Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006074.1 Corchorus capsularis cultivar CVL-1 contig06092, 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: 29244
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Found at i:3509 original size:42 final size:42
Alignment explanation
Indices: 3448--3533 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
3438 AAGGGTCAAG
* *
3448 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATGGGCCGCGCGA
1 TGGCCGGTTGAGGCCGGATGGCCCGTGCGATGGCCCGCGCGA
* * *
3490 TGGCCGGTTGAGGCTGGATGGCTCGTGCGATGGCCCGTGCGA
1 TGGCCGGTTGAGGCCGGATGGCCCGTGCGATGGCCCGCGCGA
3532 TG
1 TG
3534 TCCCATGCGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.08, C:0.26, G:0.47, T:0.20
Consensus pattern (42 bp):
TGGCCGGTTGAGGCCGGATGGCCCGTGCGATGGCCCGCGCGA
Found at i:3523 original size:12 final size:12
Alignment explanation
Indices: 3506--3548 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3496 GTTGAGGCTG
*
3506 GATGGCTCGTGC
1 GATGGCCCGTGC
3518 GATGGCCCGTGC
1 GATGGCCCGTGC
* *
3530 GATGTCCCATGC
1 GATGGCCCGTGC
*
3542 GTTGGCC
1 GATGGCC
3549 GGTCATGGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.23
Consensus pattern (12 bp):
GATGGCCCGTGC
Found at i:4706 original size:33 final size:32
Alignment explanation
Indices: 4627--4716 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
4617 TTGCAAAGAG
*
4627 TGTTTTAGATGTTGTTTGCGATGATACCAAACC
1 TGTTTTAG-TGTTGTTTGCGATGACACCAAACC
* * * *
4660 TAATTTGAGTGTTGTTTGCGATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGACACCAAACC
*
4693 TGTTTTAGCTGTTGTTTGTGATGA
1 TGTTTTAG-TGTTGTTTGCGATGA
4717 AACAAGTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
32 5 0.11
33 37 0.79
34 5 0.11
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.43
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGACACCAAACC
Found at i:5486 original size:47 final size:47
Alignment explanation
Indices: 5409--5539 Score: 133
Period size: 47 Copynumber: 2.8 Consensus size: 47
5399 CTTATTTCCA
* *
5409 CTTTTCCAAAATTGCCCTTCCTCATTGGAAGGTGTTGTCTAAGTCTG
1 CTTTTCCAAAAATGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTG
* * *
5456 CTTTTTCAAAAATGTCCTTCAC-CATCGGAAGGTGTTGTTTAAGTCTG
1 CTTTTCCAAAAATGCCCTTC-CTCATCGGAAGGTGTTGTCTAAGTCTG
* * * *
5503 CTCTT-CACAAATTGCCCTGCC-CGGTCGGAAGGTGTTG
1 CTTTTCCA-AAAATGCCCTTCCTC-ATCGGAAGGTGTTG
5540 CTTTCATTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
46 4 0.06
47 66 0.93
48 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (47 bp):
CTTTTCCAAAAATGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTG
Found at i:5618 original size:40 final size:40
Alignment explanation
Indices: 5552--5917 Score: 272
Period size: 40 Copynumber: 9.2 Consensus size: 40
5542 TTCATTATCT
* *
5552 TATTCCCAGTTTGCCTTTCCCAGTCGGAAGGTGTTGTTTA
1 TATTCCCAGTTTGCCCTTCCTAGTCGGAAGGTGTTGTTTA
* * *
5592 TATTCCCAGTTTGCCATTCTTGGTCGGAAGGTGTTGTTTA
1 TATTCCCAGTTTGCCCTTCCTAGTCGGAAGGTGTTGTTTA
* * * * *
5632 CATT-CCTGTTTTGGCGTTCCTCA-TAGGAAGGTGTTGTTTA
1 TATTCCCAG-TTTGCCCTTCCT-AGTCGGAAGGTGTTGTTTA
* * *
