Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013173.1 Corchorus capsularis cultivar CVL-1 contig13194, 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: 22717
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:2076 original size:40 final size:39
Alignment explanation
Indices: 2018--2106 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 39
2008 AGTTAAGGAG
* *
2018 AAGTAAAGAAAGCGGTT-AAAGATCTTAGTTCATAGAAATT
1 AAGTAAA-AAAGCAGTTAAAAGA-CTTAATTCATAGAAATT
*
2058 AAGTAAAAATAGCAGTTAAAAGACTTAATTCATAGTAATT
1 AAGTAAAAA-AGCAGTTAAAAGACTTAATTCATAGAAATT
2098 AAGTAAAAA
1 AAGTAAAAA
2107 CATCAGAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 2 0.05
40 37 0.84
41 5 0.11
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.27
Consensus pattern (39 bp):
AAGTAAAAAAGCAGTTAAAAGACTTAATTCATAGAAATT
Found at i:2198 original size:12 final size:12
Alignment explanation
Indices: 2181--2242 Score: 90
Period size: 12 Copynumber: 5.2 Consensus size: 12
2171 GAAATTAGGC
2181 AAAAGAAGACTG
1 AAAAGAAGACTG
2193 AAAAGAAGACTG
1 AAAAGAAGACTG
2205 AAAAGAAGACTG
1 AAAAGAAGACTG
*
2217 GAAAGAAGACTG
1 AAAAGAAGACTG
* *
2229 -ATAGAAAACTG
1 AAAAGAAGACTG
2240 AAA
1 AAA
2243 TTAGATTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.20
12 36 0.80
ACGTcount: A:0.58, C:0.08, G:0.24, T:0.10
Consensus pattern (12 bp):
AAAAGAAGACTG
Found at i:2252 original size:11 final size:11
Alignment explanation
Indices: 2236--2373 Score: 105
Period size: 11 Copynumber: 12.5 Consensus size: 11
2226 CTGATAGAAA
2236 ACTGAAATTAG
1 ACTGAAATTAG
* **
2247 ATTGAAAAAAG
1 ACTGAAATTAG
*
2258 ACTGATATTAG
1 ACTGAAATTAG
2269 ACTGAAATTAG
1 ACTGAAATTAG
** **
2280 ACTGGTAGAAG
1 ACTGAAATTAG
**
2291 ACTGGTATTAG
1 ACTGAAATTAG
2302 ACTGAAATTAG
1 ACTGAAATTAG
* *
2313 ACTGATATAAG
1 ACTGAAATTAG
* *
2324 ACTGATATTAA
1 ACTGAAATTAG
*
2335 ACTGAAATCAG
1 ACTGAAATTAG
* **
2346 ACTAAAAAGAAG
1 ACT-GAAATTAG
2358 ACTGAAATTAG
1 ACTGAAATTAG
2369 ACTGA
1 ACTGA
2374 TAAAAGACTG
Statistics
Matches: 97, Mismatches: 29, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
11 89 0.92
12 8 0.08
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (11 bp):
ACTGAAATTAG
Found at i:2264 original size:33 final size:33
Alignment explanation
Indices: 2211--2373 Score: 164
Period size: 33 Copynumber: 4.9 Consensus size: 33
2201 ACTGAAAAGA
* **
2211 AGACTGGAAAGAAGACTGATAGAAAACTGAAATT
1 AGACT-GAAAAAAGACTGATATTAAACTGAAATT
* *
2245 AGATTGAAAAAAGACTGATATTAGACTGAAATT
1 AGACTGAAAAAAGACTGATATTAAACTGAAATT
** * * *
2278 AGACTGGTAGAAGACTGGTATTAGACTGAAATT
1 AGACTGAAAAAAGACTGATATTAAACTGAAATT
* * *
2311 AGACTGATATAAGACTGATATTAAACTGAAATC
1 AGACTGAAAAAAGACTGATATTAAACTGAAATT
* * *
2344 AGACTAAAAAGAAGACTGAAATTAGACTGA
1 AGACTGAAAA-AAGACTGATATTAAACTGA
2374 TAAAAGACTG
Statistics
Matches: 108, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
33 87 0.81
34 21 0.19
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (33 bp):
AGACTGAAAAAAGACTGATATTAAACTGAAATT
Found at i:2362 original size:23 final size:25
Alignment explanation
Indices: 2335--2380 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2325 CTGATATTAA
2335 ACTGAAATCAGACT-A-AAAAGAAG
1 ACTGAAATCAGACTGATAAAAGAAG
*
2358 ACTGAAATTAGACTGATAAAAGA
1 ACTGAAATCAGACTGATAAAAGA
