Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 21 of 135
Found at i:8938652 original size:6 final size:6
Alignment explanation
Indices: 8938643--8938678 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
8938633 AATTTTGATT
8938643 TATTAC TATTTAC TATTAC TATTAC TATTAC TATTA
1 TATTAC TA-TTAC TATTAC TATTAC TATTAC TATTA
8938679 TAGTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAC
Found at i:8943104 original size:18 final size:19
Alignment explanation
Indices: 8943072--8943111 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
8943062 TATAATTTTT
8943072 TAAAAAGTTTGAAAATATA
1 TAAAAAGTTTGAAAATATA
*
8943091 TAAAAA-TTTTAAAATATA
1 TAAAAAGTTTGAAAATATA
8943109 TAA
1 TAA
8943112 TTATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAAAAGTTTGAAAATATA
Found at i:8943148 original size:19 final size:19
Alignment explanation
Indices: 8943124--8943182 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
8943114 ATAAATTTTA
*
8943124 AAAAATCAAAATAATA-TAT
1 AAAAATTAAAA-AATATTAT
*
8943143 AAAAATTGAAAAATATTAT
1 AAAAATTAAAAAATATTAT
*
8943162 AAAAATTAAAAAGTATT-T
1 AAAAATTAAAAAATATTAT
8943180 AAA
1 AAA
8943183 TTTCAAGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.23
19 27 0.77
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATTAAAAAATATTAT
Found at i:8943157 original size:18 final size:18
Alignment explanation
Indices: 8943083--8943182 Score: 63
Period size: 18 Copynumber: 5.7 Consensus size: 18
8943073 AAAAAGTTTG
*
8943083 AAAATA-TATAAAAATTTT
1 AAAATATTATAAAAA-TTA
8943101 AAAATA-TAT---AATTA
1 AAAATATTATAAAAATTA
* * *
8943115 TAAAT-TT-TAAAAAATC
1 AAAATATTATAAAAATTA
8943131 AAAATAATATATAAAAATTGA
1 AAAAT-AT-TATAAAAATT-A
8943152 AAAATATTATAAAAATTA
1 AAAATATTATAAAAATTA
8943170 AAAAGTATT-TAAA
1 AAAA-TATTATAAA
8943183 TTTCAAGTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
13 1 0.02
14 7 0.11
15 2 0.03
16 7 0.11
18 19 0.29
19 15 0.23
20 9 0.14
21 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATATTATAAAAATTA
Found at i:8943238 original size:8 final size:8
Alignment explanation
Indices: 8943227--8943285 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 8
8943217 ATTTAAATAT
8943227 TTTTAAAA
1 TTTTAAAA
*
8943235 TTTTATAA
1 TTTTAAAA
* *
8943243 TTAT-ATA
1 TTTTAAAA
8943250 TTTTAAAA
1 TTTTAAAA
*
8943258 TTTTATAA
1 TTTTAAAA
* *
8943266 TTAT-ATA
1 TTTTAAAA
8943273 TTTTAAAA
1 TTTTAAAA
8943281 TTTTA
1 TTTTA
8943286 TAAAAAATAT
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
7 8 0.22
8 29 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTTTAAAA
Found at i:8943256 original size:23 final size:23
Alignment explanation
Indices: 8943223--8943288 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
8943213 TGAAATTTAA
8943223 ATAT-TTTTAAAATTTTATAATT
1 ATATATTTTAAAATTTTATAATT
8943245 ATATATTTTAAAATTTTATAATT
1 ATATATTTTAAAATTTTATAATT
8943268 ATATATTTTAAAATTTTATAA
1 ATATATTTTAAAATTTTATAA
8943289 AAAATATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 4 0.09
23 39 0.91
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATATTTTAAAATTTTATAATT
Found at i:8943287 original size:15 final size:15
Alignment explanation
Indices: 8943227--8943287 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
8943217 ATTTAAATAT
8943227 TTTTAAAATTTTATA
1 TTTTAAAATTTTATA
* * *
8943242 -ATTATATATTTTAAAA
1 TTTTA-AAATTTT-ATA
* *
8943258 TTTTATAATTATATA
1 TTTTAAAATTTTATA
8943273 TTTTAAAATTTTATA
1 TTTTAAAATTTTATA
8943288 AAAAATATTT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
14 3 0.09
15 21 0.64
16 6 0.18
17 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAAAATTTTATA
Found at i:8943414 original size:11 final size:11
Alignment explanation
Indices: 8943400--8943424 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8943390 TTTATTTATT
8943400 TTTTTTATAAA
1 TTTTTTATAAA
8943411 TTTTTTATAAA
1 TTTTTTATAAA
8943422 TTT
1 TTT
8943425 ATATGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTATAAA
Found at i:8943456 original size:22 final size:22
Alignment explanation
Indices: 8943422--8943477 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
8943412 TTTTTATAAA
*
8943422 TTTATATGTTTTTTTAT--AGTT
1 TTTATAT-TTATTTTATGAAGTT
*
8943443 TTTATATTTATTTTATGAATTT
1 TTTATATTTATTTTATGAAGTT
8943465 TTTATATTTATTT
1 TTTATATTTATTT
8943478 CCATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 8 0.26
21 7 0.23
22 16 0.52
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTATATTTATTTTATGAAGTT
Found at i:8949453 original size:6 final size:6
Alignment explanation
Indices: 8949442--8949469 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
8949432 TTTTTCTCCC
8949442 TTCCAG TTCCAG TTCCAG TTCCAG TTCC
1 TTCCAG TTCCAG TTCCAG TTCCAG TTCC
8949470 TCCCCCACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (6 bp):
TTCCAG
Found at i:8953635 original size:18 final size:18
Alignment explanation
Indices: 8953589--8953626 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
8953579 TATAAGTATG
8953589 ATAAATTT-TCTT-ATTAA
1 ATAAATTTAT-TTGATTAA
8953606 ATAAATTTATTTGATTAA
1 ATAAATTTATTTGATTAA
8953624 ATA
1 ATA
8953627 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAAATTTATTTGATTAA
Found at i:8954054 original size:21 final size:21
Alignment explanation
Indices: 8954012--8954056 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8954002 TTGAAAATAA
*
8954012 TAAAAAATTCTAATTAATTAT
1 TAAAAAATTCTAATTAACTAT
*
8954033 TAAAAATATTTTAATT-ACTAT
1 TAAAAA-ATTCTAATTAACTAT
8954054 TAA
1 TAA
8954057 TTAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAAATTCTAATTAACTAT
Found at i:8954478 original size:23 final size:23
Alignment explanation
Indices: 8954452--8954499 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
8954442 AATATTTTGA
* * *
8954452 TTTAATCTTTTAAAATTTATAAT
1 TTTAATATTGTAAAAATTATAAT
*
8954475 TTTACTATTGTAAAAATTATAAT
1 TTTAATATTGTAAAAATTATAAT
8954498 TT
1 TT
8954500 AATTTTGACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTAATATTGTAAAAATTATAAT
Found at i:8954734 original size:23 final size:22
Alignment explanation
Indices: 8954683--8954738 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
8954673 ATAATTGAAT
** * *
8954683 TAAATATAAATTTAGAATAAGT
1 TAAATATATTTTTAGAAAAAGG
8954705 TAAATATATTTTTATGAAAAAGG
1 TAAATATATTTTTA-GAAAAAGG
8954728 TAAATATATTT
1 TAAATATATTT
8954739 AATTTCATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
TAAATATATTTTTAGAAAAAGG
Found at i:8957900 original size:15 final size:16
Alignment explanation
Indices: 8957875--8957904 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8957865 ATCTTTCTCA
8957875 ATTTGTTTTTATATTG
1 ATTTGTTTTTATATTG
8957891 ATTT-TTTTTATATT
1 ATTTGTTTTTATATT
8957905 TCATAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (16 bp):
ATTTGTTTTTATATTG
Found at i:8964420 original size:60 final size:60
Alignment explanation
Indices: 8964327--8964447 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
8964317 GGGGTCGAAA
8964327 ATGAATGTCCCTGGCTTACTCTACCATTACCATAATGCCGGTCAACCGTTCCGTTAAAGT
1 ATGAATGTCCCTGGCTTACTCTACCATTACCATAATGCCGGTCAACCGTTCCGTTAAAGT
8964387 ATGAATGTCCCTGGCTTACTCTACCATTACCATAATGCCGGTCAACCGTTCCGTTAAAGT
1 ATGAATGTCCCTGGCTTACTCTACCATTACCATAATGCCGGTCAACCGTTCCGTTAAAGT
8964447 A
1 A
8964448 GTCACTATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (60 bp):
ATGAATGTCCCTGGCTTACTCTACCATTACCATAATGCCGGTCAACCGTTCCGTTAAAGT
Found at i:8974285 original size:3 final size:3
Alignment explanation
Indices: 8974277--8974311 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
8974267 TCATTTGTTA
8974277 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8974312 ATAAATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:8975556 original size:31 final size:29
Alignment explanation
Indices: 8975478--8975558 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
