Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011004.1 Corchorus capsularis cultivar CVL-1 contig11025, 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: 49616
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3750 original size:23 final size:24
Alignment explanation
Indices: 3703--3763 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
3693 CTCGATTAAT
*
3703 CTCTGT-TTTTCTCTTCTCTTCCC
1 CTCTGTCTTTTCTCTTCGCTTCCC
3726 CTCTGTCTGTTTCTCTTCGC-T-CC
1 CTCTGTCT-TTTCTCTTCGCTTCCC
* *
3749 CTTTCTCTTTTCTCT
1 CTCTGTCTTTTCTCT
3764 ATAGACTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 7 0.21
23 14 0.42
24 2 0.06
25 10 0.30
ACGTcount: A:0.00, C:0.38, G:0.07, T:0.56
Consensus pattern (24 bp):
CTCTGTCTTTTCTCTTCGCTTCCC
Found at i:5445 original size:124 final size:124
Alignment explanation
Indices: 5315--5550 Score: 386
Period size: 124 Copynumber: 1.9 Consensus size: 124
5305 ATTAGAACAC
* *
5315 AAAATTAAGTGATCAAGACCACAATCCCTATAGCAAATGAGCTATAATCCAATTTTAAT-GGTCT
1 AAAATTAAGTGATCAAGACCACAATCCCCATAGAAAATGAGCTATAATCCAATTTTAATAGG-CT
*
5379 TAATCAACAACAACATCTAC-TTAAACATTAAGCAAAATAAAATAATGTGAAATTGAAAGG
65 TAATCAACAACAACATCT-CTTTAAACACTAAGCAAAATAAAATAATGTGAAATTGAAAGG
* *
5439 AAAATTAAGTGATCAAGACCACAATCCCCATATAAAATGATCTATAATCCAATTTTAATAGGCTT
1 AAAATTAAGTGATCAAGACCACAATCCCCATAGAAAATGAGCTATAATCCAATTTTAATAGGCTT
*
5504 AATCAACAACAATATCTCTTTAAACACTAAGCAAAATAAAATAATGT
66 AATCAACAACAACATCTCTTTAAACACTAAGCAAAATAAAATAATGT
5551 TTCAAGGAGA
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
123 1 0.01
124 101 0.97
125 2 0.02
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (124 bp):
AAAATTAAGTGATCAAGACCACAATCCCCATAGAAAATGAGCTATAATCCAATTTTAATAGGCTT
AATCAACAACAACATCTCTTTAAACACTAAGCAAAATAAAATAATGTGAAATTGAAAGG
Found at i:5598 original size:23 final size:23
Alignment explanation
Indices: 5572--5662 Score: 91
Period size: 23 Copynumber: 4.0 Consensus size: 23
5562 AAAAAAATGA
5572 CATGACATGAAACAAACCCTAAC
1 CATGACATGAAACAAACCCTAAC
*
5595 CATGAAATG--ACAAACCCTAA-
1 CATGACATGAAACAAACCCTAAC
* *
5615 C-TGAGATGAAGGCTAAACCCTAAC
1 CATGACATGAA-AC-AAACCCTAAC
5639 CATGACATGAAAGTCAAACCCTAA
1 CATGACATGAAA--CAAACCCTAA
5663 TATGTCATCC
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
19 6 0.11
20 1 0.02
21 11 0.20
22 1 0.02
23 17 0.31
24 1 0.02
25 17 0.31
26 1 0.02
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.15
Consensus pattern (23 bp):
CATGACATGAAACAAACCCTAAC
Found at i:5737 original size:31 final size:32
Alignment explanation
Indices: 5693--5756 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
5683 GCAAAAAAGA
*
5693 ATTGGAATGCCCAAATTATCCTCAAGGCTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
*
5725 ATTGG-ATGCCCAAATTACCCTCGAGGCTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
5756 A
1 A
5757 CGAAATAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (32 bp):
ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
Found at i:10690 original size:32 final size:32
Alignment explanation
Indices: 10653--10722 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
10643 GGGGAAATTT
**
10653 TATATTTTCCGCTTGTACCCTTATTTTTAAAA
1 TATATTTTCCAATTGTACCCTTATTTTTAAAA
* *
10685 TATA-TTTCCAATTGTATCCTTTTTTTTAAAA
1 TATATTTTCCAATTGTACCCTTATTTTTAAAA
*
10716 CATATTT
1 TATATTT
10723 CTAAATTACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (32 bp):
