Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007498.1 Corchorus capsularis cultivar CVL-1 contig07519, 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: 23695
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:338 original size:82 final size:82
Alignment explanation
Indices: 191--354 Score: 242
Period size: 82 Copynumber: 2.0 Consensus size: 82
181 GGCGCACTTC
* * *
191 TCCCGCCATTAGTATGTCTCAGATTTGGTTTCTAGTAGAGACAGTTGTTGAGACGGGTAAGTAGA
1 TCCCGCCAATAGTACGTCTCAGATTTGGTTTCTAGTAGAGACAGTTGTTGAGACGAGTAAGTAGA
*
256 GACATTTTTTGAAACGT
66 GACATTCTTTGAAACGT
* *
273 TCCCGCCAATAGTACGTCTCAGATTAT-GTTTGTAAGTGGAGACAGTTGTTGAGACGAGTAA-TA
1 TCCCGCCAATAGTACGTCTCAGATT-TGGTTTCT-AGTAGAGACAGTTGTTGAGACGAGTAAGTA
336 GAGACATTCTTTGAAACGT
64 GAGACATTCTTTGAAACGT
355 ACTATTTTGA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
82 48 0.65
83 26 0.35
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (82 bp):
TCCCGCCAATAGTACGTCTCAGATTTGGTTTCTAGTAGAGACAGTTGTTGAGACGAGTAAGTAGA
GACATTCTTTGAAACGT
Found at i:1749 original size:22 final size:21
Alignment explanation
Indices: 1704--1749 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1694 GGAAATTTAA
* * *
1704 AAGTTACATTAATCTACTCCT
1 AAGTTACATCAAACTAATCCT
1725 AAGTTACATCAAGACTAATCCT
1 AAGTTACATCAA-ACTAATCCT
1747 AAG
1 AAG
1750 AGATAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (21 bp):
AAGTTACATCAAACTAATCCT
Found at i:5253 original size:22 final size:22
Alignment explanation
Indices: 5223--5265 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5213 CATGAGAAAC
* *
5223 CAAGCCAAGAAAATGGGTGTCA
1 CAAGACAAGAAAAAGGGTGTCA
5245 CAAGACAAGAAAAAGGGTGTC
1 CAAGACAAGAAAAAGGGTGTC
5266 TGAGTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (22 bp):
CAAGACAAGAAAAAGGGTGTCA
Found at i:5542 original size:13 final size:14
Alignment explanation
Indices: 5482--5542 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 14
5472 AATATATATT
5482 AAATTAATAATGAGA
1 AAATTAATAAT-AGA
*
5497 ATTATTAAT-ATAGA
1 A-AATTAATAATAGA
*
5511 AAATTAATTTATAGA
1 AAATTAA-TAATAGA
5526 AAATTAATAAT-GA
1 AAATTAATAATAGA
5539 AAAT
1 AAAT
5543 AATGTTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.28
14 8 0.20
15 15 0.38
16 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.34
Consensus pattern (14 bp):
AAATTAATAATAGA
Found at i:5711 original size:67 final size:67
Alignment explanation
Indices: 5603--5734 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 67
5593 AATCTCAAAT
5603 CTAACGGATGTCTCTGATTCCGTGTCTGACAGTCAGAGACATTTTTATTCTGTCTCTGATCCTTA
1 CTAACGGATGTCTCTGATTCCGTGTCTGACAGTCAGAGACATTTTTATTCTGTCTCTGATCCTTA
5668 AA
66 AA
*
5670 CTAACGGATGTCTCTGATTCCGTGTCTGACAGTCAGAGACATTTTTGTTCTGTCTCTGATCCTTA
1 CTAACGGATGTCTCTGATTCCGTGTCTGACAGTCAGAGACATTTTTATTCTGTCTCTGATCCTTA
5735 GCAACGCCAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (67 bp):
CTAACGGATGTCTCTGATTCCGTGTCTGACAGTCAGAGACATTTTTATTCTGTCTCTGATCCTTA
AA
Found at i:7734 original size:12 final size:12
