Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018755.1 Corchorus olitorius cultivar O-4 contig18788, 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: 59416
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1440 original size:29 final size:30
Alignment explanation
Indices: 1382--1458 Score: 102
Period size: 29 Copynumber: 2.5 Consensus size: 30
1372 ATACTGTACA
1382 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTAC-TACAAAAAAGGATCAATTT
* **
1413 GGTCCCTCTACTATAAAAACTG-TCAATTT
1 GGTCCCTCTACTACAAAAAAGGATCAATTT
1442 GGTCCCTCTACTTACAA
1 GGTCCCTCTAC-TACAA
1459 TTTAGTGTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 18 0.44
30 12 0.29
31 11 0.27
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (30 bp):
GGTCCCTCTACTACAAAAAAGGATCAATTT
Found at i:1478 original size:60 final size:62
Alignment explanation
Indices: 1382--1502 Score: 153
Period size: 60 Copynumber: 2.0 Consensus size: 62
1372 ATACTGTACA
1382 GGTCCCTCTACTTACAAAAAAGGATCAATTTGGTCCCTCTAC-TATA-AAAA-CTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGATCAATTTGGTCCCTCTACTTA-ACAAAATCTGTCAATTT
***
1442 GGTCCCTCTACTTACAATTTAGTG-TCAA-TTGAGTCCCTCTACTTAACAAAATCTGTCAATT
1 GGTCCCTCTACTTACAAAAAAG-GATCAATTTG-GTCCCTCTACTTAACAAAATCTGTCAATT
1503 GATTATATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
59 3 0.06
60 34 0.64
61 7 0.13
62 9 0.17
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (62 bp):
GGTCCCTCTACTTACAAAAAAGGATCAATTTGGTCCCTCTACTTAACAAAATCTGTCAATTT
Found at i:1504 original size:31 final size:30
Alignment explanation
Indices: 1382--1502 Score: 122
Period size: 31 Copynumber: 4.0 Consensus size: 30
1372 ATACTGTACA
***
1382 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAATCTG-TCAATTT
1413 GGTCCCTCTACTATA-AAAA-CTGTCAATTT
1 GGTCCCTCTACT-TACAAAATCTGTCAATTT
** *
1442 GGTCCCTCTACTTACAATTTAGTGTCAA-TT
1 GGTCCCTCTACTTACAAAAT-CTGTCAATTT
1472 GAGTCCCTCTACTTAACAAAATCTGTCAATT
1 G-GTCCCTCTACTT-ACAAAATCTGTCAATT
1503 GATTATATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.03
29 21 0.28
30 4 0.05
31 40 0.53
32 8 0.11
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAATCTGTCAATTT
Found at i:3174 original size:13 final size:13
Alignment explanation
Indices: 3156--3182 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3146 CTCTAGAGCC
3156 TCATAAATCATAT
1 TCATAAATCATAT
3169 TCATAAATCATAT
1 TCATAAATCATAT
3182 T
1 T
3183 TATTATATTT
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:6185 original size:43 final size:43
Alignment explanation
Indices: 6067--6438 Score: 377
Period size: 43 Copynumber: 8.8 Consensus size: 43
6057 ATAATTAAAA
* * * *
6067 TCCCCAAACACAATTATAACACATGGGCAATTCTCTTTCTAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATATC-AAAG
* * *
6111 TCCTCAAACACATTTATAACACA-GAGAAATTCTATATCAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATATCAAAG
* * * * *
6153 TCCCCAAACACAATTATAACAAAGGGGCAATTCTCTCTAAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATATCAAAG
* * * *
6196 TCCTCAAATACATTTATAACACAGAGGC-A-TCCATA-CTAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATATC-AAAG
** * *
6237 TCCCCAAACACATTTATAACACAGGGGCACCTCTATTTTAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATATCAAAG
* * *
6280 TCCTCAAACACATTTATAACACAGAGGC-A-TCCATA-CTAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATATC-AAAG
**
6321 TCCCCAAACACATTTATAACACAGGGGCACCTCTAT-TCCAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATAT-CAAAG
* * *
6364 TCCTCAAACACATTTATAACACAGAGAC-A-TCTATATCAAAG
1 TCCCCAAACACATTTATAACACAGGGGCAATTCTATATCAAAG
*
6405 TCCCCAAACACATTTATAACACAAGGGCAATTCT
1 TCCCCAAACACATTTATAACACAGGGGCAATTCT
6439 CTCTATGGCA
Statistics
Matches: 267, Mismatches: 48, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
