Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 11 of 50
Found at i:5992455 original size:5 final size:5
Alignment explanation
Indices: 5992445--5992470 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5992435 TTTCTTTATG
5992445 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
5992471 GTACTATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:5993350 original size:213 final size:213
Alignment explanation
Indices: 5992955--5993356 Score: 608
Period size: 213 Copynumber: 1.9 Consensus size: 213
5992945 TCATTCATAA
* * *
5992955 TTATATATACATGAAATTAATGATATAACTTATATGTTATAATATTTTATATCAAAATTTGTATA
1 TTATATATACAT-AAATTAATGATACAAATTATATGTTAAAATATTTTATATCAAAATTTGTATA
* **
5993020 AATAATAACTAATTATAAACAATATGTTATAAAATCTAAGATGATGGCTAATAAACTTATTAAGT
65 AATAATAACTAATTATAAACAATATGTTATAAAATCTAACATGATAACTAATAAACTTATTAAGT
* * *
5993085 GTAATCATATAAATAAAATTTATTAGAAGTTATAGCAATGCTTATATATAAATTAAATATATGTA
130 GTAATCATATAAATAAAATCTATTAGAAATTATAGCAATACTTATATATAAATTAAATATATGTA
5993150 TATATAATATATTACTTTC
195 TATATAATATATTACTTTC
* * *
5993169 TTATATATATAT-AATTAATGATACAAATTATATGTTAAAATATTTTTTTATCAAAGTTTGTATA
1 TTATATATACATAAATTAATGATACAAATTATATGTTAAAATA-TTTTATATCAAAATTTGTATA
* *
5993233 AATAATAACTAATTATAAATAATATGTTATAAAATCTAACATGATAACTAATAAAGTTATTAAGT
65 AATAATAACTAATTATAAACAATATGTTATAAAATCTAACATGATAACTAATAAACTTATTAAGT
* * * * *
5993298 GTAATCATATAAATAAAGTCTATTATAAATTATAGTAATATTTATGTATAAATTAAATA
130 GTAATCATATAAATAAAATCTATTAGAAATTATAGCAATACTTATATATAAATTAAATA
5993357 NNNNNNNNNN
Statistics
Matches: 168, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
212 27 0.16
213 130 0.77
214 11 0.07
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (213 bp):
TTATATATACATAAATTAATGATACAAATTATATGTTAAAATATTTTATATCAAAATTTGTATAA
ATAATAACTAATTATAAACAATATGTTATAAAATCTAACATGATAACTAATAAACTTATTAAGTG
TAATCATATAAATAAAATCTATTAGAAATTATAGCAATACTTATATATAAATTAAATATATGTAT
ATATAATATATTACTTTC
Found at i:5993419 original size:2 final size:2
Alignment explanation
Indices: 5993412--5993463 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
5993402 NNNNNNNNNN
*
5993412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5993453 AT -T AT AT AT AT
1 AT AT AT AT AT AT
5993464 TCATAACAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5993478 original size:18 final size:20
Alignment explanation
Indices: 5993413--5993479 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 20
5993403 NNNNNNNNNA
*
5993413 TATATATATATATATATATAT
1 TATATATATATATATACA-AT
5993434 ATATATATATATATATACAAT
1 -TATATATATATATATACAAT
5993455 TATATATAT-TCATA-ACAAT
1 TATATATATAT-ATATACAAT
5993474 T-TATAT
1 TATATAT
5993480 TACGAGACAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 5 0.12
19 7 0.16
20 12 0.28
21 2 0.05
22 17 0.40
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATATATATATATACAAT
Found at i:5993738 original size:2 final size:2
Alignment explanation
Indices: 5993731--5993791 Score: 67
Period size: 2 Copynumber: 32.5 Consensus size: 2
5993721 ATTCTTCTTA
*
5993731 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5993771 -T A- AT GT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
5993792 AAAAATTAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5995780 original size:25 final size:24
Alignment explanation
Indices: 5995752--5995809 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
5995742 ATTAATCATT
*
5995752 ATAAAAACAATTATAACAAAATAAA
1 ATAAAAAAAATTA-AACAAAATAAA
* *
5995777 ATAATAAAAAATTAAATATAATAAA
1 ATAA-AAAAAATTAAACAAAATAAA
*
5995802 ATTAAAAA
1 ATAAAAAA
5995810 TATTTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 4 0.14
25 16 0.57
26 8 0.29
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (24 bp):
ATAAAAAAAATTAAACAAAATAAA
Found at i:5995792 original size:16 final size:16
Alignment explanation
Indices: 5995764--5995802 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
5995754 AAAAACAATT
5995764 ATAACAAAATAAA-ATA
1 ATAA-AAAATAAATATA
5995780 ATAAAAAATTAAATATA
1 ATAAAAAA-TAAATATA
5995797 ATAAAA
1 ATAAAA
5995803 TTAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 9 0.43
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAAAAATAAATATA
Found at i:5995803 original size:15 final size:14
Alignment explanation
Indices: 5995763--5995807 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
5995753 TAAAAACAAT
*
5995763 TATAACAAAATAAAA
1 TATAA-AAAATTAAA
5995778 TAATAAAAAATTAAA
1 T-ATAAAAAATTAAA
5995793 TATAATAAAATTAAA
1 TATAA-AAAATTAAA
5995808 AATATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
TATAAAAAATTAAA
Found at i:5995839 original size:26 final size:28
Alignment explanation
Indices: 5995787--5995841 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
5995777 ATAATAAAAA
5995787 ATTAAATATAATAAAATTAAAAATATTT
1 ATTAAATATAATAAAATTAAAAATATTT
* *
5995815 ATTAAA-ATAAT-TAATTAAAATTATTT
1 ATTAAATATAATAAAATTAAAAATATTT
5995841 A
1 A
5995842 AAAAAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.56
27 5 0.20
28 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTAAATATAATAAAATTAAAAATATTT
Found at i:6016347 original size:29 final size:28
Alignment explanation
Indices: 6016305--6016379 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 28
6016295 TTAAAATTTT
*
6016305 AAATAAATATTTATTTTT-TTATTAAATTC
1 AAATAAATTTTTATTTTTATT-TTAAA-TC
*
6016334 AATTAAATTTTTATACTTTTATTTTAAATC
1 AAATAAATTTTTAT--TTTTATTTTAAATC
6016364 AAATAAACTTTTTATT
1 AAATAAA-TTTTTATT
6016380 ATTAACAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 13 0.33
30 8 0.21
31 16 0.41
32 2 0.05
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (28 bp):
AAATAAATTTTTATTTTTATTTTAAATC
Found at i:6018178 original size:2 final size:2
Alignment explanation
Indices: 6018171--6018197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6018161 GAAGAAGAAA
6018171 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6018198 CAGAAAATCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6027476 original size:18 final size:18
Alignment explanation
Indices: 6027445--6027513 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
6027435 TTTTATGTAT
6027445 ATTAAT-AATGAAAATTAA
1 ATTAATAAAT-AAAATTAA
*
6027463 ATTAATAAATAAAAGTTAG
1 ATTAATAAATAAAA-TTAA
*
6027482 CTT-ATAAA-AAAA-TAA
1 ATTAATAAATAAAATTAA
6027497 ATTAA-AAATTAAAATTA
1 ATTAATAAA-TAAAATTA
6027514 TATTTAGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.17
16 1 0.02
17 8 0.20
18 17 0.41
19 8 0.20
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (18 bp):
ATTAATAAATAAAATTAA
Found at i:6037269 original size:14 final size:14
Alignment explanation
Indices: 6037250--6037276 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6037240 TTTTTGCTCT
6037250 ATAAATTGAGAAGC
1 ATAAATTGAGAAGC
6037264 ATAAATTGAGAAG
1 ATAAATTGAGAAG
6037277 GTCCTTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (14 bp):
ATAAATTGAGAAGC
Found at i:6045737 original size:24 final size:21
Alignment explanation
Indices: 6045708--6045754 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 21
6045698 AAAAACAATT
6045708 AATTTTTCAATAATATATAATTAA
1 AATTTTT--ATAATAT-TAATTAA
6045732 AA-TTTTATAATATTAATTAA
1 AATTTTTATAATATTAATTAA
6045752 AAT
1 AAT
6045755 ACTAATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
23 4 0.18
24 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTTATAATATTAATTAA
Found at i:6053602 original size:22 final size:22
Alignment explanation
Indices: 6053561--6053611 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
6053551 CTATGTCTAT
6053561 TATTATTACATAAAATTTTAAA
1 TATTATTACATAAAATTTTAAA
*
6053583 TATTAGTTACATAATA-TTTAAA
1 TATTA-TTACATAAAATTTTAAA
*
6053605 AATTATT
1 TATTATT
6053612 TACGATGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 9 0.35
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATTACATAAAATTTTAAA
Found at i:6054277 original size:15 final size:17
Alignment explanation
Indices: 6054247--6054279 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
6054237 TATTTTGTGT
