Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 185 of 190
Found at i:54931511 original size:4 final size:4
Alignment explanation
Indices: 54931502--54931528 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
54931492 TTTCATACTT
54931502 GATA GATA GATA GATA GATA GATA GAT
1 GATA GATA GATA GATA GATA GATA GAT
54931529 GCTATTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
GATA
Found at i:54931767 original size:16 final size:16
Alignment explanation
Indices: 54931737--54931773 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
54931727 CACCTGGAGC
*
54931737 GTATTG-TGTCCCATT
1 GTATTGATGACCCATT
54931752 GTATTGATGACCCATT
1 GTATTGATGACCCATT
54931768 GT-TTGA
1 GTATTGA
54931774 ACTGGTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (16 bp):
GTATTGATGACCCATT
Found at i:54937685 original size:5 final size:5
Alignment explanation
Indices: 54937675--54937699 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54937665 TTCCATTGCA
54937675 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
54937700 TAAAAAAATT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:54938365 original size:46 final size:46
Alignment explanation
Indices: 54938312--54938450 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
54938302 ACATTGCTAT
* *
54938312 AACTCAGTATGGTTTTCTTCACGGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
54938358 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
54938404 AACTCAGTATGGGTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
54938450 A
1 A
54938451 CTTTGCCATG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:54941858 original size:4 final size:4
Alignment explanation
Indices: 54941849--54941886 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
54941839 TGTTTATCAC
*
54941849 GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
54941887 GCAGGAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:54953352 original size:15 final size:16
Alignment explanation
Indices: 54953334--54953366 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54953324 CTAAATTAAA
54953334 AATAATG-CAAAATTG
1 AATAATGACAAAATTG
*
54953349 AATACTGACAAAATTG
1 AATAATGACAAAATTG
54953365 AA
1 AA
54953367 AAATCTAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (16 bp):
AATAATGACAAAATTG
Found at i:54954071 original size:20 final size:21
Alignment explanation
Indices: 54954032--54954071 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54954022 TCATATGGCT
*
54954032 AAATTTAATGAAATGTTATGA
1 AAATTTAATGAAATGCTATGA
*
54954053 AAATTTCATG-AATGCTATG
1 AAATTTAATGAAATGCTATG
54954072 GTATGTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (21 bp):
AAATTTAATGAAATGCTATGA
Found at i:54954271 original size:47 final size:46
Alignment explanation
Indices: 54954202--54954317 Score: 135
Period size: 47 Copynumber: 2.5 Consensus size: 46
54954192 ATTGATGAAA
* * *
54954202 AAGACCATGGTTGGACCATGGCAAT-ATGTGATATGTGATTTCCGTAT
1 AAGACCATGGTTGGGCTATGGC-ATCATGTGATATGTG-CTTCCGTAT
* * *
54954249 AAGACCATAGTTGGGCTATGGCATCGGTGTGATATGTGCTTCCGTGT
1 AAGACCATGGTTGGGCTATGGCATC-ATGTGATATGTGCTTCCGTAT
*
54954296 AAGACCATGGCTGGGCTATGGC
1 AAGACCATGGTTGGGCTATGGC
54954318 TTTGGTGTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 2 0.03
47 46 0.78
48 11 0.19
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (46 bp):
AAGACCATGGTTGGGCTATGGCATCATGTGATATGTGCTTCCGTAT
Found at i:54954325 original size:47 final size:50
Alignment explanation
Indices: 54954228--54954336 Score: 143
Period size: 47 Copynumber: 2.2 Consensus size: 50
54954218 CATGGCAATA
* *
54954228 TGTGATATGTGATTTCCGTATAAGACCATAGTTGGGCTATGGCATC-G-G
1 TGTGATATGTGACTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTG
* * * *
54954276 TGTGATATGTG-CTTCCGTGTAAGACCATGGCTGGGCTATGGCTTTGGTG
1 TGTGATATGTGACTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTG
54954325 TGTGATATGTGA
1 TGTGATATGTGA
54954337 TTATGTGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 28 0.54
48 12 0.23
49 12 0.23
ACGTcount: A:0.19, C:0.14, G:0.32, T:0.35
Consensus pattern (50 bp):
TGTGATATGTGACTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTG
Found at i:54954929 original size:25 final size:25
Alignment explanation
Indices: 54954901--54955035 Score: 149
Period size: 25 Copynumber: 5.6 Consensus size: 25
54954891 ACCTTAGCGC
54954901 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
54954926 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
** *
54954951 GCTCTCTGATTATTAGCATGTTAGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
54954976 GCTCTCCG---ATTAGCACATCTGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
54954998 GCTCTCTG--TA-TAGCACTTTAGT
1 GCTCTCTGATTATTAGCACATCAGT
54955020 GCTCTCT-ATTCATTAG
1 GCTCTCTGATT-ATTAG
54955036 TGCATAATAA
Statistics
Matches: 93, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
22 33 0.35
23 2 0.02
24 1 0.01
25 57 0.61
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATCAGT
Found at i:54960186 original size:46 final size:46
Alignment explanation
Indices: 54960085--54960323 Score: 270
Period size: 46 Copynumber: 5.4 Consensus size: 46
54960075 TACGTATGGT
* *
54960085 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
54960128 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
54960174 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
* * *
54960220 CACTTATCACTTTGTCACCGCTT-ATCA-CT---TGT-TCT--TG--AT
1 CACTTATCACTTTGTCA---CTTGATCAGATAAGTGTAGCTAATGCTAC
* *
54960259 CAGATTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CA-CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
54960306 CACTTATCACTTTGTCAC
1 CACTTATCACTTTGTCAC
54960324 CGCTTATCAC
Statistics
Matches: 165, Mismatches: 14, Indels: 31
0.79 0.07 0.15
Matches are distributed among these distances:
37 3 0.02
38 4 0.02
39 4 0.02
40 13 0.08
41 2 0.01
42 3 0.02
43 14 0.08
44 8 0.05
45 22 0.13
46 81 0.49
47 4 0.02
48 4 0.02
49 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
Found at i:54960285 original size:86 final size:86
Alignment explanation
Indices: 54960177--54960349 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
54960167 AGGCTACCAC
54960177 TTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACCGCT
1 TTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACCGCT
54960242 TATCACTTGTTCTTGATCAGA
66 TATCACTTGTTCTTGATCAGA
54960263 TTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACCGCT
1 TTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACCGCT
54960328 TATCACTTGTTCTTGATCAGA
66 TATCACTTGTTCTTGATCAGA
54960349 T
1 T
54960350 AAGTGTAGCT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (86 bp):
TTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACCGCT
TATCACTTGTTCTTGATCAGA
Found at i:54970167 original size:51 final size:51
Alignment explanation
Indices: 54970084--54970265 Score: 301
Period size: 51 Copynumber: 3.6 Consensus size: 51
54970074 CGGATCACAT
* * *
54970084 TTATCACTTGTCACTTGTCCCTAATCAGATAAGTGTAGCTAAATCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
54970135 TTATCACTTGTTACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
54970186 TTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
54970237 TTATCACTTGTCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTTGTCACTGATCAGA
54970266 AGTACTCAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 121 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:54982869 original size:2 final size:2
Alignment explanation
Indices: 54982864--54982896 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54982854 TCAAAATTTA
54982864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54982897 AAATGAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54988405 original size:2 final size:2