Alignment explanation
Indices: 7714--7749 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
7704 GACTTCACAA
7714 CCCCATCCCCGT
1 CCCCATCCCCGT
*
7726 CCCCGTCCCCGT
1 CCCCATCCCCGT
7738 CCCCCATCCCCG
1 -CCCCATCCCCG
7750 ACGGGGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.06, C:0.69, G:0.11, T:0.14
Consensus pattern (12 bp):
CCCCATCCCCGT
Found at i:7997 original size:20 final size:18
Alignment explanation
Indices: 7960--8006 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
7950 TATTTAGTAA
7960 ATTAGTAAATATTTATTT
1 ATTAGTAAATATTTATTT
*
7978 ATTAGTATATATTATTATTT
1 ATTAGTAAATA-T-TTATTT
7998 ATTAGTAAA
1 ATTAGTAAA
8007 ACATATATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTAGTAAATATTTATTT
Found at i:8083 original size:2 final size:2
Alignment explanation
Indices: 8078--8111 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
8068 TAAAAAAAAC
8078 AT AT AT AT AT AT AT -T A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8112 TTCGGGGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16208 original size:79 final size:79
Alignment explanation
Indices: 16031--16261 Score: 347
Period size: 79 Copynumber: 2.9 Consensus size: 79
16021 CATCATGCCT
* * *
16031 TCCTCAAGTTGGAGCGTGAATATTCGCAACGCCCAACTTGAATACTAAAGATTCAAATTGAT-TG
1 TCCTCAAGTTGGAGCGTGAAGATTCGCAACGCCCAACTTGAACACTAATGATTCAAATTGATCTG
16095 ATTTCATCACCCCC
66 ATTTCATCACCCCC
* *
16109 TCCTCAAGTTGGAGCGTGAAGATTTGCAACGTCCAACTTGAACACTAATGATTCAAATTGATCTG
1 TCCTCAAGTTGGAGCGTGAAGATTCGCAACGCCCAACTTGAACACTAATGATTCAAATTGATCTG
*
16174 ATTTCATCACTCCC
66 ATTTCATCACCCCC
* * * * * *
16188 TCCTTAAGTTGGCGCGTGAAGACTCGAAAGGCCCAACTTGAACACTAATGATTCAAATCGATCTG
1 TCCTCAAGTTGGAGCGTGAAGATTCGCAACGCCCAACTTGAACACTAATGATTCAAATTGATCTG
16253 ATTTCATCA
66 ATTTCATCA
16262 TAATTTACCT
Statistics
Matches: 138, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 57 0.41
79 81 0.59
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (79 bp):
TCCTCAAGTTGGAGCGTGAAGATTCGCAACGCCCAACTTGAACACTAATGATTCAAATTGATCTG
ATTTCATCACCCCC
Found at i:16407 original size:83 final size:83
Alignment explanation
Indices: 16265--16473 Score: 366
Period size: 83 Copynumber: 2.5 Consensus size: 83
16255 TTCATCATAA
**
16265 TTTACCTGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCGGCAACCAAAGCTGGTCTGCT
1 TTTACCTGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCAACAACCAAAGCTGGTCTGCT
16330 GACTCATTGTCTAACCCT
66 GACTCATTGTCTAACCCT
16348 TTTACCTGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCAACAACCAACA-CTGGTCTGC
1 TTTACCTGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCAACAACCAA-AGCTGGTCTGC
16412 TGACTCATTGTCTAACCCT
65 TGACTCATTGTCTAACCCT
* *
16431 TTTACCTGCGGTACTGTCATGACCTCTTCTCACTCATTATCCG
1 TTTACCTGCGGTAATGTAATGACCTCTTCTCACTCATTATCCG
16474 TGGCAACATA
Statistics
Matches: 121, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
83 120 0.99
84 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.33
Consensus pattern (83 bp):
TTTACCTGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCAACAACCAAAGCTGGTCTGCT
GACTCATTGTCTAACCCT
Found at i:16969 original size:42 final size:42
Alignment explanation
Indices: 16796--17462 Score: 771
Period size: 42 Copynumber: 15.9 Consensus size: 42
16786 GCTTTTGACA
* * * *
16796 AACCTCCCTTTTTCGAAAGTTCTACGCCACCCTCCCCGTAGGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCA----CCCCGCAGGAACT
* *
16842 AACCTCCCCTTTTCGAAGGTTTTACGCCAACCCCGCAAGAATT
1 AACCTCCCCTTTTCGAAGGTTTTACGCC-ACCCCGCAGGAACT
* * * * * *
16885 AACCTCCCATTTTCGAAGATTTTTACTCTACTCCGCAAGAACT
1 AACCTCCCCTTTTCGAAG-GTTTTACGCCACCCCGCAGGAACT
* * * *
16928 AACCTCCTCTTTTCGAAGGTTTTACGCCATCCTGCATGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
16970 AACCTCCCCTGTTT-GAAGGTTTTACGCCACCCCGCAGGAACT
1 AACCTCCCCT-TTTCGAAGGTTTTACGCCACCCCGCAGGAACT
* * **
17012 AACCTCCCCTTCTCGAAGGTTTTACACCACCTTGCAAGG-ACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGC-AGGAACT
* * * *
17054 AACCTCCCCTTTTTGAAGGGTTTAAGCCA----TC--GAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
17090 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
* *
17132 AACCTCCCCTTTTTGAAGGTTTTAAGCCACCCCGCAGGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
*
17174 AACCTCCCCTTTTCGAAGGTTTTACACCACCCCGCAGGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
** * * *
17216 AACCTCCTTTTTTAGAAGGTTTTACGCCAACCCGTAGGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
* **
17258 AACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTACAGGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
* *
17300 AACCTCCACTTTTCGAAGGTTTTACGCCA-CTCG--GGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
* *
17339 AACCTCCCCTTTTCGAAGGTTTTACACCACCCTGCAGGAACT
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
* * *
17381 ATCCTCCCATTTTCGAAGGTTTTTACGTCACCCCGCAGGAACT
1 AACCTCCCCTTTTCGAAGG-TTTTACGCCACCCCGCAGGAACT
* * *
17424 AACCTCCCATTTTCGAAGGTTTTACGCCAACCTGCAGGA
1 AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGA
17463 TATCCAAGGA
Statistics
Matches: 529, Mismatches: 76, Indels: 36
0.83 0.12 0.06
Matches are distributed among these distances:
35 1 0.00
36 29 0.05
38 1 0.00
39 33 0.06
40 3 0.01
41 3 0.01
42 327 0.62
43 99 0.19
44 7 0.01
46 25 0.05
47 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (42 bp):
AACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACT
Found at i:17116 original size:162 final size:161
Alignment explanation
Indices: 16829--17462 Score: 695
Period size: 162 Copynumber: 3.8 Consensus size: 161
16819 ACGCCACCCT
* * * * *
16829 CCCCGTAGGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCAACCCCGCAAGAATTAACCTCCCA
1 CCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACACC-ACCCTGCAGGAACTAACCTCCCA
* * * * *
16894 TTTTCGAAGATTTTTA-CTCTACTCCGCAAGAACTAACCTCCTCTTTTCGAAGGTTTTACGCCAT
65 TTTTTGAAGGTTTTAAGC-C-A-T---C--GAACTAACCTCCCCTTTTCGAAGGTTTTACGCCAC
*
16958 CCTGCATGAACTAACCTCCCCTGTTTGAAGGTTTTACGCCA
