Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007721.1 Corchorus capsularis cultivar CVL-1 contig07742, 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: 15420
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:205 original size:7 final size:7
Alignment explanation
Indices: 193--420 Score: 99
Period size: 7 Copynumber: 33.6 Consensus size: 7
183 CTTTACTGGA
193 TTACTCT
1 TTACTCT
200 TTACTCT
1 TTACTCT
* *
207 TCAC-CA
1 TTACTCT
213 TT-CTTCT
1 TTAC-TCT
220 TTACTGAC-
1 TTACT--CT
228 TT-CTCT
1 TTACTCT
*
234 TCACTCT
1 TTACTCT
*
241 TTACTAT
1 TTACTCT
**
248 TTTTTCT
1 TTACTCT
**
255 TTACTGA
1 TTACTCT
262 TTACTCT
1 TTACTCT
269 TTACTC-
1 TTACTCT
275 -TACTCT
1 TTACTCT
281 TTACTCT
1 TTACTCT
288 TTAC-CAT
1 TTACTC-T
**
295 TTTTTCT
1 TTACTCT
**
302 TTACTGA
1 TTACTCT
309 TTACTC-
1 TTACTCT
315 TTA-TCT
1 TTACTCT
321 TTACTCT
1 TTACTCT
328 TTACTCT
1 TTACTCT
*
335 TTACCCT
1 TTACTCT
*
342 TT-TTCT
1 TTACTCT
**
348 TTACTGA
1 TTACTCT
355 TTACTCTT
1 TTACTC-T
*
363 TTACTTT
1 TTACTCT
*
370 TTACCATTT
1 TTA-C-TCT
379 TTACT-T
1 TTACTCT
**
385 TGT--TGA
1 T-TACTCT
391 TTACTCT
1 TTACTCT
398 TTA--CT
1 TTACTCT
403 TTACTCT
1 TTACTCT
410 TTACTCT
1 TTACTCT
417 TTAC
1 TTAC
421 CATTTTTCTT
Statistics
Matches: 163, Mismatches: 35, Indels: 46
0.67 0.14 0.19
Matches are distributed among these distances:
5 16 0.10
6 17 0.10
7 112 0.69
8 11 0.07
9 7 0.04
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:255 original size:35 final size:35
Alignment explanation
Indices: 148--402 Score: 175
Period size: 35 Copynumber: 7.6 Consensus size: 35
138 GCCATTACTT
* *
148 TTTACTGATTAATATTTTACTCTTTACCATTTTTTC
1 TTTACTGATTACT-CTTTACTCTTTACCATTTTTTC
* *
184 TTTACTGGATTACTCTTTACTCTTCACCA-TTCTTC
1 TTTACT-GATTACTCTTTACTCTTTACCATTTTTTC
* *
219 TTTACTGACTT-CTCTTCACTCTTTACTATTTTTTC
1 TTTACTGA-TTACTCTTTACTCTTTACCATTTTTTC
**
254 TTTACTGATTACTCTTTACTC--TACTC-TTTACTC
1 TTTACTGATTACTCTTTACTCTTTAC-CATTTTTTC
* ** *
287 TTTAC-CA-T--T-TTT--TCTTTA-C-TGATTAC
1 TTTACTGATTACTCTTTACTCTTTACCATTTTTTC
*
313 TCTTATCT--TTACTCTTTACTCTTTACC-CTTTTTC
1 T-TTA-CTGATTACTCTTTACTCTTTACCATTTTTTC
* *
347 TTTACTGATTACTCTTTTACTTTTTACCATTTTTAC
1 TTTACTGATTACTC-TTTACTCTTTACCATTTTTTC
**
383 TTTGTTGATTACTCTTTACT
1 TTTACTGATTACTCTTTACT
403 TTACTCTTTA
Statistics
Matches: 171, Mismatches: 27, Indels: 43
0.71 0.11 0.18
Matches are distributed among these distances:
26 6 0.04
27 3 0.02
28 7 0.04
29 1 0.01
30 1 0.01
31 4 0.02
32 3 0.02
33 22 0.13
34 29 0.17
35 53 0.31
36 36 0.21
37 6 0.04
ACGTcount: A:0.17, C:0.23, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTCTTTACCATTTTTTC
Found at i:280 original size:12 final size:12
Alignment explanation
Indices: 263--287 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
253 CTTTACTGAT
263 TACTCTTTACTC
1 TACTCTTTACTC
275 TACTCTTTACTC
1 TACTCTTTACTC
287 T
1 T
288 TTACCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTCTTTACTC
Found at i:285 original size:40 final size:40
Alignment explanation
Indices: 236--414 Score: 125
Period size: 40 Copynumber: 4.2 Consensus size: 40
