.09
Consensus pattern (14 bp):
AAAAGGTACAAGAG
Found at i:11122653 original size:29 final size:29
Alignment explanation
Indices: 11122597--11122653 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
11122587 ACGTGAAAAG
**
11122597 ATACAAGAGAAAAAGTCGTACGTGAACAA
1 ATACAAGAGAAAAAGTCGTACGAAAACAA
* * *
11122626 ATACAAGAGAAGAAGTTGTATGAAAACA
1 ATACAAGAGAAAAAGTCGTACGAAAACA
11122654 GGTACAAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (29 bp):
ATACAAGAGAAAAAGTCGTACGAAAACAA
Found at i:11122991 original size:34 final size:35
Alignment explanation
Indices: 11122925--11123013 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 35
11122915 TTGTTCCACA
* * *
11122925 TGAAGTAGTACTACACTTATTCTAATTATTCTG-C
1 TGAAGTAGTATTTCACTTGTTCTAATTATTCTGTC
* * * *
11122959 TGAAGTAGTATTTCACTTGTTTTAGTTGTTCTGTG
1 TGAAGTAGTATTTCACTTGTTCTAATTATTCTGTC
* *
11122994 TGAAGTAGTGTTTCGCTTGT
1 TGAAGTAGTATTTCACTTGT
11123014 AATGGTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 27 0.60
35 18 0.40
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.46
Consensus pattern (35 bp):
TGAAGTAGTATTTCACTTGTTCTAATTATTCTGTC
Found at i:11123435 original size:19 final size:20
Alignment explanation
Indices: 11123403--11123444 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
11123393 TGTGTTATGT
11123403 TTTTATTCTTGATAATT-AAA
1 TTTTATTCTTGAT-ATTCAAA
11123423 TTTTATT-TTGATATTCAAA
1 TTTTATTCTTGATATTCAAA
11123442 TTT
1 TTT
11123445 ACTTCCCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 11 0.52
20 7 0.33
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTATTCTTGATATTCAAA
Found at i:11132441 original size:18 final size:18
Alignment explanation
Indices: 11132418--11132453 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11132408 CTGAAGAACT
11132418 ACAATACCGTTCAAAAGA
1 ACAATACCGTTCAAAAGA
* *
11132436 ACAATACCTTTTAAAAGA
1 ACAATACCGTTCAAAAGA
11132454 TGATTTTGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.22
Consensus pattern (18 bp):
ACAATACCGTTCAAAAGA
Found at i:11147281 original size:17 final size:17
Alignment explanation
Indices: 11147241--11147292 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
11147231 AGAGTCATGT
* * *
11147241 CTTAATCTGAATAGTAA
1 CTTAATTTGAATAATCA
11147258 CTTAATTTGAATAATCA
1 CTTAATTTGAATAATCA
*
11147275 CTTAATTTAAATAATCA
1 CTTAATTTGAATAATCA
11147292 C
1 C
11147293 ACTTGAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (17 bp):
CTTAATTTGAATAATCA
Found at i:11151368 original size:3 final size:3
Alignment explanation
Indices: 11151360--11151388 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11151350 AATTTGTCCA
11151360 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11151389 AATTTTACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11153029 original size:18 final size:20
Alignment explanation
Indices: 11153006--11153042 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
11152996 AACCAATAAA
11153006 GAATAAC-TAAAA-TAAAAG
1 GAATAACATAAAATTAAAAG
11153024 GAATAACATAAAATTAAAA
1 GAATAACATAAAATTAAAA
11153043 CAACTCACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19
Consensus pattern (20 bp):
GAATAACATAAAATTAAAAG
Found at i:11154050 original size:31 final size:31
Alignment explanation
Indices: 11154012--11154180 Score: 250
Period size: 31 Copynumber: 5.5 Consensus size: 31
11154002 GTCAGCGTTA
*
11154012 GCGTGTTACAACATTTTACATTATATGCATG
1 GCGTGTTACAACATTTTACGTTATATGCATG
* *
11154043 GCGTGTTACCACATTTTACATTATATGCATG
1 GCGTGTTACAACATTTTACGTTATATGCATG
11154074 GCGTGTTACCAA-ATTTTACGTTATATGCATG
1 GCGTGTTA-CAACATTTTACGTTATATGCATG
* *
11154105 GCGTGTTACCACATTCTACGTTATATGCATG
1 GCGTGTTACAACATTTTACGTTATATGCATG
* * *
11154136 ACGTGTTACCACATTATACGTTATATGCATG
1 GCGTGTTACAACATTTTACGTTATATGCATG
11154167 GCGTGTTACAACAT
1 GCGTGTTACAACAT
11154181 GACTGACAAA
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 2 0.02
31 123 0.97
32 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (31 bp):
GCGTGTTACAACATTTTACGTTATATGCATG
Found at i:11154391 original size:13 final size:13
Alignment explanation
Indices: 11154373--11154417 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
11154363 TTGTTTGTGG
11154373 GATTGATGAAGCT
1 GATTGATGAAGCT
11154386 GATTGATGAAGCT
1 GATTGATGAAGCT
11154399 GATTGATGAAGCT
1 GATTGATGAAGCT
*
11154412 GGTTGA
1 GATTGA
11154418 AGATGTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.29, C:0.07, G:0.33, T:0.31
Consensus pattern (13 bp):
GATTGATGAAGCT
Found at i:11157686 original size:30 final size:30
Alignment explanation
Indices: 11157646--11157717 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
11157636 CATGACTTGA
*
11157646 CCAAACAAATTTAAAAAATTTATGGATCAT
1 CCAATCAAATTTAAAAAATTTATGGATCAT
11157676 CCAATCAAATTTAAAAAATTTATGGATCAT
1 CCAATCAAATTTAAAAAATTTATGGATCAT
11157706 CCAATCAAATTT
1 CCAATCAAATTT
11157718 GATCTATGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (30 bp):
CCAATCAAATTTAAAAAATTTATGGATCAT
Found at i:11158056 original size:31 final size:31
Alignment explanation
Indices: 11158021--11158095 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
11158011 ATCTTGTGGT
*
11158021 GACACGCTGAGTGGAACCATATACTTGGTGC
1 GACACGCTGAGTGGAACCAGATACTTGGTGC
*
11158052 GACACGCTGAGTGGAACCAGATACTTGGTGT
1 GACACGCTGAGTGGAACCAGATACTTGGTGC
11158083 GACACGCTGAGTG
1 GACACGCTGAGTG
11158096 CATGCAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.21
Consensus pattern (31 bp):
GACACGCTGAGTGGAACCAGATACTTGGTGC
Found at i:11158059 original size:118 final size:117
Alignment explanation
Indices: 11157828--11158048 Score: 325
Period size: 118 Copynumber: 1.9 Consensus size: 117
11157818 CATGCTAAGT
* * *
11157828 GCATGCAGATTTCTGTGGTAACACGCTGACTTCTTGCAGTATTGTTGGGTGACACGGCACGCCCC
1 GCATGCAGATTTCAGTGGTAACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCC
* **
11157893 ATCTTGTGGTGACATGCTGAGTGAAACAAGATTGTTGGCATCACACGCTCAGG
66 ATCTTGTGGTGACACGCTGAGTGAAACAAGATACTTGG-ATCACACGCTCAGG
* * *
11157946 GCATGTAGATTTCAGTGGTGACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCATGCCCC
1 GCATGCAGATTTCAGTGGTAACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCC
* * *
11158011 ATCTTGTGGTGACACGCTGAGTGGAACCATATACTTGG
66 ATCTTGTGGTGACACGCTGAGTGAAACAAGATACTTGG
11158049 TGCGACACGC
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
118 91 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (117 bp):
GCATGCAGATTTCAGTGGTAACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCC
ATCTTGTGGTGACACGCTGAGTGAAACAAGATACTTGGATCACACGCTCAGG
Found at i:11158087 original size:118 final size:117
Alignment explanation
Indices: 11157833--11158073 Score: 297
Period size: 118 Copynumber: 2.0 Consensus size: 117
11157823 TAAGTGCATG
* * *
11157833 CAGATTTCTGTGGTAACACGCTGACTTCTTGCAGTATTGTTGGGTGACACGGCACGCCCCATCTT
1 CAGATTTCAGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCCATCTT
* ** **
11157898 GTGGTGACATGCTGAGTGAAACAAGATTGTTGGCATCACACGCTCAGGGCATG
66 GTGGTGACACGCTGAGTGAAACAAGATACTTGG-ATCACACGCTCAGGGCAAC
* * *
11157951 TAGATTTCAGTGGTGACACACTGACTTCTTGCAGTATTGTGGGGTGACACGGCATGCCCCATCTT
1 CAGATTTCAGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCCATCTT
* * * *
11158016 GTGGTGACACGCTGAGTGGAACCATATACTTGG-TGCGACACGCTGAGTGG-AAC
66 GTGGTGACACGCTGAGTGAAACAAGATACTTGGAT-C-ACACGCTCAG-GGCAAC
11158069 CAGAT
1 CAGAT
11158074 ACTTGGTGTG
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
116 1 0.01
117 1 0.01
118 100 0.96
119 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (117 bp):
CAGATTTCAGTGGTGACACGCTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCCATCTT
GTGGTGACACGCTGAGTGAAACAAGATACTTGGATCACACGCTCAGGGCAAC
