Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 8 of 121
Found at i:1137235 original size:2 final size:2
Alignment explanation
Indices: 1137228--1137274 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1137218 TTGTCTTCTG
1137228 CA CA CA CA CA CA C- CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1137269 CA CA CA
1 CA CA CA
1137275 TATATAGCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1139379 original size:15 final size:15
Alignment explanation
Indices: 1139359--1139388 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1139349 ATGTGAGGGT
1139359 GCTATAACCTTCCTC
1 GCTATAACCTTCCTC
1139374 GCTATAACCTTCCTC
1 GCTATAACCTTCCTC
1139389 ATATGTAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.07, T:0.33
Consensus pattern (15 bp):
GCTATAACCTTCCTC
Found at i:1144218 original size:21 final size:21
Alignment explanation
Indices: 1144194--1144299 Score: 115
Period size: 21 Copynumber: 5.0 Consensus size: 21
1144184 GAATCTTTTG
*
1144194 ATGAGAATTTTTGAGTTCTC-A
1 ATGAGAATTTTTGAATT-TCAA
*
1144215 ATGAAAATTTTTGAATTTCAA
1 ATGAGAATTTTTGAATTTCAA
* *
1144236 ATGAGAATCTTTGAATTTTAA
1 ATGAGAATTTTTGAATTTCAA
* *
1144257 ATGAAAATCTTTGAATTTCAA
1 ATGAGAATTTTTGAATTTCAA
** *
1144278 AAAAGAATCTTTGAATTTCAA
1 ATGAGAATTTTTGAATTTCAA
1144299 A
1 A
1144300 AAAAGAATCT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 2 0.03
21 72 0.97
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (21 bp):
ATGAGAATTTTTGAATTTCAA
Found at i:1144240 original size:42 final size:42
Alignment explanation
Indices: 1144194--1144294 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
1144184 GAATCTTTTG
* * * *
1144194 ATGAGAATTTTTGAGTTCTCAATGAAAATTTTTGAATTTCAA
1 ATGAGAATCTTTGAATTCTAAATGAAAATCTTTGAATTTCAA
*
1144236 ATGAGAATCTTTGAATTTTAAATGAAAATCTTTGAATTTCAA
1 ATGAGAATCTTTGAATTCTAAATGAAAATCTTTGAATTTCAA
**
1144278 AAAAGAATCTTTGAATT
1 ATGAGAATCTTTGAATT
1144295 TCAAAAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.41
Consensus pattern (42 bp):
ATGAGAATCTTTGAATTCTAAATGAAAATCTTTGAATTTCAA
Found at i:1144295 original size:42 final size:42
Alignment explanation
Indices: 1144197--1144313 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
1144187 TCTTTTGATG
* * * **
1144197 AGAATTTTTGAGTTCTC-AATGAAAATTTTTGAATTTCAAATG
1 AGAATCTTTGAATT-TCAAATGAAAATCTTTGAATTTCAAAAA
*
1144239 AGAATCTTTGAATTTTAAATGAAAATCTTTGAATTTCAAAAA
1 AGAATCTTTGAATTTCAAATGAAAATCTTTGAATTTCAAAAA
**
1144281 AGAATCTTTGAATTTCAAAAAAAGAATCTTTGA
1 AGAATCTTTGAATTTCAAATGAA-AATCTTTGA
1144314 GTTTTGAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 54 0.84
43 9 0.14
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (42 bp):
AGAATCTTTGAATTTCAAATGAAAATCTTTGAATTTCAAAAA
Found at i:1144304 original size:22 final size:21
Alignment explanation
Indices: 1144224--1144313 Score: 119
Period size: 21 Copynumber: 4.2 Consensus size: 21
1144214 AATGAAAATT
**
1144224 TTTGAATTTCAAATGAGAATC
1 TTTGAATTTCAAAAAAGAATC
* *
1144245 TTTGAATTTTAAATGAA-AATC
1 TTTGAATTTCAAA-AAAGAATC
1144266 TTTGAATTTCAAAAAAGAATC
1 TTTGAATTTCAAAAAAGAATC
1144287 TTTGAATTTCAAAAAAAGAATC
1 TTTGAATTTC-AAAAAAGAATC
1144309 TTTGA
1 TTTGA
1144314 GTTTTGAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.03
21 42 0.69
22 17 0.28
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (21 bp):
TTTGAATTTCAAAAAAGAATC
Found at i:1144422 original size:46 final size:46
Alignment explanation
Indices: 1144370--1144906 Score: 686
Period size: 46 Copynumber: 11.7 Consensus size: 46
1144360 TTGTTGAATA
* * *
1144370 AGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCACATG
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
* * * *
1144416 AGAACCTTTGA-TTTTAAATGAGAATCTTTAAGACATTTTCACATA
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
* *
1144461 AGAACCTTTAAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
* * *
1144507 AAAATCTTTGAGTCTTAAGTGAGAATCTTTAAGACGA-TTTCAAATA
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAC-ATTTTCAAATG
* * * *
1144553 AGAATCTTTGAATCTTGAATGAAAATTTTTAAGACATTTTCAAAT-
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
*
1144598 ACGAATCTTTGAGTCTTGAATGAGAATCTTTAAGACATTTTCAAATG
1 A-GAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
* * * * **
1144645 TGAATATTTGAATCTTAAATAAGAATCTTTAAGATGTTTTCAAAT-
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
1144690 ACGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
1 A-GAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
* *
1144737 AGAATCTTTGAGTCTTAAATGAAAATCTTTAAGATATTTTCAAATG
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
* * * * * ** *
1144783 CGAATATTTGAATCTTAACTGAAAATCTTTAAGATGTTTTCAAATA
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
* * * *
1144829 AAAACCTTTGAGTCTTAAATGATAATCTTTAAGACGTTTTCAAATG
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
1144875 AGAATCTTTGAGTCTTAAATGAGAATCTTTAA
1 AGAATCTTTGAGTCTTAAATGAGAATCTTTAA
1144907 AAAGAACTCA
Statistics
Matches: 430, Mismatches: 54, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
45 43 0.10
46 385 0.90
47 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (46 bp):
AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATG
Found at i:1145032 original size:42 final size:40
Alignment explanation
Indices: 1144981--1145103 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 40
1144971 CTTTTCAATT
*
1144981 CAAAAAAGCTTAAACTTTTAGATATGAATCTCCAAATTCGAA
1 CAAAAAAGCTTAAACTTTTAGATGTGAATCTCCAAATT--AA
* *
1145023 CAAAAAAGCTTAAACTTTTGGATGTGAATCTCAAAAAGTTAA
1 CAAAAAAGCTTAAACTTTTAGATGTGAATCTC-CAAA-TTAA
* *
1145065 CAAAAAAGGCTTAAGCTTCTTAGATGTGAA-CCCCAAATT
1 CAAAAAA-GCTTAAACTT-TTAGATGTGAATCTCCAAATT
1145104 TGTCAGACGT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
41 2 0.03
42 42 0.60
43 14 0.20
44 12 0.17
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (40 bp):
CAAAAAAGCTTAAACTTTTAGATGTGAATCTCCAAATTAA
Found at i:1145488 original size:40 final size:41
Alignment explanation
Indices: 1145402--1145833 Score: 521
Period size: 41 Copynumber: 10.4 Consensus size: 41
1145392 ATTGTCGAGA
* * * *
1145402 AGCATTTTATTTTCCAAAGTTGTGATACCTCTGTTTAGATG
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
* * *
1145443 AGCATTTTACTTTTCAAAGTTGTGGTG-CTTTGTTTAAAGG
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
*
1145483 AGCATTTTATTTTTTAAAGTTGTGGTGCCTCTGTTTAGA-G
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
* *
1145523 AGCA-TTTATTTTTTTAAAGTTATGGTGCCTCTGTTTAGAGG
1 AGCATTTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
* *
1145564 AGCATTTTATTTTTCAAAGTCGTGGTGCCTCTATTTAGAGG
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
*
1145605 AGTATTTTATTTTCTCAAAGTTGTGGTGCCTCTGTTTAGAGG
1 AGCATTTTATTTT-TCAAAGTTGTGGTGCCTCTGTTTAGAGG
* * * *
1145647 AGCAATTTATTTTTCAAAAGTTATGGTACCTTTGTTTAGAGG
1 AGCATTTTATTTTTC-AAAGTTGTGGTGCCTCTGTTTAGAGG
* *
1145689 AGCA-TTTATTTTCCAAAGTTGTGGTGCCTCTGCTTAGAGG
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
* * *
1145729 AGCTTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAAG
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
* * * *
1145770 AGCAATTTATTTTTCAAAAGTCGTTGAGCCTTCTGTTTAGAGG
1 AGCATTTTATTTTTC-AAAGTTGTGGTGCC-TCTGTTTAGAGG
*
1145813 AGCTTTGTTTACTTTTTCAAA
1 AGC-AT-TTTA-TTTTTCAAA
1145834 AAAAACAAAA
Statistics
Matches: 338, Mismatches: 41, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.01
40 94 0.28
41 133 0.39
42 80 0.24
43 14 0.04
45 7 0.02
46 6 0.02
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.44
Consensus pattern (41 bp):
AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
Found at i:1145502 original size:81 final size:81
Alignment explanation
Indices: 1145402--1145833 Score: 517
Period size: 81 Copynumber: 5.2 Consensus size: 81
1145392 ATTGTCGAGA
* * * * *
1145402 AGCATTTTATTTTCCAAAGTTGTGATACCTCTGTTTAGATGAGCATTTTACTTTTCAAAGTTGTG
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCA-TTTATTTTTCAAAGTTGTG
* *
1145467 GTG-CTTTGTTTAAAGG
65 GTGCCTCTGTTTAGAGG
* * *
1145483 AGCATTTTATTTTTTAAAGTTGTGGTGCCTCTGTTTAGA-GAGCATTTATTTTTTTAAAGTTATG
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCATTTA-TTTTTCAAAGTTGTG
1145547 GTGCCTCTGTTTAGAGG
65 GTGCCTCTGTTTAGAGG
* * *
1145564 AGCATTTTATTTTTCAAAGTCGTGGTGCCTCTATTTAGAGGAGTATTTTATTTTCTCAAAGTTGT
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCA-TTTATTTT-TCAAAGTTGT
1145629 GGTGCCTCTGTTTAGAGG
64 GGTGCCTCTGTTTAGAGG
* * * * *
1145647 AGCAATTTATTTTTCAAAAGTTATGGTACCTTTGTTTAGAGGAGCATTTATTTTCCAAAGTTGTG
1 AGCATTTTATTTTTC-AAAGTTGTGGTGCCTCTGTTTAGAGGAGCATTTATTTTTCAAAGTTGTG
*
1145712 GTGCCTCTGCTTAGAGG
65 GTGCCTCTGTTTAGAGG
* * * *
1145729 AGCTTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAAGAGCAATTTATTTTTCAAAAGTCGT
1 AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGC-ATTTATTTTTC-AAAGTTGT
* *
1145794 TGAGCCTTCTGTTTAGAGG
64 GGTGCC-TCTGTTTAGAGG
*
1145813 AGCTTTGTTTACTTTTTCAAA
1 AGC-AT-TTTA-TTTTTCAAA
1145834 AAAAACAAAA
Statistics
Matches: 303, Mismatches: 36, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
79 4 0.01
80 20 0.07
81 106 0.35
82 57 0.19
83 63 0.21
84 38 0.13
85 2 0.01
86 4 0.01
87 9 0.03
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.44
Consensus pattern (81 bp):
AGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCATTTATTTTTCAAAGTTGTGG
TGCCTCTGTTTAGAGG
Found at i:1147879 original size:18 final size:16
Alignment explanation
Indices: 1147837--1147872 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1147827 ATTTCATTTT
1147837 TTATTAATTTTATATA
1 TTATTAATTTTATATA
1147853 TTATTAATTTTATA-A
1 TTATTAATTTTATATA
1147868 TTATT
1 TTATT
1147873 TTTAATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTAATTTTATATA
Found at i:1151649 original size:14 final size:14
Alignment explanation
Indices: 1151630--1151671 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1151620 TTCGATTAAT
*
1151630 TTTAAATCAAATTA
1 TTTAAATTAAATTA
1151644 TTTAAAATTAAATTA
1 TTT-AAATTAAATTA
*
1151659 ATTAAATTAAATT
1 TTTAAATTAAATT
1151672 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATTAAATTA
Found at i:1151849 original size:120 final size:121
Alignment explanation
Indices: 1151660--1151882 Score: 333
Period size: 120 Copynumber: 1.9 Consensus size: 121
1151650 ATTAAATTAA
* * * * *
1151660 TTAAATTAAATTTTTTTTATTTTCATTAATTGAGTCAAATTTATTAATTTTGAAAATTAATTGAG
1 TTAAATTAAATTTATTTTATTTTCATTAATTGAATCAAATTTATTAATTTTAAAAATTAATCGAA
*
1151725 CGAATTTAAACTAACCGA-TAAACTTAATTAAATCGATTCGATTGGTTTGATTAATT
66 CGAATTTAAACTAACCGATTAAA-TGAATTAAATCGATTCGATTGGTTTGATTAATT
* *
1151781 TTAAATTAAA-TTATTTTGTTTTCGTTAATTGAATCAAATTTATTAATTTTAAAAATTAATCGAA
1 TTAAATTAAATTTATTTTATTTTCATTAATTGAATCAAATTTATTAATTTTAAAAATTAATCGAA