5672 TATTCCCAATTAGCCCTTCAC-GGTCGGAAGGTGTTGTTTA
1 TATTCCCAGTTTGCCCTTC-CTAGTCGGAAGGTGTTGTTTA
* * *
5712 CATT-CCTGTTTTGCCCTTCCTCA-CCGGAAGGTGTTGTTTA
1 TATTCCCAG-TTTGCCCTTCCT-AGTCGGAAGGTGTTGTTTA
* * * *
5752 CTCATTCCCAATTTGCCCTTCCAAGTTGGAACGTGTTGTTTA
1 -T-ATTCCCAGTTTGCCCTTCCTAGTCGGAAGGTGTTGTTTA
* * * *
5794 CATT-CCTGTTTGCTCTTCC----CAGAAGGTGTTGTTTA
1 TATTCCCAGTTTGCCCTTCCTAGTCGGAAGGTGTTGTTTA
* *
5829 CTCATT-CTAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
1 -T-ATTCCCAGTTTGCCCTTCCTAGTCGGAAGGTGTTGTTTA
* *
5870 -AGCTTCCCAGTTTGCCCTTCTTCA-TCGGAAGGTGTTCTTTA
1 TA--TTCCCAGTTTGCCCTTCCT-AGTCGGAAGGTGTTGTTTA
5911 TTATTCC
1 -TATTCC
5918 AAAAATGCCC
Statistics
Matches: 254, Mismatches: 48, Indels: 47
0.73 0.14 0.13
Matches are distributed among these distances:
35 13 0.05
37 15 0.06
38 1 0.00
39 18 0.07
40 123 0.48
41 52 0.20
42 29 0.11
43 3 0.01
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (40 bp):
TATTCCCAGTTTGCCCTTCCTAGTCGGAAGGTGTTGTTTA
Found at i:5804 original size:82 final size:79
Alignment explanation
Indices: 5560--5944 Score: 363
Period size: 80 Copynumber: 4.8 Consensus size: 79
5550 CTTATTCCCA
* * * ***
5560 GTTTGCCTTTCC-CAGTCGGAAGGTGTTGTTTATATTCCCAGTTTGCCATTCTTGGTCGGAAGGT
1 GTTTGCCCTTCCTCA-TCGGAAGGTGTTGTTTATATTCCCAATTTGCCCTTCCAAGTCGGAAGGT
5624 GTTGTTTACATTCCT
65 GTTGTTTACATTCCT
* * * * *
5639 GTTTTGGCGTTCCTCATAGGAAGGTGTTGTTTATATTCCCAATTAGCCCTT-CACGGTCGGAAGG
1 G-TTTGCCCTTCCTCATCGGAAGGTGTTGTTTATATTCCCAATTTGCCCTTCCA-AGTCGGAAGG
5703 TGTTGTTTACATTCCT
64 TGTTGTTTACATTCCT
* * *
5719 GTTTTGCCCTTCCTCACCGGAAGGTGTTGTTTACTCATTCCCAATTTGCCCTTCCAAGTTGGAAC
1 G-TTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-T-ATTCCCAATTTGCCCTTCCAAGTCGGAAG
5784 GTGTTGTTTACATTCCT
63 GTGTTGTTTACATTCCT
* * * *
5801 GTTTGCTCTTCC-CA---GAAGGTGTTGTTTACTCATT-CTAGTTTGCCCTTCCCAGTCGGAAGG
1 GTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-T-ATTCCCAATTTGCCCTTCCAAGTCGGAAGG
*
5861 TGTTGTTTA-AGCTTCCCA
64 TGTTGTTTACA--TT-CCT
* * * ** **
5879 GTTTGCCCTTCTTCATCGGAAGGTGTTCTTTATTATTCCAAAAATGCCCCTTCCCGGTCGGAAGG
1 GTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-TATTCCCAATTTG-CCCTTCCAAGTCGGAAGG
5944 T
64 T
5945 CACAGCTTTC
Statistics
Matches: 259, Mismatches: 32, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
75 1 0.00
76 30 0.12
77 22 0.08
78 12 0.05
79 3 0.01
80 97 0.37
81 16 0.06
82 58 0.22
83 20 0.08
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (79 bp):
GTTTGCCCTTCCTCATCGGAAGGTGTTGTTTATATTCCCAATTTGCCCTTCCAAGTCGGAAGGTG
TTGTTTACATTCCT
Found at i:5843 original size:37 final size:38
Alignment explanation
Indices: 5698--5889 Score: 139
Period size: 42 Copynumber: 4.9 Consensus size: 38
5688 TTCACGGTCG
5698 GAAGGTGTTGTTTA--CATTCCT-GTTTTGCCCTTCCTCA
1 GAAGGTGTTGTTTACTCATTCCTAG-TTTGCCCTTCC-CA
* * *
5735 CCGGAAGGTGTTGTTTACTCATTCCCAATTTGCCCTTCCAA
1 ---GAAGGTGTTGTTTACTCATTCCTAGTTTGCCCTTCCCA
* *
5776 GTTGGAACGTGTTGTTTA--CATTCCT-GTTTGCTCTTCCCA
1 ----GAAGGTGTTGTTTACTCATTCCTAGTTTGCCCTTCCCA
5815 GAAGGTGTTGTTTACTCATT-CTAGTTTGCCCTTCCCA
1 GAAGGTGTTGTTTACTCATTCCTAGTTTGCCCTTCCCA
