Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008981.1 Hibiscus syriacus cultivar Beakdansim tig00112343_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: 1473337
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 7 of 7
Found at i:1399946 original size:19 final size:18
Alignment explanation
Indices: 1399922--1399957 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1399912 AAATAATGTT
*
1399922 TTTGTTTGTTTTGATTTTA
1 TTTGTTT-TTTTAATTTTA
1399941 TTTGTTTTTTTAATTTT
1 TTTGTTTTTTTAATTTT
1399958 CTGAACTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTGTTTTTTTAATTTTA
Found at i:1404511 original size:29 final size:28
Alignment explanation
Indices: 1404466--1404537 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
1404456 TGACAATCAT
* * *
1404466 AGTTTAAGGATGTAATTAGAATGCTTAAA
1 AGTTT-AGGATGAAATTAAAATACTTAAA
*
1404495 AGTTTAGGAATGAAATTAAAATATTTAAA
1 AGTTTAGG-ATGAAATTAAAATACTTAAA
*
1404524 AATTTAGGGATGAA
1 AGTTTA-GGATGAA
1404538 GCTAGAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.08
29 31 0.86
30 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.19, T:0.33
Consensus pattern (28 bp):
AGTTTAGGATGAAATTAAAATACTTAAA
Found at i:1408417 original size:8 final size:8
Alignment explanation
Indices: 1408404--1408432 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1408394 ATGAGTACTT
1408404 TTTTTTTG
1 TTTTTTTG
1408412 TTTTTTT-
1 TTTTTTTG
1408419 TTTTTTTG
1 TTTTTTTG
1408427 TTTTTT
1 TTTTTT
1408433 AATATGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1408422 original size:15 final size:15
Alignment explanation
Indices: 1408402--1408432 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1408392 GTATGAGTAC
1408402 TTTTTTTTTGTTTTT
1 TTTTTTTTTGTTTTT
1408417 TTTTTTTTTGTTTTT
1 TTTTTTTTTGTTTTT
1408432 T
1 T
1408433 AATATGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (15 bp):
TTTTTTTTTGTTTTT
Found at i:1409574 original size:15 final size:15
Alignment explanation
Indices: 1409554--1409596 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1409544 ATAAGGTTAT
1409554 TTATTTTAAAATAAA
1 TTATTTTAAAATAAA
1409569 TTATTTTAAAATAAA
1 TTATTTTAAAATAAA
*
1409584 TTATTATAAAATA
1 TTATTTTAAAATA
1409597 TGGATTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATTTTAAAATAAA
Found at i:1409635 original size:32 final size:32
Alignment explanation
Indices: 1409599--1409755 Score: 138
Period size: 32 Copynumber: 5.5 Consensus size: 32
1409589 ATAAAATATG
1409599 GATTGATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
1409631 GATTGATTTATTTT-AA-AA--TA-T-G----
1 GATTGATTTATTTTAAATAATTTATTAGTATA
* *
1409653 GATTAATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
1409685 GATTGATTTA-TTT---TAA---A--A-TATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
* *
1409707 GATTGATTTATTTTAAATAATTTATTCGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
1409739 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
1409756 ATATAGATTG
Statistics
Matches: 100, Mismatches: 5, Indels: 40
0.69 0.03 0.28
Matches are distributed among these distances:
22 26 0.26
23 6 0.06
24 2 0.02
25 1 0.01
26 6 0.06
27 2 0.02
28 6 0.06
29 1 0.01
30 2 0.02
31 5 0.05
32 43 0.43
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:1409650 original size:54 final size:54
Alignment explanation
Indices: 1409584--1409772 Score: 324
Period size: 54 Copynumber: 3.5 Consensus size: 54
1409574 TTAAAATAAA
* * *
1409584 TTATTATAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* *
1409638 TTATTTTAAAATATGGATTAATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
1409692 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTCGTATGGATTGAT
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1409746 TTATTTTAAAATATAGATTGATTTATT
1 TTATTTTAAAATATAGATTGATTTATT
1409773 ATTGTAGTTG
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 129 1.00
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.52
Consensus pattern (54 bp):
TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:1409809 original size:80 final size:80
Alignment explanation
Indices: 1409703--1409852 Score: 237
Period size: 80 Copynumber: 1.9 Consensus size: 80
1409693 TATTTTAAAA
* * * * * *
1409703 TATAGATTGATTTATTTTAAATAATTTATTCGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATAAATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATAGATTGAT
1409768 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
1409783 TATAAATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATGGATTGAT
1 TATAAATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATAGATTGAT
1409848 TTATT
66 TTATT
1409853 TTAAAAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.51
Consensus pattern (80 bp):
TATAAATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATAGATTGAT
TTATTATTGTAGTTG
Found at i:1409828 original size:32 final size:32
Alignment explanation
Indices: 1409782--1409890 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 32
1409772 TATTGTAGTT
*
1409782 GTATAAATTGATTTATTTTAAAAAATTTATTA
1 GTATAGATTGATTTATTTTAAAAAATTTATTA
* *
1409814 GTATAGATTAATTTATTTT--AAAA--CA-T-
1 GTATAGATTGATTTATTTTAAAAAATTTATTA
1409840 G----GATTGATTTATTTTAAAAAATTTATTA
1 GTATAGATTGATTTATTTTAAAAAATTTATTA
*
1409868 GTATGGATTGATTTATTTTAAAA
1 GTATAGATTGATTTATTTTAAAA
1409891 TATGGATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
