Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015589.1 Corchorus capsularis cultivar CVL-1 contig15610, 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: 43950
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1725 original size:27 final size:28
Alignment explanation
Indices: 1695--1764 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
1685 AGGTGAACCT
*
1695 AAAAATGACTAAAATGCCCCTGAGTGCA
1 AAAAATGACCAAAATGCCCCTGAGTGCA
*
1723 AAAAATGACCAAAATGCCCCTGGGTGC-
1 AAAAATGACCAAAATGCCCCTGAGTGCA
1750 AAAAATGACCAAAAT
1 AAAAATGACCAAAAT
1765 ACCCTGTGCG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 15 0.38
28 25 0.62
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTGAGTGCA
Found at i:4040 original size:25 final size:25
Alignment explanation
Indices: 4010--4059 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4000 TCAAAATGCC
4010 CCAAATAAAAGACATAAGACAAGAA
1 CCAAATAAAAGACATAAGACAAGAA
*
4035 CCAAATAAAAGGCATAAGACAAGAA
1 CCAAATAAAAGACATAAGACAAGAA
4060 AGGAAATCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.62, C:0.16, G:0.14, T:0.08
Consensus pattern (25 bp):
CCAAATAAAAGACATAAGACAAGAA
Found at i:5072 original size:50 final size:48
Alignment explanation
Indices: 5018--5150 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 48
5008 TGAGGAATAA
*
5018 TGCCCATGCGTTACATATGTGTTTTGGGCCTTTGTATGTATTGTATGTAT
1 TGCCCATGCGTT--GTATGTGTTTTGGGCCTTTGTATGTATTGTATGTAT
* * * *
5068 TGCCCATGTGTTTGTATGTGTTTTGGGGCTTTTGTGTGTTTTGTATGTAT
1 TGCCCATGCG-TTGTATGTGTTTT-GGGCCTTTGTATGTATTGTATGTAT
*
5118 TGCCCAT-CTGTTGTATGTGTTTTGGGACTTTGT
1 TGCCCATGC-GTTGTATGTGTTTTGGGCCTTTGT
5151 TATTGGGTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
48 8 0.11
49 23 0.32
50 39 0.54
51 2 0.03
ACGTcount: A:0.11, C:0.12, G:0.27, T:0.50
Consensus pattern (48 bp):
TGCCCATGCGTTGTATGTGTTTTGGGCCTTTGTATGTATTGTATGTAT
Found at i:5132 original size:49 final size:50
Alignment explanation
Indices: 5033--5148 Score: 173
Period size: 50 Copynumber: 2.4 Consensus size: 50
5023 ATGCGTTACA
* *
5033 TATGTGTTTT-GGGCCTTTGTATGTATTGTATGTATTGCCCATGTGTTTG
1 TATGTGTTTTGGGGCTTTTGTATGTATTGTATGTATTGCCCATCTGTTTG
* *
5082 TATGTGTTTTGGGGCTTTTGTGTGTTTTGTATGTATTGCCCATCTG-TTG
1 TATGTGTTTTGGGGCTTTTGTATGTATTGTATGTATTGCCCATCTGTTTG
*
5131 TATGTGTTTTGGGACTTT
1 TATGTGTTTTGGGGCTTT
5149 GTTATTGGGT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 30 0.49
50 31 0.51
ACGTcount: A:0.10, C:0.09, G:0.28, T:0.53
Consensus pattern (50 bp):
TATGTGTTTTGGGGCTTTTGTATGTATTGTATGTATTGCCCATCTGTTTG
Found at i:6310 original size:33 final size:33
Alignment explanation
Indices: 6268--6335 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
6258 ACAAATAAAG
*
6268 AGACAGTTTTGATTTGCCAATCTAACGGTTATT
1 AGACAGTTTTGATATGCCAATCTAACGGTTATT
6301 AGACAGTTTTGATATGCCAATCTAACGGTTATT
1 AGACAGTTTTGATATGCCAATCTAACGGTTATT
6334 AG
1 AG
6336 GTATCCGCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (33 bp):
AGACAGTTTTGATATGCCAATCTAACGGTTATT
Found at i:7426 original size:6 final size:6
Alignment explanation
Indices: 7387--7432 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
7377 CAGGCAAAAT
7387 GAACCC GAAACCC GAATCCC GAAACCC G--CCC GAACCC GAACCC GAA
1 GAACCC G-AACCC GAA-CCC G-AACCC GAACCC GAACCC GAACCC GAA
7433 ATTACCCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.11
6 15 0.43
7 14 0.40
8 2 0.06
ACGTcount: A:0.35, C:0.46, G:0.17, T:0.02
Consensus pattern (6 bp):
GAACCC
Found at i:7426 original size:17 final size:17
