Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
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 13 of 171
Found at i:6098294 original size:34 final size:33
Alignment explanation
Indices: 6098240--6098325 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 33
6098230 ATTGAAAATA
*
6098240 TACAATATTAATATTATAATAATAAATATTTAT
1 TACAATATAAATATTATAATAATAAATATTTAT
6098273 TACAATTATAAATA-TATTAATAATAAATA-TT-T
1 TACAA-TATAAATATTA-TAATAATAAATATTTAT
* * *
6098305 TATAATATAAATGTTAAAATA
1 TACAATATAAATATTATAATA
6098326 TGTCATAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
31 11 0.24
32 7 0.15
33 9 0.20
34 19 0.41
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (33 bp):
TACAATATAAATATTATAATAATAAATATTTAT
Found at i:6098399 original size:22 final size:22
Alignment explanation
Indices: 6098374--6098416 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
6098364 AATATCTGTA
6098374 TTTTTATTTTTAAGAATTTAATT
1 TTTTTATTTTTAA-AATTTAATT
*
6098397 TTTTTATTTTTTAAATTTAA
1 TTTTTATTTTTAAAATTTAA
6098417 AAATTAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTATTTTTAAAATTTAATT
Found at i:6109533 original size:19 final size:18
Alignment explanation
Indices: 6109487--6109540 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
6109477 TTAAAAAATT
* *
6109487 AAAATATATTTAAATTAT
1 AAAATATATTTTAATTAG
* *
6109505 ATAATTTATTTTAATTACG
1 AAAATATATTTTAATTA-G
*
6109524 AAAATATATTTTTATTA
1 AAAATATATTTTAATTA
6109541 TTTCTCTAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
AAAATATATTTTAATTAG
Found at i:6117185 original size:13 final size:14
Alignment explanation
Indices: 6117158--6117188 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6117148 TTTTATAAAA
6117158 TTATAATTTATTTT
1 TTATAATTTATTTT
*
6117172 TTATATTTTATTTT
1 TTATAATTTATTTT
6117186 TTA
1 TTA
6117189 AAAATTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATAATTTATTTT
Found at i:6118628 original size:31 final size:31
Alignment explanation
Indices: 6118544--6118617 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
6118534 AAAAAAACAT
* * * **
6118544 AATAATTCAGTGACTTAAAT-AAAATTTTCA
1 AATAGTTCAATGACTTAAATGTAAACATTCA
6118574 AATAGTTCAATGACTTAAATGTAAACATTCA
1 AATAGTTCAATGACTTAAATGTAAACATTCA
*
6118605 AATATTTCAATGA
1 AATAGTTCAATGA
6118618 TTATTTTGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (31 bp):
AATAGTTCAATGACTTAAATGTAAACATTCA
Found at i:6119478 original size:20 final size:19
Alignment explanation
Indices: 6119455--6119497 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
6119445 AAAGCTTATT
*
6119455 AAAAATCGTAAAAGATTGTA
1 AAAAATAGTAAAAGATT-TA
*
6119475 AAAAATATTAAAAGATTTA
1 AAAAATAGTAAAAGATTTA
6119494 AAAA
1 AAAA
6119498 TAATATCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (19 bp):
AAAAATAGTAAAAGATTTA
Found at i:6119643 original size:21 final size:21
Alignment explanation
Indices: 6119619--6119661 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6119609 ATATATTCTA
*
6119619 ATATGAATTGAATAA-ATTTTT
1 ATATCAATT-AATAATATTTTT
*
6119640 ATATCAATTTATAATATTTTT
1 ATATCAATTAATAATATTTTT
6119661 A
1 A
6119662 AAATACATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
ATATCAATTAATAATATTTTT
Found at i:6132517 original size:3 final size:3
Alignment explanation
Indices: 6132509--6132534 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6132499 CGACTGTTGA
6132509 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
6132535 CATGTTGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:6141111 original size:30 final size:29
Alignment explanation
Indices: 6141072--6141128 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
6141062 ATTGTTTGGA
*
6141072 TATCAATGGA-ACCGGCAGGAGATCAGTTT
1 TATCAATGGAGAACGG-AGGAGATCAGTTT
*
6141101 TATCATATGGAGAATGGAGGAGATCAGT
1 TATCA-ATGGAGAACGGAGGAGATCAGT
6141129 CTAAGAAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 16 0.67
31 3 0.12
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (29 bp):
TATCAATGGAGAACGGAGGAGATCAGTTT
Found at i:6145901 original size:29 final size:30
Alignment explanation
Indices: 6145842--6145916 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
6145832 ATATTTGGAC
*
6145842 CTCTATATTATAAGAACTGAATCAAACTAAT
1 CTCTATATTATTA-AACTGAATCAAACTAAT
**
6145873 CTCTATATTATTAAA-TGAATCAATTTAAT
1 CTCTATATTATTAAACTGAATCAAACTAAT
* *
6145902 TTTTATATTATTAAA
1 CTCTATATTATTAAA
6145917 AAAAATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 25 0.64
30 2 0.05
31 12 0.31
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (30 bp):
CTCTATATTATTAAACTGAATCAAACTAAT
Found at i:6163573 original size:30 final size:29
Alignment explanation
Indices: 6163538--6163596 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
6163528 TTTTTAATAC
* *
6163538 TTTTAAATAATTGAAATTCTAAAAAATTAT
1 TTTTAAAAAATAGAAATTC-AAAAAATTAT
*
6163568 TTTTAAAAAATAGAAATTCCAAAAATTAT
1 TTTTAAAAAATAGAAATTCAAAAAATTAT
6163597 AAAAATGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTTAAAAAATAGAAATTCAAAAAATTAT
Found at i:6169935 original size:28 final size:28
Alignment explanation
Indices: 6169895--6169951 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
6169885 TCTTTAGTGA
6169895 AGGAGTTAGTTAATTCCATGGTTTTGGT
1 AGGAGTTAGTTAATTCCATGGTTTTGGT
6169923 AGGAGTTAGTTAATTCCATGGTTTTGGT
1 AGGAGTTAGTTAATTCCATGGTTTTGGT
6169951 A
1 A
6169952 TCTCCCCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (28 bp):
AGGAGTTAGTTAATTCCATGGTTTTGGT
Found at i:6177380 original size:24 final size:24
Alignment explanation
Indices: 6177347--6177397 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
6177337 AGGAATAATC
*
6177347 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
6177371 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
6177395 TTT
1 TTT
6177398 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:6177406 original size:24 final size:24
Alignment explanation
Indices: 6177359--6177407 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6177349 TCAGTTAAAC
*
6177359 TCTGTTTATTTGTTTCAATTAAAT
1 TCTGTTTATTTGTTTCAATCAAAT
* *
6177383 TCTGTTTATTTGTTTGAGTCAAAT
1 TCTGTTTATTTGTTTCAATCAAAT
6177407 T
1 T
6177408 TTTATTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.57
Consensus pattern (24 bp):
TCTGTTTATTTGTTTCAATCAAAT
Found at i:6181382 original size:6 final size:6
Alignment explanation
Indices: 6181351--6181396 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
6181341 GGAATGATGG
* *
6181351 AAGGGA AAAGGA AA-GGA AA-GGA AAGGGC AAGGGA AAGGGA AAGGGA
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA
6181397 GAAGATGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.52, C:0.02, G:0.46, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:6183640 original size:20 final size:20
Alignment explanation
Indices: 6183615--6183659 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6183605 AGACGTGAGA
*
6183615 CAAAATTAGTAAAATA-TTTT
1 CAAAATT-GTAAAACATTTTT
*
6183635 CAAAATTTTAAAACATTTTT
1 CAAAATTGTAAAACATTTTT
6183655 CAAAA
1 CAAAA
6183660 AGAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (20 bp):
CAAAATTGTAAAACATTTTT
Found at i:6191141 original size:17 final size:17
Alignment explanation
Indices: 6191121--6191154 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6191111 AATGTAAATT
* *
6191121 TAAAATATATAAATTTA
1 TAAAATAAAAAAATTTA
6191138 TAAAATAAAAAAATTTA
1 TAAAATAAAAAAATTTA
6191155 ATATTGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATAAAAAAATTTA
Found at i:6198028 original size:25 final size:25
Alignment explanation
Indices: 6197999--6198054 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
6197989 ATTTTTTTTA
* *
6197999 ATAATATTATCTTT-AAAATTTAAAT
1 ATAATATTATATTTAAAAATAT-AAT
* *
6198024 ATAATTTTTTATTTAAAAATATAAT
1 ATAATATTATATTTAAAAATATAAT
6198049 ATAATA
1 ATAATA
6198055 AGATAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
ATAATATTATATTTAAAAATATAAT
Found at i:6205800 original size:24 final size:25
Alignment explanation
Indices: 6205748--6205800 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
6205738 ACTATACTAT
*
6205748 TAAATACAAAAATATTATAAACTCA
1 TAAATACAAAAATACTATAAACTCA
*
6205773 -AAATA-AATAAATACTATAAA-TTA
1 TAAATACAA-AAATACTATAAACTCA
6205796 TAAAT
1 TAAAT
6205801 CTAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAATACAAAAATACTATAAACTCA
Found at i:6206163 original size:8 final size:8
Alignment explanation
Indices: 6206150--6206178 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6206140 AATAAATAAA
6206150 AAATTATT
1 AAATTATT
6206158 AAATTATT
1 AAATTATT
6206166 AAA-TATT
1 AAATTATT
6206173 AAATTA
1 AAATTA
6206179 ATATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAATTATT
Found at i:6206172 original size:15 final size:16
Alignment explanation
Indices: 6206154--6206191 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
6206144 AATAAAAAAT
*
6206154 TATTAAATTATTA-AA
1 TATTAAATTAATATAA
6206169 TATTAAATTAATATAA
1 TATTAAATTAATATAA
6206185 TA-TAAAT
1 TATTAAAT
6206192 ATATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTAAATTAATATAA
Found at i:6213954 original size:31 final size:31
Alignment explanation
Indices: 6213916--6213997 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
6213906 AATCTCAAAA
*
6213916 TTATACATGAACTTTAATTTAATGTGCTATT
1 TTATACATGAACTTTAATTTAATGTGCAATT
6213947 TTATACATGAACTTTAATTTAATGTGCAATT
1 TTATACATGAACTTTAATTTAATGTGCAATT
* *
6213978 GTATGCATGAACTTTAATTT
1 TTATACATGAACTTTAATTT
6213998 GATGCAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
TTATACATGAACTTTAATTTAATGTGCAATT
Found at i:6215247 original size:27 final size:25
Alignment explanation
Indices: 6215189--6215260 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
6215179 CAAAGTACTG
* * *
6215189 AACAAAGAGCATATAAGTACTGGGC
1 AACAGAGAGCACATAAGTGCTGGGC
6215214 AACAGAGAGCACATAAGTGCTGGGC
1 AACAGAGAGCACATAAGTGCTGGGC
*
6215239 AACAGAGAGCACACAAAGTGCT