* *
1151845 CGAATTTAAATTAACTGATTAAATGAATTAAATCGATT
66 CGAATTTAAACTAACCGATTAAATGAATTAAATCGATT
1151883 AAATCGATTA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
120 77 0.85
121 14 0.15
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (121 bp):
TTAAATTAAATTTATTTTATTTTCATTAATTGAATCAAATTTATTAATTTTAAAAATTAATCGAA
CGAATTTAAACTAACCGATTAAATGAATTAAATCGATTCGATTGGTTTGATTAATT
Found at i:1153453 original size:2 final size:2
Alignment explanation
Indices: 1153446--1153471 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1153436 TCTATCTATC
1153446 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
1153472 AATCAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1154049 original size:7 final size:6
Alignment explanation
Indices: 1154032--1154111 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
1154022 AAATCTATTT
* * *
1154032 TTTTTA TTTTTA TATTTTA TATTTTA TTTTTA ATTTTA TTTTTA TTATTG
1 TTTTTA TTTTTA T-TTTTA T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
1154082 TTTTTA TATATA TTCTT- CTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
1154112 CTTATGTATT
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
5 3 0.05
6 42 0.72
7 13 0.22
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:1154258 original size:20 final size:20
Alignment explanation
Indices: 1154177--1154258 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 20
1154167 TTATATGTAT
* *
1154177 ATTTATCAGATTATATGTTATA
1 ATTTATCTGATT-TAT-TTTTA
* *
1154199 ATTTATCTATTATTTAATTTTA
1 ATTTATC--TGATTTATTTTTA
* *
1154221 ATTTATCTG-TTAATTTTTTG
1 ATTTATCTGATTTA-TTTTTA
1154241 ATTTATCTGATTTATTTT
1 ATTTATCTGATTTATTTT
1154259 CATTAATATT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
19 3 0.06
20 18 0.38
21 3 0.06
22 18 0.38
23 2 0.04
24 3 0.06
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.61
Consensus pattern (20 bp):
ATTTATCTGATTTATTTTTA
Found at i:1154274 original size:18 final size:16
Alignment explanation
Indices: 1154251--1154292 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
1154241 ATTTATCTGA
1154251 TTTATTTTCATTAATATT
1 TTTATTTT-ATTAAT-TT
*
1154269 TTTATTTTATTTATTT
1 TTTATTTTATTAATTT
1154285 TTTATTTT
1 TTTATTTT
1154293 TTGATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 8 0.35
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTAATTT
Found at i:1154293 original size:17 final size:18
Alignment explanation
Indices: 1154251--1154293 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1154241 ATTTATCTGA
*
1154251 TTTATTTTCATTAATATT
1 TTTATTTTTATTAATATT
*
1154269 TTTA-TTTTATTTAT-TT
1 TTTATTTTTATTAATATT
1154285 TTTATTTTT
1 TTTATTTTT
1154294 TGATTTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 12 0.55
18 4 0.18
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTTATTAATATT
Found at i:1154299 original size:15 final size:16
Alignment explanation
Indices: 1154251--1154299 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1154241 ATTTATCTGA
*
1154251 TTTATTTTCATTAATATT
1 TTTATTTT-ATTGAT-TT
*
1154269 TTTATTTTATTTATTT
1 TTTATTTTATTGATTT
1154285 TTTATTTT-TTGATTT
1 TTTATTTTATTGATTT
1154300 ATTCGGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 6 0.21
16 10 0.34
17 5 0.17
18 8 0.28
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTGATTT
Found at i:1155109 original size:15 final size:16
Alignment explanation
Indices: 1155082--1155113 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1155072 TTTATATATA
1155082 TTTTATTTCTTTATTT
1 TTTTATTTCTTTATTT
1155098 TTTTATTT-TTTATTT
1 TTTTATTTCTTTATTT
1155113 T
1 T
1155114 CACTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTCTTTATTT
Found at i:1155265 original size:59 final size:58
Alignment explanation
Indices: 1155158--1155603 Score: 487
Period size: 59 Copynumber: 7.7 Consensus size: 58
1155148 AAATAAAATC
* *
1155158 CAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTT
1 CAAAAAAAAT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
1155217 CAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTTT
1 CAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAATTTT
* *
1155276 CAAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTTAAAAATAAATTTT
1 C-AAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
**
1155335 C-AAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
1 CAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* *** * * * * * *
1155392 --TAAAATGGTTTTTGAAGAAAAGTTGAAAGTATTAATTTT-CTTCGAAATTAAGGTTTC
1 CAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAA-ATTTT
* * ** * *
1155449 CAAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTT
1 CAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* * * * * *
1155506 C--AAAAGATATTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAGATTAAAATTT
1 CAAAAAAAATTTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* *
1155562 CTAAAAAAAATATTTTGGGGAAAAGTT-ACAAGTATCAATTTT
1 C-AAAAAAAATTTTTTGAGGAAAAGTTGA-AAGTATCAATTTT
1155604 TTCTGCACAA
Statistics
Matches: 340, Mismatches: 33, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
55 14 0.04
56 76 0.22
57 59 0.17
58 57 0.17
59 98 0.29
60 36 0.11
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (58 bp):
CAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
Found at i:1155372 original size:57 final size:57
Alignment explanation
Indices: 1155160--1155603 Score: 495
Period size: 56 Copynumber: 7.7 Consensus size: 57
1155150 ATAAAATCCA
* *
1155160 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTTC
1 AAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1155218 AAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTTTC
1 AAAAAAAA-TTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAATTTTC
*
1155277 AAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTTAAAAATAAATTTTC
1 --AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
**
1155336 AAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT-
1 AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *** * * * * * *
1155392 TAAAATGGTTTTTGAAGAAAAGTTGAAAGTATTAATTTT-CTTCGAAATTAAGGTTTCC
1 AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAA-ATTTTC
* ** * *
1155450 AAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTC
1 AAAAAAAATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * * * *
1155507 AAAAGATA-TTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAGATTAAAATTTC
1 AAAAAAAATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
1155563 TAAAAAAAATATTTTGGGGAAAAGTT-ACAAGTATCAATTTT
1 -AAAAAAAAT-TTTTGAGGAAAAGTTGA-AAGTATCAATTTT
1155604 TTCTGCACAA
Statistics
Matches: 339, Mismatches: 32, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
55 4 0.01
56 82 0.24
57 73 0.22
58 74 0.22
59 70 0.21
60 28 0.08
61 8 0.02
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (57 bp):
AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:1157188 original size:258 final size:258
Alignment explanation
Indices: 1156725--1157239 Score: 922
Period size: 258 Copynumber: 2.0 Consensus size: 258
1156715 ATATTAGATT
*
1156725 TCATTTAGGAAAATGTACATTTCATTCGTGCATCAAAGCATCATACATAAAGCATAGCATAACAT
1 TCATTCAGGAAAATGTACATTTCATTCGTGCATCAAAGCATCATACATAAAGCATAGCATAACAT
* *
1156790 TTCTAATCATAATTGTGGTGCTAAAGGTTCAAGGATAGCTCCATCTAGTGAGAACCCTGCCCATC
66 TTCTAATCATAATTATGGTGCTAAAAGTTCAAGGATAGCTCCATCTAGTGAGAACCCTGCCCATC
* *
1156855 GATACAACACAAGATCCAGAGCCAGACAAATGGAGCAGAAAAATTCTCACAGATTTGAAAAGATA
131 GATACAACACAAGATCCAGAGCCAAACAAATGGAGCAAAAAAATTCTCACAGATTTGAAAAGATA
* ** *
1156920 AAAAAAGCACAGGAGAAGATTAAAAGTGAGTTAAGTAAGATTTTGGATGCTCTTAATAAGCTA
196 AAAAAAGCACAGAAGAAGATTAAAAGTGAGTTAAACAAGATTCTGGATGCTCTTAATAAGCTA
1156983 TCATTCAGGAAAATGTACATTTCATTCGTGCATCAAAGCATCATACATAAAGCATAGCATAACAT
1 TCATTCAGGAAAATGTACATTTCATTCGTGCATCAAAGCATCATACATAAAGCATAGCATAACAT
*
1157048 TTTTAATCATAATTATGGTGCTAAAAGTTCAAGGATAGCTCCATCTAGTGAGAACCCTGCCCATC
66 TTCTAATCATAATTATGGTGCTAAAAGTTCAAGGATAGCTCCATCTAGTGAGAACCCTGCCCATC
*
1157113 GATACAACACAAGATCCAGAGCCAAACAAATGGAGTAAAAAAATTCTCACAGATTTGAAAAGATA
131 GATACAACACAAGATCCAGAGCCAAACAAATGGAGCAAAAAAATTCTCACAGATTTGAAAAGATA
*
1157178 AAAAAAGCACAGAAGAAGATTGAAAGTGAGTTAAACAAGATTCTGGATGCTCTTAATAAGCT
196 AAAAAAGCACAGAAGAAGATTAAAAGTGAGTTAAACAAGATTCTGGATGCTCTTAATAAGCT
1157240 GAATAAGGGA
Statistics
Matches: 245, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
258 245 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (258 bp):
TCATTCAGGAAAATGTACATTTCATTCGTGCATCAAAGCATCATACATAAAGCATAGCATAACAT
TTCTAATCATAATTATGGTGCTAAAAGTTCAAGGATAGCTCCATCTAGTGAGAACCCTGCCCATC
GATACAACACAAGATCCAGAGCCAAACAAATGGAGCAAAAAAATTCTCACAGATTTGAAAAGATA
AAAAAAGCACAGAAGAAGATTAAAAGTGAGTTAAACAAGATTCTGGATGCTCTTAATAAGCTA
Found at i:1159796 original size:8 final size:9
Alignment explanation
Indices: 1159783--1159831 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
1159773 AAGATGATGA
1159783 AAAAAAAT-
1 AAAAAAATG
1159791 -AAAAAATG
1 AAAAAAATG
1159799 AAAAAAATG
1 AAAAAAATG
1159808 AAAAAAATG
1 AAAAAAATG
1159817 -AAAAAATG
1 AAAAAAATG
1159825 AAAAAAA
1 AAAAAAA
1159832 AAAGATATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.18
8 8 0.21
9 23 0.61
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:1159831 original size:17 final size:17
Alignment explanation
Indices: 1159783--1159830 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
1159773 AAGATGATGA
1159783 AAAAAAAT-AAAAAATG
1 AAAAAAATGAAAAAATG
1159799 AAAAAAATGAAAAAAATG
1 AAAAAAATG-AAAAAATG
1159817 -AAAAAATGAAAAAA
1 AAAAAAATGAAAAAA
1159831 AAAAGATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.47
17 8 0.27
18 8 0.27
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (17 bp):
AAAAAAATGAAAAAATG
Found at i:1161383 original size:43 final size:42
Alignment explanation
Indices: 1161332--1161413 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 42
1161322 GCCTTTGAAC
*
1161332 TCAAATGAAAAGCTTT-GAATTTTTGGATGTGAATTTCCAAAAT
1 TCAAATGAAAAGCTTTAG-ATTTTTGGATATGAA-TTCCAAAAT
1161375 TCAAATGAAAAGCTTTAGATTTTTGGATATGAATTCCAA
1 TCAAATGAAAAGCTTTAGATTTTTGGATATGAATTCCAA
1161414 GTTTGCCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 6 0.16
43 30 0.81
44 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (42 bp):
TCAAATGAAAAGCTTTAGATTTTTGGATATGAATTCCAAAAT
Found at i:1161821 original size:41 final size:41
Alignment explanation
Indices: 1161706--1162203 Score: 502
Period size: 41 Copynumber: 12.0 Consensus size: 41
1161696 GATTGCCAAA
* * * * *
1161706 GAGCAATTTATTTTTTAAAGTTGT-GGTGCCTCTATTTATAG
1 GAGCAATTTACTTTTCAAAGTT-TCGTTGCCTCTGTTTAGAG
* ** *
1161747 GAGCAATTTACTTTCCAAAAGTTGAGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTC-AAAGTTTCGTTGCCTCTGTTTAGAG
