Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008909.1 Hibiscus syriacus cultivar Beakdansim tig00112206_pilon, 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: 2327114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:993441 original size:22 final size:22
Alignment explanation
Indices: 993416--993458 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
993406 AATTTATTAG
993416 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
993438 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
993459 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:993476 original size:86 final size:84
Alignment explanation
Indices: 993141--993490 Score: 314
Period size: 86 Copynumber: 4.1 Consensus size: 84
993131 TTTTAAAATA
* * **
993141 ATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTT-AAATA--ATTTA-TTAGTATGGA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGATTGATTTA-T-TTAA
* * *
993202 TTGATTTATTTTAAAATATAGATTG
64 AT-ATTTA-TTT--AGTATGGATTG
* *
993227 ATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGAATTGATTTA-TT--A
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG-ATTGATTTATTTAAA
* *
993289 T-TGTAGTT-GTATGGATTG
65 TATTTATTTAGTATGGATTG
* *
993307 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA--ATTTA-TTAGTATGAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGATTGATTTA-T-TTAA
* *
993368 TTGATTTATTTTAAAATATGGATTG
64 AT-ATTTA-TTT--AGTATGGATTG
993393 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-GATTGATTTA-TTTAA
*
993458 ATAATTTA-TTAGTCTGGATTG
64 AT-ATTTATTTAGTATGGATTG
993479 ATTTATTTTAAA
1 ATTTATTTTAAA
993491 ATATGGATTG
Statistics
Matches: 218, Mismatches: 25, Indels: 42
0.76 0.09 0.15
Matches are distributed among these distances:
75 3 0.01
76 4 0.02
78 1 0.00
79 5 0.02
80 48 0.22
82 3 0.01
83 4 0.02
84 3 0.01
86 110 0.50
87 10 0.05
88 3 0.01
90 17 0.08
91 7 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (84 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGATTGATTTATTTAAAT
ATTTATTTAGTATGGATTG
Found at i:993661 original size:22 final size:22
Alignment explanation
Indices: 993636--993678 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
993626 AATTTATTAG
*
993636 TATGGATTGATTTGTTTTAAAA
1 TATGGATTGATTTATTTTAAAA
993658 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
993679 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:993737 original size:31 final size:31
Alignment explanation
Indices: 993702--993792 Score: 164
Period size: 31 Copynumber: 2.9 Consensus size: 31
993692 TAGTTGTATG
993702 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTTCAGTATTGTAAAACTAA
993733 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTTCAGTATTGTAAAACTAA
* *
993764 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTGTAAAACT
993793 CTTTTAAGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.41
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTGTAAAACTAA
Found at i:995499 original size:15 final size:15
Alignment explanation
Indices: 995479--995507 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
995469 GATTTTTTTC
995479 AAAGAAATCGGATTA
1 AAAGAAATCGGATTA
995494 AAAGAAATCGGATT
1 AAAGAAATCGGATT
995508 GAGTTGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (15 bp):
AAAGAAATCGGATTA
Found at i:996791 original size:174 final size:174
Alignment explanation
Indices: 996501--996837 Score: 638
Period size: 174 Copynumber: 1.9 Consensus size: 174
996491 TCATGATTAT
996501 TGGCGGATCTATAAATATTTTTTAGGGTGAGCACATGTAGGTTAATAACATAAATTTTTTAAATA
1 TGGCGGATCTATAAATATTTTTTAGGGTGAGCACATGTAGGTTAATAACATAAATTTTTTAAATA
* * *
996566 AGATTATTACAAATAAAATTTTAGGGTGGGCATCGTTCGTAAAATAAGTAATTAATCGAAGAAAG
66 AGATTATTACAAATAAAATTTTAAGGTGGACATCGTCCGTAAAATAAGTAATTAATCGAAGAAAG
*
996631 CTTAGATTTAAGGATGAGCAGAACAAATTTCAGTTAGACTACAG
131 CTTAGATTTAAGGATGAGCACAACAAATTTCAGTTAGACTACAG
996675 TGGCGGATCTATAAATATTTTTTAGGGTGAGCACATGTAGGTTAATAACATAAATTTTTTAAATA
1 TGGCGGATCTATAAATATTTTTTAGGGTGAGCACATGTAGGTTAATAACATAAATTTTTTAAATA
996740 AGATTATTACAAATAAAATTTTAAGGTGGACATCGTCCGTAAAATAAGTAATTAATCGAAGAAAG
66 AGATTATTACAAATAAAATTTTAAGGTGGACATCGTCCGTAAAATAAGTAATTAATCGAAGAAAG
996805 CTTAGATTTAAGGATGAGCACAACAAATTTCAG
131 CTTAGATTTAAGGATGAGCACAACAAATTTCAG
996838 AGCGAATACC
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 159 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (174 bp):
TGGCGGATCTATAAATATTTTTTAGGGTGAGCACATGTAGGTTAATAACATAAATTTTTTAAATA
AGATTATTACAAATAAAATTTTAAGGTGGACATCGTCCGTAAAATAAGTAATTAATCGAAGAAAG
CTTAGATTTAAGGATGAGCACAACAAATTTCAGTTAGACTACAG
Found at i:1000164 original size:28 final size:28
Alignment explanation
Indices: 1000103--1000157 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1000093 GATTTTATGT
* * *
1000103 TAGGGGTGAAATTGAATTTTTAAAATTC
1 TAGGGGCGAAATTGAACTTATAAAATTC
*
1000131 TAGGGGCGAACTTGAACTTATAAAATT
1 TAGGGGCGAAATTGAACTTATAAAATT
1000158 ACAGGGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (28 bp):
TAGGGGCGAAATTGAACTTATAAAATTC
Found at i:1000923 original size:14 final size:14
Alignment explanation
Indices: 1000901--1000942 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1000891 GAAATCTCAC
*
1000901 ATTGCATTATTTTT
1 ATTGTATTATTTTT
*
1000915 ATTGTATTAATTATT
1 ATTGTATT-ATTTTT
1000930 -TTGTATTATTTTT
1 ATTGTATTATTTTT
1000943 TGCGGTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.21
14 14 0.58
15 5 0.21
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (14 bp):
ATTGTATTATTTTT
Found at i:1003676 original size:20 final size:20
Alignment explanation
Indices: 1003651--1003688 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1003641 TTTGGTTCAC
1003651 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1003671 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1003689 GGAATGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1003693 original size:18 final size:19
Alignment explanation
Indices: 1003651--1003694 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
1003641 TTTGGTTCAC
1003651 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
1003671 GGAATGTAAGATTACCA-G
1 GGAATGTAAGATTACCAGG
1003689 GGAATG
1 GGAATG
1003695 AGATTACTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.29
20 17 0.71
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:1003916 original size:37 final size:37
Alignment explanation
Indices: 1003843--1003917 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1003833 GTTGGAAAAT
*
1003843 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
1003880 ATTTATATAATTTT-TTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
1003917 A
1 A
1003918 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:1016741 original size:20 final size:21
Alignment explanation
Indices: 1016716--1016762 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1016706 TTTATATTTC
1016716 TATTATT-ATAATTTATTTAT
1 TATTATTAATAATTTATTTAT
*
1016736 TATTATTAATAATTTCTTTAT
1 TATTATTAATAATTTATTTAT
1016757 T-TTATT
1 TATTATT
1016763 TTTTGTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTATTAATAATTTATTTAT
Found at i:1028527 original size:10 final size:10
Alignment explanation
Indices: 1028512--1028540 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1028502 AAAGTTTAGG
1028512 TACTAAAACA
1 TACTAAAACA
1028522 TACTAAAACA
1 TACTAAAACA
1028532 TACTAAAAC
1 TACTAAAAC
1028541 TGATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (10 bp):
TACTAAAACA
Found at i:1030091 original size:18 final size:18
Alignment explanation
Indices: 1030068--1030102 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1030058 AAATGAAGGT
*
1030068 TTTCAAAGTTTGGGTTTA
1 TTTCAAAATTTGGGTTTA
*
1030086 TTTCAAAATTTGTGTTT
1 TTTCAAAATTTGGGTTT
1030103 TCATTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (18 bp):
TTTCAAAATTTGGGTTTA
Found at i:1031249 original size:20 final size:20
Alignment explanation
Indices: 1031221--1031259 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1031211 TAGTTTACGA
*
1031221 AATGGAAGATTATCAGTGAG
1 AATGGAAGATTACCAGTGAG
*
1031241 AATGTAAGATTACCAGTGA
1 AATGGAAGATTACCAGTGA
1031260 ATAGGATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.26
Consensus pattern (20 bp):
AATGGAAGATTACCAGTGAG
Found at i:1033904 original size:2 final size:2
Alignment explanation
Indices: 1033897--1033931 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1033887 AAAATTAATC
1033897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1033932 GTCTTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1038272 original size:2 final size:2
Alignment explanation