2381 CTGGCTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (25 bp):
ACTGAAATCAGACTGATAAAAGAAG
Found at i:2430 original size:36 final size:35
Alignment explanation
Indices: 2376--3107 Score: 863
Period size: 36 Copynumber: 20.7 Consensus size: 35
2366 TAGACTGATA
* *
2376 AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
2411 AATAGACTGGCTTAATTTCAAAGAAATTAAGTAAAG
1 AA-AGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
2447 AAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAG-ACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
2483 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAG
1 -AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
2519 -AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * **
2552 ACAAGACTGGCTTAATTTCAGGGAAACTAGGTTTAG
1 A-AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * *
2588 ATAGACTGGCTTAATTTCAAAGAAATTAAGTAAA-
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
2622 AAAGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAA-GACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
2658 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 -AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
2694 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAG
1 -AAAGACTGGCTTAATTTCAAGGAAATTAGGT-AAAG
* * *
2731 ATAGACGGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
2765 AAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAG-ACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
2801 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAG
1 -AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
2837 -AAGACTGCCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * *
2870 ACAAGACTGGCTTAGTTTCAGGGAAACTAGGTAAAG
1 A-AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* *
2906 ATAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
* * *
2940 AAAGGACTAGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAA-GACTGGCTTAATTTCAAGGAAATTAGGTAAAG
**
2976 AAAAGACTACCTTAATTTCAAGGAAACTT-GGTAAAG
1 -AAAGACTGGCTTAATTTCAAGGAAA-TTAGGTAAAG
*
3012 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
1 -AAAGACTGGCTTAATTTCAAGGAAATTAGGT-AAAG
* * *
3049 ATAGACGGGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
*
3083 AAAGAACTAGCTTAATTTC-AGGAAA
1 AAAG-ACTGGCTTAATTTCAAGGAAA
3108 GGAAATTAAG
Statistics
Matches: 605, Mismatches: 69, Indels: 47
0.84 0.10 0.07
Matches are distributed among these distances:
34 81 0.13
35 214 0.35
36 287 0.47
37 23 0.04
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.25
Consensus pattern (35 bp):
AAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG
Found at i:2914 original size:247 final size:245
Alignment explanation
Indices: 2375--3122 Score: 1015
Period size: 247 Copynumber: 3.0 Consensus size: 245
2365 TTAGACTGAT
*
2375 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAAGAAATTA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTA
2440 AGTAAAG-AAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAA
66 AGTAAAGAAAAG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAA
* * *
2504 GGAAATTAAGTAAAGAAG-ACTGGCTTAATTTCAAGGAAATTAAGTAAAACAAGACTGGCTTAAT
130 GGAAATTAAGTAAAAAAGAACTGGCTTAATTTCAAGGAAATTAGGTAAAAAAAGACTGGCTTAAT
* * * ** *
2568 TTCAGGGAAACTAGGTTTAGATAGACTGGCTTAATTTCAAAGAAATTAAGTAA