Alignment explanation
Indices: 54988398--54988451 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
54988388 CAATCATTTC
54988398 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
54988440 AT AT AT AT AT AT
1 AT AT AT AT AT AT
54988452 TGTGTCAGCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54998428 original size:20 final size:20
Alignment explanation
Indices: 54998372--54998428 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
54998362 ACTTTATTTT
*
54998372 AAAAATTAAAATAAAAATTTA
1 AAAAATTAAAA-AAAAATTAA
* ****
54998393 AAAAAGTATTTTAAAATTAA
1 AAAAATTAAAAAAAAATTAA
54998413 AAAAATTAAAAAAAAA
1 AAAAATTAAAAAAAAA
54998429 GTATTTTAAA
Statistics
Matches: 25, Mismatches: 11, Indels: 1
0.68 0.30 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATTAAAAAAAAATTAA
Found at i:54998430 original size:31 final size:30
Alignment explanation
Indices: 54998392--54998472 Score: 110
Period size: 33 Copynumber: 2.6 Consensus size: 30
54998382 ATAAAAATTT
54998392 AAAAAAGTATTTTAAAATTAAA-AAAATTAAA
1 AAAAAAGTATTTTAAAA--AAATAAAATTAAA
54998423 AAAAAAGTATTTTAAAAAAATTTTAAAATTAAA
1 AAAAAAGTATTTTAAAAAAA---TAAAATTAAA
54998456 AAAAAAGTATTTTAAAA
1 AAAAAAGTATTTTAAAA
54998473 GTATTTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.07
31 17 0.37
33 26 0.57
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (30 bp):
AAAAAAGTATTTTAAAAAAATAAAATTAAA
Found at i:54998439 original size:11 final size:11
Alignment explanation
Indices: 54998425--54998482 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
54998415 AAATTAAAAA
54998425 AAAAGTATTTT
1 AAAAGTATTTT
**
54998436 AAAAAAATTTT
1 AAAAGTATTTT
* ****
54998447 AAAATTAAAAA
1 AAAAGTATTTT
54998458 AAAAGTATTTT
1 AAAAGTATTTT
54998469 AAAAGTATTTT
1 AAAAGTATTTT
54998480 AAA
1 AAA
54998483 GTTAAAAATA
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:54998439 original size:15 final size:15
Alignment explanation
Indices: 54998392--54998442 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
54998382 ATAAAAATTT
54998392 AAAAAAGTATTTTAA
1 AAAAAAGTATTTTAA
* * *
54998407 AATTAAAA-AAATTAAA
1 AA--AAAAGTATTTTAA
54998423 AAAAAAGTATTTTAA
1 AAAAAAGTATTTTAA
54998438 AAAAA
1 AAAAA
54998443 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 4 0.15
15 12 0.44
16 7 0.26
17 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AAAAAAGTATTTTAA
Found at i:54998453 original size:42 final size:40
Alignment explanation
Indices: 54998372--54998459 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 40
54998362 ACTTTATTTT
*
54998372 AAAAATTAAAATAAAAATTTAAAAAAGTATTTTAAAATTAA
1 AAAAATTAAAAAAAAAATTTAAAAAAG-ATTTTAAAATTAA
54998413 AAAAATTAAAAAAAAAGTATTTTAAAAAA-ATTTTAAAATTAA
1 AAAAATTAAAAAAAAA--A-TTTAAAAAAGATTTTAAAATTAA
54998455 AAAAA
1 AAAAA
54998460 AAGTATTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
41 15 0.35
42 18 0.42
43 1 0.02
44 9 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (40 bp):
AAAAATTAAAAAAAAAATTTAAAAAAGATTTTAAAATTAA
Found at i:54998456 original size:33 final size:33
Alignment explanation
Indices: 54998414--54998495 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
54998404 TAAAATTAAA
54998414 AAAATTAAAAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAAAAGTATTTTAAAAAAATTTT
**
54998447 AAAATTAAAAAAAAAGTATTTTAAAAGTATTTT
1 AAAATTAAAAAAAAAGTATTTTAAAAAAATTTT
*
54998480 AAAGTTAAAAATAAAA
1 AAAATTAAAAA-AAAA
54998496 ATAAAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 41 0.91
34 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (33 bp):
AAAATTAAAAAAAAAGTATTTTAAAAAAATTTT
Found at i:54999903 original size:2 final size:2
Alignment explanation
Indices: 54999896--54999931 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54999886 TTGACTTCTC
54999896 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
54999932 GTAACACCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55001347 original size:46 final size:46
Alignment explanation
Indices: 55001269--55001545 Score: 491
Period size: 46 Copynumber: 6.0 Consensus size: 46
55001259 ACATTGCTAT
* *
55001269 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * * *
55001315 AACTCAATATGGTTTTCTTCGCTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
55001361 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
55001407 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
55001453 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
55001499 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
55001545 A
1 A
55001546 CTTTGCCATG
Statistics
Matches: 222, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 222 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:55002824 original size:17 final size:16
Alignment explanation
Indices: 55002777--55002818 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
55002767 TTTTAAATCG
*
55002777 CAAAAATTCACTAAAT
1 CAAAAATTCACTAATT
55002793 CACAAAATTCACTAATT
1 CA-AAAATTCACTAATT
55002810 CAAAAATTC
1 CAAAAATTC
55002819 TTCTAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (16 bp):
CAAAAATTCACTAATT
Found at i:55004062 original size:17 final size:18
Alignment explanation
Indices: 55004040--55004073 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55004030 TCATTCCAAT
*
55004040 AATTCATTCAAT-TCAAC
1 AATTCATACAATGTCAAC
55004057 AATTCATACAATGTCAA
1 AATTCATACAATGTCAA
55004074 TTCTGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (18 bp):
AATTCATACAATGTCAAC
Found at i:55004697 original size:41 final size:38
Alignment explanation
Indices: 55004599--55004700 Score: 100
Period size: 37 Copynumber: 2.6 Consensus size: 38
55004589 TCGAAGCAAT
55004599 AGTTGACACCCAGTGTCTCATCG-GCGAAGCCGAAGTA
1 AGTTGACACCCAGTGTCTCATCGAGCGAAGCCGAAGTA
** ** * *
55004636 AGTTGGTACCCAGTAACTCATCGAATCTAA-CCGAAGTAA
1 AGTTGACACCCAGTGTCTCATCG-AGCGAAGCCGAAGT-A
55004675 CAGTATGACACCCAGTGTCTCATCGA
1 -AGT-TGACACCCAGTGTCTCATCGA
55004701 CTCAAGGTCG
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
37 19 0.38
38 7 0.14
39 4 0.08
40 4 0.08
41 16 0.32
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (38 bp):
AGTTGACACCCAGTGTCTCATCGAGCGAAGCCGAAGTA
Found at i:55005269 original size:7 final size:7
Alignment explanation
Indices: 55005257--55005281 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55005247 ATTAAAACAC
55005257 AATAATT
1 AATAATT
55005264 AATAATT
1 AATAATT
55005271 AATAATT
1 AATAATT
55005278 AATA
1 AATA
55005282 GATTTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATAATT
Found at i:55013617 original size:10 final size:10
Alignment explanation
Indices: 55013604--55013654 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
55013594 ATAAAAAAAT
55013604 AAAATAGCAA
1 AAAATAGCAA
*
55013614 AAAATAGTAA
1 AAAATAGCAA
*
55013624 AAAATACCAA
1 AAAATAGCAA
55013634 GAAAATAGCAA
1 -AAAATAGCAA
*
55013645 AAAAAAGCAA
1 AAAATAGCAA
55013655 TTTTTTTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 26 0.74
11 9 0.26
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAATAGCAA
Found at i:55013640 original size:21 final size:20
Alignment explanation
Indices: 55013604--55013648 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
55013594 ATAAAAAAAT
* *
55013604 AAAATAGCAAAAAATAGTAA
1 AAAATACCAAAAAATAGCAA
55013624 AAAATACCAAGAAAATAGCAA
1 AAAATACCAA-AAAATAGCAA
55013645 AAAA
1 AAAA
55013649 AAGCAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (20 bp):
AAAATACCAAAAAATAGCAA
Found at i:55021685 original size:2 final size:2
Alignment explanation
Indices: 55021678--55021710 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
55021668 AACTACATTC
*
55021678 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55021711 GCTGTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:55038583 original size:26 final size:26
