Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015063.1 Corchorus capsularis cultivar CVL-1 contig15084, 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: 58410
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:532 original size:12 final size:12
Alignment explanation
Indices: 510--538 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
500 TTATGAAATT
510 CGTAG-TAAACC
1 CGTAGCTAAACC
521 CGTAGCTAAACC
1 CGTAGCTAAACC
533 CGTAGC
1 CGTAGC
539 AGATATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (12 bp):
CGTAGCTAAACC
Found at i:2575 original size:21 final size:21
Alignment explanation
Indices: 2549--2595 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2539 GGAGTGAGTC
2549 TAATTGCATGTTAAATTGGTA
1 TAATTGCATGTTAAATTGGTA
2570 TAATTGCATGTTAAATTGGTA
1 TAATTGCATGTTAAATTGGTA
2591 TAATT
1 TAATT
2596 TTTTCGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (21 bp):
TAATTGCATGTTAAATTGGTA
Found at i:5173 original size:12 final size:11
Alignment explanation
Indices: 5154--5195 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
5144 TTGTTTTATA
5154 ATTTGATTTAG
1 ATTTGATTTAG
5165 ATTTAGATTTAG
1 ATTT-GATTTAG
*
5177 ATTTGCTTT-G
1 ATTTGATTTAG
*
5187 CTTTGATTT
1 ATTTGATTT
5196 TTAGTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.30
11 8 0.30
12 11 0.41
ACGTcount: A:0.21, C:0.05, G:0.17, T:0.57
Consensus pattern (11 bp):
ATTTGATTTAG
Found at i:6846 original size:19 final size:18
Alignment explanation
Indices: 6813--6848 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6803 TTGAAATAAT
6813 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
6831 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
6849 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:11539 original size:2 final size:2
Alignment explanation
Indices: 11534--11572 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
11524 GGAATAATTT
*
11534 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
11573 AAAGTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11864 original size:38 final size:37
Alignment explanation
Indices: 11792--11893 Score: 116
Period size: 38 Copynumber: 2.7 Consensus size: 37
11782 AATTTGGTTT
* *
11792 TTTGTTTCCAACGTCCTGTTTAAGTTTTCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAAGTTTTCATTTTGTC
**
11829 TTTGTTTCCAATCGTTGTATTTAA-TTTTACATTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAAGTTTT-CATTTTGTC
* * *
11867 TTTGTCTCCAACATCCTATTTGAGTTT
1 TTTGTTTCCAACGTCCTATTTAAGTTT
11894 AGATAATCTG
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
37 23 0.43
38 30 0.57
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.54
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAAGTTTTCATTTTGTC
Found at i:12421 original size:436 final size:439
Alignment explanation
Indices: 11843--12707 Score: 1529
Period size: 436 Copynumber: 2.0 Consensus size: 439
11833 TTTCCAATCG
** *
11843 TTGTATTTAATTTTACATTTTGTCTTTGTCTCCAACATCCTATTTGAGTTTAGATAATCTGAAGT
1 TTGTATTTAATTTTACATTTTGTCTTTGTCTCCAACATCCTATTTGAACTTAGATAA--TGAAGC
* *
11908 AAATGGACAATTAGTTTGAATATTCAGATCTTATATCTTATTAGGCCATGACTGTATAACTATCT
64 AAATGGACAATTAATTTGAATATTCAGATCCTATATCTTATTAGGCCATGACTGTATAACTATCT
*
11973 ATATACTATATATAAAAGTACGAATAAGGGGAAACTTTACATTTTCCTATTGTATCATATTTTTT
129 ATATACTATATATAAAAGTACGAATAAGGGGAAACTTTACATTTTCCTATTGTACCATATTTTTT
*
12038 CAAATATATTTCTAAATTGAGATTATTAAAATTTATTATTTAAAAATTAATTATAAAATTTCAAT
194 CAAATATATTTCTAAATTGACATTATTAAAATTTATTATTTAAAAATTAATTATAAAATTTCAAT
**
12103 TTAGACTGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAAATTTCTACGAATAA
259 TTAGACCAAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAAATTTCTACGAATAA
*
12168 TGGGAAA-TTTATGTTTTACGATTGCACCCTTTTTTCCAAATATATTTCTAAATTTCCATTATTA
324 TGGGAAACTTTATGTTTTACGATTGCACCCATTTTTCCAAATATATTTCTAAATTTCCATTATTA
