Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006770.1 Corchorus capsularis cultivar CVL-1 contig06791, 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: 50184
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:104 original size:26 final size:26
Alignment explanation
Indices: 64--115 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
54 AACACGTTTA
* *
64 AATAAAAATATTTAAATAATTGAAATT
1 AATAAAAATAATTAAAGAATT-AAATT
91 AATAAAAA-AATTAAAGAATTAAATT
1 AATAAAAATAATTAAAGAATTAAATT
116 GTTATATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 10 0.43
27 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AATAAAAATAATTAAAGAATTAAATT
Found at i:1609 original size:37 final size:37
Alignment explanation
Indices: 1578--1653 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
1568 GTTGGAGATT
*
1578 AAGACAAAAAGTAAAATTAAATACAACGTTGGAAACA
1 AAGACAAAAAGAAAAATTAAATACAACGTTGGAAACA
* * **
1615 AAGATAAAAGGAAAAATTAAATAGGACGTTGGAAACA
1 AAGACAAAAAGAAAAATTAAATACAACGTTGGAAACA
1652 AA
1 AA
1654 AAGCAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.59, C:0.08, G:0.17, T:0.16
Consensus pattern (37 bp):
AAGACAAAAAGAAAAATTAAATACAACGTTGGAAACA
Found at i:1662 original size:31 final size:31
Alignment explanation
Indices: 1581--1663 Score: 76
Period size: 37 Copynumber: 2.5 Consensus size: 31
1571 GGAGATTAAG
*
1581 ACAAAAAGTAAAATTAAATACAACGTTGGAA
1 ACAAAAAGAAAAATTAAATACAACGTTGGAA
**
1612 ACAAAGATAAAAGGAAAAATTAAATAGGACGTTGGAA
1 AC----A-AAAA-GAAAAATTAAATACAACGTTGGAA
*
1649 ACAAAAAGCAAAATT
1 ACAAAAAGAAAAATT
1664 GACGTTCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
31 9 0.21
32 4 0.10
33 1 0.02
35 1 0.02
36 4 0.10
37 23 0.55
ACGTcount: A:0.59, C:0.08, G:0.16, T:0.17
Consensus pattern (31 bp):
ACAAAAAGAAAAATTAAATACAACGTTGGAA
Found at i:1821 original size:30 final size:32
Alignment explanation
Indices: 1775--1840 Score: 109
Period size: 30 Copynumber: 2.1 Consensus size: 32
1765 TGGCAATTTA
*
1775 GAAATATGGTTTTTTAAAAAAGGGTATAATCG
1 GAAATATGGTTTTTTAAAAAAGGGTACAATCG
1807 GAAATAT-G-TTTTTAAAAAAGGGTACAATCG
1 GAAATATGGTTTTTTAAAAAAGGGTACAATCG
1837 GAAA
1 GAAA
1841 ACATAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 25 0.76
31 1 0.03
32 7 0.21
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (32 bp):
GAAATATGGTTTTTTAAAAAAGGGTACAATCG
Found at i:1876 original size:2 final size:2
Alignment explanation
Indices: 1869--1913 Score: 63
Period size: 2 Copynumber: 21.0 Consensus size: 2
1859 TTCGTACTTT
1869 TA TA TA TA GTA TA GTA TA GTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
1912 TA
1 TA
1914 AAGAATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 34 0.85
3 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3766 original size:30 final size:32
Alignment explanation
Indices: 3707--3768 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
3697 GGGGAAACTT
* *
3707 TATATTTTCCGATTGTATCATTATTTTTAAAA
1 TATATTTTCCAATTGTACCATTATTTTTAAAA
*
3739 TATA-TTTCCAATTGTACCCTT-TTTTTAAAA
1 TATATTTTCCAATTGTACCATTATTTTTAAAA
3769 AAAAAACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 14 0.52
32 4 0.15
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.52
Consensus pattern (32 bp):
TATATTTTCCAATTGTACCATTATTTTTAAAA
Found at i:5046 original size:24 final size:24
Alignment explanation
Indices: 4984--5054 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
4974 TCAAAATTCC
4984 ATAGTGTGGTTACCAAAATTTCAT
1 ATAGTGTGGTTACCAAAATTTCAT
** *
5008 AT-G-GAAGTTATCAAAATTTCAT
1 ATAGTGTGGTTACCAAAATTTCAT