Alignment explanation
Indices: 7397--7430 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
7387 GAACCCGAAA
7397 CCCGAATCCCGAAACCCG
1 CCCGAATCCCG-AACCCG
7415 CCCGAA-CCCGAACCCG
1 CCCGAATCCCGAACCCG
7431 AAATTACCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.26, C:0.53, G:0.18, T:0.03
Consensus pattern (17 bp):
CCCGAATCCCGAACCCG
Found at i:7486 original size:16 final size:16
Alignment explanation
Indices: 7463--7518 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
7453 AAGTCAACGT
*
7463 CCCGAACCCGAAATTA
1 CCCGAACCCGAAAATA
*
7479 CTCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
* *
7495 CCCAAACCCGAGACA-A
1 CCCGAACCCGA-AAATA
7511 CCCGAACC
1 CCCGAACC
7519 TGCCCGAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 31 0.94
17 2 0.06
ACGTcount: A:0.39, C:0.41, G:0.12, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:8684 original size:21 final size:20
Alignment explanation
Indices: 8647--8685 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8637 TTTAGAAGCA
*
8647 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
8667 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
8686 GGAAGGGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:9702 original size:23 final size:23
Alignment explanation
Indices: 9672--9727 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
9662 CGAAAGTGAA
* * *
9672 CCGAACCCGACCCGGACCCGGAC
1 CCGAACCCGACACAGACCCGAAC
* *
9695 CCGAACCCAACACAGACCTGAAC
1 CCGAACCCGACACAGACCCGAAC
9718 CCGAACCCGA
1 CCGAACCCGA
9728 TCCAAGCCCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.48, G:0.20, T:0.02
Consensus pattern (23 bp):
CCGAACCCGACACAGACCCGAAC
Found at i:9718 original size:40 final size:38
Alignment explanation
Indices: 9672--9760 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 38
9662 CGAAAGTGAA
* *
9672 CCGAACCCGACCCGGACCC-GGACCCGAACCCAACACAGAC
1 CCGAACCCGACCC-GACCCAAG-CCCGAACCCAACA-AAAC
* *
9712 CTGAACCCGAACCCGATCCAAGCCCGAACCCAACAAAAC
1 CCGAACCCG-ACCCGACCCAAGCCCGAACCCAACAAAAC
9751 CCGAACCCGA
1 CCGAACCCGA
9761 AGTACCGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
38 1 0.02
39 11 0.26
40 25 0.60
41 5 0.12
ACGTcount: A:0.34, C:0.47, G:0.17, T:0.02
Consensus pattern (38 bp):
CCGAACCCGACCCGACCCAAGCCCGAACCCAACAAAAC
Found at i:9725 original size:6 final size:6
Alignment explanation
Indices: 9672--9761 Score: 50
Period size: 6 Copynumber: 15.8 Consensus size: 6
9662 CGAAAGTGAA
* * * *
9672 CCGAAC CCG-AC CCGGAC CCGGAC CCGAAC CC-AAC AC-AGAC CTGAAC
1 CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC CCGA-AC CCGAAC
* **
9718 CCGAAC CCG-AT CC-AAGC CCGAAC CC-AA- CAAAAC CCGAAC CCGAA
1 CCGAAC CCGAAC CCGAA-C CCGAAC CCGAAC CCGAAC CCGAAC CCGAA
9762 GTACCGGAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
4 1 0.02
5 18 0.27
6 44 0.67
7 3 0.05
ACGTcount: A:0.34, C:0.47, G:0.17, T:0.02
Consensus pattern (6 bp):
CCGAAC
Found at i:9755 original size:16 final size:17
Alignment explanation
Indices: 9715--9761 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
9705 CACAGACCTG
* *
9715 AACCCGAACCCGATCCA
1 AACCCGAACCCGAACAA
*
9732 AGCCCGAACCC-AACAA
1 AACCCGAACCCGAACAA
9748 AACCCGAACCCGAA
1 AACCCGAACCCGAA
9762 GTACCGGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.40, C:0.45, G:0.13, T:0.02
Consensus pattern (17 bp):
AACCCGAACCCGAACAA
Found at i:14959 original size:33 final size:33
Alignment explanation
