Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014390.1 Corchorus capsularis cultivar CVL-1 contig14411, 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: 38623
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5393 original size:18 final size:20
Alignment explanation
Indices: 5372--5423 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
5362 TTACTAAATT
*
5372 AATAATAAATAT-A-TTTTA
1 AATAATAAATATGAGTTTAA
5390 AATAATAAATAATGAGTTTAA
1 AATAATAAAT-ATGAGTTTAA
5411 AATAAATAAATAT
1 AAT-AATAAATAT
5424 TATATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 2 0.07
20 1 0.03
21 9 0.31
22 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AATAATAAATATGAGTTTAA
Found at i:5395 original size:21 final size:24
Alignment explanation
Indices: 5352--5402 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
5342 TATCTTAAAT
5352 ATAATATATATTACTAAATTAATA
1 ATAATATATATTACTAAATTAATA
*
5376 ATAA-ATATATT-TTAAA-TAATAA
1 ATAATATATATTACTAAATTAAT-A
5398 ATAAT
1 ATAAT
5403 GAGTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 9 0.38
23 7 0.29
24 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAATATATATTACTAAATTAATA
Found at i:5962 original size:171 final size:171
Alignment explanation
Indices: 5672--6019 Score: 615
Period size: 171 Copynumber: 2.0 Consensus size: 171
5662 AATTGGGATC
* *
5672 TTTGGATAGGATTCTATTAACGGAATGGAGTATATGAGGGAATAGAAATCGGTGCTACCATGACT
1 TTTGCATAGGATTCTATTAACGGAATGGAATATATGAGGGAATAGAAATCGGTGCTACCATGACT
*
5737 CGGTCTGTGGAACTCCATCCAAACTTGCTGCTGCTATTGAATTTCATGTAAGACAAGTGTGTAAA
66 CAGTCTGTGGAACTCCATCCAAACTTGCTGCTGCTATTGAATTTCATGTAAGACAAGTGTGTAAA
* * *
5802 ATACTGAATGAGGATCCAAGGTCATGCTCTTGCCGGATGGA
131 ATACCGAATGAAGATCCAAGGTCATGCTCTCGCCGGATGGA
* *
5843 TTTGCATAGGATTCTATTAACGGTATGGAATATATGGGGGAATAGAAATCGGTGCTACCATGACT
1 TTTGCATAGGATTCTATTAACGGAATGGAATATATGAGGGAATAGAAATCGGTGCTACCATGACT
*
5908 CAGTCTGTGGAACTCCATCCAAACTTGCTGCTTCTATTGAATTTCATGTAAGACAAGTGTGTAAA
66 CAGTCTGTGGAACTCCATCCAAACTTGCTGCTGCTATTGAATTTCATGTAAGACAAGTGTGTAAA
5973 ATACCGAATGAAGATCCAAGGTCATGCTCTCGCCGGATGGA
131 ATACCGAATGAAGATCCAAGGTCATGCTCTCGCCGGATGGA
6014 TTTGCA
1 TTTGCA
6020 ATGGAGACCT
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
171 168 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (171 bp):
TTTGCATAGGATTCTATTAACGGAATGGAATATATGAGGGAATAGAAATCGGTGCTACCATGACT
CAGTCTGTGGAACTCCATCCAAACTTGCTGCTGCTATTGAATTTCATGTAAGACAAGTGTGTAAA
ATACCGAATGAAGATCCAAGGTCATGCTCTCGCCGGATGGA
Found at i:8239 original size:4 final size:4
Alignment explanation
Indices: 8230--8278 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
8220 CATAATGACC
* * * *
8230 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
8278 A
1 A
8279 ATTCGGCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:8644 original size:10 final size:10
Alignment explanation
Indices: 8619--8681 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
8609 CCTATGTGGC
8619 TTTTTTAAATA
1 TTTTTT-AATA
*
8630 TTTTTTTAT-
1 TTTTTTAATA
*
8639 TATTTTTGA-A
1 T-TTTTTAATA
*
8649 TTTTTAAATA
1 TTTTTTAATA
8659 TTTTTT--TA
1 TTTTTTAATA
8667 TTTTTTAATA
1 TTTTTTAATA
8677 TTTTT
1 TTTTT
8682 AAATCGGCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
8 8 0.19
9 6 0.14
10 22 0.52
11 6 0.14
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:8660 original size:18 final size:18
Alignment explanation
Indices: 8639--8681 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
8629 ATTTTTTTAT
8639 TATTTTTGAATTTTTAAA
1 TATTTTTGAATTTTTAAA
** *
8657 TATTTTTTTATTTTTTAA
1 TATTTTTGAATTTTTAAA
8675 TATTTTT
1 TATTTTT