Found at i:11158191 original size:118 final size:118
Alignment explanation
Indices: 11158053--11158266 Score: 358
Period size: 118 Copynumber: 1.8 Consensus size: 118
11158043 ACTTGGTGCG
*
11158053 ACACGCTGAGTGGAACCAGATACTTGGTGTGACACGCTGAGTGCATGCA-ATTTTTTATGGTGAA
1 ACACGCTGAGTGGAACCAGATACTTGGTGTGACACGCTGAGTGCATGCAGA-TTTCTATGGTGAA
*
11158117 ACGCTGACTTCTTGCTGTATTGTGGGGTGACACGACATACCCCATCTTATGGTA
65 ACGCTGACTTCTTGCTATATTGTGGGGTGACACGACATACCCCATCTTATGGTA
* * **
11158171 ACACGCTGAGTGGAACCAGATACTTGGTGTGACACGTTGAGTGCATGCAGATTTCTGTGGTGACC
1 ACACGCTGAGTGGAACCAGATACTTGGTGTGACACGCTGAGTGCATGCAGATTTCTATGGTGAAA
11158236 CGCTGACTTCTTGCTATATTGTGGGGTGACA
66 CGCTGACTTCTTGCTATATTGTGGGGTGACA
11158267 TAGCATGCCC
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
118 88 0.99
119 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (118 bp):
ACACGCTGAGTGGAACCAGATACTTGGTGTGACACGCTGAGTGCATGCAGATTTCTATGGTGAAA
CGCTGACTTCTTGCTATATTGTGGGGTGACACGACATACCCCATCTTATGGTA
Found at i:11159871 original size:21 final size:21
Alignment explanation
Indices: 11159829--11159872 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11159819 ACACCGGGTT
*
11159829 CATCATCGTGCCCATCATCAG
1 CATCATCGTGCCCATCACCAG
*
11159850 CATCATCGTGGTCC-TCACCAG
1 CATCATCGT-GCCCATCACCAG
11159871 CA
1 CA
11159873 CCGTCAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (21 bp):
CATCATCGTGCCCATCACCAG
Found at i:11162005 original size:31 final size:30
Alignment explanation
Indices: 11161970--11162223 Score: 319
Period size: 31 Copynumber: 8.2 Consensus size: 30
11161960 ATGTGATAAT
*
11161970 ACGCCATGCATATAACGTAAATTGAGATAAC
1 ACGCCATGCATATAACGTAAAATGAG-TAAC
* * *
11162001 ACGCCATACATATAACGTATAATGTGATAAC
1 ACGCCATGCATATAACGTAAAATGAG-TAAC
* *
11162032 ACGCCATGCATATAACGTAGAATGTGGTAAC
1 ACGCCATGCATATAACGTAAAATG-AGTAAC
* * *
11162063 ACACCATGCATATAATGTAAATTGCAGTAAC
1 ACGCCATGCATATAACGTAAAATG-AGTAAC
* *
11162094 ACGCCATGCATATAACATAAAATGTGGTAAC
1 ACGCCATGCATATAACGTAAAATG-AGTAAC
*
11162125 ACGCCATGCATATAACGTAAAATGTGGTAAC
1 ACGCCATGCATATAACGTAAAATG-AGTAAC
11162156 ACGCCATGCATATAACGTAAAATGTAGTAAC
1 ACGCCATGCATATAACGTAAAATG-AGTAAC
*
11162187 ACGCCATGCATATAACGTAAAATGTTGTAAC
1 ACGCCATGCATATAACGTAAAATG-AGTAAC
11162218 ACGCCA
1 ACGCCA
11162224 ACGCTAACAC
Statistics
Matches: 200, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
31 199 1.00
32 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (30 bp):
ACGCCATGCATATAACGTAAAATGAGTAAC
Found at i:11162063 original size:62 final size:62
Alignment explanation
Indices: 11161959--11162223 Score: 374
Period size: 62 Copynumber: 4.3 Consensus size: 62
11161949 GTTAACCCAT
* * * * * *
11161959 AATGTGATAATACGCCATGCATATAACGTAAATTGAGATAACACGCCATACATATAACGTAT
1 AATGTGATAACACGCCATGCATATAACGTAAAATGTGGTAACACGCCATGCATATAACGTAA
* * *
11162021 AATGTGATAACACGCCATGCATATAACGTAGAATGTGGTAACACACCATGCATATAATGT-A
1 AATGTGATAACACGCCATGCATATAACGTAAAATGTGGTAACACGCCATGCATATAACGTAA
*
11162082 AAT-TGCAGTAACACGCCATGCATATAACATAAAATGTGGTAACACGCCATGCATATAACGTAA
1 AATGTG-A-TAACACGCCATGCATATAACGTAAAATGTGGTAACACGCCATGCATATAACGTAA
* *
11162145 AATGTGGTAACACGCCATGCATATAACGTAAAATGTAGTAACACGCCATGCATATAACGTAA
1 AATGTGATAACACGCCATGCATATAACGTAAAATGTGGTAACACGCCATGCATATAACGTAA
11162207 AATGTTG-TAACACGCCA
1 AATG-TGATAACACGCCA
11162224 ACGCTAACAC
Statistics
Matches: 182, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
60 2 0.01
61 4 0.02
62 168 0.92
63 6 0.03
64 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (62 bp):
AATGTGATAACACGCCATGCATATAACGTAAAATGTGGTAACACGCCATGCATATAACGTAA
Found at i:11162118 original size:93 final size:91
Alignment explanation
Indices: 11161959--11162223 Score: 395
Period size: 93 Copynumber: 2.8 Consensus size: 91
11161949 GTTAACCCAT
* * * *
11161959 AATGTGATAATACGCCATGCATATAACGTAAATTGAGATAACACGCCATACATATAACGTATAAT
1 AATGTGGTAACACGCCATGCATATAACGTAAATTGAG-TAACACGCCATGCATATAACGTAAAAT
*
11162024 GTGATAACACGCCATGCATATAACGTAG
65 GTG-TAACACGCCATGCATATAACGTAA
* * *
11162052 AATGTGGTAACACACCATGCATATAATGTAAATTGCAGTAACACGCCATGCATATAACATAAAAT
1 AATGTGGTAACACGCCATGCATATAACGTAAATTG-AGTAACACGCCATGCATATAACGTAAAAT
11162117 GTGGTAACACGCCATGCATATAACGTAA
65 GT-GTAACACGCCATGCATATAACGTAA
*
11162145 AATGTGGTAACACGCCATGCATATAACGTAAAATGTAGTAACACGCCATGCATATAACGTAAAAT
1 AATGTGGTAACACGCCATGCATATAACGTAAATTG-AGTAACACGCCATGCATATAACGTAAAAT
11162210 GTTGTAACACGCCA
65 G-TGTAACACGCCA
11162224 ACGCTAACAC
Statistics
Matches: 156, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
93 152 0.97
94 4 0.03
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (91 bp):
AATGTGGTAACACGCCATGCATATAACGTAAATTGAGTAACACGCCATGCATATAACGTAAAATG
TGTAACACGCCATGCATATAACGTAA
Found at i:11162917 original size:47 final size:47
Alignment explanation
Indices: 11162880--11163088 Score: 253
Period size: 47 Copynumber: 4.5 Consensus size: 47
11162870 GAGTCTGACA
* *
11162880 AACTATGAACGCTGACGTGTCATAGATTCCCTCCATGGCGTGTCA-C
1 AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCACC
* * * * * * *
11162926 GACTCTGAATGTTGGCGTGTCACAGATTTCTTCTATGGCGTGTCACC
1 AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCACC
* * * *
11162973 AACTTTGAACGTTGGCGTGTCACAGATTCCCTCCATAGCGTGTCACC
1 AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCACC
* * *
11163020 AACTTTGAACGCTGACATGTCACAGATTCCCTCCATGGTGTGTCACC
1 AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCACC
11163067 AACTCTGAACGCTG--GTGTCACA
1 AACTCTGAACGCTGACGTGTCACA
11163089 ACCGTGTCAC
Statistics
Matches: 139, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
45 7 0.05
46 36 0.26
47 96 0.69
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (47 bp):
AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCACC
Found at i:11163162 original size:58 final size:58
Alignment explanation
Indices: 11163037--11163238 Score: 241
Period size: 58 Copynumber: 3.5 Consensus size: 58
11163027 AACGCTGACA
* * * * * *
11163037 TGTCACAGATTCCCTCCATGGT-GTGTCACCAACTCTGAACGCTG--GTGTCACAACCG
1 TGTCACACATTCCCACCAT-GTAGTGTCACAAACTCTAAACCCTGTCGTGTCACAACTG
11163093 TGTCACACATTCCCACCATGGT-GTGTCACAAACTCTAAACCCTGTCGTGTCACAACTG
1 TGTCACACATTCCCACCAT-GTAGTGTCACAAACTCTAAACCCTGTCGTGTCACAACTG
* * * * * *
11163151 TGTCACACATTCCAATCATGTCGTGTCACAAACTCTAAACCCTTTCGTGTCACAGCTC
1 TGTCACACATTCCCACCATGTAGTGTCACAAACTCTAAACCCTGTCGTGTCACAACTG
*
11163209 TGCCACACATTCCCACCATGTAGTGTCACA
1 TGTCACACATTCCCACCATGTAGTGTCACA
11163239 CATTTTGAAC
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
56 39 0.30
57 2 0.02
58 87 0.68
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
TGTCACACATTCCCACCATGTAGTGTCACAAACTCTAAACCCTGTCGTGTCACAACTG
Found at i:11167312 original size:15 final size:16
Alignment explanation
Indices: 11167292--11167324 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11167282 TCTACACTAC
11167292 TTTCTC-TCTCTTCTT
1 TTTCTCTTCTCTTCTT
11167307 TTTCTCTTTCTCTTCTT
1 TTTCTC-TTCTCTTCTT
11167324 T
1 T
11167325 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCTCTTCTCTTCTT
Found at i:11168288 original size:19 final size:19
Alignment explanation
Indices: 11168236--11168289 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
11168226 CTTCTTCATT
11168236 TTTAATATAATGTTTAAAAAAA
1 TTTAA-ATAAT-TTT-AAAAAA
*
11168258 TTTAAATTATTTTAAAAAA
1 TTTAAATAATTTTAAAAAA
11168277 -TTAAATAAATTTT
1 TTTAAAT-AATTTT
11168290 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 11 0.38
20 3 0.10
21 4 0.14
22 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTAAATAATTTTAAAAAA
Found at i:11169762 original size:15 final size:15
Alignment explanation
Indices: 11169728--11169764 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
