Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 30 of 193
Found at i:9468023 original size:58 final size:58
Alignment explanation
Indices: 9467961--9468124 Score: 154
Period size: 59 Copynumber: 2.8 Consensus size: 58
9467951 GGATACTTGG
** *
9467961 GGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGAAATTTTGGATGTTCGA
1 GGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGAAATTTTGGACATCCGA
* ** * **
9468019 GGGTAAAATGATAATTTTTGGAAAAATCGA-GATTAAAAATAGAGTTTTTGGACATCCGA
1 GGGTAAAATGGTAA-TTTTGGAAAAATTTAGGGTTAAAAAT-GAAATTTTGGACATCCGA
* * * * *
9468078 GTGTATAATGGTAATTTT-G-AAAGTTTTGAGGTTAAAAATGGAATTTT
1 GGGTAAAATGGTAATTTTGGAAAAATTTAG-GGTTAAAAATGAAATTTT
9468125 TGGAAGTTTT
Statistics
Matches: 82, Mismatches: 20, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
56 4 0.05
57 6 0.07
58 35 0.43
59 37 0.45
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGAAATTTTGGACATCCGA
Found at i:9468241 original size:60 final size:59
Alignment explanation
Indices: 9468084--9468313 Score: 207
Period size: 60 Copynumber: 3.8 Consensus size: 59
9468074 CCGAGTGTAT
** **
9468084 AATGGTAA-TTTTGAAAGTTTTGAGGT-TAAAAATGGAATTTTTGGAAGTTTTTGGGTCAAA
1 AATGG-AATTTTTGAAAG-TTTG-GGTGTAAAAATATAATTTTTGGAAGTTTTAAGGTCAAA
* * * *
9468144 AATTGAATTTCT-AGAAGTTCAGGG-GTAAAAATATAATTTTTGGAAGTTTCAAGGTCAAA
1 AATGGAATTTTTGA-AAGTT-TGGGTGTAAAAATATAATTTTTGGAAGTTTTAAGGTCAAA
* ** * *
9468203 AAGTGGAATTTTTGAAAGTTTGGGTGCAAAAATATAATTTTTTTTAATTTTTGAGGTCAAA
1 AA-TGGAATTTTTGAAAGTTTGGGTGTAAAAATATAA-TTTTTGGAAGTTTTAAGGTCAAA
* * * *
9468264 AATGTAATTTTTGGAAGTTTGGGGGTTAAAATATAATTTTTGGATAGTTT
1 AATGGAATTTTTGAAAGTTTGGGTGTAAAAATATAATTTTTGGA-AGTTT
9468314 AGGGACCTCT
Statistics
Matches: 136, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
59 47 0.35
60 68 0.50
61 21 0.15
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.40
Consensus pattern (59 bp):
AATGGAATTTTTGAAAGTTTGGGTGTAAAAATATAATTTTTGGAAGTTTTAAGGTCAAA
Found at i:9468284 original size:29 final size:29
Alignment explanation
Indices: 9468088--9468313 Score: 140
Period size: 30 Copynumber: 7.6 Consensus size: 29
9468078 GTGTATAATG
* *
9468088 GTAA-TTTTGAAAGTTTTGAGGTTAAAAAT
1 GTAATTTTTGGAAG-TTTGAGGTCAAAAAT
*
9468117 GGAATTTTTGGAAGTTTTTG-GGTCAAAAAT
1 GTAATTTTTGGAAG--TTTGAGGTCAAAAAT
* * * *
9468147 -TGAATTTCTAGAAGTTCAGGGGT-AAAAAT
1 GT-AATTTTTGGAAGTT-TGAGGTCAAAAAT
* *
9468176 ATAATTTTTGGAAGTTTCAAGGTCAAAAAGT
1 GTAATTTTTGGAAGTTT-GAGGTCAAAAA-T
* *
9468207 GGAATTTTTGAAAGTTTG-GGTGCAAAAAT
1 GTAATTTTTGGAAGTTTGAGGT-CAAAAAT
* ** *
9468236 ATAATTTTTTTTAATTTTTGAGGTCAAAAAT
1 GTAA-TTTTTGGAA-GTTTGAGGTCAAAAAT
* *
9468267 GTAATTTTTGGAAGTTTGGGGGT-TAAAAT
1 GTAATTTTTGGAAGTTT-GAGGTCAAAAAT
*
9468296 ATAATTTTTGGATAGTTT
1 GTAATTTTTGGA-AGTTT
9468314 AGGGACCTCT
Statistics
Matches: 154, Mismatches: 28, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
28 2 0.01
29 50 0.32
30 65 0.42
31 34 0.22
32 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.41
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTTGAGGTCAAAAAT
Found at i:9469395 original size:13 final size:13
Alignment explanation
Indices: 9469377--9469442 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 13
9469367 TTTCGAATTT
9469377 TTATTATTAAAAA
1 TTATTATTAAAAA
*
9469390 TTATTATAAAAAA
1 TTATTATTAAAAA
* *
9469403 ATATTTATTACTATTAA
1 TTA-TTATTA--A-AAA
9469420 TTATTATTAAAAA
1 TTATTATTAAAAA
9469433 TTTATTATTA
1 -TTATTATTA
9469443 TTATTATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
13 16 0.38
14 15 0.36
16 7 0.17
17 4 0.10
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATTATTAAAAA
Found at i:9469422 original size:27 final size:25
Alignment explanation
Indices: 9469389--9469449 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
9469379 ATTATTAAAA
9469389 ATTATTATAAAAAAATATTTATTACT
1 ATTATTATAAAAAAA-ATTTATTACT
** *
9469415 ATTAATTATTATTAAAAATTTATTATT
1 ATT-ATTA-TAAAAAAAATTTATTACT
9469442 ATTATTAT
1 ATTATTAT
9469450 TATTAGTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 1 0.03
26 7 0.23
27 16 0.53
28 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTATTATAAAAAAAATTTATTACT
Found at i:9469448 original size:30 final size:29
Alignment explanation
Indices: 9469372--9469454 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 29
9469362 TAACCTTTCG
**
9469372 AATTT-TTATTATTAAAAATTATTATAAA
1 AATTTATTATTATTATTAATTATTATAAA
** *
9469400 AAAATATTTATTACTATTAATTATTATTAAA
1 AATTTA-TTATTATTATTAATTATTA-TAAA
9469431 AATTTATTATTATTATT-ATTATTA
1 AATTTATTATTATTATTAATTATTA
9469455 GTACTGTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 3 0.07
29 7 0.16
30 26 0.59
31 8 0.18
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
AATTTATTATTATTATTAATTATTATAAA
Found at i:9470239 original size:18 final size:17
Alignment explanation
Indices: 9470218--9470262 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
9470208 ATTTAATTTT
*
9470218 AATTTTAATTTTATAATA
1 AATTTAAATTTTAT-ATA
*
9470236 AATTTAAATTTTATGTA
1 AATTTAAATTTTATATA
9470253 AATTTAAATT
1 AATTTAAATT
9470263 CAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTTATATA
Found at i:9470241 original size:17 final size:17
Alignment explanation
Indices: 9470221--9470275 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
9470211 TAATTTTAAT
9470221 TTTAATTTTATAATAAA
1 TTTAATTTTATAATAAA
*
9470238 TTTAAATTTTAT-GTAAA
1 TTT-AATTTTATAATAAA
* * *
9470255 TTTAAATTCAAAATAAA
1 TTTAATTTTATAATAAA
9470272 TTTA
1 TTTA
9470276 TATCCCATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 5 0.16
17 18 0.58
18 8 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAATTTTATAATAAA
Found at i:9470400 original size:23 final size:24
Alignment explanation
Indices: 9470361--9470410 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
9470351 TAATAGAGAT
9470361 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
9470384 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
9470408 TTT
1 TTT
9470411 TACTTTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
24 8 0.35
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:9470574 original size:15 final size:15
Alignment explanation
Indices: 9470542--9470581 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
9470532 TATAATTAAC
9470542 CACATA-ATATTTCA
1 CACATATATATTTCA
* *
9470556 CACATATATTTTTCT
1 CACATATATATTTCA
9470571 CACATATATAT
1 CACATATATAT
9470582 CATTATATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (15 bp):
CACATATATATTTCA
Found at i:9483669 original size:4 final size:4
Alignment explanation
Indices: 9483660--9483687 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
9483650 TGACTCTGGT
9483660 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
9483688 ATGCTACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:9487351 original size:10 final size:10
Alignment explanation
Indices: 9487336--9487360 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9487326 ATTATATACC
9487336 ATATTCTCTA
1 ATATTCTCTA
9487346 ATATTCTCTA
1 ATATTCTCTA
9487356 ATATT
1 ATATT
9487361 TCATTTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (10 bp):
ATATTCTCTA
Found at i:9490193 original size:21 final size:22
Alignment explanation
Indices: 9490147--9490207 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
9490137 TGATCTAAGG
* *
9490147 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAACT
9490168 AAAAATAAAAGAAAATAGAACT
1 AAAAATAAAAGAAAATAGAACT
*
9490190 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
9490208 GAAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:9490198 original size:15 final size:16
Alignment explanation
Indices: 9490173--9490202 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9490163 GAATTAAAAA
9490173 TAAAAGAAAATAGAAC
1 TAAAAGAAAATAGAAC
9490189 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
9490203 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAATAGAAC
Found at i:9490973 original size:19 final size:19
Alignment explanation
Indices: 9490949--9490991 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9490939 AAACATAAAT
9490949 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
9490968 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
9490987 TAAAT
1 TAAAT
9490992 CCTAATATAA
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:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:9491739 original size:105 final size:103
Alignment explanation
Indices: 9491552--9491745 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 103
9491542 TTATTTTGTG
* *
9491552 AATTTTTTTCTTTCTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATAAAATGACACCA
1 AATTTTTTTCTTTCTTTTTCTTTAAGAATACATTGAACCTTTTGACGCGAAATAAAATGAAACCA
9491617 AAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTC
66 AAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTC
* * * * *
9491655 AATTTTTTTCTTCTCTTTTTTTTTGTAGAATGCATT-AACCCTTTTGACGCGAAGTGAAATGATA
1 AATTTTTTTCTT-TCTTTTTCTTT-AAGAATACATTGAA-CCTTTTGACGCGAAATAAAATGA-A
9491719 ACC-AAGCACTCCA-CCTCGGTTACTCAG
62 ACCAAAGCACTCCATCC-CGGTTACTCAG
9491746 TCTAACACAA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
103 12 0.15
104 13 0.16
105 51 0.65
106 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (103 bp):
AATTTTTTTCTTTCTTTTTCTTTAAGAATACATTGAACCTTTTGACGCGAAATAAAATGAAACCA
AAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTC
Found at i:9492292 original size:8 final size:8
Alignment explanation
Indices: 9492249--9492293 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
9492239 TTTCCTGGAC
9492249 AAAAATAA
1 AAAAATAA
*
9492257 ATAAATAA
1 AAAAATAA
*
9492265 AATAAGATAG
1 AA-AA-ATAA
9492275 AAAAATAA
1 AAAAATAA
9492283 AAAAATAA
1 AAAAATAA
9492291 AAA
1 AAA
9492294 TAATTGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 22 0.71
9 4 0.13
10 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:9495415 original size:21 final size:21
Alignment explanation
Indices: 9495389--9495428 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9495379 ATAGATGCCT
*
9495389 CAGTTTTCTTTTGAAAATCCA
1 CAGTTTGCTTTTGAAAATCCA
*
9495410 CAGTTTGCTTTTGGAAATC
1 CAGTTTGCTTTTGAAAATC
9495429 TATAGATTGC
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:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCCA
Found at i:9495438 original size:21 final size:21
Alignment explanation
Indices: 9495396--9495439 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9495386 CCTCAGTTTT
*
9495396 CTTTTGAAAATCCACAGTTTG
1 CTTTTGAAAATCCACAGATTG
* * *
9495417 CTTTTGGAAATCTATAGATTG
1 CTTTTGAAAATCCACAGATTG
9495438 CT
1 CT
9495440 GCTGAAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTTTGAAAATCCACAGATTG
Found at i:9497003 original size:22 final size:22
Alignment explanation
Indices: 9496978--9497038 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
9496968 TGATCTAAGG
*
9496978 AAAAATAAAAGAAAA-AGAATT
1 AAAAATAAAAGAAAATAGAACT
9496999 AAAAATAAAAGAAAATAGAACT
1 AAAAATAAAAGAAAATAGAACT
*
9497021 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
9497039 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 15 0.42
22 20 0.56
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:9497029 original size:15 final size:15
Alignment explanation
Indices: 9496990--9497034 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
9496980 AAATAAAAGA
* *
9496990 AAAAGAATTAAAAAT
1 AAAAGAAATAGAAAT
*
9497005 AAAAGAAAATAGAACT
1 AAAAG-AAATAGAAAT
9497021 AAAAGAAATAGAAA
1 AAAAGAAATAGAAA
9497035 ATAGGGAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.13
Consensus pattern (15 bp):
AAAAGAAATAGAAAT
Found at i:9497861 original size:19 final size:19
Alignment explanation
Indices: 9497837--9497879 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9497827 AAACATAAAT
9497837 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
9497856 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
9497875 TAAAT
1 TAAAT
9497880 CCTAATATAA
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:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:9506677 original size:19 final size:20
Alignment explanation
Indices: 9506650--9506703 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
9506640 AAAAATATAA
*
9506650 ATTTGAAATTTTTATAAA-T
1 ATTTTAAATTTTTATAAATT
*
9506669 ATTTTAAA-TTTTAAAAATT
1 ATTTTAAATTTTTATAAATT
*
9506688 ATTTTGTAATTTTTAT
1 ATTTT-AAATTTTTAT
9506704 TGAGAGAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 8 0.29
19 13 0.46
20 2 0.07
21 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTTAAATTTTTATAAATT
Found at i:9508418 original size:31 final size:31
Alignment explanation
Indices: 9508383--9508442 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
9508373 TAATATGGAC
*
9508383 ATTGTCGTTACA-AATTTTTATCATTTTAACT
1 ATTGTCCTTACATAA-TTTTATCATTTTAACT
* *
9508414 ATTGTCCTTATATGATTTTATCATTTTAA
1 ATTGTCCTTACATAATTTTATCATTTTAA
9508443 TCATGCGTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (31 bp):
ATTGTCCTTACATAATTTTATCATTTTAACT
Found at i:9511709 original size:3 final size:3
Alignment explanation
Indices: 9511703--9511731 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9511693 ATTTTGTTGT
9511703 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9511732 TGTCAAGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9521250 original size:19 final size:20
Alignment explanation
Indices: 9521211--9521256 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
9521201 TAAAAAATTA
* *
9521211 AAAATCATAATATATTTTTG
1 AAAATTATAAAATATTTTTG
9521231 AAAATTATAAAATA-TTTTG
1 AAAATTATAAAATATTTTTG
9521250 AAAATTA
1 AAAATTA
9521257 CAAGTATGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAATTATAAAATATTTTTG
Found at i:9521535 original size:21 final size:20
Alignment explanation
Indices: 9521491--9521536 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
9521481 TTTCGCATGC
9521491 TTATAATTTTAAAAATAGCTT
1 TTATAATTTTAAAAATAGC-T
9521512 TTATAATTTTCAAAAAATAG-T
1 TTATAATTTT--AAAAATAGCT
9521533 TTAT
1 TTAT
9521537 GATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (20 bp):
TTATAATTTTAAAAATAGCT
Found at i:9521606 original size:29 final size:29
Alignment explanation
Indices: 9521574--9521628 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
9521564 GTTTTAAGAT
* *
9521574 TTTTTTTTATTTTTTTAT-ATTTTATGGG
1 TTTTTTTGAATTTTTTATGATTTTATGGG
9521602 TTTTTTTGAATTTTTTATGATTTTATG
1 TTTTTTTGAATTTTTTATGATTTTATG
9521629 ATATTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (29 bp):
TTTTTTTGAATTTTTTATGATTTTATGGG
Found at i:9521635 original size:29 final size:27
Alignment explanation
Indices: 9521565--9521635 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
9521555 AATAAGTTTG
* * *
9521565 TTTTAAGATTTTTTTTTATTTTTTTATA
1 TTTTATGA-TTTTTTTGAATTTTTTATA
*
9521593 TTTTATGGGTTTTTTTGAATTTTTTATGA
1 TTTTAT-GATTTTTTTGAATTTTTTAT-A
*
9521622 TTTTATGATATTTT
1 TTTTATGATTTTTT
9521636 GTAAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 27 0.77
29 8 0.23
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (27 bp):
TTTTATGATTTTTTTGAATTTTTTATA
Found at i:9525495 original size:56 final size:56
Alignment explanation
Indices: 9525409--9525520 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
9525399 AGATTTAAAG
9525409 GTAAAATATCTTGATTCATTTCTGCAATTTCCAAATACATATATATGCATATACAA
1 GTAAAATATCTTGATTCATTTCTGCAATTTCCAAATACATATATATGCATATACAA
9525465 GTAAAATATCTTGATTCATTTCTGCAATTTCCAAATACATATATATGCATATACAA
1 GTAAAATATCTTGATTCATTTCTGCAATTTCCAAATACATATATATGCATATACAA
9525521 AAATAACAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (56 bp):
GTAAAATATCTTGATTCATTTCTGCAATTTCCAAATACATATATATGCATATACAA
Found at i:9533853 original size:59 final size:59
Alignment explanation
Indices: 9533752--9534358 Score: 913
Period size: 59 Copynumber: 10.4 Consensus size: 59
9533742 TTTGGATTCC
* *
9533752 CGGGGGTAAAATGGTAA-TTTTGGTGAAATTGGTGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* *
9533810 CTGAGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * **
9533869 CGGGGGTAAAATGATAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTAAAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * ** *
9533928 TGGGGGTAAAATGGTAATTTTTGATGAAATCAAGGTT-AAAATAGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* **
9533986 CGGGGGTAAAATGGTAATTTTTGGTAAAATCAAGGTTAAAAATGGAATTTTGG-AAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
*
9534044 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAG-AAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* *
9534101 CGGGGGTAAAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* **
9534160 TGGGGGTAAAATGGTAATTTTTGGTGAAATCATGGTTAAAAATGGAATTTT-GAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* *
9534218 TGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
** *
9534276 CAAGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
*
9534335 CAGGGGTAAAATGGTAATTTTTGG
1 CGGGGGTAAAATGGTAATTTTTGG
9534359 AAGTTTCGGG
Statistics
Matches: 499, Mismatches: 44, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
57 67 0.13
58 200 0.40
59 232 0.46
