Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 53 of 325
Found at i:19123951 original size:27 final size:27
Alignment explanation
Indices: 19123913--19123966 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19123903 GACTATCAAA
19123913 CCAAAAGTTCATTATCTAACAGTTGTC
1 CCAAAAGTTCATTATCTAACAGTTGTC
19123940 CCAAAAGTTCATTATCTAACAGTTGTC
1 CCAAAAGTTCATTATCTAACAGTTGTC
19123967 AATATTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (27 bp):
CCAAAAGTTCATTATCTAACAGTTGTC
Found at i:19124385 original size:26 final size:27
Alignment explanation
Indices: 19124330--19124385 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
19124320 TGAATTTTTA
* * *
19124330 TATATTTTTTTATATTTTATTAAAATT
1 TATATTTTTTAATAATTTATTAAAACT
*
19124357 TATA-TTTTTAATAATTTATTAGAACT
1 TATATTTTTTAATAATTTATTAAAACT
19124383 TAT
1 TAT
19124386 TATGATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TATATTTTTTAATAATTTATTAAAACT
Found at i:19124419 original size:10 final size:8
Alignment explanation
Indices: 19124393--19124497 Score: 61
Period size: 9 Copynumber: 12.0 Consensus size: 8
19124383 TATTATGATT
19124393 TTTTATAA
1 TTTTATAA
19124401 GTTTTATAA
1 -TTTTATAA
19124410 TTATTGATAA
1 TT-TT-ATAA
19124420 TTTTATAA
1 TTTTATAA
19124428 -TTTAT-A
1 TTTTATAA
19124434 TTTTATTTGAA
1 TTTTA--T-AA
*
19124445 TTTTTATAT
1 -TTTTATAA
*
19124454 TTTTATGA
1 TTTTATAA
*
19124462 TATTTATTAT
1 T-TTTA-TAA
19124472 TTTTATAA
1 TTTTATAA
*
19124480 TATTTACAAA
1 T-TTTA-TAA
19124490 TTTTATAA
1 TTTTATAA
19124498 GTTCATAGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
6 1 0.01
7 9 0.12
8 18 0.24
9 30 0.39
10 12 0.16
11 1 0.01
12 5 0.07
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (8 bp):
TTTTATAA
Found at i:19124432 original size:19 final size:19
Alignment explanation
Indices: 19124362--19124432 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
19124352 AAATTTATAT
*
19124362 TTTTAATAATTTATTAGA-AC
1 TTTT-ATAATTTATT-GATAA
* *
19124382 TTATTATGATTT-TTTATAA
1 TT-TTATAATTTATTGATAA
19124401 GTTTTATAA-TTATTGATAA
1 -TTTTATAATTTATTGATAA
19124420 TTTTATAATTTAT
1 TTTTATAATTTAT
19124433 ATTTTATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 11 0.27
19 18 0.44
20 10 0.24
21 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTATAATTTATTGATAA
Found at i:19124450 original size:19 final size:20
Alignment explanation
Indices: 19124428--19124478 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
19124418 AATTTTATAA
*
19124428 TTTATATTTTATTTGA-ATT
1 TTTATATTTTATATGATATT
19124447 TTTATATTTT-TATGATATT
1 TTTATATTTTATATGATATT
19124466 TATTAT-TTTTATA
1 T-TTATATTTTATA
19124479 ATATTTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 18 0.64
20 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTATATTTTATATGATATT
Found at i:19124474 original size:18 final size:17
Alignment explanation
Indices: 19124402--19124485 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 17
19124392 TTTTTATAAG
* *
19124402 TTTTATAATTATTGATAA
1 TTTTATAA-TATTTATAT
19124420 TTTTAT-A-ATTTATAT
1 TTTTATAATATTTATAT
* *
19124435 TTTATTTGAATTTTTATAT
1 TTT-TAT-AATATTTATAT
*
19124454 TTTTATGATATTTATTAT
1 TTTTATAATATTTA-TAT
19124472 TTTTATAATATTTA
1 TTTTATAATATTTA
19124486 CAAATTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
15 9 0.17
16 2 0.04
17 7 0.13
18 25 0.47
19 10 0.19
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTATAATATTTATAT
Found at i:19124577 original size:18 final size:18
Alignment explanation
Indices: 19124537--19124642 Score: 67
Period size: 18 Copynumber: 5.8 Consensus size: 18
19124527 ATGTTTTATT
* *
19124537 TTTTATAATTAATTAGAA
1 TTTTATAATTATTTATAA
19124555 TTTTTATAA-TATTTATAA
1 -TTTTATAATTATTTATAA
*
19124573 GTTTTTATGAATT-TTTATTAG
1 --TTTTAT-AATTATTTA-TAA
*
19124594 TTTTATAATTTTTTATAA
1 TTTTATAATTATTTATAA
* *
19124612 TATTATAAGTT-TATATAA
1 TTTTATAA-TTATTTATAA
*
19124630 TTTTGTAA-TATTT
1 TTTTATAATTATTT
19124643 TATTTTTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.01
17 2 0.03
18 32 0.45
19 27 0.38
20 6 0.08
21 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTATAATTATTTATAA
Found at i:19124586 original size:29 final size:29
Alignment explanation
Indices: 19124552--19124609 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
19124542 TAATTAATTA
19124552 GAATTTTTA-TAATATTTATAAGTTTTTAT
1 GAATTTTTATTAAT-TTTATAAGTTTTTAT
* *
19124581 GAATTTTTATTAGTTTTATAATTTTTTAT
1 GAATTTTTATTAATTTTATAAGTTTTTAT
19124610 AATATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (29 bp):
GAATTTTTATTAATTTTATAAGTTTTTAT
Found at i:19124587 original size:10 final size:9
Alignment explanation
Indices: 19124322--19124633 Score: 124
Period size: 10 Copynumber: 33.7 Consensus size: 9
19124312 CCAACAAATG
19124322 AATTTTTAT
1 AATTTTTAT
19124331 ATATTTTT-T
1 A-ATTTTTAT
*
19124340 TATATTTTATT
1 AAT-TTTTA-T
**
19124351 AAAATTTAT
1 AATTTTTAT
19124360 -ATTTTTAAT
1 AATTTTT-AT
*
19124369 AATTTATTAG
1 AATTT-TTAT
*
19124379 AACTTATTAT
1 AA-TTTTTAT
*
19124389 GATTTTTTAT
1 -AATTTTTAT
*
19124399 AAGTTTTAT
1 AATTTTTAT
*
19124408 AATTATTGAT
1 AATT-TTTAT
19124418 AA-TTTTAT
1 AATTTTTAT
19124426 AA--TTTAT
1 AATTTTTAT
*
19124433 -ATTTTATTT
1 AATTTT-TAT
19124442 GAATTTTTAT
1 -AATTTTTAT
19124452 -ATTTTTAT
1 AATTTTTAT
* *
19124460 GATATTTAT
1 AATTTTTAT
*
19124469 TATTTTTAT
1 AATTTTTAT
* *
19124478 AATATTTAC
1 AATTTTTAT
*
19124487 AAATTTTAT
1 AATTTTTAT
** *
19124496 AAGTTCATAGA
1 AA-TTTTTA-T
* *
19124507 AAGTTTTAA
1 AATTTTTAT
19124516 ATATTTTTA-
1 A-ATTTTTAT
19124525 ACATGTTTTAT
1 A-AT-TTTTAT
19124536 --TTTTTAT
1 AATTTTTAT
* *
19124543 AATTAATTAG
1 AATT-TTTAT
19124553 AATTTTTAT
1 AATTTTTAT
*
19124562 AATATTTAT
1 AATTTTTAT
19124571 AAGTTTTTAT
1 AA-TTTTTAT
19124581 GAATTTTTAT
1 -AATTTTTAT
* *
19124591 TAGTTTTAT
1 AATTTTTAT
19124600 AATTTTTTAT
1 AA-TTTTTAT
*
19124610 AA-TATTAT
1 AATTTTTAT
*
19124618 AAGTTTATAT
1 AA-TTTTTAT
19124628 AATTTT
1 AATTTT
19124634 GTAATATTTT
Statistics
Matches: 224, Mismatches: 50, Indels: 58
0.67 0.15 0.17
Matches are distributed among these distances:
6 1 0.00
7 11 0.05
8 30 0.13
9 81 0.36
10 85 0.38
11 16 0.07
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (9 bp):
AATTTTTAT
Found at i:19124606 original size:19 final size:19
Alignment explanation
Indices: 19124536--19124611 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
19124526 CATGTTTTAT
* *
19124536 TTTTTATAATTAATTAGAA-
1 TTTTTATAATT-TTTATAAG
*
19124555 TTTTTATAATATTTATAAG
1 TTTTTATAATTTTTATAAG
*
19124574 TTTTTATGAATTTTTATTAG
1 TTTTTAT-AATTTTTATAAG
19124594 -TTTTATAATTTTTTATAA
1 TTTTTATAA-TTTTTATAA
19124612 TATTATAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.15
19 31 0.65
20 10 0.21
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAG
Found at i:19129279 original size:2 final size:2
Alignment explanation
Indices: 19129272--19129310 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19129262 TTCTCTGCAA
19129272 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19129311 TTTGAAGCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19142793 original size:2 final size:2
Alignment explanation
Indices: 19142788--19142818 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19142778 TCTACATTGA
19142788 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
19142819 GTTTTTGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:19147657 original size:5 final size:5
Alignment explanation
Indices: 19147622--19147655 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