11169718 TGATATAAAT
11169728 ATATTAAAATTTATA
1 ATATTAAAATTTATA
11169743 A-ATTATAAATTT-TA
1 ATATTA-AAATTTATA
11169757 ATATTAAA
1 ATATTAAA
11169765 TTAAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATTAAAATTTATA
Found at i:11178344 original size:11 final size:11
Alignment explanation
Indices: 11178328--11178358 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11178318 ATGCAACATG
11178328 CTTTTTTTTTT
1 CTTTTTTTTTT
*
11178339 CTTTTTTCTTT
1 CTTTTTTTTTT
11178350 CTTTTTTTT
1 CTTTTTTTT
11178359 ATTTTTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:11182583 original size:17 final size:17
Alignment explanation
Indices: 11182561--11182599 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11182551 AAAGGAGTAA
* *
11182561 GAAAGAAAGAAAGAGAG
1 GAAAGAAAGAAACAAAG
*
11182578 GAAAGAAGGAAACAAAG
1 GAAAGAAAGAAACAAAG
11182595 GAAAG
1 GAAAG
11182600 GTTGCTGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAACAAAG
Found at i:11192760 original size:37 final size:37
Alignment explanation
Indices: 11192690--11192776 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 37
11192680 TGTGTCTTTT
* * **
11192690 TTGTCCCAACAGAAAGTTTATTTATAGGCCTAAGTGA
1 TTGTTCCAACAGAAAGTCTATTTATAAACCTAAGTGA
* * *
11192727 TTGTTCCAACAGAAAGTCTATTTTTAAATCTAAGTTA
1 TTGTTCCAACAGAAAGTCTATTTATAAACCTAAGTGA
* *
11192764 CTATTCCAACAGA
1 TTGTTCCAACAGA
11192777 TAATTGTGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (37 bp):
TTGTTCCAACAGAAAGTCTATTTATAAACCTAAGTGA
Found at i:11195878 original size:24 final size:24
Alignment explanation
Indices: 11195840--11195902 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
11195830 GCAACACAAC
**
11195840 TGTTTA-TTTCCAACAATTATAAT
1 TGTTTATTTTCCAACAAACATAAT
11195863 TGTTTATTTTCCAACAAACATAAT
1 TGTTTATTTTCCAACAAACATAAT
* *
11195887 TGTTTGTTTTTCAACA
1 TGTTTATTTTCCAACA
11195903 TAATTATGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 6 0.17
24 29 0.83
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (24 bp):
TGTTTATTTTCCAACAAACATAAT
Found at i:11195933 original size:17 final size:17
Alignment explanation
Indices: 11195911--11195945 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11195901 CATAATTATG
11195911 TGAACAAACATAACTTT
1 TGAACAAACATAACTTT
* *
11195928 TGAACAATCATAAGTTT
1 TGAACAAACATAACTTT
11195945 T
1 T
11195946 CAAATAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (17 bp):
TGAACAAACATAACTTT
Found at i:11196455 original size:517 final size:515
Alignment explanation
Indices: 11195480--11196494 Score: 1283
Period size: 517 Copynumber: 2.0 Consensus size: 515
11195470 GATTGAGAAG
* *
11195480 TAAGGAAATGTTAAAAAATGGCTTCAAGGCGTGTATCTATGCCACTTCCTTTAAGGTTTTATTCG
1 TAAGGAAATGTTAAAAAATGGCTTCAAGGCATGTATCTATGCCACTTCCTTTAAGATTTTATTCG
* * *
11195545 CCCTCACTTATAATGTACAAAATAGTTATTGATATATAAACCTCGAAAATACAATGAAGCCTAGT
66 CCCTCACTTATAATGTACAAAATAGTTACTGACATATAAACCTCGAAAACACAATGAAGCCTAGT
* * * * **
11195610 GATTGATTGTGTTTTGCATTGATGAAATCAATCCATTGAGCATCCACTGGTGTATGACAAGATTA
131 GATTGATTGTGTTTTGCATTAATAAAATCAATCCATCGAACATCCACCAGTGTATGACAAGATTA
* * * * *
11195675 CCTAAATTTATAAGATTTCTCTGCAACAAAATGATATAAAACAAATATGGAGAATATTGAGAAAG
196 CCTAAATTTATAAAATTTCTCTACAACAAAATAATATAAAACAAATATGAAGAATATTAAGAAAG
* *
11195740 CAATGAGAGATTGTTGCGTTTTTTATTTTGTGTCTTCTTTTGTCCCAGAAGAAAGTCTATTTATA
261 CAAAGAGAGATTGTT-CGTTTTTTATTCTGTGTCTTCTTTTGTCCCAGAAGAAAGTCTATTTATA
* * ** * * *
11195805 AGCCTAAATGACTATTTCAATAAATGCAACACAACTGTTTATTTCCAACAATTATAATTGTTTAT
325 AGCCTAAATGACGATTCCAATAAACACAACACAACTGTCTATTTCCAACAATCACAATTGTTTAT
* * *
11195870 TTTCCAACAAACATAATTGTTTGTTTTTCAACATAATTATGTGAACAAACATAACTTTTGAACAA
390 TTTCCAACAAACATAATTGTTTGTTTTCCAACATAATTATGTGAACAAACACAACTCTTGAACAA
* *
11195935 TCATAAGTT-TTCAAATAACTTTCTTCCTTTCATTTTTTCATTAGAGCACATAATTGGAAAA
455 TCATAA-TTATTCAAAGAACTTTCTTCATTTCATTTTTTCATTAGAGCACATAATTGGAAAA
** * * *
11195996 TAAGGAAATGTTAGGAAATGGCTTCAAGGCATGTGTCTATGCCATTTTCTTTAAGATTTTATTCG
1 TAAGGAAATGTTAAAAAATGGCTTCAAGGCATGTATCTATGCCACTTCCTTTAAGATTTTATTCG
** * * *
11196061 TCCC-CACTTATAATGTGTAAAATAGTTACTGACGTATAAACTTC-AAATACACAATGAAGTCTA
66 -CCCTCACTTATAATGTACAAAATAGTTACTGACATATAAACCTCGAAA-ACACAATGAAGCCTA
* * * ** *
11196124 TTGATTGTTTGTGTTTTG-TTCTAATAAAATCAATTTATCGAACATTCACCAGTGTATGACAAGA
129 GTGATTGATTGTGTTTTGCAT-TAATAAAATCAATCCATCGAACATCCACCAGTGTATGACAAGA
* * * ** * *
11196188 TTACGTAACTTATATAAAATTTCTCTATAATTAAATAATCTTAAAA-AAATCTGAAGAATATTAA
193 TTACCTAAATT-TATAAAATTTCTCTACAACAAAATAAT-ATAAAACAAATATGAAGAATATTAA
*
11196252 GAAATG-AAAGAGAGATTGTT-GTTTTCTCTATTCTGTGTCTTCTTTTGTCCCATAAGAAAGTCT
256 GAAA-GCAAAGAGAGATTGTTCGTTTT-T-TATTCTGTGTCTTCTTTTGTCCCAGAAGAAAGTCT
* * * * * *
11196315 ATTTATAGGCCTAAGTGACGATTCCAATAGACACAACACAATTGTCTATTTCCAATAGTCACAAT
318 ATTTATAAGCCTAAATGACGATTCCAATAAACACAACACAACTGTCTATTTCCAACAATCACAAT
* * *
11196380 TGTTTATTTTCTAACAAATATAATTGTTTGTTTTCCAACATAATTATTTGTAA-AAACACAACTC
383 TGTTTATTTTCCAACAAACATAATTGTTTGTTTTCCAACATAATTATGTG-AACAAACACAACTC
*
11196444 TT-AAGCAATCATAATTATTCAAAGAACTTTTTTCATTTCATTTTTTCATTA
447 TTGAA-CAATCATAATTATTCAAAGAACTTTCTTCATTTCATTTTTTCATTA
11196495 TTATTGTTGA
Statistics
Matches: 424, Mismatches: 64, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
515 9 0.02
516 169 0.40
517 238 0.56
518 8 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (515 bp):
TAAGGAAATGTTAAAAAATGGCTTCAAGGCATGTATCTATGCCACTTCCTTTAAGATTTTATTCG
CCCTCACTTATAATGTACAAAATAGTTACTGACATATAAACCTCGAAAACACAATGAAGCCTAGT
GATTGATTGTGTTTTGCATTAATAAAATCAATCCATCGAACATCCACCAGTGTATGACAAGATTA
CCTAAATTTATAAAATTTCTCTACAACAAAATAATATAAAACAAATATGAAGAATATTAAGAAAG
CAAAGAGAGATTGTTCGTTTTTTATTCTGTGTCTTCTTTTGTCCCAGAAGAAAGTCTATTTATAA
GCCTAAATGACGATTCCAATAAACACAACACAACTGTCTATTTCCAACAATCACAATTGTTTATT
TTCCAACAAACATAATTGTTTGTTTTCCAACATAATTATGTGAACAAACACAACTCTTGAACAAT
CATAATTATTCAAAGAACTTTCTTCATTTCATTTTTTCATTAGAGCACATAATTGGAAAA
Found at i:11198829 original size:21 final size:20
Alignment explanation
Indices: 11198791--11198846 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
11198781 TTGGTCTATG
11198791 AAATTGAATTACTTAATTTA
1 AAATTGAATTACTTAATTTA
11198811 AAATTGAATATGA-TTAATTT-
1 AAATTGAAT-T-ACTTAATTTA
*
11198831 AAATT-AATTAATTAAT
1 AAATTGAATTACTTAAT
11198847 AAAATTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.03
18 6 0.18
19 3 0.09
20 14 0.42
21 8 0.24
22 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTGAATTACTTAATTTA
Found at i:11201690 original size:35 final size:35
Alignment explanation
Indices: 11201651--11201826 Score: 147
Period size: 35 Copynumber: 5.2 Consensus size: 35
11201641 TAGGCTTAGT
* *
11201651 CAAAACCTTTCACAATGGTTTTT-ACCGGGATCAAC
1 CAAAACCTTTCACAATGGTTTTTCA-AGGGCTCAAC
*
11201686 CAAAACC--T-A-AAGTGGTTTTTCAAAGGCTCAAC
1 CAAAACCTTTCACAA-TGGTTTTTCAAGGGCTCAAC
* *
11201718 CACAACCTTTCACAATGGTTTTTCATGGGCTCAAC
1 CAAAACCTTTCACAATGGTTTTTCAAGGGCTCAAC
* *
11201753 CAAAACC--T-A-AAGTGATTTTTCAAAGGCTCAAC
1 CAAAACCTTTCACAA-TGGTTTTTCAAGGGCTCAAC
* * * *
11201785 CACAACC-TACAACAATGGTTTTTCACGGGATCAAC
1 CAAAACCTTTC-ACAATGGTTTTTCAAGGGCTCAAC
11201820 CAAAACC
1 CAAAACC
11201827 CAACAACTAA
Statistics
Matches: 113, Mismatches: 17, Indels: 22
0.74 0.11 0.14
Matches are distributed among these distances:
31 4 0.04
32 46 0.41
33 3 0.03
34 1 0.01
35 55 0.49
36 4 0.04
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (35 bp):
CAAAACCTTTCACAATGGTTTTTCAAGGGCTCAAC
Found at i:11201733 original size:67 final size:67
Alignment explanation
Indices: 11201654--11201826 Score: 278
Period size: 67 Copynumber: 2.6 Consensus size: 67
11201644 GCTTAGTCAA
*