** *
5852 GTCGGAAGGTGTTGTTTAAGC-TTCCCAGTTTGCCCTTC
1 ----GAAGGTGTTGTTTACTCATTCCTAGTTTGCCCTTC
5890 TTCATCGGAA
Statistics
Matches: 125, Mismatches: 15, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
35 13 0.10
36 2 0.02
37 17 0.14
39 11 0.09
40 22 0.18
41 29 0.23
42 31 0.25
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (38 bp):
GAAGGTGTTGTTTACTCATTCCTAGTTTGCCCTTCCCA
Found at i:5905 original size:117 final size:117
Alignment explanation
Indices: 5698--5910 Score: 267
Period size: 117 Copynumber: 1.8 Consensus size: 117
5688 TTCACGGTCG
**
5698 GAAGGTGTTGTTTACATTCCTGTTTTGCCCTTCCTCACCGGAAGGTGTTGTTTACTCATTCCCAA
1 GAAGGTGTTGTTTACATTCCTGTTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAGCATTCCCAA
* *
5763 TTTGCCCTTCCAAGTTGGAACGTGTTGTTTACATTCCTGTTTGCTCTTCCCA
66 TTTGCCCTTCCAAGTCGGAACGTGTTCTTTACATTCCTGTTTGCTCTTCCCA
*
5815 GAAGGTGTTGTTTACTCATT-CTAG-TTTGCCCTTCC-CAGTCGGAAGGTGTTGTTTAAGC-TTC
1 GAAGGTGTTGTTTA--CATTCCT-GTTTTGCCCTTCCTCA-CCGGAAGGTGTTGTTTAAGCATTC
* *
5876 CCAGTTTGCCCTTCTTC-A-TCGGAAGGTGTTCTTTA
62 CCAATTTGCCCTTC--CAAGTCGGAACGTGTTCTTTA
5911 TTATTCCAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
117 46 0.55
118 31 0.37
119 6 0.07
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (117 bp):
GAAGGTGTTGTTTACATTCCTGTTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAGCATTCCCAA
TTTGCCCTTCCAAGTCGGAACGTGTTCTTTACATTCCTGTTTGCTCTTCCCA
Found at i:5975 original size:48 final size:49
Alignment explanation
Indices: 5913--6092 Score: 159
Period size: 50 Copynumber: 3.7 Consensus size: 49
5903 GTTCTTTATT
5913 ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGCTTT-CTTCA-CC
1 ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAG-TTTCCTTCATCC
* * * * **
5961 ATTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTATTTG
1 ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTCCTTCA-TCC
* * * * ** *
6011 TTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTC-CTTGTTTTCTTTTTCTG
1 ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCAC-AGTTTCCTTCATC-C
* * *
6061 TTTCCCAAAATGCCCCTTCTCGGTCGGAAGGT
1 ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGT
6093 TTAGTTTTCT
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
47 3 0.03
48 38 0.33
49 2 0.02
50 71 0.62
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (49 bp):
ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTCCTTCATCC
Found at i:6028 original size:50 final size:50
Alignment explanation
Indices: 5962--6092 Score: 194
Period size: 50 Copynumber: 2.6 Consensus size: 50
5952 TTCTTCACCA
*
5962 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTATT-TGT
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTT-TTCTGT
* * *
6012 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTTTCTGT
1 TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTTTCTGT
6062 TTCCCAAAATGCCCCTT-CTCGGTCGGAAGGT
1 TTCCCAAAATGCCCCTTCCT-GGTCGGAAGGT
6093 TTAGTTTTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
49 3 0.04
50 71 0.96
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.36
