Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017884.1 Corchorus olitorius cultivar O-4 contig17917, 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: 174243
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:859 original size:33 final size:33
Alignment explanation
Indices: 743--859 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 33
733 CAATCTCATT
* *
743 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATGCGAGCTAGCTC-TTG
* *
776 TCTTCTCTCTTCTTCAACT-CGAGCTAGCTCCTG
1 TCTTCTATCTTCTTCAA-TGCGAGCTAGCTCTTG
* *
809 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATGCGAGCTAGCTCTTG
*
842 TCTTCTTTCTTCTTCAAT
1 TCTTCTATCTTCTTCAAT
860 TCTTGCAAGC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.03
33 70 0.97
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.42
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATGCGAGCTAGCTCTTG
Found at i:871 original size:33 final size:33
Alignment explanation
Indices: 743--875 Score: 124
Period size: 33 Copynumber: 4.0 Consensus size: 33
733 CAATCTCATT
* ** *
743 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTC-TTG
* * * *
776 TCTTCTCTCTTCTTCAACTCGAGCTAGCTCCTG
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
* * *
809 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
* **
842 TCTTCTTTCTTCTTCAATTCTTGCAAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
875 T
1 T
876 TGCGTTTGTA
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 1 0.01
33 82 0.99
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.42
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
Found at i:1944 original size:27 final size:27
Alignment explanation
Indices: 1906--1957 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
1896 CGTCCCTTGC
1906 ATCACCTACATTTGCATCATCTACAAA
1 ATCACCTACATTTGCATCATCTACAAA
1933 ATCACCTACATTTGCATCATCTACA
1 ATCACCTACATTTGCATCATCTACA
1958 TTTGCATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (27 bp):
ATCACCTACATTTGCATCATCTACAAA
Found at i:1967 original size:15 final size:15
Alignment explanation
Indices: 1902--1968 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
1892 TCTTCGTCCC
*
1902 TTGCATCACCTACAT
1 TTGCATCATCTACAT
1917 TTGCATCATCTACA-
1 TTGCATCATCTACAT
** *
1931 --AAATCACCTACAT
1 TTGCATCATCTACAT
1944 TTGCATCATCTACAT
1 TTGCATCATCTACAT
1959 TTGCATCATC
1 TTGCATCATC
1969 ACCAACTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 9 0.21
15 33 0.79
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (15 bp):
TTGCATCATCTACAT
Found at i:2744 original size:32 final size:32
Alignment explanation
Indices: 2701--2797 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
2691 CTGGATTGCA
* *
2701 AATTAGGGGCGTTTT-CTTC-ATAAAACGCCTCT
1 AATTAGTGGCGTTTTAC-TCAAT-AAACGCCACT
*
2733 AATTAGTGGCGTTTTACTCAATAAATGCCACT
1 AATTAGTGGCGTTTTACTCAATAAACGCCACT
*
2765 AATTAGTGGCGTTTTACTGAATAAACGCCACT
1 AATTAGTGGCGTTTTACTCAATAAACGCCACT
2797 A
1 A
2798 TTTGCAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
32 55 0.95
33 3 0.05
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (32 bp):
AATTAGTGGCGTTTTACTCAATAAACGCCACT
Found at i:2888 original size:12 final size:12
Alignment explanation
Indices: 2871--2897 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2861 AAAGATAGTG
2871 AAGAAAACTCCC
1 AAGAAAACTCCC
2883 AAGAAAACTCCC
1 AAGAAAACTCCC
2895 AAG
1 AAG
2898 TACAGCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.30, G:0.11, T:0.07
Consensus pattern (12 bp):
AAGAAAACTCCC
Found at i:10332 original size:51 final size:50
Alignment explanation
Indices: 10231--10333 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
10221 GTTCTTCATA
** *
10231 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
* * * *
10281 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
10332 TT
1 TT
10334 CTCTTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.09
51 39 0.89
52 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
Found at i:17897 original size:24 final size:25