8975468 GAATTGAATC
* *
8975478 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATC-AAAGTTCATGTATAAAATTACACA
* *
8975508 AAATCAAAGTTCGTGTATACAATTACACA
1 AAATCAAAGTTCATGTATAAAATTACACA
8975537 TTAAATCATAA-TTCATGTATAA
1 --AAATCA-AAGTTCATGTATAA
8975559 TTTTGAGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 20 0.48
30 5 0.12
31 15 0.36
32 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTACACA
Found at i:8994872 original size:6 final size:6
Alignment explanation
Indices: 8994861--8994901 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
8994851 TCCACCCACT
8994861 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
8994902 ATGTGTTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:8996692 original size:3 final size:3
Alignment explanation
Indices: 8996684--8996739 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
8996674 TCACCTCCAT
8996684 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
8996732 TTC TTC TT
1 TTC TTC TT
8996740 GCATTTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:8999693 original size:6 final size:7
Alignment explanation
Indices: 8999678--8999702 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8999668 CCTTTTCGTC
8999678 TTTTATT
1 TTTTATT
8999685 TTTTATT
1 TTTTATT
8999692 TTTTATT
1 TTTTATT
8999699 TTTT
1 TTTT
8999703 GAAAAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:9000480 original size:2 final size:2
Alignment explanation
Indices: 9000473--9000508 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9000463 TAAAATTAAG
9000473 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
9000509 TTATTCATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9007069 original size:28 final size:29
Alignment explanation
Indices: 9007021--9007075 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
9007011 TAAATACTTA
*
9007021 TTTTTATAATTAATCTGTTTTCTATATTT
1 TTTTTATAATTAATCTATTTTCTATATTT
* *
9007050 TTTTTGTAATTAAT-TATTTTTTATAT
1 TTTTTATAATTAATCTATTTTCTATAT
9007076 CATTTGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (29 bp):
TTTTTATAATTAATCTATTTTCTATATTT
Found at i:9008307 original size:2 final size:2
Alignment explanation
Indices: 9008300--9008329 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9008290 AGGTTTGCAG
9008300 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
9008330 GTTTGGGCAA
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:9011127 original size:33 final size:31
Alignment explanation
Indices: 9011056--9011142 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 31
9011046 TTTTACAATC
* *
9011056 AGGGCTTAATTGATTTTTCTATTATTTTATT
1 AGGGCTTAATTGATTTTTCTATTACTTTATA
**
9011087 ACAGCTTAATTGACTAATTTTC-ATTACTTTATA
1 AGGGCTTAATTGA-T--TTTTCTATTACTTTATA
*
9011120 AGGGCTTAATTGATTTTTTTATT
1 AGGGCTTAATTGATTTTTCTATT
9011143 CCTATTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
30 4 0.09
31 14 0.31
32 2 0.04
33 20 0.44
34 5 0.11
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.53
Consensus pattern (31 bp):
AGGGCTTAATTGATTTTTCTATTACTTTATA
Found at i:9011318 original size:19 final size:19
Alignment explanation
Indices: 9011277--9011319 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9011267 GAATGTTACT
* *
9011277 AAAATTATTAAAAATTAAT
1 AAAATTATTAAAAATAAAA
9011296 AAAATT-TTATAAAATAAAA
1 AAAATTATTA-AAAATAAAA
9011315 AAAAT
1 AAAAT
9011320 CCTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATTAAAAATAAAA
Found at i:9011868 original size:19 final size:21
Alignment explanation
Indices: 9011830--9011873 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
9011820 AATTTTTAAT
*
9011830 TTTATAATATTTTAT-TAAAA
1 TTTATAATATTTTATAAAAAA
*
9011850 TTTAT-ATATTTTCTAAAAAA
1 TTTATAATATTTTATAAAAAA
9011870 TTTA
1 TTTA
9011874 GATTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATAATATTTTATAAAAAA
Found at i:9012178 original size:8 final size:8
Alignment explanation
Indices: 9012160--9012212 Score: 53
Period size: 7 Copynumber: 7.1 Consensus size: 8
9012150 AGATGTAGCA
9012160 ATTTTTA-
1 ATTTTTAT
9012167 ATTTTTAT
1 ATTTTTAT
9012175 A--TTTAT
1 ATTTTTAT
9012181 -TTTTTAT
1 ATTTTTAT
9012188 -TTTTTAT
1 ATTTTTAT
*
9012195 AATTTTAT
1 ATTTTTAT
9012203 AATTTTTAT
1 -ATTTTTAT
9012212 A
1 A
9012213 GTATTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 5 0.13
7 19 0.49
8 8 0.21
9 7 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTAT
Found at i:9015527 original size:23 final size:23
Alignment explanation
Indices: 9015499--9015719 Score: 257
Period size: 23 Copynumber: 9.4 Consensus size: 23
9015489 ACACTAGCGC
9015499 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
9015522 TCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
9015545 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
9015568 GCTCTTTGTTTACCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
9015591 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* *
9015616 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * * * *
9015639 GTTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
9015662 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
9015685 GCTCTCTGTTGCCTAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
9015710 GCTCTCTGTT
1 GCTCTCTGTT
9015720 CAGTACTTTG
Statistics
Matches: 173, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
22 3 0.02
23 129 0.75
24 1 0.01
25 30 0.17
26 10 0.06
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:9015661 original size:94 final size:93
Alignment explanation
Indices: 9015499--9015717 Score: 255
Period size: 94 Copynumber: 2.3 Consensus size: 93
9015489 ACACTAGCGC
* * * *
9015499 GCTCTCTG-TTTAGCACTGTGTGTTCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCACTG
1 GCTCTCTGTTTTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATCAGCACTG
*
9015563 TGTGTGCTCTTTGTTTACCACGTCT-CGT
66 TGTGTGCTCTCTGTTTACCAC-TCTGCGT
* * *
9015591 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGTTCTCTGATCAGTACT
1 GCTCTCTGTT-TTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATCAGCACT
* * * *
9015656 TTGTGTGCTCTCTGTTTAGCACTTTGTGT
65 GTGTGTGCTCTCTGTTTACCACTCTGCGT
* *
9015685 GCTCTCTGTTGCCTAGCACT-TATGTGCTCTCTG
1 GCTCTCTGTT--TTAGCACTGTGTGTGCTCTCTG
9015718 TTCAGTACTT
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
92 8 0.07
93 3 0.03
94 90 0.83
95 7 0.06
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (93 bp):
GCTCTCTGTTTTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATCAGCACTG
TGTGTGCTCTCTGTTTACCACTCTGCGT
Found at i:9015664 original size:71 final size:69
Alignment explanation
Indices: 9015499--9015729 Score: 250
Period size: 71 Copynumber: 3.3 Consensus size: 69
9015489 ACACTAGCGC
* * * * *
9015499 GCTCTCTGTTTAGCACTGTGTGTTCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCACTGT
1 GCTCTCTGTTCAGTACTTTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCACTTT
9015564 GTGT
66 GTGT
* * ** * * *
9015568 GCTCTTTGTTTACCACGTCT-CGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCAC
1 GCTCTCTGTTCAGTAC-TTTGTGTGCTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGTTTAGCAC
9015632 TTTGTGT
63 TTTGTGT
* * *
9015639 GTTCTCTGATCAGTACTTTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCTAGCAC
1 GCTCTCTGTTCAGTACTTTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTT---TAGCAC
*
9015704 -TTATGT
63 TTTGTGT
9015710 GCTCTCTGTTCAGTACTTTG
1 GCTCTCTGTTCAGTACTTTG
9015730 ATACTCTCCG
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
69 45 0.33
70 6 0.04
71 78 0.58
72 6 0.04
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (69 bp):
GCTCTCTGTTCAGTACTTTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCACTTT
GTGT
Found at i:9023210 original size:25 final size:24
Alignment explanation
Indices: 9023176--9023226 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
