Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009261.1 Corchorus capsularis cultivar CVL-1 contig09282, 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: 29698
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:105 original size:32 final size:33
Alignment explanation
Indices: 64--138 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
54 ATTTTGGTCT
*
64 AGCCGCCCCACCG-GGACGGCCTG-CCGTGGCGA
1 AGCCGCCCCA-CGAGGACGGCCTGCCCATGGCGA
* * *
96 AGCCGCCCCATGAGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCACGAGGACGGCCTGCCCATGGCGA
129 AGCCGCCCCA
1 AGCCGCCCCA
139 GTGGGGAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.03
32 19 0.51
33 17 0.46
ACGTcount: A:0.15, C:0.43, G:0.35, T:0.08
Consensus pattern (33 bp):
AGCCGCCCCACGAGGACGGCCTGCCCATGGCGA
Found at i:177 original size:33 final size:33
Alignment explanation
Indices: 129--216 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
119 CCCATGGTGA
* *
129 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGCTG
* *
162 AGCCTCCCCACTGGGGAGACTCCGCCGTGGCTG
1 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGCTG
*
195 AGCCGT-CCTAGTGGGGAGGCTC
1 AGCC-TCCCCAGTGGGGAGGCTC
217 AGTGTAAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 46 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.34, G:0.39, T:0.16
Consensus pattern (33 bp):
AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGCTG
Found at i:2559 original size:19 final size:19
Alignment explanation
Indices: 2535--2580 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2525 TTTTCTTTAT
2535 AATTAAATAAT-AATAAATA
1 AATTAAA-AATAAATAAATA
* *
2554 AATTAAAATTAAATGAATA
1 AATTAAAAATAAATAAATA
2573 AATTAAAA
1 AATTAAAA
2581 TTAACTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AATTAAAAATAAATAAATA
Found at i:2709 original size:19 final size:20
Alignment explanation
Indices: 2670--2705 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2660 ATTTTTAAGT
2670 AAAAATATAATATATAAATA
1 AAAAATATAATATATAAATA
2690 AAAAAT-TAATAT-TAAA
1 AAAAATATAATATATAAA
2706 ATAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATATAATATATAAATA
Found at i:2809 original size:11 final size:11
Alignment explanation
Indices: 2793--2817 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2783 ACTAAAATCA
2793 CTACCCTAACC
1 CTACCCTAACC
2804 CTACCCTAACC
1 CTACCCTAACC
2815 CTA
1 CTA
2818 TTATATAATA
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:0.28, C:0.52, G:0.00, T:0.20
Consensus pattern (11 bp):
CTACCCTAACC
Found at i:3758 original size:136 final size:136
Alignment explanation
Indices: 3513--4051 Score: 717
Period size: 136 Copynumber: 4.0 Consensus size: 136
3503 ATAGTAATTT
*
3513 TATCCAAGATATGTCAGAAAATCTAACACAATAGCCAATAATTTCAGAGAATATAACCTTATCTC
1 TATCCAAGATATGTCAGAAAATCTAACACAATAGCCAATAATTTCAGAGAATCTAACCTTATCTC
* * * *
3578 AATTCAACCATTGGATTAAAAGTGAGATTCAAATGTGACTGTTAATTTTAATCGTTATCTGTTCC
66 AATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCGTTATCTCTTCC
3643 ACACAA
131 ACACAA
* * * *