11201654 AACCTTTCACAATGGTTTTT-ACCGGGATCAACCAAAACCTAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCTAAAGTGATTTTTCAAAGGCTCAAC
11201718 CAC
65 CAC
* *
11201721 AACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCTAAAGTGATTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCTAAAGTGATTTTTCAAAGGCTCAACC
11201786 AC
66 AC
*
11201788 AACC-TACAACAATGGTTTTTCACGGGATCAACCAAAACC
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACC
11201827 CAACAACTAA
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
66 2 0.02
67 95 0.97
68 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCTAAAGTGATTTTTCAAAGGCTCAACC
AC
Found at i:11202916 original size:19 final size:20
Alignment explanation
Indices: 11202892--11202929 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11202882 CTATAAATAC
*
11202892 CTTGAA-TTTCTAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
11202911 CTTGAATTTTCCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
11202930 GGTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:11203389 original size:223 final size:222
Alignment explanation
Indices: 11203001--11203445 Score: 829
Period size: 223 Copynumber: 2.0 Consensus size: 222
11202991 AAACTTCCAT
11203001 AACTTTCTCTCTCTAGCTCCAATTTTCATGCTTTTGGTGCACCCTTCCATAAACCCTTGTGCTAT
1 AACTTTCTCTCTCTAGCTCCAATTTTCATGCTTTTGGTGCACCCTTCCATAAACCCTTGTGCTAT
*
11203066 TTCATCTTCTCACTTCAAAAACCTTGAAATATCTTGTTTTCATACTTTCTCTCACTAGTTGGGCG
66 TTCATCTTCTCACTTCAAAAACCTTGAAATATCTTGTTTTCATACTTTCTCTCACTAGTTGGGCA
11203131 TTCTAGAAAGAGAAAGAGAGAATCACTTCATTGATTTGGAAGCTATTGGAAGAGAATCCAACTAC
131 TTCTAGAAAGAGAAAGAGAGAATCACTTCATTGATTTGGAAGCTATTGGAAGAGAATCCAACTAC
*
11203196 AAAGGAACCCTAGGGTGAGTGATGNCAC
196 AAAAGAACCCTAGGGTGAGTGATG-CAC
11203224 AACTTTCTCTCTCTAGCTCCAATTTTCATGCTTTTGGTGCACCCTTCCATAAACCCTTGTGCTAT
1 AACTTTCTCTCTCTAGCTCCAATTTTCATGCTTTTGGTGCACCCTTCCATAAACCCTTGTGCTAT
*
11203289 TTCATCTTTTCACTTCAAAAACCTTGAAATATCTTGTTTTCATACTTTCTCTCACTAGTTGGGCA
66 TTCATCTTCTCACTTCAAAAACCTTGAAATATCTTGTTTTCATACTTTCTCTCACTAGTTGGGCA
*
11203354 TTCTAGAGAGAGAAAGAGAGAATCAC-TCAATTGATTTGGAAGCTATTGGAAGAGAATCCAACTA
131 TTCTAGAAAGAGAAAGAGAGAATCACTTC-ATTGATTTGGAAGCTATTGGAAGAGAATCCAACTA
11203418 CAAAAGAACCCTAGGGTGAGTGATGCAC
195 CAAAAGAACCCTAGGGTGAGTGATGCAC
11203446 CAAGTTTGAT
Statistics
Matches: 217, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
222 5 0.02
223 212 0.98
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (222 bp):
AACTTTCTCTCTCTAGCTCCAATTTTCATGCTTTTGGTGCACCCTTCCATAAACCCTTGTGCTAT
TTCATCTTCTCACTTCAAAAACCTTGAAATATCTTGTTTTCATACTTTCTCTCACTAGTTGGGCA
TTCTAGAAAGAGAAAGAGAGAATCACTTCATTGATTTGGAAGCTATTGGAAGAGAATCCAACTAC
AAAAGAACCCTAGGGTGAGTGATGCAC
Found at i:11204014 original size:43 final size:43
Alignment explanation
Indices: 11203937--11204051 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
11203927 GTAATTATAT
* * * *
11203937 TGACTCGGCTATGTGTGAGTAGGGAGTGCGCATAAATCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCACATAAACCG-GTGA
* * *
11203980 TGACCCGGTTATGTGCGAGTAGGGAGTGTACATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCACATAAACCGGTGA
* * *
11204023 TGACCCAGCCATGTGCGAGTAGGAAGTGC
1 TGACCCGGCTATGTGCGAGTAGGGAGTGC
11204052 GCATGAGCTG
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCACATAAACCGGTGA
Found at i:11205856 original size:37 final size:37
Alignment explanation
Indices: 11205815--11205885 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
11205805 ATCAGCATCC
*
11205815 AAATCCTAACCATAAGCAATTATCACAGCAGAATGTT
1 AAATCCTAACCATAAGCAATTATCACAACAGAATGTT
*
11205852 AAATCCTAACCATCAGCAATTATCACAACAGAAT
1 AAATCCTAACCATAAGCAATTATCACAACAGAAT
11205886 ATCATAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (37 bp):
AAATCCTAACCATAAGCAATTATCACAACAGAATGTT
Found at i:11215278 original size:40 final size:38
Alignment explanation
Indices: 11215234--11215336 Score: 145
Period size: 38 Copynumber: 2.7 Consensus size: 38
11215224 CCCCAGTTCA
*
11215234 TGTGCATCCCCTCACATCGTGCACATAGCTAGA-GTCATCG
1 TGTGCATCCCCCCACATCGTGCACAT--CTA-ATGTCATCG
*
11215274 TGTGCATCCCCCCACATCGTGCACATCTAATGTCGTCG
1 TGTGCATCCCCCCACATCGTGCACATCTAATGTCATCG
*
11215312 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
11215337 CGGGCAATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
37 1 0.02
38 33 0.56
40 25 0.42
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.24
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACATCTAATGTCATCG
Found at i:11227035 original size:22 final size:22
Alignment explanation
Indices: 11227010--11227051 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11227000 ATAAATTGGC
* *
11227010 ACTTGCAATGAAAGCTTGACTT
1 ACTTGAAATCAAAGCTTGACTT
*
11227032 ACTTGAAATCAAATCTTGAC
1 ACTTGAAATCAAAGCTTGAC
11227052 GTGTCAAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (22 bp):
ACTTGAAATCAAAGCTTGACTT
Found at i:11240899 original size:106 final size:105
Alignment explanation
Indices: 11240667--11240982 Score: 560
Period size: 106 Copynumber: 3.0 Consensus size: 105
11240657 AAGTACCTTC
* * *
11240667 TCATTGACCTAGATATGAGAAACAATGGCAAAACCACAAGGAAACCAGTATGGAGAAATTTGAAA
1 TCATTGACCTAGATATGTGAAACAATGGCAAAACCGCAAGGAAACCAGAATGGAGAAATTTGAAA
*
11240732 CATGTGAATAACATAAGAAATTGAGTTGTATGAAAATGAT
66 CATGTGAATAACATAAGAAATTGAGTTCTATGAAAATGAT
* *
11240772 TCATTGACCTAGATATGTGAAACAATGGCAAAACTGCAAGGAAACCAGCATGGAGAAATTTGAAA
1 TCATTGACCTAGATATGTGAAACAATGGCAAAACCGCAAGGAAACCAGAATGGAGAAATTTGAAA
11240837 CATGTGAATTAACATAAGAAATTGAGTTCTATGAAAATGAT
66 CATGTGAA-TAACATAAGAAATTGAGTTCTATGAAAATGAT
11240878 TCATTGACCTAGATATGTGAAACAATGGCAAAACCGCAAGGAAACCAGAATGGAGAAATTTGAAA
1 TCATTGACCTAGATATGTGAAACAATGGCAAAACCGCAAGGAAACCAGAATGGAGAAATTTGAAA
*
11240943 CATGTGAATAACATAAGAAATTGAGTTTTATGAAAATGAT
66 CATGTGAATAACATAAGAAATTGAGTTCTATGAAAATGAT
11240983 ATTAATCTAC
Statistics
Matches: 202, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
105 100 0.50
106 102 0.50
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.24
Consensus pattern (105 bp):
TCATTGACCTAGATATGTGAAACAATGGCAAAACCGCAAGGAAACCAGAATGGAGAAATTTGAAA
CATGTGAATAACATAAGAAATTGAGTTCTATGAAAATGAT
Found at i:11253141 original size:40 final size:40
Alignment explanation
Indices: 11253092--11253218 Score: 100
Period size: 38 Copynumber: 3.2 Consensus size: 40
11253082 ATTTTGGGTG
11253092 ATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTA
1 ATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTA
* * ** * * * *** *
11253132 ATTCCT-AAAATTA-AGGATAGAATTT-TAATTT-TGGGTG
1 ATTCATAAAAAATAGAAAATTG-TTTTCTACTTTAAAAGTA
*
11253169 ATTCATAAAAAATAGAAAATTATTTTCTACTTTAAAAGTA
1 ATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTA
*
11253209 ATTCCTAAAA
1 ATTCATAAAA
11253219 TTAAGGATAG
Statistics
Matches: 58, Mismatches: 24, Indels: 10
0.63 0.26 0.11
Matches are distributed among these distances:
37 7 0.12
38 18 0.31
39 17 0.29
40 16 0.28
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (40 bp):
ATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTA
Found at i:11253178 original size:37 final size:37
Alignment explanation
Indices: 11253132--11253252 Score: 91
Period size: 37 Copynumber: 3.2 Consensus size: 37
11253122 TTTAAAAGTA
*
11253132 ATTCCTAAAATTAAGGATAGAATTTTAATTTTGGGTG
1 ATTCATAAAATTAAGGATAGAATTTTAATTTTGGGTG
* * * * * * *** *
11253169 ATTCATAAAA-AATAGAAAATTATTTTCTACTTTAAAAGTA
1 ATTCATAAAATTA-AGGATA-GAATTT-TAATTT-TGGGTG
*
11253209 ATTCCTAAAATTAAGGATAGAATTTTAATTTTGGGTG
1 ATTCATAAAATTAAGGATAGAATTTTAATTTTGGGTG
11253246 ATTCATA
1 ATTCATA
11253253 CAAAATAGGA
Statistics
Matches: 56, Mismatches: 23, Indels: 10
0.63 0.26 0.11
Matches are distributed among these distances:
36 1 0.02
37 21 0.38
38 9 0.16
39 9 0.16
