Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 45 of 113
Found at i:12266387 original size:15 final size:15
Alignment explanation
Indices: 12266367--12266404 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
12266357 TAATTTTCCT
12266367 AAAATAAATATTTTC
1 AAAATAAATATTTTC
*
12266382 AAAATAAAAATTTTC
1 AAAATAAATATTTTC
12266397 AAAA-AAAT
1 AAAATAAAT
12266405 TCTTTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAAATATTTTC
Found at i:12266411 original size:128 final size:130
Alignment explanation
Indices: 12266259--12266516 Score: 321
Period size: 128 Copynumber: 2.0 Consensus size: 130
12266249 TTCCTTTGAA
* * * *
12266259 AAAAATTTTCAAAAAAGAGTTTTGAAAAAAATTTAAAGTATTAATTTTTCTTAA-AAATAAAAAT
1 AAAAATTTTCAAAAAAGAGTTTTGAAAAAAACTTAAAGAATCAATTTTCCTTAACAAA-AAAAAT
* *
12266323 -TTTCAAAAAATGTTTTGAGGAAAAGTTGAAGGATTAATTTTC-CT-AA-AATAAATATTTTCAA
65 ATTTCAAAAAA--TTTTGAGAAAAAGTTGAAGGATTAATTTTCTCTAAACAAAAAATATTTTCAA
12266384 AAT
128 AAT
* *
12266387 AAAAATTTTCAAAAAA-ATTCTTTGAAAAAAACTTGAAGAATCAATTTTCCTTAACTAAAAAAAA
1 AAAAATTTTCAAAAAAGAGT-TTTGAAAAAAACTTAAAGAATCAATTTTCCTTAAC-AAAAAAAA
* ** *
12266451 TATTTTAAAAAATTTTGAGAAAAAGTTGAATTATTAATTTTCTTTAAACAAAAAATATTTTCAAA
64 TATTTCAAAAAATTTTGAGAAAAAGTTGAAGGATTAATTTTCTCTAAACAAAAAATATTTTCAAA
12266516 A
129 A
12266517 ATATTTGGGA
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
127 2 0.02
128 72 0.65
129 7 0.06
130 14 0.13
131 16 0.14
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.36
Consensus pattern (130 bp):
AAAAATTTTCAAAAAAGAGTTTTGAAAAAAACTTAAAGAATCAATTTTCCTTAACAAAAAAAATA
TTTCAAAAAATTTTGAGAAAAAGTTGAAGGATTAATTTTCTCTAAACAAAAAATATTTTCAAAAT
Found at i:12266480 original size:57 final size:56
Alignment explanation
Indices: 12266398--12266558 Score: 162
Period size: 57 Copynumber: 2.8 Consensus size: 56
12266388 AAAATTTTCA
* * * *
12266398 AAAAAATTCTTTGAAAAAAACTTGAAGAATCAATTTTCCTTAACTAAAAAAAATATTTT
1 AAAAAA-TATTTGAGAAAAAGTTGAAGTATCAATTTTCCTTAA--AAAAAAAATATTTT
* * * *
12266457 AAAAAAT-TTTGAGAAAAAGTTGAATTATTAATTTTCTTTAAACAAAAAATATTTT
1 AAAAAATATTTGAGAAAAAGTTGAAGTATCAATTTTCCTTAAAAAAAAAATATTTT
* *
12266512 CAAAAATATTTGGGAAAAAAGTTGAAAGTATCAATTTTTTCCTTAAA
1 AAAAAATATTTGAG-AAAAAGTTG-AAGTATCAA--TTTTCCTTAAA
12266559 TAAAGTATCA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
55 19 0.22
56 5 0.06
57 37 0.44
58 8 0.09
59 6 0.07
60 10 0.12
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.36
Consensus pattern (56 bp):
AAAAAATATTTGAGAAAAAGTTGAAGTATCAATTTTCCTTAAAAAAAAAATATTTT
Found at i:12266580 original size:21 final size:23
Alignment explanation
Indices: 12266536--12266583 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
12266526 AAAAAAGTTG
12266536 AAAGTATCAATTTTTTCCTTAAAT
1 AAAGTATCAATTTTTT-CTTAAAT
12266560 AAAGTATCAA-TTTTT-TTAAAT
1 AAAGTATCAATTTTTTCTTAAAT
12266581 AAA
1 AAA
12266584 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.38
23 5 0.21
24 10 0.42
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (23 bp):
AAAGTATCAATTTTTTCTTAAAT
Found at i:12266618 original size:28 final size:30
Alignment explanation
Indices: 12266554--12266619 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 30
12266544 AATTTTTTCC
12266554 TTAAATAAAGTATCAATTTTTTTAAATAAAA
1 TTAAATAAAG-ATCAATTTTTTTAAATAAAA
*
12266585 TAAAATAAA-AT-AATTTTTTTAAA-AAAGA
1 TTAAATAAAGATCAATTTTTTTAAATAAA-A
12266613 TTAAATA
1 TTAAATA
12266620 TCAAGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 3 0.09
28 19 0.59
29 2 0.06
31 8 0.25
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (30 bp):
TTAAATAAAGATCAATTTTTTTAAATAAAA
Found at i:12266628 original size:29 final size:28
Alignment explanation
Indices: 12266568--12266629 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
12266558 ATAAAGTATC
*
12266568 AATTTTTTTAAATAAAATAAAATAAAAT
1 AATTTTTTTAAATAAAATAAAATAAAAG
* *
12266596 AATTTTTTTAAA-AAAGATTAAATATCAAG
1 AATTTTTTTAAATAAA-ATAAAATA-AAAG
12266625 AATTT
1 AATTT
12266630 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.10
28 19 0.66
29 7 0.24
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (28 bp):
AATTTTTTTAAATAAAATAAAATAAAAG
Found at i:12267523 original size:57 final size:59
Alignment explanation
Indices: 12267454--12267568 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 59
12267444 GACTTAAGGG
* * *
12267454 AATGTTAAATCTTAACAAAGAGAG-TT-TCTATACCTCAATCTCACGTTAAAAAATTGT
1 AATGTTAAATCTTAACAAACAAAGTTTATATATACCTCAATCTCACGTTAAAAAATTGT
* * * *
12267511 AATGTTAAATCTTATCAGACAAAGTTTATATATACTTCAATCTCATGTTAAAAAATTG
1 AATGTTAAATCTTAACAAACAAAGTTTATATATACCTCAATCTCACGTTAAAAAATTG
12267569 AAACGATGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
57 20 0.41
58 2 0.04
59 27 0.55
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (59 bp):
AATGTTAAATCTTAACAAACAAAGTTTATATATACCTCAATCTCACGTTAAAAAATTGT
Found at i:12267589 original size:2 final size:2
Alignment explanation
Indices: 12267578--12267628 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
12267568 GAAACGATGT
12267578 TA TA -A TA TA TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12267614 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
12267629 GCTTAAACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
1 6 0.14
2 37 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:12267594 original size:5 final size:5
Alignment explanation
Indices: 12267578--12267627 Score: 75
Period size: 5 Copynumber: 9.8 Consensus size: 5
12267568 GAAACGATGT
12267578 TATAA TAT-A TATAA TATAA TATAA TATAA TATAA TATATA TATATA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATA-A TATA
12267628 TGCTTAAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.09
5 28 0.65
6 11 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:12267628 original size:10 final size:10
Alignment explanation
Indices: 12267578--12267628 Score: 60
Period size: 9 Copynumber: 5.7 Consensus size: 10
12267568 GAAACGATGT
12267578 TATA-ATATA
1 TATATATATA
12267587 TATA-ATATA
1 TATATATATA
12267596 -ATATA-ATA
1 TATATATATA
12267604 TA-ATATA-A
1 TATATATATA
12267612 TATATATATA
1 TATATATATA
12267622 TATATAT
1 TATATAT
12267629 GCTTAAACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 12 0.32
9 17 0.46
10 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:12274560 original size:246 final size:244
Alignment explanation
Indices: 12274093--12274582 Score: 928
Period size: 246 Copynumber: 2.0 Consensus size: 244
12274083 TGAAAAATCT
*
12274093 AAAAAAAGTGTAAGAGTTACACTAGTGTAAGTGAATCCCTCTTCATATGTATATTATGTAGGGAG
1 AAAAAAAGTGTAAGAGTTACACTAGTGTAAGTGAATCCCTCTTCATATGTATATTATATAGGGAG
12274158 AGAAGGGATCCATTTACTGCAGTGTTACATTTTTTTTTCACCATTAGGTTTGGATTAAAATAAAT
66 AGAAGGGATCCATTTACTGCAGTGTTACATTTTTTTTTCACCATTAGGTTTGGATTAAAATAAAT
*
12274223 ATTTTAAATCTTAACCATTTTGATCTAAGGATCAGAAAAAAAAAAGTACAACACGTACATTAATG
131 ATTTTAAATCTTAACCATTTTGATCTAAGGATCAAAAAAAAAAAAGTACAACACGTACATTAATG
12274288 TAACTAGATCTCTACCCATAATATATATATATATATATGATAGCCAACTTA
196 TAACTAGATCTCTACCC--AATATATATATATATATATGATAGCCAACTTA
12274339 AAAAAAAGTGTAAGAGTTACACTAGTGTAAGTGAATCCCTCTTCATATGTATATTATATAGGGAG
1 AAAAAAAGTGTAAGAGTTACACTAGTGTAAGTGAATCCCTCTTCATATGTATATTATATAGGGAG
12274404 AGAAGGGATCCATTTACTGCAGTGTTACATTTTTTTTTCACCATTAGGTTTGGATTAAAATAAAT
66 AGAAGGGATCCATTTACTGCAGTGTTACATTTTTTTTTCACCATTAGGTTTGGATTAAAATAAAT
12274469 ATTTTAAATCTTAACCATTTTGATCTAAGGATCAAAAAAAAAAAAAGTACAACACGTACATTAAT
131 ATTTTAAATCTTAACCATTTTGATCTAAGGATC-AAAAAAAAAAAAGTACAACACGTACATTAAT
12274534 GTAACTAGATCTCTACCC-ATATATATATATATATATGATAGCCAACTTA
195 GTAACTAGATCTCTACCCAATATATATATATATATATGATAGCCAACTTA
12274583 TACTAGTGTA
Statistics
Matches: 241, Mismatches: 2, Indels: 4
0.98 0.01 0.02
Matches are distributed among these distances:
244 31 0.13
246 162 0.67
247 48 0.20
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (244 bp):
AAAAAAAGTGTAAGAGTTACACTAGTGTAAGTGAATCCCTCTTCATATGTATATTATATAGGGAG
AGAAGGGATCCATTTACTGCAGTGTTACATTTTTTTTTCACCATTAGGTTTGGATTAAAATAAAT
ATTTTAAATCTTAACCATTTTGATCTAAGGATCAAAAAAAAAAAAGTACAACACGTACATTAATG
TAACTAGATCTCTACCCAATATATATATATATATATGATAGCCAACTTA
Found at i:12276290 original size:13 final size:12
Alignment explanation
Indices: 12276269--12276332 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
12276259 ATTGCAGGTA
12276269 TTTGTTTTTATT
1 TTTGTTTTTATT
12276281 TTTCGTTTTT-TT
1 TTT-GTTTTTATT
*
12276293 TTTGTTTTAATT
1 TTTGTTTTTATT
* *
12276305 TTTTTCTTTTCTTT
1 TTTGT-TTTT-ATT
*
12276319 TTTGGTTTTATT
1 TTTGTTTTTATT
12276331 TT
1 TT
12276333 ATATTATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 18 0.44
13 13 0.32
14 5 0.12
ACGTcount: A:0.06, C:0.05, G:0.08, T:0.81
Consensus pattern (12 bp):
TTTGTTTTTATT
Found at i:12276306 original size:14 final size:13
Alignment explanation
Indices: 12276269--12276332 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
12276259 ATTGCAGGTA
12276269 TTTGTTTT-TATTT
1 TTTGTTTTAT-TTT
*
12276282 TTCG-TTT-TTTT
1 TTTGTTTTATTTT
12276293 TTTGTTTTAATTTT
1 TTTGTTTT-ATTTT
* *
12276307 TTTCTTTTCTTTT
1 TTTGTTTTATTTT
*
12276320 TTGGTTTTATTTT
1 TTTGTTTTATTTT
12276333 ATATTATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
11 6 0.15
12 7 0.17
13 17 0.41
14 11 0.27
ACGTcount: A:0.06, C:0.05, G:0.08, T:0.81
Consensus pattern (13 bp):
TTTGTTTTATTTT
Found at i:12276319 original size:26 final size:26
Alignment explanation
Indices: 12276279--12276332 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
12276269 TTTGTTTTTA
12276279 TTTTTCGTTTTTTTTTT-GTTTTAATT
1 TTTTTCGTTTTTTTTTTGGTTTT-ATT
12276305 TTTTTC-TTTTCTTTTTTGGTTTTATT
1 TTTTTCGTTTT-TTTTTTGGTTTTATT
12276331 TT
1 TT
12276333 ATATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.15
26 17 0.65
27 5 0.19
ACGTcount: A:0.06, C:0.06, G:0.07, T:0.81
Consensus pattern (26 bp):
TTTTTCGTTTTTTTTTTGGTTTTATT
Found at i:12276370 original size:3 final size:3
Alignment explanation
Indices: 12276326--12276396 Score: 65
Period size: 3 Copynumber: 22.3 Consensus size: 3
12276316 TTTTTTGGTT
*