3649 TATCCAAGATATGTCAGGAAATCTAACACAATAGCTAATAATTTCAGAAAATCTAATCTTATCTC
1 TATCCAAGATATGTCAGAAAATCTAACACAATAGCCAATAATTTCAGAGAATCTAACCTTATCTC
* *
3714 AATTCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCGTTATCTCTTCC
66 AATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCGTTATCTCTTCC
*
3779 ACATAA
131 ACACAA
* *
3785 TATCCAAGATATGTCGGAAAATCTAACACAATAGCCAATAATTTCAGAGAATCTAACCTTATCTT
1 TATCCAAGATATGTCAGAAAATCTAACACAATAGCCAATAATTTCAGAGAATCTAACCTTATCTC
* * *** *
3850 AATCCAACCATTGGA-TAAAAGTTG-GATTCAAATGTGACCATTGATGAAAAAC-TTATCTCTTC
66 AATCCAACCATTGGATTAAAAG-TGAGATTCAAATGTGACCGTTAATTTGAATCGTTATCTCTTC
3912 CACACAA
130 CACACAA
* * * * * * * *
3919 TATCCAAGATATGTCAGAAAATATAACACAACAGTCAATAAATTGATGATAATTTAACATTATCT
1 TATCCAAGATATGTCAGAAAATCTAACACAATAGCCAATAATTTCA-GAGAATCTAACCTTATCT
* * * * * * *
3984 CAATCCAACCGTTGGATTCAAAGTGAGATTGAAATGTGATCGTT-GTTTGAATCCTTATCTTTTC
65 CAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCGTTATCTCTTC
4048 CACA
130 CACA
4052 AATTGTGTCT
Statistics
Matches: 352, Mismatches: 46, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
134 56 0.16
135 63 0.18
136 233 0.66
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (136 bp):
TATCCAAGATATGTCAGAAAATCTAACACAATAGCCAATAATTTCAGAGAATCTAACCTTATCTC
AATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACCGTTAATTTGAATCGTTATCTCTTCC
ACACAA
Found at i:5427 original size:23 final size:23
Alignment explanation
Indices: 5394--5466 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
5384 TTATTTTGTT
5394 TTTTAAATTTATTTAAGTTGTAA
1 TTTTAAATTTATTTAAGTTGTAA
*
5417 TTTTAACTTTATTTAAGTTGT--
1 TTTTAAATTTATTTAAGTTGTAA
*
5438 TTTTAAATTAATTTAAGTTGTAA
1 TTTTAAATTTATTTAAGTTGTAA
5461 TTTTAA
1 TTTTAA
5467 GTTAAGTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
21 19 0.42
23 26 0.58
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTTAAATTTATTTAAGTTGTAA
Found at i:5443 original size:21 final size:21
Alignment explanation
Indices: 5393--5458 Score: 96
Period size: 21 Copynumber: 3.0 Consensus size: 21
5383 TTTATTTTGT
5393 TTTTTAAATTTATTTAAGTTG
1 TTTTTAAATTTATTTAAGTTG
*
5414 TAATTTTAACTTTATTTAAGTTG
1 T--TTTTAAATTTATTTAAGTTG
*
5437 TTTTTAAATTAATTTAAGTTG
1 TTTTTAAATTTATTTAAGTTG
5458 T
1 T
5459 AATTTTAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
21 20 0.50
23 20 0.50
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (21 bp):
TTTTTAAATTTATTTAAGTTG
Found at i:5658 original size:12 final size:12
Alignment explanation
Indices: 5641--5685 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
5631 ATTATTCAAT
5641 ATATAAATGTAA
1 ATATAAATGTAA
**
5653 ATATAAATCAAA
1 ATATAAATGTAA
5665 ATATAAATTGTGAA
1 ATATAAA-TGT-AA
5679 ATATAAA
1 ATATAAA
5686 AAGGATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 1 0.04
14 9 0.33
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (12 bp):
ATATAAATGTAA
Found at i:5680 original size:26 final size:24
Alignment explanation
Indices: 5636--5701 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
5626 TTGTAATTAT
*
5636 TCAATATATAAATGTAAATATAAA
