Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 111 of 121
Found at i:18874285 original size:13 final size:13
Alignment explanation
Indices: 18874259--18874310 Score: 63
Period size: 14 Copynumber: 4.0 Consensus size: 13
18874249 CCGAAAAATT
18874259 TTTTAAATATATAA
1 TTTTAAA-ATATAA
18874273 TTTTAAAATATAA
1 TTTTAAAATATAA
*
18874286 -TTAAAAATATAAA
1 TTTTAAAATAT-AA
18874299 TTTTAAAA-ATAA
1 TTTTAAAATATAA
18874311 AAAAACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 11 0.32
13 10 0.29
14 13 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTTAAAATATAA
Found at i:18874307 original size:27 final size:28
Alignment explanation
Indices: 18874263--18874336 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
18874253 AAAATTTTTT
* **
18874263 AAATATATAATTTT-AAAATATAATTA-A
1 AAATATA-AATTTTAAAAATAAAAAAACA
18874290 AAATATAAATTTTAAAAATAAAAAAACA
1 AAATATAAATTTTAAAAATAAAAAAACA
* *
18874318 AAAGATAAATTTAAAAAAT
1 AAATATAAATTTTAAAAAT
18874337 TTACCCCACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 6 0.15
27 16 0.40
28 18 0.45
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (28 bp):
AAATATAAATTTTAAAAATAAAAAAACA
Found at i:18874311 original size:13 final size:14
Alignment explanation
Indices: 18874259--18874309 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
18874249 CCGAAAAATT
*
18874259 TTTTAAATATATAA
1 TTTTAAAAATATAA
18874273 TTTT-AAAATATAA
1 TTTTAAAAATATAA
18874286 --TTAAAAATATAAA
1 TTTTAAAAATAT-AA
18874299 TTTTAAAAATA
1 TTTTAAAAATA
18874310 AAAAAACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.06
12 7 0.22
13 10 0.31
14 4 0.12
15 9 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:18876855 original size:21 final size:22
Alignment explanation
Indices: 18876814--18876856 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
18876804 TTATTTAAAA
*
18876814 ATTATACAGATTTTATTAATTT
1 ATTATACAGATTTTATCAATTT
18876836 ATTATA-AGATTTT-TCCAATTT
1 ATTATACAGATTTTAT-CAATTT
18876857 GATAGCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 12 0.63
22 6 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
ATTATACAGATTTTATCAATTT
Found at i:18878556 original size:17 final size:15
Alignment explanation
Indices: 18878523--18878551 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18878513 TAATCTCTTG
18878523 TTCATAATATATACT
1 TTCATAATATATACT
18878538 TTCATAATATATAC
1 TTCATAATATATAC
18878552 ACTTTTAAAA
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:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
TTCATAATATATACT
Found at i:18879315 original size:19 final size:19
Alignment explanation
Indices: 18879288--18879329 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
18879278 ACATATTGTA
*
18879288 ATATAATATTATATATGAT
1 ATATAATATGATATATGAT
*
18879307 ATATCATATGATATATGAT
1 ATATAATATGATATATGAT
18879326 ATAT
1 ATAT
18879330 GATTAGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
ATATAATATGATATATGAT
Found at i:18881636 original size:23 final size:23
Alignment explanation
Indices: 18881606--18881657 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
18881596 TTACCTAATT
*
18881606 AAAAAAACAAACGGTGAAAAGTA
1 AAAAAAACAAACGATGAAAAGTA
*
18881629 AAAAAAACAAACGATGAAAATTA
1 AAAAAAACAAACGATGAAAAGTA
18881652 AAAAAA
1 AAAAAA
18881658 TTAAATAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAAAAACAAACGATGAAAAGTA
Found at i:18883197 original size:21 final size:21
Alignment explanation
Indices: 18883171--18883415 Score: 148
Period size: 21 Copynumber: 11.8 Consensus size: 21
18883161 AAATAAAAAC
18883171 TAATAATAATAAATATTAATT
1 TAATAATAATAAATATTAATT
* *
18883192 TAATAATATTATATATTAATT
1 TAATAATAATAAATATTAATT
* *
18883213 GAATAAT-ATTAATATT-ATT
1 TAATAATAATAAATATTAATT
* * *
18883232 TAATAATAGTCAACATTAATT
1 TAATAATAATAAATATTAATT
* * *
18883253 AAATAATATTCAAT-TTAAATT
1 TAATAATAATAAATATT-AATT
*
18883274 TAATAAT-ATTAATATTAATT
1 TAATAATAATAAATATTAATT
* * *
18883294 TCAT-ATTATGAAATATTCATT
1 TAATAATAAT-AAATATTAATT
* **
18883315 TAATAATATTAACCATT-ATT
1 TAATAATAATAAATATTAATT
* * * *
18883335 TAATAATATTGAATTTTGATT
1 TAATAATAATAAATATTAATT
* * *
18883356 TATTAATATTAAATATTGATT
1 TAATAATAATAAATATTAATT
*
18883377 TAATTTAA-ATATAAA-ATTAAAT
1 TAA--TAATA-ATAAATATTAATT
18883399 TAATAATAA-AATATATT
1 TAATAATAATAA-ATATT
18883416 TCAAAACCAG
Statistics
Matches: 175, Mismatches: 35, Indels: 28
0.74 0.15 0.12
Matches are distributed among these distances:
19 13 0.07
20 48 0.27
21 95 0.54
22 12 0.07
23 7 0.04
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATAATAATAAATATTAATT
Found at i:18883239 original size:61 final size:61
Alignment explanation
Indices: 18883171--18883406 Score: 212
Period size: 61 Copynumber: 3.8 Consensus size: 61
18883161 AAATAAAAAC
*
18883171 TAATAATAATAAATATTAATTTAATAATATTATATATTAATTGAATAATATTAATATT-ATT
1 TAATAATAATAAATATTAATTTAATAATATTA-ATATTAATTTAATAATATTAATATTAATT
* * * *
18883232 TAATAATAGTCAACATTAATTAAATAATATTCAAT-TTAAATTTAATAATATTAATATTAATT
1 TAATAATAATAAATATTAATTTAATAATATT-AATATT-AATTTAATAATATTAATATTAATT
* * * * * *
18883294 TCAT-ATTATGAAATATTCATTTAATAATATTAACCATT-ATTTAATAATATTGAATTTTGATT
1 TAATAATAAT-AAATATTAATTTAATAATATTAA-TATTAATTTAATAATATT-AATATTAATT
* * * * *
18883356 TATTAATATTAAATATTGATTTAATTTAA-ATATAAAATTAAATTAATAATA
1 TAATAATAATAAATATTAATTTAA--TAATAT-TAATATTAATTTAATAATA
18883407 AAATATATTT
Statistics
Matches: 141, Mismatches: 22, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
60 2 0.01
61 66 0.47
62 47 0.33
63 10 0.07
64 16 0.11
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (61 bp):
TAATAATAATAAATATTAATTTAATAATATTAATATTAATTTAATAATATTAATATTAATT
Found at i:18883258 original size:82 final size:81
Alignment explanation
Indices: 18883172--18883372 Score: 219
Period size: 82 Copynumber: 2.4 Consensus size: 81
18883162 AATAAAAACT
* *
18883172 AATAATAATAAATATTAATTTAATAATATTATATATTAATTGAATAATAT-TAATATT-ATTTAA
1 AATAATATTAAAT-TTAATTTAATAATATTA-ATATTAATTGAATAATATGAAATATTCATTTAA
18883235 TAATAGTCAA-CATTAATTA
64 TAATA-TCAACCATT-ATTA
* ** *
18883254 AATAATATTCAATTTAAATTTAATAATATTAATATTAATTTCATATTATGAAATATTCATTTAAT
1 AATAATATTAAATTT-AATTTAATAATATTAATATTAATTGAATAATATGAAATATTCATTTAAT
* *
18883319 AATATTAACCATTATTT
65 AATATCAACCATTATTA
* * *
18883336 AATAATATTGAATTTTGATTTATTAATATTAAATATT
1 AATAATATT-AAATTTAATTTAATAATATT-AATATT
18883373 GATTTAATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
81 17 0.17
82 59 0.58
83 25 0.25
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (81 bp):
AATAATATTAAATTTAATTTAATAATATTAATATTAATTGAATAATATGAAATATTCATTTAATA
ATATCAACCATTATTA
Found at i:18883319 original size:11 final size:10
Alignment explanation
Indices: 18883182--18883380 Score: 66
Period size: 10 Copynumber: 19.3 Consensus size: 10
18883172 AATAATAATA
18883182 AATATTAATTT
1 AATATT-ATTT
*
18883193 AATAATA-TT
1 AATATTATTT
*
18883202 ATATATTAATTG
1 A-ATATT-ATTT
*
18883214 AATAATA-TT
1 AATATTATTT
18883223 AATATTATTT
1 AATATTATTT
* * *
18883233 AATAATAGTC
1 AATATTATTT
* *
18883243 AACATTAATTA
1 AATATT-ATTT
* *
18883254 AATAATATTC
1 AATATTATTT
18883264 AAT-TTAAATTT
1 AATATT--ATTT
*
18883275 AATAATA-TT
1 AATATTATTT
18883284 AATATTAATTT
1 AATATT-ATTT
* **
18883295 CATATTATGA
1 AATATTATTT
18883305 AATATTCATTT
1 AATATT-ATTT
*
18883316 AATAATA-TT
1 AATATTATTT
*
18883325 AACCATTATTT
1 AA-TATTATTT
* *
18883336 AATAATATTG
1 AATATTATTT
*
18883346 AATTTTGATTT
1 AATATT-ATTT
* * *
18883357 ATTAATATTA
1 AATATTATTT
18883367 AATATTGATTT
1 AATATT-ATTT
18883378 AAT
1 AAT
18883381 TTAAATATAA
Statistics
Matches: 131, Mismatches: 42, Indels: 30
0.65 0.21 0.15
Matches are distributed among these distances:
9 22 0.17
10 54 0.41
11 52 0.40
12 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (10 bp):
AATATTATTT
Found at i:18884670 original size:20 final size:20
Alignment explanation
Indices: 18884645--18884692 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
18884635 TGTAATTTAT
*
18884645 TATAAA-AAATAATTAATAAA
1 TATAAATAAA-AACTAATAAA
18884665 TATAAATAAAAACTAAT-AA
1 TATAAATAAAAACTAATAAA
18884684 TAATAAATA
1 T-ATAAATA
18884693 TTAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAATAAAAACTAATAAA
Found at i:18884704 original size:21 final size:21
Alignment explanation
Indices: 18884678--18884935 Score: 247
Period size: 21 Copynumber: 12.5 Consensus size: 21
18884668 AAATAAAAAC
*
18884678 TAATAATAATAAATATTAATT
1 TAATAATATTAAATATTAATT
*
18884699 TAATAATATTATATATTAATT
1 TAATAATATTAAATATTAATT
*
18884720 GAATAATATT-AATATT-ATT
1 TAATAATATTAAATATTAATT
* * *
18884739 TAATAATAGTCAACATTAATT
1 TAATAATATTAAATATTAATT
* *
18884760 AAATAATATTCAAT-TTAAATT
1 TAATAATATTAAATATT-AATT
18884781 TAATAATATT-AATATTAATT
1 TAATAATATTAAATATTAATT
* * * *
18884801 TCATATTATGAAATATTCATT
1 TAATAATATTAAATATTAATT
**
18884822 TAATAATATTAACCATT-ATT
1 TAATAATATTAAATATTAATT
* * *
18884842 TAATAATATTGAATTTTGATT
1 TAATAATATTAAATATTAATT
* *
18884863 TATTAATATTAAATATTGATT
1 TAATAATATTAAATATTAATT
* *
18884884 TAATAATACTAAATATTAATA
1 TAATAATATTAAATATTAATT
* * *
18884905 TGATAATATTAAATCTAAATT
1 TAATAATATTAAATATTAATT
*
18884926 TAGTAATATT
1 TAATAATATT
18884936 TGAACTATTG
Statistics
Matches: 193, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
19 11 0.06
20 42 0.22
21 140 0.73
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
TAATAATATTAAATATTAATT
Found at i:18884743 original size:61 final size:61
Alignment explanation
Indices: 18884678--18884933 Score: 227
Period size: 61 Copynumber: 4.1 Consensus size: 61
18884668 AAATAAAAAC
18884678 TAATAATAATAAATATTAATTTAATAATATTATATATTAATTGAATAATATTAATATT-ATT
1 TAATAATAATAAATATTAATTTAATAATATTA-ATATTAATTGAATAATATTAATATTAATT
* * * * *
18884739 TAATAATAGTCAACATTAATTAAATAATATTCAAT-TTAAATTTAATAATATTAATATTAATT
1 TAATAATAATAAATATTAATTTAATAATATT-AATATT-AATTGAATAATATTAATATTAATT
* * * * * * *
18884801 TCAT-ATTATGAAATATTCATTTAATAATATTAACCATT-ATTTAATAATATTGAATTTTGATT
1 TAATAATAAT-AAATATTAATTTAATAATATTAA-TATTAATTGAATAATATT-AATATTAATT
* * * *
18884863 TATTAATATTAAATATTGATTTAATAATACTAAATATTAATATG-ATAATATTAA-ATCTAAATT