Indices: 1038265--1038293 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1038255 CCCAACAATA
1038265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1038294 ACTCCGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1042364 original size:22 final size:21
Alignment explanation
Indices: 1042339--1042379 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1042329 CGGATAATTA
1042339 TAAATTAATTAAAATCAAAACG
1 TAAATTAATTAAAAT-AAAACG
*
1042361 TAAATTATTTAAAATAAAA
1 TAAATTAATTAAAATAAAA
1042380 TAATAATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAATTAATTAAAATAAAACG
Found at i:1045397 original size:15 final size:14
Alignment explanation
Indices: 1045377--1045411 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1045367 TATGTTCAAA
1045377 AATATTTAATTACTT
1 AATATTTAA-TACTT
1045392 AATATTTAATACTT
1 AATATTTAATACTT
1045406 ATATAT
1 A-ATAT
1045412 CTATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTTAATACTT
Found at i:1045831 original size:18 final size:19
Alignment explanation
Indices: 1045789--1045833 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1045779 TTTGGTCCAC
*
1045789 GGAATATAAGATTATCAGT
1 GGAATAAAAGATTATCAGT
*
1045808 GAGAATAAAATATTATCAG-
1 G-GAATAAAAGATTATCAGT
1045827 GGAATAA
1 GGAATAA
1045834 GATTACTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 2 0.09
20 15 0.65
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (19 bp):
GGAATAAAAGATTATCAGT
Found at i:1048026 original size:2 final size:2
Alignment explanation
Indices: 1048019--1048044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1048009 ATAGCAGCTA
1048019 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
1048045 TTAAAAAAAA
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:1050414 original size:14 final size:13
Alignment explanation
Indices: 1050390--1050419 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1050380 TTTTTACTTT
1050390 TTAGGTTAAAATA
1 TTAGGTTAAAATA
1050403 TTAGGATTAAAATA
1 TTAGG-TTAAAATA
1050417 TTA
1 TTA
1050420 ATATTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (13 bp):
TTAGGTTAAAATA
Found at i:1064847 original size:2 final size:2
Alignment explanation
Indices: 1064834--1064872 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1064824 TGTTAAATAG
*
1064834 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1064873 TTATTGAAAA
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1069249 original size:23 final size:23
Alignment explanation
Indices: 1069221--1069265 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1069211 CCTCGTATTA
1069221 TTTTTCTCAATATGATCCTCAAT
1 TTTTTCTCAATATGATCCTCAAT
1069244 TTTTTCTCAATATGATCCTCAA
1 TTTTTCTCAATATGATCCTCAA
1069266 ACTCAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTTTCTCAATATGATCCTCAAT
Found at i:1073316 original size:17 final size:16
Alignment explanation
Indices: 1073292--1073326 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1073282 ATGGTAATTT
1073292 TAAAAAAAATATTTAAAA
1 TAAAAAAAA-A-TTAAAA
1073310 TAAAAAAAAATTAAAA
1 TAAAAAAAAATTAAAA
1073326 T
1 T
1073327 TATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAAAAATTAAAA
Found at i:1074160 original size:26 final size:26
Alignment explanation
Indices: 1074125--1074174 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1074115 ATTTTATGTT
* * *
1074125 AAGAAGTAAATTTCCAAAATTTTAAG
1 AAGAAATAAAATTACAAAATTTTAAG
*
1074151 AAGAAATAAAATTATAAAATTTTA
1 AAGAAATAAAATTACAAAATTTTA
1074175 GAATCAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (26 bp):
AAGAAATAAAATTACAAAATTTTAAG
Found at i:1078538 original size:20 final size:20
Alignment explanation
Indices: 1078502--1078539 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1078492 ATCCTATTCC
**
1078502 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1078522 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1078540 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1079220 original size:60 final size:60
Alignment explanation
Indices: 1079113--1079227 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
1079103 GAAAGAAGGT
* * * * *
1079113 ATAGTTTGGGGATGAAATTGAAATGTTCAAAAGTTTGAAGAATAATTTAAAATGATATTC
1 ATAGTTTAGGGATGAAATTAAAATATTCAAAACTTTGAAGAACAATTTAAAATGATATTC
* * *
1079173 ATAGTTTAGGGATGAAATTAAAATATTTAAAACTTT-AGAGACCAATTTGAAATGA
1 ATAGTTTAGGGATGAAATTAAAATATTCAAAACTTTGA-AGAACAATTTAAAATGA
1079228 AAATCGTACT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 45 0.98
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.34
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATTAAAATATTCAAAACTTTGAAGAACAATTTAAAATGATATTC
Found at i:1083215 original size:3 final size:3
Alignment explanation
Indices: 1083207--1083264 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
1083197 TTCTCGTTTG
* * * * *
1083207 ATA ATA ATA ATA ATA ATA ATG ATA TTA ATA TTA ATA ATA AT- TTA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1083254 AT- ATA ATA ATA
1 ATA ATA ATA ATA
1083265 TTTACATATA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 3 0.07
3 40 0.93
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:1083275 original size:18 final size:18
Alignment explanation
Indices: 1083214--1083276 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
1083204 TTGATAATAA
*
1083214 TAATA-ATAATAATGATAT
1 TAATATATAATAATAAT-T
1083232 TAATAT-TAATAATAATT
1 TAATATATAATAATAATT
*
1083249 TAAAAATATAATAAT-ATT
1 T-AATATATAATAATAATT
1083267 TACATATATA
1 TA-ATATATA
1083277 TTTAGATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.08
18 28 0.74
19 7 0.18
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TAATATATAATAATAATT
Found at i:1091601 original size:12 final size:11
Alignment explanation
Indices: 1091581--1091711 Score: 59
Period size: 11 Copynumber: 11.0 Consensus size: 11
1091571 TAATATATAG
1091581 TTTTTAAAATA
1 TTTTTAAAATA
1091592 TTTTTAAAAATA
1 TTTTT-AAAATA
*
1091604 TATATATT-ATATA
1 T-T-T-TTAAAATA
1091617 GTTTTTAAAATA
1 -TTTTTAAAATA
*
1091629 TTTTGAAAATA
1 TTTTTAAAATA
** *
1091640 AATATAATATATA
1 TTTTTAA-A-ATA
* *
1091653 ATTTTAAAACA
1 TTTTTAAAATA
1091664 TTTTTAAAAATA
1 TTTTT-AAAATA
*
1091676 TATATATT-ATATA
1 T-T-T-TTAAAATA
1091689 GTTTTTAAAATA
1 -TTTTTAAAATA
*
1091701 TTTTAAAAATA
1 TTTTTAAAATA
1091712 AATATAATAT
Statistics
Matches: 91, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
11 38 0.42
12 25 0.27
13 20 0.22
14 4 0.04
15 4 0.04
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:1091645 original size:36 final size:36
Alignment explanation
Indices: 1091547--1091811 Score: 313
Period size: 36 Copynumber: 7.3 Consensus size: 36
1091537 TTTTTTTATG
1091547 TTTT-AAACATTTTAAAAATAAATATAATATATAGT
1 TTTTAAAACATTTTAAAAATAAATATAATATATAGT
* * *
1091582 TTTTAAAATATTTTTAAAAATATATATATTATATAGT
1 TTTTAAAACA-TTTTAAAAATAAATATAATATATAGT
* * *
1091619 TTTTAAAATATTTTGAAAATAAATATAATATATA-A
1 TTTTAAAACATTTTAAAAATAAATATAATATATAGT
* *
1091654 TTTTAAAACATTTTTAAAAATATATATATTATATAGT
1 TTTTAAAACA-TTTTAAAAATAAATATAATATATAGT
* *
1091691 TTTTAAAATATTTTAAAAATAAATATAATATATAGA
1 TTTTAAAACATTTTAAAAATAAATATAATATATAGT
*
1091727 TTTTAAAACACTTTTTAAAAAT--ATATATTATATAGT
1 TTTTAAAACA--TTTTAAAAATAAATATAATATATAGT
* * * *
1091763 TTTTAAAACGTTTTGAAAATAAATATGATATATAAT
1 TTTTAAAACATTTTAAAAATAAATATAATATATAGT
1091799 TATTTGAAAACAT
1 T-TTT-AAAACAT
1091812 ATATATTATA
Statistics
Matches: 195, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
34 9 0.05
35 13 0.07
36 111 0.57
37 46 0.24
38 16 0.08
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTAAAACATTTTAAAAATAAATATAATATATAGT
Found at i:1091672 original size:72 final size:73
Alignment explanation
Indices: 1091547--1091796 Score: 391
Period size: 72 Copynumber: 3.5 Consensus size: 73
1091537 TTTTTTTATG
* *
1091547 TTTT-AAACATTTTAAAAATAAATATAATATATAGTTTTTAAAATATTTTTAAAAATATATATAT
1 TTTTAAAACATTTTAAAAATAAATATAATATATAGATTTTAAAACATTTTTAAAAATATATATAT
1091611 TATATAGT
66 TATATAGT
* *
1091619 TTTTAAAATATTTTGAAAATAAATATAATATATA-ATTTTAAAACATTTTTAAAAATATATATAT
1 TTTTAAAACATTTTAAAAATAAATATAATATATAGATTTTAAAACATTTTTAAAAATATATATAT
1091683 TATATAGT
66 TATATAGT
*
1091691 TTTTAAAATATTTTAAAAATAAATATAATATATAGATTTTAAAACACTTTTT-AAAA-ATATATA
1 TTTTAAAACATTTTAAAAATAAATATAATATATAGATTTTAAAACA-TTTTTAAAAATATATATA
1091754 TTATATAGT
65 TTATATAGT
* * *
1091763 TTTTAAAACGTTTTGAAAATAAATATGATATATA
1 TTTTAAAACATTTTAAAAATAAATATAATATATA
1091797 ATTATTTGAA
Statistics
Matches: 166, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
72 119 0.72
73 42 0.25
74 5 0.03
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (73 bp):
TTTTAAAACATTTTAAAAATAAATATAATATATAGATTTTAAAACATTTTTAAAAATATATATAT