226 ACTTCTCTTC
236 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
1 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
276 ACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTATCTTTACTCTTT
1 ACTCTTTA--C--T---ATTTTTTCTTTACTGATTA--C---TCTTTACTC--T
**
330 ACTCTTTAC-CCTTTTTCTTTACTGATTACTC-TT--T-T
1 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
* * * ** *
365 ACTTTTTACCATTTTTACTTTGTTGATTACTCTTTACTTT
1 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
405 ACTCTTTACT
1 ACTCTTTACT
415 CTTTACCATT
Statistics
Matches: 110, Mismatches: 10, Indels: 38
0.70 0.06 0.24
Matches are distributed among these distances:
35 9 0.08
36 17 0.15
37 2 0.02
38 1 0.01
39 1 0.01
40 19 0.17
41 2 0.02
42 1 0.01
44 2 0.02
46 17 0.15
47 19 0.17
49 1 0.01
52 10 0.09
54 9 0.08
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.58
Consensus pattern (40 bp):
ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
Found at i:287 original size:47 final size:47
Alignment explanation
Indices: 230--363 Score: 200
Period size: 47 Copynumber: 2.9 Consensus size: 47
220 TTACTGACTT
*
230 CTCTTCACTCTTTACTATTTTTTCTTTACTGATTACTCTTTA-CTCTA
1 CTCTTTACTCTTTAC-ATTTTTTCTTTACTGATTACTCTTTATCTCTA
*
277 CTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTC-TTATCTTTA
1 CTCTTTACTCTTTA-CATTTTTTCTTTACTGATTACTCTTTATCTCTA
**
324 CTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTT
1 CTCTTTACTCTTTACATTTTTTCTTTACTGATTACTCTTT
364 TACTTTTTAC
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
46 24 0.30
47 55 0.69
48 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.57
Consensus pattern (47 bp):
CTCTTTACTCTTTACATTTTTTCTTTACTGATTACTCTTTATCTCTA
Found at i:335 original size:19 final size:19
Alignment explanation
Indices: 262--335 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
252 TCTTTACTGA
262 TTACTCTTTACTC-TACTCT
1 TTACTCTTTACTCTTA-TCT
* *
281 TTACTCTTTACCATTTTTTCT
1 TTACTCTTTA-C-TCTTATCT
**
302 TTACTGATTACTCTTATCT
1 TTACTCTTTACTCTTATCT
321 TTACTCTTTACTCTT
1 TTACTCTTTACTCTT
336 TACCCTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 29 0.66
20 2 0.05
21 12 0.27
22 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.01, T:0.57
Consensus pattern (19 bp):
TTACTCTTTACTCTTATCT
Found at i:350 original size:20 final size:19
Alignment explanation
Indices: 325--434 Score: 62
Period size: 20 Copynumber: 5.4 Consensus size: 19
315 TTATCTTTAC
325 TCTTTACTCTTTACCCTTTT
1 TCTTTACTCTTTA-CCTTTT
**
345 TCTTTACTGATTACTCTTTT
1 TCTTTACTCTTTAC-CTTTT
* *
365 ACTTTTTACCATTTTTA-CTTTGT
1 --TCTTTA-C-TCTTTACCTTT-T
** *
388 TGATTACTCTTTA-CTTTAC
1 TCTTTACTCTTTACCTTT-T
407 TCTTTACTCTTTACCATTTT
1 TCTTTACTCTTTACC-TTTT
427 TCTTTACT
1 TCTTTACT
435 GATTACTCTT
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
19 21 0.30
20 26 0.38
21 7 0.10
22 9 0.13
23 2 0.03
24 4 0.06
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (19 bp):
TCTTTACTCTTTACCTTTT
Found at i:371 original size:27 final size:26
Alignment explanation
Indices: 309--371 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