12232 AAATTTAGTATAATTTTATTCTTTAAAAAATAATTAAAACTTATTTTTTCT
389 AAATTTAGTATAATTTTATTCTTTAAAAAATAATTAAAACTTATTTTTTCT
* *
12283 TTGTATTTAATTTTCCTTTTTGTCTTTGTCTCCAACATCCTATTTGAACTTAGAT-A-GAAGCAA
1 TTGTATTTAATTTTACATTTTGTCTTTGTCTCCAACATCCTATTTGAACTTAGATAATGAAGCAA
* * *
12346 ATGGACAATTAATTTGAATATTCATATCCTATATCTTATTAGGCCTTGACTTTATAACTATCTAT
66 ATGGACAATTAATTTGAATATTCAGATCCTATATCTTATTAGGCCATGACTGTATAACTATCTAT
12411 ATACTATATATAAAAGTACGAATAAGGGGAAACTTTACATTTTCCTATTGTACCATATTTTTTCA
131 ATACTATATATAAAAGTACGAATAAGGGGAAACTTTACATTTTCCTATTGTACCATATTTTTTCA
* *
12476 AATATTTTTCTAAATTGACATTATTAAAATTTATTATTTAAAATTTAATTATAAAATTTCAATTT
196 AATATATTTCTAAATTGACATTATTAAAATTTATTATTTAAAAATTAATTATAAAATTTCAATTT
12541 AGACCAAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAAATTTCTACGAATAATG
261 AGACCAAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAAATTTCTACGAATAATG
12606 GGAAACTTTATGTTTTACGATTGCACCCATTTTTCCAAATATATTTCTAAATTTCCATTATTAAA
326 GGAAACTTTATGTTTTACGATTGCACCCATTTTTCCAAATATATTTCTAAATTTCCATTATTAAA
*
12671 ATTTAGTATAATTTTATTCTTTAAAAATTAATTAAAA
391 ATTTAGTATAATTTTATTCTTTAAAAAATAATTAAAA
12708 TTTTCAATTT
Statistics
Matches: 406, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
436 260 0.64
437 94 0.23
439 1 0.00
440 51 0.13
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (439 bp):
TTGTATTTAATTTTACATTTTGTCTTTGTCTCCAACATCCTATTTGAACTTAGATAATGAAGCAA
ATGGACAATTAATTTGAATATTCAGATCCTATATCTTATTAGGCCATGACTGTATAACTATCTAT
ATACTATATATAAAAGTACGAATAAGGGGAAACTTTACATTTTCCTATTGTACCATATTTTTTCA
AATATATTTCTAAATTGACATTATTAAAATTTATTATTTAAAAATTAATTATAAAATTTCAATTT
AGACCAAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAAATTTCTACGAATAATG
GGAAACTTTATGTTTTACGATTGCACCCATTTTTCCAAATATATTTCTAAATTTCCATTATTAAA
ATTTAGTATAATTTTATTCTTTAAAAAATAATTAAAACTTATTTTTTCT
Found at i:12513 original size:13 final size:14
Alignment explanation
Indices: 12495--12539 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
12485 CTAAATTGAC
12495 ATTATTAAAATTT-
1 ATTATTAAAATTTA
12508 ATTATTTAAAATTTA
1 ATTA-TTAAAATTTA
12523 ATTA-TAAAATTTCA
1 ATTATTAAAATTT-A
12537 ATT
1 ATT
12540 TAGACCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.41
14 13 0.45
15 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATTAAAATTTA
Found at i:12812 original size:19 final size:20
Alignment explanation
Indices: 12785--12822 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12775 TACTATTATT
12785 TTTTGAATT-TAATATTTTAC
1 TTTTGAATTGTAAT-TTTTAC
12805 TTTT-AATTGTAATTTTTA
1 TTTTGAATTGTAATTTTTA
12823 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTGAATTGTAATTTTTAC
Found at i:13127 original size:24 final size:23
Alignment explanation
Indices: 13100--13158 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
13090 TGTGGTTACC
13100 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGGAT-AGGTTATT
* *
13124 AAAATTTCTTA-GATTGGTTATT
1 AAAATTTCATAGGATAGGTTATT
*
13146 GAAATTTCATAGG
1 AAAATTTCATAGG
13159 GTGGTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 16 0.53
23 4 0.13
24 10 0.33
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (23 bp):
AAAATTTCATAGGATAGGTTATT
Found at i:13163 original size:22 final size:22
Alignment explanation
Indices: 13100--13165 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
13090 TGTGGTTACC
13100 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGGAT--GGTTATT
*
13124 AAAATTTCTTA-GATTGGTTATT
1 AAAATTTCATAGGA-TGGTTATT
* *
13146 GAAATTTCATAGGGTGGTTA
1 AAAATTTCATAGGATGGTTA
13166 ATTATCACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 22 0.61
23 3 0.08
24 11 0.31
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (22 bp):
AAAATTTCATAGGATGGTTATT
Found at i:13226 original size:22 final size:22
Alignment explanation
Indices: 13201--14062 Score: 189