22 13 0.21
24 4 0.06
26 2 0.03
27 2 0.03
28 2 0.03
30 4 0.06
32 35 0.56
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (32 bp):
GTATAGATTGATTTATTTTAAAAAATTTATTA
Found at i:1409828 original size:134 final size:134
Alignment explanation
Indices: 1409658--1409906 Score: 417
Period size: 134 Copynumber: 1.9 Consensus size: 134
1409648 ATATGGATTA
* * * *
1409658 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAA
1 ATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATAGATTGATTTATTTTAA
* * *
1409723 ATAATTTATTCGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATAA
66 AAAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTAATTTATTATTGTAGTTGTATAA
1409788 ATTG
131 ATTG
*
1409792 ATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATGGATTGATTTATTTTAA
1 ATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATAGATTGATTTATTTTAA
*
1409857 AAAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATT
66 AAAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTAATTTATT
1409907 TTAAATAATT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 106 1.00
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (134 bp):
ATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATAGATTGATTTATTTTAA
AAAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTAATTTATTATTGTAGTTGTATAA
ATTG
Found at i:1409856 original size:54 final size:54
Alignment explanation
Indices: 1409788--1409921 Score: 223
Period size: 54 Copynumber: 2.5 Consensus size: 54
1409778 AGTTGTATAA
1409788 ATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATGG
1 ATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATGG
* * *
1409842 ATTGATTTATTTTAAAAAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
1 ATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATGG
* *
1409896 ATTAATTTATTTTAAATAATTTATTA
1 ATTGATTTATTTTAAAAAATTTATTA
1409922 TTGTAGTTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.51
Consensus pattern (54 bp):
ATTGATTTATTTTAAAAAATTTATTAGTATAGATTAATTTATTTTAAAACATGG
Found at i:1409921 original size:22 final size:22
Alignment explanation
Indices: 1409869--1409911 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1409859 AATTTATTAG
*
1409869 TATGGATTGATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
1409891 TATGGATTAATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
1409912 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:1409971 original size:31 final size:31
Alignment explanation
Indices: 1409936--1409994 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1409926 AGTTGTATGG
* *
1409936 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATATCAGTATTGCAAAACTAAA
1409967 ATTATTTAAATATCAGTATTGCAAAACT
1 ATTATTTAAATATCAGTATTGCAAAACT
1409995 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATATCAGTATTGCAAAACTAAA
Found at i:1412972 original size:95 final size:95
Alignment explanation
Indices: 1412809--1412999 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
1412799 AACGTTTTCC
1412809 TCCCTAATTTTTAAATTAAAAAGGAAGTGGAACCAAGCTATTTTTTTTAGTCGTATATTTAAGGT
1 TCCCTAATTTTTAAATTAAAAAGGAAGTGGAACCAAGCTATTTTTTTTAGTCGTATATTTAAGGT
1412874 GGACGAGTCTTTGATGGATATATATATATA
66 GGACGAGTCTTTGATGGATATATATATATA
*
1412904 TCCCTAATTTTTAAATTAAAAAGGAAGTGGATCCAAGCTATTTTTTTTAGTCGTATATTTAAGGT
1 TCCCTAATTTTTAAATTAAAAAGGAAGTGGAACCAAGCTATTTTTTTTAGTCGTATATTTAAGGT
1412969 GGACGAGTCTTTGATGGATATATATATATA
66 GGACGAGTCTTTGATGGATATATATATATA
1412999 T
1 T
1413000 ATATATATAT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (95 bp):
TCCCTAATTTTTAAATTAAAAAGGAAGTGGAACCAAGCTATTTTTTTTAGTCGTATATTTAAGGT
GGACGAGTCTTTGATGGATATATATATATA
Found at i:1412993 original size:2 final size:2
Alignment explanation
Indices: 1412986--1413031 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1412976 TCTTTGATGG
1412986 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
1413028 AT AT
1 AT AT
1413032 GAGAATTCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1414070 original size:22 final size:20
Alignment explanation
Indices: 1414045--1414097 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
1414035 TTTTGAAATT
* *
1414045 TATTTTTTAAAAAATATTATTA
1 TATTTATTAAAAAAAATTA--A
*
1414067 TATTTATAAAAAAAAATTAA
1 TATTTATTAAAAAAAATTAA
*
1414087 TATTTCTTAAA
1 TATTTATTAAA
1414098 TTATATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTATTAAAAAAAATTAA
Found at i:1418352 original size:2 final size:2
Alignment explanation
Indices: 1418345--1418370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1418335 TCTTTTTCTT
1418345 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
1418371 ATTTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1422663 original size:6 final size:6
Alignment explanation
Indices: 1422652--1422700 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
1422642 TATAGACAAA
* *
1422652 AAAATT AAAATT AAAATT AAAATT -AAA-T AAAA-T AAAATG AAATTT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
1422697 AAAA
1 AAAA
1422701 GTTCACGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 1 0.03
5 11 0.30
6 25 0.68
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:1422687 original size:21 final size:22
Alignment explanation
Indices: 1422657--1422699 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1422647 ACAAAAAAAT
