Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010631.1 Corchorus capsularis cultivar CVL-1 contig10652, 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: 92163
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2198 original size:19 final size:19
Alignment explanation
Indices: 2169--2205 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2159 AGTAATCAAT
2169 AAATCAGTAATCAAGTAAAA
1 AAATCAGTAATC-AGTAAAA
2189 AAAT-AGTAATCAGTAAA
1 AAATCAGTAATCAGTAAA
2206 TCGAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (19 bp):
AAATCAGTAATCAGTAAAA
Found at i:2714 original size:22 final size:22
Alignment explanation
Indices: 2689--3064 Score: 228
Period size: 22 Copynumber: 17.1 Consensus size: 22
2679 AAGGTATCTG
* * *
2689 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATAGTAATCAGT
2711 AAAGAGTAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
2733 AAAAAGTAAGAA-GGTAATCA--
1 AAAGAGTAA-AATAGTAATCAGT
* *
2753 ACAAGAGTAAAAGAGTAGTCAGT
1 A-AAGAGTAAAATAGTAATCAGT
* *
2776 AAAAAGT-AAATAGTAATCAAT
1 AAAGAGTAAAATAGTAATCAGT
*
2797 -AAGAGTAAAATAGTAATTAGT
1 AAAGAGTAAAATAGTAATCAGT
* * * *
2818 AAAAAGTAAAA-GGAAATCCGT
1 AAAGAGTAAAATAGTAATCAGT
* *
2839 -AAGAGTAAAAAAGTGATCAGT
1 AAAGAGTAAAATAGTAATCAGT
2860 AAAGAGTAAAA-AGCTAATCAGT
1 AAAGAGTAAAATAG-TAATCAGT
*
2882 -AAGAAGTAAAA-GGTAATCAGT
1 AAAG-AGTAAAATAGTAATCAGT
* * * *
2903 AAAAAAGCAAAA-GGCAATCAGT
1 -AAAGAGTAAAATAGTAATCAGT
* * *
2925 AAAAAGTAAAAGAGTAATCATT
1 AAAGAGTAAAATAGTAATCAGT
* *
2947 AAAAAAGGTGCAGAAAATAGTAATTAGT
1 -AAAGA-GT----AAAATAGTAATCAGT
*
2975 AAAAGAGTAAAATGGTAATCAGT
1 -AAAGAGTAAAATAGTAATCAGT
* *
2998 AAAAAGTAAGAA-GGTAATCA--
1 AAAGAGTAA-AATAGTAATCAGT
3018 ACAAGAGTAAAATAGTAATCAGT
1 A-AAGAGTAAAATAGTAATCAGT
3041 ACAA-AGTAAAGA-A-TAATCAGT
1 A-AAGAGTAAA-ATAGTAATCAGT
3062 AAA
1 AAA
3065 ATAGTGATGG
Statistics
Matches: 285, Mismatches: 43, Indels: 54
0.75 0.11 0.14
Matches are distributed among these distances:
20 22 0.08
21 94 0.33
22 118 0.41
23 30 0.11
24 2 0.01
27 2 0.01
28 17 0.06
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.20
Consensus pattern (22 bp):
AAAGAGTAAAATAGTAATCAGT
Found at i:2762 original size:43 final size:42
Alignment explanation
Indices: 2694--3050 Score: 295
Period size: 43 Copynumber: 8.1 Consensus size: 42
2684 ATCTGAAAGG
* *
2694 GTAAAATGGTAATTAGTAAAGAGTAAAATAGTAATCAGTAAAAA
1 GTAAAA-GGTAATCAAT-AAGAGTAAAATAGTAATCAGTAAAAA
* * *
2738 GTAAGAAGGTAATCAACAAGAGTAAAAGAGTAGTCAGTAAAAA
1 GTAA-AAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
*
2781 GTAAATA-GTAATCAATAAGAGTAAAATAGTAATTAGTAAAAA
1 GTAAA-AGGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
* ** * * *
2823 GTAAAAGGAAATCCGTAAGAGTAAAAAAGTGATCAGTAAAGA
1 GTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
* * *
2865 GTAAAAAGCTAATCAGTAAGAAGTAAAA-GGTAATCAGTAAAAAA
1 GT-AAAAGGTAATCAATAAG-AGTAAAATAGTAATCAGT-AAAAA
* * * * * *
2909 GCAAAAGGCAATCAGTAAAAAGTAAAAGAGTAATCATTAAAAAA
1 GTAAAAGGTAATCAAT-AAGAGTAAAATAGTAATCAGT-AAAAA
* * * *
2953 GGTGCAGAAAATAGTAATTAGTAAAAGAGTAAAATGGTAATCAGTAAAAA
1 -GT----AAAA-GGTAATCA--ATAAGAGTAAAATAGTAATCAGTAAAAA
* *
3003 GTAAGAAGGTAATCAACAAGAGTAAAATAGTAATCAGTACAAA
1 GTAA-AAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
3046 GTAAA
1 GTAAA
3051 GAATAATCAG
Statistics
Matches: 253, Mismatches: 43, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.00
42 68 0.27
43 99 0.39
44 39 0.15
45 11 0.04
46 2 0.01
49 6 0.02
50 10 0.04
51 17 0.07
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.20
Consensus pattern (42 bp):
GTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAAAA
Found at i:4432 original size:17 final size:17
Alignment explanation
Indices: 4410--4442 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4400 AATAGTAAAG
4410 GATATGGATACTAAATC
1 GATATGGATACTAAATC
4427 GATATGGATACTAAAT
1 GATATGGATACTAAAT
4443 TCGAATGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (17 bp):
GATATGGATACTAAATC
Found at i:5717 original size:30 final size:30