40 15 0.27
41 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (37 bp):
ATTCATAAAATTAAGGATAGAATTTTAATTTTGGGTG
Found at i:11253203 original size:77 final size:77
Alignment explanation
Indices: 11253076--11253316 Score: 412
Period size: 77 Copynumber: 3.1 Consensus size: 77
11253066 AATGCCATAT
11253076 ATTTTAATTTTGGGTGATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTAATTCCTAAA
1 ATTTTAATTTTGGGTGATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTAATTCCTAAA
11253141 ATTAAGGATAGA
66 ATTAAGGATAGA
*
11253153 ATTTTAATTTTGGGTGATTCATAAAAAATAGAAAATTATTTTCTACTTTAAAAGTAATTCCTAAA
1 ATTTTAATTTTGGGTGATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTAATTCCTAAA
11253218 ATTAAGGATAGA
66 ATTAAGGATAGA
* * *
11253230 ATTTTAATTTTGGGTGATTCATACAAAATAGGAAATTGTTTTCTACTTTAAACA-TAATTCATAA
1 ATTTTAATTTTGGGTGATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAA-AGTAATTCCTAA
*
11253294 AATTAAGGATAGT
65 AATTAAGGATAGA
*
11253307 ATCTTAATTT
1 ATTTTAATTT
11253317 GGAAAATTCA
Statistics
Matches: 156, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
77 155 0.99
78 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (77 bp):
ATTTTAATTTTGGGTGATTCATAAAAAATAGAAAATTGTTTTCTACTTTAAAAGTAATTCCTAAA
ATTAAGGATAGA
Found at i:11253234 original size:40 final size:40
Alignment explanation
Indices: 11253114--11253234 Score: 106
Period size: 40 Copynumber: 3.1 Consensus size: 40
11253104 TAGAAAATTG
11253114 TTTTCTACTTTAAAAGTAATTCCTAAAATTAAGGATAGAA
1 TTTTCTACTTTAAAAGTAATTCCTAAAATTAAGGATAGAA
* *** * * * * * **
11253154 -TTT-TAATTT-TGGGTGATTCATAAAA-AATAGAAAATTA
1 TTTTCTACTTTAAAAGTAATTCCTAAAATTA-AGGATAGAA
11253191 TTTTCTACTTTAAAAGTAATTCCTAAAATTAAGGATAGAA
1 TTTTCTACTTTAAAAGTAATTCCTAAAATTAAGGATAGAA
11253231 TTTT
1 TTTT
11253235 AATTTTGGGT
Statistics
Matches: 54, Mismatches: 22, Indels: 10
0.63 0.26 0.12
Matches are distributed among these distances:
36 1 0.02
37 16 0.30
38 8 0.15
39 8 0.15
40 20 0.37
41 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (40 bp):
TTTTCTACTTTAAAAGTAATTCCTAAAATTAAGGATAGAA
Found at i:11254229 original size:20 final size:19
Alignment explanation
Indices: 11254187--11254243 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
11254177 TCTTGGTATA
11254187 TTAAATTGAATTAGTTAAT
1 TTAAATTGAATTAGTTAAT
*
11254206 TTAAATTGAATGT-GATTCAT
1 TTAAATTGAAT-TAG-TTAAT
*
11254226 TTAAATT-AATTAATTAAT
1 TTAAATTGAATTAGTTAAT
11254244 AAAATTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.16
19 15 0.47
20 12 0.38
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (19 bp):
TTAAATTGAATTAGTTAAT
Found at i:11261226 original size:19 final size:20
Alignment explanation
Indices: 11261186--11261226 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11261176 TCTCCAATTA
* *
11261186 TCAACTGGCCGAGGGTTTTC
1 TCAACTGGCCCAGGGATTTC
11261206 TCAACTGGCCCA-GGATTTC
1 TCAACTGGCCCAGGGATTTC
11261225 TC
1 TC
11261227 TTTAAACCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.29
Consensus pattern (20 bp):
TCAACTGGCCCAGGGATTTC
Found at i:11261887 original size:42 final size:42
Alignment explanation
Indices: 11261759--11261890 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 42
11261749 GCATATGACT
* *
11261759 GGGTCAGCATC-AGCTTATGCGCACTCCTACTCGCACATAACC
1 GGGTTAGCATCGA-CTTATGCGCACTCCTACTCACACATAACC
** * * * * *
11261801 AAGTCAGCATCGGCTTATGCGCACTCCCACTAACACACAACC
1 GGGTTAGCATCGACTTATGCGCACTCCTACTCACACATAACC
* * *
11261843 GGGTTAGCATCGATTTATGCACACTCCTACTCACACATAGCC
1 GGGTTAGCATCGACTTATGCGCACTCCTACTCACACATAACC
11261885 GGGTTA
1 GGGTTA
11261891 ATATCATTAC
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (42 bp):
GGGTTAGCATCGACTTATGCGCACTCCTACTCACACATAACC
Found at i:11263464 original size:20 final size:19
Alignment explanation
Indices: 11263430--11263470 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
11263420 CGTCAAAATC
*
11263430 GATGGATGTTTAAATGCAT
1 GATGGATGATTAAATGCAT
*
11263449 GATGGAATGATTAAATGTAT
1 GATGG-ATGATTAAATGCAT
11263469 GA
1 GA
11263471 CGAGTGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (19 bp):
GATGGATGATTAAATGCAT
Found at i:11269003 original size:16 final size:17
Alignment explanation
Indices: 11268979--11269011 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11268969 AACACTTTAA
*
11268979 TTAATTTAAAT-ATATT
1 TTAAATTAAATCATATT
11268995 TTAAATTAAATCATATT
1 TTAAATTAAATCATATT
11269012 ACAAATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTAAATCATATT
Found at i:11270986 original size:22 final size:23
Alignment explanation
Indices: 11270947--11270993 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
11270937 ATTTCTATGC
11270947 ATTACTACAAAAACTAAGC-CAA
1 ATTACTACAAAAACTAAGCTCAA
*
11270969 ATTACTATC-AAAATTAAGCTCAA
1 ATTACTA-CAAAAACTAAGCTCAA
11270992 AT
1 AT
11270994 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (23 bp):
ATTACTACAAAAACTAAGCTCAA
Found at i:11272886 original size:25 final size:27
Alignment explanation
Indices: 11272858--11272922 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
11272848 TTTTAATTTT
11272858 TTTTTCATGAAAT-TA-TTTTTTGAAA
1 TTTTTCATGAAATATATTTTTTTGAAA
** *
11272883 TTTTTTTTGAAATATATTTTTTTTGAAT
1 TTTTTCATGAAATATA-TTTTTTTGAAA
11272911 TTTTTACATGAA
1 TTTTT-CATGAA
11272923 CCTATACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 11 0.35
26 2 0.06
28 14 0.45
29 4 0.13
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (27 bp):
TTTTTCATGAAATATATTTTTTTGAAA
Found at i:11272890 original size:12 final size:13
Alignment explanation
Indices: 11272865--11272904 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
11272855 TTTTTTTTCA
11272865 TGAAATTATTTTT
1 TGAAATTATTTTT
11272878 TGAAATT-TTTTT
1 TGAAATTATTTTT
11272890 TGAAATATATTTTT
1 TGAAAT-TATTTTT
11272904 T
1 T
11272905 TTGAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.44
13 8 0.32
14 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
TGAAATTATTTTT
Found at i:11272903 original size:27 final size:26
Alignment explanation
Indices: 11272856--11272915 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 26
11272846 AATTTTAATT
11272856 TTTTTTTCATGAAATTA-TTTTTTGAAA
1 TTTTTTT-ATGAAATTATTTTTTTG-AA
11272883 TTTTTTT-TGAAATATATTTTTTTTGAA
1 TTTTTTTATGAAAT-TA-TTTTTTTGAA
11272910 TTTTTT
1 TTTTTT
11272916 ACATGAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 6 0.20
26 2 0.07
27 15 0.50
28 7 0.23
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (26 bp):
TTTTTTTATGAAATTATTTTTTTGAA
Found at i:11278472 original size:22 final size:23
Alignment explanation
Indices: 11278433--11278479 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
11278423 ATTTCTATGC
11278433 ATTACTACAAAAGCTAAGC-CAA
1 ATTACTACAAAAGCTAAGCTCAA
*
11278455 ATTACTATCAAAA-TTAAGCTCAA
1 ATTACTA-CAAAAGCTAAGCTCAA
11278478 AT
1 AT
11278480 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.26
Consensus pattern (23 bp):
ATTACTACAAAAGCTAAGCTCAA
Found at i:11278805 original size:15 final size:15
Alignment explanation
Indices: 11278765--11278802 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
11278755 ATTTAAATTT
11278765 AAATTATTAA-ATATA
1 AAATTA-TAATATATA
11278780 AAATTATAATATATA
1 AAATTATAATATATA
11278795 AAA-TATAA
1 AAATTATAA
11278803 ATAGTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTATAATATATA
Found at i:11278855 original size:16 final size:17
Alignment explanation
Indices: 11278829--11278871 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
11278819 TACAGGATTT
11278829 TATACAATAGTTAAAT-A
1 TATA-AATAGTTAAATAA
11278846 TATAAATAGTTAAATAA
1 TATAAATAGTTAAATAA
11278863 TATAAATAG
1 TATAAATAG