19147612 TTTCTTAAGA
*
19147622 AATGT AATGT AATGT AATGT AATGT AATGC AATG
1 AATGT AATGT AATGT AATGT AATGT AATGT AATG
19147656 CATTGTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (5 bp):
AATGT
Found at i:19168599 original size:20 final size:20
Alignment explanation
Indices: 19168574--19168623 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19168564 TGGCTTAAAA
19168574 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19168594 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19168611 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19168624 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19173238 original size:20 final size:20
Alignment explanation
Indices: 19173213--19173262 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19173203 TGGCTTAAAA
19173213 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19173233 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19173250 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19173263 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19180195 original size:45 final size:45
Alignment explanation
Indices: 19180139--19180228 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
19180129 ATAGATAAAA
*
19180139 TAATATTAAAATAACCTACACTAATTAAAATTTAAGTAAAAAATT
1 TAATATTAAAATAACCTACACTAATTAAAATTTAAATAAAAAATT
**
19180184 TAATATTAAAATAATTTACACTAATTAAAATTTAAATAAAAAATT
1 TAATATTAAAATAACCTACACTAATTAAAATTTAAATAAAAAATT
19180229 AAAAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.36
Consensus pattern (45 bp):
TAATATTAAAATAACCTACACTAATTAAAATTTAAATAAAAAATT
Found at i:19201957 original size:17 final size:17
Alignment explanation
Indices: 19201935--19201968 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19201925 ATCCACTAAT
*
19201935 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
19201952 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
19201969 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:19206595 original size:17 final size:17
Alignment explanation
Indices: 19206573--19206606 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19206563 ATCCACTAAT
*
19206573 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
19206590 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
19206607 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:19208151 original size:4 final size:4
Alignment explanation
Indices: 19208142--19208171 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
19208132 CAAGAAGGAC
19208142 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
19208172 CATTCAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:19210223 original size:5 final size:5
Alignment explanation
Indices: 19210188--19210216 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
19210178 TCACAGTGAA
19210188 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
19210217 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:19213085 original size:13 final size:12
Alignment explanation
Indices: 19213067--19213155 Score: 76
Period size: 12 Copynumber: 7.4 Consensus size: 12
19213057 GATATTTTTA
19213067 ATATATTATAATT
1 ATATATTAT-ATT
19213080 ATATATTATATT
1 ATATATTATATT
* *
19213092 ATTTAATAT-TT
1 ATATATTATATT
* *
19213103 AGTATTAATATATA
1 A-TA-TATTATATT
*
19213117 ATATATCATATT
1 ATATATTATATT
*
19213129 ATTTATTATA-T
1 ATATATTATATT
19213140 -TATATTATATT
1 ATATATTATATT
19213151 ATATA
1 ATATA
19213156 ACAAAGTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
10 8 0.13
11 5 0.08
12 29 0.48
13 17 0.28
14 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (12 bp):
ATATATTATATT
Found at i:19213089 original size:5 final size:5
Alignment explanation
Indices: 19213068--19213154 Score: 65
Period size: 5 Copynumber: 17.0 Consensus size: 5
19213058 ATATTTTTAA
*
19213068 TATAT TATAA T-TA- TATAT TATAT TAT-T TAATATT TAGTAT TA-AT
1 TATAT TATAT TATAT TATAT TATAT TATAT T-ATA-T TA-TAT TATAT
* *
19213112 ATATAA TATAT CATAT TATTTAT TATAT TATAT TATAT TATAT
1 -TATAT TATAT TATAT TA--TAT TATAT TATAT TATAT TATAT
19213155 AACAAAGTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
3 1 0.01
4 8 0.12
5 44 0.66
6 5 0.07
7 9 0.13
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:19213089 original size:7 final size:7
Alignment explanation
Indices: 19213067--19213155 Score: 57
Period size: 7 Copynumber: 12.7 Consensus size: 7
19213057 GATATTTTTA
19213067 ATATATT
1 ATATATT
19213074 ATA-ATT
1 ATATATT
19213080 ATATATT
1 ATATATT
19213087 ATATTATT
1 ATA-TATT
19213095 -TAATATT
1 AT-ATATT
19213102 -TAGTATT
1 ATA-TATT
19213109 A-ATA-T
1 ATATATT
19213114 ATA-ATAT
1 ATATAT-T
19213121 ATCATATT
1 AT-ATATT
*
19213129 ATTTATT
1 ATATATT
19213136 ATAT-TAT
1 ATATAT-T
19213143 ATTATATT
1 A-TATATT
19213151 ATATA
1 ATATA
19213156 ACAAAGTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 26
0.71 0.02 0.27
Matches are distributed among these distances:
5 3 0.04
6 11 0.16
7 36 0.54
8 14 0.21
9 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (7 bp):
ATATATT
Found at i:19213122 original size:37 final size:39
Alignment explanation
Indices: 19213068--19213156 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 39
19213058 ATATTTTTAA
* *
19213068 TATATTATAATTATATATTATATTATTTAATAT-TTAGTAT
1 TATATTAT-ATAATATATCATATTATTTAATATATTA-TAT
*
19213108 TA-A-TATATAATATATCATATTATTTATTATATTATAT
1 TATATTATATAATATATCATATTATTTAATATATTATAT
19213145 TATATTATATAA
1 TATATTATATAA
19213157 CAAAGTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 26 0.60
38 7 0.16
39 8 0.19
40 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (39 bp):
TATATTATATAATATATCATATTATTTAATATATTATAT
Found at i:19214308 original size:28 final size:30
Alignment explanation
Indices: 19214277--19214332 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19214267 GCGCTCTCTG
19214277 ATTATTAGCA-ATT-AGTGCTCTCTGTTCT
1 ATTATTAGCACATTAAGTGCTCTCTGTTCT
*
19214305 ATTATTAGCACGTTAAGTGCTCTCTGTT
1 ATTATTAGCACATTAAGTGCTCTCTGTT
19214333 TAGCATATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 10 0.40
29 2 0.08
30 13 0.52
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (30 bp):
ATTATTAGCACATTAAGTGCTCTCTGTTCT
Found at i:19214366 original size:22 final size:22
Alignment explanation
Indices: 19214310--19214370 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
19214300 GTTCTATTAT
* *
19214310 TAGCACGTTAAGTGCTCTCTGTT
1 TAGCAC-TTTAGTGCTCTCTGTA
*
19214333 TAGCA-TAT-GTGCTCTCTGTA
1 TAGCACTTTAGTGCTCTCTGTA
19214353 TAGCACTTTAGTGCTCTC
1 TAGCACTTTAGTGCTCTC
19214371 GTTTCATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 16 0.50
21 3 0.09
22 8 0.25
23 5 0.16
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (22 bp):
TAGCACTTTAGTGCTCTCTGTA
Found at i:19230301 original size:46 final size:46
Alignment explanation
Indices: 19230230--19230447 Score: 357
Period size: 46 Copynumber: 4.7 Consensus size: 46
19230220 TGTCATAGTG
* * * * *
19230230 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGCTGCCATGGTA
*
19230276 TCTTTCAACTATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
19230322 TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
19230368 TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
*
19230414 TCTTTCAACCATGGCCTTACACATTTCATATCAG
1 TCTTTCAACCATGGTCTTACACATTTCATATCAG
19230448 AGAGCACACT
Statistics
Matches: 165, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
45 4 0.02
46 161 0.98
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
Found at i:19234729 original size:18 final size:19