9023166 TAATGTCGTT
9023176 TACTATTTTT-AATATTTATAAGTAA
1 TACTATTTTTAAATA-TTATAA-TAA
9023201 TACTATTTTTAAATATTATAATAA
1 TACTATTTTTAAATATTATAATAA
9023225 TA
1 TA
9023227 TATCCGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.20
25 16 0.64
26 4 0.16
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
TACTATTTTTAAATATTATAATAA
Found at i:9037058 original size:29 final size:29
Alignment explanation
Indices: 9037016--9037075 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
9037006 ATGATGTTGA
9037016 TTTTGAAAAAGTATGTTTCAAAACCATTC
1 TTTTGAAAAAGTATGTTTCAAAACCATTC
* *
9037045 TTTTGTAAAAGTATGTTTCAAAATCATTC
1 TTTTGAAAAAGTATGTTTCAAAACCATTC
9037074 TT
1 TT
9037076 ATGACAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (29 bp):
TTTTGAAAAAGTATGTTTCAAAACCATTC
Found at i:9041125 original size:20 final size:20
Alignment explanation
Indices: 9041088--9041126 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9041078 ATAATCATAC
** *
9041088 CAAAATTTTTAACCCTATAT
1 CAAAATTTCCAACACTATAT
9041108 CAAAATTTCCAACACTATA
1 CAAAATTTCCAACACTATA
9041127 CTAATACTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAAATTTCCAACACTATAT
Found at i:9049261 original size:39 final size:39
Alignment explanation
Indices: 9049206--9049320 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 39
9049196 AATAAAGATT
9049206 TGATATC--GAGGAAGAGGTGAAAACATACAGAAATCTG
1 TGATATCGAGAGGAAGAGGTGAAAACATACAGAAATCTG
9049243 TGATATCGAGAGGAAGAGGTGAAAACATACAGAAATCTG
1 TGATATCGAGAGGAAGAGGTGAAAACATACAGAAATCTG
*
9049282 TGATATCGAGAGGAAGAGATGAAAACATACAGAAATCTG
1 TGATATCGAGAGGAAGAGGTGAAAACATACAGAAATCTG
9049321 AGGCGTACCT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
37 7 0.09
39 68 0.91
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.18
Consensus pattern (39 bp):
TGATATCGAGAGGAAGAGGTGAAAACATACAGAAATCTG
Found at i:9051436 original size:8 final size:8
Alignment explanation
Indices: 9051423--9051453 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
9051413 TCTAAAAACT
*
9051423 ATGTATGA
1 ATGTATGC
9051431 ATGTATGC
1 ATGTATGC
9051439 ATGTATGC
1 ATGTATGC
9051447 ATGTATG
1 ATGTATG
9051454 GAAATGAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (8 bp):
ATGTATGC
Found at i:9059930 original size:37 final size:37
Alignment explanation
Indices: 9059880--9059952 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
9059870 ATTGTTCGAT
*
9059880 TAACAATGTAACATGAGTTGGCTAGACTACAAGATAC
1 TAACAATGTAACATGAGTTGACTAGACTACAAGATAC
*
9059917 TAACAATGTAACATGAGTTGATTAGACTACAAGATA
1 TAACAATGTAACATGAGTTGACTAGACTACAAGATA
9059953 TGTGAGTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (37 bp):
TAACAATGTAACATGAGTTGACTAGACTACAAGATAC
Found at i:9060525 original size:41 final size:39
Alignment explanation
Indices: 9060442--9060532 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 39
9060432 AAAATTTATA
* *
9060442 TTTAATACAATAAAATATTTATTATTTTTAGTTGTATGTT
1 TTTAATATAATAAAATATTTATTATATTTAG-TGTATGTT
*
9060482 TTTAAATATAATAAAATATTTATTATATTTA-TGATAGTTTT
1 TTT-AATATAATAAAATATTTATTATATTTAGTG-TA-TGTT
9060523 TTTAATATAA
1 TTTAATATAA
9060533 ATAATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
39 2 0.04
40 12 0.27
41 31 0.69
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (39 bp):
TTTAATATAATAAAATATTTATTATATTTAGTGTATGTT
Found at i:9060707 original size:12 final size:12
Alignment explanation
Indices: 9060685--9060715 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
9060675 GTTGAAATCT
9060685 TATTATATATATA
1 TATT-TATATATA
9060698 TATTTATATATA
1 TATTTATATATA
9060710 TATTTA
1 TATTTA
9060716 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTATATATA
Found at i:9061118 original size:12 final size:12
Alignment explanation
Indices: 9061101--9061148 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
9061091 GTTCACGAAC
*
9061101 AAGCTCGTTTAA
1 AAGCTCGTTTAT
9061113 AAGCTCGTTTAT
1 AAGCTCGTTTAT
**
9061125 TGGCTCGTTTAT
1 AAGCTCGTTTAT
9061137 AAGCTCGTTTAT
1 AAGCTCGTTTAT
9061149 TTATTAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:9061135 original size:24 final size:24
Alignment explanation
Indices: 9061103--9061149 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
9061093 TCACGAACAA
9061103 GCTCGTTTAAAAGCTCGTTTATTG
1 GCTCGTTTAAAAGCTCGTTTATTG
*
9061127 GCTCGTTTATAAGCTCGTTTATT
1 GCTCGTTTAAAAGCTCGTTTATT
9061150 TATTAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (24 bp):
GCTCGTTTAAAAGCTCGTTTATTG
Found at i:9061274 original size:23 final size:23
Alignment explanation
Indices: 9061243--9061329 Score: 122
Period size: 23 Copynumber: 3.8 Consensus size: 23
9061233 TCATTAACAT
* *
9061243 TGTTTGTGAACGTGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
9061266 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
9061289 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
**
9061312 -GTTAAATGAACATGTTCG
1 TGTT-CGTGAACATGTTCG
9061330 TGAACGAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 3 0.05
23 56 0.95
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.39
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:9061282 original size:12 final size:12
Alignment explanation
Indices: 9061265--9061306 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
9061255 TGTTCGATTA
9061265 ATGTTCGTGAAC
1 ATGTTCGTGAAC
*
9061277 ATGTTCGAT-TA-
1 ATGTTCG-TGAAC
9061288 ATGTTCGTGAAC
1 ATGTTCGTGAAC
9061300 ATGTTCG
1 ATGTTCG
9061307 ATTAAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 1 0.04
11 8 0.32
12 15 0.60
13 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:9071563 original size:22 final size:22
Alignment explanation
Indices: 9071538--9071579 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9071528 GCGCGCTTTA
*
9071538 CTGTTCAGCACTGTGTGTGCTT
1 CTGTTCAGCACTGTATGTGCTT
9071560 CTGTTCAGCACTGTATGTGC
1 CTGTTCAGCACTGTATGTGC
9071580 CTACTGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (22 bp):
CTGTTCAGCACTGTATGTGCTT
Found at i:9073216 original size:13 final size:11
Alignment explanation
Indices: 9073184--9073226 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
9073174 CCATTTTCTA
*
9073184 AATAAAATAAT
1 AATAAAATATT
9073195 AAT-AAATATTT
1 AATAAAATA-TT
9073206 AAGTAAAATATT
1 AA-TAAAATATT
9073218 AATAAAATA
1 AATAAAATA
9073227 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:9073607 original size:3 final size:3
Alignment explanation
Indices: 9073599--9073629 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9073589 ATACTTCTTA
9073599 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
9073630 ATGTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9073788 original size:16 final size:17
Alignment explanation
Indices: 9073767--9073799 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9073757 TTATACATTC
9073767 ACAATT-TAATTATATA
1 ACAATTATAATTATATA
9073783 ACAATTGATAATTATAT
1 ACAATT-ATAATTATAT
9073800 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
ACAATTATAATTATATA
Found at i:9075812 original size:12 final size:12
Alignment explanation
Indices: 9075795--9075821 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9075785 TTTTATTTTT
9075795 TTTGTTTTAATA
1 TTTGTTTTAATA
9075807 TTTGTTTTAATA
1 TTTGTTTTAATA
9075819 TTT
1 TTT
9075822 TTAACTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTGTTTTAATA
Found at i:9090532 original size:17 final size:18
Alignment explanation
Indices: 9090510--9090543 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9090500 CAGAATTATT
*
9090510 TTTGTTT-ATTTTTCAAA
1 TTTGTTTCATTTGTCAAA
9090527 TTTGTTTCATTTGTCAA
1 TTTGTTTCATTTGTCAA
9090544 TCAGTCGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (18 bp):
TTTGTTTCATTTGTCAAA
Found at i:9098184 original size:19 final size:20
Alignment explanation
Indices: 9098147--9098184 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9098137 AATATCTTAT