11278872 AAAGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (17 bp):
TATAAATAGTTAAATAA
Found at i:11279268 original size:49 final size:50
Alignment explanation
Indices: 11279171--11279293 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 50
11279161 ATTTTGAGGA
* * * *
11279171 AACCATT-AAAAATATATAGTAAATAAATAATTTCATAAATTTTGAAAAG
1 AACCATTAAAAAATATATAATAAATAAAGAACTTCAAAAATTTTGAAAAG
11279220 AACCATTAAAAAATATATAATAAAT-AAGAACTTCTAAAAATTTT-AAAAG
1 AACCATTAAAAAATATATAATAAATAAAGAACTTC-AAAAATTTTGAAAAG
** * *
11279269 GGCCATTAATATATATAATAATAAA
1 AACCATTAAAAAATAT-ATAATAAA
11279294 AATTAAAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
49 31 0.49
50 32 0.51
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (50 bp):
AACCATTAAAAAATATATAATAAATAAAGAACTTCAAAAATTTTGAAAAG
Found at i:11283334 original size:30 final size:31
Alignment explanation
Indices: 11283314--11283370 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
11283304 ATGTGTTTTG
11283314 TTTT-AAAA-TTTTACAATTTTATTCTTATT
1 TTTTAAAAATTTTTACAATTTTATTCTTATT
* *
11283343 TTTTAAAAATTTTTATAATTTTACTCTT
1 TTTTAAAAATTTTTACAATTTTATTCTT
11283371 TCAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 4 0.17
31 16 0.67
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTAAAAATTTTTACAATTTTATTCTTATT
Found at i:11283638 original size:2 final size:2
Alignment explanation
Indices: 11283633--11283680 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
11283623 TGGAAAGGAA
11283633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11283675 AT AT AT
1 AT AT AT
11283681 TTACCGAAAN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11289350 original size:27 final size:27
Alignment explanation
Indices: 11289320--11289374 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
11289310 AATCAAGATG
11289320 CTGAGTCAAATAACGTTTAACAAATAT
1 CTGAGTCAAATAACGTTTAACAAATAT
* *
11289347 CTGAGTCAGATAACGTTTAAGAAATAT
1 CTGAGTCAAATAACGTTTAACAAATAT
11289374 C
1 C
11289375 AGGTAACAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (27 bp):
CTGAGTCAAATAACGTTTAACAAATAT
Found at i:11292161 original size:2 final size:2
Alignment explanation
Indices: 11292156--11292184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11292146 TATAAGTATT
11292156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11292185 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11292217 original size:17 final size:17
Alignment explanation
Indices: 11292195--11292228 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11292185 TTTTTTTTTT
11292195 TTCAAACATGCATCAAG
1 TTCAAACATGCATCAAG
11292212 TTCAAACATGCATCAAG
1 TTCAAACATGCATCAAG
11292229 GATATCTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
TTCAAACATGCATCAAG
Found at i:11299013 original size:37 final size:36
Alignment explanation
Indices: 11298972--11299043 Score: 135
Period size: 37 Copynumber: 2.0 Consensus size: 36
11298962 AACCATTTTG
11298972 AAAACATTTGAGAGTTCTAACCTTCAACAGTCAATNA
1 AAAACATTTGAGAGTTCTAACCTTCAACAGTCAAT-A
11299009 AAAACATTTGAGAGTTCTAACCTTCAACAGTCAAT
1 AAAACATTTGAGAGTTCTAACCTTCAACAGTCAAT
11299044 GTAATCACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.28
Consensus pattern (36 bp):
AAAACATTTGAGAGTTCTAACCTTCAACAGTCAATA
Found at i:11300285 original size:10 final size:11
Alignment explanation
Indices: 11300261--11300293 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
11300251 TGTGAGGATA
11300261 AAGGAGAAAATG
1 AAGGA-AAAATG
11300273 AAGGAAAAA-G
1 AAGGAAAAATG
11300283 AAGGAAAAATG
1 AAGGAAAAATG
11300294 GGAGGAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 5 0.25
12 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (11 bp):
AAGGAAAAATG
Found at i:11304264 original size:11 final size:11
Alignment explanation
Indices: 11304248--11304284 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
11304238 GTTACAAAAT
11304248 ATCAACATAAA
1 ATCAACATAAA
11304259 ATCAACATAAA
1 ATCAACATAAA
*
11304270 ATCAGCA-AAA
1 ATCAACATAAA
11304280 ATCAA
1 ATCAA
11304285 GATGTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.62, C:0.19, G:0.03, T:0.16
Consensus pattern (11 bp):
ATCAACATAAA
Found at i:11304271 original size:132 final size:132
Alignment explanation
Indices: 11304029--11304271 Score: 362
Period size: 132 Copynumber: 1.8 Consensus size: 132
11304019 GTTTGTAGAA
* * *
11304029 AAGCTTTAGAGGAGATGCTTAGTGTGGTTGTGATTAAGGTAGGTAGGTTGTATTTATAGGCAGAG
1 AAGCTTTAGAGGAGATGCTTAGTGTCGTTGTGACTAAGGTAGGTAGGCTGTATTTATAGGCAGAG
* * * *
11304094 TAGAGAGTTAACATTACAAAATATCAGCATAAAATCAGCAAAAAATAAAAAAAATAAAGATGCTG
66 CAAAGAGTTAACATTACAAAATATCAACATAAAATCAACAAAAAATAAAAAAAATAAAGATGCTG
11304159 AG
131 AG
* *
11304161 AAGCTTTAGAGGAG-TGGTTCGGTGTCGTTGTGACTAAGGTAGGTAGGCTGTATTTATAGGCAGA
1 AAGCTTTAGAGGAGATGCTT-AGTGTCGTTGTGACTAAGGTAGGTAGGCTGTATTTATAGGCAGA
** *
11304225 GCAAAGAGTTAATGTTACAAAATATCAACATAAAATCAACATAAAAT
65 GCAAAGAGTTAACATTACAAAATATCAACATAAAATCAACAAAAAAT
11304272 CAGCAAAAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
131 4 0.04
132 94 0.96
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (132 bp):
AAGCTTTAGAGGAGATGCTTAGTGTCGTTGTGACTAAGGTAGGTAGGCTGTATTTATAGGCAGAG
CAAAGAGTTAACATTACAAAATATCAACATAAAATCAACAAAAAATAAAAAAAATAAAGATGCTG
AG
Found at i:11304430 original size:81 final size:81
Alignment explanation
Indices: 11304332--11304491 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 81
11304322 GAATATCAGC
* * * * *
11304332 ATAAAATCTGTGAAAAAT-TAGAGAAAATCAAGATGTTGAGAAGCTTTAAAAGAACGGCTTGGTG
1 ATAAAATCAGTGAAAAATCAAAAG-AAATCAAGATGCTGAGAAGCTTTAAAAGAACAGCTTGGTG
11304396 TGGTTATGACTAAGGAT
65 TGGTTATGACTAAGGAT
* * ** *
11304413 ATAAAATCAGTGAAAAATCAAAAGAAATCAAGATGCTGAGAAGCTTTAGAGGAGTAGCTTGTTGT
1 ATAAAATCAGTGAAAAATCAAAAGAAATCAAGATGCTGAGAAGCTTTAAAAGAACAGCTTGGTGT
11304478 GGTTATGACTAAGG
66 GGTTATGACTAAGG
11304492 TAGGTAGGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
81 65 0.96
82 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (81 bp):
ATAAAATCAGTGAAAAATCAAAAGAAATCAAGATGCTGAGAAGCTTTAAAAGAACAGCTTGGTGT
GGTTATGACTAAGGAT
Found at i:11305887 original size:11 final size:11
Alignment explanation
Indices: 11305871--11305897 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11305861 GTTACAGAAT
11305871 ATCAACATAAA
1 ATCAACATAAA
11305882 ATCAACATAAA
1 ATCAACATAAA
11305893 ATCAA
1 ATCAA
11305898 TGAAAATCAA
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:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (11 bp):
ATCAACATAAA
Found at i:11312052 original size:36 final size:36
Alignment explanation
Indices: 11312012--11312083 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
11312002 TAAAAAGATT
11312012 GTAAGATAACCAAATCAACGATAATATTGTAATCTA
1 GTAAGATAACCAAATCAACGATAATATTGTAATCTA
* *
11312048 GTAAGATAACTAAATCAATGATAATATTGTAATCTA
1 GTAAGATAACCAAATCAACGATAATATTGTAATCTA
11312084 ACAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (36 bp):
GTAAGATAACCAAATCAACGATAATATTGTAATCTA
Found at i:11314044 original size:19 final size:19
Alignment explanation
Indices: 11314020--11314069 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
11314010 CATAAATATG
*
11314020 TACATTGGATATGGGGAGA
1 TACATTGGATATGGGGAAA
* * *
11314039 TACATTGGGTATTGTGAAA
1 TACATTGGATATGGGGAAA
*
11314058 TACAATGGATAT
1 TACATTGGATAT
11314070 TCACATATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (19 bp):
TACATTGGATATGGGGAAA
Found at i:11319168 original size:3 final size:3
Alignment explanation
Indices: 11319160--11319185 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11319150 TCTGTTCCTT
11319160 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