1 TCAAAATATAAATGTAAATATAAA
5660 TCAAAATATAAATTGTGAAATATAAA
1 TCAAAATATAAA-TGT-AAATATAAA
*
5686 --AAGGATATAAATGTAA
1 TCAA-AATATAAATGTAA
5702 TTAAAGGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 10 0.27
26 9 0.24
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (24 bp):
TCAAAATATAAATGTAAATATAAA
Found at i:9030 original size:68 final size:68
Alignment explanation
Indices: 8951--9086 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
8941 TTCGCATAAA
*
8951 CATCATGCTCAATCTATTGGACCGTTCCCATGCTTTATAGTGCCACTTCCCATCCTCACTGCTTT
1 CATCATGCTCAATCTATTGGACCGTTCCCATGCTTTATAGTGCCACTTCCCATCCTCACCGCTTT
9016 CAT
66 CAT
* * * *
9019 CATCATGCTCAATCTATTGGACTGTTCTCATGCTTTATAGTGCCACTTCTCATCCTCACCGTTTT
1 CATCATGCTCAATCTATTGGACCGTTCCCATGCTTTATAGTGCCACTTCCCATCCTCACCGCTTT
9084 CAT
66 CAT
9087 TAGTAAAAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.38
Consensus pattern (68 bp):
CATCATGCTCAATCTATTGGACCGTTCCCATGCTTTATAGTGCCACTTCCCATCCTCACCGCTTT
CAT
Found at i:9264 original size:13 final size:13
Alignment explanation
Indices: 9246--9270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9236 ACAATACATA
9246 TACATGCTTAGAT
1 TACATGCTTAGAT
9259 TACATGCTTAGA
1 TACATGCTTAGA
9271 AATGGTGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TACATGCTTAGAT
Found at i:9985 original size:2 final size:2
Alignment explanation
Indices: 9980--10024 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
9970 ATTTTGATTG
* * *
9980 TA TA TA TA TA TA TA TA TG TA TA TG TA TA TG 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 TA
10022 TA T
1 TA T
10025 TTTGTAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11272 original size:22 final size:22
Alignment explanation
Indices: 11242--11452 Score: 178
Period size: 22 Copynumber: 9.6 Consensus size: 22
11232 TCTAGCGTAG
*
11242 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* *
11265 AAATTTGATAACCTCATTATG-
1 AAATTTGATAACCACACTATGA
* * *
11286 AAATTTCAATAACCTCCCTATGA
1 AAATTT-GATAACCACACTATGA
11309 AAATTTGATAACCACACTATGA
1 AAATTTGATAACCACACTATGA
* * * *
11331 AATTTTGATAACCTCAGTGTGA
1 AAATTTGATAACCACACTATGA
* * * *
11353 AATTTTGATAATCTCCCTAT-A
1 AAATTTGATAACCACACTATGA
*
11374 AAATTTTGATAATCACACTAT-A
1 AAA-TTTGATAACCACACTATGA
* * *
11396 TAA-TTGGTAACCACACTATAA
1 AAATTTGATAACCACACTATGA
* *
11417 AAATTTTAATAACCACACCATGA
1 AAA-TTTGATAACCACACTATGA
11440 AAATTTGATAACC
1 AAATTTGATAACC
11453 TCTCTATAAG
Statistics
Matches: 153, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
20 14 0.09
21 12 0.08
22 100 0.65
23 27 0.18
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:11289 original size:44 final size:44
Alignment explanation
Indices: 11241--11459 Score: 208
Period size: 44 Copynumber: 5.0 Consensus size: 44
11231 CTCTAGCGTA
* * *
11241 GAAATATTGATAACCACACTGTGAAAATTTGATAACCTCATTAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTAT
** * * *
11285 GAAATTTCAATAACCTCCCTATGAAAATTTGATAACCACACTAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTAT
* * * * * *