Indices: 14917--15024 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 33
14907 GTGTTTTAGA
*
14917 TGTTGTTTGCGATAATACTAAACCTAATTTGAG
1 TGTTGTTTGCAATAATACTAAACCTAATTTGAG
* *
14950 TGTTGTTTGCAATGATACTAAACCTAACTTGAG
1 TGTTGTTTGCAATAATACTAAACCTAATTTGAG
* * ** *
14983 TGTTCTTTGCAATGAA-ACTAAATCTGCTTTAAG
1 TGTTGTTTGCAAT-AATACTAAACCTAATTTGAG
15016 TGTTGTTTG
1 TGTTGTTTG
15025 TGATAAAACA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 62 0.98
34 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (33 bp):
TGTTGTTTGCAATAATACTAAACCTAATTTGAG
Found at i:15112 original size:33 final size:33
Alignment explanation
Indices: 15075--15146 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
15065 AACAAATCTA
**
15075 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
1 TTTTGGTTGATCATAGCATTAAAAATAATTCTG
* *
15108 TTTTGGTTGATTATGGCATTAAAAATAATTCTG
1 TTTTGGTTGATCATAGCATTAAAAATAATTCTG
15141 TTTTGG
1 TTTTGG
15147 GTGAAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.46
Consensus pattern (33 bp):
TTTTGGTTGATCATAGCATTAAAAATAATTCTG
Found at i:19366 original size:13 final size:13
Alignment explanation
Indices: 19350--19380 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
19340 ATATAAATAA
19350 ATTTAAATATTAT
1 ATTTAAATATTAT
19363 ATTTAAATATTAT
1 ATTTAAATATTAT
19376 ATTTA
1 ATTTA
19381 TCTTATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAAATATTAT
Found at i:19443 original size:29 final size:29
Alignment explanation
Indices: 19384--19443 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
19374 ATATTTATCT
* *
19384 TATAATGGGTAGTTTTTTTCTAAAATTGG
1 TATAATGGGTAGTTTTTATCTAAAATGGG
*
19413 TATAATGGGTAGTTTTTATCTAAGATGGG
1 TATAATGGGTAGTTTTTATCTAAAATGGG
19442 TA
1 TA
19444 GTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.45
Consensus pattern (29 bp):
TATAATGGGTAGTTTTTATCTAAAATGGG
Found at i:21217 original size:17 final size:17
Alignment explanation
Indices: 21195--21228 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21185 TGAGGGAATC
21195 AGATTACCATATTTGGT
1 AGATTACCATATTTGGT
21212 AGATTACCATATTTGGT
1 AGATTACCATATTTGGT
21229 TAACATGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
AGATTACCATATTTGGT
Found at i:24206 original size:11 final size:11
Alignment explanation
Indices: 24181--24214 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
24171 TGATTTGAAC
24181 CTTACAAATATT
1 CTTACAAA-ATT
24193 CTTACAAAATT
1 CTTACAAAATT
24204 CTTACAAAATT
1 CTTACAAAATT
24215 ATATTGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (11 bp):
CTTACAAAATT
Found at i:24495 original size:57 final size:57
Alignment explanation
Indices: 24407--24520 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
24397 ATCTTGCCCC
24407 AGGTAAAAGATTTGAGTGACAAAAATGAAACGTATATGTAATATTGCTGAATCAATT
1 AGGTAAAAGATTTGAGTGACAAAAATGAAACGTATATGTAATATTGCTGAATCAATT
24464 AGGTAAAAGATTTGAGTGACAAAAATGAAACGTATATGTAATATTGCTGAATCAATT
1 AGGTAAAAGATTTGAGTGACAAAAATGAAACGTATATGTAATATTGCTGAATCAATT
24521 TGATCAAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (57 bp):
AGGTAAAAGATTTGAGTGACAAAAATGAAACGTATATGTAATATTGCTGAATCAATT
Found at i:28752 original size:22 final size:21
Alignment explanation
Indices: 28727--28906 Score: 110
Period size: 22 Copynumber: 8.2 Consensus size: 21
28717 CCCAAATTAT
28727 ATAGAAAGATTATCAAAATTTC
1 ATAGAAAG-TTATCAAAATTTC
*** *
28749 ATAGTGTGGTTACCAAAATTTC
1 ATAG-AAAGTTATCAAAATTTC
* * *
28771 ATATAGAGGTTATCAAAACTTC
1 ATAGA-AAGTTATCAAAATTTC
**
28793 ATAGTGTAGTTATCAAAATTTC