**
9098147 TATTTCAGTTTTATCTATAA
1 TATTTCAGTTTTAGATATAA
9098167 TATTT-AGTTTTAGATATA
1 TATTTCAGTTTTAGATATA
9098185 CTTTGAACCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (20 bp):
TATTTCAGTTTTAGATATAA
Found at i:9101140 original size:90 final size:90
Alignment explanation
Indices: 9100987--9101169 Score: 321
Period size: 90 Copynumber: 2.0 Consensus size: 90
9100977 GCCATCAATA
* *
9100987 GATGGTTCCATGAAAGAAGCATTGCATAGGTTCTTAGGTTAGACAATAGAGCAATTTGAAAATGA
1 GATGGTTCCATGAAAGAAGCATTGCATAGATTCTTAGATTAGACAATAGAGCAATTTGAAAATGA
* *
9101052 AGTGAAAATGATCTTGATGAGGGTT
66 ACTGAAAATGATCTTGATGAGGGAT
*
9101077 GATGGTTCCATGAAAGAAGCATTGCATAGATTCTTAGATTAGACAGTAGAGCAATTTGAAAATGA
1 GATGGTTCCATGAAAGAAGCATTGCATAGATTCTTAGATTAGACAATAGAGCAATTTGAAAATGA
9101142 ACTGAAAATGATCTTGATGAGGGAT
66 ACTGAAAATGATCTTGATGAGGGAT
9101167 GAT
1 GAT
9101170 ATTTTTCCCA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (90 bp):
GATGGTTCCATGAAAGAAGCATTGCATAGATTCTTAGATTAGACAATAGAGCAATTTGAAAATGA
ACTGAAAATGATCTTGATGAGGGAT
Found at i:9108136 original size:3 final size:3
Alignment explanation
Indices: 9108128--9108155 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9108118 TCACTCCAAA
9108128 CCG CCG CCG CCG CCG CCG CCG CCG CCG C
1 CCG CCG CCG CCG CCG CCG CCG CCG CCG C
9108156 TACCACCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.32, T:0.00
Consensus pattern (3 bp):
CCG
Found at i:9111422 original size:21 final size:21
Alignment explanation
Indices: 9111393--9111433 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9111383 ACCACTAATA
*
9111393 ACCCCACCTAAGTAGAAATCT
1 ACCCAACCTAAGTAGAAATCT
*
9111414 ACCCAACCTACGTAGAAATC
1 ACCCAACCTAAGTAGAAATC
9111434 CTCCGACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.34, G:0.10, T:0.17
Consensus pattern (21 bp):
ACCCAACCTAAGTAGAAATCT
Found at i:9111964 original size:2 final size:2
Alignment explanation
Indices: 9111959--9111996 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
9111949 TTCAAATAGA
9111959 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9111997 CGGTGTTGTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9116827 original size:6 final size:6
Alignment explanation
Indices: 9116816--9116842 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9116806 TCAACTATTT
9116816 AAATTG AAATTG AAATTG AAATTG AAA
1 AAATTG AAATTG AAATTG AAATTG AAA
9116843 CAACATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (6 bp):
AAATTG
Found at i:9117329 original size:6 final size:6
Alignment explanation
Indices: 9117321--9117359 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
9117311 CCCCCCCGTA
*
9117321 CCAGTA CCAGTC CCAGTC CCAGTC CCAGTC CCAGTC CCA
1 CCAGTC CCAGTC CCAGTC CCAGTC CCAGTC CCAGTC CCA
9117360 CTACGCCCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.21, C:0.49, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAGTC
Found at i:9121151 original size:26 final size:26
Alignment explanation
Indices: 9121112--9121164 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
9121102 TATTCATTAG
9121112 ACATAGTTGCTTGATTTGGGTGCACA
1 ACATAGTTGCTTGATTTGGGTGCACA
*
9121138 ACATAGTTGTTTGATTTGGGTGCACA
1 ACATAGTTGCTTGATTTGGGTGCACA
9121164 A
1 A
9121165 ATTCTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (26 bp):
ACATAGTTGCTTGATTTGGGTGCACA
Found at i:9124439 original size:23 final size:23
Alignment explanation
Indices: 9124404--9124471 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 23
9124394 TTTTCGATAC
*
9124404 TAAATGCTA-TTATCAAAAAGCTG
1 TAAATG-TACTTATAAAAAAGCTG
9124427 TAAATGTACTTATAAAAAAAAAGCTG
1 TAAATGTACTTAT---AAAAAAGCTG
*
9124453 CAAATGTACTTATAAAAAA
1 TAAATGTACTTATAAAAAA
9124472 AAAGCTGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 2 0.05
23 16 0.41
26 21 0.54
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (23 bp):
TAAATGTACTTATAAAAAAGCTG
Found at i:9124457 original size:26 final size:26
Alignment explanation
Indices: 9124418--9124486 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
9124408 TGCTATTATC
*
9124418 AAAAAGCTGTAAATGTACTTATAAAA
1 AAAAAGCTGCAAATGTACTTATAAAA
9124444 AAAAAGCTGCAAATGTACTTATAAAA
1 AAAAAGCTGCAAATGTACTTATAAAA
9124470 AAAAAGCTGCAAATGTA
1 AAAAAGCTGCAAATGTA
9124487 AATATCTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (26 bp):
AAAAAGCTGCAAATGTACTTATAAAA
Found at i:9126863 original size:19 final size:17
Alignment explanation
Indices: 9126824--9126871 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
9126814 ACCGAAATAA
*
9126824 ATAATATA-TATTATAT
1 ATAATATATTTTTATAT
9126840 ATAATATATTTTTATATT
1 ATAATATATTTTTATA-T
*
9126858 AGTAATTTATTTTT
1 A-TAATATATTTTT
9126872 TGAACTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 2 0.07
19 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATAATATATTTTTATAT
Found at i:9140307 original size:16 final size:16
Alignment explanation
Indices: 9140286--9140355 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
9140276 TTTGGTTCGT
* *
9140286 TGTAATGAAATAGAAG
1 TGTAATGGAATAGAAC
9140302 TGTAATGGAATAGAAC
1 TGTAATGGAATAGAAC
* *
9140318 TGTAATGGAATATAGC
1 TGTAATGGAATAGAAC
* *
9140334 TATAATGGAATAGAGC
1 TGTAATGGAATAGAAC
9140350 TGTAAT
1 TGTAAT
9140356 CAGTAATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAAC
Found at i:9140394 original size:46 final size:44
Alignment explanation
Indices: 9140337--9140430 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
9140327 ATATAGCTAT
* *
9140337 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
9140383 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
9140427 AATG
1 AATG
9140431 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:9140592 original size:58 final size:55
Alignment explanation
Indices: 9140525--9140670 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 55
9140515 AATTTTAATG
*
9140525 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
9140583 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
9140641 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
9140671 TATAATATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
57 3 0.04
58 40 0.52
59 17 0.22
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:9144222 original size:6 final size:6
Alignment explanation
Indices: 9144211--9144237 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9144201 TGCATGCTAC
9144211 TATGGA TATGGA TATGGA TATGGA TAT
1 TATGGA TATGGA TATGGA TATGGA TAT
9144238 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (6 bp):
TATGGA
Found at i:9152703 original size:19 final size:18
Alignment explanation
Indices: 9152672--9152718 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
9152662 AGCATCTCCA
*
9152672 TTTT-TTCTCTTCTCCTCT
1 TTTTCTTCTTTTCTCCT-T
*
9152690 TTTTCTTCTTTTCTTCTT
1 TTTTCTTCTTTTCTCCTT
9152708 TTTCTCTTCTT
1 TTT-TCTTCTT
9152719 AAACCCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTCTTCTTTTCTCCTT
Found at i:9155649 original size:47 final size:47
Alignment explanation
Indices: 9155542--9155700 Score: 225
Period size: 47 Copynumber: 3.4 Consensus size: 47
9155532 ATAAAAATTA
* * *
9155542 AAATGGATCTAATATTATTATCTAAAGTTAAATTTAATTTATATTTT
1 AAATAGATCTAATATTATTATTTAAAGTTAAATTCAATTTATATTTT
** *
9155589 AAACGGA--T-ATATTATTATTTTAAGTTAAATTCAATTTATATTTT
1 AAATAGATCTAATATTATTATTTAAAGTTAAATTCAATTTATATTTT
* *
9155633 AAATAGATCTAATATTATTATTTAAAATTAAATTCAATTCATATTTT
1 AAATAGATCTAATATTATTATTTAAAGTTAAATTCAATTTATATTTT
9155680 AAATAGATCTAATATTATTAT
1 AAATAGATCTAATATTATTAT
9155701 CTGAAATTAT
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
44 38 0.38
45 1 0.01
46 1 0.01
47 60 0.60
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (47 bp):
AAATAGATCTAATATTATTATTTAAAGTTAAATTCAATTTATATTTT
Found at i:9155683 original size:23 final size:23
Alignment explanation
Indices: 9155604--9155683 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 23
