Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006222.1 Hibiscus syriacus cultivar Beakdansim tig00014825_pilon, 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: 65527
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:493 original size:19 final size:19
Alignment explanation
Indices: 471--507 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
461 AGTATCTAAT
471 TGCGAAAGTAAGTATCGCG
1 TGCGAAAGTAAGTATCGCG
*
490 TGCGAAAGTCAGTATCGC
1 TGCGAAAGTAAGTATCGC
508 ATTGCGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (19 bp):
TGCGAAAGTAAGTATCGCG
Found at i:525 original size:20 final size:22
Alignment explanation
Indices: 497--558 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 22
487 GCGTGCGAAA
497 GTCAGTATCGCATTGCGATTTT
1 GTCAGTATCGCATTGCGATTTT
* *
519 GT-A-TATCGCGTTGCGA--TA
1 GTCAGTATCGCATTGCGATTTT
537 GTCAGTATCGCATTGCGATTTT
1 GTCAGTATCGCATTGCGATTTT
559 CCAAATTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.09
19 1 0.03
20 24 0.75
21 1 0.03
22 3 0.09
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (22 bp):
GTCAGTATCGCATTGCGATTTT
Found at i:526 original size:39 final size:40
Alignment explanation
Indices: 425--558 Score: 143
Period size: 39 Copynumber: 3.4 Consensus size: 40
415 CGCTTTGAAA
* *
425 ATCGCATTGCGATTATGTATTAT-TCGTTGCG-AAGTCAGT
1 ATCGCATTGCGATTTTGTA-TATCGCGTTGCGAAAGTCAGT
** **
464 ATCTAATTGCGA--AAGTAAGTATCGCG-TGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-A-TATCGCGTTGCGAAAGTCAGT
*
503 ATCGCATTGCGATTTTGTATATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATATCGCGTTGCGAAAGTCAGT
543 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
559 CCAAATTCGC
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
37 3 0.04
38 8 0.10
39 37 0.47
40 29 0.37
41 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (40 bp):
ATCGCATTGCGATTTTGTATATCGCGTTGCGAAAGTCAGT
Found at i:608 original size:21 final size:20
Alignment explanation
Indices: 583--637 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
573 TGATTTACTT
583 AATCGCAATGCGAATTGGGAA
1 AATCGCAATGCGAATT-GGAA
*
604 AATCGCAACGCGAAATTGGAA
1 AATCGCAATGCG-AATTGGAA
*
625 AATCGCATTGCGA
1 AATCGCAATGCGA
638 TAGTAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 25 0.83
22 4 0.13
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
AATCGCAATGCGAATTGGAA
Found at i:3545 original size:33 final size:33
Alignment explanation
Indices: 3480--3560 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
3470 TTGTTTGTTG
3480 AAGTTATATTATAAAAAAATTAGTTAATTAGTTT
1 AAGTTATA-TATAAAAAAATTAGTTAATTAGTTT
*
3514 AAGTTATATATAATAAATAA-TAGTTTA-TAGTTT
1 AAGTTATATATAA-AAA-AATTAGTTAATTAGTTT
3547 AAGTTATATA-AAAA
1 AAGTTATATATAAAA
3561 TTATGGCGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 21 0.48
34 17 0.39
35 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (33 bp):
AAGTTATATATAAAAAAATTAGTTAATTAGTTT
Found at i:5373 original size:14 final size:14
Alignment explanation
Indices: 5356--5386 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5346 CAATAGTTCA
5356 TTGATTATAGAGTT
1 TTGATTATAGAGTT
5370 TTGATTATAGAGTT
1 TTGATTATAGAGTT
5384 TTG
1 TTG
5387 CTTTGTCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (14 bp):
TTGATTATAGAGTT
Found at i:5880 original size:45 final size:43
Alignment explanation
Indices: 5780--5880 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 43
5770 GTATCGATAC
*
5780 TACTAATGATTTA-TTATTAAAATTTAATGATTTAGTAATGAT
1 TACTAATGATTTATTTATTAAAATTTAATGATTCAGTAATGAT
* *
5822 TACTAAT-AATTATTTATTATAAATATTTAATGATTCAG-ATTTGA-
1 TACTAATGATTTATTTA-T-TAAA-ATTTAATGATTCAGTA-ATGAT