1 ATAG-AAAGTTATCAAAATTTC
* * *
28815 ATACATAGGTTACCAAAATTTC
1 ATAGA-AAGTTATCAAAATTTC
* *
28837 ATAAAAAGTTTACCAAAATTTC
1 ATAGAAAG-TTATCAAAATTTC
* * *
28859 TTAGGGATGTTAAT-AAAATTTC
1 ATA-GAAAGTT-ATCAAAATTTC
*
28881 ATATGAAAGTTAACAAAATTTC
1 ATA-GAAAGTTATCAAAATTTC
28903 ATAG
1 ATAG
28907 GGAGGGAGTT
Statistics
Matches: 119, Mismatches: 31, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
21 4 0.03
22 111 0.93
23 4 0.03
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (21 bp):
ATAGAAAGTTATCAAAATTTC
Found at i:28768 original size:44 final size:43
Alignment explanation
Indices: 28720--28839 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 43
28710 CAATAAACCC
* *
28720 AAATTATATAGAAAGATTATCAAAATTTCATAGTGTGGTTACCA
1 AAATTATATAG-AAGGTTATCAAAATTTCATAGTGTAGTTACCA
* *
28764 AAATTTCATATAG-AGGTTATCAAAACTTCATAGTGTAGTTATCA
1 AAA-TT-ATATAGAAGGTTATCAAAATTTCATAGTGTAGTTACCA
* *
28808 AAATT-TCATACATAGGTTACCAAAATTTCATA
1 AAATTAT-ATAGA-AGGTTATCAAAATTTCATA
28840 AAAAGTTTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.02
42 3 0.05
43 2 0.03
44 50 0.78
45 2 0.03
46 6 0.09
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (43 bp):
AAATTATATAGAAGGTTATCAAAATTTCATAGTGTAGTTACCA
Found at i:28854 original size:44 final size:44
Alignment explanation
Indices: 28757--28905 Score: 122
Period size: 44 Copynumber: 3.4 Consensus size: 44
28747 TCATAGTGTG
* * ***
28757 GTTACCAAAATTTCATATAGAGGTTATCAAAACTTCATAGTGTA
1 GTTACCAAAATTTCATACAGAGGTTACCAAAACTTCATAGAAAA
* * *
28801 GTTATCAAAATTTCATACATAGGTTACCAAAATTTCATA-AAAA
1 GTTACCAAAATTTCATACAGAGGTTACCAAAACTTCATAGAAAA
* ** * ** *
28844 GTTTACCAAAATTTCTTAGGGATGTTAATAAAATTTCATATG-AAA
1 G-TTACCAAAATTTCATACAGAGGTTACCAAAACTTCATA-GAAAA
*
28889 GTTAACAAAATTTCATA
1 GTTACCAAAATTTCATA
28906 GGGAGGGAGT
Statistics
Matches: 84, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
43 2 0.02
44 78 0.93
45 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (44 bp):
GTTACCAAAATTTCATACAGAGGTTACCAAAACTTCATAGAAAA
Found at i:28854 original size:66 final size:65
Alignment explanation
Indices: 28736--28905 Score: 166
Period size: 66 Copynumber: 2.6 Consensus size: 65
28726 TATAGAAAGA
* * * * * *
28736 TTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATAGAGGTTATCAAAACTTCATAGTG-T
1 TTATCAAAATTTCATAAT-AGGTTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGGAT
28800 AG
65 -G
* * *
28802 TTATCAAAATTTCATACATAGGTTACCAAAATTTCATAAAAAGTTTACCAAAATTTCTTAGGGAT
1 TTATCAAAATTTCATA-ATAGGTTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGGAT
28867 G
65 G
* *
28868 TTAAT-AAAATTTCAT-ATGAAAGTTAACAAAATTTCATA
1 TT-ATCAAAATTTCATAAT--AGGTTACCAAAATTTCATA
28906 GGGAGGGAGT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
64 2 0.02
66 82 0.93
67 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (65 bp):
TTATCAAAATTTCATAATAGGTTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGGATG
Found at i:28987 original size:22 final size:22
Alignment explanation
Indices: 28931--29278 Score: 133
Period size: 22 Copynumber: 15.6 Consensus size: 22
28921 AAATTTGTGC
**
28931 TTATCAAAATTTCCTAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
*
28953 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
* *
28975 TTATGAAAATTTTAT-GGAGAGC
1 TTATCAAAATTTTATAGG-GAGG
* ** *
28997 TTATTGAAAA-TAAATAGAGAGG
1 TTA-TCAAAATTTTATAGGGAGG
* * *
29019 ATATCACAGTTTCATTCTCATAGGGAGG
1 TTATCA-A----AATT-TTATAGGGAGG
* *
29047 TTATCAAAATTTCAT-GGTGTGG