TATATAGT
Found at i:1093148 original size:19 final size:18
Alignment explanation
Indices: 1093124--1093168 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1093114 TGATCCTTTT
* *
1093124 TTATTTTTTTCGTTTTTCA
1 TTATTTTTTT-ATTTCTCA
1093143 TTATTTATTTTATTTCTCA
1 TTATTT-TTTTATTTCTCA
1093162 TTATTTT
1 TTATTTT
1093169 ACTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 18 0.78
20 4 0.17
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (18 bp):
TTATTTTTTTATTTCTCA
Found at i:1097115 original size:325 final size:324
Alignment explanation
Indices: 1096528--1097738 Score: 1497
Period size: 325 Copynumber: 3.8 Consensus size: 324
1096518 AGAGAATATA
* * *
1096528 TATTTGGAACTTTCTTTCCTATAAGCAATAAGTATAGAGATGTTCTCTTGAATAGAGA-TAAGGT
1 TATTTAGAACTTTCTTTTCTATAAGCAATAAGTATAGAGATGTTCTCTTGAATAGAGAGGAAGGT
* *
1096592 GATGAAGTATATGAGGTAATTATGACTGGTTTCAGCCTCGATGTTTTCATGGTGTAGCTAGCCTA
66 GATGAAGTATAGGAGGTAATTATGACTGGTTTCAGCCTCGATGTTTTCCT-G-GT-GC-AGCCTA
* * *
1096657 TTTCTGCTGTGCCGAACATCTGAGGGTTGTTTGGC----TG-------AACTTCCTACTTTCTGA
127 TTTGTGTTGTGCCGAACATCTGAGGGTTGTTTGGCTGAATGAATATACAACTTCCTACTTTCTAA
* * *
1096711 TTCATTCTTTATTCTTATAAGTTGTAACTCCAATTTCACATCT-TTCCACAAATGATGGTGGCCA
192 TTCATTCTCTATTATTATAA-TTATAACTCCAATTTCACATCTCTT-CACAAATGATGGTGGCCA
* ** *
1096775 AATGATTTTCAGCAGATA-GAAATATATGTCCCGAGCACCAAAATAATATATTTTTTCTTTGTAA
255 AATGATTTTCAGCAGATAGGGAATAGGTGTTCCGAGCACCAAAATAATATATTTTTTCTTTGTAA
1096839 TATTC
320 TATTC
* *
1096844 TATTTAGAACTTTCTTTTCTATAAGCAATAAGTATAGAGATGTTCTCTTGAATAGAAAGGAAGGG
1 TATTTAGAACTTTCTTTTCTATAAGCAATAAGTATAGAGATGTTCTCTTGAATAGAGAGGAAGGT
* * * *
1096909 GATGGAGTACAGGAGGTAATTATGACCGGTTTCAGCCTCGATGTTTTTCTGGTGCAGCCTATTTG
66 GATGAAGTATAGGAGGTAATTATGACTGGTTTCAGCCTCGATGTTTTCCTGGTGCAGCCTATTTG
* * *
1096974 TGATGTGCCAAACATCTGGGGGGTTGTTTGGCTGAATGAATATACAACTTCCTACTTTCTAATTC
131 TGTTGTGCCGAACATCT-GAGGGTTGTTTGGCTGAATGAATATACAACTTCCTACTTTCTAATTC
***
1097039 ATTCTCTATTATTATAATTTATAACTCCAATTTCACATCTCTTCACAAATGACAATGGCCAAATG
195 ATTCTCTATTATTATAA-TTATAACTCCAATTTCACATCTCTTCACAAATGATGGTGGCCAAATG
* *
1097104 ATTTTCAGCAGATAGGGAATCGGTGTTCCGAGCACCAAAATAATATTTTTTTTCTTTGTAATA-T
259 ATTTTCAGCAGATAGGGAATAGGTGTTCCGAGCACCAAAATAATATATTTTTTCTTTGTAATATT
1097168 C
324 C
* * *
1097169 TTATTTA-AACTTTTTTTTCTATAAGAAATAAGCATAGAGATGTTCTCTTGAATAGAGAGGAAGG
1 -TATTTAGAACTTTCTTTTCTATAAGCAATAAGTATAGAGATGTTCTCTTGAATAGAGAGGAAGG
** * *
1097233 TGATGAAGTATAGGAGGTAATTATGACTGGTTTCAAACTTGATATTTTCCTGGTGCAGCCTATTT
65 TGATGAAGTATAGGAGGTAATTATGACTGGTTTCAGCCTCGATGTTTTCCTGGTGCAGCCTATTT
* * * *
1097298 GTGTTGTGTCGAACATCTG-GGATTGTTTGGCTAAATGAATATACAACTTCATACTTT-TAATTC
130 GTGTTGTGCCGAACATCTGAGGGTTGTTTGGCTGAATGAATATACAACTTCCTACTTTCTAATTC
* * *
1097361 ATTATC---TA-T-T-ATTATAACTCCAATTTCACATCTCTCCACAAATGATGGTGGCCAAATAA
195 ATTCTCTATTATTATAATTATAACTCCAATTTCACATCTCTTCACAAATGATGGTGGCCAAATGA
* *
1097420 TTTTCAGCAGATATGGAATAGGTGTTCCGAGCA-CAAAAT-A-A-ATTTTTTCTTTGTAATATCC
260 TTTTCAGCAGATAGGGAATAGGTGTTCCGAGCACCAAAATAATATATTTTTTCTTTGTAATATTC
* * * * * *
1097481 TATTTGGAACTTTCTTTTCTATAAGTAATAAGTACAGAGATTTTTTTCTTGAATAGAGCGGAAGG
1 TATTTAGAACTTTCTTTTCTATAAGCAATAAGTATAGAGA-TGTTCTCTTGAATAGAGAGGAAGG
* * * * *
1097546 TGATGAAGTATAGGAGGTAATTATGAATGGTTTCATCCTCGATGTTTTCCTGGAGTAGTCTATTT
65 TGATGAAGTATAGGAGGTAATTATGACTGGTTTCAGCCTCGATGTTTTCCTGGTGCAGCCTATTT
* ** * *
1097611 GTGTTGTGCCGGACATCTGAAAGTTGTTTGGCTGAATGAATATACAACTT-CTACTTTTTGATTC
130 GTGTTGTGCCGAACATCTGAGGGTTGTTTGGCTGAATGAATATACAACTTCCTACTTTCTAATTC
* * *
1097675 ATTCTC---TA-T-T-CTTACAACTCCAATTTCATATCTC--CACAAATGATGGTGGCCAAATGA
195 ATTCTCTATTATTATAATTATAACTCCAATTTCACATCTCTTCACAAATGATGGTGGCCAAATGA
1097732 TTTTCAG
260 TTTTCAG
1097739 TAAATAAGTA
Statistics
Matches: 787, Mismatches: 87, Indels: 46
0.86 0.09 0.05
Matches are distributed among these distances:
311 21 0.03
312 60 0.08
313 126 0.16
314 82 0.10
315 76 0.10
316 57 0.07
317 49 0.06
318 3 0.00
319 2 0.00
322 11 0.01
323 35 0.04
324 1 0.00
325 214 0.27
326 50 0.06
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (324 bp):
TATTTAGAACTTTCTTTTCTATAAGCAATAAGTATAGAGATGTTCTCTTGAATAGAGAGGAAGGT
GATGAAGTATAGGAGGTAATTATGACTGGTTTCAGCCTCGATGTTTTCCTGGTGCAGCCTATTTG
TGTTGTGCCGAACATCTGAGGGTTGTTTGGCTGAATGAATATACAACTTCCTACTTTCTAATTCA
TTCTCTATTATTATAATTATAACTCCAATTTCACATCTCTTCACAAATGATGGTGGCCAAATGAT
TTTCAGCAGATAGGGAATAGGTGTTCCGAGCACCAAAATAATATATTTTTTCTTTGTAATATTC
Found at i:1098456 original size:20 final size:20
Alignment explanation
Indices: 1098416--1098456 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1098406 ATTTTTGAAA
*
1098416 AAATCATAAAATTTATTAAT
1 AAATCATAAAATTTATAAAT
1098436 AAATCAATAAAATTT-TAAAT
1 AAATC-ATAAAATTTATAAAT
1098456 A
1 A
1098457 TATTTGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATCATAAAATTTATAAAT
Found at i:1098980 original size:30 final size:30
Alignment explanation
Indices: 1098938--1098994 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1098928 GATTTCTTAA
**
1098938 TTCAAACTGAATTATTTGGAATTTAAATTCG
1 TTCAAACTGAATTAAAT-GAATTTAAATTCG
1098969 TTCAAA-TGAATTAAATGAATTTAAAT
1 TTCAAACTGAATTAAATGAATTTAAAT
1098995 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 8 0.33
31 6 0.25
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (30 bp):
TTCAAACTGAATTAAATGAATTTAAATTCG
Found at i:1101339 original size:2 final size:2
Alignment explanation
Indices: 1101332--1101368 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1101322 TATCGCAGTG
1101332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1101369 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1107392 original size:23 final size:22
Alignment explanation
Indices: 1107349--1107393 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1107339 TAACATACCT
1107349 TGAATCTTCAAAAGAGCAGAAGG
1 TGAATCTTCAAAAGA-CAGAAGG
1107372 TGAATCCTTCAACAAGA-AGAAG
1 TGAAT-CTTCAA-AAGACAGAAG
1107394 CGGATCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.50
24 6 0.30
25 4 0.20
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (22 bp):
TGAATCTTCAAAAGACAGAAGG
Found at i:1107466 original size:52 final size:53
Alignment explanation
Indices: 1107388--1107497 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 53
1107378 CTTCAACAAG
*
1107388 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCC-AATGGAGACTTTAAA
1 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
1107440 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
1 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
1107493 AAGAA
1 AAGAA
1107498 ACAGTGCCGA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 37 0.66
53 19 0.34
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (53 bp):
AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
Found at i:1114048 original size:216 final size:216
Alignment explanation
Indices: 1113658--1114087 Score: 808
Period size: 215 Copynumber: 2.0 Consensus size: 216
1113648 AAGGCAATGG
1113658 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
1 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
1113723 GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
66 GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
1113788 TCCCATATGTAATGGGGTAAGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAACA
131 TCCCATATGTAATGGGGTAAGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAACA
*
1113853 GCTTCCGTAAGAGACCTCCGA
196 GCTTCCGTAAAAGACCTCCGA
1113874 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGG-ATTCAAACATTTGACCTTACTTAAG
1 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
* *
1113938 TGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGCTTACCCTTAT
66 GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
*
1114003 TCCCATATGTAATGGGGTAAGGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAGC
131 TCCCATATGTAATGGGGTAA-GGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAAC
1114068 AGCTTCCGTAAAAGACCTCC
195 AGCTTCCGTAAAAGACCTCC
1114088 AAATTATGAA
Statistics
Matches: 209, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
215 108 0.52
216 101 0.48
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (216 bp):
CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
TCCCATATGTAATGGGGTAAGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAACA
GCTTCCGTAAAAGACCTCCGA
Found at i:1117023 original size:2 final size:2
Alignment explanation
Indices: 1117018--1117077 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1117008 ACACACAATC
1117018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1117060 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1117078 ATAAACTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1119988 original size:37 final size:37