Period size: 22 Copynumber: 38.7 Consensus size: 22
13191 ATCAAAGAGA
* *
13201 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
13223 TTAT-AAGAATTTCATAGTGTGC
1 TTATCAA-AATTTCATAGTGAGG
* *
13245 TTAACAAAATTCCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* *
13267 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
13289 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
13311 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
13333 TTAT-AAAAGTCTCAATTTCA-TAAGGG
1 TTATCAAAA-TTTC-A--T-AGTGA-GG
* * * * **
13359 GTACCAAAATTTGATAG-AAAA
1 TTATCAAAATTTCATAGTGAGG
* * * *
13380 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
13401 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCAT--AG-TGAGG
*
13426 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTG-AGG
13447 TTATCAAAATTTCATAGT---G
1 TTATCAAAATTTCATAGTGAGG
* *
13466 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
13488 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
13510 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * **
13532 TGAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
13554 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
13576 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
**
13598 TTA-CAAAAATTTCATAGTGATA
1 TTATC-AAAATTTCATAGTGAGG
** * * ***
13620 TT-TCTAGGGAGGTTATCAAAAT-TTC
1 TTATC-A---AAATT-TCATAGTGAGG
* *** *
13645 ATAGT-ATGGTTATCAAATTAG-GAAGA
1 TTA-TCAAAATT-TC--A-TAGTG-AGG
* *
13671 TTATTATAAACTTTTATTA-TG-GAG
1 TTATCA-AAA-TTTCA-TAGTGAG-G
* * *
13695 TAATCAAAATTTC--AGGGAGA
1 TTATCAAAATTTCATAGTGAGG
*
13715 ATATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
13737 TTATCAAAATTTCATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* * * *
13758 TAGATCACAATTTCATAGGGAGA
1 T-TATCAAAATTTCATAGTGAGG
* * *
13781 TTAACAAAATTTAATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
** *
13803 TTATCAAAAAATCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
13825 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
13847 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
13869 TTATCAAAATTTCAAAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
*
13891 TTA-CTAACGA-TTCATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
* * * * ** *
13913 TTTTTAAATTTTCACAACGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
13935 TTATCAATATATCGTA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * * *
13957 CTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
13980 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCATAGTGAGG
*
14002 TTATCAAAATTTCATATTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
14024 TCT-TCAAAATTCCTTAGGGAAG
1 T-TATCAAAATTTCATAGTGAGG
*
14046 TTAACAAAAATTTCATA
1 TTATC-AAAATTTCATA
14063 AGAAGGTTAA
Statistics
Matches: 604, Mismatches: 172, Indels: 127
0.67 0.19 0.14
Matches are distributed among these distances:
19 17 0.03
20 21 0.03
21 45 0.07
22 416 0.69
23 43 0.07
24 9 0.01
25 29 0.05
26 16 0.03
27 6 0.01
28 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:13447 original size:21 final size:24
Alignment explanation
Indices: 13363--13463 Score: 94
Period size: 21 Copynumber: 4.5 Consensus size: 24
13353 TAAGGGGTAC
*
13363 CAAAATTTGATAGA-A-A-ATTAT
1 CAAAATTTCATAGAGACAGATTAT
* *
13384 C-AAATCTCATAGAG--TGATTAT
1 CAAAATTTCATAGAGACAGATTAT
*
13405 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGA-CAGATTAT
13430 CAAAATTT-ATAG-GA-AGATTAT
1 CAAAATTTCATAGAGACAGATTAT
13451 CAAAATTTCATAG
1 CAAAATTTCATAG
13464 TGTTATCAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
20 10 0.15
21 22 0.33
22 16 0.24
23 2 0.03
24 4 0.06
25 13 0.19
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (24 bp):
CAAAATTTCATAGAGACAGATTAT
Found at i:23002 original size:13 final size:12
Alignment explanation
