Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015668.1 Corchorus capsularis cultivar CVL-1 contig15689, 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: 85639
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4752 original size:1 final size:1
Alignment explanation
Indices: 4746--4799 Score: 72
Period size: 1 Copynumber: 54.0 Consensus size: 1
4736 AAGGGGATTG
*** *
4746 AAAAAAAAAAAAAAATTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4800 CAACAACAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.93, C:0.02, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:4804 original size:3 final size:3
Alignment explanation
Indices: 4793--4832 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
4783 AAAAAAAAAA
4793 AAC AA- AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
4833 TCAGAAGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:6187 original size:20 final size:20
Alignment explanation
Indices: 6162--6201 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6152 TTATTTTTCA
**
6162 AAAATAAATTTCAATAAAAT
1 AAAATAAATTAAAATAAAAT
*
6182 AAAATATATTAAAATAAAAT
1 AAAATAAATTAAAATAAAAT
6202 TATTTAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAATTAAAATAAAAT
Found at i:6194 original size:15 final size:14
Alignment explanation
Indices: 6162--6205 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
6152 TTATTTTTCA
* *
6162 AAAATAAATTTCAAT
1 AAAATAAAATT-ATT
6177 AAAATAAAATATATT
1 AAAATAAAAT-TATT
6192 AAAATAAAATTATT
1 AAAATAAAATTATT
6206 TAATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 21 0.81
16 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAAAATTATT
Found at i:6208 original size:15 final size:15
Alignment explanation
Indices: 6176--6205 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6166 TAAATTTCAA
6176 TAAAATAAAATATAT
1 TAAAATAAAATATAT
6191 TAAAATAAAAT-TAT
1 TAAAATAAAATATAT
6205 T
1 T
6206 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:10757 original size:3 final size:3
Alignment explanation
Indices: 10749--10794 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
10739 GATTAGAAGT
10749 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10795 ATAAATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10799 original size:4 final size:4
Alignment explanation
Indices: 10790--10821 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
10780 TAATAATAAT
10790 AATA AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA
10822 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:21691 original size:19 final size:18
Alignment explanation
Indices: 21646--21696 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
21636 AATGGGGTTG
*
21646 AAGGAAAGAGAAGAACAA
1 AAGGAAAGAAAAGAACAA
21664 AAGGAAAAGAAAAG-ACAGGA
1 AAGG-AAAGAAAAGAACA--A
*
21684 AAGGAAAGGAAAG
1 AAGGAAAGAAAAG
21697 CAAAAAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 7 0.25
19 16 0.57
20 5 0.18
ACGTcount: A:0.65, C:0.04, G:0.31, T:0.00
Consensus pattern (18 bp):
AAGGAAAGAAAAGAACAA
Found at i:34253 original size:162 final size:162
Alignment explanation
Indices: 34059--34502 Score: 561
Period size: 162 Copynumber: 2.7 Consensus size: 162
34049 TCGGAGCCCT
* * * *
34059 TTCACTGTCTTTGTCTTTTGCG-GCATCTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTT
1 TTCACTATCTTCGTCTGTTG-GTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTT
34123 TCAGTTTTTGTAGCTTCTTCACTATCTTTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGC
65 TCAGTTTTTGTAGCTTCTTCACTATCTTTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGC
* *
34188 TTGAGTGTCATTGGTTTCAGTTTTTGTAGCTTC
130 TTGAATGTCATTGGTTTCAGTCTTTGTAGCTTC
** * * * *** * ***
34221 TTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCA-GCTTTGCATCAGAACCCTTCAAT
1 TTCACTATCTTCGTCTGTTGGTGCAACTTCTAATGACTG-AGGCTTTGCTTGAGTGTCATTGGTT
