Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007805.1 Hibiscus syriacus cultivar Beakdansim tig00110123_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: 2708727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:992344 original size:28 final size:27
Alignment explanation
Indices: 992281--992350 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
992271 AGACATTTAA
* *
992281 TGTAATTTATGAAAAGTATGTCATTAT
1 TGTAATTTATAAAAAGTATCTCATTAT
* *
992308 TGTAATTTATAAAAAGTTTCTCTTTGAT
1 TGTAATTTATAAAAAGTATCTCATT-AT
992336 TGTAATTTATAAAAA
1 TGTAATTTATAAAAA
992351 AATTGACGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (27 bp):
TGTAATTTATAAAAAGTATCTCATTAT
Found at i:992366 original size:28 final size:27
Alignment explanation
Indices: 992334--992408 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 27
992324 TTTCTCTTTG
*
992334 ATTGTAATTTATAAAAAAATTGACGTT
1 ATTGTAATTTATAAAAAAATAGACGTT
* *
992361 AGTTGTAATTTATAGAAAGAAAATAGTCTTT
1 A-TTGTAATTTAT--AAA-AAAATAGACGTT
992392 ATTGTAATTTATAAAAA
1 ATTGTAATTTATAAAAA
992409 GTTGTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 3 0.07
28 14 0.34
30 14 0.34
31 10 0.24
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (27 bp):
ATTGTAATTTATAAAAAAATAGACGTT
Found at i:992399 original size:30 final size:29
Alignment explanation
Indices: 992328--992407 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
992318 AAAAAGTTTC
*
992328 TCTTTGATTGTAATTTAT-AAA-AAAATTG
1 TCTTT-ATTGTAATTTATAAAAGAAAATAG
* *
992356 ACGTTAGTTGTAATTTATAGAAAGAAAATAG
1 TCTTTA-TTGTAATTTATA-AAAGAAAATAG
992387 TCTTTATTGTAATTTATAAAA
1 TCTTTATTGTAATTTATAAAA
992408 AGTTGTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.02
28 14 0.33
29 3 0.07
30 15 0.35
31 10 0.23
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.42
Consensus pattern (29 bp):
TCTTTATTGTAATTTATAAAAGAAAATAG
Found at i:992603 original size:15 final size:17
Alignment explanation
Indices: 992568--992604 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
992558 TAATTGTGAC
*
992568 ATTATTAGTGACAATAA
1 ATTATTAATGACAATAA
992585 ATTATTAATGA-AA-AA
1 ATTATTAATGACAATAA
992600 ATTAT
1 ATTAT
992605 ACTTTTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 2 0.11
17 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (17 bp):
ATTATTAATGACAATAA
Found at i:993679 original size:20 final size:19
Alignment explanation
Indices: 993642--993683 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
993632 GAATATTTTT
993642 TTAATTAAAAAAATTATAA
1 TTAATTAAAAAAATTATAA
* *
993661 TTAATTTAAATAATATATAA
1 TTAATTAAAAAAAT-TATAA
993681 TTA
1 TTA
993684 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATTAAAAAAATTATAA
Found at i:993849 original size:9 final size:9
Alignment explanation
Indices: 993827--993860 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
993817 TATTTAAAAT
993827 TTAATTTCGG
1 TTAATTT-GG
993837 TTAATTTGG
1 TTAATTTGG
*
993846 TTAATTCGG
1 TTAATTTGG
993855 TTAATT
1 TTAATT
993861 AACCGATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (9 bp):
TTAATTTGG
Found at i:998611 original size:14 final size:13
Alignment explanation
Indices: 998593--998634 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
998583 TTTATCAATA
998593 ATAATAATATAAT
1 ATAATAATATAAT
998606 ACTAATAATATAA-
1 A-TAATAATATAAT
998619 AT-ATAATATAAT
1 ATAATAATATAAT
998631 ATAA
1 ATAA
998635 ATTCGGACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 3 0.12
14 11 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:998931 original size:80 final size:80
Alignment explanation
Indices: 998836--999189 Score: 393
Period size: 80 Copynumber: 4.4 Consensus size: 80
998826 GGATGACGAG
* * * * * * * * *
998836 TCTACTCCTCTATTCATTTAGAGAATATCAGACTTGATCTGTGCCATTTTTTTGGGTATTCATAT
1 TCTACTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTCGGGTATTCAGAT
* * * *
998901 CAACTTGAATACTTA
66 AAACTTAAAGACATA
* * * * *
998916 TTTTCTCCACCATTCATTCAGGGGAGATCAGACCGGATTTGTGCCACTTTTTCGGGTATTCAGAT
1 TCTACTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTCGGGTATTCAGAT
998981 AAACTTAAAGACATA
66 AAACTTAAAGACATA
* * * * * ** *
998996 TTTTCTCCACTATTCATTCAGGGGAGATCAGACTAGATATGTGTCACTTTTTCGATTATTTAGAT
1 TCTACTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTCGGGTATTCAGAT
* * *
999061 AAATTTGAAGACTTA
66 AAACTTAAAGACATA
* * * *
999076 TCTACTCCACTATTCATTCATGGGAGATCAGACTGGATCTTTACCATTTTTTCGGGTATTCAGAT
1 TCTACTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTCGGGTATTCAGAT
*
999141 CAACTTAAAGACATA
66 AAACTTAAAGACATA
*
999156 TCTACTCCACTATTCATTCAGGAGAGATCAGACT
1 TCTACTCCACTATTCATTCAGGGGAGATCAGACT
999190 CATAAATTCT
Statistics
Matches: 227, Mismatches: 47, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
80 227 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (80 bp):
TCTACTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTCGGGTATTCAGAT
AAACTTAAAGACATA
Found at i:1004732 original size:13 final size:13
Alignment explanation
Indices: 1004693--1004734 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1004683 ATAAATCTAA
1004693 GACGCGCATTTAT
1 GACGCGCATTTAT
*
1004706 GACAC-CATTTAT
1 GACGCGCATTTAT
*
1004718 GACGCGCATTAAT
1 GACGCGCATTTAT
1004731 GACG
1 GACG
1004735 TTCATTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (13 bp):
GACGCGCATTTAT
Found at i:1004990 original size:2 final size:2
Alignment explanation
Indices: 1004983--1005029 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1004973 TTTTGTAAAT
* *
1004983 TA TA TA TA AA TA TA AA 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
1005025 TA TA T
1 TA TA T
1005030 TGTAGATTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1007411 original size:39 final size:38
Alignment explanation
Indices: 1007335--1007451 Score: 96
Period size: 39 Copynumber: 3.0 Consensus size: 38
1007325 TCATCCTCCT
* * **
1007335 CCTTTGTGGTGTTCCCTCCTCATTTTCTTTCTT-TTTTTC
1 CCTTTGT-GTG-TCCCTTCTCATTTACCCTCTTCTTTTTC
* *
1007374 CCTCTTCG-GTGTCCCTTCTCCTTT-CTCCTCTTCTTTTTT
1 CCT-TT-GTGTGTCCCTTCTCATTTAC-CCTCTTCTTTTTC
*
1007413 CCTTTGTTGTGTCCCTTCTCATTTACCCTCTTCATTTTC
1 CCTTTG-TGTGTCCCTTCTCATTTACCCTCTTCTTTTTC
1007452 TTTCTCTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
37 2 0.03
38 17 0.27
39 40 0.63
40 3 0.05
41 1 0.02
ACGTcount: A:0.03, C:0.33, G:0.09, T:0.55
Consensus pattern (38 bp):
CCTTTGTGTGTCCCTTCTCATTTACCCTCTTCTTTTTC
Found at i:1018724 original size:3 final size:3
Alignment explanation
Indices: 1018718--1018773 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
1018708 ATGTATTATT
* *
1018718 TAA TAA TAA TAA TTA TAA TAA TAA T-A TAA TAC TAA TAA T-A TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
1018764 TAA T-A TAA TA
1 TAA TAA TAA TA
1018774 TAAACTCGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 7 0.16
3 36 0.82
4 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1018922 original size:18 final size:19
Alignment explanation
Indices: 1018887--1018923 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1018877 CACGGAATGT
1018887 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1018907 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1018924 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1019095 original size:15 final size:15
Alignment explanation
Indices: 1019077--1019107 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1019067 AAATTCTAAA
1019077 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1019092 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1019107 T
1 T
1019108 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1024232 original size:19 final size:19
Alignment explanation
Indices: 1024197--1024234 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1024187 CTCACATTTC
*
1024197 ATATAGATTTTAAACTTTT
1 ATATAGATTTAAAACTTTT
1024216 ATATA-ATTTAAATACTTTT
1 ATATAGATTTAAA-ACTTTT
1024235 TATTGATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (19 bp):
ATATAGATTTAAAACTTTT
Found at i:1026432 original size:19 final size:19
Alignment explanation
Indices: 1026408--1026486 Score: 140
Period size: 19 Copynumber: 4.2 Consensus size: 19
1026398 GCGCTGCAGG
1026408 GGGCGCTCCTTACTACAAA
1 GGGCGCTCCTTACTACAAA
1026427 GGGCGCTCCTTACTACAAA
1 GGGCGCTCCTTACTACAAA
*
1026446 GGGCGTTCCTTACTACAAA
1 GGGCGCTCCTTACTACAAA
*
1026465 GGGCGCTCCTTACTGCAAA
1 GGGCGCTCCTTACTACAAA
1026484 GGG
1 GGG
1026487 TGTTAGATCG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 57 1.00
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (19 bp):
GGGCGCTCCTTACTACAAA
Found at i:1028173 original size:199 final size:199
Alignment explanation
Indices: 1027827--1028226 Score: 746
Period size: 199 Copynumber: 2.0 Consensus size: 199
1027817 TGGCCAGATC
1027827 CAACGGCCCCAAGTGTAACCAGCAGAAACCCTAGGGCACTCATTGTAACCCTAGGGCTATTTCGG
1 CAACGGCCCCAAGTGTAACCAGCAGAAACCCTAGGGCACTCATTGTAACCCTAGGGCTATTTCGG
* * *
1027892 CCGCTGCCATAGTGTTATGATGCCTCCGTCGCCGAACGCTCCAACCAACAGATGCCACGACACTA
66 CCGCCGCCATAGTATTATGATGCCTCCGTCGCCGAACGCTCCAACCAACAGATGCCACGACAATA
1027957 CCACGTCATAACCGGATCCACGAGATCTGGGTGCATTTAATACACCCAGTCCCTCCACCGCACAG
131 CCACGTCATAACCGGATCCACGAGATCTGGGTGCATTTAATACACCCAGTCCCTCCACCGCACAG
1028022 CTCA
196 CTCA
1028026 CAACGGCCCCAAGTGTAACCAGCAGAAACCCTAGGGCACTCATTGTAACCCTAGGGCTATTTCGG
1 CAACGGCCCCAAGTGTAACCAGCAGAAACCCTAGGGCACTCATTGTAACCCTAGGGCTATTTCGG
1028091 CCGCCGCCATAGTATTATGATGCCTCCGTCGCCGAACGCTCCAACCAACAGATGCCACGACAATA
66 CCGCCGCCATAGTATTATGATGCCTCCGTCGCCGAACGCTCCAACCAACAGATGCCACGACAATA
* **
1028156 CCACGTCGTCGCCGGATCCACGAGATCTGGGTGCATTTAATACACCCAGTCCCTCCACCGCACAG
131 CCACGTCATAACCGGATCCACGAGATCTGGGTGCATTTAATACACCCAGTCCCTCCACCGCACAG
1028221 CTCA
196 CTCA
1028225 CA
1 CA
1028227 GCCCCTAGGG
Statistics
Matches: 195, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
199 195 1.00
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.18
Consensus pattern (199 bp):
CAACGGCCCCAAGTGTAACCAGCAGAAACCCTAGGGCACTCATTGTAACCCTAGGGCTATTTCGG
CCGCCGCCATAGTATTATGATGCCTCCGTCGCCGAACGCTCCAACCAACAGATGCCACGACAATA
CCACGTCATAACCGGATCCACGAGATCTGGGTGCATTTAATACACCCAGTCCCTCCACCGCACAG
CTCA
Found at i:1029173 original size:18 final size:18
Alignment explanation
Indices: 1029150--1029184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1029140 ACTAATTATA
* *
1029150 ATATTAGTATAATTTTAC
1 ATATTAGGATAACTTTAC
1029168 ATATTAGGATAACTTTA
1 ATATTAGGATAACTTTA
1029185 TAATATAGTT
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:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
ATATTAGGATAACTTTAC
Found at i:1040605 original size:66 final size:65
Alignment explanation
Indices: 1040528--1040688 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 65
1040518 GAAAAAATTG
* * *
1040528 AACATCGAATGCATTAT-ATGCATCGATGCACATA-CCATTCATCGATGCACTCAGGTTTTTTAT
1 AACATCGAATGCATTATCATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTTGTT-T
1040591 GAA
64 G-A
* *
1040594 AACATCGAATGCATT-TGATGCATCGATGCACAAGCCATGCATCGATGCACTCGGGCTTGTTTGA
1 AACATCGAATGCATTATCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
* *
1040658 AACATCGAATGCA-CATCATGCATCAATGCAC
1 AACATCGAATGCATTATCATGCATCGATGCAC
1040689 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
64 28 0.33
65 4 0.05
66 53 0.62
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTATCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
Found at i:1046558 original size:44 final size:44
Alignment explanation
Indices: 1046466--1046560 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
1046456 GTGCTTAATG
* * *
1046466 CATCGATACATTGAACAGTGCATCGATGCATCCCTTTGTATGTG
1 CATCGATACATTGAACAGTGCACCGATGCATCCCTTTGAATGTA
*
1046510 CATCGATACATCATGAAGA-TGCACCGATGCA-CTCC-TTGAATGTA
1 CATCGATACAT--TGAACAGTGCACCGATGCATC-CCTTTGAATGTA
1046554 CATCGAT