1 AACAGAGAGCACA-TAAGTGCT
6215261 AAACGGAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 35 0.83
26 7 0.17
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.12
Consensus pattern (25 bp):
AACAGAGAGCACATAAGTGCTGGGC
Found at i:6215358 original size:25 final size:23
Alignment explanation
Indices: 6215284--6215409 Score: 155
Period size: 23 Copynumber: 5.3 Consensus size: 23
6215274 ACAAAGTACT
* *
6215284 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAAACAGA
* *
6215307 AAGCACACGAAAGTGCTAATCACAGA
1 GAGCACAC-ACAGTGCTAA--ACAGA
*
6215333 GAGCACGAGAC-GTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAAACAGA
*
6215356 GAGCACACACAGTGCTGAACAGA
1 GAGCACACACAGTGCTAAACAGA
6215379 GAGCACACACAGTGCTAAACAGA
1 GAGCACACACAGTGCTAAACAGA
6215402 GAGCACAC
1 GAGCACAC
6215410 TAGCGTTCCT
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
22 3 0.03
23 59 0.66
24 10 0.11
25 7 0.08
26 10 0.11
27 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.10
Consensus pattern (23 bp):
GAGCACACACAGTGCTAAACAGA
Found at i:6215615 original size:21 final size:21
Alignment explanation
Indices: 6215591--6215631 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6215581 TTTCACCAAT
6215591 TAATTACACAATC-AATATTTA
1 TAATTA-ACAATCTAATATTTA
*
6215612 TAATTAACCATCTAATATTT
1 TAATTAACAATCTAATATTT
6215632 CACCCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATTAACAATCTAATATTTA
Found at i:6221234 original size:134 final size:133
Alignment explanation
Indices: 6221037--6221279 Score: 405
Period size: 134 Copynumber: 1.8 Consensus size: 133
6221027 TACGAACCCG
* * *
6221037 AACATAATAATAAAATTGACATGACAAATACTAAAAAATATTAAATAGTAAGAGAATTTTTTAAT
1 AACATAACAATAAAATTGACATGAAAAATACTAAAAAATATTAAATAGTAAGAGAAATTTTTAAT
** *
6221102 ATATAAAAATTTTCAGGAAAATTATAATATTTTTTATTTTTCTAATACTAATAAAATAGTGGTAA
66 ATATAAAAATTCGCAGGAAAATTATAATATTTTCTATTTTTCTAATACTAATAAAATAGTGGTAA
6221167 GCT
131 GCT
*
6221170 AACATAACAATAAAATTGATATGAAAAATACTAAAAAAATATTAAATAGTAAGAGAAATTTTTAA
1 AACATAACAATAAAATTGACATGAAAAATACT-AAAAAATATTAAATAGTAAGAGAAATTTTTAA
*
6221235 TATATAAAAATTCGCAGGAAAATTATAATATTTTCTGTTTTTCTA
65 TATATAAAAATTCGCAGGAAAATTATAATATTTTCTATTTTTCTA
6221280 CTTGATGTGT
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
133 29 0.29
134 72 0.71
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (133 bp):
AACATAACAATAAAATTGACATGAAAAATACTAAAAAATATTAAATAGTAAGAGAAATTTTTAAT
ATATAAAAATTCGCAGGAAAATTATAATATTTTCTATTTTTCTAATACTAATAAAATAGTGGTAA
GCT
Found at i:6234868 original size:3 final size:3
Alignment explanation
Indices: 6234860--6234885 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6234850 AGAAAGGCAG
6234860 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
6234886 TGAAGGCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:6249846 original size:6 final size:6
Alignment explanation
Indices: 6249835--6249886 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
6249825 GCAAATGTTG
6249835 ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA
1 ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA ATGGTA
6249883 ATGG
1 ATGG
6249887 AAGGTTTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (6 bp):
ATGGTA
Found at i:6252613 original size:12 final size:12
Alignment explanation
Indices: 6252596--6252632 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
6252586 GTTGTCGTGG
*
6252596 TCATCATCATCA
1 TCATCACCATCA
6252608 TCATCACCATCA
1 TCATCACCATCA
*
6252620 CCATCACCATCA
1 TCATCACCATCA
6252632 T
1 T
6252633 ACATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (12 bp):
TCATCACCATCA
Found at i:6255693 original size:23 final size:24
Alignment explanation
Indices: 6255652--6255702 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
6255642 TTCAAACATA
6255652 AAATAATTTTCACCTATAA-AATT
1 AAATAATTTTCACCTATAATAATT
*
6255675 AAATAAATTTTCTCC-ATAATTAATT
1 AAAT-AATTTTCACCTATAA-TAATT
6255700 AAA
1 AAA
6255703 AGATTATAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.33
24 9 0.38
25 7 0.29
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATAATTTTCACCTATAATAATT
Found at i:6260250 original size:23 final size:24
Alignment explanation
Indices: 6260224--6260269 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
6260214 AAAATTTAAA
6260224 ATATAATAC-AATAAAATAAAAAT
1 ATATAATACAAATAAAATAAAAAT
* *
6260247 ATATACTACAAATAGAATAAAAA
1 ATATAATACAAATAAAATAAAAA
6260270 AATTTTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (24 bp):
ATATAATACAAATAAAATAAAAAT
Found at i:6266055 original size:27 final size:28
Alignment explanation
Indices: 6266007--6266061 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
6265997 TTGGGCAATA
6266007 TTAAAATTATTTTTATCCTTTT-AAATT
1 TTAAAATTATTTTTATCCTTTTCAAATT
* *
6266034 TTAAAATTTTATTTTAT-GTTTTCAAATT
1 TTAAAATTAT-TTTTATCCTTTTCAAATT
6266062 ATAGTTAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (28 bp):
TTAAAATTATTTTTATCCTTTTCAAATT
Found at i:6268446 original size:51 final size:51
Alignment explanation
Indices: 6268369--6268482 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
6268359 TGTAAAAAAG
* *
6268369 TTAAAGT-ACACAATGGATAAATATTGA-AAGCTAATTTGTTGGAATCAAGT
1 TTAAAGTGACACAATGGATAAACATTGAGAA-CTAATTTGTTGGAATCAAGA
* * * * *
6268419 TTAAAGTGACATAATGTATAAACATTGAGAATTATTTTTTTGGAATCAAGA
1 TTAAAGTGACACAATGGATAAACATTGAGAACTAATTTGTTGGAATCAAGA
*
6268470 TTAAATTGACACA
1 TTAAAGTGACACA
6268483 GTATGTAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
50 7 0.13
51 44 0.83
52 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (51 bp):
TTAAAGTGACACAATGGATAAACATTGAGAACTAATTTGTTGGAATCAAGA
Found at i:6270697 original size:31 final size:32
Alignment explanation
Indices: 6270640--6270702 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
6270630 GTTATGTTTA
*
6270640 CATTTTTATTTTGATCATCTAA-TTTTTAAAT
1 CATTTTCATTTTGATCATCTAATTTTTTAAAT
6270671 CATTTTCATTTTGATCA-CTAATTTTTTTAAAT
1 CATTTTCATTTTGATCATCTAA-TTTTTTAAAT
6270703 ATTGATTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.14
31 16 0.55
32 9 0.31
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (32 bp):
CATTTTCATTTTGATCATCTAATTTTTTAAAT
Found at i:6274682 original size:8 final size:8
Alignment explanation
Indices: 6274669--6274699 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
6274659 ATTAATTAAA
6274669 AATAAAAT
1 AATAAAAT
6274677 AATAAAAT
1 AATAAAAT
6274685 AATAAAAT
1 AATAAAAT
6274693 AA-AAAAT
1 AATAAAAT
6274700 TCAAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAAAAT
Found at i:6276864 original size:16 final size:17
Alignment explanation
Indices: 6276845--6276876 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6276835 AGAGGATCTC
6276845 AACAGTACC-GAGCTCT
1 AACAGTACCTGAGCTCT
6276861 AACAGTACCTGAGCTC
1 AACAGTACCTGAGCTC
6276877 ACCCAGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (17 bp):
AACAGTACCTGAGCTCT
Found at i:6277727 original size:73 final size:73
Alignment explanation
Indices: 6277636--6277805 Score: 322
Period size: 73 Copynumber: 2.3 Consensus size: 73
6277626 TTTACTTGTT
6277636 GATACAAGTTGTTTAATGAAGAAACCCCGAAAATCTTGAGTATATGTTGATAGTTTAAACAATCA
1 GATACAAGTTGTTTAATGAAGAAACCCCGAAAATCTTGAGTATATGTTGATAGTTTAAACAATCA
6277701 TTTTCTTG
66 TTTTCTTG
6277709 GATACAAGTTGTTTAATGAAGAAACCCCGAAAATCTTGAGTATATGTTGATAGTTTAAACAATCA
1 GATACAAGTTGTTTAATGAAGAAACCCCGAAAATCTTGAGTATATGTTGATAGTTTAAACAATCA
6277774 TTTTCTTG
66 TTTTCTTG
* *
6277782 GATGCAACTTGTTTAATGAAGAAA
1 GATACAAGTTGTTTAATGAAGAAA
6277806 AATTACAAAA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 95 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (73 bp):
GATACAAGTTGTTTAATGAAGAAACCCCGAAAATCTTGAGTATATGTTGATAGTTTAAACAATCA
TTTTCTTG
Found at i:6296011 original size:2 final size:2
Alignment explanation
Indices: 6296004--6296039 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6295994 TTTTGTATTA
6296004 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
6296040 TGTAAAATTT
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:6297277 original size:18 final size:18
Alignment explanation
Indices: 6297254--6297294 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6297244 AATGATTCAA
6297254 ATTTATCATATTTAAAAT
1 ATTTATCATATTTAAAAT
**
6297272 ATTTATTTTATTTAAAAT
1 ATTTATCATATTTAAAAT
*
6297290 TTTTA
1 ATTTA
6297295 AATTTATGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTATCATATTTAAAAT
Found at i:6297379 original size:24 final size:24
Alignment explanation
Indices: 6297341--6297387 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6297331 AATAAAATTT
6297341 TAATTTCTATTAATTTAAATTAAA
1 TAATTTCTATTAATTTAAATTAAA
*
6297365 TAATTTC-ATTCAATTTAATTTAA
1 TAATTTCTATT-AATTTAAATTAA
6297388 TTTAACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATTTCTATTAATTTAAATTAAA
Found at i:6299621 original size:21 final size:21
Alignment explanation
Indices: 6299595--6299637 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6299585 TATTGTAGTT
6299595 TGGTCTTTTATGTATCTGCAA
1 TGGTCTTTTATGTATCTGCAA
6299616 TGGTCTTTTATGTATCTGCAA
1 TGGTCTTTTATGTATCTGCAA
6299637 T
1 T
6299638 CAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (21 bp):
TGGTCTTTTATGTATCTGCAA
Found at i:6320768 original size:14 final size:15
Alignment explanation
Indices: 6320749--6320781 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6320739 CAGCCCACAC
6320749 ATATTA-AATTTTTT
1 ATATTATAATTTTTT
*
6320763 ATATTATTATTTTTT
1 ATATTATAATTTTTT
6320778 ATAT
1 ATAT
6320782 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTATAATTTTTT
Found at i:6321764 original size:17 final size:19
Alignment explanation
Indices: 6321742--6321785 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
6321732 CAAAGCATAG
*
6321742 TAAAAATTAAAAA-AA-AT
1 TAAAAAATAAAAATAATAT
6321759 TAAAAAATAAAAATAATAT
1 TAAAAAATAAAAATAATAT
6321778 TAAAAAAT
1 TAAAAAAT
6321786 GTTTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.50
18 2 0.08
19 10 0.42