Alignment explanation
Indices: 55038533--55038589 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
55038523 ATATTAATAT
* *
55038533 AAAATACAATGGATTAAATAGTTAAA
1 AAAATACAACGGATTAAAAAGTTAAA
* *
55038559 AAAATATAACGGATTAAAAATTTAAA
1 AAAATACAACGGATTAAAAAGTTAAA
*
55038585 TAAAT
1 AAAAT
55038590 TTGGATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.28
Consensus pattern (26 bp):
AAAATACAACGGATTAAAAAGTTAAA
Found at i:55042989 original size:4 final size:4
Alignment explanation
Indices: 55042974--55043002 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
55042964 GTTGCATTCT
55042974 TTAA TTAA -TAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
55043003 GTTTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:55060645 original size:2 final size:2
Alignment explanation
Indices: 55060638--55060672 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55060628 GCTACTAATC
55060638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55060673 GCAACATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55068540 original size:31 final size:30
Alignment explanation
Indices: 55068505--55068600 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
55068495 TCAATATATT
*
55068505 ATTTGGTACCTAAGTTTAGTTTCAATATTCA
1 ATTTGATACCTAAGTTT-GTTTCAATATTCA
** * *
55068536 ATTTGATATTTAAGTTT-TTT--TTTTCTCA
1 ATTTGATACCTAAGTTTGTTTCAATAT-TCA
* *
55068564 ATTTGATACCTGAGTTTGGTTTCAATGTTCA
1 ATTTGATACCTAAGTTT-GTTTCAATATTCA
55068595 ATTTGA
1 ATTTGA
55068601 AATTCAGACC
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
27 2 0.04
28 17 0.34
29 3 0.06
30 3 0.06
31 23 0.46
32 2 0.04
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (30 bp):
ATTTGATACCTAAGTTTGTTTCAATATTCA
Found at i:55070708 original size:20 final size:20
Alignment explanation
Indices: 55070657--55070708 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
55070647 AAATCATTGC
55070657 AATATATGTAAAAATAATTT
1 AATATATGTAAAAATAATTT
* *
55070677 AA-A-ATATAAAAAT-TTATT
1 AATATATGTAAAAATAAT-TT
55070695 AATATATGTAAAAA
1 AATATATGTAAAAA
55070709 CAACTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.04
18 13 0.50
19 2 0.08
20 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AATATATGTAAAAATAATTT
Found at i:55070823 original size:20 final size:20
Alignment explanation
Indices: 55070798--55070837 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55070788 AATATTTTCC
*
55070798 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55070818 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
55070838 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55070839 original size:34 final size:35
Alignment explanation
Indices: 55070786--55070852 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
55070776 CAAACACCAG
*
55070786 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
55070821 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55070853 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55070844 original size:14 final size:14
Alignment explanation
Indices: 55070821--55070860 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55070811 ACAGAAAAGT
*
55070821 AAAACATTTTTCAG
1 AAAACATTTTACAG
* *
55070835 AAATCATTTTACGG
1 AAAACATTTTACAG
55070849 AAAACATTTTAC
1 AAAACATTTTAC
55070861 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:55085920 original size:21 final size:23
Alignment explanation
Indices: 55085895--55085936 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
55085885 AAATTTAAAA
55085895 TAATTAAAT-AT-TAAATTATGC
1 TAATTAAATAATATAAATTATGC
55085916 TAATTAAATAATATAAATTAT
1 TAATTAAATAATATAAATTAT
55085937 AATTTACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATTAAATAATATAAATTATGC
Found at i:55086391 original size:29 final size:30
Alignment explanation
Indices: 55086332--55086395 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
55086322 AATCTATATA
* *
55086332 TTTATAATTTTTAAAGGATTAAATTAAAAT
1 TTTATAATTTTTAAAGGATCAAAATAAAAT
* * *
55086362 TTTATAA-TTTTAATGGGTCAAAATATAAT
1 TTTATAATTTTTAAAGGATCAAAATAAAAT
55086391 TTTAT
1 TTTAT
55086396 CTTTATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGATCAAAATAAAAT
Found at i:55087230 original size:25 final size:26
Alignment explanation
Indices: 55087193--55087254 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
55087183 CTAGTATTTT
* * *
55087193 AAAATTTATTATTATATTTTCTTGAA
1 AAAATATATTATTATATATACTTGAA
* *
55087219 AAAATATA-TATTTTATATACTTTAA
1 AAAATATATTATTATATATACTTGAA
55087244 AAAATAT-TTAT
1 AAAATATATTAT
55087255 GTATTTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (26 bp):
AAAATATATTATTATATATACTTGAA
Found at i:55095085 original size:2 final size:2
Alignment explanation
Indices: 55095078--55095103 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55095068 GTAGAACTCA
55095078 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
55095104 CTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55097673 original size:15 final size:16
Alignment explanation
Indices: 55097624--55097676 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
55097614 CTTAAGCTAA
55097624 GTTGAAAAAATTAAGT
1 GTTGAAAAAATTAAGT
* * *
55097640 GCTAAAAAAATTAAAT
1 GTTGAAAAAATTAAGT
55097656 GTTGAAAAAA-TAAGT
1 GTTGAAAAAATTAAGT
55097671 GTTGAA
1 GTTGAA
55097677 TTTAAGTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 10 0.32
16 21 0.68
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.28
Consensus pattern (16 bp):
GTTGAAAAAATTAAGT
Found at i:55113555 original size:13 final size:14
Alignment explanation
Indices: 55113536--55113569 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
55113526 ACATTTTTTT
55113536 TTCTAACGATACTA
1 TTCTAACGATACTA
55113550 -TCTAACGATACTA
1 TTCTAACGATACTA
55113563 TTCTAAC
1 TTCTAAC
55113570 ATGTAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:55118409 original size:45 final size:45
Alignment explanation
Indices: 55118268--55118420 Score: 216
Period size: 45 Copynumber: 3.4 Consensus size: 45
55118258 CACCAGTATA
* * *
55118268 CAGTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAC
1 CAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* * * *
55118314 CTGTAATAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
55118359 TAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCAAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
55118404 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
55118421 GTCGGCACAT
Statistics
Matches: 93, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
45 88 0.95
46 5 0.05
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:55128535 original size:26 final size:26
Alignment explanation
Indices: 55128505--55128556 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
55128495 TCATAGCTGA
* *
55128505 AATGAATTATATGTATAAATGTTTAT
1 AATGAACTATATGTATAAATGATTAT
55128531 AATGAACTATATGTATAAATGATTAT
1 AATGAACTATATGTATAAATGATTAT
55128557 GAATCTCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (26 bp):
AATGAACTATATGTATAAATGATTAT
Found at i:55128664 original size:26 final size:26
Alignment explanation
Indices: 55128630--55128681 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
55128620 CTTGAGATTC
* *
55128630 ATAATCATTTATACATATAGTTCATT
1 ATAAACATTTATACATATAATTCATT
55128656 ATAAACATTTATACATATAATTCATT
1 ATAAACATTTATACATATAATTCATT
55128682 TCATTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAAACATTTATACATATAATTCATT
Found at i:55138377 original size:12 final size:12
Alignment explanation
Indices: 55138360--55138384 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55138350 TCGGCAGATC
55138360 AGCAAGTAGAAG
1 AGCAAGTAGAAG