12276326 TTA TT- TTA -TA TTA TTT TTA TTTA TTTA TTTA TGTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA -TTA -TTA T-TA -TTA TTA TTA
12276371 TTA TTA TTA TTA TTA TTA TTAA TTA T
1 TTA TTA TTA TTA TTA TTA TT-A TTA T
12276397 AGATTGAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
2 4 0.07
3 37 0.62
4 18 0.30
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12287056 original size:21 final size:21
Alignment explanation
Indices: 12287028--12287072 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
12287018 CCAGCCCTCT
* *
12287028 TTTTTTTTTTTTTTAATG-AA
1 TTTTCTTTTTTATTAATGTAA
12287048 TTTTCTTTTTTATTAATGTAA
1 TTTTCTTTTTTATTAATGTAA
12287069 TTTT
1 TTTT
12287073 GTTAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTCTTTTTTATTAATGTAA
Found at i:12288196 original size:46 final size:46
Alignment explanation
Indices: 12288129--12288219 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
12288119 AGTTTGATGG
* * *
12288129 TAGAATATTAAGATTTTAAAAATTATTATGATAATTTATTTATTAA
1 TAGAATATTAAGATTTTAAAAATCATCATGATAATTTAATTATTAA
12288175 TAGAATATTAA-ATTTTTAAAAATCATCATGATAATTTAATTATTA
1 TAGAATATTAAGA-TTTTAAAAATCATCATGATAATTTAATTATTA
12288220 TTAAAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 1 0.02
46 40 0.98
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (46 bp):
TAGAATATTAAGATTTTAAAAATCATCATGATAATTTAATTATTAA
Found at i:12291171 original size:9 final size:8
Alignment explanation
Indices: 12291152--12291176 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12291142 TCAACCAAAA
12291152 TTTTTTAT
1 TTTTTTAT
12291160 TTTTTTAT
1 TTTTTTAT
12291168 TTTTTTAT
1 TTTTTTAT
12291176 T
1 T
12291177 GAAAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:12291296 original size:24 final size:25
Alignment explanation
Indices: 12291260--12291307 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
12291250 AATTCACTTA
12291260 AAAATTTTATAAAAACTTATCATTT
1 AAAATTTTATAAAAACTTATCATTT
**
12291285 AAAATTTT-TAAAATTTTATCATT
1 AAAATTTTATAAAAACTTATCATT
12291308 AGATAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAATTTTATAAAAACTTATCATTT
Found at i:12291456 original size:31 final size:32
Alignment explanation
Indices: 12291398--12291457 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
12291388 AATGAAAATC
*
12291398 ATAAAACAAAGTGAATAAATAAACAATTATGG
1 ATAAAACAAAGTGAATAAACAAACAATTATGG
* *
12291430 ATAAAACAAA-TGAATAAGCAATCAATTA
1 ATAAAACAAAGTGAATAAACAAACAATTA
12291458 AAGAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22
Consensus pattern (32 bp):
ATAAAACAAAGTGAATAAACAAACAATTATGG
Found at i:12292521 original size:43 final size:43
Alignment explanation
Indices: 12292474--12292620 Score: 163
Period size: 43 Copynumber: 3.4 Consensus size: 43
12292464 TAACTTTTGG
* *
12292474 AAAAATAAATACAA-ATCCTCTAAACAGAGGTTCAATGACTTCT
1 AAAAATAAATA-AAGCTCCTCTAATCAGAGGTTCAATGACTTCT
* * *
12292517 AAAAATAAATAAAGCTCCTCCAATCAAAGATTCAATGACTTCT
1 AAAAATAAATAAAGCTCCTCTAATCAGAGGTTCAATGACTTCT
* * * * *
12292560 GAAAATAAATAAAGCTCCTCTAATTAGAGGTTCGATAAATT-T
1 AAAAATAAATAAAGCTCCTCTAATCAGAGGTTCAATGACTTCT
* *
12292602 GAAAATACATAAAGCTCCT
1 AAAAATAAATAAAGCTCCT
12292621 TTACAATCTC
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
42 21 0.24
43 68 0.76
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.27
Consensus pattern (43 bp):
AAAAATAAATAAAGCTCCTCTAATCAGAGGTTCAATGACTTCT
Found at i:12293382 original size:21 final size:21
Alignment explanation
Indices: 12293356--12293429 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
12293346 GGTTTCACAT
12293356 CTCAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
*
12293377 CTCAAAGATTCTCATATGAAAA
1 CTCAAAGATTCTCATTTG-AAA
* * *
12293399 CTCAAATATTCTCATTTCATA
1 CTCAAAGATTCTCATTTGAAA
12293420 CTCAAAGATT
1 CTCAAAGATT
12293430 TTCAAAGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 28 0.61
22 18 0.39
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:12293457 original size:22 final size:22
Alignment explanation
Indices: 12293431--12293487 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
12293421 TCAAAGATTT
* *
12293431 TCAAAGATACTTATTTGAAAAC
1 TCAAAGATACTCATTTAAAAAC
*
12293453 TCAAAGATTCTCATTTAAAAAC
1 TCAAAGATACTCATTTAAAAAC
* *
12293475 TTAAAGATTCTCA
1 TCAAAGATACTCA
12293488 AAAATTCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (22 bp):
TCAAAGATACTCATTTAAAAAC
Found at i:12293488 original size:32 final size:32
Alignment explanation
Indices: 12293452--12293517 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
12293442 TATTTGAAAA
* *
12293452 CTCAAAGATTCTCATTTAAAAACTTAAAGATT
1 CTCAAAAATTCTCATTTAAAAACTCAAAGATT
*
12293484 CTCAAAAATTCTCATTTGAAAACTCAAAGATT
1 CTCAAAAATTCTCATTTAAAAACTCAAAGATT
12293516 CT
1 CT
12293518 TATTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (32 bp):
CTCAAAAATTCTCATTTAAAAACTCAAAGATT
Found at i:12293505 original size:54 final size:54
Alignment explanation
Indices: 12293377--12293540 Score: 206
Period size: 54 Copynumber: 3.1 Consensus size: 54
12293367 TCATTTGAAA
* * * * *
12293377 CTCAAAGATTCTCATATGAAAACTCAAATATTCTCATTT-CATACTCAAAGATT
1 CTCAAAGATTCTCATTTGAAAACTCAAAGATTCTCATTTAAAAACTAAAAGATT
* * * *
12293430 TTCAAAGATACTTATTTGAAAACTCAAAGATTCTCATTTAAAAACTTAAAGATT
1 CTCAAAGATTCTCATTTGAAAACTCAAAGATTCTCATTTAAAAACTAAAAGATT
* * *
12293484 CTCAAAAATTCTCATTTGAAAACTCAAAGATTCTTATTTAAAAA-TAAAATATT
1 CTCAAAGATTCTCATTTGAAAACTCAAAGATTCTCATTTAAAAACTAAAAGATT
12293537 CTCA
1 CTCA
12293541 TTTGAAAACT
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 45 0.47
54 50 0.53
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (54 bp):
CTCAAAGATTCTCATTTGAAAACTCAAAGATTCTCATTTAAAAACTAAAAGATT
Found at i:12293539 original size:43 final size:42
Alignment explanation
Indices: 12293487--12293570 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 42
12293477 AAAGATTCTC
12293487 AAAAATTCTCATTTGAAAACTCAAAGATTCTTATTTAAAAAT
1 AAAAATTCTCATTTGAAAACTCAAAGATTCTTATTTAAAAAT
* * *
12293529 AAAATATTCTCATTTGAAAACTCAAAGTTTCTTGTTTGAAAA
1 AAAA-ATTCTCATTTGAAAACTCAAAGATTCTTATTTAAAAA
12293571 CTCAAAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 4 0.11
43 34 0.89
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (42 bp):
AAAAATTCTCATTTGAAAACTCAAAGATTCTTATTTAAAAAT
Found at i:12293577 original size:22 final size:22
Alignment explanation
Indices: 12293492--12293580 Score: 101
Period size: 22 Copynumber: 4.1 Consensus size: 22
12293482 TTCTCAAAAA
* *
12293492 TTCTCATTTGAAAACTCAAAGA
1 TTCTTATTTGAAAACTCAAAGT
* *
12293514 TTCTTATTT-AAAAAT-AAAAT
1 TTCTTATTTGAAAACTCAAAGT
*
12293534 ATTCTCATTTGAAAACTCAAAGT
1 -TTCTTATTTGAAAACTCAAAGT
*
12293557 TTCTTGTTTGAAAACTCAAAGT
1 TTCTTATTTGAAAACTCAAAGT
12293579 TT
1 TT
12293581 TATCTTAAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
20 3 0.05
21 13 0.24
22 35 0.64
23 4 0.07
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (22 bp):
TTCTTATTTGAAAACTCAAAGT
Found at i:12295343 original size:14 final size:14
Alignment explanation
Indices: 12295324--12295354 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12295314 GTAAAAGAAA
12295324 TATGATTATTTTTT
1 TATGATTATTTTTT
12295338 TATGATTATTTTTT
1 TATGATTATTTTTT
12295352 TAT
1 TAT
12295355 CTCAAACGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TATGATTATTTTTT
Found at i:12299056 original size:26 final size:24
Alignment explanation
Indices: 12299027--12299085 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
12299017 TAAATTTAGA
*
12299027 AAAAATTTCTCACATAGGAATTTTAT
1 AAAAATTTCTCA-ATAGAAATTTT-T
* * *
12299053 AAAAATTTATCATTTGAAATTTTT
1 AAAAATTTCTCAATAGAAATTTTT
12299077 AAAAATTTC
1 AAAAATTTC
12299086 ATCATTGGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 9 0.32
25 8 0.29
26 11 0.39
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (24 bp):
AAAAATTTCTCAATAGAAATTTTT
Found at i:12299240 original size:31 final size:32
Alignment explanation
Indices: 12299181--12299241 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
12299171 TAACAAAAAC
*
12299181 CATAAAACAAAGTGAATAAATAAACAATTATT
1 CATAAAACAAAGTGAATAAACAAACAATTATT
* * *
12299213 CATAACACAAA-TGAATAAGCAATCAATTA
1 CATAAAACAAAGTGAATAAACAAACAATTA
12299242 AAGAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (32 bp):
CATAAAACAAAGTGAATAAACAAACAATTATT
Found at i:12300690 original size:119 final size:118
Alignment explanation
Indices: 12300517--12300756 Score: 372
Period size: 119 Copynumber: 2.0 Consensus size: 118
12300507 TACAGTTAAG
*
12300517 TTTGATCACCTCATTTTGAAATGCAAATTAGAGAAACAAAAAGAACAAACAATTGCATAATTTCT
1 TTTGATCACCTCATTTTGAAATGCAAATTAGAGAAACAAAAAAAACAAACAATTGCATAATTTCT
* *
12300582 TGAAAGATTGAAGATTAAGATAGCTAATATGGTACAGCTACAACCTTATTAGA
66 TGAAAGATTAAAGATTAAGATAGCTAATATGGTACAACTACAACCTTATTAGA
* * *
12300635 TTTGATCACCTCATTTTGAAATGCAAAATTAGAGAAATAAAAAAAACAAATAATTGCATAATTTT
1 TTTGATCACCTCATTTTGAAATGC-AAATTAGAGAAACAAAAAAAACAAACAATTGCATAATTTC
* * * * *
12300700 TTGGAGGGTTAAAGATTAAGATAGCTAATATGGTACAATTACAACCTTATTGGA
65 TTGAAAGATTAAAGATTAAGATAGCTAATATGGTACAACTACAACCTTATTAGA
12300754 TTT
1 TTT
12300757 TTAACAATGT
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
118 24 0.22
119 86 0.78
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (118 bp):
TTTGATCACCTCATTTTGAAATGCAAATTAGAGAAACAAAAAAAACAAACAATTGCATAATTTCT
TGAAAGATTAAAGATTAAGATAGCTAATATGGTACAACTACAACCTTATTAGA
Found at i:12302632 original size:293 final size:292
Alignment explanation
Indices: 12301984--12302640 Score: 717
Period size: 293 Copynumber: 2.2 Consensus size: 292
12301974 GCGCATGTGT
* * * * *
12301984 GTGGATAGTAAGGA-AATCAATAAAATCATGATTGACTATCACTTTCCTCTTTTGTGCTTGGATG
1 GTGGATAGTAA-GACAATCAATAAAATCATGATTGACTATCAC-TTCTTATTCTATGCTTAGATG
* * * * *
12302048 ACTTACTAGACCAATTACATGGAACAATTATTTTCTTCAAGATAGACCTATGTAATGGCTATCAT
64 ACTTGCTAGACCAACTACATAGAACAACTATTTTCTTCAAGATAGACCTATGCAATGGCTATCAT
* * * * * * * *
12302113 CAATCAAAATGAGGCTTGGAGATGAATGAAAAATAGCTTTCAAGATAAGGGATGGTGTCTGTGAA
129 CAATCAAAATAAGGCCTAGAGATGAATGAAAAATAGCCTTCAAGACAAGGAATGATGTCTATGAA
* * * ** * ** * * *
12302178 TGGATGGTAATGCTTTTTGGTTTATCCAATGTTCTTTGTATTTTCATAAGGTTTATGACGCTTTT