Indices: 22975--23042 Score: 100
Period size: 12 Copynumber: 5.5 Consensus size: 12
22965 TTAATACAGG
*
22975 TATCGACGAATA
1 TATCGACGGATA
22987 TATCGAACGGATA
1 TATCG-ACGGATA
*
23000 TATCGAACAGATA
1 TATCG-ACGGATA
23013 TATCGACGGATA
1 TATCGACGGATA
23025 TATCGACGGATA
1 TATCGACGGATA
23037 TATCGA
1 TATCGA
23043 GGTATCGATG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
12 29 0.56
13 23 0.44
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:25247 original size:14 final size:14
Alignment explanation
Indices: 25228--25273 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
25218 ACAAAGGTGC
*
25228 TGACGTGTACTGGT
1 TGACGTGTACTTGT
* *
25242 TGACGTGTCCTTGC
1 TGACGTGTACTTGT
25256 TGACGTGTACTTGT
1 TGACGTGTACTTGT
25270 TGAC
1 TGAC
25274 TTTTGACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.13, C:0.20, G:0.30, T:0.37
Consensus pattern (14 bp):
TGACGTGTACTTGT
Found at i:30732 original size:21 final size:20
Alignment explanation
Indices: 30708--30880 Score: 126
Period size: 21 Copynumber: 8.4 Consensus size: 20
30698 ACTCTTTGAA
*
30708 TTACTGATCACCTTTTACTC
1 TTACTGATTACCTTTTACTC
*
30728 TTTACTGATTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
* * *
30750 TAACTAATTACCATTTTGCTC
1 TTACTGATTACC-TTTTACTC
*
30771 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
30792 TTACTGATTACC---T--T-
1 TTACTGATTACCTTTTACTC
30806 TTACTGATTA-CTATTTAACTC
1 TTACTGATTACCT-TTT-ACTC
*
30827 TTTACTGATTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
*
30849 TTTACTGATTACCTTCTTACTTT
1 -TTACTGATTACCTT-TTAC-TC
30872 TTACTGATT
1 TTACTGATT
30881 TCTATTTTTA
Statistics
Matches: 122, Mismatches: 14, Indels: 31
0.73 0.08 0.19
Matches are distributed among these distances:
13 1 0.01
14 10 0.08
15 1 0.01
17 2 0.02
20 1 0.01
21 55 0.45
22 47 0.39
23 4 0.03
24 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:30775 original size:42 final size:43
Alignment explanation
Indices: 30708--30896 Score: 175
Period size: 42 Copynumber: 4.6 Consensus size: 43
30698 ACTCTTTGAA
*
30708 TTACTGATCACC-TTTTACTCTTTACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
* * *
30750 TAACTAATTACCATTTTGCTC-TTACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
*
30792 TTACTGATTA-C------CT-TTTACTGATTACTATTTAACTC
1 TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
* * *
30827 TTTACTGATTACTATTTTACTCTTTACTGATTACCT-TCTTACTTT
1 -TTACTGATTACCATTTTACTCTTTACTGATTA-CTATTTTAC-TC
* *
30872 TTACTGATTTCTATTTTTACTCTTT
1 TTACTGATTACCA-TTTTACTCTTT
30897 TTTACTTATT
Statistics
Matches: 121, Mismatches: 12, Indels: 25
0.77 0.08 0.16
Matches are distributed among these distances:
35 22 0.18
36 10 0.08
41 1 0.01
42 38 0.31
43 9 0.07
44 27 0.22
45 14 0.12
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (43 bp):
TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
Found at i:30810 original size:35 final size:37
Alignment explanation
Indices: 30771--30847 Score: 122
Period size: 35 Copynumber: 2.1 Consensus size: 37
30761 CATTTTGCTC
* *
30771 TTACTGATTACTATTTTACTC-TTACTGATTAC-CTT
1 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
30806 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
1 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
30843 TTACT
1 TTACT
30848 CTTTACTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 20 0.53
36 11 0.29
37 7 0.18
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (37 bp):
TTACTGATTACTATTTAACTCTTTACTGATTACTATT
Found at i:30831 original size:22 final size:22
Alignment explanation
Indices: 30805--30896 Score: 123
Period size: 22 Copynumber: 4.1 Consensus size: 22
30795 CTGATTACCT
*
30805 TTTACTGATTACTATTTAACTC
1 TTTACTGATTACTATTTTACTC
30827 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
30849 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
