Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006815.1 Corchorus capsularis cultivar CVL-1 contig06836, 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: 23202
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:3441 original size:29 final size:29
Alignment explanation
Indices: 3402--3478 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
3392 AGTTCCTTAT
3402 AAAAATATTGCATTAATCTGATGCCAAAA
1 AAAAATATTGCATTAATCTGATGCCAAAA
3431 AAAAATATTGCATTAATCTGATGCCAAAA
1 AAAAATATTGCATTAATCTGATGCCAAAA
3460 AAAAATATTGCATTAATCT
1 AAAAATATTGCATTAATCT
3479 AAAAGTTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (29 bp):
AAAAATATTGCATTAATCTGATGCCAAAA
Found at i:3558 original size:2 final size:2
Alignment explanation
Indices: 3551--3584 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3541 AGTAAAGTAA
3551 AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3585 TCTACATATT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3614 original size:20 final size:17
Alignment explanation
Indices: 3592--3625 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3582 TATTCTACAT
3592 ATTATTTTTATAACCAC
1 ATTATTTTTATAACCAC
3609 ATTATTTTTATAACCAC
1 ATTATTTTTATAACCAC
3626 GTGAAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTATTTTTATAACCAC
Found at i:4910 original size:22 final size:22
Alignment explanation
Indices: 4885--5101 Score: 75
Period size: 22 Copynumber: 9.8 Consensus size: 22
4875 ATGATCCCAT
4885 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** **
4907 TATGAAATTTTAATAATGATAT
1 TATGAAATTTTGATAACCTTCC
* * * * **
4929 TATGGAATCTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
4951 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
4973 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
4995 TAAGGAATTTTGA-AGATC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
5017 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
5039 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
5062 TATTGAGATGTTGATAACC-TCC
1 TA-TGAAATTTTGATAACCTTCC
* *
5084 ATATGATATATTGATAAC
1 -TATGAAATTTTGATAAC
5102 AGTAGACACT
Statistics
Matches: 141, Mismatches: 43, Indels: 22
0.68 0.21 0.11
Matches are distributed among these distances:
21 5 0.04
22 111 0.79
23 11 0.08
24 14 0.10
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:5233 original size:26 final size:26
Alignment explanation
Indices: 5170--5248 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
5160 GGCATTAGGG
*
5170 TCAC-CTAGGGGGCATTTTGGTCATCT
1 TCACACTAAGGGGCATTTTGGTCAT-T
*
5196 TTACACTAA-GGGCATTTTGGTCATT
1 TCACACTAAGGGGCATTTTGGTCATT
* * *
5221 TGCACATTCAGGGGCATTTTAGTCATT
1 T-CACACTAAGGGGCATTTTGGTCATT
5248 T
1 T
5249 TAAGTCCAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.05
26 23 0.52
27 19 0.43
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (26 bp):
TCACACTAAGGGGCATTTTGGTCATT
Found at i:7948 original size:2 final size:2
Alignment explanation
Indices: 7912--7938 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7902 CTTGAATCGG
7912 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
7939 TCATTCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10484 original size:23 final size:23
Alignment explanation
Indices: 10453--10537 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
10443 GATAACCTGA
*
10453 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
10476 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
10499 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* *
10521 TTATAAAATCTTGATAA
1 CTATAAAATTTTGATAA
10538 CTACAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 17 0.31
23 37 0.69
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:10593 original size:22 final size:22
Alignment explanation
Indices: 10434--10660 Score: 87
Period size: 22 Copynumber: 10.5 Consensus size: 22
10424 AATCACACTC
* * *
10434 TGAAATTGTGATAACCTGACTA
1 TGAAATTTTGATAACCTCATTA
* *
10456 TGAAATTTTGATAAATCTTC-CTA
1 TGAAATTTTGAT-AA-CCTCATTA
* **
10479 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCATTA
* *
10502 TAAAATTTTGATAACTTTC-TTA
1 TGAAATTTTGATAAC-CTCATTA