Alignment explanation
Indices: 5677--5735 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5667 TGTCTTCAAG
5677 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
5707 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
5736 CTCCCCCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:6160 original size:33 final size:33
Alignment explanation
Indices: 6114--6199 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
6104 TTCTTTTCAT
* *
6114 CCAAAACATAATTATTTTTAATGATATAATCAA
1 CCAAAACAGAATTATTTTCAATGATATAATCAA
* * *
6147 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGATATAATCAA
*
6180 TCAAAACAGAATTATTTTCA
1 CCAAAACAGAATTATTTTCA
6200 TCACAATTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGATATAATCAA
Found at i:6252 original size:33 final size:33
Alignment explanation
Indices: 6214--6310 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
6204 AATTAGCATC
*
6214 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * * *
6247 TAAAACAGATTTAGTGTCATTGCCAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** *
6280 CAAATTAGGTTTAGTATCATCGCAAACAACA
1 CAAAACAGATTTAGTATCATCGCAAACAACA
6311 TCTAAAAGAC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:7946 original size:8 final size:8
Alignment explanation
Indices: 7918--7951 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
7908 GAATCGGCTA
7918 TGAATTTT
1 TGAATTTT
*
7926 TGAAGTTTC
1 TGAA-TTTT
7935 TGAATTTT
1 TGAATTTT
7943 TGAATTTT
1 TGAATTTT
7951 T
1 T
7952 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:15924 original size:190 final size:189
Alignment explanation
Indices: 15553--15924 Score: 457
Period size: 190 Copynumber: 2.0 Consensus size: 189
15543 TAAAATCGCT
* *
15553 TATTTTTTTTTCTCTTTTCATTTTAACTAATATCTTTTTTAGACATTTTATCTTTCTATTACATT
1 TATTTTTTTTTCTCTTTTCATTTTAACTAATATCTTTTTTAGACATTTTATCTTTCTATCACAAT
* * *
15618 TTTCTACAATAATACCAAACATTAATTACATTTTATACCTCCATTTCAAAAAGCACTTTCCAAAA
66 TTTCTACAACAATACCAAACATTAATTACATTTTATAACTCAATTTCAAAAAGCACTTTCCAAAA
* * * *
15683 ACACTTCTCCCAAACCGAATTTTTTCAAACCGCAACCTCAATATCAAACTAGTCCTAAA
131 ACACTTCTCCCAAACCGAACTTTTTCAAACCACAAACTCAATATAAAACTAGTCCTAAA
* *
15742 TATTTTTTTTT-TCTTTTCTCTTGTTAACTAATGTCTTTTTTAGACATTTTATCTTTCTATCACC
1 TATTTTTTTTTCTCTTTTC-ATT-TTAACTAATATCTTTTTTAGACATTTTATCTTTCTATCA-C
* * * * * *
15806 AATTTT-TATAGCAATACCAAATATTAATTATATTTT-TCAACTGCAATTTCAAAAAGTA-TTTT
63 AATTTTCTACAACAATACCAAACATTAATTACATTTTAT-AACT-CAATTTCAAAAAGCACTTTC
* * * * *
15868 CAAAAACACTT-TTCTATATCGAACTTTTTCAAACTACAAACTCAATACTAAAACTAG
126 CAAAAACACTTCTCCCAAACCGAACTTTTTCAAACCACAAACTCAATA-TAAAACTAG
15925 CCCAAAACTC
Statistics
Matches: 155, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
188 7 0.05
189 42 0.27
190 87 0.56
191 19 0.12
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.43
Consensus pattern (189 bp):
TATTTTTTTTTCTCTTTTCATTTTAACTAATATCTTTTTTAGACATTTTATCTTTCTATCACAAT
TTTCTACAACAATACCAAACATTAATTACATTTTATAACTCAATTTCAAAAAGCACTTTCCAAAA
ACACTTCTCCCAAACCGAACTTTTTCAAACCACAAACTCAATATAAAACTAGTCCTAAA
Found at i:23949 original size:11 final size:11
Alignment explanation
Indices: 23933--23963 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
23923 AATAGTAGTC
23933 TTTTTATCCTA
1 TTTTTATCCTA
23944 TTTTTATCCTA
1 TTTTTATCCTA
23955 TTTTTATCC
1 TTTTTATCC
23964 AGAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTTATCCTA
Found at i:25338 original size:33 final size:33
Alignment explanation
Indices: 25296--25362 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
25286 CCAAATTAAA
*
25296 TCCAGTCATAGTTTGAGTTGATACTCATAACTT
1 TCCAGTCATAGTCTGAGTTGATACTCATAACTT
25329 TCCAGTCATAGTCTGAGTTGATACTCATAACTT
1 TCCAGTCATAGTCTGAGTTGATACTCATAACTT
25362 T
1 T
25363 TTTCTTTTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (33 bp):
TCCAGTCATAGTCTGAGTTGATACTCATAACTT
Found at i:31358 original size:129 final size:128
Alignment explanation
Indices: 31044--31358 Score: 386
