Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013451.1 Corchorus capsularis cultivar CVL-1 contig13472, 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: 50049
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7136 original size:6 final size:6
Alignment explanation
Indices: 7120--7166 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
7110 AAAACAAAGC
7120 AAATC- AAATCT AAATCT AAATCT AAAATCTT AAATCT AAAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT -AAATC-T AAATCT -AAATCT AAA
7167 GCAAGATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.13
6 16 0.42
7 16 0.42
8 1 0.03
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:7149 original size:7 final size:7
Alignment explanation
Indices: 7125--7166 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
7115 AAAGCAAATC
7125 AAATCT-
1 AAATCTA
7131 AAATCT-
1 AAATCTA
7137 AAATCTA
1 AAATCTA
*
7144 AAATCTT
1 AAATCTA
7151 AAATCTA
1 AAATCTA
7158 AAATCTA
1 AAATCTA
7165 AA
1 AA
7167 GCAAGATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATCTA
Found at i:7179 original size:13 final size:13
Alignment explanation
Indices: 7163--7197 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
7153 ATCTAAAATC
7163 TAAAGCAAGA-TAA
1 TAAAGCAA-ATTAA
7176 TAAAGCAAATTAA
1 TAAAGCAAATTAA
7189 TAAAGCAAA
1 TAAAGCAAA
7198 CAATAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:10409 original size:23 final size:22
Alignment explanation
Indices: 10338--10409 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
10328 GTGGTGGCGC
*
10338 GGCATGGTGCGCGG-ATGGCTT
1 GGCATGGTGCGCGGCATGGCTG
* *
10359 GGCAAGG-GC-CGGGCATGGCGG
1 GGCATGGTGCGC-GGCATGGCTG
*
10380 GGCATGGTGCGCGGACATAGCTG
1 GGCATGGTGCGCGG-CATGGCTG
10403 GGCATGG
1 GGCATGG
10410 CTTGGTGATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.03
20 4 0.10
21 17 0.43
22 4 0.10
23 14 0.35
ACGTcount: A:0.14, C:0.21, G:0.50, T:0.15
Consensus pattern (22 bp):
GGCATGGTGCGCGGCATGGCTG
Found at i:13965 original size:15 final size:15
Alignment explanation
Indices: 13947--13992 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
13937 CTAATCTCTC
13947 TTCACTTTTTCTCAA
1 TTCACTTTTTCTCAA
**
13962 TTCACTTTTTCTCTC
1 TTCACTTTTTCTCAA
13977 TTCACTTTTTCTCAA
1 TTCACTTTTTCTCAA
13992 T
1 T
13993 AGCTAGGGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCACTTTTTCTCAA
Found at i:14193 original size:7 final size:7
Alignment explanation
Indices: 14175--14210 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
14165 AAAGCAAAGC
14175 AAATCT-
1 AAATCTA
14181 AAATCTA
1 AAATCTA
*
14188 AAATCTT
1 AAATCTA
14195 AAATCTA
1 AAATCTA
14202 AAATCTA
1 AAATCTA
14209 AA
1 AA
14211 GCAAGATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATCTA
Found at i:14223 original size:13 final size:13
Alignment explanation
Indices: 14207--14241 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
14197 ATCTAAAATC
14207 TAAAGCAAGA-TAA
1 TAAAGCAA-ATTAA
14220 TAAAGCAAATTAA
1 TAAAGCAAATTAA
14233 TAAAGCAAA
1 TAAAGCAAA
14242 CAATAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:15166 original size:10 final size:10
Alignment explanation
Indices: 15151--15175 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15141 GAGGACTCTA
15151 GAATTTTCTG
1 GAATTTTCTG
15161 GAATTTTCTG
1 GAATTTTCTG
15171 GAATT
1 GAATT
15176 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:18211 original size:33 final size:33
Alignment explanation