30871 TTTACTGATTTCTATTTTTACTC
1 TTTACTGATTACTA-TTTTACTC
30894 TTT
1 TTT
30897 TTTACTTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
21 2 0.03
22 48 0.79
23 11 0.18
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:30925 original size:27 final size:26
Alignment explanation
Indices: 30868--31076 Score: 185
Period size: 27 Copynumber: 7.8 Consensus size: 26
30858 TACCTTCTTA
* * *
30868 CTTTTTACTGATTTCTA-TTTTTACT
1 CTTTTTACTGAATACCATTTTTTACT
* *
30893 CTTTTTTACTTATTACCATTTTCTTACT
1 C-TTTTTACTGAATACCATTTT-TTACT
*
30921 CTTTTTACTGATTATCC-TTTTCTTACT
1 CTTTTTACTGAATA-CCATTTT-TTACT
30948 -TTTTTACTGAATACCATTTTTTACT
1 CTTTTTACTGAATACCATTTTTTACT
*
30973 CTTTTTTACTGAATACCA-TTTTTATT
1 C-TTTTTACTGAATACCATTTTTTACT
*
30999 CTTTTTACCACTGAATACCA-TTTTAACT
1 CTTTTT---ACTGAATACCATTTTTTACT
* *
31027 CCTTTTTTACTAAATACCATTTTTTATT
1 -C-TTTTTACTGAATACCATTTTTTACT
*
31055 CTTTTCTACTGATTACCATTTT
1 CTTTT-TACTGAATACCATTTT
31077 CACTTTACTA
Statistics
Matches: 157, Mismatches: 13, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
25 13 0.08
26 41 0.26
27 66 0.42
28 31 0.20
29 1 0.01
30 5 0.03
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (26 bp):
CTTTTTACTGAATACCATTTTTTACT
Found at i:30927 original size:53 final size:53
Alignment explanation
Indices: 30827--31077 Score: 190
Period size: 53 Copynumber: 4.8 Consensus size: 53
30817 TATTTAACTC
30827 TTTACTGATTACTA-TTTTACTC---TTTACTGATTACC---TTCTTA--CTT
1 TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTT
* *
30871 TTTACTGATTTCTATTTTTACTCTTTTTTACTTATTACCATTTTCTTACTCTT
1 TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTT
*
30924 TTTACTGATTATCCT-TTTCTTA--CTTTTTTACTGAATACCATTTT-TTACTCTTT
1 TTTACTGATTA--CTATTT-TTACTCTTTTTTACTGATTACCATTTTCTTACTC-TT
* * * * * *
30977 TTTACTGAATACCATTTTTATTCTTTTTACCACTGAATACCA-TTT-TAACTCCTTT
1 TTTACTGATTACTATTTTTACTCTTTTT--TACTGATTACCATTTTCTTACT-C-TT
* * * * *
31032 TTTACTAAATACCATTTTTTATTCTTTTCTACTGATTACCATTTTC
1 TTTACTGATTACTA-TTTTTACTCTTTTTTACTGATTACCATTTTC
31078 ACTTTACTAA
Statistics
Matches: 172, Mismatches: 13, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
44 13 0.08
45 8 0.05
48 12 0.07
51 10 0.06
52 9 0.05
53 51 0.30
54 20 0.12
55 36 0.21
56 13 0.08
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (53 bp):
TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTT
Found at i:31033 original size:55 final size:53
Alignment explanation
Indices: 30953--31076 Score: 169
Period size: 55 Copynumber: 2.3 Consensus size: 53
30943 TTACTTTTTT
* *
30953 ACTGAATACCATTTTTTACTCTTTTTTACTGAATACCA-TTTTTATTCTTTTTACC
1 ACTGAATACCA-TTTTAACTCTTTTTTACTAAATACCATTTTTTATTC-TTTT-CC
*
31008 ACTGAATACCATTTTAACTCCTTTTTTACTAAATACCATTTTTTATTCTTTTCT
1 ACTGAATACCATTTTAACT-CTTTTTTACTAAATACCATTTTTTATTCTTTTCC
*
31062 ACTGATTACCATTTT
1 ACTGAATACCATTTT
31077 CACTTTACTA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
54 22 0.35
55 32 0.51
56 9 0.14
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.52
Consensus pattern (53 bp):
ACTGAATACCATTTTAACTCTTTTTTACTAAATACCATTTTTTATTCTTTTCC
Found at i:31085 original size:21 final size:21
Alignment explanation
Indices: 31061--31105 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31051 TATTCTTTTC
* *
31061 TACTGATTACCATTTTCACTT
1 TACTAATTACCATTTACACTT
* *
31082 TACTAATTACTATTTACTCTT
1 TACTAATTACCATTTACACTT
31103 TAC
1 TAC
31106 CATTTTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (21 bp):
TACTAATTACCATTTACACTT
Found at i:31127 original size:36 final size:36
Alignment explanation
Indices: 31067--31334 Score: 405
Period size: 36 Copynumber: 7.5 Consensus size: 36
31057 TTTCTACTGA
* * * *
31067 TTACCATTTT-CACTTTACTAATTACTATTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
31102 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