Period size: 129 Copynumber: 2.5 Consensus size: 128
31034 ATGGCTTTAT
* * * * * *
31044 TAATAGTTGCTGCAATTCCTCAACAAGTTCACTTCTCGCAATC--ACTTCCTTATTGGTGCTTTT
1 TAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCATACCTCCTTAGTGGTGCTTTT
* * *
31107 TAATAGCTGCTGCAGTTCCTCAATAAGTTTACTCCTCAGAATCACTTCCTCGTGGGTGCTTTT
66 TAATAGCTGCTGCAGTTCCTCAAAAAGTTTACTCCTCAGAATCACTTCCTCATGGGTGCTTTC
* * * *
31170 TAA-ACGCTGCTGCACTTCCTCAACAAGTTTACCTCTCGGAATCACTACCTCATTTGTGGTGCTT
1 TAATA-GCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCA-TACCTCCTTAGTGGTGCTT
* * * * * *
31234 TTTAATCGCTGCTGCAGTTCTTCAAAAAGTTTACTTCTCGGAATCA-TATCCTCATTGGTGGTTT
64 TTTAATAGCTGCTGCAGTTCCTCAAAAAGTTTACTCCTCAGAATCACT-TCCTCATGGGTGCTTT
31298 C
128 C
*
31299 TAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCATATCCTCCTTGGTGGT
1 TAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCATA-CCTCCTTAGTGGT
31359 TTCTACCTTC
Statistics
Matches: 160, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
125 1 0.01
126 36 0.22
128 3 0.02
129 119 0.74
130 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.37
Consensus pattern (128 bp):
TAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCATACCTCCTTAGTGGTGCTTTT
TAATAGCTGCTGCAGTTCCTCAAAAAGTTTACTCCTCAGAATCACTTCCTCATGGGTGCTTTC
Found at i:31363 original size:63 final size:64
Alignment explanation
Indices: 31037--31356 Score: 357
Period size: 63 Copynumber: 5.0 Consensus size: 64
31027 CCCTTTCATG
* * * * *
31037 GCTTTATTAATAGTTGCTGCAATTCCTCAACAAGTTCACTTCTCGCAATCACT-TCCTTATTGGT
1 GCTTT-TTAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCACTATCCTCATTGGT
* * * * *
31101 GCTTTTTAATAGCTGCTGCAGTTCCTCAATAAGTTTACTCCTC-AGAATCACT-TCCTCGTGGGT
1 GCTTTTTAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGA-AATCACTATCCTCATTGGT
* *
31164 GCTTTTTAA-ACGCTGCTGCACTTCCTCAACAAGTTTACCTCTCGGAATCACTA-CCTCATTTGT
1 GCTTTTTAATA-GCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCACTATCCTCA--T-T
31227 GGT
62 GGT
* * * * *
31230 GCTTTTTAATCGCTGCTGCAGTTCTTCAAAAAGTTTACTTCTCGGAATCA-TATCCTCATTGGT
1 GCTTTTTAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCACTATCCTCATTGGT
* * *
31293 GGTTTCTAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCA-TATCCTCCTTGGT
1 GCTTTTTAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCACTATCCTCATTGGT
31356 G
1 G
31357 GTTTCTACCT
Statistics
Matches: 218, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.00
63 156 0.72
64 6 0.03
65 3 0.01
66 52 0.24
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (64 bp):
GCTTTTTAATAGCTGCTGCACTTCCTCAACAAGTTTACTTCTCGAAATCACTATCCTCATTGGT
Found at i:32344 original size:2 final size:2
Alignment explanation
Indices: 32337--32361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32327 TTGATTTGGA
32337 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
32362 AATTCAACTG
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:32890 original size:33 final size:33
Alignment explanation
Indices: 32848--32914 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
32838 CAATTCCAAG
*
32848 ACTCATACCAACAGCTGGAACCTGCTTTGTGCC
1 ACTCATACCAACAGCTGGAACCGGCTTTGTGCC
32881 ACTCATACCAACAGCTGGAACCGGCTTTGTGCC
1 ACTCATACCAACAGCTGGAACCGGCTTTGTGCC
32914 A
1 A
32915 AAATTTCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (33 bp):
ACTCATACCAACAGCTGGAACCGGCTTTGTGCC
Found at i:33670 original size:1 final size:1
Alignment explanation
Indices: 33664--33698 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
33654 AGACCATTGC
33664 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33699 GAAGAGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38425 original size:29 final size:29
Alignment explanation
Indices: 38360--38447 Score: 131
Period size: 29 Copynumber: 2.9 Consensus size: 29
38350 TCACTGAGGG
38360 TATGTTGGTTTCTTAAAGAAATTAACAAAAAGA
1 TATGTTGGTTTCTTAAAG--A--AACAAAAAGA
*
38393 TATGTTGGTTTCTTAAAGAAACAAAGAGA
1 TATGTTGGTTTCTTAAAGAAACAAAAAGA
38422 TATGTTGGTTTCTTAAAGAAACAAAA