5030 ATAGTGTGGTTACCAAAATTTCAT
1 ATAGTGTGGTTACCAAAATTTCAT
5054 A
1 A
5055 GGATTAGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 18 0.46
23 2 0.05
24 19 0.49
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (24 bp):
ATAGTGTGGTTACCAAAATTTCAT
Found at i:5086 original size:46 final size:44
Alignment explanation
Indices: 4956--5102 Score: 156
Period size: 46 Copynumber: 3.2 Consensus size: 44
4946 TGGTTATTAT
* *
4956 AATTTCATGAGG-AGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCAT-AGGAAGGTTATCAAAATTTCTTAGTGTGGTTACCAA
5000 AATTTCATATGGAA-GTTATCAAAATTTCATATAGTGTGGTTACCAA
1 AATTTCATA-GGAAGGTTATCAAAATTTC-T-TAGTGTGGTTACCAA
* ***
5046 AATTTCATAGGATTAGGTTATTAAAATTTCTTAG-GTTGGTTATTGA
1 AATTTCATAGGA--AGGTTATCAAAATTTCTTAGTG-TGGTTACCAA
5092 AATTTCATAGG
1 AATTTCATAGG
5103 GTGGTTAACT
Statistics
Matches: 89, Mismatches: 6, Indels: 14
0.82 0.06 0.13
Matches are distributed among these distances:
43 1 0.01
44 23 0.26
45 5 0.06
46 45 0.51
47 2 0.02
48 13 0.15
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (44 bp):
AATTTCATAGGAAGGTTATCAAAATTTCTTAGTGTGGTTACCAA
Found at i:5107 original size:22 final size:22
Alignment explanation
Indices: 4924--5109 Score: 119
Period size: 22 Copynumber: 8.3 Consensus size: 22
4914 TCTCTCTATG
* *
4924 TGGTTATTAAAA-TTCTATAAGA
1 TGGTTATTAAAATTTC-ATAGGT
*
4946 TGGTTATTATAATTTCATGAGG-
1 TGGTTATTAAAATTTCAT-AGGT
* * *
4968 AGGTTATCAAAATTCCATA-GT
1 TGGTTATTAAAATTTCATAGGT
**
4989 GTGGTTACCAAAATTTCATATGG-
1 -TGGTTATTAAAATTTCATA-GGT
** * *
5012 AAGTTATCAAAATTTCATATAGT
1 TGGTTATTAAAATTTCATA-GGT
**
5035 GTGGTTACCAAAATTTCATAGGAT
1 -TGGTTATTAAAATTTCATAGG-T
*
5059 TAGGTTATTAAAATTTCTTAGGT
1 T-GGTTATTAAAATTTCATAGGT
* *
5082 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGT
5104 TGGTTA
1 TGGTTA
5110 ACTATCACAA
Statistics
Matches: 131, Mismatches: 23, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 85 0.65
23 9 0.07
24 35 0.27
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGT
Found at i:5170 original size:22 final size:21
Alignment explanation
Indices: 5145--6119 Score: 294
Period size: 22 Copynumber: 44.8 Consensus size: 21
5135 ATCAAAGAGA
*
5145 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
**
5167 TTAT-AAGAATTTCATAGTGTTG
1 TTATCAA-AATTTCATAG-GAGG
*
5189 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
5211 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* ***
5233 TTATCAAAATTTTATAGTGTTA
1 TTATCAAAATTTCATAG-GAGG
*
5255 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
5277 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
5302 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
5324 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
5344 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
*
5370 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGG-AGG
**
5391 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
5413 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
5435 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
5457 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
5479 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
5501 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGGA-GG
*
5523 TTA-CCAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* * *
5540 TTATTAAACTTTTATTATGGA-G
1 TTATCAAAATTTCA-TA-GGAGG
* * *
5562 TAATCAGAATTT--TAGGGATG
1 TTATCAAAATTTCATA-GGAGG
* * *
5582 ATATTAAAATTTCA-GGGAGG
1 TTATCAAAATTTCATAGGAGG
* *
5602 ATATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG--GAGG