122 CCTGCAGGAACTAACCTCCCCT-TTTGAAGGTTTTACGCCA
* * *
16999 CCCCGCAGGAACTAACCTCCCCTTCTCGAAGGTTTTACACCACCTTGCAAGG-ACTAACCTCCCC
1 CCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCTGC-AGGAACTAACCTCCCA
* *
17063 TTTTTGAAGGGTTTAAGCCATCGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGG
65 TTTTTGAAGGTTTTAAGCCATCGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCTGCAGG
*
17128 AACTAACCTCCCCTTTTTGAAGGTTTTAAGCCA
130 AACTAACCTCCCC-TTTTGAAGGTTTTACGCCA
* *
17161 CCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCCGCAGGAACTAACCT-CCTT
1 CCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCTGCAGGAACTAACCTCCCAT
* * *
17225 TTTTAGAAGGTTTTACGCCAACCCGTAGGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCC
66 TTTT-GAAGGTTTTAAGCC-A----T-CGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCC
* *
17290 TACAGGAACTAACCTCCACTTTTCGAAGGTTTTACGCCA
124 TGCAGGAACTAACCTCCCCTTTT-GAAGGTTTTACGCCA
* *
17329 -CTCG--GGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCTGCAGGAACTATCCTCCCAT
1 CCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCTGCAGGAACTAACCTCCCAT
* * ** * *
17391 TTTCGAAGGTTTTTACGTCACCCCGCAGGAACTAACCTCCCATTTTCGAAGGTTTTACGCCAACC
66 TTTTGAAGG-TTTTA----AGCCATC--GAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCC
17456 TGCAGGA
124 TGCAGGA
17463 TATCCAAGGA
Statistics
Matches: 401, Mismatches: 43, Indels: 44
0.82 0.09 0.09
Matches are distributed among these distances:
161 10 0.02
162 134 0.33
163 2 0.00
164 1 0.00
165 56 0.14
166 51 0.13
167 9 0.02
168 67 0.17
169 28 0.07
170 43 0.11
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (161 bp):
CCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCTGCAGGAACTAACCTCCCAT
TTTTGAAGGTTTTAAGCCATCGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCTGCAGGA
ACTAACCTCCCCTTTTGAAGGTTTTACGCCA
Found at i:17276 original size:246 final size:248
Alignment explanation
Indices: 16836--17462 Score: 861
Period size: 246 Copynumber: 2.5 Consensus size: 248
16826 CCTCCCCGTA
* *
16836 GGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCAACCCCGCAAGAATTAACCTCCCATTTTCGA
1 GGAACTAACCTCCCCTTTTCGAAGGTTTTACGCC-ACCCCGCAGGAACTAACCTCCCATTTTCGA
* * * * * * *
16901 AGATTTTTA-CTCTACTCCGCAAGAACTAACCTCCTCTTTTCGAAGGTTTTACGCCATCCTGCAT
65 AGGTTTTAAGC-C-ACCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCAACCTGCAG
*
16965 GAACTAACCTCCCCTGTTTGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCCTTCTCGAAG
128 GAACTAACCTCCCCTGTTTGAAGGTTTTACGCCAACCCGCAGGAACTAACCTCCCCTTCTCGAAG
* * * *
17030 GTTTTACA-CCACCTTGCAAGG-ACTAACCTCCCCTTTTTGAAGGGTTTAAGCCA-TC
193 GTTTTA-AGCCACCCTAC-AGGAACTAACCTCCACTTTTCGAAGGGTTTAAGCCACTC
* *
17085 -GAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCCTTTTTGAA
1 GGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCATTTTCGAA
* * *
17149 GGTTTTAAGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCCGCAGGAA
66 GGTTTTAAGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCAACCTGCAGGAA
* * * *