41 100 0.37
42 27 0.10
43 118 0.44
44 22 0.08
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.24
Consensus pattern (43 bp):
TCCCCAAACACATTTATAACACAGGGGCAATTCTATATCAAAG
Found at i:6263 original size:84 final size:83
Alignment explanation
Indices: 6062--6443 Score: 489
Period size: 84 Copynumber: 4.5 Consensus size: 83
6052 ACCCAATAAT
* * *
6062 TAAAATCCCCAAACACAATTATAACACATGGGCAATTCTCTTTCT-AAAGTCCTCAAACACATTT
1 TAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTC--TCTAAAAGTCCTCAAACACATTT
* *
6126 ATAACACAGAGAAATTCTATA
64 ATAACACAGAGACA-TCCATA
* * *
6147 TCAAAGTCCCCAAACACAATTATAACAAAGGGGCAATTCTCTCTAAAAGTCCTCAAATACATTTA
1 T-AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAACACATTTA
*
6212 TAACACAGAGGCATCCATA
65 TAACACAGAGACATCCATA
** * * *
6231 CTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTTTAAAGTCCTCAAACACATTTA
1 -TAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAACACATTTA
*
6296 TAACACAGAGGCATCCATA
65 TAACACAGAGACATCCATA
** * *
6315 CTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTAT-TCCAAAGTCCTCAAACACATTT
1 -TAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCT-AAAAGTCCTCAAACACATTT
*
6379 ATAACACAGAGACATCTATA
64 ATAACACAGAGACATCCATA
*
6399 TCAAAGTCCCCAAACACATTTATAACACAAGGGCAATTCTCTCTA
1 T-AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTA
6444 TGGCAAAGGC
Statistics
Matches: 268, Mismatches: 23, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
83 2 0.01
84 197 0.74
85 33 0.12
86 36 0.13
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.24
Consensus pattern (83 bp):
TAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAACACATTTAT
AACACAGAGACATCCATA
Found at i:16662 original size:12 final size:13
Alignment explanation
Indices: 16634--16662 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16624 AAAGGCCACT
16634 AAATTGTTTACCA
1 AAATTGTTTACCA
16647 AAATTGTTTA-CA
1 AAATTGTTTACCA
16659 AAAT
1 AAAT
16663 CTAACTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (13 bp):
AAATTGTTTACCA
Found at i:17905 original size:19 final size:20
Alignment explanation
Indices: 17877--17915 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
17867 ATTTATAATT
*
17877 AAATATATATTATATATAAA
1 AAATATATATTAGATATAAA
17897 AAATA-ATATTAGATATAAA
1 AAATATATATTAGATATAAA
17916 TAATTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATATATATTAGATATAAA
Found at i:18657 original size:3 final size:3
Alignment explanation
Indices: 18645--18678 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
18635 TTATATTATT
*
18645 ATA ATT ATA ATA ATA ATA ATA ATA ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
18679 TACTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:20166 original size:54 final size:54
Alignment explanation
Indices: 20069--20241 Score: 294
Period size: 54 Copynumber: 3.2 Consensus size: 54
20059 TGGATCAAAT
* * *
20069 TGGAGATCAACTCTGATCATCGAAAACTTCTTG-AACGAGCACACTGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACCGGATCATC
20122 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACCGGATCATC
* *
20176 TGAAGATCAACTCTGATCTTCGAAATCTTCTTGAAACGACCACACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACCGGATCATC
20230 TGGAGATCAACT
1 TGGAGATCAACT
20242 TTGAAAACTT
Statistics
Matches: 113, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 32 0.28
54 81 0.72
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACCGGATCATC
Found at i:20354 original size:54 final size:54
Alignment explanation
Indices: 20271--20530 Score: 362
Period size: 54 Copynumber: 4.8 Consensus size: 54
20261 ACCGCACTCG
* * * * * *
20271 AAAACTTCTTGTAAGGACCGCAATTGATCATCTG-GAGATCAACTCTAATCATCA