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
TAAAAAATAAAAATAATAT
Found at i:6321994 original size:16 final size:15
Alignment explanation
Indices: 6321972--6322016 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
6321962 TGAGTTCTCC
6321972 AAAAATATTTTTTGA
1 AAAAATATTTTTTGA
*
6321987 ACAAAATATGTTTTGA
1 A-AAAATATTTTTTGA
*
6322003 AAAAGTATTTTTTG
1 AAAAATATTTTTTG
6322017 TGTAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (15 bp):
AAAAATATTTTTTGA
Found at i:6325180 original size:37 final size:37
Alignment explanation
Indices: 6325130--6325205 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
6325120 ACTAAGAGAG
*
6325130 GATGCTGTTCTACTTAGAAAGGTGATAGGTTACATTT
1 GATGCTGTTCTACTTAAAAAGGTGATAGGTTACATTT
6325167 GATGCTGTTCTACTTAAAAAGGTGATAGGTTACATTT
1 GATGCTGTTCTACTTAAAAAGGTGATAGGTTACATTT
6325204 GA
1 GA
6325206 GAAGGTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (37 bp):
GATGCTGTTCTACTTAAAAAGGTGATAGGTTACATTT
Found at i:6333056 original size:39 final size:39
Alignment explanation
Indices: 6332928--6333107 Score: 132
Period size: 39 Copynumber: 4.6 Consensus size: 39
6332918 CTCAAGGTCG
* * *
6332928 CTCACCACCTACACAAGCTCATTCACCGCCAACGCAATA
1 CTCACCACCTACACAAGCTCATCCACCACCAACACAATA
* * * * * * * *
6332967 CTCGCCACCCACTCAAACTCATCCGCCACCTACTCAAGGTTG
1 CTCACCACCTACACAAGCTCATCCACCACCAACACAA---TA
* * *
6333009 CACCCCACCTACCCAAGCTCATCCACCACCAACACAATA
1 CTCACCACCTACACAAGCTCATCCACCACCAACACAATA
* * *
6333048 CTCACCACCT--A-TAGCTCATCCTCCACCAAGACAATA
1 CTCACCACCTACACAAGCTCATCCACCACCAACACAATA
* * *
6333084 CCCACCACCCACACAAACTCATCC
1 CTCACCACCTACACAAGCTCATCC
6333108 TCAACCACCC
Statistics
Matches: 106, Mismatches: 29, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
36 30 0.28
38 1 0.01
39 45 0.42
42 30 0.28
ACGTcount: A:0.32, C:0.47, G:0.06, T:0.15
Consensus pattern (39 bp):
CTCACCACCTACACAAGCTCATCCACCACCAACACAATA
Found at i:6333074 original size:36 final size:36
Alignment explanation
Indices: 6333024--6333092 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
6333014 CACCTACCCA
*
6333024 AGCTCATCCACCACCAACACAATACTCACCACCTAT
1 AGCTCATCCACCACCAACACAATACCCACCACCTAT
* *
6333060 AGCTCATCCTCCACCAAGACAATACCCACCACC
1 AGCTCATCCACCACCAACACAATACCCACCACC
6333093 CACACAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.35, C:0.46, G:0.04, T:0.14
Consensus pattern (36 bp):
AGCTCATCCACCACCAACACAATACCCACCACCTAT
Found at i:6333138 original size:24 final size:24
Alignment explanation
Indices: 6333085--6333138 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
6333075 AAGACAATAC
* *
6333085 CCACCACCCACACAAACTCATCCT
1 CCACCACCCACACAAACACATCCA
* *
6333109 CAACCACCCACTCAAACACATCCA
1 CCACCACCCACACAAACACATCCA
6333133 CCACCA
1 CCACCA
6333139 ATGCAATACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.54, G:0.00, T:0.09
Consensus pattern (24 bp):
CCACCACCCACACAAACACATCCA
Found at i:6333161 original size:39 final size:39
Alignment explanation
Indices: 6333112--6333930 Score: 411
Period size: 39 Copynumber: 21.2 Consensus size: 39
6333102 TCATCCTCAA
* *
6333112 CCACCCACTCAAACACATCCACCACCAATGCAATACTCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* *
6333151 CCGCCAACTC-AA-AC-T---CCACCAAGGCAATACCCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * * *
6333184 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCA
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * * *
6333223 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCA
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* *
6333262 CCACCCACTCAAACACATCCACCACCAATGCAATACTCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * * ** *
6333301 CCGCCCACTCAAGGC-CATCCGCCACCAACTCAA-ACTCCT
1 CCACCCACTCAA-ACACATCCACCACCAAGGCAATAC-CCG
* ** * ** *
6333340 CCACCAAGGC--A-ATATCCACCACCAACACAATACTCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * * ** * *
6333376 CCACCCACTCAAGGC-CATCCGCCACCCACTCAAACACATCCA
1 CCACCCACTCAA-ACACATCCACCACCAAGGC-AATAC--CCG
* * *
6333418 CCACCAACTC-AA-AC-TCCTCCACCAAGGCAATACCCA
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * * * ** *
6333454 CCACCAACTCAAGCTCATCCACCACCCACTCAA-ACACATTCA
1 CCACCCACTCAAACACATCCACCACCAAGGCAATAC-C---CG
* * * * * *
6333496 CCACCAACACAATACTC-GCCACCCACTCAA-GC--TCATCCT
1 CCACCCACTCAA-ACACATCCA-CCAC-CAAGGCAAT-ACCCG
* ** * * * *
6333535 CCACCAAGGCAATACCCA-CCACCCATTCAA-GC--TCATCCA
1 CCACCCACTCAA-ACACATCCA-CCA-CCAAGGCAAT-ACCCG
* ** * * * *
6333574 CCACCAAGGCAATACTC-GCCACCCACTCAAGGC--CACCCA
1 CCACCCACTCAA-ACACATCCA-CCAC-CAAGGCAATACCCG
* * ** * * * **
6333613 CCACCCTCACAAATTCATCCTCCACCAAGACAATGCCAA
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* *
6333652 CCACCCACTCAAACACATCCACCACCAATGCAATACTCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * *
6333691 CCACCAACTC-AA-AC-TTCTCCACCAAGGCAATACCCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * *
6333727 CCACCCACTCAAGCTCATCCACCACCAAGGCTATACCCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* *
6333766 CCACCCATTCAAACACATCCACCACCAACGCAATACCCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
** * *
6333805 CCACCTGCTCAAACACATCCACCACCAACGCAATACTCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
*
6333844 CCACCCACTCAAACACATCCACCACCAAGGCAATACTCG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
* * * *
6333883 CCACCCATTCAAACACATCCACCACCAATGCAACACACG
1 CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
6333922 CCACCCACT
1 CCACCCACT
6333931 AAAGGTTGTG
Statistics
Matches: 617, Mismatches: 122, Indels: 82
0.75 0.15 0.10
Matches are distributed among these distances:
33 24 0.04
34 1 0.00
35 1 0.00
36 65 0.11
37 13 0.02
38 21 0.03
39 445 0.72
40 8 0.01
41 1 0.00
42 27 0.04
43 9 0.01
44 2 0.00
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.12
Consensus pattern (39 bp):
CCACCCACTCAAACACATCCACCACCAAGGCAATACCCG
Found at i:6333170 original size:78 final size:74
Alignment explanation
Indices: 6333088--6333312 Score: 206
Period size: 78 Copynumber: 3.0 Consensus size: 74
6333078 ACAATACCCA
6333088 CCACCCACACAAACTCATCCTCAACCACCCACTCAAACACATCCACCACCAATGCAATACTCGCC
1 CCACCCACAC-AA-TCATCC-C-ACCACCCACTCAAACACATCCACCACCAATGCAATACTCGCC
*
6333153 GCCAACTCAAACT
62 GCCCACTCAAACT
* ** * * * * * * * *
6333166 CCACCAAGGCAAT-A-CCCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCC
1 CCACCCACACAATCATCCCACCACCCACTCAAACACATCCACCACCAATGCAATACTCGCCGCCC
*
6333229 ACTCAAGCT
66 ACTCAAACT
*
6333238 -CATCCTC-CACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAATGCAATACTCG
1 CCA-CC-CACA-CAA-TC-AT-CCCACCACCCACTCAAACACATCCACCACCAATGCAATACTCG
6333301 CCGCCCACTCAA
60 CCGCCCACTCAA
6333313 GGCCATCCGC
Statistics
Matches: 114, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
71 2 0.02
72 47 0.41
73 4 0.04
74 2 0.02
75 1 0.01
76 2 0.02
77 2 0.02
78 54 0.47
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (74 bp):
CCACCCACACAATCATCCCACCACCCACTCAAACACATCCACCACCAATGCAATACTCGCCGCCC
ACTCAAACT
Found at i:6333208 original size:21 final size:21
Alignment explanation
Indices: 6333184--6333248 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
6333174 GCAATACCCG
6333184 CCACCCACTCAAGCTCATCCT
1 CCACCCACTCAAGCTCATCCT
* ** * *
6333205 CCACCAAGGCAA--T-ACCCA
1 CCACCCACTCAAGCTCATCCT
6333223 CCACCCACTCAAGCTCATCCT
1 CCACCCACTCAAGCTCATCCT
6333244 CCACC
1 CCACC
6333249 AAGGCAATAC
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 12 0.39
19 1 0.03
20 1 0.03
21 17 0.55
ACGTcount: A:0.28, C:0.52, G:0.06, T:0.14
Consensus pattern (21 bp):
CCACCCACTCAAGCTCATCCT
Found at i:6333259 original size:174 final size:170
Alignment explanation
Indices: 6333013--6333791 Score: 538
Period size: 174 Copynumber: 4.6 Consensus size: 170
6333003 AGGTTGCACC
* * * ** * * *
6333013 CCACCTACCCAAGCTCATCCACCACCAACACAATACTCACCACCTA-T--AGCTCATCCTCCACC
1 CCACCAACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAGCTCATCCACCACC
* * *
6333075 AAGACAATACCCACCACCCACACAAACTCATCCTCAACCACCCACTCAAACACATCCACCACCAA
66 AAGGCAATACCCACCACCCACTCAAACTCA-CC-C-ACCACCCACTCAAACTCATCCACCACCAA
*
6333140 TGCAATACTCGCCGCCAACTCAAACTCCACCAAGGCAATACCCG
128 TGCAATAC-CGCCACCAACTCAAACTCCACCAAGGCAATACCCG
* *
6333184 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAGCTCATCCTCCACC
1 CCACCAACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAGCTCATCCACCACC
* * * * *
6333249 AAGGCAATACCCACCACCCACTCAAACACATCCACCA-CCAATGCAATACTC-GCCGCCCACTCA
66 AAGGCAATACCCACCACCCACTCAAACTCACCCACCACCCACT-CAA-ACTCATCC-ACCAC-CA
* * * *
6333312 AGGCCAT-CCGCCACCAACTCAAACTCCTCCACCAAGGCAATATCCA
127 ATGCAATACCGCCACCAACTCAAA---CTCCACCAAGGCAATACCCG
* * * * * * * *
6333358 CCACCAACACAATACTC-GCCACCCACTCAAGGCCAT--CCGCCACCCACTCAAACACATCCACC
1 CCACCAACTCAA-GCTCATCC-TCCAC-CAAGGCAATACCCACCACCCACTCAAGCTCATCCACC
** * * ** * *
6333420 ACCAACTCAA-ACTCCTCCACCAAGGC-AA-T-ACCCACCACCAACTCAAGCTCATCCACCACCC
63 ACCAAGGCAATAC-CCACCACCCACTCAAACTCACCCACCACCCACTCAAACTCATCCACCA-CC
* * ** *
6333481 ACT-CAA-A----CA-C-ATTC--A--CCACCAACACAATACTCG
126 AATGCAATACCGCCACCAACTCAAACTCCACCAAGGCAATACCCG
* *
6333514 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCATTCAAGCTCATCCACCACC
1 CCACCAACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAGCTCATCCACCACC
* * * * * * *
6333579 AAGGCAATACTCGCCACCCACTCAAGGC-CACCCACCACCCTCACAAATTCATCCTCCACCAA-G
66 AAGGCAATACCCACCACCCACTCAA-ACTCACCCACCACCCACTCAAACTCATCCACCACCAATG
* * * * *
6333642 ACAATGCCAACCACCCACTCAAACACATCCACCACCAATGCAATACTCG
130 -CAATACC-GCCACCAACTC-AA-AC-T---CCACCAAGGCAATACCCG
* *
6333691 CCACCAACTCAAACT--T-CTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCACC
1 CCACCAACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAGCTCATCCACCACC
* * * * *
6333753 AAGGCTATACCCGCCACCCATTCAAACACATCCACCACC
66 AAGGCAATACCCACCACCCACTCAAACTCACCCACCACC
6333792 AACGCAATAC
Statistics
Matches: 471, Mismatches: 90, Indels: 91
0.72 0.14 0.14
Matches are distributed among these distances:
154 8 0.02
155 7 0.01
156 63 0.13
157 3 0.01
158 3 0.01
159 26 0.06
161 1 0.00
163 3 0.01
164 1 0.00
165 4 0.01
166 1 0.00
167 3 0.01
169 2 0.00
170 12 0.03
171 76 0.16
172 13 0.03
173 13 0.03
174 187 0.40
175 8 0.02
176 8 0.02
177 29 0.06
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (170 bp):
CCACCAACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAGCTCATCCACCACC
AAGGCAATACCCACCACCCACTCAAACTCACCCACCACCCACTCAAACTCATCCACCACCAATGC
AATACCGCCACCAACTCAAACTCCACCAAGGCAATACCCG
Found at i:6333266 original size:96 final size:96
Alignment explanation
Indices: 6333166--6333557 Score: 286
Period size: 96 Copynumber: 4.1 Consensus size: 96
6333156 AACTCAAACT
** * *
6333166 CCACCAAGGCAATACCCGCCACCCACTCAAG-CTCATCCTCCACCAAGGCAATACCCACCACCCA
1 CCACCAACTCAATACCCGCCACCCACTCAAGACTCATCCACCACCAACGCAATACCCACCACCCA
6333230 CTCAAGCTCATCCTCCACCAAGGCAATACCCA
66 CTCAA-CTCATCCTCCACCAAGGCAATACCCA
* ** * * * * * * *
6333262 CCACCCACTCAA-ACACATCCACCACCAATGCAATACTC-GCCGCCCACTCAAGGCCAT--CCGC
1 CCACCAACTCAATAC-CCGCCA-C-CCACT-CAAGACTCATCC-ACCAC-CAACGCAATACCCAC
* * *
6333323 CACCAACTCAA-AC-TCCTCCACCAAGGCAATATCCA
60 CACCCACTCAACTCATCCTCCACCAAGGCAATACCCA
* * * * * * *
6333358 CCACCAACACAATACTCGCCACCCACTCAAGGC-CATCCGCCACCCACTCAA-ACACATCCA-CC
1 CCACCAACTCAATACCCGCCACCCACTCAAGACTCATCCACCACCAACGCAATACCCA-CCACCC
6333420 AC-CAACTCAAACTCCTCCACCAAGGCAATACCCA
65 ACTCAACTC--A-TCCTCCACCAAGGCAATACCCA
* * * * * * *
6333454 CCACCAACTCAAGCTCATCCACCACCCACTCAA-ACACATTCACCACCAACACAATACTCGCCAC
1 CCACCAACTCAA--T-ACCCGCCACCCACTCAAGACTCATCCACCACCAACGCAATACCCACCAC
6333518 CCACTCAAGCTCATCCTCCACCAAGGCAATACCCA
63 CCACTCAA-CTCATCCTCCACCAAGGCAATACCCA
6333553 CCACC
1 CCACC
6333558 CATTCAAGCT
Statistics
Matches: 227, Mismatches: 44, Indels: 47
0.71 0.14 0.15
Matches are distributed among these distances:
91 7 0.03
92 10 0.04
93 9 0.04
94 4 0.02
95 3 0.01
96 79 0.35
97 4 0.02
98 6 0.03
99 76 0.33
100 15 0.07
101 11 0.05
102 3 0.01
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (96 bp):
CCACCAACTCAATACCCGCCACCCACTCAAGACTCATCCACCACCAACGCAATACCCACCACCCA
CTCAACTCATCCTCCACCAAGGCAATACCCA
Found at i:6333345 original size:18 final size:19
Alignment explanation
Indices: 6333322--6333525 Score: 98
Period size: 18 Copynumber: 10.6 Consensus size: 19
6333312 AGGCCATCCG
*
6333322 CCACCAACTCAA-ACTCCT
1 CCACCAACTCAATACTCCA
**
6333340 CCACCAAGGCAATA-TCCA
1 CCACCAACTCAATACTCCA
* *
6333358 CCACCAACACAATACT-CG
1 CCACCAACTCAATACTCCA
* ** *
6333376 CCACCCACTCAAGGCCATCCG
1 CCACCAACTCAA-TAC-TCCA
* *
6333397 CCACCCACTCAAACACATCCA
1 CCACCAACTC-AATAC-TCCA
*
6333418 CCACCAACTCAA-ACTCCT
1 CCACCAACTCAATACTCCA
**
6333436 CCACCAAGGCAATAC-CCA
1 CCACCAACTCAATACTCCA
6333454 CCACCAACTCAAGCT-CATCCA
1 CCACCAACTCAA--TAC-TCCA
* * *
6333475 CCACCCACTCAAACACATTCA
1 CCACCAACTC-AATAC-TCCA
* *
6333496 CCACCAACACAATACT-CG
1 CCACCAACTCAATACTCCA
*
6333514 CCACCCACTCAA
1 CCACCAACTCAA
6333526 GCTCATCCTC
Statistics
Matches: 144, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
18 72 0.50
19 9 0.06
20 8 0.06
21 51 0.35
22 4 0.03
ACGTcount: A:0.35, C:0.48, G:0.05, T:0.12
Consensus pattern (19 bp):
CCACCAACTCAATACTCCA
Found at i:6333388 original size:75 final size:75
Alignment explanation
Indices: 6333278--6333420 Score: 232
Period size: 75 Copynumber: 1.9 Consensus size: 75
6333268 ACTCAAACAC
** * * *
6333278 ATCCACCACCAATGCAATACTCGCCGCCCACTCAAGGCCATCCGCCACCAACTCAAACTCCTCCA
1 ATCCACCACCAACACAATACTCGCCACCCACTCAAGGCCATCCGCCACCAACTCAAACACATCCA
6333343 CCAAGGCAAT
66 CCAAGGCAAT
*
6333353 ATCCACCACCAACACAATACTCGCCACCCACTCAAGGCCATCCGCCACCCACTCAAACACATCCA
1 ATCCACCACCAACACAATACTCGCCACCCACTCAAGGCCATCCGCCACCAACTCAAACACATCCA
6333418 CCA
66 CCA
6333421 CCAACTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.32, C:0.48, G:0.08, T:0.12
Consensus pattern (75 bp):
ATCCACCACCAACACAATACTCGCCACCCACTCAAGGCCATCCGCCACCAACTCAAACACATCCA
CCAAGGCAAT
Found at i:6333415 original size:21 final size:20
Alignment explanation
Indices: 6333374--6333431 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
6333364 ACACAATACT
*
6333374 CGCCACCCACTCAAGGCCATC
1 CGCCACCCACTCAA-ACCATC
6333395 CGCCACCCACTCAAACACATC
1 CGCCACCCACTCAAAC-CATC
* *
6333416 CACCACCAACTCAAAC
1 CGCCACCCACTCAAAC
6333432 TCCTCCACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.33, C:0.52, G:0.07, T:0.09
Consensus pattern (20 bp):
CGCCACCCACTCAAACCATC
Found at i:6333438 original size:21 final size:21
Alignment explanation
Indices: 6333391--6333580 Score: 91
Period size: 21 Copynumber: 9.6 Consensus size: 21
6333381 CACTCAAGGC
* * *
6333391 CATCCGCCACCCACTCAAACA
1 CATCCACCACCAACTCAAACT
6333412 CATCCACCACCAACTCAAA--
1 CATCCACCACCAACTCAAACT
* **
6333431 C-TCCTCCACCAAGGC-AA-T
1 CATCCACCACCAACTCAAACT
* *
6333449 -ACCCACCACCAACTCAAGCT
1 CATCCACCACCAACTCAAACT
* *
6333469 CATCCACCACCCACTCAAACA
1 CATCCACCACCAACTCAAACT
* *
6333490 CATTCACCACCAACACAATACT
1 CATCCACCACCAACTCAA-ACT
* *
6333512 C-GCCA-C-CC-ACTCAAGCT
1 CATCCACCACCAACTCAAACT
* **
6333529 CATCCTCCACCAAGGC-AA-T
1 CATCCACCACCAACTCAAACT
* * * *
6333548 -ACCCACCACCCATTCAAGCT
1 CATCCACCACCAACTCAAACT
6333568 CATCCACCACCAA
1 CATCCACCACCAA
6333581 GGCAATACTC
Statistics
Matches: 121, Mismatches: 35, Indels: 26
0.66 0.19 0.14
Matches are distributed among these distances:
17 5 0.04
18 38 0.31
19 7 0.06
20 6 0.05
21 62 0.51
22 3 0.02
ACGTcount: A:0.34, C:0.48, G:0.05, T:0.13
Consensus pattern (21 bp):
CATCCACCACCAACTCAAACT
Found at i:6333520 original size:138 final size:138
Alignment explanation
Indices: 6333112--6333752 Score: 425
Period size: 138 Copynumber: 4.8 Consensus size: 138
6333102 TCATCCTCAA
* * * *
6333112 CCACCCACTCAAACACATCCACCA-CCAATGC-AATAC-T-CGCCGCCAACTCAAA---CTCCAC
1 CCACCCACTCAAGCACATCCACCACCCAAT-CAAACACATCCACCACCAACTCAAACTCCTCCAC
* * ** * * *
6333170 CAAGGCAATACCCGCCACCCACTCAAGCTCATCCTCCACCAAGGC-AATAC--CCACCACCCACT
65 CAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCACCCACACAAACACATCCACCACCAACA
* *
6333232 CAA-GCTCAT
130 CAATACTC-G
* *
6333241 CC-TCCAC-CAAGGCA-ATACCCACCACCCACTCAAACACATCCACCACCAA-TGCAATACTCGC
1 CCACCCACTCAA-GCACAT--CCACCACCCAATCAAACACATCCACCACCAACT-CAA-ACT--C
* * * * * ** *
6333302 CGCCCACTCAAGGCCAT--CCGCCACCAACTCAAACTCCTCCACCA---AGGC--A-ATATCCAC
59 C-TCCAC-CAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCACCCACACAAACACATCCAC
6333359 CACCAACACAATACTCG
122 CACCAACACAATACTCG
* *
6333376 CCACCCACTCAAGGC-CATCCGCCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCAC
1 CCACCCACTCAA-GCACATCCACCACCCAATCAAACACATCCACCACCAACTCAAACTCCTCCAC
* * * *
6333440 CAAGGCAATACCCACCACCAACTCAAGCTCATCCACCACCCACTCAAACACATTCACCACCAACA
65 CAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCACCCACACAAACACATCCACCACCAACA
6333505 CAATACTCG
130 CAATACTCG
* * * * * *
6333514 CCACCCACTCAAGCTCATCCTCCA-CCAAGGCAATACCCA-CCACCCATTCAAGCTC--A-TCCA
1 CCACCCACTCAAGCACATCCACCACCCAA-TCAA-ACACATCCA-CCA-CCAA-CTCAAACTCCT
* * * ** *
6333574 CCACCAAGGCAATACTCGCCACCCACTCAAGGC-CACCCACCACCCTCACAAATTCATCCTCCAC
61 CCACCAAGGCAATACCCGCCACCCACTCAA-GCTCATCCACCACCCACACAAACACATCCACCAC
* * *
6333638 CAAGACAATGC-CAA
125 CAACACAATACTC-G
* * * *
6333652 CCACCCACTCAAACACATCCACCA-CCAATGC-AATAC-T-CGCCACCAACTCAAACTTCTCCAC
1 CCACCCACTCAAGCACATCCACCACCCAAT-CAAACACATCCACCACCAACTCAAACTCCTCCAC
6333713 CAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCACC
65 CAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCACC
6333753 AAGGCTATAC
Statistics
Matches: 408, Mismatches: 59, Indels: 84
0.74 0.11 0.15
Matches are distributed among these distances:
127 5 0.01
128 6 0.01
129 9 0.02
130 16 0.04
131 6 0.01
132 39 0.10
133 5 0.01
134 10 0.02
135 96 0.24
136 10 0.02
137 16 0.04
138 162 0.40
139 14 0.03
140 11 0.03
141 3 0.01
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (138 bp):
CCACCCACTCAAGCACATCCACCACCCAATCAAACACATCCACCACCAACTCAAACTCCTCCACC
AAGGCAATACCCGCCACCCACTCAAGCTCATCCACCACCCACACAAACACATCCACCACCAACAC
AATACTCG
Found at i:6333617 original size:99 final size:96
Alignment explanation
Indices: 6333218--6333702 Score: 444
Period size: 99 Copynumber: 5.0 Consensus size: 96
6333208 CCAAGGCAAT
*
6333218 ACCCACCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCA
1 ACCCACCACCCACTCAA--TCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACTCATCCA
* *
6333283 CCACCAATGCAATACTCGCCGCCCACTCAAGGCC
64 CCACCAAGGCAATACTCGCCACCCACTCAA-GCC
* * * * * * * *
6333317 ATCCGCCACCAACTCAAAC-TCCTCCACCAAGGCAATATCCACCACCAACACAATACTC-GCCAC
1 ACCCACCACCCACTCAATCATCCTCCACCAAGGCAATACCCACCACCCACTCAA-ACTCATCCA-
* *
6333380 CCACTCAAGGCCAT-C-CGCCACCCACTCAAACAC
64 CCAC-CAAGGCAATACTCGCCACCCACTCAAGC-C
* * * * *
6333413 ATCCACCACCAACTCAAAC-TCCTCCACCAAGGCAATACCCACCACCAACTCAAGCTCATCCACC
1 ACCCACCACCCACTCAATCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACTCATCCACC
* ** * * * * *
6333477 ACCCACTCAAACACATTCACCACCAACACAA--T
66 ACCAAGGC-AATAC--TCGCCACCCACTCAAGCC
* * * *
6333509 ACTCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCATTCAAGCTCATCCA
1 ACCCACCACCCACTCAA--TCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACTCATCCA
6333574 CCACCAAGGCAATACTCGCCACCCACTCAAGGCC
64 CCACCAAGGCAATACTCGCCACCCACTCAA-GCC
* * * * * *
6333608 ACCCACCACCCTCACAAATTCATCCTCCACCAAGACAATGCCAACCACCCACTCAAACACATCCA
1 ACCCACCACCCACTC-AA-TCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACTCATCCA
* *
6333673 CCACCAATGCAATACTCGCCACCAACTCAA
64 CCACCAAGGCAATACTCGCCACCCACTCAA
6333703 ACTTCTCCAC
Statistics
Matches: 314, Mismatches: 55, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
94 3 0.01
95 9 0.03
96 127 0.40
97 9 0.03
98 12 0.04
99 152 0.48
100 2 0.01
ACGTcount: A:0.34, C:0.48, G:0.07, T:0.12
Consensus pattern (96 bp):
ACCCACCACCCACTCAATCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACTCATCCACC
ACCAAGGCAATACTCGCCACCCACTCAAGCC
Found at i:6333696 original size:18 final size:18
Alignment explanation