1 CATCGAT
1046561 GCACAAAGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
44 26 0.59
45 13 0.30
46 5 0.11
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
CATCGATACATTGAACAGTGCACCGATGCATCCCTTTGAATGTA
Found at i:1049369 original size:64 final size:65
Alignment explanation
Indices: 1049255--1049375 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 65
1049245 AATGCATTAT
* * *
1049255 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACAAGCC
1 ATGCATCGATGCACTCAGGTTGTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGCC
*
1049320 ATGCATCGATGCACTCGGGCTTGTT-TG-AAACATCGAATGCACTTCATGCATCGATG
1 ATGCATCGATGCACTCAGG-TTGTTATGAAAACATCGAATGCACTTCATGCATCGATG
1049376 GACTCTTAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 27 0.53
65 20 0.39
66 4 0.08
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (65 bp):
ATGCATCGATGCACTCAGGTTGTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGCC
Found at i:1050529 original size:36 final size:36
Alignment explanation
Indices: 1050474--1050647 Score: 235
Period size: 36 Copynumber: 4.8 Consensus size: 36
1050464 TTTTCAAGTC
* * *
1050474 AATCAAGGCTTCACTAAAGAGTAGTGAAGCAATACG
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCGATACG
*
1050510 AATCAAGCCTTCCCAAAAGAGTAGTGAAGCGATACG
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCGATACG
*
1050546 AATCAAGCCTTCACAAAAGAGTAGTGAAGCGATACA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCGATACG
* * *
1050582 AATCAAGCTTTCACAAAAGAGTAGTAAAGCGATGC-
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCGATACG
*
1050617 ACATCCAA-CCTTCACAAAAGAGTAATGAAGC
1 A-AT-CAAGCCTTCACAAAAGAGTAGTGAAGC
1050648 AGGAACAAAT
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
35 1 0.01
36 120 0.97
37 3 0.02
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (36 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCGATACG
Found at i:1050852 original size:13 final size:13
Alignment explanation
Indices: 1050834--1050865 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1050824 TTATAAGTAT
1050834 TATTATTATATAA
1 TATTATTATATAA
*
1050847 TATTATTATATTA
1 TATTATTATATAA
1050860 TATTAT
1 TATTAT
1050866 ATTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTATTATATAA
Found at i:1052000 original size:2 final size:2
Alignment explanation
Indices: 1051993--1052036 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1051983 CACTGCTACG
1051993 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
1052035 TA
1 TA
1052037 GGGTACAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1052780 original size:22 final size:23
Alignment explanation
Indices: 1052736--1052781 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1052726 GACATTAAAA
*
1052736 ATTAATTAAATAAATCATTTATT
1 ATTAATTAAAAAAATCATTTATT
*
1052759 ATTATTTAAAAAAAT-ATTTATT
1 ATTAATTAAAAAAATCATTTATT
1052781 A
1 A
1052782 GATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTAATTAAAAAAATCATTTATT
Found at i:1052808 original size:17 final size:18
Alignment explanation
Indices: 1052773--1052813 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1052763 TTTAAAAAAA
*
1052773 TATTTATTAGATTATTAT
1 TATTTATTAGATAATTAT
1052791 T-TTTATT-GATAATATAT
1 TATTTATTAGATAAT-TAT
1052808 TATTTA
1 TATTTA
1052814 ATAAAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.25
17 10 0.50
18 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TATTTATTAGATAATTAT
Found at i:1053909 original size:30 final size:30
Alignment explanation
Indices: 1053873--1053937 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1053863 AGTGAATCGG
**
1053873 CGGTTCAAACC-GGTTTTGTCGGTTTTCAGC
1 CGGTTC-AACCTGGTTTTACCGGTTTTCAGC
* *
1053903 CGGTTCACCCTGGTTTTACCGGTTTTCAGT
1 CGGTTCAACCTGGTTTTACCGGTTTTCAGC
1053933 CGGTT
1 CGGTT
1053938 TATTGCCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.11, C:0.25, G:0.26, T:0.38
Consensus pattern (30 bp):
CGGTTCAACCTGGTTTTACCGGTTTTCAGC
Found at i:1060016 original size:26 final size:25
Alignment explanation
Indices: 1059987--1060067 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
1059977 TTAATTTAAA
1059987 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
* * *
1060013 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTT-AT
1060038 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
1060064 CTAA
1 CTAA
1060068 CTTTCTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Found at i:1060029 original size:25 final size:24
Alignment explanation
Indices: 1060001--1060081 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
1059991 ACTACTTAGT
1060001 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * *
1060026 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
1060051 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
1060077 AGTTA
1 AGTTA
1060082 GTGTTATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 2 0.05
25 22 0.51
26 17 0.40
27 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:1060053 original size:51 final size:51
Alignment explanation
Indices: 1059977--1060081 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
1059967 GAACAAGTAT
1059977 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
*
1060028 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1060079 TTA
1 TTA
1060082 GTGTTATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:1060973 original size:20 final size:20
Alignment explanation
Indices: 1060948--1061046 Score: 101
Period size: 20 Copynumber: 4.7 Consensus size: 20
1060938 AAAAGCCTGA
*
1060948 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGTCAT
1060968 GTGCATCGATGCATGGTCAT
1 GTGCATCGATGCATGGTCAT
**
1060988 GTGCATCGATGCATCAAATGCACT
1 GTGCATCGATGCAT--GGT-CA-T
*
1061012 GAGTGCATTGATGCATGGT-AT
1 --GTGCATCGATGCATGGTCAT
1061033 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1061047 AAAATGCATT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.20
20 33 0.50
21 1 0.02
22 2 0.03
23 2 0.03
24 2 0.03
26 13 0.20
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATGGTCAT
Found at i:1061046 original size:45 final size:46
Alignment explanation
Indices: 1060968--1061054 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 46
1060958 GCATGGTCTT
*
1060968 GTGCATCGATGCATGGTCATGTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTGA
*
1061014 GTGCATTGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 GTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
1061055 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 23 0.59
46 16 0.41
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (46 bp):
GTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTGA
Found at i:1061102 original size:20 final size:20
Alignment explanation
Indices: 1061074--1061112 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1061064 CTAGAAATTA
1061074 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
1061094 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1061113 CCCTTGAAAA
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:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:1062182 original size:18 final size:18
Alignment explanation
Indices: 1062159--1062201 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1062149 GTCAGAAGCC
1062159 GGAGCAGGAGGAGGAG-GA
1 GGAGCAGGA-GAGGAGCGA
* *
1062177 GGAGCACGAGAGGAGCTA
1 GGAGCAGGAGAGGAGCGA
1062195 GGAGCAG
1 GGAGCAG
1062202 CTCATGAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.33, C:0.12, G:0.53, T:0.02
Consensus pattern (18 bp):
GGAGCAGGAGAGGAGCGA
Found at i:1069750 original size:45 final size:46
Alignment explanation
Indices: 1069661--1069751 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
1069651 TTAAAAAAGC
* * *
1069661 CTGAGTGCATCGATGCATGGTCTTGTGCATAAATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATAAATGCATAAAATGCA
**
1069707 CTGAGTGCATCGATGCATGGT-ATATGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATAAATGCATAAAATGCA
1069752 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 19 0.47
46 21 0.52
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATATGCATAAATGCATAAAATGCA
Found at i:1074734 original size:25 final size:26
Alignment explanation
Indices: 1074706--1074774 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
1074696 TTATCCTTAT
1074706 CTAACTTTCTAAGAGTTAAT-TTAAA
1 CTAACTTTCTAAGAGTTAATCTTAAA
* * * *
1074731 CTAAAC-TACTTAGTAGTT-ATCTTTAT
1 CT-AACTTTCTAAG-AGTTAATCTTAAA
1074757 CTAACTTTCTAAGAGTTA
1 CTAACTTTCTAAGAGTTA
1074775 GTGTTATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (26 bp):
CTAACTTTCTAAGAGTTAATCTTAAA
Found at i:1074751 original size:51 final size:51
Alignment explanation
Indices: 1074674--1074811 Score: 177
Period size: 51 Copynumber: 2.7 Consensus size: 51
1074664 AAGTATTTAG
*
1074674 TTTAAAATAAACTACTTAGTATTTATCCTTATCTAACTTTCTAAGAGTTAA
1 TTTAAAATAAACTACTTAGTAATTATCCTTATCTAACTTTCTAAGAGTTAA
* * * *
1074725 TTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAGTTAG
1 TTTAAAATAAACTACTTAGTAATTATCCTTATCTAACTTTCTAAGAGTTAA
* * * * *
1074776 TGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 T-TTAAAATAAACTACTTAGTAATTATCCTTATCTA
1074812 TTGCATAACC
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 48 0.64
52 27 0.36
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (51 bp):
TTTAAAATAAACTACTTAGTAATTATCCTTATCTAACTTTCTAAGAGTTAA
Found at i:1074760 original size:26 final size:26
Alignment explanation
Indices: 1074681--1074760 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
1074671 TAGTTTAAAA
* *
1074681 TAAACTACTTAGTATTTATCCTTATC
1 TAAACTACTTAGTAGTTATCTTTATC
* * * *
1074707 T-AACTTTCTAAG-AGTTAAT-TTAAAC
1 TAAAC-TACTTAGTAGTT-ATCTTTATC
1074732 TAAACTACTTAGTAGTTATCTTTATC
1 TAAACTACTTAGTAGTTATCTTTATC
1074758 TAA
1 TAA
1074761 CTTTCTAAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
25 17 0.44
26 22 0.56
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (26 bp):
TAAACTACTTAGTAGTTATCTTTATC
Found at i:1074781 original size:25 final size:23
Alignment explanation
Indices: 1074702--1074774 Score: 58
Period size: 25 Copynumber: 3.0 Consensus size: 23
1074692 GTATTTATCC
1074702 TTATCTAACTTTCTAAGAGTTAAT
1 TTATCTAACTTTCTAAGAGTT-AT
* * *
1074726 TTAAACTAAAC-TACTTAGTAGTTATCT
1 TT-ATCT-AACTTTCTAAG-AGTTA--T
1074753 TTATCTAACTTTCTAAGAGTTA
1 TTATCTAACTTTCTAAGAGTTA
1074775 GTGTTATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 2 0.05
25 17 0.46
26 15 0.41
27 3 0.08
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (23 bp):
TTATCTAACTTTCTAAGAGTTAT
Found at i:1075947 original size:46 final size:46
Alignment explanation
Indices: 1075875--1075983 Score: 209
Period size: 46 Copynumber: 2.4 Consensus size: 46
1075865 ATACTGGTTA
*
1075875 ACATGTTCATCATATATACTTTCACAATCTGTTCTTGTTTGTACAT
1 ACATGTTCATCATATATACTTCCACAATCTGTTCTTGTTTGTACAT
1075921 ACATGTTCATCATATATACTTCCACAATCTGTTCTTGTTTGTACAT
1 ACATGTTCATCATATATACTTCCACAATCTGTTCTTGTTTGTACAT
1075967 ACATGTTCATCATATAT
1 ACATGTTCATCATATAT
1075984 CCTTGTTGTG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (46 bp):
ACATGTTCATCATATATACTTCCACAATCTGTTCTTGTTTGTACAT
Found at i:1083765 original size:14 final size:15
Alignment explanation
Indices: 1083748--1083785 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1083738 AAAATGCAAT
1083748 AATTAAAGGACT-AA
1 AATTAAAGGACTGAA
*
1083762 AATTAAAGTACTGAA
1 AATTAAAGGACTGAA
*
1083777 AAATAAAGG
1 AATTAAAGG
1083786 GCAAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (15 bp):
AATTAAAGGACTGAA
Found at i:1085535 original size:22 final size:22
Alignment explanation
Indices: 1085507--1085557 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1085497 CTTTATGAAC
*
1085507 TTCTTCTCACTCCTTAAACAAG
1 TTCTTCTCACTCCTCAAACAAG
**
1085529 TTCTTCTCACTCCTCAAATGAG