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:9534159 original size:116 final size:118
Alignment explanation
Indices: 9533752--9534358 Score: 913
Period size: 117 Copynumber: 5.2 Consensus size: 118
9533742 TTTGGATTCC
* * * *
9533752 CGGGGGTAAAATGGTAA-TTTTGGTGAAATTGGTGTTAAAAATGGAATTTTGGAAAGTTCTGAGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGG
9533816 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
66 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * ** *
9533869 CGGGGGTAAAATGATAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTAAAAAGTTTGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGG
* ** *
9533934 TAAAATGGTAATTTTTGATGAAATCAAGGTT-AAAATAGAATTTTGGAAAGTT
66 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* **
9533986 CGGGGGTAAAATGGTAATTTTTGGTAAAATCAAGGTTAAAAATGGAATTTTGG-AAGTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGG
*
9534050 TAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAG-AAGTT
66 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * *
9534101 CGGGGGTAAAATGGTAATTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGG
**
9534166 TAAAATGGTAATTTTTGGTGAAATCATGGTTAAAAATGGAATTTT-GAAAGTT
66 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * **
9534218 TGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTCAAGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGG
*
9534282 TAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAGTT
66 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
*
9534335 CAGGGGTAAAATGGTAATTTTTGG
1 CGGGGGTAAAATGGTAATTTTTGG
9534359 AAGTTTCGGG
Statistics
Matches: 440, Mismatches: 45, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
115 53 0.12
116 157 0.36
117 163 0.37
118 67 0.15
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (118 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGG
TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:9534702 original size:162 final size:162
Alignment explanation
Indices: 9534428--9534766 Score: 475
Period size: 162 Copynumber: 2.1 Consensus size: 162
9534418 AGGCATCCAG
* * * * * * *
9534428 CAGTCAAGGGATTAATTTGTAAACCTTGAAAAATTCTTGGGCCAATTTTATGATTAAATAAGAGT
1 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATGCTTGGGCCAATTTTATAATTAAATAAAAGA
* *
9534493 TGATTTGGGGATTAAATTAAAACAAATCCAAAATGTCAGGGACTAAATGAC-TAAATAAGCCAAA
66 TGATTTAGGGATTAAATTAAAACAAATCCAAAATGTCAGGAACTAAAT-ACATAAATAAGCCAAA
* * * **
9534557 AAGTGACACGTGTCAGCCTCTGGTGTAGTCAAA
130 AAGTGACACGTGGCAACCTCTAGTACAGTCAAA
* *
9534590 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATGGTTGGGCCAATTTTGTAATTAAATAAAAGA
1 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATGCTTGGGCCAATTTTATAATTAAATAAAAGA
* *
9534655 TGATTTAGGGATTAAATTAAAACAAAT-TAAAACTGTCAGGAACTAAATACATAAATAATCCAAA
66 TGATTTAGGGATTAAATTAAAACAAATCCAAAA-TGTCAGGAACTAAATACATAAATAAGCCAAA
9534719 AAGTGACACGTGGCAACCTCTAGTACAGTCAAA
130 AAGTGACACGTGGCAACCTCTAGTACAGTCAAA
*
9534752 TAGTCAAAGGACTAA
1 CAGTCAAAGGACTAA
9534767 ATTGAAAGCT
Statistics
Matches: 156, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
161 6 0.04
162 150 0.96
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (162 bp):
CAGTCAAAGGACTAATTTATAAACCTTGAAAAATGCTTGGGCCAATTTTATAATTAAATAAAAGA
TGATTTAGGGATTAAATTAAAACAAATCCAAAATGTCAGGAACTAAATACATAAATAAGCCAAAA
AGTGACACGTGGCAACCTCTAGTACAGTCAAA
Found at i:9537161 original size:17 final size:17
Alignment explanation
Indices: 9537139--9537172 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9537129 CTTACAATAA
*
9537139 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
9537156 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
9537173 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:9543452 original size:21 final size:22
Alignment explanation
Indices: 9543417--9543458 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
9543407 AATTAAAAAA
9543417 AATCACAATTAATTAAACCATT
1 AATCACAATTAATTAAACCATT
* *
9543439 AATCA-AATTGATTACACCAT
1 AATCACAATTAATTAAACCAT
9543459 CAATTTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (22 bp):
AATCACAATTAATTAAACCATT
Found at i:9543600 original size:25 final size:26
Alignment explanation
Indices: 9543543--9543605 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
9543533 GTTAAACCAC
*
9543543 ATTTAACTAAAAAAATAATAAAGATGA
1 ATTTAAC-AAAAAAATAATAAAAATGA
*
9543570 AATTAACAAAAAAAT-ATAAAAAT-A
1 ATTTAACAAAAAAATAATAAAAATGA
*
9543594 TATTTAATAAAA
1 -ATTTAACAAAA
9543606 TATCATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 1 0.03
25 16 0.52
26 8 0.26
27 6 0.19
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (26 bp):
ATTTAACAAAAAAATAATAAAAATGA
Found at i:9548954 original size:63 final size:59
Alignment explanation
Indices: 9548864--9549025 Score: 222
Period size: 58 Copynumber: 2.7 Consensus size: 59
9548854 TTATTTATTT
*
9548864 ATTTATTTATCTATATTCATAAAATAATAAATAAATAATAAAATAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAAT----TTAATATTATTTTAC
* *
9548927 ATTTATTTATTTATATTCATACAATAATAAAT-AATAA-ACAAATTTAATATTATTTTAT
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATA-AAATTTAATATTATTTTAC
9548985 ATTTATTTATTTATATTCATAAAAATAATAAATAAA-AATAA
1 ATTTATTTATTTATATTCAT-AAAATAATAAATAAATAATAA
9549026 CAAGAAAAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
58 34 0.37
59 14 0.15
60 3 0.03
61 1 0.01
62 9 0.10
63 30 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (59 bp):
ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAATTTAATATTATTTTAC
Found at i:9554503 original size:32 final size:32
Alignment explanation
Indices: 9554467--9554528 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
9554457 CAAATATCTA
* *
9554467 GATTTGATTTGTTTCAAATCAATTTGATTTTT
1 GATTTGATTTGATTCAAATCAAATTGATTTTT
* *
9554499 GATTTGATTTGATTCTATTCAAATTGATTT
1 GATTTGATTTGATTCAAATCAAATTGATTT
9554529 AAAGACTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (32 bp):
GATTTGATTTGATTCAAATCAAATTGATTTTT
Found at i:9557941 original size:20 final size:19
Alignment explanation
Indices: 9557880--9557939 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
9557870 ACCAAAATTA
*
9557880 AAAAAGTTCAAAAATAATTTCT
1 AAAAA-TTC-AAAAT-ATTTAT
9557902 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
9557921 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
9557939 A
1 A
9557940 TATATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.19
19 16 0.44
20 5 0.14
21 3 0.08
22 5 0.14
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:9566520 original size:51 final size:51
Alignment explanation
Indices: 9566439--9566624 Score: 273
Period size: 51 Copynumber: 3.6 Consensus size: 51
9566429 GCTATAAACG
9566439 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
9566490 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * * * *
9566541 AAAGGTCTAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
9566592 AAATGGTCCGATGACAAAATGTCATCGTTAGTA
1 AAA-GGTCCGATGACTAAGTGTCATCGTGAGTA
9566625 TTAAATGAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
51 97 0.80
52 24 0.20
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:9577456 original size:2 final size:2
Alignment explanation
Indices: 9577449--9577482 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9577439 AACTACTGAT
9577449 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
9577483 CTTAACTAAG
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:9580398 original size:13 final size:13
Alignment explanation
Indices: 9580380--9580405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9580370 GAGAAGTTAG
9580380 ACTTCGAAATCTC
1 ACTTCGAAATCTC
9580393 ACTTCGAAATCTC
1 ACTTCGAAATCTC
9580406 CCCTCCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
ACTTCGAAATCTC
Found at i:9582822 original size:26 final size:25
Alignment explanation
Indices: 9582764--9582823 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
9582754 TTTCTTTCTC
*
9582764 TTTCTCCTTTCATTTTTAGGTTAGGT
1 TTTCT-CTTTCATTTTTAGGTTAGAT
*
9582790 TTTCTCTTTTATTTTTAGAG-TAGAT
1 TTTCTCTTTCATTTTTAG-GTTAGAT
9582815 TTTACTCTT
1 TTT-CTCTT
9582824 GTAGTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 19 0.63
26 11 0.37
ACGTcount: A:0.15, C:0.13, G:0.12, T:0.60
Consensus pattern (25 bp):
TTTCTCTTTCATTTTTAGGTTAGAT
Found at i:9584713 original size:16 final size:16
Alignment explanation
Indices: 9584694--9584724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9584684 AAAAATCAAA
*
9584694 TTAACCTAAAAATTAT
1 TTAAACTAAAAATTAT
9584710 TTAAACTAAAAATTA
1 TTAAACTAAAAATTA