11329 GAAATTTTGATAACCTCAGTGTGAAATTTTGATAATCTCCCTAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTAT
* * * * *
11373 AAAATTTTGATAATCACACTAT-ATAA-TTGGTAACCACACTAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTAT
* * * *
11415 AAAAATTTTAATAACCACACCATGAAAATTTGATAACCTCTCTAT
1 -GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTAT
11460 AAGAATGAAA
Statistics
Matches: 137, Mismatches: 35, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
42 12 0.09
43 21 0.15
44 91 0.66
45 13 0.09
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (44 bp):
GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTAT
Found at i:11338 original size:66 final size:65
Alignment explanation
Indices: 11242--11452 Score: 223
Period size: 66 Copynumber: 3.2 Consensus size: 65
11232 TCTAGCGTAG
* * *
11242 AAATATTGATAACCACACTGTGAAAATTTGATAACCTCATTATGAAATTTCAATAACCTCCCTAT
1 AAAT-TTGATAACCACACTATG-AAATTTGATAACCTCACTATGAAATTTTAATAACCTCCCTAT
11307 GA
64 GA
* * * *
11309 AAATTTGATAACCACACTATGAAATTTTGATAACCTCAGTGTGAAATTTTGATAATCTCCCTAT-
1 AAATTTGATAACCACACTATGAAA-TTTGATAACCTCACTATGAAATTTTAATAACCTCCCTATG
11373 A
65 A
* * * * *
11374 AAATTTTGATAATCACACTAT-ATAA-TTGGTAACCACACTATAAAAATTTTAATAACCACACC-
1 AAA-TTTGATAACCACACTATGA-AATTTGATAACCTCACTAT-GAAATTTTAATAACCTC-CCT
11436 ATGA
62 ATGA
11440 AAATTTGATAACC
1 AAATTTGATAACC
11453 TCTCTATAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
64 12 0.10
65 32 0.26
66 74 0.61
67 4 0.03
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (65 bp):
AAATTTGATAACCACACTATGAAATTTGATAACCTCACTATGAAATTTTAATAACCTCCCTATGA
Found at i:11600 original size:26 final size:23
Alignment explanation
Indices: 11571--11630 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
11561 TGATAAGCAT
11571 AAATTTTGATAAATTCCCTCCTTATG
1 AAATTTTGATAAA---CCTCCTTATG
* *
11597 AAATTTTG-TTAACCTTCTTATG
1 AAATTTTGATAAACCTCCTTATG
11619 AAATTTTGATAA
1 AAATTTTGATAA
11631 TCAAACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 17 0.57
23 2 0.07
25 3 0.10
26 8 0.27
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCTTATG
Found at i:11616 original size:22 final size:22
Alignment explanation
Indices: 11591--11823 Score: 134
Period size: 22 Copynumber: 10.6 Consensus size: 22
11581 AAATTCCCTC
*
11591 CTTATGAAATTTTGTTAACCTT
1 CTTATGAAATTTTGATAACCTT
***
11613 CTTATGAAATTTTGATAATCAAA
1 CTTATGAAATTTTGATAA-CCTT
* * **
11636 C-TATAAAATTTCGATAAGTTT
1 CTTATGAAATTTTGATAACCTT
* * * *
11657 CGTATAAAATTTTGCTAACCTC
1 CTTATGAAATTTTGATAACCTT
* * *
11679 CCTAGGAAATTTTGATAATCTT
1 CTTATGAAATTTTGATAACCTT
* * *
11701 TTTATGAAAATTTGGTAACCTT
1 CTTATGAAATTTTGATAACCTT
*
11723 -TGTATGAAATTTTGATAA-CTA
1 CT-TATGAAATTTTGATAACCTT
* * *
11744 CACTATGAAGTTTTGATAATCTT
1 C-TTATGAAATTTTGATAACCTT
* * * *
11767 CATATAAAATTTTGGTAACC-A
1 CTTATGAAATTTTGATAACCTT
* *
11788 CACTATAAAATTTTGATAACCTT
1 C-TTATGAAATTTTGATAACCTT
*
11811 C-TATGTAATTTTG
1 CTTATGAAATTTTG
11824 GTTTGATTGT
Statistics
Matches: 159, Mismatches: 44, Indels: 17
0.72 0.20 0.08
Matches are distributed among these distances:
21 15 0.09