Alignment explanation
Indices: 1119946--1120019 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
1119936 CTAAAAAATC
* *
1119946 GGGTCGAGTCAGAGTTGG-TG-AAGAATATATATTTTTT
1 GGGTCGAGTC-GAGTCGGATGTAAG-ATATAAATTTTTT
1119983 GGGTCGAGTCGAGTCGGATGTAAGATATAAATTTTTT
1 GGGTCGAGTCGAGTCGGATGTAAGATATAAATTTTTT
1120020 TGACCGGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 6 0.18
37 24 0.73
38 3 0.09
ACGTcount: A:0.27, C:0.07, G:0.30, T:0.36
Consensus pattern (37 bp):
GGGTCGAGTCGAGTCGGATGTAAGATATAAATTTTTT
Found at i:1126148 original size:21 final size:21
Alignment explanation
Indices: 1126096--1126142 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1126086 GTTTCCAGAT
*
1126096 TCGCAACACGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
1126117 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
1126138 TCGCA
1 TCGCA
1126143 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1126183 original size:21 final size:21
Alignment explanation
Indices: 1126157--1126203 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1126147 GATTTACATA
* *
1126157 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTACGATAGTCAAAG
1126178 TTCGCATTACGATAGTCAAAG
1 TTCGCATTACGATAGTCAAAG
1126199 TTCGC
1 TTCGC
1126204 GTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (21 bp):
TTCGCATTACGATAGTCAAAG
Found at i:1126297 original size:21 final size:21
Alignment explanation
Indices: 1126267--1126340 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
1126257 GATTTACATA
* *
1126267 TTCGCATTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** * *
1126288 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
1126309 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
1126328 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1126341 TTATTCCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 15 0.37
21 26 0.63
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:1126316 original size:19 final size:19
Alignment explanation
Indices: 1126292--1126361 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 19
1126282 TCGAAGTTCG
1126292 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** * *
1126311 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
1126330 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
1126353 CGTTGCGAT
1 CGTTGCGAT
1126362 AGTCCAAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 15 0.38
20 1 0.03
21 16 0.41
22 1 0.03
23 6 0.15
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:1126326 original size:40 final size:42
Alignment explanation
Indices: 1126273--1126365 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 42
1126263 CATATTCGCA
*
1126273 TTGCAATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1126313 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1126355 TTGCGATAGTC
1 TTGCGATAGTC
1126366 CAAATCACAC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 26 0.52
41 2 0.04
42 22 0.44
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1126369 original size:19 final size:19
Alignment explanation
Indices: 1126292--1126370 Score: 77
Period size: 19 Copynumber: 3.9 Consensus size: 19
1126282 TCGAAGTTCG
**
1126292 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
* *
1126311 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATAGTCCAAATT
*
1126330 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA--TAGTCCAAATT
1126353 CGTTGCGATAGTCCAAAT
1 CGTTGCGATAGTCCAAAT
1126371 CACACGACTG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
19 24 0.50
21 16 0.33
23 8 0.17
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:1127510 original size:30 final size:30
Alignment explanation
Indices: 1127476--1127542 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
1127466 TCAACCCGAA
1127476 AATTAATATAAATTTACCTTATATATATAG
1 AATTAATATAAATTTACCTTATATATATAG
1127506 AATTAATATAAATTTACCTTATATATATAG
1 AATTAATATAAATTTACCTTATATATATAG
1127536 AATTAAT
1 AATTAAT
1127543 TTCAATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (30 bp):
AATTAATATAAATTTACCTTATATATATAG
Found at i:1127563 original size:34 final size:30
Alignment explanation
Indices: 1127476--1127568 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 30
1127466 TCAACCCGAA
* *
1127476 AATTAATATAAATTTACCTTATATATATAG
1 AATTAATATAAAATAACCTTATATATATAG
* *
1127506 AATTAATATAAATTTACCTTATATATATAG
1 AATTAATATAAAATAACCTTATATATATAG
*
1127536 AATTAATTTCAATAATAATCCTATATATATATA
1 AATTAATAT-AA-AATAA-CCT-TATATATATA
1127569 TATATATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 38 0.68
31 2 0.04
32 3 0.05
33 3 0.05
34 10 0.18
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (30 bp):
AATTAATATAAAATAACCTTATATATATAG
Found at i:1127564 original size:2 final size:2
Alignment explanation
Indices: 1127557--1127581 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1127547 ATAATAATCC
1127557 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 T
1127582 TTCAATTAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1132255 original size:14 final size:14
Alignment explanation
Indices: 1132236--1132267 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1132226 AAAGCTAGTA
1132236 TATTATCATAAATT
1 TATTATCATAAATT
*
1132250 TATTATCATAACTT
1 TATTATCATAAATT
1132264 TATT
1 TATT
1132268 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:1137813 original size:13 final size:13
Alignment explanation
Indices: 1137791--1137853 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
1137781 ACAACTTATT
*
1137791 ACCATGTATGGAC
1 ACCATCTATGGAC
1137804 ACCATCTATGGAC
1 ACCATCTATGGAC
* *
1137817 A-CAACT-T--ATT
1 ACCATCTATGGA-C
*
1137827 ACCATGTATGGAC
1 ACCATCTATGGAC
1137840 ACCATCTATGGAC
1 ACCATCTATGGAC
1137853 A
1 A
1137854 ACTTATTACC
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
9 1 0.03
10 1 0.03
11 4 0.11
12 5 0.13
13 26 0.68
14 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (13 bp):
ACCATCTATGGAC
Found at i:1137814 original size:36 final size:36
Alignment explanation
Indices: 1137771--1137875 Score: 178
Period size: 36 Copynumber: 3.0 Consensus size: 36
1137761 ACTAATTACA
1137771 ATCTATGGACACAACTTATTACCATGTATGGACACC
1 ATCTATGGACACAACTTATTACCATGTATGGACACC
1137807 ATCTATGGACACAACTTATTACCATGTATGGACACC
1 ATCTATGGACACAACTTATTACCATGTATGGACACC
* *
1137843 ATCTATGG--ACAACTTATTACCATCTATGAACAC
1 ATCTATGGACACAACTTATTACCATGTATGGACAC
1137876 AACTGAATTG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 23 0.34
36 44 0.66
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (36 bp):
ATCTATGGACACAACTTATTACCATGTATGGACACC
Found at i:1145520 original size:14 final size:13
Alignment explanation
Indices: 1145498--1145531 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1145488 GATATTATGG
1145498 AATTATATA-AAA
1 AATTATATATAAA
1145510 AATTATATATAAA
1 AATTATATATAAA
1145523 AATTATATA
1 AATTATATA
1145532 CGACTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTATATATAAA
Found at i:1147127 original size:19 final size:19
Alignment explanation
Indices: 1147092--1147128 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1147082 CGTTACACTT
*
1147092 GTTTAAATTACATAAATTG
1 GTTTAAATTACAGAAATTG
*
1147111 GTTTAAATTTCAGAAATT
1 GTTTAAATTACAGAAATT
1147129 AAAACGACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (19 bp):
GTTTAAATTACAGAAATTG
Found at i:1153779 original size:21 final size:21
Alignment explanation
Indices: 1153755--1153803 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1153745 CATATTCGTA
1153755 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
1153776 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
1153797 TTGCGAT
1 TTGCGAT
1153804 TTATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:1153867 original size:42 final size:42
Alignment explanation
Indices: 1153774--1153956 Score: 276
Period size: 42 Copynumber: 4.2 Consensus size: 42
1153764 TCGAAGTTCG
1153774 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCG------ATTTATTCCAAATT
1153822 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
1153864 CGTTGTGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
1153906 CGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1153948 CGTTGCGAT
1 CGTTGCGAT
1153957 TTGTTTCTTA
Statistics
Matches: 131, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
42 103 0.79
48 28 0.21
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:1153951 original size:21 final size:21
Alignment explanation
Indices: 1153808--1153958 Score: 118
Period size: 21 Copynumber: 7.2 Consensus size: 21