*
1161789 GAGCAATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAG
*
1161830 GAGCAATTTACTTTTCAAAG--TCGTGGTACCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGTTTCGT--TGCCTCTGTTTAGAG
* *
1161871 GAGCAATTTACTTTCCAAAGTTGT-GGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGTT-TCGTTGCCTCTGTTTAGAG
*
1161912 GAG-ATATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAG
1 GAGCA-ATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAG
1161953 GAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGTTTCGT--TGCCTCTGTTTAGAG
* * *
1161994 GAGCAATTTACTTTCCAAAGTCAT-GGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGT-TTCGTTGCCTCTGTTTAGAG
*
1162035 GAGCAATTTACTTTTCAAAAG--TCGTGGTGCCTCTGTTTAGAC
1 GAGCAATTTACTTTTC-AAAGTTTCGT--TGCCTCTGTTTAGAG
1162077 GAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGTTTCGT--TGCCTCTGTTTAGAG
* ** * *
1162118 GAGTAATTTACTTTTCAAAAGTTGAGGTGCCTCTGATTAGAG
1 GAGCAATTTACTTTTC-AAAGTTTCGTTGCCTCTGTTTAGAG
* * *
1162160 GAGCCATTTATTTTTTCAAAG--TCGTTGAGCCTCTGCTTAGAG
1 GAGCAATTTA-CTTTTCAAAGTTTCGTT--GCCTCTGTTTAGAG
1162202 GA
1 GA
1162204 ATTTTGATCA
Statistics
Matches: 396, Mismatches: 36, Indels: 49
0.82 0.07 0.10
Matches are distributed among these distances:
39 9 0.02
40 5 0.01
41 256 0.65
42 116 0.29
43 7 0.02
44 3 0.01
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (41 bp):
GAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAG
Found at i:1161881 original size:82 final size:82
Alignment explanation
Indices: 1161706--1162203 Score: 614
Period size: 82 Copynumber: 6.0 Consensus size: 82
1161696 GATTGCCAAA
* * * * * *
1161706 GAGCAATTTATTTTTTAAAGTTGT-GGTGCCTCTATTTATAGGAGCAATTTACTTTCCAAAAGTT
1 GAGCAATTTACTTTTCAAAGTT-TCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTC
*
1161770 GAGGTGCCTCTGTTTAGAG
64 GTGGTGCCTCTGTTTAGAG
* *
1161789 GAGCAATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT
1 GAGCAATTTACTTTTCAAAGTTTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT
*
1161854 GGTACCTCTGTTTAGAG
66 GGTGCCTCTGTTTAGAG
* *
1161871 GAGCAATTTACTTTCCAAAGTTGT-GGTGCCTCTGTTTAGAGGAG-ATATTTACTTTACAAAGTT
1 GAGCAATTTACTTTTCAAAGTT-TCGGTGCCTCTGTTTAGAGGAGCA-ATTTACTTTTCAAAG--
1161934 TCGT--TGCCTCTGTTTAGAG
62 TCGTGGTGCCTCTGTTTAGAG
* * *
1161953 GAGCAATTTACTTTTCAAAGTCGT-GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCA
1 GAGCAATTTACTTTTCAAAGT-TTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCG
1162017 TGGTGCCTCTGTTTAGAG
65 TGGTGCCTCTGTTTAGAG
* *
1162035 GAGCAATTTACTTTTCAAAAGTCGT-GGTGCCTCTGTTTAGACGAGCAATTTACTTTTCAAAGTC
1 GAGCAATTTACTTTTC-AAAGT-TTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
1162099 GTGGTGCCTCTGTTTAGAG
64 GTGGTGCCTCTGTTTAGAG
* ** * * *
1162118 GAGTAATTTACTTTTCAAAAGTTGAGGTGCCTCTGATTAGAGGAGCCATTTATTTTTTCAAAGTC
1 GAGCAATTTACTTTTC-AAAGTTTCGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTTCAAAGTC
* * *
1162183 GTTGAGCCTCTGCTTAGAG
64 GTGGTGCCTCTGTTTAGAG
1162202 GA
1 GA
1162204 ATTTTGATCA
Statistics
Matches: 372, Mismatches: 31, Indels: 23
0.87 0.07 0.05
Matches are distributed among these distances:
80 3 0.01
81 1 0.00
82 177 0.48
83 158 0.42
84 33 0.09
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (82 bp):
GAGCAATTTACTTTTCAAAGTTTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT
GGTGCCTCTGTTTAGAG
Found at i:1161935 original size:123 final size:123
Alignment explanation
Indices: 1161706--1162203 Score: 711
Period size: 123 Copynumber: 4.0 Consensus size: 123
1161696 GATTGCCAAA
* * * * *
1161706 GAGCAATTTATTTTTTAAAGTTGTGGTGCCTCTATTTATAGGAGCAATTTACTTTCCAAAAGTTG
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC-AAAGTTG
1161771 AGGTGCCTCTGTTTAGAGGAGCAATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAG
65 AGGTGCCTCTGTTTAGAGGAGCAATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAG
* *
1161830 GAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTGT
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTGA
1161895 GGTGCCTCTGTTTAGAGGAG-ATATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAG
66 GGTGCCTCTGTTTAGAGGAGCA-ATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAG
*
1161953 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TCA
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTGA
* *
1162017 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAG--TCGTGGTGCCTCTGTTTAGAC
66 -GGTGCCTCTGTTTAGAGGAGCAATTTACTTTAC-AAAGTTTCGT--TGCCTCTGTTTAGAG
* *
1162077 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGTAATTTACTTTTCAAAAGTTG
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTTG
* * * * *
1162142 AGGTGCCTCTGATTAGAGGAGCCATTTATTTTTTCAAAG--TCGTTGAGCCTCTGCTTAGAG
65 AGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTACAAAGTTTCGTT--GCCTCTGTTTAGAG
1162202 GA
1 GA
1162204 ATTTTGATCA
Statistics
Matches: 343, Mismatches: 20, Indels: 21
0.89 0.05 0.05
Matches are distributed among these distances:
122 6 0.02
123 154 0.45
124 121 0.35
125 55 0.16
126 7 0.02
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (123 bp):
GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTGA
GGTGCCTCTGTTTAGAGGAGCAATTTACTTTACAAAGTTTCGTTGCCTCTGTTTAGAG
Found at i:1162397 original size:13 final size:11
Alignment explanation
Indices: 1162381--1162414 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
1162371 TTTCTTTATT
1162381 TTTTTATTTTACA
1 TTTTTATTTT--A
1162394 TTTTTATTTTA
1 TTTTTATTTTA
1162405 TTTTTATTTT
1 TTTTTATTTT
1162415 TATTATTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:1162402 original size:6 final size:6
Alignment explanation
Indices: 1162381--1162452 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
1162371 TTTCTTTATT
* * *
1162381 TTTTTA TTTTACA TTTTTA -TTTTA TTTTTA TTTTTA TTATTG TTTTTA
1 TTTTTA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
1162429 TATATA TTCTT- CTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
1162453 CTTATGTATT
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
5 8 0.16
6 36 0.73
7 5 0.10
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:1162578 original size:12 final size:12
Alignment explanation
Indices: 1162540--1162579 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1162530 TTATATGTTA
1162540 TAATTTATCTGT
1 TAATTTATCTGT
1162552 T-ATTTAAT-T-T
1 TAATTT-ATCTGT
1162562 TAATTTATCTGT
1 TAATTTATCTGT
1162574 TAATTT
1 TAATTT
1162580 TTTGATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (12 bp):
TAATTTATCTGT
Found at i:1162587 original size:20 final size:20
Alignment explanation
Indices: 1162540--1162602 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 20
1162530 TTATATGTTA
*
1162540 TAATTTATCTGTTATTTAATTT
1 TAATTTATCTGTTAATT--TTT
1162562 TAATTTATCTGTTAATTTTT
1 TAATTTATCTGTTAATTTTT
* *
1162582 TGATTTATCTGATTTATTTTT
1 TAATTTATCTG-TTAATTTTT
1162603 ATTAATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.35
21 8 0.22
22 16 0.43
ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65
Consensus pattern (20 bp):
TAATTTATCTGTTAATTTTT
Found at i:1164135 original size:9 final size:9
Alignment explanation
Indices: 1164121--1164151 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
1164111 TTCCAGTTTC
1164121 TTTTATATA
1 TTTTATATA
1164130 TTTTATATA
1 TTTTATATA
1164139 TTTTATATA
1 TTTTATATA
1164148 TTTT
1 TTTT
1164152 TTTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTATATA
Found at i:1164158 original size:18 final size:17
Alignment explanation
Indices: 1164121--1164251 Score: 92
Period size: 16 Copynumber: 7.8 Consensus size: 17
1164111 TTCCAGTTTC
* *
1164121 TTTTATATATTTTATATA
1 TTTT-TATATTTTTTTTA
1164139 TTTTATATATTTTTTTTA
1 TTTT-TATATTTTTTTTA
* * * *
1164157 TTATTAGATTATGTTTA
1 TTTTTATATTTTTTTTA
* *
1164174 -TTTAATA-TTCTTTTA
1 TTTTTATATTTTTTTTA
*
1164189 TTTTTATCTTTATTTTTA
1 TTTTTATATTT-TTTTTA
1164207 -TTTT-TATTTTTTTTA
1 TTTTTATATTTTTTTTA
* *
1164222 TTTTTA-CTTTTCTTTA
1 TTTTTATATTTTTTTTA
*
1164238 TTTTTTTATTTTTT
1 TTTTTATATTTTTT
1164252 ATTTTCACTT
Statistics
Matches: 86, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
15 11 0.13
16 30 0.35
17 21 0.24
18 24 0.28
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTATATTTTTTTTA
Found at i:1164193 original size:6 final size:6
Alignment explanation
Indices: 1164184--1164286 Score: 83
Period size: 6 Copynumber: 17.5 Consensus size: 6
1164174 TTTAATATTC
* *
1164184 TTTTAT TTTTAT CTTTAT TTTTAT TTTTA- -TTT-T TTTTAT TTTTAC
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * *
1164229 TTTTCT TTATT-T TTTTATT TTTTAT TTTCAC TTTTAT TTTGT-T TTATTA-
1 TTTTAT TT-TTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTT-TAT TT-TTAT
1164278 TTTTAT TTT
1 TTTTAT TTT
1164287 CTTTAAATAA
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
4 3 0.04
5 8 0.10
6 57 0.73
7 10 0.13
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:1164207 original size:33 final size:32
Alignment explanation
Indices: 1164144--1164286 Score: 91
Period size: 32 Copynumber: 4.5 Consensus size: 32
1164134 ATATATTTTA
* * ** *
1164144 TATATTTTTTTTATTATTAGATTATGTTTATT
1 TATATTTCTTTTATTTTTACTTTATCTTTATT
*
1164176 TA-ATATTCTTTTATTTTTATCTTTATTTTTATT
1 TATAT-TTCTTTTATTTTTA-CTTTATCTTTATT
* *
1164209 TTTATTTTTTTTATTTTTACTTT-TCTTTATT
1 TATATTTCTTTTATTTTTACTTTATCTTTATT
* * * *
1164240 T-TTTTATTTTTTATTTTCACTTTTAT-TTTGTT
1 TATATT-TCTTTTATTTTTAC-TTTATCTTTATT
*
1164272 T-TA-TTATTTTATTTT
1 TATATTTCTTTTATTTT
1164287 CTTTAAATAA
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
30 13 0.14
31 24 0.26
32 28 0.30
33 25 0.27
34 2 0.02
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (32 bp):
TATATTTCTTTTATTTTTACTTTATCTTTATT
Found at i:1164237 original size:25 final size:25
Alignment explanation
Indices: 1164209--1164291 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 25
1164199 TATTTTTATT
1164209 TTTATTTTTTTTA-TTTTTACTTTTC
1 TTTATTTTTTTTATTTTTTA-TTTTC
1164234 TTTA-TTTTTTTATTTTTTATTTTCAC
1 TTTATTTTTTTTATTTTTTATTTT--C
1164260 TTTTATTTTGTTTTATTATTTTATTTTC
1 -TTTATTTT-TTTTATT-TTTTATTTTC
1164288 TTTA
1 TTTA
1164292 AATAAAATCC
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
24 12 0.24
25 10 0.20
26 1 0.02
27 8 0.16
28 4 0.08
29 7 0.14
30 9 0.18
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (25 bp):
TTTATTTTTTTTATTTTTTATTTTC
Found at i:1164264 original size:37 final size:35
Alignment explanation
Indices: 1164195--1164286 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 35
1164185 TTTATTTTTA
* *
1164195 TCTTTATTTTTATT-TTTATTTTTTTTATTTTTACTTT
1 TCTTTATTTTT-TTATTT-TTTTTTTCACTTTTA-TTT
1164232 TCTTTATTTTTTTATTTTTTATTTTCACTTTTATTT
1 TCTTTATTTTTTTATTTTTT-TTTTCACTTTTATTT
* *
1164268 TGTTTTATTATTTTATTTT
1 T-CTTTATTTTTTTATTTT