11319186 GATTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11329224 original size:14 final size:15
Alignment explanation
Indices: 11329198--11329226 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11329188 TTTAGTTAAA
11329198 TTTTTTTATTAAGTT
1 TTTTTTTATTAAGTT
11329213 TTTTTTTA-TAAGTT
1 TTTTTTTATTAAGTT
11329227 ATCATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTTTATTAAGTT
Found at i:11337418 original size:13 final size:14
Alignment explanation
Indices: 11337396--11337451 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
11337386 TGAATAAAAA
11337396 TTAATATATTAAAT
1 TTAATATATTAAAT
* *
11337410 TTAATTATTAATAAAAA
1 TTAA-TA-T-ATTAAAT
11337427 TTAATATATTAAAT
1 TTAATATATTAAAT
11337441 TTAAT-TATTAA
1 TTAATATATTAA
11337452 TAAAAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 6 0.17
14 14 0.40
15 3 0.09
16 3 0.09
17 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATATATTAAAT
Found at i:11337426 original size:31 final size:31
Alignment explanation
Indices: 11337388--11337458 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
11337378 GAGATAGATG
11337388 AATAAAAATTAATATATTAAATTTAATTATT
1 AATAAAAATTAATATATTAAATTTAATTATT
11337419 AATAAAAATTAATATATTAAATTTAATTATT
1 AATAAAAATTAATATATTAAATTTAATTATT
11337450 AATAAAAAT
1 AATAAAAAT
11337459 AATTTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AATAAAAATTAATATATTAAATTTAATTATT
Found at i:11337427 original size:18 final size:18
Alignment explanation
Indices: 11337406--11337458 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
11337396 TTAATATATT
11337406 AAATTTAATTATTAATAA
1 AAATTTAATTATTAATAA
*
11337424 AAA-TTAA-TA-T-AT-T
1 AAATTTAATTATTAATAA
11337437 AAATTTAATTATTAATAA
1 AAATTTAATTATTAATAA
11337455 AAAT
1 AAAT
11337459 AATTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.11
14 6 0.21
15 3 0.11
16 3 0.11
17 6 0.21
18 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAATTATTAATAA
Found at i:11337822 original size:21 final size:21
Alignment explanation
Indices: 11337798--11337841 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11337788 ATTTCTATTT
*
11337798 AAACTTATAATAC-TAAATATA
1 AAAC-TATAACACATAAATATA
*
11337819 AAACTATGACACATAAATATA
1 AAACTATAACACATAAATATA
11337840 AA
1 AA
11337842 TAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (21 bp):
AAACTATAACACATAAATATA
Found at i:11338284 original size:13 final size:14
Alignment explanation
Indices: 11338260--11338297 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
11338250 CATATGAGCA
*
11338260 AATAGTATAAAAAT
1 AATAATATAAAAAT
*
11338274 ATTAA-ATAAAAAT
1 AATAATATAAAAAT
11338287 AATAATATAAA
1 AATAATATAAA
11338298 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AATAATATAAAAAT
Found at i:11338322 original size:21 final size:22
Alignment explanation
Indices: 11338266--11338325 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 22
11338256 AGCAAATAGT
11338266 ATAAAAATATTAAATAAAAATAATA
1 ATAAAAAT-TT-AA-AAAAATAATA
*
11338291 ATATAAATTTAAAAAAATAA-A
1 ATAAAAATTTAAAAAAATAATA
11338312 A-AAAAACTTTAAAA
1 ATAAAAA-TTTAAAA
11338326 TTGAATAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 9 0.28
22 8 0.25
23 2 0.06
24 2 0.06
25 7 0.22
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAAAAATTTAAAAAAATAATA
Found at i:11339810 original size:37 final size:37
Alignment explanation
Indices: 11339750--11339820 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
11339740 GTTAAAAATG
*
11339750 AAACCACAATTAAACCTAATGGCATGGGTCAGAATCA
1 AAACCACAATTAAACCTAATGGCATAGGTCAGAATCA
*
11339787 AAACCACAATT-AACTCTAGTGGCATAGGTCAGAA
1 AAACCACAATTAAAC-CTAATGGCATAGGTCAGAA
11339821 GTATATCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (37 bp):
AAACCACAATTAAACCTAATGGCATAGGTCAGAATCA
Found at i:11340838 original size:33 final size:34
Alignment explanation
Indices: 11340792--11340865 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
11340782 TTAAAAGACA
*
11340792 AAAT-ATACTCTTCATTAAATTTA-AATAATACT
1 AAATAATAATCTTCATTAAATTTATAATAATACT
*
11340824 AAATAATAATCTTCATTAAATTTATAATAATATT
1 AAATAATAATCTTCATTAAATTTATAATAATACT
11340858 AAATAATA
1 AAATAATA
11340866 TTCCTTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 4 0.11
33 18 0.47
34 16 0.42
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (34 bp):
AAATAATAATCTTCATTAAATTTATAATAATACT
Found at i:11340864 original size:10 final size:10
Alignment explanation
Indices: 11340849--11340923 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
11340839 TTAAATTTAT
11340849 AATAATATTA
1 AATAATATTA
*
11340859 AATAATATTCCT
1 AATAATATT--A
*
11340871 TATAATATT-
1 AATAATATTA
* *
11340880 TATTATAGTTA
1 AATAATA-TTA
11340891 AATAATATT-
1 AATAATATTA
11340900 AAT-ATATTA
1 AATAATATTA
11340909 AATAATATTTA
1 AATAATA-TTA
11340920 AATA
1 AATA
11340924 TTTTCATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 12 0.23
10 16 0.30
11 12 0.23
12 8 0.15
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (10 bp):
AATAATATTA
Found at i:11340881 original size:34 final size:34
Alignment explanation
Indices: 11340792--11340899 Score: 113
Period size: 34 Copynumber: 3.3 Consensus size: 34
11340782 TTAAAAGACA
* *
11340792 AAAT-ATACTCTTCATTAAATTTA-AATAATACT
1 AAATAATATTCTTCATTAAATTTATAATAATATT
*
11340824 AAATAATAATCTTCATTAAATTTATAATAATATT
1 AAATAATATTCTTCATTAAATTTATAATAATATT
11340858 AAATAATATTCCTT-A-TAATATTTAT--T-ATAGTT
1 AAATAATATT-CTTCATTAA-ATTTATAATAATA-TT
11340890 AAATAATATT
1 AAATAATATT
11340900 AATATATTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
31 3 0.04
32 17 0.25
33 21 0.31
34 24 0.35
35 3 0.04
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (34 bp):
AAATAATATTCTTCATTAAATTTATAATAATATT
Found at i:11340911 original size:18 final size:19
Alignment explanation
Indices: 11340872--11340917 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
11340862 AATATTCCTT
*
11340872 ATAATATTTATTATAGTTAA
1 ATAATA-TTAATATAGTTAA
11340892 ATAATATTAATATA-TTAA
1 ATAATATTAATATAGTTAA
11340910 ATAATATT
1 ATAATATT
11340918 TAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 7 0.28
20 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATAATATTAATATAGTTAA
Found at i:11340916 original size:12 final size:11
Alignment explanation
Indices: 11340810--11340923 Score: 59
Period size: 11 Copynumber: 10.8 Consensus size: 11
11340800 TCTTCATTAA
11340810 ATTTAAATAAT
1 ATTTAAATAAT
*
11340821 A-CTAAATAAT
1 ATTTAAATAAT
* *
11340831 AATCTTCATTAA-
1 -AT-TTAAATAAT
11340843 ATTTATAATAAT
1 ATTTA-AATAAT
11340855 A-TTAAATAAT
1 ATTTAAATAAT
*
11340865 ATTCCT-TATAAT
1 ATT--TAAATAAT
*
11340877 ATTT--ATTAT
1 ATTTAAATAAT
*
11340886 AGTTAAATAAT
1 ATTTAAATAAT
11340897 A-TT-AAT-AT
1 ATTTAAATAAT
11340905 A-TTAAATAAT
1 ATTTAAATAAT
11340915 ATTTAAATA
1 ATTTAAATA
11340924 TTTTCATTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
8 5 0.06
9 13 0.16
10 23 0.29
11 24 0.30
12 9 0.11
13 6 0.08
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (11 bp):
ATTTAAATAAT
Found at i:11340924 original size:18 final size:18
Alignment explanation
Indices: 11340872--11340925 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
11340862 AATATTCCTT
*
11340872 ATAATATTTATTATAGTTAA
1 ATAATATTTA-AATA-TTAA
11340892 ATAATA-TTAATATATTAA
1 ATAATATTTAA-ATATTAA
11340910 ATAATATTTAAATATT
1 ATAATATTTAAATATT
11340926 TTCATTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAATATTTAAATATTAA
Found at i:11361634 original size:23 final size:23
Alignment explanation
Indices: 11361608--11361659 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
11361598 ATATATGGAG
* *
11361608 TGGCGTTACTAGTTATTATAGAA
1 TGGCGTGACTAGTTATTATAAAA
* * *