Consensus pattern (50 bp):
TTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTTTCTGT
Found at i:12551 original size:95 final size:96
Alignment explanation
Indices: 12435--12624 Score: 303
Period size: 95 Copynumber: 2.0 Consensus size: 96
12425 GTAAAAGAGG
* * *
12435 AAGTAATCAGTAAAATGGAGTAAAAGTAAAAGAAA-TAATCAGTAGAATGGAGTAAAAGTAAAAG
1 AAGTAATCAATAAAATGGAGTAAAAGTAAAA-AAAGTAATCAGCAGAATGGAATAAAAGTAAAAG
12499 AAGTAATCAGTA-AATGGAGTAAAAGTAAAAT
65 AAGTAATCAGTAGAATGGAGTAAAAGTAAAAT
* * *
12530 AAGTAATCAATAGAATTGAGTAAAAGTAAAAAAAGTAATCAGCAGAATGGAATAAGAGTAAAAGA
1 AAGTAATCAATAAAATGGAGTAAAAGTAAAAAAAGTAATCAGCAGAATGGAATAAAAGTAAAAGA
12595 AGTAATCAGTAGAATGGAGTAAAAGTAAAA
66 AGTAATCAGTAGAATGGAGTAAAAGTAAAA
12625 GAAGAAATAA
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
94 3 0.03
95 66 0.76
96 18 0.21
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (96 bp):
AAGTAATCAATAAAATGGAGTAAAAGTAAAAAAAGTAATCAGCAGAATGGAATAAAAGTAAAAGA
AGTAATCAGTAGAATGGAGTAAAAGTAAAAT
Found at i:12628 original size:32 final size:32
Alignment explanation
Indices: 12434--12643 Score: 305
Period size: 32 Copynumber: 6.6 Consensus size: 32
12424 AGTAAAAGAG
*
12434 GAAGTAATCAGTAAAATGGAGTAAAAGTAAAA
1 GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
*
12466 GAAATAATCAGTAGAATGGAGTAAAAGTAAAA
1 GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
12498 GAAGTAATCAGTA-AATGGAGTAAAAGTAAAA
1 GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
* * *
12529 TAAGTAATCAATAGAATTGAGTAAAAGTAAAA
1 GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
* * * *
12561 AAAGTAATCAGCAGAATGGAATAAGAGTAAAA
1 GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
12593 GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
1 GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
* * *
12625 GAAGAAATAAGAAGAATGG
1 GAAGTAATCAGTAGAATGG
12644 GGTGAAAGGA
Statistics
Matches: 158, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
31 29 0.18
32 129 0.82
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.19
Consensus pattern (32 bp):
GAAGTAATCAGTAGAATGGAGTAAAAGTAAAA
Found at i:12694 original size:127 final size:127
Alignment explanation
Indices: 12435--12666 Score: 320
Period size: 127 Copynumber: 1.8 Consensus size: 127
12425 GTAAAAGAGG
* *
12435 AAGTAATCAGTAAAATGGAGTAAAAGTAAAAGAAATAATCAGTAGAATGGAGTAAAAGTAAAAGA
1 AAGTAATCAGCAAAATGGAATAAAAGTAAAAGAAATAATCAGTAGAATGGAGTAAAAGTAAAAGA
* * * * * *
12500 AGTAATCAGTAAATGGAGTAAAAGTAAAATAAGTAATCAATAGAATTGAGTAAAAGTAAAAA
66 AGAAATAAGAAAATGGAGTAAAAGGAAAAGAAGTAAGCAATAGAATTGAGTAAAAGTAAAAA
* * *
12562 AAGTAATCAGCAGAATGGAATAAGAGTAAAAGAAGTAATCAGTAGAATGGAGTAAAAGTAAAAGA
1 AAGTAATCAGCAAAATGGAATAAAAGTAAAAGAAATAATCAGTAGAATGGAGTAAAAGTAAAAGA
* * * *
12627 AGAAATAAGAAGAATGGGGTGAAAGGACAAGAATTAAGCA
66 AGAAATAAGAA-AATGGAGTAAAAGGAAAAGAAGTAAGCA
12667 GTAACTTGGT
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
127 68 0.76
128 21 0.24
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.18
Consensus pattern (127 bp):
AAGTAATCAGCAAAATGGAATAAAAGTAAAAGAAATAATCAGTAGAATGGAGTAAAAGTAAAAGA