6054247 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
6054264 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
6054279 T
1 T
6054280 TAATTACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:6059513 original size:2 final size:2
Alignment explanation
Indices: 6059506--6059539 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6059496 AAAGGAACAC
6059506 TA TA TA TA TA TA TA 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
6059540 GAATACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6062114 original size:23 final size:23
Alignment explanation
Indices: 6062068--6062115 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6062058 TTATATATAT
**
6062068 GTACAAATGATTTTAAATGTAAA
1 GTACAAATGATTTTAAATACAAA
6062091 GTACAAAT-ATTTTTAAATACAAA
1 GTACAAATGA-TTTTAAATACAAA
6062114 GT
1 GT
6062116 TTAAAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (23 bp):
GTACAAATGATTTTAAATACAAA
Found at i:6065929 original size:7 final size:7
Alignment explanation
Indices: 6065908--6065949 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
6065898 TATATATATA
6065908 AATAAAT
1 AATAAAT
6065915 AA-AAAT
1 AATAAAT
6065921 AATAAAT
1 AATAAAT
6065928 AATAAAT
1 AATAAAT
*
6065935 AACAAAT
1 AATAAAT
6065942 AATCAAAT
1 AAT-AAAT
6065950 TTTTAGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 6 0.19
7 21 0.68
8 4 0.13
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:6088152 original size:21 final size:21
Alignment explanation
Indices: 6088086--6088152 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
6088076 AGCAGCACCT
*
6088086 GCAGCAGCAACAAAAACAACA
1 GCAGCAGCAACAAAAGCAACA
* * *
6088107 TCAACAGCAACAAAAGCAAGA
1 GCAGCAGCAACAAAAGCAACA
*
6088128 GCAGCAGCAACAGAAGCAACA
1 GCAGCAGCAACAAAAGCAACA
6088149 GCAG
1 GCAG
6088153 AAGAAGAAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.52, C:0.27, G:0.19, T:0.01
Consensus pattern (21 bp):
GCAGCAGCAACAAAAGCAACA
Found at i:6099312 original size:15 final size:16
Alignment explanation
Indices: 6099292--6099326 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6099282 CTATTATGTG
*
6099292 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
6099307 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
6099323 AATT
1 AATT
6099327 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:6099504 original size:21 final size:22
Alignment explanation
Indices: 6099480--6099526 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
6099470 GCTTTATGTT
*
6099480 TTATATTTAGTTAAAA-AA-AAA
1 TTATATTGAG-TAAAAGAAGAAA
*
6099501 TTATCTTGAGTAAAAGAAGAAA
1 TTATATTGAGTAAAAGAAGAAA
6099523 TTAT
1 TTAT
6099527 TAATTCTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (22 bp):
TTATATTGAGTAAAAGAAGAAA
Found at i:6101268 original size:17 final size:18
Alignment explanation
Indices: 6101243--6101289 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
6101233 AAATAATTCA
*
6101243 TTAATTATTTTTT-ACTT
1 TTAAATATTTTTTAACTT
*
6101260 TTAAATATTTTTTAATTT
1 TTAAATATTTTTTAACTT
*
6101278 TTATATATTTTT
1 TTAAATATTTTT
6101290 AATCTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTAAATATTTTTTAACTT
Found at i:6101290 original size:17 final size:17
Alignment explanation
Indices: 6101243--6101292 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
6101233 AAATAATTCA
* * *
6101243 TTAATTATTTTTTACTT
1 TTAAATATTTTTAATTT
6101260 TTAAATATTTTTTAATTT
1 TTAAATA-TTTTTAATTT
*
6101278 TTATATATTTTTAAT
1 TTAAATATTTTTAAT
6101293 CTAATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTAAATATTTTTAATTT
Found at i:6105267 original size:20 final size:20
Alignment explanation
Indices: 6105223--6105267 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6105213 TATTCATTAC
6105223 TTAATATTTAATTATAAATA
1 TTAATATTTAATTATAAATA
* *
6105243 ATAATATTTAA-TATTAAATT
1 TTAATATTTAATTA-TAAATA
6105263 TTAAT
1 TTAAT
6105268 TATATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATATTTAATTATAAATA
Found at i:6109378 original size:16 final size:16
Alignment explanation
Indices: 6109357--6109401 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
6109347 ATTAATTTTT
6109357 TATAATATATTATATA
1 TATAATATATTATATA
* *
6109373 TATAATATATAATATT
1 TATAATATATTATATA
*
6109389 TTTATATATATTA
1 TATA-ATATATTA
6109402 AGAAGAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAATATATTATATA
Found at i:6109516 original size:22 final size:22
Alignment explanation
Indices: 6109491--6109532 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6109481 AATCATAGGA
*
6109491 ATTTAATTTTAATTAAATATTT
1 ATTTAAATTTAATTAAATATTT
* *
6109513 ATTTAAATTTATTTTAATAT
1 ATTTAAATTTAATTAAATAT
6109533 AAAATTACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAAATTTAATTAAATATTT
Found at i:6110107 original size:224 final size:220
Alignment explanation
Indices: 6109719--6110126 Score: 522
Period size: 224 Copynumber: 1.8 Consensus size: 220
6109709 AACATTATTA
* * * *
6109719 TAACTTATAATAAATTTTATTTCTATGATTACACTAAATAATTTTATTAATTATCACTTTAGTTT
1 TAACTTATAATAAACTTTATTTATATGATTACACTAAATAATTTTATTAATTATCACCTCAGTTT
*
6109784 TTGCAACATATTGTTTATAAATAGTTATTATTTATACAAATTTTGATATAAAACATTATAAAATA
66 TTGCAACATATTGTTTATAAATAGTTATTATTTATACAAATTTTAATATAAAACATTATAAAATA
*
6109849 TAAATTATATCATTAATTTTATATATACATAATAAAATAATACATATTATATATATATAAATACA
131 TAAATTATATCATTAA-TTTATATATA-ATAATAAAATAAT--ATATTATACATATATAAATACA
6109914 TATATTTAATTTATACATAAATTTCACTG
192 TATATTTAATTTATACATAAATTTCACTG
* * *
6109943 TAACTTATAATAAGCTTTATTTATATGATTACACTTAATAATTTTTTTAATTATCATCCTCA-TT
1 TAACTTATAATAAACTTTATTTATATGATTACACTAAATAATTTTATTAATTATCA-CCTCAGTT
* * * *
6110007 TTT-TAATATATTGTTTATAACTAGTTATTA-TTATATAAATTTTAATATAAAA-ATTAAAATAT
65 TTTGCAACATATTGTTTATAAATAGTTATTATTTATACAAATTTTAATATAAAACATT---ATA-
* * *
6110069 TTAACATATAAGTTATGTCATTAA-TTATATAT-ATAATAAAGTAATATATTATACATAT
126 --AA-ATATAAATTATATCATTAATTTATATATAATAATAAAATAATATATTATACATAT
6110127 CTATATTTAA
Statistics
Matches: 160, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
221 3 0.02
222 32 0.20
223 24 0.15
224 71 0.44
225 3 0.02
226 8 0.05
227 2 0.01
228 17 0.11
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (220 bp):
TAACTTATAATAAACTTTATTTATATGATTACACTAAATAATTTTATTAATTATCACCTCAGTTT
TTGCAACATATTGTTTATAAATAGTTATTATTTATACAAATTTTAATATAAAACATTATAAAATA
TAAATTATATCATTAATTTATATATAATAATAAAATAATATATTATACATATATAAATACATATA
TTTAATTTATACATAAATTTCACTG
Found at i:6110696 original size:96 final size:96
Alignment explanation
Indices: 6110532--6110724 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
6110522 ATTCTCAGCT
*
6110532 TCCATCAATCATAAAGGTTAGGCATGACGAAGACAGATAGGAAAAGCAAGGACATAACTGATATT
1 TCCATCAATCATAAAGGTGAGGCATGACGAAGACAGATAGGAAAAGCAAGGACATAACTGATATT
6110597 CACAGCATGAAGCTTTTCTGAAAGTCTGGAA
66 CACAGCATGAAGCTTTTCTGAAAGTCTGGAA
6110628 TCCATCAATCATAAAGGTGAGGCATGACGAAGACAGATAGGAAAAGCAAGGACATAACTGATATT
1 TCCATCAATCATAAAGGTGAGGCATGACGAAGACAGATAGGAAAAGCAAGGACATAACTGATATT
6110693 CACAGCATGAAGCTTTTCTGAAAGTCTGGAA
66 CACAGCATGAAGCTTTTCTGAAAGTCTGGAA
6110724 T
1 T
6110725 AACAGCTAAT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (96 bp):
TCCATCAATCATAAAGGTGAGGCATGACGAAGACAGATAGGAAAAGCAAGGACATAACTGATATT
CACAGCATGAAGCTTTTCTGAAAGTCTGGAA
Found at i:6113831 original size:58 final size:58
Alignment explanation
Indices: 6113762--6113880 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
6113752 TAGTTGTTCA
6113762 ATTTTGCTTCTCAAATAAAAGAAATTAAAGAATGAATTATATTTATATACCGTTATAC
1 ATTTTGCTTCTCAAATAAAAGAAATTAAAGAATGAATTATATTTATATACCGTTATAC
6113820 ATTTTGCTTCTCAAATAAAAGAAATTAAAGAATGAATTATATTTATATACCGTTATAC
1 ATTTTGCTTCTCAAATAAAAGAAATTAAAGAATGAATTATATTTATATACCGTTATAC
6113878 ATT
1 ATT
6113881 CTTTGCCATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (58 bp):
ATTTTGCTTCTCAAATAAAAGAAATTAAAGAATGAATTATATTTATATACCGTTATAC
Found at i:6130639 original size:2 final size:2
Alignment explanation
Indices: 6130632--6130664 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6130622 TTCCGAATTT