9584725 ACCAATTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAACTAAAAATTAT
Found at i:9584840 original size:44 final size:44
Alignment explanation
Indices: 9584790--9584884 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
9584780 AGTTATCCTT
*
9584790 ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAATTA
1 ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAACTA
* *
9584834 ATTAACTTCAAAATTCGAGTTTTATTGGGTTAGCTAATTAACTA
1 ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAACTA
9584878 ATTAACT
1 ATTAACT
9584885 AATCGACCAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (44 bp):
ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAACTA
Found at i:9586065 original size:12 final size:13
Alignment explanation
Indices: 9586048--9586076 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
9586038 GCAAGCTCAC
9586048 ATAAAAACA-AAA
1 ATAAAAACACAAA
9586060 ATAAAAACACAAA
1 ATAAAAACACAAA
9586073 ATAA
1 ATAA
9586077 CGAAAAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (13 bp):
ATAAAAACACAAA
Found at i:9587807 original size:1 final size:1
Alignment explanation
Indices: 9587801--9587830 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
9587791 CCAAAGTAAG
9587801 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
9587831 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:9587952 original size:2 final size:2
Alignment explanation
Indices: 9587945--9587985 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9587935 ACAAGCAACC
9587945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9587986 AAAGGTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9590616 original size:4 final size:4
Alignment explanation
Indices: 9590607--9590636 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
9590597 TTTTATATAT
9590607 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
9590637 GTTTATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:9591516 original size:21 final size:22
Alignment explanation
Indices: 9591478--9591520 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
9591468 ATACTTTTCT
*
9591478 AATAATTTAATGATTTTTTAAA
1 AATAATTTAATGAATTTTTAAA
*
9591500 AATAATTT-TTGAATTTTTAAA
1 AATAATTTAATGAATTTTTAAA
9591521 CTTTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
AATAATTTAATGAATTTTTAAA
Found at i:9592039 original size:10 final size:10
Alignment explanation
Indices: 9592013--9592071 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
9592003 ATTCTAATTC
*
9592013 TTTATAAAAA
1 TTTAAAAAAA
9592023 TTATAAAAAAA
1 TT-TAAAAAAA
9592034 TTTAAAAAAA
1 TTTAAAAAAA
*
9592044 TTCTAAAGAATA
1 TT-TAAA-AAAA
*
9592056 TATAAAAAAA
1 TTTAAAAAAA
9592066 TTTAAA
1 TTTAAA
9592072 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
10 20 0.49
11 17 0.41
12 4 0.10
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:9592042 original size:21 final size:21
Alignment explanation
Indices: 9592013--9592071 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
9592003 ATTCTAATTC
*
9592013 TTTATAAAAATTATAAA-AAAA
1 TTTAAAAAAATT-TAAAGAAAA
*
9592034 TTTAAAAAAATTCTAAAGAATA
1 TTTAAAAAAATT-TAAAGAAAA
*
9592056 TATAAAAAAATTTAAA
1 TTTAAAAAAATTTAAA
9592072 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
TTTAAAAAAATTTAAAGAAAA
Found at i:9592670 original size:19 final size:19
Alignment explanation
Indices: 9592624--9592671 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
9592614 TTAACAAATG
9592624 TTTTTATAAAAATATAATAA
1 TTTTT-TAAAAATATAATAA
** * *
9592644 AATATTAAAAATATATTAA
1 TTTTTTAAAAATATAATAA
9592663 TTTTTTAAA
1 TTTTTTAAA
9592672 TATACTTAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTTTAAAAATATAATAA
Found at i:9608800 original size:20 final size:20
Alignment explanation
Indices: 9608770--9608819 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
9608760 ATTAGCATGA
*
9608770 TTTATATTAAGTTTAAATAG-G
1 TTTA-ATTAAGATTAAA-AGTG
9608791 TTTAATTAAGATTAAAAGTG
1 TTTAATTAAGATTAAAAGTG
*
9608811 ATTAATTAA
1 TTTAATTAA
9608820 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (20 bp):
TTTAATTAAGATTAAAAGTG
Found at i:9616800 original size:25 final size:25
Alignment explanation
Indices: 9616753--9616823 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
9616743 ATGTAGAAAC
*
9616753 TCTGT-TTAGCTCGTACGAGCGATAT
1 TCTGTCTTA-CTCGTAAGAGCGATAT
* *
9616778 TTTGTCTTACTCGTAAGATCGATAT
1 TCTGTCTTACTCGTAAGAGCGATAT
** *
9616803 TCTGTCTGGCTCGTGAGAGCG
1 TCTGTCTTACTCGTAAGAGCG
9616824 TTAATCTATC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 34 0.92
26 3 0.08
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (25 bp):
TCTGTCTTACTCGTAAGAGCGATAT
Found at i:9619250 original size:17 final size:18
Alignment explanation
Indices: 9619216--9619251 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9619206 GTAAAATTTA
9619216 ATTTGAAATATAAACTAT
1 ATTTGAAATATAAACTAT
*
9619234 ATTTTAAATAT-AACTAT
1 ATTTGAAATATAAACTAT
9619251 A
1 A
9619252 ACCGTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTTGAAATATAAACTAT
Found at i:9623977 original size:43 final size:43
Alignment explanation
Indices: 9623937--9624020 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
9623927 AAGTGTTTAT
** * *
9623937 GGAGAGTGTGAGCATTCGTGCTACACTTATAGGCAATGTTTTC
1 GGAGAGTGCAAGCATTCATGCTACACTTACAGGCAATGTTTTC
* * *
9623980 GGAGAGTGCAAGTATTCATGCTGCACTTACAGGCAGTGTTT
1 GGAGAGTGCAAGCATTCATGCTACACTTACAGGCAATGTTT
9624021 CAAGAGATCC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (43 bp):
GGAGAGTGCAAGCATTCATGCTACACTTACAGGCAATGTTTTC
Found at i:9624211 original size:15 final size:15
Alignment explanation
Indices: 9624160--9624212 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
9624150 TATCTGCTAT
*
9624160 CTGTTTATATGTGAA
1 CTGTTTATATGCGAA
** *
9624175 CTGTTTACGTGCAAA
1 CTGTTTATATGCGAA
* *
9624190 ATATTTATATGCGAA
1 CTGTTTATATGCGAA
9624205 CTGTTTAT
1 CTGTTTAT
9624213 TTACGAATTC
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (15 bp):
CTGTTTATATGCGAA
Found at i:9625092 original size:3 final size:3
Alignment explanation
Indices: 9625086--9625116 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
9625076 ATTATTATTA
*
9625086 TTG TTG TTG TTG TTG TTA TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
9625117 CCAAGCCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:9625983 original size:166 final size:164
Alignment explanation
Indices: 9625677--9625992 Score: 356
Period size: 166 Copynumber: 1.9 Consensus size: 164
9625667 TTATCTTTTT
* *
9625677 ATCTCTACTAATATTAAGTCATTTACTAAGTTTGGCATCACGACTTGTGACACCATCTCTGTTGG
1 ATCTCTACTAATATTAAGTCATTTACTAAGTTTGGCATCACGACTTGTGACACCATCTCTGCTAG
* * *
9625742 TTAAATTACTAATTAACCTCTTATTTTTTGAAATAAGTTATATTATTAAGATGGAATTTTTATCT
66 TTAAATTACTAATTAACCTCTTATTATTTAAAATAAGTTATACTATTAAGATGGAATTTTTATCT
*
9625807 TTGCATATTTTCGAAGAAAACCTAAAAAAATTAA
131 TTGCATATTTTCAAAGAAAACCTAAAAAAATTAA
* * * *
9625841 ATCTCTACTAATATTAAGTCGTTTACTGAGTTTGGTGA-CACGAGTTAAGTGACACCAAT-T-TA
1 ATCTCTACTAATATTAAGTCATTTACTAAGTTTGG-CATCACGACTT--GTGACACC-ATCTCT-
* * **
9625903 GCTAGTTAAATTAGTAATTAA-CTCTT-TCATATTTAAAATAAGTTTTACTATTGTGAT-GATAT
61 GCTAGTTAAATTACTAATTAACCTCTTAT--TATTTAAAATAAGTTATACTATTAAGATGGA-AT
* ** *
9625965 TTTTATGTTTTTATATTTTTAAAGAAAA
123 TTTTATCTTTGCATATTTTCAAAGAAAA
9625993 TTAATAAAAA
Statistics
Matches: 126, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
164 41 0.33
165 9 0.07
166 74 0.59
167 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (164 bp):
ATCTCTACTAATATTAAGTCATTTACTAAGTTTGGCATCACGACTTGTGACACCATCTCTGCTAG
TTAAATTACTAATTAACCTCTTATTATTTAAAATAAGTTATACTATTAAGATGGAATTTTTATCT
TTGCATATTTTCAAAGAAAACCTAAAAAAATTAA
Found at i:9628980 original size:23 final size:23
Alignment explanation
Indices: 9628954--9629011 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
9628944 TGATGTGGCA
9628954 TCCAGTCAGCAACTTCTAGAAGG
1 TCCAGTCAGCAACTTCTAGAAGG
* *
9628977 TCCAGTCAACAGCTTCTAGAAGG
1 TCCAGTCAGCAACTTCTAGAAGG
*
9629000 TCCAATCAGCAA
1 TCCAGTCAGCAA
9629012 GGATGGACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
TCCAGTCAGCAACTTCTAGAAGG
Found at i:9629858 original size:12 final size:12
Alignment explanation
Indices: 9629841--9629865 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9629831 GATACTTATA
9629841 TTAAATTTCTTT
1 TTAAATTTCTTT
9629853 TTAAATTTCTTT
1 TTAAATTTCTTT
9629865 T
1 T
9629866 CTTTAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAAATTTCTTT
Found at i:9661112 original size:12 final size:12
Alignment explanation