Alignment explanation
Indices: 17865--17913 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
17855 GACATCTCTT
*
17865 CCGCCGCAGCAAA-GGAAGAAGAAA
1 CCGCAGCAGCAAAGGGAAGAAGAAA
17889 CCGCAGCAGCAAAGGGAAGAAGAAA
1 CCGCAGCAGCAAAGGGAAGAAGAAA
17914 GAAATGGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.47, C:0.22, G:0.31, T:0.00
Consensus pattern (25 bp):
CCGCAGCAGCAAAGGGAAGAAGAAA
Found at i:21424 original size:40 final size:40
Alignment explanation
Indices: 21380--21462 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
21370 AAAGGGTTTG
21380 TTGGCTCTTAAATTCAAGAACATGTGTTATGAGATTTTAA
1 TTGGCTCTTAAATTCAAGAACATGTGTTATGAGATTTTAA
*
21420 TTGGCTCTTAGATTCAAGAACATGTGTTATGAGATTTTAA
1 TTGGCTCTTAAATTCAAGAACATGTGTTATGAGATTTTAA
21460 TTG
1 TTG
21463 TATTTGTTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (40 bp):
TTGGCTCTTAAATTCAAGAACATGTGTTATGAGATTTTAA
Found at i:27126 original size:3 final size:3
Alignment explanation
Indices: 27118--27166 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
27108 TACTTATTGC
27118 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
27166 C
1 C
27167 CTCATTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:28697 original size:2 final size:2
Alignment explanation
Indices: 28690--28729 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
28680 ATGGACAGGT
* *
28690 TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28730 ATATGTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:35536 original size:36 final size:36
Alignment explanation
Indices: 35495--35564 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
35485 ATTTTCTCTA
35495 ATTTATTTCATCAACGTCTAAAGACATTGACTAATC
1 ATTTATTTCATCAACGTCTAAAGACATTGACTAATC
* * *
35531 ATTTATTTCATCAATGTCTCAAGACATTGGCTAA
1 ATTTATTTCATCAACGTCTAAAGACATTGACTAA
35565 ATCTTCATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (36 bp):
ATTTATTTCATCAACGTCTAAAGACATTGACTAATC
Found at i:40109 original size:2 final size:2
Alignment explanation
Indices: 40102--40129 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40092 CTAAAACTAG
40102 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40130 ATTCTCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40768 original size:31 final size:31
Alignment explanation
Indices: 40730--40791 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
40720 GAGTTTTGTA
40730 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
*
40761 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
40792 TTTTAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTATT
Found at i:41570 original size:93 final size:93
Alignment explanation
Indices: 41411--41595 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
41401 TTGTTTAAAT
*
41411 TTTTATAGTTTTAGTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
41476 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
41504 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
41569 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
41596 ATTAAAAAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:43692 original size:52 final size:52
Alignment explanation
Indices: 43633--43752 Score: 240
Period size: 52 Copynumber: 2.3 Consensus size: 52
43623 AAAAGTAAAT
43633 ATTTAACGTCTTGAGACGAGATTGAAAGAAAAGAAAAACTCGCGGAGAGTTG
1 ATTTAACGTCTTGAGACGAGATTGAAAGAAAAGAAAAACTCGCGGAGAGTTG
43685 ATTTAACGTCTTGAGACGAGATTGAAAGAAAAGAAAAACTCGCGGAGAGTTG
1 ATTTAACGTCTTGAGACGAGATTGAAAGAAAAGAAAAACTCGCGGAGAGTTG
43737 ATTTAACGTCTTGAGA
1 ATTTAACGTCTTGAGA
43753 TGAAATTAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (52 bp):
ATTTAACGTCTTGAGACGAGATTGAAAGAAAAGAAAAACTCGCGGAGAGTTG
Found at i:44499 original size:27 final size:27
Alignment explanation
Indices: 44461--44546 Score: 111
Period size: 27 Copynumber: 3.1 Consensus size: 27
44451 ATTTACTTCT
* *
44461 CATTTTGGTCATTTGCAT-GCTTAGGGG
1 CATTTTGGTCATTTGCATATC-CAGGGG
*
44488 CATTTTGATCATTTGCATATCCAGGGG
1 CATTTTGGTCATTTGCATATCCAGGGG
*
44515 CATTTTGGTCATTTGCACATCCAGGGGG
1 CATTTTGGTCATTTGCATATCCA-GGGG