* * * * * * *
34285 TCAGCTTTTGCAGCTTCATCACTATTTTTG-CTTGTTGGAGTAACTTCCAATGACTGAGGCTTTG
65 TCAGTTTTTGTAGCTTCTTCACTATCTTTGTC-TGTTGGTGCAACTTCTAATGACTGAGGCTTTG
34349 CTTGAATGTCATTGGTTTCAGTCTTTGTAGCTTC
129 CTTGAATGTCATTGGTTTCAGTCTTTGTAGCTTC
* *
34383 TTCACTATCTTTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCGTTGGTTT
1 TTCACTATCTTCGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTT
** * *
34448 CAGTTTTTGTAGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTG
66 CAGTTTTTGTAGCTTCTTCACTATCTTTGTCTGTTGGTGCAACTTCTAATGACTG
34503 TAGCTTCGCA
Statistics
Matches: 228, Mismatches: 49, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
161 3 0.01
162 224 0.98
163 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (162 bp):
TTCACTATCTTCGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTT
CAGTTTTTGTAGCTTCTTCACTATCTTTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCT
TGAATGTCATTGGTTTCAGTCTTTGTAGCTTC
Found at i:34386 original size:243 final size:243
Alignment explanation
Indices: 34085--34592 Score: 926
Period size: 243 Copynumber: 2.1 Consensus size: 243
34075 TTTGCGGCAT
* * *
34085 CTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGTAGCTTCTTCACTATCT
1 CTTCCAATGACTGAGGCTTTGCTTGAATGTCATTGGTTTCAGTCTTTGTAGCTTCTTCACTATCT
34150 TTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
66 TTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
* *
34215 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTTGCATCAGAACCCT
131 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTCGCATCAGAACCCC
* *
34280 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGCTTGTTGGAGTAA
196 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
34328 CTTCCAATGACTGAGGCTTTGCTTGAATGTCATTGGTTTCAGTCTTTGTAGCTTCTTCACTATCT
1 CTTCCAATGACTGAGGCTTTGCTTGAATGTCATTGGTTTCAGTCTTTGTAGCTTCTTCACTATCT
*
34393 TTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCGTTGGTTTCAGTTTTTGT
66 TTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
*
34458 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGTAGCTTCGCATCAGAACCCC
131 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTCGCATCAGAACCCC
34523 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
196 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
*
34571 CTTCCAATGACTGAGACTTTGC
1 CTTCCAATGACTGAGGCTTTGC
34593 ATTAGAGTCC
Statistics
Matches: 255, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 255 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (243 bp):
CTTCCAATGACTGAGGCTTTGCTTGAATGTCATTGGTTTCAGTCTTTGTAGCTTCTTCACTATCT
TTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTCGCATCAGAACCCC
TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
Found at i:34531 original size:81 final size:81
Alignment explanation
Indices: 34059--34594 Score: 481
Period size: 81 Copynumber: 6.6 Consensus size: 81
34049 TCGGAGCCCT
* * * * **
34059 TTCACTGTCTTTGTCTT-TTGCG-GCATCTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGT
1 TTCACTATCTTTGT-TTGTTG-GTGCAACTTCTAATGACTGAGGCTTTGCATCAGAATCATTGGT
34122 TTCAGTTTTTGTAGCTTC
64 TTCAGTTTTTGTAGCTTC
* * * **
34140 TTCACTATCTTTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTT
1 TTCACTATCTTTGTTTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCATCAGAATCATTGGTTT
34205 CAGTTTTTGTAGCTTC
66 CAGTTTTTGTAGCTTC
** * * * ***
34221 TTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCA-GCTTTGCATCAGAACCCTTCAAT
1 TTCACTATCTTTGTTTGTTGGTGCAACTTCTAATGACTG-AGGCTTTGCATCAGAATCATTGGTT
* *
34285 TCAGCTTTTGCAGCTTC
65 TCAGTTTTTGTAGCTTC
* * * * * * *
34302 ATCACTATTTTTGCTTGTTGGAGTAACTTCCAATGACTGAGGCTTTGC-T-TGAATGTCATTGGT
1 TTCACTATCTTTGTTTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCATCAGAA--TCATTGGT
*
34365 TTCAGTCTTTGTAGCTTC
64 TTCAGTTTTTGTAGCTTC
* * * ** *