1 TTCTTCTCACTCCTCAAACAAG
1085551 TTCTTCT
1 TTCTTCT
1085558 TATTCTGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (22 bp):
TTCTTCTCACTCCTCAAACAAG
Found at i:1085880 original size:66 final size:66
Alignment explanation
Indices: 1085738--1086060 Score: 328
Period size: 67 Copynumber: 4.9 Consensus size: 66
1085728 AAGAAATTTG
* * * * * * *
1085738 TTTCAAGAGAAGCTATCTCATGTGAGATAAATTTTTGTTTCGAGTGAAACAATCTCAAAGGTTTA
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAA-ATTTGTTTCGAGAGAAACAATCTCAAAGGTTTA
*
1085803 TG
65 TA
* ** ** * * *
1085805 TTTCCAGAGAAACCATCTCAAGCGAGATGAAATTTATTTTGAGAGAAAAAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
1085870 A
66 A
* * * *
1085871 TTTCAAGAGAAATTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAATAATATCAAAGGTTTA
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTCGAGAGAAACAATCTCAAAGGTTTA
1085936 TGA
65 T-A
* * * * *
1085939 -TTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTGTTTAGAGATAAACAATATCAAAGG-TT-T
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
1086001 A
66 A
* * * * *
1086002 TGTCAAGTGAAACTGTCTCAAGCCAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAG
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCGAGAGAAACAATCTCAAAG
1086061 CAGACAGACA
Statistics
Matches: 213, Mismatches: 40, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
63 1 0.00
64 49 0.23
65 2 0.01
66 79 0.37
67 81 0.38
68 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (66 bp):
TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
A
Found at i:1085995 original size:133 final size:130
Alignment explanation
Indices: 1085771--1086060 Score: 373
Period size: 133 Copynumber: 2.2 Consensus size: 130
1085761 GAGATAAATT
* * * * * * **
1085771 TTTGTTTCGAGTGAAACAATCTCAAAGGTTTATGTTTCCAGAGAAACCATCTCAAGCGAGATGAA
1 TTTGTTTCAAGAGAAATAATCTCAAAGGTTTATGATTCAAGAGAAACCATCTCAAGAGAGAAAAA
* * * * *
1085836 ATTTATTTTGAGAGAAAAAATCTCAAAGGTTTATATTTCAAGAGAAATTGTCTCAAGCGAGACAA
66 ATTTATTTAGAGAGAAAAAATATCAAAGG-TT-TATGTCAAGAGAAACTGTCTCAAGCCAGACAA
1085901 AA
129 AA
* **
1085903 CTTTGTTTCAAGAGAAATAATATCAAAGGTTTATGATTCAAGAGAAACTGTCTCAAGAGAGAAAA
1 -TTTGTTTCAAGAGAAATAATCTCAAAGGTTTATGATTCAAGAGAAACCATCTCAAGAGAGAAAA
* * * *
1085968 AATTTGTTTAGAGATAAACAATATCAAAGGTTTATGTCAAGTGAAACTGTCTCAAGCCAGACAAA
65 AATTTATTTAGAGAGAAAAAATATCAAAGGTTTATGTCAAGAGAAACTGTCTCAAGCCAGACAAA
1086033 A
130 A
1086034 TTTGTTTCAAGAGAAATAATCTCAAAG
1 TTTGTTTCAAGAGAAATAATCTCAAAG
1086061 CAGACAGACA
Statistics
Matches: 136, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
130 26 0.19
131 30 0.22
132 2 0.01
133 78 0.57
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (130 bp):
TTTGTTTCAAGAGAAATAATCTCAAAGGTTTATGATTCAAGAGAAACCATCTCAAGAGAGAAAAA
ATTTATTTAGAGAGAAAAAATATCAAAGGTTTATGTCAAGAGAAACTGTCTCAAGCCAGACAAAA
Found at i:1091556 original size:14 final size:14
Alignment explanation
Indices: 1091537--1091566 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1091527 GCAATGCAAT
*
1091537 AATTAAAGGACTAA
1 AATTAAAGCACTAA
1091551 AATTAAAGCACTAA
1 AATTAAAGCACTAA
1091565 AA
1 AA
1091567 AGTAAAGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (14 bp):
AATTAAAGCACTAA
Found at i:1092282 original size:24 final size:24
Alignment explanation
Indices: 1092246--1092292 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
1092236 TCTTCTTTTC
1092246 TTTATTTTCAAGTTTTCATTTTTAT
1 TTTATTTTCAAGTTTT-ATTTTTAT
1092271 TTTATTTT-AAGTTTTATTTTTA
1 TTTATTTTCAAGTTTTATTTTTA
1092293 AACATGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATTTTCAAGTTTTATTTTTAT
Found at i:1092285 original size:12 final size:12
Alignment explanation
Indices: 1092246--1092290 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
1092236 TCTTCTTTTC
1092246 TTTATTTTCAAGT
1 TTTATTTT-AAGT
*
1092259 TTTCATTTTTA-T
1 TTT-ATTTTAAGT
1092271 TTTATTTTAAGT
1 TTTATTTTAAGT
1092283 TTTATTTT
1 TTTATTTT
1092291 TAAACATGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 13 0.46
13 4 0.14
14 5 0.18
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTATTTTAAGT
Found at i:1093303 original size:18 final size:18
Alignment explanation
Indices: 1093280--1093318 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1093270 ACAACAACAA
* *
1093280 TCAGATCTATAATCGAGT
1 TCAGATCTAGAATCAAGT
*
1093298 TCAGATTTAGAATCAAGT
1 TCAGATCTAGAATCAAGT
1093316 TCA
1 TCA
1093319 AGTGAATCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (18 bp):
TCAGATCTAGAATCAAGT
Found at i:1093596 original size:30 final size:29
Alignment explanation
Indices: 1093565--1093632 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1093555 AAAAATAAAT
1093565 AAATAAATATAATAGTGGCTAAATTGGAATA
1 AAATAAA-A-AATAGTGGCTAAATTGGAATA
* **
1093596 AAATAAAACATAGTGGCTAAATTAAAATA
1 AAATAAAAAATAGTGGCTAAATTGGAATA
1093625 AAATAAAA
1 AAATAAAA
1093633 CAATGTGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 26 0.76
30 1 0.03
31 7 0.21
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (29 bp):
AAATAAAAAATAGTGGCTAAATTGGAATA
Found at i:1093611 original size:29 final size:29
Alignment explanation
Indices: 1093576--1093634 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1093566 AATAAATATA
**
1093576 ATAGTGGCTAAATTGGAATAAAATAAAAC
1 ATAGTGGCTAAATTAAAATAAAATAAAAC
1093605 ATAGTGGCTAAATTAAAATAAAATAAAAC
1 ATAGTGGCTAAATTAAAATAAAATAAAAC
1093634 A
1 A
1093635 ATGTGAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.24
Consensus pattern (29 bp):
ATAGTGGCTAAATTAAAATAAAATAAAAC
Found at i:1098000 original size:20 final size:21
Alignment explanation
Indices: 1097955--1098003 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
1097945 TTTTCATCCA
1097955 TTTGTAACTCGTGTAATTACAC
1 TTTGTAACTCGTGTAATTA-AC
*
1097977 TTTGTAACTCTTGTAATT-AC
1 TTTGTAACTCGTGTAATTAAC
1097997 TTTGTAA
1 TTTGTAA
1098004 TTGGCACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 9 0.35
22 17 0.65
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTGTAACTCGTGTAATTAAC
Found at i:1099523 original size:41 final size:41
Alignment explanation
Indices: 1099465--1099584 Score: 161
Period size: 40 Copynumber: 3.0 Consensus size: 41
1099455 GTTCAAAAAA
* *
1099465 AAAAAAAACTTGCTCCTCCATCTTGAGGTCTTGACACTTTG
1 AAAAATAACTTGTTCCTCCATCTTGAGGTCTTGACACTTTG
*
1099506 AAAAATAACTTGTTCCT-CATCTTGAAGTCTTGACACTTTG
1 AAAAATAACTTGTTCCTCCATCTTGAGGTCTTGACACTTTG
* * * * *
1099546 AAAAATAATTTGTTCGTCTATCTTAAGGTCGTGACACTT
1 AAAAATAACTTGTTCCTCCATCTTGAGGTCTTGACACTT
1099585 CAAAATATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 37 0.54
41 32 0.46
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (41 bp):
AAAAATAACTTGTTCCTCCATCTTGAGGTCTTGACACTTTG
Found at i:1106624 original size:19 final size:19
Alignment explanation
Indices: 1106600--1106638 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1106590 ATTTAATCAA
1106600 ACGTTAAGAGTATTTTTTG
1 ACGTTAAGAGTATTTTTTG
* **
1106619 ACGTTATGCTTATTTTTTG
1 ACGTTAAGAGTATTTTTTG
1106638 A
1 A
1106639 GGTAACAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (19 bp):
ACGTTAAGAGTATTTTTTG
Found at i:1109191 original size:21 final size:20
Alignment explanation
Indices: 1109140--1109192 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1109130 CATACCACTA
1109140 CTGTAGGGTTACATACCGAG
1 CTGTAGGGTTACATACCGAG
* *
1109160 ATCGTAGGGTTACATATCGAG
1 CT-GTAGGGTTACATACCGAG
*
1109181 CCTGTAAGGTTA
1 -CTGTAGGGTTA
1109193 AATTCTAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
CTGTAGGGTTACATACCGAG
Found at i:1111633 original size:15 final size:16
Alignment explanation
Indices: 1111613--1111645 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1111603 ATTACCGTTC
1111613 TTTCTTTC-TGTACTA
1 TTTCTTTCTTGTACTA
1111628 TTTCTTTCTTGTACTA
1 TTTCTTTCTTGTACTA
1111644 TT
1 TT
1111646 CTTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.12, C:0.18, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTCTTTCTTGTACTA
Found at i:1111705 original size:12 final size:11
Alignment explanation
Indices: 1111684--1111729 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1111674 ATTCTTTTTC
1111684 TTTT-CTATAT
1 TTTTACTATAT
1111694 CTTTTACTATAT
1 -TTTTACTATAT
*
1111706 TGTTA-TAT-T
1 TTTTACTATAT
1111715 TTTTACTATAT
1 TTTTACTATAT
1111726 TTTT
1 TTTT
1111730 TCTTTTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 5 0.17
10 6 0.20
11 13 0.43
12 6 0.20
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTTACTATAT
Found at i:1111718 original size:20 final size:20
Alignment explanation
Indices: 1111689--1111726 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1111679 TTTTCTTTTC
1111689 TATATCTTTTACTATATTGT
1 TATATCTTTTACTATATTGT
*
1111709 TATATTTTTTACTATATT
1 TATATCTTTTACTATATT
1111727 TTTTCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TATATCTTTTACTATATTGT
Found at i:1116710 original size:33 final size:33
Alignment explanation
Indices: 1116673--1116746 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1116663 TATGCCTTTA
1116673 TGTATAACAATGTAACTTAGGTGCTTATATGCT
1 TGTATAACAATGTAACTTAGGTGCTTATATGCT
*
1116706 TGTATAACAATGTAACTTTGGTGCTTATATGCT
1 TGTATAACAATGTAACTTAGGTGCTTATATGCT
*
1116739 TGTGTAAC
1 TGTATAAC
1116747 GATGGAAACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (33 bp):
TGTATAACAATGTAACTTAGGTGCTTATATGCT
Found at i:1119475 original size:19 final size:19
Alignment explanation
Indices: 1119453--1119553 Score: 55
Period size: 19 Copynumber: 5.3 Consensus size: 19
1119443 AGGTTGCAAC
*
1119453 TGAAAATCTAGTTTCCATA
1 TGAAAATCTAGTTTCAATA
* *
1119472 TGAAAAATC-ATGTTGCAATC
1 TG-AAAATCTA-GTTTCAATA
* * *
1119492 T-TAAATCTGGTTTCCATA
1 TGAAAATCTAGTTTCAATA
* *
1119510 TGAAAATC-AGGTTGCAATC
1 TGAAAATCTA-GTTTCAATA
* * *
1119529 TAAAAATCTGGTTTCTATA
1 TGAAAATCTAGTTTCAATA
1119548 TGAAAA
1 TGAAAA
1119554 ATCAGGTTGC
Statistics
Matches: 57, Mismatches: 19, Indels: 12
0.65 0.22 0.14
Matches are distributed among these distances:
18 12 0.21
19 32 0.56
20 13 0.23
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (19 bp):
TGAAAATCTAGTTTCAATA
Found at i:1119572 original size:19 final size:19
Alignment explanation
Indices: 1119474--1119572 Score: 74
Period size: 19 Copynumber: 5.2 Consensus size: 19
1119464 TTTCCATATG
*
1119474 AAAAATCATGTTGCAATCT
1 AAAAATCAGGTTGCAATCT
* * * * *
1119493 -TAAATCTGGTTTCCATAT
1 AAAAATCAGGTTGCAATCT
*
1119511 GAAAATCAGGTTGCAATCT
1 AAAAATCAGGTTGCAATCT
* * * *
1119530 AAAAATCTGGTTTCTATAT
1 AAAAATCAGGTTGCAATCT
*
1119549 GAAAAATCAGGTTGCAACCT
1 -AAAAATCAGGTTGCAATCT
1119569 AAAA
1 AAAA
1119573 TGTTGTTTTT
Statistics
Matches: 57, Mismatches: 21, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
18 12 0.21
19 31 0.54
20 14 0.25
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (19 bp):
AAAAATCAGGTTGCAATCT
Found at i:1119655 original size:38 final size:38
Alignment explanation
Indices: 1119436--1119645 Score: 235
Period size: 38 Copynumber: 5.5 Consensus size: 38
1119426 ATTTCAATAC
* * *
1119436 AAAAATTAGGTTGCAA-CTGAAAATCTAGTTTCCATATG
1 AAAAATCAGGTTGCAATCT-AAAATCTGGTTTCTATATG
* * *
1119474 AAAAATCATGTTGCAATCTTAAATCTGGTTTCCATATG
1 AAAAATCAGGTTGCAATCTAAAATCTGGTTTCTATATG
1119512 -AAAATCAGGTTGCAATCTAAAAATCTGGTTTCTATATG
1 AAAAATCAGGTTGCAATCT-AAAATCTGGTTTCTATATG
* * * *
1119550 AAAAATCAGGTTGCAACCTAAAATGTTGTTTTTATATG
1 AAAAATCAGGTTGCAATCTAAAATCTGGTTTCTATATG
* * * * *
1119588 AAAAATCAGGTTGTAACCTAAATTATGGTTTCTATTTG
1 AAAAATCAGGTTGCAATCTAAAATCTGGTTTCTATATG
* *
1119626 AAAAACCAGTTTGCAATCTA
1 AAAAATCAGGTTGCAATCTA
1119646 TAAAGTGGTT
Statistics
Matches: 148, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
37 17 0.11
38 112 0.76
39 19 0.13
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (38 bp):
AAAAATCAGGTTGCAATCTAAAATCTGGTTTCTATATG
Found at i:1119655 original size:114 final size:114