44543 CATT
1 CATT
44547 CCGGTCACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 43 0.83
28 9 0.17
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (27 bp):
CATTTTGGTCATTTGCATATCCAGGGG
Found at i:44552 original size:28 final size:27
Alignment explanation
Indices: 44496--44553 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
44486 GGCATTTTGA
* **
44496 TCATTTGCATATCCAGGGGCATTTTGG
1 TCATTTGCACATCCAGGGGCATTCCGG
44523 TCATTTGCACATCCAGGGGGCATTCCGG
1 TCATTTGCACATCCA-GGGGCATTCCGG
44551 TCA
1 TCA
44554 CTTCAAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (27 bp):
TCATTTGCACATCCAGGGGCATTCCGG
Found at i:47636 original size:2 final size:2
Alignment explanation
Indices: 47629--47660 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47619 CAATTGGGTG
47629 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
47661 GCTTATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52555 original size:128 final size:129
Alignment explanation
Indices: 52403--52651 Score: 383
Period size: 128 Copynumber: 1.9 Consensus size: 129
52393 TTATTTAAAC
* * * *
52403 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTGATAACTA
1 TTTTATAATTTTACTCAACAAAAAACTCTATTTCTATTTAATAAAATCTAATATCCTGATAACTA
** *
52468 TTTTATTTTTACTGTTTTACTATTTTAATTAAAAAAATT-ATATATTAGAATTTTTTAATATAT
66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAATTAATATATTAGAATTTTTTAATATAT
* * *
52531 TTTTATAATTTTACTCAACAAAAAACTCTATTTCTATTTAATAAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACAAAAAACTCTATTTCTATTTAATAAAATCTAATATCCTGATAACTA
*
52596 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTT
66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAATTA-ATATATTAGAATTTT
52652 AAAATAAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 93 0.86
130 15 0.14
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (129 bp):
TTTTATAATTTTACTCAACAAAAAACTCTATTTCTATTTAATAAAATCTAATATCCTGATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAATTAATATATTAGAATTTTTTAATATAT
Found at i:57617 original size:17 final size:17
Alignment explanation
Indices: 57589--57652 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 17
57579 GCCCAGCGTC
*
57589 GAAAAA-AAAAAG-AGA
1 GAAAAAGAAAAAGAAAA
57604 GAAAAAGGAAAAAGAAAA
1 GAAAAA-GAAAAAGAAAA
57622 GAAAAAGAAAAAGGAAAAA
1 GAAAAAGAAAAA-G-AAAA
57641 GAAAAAGAAAAA
1 GAAAAAGAAAAA
57653 ATAGAAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
15 6 0.14
17 12 0.28
18 9 0.21
19 16 0.37
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAA
Found at i:57630 original size:24 final size:25
Alignment explanation
Indices: 57603--57652 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
57593 AAAAAAAGAG
57603 AGAAAAAGGAAAAAG-AAAAGAAAA
1 AGAAAAAGGAAAAAGAAAAAGAAAA
57627 AGAAAAAGGAAAAAGAAAAAGAAAA
1 AGAAAAAGGAAAAAGAAAAAGAAAA
57652 A
1 A
57653 ATAGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (25 bp):
AGAAAAAGGAAAAAGAAAAAGAAAA
Found at i:57653 original size:13 final size:13
Alignment explanation
Indices: 57589--57653 Score: 71
Period size: 13 Copynumber: 5.0 Consensus size: 13
57579 GCCCAGCGTC
*
57589 GAAAAAAAAAAGAGA
1 GAAAAAGAAAA-A-A
*
57604 GAAAAAGGAAAAA
1 GAAAAAGAAAAAA
57617 G-AAAAG-AAAAA
1 GAAAAAGAAAAAA
*
57628 GAAAAAGGAAAAA
1 GAAAAAGAAAAAA
57641 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
57654 TAGAAAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
11 6 0.13
12 10 0.22
13 19 0.42
14 1 0.02
15 9 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAAA
Found at i:57661 original size:7 final size:6
Alignment explanation
Indices: 57603--57652 Score: 75
Period size: 6 Copynumber: 8.2 Consensus size: 6
57593 AAAAAAAGAG
57603 AGAAAA AGGAAAA AG-AAA AGAAAA AGAAAA AGGAAAA AGAAAA AGAAAA
1 AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA A-GAAAA AGAAAA AGAAAA
57652 A
1 A
57653 ATAGAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.12
6 24 0.59
7 12 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:58617 original size:28 final size:28