TATATTTTCCAATTGTACCCTTATTTTTAAAA
Found at i:10700 original size:31 final size:31
Alignment explanation
Indices: 10665--10723 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
10655 TATTTTCCGC
*
10665 TTGTACCCTTATTTTTAAAATATATTTCCAA
1 TTGTACCCTTATTTTTAAAACATATTTCCAA
* *
10696 TTGTATCCTTTTTTTTAAAACATATTTC
1 TTGTACCCTTATTTTTAAAACATATTTC
10724 TAAATTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (31 bp):
TTGTACCCTTATTTTTAAAACATATTTCCAA
Found at i:12158 original size:22 final size:22
Alignment explanation
Indices: 12130--12310 Score: 97
Period size: 22 Copynumber: 8.3 Consensus size: 22
12120 TGTCTCTATG
12130 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
12152 TGGTTATTACAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
12175 -GGTTATCAAAA-TTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
12195 TGGTTACCAAAATTTCAT---A
1 TGGTTATCAAAATTTCATAAGA
* *
12214 TGGAATATCAAAATTTCAT-AGTG
1 TGG-TTATCAAAATTTCATAAG-A
* *
12237 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
12259 TCATGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
12283 TGGTTATTGAGATTTCATAAGG
1 TGGTTATCAAAATTTCATAAGA
12305 TGGTTA
1 TGGTTA
12311 ATTATCACAA
Statistics
Matches: 121, Mismatches: 27, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.03
20 13 0.11
21 15 0.12
22 65 0.54
23 7 0.06
24 17 0.14
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:12414 original size:22 final size:22
Alignment explanation
Indices: 12389--12471 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
12379 TCCATAGTCT
12389 GGTTATCAAAATTTCATTAGGA
1 GGTTATCAAAATTTCATTAGGA
* * **
12411 GGTTA-CTAATATTTGATGGGGA
1 GGTTATC-AAAATTTCATTAGGA
* *
12433 GGTTATCAAAATTTTA-TAGTGT
1 GGTTATCAAAATTTCATTAG-GA
*
12455 GATTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
12472 ATGAAGCTTA
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.04
22 43 0.93
23 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATTAGGA
Found at i:12482 original size:22 final size:22
Alignment explanation
Indices: 12342--12472 Score: 63
Period size: 22 Copynumber: 5.9 Consensus size: 22
12332 GGTTATCAAA
*
12342 GAGATTATCAAAATGTT-ATAGC
1 GAGATTATCAAAAT-TTCATAGT
* *
12364 GAGGTTTAT-AAGAATTCCATAGT
1 GA-GATTATCAA-AATTTCATAGT
** *
12387 CTGGTTATCAAAATTTCATTAG-
1 GAGATTATCAAAATTTCA-TAGT
* * * * *
12409 GAGGTTA-CTAATATTTGATGGG
1 GAGATTATC-AAAATTTCATAGT
* *
12431 GAGGTTATCAAAATTTTATAGT
1 GAGATTATCAAAATTTCATAGT
*
12453 GTGATTATCAAAATTTCATA
1 GAGATTATCAAAATTTCATA
12473 TGAAGCTTAT
Statistics
Matches: 82, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
21 3 0.04
22 61 0.74
23 18 0.22
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.37
Consensus pattern (22 bp):
GAGATTATCAAAATTTCATAGT
Found at i:12579 original size:25 final size:22
Alignment explanation
Indices: 12543--12604 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 22
12533 ATCTCAAAGT
*
12543 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAG-GA--A
*
12568 TATTATCAAAATTT-ATAGGAA
1 GATTATCAAAATTTCATAGGAA
12589 GATTATCAAAATTTCA
1 GATTATCAAAATTTCA
12605 GTATCAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 14 0.42
22 1 0.03
23 2 0.06
24 4 0.12
25 12 0.36
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGGAA
Found at i:12611 original size:14 final size:14
Alignment explanation