194 TGGATAGTAATACCTTTTGGTTTATCCAATACTCCTAATACTTTCATAAGATTTATGACCCTTTT
* * * **
12302243 AGTGCCTAAAAAGAATGGATTATGGCACATGTGT
259 AGTGCCTAAAAAGAATAGATTATGACACATCTAC
* * * * * * ** * * *
12302277 GTGGATGGTAGGGCAATTAACAAAATTACAATTGATTATCA-TTTTCTATTCCATGCTTAGATGA
1 GTGGATAGTAAGACAATCAATAAAATCATGATTGACTATCACTTCT-TATTCTATGCTTAGATGA
* * *
12302341 CTTGCTAGACCAACTACATAGAGCAACTATTTTCTTCAAGATAGACTTATGCAATGGCTATTATC
65 CTTGCTAGACCAACTACATAGAACAACTATTTTCTTCAAGATAGACCTATGCAATGGCTATCATC
* * * * *
12302406 AAATCAGAATAAGGCCTAGAGATGAGTGAAAAATAGCCTTCAAGACAATGAATGATTTTTATGAA
130 -AATCAAAATAAGGCCTAGAGATGAATGAAAAATAGCCTTCAAGACAAGGAATGATGTCTATGAA
* *
12302471 TGGATAGTAATACCTTTTGGTTTATCCAATACTCCTAATGCTTTCATGAGATTTATGACCCTTTT
194 TGGATAGTAATACCTTTTGGTTTATCCAATACTCCTAATACTTTCATAAGATTTATGACCCTTTT
**
12302536 AGTGCCTAAATAAG-ATAGATTATGATGCATCTAC
259 AGTGCCTAAA-AAGAATAGATTATGACACATCTAC
* *
12302570 GTGGATAGTAAAACAATCAATAAAATCATGATTGACTATCACTTCTTATTCTATGTTTAGATGAC
1 GTGGATAGTAAGACAATCAATAAAATCATGATTGACTATCACTTCTTATTCTATGCTTAGATGAC
12302635 TTGCTA
66 TTGCTA
12302641 TGTTGAGCAA
Statistics
Matches: 289, Mismatches: 70, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
291 2 0.01
292 71 0.25
293 210 0.73
294 6 0.02
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (292 bp):
GTGGATAGTAAGACAATCAATAAAATCATGATTGACTATCACTTCTTATTCTATGCTTAGATGAC
TTGCTAGACCAACTACATAGAACAACTATTTTCTTCAAGATAGACCTATGCAATGGCTATCATCA
ATCAAAATAAGGCCTAGAGATGAATGAAAAATAGCCTTCAAGACAAGGAATGATGTCTATGAATG
GATAGTAATACCTTTTGGTTTATCCAATACTCCTAATACTTTCATAAGATTTATGACCCTTTTAG
TGCCTAAAAAGAATAGATTATGACACATCTAC
Found at i:12305487 original size:15 final size:15
Alignment explanation
Indices: 12305450--12305489 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12305440 AAATATTAAT
*
12305450 AAAGGAAAGGAAACG
1 AAAGGAAAGGAAAAG
12305465 AAAGGAAAGGAAAAG
1 AAAGGAAAGGAAAAG
*
12305480 CAAAGAAAAG
1 -AAAGGAAAG
12305490 AAAGTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.65, C:0.05, G:0.30, T:0.00
Consensus pattern (15 bp):
AAAGGAAAGGAAAAG
Found at i:12305960 original size:25 final size:24
Alignment explanation
Indices: 12305926--12305987 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
12305916 TCTAGTCTCA
12305926 ATATTCTATCATTATTTAAATTTTT
1 ATATT-TATCATTATTTAAATTTTT
* *
12305951 ATATGTTATC-TTTTTTTAATTTTT
1 ATAT-TTATCATTATTTAAATTTTT
* *
12305975 TTATTTATAATTA
1 ATATTTATCATTA
12305988 ATTTTTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 4 0.13
24 17 0.57
25 8 0.27
26 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (24 bp):
ATATTTATCATTATTTAAATTTTT
Found at i:12307415 original size:14 final size:13
Alignment explanation
Indices: 12307390--12307430 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
12307380 TTTTTATCAC
12307390 TAATTTTGAATAA
1 TAATTTTGAATAA
12307403 TAATTTTG--TAA
1 TAATTTTGAATAA
*
12307414 TAATTTTCATATAA
1 TAATTTTGA-ATAA
12307428 TAA
1 TAA
12307431 AATAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 10 0.42
13 8 0.33
14 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (13 bp):
TAATTTTGAATAA
Found at i:12308097 original size:20 final size:20
Alignment explanation
Indices: 12308068--12308129 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
12308058 ATAATATATC
*
12308068 AATATTTTTAAAAAAATAAT
1 AATATATTTAAAAAAATAAT
* * *
12308088 AATATATTTACATAAATCAT
1 AATATATTTAAAAAAATAAT
* *
12308108 AATA-ATCTAAAAAGATAAT
1 AATATATTTAAAAAAATAAT
12308127 AAT
1 AAT
12308130 CAATTTTTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (20 bp):
AATATATTTAAAAAAATAAT
Found at i:12308119 original size:64 final size:63
Alignment explanation
Indices: 12308017--12308158 Score: 150
Period size: 64 Copynumber: 2.2 Consensus size: 63
12308007 TTTTAAAGTT
12308017 AAATAATAATT-TATTAATAAATAATAAAAACTAATAAAATA-ATAATATATCAATATTTTTA-A
1 AAATAATAATTAT-TTAATAAATAATAAAAACTAATAAAA-AGATAATA-ATCAAT-TTTTTATA
12308079 AA
62 AA
* * * **
12308081 AAATAATAATATATTTACATAAATCATAATAA-T-CTAAAAAGATAATAATCAATTTTTTATGGA
1 AAATAATAAT-TATTTA-ATAAATAATAAAAACTAATAAAAAGATAATAATCAATTTTTTATAAA
12308144 AAATAATAATTATTT
1 AAATAATAATTATTT
12308159 TTTATTCAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
62 11 0.16
63 18 0.26
64 21 0.31
65 5 0.07
66 13 0.19
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.37
Consensus pattern (63 bp):
AAATAATAATTATTTAATAAATAATAAAAACTAATAAAAAGATAATAATCAATTTTTTATAAA
Found at i:12308162 original size:23 final size:23
Alignment explanation
Indices: 12308122--12308177 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
12308112 ATCTAAAAAG
* *
12308122 ATAATAATCAATTTTTTATGGAAA
1 ATAATAAT-TATTTTTTATGCAAA
*
12308146 ATAATAATTATTTTTTATTCAAA
1 ATAATAATTATTTTTTATGCAAA
*
12308169 ATAAAAATT
1 ATAATAATT
12308178 TTATCGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (23 bp):
ATAATAATTATTTTTTATGCAAA
Found at i:12310592 original size:21 final size:20
Alignment explanation
Indices: 12310568--12310608 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
12310558 TATAAGTTAC
12310568 ATTTTTTTTAATATATGTAAA
1 ATTTTTTTT-ATATATGTAAA
*
12310589 ATTTTTGTTTATATTTGTAA
1 ATTTTT-TTTATATATGTAA
12310609 GATATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
ATTTTTTTTATATATGTAAA
Found at i:12310945 original size:22 final size:22
Alignment explanation
Indices: 12310920--12310963 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12310910 TATAGAGATT
* *
12310920 TATATTTGATGTACTATTAATA
1 TATATTTGATATACTATCAATA
*
12310942 TATATTTTATATACTATCAATA
1 TATATTTGATATACTATCAATA
12310964 AATTAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
TATATTTGATATACTATCAATA
Found at i:12311186 original size:104 final size:102
Alignment explanation
Indices: 12311006--12311334 Score: 353
Period size: 104 Copynumber: 3.2 Consensus size: 102
12310996 AATGTTTCTG
* * *
12311006 ATTAAAGAAGCTCTTTTT-AAATGAGATTACTTTTAAAAGTTTCAATACCTCTGTTTAAGAGGAT
1 ATTAAAGAAGCT-TTTTTCAAATGAGATTTCTTTTAAAAGTTTCAATACCTATGTTTAAGA-GAA
12311070 CTTTCTTT-ATATAAGAGTTTTAAAATTTCAATGCCTTTA
64 CTTT-TTTCATATAAGAGTTTTAAAATTTCAATGCCTTTA
* * * * * *
12311109 ATTAAAGAAGCTTTTTTCAAGTGACATTTTCTTTTAAAAGTTTTAATATCTTTGTTTAAGATGAG
1 ATTAAAGAAGCTTTTTTCAAATGAGA-TTTCTTTTAAAAGTTTCAATACCTATGTTTAAGA-GAA
* *
12311174 CTTTTTTCATATAAGAGTTTTAAAATTTCAATGCATTTT
64 CTTTTTTCATATAAGAGTTTTAAAATTTCAATGCCTTTA
* * *
12311213 ATTAGAGGAA-C-TTTTTCAAATGAGATTTCTTTTAAAAGTTTCAA-AGCATATATTTAAGAGAA
1 ATTA-AAGAAGCTTTTTTCAAATGAGATTTCTTTTAAAAGTTTCAATA-CCTATGTTTAAGAG-A
* * * ** *
12311275 ACTTTCTTCAGATAAGAGTTTTAAAGTTTCAATATCTTTG
63 ACTTTTTTCATATAAGAGTTTTAAAATTTCAATGCCTTTA
*
12311315 TTTAAGAGAAGCTTTTTTCA
1 ATTAA-AGAAGCTTTTTTCA
12311335 GATAAAACTT
Statistics
Matches: 189, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
101 3 0.02
102 71 0.38
103 34 0.18
104 77 0.41
105 4 0.02
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (102 bp):
ATTAAAGAAGCTTTTTTCAAATGAGATTTCTTTTAAAAGTTTCAATACCTATGTTTAAGAGAACT
TTTTTCATATAAGAGTTTTAAAATTTCAATGCCTTTA
Found at i:12311303 original size:50 final size:49
Alignment explanation
Indices: 12311241--12311360 Score: 150
Period size: 50 Copynumber: 2.4 Consensus size: 49
12311231 AATGAGATTT
*
12311241 CTTTTAAAAGTTTCAAAGCATATATTTAAGAGAAACTTTCTTCAGATAAGA
1 CTTTT-AAAGTTTCAAAGC-TATATTTAAGAGAAACTTTCTTCAGATAAAA
* * * * * *
12311292 GTTTTAAAGTTTCAATATCTTTGTTTAAGAGAAGCTTTTTTCAGATAAAA
1 CTTTTAAAGTTTCAA-AGCTATATTTAAGAGAAACTTTCTTCAGATAAAA
12311342 CTTTTAAAGTTTCAAAGCT
1 CTTTTAAAGTTTCAAAGCT
12311361 TCTAATTAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 3 0.05
50 50 0.85
51 6 0.10
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (49 bp):
CTTTTAAAGTTTCAAAGCTATATTTAAGAGAAACTTTCTTCAGATAAAA
Found at i:12311472 original size:153 final size:152
Alignment explanation
Indices: 12311140--12311461 Score: 391
Period size: 152 Copynumber: 2.1 Consensus size: 152
12311130 TGACATTTTC
* * * * *
12311140 TTTTAAAAGTTTTAATATCTTTGTTTAAGATGAGCTTTTTTCATATAAGAGTTTTAAAATTTCAA
1 TTTTTAAAGTTTCAATATCTTTGTTTAAGATGAGCTTTTTTCAGATAAAACTTTTAAAATTTCAA
* * * * *
12311205 TGCATTTTATTAGAGGAACTTTTTCAAATGAGATTTCTTTTAAAAGTTTCAAAGCATATATTTAA
66 AGCATTTAATTAGAAGAACTTTTTCAAATGAGATTTATTTTAAAAATTTCAAAGCATATATTTAA
12311270 GAGAAACTTTCTTCAGATAAGA
131 GAGAAACTTTCTTCAGATAAGA
* *
12311292 GTTTTAAAGTTTCAATATCTTTGTTTAAGA-GAAGCTTTTTTCAGATAAAACTTTTAAAGTTTCA
1 TTTTTAAAGTTTCAATATCTTTGTTTAAGATG-AGCTTTTTTCAGATAAAACTTTTAAAATTTCA
** * * * * *
12311356 AAGC-TTCTAATTAGAAGAGTTATTTTTAAATGAGATTTATTTTAAAAATTTCAATGCCTCTGTT
65 AAGCATT-TAATTAGAAGAACT-TTTTCAAATGAGATTTATTTTAAAAATTTCAAAGCATATATT
*
12311420 TAAGATAAACTTTCCTT-AGATGAA-A
128 TAAGAGAAACTTT-CTTCAGAT-AAGA
12311445 TTTTTAAAGTTTCAATA
1 TTTTTAAAGTTTCAATA
12311462 CCTCTATTTA
Statistics
Matches: 144, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
151 3 0.02
152 68 0.47
153 68 0.47
154 5 0.03
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (152 bp):
TTTTTAAAGTTTCAATATCTTTGTTTAAGATGAGCTTTTTTCAGATAAAACTTTTAAAATTTCAA
AGCATTTAATTAGAAGAACTTTTTCAAATGAGATTTATTTTAAAAATTTCAAAGCATATATTTAA
GAGAAACTTTCTTCAGATAAGA
Found at i:12311515 original size:49 final size:47
Alignment explanation
Indices: 12311394--12311572 Score: 126
Period size: 50 Copynumber: 3.6 Consensus size: 47
12311384 AATGAGATTT
* ** * *
12311394 ATTTTAAAAATTTCAATGCCTCTGTTTAAGATAAACTTTCCTT-AGATGAA
1 ATTTT-AAAATTTCAATGCCTCTATTTAA-A-AAAAGTT-CTTCAAATGAG
* *
12311444 ATTTTTAAAGTTTCAATACCTCTATTTAAAAAAAGTTACTTGCAAATGAG
1 A-TTTTAAAATTTCAATGCCTCTATTTAAAAAAAGTT-CTT-CAAATGAG
* ** * *
12311494 ATTTTAAAATTTCAATGCCTCTATTCAAAATGAGCTTTTTTCATATGAG
1 ATTTTAAAATTTCAATGCCTCTATTTAAAAAAAG--TTCTTCAAATGAG
* * *
12311543 ATTCTTAAAGTTTCAAGGCCTCTAATTAAA
1 ATT-TTAAAATTTCAATGCCTCTATTTAAA
12311573 GTAGTTTTCT
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
48 8 0.08
49 39 0.38
50 51 0.49
51 6 0.06
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (47 bp):
ATTTTAAAATTTCAATGCCTCTATTTAAAAAAAGTTCTTCAAATGAG
Found at i:12311542 original size:153 final size:152