Alignment explanation
Indices: 58557--58609 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
58547 CCTATCATGA
* * *
58557 AAAATTATTGTTTTGCCCTTTGTCGAAT
1 AAAATTACTGTTTTGCCCTCTGTAGAAT
58585 AAAATTACTGTTTTGCCC-CTGTAGA
1 AAAATTACTGTTTTGCCCTCTGTAGA
58610 CCTAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (28 bp):
AAAATTACTGTTTTGCCCTCTGTAGAAT
Found at i:61369 original size:42 final size:43
Alignment explanation
Indices: 61318--61411 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
61308 AGTGCATTAC
*
61318 CTAA-ATTCTA-CTACATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAG
*
61359 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTACATCTCTAGATAATTCATCAAAATAAAG
61404 CTAATATT
1 CTAATATT
61412 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAG
Found at i:64649 original size:32 final size:32
Alignment explanation
Indices: 64613--64675 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
64603 TCGGTCAAAC
64613 CGGTTGTTGACCGAGTCTTGACCGGGCTAAAT
1 CGGTTGTTGACCGAGTCTTGACCGGGCTAAAT
64645 CGGTTGTTGACCGAGTCTTGACCGGGCTAAA
1 CGGTTGTTGACCGAGTCTTGACCGGGCTAAA
64676 CCTCCCTCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (32 bp):
CGGTTGTTGACCGAGTCTTGACCGGGCTAAAT
Found at i:64773 original size:73 final size:75
Alignment explanation
Indices: 64650--64788 Score: 246
Period size: 73 Copynumber: 1.9 Consensus size: 75
64640 TAAATCGGTT
*
64650 GTTGACCGAGTCTTGACCGGGCTAAACCTCCCTCGGTTAACCCCCCTTTCCGGACCGGATAGGCC
1 GTTGACCGAGTCTTGACCAGGCTAAACCTCCCTCGGTTAACCCCCCTTTCCGGACCGGATAGGCC
64715 TTAACCGGCG
66 TTAACCGGCG
*
64725 GTTGACCGAGTCTTGACCAGGCTCAACC-CCC-CGGTTAACCCCCCTTTCCGGACCGGATAGGCC
1 GTTGACCGAGTCTTGACCAGGCTAAACCTCCCTCGGTTAACCCCCCTTTCCGGACCGGATAGGCC
64788 T
66 T
64789 CAGGGTCCCG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
73 33 0.53
74 3 0.05
75 26 0.42
ACGTcount: A:0.17, C:0.37, G:0.24, T:0.21
Consensus pattern (75 bp):
GTTGACCGAGTCTTGACCAGGCTAAACCTCCCTCGGTTAACCCCCCTTTCCGGACCGGATAGGCC
TTAACCGGCG
Found at i:65090 original size:42 final size:43
Alignment explanation
Indices: 65038--65131 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 43
65028 AGTGCATTAC
65038 CTAA-ATTCTACT-CCATCTCTACG-TAATTCATCAAAATAAAG
1 CTAATATTCTACTCCCATCTCTA-GATAATTCATCAAAATAAAG
*
65079 CTAATATTCTACTCCCCCATCTCTAGATGATTCATCAAAATAAAG
1 CTAATATTCTACT--CCCATCTCTAGATAATTCATCAAAATAAAG
65124 CTAATATT
1 CTAATATT
65132 GATTGTTGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 34 0.72
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:67407 original size:13 final size:13
Alignment explanation
Indices: 67389--67425 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
67379 GGTTTTGTCC
67389 GAAAATTAAAATG
1 GAAAATTAAAATG
67402 GAAAATTAAAATG
1 GAAAATTAAAATG
*
67415 GAAAATCAAAA
1 GAAAATTAAAA
67426 GATTGTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.65, C:0.03, G:0.14, T:0.19
Consensus pattern (13 bp):
GAAAATTAAAATG
Found at i:69594 original size:21 final size:21
Alignment explanation
Indices: 69570--69609 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
69560 AGCCGCTCGA
69570 TGCT-TGGCTCAAGGATATGCC
1 TGCTATGGCTCAA-GATATGCC
*
69591 TGCTATGGCTTAAGATATG
1 TGCTATGGCTCAAGATATG
69610 GTCTATGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (21 bp):
TGCTATGGCTCAAGATATGCC
Found at i:70533 original size:5 final size:5
Alignment explanation
Indices: 70523--70589 Score: 134
Period size: 5 Copynumber: 13.4 Consensus size: 5
70513 TTTGTGGTCC
70523 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
70573 CAACA CAACA CAACA CA
1 CAACA CAACA CAACA CA
70590 TGTAAGCTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 62 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
CAACA
Found at i:75220 original size:2 final size:2
Alignment explanation
Indices: 75215--75241 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
75205 TATATATATA
75215 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
75242 ATAAATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:75268 original size:2 final size:2