1 TAATAATAATAAATATTAATTTAATAATA-TTAATATTAAT-TGAATAATATTAATAT-T-AATT
*
18884926 TAGTAATA
1 TAATAATA
18884934 TTTGAACTAT
Statistics
Matches: 156, Mismatches: 26, Indels: 24
0.76 0.13 0.12
Matches are distributed among these distances:
60 2 0.01
61 67 0.43
62 58 0.37
63 28 0.18
64 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (61 bp):
TAATAATAATAAATATTAATTTAATAATATTAATATTAATTGAATAATATTAATATTAATT
Found at i:18884765 original size:82 final size:79
Alignment explanation
Indices: 18884679--18884901 Score: 241
Period size: 82 Copynumber: 2.7 Consensus size: 79
18884669 AATAAAAACT
* * *
18884679 AATAATAATAAATATTAATTTAATAATATTATATATTAATTGAATAATATTAATATTATTTAATA
1 AATAATATTAAAT-TTAATTTAATAATATTA-ATATTAATTTAATAATATAAATATTATTTAATA
18884744 ATAGTCAA-CATTAATTA
64 ATA-TCAACCATT-ATTA
* * *
18884761 AATAATATTCAATTTAAATTTAATAATATTAATATTAATTTCATATTATGAAATATTCATTTAAT
1 AATAATATTAAATTT-AATTTAATAATATTAATATTAATTTAATAATAT-AAATATT-ATTTAAT
* *
18884826 AATATTAACCATTATTT
63 AATATCAACCATTATTA
* * * *
18884843 AATAATATTGAATTTTGATTTATTAATATTAAATATTGATTTAATAATACTAAATATTA
1 AATAATATT-AAATTTAATTTAATAATATT-AATATTAATTTAATAATA-TAAATATTA
18884902 ATATGATAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
81 17 0.14
82 60 0.50
83 41 0.34
84 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (79 bp):
AATAATATTAAATTTAATTTAATAATATTAATATTAATTTAATAATATAAATATTATTTAATAAT
ATCAACCATTATTA
Found at i:18884826 original size:11 final size:10
Alignment explanation
Indices: 18884689--18884888 Score: 68
Period size: 10 Copynumber: 19.4 Consensus size: 10
18884679 AATAATAATA
18884689 AATATTAATTT
1 AATATT-ATTT
*
18884700 AATAATA-TT
1 AATATTATTT
*
18884709 ATATATTAATTG
1 A-ATATT-ATTT
*
18884721 AATAATA-TT
1 AATATTATTT
18884730 AATATTATTT
1 AATATTATTT
* * *
18884740 AATAATAGTC
1 AATATTATTT
* *
18884750 AACATTAATTA
1 AATATT-ATTT
* *
18884761 AATAATATTC
1 AATATTATTT
18884771 AAT-TTAAATTT
1 AATATT--ATTT
*
18884782 AATAATA-TT
1 AATATTATTT
18884791 AATATTAATTT
1 AATATT-ATTT
* **
18884802 CATATTATGA
1 AATATTATTT
18884812 AATATTCATTT
1 AATATT-ATTT
*
18884823 AATAATA-TT
1 AATATTATTT
*
18884832 AACCATTATTT
1 AA-TATTATTT
* *
18884843 AATAATATTG
1 AATATTATTT
*
18884853 AATTTTGATTT
1 AATATT-ATTT
* * *
18884864 ATTAATATTA
1 AATATTATTT
18884874 AATATTGATTT
1 AATATT-ATTT
18884885 AATA
1 AATA
18884889 ATACTAAATA
Statistics
Matches: 132, Mismatches: 42, Indels: 30
0.65 0.21 0.15
Matches are distributed among these distances:
9 22 0.17
10 54 0.41
11 53 0.40
12 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (10 bp):
AATATTATTT
Found at i:18885171 original size:22 final size:22
Alignment explanation
Indices: 18885113--18885213 Score: 93
Period size: 22 Copynumber: 4.8 Consensus size: 22
18885103 TGTGATATTA
* *
18885113 AATAATATGATAATAATA-TTT
1 AATAATATGTTAATATTATTTT
* *
18885134 --TAATAT-TTAGTATTATTTG
1 AATAATATGTTAATATTATTTT
*
18885153 CATAATATGTTAATATTATTTT
1 AATAATATGTTAATATTATTTT
**
18885175 AATAGCATGTTAATATTATTTT
1 AATAATATGTTAATATTATTTT
* *
18885197 AATGATATTTTAATATT
1 AATAATATGTTAATATT
18885214 TCATATTATT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
18 6 0.10
19 8 0.13
21 6 0.10
22 43 0.68
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
AATAATATGTTAATATTATTTT
Found at i:18885178 original size:11 final size:11
Alignment explanation
Indices: 18885139--18885213 Score: 62
Period size: 11 Copynumber: 6.8 Consensus size: 11
18885129 TATTTTAATA
*
18885139 TTTAGTATTAT
1 TTTAATATTAT
** *
18885150 TTGCATAATAT
1 TTTAATATTAT
*
18885161 GTTAATATTAT
1 TTTAATATTAT
**
18885172 TTTAATAGCAT
1 TTTAATATTAT
*
18885183 GTTAATATTAT
1 TTTAATATTAT
18885194 TTTAATGA-TAT
1 TTTAAT-ATTAT
18885205 TTTAATATT
1 TTTAATATT
18885214 TCATATTATT
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
10 1 0.02
11 45 0.96
12 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.55
Consensus pattern (11 bp):
TTTAATATTAT
Found at i:18885293 original size:18 final size:20
Alignment explanation
Indices: 18885262--18885299 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
18885252 TTATTGTTAT
*
18885262 TTTATAATATTTAAATATTA
1 TTTATAATATTTAAAAATTA
18885282 TTTA-AATA-TTAAAAATTA
1 TTTATAATATTTAAAAATTA
18885300 AGTGAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATAATATTTAAAAATTA
Found at i:18885440 original size:37 final size:37
Alignment explanation
Indices: 18885373--18885446 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
18885363 TTTATTCTTT
* * **
18885373 TAATAAATTCTAATGTTATTTTTATTATTAAATATTA
1 TAATAAATTCTAATATTATTTTAAGCATTAAATATTA
*
18885410 TAATAATATTCTAATATTA-TTTAAGCATTAAGTATTA
1 TAATAA-ATTCTAATATTATTTTAAGCATTAAATATTA
18885447 ATTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 20 0.65
38 11 0.35
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (37 bp):
TAATAAATTCTAATATTATTTTAAGCATTAAATATTA
Found at i:18892462 original size:42 final size:42
Alignment explanation
Indices: 18892415--18892498 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
18892405 CCCTCTTGCT
*
18892415 CTTGTTTTGTTTGTTTGTGAATTTATTGCCCTATATAAACAA
1 CTTGTTTTGTTTGCTTGTGAATTTATTGCCCTATATAAACAA
*
18892457 CTTGTTTTGTTTGCTTGTGAGTTTATTGCCCTATATAAACAA
1 CTTGTTTTGTTTGCTTGTGAATTTATTGCCCTATATAAACAA
18892499 TCATTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (42 bp):
CTTGTTTTGTTTGCTTGTGAATTTATTGCCCTATATAAACAA
Found at i:18897428 original size:44 final size:44
Alignment explanation
Indices: 18897361--18897456 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
18897351 GTCTGCCAAA
18897361 AGTGTGATTCTCTAATTCCTACCTTATATAACATTAATTAAATG
1 AGTGTGATTCTCTAATTCCTACCTTATATAACATTAATTAAATG
*
18897405 AGTGTGATTCTCTAATTCTTACCTTATATAACATTAATTAAATG
1 AGTGTGATTCTCTAATTCCTACCTTATATAACATTAATTAAATG
*
18897449 AGTATGAT
1 AGTGTGAT
18897457 ATAAGCCACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
AGTGTGATTCTCTAATTCCTACCTTATATAACATTAATTAAATG
Found at i:18902657 original size:30 final size:31
Alignment explanation
Indices: 18902599--18902658 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
18902589 AAAAAATTTA
*
18902599 TTCATTAATAAAATAACATCATTCGATTCAC
1 TTCATTAATAAAATAACATAATTCGATTCAC
*
18902630 TTCATTAAT-AAATAATATTAATT-GATTCA
1 TTCATTAATAAAATAACA-TAATTCGATTCA
18902659 TTAACGGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.40
Consensus pattern (31 bp):
TTCATTAATAAAATAACATAATTCGATTCAC
Found at i:18904713 original size:31 final size:31
Alignment explanation
Indices: 18904674--18904748 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
18904664 TTTGCATTTA
*
18904674 AAAT-AAATTCTT-AATTTTTAATTTAAATCC
1 AAATAAAATT-TTAAATTATTAATTTAAATCC
** *
18904704 AAATAAAATTTTAAATTATTAATTTGTATCT
1 AAATAAAATTTTAAATTATTAATTTAAATCC
*
18904735 AAATAAAAATTTAA
1 AAATAAAATTTTAA
18904749 CATAGATCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (31 bp):
AAATAAAATTTTAAATTATTAATTTAAATCC
Found at i:18904782 original size:17 final size:18
Alignment explanation
Indices: 18904762--18904795 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18904752 AGATCATTAT
18904762 TTTATTTGAA-ATAAATA
1 TTTATTTGAATATAAATA
18904779 TTTATTTGAATATAAAT
1 TTTATTTGAATATAAAT
18904796 CAAAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTATTTGAATATAAATA
Found at i:18906520 original size:26 final size:27
Alignment explanation
Indices: 18906476--18906545 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
18906466 CCAATTATCC
* *
18906476 AATGATAAAATT-CTTAGAAAT-TTCA
1 AATGATAAATTTCCTAAGAAATCTTCA
*
18906501 AATGATAAATTTCCTAAGAAATCTTTA
1 AATGATAAATTTCCTAAGAAATCTTCA
* *
18906528 AGTGAGAAATTTCTCTAA
1 AATGATAAATTTC-CTAA
18906546 ATTTGTCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.30
26 8 0.22
27 14 0.38
28 4 0.11
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
AATGATAAATTTCCTAAGAAATCTTCA
Found at i:18906713 original size:27 final size:25
Alignment explanation
Indices: 18906662--18906718 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
18906652 AATGATGAGA
*
18906662 TTCTTAAAAATTTCTAATGAAAAAT
1 TTCTTAAAAATCTCTAATGAAAAAT
*
18906687 TTCTTAAGAAATCTCTAGATGATAAAT
1 TTCTTAA-AAATCTCTA-ATGAAAAAT
18906714 TTCTT
1 TTCTT
18906719 TAAATTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.25
26 8 0.29
27 13 0.46
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (25 bp):
TTCTTAAAAATCTCTAATGAAAAAT
Found at i:18906877 original size:47 final size:47
Alignment explanation
Indices: 18906812--18906910 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 47
18906802 AACAAAAAAG
* *
18906812 AAAA-AAATTTTTAAATAGACTCAAATGATAAAAAATTTAGAAATCA
1 AAAAGAAATTTCTAAATAGACTCAAATAATAAAAAATTTAGAAATCA
* * *
18906858 AAAAGAAATTTCTAAATAGATTCAAATAATGAAAAATTTAGAAATTA
1 AAAAGAAATTTCTAAATAGACTCAAATAATAAAAAATTTAGAAATCA
18906905 AAAAGA
1 AAAAGA
18906911 GAAAATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 4 0.09
47 43 0.91
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (47 bp):
AAAAGAAATTTCTAAATAGACTCAAATAATAAAAAATTTAGAAATCA
Found at i:18912313 original size:12 final size:12
Alignment explanation
Indices: 18912289--18912326 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
18912279 TACATTTTTG
18912289 TTATTTT-TATT
1 TTATTTTATATT
18912300 TTATTTTATATT
1 TTATTTTATATT
*
18912312 TTATGTATATATT
1 TTAT-TTTATATT
18912325 TT
1 TT
18912327 CCTTTATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 7 0.29
12 8 0.33
13 9 0.38
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TTATTTTATATT
Found at i:18912368 original size:28 final size:28
Alignment explanation
Indices: 18912337--18912391 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
18912327 CCTTTATATC
* *
18912337 CTATGTATTTAT-TATTTATTTATTATTA
1 CTATGTATTAATATATATATTT-TTATTA
*
18912365 CTATTTATTAATATATATATTTTTATT
1 CTATGTATTAATATATATATTTTTATT
18912392 TTATTTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (28 bp):
CTATGTATTAATATATATATTTTTATTA
Found at i:18912456 original size:24 final size:22
Alignment explanation
Indices: 18912429--18912555 Score: 97