Indices: 6333673--6333731 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
6333663 AACACATCCA
6333673 CCACCAATGCAATACTCG
1 CCACCAATGCAATACTCG
*
6333691 CCACCAACT-CAA-ACTTCT
1 CCACCAA-TGCAATAC-TCG
* *
6333709 CCACCAAGGCAATACCCG
1 CCACCAATGCAATACTCG
6333727 CCACC
1 CCACC
6333732 CACTCAAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.06
18 28 0.85
19 3 0.09
ACGTcount: A:0.32, C:0.46, G:0.08, T:0.14
Consensus pattern (18 bp):
CCACCAATGCAATACTCG
Found at i:6333730 original size:330 final size:329
Alignment explanation
Indices: 6333166--6334032 Score: 875
Period size: 330 Copynumber: 2.6 Consensus size: 329
6333156 AACTCAAACT
* * *
6333166 CCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCAC
1 CCACCAACGCAATACTCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCAT
* * * * * *
6333231 TCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAA-ACACATCCACCACCAATGCA-
66 TCAAGCTCATCCACCACCAAGGCAATACACGCCACCCACTCAAGGC-CATCCACCACC-CTACAC
* * * * * * * *
6333294 ATACTC-GCCGCCCACTCAAGGCCATCCGCCACCAACTC-AA-AC-TCCTCCACCAAGGCAATA-
129 AAACTCATCC-TCCAC-CAAGGCAATCCACCACCCACTCAAACACATCCACCACCAACGCAATAC
* * *
6333354 TCCACCACCAACACAATACTCGCCACCCACTCAAGGCCATCCGCCACCCACTCAAACACATCCAC
192 T-CGCCACCAACTCAATACTC-CCACCCACTCAAGGCAATCCGCCACCCACTCAAACACATCCAC
* * * *
6333419 CACCAA-CTCAAACTCCTCCACCAAGGC-AATAC-CCACCACCAACTCAAGCTCATCCACCACCC
255 CACCAAGCT-AAAC-CCGCCACCAAGGCAAACACACCACCACCAACGCAA--T-ACCCACCACCC
*
6333481 ACTCAAACACATTCA
315 ACTCAAACACATCCA
*
6333496 CCACCAACACAATACTCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCAT
1 CCACCAACGCAATACTCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCAT
* *
6333561 TCAAGCTCATCCACCACCAAGGCAATACTCGCCACCCACTCAAGGCCACCCACCACCCT-CACAA
66 TCAAGCTCATCCACCACCAAGGCAATACACGCCACCCACTCAAGGCCATCCACCACCCTACACAA
* * *
6333625 ATTCATCCTCCACCAAGACAATGCCAACCACCCACTCAAACACATCCACCACCAATGCAATACTC
131 ACTCATCCTCCACCAAGGCAAT-CC-ACCACCCACTCAAACACATCCACCACCAACGCAATACTC
* * * *
6333690 GCCACCAACTCAA-ACT-TC-TCCAC-CAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCA
194 GCCACCAACTCAATACTCCCACCCACTCAAGGCAAT--CCGCCACCCACTCAAACACATCCACCA
* * ** * **
6333751 CCAAGGCTATACCCGCCACCCATTCAAACACATCCACCACCAACGCAATACCCGCCACCTGCTCA
257 CCAA-GCTAAACCCGCCACCAAGGCAAACACA-CCACCACCAACGCAATACCCACCACCCACTCA
6333816 AACACATCCA
320 AACACATCCA
* * * * *
6333826 CCACCAACGCAATACTCGCCACCCACTCAAACACATCCACCACCAAGGCAATACTCGCCACCCAT
1 CCACCAACGCAATACTCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCAT
* * * * * *** ** *
6333891 TCAAACACATCCACCACCAATGCAACACACGCCACCCACTAAAGGTTGTGAACCA-CCTACTCAA
66 TCAAGCTCATCCACCACCAAGGCAATACACGCCACCCACTCAAGGCCATCCACCACCCTACACAA
* * * * *
6333955 GCTCATCCTCCACCAAGGCAATACTCACCTCCCACTCAAACTCATCCACCACCAACACAGTACTC
131 ACTCATCCTCCACCAAGGCAAT-C-CACCACCCACTCAAACACATCCACCACCAACGCAATACTC
*
6334020 GCCACCCACTCAA
194 GCCACCAACTCAA
6334033 GGTCATACAC
Statistics
Matches: 451, Mismatches: 68, Indels: 36
0.81 0.12 0.06
Matches are distributed among these distances:
328 17 0.04
329 18 0.04
330 354 0.78
331 12 0.03
332 7 0.02
333 42 0.09
334 1 0.00
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (329 bp):
CCACCAACGCAATACTCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCAT
TCAAGCTCATCCACCACCAAGGCAATACACGCCACCCACTCAAGGCCATCCACCACCCTACACAA
ACTCATCCTCCACCAAGGCAATCCACCACCCACTCAAACACATCCACCACCAACGCAATACTCGC
CACCAACTCAATACTCCCACCCACTCAAGGCAATCCGCCACCCACTCAAACACATCCACCACCAA
GCTAAACCCGCCACCAAGGCAAACACACCACCACCAACGCAATACCCACCACCCACTCAAACACA
TCCA
Found at i:6333907 original size:21 final size:21
Alignment explanation
Indices: 6333766--6333908 Score: 70
Period size: 21 Copynumber: 7.2 Consensus size: 21
6333756 GCTATACCCG
*
6333766 CCACCCATTCAAACACATCCA
1 CCACCCACTCAAACACATCCA
* * * *
6333787 CCACCAACGC-AATAC--CCG
1 CCACCCACTCAAACACATCCA
**
6333805 CCACCTGCTCAAACACATCCA
1 CCACCCACTCAAACACATCCA
* * * *
6333826 CCACCAACGC-AATAC-T-CG
1 CCACCCACTCAAACACATCCA
6333844 CCACCCACTCAAACACATCCA
1 CCACCCACTCAAACACATCCA
* ** * *
6333865 CCACCAAGGC-AATAC-T-CG
1 CCACCCACTCAAACACATCCA
*
6333883 CCACCCATTCAAACACATCCA
1 CCACCCACTCAAACACATCCA
6333904 CCACC
1 CCACC
6333909 AATGCAACAC
Statistics
Matches: 84, Mismatches: 29, Indels: 18
0.64 0.22 0.14
Matches are distributed among these distances:
18 26 0.31
19 14 0.17
20 14 0.17
21 30 0.36
ACGTcount: A:0.35, C:0.48, G:0.06, T:0.11
Consensus pattern (21 bp):
CCACCCACTCAAACACATCCA
Found at i:6333907 original size:291 final size:291
Alignment explanation
Indices: 6333112--6333910 Score: 837
Period size: 291 Copynumber: 2.8 Consensus size: 291
6333102 TCATCCTCAA
* * * * *
6333112 CCACCCACTCAAACACATCCACCACCAATGCAATACT-CGCCGCCAACTC-A-A---A-CTCCAC
1 CCACCAACTCAAACACATCCACCACCAACGCAA-ACTCCGCCACCAACGCAATACCCACCACCAC
* * * * * *
6333170 CAAGGCAATACCCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAA
65 CAAGGCTATACCCGCCACCCACTCAAACACATCCACCACCAACGCAATACCCGCCACCCACTCAA
*
6333235 GCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAATGCAATACTC
130 GCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAGGCAATACTC
* * * * *
6333300 GCCGCCCACTCAAGGCCATCCGCCACCAACTCAAACTCCTCCACCAAGGCAATATCCACCACCAA
195 GCCACCCACTCAAGGCCATCCACCACCAACACAAACTCCTCCACCAAGACAATAGCCACCACCAA
* *
6333365 CACAATACTCGCCACCCACTCAAGGCCATCCG
260 CACAATACACGCCACCCACTCAAGGCAATCCG
* * * *
6333397 CCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACCAAGGCAATACCCACCACCAAC
1 CCACCAACTCAAACACATCCACCACCAACGCAAACTCCGCCACCAACGCAATACCCACCACC-AC
* * * *
6333462 TCAA-GCTCAT--CCACCACCCACTCAAACACATTCACCACCAACACAATACTCGCCACCCACTC
65 -CAAGGCT-ATACCCGCCACCCACTCAAACACATCCACCACCAACGCAATACCCGCCACCCACTC
* * *
6333524 AAGCTCATCCTCCACCAAGGCAATACCCACCACCCATTCAAGCTCATCCACCACCAAGGCAATAC
128 AAGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAGGCAATAC
* **
6333589 TCGCCACCCACTCAAGGCCACCCACCACCCTCACAAATTCATCCTCCACCAAGACAAT-GCCAAC
193 TCGCCACCCACTCAAGGCCATCCACCACCAACACAAA--C-TCCTCCACCAAGACAATAGCC-AC
* * * *
6333653 CACCCACTCAA-ACACATCCA-CCAC-CAATGCAATACTCG
254 CACCAACACAATACAC-GCCACCCACTCAAGGCAAT-C-CG
* * * * * * *
6333691 CCACCAACTC-AA-AC-TTCTCCACCAAGGCAATAC-CCGCCACCCACTCAA-GCTCATCCACCA
1 CCACCAACTCAAACACATCCACCACCAACGCAA-ACTCCGCCACCAACGCAATACCCA-CCACCA
* **
6333751 CCAAGGCTATACCCGCCACCCATTCAAACACATCCACCACCAACGCAATACCCGCCACCTGCTCA
64 CCAAGGCTATACCCGCCACCCACTCAAACACATCCACCACCAACGCAATACCCGCCACCCACTCA
* * * * * *
6333816 AACACATCCACCACCAACGCAATACTCGCCACCCACTCAAACACATCCACCACCAAGGCAATACT
129 AGCTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAGGCAATACT
* *
6333881 CGCCACCCATTCAA-ACACATCCACCACCAA
194 CGCCACCCACTCAAGGC-CATCCACCACCAA
6333911 TGCAACACAC
Statistics
Matches: 424, Mismatches: 67, Indels: 40
0.80 0.13 0.08
Matches are distributed among these distances:
284 3 0.01
285 39 0.09
286 1 0.00
287 1 0.00
289 5 0.01
290 10 0.02
291 291 0.69
292 15 0.04
293 18 0.04
294 41 0.10
ACGTcount: A:0.34, C:0.47, G:0.07, T:0.12
Consensus pattern (291 bp):
CCACCAACTCAAACACATCCACCACCAACGCAAACTCCGCCACCAACGCAATACCCACCACCACC
AAGGCTATACCCGCCACCCACTCAAACACATCCACCACCAACGCAATACCCGCCACCCACTCAAG
CTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAGGCAATACTCG
CCACCCACTCAAGGCCATCCACCACCAACACAAACTCCTCCACCAAGACAATAGCCACCACCAAC
ACAATACACGCCACCCACTCAAGGCAATCCG
Found at i:6333992 original size:39 final size:39
Alignment explanation
Indices: 6333942--6334191 Score: 148
Period size: 39 Copynumber: 6.3 Consensus size: 39
6333932 AAGGTTGTGA
* * **
6333942 ACCACCTACTCAAGCTCATCCTCCACCAAGGCAATACTC
1 ACCACCCACTCAAGCTCATCCACCACCAACACAATACTC
* * *
6333981 ACCTCCCACTCAAACTCATCCACCACCAACACAGTACTC
1 ACCACCCACTCAAGCTCATCCACCACCAACACAATACTC
* * * * * *
6334020 GCCACCCACTCAAGGTCATACACCACCTACTCAA-GCTC
1 ACCACCCACTCAAGCTCATCCACCACCAACACAATACTC
* * * * * *
6334058 ATCCA-CCAC-CAACGCAACATTCACCGCCCACTCAAGGTCACAC
1 A-CCACCCACTCAA-GC-TCATCCACCACCAACACAA--T-ACTC
* * * **
6334101 GCCACCTACTCAAGTTCATCCACCACCAAGTCAATACTC
1 ACCACCCACTCAAGCTCATCCACCACCAACACAATACTC
* * * *
6334140 GCCGCCCACTCAAAG-TCATCCAACACCAACGCAATACTC
1 ACCACCCACTC-AAGCTCATCCACCACCAACACAATACTC
*
6334179 ACCACCTACTCAA
1 ACCACCCACTCAA
6334192 ATTCATCCGC
Statistics
Matches: 160, Mismatches: 41, Indels: 21
0.72 0.18 0.09
Matches are distributed among these distances:
37 3 0.02
38 10 0.06
39 117 0.73
40 4 0.03
42 17 0.11
43 6 0.04
44 3 0.02
ACGTcount: A:0.32, C:0.45, G:0.08, T:0.16
Consensus pattern (39 bp):
ACCACCCACTCAAGCTCATCCACCACCAACACAATACTC
Found at i:6334045 original size:21 final size:21
Alignment explanation
Indices: 6334021--6334127 Score: 85
Period size: 21 Copynumber: 5.2 Consensus size: 21
6334011 ACAGTACTCG
6334021 CCACCCACTCAAGGTCATACA
1 CCACCCACTCAAGGTCATACA
* * *
6334042 CCACCTACTCAAGCTCATCCA
1 CCACCCACTCAAGGTCATACA
* * *
6334063 CCACCAACGCAA---CATTCA
1 CCACCCACTCAAGGTCATACA
* * *
6334081 CCGCCCACTCAAGGTCACACG
1 CCACCCACTCAAGGTCATACA
* * *
6334102 CCACCTACTCAAGTTCATCCA
1 CCACCCACTCAAGGTCATACA
6334123 CCACC
1 CCACC
6334128 AAGTCAATAC
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
18 14 0.22
21 51 0.78
ACGTcount: A:0.30, C:0.47, G:0.08, T:0.15
Consensus pattern (21 bp):
CCACCCACTCAAGGTCATACA
Found at i:6334052 original size:60 final size:60
Alignment explanation
Indices: 6333988--6334184 Score: 216
Period size: 60 Copynumber: 3.3 Consensus size: 60
6333978 CTCACCTCCC
* *
6333988 ACTCAAACTCATCCACCACCAACACAGTACTCGCCACCCACTCAAGGTCATACACCACCT
1 ACTCAAACTCATCCACCACCAACACAATACTCGCCGCCCACTCAAGGTCATACACCACCT
* * * * * * *
6334048 ACTCAAGCTCATCCACCACCAACGCAACATTCACCGCCCACTCAAGGTCACACGCCACCT
1 ACTCAAACTCATCCACCACCAACACAATACTCGCCGCCCACTCAAGGTCATACACCACCT
** ** * * * *
6334108 ACTCAAGTTCATCCACCACCAAGTCAATACTCGCCGCCCACTCAAAGTCATCCAACACCA
1 ACTCAAACTCATCCACCACCAACACAATACTCGCCGCCCACTCAAGGTCATACACCACCT
*
6334168 ACGCAATACTCA-CCACC
1 ACTCAA-ACTCATCCACC
6334185 TACTCAAATT
Statistics
Matches: 112, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
60 109 0.97
61 3 0.03