Alignment explanation
Indices: 75263--75297 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
75253 TATATATATA
75263 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
75298 ACTAGACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:80857 original size:2 final size:2
Alignment explanation
Indices: 80852--80882 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80842 AGAAAGAAGA
80852 AG AG AG 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 AG AG AG A
80883 AGACAGACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:83053 original size:2 final size:2
Alignment explanation
Indices: 83046--83083 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
83036 GCAATCCAGT
83046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
83084 TGGTCCTCTA
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:86569 original size:11 final size:11
Alignment explanation
Indices: 86554--86583 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
86544 TATGTGATCA
86554 AAGTTCAAGAT
1 AAGTTCAAGAT
*
86565 TAGTTCAAGAT
1 AAGTTCAAGAT
86576 AAGTTCAA
1 AAGTTCAA
86584 TCAGATTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (11 bp):
AAGTTCAAGAT
Found at i:86759 original size:95 final size:95
Alignment explanation
Indices: 86596--86883 Score: 567
Period size: 95 Copynumber: 3.0 Consensus size: 95
86586 AGATTGTGAT
86596 CAAACCTACCTAATAAGCTCAAATGTTTGTATTTAGCCATATATTAATCAATTTCATCATATTAG
1 CAAACCTACCTAATAAGCTCAAATGTTTGTATTTAGCCATATATTAATCAATTTCATCATATTAG
86661 TTTCAATTGTTGATCTTATACAAGAGTTGA
66 TTTCAATTGTTGATCTTATACAAGAGTTGA
86691 CAAACCTACCTAATAAGCTCAAATGTTTGTATTTAGCCATATATTAATCAATTTCATCATATTAG
1 CAAACCTACCTAATAAGCTCAAATGTTTGTATTTAGCCATATATTAATCAATTTCATCATATTAG
*
86756 TTTCAATTATTGATCTTATACAAGAGTTGA
66 TTTCAATTGTTGATCTTATACAAGAGTTGA
86786 CAAACCTACCTAATAAGCTCAAATGTTTGTATTTAGCCATATATTAATCAATTTCATCATATTAG
1 CAAACCTACCTAATAAGCTCAAATGTTTGTATTTAGCCATATATTAATCAATTTCATCATATTAG
86851 TTTCAATTGTTGATCTTATACAAGAGTTGA
66 TTTCAATTGTTGATCTTATACAAGAGTTGA
86881 CAA
1 CAA
86884 GCATAAGCTC
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 191 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (95 bp):
CAAACCTACCTAATAAGCTCAAATGTTTGTATTTAGCCATATATTAATCAATTTCATCATATTAG
TTTCAATTGTTGATCTTATACAAGAGTTGA
Found at i:91083 original size:11 final size:11
Alignment explanation
Indices: 91059--91093 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
91049 TTGACAGCGC
91059 AACAAAAACAA
1 AACAAAAACAA
* *
91070 AACGAAAACGA
1 AACAAAAACAA
91081 AACAAAAACAA
1 AACAAAAACAA
91092 AA
1 AA
91094 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:98106 original size:17 final size:19
Alignment explanation
Indices: 98073--98108 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
98063 TTTTTCTTAC
98073 TTATCTAATTATTAATTTA
1 TTATCTAATTATTAATTTA
98092 TTAT-TAATT-TTAATTTA
1 TTATCTAATTATTAATTTA
98109 CATAAAACGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATCTAATTATTAATTTA
Found at i:102320 original size:7 final size:7
Alignment explanation
Indices: 102308--102335 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
102298 TTTGTGTTCG
102308 AATCCAA
1 AATCCAA
102315 AATCCAA
1 AATCCAA
102322 AATCCAA
1 AATCCAA
102329 AATCCAA
1 AATCCAA
102336 CCCCACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (7 bp):
AATCCAA
Found at i:102543 original size:5 final size:5
Alignment explanation
Indices: 102533--102564 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
102523 TATTATTATT
102533 ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA AT
102565 TAAATACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:103331 original size:2 final size:2
Alignment explanation
Indices: 103324--103350 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103314 TTTAATATTA
103324 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
103351 ATAATCACTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103922 original size:33 final size:33
Alignment explanation