Alignment explanation
Indices: 12311224--12311545 Score: 330
Period size: 153 Copynumber: 2.1 Consensus size: 152
12311214 TTAGAGGAAC
* *
12311224 TTTTTCAAATGAGATTTCTTTTAAAAGTTTCAAAGCATATATTTAAGAGAAACTTTCTTCAGATA
1 TTTTTCAAATGAGATTTATTTTAAAAATTTCAAAGCATATATTTAAGAGAAACTTTCTTCAGATA
* * * * * * * * *
12311289 AGAGTTTTAAAGTTTCAATATCTTTGTTTAAGAGAAGCTTTTTTCAGATAAAACTTTTAAAGTTT
66 AGAGTTTTAAAGTTTCAATACCTCTATTTAAAAAAAGCTTCTTGCAAATAAAACTTTTAAAATTT
* *
12311354 CAAAGCTTCTAATTAGAAGAGT
131 CAAAGCCTCTAATTAAAAGAGT
* * * * * *
12311376 TATTTTTAAATGAGATTTATTTTAAAAATTTCAATGCCTCTGTTTAAGATAAACTTTCCTT-AGA
1 T-TTTTCAAATGAGATTTATTTTAAAAATTTCAAAGCATATATTTAAGAGAAACTTT-CTTCAGA
* * *
12311440 TGAA-ATTTTTAAAGTTTCAATACCTCTATTTAAAAAAAG-TTACTTGCAAATGAGA-TTTTAAA
64 T-AAGAGTTTTAAAGTTTCAATACCTCTATTTAAAAAAAGCTT-CTTGCAAATAAAACTTTTAAA
*
12311502 ATTTCAATGCCTCT-ATTCAAAATGAGCT
127 ATTTCAAAGCCTCTAATT-AAAA-GAG-T
*
12311530 TTTTTCATATGAGATT
1 TTTTTCAAATGAGATT
12311546 CTTAAAGTTT
Statistics
Matches: 138, Mismatches: 25, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
151 3 0.02
152 24 0.17
153 104 0.75
154 7 0.05
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (152 bp):
TTTTTCAAATGAGATTTATTTTAAAAATTTCAAAGCATATATTTAAGAGAAACTTTCTTCAGATA
AGAGTTTTAAAGTTTCAATACCTCTATTTAAAAAAAGCTTCTTGCAAATAAAACTTTTAAAATTT
CAAAGCCTCTAATTAAAAGAGT
Found at i:12311621 original size:49 final size:49
Alignment explanation
Indices: 12311439--12311622 Score: 178
Period size: 49 Copynumber: 3.7 Consensus size: 49
12311429 CTTTCCTTAG
* * * *
12311439 ATGAAATTTTTAAAGTTTCAATACCTCTATTTAAAAAAAG-TTACTTGCAA
1 ATGAGATTTTTAAAGTTTCAATACCTCTATTT-AAAATAGTTTTCTT-CAT
* * *
12311489 ATGAGA-TTTTAAAATTTCAATGCCTCTATTCAAAATGAGCTTTT-TTCAT
1 ATGAGATTTTTAAAGTTTCAATACCTCTATTTAAAAT-AG-TTTTCTTCAT
* ** * * *
12311538 ATGAGATTCTTAAAGTTTCAAGGCCTCTAATTAAAGTAGTTTTCTTTAT
1 ATGAGATTTTTAAAGTTTCAATACCTCTATTTAAAATAGTTTTCTTCAT
12311587 ATGAGATTTTTAAAGTTTCAATACCT-TAGTTTAAAA
1 ATGAGATTTTTAAAGTTTCAATACCTCTA-TTTAAAA
12311623 GGAACCACTT
Statistics
Matches: 109, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
48 10 0.09
49 66 0.61
50 31 0.28
51 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (49 bp):
ATGAGATTTTTAAAGTTTCAATACCTCTATTTAAAATAGTTTTCTTCAT
Found at i:12311669 original size:98 final size:98
Alignment explanation
Indices: 12311567--12311755 Score: 245
Period size: 98 Copynumber: 1.9 Consensus size: 98
12311557 AAGGCCTCTA
* * * * *
12311567 ATTAAAGTAGTTTTCTTTATATGAGATTTTTAAAGTTTCAATACCTTA-GTTTAAAAGGAACCAC
1 ATTAAAGGAGCTTTCTTCATATAAGATTTTTAAAGTTTCAAT-CCATATGTTTAAAAGGAACCAC
*
12311631 TTGCAAATAAGGTTTTAAAGTTTCAATTTCTTTT
65 TTGCAAATAAGATTTTAAAGTTTCAATTTCTTTT
* * * * *
12311665 ATTAAAGGAGCTTTCTTCATATAAGATTTTTGAAGTTTTAATGCATATGTTTAAAAGGAGCCATT
1 ATTAAAGGAGCTTTCTTCATATAAGATTTTTAAAGTTTCAATCCATATGTTTAAAAGGAACCACT
* *
12311730 TGTAAATGAGATTTTAAAGTTTCAAT
66 TGCAAATAAGATTTTAAAGTTTCAAT
12311756 GCTTTTGTTA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 3 0.04
98 74 0.96
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (98 bp):
ATTAAAGGAGCTTTCTTCATATAAGATTTTTAAAGTTTCAATCCATATGTTTAAAAGGAACCACT
TGCAAATAAGATTTTAAAGTTTCAATTTCTTTT
Found at i:12313886 original size:41 final size:44
Alignment explanation
Indices: 12313842--12313931 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
12313832 AGTAAATTAA
* *
12313842 AAAAATG-TGTATGAAAAAT-AT-ATAA-TATAACAATAATAAT
1 AAAAATGATGTATAAAAAATAATAATAACAATAACAATAATAAT
12313882 AAAAATGATGTATAAAAAATAATAATAACAATAACAATAATAAT
1 AAAAATGATGTATAAAAAATAATAATAACAATAACAATAATAAT
*
12313926 GAAAAT
1 AAAAAT
12313932 CTCCAACGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 7 0.16
41 11 0.26
42 2 0.05
43 4 0.09
44 19 0.44
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (44 bp):
AAAAATGATGTATAAAAAATAATAATAACAATAACAATAATAAT
Found at i:12313914 original size:12 final size:12
Alignment explanation
Indices: 12313855--12313921 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
12313845 AATGTGTATG
12313855 AAAAATATATAAT
1 AAAAATA-ATAAT
12313868 ATAACAATAATAAT
1 A-AA-AATAATAAT
* *
12313882 AAAAATGATGTAT
1 AAAAATAAT-AAT
12313895 AAAAAATAATAAT
1 -AAAAATAATAAT
* *
12313908 AACAATAACAAT
1 AAAAATAATAAT
12313920 AA
1 AA
12313922 TAATGAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 17 0.39
13 7 0.16
14 16 0.36
15 4 0.09
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.25
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:12313921 original size:38 final size:41
Alignment explanation
Indices: 12313842--12313927 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 41
12313832 AGTAAATTAA
* *
12313842 AAAAATG-TGTATGAAAAATATATAATATAACAATAATAAT
1 AAAAATGATGTATAAAAAATATATAATATAACAATAACAAT
12313882 AAAAATGATGTATAAAAAATA-AT-A-ATAACAATAACAAT
1 AAAAATGATGTATAAAAAATATATAATATAACAATAACAAT
*
12313920 AATAATGA
1 AAAAATGA
12313928 AAATCTCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 20 0.48
39 1 0.02
40 9 0.21
41 12 0.29
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (41 bp):
AAAAATGATGTATAAAAAATATATAATATAACAATAACAAT
Found at i:12315602 original size:5 final size:5
Alignment explanation
Indices: 12315592--12315616 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12315582 CCATCGATTC
12315592 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
12315617 TCTATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:12316743 original size:2 final size:2
Alignment explanation
Indices: 12316736--12316762 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12316726 GTTTGTATTT
12316736 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12316763 GGAGTTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12319241 original size:21 final size:20
Alignment explanation
Indices: 12319210--12319259 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
12319200 ATTATCAAAC
12319210 TTAATTAAATTTTTA-TATT
1 TTAATTAAATTTTTATTATT
12319229 TTAATATATAATTTTTATTATT
1 TTAAT-TA-AATTTTTATTATT
*
12319251 GTAATTAAA
1 TTAATTAAA
12319260 AAAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 10 0.37
22 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTAATTAAATTTTTATTATT
Found at i:12321026 original size:62 final size:62
Alignment explanation
Indices: 12320960--12321176 Score: 244
Period size: 62 Copynumber: 3.5 Consensus size: 62
12320950 GCGAAACGCT
* * *
12320960 TTAATTGATCTTATTATAAATTTATAAAGAGGTTAATTAAGGCATTTGGCTACACAAATATC
1 TTAATTGATCTAATTATAAATTTATAAAGAGATCAATTAAGGCATTTGGCTACACAAATATC
* * * *
12321022 TTAATGGATCCAATATGTAAATTATATATAA-ATGATCAATTAAGGCATTTGGTTACACAAACT-
1 TTAATTGATCTAAT-TATAAATT-TATA-AAGA-GATCAATTAAGGCATTTGGCTACACAAA-TA
*
12321085 CC
61 TC
* * *
12321087 TTAATTGATCTTATTATAAATTTATAATGAGATCAATTAAGGCGA-TTGGCTACACAAACATC
1 TTAATTGATCTAATTATAAATTTATAAAGAGATCAATTAAGGC-ATTTGGCTACACAAATATC
12321149 TTAATTGATCTAATTTATAAA-TTATAAA
1 TTAATTGATCTAA-TTATAAATTTATAAA
12321177 TTAAAAACAA
Statistics
Matches: 128, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
62 56 0.44
63 20 0.16
64 12 0.09
65 39 0.30
66 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (62 bp):
TTAATTGATCTAATTATAAATTTATAAAGAGATCAATTAAGGCATTTGGCTACACAAATATC
Found at i:12324895 original size:14 final size:15
Alignment explanation
Indices: 12324873--12325198 Score: 73
Period size: 15 Copynumber: 20.3 Consensus size: 15
12324863 ATACTCAAAA
*
12324873 TAATTATATTT-TAT
1 TAATAATATTTATAT
12324887 TAATAATATTTAATAT
1 TAATAATATTT-ATAT
*
12324903 TAAAATATTATGTTAATAT
1 T--AATAATAT-TT-ATAT
* * * *
12324922 AAAAAATATTTAAAA
1 TAATAATATTTATAT
12324937 TAA-AACTATTTATTAT
1 TAATAA-TATTTA-TAT
** * *
12324953 TCTTTATATTATTTAT
1 TAATAATATT-TATAT
12324969 TAAT-ATATTATATATT
1 TAATAATATT-TATA-T
*
12324985 TATTAATATATTATAT
1 TAATAATAT-TTATAT
12325001 TAATAGTATACTATT-TAT
1 TAATA--ATA-T-TTATAT
12325019 TAATAATATATTAT-T
1 TAATAATAT-TTATAT
* *
12325034 TAGTAATA-GTATAT
1 TAATAATATTTATAT
* *
12325048 TTAT-TTATTAATATAT
1 TAATAATATT--TATAT
*
12325064 TAAT-ATATTATTTAT
1 TAATAATATT-TATAT
12325079 TAATATATGATTTATTAAT
1 TAATA-AT-ATTTA-T-AT
*
12325098 ATAATATTATTTATTTATT
1 -TAATAATATTTA--TA-T
*
12325117 TACTAATATTAATATAT
1 TAATAATATT--TATAT
12325134 TAGTATAATATTTAT-T
1 TA--ATAATATTTATAT
*
12325150 T-ATAATAATTAT-T
1 TAATAATATTTATAT
*
12325163 TATTAATATATTAT-T
1 TAATAATAT-TTATAT
* *
12325178 TATTAATATATTGTAT
1 TAATAATAT-TTATAT
12325194 TAATA
1 TAATA
12325199 GTATATTATT
Statistics
Matches: 239, Mismatches: 38, Indels: 68
0.69 0.11 0.20
Matches are distributed among these distances:
13 17 0.07
14 20 0.08
15 58 0.24
16 49 0.21
17 25 0.10
18 39 0.16
19 24 0.10
20 7 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (15 bp):
TAATAATATTTATAT
Found at i:12324965 original size:19 final size:19
Alignment explanation
Indices: 12324943--12325241 Score: 125
Period size: 18 Copynumber: 16.0 Consensus size: 19
12324933 AAAATAAAAC
* *
12324943 TATTTATTATTCT-TTATA
1 TATTTATTAATATATTATA
12324961 TTATTTATTAATATATTATA
1 -TATTTATTAATATATTATA
12324981 TATTTATT-A-ATA-TAT-
1 TATTTATTAATATATTATA
*
12324996 TA--TATTAATAGTA-TA-C
1 TATTTATTAATA-TATTATA
12325012 TATTTATTAATA-A-TATA
1 TATTTATTAATATATTATA
* *
12325029 TTATTTAGTAATAGTA-TATT
1 -TATTTATTAATA-TATTATA
12325049 TATTTATTAATATATTA-A
1 TATTTATTAATATATTATA
* *
12325067 TATATTATTTAT-TAATATA
1 TAT-TTATTAATATATTATA
*
12325086 TGATTTATTAATATAATAT-
1 T-ATTTATTAATATATTATA
* * *
12325105 TATTTATTTATTTACTAATA
1 TATTTATTAATATA-TTATA
* * * *
12325125 TTAATATATTAGTATAATATT
1 -T-ATTTATTAATATATTATA
*
12325146 TATTTA-TAATA-ATTATT
1 TATTTATTAATATATTATA
* *
12325163 TATTAATATATTATTTATTAATA
1 TATT--TAT-TAATATATT-ATA
12325186 TATTGTATTAATAGTA-TAT-
1 TATT-TATTAATA-TATTATA
* * *
12325205 TATTTATTCATGTAATAT-
1 TATTTATTAATATATTATA
*
12325223 TATTTATTAATATGTTATA
1 TATTTATTAATATATTATA
12325242 ATATAATATC
Statistics
Matches: 215, Mismatches: 36, Indels: 58
0.70 0.12 0.19
Matches are distributed among these distances:
13 4 0.02
14 1 0.00
15 3 0.01
16 12 0.06
17 14 0.07
18 67 0.31
19 61 0.28
20 20 0.09
21 10 0.05
22 17 0.08