9155594 GATATATTAT
*
9155604 TATTTTAAGTTAAATTCAATTTA
1 TATTTTAAATTAAATTCAATTTA
*
9155627 TATTTTAAA-TAGA-TCTAATATTA
1 TATTTTAAATTAAATTC-AAT-TTA
* *
9155650 TTATTTAAAATTAAATTCAATTCA
1 -TATTTTAAATTAAATTCAATTTA
9155674 TATTTTAAAT
1 TATTTTAAAT
9155684 AGATCTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
21 2 0.04
22 6 0.13
23 20 0.43
24 10 0.22
25 6 0.13
26 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (23 bp):
TATTTTAAATTAAATTCAATTTA
Found at i:9155707 original size:24 final size:24
Alignment explanation
Indices: 9155627--9155700 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
9155617 ATTCAATTTA
*
9155627 TATTTTAAATAGATCTAATATTAT
1 TATTTAAAATAGATCTAATATTAT
* *
9155651 TATTTAAAATTAAAT-TCAAT-TCA-
1 TATTTAAAA-TAGATCT-AATATTAT
*
9155674 TATTTTAAATAGATCTAATATTAT
1 TATTTAAAATAGATCTAATATTAT
9155698 TAT
1 TAT
9155701 CTGAAATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
22 7 0.18
23 11 0.28
24 14 0.36
25 7 0.18
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (24 bp):
TATTTAAAATAGATCTAATATTAT
Found at i:9159472 original size:58 final size:59
Alignment explanation
Indices: 9159384--9159531 Score: 156
Period size: 59 Copynumber: 2.5 Consensus size: 59
9159374 AAATAGTAAT
* * ** * *
9159384 TTAGAC-TCTCGAGGGGCAAAATGGTAATTTTGGGAAATTTTGGGATTAAAAAT-GAAACC
1 TTAGACAT-TCGA-GGGTAAAATGGTAATTTTGAGAAAGATCGGGATCAAAAATAGAAACC
* * ***
9159443 TTAGACATTCGAGGGTAAAATGATAATTTTTAGAAAGATCGGGATCAAAAATAGAATTT
1 TTAGACATTCGAGGGTAAAATGGTAATTTTGAGAAAGATCGGGATCAAAAATAGAAACC
*
9159502 TTGGACATTCGAGGGTAAAATGGTAATTTT
1 TTAGACATTCGAGGGTAAAATGGTAATTTT
9159532 TAAAAGGTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
58 32 0.43
59 41 0.55
60 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (59 bp):
TTAGACATTCGAGGGTAAAATGGTAATTTTGAGAAAGATCGGGATCAAAAATAGAAACC
Found at i:9159529 original size:29 final size:29
Alignment explanation
Indices: 9159443--9159533 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
9159433 AAATGAAACC
*
9159443 TTAGACATTCGAGGGTAAAATGATAATTT
1 TTAGACATTCGAGGGTAAAATGGTAATTT
* * * *
9159472 TTAGAAAGATCG-GGATCAAAAATAG-AATTT
1 TTAGACA-TTCGAGGGT--AAAATGGTAATTT
*
9159502 TTGGACATTCGAGGGTAAAATGGTAATTT
1 TTAGACATTCGAGGGTAAAATGGTAATTT
9159531 TTA
1 TTA
9159534 AAAGGTTTGG
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
28 6 0.13
29 19 0.41
30 16 0.35
31 5 0.11
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (29 bp):
TTAGACATTCGAGGGTAAAATGGTAATTT
Found at i:9159546 original size:29 final size:29
Alignment explanation
Indices: 9159514--9159767 Score: 166
Period size: 29 Copynumber: 8.8 Consensus size: 29
9159504 GGACATTCGA
**
9159514 GGGT-AAAATGGTAATTTTTAAAAGGTTTG
1 GGGTCAAAAT-GTAATTTTTGGAAGGTTTG
* * * *
9159543 GGGTTAAAAAAGGAGTTTTTGGAA-GTTTGG
1 GGG-TCAAAATGTAATTTTTGGAAGGTTT-G
** * *
9159573 GGGT-AAAAAATAATTTTT-GAAGTTTTA
1 GGGTCAAAATGTAATTTTTGGAAGGTTTG
** *
9159600 GGGTCAAAAATAG-AAAATTT-GAAAGTTTGG
1 GGGTC-AAAAT-GTAATTTTTGGAAGGTTT-G
* *
9159630 GGGTCAAAATGTAATTTTTGGAAGTTTTA
1 GGGTCAAAATGTAATTTTTGGAAGGTTTG
9159659 GGGTCAAAATGTAATTTTTGGAA-GTTTG
1 GGGTCAAAATGTAATTTTTGGAAGGTTTG
* *
9159687 GGGT-AAAATGTAATTTTTGAAAGTTTTG
1 GGGTCAAAATGTAATTTTTGGAAGGTTTG
* * * *
9159715 GAGTCAAAAATATAA-TTTTGGAGAAGTTTAA
1 GGGTC-AAAATGTAATTTTTGGA-AGGTTT-G
*
9159746 GGGTCAAAATATAATTTTTGGA
1 GGGTCAAAATGTAATTTTTGGA
9159768 CAGTGTAAGG
Statistics
Matches: 176, Mismatches: 33, Indels: 30
0.74 0.14 0.13
Matches are distributed among these distances:
27 24 0.14
28 29 0.16
29 62 0.35
30 46 0.26
31 15 0.09
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTGGAAGGTTTG
Found at i:9159552 original size:59 final size:58
Alignment explanation
Indices: 9159453--9159764 Score: 269
Period size: 59 Copynumber: 5.3 Consensus size: 58
9159443 TTAGACATTC
* * * *
9159453 GAGGGTAAAATGATAATTTTTAGAAAG-ATCGGGATCAAAAATAGAATTTTTGGACA-TTC
1 GAGGGTAAAATG-TAATTTTTA-AAAGTTTTGGGGTCAAAAATAGAATTTTTGGA-AGTTT
* * *
9159512 GAGGGTAAAATGGTAATTTTTAAAAGGTTTGGGGTTAAAAA-AGGAGTTTTTGGAAGTTT
1 GAGGGTAAAAT-GTAATTTTTAAAAGTTTTGGGGTCAAAAATA-GAATTTTTGGAAGTTT
* ** * * ** *
9159571 GGGGGTAAAAAATAATTTTT-GAAGTTTTAGGGTCAAAAATAGAAAATTTGAAAGTTT
1 GAGGGTAAAATGTAATTTTTAAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAGTTT
* ** *
9159628 GGGGGTCAAAATGTAATTTTTGGAAGTTTTAGGGTC-AAAAT-GTAATTTTTGGAAGTTT
1 GAGGGT-AAAATGTAATTTTTAAAAGTTTTGGGGTCAAAAATAG-AATTTTTGGAAGTTT
* * * *
9159686 G-GGGTAAAATGTAATTTTTGAAAGTTTTGGAGTCAAAAATATAATTTTGGAGAAGTTT
1 GAGGGTAAAATGTAATTTTTAAAAGTTTTGGGGTCAAAAATAGAATTTTTG-GAAGTTT
* *
9159744 AAGGGTCAAAATATAATTTTT
1 GAGGGT-AAAATGTAATTTTT
9159765 GGACAGTGTA
Statistics
Matches: 211, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
56 26 0.12
57 50 0.24
58 52 0.25
59 69 0.33
60 14 0.07
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
GAGGGTAAAATGTAATTTTTAAAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAGTTT
Found at i:9159684 original size:58 final size:58
Alignment explanation
Indices: 9159487--9159767 Score: 243
Period size: 57 Copynumber: 4.8 Consensus size: 58
9159477 AAGATCGGGA
* * * ** * *
9159487 TCAAAAATAG-AATTTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTAAAAGGTTTGGGG
1 TCAAAAAT-GTAATTTTTGGA-AGTTTGGGGGTAAAAT-ATAATTTTTGGAAGTTTTAGGG
* * * * *
9159546 TTAAAAAAGGAGTTTTTGGAAGTTTGGGGGTAAAAAATAATTTTT-GAAGTTTTAGGG
1 TCAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAATATAATTTTTGGAAGTTTTAGGG
** * *
9159603 TCAAAAATAG-AAAATTTGAAAGTTTGGGGGTCAAAATGTAATTTTTGGAAGTTTTAGGG
1 TCAAAAAT-GTAATTTTTGGAAGTTTGGGGGT-AAAATATAATTTTTGGAAGTTTTAGGG
* *
9159662 TC-AAAATGTAATTTTTGGAAGTTT-GGGGTAAAATGTAATTTTTGAAAGTTTT-GGAG
1 TCAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAATATAATTTTTGGAAGTTTTAGG-G
* * **
9159718 TCAAAAATATAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTTGGA
1 TCAAAAATGTAATTTTTG-GAAGTTTGGGGGT-AAAATATAATTTTTGGA
9159768 CAGTGTAAGG
Statistics
Matches: 184, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
55 2 0.01
56 25 0.14
57 51 0.28
58 47 0.26
59 44 0.24
60 15 0.08
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
TCAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAATATAATTTTTGGAAGTTTTAGGG
Found at i:9159761 original size:87 final size:87
Alignment explanation
Indices: 9159490--9159767 Score: 264
Period size: 87 Copynumber: 3.2 Consensus size: 87
9159480 ATCGGGATCA
* * * * * *
9159490 AAAATAGAATTTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTAAAAGGTTTGGGGTTAAAAA-
1 AAAATATAATTTTTGGA-AGTTTG-GGGTAAAATAGTAATTTTTGAAAGTTTTGGGGTCAAAAAT
* * **
9159553 AGGAGTTTTTGGAAGTTTGGGGGT-
64 A-TAATTTTTGGAAGTTTAAGGGTC
* * ** *
9159577 AAAAAATAATTTTT-GAAGTTTTAGGGTCAAAAATAG-AAAATTTGAAAGTTTGGGGGTC-AAAA
1 AAAATATAATTTTTGGAAG-TTTGGGGT--AAAATAGTAATTTTTGAAAGTTTTGGGGTCAAAAA
* *
9159639 TGTAATTTTTGGAAGTTTTAGGGTC
63 TATAATTTTTGGAAGTTTAAGGGTC
* *
9159664 AAAATGTAATTTTTGGAAGTTTGGGGTAAAAT-GTAATTTTTGAAAGTTTTGGAGTCAAAAATAT
1 AAAATATAATTTTTGGAAGTTTGGGGTAAAATAGTAATTTTTGAAAGTTTTGGGGTCAAAAATAT
*
9159728 AATTTTGGAGAAGTTTAAGGGTC
66 AATTTTTG-GAAGTTTAAGGGTC
9159751 AAAATATAATTTTTGGA
1 AAAATATAATTTTTGGA
9159768 CAGTGTAAGG
Statistics
Matches: 154, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
84 1 0.01
85 24 0.16
86 41 0.27
87 78 0.51
88 10 0.06
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (87 bp):
AAAATATAATTTTTGGAAGTTTGGGGTAAAATAGTAATTTTTGAAAGTTTTGGGGTCAAAAATAT
AATTTTTGGAAGTTTAAGGGTC
Found at i:9159777 original size:30 final size:28
Alignment explanation
Indices: 9159558--9159767 Score: 185
Period size: 29 Copynumber: 7.3 Consensus size: 28
9159548 AAAAAAGGAG
* **
9159558 TTTTTGGAAGTTTGGGGGT-AAAAAATAA
1 TTTTTGGAAGTTT-AGGGTCAAAATGTAA
9159586 TTTTT-GAAGTTTTAGGGTCAAAAATAG-AA
1 TTTTTGGAAG-TTTAGGGTC-AAAAT-GTAA
** * *
9159615 AATTTGAAAGTTTGGGGGTCAAAATGTAA