Period size: 21 Copynumber: 5.8 Consensus size: 22
18912419 TCATTTTATT
18912429 TTATATGTATTTTTATTTATCTAA
1 TTATAT-TATTTTTATTTATCT-A
*
18912453 TTATA-TA--TTTATTTATCTG
1 TTATATTATTTTTATTTATCTA
18912472 TTATTATTATTTTTTATTTATC--
1 TTA-TATTA-TTTTTATTTATCTA
* *
18912494 TTATAATATTGTTGATTTATCT-
1 TTATATTATT-TTTATTTATCTA
*
18912516 TTATTATTATTTTCTAATTATCTA
1 TTA-TATTATTTT-TATTTATCTA
*
18912540 TTAAATT-TTTTTATTT
1 TTATATTATTTTTATTT
18912556 GATTTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
19 3 0.04
20 15 0.18
21 19 0.22
22 14 0.16
23 16 0.19
24 18 0.21
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (22 bp):
TTATATTATTTTTATTTATCTA
Found at i:18912465 original size:20 final size:20
Alignment explanation
Indices: 18912440--18912541 Score: 63
Period size: 20 Copynumber: 5.1 Consensus size: 20
18912430 TATATGTATT
18912440 TTTATTTATCTAATTATATA
1 TTTATTTATCTAATTATATA
* *
18912460 TTTATTTATCTGTTATTATTATTT
1 TTTATTTATC--TAATTA-TA-TA
* *
18912484 TTTATTTATCTTATAATAT-
1 TTTATTTATCTAATTATATA
18912503 TGTTGATTTATCT--TTAT-TA
1 T-TT-ATTTATCTAATTATATA
*
18912522 -TTATTT-TCTAATTATCTA
1 TTTATTTATCTAATTATATA
18912540 TT
1 TT
18912542 AAATTTTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 23
0.71 0.04 0.24
Matches are distributed among these distances:
15 3 0.04
16 4 0.06
17 6 0.09
18 3 0.04
19 5 0.07
20 13 0.19
21 10 0.15
22 10 0.15
23 2 0.03
24 11 0.16
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTATTTATCTAATTATATA
Found at i:18912489 original size:44 final size:44
Alignment explanation
Indices: 18912423--18912539 Score: 136
Period size: 44 Copynumber: 2.7 Consensus size: 44
18912413 TCTTTTTCAT
*
18912423 TTTAT-TTTA-TATGTA-TTTTTATTTATCTAATTATATAT-TT-A
1 TTTATCTTTATTAT-TATTTTTTATTTATCTAATAATAT-TGTTGA
*
18912464 TTTATCTGTTATTATTATTTTTTATTTATCTTATAATATTGTTGA
1 TTTATCT-TTATTATTATTTTTTATTTATCTAATAATATTGTTGA
* *
18912509 TTTATCTTTATTATTATTTTCTAATTATCTA
1 TTTATCTTTATTATTATTTTTTATTTATCTA
18912540 TTAAATTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
41 5 0.08
42 1 0.02
43 6 0.09
44 45 0.69
45 8 0.12
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.65
Consensus pattern (44 bp):
TTTATCTTTATTATTATTTTTTATTTATCTAATAATATTGTTGA
Found at i:18913643 original size:59 final size:57
Alignment explanation
Indices: 18913551--18914138 Score: 659
Period size: 59 Copynumber: 10.1 Consensus size: 57
18913541 TATTATTTTA
* * * **
18913551 TTTTCTT-TAAATAAA-ATTCAAAAAATATTTTTGAAAAAAAGTTGAAACGTATCAAT
1 TTTTCTTAAAAATAAATTTTCAAAAAAAATTTTTGAGGAAAAGTTGAAA-GTATCAAT
* * *
18913607 TTTTCTTAAAAATAGATTTTTAAAAAAAAGTTTTTGAGGGAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAATAAATTTTCAAAAAAAA-TTTTTGAGGAAAAGTTGAAAGTATCAAT
* * * *
18913664 TTTTCTTTGAAAATCAAAGTTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
1 TTTTC-TTAAAAAT-AAA-TTTTCAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAAT
** *
18913724 TTTTCTTAAAAATAAATTTTCAAAAAAGGGTTTTTGAGGAAAAGTTAAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTCAAAAAA-AATTTTTGAGGAAAAGTTGAAAGTATCAAT
* ** * *
18913782 TTTCCTCGAAAATCAAAGTTTTCAAAAAATATTTTTG-GGAAAAAGTTAAAAGTATCAAT
1 TTTTCTTAAAAAT-AAA-TTTTCAAAAAAAATTTTTGAGG-AAAAGTTGAAAGTATCAAT
*
18913841 TTTCCTTAAAAATAAATTTTCAAAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTC-AAAAAAAA--TTTTTGAGGAAAAGTTGAAAGTATCAAT
18913901 TTTTCTTAAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAATAAATTTTCAAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAAT
**
18913958 TTTTCTCGAAAATCAAAGTTTTCAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAAT-AAA-TTTTCAAAAAAA-ATTTTTGAGG-AAAAGTTGAAAGTATCAAT
*
18914018 TTTTCTTAAAAATAAATTTTCAAAAAAATCAATTTTTGAGGAAAAGTTGAAAATATCAAT
1 TTTTCTTAAAAATAAATTTTC-AAAAAA--AATTTTTGAGGAAAAGTTGAAAGTATCAAT
* ** * * *
18914078 TTTCCTCGAAATTAAAGTTTCAAAAGAATATTTTT-AGGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTCAAAA-AAAATTTTTGA-GGAAAAGTTGAAAGTATCAAT
18914136 TTT
1 TTT
18914139 CCCTGCACAA
Statistics
Matches: 463, Mismatches: 43, Indels: 50
0.83 0.08 0.09
Matches are distributed among these distances:
56 7 0.02
57 38 0.08
58 140 0.30
59 148 0.32
60 125 0.27
61 5 0.01
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (57 bp):
TTTTCTTAAAAATAAATTTTCAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:18913757 original size:117 final size:117
Alignment explanation
Indices: 18913569--18914139 Score: 683
Period size: 117 Copynumber: 4.8 Consensus size: 117
18913559 AAATAAAATT
** * *
18913569 CAAAAAATATTTTTGAAAAAAAGTTGAAACGTATCAATTTTTCTTAAAAATAGATTTTTAAAAAA
1 CAAAAAATATTTTTGAGGAAAAGTTGAAA-GTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA
* *
18913634 A-AGTTTTTGAGGGAAAGTTGAAAGTATCAATTTTCT-TTGAAAATCAAAGTTTC
65 AGA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTTAAAAAT-AAAGTTTC
* *
18913687 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAG
1 CAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAA
* * ** *
18913752 GGTTTTTGAGGAAAAGTTAAAAGTATCAATTTTC-CTCGAAAATCAAAGTTTT
66 GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTTAAAAAT-AAAGTTTC
* *
18913804 CAAAAAATATTTTTG-GGAAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
1 CAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC--AAAA
* *
18913868 AAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TCTTAAAAATAAATTTTC
63 AAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTTAAAAATAAAGTTTC
* **
18913922 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTCGAAAATCAAAGTTTTCAAAAA
1 CAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAA-TTTTCAAAAA
* *
18913986 AATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTT-TCTTAAAAATAAATTTTC
64 AAGATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCTCTTAAAAATAAAGTTTC
* * * ** * * *
18914039 AAAAAAATCAATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCGAAATTAAAGTTTCAAAAG
1 CAAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAA
*
18914104 AATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTC
64 AAGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTC
18914140 CCTGCACAAG
Statistics
Matches: 405, Mismatches: 32, Indels: 31
0.87 0.07 0.07
Matches are distributed among these distances:
116 4 0.01
117 202 0.50
118 105 0.26
119 83 0.20
120 11 0.03
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (117 bp):
CAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAA
GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTTAAAAATAAAGTTTC
Found at i:18913908 original size:177 final size:174
Alignment explanation
Indices: 18913551--18914140 Score: 744
Period size: 177 Copynumber: 3.4 Consensus size: 174
18913541 TATTATTTTA
* * ** * * *
18913551 TTTTCTT-TAAATAAA-ATTCAAAAAATATTTTTGAAAAAAAGTTGAAACGTATCAATTTTTCTT
1 TTTTCTTAAAAATAAATTTTCAAAAAATATTTTTGAGGAAAAGTT-AAAAGTATCAATTTTCCTC
* * * * * * *
18913614 AAAAAT-AGA-TTTTTAAAAAAAAGTTTTTGAGG-GAAAGTTGAAAGTATCAATTTTCTTTGAAA
65 GAAAATCAAAGTTTTCAAAAAATA-TTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAA
* * * *
18913676 ATCAAAGTTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
128 AT-AAATTTTCAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAAT
**
18913724 TTTTCTTAAAAATAAATTTTCAAAAAAGGGTTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTC
1 TTTTCTTAAAAATAAATTTTCAAAAAA-TATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTC
*
18913789 GAAAATCAAAGTTTTCAAAAAATATTTTTGGGAAAAAGTTAAAAGTATCAATTTTCCTTAAAAAT
65 GAAAATCAAAGTTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
18913854 AAATTTTCAAAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAAT
130 AAATTTTCAAAAAAAAA--TTTTTGAGGAAAAGTTGAAAGTATCAAT
*
18913901 TTTTCTTAAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTC
1 TTTTCTTAAAAATAAATTTTC-AAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTC
*
18913965 GAAAATCAAAGTTTTCAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
65 GAAAATCAAAGTTTTC-AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
*
18914030 TAAATTTTCAAAAAAATCAATTTTTGAGGAAAAGTTGAAAATATCAAT
129 TAAATTTTCAAAAAAA--AATTTTTGAGGAAAAGTTGAAAGTATCAAT
* ** * * *
18914078 TTTCCTCGAAATTAAAGTTTCAAAAGAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCC
1 TTTTCTTAAAAATAAATTTTCAAAA-AATATTTTTGA-GGAAAAGTTAAAAGTATCAATTTTCC
18914141 CTGCACAAGA
Statistics
Matches: 370, Mismatches: 32, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
173 7 0.02
174 7 0.02
175 46 0.12
176 74 0.20
177 227 0.61
178 7 0.02
179 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (174 bp):
TTTTCTTAAAAATAAATTTTCAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTCG
AAAATCAAAGTTTTCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
AATTTTCAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:18914054 original size:17 final size:17
Alignment explanation
Indices: 18914012--18914054 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
18914002 AGTTGAAAGT
**
18914012 ATCAATTTTTCTTAAAA
1 ATCAATTTTTCAAAAAA
*
18914029 AT-AAATTTTCAAAAAA
1 ATCAATTTTTCAAAAAA
18914045 ATCAATTTTT
1 ATCAATTTTT
18914055 GAGGAAAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
ATCAATTTTTCAAAAAA
Found at i:18914139 original size:58 final size:56
Alignment explanation
Indices: 18913559--18914140 Score: 646
Period size: 58 Copynumber: 9.9 Consensus size: 56
18913549 TATTTTCTTT
* ** *
18913559 AAATAAA-ATTCAAAAAATATTTTTGAAAAAAAGTTGAAACGTATCAATTTTTCTTAA
1 AAATAAATTTTCAAAAAATATTTTTG-GGAAAAGTTGAAA-GTATCAATTTTCCTTAA
* * * * * *
18913616 AAATAGATTTTTAAAAAAAAGTTTTTGAGGGAAAGTTGAAAGTATCAATTTTCTTTGA
1 AAATAAATTTTCAAAAAATA-TTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA
* *
18913674 AAATCAAAGTTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAAT-AAA-TTTTCAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAA
** * **
18913733 AAATAAATTTTCAAAAAAGGGTTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTCGA
1 AAATAAATTTTCAAAAAA-TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA
*
18913791 AAATCAAAGTTTTCAAAAAATATTTTTGGGAAAAAGTTAAAAGTATCAATTTTCCTTAA
1 AAAT-AAA-TTTTCAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAA
* *
18913850 AAATAAATTTTCAAAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAATAAATTTTC-AAAAAATA--TTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA
**
18913910 AAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTCGA
1 AAATAAATTTTC-AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA
*
18913967 AAATCAAAGTTTTCAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAAT-AAA-TTTTC-AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAA
* **
18914027 AAATAAATTTTCAAAAAAATCAATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCGA
1 AAATAAATTTTC-AAAAAAT--ATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA
* *
18914087 AATTAAAGTTTCAAAAGAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAATAAATTTTCAAAA-AATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCC
18914141 CTGCACAAGA
Statistics
Matches: 458, Mismatches: 44, Indels: 45
0.84 0.08 0.08
Matches are distributed among these distances:
57 29 0.06
58 157 0.34
59 143 0.31
60 125 0.27
61 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (56 bp):
AAATAAATTTTCAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAA
Found at i:18914187 original size:14 final size:13
Alignment explanation
Indices: 18914163--18914198 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
18914153 AATCATTCTT
18914163 TTCTTTTTTTTTA
1 TTCTTTTTTTTTA
18914176 TTCTTATTTTTTTA
1 TTCTT-TTTTTTTA
18914190 TT-TTTTTTT
1 TTCTTTTTTT
18914199 CTTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 7 0.32
14 10 0.45
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.86
Consensus pattern (13 bp):
TTCTTTTTTTTTA
Found at i:18914193 original size:21 final size:21
Alignment explanation
Indices: 18914161--18914201 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18914151 ACAATCATTC
18914161 TTTTCTTTTTTTTTATTCTTA
1 TTTTCTTTTTTTTTATTCTTA
*
18914182 TTTT-TTTATTTTTTTTTCTT
1 TTTTCTTT-TTTTTTATTCTT
18914202 TAAATAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTCTTTTTTTTTATTCTTA
Found at i:18914203 original size:14 final size:14
Alignment explanation
Indices: 18914166--18914203 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
18914156 CATTCTTTTC
18914166 TTTTTTTTTATTCT
1 TTTTTTTTTATTCT
*
18914180 TATTTTTTTATT-T
1 TTTTTTTTTATTCT
18914193 TTTTTTCTTTA
1 TTTTTT-TTTA
18914204 AATAATCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTATTCT
Found at i:18915488 original size:15 final size:15
Alignment explanation
Indices: 18915470--18915499 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18915460 CATGCATTTT
*
18915470 TCATTCATTGCATTC
1 TCATTCATTACATTC
18915485 TCATTCATTACATTC
1 TCATTCATTACATTC
18915500 AACAAAGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (15 bp):
TCATTCATTACATTC
Found at i:18918257 original size:12 final size:12
Alignment explanation
Indices: 18918240--18918295 Score: 75
Period size: 10 Copynumber: 4.9 Consensus size: 12
18918230 AACAATAGAT
18918240 AAAAAATGAGAA
1 AAAAAATGAGAA
18918252 AAAAAATGATGAA
1 AAAAAATGA-GAA
18918265 AAAAAATGA-AA
1 AAAAAATGAGAA
18918276 AAAAAA-GA-AA
1 AAAAAATGAGAA
18918286 AAAAAA-GAGA
1 AAAAAATGAGA
18918296 TTCAAATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
10 12 0.29
11 9 0.21
12 9 0.21
13 12 0.29
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAATGAGAA
Found at i:18920026 original size:41 final size:40
Alignment explanation
Indices: 18919991--18920452 Score: 401
Period size: 42 Copynumber: 11.5 Consensus size: 40
18919981 AAAGTTGCGT
* *
18919991 TGCCTCTGTTTAGAGGACCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT-ATGG
18920032 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGG
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT-ATGG
18920073 TGCCTCTGTTTAGAGGAGCAATTTTACTTTTCAAAGTCATGG
1 TGCCTCTGTTTAGAGGAGCAA-TTTACTTTTCAAAGT-ATGG
*
18920115 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCATGG
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGT-ATGG
* *
18920157 TGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTA-CTTTTCAAAGT-ATGG
* *
18920199 TGCCTCTGTTTAGAGGAACAATTTAC-TTTCCAA--A--G
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTATGG
* * * * *** ** ****
18920234 T-CGT-AG--TA-AGCA--ATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTATGG
18920267 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGG
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT-ATGG
* *
18920308 TGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT-ATGG
** *
18920349 TGCCTCTGTTTAGAGGAGCAATTTGTTTTTTTAAAGT-TGTTG
1 TGCCTCTGTTTAGAGGAGCAATTT-ACTTTTCAAAGTATG--G
* * * * *
18920391 AGCCTCTGATTAGAGGAGCCATTTATGTTTCTCAAAGTCATTG
1 TGCCTCTGTTTAGAGGAGCAATTTA-CTTT-TCAAAGT-ATGG
* *
18920434 AGCCTCTGCTTAGAGGAGC
1 TGCCTCTGTTTAGAGGAGC
18920453 TTTGGTCAAA
Statistics
Matches: 349, Mismatches: 49, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
28 3 0.01
29 3 0.01
30 3 0.01
31 2 0.01
33 3 0.01
34 4 0.01
35 3 0.01
37 2 0.01
38 3 0.01
40 16 0.05
41 134 0.38
42 143 0.41
43 29 0.08
45 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (40 bp):
TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTATGG
Found at i:18920283 original size:68 final size:69
Alignment explanation
Indices: 18920173--18920303 Score: 228
Period size: 68 Copynumber: 1.9 Consensus size: 69
18920163 TGTTTAGAGG
*
18920173 AGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTCGT
1 AGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTCGT
18920238 AGTA
66 AGTA
* *
18920242 AGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
1 AGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTC
18920304 ATGGTGCCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
68 50 0.85
69 9 0.15
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (69 bp):
AGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTCGT
AGTA
Found at i:18920428 original size:235 final size:235
Alignment explanation
Indices: 18920009--18920450 Score: 706
Period size: 235 Copynumber: 1.9 Consensus size: 235
18919999 TTTAGAGGAC
18920009 CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGT
1 CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGT
*
18920074 GCCTCTGTTTAGAGGAGCAATTTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTT
66 GCCTCTATTTAGAGGAGCAATTTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTT
* * * * *
18920139 ACTTTCCAAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCT
131 ACTTTCCAAAAGTCATGGAGCCTCTGATTAGAGGAGCAATTTATTTTCTCAAAGTCATGGAGCCT
*
18920204 CTGTTTAGAGGAACAATTTACTTTCCAAAGTCGTAGTAAG
196 CTGCTTAGAGGAACAATTTACTTTCCAAAGTCGTAGTAAG
18920244 CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGT
1 CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGT
*
18920309 GCCTCTATTTAGAGGAGCAA-TTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTT
66 GCCTCTATTTAGAGGAGCAATTTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTT
** *** ** * * *
18920373 GTTTTTTTAAAGTTGTTGAGCCTCTGATTAGAGGAGCCATTTATGTTTCTCAAAGTCATTGAGCC
131 ACTTTCCAAAAGTCATGGAGCCTCTGATTAGAGGAGCAATTTAT-TTTCTCAAAGTCATGGAGCC
18920438 TCTGCTTAGAGGA
195 TCTGCTTAGAGGA
18920451 GCTTTGGTCA
Statistics
Matches: 188, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
234 76 0.40
235 112 0.60
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (235 bp):
CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGT
GCCTCTATTTAGAGGAGCAATTTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTT
ACTTTCCAAAAGTCATGGAGCCTCTGATTAGAGGAGCAATTTATTTTCTCAAAGTCATGGAGCCT
CTGCTTAGAGGAACAATTTACTTTCCAAAGTCGTAGTAAG
Found at i:18920440 original size:43 final size:41
Alignment explanation
Indices: 18920242--18920452 Score: 226
Period size: 41 Copynumber: 5.1 Consensus size: 41
18920232 AGTCGTAGTA
* * *
18920242 AGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTCAAAGTCATGGAGCCTCTGATTAGAGG
*
18920283 AGCAATTTACTTTTCAAAGTCATGGTGCCTCT-ATTTAGAGG
1 AGCAATTTACTTTTCAAAGTCATGGAGCCTCTGA-TTAGAGG
* * *
18920324 AGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTCAAAGTCATGGAGCCTCTGATTAGAGG
** * ** *
18920365 AGCAATTTGTTTTTTTAAAGTTGTTGAGCCTCTGATTAGAGG
1 AGCAATTT-ACTTTTCAAAGTCATGGAGCCTCTGATTAGAGG
* * * *
18920407 AGCCATTTATGTTTCTCAAAGTCATTGAGCCTCTGCTTAGAGG
1 AGCAATTTA-CTTT-TCAAAGTCATGGAGCCTCTGATTAGAGG
18920450 AGC
1 AGC
18920453 TTTGGTCAAA
Statistics
Matches: 147, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
41 84 0.57
42 36 0.24
43 27 0.18
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
AGCAATTTACTTTTCAAAGTCATGGAGCCTCTGATTAGAGG
Found at i:18920790 original size:21 final size:20
Alignment explanation
Indices: 18920766--18920871 Score: 90
Period size: 21 Copynumber: 5.0 Consensus size: 20
18920756 TCTTTTTCAT
*
18920766 TTTATTTTATATGTATTTTTA
1 TTTATCTTATAT-TATTTTTA
18920787 TTTATC-TA-ATTATATATTTA
1 TTTATCTTATATTAT-T-TTTA
18920807 TTTATCTGTTATTATTATTTTTTA
1 TTTATC--TTA-TATTA-TTTTTA
* *
18920831 TTTATCTTATAATATTGTTGA
1 TTTATCTTATATTATT-TTTA
18920852 TTTATCTTATTATTATTTTT
1 TTTATCTTA-TATTATTTTT
18920872 CTAATTATCT
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.04
19 3 0.04
20 14 0.20
21 23 0.33
22 9 0.13
23 2 0.03
24 10 0.14
25 5 0.07
26 1 0.01
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTATCTTATATTATTTTTA
Found at i:18920799 original size:24 final size:22
Alignment explanation
Indices: 18920772--18920897 Score: 84
Period size: 24 Copynumber: 5.7 Consensus size: 22
18920762 TCATTTTATT
18920772 TTATATGTATTTTTATTTATCTAA
1 TTATAT-TATTTTTATTTATCT-A
*
18920796 TTATA-TA--TTTATTTATCTG
1 TTATATTATTTTTATTTATCTA
18920815 TTATTATTATTTTTTATTTATC--
1 TTA-TATTA-TTTTTATTTATCTA
* *
18920837 TTATAATATTGTTGATTTATCTTA
1 TTATATTATT-TTTATTTATC-TA
* *
18920861 TTATTATT-TTTCTAATTATCTA
1 TTA-TATTATTTTTATTTATCTA
* *
18920883 TTAAATTTTTTTTAT
1 TTATATTATTTTTAT
18920898 CTGATTTTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
19 3 0.04
20 15 0.19
21 18 0.22
22 15 0.19
23 7 0.09
24 20 0.25
25 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (22 bp):
TTATATTATTTTTATTTATCTA