1153798 TGCGATTTAT
1153808 ATTTATTCCAAATTCGTTGCG
1 ATTTATTCCAAATTCGTTGCG
* * *
1153829 A--TAGTCGAAGTTCGCGTTGCG
1 ATTTATTCCAAATT--CGTTGCG
*
1153850 ATTTATTCCAAATTCGTTGTG
1 ATTTATTCCAAATTCGTTGCG
*
1153871 A--TAGT-CAAAGTTCGCGTTGCG
1 ATTTATTCCAAA-TT--CGTTGCG
*
1153892 ATTTATTCCAAATTCGTTGTG
1 ATTTATTCCAAATTCGTTGCG
* *
1153913 A--TAGTCCAAGTTCGCGTTGCG
1 ATTTATTCCAAATT--CGTTGCG
1153934 ATTTATTCCAAATTCGTTGCG
1 ATTTATTCCAAATTCGTTGCG
1153955 ATTT
1 ATTT
1153959 GTTTCTTAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 28
0.69 0.11 0.19
Matches are distributed among these distances:
18 4 0.04
19 22 0.22
21 48 0.48
23 22 0.22
24 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.39
Consensus pattern (21 bp):
ATTTATTCCAAATTCGTTGCG
Found at i:1154665 original size:21 final size:21
Alignment explanation
Indices: 1154636--1154751 Score: 139
Period size: 21 Copynumber: 5.6 Consensus size: 21
1154626 GATTTACATA
*
1154636 TTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
1154657 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1154678 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
1154698 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
1154719 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
1154740 TTCGCATTGCGA
1 TTCGCATTGCGA
1154752 ATCTGGAAAC
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.21
21 64 0.78
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1155940 original size:29 final size:29
Alignment explanation
Indices: 1155907--1155963 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1155897 ATAGTCGTGT
* * *
1155907 GACCATTTTGTTACTTTTAATATTTGAGA
1 GACCATTTTATAACTTTTAATAGTTGAGA
1155936 GACCATTTTATAACTTTTAATAGTTGAG
1 GACCATTTTATAACTTTTAATAGTTGAG
1155964 GGATTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (29 bp):
GACCATTTTATAACTTTTAATAGTTGAGA
Found at i:1157038 original size:22 final size:24
Alignment explanation
Indices: 1157001--1157047 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1156991 TATATAATCT
* *
1157001 ATTTATTTTAATTTTATATTTTAA
1 ATTTATTTTAATTTTAAATTATAA
1157025 ATTT-TTTTAA-TTTAAATTATAA
1 ATTTATTTTAATTTTAAATTATAA
1157047 A
1 A
1157048 CCAACCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 6 0.29
24 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATTTTAATTTTAAATTATAA
Found at i:1159939 original size:20 final size:19
Alignment explanation
Indices: 1159914--1159967 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1159904 ACGAAATAAA
1159914 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
*
1159934 AATCGCAAAC-CAGTTCCCAG
1 AATCGC-AACGC-GATCCCAG
1159954 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1159968 AGTACAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 5 0.17
20 18 0.62
21 6 0.21
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1160021 original size:20 final size:20
Alignment explanation
Indices: 1159996--1160048 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1159986 GATTTTCCAG
* *
1159996 AATCGCAACGTGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
1160016 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
1160036 AATCGCAACGCGA
1 AATCGCAACGCGA
1160049 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:1160080 original size:20 final size:20
Alignment explanation
Indices: 1160057--1160126 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1160047 GATTCTGACT
1160057 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
1160077 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
1160098 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
*
1160118 ATTGCAACG
1 ATCGCAACG
1160127 CGATCGATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 25 0.61
21 16 0.39
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:1160265 original size:20 final size:20
Alignment explanation
Indices: 1160240--1160295 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1160230 TTTTCTTAAT
1160240 TCGCAACGCGATTAC-GTAAA
1 TCGCAACGCGATT-CTGTAAA
* *
1160260 TCGCAATGCGAATCTGTAAA
1 TCGCAACGCGATTCTGTAAA
* *
1160280 TCACAACGAGATTCTG
1 TCGCAACGCGATTCTG
1160296 ACTATCGCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATTCTGTAAA
Found at i:1161170 original size:24 final size:24
Alignment explanation
Indices: 1161143--1161196 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1161133 GTATTCGAAA
1161143 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1161167 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1161191 TTTGAT
1 TTTGAT
1161197 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1163653 original size:20 final size:20
Alignment explanation
Indices: 1163628--1163716 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
1163618 CAACGTGGAA
1163628 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
1163648 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
1163668 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
1163688 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
1163708 ATCGCAACG
1 ATCGCAACG
1163717 AGAGAATCGT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1163753 original size:19 final size:19
Alignment explanation
Indices: 1163721--1163883 Score: 221
Period size: 19 Copynumber: 8.8 Consensus size: 19
1163711 GCAACGAGAG
*
1163721 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1163740 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1163759 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1163778 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1163797 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
1163815 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
1163834 AATCGCAA--CG-GGTG--
1 AATCGCAATGCGAAATGAA
1163848 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1163868 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
1163884 CGTTGCGATT
Statistics
Matches: 127, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
14 8 0.06
16 4 0.03
17 2 0.02
18 20 0.16
19 82 0.65
20 11 0.09
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1164058 original size:14 final size:14
Alignment explanation
Indices: 1164039--1164075 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1164029 CAACAATTAA
1164039 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1164053 ACAAATCATCTTTT
1 ACAAATCAACATTT
1164067 ACAAATCAA
1 ACAAATCAA
1164076 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1165536 original size:42 final size:42
Alignment explanation
Indices: 1165431--1165540 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
1165421 TAGAATGTTG
* * *
1165431 GGAGGGACCTCTTCAACGATGACAGTGGCCTATTGAACCGTA
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTATTGAACCGTA
* ** * *
1165473 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAA-CGATA
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTATTGAACCG-TA
1165515 GG-GGAGGCCTCTTGAACGATGACAGG
1 GGAGG-GGCCTCTTGAACGATGACAGG
1165541 TGAGTCAGGC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 4 0.07
42 50 0.93
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.20
Consensus pattern (42 bp):
GGAGGGGCCTCTTGAACGATGACAGGGGCCTATTGAACCGTA
Found at i:1166066 original size:20 final size:20
Alignment explanation
Indices: 1166019--1166067 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1166009 GAAACTTAAA
*
1166019 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
1166039 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
1166059 ATCGCAATG
1 ATCGCAATG
1166068 TGAATTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1166079 original size:20 final size:20
Alignment explanation
Indices: 1166019--1166085 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
1166009 GAAACTTAAA
* *
1166019 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATAACT
*
1166039 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATAACT
* **
1166059 ATCGCAATGTGAATTTAACT
1 ATCGCAATGCGAAAATAACT
1166079 ATCGCAA
1 ATCGCAA
1166086 CGAGAGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATAACT
Found at i:1166142 original size:19 final size:19
Alignment explanation
Indices: 1166120--1166163 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1166110 AAATCGCAAC
*
1166120 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCATT
* *
1166139 GCGATTTTGGTTTCGCATT
1 GCGATTATAGTTTCGCATT
1166158 GCGATT
1 GCGATT
1166164 TTGTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCATT
Found at i:1166164 original size:19 final size:19
Alignment explanation
Indices: 1166129--1166166 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1166119 CGCGATTATA