1 TATGTTGGTTTCTTAAAGAAACAAAA
38448 GAGTTATACC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
29 34 0.64
31 1 0.02
33 18 0.34
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (29 bp):
TATGTTGGTTTCTTAAAGAAACAAAAAGA
Found at i:43831 original size:1 final size:1
Alignment explanation
Indices: 43825--43853 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
43815 TAGATTCTGC
43825 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43854 GGACGGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50736 original size:17 final size:17
Alignment explanation
Indices: 50714--50748 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
50704 ATCAAGTAAT
50714 TCTGTGGCAGTAGTTAC
1 TCTGTGGCAGTAGTTAC
*
50731 TCTGTGGGAGTAGTTAC
1 TCTGTGGCAGTAGTTAC
50748 T
1 T
50749 TTTTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.31, T:0.37
Consensus pattern (17 bp):
TCTGTGGCAGTAGTTAC
Found at i:50830 original size:20 final size:21
Alignment explanation
Indices: 50794--50832 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50784 GAGTAGTTAC
50794 TTTTTCAAATTGAAATTAACA
1 TTTTTCAAATTGAAATTAACA
*
50815 TTTTTCAATTTG-AATTAA
1 TTTTTCAAATTGAAATTAA
50833 ACCGTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTTTCAAATTGAAATTAACA
Found at i:53056 original size:79 final size:79
Alignment explanation
Indices: 52922--53083 Score: 297
Period size: 79 Copynumber: 2.1 Consensus size: 79
52912 TACAAAACAT
* *
52922 AGATCCTATTCCTACTTAGCTCTTGGTTACTAATCATGGGGGCAACAACAGCATCCTTATTCCAA
1 AGATCCTATTCCTACTTAGCTCTTGGCTACTAATCATGGGGGCAACAACACCATCCTTATTCCAA
52987 ATACCAACTAGTGA
66 ATACCAACTAGTGA
53001 AGATCCTATTCCTACTTAGCTCTTGGCTACTAATCATGGGGGCAACAACACCATCCTTATTCCAA
1 AGATCCTATTCCTACTTAGCTCTTGGCTACTAATCATGGGGGCAACAACACCATCCTTATTCCAA
*
53066 ATACCAGCTAGTGA
66 ATACCAACTAGTGA
53080 AGAT
1 AGAT
53084 GGTTTTTGTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (79 bp):
AGATCCTATTCCTACTTAGCTCTTGGCTACTAATCATGGGGGCAACAACACCATCCTTATTCCAA
ATACCAACTAGTGA
Found at i:53933 original size:21 final size:20
Alignment explanation
Indices: 53857--53945 Score: 88
Period size: 21 Copynumber: 4.3 Consensus size: 20
53847 CTGATCACCC
53857 TTTACTCTTACTGATTACTAT
1 TTTACTCTTACTGATTA-TAT
* * *
53878 TTGACTCTTACTAATTATCAC
1 TTTACTCTTACTGATTAT-AT
* *
53899 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTGATTA-TAT
* *
53920 TTTACTCTTACTGGTTATCT
1 TTTACTCTTACTGATTATAT
53940 TTTACT
1 TTTACT
53946 GATTACTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.16
21 46 0.82
22 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTACTCTTACTGATTATAT
Found at i:53970 original size:22 final size:22
Alignment explanation
Indices: 53940--54298 Score: 181
Period size: 22 Copynumber: 16.1 Consensus size: 22
53930 CTGGTTATCT
*
53940 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACCATTTTACTC
* *
53962 TTTGCTGATTACC-TTCTTACTT
1 TTTACTGATTACCATT-TTACTC
53984 TTTACTGATTACCATTTTACTC
1 TTTACTGATTACCATTTTACTC
*
54006 TTTTACTGATTACCATTTTCTGCTCCC
1 -TTTACTGATTACCA-TTT-TACT--C
*
54033 TTTTTACTGATTACTC-TTTTACTT
1 --TTTACTGATTAC-CATTTTACTC
** * *
54057 TTTACTGATTGTC-TTTTGCTT
1 TTTACTGATTACCATTTTACTC
* *
54078 TTTACTGATTACCTTTTTA-TT
1 TTTACTGATTACCATTTTACTC
* *
54099 TCTTACTGATTAGCTTTTTACTC
1 T-TTACTGATTACCATTTTACTC
*
54122 TTTACTGATCACC-TTTTCACTC
1 TTTACTGATTACCATTTT-ACTC
*
54144 -TTACTGATTTCC-TTTTACT-
1 TTTACTGATTACCATTTTACTC
**
54163 TCTTACTTG-TTACTTTTTTTTTACTC
1 T-TTAC-TGATTAC---CATTTTACTC
** *
54189 -TTACTGATTAATATTTTACTTT
1 TTTACTGATTACCATTTTAC-TC
* * * *
54211 TTTACGGACTACTATTTCACTC
1 TTTACTGATTACCATTTTACTC
*
54233 TTGT--TGATTACC-TTCTTACTT
1 TT-TACTGATTACCATT-TTACTC
*
54254 TTTAATGATTACC-TTTTACTC
1 TTTACTGATTACCATTTTACTC
* * *
54275 -TTACTAACTACCATTTTACCC
1 TTTACTGATTACCATTTTACTC
54296 TTT
1 TTT
54299 CAGATACTTT
Statistics
Matches: 267, Mismatches: 40, Indels: 60
0.73 0.11 0.16
Matches are distributed among these distances:
20 15 0.06
21 79 0.30
22 96 0.36
23 36 0.13
24 10 0.04