1164287 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 9 0.19
37 39 0.81
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.79
Consensus pattern (35 bp):
TCTTTATTTTTTTATTTTTTTTTTCACTTTTATTT
Found at i:1164278 original size:13 final size:13
Alignment explanation
Indices: 1164137--1164286 Score: 52
Period size: 12 Copynumber: 11.5 Consensus size: 13
1164127 ATATTTTATA
1164137 TATTTTATATATTT
1 TATTTTAT-TATTT
1164151 T-TTTTATTATTAGAT
1 TATTTTATTATT---T
**
1164166 TATGTTTATT-TAA
1 TAT-TTTATTATTT
1164179 TATTCTT-TTATTTT
1 TATT-TTATTA-TTT
1164193 TATCTTTA-T-TTT
1 TAT-TTTATTATTT
1164205 TATTTTTATT-TTT
1 TA-TTTTATTATTT
*
1164218 T-TTATTTTTACTTT
1 TATT-TTATTA-TTT
* *
1164232 T-CTTTATTTTTT
1 TATTTTATTATTT
1164244 TATTTT-TTATTT
1 TATTTTATTATTT
*
1164256 TCA-CTT-TTATTT
1 T-ATTTTATTATTT
*
1164268 TGTTTTATTATTT
1 TATTTTATTATTT
1164281 TATTTT
1 TATTTT
1164287 CTTTAAATAA
Statistics
Matches: 103, Mismatches: 14, Indels: 39
0.66 0.09 0.25
Matches are distributed among these distances:
11 2 0.02
12 41 0.40
13 36 0.35
14 13 0.13
15 3 0.03
16 2 0.02
17 6 0.06
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (13 bp):
TATTTTATTATTT
Found at i:1164375 original size:58 final size:57
Alignment explanation
Indices: 1164303--1164630 Score: 374
Period size: 58 Copynumber: 5.7 Consensus size: 57
1164293 ATAAAATCCA
* * *
1164303 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCGATTTTTCTTAAAAATAAATTTTC
1 AAAAAAA-ATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
1164361 AAAAAAAAAATTTTGAGAAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 -AAAAAAAATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * *
1164419 AAAAAAAAAGTTTTTGAAGAAAAATTTAAAGTATTAATTTTTCTTAAAAATAAATTTTC
1 -AAAAAAAA-TTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
1164478 AAAAAAAGTTTTTG-GGAAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTT-
1 AAAAAAAATTTTTGAGG-AAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *** * * ** * *
1164534 TAAAACGGTTTTTGAGGAAAAGTTGAAAGTATAAATTTTCCTCGAAATTAAGGTTTTC
1 AAAAAAAATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAATAA-ATTTTC
* *
1164592 AAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAATTTTTGAG-GAAAAATTGAAAGTATCAATTTT
1164631 TTCTGCACAA
Statistics
Matches: 233, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
56 41 0.18
57 49 0.21
58 93 0.40
59 50 0.21
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (57 bp):
AAAAAAAATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:1165627 original size:29 final size:30
Alignment explanation
Indices: 1165582--1165638 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1165572 TTTTGTCCAT
*
1165582 TTAATTGAGTTGAAATAGAAGATTAAAAGC
1 TTAATTGAGTTGAAATAAAAGATTAAAAGC
* *
1165612 TTAATTGA-TTGTAATAAAATATTAAAA
1 TTAATTGAGTTGAAATAAAAGATTAAAA
1165639 ATTTAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (30 bp):
TTAATTGAGTTGAAATAAAAGATTAAAAGC
Found at i:1165644 original size:29 final size:29
Alignment explanation
Indices: 1165580--1165650 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1165570 GATTTTGTCC
*
1165580 ATTTAATTGAGTTGAAATAGAAGATTAAAA
1 ATTTAATTGA-TTGAAATAAAAGATTAAAA
** * *
1165610 GCTTAATTGATTGTAATAAAATATTAAAA
1 ATTTAATTGATTGAAATAAAAGATTAAAA
*
1165639 ATTTAAATGATT
1 ATTTAATTGATT
1165651 ATTAAATTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (29 bp):
ATTTAATTGATTGAAATAAAAGATTAAAA
Found at i:1166101 original size:42 final size:41
Alignment explanation
Indices: 1166012--1166101 Score: 92
Period size: 42 Copynumber: 2.2 Consensus size: 41
1166002 TACAACAATG
* * * **
1166012 TCTTACTTTCTGTAAAACTATATCTCTACTTAATTTCTTAT
1 TCTTTCTTTCTGTAAAACCATATCTCAACTTAATTTCCCAT
* *
1166053 TATTTCTTTACTGTACAACCATATCTCAACTTAA-TTCCCAT
1 TCTTTCTTT-CTGTAAAACCATATCTCAACTTAATTTCCCAT
1166094 CTCTTTCT
1 -TCTTTCT
1166102 CATACTTTGG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
41 12 0.31
42 27 0.69
ACGTcount: A:0.26, C:0.24, G:0.02, T:0.48
Consensus pattern (41 bp):
TCTTTCTTTCTGTAAAACCATATCTCAACTTAATTTCCCAT
Found at i:1183070 original size:40 final size:40
Alignment explanation
Indices: 1183015--1183128 Score: 192
Period size: 40 Copynumber: 2.9 Consensus size: 40
1183005 TTAGGACTTG
1183015 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
* *
1183055 GCCAATCATGAGACTGGCTCTCAAGGCTTTTATTTTCTTA
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
* *
1183095 GCTAATCACGAGACTGGTTCTCAAGGCTTTTATT
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATT
1183129 CTACTATTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (40 bp):
GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
Found at i:1185492 original size:4 final size:4
Alignment explanation
Indices: 1185485--1185520 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1185475 ATATATATAT
* *
1185485 ATAC ATAC ATAC ACAC ACAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1185521 TAGTTTTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (4 bp):
ATAC
Found at i:1185707 original size:21 final size:20
Alignment explanation
Indices: 1185681--1185790 Score: 53
Period size: 21 Copynumber: 5.3 Consensus size: 20
1185671 GATATATTTT
1185681 AATTTTGATAACCTTTGATAA
1 AATTTTGATAA-CTTTGATAA
* *
1185702 AATTTTGGA-AACCTTCA-ATA
1 AATTTT-GATAACTTTGATA-A
* * *
1185722 TATTTTGGTAACTTATGATAT
1 AATTTTGATAACTT-TGATAA
* * **
1185743 AAGTTTGGTAACTATTGATGC
1 AATTTTGATAACT-TTGATAA
* *
1185764 AATTTTAATAATTTTTGATAA
1 AATTTTGATAA-CTTTGATAA
1185785 AATTTT
1 AATTTT
1185791 AATACTCTCT
Statistics
Matches: 65, Mismatches: 17, Indels: 14
0.68 0.18 0.15
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 44 0.68
22 5 0.08
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (20 bp):
AATTTTGATAACTTTGATAA
Found at i:1185791 original size:21 final size:22
Alignment explanation
Indices: 1185764--1185817 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1185754 CTATTGATGC
*
1185764 AATTTTAATAAT-TTTTGATAA
1 AATTTTAATAATCTCTTGATAA
* **
1185785 AATTTTAATACTCTCTTGATGT
1 AATTTTAATAATCTCTTGATAA
1185807 AATTTTAATAA
1 AATTTTAATAA
1185818 GCTTTAGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTTTAATAATCTCTTGATAA
Found at i:1185810 original size:22 final size:21
Alignment explanation
Indices: 1185757--1185817 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1185747 TTGGTAACTA
* *
1185757 TTGATGCAATTTTAATAATTT
1 TTGATGAAATTTTAATAATTC
* *
1185778 TTGATAAAATTTTAATACTCTC
1 TTGATGAAATTTTAATAAT-TC
*
1185800 TTGATGTAATTTTAATAA
1 TTGATGAAATTTTAATAA
1185818 GCTTTAGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (21 bp):
TTGATGAAATTTTAATAATTC
Found at i:1185948 original size:19 final size:21
Alignment explanation
Indices: 1185921--1185963 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1185911 TCAGTTCTAA
*
1185921 TATAAAAT-A-ATTTTTATTT
1 TATAAAATAACATTATTATTT
*
1185940 TATATAATAACATTATTATTT
1 TATAAAATAACATTATTATTT
1185961 TAT
1 TAT
1185964 TCAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATAAAATAACATTATTATTT
Found at i:1186076 original size:44 final size:44
Alignment explanation
Indices: 1186028--1186201 Score: 125
Period size: 44 Copynumber: 4.0 Consensus size: 44
1186018 ACAATTTAGT
* ** * **
1186028 TATCATTGATTTATTATTATGTTATTAATGATTTGTTACTAAAC
1 TATCATTGATTTATTAATAAATTATTAATAATTTACTACTAAAC
* * *
1186072 TATCAATGATATATTAATAAATTATTAATAATTTACTACTAAAT
1 TATCATTGATTTATTAATAAATTATTAATAATTTACTACTAAAC
* * * * * * *
1186116 TA-CTATTGATTTAATACTAATTTGTAAATGATTTACTACTAAAT
1 TATC-ATTGATTTATTAATAAATTATTAATAATTTACTACTAAAC
* * * * * * *
1186160 TATTACTGATTTACTACTAAATTGTTGATGATTTACTACTAA
1 TATCATTGATTTATTAATAAATTATTAATAATTTACTACTAA
1186202 GTTACTAATG
Statistics
Matches: 105, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
43 1 0.01
44 104 0.99
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (44 bp):
TATCATTGATTTATTAATAAATTATTAATAATTTACTACTAAAC
Found at i:1186117 original size:22 final size:22
Alignment explanation
Indices: 1186049--1186211 Score: 155
Period size: 22 Copynumber: 7.4 Consensus size: 22
1186039 TATTATTATG
**
1186049 TTATTAATGATTTGTTACTAAA
1 TTATTAATGATTTACTACTAAA
* * * * *
1186071 CTATCAATGATATATTAATAAA
1 TTATTAATGATTTACTACTAAA
*
1186093 TTATTAATAATTTACTACTAAA
1 TTATTAATGATTTACTACTAAA
* * * *
1186115 TTACTATTGATTTAATACTAAT
1 TTATTAATGATTTACTACTAAA
* *
1186137 TTGTAAATGATTTACTACTAAA
1 TTATTAATGATTTACTACTAAA
*
1186159 TTATTACTGATTTACTACTAAA
1 TTATTAATGATTTACTACTAAA
* * *
1186181 TTGTTGATGATTTACTACTAAG
1 TTATTAATGATTTACTACTAAA
*
1186203 TTACTAATG
1 TTATTAATG
1186212 GTTGATTATA
Statistics
Matches: 109, Mismatches: 32, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 109 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (22 bp):
TTATTAATGATTTACTACTAAA
Found at i:1186138 original size:11 final size:11
Alignment explanation
Indices: 1186100--1186179 Score: 54
Period size: 11 Copynumber: 7.3 Consensus size: 11
1186090 AAATTATTAA
1186100 TAATTTACTAC
1 TAATTTACTAC
* *
1186111 TAAATTACTAT
1 TAATTTACTAC
* *
1186122 TGATTTAATAC
1 TAATTTACTAC
* *
1186133 TAATTT-GTAAA
1 TAATTTACT-AC
*
1186144 TGATTTACTAC
1 TAATTTACTAC
* *
1186155 TAAATTATTAC
1 TAATTTACTAC
*
1186166 TGATTTACTAC
1 TAATTTACTAC
1186177 TAA
1 TAA
1186180 ATTGTTGATG
Statistics
Matches: 48, Mismatches: 19, Indels: 4
0.68 0.27 0.06
Matches are distributed among these distances:
10 1 0.02
11 46 0.96
12 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (11 bp):
TAATTTACTAC
Found at i:1186338 original size:44 final size:44
Alignment explanation
Indices: 1186290--1186379 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
1186280 AACTAATTAG
* * *
1186290 CTACTAAATTATCACTTATTTATCA-CTAAATTATTAGTAATTTA
1 CTACTAAATTATCAATAATTTA-CATCTAAATTATCAGTAATTTA
* * *
1186334 CTACTAAGTTATTAATAATTTACATCTAAATTATCATTAATTTA
1 CTACTAAATTATCAATAATTTACATCTAAATTATCAGTAATTTA
1186378 CT
1 CT
1186380 GTTATGTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.05
44 37 0.95
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (44 bp):
CTACTAAATTATCAATAATTTACATCTAAATTATCAGTAATTTA
Found at i:1186389 original size:22 final size:22
Alignment explanation
Indices: 1186290--1186425 Score: 84
Period size: 22 Copynumber: 6.2 Consensus size: 22
1186280 AACTAATTAG
*
1186290 CTACTAAATTATCACTT-ATTTA
1 CTACTATATTATCA-TTAATTTA
* * *
1186312 -TCACTAAATTATTAGTAATTTA
1 CT-ACTATATTATCATTAATTTA
* *
1186334 CTACTA-AGTTATTAATAATTTA
1 CTACTATA-TTATCATTAATTTA
*
1186356 C-ATCTAAATTATCATTAATTTA
1 CTA-CTATATTATCATTAATTTA
** * *
1186378 CTGTTATGTTATTA-TACATTTA
1 CTACTATATTATCATTA-ATTTA
*
1186400 CTACTATATTATCATTGATTTA
1 CTACTATATTATCATTAATTTA
1186422 CTAC
1 CTAC
1186426 ATAGCTTTTG
Statistics