55138372 AGCAAGTAGAAG
1 AGCAAGTAGAAG
55138384 A
1 A
55138385 TGAGTTGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.32, T:0.08
Consensus pattern (12 bp):
AGCAAGTAGAAG
Found at i:55146350 original size:15 final size:13
Alignment explanation
Indices: 55146318--55146342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55146308 TCATCAATTG
55146318 GTAATTTAGTTAT
1 GTAATTTAGTTAT
55146331 GTAATTTAGTTA
1 GTAATTTAGTTA
55146343 AATGTAATAT
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
GTAATTTAGTTAT
Found at i:55166388 original size:24 final size:25
Alignment explanation
Indices: 55166361--55166410 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
55166351 TCTTCACCTA
*
55166361 TTTATTAATTT-TTTTGTTAAAAAT
1 TTTATTAATTTGTATTGTTAAAAAT
*
55166385 TTTATTTATTTGTATTGTTAAAAAT
1 TTTATTAATTTGTATTGTTAAAAAT
55166410 T
1 T
55166411 GGTGTAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (25 bp):
TTTATTAATTTGTATTGTTAAAAAT
Found at i:55167022 original size:4 final size:4
Alignment explanation
Indices: 55167013--55167041 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
55167003 GTTCCATTTC
55167013 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
55167042 GTATGCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:55186784 original size:95 final size:95
Alignment explanation
Indices: 55186640--55186814 Score: 273
Period size: 95 Copynumber: 1.8 Consensus size: 95
55186630 TTTTTGTTAA
*
55186640 GAAATCTCAATTGAGGAATTTAAACAAGATTCCATCAACTCATACTATTATTCAAATTACAGATT
1 GAAATATCAATTGAGGAATTTAAACAAGATTCCATCAACTCATACTATTATTCAAATTACAGATT
55186705 T-AAAGATGCATTCGTCAATGCAATTTCATT
66 TGAAA-ATGCATTCGTCAATGCAATTTCATT
* * * *
55186735 GAAATATCAATTGAGGAA-TTAAACAATATTTCATCAACTCGTAATTATTATTCAAATTACAGAT
1 GAAATATCAATTGAGGAATTTAAACAAGATTCCATCAACTCAT-ACTATTATTCAAATTACAGAT
55186799 TTGAAAATGCATTCGT
65 TTGAAAATGCATTCGT
55186815 TCATCAACGC
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
94 21 0.29
95 49 0.67
96 3 0.04
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (95 bp):
GAAATATCAATTGAGGAATTTAAACAAGATTCCATCAACTCATACTATTATTCAAATTACAGATT
TGAAAATGCATTCGTCAATGCAATTTCATT
Found at i:55189575 original size:22 final size:21
Alignment explanation
Indices: 55189547--55189599 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
55189537 GCCCGGACCG
55189547 ATTTTTAATAAACACAAAAAAT
1 ATTTTTAATAAACA-AAAAAAT
*
55189569 ATTTTTAAAATAAATAAAAAAAT
1 ATTTTT--AATAAACAAAAAAAT
55189592 ATTTTTAA
1 ATTTTTAA
55189600 AGTATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 2 0.07
22 6 0.21
23 13 0.46
24 7 0.25
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTTTTAATAAACAAAAAAAT
Found at i:55189588 original size:23 final size:24
Alignment explanation
Indices: 55189553--55189600 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
55189543 ACCGATTTTT
55189553 AATAAACACAAAAAATATTTTTAA
1 AATAAACACAAAAAATATTTTTAA
*
55189577 AATAAATA-AAAAAATATTTTTAA
1 AATAAACACAAAAAATATTTTTAA
55189600 A
1 A
55189601 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
AATAAACACAAAAAATATTTTTAA
Found at i:55194466 original size:5 final size:5
Alignment explanation
Indices: 55194456--55194488 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
55194446 AGCATCTAAG
55194456 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
55194489 AAGAACCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:55201858 original size:20 final size:20
Alignment explanation
Indices: 55201820--55201858 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55201810 ATGAAATATA
**
55201820 TTTAAAACATATTTTATTTT
1 TTTAAAACATATTAAATTTT
55201840 TTTAAAACATATTAAATTT
1 TTTAAAACATATTAAATTT
55201859 AAGTTAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAAACATATTAAATTTT
Found at i:55203850 original size:38 final size:38
Alignment explanation
Indices: 55203808--55203882 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
55203798 CAAATATAAT
*
55203808 AAATATATTTTTTA-ATTTTTAATTTTAAAATACTTTTA
1 AAATAT-TTTTTTATATTTTTAATTTTAAAATAATTTTA
* *
55203846 AAATATTTTTTTATTTTTTTATTTTTAAAATAATTTT
1 AAATATTTTTTTATATTTTTAATTTTAAAATAATTTT
55203883 TTAATGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 7 0.21
38 26 0.79
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (38 bp):
AAATATTTTTTTATATTTTTAATTTTAAAATAATTTTA
Found at i:55203892 original size:26 final size:27
Alignment explanation
Indices: 55203841--55203903 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
55203831 TTTAAAATAC
* * *
55203841 TTTTAAAATATTTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
55203868 TTTTAAAATAATTTTTTA-ATGTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
*
55203894 TTTAAAAATA
1 TTTTAAAATA
55203904 GGCCGGGCCG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTATATGTTTAT
Found at i:55205378 original size:8 final size:8
Alignment explanation
Indices: 55205365--55205393 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
55205355 AACTGCCAAT
55205365 TAAAAAAA
1 TAAAAAAA
55205373 T-AAAAAA
1 TAAAAAAA
55205380 TAAAAAAA
1 TAAAAAAA
55205388 TAAAAA
1 TAAAAA
55205394 TATGAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:55205385 original size:15 final size:15
Alignment explanation
Indices: 55205365--55205393 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55205355 AACTGCCAAT
55205365 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
55205380 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
55205394 TATGAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:55207266 original size:30 final size:30
Alignment explanation
Indices: 55207232--55207293 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
55207222 TTGGTGCCAA
*
55207232 TGGATTTGGGGATTCATCATTGATCTTCTC
1 TGGATTTGGGGATTCATCACTGATCTTCTC
*
55207262 TGGATTTGGGGTTTCATCACTGATCTTCTC
1 TGGATTTGGGGATTCATCACTGATCTTCTC
55207292 TG
1 TG
55207294 CCATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (30 bp):
TGGATTTGGGGATTCATCACTGATCTTCTC
Found at i:55210313 original size:17 final size:17
Alignment explanation
Indices: 55210272--55210318 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
55210262 TTGACTAGAG
55210272 AAAATATCTTTTTCTTAA
1 AAAATAT-TTTTTCTTAA
* *
55210290 AATAATATTTTTTGTTTA
1 AA-AATATTTTTTCTTAA
55210308 AAAATATTTTT
1 AAAATATTTTT
55210319 GAGAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
19 5 0.19
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
AAAATATTTTTTCTTAA
Found at i:55211432 original size:30 final size:31
Alignment explanation
Indices: 55211393--55211452 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
55211383 AGAGGTGGGA
*
55211393 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* *
55211424 TGGG-AGGGAGTAAAAATTTTGGGGAAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
55211453 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:55225281 original size:51 final size:51
Alignment explanation
Indices: 55225177--55225281 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
55225167 ACATTTTATG
* * * **
55225177 AATATTTACACATTTTATCAATTTGATCTTCATTTAACACATTTAGCTTGC
1 AATATTTACACATTTTAGCAATTTGATCTTCATTTAACAAATTTAACCCGC
*
55225228 AATATTTACATATTCTT-GCAATTTGATCCTT-ATTTAACAAATTTAACCCGC
1 AATATTTACACATT-TTAGCAATTTGAT-CTTCATTTAACAAATTTAACCCGC
55225279 AAT
1 AAT
55225282 TTTCAACATC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 41 0.89
52 5 0.11
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (51 bp):
AATATTTACACATTTTAGCAATTTGATCTTCATTTAACAAATTTAACCCGC
Found at i:55228790 original size:2 final size:2
Alignment explanation
Indices: 55228783--55228828 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
55228773 ACATCATTAA
55228783 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