Alignment explanation
Indices: 19234695--19234744 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
19234685 AATATTTAAG
*
19234695 TATTAATATATAATATATCA
1 TATT-ATATATATTATATCA
*
19234715 TATTAT-TATATTATATTA
1 TATTATATATATTATATCA
19234733 TATTATATATAT
1 TATTATATATAT
19234745 AAAACATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 16 0.59
19 7 0.26
20 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATATATATTATATCA
Found at i:19234734 original size:23 final size:23
Alignment explanation
Indices: 19234695--19234740 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
19234685 AATATTTAAG
19234695 TATTAATATATAATATATCATAT
1 TATTAATATATAATATATCATAT
* *
19234718 TATT-ATATTATATTATATTATAT
1 TATTAATA-TATAATATATCATAT
19234741 ATATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTAATATATAATATATCATAT
Found at i:19234743 original size:39 final size:40
Alignment explanation
Indices: 19234659--19234746 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 40
19234649 TAATATAAAA
* *
19234659 ATATATATTATATATTATATTAATTTAATATTTAAGTATT
1 ATATATATAATATATCATATTAATTTAATATTTAAGTATT
*
19234699 A-ATATATAATATATCATATT-ATTATATTATATT-A-TATT
1 ATATATATAATATATCATATTAATT-TAATAT-TTAAGTATT
19234737 ATATATATAA
1 ATATATATAA
19234747 AACATAAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 8 0.19
39 31 0.74
40 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (40 bp):
ATATATATAATATATCATATTAATTTAATATTTAAGTATT
Found at i:19235923 original size:29 final size:30
Alignment explanation
Indices: 19235891--19235947 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
19235881 GCGCTCTCTG
19235891 ATTATTAGCACATT-AGTGCTCTCTGTTCT
1 ATTATTAGCACATTAAGTGCTCTCTGTTCT
*
19235920 ATTATTAGCACGTTAAGTGCTCTCTGTT
1 ATTATTAGCACATTAAGTGCTCTCTGTT
19235948 TAGCACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (30 bp):
ATTATTAGCACATTAAGTGCTCTCTGTTCT
Found at i:19235964 original size:22 final size:22
Alignment explanation
Indices: 19235935--19235991 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
19235925 TAGCACGTTA
19235935 AGTGCTCTCTGTTTAGCAC-AT
1 AGTGCTCTCTGTTTAGCACTAT
* *
19235956 ATGTGCTCTCTGTATAGCACTTT
1 A-GTGCTCTCTGTTTAGCACTAT
19235979 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
19235992 CATTTGTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTAT
Found at i:19238788 original size:17 final size:16
Alignment explanation
Indices: 19238766--19238797 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
19238756 CCAATTTGTG
19238766 AAAAAATAAAATAAAAT
1 AAAAAATAAAA-AAAAT
19238783 AAAAAATAAAAAAAA
1 AAAAAATAAAAAAAA
19238798 CACAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:19240709 original size:10 final size:10
Alignment explanation
Indices: 19240694--19240725 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
19240684 GTATTAATTA
19240694 AATTATTTTT
1 AATTATTTTT
19240704 AATTATTTTT
1 AATTATTTTT
*
19240714 AATTTTTTTT
1 AATTATTTTT
19240724 AA
1 AA
19240726 AAATTATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTATTTTT
Found at i:19241813 original size:22 final size:22
Alignment explanation
Indices: 19241785--19241826 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19241775 ATAGCTAATG
19241785 GAATTTATTCTAAAATTAAAAA
1 GAATTTATTCTAAAATTAAAAA
*
19241807 GAATTTATTTTAAAATTAAA
1 GAATTTATTCTAAAATTAAA
19241827 GCATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
GAATTTATTCTAAAATTAAAAA
Found at i:19243975 original size:3 final size:3
Alignment explanation
Indices: 19243969--19243994 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19243959 TACTAAATAA
19243969 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
19243995 AACCTAGCCA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19245913 original size:56 final size:56
Alignment explanation
Indices: 19245827--19245955 Score: 195
Period size: 56 Copynumber: 2.3 Consensus size: 56
19245817 CGGCTGTGTC
* * *
19245827 AGTCAGTATGCTCACACAGCCTAGCACACGGGCGTGTGGCTTGGCCGTGTGACCTA
1 AGTCAGTATACTCACACAGCCTAGCACACGGGCGTATGGCTTGGCCGTGTGACCCA
* * *
19245883 AGTCAGTATACTCATACAGTCTAGCACACGGGCGTATGGTTTGGCCGTGTGACCCA
1 AGTCAGTATACTCACACAGCCTAGCACACGGGCGTATGGCTTGGCCGTGTGACCCA
*
19245939 AGTTAGTATACTCACAC
1 AGTCAGTATACTCACAC
19245956 GGGCATGGAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 65 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.24
Consensus pattern (56 bp):
AGTCAGTATACTCACACAGCCTAGCACACGGGCGTATGGCTTGGCCGTGTGACCCA
Found at i:19247277 original size:19 final size:19
Alignment explanation
Indices: 19247250--19247310 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
19247240 CTTGTTAATG
*
19247250 GTGTTTGATTAGTGGAATT
1 GTGTCTGATTAGTGGAATT
* *
19247269 GTGTCTGATTAATGGAACT
1 GTGTCTGATTAGTGGAATT
* *
19247288 GCGTGTGATTAGTGGAATT
1 GTGTCTGATTAGTGGAATT
19247307 GTGT
1 GTGT
19247311 ATGCATGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.41
Consensus pattern (19 bp):
GTGTCTGATTAGTGGAATT
Found at i:19251337 original size:18 final size:17
Alignment explanation
Indices: 19251302--19251339 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
19251292 GAAATTTATT
19251302 ATTTTATAAATTTAAAA
1 ATTTTATAAATTTAAAA
*
19251319 ATTTTATATAATTTTAAA
1 ATTTTATA-AATTTAAAA
19251337 ATT
1 ATT
19251340 CTTTTAGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTATAAATTTAAAA
Found at i:19251499 original size:2 final size:2
Alignment explanation
Indices: 19251492--19251518 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19251482 AACGAAATTA
19251492 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 A
19251519 AATGCAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19253813 original size:19 final size:18
Alignment explanation
Indices: 19253786--19253825 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
19253776 TCTCATTTTA
*
19253786 TCATTTCATATTTCATTTC
1 TCATCTCATA-TTCATTTC
19253805 TCATCTCATATTCATTTC
1 TCATCTCATATTCATTTC
19253823 TCA
1 TCA
19253826 ACTTTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.53
Consensus pattern (18 bp):
TCATCTCATATTCATTTC
Found at i:19260902 original size:29 final size:30
Alignment explanation
Indices: 19260840--19260902 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
19260830 AATTATATTT
* * *
19260840 TTATAATTTTTAAATGATTAAATCAAAATC
1 TTATAATTTTTAAAGGATAAAATCAAAATA
* *
19260870 TTATCATTTTTAAAGGATAAAAT-ATAATA
1 TTATAATTTTTAAAGGATAAAATCAAAATA
19260899 TTAT
1 TTAT
19260903 TATTAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
TTATAATTTTTAAAGGATAAAATCAAAATA
Found at i:19262905 original size:30 final size:28
Alignment explanation
Indices: 19262837--19262892 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
19262827 AACAATAATG
* *
19262837 TAAGTGACTAAAATGTAAAATTTTAAACA
1 TAAGTGACTAAAATCT-AAATTTAAAACA
19262866 TAAGTGACTAAAATCT-AATTTAAAACA
1 TAAGTGACTAAAATCTAAATTTAAAACA
19262893 AATAAAGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.40
29 15 0.60
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (28 bp):
TAAGTGACTAAAATCTAAATTTAAAACA
Found at i:19264289 original size:3 final size:3
Alignment explanation
Indices: 19264281--19264317 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
19264271 GAGATCATCT
19264281 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19264318 TTAAAAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19277879 original size:46 final size:46
Alignment explanation
Indices: 19277773--19278093 Score: 417
Period size: 46 Copynumber: 7.0 Consensus size: 46
