Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1187054 original size:20 final size:23
Alignment explanation
Indices: 1187033--1187075 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1187023 TATAATAATA
1187033 TTTTA-ATTTAAA-ATTATTTATT
1 TTTTATATTTAAACATTATTTA-T
1187055 TTTTATATTTAAACATTATTT
1 TTTTATATTTAAACATTATTT
1187076 TAGCCTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTATATTTAAACATTATTTAT
Found at i:1187902 original size:31 final size:31
Alignment explanation
Indices: 1187867--1187929 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1187857 AAGTAATCTT
1187867 AAGCGTAATTTACCCTTTAAAAATAAGTTTA
1 AAGCGTAATTTACCCTTTAAAAATAAGTTTA
*
1187898 AAGCGTAATTTATCCTTTAAAAATAAGTTTA
1 AAGCGTAATTTACCCTTTAAAAATAAGTTTA
1187929 A
1 A
1187930 CTTTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.37
Consensus pattern (31 bp):
AAGCGTAATTTACCCTTTAAAAATAAGTTTA
Found at i:1189747 original size:32 final size:32
Alignment explanation
Indices: 1189693--1189764 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
1189683 TCCAATGATT
* * *
1189693 TACCCAAGGGAGTGTCTTGGGGCAT-GAGATCC
1 TACCCAAGAGAGTGTCTCGGGGCATCG-GAGCC
* * *
1189725 TACCCAAGATAGTTTCTCGGGGCCTCGGAGCC
1 TACCCAAGAGAGTGTCTCGGGGCATCGGAGCC
1189757 TACCCAAG
1 TACCCAAG
1189765 GGTCATCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (32 bp):
TACCCAAGAGAGTGTCTCGGGGCATCGGAGCC
Found at i:1192027 original size:19 final size:19
Alignment explanation
Indices: 1192003--1192071 Score: 102
Period size: 19 Copynumber: 3.6 Consensus size: 19
1191993 GATCAACTAT
*
1192003 GGTCAAAGTCAATGGGTTG
1 GGTCAAAGTCAATGGGTCG
**
1192022 GGTCAAAGTCAACAGGTCG
1 GGTCAAAGTCAATGGGTCG
*
1192041 GGTAAAAGTCAATGGGTCG
1 GGTCAAAGTCAATGGGTCG
1192060 GGTCAAAGTCAA
1 GGTCAAAGTCAA
1192072 CGAGTCAGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.20
Consensus pattern (19 bp):
GGTCAAAGTCAATGGGTCG
Found at i:1205694 original size:169 final size:170
Alignment explanation
Indices: 1205410--1205745 Score: 665
Period size: 169 Copynumber: 2.0 Consensus size: 170
1205400 GGTCTGAAGA
1205410 AAAATTTATTATCCTACGGATTGTTGGATAATAATGCTAGCAAGATTGAAACACGGAAATGAATC
1 AAAATTTATTATCCTACGGATTGTTGGATAATAATGCTAGCAAGATTGAAACACGGAAATGAATC
1205475 ATGAAGGTGTTCCGTGGAGCGCTTGTGGTGCTGAAAGATGAAAAGATAGCTACAAACTTGTACAT
66 ATGAAGGTGTTCCGTGGAGCGCTTGTGGTGCTGAAAGATGAAAAGATAGCTACAAACTTGTACAT
1205540 GCTGAAGGGAAAGACATTGTTAGAAGCAGAAGCCTCTAAG
131 GCTGAAGGGAAAGACATTGTTAGAAGCAGAAGCCTCTAAG
1205580 AAAA-TTATTATCCTACGGATTGTTGGATAATAATGCTAGCAAGATTGAAACACGGAAATGAATC
1 AAAATTTATTATCCTACGGATTGTTGGATAATAATGCTAGCAAGATTGAAACACGGAAATGAATC
1205644 ATGAAGGTGTTCCGTGGAGCGCTTGTGGTGCTGAAAGATGAAAAGATAGCTACAAACTTGTACAT
66 ATGAAGGTGTTCCGTGGAGCGCTTGTGGTGCTGAAAGATGAAAAGATAGCTACAAACTTGTACAT
1205709 GCTGAAGGGAAAGACATTGTTAGAAGCAGAAGCCTCT
131 GCTGAAGGGAAAGACATTGTTAGAAGCAGAAGCCTCT
1205746 GTTGCCTCAT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 162 0.98
170 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (170 bp):
AAAATTTATTATCCTACGGATTGTTGGATAATAATGCTAGCAAGATTGAAACACGGAAATGAATC
ATGAAGGTGTTCCGTGGAGCGCTTGTGGTGCTGAAAGATGAAAAGATAGCTACAAACTTGTACAT
GCTGAAGGGAAAGACATTGTTAGAAGCAGAAGCCTCTAAG
Found at i:1216391 original size:16 final size:16
Alignment explanation
Indices: 1216370--1216408 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1216360 GGTATTACCC
*
1216370 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
* *
1216386 GACCTGTTATGAATCT
1 GACCTGTTATCAACCT
1216402 GACCTGT
1 GACCTGT
1216409 AATTGACTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:1217231 original size:23 final size:23
Alignment explanation
Indices: 1217201--1217253 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1217191 CAACAACCGA
*
1217201 CAAGCATTAATGAACCAATTCAT
1 CAAGCATTAATGAACCAATTCAG
* * *
1217224 CAAGCATTATTGCATCAATTCAG
1 CAAGCATTAATGAACCAATTCAG
1217247 CAAGCAT
1 CAAGCAT
1217254 CCTGCATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (23 bp):
CAAGCATTAATGAACCAATTCAG
Found at i:1220004 original size:25 final size:25
Alignment explanation
Indices: 1219967--1220032 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
1219957 AAAATGTATT
* * *
1219967 TATATATATTAATATTAAAATAAGA
1 TATATTTAATAATATTAAAATAACA
* *
1219992 TATATTTAATAATATTAATATAACT
1 TATATTTAATAATATTAAAATAACA
*
1220017 TATATTAATATAATAT
1 TATATTTA-ATAATAT
1220033 AGTTATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 27 0.79
26 7 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TATATTTAATAATATTAAAATAACA
Found at i:1220091 original size:30 final size:29
Alignment explanation
Indices: 1220046--1220119 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
1220036 TATAATTTGT
1220046 AATTAATATTAATATAAAATATA-GTCTATAA
1 AATTAATA-TAATATAAAATATATGT-TAT-A
*
1220077 AATTAATATAATATAAACTATATGTTATA
1 AATTAATATAATATAAAATATATGTTATA
*
1220106 AATT-ATATTATATA
1 AATTAATATAATATA
1220120 GTTTATAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 9 0.22
29 5 0.12
30 16 0.40
31 10 0.25
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
AATTAATATAATATAAAATATATGTTATA
Found at i:1220093 original size:16 final size:17
Alignment explanation
Indices: 1220046--1220093 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
1220036 TATAATTTGT
*
1220046 AATTAATATTAATATAA
1 AATTAATAGTAATATAA
*
1220063 AA-T-ATAGT-CTATAA
1 AATTAATAGTAATATAA
1220077 AATTAATA-TAATATAA
1 AATTAATAGTAATATAA
1220093 A
1 A
1220094 CTATATGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 10 0.40
17 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AATTAATAGTAATATAA
Found at i:1220119 original size:14 final size:14
Alignment explanation
Indices: 1220046--1220155 Score: 55
Period size: 14 Copynumber: 7.5 Consensus size: 14
1220036 TATAATTTGT
1220046 AATTAATATTAATATA
1 AATT-ATATT-ATATA
*
1220062 AAATATAGTCTATA-A
1 AATTATA-T-TATATA
*
1220077 AATTAATATAATATA
1 AATT-ATATTATATA
*
1220092 AACTATATGT-TATA
1 AATTATAT-TATATA
1220106 AATTATATTATATA
1 AATTATATTATATA
** *
1220120 GTTTATA-AACTATA
1 AATTATATTA-TATA
* *
1220134 TACTATATTAATATA
1 AATTATATT-ATATA
1220149 AATTATA
1 AATTATA
1220156 GTTAAGATAT
Statistics
Matches: 70, Mismatches: 15, Indels: 19
0.67 0.14 0.18
Matches are distributed among these distances:
13 2 0.03
14 35 0.50
15 21 0.30
16 11 0.16
17 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (14 bp):
AATTATATTATATA
Found at i:1220119 original size:21 final size:21
Alignment explanation
Indices: 1220088--1220155 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1220078 ATTAATATAA
*
1220088 TATAAACTATATGTTATAAAT
1 TATATACTATATGTTATAAAT
*
1220109 TATAT--TATATAGTTTATAAAC
1 TATATACTATAT-G-TTATAAAT
1220130 TATATACTATAT-TAATATAAAT
1 TATATACTATATGT--TATAAAT
1220152 TATA
1 TATA
1220156 GTTAAGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 16 0.42
22 10 0.26
23 5 0.13
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (21 bp):
TATATACTATATGTTATAAAT
Found at i:1220226 original size:80 final size:80
Alignment explanation
Indices: 1220137--1220288 Score: 222
Period size: 80 Copynumber: 1.9 Consensus size: 80
1220127 AACTATATAC
*
1220137 TATATTAATATAAATTATAGTTAAGAT-ATTAACATTAA-ATAAACTATA-TAGTATT-ATATAA
1 TATATTAATAT-AA--ATAGTTAAGATAATTAACATTAATATAAACTATAGTA-CATTAATATAA
1220198 AATATAGTTTAAACAAATA
62 AATATAGTTTAAACAAATA
*
1220217 TATATTAATATAAATAGTTAAGATAATTAATATTAATATAAACTATAGTACATTAATATAAAATA
1 TATATTAATATAAATAGTTAAGATAATTAACATTAATATAAACTATAGTACATTAATATAAAATA
1220282 TAGTTTA
66 TAGTTTA
1220289 TAAATTATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
77 11 0.17
78 10 0.15
79 15 0.23
80 30 0.45
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.39
Consensus pattern (80 bp):
TATATTAATATAAATAGTTAAGATAATTAACATTAATATAAACTATAGTACATTAATATAAAATA
TAGTTTAAACAAATA
Found at i:1220273 original size:20 final size:20
Alignment explanation
Indices: 1220248--1220285 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1220238 GATAATTAAT
*
1220248 ATTAATATAAACTATAGTAC
1 ATTAATATAAAATATAGTAC
1220268 ATTAATATAAAATATAGT
1 ATTAATATAAAATATAGT
1220286 TTATAAATTA
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:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTAATATAAAATATAGTAC
Found at i:1220337 original size:15 final size:17
Alignment explanation
Indices: 1220314--1220524 Score: 102
Period size: 18 Copynumber: 12.1 Consensus size: 17
1220304 GGTTAAAGTA
1220314 ATATATAGTTTATATAT
1 ATATATAGTTTATATAT
1220331 -T-TATAGTTTATATAT
1 ATATATAGTTTATATAT
1220346 ACTATATAGTTT-TATAT
1 A-TATATAGTTTATATAT
**
1220363 ATA-AT-GAACTATATA-
1 ATATATAG-TTTATATAT
* * *
1220378 ACATATATTTTGTATACCAT
1 ATATATA-GTT-TATA-TAT
*
1220398 ATATATAGTATATACTACT
1 ATATATAGTTTATA-TA-T
*
1220417 GAACTATATATTATATATATAT
1 --A-TATATAGT-T-TATATAT
1220439 ATATATAGTTTATATAT
1 ATATATAGTTTATATAT
**
1220456 ACTA-AT-GAACTATATAT
1 A-TATATAG-TTTATATAT
*
1220473 AATGTATAGTTTATATAT
1 -ATATATAGTTTATATAT
1220491 ATCATATA---TATATAT
1 AT-ATATAGTTTATATAT
1220506 ATCATATAGTTTATATAT
1 AT-ATATAGTTTATATAT
1220524 A
1 A
1220525 CTAATAAACT
Statistics
Matches: 148, Mismatches: 20, Indels: 51
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.01
15 34 0.23
16 10 0.07
17 27 0.18
18 43 0.29
19 11 0.07
20 7 0.05
21 1 0.01
22 8 0.05
23 2 0.01
24 4 0.03
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
ATATATAGTTTATATAT
Found at i:1220376 original size:33 final size:31
Alignment explanation
Indices: 1220314--1220551 Score: 150
Period size: 33 Copynumber: 7.4 Consensus size: 31
1220304 GGTTAAAGTA
* *
1220314 ATATATAGTTTATATAT-TTATAGTTTATATAT
1 ATATATAGTTTATATATATAATA--ATATATAT