ACGTcount: A:0.32, C:0.45, G:0.08, T:0.15
Consensus pattern (60 bp):
ACTCAAACTCATCCACCACCAACACAATACTCGCCGCCCACTCAAGGTCATACACCACCT
Found at i:6334106 original size:99 final size:99
Alignment explanation
Indices: 6333844--6334092 Score: 284
Period size: 99 Copynumber: 2.5 Consensus size: 99
6333834 GCAATACTCG
* * * * * * * * *
6333844 CCACCCACTCAAACACATCCACCACCAAGGCAATACTCGCCACCCATTCAAACACATCCACCACC
1 CCACCTACTCAAGCTCATCCACCACCAACGCAACACTCACCGCCCACTCAAACTCATCCACCACC
** ** * **
6333909 AATGCAACACACGCCACCCACTAAAGGTTGTGAA
66 AACACAGTACTCGCCACCCACTAAAGGTCATGAA
* * * *
6333943 CCACCTACTCAAGCTCATCCTCCACCAAGGCAATACTCACCTCCCACTCAAACTCATCCACCACC
1 CCACCTACTCAAGCTCATCCACCACCAACGCAACACTCACCGCCCACTCAAACTCATCCACCACC
*
6334008 AACACAGTACTCGCCACCCACTCAAGGTCAT-ACA
66 AACACAGTACTCGCCACCCACTAAAGGTCATGA-A
*
6334042 CCACCTACTCAAGCTCATCCACCACCAACGCAACATTCACCGCCCACTCAA
1 CCACCTACTCAAGCTCATCCACCACCAACGCAACACTCACCGCCCACTCAA
6334093 GGTCACACGC
Statistics
Matches: 128, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
98 1 0.01
99 127 0.99
ACGTcount: A:0.33, C:0.45, G:0.08, T:0.14
Consensus pattern (99 bp):
CCACCTACTCAAGCTCATCCACCACCAACGCAACACTCACCGCCCACTCAAACTCATCCACCACC
AACACAGTACTCGCCACCCACTAAAGGTCATGAA
Found at i:6345638 original size:173 final size:169
Alignment explanation
Indices: 6345346--6345670 Score: 497
Period size: 173 Copynumber: 1.9 Consensus size: 169
6345336 ATTATTTGAC
* **
6345346 TCGAGTTTTTTGAGTTAAACGAATTAAATTAAATTTTTTTCGAATTTTGAGTTCGAATCGAGTTG
1 TCGAGTTTTTCGAGTTAAACGAATTAAATTAAATTTTTTTCGAATTTCAAGTTCGAATCGAGTTG
* * *
6345411 AATTTTCGAATTTGAATAATTCGATTAAACCGAATAAAATTATATTACTTTTAATTTCAAATTTA
66 AATTTTCGAATTCGAATAATTCGAATAAACCGAATAAAACTATATTACTTTTAATTTCAAATTTA
6345476 TATTACCCAAACTCAAATATTAATTTCAAATTATTCGGA
131 TATTACCCAAACTCAAATATTAATTTCAAATTATTCGGA
* * *
6345515 TCGAGTTTTTCGAGTTAAACGAATTAAGTTGAATTTTTTTTTTTCGAATTTCAAGTTTGAATCGA
1 TCGAGTTTTTCGAGTTAAACGAATTAAATT-AA---ATTTTTTTCGAATTTCAAGTTCGAATCGA
* **
6345580 GTTGAATTTTCGAATTCGAATAATTCGAATAAACCGAATAAAACTATATTATTTTTAATTTTTAA
62 GTTGAATTTTCGAATTCGAATAATTCGAATAAACCGAATAAAACTATATTACTTTTAATTTCAAA
*
6345645 TTTATTTTACCCAAACTCAAATATTA
127 TTTATATTACCCAAACTCAAATATTA
6345671 TTATTTTACC
Statistics
Matches: 139, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
169 28 0.20
170 2 0.01
173 109 0.78
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (169 bp):
TCGAGTTTTTCGAGTTAAACGAATTAAATTAAATTTTTTTCGAATTTCAAGTTCGAATCGAGTTG
AATTTTCGAATTCGAATAATTCGAATAAACCGAATAAAACTATATTACTTTTAATTTCAAATTTA
TATTACCCAAACTCAAATATTAATTTCAAATTATTCGGA
Found at i:6346042 original size:34 final size:34
Alignment explanation
Indices: 6345997--6346078 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
6345987 TAAATTAAAT
*
6345997 CCAAATGTTTTTTATTTTTTACCTTTTA-TCTTAC
1 CCAAATATTTTTTATTTTTTACCTTTTACT-TTAC
* *
6346031 CCAAATATTTTTAATTTTTTATCTTTTACTTTAC
1 CCAAATATTTTTTATTTTTTACCTTTTACTTTAC
*
6346065 CCAAATATTGTTTA
1 CCAAATATTTTTTA
6346079 ATTGGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 41 0.98
35 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (34 bp):
CCAAATATTTTTTATTTTTTACCTTTTACTTTAC
Found at i:6348161 original size:21 final size:21
Alignment explanation
Indices: 6348135--6348216 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 21
6348125 TTTTGAATTG
* *
6348135 ATTGTTTATATATTTAAATCA
1 ATTGTTTATATGTTGAAATCA
*
6348156 ATTG--T-TATGTTGGAAT--
1 ATTGTTTATATGTTGAAATCA
*
6348172 ACTGTTTAT-T-TTG-AATCA
1 ATTGTTTATATGTTGAAATCA
*
6348190 ATTGTTTATATGTTTAAATCA
1 ATTGTTTATATGTTGAAATCA
6348211 ATTGTT
1 ATTGTT
6348217 ATGTAGCACG
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
16 6 0.13
17 3 0.06
18 18 0.38
19 3 0.06
20 2 0.04
21 15 0.32
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.52
Consensus pattern (21 bp):
ATTGTTTATATGTTGAAATCA
Found at i:6348170 original size:55 final size:55
Alignment explanation
Indices: 6348101--6348220 Score: 177
Period size: 55 Copynumber: 2.2 Consensus size: 55
6348091 CCCAAAATTG
* * **
6348101 ATTGTTATGATGGAATACTACTTGTTTTGAATTGATTGTTTATATATTTAAATCA
1 ATTGTTATGTTGGAATACTACTTATTTTGAATCAATTGTTTATATATTTAAATCA
** *
6348156 ATTGTTATGTTGGAATACTGTTTATTTTGAATCAATTGTTTATATGTTTAAATCA
1 ATTGTTATGTTGGAATACTACTTATTTTGAATCAATTGTTTATATATTTAAATCA
6348211 ATTGTTATGT
1 ATTGTTATGT
6348221 AGCACGTCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (55 bp):
ATTGTTATGTTGGAATACTACTTATTTTGAATCAATTGTTTATATATTTAAATCA
Found at i:6354547 original size:27 final size:28
Alignment explanation
Indices: 6354476--6354550 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
6354466 CAAATAATTT
* *
6354476 TAAAATTTTTAGAATTATTTTTTTTAAATA
1 TAAAATTATTAAAATTA--TTTTTTAAATA
*
6354506 TAAAATTATTAAAATTATTTTTTGAAT-
1 TAAAATTATTAAAATTATTTTTTAAATA
6354533 TAATAATTATT-AAATTAT
1 TAA-AATTATTAAAATTAT
6354551 AATATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.24
28 16 0.39
30 15 0.37
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTTAAATA
Found at i:6355201 original size:25 final size:25
Alignment explanation
Indices: 6355171--6355223 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
6355161 GTTGTTTTAT
6355171 TTTTATATATT-T-ATTATTTTAAATA
1 TTTTATA-ATTATAATT-TTTTAAATA
*
6355196 TTTTATAATTATAATTTTTTTAATA
1 TTTTATAATTATAATTTTTTAAATA
6355221 TTT
1 TTT
6355224 AAAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 3 0.12
25 19 0.76
26 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTATAATTATAATTTTTTAAATA
Found at i:6355587 original size:22 final size:23
Alignment explanation
Indices: 6355557--6355611 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
6355547 ATTCAATCAT
* *
6355557 TATTTTAAATATTTAAAAATT-A
1 TATTATAAATATTAAAAAATTAA
6355579 TATTATAAAATATTAAAAAATTAA
1 TATTAT-AAATATTAAAAAATTAA
*
6355603 AATTATAAA
1 TATTATAAA
6355612 AATAAAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 17 0.61
24 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATTATAAATATTAAAAAATTAA
Found at i:6355597 original size:23 final size:24
Alignment explanation
Indices: 6355563--6355612 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
6355553 TCATTATTTT
* *
6355563 AAATATTTAAAAATT-ATATTATA
1 AAATATTAAAAAATTAAAATTATA
6355586 AAATATTAAAAAATTAAAATTATA
1 AAATATTAAAAAATTAAAATTATA
6355610 AAA
1 AAA
6355613 ATAAAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATATTAAAAAATTAAAATTATA
Found at i:6361261 original size:17 final size:17
Alignment explanation
Indices: 6361231--6361264 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6361221 TAGCTTTAAG
6361231 GTTGAATTTAATCTAAA
1 GTTGAATTTAATCTAAA
6361248 GTTG-ATTTATATCTAAA
1 GTTGAATTTA-ATCTAAA
6361265 TAGATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
GTTGAATTTAATCTAAA
Found at i:6371700 original size:25 final size:23
Alignment explanation
Indices: 6371672--6371724 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
6371662 AGCACGTCTC
6371672 GTGCTATCTGTTATTAGCACTGCGT
1 GTGCTATCTG--ATTAGCACTGCGT
* **
6371697 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTATCTGATTAGCACTGCGT
6371720 GTGCT
1 GTGCT
6371725 CAGTACTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
25 9 0.36
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.42
Consensus pattern (23 bp):
GTGCTATCTGATTAGCACTGCGT
Found at i:6371759 original size:23 final size:23
Alignment explanation
Indices: 6371724--6371817 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
6371714 CTTTGTGTGC
*
6371724 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
6371747 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
*
6371770 TACCCAACACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
*
6371795 TCAGTACTTTG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
6371817 T
1 T
6371818 TGTTCCGTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 2 0.03
22 15 0.26
23 21 0.36
25 9 0.16
26 6 0.10
27 4 0.07
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:6373793 original size:5 final size:5
Alignment explanation
Indices: 6373783--6373811 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
6373773 TCGACTAAAC
6373783 TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
6373812 AAAAATTTCA
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:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (5 bp):
TCGAT
Found at i:6376406 original size:2 final size:2
Alignment explanation
Indices: 6376401--6376443 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6376391 GCAAAAAAGA
6376401 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6376443 A
1 A
6376444 AAGGCTAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6413250 original size:23 final size:22
Alignment explanation
Indices: 6413224--6413285 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
6413214 TTAATAATCC
6413224 AATAATTTAAATAAAATTTTTT
1 AATAATTTAAATAAAATTTTTT
* *
6413246 AAATAA-TTCAATAATTATTTTTT
1 -AATAATTTAAATAA-AATTTTTT
*
6413269 -ATAATTTAATTAAAATT
1 AATAATTTAAATAAAATT
6413286 AAAGGACTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 7 0.22
22 13 0.41
23 12 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATAATTTAAATAAAATTTTTT
Found at i:6415670 original size:22 final size:20
Alignment explanation
Indices: 6415628--6415664 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
6415618 AATAAAAATA
6415628 AAAATAAATAA-T-CTTTTC
1 AAAATAAATAATTACTTTTC
6415646 AAAATAAATAATTACTTTT
1 AAAATAAATAATTACTTTT
6415665 ATCAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 1 0.06
20 5 0.29
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAAATAATTACTTTTC
Found at i:6415697 original size:13 final size:13
Alignment explanation
Indices: 6415679--6415703 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6415669 AATAACATAA
6415679 TTATATTTAGTAC
1 TTATATTTAGTAC
6415692 TTATATTTAGTA
1 TTATATTTAGTA
6415704 ATTTATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