19277763 TTTGACATGA
* * * * ** * * *
19277773 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
** * *
19277820 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*** *** * *
19277866 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
19277912 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
19277958 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
* *
19278004 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
19278050 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
19278094 AGAGCACACT
Statistics
Matches: 250, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 221 0.88
47 29 0.12
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:19280266 original size:18 final size:20
Alignment explanation
Indices: 19280251--19280287 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19280241 TAATAATAAA
*
19280251 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
19280271 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
19280288 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:19282197 original size:93 final size:93
Alignment explanation
Indices: 19282037--19282208 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
19282027 AGGATATTTG
* *
19282037 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAAATGCGAATGTCCGAACTCGTTAAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAAATGCGAACGCCCGAACTCGTTAAG
19282102 TTGAGGCCGAGTTCGAGAGATGTAACTA
66 TTGAGGCCGAGTTCGAGAGATGTAACTA
* ** * *
19282130 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAAATGCGAACGCCCGAACTCGTTAAG
*
19282195 TTGAGTCCGAGTTC
66 TTGAGGCCGAGTTC
19282209 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAAATGCGAACGCCCGAACTCGTTAAG
TTGAGGCCGAGTTCGAGAGATGTAACTA
Found at i:19282215 original size:46 final size:46
Alignment explanation
Indices: 19282042--19282216 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 46
19282032 ATTTGGGCAT
** * *
19282042 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAAATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *** * * * *
19282088 CCGAACTCGTTAAGTTGAGGCCGAGTTCGAGAGATGTA-AC-TAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAACGC
*
19282133 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
19282181 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19282217 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
45 2 0.02
46 68 0.66
47 30 0.29
48 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:19302515 original size:21 final size:21
Alignment explanation
Indices: 19302489--19302531 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
19302479 TTAGTATTTA
*
19302489 TTAATTTTTTTATTTTAAAAT
1 TTAATTTTTTTAGTTTAAAAT
19302510 TTAATTTTTTTAGTTTAAAAT
1 TTAATTTTTTTAGTTTAAAAT
19302531 T
1 T
19302532 ACTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTAATTTTTTTAGTTTAAAAT
Found at i:19321990 original size:19 final size:19
Alignment explanation
Indices: 19321962--19321998 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19321952 CTTTGAGTAG
*
19321962 AAACCAAAAACTTTAACAC
1 AAACCAAAAACTTCAACAC
*
19321981 AAACCTAAAACTTCAACA
1 AAACCAAAAACTTCAACA
19321999 ATAACAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (19 bp):
AAACCAAAAACTTCAACAC
Found at i:19325071 original size:15 final size:15
Alignment explanation
Indices: 19325030--19325071 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
19325020 CATAAGTGAC
19325030 TAAAATATAAT-ATT
1 TAAAATATAATAATT
*
19325044 TCAAATATAAATAATT
1 TAAAATAT-AATAATT
19325060 TAAAATATAATA
1 TAAAATATAATA
19325072 TAAGACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 7 0.29
16 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATAATAATT
Found at i:19327388 original size:18 final size:18
Alignment explanation
Indices: 19327367--19327402 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19327357 TATTTAAATT
* *
19327367 AAAATTTCAAAATTCAAA
1 AAAATTTAAAAAATCAAA
19327385 AAAATTTAAAAAATCAAA
1 AAAATTTAAAAAATCAAA
19327403 TTAAAATATG
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:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTTAAAAAATCAAA
Found at i:19329254 original size:6 final size:6
Alignment explanation
Indices: 19329245--19329271 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19329235 TTCGAGTGGA
19329245 CCAGAT CCAGAT CCAGAT CCAGAT CCA
1 CCAGAT CCAGAT CCAGAT CCAGAT CCA
19329272 AACAAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.37, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAGAT
Found at i:19336590 original size:89 final size:89
Alignment explanation
Indices: 19336438--19336606 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
19336428 CATGGCCATC
19336438 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
1 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
19336503 AAGTATATATTCTTGTAATTTATT
66 AAGTATATATTCTTGTAATTTATT
* * * * *
19336527 GTGCTTACTACCAAGGCTTGAAAATTTCCTCTAGA-TTCAATGGATTCATACTTTAAAGTTCAAT
1 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTT-AATGAACTCATACTTCAAAGCTCAAT
* * *
19336591 CATGTTTTTATTCTTG
65 CAAGTATATATTCTTG
19336607 AATCCTTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 2 0.03
89 69 0.97
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (89 bp):
GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
AAGTATATATTCTTGTAATTTATT
Found at i:19338717 original size:52 final size:48
Alignment explanation
Indices: 19338653--19338798 Score: 145
Period size: 52 Copynumber: 3.0 Consensus size: 48
19338643 AAATGTGATT
* *
19338653 TCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATACGTGC
1 TCCGTATAAGACCATAGCTGGGCTATGGCATCGGAG---TGTGATACGTGA
* * *
19338704 TACTGTATAAGACCATATCTGGGATATGGCATC--AGTGTGATACGTGA
1 T-CCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGTGATACGTGA
* * * *
19338751 TCCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTA-TGTGATATGTGA
1 TCCGTATAAGACCATAGCTGGGCTATGGCATCGG-AGTGTGATACGTGA
19338799 CTATGTGCAA
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
46 25 0.32
47 12 0.15
48 11 0.14
49 1 0.01
50 2 0.03
51 1 0.01
52 27 0.34
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (48 bp):
TCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGTGATACGTGA
Found at i:19340794 original size:13 final size:14
Alignment explanation
Indices: 19340773--19340805 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19340763 TATAATATTT
19340773 AAAAA-TATTT-AA
1 AAAAATTATTTCAA
19340785 AAAAATTATTTCAA
1 AAAAATTATTTCAA
19340799 AAAAATT
1 AAAAATT
19340806 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 5 0.26
14 9 0.47
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTATTTCAA
Found at i:19340817 original size:11 final size:11
Alignment explanation
Indices: 19340766--19340817 Score: 54
Period size: 10 Copynumber: 4.6 Consensus size: 11
19340756 TAAATTATAT
19340766 AATATTT-AAA
1 AATATTTAAAA
19340776 AATATTTAAAAA
1 AATATTT-AAAA
19340788 AATTATTTCAAAA
1 AA-TATTT-AAAA
19340801 AA-ATTTAAAA
1 AATATTTAAAA
*
19340811 TATATTT
1 AATATTT
19340818 TCTAAATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 12 0.33
11 8 0.22
12 5 0.14
13 11 0.31
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:19364472 original size:13 final size:13
Alignment explanation
Indices: 19364441--19364475 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19364431 ACAAATAAAA
19364441 AAAATTATA-AAT
1 AAAATTATATAAT
*
19364453 TAAATTATATAAT
1 AAAATTATATAAT
19364466 AAAATTATAT
1 AAAATTATAT