1220346 ACTATATAGTTT-TATATATAATGAACTATATA-
1 A-TATATAGTTTATATATATAAT-AA-TATATAT
* * **
1220378 ACATATA-TTT-TGTATACCAT-ATATATAGT
1 ATATATAGTTTATATATATAATAATATATA-T
* ** *
1220407 ATATACTACTGAACTATATATTAT-ATATATAT
1 ATATA-TAGTTTA-TATATATAATAATATATAT
1220439 ATATATAGTTTATATATACTAATGAACTATATAT
1 ATATATAGTTTATATATA-TAAT-AA-TATATAT
* *
1220473 AATGTATAGTTTATATATATCATATATATATAT
1 -ATATATAGTTTATATATATAATA-ATATATAT
1220506 ATCATATAGTTTATATATACTAATAA-ACTATAT
1 AT-ATATAGTTTATATATA-TAATAATA-TATAT
*
1220539 AATGTATAGTTTA
1 -ATATATAGTTTA
1220552 GGGTTTAGGG
Statistics
Matches: 165, Mismatches: 21, Indels: 39
0.73 0.09 0.17
Matches are distributed among these distances:
27 6 0.04
28 1 0.01
29 4 0.02
30 18 0.11
31 13 0.08
32 16 0.10
33 72 0.44
34 18 0.11
35 17 0.10
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (31 bp):
ATATATAGTTTATATATATAATAATATATAT
Found at i:1220437 original size:11 final size:11
Alignment explanation
Indices: 1220421--1220524 Score: 62
Period size: 11 Copynumber: 9.5 Consensus size: 11
1220411 ACTACTGAAC
1220421 TATATATTATA
1 TATATATTATA
1220432 TATATA-TATA
1 TATATATTATA
1220442 TATAGT-TTATA
1 TATA-TATTATA
*
1220453 TATACTAATGA-A
1 TATA-T-ATTATA
1220465 CTATATA-TA-A
1 -TATATATTATA
*
1220475 TGTATAGTT-TA
1 TATATA-TTATA
*
1220486 TATATATCATA
1 TATATATTATA
1220497 TATATA-TATA
1 TATATATTATA
1220507 TCATATAGTT-TA
1 T-ATATA-TTATA
1220519 TATATA
1 TATATA
1220525 CTAATAAACT
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
9 5 0.07
10 15 0.20
11 42 0.57
12 5 0.07
13 7 0.09
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (11 bp):
TATATATTATA
Found at i:1220535 original size:68 final size:63
Alignment explanation
Indices: 1220421--1220551 Score: 208
Period size: 68 Copynumber: 2.0 Consensus size: 63
1220411 ACTACTGAAC
*
1220421 TATATATTATATATATATATATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTA
1 TATATATTATATATATATATATATAGTTTATATATACTAATAAAC--TATATAATGTATAGTTTA
1220486 TATATATCATATATATATATATCATATAGTTTATATATACTAATAAACTATATAATGTATAGTTT
1 TATATAT--TATATATATATAT-ATATAGTTTATATATACTAATAAACTATATAATGTATAGTTT
1220551 A
63 A
1220552 GGGTTTAGGG
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
65 7 0.11
66 18 0.29
67 13 0.21
68 24 0.39
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (63 bp):
TATATATTATATATATATATATATAGTTTATATATACTAATAAACTATATAATGTATAGTTTA
Found at i:1220539 original size:2 final size:2
Alignment explanation
Indices: 1220421--1220524 Score: 72
Period size: 2 Copynumber: 50.0 Consensus size: 2
1220411 ACTACTGAAC
*
1220421 TA TA TA T- TA TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA -A TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA T-A
* *
1220464 -A CTA TA TA TA -A TG TA TA GTT TA TA TA TA TCA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA
*
1220505 TA TCA TA TA GTT TA TA TA TA
1 TA T-A TA TA -TA TA TA TA TA
1220525 CTAATAAACT
Statistics
Matches: 82, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
1 4 0.05
2 67 0.82
3 11 0.13
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1220777 original size:18 final size:18
Alignment explanation
Indices: 1220754--1220846 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 18
1220744 ATAGTTATTA
*
1220754 TATAGTTCATTTGTAAAC
1 TATAGTTCATATGTAAAC
1220772 TATAGTTCATATGTAAATATCAAC
1 TATAGTTCATATG----TA--AAC
*
1220796 TATAGTT-TTATGTAAAC
1 TATAGTTCATATGTAAAC
*
1220813 TATAGTT-AGTA-ATAAAC
1 TATAGTTCA-TATGTAAAC
*
1220830 TATAGTTCATATATAAA
1 TATAGTTCATATGTAAA
1220847 TATCAACCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
17 24 0.39
18 20 0.32
19 2 0.03
22 2 0.03
23 4 0.06
24 10 0.16
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:1220937 original size:31 final size:31
Alignment explanation
Indices: 1220889--1220951 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
1220879 TAGTTCATAG
*
1220889 TAAATTATAGTTCATAT-ATAGTATATAAATA
1 TAAACTATAGTTCATATAATAGTATA-AAATA
1220920 TAAACTATAGATT-ATATAAATAGTATAAAATA
1 TAAACTATAG-TTCATAT-AATAGTATAAAATA
1220952 GTATTAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 13 0.46
32 7 0.25
33 8 0.29
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (31 bp):
TAAACTATAGTTCATATAATAGTATAAAATA
Found at i:1220957 original size:24 final size:22
Alignment explanation
Indices: 1220910--1220964 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
1220900 TCATATATAG
*
1220910 TATATAAATATAAACTATAGAT
1 TATATAAATATAAACAATAGAT
1220932 TATATAAATAGTATAA-AATAGTAT
1 TATATAAATA-TA-AACAATAG-AT
*
1220956 TAAATAAAT
1 TATATAAAT
1220965 TATAGTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.36
23 6 0.21
24 12 0.43
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (22 bp):
TATATAAATATAAACAATAGAT
Found at i:1221036 original size:20 final size:18
Alignment explanation
Indices: 1221008--1221063 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
1220998 CCTAAACCCT
*
1221008 AAACCATATATATATATATA
1 AAACTATATA-AT-TATATA
1221028 AAACTATATAATTATATA
1 AAACTATATAATTATATA
*
1221046 ATAAATATATAATT-TATA
1 A-AACTATATAATTATATA
1221064 CAATATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 11 0.33
19 13 0.39
20 9 0.27
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAACTATATAATTATATA
Found at i:1221037 original size:18 final size:16
Alignment explanation
Indices: 1221013--1221097 Score: 62
Period size: 18 Copynumber: 4.8 Consensus size: 16
1221003 ACCCTAAACC
1221013 ATATATATATATATAAA
1 ATATATA-ATATATAAA
1221030 ACTATATAATTATATAATAA
1 A-TATATAA-TATAT-A-AA
* *
1221050 ATATATAATTTATACA
1 ATATATAATATATAAA
*
1221066 ATATATTATATTTATAATTA
1 ATATA-TA-ATATATAA--A
1221086 ATATATAATATA
1 ATATATAATATA
1221098 ATGTTAGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
16 6 0.11
17 5 0.09
18 26 0.46
19 10 0.18
20 9 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATAATATATAAA
Found at i:1221204 original size:27 final size:28
Alignment explanation
Indices: 1221172--1221252 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 28
1221162 ATATATAAAC
*
1221172 TATATAGTATTATAGTTTATACAT-GTA
1 TATATAGTATTATAGTTTATACATAATA
*
1221199 TATATAGT-TTATATTTTATACATAATA
1 TATATAGTATTATAGTTTATACATAATA
* * *
1221226 TATATA-AACTATAGTTTATATATAATA
1 TATATAGTATTATAGTTTATACATAATA
1221253 CATACTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.30
27 32 0.70
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATAGTTTATACATAATA
Found at i:1221226 original size:25 final size:27
Alignment explanation
Indices: 1221172--1221229 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1221162 ATATATAAAC
*
1221172 TATATAGTATTATAGTTTATACATGTA
1 TATATAGTATTATAGTTTATACATGAA
*
1221199 TATATAGT-TTATATTTTATACAT-AA
1 TATATAGTATTATAGTTTATACATGAA
1221224 TATATA
1 TATATA
1221230 TAAACTATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.24
26 14 0.48
27 8 0.28
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (27 bp):
TATATAGTATTATAGTTTATACATGAA
Found at i:1221240 original size:34 final size:33
Alignment explanation
Indices: 1221201--1221282 Score: 112
Period size: 34 Copynumber: 2.5 Consensus size: 33
1221191 TACATGTATA
* *
1221201 TATAGTTTATATTTTATACATAATATATATAAAC-
1 TATAGTTTATATATAATACATAAT-T-TATAAACT
*
1221235 TATAGTTTATATATAATACATACTTTATAAACT
1 TATAGTTTATATATAATACATAATTTATAAACT
1221268 TATAGTTTATATATA
1 TATAGTTTATATATA
1221283 TTATATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.16
33 16 0.36
34 21 0.48
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (33 bp):
TATAGTTTATATATAATACATAATTTATAAACT
Found at i:1221245 original size:18 final size:18
Alignment explanation
Indices: 1221224--1221282 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
1221214 TTATACATAA
1221224 TATATATAAACTATAGTT
1 TATATATAAACTATAGTT
*
1221242 TATATATAATAC-ATA--C
1 TATATATAA-ACTATAGTT
1221258 T-T-TATAAACTTATAGTT
1 TATATATAAAC-TATAGTT
1221275 TATATATA
1 TATATATA
1221283 TTATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 13
0.68 0.04 0.28
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 4 0.12
16 1 0.03
17 1 0.03
18 13 0.41
19 6 0.19
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (18 bp):
TATATATAAACTATAGTT
Found at i:1221684 original size:206 final size:210
Alignment explanation
Indices: 1221322--1221912 Score: 807
Period size: 206 Copynumber: 2.8 Consensus size: 210
1221312 GTTTTTCTCA
* * * * *
1221322 ACTTATTACGTATTTTTATTATT-AATTGGCCTATAACTTTTT-AATGAGTATAATTTAGTACAT
1 ACTTATTACTTATTTCTATTTTTAAATT-GCCCATAACTTTTTAAATGGGTATAATTTAGTAC-T
*
1221385 TCTTGGATTAATTTCAACCTCA-AATTTAAAAATTATTTCGATTGAT-CC-CT---T-TGTGTTG
64 T-TTTGATTAATTTCAACCTCACAATTT-AAAATTATTTCGATT-ATCCCTCTCAATGTGTGTTG
* *
1221443 TTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTTCTCCAAA-TTTA-T
126 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
1221506 TGCATATGAAATTGACCCAT
191 TGCATATGAAATTGACCCAT
1221526 ACTTATTACTTATTTCTATTTTTAAATTGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTT
1 ACTTATTACTTATTTCTATTTTTAAATTGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTT
*
1221591 TTGATTAATTTCAACATCACAATTT-AAATTATTTCGATT-TCCCTCGTCAATGTGTGTTGTTT-
66 TTGATTAATTTCAACCTCACAATTTAAAATTATTTCGATTATCCCTC-TCAATGTGTGTTGTTTA
*
1221653 ATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTAAATTTAGTCCTCCAAATTTTATTTGCA
130 ATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCA
*
1221718 TATGAAATTGATCCAT
195 TATGAAATTGACCCAT
* *
1221734 ACTTATTACTTAATTCTATTTTTGTAATTTGCCCATAACTTTTTAAATGGGTATAATTTAGTA-T
1 ACTTATTACTTATTTCTA-TTTT-TAAATTGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
*