34383 TTCACTATCTTTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCGTTGGTTT
1 TTCACTATCTTTGTTTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCATCAGAATCATTGGTTT
34448 CAGTTTTTGTAGCTTC
66 CAGTTTTTGTAGCTTC
** * * * ** ***
34464 TTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGTA-GCTTCGCATCAGAACCCCTCAAT
1 TTCACTATCTTTGTTTGTTGGTGCAACTTCTAATGACTG-AGGCTTTGCATCAGAATCATTGGTT
* *
34528 TCAGCTTTTGCAGCTTC
65 TCAGTTTTTGTAGCTTC
* * * * * * * *
34545 ATCACTATTTTTGATTGTCGGAGTAACTTCCAATGACTGAGACTTTGCAT
1 TTCACTATCTTTGTTTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCAT
34595 TAGAGTCCTT
Statistics
Matches: 368, Mismatches: 77, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
79 3 0.01
80 5 0.01
81 356 0.97
82 3 0.01
83 1 0.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (81 bp):
TTCACTATCTTTGTTTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCATCAGAATCATTGGTTT
CAGTTTTTGTAGCTTC
Found at i:34673 original size:243 final size:243
Alignment explanation
Indices: 34085--34675 Score: 726
Period size: 243 Copynumber: 2.4 Consensus size: 243
34075 TTTGCGGCAT
* * * *** ** * * *
34085 CTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGTAGCTTCTTCACTATCT
1 CTTCCAATGACTGAGACTTTGCTTGAATGTCATTCACTTCAGACTCTGCAGCTTCTTCACTATCC
* * * * * *
34150 TTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
66 TTGTCTGGTGGTACAACATCCAATGACTCAAGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
* *
34215 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTTGCATCAGAACCCT
131 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTCGCATCAGAACCCC
* *
34280 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGCTTGTTGGAGTAA
196 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
* *** * * * *
34328 CTTCCAATGACTGAGGCTTTGCTTGAATGTCATTGGTTTCAGTCTTTGTAGCTTCTTCACTATCT
1 CTTCCAATGACTGAGACTTTGCTTGAATGTCATTCACTTCAGACTCTGCAGCTTCTTCACTATCC
* * * * * * *
34393 TTGTCTGTTGGTGCAACTTCTAATGACTGAGGCTTTGCTTGAGTGTCGTTGGTTTCAGTTTTTGT
66 TTGTCTGGTGGTACAACATCCAATGACTCAAGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
*
34458 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGTAGCTTCGCATCAGAACCCC
131 AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTCGCATCAGAACCCC
34523 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
196 TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
* *
34571 CTTCCAATGACTGAGACTTTGCATT-AGA-GTCCTTCACTTCAGACTCTGCAGC-TCTTTCAGTA
1 CTTCCAATGACTGAGACTTTGC-TTGA-ATGTCATTCACTTCAGACTCTGCAGCTTC-TTCACTA
*
34633 TCCTTGT-TGGT-GTCACTAACATCCAGA-GATTCAAGCTTTGCTT
63 TCCTTGTCTGGTGGT-AC-AACATCCA-ATGACTCAAGCTTTGCTT
34676 CAGTCTTTGT
Statistics
Matches: 316, Mismatches: 26, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
241 2 0.01
242 6 0.02
243 304 0.96
244 4 0.01
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (243 bp):
CTTCCAATGACTGAGACTTTGCTTGAATGTCATTCACTTCAGACTCTGCAGCTTCTTCACTATCC
TTGTCTGGTGGTACAACATCCAATGACTCAAGCTTTGCTTGAGTGTCATTGGTTTCAGTTTTTGT
AGCTTCTTTGCTATCTTCGTTTGTTGGTGCAACTTCTAATGACTGCAGCTTCGCATCAGAACCCC
TCAATTCAGCTTTTGCAGCTTCATCACTATTTTTGATTGTCGGAGTAA
Found at i:45269 original size:2 final size:2
Alignment explanation
Indices: 45264--45294 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45254 TTTGCTTGTA
45264 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 T
45295 ATAGGTTTCT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:45323 original size:10 final size:10
Alignment explanation
Indices: 45308--45338 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
45298 GGTTTCTATC
45308 TTATATGGCT
1 TTATATGGCT
45318 TTATATGGCT
1 TTATATGGCT
45328 TTATATGGCT
1 TTATATGGCT
45338 T
1 T
45339 CAGTTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (10 bp):
TTATATGGCT
Found at i:53264 original size:5 final size:5
Alignment explanation