299 TCTTTACTGA
* * *
309 TTACTCTTATCTTTACTCTTTACTCT
1 TTACTTTTTTCTTTACTCATTACTCT
* *
335 TTACCCTTTTTCTTTACTGATTACTCTT
1 TTA-CTTTTTTCTTTACTCATTACTC-T
363 TTACTTTTT
1 TTACTTTTT
372 ACCATTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 22 0.76
28 4 0.14
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (26 bp):
TTACTTTTTTCTTTACTCATTACTCT
Found at i:373 original size:82 final size:81
Alignment explanation
Indices: 163--444 Score: 331
Period size: 82 Copynumber: 3.4 Consensus size: 81
153 TGATTAATAT
* *
163 TTTACTCTTTACCATTTTTTCTTTACTGGATTACTCTTTACTCTTCACCA-TTCTTCTTTACTGA
1 TTTACTCTTTACCA-TTTTTCTTTACT-GATTACTCTTTACTCTTTACCATTTTTTCTTTACTGA
*
227 CTT-CTCTTCACTCTTTACTA
64 -TTACTCTT-A-TCTTTACTC
** * ** *
247 TTTTTTCTTTACTGATTACTCTTTACT--CTACTCTTTACTCTTTACCATTTTTTCTTTACTGAT
1 TTTACTCTTTAC-CATTTTTCTTTACTGATTACTCTTTACTCTTTACCATTTTTTCTTTACTGAT
310 TACTCTTATCTTTACTC
65 TACTCTTATCTTTACTC
* * * **
327 TTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTTACTTTGTTGAT
1 TTTACTCTTTACCATTTTTCTTTACTGATTACTC-TTTACTCTTTACCATTTTTTCTTTACTGAT
392 TACTCTT-TACTTTACTC
65 TACTCTTAT-CTTTACTC
409 TTTACTCTTTACCATTTTTCTTTACTGATTACTCTT
1 TTTACTCTTTACCATTTTTCTTTACTGATTACTCTT
445 GTCTGAATAC
Statistics
Matches: 170, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
79 10 0.06
80 18 0.11
81 29 0.17
82 92 0.54
84 20 0.12
85 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.56
Consensus pattern (81 bp):
TTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTTTACCATTTTTTCTTTACTGATT
ACTCTTATCTTTACTC
Found at i:456 original size:48 final size:49
Alignment explanation
Indices: 345--459 Score: 148
Period size: 47 Copynumber: 2.4 Consensus size: 49
335 TTACCCTTTT
* **
345 TCTTTACTGATTACTCTTTTACTTTTTACCATTTTTACTTTGTTGATTAC
1 TCTTTACTGATTACTC-TTTACTCTTTACCATTTTTACTTTACTGATTAC
395 TCTTTACT--TTACTCTTTACTCTTTACCATTTTT-CTTTACTGATTAC
1 TCTTTACTGATTACTCTTTACTCTTTACCATTTTTACTTTACTGATTAC
*
441 TCTTGT-CTGAATACTCTTT
1 TCTT-TACTGATTACTCTTT
460 TACTTTTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
46 17 0.29
47 19 0.33
48 14 0.24
50 8 0.14
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (49 bp):
TCTTTACTGATTACTCTTTACTCTTTACCATTTTTACTTTACTGATTAC
Found at i:566 original size:7 final size:7
Alignment explanation
Indices: 554--578 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
544 CCTTTGCTGA
554 TTACTCT
1 TTACTCT
561 TTACTCT
1 TTACTCT
568 TTACTCT
1 TTACTCT
575 TTAC
1 TTAC
579 CATTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:614 original size:22 final size:22
Alignment explanation
Indices: 560--807 Score: 156
Period size: 22 Copynumber: 11.5 Consensus size: 22
550 CTGATTACTC
* **
560 TTTACTCTTTACTCTTTACCAT
1 TTTACTTTTTACTGATTACCAT
* *
582 TTT-TTTCTTTACTGATTGCTC-T
1 TTTACTT-TTTACTGATTAC-CAT
*
604 TTTACTTTTTATTGATTACCAT
1 TTTACTTTTTACTGATTACCAT
* *
626 TTTACTCTTTT-CTAATTACTAT
1 TTTACT-TTTTACTGATTACCAT
* *
648 TTTACCTTTTACTGATTACCTT
1 TTTACTTTTTACTGATTACCAT
**
670 TTTACTTTTTACAAATTACCA-
1 TTTACTTTTTACTGATTACCAT