Indices: 12592--12618 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12582 ATAGGAAGAT
12592 TATCAAAATTTCAG
1 TATCAAAATTTCAG
12606 TATCAAAATTTCA
1 TATCAAAATTTCA
12619 AAACAAGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
TATCAAAATTTCAG
Found at i:12702 original size:22 final size:22
Alignment explanation
Indices: 12606--12730 Score: 117
Period size: 22 Copynumber: 5.6 Consensus size: 22
12596 AAAATTTCAG
*
12606 TATCAAAATTTCA-AAACAAGGT
1 TATCAAAATTTCATAAA-GAGGT
* * *
12628 TATCAAAATTACATAATGTGTGAT
1 TATCAAAATTTCATAAAGAG-G-T
* * *
12652 TATCAGAATTTCATAGAGGGGT
1 TATCAAAATTTCATAAAGAGGT
* * *
12674 CAACAAAATTTTATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
12696 TATCAAAATTTCATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
*
12718 TATCAAATTTTCA
1 TATCAAAATTTCA
12731 AAATGTGATT
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
22 61 0.75
23 4 0.05
24 16 0.20
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
TATCAAAATTTCATAAAGAGGT
Found at i:12884 original size:22 final size:22
Alignment explanation
Indices: 12856--13315 Score: 126
Period size: 22 Copynumber: 21.1 Consensus size: 22
12846 TCAGGGAGGA
*
12856 TATCAAAATTCCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
12878 TATCAAAATTTCATAATTTA-GT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
12900 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
12922 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * * **
12943 AGATCAAGATTTCATAGGGACAT
1 -TATCAAAATTTCATATGAAGGT
* *
12966 TAACAAAATTTCGTAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
12988 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
13010 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
13026 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
13048 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
13071 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
** ** *
13093 TATCTCAATTTCATATGGTGAT
1 TATCAAAATTTCATATGAAGGT
* * * * *
13115 TATTAAAATTTTAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
13137 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
13159 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * * * *
13181 TATCGATATATCATATGGAGAT
1 TATCAAAATTTCATATGAAGGT
* * ***
13203 TATCAATATCTCATAGTGTTCGT
1 TATCAAAATTTCATA-TGAAGGT
*
13226 TATCAAAATTTCAT-TGGAAAGT
1 TATCAAAATTTCATAT-GAAGGT
*
13248 TATCAAAATTTCATATTG-AGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
13270 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
13292 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
13314 TA
1 TA
13316 AAAAAAATTT
Statistics
Matches: 316, Mismatches: 92, Indels: 60
0.68 0.20 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 2 0.01
21 16 0.05
22 235 0.74
23 49 0.16
24 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:12955 original size:44 final size:43
Alignment explanation
Indices: 12856--13058 Score: 141
Period size: 44 Copynumber: 4.8 Consensus size: 43
12846 TCAGGGAGGA
* * *
12856 TATCAAAATTCCATATGAAGGTTATCAAAATTTCATAATTTAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAATGTAG
* *
12899 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATA--ATGTAG
* * * ** * *
12945 -ATCAAGATTTCATAGGGACATTAACAAAATTTCGTAATG-AGG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAATGTA-G
** * * *
12987 TTATCAAAAAATCATAGGGAGGTTATCAAAATTT-GT-A-GT--