Found at i:18920828 original size:43 final size:42
Alignment explanation
Indices: 18920766--18920871 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 42
18920756 TCTTTTTCAT
* *
18920766 TTTATTTTA-TATGTATTTTTATTTATCTAATTATATAT-TT-A
1 TTTATCTTATTAT-TATTTTTATTTATCTAATAATAT-TGTTGA
*
18920807 TTTATCTGTTATTATTATTTTTTATTTATCTTATAATATTGTTGA
1 TTTATC--TTATTATTA-TTTTTATTTATCTAATAATATTGTTGA
18920852 TTTATCTTATTATTATTTTT
1 TTTATCTTATTATTATTTTT
18920872 CTAATTATCT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
41 5 0.09
42 5 0.09
43 15 0.27
44 24 0.43
45 7 0.12
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (42 bp):
TTTATCTTATTATTATTTTTATTTATCTAATAATATTGTTGA
Found at i:18920831 original size:44 final size:42
Alignment explanation
Indices: 18920781--18920909 Score: 136
Period size: 44 Copynumber: 3.0 Consensus size: 42
18920771 TTTATATGTA
18920781 TTTTTATTTATCTAATTATATATTTATTTATCTGTTATTATTAT
1 TTTTTATTTATCT-ATTATAT-TTTATTTATCTGTTATTATTAT
*
18920825 TTTTTATTTATCTTATAATATTGTTGATTTATC--TTATTATTAT
1 TTTTTATTTATC-TATTATATT-TT-ATTTATCTGTTATTATTAT
* * * *
18920868 TTTTCTAATTATCTATTAAATTTTTTTTATCTGATTTTTATT
1 TTTT-TATTTATCTATTATATTTTATTTATCTG-TTATTATT
18920910 TTGGAAGGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
41 6 0.08
42 2 0.03
43 22 0.31
44 34 0.47
45 8 0.11
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (42 bp):
TTTTTATTTATCTATTATATTTTATTTATCTGTTATTATTAT
Found at i:18921819 original size:17 final size:17
Alignment explanation
Indices: 18921799--18921833 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18921789 TTTAATGTTC
18921799 TTTTATCTTTATTTTAT
1 TTTTATCTTTATTTTAT
* *
18921816 TTTTATTTTTGTTTTAT
1 TTTTATCTTTATTTTAT
18921833 T
1 T
18921834 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTATCTTTATTTTAT
Found at i:18921928 original size:13 final size:14
Alignment explanation
Indices: 18921900--18921929 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18921890 TCAATTTTCC
*
18921900 TTAAAAATAGATTT
1 TTAAAAAAAGATTT
18921914 TTAAAAAAAGATTT
1 TTAAAAAAAGATTT
18921928 TT
1 TT
18921930 GAGGGAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TTAAAAAAAGATTT
Found at i:18921928 original size:58 final size:58
Alignment explanation
Indices: 18921859--18922190 Score: 424
Period size: 58 Copynumber: 5.7 Consensus size: 58
18921849 AATAAAATCC
* * * *
18921859 AAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAGATTTTTA
1 AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCA
* * * *
18921917 AAAAAAGATTTTT-GAGGGAAAGTTAAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTC-
1 AAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAA-TTTTCA
18921976 AAAAAATATTTTTGG-GAAAAAGTTGAAAGTATCAATTTTCCTT-AAAAGTAAATTTTCA
1 AAAAAATATTTTTGGAG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAA-TAAATTTTCA
18922034 AAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTT-CTTCGAAAATCAAAGTTTTCA
1 AAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT-AAA-TTTTCA
* * *
18922094 AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCA
1 AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCA
* *
18922152 AAAGAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT
18922191 TTCTGCACAA
Statistics
Matches: 242, Mismatches: 17, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
57 11 0.05
58 126 0.52
59 49 0.20
60 52 0.21
61 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCA
Found at i:18921981 original size:117 final size:118
Alignment explanation
Indices: 18921858--18922191 Score: 512
Period size: 117 Copynumber: 2.8 Consensus size: 118
18921848 AAATAAAATC
* *
18921858 CAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAGATTTTTAAAAAAA
1 CAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
* * *
18921923 GATTTTTGAGGGAAAGTTAAAAGTATCAATTTTTCTT-GAAAATCAAAGTTTT
66 TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTCGAAAATCAAAGTTTT
* *
18921975 CAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTCAAAAAAA
1 CAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
18922040 TATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTCGAAAATCAAAGTTTT
66 TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTCGAAAATCAAAGTTTT
* ** * * *
18922092 CAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCAAAAGA
1 C-AAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
18922157 ATATTTTT-AGAGAAAAGTTGAAAGTATCAATTTTT
65 ATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTT
18922192 TCTGCACAAG
Statistics
Matches: 199, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
116 7 0.04
117 105 0.53
118 83 0.42
119 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (118 bp):
CAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTCGAAAATCAAAGTTTT
Found at i:18922189 original size:27 final size:27
Alignment explanation
Indices: 18922101--18922191 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
18922091 TCAAAAAAAT
*
18922101 ATTTTTGGAGAAAAGTTGAAAGTATCA
1 ATTTTTAGAGAAAAGTTGAAAGTATCA
* * * *
18922128 ATTTTCCTCGAAATTAAAGTTTCAAAAGAAT--
1 ATTTT--TAGAGA--AAAG-TT-GAAAGTATCA
18922159 ATTTTTAGAGAAAAGTTGAAAGTATCA
1 ATTTTTAGAGAAAAGTTGAAAGTATCA
18922186 ATTTTT
1 ATTTTT
18922192 TCTGCACAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
25 6 0.12
26 2 0.04
27 15 0.31
29 8 0.17
31 9 0.19
32 2 0.04
33 6 0.12
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (27 bp):
ATTTTTAGAGAAAAGTTGAAAGTATCA
Found at i:18922238 original size:14 final size:14
Alignment explanation
Indices: 18922215--18922254 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
18922205 AATCATTCTT
*
18922215 TTCTTCTTTTTTTA
1 TTCTTATTTTTTTA
18922229 TTCTTATTTTTTTA
1 TTCTTATTTTTTTA
*
18922243 TTTTTATTTTTT
1 TTCTTATTTTTT
18922255 CTTTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (14 bp):
TTCTTATTTTTTTA
Found at i:18923566 original size:8 final size:8
Alignment explanation
Indices: 18923519--18923569 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
18923509 TTAATAATGG
18923519 ATGAAAAA
1 ATGAAAAA
18923527 AT-AAGAAA
1 ATGAA-AAA
*
18923535 ATAAAAAA
1 ATGAAAAA
18923543 ATGAAAAATA
1 ATG-AAAA-A
*
18923553 AAGAAAAA
1 ATGAAAAA
18923561 ATGAAAAA
1 ATGAAAAA
18923569 A
1 A
18923570 ATGTAAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 2 0.06
8 21 0.58
9 10 0.28
10 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (8 bp):
ATGAAAAA
Found at i:18923577 original size:27 final size:27
Alignment explanation
Indices: 18923532--18923589 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
18923522 AAAAAATAAG
18923532 AAAATAAAAAAATGAAAAAT-AAAGAA
1 AAAATAAAAAAATGAAAAATGAAAGAA
* *
18923558 AAAATGAAAAAAATGTAAAATGAGAGAA
1 AAAAT-AAAAAAATGAAAAATGAAAGAA
18923586 AAAA
1 AAAA
18923590 AAGACTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.18
27 14 0.50
28 9 0.32
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (27 bp):
AAAATAAAAAAATGAAAAATGAAAGAA
Found at i:18924985 original size:44 final size:44
Alignment explanation
Indices: 18924926--18925377 Score: 345
Period size: 44 Copynumber: 10.5 Consensus size: 44
18924916 AATTATCGAT
*
18924926 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTATTTATGA-
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGTTTA-GAG
* * * * * *
18924970 GAGCTTTATTTA-TTTTTCAAAGTC-ATGAGCCTCTATTTAGAT
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGTTTAGAG
* * *
18925012 GAGCTTTATTTATTTTTCAAAAGTTGTTGAGCTTCTGTTTAGAG
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGTTTAGAG
* * * * * *
18925056 GAACATTACTTATTTTTTTAAAGTC-ATGAGTCTT-TGTTTAAAG
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAG-CTTCTGTTTAGAG
* * * *
18925099 GAGCCTT-TTTA-TTTTTCAAAGTCG-TGAGCCTCTGCTTAAAG
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGTTTAGAG
* **
18925140 AAGCCTTATTTA-TTTTTCGAAGTCGTTGAGCTTCTGTTTAGAG
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGTTTAGAG
* * * **
18925183 GAGCCTTATTTCTTTTTCAAAAATTATTGAGCTTCT-TCTTAGAG
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGT-TTAGAG
* * *
18925227 GAGCCTTATTTACTTTTCT-AAAGTCGTTAAGCCTCTGTTTAGAG
1 GAGCCTTATTTA-TTTTTTAAAAGTCGTTGAGCTTCTGTTTAGAG
* * * * ** * * *
18925271 AAGCTTTAGTTATTTTTCAAAA-TTATTGAGCCTCTGCTTAGAA
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGTTTAGAG
* * * * * *
18925314 GAACCTTATTTATTTTTTAAAAGTTGTTAAGTCTT-TGCTTAAAA
1 GAGCCTTATTTATTTTTTAAAAGTCGTTGAG-CTTCTGTTTAGAG
*
18925358 GAGTCTTATTTATTTTTTAA
1 GAGCCTTATTTATTTTTTAA
18925378 TGTTATTGAG
Statistics
Matches: 326, Mismatches: 67, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
40 2 0.01
41 31 0.10
42 44 0.13
43 99 0.30
44 143 0.44
45 7 0.02
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (44 bp):
GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTGTTTAGAG
Found at i:18925035 original size:43 final size:43
Alignment explanation
Indices: 18924926--18925452 Score: 325
Period size: 43 Copynumber: 12.2 Consensus size: 43
18924916 AATTATCGAT
* * * *
18924926 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTATTTATGA-
1 GAGCCTTATTTATTTTTCAAAAGTC-ATGAGCCTCTGTTTA-GAG
* * *
18924970 GAGCTTTATTTATTTTTC-AAAGTCATGAGCCTCTATTTAGAT
1 GAGCCTTATTTATTTTTCAAAAGTCATGAGCCTCTGTTTAGAG
* ** *
18925012 GAGCTTTATTTATTTTTCAAAAGTTGTTGAGCTTCTGTTTAGAG
1 GAGCCTTATTTATTTTTCAAAAG-TCATGAGCCTCTGTTTAGAG
* * * ** * * *
18925056 GAACATTACTTATTTTTTTAAAGTCATGAGTCTTTGTTTAAAG
1 GAGCCTTATTTATTTTTCAAAAGTCATGAGCCTCTGTTTAGAG
* * *
18925099 GAGCCTT-TTTATTTTTC-AAAGTCGTGAGCCTCTGCTTAAAG
1 GAGCCTTATTTATTTTTCAAAAGTCATGAGCCTCTGTTTAGAG
* * * *
18925140 AAGCCTTATTTATTTTTC-GAAGTCGTTGAGCTTCTGTTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTC-ATGAGCCTCTGTTTAGAG
* * * *
18925183 GAGCCTTATTTCTTTTTCAAAAATTATTGAGCTTCT-TCTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTCA-TGAGCCTCTGT-TTAGAG
* * * *
18925227 GAGCCTTATTTACTTTTCTAAAGTCGTTAAGCCTCTGTTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTC-ATGAGCCTCTGTTTAGAG
* * * * * *
18925271 AAGCTTTAGTTATTTTTCAAAA-TTATTGAGCCTCTGCTTAGAA
1 GAGCCTTATTTATTTTTCAAAAGTCA-TGAGCCTCTGTTTAGAG