31138 TTACCATTTTACCCTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
31174 TTACCATTTTACCCTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
31210 TTACCATTTTACCCTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* *
31246 TCACCATTTTACTCTTTACTGATTACTATTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* *
31282 TTACCATTTTACTCTTTACTGATTACCCTTT-GTTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTT-T
31318 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
31335 TTAACTTGAT
Statistics
Matches: 217, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
35 12 0.06
36 205 0.94
ACGTcount: A:0.20, C:0.24, G:0.03, T:0.54
Consensus pattern (36 bp):
TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
Found at i:31465 original size:32 final size:32
Alignment explanation
Indices: 31429--31686 Score: 199
Period size: 32 Copynumber: 7.8 Consensus size: 32
31419 CTACTGCTCC
*
31429 CTTCTTTTACTTTTACTCCATTCTACTAATAT
1 CTTCTTTTACTTTTACTCCATTCTACTGATAT
*
31461 CTTCTTTTACCTTGATTCTTAATTACCCATT-TACTGAT-T
1 CTTCTTTTA-C----TT-TT-ACT--CCATTCTACTGATAT
* * *
31500 ACTTCTTTTACTCTTACTCCATTCTGCTGAGTAC
1 -CTTCTTTTACTTTTACTCCATTCTACTGA-TAT
* *
31534 CTT-TTTTACTTTTACTCAATTCTATTGATA-
1 CTTCTTTTACTTTTACTCCATTCTACTGATAT
*
31564 CTTATTTTACTTTTACTCCATTCTACTGATTAT
1 CTTCTTTTACTTTTACTCCATTCTACTGA-TAT
*
31597 -TTCTTTTACTTTTACTCCATTTTACTGAT-T
1 CTTCTTTTACTTTTACTCCATTCTACTGATAT
*
31627 ACTTCCTCTTACTTTTACTCCATT-TACTGAT-T
1 -CTT-CTTTTACTTTTACTCCATTCTACTGATAT
* * *
31659 ACTTCCTCTTGCTTTCACTCCATTCTAC
1 -CTT-CTTTTACTTTTACTCCATTCTAC
31687 GGATTACTTC
Statistics
Matches: 189, Mismatches: 17, Indels: 39
0.77 0.07 0.16
Matches are distributed among these distances:
30 4 0.02
31 31 0.16
32 95 0.50
33 28 0.15
34 2 0.01
35 1 0.01
37 2 0.01
38 2 0.01
39 4 0.02
40 15 0.08
41 5 0.03
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (32 bp):
CTTCTTTTACTTTTACTCCATTCTACTGATAT
Found at i:31470 original size:72 final size:71
Alignment explanation
Indices: 31389--31613 Score: 227
Period size: 72 Copynumber: 3.3 Consensus size: 71
31379 ATAGTGACTA
* *
31389 CTTCTTTTACTTTTACTCTTAATTACCAATCTACTGCTCCCTTCTTTTACTTTTACTCCATTCTA
1 CTTCTTTTACTTTTACTCTTAATTACC-ATCTACTGAT-ACTTCTTTTACTTTTACTCCATTCTA
31454 CT-AATAT
64 CTGAATAT
* * * * * *
31461 CTTCTTTTACCTTGATTCTTAATTACCCATTTACTGATTACTTCTTTTACTCTTACTCCATTCTG
1 CTTCTTTTACTTTTACTCTTAATTA-CCATCTACTGA-TACTTCTTTTACTTTTACTCCATTCTA
* *
31526 CTGAGTAC
64 CTGAATAT
* *
31534 CTT-TTTTACTTTTACTC--AA-T----TCTATTGATACTTATTTTACTTTTACTCCATTCTACT
1 CTTCTTTTACTTTTACTCTTAATTACCATCTACTGATACTTCTTTTACTTTTACTCCATTCTACT
*
31591 GATTAT
66 GAATAT
31597 -TTCTTTTACTTTTACTC
1 CTTCTTTTACTTTTACTC
31614 CATTTTACTG
Statistics
Matches: 129, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
62 2 0.02
63 44 0.34
64 6 0.05
69 1 0.01
70 2 0.02
72 65 0.50
73 9 0.07
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (71 bp):
CTTCTTTTACTTTTACTCTTAATTACCATCTACTGATACTTCTTTTACTTTTACTCCATTCTACT
GAATAT
Found at i:31638 original size:17 final size:17
Alignment explanation
Indices: 31618--31668 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
31608 TTACTCCATT
31618 TTACTGATTACTTCCTC
1 TTACTGATTACTTCCTC
*
31635 TTACT-TTTAC-TCCAT-
1 TTACTGATTACTTCC-TC
31650 TTACTGATTACTTCCTC
1 TTACTGATTACTTCCTC
31667 TT
1 TT
31669 GCTTTCACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 8 0.29
16 10 0.36
17 10 0.36
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.51
Consensus pattern (17 bp):
TTACTGATTACTTCCTC
Found at i:31650 original size:65 final size:65
Alignment explanation
Indices: 31483--31701 Score: 243
Period size: 63 Copynumber: 3.4 Consensus size: 65
31473 TGATTCTTAA
* * * * *
31483 TTAC-CCATT-TACTGATTACTTCTTTTACTCTTACTCCATTCTGCTGAGTACCTT-TTTTACTT