* *
10524 TAAAATCTTGATAA---C--TA
1 TGAAATTTTGATAACCTCATTA
* *
10541 -CAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCATTA
**
10562 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCATTA
* * * **
10584 TGAAAATTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCTCATTA
* * *
10606 TGAAATTTTGATCTACAT-ACTA
1 TGAAATTTTGAT-AACCTCATTA
*
10628 TGAAATTTTGGTAAACCTC-TTA
1 TGAAATTTTGAT-AACCTCATTA
* *
10650 TAAAAATTTGA
1 TGAAATTTTGA
10661 AAACTAAACT
Statistics
Matches: 158, Mismatches: 35, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
19 1 0.01
21 2 0.01
22 101 0.64
23 38 0.24
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCATTA
Found at i:10920 original size:66 final size:65
Alignment explanation
Indices: 10782--10934 Score: 164
Period size: 66 Copynumber: 2.3 Consensus size: 65
10772 CCAGAAATAC
* * * * *
10782 CACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATAAAATTTTGTTGACC
1 CACTATGAAA-TTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGATAACA
*
10847 C
65 A
* * * * *
10848 CTCTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAAC
1 CACTATGAAATTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATAAAATTTTGATAAC
10912 AA
64 AA
10914 CACTATGAAATTTTGTTAATC
1 CACTATGAAATTTTG-TAATC
10935 TTCCTATAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 4 0.06
66 65 0.92
67 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (65 bp):
CACTATGAAATTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGATAACAA
Found at i:10922 original size:22 final size:22
Alignment explanation
Indices: 10782--11001 Score: 108
Period size: 22 Copynumber: 10.0 Consensus size: 22
10772 CCAGAAATAC
10782 CACTATGAAATTTTTG-TAATCA
1 CACTATGAAA-TTTTGATAATCA
* * * * *
10804 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAATCA
** * * * * *
10826 CTTTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAATCA
* *
10848 CTCTATGAAATTCTGATAATCA
1 CACTATGAAATTTTGATAATCA
* * * *
10870 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
* *
10892 CGCTTTGAAATTTTGATAA-CAA
1 CACTATGAAATTTTGATAATC-A
* *
10914 CACTATGAAATTTTGTTAATCTT
1 CACTATGAAATTTTGATAATC-A
10937 C-CTAT-AAATTTTGATAATCTGA
1 CACTATGAAATTTTGATAATC--A
* * *
10959 TCTCTATGAAACTTCGATAATCA
1 -CACTATGAAATTTTGATAATCA
* *
10982 CTCTATGAGA-TTTGATAATC
1 CACTATGAAATTTTGATAATC
11002 TTCTATCAAA
Statistics
Matches: 149, Mismatches: 42, Indels: 15
0.72 0.20 0.07
Matches are distributed among these distances:
21 27 0.18
22 102 0.68
23 4 0.03
24 4 0.03
25 12 0.08
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
CACTATGAAATTTTGATAATCA
Found at i:11135 original size:22 final size:21
Alignment explanation
Indices: 11079--11131 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
11069 CCACATTATA
*
11079 AAATTTTGATAACCTCCCCATG
1 AAATTTTG-TAACCTCCCAATG
* * *
11101 AAACATTAGTAACCTCCTAATG
1 AAA-TTTTGTAACCTCCCAATG
11123 AAATTTTGT
1 AAATTTTGT
11132 TAACTACACT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.17
22 17 0.71
23 3 0.12
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
AAATTTTGTAACCTCCCAATG
Found at i:11247 original size:22 final size:22
Alignment explanation
Indices: 11215--11398 Score: 106
Period size: 22 Copynumber: 8.3 Consensus size: 22
11205 TTGTGATAAT
* *
11215 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
11237 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
11259 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
*
11283 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
** **
11305 TAA-CTTCCATATGAAATTTTGG
1 TAACCAACC-TATGAAATTTTAA
* *
11327 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* **
11349 TAACC-TCCTCATGAAATCATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
11371 TAATCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
11393 TAACCA
1 TAACCA
11399 CATAGAGACA
Statistics
Matches: 128, Mismatches: 25, Indels: 18
0.75 0.15 0.11
Matches are distributed among these distances:
21 5 0.04
22 100 0.78
23 5 0.04
24 18 0.14
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:11287 original size:46 final size:44
Alignment explanation