Indices: 18168--18248 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
18158 CGAGTGACCA
*
18168 GCCATGCGACTTGGAGAAGCCC-GACCAACACCG
1 GCCACGCGACTTGGAGAAGCCCAG-CCAACACCG
* * * *
18201 GCCACGCGACTCGAAGATGCCCAGCCATCACCG
1 GCCACGCGACTTGGAGAAGCCCAGCCAACACCG
*
18234 GCCACGCGACATGGA
1 GCCACGCGACTTGGA
18249 CATGTCCGGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 38 0.97
34 1 0.03
ACGTcount: A:0.26, C:0.38, G:0.27, T:0.09
Consensus pattern (33 bp):
GCCACGCGACTTGGAGAAGCCCAGCCAACACCG
Found at i:23890 original size:23 final size:23
Alignment explanation
Indices: 23846--23895 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
23836 CGAGTGACCG
* * *
23846 GCCATGCGACTTGGAGAAGCCCA
1 GCCACGCGACTCGAAGAAGCCCA
* *
23869 GCCACGCGACTCGAAGATGCCCG
1 GCCACGCGACTCGAAGAAGCCCA
23892 GCCA
1 GCCA
23896 TCACCGGCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.36, G:0.30, T:0.10
Consensus pattern (23 bp):
GCCACGCGACTCGAAGAAGCCCA
Found at i:27367 original size:11 final size:11
Alignment explanation
Indices: 27351--27375 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27341 TAATTCTTTT
27351 GTGTGTATTCA
1 GTGTGTATTCA
27362 GTGTGTATTCA
1 GTGTGTATTCA
27373 GTG
1 GTG
27376 AAGAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (11 bp):
GTGTGTATTCA
Found at i:29602 original size:13 final size:13
Alignment explanation
Indices: 29584--29613 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
29574 TGGACCAATT
29584 AGAATGCACATGG
1 AGAATGCACATGG
29597 AGAATGCACATGG
1 AGAATGCACATGG
29610 AGAA
1 AGAA
29614 AATGACCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.13
Consensus pattern (13 bp):
AGAATGCACATGG
Found at i:34693 original size:18 final size:19
Alignment explanation
Indices: 34658--34702 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
34648 ATTTTCTTCT
34658 TTTATTTAGCTATCATCTA
1 TTTATTTAGCTATCATCTA
*
34677 TTTATTTA-CTATTATCTA
1 TTTATTTAGCTATCATCTA
34695 TTTATTTA
1 TTTATTTA
34703 TTTATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTATTTAGCTATCATCTA
Found at i:34732 original size:4 final size:4
Alignment explanation
Indices: 34675--34713 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
34665 AGCTATCATC
*
34675 TATT TATT TACTAT TATC TATT TATT TATT TATT TATT T
1 TATT TATT TA-T-T TATT TATT TATT TATT TATT TATT T
34714 TTACCTACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 26 0.84
5 2 0.06
6 3 0.10
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:38152 original size:20 final size:22
Alignment explanation
Indices: 38116--38155 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
38106 CTATTCGGAC
38116 TCGACTCGAGAAAAATTCGAGT
1 TCGACTCGAGAAAAATTCGAGT
38138 TCGACTCG-G-AAAATTCGA
1 TCGACTCGAGAAAAATTCGA
38156 ACCGAGCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (22 bp):
TCGACTCGAGAAAAATTCGAGT
Found at i:43401 original size:2 final size:2
Alignment explanation
Indices: 43389--43429 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
43379 CTAATTGTAT
43389 TA TA T- TA TA TA TA TA TA TA TA TA -A TA TA TA T- 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
43428 TA
1 TA
43430 AAAGAGATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46716 original size:22 final size:22
Alignment explanation
Indices: 46691--46973 Score: 102
Period size: 22 Copynumber: 13.0 Consensus size: 22
46681 GAATTGTTAG
*
46691 TAATCACACTTTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* **
46713 TAATCACACTATAAAATTGCGA