19364476 TTTGACCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTATATAAT
Found at i:19368203 original size:32 final size:32
Alignment explanation
Indices: 19368167--19368227 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
19368157 AGGCTGAACT
19368167 GAAGCTCATAAGAGCTAAAC-AGAAACCCAACG
1 GAAGCTCATAAGAGCTAAACGA-AAACCCAACG
** *
19368199 GAAGCTTGTAAGAGCTGAACGAAAACCCA
1 GAAGCTCATAAGAGCTAAACGAAAACCCA
19368228 TAAGGGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.11
Consensus pattern (32 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCAACG
Found at i:19368231 original size:21 final size:21
Alignment explanation
Indices: 19368207--19368267 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
19368197 CGGAAGCTTG
19368207 TAAGAGCTGAACGAAAACCCA
1 TAAGAGCTGAACGAAAACCCA
* * * * *
19368228 TAAGGGTTAAAC-AGAAGCTCA
1 TAAGAGCTGAACGA-AAACCCA
*
19368249 AAAGAGCTGAACGAAAACC
1 TAAGAGCTGAACGAAAACC
19368268 TATTAGGGTT
Statistics
Matches: 27, Mismatches: 11, Indels: 4
0.64 0.26 0.10
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (21 bp):
TAAGAGCTGAACGAAAACCCA
Found at i:19382298 original size:21 final size:22
Alignment explanation
Indices: 19382281--19382322 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19382271 ACCTAAATTT
19382281 TTAAA-TTTAAAAAATAAATAA
1 TTAAATTTTAAAAAATAAATAA
*
19382302 TTAAATTTTTAAAAATAAATA
1 TTAAATTTTAAAAAATAAATA
19382323 TATAGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAATTTTAAAAAATAAATAA
Found at i:19383086 original size:18 final size:20
Alignment explanation
Indices: 19383055--19383091 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
19383045 AAAATTATTT
19383055 AAAAAATCAACATT-TAAAA
1 AAAAAATCAACATTATAAAA
*
19383074 AAAAAATC-TCATTATAAA
1 AAAAAATCAACATTATAAA
19383092 GAATTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAATCAACATTATAAAA
Found at i:19385839 original size:20 final size:21
Alignment explanation
Indices: 19385805--19385858 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
19385795 TGATGATATT
*
19385805 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
19385826 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
19385846 TTTTATTATTTTA
1 TTATATTATTTTA
19385859 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:19385864 original size:11 final size:11
Alignment explanation
Indices: 19385848--19385875 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
19385838 ATGAGATATT
19385848 TTATTATTTTA
1 TTATTATTTTA
19385859 TTATTATTTTA
1 TTATTATTTTA
19385870 TTATTA
1 TTATTA
19385876 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:19387611 original size:25 final size:25
Alignment explanation
Indices: 19387583--19387657 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
19387573 AGATGCTTGA
19387583 GATTGCATGTTATTGATGTGAATAT
1 GATTGCATGTTATTGATGTGAATAT
*
19387608 GATTTGAATG-TA--GATGCT---TGA-
1 GA-TTGCATGTTATTGATG-TGAAT-AT
19387629 GATTGCATGTTATTGATGTGAATAT
1 GATTGCATGTTATTGATGTGAATAT
19387654 GATT
1 GATT
19387658 TGAATGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 20
0.63 0.03 0.33
Matches are distributed among these distances:
20 6 0.16
21 5 0.13
22 2 0.05
23 8 0.21
24 2 0.05
25 9 0.24
26 6 0.16
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (25 bp):
GATTGCATGTTATTGATGTGAATAT
Found at i:19387625 original size:46 final size:46
Alignment explanation
Indices: 19387572--19387664 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
19387562 ATTATATTCT
19387572 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
1 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
19387618 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
1 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
19387664 T
1 T
19387665 TCATTGTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (46 bp):
TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
Found at i:19388097 original size:46 final size:46
Alignment explanation
Indices: 19388044--19388225 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
19388034 AGTGTGCTCT
*
19388044 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
19388090 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *
19388136 GTGATATGAAATGAACAAGACCATGGTTGAAAGATAACATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
19388182 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
19388226 TCATGTCAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 119 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:19388946 original size:17 final size:17
Alignment explanation
Indices: 19388924--19388959 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
19388914 TCCCTCTCTC
19388924 CATAGCTAGGGTTTCTT
1 CATAGCTAGGGTTTCTT
19388941 CATAGCTAGGGTTTCTT
1 CATAGCTAGGGTTTCTT
19388958 CA
1 CA
19388960 ACTTTCAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (17 bp):
CATAGCTAGGGTTTCTT
Found at i:19389621 original size:46 final size:45
Alignment explanation
Indices: 19389569--19389743 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
19389559 TGGTTGAGCA
* *
19389569 TCCGAACTCGTTGAGTTAAGTTCGAGTTCACTTACGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * *
19389615 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
*
19389660 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* *
19389708 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
19389744 GGCGGGTTAC
Statistics
Matches: 107, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 58 0.54
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:19389725 original size:93 final size:93
Alignment explanation
Indices: 19389566--19389736 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
19389556 GGATGGTTGA
* * **
19389566 GCATCCGAACTCGTTGAGTTAAGTTCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
19389631 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
19389659 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
19389724 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
19389737 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:19398350 original size:17 final size:17
Alignment explanation
Indices: 19398328--19398360 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19398318 TAATTAATTA
*
19398328 ATTATATTTTATTTATT
1 ATTATATTATATTTATT
19398345 ATTATATTATATTTAT
1 ATTATATTATATTTAT
19398361 CTTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATATTATATTTATT
Found at i:19401255 original size:18 final size:19
Alignment explanation
Indices: 19401221--19401256 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19401211 TTAGTCTCTC
*
19401221 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTATAAAAT
19401240 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
19401257 ATTATAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAT
Found at i:19401257 original size:19 final size:19
Alignment explanation
Indices: 19401221--19401259 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19401211 TTAGTCTCTC
*
19401221 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTTAAAAAT
19401240 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TAAAAAT
19401259 T
1 T
19401260 ATAACATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TCAAAATAATTTTAAAAAT
Found at i:19401802 original size:29 final size:29
Alignment explanation
Indices: 19401770--19401830 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
19401760 TAGTTTTTGT
19401770 AATAGATTTA-ATACTTTTTTATTTTTAAA
1 AATA-ATTTATATACTTTTTTATTTTTAAA
* * *
19401799 AATATTTTATATAGTTTTTTATTTTTTAA