Alignment explanation
Indices: 1119436--1119645 Score: 262
Period size: 114 Copynumber: 1.8 Consensus size: 114
1119426 ATTTCAATAC
* * * *
1119436 AAAAATTAGGTTGCAACTGAAAATCTAGTTTCCATATGAAAAATCATGTTGCAATCTTAAATCTG
1 AAAAATCAGGTTGCAACTGAAAATCTAGTTTCCATATGAAAAATCAGGTTGCAATCCTAAATATG
*
1119501 GTTTCCATATGAAAATCAGGTTGCAATCTAAAAATCTGGTTTCTATATG
66 GTTTCCATATGAAAACCAGGTTGCAATCTAAAAATCTGGTTTCTATATG
* * ** *
1119550 AAAAATCAGGTTGCAACCT-AAAATGTTGTTTTTATATGAAAAATCAGGTTGTAA-CCTAAATTA
1 AAAAATCAGGTTGCAA-CTGAAAATCTAGTTTCCATATGAAAAATCAGGTTGCAATCCTAAA-TA
* * *
1119613 TGGTTTCTATTTGAAAAACCAGTTTGCAATCTA
64 TGGTTTCCATATG-AAAACCAGGTTGCAATCTA
1119646 TAAAGTGGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
113 5 0.06
114 56 0.70
115 19 0.24
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (114 bp):
AAAAATCAGGTTGCAACTGAAAATCTAGTTTCCATATGAAAAATCAGGTTGCAATCCTAAATATG
GTTTCCATATGAAAACCAGGTTGCAATCTAAAAATCTGGTTTCTATATG
Found at i:1120500 original size:107 final size:108
Alignment explanation
Indices: 1120304--1120519 Score: 416
Period size: 107 Copynumber: 2.0 Consensus size: 108
1120294 ATGGTAAAAC
1120304 GAAGAGAATGTAAGCTTATATAGTTTAGTGAGGTAGCAAACACAAAACAAATCAAATGCAAATGA
1 GAAGAGAA-GTAAGCTTATATAGTTTAGTGAGGTAGCAAACACAAAACAAATCAAATGCAAATGA
1120369 CATACTTGGTTGTTCTTGATATACTTGAATGGAAAATGACAAAT
65 CATACTTGGTTGTTCTTGATATACTTGAATGGAAAATGACAAAT
1120413 GAAGAGAA-TAAGCTTATATAGTTTAGTGAGGTAGCAAACACAAAACAAATCAAATGCAAATGAC
1 GAAGAGAAGTAAGCTTATATAGTTTAGTGAGGTAGCAAACACAAAACAAATCAAATGCAAATGAC
1120477 ATACTTGGTTGTTCTTGATATACTTGAATGGAAAATGACAAAT
66 ATACTTGGTTGTTCTTGATATACTTGAATGGAAAATGACAAAT
1120520 AATAGATATT
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 99 0.93
109 8 0.07
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (108 bp):
GAAGAGAAGTAAGCTTATATAGTTTAGTGAGGTAGCAAACACAAAACAAATCAAATGCAAATGAC
ATACTTGGTTGTTCTTGATATACTTGAATGGAAAATGACAAAT
Found at i:1121146 original size:21 final size:21
Alignment explanation
Indices: 1121122--1121176 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1121112 TAGACACCTT
1121122 GAGTATCGGTACTCGGGCTTG
1 GAGTATCGGTACTCGGGCTTG
1121143 GAGTATCGGTACTCGGGCTTG
1 GAGTATCGGTACTCGGGCTTG
1121164 GAGTATCGGTACT
1 GAGTATCGGTACT
1121177 GCCTTACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.16, C:0.18, G:0.36, T:0.29
Consensus pattern (21 bp):
GAGTATCGGTACTCGGGCTTG
Found at i:1122087 original size:30 final size:30
Alignment explanation
Indices: 1122047--1122123 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
1122037 AGAATGGTCC
* *
1122047 CCCTCTAACATCGCCAATGATCAATAACAT
1 CCCTCAAACATCGCCAATGACCAATAACAT
* *
1122077 CCCTCCAACATCGTCAATGACCAATAACAT
1 CCCTCAAACATCGCCAATGACCAATAACAT
* *
1122107 TCCTCAAACATTGCCAA
1 CCCTCAAACATCGCCAA
1122124 ATAAGGATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.36, C:0.35, G:0.06, T:0.22
Consensus pattern (30 bp):
CCCTCAAACATCGCCAATGACCAATAACAT
Found at i:1130647 original size:19 final size:19
Alignment explanation
Indices: 1130623--1130659 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1130613 ACGTATAAAG
1130623 CTGAAAGAA-CTTGATCGAT
1 CTGAAAGAATCTT-ATCGAT
1130642 CTGAAAGAATCTTATCGA
1 CTGAAAGAATCTTATCGA
1130660 GGAGATGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (19 bp):
CTGAAAGAATCTTATCGAT
Found at i:1131721 original size:128 final size:128
Alignment explanation
Indices: 1131583--1131840 Score: 516
Period size: 128 Copynumber: 2.0 Consensus size: 128
1131573 TTGCTGATAC
1131583 AATAACATTTTAACGTTTTAATTTAATTAATTAATTTAATGCATGATTATTAGTTTAAAAATTAA
1 AATAACATTTTAACGTTTTAATTTAATTAATTAATTTAATGCATGATTATTAGTTTAAAAATTAA
1131648 TTTGTGTAATTATTTATATTTTAGTAGAGATATTGTATATTAGATCCTTTTATTAAGAACCTT
66 TTTGTGTAATTATTTATATTTTAGTAGAGATATTGTATATTAGATCCTTTTATTAAGAACCTT
1131711 AATAACATTTTAACGTTTTAATTTAATTAATTAATTTAATGCATGATTATTAGTTTAAAAATTAA
1 AATAACATTTTAACGTTTTAATTTAATTAATTAATTTAATGCATGATTATTAGTTTAAAAATTAA
1131776 TTTGTGTAATTATTTATATTTTAGTAGAGATATTGTATATTAGATCCTTTTATTAAGAACCTT
66 TTTGTGTAATTATTTATATTTTAGTAGAGATATTGTATATTAGATCCTTTTATTAAGAACCTT
1131839 AA
1 AA
1131841 GTTAGTTATA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 130 1.00
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (128 bp):
AATAACATTTTAACGTTTTAATTTAATTAATTAATTTAATGCATGATTATTAGTTTAAAAATTAA
TTTGTGTAATTATTTATATTTTAGTAGAGATATTGTATATTAGATCCTTTTATTAAGAACCTT
Found at i:1133691 original size:3 final size:3
Alignment explanation
Indices: 1133685--1133725 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1133675 GGATGACGAA
* * *
1133685 GAT GAT GAT GAC GAT GAT GAT GAT GGT GGT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1133726 CAATGAGGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.02, G:0.39, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:1133717 original size:15 final size:15
Alignment explanation
Indices: 1133676--1133731 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
1133666 GGAGGAGGAG
*
1133676 GATGACGAAGATGAT
1 GATGACGATGATGAT
1133691 GATGACGATGATGAT
1 GATGACGATGATGAT
** *
1133706 GATGGTGGTGATGAT
1 GATGACGATGATGAT
*
1133721 GATGACAATGA
1 GATGACGATGA
1133732 GGAGTCACAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (15 bp):
GATGACGATGATGAT
Found at i:1133866 original size:24 final size:25
Alignment explanation
Indices: 1133839--1133895 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
1133829 TTTATACTTG
*
1133839 TATTTA-GTACTTTTTTATTGTAGT
1 TATTTATGGACTTTTTTATTGTAGT
*
1133863 TATTTATTGGACTTTTTTATTGTAAT
1 TATTTA-TGGACTTTTTTATTGTAGT
*
1133889 TTTTTAT
1 TATTTAT
1133896 TTATCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 1 0.04
26 21 0.75
ACGTcount: A:0.21, C:0.04, G:0.11, T:0.65
Consensus pattern (25 bp):
TATTTATGGACTTTTTTATTGTAGT
Found at i:1133882 original size:26 final size:26
Alignment explanation
Indices: 1133847--1133896 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1133837 TGTATTTAGT
*
1133847 ACTTTTTTATTGTAGTTATTTATTGG
1 ACTTTTTTATTGTAATTATTTATTGG
*
1133873 ACTTTTTTATTGTAATTTTTTATT
1 ACTTTTTTATTGTAATTATTTATT
1133897 TATCATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.66
Consensus pattern (26 bp):
ACTTTTTTATTGTAATTATTTATTGG
Found at i:1133904 original size:14 final size:13
Alignment explanation
Indices: 1133849--1133896 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
1133839 TATTTAGTAC
*
1133849 TTTTTTATTGTAG
1 TTTTTTATTGTAA
* * *
1133862 TTATTTATTGGAC
1 TTTTTTATTGTAA
1133875 TTTTTTATTGTAA
1 TTTTTTATTGTAA
1133888 TTTTTTATT
1 TTTTTTATT
1133897 TATCATTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (13 bp):
TTTTTTATTGTAA
Found at i:1138819 original size:26 final size:28
Alignment explanation
Indices: 1138757--1138819 Score: 67
Period size: 31 Copynumber: 2.2 Consensus size: 28
1138747 TGAGTATTGT
*
1138757 TGAGCTCGACTCGACTCGAAAACTTTGAAA
1 TGAGCTCGACTCGACTCGAAAACTTCG--A
*
1138787 TAAAGCTCGACTCGACTCGAAAAC-TCG-
1 T-GAGCTCGACTCGACTCGAAAACTTCGA
1138814 TGAGCT
1 TGAGCT
1138820 TAAAATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 3 0.10
31 21 0.72
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCGAAAACTTCGA
Found at i:1140032 original size:16 final size:17
Alignment explanation
Indices: 1140010--1140047 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1140000 AAACGTCTTT
1140010 TAAAATTAATTTTAAGA
1 TAAAATTAATTTTAAGA
**
1140027 -AAAATTGTTTTTAAGA
1 TAAAATTAATTTTAAGA
1140043 TAAAA
1 TAAAA
1140048 GTTGGTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (17 bp):
TAAAATTAATTTTAAGA
Found at i:1140403 original size:30 final size:29
Alignment explanation
Indices: 1140282--1140419 Score: 79
Period size: 30 Copynumber: 4.7 Consensus size: 29
1140272 ATAATAAATC
*
1140282 TAGAAAAAACATG-AACTTAAAGGATTAAAA
1 TAGAAAAAACA-GAAACTT-AAGGACTAAAA
* * *
1140312 TGGTAAAAACAAAAACTTAAAAGG-CTAAAA
1 TAGAAAAAACAGAAACTT--AAGGACTAAAA
* ** * *
1140342 CAGCTAAAACATAAATTTAAAGGAC-ATAAA
1 TAGAAAAAACAGAAACTT-AAGGACTA-AAA
1140372 TAGAAAAAACAGAAACTTAAGTGACTAAAA
1 TAGAAAAAACAGAAACTTAAG-GACTAAAA
* *
1140402 TA-AAATAAGAGAAA-TTAA
1 TAGAAAAAACAGAAACTTAA
1140420 AATGTCAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
28 4 0.05
29 19 0.22
30 56 0.66
31 6 0.07
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (29 bp):
TAGAAAAAACAGAAACTTAAGGACTAAAA
Found at i:1141184 original size:3 final size:3
Alignment explanation
Indices: 1141176--1141207 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1141166 TGGTTTTAAT
1141176 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1141208 TTTTTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1141679 original size:46 final size:44
Alignment explanation
Indices: 1141477--1142149 Score: 328
Period size: 46 Copynumber: 15.8 Consensus size: 44
1141467 AGTTTTGGTC
* * *
1141477 GGGTGATGACACGGTTCCTACGCGATGAGAACGACAGGTCATCT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
* * * * * **
1141521 AAGGATAATAACACGGTTCCTACGTGATGAGGATGACTGGTTATTCT
1 --GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCA-TCT
* *** *
1141568 GGG-GTTGACACAACTCCTACGTGATGAGGA-TATCAGG---T-T
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGA-CAGGCCATCT
* *
1141607 GGGTGATGTCACGGTTCCTACATGATGAGGACGACAGGCCATCT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
* * * ** *
1141651 AAGGGTGATAACACGGTTCCTGCGTGATGAGGATTG-TTGGCTATCT
1 --GGGTGATGACACGGTTCCTACGTGATGAGGA-CGACAGGCCATCT
* **
1141697 GGG-GTTGACACGACTCCTACGTGATGAGGA-GATCAGG---TC-
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGA-CAGGCCATCT
* * *
1141736 GGGTGATGACACAGTTCCTACGTGATGAGGAAGACATGCCATCT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
* * * * * * **
1141780 AAGAGTGATAACATGGTTTCTACGTGATGAGGACGGCTGGTTATCT
1 --GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
*
1141826 AGGGT--TGACACGGTTCCTACGCGATGAGGA-GATCAGG---TC-
1 -GGGTGATGACACGGTTCCTACGTGATGAGGACGA-CAGGCCATCT
* * * * **
1141865 GGGTGATGACACGATTCCTACGTGATGAGGATGGCTGGTTATCT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
* **
1141909 GGG-GTTGACACGGTTCCTACGTGATGAGGACGGTAGGCCATCT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
* * * * * **
1141952 AAGGGTGATAACACGATTCCTATGTGATGAGGACGGCTGGTTATCT
1 --GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
* * * * *
1141998 GGG-GCTGACATGGTTCCAATGTGATGAGGA-AATCAGG---TC-
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGA-CAGGCCATCT
*
1142037 GGGTGATGACACGGTTCCTA-G-GA--A--A--TCAGG---TC-
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
*
1142069 GGGTGATGACACGGTTCCTACGCGATGAGGACGACAGGCCATCT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
* * *
1142113 AAGGGTGAT-AGCACGATACCTACATGATGAGGACGAC
1 --GGGTGATGA-CACGGTTCCTACGTGATGAGGACGAC
1142150 TGATCATCTA
Statistics
Matches: 480, Mismatches: 98, Indels: 98
0.71 0.14 0.14
Matches are distributed among these distances:
32 26 0.05
33 1 0.00
34 3 0.01
36 2 0.00
38 7 0.01
39 11 0.02
40 101 0.21
41 5 0.01
42 1 0.00
43 114 0.24
44 34 0.07
45 10 0.02
46 161 0.34
47 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (44 bp):
GGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCT
Found at i:1141755 original size:40 final size:41
Alignment explanation
Indices: 1141403--1142099 Score: 205
Period size: 40 Copynumber: 16.6 Consensus size: 41
1141393 CGTCTAAGGG
* * *
1141403 TGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGG-GA
1 TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
** * * * * * **
1141443 TGACACGACTCATACATTATGAAGAGTTTTGGTC-GGGTGA
1 TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
* * * *
1141483 TGACACGGTTCCTACGCGATGAGAACGA-CAGGTCATCTAAGGATAA
1 TGACACGGTTCCTACGTGATGAGGA-GATCAGG---TC--AGGGTGA
* * * *
1141529 TAACACGGTTCCTACGTGATGAGGATGA-CTGGTTATTCTGGG-GT