1 TTACTCCATTCTACTGATTACTTCTCTTACTTTTACTCCATTCTACTGATTACTTTCTTTTACTT
* * * *
31545 TTACTCAATTCTATTGA-TACTTATTTTACTTTTACTCCATTCTACTGATTA-TTTCTTTTACTT
1 TTACTCCATTCTACTGATTACTTCTCTTACTTTTACTCCATTCTACTGATTACTTTCTTTTACTT
* * * *
31608 TTACTCCATTTTACTGATTACTTCCTCTTACTTTTACTCCATT-TACTGATTACTTCCTCTTGCT
1 TTACTCCATTCTACTGATTACTT-CTCTTACTTTTACTCCATTCTACTGATTACTTTCTTTTACT
31672 T
65 T
* *
31673 TCACTCCATTCTACGGATTACTTCCTCTT
1 TTACTCCATTCTACTGATTACTT-CTCTT
31702 TTACTTCTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
62 6 0.05
63 56 0.42
64 19 0.14
65 52 0.39
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.51
Consensus pattern (65 bp):
TTACTCCATTCTACTGATTACTTCTCTTACTTTTACTCCATTCTACTGATTACTTTCTTTTACTT
Found at i:35188 original size:26 final size:26
Alignment explanation
Indices: 35146--35215 Score: 97
Period size: 25 Copynumber: 2.7 Consensus size: 26
35136 TAATGAATTA
* * *
35146 AAAATGACTAAAGTGCCCCCTAGTTC
1 AAAATGACCAAAATGCCCCATAGTTC
*
35172 AAAATGACCAAAATG-CCCATGGTTC
1 AAAATGACCAAAATGCCCCATAGTTC
35197 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
35216 TAGGTGACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 23 0.59
26 16 0.41
ACGTcount: A:0.40, C:0.27, G:0.14, T:0.19
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCATAGTTC
Found at i:35323 original size:14 final size:14
Alignment explanation
Indices: 35291--35337 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
35281 GGTGTCTACA
35291 CTGACGTGTAC-TG
1 CTGACGTGTACTTG
* *
35304 TTTGACGTGTCCTTG
1 -CTGACGTGTACTTG
35319 CTGACGTGTACTTG
1 CTGACGTGTACTTG
*
35333 TTGAC
1 CTGAC
35338 TTTTGACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (14 bp):
CTGACGTGTACTTG
Found at i:36510 original size:23 final size:23
Alignment explanation
Indices: 36463--36510 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
36453 TATTGATAAA
**
36463 TTAATATATGTTCATGAACGTGT
1 TTAATATATGTTCATGAACCCGT
36486 TTAAT-TAGTGTTCATGAACCCGT
1 TTAATATA-TGTTCATGAACCCGT
36509 TT
1 TT
36511 GTTCATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (23 bp):
TTAATATATGTTCATGAACCCGT
Found at i:36777 original size:22 final size:22
Alignment explanation
Indices: 36762--36806 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
36752 TAATCTGAAG
36762 GAGGTTTAAACTTAATCAAGAA
1 GAGGTTTAAACTTAATCAAGAA
36784 GAGGTTTAAACTTAATCAAGAA
1 GAGGTTTAAACTTAATCAAGAA
36806 G
1 G
36807 GCTTATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (22 bp):
GAGGTTTAAACTTAATCAAGAA
Found at i:40907 original size:2 final size:2
Alignment explanation
Indices: 40900--40949 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
40890 TGAGACATAA
40900 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40942 AG AG AG AG
1 AG AG AG AG
40950 TTTTGAACAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41803 original size:13 final size:13
Alignment explanation
Indices: 41787--41814 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41777 AGGAAAAAAG
41787 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
41800 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
41813 AA
1 AA
41815 CCCAACAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:41814 original size:11 final size:11
Alignment explanation
Indices: 41780--41807 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41770 CCAAAAGAGG
41780 AAAAAAGAAAA
1 AAAAAAGAAAA
41791 AAAAAAGAAAA
1 AAAAAAGAAAA
41802 AAAAAA
1 AAAAAA
41808 AAGAAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:42733 original size:7 final size:7
Alignment explanation
Indices: 42723--42760 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
42713 AATTTGTCAT
42723 TTATATA
1 TTATATA
*
42730 TTAT-TT
1 TTATATA
42736 TATATATA
1 T-TATATA
42744 TTATATA
1 TTATATA
42751 TTATATA
1 TTATATA
42758 TTA
1 TTA
42761 AACCTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 2 0.07