Indices: 53254--53300 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
53244 TTAATTAGCT
53254 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
53301 ATACTAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:54076 original size:40 final size:40
Alignment explanation
Indices: 54022--54100 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
54012 ATTTGATTTT
* * *
54022 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGATA
54062 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGA
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTGA
54101 AGACTTGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 15 0.44
41 18 0.53
42 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGATA
Found at i:54439 original size:91 final size:91
Alignment explanation
Indices: 54284--54507 Score: 299
Period size: 91 Copynumber: 2.5 Consensus size: 91
54274 TCTTTGATAA
* * * *
54284 TTTGAAAGAATAATCCTCCACATACGTGGATCTTCTTTCAATAATTTCCCAATAATTGGGTCTTC
1 TTTGAAAGAAAAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTC
* *
54349 AGTAATTCTGCAATAATTG-GATTTTC
66 AGTAATTCTCCAATAATTGAG-TCTTC
* *
54375 TTTGAAAGAAAAATACTCCGCATACATGGATCTTCTTTCAATAA-CTCCCAAATAACTGGGTCTT
1 TTTGAAAGAAAAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCC-AATAACTGGGTCTT
54439 CAGTAATTCTCCAATAATTGAGTCTTC
65 CAGTAATTCTCCAATAATTGAGTCTTC
* ** * *
54466 TTTGAAAGAAGAATTTTCCACATATGTGAATCTTCTTTCAAT
1 TTTGAAAGAAAAATACTCCACATACGTGGATCTTCTTTCAAT
54508 CTTCTTAAGT
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
90 4 0.03
91 111 0.96
92 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (91 bp):
TTTGAAAGAAAAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTC
AGTAATTCTCCAATAATTGAGTCTTC
Found at i:65670 original size:69 final size:69
Alignment explanation
Indices: 65546--65675 Score: 181
Period size: 69 Copynumber: 1.9 Consensus size: 69
65536 CCAAAGTATG
* * ** *
65546 TTCACCTACTGAAAATATTACAAATTCAAATGATGTCACTGGTCACAAGGTAATAAAAATCTTAA
1 TTCACCTACTGAAAATATTACAAATGCAAAGGATGTCACCAGTCACAAGGCAATAAAAATCTTAA
65611 TGTT
66 TGTT
* *
65615 TTCACCTACTGAAAATATTACATATGCAAAGGATGTCACCAGT-AGTAAGGCAATAAAAATC
1 TTCACCTACTGAAAATATTACAAATGCAAAGGATGTCACCAGTCA-CAAGGCAATAAAAATC
65676 ATAAAGAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
68 1 0.02
69 52 0.98
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (69 bp):
TTCACCTACTGAAAATATTACAAATGCAAAGGATGTCACCAGTCACAAGGCAATAAAAATCTTAA
TGTT
Found at i:68199 original size:19 final size:19
Alignment explanation
Indices: 68175--68214 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
68165 CTACACATAT
*
68175 TGTAAGACTTTCACAGGAA
1 TGTAAGACTTCCACAGGAA
68194 TGTAAGACTTCCACAGGAA
1 TGTAAGACTTCCACAGGAA
68213 TG
1 TG
68215 AATAAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (19 bp):
TGTAAGACTTCCACAGGAA
Found at i:74211 original size:55 final size:56
Alignment explanation
Indices: 74108--74221 Score: 169
Period size: 55 Copynumber: 2.0 Consensus size: 56
74098 AGAGGTTATA
* *
74108 AGACAACTTAATCTACGAAAGAATAGAAGTTTCATGAATATAATTCATTATAAAA-AAT
1 AGACAACTTAATCGACAAAAGAAT--AAGTTTCATGAATATAATTCATTA-AAAAGAAT
74166 AGACAACTTAATCGACAAAAGAAT-AGTTTCATGAATATAATTCATTAAAAAGAAT
1 AGACAACTTAATCGACAAAAGAATAAGTTTCATGAATATAATTCATTAAAAAGAAT
74221 A
1 A
74222 TATTACTGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
54 4 0.08
55 27 0.51
58 22 0.42
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (56 bp):
AGACAACTTAATCGACAAAAGAATAAGTTTCATGAATATAATTCATTAAAAAGAAT
Found at i:76123 original size:21 final size:21
Alignment explanation
Indices: 76097--76138 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
76087 TATTTTACAG
76097 AGTACATAAGTTTTAAGCAAT
1 AGTACATAAGTTTTAAGCAAT
*
76118 AGTACATGAGTTTTAAGCAAT
1 AGTACATAAGTTTTAAGCAAT
76139 TTCCTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
AGTACATAAGTTTTAAGCAAT
Done.