Matches: 90, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
21 6 0.07
22 81 0.90
23 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (22 bp):
CTACTATATTATCATTAATTTA
Found at i:1186389 original size:44 final size:44
Alignment explanation
Indices: 1186307--1186425 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 44
1186297 ATTATCACTT
* *
1186307 ATTTATCA-CTAAATTATTAGTAATTTACTACTAAGTTATTAATA-
1 ATTTA-CATCTAAATTATCATTAATTTACTACTAAGTTATT-ATAC
** *
1186351 ATTTACATCTAAATTATCATTAATTTACTGTTATGTTATTATAC
1 ATTTACATCTAAATTATCATTAATTTACTACTAAGTTATTATAC
* *
1186395 ATTTAC-TACTATATTATCATTGATTTACTAC
1 ATTTACAT-CTAAATTATCATTAATTTACTAC
1186426 ATAGCTTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
43 6 0.10
44 57 0.90
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (44 bp):
ATTTACATCTAAATTATCATTAATTTACTACTAAGTTATTATAC
Found at i:1186485 original size:22 final size:21
Alignment explanation
Indices: 1186439--1186478 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1186429 GCTTTTGATT
1186439 ATTTACTACAAAATCATAACAA
1 ATTTACTACAAAAT-ATAACAA
*
1186461 ATTTATTACAAAAT-TAAC
1 ATTTACTACAAAATATAAC
1186479 CATAATTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
22 13 0.76
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTTACTACAAAATATAACAA
Found at i:1186549 original size:22 final size:22
Alignment explanation
Indices: 1186496--1186800 Score: 137
Period size: 22 Copynumber: 13.8 Consensus size: 22
1186486 CGTTATCAAG
1186496 TTATCATTGATTTA-TATTAAA
1 TTATCATTGATTTACTATTAAA
*
1186517 TTATCCA-TGATTTACTCTTAAA
1 TTAT-CATTGATTTACTATTAAA
* *
1186539 TTATCATTGATTAACTATTAAGT
1 TTATCATTGATTTACTATTAA-A
* * *
1186562 TTTTGA-TGATTAACTACTATTAAG
1 TTATCATTGATT---TACTATTAAA
* * * *
1186586 TCAT-GTTGATTTACTTTTAAG
1 TTATCATTGATTTACTATTAAA
* * * *
1186607 TTTTCAATGATTAACTACTAAA
1 TTATCATTGATTTACTATTAAA
*
1186629 TTATCATTGATTTACTATTAAG
1 TTATCATTGATTTACTATTAAA
* * * * *
1186651 CTAT-TTATGAGTAACTACTAAA
1 TTATCAT-TGATTTACTATTAAA
* *
1186673 TTAATTAATT-AATTACTATTAAA
1 TT-A-TCATTGATTTACTATTAAA
* * *
1186696 TTGA-AACTAATTTACTATTAAA
1 TT-ATCATTGATTTACTATTAAA
*
1186718 TTATCATTAATTTACTATTAAA
1 TTATCATTGATTTACTATTAAA
*
1186740 TTATCAGTT-A-TTACCTA-AAAA
1 TTATCA-TTGATTTA-CTATTAAA
** *
1186761 GTTATCACTT-ATTTTTTATTAAC
1 -TTATCA-TTGATTTACTATTAAA
*
1186784 GTATCATTGATTTACTA
1 TTATCATTGATTTACTA
1186801 ATATGTTGTT
Statistics
Matches: 213, Mismatches: 50, Indels: 41
0.70 0.16 0.13
Matches are distributed among these distances:
21 37 0.17
22 134 0.63
23 24 0.11
24 9 0.04
25 9 0.04
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (22 bp):
TTATCATTGATTTACTATTAAA
Found at i:1186666 original size:44 final size:44
Alignment explanation
Indices: 1186496--1186738 Score: 166
Period size: 44 Copynumber: 5.5 Consensus size: 44
1186486 CGTTATCAAG
* *
1186496 TTATCATTGATTTA-TATTAA--ATTATCCATGATTTACT-CTTAAA
1 TTATCATTGATTTACTATTAAGTATT-T-AATGATTAACTAC-TAAA
* * *
1186539 TTATCATTGATTAACTATTAAGTTTTTGATGATTAACTACT--A
1 TTATCATTGATTTACTATTAAGTATTTAATGATTAACTACTAAA
*
1186581 TTAAGTCATGTTGATTTACTTTTAAGT-TTTCAATGATTAACTACTAAA
1 TT-A-TCA--TTGATTTACTATTAAGTATTT-AATGATTAACTACTAAA
*
1186629 TTATCATTGATTTACTATTAAGCTATTT-ATGAGTAACTACTAAA
1 TTATCATTGATTTACTATTAAG-TATTTAATGATTAACTACTAAA
* * * * * *
1186673 TTAATTAATT-AATTACTATTAA--ATTGAAACTAATTTACTATTAAA
1 TT-A-TCATTGATTTACTATTAAGTATT-TAA-TGATTAACTACTAAA
*
1186718 TTATCATTAATTTACTATTAA
1 TTATCATTGATTTACTATTAA
1186739 ATTATCAGTT
Statistics
Matches: 163, Mismatches: 18, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
42 6 0.04
43 18 0.11
44 64 0.39
45 31 0.19
46 40 0.25
47 1 0.01
48 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (44 bp):
TTATCATTGATTTACTATTAAGTATTTAATGATTAACTACTAAA
Found at i:1187239 original size:9 final size:9
Alignment explanation
Indices: 1187225--1187250 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1187215 ATTTTTCATT
1187225 ATTATTATG
1 ATTATTATG
1187234 ATTATTATG
1 ATTATTATG
1187243 ATTATTAT
1 ATTATTAT
1187251 TTATCTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
ATTATTATG
Found at i:1187271 original size:21 final size:22
Alignment explanation
Indices: 1187247--1187337 Score: 107
Period size: 21 Copynumber: 4.3 Consensus size: 22
1187237 ATTATGATTA
1187247 TTATTTATCTATTAA-TATTTT
1 TTATTTATCTATTAATTATTTT
* *
1187268 TTATTTACCTATTAATTTTTTT
1 TTATTTATCTATTAATTATTTT
* *
1187290 TTAGTTATCTATTAA-TATATT
1 TTATTTATCTATTAATTATTTT
* *
1187311 TTA-TTATTTATCAATTATTTT
1 TTATTTATCTATTAATTATTTT
1187332 TTATTT
1 TTATTT
1187338 TTATCTTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.16
21 29 0.50
22 20 0.34
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (22 bp):
TTATTTATCTATTAATTATTTT
Found at i:1187332 original size:43 final size:43
Alignment explanation
Indices: 1187251--1187334 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
1187241 TGATTATTAT
* *
1187251 TTATCTATTAATATTTTTTATTTACCTATTAATTTTTTTTTAG
1 TTATCTATTAATATATTTTATTTACCTATCAATTTTTTTTTAG
** *
1187294 TTATCTATTAATATATTTTA-TTATTTATCAATTATTTTTTA
1 TTATCTATTAATATATTTTATTTACCTATCAATTTTTTTTTA
1187335 TTTTTATCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 17 0.47
43 19 0.53
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (43 bp):
TTATCTATTAATATATTTTATTTACCTATCAATTTTTTTTTAG
Found at i:1187349 original size:18 final size:20
Alignment explanation
Indices: 1187212--1187342 Score: 68
Period size: 22 Copynumber: 6.0 Consensus size: 20
1187202 ATTTAATTTA
* *
1187212 ATTATTTTTCATTATTATTATG
1 ATTATTTTTTATTA-T-TTATC
*
1187234 ATTATTATGATTATTATTTATC
1 ATTATT-T-TTTATTATTTATC
* *
1187256 TATTAATATTTT-TTATTTACC
1 -ATT-ATTTTTTATTATTTATC
* *
1187277 TATTAATTTTTTTTTAGTTATC
1 -ATT-ATTTTTTATTATTTATC
1187299 TATTAATATATTTTATTATTTATC
1 -ATT-AT-T-TTTTATTATTTATC
1187323 AATTATTTTTTATT-TTTATC
1 -ATTATTTTTTATTATTTATC
1187343 TTTTTTTCTT
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
20 6 0.07
21 26 0.29
22 27 0.30
23 9 0.10
24 22 0.24
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTATTTTTTATTATTTATC
Found at i:1188129 original size:17 final size:17
Alignment explanation
Indices: 1188107--1188139 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1188097 CGATTCAAGG
1188107 TTTATT-TTATTTATTTA
1 TTTATTATTA-TTATTTA
1188124 TTTATTATTATTATTT
1 TTTATTATTATTATTT
1188140 TAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTATTATTATTTA
Found at i:1203621 original size:22 final size:22
Alignment explanation
Indices: 1203570--1203631 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1203560 NNNNNNNNNN
*
1203570 ATTGATTTACTATTAAATTATC
1 ATTGATTTACTATTAAGTTATC
* *
1203592 ACTAATTTACTATTAAGTTATC
1 ATTGATTTACTATTAAGTTATC
* *
1203614 ATTGATTTATTACTAAGT
1 ATTGATTTACTATTAAGT
1203632 GATTAATAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTGATTTACTATTAAGTTATC
Found at i:1203799 original size:44 final size:44
Alignment explanation
Indices: 1203741--1203833 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
1203731 TTATTATTGT
*
1203741 ATTATTATAAATTTACTAAAAAGTTATCAACT-ATTAACTATTAA
1 ATTATTATAAATTTACTAAAAAGTTAT-AAATAATTAACTATTAA
** ** * *
1203785 ATTATTATTCATTTACTATTAAGTTATAAATAATTTATTATTAA
1 ATTATTATAAATTTACTAAAAAGTTATAAATAATTAACTATTAA
1203829 ATTAT
1 ATTAT
1203834 CTATGATTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.07
44 38 0.93
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (44 bp):
ATTATTATAAATTTACTAAAAAGTTATAAATAATTAACTATTAA
Found at i:1203802 original size:22 final size:22
Alignment explanation
Indices: 1203777--1203833 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1203767 TCAACTATTA
* * *
1203777 ACTATTAAATTATTATTCATTT
1 ACTATTAAATTATAAATAATTT
*
1203799 ACTATTAAGTTATAAATAATTT
1 ACTATTAAATTATAAATAATTT
*
1203821 ATTATTAAATTAT
1 ACTATTAAATTAT
1203834 CTATGATTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
ACTATTAAATTATAAATAATTT
Found at i:1203899 original size:22 final size:21
Alignment explanation
Indices: 1203777--1203900 Score: 65
Period size: 22 Copynumber: 5.8 Consensus size: 21
1203767 TCAACTATTA
* * *
1203777 ACTATTAAATTATTATTCATTT
1 ACTATTAAGTTATTAATGA-TT
* *
1203799 ACTATTAAGTTATAAATAATTT
1 ACTATTAAGTTATTAATGA-TT
* *
1203821 ATTATTAAATTATCT-ATGATT
1 ACTATTAAGTTAT-TAATGATT
* *
1203842 ACTACTAAGTTA-TATTGATT
1 ACTATTAAGTTATTAATGATT
* * *
1203862 A-TGTTTGAGTTTTTAATGATT
1 ACT-ATTAAGTTATTAATGATT
*
1203883 AATTATTAAGTTATTAAT
1 -ACTATTAAGTTATTAAT
1203901 TATCCATTAC
Statistics
Matches: 76, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.03
20 11 0.14
21 18 0.24
22 44 0.58
23 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
ACTATTAAGTTATTAATGATT
Found at i:1204410 original size:104 final size:105
Alignment explanation
Indices: 1204229--1204439 Score: 370
Period size: 104 Copynumber: 2.0 Consensus size: 105
1204219 CCTCAACTTA
1204229 TATAACAGCAACTTGATCAACAAATGAATGATTATAAAACTCGTTAATCTAGATTAGTATTTCTA
1 TATAACAGCAACTTGATCAACAAATGAATGATTATAAAACTCGTTAATCTAGATTAGTATTTCTA
*
1204294 TGATACAAATTTCAAAATCTTCAAAAAGAGATATATTCTT
66 TGATACAAATTTCAAAATCCTCAAAAAGAGATATATTCTT
*
1204334 TATAATAGCAACTTGATCAACAAATGAATGATTAT-AAACTCGTTAATCTAGATTAGTATTTCTA
1 TATAACAGCAACTTGATCAACAAATGAATGATTATAAAACTCGTTAATCTAGATTAGTATTTCTA
* * *
1204398 TTATACAAATTTCAAAATCCTCAAAAGGAGATATATTTTT
66 TGATACAAATTTCAAAATCCTCAAAAAGAGATATATTCTT
1204438 TA
1 TA
1204440 ATCTCTGCAA
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
104 67 0.66
105 34 0.34
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (105 bp):
TATAACAGCAACTTGATCAACAAATGAATGATTATAAAACTCGTTAATCTAGATTAGTATTTCTA
TGATACAAATTTCAAAATCCTCAAAAAGAGATATATTCTT
Found at i:1205918 original size:17 final size:16
Alignment explanation
Indices: 1205871--1205918 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
1205861 TTAATTTTTC
1205871 TTTTATT-TA-AAAAA
1 TTTTATTATACAAAAA
*
1205885 TTTTATTATACATAAA
1 TTTTATTATACAAAAA
*
1205901 TTCTTATTATATAAAAA
1 TT-TTATTATACAAAAA
1205918 T
1 T
1205919 ATTAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.25
15 2 0.07
16 6 0.21
17 13 0.46
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTATTATACAAAAA
Found at i:1207144 original size:57 final size:57
Alignment explanation
Indices: 1206891--1207570 Score: 939
Period size: 57 Copynumber: 11.7 Consensus size: 57
1206881 TTGTGTAGGA
* *
1206891 AAAATTGATACTTTCAACTTTTCCCCAAAAATATCTTTTTTGGAAATTTAATTTTT-AGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGAAAATTT-ATTTTTAAGG
* * * * * *
1206950 AAAATTGATACTTCCAACTTTTCCTCAAAATTTTTTTTTTGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAA-ATATTTTTTGAAAATTT-ATTTTTAAGG
* * *