*
1166129 GTTTCGCGTTGCGATTTTG
1 GTTTCGCATTGCGATTTTG
1166148 GTTTCGCATTGCGATTTTG
1 GTTTCGCATTGCGATTTTG
1166167 TCGTTGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
GTTTCGCATTGCGATTTTG
Found at i:1166204 original size:33 final size:33
Alignment explanation
Indices: 1166135--1166226 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
1166125 TATAGTTTCG
** * * *
1166135 CGTTGCGATTTTGGTTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1166168 CGTTGCAATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1166201 CGTTACGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
1166227 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 18 0.35
33 33 0.65
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1166226 original size:17 final size:17
Alignment explanation
Indices: 1166178--1166226 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
1166168 CGTTGCAATT
1166178 TTCATTTCGCGTTGCGA
1 TTCATTTCGCGTTGCGA
* *
1166195 TTC---TCTCGTTACGA
1 TTCATTTCGCGTTGCGA
1166209 TTCATTTCGCGTTGCGA
1 TTCATTTCGCGTTGCGA
1166226 T
1 T
1166227 AGTCATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 12 0.48
17 13 0.52
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (17 bp):
TTCATTTCGCGTTGCGA
Found at i:1166460 original size:94 final size:94
Alignment explanation
Indices: 1166314--1166693 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
1166304 ATGGATTGCA
* * * *
1166314 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTTATAGTATTAAAGAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1166378 TTATCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1166407 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1166472 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1166501 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1166566 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1166595 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1166659 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1166689 TTACT
1 TTACT
1166694 AAGCAATCTA
Statistics
Matches: 276, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
93 23 0.08
94 253 0.92
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1172403 original size:33 final size:32
Alignment explanation
Indices: 1172346--1172412 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1172336 ACCCGGATAA
1172346 CAAGCAAGCAAAGCAATCACGCTTTAATTAAG
1 CAAGCAAGCAAAGCAATCACGCTTTAATTAAG
1172378 CAAGCAAGC-AAGCAAGATCACGCTTTAATTAAG
1 CAAGCAAGCAAAGC-A-ATCACGCTTTAATTAAG
1172411 CA
1 CA
1172413 CGAGGATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
31 4 0.12
32 10 0.30
33 19 0.58
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (32 bp):
CAAGCAAGCAAAGCAATCACGCTTTAATTAAG
Found at i:1173460 original size:34 final size:34
Alignment explanation
Indices: 1173410--1173486 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
1173400 AATGTTATTG
1173410 AACTGCATCTCGTTGGAAATTT-TCAGTGTCATTC
1 AACTGCATCTCGTTGG-AATTTATCAGTGTCATTC
* * * *
1173444 AACTGCGTCTCTTTGGAATTTATCAGTGTTATTG
1 AACTGCATCTCGTTGGAATTTATCAGTGTCATTC
1173478 AACTGCATC
1 AACTGCATC
1173487 CCCATTCAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (34 bp):
AACTGCATCTCGTTGGAATTTATCAGTGTCATTC
Found at i:1174944 original size:26 final size:26
Alignment explanation
Indices: 1174906--1174958 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1174896 AATTTTTATT
*
1174906 TGTTTAAAGTGATAATTTAATATATA
1 TGTTTAAAGTGATAATGTAATATATA
* *
1174932 TGTTATAAA-TGATGATGTGATATATA
1 TGTT-TAAAGTGATAATGTAATATATA
1174958 T
1 T
1174959 CATGTGCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (26 bp):
TGTTTAAAGTGATAATGTAATATATA
Found at i:1176182 original size:2 final size:2
Alignment explanation
Indices: 1176138--1176167 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1176128 TTTTATACCA
1176138 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1176168 ACATTATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1176319 original size:2 final size:2
Alignment explanation
Indices: 1176312--1176338 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1176302 TTGGATGAAT
1176312 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
1176339 TTAAATTGTG
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:1192974 original size:130 final size:130
Alignment explanation
Indices: 1192659--1192967 Score: 415
Period size: 130 Copynumber: 2.3 Consensus size: 130
1192649 TCAACATCAA
*
1192659 CTGACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCA
1 CTGACCAGATC-TCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAACCAGCCGTCCTCATCA
* * * * *
1192723 CGTAGGAACCGAGTTATCACCCTTCCTAAAGGTGGCCAGAGTTTTTCATCATGTATGAACCGTGT
64 CGTAGGAACCGAGTTATCA--C--CCTAAAGATGGCCAGAATTCTTCATCATGTAGGAACAGTGT
1192788 CATCCC
125 CATCCC
* * * *
1192794 CAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACG
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACG
* *
1192859 TAGGAACCGTGTTATCA-CCTAAAGATGGCCAAGAATTCTTCATCATGTAGGAGCAGTGTCATCC
66 TAGGAACCGAGTTATCACCCTAAAGATGGCC-AGAATTCTTCATCATGTAGGAACAGTGTCATCC
*
1192923 T
130 C
*
1192924 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGA
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
1192968 CGACCAGACC
Statistics
Matches: 154, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
129 12 0.08
130 67 0.44
134 39 0.25
135 35 0.23
136 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (130 bp):
CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACG
TAGGAACCGAGTTATCACCCTAAAGATGGCCAGAATTCTTCATCATGTAGGAACAGTGTCATCCC
Found at i:1193174 original size:9 final size:10
Alignment explanation
Indices: 1193156--1193213 Score: 68
Period size: 9 Copynumber: 5.8 Consensus size: 10
1193146 GTCTTTTTTA
1193156 TATTATTTAAT
1 TATTA-TTAAT
1193167 T-TTATTAAT
1 TATTATTAAT
1193176 TATTATT-AT
1 TATTATTAAT
1193185 TATTATT-AT
1 TATTATTAAT
1193194 TATTATTAAAT
1 TATTATT-AAT
1193205 TATATATTA
1 TAT-TATTA
1193214 CAAATTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
9 24 0.56
10 8 0.19
11 7 0.16
12 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:1193180 original size:3 final size:3
Alignment explanation
Indices: 1193156--1193201 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
1193146 GTCTTTTTTA
*
1193156 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
1193200 TA
1 TA
1193202 AATTATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 3 0.08
3 32 0.84
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1193359 original size:25 final size:25
Alignment explanation
Indices: 1193330--1193428 Score: 159
Period size: 25 Copynumber: 4.0 Consensus size: 25
1193320 GAACCAACCC
1193330 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1193355 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1193380 ATCAGATTAGGGTTTCAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
1193406 AT-A-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
1193429 TCCCCTAACT
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
23 2 0.03
24 7 0.10
25 59 0.82
26 4 0.06
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1200274 original size:21 final size:21
Alignment explanation
Indices: 1200216--1200274 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1200206 TATTAATTAA
** *
1200216 AATATTTAAAATATATTTATT
1 AATATTTCTAATATATATATT
1200237 AATATTTCTAATATATATATT
1 AATATTTCTAATATATATATT
*
1200258 -ATATTTTTAATAT-TATA
1 AATATTTCTAATATATATA
1200275 ATAAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.12
20 12 0.35
21 18 0.53
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTTCTAATATATATATT
Found at i:1200312 original size:18 final size:17
Alignment explanation
Indices: 1200279--1200314 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1200269 ATTATAATAA
*
1200279 AATAATAAATATATTAT
1 AATAATAAAGATATTAT
1200296 AATAATACAAGATATTAT
1 AATAATA-AAGATATTAT
1200314 A
1 A
1200315 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AATAATAAAGATATTAT
Found at i:1200417 original size:19 final size:18
Alignment explanation
Indices: 1200333--1200461 Score: 54
Period size: 18 Copynumber: 7.1 Consensus size: 18
1200323 TTAATAACAT
1200333 ATAATAA-ATTATTAATA
1 ATAATAATATTATTAATA
* *
1200350 A-AATTTATATTATTTATTA
1 ATAA-TAATATTA-TTAATA
* * * *
1200369 AT-TTCATATAAATAATA
1 ATAATAATATTATTAATA
* *
1200386 TTATTAA-ATTATTAATA
1 ATAATAATATTATTAATA
*
1200403 ATGAATAATATTATTTAT-
1 AT-AATAATATTATTAATA
*
1200421 ATATTTAATATTAATATAATA
1 ATA-ATAATATT-AT-TAATA
1200442 ATCTAATAATATT-TTAATA
1 A--TAATAATATTATTAATA
1200461 A