1 TTTTTGGAAGTTT-AGGGTCAAAATGTAA
9159644 TTTTTGGAAGTTTTAGGGTCAAAATGTAA
1 TTTTTGGAAG-TTTAGGGTCAAAATGTAA
*
9159673 TTTTTGGAAGTTTGGGGT-AAAATGTAA
1 TTTTTGGAAGTTTAGGGTCAAAATGTAA
* * *
9159700 TTTTTGAAAGTTTTGGAGTCAAAAATATAA
1 TTTTTGGAAGTTTAGG-GTC-AAAATGTAA
* *
9159730 TTTTGGAGAAGTTTAAGGGTCAAAATATAA
1 TTTTTG-GAAGTTT-AGGGTCAAAATGTAA
9159760 TTTTTGGA
1 TTTTTGGA
9159768 CAGTGTAAGG
Statistics
Matches: 150, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
27 31 0.21
28 18 0.12
29 52 0.35
30 38 0.25
31 9 0.06
32 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (28 bp):
TTTTTGGAAGTTTAGGGTCAAAATGTAA
Found at i:9160735 original size:17 final size:17
Alignment explanation
Indices: 9160715--9160824 Score: 141
Period size: 17 Copynumber: 6.4 Consensus size: 17
9160705 TGGATTTTAT
* *
9160715 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
9160732 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
9160750 TTTAAATTCAAATTAAA
1 TTTAAATTTAAAATAAA
9160767 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
9160784 TTTAAATTTTAAGATAAA
1 TTTAAA-TTTAAAATAAA
9160802 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
9160819 TTTAAA
1 TTTAAA
9160825 ATGAGTTTGG
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
16 1 0.01
17 51 0.63
18 29 0.36
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:9160754 original size:35 final size:34
Alignment explanation
Indices: 9160715--9160824 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 34
9160705 TGGATTTTAT
*
9160715 TTTAAATTTATAATAATTTTAAATTTAAAAATAAA
1 TTTAAATTTATAATAAATTTAAATTT-AAAATAAA
*
9160750 TTTAAATTCA-AATTAAATTTAAATTTAAAATAAA
1 TTTAAATTTATAA-TAAATTTAAATTTAAAATAAA
9160784 TTTAAATTT-TAAGATAAATTT-AATCTTAAAATAAA
1 TTTAAATTTAT-A-ATAAATTTAAAT-TTAAAATAAA
9160819 TTTAAA
1 TTTAAA
9160825 ATGAGTTTGG
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
34 21 0.31
35 45 0.67
36 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (34 bp):
TTTAAATTTATAATAAATTTAAATTTAAAATAAA
Found at i:9160801 original size:52 final size:52
Alignment explanation
Indices: 9160715--9160824 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 52
9160705 TGGATTTTAT
* * *
9160715 TTTAAATTTATAATAATTTTAAATTTAAAAATAAATTTAAAT-TCAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTT-AATCTCAAAATAAA
* * *
9160767 TTTAAATTTAAAATAAATTTAAATTTTAAGATAAATTTAATCTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAATCTCAAAATAAA
9160819 TTTAAA
1 TTTAAA
9160825 ATGAGTTTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 3 0.06
52 48 0.94
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAATCTCAAAATAAA
Found at i:9171035 original size:18 final size:18
Alignment explanation
Indices: 9171014--9171048 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9171004 ATTTAAATTA
*
9171014 ATAATTGAAATTAATTTT
1 ATAATTCAAATTAATTTT
*
9171032 ATAATTCAAATTGATTT
1 ATAATTCAAATTAATTT
9171049 AAATAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
ATAATTCAAATTAATTTT
Found at i:9177172 original size:14 final size:14
Alignment explanation
Indices: 9177153--9177180 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9177143 AACAAGCATA
9177153 ATTTATTTATTTAT
1 ATTTATTTATTTAT
9177167 ATTTATTTATTTAT
1 ATTTATTTATTTAT
9177181 GATCCAGTTG
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:0.00, T:0.71
Consensus pattern (14 bp):
ATTTATTTATTTAT
Found at i:9178117 original size:2 final size:2
Alignment explanation
Indices: 9178110--9178147 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9178100 GTGTTTTTAC
9178110 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
9178148 GAGAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9179152 original size:30 final size:31
Alignment explanation
Indices: 9179086--9179153 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
9179076 AATTTATTAA
* *
9179086 TTAATAAATGATCAAATTATACTTTAGTCCCT
1 TTAA-AAATGATCAAATTATAATTTAATCCCT
*
9179118 TTAAAAATGAT-AAATTTTAAATTTAATCCC-
1 TTAAAAATGATCAAATTAT-AATTTAATCCCT
9179148 TTAAAA
1 TTAAAA
9179154 TTTATAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 12 0.38
31 16 0.50
32 4 0.12
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (31 bp):
TTAAAAATGATCAAATTATAATTTAATCCCT
Found at i:9180298 original size:33 final size:33
Alignment explanation
Indices: 9180260--9180326 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
9180250 GGTATAGTTG
9180260 TACACATTGATTGTGCTCTTATTCTCAAATACA
1 TACACATTGATTGTGCTCTTATTCTCAAATACA
9180293 TACACATTGATTGTGCTCTTATTCTCAAATACA
1 TACACATTGATTGTGCTCTTATTCTCAAATACA
9180326 T
1 T
9180327 GAATTGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (33 bp):
TACACATTGATTGTGCTCTTATTCTCAAATACA
Found at i:9182614 original size:10 final size:8
Alignment explanation
Indices: 9182592--9182662 Score: 56
Period size: 8 Copynumber: 8.5 Consensus size: 8
9182582 ATTTTAGTAC
9182592 TTTTTATA
1 TTTTTATA
9182600 TTTTTATA
1 TTTTTATA
* *
9182608 TTGTTTTTG
1 TT-TTTATA
9182617 TGATTTTATA
1 T--TTTTATA
9182627 TTTTTAATA
1 TTTTT-ATA
*
9182636 GTTTTATA
1 TTTTTATA
9182644 GTTTTT-TA
1 -TTTTTATA
9182652 TTTTTAT-
1 TTTTTATA
9182659 TTTT
1 TTTT
9182663 GTAATTTCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
7 9 0.18
8 20 0.39
9 16 0.31
10 5 0.10
11 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (8 bp):
TTTTTATA
Found at i:9182650 original size:27 final size:27
Alignment explanation
Indices: 9182592--9182658 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
9182582 ATTTTAGTAC
*
9182592 TTTTTATATTTTTATATTGTTTTTGTG
1 TTTTTATATTTTTATATAGTTTTTGTG
* *
9182619 ATTTTATATTTTTA-ATAGTTTTAT-AG
1 TTTTTATATTTTTATATAGTTTT-TGTG
9182645 TTTTT-TATTTTTAT
1 TTTTTATATTTTTAT
9182659 TTTTGTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 8 0.24
26 12 0.35
27 14 0.41
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (27 bp):
TTTTTATATTTTTATATAGTTTTTGTG
Found at i:9187059 original size:40 final size:40
Alignment explanation
Indices: 9187004--9187085 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
9186994 ATTAGTGTCA
9187004 TAGGGGTATTAATGTTTTTAGCACACCACACGCGACTTGG
1 TAGGGGTATTAATGTTTTTAGCACACCACACGCGACTTGG
9187044 TAGGGGTATTAATGTTTTTAGCACACCACACGCGACTTGG
1 TAGGGGTATTAATGTTTTTAGCACACCACACGCGACTTGG
9187084 TA
1 TA
9187086 TAACATTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (40 bp):
TAGGGGTATTAATGTTTTTAGCACACCACACGCGACTTGG
Found at i:9187621 original size:16 final size:14
Alignment explanation
Indices: 9187582--9187640 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 14
9187572 TTTTAAAAAT
9187582 ATTTATATTATTTTA
1 ATTTATA-TATTTTA
9187597 ATTTA-ATATTTAATA
1 ATTTATATATTT--TA
9187612 ATTTATATATTTTA
1 ATTTATATATTTTA
*
9187626 ATTTAATAAATTTTA
1 ATTT-ATATATTTTA
9187641 TATAATCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 5 0.13
14 7 0.18
15 21 0.54
16 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATATATTTTA
Found at i:9195745 original size:47 final size:47
Alignment explanation
Indices: 9195671--9195771 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 47
9195661 GGGTAAGTCG
*
9195671 AATTCTGGTTTAGAATTATTATCATTTGGAAGGTTATCCATAAATTC
1 AATTATGGTTTAGAATTATTATCATTTGGAAGGTTATCCATAAATTC
*
9195718 AATTATGGTTTAGAATTATTATCATTTGGAAGGTTATTCATAAATTC
1 AATTATGGTTTAGAATTATTATCATTTGGAAGGTTATCCATAAATTC
9195765 AATTATG
1 AATTATG
9195772 TCTTATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.44
Consensus pattern (47 bp):
AATTATGGTTTAGAATTATTATCATTTGGAAGGTTATCCATAAATTC
Found at i:9199897 original size:32 final size:32
Alignment explanation
Indices: 9199827--9199897 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
9199817 TTTAACAACC
* * *
9199827 CAATGA-TTTAAATAAAAACTTTCGAATAGTT
1 CAATGACTTAAAATAAAAACTTTCAAATAATT
* *
9199858 CAGTGACTTAAAATGAAAACTTTCAAATAATT
1 CAATGACTTAAAATAAAAACTTTCAAATAATT
*
9199890 TAATGACT