195 TTCAAGGAAATTAAGTAAAGA-AGACT-GCTTAATTTCAAGGAAATTAAGTAA
* * *
2621 AAAAGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
1 AAAA-GACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATT
* * * * *
2686 AGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAA-AGATAGACGGGCTTAATTTCA
65 AAGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGA-AAAGACTGGCTTAATTTCA
* *
2750 AGGAAATTAAGTAAAAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTA
129 AGGAAATTAAGTAAAAAAGAACTGGCTTAATTTCAAGGAAATTAGGTAAA-AAAAGACTGGCTTA
2815 ATTTCAAGGAAATTAAGTAAAGAAGACTGCCTTAATTTCAAGGAAATTAAGTAA
193 ATTTCAAGGAAATTAAGTAAAGAAGACTG-CTTAATTTCAAGGAAATTAAGTAA
*
2869 AACAAGACTGGCTTAGTTTCAGGGAAACTAGGTAAAG-ATAGACTGGCTTAATTTCAAGGAAATT
1 AA-AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATT
* * **
2933 AAGTAAA-AAAGGACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTACCTTAATTTCAA
65 AAGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAA
* * * *
2997 GGAAACTT-GGTAAAGAAA-AGACTGACTTAATTTCAAGGAAATTAGGTAAAAGATAGACGGGCT
130 GGAAA-TTAAGTAAA-AAAGA-ACTGGCTTAATTTCAAGGAAATTAGGTAAAA-AAAGACTGGCT
*
3060 TAATTTCAAGGAAATTAAGTAAAAAAGAACTAGCTTAATTTCAGGAAAGGAAATTAAGTAA
191 TAATTTCAAGGAAATTAAGTAAAGAAG-ACT-GCTTAATTTC----AAGGAAATTAAGTAA
3121 AA
1 AA
3123 TAAAGAATTT
Statistics
Matches: 444, Mismatches: 40, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
246 64 0.14
247 225 0.51
248 104 0.23
249 34 0.08
252 17 0.04
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (245 bp):
AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTA
AGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAG
GAAATTAAGTAAAAAAGAACTGGCTTAATTTCAAGGAAATTAGGTAAAAAAAGACTGGCTTAATT
TCAAGGAAATTAAGTAAAGAAGACTGCTTAATTTCAAGGAAATTAAGTAA
Found at i:2955 original size:318 final size:318
Alignment explanation
Indices: 2375--3107 Score: 1281
Period size: 318 Copynumber: 2.3 Consensus size: 318
2365 TTAGACTGAT
* * * *
2375 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGT-AAAGAATAGACTGGCTTAATTTCAAAGAAATT
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAG-ATAGACGGGCTTAATTTCAAGGAAATT
2439 AAGTAAAGAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAA
65 AAGTAAA-AAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAA
*
2504 GGAAATTAAGTAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAACAAGACTGGCTTAATT
129 GGAAATTAAGTAAAGAAGACTGCCTTAATTTCAAGGAAATTAAGTAAAACAAGACTGGCTTAATT
** *
2569 TCAGGGAAACTAGGTTTAGATAGACTGGCTTAATTTCAAAGAAATTAAGTAAAAAAGGACTGGCT
194 TCAGGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAAGAAATTAAGTAAAAAAGGACTAGCT
** *
2634 TAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
259 TAGTTTCAAGGAAACTAGGTAAAGAAAAGACTACCTTAATTTCAAGGAAACTAGGTAAAG
2694 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGATAGACGGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGATAGACGGGCTTAATTTCAAGGAAATTA
2759 AGTAAAAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGG
66 AGTAAAAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGG
*
2824 AAATTAAGTAAAGAAGACTGCCTTAATTTCAAGGAAATTAAGTAAAACAAGACTGGCTTAGTTTC
131 AAATTAAGTAAAGAAGACTGCCTTAATTTCAAGGAAATTAAGTAAAACAAGACTGGCTTAATTTC
*
2889 AGGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAGGACTAGCTTA
196 AGGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAAGAAATTAAGTAAAAAAGGACTAGCTTA
*
2954 GTTTCAAGGAAACTAGGTAAAGAAAAGACTACCTTAATTTCAAGGAAACTTGGTAAAG
261 GTTTCAAGGAAACTAGGTAAAGAAAAGACTACCTTAATTTCAAGGAAACTAGGTAAAG
*
3012 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGATAGACGGGCTTAATTTCAAGGAAATTA
1 AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGATAGACGGGCTTAATTTCAAGGAAATTA
* *
3077 AGTAAAAAAGAACTAGCTTAATTTC-AGGAAA
66 AGTAAAAAAGAACTGGCTTAGTTTCAAGGAAA
3108 GGAAATTAAG
Statistics
Matches: 396, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
317 6 0.02
318 324 0.82
319 62 0.16
320 4 0.01
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (318 bp):
AAAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGATAGACGGGCTTAATTTCAAGGAAATTA
AGTAAAAAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGG
AAATTAAGTAAAGAAGACTGCCTTAATTTCAAGGAAATTAAGTAAAACAAGACTGGCTTAATTTC
AGGGAAACTAGGTAAAGATAGACTGGCTTAATTTCAAAGAAATTAAGTAAAAAAGGACTAGCTTA
GTTTCAAGGAAACTAGGTAAAGAAAAGACTACCTTAATTTCAAGGAAACTAGGTAAAG
Found at i:3391 original size:12 final size:13
Alignment explanation
Indices: 3340--3405 Score: 50
Period size: 14 Copynumber: 5.0 Consensus size: 13
3330 TATGACGTGG
3340 CTTTTTCTTTTC-
1 CTTTTTCTTTTCT
3352 CTTTTTCATTTTCAT
1 CTTTTTC-TTTTC-T
*
3367 -TTTTATTTTTTCT
1 CTTTT-TCTTTTCT
3380 CTTTTT-TTTTCT
1 CTTTTTCTTTTCT
3392 -TTTTCTCTTCTTCT
1 CTTTT-TCTT-TTCT
3406 TTCTCAACCC
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
11 4 0.09
12 14 0.31
13 9 0.20
14 17 0.38
15 1 0.02
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTCTTTTCT
Found at i:3394 original size:6 final size:6
Alignment explanation
Indices: 3340--3407 Score: 57
Period size: 6 Copynumber: 10.7 Consensus size: 6
3330 TATGACGTGG
* * *
3340 CTTTTT CTTTTC CTTTTT CATTTT CATTTTT ATTTTTT CTCTTTT -TTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT -CTTTTT CT-TTTT CTTTTT
3390 CTTTTT CTCTTCTT CTTT
1 CTTTTT CT-TT-TT CTTT
3408 CTCAACCCGA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
5 4 0.08
6 25 0.50
7 17 0.34
8 4 0.08
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:5729 original size:13 final size:13
Alignment explanation
Indices: 5711--5737 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5701 CTGACATCAA
5711 GAAGAAGAAGACC
1 GAAGAAGAAGACC
5724 GAAGAAGAAGACC
1 GAAGAAGAAGACC
5737 G
1 G
5738 TTTTTAACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGACC
Found at i:6278 original size:30 final size:31
Alignment explanation
Indices: 6200--6278 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
6190 ATTACAATTG
*
6200 AAACGTTTGGTCCCAAATCAAGCATCGCGGC
1 AAACGTTTGGCCCCAAATCAAGCATCGCGGC
6231 AAACGTTTGGCCCCAAATCAAGCATCGCGGC
1 AAACGTTTGGCCCCAAATCAAGCATCGCGGC
6262 AAACGTTTGG-CCCAAAT
1 AAACGTTTGGCCCCAAAT
6279 TGAGCCTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 7 0.15
31 40 0.85
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (31 bp):
AAACGTTTGGCCCCAAATCAAGCATCGCGGC
Found at i:6389 original size:36 final size:34
Alignment explanation
Indices: 6292--6389 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 34
6282 GCCTTTTGCC
*
6292 TAATTAAGTGAAGTCAATAAAAGGCTTAATTCAGGG
1 TAATTAAGTG-AGTCAATAAAA-GCTTAATTCAAGG
*
6328 TAATTAAGT-AG--AATAAAAAACTTAATTCAAGG
1 TAATTAAGTGAGTCAAT-AAAAGCTTAATTCAAGG