55228825 AT AT
1 AT AT
55228829 CTGTGTTAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55232596 original size:11 final size:11
Alignment explanation
Indices: 55232582--55232646 Score: 70
Period size: 11 Copynumber: 6.4 Consensus size: 11
55232572 TATTTTTAAA
55232582 TTTTAAAATAT
1 TTTTAAAATAT
55232593 TTTTAAAATAT
1 TTTTAAAATAT
55232604 TTTTAAAAT-T
1 TTTTAAAATAT
55232614 TTTT---A-A-
1 TTTTAAAATAT
55232620 TTTTAAAATAT
1 TTTTAAAATAT
*
55232631 TTTAAAAATACT
1 TTTTAAAATA-T
55232643 TTTT
1 TTTT
55232647 TTAATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
6 4 0.09
7 1 0.02
9 1 0.02
10 6 0.13
11 29 0.64
12 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:55232607 original size:38 final size:39
Alignment explanation
Indices: 55232565--55232658 Score: 129
Period size: 38 Copynumber: 2.4 Consensus size: 39
55232555 AAAATACTTT
*
55232565 TTTTTATTATTTTTAAATTTTAAAATATTTTTAAAATA-
1 TTTTTATTATTTTTAAATTTTAAAATATTTTAAAAATAC
** *
55232603 TTTTTAAAATTTTTTAATTTTAAAATATTTTAAAAATAC
1 TTTTTATTATTTTTAAATTTTAAAATATTTTAAAAATAC
55232642 TTTTT-TTAATTTTTAAA
1 TTTTTATT-ATTTTTAAA
55232659 ATAAATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
38 34 0.72
39 13 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (39 bp):
TTTTTATTATTTTTAAATTTTAAAATATTTTAAAAATAC
Found at i:55232667 original size:21 final size:21
Alignment explanation
Indices: 55232629--55232668 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55232619 ATTTTAAAAT
**
55232629 ATTTTAAAAATACTTTTTTTA
1 ATTTTAAAAATAAATTTTTTA
*
55232650 ATTTTTAAAATAAATTTTT
1 ATTTTAAAAATAAATTTTT
55232669 AGTATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTAAAAATAAATTTTTTA
Found at i:55232675 original size:70 final size:69
Alignment explanation
Indices: 55232531--55232661 Score: 160
Period size: 70 Copynumber: 1.9 Consensus size: 69
55232521 TAAATATATT
* ***
55232531 TATTTTTAAATTTTTTTTAATTTTAAAATACTTTTTTTTATTATTTTTAAATTTTAAAATATTTT
1 TATTTTTAAATATTTTTTAATTTTAAAATACTTTTAAATATTATTTTTAAATTTTAAAATATTTT
55232596 TAAAA
66 T-AAA
*
55232601 TATTTTTAAA-ATTTTTTAATTTTAAAATA-TTTTAAAAATACTT-TTTTTAATTTTTAAAATA
1 TATTTTTAAATATTTTTTAATTTTAAAATACTTTT--AAATA-TTATTTTTAAATTTTAAAATA
55232662 AATTTTTAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
68 4 0.08
69 18 0.34
70 29 0.55
71 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (69 bp):
TATTTTTAAATATTTTTTAATTTTAAAATACTTTTAAATATTATTTTTAAATTTTAAAATATTTT
TAAA
Found at i:55232848 original size:11 final size:10
Alignment explanation
Indices: 55232820--55232859 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
55232810 ATTCAGGATA
55232820 AAAAATTATT
1 AAAAATTATT
*
55232830 CAAAATTATT
1 AAAAATTATT
55232840 AAAATATTATT
1 AAAA-ATTATT
55232851 AAATAATTA
1 AAA-AATTA
55232860 GAAAAAGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 12 0.46
11 13 0.50
12 1 0.04
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAAATTATT
Found at i:55232848 original size:21 final size:22
Alignment explanation
Indices: 55232818--55232859 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
55232808 GTATTCAGGA
*
55232818 TAAAAAATTATTCAA-AATTAT
1 TAAAAAATTATTAAATAATTAT
*
55232839 TAAAATATTATTAAATAATTA
1 TAAAAAATTATTAAATAATTA
55232860 GAAAAAGGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAAATTATTAAATAATTAT
Found at i:55233068 original size:2 final size:2
Alignment explanation
Indices: 55233061--55233089 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55233051 AAGGTAGGTA
55233061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55233090 AAACAATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55237294 original size:2 final size:2
Alignment explanation
Indices: 55237287--55237319 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55237277 ATAAATATCA
55237287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55237320 AAAAATTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55241105 original size:9 final size:10
Alignment explanation
Indices: 55241076--55241136 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
55241066 ACTCAAACAC
55241076 TTTAAAAATAT
1 TTTAAAAA-AT
55241087 TTTAAAAAAT
1 TTTAAAAAAT
55241097 TTTAAAAATACT
1 TTTAAAAA-A-T
****
55241109 TTTTTTTAAT
1 TTTAAAAAAT
*
55241119 TTTAAAATAT
1 TTTAAAAAAT
55241129 TTTAAAAA
1 TTTAAAAA
55241137 TACTTTTTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
10 23 0.61
11 10 0.26
12 5 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTAAAAAAT
Found at i:55241110 original size:32 final size:32
Alignment explanation
Indices: 55241074--55241142 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
55241064 TTACTCAAAC
55241074 ACTTTAAAA-ATATTTTAAAAAATTTTAAAAAT
1 ACTTTAAAATA-ATTTTAAAAAATTTTAAAAAT
**** *
55241106 ACTTTTTTTTAATTTTAAAATATTTTAAAAAT
1 ACTTTAAAATAATTTTAAAAAATTTTAAAAAT
55241138 ACTTT
1 ACTTT
55241143 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (32 bp):
ACTTTAAAATAATTTTAAAAAATTTTAAAAAT
Found at i:55241143 original size:32 final size:32
Alignment explanation
Indices: 55241085--55241170 Score: 112
Period size: 32 Copynumber: 2.9 Consensus size: 32
55241075 CTTTAAAAAT
*
55241085 ATTTTAAAAAATTTTAAAAATACTTTTTTTTA
1 ATTTTAAAATATTTTAAAAATACTTTTTTTTA
55241117 ATTTTAAAATATTTTAAAAATAC---TTTTTA
1 ATTTTAAAATATTTTAAAAATACTTTTTTTTA
*
55241146 AATTT-AAATATTTT--AAATACTTTTT
1 ATTTTAAAATATTTTAAAAATACTTTTT
55241171 AAATTTTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.12
28 9 0.18
29 12 0.24
32 22 0.45
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTTTAAAATATTTTAAAAATACTTTTTTTTA
Found at i:55241179 original size:28 final size:29
Alignment explanation
Indices: 55241085--55241188 Score: 106
Period size: 32 Copynumber: 3.5 Consensus size: 29
55241075 CTTTAAAAAT
* * *
55241085 ATTTTAAAAAATTTTAAAAATACTTTTTTTTA
1 ATTTTTAAATATTTT-AAAATAC--TTTTTAA
*
55241117 ATTTTAAAATATTTTAAAAATACTTTTTAA
1 ATTTTTAAATATTTT-AAAATACTTTTTAA
55241147 A--TTTAAATATTTT-AAATACTTTTTAA
1 ATTTTTAAATATTTTAAAATACTTTTTAA
55241173 ATTTTTAAATAATTTT
1 ATTTTTAAAT-ATTTT
55241189 GTATTTATTA
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
26 14 0.21
28 18 0.27
29 5 0.08
30 7 0.11
32 22 0.33
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTTTAAATATTTTAAAATACTTTTTAA
Found at i:55241180 original size:19 final size:20
Alignment explanation
Indices: 55241148--55241188 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
55241138 ACTTTTTAAA
*
55241148 TTTAAATATTTTAAATACTT
1 TTTAAATATTTTAAATAATT
55241168 TTTAAAT-TTTTAAATAATT
1 TTTAAATATTTTAAATAATT
55241187 TT
1 TT
55241189 GTATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAATATTTTAAATAATT
Found at i:55242293 original size:18 final size:18
Alignment explanation
Indices: 55242241--55242294 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
55242231 ATTCACCTAA
*
55242241 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCAAACCCAATT
* * *
55242260 ATCCAACCTAATCCAATT
1 ACCCAACCAAACCCAATT
*
55242278 ACCCAACCCAACCCAAT
1 ACCCAACCAAACCCAAT
55242295 CATAAAAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.41, C:0.43, G:0.02, T:0.15
Consensus pattern (18 bp):
ACCCAACCAAACCCAATT
Found at i:55265767 original size:23 final size:22
Alignment explanation
Indices: 55265732--55265776 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
55265722 GATTATTGAG
**
55265732 ATAAATTGGATTTAAAATTTAAA
1 ATAAATTAAATTT-AAATTTAAA
*
55265755 ATAAATTAAATTTATATTTAAA
1 ATAAATTAAATTTAAATTTAAA
55265777 TATTTTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
ATAAATTAAATTTAAATTTAAA
Found at i:55266807 original size:17 final size:16
Alignment explanation
Indices: 55266794--55266830 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