1 CAATGACT
9199898 ATTTTATAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (32 bp):
CAATGACTTAAAATAAAAACTTTCAAATAATT
Found at i:9209284 original size:13 final size:13
Alignment explanation
Indices: 9209264--9209298 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
9209254 ATGGGAAAAG
9209264 AACAATCTTGAGC
1 AACAATCTTGAGC
*
9209277 AGCAATCTTGAGC
1 AACAATCTTGAGC
9209290 AACAATCTT
1 AACAATCTT
9209299 CAGAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (13 bp):
AACAATCTTGAGC
Found at i:9248156 original size:232 final size:232
Alignment explanation
Indices: 9247750--9248213 Score: 919
Period size: 232 Copynumber: 2.0 Consensus size: 232
9247740 CTTGAGCTTT
*
9247750 GTCGATGCACAAAGCCTGTTGCAGTTGACATTTGCGGTGTCTAATATTATTATAATCGTGGGCCC
1 GTCGATGCACAAAGCCTGTTGCAGTTGACATTTGCGGTGTCTAATATTATTATAATCGTGAGCCC
9247815 TATATCGGATGCCTTTCTTGGCTAATATCAAACACCTGTCATAGGTTTTCCCACTAGTGAACAGG
66 TATATCGGATGCCTTTCTTGGCTAATATCAAACACCTGTCATAGGTTTTCCCACTAGTGAACAGG
9247880 TGATAACATCTAATCTTTGTCCACAATTATTTGATTTTTTTGTATGTAAATTTGATGTTATAAGT
131 TGATAACATCTAATCTTTGTCCACAATTATTTGATTTTTTTGTATGTAAATTTGATGTTATAAGT
9247945 TGTTTTTTGTAGATGGCGTGGGAATCCGAATATCGGA
196 TGTTTTTTGTAGATGGCGTGGGAATCCGAATATCGGA
9247982 GTCGATGCACAAAGCCTGTTGCAGTTGACATTTGCGGTGTCTAATATTATTATAATCGTGAGCCC
1 GTCGATGCACAAAGCCTGTTGCAGTTGACATTTGCGGTGTCTAATATTATTATAATCGTGAGCCC
9248047 TATATCGGATGCCTTTCTTGGCTAATATCAAACACCTGTCATAGGTTTTCCCACTAGTGAACAGG
66 TATATCGGATGCCTTTCTTGGCTAATATCAAACACCTGTCATAGGTTTTCCCACTAGTGAACAGG
9248112 TGATAACATCTAATCTTTGTCCACAATTATTTGATTTTTTTGTATGTAAATTTGATGTTATAAGT
131 TGATAACATCTAATCTTTGTCCACAATTATTTGATTTTTTTGTATGTAAATTTGATGTTATAAGT
9248177 TGTTTTTTGTAGATGGCGTGGGAATCCGAATATCGGA
196 TGTTTTTTGTAGATGGCGTGGGAATCCGAATATCGGA
9248214 AGGTCATTCA
Statistics
Matches: 231, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 231 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (232 bp):
GTCGATGCACAAAGCCTGTTGCAGTTGACATTTGCGGTGTCTAATATTATTATAATCGTGAGCCC
TATATCGGATGCCTTTCTTGGCTAATATCAAACACCTGTCATAGGTTTTCCCACTAGTGAACAGG
TGATAACATCTAATCTTTGTCCACAATTATTTGATTTTTTTGTATGTAAATTTGATGTTATAAGT
TGTTTTTTGTAGATGGCGTGGGAATCCGAATATCGGA
Found at i:9249400 original size:23 final size:23
Alignment explanation
Indices: 9249330--9249452 Score: 135
Period size: 23 Copynumber: 5.3 Consensus size: 23
9249320 ACGGAACAAG
* *
9249330 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
*
9249351 CAGAGAGCACA-TAAGTGCTAGGCAA
1 CAGAGAGCACACAAAGTGCTA---AA
*
9249376 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* *
9249399 CAGAGAGTACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
9249422 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
9249445 CAGAGAGC
1 CAGAGAGC
9249453 GCGCTAGTGT
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
21 15 0.17
23 52 0.60
25 13 0.15
26 7 0.08
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:9256714 original size:23 final size:23
Alignment explanation
Indices: 9256642--9256764 Score: 153
Period size: 23 Copynumber: 5.3 Consensus size: 23
9256632 ACGGAACAAG
* *
9256642 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
* *
9256663 CAGAGAGCACA-TAAGTGCTAGGCAA
1 CAGAGAGCACACAAAGTGCTA---AT
*
9256688 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
9256711 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
9256734 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
9256757 CAGAGAGC
1 CAGAGAGC
9256765 GCGCTAGTGT
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
21 16 0.18
23 54 0.61
24 1 0.01
25 11 0.12
26 7 0.08
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:9259046 original size:6 final size:6
Alignment explanation
Indices: 9259035--9259075 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
9259025 TAGAATTAAA
*
9259035 TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
9259076 ATGCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:9262136 original size:9 final size:9
Alignment explanation
Indices: 9262122--9262146 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
9262112 ATAATAATAT
9262122 AAAATTAAA
1 AAAATTAAA
9262131 AAAATTAAA
1 AAAATTAAA
9262140 AAAATTA
1 AAAATTA
9262147 GCACCACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:9263272 original size:14 final size:14
Alignment explanation
Indices: 9263255--9263303 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
9263245 ATTATTTAAG
9263255 TTATTTTTTTTGTA
1 TTATTTTTTTTGTA
* **
9263269 TTATATTCTGGTGTA
1 TTAT-TTTTTTTGTA
*
9263284 TAATTTTTTTTGTA
1 TTATTTTTTTTGTA
9263298 TTATTT
1 TTATTT
9263304 AGGTAAAAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.18, C:0.02, G:0.10, T:0.69
Consensus pattern (14 bp):
TTATTTTTTTTGTA
Found at i:9265189 original size:17 final size:16
Alignment explanation
Indices: 9265150--9265200 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
9265140 TTAAAATGAT
9265150 AAATTTT-TAATTTAA
1 AAATTTTATAATTTAA
*
9265165 AATTTTTTATAATTTATA
1 AA-ATTTTATAATTTA-A
9265183 AAATTTTA-AA-TTAA
1 AAATTTTATAATTTAA
9265197 AAAT
1 AAAT
9265201 ATTAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
15 5 0.16
16 6 0.19
17 12 0.39
18 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTTTATAATTTAA
Found at i:9268916 original size:118 final size:117
Alignment explanation
Indices: 9268762--9268985 Score: 349
Period size: 118 Copynumber: 1.9 Consensus size: 117
9268752 CCCCTTCTAT
* *
9268762 AAGAACTTTTCAACCCAAAAGCAATGAATAACACTTGGTTTTAGTCAAAAGTATTGTTTGAAAGT
1 AAGAACTTTTCAACCCAAAAGCAATGAAGAACACTTGGTTTTAGTCAAAAGTACTGTTTGAAAGT
* *
9268827 GTTTTTCCACCTGAACGCAAAAGTTGAAATTTAAGTATTTTTTACTTTTCAA
66 CTTTTTCCACCTAAACGCAAAAGTTGAAATTTAAGTATTTTTTACTTTTCAA
* *
9268879 AAGAATTTTTCATCCCTAAAAGCAATGAAGAACACTTGGTTTTAGTCAAAAGTACTGTTTGAAAG
1 AAGAACTTTTCAACCC-AAAAGCAATGAAGAACACTTGGTTTTAGTCAAAAGTACTGTTTGAAAG
* * * *
9268944 TCTTTTTCTACCTAAACGTAAAAGTTGAGATTTAAGTGTTTT
65 TCTTTTTCCACCTAAACGCAAAAGTTGAAATTTAAGTATTTT
9268986 AGTATTTGCT
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
117 14 0.15
118 82 0.85
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (117 bp):
AAGAACTTTTCAACCCAAAAGCAATGAAGAACACTTGGTTTTAGTCAAAAGTACTGTTTGAAAGT
CTTTTTCCACCTAAACGCAAAAGTTGAAATTTAAGTATTTTTTACTTTTCAA
Found at i:9269980 original size:20 final size:22
Alignment explanation
Indices: 9269955--9269996 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9269945 CTATGGTTGA
*
9269955 GAAATTGA-A-GAATTAGGCTT
1 GAAATTGATAGGAATTAAGCTT
9269975 GAAATTGATAGGAATTAAGCTT
1 GAAATTGATAGGAATTAAGCTT
9269997 AGATTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (22 bp):
GAAATTGATAGGAATTAAGCTT
Found at i:9271725 original size:5 final size:5
Alignment explanation
Indices: 9271699--9271743 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
9271689 TAAAGTTCGA
9271699 AATA- AATA- AATA- AATA- AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
9271744 CAAAAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 16 0.40
5 24 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:9271987 original size:7 final size:7
Alignment explanation
Indices: 9271977--9272007 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
9271967 AAAGGAAAAA
9271977 GGGAAGC
1 GGGAAGC
9271984 GGGAAGC
1 GGGAAGC
9271991 GGGAAGC
1 GGGAAGC
9271998 GGGAAGC
1 GGGAAGC
9272005 GGG
1 GGG
9272008 GGGTAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.61, T:0.00
Consensus pattern (7 bp):
GGGAAGC
Found at i:9274537 original size:31 final size:31
Alignment explanation
Indices: 9274493--9274570 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
9274483 ATTGCGCAAA
* * *
9274493 AAAATAAAAATAAAAATAAT-TAAATGATTAG
1 AAAATTAATATAAAAACAATGTAAATGATT-G
* *
9274524 AAAATTAATATAAATACAATGTAAATGCTTG
1 AAAATTAATATAAAAACAATGTAAATGATTG
*
9274555 AATATTAATATAAAAA
1 AAAATTAATATAAAAA