22 138 0.87
23 6 0.04
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (22 bp):
CTTATGAAATTTTGATAACCTT
Found at i:11733 original size:66 final size:66
Alignment explanation
Indices: 11593--11823 Score: 195
Period size: 66 Copynumber: 3.5 Consensus size: 66
11583 ATTCCCTCCT
* * * * * *
11593 TATGAAATTTTGTTAACCTTCTTATGAAATTTTGATAATC-AAACTATAAAATTTCGATAA-GTT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAATCTTAA-TATAAAATTT-GGTAACCTT
11656 TCG
64 TCG
* * * **
11659 TATAAAATTTTGCTAACCTCCCTAGGAAATTTTGATAATCTTTTTATGAAAATTTGGTAACCTTT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAATCTTAATAT-AAAATTTGGTAACCTTT
11724 -G
65 CG
* * * **
11725 TATGAAATTTTGATAA-CTACACTATGAAGTTTTGATAATCTTCATATAAAATTTTGGTAACCAC
1 TATGAAATTTTGATAACCT-CCCTATGAAATTTTGATAATCTTAATATAAAA-TTTGGTAACCTT
*
11789 AC-
64 TCG
* * *
11791 TATAAAATTTTGATAACCT-TCTATGTAATTTTG
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTG
11824 GTTTGATTGT
Statistics
Matches: 134, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
65 17 0.13
66 105 0.78
67 12 0.09
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (66 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAATCTTAATATAAAATTTGGTAACCTTTC
G
Found at i:13225 original size:22 final size:23
Alignment explanation
Indices: 13179--13325 Score: 72
Period size: 22 Copynumber: 6.6 Consensus size: 23
13169 TAGAACAATC
*
13179 TTGATAATCACACTGTGAAAAAT
1 TTGATAATCTCACTGTGAAAAAT
* *
13202 TTGATAACCTCACTGT-TAAAAT
1 TTGATAATCTCACTGTGAAAAAT
* * *
13224 TTGTTAATCTCATTATG--AAAT
1 TTGATAATCTCACTGTGAAAAAT
* * * *
13245 TTCAATAACCTCCCTATG-AAAAT
1 TT-GATAATCTCACTGTGAAAAAT
* * * * **
13268 TTAATAACCACACTATG-AACTT
1 TTGATAATCTCACTGTGAAAAAT
* *
13290 TTGATAATCTCAGTGTG-AAATT
1 TTGATAATCTCACTGTGAAAAAT
*
13312 TTGATAATCACACT
1 TTGATAATCTCACT
13326 ATATAATTGG
Statistics
Matches: 97, Mismatches: 24, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
21 6 0.06
22 71 0.73
23 20 0.21
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (23 bp):
TTGATAATCTCACTGTGAAAAAT
Found at i:13471 original size:22 final size:22
Alignment explanation
Indices: 13411--13471 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
13401 ACCATAATAT
* * *
13411 CCTCTCTATGTAATTTTGATAA
1 CCTCTATATGAAATTTTCATAA
*
13433 CCTCTACAT-AAAGTTTTCATAA
1 CCTCTATATGAAA-TTTTCATAA
13455 CCCTCT-TATGAAATTTT
1 -CCTCTATATGAAATTTT
13472 GTAAACGTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 2 0.06
22 21 0.68
23 8 0.26
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.43
Consensus pattern (22 bp):
CCTCTATATGAAATTTTCATAA
Found at i:13532 original size:26 final size:23
Alignment explanation
Indices: 13503--13562 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
13493 TGATAAGCAT
13503 AAATTTTGATAAATTGCCTCCTTATG
1 AAATTTTGATAAA---CCTCCTTATG
* *
13529 AAATTTTG-TTAACCTTCTTATG
1 AAATTTTGATAAACCTCCTTATG
13551 AAATTTTGATAA
1 AAATTTTGATAA
13563 CCAAACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 17 0.57
23 2 0.07
25 3 0.10
26 8 0.27