25 10 0.04
26 3 0.01
27 4 0.01
28 13 0.05
29 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.54
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTC
Found at i:53992 original size:44 final size:44
Alignment explanation
Indices: 53939--54276 Score: 223
Period size: 44 Copynumber: 7.6 Consensus size: 44
53929 ACTGGTTATC
*
53939 TTTTACTGATTACTATTTTACTCTTTGCTGATTACCTTCTTACT
1 TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACT
* *
53983 TTTTACTGATTACCATTTTACTCTTTTACTGATTACCATTTTCTGCTCCCT
1 TTTTACTGATTACTATTTTACTC-TTTACTGATTACC---TTCT--T-ACT
* * ** *
54034 TTTTACTGATTACTCTTTTACTTTTTACTGATTGTCTT-TTGCT
1 TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACT
* * *
54077 TTTTACTGATTACCT-TTTTA-TTTCTTACTGATTAGCTTTTTACT
1 TTTTACTGATTA-CTATTTTACTCT-TTACTGATTACCTTCTTACT
* * * *
54121 CTTTACTGATCACCT-TTTCACTC-TTACTGATTTCCTT-TTACT
1 TTTTACTGATTA-CTATTTTACTCTTTACTGATTACCTTCTTACT
* * * *
54163 TCTTACTTG-TTACTTTTTTTTTACTC-TTACTGATTA-ATATTTTACTT
1 TTTTAC-TGATTAC---TATTTTACTCTTTACTGATTACCT-TCTTAC-T
* * *
54210 TTTTACGGACTACTATTTCACTCTTGT--TGATTACCTTCTTACT
1 TTTTACTGATTACTATTTTACTCTT-TACTGATTACCTTCTTACT
* *
54253 TTTTAATGATTAC-CTTTTACTCTT
1 TTTTACTGATTACTATTTTACTCTT
54277 ACTAACTACC
Statistics
Matches: 235, Mismatches: 36, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
41 1 0.00
42 23 0.10
43 56 0.24
44 67 0.29
45 32 0.14
46 7 0.03
47 11 0.05
48 4 0.02
50 12 0.05
51 22 0.09
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (44 bp):
TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACT
Found at i:54018 original size:15 final size:15
Alignment explanation
Indices: 54000--54055 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
53990 GATTACCATT
54000 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
54015 TTAC-CATTTT-CTGC
1 TTACTC-TTTTACTGA
**
54029 TCCCT-TTTTACTGA
1 TTACTCTTTTACTGA
54043 TTACTCTTTTACT
1 TTACTCTTTTACT
54056 TTTTACTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
13 4 0.13
14 12 0.39
15 15 0.48
ACGTcount: A:0.16, C:0.25, G:0.05, T:0.54
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:54058 original size:21 final size:21
Alignment explanation
Indices: 54034--54279 Score: 121
Period size: 21 Copynumber: 11.3 Consensus size: 21
54024 TCTGCTCCCT
54034 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTACTCTTTTAC
* *
54055 TTTTTACTGATT-GTCTTTTGC
1 -TTTTACTGATTACTCTTTTAC
*
54076 TTTTTACTGATTAC-CTTTTTAT
1 -TTTTACTGATTACTC-TTTTAC
54098 TTCTTACTGATTAGCT-TTTTAC
1 TT-TTACTGATTA-CTCTTTTAC
*
54120 TCTTTACTGATCAC-CTTTTCAC
1 T-TTTACTGATTACTCTTTT-AC
* *
54142 TCTTACTGATTTC-CTTTTAC
1 TTTTACTGATTACTCTTTTAC
*
54162 TTCTTACTTG-TTACTTTTTTTTTAC
1 TT-TTAC-TGATTAC---TCTTTTAC
* * *
54187 TCTTACTGATTAATATTTTAC
1 TTTTACTGATTACTCTTTTAC
* * * *
54208 TTTTTTACGGACTACTATTTCAC
1 --TTTTACTGATTACTCTTTTAC
* **
54231 TCTTGTTGATTAC-CTTCTTAC
1 TTTTACTGATTACTCTT-TTAC
*
54252 TTTTTAATGATTAC-CTTTTAC
1 -TTTTACTGATTACTCTTTTAC
*
54273 TCTTACT
1 TTTTACT
54280 AACTACCATT
Statistics
Matches: 172, Mismatches: 33, Indels: 40
0.70 0.13 0.16
Matches are distributed among these distances:
20 10 0.06
21 70 0.41
22 58 0.34
23 20 0.12
24 7 0.04
25 7 0.04
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTACTGATTACTCTTTTAC
Found at i:54205 original size:24 final size:25
Alignment explanation
Indices: 54156--54205 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
54146 ACTGATTTCC
* *
54156 TTTTACTTCTTACTTGTTACTTTTT
1 TTTTACTTCTTACTTGTTAATATTT
54181 TTTTAC-TCTTAC-TGATTAATATTT
1 TTTTACTTCTTACTTG-TTAATATTT
54205 T
1 T
54206 ACTTTTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 2 0.09
24 14 0.64
25 6 0.27
ACGTcount: A:0.18, C:0.14, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTTACTTCTTACTTGTTAATATTT
Found at i:54509 original size:22 final size:24
Alignment explanation
Indices: 54482--54525 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
54472 TTAACCACTC
54482 AACTCTTAATTAT-GA-TCACTTT