1 A
1200462 AGATATTTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 24
0.67 0.14 0.20
Matches are distributed among these distances:
16 2 0.02
17 18 0.22
18 26 0.32
19 22 0.27
20 4 0.05
21 1 0.01
22 7 0.09
23 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (18 bp):
ATAATAATATTATTAATA
Found at i:1200436 original size:27 final size:27
Alignment explanation
Indices: 1200356--1200441 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 27
1200346 AATAAAATTT
*
1200356 ATATTATTTAT-TAATTTCATATAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
1200383 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
1200410 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
1200439 ATA
1 ATA
1200442 ATCTAATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 20 0.43
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:1200482 original size:23 final size:24
Alignment explanation
Indices: 1200456--1200501 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1200446 AATAATATTT
1200456 TAATAAAGA-TATTTAAAATATAC
1 TAATAAAGATTATTTAAAATATAC
* * *
1200479 TAATTAATATTTTTTAAAATATA
1 TAATAAAGATTATTTAAAATATA
1200502 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAAGATTATTTAAAATATAC
Found at i:1200617 original size:11 final size:11
Alignment explanation
Indices: 1200601--1200628 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1200591 AAAATTATAA
1200601 AAATAATAAAT
1 AAATAATAAAT
1200612 AAATAATAAAT
1 AAATAATAAAT
1200623 AAATAA
1 AAATAA
1200629 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:1210293 original size:3 final size:3
Alignment explanation
Indices: 1210285--1210324 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1210275 ATGAAATCTT
1210285 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
1210325 GAAGTGTTTA
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:1218240 original size:30 final size:30
Alignment explanation
Indices: 1218204--1218265 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1218194 CATGATACTT
1218204 TGAAAATGCTGTTGCACATTATTTCACCAA
1 TGAAAATGCTGTTGCACATTATTTCACCAA
1218234 TGAAAATGCTGTTGCACATTATTTCACCAA
1 TGAAAATGCTGTTGCACATTATTTCACCAA
1218264 TG
1 TG
1218266 CTGTTGTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (30 bp):
TGAAAATGCTGTTGCACATTATTTCACCAA
Found at i:1218321 original size:17 final size:16
Alignment explanation
Indices: 1218295--1218326 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1218285 TTGCCTGCTG
1218295 GCCGCTGCCGCCGCCC
1 GCCGCTGCCGCCGCCC
1218311 GCCGTCTGCCGCCGCC
1 GCCG-CTGCCGCCGCC
1218327 GTCAGCCGTC
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:0.00, C:0.59, G:0.31, T:0.09
Consensus pattern (16 bp):
GCCGCTGCCGCCGCCC
Found at i:1218326 original size:20 final size:20
Alignment explanation
Indices: 1218296--1218343 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1218286 TGCCTGCTGG
* *
1218296 CCGCTGCCGCCGCCCGCCGT
1 CCGCCGCCGCCGCCAGCCGT
* *
1218316 CTGCCGCCGCCGTCAGCCGT
1 CCGCCGCCGCCGCCAGCCGT
1218336 CCGCCGCC
1 CCGCCGCC
1218344 ACACTCTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.58, G:0.29, T:0.10
Consensus pattern (20 bp):
CCGCCGCCGCCGCCAGCCGT
Found at i:1220659 original size:1 final size:1
Alignment explanation
Indices: 1220653--1220683 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1220643 AACTTCTATC
1220653 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1220684 GTAAGGTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1232446 original size:94 final size:94
Alignment explanation
Indices: 1232327--1232516 Score: 353
Period size: 94 Copynumber: 2.0 Consensus size: 94
1232317 CAAAATTTCT
* * *
1232327 TAAAAAGGACACGTATTAGTTTATTTAATTTAATTTTCCACCAATAATCAGTAAGTGGAATCAAT
1 TAAAAAGGACACGTATTAATCTATTTAATTTAATTTCCCACCAATAATCAGTAAGTGGAATCAAT
1232392 GAAATTTACCCCTACATCTCAATTGAAGA
66 GAAATTTACCCCTACATCTCAATTGAAGA
1232421 TAAAAAGGACACGTATTAATCTATTTAATTTAATTTCCCACCAATAATCAGTAAGTGGAATCAAT
1 TAAAAAGGACACGTATTAATCTATTTAATTTAATTTCCCACCAATAATCAGTAAGTGGAATCAAT
1232486 GAAATTTACCCCTACATCTCAATTGAAGA
66 GAAATTTACCCCTACATCTCAATTGAAGA
1232515 TA
1 TA
1232517 TTATTAGGTC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (94 bp):
TAAAAAGGACACGTATTAATCTATTTAATTTAATTTCCCACCAATAATCAGTAAGTGGAATCAAT
GAAATTTACCCCTACATCTCAATTGAAGA
Found at i:1233902 original size:14 final size:14
Alignment explanation
Indices: 1233883--1233912 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1233873 CAGACAGAAC
1233883 GGCATGTAATTAGG
1 GGCATGTAATTAGG
1233897 GGCATGTAATTAGG
1 GGCATGTAATTAGG
1233911 GG
1 GG
1233913 TGTAATCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.40, T:0.27
Consensus pattern (14 bp):
GGCATGTAATTAGG
Found at i:1233918 original size:12 final size:13
Alignment explanation
Indices: 1233886--1233918 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1233876 ACAGAACGGC
1233886 ATGTAATTAGGGG
1 ATGTAATTAGGGG
1233899 CATGTAATTAGGGG
1 -ATGTAATTAGGGG
1233913 -TGTAAT
1 ATGTAAT
1233919 CGAGCCGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
14 13 0.68
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (13 bp):
ATGTAATTAGGGG
Found at i:1234007 original size:26 final size:27
Alignment explanation
Indices: 1233944--1234007 Score: 67
Period size: 31 Copynumber: 2.3 Consensus size: 27
1233934 TCGAGTATTG
1233944 ATGAGCTCGACTCGACTCAAAAACTCTGAA
1 ATGAGCTCGACTCGACTCAAAAACTC---A
* *
1233974 ATGAAGCTCGACTTGACTCGAAAACTC-
1 ATG-AGCTCGACTCGACTCAAAAACTCA
1234001 ATGAGCT
1 ATGAGCT
1234008 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 4 0.13
27 3 0.10
30 3 0.10
31 21 0.68
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (27 bp):
ATGAGCTCGACTCGACTCAAAAACTCA
Found at i:1238251 original size:34 final size:34
Alignment explanation
Indices: 1238208--1238332 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
1238198 TTCGTCCTAC
1238208 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
1238242 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1238277 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
1238306 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
1238333 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1238738 original size:34 final size:32
Alignment explanation
Indices: 1238666--1238759 Score: 91
Period size: 34 Copynumber: 2.9 Consensus size: 32
1238656 TTTTTCCTAC
* *
1238666 TTTATT-ATTCTTGTTATATATGCATATTACTT
1 TTTATTAATT-TTATTATATATGTATATTACTT
* *
1238698 TCTATTAATTTTATTATATATGTATATATATTTT
1 TTTATTAATTTTATTATATATGTATAT-TA-CTT
* * *
1238732 TTTATTAGTGTTATTATATATATATATT
1 TTTATTAATTTTATTATATATGTATATT
1238760 TATATATTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 20 0.39
33 6 0.12
34 25 0.49
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (32 bp):
TTTATTAATTTTATTATATATGTATATTACTT
Found at i:1238749 original size:22 final size:21
Alignment explanation
Indices: 1238700--1238750 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
1238690 TATTACTTTC
1238700 TATTA-ATTTTATTATATATG
1 TATTATATTTTATTATATATG
*
1238720 TATATATATTTTTTTAT-TAGTG
1 TAT-TATATTTTATTATATA-TG
1238742 TTATTATAT
1 -TATTATAT
1238751 ATATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 4 0.15
22 16 0.62
23 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (21 bp):
TATTATATTTTATTATATATG
Found at i:1238854 original size:20 final size:20
Alignment explanation
Indices: 1238829--1238866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1238819 ATTATTATTA
1238829 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
1238849 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
1238867 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:1238898 original size:16 final size:18
Alignment explanation
Indices: 1238877--1238911 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1238867 TTTACTCATT
1238877 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
1238893 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
1238911 T
1 T
1238912 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:1239045 original size:16 final size:16
Alignment explanation
Indices: 1239007--1239045 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1238997 TTATTGTTTT
1239007 TTTATTTTATATTCTA
1 TTTATTTTATATTCTA
*
1239023 TTCATTTTATATT-TA
1 TTTATTTTATATTCTA
1239038 CTTTATTT
1 -TTTATTT
1239046 CTTTCTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTTATATTCTA
Found at i:1242104 original size:16 final size:16
Alignment explanation
Indices: 1242078--1242160 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
1242068 AGATCCAATC