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGAG-GATCAACTCTGATCATTA
* *
20325 AAAACTTCTTCGAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTG
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
* *
20379 AAAACTTCTTGGAATGACCGCACTAGATCATCT-ACGGATCAATTCTGATCATTA
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGA-GGATCAACTCTGATCATTA
* * *
20433 TAAATTTCTTGGAATGACCACACTGGATCATCTGAGGATCAACTCTGATCATTA
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
*
20487 AAAACTTCTTGGAATGACCACACTGGATCATCTGAGGATCAACT
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACT
20531 TTCTACAAAA
Statistics
Matches: 184, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 181 0.98
55 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (54 bp):
AAAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
Found at i:21449 original size:12 final size:12
Alignment explanation
Indices: 21432--21461 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21422 TTCTTTTTCC
21432 TTTTTTTC-TCT
1 TTTTTTTCTTCT
21443 TTTTTTTCTTCT
1 TTTTTTTCTTCT
21455 TTTTTTT
1 TTTTTTT
21462 TTGAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:25292 original size:16 final size:16
Alignment explanation
Indices: 25259--25292 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25249 TTACTCTGCT
*
25259 ATATTGATGCAGTCAA
1 ATATTGATGCACTCAA
*
25275 ATATTGATGCACTGAA
1 ATATTGATGCACTCAA
25291 AT
1 AT
25293 GTTTGCAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (16 bp):
ATATTGATGCACTCAA
Found at i:25811 original size:28 final size:27
Alignment explanation
Indices: 25771--25842 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 27
25761 AATGGAGTAG
*
25771 AAATGA-TCAAAATGCCCAAGGACGTGC
1 AAATGACT-AAAATGCCCAAGAACGTGC
* ** *
25798 AAAATGACTAAAATACCCCTGAATGTGC
1 -AAATGACTAAAATGCCCAAGAACGTGC
*
25826 AAATGACCAAAATGCCC
1 AAATGACTAAAATGCCC
25843 CTGGATTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 15 0.42
28 20 0.56
29 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACTAAAATGCCCAAGAACGTGC
Found at i:27306 original size:37 final size:41
Alignment explanation
Indices: 27289--27378 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
27279 ATCAGGGGGG
27289 AAATTGAATCAATAAATAAATATTACTCTAAATCAGGGACA
1 AAATTGAATCAATAAATAAATATTACTCTAAATCAGGGACA
* * * * * *
27330 AAATTGAATCAATTAACAAACATAACCCTAAATCAGGGACT
1 AAATTGAATCAATAAATAAATATTACTCTAAATCAGGGACA
*
27371 ATATTGAA
1 AAATTGAA
27379 AACGGAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (41 bp):
AAATTGAATCAATAAATAAATATTACTCTAAATCAGGGACA
Found at i:27310 original size:41 final size:41
Alignment explanation
Indices: 27265--27378 Score: 104
Period size: 41 Copynumber: 2.8 Consensus size: 41
27255 ATAAATCAAA
***
27265 AAATAAAA-TCTTAAATCAGGGGGGAAATTGAATCAATAAAT
1 AAATAAAACTC-TAAATCAGGGACAAAATTGAATCAATAAAT
** * *
27306 AAATATTACTCTAAATCAGGGACAAAATTGAATCAATTAAC
1 AAATAAAACTCTAAATCAGGGACAAAATTGAATCAATAAAT
* * * * *
27347 AAACATAACCCTAAATCAGGGACTATATTGAA
1 AAATAAAACTCTAAATCAGGGACAAAATTGAA
27379 AACGGAAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 58 0.97
42 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (41 bp):
AAATAAAACTCTAAATCAGGGACAAAATTGAATCAATAAAT
Found at i:28417 original size:43 final size:44
Alignment explanation
Indices: 28329--28419 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 44
28319 TCTCCCGGGA
* *
28329 AGAGAGGATATAGCCAGAGAATTTTGTAGATAGAGAGTCCCCAG
1 AGAGAAGATATAGCCAGAGAATTTTGTAGAGAGAGAGTCCCCAG
*
28373 AGAGAAGATATAGCCAGAGAA-TTTGTAGAGAGAGAGTCCGCAG
1 AGAGAAGATATAGCCAGAGAATTTTGTAGAGAGAGAGTCCCCAG
28416 AGAG
1 AGAG
28420 TGAATCGAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 24 0.55
44 20 0.45
ACGTcount: A:0.38, C:0.12, G:0.32, T:0.18