1221798 ATTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAACGTGTGT
64 -TTTTG-ATTAATTTCAACCTCACAATTTAAAATTATTTCGA-TT-ATCCCTC-TCAATGTGTGT
* * *
1221863 TGTTTAATTTATTTAAAATTTTAGTTATAATTTCATATTTGTTCAATTTA
124 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1221913 ATTATTAAAT
Statistics
Matches: 346, Mismatches: 20, Indels: 30
0.87 0.05 0.08
Matches are distributed among these distances:
200 1 0.00
201 2 0.01
202 15 0.04
203 19 0.05
204 40 0.12
205 22 0.06
206 52 0.15
207 14 0.04
208 37 0.11
209 5 0.01
210 43 0.12
211 21 0.06
212 12 0.03
213 2 0.01
215 21 0.06
216 40 0.12
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (210 bp):
ACTTATTACTTATTTCTATTTTTAAATTGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTT
TTGATTAATTTCAACCTCACAATTTAAAATTATTTCGATTATCCCTCTCAATGTGTGTTGTTTAA
TTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCAT
ATGAAATTGACCCAT
Found at i:1222368 original size:25 final size:26
Alignment explanation
Indices: 1222323--1222371 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1222313 GGTGTCAAAA
* *
1222323 TTTACCTGACTTGACCTGTATCCGAT
1 TTTACCTGACCTGACCAGTATCCGAT
1222349 TTTACCTGACCTG-CCAGTATCCG
1 TTTACCTGACCTGACCAGTATCCG
1222372 TCTGAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (26 bp):
TTTACCTGACCTGACCAGTATCCGAT
Found at i:1222811 original size:2 final size:2
Alignment explanation
Indices: 1222804--1222828 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1222794 TTCTAATCAA
1222804 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1222829 AGCACAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1222929 original size:2 final size:2
Alignment explanation
Indices: 1222922--1222946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1222912 GAAACAATAC
1222922 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1222947 TTTATGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1223694 original size:17 final size:18
Alignment explanation
Indices: 1223657--1223697 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1223647 TTTAAGGAAG
* *
1223657 TAGAATCTGTGAAATAAT
1 TAGAATATGTGAAAGAAT
1223675 TAGAATATGTG-AAGAAT
1 TAGAATATGTGAAAGAAT
1223692 TAGAAT
1 TAGAAT
1223698 CAAATTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (18 bp):
TAGAATATGTGAAAGAAT
Found at i:1224826 original size:2 final size:2
Alignment explanation
Indices: 1224819--1224884 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1224809 CCTCCTCTTC
1224819 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1224861 CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
1224885 ATAGAATGGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1226981 original size:72 final size:73
Alignment explanation
Indices: 1226892--1227026 Score: 218
Period size: 73 Copynumber: 1.9 Consensus size: 73
1226882 AACATAAGTT
* * *
1226892 TTGATATTTTAAAGTTA-TTTTGAAATTAAAGTTTCCTACGAGTATCGAACATCATAGCATAAGT
1 TTGATATTTTAAAGTTATTTTTGAAATTAAACTTTCATACAAGTATCGAACATCATAGCATAAGT
1226956 TTTGATAC
66 TTTGATAC
* *
1226964 TTGATATTTTTATGTTATTTTTGAAATTAAACTTTCATACAAGTATCGAACATCATAGCATAA
1 TTGATATTTTAAAGTTATTTTTGAAATTAAACTTTCATACAAGTATCGAACATCATAGCATAA
1227027 ATTTCAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
72 15 0.26
73 42 0.74
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (73 bp):
TTGATATTTTAAAGTTATTTTTGAAATTAAACTTTCATACAAGTATCGAACATCATAGCATAAGT
TTTGATAC
Found at i:1236871 original size:13 final size:13
Alignment explanation
Indices: 1236848--1236938 Score: 119
Period size: 13 Copynumber: 7.0 Consensus size: 13
1236838 AATGACGCGC
*
1236848 AATGAGCGTCATA
1 AATGCGCGTCATA
*
1236861 AATGCGTGTCATA
1 AATGCGCGTCATA
*
1236874 AATGAGCGTCATA
1 AATGCGCGTCATA
*
1236887 AATGCGTGTCATA
1 AATGCGCGTCATA
*
1236900 AATGAGCGTCATA
1 AATGCGCGTCATA
*
1236913 AATGCGTGTCATA
1 AATGCGCGTCATA
*
1236926 AATACGCGTCATA
1 AATGCGCGTCATA
1236939 GATTTATGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 66 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1236877 original size:26 final size:26
Alignment explanation
Indices: 1236848--1236938 Score: 166
Period size: 26 Copynumber: 3.5 Consensus size: 26
1236838 AATGACGCGC
1236848 AATGAGCGTCATAAATGCGTGTCATA
1 AATGAGCGTCATAAATGCGTGTCATA
1236874 AATGAGCGTCATAAATGCGTGTCATA
1 AATGAGCGTCATAAATGCGTGTCATA
1236900 AATGAGCGTCATAAATGCGTGTCATA
1 AATGAGCGTCATAAATGCGTGTCATA
1236926 AAT-ACGCGTCATA
1 AATGA-GCGTCATA
1236939 GATTTATGAC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 1 0.02
26 63 0.98
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGTGTCATA
Found at i:1243348 original size:23 final size:23
Alignment explanation
Indices: 1243322--1243398 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
1243312 ACCACAGCTT
*
1243322 ATATAATTGCACTGAAGTGCCAC
1 ATATAATTGCACCGAAGTGCCAC
* *
1243345 ATATAATTGCACCGGAGTGCCGC
1 ATATAATTGCACCGAAGTGCCAC
* * * *
1243368 GTAGAATTGCACCGTAGTGCCAT
1 ATATAATTGCACCGAAGTGCCAC
1243391 ATAATAAT
1 AT-ATAAT
1243399 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (23 bp):
ATATAATTGCACCGAAGTGCCAC
Found at i:1243576 original size:103 final size:103
Alignment explanation
Indices: 1243405--1243622 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1243395 TAATGTCCAT
* *
1243405 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1243470 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1243508 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1243573 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1243611 AAGGACCACATA
1 AAGGACCACATA
1243623 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1244510 original size:64 final size:64
Alignment explanation
Indices: 1244359--1244515 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
1244349 TAATGAAGGT
* ** *
1244359 ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAAAGAG
* * * *
1244423 ATGCATCGATGTA-TTCATTATGCATCGATGCACT-AATTGCATTCGATGTATT-TATT-TTAAA
1 ATGCATCGATGCACTAC-TAATGCATCGATGCA-TAAAATGCATTCGATGT-TTGT-TTATTAAA
1244484 -AG
62 GAG
1244486 AGTGCATCGATGCACTACTAATGCATCGAT
1 A-TGCATCGATGCACTACTAATGCATCGAT
1244516 ACACCTTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
63 4 0.05
64 66 0.86
65 7 0.09
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAAAGAG
Found at i:1249276 original size:23 final size:23
Alignment explanation
Indices: 1249250--1249327 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
1249240 CACCACAGCT
1249250 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1249273 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
1249296 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1249319 TATAATAAT
1 CAT-ATAAT
1249328 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1249505 original size:103 final size:103
Alignment explanation
Indices: 1249334--1249551 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1249324 TAATGTCCAT
* *
1249334 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1249399 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1249437 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1249502 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1249540 AAGGACCACATA
1 AAGGACCACATA
1249552 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1250421 original size:64 final size:64
Alignment explanation
Indices: 1250283--1250444 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
1250273 TCTTTTAATG
*
1250283 AAGGTATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAC
1 AAGG-ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAA
* * * * *
1250348 TAGGATGCATCGATGCATTCCTTATGCATCGATGCACT-AATTGCATTCGATGTATT-TATT-TT
1 AAGGATGCATCGATGCACTACTGATGCATCGATGCA-TAAAATGCATTCGATGT-TTGT-TTATT
1250410 AA
63 AA
**
1250412 AA-GAGTGCATCGATGCACTACCAATGCATCGAT
1 AAGGA-TGCATCGATGCACTACTGATGCATCGAT
1250445 ACACCTTCAA
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
63 2 0.02
64 72 0.88
65 8 0.10
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
AAGGATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAA
Found at i:1258690 original size:78 final size:78
Alignment explanation
Indices: 1258595--1258754 Score: 268
Period size: 78 Copynumber: 2.1 Consensus size: 78
1258585 TAGCATTGAA
**
1258595 ATTTTCTAAACCGCTACAGATCGACTTTTTCTTCTTTATACTACATTCATATCTTATTTAATTGA
1 ATTTTCTAAACCGCTACAGATCGACCCTTTCTTCTTTATACTACATTCATATCTTATTTAATTGA
1258660 GAAAAAATATTTT
66 GAAAAAATATTTT
*
1258673 ATTTTCTAAAGCC-CTACAGATCGACCCTTTCTTCTTTATACTACATTTATATCTTATTTAATTG
1 ATTTTCTAAA-CCGCTACAGATCGACCCTTTCTTCTTTATACTACATTCATATCTTATTTAATTG
*
1258737 AGGAAAAATATTTT
65 AGAAAAAATATTTT
1258751 ATTT
1 ATTT
1258755 ATTTAAAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
78 75 0.97
79 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (78 bp):
ATTTTCTAAACCGCTACAGATCGACCCTTTCTTCTTTATACTACATTCATATCTTATTTAATTGA
GAAAAAATATTTT
Found at i:1266425 original size:38 final size:33
Alignment explanation
Indices: 1266342--1266407 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1266332 AGTTGACAAG
*
1266342 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCAAACTTA
1266375 TTGGAAATTTCATCTTGGTTGGTGGCTAAACTT
1 TTGGAAATTTCATCTTGGTTGGTGGC-AAACTT
1266408 TGAATATGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCAAACTTA
Found at i:1272032 original size:32 final size:33
Alignment explanation
Indices: 1271958--1272035 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 33
1271948 GGCCTAAGAT
* *
1271958 CTTTCTTGGGTAGGCCCTGCTGCCCCGAGATGA
1 CTTTCTTGGGTAGGCCCCGCTGCCCCGAGATAA
1271991 --TTCTTGGGTAGGCCCCG-TGACCCCGAG-TAA
1 CTTTCTTGGGTAGGCCCCGCTG-CCCCGAGATAA
1272021 CTTTCTTGGGTAGGC
1 CTTTCTTGGGTAGGC