1 TAATCACACTATGAAATTTTGA
* * *
46735 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
46757 TAAATCTTC-TTATAAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * * *
46780 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
** * *
46803 TAACTTTC-TTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
46824 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
46841 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
46863 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
46885 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
46907 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* *
46929 TAA-CCCTCTTATGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
46951 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
46973 T
1 T
46974 TACTCCATAA
Statistics
Matches: 194, Mismatches: 50, Indels: 33
0.70 0.18 0.12
Matches are distributed among these distances:
16 7 0.04
17 2 0.01
18 1 0.01
19 2 0.01
21 8 0.04
22 135 0.70
23 37 0.19
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:46773 original size:45 final size:45
Alignment explanation
Indices: 46722--46819 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
46712 ATAATCACAC
* *
46722 TATAAAATTGCGAT-AACCTCGCTATGAAATTTTGATAAATCTTCT
1 TATAAAATTGCGATAAACCTCCCTATAAAATTTTGATAAAT-TTCT
** *
46767 TATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCT
1 TATAAAATTGCGATAAACCTCCCTATAAAATTTTGATAAATTTCT
*
46812 TATGAAAT
1 TATAAAAT
46820 CTTGATAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 23 0.50
46 23 0.50
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (45 bp):
TATAAAATTGCGATAAACCTCCCTATAAAATTTTGATAAATTTCT
Found at i:46775 original size:23 final size:23
Alignment explanation
Indices: 46748--46827 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
46738 CCTCGCTATG
46748 AAATTTTGATAAATCTTCTTATA
1 AAATTTTGATAAATCTTCTTATA
* * *
46771 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCTTATA
* *
46794 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCTTATA
*
46816 AAATCTTGATAA
1 AAATTTTGATAA
46828 CTACAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 16 0.33
23 32 0.67
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCTTATA
Found at i:46920 original size:44 final size:43
Alignment explanation
Indices: 46832--46979 Score: 133
Period size: 44 Copynumber: 3.4 Consensus size: 43
46822 TGATAACTAC
** * * *
46832 AAATTTTGATAACCTCCCTATGATTTTTTGAT-AACCTCATTATG
1 AAATTTTGATAA-CTCCCTATGAAATTTTGATCTACAT-ACTATG
*
46876 AAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACTATG
1 AAATTTTGATAA-CTCCCTATGAAATTTTGATCTACATACTATG
*
46920 AAATTTTGATAAC-CCTCTTATGAAATTTTGAAAACTA-A-ACTATG
1 AAATTTTGATAACTCC-C-TATGAAATTTTG--ATCTACATACTATG
*
46964 AAATTTTGATTACTCC
1 AAATTTTGATAACTCC
46980 ATAATAAAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 74 0.84
45 6 0.07
46 4 0.05
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (43 bp):
AAATTTTGATAACTCCCTATGAAATTTTGATCTACATACTATG
Found at i:46921 original size:104 final size:106
Alignment explanation
Indices: 46733--46932 Score: 246
Period size: 104 Copynumber: 1.9 Consensus size: 106
46723 ATAAAATTGC
* *
46733 GATAACCTCGCTATGAAATTTTGATAAATCTTCTTATAAAATTTTGATAAACCTCCCTATAAAAT
1 GATAACCTCCCTATGAAATTTTGATAAATCCTCTTATAAAATTTTGATAAACCTCCCTATAAAAT
* *
46798 TTTGATAACTTTCTTATGAAATCTTGATAACTACAAATTTT
66 TTTGATAACATACTTATGAAATCTTGATAACTACAAATTTT