Consensus pattern (44 bp):
AGAGAAGATATAGCCAGAGAATTTTGTAGAGAGAGAGTCCCCAG
Found at i:29385 original size:25 final size:25
Alignment explanation
Indices: 29357--29407 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29347 TTGGCCCAAT
* * *
29357 GTGCCAGGCCGGCACGCTAGCCAGC
1 GTGCCAAGCCAGCACGCGAGCCAGC
*
29382 GTGCCAAGCCAGCACGCGGGCCAGC
1 GTGCCAAGCCAGCACGCGAGCCAGC
29407 G
1 G
29408 CGGCCCAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.39, G:0.37, T:0.06
Consensus pattern (25 bp):
GTGCCAAGCCAGCACGCGAGCCAGC
Found at i:30862 original size:25 final size:25
Alignment explanation
Indices: 30808--30862 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
30798 CCCGTTGAGG
* *
30808 AAATGTTTTATTACTGTTTTTACAT
1 AAATGATTTATTAATGTTTTTACAT
* *
30833 GAATGATTTATATAATGTTTTT-GAT
1 AAATGATTTAT-TAATGTTTTTACAT
30858 AAATG
1 AAATG
30863 TTTTGGGTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (25 bp):
AAATGATTTATTAATGTTTTTACAT
Found at i:44337 original size:2 final size:2
Alignment explanation
Indices: 44330--44358 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
44320 ACCTAGTTGC
44330 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44359 AGATTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52493 original size:51 final size:51
Alignment explanation
Indices: 52373--52506 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 51
52363 TTTATGGTTG
*
52373 TTTGGTTAATCTTTGGTTTGATTTGTGAATGGCAGCAATACAAATATGCAAT
1 TTTGGTTAATATTTGGTTTGA-TTGTGAATGGCAGCAATACAAATATGCAAT
** ** **
52425 TTTGGTTAATATTTGGTTTGATTAGTGAATGGCAGC-ATGGATTTATGCCTT
1 TTTGGTTAATATTTGGTTTGATT-GTGAATGGCAGCAATACAAATATGCAAT
* *
52476 TTTGCTTAATATTTGGTTGGATGTGTGAATG
1 TTTGGTTAATATTTGGTTTGAT-TGTGAATG
52507 ATTTATGGCT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
51 38 0.54
52 33 0.46
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.44
Consensus pattern (51 bp):
TTTGGTTAATATTTGGTTTGATTGTGAATGGCAGCAATACAAATATGCAAT
Found at i:54572 original size:24 final size:24
Alignment explanation
Indices: 54544--54590 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
54534 TTGGTGTAAA
*
54544 TTATGTTGAACTTGAATTATGTTT
1 TTATGTTGAACATGAATTATGTTT
*
54568 TTATGTTGGACATGAATTATGTT
1 TTATGTTGAACATGAATTATGTT
54591 GCATTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (24 bp):
TTATGTTGAACATGAATTATGTTT
Found at i:54618 original size:38 final size:39
Alignment explanation
Indices: 54542--54668 Score: 159
Period size: 38 Copynumber: 3.3 Consensus size: 39
54532 GTTTGGTGTA
* *
54542 AATTATGTTGAACTTGAATTATGTTTTTATGTTGGACATG
1 AATTATGTTGCATTTGAATTATG-TTTTATGTTGGACATG
*
54582 AATTATGTTGCATTTGAATGATG-TTTATGTTGGACATG
1 AATTATGTTGCATTTGAATTATGTTTTATGTTGGACATG
* ** *
54620 AAATATGTTGCACTTT-AATTATGAATCATGTTGGACATG
1 AATTATGTTGCA-TTTGAATTATGTTTTATGTTGGACATG
54659 AATTATGTTG
1 AATTATGTTG
54669 AACTTTATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
38 32 0.42
39 25 0.32
40 20 0.26
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.44
Consensus pattern (39 bp):
AATTATGTTGCATTTGAATTATGTTTTATGTTGGACATG
Found at i:54659 original size:39 final size:38
Alignment explanation
Indices: 54570--54675 Score: 142
Period size: 39 Copynumber: 2.8 Consensus size: 38
54560 TTATGTTTTT
* *
54570 ATGTTGGACATGAATTATGTTGCA-TTTGAATGATGTTT
1 ATGTTGGACATGAATTATGTTGCACTTT-AATGATGATC
* *
54608 ATGTTGGACATGAAATATGTTGCACTTTAATTATGAATC
1 ATGTTGGACATGAATTATGTTGCACTTTAATGATG-ATC
*
54647 ATGTTGGACATGAATTATGTTGAACTTTA
1 ATGTTGGACATGAATTATGTTGCACTTTA
54676 TTAATTGATT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 29 0.48
39 31 0.52
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.42
Consensus pattern (38 bp):
ATGTTGGACATGAATTATGTTGCACTTTAATGATGATC
Done.