* **
5624 TTTTCAAAATTTCATAATAGGG
1 TTATCAAAATTTCATAGGA-GG
*
5646 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATA-GGAGG
* *
5668 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCAT-AGGAGG
**
5690 TTATCAAAAAAATCATATGGAGG
1 TTATC-AAAATTTCATA-GGAGG
*
5713 TTATCAAAA-TT--T-GTA-G
1 TTATCAAAATTTCATAGGAGG
* * *
5729 TTATCAAGATTTCATAAGAAAG
1 TTATCAAAATTTCAT-AGGAGG
*
5751 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
5773 TTTATCAAAATTTTATAGGAAGAT
1 -TTATCAAAATTTCATAGG-AG-G
*
5797 TTATCAAAATTTTATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
5819 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
* * * *
5841 TTATCAAAATTTCAGACTGTGA
1 TTATCAAAATTTCATA-GGAGG
*
5863 TTA-CTAACAA-TTCATATGTAGG
1 TTATC-AA-AATTTCATA-GGAGG
* * * * *
5885 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
5907 TTATTAATATATCATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
5929 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-G-AGG
* * *
5952 TTATCAAAATTTCGTTGGGAAG
1 TTATCAAAATTTC-ATAGGAGG
*
5974 TTATCAAAATTTCATATTGAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
5996 TCT-TCAAAA-TTCCTTGGTGG
1 T-TATCAAAATTTCATAGGAGG
* * *
6016 TTAACAAAATTTCGTAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
** **
6038 TTAAAAAAAATTT-ATAAAAAGG
1 TT-ATCAAAATTTCAT-AGGAGG
* * * **
6060 TTCTCAAAATTCCATAGTATCA
1 TTATCAAAATTTCATAGGA-GG
*
6082 TTATTAAAATTTCATAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
6104 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
6120 ATGGGATCAT
Statistics
Matches: 700, Mismatches: 172, Indels: 162
0.68 0.17 0.16
Matches are distributed among these distances:
16 9 0.01
17 12 0.02
18 3 0.00
19 11 0.02
20 55 0.08
21 61 0.09
22 409 0.58
23 101 0.14
24 10 0.01
25 16 0.02
26 2 0.00
27 2 0.00
28 9 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:5598 original size:20 final size:20
Alignment explanation
Indices: 5564--5615 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
5554 TTATGGAGTA
* * *
5564 ATCAGAATTTTAGGGATGAT
1 ATCAAAATTTCAGGGAGGAT
*
5584 ATTAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
5604 ATCAAAATTTCA
1 ATCAAAATTTCA
5616 TAGTTTAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:5721 original size:45 final size:44
Alignment explanation
Indices: 5627--5724 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
5617 AGTTTAGTTT
**
5627 TCAAAATTTCATAATAGGGTTATCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAATAGGGTTATCAAAAAATCATAGGGAGATTA
* * *
5671 ACAAAATTTCATAAT-GAGGTTATCAAAAAAATCATATGGAGGTTA
1 TCAAAATTTCATAATAG-GGTTATC-AAAAAATCATAGGGAGATTA
5716 TCAAAATTT
1 TCAAAATTT
5725 GTAGTTATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.02
44 21 0.46
45 24 0.52
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (44 bp):
TCAAAATTTCATAATAGGGTTATCAAAAAATCATAGGGAGATTA
Found at i:5781 original size:23 final size:23
Alignment explanation
Indices: 5751--5852 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
5741 CATAAGAAAG
5751 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
5774 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
*
5797 TTATCAAAATTTTATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * * *
5819 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
5841 TTATCAAAATTT
1 TTATCAAAATTT
5853 CAGACTGTGA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 1 0.01
22 27 0.40
23 40 0.59
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:18323 original size:2 final size:2