23 6 0.03
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (19 bp):
TATTTATTAATATATTATA
Found at i:12324975 original size:15 final size:15
Alignment explanation
Indices: 12324957--12325302 Score: 204
Period size: 15 Copynumber: 22.8 Consensus size: 15
12324947 TATTATTCTT
12324957 TATATTATTTATTAATA
1 TATATTATTTATT-A-A
12324974 TATTATATATTTATTAA
1 TA-TAT-TATTTATTAA
* *
12324991 TATATTATATTAATAG
1 TATATTAT-TTATTAA
*
12325007 TATACTATTTATTAATAA
1 TATATTATTTA-T--TAA
*
12325025 TATATTATTTAGTAA
1 TATATTATTTATTAA
12325040 TAGTA-TATTTATT--
1 TA-TATTATTTATTAA
* *
12325053 TAT-TAATATATTAA
1 TATATTATTTATTAA
12325067 TATATTATTTATTAA
1 TATATTATTTATTAA
*
12325082 TATATGATTTATTAA
1 TATATTATTTATTAA
*
12325097 TATAATA-TTATT--
1 TATATTATTTATTAA
*
12325109 TAT-TTATTTACTAA
1 TATATTATTTATTAA
*
12325123 TATTAATATATTAGTATAA
1 TA-TATTAT-TTA-T-TAA
12325142 TAT-TTATTTA-TAA
1 TATATTATTTATTAA
12325155 TA-ATTATTTATTAA
1 TATATTATTTATTAA
12325169 TATATTATTTATTAA
1 TATATTATTTATTAA
* * *
12325184 TATATTGTATTAATAG
1 TATATTAT-TTATTAA
*
12325200 TATATTATTTATTCATG
1 TATATTATTTATT-A-A
12325217 TAATATTATTTATTAA
1 T-ATATTATTTATTAA
* *
12325233 TATGTTA-TAATATAA
1 TATATTATTTAT-TAA
*
12325248 TATCATTTATTAATATAA
1 TAT-A-TTATTTAT-TAA
*
12325266 TATAATA-TTATT--
1 TATATTATTTATTAA
* *
12325278 TAT-TTATTTGTTTA
1 TATATTATTTATTAA
12325292 -ATATTATTTAT
1 TATATTATTTAT
12325303 AAGTAAAATT
Statistics
Matches: 261, Mismatches: 34, Indels: 71
0.71 0.09 0.19
Matches are distributed among these distances:
11 4 0.02
12 21 0.08
13 16 0.06
14 26 0.10
15 84 0.32
16 39 0.15
17 18 0.07
18 40 0.15
19 13 0.05
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (15 bp):
TATATTATTTATTAA
Found at i:12325041 original size:68 final size:67
Alignment explanation
Indices: 12324957--12325281 Score: 254
Period size: 68 Copynumber: 4.9 Consensus size: 67
12324947 TATTATTCTT
*
12324957 TATATTATTTATTAATATATTATATATTTATTAATATATTATATTAATAGTATACTATTTATTAA
1 TATATTATTTATTAATATATTATATATTTATTAATATATTATA-TAATAGTATATTATTTATTAA
12325022 TAA
65 TAA
* *
12325025 TATATTATTTAGTAATAGTA-TATTTATTTATT-A-ATA-TAT-T-A-A-TATATTATTTATTAA
1 TATATTATTTATTAATA-TATTATATATTTATTAATATATTATATAATAGTATATTATTTATTAA
12325082 T-A
65 TAA
* * * * * *
12325084 TATGATTTATTAATATAATATTATTTATTTATTTACTAATAT-TAATATATTAGTATAATATTTA
1 TAT-A-TTATTTAT-TAATA-TA-TTATATATTTATTAATATATTATATAATAGTATATTATTTA
*
12325148 TTTATAA
61 TTAATAA
* *
12325155 TA-ATTATTTATT-A-ATA-TAT-TATTTATTAATATATTGTATTAATAGTATATTATTTATTCA
1 TATATTATTTATTAATATATTATATATTTATTAATATATTATA-TAATAGTATATTATTTATTAA
*
12325215 T-G
65 TAA
* * * *
12325217 TAATATTATTTATTAATATGTTATA-ATATAATATCATTTATTAATATAATA-TAATATTATTTA
1 T-ATATTATTTATTAATATATTATATAT-TTAT-TAATATATT-ATATAATAGT-ATATTATTTA
12325280 TT
61 TT
12325282 TATTTGTTTA
Statistics
Matches: 207, Mismatches: 24, Indels: 51
0.73 0.09 0.18
Matches are distributed among these distances:
59 4 0.02
60 16 0.08
61 19 0.09
62 15 0.07
63 21 0.10
64 23 0.11
65 6 0.03
66 10 0.05
67 8 0.04
68 38 0.18
69 28 0.14
70 16 0.08
71 3 0.01
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (67 bp):
TATATTATTTATTAATATATTATATATTTATTAATATATTATATAATAGTATATTATTTATTAAT
AA
Found at i:12325255 original size:28 final size:28
Alignment explanation
Indices: 12325217--12325273 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
12325207 TTTATTCATG
* **
12325217 TAATATTATTTATTAATATGTTATAATA
1 TAATATCATTTATTAATATAATATAATA
12325245 TAATATCATTTATTAATATAATATAATA
1 TAATATCATTTATTAATATAATATAATA
12325273 T
1 T
12325274 TATTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
TAATATCATTTATTAATATAATATAATA
Found at i:12325262 original size:64 final size:63
Alignment explanation
Indices: 12324960--12325174 Score: 116
Period size: 57 Copynumber: 3.5 Consensus size: 63
12324950 TATTCTTTAT
* * *
12324960 ATTATTTATTAATATATTATATATTTATTAATATATTATATTAATAGTATACTATTTATTAATAA
1 ATTATTTATTAATATA-T-TATA--TATTAATATATTGTATTAATAGTATAATATTTATTTATAA
12325025 TA
62 TA
* * * * * *
12325027 TATTATTTAGTAATAGTA-TATTTATTTAT-TAATATATTAATA-TAT--TATTTATTAAT-AT-
1 -ATTATTTATTAATA-TATTATATATTAATATATTGTATTAATAGTATAATATTTATTTATAATA
* * * * * *
12325085 ATGATTTATTAATATAATAT-TATTTATTTATT-TACTAATA-T-TAATATATTA-GTATAATA
1 ATTATTTATTAATATATTATATATTAATATATTGTATTAATAGTATAATAT-TTATTTATAATA
* *
12325144 TTTATTTA-TAATA-ATTATTTATTAATATATT
1 ATTATTTATTAATATATTATATATTAATATATT
12325175 ATTTATTAAT
Statistics
Matches: 123, Mismatches: 15, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
55 1 0.01
56 17 0.14
57 27 0.22
58 20 0.16
59 8 0.07
60 11 0.09
62 3 0.02
63 12 0.10
64 6 0.05
66 3 0.02
68 13 0.11
69 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (63 bp):
ATTATTTATTAATATATTATATATTAATATATTGTATTAATAGTATAATATTTATTTATAATA
Found at i:12325267 original size:46 final size:48
Alignment explanation
Indices: 12324958--12325277 Score: 195
Period size: 46 Copynumber: 6.6 Consensus size: 48
12324948 ATTATTCTTT
* * *
12324958 ATATTATTTATTAATATATTATATATTTATTAATATATTATATTAATAGT-
1 ATATTATTTATT-ATATAATAT-TATTTATTAATATAGTGTATTAATA-TA
* * *
12325008 ATACTATTTATTA-ATAATA-TA-TTATTTAGTAATAGTATATT--TAT-
1 ATATTATTTATTATATAATATTATTTA-TTAAT-ATAGTGTATTAATATA
* * *
12325052 TTATTAATATATTA-AT-ATATTATTTATTAATATATGATTTATTAATATA
1 ATATT-ATTTATTATATAATATTATTTATTAATATA-G-TGTATTAATATA
* * * * *
12325101 ATATTATTTATTTATTTACTAATATTAATATATTAGTATAATAT-TTATTTATA
1 ATATTATTTA-TTA--TA-TAATATT-ATTTATTAATATAGTGTATTA-ATATA
*
12325154 ATAATTATTTATTA-AT-ATATTATTTATTAATATATTGTATTAATAGT-
1 AT-ATTATTTATTATATAATATTATTTATTAATATAGTGTATTAATA-TA
*
12325201 ATATTATTTATTCATGTAATATTATTTATTAATAT-GT-TA-TAATATA
1 ATATTATTTATT-ATATAATATTATTTATTAATATAGTGTATTAATATA
* *
12325247 ATATCATTTATTAATATAATATAATATTATT
1 ATATTATTTATT-ATATAATATTAT-TTATT
12325278 TATTTATTTG
Statistics
Matches: 217, Mismatches: 27, Indels: 55
0.73 0.09 0.18
Matches are distributed among these distances:
44 10 0.05
45 22 0.10
46 50 0.23
47 34 0.16
48 23 0.11
49 26 0.12
50 12 0.06
52 4 0.02
53 12 0.06
54 13 0.06
55 11 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (48 bp):
ATATTATTTATTATATAATATTATTTATTAATATAGTGTATTAATATA
Found at i:12326244 original size:14 final size:13
Alignment explanation
Indices: 12326215--12326255 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
12326205 CTTTCACAAT
*
12326215 AAAAATTACA-TA
1 AAAAATTAAATTA
12326227 AAAAATTTAAATTA
1 AAAAA-TTAAATTA
12326241 AAAAATTAAATTA
1 AAAAATTAAATTA
12326254 AA
1 AA
12326256 TCTATCACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 14 0.54
14 7 0.27
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAATTAAATTA
Found at i:12326747 original size:499 final size:496
Alignment explanation
Indices: 12325826--12326754 Score: 1367
Period size: 497 Copynumber: 1.9 Consensus size: 496
12325816 ATAGTTTTGT
*
12325826 AATTTAATGGTAGAATACTATGCTTTTAAAGATCATTTTGATAATTTATTTATTAATAGAATACT
1 AATTTAATGGTAGAATACTATGCTTTTAAAGATCATTGTGATAATTTATTTATTAATAGAATACT
* * * * *
12325891 AAATTTTTAAAAATTATCGTGATAATTTAATTATTATTACAGTTATCTTATAATTCATTATTCGA
66 AAACTTTTAAAAATTATCATGATAATTTAATTATTATTACAATTATCTTATAATTCATGATTAGA
* * * *
12325956 ATCACTTTTTTTTAACTATAATTATTTCTCAGAACTTAAAAATTATTATGTTTGATGTTATTGAA
131 ATCAC-TTTTTTTAACTATAATTAGTTCTCAAAACTTAAAAATTATTATGTTTGATATTATTAAA
* * *
12326021 AATTAAAAATTATTTTATTTAAAAGTTTTAAAATAGTCATATTATCATAGCACAAAAGTAATATT
195 AAATAAAAATTATTTTATTTAAAAGTATTAAAATAATCATATTATCATAGCACAAAAGTAATATT
*
12326086 TCAATGTTATATAAATCAACATAACTATATGCAAAATATCAGTAATATTTTATTTTCTTGATAAT
260 TCAATGTTATATAAAT-AACATAAC-ATATGCAAAATATCAATAATATTTTATTTTCTTGATAAT
* * *
12326151 AATATATAAATAACATTTTAGATTAATAAATATATTTATTGATAAATGAAATAACTTTCACAATA
323 AAGATATAAATAACATTTTAAATTAATAAATATATTTATTAATAAATGAAATAACTTTCACAATA
12326216 AAAATTACATAAAAAATTTAAATTAAAAAATTAAATTAAATCTATCACTACCAAATTTTAGTTTA
388 AAAATTACATAAAAAATTTAAATTAAAAAATTAAATTAAATCTATCACTACCAAATTTTAGTTTA
12326281 ATATGGACAAAGTTTTGTCAGTAATTATCAAGTGTTATTGATAA
453 ATATGGACAAAGTTTTGTCAGTAATTATCAAGTGTTATTGATAA
* * *
12326325 AATTTAATGGTA-AAGTACTATGCTTTTGAAGATCATTGTGATAATTTATTTATTAGTA-ATTTA
1 AATTTAATGGTAGAA-TACTATGCTTTTAAAGATCATTGTGATAATTTATTTATTAATAGA-ATA
* * *
12326388 TTAAACTTTTAAAAATTATCATGATAATTTAATT-TTGTTACAATTATCTTATAATTCGTGATTT
64 CTAAACTTTTAAAAATTATCATGATAATTTAATTATTATTACAATTATCTTATAATTCATGA-TT
*
12326452 AGAATCA-TTTTTTTAA-TGATAATTAGTTCTCAAAACTTATAAATTATTATGTTTGATATTATT
128 AGAATCACTTTTTTTAACT-ATAATTAGTTCTCAAAACTTAAAAATTATTATGTTTGATATTATT
* *
12326515 AAAAAATAAAAATTATTTTATTTAAAGGTATTACAATAATCATATTATCATAGCACAAAAGTAAT
192 AAAAAATAAAAATTATTTTATTTAAAAGTATTAAAATAATCATATTATCATAGCACAAAAGTAAT
* *
12326580 AATTTCAATGTTATTTACAAT-A-A-AA-ATATGTAAAATATCAATAATATTTTATTTTCTTGAT
257 -ATTTCAATGTTATATA-AATAACATAACATATGCAAAATATCAATAATATTTTATTTTCTTGAT
* *
12326641 AATAAGATATAAATAA-ATTTTAAATTAATAAATATATTTATTAATAAAT-AAATTAACTTTTAT
320 AATAAGATATAAATAACATTTTAAATTAATAAATATATTTATTAATAAATGAAA-TAACTTTCAC
* * * *
12326704 AATAAAGATTACATAAAAATTATTTGAATTAGAAAATAAAATTAAATCTAT
384 AATAAAAATTACATAAAAA--ATTTAAATTAAAAAATTAAATTAAATCTAT
12326755 TGGTAGAATT
Statistics
Matches: 387, Mismatches: 34, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
491 3 0.01
492 57 0.15
493 49 0.13
494 27 0.07
495 2 0.01
496 2 0.01
497 110 0.28
498 41 0.11
499 96 0.25
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (496 bp):
AATTTAATGGTAGAATACTATGCTTTTAAAGATCATTGTGATAATTTATTTATTAATAGAATACT
AAACTTTTAAAAATTATCATGATAATTTAATTATTATTACAATTATCTTATAATTCATGATTAGA
ATCACTTTTTTTAACTATAATTAGTTCTCAAAACTTAAAAATTATTATGTTTGATATTATTAAAA
AATAAAAATTATTTTATTTAAAAGTATTAAAATAATCATATTATCATAGCACAAAAGTAATATTT
CAATGTTATATAAATAACATAACATATGCAAAATATCAATAATATTTTATTTTCTTGATAATAAG
ATATAAATAACATTTTAAATTAATAAATATATTTATTAATAAATGAAATAACTTTCACAATAAAA
ATTACATAAAAAATTTAAATTAAAAAATTAAATTAAATCTATCACTACCAAATTTTAGTTTAATA
TGGACAAAGTTTTGTCAGTAATTATCAAGTGTTATTGATAA
Found at i:12328209 original size:21 final size:22
Alignment explanation
Indices: 12328170--12328211 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12328160 ACCGATATGA