1242078 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
1242093 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
* *
1242110 AA-AAAAAACAAAGAAA
1 AAGAACAAA-AAAGCAA
1242126 AAGAGA-AACAAGAA-CAA
1 AAGA-ACAA-AA-AAGCAA
1242143 AAGAA-AAAAAGAGCAA
1 AAGAACAAAAA-AGCAA
1242159 AA
1 AA
1242161 ATCAAAAAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.02
15 11 0.20
16 26 0.46
17 14 0.25
18 4 0.07
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:1242126 original size:22 final size:23
Alignment explanation
Indices: 1242101--1242184 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 23
1242091 AAAAGAAGCA
1242101 AAAAAGCA-AAAAAAAAAC-AAAG
1 AAAAAG-AGAAAAAAAAACAAAAG
* *
1242123 AAAAAGAGAAACAAGAACAAAAG
1 AAAAAGAGAAAAAAAAACAAAAG
* ** *
1242146 AAAAAAAGAGCAAAAATCAAAAAG
1 AAAAAGAGAAAAAAAAAC-AAAAG
* *
1242170 AAAAAGGGACAAAAA
1 AAAAAGAGAAAAAAA
1242185 GCACATGCAA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.02
22 14 0.30
23 16 0.34
24 16 0.34
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.01
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAAACAAAAG
Found at i:1242836 original size:22 final size:22
Alignment explanation
Indices: 1242811--1242859 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1242801 CCATCAATCT
* *
1242811 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
1242833 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
1242855 TTTGA
1 TTTGA
1242860 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:1243842 original size:21 final size:21
Alignment explanation
Indices: 1243816--1243855 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1243806 GACAGTTTCC
*
1243816 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTCGTCTCT
1243837 CTTGAAACAAATTTCGTCT
1 CTTGAAACAAATTTCGTCT
1243856 ATCTGGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (21 bp):
CTTGAAACAAATTTCGTCTCT
Found at i:1243885 original size:36 final size:36
Alignment explanation
Indices: 1243837--1244057 Score: 197
Period size: 36 Copynumber: 6.3 Consensus size: 36
1243827 TTTTGTCTCT
*
1243837 CTTGAAACAAATTTCGTCTATCTGGAGACAGTTTCC
1 CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCC
* * *
1243873 CTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCC
* * *
1243909 CTTGAAACAAA------ATAT-TTGA-ATATGTTTTC
1 CTTGAAACAAATTTCGTCTATCTTGAGACA-GTTTCC
* * ** *
1243938 TTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCT
1 CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCC
* * * * * *
1243974 TTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAAC-AAATTTCGTCTATCTTGAGACAGTTTCC
*
1244011 CTTGAAACAATTTTCGTCTATCTTGAGACAGTTTCC
1 CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCC
1244047 CTTGAAACAAA
1 CTTGAAACAAA
1244058 ACCTTTGAAT
Statistics
Matches: 147, Mismatches: 28, Indels: 20
0.75 0.14 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.13
30 2 0.01
35 1 0.01
36 91 0.62
37 32 0.22
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (36 bp):
CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCC
Found at i:1244015 original size:102 final size:101
Alignment explanation
Indices: 1243838--1244020 Score: 276
Period size: 102 Copynumber: 1.8 Consensus size: 101
1243828 TTTGTCTCTC
* *
1243838 TTGAAACAAATTTCGTCTATCTGGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 TTGAAACAAATTCCGTCTACCTGGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1243903 GTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
66 GTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
* * ** * *
1243939 TTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTCCGTCTACCTGGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGAC
*
1244004 AGTTTCTCTTGAAACAA
65 AGTTTCCCTTGAAACAA
1244021 TTTTCGTCTA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 32 0.44
102 40 0.56
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (101 bp):
TTGAAACAAATTCCGTCTACCTGGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
GTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
Found at i:1244046 original size:138 final size:138
Alignment explanation
Indices: 1243852--1244108 Score: 354
Period size: 138 Copynumber: 1.9 Consensus size: 138
1243842 AACAAATTTC
*
1243852 GTCTATCTGGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTATCTGGAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAAC
* * * ** * *
1243917 AAAATATTTGAATATGTTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAACATTTGAATATATTTCCCCTAAAACAAATTCCATCTCCCTTGAGACAGTTTCTTTTGGAAC
1243982 TAAGTTTT
131 TAAGTTTT
* * * *
1243990 GTCTCTCTTGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAA
1 GTCTATCTGGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAA
* * **
1244054 CAAAACCTTTGAATTTATTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAGTT
65 CAAAACATTTGAATATATTTCCCCTAAAACAAATTCCATCTCCCTTGAGACAGTT
1244109 ACTCTTGAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
137 6 0.06
138 96 0.94
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (138 bp):
GTCTATCTGGAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAAC
AAAACATTTGAATATATTTCCCCTAAAACAAATTCCATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:1244150 original size:67 final size:68
Alignment explanation
Indices: 1244032--1244188 Score: 203
Period size: 68 Copynumber: 2.4 Consensus size: 68
1244022 TTTCGTCTAT
* **
1244032 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTTATC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
1244094 TCC
66 TCC
* * * * *
1244097 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
1244162 TCC
66 TCC
* *
1244165 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1244189 ACAGATATCT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.36
68 31 0.40
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
TCC
Found at i:1245147 original size:98 final size:101
Alignment explanation
Indices: 1244827--1245239 Score: 368
Period size: 105 Copynumber: 4.0 Consensus size: 101
1244817 TCGTGCCACT
* * *
1244827 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACGAACAACTTTCCAAT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCAGT
** * * * ** * * *
1244892 -TTCAAAGCTGATTTTCCACGACGGAGGATATCATGCTACC
65 GAGCCAATCTCAACTT-CACAACGAAGGATAT--TG-GACC
* *
1244932 TATGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAGT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CCAG-
* * * *
1244996 TTCAGGGCCAATTTCAACTTCACAGCGGAGGATATTGGACC
64 -T--GAGCCAATCTCAACTTCACAACGAAGGATATTGGACC
* * * * **
1245037 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTT-C-G-G
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTG
*
1245099 AGCCAATCTCAACTTCACAACGAAGGATATTGGACT
66 AGCCAATCTCAACTTCACAACGAAGGATATTGGACC
* *
1245135 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCGGT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCAG-
* * * *
1245200 TTCAGAGCCAATTTCAACTTCACGACGGACGATATTGGAC
64 -T--GAGCCAATCTCAACTTCACAACGAAGGATATTGGAC
1245240 TTGGAACAAT
Statistics
Matches: 254, Mismatches: 39, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
98 81 0.32
99 3 0.01
100 1 0.00
101 1 0.00
103 4 0.02
104 9 0.04
105 92 0.36
106 43 0.17
108 13 0.05
109 7 0.03
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (101 bp):
CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTG
AGCCAATCTCAACTTCACAACGAAGGATATTGGACC
Found at i:1245832 original size:34 final size:34
Alignment explanation
Indices: 1245789--1245913 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
1245779 TTCGTCCTAC
1245789 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
1245823 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
*
1245858 GCTAGGATTC--A-----AAAAATAGGATATAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
1245887 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
1245914 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 12 0.16
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1246318 original size:34 final size:34
Alignment explanation
Indices: 1246246--1246345 Score: 98
Period size: 34 Copynumber: 3.0 Consensus size: 34
1246236 TTTTTCCTAC
* * *
1246246 TTTATT-ATTCTTGTTATATATGCATAT-TA-CTT
1 TTTATTAATT-TTATTATATATGTATATATATTTT
*
1246278 TCTATTAATTTTATTATATATGTATATATATTTT
1 TTTATTAATTTTATTATATATGTATATATATTTT
* * *
1246312 TTTATTAGTGTTATTATATATATATTATATATTT
1 TTTATTAATTTTATTATATATGTA-TATATATTT
1246346 CCTATTTTGC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
32 20 0.36
33 5 0.09
34 22 0.39
35 9 0.16
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (34 bp):
TTTATTAATTTTATTATATATGTATATATATTTT
Done.