AGAAATAAGAAAATGGAGTAAAAGGAAAAGAAGTAAGCAATAGAATTGAGTAAAAGTAAAAA
Found at i:12744 original size:40 final size:39
Alignment explanation
Indices: 12665--12868 Score: 171
Period size: 40 Copynumber: 5.1 Consensus size: 39
12655 AAGAATTAAG
* * * **
12665 CAGTAACTTGGTAATTAAGTGTA-AAAGTAAAAGGGGTAAT
1 CAGTAAATTGATAATTAAGAG-AGAAAGTAAAA-AAGTAAT
* * * * *
12705 CGGTAAATTGGTAACTAAAAGTGAAAGTAAGAAAAGTAAT
1 CAGTAAATTGATAATTAAGAGAGAAAGTAA-AAAAGTAAT
*
12745 CAGTAAATTGATAATTAAGAGAGGAAGTAAAAGAAGTAAT
1 CAGTAAATTGATAATTAAGAGAGAAAGTAAAA-AAGTAAT
* * *
12785 CAGTCAA-TCAGTAATTAAGAGTA-AAAGTAAAAAAAATTAAT
1 CAGTAAATTGA-TAATTAAGAG-AGAAAGT--AAAAAAGTAAT
*
12826 CAGTAAATTGATAATTAAGAGAGAAAGTTAAAGAAGTAAT
1 CAGTAAATTGATAATTAAGAGAGAAAG-TAAAAAAGTAAT
12866 CAG
1 CAG
12869 AAAAATGGCA
Statistics
Matches: 132, Mismatches: 22, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
39 4 0.03
40 92 0.70
41 29 0.22
42 7 0.05
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (39 bp):
CAGTAAATTGATAATTAAGAGAGAAAGTAAAAAAGTAAT
Found at i:12749 original size:80 final size:81
Alignment explanation
Indices: 12665--12868 Score: 241
Period size: 80 Copynumber: 2.5 Consensus size: 81
12655 AAGAATTAAG
* * * ** * ** *
12665 CAGTAACTTGGTAATTAAGTGTA-AAAGTAAAAGGGGTAATCGGTAAATTGGTAACTAAAAGTGA
1 CAGTAAATTGATAATTAAGAG-AGAAAGTAAAAGAAGTAATCAGTAAATCAGTAACTAAAAGTAA
*
12729 AAGT-AAGAAAAGTAAT
65 AAGTAAAAAAAAGTAAT
* * * *
12745 CAGTAAATTGATAATTAAGAGAGGAAGTAAAAGAAGTAATCAGTCAATCAGTAATTAAGAGTAAA
1 CAGTAAATTGATAATTAAGAGAGAAAGTAAAAGAAGTAATCAGTAAATCAGTAACTAAAAGTAAA
*
12810 AGTAAAAAAAATTAAT
66 AGTAAAAAAAAGTAAT
*
12826 CAGTAAATTGATAATTAAGAGAGAAAGTTAAAGAAGTAATCAG
1 CAGTAAATTGATAATTAAGAGAGAAAGTAAAAGAAGTAATCAG
12869 AAAAATGGCA
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
79 1 0.01
80 53 0.50
81 51 0.49
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (81 bp):
CAGTAAATTGATAATTAAGAGAGAAAGTAAAAGAAGTAATCAGTAAATCAGTAACTAAAAGTAAA
AGTAAAAAAAAGTAAT
Found at i:12976 original size:40 final size:40
Alignment explanation
Indices: 12932--13034 Score: 95
Period size: 40 Copynumber: 2.6 Consensus size: 40
12922 GTAAAAGAAG
*
12932 AAATTAGTAGAAT-GGAGTAAAAGTAAAAGAAGGGAG-CAGT
1 AAATTAGTA-AATAAGAGTAAAAGTAAAAGAA-GGAGTCAGT
* * * *
12972 AAATTGGTAATTAAGTGTAAAAGTAAAAGAAGTAGTCAGT
1 AAATTAGTAAATAAGAGTAAAAGTAAAAGAAGGAGTCAGT
* *
13012 AAATCAGTAATTAA-AGTCAAAAG
1 AAATTAGTAAATAAGAGT-AAAAG
13035 ATGGTATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
39 7 0.13
40 45 0.87
ACGTcount: A:0.50, C:0.04, G:0.23, T:0.22
Consensus pattern (40 bp):
AAATTAGTAAATAAGAGTAAAAGTAAAAGAAGGAGTCAGT
Found at i:13113 original size:29 final size:29
Alignment explanation
Indices: 13079--13334 Score: 173
Period size: 29 Copynumber: 8.4 Consensus size: 29
13069 TGGTAAGAAA
*
13079 GTAAAGAGTAATCAGTAAATAGTAAAATG
1 GTAAAGAGTAATCAGTAAAGAGTAAAATG
13108 GTAAAGAGTAATCAGTAAAGAGTAAAATG
1 GTAAAGAGTAATCAGTAAAGAGTAAAATG
13137 GTAAAGAACAATGAGTAATCAGTAAAGAGTAAAATG
1 GT-----A-AA-GAGTAATCAGTAAAGAGTAAAATG
** *
13173 GTAAAGAGTAAAGAGTAAAGAGT--AATCA