6130632 TA 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 T
6130665 TACTTTTCAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6133464 original size:45 final size:45
Alignment explanation
Indices: 6133413--6133550 Score: 258
Period size: 45 Copynumber: 3.1 Consensus size: 45
6133403 AAAAAAAAGA
*
6133413 TGTCCTAGCTTTGGAGCCATGCCAGGTGATAAAAGAGGAAGTCCT
1 TGTCCTAGCTTTGGAGCCATACCAGGTGATAAAAGAGGAAGTCCT
*
6133458 TGTCCTAGCTTTGGAGCCATACCAGGTGCTAAAAGAGGAAGTCCT
1 TGTCCTAGCTTTGGAGCCATACCAGGTGATAAAAGAGGAAGTCCT
6133503 TGTCCTAGCTTTGGAGCCATACCAGGTGATAAAAGAGGAAGTCCT
1 TGTCCTAGCTTTGGAGCCATACCAGGTGATAAAAGAGGAAGTCCT
6133548 TGT
1 TGT
6133551 ACCACTGGAT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 90 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (45 bp):
TGTCCTAGCTTTGGAGCCATACCAGGTGATAAAAGAGGAAGTCCT
Found at i:6134695 original size:17 final size:16
Alignment explanation
Indices: 6134667--6134699 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
6134657 CACATAATGG
6134667 TTAAATATATAAATAA
1 TTAAATATATAAATAA
6134683 TTAAATAATATAAATAA
1 TTAAAT-ATATAAATAA
6134700 AATGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TTAAATATATAAATAA
Found at i:6137243 original size:23 final size:23
Alignment explanation
Indices: 6137190--6137251 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
6137180 ATAATCTAGA
* *
6137190 ATTTAATTAAAATATTAATAATT
1 ATTTAATTTAAATATTAACAATT
* * *
6137213 A-ATCATTTAAATATTAACATTT
1 ATTTAATTTAAATATTAACAATT
6137235 ATTTAATTTAAATATTA
1 ATTTAATTTAAATATTA
6137252 TTATNNNNNN
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATTTAAATATTAACAATT
Found at i:6137550 original size:21 final size:22
Alignment explanation
Indices: 6137508--6137551 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
6137498 TTTATTAAAA
*
6137508 TATTAATAATTGATGATTTAAT
1 TATTAATAATTGATGATCTAAT
* *
6137530 TATTAAT-ATTGTTTATCTAAT
1 TATTAATAATTGATGATCTAAT
6137551 T
1 T
6137552 TAAATGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
TATTAATAATTGATGATCTAAT
Found at i:6137891 original size:17 final size:17
Alignment explanation
Indices: 6137869--6137905 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6137859 AAAAATTTTA
6137869 AAAAATAATTATTTCAT
1 AAAAATAATTATTTCAT
*
6137886 AAAAATAATTATTTCTT
1 AAAAATAATTATTTCAT
6137903 AAA
1 AAA
6137906 TTATTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAATAATTATTTCAT
Found at i:6146783 original size:13 final size:13
Alignment explanation
Indices: 6146765--6146789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6146755 GATAAATTTC
6146765 TTTTTATAAGTTT
1 TTTTTATAAGTTT
6146778 TTTTTATAAGTT
1 TTTTTATAAGTT
6146790 ATAATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTTTATAAGTTT
Found at i:6146809 original size:18 final size:20
Alignment explanation
Indices: 6146768--6146809 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
6146758 AAATTTCTTT
* *
6146768 TTATAAGTTTTTTTTATAAG
1 TTATAAGTTTTTATTATAAA
6146788 TTATAA-TTTTTATTA-AAA
1 TTATAAGTTTTTATTATAAA
6146806 TTAT
1 TTAT
6146810 CATAAAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATAAGTTTTTATTATAAA
Found at i:6148070 original size:2 final size:2
Alignment explanation
Indices: 6148058--6148127 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
6148048 TTCATATGAA
* *
6148058 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6148099 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6148128 GAGTGTAGCA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:6148392 original size:27 final size:27
Alignment explanation
Indices: 6148347--6148438 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
6148337 TTAAATTTTT
* * *
6148347 TATTTTTCTATAT-ATTTTTTCTTTTAA
1 TATTTTTCAAAATAATTTTTT-ATTTAA
6148374 TATTTTTCAAAATAATTTTTTATTTAA
1 TATTTTTCAAAATAATTTTTTATTTAA
**
6148401 TAATTAAT-ATAAATATATTTTTTATTTATTA
1 T-ATTTTTCA-AAATA-ATTTTTTATTTA--A
6148432 TATTTTT
1 TATTTTT
6148439 TTTCTCTTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
27 18 0.35
28 16 0.31
29 12 0.23
30 4 0.08
31 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTTTCAAAATAATTTTTTATTTAA
Found at i:6148463 original size:32 final size:32
Alignment explanation
Indices: 6148426--6148490 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
6148416 TATTTTTTAT
* * *
6148426 TTATTA-TATTTTTTTTCTCTTCTTTATTATTC
1 TTATTATTAGTTTATTTCT-TTCATTATTATTC
6148458 TTATTATTAGTTTATTTCTTTCATTATTATTC
1 TTATTATTAGTTTATTTCTTTCATTATTATTC
6148490 T
1 T
6148491 ATTCACTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.69
Consensus pattern (32 bp):
TTATTATTAGTTTATTTCTTTCATTATTATTC
Found at i:6151044 original size:19 final size:19
Alignment explanation
Indices: 6151022--6151058 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6151012 ATCATAAACT
6151022 TATGGATAAAGAATTACCA
1 TATGGATAAAGAATTACCA
6151041 TATGGATAAAGAATTACC
1 TATGGATAAAGAATTACC
6151059 TCAATGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
TATGGATAAAGAATTACCA
Found at i:6161744 original size:38 final size:40
Alignment explanation
Indices: 6161655--6161760 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 40
6161645 CACACTCAAC
* *
6161655 TCATATACATCCCCCCACATCGTGCACATAGCCGGCGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
* * * *
6161695 TCATGTTCATCCTCCCACATCGTGCACA-A-TCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
* *
6161733 TCGTGTACATCCCCCCACATCATGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
6161761 CGGGCACTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 30 0.54
39 1 0.02
40 25 0.45
ACGTcount: A:0.25, C:0.41, G:0.13, T:0.22
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
Found at i:6161889 original size:2 final size:2
Alignment explanation
Indices: 6161876--6161909 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6161866 ATCATGCACA
*
6161876 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6161910 CATCATAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6162315 original size:20 final size:20
Alignment explanation
Indices: 6162290--6162330 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6162280 TAGAGTCAAT
6162290 ACACAATCTCAA-CAATAAAC
1 ACACAAT-TCAATCAATAAAC
*
6162310 ACACAATTCAATCAGTAAAC
1 ACACAATTCAATCAATAAAC
6162330 A
1 A
6162331 TTATCAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.54, C:0.27, G:0.02, T:0.17
Consensus pattern (20 bp):
ACACAATTCAATCAATAAAC
Found at i:6167455 original size:21 final size:19
Alignment explanation
Indices: 6167429--6167476 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
6167419 AGAGAGATAG
*
6167429 AGAAAGAAAAGGTAGAAATAA
1 AGAAAGAAAAGGAAG-AA-AA
*
6167450 AGAAAGAAGAGGAAGAAAA
1 AGAAAGAAAAGGAAGAAAA
6167469 AGAAAGAA
1 AGAAAGAA
6167477 TTATTATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (19 bp):
AGAAAGAAAAGGAAGAAAA
Found at i:6168325 original size:22 final size:22
Alignment explanation
Indices: 6168276--6168342 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 22
6168266 GAAAAAAAAT
*
6168276 AAATTAATAATTTAAGTTAATTTA
1 AAATTAATAATTT-AGTT-ATATA
*
6168300 ATAATTTTATATATTTAGTTATATA
1 A-AA-TTAATA-ATTTAGTTATATA
6168325 AAATTAATAATTTAGTTA
1 AAATTAATAATTTAGTTA
6168343 CCAATGGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 9 0.24
23 5 0.14
24 3 0.08
25 7 0.19
26 9 0.24
27 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
AAATTAATAATTTAGTTATATA
Found at i:6168665 original size:28 final size:28
Alignment explanation
Indices: 6168633--6168686 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
6168623 AATTGAAACT
*
6168633 TTATTTATGTTTGATGTAATTTATTTAC
1 TTATTTATATTTGATGTAATTTATTTAC
*
6168661 TTATTTATATTTGGTGTAATTTATTT
1 TTATTTATATTTGATGTAATTTATTT
6168687 GTTTGTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (28 bp):
TTATTTATATTTGATGTAATTTATTTAC
Found at i:6172160 original size:17 final size:16
Alignment explanation
Indices: 6172117--6172160 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
6172107 TCATTTTATT
*
6172117 AATAAATAAATTTAAA
1 AATAAATAATTTTAAA
* *