8682 AAATCGGCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TATTTTTGAATTTTTAAA
Found at i:8662 original size:29 final size:28
Alignment explanation
Indices: 8620--8685 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 28
8610 CTATGTGGCT
*
8620 TTTTTAAATATTTTTTTATTATTTTTGA-A
1 TTTTTAAATATTTTTTTA-T-TTTTTAATA
8649 TTTTTAAATATTTTTTTATTTTTTAATA
1 TTTTTAAATATTTTTTTATTTTTTAATA
8677 TTTTTAAAT
1 TTTTTAAAT
8686 CGGCTCAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 6 0.17
28 11 0.31
29 18 0.51
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (28 bp):
TTTTTAAATATTTTTTTATTTTTTAATA
Found at i:18050 original size:3 final size:3
Alignment explanation
Indices: 18042--18089 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
18032 TAATTATTTT
18042 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18090 TTTTTGTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:24317 original size:30 final size:31
Alignment explanation
Indices: 24283--24361 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
24273 ATGTTTTCCG
*
24283 ATTGTACCTTATTTTTAAAACATATTT-TCA
1 ATTGTACCTTATTTTTAAAACATATTTCTAA
*
24313 ATTGTATCATT-TTCTTTAAAACATATTTCTAA
1 ATTGTA-CCTTATT-TTTAAAACATATTTCTAA
24345 ATTG--CCATTATTTTTAA
1 ATTGTACC-TTATTTTTAA
24362 TTATTTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
29 1 0.02
30 15 0.37
31 19 0.46
32 6 0.15
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.51
Consensus pattern (31 bp):
ATTGTACCTTATTTTTAAAACATATTTCTAA
Found at i:24524 original size:38 final size:35
Alignment explanation
Indices: 24460--24536 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
24450 AATTTGACTT
24460 TTTGTTTCCAACATCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACATCCTATTTAATTTTG-C-TTTGTC
**
24497 TTTGTTTCCAATCATTGTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CATCCTATTTAATTTTGCTTTGTC
24533 TTTG
1 TTTG
24537 GTCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 12 0.32
38 15 0.41
ACGTcount: A:0.16, C:0.17, G:0.10, T:0.57
Consensus pattern (35 bp):
TTTGTTTCCAACATCCTATTTAATTTTGCTTTGTC
Found at i:24689 original size:19 final size:20
Alignment explanation
Indices: 24662--24699 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
24652 TACTATTATT
24662 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
24682 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
24700 AATATCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:25024 original size:22 final size:22
Alignment explanation
Indices: 24864--25026 Score: 116
Period size: 22 Copynumber: 7.3 Consensus size: 22
24854 TTGTCTCTAT
* *
24864 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATTTCATAGG
* *
24886 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * *
24908 GAGGTTATCAAAA-TTCTATAGT
1 GTGGTTATTAAAATTTC-ATAGG
** *
24930 GTGGTTACCAAAATTTCATAGT
1 GTGGTTATTAAAATTTCATAGG
**
24952 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
* *
24974 ATCAGGTTATTAAAATCT-ATTAGG
1 GT--GGTTATTAAAATTTCA-TAGG
* *
24998 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
25020 GTGGTTA
1 GTGGTTA
25027 ATTATCACAA
Statistics
Matches: 113, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
21 3 0.03
22 88 0.78
23 6 0.05
24 16 0.14
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:25087 original size:22 final size:22
Alignment explanation
Indices: 25062--25437 Score: 167
Period size: 22 Copynumber: 16.9 Consensus size: 22
25052 ATCAAAGAGA
* *
25062 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
25084 TTAT-AAGAATTTTATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