Alignment explanation
Indices: 18307--18371 Score: 53
Period size: 2 Copynumber: 33.0 Consensus size: 2
18297 CTAAAGCAAG
* * * *
18307 TA TA -A TA TA -A TA TA TA TA TA TA TA TG TG TG TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
18347 TA TA TA TA TT TGA GA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA
18372 GCATATGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (2 bp):
TA
Found at i:19410 original size:12 final size:12
Alignment explanation
Indices: 19393--19425 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19383 TCCTTCCAAC
*
19393 TATTATTTTTTT
1 TATTATTTATTT
19405 TATTATTTATTT
1 TATTATTTATTT
19417 TATT-TTTAT
1 TATTATTTAT
19426 AATAAGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:21736 original size:5 final size:5
Alignment explanation
Indices: 21726--21764 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
21716 CATGCAACAA
*
21726 AAAAG AAAAG AAAAG AAAAG AACAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
21765 AAGAAGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:21771 original size:15 final size:14
Alignment explanation
Indices: 21726--21772 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
21716 CATGCAACAA
21726 AAAAGAAAAGAAAAG
1 AAAAGAAAA-AAAAG
*
21741 AAAAGAACAGAAAAG
1 AAAAGAA-AAAAAAG
21756 AAAAGAAAAAAGAAG
1 AAAAGAAAAAA-AAG
21771 AA
1 AA
21773 TAAAAGAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 3 0.11
15 24 0.86
16 1 0.04
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:23926 original size:31 final size:31
Alignment explanation
Indices: 23885--23950 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
23875 GACTTCAAGG
*
23885 GACTGATTTGAGCCGATTTTGCAATGTTAGA
1 GACTGATTTGAGCCGATTTTACAATGTTAGA
* *
23916 GACTGGTTTGAGCCGATTTTACAATGTTAGG
1 GACTGATTTGAGCCGATTTTACAATGTTAGA
23947 GACT
1 GACT
23951 TAATTAACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (31 bp):
GACTGATTTGAGCCGATTTTACAATGTTAGA
Found at i:25017 original size:26 final size:26
Alignment explanation
Indices: 24965--25016 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
24955 CACTTTTCAA
24965 TACATATTTTTTTTAAAAATAAATTT
1 TACATATTTTTTTTAAAAATAAATTT
* *
24991 TACA-ATTTTTTTTATAAATAATTTT
1 TACATATTTTTTTTAAAAATAAATTT
25016 T
1 T
25017 TTTGAGAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
TACATATTTTTTTTAAAAATAAATTT
Found at i:26229 original size:197 final size:198
Alignment explanation
Indices: 25851--26372 Score: 663
Period size: 197 Copynumber: 2.6 Consensus size: 198
25841 AAATAACTTT
* * * *
25851 ATATAATTTTTCTTATAGGATTTTTATAGAATACACTTTTCAGTGTAAATTTTGGATTCCATAAG
1 ATATAATTTTTCTTATAAGATTATTATACAATACA-TTATCAGTGTAAATTTTGGATTCCATAAG
* *
25916 CGGGTTAAGAAGTTGACACATACCCCATTTAATAATCAATTAAATATTTAATATTAATACATATT
65 CGGGTTAAGAAGTTGACACATACCCCATTTTATAATAAATTAAATATTTAATATTAATACATATT
* * * * *
25981 CCTTAAGGGGACATATGTCAACCCTTAAACATTGCACGTGCAGTATGCTAAA-CGACTGGCAG-T
130 CCCTAAGGGAACACATGTCAACCCTTAAACATCGCACGTGCAGTATGCTAAACCGACTGAC-GTT
*
26044 GTATA
194 GCATA
* *
26049 GTATAATTTTTCTTATAAGATTATTATACAATCCATTATCAGTGTAAATTTTGGATTCCATAAGC
1 ATATAATTTTTCTTATAAGATTATTATACAATACATTATCAGTGTAAATTTTGGATTCCATAAGC
* * * *
26114 GGGTTAAGAAGTTGACATATACCCCATTTTATAATTAATTACATATTTAATATTAATATATATTC
66 GGGTTAAGAAGTTGACACATACCCCATTTTATAATAAATTAAATATTTAATATTAATACATATTC
* * * * * * *
26179 CCTAAGGGAACACATGTCAACCTTTAAACCTCGCATGTTCAGTCTGCTAAACTCTACTTACGTTG
131 CCTAAGGGAACACATGTCAACCCTTAAACATCGCACGTGCAGTATGCTAAAC-CGACTGACGTTG
26244 CATA
195 CATA
* * * * * * *