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCTTATG
Found at i:13548 original size:22 final size:22
Alignment explanation
Indices: 13523--13643 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
13513 AAATTGCCTC
* *
13523 CTTATGAAATTTTGTTAACCTT
1 CTTATAAAATTTTGATAACCTT
* **
13545 CTTATGAAATTTTGATAACCAAA
1 CTTATAAAATTTTGATAACC-TT
**
13568 C-TATAAAATTTTGATAATTTT
1 CTTATAAAATTTTGATAACCTT
* * *
13589 CGTATAAAATTTTGTTAACCTC
1 CTTATAAAATTTTGATAACCTT
* ** *
13611 CCTAGGAAATTTTGATAATCTT
1 CTTATAAAATTTTGATAACCTT
*
13633 TTTATAAAATT
1 CTTATAAAATT
13644 AAAAATATTA
Statistics
Matches: 75, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
21 1 0.01
22 73 0.97
23 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.45
Consensus pattern (22 bp):
CTTATAAAATTTTGATAACCTT
Found at i:13599 original size:44 final size:44
Alignment explanation
Indices: 13529--13643 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 44
13519 CCTCCTTATG
* * * *
13529 AAATTTTGTTAACCTTCT-TATGAAATTTTGATAACCAAACTATA
1 AAATTTTGATAATCTT-TGTATAAAATTTTGATAACCAAACTAGA
* *** *
13573 AAATTTTGATAAT-TTTCGTATAAAATTTTGTTAACCTCCCTAGG
1 AAATTTTGATAATCTTT-GTATAAAATTTTGATAACCAAACTAGA
*
13617 AAATTTTGATAATCTTTTTATAAAATT
1 AAATTTTGATAATCTTTGTATAAAATT
13644 AAAAATATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 1 0.02
43 2 0.03
44 52 0.90
45 3 0.05
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (44 bp):
AAATTTTGATAATCTTTGTATAAAATTTTGATAACCAAACTAGA
Found at i:13731 original size:14 final size:13
Alignment explanation
Indices: 13712--13745 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
13702 GGCTCTACAC
13712 AAAAAAAATAAAA
1 AAAAAAAATAAAA
13725 TAAAAAAAATAAAA
1 -AAAAAAAATAAAA
13739 AAAAAAA
1 AAAAAAA
13746 CTACTAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAAAAAATAAAA
Found at i:14307 original size:5 final size:5
Alignment explanation
Indices: 14294--14346 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
14284 TATATATATA
* * *
14294 ATAAA ATAAG ATAAG ATAAG GTAAG ATAAG ATATG ATAAG AT-AG ATAAG
1 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG
14343 ATAA
1 ATAA
14347 AATAGTAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
4 4 0.10
5 38 0.90
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (5 bp):
ATAAG
Found at i:18099 original size:15 final size:15
Alignment explanation
Indices: 18079--18109 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18069 TCAATTTGGC
18079 CAAATTACCGCTGCT
1 CAAATTACCGCTGCT
18094 CAAATTACCGCTGCT
1 CAAATTACCGCTGCT
18109 C
1 C
18110 CTTATCGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (15 bp):
CAAATTACCGCTGCT
Found at i:18943 original size:2 final size:2
Alignment explanation
Indices: 18936--19011 Score: 53
Period size: 2 Copynumber: 42.5 Consensus size: 2
18926 GTTTAATAAT
*
18936 TA TA TA TA T- TA T- TA TA TA TA TA -A T- TA TA TA TA TC TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
18973 TA T- TA T- TA TA TA TA TA AA AA TA TA TA TT TA -A T- 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
19011 T