*
1422657 TAAAATTAAAATTAAAATTAAA
1 TAAAATTAAAATGAAAATTAAA
*
1422679 TAAAA-TAAAATGAAATTTAAA
1 TAAAATTAAAATGAAAATTAAA
1422700 AGTTCACGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAAATTAAAATGAAAATTAAA
Found at i:1425841 original size:6 final size:6
Alignment explanation
Indices: 1425830--1425882 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
1425820 CGTGGAGTCC
1425830 GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT
1 GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT
1425878 GGATT
1 GGATT
1425883 AGGCACGTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (6 bp):
GGATTT
Found at i:1428128 original size:135 final size:135
Alignment explanation
Indices: 1427874--1428134 Score: 310
Period size: 135 Copynumber: 1.9 Consensus size: 135
1427864 TTCACATGGG
* * * * * * * *
1427874 CATGCAGGATCCTCATAGCTAATAGACTTGAAAATTTACTCACCCCTCTCCCTTGCTTTTTTAGG
1 CATGCAGGACCCTCATAACTAAAAGACCTGAAAATTCACTCACCCCTCTCCATTGCTTGTTTAGA
* * * ***
1427939 TTTTCTTTCCGTTTTCGCAGATTCAGCTTGAGCTGCCGTGTCAAGGAAATAACAAATTATTAGCC
66 TTTTCTTTCCATTTTCGCAGAGTCAGATTGAGCTGCCACATCAAGGAAATAACAAATTATTAGCC
1428004 AAAAT
131 AAAAT
* *
1428009 CATGCAGGACCCTCATAACTAAAAGACCTGAAAATTCACTTACCCTTCTCCATTGCTTGTTTAGA
1 CATGCAGGACCCTCATAACTAAAAGACCTGAAAATTCACTCACCCCTCTCCATTGCTTGTTTAGA
* * * *
1428074 TTTTGTTTCCAATTTT-GTAGAGTCAGATTGAGCTGCCACATCAGGGGAAA-AACAATTTATT
66 TTTTCTTTCC-ATTTTCGCAGAGTCAGATTGAGCTGCCACATCA-AGGAAATAACAAATTATT
1428135 CAAGCAGTGA
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
135 95 0.91
136 9 0.09
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (135 bp):
CATGCAGGACCCTCATAACTAAAAGACCTGAAAATTCACTCACCCCTCTCCATTGCTTGTTTAGA
TTTTCTTTCCATTTTCGCAGAGTCAGATTGAGCTGCCACATCAAGGAAATAACAAATTATTAGCC
AAAAT
Found at i:1429614 original size:68 final size:64
Alignment explanation
Indices: 1429491--1429672 Score: 265
Period size: 68 Copynumber: 2.7 Consensus size: 64
1429481 TTCCTCCTCC
*
1429491 TCTTCCTTTTCCTCTTCTTTCTCTTCTTCTTTTGAACTTTCAGCATTTGTGGAAACAGGATCATC
1 TCTTCCTTTTCCTCTTCTTTCTC-T-TTCTTTTGAACTTTCAGCATTTGTAGAAACAGGATCATC
1429556 A
64 A
1429557 TCGTCTTCCTTTTCCTCTTCTTTCTCTTTGCTTTTGAACTTTCAGCATTTGTAGAAACAGGATCA
1 ---TCTTCCTTTTCCTCTTCTTTCTCTTT-CTTTTGAACTTTCAGCATTTGTAGAAACAGGATCA
1429622 TCA
62 TCA
* *
1429625 TCTTCCTTTTCCTCTTCTTTCTCCTCTTCCTTTGCACTTTCAGCATTT
1 TCTTCCTTTTCCTCTTCTTTCT-CT-TTCTTTTGAACTTTCAGCATTT
1429673 AAGGAGACAG
Statistics
Matches: 107, Mismatches: 3, Indels: 9
0.90 0.03 0.08
Matches are distributed among these distances:
65 22 0.21
66 20 0.19
67 4 0.04
68 38 0.36
69 23 0.21
ACGTcount: A:0.14, C:0.28, G:0.09, T:0.48
Consensus pattern (64 bp):
TCTTCCTTTTCCTCTTCTTTCTCTTTCTTTTGAACTTTCAGCATTTGTAGAAACAGGATCATCA
Found at i:1432068 original size:20 final size:21
Alignment explanation
Indices: 1432045--1432084 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1432035 ATATAATCTA
*
1432045 TTTTT-ATTTT-ATATTATTT
1 TTTTTAATTTTCAAATTATTT
1432064 TTTTTAATTTTCAAATTATTT
1 TTTTTAATTTTCAAATTATTT
1432085 CATCCTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTAATTTTCAAATTATTT
Found at i:1432612 original size:14 final size:13
Alignment explanation
Indices: 1432588--1432618 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1432578 GAGTTATTCA
1432588 ATTTTTTATAATT
1 ATTTTTTATAATT
1432601 ATTTTGTTATAATT
1 ATTTT-TTATAATT
1432615 ATTT
1 ATTT
1432619 GACTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
ATTTTTTATAATT
Found at i:1435403 original size:3 final size:3
Alignment explanation
Indices: 1435395--1435428 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1435385 CATTCAAAAC
1435395 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1435429 AACAGATCAG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1440826 original size:213 final size:213
Alignment explanation
Indices: 1440416--1440833 Score: 680
Period size: 213 Copynumber: 2.0 Consensus size: 213
1440406 CATGTGCTGA
*
1440416 TTCTGCAAGCTGAATGTCTTTACACTTCATCGCATCAAGACGATTACGGTTTGCCTCTGATAGTC
1 TTCTGCAAGCTGAATGTCCTTACACTTCATCGCATCAAGACGATTACGGTTTGCCTCTGATAGTC
1440481 TATTCACAACTACAAAAGCAGCAGTTGAACAAGCAGATGCATTTCTTAAGTCACCTTCAGCAATC
66 TATTCACAACTACAAAAGCAGCAGTTGAACAAGCAGATGCATTTCTTAAGTCACCTTCAGCAATC
* * *
1440546 TTCATTCTATCCTCGAGCTTTGTAATGATTGATGTTTTTTCATTCAGTTCTTTCTTCAATTGAAC
131 TTCATTCTATCCTCAAGCTTTGTAATGATTGATGTTTTTTCATTCAATTCTTTCTTCAATAGAAC
1440611 AATTTCTTTCACATTTTC
196 AATTTCTTTCACATTTTC
* * * *
1440629 TTCTGCCAGCTGGATGTCCTTAC-CTTTCAAT-GCATCGAGATGATTACGGTTTGCCTCTGATAG
1 TTCTGCAAGCTGAATGTCCTTACAC-TTC-ATCGCATCAAGACGATTACGGTTTGCCTCTGATAG
*
1440692 TCTATTCACAACTACAAAAGCCA-CAGTTGCACAAGCAGATGCATTTCTTAAGTCACCTTCAGCA
64 TCTATTCACAACTACAAAAG-CAGCAGTTGAACAAGCAGATGCATTTCTTAAGTCACCTTCAGCA
* * *
1440756 ATCTTCATTCTATGCTCAAGCTTTGTAATGATTGCTGTTTTTTCATTCAATTCTTTCTTCAGTAG
128 ATCTTCATTCTATCCTCAAGCTTTGTAATGATTGATGTTTTTTCATTCAATTCTTTCTTCAATAG
1440821 AACAATTTCTTTC
193 AACAATTTCTTTC
1440834 TCCTTTTCAT
Statistics
Matches: 190, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
212 1 0.01
213 185 0.97
214 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (213 bp):
TTCTGCAAGCTGAATGTCCTTACACTTCATCGCATCAAGACGATTACGGTTTGCCTCTGATAGTC
TATTCACAACTACAAAAGCAGCAGTTGAACAAGCAGATGCATTTCTTAAGTCACCTTCAGCAATC
TTCATTCTATCCTCAAGCTTTGTAATGATTGATGTTTTTTCATTCAATTCTTTCTTCAATAGAAC