6172133 AATTAAGAATTTTAAAA
1 AATAAATAATTTT-AAA
6172150 AATAAATAATT
1 AATAAATAATT
6172161 ATAATTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AATAAATAATTTTAAA
Found at i:6172729 original size:23 final size:23
Alignment explanation
Indices: 6172679--6172739 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
6172669 TTGACCTTTT
* *
6172679 CTTCTCCTTCTTGCCTTCTTCAC
1 CTTCTTCTTCTTGCCTTCGTCAC
* * *
6172702 TTTCTTCTTCTTGTCTTCGTCTC
1 CTTCTTCTTCTTGCCTTCGTCAC
6172725 CTTCTTGCTTCTTGC
1 CTTCTT-CTTCTTGC
6172740 TTTTTTCTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.02, C:0.36, G:0.08, T:0.54
Consensus pattern (23 bp):
CTTCTTCTTCTTGCCTTCGTCAC
Found at i:6173153 original size:20 final size:20
Alignment explanation
Indices: 6173128--6173178 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
6173118 GTTATTTATT
*
6173128 TATCGATAGATAGTATAATA
1 TATCGATAGATAATATAATA
* *
6173148 TATCGATAGATAATATGATC
1 TATCGATAGATAATATAATA
6173168 TATCGATAGAT
1 TATCGATAGAT
6173179 TTGTCTTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATAGATAATATAATA
Found at i:6183570 original size:2 final size:2
Alignment explanation
Indices: 6183563--6183590 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6183553 ACCAAGGAAG
6183563 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6183591 AAATCCTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6185504 original size:3 final size:3
Alignment explanation
Indices: 6185493--6185528 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
6185483 ACAATTTTTT
*
6185493 TTA TCA TTA TTA TTA TTA TTA TTA TTA TATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT
6185529 TTGGCCTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:6186592 original size:2 final size:2
Alignment explanation
Indices: 6186579--6186608 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6186569 TGAGTGTTCA
*
6186579 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6186609 TTTGAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6187025 original size:13 final size:13
Alignment explanation
Indices: 6186986--6187027 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
6186976 ATTAGGAGAA
*
6186986 ATATTTGTATTTG
1 ATATTTATATTTG
* *
6186999 ATTTTTCT-TTTG
1 ATATTTATATTTG
6187011 ATATTTATATTTG
1 ATATTTATATTTG
6187024 ATAT
1 ATAT
6187028 ATTGTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:6188169 original size:15 final size:16
Alignment explanation
Indices: 6188151--6188181 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6188141 TTTTTTAACA
6188151 TAAATTATT-AATATT
1 TAAATTATTCAATATT
6188166 TAAATTATTCAATATT
1 TAAATTATTCAATATT
6188182 ATTAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTATTCAATATT
Found at i:6188651 original size:27 final size:25
Alignment explanation
Indices: 6188609--6188658 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
6188599 ACAAAAAATA
6188609 ATAATTTTTTTATAAAATATTTTAT
1 ATAATTTTTTTATAAAATATTTTAT
*
6188634 ATAATTTTTTTTAATAAATTATTTT
1 ATAA-TTTTTTT-ATAAAATATTTT
6188659 TCAGTTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 7 0.32
27 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATAATTTTTTTATAAAATATTTTAT
Found at i:6190067 original size:10 final size:10
Alignment explanation
Indices: 6190054--6190147 Score: 54
Period size: 10 Copynumber: 9.2 Consensus size: 10
6190044 AAAAAAAAAG
6190054 AGAAAAGGAA
1 AGAAAAGGAA
*
6190064 AGAAACTGGGAGA
1 AGAAA--AGGA-A
*
6190077 GAGAAAGGGAA
1 -AGAAAAGGAA
6190088 AGAAAAGGAA
1 AGAAAAGGAA
6190098 A-AGAAAGTGAA
1 AGA-AAAG-GAA
*
6190109 AGAAAAGGGGA
1 AGAAAA-GGAA
6190120 AG-AAAGGAA
1 AGAAAAGGAA
6190129 A-AAAA-GAA
1 AGAAAAGGAA
*
6190137 A-AAAAGAAA
1 AGAAAAGGAA
6190146 AG
1 AG
6190148 GGTGAGGAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
8 8 0.12
9 11 0.16
10 22 0.32
11 12 0.18
12 9 0.13
13 1 0.01
14 5 0.07
ACGTcount: A:0.65, C:0.01, G:0.32, T:0.02
Consensus pattern (10 bp):
AGAAAAGGAA
Found at i:6190104 original size:21 final size:21
Alignment explanation
Indices: 6190078--6190142 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
6190068 ACTGGGAGAG
6190078 AGAAAGGGAAAGAAAAGGAAA
1 AGAAAGGGAAAGAAAAGGAAA
* **
6190099 AGAAAGTGAAAGAAAAGGGGA
1 AGAAAGGGAAAGAAAAGGAAA
6190120 AGAAA-GGAAA-AAAA-GAAA
1 AGAAAGGGAAAGAAAAGGAAA
6190138 A-AAAG
1 AGAAAG
6190143 AAAAGGGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 3 0.08
18 3 0.08
19 4 0.11
20 4 0.11
21 23 0.62
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (21 bp):
AGAAAGGGAAAGAAAAGGAAA
Found at i:6190143 original size:42 final size:44
Alignment explanation
Indices: 6190037--6190145 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 44
6190027 AGAAATTGAG
* * *
6190037 GAAAGGAAAAAAA-AAAGAGA-AAAGGAAAGAAACTGGGAGAGA
1 GAAAGGAAAAAAAGAAAAAAAGAAAGGAAAGAAACAGGGAGAGA
*
6190079 GAAAGGGAAAGAAAAG--GAAAAGAAAGTGAAAGAAA-AGGG-GA-A
1 GAAA-GGAAA-AAAAGAAAAAAAGAAAG-GAAAGAAACAGGGAGAGA
6190121 GAAAGGAAAAAAAGAAAAAAAGAAA
1 GAAAGGAAAAAAAGAAAAAAAGAAA
6190146 AGGGTGAGGA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
40 5 0.09
41 5 0.09
42 17 0.31
43 9 0.16
44 11 0.20
45 8 0.15
ACGTcount: A:0.67, C:0.01, G:0.30, T:0.02
Consensus pattern (44 bp):
GAAAGGAAAAAAAGAAAAAAAGAAAGGAAAGAAACAGGGAGAGA
Found at i:6207821 original size:21 final size:21
Alignment explanation
Indices: 6207797--6207836 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6207787 AAAAGTGAAC
*
6207797 ATATTACATCACTATGTCATA
1 ATATTACATCAATATGTCATA
*
6207818 ATATTATATCAATATGTCA
1 ATATTACATCAATATGTCA
6207837 CGTCATCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
ATATTACATCAATATGTCATA
Found at i:6208806 original size:22 final size:19
Alignment explanation
Indices: 6208758--6208799 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
6208748 ATTTTTTGTA
6208758 AAATTGTAGTGATAATAAG
1 AAATTGTAGTGATAATAAG
*
6208777 AAATTGTATTGATAATAAG
1 AAATTGTAGTGATAATAAG
6208796 AAAT
1 AAAT
6208800 GAGTGTAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (19 bp):
AAATTGTAGTGATAATAAG
Found at i:6210457 original size:2 final size:2
Alignment explanation
Indices: 6210452--6210481 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6210442 TGTGTATGTT
6210452 TA TA TA TA TA 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
6210482 AAGAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6211733 original size:3 final size:3
Alignment explanation
Indices: 6211725--6211754 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6211715 CTAGCTACAG
*
6211725 CAC CAC CAC AAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
6211755 TACAGACGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:6218121 original size:17 final size:17
Alignment explanation
Indices: 6218080--6218121 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
6218070 TATGTAAATT
*
6218080 TATTATTTTTTAATATA
1 TATTATTTTTTAACATA
*
6218097 TATCATTTTTTAACA-A
1 TATTATTTTTTAACATA
6218113 TGATTATTT
1 T-ATTATTT
6218122 GACTTAACGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTTTTTAACATA
Found at i:6219297 original size:2 final size:2
Alignment explanation
Indices: 6219290--6219316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6219280 NNNNNNNNNN
6219290 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 T
6219317 TATTTTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6222301 original size:35 final size:34
Alignment explanation
Indices: 6222261--6222506 Score: 235
Period size: 35 Copynumber: 7.1 Consensus size: 34
6222251 GCAGAGGAAT
* *
6222261 AGTGAAATCTGGGTTTGTTTGCCGCCGGTAGAAGG
1 AGTGAAATCTGGG-TGGTTTGCCGCCGGTAGGAGG
* *
6222296 AGTGAAATTTGGGGTTGTTTGCCGCCGGTTAGGAGG
1 AGTGAAATCT-GGGTGGTTTGCCGCCGG-TAGGAGG
* * * * *
6222332 AGTCACAGCTTGGAGGTTTGCCGCCGGTAGGAGG
1 AGTGAAATCTGGGTGGTTTGCCGCCGGTAGGAGG
* * *
6222366 AGTGAAATCTGGAG-CGTTTGCTGCCGGCAGGAGG
1 AGTGAAATCTGG-GTGGTTTGCCGCCGGTAGGAGG
*
6222400 AGTGAAATCTGGGTTGGTTTGTCGCCCGGTAGGAGG
1 AGTGAAATCTGGG-TGGTTTGCCG-CCGGTAGGAGG
* * * * * *
6222436 AG-CAACAGCTTGGAGGTTGGTCGCCGGTAGGAGG