Indices: 9661078--9661137 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
9661068 GAGGCAATTA
9661078 TTTCTTCCTTTTCC
1 TTTCTT-CTTTT-C
9661092 TTCTCTTCTTTTC
1 TT-TCTTCTTTTC
*
9661105 TTTCTTCTTCTC
1 TTTCTTCTTTTC
9661117 TTGT-TTCTTTTC
1 TT-TCTTCTTTTC
*
9661129 CTTCTTCTT
1 TTTCTTCTT
9661138 CCTCTACCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.03
12 24 0.60
13 4 0.10
14 7 0.17
15 4 0.10
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTCTTCTTTTC
Found at i:9661113 original size:15 final size:15
Alignment explanation
Indices: 9661079--9661125 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9661069 AGGCAATTAT
*
9661079 TTCTTCCTTTTCCTTC
1 TTCTT-CTTTTCTTTC
9661095 -TCTTCTTTTCTTTC
1 TTCTTCTTTTCTTTC
* *
9661109 TTCTTCTCTTGTTTC
1 TTCTTCTTTTCTTTC
9661124 TT
1 TT
9661126 TTCCTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (15 bp):
TTCTTCTTTTCTTTC
Found at i:9666414 original size:52 final size:51
Alignment explanation
Indices: 9666230--9666415 Score: 230
Period size: 51 Copynumber: 3.6 Consensus size: 51
9666220 GCTATAAACG
* * *
9666230 AAAGGTTCGGTGACTAAGTGTCATCGTGAGTAAATGAATCTTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** *
9666281 AAAGGTCCGATGACTAAGTGTCATCGTGACCAAAGGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
9666332 AAAAGTCCGATGACTAAGTGTGATCGTGAGTAAATGAATCCATCACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
9666383 AAATGGTCCGATGAC-AATATGTCATCATGAGTA
1 AAA-GGTCCGATGACTAA-GTGTCATCGTGAGTA
9666416 TTAAATAAAA
Statistics
Matches: 115, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
51 93 0.81
52 22 0.19
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:9672103 original size:33 final size:33
Alignment explanation
Indices: 9672022--9672103 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 33
9672012 ATTACCCTAT
* * * **
9672022 TTACTTAAAATAAATAATTTTAGTCAAAATGAAA
1 TTAC-TAAAATAAACAAATTTAATCAAAACAAAA
**
9672056 TTAGGAAAAT-AACAAATTTAATCAAAACAAAA
1 TTACTAAAATAAACAAATTTAATCAAAACAAAA
9672088 TTACTAAAATAAACAA
1 TTACTAAAATAAACAA
9672104 CTTTGACTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
32 25 0.66
33 10 0.26
34 3 0.08
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.28
Consensus pattern (33 bp):
TTACTAAAATAAACAAATTTAATCAAAACAAAA
Found at i:9683777 original size:24 final size:24
Alignment explanation
Indices: 9683716--9683778 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
9683706 TAGAGTAATA
* * *
9683716 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
9683740 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
9683764 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
9683779 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:9685111 original size:18 final size:18
Alignment explanation
Indices: 9685088--9685124 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9685078 ACCTCCTGCA
9685088 ATACCCTATTTACGAGGC
1 ATACCCTATTTACGAGGC
*
9685106 ATACCCTATTTGCGAGGC
1 ATACCCTATTTACGAGGC
9685124 A
1 A
9685125 AAACTGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (18 bp):
ATACCCTATTTACGAGGC
Found at i:9685699 original size:24 final size:24
Alignment explanation
Indices: 9685638--9685700 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
9685628 TAGAGTAATA
* *
9685638 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
9685662 AGAGTTTAATTGAAACACATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
9685686 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
9685701 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:9691459 original size:38 final size:38
Alignment explanation
Indices: 9691417--9691492 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
9691407 TAAGAAAACC
9691417 ACATTCATTTGCAAATAATCCAATTTTCTCCATTTTCA
1 ACATTCATTTGCAAATAATCCAATTTTCTCCATTTTCA
*
9691455 ACATTCATTTGCAAATGATCCAATTTTCTCCATTTTCA
1 ACATTCATTTGCAAATAATCCAATTTTCTCCATTTTCA
9691493 TTTTCATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.42
Consensus pattern (38 bp):
ACATTCATTTGCAAATAATCCAATTTTCTCCATTTTCA
Found at i:9701080 original size:2 final size:2
Alignment explanation
Indices: 9701073--9701107 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
9701063 GGATACCTCT
* *
9701073 TA TA TA TA TA TA TA TA TA TA CA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9701108 GTAACGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9702136 original size:18 final size:18
Alignment explanation
Indices: 9702110--9702146 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9702100 GTAAATTTTA
9702110 ATTTGAAATATAAACTAT
1 ATTTGAAATATAAACTAT
* *
9702128 ATTTTAAATATTAACTAT
1 ATTTGAAATATAAACTAT
9702146 A
1 A
9702147 ACCATTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTTGAAATATAAACTAT
Found at i:9702267 original size:22 final size:22
Alignment explanation
Indices: 9702240--9702286 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
9702230 ACATAAAGAG
9702240 AAAACCTTTGCATTTGAAATTA
1 AAAACCTTTGCATTTGAAATTA
9702262 AAAACCTTTGCATTTGAAATTA
1 AAAACCTTTGCATTTGAAATTA
9702284 AAA
1 AAA
9702287 GCATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (22 bp):
AAAACCTTTGCATTTGAAATTA
Found at i:9705791 original size:18 final size:19
Alignment explanation
Indices: 9705768--9705822 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
9705758 GGAGTCGTGC
*
9705768 ACATGGTCATGA-TGATGG
1 ACATGGTCATGAGTCATGG
9705786 ACATGGTCAT-AGTCATGG
1 ACATGGTCATGAGTCATGG
*
9705804 ACATGGACATG-GTCATGG
1 ACATGGTCATGAGTCATGG
9705822 A
1 A
9705823 GGTGAGGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 32 0.97
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (19 bp):
ACATGGTCATGAGTCATGG
Found at i:9705820 original size:12 final size:12
Alignment explanation
Indices: 9705782--9705822 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
9705772 GGTCATGATG
9705782 ATGGACATGGTC
1 ATGGACATGGTC
* * *
9705794 ATAGTCATGGAC
1 ATGGACATGGTC
9705806 ATGGACATGGTC
1 ATGGACATGGTC
9705818 ATGGA
1 ATGGA
9705823 GGTGAGGATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (12 bp):
ATGGACATGGTC
Found at i:9707329 original size:24 final size:26
Alignment explanation
Indices: 9707302--9707350 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
9707292 TCATCCTTTA
9707302 TTATTATTAT-TTTT-ATT-AATTTGG
1 TTATTATT-TGTTTTAATTAAATTTGG
9707326 TTATTATTTGTTTTAATTAAATTTG
1 TTATTATTTGTTTTAATTAAATTTG
9707351 ATGTTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 1 0.05
24 12 0.55
25 3 0.14
26 6 0.27
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (26 bp):
TTATTATTTGTTTTAATTAAATTTGG
Found at i:9708315 original size:11 final size:13
Alignment explanation
Indices: 9708291--9708325 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
9708281 TTTACTATTT
9708291 ATATATTAATAAA
1 ATATATTAATAAA
9708304 ATAT-TTAA-AAA
1 ATATATTAATAAA
9708315 ATATATTAATA
1 ATATATTAATA
9708326 TTTATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.35
12 8 0.40
13 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATTAATAAA
Found at i:9715736 original size:5 final size:5
Alignment explanation
Indices: 9715705--9715735 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
9715695 GTAGGGTATA
*
9715705 ATTAT ATTAT ATTAT ATTAT ATTAT AATAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
9715736 AAGAATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTAT
Found at i:9717099 original size:36 final size:36
Alignment explanation
Indices: 9717046--9717167 Score: 131
Period size: 36 Copynumber: 3.4 Consensus size: 36
9717036 TCTACTGGAC
* *
9717046 CTTCAACCTCG-CATTCATATGCACGTCGGGGTTGAT
1 CTTCAGCCTCGTC-TTCATGTGCACGTCGGGGTTGAT
* * *
9717082 CTTCAGCGTCGTCTTCATGTGCACATCAGGGTTGAT
1 CTTCAGCCTCGTCTTCATGTGCACGTCGGGGTTGAT
* * *
9717118 CTT-TGACCTCATCTTCATGTGCACGTCGAGGTTGAT
1 CTTCAG-CCTCGTCTTCATGTGCACGTCGGGGTTGAT
*
9717154 CTTCGGCCTCGTCT
1 CTTCAGCCTCGTCT
9717168 CCTCTCTCCA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
35 1 0.01
36 67 0.96
37 2 0.03
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.34
Consensus pattern (36 bp):
CTTCAGCCTCGTCTTCATGTGCACGTCGGGGTTGAT
Found at i:9729129 original size:21 final size:21
Alignment explanation
Indices: 9729082--9729141 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
9729072 AACTATGCAG
**
9729082 ATTTCTACCGATACTTGTACT
1 ATTTCTACCGATACAAGTACT
*
9729103 AGTTCTACCGATACAAGTA-T
1 ATTTCTACCGATACAAGTACT
*
9729123 AATTTCTACCGAAACAAGT
1 -ATTTCTACCGATACAAGT
9729142 CATTCAACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (21 bp):