1 T
19012 TAACTAAACG
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
1 9 0.15
2 50 0.85
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18951 original size:12 final size:12
Alignment explanation
Indices: 18934--19011 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
18924 CCGTTTAATA
18934 ATTATATATATT
1 ATTATATATATT
*
18946 ATTATATATATA
1 ATTATATATATT
18958 ATTATATATATCT
1 ATTATATATAT-T
18971 A--ATAT-TATT
1 ATTATATATATT
**
18980 A-TATATATAAA
1 ATTATATATATT
*
18991 AATATATAT-TT
1 ATTATATATATT
19002 AATTATATAT
1 -ATTATATAT
19012 TAACTAAACG
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
11 7 0.13
12 37 0.69
13 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTATATATATT
Found at i:18979 original size:31 final size:31
Alignment explanation
Indices: 18941--19013 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
18931 ATAATTATAT
**
18941 ATATTATTATATATATAATTATATATATCTA
1 ATATTATTATATATATAAAAATATATATCTA
*
18972 ATATTATTATATATATAAAAATATATATTTA
1 ATATTATTATATATATAAAAATATATATCTA
19003 ATTATATATTA
1 A-TAT-TATTA
19014 ACTAAACGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 29 0.78
32 3 0.08
33 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATTATTATATATATAAAAATATATATCTA
Found at i:24036 original size:257 final size:257
Alignment explanation
Indices: 23580--24095 Score: 1005
Period size: 257 Copynumber: 2.0 Consensus size: 257
23570 CTGAGTGAAC
23580 TCTGTCGAATTGAAAATCGTAATTCATCATGCCCATTAGTGATTCTCTTCTTGGTTTATTTCAGC
1 TCTGTCGAATTGAAAATCGTAATTCATCATGCCCATTAGTGATTCTCTTCTTGGTTTATTTCAGC
23645 AAAGCAACCAAATTGAGCACCATGGCAGCCGCCTTGCCTCCCATTTCTGCTTCACCATTCACCAA
66 AAAGCAACCAAATTGAGCACCATGGCAGCCGCCTTGCCTCCCATTTCTGCTTCACCATTCACCAA
23710 CATAGCGCATTGCTAAGAATTCGGGGGATTTGCAATGAGAAAGGTTGATCTCCCATGTTATTTAA
131 CATAGCGCATTGCTAAGAATTCGGGGGATTTGCAATGAGAAAGGTTGATCTCCCATGTTATTTAA
23775 TGAGGAACTTGGTGAATCGCTCATGTTCTGTAGAGCATGCATGTATTATGCAACCCAGGGAA
196 TGAGGAACTTGGTGAATCGCTCATGTTCTGTAGAGCATGCATGTATTATGCAACCCAGGGAA
*
23837 TCTGTCGAATTGAAAATTGTAATTCATCATGCCCATTAGTGATTCTCTTCTTGGTTTATTTCAGC
1 TCTGTCGAATTGAAAATCGTAATTCATCATGCCCATTAGTGATTCTCTTCTTGGTTTATTTCAGC
*
23902 AAAGCAACCAAATTGAGCACCATGGCAGCCGCCTTGCGTCCCATTTCTGCTTCACCATTCACCAA
66 AAAGCAACCAAATTGAGCACCATGGCAGCCGCCTTGCCTCCCATTTCTGCTTCACCATTCACCAA
*
23967 CATAGCGCATTGCTAAGAATTCGGGGGATTTGCAATGAGAAAGGTTGATCTCCCTTGTTATTTAA
131 CATAGCGCATTGCTAAGAATTCGGGGGATTTGCAATGAGAAAGGTTGATCTCCCATGTTATTTAA
24032 TGAGGAACTTGGTGAATCGCTCATGTTCTGTAGAGCATGCATGTATTATGCAACCCAGGGAA
196 TGAGGAACTTGGTGAATCGCTCATGTTCTGTAGAGCATGCATGTATTATGCAACCCAGGGAA
24094 TC
1 TC
24096 AGACAGAAGA
Statistics
Matches: 256, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
257 256 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (257 bp):
TCTGTCGAATTGAAAATCGTAATTCATCATGCCCATTAGTGATTCTCTTCTTGGTTTATTTCAGC
AAAGCAACCAAATTGAGCACCATGGCAGCCGCCTTGCCTCCCATTTCTGCTTCACCATTCACCAA
CATAGCGCATTGCTAAGAATTCGGGGGATTTGCAATGAGAAAGGTTGATCTCCCATGTTATTTAA
TGAGGAACTTGGTGAATCGCTCATGTTCTGTAGAGCATGCATGTATTATGCAACCCAGGGAA
Done.