* *
691 -TTGCTTCTTACTGATTA-C-T
1 TTTACTTTTTACTGATTACCAT
* * *
710 ATTACTTTCTACTGATTATCACT
1 TTTACTTTTTACTGATTACCA-T
* *
733 TTTACTCTTTACTAATTACCAT
1 TTTACTTTTTACTGATTACCAT
* * *
755 TTTAGC-CTTT-CAGA-TACCTT
1 TTTA-CTTTTTACTGATTACCAT
* *
775 TTTACTTTTTACTGATTGCCCTT
1 TTTACTTTTTACTGATT-ACCAT
798 TTTACTTTTT
1 TTTACTTTTT
808 TGGAACTTAA
Statistics
Matches: 173, Mismatches: 37, Indels: 31
0.72 0.15 0.13
Matches are distributed among these distances:
19 2 0.01
20 39 0.23
21 12 0.07
22 81 0.47
23 39 0.23
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTACTTTTTACTGATTACCAT
Found at i:707 original size:20 final size:20
Alignment explanation
Indices: 653--727 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 20
643 ACTATTTTAC
*
653 CTTT-TACTGATTACCTTTTTA
1 CTTTCTACTGATTACC--ATTA
* ** *
674 CTTTTTACAAATTACCATTG
1 CTTTCTACTGATTACCATTA
*
694 C-TTCTTACTGATTACTATTA
1 CTTTC-TACTGATTACCATTA
714 CTTTCTACTGATTA
1 CTTTCTACTGATTA
728 TCACTTTTAC
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.05
20 24 0.57
21 7 0.17
22 9 0.21
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (20 bp):
CTTTCTACTGATTACCATTA
Found at i:745 original size:23 final size:22
Alignment explanation
Indices: 711--758 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
701 CTGATTACTA
* *
711 TTACTTTCTACTGATTATCACTT
1 TTACTTTCTACTAATTACCA-TT
734 TTACTCTT-TACTAATTACCATT
1 TTACT-TTCTACTAATTACCATT
756 TTA
1 TTA
759 GCCTTTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 15 0.68
24 2 0.09
ACGTcount: A:0.25, C:0.21, G:0.02, T:0.52
Consensus pattern (22 bp):
TTACTTTCTACTAATTACCATT
Found at i:2676 original size:47 final size:47
Alignment explanation
Indices: 2623--2718 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
2613 TTCTGCAATG
2623 TCCTGTTTTTTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAAT
1 TCCTGTTTTTTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAAT
2670 TCCTGTTTTTTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAAT
1 TCCTGTTTTTTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAAT
2717 TC
1 TC
2719 ATCCCTCTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.10, C:0.14, G:0.25, T:0.51
Consensus pattern (47 bp):
TCCTGTTTTTTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAAT
Found at i:2730 original size:47 final size:47
Alignment explanation
Indices: 2632--2731 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 47
2622 GTCCTGTTTT
* *** *
2632 TTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAATTCCTGTTTT
1 TTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAATTCATCCCTC
2679 TTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAATTCATCCCTC
1 TTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAATTCATCCCTC
2726 TTGAAT
1 TTGAAT
2732 TTTGTCTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.48
Consensus pattern (47 bp):
TTGAATGTGATTGGGTTTGCTGCTTTGGTTCCTTGAATTCATCCCTC
Found at i:4114 original size:62 final size:62
Alignment explanation
Indices: 4037--4156 Score: 206
Period size: 62 Copynumber: 1.9 Consensus size: 62