1 AACTCTTAATTATCGATTCACTTT
54504 AACTCTTAATTATCGATTCACT
1 AACTCTTAATTATCGATTCACT
54526 GATTACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (24 bp):
AACTCTTAATTATCGATTCACTTT
Found at i:54672 original size:55 final size:56
Alignment explanation
Indices: 54608--54723 Score: 182
Period size: 56 Copynumber: 2.1 Consensus size: 56
54598 TATCTTTTAC
*
54608 CTGA-TTACTGATTACTATTACCTTAACTC-TGATTAATCTCTTTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACTCATGATTAATCTCTTTTTACTTAATTA
* * *
54662 CTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACTCATGATTAATCTCTTTTTACTTAATTA
54718 CTGATT
1 CTGATT
54724 GCCCCCTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 4 0.07
55 21 0.38
56 31 0.55
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (56 bp):
CTGATTTACTGATTACTACTACCTTAACTCATGATTAATCTCTTTTTACTTAATTA
Found at i:55682 original size:10 final size:11
Alignment explanation
Indices: 55657--55685 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
55647 AGATTAGTCC
55657 TTTATCACCAA
1 TTTATCACCAA
55668 TTTATCACC-A
1 TTTATCACCAA
55678 TTTATCAC
1 TTTATCAC
55686 TAAAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (11 bp):
TTTATCACCAA
Found at i:57906 original size:22 final size:21
Alignment explanation
Indices: 57874--57927 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
57864 ACTCTTCTTA
* *
57874 TTTTTGCTATTTTTA-TTATTT
1 TTTTTGTTATTATTACTT-TTT
57895 TATTTTGTTATTATTACTTTTT
1 T-TTTTGTTATTATTACTTTTT
57917 TTTTTGCTTAT
1 TTTTTG-TTAT
57928 GCGAGTGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.21
22 20 0.71
23 2 0.07
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (21 bp):
TTTTTGTTATTATTACTTTTT
Found at i:58421 original size:28 final size:28
Alignment explanation
Indices: 58362--58431 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
58352 AGGTGAACCC
* *
58362 AAAAATGACTAAAATGCCCCTGAGTACA
1 AAAAATGACCAAAATGCCCATGAGTACA
* *
58390 AAAAATGACCAAAATGCCCATGGGTGC-
1 AAAAATGACCAAAATGCCCATGAGTACA
*
58417 GAAAATGACCAAAAT
1 AAAAATGACCAAAAT
58432 ACCCTTGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 14 0.38
28 23 0.62
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCATGAGTACA
Found at i:67431 original size:30 final size:31
Alignment explanation
Indices: 67397--67455 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
67387 CACGGGCCAC
* *
67397 GCCACATGTCCTTTTTT-GTACACGTGGCGT
1 GCCACACGTCATTTTTTGGTACACGTGGCGT
* *
67427 GCCACGCGTCATTTTTTGGTATACGTGGC
1 GCCACACGTCATTTTTTGGTACACGTGGC
67456 ATCTCACGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (31 bp):
GCCACACGTCATTTTTTGGTACACGTGGCGT
Found at i:70987 original size:15 final size:15
Alignment explanation
Indices: 70967--71001 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
70957 ACTAGCTCAG
*
70967 CAAACTCAACAGACT
1 CAAACTAAACAGACT
*
70982 CAAACTAAACTGACT
1 CAAACTAAACAGACT
70997 CAAAC
1 CAAAC
71002 ATCCAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
CAAACTAAACAGACT
Found at i:72044 original size:6 final size:6
Alignment explanation
Indices: 72032--72072 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
72022 AAATAGGAAA
* *
72032 AAAAAG GAAAAG GAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
72073 ATTAAAGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:72048 original size:12 final size:11
Alignment explanation
Indices: 72028--72071 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
72018 GAGAAAATAG
*
72028 GAAAAA-AAAG
1 GAAAAAGAAAA
*
72038 GAAAAGGAAAA
1 GAAAAAGAAAA
72049 GAAAAAGAAAAA
1 GAAAAAG-AAAA
72061 GAAAAAGAAAA
1 GAAAAAGAAAA
72072 AATTAAAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 5 0.17
11 13 0.45
12 11 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:73761 original size:17 final size:17
Alignment explanation
Indices: 73741--73786 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
73731 TGCTGCCACG
73741 TGATTCCTGTTGTAGTC
1 TGATTCCTGTTGTAGTC
*
73758 TGATTCCTGTTGTAGTG