1 TGACACGGTTCCTACGTGATGAGGA-GATCAGG----TCAGGGTGA
*** * *
1141573 TGACACAACTCCTACGTGATGAGGATATCAGGT-TGGGTGA
1 TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
* *
1141613 TGTCACGGTTCCTACATGATGAGGACGA-CAGGCCATCTAAGGGTGA
1 TGACACGGTTCCTACGTGATGAGGA-GATCAGG---TC--AGGGTGA
* * * * *
1141659 TAACACGGTTCCTGCGTGATGAGGATTG-T-TGGCTATCTGGG-GT
1 TGACACGGTTCCTACGTGATGAGGA--GATCAGG---TCAGGGTGA
**
1141702 TGACACGACTCCTACGTGATGAGGAGATCAGGTC-GGGTGA
1 TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
* * *
1141742 TGACACAGTTCCTACGTGATGAGGAAGA-CATGCCATCTAAGAGTGA
1 TGACACGGTTCCTACGTGATGAGG-AGATCA-G--GTC--AGGGTGA
* * * * *
1141788 TAACATGGTTTCTACGTGATGAGGACG-GCTGGTTATCTAGGGT--
1 TGACACGGTTCCTACGTGATGAGGA-GATCAGG---TC-AGGGTGA
*
1141831 TGACACGGTTCCTACGCGATGAGGAGATCAGGTC-GGGTGA
1 TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
* * * * *
1141871 TGACACGATTCCTACGTGATGAGGATG-GCTGGTTATCTGGG-GT
1 TGACACGGTTCCTACGTGATGAGGA-GATCAGG---TCAGGGTGA
*
1141914 TGACACGGTTCCTACGTGATGAGGACGGT-AGGCCATCTAAGGGTGA
1 TGACACGGTTCCTACGTGATGAGGA-GATCAGG---TC--AGGGTGA
* * * * * * *
1141960 TAACACGATTCCTATGTGATGAGGACG-GCTGGTTATCTGGG-GC
1 TGACACGGTTCCTACGTGATGAGGA-GATCAGG---TCAGGGTGA
* * * *
1142003 TGACATGGTTCCAATGTGATGAGGAAATCAGGTC-GGGTGA
1 TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
1142043 TGACACGGTTCCTA---G--GA--A-ATCAGGTC-GGGTGA
1 TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
*
1142075 TGACACGGTTCCTACGCGATGAGGA
1 TGACACGGTTCCTACGTGATGAGGA
1142100 CGACAGGCCA
Statistics
Matches: 488, Mismatches: 112, Indels: 115
0.68 0.16 0.16
Matches are distributed among these distances:
32 28 0.06
33 1 0.00
35 3 0.01
37 3 0.01
38 4 0.01
39 14 0.03
40 142 0.29
41 8 0.02
42 2 0.00
43 112 0.23
44 33 0.07
45 11 0.02
46 123 0.25
47 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (41 bp):
TGACACGGTTCCTACGTGATGAGGAGATCAGGTCAGGGTGA
Found at i:1141762 original size:129 final size:128
Alignment explanation
Indices: 1141473--1141938 Score: 587
Period size: 129 Copynumber: 3.6 Consensus size: 128
1141463 GAAGAGTTTT
* * * * *
1141473 GGTCGGGTGATGACACGGTTCCTACGCGATGAGAACGACAGGTCATCTAAGGATAATAACACGGT
1 GGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCTAAGGGTGATAACACGGT
* *
1141538 TCCTACGTGATGAGGATGACTGGTTATTCTGGGGTTGACACAACTCCTACGTGATGAGGATATCA
66 TCCTACGTGATGAGGATG-CTGGTTA-TCTGGGGTTGACACGACTCCTACGTGATGAGGAGATCA
* * *
1141603 GGTTGGGTGATGTCACGGTTCCTACATGATGAGGACGACAGGCCATCTAAGGGTGATAACACGGT
1 GGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCTAAGGGTGATAACACGGT
* * *
1141668 TCCTGCGTGATGAGGATTGTTGGCTATCTGGGGTTGACACGACTCCTACGTGATGAGGAGATCA
66 TCCTACGTGATGAGGA-TGCTGGTTATCTGGGGTTGACACGACTCCTACGTGATGAGGAGATCA
* * * * *
1141732 GGTCGGGTGATGACACAGTTCCTACGTGATGAGGAAGACATGCCATCTAAGAGTGATAACATGGT
1 GGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCTAAGGGTGATAACACGGT
* * * ** *
1141797 TTCTACGTGATGAGGACGGCTGGTTATCTAGGGTTGACACGGTTCCTACGCGATGAGGAGATCA
66 TCCTACGTGATGAGGA-TGCTGGTTATCTGGGGTTGACACGACTCCTACGTGATGAGGAGATCA
* * * * ** * *
1141861 GGTCGGGTGATGACACGATTCCTACGTGATGAGGATGGCTGGTTATCT--GGG-GTTGACACGGT
1 GGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCTAAGGGTGATAACACGGT
1141923 TCCTACGTGATGAGGA
66 TCCTACGTGATGAGGA
1141939 CGGTAGGCCA
Statistics
Matches: 291, Mismatches: 44, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
126 23 0.08
127 2 0.01
129 187 0.64
130 77 0.26
131 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (128 bp):
GGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGCCATCTAAGGGTGATAACACGGT
TCCTACGTGATGAGGATGCTGGTTATCTGGGGTTGACACGACTCCTACGTGATGAGGAGATCA
Found at i:1141901 original size:83 final size:83
Alignment explanation
Indices: 1141531--1142056 Score: 361
Period size: 89 Copynumber: 6.1 Consensus size: 83
1141521 AAGGATAATA
* * * ***
1141531 ACACGGTTCCTACGTGATGAGGATGACTGGTTATTCTGGGGTTGACACAACTCCTACGTGATGAG
1 ACACGATTCCTACGTGATGAGGACGGCTGGTTA-TCTGGGGTTGACACGGTTCCTACGTGATGAG
* *
1141596 GATATCAGGTTGGGTGATG
65 GAGATCAGGTCGGGTGATG
* * * * * ** * * *
1141615 TCACGGTTCCTACATGATGAGGACGACAGGCCATCTAAGGGTGATAACACGGTTCCTGCGTGATG
1 ACACGATTCCTACGTGATGAGGACGGCTGGTTATCT--GGG-GTTGACACGGTTCCTACGTGATG
* *
1141680 AGGATTG-T-TGGCTATCTGGG-GTTG
63 AGGA--GATCAGG---TC-GGGTGATG
* * * * *
1141704 ACACGACTCCTACGTGATGAGGA-GATCAGG---TC-GGGTGATGACACAGTTCCTACGTGATGA
1 ACACGATTCCTACGTGATGAGGACG-GCTGGTTATCTGGG-GTTGACACGGTTCCTACGTGATGA
* * *
1141764 GGAAGA-CATGCCATCTAAGAGTGATA
64 GG-AGATCA-G--GTC---GGGTGATG
* * * * *
1141790 ACATGGTTTCTACGTGATGAGGACGGCTGGTTATCTAGGGTTGACACGGTTCCTACGCGATGAGG
1 ACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACACGGTTCCTACGTGATGAGG
1141855 AGATCAGGTCGGGTGATG
66 AGATCAGGTCGGGTGATG
*
1141873 ACACGATTCCTACGTGATGAGGATGGCTGGTTATCTGGGGTTGACACGGTTCCTACGTGATGAGG
1 ACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACACGGTTCCTACGTGATGAGG
* *
1141938 ACGGT-AGGCCATCTAAGGGTGATA
66 A-GATCAGG---TC---GGGTGATG
* * * * *
1141962 ACACGATTCCTATGTGATGAGGACGGCTGGTTATCTGGGGCTGACATGGTTCCAATGTGATGAGG
1 ACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACACGGTTCCTACGTGATGAGG
*
1142027 AAATCAGGTCGGGTGATG
66 AGATCAGGTCGGGTGATG
*
1142045 ACACGGTTCCTA
1 ACACGATTCCTA
1142057 GGAAATCAGG
Statistics
Matches: 348, Mismatches: 61, Indels: 67
0.73 0.13 0.14
Matches are distributed among these distances:
82 1 0.00
83 119 0.34
84 31 0.09
85 5 0.01
86 55 0.16
87 2 0.01
88 6 0.02
89 124 0.36
90 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (83 bp):
ACACGATTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACACGGTTCCTACGTGATGAGG
AGATCAGGTCGGGTGATG
Found at i:1141935 original size:172 final size:172
Alignment explanation
Indices: 1141742--1142147 Score: 476
Period size: 172 Copynumber: 2.4 Consensus size: 172
1141732 GGTCGGGTGA
* * * *
1141742 TGACACAGTTCCTACGTGATGAGGAAGACATGCCATCTAAGAGTGATAACATGGTTTCTACGTGA
1 TGACACAGTTCCTACGTGATGAGGAAGACAGGCCATCTAAGAGTGATAACACGATTCCTACGTGA
* * *
1141807 TGAGGACGGCTGGTTATCTAGGGTTGACACGGTTCCTACGCGATGAGGAGATCAGGTCGGGTGAT
66 TGAGGACGGCTGGTTATCTAGGGCTGACACGGTTCCAACGCGATGAGGAAATCAGGTCGGGTGAT
1141872 GACACGATTCCTACGTGATGAGGATGGCTGGTTATCTGGGGT
131 GACACGATTCCTACGTGATGAGGATGGCTGGTTATCTGGGGT
* * ** * *
1141914 TGACACGGTTCCTACGTGATGAGGACGGTAGGCCATCTAAGGGTGATAACACGATTCCTATGTGA
1 TGACACAGTTCCTACGTGATGAGGAAGACAGGCCATCTAAGAGTGATAACACGATTCCTACGTGA
* * * *
1141979 TGAGGACGGCTGGTTATCTGGGGCTGACATGGTTCCAATGTGATGAGGAAATCAGGTCGGGTGAT
66 TGAGGACGGCTGGTTATCTAGGGCTGACACGGTTCCAACGCGATGAGGAAATCAGGTCGGGTGAT
* * *
1142044 GACACGGTTCCTA-G-GA--A--AT--CAGG---TC-GGGTGA
131 GACACGATTCCTACGTGATGAGGATGGCTGGTTATCTGGG-GT
* * * * * * *
1142075 TGACACGGTTCCTACGCGATGAGGACGACAGGCCATCTAAGGGTGATAGCACGATACCTACATGA
1 TGACACAGTTCCTACGTGATGAGGAAGACAGGCCATCTAAGAGTGATAACACGATTCCTACGTGA
1142140 TGAGGACG
66 TGAGGACG
1142148 ACTGATCATC
Statistics
Matches: 206, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
160 3 0.01
161 69 0.33
164 3 0.01
166 2 0.01
168 1 0.00
170 2 0.01
171 1 0.00
172 125 0.61
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (172 bp):
TGACACAGTTCCTACGTGATGAGGAAGACAGGCCATCTAAGAGTGATAACACGATTCCTACGTGA
TGAGGACGGCTGGTTATCTAGGGCTGACACGGTTCCAACGCGATGAGGAAATCAGGTCGGGTGAT
GACACGATTCCTACGTGATGAGGATGGCTGGTTATCTGGGGT
Found at i:1142065 original size:32 final size:32
Alignment explanation
Indices: 1142024--1142088 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1142014 CAATGTGATG
1142024 AGGAAATCAGGTCGGGTGATGACACGGTTCCT
1 AGGAAATCAGGTCGGGTGATGACACGGTTCCT
1142056 AGGAAATCAGGTCGGGTGATGACACGGTTCCT
1 AGGAAATCAGGTCGGGTGATGACACGGTTCCT
1142088 A
1 A
1142089 CGCGATGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (32 bp):
AGGAAATCAGGTCGGGTGATGACACGGTTCCT
Found at i:1142525 original size:33 final size:33
Alignment explanation
Indices: 1142472--1142552 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
1142462 ACAAGATTTT
* * * *
1142472 TTTCAAGAGAAACAATCTCAAAGATGGTTGTTG
1 TTTCAAGTGAAACAAACTCAAAGATGATTGTTA
* * *
1142505 TTTCCAGTGAAACAAACTCAAAGATTATTTTTA
1 TTTCAAGTGAAACAAACTCAAAGATGATTGTTA
1142538 TTTCAAGTGAAACAA
1 TTTCAAGTGAAACAA
1142553 TTTCAGAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (33 bp):
TTTCAAGTGAAACAAACTCAAAGATGATTGTTA
Found at i:1143021 original size:134 final size:134
Alignment explanation
Indices: 1142873--1143168 Score: 450
Period size: 134 Copynumber: 2.2 Consensus size: 134
1142863 AGAGAAAAAT
* * *
1142873 TGTCTCAAGCGAGACGAAATTTGTTTTGAGAAATTGTCTTAAGTGAGACGAAATTTGTGTTAAGA
1 TGTCTCAAGTGAGAC-AAATTTGTTTTGAGAAATTGTCTCAAGTGAGACAAAATTTGTGTTAAGA
*
1142938 AATTATCTCAAGTGAGACGAAATTTGTTTTGAGAAATTG-TCAAGTAAGACGAAATTTGTTTTGA
65 AATTATCTCAAGTGAGACGAAATTTGTTTTGAGAAATTGCTCAAGTAAGACAAAATTTGTTTTGA
1143002 GAAAG
130 GAAAG
* * *
1143007 TGTCTCAAGTGAGACAAAATTTGTTTTGAGAAATTTTCTCAAGTGAGACAAAATTTGTTTTGAGA
1 TGTCTCAAGTGAGAC-AAATTTGTTTTGAGAAATTGTCTCAAGTGAGACAAAATTTGTGTTAAGA
* *
1143072 AATTGTCTCAAGTGAGACGAAATTTGTTTTGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTTG
65 AATTATCTCAAGTGAGACGAAATTTGTTTTGAGAAATTG-CTCAAGTAAGACAAAATTTGTTTTG
*
1143137 AGAAAT
129 AGAAAG
* *
1143143 TGTCTCAAGTAAGACAAATTTTTTTT
1 TGTCTCAAGTGAGACAAATTTGTTTT
1143169 TGAAGAGAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
134 96 0.65
135 10 0.07
136 41 0.28
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (134 bp):
TGTCTCAAGTGAGACAAATTTGTTTTGAGAAATTGTCTCAAGTGAGACAAAATTTGTGTTAAGAA
ATTATCTCAAGTGAGACGAAATTTGTTTTGAGAAATTGCTCAAGTAAGACAAAATTTGTTTTGAG
AAAG
Found at i:1143171 original size:34 final size:34
Alignment explanation
Indices: 1142869--1143168 Score: 462
Period size: 34 Copynumber: 8.9 Consensus size: 34
1142859 TCTCAGAGAA
*
1142869 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
* * *
1142903 AAATTGTCTTAAGTGAGACGAAATTTGTGTTAAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
*
1142937 AAATTATCTCAAGTGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
*
1142971 AAATTG--TCAAGTAAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
* *
1143003 AAAGTGTCTCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
* *
1143037 AAATTTTCTCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
1143071 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
*
1143105 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
* *
1143139 AAATTGTCTCAAGTAAGAC-AAATTTTTTTT
1 AAATTGTCTCAAGTGAGACGAAATTTGTTTT
1143169 TGAAGAGAAA
Statistics
Matches: 244, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
32 30 0.12
33 10 0.04
34 204 0.84
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (34 bp):
AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
Found at i:1143329 original size:32 final size:32
Alignment explanation
Indices: 1143260--1143345 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
1143250 TCACATCAGG
*
1143260 ATGTTGAATCCCTAAATATGCCCCAATATTCA
1 ATGTTGAATCTCTAAATATGCCCCAATATTCA
**
1143292 ATGTTGAATCTCTAAATATGCCCCAATATTTG
1 ATGTTGAATCTCTAAATATGCCCCAATATTCA
* * *
1143324 TTGTTGAATCTTTAAAGATGCC
1 ATGTTGAATCTCTAAATATGCC
1143346 TGTTGTTCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (32 bp):
ATGTTGAATCTCTAAATATGCCCCAATATTCA
Found at i:1144803 original size:52 final size:51
Alignment explanation
Indices: 1144665--1144820 Score: 149
Period size: 52 Copynumber: 3.0 Consensus size: 51
1144655 AGTGGGATTA
* *
1144665 TTAGTGGAGTAGTGGAGGATTTATTTAATTGGTAGTGGTAGATAGTGG--G
1 TTAGTGGAGTAGTGGATGATTTATTTAATTGGTAGTGGTAGATAGTGGTTT
** * * * * *
1144714 TTAGTGGTAGGTTA-T-TTTAATGTTATGATAGTGGGTAGTGGTGGATAGTGGATTT
1 TTAGTGG-A-G-TAGTGGATGAT-TTAT-TTAATTGGTAGTGGTAGATAGTGG-TTT
1144769 TTAGTGGAGTAGTGGATGATTTATTTAATTGGTAGTGGTAGATAGTGGTTT
1 TTAGTGGAGTAGTGGATGATTTATTTAATTGGTAGTGGTAGATAGTGGTTT
1144820 T
1 T
1144821 AATTAATAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