** * * * *
46839 GATAACCTCCCTATGATTTTTTGAT-AA-CCTCATTATGAAATTTTG-TTAATCTCCCTATGAAA
1 GATAACCTCCCTATGAAATTTTGATAAATCCTC-TTATAAAATTTTGATAAACCTCCCTATAAAA
* *
46901 TTTTGATCTACATAC-TATGAAATTTTGATAAC
65 TTTTGAT-AACATACTTATGAAATCTTGATAAC
46933 CCTCTTATGA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
104 40 0.50
105 18 0.22
106 22 0.28
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (106 bp):
GATAACCTCCCTATGAAATTTTGATAAATCCTCTTATAAAATTTTGATAAACCTCCCTATAAAAT
TTTGATAACATACTTATGAAATCTTGATAACTACAAATTTT
Found at i:47103 original size:22 final size:22
Alignment explanation
Indices: 47071--47317 Score: 125
Period size: 22 Copynumber: 11.3 Consensus size: 22
47061 ATTATTGTTT
*
47071 TGAAAATTTGATAATCTCTTTA
1 TGAAATTTTGATAATCTCTTTA
* *
47093 TGAAATCTTGATAACCTCTTTA
1 TGAAATTTTGATAATCTCTTTA
* * * * * *
47115 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCTCTTTA
* * *
47137 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAATCTCTTTA
* *
47159 TGTAATTTTGATAATCTCGCTT-
1 TGAAATTTTGATAATCTC-TTTA
* **
47181 TGAAATTTTGATAA-CAGCACTA
1 TGAAATTTTGATAATC-TCTTTA
*
47203 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAATCTCT-TTA
* *
47225 T-AAATTTTGATAATTTGATCTCTA
1 TGAAATTTTGATAA--T-CTCTTTA
* * *
47249 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAATCTCTTTA
*
47271 TGAGA-TTTGATAA-C-CTTCTA
1 TGAAATTTTGATAATCTCTT-TA
* * *
47291 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAATCTCTTTA
47311 TGAAATT
1 TGAAATT
47318 GAGACTTTTA
Statistics
Matches: 173, Mismatches: 39, Indels: 28
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.01
20 16 0.09
21 28 0.16
22 105 0.61
23 5 0.03
24 5 0.03
25 12 0.07
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCTTTA
Found at i:47187 original size:66 final size:65
Alignment explanation
Indices: 47074--47218 Score: 148
Period size: 66 Copynumber: 2.2 Consensus size: 65
47064 ATTGTTTTGA
* * * * * * *
47074 AAATTTGATAATCTCTTTATGAAATCTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATG
1 AAATTTGATAATCACATTATGAAATCTTGATAACCTCCTTATAAAATTTTGATAACACCACTATG
* * * * *
47139 AAATTCTGATAATCACATTATGTAATTTTGATAATCTCGCTT-TGAAATTTTGATAACAGCACTA
1 AAATT-TGATAATCACATTATGAAATCTTGATAACCTC-CTTATAAAATTTTGATAACACCACTA
47203 TG
64 TG
47205 AAATTTTGATAATC
1 AAA-TTTGATAATC
47219 TTCCTATAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
65 5 0.08
66 56 0.86
67 4 0.06
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (65 bp):
AAATTTGATAATCACATTATGAAATCTTGATAACCTCCTTATAAAATTTTGATAACACCACTATG
Found at i:47231 original size:21 final size:22
Alignment explanation
Indices: 47071--47466 Score: 123
Period size: 22 Copynumber: 17.8 Consensus size: 22
47061 ATTATTGTTT
* **
47071 TGAAAATTTGATAATCTCTTTA
1 TGAAATTTTGATAATCTCACTA
* * **
47093 TGAAATCTTGATAACCTCTTTA
1 TGAAATTTTGATAATCTCACTA
* * * * * *
47115 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCTCACTA
* * *
47137 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAATCTCACTA
* * *
47159 TGTAATTTTGATAATCTCGCTT
1 TGAAATTTTGATAATCTCACTA
*
47181 TGAAATTTTGATAA-CAGCACTA
1 TGAAATTTTGATAATC-TCACTA
47203 TGAAATTTTGATAATCTTC-CTA
1 TGAAATTTTGATAATC-TCACTA
* *
47225 T-AAATTTTGATAATTTGATCTCTA
1 TGAAATTTTGATAA--T-CTCACTA
* * *
47249 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAATCTCACTA
* * *
47271 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAATCTCACTA
* *
47291 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAATCTCAC-TA
* *