1 TGATTCCTGTTGTAGTC
73775 TGATTCCTGTTG
1 TGATTCCTGTTG
73787 CAGCGTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.11, C:0.15, G:0.26, T:0.48
Consensus pattern (17 bp):
TGATTCCTGTTGTAGTC
Found at i:73794 original size:17 final size:17
Alignment explanation
Indices: 73722--73796 Score: 82
Period size: 17 Copynumber: 4.4 Consensus size: 17
73712 CCGGTCCTTC
*
73722 CGTGATTCCTGCTGCCA-
1 CGTGATTCCTGTTG-CAG
*
73739 CGTGATTCCTGTTGTAG
1 CGTGATTCCTGTTGCAG
*
73756 TC-TGATTCCTGTTGTAG
1 -CGTGATTCCTGTTGCAG
*
73773 TGTGATTCCTGTTGCAG
1 CGTGATTCCTGTTGCAG
73790 CGTGATT
1 CGTGATT
73797 GTTGTTGTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.02
17 48 0.96
18 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.40
Consensus pattern (17 bp):
CGTGATTCCTGTTGCAG
Found at i:73796 original size:34 final size:34
Alignment explanation
Indices: 73740--73806 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
73730 CTGCTGCCAC
*
73740 GTGATTCCTGTTGTAGTCTGATTCCTGTTGTAGT
1 GTGATTCCTGTTGCAGTCTGATTCCTGTTGTAGT
**
73774 GTGATTCCTGTTGCAG-CGTGATTGTTGTTGTAG
1 GTGATTCCTGTTGCAGTC-TGATTCCTGTTGTAG
73807 CCTGACTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.12, C:0.13, G:0.30, T:0.45
Consensus pattern (34 bp):
GTGATTCCTGTTGCAGTCTGATTCCTGTTGTAGT
Found at i:75058 original size:30 final size:30
Alignment explanation
Indices: 75023--75094 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
75013 GATTAAAATA
75023 TGTATCCATCTAGAATTCGAAAAATATATG
1 TGTATCCATCTAGAATTCGAAAAATATATG
75053 TGTATCCATCTAGAATTCGAAAAATATATG
1 TGTATCCATCTAGAATTCGAAAAATATATG
*
75083 TATATCCATCTA
1 TGTATCCATCTA
75095 AATAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (30 bp):
TGTATCCATCTAGAATTCGAAAAATATATG
Found at i:75103 original size:28 final size:30
Alignment explanation
Indices: 75025--75105 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
75015 TTAAAATATG
** *
75025 TATCCATCTAGAATTCGAAAAATATATGTG
1 TATCCATCTAGAATTAAAAAAATATATGTA
**
75055 TATCCATCTAGAATTCGAAAAATATATGTA
1 TATCCATCTAGAATTAAAAAAATATATGTA
*
75085 TATCCATCTA-AATAAAAAAAA
1 TATCCATCTAGAATTAAAAAAA
75106 AAAAAACCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 8 0.17
30 39 0.83
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (30 bp):
TATCCATCTAGAATTAAAAAAATATATGTA
Found at i:82367 original size:13 final size:14
Alignment explanation
Indices: 82337--82371 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
82327 TTTCTTTTGC
82337 TTTTTCGTTGTTTA
1 TTTTTCGTTGTTTA
82351 TTTTT-GTT-TTTA
1 TTTTTCGTTGTTTA
82363 TTTTTCGTT
1 TTTTTCGTT
82372 AAGTGCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.45
13 6 0.30
14 5 0.25
ACGTcount: A:0.06, C:0.06, G:0.11, T:0.77
Consensus pattern (14 bp):
TTTTTCGTTGTTTA
Found at i:84615 original size:21 final size:21
Alignment explanation
Indices: 84591--84639 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
84581 TAGTTGGGCC
*
84591 CCCAGGTCGCAAGCCTGAACA
1 CCCAGGCCGCAAGCCTGAACA
* * *
84612 CCCAGCCCGTAAGCCTGAGCA
1 CCCAGGCCGCAAGCCTGAACA
84633 CCCAGGC
1 CCCAGGC
84640 GCGAGCTACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.43, G:0.24, T:0.08
Consensus pattern (21 bp):
CCCAGGCCGCAAGCCTGAACA
Found at i:86439 original size:6 final size:6
Alignment explanation
Indices: 86424--86454 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
86414 TATGGTTAGG
*
86424 CGGATA CGGATT CGGATT CGGATT CGGATT C
1 CGGATT CGGATT CGGATT CGGATT CGGATT C
86455 TAAATGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.29
Consensus pattern (6 bp):
CGGATT
Found at i:87569 original size:21 final size:21
Alignment explanation
Indices: 87545--87584 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
87535 ACTGCCTACC
*
87545 TGGGTGATCAGGCAAACCACA
1 TGGGTCATCAGGCAAACCACA
* *
87566 TGGGTCTTCAGTCAAACCA
1 TGGGTCATCAGGCAAACCA
87585 TGTGGGTGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (21 bp):
TGGGTCATCAGGCAAACCACA
Found at i:90263 original size:28 final size:28