1 GTAAAGAGTAATCAGTAAAGAGTAAAAT-G
* * *
13201 GTAAAGAGTAAAAT-GGTAAAAAGTAAAGT-
1 GTAAAGAGT--AATCAGTAAAGAGTAAAATG
** **
13230 GTAATCAGTAAAGAGTAAA-ATGGTAAAA-G
1 GTAAAGAGTAATCAGTAAAGA--GTAAAATG
*
13259 GTAAAGAGTAATCAGTAAAGGGTAAAATG
1 GTAAAGAGTAATCAGTAAAGAGTAAAATG
*
13288 GTAAAAAGAAAAGAGTAATCAGTAAAAAGTAAAATG
1 GT-------AAAGAGTAATCAGTAAAGAGTAAAATG
*
13324 ATAAAGAGTAA
1 GTAAAGAGTAA
13335 ATAGTAATTA
Statistics
Matches: 181, Mismatches: 21, Indels: 50
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.03
28 20 0.11
29 93 0.51
30 4 0.02
31 3 0.02
34 1 0.01
35 2 0.01
36 52 0.29
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (29 bp):
GTAAAGAGTAATCAGTAAAGAGTAAAATG
Found at i:13125 original size:36 final size:36
Alignment explanation
Indices: 13058--13362 Score: 322
Period size: 36 Copynumber: 8.5 Consensus size: 36
13048 ATTAAGTTAA
* *
13058 AAAGAGTAGAATGGTAAGAAAGTAAAGAGTAATCAGT
1 AAAGAGTAAAATGGTAA-AGAGTAAAGAGTAATCAGT
*
13095 AAATAGTAAAA---T---G-GTAAAGAGTAATCAGT
1 AAAGAGTAAAATGGTAAAGAGTAAAGAGTAATCAGT
** *
13124 AAAGAGTAAAATGGTAAAGAACAATGAGTAATCAGT
1 AAAGAGTAAAATGGTAAAGAGTAAAGAGTAATCAGT
13160 AAAGAGTAAAATGGTAAAGAGTAAAGAGTAAAGAGTAATCAGT
1 AAAGAGTAAAA---T---G-GTAAAGAGTAAAGAGTAATCAGT
* *
13203 AAAGAGTAAAATGGTAAAAAGTAAAGTGTAATCAGT
1 AAAGAGTAAAATGGTAAAGAGTAAAGAGTAATCAGT
13239 AAAGAGTAAAATGGTAAA-AGGTAAAGAGTAATCAGT
1 AAAGAGTAAAATGGTAAAGA-GTAAAGAGTAATCAGT
* * *
13275 AAAGGGTAAAATGGTAAAAAGAAAAGAGTAATCAGT
1 AAAGAGTAAAATGGTAAAGAGTAAAGAGTAATCAGT
* * * *
13311 AAAAAGTAAAATGATAAAGAGTAAATAGTAATTAGT
1 AAAGAGTAAAATGGTAAAGAGTAAAGAGTAATCAGT
*
13347 AAAGTG-AAAATGGTAA
1 AAAGAGTAAAATGGTAA
13363 TCAGTAGAAA
Statistics
Matches: 227, Mismatches: 25, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
29 26 0.11
32 1 0.00
34 1 0.00
35 11 0.05
36 143 0.63
37 11 0.05
39 1 0.00
40 1 0.00
42 1 0.00
43 31 0.14
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (36 bp):
AAAGAGTAAAATGGTAAAGAGTAAAGAGTAATCAGT
Found at i:13347 original size:29 final size:28
Alignment explanation
Indices: 13288--13374 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
13278 GGGTAAAATG
13288 GTAAAAAGAAAAGAGTAATCAGTAAAAA
1 GTAAAAAGAAAAGAGTAATCAGTAAAAA
* **
13316 GTAAAATGATAAAGAGTAAAT-AGTAATTA
1 GTAAAAAGA-AAAGAGT-AATCAGTAAAAA
**
13345 GTAAAGTGAAAATG-GTAATCAGTAGAAAA
1 GTAAAAAGAAAA-GAGTAATCAGTA-AAAA
13374 G
1 G
13375 AGTAAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.06
28 17 0.35
29 25 0.52
30 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (28 bp):
GTAAAAAGAAAAGAGTAATCAGTAAAAA
Found at i:13387 original size:27 final size:27
Alignment explanation
Indices: 13353--13575 Score: 216
Period size: 27 Copynumber: 8.0 Consensus size: 27
13343 TAGTAAAGTG
*
13353 AAAATGGTAATCAGTAGAAAAGAGTAA
1 AAAATGGTAATCAGTAAAAAAGAGTAA
* *
13380 AAAATGGTATTCAGTAAAAAAGAGAAA
1 AAAATGGTAATCAGTAAAAAAGAGTAA
* *
13407 AAAATGGTATTCAGTAAAAGAAAAAAGTAA
1 AAAATGGTAATCAGT--AA-AAAAGAGTAA
*
13437 GAAAAGGGTAATCAGTAAAAACAGAGTAA
1 -AAAATGGTAATCAGTAAAAA-AGAGTAA
* * *
13466 GAAAAGGGTAATTAGTAAAAAATAGTAA