25106 TTAACAAAATTTCAT-GGGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
25128 TTATTAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
25150 TTATCAAAATTTCA-AATGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
25172 TTATAAAAGCCTCAATTTCATAAG-GA-G
1 TTAT-CAA-----AATTTCATA-GTGAGG
* * *
25199 -TACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
25219 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
25240 TTATCGAAATTTCATAGAGATCGCA
1 TTATCAAAATTTCATAGTGA--G-G
**
25265 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* *
25287 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
25309 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
25331 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * **
25353 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
25375 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
25397 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
25419 TTA-CAAAAATTTCATAGTG
1 TTATC-AAAATTTCATAGTG
25438 GTATTTTTGG
Statistics
Matches: 264, Mismatches: 69, Indels: 42
0.70 0.18 0.11
Matches are distributed among these distances:
19 2 0.01
20 18 0.07
21 17 0.06
22 187 0.71
23 6 0.02
24 1 0.00
25 20 0.08
26 2 0.01
27 1 0.00
28 8 0.03
29 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:25335 original size:44 final size:44
Alignment explanation
Indices: 25060--25432 Score: 201
Period size: 44 Copynumber: 8.4 Consensus size: 44
25050 TTATCAAAGA
* * * * *
25060 GATTATCAAAATGTCATAGCGAGGTTAT-AAGAATTTTATAGTGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAA-AATTTCATAATGT
* * * * * * *
25104 GGTTAACAAAATTTC-ATGGGAAGGTTATTAAAATTTTATAGTGT
1 GATTATCAAAATTTCAAAGAG-AGGTTATCAAAATTTCATAATGT
* *
25148 GGTTATCAAAATTTCAAATGA-AGGTTATAAAAGCCTCAATTTCATAA-G-
1 GATTATCAAAATTTCAAA-GAGAGGTTAT-CAA-----AATTTCATAATGT
* * * * *
25196 GAGTACCAAAATTTGATAGA-AGGTTATC-AAATCTCATAGA-GT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATA-ATGT
* * * *
25238 GATTATCGAAATTTCATAGAGATCGCATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGA--G-GTTATCAAAATTTCATAATG-T
* *
25286 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
25329 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
25373 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
25417 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
25433 TAGTGGTATT
Statistics
Matches: 253, Mismatches: 54, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
40 8 0.03
41 2 0.01
42 16 0.06
43 6 0.02
44 146 0.58
45 9 0.04
46 6 0.02
47 36 0.14
48 15 0.06
49 1 0.00
50 8 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:25563 original size:22 final size:22
Alignment explanation
Indices: 25507--25968 Score: 178
Period size: 22 Copynumber: 21.1 Consensus size: 22
25497 AACCTTTTAT
*
25507 TATGGA-GTAATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
25528 -A-GGAGGATATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
* *
25548 TATGAAGGTTATCAAAATTTTA
1 TATGGAGGTTATCAAAATTTCA
** *
25570 TAGTTTA-GTTTTCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
* *
25592 CA-AGAGGGTTATCAAAATTTCA
1 TATGGA-GGTTATCAAAATTTCA
* * *
25614 TA-GTATGTAGATCAAAATTTCA
1 TATGGAGGT-TATCAAAATTTCA
* * * *
25636 AAGGGAGATTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
***
25658 TAAT-GAGGTTATCAAAAAACCA
1 T-ATGGAGGTTATCAAAATTTCA
* *
25680 TAGGGAGGTTAACAAAA--T--
1 TATGGAGGTTATCAAAATTTCA
* *
25698 T-TGTA-GTTATCAAGATTTCA
1 TATGGAGGTTATCAAAATTTCA
* * * *
25718 TAAGAAAGTTATCAAAATTTTA
1 TATGGAGGTTATCAAAATTTCA
* *
25740 TAGGGAGGTTTATCAAAATTTTA
1 TATGGAGG-TTATCAAAATTTCA
25763 TA-GGAAGCTGATTTATCAAAATTTCA
1 TATGG-AG--G--TTATCAAAATTTCA