AATTTCTTTCACATTTTC
Found at i:1448838 original size:19 final size:19
Alignment explanation
Indices: 1448814--1448862 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1448804 ACCAACTAAA
1448814 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
1448833 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
*
1448852 TCGCAACGCGA
1 TCGCAATGCGA
1448863 CTCCGGTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:1449030 original size:42 final size:42
Alignment explanation
Indices: 1448936--1449075 Score: 160
Period size: 42 Copynumber: 3.4 Consensus size: 42
1448926 ACATATTCAT
* ** * *
1448936 ATTGCGATAGTCCAAGTTTGCGTTGCGA---ATCTGGAAACTG
1 ATTGCGATAGTCCAAGTTCGCGTTGCGATTTAT-TACAAATTC
* *
1448976 ATTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTACAAATTC
1 A-TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTC
* *
1449019 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
1 ATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTC
1449061 ATTGCGATAGTCCAA
1 ATTGCGATAGTCCAA
1449076 AATTGCAACG
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 24 0.29
42 52 0.62
43 5 0.06
44 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (42 bp):
ATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTC
Found at i:1449042 original size:21 final size:21
Alignment explanation
Indices: 1448978--1449047 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1448968 GGAAACTGAT
*
1448978 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* * * *
1448999 TTGTGATTTATTACAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
1449020 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
1449041 TTGCGAT
1 TTGCGAT
1449048 TTATTCCAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 8 0.22
21 21 0.58
23 7 0.19
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:1449076 original size:19 final size:19
Alignment explanation
Indices: 1449012--1449076 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
1449002 TGATTTATTA
1449012 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
* *
1449031 CAAGTTCGCGTTGCGATTTATTC
1 CAAATT--CGTTGCGA--TAGTC
*
1449054 CAAATTCATTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
1449073 CAAA
1 CAAA
1449077 ATTGCAACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 13 0.35
21 15 0.41
23 9 0.24
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (19 bp):
CAAATTCGTTGCGATAGTC
Found at i:1449983 original size:42 final size:42
Alignment explanation
Indices: 1449920--1450249 Score: 565
Period size: 42 Copynumber: 7.9 Consensus size: 42
1449910 TGCGATTTTG
*
1449920 GACTATCGCAACGAACATGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1449962 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1450004 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1450046 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1450088 GAATATCGCAACGAACTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1450130 GACTATCGCAACGAACTTGGAATAAATCGCAAAGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1450172 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1450214 GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
1450250 TTTGGAATAA
Statistics
Matches: 272, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
40 13 0.05
42 259 0.95
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1450264 original size:42 final size:41
Alignment explanation
Indices: 1449920--1450289 Score: 510
Period size: 42 Copynumber: 8.8 Consensus size: 41
1449910 TGCGATTTTG
*
1449920 GACTATCGCAACGAACATGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
1449962 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
1450004 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* *
1450046 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* *
1450088 GAATATCGCAACGAACTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
1450130 GACTATCGCAACGAACTTGGAATAAATCGCAAAGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
1450172 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* * *
1450214 GACTATCGCAACGAACTTGGACT-ATCGCAACGCGAATTTG
1 GACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTC
* *
1450254 GAATAAATCGCAACGCGAACTTGGACT-ATCGCAACG
1 GACT--ATCGCAA--CGAACTTGGAATAATCGCAACG
1450290 AATTTGGAAA
Statistics
Matches: 305, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
40 18 0.06
42 266 0.87
44 21 0.07
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
GACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTC
Found at i:1450332 original size:21 final size:21
Alignment explanation
Indices: 1450306--1450353 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1450296 GAAAATAGCA
*
1450306 TTGCGATAGTCGAA-GTTTGCG
1 TTGCGATAGTC-AATGTTCGCG
1450327 TTGCGATAGTCAATGTTCGCG
1 TTGCGATAGTCAATGTTCGCG
1450348 TTGCGA
1 TTGCGA
1450354 ATCTGGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (21 bp):
TTGCGATAGTCAATGTTCGCG
Found at i:1450849 original size:109 final size:109
Alignment explanation
Indices: 1450712--1450924 Score: 338
Period size: 109 Copynumber: 2.0 Consensus size: 109
1450702 ATTTTTCGAT
* * *
1450712 TAGATATTATGAATAGAGTAAACTGGAATGAGATGATATTTTCATAATAAATTTTTATAATATTG
1 TAGATATTATGAATAGAATAAACTGGAATGAGAGGATATTTTCATAATAAATTTTTATAATATTA
* *
1450777 AAACGAAACTAATATGTTCG-TAAATTAAATAGAATGTTTGAATA