55266784 AAAAATATGT
55266794 AAAATCATAAAATATC
1 AAAATCATAAAATATC
*
55266810 ACAATCATAAAATATCC
1 AAAATCATAAAATAT-C
55266827 AAAA
1 AAAA
55266831 ATATTACTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATCATAAAATATC
Found at i:55270821 original size:10 final size:10
Alignment explanation
Indices: 55270791--55270928 Score: 62
Period size: 10 Copynumber: 13.0 Consensus size: 10
55270781 ATATTGATTT
*
55270791 TTTATTAAAA
1 TTTATAAAAA
* *
55270801 TTGATATAAA
1 TTTATAAAAA
55270811 TTTATAAAAA
1 TTTATAAAAA
55270821 TTCTAATAAAGCATA
1 TT-T-ATAAA--A-A
*
55270836 TTTTTATAAAA
1 TTTATA-AAAA
*
55270847 TTAATAAAACA
1 TTTATAAAA-A
**
55270858 TATT-TAAATT
1 T-TTATAAAAA
55270868 TTTATAAAAA
1 TTTATAAAAA
* *
55270878 TGTATTAAAA
1 TTTATAAAAA
* *
55270888 TTGATATAAA
1 TTTATAAAAA
*
55270898 CTTATAAAAA
1 TTTATAAAAA
*
55270908 TTATTTAAAAA
1 TT-TATAAAAA
*
55270919 ATTATAAAAA
1 TTTATAAAAA
55270929 CTTGAACTGG
Statistics
Matches: 92, Mismatches: 26, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
9 2 0.02
10 54 0.59
11 20 0.22
12 7 0.08
13 2 0.02
14 4 0.04
15 3 0.03
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:55271481 original size:29 final size:25
Alignment explanation
Indices: 55271434--55271486 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 25
55271424 AAATATGTTT
55271434 TATTTAATTTTATATTTTTATATTA
1 TATTTAATTTTATATTTTTATATTA
55271459 TATTGTAATATTTATAATATTTTATATT
1 TATT-TAAT-TTTAT-AT-TTTTATATT
55271487 TTTATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 5 0.21
28 2 0.08
29 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTTAATTTTATATTTTTATATTA
Found at i:55274120 original size:18 final size:18
Alignment explanation
Indices: 55274085--55274123 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55274075 ATACCAGGTG
*
55274085 TGTATCCTAGCCCTTATA
1 TGTATCCTAGACCTTATA
55274103 TGTATCCTA-ACCTATATA
1 TGTATCCTAGACCT-TATA
55274121 TGT
1 TGT
55274124 TTCTTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (18 bp):
TGTATCCTAGACCTTATA
Found at i:55274563 original size:24 final size:24
Alignment explanation
Indices: 55274530--55274595 Score: 114
Period size: 24 Copynumber: 2.7 Consensus size: 24
55274520 TAAAATTTGT
55274530 TTTTTAATATTTTAATAGTAATTTA
1 TTTTT-ATATTTTAATAGTAATTTA
55274555 TTTTTATATTTTAATAGTAATTTA
1 TTTTTATATTTTAATAGTAATTTA
55274579 TTTTTATATTTTTAATA
1 TTTTTATA-TTTTAATA
55274596 TATTTGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 27 0.68
25 13 0.32
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (24 bp):
TTTTTATATTTTAATAGTAATTTA
Found at i:55274674 original size:24 final size:23
Alignment explanation
Indices: 55274531--55274687 Score: 99
Period size: 24 Copynumber: 6.7 Consensus size: 23
55274521 AAAATTTGTT
55274531 TTTTAATATTTTAATAGTAATTTA
1 TTTTAATATTTTAATA-TAATTTA
*
55274555 TTTTTATATTTTAATAGTAATTTA
1 TTTTAATATTTTAATA-TAATTTA
* *
55274579 TTTTTATATTTTTAATAT-ATTTG
1 TTTTAATA-TTTTAATATAATTTA
* * * **
55274602 TATAAATTATTTTTATATTGTTTCA
1 TTTTAA-TATTTTAATATAATTT-A
* * *
55274627 -TTTAATA---AAATAAAAGTTA
1 TTTTAATATTTTAATATAATTTA
55274646 TTTTTAATATTTTAATATTAATTTA
1 -TTTTAATATTTTAATA-TAATTTA
*
55274671 TTTTTATATTTTTAATA
1 TTTTAATA-TTTTAATA
55274688 AAATAAAAGT
Statistics
Matches: 102, Mismatches: 20, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 5 0.05
21 7 0.07
23 17 0.17
24 51 0.50
25 21 0.21
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.61
Consensus pattern (23 bp):
TTTTAATATTTTAATATAATTTA
Found at i:55274684 original size:117 final size:117
Alignment explanation
Indices: 55274470--55274687 Score: 366
Period size: 117 Copynumber: 1.9 Consensus size: 117
55274460 AACATTGAAT
* *
55274470 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTCCATTTAATAAAATAAAATTTGTTTTTT
1 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTCCATTTAATAAAATAAAAGTTGATTTTT
55274535 AATATTTTAATAGTAATTTATTTTTATATTTTAATAGTAATTTATTTTTATA
66 AATATTTTAATAGTAATTTATTTTTATATTTTAATAGTAATTTATTTTTATA
* * *
55274587 TTTTTAATATATTTGTATAAATTATTTTTATATTGTTTCATTTAATAAAATAAAAGTT-ATTTTT
1 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTCCATTTAATAAAATAAAAGTTGATTTTT
*
55274651 AATATTTTAATATTAATTTATTTTTATATTTTTAATA
66 AATATTTTAATAGTAATTTATTTTTATA-TTTTAATA
55274688 AAATAAAAGT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
116 32 0.34
117 62 0.66
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (117 bp):
TTTTTAATATATTTGTACAAACTATTTTTATATTGTTCCATTTAATAAAATAAAAGTTGATTTTT
AATATTTTAATAGTAATTTATTTTTATATTTTAATAGTAATTTATTTTTATA
Found at i:55274696 original size:54 final size:54
Alignment explanation
Indices: 55274510--55274747 Score: 169
Period size: 54 Copynumber: 4.2 Consensus size: 54
55274500 TATTGTTCCA
* * *
55274510 TTTAATAAAATAAAATTTGTTTTTTAATATTTTAATAGTAATTTATTTTTATA-T
1 TTTAATAAAATAAAAGTT-ATTTTTAATATTTTAATATTAATTTATTTTTATATT
* **** * *
55274564 TTTAATAGTAATTTATTTTTATATTTTTAATATATTT-GTA-TAAATTATTTTTATATTGTTT
1 TTTAATA--AA-ATAAAAGT-TATTTTTAATAT-TTTAATATTAATTTATTTTTATA----TT
55274625 CATTTAATAAAATAAAAGTTATTTTTAATATTTTAATATTAATTTATTTTTATATT
1 --TTTAATAAAATAAAAGTTATTTTTAATATTTTAATATTAATTTATTTTTATATT
* * **** *
55274681 TTTAATAAAATAAAAGTTCTTTTGAATAAGAAAATATT-TTTAATATTTTTATATT
1 TTTAATAAAATAAAAGTTATTTTTAATATTTTAATATTAATT--TATTTTTATATT
55274736 TTTAATAAAATA
1 TTTAATAAAATA
55274748 TAATTAATGT
Statistics
Matches: 147, Mismatches: 21, Indels: 31
0.74 0.11 0.16
Matches are distributed among these distances:
53 2 0.01
54 39 0.27
55 24 0.16
56 18 0.12
57 16 0.11
58 7 0.05
59 14 0.10
60 17 0.12
61 3 0.02
63 7 0.05
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (54 bp):
TTTAATAAAATAAAAGTTATTTTTAATATTTTAATATTAATTTATTTTTATATT
Found at i:55274729 original size:8 final size:9
Alignment explanation
Indices: 55274713--55274742 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55274703 TGAATAAGAA
55274713 AATATTTTT
1 AATATTTTT
55274722 AATATTTTT
1 AATATTTTT
55274731 -ATATTTTT
1 AATATTTTT
55274739 AATA
1 AATA
55274743 AAATATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:55278636 original size:36 final size:36
Alignment explanation
Indices: 55278596--55278669 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
55278586 CCTAGCGTCA
*
55278596 GCCGATTTGCTCCCAATTTATTTTCTTTTTTTTTCT
1 GCCGATTTGCTCCCAATTTATTTTCTTTTCTTTTCT
*
55278632 GCCGATTTGCTCCCAGTTTATTTTCTTTTCTTTTCT
1 GCCGATTTGCTCCCAATTTATTTTCTTTTCTTTTCT
55278668 GC
1 GC
55278670 AGAATAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.09, C:0.24, G:0.11, T:0.55
Consensus pattern (36 bp):
GCCGATTTGCTCCCAATTTATTTTCTTTTCTTTTCT
Found at i:55281660 original size:91 final size:91
Alignment explanation
Indices: 55281513--55281720 Score: 312
Period size: 91 Copynumber: 2.3 Consensus size: 91
55281503 TTGATTTTAG
*
55281513 TAAATTCATATAAGAACATTATATTATTAAGAAATTTATGAAATTATATATCATTATTAAATCAT
1 TAAATTCATATAAGAAAATT-TATTATTAAGAAATTTATGAAATTATATATCATTATTAAATCAT
* * *
55281578 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* *
55281605 TAAATTCATATAAGAAAATTTATT-TTCAAGAATATTT-TGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATT-AAGAA-ATTTATGAAATTATATATCATTATTAAATCA
55281668 TATGTAATAATAATTATTTTAAATTATA
64 TATGTAATAATAATTATTTTAAATTATA
*
55281696 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
55281721 GTTATAATTA
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
90 2 0.02
91 81 0.76
92 23 0.22
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAAATTTATGAAATTATATATCATTATTAAATCATA
TGTAATAATAATTATTTTAAATTATA
Found at i:55281660 original size:101 final size:97
Alignment explanation
Indices: 55281554--55281809 Score: 262
Period size: 91 Copynumber: 2.6 Consensus size: 97
55281544 AAATTTATGA