Indices: 103846--103935 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 33
103836 TTTTGATATT
103846 TAAACTCTCAAAACTCCTTCAAACTTCATTTTC
1 TAAACTCTCAAAACTCCTTCAAACTTCATTTTC
103879 T-AACTCTCAAAACTCCTTCAAACTTCATTTTC
1 TAAACTCTCAAAACTCCTTCAAACTTCATTTTC
*
103911 TAAACTCTCAAAACTTCTTCAAACT
1 TAAACTCTCAAAACTCCTTCAAACT
103936 CTCTAAAACT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (33 bp):
TAAACTCTCAAAACTCCTTCAAACTTCATTTTC
Found at i:103945 original size:20 final size:19
Alignment explanation
Indices: 103847--103953 Score: 85
Period size: 19 Copynumber: 6.2 Consensus size: 19
103837 TTTGATATTT
*
103847 AAACTCTCAAAACTCCTTC
1 AAACTCTCAAAACTTCTTC
103866 AAACT-TC---A-TT-TTC
1 AAACTCTCAAAACTTCTTC
* *
103879 TAACTCTCAAAACTCCTTC
1 AAACTCTCAAAACTTCTTC
103898 AAACT-TC---A-TT-TTC
1 AAACTCTCAAAACTTCTTC
103911 TAAACTCTCAAAACTTCTTC
1 -AAACTCTCAAAACTTCTTC
103931 AAACTCTCTAAAACTTCTTC
1 AAACTCTC-AAAACTTCTTC
103951 AAA
1 AAA
103954 GAACATCATG
Statistics
Matches: 69, Mismatches: 5, Indels: 27
0.68 0.05 0.27
Matches are distributed among these distances:
13 10 0.14
14 9 0.13
15 4 0.06
17 1 0.01
18 6 0.09
19 22 0.32
20 17 0.25
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.35
Consensus pattern (19 bp):
AAACTCTCAAAACTTCTTC
Found at i:104378 original size:17 final size:18
Alignment explanation
Indices: 104348--104388 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
104338 TAGTTATTTT
104348 ATTATTTGACTATAATTA
1 ATTATTTGACTATAATTA
104366 ATTATTT-ACTATAATTA
1 ATTATTTGACTATAATTA
*
104383 TTTATT
1 ATTATT
104389 ATTCTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTGACTATAATTA
Found at i:110717 original size:3 final size:3
Alignment explanation
Indices: 110709--110740 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
110699 AAGCTTGATA
110709 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
110741 GCTTATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:111328 original size:20 final size:20
Alignment explanation
Indices: 111291--111333 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
111281 TTATAGGTAG
*
111291 TACATATTATATTTTATATT
1 TACATATTATATTTTATAAT
111311 TACA-ATTATATTTATATAAT
1 TACATATTATATTT-TATAAT
111331 TAC
1 TAC
111334 TTAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TACATATTATATTTTATAAT
Found at i:111359 original size:17 final size:18
Alignment explanation
Indices: 111327--111361 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
111317 TATATTTATA
*
111327 TAATTACTTAATATAATT
1 TAATTACTTAAAATAATT
111345 TAATT-CTTAAAATAATT
1 TAATTACTTAAAATAATT
111362 ATTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTACTTAAAATAATT
Found at i:122470 original size:12 final size:12
Alignment explanation
Indices: 122453--122500 Score: 78
Period size: 12 Copynumber: 3.9 Consensus size: 12
122443 CATCGATACC
122453 TCGATATATCCG
1 TCGATATATCCG
*
122465 TCGATATATCCA
1 TCGATATATCCG
122477 TCGATATATCCG
1 TCGATATATCCG
122489 TTCGATATATCC
1 -TCGATATATCC
122501 ATGGATACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:122499 original size:25 final size:24
Alignment explanation
Indices: 122453--122507 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
122443 CATCGATACC
122453 TCGATATATCCGTCGATATATCCA
1 TCGATATATCCGTCGATATATCCA
122477 TCGATATATCCGTTCGATATATCCA
1 TCGATATATCCG-TCGATATATCCA
*
122502 TGGATA
1 TCGATA
122508 CCTGTGGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (24 bp):
TCGATATATCCGTCGATATATCCA
Found at i:137795 original size:24 final size:24
Alignment explanation
Indices: 137768--137814 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
137758 TACCACAAGT
*
137768 GATGACTGCGCTGAA-AGTGATGAA
1 GATGACTGCACTGAACA-TGATGAA
137792 GATGACTGCACTGAACATGATGA
1 GATGACTGCACTGAACATGATGA
137815 TGAGCAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (24 bp):
GATGACTGCACTGAACATGATGAA
Found at i:138329 original size:2 final size:2
Alignment explanation
Indices: 138322--138355 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