* * ** * * * * * *
18925314 GAACCTTATTTATTTTTTAAAAGTTGTTAAGTCTTTGCTTAAAA
1 GAGCCTTATTTATTTTTCAAAAG-TCATGAGCCTCTGTTTAGAG
* * * * * *
18925358 GAGTCTTATTTATTTTT-TAATGTTATTGAGTCTCTGCTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTCA-TGAGCCTCTGTTTAGAG
** * * **
18925401 GAGTTTTATTTAGTTTTC-AAAGTTATTGAGCCTCTACTTAGAG
1 GAGCCTTATTTATTTTTCAAAAGTCA-TGAGCCTCTGTTTAGAG
*
18925444 GAGCTTTAT
1 GAGCCTTAT
18925453 GTTTCAGAAG
Statistics
Matches: 383, Mismatches: 85, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
41 28 0.07
42 55 0.14
43 153 0.40
44 145 0.38
45 2 0.01
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (43 bp):
GAGCCTTATTTATTTTTCAAAAGTCATGAGCCTCTGTTTAGAG
Found at i:18925244 original size:87 final size:86
Alignment explanation
Indices: 18924926--18925452 Score: 361
Period size: 87 Copynumber: 6.1 Consensus size: 86
18924916 AATTATCGAT
* * ** *
18924926 GAGCCTTATTTATTTTTTAAAAGTCGTTGAGCTTCTAT-TTATGA-GAGCTTTATTTATTTTTCA
1 GAGCCTTATTTATTTTTCAAAAATTATTGAGCTTCT-TCTTA-GAGGAGCCTTATTTATTTTTCA
* *
18924989 AAGTCATGAGCCTCTATTTAGAT
64 AAGTCATGAGCCTCTGTTTAGAG
* * * * * * *
18925012 GAGCTTTATTTATTTTTCAAAAGTTGTTGAGCTTCTGT-TTAGAGGAACATTACTTATTTTTTTA
1 GAGCCTTATTTATTTTTCAAAAATTATTGAGCTTCT-TCTTAGAGGAGCCTTATTTA-TTTTTCA
* * *
18925076 AAGTCATGAGTCTTTGTTTAAAG
64 AAGTCATGAGCCTCTGTTTAGAG
* ** * * * * *
18925099 GAGCCTT-TTTATTTTTC--AAAGTCGTGAGCCTCTGCTTAAAGAAGCCTTATTTATTTTTCGAA
1 GAGCCTTATTTATTTTTCAAAAATTATTGAGCTTCTTCTTAGAGGAGCCTTATTTATTTTTCAAA
* *
18925161 GTCGTTGAGCTTCTGTTTAGAG
66 GTC-ATGAGCCTCTGTTTAGAG
* *
18925183 GAGCCTTATTTCTTTTTCAAAAATTATTGAGCTTCTTCTTAGAGGAGCCTTATTTACTTTTCTAA
1 GAGCCTTATTTATTTTTCAAAAATTATTGAGCTTCTTCTTAGAGGAGCCTTATTTATTTTTC-AA
* *
18925248 AGTCGTTAAGCCTCTGTTTAGAG
65 AGTC-ATGAGCCTCTGTTTAGAG
* * * * * * * *
18925271 AAGCTTTAGTTATTTTTC-AAAATTATTGAGCCTCTGCTTAGAAGAACCTTATTTATTTTTTAAA
1 GAGCCTTATTTATTTTTCAAAAATTATTGAGCTTCTTCTTAGAGGAGCCTTATTTA-TTTTTCAA
** * * * * * *
18925335 AGTTGTTAAGTCTTTGCTTAAAA
65 AG-TCATGAGCCTCTGTTTAGAG
* * ** * ** *
18925358 GAGTCTTATTTATTTTT-TAATGTTATTGAG-TCTCTGCTTAGAGGAGTTTTATTTAGTTTTCAA
1 GAGCCTTATTTATTTTTCAAAAATTATTGAGCT-TCTTCTTAGAGGAGCCTTATTTATTTTTCAA
* **
18925421 AGTTATTGAGCCTCTACTTAGAG
65 AGTCA-TGAGCCTCTGTTTAGAG
*
18925444 GAGCTTTAT
1 GAGCCTTAT
18925453 GTTTCAGAAG
Statistics
Matches: 345, Mismatches: 83, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
83 10 0.03
84 44 0.13
85 12 0.03
86 82 0.24
87 156 0.45
88 41 0.12
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (86 bp):
GAGCCTTATTTATTTTTCAAAAATTATTGAGCTTCTTCTTAGAGGAGCCTTATTTATTTTTCAAA
GTCATGAGCCTCTGTTTAGAG
Found at i:18925946 original size:20 final size:21
Alignment explanation
Indices: 18925899--18925944 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
18925889 AACCAAGCCT
18925899 AAAAAAT-CACATAAAAAGTA
1 AAAAAATACACATAAAAAGTA
*
18925919 AAAAAATACACATAAAAAGGA
1 AAAAAATACACATAAAAAGTA
18925940 AAAAA
1 AAAAA
18925945 TATAGTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.11
Consensus pattern (21 bp):
AAAAAATACACATAAAAAGTA
Found at i:18926039 original size:20 final size:21
Alignment explanation
Indices: 18926014--18926055 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
18926004 AAACTAGAAA
*
18926014 TTTTTAGATTTTGATGA-ATT
1 TTTTTAGATTTCGATGACATT
18926034 TTTTTAGATTTCGATGACATT
1 TTTTTAGATTTCGATGACATT
18926055 T
1 T
18926056 GAATTTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (21 bp):
TTTTTAGATTTCGATGACATT
Found at i:18927056 original size:26 final size:26
Alignment explanation
Indices: 18927022--18927075 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
18927012 AATTATGAGA
*
18927022 TTCTTAGAAATTTC-AAAT-AGTAAAT
1 TTCTTAGAAATCTCTAAATGAG-AAAT
18927047 TTCTTAAGAAATCTCTAAATGAGAAAT
1 TTCTT-AGAAATCTCTAAATGAGAAAT
18927074 TT
1 TT
18927076 ATTTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 5 0.20
26 8 0.32
27 10 0.40
28 2 0.08
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (26 bp):
TTCTTAGAAATCTCTAAATGAGAAAT
Found at i:18929278 original size:2 final size:2
Alignment explanation
Indices: 18929265--18929301 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18929255 TGCGCGTATG
*
18929265 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18929302 TTCAGAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18931815 original size:2 final size:2
Alignment explanation
Indices: 18931808--18931836 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18931798 AGGTCATGTC
18931808 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
18931837 GCTTGGAAAA
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:18932337 original size:2 final size:2
Alignment explanation
Indices: 18932330--18932358 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18932320 AACTTTTTGA
18932330 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
18932359 ATTACTATAG
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:18933353 original size:2 final size:2
Alignment explanation
Indices: 18933346--18933378 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18933336 TGTATCCAAC
18933346 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
18933379 AAACTTTTCT
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:18933512 original size:87 final size:87
Alignment explanation
Indices: 18933366--18933541 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
18933356 ATATATATAT
*
18933366 ATATATATATATAAAACTTTTCTAGCATAAAGTAGATATGGTATAAACTAGGTGAAGGATCGATA
1 ATATATATATATAAAACTTTTCTAGCATAAAGTAGATATGGCATAAACTAGGTGAAGGATCGATA
18933431 TGAACTATAAATGCATGCATGC
66 TGAACTATAAATGCATGCATGC
18933453 ATATATATATATAAAACTTTTCTAGCATAAAGTAGATATGGCATAAACTAGGTGAAGGATCGATA
1 ATATATATATATAAAACTTTTCTAGCATAAAGTAGATATGGCATAAACTAGGTGAAGGATCGATA
18933518 TGAACTATAAATGCATGCATGC
66 TGAACTATAAATGCATGCATGC
18933540 AT
1 AT
18933542 GCATGCATGA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (87 bp):
ATATATATATATAAAACTTTTCTAGCATAAAGTAGATATGGCATAAACTAGGTGAAGGATCGATA
TGAACTATAAATGCATGCATGC
Found at i:18933628 original size:2 final size:2
Alignment explanation
Indices: 18933584--18933609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18933574 TAAGGGAGAC
18933584 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
18933610 TACGGTCAAG
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:18948862 original size:15 final size:15
Alignment explanation
Indices: 18948844--18948873 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18948834 TTATTTAGTC
*
18948844 AAATTTAATAATAAA
1 AAATTTAAAAATAAA
18948859 AAATTTAAAAATAAA
1 AAATTTAAAAATAAA
18948874 TTAATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTTAAAAATAAA
Found at i:18949492 original size:28 final size:28
Alignment explanation
Indices: 18949434--18949492 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
18949424 TGAGTTTTAA
* **
18949434 TTTCTCAATAATAAATTTATGAAAATTT
1 TTTCTCAAAAATAAATTTATGAAAAGCT
* * *
18949462 TTTCTTAAAAATAGATTTTTGAAAAGCT
1 TTTCTCAAAAATAAATTTATGAAAAGCT
18949490 TTT
1 TTT
18949493 ATAGCTCTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (28 bp):
TTTCTCAAAAATAAATTTATGAAAAGCT
Found at i:18949589 original size:15 final size:15
Alignment explanation
Indices: 18949569--18949616 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
18949559 TTTTAAAGAT
*
18949569 TTTTTAAAAATAAAG
1 TTTTTAAAAATAAAA
***
18949584 TTTTTAATTTTAAAA
1 TTTTTAAAAATAAAA
18949599 TTTTTAAAAATAAAA
1 TTTTTAAAAATAAAA
18949614 TTT
1 TTT
18949617 CGAAAATTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTTTAAAAATAAAA
Found at i:18949625 original size:32 final size:33
Alignment explanation
Indices: 18949554--18949625 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 33
18949544 ATTTATTTTG
*
18949554 GAAAATTTTAAAGATTTTTTAAAAATAAAGTTT
1 GAAAATTTTAAAGATTTTTTAAAAATAAAATTT
**
18949587 -TTAATTTTAAA-A-TTTTTAAAAATAAAATTT
1 GAAAATTTTAAAGATTTTTTAAAAATAAAATTT
18949617 CGAAAATTT
1 -GAAAATTT
18949626 ACGCAAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 17 0.53
31 1 0.03
32 14 0.44
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (33 bp):
GAAAATTTTAAAGATTTTTTAAAAATAAAATTT
Found at i:18972793 original size:12 final size:12
Alignment explanation
Indices: 18972776--18972801 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18972766 CAAGAAAATG
18972776 AAGAAAATTTCA
1 AAGAAAATTTCA
18972788 AAGAAAATTTCA
1 AAGAAAATTTCA
18972800 AA
1 AA
18972802 ATGGTCGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (12 bp):
AAGAAAATTTCA
Found at i:18981773 original size:25 final size:25
Alignment explanation
Indices: 18981739--18981796 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
18981729 TGCAACATGG
* *
18981739 AGGTTAAAGATATTTCATCTAAGTT
1 AGGTTAAAGATACTACATCTAAGTT
18981764 AGGTTAAAGATACTACATCTAAGTT
1 AGGTTAAAGATACTACATCTAAGTT
*
18981789 AAGTTAAA
1 AGGTTAAA
18981797 ACACACCTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (25 bp):
AGGTTAAAGATACTACATCTAAGTT
Found at i:18988194 original size:11 final size:11
Alignment explanation
Indices: 18988166--18988208 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
18988156 TGATAATTTA
18988166 AAATATAATAT
1 AAATATAATAT
18988177 ATTAATATAATAT
1 A--AATATAATAT
*
18988190 AAATATGATAT
1 AAATATAATAT
*
18988201 AAAAATAA
1 AAATATAA
18988209 AATATGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 16 0.59
13 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:18988200 original size:24 final size:24
Alignment explanation
Indices: 18988166--18988226 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
18988156 TGATAATTTA
** *
18988166 AAATATAATATATTAATATAATAT
1 AAATATAATATAAAAATAAAATAT
*
18988190 AAATATGATATAAAAATAAAATAT
1 AAATATAATATAAAAATAAAATAT
* *
18988214 GAATATTATATAA
1 AAATATAATATAA
18988227 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
AAATATAATATAAAAATAAAATAT
Found at i:18988319 original size:25 final size:25
Alignment explanation
Indices: 18988290--18988351 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
18988280 TTTTATGTTT