1272036 TCTCAGGCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 4 0.10
31 23 0.57
32 13 0.32
ACGTcount: A:0.13, C:0.28, G:0.31, T:0.28
Consensus pattern (33 bp):
CTTTCTTGGGTAGGCCCCGCTGCCCCGAGATAA
Found at i:1275619 original size:59 final size:59
Alignment explanation
Indices: 1275542--1275656 Score: 194
Period size: 59 Copynumber: 1.9 Consensus size: 59
1275532 ACTTAATTGC
*
1275542 TTATCTACACACACAGAATTAGATATCCATACCAGTGAATTCTAGGCTATAGAAGAAAT
1 TTATCTACACACACAGAATTAGATATCCATACCAGTGAATTCTAGGCTATACAAGAAAT
* **
1275601 TTATCTACACACAGAGAATTAGATATCCATATTAGTGAATTCTAGGCTATACAAGA
1 TTATCTACACACACAGAATTAGATATCCATACCAGTGAATTCTAGGCTATACAAGA
1275657 TCTATATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (59 bp):
TTATCTACACACACAGAATTAGATATCCATACCAGTGAATTCTAGGCTATACAAGAAAT
Found at i:1281476 original size:17 final size:16
Alignment explanation
Indices: 1281456--1281489 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1281446 TTAAAGACTA
*
1281456 TTTGTACTATTTCTCTC
1 TTTGTAATATTTC-CTC
1281473 TTTGTAATATTTCCTC
1 TTTGTAATATTTCCTC
1281489 T
1 T
1281490 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTGTAATATTTCCTC
Found at i:1287891 original size:16 final size:16
Alignment explanation
Indices: 1287870--1287900 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1287860 GTTTAAATTG
1287870 AAATAATCAATAAAAT
1 AAATAATCAATAAAAT
*
1287886 AAATAATTAATAAAA
1 AAATAATCAATAAAA
1287901 ACTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATCAATAAAAT
Found at i:1288877 original size:2 final size:2
Alignment explanation
Indices: 1288870--1288898 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1288860 AGTTTACCAT
1288870 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
1288899 TATGTGTAAA
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:1300918 original size:30 final size:30
Alignment explanation
Indices: 1300884--1300951 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
1300874 TGTTTCTCAT
*
1300884 AGCTCTTTCTCTCTTTATCACCTCCATCCC
1 AGCTCTTCCTCTCTTTATCACCTCCATCCC
1300914 AGCTCTTCCTCTCTTTATCACCTCCATCCC
1 AGCTCTTCCTCTCTTTATCACCTCCATCCC
1300944 AGCTCTTC
1 AGCTCTTC
1300952 ACTGGGAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.13, C:0.44, G:0.04, T:0.38
Consensus pattern (30 bp):
AGCTCTTCCTCTCTTTATCACCTCCATCCC
Found at i:1311849 original size:16 final size:16
Alignment explanation
Indices: 1311830--1311863 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1311820 CAATATACGA
1311830 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1311846 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1311862 AT
1 AT
1311864 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1311932 original size:17 final size:17
Alignment explanation
Indices: 1311904--1311936 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1311894 TATTAATGTA
1311904 TGAATCATTTATATTTTT
1 TGAATCATTTAT-TTTTT
1311922 TGAAT-ATTTATTTTT
1 TGAATCATTTATTTTT
1311937 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTTATTTTTT
Found at i:1312609 original size:130 final size:130
Alignment explanation
Indices: 1312405--1312652 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
1312395 AATTTTCTTC
* *
1312405 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
1312470 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
1312535 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
1312600 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1312653 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1313100 original size:35 final size:35
Alignment explanation
Indices: 1313050--1313125 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
1313040 AATTGAATTT
* *
1313050 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1313085 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1313120 AATTGA
1 AATTGA
1313126 GGATTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1324454 original size:21 final size:20
Alignment explanation
Indices: 1324430--1324470 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1324420 TTTTACCTAA
*
1324430 TCTCTATCTTTCTCTCTGTTT
1 TCTCTATCTCTCTCTC-GTTT
*
1324451 TCTCTTTCTCTCTCTCGTTT
1 TCTCTATCTCTCTCTCGTTT
1324471 ATCTGTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.02, C:0.32, G:0.05, T:0.61
Consensus pattern (20 bp):
TCTCTATCTCTCTCTCGTTT
Found at i:1325924 original size:21 final size:21
Alignment explanation
Indices: 1325898--1325967 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
1325888 GACTATCGCA
1325898 TTGCGATTTATTCCAAGTTCG
1 TTGCGATTTATTCCAAGTTCG
* *
1325919 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAGTT--CG
*
1325940 TTGCGATTTATTTCAAGTTCG
1 TTGCGATTTATTCCAAGTTCG
1325961 TTGCGAT
1 TTGCGAT
1325968 AGTCGAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 9 0.22
21 23 0.57
23 8 0.20
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (21 bp):
TTGCGATTTATTCCAAGTTCG
Found at i:1325945 original size:42 final size:42
Alignment explanation
Indices: 1325893--1325974 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1325883 ACTTCGACTA
1325893 TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGT
* *
1325935 TCGCGTTGCGATTTATTTCAAGTTCGTTGCGATAGTCGAA
1 TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAA
1325975 AATCGCAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TCGCATTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGT
Found at i:1326727 original size:21 final size:21
Alignment explanation
Indices: 1326703--1327003 Score: 206
Period size: 21 Copynumber: 14.6 Consensus size: 21
1326693 TTTGGAATAA
1326703 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTTGACT
*
1326724 ATCGCAA--CGAA-TTTGGAAT
1 ATCGCAACGCGAACTTT-GACT
*
1326743 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTTGACT
*
1326766 ATCGCAA--CGAA-TTTGGAAT
1 ATCGCAACGCGAACTTT-GACT
*
1326785 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTTGACT
**
1326808 ATCGCAA--CGAA-TTTGGAAA
1 ATCGCAACGCGAACTTT-GACT
*
1326827 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTTGACT
*
1326848 ATCGCAA--CGAA-TTTGGAAT
1 ATCGCAACGCGAACTTT-GACT
*
1326867 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTTGACT
**
1326890 ATCGCAA--CGAA-TTTAGAAA
1 ATCGCAACGCGAACTTT-GACT
* *
1326909 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTTGACT
**
1326930 ATCGCAA--CGAA-TTTGGAAA
1 ATCGCAACGCGAACTTT-GACT
*
1326949 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTTGACT
*
1326970 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTTGACT
*
1326991 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1327004 TATGTAAAGC
Statistics
Matches: 219, Mismatches: 31, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
18 13 0.06
19 60 0.27
21 113 0.52
22 6 0.03
23 21 0.10
24 6 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTTGACT
Found at i:1326840 original size:40 final size:42
Alignment explanation
Indices: 1326678--1326978 Score: 524
Period size: 42 Copynumber: 7.3 Consensus size: 42
1326668 TGCGATTTTG
* *
1326678 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1326720 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1326762 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1326804 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1326844 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1326886 GACTATCGCAACGAATTTAG-A-AAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1326926 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1326966 GACTATCGCAACG
1 GACTATCGCAACG
1326979 CGAACTTGGA
Statistics
Matches: 251, Mismatches: 6, Indels: 6
0.95 0.02 0.02
Matches are distributed among these distances:
40 108 0.43
41 3 0.01
42 140 0.56
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1326997 original size:82 final size:82
Alignment explanation
Indices: 1326678--1326978 Score: 534
Period size: 82 Copynumber: 3.7 Consensus size: 82
1326668 TGCGATTTTG
* *
1326678 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTTGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG-A-
1326743 AAATCGCAACGCGAACTTC
64 AAATCGCAACGCGAACTTC
1326762 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1326827 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
*
1326844 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
1326909 ATCGCAACACGAACTTC
66 ATCGCAACGCGAACTTC
1326926 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
1326979 CGAACTTGGA
Statistics
Matches: 213, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
80 32 0.15
81 1 0.00
82 119 0.56
83 1 0.00
84 60 0.28
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
ATCGCAACGCGAACTTC
Found at i:1327038 original size:21 final size:21
Alignment explanation
Indices: 1327013--1327064 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1327003 ATATGTAAAG
1327013 CGCATTGCGATAGTCCAAGTT
1 CGCATTGCGATAGTCCAAGTT
*
1327034 CGCATTGCGATAGTCGAAGTT
1 CGCATTGCGATAGTCCAAGTT
*
1327055 CGCGTTGCGA
1 CGCATTGCGA
1327065 ATATGGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (21 bp):
CGCATTGCGATAGTCCAAGTT
Found at i:1328589 original size:18 final size:18
Alignment explanation
Indices: 1328566--1328609 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1328556 GAGGCGGTGT
*
1328566 TATTATTATTTAATAAAA
1 TATTATTATTTAAGAAAA
*
1328584 TATTATTATTTGAGAAAA
1 TATTATTATTTAAGAAAA
1328602 TATTATTA
1 TATTATTA
1328610 GTAAATGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATTATTATTTAAGAAAA
Found at i:1329617 original size:10 final size:10
Alignment explanation
Indices: 1329602--1329626 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1329592 TAATAATGTT