47311 TGAAATTGAGACTTTTATAACCTTCA-TA
1 TGAAA-T-----TTTGATAATC-TCACTA
* * *
47339 TGATATTTTGATAACCACACTA
1 TGAAATTTTGATAATCTCACTA
* * * *
47361 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAATCTCACTA
*
47383 TGAAATATT-AGTAATCTC-CTAA
1 TGAAATTTTGA-TAATCTCACT-A
* * *
47405 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAATCTCACTA
* * *
47427 TGAAACTCTT-ATAACCTCGCTA
1 TGAAA-TTTTGATAATCTCACTA
* * *
47449 TGACATTTTAATGATCTC
1 TGAAATTTTGATAATCTC
47467 TTTGATAACC
Statistics
Matches: 280, Mismatches: 67, Indels: 54
0.70 0.17 0.13
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 34 0.12
22 188 0.67
23 11 0.04
24 4 0.01
25 11 0.04
26 4 0.01
27 2 0.01
28 7 0.03
29 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCACTA
Found at i:47682 original size:22 final size:23
Alignment explanation
Indices: 47657--47711 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
47647 TGTAATCACA
47657 TTTTGAAAATTT-GATAACCTCT
1 TTTTGAAAATTTCGATAACCTCT
*
47679 TTTTG-GAATTTCGATAACCTCT
1 TTTTGAAAATTTCGATAACCTCT
*
47701 TTAT-AAAATTT
1 TTTTGAAAATTT
47712 TGTTGACCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTTGAAAATTTCGATAACCTCT
Found at i:47946 original size:22 final size:22
Alignment explanation
Indices: 47749--48014 Score: 74
Period size: 22 Copynumber: 11.8 Consensus size: 22
47739 ATAATCACAT
* *
47749 TATGTAATTTTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-A
* *
47771 TTTGAAATTTTGATAACAAC-ACA
1 TATGAAATTTTGATAAC--CTTCA
* *
47794 -ATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTCA
*
47815 TAT-AAATTTTGATAATATGATCTCTC-
1 TATGAAATTTTG---ATA--ACCT-TCA
*
47841 TATGAAATTTCGATAATCAC-TCA
1 TATGAAATTTTGATAA-C-CTTCA
*
47864 -ATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* *
47883 TATCAAATTTTGAT-ACTCTTTA
1 TATGAAATTTTGATAAC-CTTCA
*
47905 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
*
47931 TATGAAATTTTGATAACCAT-A
1 TATGAAATTTTGATAACCTTCA
* * *
47952 CTATAAAATTTTGATAACCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * *
47975 CATGAAATATT-AGTAACC-TCC
1 TATGAAATTTTGA-TAACCTTCA
*
47996 TAATGAAATTTTGTTAACC
1 T-ATGAAATTTTGATAACC
48015 ACATCGAAAA
Statistics
Matches: 182, Mismatches: 31, Indels: 62
0.66 0.11 0.23
Matches are distributed among these distances:
19 1 0.01
20 10 0.05
21 34 0.19
22 94 0.52
23 1 0.01
24 9 0.05
25 1 0.01
26 16 0.09
27 16 0.09
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:48409 original size:22 final size:22
Alignment explanation
Indices: 48384--48441 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
48374 AACACTATGG
48384 AATTTTGATAACC-TCCTCATGA
1 AATTTTGATAACCAT-CTCATGA
* * *
48406 AATTATAATAACCATCTTATGA
1 AATTTTGATAACCATCTCATGA
48428 AATTTTGATAACCA
1 AATTTTGATAACCA
48442 CATAGAGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (22 bp):
AATTTTGATAACCATCTCATGA
Found at i:49826 original size:37 final size:37
Alignment explanation
Indices: 49785--49876 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 37
49775 ATCTAAGCCC
* * *
49785 AAATAGGACGTTGGAGACAAAGACAAAAAG-CTAAATT
1 AAATAGGATGTTGGAAACAAAGA-AAAAAGACAAAATT
** *
49822 AAATACAATGATTGGAAACAAAGATAAAAGACAAAATT
1 AAATAGGATG-TTGGAAACAAAGAAAAAAGACAAAATT
49860 AAATAGGATGTTGGAAA
1 AAATAGGATGTTGGAAA
49877 TAAAAAGGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 19 0.42
38 26 0.58
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (37 bp):
AAATAGGATGTTGGAAACAAAGAAAAAAGACAAAATT
Done.