18988290 TATTTTTATTTAA-ATTATAATAT-A
1 TATTTTTATTTAAGA-TATAATATAA
* *
18988314 TAATTTTTGTATAAGATATAATATAA
1 T-ATTTTTATTTAAGATATAATATAA
18988340 TATTTTATATTT
1 TATTTT-TATTT
18988352 TACAAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 1 0.03
25 23 0.77
26 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TATTTTTATTTAAGATATAATATAA
Found at i:18988922 original size:19 final size:18
Alignment explanation
Indices: 18988831--18988923 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 18
18988821 AGATATCAAT
18988831 TTATTAAT-AAATAAATA
1 TTATTAATAAAATAAATA
**
18988848 TTAATTTTTAAAATAAATA
1 TT-ATTAATAAAATAAATA
* *
18988867 -TA-TAAAAAAATTAATA
1 TTATTAATAAAATAAATA
***
18988883 TTATT--TAAAATTTTTA
1 TTATTAATAAAATAAATA
18988899 TTTATTAATAAAAATAAATA
1 -TTATTAAT-AAAATAAATA
18988919 TTATT
1 TTATT
18988924 TTATTTTATT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
16 18 0.32
17 10 0.18
18 6 0.11
19 15 0.27
20 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTAATAAAATAAATA
Found at i:18988931 original size:29 final size:27
Alignment explanation
Indices: 18988894--18988964 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
18988884 TATTTAAAAT
18988894 TTTTATTTATTAATAAAAATAAATATTA
1 TTTTATTTATTAATAAAAAT-AATATTA
18988922 TTTTATTTTATTAAT-AAAATAATATTA
1 TTTTA-TTTATTAATAAAAATAATATTA
*
18988949 TTTAATTTATTAATAA
1 TTTTATTTATTAATAA
18988965 TATATAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 9 0.22
27 12 0.30
28 10 0.25
29 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTATTTATTAATAAAAATAATATTA
Found at i:18988959 original size:26 final size:28
Alignment explanation
Indices: 18988892--18988964 Score: 105
Period size: 26 Copynumber: 2.6 Consensus size: 28
18988882 ATTATTTAAA
*
18988892 ATTTTTATTTATTAATAAAAATAAATATT
1 ATTTTAATTTATTAAT-AAAATAAATATT
*
18988921 ATTTTATTTTATTAATAAAAT-AATATT
1 ATTTTAATTTATTAATAAAATAAATATT
18988948 A-TTTAATTTATTAATAA
1 ATTTTAATTTATTAATAA
18988965 TATATAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 15 0.37
27 7 0.17
28 5 0.12
29 14 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTTAATTTATTAATAAAATAAATATT
Found at i:18988978 original size:29 final size:27
Alignment explanation
Indices: 18988888--18988975 Score: 101
Period size: 26 Copynumber: 3.3 Consensus size: 27
18988878 TAATATTATT
*
18988888 TAAAATT-TTT-ATTTATTAATAAAAA
1 TAAAATTATTTAATTTATTAATAAATA
*
18988913 TAAATATTATTTTATTTTATTAATAAA-A
1 TAAA-ATTA-TTTAATTTATTAATAAATA
*
18988941 TAATATTATTTAATTTATTAATAATATA
1 TAAAATTATTTAATTTATTAATAA-ATA
18988969 TAAAATT
1 TAAAATT
18988976 TATATATAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 4 0.08
26 18 0.34
27 5 0.09
28 14 0.26
29 12 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAAATTATTTAATTTATTAATAAATA
Found at i:18989610 original size:17 final size:18
Alignment explanation
Indices: 18989576--18989619 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
18989566 TTTATATATA
*
18989576 ATTAAATAAGTAATATTC
1 ATTAAATATGTAATATTC
*
18989594 ATTAAATATTTAA-ATTC
1 ATTAAATATGTAATATTC
*
18989611 GTTAAATAT
1 ATTAAATAT
18989620 ATGTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
ATTAAATATGTAATATTC
Found at i:18990640 original size:22 final size:22
Alignment explanation
Indices: 18990601--18990653 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
18990591 AATATTTTAA
*
18990601 AATATTAT-TATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
*
18990622 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTAAAAAAAT
18990644 AATATTTTAT
1 AATATTTTAT
18990654 TAATTTCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:18990650 original size:15 final size:16
Alignment explanation
Indices: 18990586--18990630 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
18990576 ATACATTTAT
18990586 ATAATAATATTTTAAA
1 ATAATAATATTTTAAA
* *
18990602 ATATTATTA-TTTAAA
1 ATAATAATATTTTAAA
*
18990617 AAAATAATATTTTA
1 ATAATAATATTTTA
18990631 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATAATATTTTAAA
Found at i:18997550 original size:11 final size:11
Alignment explanation
Indices: 18997536--18997569 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18997526 ATTAAAATAT
18997536 TTTTAATAAAA
1 TTTTAATAAAA
18997547 TTTTAATAAAA
1 TTTTAATAAAA
18997558 -TTTAATTAAAA
1 TTTTAA-TAAAA
18997569 T
1 T
18997570 GATTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTTAATAAAA
Found at i:18998900 original size:22 final size:22
Alignment explanation
Indices: 18998869--18998945 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
18998859 ACTATTAAAC
*
18998869 TAAAACTAAATCATTAATAATT
1 TAAAAGTAAATCATTAATAATT
* *
18998891 TAAAAGTAAATCATTCATAACT
1 TAAAAGTAAATCATTAATAATT
* * **
18998913 TAACAGTAAATCAATGTTAATT
1 TAAAAGTAAATCATTAATAATT
*
18998935 TAATAGTAAAT
1 TAAAAGTAAAT
18998946 TATTGATATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (22 bp):
TAAAAGTAAATCATTAATAATT
Found at i:19017428 original size:16 final size:16
Alignment explanation
Indices: 19017407--19017438 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19017397 AAAATCATCG
19017407 TAAATCATCATTATCA
1 TAAATCATCATTATCA
19017423 TAAATCATCATTATCA
1 TAAATCATCATTATCA
19017439 ATCAAATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATCATCATTATCA
Found at i:19017453 original size:15 final size:15
Alignment explanation
Indices: 19017433--19017465 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19017423 TAAATCATCA
19017433 TTATCAATCAAATCG
1 TTATCAATCAAATCG
*
19017448 TTATCATTCAAATCG
1 TTATCAATCAAATCG
19017463 TTA
1 TTA
19017466 GCTACGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTATCAATCAAATCG
Found at i:19022538 original size:15 final size:15
Alignment explanation
Indices: 19022518--19022550 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19022508 AAAATCATCA
19022518 TTATCAATCAAATCG
1 TTATCAATCAAATCG
*
19022533 TTATCATTCAAATCG
1 TTATCAATCAAATCG
19022548 TTA
1 TTA
19022551 GCTACGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTATCAATCAAATCG
Found at i:19027631 original size:15 final size:15
Alignment explanation
Indices: 19027611--19027643 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19027601 TAAATCATCA
19027611 TTATCAATCAAATCG
1 TTATCAATCAAATCG
*
19027626 TTATCATTCAAATCG
1 TTATCAATCAAATCG
19027641 TTA
1 TTA
19027644 GCTACGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTATCAATCAAATCG
Found at i:19032715 original size:16 final size:16
Alignment explanation
Indices: 19032694--19032725 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19032684 AAAATCATCG
19032694 TAAATCATCATTATCA
1 TAAATCATCATTATCA
19032710 TAAATCATCATTATCA
1 TAAATCATCATTATCA
19032726 ATCAAATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATCATCATTATCA
Found at i:19032740 original size:15 final size:15
Alignment explanation
Indices: 19032720--19032752 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19032710 TAAATCATCA
19032720 TTATCAATCAAATCG
1 TTATCAATCAAATCG
*
19032735 TTATCATTCAAATCG
1 TTATCAATCAAATCG
19032750 TTA
1 TTA
19032753 GCTACGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTATCAATCAAATCG
Found at i:19040841 original size:21 final size:21
Alignment explanation
Indices: 19040792--19040919 Score: 62
Period size: 20 Copynumber: 6.3 Consensus size: 21
19040782 GTACAAATTT
* *
19040792 AATATTATATAAAATCATAATC
1 AATATTATTTAAAAT-ATAATA
19040814 AAT-TTATTTAAAAT-TAATAA
1 AATATTATTTAAAATATAAT-A
*
19040834 AATATTATTT-TAATATAA-A
1 AATATTATTTAAAATATAATA
19040853 ATATAATT-TTT-AAATATAA-A
1 A-AT-ATTATTTAAAATATAATA
* *
19040873 TATAATA-TTAAATATATAA-A
1 AATATTATTTAAA-ATATAATA
* *
19040893 AAAATTATAT-AAATAT-ATA
1 AATATTATTTAAAATATAATA
19040912 TAATATTA
1 -AATATTA
19040920 ACAAATAATA
Statistics
Matches: 84, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
18 5 0.06
19 15 0.18
20 38 0.45
21 23 0.27
22 3 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATTATTTAAAATATAATA
Found at i:19040851 original size:18 final size:20
Alignment explanation
Indices: 19040830--19040888 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 20
19040820 TTTAAAATTA
*
19040830 ATAAAATATTA-TTTT-AAT
1 ATAAAATATAATTTTTAAAT
19040848 ATAAAATATAATTTTTAAAT
1 ATAAAATATAATTTTTAAAT
*
19040868 AT-AAATATAA-TATTAAAT
1 ATAAAATATAATTTTTAAAT
19040886 ATA
1 ATA
19040889 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 19 0.53
19 12 0.33
20 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAAATATAATTTTTAAAT
Found at i:19040865 original size:19 final size:19
Alignment explanation
Indices: 19040830--19040888 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
19040820 TTTAAAATTA
*
19040830 ATAAAATATTA-TTTTAAT
1 ATAAAATATAATTTTTAAT
19040848 ATAAAATATAATTTTTAA-
1 ATAAAATATAATTTTTAAT
* *
19040866 ATATAAATATAATATTAAAT
1 ATA-AAATATAATTTTTAAT
19040886 ATA
1 ATA
19040889 TAAAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 13 0.37
19 19 0.54
20 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATATAATTTTTAAT
Found at i:19040886 original size:12 final size:11
Alignment explanation
Indices: 19040865--19040914 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
19040855 ATAATTTTTA
19040865 AATATAAATAT
1 AATATAAATAT
19040876 AATATTAAATAT
1 AATA-TAAATAT
* *
19040888 -ATAAAAAAAT
1 AATATAAATAT
*
19040898 TATATAAATAT
1 AATATAAATAT
19040909 -ATATAA
1 AATATAA
19040915 TATTAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 11 0.33
11 15 0.45
12 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:19040931 original size:39 final size:38
Alignment explanation
Indices: 19040863--19040961 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 38
19040853 ATATAATTTT
*
19040863 TAAATATAAATATAATATTAAATATATAAAAAA-ATTATA
1 TAAATAT--ATATAATATTAAAAATATAAAAAACATTATA
*
19040902 TAAATATATATAATATTAACAAATAATAAAAAACTATTTTA
1 TAAATATATATAATATTAA-AAAT-ATAAAAAAC-ATTATA
* *
19040943 TATATATATAT-CTATTAAA
1 TAAATATATATAATATTAAA
19040962 TAAAAAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
37 12 0.23
38 3 0.06
39 16 0.31
40 6 0.12
41 15 0.29