* *
25789 TA-GCGAGATTATCACAATTTCA
1 TATG-GAGGTTATCAAAATTTCA
25811 TAGTGTGA--TTATCAAAATTTCA
1 TA-TG-GAGGTTATCAAAATTTCA
* * *
25833 GAGTCTGA--TTA-CTAACAA-TTAA
1 TA-T-GGAGGTTATC-AA-AATTTCA
* * *
25855 TATGGAGGTTTTTAAATTTTCA
1 TATGGAGGTTATCAAAATTTCA
* * *
25877 TAAT-GTGGTTATCAATATATCA
1 T-ATGGAGGTTATCAAAATTTCA
* *
25899 TATGGAGGTTATCAACATCTCA
1 TATGGAGGTTATCAAAATTTCA
**
25921 TAGTGTTGGTTATCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
*
25944 T-TGGGAAGTTATCAAAATTTCA
1 TAT-GGAGGTTATCAAAATTTCA
25966 TAT
1 TAT
25969 TAAGGTCTTC
Statistics
Matches: 330, Mismatches: 75, Indels: 70
0.69 0.16 0.15
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
19 3 0.01
20 18 0.05
21 12 0.04
22 215 0.65
23 46 0.14
24 3 0.01
25 1 0.00
26 19 0.06
27 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATGGAGGTTATCAAAATTTCA
Found at i:25784 original size:26 final size:23
Alignment explanation
Indices: 25704--25791 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
25694 AAATTTGTAG
* * * *
25704 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAGGAAGGT
*
25726 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGGT
25749 TTATCAAAATTTTATAGGAAGCTGAT
1 TTATCAAAATTTTATAGGAAG--G-T
*
25775 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
25792 CGAGATTATC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 17 0.31
23 20 0.36
25 1 0.02
26 17 0.31
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:25955 original size:45 final size:44
Alignment explanation
Indices: 25874--25967 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
25864 TTTTAAATTT
* * *
25874 TCATAATGTGGTTATCAATATATCATATGGAGGTTATCAACATC
1 TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
* * *
25918 TCATAGTGTTGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATT
1 TCATAATG-TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATC
25963 TCATA
1 TCATA
25968 TTAAGGTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
44 8 0.19
45 34 0.81
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
Found at i:26265 original size:30 final size:31
Alignment explanation
Indices: 26231--26295 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
26221 AACTTTATGT
*
26231 TTTCCGATTGTACCCTTATT-TTTAAAA-ATA
1 TTTCCAATTGTA-CCTTATTCTTTAAAACATA
*
26261 TTTCCAATTGTACCTTTTTCTTTAAAACATA
1 TTTCCAATTGTACCTTATTCTTTAAAACATA
26292 TTTC
1 TTTC
26296 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 6 0.19
30 18 0.58
31 7 0.23
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCTTATTCTTTAAAACATA
Found at i:26628 original size:19 final size:21
Alignment explanation
Indices: 26596--26638 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
26586 TTCTTTACTA
26596 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
26617 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
26636 TTA
1 TTA
26639 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:26875 original size:22 final size:22
Alignment explanation
Indices: 26789--26894 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
26779 TTATCTCTAA
*
26789 GTGGTTATCAAAATTTCATAAG-
1 GTGGTTACCAAAATTTCAT-AGC
* ** *
26811 ATGGTTATTATAATTTCATGAG-
1 GTGGTTACCAAAATTTCAT-AGC
* * *
26833 GAGGTTATCAAAATTCCATAGC
1 GTGGTTACCAAAATTTCATAGC
* *
26855 GTGGTTACCAAATTTTCATAGT
1 GTGGTTACCAAAATTTCATAGC
*
26877 GTGATTACCAAAATTTCA
1 GTGGTTACCAAAATTTCA
26895 CAGGATCAGG
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
21 2 0.03
22 65 0.97
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (22 bp):
GTGGTTACCAAAATTTCATAGC
Found at i:27078 original size:22 final size:22