1 AGTGAA-ATCTGGGTGGTTTGCCGCCGGTAGGAGG
6222470 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGG
1 AGTGAAATCTGGG-TGGTTTGCCGCCGGTAGGAGG
6222505 AG
1 AG
6222507 CAACAGCTTG
Statistics
Matches: 171, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
33 1 0.01
34 62 0.36
35 76 0.44
36 32 0.19
ACGTcount: A:0.19, C:0.15, G:0.41, T:0.24
Consensus pattern (34 bp):
AGTGAAATCTGGGTGGTTTGCCGCCGGTAGGAGG
Found at i:6222368 original size:34 final size:34
Alignment explanation
Indices: 6222277--6222600 Score: 244
Period size: 34 Copynumber: 9.4 Consensus size: 34
6222267 ATCTGGGTTT
* ** *
6222277 GTTTGCCGCCGGTAGAAGGAGTGA-AATTTGGGG
1 GTTTGCCGCCGGTAGGAGGAGTGACAGCTTGGAG
*
6222310 TTGTTTGCCGCCGGTTAGGAGGAGTCACAGCTTGGAG
1 --GTTTGCCGCCGG-TAGGAGGAGTGACAGCTTGGAG
* *
6222347 GTTTGCCGCCGGTAGGAGGAGTGAAATC-TGGAG
1 GTTTGCCGCCGGTAGGAGGAGTGACAGCTTGGAG
* * * * * *
6222380 CGTTTGCTGCCGGCAGGAGGAGTGAAATCTGGGTTG
1 -GTTTGCCGCCGGTAGGAGGAGTGACAGCTTGG-AG
* **
6222416 GTTTGTCGCCCGGTAGGAGGAGCAACAGCTTGGAG
1 GTTTGCCG-CCGGTAGGAGGAGTGACAGCTTGGAG
* * * * * *
6222451 GTTGGTCGCCGGTAGGAGGAGTGAAATCTGGGTTG
1 GTTTGCCGCCGGTAGGAGGAGTGACAGCTTGG-AG
**
6222486 GTTTGCCGCCGGTAGGAGGAGCAACAGCTTGGAG
1 GTTTGCCGCCGGTAGGAGGAGTGACAGCTTGGAG
* * *
6222520 GTTTGCTGCCGG-AGAGAGGAGTAACAGCTTGGGG
1 GTTTGCCGCCGGTAG-GAGGAGTGACAGCTTGGAG
* * *
6222554 GTTTGCCGTCGGT-GAGAGGAGTAATAGC-TGGAG
1 GTTTGCCGCCGGTAG-GAGGAGTGACAGCTTGGAG
*
6222587 TGTTAGCCGCCGGT
1 -GTTTGCCGCCGGT
6222601 GGGGGATGAT
Statistics
Matches: 234, Mismatches: 45, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
33 11 0.05
34 122 0.52
35 66 0.28
36 29 0.12
37 6 0.03
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (34 bp):
GTTTGCCGCCGGTAGGAGGAGTGACAGCTTGGAG
Found at i:6222429 original size:70 final size:69
Alignment explanation
Indices: 6222261--6222541 Score: 288
Period size: 70 Copynumber: 4.0 Consensus size: 69
6222251 GCAGAGGAAT
* * * * * *
6222261 AGTGAAATCTGGGTTTGTTTGCCGCCGGTAGAAGGAGTGAA-A-TTTGGGGTTGTTTGCCGCCGG
1 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAG-CAACAGCTTGGAG--GTTTGCTGCCGG
6222324 TTAGGAGG
63 -TAGGAGG
* * * * * * * *
6222332 AGTCACAGCTTGG-AGGTTTGCCGCCGGTAGGAGGAGTGAA-ATC-TGGAGCGTTTGCTGCCGGC
1 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAG-CAACAGCTTGGAG-GTTTGCTGCCGGT
6222394 AGGAGG
64 AGGAGG
* *
6222400 AGTGAAATCTGGGTTGGTTTGTCGCCCGGTAGGAGGAGCAACAGCTTGGAGG-TTGGTCGCCGGT
1 AGTGAAATCTGGGTTGGTTTGCCG-CCGGTAGGAGGAGCAACAGCTTGGAGGTTTGCT-GCCGGT
6222464 AGGAGG
64 AGGAGG
6222470 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAGCAACAGCTTGGAGGTTTGCTGCCGG-AG
1 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAGCAACAGCTTGGAGGTTTGCTGCCGGTAG
6222534 AGAGG
66 -GAGG
6222539 AGT
1 AGT
6222542 AACAGCTTGG
Statistics
Matches: 178, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
68 17 0.10
69 64 0.36
70 83 0.47
71 14 0.08
ACGTcount: A:0.19, C:0.16, G:0.41, T:0.24
Consensus pattern (69 bp):
AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAGCAACAGCTTGGAGGTTTGCTGCCGGTAG
GAGG
Found at i:6222523 original size:104 final size:101
Alignment explanation
Indices: 6222261--6222575 Score: 309
Period size: 104 Copynumber: 3.0 Consensus size: 101
6222251 GCAGAGGAAT
* * * *
6222261 AGTGAAATCTGGGTTTGTTTGCCGCCGGTAGAAGGAGTGAAATTTGGGGTTGTTTGCCGCCGGTT
1 AGTGAAATCTGGGTTCGTTTGCCGCCGGTAGGAGGAGTGAAACTTGGAG--GTTTG-CGCCGG-T
*
6222326 AGGAGGAGTC-ACAGCTTGGAGGTTTGCCGCCGGTAGGAGG
62 AGGAGGAG-CAACAGCTTGGAGGTTGGCCGCCGGTAGGAGG
* * * *
6222366 AGTGAAATCTGGAG--CGTTTGCTGCCGGCAGGAGGAGTGAAATCTGGGTTGGTTTGTCGCCCGG
1 AGTGAAATCTGG-GTTCGTTTGCCGCCGGTAGGAGGAGTGAAA-CTTGG-AGGTTTG-CG-CCGG
*
6222429 TAGGAGGAGCAACAGCTTGGAGGTTGGTCGCCGGTAGGAGG
61 TAGGAGGAGCAACAGCTTGGAGGTTGGCCGCCGGTAGGAGG
* *
6222470 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAG-CAACAGCTTGGAGGTTTGCTGCCGG-A
1 AGTGAAATCTGGGTTCGTTTGCCGCCGGTAGGAGGAGTGAA-A-CTTGGAGGTTTGC-GCCGGTA
* * * *
6222533 GAGAGGAGTAACAGCTTGGGGGTTTGCCGTCGGT-GAGAGG
63 G-GAGGAGCAACAGCTTGGAGGTTGGCCGCCGGTAG-GAGG
6222573 AGT
1 AGT
6222576 AATAGCTGGA
Statistics
Matches: 177, Mismatches: 22, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
102 3 0.02
103 41 0.23
104 88 0.50
105 43 0.24
106 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.24
Consensus pattern (101 bp):
AGTGAAATCTGGGTTCGTTTGCCGCCGGTAGGAGGAGTGAAACTTGGAGGTTTGCGCCGGTAGGA
GGAGCAACAGCTTGGAGGTTGGCCGCCGGTAGGAGG
Found at i:6240615 original size:2 final size:2
Alignment explanation
Indices: 6240608--6240636 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6240598 TTGTTTTTAT
6240608 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 T
6240637 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6243097 original size:11 final size:11
Alignment explanation
Indices: 6243081--6243106 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6243071 TGCAGACTTC
6243081 AAGAGCAAAAG
1 AAGAGCAAAAG
6243092 AAGAGCAAAAG
1 AAGAGCAAAAG
6243103 AAGA
1 AAGA
6243107 AAAAAAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAGCAAAAG
Found at i:6251872 original size:14 final size:14
Alignment explanation
Indices: 6251855--6251885 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6251845 TTTTTACATT
6251855 GAAGTCTTCACTCA
1 GAAGTCTTCACTCA
6251869 GAAGTCTTCACTCA
1 GAAGTCTTCACTCA
6251883 GAA
1 GAA
6251886 ATATGGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (14 bp):
GAAGTCTTCACTCA
Found at i:6287105 original size:203 final size:203
Alignment explanation
Indices: 6286768--6287155 Score: 643
Period size: 203 Copynumber: 1.9 Consensus size: 203
6286758 ATTTTTTATT
* *
6286768 AAAATAAAAAAAAATCCTTCAAATGTCAAAAACAACTTATTTTTGACATAAAATGTAAAAAAAAT
1 AAAACAAAAAAAAACCCTTCAAATGTCAAAAACAACTTATTTTTGACATAAAATGTAAAAAAAAT
* *
6286833 TAATTCAATAGAAAACGAAAGGTCAAAAAAATAAAAAAGTGTTCTAATTGAATGACACTTATCAT
66 TAATTCAATAGAAAACGAAAGGTCAAAAAAATAAAAAAGAGTTCTAATTGAATAACACTTATCAT
*
6286898 TCAATCGAAAACTCAATTGAAAAAAATTGAAATATCCTACTTTTATATATATTATTATATAAATA
131 TCAATCGAAAACTCAATTGAAAAAAATTGAAACATCCTACTTTTATATATATTATTATATAAATA
6286963 AAAGTAAA
196 AAAGTAAA
*
6286971 AAAACAAAAAAAAACCCTTCAAATGAT-AAAAACAACTTATTTTTGACATAAGATGTAAAAAAAA
1 AAAACAAAAAAAAACCCTTCAAATG-TCAAAAACAACTTATTTTTGACATAAAATGTAAAAAAAA
* * * *
6287035 TTAATTCAATAGAAAACGAATGGTTAAAAAAATAAAAAAGAGTTCTAATTGAATAACACTTGTTA
65 TTAATTCAATAGAAAACGAAAGGTCAAAAAAATAAAAAAGAGTTCTAATTGAATAACACTTATCA
* * *
6287100 TTCAATTGAAGACTCAATTGAAAAAAATTGAAACATCTTACTTTTATATATATTAT
130 TTCAATCGAAAACTCAATTGAAAAAAATTGAAACATCCTACTTTTATATATATTAT
6287156 AGATGTTATC
Statistics
Matches: 171, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
203 170 0.99
204 1 0.01
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29
Consensus pattern (203 bp):
AAAACAAAAAAAAACCCTTCAAATGTCAAAAACAACTTATTTTTGACATAAAATGTAAAAAAAAT
TAATTCAATAGAAAACGAAAGGTCAAAAAAATAAAAAAGAGTTCTAATTGAATAACACTTATCAT
TCAATCGAAAACTCAATTGAAAAAAATTGAAACATCCTACTTTTATATATATTATTATATAAATA
AAAGTAAA
Found at i:6287445 original size:20 final size:21
Alignment explanation
Indices: 6287420--6287458 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
6287410 TATAAGAGAT
6287420 TAAATAACTGA-AAAATAAAA
1 TAAATAACTGAGAAAATAAAA
6287440 TAAATAACTGAGAAAATAA
1 TAAATAACTGAGAAAATAA
6287459 GTTTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (21 bp):
TAAATAACTGAGAAAATAAAA
Found at i:6289586 original size:22 final size:22
Alignment explanation
Indices: 6289561--6289607 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
6289551 AAGTCCTGTA
*
6289561 TGAAATGAGATAATGGAGTAGT
1 TGAAATGAGAGAATGGAGTAGT
6289583 TGAAATGAGAGAATGGAGTAGT
1 TGAAATGAGAGAATGGAGTAGT
6289605 TGA
1 TGA
6289608 GCTGCTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (22 bp):
TGAAATGAGAGAATGGAGTAGT
Found at i:6293006 original size:191 final size:190
Alignment explanation
Indices: 6292677--6293054 Score: 625
Period size: 191 Copynumber: 2.0 Consensus size: 190
6292667 TAATTTATAA
6292677 CTTTTAATACTTAGAAGATAAATTCATTTAATATTTATCAATTAAAATTTAATATTATTTTTCAT