1 TTATCAAAATTTTATAGG-GAGG
29069 TTATCAAAATTTTAT---GAGG
1 TTATCAAAATTTTATAGGGAGG
* *
29088 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAATTTT-ATAGGGAGG
* * * *
29111 TTA-C-CAATTTTATTTAGTGTGA
1 TTATCAAAATTTTA--TAGGGAGG
* * *
29133 TTATTAAAATTTTATAGGCAGA
1 TTATCAAAATTTTATAGGGAGG
* * ***
29155 TTATCAAAATTTCACACTAAGG
1 TTATCAAAATTTTATAGGGAGG
* * *
29177 TTATCGAAATTTCATA-GTATGG
1 TTATCAAAATTTTATAGGGA-GG
* * * *
29199 TTACCAAAAGTTTTCACAGTGTGG
1 TTATCAAAA-TTTT-ATAGGGAGG
29223 TTATC-AAATTTTCATAGGGAGG
1 TTATCAAAATTTT-ATAGGGAGG
* **
29245 TTATCAAAATTTCATAATGAGG
1 TTATCAAAATTTTATAGGGAGG
29267 TTATC-AAATTTT
1 TTATCAAAATTTT
29279 CAAAATGTGG
Statistics
Matches: 246, Mismatches: 56, Indels: 49
0.70 0.16 0.14
Matches are distributed among these distances:
19 16 0.07
20 3 0.01
21 19 0.08
22 149 0.61
23 28 0.11
24 15 0.06
26 1 0.00
27 2 0.01
28 13 0.05
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:29091 original size:19 final size:20
Alignment explanation
Indices: 29043--29100 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
29033 TTCTCATAGG
*
29043 GAGGTTATCAAAATTTCATGGT
1 GAGGTTATCAAAATTT--TGAT
*
29065 GTGGTTATCAAAATTTT-AT
1 GAGGTTATCAAAATTTTGAT
29084 GAGGTTATCAAAATTTT
1 GAGGTTATCAAAATTTT
29101 CATAGTGCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.52
20 1 0.03
22 15 0.45
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (20 bp):
GAGGTTATCAAAATTTTGAT
Found at i:29247 original size:46 final size:44
Alignment explanation
Indices: 29159--29280 Score: 131
Period size: 46 Copynumber: 2.7 Consensus size: 44
29149 GGCAGATTAT
* * *
29159 CAAAATTTCACACTAAGGTTATCGAAA-TTTCATAGTATGGTTAC
1 CAAAATTTCACAATGAGGTTATC-AAATTTTCATAGGATGGTTAC
* * *
29203 CAAAAGTTTTCACAGTGTGGTTATCAAATTTTCATAGGGA-GGTTAT
1 CAAAA--TTTCACAATGAGGTTATCAAATTTTCATA-GGATGGTTAC
*
29249 CAAAATTTCATAATGAGGTTATCAAATTTTCA
1 CAAAATTTCACAATGAGGTTATCAAATTTTCA
29281 AAATGTGGCT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
44 29 0.44
45 3 0.05
46 32 0.48
47 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (44 bp):
CAAAATTTCACAATGAGGTTATCAAATTTTCATAGGATGGTTAC
Found at i:29269 original size:68 final size:67
Alignment explanation
Indices: 29174--29301 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 67
29164 TTTCACACTA
* * * * *
29174 AGGTTATCGAAATTTCATAGTATGGTTACCAAAAGTTTTCACAGTGTGGTTATCAA-ATTTTCAT
1 AGGTTATCAAAATTTCATAATATGGTTACC-AAA-TTTTCAAAATGTGGCTATCAATATTTTCAT
29238 AGGG
64 AGGG
*
29242 AGGTTATCAAAATTTCATAATGA-GGTTATCAAATTTTCAAAATGTGGCTATCAATATTTT
1 AGGTTATCAAAATTTCATAAT-ATGGTTACCAAATTTTCAAAATGTGGCTATCAATATTTT
29302 TACATTGAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
66 18 0.35
67 8 0.15
68 25 0.48
69 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (67 bp):
AGGTTATCAAAATTTCATAATATGGTTACCAAATTTTCAAAATGTGGCTATCAATATTTTCATAG
GG
Found at i:29279 original size:22 final size:22
Alignment explanation
Indices: 29036--29280 Score: 157
Period size: 22 Copynumber: 11.1 Consensus size: 22
29026 AGTTTCATTC
* *
29036 TCATAGGGAGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAATTT
* * *
29058 TCATGGTGTGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAATTT
29080 T--TA-TGAGGTTATCAAAATTT
1 TCATAGTGAGGTTATC-AAATTT
* *
29100 TCATAGTGCGGTTA-CCAATTT
1 TCATAGTGAGGTTATCAAATTT
* * *
29121 T-ATTTAGTGTGATTATTAAAATTT
1 TCA--TAGTGAGGTTA-TCAAATTT
* *
29145 T-ATAG-GCAGATTATCAAAATT
1 TCATAGTG-AGGTTATCAAATTT
* * *
29166 TCACACTAAGGTTATCGAAA-TT