4027 AGAACTTCTC
*
4037 TTTCTCTTCTCTTCTTTTCTTTTTTTTTAAAC-TTTTTCAATTCCCATTTTTGTATTTTTGTA
1 TTTCTCTTCTCTTCTTTT-TTTTTTTTCAAACTTTTTTCAATTCCCATTTTTGTATTTTTGTA
*
4099 TTTCTCTTCTTTTCTTTTTTTTTTTTCAAACTTTTTTCAATTCCCATTTTTGTATTTT
1 TTTCTCTTCTCTTCTTTTTTTTTTTTCAAACTTTTTTCAATTCCCATTTTTGTATTTT
4157 GAATTTTTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 12 0.22
62 43 0.78
ACGTcount: A:0.12, C:0.17, G:0.03, T:0.68
Consensus pattern (62 bp):
TTTCTCTTCTCTTCTTTTTTTTTTTTCAAACTTTTTTCAATTCCCATTTTTGTATTTTTGTA
Found at i:9142 original size:30 final size:31
Alignment explanation
Indices: 9086--9150 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
9076 AATTTTACGT
*
9086 TTTCCTATTGTACCCTTTTTTGTAAAACATA
1 TTTCCGATTGTACCCTTTTTTGTAAAACATA
9117 TTTCCGATTGTACCCTTTTTT-TAAAACATA
1 TTTCCGATTGTACCCTTTTTTGTAAAACATA
9147 TTTC
1 TTTC
9151 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (31 bp):
TTTCCGATTGTACCCTTTTTTGTAAAACATA
Found at i:11798 original size:45 final size:45
Alignment explanation
Indices: 11745--11838 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
11735 GCAGAAATAT
11745 AAAA-GTTTTAAATAATTGTTGTTATGTGTGTTACATGTAAAAAA
1 AAAAGGTTTTAAATAATTGTTGTTATGTGTGTTACATGTAAAAAA
*
11789 AAAAGGTTTTAAATAATTGTTGTTATGTGTGTTACATGTTAAAAA
1 AAAAGGTTTTAAATAATTGTTGTTATGTGTGTTACATGTAAAAAA
11834 AAAAG
1 AAAAG
11839 AGTGAAAGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 4 0.08
45 44 0.92
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (45 bp):
AAAAGGTTTTAAATAATTGTTGTTATGTGTGTTACATGTAAAAAA
Found at i:12587 original size:16 final size:16
Alignment explanation
Indices: 12568--12630 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
12558 TCCGACCCTA
12568 AACCCGAATGACCCGT
1 AACCCGAATGACCCGT
** *
12584 AACCC-AGATGACTTGA
1 AACCCGA-ATGACCCGT
*
12600 AACCCGAATGACACGT
1 AACCCGAATGACCCGT
*
12616 AACCCGAGTGACCCG
1 AACCCGAATGACCCG
12631 AGACCTGTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.33, C:0.33, G:0.21, T:0.13
Consensus pattern (16 bp):
AACCCGAATGACCCGT
Found at i:13483 original size:16 final size:16
Alignment explanation
Indices: 13464--13531 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
13454 CCCAGTTGAT
*
13464 CCGAAACCCGAGTGAC
1 CCGAAACCCGAATGAC
*
13480 CCGAGACCCGAATGAC
1 CCGAAACCCGAATGAC
* * *
13496 TCGGAACCCGAATAAC
1 CCGAAACCCGAATGAC
* *
13512 CTGAAACCCGAATGAT
1 CCGAAACCCGAATGAC
13528 CCGA
1 CCGA
13532 GAAAACTGCC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.34, C:0.34, G:0.22, T:0.10
Consensus pattern (16 bp):
CCGAAACCCGAATGAC
Found at i:13857 original size:17 final size:16
Alignment explanation
Indices: 13818--13862 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
13808 GTTGGTTGGG
*
13818 AGGAAA-GAAATAAGA
1 AGGAAAGGAAATAACA
13833 AGGAAAGGAAATAACA
1 AGGAAAGGAAATAACA
13849 AGAGAAAGGAAATA
1 AG-GAAAGGAAATA
13863 GGGAGAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 6 0.22
16 10 0.37
17 11 0.41
ACGTcount: A:0.64, C:0.02, G:0.27, T:0.07
Consensus pattern (16 bp):
AGGAAAGGAAATAACA
Done.