138312 AAATGCAACC
138322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
138356 AAAGTTAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:141653 original size:16 final size:16
Alignment explanation
Indices: 141632--141666 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
141622 AATTTTGAAA
*
141632 TAAAATAAAATTTATT
1 TAAAATAAAATTCATT
*
141648 TAAAATTAAATTCATT
1 TAAAATAAAATTCATT
141664 TAA
1 TAA
141667 CAAAAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATAAAATTCATT
Found at i:142779 original size:18 final size:18
Alignment explanation
Indices: 142756--142790 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
142746 TCCAAAAGAT
142756 TCTGCCCC-ACATTGACGG
1 TCTGCCCCTA-ATTGACGG
142774 TCTGCCCCTAATTGACG
1 TCTGCCCCTAATTGACG
142791 CGAATTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.17, C:0.37, G:0.20, T:0.26
Consensus pattern (18 bp):
TCTGCCCCTAATTGACGG
Found at i:143144 original size:28 final size:28
Alignment explanation
Indices: 143086--143154 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
143076 GGACTTAAGT
143086 AAGGATCCAACC-ATTTTTTTTTCGGTG
1 AAGGATCCAACCAATTTTTTTTTCGGTG
143113 AAGGATCCAACCAATTTTTTTTT-GGTG
1 AAGGATCCAACCAATTTTTTTTTCGGTG
143140 AAAGGATCCAACCAA
1 -AAGGATCCAACCAA
143155 ATTTGGTCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.40
28 24 0.60
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (28 bp):
AAGGATCCAACCAATTTTTTTTTCGGTG
Found at i:144139 original size:22 final size:22
Alignment explanation
Indices: 144105--144289 Score: 120
Period size: 22 Copynumber: 8.5 Consensus size: 22
144095 TAAATATTTT
144105 TATGAAA-TTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* *
144126 TATTAAATTTTGATAA-TCACGC
1 TATGAAATTTTGATAACT-ACCC
* *
144148 TATGGAATTTTGATAATTA-CC
1 TATGAAATTTTGATAACTACCC
*
144169 TATG-AATTTGTGATAAACT-CCA
1 TATGAAATTT-TGAT-AACTACCC
*
144191 TATGAAATTTTGATAACCTA-AC
1 TATGAAATTTTGATAA-CTACCC
** **
144213 TATGAAATTTCAATAAACTTTCC
1 TATGAAATTTTGAT-AACTACCC
*
144236 TATGAAATTTTG-TAACCT-TCC
1 TATGAAATTTTGATAA-CTACCC
*
144257 TATG-ATTTTTGATAACCT-CCC
1 TATGAAATTTTGATAA-CTACCC
*
144278 TATGAGATTTTG
1 TATGAAATTTTG
144290 TTAATCTCCT
Statistics
Matches: 131, Mismatches: 19, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
20 11 0.08
21 39 0.30
22 62 0.47
23 19 0.15
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:144171 original size:43 final size:44
Alignment explanation
Indices: 144105--144207 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 44
144095 TAAATATTTT
*
144105 TATGAAA-TTTGATAACTACCCTATTAAATTT-TGATAATCACGC-
1 TATGAAATTTTGATAACTACCCTA-TAAATTTGTGATAAACAC-CA
* * * *
144148 TATGGAATTTTGATAATTA-CCTATGAATTTGTGATAAACTCCA
1 TATGAAATTTTGATAACTACCCTATAAATTTGTGATAAACACCA
144191 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
144208 CTAACTATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 7 0.14
43 33 0.66
44 10 0.20
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCCTATAAATTTGTGATAAACACCA
Found at i:144258 original size:21 final size:21
Alignment explanation
Indices: 144191--144290 Score: 85
Period size: 21 Copynumber: 4.6 Consensus size: 21
144181 ATAAACTCCA
**
144191 TATGAAATTTTGATAACCTAAC
1 TATGAAATTTTG-TAACCTTCC
** *
144213 TATGAAATTTCAATAAACTTTCC
1 TATGAAATTT-TGT-AACCTTCC
144236 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTGTAACCTTCC
* *
144257 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTG-TAACCTTCC
*
144278 TATGAGATTTTGT
1 TATGAAATTTTGT
144291 TAATCTCCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
20 6 0.10
21 24 0.39
22 17 0.27
23 15 0.24
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Found at i:144298 original size:22 final size:20
Alignment explanation
Indices: 144234--144308 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
144224 AATAAACTTT
*
144234 CCTATGAAATTTTGTAACCTT
1 CCTATG-AATTTTGTAACCTC
*
144255 CCTATGATTTTTGATAACCTC
1 CCTATGAATTTTG-TAACCTC
*
144276 CCTATGAGATTTTGTTAATCTC