7 23 0.85
8 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTATATA
Found at i:43177 original size:17 final size:18
Alignment explanation
Indices: 43139--43178 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
43129 TGAATAAGAA
43139 CAAT-TTTTCTCCTTCTT
1 CAATATTTTCTCCTTCTT
*
43156 C-ATATTTTCTTCTTC-T
1 CAATATTTTCTCCTTCTT
43172 CAATATT
1 CAATATT
43179 CTATTGTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (18 bp):
CAATATTTTCTCCTTCTT
Found at i:43351 original size:3 final size:3
Alignment explanation
Indices: 43343--43373 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
43333 GAAGTTCTAG
43343 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43374 CTATACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50435 original size:8 final size:8
Alignment explanation
Indices: 50424--50477 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
50414 GCTATTAGCT
50424 TATTATTA
1 TATTATTA
50432 TATTATTA
1 TATTATTA
50440 -ATTA--A
1 TATTATTA
*
50445 TAATATTA
1 TATTATTA
50453 -ATATATTA
1 TAT-TATTA
50461 TATTATTA
1 TATTATTA
50469 TATATATTA
1 TAT-TATTA
50478 CTAGTTTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
5 1 0.03
6 3 0.08
7 5 0.13
8 22 0.58
9 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTATTA
Found at i:50563 original size:22 final size:22
Alignment explanation
Indices: 50538--50641 Score: 106
Period size: 22 Copynumber: 4.8 Consensus size: 22
50528 TTGAATATTT
50538 CTATGAAATTTTGATAATTACC
1 CTATGAAATTTTGATAATTACC
* * *
50560 CTATTAAATTTTGATAACTACG
1 CTATGAAATTTTGATAATTACC
* *
50582 TTATGAAATTTAGATAATTA-C
1 CTATGAAATTTTGATAATTACC
* *
50603 CTATGAAATTGTAATAA--ACTC
1 CTATGAAATTTTGATAATTAC-C
50624 CATATGAAATTTTGATAA
1 C-TATGAAATTTTGATAA
50642 CCTAATGTGA
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
21 15 0.23
22 49 0.75
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAATTACC
Found at i:50630 original size:43 final size:44
Alignment explanation
Indices: 50539--50641 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
50529 TGAATATTTC
* * * **
50539 TATGAAATTTTGATAATTACCCTATTAAATTTTGATAACTACGT
1 TATGAAATTTTGATAATTACCCTATGAAATTGTAATAACTACCA
*
50583 TATGAAATTTAGATAATTA-CCTATGAAATTGTAATAAACT-CCA
1 TATGAAATTTTGATAATTACCCTATGAAATTGTAAT-AACTACCA
50626 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
50642 CCTAATGTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 29 0.57
44 22 0.43
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGATAATTACCCTATGAAATTGTAATAACTACCA
Found at i:50653 original size:43 final size:43
Alignment explanation
Indices: 50606--50687 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
50596 TAATTACCTA
50606 TGAAATTGTAATAAA-C-TCCATATGAAATTTTGATAACCTAATG
1 TGAAATTGTAATAAACCTTCC-TATGAAATTTTG-TAACCTAATG
*
50649 TGAAATTTTAATAAACCTTCCTATGAAATTTTGTAACCT
1 TGAAATTGTAATAAACCTTCCTATGAAATTTTGTAACCT
50688 CCCTATAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
43 20 0.56
44 13 0.36
45 3 0.08
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (43 bp):
TGAAATTGTAATAAACCTTCCTATGAAATTTTGTAACCTAATG
Found at i:50714 original size:22 final size:21
Alignment explanation
Indices: 50602--50714 Score: 68
Period size: 22 Copynumber: 5.2 Consensus size: 21
50592 TAGATAATTA
** *
50602 CCTATGAAATTGTAATAAACTC
1 CCTATGAAATT-TTGTAACCTC
*
50624 CATATGAAATTTTGATAACCT-
1 CCTATGAAATTTTG-TAACCTC
** * * *
50645 AATGTGAAATTTTAATAAACCTT
1 CCTATGAAATTTT-GT-AACCTC
50668 CCTATGAAATTTTGTAACCTC
1 CCTATGAAATTTTGTAACCTC
*
50689 CCTAT-AAGATTTTGTTAATCTC
1 CCTATGAA-ATTTTG-TAACCTC
50711 CCTA
1 CCTA
50715 ATTTCTTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
20 2 0.03
21 29 0.40
22 31 0.43
23 10 0.14
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (21 bp):
CCTATGAAATTTTGTAACCTC
Done.