Alignment explanation
Indices: 27053--27118 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
27043 TTCATTAAAT
*
27053 ATTTAATGGGGAGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
27075 ATTTTATAGTGTGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
27097 ATTTCATATGAAGGTTAT-AAA
1 ATTTAATAGGGAGGTTATCAAA
27118 A
1 A
27119 GTTTCAATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTAATAGGGAGGTTATCAAA
Found at i:27080 original size:23 final size:22
Alignment explanation
Indices: 27061--27118 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
27051 ATATTTAATG
27061 GGGAGGTTATCAAAATTTTATA
1 GGGAGGTTATCAAAATTTTATA
* * *
27083 GTGTGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
27105 TGAAGGTTAT-AAAA
1 GGGAGGTTATCAAAA
27119 GTTTCAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (22 bp):
GGGAGGTTATCAAAATTTTATA
Found at i:27197 original size:22 final size:22
Alignment explanation
Indices: 27162--27399 Score: 146
Period size: 22 Copynumber: 10.8 Consensus size: 22
27152 TGATAGAAGG
*
27162 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
27183 TTATCGAAATTTCATAGAGATCGGA
1 TTATCAAAATTTCATAGAG-T--GA
**
27208 TTATCAAAATTT-ATAGAAAGA
1 TTATCAAAATTTCATAGAGTGA
*
27229 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAG-TGA
* * * *
27251 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGAGTGA
*
27273 TTATCAAAATTACATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTGA
* * *
27295 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGAGTGA
* * * * * *
27317 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGAGTGA
* ** *
27339 TTATCAAAATTTCATAAAAAGG
1 TTATCAAAATTTCATAGAGTGA
* *
27361 TTATCAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAGA-GTGA
27383 TTA-CAAAAATTTCATAG
1 TTATC-AAAATTTCATAG
27400 TGGTATTTCT
Statistics
Matches: 170, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
21 24 0.14
22 124 0.73
23 4 0.02
24 5 0.03
25 13 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:27299 original size:44 final size:44
Alignment explanation
Indices: 27206--27770 Score: 169
Period size: 44 Copynumber: 12.9 Consensus size: 44
27196 ATAGAGATCG
* * *
27206 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCATAATG-T
** *
27250 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCATAATGT
* * ** * * * * *
27293 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCATAATGT
* * *
27337 GGTTATCAAAATTTCATAA-AAAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAAAGGTTATCAAAATTTCATAATGT
** * *
27381 GATTA-CAAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCATAGTAT
1 GATTATC-AAAATTTCA-A-----A------GAAAGGTTATCAAAATTTCATAATGT
* * * * * *
27437 GGTTA-CCAAA-TT---AGAAAGGTTATTAAACTTTTATTATG-
1 GATTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCATAATGT
* * * *
27475 GAGTAATCAAAATTTCAATG--AGGATATCAAAA-TTCAGTGA-G-
1 GA-TTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCA-TAATGT
* *
27516 GA-TATCAAAATTTCATATG-AAGGTTATCAAAATTTCATAGT-T
1 GATTATCAAAATTTCA-AAGAAAGGTTATCAAAATTTCATAATGT
* * *
27558 TAGTTTTCAAAATTTCACAAG-AGGGTTATCAAAATTTCATAGTATGT
1 GA-TTATCAAAATTTCA-AAGAAAGGTTATCAAAATTTCATA--ATGT
* * ** * * *
27605 -A-GATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA
1 GATTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCATAATGT
** * ** *
27647 GATTATCAAAAAATCATAGGGAGGTTATCAAAATTT-GT-A---
1 GATTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCATAATGT
* * ** *
27686 G-TTATCAAGATTTCATAAGAAA-GTTATCAAAATTTTATAGGGAG
1 GATTATCAAAATTTCA-AAGAAAGGTTATCAAAATTTCATAATG-T
* * * * *