49 7 0.09
50 3 0.04
51 10 0.12
52 44 0.54
53 6 0.07
54 4 0.05
55 7 0.09
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (51 bp):
TTAGTGGAGTAGTGGATGATTTATTTAATTGGTAGTGGTAGATAGTGGTTT
Found at i:1144832 original size:3 final size:3
Alignment explanation
Indices: 1144824--1144877 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
1144814 TGGTTTTAAT
*
1144824 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1144870 TAA TAA TA
1 TAA TAA TA
1144878 TTTTTTAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1148161 original size:13 final size:12
Alignment explanation
Indices: 1148128--1148161 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1148118 GCCAAATACC
*
1148128 TAAAAATACTTT
1 TAAAAATAATTT
1148140 TAAAAATAATTT
1 TAAAAATAATTT
1148152 TAAAAGATAA
1 TAAAA-ATAA
1148162 AAACTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (12 bp):
TAAAAATAATTT
Found at i:1151590 original size:21 final size:21
Alignment explanation
Indices: 1151548--1151590 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1151538 AGCTGAAGTT
**
1151548 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCAATAC
1151569 ACTGTAGCAGTGCATCAATAC
1 ACTGTAGCAGTGCATCAATAC
1151590 A
1 A
1151591 TAATTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCAATAC
Found at i:1155046 original size:3 final size:3
Alignment explanation
Indices: 1155038--1155071 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1155028 GTAAATTATT
1155038 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1155072 TGGGACGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1155793 original size:164 final size:161
Alignment explanation
Indices: 1155613--1155929 Score: 377
Period size: 164 Copynumber: 2.0 Consensus size: 161
1155603 ACCAAATTTG
* * * *
1155613 AAAGATTGATTTCTCTTCACGAGAAAGTCAAGAATTTATTCCTCTTCGCGAGGGAGTCAAGAATA
1 AAAGATTGATTTCTCTTCACAAGAAAGTCAAGAATTGATTCCACTTCACGAGGGAGTCAAGAATA
* * * * *
1155678 ACAAAGATTGACTCCTCTTCATGAGGATGTGAATAATTGACACCACTTTAGGAATAGA-AAATAT
66 ACAAAGATAGACTCCTCTTCACGAGGAAGTCAATAATTGACACCACTTTAGGAATA-ACAAAGAT
*
1155742 TGACTTCTCCTCTTCACGAGGGAGTCATGAATAAA
130 TGAC-T-T-CTCTTCACGAGGAAGTCATGAATAAA
* * * * *
1155777 AAAGATTG-TCTTCTCTTCATAAGGAAGTCAAGGATTGATTCCACTTCACTAGGGAGTCATGAAT
1 AAAGATTGAT-TTCTCTTCACAAGAAAGTCAAGAATTGATTCCACTTCACGAGGGAGTCAAGAAT
* * * ** * *
1155841 AACAAAGATAGACTTCTCTTTACGAGTAAGTCAATAATTGACTTCTCTTTAGGATTAACAAAGAT
65 AACAAAGATAGACTCCTCTTCACGAGGAAGTCAATAATTGACACCACTTTAGGAATAACAAAGAT
1155906 TGACTTCTCTTCACGAGGAAGTCA
130 TGACTTCTCTTCACGAGGAAGTCA
1155930 AGGATTGGTT
Statistics
Matches: 129, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
161 17 0.13
162 1 0.01
163 3 0.02
164 108 0.84
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (161 bp):
AAAGATTGATTTCTCTTCACAAGAAAGTCAAGAATTGATTCCACTTCACGAGGGAGTCAAGAATA
ACAAAGATAGACTCCTCTTCACGAGGAAGTCAATAATTGACACCACTTTAGGAATAACAAAGATT
GACTTCTCTTCACGAGGAAGTCATGAATAAA
Found at i:1155915 original size:27 final size:27
Alignment explanation
Indices: 1155840--1155922 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
1155830 GAGTCATGAA
*
1155840 TAACAAAGATAGACTTCTCTTTACGAG
1 TAACAAAGATTGACTTCTCTTTACGAG
* *
1155867 TAAGTCAATA-ATTGACTTCTCTTTAGGAT
1 TAA--CAA-AGATTGACTTCTCTTTACGAG
*
1155896 TAACAAAGATTGACTTCTCTTCACGAG
1 TAACAAAGATTGACTTCTCTTTACGAG
1155923 GAAGTCAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 1 0.02
27 22 0.48
29 22 0.48
30 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (27 bp):
TAACAAAGATTGACTTCTCTTTACGAG
Found at i:1155928 original size:56 final size:56
Alignment explanation
Indices: 1155837--1156976 Score: 440
Period size: 56 Copynumber: 18.8 Consensus size: 56
1155827 AGGGAGTCAT
* * * **
1155837 GAATAACAAAGATAGACTTCTCTTTACGAGTAAGTCAATAATTGACTTCTCTTTAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* *
1155893 GATTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTG-GTTCCTCTTCACGAGGGAGT
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTT-CTCTT----------T
*
1155957 CAT
55 -AG
* * * * * *
1155960 GAATAATAAAAATTAACTTCTCTTCATGAGGAAGTCAATGATTG-GTTCCTCTTCACGAGGGAGT
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTT-CTCTT----------T
*
1156024 CAA
55 -AG
* *
1156027 GAATAATAAAGATTGATTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * * *
1156083 GAATAACAAATATCGACTTCTATTCACGAGGAAGTCAAGGATTG-GTTCCTCTTCACGAGGGAGT
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTT-CTCTT----------T
*
1156147 CAT
55 -AG
* * * *
1156150 GAATAATAAAGATTGACTTCTCTTCAAGAGGAATTCAAGGATTGACTTCTTTTTAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* ** * * * * * * * *
1156206 GAACAGTAAAGATTAACGTCTTTTTATGAGGAAGTCAAGCATTGGCTCCTCTTCACGAGGAAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTT----------T-
*
1156271 AT
55 AG
*** * *
1156273 GAATAACAAAGATTGACTTCTCTTCTTAAGGAAGTCAAGGATTGACTCCTATTTAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * * * *
1156329 GAATAGCAAAGATTAATTTTTCTTCACGAGGAAGTCAAGGATTG-GTTCCTCTTCACAAGGGAGT
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTT-CTCTT----------T
*
1156393 CAT
55 -AG
*
1156396 GAATAACAAAGATTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTTCTCTTTAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* *
1156452 GAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAGGATTG-GTTCCTCTTCATGAGGGAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTT-CTCTT--T-----AG
* ** ** * *
1156515 TTATGAATAATAAAGATTGACTTCTCTTCGTGAGGAAGTCAACAACTAACTTCTCTTTAG
1 ----GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * * * ** ** * *
1156575 GAATATCAAAGATTGACTTTTCTTCA--AGG-A-T--TGGTTTCTCTTCATGAGGGAGTCAT
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTC-T-----CTTTAG
1156631 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * * *
1156687 GAATATCAAAGATTGAATTCTCTTCATGAGGAAGTTAAGGATTTG--TTCCTCTTTACGAGG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGA-TTGACTT-CTCTTT---A-G
* * * *
1156747 GAGTCATGAATGATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCAG
1 GA---AT--A--ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
* *
1156810 GAATAAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTG-TTTCCTCTTCATGAGGGAGT
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTT-CTC-T--T-------T
1156874 CAG
55 -AG
* ** * * *
1156877 GAATGAA-AAAGATTAACTTCTCTTTGCGAGGAAGACATGGATTGAC-TCTATTTCAG
1 GAAT-AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTT-AG
* * *
1156933 GAATAACAAAGATTAACTTCTCTTCACAAGAAAGTCAAGGATTG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTG
1156977 GTTCCTCTTC
Statistics
Matches: 832, Mismatches: 147, Indels: 210
0.70 0.12 0.18
Matches are distributed among these distances:
50 5 0.01
51 1 0.00
52 1 0.00
53 1 0.00
54 3 0.00
55 12 0.01
56 392 0.47
57 8 0.01
58 5 0.01
59 3 0.00
60 8 0.01
61 1 0.00
62 8 0.01
63 8 0.01
64 1 0.00
65 3 0.00
66 9 0.01
67 352 0.42
68 11 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (56 bp):
GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
Found at i:1155982 original size:190 final size:190
Alignment explanation
Indices: 1155749--1156900 Score: 931
Period size: 190 Copynumber: 6.2 Consensus size: 190
1155739 TATTGACTTC
* * *
1155749 TCCTCTTCACGAGGGAGTCATGAATAAAAAAGATTGTCTTCTCTTCATAAGGAAGTCAAGGATTG
1 TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTG
* * * **
1155814 ATTCCACTTCACTAGGGAGTCATGAATAACAAAGATAGACTTCTCTTTACGAGTAAGTCAATAAT
66 ATTCCTCTTCACTAGGGAGTCATGAATAACAAAGATAGACTTCTCTTCACGAGGAAGTCAAGGAT
*
1155879 TGACTTCTCTTTAGGATTAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGT
131 TGACTTCTCTTTAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGT
* * *
1155939 TCCTCTTCACGAGGGAGTCATGAATAATAAAAATTAACTTCTCTTCATGAGGAAGTCAATGATTG
1 TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTG
* * * * * *
1156004 GTTCCTCTTCACGAGGGAGTCAAGAATAATAAAGATTGATTTCTCTTCACGAGGAAGTCAAGGAT
66 ATTCCTCTTCACTAGGGAGTCATGAATAACAAAGATAGACTTCTCTTCACGAGGAAGTCAAGGAT
* * *
1156069 TGACTTCTCTTTAGGAATAACAAATATCGACTTCTATTCACGAGGAAGTCAAGGATTGGT
131 TGACTTCTCTTTAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGT
* *
1156129 TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCAAGAGGAATTCAAGGATTG
1 TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTG
* * * * * * *
1156194 ACTT-CT-TT--TTA-GGA-ACA-G--T---AAAGATTA-ACGTCTTTTTATGAGGAAGTCAAGC
66 A-TTCCTCTTCACTAGGGAGTCATGAATAACAAAGA-TAGACTTCTCTTCACGAGGAAGTCAAGG
* * * ***
1156246 ATTGGCTCCTCTTCACGAGGAAGTCATGAATAACAAAGATTGACTTCTCTTCTTAAGGAAGTCAA
129 ATTGACTTCTCTT----------T-AGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
**
1156311 GGATTGAC
183 GGATTGGT
* * ** * * * *
1156319 TCCTATT----------T-AGGAATAGCAAAGATTAATTTTTCTTCACGAGGAAGTCAAGGATTG
1 TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTG
* * * *
1156373 GTTCCTCTTCACAAGGGAGTCATGAATAACAAAGATTGACTTCTCTTCACAAGGAAGTCAAGGAT
66 ATTCCTCTTCACTAGGGAGTCATGAATAACAAAGATAGACTTCTCTTCACGAGGAAGTCAAGGAT
*
1156438 TGACTTCTCTTTAGGAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAGGATTGGT
131 TGACTTCTCTTTAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGT
* * * ** * *
1156498 TCCTCTTCATGAGGGAGTTATGAATAATAAAGATTGACTTCTCTTCGTGAGGAAGTCAACAACTA
1 TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTG
* * * *
1156563 ACTT-CTCTT---TA-GGA---AT--AT--CAAAGATTGACTTTTCTTCA--AGG-A-T--TGGT
66 A-TTCCTCTTCACTAGGGAGTCATGAATAACAAAGATAGACTTCTCTTCACGAGGAAGTCAAGGA
** ** * *
1156610 TTCTCTTCATGAGGGAGTCATGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTG
130 TTGACTTC-T-----CTTTAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTG
*
1156675 ACT
189 -GT
* * * *
1156678 T-CTCTT---TA-GGA---AT--AT--CAAAGATTGAATTCTCTTCATGAGGAAGTTAAGGATTT
1 TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGA-TT
* * * * * *
1156731 G-TTCCTCTTTACGAGGGAGTCATGAATGATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGA
65 GATTCCTCTTCACTAGGGAGTCATGAATAACAAAGATAGACTTCTCTTCACGAGGAAGTCAAGGA
* * * *
1156795 TTGACTCCTCTTCAGGAATAAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGTT
130 TTGACTTCTCTTTAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGT
* * *
1156856 TCCTCTTCATGAGGGAGTCAGGAATGAA-AAAGATTAACTTCTCTT
1 TCCTCTTCACGAGGGAGTCATGAAT-AATAAAGATTGACTTCTCTT
1156901 TGCGAGGAAG
Statistics
Matches: 756, Mismatches: 129, Indels: 154
0.73 0.12 0.15
Matches are distributed among these distances:
167 2 0.00
168 34 0.04
169 1 0.00
170 2 0.00
171 1 0.00
172 5 0.01
173 8 0.01
174 1 0.00
175 6 0.01
176 2 0.00
177 5 0.01
178 4 0.01
179 260 0.34
180 7 0.01
181 5 0.01
182 4 0.01
183 9 0.01
184 4 0.01
185 10 0.01
186 7 0.01
187 3 0.00
188 2 0.00
189 5 0.01
190 365 0.48
191 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (190 bp):
TCCTCTTCACGAGGGAGTCATGAATAATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTG
ATTCCTCTTCACTAGGGAGTCATGAATAACAAAGATAGACTTCTCTTCACGAGGAAGTCAAGGAT
TGACTTCTCTTTAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGT
Found at i:1156012 original size:123 final size:123
Alignment explanation
Indices: 1155777--1156003 Score: 330
Period size: 123 Copynumber: 1.8 Consensus size: 123
1155767 CATGAATAAA
* * *
1155777 AAAGATTGTCTTCTCTTCATAAGGAAGTCAAGGATTGATTCCACTTCACTAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGGATTGATTCCACTTCACGAGGGAGTCATGAATA
* * *
1155842 ACAAAGATAGACTTCTCTTTACGAGTAAGTCAATAATTGACTTCTCTTTAGGATTAAC
66 ACAAAAATAGACTTCTCTTCACGAGGAAGTCAATAATTGACTTCTCTTTAGGATTAAC
* * *
1155900 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGGATTGATTCCACTTCACGAGGGAGTCATGAATA
* * *
1155965 ATAAAAATTA-ACTTCTCTTCATGAGGAAGTCAATGATTG
66 ACAAAAA-TAGACTTCTCTTCACGAGGAAGTCAATAATTG
1156004 GTTCCTCTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 89 0.98