Indices: 11222--11365 Score: 168
Period size: 44 Copynumber: 3.2 Consensus size: 44
11212 AATTAACCAC
*** * *
11222 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAACCT--T
11268 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-CTT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
*
11311 CCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-T
1 CC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
11355 CCTCATGAAAT
1 CCT-ATGAAAT
11366 CATAATAATC
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
43 4 0.05
44 47 0.53
45 3 0.03
46 33 0.38
47 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
Found at i:11547 original size:6 final size:6
Alignment explanation
Indices: 11536--11567 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
11526 AGTATTGTAC
11536 GTGTTA GTGTTA GTGTTA GTGTTA GTGTTA GT
1 GTGTTA GTGTTA GTGTTA GTGTTA GTGTTA GT
11568 TTAATCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
GTGTTA
Found at i:11619 original size:19 final size:20
Alignment explanation
Indices: 11588--11625 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
11578 TATTGATATT
11588 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
11607 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
11626 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:13637 original size:24 final size:27
Alignment explanation
Indices: 13578--13635 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 27
13568 GGAGACAAAG
13578 ACAAAAAGCAAAATTAAATATTGGAAACTC
1 ACAAAAA-CAAAATTAAATATTGGAAA--C
13608 ACCAAAAA-AAAATTAAATATTGGAAAC
1 A-CAAAAACAAAATTAAATATTGGAAAC
13635 A
1 A
13636 AAGACAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.07
29 18 0.67
30 1 0.04
31 6 0.22
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (27 bp):
ACAAAAACAAAATTAAATATTGGAAAC
Found at i:13833 original size:30 final size:31
Alignment explanation
Indices: 13798--13862 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
13788 TGACAATTTT
* *
13798 GAAATATGTTTTAAAAA-AATGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
13828 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
13859 GAAA
1 GAAA
13863 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:14288 original size:31 final size:32
Alignment explanation
Indices: 14252--14318 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
14242 TGACAATTTA
* *
14252 GAAATATGTTTT--AAAATAAAGGGTACAATTG
1 GAAATATGTTTTAGAAAAT-AAGGATACAATCG
14283 GAAATATGTTTTAGAAAATAAGGATACAATCG
1 GAAATATGTTTTAGAAAATAAGGATACAATCG
14315 GAAA
1 GAAA
14319 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 12 0.38
32 15 0.47
33 5 0.16
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.28
Consensus pattern (32 bp):
GAAATATGTTTTAGAAAATAAGGATACAATCG
Found at i:18429 original size:27 final size:28
Alignment explanation
Indices: 18375--18429 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
18365 ATTAATACAC
*
18375 CTTTCATCCCCTTTTATCTGTCGGTTTT
1 CTTTCATCCCCTTTTATCTGTCAGTTTT
* *
18403 CTTT-ATCCCTTTTTATCTGTCATTTTT
1 CTTTCATCCCCTTTTATCTGTCAGTTTT
18430 GAACATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.09, C:0.25, G:0.07, T:0.58
Consensus pattern (28 bp):
CTTTCATCCCCTTTTATCTGTCAGTTTT
Found at i:20135 original size:60 final size:60
Alignment explanation
Indices: 20068--20279 Score: 245
Period size: 60 Copynumber: 3.7 Consensus size: 60
20058 GCTAATTGCT
* *
20068 CAAATAAGGGCCTAACGTTTGTC-AAAATGCTCGAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * **
20128 CAAATAAGAGTCTAACGTTATCGAAAATGCTCAAAT-A--G---G--C---TAA-TTGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
20176 CAAATAAGGGCCTAACGTTTGTC-AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
20236 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCC
20280 AGTGTCAGTT
Statistics
Matches: 125, Mismatches: 12, Indels: 30
0.75 0.07 0.18
Matches are distributed among these distances:
48 31 0.25
49 8 0.06
51 1 0.01
52 1 0.01
54 2 0.02
56 1 0.01
57 1 0.01
59 12 0.10
60 68 0.54
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:20210 original size:31 final size:30