1329602 ATTTAAATTA
1 ATTTAAATTA
1329612 ATTTAAATTA
1 ATTTAAATTA
1329622 ATTTA
1 ATTTA
1329627 TTTAACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTAAATTA
Found at i:1329629 original size:14 final size:14
Alignment explanation
Indices: 1329607--1329657 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1329597 ATGTTATTTA
*
1329607 AATTAATTTAAATT
1 AATTTATTTAAATT
1329621 AATTTATTTAACATT
1 AATTTATTTAA-ATT
*
1329636 -ATTTATTT-ATTT
1 AATTTATTTAAATT
1329648 ATATTTATTT
1 A-ATTTATTT
1329658 CTTTGCTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 2 0.06
13 1 0.03
14 26 0.81
15 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTATTTAAATT
Found at i:1331044 original size:148 final size:149
Alignment explanation
Indices: 1330778--1331062 Score: 412
Period size: 148 Copynumber: 1.9 Consensus size: 149
1330768 AAATGAGGAC
* * *
1330778 TAAATTGATAGAATATATAAGTAAAAATTACCAAATGTGTAATTATATCAATTTGATTAAATTTT
1 TAAATTGATAGAATATATAAGTAAAAATGACCAAATGTGTAATTATATCAATTTGATGAAAATTT
* * * *
1330843 AAAAGTTAAGACGAGATAAAATATACGTGATGAATGTTAGATAATAATAAAAAATTATATTTTT-
66 AAAAGTTAAGACGAGATAAAATATACATGATGAATGTTAGATAAGAATAAAAAATCAAATTTTTA
1330907 AATAAATAACAATAAAATA
131 AATAAATAACAATAAAATA
* * *
1330926 TAAATTGATAGAATCTATAAGTAAAAATGACCAAATGTGTAATTATATCAGTTTTATGAAAATTT
1 TAAATTGATAGAATATATAAGTAAAAATGACCAAATGTGTAATTATATCAATTTGATGAAAATTT
* * **
1330991 AAAAGTTAAGATGAGATAAAATATATAT-ATTTTTATGTTAGATAAGAATAAAAAATCAAATTTT
66 AAAAGTTAAGACGAGATAAAATATACATGA--TGAATGTTAGATAAGAATAAAAAATCAAATTTT
1331055 TAAATAAA
129 TAAATAAA
1331063 ATTAAAATAT
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
147 1 0.01
148 84 0.70
149 29 0.24
150 6 0.05
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (149 bp):
TAAATTGATAGAATATATAAGTAAAAATGACCAAATGTGTAATTATATCAATTTGATGAAAATTT
AAAAGTTAAGACGAGATAAAATATACATGATGAATGTTAGATAAGAATAAAAAATCAAATTTTTA
AATAAATAACAATAAAATA
Found at i:1331205 original size:20 final size:19
Alignment explanation
Indices: 1331182--1331249 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
1331172 AAAATACATA
1331182 AATTATTATAAAATAAAGTT
1 AATTATTATAAAAT-AAGTT
*
1331202 AATTATTAT-ACAT-A---
1 AATTATTATAAAATAAGTT
1331216 AATTATTATAAAATTAAGTT
1 AATTATTATAAAA-TAAGTT
1331236 AATTATTATAAAAT
1 AATTATTATAAAAT
1331250 CAAATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 9 0.22
15 2 0.05
16 1 0.03
17 2 0.05
19 4 0.10
20 22 0.55
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (19 bp):
AATTATTATAAAATAAGTT
Found at i:1331213 original size:34 final size:34
Alignment explanation
Indices: 1331175--1331245 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
1331165 ATACTAAAAA
1331175 ATACATAAATTATTATAAAATAAAGTTAATTATT
1 ATACATAAATTATTATAAAATAAAGTTAATTATT
*
1331209 ATACATAAATTATTATAAAATTAAGTTAATTATT
1 ATACATAAATTATTATAAAATAAAGTTAATTATT
1331243 ATA
1 ATA
1331246 AAATCAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (34 bp):
ATACATAAATTATTATAAAATAAAGTTAATTATT
Found at i:1331261 original size:14 final size:16
Alignment explanation
Indices: 1331181--1331280 Score: 68
Period size: 20 Copynumber: 6.1 Consensus size: 16
1331171 AAAAATACAT
1331181 AAATTATTATAAAAT-
1 AAATTATTATAAAATC
*
1331196 AAAGTTAATTATTATACAT-
1 AAA-TT-ATTA-TA-AAATC
*
1331215 AAATTATTATAAAATTA
1 AAATTATTATAAAA-TC
1331232 AGTTAATTATTATAAAATC
1 A---AATTATTATAAAATC
1331251 AAA-TA-TAT-AAAT-
1 AAATTATTATAAAATC
1331263 AAATTATTATAAAATC
1 AAATTATTATAAAATC
1331279 AA
1 AA
1331281 GTTAATTGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
12 3 0.04
13 6 0.09
14 6 0.09
15 11 0.16
16 9 0.13
17 9 0.13
18 4 0.06
19 8 0.12
20 13 0.19
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATTATTATAAAATC
Found at i:1333256 original size:18 final size:18
Alignment explanation
Indices: 1333216--1333250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1333206 TATCATTTCA
*
1333216 TTATTCTTATTAATATTC
1 TTATTATTATTAATATTC
*
1333234 TTATTATTATTTATATT
1 TTATTATTATTAATATT
1333251 TATATTTCTT
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:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATTATTAATATTC
Found at i:1333480 original size:23 final size:23
Alignment explanation
Indices: 1333450--1333502 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1333440 GTCATATAAA
1333450 TGCACCGAAATGCCACGTAGAAT
1 TGCACCGAAATGCCACGTAGAAT
* * *
1333473 TGCACCGAAGTGTCTCGTAGAAT
1 TGCACCGAAATGCCACGTAGAAT
1333496 TGCACCG
1 TGCACCG
1333503 TAGTGCCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
TGCACCGAAATGCCACGTAGAAT
Found at i:1334337 original size:2 final size:2
Alignment explanation
Indices: 1334330--1334355 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1334320 CCTTGTTATC
1334330 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1334356 TCACATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1337633 original size:13 final size:13
Alignment explanation
Indices: 1337615--1337647 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1337605 AATGGACAAT
1337615 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
1337628 TTTGAAAACAAGG
1 TTTGAAAACAAGG
1337641 TTTGAAA
1 TTTGAAA
1337648 GTCAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:1338176 original size:22 final size:23
Alignment explanation
Indices: 1338129--1338184 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1338119 GATTCCCTAC
1338129 AGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGGTTCCCATTCAA
*
1338152 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCATTCAA
*
1338174 AGGGGGTATCG
1 AGGGGGAATCG
1338185 AGTCCTCCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCATTCAA
Found at i:1342031 original size:21 final size:22
Alignment explanation
Indices: 1342007--1342049 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1341997 AAGACTGTTT
1342007 TCATTTTTCAATTTT-AAAATA
1 TCATTTTTCAATTTTGAAAATA
**
1342028 TCATTTTTGTATTTTGAAAATA
1 TCATTTTTCAATTTTGAAAATA
1342050 GAGTCTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
TCATTTTTCAATTTTGAAAATA
Found at i:1348958 original size:27 final size:27
Alignment explanation
Indices: 1348926--1348978 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1348916 TATTTTTGCA
*
1348926 CGTCCCCTCTTGCTCCCCGCTGCATGC
1 CGTCCCCTCCTGCTCCCCGCTGCATGC
*
1348953 CGTCCCCTCCTGCTCCCCGTTGCATG
1 CGTCCCCTCCTGCTCCCCGCTGCATG
1348979 TCGCTGCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.04, C:0.51, G:0.19, T:0.26
Consensus pattern (27 bp):
CGTCCCCTCCTGCTCCCCGCTGCATGC
Found at i:1349179 original size:26 final size:26
Alignment explanation
Indices: 1349150--1349207 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
1349140 ACATAAAAGA
*
1349150 AAGAAAGGGAGAAGAGATTGCAGCCG
1 AAGAAAGGGAGAAGAGAGTGCAGCCG
* *
1349176 AAGAAAGGGAGAAGATAGTGTAGCCG
1 AAGAAAGGGAGAAGAGAGTGCAGCCG
1349202 -AGAAAG
1 AAGAAAG
1349208 AAAGAAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.45, C:0.09, G:0.38, T:0.09
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAGAGTGCAGCCG
Found at i:1349245 original size:14 final size:13
Alignment explanation
Indices: 1349202--1349247 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1349192 AGTGTAGCCG
*
1349202 AGAAAGAAAG-AA
1 AGAAAGGAAGAAA
*
1349214 AGAAAGGGAGAAA
1 AGAAAGGAAGAAA
1349227 AGAAAGGAAGAAGA
1 AGAAAGGAAGAA-A
1349241 AGAAAGG
1 AGAAAGG
1349248 GATATAAGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
AGAAAGGAAGAAA
Found at i:1349515 original size:44 final size:47
Alignment explanation
Indices: 1349455--1349543 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 47
1349445 TTATATAGTT
* *
1349455 AAAATTAACTAATTAGTTTGT-TTTGTT-AGTAGTT-AGTTATATAA
1 AAAATTAACTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
**
1349499 AAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAATTAACTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1349544 TTGTTTGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 19 0.50
45 5 0.13
46 6 0.16
47 8 0.21
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.48
Consensus pattern (47 bp):
AAAATTAACTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:1349526 original size:38 final size:38
Alignment explanation
Indices: 1349415--1349527 Score: 95
Period size: 38 Copynumber: 2.8 Consensus size: 38
1349405 TACATAAATA
* *
1349415 AAAAAATTATTTAATTAGTATGT-TT-GATAGTTATAT
1 AAAAAATTATTTAATTAGTTTGTGTTAGTTAGTTATAT
* **
1349451 AGTTAAAATTAACTAATTAGTTTGTTTTGTTAGTAGTTAGTTATAT
1 A--AAAAATTATTTAATTAGTTTG---TG-T--TAGTTAGTTATAT
1349497 AAAAAATTATTTAATTAGTTTGTGTTAGTTA
1 AAAAAATTATTTAATTAGTTTGTGTTAGTTA
1349528 AATAGTTAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
36 1 0.02
38 23 0.39
40 1 0.02
41 3 0.05
43 1 0.02
44 18 0.31
45 1 0.02
46 11 0.19
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (38 bp):
AAAAAATTATTTAATTAGTTTGTGTTAGTTAGTTATAT
Found at i:1349733 original size:15 final size:16
Alignment explanation
Indices: 1349705--1349738 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1349695 AAAGTTTACT
1349705 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
1349721 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
1349736 TTA
1 TTA
1349739 AATTTTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:1352058 original size:14 final size:14
Alignment explanation
Indices: 1352037--1352354 Score: 200
Period size: 14 Copynumber: 24.1 Consensus size: 14
1352027 ATTAGTAATA
1352037 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1352051 AGTATTAAATCATT
1 ATTATTAAATCATT
*
1352065 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