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (38 bp):
TAAATATATATAATATTAAAAATATAAAAAACATTATA
Found at i:19040963 original size:37 final size:36
Alignment explanation
Indices: 19040860--19040974 Score: 117
Period size: 37 Copynumber: 3.1 Consensus size: 36
19040850 AAAATATAAT
* *
19040860 TTTTAAATATAAATATAATATTAAATATATAAAAAAA
1 TTTTATATATATATATAATATTAAATA-ATAAAAAAA
* *
19040897 TTATATAAATATATATAATATTAACAAATAATAAAAAACTA
1 TTTTATATATATATATAATATT---AAATAATAAAAAA--A
*
19040938 TTTTATATATATATAT-CTATTAAATAA-AAAAAAA
1 TTTTATATATATATATAATATTAAATAATAAAAAAA
19040972 TTT
1 TTT
19040975 ACCTAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
34 4 0.06
36 6 0.09
37 24 0.36
39 8 0.12
40 9 0.14
41 15 0.23
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (36 bp):
TTTTATATATATATATAATATTAAATAATAAAAAAA
Found at i:19049688 original size:23 final size:21
Alignment explanation
Indices: 19049648--19049692 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
19049638 ATAAAATATA
19049648 TATTTTAAATTTTATTAAATT
1 TATTTTAAATTTTATTAAATT
*
19049669 TATTTTAATTTTTTATTTAAATT
1 TATTTTAA-ATTTTA-TTAAATT
19049692 T
1 T
19049693 TAAATAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTAAATTTTATTAAATT
Found at i:19049756 original size:26 final size:25
Alignment explanation
Indices: 19049702--19049768 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 25
19049692 TTAAATAATG
*
19049702 TTATTTTTATATAT-TTTATTCATA
1 TTATTTTTATATATCATTATTCATA
*
19049726 TTATTTTTATATATCATTA-TCATG
1 TTATTTTTATATATCATTATTCATA
19049750 TTATATTTTATATTATCAT
1 TTAT-TTTTATA-TATCAT
19049769 GTCATTATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 22 0.58
25 10 0.26
26 6 0.16
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (25 bp):
TTATTTTTATATATCATTATTCATA
Found at i:19049773 original size:25 final size:23
Alignment explanation
Indices: 19049699--19049773 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
19049689 ATTTTAAATA
* *
19049699 ATGTTATTTTTATATATTTTATTC
1 ATGTTATTTTTATAT-TATCATTC
*
19049723 ATATTATTTTTATA-TATCATTATC
1 ATGTTATTTTTATATTATCA-T-TC
19049747 ATGTTATATTTTATATTATCATGTC
1 ATGTTAT-TTTTATATTATCAT-TC
19049772 AT
1 AT
19049774 TATCATCTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 3 0.07
23 1 0.02
24 21 0.50
25 12 0.29
26 5 0.12
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (23 bp):
ATGTTATTTTTATATTATCATTC
Found at i:19061506 original size:18 final size:18
Alignment explanation
Indices: 19061480--19061537 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
19061470 ATCACAAAAA
19061480 ATATTATATTTATATTAT
1 ATATTATATTTATATTAT
* ** *
19061498 ATTTTATATAAAAATTAT
1 ATATTATATTTATATTAT
19061516 ATATTATAATTTATATTA-
1 ATATTAT-ATTTATATTAT
19061534 ATAT
1 ATAT
19061538 AAAAATATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 24 0.77
19 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTATATTTATATTAT
Found at i:19061538 original size:31 final size:32
Alignment explanation
Indices: 19061477--19061557 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 32
19061467 ATGATCACAA
*
19061477 AAAATATTATAT-TTAT-A-TTATATTTTATAT
1 AAAA-ATTATATATTATAATTTATATTTAATAT
19061507 AAAAATTATATATTATAATTTATA-TTAATAT
1 AAAAATTATATATTATAATTTATATTTAATAT
* *
19061538 AAAAA-TATAAAATATAATTT
1 AAAAATTATATATTATAATTT
19061558 TTTAATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 7 0.16
30 21 0.47
31 12 0.27
32 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
AAAAATTATATATTATAATTTATATTTAATAT
Found at i:19061615 original size:11 final size:11
Alignment explanation
Indices: 19061601--19061644 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
19061591 AAATTTTAAA
19061601 TTATATTATTT
1 TTATATTATTT
*
19061612 TTATATTTTATAT
1 TTATA--TTATTT
19061625 TTATATTATTT
1 TTATATTATTT
*
19061636 ATATATTAT
1 TTATATTAT
19061645 ATTACTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTATTT
Found at i:19061625 original size:15 final size:17
Alignment explanation
Indices: 19061601--19061662 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 17
19061591 AAATTTTAAA
*
19061601 TTATATTATTTTTA-TAT
1 TTATA-TATTTATATTAT
19061618 TT-TATATTTATATTAT
1 TTATATATTTATATTAT
19061634 TTATATA-TTATATTACT
1 TTATATATTTATATTA-T
*
19061651 GTATCATATTTA
1 TTAT-ATATTTA
19061663 AAATTTACCT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 7 0.18
16 15 0.39
17 10 0.26
18 3 0.08
19 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (17 bp):
TTATATATTTATATTAT
Found at i:19061633 original size:24 final size:24
Alignment explanation
Indices: 19061575--19061642 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
19061565 TTATTCAATT
* *
19061575 TATTTATATT-TTTATAAAATTTTA
1 TATTTATATTATTT-TTATATTTTA
*
19061599 -AATTATATTATTTTTATATTTTA
1 TATTTATATTATTTTTATATTTTA
*
19061622 TATTTATATTATTTATATATT
1 TATTTATATTATTTTTATATT
19061643 ATATTACTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 16 0.43
24 21 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTATATTATTTTTATATTTTA
Found at i:19061644 original size:16 final size:15
Alignment explanation
Indices: 19061595--19061648 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
19061585 TTTATAAAAT
* *
19061595 TTTAAATTATATTATT
1 TTTATATTAT-TTATA
19061611 TTTATA-T-TTTATA
1 TTTATATTATTTATA
19061624 TTTATATTATTTATA
1 TTTATATTATTTATA
19061639 TATTATATTA
1 T-TTATATTA
19061649 CTGTATCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 10 0.30
14 2 0.06
15 8 0.24
16 13 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATATTATTTATA
Found at i:19069693 original size:14 final size:14
Alignment explanation
Indices: 19069674--19069701 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19069664 AACATTAAAG
19069674 GTGGAGAGATTGTA
1 GTGGAGAGATTGTA
19069688 GTGGAGAGATTGTA
1 GTGGAGAGATTGTA
19069702 AAGAGAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (14 bp):
GTGGAGAGATTGTA
Found at i:19069965 original size:103 final size:104
Alignment explanation
Indices: 19069837--19070023 Score: 277
Period size: 103 Copynumber: 1.8 Consensus size: 104
19069827 AGATTGTAAT
* * ** *
19069837 GCCCCAAATCCACATTAGAAGAATGTGTGGATAAAAAATAATATATATGTAGAAACTTAATCCCA
1 GCCCCAAATCCACATCAGAAAAATGTGTAAATAAAAAATAATATATATGCAGAAACTTAATCCCA
*
19069902 AACTTGTGAAACACCTTTTATAGGATAAAACTGCGAGAC
66 AACTTGTGAAACACATTTTATAGGATAAAACTGCGAGAC
* *
19069941 GCCCC-AATCCACATCAGAAAAATGTGTAAATAAAAAATAATATATATGCAGAGACTTAATCTCA
1 GCCCCAAATCCACATCAGAAAAATGTGTAAATAAAAAATAATATATATGCAGAAACTTAATCCCA
* *
19070005 AAGTTGTGAGACACATTTT
66 AACTTGTGAAACACATTTT
19070024 GTAAAATAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
103 68 0.93
104 5 0.07
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (104 bp):
GCCCCAAATCCACATCAGAAAAATGTGTAAATAAAAAATAATATATATGCAGAAACTTAATCCCA
AACTTGTGAAACACATTTTATAGGATAAAACTGCGAGAC
Found at i:19075602 original size:2 final size:2
Alignment explanation
Indices: 19075584--19075617 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
19075574 CAAATTTATG
* *
19075584 TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19075618 GACACACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:19088034 original size:24 final size:25
Alignment explanation
Indices: 19087980--19088034 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
19087970 GAATAATAAT
19087980 AAATTTATTATAATTATGATTGAAA
1 AAATTTATTATAATTATGATTGAAA
19088005 AAATTTATTATAATTATGATT-AAA
1 AAATTTATTATAATTATGATTGAAA
19088029 AAATTT
1 AAATTT
19088035 TTAATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (25 bp):
AAATTTATTATAATTATGATTGAAA
Found at i:19094100 original size:14 final size:14
Alignment explanation
Indices: 19094081--19094112 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
19094071 AATCAAATTC
19094081 AAATTTATTTTTTA
1 AAATTTATTTTTTA
19094095 AAATTTATTTTTTA
1 AAATTTATTTTTTA
19094109 AAAT
1 AAAT
19094113 ATAGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AAATTTATTTTTTA
Found at i:19094120 original size:15 final size:14
Alignment explanation
Indices: 19094081--19094124 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
19094071 AATCAAATTC
*
19094081 AAATTTATTTTTTA
1 AAATATATTTTTTA
*
19094095 AAATTTATTTTTTA
1 AAATATATTTTTTA
*
19094109 AAATATA-GTTTTA
1 AAATATATTTTTTA
19094122 AAA
1 AAA
19094125 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
AAATATATTTTTTA
Found at i:19094439 original size:18 final size:17
Alignment explanation
Indices: 19094416--19094450 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19094406 TAAAATATTT
19094416 ATAAAAAATATTATTTAA
1 ATAAAAAATA-TATTTAA
*
19094434 ATAAAAATTATATTTAA
1 ATAAAAAATATATTTAA
19094451 TTTATATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAAAATATATTTAA
Found at i:19094454 original size:22 final size:25
Alignment explanation
Indices: 19094428--19094473 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 25
19094418 AAAAAATATT
19094428 ATTTAAATA-AAAAT-TA-TATTTA
1 ATTTAAATAGAAAATATAGTATTTA
*
19094450 ATTTATATAGAAAATATAGTATTT
1 ATTTAAATAGAAAATATAGTATTT
19094474 TTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
24 2 0.10
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTTAAATAGAAAATATAGTATTTA
Found at i:19094479 original size:26 final size:22
Alignment explanation
Indices: 19094426--19094486 Score: 59
Period size: 26 Copynumber: 2.6 Consensus size: 22
19094416 ATAAAAAATA
19094426 TTATTTAAATAAAAATTATATT
1 TTATTTAAATAAAAATTATATT
* *
19094448 TAATTTATATAGAAAATATAGTATTT
1 TTATTTAAATA-AAAAT-TA-TA-TT
*
19094474 TTATTTAATTAAA
1 TTATTTAAATAAA
19094487 TTATTAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 2 0.07
25 4 0.13
26 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TTATTTAAATAAAAATTATATT
Found at i:19094561 original size:2 final size:2
Alignment explanation
Indices: 19094554--19094578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19094544 TAAAATTTAT
19094554 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19094579 CCCGGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.