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAATGTAG
* *
13026 TATCAAGATTTCATAAGAAAGTTATCAAAATTT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTT
13059 TATAGGAAGA
Statistics
Matches: 127, Mismatches: 26, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
38 27 0.21
41 2 0.02
42 5 0.04
43 2 0.02
44 86 0.68
46 5 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAATGTAG
Found at i:13316 original size:22 final size:22
Alignment explanation
Indices: 13288--13336 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
13278 TTCCTTAGGG
* *
13288 AGGTT-AACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTT-ATAAAA
13310 AGGTTAAAAAAAATTTATAAAA
1 AGGTTAAAAAAAATTTATAAAA
13332 AGGTT
1 AGGTT
13337 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAAATTTATAAAA
Found at i:26698 original size:6 final size:6
Alignment explanation
Indices: 26687--26712 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
26677 ATTTTAACAA
26687 TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TT
26713 CATTTAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCCT
Found at i:27287 original size:20 final size:21
Alignment explanation
Indices: 27258--27297 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27248 AATGGCACCA
27258 AAAAAGAAAT-TCTACCAAAAG
1 AAAAAGAAATGTC-ACCAAAAG
27279 AAAAA-AAATGTCACCAAAA
1 AAAAAGAAATGTCACCAAAA
27298 TTTCCCGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.65, C:0.15, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAAAGAAATGTCACCAAAAG
Found at i:28876 original size:16 final size:17
Alignment explanation
Indices: 28843--28876 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28833 AGGTGCTTTG
*
28843 ATGAAACCTTCAAGAAA
1 ATGAAACCATCAAGAAA
28860 ATGAAACCATC-AGAAA
1 ATGAAACCATCAAGAAA
28876 A
1 A
28877 GGTTAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.15
Consensus pattern (17 bp):
ATGAAACCATCAAGAAA
Found at i:30262 original size:24 final size:25
Alignment explanation
Indices: 30235--30289 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
30225 AAAATTGTGA
30235 TTTTTAAAT-TTTGCACTTTCCTTC
1 TTTTTAAATCTTTGCACTTTCCTTC
* *
30259 TTTTT-AGTCTTTGCACTTTCTTTC
1 TTTTTAAATCTTTGCACTTTCCTTC
*
30283 TATTTAA
1 TTTTTAA
30290 GTGCTAGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.08
24 23 0.88
25 1 0.04
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.60
Consensus pattern (25 bp):
TTTTTAAATCTTTGCACTTTCCTTC
Found at i:31694 original size:4 final size:4
Alignment explanation
Indices: 31685--31715 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
31675 TATTCAACCC
31685 GTTT GTTT GTTT GTTT -TTT GTTT GTTT GTTT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT
31716 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
GTTT
Found at i:31706 original size:15 final size:15
Alignment explanation
Indices: 31686--31731 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
31676 ATTCAACCCG
31686 TTTGTTTGTTTGTTT
1 TTTGTTTGTTTGTTT
31701 TTTGTTTGTTTGTTT
1 TTTGTTTGTTTGTTT
31716 TTT-TTT-TTT-TTT
1 TTTGTTTGTTTGTTT
31728 TTTG
1 TTTG
31732 CATGAGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.20
13 3 0.10
14 3 0.10
15 18 0.60
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (15 bp):
TTTGTTTGTTTGTTT
Found at i:31722 original size:19 final size:19