1352076 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1352090 ACTATTAAATCATT
1 ATTATTAAATCATT
*
1352104 ATTA-T-AATGATT
1 ATTATTAAATCATT
1352116 ATTATT-AA--ATT
1 ATTATTAAATCATT
1352127 ATT-TT--ATCATT
1 ATTATTAAATCATT
1352138 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1352152 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1352164 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1352178 ATTA-T-AATAATT
1 ATTATTAAATCATT
*
1352190 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1352204 ATTA-T-AATGATT
1 ATTATTAAATCATT
* *
1352216 ATTATCAAGTCATT
1 ATTATTAAATCATT
*
1352230 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
* *
1352249 AAATATTAAA--ATC
1 -ATTATTAAATCATT
*
1352262 GTTATTAAATCATT
1 ATTATTAAATCATT
*
1352276 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1352288 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1352302 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1352314 ATTATCAAATCATT
1 ATTATTAAATCATT
* *
1352328 ACTA-T-AATGATT
1 ATTATTAAATCATT
*
1352340 ATTATCAAATCATT
1 ATTATTAAATCATT
1352354 A
1 A
1352355 CTAAATCATC
Statistics
Matches: 240, Mismatches: 35, Indels: 58
0.72 0.11 0.17
Matches are distributed among these distances:
9 1 0.00
10 2 0.01
11 18 0.08
12 82 0.34
13 18 0.08
14 100 0.42
15 6 0.03
16 1 0.00
18 1 0.00
19 10 0.04
20 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1352116 original size:26 final size:26
Alignment explanation
Indices: 1352037--1352354 Score: 304
Period size: 26 Copynumber: 12.6 Consensus size: 26
1352027 ATTAGTAATA
* *
1352037 ATTATTAAATCATTAGTATTAAATCATT
1 ATTATTAAATCATTATTA-T-AATGATT
* * *
1352065 ATTATAAAATCATTACTA-AATCATT
1 ATTATTAAATCATTATTATAATGATT
*
1352090 ACTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* *
1352116 ATTATT-AA--ATTATT-TTATCATT
1 ATTATTAAATCATTATTATAATGATT
1352138 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* *
1352164 ATTACTAAATCATTATTATAATAATT
1 ATTATTAAATCATTATTATAATGATT
*
1352190 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* * * * *
1352216 ATTATCAAGTCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATGAT--T
*
1352243 ATCATTAAAT-ATTA--A-AATCG---
1 ATTATTAAATCATTATTATAAT-GATT
1352263 -TTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
*
1352288 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* *
1352314 ATTATCAAATCATTACTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
*
1352340 ATTATCAAATCATTA
1 ATTATTAAATCATTA
1352355 CTAAATCATC
Statistics
Matches: 245, Mismatches: 29, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.03
20 4 0.02
22 14 0.06
23 11 0.04
24 4 0.02
25 35 0.14
26 146 0.60
27 7 0.03
28 16 0.07
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATGATT
Found at i:1352273 original size:124 final size:124
Alignment explanation
Indices: 1352037--1352412 Score: 465
Period size: 124 Copynumber: 3.0 Consensus size: 124
1352027 ATTAGTAATA
* * * * * * *
1352037 ATTATTAAATCATTAGTATTAAATCATTATTATAAAATCATTACTA-AATCATTACTATTAAATC
1 ATTACTAAATCATTATTA-T-AATAATTATTATCAAATCATTACTATAATGATTATTATCAAATC
* * * * ** *
1352101 ATTATTATAATGAT--TATTATTAAATTATTTTATCATTATTATTAAATCATTATTATAATGATT
64 ATTACTA-AATCATCAAATCATTAAA-TA--TTAAAATCATTATTAAATCATTATTATAATGATT
* *
1352164 ATTACTAAATCATTATTATAATAATTATTA-CTAAATCATTATTATAATGATTATTATCAAGTCA
1 ATTACTAAATCATTATTATAATAATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
*
1352228 TTACTAAATCATCAAATCATTAAATATTAAAATCGTTATTAAATCATTATTATAATGATT
65 TTACTAAATCATCAAATCATTAAATATTAAAATCATTATTAAATCATTATTATAATGATT
*
1352288 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTACTAAATCATTATTATAATAATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
* *
1352353 TACTAAATCATCAAATCATTAAATATTAAATTCATTATTAAATTCATTATTA-AATCATT
66 TACTAAATCATCAAATCATTAAATATTAAAATCATTATTAAA-TCATTATTATAATGATT
1352412 A
1 A
1352413 ATAAATTATT
Statistics
Matches: 220, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
124 137 0.62
125 36 0.16
126 23 0.10
127 24 0.11
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTACTAAATCATTATTATAATAATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATCATTAAATATTAAAATCATTATTAAATCATTATTATAATGATT
Found at i:1352393 original size:12 final size:12
Alignment explanation
Indices: 1352376--1352419 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
1352366 AATCATTAAA
1352376 TATTAAATTCAT
1 TATTAAATTCAT
1352388 TATTAAATTCAT
1 TATTAAATTCAT
1352400 TATTAAA-TCAT
1 TATTAAATTCAT
*
1352411 TAATAAATT
1 TATTAAATT
1352420 ATTTTTATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:1352631 original size:21 final size:21
Alignment explanation
Indices: 1352607--1352691 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 21
1352597 AATTATTATT
1352607 ATTATTTCATTATTACTAATA
1 ATTATTTCATTATTACTAATA
* ** * *
1352628 ATTACTAAATCATTACTATTA
1 ATTATTTCATTATTACTAATA
* *
1352649 A--A--TCATTAAATATTAATA
1 ATTATTTCATT-ATTACTAATA
*
1352667 ATAATTTCATTATTACTAATA
1 ATTATTTCATTATTACTAATA
1352688 ATTA
1 ATTA
1352692 CTATCAAATC
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
17 2 0.04
18 8 0.18
19 1 0.02
20 1 0.02
21 28 0.62
22 5 0.11
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTTCATTATTACTAATA
Found at i:1352686 original size:18 final size:17
Alignment explanation
Indices: 1352659--1352833 Score: 62
Period size: 18 Copynumber: 10.6 Consensus size: 17
1352649 AATCATTAAA
*
1352659 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
*
1352677 TATTACTAATAATT-AC
1 TATTACTAATAATTCAT
* * * *
1352693 TA-T-CAAATCATTAAA
1 TATTACTAATAATTCAT
*
1352708 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
* *
1352726 TATTACTAATCATT-AC
1 TATTACTAATAATTCAT
* * * *
1352742 TA-T-CAAATCATTAAA
1 TATTACTAATAATTCAT
*
1352757 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
* *
1352775 TATTACTAATCATT-AC
1 TATTACTAATAATTCAT
* * * *
1352791 TA-T-CAAATCATTAAA
1 TATTACTAATAATTCAT
*
1352806 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
1352824 TATTACTAAT
1 TATTACTAAT
1352834 CATTACTATC
Statistics
Matches: 114, Mismatches: 31, Indels: 24
0.67 0.18 0.14
Matches are distributed among these distances:
14 23 0.20
15 12 0.11
16 12 0.11
17 18 0.16
18 49 0.43
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTACTAATAATTCAT
Found at i:1352695 original size:49 final size:49
Alignment explanation
Indices: 1352628--1352865 Score: 449
Period size: 49 Copynumber: 4.8 Consensus size: 49
1352618 ATTACTAATA
*
1352628 ATTACTAAATCATTACTATTAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
1352678 ATTACTAATAATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1352727 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1352776 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1352825 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1352866 TATGGGTGCC
Statistics
Matches: 185, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
49 179 0.97
50 6 0.03
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:1356738 original size:28 final size:30
Alignment explanation
Indices: 1356698--1356760 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
1356688 ATTTTTTATA
1356698 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1356728 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1356756 TAATA
1 TAATA
1356761 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1356767 original size:28 final size:28
Alignment explanation
Indices: 1356702--1356767 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1356692 TTTATATAAT
1356702 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
1356730 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
1356758 ATAATTTATA
1 ATAATATATA
1356768 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:1356770 original size:21 final size:21
Alignment explanation
Indices: 1356737--1356785 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1356727 CTAATATAAT
1356737 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1356758 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1356779 ATTAACT
1 A-TAACT
1356786 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1357385 original size:29 final size:29
Alignment explanation
Indices: 1357351--1357418 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1357341 CATGCATCCA
* **
1357351 CTCCTTGGTCGCCCGGAGTGCATGGTAAC
1 CTCCTTGGTCGCCCGGAATGCATGACAAC
* *
1357380 CTCCTTGGTCGCCCGTAATGCATGACGAC
1 CTCCTTGGTCGCCCGGAATGCATGACAAC
1357409 CTCCTTGGTC
1 CTCCTTGGTC
1357419 ACTGTAGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (29 bp):
CTCCTTGGTCGCCCGGAATGCATGACAAC
Found at i:1358732 original size:5 final size:5
Alignment explanation
Indices: 1358722--1358791 Score: 140
Period size: 5 Copynumber: 14.0 Consensus size: 5
1358712 TCTTTTGTCT
1358722 TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC
1 TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC
1358772 TAAAC TAAAC TAAAC TAAAC
1 TAAAC TAAAC TAAAC TAAAC
1358792 ATATTAATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 65 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAC
Found at i:1359953 original size:2 final size:2
Alignment explanation
Indices: 1359948--1359974 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1359938 ATTAAAAAAT
1359948 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1359975 GATCTTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1361970 original size:2 final size:2
Alignment explanation
Indices: 1361958--1361990 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1361948 AATATTGTAC
1361958 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1361991 GATGTATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1362253 original size:2 final size:2