27730 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATA
1 GATTATCAAAATTTCAAAGAAAG-GTTATCAAAATTTCATA
27771 GCGAGGTTAT
Statistics
Matches: 383, Mismatches: 92, Indels: 90
0.68 0.16 0.16
Matches are distributed among these distances:
38 25 0.07
39 36 0.09
40 7 0.02
41 20 0.05
42 20 0.05
43 19 0.05
44 194 0.51
45 14 0.04
46 17 0.04
47 1 0.00
49 1 0.00
54 2 0.01
55 3 0.01
56 24 0.06
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAAAGGTTATCAAAATTTCATAATGT
Found at i:27374 original size:66 final size:65
Alignment explanation
Indices: 27162--27371 Score: 172
Period size: 66 Copynumber: 3.2 Consensus size: 65
27152 TGATAGAAGG
* * * * * * * *
27162 TTATCAAATCTCATAGAGTGATTATCGAAATTTCATAGAGATCGGATTATCAAAATTT-ATAGAA
1 TTATCAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGA--GG-TTATCAAAATTTCATAAAA
27226 AGA
63 AGA
* ** * * * * ***
27229 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTG
1 TTATC-AAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTTCATAAAAAG
27294 A
65 A
*
27295 TTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAA-AGAGGTTATCAAAATTTCATAAAAA
1 TTATCA-AATTTCATAGAGGGGTCAACAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAAAAA
*
27359 GG
64 GA
27361 TTATCAAATTT
1 TTATCAAATTT
27372 TCAAAATGTG
Statistics
Matches: 115, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
65 17 0.15
66 62 0.54
67 7 0.06
68 29 0.25
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (65 bp):
TTATCAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTTCATAAAAAGA
Found at i:27515 original size:19 final size:19
Alignment explanation
Indices: 27480--27549 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
27470 TTATGGAGTA
27480 ATCAAAATTTCAATGAGGAT
1 ATCAAAA-TTCAATGAGGAT
*
27500 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAATGAGGAT
*
27519 ATCAAAATTTCATATGAAGGTT
1 ATCAAAA-TTCA-ATG-AGGAT
27541 ATCAAAATT
1 ATCAAAATT
27550 TCATAGTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
19 18 0.41
20 11 0.25
21 4 0.09
22 11 0.25
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.31
Consensus pattern (19 bp):
ATCAAAATTCAATGAGGAT
Found at i:27546 original size:22 final size:22
Alignment explanation
Indices: 27480--28076 Score: 215
Period size: 22 Copynumber: 27.5 Consensus size: 22
27470 TTATGGAGTA
*
27480 ATCAAAATTTCA-ATG-AGGAT
1 ATCAAAATTTCATATGAAGGTT
* *
27500 ATCAAAA-TTCA-GTG-AGGAT
1 ATCAAAATTTCATATGAAGGTT
27519 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
27541 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
27563 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
27585 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
27607 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
* *
27629 AACAAAATTTCATAATG-AGATT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
27651 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
27673 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
27689 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
27711 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
27734 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
*
27757 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
27779 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
27801 ATCAAAATTTCAGAGTGTAA--TT
1 ATCAAAATTTCATA-TG-AAGGTT
* *
27823 -GCTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
27845 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
27867 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * ** *
27889 ATCAACATCTCATAGTGTTGGTC
1 ATCAAAATTTCATA-TGAAGGTT
27912 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