ATTTCTACCGATACAAGTACT
Found at i:9738793 original size:25 final size:25
Alignment explanation
Indices: 9738765--9738815 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
9738755 AAATAATAGA
9738765 TATCATTATAATAATATTTTTTTAC
1 TATCATTATAATAATATTTTTTTAC
9738790 TATCATTATAATAATATTTTTTTAC
1 TATCATTATAATAATATTTTTTTAC
9738815 T
1 T
9738816 TTAACTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (25 bp):
TATCATTATAATAATATTTTTTTAC
Found at i:9738951 original size:15 final size:16
Alignment explanation
Indices: 9738928--9738969 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
9738918 TTGATTGTTG
*
9738928 AATAAATTTTT-TATA
1 AATATATTTTTATATA
9738943 AATATATTTTTAATATA
1 AATATATTTTT-ATATA
*
9738960 AGTATATTTT
1 AATATATTTT
9738970 CCACCCCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
17 13 0.57
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATATATTTTTATATA
Found at i:9741793 original size:17 final size:19
Alignment explanation
Indices: 9741766--9741800 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9741756 ATATAATTAT
9741766 TATAGGTATAAA-TACAAG
1 TATAGGTATAAACTACAAG
9741784 TATA-GTATAAACTACAA
1 TATAGGTATAAACTACAA
9741801 ATGATACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (19 bp):
TATAGGTATAAACTACAAG
Found at i:9750295 original size:59 final size:60
Alignment explanation
Indices: 9750169--9750299 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
9750159 AAAAAAATTA
* *
9750169 GGTGTTGACCATGCAATGGTCGACACCCTTTTTTAATCTGATTAAAAAATTAAATTTTTG
1 GGTGTTGGCCATGCAATGGTCGACACCCTTTTTTAATCGGATTAAAAAATTAAATTTTTG
* * * ** *
9750229 GGGGTTGGCCATGTAATGGTCGACACTCTTTTTTTGTCGGA-TAAAAAA-TACAATTTTTT
1 GGTGTTGGCCATGCAATGGTCGACACCCTTTTTTAATCGGATTAAAAAATTA-AATTTTTG
*
9750288 TGTGTTGGCCAT
1 GGTGTTGGCCAT
9750300 TGCATGGGCA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 2 0.03
59 24 0.40
60 34 0.57
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (60 bp):
GGTGTTGGCCATGCAATGGTCGACACCCTTTTTTAATCGGATTAAAAAATTAAATTTTTG
Found at i:9750609 original size:63 final size:61
Alignment explanation
Indices: 9750413--9750752 Score: 347
Period size: 62 Copynumber: 5.6 Consensus size: 61
9750403 TTTATCAAAT
* * ** * *
9750413 AAAAAATTT-AA-TTTTTTGGTATTGGTCATGCAATGACCGACA-CCCCTATTTATCTGAT-
1 AAAAAATTTAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCCT-TTTCTCAGATA
* * * * * *
9750471 AAAAAA--TCAATTTTTTGGGTGTTAGTCATGCAATGGCCGACACCCCCTGTTCTCAGATA
1 AAAAAATTTAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCTCAGATA
* *
9750530 AAAAAATTTCAAATTTTTTTGGTGTTGCCCATGCAATGGTCGACACCCCCTTTTCTCAAATA
1 AAAAAATTT-AAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCTCAGATA
9750592 AAAAAATTTTAAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCTCAGATAA
1 AAAAAA-TTT-AAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCTCAGAT-A
** * * ** *
9750656 AAAAAATTTAAATTTTTTTGGTGTTGGTTATGCAATGATTGACACCCCCTTTTTCTTTGGT-
1 AAAAAATTTAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCC-TTTTCTCAGATA
* * *
9750717 AAAATA-TTAAA-TTTTTTGGTGTTGGTCATGTAATGG
1 AAAAAATTTAAATTTTTTTGGTGTTGGCCATGCAATGG
9750753 CTGACATCAA
Statistics
Matches: 243, Mismatches: 29, Indels: 19
0.84 0.10 0.07
Matches are distributed among these distances:
56 1 0.00
57 2 0.01
58 40 0.16
59 33 0.14
60 5 0.02
61 6 0.02
62 86 0.35
63 63 0.26
64 7 0.03
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (61 bp):
AAAAAATTTAAATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCTCAGATA
Found at i:9750643 original size:125 final size:125
Alignment explanation
Indices: 9750479--9750708 Score: 354
Period size: 125 Copynumber: 1.8 Consensus size: 125
9750469 ATAAAAAATC
*
9750479 AATTTTTTGGGTGTTAGTCATGCAATGGCCGACACCCCCTGTTCTCAGAT-AAAAAAATTTCAAA
1 AATTTTTTGGGTGTTAGCCATGCAATGGCCGACACCCCCTGTTCTCAGATAAAAAAAATTT-AAA
*
9750543 TTTTTTTGGTGTTGCCCATGCAATGGTCGACACCCCCTTTTCTCAAATAAAAAAATTTTAA
65 TTTTTTTGGTGTTGCCCATGCAATGATCGACACCCCCTTTTCTCAAATAAAAAAATTTTAA
* * * *
9750604 AATTTTTTTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTCTCAGATAAAAAAAATTTAAAT
1 AATTTTTTGGGTGTTAGCCATGCAATGGCCGACACCCCCTGTTCTCAGATAAAAAAAATTTAAAT
*** *
9750669 TTTTTTGGTGTTGGTTATGCAATGATTGACACCCCCTTTT
66 TTTTTTGGTGTTGCCCATGCAATGATCGACACCCCCTTTT
9750709 TCTTTGGTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 84 0.89
126 10 0.11
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (125 bp):
AATTTTTTGGGTGTTAGCCATGCAATGGCCGACACCCCCTGTTCTCAGATAAAAAAAATTTAAAT
TTTTTTGGTGTTGCCCATGCAATGATCGACACCCCCTTTTCTCAAATAAAAAAATTTTAA
Found at i:9751594 original size:17 final size:17
Alignment explanation
Indices: 9751572--9751623 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
9751562 AAAAATAATT
9751572 ATTAGAATATACAGGAA
1 ATTAGAATATACAGGAA
9751589 ATTAGAA-A-A-A--AA
1 ATTAGAATATACAGGAA
*
9751601 A-TAAAATATACAGGAA
1 ATTAGAATATACAGGAA
9751617 ATTAGAA
1 ATTAGAA
9751624 ATTAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
11 4 0.15
12 4 0.15
13 1 0.04
14 2 0.07
15 1 0.04
16 4 0.15
17 11 0.41
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.21
Consensus pattern (17 bp):
ATTAGAATATACAGGAA
Found at i:9751630 original size:28 final size:28
Alignment explanation
Indices: 9751577--9751660 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
9751567 TAATTATTAG
**
9751577 AATATACAGGAAATTAGAAAAAAAATAA
1 AATATACAGGAAATTAGAAATTAAATAA
9751605 AATATACAGGAAATTAGAAATTAAATTTAA
1 AATATACAGGAAATTAGAAATTAAA--TAA
* * * *
9751635 AATAAAAACGAAATTACAAATTAAAT
1 AATATACAGGAAATTAGAAATTAAAT
9751661 TTAAAAAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.50
30 24 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (28 bp):
AATATACAGGAAATTAGAAATTAAATAA
Found at i:9751638 original size:30 final size:30
Alignment explanation
Indices: 9751577--9751666 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
9751567 TAATTATTAG
**
9751577 AATATACAGGAAATTAGAAA--AAAAATAA
1 AATATACAGGAAATTAGAAATTAAATTTAA
9751605 AATATACAGGAAATTAGAAATTAAATTTAA
1 AATATACAGGAAATTAGAAATTAAATTTAA
* * * *
9751635 AATAAAAACGAAATTACAAATTAAATTTAA
1 AATATACAGGAAATTAGAAATTAAATTTAA
9751665 AA
1 AA
9751667 AGTAAACGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 20 0.37
30 34 0.63
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (30 bp):
AATATACAGGAAATTAGAAATTAAATTTAA
Found at i:9752867 original size:21 final size:20
Alignment explanation
Indices: 9752826--9752887 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
9752816 TTTTAAAAAA
* *
9752826 TTTGAAAATATAAAAATTAT
1 TTTGAAAATAAAAAAAATAT
9752846 TTTGAAAATAGAAAAAAATAT
1 TTTGAAAATA-AAAAAAATAT
* * *
9752867 TATAAAAACTAAAAAATATAT
1 TTTGAAAA-TAAAAAAAATAT
9752888 CTTACATCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 10 0.29
21 23 0.66
22 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
TTTGAAAATAAAAAAAATAT
Found at i:9754306 original size:85 final size:85
Alignment explanation
Indices: 9754053--9754612 Score: 853
Period size: 85 Copynumber: 6.6 Consensus size: 85
9754043 ATTTAAAATC
* * *
9754053 TGATAAAAATTGTAATATAATAATAA-TTGTTGATTTAAATATTTAAATTTAGTAAATAATGTAT
1 TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAACGTAT
9754117 TGTCAAATCAACACATTATT
66 TGTCAAATCAACACATTATT
*
9754137 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAGATAACGTA
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTTATTTAAATATTTAAATTTAGTAAATAACGTA
9754202 TTGTCAAATCAACACATTATT
65 TTGTCAAATCAACACATTATT
9754223 TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAACGTAT
1 TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAACGTAT
9754288 TGTCAAATCAACACATTATT
66 TGTCAAATCAACACATTATT
* *
9754308 TGACAAAAATTGTAATATAATAATAATCTTTTTATTTAAATATTTAAATTTAGTAAATAACGTAT
1 TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAACGTAT
9754373 TGTCAAATCAACACATTATT
66 TGTCAAATCAACACATTATT
* **
9754393 TGATAAAAATTATAATATAATAAT-A-TTTTTTATTTAAATATTTAAATTTAGTAAATAATATAT
1 TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAACGTAT
*
9754456 TGTCAAATCAATACATTATT
66 TGTCAAATCAACACATTATT
* * ** *
9754476 TGATAAAAAATT-TAATATAATAATAA-TTTGTAATTTAAATATGAAAATTT-GATAAATAATGT
1 TGAT-AAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAG-TAAATAACGT
* * *
9754538 ATTGTCAAATGAACATAATATT
64 ATTGTCAAATCAACACATTATT
*
9754560 TGATATAAATTGTAATATAATAATAATTTTTTTTATTTAAATAATATTAAATT
1 TGATAAAAATTGTAATATAATAATAA-TTTTTTTATTTAAAT-AT-TTAAATT
9754613 AATTTTAAAT
Statistics
Matches: 439, Mismatches: 27, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
83 77 0.18
84 100 0.23
85 162 0.37