1207009 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGAAAATTTATTTTTAAGG
* * *
1207068 AAAATTGATACTTTTAACTTTTCCCCAAAAATAATTTTCGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
* * *
1207125 AAAATTGATACTTCCAACTTTTCCTCAAAAATATTTTTTTTAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTATTTTTAAGG
1207183 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
* * *
1207240 AAAATTGATACTTTTAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
* *
1207297 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTCATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
* *
1207354 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
* * * * ***
1207411 AAAATTGATACTTTCAACTTGTCCTCAAAAAAATTTTTTTTGAAACTTTGATTTCCGAGG
1 AAAATTGATACTTTCAACTTTTCC-C-CAAAAATATTTTTTGAAAATTT-ATTTTTAAGG
* *
1207471 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGAAAATTTATTTTTAAGG
1207530 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGA
1207571 TTTTTATTTA
Statistics
Matches: 554, Mismatches: 57, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
57 266 0.48
58 75 0.14
59 152 0.27
60 61 0.11
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
Found at i:1207608 original size:22 final size:22
Alignment explanation
Indices: 1207583--1207624 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1207573 TTTATTTAAA
1207583 GAAAATAGAACAAA-ATAAAAGT
1 GAAAATA-AACAAAGATAAAAGT
*
1207605 GAAAATAAATAAAGATAAAA
1 GAAAATAAACAAAGATAAAA
1207625 AAAATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14
Consensus pattern (22 bp):
GAAAATAAACAAAGATAAAAGT
Found at i:1207618 original size:15 final size:15
Alignment explanation
Indices: 1207606--1207673 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
1207596 AATAAAAGTG
*
1207606 AAAATAAATAAAGAT
1 AAAAAAAATAAAGAT
1207621 AAAAAAAATAAAGA-
1 AAAAAAAATAAAGAT
* * *
1207635 AAAGTAAAACAAAAAT
1 AAA-AAAAATAAAGAT
*
1207651 AAAAATTAGATAAAGAT
1 AAAAA--AAATAAAGAT
1207668 AAAAAA
1 AAAAAA
1207674 TATTAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
14 3 0.07
15 23 0.56
16 3 0.07
17 12 0.29
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.15
Consensus pattern (15 bp):
AAAAAAAATAAAGAT
Found at i:1207642 original size:19 final size:21
Alignment explanation
Indices: 1207606--1207664 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1207596 AATAAAAGTG
*
1207606 AAAATAAATAAAGAT-AAA-A
1 AAAATAAAAAAAGATAAAACA
1207625 AAAATAAAGAAAAG-TAAAACA
1 AAAATAAA-AAAAGATAAAACA
*
1207646 AAAATAAAAATTAGATAAA
1 AAAATAAAAA-AAGATAAA
1207665 GATAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 9 0.27
20 9 0.27
21 11 0.33
22 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAATAAAAAAAGATAAAACA
Found at i:1207711 original size:47 final size:46
Alignment explanation
Indices: 1207606--1207729 Score: 110
Period size: 47 Copynumber: 2.7 Consensus size: 46
1207596 AATAAAAGTG
*
1207606 AAAATAAATAAAGATAAAAAAAATAAAGAAAAGTAAAACAAAAATA
1 AAAATAAATAAAGATAAAAAAAATAAAGAAAACTAAAACAAAAATA
* * * * * * *
1207652 AAAATTAGATAAAGATAAAAAATATTAAATAAATCT-AATCTAATATA
1 AAAA-TAAATAAAGATAAAAAA-AATAAAGAAAACTAAAACAAAAATA
* *
1207699 ATAAATAAAT-AA-ATAAAACAAATAAATAAAA
1 A-AAATAAATAAAGATAAAAAAAATAAAGAAAA
1207730 AAATTCCAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
44 9 0.14
45 7 0.11
46 6 0.10
47 29 0.46
48 12 0.19
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (46 bp):
AAAATAAATAAAGATAAAAAAAATAAAGAAAACTAAAACAAAAATA
Found at i:1207721 original size:13 final size:12
Alignment explanation
Indices: 1207693--1207733 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
1207683 AATCTAATCT
*
1207693 AATATAATAAATA
1 AATA-AATAAAAA
1207706 AATAAATAAAACA
1 AATAAATAAAA-A
1207719 AATAAATAAAAA
1 AATAAATAAAAA
1207731 AAT
1 AAT
1207734 TCCAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (12 bp):
AATAAATAAAAA
Found at i:1207721 original size:17 final size:16
Alignment explanation
Indices: 1207701--1207732 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1207691 CTAATATAAT
1207701 AAATAAATAAATAAAAC
1 AAATAAATAAA-AAAAC
1207718 AAATAAATAAAAAAA
1 AAATAAATAAAAAAA
1207733 TTCCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAAATAAAAAAAC
Found at i:1208632 original size:19 final size:19
Alignment explanation
Indices: 1208587--1208632 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1208577 AAAAAATAAT
*
1208587 AATAATAATCAGATAATCG
1 AATAAAAATCAGATAATCG
1208606 AA-AAAAATCAGATAAAT-G
1 AATAAAAATCAGAT-AATCG
1208624 AATAAAAAT
1 AATAAAAAT
1208633 AAAATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.22
Consensus pattern (19 bp):
AATAAAAATCAGATAATCG
Found at i:1208752 original size:20 final size:21
Alignment explanation
Indices: 1208681--1208760 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
1208671 TAACTATATA
* *
1208681 AATAAAATACATGTAAATATT
1 AATAAAATACATATAAATAAT
* *
1208702 AACAAAATA-AAATAAATAAAT
1 AATAAAATACATATAAAT-AAT
*
1208723 AA-AGACATACATAT-AATAAT
1 AATA-AAATACATATAAATAAT
1208743 AATAAAATACATA-AAATA
1 AATAAAATACATATAAATA
1208761 CAAAAGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 24 0.51
21 20 0.43
22 3 0.06
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (21 bp):
AATAAAATACATATAAATAAT
Found at i:1208773 original size:15 final size:16
Alignment explanation
Indices: 1208755--1208796 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1208745 TAAAATACAT
1208755 AAAATACAAAAGAAAA
1 AAAATACAAAAGAAAA
*
1208771 AAAATA-AAAATAAAA
1 AAAATACAAAAGAAAA
*
1208786 ATAATACAAAA
1 AAAATACAAAA
1208797 TAAAGATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAATACAAAAGAAAA
Found at i:1208797 original size:16 final size:16
Alignment explanation
Indices: 1208755--1208800 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1208745 TAAAATACAT
*
1208755 AAAATACAAAAGAAAA
1 AAAATACAAAATAAAA
1208771 AAAATA-AAAATAAAA
1 AAAATACAAAATAAAA
*
1208786 ATAATACAAAATAAA
1 AAAATACAAAATAAA
1208801 GATTGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (16 bp):
AAAATACAAAATAAAA
Found at i:1208995 original size:9 final size:9
Alignment explanation
Indices: 1208955--1209000 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
1208945 AACATTGTCA
1208955 TTTTTTGTT
1 TTTTTTGTT
*
1208964 TTTTGTGTT
1 TTTTTTGTT
*
1208973 TTTTGTGTT
1 TTTTTTGTT
1208982 TTTTTTGTT
1 TTTTTTGTT
1208991 TTTTTT-TT
1 TTTTTTGTT
1208999 TT
1 TT
1209001 GACCAAAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 4 0.11
9 31 0.89
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:1209101 original size:41 final size:41
Alignment explanation
Indices: 1209008--1209220 Score: 259
Period size: 41 Copynumber: 5.1 Consensus size: 41
1208998 TTTGACCAAA
* *
1209008 GCTCCTCTAAACAGAGGCT-CAACAACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGG-TACCACGACTTTGA-AAA-ATAAATT
* *
1209051 GCTCCTCTAAACAGAGGTAGCACGATTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATT
* **
1209092 GCTCCTCTAAGCAGAGGTACCACGACTTTGAAAGGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATT
* *
1209133 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATT
* * * *
1209174 GCTCATCTAAACAGAGGCAACA-GAACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGTACCACG-ACTTTGAAAAATAAATT
1209215 GCTCCT
1 GCTCCT
1209221 TGACAATCAT
Statistics
Matches: 151, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 121 0.80
42 4 0.03
43 25 0.17
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATT
Found at i:1209504 original size:55 final size:55
Alignment explanation
Indices: 1209442--1209615 Score: 173
Period size: 55 Copynumber: 3.4 Consensus size: 55
1209432 GGAGGCTCAC
1209442 ATCCAAAAGT-TCAAAGCTTTTTTAAAGGTTCTTATTTGGCAAACTTGGAATTCAT
1 ATCCAAAAGTCT-AAAGCTTTTTTAAAGGTTCTTATTTGGCAAACTTGGAATTCAT
* * *
1209497 ATCCAAAAGTCTAAAGC--TTTT-CA--TT-TGAATTTTGG---A-----AATTCAC
1 ATCCAAAAGTCTAAAGCTTTTTTAAAGGTTCT-TA-TTTGGCAAACTTGGAATTCAT
1209540 ATCCAAAAGTTC-AAAGCTTTTTTAAAGGTTCTTATTTGGCAAACTTGGAATTCAT
1 ATCCAAAAG-TCTAAAGCTTTTTTAAAGGTTCTTATTTGGCAAACTTGGAATTCAT
1209595 ATCCAAAAGTCTAAAGCTTTT
1 ATCCAAAAGTCTAAAGCTTTT
1209616 CATTTGAATT
Statistics
Matches: 94, Mismatches: 6, Indels: 38
0.68 0.04 0.28
Matches are distributed among these distances:
43 20 0.21
44 2 0.02
45 4 0.04
46 1 0.01
47 5 0.05
48 4 0.04
49 2 0.02
50 4 0.04
51 5 0.05
52 1 0.01
53 4 0.04
54 2 0.02
55 39 0.41
56 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (55 bp):
ATCCAAAAGTCTAAAGCTTTTTTAAAGGTTCTTATTTGGCAAACTTGGAATTCAT
Found at i:1209523 original size:44 final size:44
Alignment explanation
Indices: 1209475--1209665 Score: 142
Period size: 43 Copynumber: 4.1 Consensus size: 44
1209465 AAAGGTTCTT
1209475 ATTTGGCAAACTTGG-AATTCATATCCAAAAG-TCTAAAGCTTTTC
1 ATTTGG-AAACTTGGAAATTCATATCCAAAAGTTC-AAAGCTTTTC
** *
1209519 ATTT-GAATTTTGGAAATTCACATCCAAAAGTTCAAAGCTTTTTTAAAGGTTC
1 ATTTGGAAACTTGGAAATTCATATCCAAAAGTTCAAAGC----TT-----TTC
1209571 TTATTTGGCAAACTTGG-AATTCATATCCAAAAG-TCTAAAGCTTTTC
1 --ATTTGG-AAACTTGGAAATTCATATCCAAAAGTTC-AAAGCTTTTC
** *
1209617 ATTT-GAATTTTGGAAATTCATATCCAAAAAATTCAAAGCTTTTC
1 ATTTGGAAACTTGGAAATTCATATCC-AAAAGTTCAAAGCTTTTC
1209661 ATTTG
1 ATTTG
1209666 AGTTCAAAGG
Statistics
Matches: 118, Mismatches: 9, Indels: 39
0.71 0.05 0.23
Matches are distributed among these distances:
42 12 0.10
43 33 0.28
44 28 0.24
45 2 0.02
46 3 0.03
47 2 0.02
51 2 0.02
52 3 0.03
54 6 0.05
55 21 0.18
56 6 0.05
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (44 bp):
ATTTGGAAACTTGGAAATTCATATCCAAAAGTTCAAAGCTTTTC
Found at i:1209588 original size:98 final size:98
Alignment explanation
Indices: 1209419--1209659 Score: 428
Period size: 98 Copynumber: 2.4 Consensus size: 98
1209409 TCAAAGATCC
***
1209419 TCATTTGAATTTTGGAGGCTCACATCCAAAAGTTCAAAGCTTTTTTAAAGGTTCTTATTTGGCAA
1 TCATTTGAATTTTGGAAATTCACATCCAAAAGTTCAAAGCTTTTTTAAAGGTTCTTATTTGGCAA
1209484 ACTTGGAATTCATATCCAAAAGTCTAAAGCTTT
66 ACTTGGAATTCATATCCAAAAGTCTAAAGCTTT
1209517 TCATTTGAATTTTGGAAATTCACATCCAAAAGTTCAAAGCTTTTTTAAAGGTTCTTATTTGGCAA
1 TCATTTGAATTTTGGAAATTCACATCCAAAAGTTCAAAGCTTTTTTAAAGGTTCTTATTTGGCAA
1209582 ACTTGGAATTCATATCCAAAAGTCTAAAGCTTT
66 ACTTGGAATTCATATCCAAAAGTCTAAAGCTTT
* *
1209615 TCATTTGAATTTTGGAAATTCATATCCAAAAAATTCAAAGCTTTT
1 TCATTTGAATTTTGGAAATTCACATCC-AAAAGTTCAAAGCTTTT
1209660 CATTTGAGTT
Statistics
Matches: 137, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
98 121 0.88
99 16 0.12
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (98 bp):
TCATTTGAATTTTGGAAATTCACATCCAAAAGTTCAAAGCTTTTTTAAAGGTTCTTATTTGGCAA
ACTTGGAATTCATATCCAAAAGTCTAAAGCTTT
Found at i:1209666 original size:44 final size:42
Alignment explanation
Indices: 1209584--1209666 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 42
1209574 TTTGGCAAAC