*
55281554 AATTATATATCATTATTAAATCATATTTAATATTAATTATTTTAAATTGTATAAATTCATATAAG
1 AATTATATAT-ATTATTAAAT-ATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAG
*
55281619 AAAATTTATT-TTCA-AGAATATTTTGAA----ATT
64 AAAATTTATTATT-ATA-AATATTTTAAATTTTATT
* * *
55281649 -A-TATAT-TATTATTAAATTATATGTAATAATAATTATTTTAAATTATACAAATTCATATAAGA
1 AATTATATATATTATTAAA-TATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGA
*
55281711 AAATTTATTAGTTATAATTATTTTAAATTTTATT
65 AAATTTATTA-TTATAAATATTTTAAATTTTATT
* * * *
55281745 AAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTTTATTAAATT-ATATA
1 -AATTATATATATT-ATT-AAATATATTTAATATTAATTATTTTAAATTATA-TAAATTCATATA
55281809 A
62 A
55281810 TATAGTATCA
Statistics
Matches: 133, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
91 58 0.44
92 12 0.09
93 8 0.06
94 1 0.01
96 3 0.02
98 1 0.01
99 4 0.03
100 3 0.02
101 35 0.26
102 8 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (97 bp):
AATTATATATATTATTAAATATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAA
AATTTATTATTATAAATATTTTAAATTTTATT
Found at i:55281754 original size:28 final size:27
Alignment explanation
Indices: 55281723--55281810 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
55281713 ATTTATTAGT
55281723 TATAATTATTTTAAATTTTATTAAATCA
1 TATAATTATTTTAAATTTTATTAAAT-A
* * *
55281751 TAT-ATT-TTAATTAAAATATATTTAATA
1 TATAATTATT--TTAAATTTTATTAAATA
*
55281778 T-TAATTATTTCAAATTTTATTAAATTA
1 TATAATTATTTTAAATTTTATTAAA-TA
55281805 TATAAT
1 TATAAT
55281811 ATAGTATCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
26 14 0.30
27 11 0.23
28 22 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TATAATTATTTTAAATTTTATTAAATA
Found at i:55281897 original size:14 final size:15
Alignment explanation
Indices: 55281876--55281924 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
55281866 AATTTTATTA
55281876 AATT-ATATAT-TTT
1 AATTAATATATGTTT
55281889 AATTAATATATGTTT
1 AATTAATATATGTTT
*
55281904 AA-TAATAATTATGTTA
1 AATTAAT-A-TATGTTT
55281920 AATTA
1 AATTA
55281925 TCTTTTATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 10 0.33
15 6 0.20
16 8 0.27
17 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AATTAATATATGTTT
Found at i:55285184 original size:79 final size:79
Alignment explanation
Indices: 55285026--55285206 Score: 265
Period size: 79 Copynumber: 2.3 Consensus size: 79
55285016 TGTATCTAAC
* * * * *
55285026 CTTTTATTACTTT-AGACAAGTTCCGTTTTGCAGTTTGAAAGGAATGAGGCAGGAGGGTGGTTGA
1 CTTTTATTCCTTTCAGTCGAGTTCCGTTTTGCAGTTTGAAAGGAAAGAAGCAGGAGGGTGGTTGA
55285090 GGAATGAAGGATAT
66 GGAATGAAGGATAT
* *
55285104 CTTTTATTCCTTTCAGTCGAGTTTCGTTTTGCAGTTTGAAAGGAAAGAAGCGGGAGGGTGGTTGA
1 CTTTTATTCCTTTCAGTCGAGTTCCGTTTTGCAGTTTGAAAGGAAAGAAGCAGGAGGGTGGTTGA
*
55285169 GGAATGAAGGGTAT
66 GGAATGAAGGATAT
*
55285183 CTTTTATTCCTTTCAATCGTAGTT
1 CTTTTATTCCTTTCAGTCG-AGTT
55285207 AGTAATCTCT
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 12 0.13
79 76 0.83
80 4 0.04
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (79 bp):
CTTTTATTCCTTTCAGTCGAGTTCCGTTTTGCAGTTTGAAAGGAAAGAAGCAGGAGGGTGGTTGA
GGAATGAAGGATAT
Found at i:55286873 original size:34 final size:34
Alignment explanation
Indices: 55286830--55286897 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
55286820 AGTGTGAAGT
55286830 CTTGATGTAGCATGACTATTTAGCATAGCCCTGC
1 CTTGATGTAGCATGACTATTTAGCATAGCCCTGC
55286864 CTTGATGTAGCATGACTATTTAGCATAGCCCTGC
1 CTTGATGTAGCATGACTATTTAGCATAGCCCTGC
55286898 TTGTCATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (34 bp):
CTTGATGTAGCATGACTATTTAGCATAGCCCTGC
Found at i:55289465 original size:28 final size:29
Alignment explanation
Indices: 55289429--55289502 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
55289419 TTAACGATTC
* *
55289429 AGTGGCTAAAATATTACATGTT-AACATA
1 AGTGACTAAAATATAACATGTTAAACATA
** * *
55289457 AGTGACTAAAACGTAATATTTTAAACATA
1 AGTGACTAAAATATAACATGTTAAACATA
*
55289486 AGTGATTAAAATATAAC
1 AGTGACTAAAATATAAC
55289503 CCGAAATAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
28 16 0.46
29 19 0.54
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (29 bp):
AGTGACTAAAATATAACATGTTAAACATA
Found at i:55300049 original size:25 final size:24
Alignment explanation
Indices: 55300021--55300076 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
55300011 AACATGTTTT
55300021 AAAT-TTTTTTAAAATTCGAAAATAA
1 AAATATTTTTTAAAA-T-GAAAATAA
*
55300046 AAATTATTTTTTAAAATGAAAATAT
1 AAA-TATTTTTTAAAATGAAAATAA
55300071 AAATAT
1 AAATAT
55300077 AAAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 3 0.11
25 13 0.46
26 2 0.07
27 10 0.36
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATTTTTTAAAATGAAAATAA
Found at i:55300060 original size:27 final size:25
Alignment explanation
Indices: 55300025--55300074 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
55300015 TGTTTTAAAT
55300025 TTTTTTAAAATTCGAAAATAAAAATTA
1 TTTTTTAAAA-T-GAAAATAAAAATTA
*
55300052 TTTTTTAAAATGAAAATATAAAT
1 TTTTTTAAAATGAAAATAAAAAT
55300075 ATAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
27 10 0.45
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
TTTTTTAAAATGAAAATAAAAATTA
Found at i:55313372 original size:12 final size:12
Alignment explanation
Indices: 55313351--55313400 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
55313341 AAAAACAAAA
*
55313351 TGATTAAAAACT
1 TGATGAAAAACT
* *
55313363 TGATGGAAAATT
1 TGATGAAAAACT
*
55313375 TTATGAAAATACT
1 TGATGAAAA-ACT
55313388 TGATGAAAAACT
1 TGATGAAAAACT
55313400 T
1 T
55313401 AAAAAGAACT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:55313490 original size:18 final size:18
Alignment explanation
Indices: 55313467--55313504 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
55313457 AGAACTAAAT
*
55313467 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
55313485 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
55313503 GA
1 GA
55313505 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:55314390 original size:19 final size:20
Alignment explanation
Indices: 55314356--55314394 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
55314346 TTAAAAAGTA
55314356 TATATTAAATAAATATATTT
1 TATATTAAATAAATATATTT
*
55314376 TATATTATA-AAATATATTT
1 TATATTAAATAAATATATTT
55314395 AAAATAATGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTAAATAAATATATTT
Found at i:55316977 original size:26 final size:25
Alignment explanation
Indices: 55316915--55316974 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
55316905 AATCATTTCA
*
55316915 ATTTGGATTTT-AAAATTTAATGGAT
1 ATTTGG-TTTTAAAAATTTAATGCAT
55316940 ATTTGGTTTTAAAAATTTTAATGCAT
1 ATTTGGTTTTAAAAA-TTTAATGCAT
55316966 -TTTGGTTTT
1 ATTTGGTTTT
55316975 TAAGAGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.12
25 19 0.59
26 9 0.28
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (25 bp):
ATTTGGTTTTAAAAATTTAATGCAT
Found at i:55341165 original size:30 final size:27
Alignment explanation
Indices: 55341099--55341162 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
55341089 ACTGTTATGT
* *
55341099 TACCTTCATCATCATCACCAAACCCAC
1 TACCTTCTTCATCATCAACAAACCCAC
*
55341126 TACCTTCTTCATCATCAACAAACCCTC
1 TACCTTCTTCATCATCAACAAACCCAC
*
55341153 TATCTTCTTC
1 TACCTTCTTC
55341163 TTCTGCTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (27 bp):
TACCTTCTTCATCATCAACAAACCCAC
Found at i:55349456 original size:31 final size:31
Alignment explanation
Indices: 55349419--55349485 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
55349409 TTGAAATCAA
55349419 AAAAATAG-AGAGACTAAATTTCAATTTTATG
1 AAAAATAGAAG-GACTAAATTTCAATTTTATG
*
55349450 AAAAATATAAGGACTAAATTTCAATTTTATG
1 AAAAATAGAAGGACTAAATTTCAATTTTATG
55349481 AAAAA
1 AAAAA