12328170 TTTAAAAAAACTAAAAATCAACT
1 TTTAAAAAAAC-AAAAATCAACT
*
12328193 TTTAAAAAAA-AATAATCAA
1 TTTAAAAAAACAAAAATCAA
12328212 AATTGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (22 bp):
TTTAAAAAAACAAAAATCAACT
Found at i:12336945 original size:26 final size:27
Alignment explanation
Indices: 12336913--12336963 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
12336903 GAGATTAATT
12336913 TTAATAA-AAAAAAAAAATAAAATTAA
1 TTAATAATAAAAAAAAAATAAAATTAA
* * *
12336939 TTAATAATATAATAAAATTAAAATT
1 TTAATAATAAAAAAAAAATAAAATT
12336964 GATGATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
TTAATAATAAAAAAAAAATAAAATTAA
Found at i:12337182 original size:21 final size:21
Alignment explanation
Indices: 12337147--12337190 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12337137 AACAATAATG
12337147 TATTAAATAGCAATT-TTATTA
1 TATTAAATAGCAATTATT-TTA
12337168 TATTAAATTAG-AATTATTTTA
1 TATTAAA-TAGCAATTATTTTA
12337189 TA
1 TA
12337191 AATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
TATTAAATAGCAATTATTTTA
Found at i:12337852 original size:2 final size:2
Alignment explanation
Indices: 12337847--12337871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12337837 ATAAAAAAAA
12337847 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12337872 GTTGACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12340584 original size:18 final size:18
Alignment explanation
Indices: 12340557--12340621 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
12340547 GTCTTTCTCG
12340557 TCATAATATTCATCATCA
1 TCATAATATTCATCATCA
*
12340575 TCATAGTATTCATCATCGTCA
1 TCATAATATTCATCA---TCA
* * *
12340596 TCTTCATAGTCATCATCA
1 TCATAATATTCATCATCA
12340614 TCATAATA
1 TCATAATA
12340622 ATATTCTTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 23 0.62
21 14 0.38
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (18 bp):
TCATAATATTCATCATCA
Found at i:12340596 original size:21 final size:20
Alignment explanation
Indices: 12340566--12340633 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
12340556 GTCATAATAT
12340566 TCATCATCATCATAGTATTCA
1 TCATCATCATCATA-TATTCA
* * *
12340587 TCATCGTCATCTTCATAGTCA
1 TCATCATCATCAT-ATATTCA
* *
12340608 TCATCATCATAATAATATTCT
1 TCATCATCATCAT-ATATTCA
12340629 TCATC
1 TCATC
12340634 TTCTTTGTCT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (20 bp):
TCATCATCATCATATATTCA
Found at i:12340602 original size:12 final size:12
Alignment explanation
Indices: 12340569--12340615 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
12340559 ATAATATTCA
*
12340569 TCATCATCATAG
1 TCATCATCATCG
12340581 T-ATTCATCATCG
1 TCA-TCATCATCG
* *
12340593 TCATCTTCATAG
1 TCATCATCATCG
12340605 TCATCATCATC
1 TCATCATCATC
12340616 ATAATAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:12340602 original size:24 final size:24
Alignment explanation
Indices: 12340569--12340615 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12340559 ATAATATTCA
12340569 TCATCATCATAGT-ATTCATCATCG
1 TCATCATCATAGTCA-TCATCATCG
*
12340593 TCATCTTCATAGTCATCATCATC
1 TCATCATCATAGTCATCATCATC
12340616 ATAATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (24 bp):
TCATCATCATAGTCATCATCATCG
Found at i:12342000 original size:6 final size:6
Alignment explanation
Indices: 12341989--12342034 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
12341979 GTTTTTTGGG
12341989 GTATGT GTATGT GT-TGT GTATGT GTATGT GTATGT GT-TGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
12342035 ATGCATGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.26
6 28 0.74
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (6 bp):
GTATGT
Found at i:12342011 original size:17 final size:18
Alignment explanation
Indices: 12341989--12342034 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
12341979 GTTTTTTGGG
12341989 GTATGTGTATGTGT-TGT
1 GTATGTGTATGTGTATGT
12342006 GTATGTGTATGTGTATGT
1 GTATGTGTATGTGTATGT
12342024 GT-TGTGTATGT
1 GTATGTGTATGT
12342035 ATGCATGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (18 bp):
GTATGTGTATGTGTATGT
Found at i:12342015 original size:23 final size:23
Alignment explanation
Indices: 12341989--12342034 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12341979 GTTTTTTGGG
12341989 GTATGTGTATGTGTTGTGTATGT
1 GTATGTGTATGTGTTGTGTATGT
12342012 GTATGTGTATGTGTTGTGTATGT
1 GTATGTGTATGTGTTGTGTATGT
12342035 ATGCATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (23 bp):
GTATGTGTATGTGTTGTGTATGT
Found at i:12345838 original size:3 final size:3
Alignment explanation
Indices: 12345830--12345869 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12345820 CAATTTGGAG
12345830 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12345870 GTTTATGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12346314 original size:32 final size:32
Alignment explanation
Indices: 12346270--12346334 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
12346260 AGCTCAAATT
*
12346270 AAAGATTAGGATTTGATTCGAAACAGTTATAA
1 AAAGATTAGGATTTGATTCAAAACAGTTATAA
* *
12346302 AAAGATTGGGATTTGATTCAAAACATTTATAA
1 AAAGATTAGGATTTGATTCAAAACAGTTATAA
12346334 A
1 A
12346335 TTTTCCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (32 bp):
AAAGATTAGGATTTGATTCAAAACAGTTATAA
Found at i:12346393 original size:20 final size:21
Alignment explanation
Indices: 12346365--12346407 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12346355 TTAGGGAAGC
12346365 TTCTATTTAAATCTTT-TTTT
1 TTCTATTTAAATCTTTCTTTT
* *
12346385 TTCTCTTTACATCTTTCTTTT
1 TTCTATTTAAATCTTTCTTTT
12346406 TT
1 TT
12346408 TTTTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTCTATTTAAATCTTTCTTTT
Found at i:12349769 original size:6 final size:6
Alignment explanation
Indices: 12349758--12349807 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
12349748 TGTTTTTTGG
*
12349758 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTTT GTGTAT
1 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT
12349806 GT
1 GT
12349808 ATGCATGGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (6 bp):
GTGTAT
Found at i:12352972 original size:25 final size:25
Alignment explanation
Indices: 12352935--12352990 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
12352925 TGTTTAATTA
*
12352935 AATTATAGTTTTAAGTTGAT-TATAAT
1 AATTATAGATTTAA-TT-ATATATAAT
12352961 AATTATA-ATTTAATTATAATATAAT
1 AATTATAGATTTAATTAT-ATATAAT
12352986 AATTA
1 AATTA
12352991 ATTATTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 16 0.59
26 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (25 bp):
AATTATAGATTTAATTATATATAAT
Found at i:12352988 original size:14 final size:14
Alignment explanation
Indices: 12352955--12352990 Score: 51
Period size: 11 Copynumber: 2.8 Consensus size: 14
12352945 TTAAGTTGAT
12352955 TATAATAATTATAA
1 TATAATAATTATAA
12352969 T-T--TAATTATAA
1 TATAATAATTATAA
12352980 TATAATAATTA
1 TATAATAATTA
12352991 ATTATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 1 0.05
14 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAATAATTATAA
Found at i:12353594 original size:3 final size:3
Alignment explanation
Indices: 12353586--12353625 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12353576 CAATTTGGAG
12353586 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12353626 GTTTATGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12354070 original size:32 final size:32
Alignment explanation
Indices: 12354026--12354090 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
12354016 AGCTCAAATT
*
12354026 AAAGATTAGGATTTGATTCGAAACAGTTATAA
1 AAAGATTAGGATTTGATTCAAAACAGTTATAA
* *
12354058 AAAGATTGGGATTTGATTCAAAACATTTATAA
1 AAAGATTAGGATTTGATTCAAAACAGTTATAA
12354090 A
1 A
12354091 TTTTCCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (32 bp):
AAAGATTAGGATTTGATTCAAAACAGTTATAA
Found at i:12354148 original size:21 final size:22
Alignment explanation
Indices: 12354119--12354163 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
12354109 TTAGGGAAGC
12354119 TTCTATTTAAATCTTT-TTTTT
1 TTCTATTTAAATCTTTCTTTTT
* *
12354140 TTCTCTTTACATCTTTCTTTTT
1 TTCTATTTAAATCTTTCTTTTT
12354162 TT
1 TT
12354164 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTATTTAAATCTTTCTTTTT
Found at i:12355392 original size:34 final size:34
Alignment explanation
Indices: 12355329--12355394 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
12355319 GAAAACTTTA
* * *
12355329 AAAGCTTTTGGAAATATAAATTCATAAGTTTTTG
1 AAAGCTTATGAAAATATAAATCCATAAGTTTTTG
12355363 AAAGCTTATGAAAATATAAATCCGA-AAGTTTT
1 AAAGCTTATGAAAATATAAATCC-ATAAGTTTT
12355395 CAAAAGATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (34 bp):
AAAGCTTATGAAAATATAAATCCATAAGTTTTTG
Found at i:12357550 original size:29 final size:28
Alignment explanation
Indices: 12357488--12357555 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
12357478 TTTGTTTAAA
*
12357488 TTTATTATGATTAAAAATACTATTAAAAT
1 TTTAATAT-ATTAAAAATACTATTAAAAT
* * *
12357517 ATTAATATATTAAAAATAACTATTGATAT
1 TTTAATATATTAAAAAT-ACTATTAAAAT
*
12357546 TTTAAAATAT
1 TTTAATATAT
12357556 ATATTAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 9 0.28
29 23 0.72
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (28 bp):
TTTAATATATTAAAAATACTATTAAAAT
Found at i:12357560 original size:20 final size:20
Alignment explanation
Indices: 12357514--12357573 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
12357504 ATACTATTAA
12357514 AATATTAATATATTAAAAAT
1 AATATTAATATATTAAAAAT
* *
12357534 AACTATTGATAT-TTTAAAAT
1 AA-TATTAATATATTAAAAAT
12357554 ATATATTAA-A-A-TAAAAAT
1 A-ATATTAATATATTAAAAAT
12357572 AA
1 AA
12357574 AATAGATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 1 0.03
20 15 0.45
21 9 0.27
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATTAATATATTAAAAAT
Found at i:12358432 original size:42 final size:42
Alignment explanation
Indices: 12358386--12358469 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
12358376 TTTAACCCTA
*
12358386 AAACAGATTTAAATTATTTTTCTTTTTTAAATTTAATTGGCT
1 AAACAGATTTAAATTATTTTTATTTTTTAAATTTAATTGGCT