1 CTTTTAATACTTAGAAGATAAATTCATTTAATATTTATCAATTAAAATTTAATATTATTTTTCAT
* *
6292742 CTATATTCTCTTATTCTGCATGAACTTGAATCTATAGTATTTAGACATCTATTTTATACATGAAT
66 CTATATTCTCTTATTCTGCATCAACTTGAATCTATAGTATGTAGACATCTATTTTATACATGAAT
6292807 GATTAAATT-TCAATAAATAGTCATCCAATGCATTAAACAAAATAAAAAAATAAAAAAATC
131 GATTAAATTCT-AATAAATAGTCATCCAATGCATTAAACAAAATAAAAAAATAAAAAAATC
* *
6292867 CNTTTTAATGA-TTAGAAGATAGATTCATTTAATATTTATCAATTACAATTTAATATTATTTTTC
1 C-TTTTAAT-ACTTAGAAGATAAATTCATTTAATATTTATCAATTAAAATTTAATATTATTTTTC
* * *
6292931 ATCTATATTCTCTTATTCTGCATCAACTTGAATTTATAGTATGTAGACATCTTTTTTGTACATGA
64 ATCTATATTCTCTTATTCTGCATCAACTTGAATCTATAGTATGTAGACATCTATTTTATACATGA
* * *
6292996 ATGTTTAAATTCTAATAAATATTCATCCAATTCATTAAACAAAATAAAAAAATAAAAAA
129 ATGATTAAATTCTAATAAATAGTCATCCAATGCATTAAACAAAATAAAAAAATAAAAAA
6293055 GGTCTACTCA
Statistics
Matches: 175, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
190 1 0.01
191 172 0.98
192 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (190 bp):
CTTTTAATACTTAGAAGATAAATTCATTTAATATTTATCAATTAAAATTTAATATTATTTTTCAT
CTATATTCTCTTATTCTGCATCAACTTGAATCTATAGTATGTAGACATCTATTTTATACATGAAT
GATTAAATTCTAATAAATAGTCATCCAATGCATTAAACAAAATAAAAAAATAAAAAAATC
Found at i:6294479 original size:25 final size:25
Alignment explanation
Indices: 6294451--6294500 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
6294441 AAAAATGATA
*
6294451 AATTAGTTATAAAAATTTATTTAAT
1 AATTAATTATAAAAATTTATTTAAT
6294476 AATTAATTATAAAAATTTATTTAAT
1 AATTAATTATAAAAATTTATTTAAT
6294501 TTCGTCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTAATTATAAAAATTTATTTAAT
Found at i:6325958 original size:34 final size:34
Alignment explanation
Indices: 6325915--6325982 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
6325905 ATTGTGAAAG
*
6325915 TATTTTTAATAAATCACGTTGAAATTTGAATGCT
1 TATTTTTAATAAATCACGGTGAAATTTGAATGCT
6325949 TATTTTTAATAAATCACGGTGAAATTTGAATGCT
1 TATTTTTAATAAATCACGGTGAAATTTGAATGCT
6325983 GCATAGTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (34 bp):
TATTTTTAATAAATCACGGTGAAATTTGAATGCT
Found at i:6327007 original size:43 final size:44
Alignment explanation
Indices: 6326960--6327048 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
6326950 TAAGTGGTTT
6326960 TTAATATTGAATTG-TTTTTTTTTTATAATTAGAAGAATGGGGA
1 TTAATATTGAATTGTTTTTTTTTTTATAATTAGAAGAATGGGGA
6327003 TTAATATTGAATTGTTTTTTTTTTTATAATTAGAAGAATGGGGA
1 TTAATATTGAATTGTTTTTTTTTTTATAATTAGAAGAATGGGGA
6327047 TT
1 TT
6327049 CGAACTCTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 14 0.31
44 31 0.69
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (44 bp):
TTAATATTGAATTGTTTTTTTTTTTATAATTAGAAGAATGGGGA
Found at i:6328847 original size:131 final size:130
Alignment explanation
Indices: 6328612--6328873 Score: 515
Period size: 131 Copynumber: 2.0 Consensus size: 130
6328602 AAATTATATA
6328612 TATATATATAGAATACGGATTAGTTATTTTATTAAAAAATACTACTGATTAAAAATTGAAGTGTC
1 TATATATATAGAATACGGATTAGTTATTTTATTAAAAAATACTACTGATTAAAAATTGAAGTGTC
6328677 CATTTCAGAGATGATTGTATAATTGCTAATACTGTTACCTTAATCACCGGAACCTATTTGTCTTG
66 CATTTCAGAGATGATTGTATAATTGCTAATACTGTTACCTTAATCACCGGAACCTATTTGTCTTG
6328742 TNATATATATAGAATACGGATTAGTTATTTTATTAAAAAATACTACTGATTAAAAATTGAAGTGT
1 T-ATATATATAGAATACGGATTAGTTATTTTATTAAAAAATACTACTGATTAAAAATTGAAGTGT
6328807 CCATTTCAGAGATGATTGTATAATTGCTAATACTGTTACCTTAATCACCGGAACCTATTTGTCTT
65 CCATTTCAGAGATGATTGTATAATTGCTAATACTGTTACCTTAATCACCGGAACCTATTTGTCTT
6328872 G
130 G
6328873 T
1 T
6328874 CCTCTCTCTC
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
130 1 0.01
131 130 0.99
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (130 bp):
TATATATATAGAATACGGATTAGTTATTTTATTAAAAAATACTACTGATTAAAAATTGAAGTGTC
CATTTCAGAGATGATTGTATAATTGCTAATACTGTTACCTTAATCACCGGAACCTATTTGTCTTG
Found at i:6329807 original size:2 final size:2
Alignment explanation
Indices: 6329800--6329843 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
6329790 TTCCACCTAC
6329800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6329842 AT
1 AT
6329844 GCATGTTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6337904 original size:18 final size:18
Alignment explanation
Indices: 6337877--6337944 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
6337867 GGGTTTCACT
*
6337877 TCTTCTTCTTCTTCTTCA
1 TCTTCATCTTCTTCTTCA
*
6337895 TCTTCATCTTCATCTTCA
1 TCTTCATCTTCTTCTTCA
* *
6337913 TCTTCATCTTCCTCTTCC
1 TCTTCATCTTCTTCTTCA
* *
6337931 TCTCCCTCTTCTTC
1 TCTTCATCTTCTTC
6337945 ATCACTCTCG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTCATCTTCTTCTTCA
Found at i:6337933 original size:6 final size:6
Alignment explanation
Indices: 6337877--6337929 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
6337867 GGGTTTCACT
* * *
6337877 TCTTCT TCTTCT TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA
6337925 TCTTC
1 TCTTC
6337930 CTCTCCCTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (6 bp):
TCTTCA
Found at i:6337938 original size:12 final size:12
Alignment explanation
Indices: 6337889--6337941 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
6337879 TTCTTCTTCT
* *
6337889 TCTTCATCTTCA
1 TCTTCATCTCCC
* *
6337901 TCTTCATCTTCA
1 TCTTCATCTCCC
*
6337913 TCTTCATCTTCC
1 TCTTCATCTCCC
*
6337925 TCTTCCTCTCCC
1 TCTTCATCTCCC
6337937 TCTTC
1 TCTTC
6337942 TTCATCACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.09, C:0.42, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTTCATCTCCC
Found at i:6349916 original size:2 final size:2
Alignment explanation
Indices: 6349909--6349941 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6349899 TATGGATAGA
6349909 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6349942 TTACATGAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6351030 original size:30 final size:29
Alignment explanation
Indices: 6350996--6351057 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
6350986 TATTTTTAAC
6350996 AAATTTTATAATTTTA-CTTCTCCAAATATT
1 AAATTTTATAATTTTATCTT-TCCAAAT-TT
* * *
6351026 AAATTTTTTATTTTTATCTTTTCAAATTT
1 AAATTTTATAATTTTATCTTTCCAAATTT
6351055 AAA
1 AAA
6351058 ATCCTAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.18
30 20 0.71
31 3 0.11
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (29 bp):
AAATTTTATAATTTTATCTTTCCAAATTT
Found at i:6356930 original size:22 final size:22
Alignment explanation
Indices: 6356888--6356930 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
6356878 GTGGAGAATT
* *
6356888 TCAAGAGAAAAAGTGTGAAAAA
1 TCAAGAAAAAAAGTGTAAAAAA
6356910 TCAAGAAAAACAAGTG-AAAAA
1 TCAAGAAAAA-AAGTGTAAAAA
6356931 TGTAGGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.63, C:0.07, G:0.19, T:0.12
Consensus pattern (22 bp):
TCAAGAAAAAAAGTGTAAAAAA
Found at i:6366620 original size:43 final size:44
Alignment explanation
Indices: 6366554--6366639 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 44
6366544 AAATGTTAGA
*
6366554 CAAACAAAATGAAAGAGCTTTAATAATCAT-ATGCTTCTCTATC
1 CAAACAAAATGAAAGAGCGTTAATAATCATAATGCTTCTCTATC
*
6366597 CAAACAAAGTGAAAGAGCGTTAATAATCATAATGCTTCTCTAT
1 CAAACAAAATGAAAGAGCGTTAATAATCATAATGCTTCTCTAT
6366640 ATAGTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 28 0.70
44 12 0.30
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (44 bp):
CAAACAAAATGAAAGAGCGTTAATAATCATAATGCTTCTCTATC
Found at i:6371445 original size:65 final size:65
Alignment explanation
Indices: 6371365--6371496 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
6371355 TAATATGAGA
6371365 TATTTAACCTTCAACTTGTGAAATGTGAAATGTTTTTACAAGACAAATCAGTAAAACTAGTGAAC
1 TATTTAACCTTCAACTTGTGAAATGTGAAATGTTTTTACAAGACAAATCAGTAAAACTAGTGAAC
6371430 TATTTAACCTTCAACTTGTGAAATGTGAAATGTTTTTACAAGACAAATCAGTAAAACTAGTGAAC
1 TATTTAACCTTCAACTTGTGAAATGTGAAATGTTTTTACAAGACAAATCAGTAAAACTAGTGAAC
6371495 TA
1 TA
6371497 AAACGGGCAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (65 bp):
TATTTAACCTTCAACTTGTGAAATGTGAAATGTTTTTACAAGACAAATCAGTAAAACTAGTGAAC
Found at i:6372163 original size:2 final size:2
Alignment explanation
Indices: 6372156--6372193 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