124 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (123 bp):
AAAGATTGACTTCTCTTCACAAGGAAGTCAAGGATTGATTCCACTTCACGAGGGAGTCATGAATA
ACAAAAATAGACTTCTCTTCACGAGGAAGTCAATAATTGACTTCTCTTTAGGATTAAC
Found at i:1156181 original size:123 final size:123
Alignment explanation
Indices: 1155960--1157035 Score: 1300
Period size: 123 Copynumber: 8.8 Consensus size: 123
1155950 AGGGAGTCAT
* * * * *
1155960 GAATAATAAAAATTAACTTCTCTTCATGAGGAAGTCAATGATTGGTTCCTCTTCACGAGGGAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
* * * *
1156025 AAGAATAATAAAGATTGATTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
66 ATGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * *
1156083 GAATAACAAATATCGACTTCTATTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
* * *
1156148 ATGAATAATAAAGATTGACTTCTCTTCAAGAGGAATTCAAGGATTGACTTCTTTTTAG
66 ATGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGGATTGACTTCTCTTTAG
* ** * * * * * * * *
1156206 GAACAGTAAAGATTAACGTCTTTTTATGAGGAAGTCAAGCATTGGCTCCTCTTCACGAGGAAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
* * *
1156271 ATGAATAACAAAGATTGACTTCTCTTCTTA-AGGAAGTCAAGGATTGACTCCTATTTAG
66 ATGAATAACAAAGATTGACTTCTCTTC-AAGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * * * *
1156329 GAATAGCAAAGATTAATTTTTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
1156394 ATGAATAACAAAGATTGACTTCTCTTCACA-AGGAAGTCAAGGATTGACTTCTCTTTAG
66 ATGAATAACAAAGATTGACTTCTCTTCA-AGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * *
1156452 GAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAGGATTGGTTCCTCTTCATGAGGGAGTT
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
* ** ** * *
1156517 ATGAATAATAAAGATTGACTTCTCTTCGTGAGGAAGTCAACAACTAACTTCTCTTTAG
66 ATGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * * *
1156575 GAATATCAAAGATTGAC-T-T-TT--C------TTCAAGGATTGGTTTCTCTTCATGAGGGAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
*
1156629 ATGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTTCTCTTTAG
66 ATGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * * * * *
1156687 GAATATCAAAGATTGAATTCTCTTCATGAGGAAGTTAAGGATTTGTTCCTCTTTACGAGGGAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
* * * * *
1156752 ATGAATGATAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCAG
66 ATGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGGATTGACTTCTCTTTAG
* * *
1156810 GAATAAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGTTTCCTCTTCATGAGGGAGTC
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
* * *** * * *
1156875 AGGAATGAA-AAAGATTAACTTCTCTTTGCGAGGAAGACATGGATTGAC-TCTATTTCAG
66 ATGAAT-AACAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGGATTGACTTCTCTTT-AG
* * * **
1156933 GAATAACAAAGATTAACTTCTCTTCACAAGAAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGAG
1 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
** *
1156998 AAAAATAACAAAGATTGACTTCTCTTCATGAGGAAGTC
66 ATGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTC
1157036 TAGTTGAAGA
Statistics
Matches: 817, Mismatches: 119, Indels: 34
0.84 0.12 0.04
Matches are distributed among these distances:
112 96 0.12
113 1 0.00
114 1 0.00
115 2 0.00
118 1 0.00
120 2 0.00
121 1 0.00
122 7 0.01
123 704 0.86
124 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (123 bp):
GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACGAGGGAGTC
ATGAATAACAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGGATTGACTTCTCTTTAG
Found at i:1156466 original size:27 final size:27
Alignment explanation
Indices: 1156396--1156477 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
1156386 AGGGAGTCAT
*
1156396 GAATAACAAAGATTGACTTCTCTTCACAAG
1 GAATAACAAAGATTGACTTCTCTT---TAG
*
1156426 GAAGT--CAAGGATTGACTTCTCTTTAG
1 GAA-TAACAAAGATTGACTTCTCTTTAG
1156452 GAATAACAAAGATTGACTTCTCTTTA
1 GAATAACAAAGATTGACTTCTCTTTA
1156478 CGAGGAAGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.02
26 5 0.11
27 19 0.41
29 17 0.37
30 3 0.07
31 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (27 bp):
GAATAACAAAGATTGACTTCTCTTTAG
Found at i:1156683 original size:29 final size:29
Alignment explanation
Indices: 1156641--1156875 Score: 135
Period size: 29 Copynumber: 7.9 Consensus size: 29
1156631 GAATAACAAA
1156641 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTTCTCTTCACGAGGAAGTCAAG
* * *
1156670 GATTGACTTCTCTT---TAGGAATATCAAA
1 GATTGACTTCTCTTCACGAGGAA-GTCAAG
* * *
1156697 GATTGAATTCTCTTCATGAGGAAGTTAAG
1 GATTGACTTCTCTTCACGAGGAAGTCAAG
* *
1156726 GATTTG--TTCCTCTTTACGAGGGAGTCATGAATG
1 GA-TTGACTT-CTCTTCACGAGGAAGTC---AA-G
*
1156759 ATAAAGATTGACTTCTCTTCATGAGGAAGTCAAG
1 -----GATTGACTTCTCTTCACGAGGAAGTCAAG
* * ** * *
1156793 GATTGACTCCTCTTCAGGAATAA--AAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAG
1156820 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTTCTCTTCACGAGGAAGTCAAG
* * *
1156849 GATTG-TTTCCTCTTCATGAGGGAGTCA
1 GATTGACTT-CTCTTCACGAGGAAGTCA
1156876 GGAATGAAAA
Statistics
Matches: 156, Mismatches: 30, Indels: 40
0.69 0.13 0.18
Matches are distributed among these distances:
26 5 0.03
27 38 0.24
28 4 0.03
29 74 0.47
30 8 0.05
32 2 0.01
33 1 0.01
34 1 0.01
35 2 0.01
37 3 0.02
38 16 0.10
39 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (29 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAG
Found at i:1156804 original size:67 final size:63
Alignment explanation
Indices: 1156598--1157035 Score: 292
Period size: 56 Copynumber: 7.0 Consensus size: 63
1156588 TGACTTTTCT
* * * *
1156598 TCAAGGATTGGTTTCTCTTCATGAGGGAGTCATGAATAACAAAGATTGACTTCTCTTCACGAGGA
1 TCAAGGATTGATTCCTCTTTACGAGGGAG--AT-AAT-ACAAAGATTGACTTCTCTTCACGAGGA
1156663 AG
62 AG
* *
1156665 TCAAGGATTGACTT-CTCTTT---A-GGA-AT-AT-CAAAGATTGAATTCTCTTCATGAGGAAG
1 TCAAGGATTGA-TTCCTCTTTACGAGGGAGATAATACAAAGATTGACTTCTCTTCACGAGGAAG
* * *
1156721 TTAAGGATTTG-TTCCTCTTTACGAGGGAGTCATGAATGATAAAGATTGACTTCTCTTCATGAGG
1 TCAAGGA-TTGATTCCTCTTTACGAGGGAG--AT-AAT-ACAAAGATTGACTTCTCTTCACGAGG
1156785 AAG
61 AAG
*
1156788 TCAAGGATTGACTCCTC-TT-C-A-GGA-ATAA-A-AAAGATTGACTTCTCTTCACGAGGAAG
1 TCAAGGATTGATTCCTCTTTACGAGGGAGATAATACAAAGATTGACTTCTCTTCACGAGGAAG
* * * * * * **
1156844 TCAAGGATTGTTTCCTCTTCATGAGGGAGTCAGGAATGAAAAAGATTAACTTCTCTTTGCGAGGA
1 TCAAGGATTGATTCCTCTTTACGAGGGAG--A-TAAT-ACAAAGATTGACTTCTCTTCACGAGGA
1156909 AG
62 AG
* * * * * * *
1156911 ACATGGATTGACT-CTATTT-C-A-GGA-AT-A-ACAAAGATTAACTTCTCTTCACAAGAAAG
1 TCAAGGATTGATTCCTCTTTACGAGGGAGATAATACAAAGATTGACTTCTCTTCACGAGGAAG
* * * *
1156967 TCAAGGATTGGTTCCTCTTCACGAGGGAGAGAAAAATAACAAAGATTGACTTCTCTTCATGAGGA
1 TCAAGGATTGATTCCTCTTTACGA-GG-GAG-ATAAT-ACAAAGATTGACTTCTCTTCACGAGGA
1157032 AG
62 AG
1157034 TC
1 TC
1157036 TAGTTGAAGA
Statistics
Matches: 292, Mismatches: 42, Indels: 74
0.72 0.10 0.18
Matches are distributed among these distances:
55 2 0.01
56 112 0.38
57 9 0.03
58 4 0.01
59 5 0.02
60 11 0.04
61 1 0.00
62 2 0.01
63 12 0.04
64 6 0.02
65 4 0.01
66 10 0.03
67 112 0.38
68 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (63 bp):
TCAAGGATTGATTCCTCTTTACGAGGGAGATAATACAAAGATTGACTTCTCTTCACGAGGAAG
Found at i:1159321 original size:2 final size:2
Alignment explanation
Indices: 1159314--1159342 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1159304 AATCCAACAT
1159314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1159343 CATTTATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1162215 original size:24 final size:24
Alignment explanation
Indices: 1162180--1162231 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1162170 ATGTTCAACT
* *
1162180 ATGTTCCCATGTGAAGCGGTTTTC
1 ATGTTCCAATGTGAAGCGGTTCTC
*
1162204 ATGTTCCAATGTGAAGCTGTTCTC
1 ATGTTCCAATGTGAAGCGGTTCTC
1162228 ATGT
1 ATGT
1162232 GAACGATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (24 bp):
ATGTTCCAATGTGAAGCGGTTCTC
Found at i:1163926 original size:18 final size:18
Alignment explanation
Indices: 1163891--1163926 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1163881 AACAAATACA
**
1163891 TAAAATATAAAATTTATT
1 TAAAATATAAAAGATATT
1163909 TAAAATATAAAAGATATT
1 TAAAATATAAAAGATATT
1163927 ATTTTATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TAAAATATAAAAGATATT
Found at i:1175232 original size:13 final size:13
Alignment explanation
Indices: 1175214--1175238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1175204 CCTTATTTTG
1175214 TTGTTGTTATTGC
1 TTGTTGTTATTGC
1175227 TTGTTGTTATTG
1 TTGTTGTTATTG
1175239 ATGATTGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.04, G:0.24, T:0.64
Consensus pattern (13 bp):
TTGTTGTTATTGC
Found at i:1175755 original size:6 final size:6
Alignment explanation
Indices: 1175744--1175782 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1175734 GACACGTATT
1175744 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1175783 TGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1176322 original size:6 final size:6
Alignment explanation
Indices: 1176281--1176325 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1176271 GTCTGTCTCG
* * *
1176281 GGTCGG GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1176326 AATACGTGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.58, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:1176432 original size:20 final size:20
Alignment explanation
Indices: 1176407--1176473 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
1176397 CCACCAGTCG
1176407 TTGCGATTTCGACTATCGCA
1 TTGCGATTTCGACTATCGCA
1176427 TTGCGATTTCGACTATCGCA
1 TTGCGATTTCGACTATCGCA
1176447 TTGCGATTT--ACATATTCGCA
1 TTGCGATTTCGAC-TA-TCGCA
1176467 TTGCGAT
1 TTGCGAT
1176474 AGTCCAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 41 0.91
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGCGATTTCGACTATCGCA
Found at i:1180879 original size:3 final size:3
Alignment explanation
Indices: 1180871--1180945 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
1180861 ATTGATTTAT
* * * *
1180871 TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1180919 ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1180946 AATATATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1180953 original size:12 final size:14
Alignment explanation
Indices: 1180878--1180954 Score: 81
Period size: 15 Copynumber: 5.6 Consensus size: 14
1180868 TATTTATTAT
1180878 TATTATTATTATAA
1 TATTATTATTATAA
1180892 TAATTATTATTAT--
1 T-ATTATTATTATAA
*
1180905 TATAATTATTATAAA
1 TATTATTATTAT-AA
*
1180920 TATTATTATTATTAT
1 TATTATTATTA-TAA
1180935 TATTATTATTA-AA
1 TATTATTATTATAA
1180948 TA-TATTA
1 TATTATTA
1180955 AATATAGATA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
12 15 0.28
13 4 0.07
14 1 0.02
15 33 0.61
16 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATTATTATAA
Found at i:1180982 original size:13 final size:14
Alignment explanation
Indices: 1180966--1180998 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1180956 ATATAGATAT
1180966 AAATAATAATAA-A
1 AAATAATAATAATA
1180979 AAATAATAATAATA
1 AAATAATAATAATA
1180993 AAATAA
1 AAATAA
1180999 ATTACAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:1193704 original size:9 final size:9
Alignment explanation
Indices: 1193684--1193755 Score: 76
Period size: 9 Copynumber: 7.9 Consensus size: 9
1193674 ATGCTTGAAG
1193684 AAAAAAAG-
1 AAAAAAAGA
1193692 -AAAAAAGA
1 AAAAAAAGA
1193700 AAAAAAAGA
1 AAAAAAAGA
1193709 GAAAAAAAGA
1 -AAAAAAAGA
*
1193719 GAAAAAAGAAA
1 -AAAAAA-AGA
1193730 AAAAAAAGA
1 AAAAAAAGA
*
1193739 GAAAAAAGA
1 AAAAAAAGA
*
1193748 AGAAAAAG
1 AAAAAAAG
1193756 GGGGGGGTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
7 7 0.13
9 24 0.44
10 22 0.40
11 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:1193705 original size:10 final size:10
Alignment explanation
Indices: 1193692--1193754 Score: 74