1 TCATAGTGAGGTTATC-AAATTT
*
29188 TCATAGT-ATGGTTACCAAAAGTTT
1 TCATAGTGA-GGTTATC-AAA-TTT
* *
29212 TCACAGTGTGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAATTT
* *
29234 TCATAGGGAGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAATTT
*
29256 TCATAATGAGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAATTT
29278 TCA
1 TCA
29281 AAATGTGGCT
Statistics
Matches: 174, Mismatches: 33, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
19 9 0.05
20 8 0.05
21 15 0.09
22 108 0.62
23 13 0.07
24 21 0.12
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (22 bp):
TCATAGTGAGGTTATCAAATTT
Found at i:29280 original size:90 final size:88
Alignment explanation
Indices: 29045--29280 Score: 236
Period size: 90 Copynumber: 2.7 Consensus size: 88
29035 CTCATAGGGA
* *
29045 GGTTATCAAAATTTCAT-GGTGTGGTTATCAAAATTT--T-ATGAGGTTATCAAAATTTTCATAG
1 GGTTATCAAATTTTCATAGG-GAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTTCATAG
* *
29106 TGCGGTTACCAATTTTATTTAGTGT
65 TACGGTTACCAATTTTA-TCAGTGT
* * * * * * * *
29131 GATTATTAAAATTTT-ATAGGCAGATTATCAAAATTTCACACTAAGGTTATCGAAA-TTTCATAG
1 GGTTA-TCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTTCATAG
*
29194 TATGGTTACCAAAAGTTTTCA-CAGTGT
65 TACGGTTACC--AA-TTTT-ATCAGTGT
29221 GGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATC-AAATTTTCA
1 GGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTTCA
29281 AAATGTGGCT
Statistics
Matches: 119, Mismatches: 20, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
86 19 0.16
87 9 0.08
88 16 0.13
89 23 0.19
90 47 0.39
91 4 0.03
92 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (88 bp):
GGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTTCATAGT
ACGGTTACCAATTTTATCAGTGT
Found at i:30321 original size:21 final size:21
Alignment explanation
Indices: 30292--30355 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
30282 AGGTGCATAA
*
30292 CCTATAATCGATTGGAATATT
1 CCTAGAATCGATTGGAATATT
* * *
30313 CCTAGAATCGATTGTAGTAAT
1 CCTAGAATCGATTGGAATATT
*
30334 CATAGAATCGATTGGAATATT
1 CCTAGAATCGATTGGAATATT
30355 C
1 C
30356 TTGCTCCAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (21 bp):
CCTAGAATCGATTGGAATATT
Found at i:31846 original size:30 final size:30
Alignment explanation
Indices: 31810--31872 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
31800 TGTCTTCAAG
31810 TCCATGATAAGTCCTT-GGCGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
31840 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
31870 TCC
1 TCC
31873 CCCTTGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:32815 original size:980 final size:986
Alignment explanation
Indices: 30905--32844 Score: 3007
Period size: 980 Copynumber: 2.0 Consensus size: 986
30895 AGCAATCGGT
*
30905 TCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGGATCACCAAACTTCTAGACTTGTATGTC
1 TCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAATCACCAAACTTCTAGACTTGTATGTC
*
30970 GACAATCTTCACTAAGTAAACCCTCATTCGTTCGTCGGCCTTAGACCCTCAATTAGACCTGCAAT
66 GACAATCTTCACTAAGTAAACCCTCATTCGTACGTCGGCCTTAGACCCTCAATTAGACCTGCAAT
* *
31035 TGAACACCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTTCTAGGAG
131 TGAACACCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGAC
31100 TCTACAAGATTGAAGAACCCTAAAGTATGCTCAAATTAGAACAATGAAGCCAAGATAATCAATTT
196 TCTACAAGATTGAAGAACCCTAAAGTATGCTCAAATTAGAACAATGAAGCCAAGATAATCAATTT
* *
31165 GGATGTATAAACCTCAATTTTATTAATCAACTCAACTTATGTTTATAAGAGATATTGCTGGCCTT