*
6360 TAATTAAGTGGAGTCAATAAAGAGTTTAAT
1 TAATTAAGT-GAGTCAATAAA-AGCTTAAT
6390 CTAGAAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
32 23 0.44
33 4 0.08
34 4 0.08
35 3 0.06
36 18 0.35
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (34 bp):
TAATTAAGTGAGTCAATAAAAGCTTAATTCAAGG
Found at i:6460 original size:61 final size:61
Alignment explanation
Indices: 6385--6504 Score: 240
Period size: 61 Copynumber: 2.0 Consensus size: 61
6375 AATAAAGAGT
6385 TTAATCTAGAAAAGAGATTAAGCAAAACAATAAAAGGGCTTGATTTATAAAAATTAAGTGC
1 TTAATCTAGAAAAGAGATTAAGCAAAACAATAAAAGGGCTTGATTTATAAAAATTAAGTGC
6446 TTAATCTAGAAAAGAGATTAAGCAAAACAATAAAAGGGCTTGATTTATAAAAATTAAGT
1 TTAATCTAGAAAAGAGATTAAGCAAAACAATAAAAGGGCTTGATTTATAAAAATTAAGT
6505 CAATAAAGGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (61 bp):
TTAATCTAGAAAAGAGATTAAGCAAAACAATAAAAGGGCTTGATTTATAAAAATTAAGTGC
Found at i:9151 original size:39 final size:38
Alignment explanation
Indices: 9070--9163 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 38
9060 TCTCTCCCCG
* * *
9070 AAGTCCCCAAACACATATAACACAGGGGCAACTCTCTCA
1 AAGT-CCCAAACACATATAACACAGGAGAAACTATCTCA
9109 AAGTCCTCAAACACATATAACACA-GAGAAATCTATACT-A
1 AAGTCC-CAAACACATATAACACAGGAGAAA-CTAT-CTCA
9148 AAGTCCCTAAACACAT
1 AAGTCCC-AAACACAT
9164 GCAACACAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 7 0.15
39 39 0.81
40 2 0.04
ACGTcount: A:0.44, C:0.29, G:0.10, T:0.18
Consensus pattern (38 bp):
AAGTCCCAAACACATATAACACAGGAGAAACTATCTCA
Found at i:9529 original size:15 final size:16
Alignment explanation
Indices: 9497--9530 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9487 AAGAAGAATT
*
9497 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
9513 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
9528 TAA
1 TAA
9531 GAGAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:11777 original size:20 final size:21
Alignment explanation
Indices: 11748--11793 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
11738 GCTCCATACA
*
11748 AAGAATCACAAT-ACAATATC
1 AAGAACCACAATCACAATATC
* *
11768 AAGAACCACAATCTCCATATC
1 AAGAACCACAATCACAATATC
11789 AAGAA
1 AAGAA
11794 TCATCATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.52, C:0.24, G:0.07, T:0.17
Consensus pattern (21 bp):
AAGAACCACAATCACAATATC
Found at i:11789 original size:21 final size:21
Alignment explanation
Indices: 11722--11796 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
11712 CACTACTCAT
* *
11722 ATATCAAGCATCACAAGCTCC
1 ATATCAAGAATCACAATCTCC
* *
11743 ATA-CAAAGAATCACAAT-ACA
1 ATATC-AAGAATCACAATCTCC
*
11763 ATATCAAGAACCACAATCTCC
1 ATATCAAGAATCACAATCTCC
11784 ATATCAAGAATCA
1 ATATCAAGAATCA
11797 TCATCATCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 16 0.37
21 27 0.63
ACGTcount: A:0.48, C:0.27, G:0.07, T:0.19
Consensus pattern (21 bp):
ATATCAAGAATCACAATCTCC
Found at i:16725 original size:16 final size:16
Alignment explanation
Indices: 16684--16728 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
16674 TCGGATTTTG
**
16684 TCGGTTTCGGGTTATC
1 TCGGTTTCGGGTTAAA
*
16700 TC-GATTCGGGTTAAA
1 TCGGTTTCGGGTTAAA
16715 TCGGTTTCGGGTTA
1 TCGGTTTCGGGTTA
16729 TAGTACTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40
Consensus pattern (16 bp):
TCGGTTTCGGGTTAAA
Done.