11361631 TGGCGTGAGTATTTATTCTAAAA
1 TGGCGTGACTAGTTATTATAAAA
11361654 TGGCGT
1 TGGCGT
11361660 AAGTAGAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (23 bp):
TGGCGTGACTAGTTATTATAAAA
Found at i:11361664 original size:23 final size:23
Alignment explanation
Indices: 11361620--11361664 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11361610 GCGTTACTAG
* *
11361620 TTATTATAGAATGGCGTGAGTAT
1 TTATTATAAAATGGCGTAAGTAT
*
11361643 TTATTCTAAAATGGCGTAAGTA
1 TTATTATAAAATGGCGTAAGTA
11361665 GAAAAATGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (23 bp):
TTATTATAAAATGGCGTAAGTAT
Found at i:11364671 original size:78 final size:78
Alignment explanation
Indices: 11364582--11364749 Score: 228
Period size: 78 Copynumber: 2.2 Consensus size: 78
11364572 TTTGAGAGAG
* * * *
11364582 ACATCTTGTGTTTTAGATTTGTTTTTCCCCCAGTCACCCCACTCAGTTTGCTTCGTTGTACTGGT
1 ACATCTTGTGTTTTAGATTTGATTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
11364647 CACAACTGCTGCA
66 CACAACTGCTGCA
* * * * * *
11364660 ACATCTTGTGTTTTAGATTTGATTGTCCCCCAATCATAGCAGTCATTTTGTTTCGTTGTTCTGGT
1 ACATCTTGTGTTTTAGATTTGATTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
*
11364725 CACAATTGCTGCA
66 CACAACTGCTGCA
*
11364738 ACATCATGTGTT
1 ACATCTTGTGTT
11364750 GCAAATATCA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.40
Consensus pattern (78 bp):
ACATCTTGTGTTTTAGATTTGATTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
CACAACTGCTGCA
Found at i:11368163 original size:118 final size:118
Alignment explanation
Indices: 11368006--11368399 Score: 516
Period size: 118 Copynumber: 3.4 Consensus size: 118
11367996 AATGCCTAAT
* * * *** *
11368006 AACTAGTGAACAAATGCC-CAAAACAAGAGGCGAATTGCACAAGTCACGCCCCACCACTCTCGCA
1 AACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCTCGCA
* *
11368070 ATACATAACAACAGGTTATGCAATATATAAAAACCAGTCACGCAAGCCTAAAA
66 ATACATAACAACAGGTAACGCAATATATAAAAACCAGTCACGCAAGCCTAAAA
* * * * *
11368123 AACTATTGAACAAAAGTCTCAAAACAACATATGAATTGCACAAGTCATGCGTCACCACTCTCGCA
1 AACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCTCGCA
* * * *
11368188 ATACATAAAAACAGGTCACGCAATATATAAAAACCAGTCATGCAAGCCTTAAA
66 ATACATAACAACAGGTAACGCAATATATAAAAACCAGTCACGCAAGCCTAAAA
*
11368241 AACTACTAAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCT----
1 AACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCTCGCA
* * *
11368302 -TGC-T-ACAACAGGTAACGCAATATATAAAAACCAATCACGCACTGCCTAAAA
66 ATACATAACAACAGGTAACGCAATATATAAAAACCAGTCACGCA-AGCCTAAAA
*
11368353 AACTACTGAACAAAAGCCTCAAAACAACACATAAATTGCACAAGTCA
1 AACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCA
11368400 ATCACGCACC
Statistics
Matches: 245, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
111 33 0.13
112 53 0.22
113 2 0.01
117 15 0.06
118 142 0.58
ACGTcount: A:0.44, C:0.27, G:0.12, T:0.17
Consensus pattern (118 bp):
AACTACTGAACAAAAGCCTCAAAACAACACATGAATTGCACAAGTCACGCGCCACCACTCTCGCA
ATACATAACAACAGGTAACGCAATATATAAAAACCAGTCACGCAAGCCTAAAA
Found at i:11368681 original size:9 final size:9
Alignment explanation
Indices: 11368667--11368741 Score: 87
Period size: 9 Copynumber: 8.3 Consensus size: 9
11368657 ACACGATTAA
*
11368667 TAACACGTT
1 TAACACGAT
11368676 TAACACGAT
1 TAACACGAT
*
11368685 TAACACGTT
1 TAACACGAT
*
11368694 TAATACGAT
1 TAACACGAT
*
11368703 TAACACGTT
1 TAACACGAT
*
11368712 TAACACAAT
1 TAACACGAT
* *
11368721 TAATACGTT
1 TAACACGAT
11368730 TAACACGAT
1 TAACACGAT
11368739 TAA
1 TAA
11368742 ATAAAAATAT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (9 bp):
TAACACGAT
Found at i:11368690 original size:18 final size:18
Alignment explanation
Indices: 11368667--11368741 Score: 123
Period size: 18 Copynumber: 4.2 Consensus size: 18
11368657 ACACGATTAA
11368667 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
*
11368685 TAACACGTTTAATACGAT
1 TAACACGTTTAACACGAT
*
11368703 TAACACGTTTAACACAAT
1 TAACACGTTTAACACGAT
*
11368721 TAATACGTTTAACACGAT
1 TAACACGTTTAACACGAT
11368739 TAA
1 TAA
11368742 ATAAAAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:11368714 original size:27 final size:27
Alignment explanation
Indices: 11368675--11368741 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
11368665 AATAACACGT
**
11368675 TTAACACGATTAACACGTTTAATACGA
1 TTAACACGATTAACACAATTAATACGA
* *
11368702 TTAACACGTTTAACACAATTAATACGT
1 TTAACACGATTAACACAATTAATACGA
11368729 TTAACACGATTAA
1 TTAACACGATTAA
11368742 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (27 bp):
TTAACACGATTAACACAATTAATACGA
Found at i:11368762 original size:20 final size:20
Alignment explanation
Indices: 11368737--11368826 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
11368727 GTTTAACACG
11368737 ATTAAATAAAAATATTTATA
1 ATTAAATAAAAATATTTATA
*
11368757 ATTAAAT-ATAAT-TTTATTA
1 ATTAAATAAAAATATTTA-TA
* ** *
11368776 TTTAAATTTAAA-ATCTATA
1 ATTAAATAAAAATATTTATA
*
11368795 ATT--ATAAAAATAATTATA
1 ATTAAATAAAAATATTTATA
* *
11368813 ATAAAACAAAAATA
1 ATTAAATAAAAATA
11368827 GTAATAACAT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.10
18 11 0.21
19 16 0.31
20 20 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAAATAAAAATATTTATA
Found at i:11369046 original size:18 final size:18
Alignment explanation
Indices: 11369011--11369074 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
11369001 TGTCACATAT
* *
11369011 ACACGTTTAAACATGATA
1 ACACGATTAAACACGATA
* *
11369029 ATACGATTGAACACGATA
1 ACACGATTAAACACGATA
11369047 ACACGATTAAACACGATA
1 ACACGATTAAACACGATA
11369065 ACACGATTAA
1 ACACGATTAA
11369075 GTAAACGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:11369059 original size:10 final size:9
Alignment explanation
Indices: 11369031--11369074 Score: 56
Period size: 8 Copynumber: 4.9 Consensus size: 9
11369021 ACATGATAAT
11369031 ACGATTGAAC
1 ACGATT-AAC
11369041 ACGA-TAAC
1 ACGATTAAC
11369049 ACGATTAAAC
1 ACGATT-AAC
11369059 ACGA-TAAC
1 ACGATTAAC
11369067 ACGATTAA
1 ACGATTAA
11369075 GTAAACGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 14 0.45
9 6 0.19
10 11 0.35
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (9 bp):
ACGATTAAC
Found at i:11370645 original size:26 final size:26
Alignment explanation
Indices: 11370616--11370740 Score: 86
Period size: 26 Copynumber: 5.1 Consensus size: 26
11370606 CACGTCATGC
11370616 AATGCTCAACAAATATTCAGTCACGT
1 AATGCTCAACAAATATTCAGTCACGT
* * * *
11370642 AATGC-CTATAAATA---AGTCAAGC
1 AATGCTCAACAAATATTCAGTCACGT
* *
11370664 AACGCTTAACAAATATTCAGTCACGT
1 AATGCTCAACAAATATTCAGTCACGT
* * * * * *
11370690 AAT-TTCTATAAACA---AGTCATGC
1 AATGCTCAACAAATATTCAGTCACGT
11370712 AATGCTCAACAAATATTCAGTCACGT
1 AATGCTCAACAAATATTCAGTCACGT
11370738 AAT
1 AAT
11370741 ATACAGGAAC
Statistics
Matches: 67, Mismatches: 24, Indels: 16
0.63 0.22 0.15
Matches are distributed among these distances:
22 19 0.28
23 13 0.19
25 13 0.19
26 22 0.33
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (26 bp):
AATGCTCAACAAATATTCAGTCACGT
Found at i:11370675 original size:48 final size:48
Alignment explanation
Indices: 11370586--11370740 Score: 229
Period size: 48 Copynumber: 3.2 Consensus size: 48
11370576 AGGTAGATAA
* * *
11370586 AGTCACGCAATGCCTACAAACACGTCATGCAATGCTCAACAAATATTC
1 AGTCACGTAATGCCTATAAACAAGTCATGCAATGCTCAACAAATATTC
* * * *
11370634 AGTCACGTAATGCCTATAAATAAGTCAAGCAACGCTTAACAAATATTC
1 AGTCACGTAATGCCTATAAACAAGTCATGCAATGCTCAACAAATATTC
**
11370682 AGTCACGTAATTTCTATAAACAAGTCATGCAATGCTCAACAAATATTC
1 AGTCACGTAATGCCTATAAACAAGTCATGCAATGCTCAACAAATATTC
11370730 AGTCACGTAAT
1 AGTCACGTAAT
11370741 ATACAGGAAC
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (48 bp):
AGTCACGTAATGCCTATAAACAAGTCATGCAATGCTCAACAAATATTC
Done.