261 GGATGTATAAACCTCAATTTTATTAATCAACTCAACTTATGTTTACAAGAGATATTGCTGCCCTT
* * *
31230 ATATAGGCACAAAGTCGACACAATACCCCCTAAACCGACCTAGGCCTTCAATACAAAGGTGAAGG
326 ATATAGGCACAAAGTCGACACAATACCCCCTAAACC-ACCTAGACCTTCAATACAAAGATGAAAG
** * * *
31295 GCGGTTTAGCATAGAACAATCTAGAGACTATCCTAAAATACAACCAATAGGAAAAATAGCTAAGG
390 GC-GTACAGCAAAGAACAATCTAGAAACTATCCAAAAATACAACCAATAGGAAAAATAGCTAAGG
* * * ** * *
31360 ATTGGACTTAATTAAACAAGGCCCAACCCTAAACAAGGTCCAAACTATATAATCAACTAATTTAA
454 ATTAGACTTAATCAAACAAGGCCAAACCCTAAACAACATCCAAACTATAAAATCAACTAATCTAA
* *
31425 GATAGAATTAAGCCCAAACAAAGCAAACTAAAGCTAATGGGCTCATGCCATGATGTCAATCCGGC
519 GATAGAATTAAGCCCAAACAAAGCAAACTAAAGCTAATGGACTCATGCCACGATGTCAATCCGGC
* *
31490 CATCTAGAATAAATAGCAAGCAAAGTGATGAACTTGTAATTGATTGGTGTTTTCTTGCTCAAATC
584 AATCTAGAATAAATAGCAAGCAAAGTGATGAACATGTAATTGATTGGTGTTTTCTTGCTCAAATC
* *
31555 ATCATCAAAGCTCTTCAATTGAACTTGAATGGTCTTCATATCATAGAGATGAGTTCGAACAAGGC
649 ATCATCAAAGCTCTTCAATTGAACTTGAATAGTCTTCATATCATAGAGATGAGTTCGAACAACGC
* *
31620 CCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCATGTCATCGGACCTAATGGCATCATCAAT
714 CCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCATCTCATCGGACCTAATGGCATCATCAAC
* * *
31685 GGATCAAATGACATCTTCTTGGTGCTTGGTACATGCTCAACGATATCTCCATGATCTTCATGCAT
779 GGATCAAATGACATCTTCTTGGTGCTTGGAACATGATCAACAATATCTCCATGATCTTCATGCAT
*
31750 CTTCATGCTTCCTTGCAGCCCATGCACATCCTTTCCATGCTCTCCGTGCTTGTCTTCAAGTCCAT
844 CTCCATGCTTCCTTGCAGCCCATGCACATCCTTTCCATGCTCTCCGTGCTTGTCTTCAAGTCCAT
*
31815 GATAAGTCCTTGGCGCATCATTCCCTCCATGATAAGCCTTGGGCGCATCATTCCCTCCCCCTTGA
909 AATAAGTCCTTGGCGCATCATTCCCTCCATGATAAGCCTTGGGCGCATCATTCCCTCCCCCTTGA
31880 AGACGATTTGTCC
974 AGACGATTTGTCC
*
31893 TCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAATCACCAAACTTCTAGATTTGTATGTC
1 TCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAATCACCAAACTTCTAGACTTGTATGTC
*
31958 GACAATCTTCACTAAGTAAACCCTCCTTCGTACGTCGGCCTTAGACCCTCAATTAGACCTGCAAT
66 GACAATCTTCACTAAGTAAACCCTCATTCGTACGTCGGCCTTAGACCCTCAATTAGACCTGCAAT
* *
32023 TGAACACCTATGATCACAAGATTCACAAACAATTAAGCTATCACAACCTAATTGTTTGCTAGGAC
131 TGAACACCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGAC
*
32088 TCTACAAGATTGAAGAACCCTAAAGTATGCTCAAATTAGAACAATGAAGTCAAGATAATCAATTT
196 TCTACAAGATTGAAGAACCCTAAAGTATGCTCAAATTAGAACAATGAAGCCAAGATAATCAATTT
* *
32153 GGGTGTATAAACCTCAATTTTATTAATCAACTCAACTTATGTTTACAAGAGATATTGGTGCCCTT
261 GGATGTATAAACCTCAATTTTATTAATCAACTCAACTTATGTTTACAAGAGATATTGCTGCCCTT
* * * ** * * *
32218 ATATAGGCACAAAGAT-TACGC-ATAACCTACTCTAAA-C-CCTA-ATTTTC-GTCCAAATAT-A
326 ATATAGGCACAAAG-TCGACACAAT-ACC--CCCTAAACCACCTAGACCTTCAATACAAAGATGA
* ** **
32276 AAGGC-TACA-CAAAAGATCCTTCTAGAAACTATCCAAAAATACAATGAATA-GAAAAATAGCTA
387 AAGGCGTACAGC-AAAGAACAATCTAGAAACTATCCAAAAATACAACCAATAGGAAAAATAGCTA
*
32338 AGGATTAGAC-TAAGTCAAACAAGGCCAAACCC-AAATAACATCCAAACT-TAAAAAT-AAGCTA
451 AGGATTAGACTTAA-TCAAACAAGGCCAAACCCTAAACAACATCCAAACTAT-AAAATCAA-CTA
*
32399 ATCTAAGATAGAATTAAGCCCAAACAAAGCAAACTAATGCTAATGGACTCATGCCACGATGTCAA
513 ATCTAAGATAGAATTAAGCCCAAACAAAGCAAACTAAAGCTAATGGACTCATGCCACGATGTCAA
* * *
32464 TCCGGCAATTTAGAATCAATAGCAAGTAAAGTGATGAACATGTAATTTG-TTGGTGTTTTCTTGC
578 TCCGGCAATCTAGAATAAATAGCAAGCAAAGTGATGAACATGTAA-TTGATTGGTGTTTTCTTGC
*
32528 TCAAATCATCATCAAAGCTCTTCAATTGAACTTGAATAGTCTTCATGTCATCAG-GATGAGTTCG
642 TCAAATCATCATCAAAGCTCTTCAATTGAACTTGAATAGTCTTCATATCAT-AGAGATGAGTTCG
*
32592 AACAACGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTCTCATCGGACCTAATGGCA
706 AACAACGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCATCTCATCGGACCTAATGGCA
* * * * *
32657 TCTTTAACGGATCGAATGGCATCCTT-TTGGTGCTTGGAACATGATCATCAATATCTCCATGATC
771 TCATCAACGGATCAAATGACAT-CTTCTTGGTGCTTGGAACATGATCAACAATATCTCCATGATC
*
32721 TTCATGCATCTCCATGCTTCCTTGCAGCCCTTGCACATCCTTTCCATGCTCT-CGATGCTTGTCT
835 TTCATGCATCTCCATGCTTCCTTGCAGCCCATGCACATCCTTTCCATGCTCTCCG-TGCTTGTCT
* *
32785 TCAAGTTCATAATAAGTCCTTGGTGCATCATTCCCTCCATGATAAGCCTTGGGCGCATCA
899 TCAAGTCCATAATAAGTCCTTGGCGCATCATTCCCTCCATGATAAGCCTTGGGCGCATCA
32845 GTAACCAACG
Statistics
Matches: 871, Mismatches: 69, Indels: 32
0.90 0.07 0.03
Matches are distributed among these distances:
979 5 0.01
980 427 0.49
981 46 0.05
982 33 0.04
984 5 0.01
985 6 0.01
986 3 0.00
987 6 0.01
988 332 0.38
989 2 0.00
990 6 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (986 bp):
TCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAATCACCAAACTTCTAGACTTGTATGTC
GACAATCTTCACTAAGTAAACCCTCATTCGTACGTCGGCCTTAGACCCTCAATTAGACCTGCAAT
TGAACACCTAAGATCACAAGATTCACAAACAATTAAGCAATCACAACCTAATTGTTTGCTAGGAC
TCTACAAGATTGAAGAACCCTAAAGTATGCTCAAATTAGAACAATGAAGCCAAGATAATCAATTT
GGATGTATAAACCTCAATTTTATTAATCAACTCAACTTATGTTTACAAGAGATATTGCTGCCCTT
ATATAGGCACAAAGTCGACACAATACCCCCTAAACCACCTAGACCTTCAATACAAAGATGAAAGG
CGTACAGCAAAGAACAATCTAGAAACTATCCAAAAATACAACCAATAGGAAAAATAGCTAAGGAT
TAGACTTAATCAAACAAGGCCAAACCCTAAACAACATCCAAACTATAAAATCAACTAATCTAAGA
TAGAATTAAGCCCAAACAAAGCAAACTAAAGCTAATGGACTCATGCCACGATGTCAATCCGGCAA
TCTAGAATAAATAGCAAGCAAAGTGATGAACATGTAATTGATTGGTGTTTTCTTGCTCAAATCAT
CATCAAAGCTCTTCAATTGAACTTGAATAGTCTTCATATCATAGAGATGAGTTCGAACAACGCCC
ATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCATCTCATCGGACCTAATGGCATCATCAACGG
ATCAAATGACATCTTCTTGGTGCTTGGAACATGATCAACAATATCTCCATGATCTTCATGCATCT
CCATGCTTCCTTGCAGCCCATGCACATCCTTTCCATGCTCTCCGTGCTTGTCTTCAAGTCCATAA
TAAGTCCTTGGCGCATCATTCCCTCCATGATAAGCCTTGGGCGCATCATTCCCTCCCCCTTGAAG
ACGATTTGTCC
Found at i:38173 original size:2 final size:2
Alignment explanation
Indices: 38166--38202 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38156 ATCAGTAGTG
*
38166 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38203 TATTTTTGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38357 original size:11 final size:11
Alignment explanation
Indices: 38341--38383 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
38331 TATACTATAT
38341 CTAATTAATAG
1 CTAATTAATAG
*
38352 CTAATTAATAT
1 CTAATTAATAG
38363 CTAATTAATAG
1 CTAATTAATAG
*
38374 TTAATTAATA
1 CTAATTAATA
38384 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:38362 original size:22 final size:22
Alignment explanation
Indices: 38337--38383 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
38327 CCATTATACT
38337 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
38359 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
38381 ATA
1 ATA
38384 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:40070 original size:42 final size:42
Alignment explanation
Indices: 40011--40099 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
40001 AAATCATGGA
40011 TTGTTCCTTTGCCTTATTATATCCACGTACTCCCCAACTTCC
1 TTGTTCCTTTGCCTTATTATATCCACGTACTCCCCAACTTCC
* * *
40053 TTGTTCCTTTGCCTTATTATGTCCACGTAGTCCTCAACTTCC
1 TTGTTCCTTTGCCTTATTATATCCACGTACTCCCCAACTTCC
40095 TTGTT
1 TTGTT
40100 ACCTAGTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.15, C:0.31, G:0.10, T:0.44
Consensus pattern (42 bp):
TTGTTCCTTTGCCTTATTATATCCACGTACTCCCCAACTTCC
Done.