1 CCTATGA-ATTTTG-TAACCTC
*
144298 CTTAT-AATTTT
1 CCTATGAATTTT
144309 TTGATACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
20 11 0.24
21 20 0.43
22 15 0.33
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (20 bp):
CCTATGAATTTTGTAACCTC
Found at i:144603 original size:45 final size:45
Alignment explanation
Indices: 144552--144641 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
144542 AATCTAATCT
* *
144552 GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAGTTTAACTCC
1 GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTCC
*
144597 GGTTTAGTTCTTATAGTATGATTATACGTTTAAAAATTCAACTCC
1 GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTCC
144642 TTTGAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (45 bp):
GGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTCC
Found at i:146550 original size:18 final size:18
Alignment explanation
Indices: 146529--146584 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 18
146519 ACTTATGGTT
146529 ATATAAGTTTTTTTTTCA
1 ATATAAGTTTTTTTTTCA
146547 ATATAAGTAATTTTTTTGTTCA
1 ATATAAG---TTTTTTT-TTCA
146569 ATATAAGTATTTTTTT
1 ATATAAGT-TTTTTTT
146585 AAAGTCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 7 0.21
19 2 0.06
20 6 0.18
21 7 0.21
22 11 0.33
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (18 bp):
ATATAAGTTTTTTTTTCA
Found at i:146568 original size:22 final size:20
Alignment explanation
Indices: 146536--146615 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 20
146526 GTTATATAAG
146536 TTTTTTTTTCAATATAAGTAA
1 TTTTTTTTTCAATATAAGT-A
146557 TTTTTTTGTTCAATATAAGTA
1 TTTTTTT-TTCAATATAAGTA
*
146578 TTTTTTTAAAGTCAAATATAAGGT-
1 TTTTTTT---TTC-AATATAA-GTA
146602 TTTTTTTTTCAATA
1 TTTTTTTTTCAATA
146616 CATATACAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.08
21 17 0.33
22 12 0.24
23 2 0.04
24 14 0.27
25 2 0.04
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTTTTTTTCAATATAAGTA
Found at i:152721 original size:22 final size:21
Alignment explanation
Indices: 152693--152735 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
152683 TTGTTGTGCT
152693 AAAAAAAAGTTGCTTTTCATTA
1 AAAAAAAAGTTGCTTTT-ATTA
152715 AAAAAAAAGTTGCTTTTATTA
1 AAAAAAAAGTTGCTTTTATTA
152736 GAATCCCGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (21 bp):
AAAAAAAAGTTGCTTTTATTA
Found at i:159725 original size:21 final size:20
Alignment explanation
Indices: 159695--159733 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
159685 TATAGTATGA
*
159695 AAGCATTGTCATAATGAAGGT
1 AAGCAATGTCATAA-GAAGGT
*
159716 AAGCAATGTCTTAAGAAG
1 AAGCAATGTCATAAGAAG
159734 TGGTCGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (20 bp):
AAGCAATGTCATAAGAAGGT
Found at i:162808 original size:37 final size:35
Alignment explanation
Indices: 162735--162806 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
162725 AATACCGGTC
162735 GTTGTGGTTCATGCTCTTTTAGTGTGTGTATGTGT
1 GTTGTGGTTCATGCTCTTTTAGTGTGTGTATGTGT
162770 GTTGTGGTTCATGCTCTTTTAGTGTGTGTATGTGT
1 GTTGTGGTTCATGCTCTTTTAGTGTGTGTATGTGT
162805 GT
1 GT
162807 GTGCGCGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.51
Consensus pattern (35 bp):
GTTGTGGTTCATGCTCTTTTAGTGTGTGTATGTGT
Found at i:166972 original size:24 final size:24
Alignment explanation
Indices: 166920--166977 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
166910 CCACCTGCAC
*
166920 TTCCTCCACCTCAGAATCGGAACG
1 TTCCTCCACCTCAGAATCGGAACA
* *
166944 CTCCTCCACCTCAGAATCGGAATA
1 TTCCTCCACCTCAGAATCGGAACA
166968 TTCCTCCACC
1 TTCCTCCACC
166978 GATTCCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.22
Consensus pattern (24 bp):
TTCCTCCACCTCAGAATCGGAACA
Found at i:172907 original size:20 final size:20
Alignment explanation
Indices: 172882--172920 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
172872 GTCTTTCCCT
172882 TTTCTAAACCCATCAAATTG
1 TTTCTAAACCCATCAAATTG
172902 TTTCTAAACCCATCAAATT
1 TTTCTAAACCCATCAAATT
172921 TTTGTTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (20 bp):
TTTCTAAACCCATCAAATTG
Done.