1 AATAATTTATATACTTTTTTATTTTTAAA
19401828 AAT
1 AAT
19401831 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AATAATTTATATACTTTTTTATTTTTAAA
Found at i:19402562 original size:18 final size:16
Alignment explanation
Indices: 19402534--19402568 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
19402524 CTAACGGCGG
19402534 AAATAATATTTATATTA
1 AAATAATATTTAT-TTA
19402551 AAATATATATTTATTTA
1 AAATA-ATATTTATTTA
19402568 A
1 A
19402569 CAATTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATAATATTTATTTA
Found at i:19402808 original size:15 final size:15
Alignment explanation
Indices: 19402778--19402821 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
19402768 TAAAATAAAA
*
19402778 TAAAATATTTAAATTT
1 TAAAAT-TTAAAATTT
19402794 TAAAATTTAAAATTT
1 TAAAATTTAAAATTT
*
19402809 TATAATTTAAAAT
1 TAAAATTTAAAAT
19402822 CTATATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTAAAATTT
Found at i:19402909 original size:15 final size:15
Alignment explanation
Indices: 19402886--19402927 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
19402876 ATAATTTAAA
*
19402886 TTCAGTACTTAAAAT
1 TTCAATACTTAAAAT
*
19402901 TTCAATACTTAATAT
1 TTCAATACTTAAAAT
*
19402916 TTCAACACTTAA
1 TTCAATACTTAA
19402928 TTTGTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (15 bp):
TTCAATACTTAAAAT
Found at i:19430192 original size:38 final size:41
Alignment explanation
Indices: 19430121--19430201 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 41
19430111 TAATTCATAA
*
19430121 AAATTCAAAAAAAGTTTAATTAAAAAAATTTAAAATTTAAC
1 AAATTCAAAAAAAGTTTAATTAAAAAAATTTAAAAATTAAC
* **
19430162 AAATTC-AAAAAAG-TTCA-TAAAAACTTTTAAAAATTAAC
1 AAATTCAAAAAAAGTTTAATTAAAAAAATTTAAAAATTAAC
19430200 AA
1 AA
19430202 CCTAATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 20 0.56
39 3 0.08
40 7 0.19
41 6 0.17
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (41 bp):
AAATTCAAAAAAAGTTTAATTAAAAAAATTTAAAAATTAAC
Found at i:19431933 original size:56 final size:56
Alignment explanation
Indices: 19431870--19431982 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
19431860 TTAATCAAAA
*
19431870 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAGCAATTTT
1 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
19431926 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
1 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
19431982 C
1 C
19431983 TTACATATGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.29, C:0.17, G:0.01, T:0.53
Consensus pattern (56 bp):
CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
Found at i:19450652 original size:27 final size:27
Alignment explanation
Indices: 19450619--19450692 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
19450609 GAGGGCATGT
** *
19450619 CACAGGCGGCACCGGTGGTGGGGGTGC
1 CACAGGCGGCACCAATGGAGGGGGTGC
* * *
19450646 CAGAGGCGGCACCAATGGAGGGGTTGT
1 CACAGGCGGCACCAATGGAGGGGGTGC
19450673 CACAGGCGGCACCAATGGAG
1 CACAGGCGGCACCAATGGAG
19450693 AAGAAAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.20, C:0.24, G:0.45, T:0.11
Consensus pattern (27 bp):
CACAGGCGGCACCAATGGAGGGGGTGC
Found at i:19450725 original size:14 final size:14
Alignment explanation
Indices: 19450690--19450718 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19450680 GGCACCAATG
19450690 GAGAAGAA-AAGAA
1 GAGAAGAAGAAGAA
19450703 GAGAAGAAGAAGAA
1 GAGAAGAAGAAGAA
19450717 GA
1 GA
19450719 ACAGAAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAGAAGAAGAAGAA
Found at i:19451423 original size:6 final size:6
Alignment explanation
Indices: 19451414--19451438 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19451404 TATTTTTGTT
19451414 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
19451439 AATATTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:19451446 original size:20 final size:20
Alignment explanation
Indices: 19451404--19451446 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
19451394 TGGGATAGCC
* * * *
19451404 TATTTTTGTTTTTTTATTTT
1 TATTTTTATTTTTATAATAT
19451424 TATTTTTATTTTTATAATAT
1 TATTTTTATTTTTATAATAT
19451444 TAT
1 TAT
19451447 GGTAAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TATTTTTATTTTTATAATAT
Found at i:19452051 original size:24 final size:24
Alignment explanation
Indices: 19452024--19452069 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
19452014 GAGAGAATTT
19452024 TTAT-TTTATTTAATATCAATATAA
1 TTATATTTA-TTAATATCAATATAA
*
19452048 TTATATTTATTAATATTAATAT
1 TTATATTTATTAATATCAATAT
19452070 TAATATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATTTATTAATATCAATATAA
Found at i:19452064 original size:6 final size:6
Alignment explanation
Indices: 19452055--19452081 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19452045 TAATTATATT
19452055 TATTAA TATTAA TATTAA TATTAA TAT
1 TATTAA TATTAA TATTAA TATTAA TAT
19452082 AAAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:19452100 original size:18 final size:19
Alignment explanation
Indices: 19452055--19452092 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
19452045 TAATTATATT
* *
19452055 TATTAATAT-TAATATTAA
1 TATTAATATAAAATATAAA
19452073 TATTAATATAAAATATAAA
1 TATTAATATAAAATATAAA
19452092 T
1 T
19452093 TTATTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTAATATAAAATATAAA
Found at i:19464001 original size:21 final size:19
Alignment explanation
Indices: 19463976--19464029 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
19463966 AACCCAAAAA
19463976 AAATAGCAAAATCAAAATACC
1 AAATAGCAAAATCAAAAT--C
19463997 AAATAGCAAACAATCAAAATC
1 AAATAGC-AA-AATCAAAATC
19464018 AAATCAGCAAAA
1 AAAT-AGCAAAA
19464030 AAAGAACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.07
21 14 0.47
22 5 0.17
23 9 0.30
ACGTcount: A:0.63, C:0.19, G:0.06, T:0.13
Consensus pattern (19 bp):
AAATAGCAAAATCAAAATC
Found at i:19466351 original size:2 final size:2
Alignment explanation
Indices: 19466344--19466386 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
19466334 GAGAAACCTA
* *
19466344 AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG A- AG TG AG A- AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19466384 AG A
1 AG A
19466387 ACTAAAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:19476127 original size:15 final size:15
Alignment explanation
Indices: 19476109--19476147 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
19476099 TTATATAATC
*
19476109 AATATATTTATATTA
1 AATATATTTAAATTA
*
19476124 AATATATTAAAATTA
1 AATATATTTAAATTA
*
19476139 AATAAATTT
1 AATATATTT
19476148 TTGGTCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATTTAAATTA
Found at i:19484396 original size:52 final size:50
Alignment explanation
Indices: 19484298--19484396 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 50
19484288 TGAAGTAAAC
* * * * *
19484298 AAGAAAACAAGAAAGCTTTGAGTAAATTTTCTAAGGTCGCATGGTTAATT
1 AAGAAAACAAGAAAGCTTTGAGTAAACTCTCTAAGGCCACACGGTTAATT
*
19484348 AAGAAAACTCAAGAAATCTTTGAGTAAACTCTCTAAGGCCACACGGTTA
1 AAGAAAA--CAAGAAAGCTTTGAGTAAACTCTCTAAGGCCACACGGTTA
19484397 GTTCGACTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 7 0.17
52 34 0.83
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (50 bp):
AAGAAAACAAGAAAGCTTTGAGTAAACTCTCTAAGGCCACACGGTTAATT
Found at i:19485395 original size:22 final size:21
Alignment explanation
Indices: 19485369--19485409 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19485359 TTGTTAACTA
19485369 TTTACAATTTTTTAATAATTAT
1 TTTACAA-TTTTTAATAATTAT
*
19485391 TTTACGATTTTTAATAATT