1 -AAAATGGTAATCAGTAAAAAAGAGTAA
*
13494 AAAA-GGTAATCAAT-AAAAAGAGTAA
1 AAAATGGTAATCAGTAAAAAAGAGTAA
* * *
13519 GAAAATGGTAGTTAGTAAAAGAAGAAGGTAG
1 -AAAATGGTAATCAGTAAAA-AAG-A-GTAA
*
13550 AAAATGGTAATCAGTAAAAAGGAGTA
1 AAAATGGTAATCAGTAAAAAAGAGTA
13576 GGATAGATTA
Statistics
Matches: 165, Mismatches: 20, Indels: 22
0.80 0.10 0.11
Matches are distributed among these distances:
25 10 0.06
26 12 0.07
27 53 0.32
28 13 0.08
29 35 0.21
30 26 0.16
31 16 0.10
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.18
Consensus pattern (27 bp):
AAAATGGTAATCAGTAAAAAAGAGTAA
Found at i:13457 original size:57 final size:55
Alignment explanation
Indices: 13352--13575 Score: 217
Period size: 57 Copynumber: 4.0 Consensus size: 55
13342 TTAGTAAAGT
* * *
13352 GAAAATGGTAATCAGT-AGAAAAGAGTAAAAAATGGTATTCAGTAAAAAAGAG-AA
1 GAAAATGGT-ATTAGTAAGAAAAAAGTAAAAAATGGTAATCAGTAAAAAAGAGTAA
* *
13406 AAAAATGGTATTCAGTAAAAGAAAAAAGTAAGAAAAGGGTAATCAGTAAAAACAGAGTAA
1 GAAAATGGTATT-AGT--AAGAAAAAAGTAA-AAAATGGTAATCAGTAAAAA-AGAGTAA
* * *
13466 GAAAAGGGTAATTAGTAA-AAAATAGTAAAAAA-GGTAATCAAT-AAAAAGAGTAA
1 GAAAATGGT-ATTAGTAAGAAAAAAGTAAAAAATGGTAATCAGTAAAAAAGAGTAA
* *
13519 GAAAATGGTAGTTAGTAA-AAGAAGAAGGTAGAAAATGGTAATCAGTAAAAAGGAGTA
1 GAAAATGGTA-TTAGTAAGAA-AA-AA-GTAAAAAATGGTAATCAGTAAAAAAGAGTA
13576 GGATAGATTA
Statistics
Matches: 142, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
52 1 0.01
53 26 0.18
54 17 0.12
55 10 0.07
56 11 0.08
57 29 0.20
58 29 0.20
59 4 0.03
60 12 0.08
61 3 0.02
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.18
Consensus pattern (55 bp):
GAAAATGGTATTAGTAAGAAAAAAGTAAAAAATGGTAATCAGTAAAAAAGAGTAA
Found at i:13524 original size:113 final size:113
Alignment explanation
Indices: 13352--13569 Score: 298
Period size: 113 Copynumber: 1.9 Consensus size: 113
13342 TTAGTAAAGT
* * * *
13352 GAAAATGGTAATCAGTAGAAAAGAGTAAAAAATGGTATTCAGTAAAAAAGAGAAAAAAATGGTA-
1 GAAAAGGGTAATCAGTAAAAAAGAGTAAAAAATGGTAATCAATAAAAAAGAGAAAAAAATGGTAG
13416 TTCAGTAAAAGAAAAAAGTAAGAAAAGGGTAATCAGTAAAAACAGAGTAA
66 TT-AGTAAAAGAAAAAAGT-AGAAAAGGGTAATCAGTAAAAACAGAGTAA
* * *
13466 GAAAAGGGTAATTAGTAAAAAATAGTAAAAAA-GGTAATCAAT-AAAAAGAGTAAGAAAATGGTA
1 GAAAAGGGTAATCAGTAAAAAAGAGTAAAAAATGGTAATCAATAAAAAAGAG-AAAAAAATGGTA
* * *
13529 GTTAGTAAAAGAAGAAGGTAGAAAATGGTAATCAGTAAAAA
65 GTTAGTAAAAGAAAAAAGTAGAAAAGGGTAATCAGTAAAAA
13570 GGAGTAGGAT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
112 29 0.32
113 33 0.36
114 30 0.33
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.18
Consensus pattern (113 bp):
GAAAAGGGTAATCAGTAAAAAAGAGTAAAAAATGGTAATCAATAAAAAAGAGAAAAAAATGGTAG
TTAGTAAAAGAAAAAAGTAGAAAAGGGTAATCAGTAAAAACAGAGTAA
Found at i:14429 original size:48 final size:48
Alignment explanation
Indices: 14370--14500 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 48
14360 CTTGTTTCCA
*
14370 CTTTTCCAAAATTGCCCTTCCTCATTGG-AAGGTGTTGTCTAAGTCTG
1 CTTTTCCAAAATTGCCCTTCCTCATCGGAAAGGTGTTGTCTAAGTCTG
* * * *
14417 CTTTTCCAAAAATGTCCTTCGTCATCGGAAAGGTGTTGTTTAAGTCTG
1 CTTTTCCAAAATTGCCCTTCCTCATCGGAAAGGTGTTGTCTAAGTCTG
* * *
14465 CTCTTCCCAAATTG-CCTTTC-CAGTCGG-AAGGTGTTG