1209584 TTGGAATTCATATCCAAAAGTCTAAAGCTTTTCATTTGAATT
1 TTGGAATTCATATCCAAAAGTCTAAAGCTTTTCATTTGAATT
*
1209626 TTGGAAATTCATATCCAAAAAAT-TCAAAGCTTTTCATTTGA
1 TTGG-AATTCATATCC-AAAAGTCT-AAAGCTTTTCATTTGA
1209667 GTTCAAAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 4 0.11
43 12 0.32
44 21 0.57
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (42 bp):
TTGGAATTCATATCCAAAAGTCTAAAGCTTTTCATTTGAATT
Found at i:1209898 original size:22 final size:22
Alignment explanation
Indices: 1209850--1209908 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1209840 GGTTTCACTC
*
1209850 CTCAAAGATTCCCATTTTGAAAT
1 CTCAAAGATTCTCA-TTTGAAAT
**
1209873 -TCAAAGATTCTCATTTGAGTT
1 CTCAAAGATTCTCATTTGAAAT
*
1209894 CTCAAAAATTCTCAT
1 CTCAAAGATTCTCAT
1209909 CAAAACATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (22 bp):
CTCAAAGATTCTCATTTGAAAT
Found at i:1211011 original size:16 final size:16
Alignment explanation
Indices: 1210992--1211024 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1210982 CTTTTTTCCA
1210992 TTTTC-TCATTCTTTTT
1 TTTTCATCA-TCTTTTT
1211008 TTTTCATCATCTTTTT
1 TTTTCATCATCTTTTT
1211024 T
1 T
1211025 CTTTTTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCATCATCTTTTT
Found at i:1215102 original size:59 final size:59
Alignment explanation
Indices: 1214915--1215308 Score: 498
Period size: 59 Copynumber: 6.7 Consensus size: 59
1214905 TCTTGTGTAG
* *
1214915 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAC--TTTTTTGGAAATTTAATTTTT-A
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTTTGAAAATTT-ATTTTTAA
* * * * * *
1214973 GAAAAATTGATACTTCCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTCGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTTTGAAAATT-TATTTTTAA
1215034 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
* ** * *
1215093 GGAAAATTGATACTTTCAACTTTTTCCT-AAAAAT-ATTTTTCAGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATCTTTTTTTTGAAAATTT-ATTTTTAA
* * * *
1215152 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
1215209 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
* *
1215268 GGAAAATTAATACTTTCAACTTTT-CTCAAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATCTTTTTT
1215309 GATTTTTATT
Statistics
Matches: 292, Mismatches: 34, Indels: 19
0.85 0.10 0.06
Matches are distributed among these distances:
57 38 0.13
58 63 0.22
59 121 0.41
60 37 0.13
61 33 0.11
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
Found at i:1215243 original size:175 final size:176
Alignment explanation
Indices: 1214915--1215307 Score: 580
Period size: 175 Copynumber: 2.2 Consensus size: 176
1214905 TCTTGTGTAG
* * ** *
1214915 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTGGAAATTTAATTTTTAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTTCCAAAAAATA-TTTTTCAGAAATTTAATTTTAAGAAAAAT
* *
1214980 TGATACTTCCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTCGATTTTCAAGGAAAATTGAT
65 TGATACTTCCAACTTTTCCCCAAAAATA-TTTTTTTGGAAACTTCGATTTTCAAGGAAAATTGAT
1215045 ACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
129 ACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
* * *
1215093 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTCAGAAATTTTGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTTCCAAAAAATATTTTTCAGAAA-TTTAATTTT-AAGAAAAA
* *
1215158 TTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAA-TT-TA-TTTCTAAGGAAAATTGA
64 TTGATACTTCCAACTTTTCCCCAAAAATATTTTTTTGGAAACTTCGATTTTC-AAGGAAAATTGA
1215219 TACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
128 TACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
*
1215268 GGAAAATTAATACTTTCAAC-TTTTCTCAAAAAATATTTTT
1 GGAAAATTGATACTTTCAACTTTTTC-CAAAAAATATTTTT
1215308 TGATTTTTAT
Statistics
Matches: 198, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
174 9 0.05
175 94 0.47
176 2 0.01
177 19 0.10
178 41 0.21
179 33 0.17
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (176 bp):
GGAAAATTGATACTTTCAACTTTTTCCAAAAAATATTTTTCAGAAATTTAATTTTAAGAAAAATT
GATACTTCCAACTTTTCCCCAAAAATATTTTTTTGGAAACTTCGATTTTCAAGGAAAATTGATAC
TTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
Found at i:1215348 original size:22 final size:22
Alignment explanation
Indices: 1215323--1215364 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1215313 TTTATTTAAA
1215323 GAAAATAGAACAAA-ATAAAAGT
1 GAAAATA-AACAAAGATAAAAGT
*
1215345 GAAAATAAATAAAGATAAAA
1 GAAAATAAACAAAGATAAAA
1215365 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14
Consensus pattern (22 bp):
GAAAATAAACAAAGATAAAAGT
Found at i:1216314 original size:19 final size:19
Alignment explanation
Indices: 1216269--1216314 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1216259 AAAAAATAAT
*
1216269 AATAATAATCAGATAATCG
1 AATAAAAATCAGATAATCG
1216288 AA-AAAAATCAGATAAAT-G
1 AATAAAAATCAGAT-AATCG
1216306 AATAAAAAT
1 AATAAAAAT
1216315 AAAATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.22
Consensus pattern (19 bp):
AATAAAAATCAGATAATCG
Found at i:1216492 original size:12 final size:12
Alignment explanation
Indices: 1216434--1216524 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 12
1216424 ATATTAACAA
1216434 AATAAAATAAAT
1 AATAAAATAAAT
*
1216446 AA-ATAAATAAAG
1 AATA-AAATAAAT
*
1216458 ACAT-ACATATAAT
1 A-ATAAAATA-AAT
1216471 AATAATAATAAAT
1 AATAA-AATAAAT
1216484 AATAAAATACAA-
1 AATAAAATA-AAT
* *
1216496 AAGAAAAAAAAT
1 AATAAAATAAAT
1216508 AATAAAAATAAA-
1 AAT-AAAATAAAT
1216520 AATAA
1 AATAA
1216525 TACAAAATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
11 5 0.08
12 32 0.52
13 22 0.35
14 3 0.05
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:1220157 original size:2 final size:2
Alignment explanation
Indices: 1220150--1220201 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
1220140 TAAGAACAAT
1220150 TA TA TA TA TA TA TA TA -A T- 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 TA TA TA TA
1220190 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1220202 CCTTTTCCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1225415 original size:2 final size:2
Alignment explanation
Indices: 1225408--1225445 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1225398 TTCCCTACAT
1225408 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1225446 AAATTTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1226827 original size:2 final size:2
Alignment explanation
Indices: 1226820--1226845 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1226810 GTTTATAACC
1226820 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
1226846 GTCATGCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1228512 original size:40 final size:40
Alignment explanation
Indices: 1228457--1228571 Score: 185
Period size: 40 Copynumber: 2.9 Consensus size: 40
1228447 TTAGGACTTG
1228457 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTCCCTTA
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTCCCTTA
* **
1228497 GCCAATCATGAGACTGGCTCTCAAGGCTTTTATTTTCTTA
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTCCCTTA
* *
1228537 GCTAATCACGAGACTGGTTCTCAAGGCTTTTATTC
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTC
1228572 TACTATTAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (40 bp):
GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTCCCTTA
Found at i:1229599 original size:25 final size:25
Alignment explanation
Indices: 1229565--1229617 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1229555 ATAATTAAAA
1229565 ATATCCAAGCCCATATTTTTTTATT
1 ATATCCAAGCCCATATTTTTTTATT
1229590 ATATCCAAGCCCATATTTTTTTATT
1 ATATCCAAGCCCATATTTTTTTATT
1229615 ATA
1 ATA
1229618 ATTAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (25 bp):
ATATCCAAGCCCATATTTTTTTATT
Found at i:1230573 original size:12 final size:12
Alignment explanation
Indices: 1230537--1230575 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1230527 AATATATATG
1230537 TACATACACACA
1 TACATACACACA
* *
1230549 CACACACACACA
1 TACATACACACA
*
1230561 TACATACATACA
1 TACATACACACA
1230573 TAC
1 TAC
1230576 TAGTTTTTGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (12 bp):
TACATACACACA
Found at i:1230844 original size:21 final size:22
Alignment explanation
Indices: 1230820--1230873 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1230810 CTATTGATGC
*
1230820 AATTTTAATAATTTC-TGATAA
1 AATTTTAATAATCTCTTGATAA
**
1230841 AATTTTAATAATCTCTTGATGT
1 AATTTTAATAATCTCTTGATAA
1230863 AATTTTAATAA
1 AATTTTAATAA
1230874 GCTTTAGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (22 bp):
AATTTTAATAATCTCTTGATAA
Found at i:1230866 original size:22 final size:22
Alignment explanation
Indices: 1230813--1230873 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
1230803 TTGGTAACTA
* *
1230813 TTGATGCAATTTTAATAATTTC
1 TTGATGAAATTTTAATAATCTC
*
1230835 -TGATAAAATTTTAATAATCTC
1 TTGATGAAATTTTAATAATCTC
*
1230856 TTGATGTAATTTTAATAA
1 TTGATGAAATTTTAATAA
1230874 GCTTTAGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (22 bp):
TTGATGAAATTTTAATAATCTC
Found at i:1231132 original size:44 final size:44
Alignment explanation
Indices: 1231084--1231214 Score: 111
Period size: 44 Copynumber: 3.0 Consensus size: 44
1231074 ACAATTTAGT
* ** * **
1231084 TATCATTGATTTATTATTATGTTATTAATGATTTGTTACTAAAC
1 TATCATTGATTTATTAATAAATTATTAATAATTTACTACTAAAC
* * *
1231128 TATCAATGATATATTAATAAATTATTAATAATTTACTACTAAAT
1 TATCATTGATTTATTAATAAATTATTAATAATTTACTACTAAAC
* * * * * *
1231172 TA-CTATTGATTTAATACTAATTTGTAAATGATTTACTACTAAA
1 TATC-ATTGATTTATTAATAAATTATTAATAATTTACTACTAAA
1231215 TTATTACTAA
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
43 1 0.01
44 68 0.99
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (44 bp):
TATCATTGATTTATTAATAAATTATTAATAATTTACTACTAAAC
Found at i:1231173 original size:22 final size:22
Alignment explanation
Indices: 1231145--1231339 Score: 110
Period size: 22 Copynumber: 9.0 Consensus size: 22
1231135 GATATATTAA
1231145 TAAATTATTAATAATTTACTAC
1 TAAATTATTAATAATTTACTAC
* * * *
1231167 TAAATTACTATTGATTTAATAC
1 TAAATTATTAATAATTTACTAC
* * * *
1231189 TAATTTGTAAATGATTTACTAC
1 TAAATTATTAATAATTTACTAC
*
1231211 TAAATTATTACTAATTTACTAC
1 TAAATTATTAATAATTTACTAC
* * * *
1231233 AAAATTGTTGATGATTTACTAC
1 TAAATTATTAATAATTTACTAC
* * ** * *
1231255 TAAGTTACT-ATGGTTGATTA-
1 TAAATTATTAATAATTTACTAC
* *
1231275 TAAGTTA-TAACTAATTTACTAT
1 TAAATTATTAA-TAATTTACTAC
* ***
1231297 TAATTTATCGGTAATTTACTA-
1 TAAATTATTAATAATTTACTAC
*
1231318 TAAAGTTATTAATAATTAACTA
1 TAAA-TTATTAATAATTTACTA
1231340 ATTAGCTACT
Statistics
Matches: 128, Mismatches: 40, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
19 1 0.01
20 8 0.06
21 17 0.13
22 102 0.80
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (22 bp):