6372146 GGGATCAAAT
6372156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6372194 TGGGCATTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6373462 original size:27 final size:29
Alignment explanation
Indices: 6373392--6373462 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 29
6373382 AACATACAAA
6373392 CATGTTATATCACAATTCATTATAACATAT
1 CATG-TATATCACAATTCATTATAACATAT
* * *
6373422 TATGTA-A-AATAATTCATTATAACATAT
1 CATGTATATCACAATTCATTATAACATAT
6373449 CA-GTATATCA-AATT
1 CATGTATATCACAATT
6373463 AATATTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
26 3 0.09
27 24 0.71
28 2 0.06
29 2 0.06
30 3 0.09
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (29 bp):
CATGTATATCACAATTCATTATAACATAT
Found at i:6377876 original size:2 final size:2
Alignment explanation
Indices: 6377869--6377899 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6377859 GTATGACCAC
6377869 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 A
6377900 AATTTCATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6383679 original size:18 final size:19
Alignment explanation
Indices: 6383652--6383691 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6383642 TTCAATTTGC
* *
6383652 AAAAAGAAAAAGCAACA-A
1 AAAAAAAAAAAGAAACAGA
6383670 AAAAAAAAAAAGAAACAGA
1 AAAAAAAAAAAGAAACAGA
6383689 AAA
1 AAA
6383692 TTATAGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAGAAACAGA
Found at i:6384352 original size:6 final size:6
Alignment explanation
Indices: 6384341--6384373 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
6384331 GCCATGGAAA
6384341 TTATGT TTATGT TTATGT TTATGT TTATTGT TT
1 TTATGT TTATGT TTATGT TTATGT TTA-TGT TT
6384374 TTTTTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (6 bp):
TTATGT
Found at i:6393817 original size:22 final size:21
Alignment explanation
Indices: 6393788--6393828 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6393778 GGACAAGTGT
*
6393788 ATGGTGAAAATTTGAAAACAA
1 ATGGTGAAAATTTAAAAACAA
6393809 ATGGATGAAAATTTAAAAAC
1 ATGG-TGAAAATTTAAAAAC
6393829 GGGCCAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (21 bp):
ATGGTGAAAATTTAAAAACAA
Found at i:6398706 original size:13 final size:13
Alignment explanation
Indices: 6398688--6398712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6398678 TACAAGATAA
6398688 TTAGAGAGAGAAT
1 TTAGAGAGAGAAT
6398701 TTAGAGAGAGAA
1 TTAGAGAGAGAA
6398713 GCTCTCAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TTAGAGAGAGAAT
Found at i:6398996 original size:17 final size:17
Alignment explanation
Indices: 6398945--6398998 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
6398935 ATAAGAATAG
* *
6398945 GTACAAGAGAAGAAGCT
1 GTACATGAGAATAAGCT
6398962 GTAC--GAGAAT-AG--
1 GTACATGAGAATAAGCT
6398974 GTACATGAGAATAAGCT
1 GTACATGAGAATAAGCT
6398991 GTACATGA
1 GTACATGA
6398999 ATAAGTATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
12 4 0.13
14 8 0.26
15 7 0.23
17 12 0.39
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.19
Consensus pattern (17 bp):
GTACATGAGAATAAGCT
Found at i:6399001 original size:29 final size:29
Alignment explanation
Indices: 6398938--6398994 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
6398928 GAGGTGTATA
6398938 AGAATAGGTACAAGAGAAGAAGCTGTACG
1 AGAATAGGTACAAGAGAAGAAGCTGTACG
* *
6398967 AGAATAGGTACATGAGAATAAGCTGTAC
1 AGAATAGGTACAAGAGAAGAAGCTGTAC
6398995 ATGAATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.18
Consensus pattern (29 bp):
AGAATAGGTACAAGAGAAGAAGCTGTACG
Found at i:6399012 original size:29 final size:29
Alignment explanation
Indices: 6398938--6399013 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
6398928 GAGGTGTATA
* *
6398938 AGAATAGGTACAAGAGAAGAAGCTGTACG
1 AGAATAAGTACACGAGAAGAAGCTGTACG
* * *
6398967 AGAATAGGTACATGAGAATAAGCTGTAC-
1 AGAATAAGTACACGAGAAGAAGCTGTACG
*
6398995 ATGAATAAGTATACGAGAA
1 A-GAATAAGTACACGAGAA
6399014 CAAGATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.18
Consensus pattern (29 bp):
AGAATAAGTACACGAGAAGAAGCTGTACG
Found at i:6399343 original size:35 final size:35
Alignment explanation
Indices: 6399297--6399373 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
6399287 AGCACTTCAC
* *
6399297 TTATTCTGCGTGAAGTAGCGCTTCACTTGTTCTAG
1 TTATTCTGCGTGAAGTAACACTTCACTTGTTCTAG
*
6399332 TTATTCTGCGTGAAGTAACACTTCACTTGTTCTGG
1 TTATTCTGCGTGAAGTAACACTTCACTTGTTCTAG
*
6399367 TTGTTCT
1 TTATTCT
6399374 CTGTACAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (35 bp):
TTATTCTGCGTGAAGTAACACTTCACTTGTTCTAG
Found at i:6407438 original size:36 final size:36
Alignment explanation
Indices: 6407390--6407464 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
6407380 TGCCCGATAA
* * *
6407390 CTAATGTCTGTTCTACAAGGGCACGAGAAGTATCTG
1 CTAATGTATGTTCTACAAGGGAACGAGAAGTATCAG
*
6407426 CTAATGTATGTTCTACAAGGGAATGAGAAGTATCAG
1 CTAATGTATGTTCTACAAGGGAACGAGAAGTATCAG
6407462 CTA
1 CTA
6407465 CCACTAAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (36 bp):
CTAATGTATGTTCTACAAGGGAACGAGAAGTATCAG
Found at i:6414277 original size:2 final size:2
Alignment explanation
Indices: 6414270--6414298 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6414260 TAGGTTTGTA
6414270 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
6414299 CACCCACACA
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:6418064 original size:31 final size:30
Alignment explanation
Indices: 6418022--6418100 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
6418012 CCATAGGGAT
6418022 TAAATTGAATAAAAATATATAATACAGAAAC
1 TAAATTGAATAAAAATATATAATA-AGAAAC
* * * * *
6418053 TAAATTAAATAAAATTAAAATATTAAGAGAC
1 TAAATTGAATAAAAAT-ATATAATAAGAAAC
6418084 TAAATTGAA-AAAAATAT
1 TAAATTGAATAAAAATAT
6418101 TTTAAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 1 0.03
30 5 0.13
31 27 0.69
32 6 0.15
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (30 bp):
TAAATTGAATAAAAATATATAATAAGAAAC
Found at i:6418586 original size:19 final size:19
Alignment explanation
Indices: 6418564--6418617 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
6418554 TTTTCAATTA
6418564 TTTATTTATTTTTTATATT
1 TTTATTTATTTTTTATATT
* *
6418583 TTTATTT-TGTTTAATATT
1 TTTATTTATTTTTTATATT
*
6418601 TCATATTATATTTTTTA
1 T-TTATT-TATTTTTTA
6418618 GGTTGAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 1 0.04
21 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTATTTATTTTTTATATT
Found at i:6418601 original size:18 final size:19
Alignment explanation
Indices: 6418564--6418601 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6418554 TTTTCAATTA
* *
6418564 TTTATTTATTTTTTATATT
1 TTTATTTATGTTTAATATT
6418583 TTTATTT-TGTTTAATATT
1 TTTATTTATGTTTAATATT
6418601 T
1 T
6418602 CATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTATTTATGTTTAATATT
Found at i:6419255 original size:19 final size:17
Alignment explanation
Indices: 6419231--6419272 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
6419221 ATTAATAAGT
6419231 ATATTTATCATTTATTTAA
1 ATATTTAT-ATTT-TTTAA
*
6419250 ATATTTATATTTTTTTA
1 ATATTTATATTTTTTAA
6419267 ATATTT
1 ATATTT
6419273 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTATATTTTTTAA
Found at i:6442462 original size:53 final size:53
Alignment explanation
Indices: 6442382--6442487 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
6442372 AATCTGCATG
6442382 TGCTTTATCTGTTGATTTATTGGTAGTCATGAAGTACAGGTGGTAAAAGCAGA
1 TGCTTTATCTGTTGATTTATTGGTAGTCATGAAGTACAGGTGGTAAAAGCAGA
6442435 TGCTTTATCTGTTGATTTATTGGTAGTCATGAAGTACAGGTGGTAAAAGCAGA
1 TGCTTTATCTGTTGATTTATTGGTAGTCATGAAGTACAGGTGGTAAAAGCAGA
6442488 CCCAAACAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (53 bp):
TGCTTTATCTGTTGATTTATTGGTAGTCATGAAGTACAGGTGGTAAAAGCAGA
Found at i:6447860 original size:218 final size:217
Alignment explanation
Indices: 6447628--6448267 Score: 846
Period size: 210 Copynumber: 3.0 Consensus size: 217
6447618 TAATTATATA
* * *
6447628 AATATATTATATATACATATATTTAATTTATACATAAGGATTACTATAATTTATCATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTA
* * ** * *
6447693 TTTATCTAATTACATTTGGTAACTTTATTAATTATCACATTAGATTTTATAACATATTGTTTATA
66 TTTATATAATTACACTTAATAACTTTATTAGTTATCACATTAAATTTTATAACATATTGTTTATA
* * *
6447758 ATTAGTTATTATTTATATAAACTGTGATATAAAACGTTATAACATATAAGCTATGTGATTAATTT
131 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAG-TATGTGATTAATTT
6447823 CATATATATATATATAACAAAAT
195 CATATATATATATATAACAAAAT
* ** * *
6447846 CATATATTATATATACATATATTTAATTTATACATAAATATAACTATAACTTATAATAGACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTA
* * *
6447911 TTTATATGATTACACTTAATAACTTTATTAGTTGTCACATTAAATTTTATAACATATTATTTATA
66 TTTATATAATTACACTTAATAACTTTATTAGTTATCACATTAAATTTTATAACATATTGTTTATA
* * * *
6447976 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTTTATCAAATAA-T-TG-G-TATCA-TT
131 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTATGTGAT-TAATTT
* * **
6448036 -A-AT-TATACATATAATAAGGT
195 CATATATATATATATAACAAAAT
* * *
6448056 AATATATCATATATACATATATTTAATTTATACATAAGCATTAGTATAACTTATAATGAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTA
** * * *
6448121 TTTATATAATTACACTTAATATGTTTTTTAGCTATCACCTTAAATTTTATAACATATTGTTTATA
66 TTTATATAATTACACTTAATAACTTTATTAGTTATCACATTAAATTTTATAACATATTGTTTATA
* * *
6448186 ATTAGTTATTATTTATACAAATTTTGATATAAAACATTATAACATATAAGTTATATTATTAATTT
131 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAG-TATGTGATTAATTT
6448251 CATATATATATATATAA
195 CATATATATATATATAA
6448268 TTATGGATAA
Statistics
Matches: 361, Mismatches: 51, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
210 172 0.48
211 2 0.01
212 2 0.01
213 4 0.01
214 5 0.01
215 5 0.01
216 2 0.01
217 2 0.01
218 167 0.46
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (217 bp):
AATATATTATATATACATATATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTA
TTTATATAATTACACTTAATAACTTTATTAGTTATCACATTAAATTTTATAACATATTGTTTATA
ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTATGTGATTAATTTC
ATATATATATATATAACAAAAT
Found at i:6450222 original size:26 final size:26
Alignment explanation
Indices: 6450184--6450262 Score: 149
Period size: 26 Copynumber: 3.0 Consensus size: 26
6450174 GCTTGGTTAA
6450184 AAACGGTGTTGAATTATGAAGGTGAT
1 AAACGGTGTTGAATTATGAAGGTGAT
*
6450210 AAACGGTGCTGAATTATGAAGGTGAT
1 AAACGGTGTTGAATTATGAAGGTGAT
6450236 AAACGGTGTTGAATTATGAAGGTGAT
1 AAACGGTGTTGAATTATGAAGGTGAT
6450262 A
1 A
6450263 CTGATAATAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.29
Consensus pattern (26 bp):
AAACGGTGTTGAATTATGAAGGTGAT
Found at i:6465551 original size:28 final size:30
Alignment explanation
Indices: 6465519--6465581 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
6465509 AAAATATAAA
6465519 ATATAAATTAATAATAAAAAT-ATATATTTT
1 ATATAAATTAATAA-AAAAATAATATATTTT
*
6465549 ATATAAATT--TAAAATAATAATATATTTT
1 ATATAAATTAATAAAAAAATAATATATTTT
6465577 ATATA
1 ATATA
6465582 TTAATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.16
28 17 0.55
30 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATAAATTAATAAAAAAATAATATATTTT
Found at i:6465555 original size:30 final size:30
Alignment explanation
Indices: 6465519--6465596 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 30
6465509 AAAATATAAA
6465519 ATATAAATTAATAATAAAAATATATATTT-T
1 ATATAAATTAATAATAAAAATATAT-TTTAT
*
6465549 ATATAAATTTAA-AATAATAATATATTTTAT
1 ATATAAA-TTAATAATAAAAATATATTTTAT
*
6465579 ATATTAATATATATAATA
1 ATATAAAT-TA-ATAATA
6465597 TTAGTTTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 4 0.10
30 28 0.68
31 5 0.12
32 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATAAATTAATAATAAAAATATATTTTAT
Found at i:6468941 original size:16 final size:15
Alignment explanation
Indices: 6468899--6468951 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
6468889 AAGAAATGAA
6468899 AAAAAATATATATTT
1 AAAAAATATATATTT
6468914 AATTAAAA-ATATATTT
1 AA--AAAATATATATTT
*
6468930 AAAAAATGATATTATAT
1 AAAAAAT-ATA-TATTT
6468947 AAAAA
1 AAAAA
6468952 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 13 0.41
17 13 0.41
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AAAAAATATATATTT
Found at i:6469154 original size:15 final size:15
Alignment explanation
Indices: 6469128--6469167 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
6469118 TCTTCCCTAC
* *
6469128 AATCATATTACCTGT
1 AATCACATTACCTCT
*
6469143 AATTACATTACCTCT
1 AATCACATTACCTCT
6469158 AATCACATTA
1 AATCACATTA
6469168 TATTGTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.38
Consensus pattern (15 bp):
AATCACATTACCTCT
Found at i:6474465 original size:48 final size:48
Alignment explanation
Indices: 6474408--6474502 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
6474398 ACATATTAAG
*
6474408 TCAATTCATGCACAATCCTCCG-CAATCACACTTAGATGCAGCTTTTCT
1 TCAATTCATGCACAACCCT-CGACAATCACACTTAGATGCAGCTTTTCT
*
6474456 TCAATTCATGCACAACCCTCGATAATCACACTTAGATGCAGCTTTTC
1 TCAATTCATGCACAACCCTCGACAATCACACTTAGATGCAGCTTTTC
6474503 GTGTGCTTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 2 0.05
48 42 0.95
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (48 bp):
TCAATTCATGCACAACCCTCGACAATCACACTTAGATGCAGCTTTTCT
Found at i:6480973 original size:2 final size:2
Alignment explanation
Indices: 6480966--6481001 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6480956 CGACAGGCAT
6480966 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6481002 AAAGTATCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6492762 original size:138 final size:138
Alignment explanation
Indices: 6492559--6492809 Score: 337
Period size: 138 Copynumber: 1.8 Consensus size: 138
6492549 GCAAATGAAG
* *
6492559 CAAAGCAACATCTTGAGTCTCAACTCAGTAGCATGGAAACAGATGCAGAGACAATGTCGTCAAAG
1 CAAAGCAACATCTTGAGTCTCAACTCAGTAGCATCGAAACAGAGGCAGAGACAATGTCGTCAAAG
* *
6492624 ATTGACTCATT-AAAAGCAGAAATTGAAAAGGAAATGGCCCTGTCAGCAGAAGTTTCAGTTAATG
66 ATTGACTCATTGAAAA-CAGAAATTGAAAAGGAAAGGGCACTGTCAGCAGAAGTTTCAGTTAATG
6492688 CAACCGAAT
130 CAACCGAAT
* * * *
6492697 CAAAGCAACTTCTTGAGTCTCAACTCATTAGCATCGAAGCAGAGGCTCG-GACAATGTC-TGCAA
1 CAAAGCAACATCTTGAGTCTCAACTCAGTAGCATCGAAACAGAGGC-AGAGACAATGTCGT-CAA
* * * * *
6492760 AGATTGATTCATTGGAAACAGAAGTTGAAACGGAAAGGGCATTGTCAGCA
64 AGATTGACTCATTGAAAACAGAAATTGAAAAGGAAAGGGCACTGTCAGCA
6492810 CAAATTACAG
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
137 1 0.01
138 92 0.95
139 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (138 bp):
CAAAGCAACATCTTGAGTCTCAACTCAGTAGCATCGAAACAGAGGCAGAGACAATGTCGTCAAAG
ATTGACTCATTGAAAACAGAAATTGAAAAGGAAAGGGCACTGTCAGCAGAAGTTTCAGTTAATGC
AACCGAAT
Found at i:6497227 original size:18 final size:18
Alignment explanation
Indices: 6497204--6497240 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6497194 TCAAAGAATG
6497204 ATTATCCTACCCTGATGT
1 ATTATCCTACCCTGATGT
6497222 ATTATCCTACCCTGATGT
1 ATTATCCTACCCTGATGT
6497240 A
1 A
6497241 AGCTTCTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTATCCTACCCTGATGT
Found at i:6506832 original size:24 final size:22
Alignment explanation
Indices: 6506805--6506863 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
6506795 GTTATTATAC
6506805 AATACTATTACGTAGTTAAACTAT
1 AATACTATTA-G-AGTTAAACTAT
* *
6506829 AATATCTTATTAGAGTTATATTAT
1 AATA-C-TATTAGAGTTAAACTAT
*
6506853 AATATTATTAG
1 AATACTATTAG
6506864 TTAGAGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 6 0.20
24 17 0.57
25 2 0.07
26 5 0.17
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (22 bp):
AATACTATTAGAGTTAAACTAT
Found at i:6506871 original size:26 final size:25
Alignment explanation
Indices: 6506818--6506890 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 25
6506808 ACTATTACGT
* *
6506818 AGTTAAACTATAATA-TCTTATTAG
1 AGTTATACTATAATATTATTATTAG
*
6506842 AGTTATATTATAATATTATTAGTTAG
1 AGTTATACTATAATATTATTA-TTAG
* *
6506868 AGTTATACTATATTGTTATTATT
1 AGTTATACTATAATATTATTATT
6506891 TGTCAACCGG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 13 0.32
25 6 0.15
26 22 0.54
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (25 bp):
AGTTATACTATAATATTATTATTAG
Done.