1 CTTTTCCAAAATTGCCCTTCCTCA-TCGGAAAGGTGTTG
14501 CTTTCATTGT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 11 0.15
47 32 0.44
48 29 0.40
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (48 bp):
CTTTTCCAAAATTGCCCTTCCTCATCGGAAAGGTGTTGTCTAAGTCTG
Found at i:14573 original size:40 final size:40
Alignment explanation
Indices: 14513--14843 Score: 307
Period size: 40 Copynumber: 8.2 Consensus size: 40
14503 TTCATTGTCT
14513 TATTCCCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
1 TATTCCCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
* *
14553 TATTCCCAGTTTGCCATTCCCGGTCGGAAGGTGTTGTTTA
1 TATTCCCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
* * * * *
14593 CATTCCTATTTTGGCGTTCCTCA--CAGGAAGGTGTTGTTTA
1 TATTCCCAGTTTGCCCTTCC-CAGTC-GGAAGGTGTTGTTTA
* * * * * *
14633 TATTCGCAATTTGCCCTTCACGGTCCGAAGGGGTTGTTTA
1 TATTCCCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
* * * * *
14673 CATT-GCTGTTTTGCCCTTCCTCA-CCGGAAGGTGTTGGTTA
1 TATTCCCAG-TTTGCCCTTCC-CAGTCGGAAGGTGTTGTTTA
* *
14713 CTCATTCCCAATTTGCCCTTCCAAGTCGGAAGGTGTTGTTTA
1 -T-ATTCCCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
14755 CTCATT-CCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
1 -T-ATTCCCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
* *
14796 -AGCTTCCCAGTTTGCCCTTCTTCA-TCGGAAGCTGTTGTTTA
1 TA--TTCCCAGTTTGCCCTTC-CCAGTCGGAAGGTGTTGTTTA
14837 TTATTCC
1 -TATTCC
14844 AAAAATGCCC
Statistics
Matches: 237, Mismatches: 38, Indels: 31
0.77 0.12 0.10
Matches are distributed among these distances:
38 1 0.00
39 4 0.02
40 122 0.51
41 71 0.30
42 37 0.16
43 2 0.01
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (40 bp):
TATTCCCAGTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTA
Found at i:14953 original size:50 final size:49
Alignment explanation
Indices: 14888--15019 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 49
14878 TTCTTCTCTA
* *
14888 TTCCAAAAATGCCCCTTCATGGTCGGAAGGTCCCTGTTTCCTTTATTTGT
1 TTCCCAAAATGCCCCTTC-TGGTCGGAAGGTCCCTGTTTCCTTTATCTGT
* * * *
14938 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTCTGT
1 TTCCCAAAATGCCCCTT-CTGGTCGGAAGGTCCCTGTTTCCTTTATCTGT
14988 TTCCCAAAATGCCCCTTCTCGGTCGGAAGGTC
1 TTCCCAAAATGCCCCTTCT-GGTCGGAAGGTC
15020 TAGTTTTCTC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 1 0.01
50 71 0.97
51 1 0.01
ACGTcount: A:0.16, C:0.30, G:0.20, T:0.35
Consensus pattern (49 bp):
TTCCCAAAATGCCCCTTCTGGTCGGAAGGTCCCTGTTTCCTTTATCTGT
Found at i:27564 original size:33 final size:33
Alignment explanation
Indices: 27527--27606 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
27517 AGCACTTGTG
**
27527 ACCGGCCACGCGACTTGGAGATGCCCGTGCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCAAC
* *
27560 ACCGGCCATGCGACTTGGAGATGCCCGACCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCAAC
27593 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
27607 AAGGTCATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.21, C:0.39, G:0.29, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGACCAAC
Done.