TAAATTATTAATAATTTACTAC
Found at i:1231194 original size:11 final size:11
Alignment explanation
Indices: 1231156--1231232 Score: 57
Period size: 11 Copynumber: 7.0 Consensus size: 11
1231146 AAATTATTAA
1231156 TAATTTACTAC
1 TAATTTACTAC
* *
1231167 TAAATTACTAT
1 TAATTTACTAC
* *
1231178 TGATTTAATAC
1 TAATTTACTAC
* *
1231189 TAATTT-GTAAA
1 TAATTTACT-AC
*
1231200 TGATTTACTAC
1 TAATTTACTAC
* *
1231211 TAAATTATTAC
1 TAATTTACTAC
1231222 TAATTTACTAC
1 TAATTTACTAC
1231233 AAAATTGTTG
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
10 1 0.02
11 45 0.96
12 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (11 bp):
TAATTTACTAC
Found at i:1231215 original size:44 final size:44
Alignment explanation
Indices: 1231158--1231265 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 44
1231148 ATTATTAATA
* * *
1231158 ATTTACTACTAAATTACTATTGATTTAATACTAATTTGTAAATG
1 ATTTACTACTAAATTACTATTAATTTAATACAAAATTGTAAATG
* * * **
1231202 ATTTACTACTAAATTATTACTAATTTACTACAAAATTGTTGATG
1 ATTTACTACTAAATTACTATTAATTTAATACAAAATTGTAAATG
*
1231246 ATTTACTACTAAGTTACTAT
1 ATTTACTACTAAATTACTAT
1231266 GGTTGATTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.44
Consensus pattern (44 bp):
ATTTACTACTAAATTACTATTAATTTAATACAAAATTGTAAATG
Found at i:1231444 original size:22 final size:22
Alignment explanation
Indices: 1231345--1231481 Score: 111
Period size: 22 Copynumber: 6.2 Consensus size: 22
1231335 AACTAATTAG
1231345 CTACTAAATTATCACTT-ATTTA
1 CTACTAAATTATCA-TTAATTTA
* *
1231367 -TCACTAAATTATTAGTAATTTA
1 CT-ACTAAATTATCATTAATTTA
* * *
1231389 CTACTAAGTTATTAATAATTTA
1 CTACTAAATTATCATTAATTTA
1231411 C-ATCTAAATTATCATTAATTTA
1 CTA-CTAAATTATCATTAATTTA
* ** *
1231433 CTATTATGTTATTA-TACATTTA
1 CTACTAAATTATCATTA-ATTTA
* *
1231455 CTACTATATTATCATTGATTTA
1 CTACTAAATTATCATTAATTTA
1231477 CTACT
1 CTACT
1231482 TAGCTTTTGA
Statistics
Matches: 93, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
21 5 0.05
22 85 0.91
23 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.47
Consensus pattern (22 bp):
CTACTAAATTATCATTAATTTA
Found at i:1231444 original size:44 final size:44
Alignment explanation
Indices: 1231362--1231481 Score: 138
Period size: 44 Copynumber: 2.7 Consensus size: 44
1231352 ATTATCACTT
* *
1231362 ATTTATCA-CTAAATTATTAGTAATTTACTACTAAGTTATTAATA-
1 ATTTA-CATCTAAATTATCATTAATTTACTACTAAGTTATT-ATAC
* *
1231406 ATTTACATCTAAATTATCATTAATTTACTATTATGTTATTATAC
1 ATTTACATCTAAATTATCATTAATTTACTACTAAGTTATTATAC
* *
1231450 ATTTAC-TACTATATTATCATTGATTTACTACT
1 ATTTACAT-CTAAATTATCATTAATTTACTACT
1231482 TAGCTTTTGA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
43 6 0.09
44 60 0.91
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (44 bp):
ATTTACATCTAAATTATCATTAATTTACTACTAAGTTATTATAC
Found at i:1231604 original size:22 final size:22
Alignment explanation
Indices: 1231551--1231800 Score: 136
Period size: 22 Copynumber: 11.3 Consensus size: 22
1231541 CGTTATCAAG
1231551 TTATCATTGATTTA-TATTAAA
1 TTATCATTGATTTACTATTAAA
*
1231572 TTATCCA-TGATTTACTCTTAAA
1 TTAT-CATTGATTTACTATTAAA
* *
1231594 TTATCATTGATTAACTATTAAGT
1 TTATCATTGATTTACTATTAA-A
* * *
1231617 TTTTGA-TGATTAACTACTATTAAG
1 TTATCATTGATT---TACTATTAAA
* * * *
1231641 TCAT-GTTGATTTACTTTTAAG
1 TTATCATTGATTTACTATTAAA
* * * *
1231662 TTTTCAATGATTAACTACTAAA
1 TTATCATTGATTTACTATTAAA
*
1231684 TTATCATTGATTTACTATTAAG
1 TTATCATTGATTTACTATTAAA
* * * * *
1231706 CTAT-TTATGAGTAACTACTAAA
1 TTATCAT-TGATTTACTATTAAA
* *
1231728 TTAATTAATT-AATTACTATTAAA
1 TT-A-TCATTGATTTACTATTAAA
* *
1231751 TTGA-AACTGATTTACTATTAAA
1 TT-ATCATTGATTTACTATTAAA
* *
1231773 TTATCACTAATTTACTATTAAA
1 TTATCATTGATTTACTATTAAA
1231795 TTATCA
1 TTATCA
1231801 GTTATTACCT
Statistics
Matches: 173, Mismatches: 41, Indels: 29
0.71 0.17 0.12
Matches are distributed among these distances:
21 29 0.17
22 108 0.62
23 18 0.10
24 9 0.05
25 9 0.05
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (22 bp):
TTATCATTGATTTACTATTAAA
Found at i:1231721 original size:44 final size:44
Alignment explanation
Indices: 1231551--1231793 Score: 166
Period size: 44 Copynumber: 5.5 Consensus size: 44
1231541 CGTTATCAAG
* *
1231551 TTATCATTGATTTA-TATTAA--ATTATCCATGATTTACT-CTTAAA
1 TTATCATTGATTTACTATTAAGTATT-T-AATGATTAACTAC-TAAA
* * *
1231594 TTATCATTGATTAACTATTAAGTTTTTGATGATTAACTACT--A
1 TTATCATTGATTTACTATTAAGTATTTAATGATTAACTACTAAA
*
1231636 TTAAGTCATGTTGATTTACTTTTAAGT-TTTCAATGATTAACTACTAAA
1 TT-A-TCA--TTGATTTACTATTAAGTATTT-AATGATTAACTACTAAA
*
1231684 TTATCATTGATTTACTATTAAGCTATTT-ATGAGTAACTACTAAA
1 TTATCATTGATTTACTATTAAG-TATTTAATGATTAACTACTAAA
* * * * *
1231728 TTAATTAATT-AATTACTATTAA--ATTGAAACTGATTTACTATTAAA
1 TT-A-TCATTGATTTACTATTAAGTATT-TAA-TGATTAACTACTAAA
* *
1231773 TTATCACTAATTTACTATTAA
1 TTATCATTGATTTACTATTAA
1231794 ATTATCAGTT
Statistics
Matches: 163, Mismatches: 18, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
42 6 0.04
43 17 0.10
44 64 0.39
45 32 0.20
46 40 0.25
47 1 0.01
48 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (44 bp):
TTATCATTGATTTACTATTAAGTATTTAATGATTAACTACTAAA
Found at i:1232290 original size:9 final size:9
Alignment explanation
Indices: 1232276--1232301 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1232266 ATTTTTCATT
1232276 ATTATTATG
1 ATTATTATG
1232285 ATTATTATG
1 ATTATTATG
1232294 ATTATTAT
1 ATTATTAT
1232302 TTATCTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
ATTATTATG
Found at i:1232322 original size:21 final size:21
Alignment explanation
Indices: 1232298--1232387 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 21
1232288 ATTATGATTA
1232298 TTATTTATCTATTAATATTTT
1 TTATTTATCTATTAATATTTT
* *
1232319 TTATTTACCTATTAATTTTTT
1 TTATTTATCTATTAATATTTT
* *
1232340 TTAGTTATCTATTAATATATT
1 TTATTTATCTATTAATATTTT
* *
1232361 TTA-TTATTTATCAATTATTTT
1 TTATTTATCTATTAA-TATTTT
1232382 TTATTT
1 TTATTT
1232388 TTATCTTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.16
21 47 0.81
22 2 0.03
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.66
Consensus pattern (21 bp):
TTATTTATCTATTAATATTTT
Found at i:1232399 original size:18 final size:20
Alignment explanation
Indices: 1232263--1232392 Score: 68
Period size: 21 Copynumber: 6.0 Consensus size: 20
1232253 ATTTAATTTA
* *
1232263 ATTATTTTTCATTATTATTATG
1 ATTATTTTTTATTA-T-TTATC
*
1232285 ATTATTATGATTATTATTTATC
1 ATTATT-T-TTTATTATTTATC
* *
1232307 TATTAATATTTT-TTATTTACC
1 -ATT-ATTTTTTATTATTTATC
*
1232328 TATTAATTTTTT-TTAGTTATC
1 -ATT-ATTTTTTATTATTTATC
1232349 TATTAATATATTTTATTATTTATC
1 -ATT-AT-T-TTTTATTATTTATC
1232373 AATTATTTTTTATT-TTTATC
1 -ATTATTTTTTATTATTTATC
1232393 TTTTTTTCTT
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.07
21 40 0.44
22 14 0.16
23 12 0.13
24 18 0.20
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTATTTTTTATTATTTATC
Found at i:1233206 original size:17 final size:17
Alignment explanation
Indices: 1233184--1233216 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1233174 CGATTCAAGG
1233184 TTTATT-TTATTTATTTA
1 TTTATTATTA-TTATTTA
1233201 TTTATTATTATTATTT
1 TTTATTATTATTATTT
1233217 TAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTATTATTATTTA
Found at i:1245040 original size:40 final size:40
Alignment explanation
Indices: 1244985--1245099 Score: 185
Period size: 40 Copynumber: 2.9 Consensus size: 40
1244975 TTAGGACTTG
*
1244985 GCCAATAATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
* *
1245025 GCCAATCATGAGACTGGCTCTCAAGGCTTTTATTTTCTTA
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
* *
1245065 GCTAATCACGAGACTGGTTCTCAAGGCTTTTATTT
1 GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTT
1245100 ACTATTAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.37
Consensus pattern (40 bp):
GCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTCCTTA
Found at i:1247098 original size:2 final size:2
Alignment explanation
Indices: 1247091--1247129 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1247081 CTTTTCTTAT
*
1247091 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1247130 TACATACTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:1247134 original size:12 final size:12
Alignment explanation
Indices: 1247091--1247136 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1247081 CTTTTCTTAT
*
1247091 ACACACACACAC
1 ACACACATACAC
*
1247103 ACACACACACAC
1 ACACACATACAC
1247115 ACACACATACAC
1 ACACACATACAC
*
1247127 ACATACATAC
1 ACACACATAC
1247137 TAGTTTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (12 bp):
ACACACATACAC
Found at i:1247406 original size:21 final size:22
Alignment explanation
Indices: 1247380--1247433 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1247370 CTATTGATGC
*
1247380 AATTTTAATAATTTC-TAATAA
1 AATTTTAATAATCTCTTAATAA
**
1247401 AATTTTAATAATCTCTTAATGT
1 AATTTTAATAATCTCTTAATAA
1247423 AATTTTAATAA
1 AATTTTAATAA
1247434 GCTTTAGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTTTAATAATCTCTTAATAA
Found at i:1247689 original size:22 final size:22
Alignment explanation
Indices: 1247642--1247812 Score: 121
Period size: 22 Copynumber: 7.8 Consensus size: 22
1247632 GACAATTTAG
* * **
1247642 TTATCATTGATTTATTATTATG
1 TTATCAATGATTTATTACTAAA
1247664 TTATCAATGATTTATTACTAAA
1 TTATCAATGATTTATTACTAAA
* *
1247686 TTATCAATGATATATTAATAAA
1 TTATCAATGATTTATTACTAAA
* * *
1247708 TTATTAATAATTTACTACTAAA
1 TTATCAATGATTTATTACTAAA
* * *
1247730 TTA-CTATTGATTTAATACTAAT
1 TTATC-AATGATTTATTACTAAA
* * *
1247752 TTATAAATGATTTACTACTAAT
1 TTATCAATGATTTATTACTAAA
* * * * *
1247774 TTATTACTAATTTACTACTAAG
1 TTATCAATGATTTATTACTAAA
*
1247796 TTA-CTAATGATTGATTA
1 TTATC-AATGATTTATTA
1247813 TAAGTTACAA
Statistics
Matches: 118, Mismatches: 28, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
22 118 1.00
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (22 bp):
TTATCAATGATTTATTACTAAA
Found at i:1247733 original size:11 final size:11
Alignment explanation
Indices: 1247715--1247841 Score: 96
Period size: 11 Copynumber: 11.6 Consensus size: 11
1247705 AAATTATTAA
1247715 TAATTTACTAC
1 TAATTTACTAC
* *
1247726 TAAATTACTAT
1 TAATTTACTAC
* *
1247737 TGATTTAATAC
1 TAATTTACTAC
*
1247748 TAATTTA-TAAA
1 TAATTTACT-AC
*
1247759 TGATTTACTAC
1 TAATTTACTAC
*
1247770 TAATTTATTAC
1 TAATTTACTAC
1247781 TAATTTACTAC
1 TAATTTACTAC
* *
1247792 TAAGTTACTAA
1 TAATTTACTAC
* * *
1247803 TGATTGATTA-
1 TAATTTACTAC
* *
1247813 TAAGTTACAAC
1 TAATTTACTAC
*
1247824 TAATTTACTAT
1 TAATTTACTAC
1247835 TAATTTA
1 TAATTTA
1247842 TCGGTAATTT
Statistics
Matches: 86, Mismatches: 27, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
10 6 0.07
11 79 0.92
12 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (11 bp):
TAATTTACTAC
Done.