26248 ATATAATTTTTCTTATATGATTATTATACAATAAACTGTCAGTGTAAATTTTGGACTCGATGAGC
1 ATATAATTTTTCTTATAAGATTATTATACAATACATTATCAGTGTAAATTTTGGATTCCATAAGC
* * * *
26313 GAGTTAAGAAGTTGACACATACCTCATTTCT-TAACAAAATAAATATTTAATATTAATACA
66 GGGTTAAGAAGTTGACACATACCCCATTT-TATAATAAATTAAATATTTAATATTAATACA
26373 ATTATACCTC
Statistics
Matches: 279, Mismatches: 41, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
197 131 0.47
198 31 0.11
199 116 0.42
200 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (198 bp):
ATATAATTTTTCTTATAAGATTATTATACAATACATTATCAGTGTAAATTTTGGATTCCATAAGC
GGGTTAAGAAGTTGACACATACCCCATTTTATAATAAATTAAATATTTAATATTAATACATATTC
CCTAAGGGAACACATGTCAACCCTTAAACATCGCACGTGCAGTATGCTAAACCGACTGACGTTGC
ATA
Found at i:28479 original size:28 final size:28
Alignment explanation
Indices: 28435--28490 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
28425 TAAGTAAATA
*
28435 CTCCCTCTGTTCCTTTTTAATTGTCCCT
1 CTCCCTCTATTCCTTTTTAATTGTCCCT
28463 CTCCCT-TATTCCTTTTTAATTGTCCCT
1 CTCCCTCTATTCCTTTTTAATTGTCCCT
28490 C
1 C
28491 ATTTTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.09, C:0.36, G:0.05, T:0.50
Consensus pattern (28 bp):
CTCCCTCTATTCCTTTTTAATTGTCCCT
Found at i:30704 original size:31 final size:32
Alignment explanation
Indices: 30664--30737 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
30654 TTGTCTGACA
* *
30664 TGGCCTTGCCATGTGACATTTTT-GTCCAACG
1 TGGCATTGCCATGCGACATTTTTGGTCCAACG
* *
30695 TGGCATTGCCATGCGGCATTTTTGGTCCGACG
1 TGGCATTGCCATGCGACATTTTTGGTCCAACG
*
30727 TGACATTGCCA
1 TGGCATTGCCA
30738 CGTCAACAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 20 0.54
32 17 0.46
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (32 bp):
TGGCATTGCCATGCGACATTTTTGGTCCAACG
Found at i:30734 original size:32 final size:31
Alignment explanation
Indices: 30669--30737 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
30659 TGACATGGCC
* *
30669 TTGCCATGTGACATTTTTGTCCAACGTGGCA
1 TTGCCATGCGACATTTTTGTCCAACGTGACA
* *
30700 TTGCCATGCGGCATTTTTGGTCCGACGTGACA
1 TTGCCATGCGACATTTTT-GTCCAACGTGACA
30732 TTGCCA
1 TTGCCA
30738 CGTCAACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (31 bp):
TTGCCATGCGACATTTTTGTCCAACGTGACA
Found at i:31711 original size:3 final size:3
Alignment explanation
Indices: 31703--31728 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31693 AAAATCCTAC
31703 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
31729 CAAAATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:38094 original size:10 final size:11
Alignment explanation
Indices: 38077--38108 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
38067 AAACAACAGA
38077 ATTTTTATTTT
1 ATTTTTATTTT
38088 A-TTTTATTTT
1 ATTTTTATTTT
38098 ATTTTTATTTT
1 ATTTTTATTTT
38109 TTTGTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:38109 original size:6 final size:5
Alignment explanation
Indices: 38079--38108 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
38069 ACAACAGAAT
38079 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
38109 TTTGTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:38365 original size:20 final size:22
Alignment explanation
Indices: 38328--38373 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
38318 GGTACGTTTC
38328 TTTCTTTCTTCATCTTTTTCTT
1 TTTCTTTCTTCATCTTTTTCTT
*
38350 TTTCTTTC-TC-TGTTTTTCTT
1 TTTCTTTCTTCATCTTTTTCTT
38370 TTTC
1 TTTC
38374 CACAACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
21 2 0.09
22 8 0.35
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTCTTTCTTCATCTTTTTCTT
Done.