66 AAACGAAACTAATAAGTT-GATAAATTAAATAAAATGTTTGAATA
* *
1450821 TAGATATTATGAATAGAATAAACTGGAATGAGAGGATCTTTTCATAATAACTTTTTATAATATTA
1 TAGATATTATGAATAGAATAAACTGGAATGAGAGGATATTTTCATAATAAATTTTTATAATATTA
*
1450886 AAACGAAATTAATAAGTTGATAAATTAAATAAAATGTTT
66 AAACGAAACTAATAAGTTGATAAATTAAATAAAATGTTT
1450925 AACAACCTCT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 1 0.01
109 94 0.99
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.37
Consensus pattern (109 bp):
TAGATATTATGAATAGAATAAACTGGAATGAGAGGATATTTTCATAATAAATTTTTATAATATTA
AAACGAAACTAATAAGTTGATAAATTAAATAAAATGTTTGAATA
Found at i:1454498 original size:55 final size:54
Alignment explanation
Indices: 1454452--1454830 Score: 382
Period size: 55 Copynumber: 7.0 Consensus size: 54
1454442 CTTGAAAAAT
* * * *
1454452 TCTTCAAAATCGGGTTCGCTCCCTATCTCTTCAGAGAGTATAAGACTCGAACAA
1 TCTTCAAAATTGCGTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
*
1454506 TCTTCAACGATTGCG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 TCTTCAA-AATTGCGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * * *
1454561 TCCTCAACGATTGTG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1 TCTTCAA-AATTGCGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
*
1454614 TCTTCATCAATTGCGTAT-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 TCTTCA-AAATTGCGT-TCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * *
1454669 TCTTCAACGATTGTG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1 TCTTCAA-AATTGCGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * *
1454722 TCTTCATCAATCGCG-TCTACCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 TCTTCA-AAATTGCGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * * * * *
1454777 TCTTCAACAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTAT-AGAACTCGAACA
1 TCTTCAA-AATTGCGTTCGCCCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACA
1454831 TCTCTTCACG
Statistics
Matches: 277, Mismatches: 32, Indels: 31
0.81 0.09 0.09
Matches are distributed among these distances:
53 89 0.32
54 15 0.05
55 171 0.62
56 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (54 bp):
TCTTCAAAATTGCGTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
Found at i:1454640 original size:53 final size:55
Alignment explanation
Indices: 1454472--1454784 Score: 481
Period size: 55 Copynumber: 5.8 Consensus size: 55
1454462 CGGGTTCGCT
*
1454472 CCCTATCTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
* *
1454527 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCCTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
* * * *
1454582 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATTGCGTATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
*
1454635 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
* * * * *
1454690 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTACC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1454743 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1454785 AAATGGGTTC
Statistics
Matches: 232, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
53 92 0.40
54 4 0.02
55 136 0.59
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
Found at i:1454649 original size:108 final size:108
Alignment explanation
Indices: 1454472--1454784 Score: 536
Period size: 108 Copynumber: 2.9 Consensus size: 108
1454462 CGGGTTCGCT
* * * *
1454472 CCCTATCTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATTGCGTCTGCCCCCTATTTCT
*
1454537 TCAGAGAGTATAAGACTCGAACAATCCTCAACGATTGTGTCTGCC
64 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
*
1454582 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTATGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTC
1454647 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
* *
1454690 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTACCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTC
1454755 AGAGAGTATAAGACTCGAACAATCTTCAAC
66 AGAGAGTATAAGACTCGAACAATCTTCAAC
1454785 AAATGGGTTC
Statistics
Matches: 194, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
108 168 0.87
109 1 0.01
110 25 0.13
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTC
AGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
Found at i:1454779 original size:163 final size:163
Alignment explanation
Indices: 1454465--1454830 Score: 506
Period size: 163 Copynumber: 2.2 Consensus size: 163
1454455 TCAAAATCGG
* *
1454465 GTTCGCTCCCTATCTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
1 GTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
* * * *
1454530 TATTTCTTCAGAGAGTATAAGACTCGAACAATCCTCAACGATTGTGTCTGCCCCCTATTTCTTCA
66 TATTTCTTCAGAGAGTATAAGACTCGAACAATCCTCAACAATCGCGTCTACCCCCTATTTCTTCA
* * *
1454595 GAGAGTATAAGACCCACAATCTTCATCAATTGC
131 GAGAGTATAAGACCAACAATCTTCAACAAATGC
*
1454628 GTAT-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCCCC
1 GT-TCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCC
* * *
1454692 CTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTACCCCCTATTTCTTC
65 CTATTTCTTCAGAGAGTATAAGACTCGAACAATCCTCAACAATCGCGTCTACCCCCTATTTCTTC
*
1454755 AGAGAGTATAAGACTCGAACAATCTTCAACAAATGG
130 AGAGAGTATAAGAC-C-AACAATCTTCAACAAATGC
* * * *
1454791 GTTCGCTCCCTCTTTCTTTAGGGAGTAT-AGAACTCGAACA
1 GTTCGCCCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACA
1454831 TCTCTTCACG
Statistics
Matches: 180, Mismatches: 18, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
161 45 0.25
162 5 0.03
163 129 0.72
164 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (163 bp):
GTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
TATTTCTTCAGAGAGTATAAGACTCGAACAATCCTCAACAATCGCGTCTACCCCCTATTTCTTCA
GAGAGTATAAGACCAACAATCTTCAACAAATGC
Found at i:1454807 original size:108 final size:108
Alignment explanation
Indices: 1454472--1454819 Score: 500
Period size: 108 Copynumber: 3.2 Consensus size: 108
1454462 CGGGTTCGCT
* * * *
1454472 CCCTATCTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATTGCGTCTGCCCCCTATTTCT
* * * *
1454537 TCAGAGAGTATAAGACTCGAACAATCCTCAACGATTGTGTCTGCC
64 TCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGGGTCTGCC
*
1454582 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTATGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTC
* * *
1454647 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
66 AGAGAGTATAAGACTCGAACAATCTTCAACAAATGGGTCTGCC
* *
1454690 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTACCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTC
*
1454755 AGAGAGTATAAGACTCGAACAATCTTCAACAAATGGGT-TCGCT
66 AGAGAGTATAAGACTCGAACAATCTTCAACAAATGGGTCT-GCC
* * *
1454798 CCCTCTTTCTTTAGGGAGTATA
1 CCCTATTTCTTCAGAGAGTATA
1454820 GAACTCGAAC
Statistics
Matches: 221, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
107 1 0.00
108 194 0.88
109 1 0.00
110 25 0.11
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTC
AGAGAGTATAAGACTCGAACAATCTTCAACAAATGGGTCTGCC
Found at i:1454864 original size:51 final size:52
Alignment explanation
Indices: 1454789--1455398 Score: 618
Period size: 51 Copynumber: 11.7 Consensus size: 52
1454779 TTCAACAAAT
1454789 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTC-AC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCAAC
* *
1454840 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACA--TCTTCAAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCAAC
* * * *
1454890 TGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTAC
1 -GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATC-TCTTC-AAC
* * **
1454945 GGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACA--TCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTC-AAC
* * * * * *
1454996 GGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAACTCG--GATATCTTCACAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCA-AC
* *
1455047 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGA-ACATCTCTTC-AAC
* * *
1455100 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCG--CATATCTTCACAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCA-AC
* * *
1455151 GGGTTCGCTCCCGCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGA-ACATCTCTTC-AAC
* ** * *
1455204 GGGTTCGCTCCTTCTTTCTTTAAAGAGTATGGAACTCGAACATCT-TTAAAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCAAC
* * * * **
1455255 GGGTTCGCTCCTTCTTTCTTTAAGGAAGTATAGAACTTGAATGATCTTCTGAAAAC
1 GGGTTCGCTCCCTCTTTCTTT-AGGGAGTATAGAACTCGAA-CATC-TCT-TCAAC
* * *
1455311 GGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-A-ATCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTC-AAC
* * *
1455362 GGGTTCGCTCCTTCTTTCTCTAGGGAGTATGGAACTC
1 GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTC
1455399 AAATAATCTT
Statistics
Matches: 468, Mismatches: 65, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
49 6 0.01
50 4 0.01
51 262 0.56
52 16 0.03
53 94 0.20
54 44 0.09
55 20 0.04
56 22 0.05
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (52 bp):
GGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCAAC
Found at i:1454953 original size:156 final size:154
Alignment explanation
Indices: 1454784--1455407 Score: 726
Period size: 156 Copynumber: 4.0 Consensus size: 154
1454774 CAATCTTCAA
* * *
1454784 CAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCACGGGTTCGCT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCACGGGTTCGCT
1454849 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTC-AACTGGGTTCGCTCCCTCTTTCT-TC
66 CCCTCTTTCT-TAGGGAGTATGGAACTCGAACATCTTCAAAC-GGGTTCGCTCCCTCTTTCTCT-
*
1454912 AGGGAGTATAGAACTCAAAAATCTTCTT
128 AGGGAGTATGGAACTCAAAAATC-TCTT
** * *
1454940 CTTACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCG
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTC--ACGGGTTCG
* * * * *
1455003 CTCCTTCTTTCATTAAGGAGTATGGAACTCGGATATCTTCACACGGGTTCGCTCCCTCTTTCTCT
64 CTCCCTCTTTC-TTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
1455068 AGGGAGTATGGAACTCAGACATCTCTT
128 AGGGAGTATGGAACTCAAAAATCTCTT
*
1455095 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCG--CATATCTTCACACGGGTTCG
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTT--CACGGGTTCG
* *
1455158 CTCCCGCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAACGGGTTCGCTCCTTCTTTC
64 CTCCCTCTTTCT-TAGGGAGTATGGAACTCGA-ACA--TCTTCAAACGGGTTCGCTCCCTCTTTC
* ** * *
1455222 TTTAAAGAGTATGGAACTCGAACATCT-TT
125 TCTAGGGAGTATGGAACTCAAAAATCTCTT
* * **
1455251 -AAACGGGTTCGCTCCTTCTTTCTTTAAGGAAGTATAGAACTTGAATGATCTTCTGAAAACGGGT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGG-AGTATAGAACTCGAA-CATC-TCT--TCACGGGT
* * * *
1455315 TCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTTTC
61 TCGCTCCCTCTTTCTT-AGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTC
1455380 TCTAGGGAGTATGGAACTCAAATAATCT
125 TCTAGGGAGTATGGAACTCAAA-AATCT
1455408 TCATTTGCTT
Statistics
Matches: 400, Mismatches: 45, Indels: 43
0.82 0.09 0.09
Matches are distributed among these distances:
153 2 0.00
154 6 0.01
155 112 0.28
156 136 0.34
157 52 0.13
158 45 0.11
159 7 0.02
160 39 0.10
161 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (154 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCACGGGTTCGCT
CCCTCTTTCTTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
GAGTATGGAACTCAAAAATCTCTT
Found at i:1455123 original size:104 final size:103
Alignment explanation
Indices: 1454784--1455399 Score: 697
Period size: 104 Copynumber: 5.9 Consensus size: 103
1454774 CAATCTTCAA
* * * *
1454784 CAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATC-TCTTCACGGGTTCGC
1 CAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC-ACACGGGTTCGC
1454848 TCCCTCTTTCTCTAGGGAGTATGGAACTC-GAA-CATCTT
65 TCCCTCTTTCTCTAGGGAGTATGGAACTCAGAATC-TCTT
* * * *
1454886 C-AACTGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTT
1 CAAAC-GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC-AC--ACGGGTT
* * * ** *
1454950 CGCTCCTTCTCTCTTTAAAGAGTATAGAACTC-GAA-CATCTT
62 CGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGAATC-TCTT
* * * * *
1454991 CAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAACTCGGATATCTTCACACGGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCACACGGGTTCGCT
1455056 CCCTCTTTCTCTAGGGAGTATGGAACTCAGACATCTCTT
66 CCCTCTTTCTCTAGGGAGTATGGAACTCAGA-ATCTCTT
* * *
1455095 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCACACGGGTTCGCT
*
1455160 CCCGCTTTCTCTAGGGAGTATGGAACTCAGACATCTCTT
66 CCCTCTTTCTCTAGGGAGTATGGAACTCAGA-ATCTCTT
* * * * * *
1455199 CAAACGGGTTCGCTCCTTCTTTCTTTAAAGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCACACGGGTTCGCT
* * * * * *
1455264 CCTTCTTTCTTTAAGGAAGTATAGAACT-TGAATGATCTT
66 CCCTCTTTCTCT-AGGGAGTATGGAACTCAGAAT-CTCTT
* * * *
1455303 CTGAAAACGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTC
1 C---AAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCACACGGGTTC
*
1455368 GCTCCTTCTTTCTCTAGGGAGTATGGAACTCA
63 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
1455400 AATAATCTTC
Statistics
Matches: 446, Mismatches: 54, Indels: 23
0.85 0.10 0.04
Matches are distributed among these distances:
101 2 0.00
102 75 0.17
103 9 0.02
104 181 0.41
105 96 0.22
106 16 0.04
107 67 0.15
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (103 bp):
CAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCACACGGGTTCGCT
CCCTCTTTCTCTAGGGAGTATGGAACTCAGAATCTCTT
Found at i:1455838 original size:36 final size:36
Alignment explanation
Indices: 1455780--1456009 Score: 284
Period size: 36 Copynumber: 6.4 Consensus size: 36
1455770 ACTCTTCTGA
* * **
1455780 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * *
1455817 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
1455853 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
1455889 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
1455925 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
1455961 GAAGGCTTAGGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
1455997 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
1456010 TGACTTGCTC
Statistics
Matches: 172, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
35 2 0.01
36 157 0.91
37 13 0.08
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:1455944 original size:108 final size:109
Alignment explanation
Indices: 1455780--1456018 Score: 315
Period size: 108 Copynumber: 2.2 Consensus size: 109
1455770 ACTCTTCTGA
* * **
1455780 GAAGGCTTAAAATGGA-TCTGCTTCACTACTT-TTTGGTGAAGACTTAAGATGGTTTGCTTCACT
1 GAAGGCTTAAGATTGACT-TGCTTCACTA-TTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACT
* *
1455843 ACTCTCTGGTGAAGACTTATGATGGTTTGCTTCACTAT-TCTCCGGT
64 ACTCTCCGGTGAAGACTTAGGATGGTTTGCTTCACT-TCTCTCCGGT
* * * *
1455889 GAAGGCTTCAGATTGA-TTGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTAT
1 GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTAC
* *
1455953 TCTCCGGTGAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGGT
66 TCTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
1455997 GAAGGCTTAAGATTGACTTGCT
1 GAAGGCTTAAGATTGACTTGCT
1456019 CCAATCTCAT
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
107 3 0.03
108 92 0.81
109 19 0.17
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (109 bp):
GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTAC
TCTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
Found at i:1457415 original size:125 final size:125
Alignment explanation
Indices: 1457209--1457445 Score: 359
Period size: 125 Copynumber: 1.9 Consensus size: 125
1457199 TATTTTATTC
*
1457209 TGGTACGGGCCTTCAAAATGCCTCAATATCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTGG
1 TGGTACGGGCCTTCAAAATGCCTCAATACCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTGG
** * *
1457274 TCTGAATCTTGTCATTTCATCATGATGTGGGTTCAGTCGCGCCCCAACATTATCTCATAT
66 TCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGCGCCCCAACATTATCTCATAT
* * ** *
1457334 TGGTACGGGCCTTCAAAATGCC-CCATCACCTCAAATTGTAAGGCTCATTCTTGATGCCTTCTTT
1 TGGTACGGGCCTTCAAAATGCCTCAAT-ACCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTG
*
1457398 GTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGTGCCCCAA
65 GTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGCGCCCCAA
1457446 TGTGGGTATT
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
124 3 0.03
125 97 0.97
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (125 bp):
TGGTACGGGCCTTCAAAATGCCTCAATACCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTGG
TCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGCGCCCCAACATTATCTCATAT
Found at i:1468007 original size:19 final size:19
Alignment explanation
Indices: 1467983--1468040 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
1467973 ATGACCAACA
1467983 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
1468002 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
1468021 AAATCGCAACGCGATCTCT
1 AAATCGCAATGCGATCTCT
1468040 A
1 A
1468041 GTATCGCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:1468108 original size:21 final size:20
Alignment explanation
Indices: 1468055--1468109 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1468045 CGCAAATCAG
* *
1468055 TTTCCAGATTCGCGTTGCGA
1 TTTCCAAATTCGCATTGCGA
* *
1468075 TTTACATATTCGCATTGCGA
1 TTTCCAAATTCGCATTGCGA
1468095 TTTTCCAAATTCGCA
1 -TTTCCAAATTCGCA
1468110 ACGCGATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (20 bp):
TTTCCAAATTCGCATTGCGA
Found at i:1468197 original size:20 final size:20
Alignment explanation
Indices: 1468125--1468189 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
1468115 ATAATACATA
*
1468125 ATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1468145 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1468165 ATTGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1468185 ATCGC
1 ATCGC
1468190 GTTGCGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1468718 original size:40 final size:40
Alignment explanation
Indices: 1468674--1468768 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 40
1468664 CACCTCACCC
1468674 AGAGCCATCACCTGATCGACCAC-ACTATACCTCTACAACG
1 AGAGCCATCACCTGATCGACCACTA-TATACCTCTACAACG
1468714 AGAGCCATATCACCTGATCGACCACTATATACCTCTACAACG
1 AGAGCC--ATCACCTGATCGACCACTATATACCTCTACAACG
1468756 AGAGCCATCACCT
1 AGAGCCATCACCT
1468769 ATTCCATCAC
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
40 13 0.25
42 38 0.73
43 1 0.02
ACGTcount: A:0.33, C:0.36, G:0.13, T:0.19
Consensus pattern (40 bp):
AGAGCCATCACCTGATCGACCACTATATACCTCTACAACG
Found at i:1469302 original size:20 final size:20
Alignment explanation
Indices: 1469277--1469345 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
1469267 AAACTTAAAA
1469277 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1469297 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1469317 ATCGCAACACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1469337 ATCGCAACG
1 ATCGCAACG
1469346 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1470669 original size:14 final size:14
Alignment explanation
Indices: 1470650--1470676 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1470640 TCCCGTGGCA
1470650 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
1470664 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
1470677 TTTCTTCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1470682 original size:12 final size:13
Alignment explanation
Indices: 1470651--1470683 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1470641 CCCGTGGCAT
1470651 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
1470664 TTTTCTTCGGGGA-
1 -TTTCTTCGGGGAC
1470677 TTTCTTC
1 TTTCTTC
1470684 TTATTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:1470940 original size:24 final size:24
Alignment explanation
Indices: 1470873--1470932 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1470863 CTGAAACATC
1470873 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
1470897 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
1470921 ATCAAATTTCGA
1 ATCAAAATTCGA
1470933 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:1471769 original size:20 final size:20
Alignment explanation
Indices: 1471744--1471830 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
1471734 GGAATTCAGT
* *
1471744 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAAAATCGC
*
1471764 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAAAATCGC
* *
1471784 GTTACGATACTCAAAATCGC
1 GTTGCGATAGTCAAAATCGC
* *
1471804 ATTGAGATAGTCAAAATCGC
1 GTTGCGATAGTCAAAATCGC
1471824 GTTGCGA
1 GTTGCGA
1471831 ATCTGGAAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (20 bp):
GTTGCGATAGTCAAAATCGC
Found at i:1471868 original size:20 final size:19
Alignment explanation
Indices: 1471845--1471890 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1471835 GGAAACTGAT
* *
1471845 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1471865 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1471884 TTGCGAT
1 TTGCGAT
1471891 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1471880 original size:19 final size:19
Alignment explanation
Indices: 1471856--1471892 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1471846 TGCGATACTG
*
1471856 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1471875 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1471893 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Done.