86 93 0.21
87 2 0.00
88 5 0.01
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (85 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAACGTAT
TGTCAAATCAACACATTATT
Found at i:9754747 original size:16 final size:17
Alignment explanation
Indices: 9754726--9754760 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
9754716 ATTAATTTTC
*
9754726 AAATTAATT-TCAACTT
1 AAATTAATTATCAAATT
9754742 AAATTAATTATCAAATT
1 AAATTAATTATCAAATT
9754759 AA
1 AA
9754761 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTAATTATCAAATT
Found at i:9754773 original size:28 final size:28
Alignment explanation
Indices: 9754716--9754773 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
9754706 AAACATGTTC
* **
9754716 ATTAATTTTCAAATTAATTTCAACTTAA
1 ATTAATTATCAAATTAATTTCAACACAA
**
9754744 ATTAATTATCAAATTAATTTTTACACAA
1 ATTAATTATCAAATTAATTTCAACACAA
9754772 AT
1 AT
9754774 ATTCTTCATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTATCAAATTAATTTCAACACAA
Found at i:9758542 original size:59 final size:59
Alignment explanation
Indices: 9758441--9758576 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 59
9758431 GCCATTATGT
** * *
9758441 GGCCAACACCAAAAAAATTTAATTTTTTACCAAATAAAAAGGGAGTCTCGGCCATGACAC
1 GGCCAACA-CAAAAAAATCGAATTTTTTACCAAACAAAAAGGGAGTCTCGACCATGACAC
* ** * * * * *
9758501 GGCCAACACAAAAAAATCGAATTTTTTATCTGACGAAAAGGGGGTGTCGACCATGGCAT
1 GGCCAACACAAAAAAATCGAATTTTTTACCAAACAAAAAGGGAGTCTCGACCATGACAC
*
9758560 GGCCAACACCAAAAAAT
1 GGCCAACACAAAAAAAT
9758577 TTTGAAATTT
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 55 0.87
60 8 0.13
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (59 bp):
GGCCAACACAAAAAAATCGAATTTTTTACCAAACAAAAAGGGAGTCTCGACCATGACAC
Found at i:9758683 original size:62 final size:61
Alignment explanation
Indices: 9758440--9758722 Score: 249
Period size: 62 Copynumber: 4.7 Consensus size: 61
9758430 GGCCATTATG
* ** * ** * *
9758440 TGGCCAACACCAAAAAAATTT--AA-TTTTTTACCAAATAAAAAGGGAGTCTCGGCCATGACA
1 TGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGA-GAAAAGGG-GGGTCGACCATGGCA
* *
9758500 CGGCCAACA-CAAAAAAA-TCG-AA-TTTTTTATCTGACGAAAAGGGGGTGTCGACCATGGCA
1 TGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGA-GAAAAGGGGG-GTCGACCATGGCA
* * * *** * *
9758559 TGGCCAACACCAAAAAATTTTGAAATTTTTTTATCAGAAAAAAGGATTGTAGGCCATGGCA
1 TGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGGGGTCGACCATGGCA
* * * *
9758620 TGACCAACACCAAAAGAAATTTGAAATTTTTTTATCTGAGAACAGGGGGGTCGCCCATTGCA
1 TGGCCAACACCAAAA-AAATTTGAAATTTTTTTATCTGAGAAAAGGGGGGTCGACCATGGCA
* *
9758682 TGGCTAACA-CAAAAAAATTTAAAATTTTTTTATCTGAGAAA
1 TGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAA
9758723 TGATCGACAC
Statistics
Matches: 180, Mismatches: 36, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
58 2 0.01
59 44 0.24
60 40 0.22
61 32 0.18
62 51 0.28
63 11 0.06
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (61 bp):
TGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGGGGTCGACCATGGCA
Found at i:9758844 original size:60 final size:57
Alignment explanation
Indices: 9758732--9758945 Score: 207
Period size: 58 Copynumber: 3.6 Consensus size: 57
9758722 ATGATCGACA
* * * * *
9758732 CCCAAAAATTTGATTTTTTTATCAGATAAATAAGGGTGTCGGTCATTGCATGGCCAAC
1 CCCAAAAAATTAAATTTTTTATCTGATAAAAAAGGGTGTC-GTCATTGCATGGCCAAC
*
9758790 CCCAAAAAATTAAATTTTTTATCTGATAAAAAAGGGAGTGTCAGTCATTACATGGCCAAC
1 CCCAAAAAATTAAATTTTTTATCTGATAAAAAA-GG-GTGTC-GTCATTGCATGGCCAAC
* **
9758850 ACCCAAAAATTTGATTTTTTTTAT-TAGATTAAAAAAGGGTGTCGATCA-TGCAATGGCCAAC
1 -CCCAAAAAATT-AAATTTTTTATCT-GA-TAAAAAAGGGTGTCG-TCATTGC-ATGGCCAAC
* * * *
9758911 ACAAAAAAATTATATTTTTTATCTGACAAAAAAGG
1 CCCAAAAAATTAAATTTTTTATCTGATAAAAAAGG
9758946 AATGGCCAAC
Statistics
Matches: 131, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
58 36 0.27
59 14 0.11
60 33 0.25
61 28 0.21
62 13 0.10
63 7 0.05
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (57 bp):
CCCAAAAAATTAAATTTTTTATCTGATAAAAAAGGGTGTCGTCATTGCATGGCCAAC
Found at i:9758906 original size:61 final size:59
Alignment explanation
Indices: 9758729--9758930 Score: 191
Period size: 61 Copynumber: 3.4 Consensus size: 59
9758719 GAAATGATCG
* * *
9758729 ACACCCAAAAATTTGA-TTTTTTTATCAGATAAATAAGGGTGTCGGTCATTGC-ATGGCCA
1 ACACCCAAAAATTT-ATTTTTTTTATTAGATAAAAAAGGGTGTCGATCA-TGCAATGGCCA
* ** *
9758788 AC-CCCAAAAAATTAAATTTTTTATCT-GATAAAAAAGGGAGTGTC-AGTCAT-TACATGGCCA
1 ACACCCAAAAATTTATTTTTTTTAT-TAGATAAAAAA-GG-GTGTCGA-TCATGCA-ATGGCCA
9758848 ACACCCAAAAATTTGATTTTTTTTATTAGATTAAAAAAGGGTGTCGATCATGCAATGGCCA
1 ACACCCAAAAATTT-ATTTTTTTTATTAGA-TAAAAAAGGGTGTCGATCATGCAATGGCCA
**
9758909 ACACAAAAAAATTATATTTTTT
1 ACACCCAAAAATT-TATTTTTT
9758931 ATCTGACAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
57 1 0.01
58 26 0.22
59 5 0.04
60 17 0.15
61 45 0.38
62 16 0.14
63 7 0.06
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (59 bp):
ACACCCAAAAATTTATTTTTTTTATTAGATAAAAAAGGGTGTCGATCATGCAATGGCCA
Found at i:9758942 original size:121 final size:119
Alignment explanation
Indices: 9758729--9758945 Score: 337
Period size: 121 Copynumber: 1.8 Consensus size: 119
9758719 GAAATGATCG
* * * *
9758729 ACACCCAAAAATTTGATTTTTTTATCAGATAAATAAGGGTGTCGGTCATTGCATGGCCAACCCCA
1 ACACCCAAAAATTTGATTTTTTTATCAGATAAAAAAGGGTGTCGATCATTGCATGGCCAACACAA
*
9758794 AAAAATTAAATTTTTTATCTGATAAAAAAGGGAGTGTCAGTCATTACATGGCCA
66 AAAAATTAAATTTTTTATCTGACAAAAAAGGGAGTGTCAGTCATTACATGGCCA
*
9758848 ACACCCAAAAATTTGATTTTTTTTATTAGATTAAAAAAGGGTGTCGATCA-TGCAATGGCCAACA
1 ACACCCAAAAATTTGA-TTTTTTTATCAGA-TAAAAAAGGGTGTCGATCATTGC-ATGGCCAACA
*
9758912 CAAAAAAATTATATTTTTTATCTGACAAAAAAGG
63 CAAAAAAATTAAATTTTTTATCTGACAAAAAAGG
9758946 AATGGCCAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
119 16 0.18
120 15 0.17
121 57 0.65
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (119 bp):
ACACCCAAAAATTTGATTTTTTTATCAGATAAAAAAGGGTGTCGATCATTGCATGGCCAACACAA
AAAAATTAAATTTTTTATCTGACAAAAAAGGGAGTGTCAGTCATTACATGGCCA
Found at i:9760498 original size:9 final size:9
Alignment explanation
Indices: 9760480--9760532 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
9760470 ATCAACAAAT
9760480 AATT-TTAA
1 AATTATTAA
9760488 AATTATTAA
1 AATTATTAA
9760497 AATTATT--
1 AATTATTAA
9760504 --TT-TTAA
1 AATTATTAA
9760510 AA-TA-TAA
1 AATTATTAA
9760517 AATTATTAA
1 AATTATTAA
9760526 AATTATT
1 AATTATT
9760533 TTTTTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.16
8 6 0.16
9 21 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:9760504 original size:20 final size:20
Alignment explanation
Indices: 9760476--9760532 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
9760466 TCAAATCAAC
*
9760476 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
9760496 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
9760516 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
9760533 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:9760518 original size:29 final size:31
Alignment explanation
Indices: 9760485--9760557 Score: 132
Period size: 29 Copynumber: 2.4 Consensus size: 31
9760475 CAAATAATTT
9760485 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
9760514 TAAAATTATTAAAATTATTTTTTTAAAATAA
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
9760545 TAAAATTATTAAA
1 TAAAATTATTAAA
9760558 TAATTTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 17 0.40
30 11 0.26
31 14 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAA
Found at i:9760564 original size:30 final size:29
Alignment explanation
Indices: 9760485--9760564 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 29
9760475 CAAATAATTT
*
9760485 TAAAATTATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
*
9760514 TAAAATTATTAAAATTATTTTTTTAAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
9760545 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
9760565 AATTTTTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.22
30 23 0.51
31 12 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:9761728 original size:9 final size:9
Alignment explanation
Indices: 9761716--9761768 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
9761706 TATTTTAAAC
9761716 AATAATTTT
1 AATAATTTT
9761725 AATAATTTT
1 AATAATTTT
9761734 -AT-ATTTT
1 AATAATTTT
9761741 AA-AA----
1 AATAATTTT
9761745 AATAATTTT
1 AATAATTTT
9761754 AATAATTTT
1 AATAATTTT
9761763 AA-AATT
1 AATAATT
9761769 ATTTGTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 5 0.14
8 8 0.22
9 20 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AATAATTTT
Found at i:9761738 original size:29 final size:29