Alignment explanation
Indices: 20172--20278 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 30
20162 ATAGGCTAAT
20172 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-TCAAAA
* * **
20203 TGCTCAAATAAGGGCCCGATC-TTTT-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTTCAAAA
*
20232 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTTC-AAAA
20263 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
20279 CAGTGTCAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.07
29 16 0.26
30 5 0.08
31 32 0.52
32 4 0.07
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTTCAAAA
Found at i:20251 original size:108 final size:108
Alignment explanation
Indices: 20057--20272 Score: 405
Period size: 108 Copynumber: 2.0 Consensus size: 108
20047 AATTTGGTTC
*
20057 GGCTAATTGCTCAAATAAGGGCCTAACGTTTGTCAAAATGCTCGAATAAGGGCCCGATCTTTTAA
1 GGCTAATTGCTCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAA
*
20122 TTTGGCCAAATAAGAGTCTAACGTTATCGAAAATGCTCAAATA
66 TTTGGCCAAATAAGAGCCTAACGTTATCGAAAATGCTCAAATA
20165 GGCTAATTGCTCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAA
1 GGCTAATTGCTCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAA
*
20230 TTTGGCCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATA
66 TTTGGCCAAATAAGAGCCTAACGTTATCGAAAATGCTCAAATA
20273 AGGGCCCAGT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (108 bp):
GGCTAATTGCTCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAA
TTTGGCCAAATAAGAGCCTAACGTTATCGAAAATGCTCAAATA
Found at i:20344 original size:31 final size:30
Alignment explanation
Indices: 20309--20414 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 30
20299 TGTGAGACAA
*
20309 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT-GCAAAAGTTAG
** *
20340 GCCCTTATTTG-GCCAAATT--AAAAGATCAG
1 GCCCTTATTTGAG-CATTTTGCAAAAG-TTAG
* *
20369 ACCCTTATTTGAGCATTTTGTCAAATGTTAG
1 GCCCTTATTTGAGCATTTTG-CAAAAGTTAG
20400 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
20415 ATTAGCCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.07
29 17 0.29
30 2 0.03
31 32 0.54
32 4 0.07
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTGCAAAAGTTAG
Found at i:20720 original size:20 final size:21
Alignment explanation
Indices: 20685--20730 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
20675 TATTATATTA
*
20685 TTTATCCTATAATGGGTAGTT
1 TTTATCCTAAAATGGGTAGTT
20706 TTTAT-CTAAAATGGGTAGTT
1 TTTATCCTAAAATGGGTAGTT
20726 TTTAT
1 TTTAT
20731 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTATCCTAAAATGGGTAGTT
Found at i:20847 original size:15 final size:15
Alignment explanation
Indices: 20811--20862 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
20801 TTATAATTAG
*
20811 TATAGATGTGTACAA
1 TATATATGTGTACAA
* *
20826 CACATATGTTGTA-AA
1 TATATATG-TGTACAA
*
20841 TATATATGTGTACGA
1 TATATATGTGTACAA
20856 TATATAT
1 TATATAT
20863 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 4 0.14
15 21 0.72
16 4 0.14
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (15 bp):
TATATATGTGTACAA
Found at i:20953 original size:3 final size:3
Alignment explanation
Indices: 20945--20987 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
20935 TTTGAAAAAT
20945 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 A
20988 CCAAACACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21193 original size:2 final size:2
Alignment explanation
Indices: 21186--21225 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
21176 GTTTAGAATG
* *
21186 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TT 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
21226 AGTACTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:22099 original size:32 final size:31
Alignment explanation
Indices: 22058--22122 Score: 121
Period size: 32 Copynumber: 2.1 Consensus size: 31
22048 AGCCATCATC
22058 ATCCACTAGTCAATGCCACGTGACATTTTCAA
1 ATCCACTAGTCAATGCCACGTGAC-TTTTCAA
22090 ATCCACTAGTCAATGCCACGTGACTTTTCAA
1 ATCCACTAGTCAATGCCACGTGACTTTTCAA
22121 AT
1 AT
22123 GACGTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (31 bp):
ATCCACTAGTCAATGCCACGTGACTTTTCAA
Done.