27934 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * *
27957 -TCAAAATTCCTTAGGGAA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
27978 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
** **
28000 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * * **
28021 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATATG-AAGGTT
* *
28043 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
28065 ATCAAAATTTCA
1 ATCAAAATTTCA
28077 AAATGGGATC
Statistics
Matches: 433, Mismatches: 101, Indels: 84
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
19 18 0.04
20 14 0.03
21 36 0.08
22 282 0.65
23 68 0.16
24 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:27595 original size:66 final size:66
Alignment explanation
Indices: 27518--27947 Score: 253
Period size: 66 Copynumber: 6.6 Consensus size: 66
27508 TCAGTGAGGA
* * * * *
27518 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCACAAGAGG
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-GTAGATTATCAAAATTTCATAAGAGG
27582 GT
65 GT
* * * * *
27584 TATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA-
1 TATCAAAATTTCATAGGGAGGT-TATCAAAATTTCATAGGTAGATTATCAAAATTTCATAA-GAG
*
27647 GAT
64 GGT
** * **
27650 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T--GTAG-TTATCAAGATTTCATAAGAAAG
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGTAGATTATCAAAATTTCATAAGAGGG
27709 T
66 T
* * * *
27710 TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCAT-AGCG
1 TATCAAAATTTCATAGGGAGG-TTATCAAAATTTCATAGGTAGA-TTATCAAAATTTCATAAGAG
27774 AGGT
64 -GGT
* * * * * * *
27778 TATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTA-ATT-GCTAACAA-TTCATATG-
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-GTAGATTATC-AA-AATTTCATAAGA
27839 GAGGT
63 G-GGT
* * * ** * * * * * * *
27844 TTTTAAATTTTCATAACGTGGTTATCAATATATCATATGG-AGGTTATCAACATCTCAT-AGTGT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATA-GGTAGATTATCAAAATTTCATAAGAG-
27907 TGGT
64 -GGT
* * *
27911 CATCAAAATTTCATTGGGAAGTTATCAAAATTTCATA
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATA
27948 TTGAGGTCTT
Statistics
Matches: 276, Mismatches: 64, Indels: 47
0.71 0.17 0.12
Matches are distributed among these distances:
59 2 0.01
60 34 0.12
61 12 0.04
62 2 0.01
63 1 0.00
64 1 0.00
65 12 0.04
66 120 0.43
67 58 0.21
68 34 0.12
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (66 bp):
TATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGTAGATTATCAAAATTTCATAAGAGGG
T
Found at i:28795 original size:24 final size:24
Alignment explanation
Indices: 28763--28811 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28753 TATATTAACT
* * *
28763 ACAATAATTAGGCTTTTTTTTGAC
1 ACAATAATTAGCCTTATGTTTGAC
28787 ACAATAATTAGCCTTATGTTTGAC
1 ACAATAATTAGCCTTATGTTTGAC
28811 A
1 A
28812 ATTAGACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (24 bp):
ACAATAATTAGCCTTATGTTTGAC
Found at i:29495 original size:14 final size:14
Alignment explanation
Indices: 29476--29503 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29466 AGAGTAATTA
29476 GATATTGCCCTATC
1 GATATTGCCCTATC
29490 GATATTGCCCTATC
1 GATATTGCCCTATC
29504 AAATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (14 bp):
GATATTGCCCTATC
Found at i:31232 original size:10 final size:10
Alignment explanation
Indices: 31204--31236 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
31194 TGCTATAGTG
31204 GATTTGCAAC
1 GATTTGCAAC
31214 GACTTTGCAAC
1 GA-TTTGCAAC
31225 GATTTGCAAC
1 GATTTGCAAC
31235 GA
1 GA
31237 ATTTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (10 bp):
GATTTGCAAC