12358428 AAACAGATTTAAATTATTTTTATTTTTTAAATTTAATTGGCT
1 AAACAGATTTAAATTATTTTTATTTTTTAAATTTAATTGGCT
12358470 TAGTATTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (42 bp):
AAACAGATTTAAATTATTTTTATTTTTTAAATTTAATTGGCT
Found at i:12365232 original size:28 final size:28
Alignment explanation
Indices: 12365154--12365232 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
12365144 TTAAGGTTTA
* *
12365154 AAATATTTATTTTTTTAATTGAGCCTTT
1 AAATATTTATTTTTTCAATTGAACCTTT
* * *
12365182 AAGTTTTTTTTTTTTATCAAATTGAACC-TT
1 AA-ATATTTATTTTT-TC-AATTGAACCTTT
12365212 AAATATTTATTTTATTCAATT
1 AAATATTTATTTT-TTCAATT
12365233 AAACTTTCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
28 6 0.15
29 19 0.49
30 6 0.15
31 8 0.21
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (28 bp):
AAATATTTATTTTTTCAATTGAACCTTT
Found at i:12366004 original size:12 final size:13
Alignment explanation
Indices: 12365971--12366013 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
12365961 GGTTAGCTAG
12365971 ATAATTAT-TTAT
1 ATAATTATATTAT
12365983 ATATATTTATATT-T
1 ATA-A-TTATATTAT
12365997 ATAATTATATTAT
1 ATAATTATATTAT
12366010 ATAA
1 ATAA
12366014 AAATATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 8 0.30
15 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAATTATATTAT
Found at i:12366574 original size:13 final size:14
Alignment explanation
Indices: 12366556--12366595 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
12366546 TATTTTTAAA
12366556 TTTATTTATATA-T
1 TTTATTTATATATT
12366569 TTTATTTATATTATT
1 TTTATTTATA-TATT
12366584 TTTATATTATAT
1 TTTAT-TTATAT
12366596 TATCATATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 7 0.29
16 5 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTATATATT
Found at i:12366596 original size:13 final size:12
Alignment explanation
Indices: 12366546--12366596 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
12366536 TAAAAAAATA
*
12366546 TATTTTTAAATT
1 TATTTTTATATT
*
12366558 TATTTATATATT
1 TATTTTTATATT
*
12366570 T-TATTTATA-T
1 TATTTTTATATT
12366580 TATTTTTATATT
1 TATTTTTATATT
12366592 ATATT
1 -TATT
12366597 ATCATATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.06
11 13 0.42
12 12 0.39
13 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTTTATATT
Found at i:12369255 original size:32 final size:32
Alignment explanation
Indices: 12369210--12369271 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
12369200 ACATATCAAA
12369210 TATAAAATAATATTAT-TTAATTTAATTATATT
1 TATAAAATAATATTATATT-ATTTAATTATATT
* * *
12369242 TATAATATTATATTATATTATTTTATTATA
1 TATAAAATAATATTATATTATTTAATTATA
12369272 ATTTTATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATAAAATAATATTATATTATTTAATTATATT
Found at i:12369257 original size:13 final size:13
Alignment explanation
Indices: 12369234--12369278 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
12369224 ATTTAATTTA
12369234 ATTATATTTATAAT
1 ATTATA-TTATAAT
*
12369248 ATTATATTATATT
1 ATTATATTATAAT
*
12369261 ATTTTATTATAAT
1 ATTATATTATAAT
*
12369274 TTTAT
1 ATTAT
12369279 GTATCGAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATTATAAT
Found at i:12369339 original size:6 final size:6
Alignment explanation
Indices: 12369328--12369352 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12369318 CCCGAAGAAT
12369328 AGTGGG AGTGGG AGTGGG AGTGGG A
1 AGTGGG AGTGGG AGTGGG AGTGGG A
12369353 CGGTGTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.64, T:0.16
Consensus pattern (6 bp):
AGTGGG
Found at i:12388083 original size:27 final size:28
Alignment explanation
Indices: 12388053--12388116 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
12388043 ATTTTTTTGA
12388053 TTAAATTATATAATTA-T-TATTATAATT
1 TTAAATTATATAATTATTATATTAT-ATT
* * *
12388080 TTAAATTATTTTATTTTTATATTATATT
1 TTAAATTATATAATTATTATATTATATT
12388108 TTAAATTAT
1 TTAAATTAT
12388117 CAAATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 13 0.41
28 13 0.41
29 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTAAATTATATAATTATTATATTATATT
Found at i:12388087 original size:16 final size:15
Alignment explanation
Indices: 12388068--12388116 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 15
12388058 TTATATAATT
12388068 ATTATTATAATTTTAA
1 ATTATTAT-ATTTTAA
* *
12388084 ATTATTTTATTTT-T
1 ATTATTATATTTTAA
12388098 A-TATTATATTTTAA
1 ATTATTATATTTTAA
12388112 ATTAT
1 ATTAT
12388117 CAAATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
15 8 0.30
16 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATATTTTAA
Found at i:12388916 original size:34 final size:33
Alignment explanation
Indices: 12388838--12388925 Score: 79
Period size: 33 Copynumber: 2.6 Consensus size: 33
12388828 TTCTACAGGC
* * * * * *
12388838 TTTCGGATTTATATTTTCAAGAATTTTTAAAAGT
1 TTTCAGATGTATATTTTGAA-AAGTTCTAAAAAT
*
12388872 TTTTAGATGTATATTTTGAAAAGTTCTAAAAAT
1 TTTCAGATGTATATTTTGAAAAGTTCTAAAAAT
*
12388905 TTTCAGAATGTA-AATTTGAAA
1 TTTCAG-ATGTATATTTTGAAA
12388926 GCTTGCAAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
33 23 0.52
34 21 0.48
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (33 bp):
TTTCAGATGTATATTTTGAAAAGTTCTAAAAAT
Found at i:12390132 original size:17 final size:17
Alignment explanation
Indices: 12390110--12390143 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12390100 TTGATCGATT
* *
12390110 ATTTATATTTGAAATTA
1 ATTTATAATTAAAATTA
12390127 ATTTATAATTAAAATTA
1 ATTTATAATTAAAATTA
12390144 TTAATTCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTATAATTAAAATTA
Found at i:12392211 original size:22 final size:22
Alignment explanation
Indices: 12392183--12392228 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12392173 GTTGGATCTG
12392183 TCTTGAAGTTCTTTAGTAGTTT
1 TCTTGAAGTTCTTTAGTAGTTT
12392205 TCTTGAAGTTCTTTAGTAGTTT
1 TCTTGAAGTTCTTTAGTAGTTT
12392227 TC
1 TC
12392229 CCTGCCGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (22 bp):
TCTTGAAGTTCTTTAGTAGTTT
Found at i:12405205 original size:17 final size:17
Alignment explanation
Indices: 12405183--12405215 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12405173 ATTTATTTTT
12405183 AAAAT-ATAATAAAATAA
1 AAAATAATAA-AAAATAA
12405200 AAAATAATAAAAAATA
1 AAAATAATAAAAAATA
12405216 TATTAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAATAAAAAATAA
Found at i:12405206 original size:15 final size:15
Alignment explanation
Indices: 12405182--12405211 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12405172 AATTTATTTT
*
12405182 TAAAATATAATAAAA
1 TAAAAAATAATAAAA
12405197 TAAAAAATAATAAAA
1 TAAAAAATAATAAAA
12405212 AATATATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAATAATAAAA
Found at i:12405285 original size:21 final size:22
Alignment explanation
Indices: 12405245--12405285 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12405235 TTTGTAAAAT
* *
12405245 TAAAAATTTTACTCATAATATA
1 TAAAAAATTAACTCATAATATA
12405267 TAAAAAATTAACTCA-AATA
1 TAAAAAATTAACTCATAATA
12405286 AATATATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAAAATTAACTCATAATATA
Found at i:12409710 original size:14 final size:14
Alignment explanation
Indices: 12409691--12409718 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12409681 CTTGCTGTAA
12409691 CCTTTAAATGCAAT
1 CCTTTAAATGCAAT
12409705 CCTTTAAATGCAAT
1 CCTTTAAATGCAAT
12409719 TTTGTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CCTTTAAATGCAAT
Found at i:12419337 original size:22 final size:22
Alignment explanation
Indices: 12419312--12419435 Score: 63
Period size: 22 Copynumber: 5.6 Consensus size: 22
12419302 ATTGGTGATG
*
12419312 ACTTAATAGTAAATAAATTATA
1 ACTTAATAGTAAATAAATAATA
* * *
12419334 ACTTAGTAGTTAATAACTAATA
1 ACTTAATAGTAAATAAATAATA
** * *
12419356 ACTTTTTAATAAATCAATAATA
1 ACTTAATAGTAAATAAATAATA
* * **
12419378 A-TACAATAATAAATGCATAATA
1 ACT-TAATAGTAAATAAATAATA
** * *
12419400 TTTTAATAGTAAATCAATTATA
1 ACTTAATAGTAAATAAATAATA
*
12419422 A-TATAATTGTAAAT
1 ACT-TAATAGTAAAT
12419436 GTATAACAAT
Statistics
Matches: 76, Mismatches: 23, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
21 2 0.03
22 73 0.96
23 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (22 bp):
ACTTAATAGTAAATAAATAATA
Found at i:12419854 original size:44 final size:43
Alignment explanation
Indices: 12419755--12419866 Score: 109
Period size: 44 Copynumber: 2.6 Consensus size: 43
12419745 GGTAAATTGG
** * *
12419755 TGATAATTTTGTAATAAATAATAAAAATGAAGTAGTAAATCAA
1 TGATAATTTAATAATAAATAATAAAAATGAAATAATAAATCAA
** * *
12419798 TGATAAAATAATATTAAATACATAAAAAT-ATAATAATAAATCAT
1 TGATAATTTAATAATAAATA-ATAAAAATGA-AATAATAAATCAA
*
12419842 TGATAATTTAATAGTAAATTAATAA
1 TGATAATTTAATAATAAA-TAATAA
12419867 CTTAGTAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
43 16 0.29
44 37 0.67
45 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (43 bp):
TGATAATTTAATAATAAATAATAAAAATGAAATAATAAATCAA
Found at i:12419999 original size:68 final size:68
Alignment explanation
Indices: 12419916--12420043 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 68
12419906 AATTACTTAA
* *
12419916 TTATAAATCAGTGATAATTTAATTACAAATTGATTAATCATTAATAACTTTTTAGTAAATTAACT
1 TTATAAATCAATGATAATTTAATAACAAATTGATTAATCATTAATAACTTTTTAGTAAATTAACT
12419981 TGG
66 TGG
* *
12419984 TTATAAATCAATGATAATTTAATAATAAATTGGTTAATCATTAATAACTTTTTAGTAAAT
1 TTATAAATCAATGATAATTTAATAACAAATTGATTAATCATTAATAACTTTTTAGTAAAT
12420044 AATATGTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (68 bp):
TTATAAATCAATGATAATTTAATAACAAATTGATTAATCATTAATAACTTTTTAGTAAATTAACT
TGG
Found at i:12420043 original size:30 final size:30
Alignment explanation
Indices: 12419942--12420043 Score: 71
Period size: 30 Copynumber: 3.1 Consensus size: 30
12419932 ATTTAATTAC
*
12419942 AAATTGATTAATCATTAATAACTTTTTAGT
1 AAATTGGTTAATCATTAATAACTTTTTAGT
* * * *
12419972 AAATTAACTTGGTTATAAATCAATGATAA-TTTAATAAT
1 --A--AA-TTGG-T-T-AATCATTAATAACTTT-TTAGT
12420010 AAATTGGTTAATCATTAATAACTTTTTAGT
1 AAATTGGTTAATCATTAATAACTTTTTAGT
12420040 AAAT
1 AAAT
12420044 AATATGTAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 18