Alignment explanation
Indices: 31685--31721 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31675 TATTCAACCC
31685 GTTTGTTTGTTTGTTTTTT
1 GTTTGTTTGTTTGTTTTTT
31704 GTTTGTTTGTTT-TTTTTT
1 GTTTGTTTGTTTGTTTTTT
31722 TTTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (19 bp):
GTTTGTTTGTTTGTTTTTT
Found at i:31724 original size:8 final size:8
Alignment explanation
Indices: 31686--31730 Score: 51
Period size: 7 Copynumber: 6.0 Consensus size: 8
31676 ATTCAACCCG
*
31686 TTTGTTTG
1 TTTGTTTT
31694 TTTG-TTT
1 TTTGTTTT
*
31701 TTTGTTTG
1 TTTGTTTT
31709 TTTGTTTT
1 TTTGTTTT
31717 TTT-TTTT
1 TTTGTTTT
31724 TTT-TTTT
1 TTTGTTTT
31731 GCATGAGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 17 0.52
8 16 0.48
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTGTTTT
Found at i:33901 original size:3 final size:3
Alignment explanation
Indices: 33889--33931 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
33879 AACCCTTCAG
33889 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
33932 ATAATATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:38619 original size:95 final size:95
Alignment explanation
Indices: 38452--38641 Score: 362
Period size: 95 Copynumber: 2.0 Consensus size: 95
38442 ATGCTATAAT
38452 TTCTAGTTTGGATTGAATTCTCATTTAGATGTTTGGACATAGAGATTTATTTGAATGAACTGTAA
1 TTCTAGTTTGGATTGAATTCTCATTTAGATGTTTGGACATAGAGATTTATTTGAATGAACTGTAA
38517 TGAGATTTCACTAGGTTTGTTTGTTGGGGA
66 TGAGATTTCACTAGGTTTGTTTGTTGGGGA
*
38547 TTCTAGTTTGGATTGAATTCTCATTTAGATGTTTGGACATAGATATTTATTTGAATGAACTGTAA
1 TTCTAGTTTGGATTGAATTCTCATTTAGATGTTTGGACATAGAGATTTATTTGAATGAACTGTAA
*
38612 TGGGATTTCACTAGGTTTGTTTGTTGGGGA
66 TGAGATTTCACTAGGTTTGTTTGTTGGGGA
38642 AGGGGTTTGT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (95 bp):
TTCTAGTTTGGATTGAATTCTCATTTAGATGTTTGGACATAGAGATTTATTTGAATGAACTGTAA
TGAGATTTCACTAGGTTTGTTTGTTGGGGA
Found at i:39311 original size:18 final size:18
Alignment explanation
Indices: 39288--39352 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
39278 AAAGTGCCTT
39288 TAAAATTATTTTCCCATC
1 TAAAATTATTTTCCCATC
** * *
39306 TAAAATTATCAAAGTGCC-TT
1 TAAAATTAT---TTTCCCATC
39326 TAAAATTATTTTCCCATC
1 TAAAATTATTTTCCCATC
39344 TAAAATTAT
1 TAAAATTAT
39353 CAAAACAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
17 3 0.09
18 19 0.54
20 10 0.29
21 3 0.09
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (18 bp):
TAAAATTATTTTCCCATC
Found at i:39319 original size:38 final size:38
Alignment explanation
Indices: 39277--39356 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
39267 AGATGTCCTA
39277 CAAAGTGCCTTTAAAATTATTTTCCCATCTAAAATTAT
1 CAAAGTGCCTTTAAAATTATTTTCCCATCTAAAATTAT
39315 CAAAGTGCCTTTAAAATTATTTTCCCATCTAAAATTAT
1 CAAAGTGCCTTTAAAATTATTTTCCCATCTAAAATTAT
39353 CAAA
1 CAAA
39357 ACAAACCATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.38
Consensus pattern (38 bp):
CAAAGTGCCTTTAAAATTATTTTCCCATCTAAAATTAT
Found at i:46330 original size:27 final size:27
Alignment explanation
Indices: 46289--46351 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
46279 TGCAATAATT
*
46289 GCTCAGAGCTCCTCTAAGAAGAAGCAA
1 GCTCAGAGTTCCTCTAAGAAGAAGCAA
*
46316 GCTCAGAGTTTCTCTAAGAAGAAGCAA
1 GCTCAGAGTTCCTCTAAGAAGAAGCAA
46343 GCTCAGAGT
1 GCTCAGAGT
46352 CCCAGTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
GCTCAGAGTTCCTCTAAGAAGAAGCAA
Done.