9274571 GAAAAGTATC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 31 0.79
32 8 0.21
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (31 bp):
AAAATTAATATAAAAACAATGTAAATGATTG
Found at i:9279986 original size:5 final size:5
Alignment explanation
Indices: 9279978--9280006 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9279968 ATTTCAACAA
9279978 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
9280007 AACTTCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:9282645 original size:21 final size:21
Alignment explanation
Indices: 9282606--9282645 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9282596 TGATTTTTTT
* *
9282606 TTCAATGTGAAAATGTTGAAA
1 TTCAATATGAAAATATTGAAA
*
9282627 TTCAATATGAAATTATTGA
1 TTCAATATGAAAATATTGA
9282646 TGTGACAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (21 bp):
TTCAATATGAAAATATTGAAA
Found at i:9289300 original size:19 final size:18
Alignment explanation
Indices: 9289256--9289302 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
9289246 AAATTTAAAA
*
9289256 ATATTTTTTATAATTTGT
1 ATATTTTTTATAATTTAT
*
9289274 ATTCTTTTTTAATAATTTAT
1 A-TATTTTTT-ATAATTTAT
9289294 ATATTTTTT
1 ATATTTTTT
9289303 TGAACTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 9 0.38
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
ATATTTTTTATAATTTAT
Found at i:9289301 original size:20 final size:21
Alignment explanation
Indices: 9289240--9289303 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
9289230 AATTAATTAA
* *
9289240 TTTTTAA-AATTTAAAAATAT
1 TTTTTAATAATTTATATATAT
* *
9289260 TTTTT-ATAATTTGTAT-TCT
1 TTTTTAATAATTTATATATAT
9289279 TTTTTAATAATTTATATAT-T
1 TTTTTAATAATTTATATATAT
9289299 TTTTT
1 TTTTT
9289304 GAACTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 8 0.22
20 27 0.75
21 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTAATAATTTATATATAT
Found at i:9295281 original size:31 final size:31
Alignment explanation
Indices: 9295246--9295318 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
9295236 AAATTTATTA
* *
9295246 TTTAGTCACTCCCGTTAGATAAGTTGTTAAT
1 TTTAGTCACTCCCGGTAGATAAGTTGTCAAT
**
9295277 TTTAGTCACTCTTGGTAGATAAGTTGTCAAT
1 TTTAGTCACTCCCGGTAGATAAGTTGTCAAT
*
9295308 TTTAATCACTC
1 TTTAGTCACTC
9295319 TATTGTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTAGTCACTCCCGGTAGATAAGTTGTCAAT
Found at i:9297945 original size:2 final size:2
Alignment explanation
Indices: 9297938--9297963 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9297928 CAAACACTTG
9297938 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
9297964 TTGAATTTAT
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:9299771 original size:3 final size:3
Alignment explanation
Indices: 9299763--9299801 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
9299753 ATCTGGTTGA
9299763 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
9299802 ATAAGTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:9310549 original size:2 final size:2
Alignment explanation
Indices: 9310542--9310571 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9310532 GAAGAAGGAG
9310542 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
9310572 AAGCTAATCT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9312077 original size:4 final size:4
Alignment explanation
Indices: 9312070--9312103 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
9312060 ATATGCATGC
* *
9312070 ATGT ATGT TTGT TTGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
9312104 AGACACAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.56
Consensus pattern (4 bp):
ATGT
Found at i:9314615 original size:20 final size:20
Alignment explanation
Indices: 9314578--9314616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9314568 TTGTACGGGT
* *
9314578 TTGCACTTTGGTGCCTCTGA
1 TTGCACCTTGATGCCTCTGA
*
9314598 TTGCACCTTGATGTCTCTG
1 TTGCACCTTGATGCCTCTG
9314617 TTAACACTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.10, C:0.26, G:0.23, T:0.41
Consensus pattern (20 bp):
TTGCACCTTGATGCCTCTGA
Found at i:9317364 original size:17 final size:18
Alignment explanation
Indices: 9317334--9317374 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
9317324 AAGCCCTTTT
* *
9317334 AAAATTTATAAATTATTA
1 AAAAATTATAAATTATAA
9317352 AAAAATTAT-AATTATAA
1 AAAAATTATAAATTATAA
9317369 AAAAAT
1 AAAAAT
9317375 AAGTTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATTATAAATTATAA
Found at i:9317572 original size:20 final size:21
Alignment explanation
Indices: 9317521--9317572 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
9317511 AAAATTAAAA
*
9317521 TTTTATAAATTTTTTTATAGTT
1 TTTTA-AAATTTTTTAATAGTT
**
9317543 TTTT-TGATTTTTTAATA-TT
1 TTTTAAAATTTTTTAATAGTT
9317562 TTTTAAAATTT
1 TTTTAAAATTT
9317573 AAAAAGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
22 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTAAAATTTTTTAATAGTT
Found at i:9320987 original size:29 final size:29
Alignment explanation
Indices: 9320928--9321011 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 29
9320918 ATCTCAAAAC
* *
9320928 TATACATGAATTTTGATTTAATGTGAAATTA
1 TATACATGAATTTTAATTT--GGTGAAATTA
*
9320959 TATACATGAATTTTAATTTGGTGCAATTA
1 TATACATGAATTTTAATTTGGTGAAATTA
*
9320988 TACACATGAAATTTTAATTGTGGT
1 TATACATG-AATTTTAATT-TGGT
9321012 TCAAATGTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 15 0.32
30 10 0.21
31 22 0.47
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (29 bp):
TATACATGAATTTTAATTTGGTGAAATTA
Found at i:9321003 original size:30 final size:30
Alignment explanation
Indices: 9320954--9321011 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
9320944 TTTAATGTGA
*
9320954 AATTATATACATGAATTTTAATT-TGGTGC
1 AATTATACACATGAATTTTAATTGTGGTGC
9320983 AATTATACACATGAAATTTTAATTGTGGT
1 AATTATACACATG-AATTTTAATTGTGGT
9321012 TCAAATGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.46
30 10 0.38
31 4 0.15
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (30 bp):
AATTATACACATGAATTTTAATTGTGGTGC
Found at i:9322607 original size:3 final size:3
Alignment explanation
Indices: 9322599--9322625 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9322589 AGAAATGACA
9322599 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
9322626 AGGAAGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:9335035 original size:29 final size:31
Alignment explanation
Indices: 9335003--9335084 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 31
9334993 TTAAATTTAA
*
9335003 AAAAATTATGAAAATTATTTTTAAAAA-T-T
1 AAAAATTATAAAAATTATTTTTAAAAAGTAT
* * *
9335032 AAAAATCATTAACATTA--TTTAAAAAGTAT
1 AAAAATTATAAAAATTATTTTTAAAAAGTAT
*
9335061 AAAAA-TATAAAAAATATTTTTAAA
1 AAAAATTATAAAAATTATTTTTAAA
9335085 TATTTTTGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
27 8 0.19
28 8 0.19
29 20 0.48
30 6 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (31 bp):
AAAAATTATAAAAATTATTTTTAAAAAGTAT
Found at i:9335078 original size:28 final size:27
Alignment explanation
Indices: 9335022--9335079 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
9335012 GAAAATTATT
* * *
9335022 TTTAAAAATTAAAAATCATTAACATTA
1 TTTAAAAATTAAAAATCATAAAAAATA
9335049 TTTAAAAAGTATAAAAAT-ATAAAAAATA
1 TTTAAAAA-T-TAAAAATCATAAAAAATA
9335077 TTT
1 TTT
9335080 TTAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.31
28 11 0.42
29 7 0.27
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (27 bp):
TTTAAAAATTAAAAATCATAAAAAATA
Found at i:9335338 original size:23 final size:23
Alignment explanation
Indices: 9335311--9335358 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
9335301 CCTAGTAACC
*
9335311 ATAAACTTAAATTTAACAATATA
1 ATAAACTTAAATTTAACAAAATA
*
9335334 ATAAATTTAAATTTAACAAAATA
1 ATAAACTTAAATTTAACAAAATA
9335357 AT
1 AT
9335359 TTGAACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAAACTTAAATTTAACAAAATA
Done.