0.66 0.11 0.22
Matches are distributed among these distances:
30 17 0.32
31 4 0.08
32 2 0.04
33 4 0.08
34 4 0.08
35 3 0.06
36 2 0.04
37 4 0.08
38 13 0.25
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (30 bp):
AAATTGGTTAATCATTAATAACTTTTTAGT
Found at i:12420083 original size:22 final size:22
Alignment explanation
Indices: 12420027--12420099 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
12420017 TTAATCATTA
* * *
12420027 ATAACTTTTTAGTAAATAATAT
1 ATAACTTTATAATAAATAATTT
* *
12420049 GTAA-TTTAGTAATAAATTATTT
1 ATAACTTTA-TAATAAATAATTT
* *
12420071 ATAACTTTATAATAAATCATTA
1 ATAACTTTATAATAAATAATTT
12420093 ATAACTT
1 ATAACTT
12420100 AGTGGTAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.07
22 34 0.83
23 4 0.10
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (22 bp):
ATAACTTTATAATAAATAATTT
Found at i:12420542 original size:11 final size:11
Alignment explanation
Indices: 12420494--12420561 Score: 75
Period size: 11 Copynumber: 6.3 Consensus size: 11
12420484 CTAAATAGTT
*
12420494 AATTATTAATA
1 AATTAATAATA
* *
12420505 ACTTAATAACA
1 AATTAATAATA
12420516 AA-TAATAATA
1 AATTAATAATA
* *
12420526 ATTTAATAGTA
1 AATTAATAATA
12420537 AATTAATAATA
1 AATTAATAATA
*
12420548 ATTTAATAATA
1 AATTAATAATA
12420559 AAT
1 AAT
12420562 CAGTTTCAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
10 8 0.18
11 37 0.82
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (11 bp):
AATTAATAATA
Found at i:12420546 original size:22 final size:22
Alignment explanation
Indices: 12420487--12420646 Score: 103
Period size: 22 Copynumber: 7.3 Consensus size: 22
12420477 GCGACAGCTA
* * *
12420487 AATAGTTAATTATTAATAACTT
1 AATAGTAAATTAATAATAATTT
**
12420509 AATAACAAA-TAATAATAATTT
1 AATAGTAAATTAATAATAATTT
12420530 AATAGTAAATTAATAATAATTT
1 AATAGTAAATTAATAATAATTT
* * * * *
12420552 AATAATAAATCAGT-TTCAGTTT
1 AATAGTAAATTAATAAT-AATTT
*
12420574 AATAGT-AATTAATTGATAAATTT
1 AATAGTAAATTAA-TAAT-AATTT
** *
12420597 AATAGTAAA-CCATAAATAACTT
1 AATAGTAAATTAAT-AATAATTT
* *
12420619 AGTAGTAAATCAATAATAATTT
1 AATAGTAAATTAATAATAATTT
*
12420641 AGTAGT
1 AATAGT
12420647 TAATAATTAG
Statistics
Matches: 106, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
21 22 0.21
22 65 0.61
23 17 0.16
24 2 0.02
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (22 bp):
AATAGTAAATTAATAATAATTT
Found at i:12420763 original size:43 final size:43
Alignment explanation
Indices: 12420707--12420805 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
12420697 TATCAATAAA
* * *
12420707 TTAATAGTTAATCAATGATAACTTACTAGTAAATCATGAACAAT
1 TTAATA-TAAATCAATGATAACTTAATAATAAATCATGAACAAT
* * * **
12420751 TTAATATAAATCAATTATGACTTAATAATGAATCATGATTAAT
1 TTAATATAAATCAATGATAACTTAATAATAAATCATGAACAAT
12420794 TTAATAATAAAT
1 TTAAT-ATAAAT
12420806 GTAGGATGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 34 0.74
44 12 0.26
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (43 bp):
TTAATATAAATCAATGATAACTTAATAATAAATCATGAACAAT
Found at i:12420899 original size:21 final size:22
Alignment explanation
Indices: 12420868--12420918 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
12420858 ACATAGTAAC
* *
12420868 AAATTACTAATAATTTAGTTGT
1 AAATTAGTAATAATTTAGTAGT
12420890 -AATTAGTAATAATTTAGTAGT
1 AAATTAGTAATAATTTAGTAGT
12420911 AAATTAGT
1 AAATTAGT
12420919 TAATTATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (22 bp):
AAATTAGTAATAATTTAGTAGT
Found at i:12420906 original size:11 final size:11
Alignment explanation
Indices: 12420861--12421032 Score: 61
Period size: 11 Copynumber: 16.0 Consensus size: 11
12420851 AATGATAACA
*
12420861 TAGTAACAAAT
1 TAGTAATAAAT
* *
12420872 TACTAATAATT
1 TAGTAATAAAT
**
12420883 TAGTTGT-AAT
1 TAGTAATAAAT
*
12420893 TAGTAATAATT
1 TAGTAATAAAT
*
12420904 TAGTAGTAAAT
1 TAGTAATAAAT
12420915 TAGT--T-AAT
1 TAGTAATAAAT
* * *
12420923 TATTGATAACTT
1 TAGTAATAA-AT
*
12420935 TA-TAGTAAAT
1 TAGTAATAAAT
* *
12420945 TA-TCATAACT
1 TAGTAATAAAT
12420955 TAGTAATAAAT
1 TAGTAATAAAT
* *
12420966 CA-TCAATAATT
1 TAGT-AATAAAT
*
12420977 TAGTAGTAAAT
1 TAGTAATAAAT
* * * *
12420988 CATTTATAACT
1 TAGTAATAAAT
*
12420999 TAGTAGTAAAT
1 TAGTAATAAAT
* *
12421010 TATTTATAAAT
1 TAGTAATAAAT
12421021 TAAGTAATAAAT
1 T-AGTAATAAAT
12421033 CAATACTAAT
Statistics
Matches: 110, Mismatches: 42, Indels: 17
0.65 0.25 0.10
Matches are distributed among these distances:
8 6 0.05
9 1 0.01
10 19 0.17
11 72 0.65
12 12 0.11
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (11 bp):
TAGTAATAAAT
Found at i:12420941 original size:30 final size:30
Alignment explanation
Indices: 12420889--12420963 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 30
12420879 AATTTAGTTG
12420889 TAATTAGTAATAATTTAGTAGTAAATTAGT
1 TAATTAGTAATAATTTAGTAGTAAATTAGT
* *
12420919 TAATTATTGATAACTTTA-TAGTAAATTA-T
1 TAATTAGTAATAA-TTTAGTAGTAAATTAGT
12420948 CATAACTTAGTAATAA
1 --TAA-TTAGTAATAA
12420964 ATCATCAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 1 0.03
30 21 0.57
31 7 0.19
32 8 0.22
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (30 bp):
TAATTAGTAATAATTTAGTAGTAAATTAGT
Found at i:12420945 original size:22 final size:22
Alignment explanation
Indices: 12420915--12421134 Score: 176
Period size: 22 Copynumber: 9.8 Consensus size: 22
12420905 AGTAGTAAAT
*
12420915 TAGTTAATTATTGATAACTTTA-
1 TAGTAAATTATTGATAA-TTTAG
* *
12420937 TAGTAAATTA-TCATAACTTAG
1 TAGTAAATTATTGATAATTTAG
* * **
12420958 TAATAAATCATCAATAATTTAG
1 TAGTAAATTATTGATAATTTAG
* * *
12420980 TAGTAAATCATTTATAACTTAG
1 TAGTAAATTATTGATAATTTAG
* *
12421002 TAGTAAATTATTTATAAATTAAG
1 TAGTAAATTATTGAT-AATTTAG
* * *
12421025 TAATAAATCAAT-ACTAATTTAG
1 TAGTAAATTATTGA-TAATTTAG
*
12421047 TATGTAATAAATCATTGATAATTTAG
1 TA-G---TAAATTATTGATAATTTAG
12421073 TAGTAAATTATTGATAATTTAG
1 TAGTAAATTATTGATAATTTAG
*
12421095 TAGTAAATTATTGATAACTTAG
1 TAGTAAATTATTGATAATTTAG
** *
12421117 TACCAAATTGTTGATAAT
1 TAGTAAATTATTGATAAT
12421135 ATAATAGCAA
Statistics
Matches: 162, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
20 3 0.02
21 13 0.08
22 111 0.69
23 15 0.09
25 1 0.01
26 18 0.11
27 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (22 bp):
TAGTAAATTATTGATAATTTAG
Found at i:12421054 original size:26 final size:25
Alignment explanation
Indices: 12421023--12421100 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 25
12421013 TTATAAATTA
12421023 AGTAATAAATCAAT-ACTAATTTAGT
1 AGTAATAAATCAATGA-TAATTTAGT
*
12421048 ATGTAATAAATCATTGATAATTTAGT
1 A-GTAATAAATCAATGATAATTTAGT
* *
12421074 AG---TAAATTATTGATAATTTAGT
1 AGTAATAAATCAATGATAATTTAGT
12421096 AGTAA
1 AGTAA
12421101 ATTATTGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
22 21 0.46
25 2 0.04
26 22 0.48
27 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.40
Consensus pattern (25 bp):
AGTAATAAATCAATGATAATTTAGT
Found at i:12421081 original size:71 final size:66
Alignment explanation
Indices: 12420915--12421102 Score: 202
Period size: 71 Copynumber: 2.8 Consensus size: 66
12420905 AGTAGTAAAT
* * *
12420915 TAGTTAATTATTGATAACTTTA-TAGTAAATTA-TCATAACTTAGTAATAAATCATCAATAATTT
1 TAGTAAATCATTGATAA-TTTAGTAGTAAATTATTCATAAATTAGTAATAAATCATCAATAATTT
12420978 AG
65 AG
* * * *
12420980 TAGTAAATCATTTATAACTTAGTAGTAAATTATTTATAAATTAAGTAATAAATCAAT-ACTAATT
1 TAGTAAATCATTGATAATTTAGTAGTAAATTATTCATAAATT-AGTAATAAATC-ATCAATAATT
12421044 TAG
64 TAG
* * *
12421047 TATGTAATAAATCATTGATAATTTAGTAGTAAATTATTGATAATTTAGTAGTAAAT
1 TA-G---TAAATCATTGATAATTTAGTAGTAAATTATTCATAAATTAGTAATAAAT
12421103 TATTGATAAC
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
64 3 0.03
65 24 0.23
66 7 0.07
67 22 0.21
68 3 0.03
70 9 0.09
71 35 0.34
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.41
Consensus pattern (66 bp):
TAGTAAATCATTGATAATTTAGTAGTAAATTATTCATAAATTAGTAATAAATCATCAATAATTTA
G
Found at i:12421117 original size:44 final size:44
Alignment explanation
Indices: 12420915--12421159 Score: 172
Period size: 44 Copynumber: 5.5 Consensus size: 44
12420905 AGTAGTAAAT
* * *
12420915 TAGTTAATTATTGATAACTTTA-TAGTAAATTA-TCATAACTTAG
1 TAGTAAATTATTGATAAC-TTAGTAGTAAATTATTGATAATTTAG
* * ** * * * *
12420958 TAATAAATCATCAATAATTTAGTAGTAAATCATTTATAACTTAG
1 TAGTAAATTATTGATAACTTAGTAGTAAATTATTGATAATTTAG
* * * * *
12421002 TAGTAAATTATTTATAAATTAAGTAATAAATCAAT-ACTAATTTAG
1 TAGTAAATTATTGATAACTT-AGTAGTAAATTATTGA-TAATTTAG
* *
12421047 TATGTAATAAATCATTGATAATTTAGTAGTAAATTATTGATAATTTAG
1 TA-G---TAAATTATTGATAACTTAGTAGTAAATTATTGATAATTTAG
** * * *
12421095 TAGTAAATTATTGATAACTTAGTACCAAATTGTTGATAATATAA
1 TAGTAAATTATTGATAACTTAGTAGTAAATTATTGATAATTTAG
* * *
12421139 TAGCAAATAAATGATAACTTA
1 TAGTAAATTATTGATAACTTA
12421160 ATTTACAATC
Statistics
Matches: 161, Mismatches: 32, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
42 3 0.02
43 21 0.13
44 78 0.48
45 21 0.13
46 1 0.01
47 1 0.01
48 21 0.13
49 15 0.09
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.40
Consensus pattern (44 bp):
TAGTAAATTATTGATAACTTAGTAGTAAATTATTGATAATTTAG
Found at i:12421435 original size:21 final size:20
Alignment explanation
Indices: 12421410--12421465 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
12421400 TATGTAAATT
12421410 TTATCAATAATTATAAAAAA
1 TTATCAATAATTATAAAAAA
*
12421430 TATATC-ATAAGTTATCAAAAGA
1 T-TATCAATAA-TTAT-AAAAAA
*
12421452 TTATTAA-AATTATA
1 TTATCAATAATTATA
12421466 TCAATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 13 0.43
22 7 0.23
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (20 bp):
TTATCAATAATTATAAAAAA
Found at i:12421497 original size:21 final size:21
Alignment explanation
Indices: 12421441--12421505 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 21
12421431 ATATCATAAG
*
12421441 TTATCAAAAGATTATTAAAATT
1 TTATCAAAA-ATTACTAAAATT
*
12421463 ATATCAATAAATTACTAAAATT
1 TTATCAA-AAATTACTAAAATT
12421485 TTATCAAAAATTACTAAAATT
1 TTATCAAAAATTACTAAAATT
12421506 GTGTTAATGG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.36
22 23 0.59
23 2 0.05
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (21 bp):
TTATCAAAAATTACTAAAATT
Done.