1 TTTACAATTTTTAATAATT
19485410 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTACAATTTTTAATAATTAT
Found at i:19485426 original size:40 final size:39
Alignment explanation
Indices: 19485382--19485459 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
19485372 ACAATTTTTT
* *
19485382 AATAATTATTTTACGATTTTTAATAATTTTTAAAAAATTA
1 AATAA-TATTTTACAACTTTTAATAATTTTTAAAAAATTA
* * *
19485422 AATAATGTTTTATAACTTTTAATAATTTTTTAAAAATT
1 AATAATATTTTACAACTTTTAATAATTTTTAAAAAATT
19485460 TTAAATATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (39 bp):
AATAATATTTTACAACTTTTAATAATTTTTAAAAAATTA
Found at i:19485445 original size:20 final size:19
Alignment explanation
Indices: 19485399--19485488 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
19485389 ATTTTACGAT
19485399 TTTTAATAATTTTTAAAAA
1 TTTTAATAATTTTTAAAAA
* * * *
19485418 ATTAAATAATGTTTTATAAC
1 TTTTAATAAT-TTTTAAAAA
19485438 TTTTAATAATTTTTTAAAAA
1 TTTTAATAA-TTTTTAAAAA
*
19485458 TTTTAA-ATATTTTAAAAAA
1 TTTTAATA-ATTTTTAAAAA
*
19485477 TATTTAAAAATT
1 T-TTTAATAATT
19485489 ATTACAATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
19 19 0.33
20 36 0.63
21 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
TTTTAATAATTTTTAAAAA
Found at i:19485487 original size:10 final size:9
Alignment explanation
Indices: 19485449--19485488 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
19485439 TTTAATAATT
19485449 TTTTAAAAA
1 TTTTAAAAA
*
19485458 TTTTAAATA
1 TTTTAAAAA
19485467 TTTTAAAAAA
1 TTTT-AAAAA
19485477 TATTTAAAAA
1 T-TTTAAAAA
19485487 TT
1 TT
19485489 ATTACAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 13 0.48
10 11 0.41
11 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:19500801 original size:43 final size:43
Alignment explanation
Indices: 19500753--19500838 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
19500743 ATCCGAGGTC
*
19500753 TCGATACCTCGTTTTCAACCAAATTTATCTGATTAATTTTTTT
1 TCGATACCTCATTTTCAACCAAATTTATCTGATTAATTTTTTT
19500796 TCGATACCTCATTTTCAACCAAATTTATCTGATTAATTTTTTT
1 TCGATACCTCATTTTCAACCAAATTTATCTGATTAATTTTTTT
19500839 AAAATCGCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.49
Consensus pattern (43 bp):
TCGATACCTCATTTTCAACCAAATTTATCTGATTAATTTTTTT
Found at i:19501163 original size:17 final size:16
Alignment explanation
Indices: 19501136--19501196 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
19501126 GAGCAAAGGT
19501136 AAATATAATATTATAAAA
1 AAAT-TAATATTA-AAAA
*
19501154 AAATTAATA-TAAATA
1 AAATTAATATTAAAAA
* *
19501169 AAATTAACATTAAAAT
1 AAATTAATATTAAAAA
19501185 AAATTAAT-TTAA
1 AAATTAATATTAA
19501197 CAATATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 15 0.41
16 13 0.35
17 5 0.14
18 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATTAATATTAAAAA
Found at i:19501173 original size:15 final size:14
Alignment explanation
Indices: 19501147--19501192 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
19501137 AATATAATAT
19501147 TATAAAAAAATTAA
1 TATAAAAAAATTAA
19501161 TATAAATAAAATTAA
1 TATAAA-AAAATTAA
*
19501176 CATTAAAATAAATTAA
1 TA-TAAAA-AAATTAA
19501192 T
1 T
19501193 TTAACAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 10 0.37
16 11 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
TATAAAAAAATTAA
Found at i:19501186 original size:21 final size:22
Alignment explanation
Indices: 19501155--19501213 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
19501145 ATTATAAAAA
*
19501155 AATTAATATAAATAAAATTAAC
1 AATTAAAATAAATAAAATTAAC
* *
19501177 -ATTAAAATAAATTAATTTAAC
1 AATTAAAATAAATAAAATTAAC
*
19501198 AATATATAATAAATAA
1 AAT-TAAAATAAATAA
19501214 CTTATAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 18 0.60
22 2 0.07
23 10 0.33
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (22 bp):
AATTAAAATAAATAAAATTAAC
Found at i:19501230 original size:23 final size:23
Alignment explanation
Indices: 19501182--19501243 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
19501172 TTAACATTAA
*
19501182 AATAAATTAATTTAACAATATAT
1 AATAAATTAATTTAAAAATATAT
19501205 AATAAA-TAACTTATAAAAATAT-T
1 AATAAATTAA-TT-TAAAAATATAT
19501228 AATAACATT-ATTTAAA
1 AATAA-ATTAATTTAAA
19501244 TTACAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 7 0.21
23 16 0.47
24 10 0.29
25 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAATTAATTTAAAAATATAT
Found at i:19508850 original size:19 final size:20
Alignment explanation
Indices: 19508814--19508852 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19508804 ACGATTAATA
*
19508814 ATAATTTTTTTCGGTACAATC
1 ATAATTTTTTTC-ATACAATC
19508835 ATAATTTTTTT-ATACAAT
1 ATAATTTTTTTCATACAAT
19508853 TATCAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
ATAATTTTTTTCATACAATC
Found at i:19518483 original size:13 final size:13
Alignment explanation
Indices: 19518465--19518491 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19518455 ACAAATATCA
19518465 TACTTGTTTTGAG
1 TACTTGTTTTGAG
19518478 TACTTGTTTTGAG
1 TACTTGTTTTGAG
19518491 T
1 T
19518492 GTCTATTTAT
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:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TACTTGTTTTGAG
Found at i:19530834 original size:19 final size:18
Alignment explanation
Indices: 19530812--19530854 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
19530802 TTTTTTAAAA
19530812 TTTAATAATTTTTATATCT
1 TTTAATAATTTTTATAT-T
* * *
19530831 TTTATTGATTTTTATCTT
1 TTTAATAATTTTTATATT
19530849 TTTAAT
1 TTTAAT
19530855 TTTTTTGTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTAATAATTTTTATATT
Found at i:19540622 original size:20 final size:20
Alignment explanation
Indices: 19540594--19540632 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19540584 CGACCACGAG
19540594 CCTACCCACACGGGCGTGTC
1 CCTACCCACACGGGCGTGTC
*
19540614 CCTATCCACACGGGCGTGT
1 CCTACCCACACGGGCGTGT
19540633 GGCCCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.26, T:0.18
Consensus pattern (20 bp):
CCTACCCACACGGGCGTGTC
Found at i:19542527 original size:42 final size:42
Alignment explanation
Indices: 19542464--19542627 Score: 195
Period size: 42 Copynumber: 3.7 Consensus size: 42
19542454 CTTCGTTTTC
** *
19542464 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* *
19542507 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
19542548 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
*
19542597 TCGATGCTATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
19542628 GAATCACATA
Statistics
Matches: 105, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
41 2 0.02
42 63 0.60
43 1 0.01
45 2 0.02
48 1 0.01
49 36 0.34
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:19542609 original size:49 final size:48
Alignment explanation
Indices: 19542534--19542670 Score: 179
Period size: 49 Copynumber: 2.9 Consensus size: 48
19542524 TATGGTCTTA
*
19542534 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AAT
*
19542584 CACATATCACATATCGATGCTATAGCCCAGCTATGGTCTTACACGAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
* * * * *
19542632 CACATATCTCA-CT-GATGTCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
19542671 TACAGCAGCA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 22 0.28
47 1 0.01
48 13 0.16
49 37 0.47
50 6 0.08
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
Found at i:19542774 original size:31 final size:31
Alignment explanation
Indices: 19542739--19542887 Score: 190
Period size: 31 Copynumber: 4.8 Consensus size: 31
19542729 CTTGTCACTT
* *
19542739 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * * *
19542770 GTAGCCGGAGTTATCATTTTTCACTGGTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
19542801 GTAGCCGGAGCTACCACTTTTCACTGATCTG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
19542832 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
19542863 GCAGCCGAAGCTATCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
19542888 TGTCATTTGT
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:19542963 original size:50 final size:50
Alignment explanation
Indices: 19542865--19543039 Score: 287
Period size: 50 Copynumber: 3.5 Consensus size: 50
19542855 CTGATCAGGC
*
19542865 AGCCGAAGCTATCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGT
* * *
19542916 AGCTGAAGCTATCACTTATCACTTTCACTTGTCCTTTATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
*
19542966 AGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
*
19543016 AGCCGAAGCTATTACTTATCACTT
1 AGCCGAAGCTATCACTTATCACTT
19543040 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 94 0.81
51 22 0.19
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (50 bp):
AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
Found at i:19543589 original size:6 final size:6
Alignment explanation
Indices: 19543550--19543576 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19543540 TTTATATTTA
19543550 ATTGTT ATTGTT ATTGTT ATTGTT ATT
1 ATTGTT ATTGTT ATTGTT ATTGTT ATT
19543577 TAAATTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
ATTGTT
Found at i:19544196 original size:23 final size:21
Alignment explanation
Indices: 19544149--19544189 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
19544139 TTTGGTTAAA
19544149 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
19544171 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
19544190 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:19544567 original size:15 final size:15
Alignment explanation
Indices: 19544519--19544568 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
19544509 TTTATCAAAT
19544519 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
19544534 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
19544549 TTATATTGATTGAAA
1 TTATATTGATTGAAA
19544564 TTATA
1 TTATA
19544569 ATATATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:19545091 original size:23 final size:23
Alignment explanation
Indices: 19545063--19545149 Score: 111
Period size: 23 Copynumber: 3.5 Consensus size: 23
19545053 TAATATTCCG
19545063 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
19545086 GGTGTGTTTGGGTTGAATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
19545109 GGTGTGTTTGGGTTTGGGTTGGATATTCT
1 -G-GTG--T--GTTTGGGTTGGATATTCT
19545138 GGTGTGTTTGGG
1 GGTGTGTTTGGG
19545150 AGGAATCGTC
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
23 29 0.52
24 1 0.02
25 4 0.07
27 4 0.07
28 1 0.02
29 17 0.30
ACGTcount: A:0.08, C:0.03, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:19545134 original size:29 final size:29
Alignment explanation
Indices: 19545068--19545149 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
19545058 TTCCGGGTGT
19545068 GTTTGGGTTGGATATTCT-G-GTG--T--
1 GTTTGGGTTGGATATTCTGGTGTGTTTGG
*
19545091 GTTTGGGTTGAATATTCTGGTGTGTTTGG
1 GTTTGGGTTGGATATTCTGGTGTGTTTGG
19545120 GTTTGGGTTGGATATTCTGGTGTGTTTGG
1 GTTTGGGTTGGATATTCTGGTGTGTTTGG
19545149 G
1 G
19545150 AGGAATCGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
23 17 0.33
24 1 0.02
25 3 0.06
27 1 0.02
29 29 0.57
ACGTcount: A:0.09, C:0.04, G:0.40, T:0.48
Consensus pattern (29 bp):
GTTTGGGTTGGATATTCTGGTGTGTTTGG
Found at i:19545275 original size:18 final size:19
Alignment explanation
Indices: 19545254--19545294 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
19545244 AATGAAATGA
19545254 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
19545272 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
19545291 GAAA
1 GAAA
19545295 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:19553774 original size:40 final size:40
Alignment explanation
Indices: 19553707--19553793 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
19553697 AATTCATTAC
* * *
19553707 TTCAGTAATTTCACAGTTCAGTGCAGTACACATAACAATA
1 TTCAGTAATTTCACAATTCAATGCAGTACACAAAACAATA
* **
19553747 TTCAGTAACTTT-ACAATTCAATTCAGTATTCAAAACAATA
1 TTCAGTAA-TTTCACAATTCAATGCAGTACACAAAACAATA
19553787 TTCAGTA
1 TTCAGTA
19553794 TTCCATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (40 bp):
TTCAGTAATTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:19554608 original size:14 final size:13
Alignment explanation
Indices: 19554571--19554622 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
19554561 TTCTTCTTTA
* *
19554571 CTTTGTTTTGTTT
1 CTTTATTTTATTT
19554584 CTTTATTTTATTT
1 CTTTATTTTATTT
*
19554597 CATTTCTTTTATTAT
1 C-TTTATTTTATT-T
19554612 -TTTATTTTATT
1 CTTTATTTTATT
19554623 AACTTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
14 10 0.30
15 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (13 bp):
CTTTATTTTATTT
Found at i:19554667 original size:19 final size:19
Alignment explanation
Indices: 19554626--19554678 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
19554616 TTTTATTAAC
19554626 TTAATAAT-AATA-ATTAT
1 TTAATAATAAATATATTAT
*
19554643 TATAATAATAAATATCTTAT
1 T-TAATAATAAATATATTAT
*
19554663 TTAATAACAAATATAT
1 TTAATAATAAATATAT
19554679 ATATATTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 7 0.23
19 17 0.57
20 5 0.17
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATAATAAATATATTAT
Found at i:19554918 original size:20 final size:20
Alignment explanation
Indices: 19554893--19554953 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
19554883 TTATTTTTAA
*
19554893 TAATAATAATAATCATAATT
1 TAATAATAATAATAATAATT
*
19554913 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATAATAATT
*
19554933 TGATAGAATAATAATAATAAT
1 T-A-ATAATAATAATAATAAT
19554954 GATAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 1 0.03
22 12 0.35
23 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (20 bp):
TAATAATAATAATAATAATT
Found at i:19555106 original size:25 final size:27
Alignment explanation
Indices: 19555072--19555133 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 27
19555062 TGGCTTTAAT
*
19555072 TTAATTTAATTCATAATATGATATTTATAA
1 TTAA-TTAATTAATAATAT-AT-TTTATAA
19555102 TTAATTAATTTAATAATATATTTTATAA
1 TTAATTAA-TTAATAATATATTTTATAA
19555130 TTAA
1 TTAA
19555134 ATTATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 6 0.20
30 13 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTAATTAATTAATAATATATTTTATAA
Found at i:19555144 original size:24 final size:23
Alignment explanation
Indices: 19555103--19555157 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
19555093 TATTTATAAT
* **
19555103 TAATTAATTTAATAATATATTTTA
1 TAATTAAATTAATAATAT-TTACA
19555127 TAATTAAATT-ATATATATTTACA
1 TAATTAAATTAATA-ATATTTACA
19555150 TAATTAAA
1 TAATTAAA
19555158 ATCTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTAAATTAATAATATTTACA
Found at i:19555212 original size:16 final size:16
Alignment explanation
Indices: 19555191--19555258 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
19555181 TTTGGTTCGC
*
19555191 TGTATTAAATTAGAGG
1 TGTATTGAATTAGAGG
*
19555207 TGTATTGGATTAGAGG
1 TGTATTGAATTAGAGG
* *
19555223 TGTATTGGATTAAAGG
1 TGTATTGAATTAGAGG
19555239 TGTATTGAATTAGAGG
1 TGTATTGAATTAGAGG
19555255 TGTA
1 TGTA
19555259 ATAGCAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
TGTATTGAATTAGAGG
Done.