55349486 ATATAAAGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.31
Consensus pattern (31 bp):
AAAAATAGAAGGACTAAATTTCAATTTTATG
Found at i:55349491 original size:32 final size:32
Alignment explanation
Indices: 55349417--55349496 Score: 119
Period size: 32 Copynumber: 2.5 Consensus size: 32
55349407 TTTTGAAATC
55349417 AAAAAA-ATAGAGAGACTAAATTTCAATTTTATG
1 AAAAAATATA-AG-GACTAAATTTCAATTTTATG
55349450 -AAAAATATAAGGACTAAATTTCAATTTTATG
1 AAAAAATATAAGGACTAAATTTCAATTTTATG
*
55349481 AAAAAATATAAAGACT
1 AAAAAATATAAGGACT
55349497 TATTGCATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
31 20 0.45
32 21 0.48
33 3 0.07
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.30
Consensus pattern (32 bp):
AAAAAATATAAGGACTAAATTTCAATTTTATG
Found at i:55349509 original size:32 final size:31
Alignment explanation
Indices: 55349419--55349510 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
55349409 TTGAAATCAA
* * *
55349419 AAAAATAGAGAGACTAAATTTCAATTTTATG
1 AAAAATATAAAGACTAAATTGCAATTTTATG
* *
55349450 AAAAATATAAGGACTAAATTTCAATTTTATG
1 AAAAATATAAAGACTAAATTGCAATTTTATG
*
55349481 AAAAAATATAAAGACT-TATTGCATATTTTA
1 -AAAAATATAAAGACTAAATTGCA-ATTTTA
55349511 ACCTATTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.62
32 20 0.38
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.35
Consensus pattern (31 bp):
AAAAATATAAAGACTAAATTGCAATTTTATG
Found at i:55350123 original size:11 final size:11
Alignment explanation
Indices: 55350107--55350150 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
55350097 ATTGGCTCTT
55350107 ATTTTAAATTA
1 ATTTTAAATTA
55350118 ATTTTAAATTA
1 ATTTTAAATTA
55350129 A-TTT-AATTA
1 ATTTTAAATTA
55350138 CATTTTTAAATTA
1 -A-TTTTAAATTA
55350151 TCAATATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.17
10 4 0.14
11 12 0.41
12 3 0.10
13 5 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:55356560 original size:30 final size:33
Alignment explanation
Indices: 55356500--55356560 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
55356490 TGTACTAAAA
*
55356500 AAAATGAGCAAATTAGTTCATGTATGTTACATC
1 AAAATGAGCAAACTAGTTCATGTATGTTACATC
*
55356533 AAAA-GAGCAAACTAG-TCAT-TCTGTTACA
1 AAAATGAGCAAACTAGTTCATGTATGTTACA
55356561 AATTCTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 4 0.15
32 10 0.38
33 4 0.15
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (33 bp):
AAAATGAGCAAACTAGTTCATGTATGTTACATC
Found at i:55365849 original size:94 final size:94
Alignment explanation
Indices: 55365688--55365876 Score: 369
Period size: 94 Copynumber: 2.0 Consensus size: 94
55365678 TTATTCACCC
55365688 AGTAAAATTCAAAATCTGACTTTCAAGTTCCATTTTCTTTTACAGATTCCAAAATGGAACAATCA
1 AGTAAAATTCAAAATCTGACTTTCAAGTTCCATTTTCTTTTACAGATTCCAAAATGGAACAATCA
55365753 AATTCCACATAAAAATAATAAACAACTAA
66 AATTCCACATAAAAATAATAAACAACTAA
*
55365782 AGTAAAATTCAAAATCTGACTTTCAAGTTCCATTTTCTTTTACAGATTCCACAATGGAACAATCA
1 AGTAAAATTCAAAATCTGACTTTCAAGTTCCATTTTCTTTTACAGATTCCAAAATGGAACAATCA
55365847 AATTCCACATAAAAATAATAAACAACTAA
66 AATTCCACATAAAAATAATAAACAACTAA
55365876 A
1 A
55365877 ACGAATTAAA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (94 bp):
AGTAAAATTCAAAATCTGACTTTCAAGTTCCATTTTCTTTTACAGATTCCAAAATGGAACAATCA
AATTCCACATAAAAATAATAAACAACTAA
Found at i:55366473 original size:3 final size:3
Alignment explanation
Indices: 55366465--55366503 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
55366455 ACTTCATCCA
*
55366465 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA
55366504 CACCACCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55366681 original size:22 final size:23
Alignment explanation
Indices: 55366656--55366699 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
55366646 ACTTTTAATT
*
55366656 TTTTATATA-TTTAAAAATTATG
1 TTTTATATAGATTAAAAATTATG
*
55366678 TTTTCTATAGATTAAAAATTAT
1 TTTTATATAGATTAAAAATTAT
55366700 ACTTCATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
TTTTATATAGATTAAAAATTATG
Found at i:55376556 original size:31 final size:30
Alignment explanation
Indices: 55376492--55376557 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
55376482 ATTTTTTTAG
* *
55376492 TCAAATTAGATACCTGAACTTGACTTTTGGT
1 TCAAATTAGATA-CTGAACTTGACTTATAGT
55376523 TCAAATTAGTATA-TGAACTTGACTTCATAGT
1 TCAAATTAG-ATACTGAACTTGACTT-ATAGT
55376554 TCAA
1 TCAA
55376558 TTAAGTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 12 0.39
31 16 0.52
32 3 0.10
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (30 bp):
TCAAATTAGATACTGAACTTGACTTATAGT
Found at i:55382282 original size:26 final size:27
Alignment explanation
Indices: 55382230--55382288 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
55382220 AATCGAATTA
* * *
55382230 ATATTTATTTTTTTAATTATTTTAAAT
1 ATATTTATATTTATAATCATTTTAAAT
55382257 ATATTTATATTTAT-ATCATTTTAAAT
1 ATATTTATATTTATAATCATTTTAAAT
*
55382283 AAATTT
1 ATATTT
55382289 GTTAATTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
ATATTTATATTTATAATCATTTTAAAT
Found at i:55383364 original size:31 final size:31
Alignment explanation
Indices: 55383329--55383387 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
55383319 CCCTAAACTT
55383329 CTTTTATC-ATATTAGT-CCTGGAACTTAGTAA
1 CTTTTATCAAT-TTAGTCCCT-GAACTTAGTAA
*
55383360 CTTTTCTCAATTTAGTCCCTGAACTTAG
1 CTTTTATCAATTTAGTCCCTGAACTTAG
55383388 ATTCAAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (31 bp):
CTTTTATCAATTTAGTCCCTGAACTTAGTAA
Found at i:55391902 original size:31 final size:31
Alignment explanation
Indices: 55391849--55391907 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
55391839 ATGATTATTC
**
55391849 AACTATTTGAAAGCTTTCATTTAAGTCACTA
1 AACTATTCAAAAGCTTTCATTTAAGTCACTA
* *
55391880 AACTATTCAAAAGTTTTTATTTAAGTCA
1 AACTATTCAAAAGCTTTCATTTAAGTCA
55391908 TTAGGTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (31 bp):
AACTATTCAAAAGCTTTCATTTAAGTCACTA
Found at i:55395759 original size:4 final size:4
Alignment explanation
Indices: 55395752--55395786 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
55395742 TTATGTTGTT
55395752 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
55395787 TGGGCTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:55407866 original size:13 final size:13
Alignment explanation
Indices: 55407848--55407874 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55407838 AGTATGTTTT
55407848 ATACTTTTATTAA
1 ATACTTTTATTAA
55407861 ATACTTTTATTAA
1 ATACTTTTATTAA
55407874 A
1 A
55407875 ATGGATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
ATACTTTTATTAA
Found at i:55410996 original size:85 final size:86
Alignment explanation
Indices: 55410871--55411041 Score: 326
Period size: 85 Copynumber: 2.0 Consensus size: 86
55410861 AATCCATGCA
55410871 ACCTGCGAAACGATTACACCAAACAAAATCTATTAAAATACGTAATTAAAACAGGAGAAACATCA
1 ACCTGCGAAACGATTACACCAAACAAAATCTATTAAAATACGTAATTAAAACAGGAGAAACATCA
55410936 GTAGCTAGATCAAGGAAAAGT
66 GTAGCTAGATCAAGGAAAAGT
*
55410957 ACCTGCGAAACGTTTACACCAAA-AAAATCTATTAAAATACGTAATTAAAACAGGAGAAACATCA
1 ACCTGCGAAACGATTACACCAAACAAAATCTATTAAAATACGTAATTAAAACAGGAGAAACATCA
55411021 GTAGCTAGATCAAGGAAAAGT
66 GTAGCTAGATCAAGGAAAAGT
55411042 GAAGCAAAAC
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 62 0.74
86 22 0.26
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (86 bp):
ACCTGCGAAACGATTACACCAAACAAAATCTATTAAAATACGTAATTAAAACAGGAGAAACATCA
GTAGCTAGATCAAGGAAAAGT
Found at i:55412617 original size:17 final size:17
Alignment explanation
Indices: 55412595--55412628 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55412585 GTTTTAGCAT
*
55412595 ATTTTTTCTATTTTTAA
1 ATTTTTTATATTTTTAA
*
55412612 ATTTTTTATGTTTTTAA
1 ATTTTTTATATTTTTAA
55412629 TTATTATTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTTTTATATTTTTAA
Done.