Alignment explanation
Indices: 1362185--1362235 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1362175 TTTTATAAAC
1362185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1362227 AT AT AT AT A
1 AT AT AT AT A
1362236 CCGTCACATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1363492 original size:2 final size:2
Alignment explanation
Indices: 1363485--1363518 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1363475 CTTATATTAA
*
1363485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1363519 TTTACTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1363636 original size:2 final size:2
Alignment explanation
Indices: 1363629--1363666 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1363619 CAAGCTAATG
1363629 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1363667 CTTCCCTCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1367062 original size:17 final size:19
Alignment explanation
Indices: 1367034--1367071 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1367024 ATATTTTGTA
1367034 TTTTTATATTT-CATGTTT
1 TTTTTATATTTCCATGTTT
1367052 TTTTTAT-TTTCCATGTTT
1 TTTTTATATTTCCATGTTT
1367070 TT
1 TT
1367072 ACATTCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTATATTTCCATGTTT
Found at i:1367466 original size:39 final size:39
Alignment explanation
Indices: 1367412--1367490 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
1367402 CACCCGGAGT
* * *
1367412 ATTACCCGGGGACTCATCCGCTACTAAAGGGAAAGCTGC
1 ATTACCCGAGGACTCATCCGCTACCAAAGCGAAAGCTGC
* * *
1367451 ATTACCCGAGGACTCATTCGTTACCAAAGCGAAAGTTGC
1 ATTACCCGAGGACTCATCCGCTACCAAAGCGAAAGCTGC
1367490 A
1 A
1367491 CCTGCTGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (39 bp):
ATTACCCGAGGACTCATCCGCTACCAAAGCGAAAGCTGC
Found at i:1375016 original size:43 final size:43
Alignment explanation
Indices: 1374968--1375127 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
1374958 CAGAGCCAAT
1374968 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * *
1375011 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCGATAAACAATTCCAGAGCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---C---G-CAAG
1375066 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
1375109 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
1375128 GACCGCTGGT
Statistics
Matches: 86, Mismatches: 19, Indels: 24
0.67 0.15 0.19
Matches are distributed among these distances:
43 37 0.43
44 4 0.05
45 3 0.03
46 2 0.02
47 1 0.01
48 5 0.06
50 5 0.06
51 1 0.01
52 2 0.02
53 3 0.03
54 4 0.05
55 19 0.22
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:1375083 original size:55 final size:53
Alignment explanation
Indices: 1375006--1375378 Score: 167
Period size: 55 Copynumber: 7.5 Consensus size: 53
1374996 TCCAGACAAC
* * *
1375006 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCGATAAACAATTCCAGA
1 GCAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAATT-CAGA
*** * * *
1375060 GCCAATTTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA--C---
1 G-CAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAATTCAGA
* * *
1375104 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCGATAAACAATTTCAGA
1 GCAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAA-TTCAGA
*** * * *
1375158 GTCAATTTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA-T----
1 G-CAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAATTCAGA
* * *
1375202 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTCGTCGATAAACAATTTCAGAA
1 GCAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAA-TTCAG-A
* * * *** * *
1375257 CCAATTTTAACTTCACAATGAA-GGA-TATTGG-ACTCCAT--ACAA-T----
1 GCAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAATTCAGA
* * * *
1375300 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCAGA
1 GCAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAA-TTCAGA
1375354 GCCAATTTCAACTTCACAACGAAGG
1 G-CAATTTCAACTTCACAACGAAGG
1375379 ATATTGGACT
Statistics
Matches: 222, Mismatches: 60, Indels: 73
0.63 0.17 0.21
Matches are distributed among these distances:
43 55 0.25
44 11 0.05
45 9 0.04
46 8 0.04
47 1 0.00
48 16 0.07
50 16 0.07
51 1 0.00
52 8 0.04
53 9 0.04
54 12 0.05
55 76 0.34
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (53 bp):
GCAATTTCAACTTCACAACGAAGGGACCGCTGGTAGTCGATAAACAATTCAGA
Found at i:1375126 original size:98 final size:98
Alignment explanation
Indices: 1374958--1375577 Score: 1049
Period size: 98 Copynumber: 6.4 Consensus size: 98
1374948 AGGTTTTACC
1374958 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1375023 ACGAAGGGACCGCTGGTTGTCGATAAACAATTC
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
1375056 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1375121 ACGAAGGGACCGCTGGTTGTCGATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
* *
1375154 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1375219 ACGAAGGGACCGCTGGTCGTCGATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
* * * * *
1375252 CAGAACCAATTTTAACTTCACAATGAAGGATATTGGACTCCATACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1375317 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
1375350 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1375415 ACGAAGGGACCGCTGGTTGTCAATCAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
1375448 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1375509 ACGAAGGGACCGCTGGTTGTCAATCAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
1375542 C----CCAATTTCAACTTCACAACGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1375578 GGAACAATAC
Statistics
Matches: 504, Mismatches: 18, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
94 128 0.25
98 376 0.75
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (98 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
Found at i:1375421 original size:43 final size:43
Alignment explanation
Indices: 1375360--1375515 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 43
1375350 CAGAGCCAAT
1375360 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * * * *
1375403 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-CA-ACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA----T-ATTG-GACTCCAGACAA---CGCAAG
1375454 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
1375497 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
1375516 GACCGCTGGT
Statistics
Matches: 88, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
43 38 0.43
44 5 0.06
45 5 0.06
46 5 0.06
48 5 0.06
49 5 0.06
50 5 0.06
51 20 0.23
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:1375924 original size:2 final size:2
Alignment explanation
Indices: 1375878--1375908 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1375868 TTTTATAAAC
*
1375878 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1375909 CACGTCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
AT
Found at i:1382789 original size:21 final size:21
Alignment explanation
Indices: 1382759--1382798 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1382749 ATATTTTACT
1382759 TTTTAGTTTCCATAATTTTTA
1 TTTTAGTTTCCATAATTTTTA
* *
1382780 TTTTATTTTCCATTATTTT
1 TTTTAGTTTCCATAATTTT
1382799 AGAAAAGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTAGTTTCCATAATTTTTA
Found at i:1386804 original size:81 final size:81
Alignment explanation
Indices: 1386669--1386833 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 81
1386659 CTTATATAAA
*
1386669 TCTGAAACTGTTGGAGTCATACGGATGAATGTGGAAAGCATCATGCTGCATTTGCAGTTCTGCAG
1 TCTGAAACTGTAGGAGTCATACGGATGAATGTGGAAAGCATCATGCTGCATTTGCAGTTCTGCAG
1386734 AAGTACCATAACACAT
66 AAGTACCATAACACAT
1386750 TCTGAAACTGTAGGAGTCATACGGATGAATGTGGAAAGCATCATGCTGCATTTGCAGTTCTGCAG
1 TCTGAAACTGTAGGAGTCATACGGATGAATGTGGAAAGCATCATGCTGCATTTGCAGTTCTGCAG
1386815 AAGTACCATAACACAT
66 AAGTACCATAACACAT
1386831 TCT
1 TCT
1386834 TATTATCATT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (81 bp):
TCTGAAACTGTAGGAGTCATACGGATGAATGTGGAAAGCATCATGCTGCATTTGCAGTTCTGCAG
AAGTACCATAACACAT
Found at i:1386927 original size:83 final size:84
Alignment explanation
Indices: 1386788--1386959 Score: 319
Period size: 83 Copynumber: 2.1 Consensus size: 84
1386778 ATGTGGAAAG
*
1386788 CATCATGCTGCATTTGCAGTTCTGCAGAAGTACCATAACACATTCTTATTATCATTA-TTTTTTT
1 CATCATGCTGCATTTGCAGTTCTGCAGAAGTACCATAACACATTCTTATCATCATTATTTTTTTT
1386852 AATGTTCTTAATTCTGGTC
66 AATGTTCTTAATTCTGGTC
1386871 CATCATGCTGCATTTGCAGTTCTGCAGAAGTACCATAACACATTCTTATCATCATTATTTTTTTT
1 CATCATGCTGCATTTGCAGTTCTGCAGAAGTACCATAACACATTCTTATCATCATTATTTTTTTT
1386936 AATGTTCTTAATTCTGGTC
66 AATGTTCTTAATTCTGGTC
*
1386955 TATCA
1 CATCA
1386960 GCTTCAAATG
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
83 56 0.65
84 30 0.35
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.43
Consensus pattern (84 bp):
CATCATGCTGCATTTGCAGTTCTGCAGAAGTACCATAACACATTCTTATCATCATTATTTTTTTT
AATGTTCTTAATTCTGGTC
Found at i:1390539 original size:37 final size:37
Alignment explanation
Indices: 1390484--1390641 Score: 131
Period size: 42 Copynumber: 4.0 Consensus size: 37
1390474 TTTGAGAACA
* **
1390484 AAAAACTCCGCAAAAGGTCGTTATCTATAGCGGCGTT
1 AAAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTT
*
1390521 AAAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTT
1 AAAAACGCCGCAAAAGGTCGAGATCTATAGCGGCG---TT
*
1390561 GGAATAAATGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTCT
1 --AA-AAACGCCGCAAAAGGTCGAGATCTATAGCGGCG--T-T
* *
1390603 AGAACAAACGCTGTAAAAGGTC-AGATCTATAGCGGCGTT
1 --AA-AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTT
1390642 TTTTTGATAC
Statistics
Matches: 103, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
37 31 0.30
39 1 0.01
40 3 0.03
41 3 0.03
42 50 0.49
43 15 0.15
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (37 bp):
AAAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTT
Found at i:1390716 original size:43 final size:43
Alignment explanation
Indices: 1390523--1390826 Score: 398
Period size: 43 Copynumber: 7.1 Consensus size: 43
1390513 GCGGCGTTAA
* *
1390523 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGA-AT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * *
1390566 AAATGCCGCAAAAGGTCAGATCTATAGCGGCGTTTCTAGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * *
1390608 AAACGCTGTAAAAGGTCAGATCTATAGCGGCGTTTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGATAC
* * * *
1390652 AAACGCCGTAAAAGGTCA-ATCTGTAGCGGCATTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * *
1390694 AAACGCCGCAAAAGGTCAAATCTATAGCGGAGTTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* *
1390737 AAACGCCGCAAAAGGTTAGATCTATAGCGGCGTTTTTGGATAT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* *
1390780 AAACGCCGCAAAAGGTCAAATCTATAGCGACGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
1390823 AAAC
1 AAAC
1390827 TATGTATTTA
Statistics
Matches: 232, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
42 79 0.34
43 134 0.58
44 19 0.08
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
Found at i:1390980 original size:21 final size:21
Alignment explanation
Indices: 1390936--1390996 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1390926 ATTATCCAAT
* *
1390936 AAACTTGACAT-CATAACAAC
1 AAACTTGAAATCCATAATAAC
*
1390956 AAACTTGAAATCCATAATAAG
1 AAACTTGAAATCCATAATAAC
1390977 AAACTTGAAATCCATAATAA
1 AAACTTGAAATCCATAATAA
1390997 TAAATCAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
20 10 0.27
21 27 0.73
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (21 bp):
AAACTTGAAATCCATAATAAC
Found at i:1392051 original size:66 final size:66
Alignment explanation
Indices: 1391939--1392069 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 66
1391929 CCAAGCTAAA
*
1391939 TGCAACAATCAGAAACAATAAACCATCCTCATCTAGACTTGAAAGGATA-TTCACATTGAATCAA
1 TGCAACAATCAGAAACAATAAACCATCCTCACCTAGACTTGAAAGGA-ACTTCACATTGAATCAA
1392003 AG
65 AG
* *
1392005 TGCATCAATCAGAAACAATAAACCATCCTCACCTAGACTTGCAAGGAACTTCACATTGAATCAAA
1 TGCAACAATCAGAAACAATAAACCATCCTCACCTAGACTTGAAAGGAACTTCACATTGAATCAAA
1392070 TTTTCTATCC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 1 0.02
66 60 0.98
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (66 bp):
TGCAACAATCAGAAACAATAAACCATCCTCACCTAGACTTGAAAGGAACTTCACATTGAATCAAA
G
Found at i:1394011 original size:41 final size:41
Alignment explanation
Indices: 1393920--1394304 Score: 406
Period size: 41 Copynumber: 9.4 Consensus size: 41
1393910 GCAATTGCAG
* *
1393920 CACGAGTCTATAGCGGCTTTTGTAAACACAAACGCCACTAAAGT
1 CACGAGTCTATAGCGGCGTTTGTATA-A-AAACGCCACTAAA-T
* *
1393964 -ATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGT
1 CACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA-T
** *
1394005 -ACGAGTCTATAGCATCGTTTGTATAAAAATGCCACTAAAT
1 CACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
* * *
1394045 CACGATTCTTTAGCGGCGTTTGTA-AAAAAAGCCACTAAAT
1 CACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
* *
1394085 CAC-AGTCTTTAGCAGCGTTTGTATAAAAACGCCACTAAAT
1 CACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
* * **
1394125 CATGAGTCTATAGCAGCGTTTGTATAAAAATTCCACTAAAT
1 CACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
*
1394166 CACGAGTCTATAACGGCGTTTGTATAAAAACGCCACTAAAT
1 CACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
* *
1394207 CACGAGTCTATAGCGGCGTTTTTGA-AACAAACGCCGCTAAA-
1 CACGAGTCTATAGCGGCGTTTGT-ATAA-AAACGCCACTAAAT
* ** * * * *
1394248 GACTCGTACTATTGCGACGTTTGTATAGAAATGCCACTAAAT
1 CACGAGT-CTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
* *
1394290 TAC-AGTCTTTAGCGG
1 CACGAGTCTATAGCGG
1394305 GAATGTCATT
Statistics
Matches: 290, Mismatches: 43, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
39 18 0.06
40 42 0.14
41 179 0.62
42 30 0.10
43 21 0.07
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (41 bp):
CACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
Found at i:1395216 original size:96 final size:96
Alignment explanation
Indices: 1395052--1395244 Score: 298
Period size: 96 Copynumber: 2.0 Consensus size: 96
1395042 TGCACCTTTG
* * * *
1395052 CATGTGTGATGCTCGAACATGATACCTTAAGGGATAAGAAAAATCCTTTAACCACTGAGGTCGTA
1 CATGTGTGATGATAGAACATGATACCTTAAGGGATAACAAAAATCCTTTAACCACCGAGGTCGTA
*
1395117 TAATAAATGGTATTTATTTTTACACAATTTA
66 TAATAAATGATATTTATTTTTACACAATTTA
* *
1395148 CATGTGTGGTGATAGAACATGATACCTTAAGGGATAACAACAAT-CTCTTAACCACCGAGGTCGT
1 CATGTGTGATGATAGAACATGATACCTTAAGGGATAACAAAAATCCT-TTAACCACCGAGGTCGT
*
1395212 ATAATAAATGATATTTATTTTTGCACAATTTA
65 ATAATAAATGATATTTATTTTTACACAATTTA
1395244 C
1 C
1395245 TTAAAAGTAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 2 0.02
96 86 0.98
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (96 bp):
CATGTGTGATGATAGAACATGATACCTTAAGGGATAACAAAAATCCTTTAACCACCGAGGTCGTA
TAATAAATGATATTTATTTTTACACAATTTA
Found at i:1398944 original size:23 final size:24
Alignment explanation
Indices: 1398898--1398950 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
1398888 AAAAAACAAA
1398898 ATAATTTTAAATAAAGATTATTTT
1 ATAATTTTAAATAAAGATTATTTT
* *
1398922 ATAATTTTGAAT-AATATTATTTT
1 ATAATTTTAAATAAAGATTATTTT
1398945 ATAATT
1 ATAATT
1398951 GATTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
ATAATTTTAAATAAAGATTATTTT
Found at i:1402802 original size:20 final size:20
Alignment explanation
Indices: 1402777--1402975 Score: 102
Period size: 20 Copynumber: 9.8 Consensus size: 20
1402767 GATTTTCCAG
1402777 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
1402797 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
1402817 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* * * * **
1402837 TATCGTAACGAGTATCCGTAA
1 AATCGCAACGCGAATATG-AA
* *
1402858 AATCGCAACGCGTAT-TCGTA
1 AATCGCAACGCGAATAT-GAA
*
1402878 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* *
1402899 AATCGCAACGCGTAT-TCGTA
1 AATCGCAACGCGAATAT-GAA
* *
1402919 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* ** *
1402940 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
1402960 AATCGCAACGCGAATA
1 AATCGCAACGCGAATA
1402976 CGTCATTGCG
Statistics
Matches: 133, Mismatches: 33, Indels: 26
0.69 0.17 0.14
Matches are distributed among these distances:
19 1 0.01
20 87 0.65
21 45 0.34
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:1402862 original size:21 final size:20
Alignment explanation
Indices: 1402838--1402969 Score: 120
Period size: 21 Copynumber: 6.5 Consensus size: 20
1402828 GATTCTGACT
* *
1402838 ATCGTAACGAGTATCCGTAAA
1 ATCGCAACGAGTATACGT-AA
* *
1402859 ATCGCAACGCGTATTCGTAA
1 ATCGCAACGAGTATACGTAA
**
1402879 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATACGT-AA
* *
1402900 ATCGCAACGCGTATTCGTAA
1 ATCGCAACGAGTATACGTAA
* **
1402920 ATCGCAATGACAATACGTAAA
1 ATCGCAACGAGTATACGT-AA
* *
1402941 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATACGTAA
1402961 ATCGCAACG
1 ATCGCAACG
1402970 CGAATACGTC
Statistics
Matches: 88, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
20 42 0.48
21 46 0.52
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATACGTAA
Found at i:1402888 original size:41 final size:41
Alignment explanation
Indices: 1402777--1402978 Score: 218
Period size: 41 Copynumber: 5.0 Consensus size: 41
1402767 GATTTTCCAG
* * * *
1402777 AATCGCAACGCGAATAT-GAAAATCGCAACG-CGA-ACATATA
1 AATCGCAACGCGTAT-TCGTAAATCGCAACGACAATACGTA-A
* * ** *
1402817 AATCGCAACGCG-ATTC-TGACTATCGTAACGAGTATCCGTAA
1 AATCGCAACGCGTATTCGT-A-AATCGCAACGACAATACGTAA
1402858 AATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTAA
*
1402899 AATCGCAACGCGTATTCGTAAATCGCAATGACAATACGTAA
1 AATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTAA
*
1402940 AATCGCAACGCGTATCCGTAAATCGCAACG-CGAATACGT
1 AATCGCAACGCGTATTCGTAAATCGCAACGAC-AATACGT
1402979 CATTGCGATT
Statistics
Matches: 139, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 21 0.15
41 105 0.76
42 8 0.06
43 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
AATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTAA
Found at i:1403872 original size:24 final size:24
Alignment explanation
Indices: 1403821--1403874 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1403811 GTATTCGAAA
*
1403821 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1403845 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1403869 TTTGAT
1 TTTGAT
1403875 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1406327 original size:19 final size:19
Alignment explanation
Indices: 1406303--1406434 Score: 104
Period size: 19 Copynumber: 7.4 Consensus size: 19
1406293 CTTAATGTCT
*
1406303 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
1406322 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1406336 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1406355 ATCGCAA--CG---TGAAA
1 ATCGCAATGCGAAATGAAA
* *
1406369 ATCGCAATGCAAATATGAAT
1 ATCGCAATGCGAA-ATGAAA
* **
1406389 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
*
1406409 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1406428 ATCGCAA
1 ATCGCAA
1406435 CGAGAGAATC
Statistics
Matches: 88, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 3 0.03
17 4 0.05
18 1 0.01
19 30 0.34
20 26 0.30
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Done.