TTATATTTAGTAC
Found at i:6416975 original size:18 final size:20
Alignment explanation
Indices: 6416949--6416989 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
6416939 TGATATTATG
6416949 TTTTATTTT-TTA-ATTTCT
1 TTTTATTTTATTATATTTCT
* *
6416967 TTTTGTTTTATTATTTTTCT
1 TTTTATTTTATTATATTTCT
6416987 TTT
1 TTT
6416990 ACCTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTATTTTATTATATTTCT
Found at i:6418581 original size:5 final size:5
Alignment explanation
Indices: 6418571--6418595 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6418561 TTTCACCAAA
6418571 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
6418596 GATTCACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:6419158 original size:12 final size:12
Alignment explanation
Indices: 6419143--6419176 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6419133 TTCTAATATA
6419143 TTATAAAATAAT
1 TTATAAAATAAT
*
6419155 TTATAGAATAAT
1 TTATAAAATAAT
6419167 TTATATAAAT
1 TTATA-AAAT
6419177 TATAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TTATAAAATAAT
Found at i:6419223 original size:21 final size:22
Alignment explanation
Indices: 6419198--6419240 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6419188 TTCAGAATAT
6419198 TTAAAATT-TTATAAAAA-CATA
1 TTAAAATTCTT-TAAAAATCATA
6419219 TTAAAATTCTTTAAAAATCATA
1 TTAAAATTCTTTAAAAATCATA
6419241 AAACTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATTCTTTAAAAATCATA
Found at i:6419284 original size:20 final size:21
Alignment explanation
Indices: 6419231--6419286 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
6419221 AAAATTCTTT
6419231 AAAAATCAT-AAAAC-TACTA
1 AAAAATCATAAAAACTTACTA
* * *
6419250 AAAATTAATATAAACTTA-TA
1 AAAAATCATAAAAACTTACTA
6419270 AAAAATCATAAAAACTT
1 AAAAATCATAAAAACTT
6419287 GAATTGAACC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 7 0.24
20 20 0.69
21 2 0.07
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATCATAAAAACTTACTA
Found at i:6419676 original size:9 final size:9
Alignment explanation
Indices: 6419654--6419752 Score: 69
Period size: 9 Copynumber: 10.7 Consensus size: 9
6419644 CCAATTCAAG
6419654 ATTTT-ATA
1 ATTTTAATA
6419662 ATTTTAATA
1 ATTTTAATA
*
6419671 AGTTTATATCA
1 ATTTTA-AT-A
6419682 ATTTTAATA
1 ATTTTAATA
*
6419691 TTTTTAATA
1 ATTTTAATA
*
6419700 ATTCTAATA
1 ATTTTAATA
*
6419709 CGCTTTTTAA-A
1 ---ATTTTAATA
*
6419720 ATTTAAAT-
1 ATTTTAATA
6419728 ATTTTAATA
1 ATTTTAATA
*
6419737 ACTTTTATTA
1 A-TTTTAATA
6419747 ATTTTA
1 ATTTTA
6419753 TAAATTTGTT
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
8 17 0.24
9 30 0.42
10 12 0.17
11 7 0.10
12 5 0.07
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (9 bp):
ATTTTAATA
Found at i:6419696 original size:20 final size:18
Alignment explanation
Indices: 6419659--6419708 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
6419649 TCAAGATTTT
6419659 ATAATTTTAATAAGTTTA
1 ATAATTTTAATAAGTTTA
**
6419677 TATCAATTTTAATATTTTTA
1 -AT-AATTTTAATAAGTTTA
*
6419697 ATAATTCTAATA
1 ATAATTTTAATA
6419709 CGCTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.33
19 4 0.15
20 14 0.52
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (18 bp):
ATAATTTTAATAAGTTTA
Found at i:6419701 original size:38 final size:36
Alignment explanation
Indices: 6419654--6419756 Score: 100
Period size: 38 Copynumber: 2.8 Consensus size: 36
6419644 CCAATTCAAG
* *
6419654 ATTTT-ATAATTTTAATAAGTTTATATCAATTTTAAT
1 ATTTTAATAATTTTAATAAGTTTATA-AAATTTAAAT
* * *
6419690 ATTTTTAATAATTCTAATACGCTTTTTAAAATTTAAAT
1 A-TTTTAATAATTTTAATAAG-TTTATAAAATTTAAAT
* *
6419728 ATTTTAATAACTTTTATTAATTTTATAAA
1 ATTTTAATAA-TTTTAATAAGTTTATAAA
6419757 TTTGTTTATA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
36 1 0.02
37 20 0.38
38 27 0.51
39 5 0.09
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (36 bp):
ATTTTAATAATTTTAATAAGTTTATAAAATTTAAAT
Found at i:6419811 original size:10 final size:9
Alignment explanation
Indices: 6419655--6419814 Score: 51
Period size: 9 Copynumber: 17.1 Consensus size: 9
6419645 CAATTCAAGA
6419655 TTTTATAAT
1 TTTTATAAT
*
6419664 TTTAATAAGT
1 TTTTATAA-T
*
6419674 TTATATCAAT
1 TTTTAT-AAT
*
6419684 TTTAAT-AT
1 TTTTATAAT
6419692 TTTTAATAAT
1 TTTT-ATAAT
* * *
6419702 TCTAATACGCT
1 TTTTATA--AT
*
6419713 TTTTAAAAT
1 TTTTATAAT
**
6419722 TTAAAT-AT
1 TTTTATAAT
* *
6419730 TTTAATAAC
1 TTTTATAAT
6419739 TTTTATTAA-
1 TTTTA-TAAT
6419748 TTTTATAAATT
1 TTTTAT-AA-T
6419759 TGTTTATAAAT
1 T-TTTAT-AAT
* * *
6419770 TATTAGACT
1 TTTTATAAT
6419779 TTTTAT--T
1 TTTTATAAT
6419786 TTTTATAAT
1 TTTTATAAT
*
6419795 ATTTATAAGT
1 TTTTATAA-T
6419805 TTTTATAAT
1 TTTTATAAT
6419814 T
1 T
6419815 CAAAAAGCTT
Statistics
Matches: 110, Mismatches: 26, Indels: 30
0.66 0.16 0.18
Matches are distributed among these distances:
7 7 0.06
8 13 0.12
9 44 0.40
10 28 0.25
11 10 0.09
12 8 0.07
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (9 bp):
TTTTATAAT
Found at i:6436240 original size:14 final size:15
Alignment explanation
Indices: 6436221--6436249 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6436211 AACAATAACA
6436221 ATTAAATCC-ATTAG
1 ATTAAATCCAATTAG
6436235 ATTAAATCCAATTAG
1 ATTAAATCCAATTAG
6436250 TAATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (15 bp):
ATTAAATCCAATTAG
Found at i:6436328 original size:17 final size:17
Alignment explanation
Indices: 6436298--6436340 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
6436288 TATTATTTAA
*
6436298 TTAAATTATTTTAAATTT
1 TTAAATT-TTTTAAAATT
6436316 TTAAATTTTTTAAAATT
1 TTAAATTTTTTAAAATT
6436333 TT-AATTTT
1 TTAAATTTT
6436341 AATAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 6 0.25
17 11 0.46
18 7 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTAAATTTTTTAAAATT
Found at i:6438216 original size:2 final size:2
Alignment explanation
Indices: 6438209--6438235 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6438199 ATTAGTTTTA
6438209 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6438236 ATAAAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6443861 original size:3 final size:3
Alignment explanation
Indices: 6443820--6443849 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6443810 CAGCCCTCTG
*
6443820 GCT GCT GCT GCT GCT GCT GCT GCC GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
6443850 TGGCTTGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.33, T:0.30
Consensus pattern (3 bp):
GCT
Found at i:6452840 original size:22 final size:20
Alignment explanation
Indices: 6452815--6452854 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
6452805 AAATACATAT
6452815 AAATTATTTTATAATTATAATC
1 AAATTA-TTTA-AATTATAATC
6452837 AAATTATTTAAATTATAA
1 AAATTATTTAAATTATAA
6452855 CTAATGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATTTAAATTATAATC
Found at i:6454051 original size:2 final size:2
Alignment explanation
Indices: 6454044--6454077 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6454034 TGAATGGAAT
6454044 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6454078 GGTGTTTTAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6461387 original size:18 final size:19
Alignment explanation
Indices: 6461366--6461402 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6461356 TTTATGGCCT
6461366 TATTAAAAT-TTAATTTTA
1 TATTAAAATATTAATTTTA
*
6461384 TATTAAAATATTTATTTTA
1 TATTAAAATATTAATTTTA
6461403 GTTTATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTAAAATATTAATTTTA
Found at i:6461675 original size:18 final size:19
Alignment explanation
Indices: 6461654--6461695 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
6461644 TTTAAGTTAT
*
6461654 TTATTATTTT-ATTAAAAA
1 TTATTATTTTAAATAAAAA
6461672 TTA-TATTTTAAATAAAAA
1 TTATTATTTTAAATAAAAA
*
6461690 TAATTA
1 TTATTA
6461696 AATTTTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 12 0.60
19 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTATTTTAAATAAAAA
Found at i:6462292 original size:25 final size:23
Alignment explanation
Indices: 6462259--6462305 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
6462249 TTATGATGTT
6462259 TTGTCAAA-TCAACTTTTTTTAATA
1 TTGTCAAATTC-A-TTTTTTTAATA
6462283 TTGTCCAAATTCATTTTTTTAAT
1 TTGT-CAAATTCATTTTTTTAAT
6462306 TTCATTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 14 0.67
25 5 0.24
26 2 0.10
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.53
Consensus pattern (23 bp):
TTGTCAAATTCATTTTTTTAATA
Found at i:6463085 original size:47 final size:47
Alignment explanation
Indices: 6463005--6463120 Score: 178
Period size: 47 Copynumber: 2.5 Consensus size: 47
6462995 TCATTAACAT
* * **
6463005 TGTTTGTGAACATGTTCAATTATATGTTCATGAACATGATTGTTTAA
1 TGTTCGTGAACATGTTCAATTATATATTCATGAACATGATCATTTAA
*
6463052 TGTTCGTGAACATGTTCAATTATATATTTATGAACATGATCATTTAA
1 TGTTCGTGAACATGTTCAATTATATATTCATGAACATGATCATTTAA
*
6463099 TGTTCGTGAACATGTTCGATTA
1 TGTTCGTGAACATGTTCAATTA
6463121 AATTAAATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (47 bp):
TGTTCGTGAACATGTTCAATTATATATTCATGAACATGATCATTTAA
Found at i:6463121 original size:23 final size:23
Alignment explanation
Indices: 6463005--6463121 Score: 110
Period size: 23 Copynumber: 5.0 Consensus size: 23
6462995 TCATTAACAT
*
6463005 TGTTTGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
6463029 TGTTCATGAACATGATT-GTTTAA
1 TGTTCGTGAACATG-TTCAATTAA
6463052 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* ** * *
6463076 TATTTATGAACATGATCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
6463099 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCAATTAA
6463122 ATTAAATAAA
Statistics
Matches: 72, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
22 2 0.03
23 35 0.49
24 33 0.46
25 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:6463148 original size:23 final size:23
Alignment explanation
Indices: 6463107--6463150 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
6463097 AATGTTCGTG