Alignment explanation
Indices: 90193--90265 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
90183 CATTTTACTC
*
90193 TTTTACTGATTACTATTTTCTGCTCCTT
1 TTTTACTGATTACTCTTTTCTGCTCCTT
90221 TTTTACTGATTACTCTTTTCTGCTCCTT
1 TTTTACTGATTACTCTTTTCTGCTCCTT
90249 TTTTACTGATTACTCTT
1 TTTTACTGATTACTCTT
90266 GCTTTTTACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.58
Consensus pattern (28 bp):
TTTTACTGATTACTCTTTTCTGCTCCTT
Found at i:90318 original size:21 final size:21
Alignment explanation
Indices: 90271--90451 Score: 125
Period size: 21 Copynumber: 8.4 Consensus size: 21
90261 CTCTTGCTTT
90271 TTACTGATTACCT-TTTTACTTC
1 TTACTGATTA-CTATTTTAC-TC
*
90293 TTACTGATTACTATTTTACCC
1 TTACTGATTACTATTTTACTC
** *
90314 TTACTGATTACTATTTATTTTTT
1 TTACTGATTACTA-TT-TTACTC
**
90337 TTACTGGCTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
** * *
90358 TTGTTGATTACCT-TCTTACTTT
1 TTACTGATTA-CTATTTTAC-TC
90380 TTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
* * *
90401 TTACTAATTACCATTTTACCC
1 TTACTGATTACTATTTTACTC
* * * *
90422 TTTCAGATAACT-TTTTACTTT
1 TTACTGATTACTATTTTAC-TC
90443 TTACTGATT
1 TTACTGATT
90452 GCATGCTATT
Statistics
Matches: 119, Mismatches: 33, Indels: 15
0.71 0.20 0.09
Matches are distributed among these distances:
20 6 0.05
21 64 0.54
22 36 0.30
23 13 0.11
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.54
Consensus pattern (21 bp):
TTACTGATTACTATTTTACTC
Found at i:90412 original size:43 final size:42
Alignment explanation
Indices: 90121--90205 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
90111 CTGACTATTC
* **
90121 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCT
*
90163 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTAC
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTACTGATTAC
90206 TATTTTCTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.03
43 26 0.72
45 9 0.25
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCT
Found at i:90779 original size:55 final size:55
Alignment explanation
Indices: 90718--90926 Score: 355
Period size: 55 Copynumber: 3.8 Consensus size: 55
90708 TATCAATTTA
* * * *
90718 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACT
*
90773 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACT
* *
90828 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACT
90883 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTA
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTA
90927 CCTCTTTTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 145 1.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACT
Found at i:90939 original size:36 final size:37
Alignment explanation
Indices: 90892--90963 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
90882 TCTGATTAAT
*
90892 CTCTTTTTACTTTATTACTGA-TTTACTGATTACTAC
1 CTCTTTTTACTTAATTACTGATTTTACTGATTACTAC
90928 CTCTTTTTACTTAATTACTGATTTTACTGATTACTA
1 CTCTTTTTACTTAATTACTGATTTTACTGATTACTA
90964 TTACCTTGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 20 0.59
37 14 0.41
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (37 bp):
CTCTTTTTACTTAATTACTGATTTTACTGATTACTAC
Found at i:90977 original size:92 final size:91
Alignment explanation
Indices: 90837--91006 Score: 304
Period size: 92 Copynumber: 1.9 Consensus size: 91
90827 TCTGATTAAT
90837 CTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTAC
1 CTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTAC
*
90902 TTTATTACTGATTTACTGATTACTAC
66 TTAATTACTGATTTACTGATTACTAC
**
90928 CTCTTTTTACTTAATTACTGATTTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTA
1 CTCTTTTTACTTAATTACTGA-TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTA
90993 CTTAATTACTGATT
65 CTTAATTACTGATT
91007 GCCCTTTTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 21 0.28
92 54 0.72
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (91 bp):
CTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTAC
TTAATTACTGATTTACTGATTACTAC
Done.