17214 CTAACCT-CCTTTTTTAGAAGGTTTTACGCCAACCCGTAGGAACTAACCTCCCCTTTTCGAAGGT
131 CTAACCTCCCCTGTTT-GAAGGTTTTACGCCAACCCGCAGGAACTAACCTCCCCTTCTCGAAGGT
* *
17278 TTTAAGCCACCCTACAGGAACTAACCTCCACTTTTCGAAGGTTTTACGCCACTC
195 TTTAAGCCACCCTACAGGAACTAACCTCCACTTTTCGAAGGGTTTAAGCCACTC
* * *
17332 GGGAACTAACCTCCCCTTTTCGAAGGTTTTACACCACCCTGCAGGAACTATCCTCCCATTTTCGA
1 -GGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCATTTTCGA
* * *
17397 AGGTTTTTACGTCACCCCGCAGGAACTAACCTCCCATTTTCGAAGGTTTTACGCCAACCTGCAGG
65 AGG-TTTTAAGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCAACCTGCAGG
17462 A
129 A
17463 TATCCAAGGA
Statistics
Matches: 335, Mismatches: 35, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
245 10 0.03
246 138 0.41
247 36 0.11
248 34 0.10
249 61 0.18
250 56 0.17
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (248 bp):
GGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCATTTTCGAA
GGTTTTAAGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAGGTTTTACGCCAACCTGCAGGAA
CTAACCTCCCCTGTTTGAAGGTTTTACGCCAACCCGCAGGAACTAACCTCCCCTTCTCGAAGGTT
TTAAGCCACCCTACAGGAACTAACCTCCACTTTTCGAAGGGTTTAAGCCACTC
Found at i:17588 original size:60 final size:60
Alignment explanation
Indices: 17524--17692 Score: 320
Period size: 60 Copynumber: 2.8 Consensus size: 60
17514 TCTCTGACAA
* *
17524 ATCTACCAGAGGATGCAAATTCGCTGCTCTCTCTGTTAGATCTGGCCATCTCTCTGTCTG
1 ATCTACTAGAGGATGCAGATTCGCTGCTCTCTCTGTTAGATCTGGCCATCTCTCTGTCTG
17584 ATCTACTAGAGGATGCAGATTCGCTGCTCTCTCTGTTAGATCTGGCCATCTCTCTGTCTG
1 ATCTACTAGAGGATGCAGATTCGCTGCTCTCTCTGTTAGATCTGGCCATCTCTCTGTCTG
17644 ATCTACTAGAGGATGCAGATTCGCTGCTCTCTCTGTTAGATCTGGCCAT
1 ATCTACTAGAGGATGCAGATTCGCTGCTCTCTCTGTTAGATCTGGCCAT
17693 GGCTTTACCA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 107 1.00
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (60 bp):
ATCTACTAGAGGATGCAGATTCGCTGCTCTCTCTGTTAGATCTGGCCATCTCTCTGTCTG
Found at i:19928 original size:46 final size:47
Alignment explanation
Indices: 19841--19941 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 47
19831 GAAATTGTAA
*
19841 AACAAGCTATAACGCAAAAAAGAAACAACTATAAAAAGCTATACTCT
1 AACAAGCTATAACGCAAAAAAGAAACAACTACAAAAAGCTATACTCT
* * * **
19888 CACAAGCTATAGCTC-AAAAAGAAACAACTACAAATGGCTATACTCT
1 AACAAGCTATAACGCAAAAAAGAAACAACTACAAAAAGCTATACTCT
19934 AACAAGCT
1 AACAAGCT
19942 TTAATGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 35 0.74
47 12 0.26
ACGTcount: A:0.50, C:0.22, G:0.10, T:0.18
Consensus pattern (47 bp):
AACAAGCTATAACGCAAAAAAGAAACAACTACAAAAAGCTATACTCT
Found at i:20986 original size:26 final size:27
Alignment explanation
Indices: 20954--21008 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
20944 AAAAGAAAGC
20954 AATTAAA-CTAAAAACTA-AGCAAAATA
1 AATTAAATCT-AAAACTATAGCAAAATA
*
20980 AATTAAATCTAAAACTATAGCAAATTA
1 AATTAAATCTAAAACTATAGCAAAATA
21007 AA
1 AA
21009 AAAAGCATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.62, C:0.11, G:0.04, T:0.24
Consensus pattern (27 bp):
AATTAAATCTAAAACTATAGCAAAATA
Done.