Period size: 10 Copynumber: 6.2 Consensus size: 10
1193682 AGAAAAAAAG
1193692 AAAAAAGAAA
1 AAAAAAGAAA
1193702 AAAAAGAGAAA
1 AAAAA-AGAAA
*
1193713 AAAAGAGAAA
1 AAAAAAGAAA
1193723 AAAGAAA-AAA
1 AAA-AAAGAAA
*
1193733 AAAAGAGAAA
1 AAAAAAGAAA
*
1193743 AAAGAAGAAA
1 AAAAAAGAAA
1193753 AA
1 AA
1193755 GGGGGGGGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 2 0.04
10 32 0.71
11 11 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1193723 original size:20 final size:20
Alignment explanation
Indices: 1193684--1193754 Score: 80
Period size: 19 Copynumber: 3.7 Consensus size: 20
1193674 ATGCTTGAAG
1193684 AAAAAA-AG-AAAAAAGA-A
1 AAAAAAGAGAAAAAAAGAGA
1193701 AAAAAAGAGAAAAAAAGAG-
1 AAAAAAGAGAAAAAAAGAGA
*
1193720 AAAAAAGA-AAAAAAAAAGA
1 AAAAAAGAGAAAAAAAGAGA
1193739 GAAAAAAGAAGAAAAA
1 -AAAAAAG-AGAAAAA
1193755 GGGGGGGGTC
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
17 6 0.13
18 11 0.24
19 16 0.35
20 7 0.15
21 1 0.02
22 5 0.11
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAGAGAAAAAAAGAGA
Found at i:1194106 original size:16 final size:16
Alignment explanation
Indices: 1194078--1194114 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1194068 CAATTCTATC
1194078 TATTTCAAGTTCAATT
1 TATTTCAAGTTCAATT
1194094 TATTT-AAGATTCAATT
1 TATTTCAAG-TTCAATT
1194110 TATTT
1 TATTT
1194115 TCGAAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
TATTTCAAGTTCAATT
Found at i:1195232 original size:85 final size:85
Alignment explanation
Indices: 1194912--1195841 Score: 1532
Period size: 85 Copynumber: 11.0 Consensus size: 85
1194902 AACAAATGCC
* * * *
1194912 ATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
*
1194976 CATTGAATTTGG-AAGATGA
66 TATTGAATTTGGAAAGATGA
* * * * *
1194995 ATATGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
* *
1195059 CATTGAATTTGG-AAGAGGA
66 TATTGAATTTGGAAAGATGA
* * * * *
1195078 ATG-ACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
*
1195142 CATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
1195162 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1195227 TATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
*
1195247 ATGTACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1195312 TATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
1195332 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1195397 TATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
*
1195417 ATGTG-CTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1195481 TATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
1195501 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1195566 TATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
*
1195586 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAACCAGT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1195651 TATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
* * *
1195671 ATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGTAAAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
*
1195736 CATTGAATTTGGAAAGATGA
66 TATTGAATTTGGAAAGATGA
* * * *
1195756 ATGTGCCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTAATCTAGTTTGGTAAAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
* *
1195821 CATTGAATTT-AAAAGATGA
66 TATTGAATTTGGAAAGATGA
1195840 AT
1 AT
1195842 TTGCTCATAG
Statistics
Matches: 816, Mismatches: 27, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
82 3 0.00
83 151 0.19
84 102 0.12
85 560 0.69
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (85 bp):
ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
TATTGAATTTGGAAAGATGA
Found at i:1195537 original size:339 final size:339
Alignment explanation
Indices: 1194920--1195841 Score: 1575
Period size: 339 Copynumber: 2.7 Consensus size: 339
1194910 CCATGTGCTC
* * * *
1194920 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
*
1194985 TGG-AAGATGAATATGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
66 TGGAAAGATGAATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
* * * *
1195048 GCAGAACCAATCATTGAATTTGG-AAGAGGAATG-ACTCAATAGCATCTTCTGGAAGTGTTCTTT
131 GTAAAACCAATCATTGAATTTGGAAAGATGAATGTGCT-AATAGCATCTTCTGGAAGTGTTCTTT
* *
1195111 GAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAAGATGAATGTGCCCAATAGC
195 GAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAAGATGAATGTGCCCAATAGC
1195176 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAA
260 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAA
1195241 AGATGAATGTACCCA
325 AGATGAATGTACCCA
1195256 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
*
1195321 TGGAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
66 TGGAAAGATGAATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
* *
1195386 GTAAAACCAGTTATTGAATTTGGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTG
131 GTAAAACCAATCATTGAATTTGGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTG
* *
1195451 AGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAAGATGAATGTGCCCAATAGCA
196 AGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAAGATGAATGTGCCCAATAGCA
1195516 TCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAA
261 TCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAA
*
1195581 GATGAATGTGCCCA
326 GATGAATGTACCCA
*
1195595 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAACCAGTTATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
*
1195660 TGGAAAGATGAATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTG
66 TGGAAAGATGAATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
* *
1195725 GTAAAACCAATCATTGAATTTGGAAAGATGAATGTGCCCAATAGCATCTTCTGGAAATGTTCTTT
131 GTAAAACCAATCATTGAATTTGGAAAGATGAATGTG-CTAATAGCATCTTCTGGAAGTGTTCTTT
* * *
1195790 GAGTTATCTAATCTAGTTTGGTAAAACCAATCATTGAATTT-AAAAGATGAAT
195 GAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAAGATGAAT
1195842 TTGCTCATAG
Statistics
Matches: 552, Mismatches: 29, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
336 64 0.12
337 13 0.02
338 64 0.12
339 346 0.63
340 65 0.12
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (339 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
TGGAAAGATGAATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
GTAAAACCAATCATTGAATTTGGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTG
AGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAAGATGAATGTGCCCAATAGCA
TCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAA
GATGAATGTACCCA
Found at i:1196831 original size:113 final size:113
Alignment explanation
Indices: 1196633--1197181 Score: 771
Period size: 113 Copynumber: 4.8 Consensus size: 113
1196623 GCAAAGATTT
* ***
1196633 AAATCCATCA-TTCAATGGATCAACTTTTCCAGTTCAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAA
* *
1196697 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
1196746 AAATCCATCACTTGATGGATTAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
*
1196811 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* **
1196859 AAATACATCACTTGATGGATCCGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1196924 AAGGATA-AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGA-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
1196972 AAATCTATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAA
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
1197037 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * *
1197085 GAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGGA-AGTTCATAATGAGAAGAA--C-TCATCT
*
1197149 AAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1197182 CTCATCTGAA
Statistics
Matches: 394, Mismatches: 35, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
112 3 0.01
113 351 0.89
114 2 0.01
115 1 0.00
116 37 0.09
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:1197200 original size:40 final size:42
Alignment explanation
Indices: 1197121--1197221 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 42
1197111 TGCCAGGTAG
1197121 AGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGGAAGAAGA
1 AGTTCATAATGAGAAGAAC-CGTCATCTAAAGAAGGAAGAAGA
* *
1197164 AGTTCATAATGAGAAGAA-C-TCATCTGAAGAATGAAGAAGA
1 AGTTCATAATGAGAAGAACCGTCATCTAAAGAAGGAAGAAGA
*
1197204 AATTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
1197222 TTTGTTCAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 36 0.65
41 1 0.02
43 18 0.33
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.20
Consensus pattern (42 bp):
AGTTCATAATGAGAAGAACCGTCATCTAAAGAAGGAAGAAGA
Found at i:1197200 original size:156 final size:153
Alignment explanation
Indices: 1197007--1197334 Score: 458
Period size: 156 Copynumber: 2.1 Consensus size: 153
1196997 TTTCCAGAGA
*
1197007 AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
* * * ** * *
1197072 CAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAG
66 CAACCTTTCGCTCAAATCCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAG
1197137 AACTCGTCATCTAAAGAAGGAAGAAG
131 AA--C-TCATCTAAAGAAGGAAGAAG
* * *
1197163 AAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
* * * * * *
1197228 CAACCTTTCGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAG
66 CAACCTTTCGCTCAAATCCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAG
*
1197293 AACTCATCTGAAGAAGGAAGAAG
131 AACTCATCTAAAGAAGGAAGAAG
*
1197316 AAATTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
1197335 TTTGTTCAAC
Statistics
Matches: 153, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
153 37 0.24
154 1 0.01
156 115 0.75
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (153 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
CAACCTTTCGCTCAAATCCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAG
AACTCATCTAAAGAAGGAAGAAG
Found at i:1197213 original size:269 final size:266
Alignment explanation
Indices: 1196893--1197447 Score: 842
Period size: 269 Copynumber: 2.1 Consensus size: 266
1196883 TTTTCCAGAG
*
1196893 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATAAAGAAGTTCATAATGAGAAGAATTTGT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATAAAGAAATTCATAATGAGAAGAATTTGT
* * *
1196958 TCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAA
66 TCAACCTTTCGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAA
* * * **
1197023 GAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAA
131 GAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAA
* * ** *
1197088 TTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAG
196 TCCATCATCTGATGGATCAACATTGCCAGAAAAAGTTCATAATGAGAAGAA--C-TCATCTAAAG
1197153 AAGGAAGAA
258 AAGGAAGAA
*
1197162 GAAGTTCATAATGAGAAGAACTCATCTGAAGAATGA-AGAAGAAATTCATAATGAGAAGAATTTG
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATA-AAGAAATTCATAATGAGAAGAATTTG
****
1197226 TTCAACCTTTCGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGA
65 TTCAACCTTTCGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGA
* *
1197291 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAA
130 AGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAA
* * * *
1197356 ATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
195 ATCCATCATCTGATGGATCAACATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAA
1197421 GGAAGAA
260 GGAAGAA
1197428 GAAGTTCATAATGAGAAGAA
1 GAAGTTCATAATGAGAAGAA
1197448 TTTGTTCAAC
Statistics
Matches: 260, Mismatches: 25, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
266 38 0.15
267 1 0.00
268 1 0.00
269 220 0.85
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (266 bp):
GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATAAAGAAATTCATAATGAGAAGAATTTGT
TCAACCTTTCGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAA
GAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAA
TCCATCATCTGATGGATCAACATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAG
GAAGAA
Done.