Alignment explanation
Indices: 9761706--9761763 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
9761696 AATATTTAAT
*
9761706 TATTTTAAACAATAATTTTAATAATTTTA
1 TATTTTAAAAAATAATTTTAATAATTTTA
9761735 TATTTTAAAAAATAATTTTAATAATTTTA
1 TATTTTAAAAAATAATTTTAATAATTTTA
9761764 AAATTATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TATTTTAAAAAATAATTTTAATAATTTTA
Found at i:9761750 original size:20 final size:22
Alignment explanation
Indices: 9761725--9761766 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
9761715 CAATAATTTT
9761725 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
9761745 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
9761767 TTATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:9761767 original size:20 final size:20
Alignment explanation
Indices: 9761716--9761772 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
9761706 TATTTTAAAC
9761716 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
9761734 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
9761754 AATAATTTTAAAATTATTT
1 AATAATTTTAAAATAATTT
9761773 GTTGATGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:9762581 original size:3 final size:3
Alignment explanation
Indices: 9762573--9762601 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9762563 AGAAACAACT
9762573 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
9762602 ATAGAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:9763686 original size:6 final size:6
Alignment explanation
Indices: 9763677--9763707 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
9763667 AACTCCAACT
9763677 GCAGTA GCAGTA GCAGTA GCAGTA GCAGTA G
1 GCAGTA GCAGTA GCAGTA GCAGTA GCAGTA G
9763708 GAGATCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (6 bp):
GCAGTA
Found at i:9766169 original size:30 final size:30
Alignment explanation
Indices: 9766133--9766195 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
9766123 ATTTAACAAG
* *
9766133 CAAATGTCTCTCAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATGAA
9766163 CAAATGTCTCTAAAATAATAACAAAATGAA
1 CAAATGTCTCTAAAATAATAACAAAATGAA
9766193 CAA
1 CAA
9766196 TAAAACAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.24
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATGAA
Found at i:9773007 original size:21 final size:21
Alignment explanation
Indices: 9772983--9773032 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
9772973 ACTTTTACTA
*
9772983 ATACAAGTGACAGTTCTACCG
1 ATACAAGTGACACTTCTACCG
*
9773004 ATACAAGTGACTCTTCTACCG
1 ATACAAGTGACACTTCTACCG
*
9773025 AAACAAGT
1 ATACAAGT
9773033 CTTGCTTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (21 bp):
ATACAAGTGACACTTCTACCG
Found at i:9773228 original size:21 final size:21
Alignment explanation
Indices: 9773203--9773242 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9773193 TACCCTGTAT
* *
9773203 TTCTACCGATACATGTATGGG
1 TTCTACCGAAACAAGTATGGG
9773224 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
9773243 CAGAATCTCA
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:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGG
Found at i:9775447 original size:23 final size:23
Alignment explanation
Indices: 9775414--9775471 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
9775404 GGTTGTTAGA
*
9775414 TTTGATGATTTTGTAAAGTAGTT
1 TTTGATGATTTTGTAAAGTAATT
*
9775437 TTTGATTATTTTGTAAAGTAATT
1 TTTGATGATTTTGTAAAGTAATT
9775460 TTTGATGATTTT
1 TTTGATGATTTT
9775472 AATGTTTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (23 bp):
TTTGATGATTTTGTAAAGTAATT
Found at i:9776595 original size:23 final size:23
Alignment explanation
Indices: 9776565--9776645 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
9776555 GTGCTGGGGA
9776565 AAAT-AGTAAGCACACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
* * *
9776587 AAATCAGTAAGCATATATAGTGC
1 AAATCAGTAAGCACACACAGTGC
*
9776610 GAATCAGTAAGCACACACAGTGC
1 AAATCAGTAAGCACACACAGTGC
*
9776633 TGAA-CAGTAAGCA
1 -AAATCAGTAAGCA
9776646 AGCTAATGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 4 0.08
23 43 0.86
24 3 0.06
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (23 bp):
AAATCAGTAAGCACACACAGTGC
Found at i:9778694 original size:191 final size:194
Alignment explanation
Indices: 9778345--9778786 Score: 524
Period size: 191 Copynumber: 2.3 Consensus size: 194
9778335 GATGCTACAC
* * * * *
9778345 GATGGCTAAGGTACCGTATA-TGTTGCGAGTCCTCGACAGCTCATGTGAGTAGCATCGTGAGTTA
1 GATGGCTGAGGTACCGCATACAG-TGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTTA
* * *
9778409 GGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCTATACGATGGCTGAGATTTATGCATAAGT
65 GGAAAAGAGAAAAGAATCCAAGAATGGATTACAGGCTATACGATGGCTGAAATTTATGCATAAAT
* * *
9778474 GCATATTCTCGATAGCTCATGTGAGCAGCATCGTTAGGGAACAA-TTATATGCACAGATACT-TA
130 GCATATTCTCGACAGCTCATATGAGCAGCATCGTTAGGGAACAATTTATA-G-ACAGAGACTGTA
9778537 -T
193 CT
* * *
9778538 CGAT-GCTGAGGTATCGCATATAGTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATTGTGAGTT-
1 -GATGGCTGAGGTACCGCATACAGTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTTA
* * * * * *
9778601 GGAAAAGAGATATGAATCCTA-AATGGATTATAGGTCCTA-A-GATGGCTTAAATTTATGCTTAA
65 GGAAAAGAGAAAAGAATCCAAGAATGGATTACAGG--CTATACGATGGCTGAAATTTATGCATAA
* * *
9778663 ATGCATATTCTCGACAGCTCGTATGAGCAGCATCGTTAGGGGACAGTTTATAGACAGAGACTGTA
128 ATGCATATTCTCGACAGCTCATATGAGCAGCATCGTTAGGGAACAATTTATAGACAGAGACTGTA
9778728 CT
193 CT
* * * *
9778730 GATGGCTGGGGTACCGCATACATTGCGAGTCCTTGACAGCTCGTGTGAGCAACATCG
1 GATGGCTGAGGTACCGCATACAGTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
9778787 GGTACTAGTA
Statistics
Matches: 212, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
190 8 0.04
191 77 0.36
192 70 0.33
193 53 0.25
194 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (194 bp):
GATGGCTGAGGTACCGCATACAGTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTTAG
GAAAAGAGAAAAGAATCCAAGAATGGATTACAGGCTATACGATGGCTGAAATTTATGCATAAATG
CATATTCTCGACAGCTCATATGAGCAGCATCGTTAGGGAACAATTTATAGACAGAGACTGTACT
Found at i:9779510 original size:21 final size:21
Alignment explanation
Indices: 9779480--9779529 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
9779470 TTTTTAGTAC
* * * *
9779480 CGGTAAAAGCATGATTTGTTT
1 CGGTAGAAGCATCACTTGTAT
*
9779501 CGGTAGAAGCTTCACTTGTAT
1 CGGTAGAAGCATCACTTGTAT
9779522 CGGTAGAA
1 CGGTAGAA
9779530 CTGTCATAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (21 bp):
CGGTAGAAGCATCACTTGTAT
Found at i:9779706 original size:2 final size:2
Alignment explanation
Indices: 9779699--9779727 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9779689 ATTATAAATG
9779699 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 T
9779728 TATTAAATCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9783144 original size:8 final size:8
Alignment explanation
Indices: 9783131--9783155 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9783121 TAATATTTAG
9783131 TTGTAATA
1 TTGTAATA
9783139 TTGTAATA
1 TTGTAATA
9783147 TTGTAATA
1 TTGTAATA
9783155 T
1 T
9783156 ATGGAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTAATA
Found at i:9785934 original size:6 final size:6
Alignment explanation
Indices: 9785923--9785947 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9785913 TGAATGATCC
9785923 AATCTT AATCTT AATCTT AATCTT A
1 AATCTT AATCTT AATCTT AATCTT A
9785948 TAGGGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
AATCTT
Found at i:9786613 original size:15 final size:15
Alignment explanation
Indices: 9786575--9786625 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
9786565 ATAAAACGAT
* *
9786575 AATATAAATGAGTAA
1 AATATAAATAATTAA
* * *
9786590 AATGT-AATATTTTA
1 AATATAAATAATTAA
9786604 AATATAAATAATTAA
1 AATATAAATAATTAA
9786619 AATATAA
1 AATATAA
9786626 TATGAGACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:9792916 original size:52 final size:53
Alignment explanation
Indices: 9792838--9792943 Score: 169
Period size: 52 Copynumber: 2.0 Consensus size: 53
9792828 CTGATGCAAT
* * * *
9792838 GTCTTCTATTTGTTAGGAACATTGGCAGTT-TAACTTTGTGCATGGTTCTTGA
1 GTCTTCTATTTATTAGGAACATTGGCAGTTCAAACTTTGTCCACGGTTCTTGA
9792890 GTCTTCTATTTATTAGGAACATTGGCAGTTCAAACTTTGTCCACGGTTCTTGA
1 GTCTTCTATTTATTAGGAACATTGGCAGTTCAAACTTTGTCCACGGTTCTTGA
9792943 G
1 G
9792944 ATGTGAAGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 29 0.59
53 20 0.41
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.42
Consensus pattern (53 bp):
GTCTTCTATTTATTAGGAACATTGGCAGTTCAAACTTTGTCCACGGTTCTTGA
Done.