*
6463107 AACATGTTCGATTAAATTAAATA
1 AACATGTTCGATGAAATTAAATA
6463130 AACATGTTCG-TGAACATTAAA
1 AACATGTTCGATGAA-ATTAAA
6463151 CGAACGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (23 bp):
AACATGTTCGATGAAATTAAATA
Found at i:6468058 original size:66 final size:66
Alignment explanation
Indices: 6467981--6468389 Score: 642
Period size: 66 Copynumber: 6.2 Consensus size: 66
6467971 GGATTGTCTT
*
6467981 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCA
1 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
6468046 C
66 C
*
6468047 CCCTTTGTCGTTCCAAACCATCATCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATT-TGC
1 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCT-C
6468111 TC
65 TC
6468113 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
1 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
6468178 C
66 C
* *
6468179 CCCTTTGTCCTTCCAAACCATCATCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
1 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
*
6468244 T
66 C
*
6468245 CCCTTTGTTGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
1 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
6468310 C
66 C
** ** * * * * *
6468311 CCCTTTGTCGTTCCAAAAGATTTGCTTTCCCTT-TCCATTTAGCCGCTTGATCTTCAACGTTCTC
1 CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGT-CGTTTCGCCGTTTGATCTTCAACATTCTC
*
6468375 CC
65 TC
6468377 CCCTTTGTCGTTC
1 CCCTTTGTCGTTC
6468390 TAAAACATTT
Statistics
Matches: 319, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
65 2 0.01
66 316 0.99
67 1 0.00
ACGTcount: A:0.15, C:0.34, G:0.12, T:0.39
Consensus pattern (66 bp):
CCCTTTGTCGTTCCAAACCATCAGCATTCCCTTGTCGTTTCGCCGTTTGATCTTCAACATTCTCT
C
Found at i:6469402 original size:32 final size:32
Alignment explanation
Indices: 6469365--6469426 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
6469355 TTGGATTTGA
*
6469365 TTGGGCCAATTTGCTTTAGACTCCATCCAAAT
1 TTGGGCCAATTTGCCTTAGACTCCATCCAAAT
6469397 TTGGGCCAATTTGCCTTAGACTCCATCCAA
1 TTGGGCCAATTTGCCTTAGACTCCATCCAA
6469427 TTGAGCCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGGGCCAATTTGCCTTAGACTCCATCCAAAT
Found at i:6477101 original size:77 final size:77
Alignment explanation
Indices: 6477012--6477166 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 77
6477002 CTGAAACAAA
*
6477012 CAAAAGTTACTATTTTGATAATTTACTCTAAAAATAATTACATAAATCAATTAAATTAAATTTAA
1 CAAAAGTGACTATTTTGATAATTTACTCTAAAAATAATTACATAAATCAATTAAATTAAATTTAA
6477077 AAATTTGACTCT
66 AAATTTGACTCT
6477089 CAAAAGTGACTATTTTGATAATTTACTCTAAAAATAATTACATAAATCAATTAAATTAAATTTAA
1 CAAAAGTGACTATTTTGATAATTTACTCTAAAAATAATTACATAAATCAATTAAATTAAATTTAA
*
6477154 AAGTTTGACTCT
66 AAATTTGACTCT
6477166 C
1 C
6477167 CATACCTTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (77 bp):
CAAAAGTGACTATTTTGATAATTTACTCTAAAAATAATTACATAAATCAATTAAATTAAATTTAA
AAATTTGACTCT
Found at i:6478139 original size:29 final size:30
Alignment explanation
Indices: 6478106--6478179 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
6478096 TTATAGGATC
6478106 GGATCAAATTAATCACTT-T-ATCATT-AAAT
1 GGATCAAATTAATC-CTTATGAT-ATTAAAAT
*
6478135 GGATCAATTTAATCCTTATGATATTAAAAT
1 GGATCAAATTAATCCTTATGATATTAAAAT
* *
6478165 GAATCAAATAAATCC
1 GGATCAAATTAATCC
6478180 AATTTTAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 3 0.08
29 17 0.45
30 18 0.47
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (30 bp):
GGATCAAATTAATCCTTATGATATTAAAAT
Found at i:6480417 original size:2 final size:2
Alignment explanation
Indices: 6480410--6480449 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6480400 AAAAACACAA
6480410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6480450 AATGTCTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6484006 original size:129 final size:129
Alignment explanation
Indices: 6483650--6484034 Score: 524
Period size: 130 Copynumber: 3.0 Consensus size: 129
6483640 AAGGTTAAAG
* * * * *
6483650 TCTTAATAAGAATGTGATTAGTGTAATTTTTAAGTCACATTTGAGGTAGTGAATATTTTAATTAT
1 TCTTAATAATAATGTGATTAGTGTAATTTTTAGGTCATATTTGAGGAAGTGAATATTTTAATCAT
* * *
6483715 CAAGTCAATATACGAGGTTCAGTTAAAGTATTTAAGTTTAATATAACATTTGGTATTTGAAAAAG
66 CAAGTCAATATACG-GGTTCAGTTAAAGTATTTAGGTTTAATATAATATTTGGTATTTGAAAAAA
* * *
6483780 T-TCTAATAATAATGTGATTAGTATAATTTTTAGGTCGTATTTG-GAGAAGTGAATATCTTAATC
1 TCT-TAATAATAATGTGATTAGTGTAATTTTTAGGTCATATTTGAG-GAAGTGAATATTTTAATC
*
6483843 ATTAAGTCAATATACGGGATTCAGTTAAAGTATTTAGGTTTAATATAATATTTGGTATTTGAAAA
64 ATCAAGTCAATATACGGG-TTCAGTTAAAGTATTTAGGTTTAATATAATATTTGGTATTTGAAAA
6483908 AA
128 AA
** * * *
6483910 TCTTAATAATAATACGATT-GTGTAATTTTTAGGTTATACTTGAGGCAGTGAATATTTTAATCAT
1 TCTTAATAATAATGTGATTAGTGTAATTTTTAGGTCATATTTGAGGAAGTGAATATTTTAATCAT
* * *
6483974 CAGGTCAATATACAGGGTTCAGTTAAAGTATTTAGGCTTAATATAATATTTGGTATCTGAA
66 CAAGTCAATATAC-GGGTTCAGTTAAAGTATTTAGGTTTAATATAATATTTGGTATTTGAA
6484035 CTTGATATAT
Statistics
Matches: 225, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
129 94 0.42
130 130 0.58
131 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (129 bp):
TCTTAATAATAATGTGATTAGTGTAATTTTTAGGTCATATTTGAGGAAGTGAATATTTTAATCAT
CAAGTCAATATACGGGTTCAGTTAAAGTATTTAGGTTTAATATAATATTTGGTATTTGAAAAAA
Found at i:6488371 original size:16 final size:15
Alignment explanation
Indices: 6488328--6488371 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
6488318 GTCCGGCCCA
*
6488328 ATTAATTTTTAAGTT
1 ATTAATTTTTATGTT
6488343 ATTAATATTTTATGTT
1 ATTAAT-TTTTATGTT
*
6488359 ATGTTATTTTTAT
1 AT-TAATTTTTAT
6488372 ATATTATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 16 0.64
17 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (15 bp):
ATTAATTTTTATGTT
Found at i:6490439 original size:21 final size:21
Alignment explanation
Indices: 6490406--6490453 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
6490396 TTTTTACATC
*
6490406 ATAAA-AATTAAAAT-TAATT
1 ATAAATAATTAAAATAAAATT
6490425 ATAAATAATATAAAATAAAATT
1 ATAAATAAT-TAAAATAAAATT
6490447 -TAAATAA
1 ATAAATAA
6490454 ATTTCAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 3 0.12
21 13 0.52
22 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATAATTAAAATAAAATT
Found at i:6502756 original size:11 final size:10
Alignment explanation
Indices: 6502720--6502763 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
6502710 TAAAATGATT
*
6502720 AAAAATTATG
1 AAAAATTATA
6502730 AAAAATTCA-A
1 AAAAATT-ATA
6502740 AAAAATTATA
1 AAAAATTATA
6502750 AATAAATTATA
1 AA-AAATTATA
6502761 AAA
1 AAA
6502764 TTAATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 1 0.03
10 18 0.60
11 11 0.37
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAATTATA
Found at i:6502763 original size:20 final size:20
Alignment explanation
Indices: 6502719--6502773 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
6502709 ATAAAATGAT
*
6502719 TAAAAATTATGAAAAATTCA
1 TAAAAATTATAAAAAATTCA
*
6502739 AAAAAATTATAAATAAATT-A
1 TAAAAATTATAAA-AAATTCA
6502759 T-AAAATTAATAAAAA
1 TAAAAATT-ATAAAAA
6502774 CATATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 8 0.27
20 17 0.57
21 5 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAAAATTATAAAAAATTCA
Found at i:6503548 original size:16 final size:16
Alignment explanation
Indices: 6503501--6503550 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
6503491 ATTTTTCATC
*
6503501 CTTTTTAATAATTTTCTG
1 CTTTTTAA-AATTTT-TA
* *
6503519 CTTTTTATATTTTTTA
1 CTTTTTAAAATTTTTA
6503535 CTTTTTAAAATTTTTA
1 CTTTTTAAAATTTTTA
6503551 TAGGTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 15 0.56
17 5 0.19
18 7 0.26
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (16 bp):
CTTTTTAAAATTTTTA
Found at i:6517996 original size:27 final size:26
Alignment explanation
Indices: 6517965--6518032 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 26
6517955 CGTTCCGGGT
6517965 TCGGGTCCTTTAGAAAGAGGGTTCATG
1 TCGGGTCCTTT-GAAAGAGGGTTCATG
* *
6517992 TCGGGTCCGATTGAGAGAGGGTTCATG
1 TCGGGTCC-TTTGAAAGAGGGTTCATG
6518019 TCGGGTCCTCTTGA
1 TCGGGTCCT-TTGA
6518033 TAACACTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 34 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (26 bp):
TCGGGTCCTTTGAAAGAGGGTTCATG
Found at i:6536812 original size:18 final size:21
Alignment explanation
Indices: 6536774--6536814 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
6536764 AATTTTGACA
6536774 AAAAAATTTAAATATTAATTT
1 AAAAAATTTAAATATTAATTT
6536795 AAAAAA-TT-AATA-TAATTT
1 AAAAAATTTAAATATTAATTT
6536813 AA
1 AA
6536815 GTATTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 2 0.10
21 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAAATTTAAATATTAATTT
Found at i:6537208 original size:7 final size:7
Alignment explanation
Indices: 6537196--6537226 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
6537186 CTTTTTCGCC
6537196 CAAAAAG
1 CAAAAAG
6537203 CAAAAAG
1 CAAAAAG
6537210 CAAAAAG
1 CAAAAAG
6537217 CAAAAAG
1 CAAAAAG
6537224 CAA
1 CAA
6537227 TCTAAAGAAA
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:0.71, C:0.16, G:0.13, T:0.00
Consensus pattern (7 bp):
CAAAAAG
Found at i:6547030 original size:18 final size:18
Alignment explanation
Indices: 6546992--6547030 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6546982 ATTGCTTCTC
* *
6546992 AAAAGCACTTTTGGGACA
1 AAAAACACTTTTGAGACA
*
6547010 AAAAACACTTTTGAGATA
1 AAAAACACTTTTGAGACA
6547028 AAA
1 AAA
6547031 GCATTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAAACACTTTTGAGACA
Found at i:6549931 original size:29 final size:30
Alignment explanation
Indices: 6549874--6549944 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
6549864 ATATCAAAAT
*
6549874 TATACATAAAATTTAATTTAATGTATAATTA
1 TATACATGAAATTTAATTT-ATGTATAATTA
* *
6549905 TATACATGAATTTTAATTT-TGTGTAATTA
1 TATACATGAAATTTAATTTATGTATAATTA
**
6549934 TGCACATGAAA
1 TATACATGAAA
6549945 CTTTTATTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (30 bp):
TATACATGAAATTTAATTTATGTATAATTA
Done.