Found at i:31240 original size:11 final size:11
Alignment explanation
Indices: 31205--31240 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
31195 GCTATAGTGG
31205 ATTTGCAACGA
1 ATTTGCAACGA
*
31216 CTTTGCAACG-
1 ATTTGCAACGA
31226 ATTTGCAACGA
1 ATTTGCAACGA
31237 ATTT
1 ATTT
31241 TCCATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (11 bp):
ATTTGCAACGA
Found at i:31552 original size:18 final size:18
Alignment explanation
Indices: 31520--31554 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31510 GAAATTTTGC
* *
31520 AACAAATTTAGTTTTCAT
1 AACAAATTAAATTTTCAT
31538 AACAAATTAAATTTTCA
1 AACAAATTAAATTTTCA
31555 ATTCCCGCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (18 bp):
AACAAATTAAATTTTCAT
Found at i:31577 original size:103 final size:102
Alignment explanation
Indices: 31408--31716 Score: 377
Period size: 103 Copynumber: 3.0 Consensus size: 102
31398 AATTTGCTGC
* * * * * * *
31408 AAATTTTGCCACGAAA-TTAGTTTTCGTGGCAAATTAAAATTTGAATTTCCACTCACTCAAAAAT
1 AAATTTTGCAAC-AAATTTAGTTTTCGTGACAAATT-AAATTTCAATTCCCGCTCGCTCAAATAT
* * *
31472 TTTGCGCCAAAATTAATTTTTGCAACGGAAATTATTACG
64 TTTGCGCCAAAATAAATTTTTGCAACGGAAATTACTACA
* * *
31511 AAATTTTGCAACAAATTTAGTTTTCATAACAAATTAAATTTTCAATTCCCGCTCGCTTAAATATT
1 AAATTTTGCAACAAATTTAGTTTTCGTGACAAATTAAA-TTTCAATTCCCGCTCGCTCAAATATT
31576 TTGCGCCAAAATAAATTTTTGCAACGGAAATTACTACA
65 TTGCGCCAAAATAAATTTTTGCAACGGAAATTACTACA
* * * * * *
31614 AAATTTTGCAACGATTTTAATTTTCGTGACAAATTAAAATTCGAATTCCCGCTAGCCCAAATATT
1 AAATTTTGCAACAAATTTAGTTTTCGTGACAAATTAAATTTC-AATTCCCGCTCGCTCAAATATT
* * *
31679 TTCCGCCAAAATAAATTGTTCCAACGGAAATTACTACA
65 TTGCGCCAAAATAAATTTTTGCAACGGAAATTACTACA
31717 TAAAAATCTG
Statistics
Matches: 178, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
102 9 0.05
103 169 0.95
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (102 bp):
AAATTTTGCAACAAATTTAGTTTTCGTGACAAATTAAATTTCAATTCCCGCTCGCTCAAATATTT
TGCGCCAAAATAAATTTTTGCAACGGAAATTACTACA
Found at i:34120 original size:21 final size:21
Alignment explanation
Indices: 34096--34136 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
34086 AAACTGGCGG
34096 GTTTTACTTGCTGAGGAAGGT
1 GTTTTACTTGCTGAGGAAGGT
34117 GTTTTACTTGCTGAGGAAGG
1 GTTTTACTTGCTGAGGAAGG
34137 CGAACTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.34, T:0.37
Consensus pattern (21 bp):
GTTTTACTTGCTGAGGAAGGT
Found at i:34331 original size:17 final size:17
Alignment explanation
Indices: 34293--34325 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34283 CTTATAGTAC
*
34293 CTAGTTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
34310 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
34326 GATAGGCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.33
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:36557 original size:6 final size:6
Alignment explanation
Indices: 36548--36580 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
36538 TATATATATA
36548 TATCTT TATCTT TATCTT TATCTT TATCTT TAT
1 TATCTT TATCTT TATCTT TATCTT TATCTT TAT
36581 ATTATATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (6 bp):
TATCTT
Found at i:37786 original size:40 final size:40
Alignment explanation
Indices: 37731--37811 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
37721 TTTAGGTTTG
37731 ATTCAACATGTCAAGGACATGCATATATAGTAAAATAAAT
1 ATTCAACATGTCAAGGACATGCATATATAGTAAAATAAAT
*
37771 ATTCAACATGTCAAGGACATGCATATATAGTAATATAAAT
1 ATTCAACATGTCAAGGACATGCATATATAGTAAAATAAAT
37811 A
1 A
37812 CAATTTCTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (40 bp):
ATTCAACATGTCAAGGACATGCATATATAGTAAAATAAAT
Done.