5866 TACTAATGATTTATT
1 TACTAATGATTTATT
5881 AATGATTACT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
41 4 0.08
42 10 0.20
43 1 0.02
44 12 0.24
45 22 0.45
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (43 bp):
TACTAATGATTTATTTATTAAAATTTAATGATTCAGTAATGAT
Found at i:6174 original size:15 final size:15
Alignment explanation
Indices: 6154--6182 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6144 TTTATTATTA
6154 ATATTTAATGATTTG
1 ATATTTAATGATTTG
6169 ATATTTAATGATTT
1 ATATTTAATGATTT
6183 AGTAATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
ATATTTAATGATTTG
Found at i:6191 original size:21 final size:21
Alignment explanation
Indices: 6167--6227 Score: 52
Period size: 24 Copynumber: 2.8 Consensus size: 21
6157 TTTAATGATT
6167 TGATATTTAATGATTTAGTAA
1 TGATATTTAATGATTTAGTAA
* *
6188 TGAT-TCCTAATAATGATTTATTAT
1 TGATAT--T--TAATGATTTAGTAA
*
6212 TAATATTTAATGATTT
1 TGATATTTAATGATTT
6228 GATACTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
20 1 0.03
21 13 0.41
22 1 0.03
23 1 0.03
24 15 0.47
25 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (21 bp):
TGATATTTAATGATTTAGTAA
Found at i:6236 original size:21 final size:22
Alignment explanation
Indices: 6198--6242 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
6188 TGATTCCTAA
*
6198 TAATGATTTATTATTAAT-ATT
1 TAATGATTTATTACTAATGATT
6219 TAATGATTTGA-TACTAATGATT
1 TAATGATTT-ATTACTAATGATT
6241 TA
1 TA
6243 GTAATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
TAATGATTTATTACTAATGATT
Found at i:6262 original size:59 final size:60
Alignment explanation
Indices: 6132--6262 Score: 219
Period size: 60 Copynumber: 2.2 Consensus size: 60
6122 ATAGTACCGA
* * *
6132 TACTACTAATTATTTATTATTAATATTTAATGATTTGATATTTAATGATTTAGTAATGAT
1 TACTAATAATGATTTATTATTAATATTTAATGATTTGATATCTAATGATTTAGTAATGAT
*
6192 TCCTAATAATGATTTATTATTAATATTTAATGATTTGATA-CTAATGATTTAGTAATGAT
1 TACTAATAATGATTTATTATTAATATTTAATGATTTGATATCTAATGATTTAGTAATGAT
6251 TACTAATAATGA
1 TACTAATAATGA
6263 ACTTATAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 29 0.44
60 37 0.56
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (60 bp):
TACTAATAATGATTTATTATTAATATTTAATGATTTGATATCTAATGATTTAGTAATGAT
Found at i:6271 original size:24 final size:24
Alignment explanation
Indices: 6233--6324 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
6223 GATTTGATAC
* *
6233 TAATGATTTAGTAATGATTACTAA
1 TAATGACTTAATAATGATTACTAA
*
6257 TAATGAACTT-ATAATAATTACTAA
1 TAATG-ACTTAATAATGATTACTAA
* * *
6281 TCATGATTTAATAACGATTACTAA
1 TAATGACTTAATAATGATTACTAA
* *
6305 TAATTATTTAATAATGATTA
1 TAATGACTTAATAATGATTA
6325 AATATTTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 3 0.05
24 50 0.89
25 3 0.05
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATGACTTAATAATGATTACTAA
Found at i:6299 original size:11 final size:11
Alignment explanation
Indices: 6174--6328 Score: 73
Period size: 11 Copynumber: 13.2 Consensus size: 11
6164 ATTTGATATT
*
6174 TAATGATTTAG
1 TAATGATTTAA
6185 TAATGATTCCTAA
1 TAATGATT--TAA
*
6198 TAATGATTTAT
1 TAATGATTTAA
* *
6209 TATTAATATT--
1 TAATGAT-TTAA
6219 TAATGATTTGATA
1 TAATGATTT-A-A
*
6232 CTAATGATTTAG
1 -TAATGATTTAA
6244 TAATGATTACTAA
1 TAATGATT--TAA
6257 TAATGAACTTATAA
1 TAATG-A-TT-TAA
* *
6271 TAATTA-CTAA
1 TAATGATTTAA
*
6281 TCATGATTTAA
1 TAATGATTTAA
*
6292 TAACGATTACTAA
1 TAATGATT--TAA
*
6305 TAATTATTTAA
1 TAATGATTTAA
*
6316 TAATGATTAAA
1 TAATGATTTAA
6327 TA
1 TA
6329 TTTAAATAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 30
0.69 0.13 0.19
Matches are distributed among these distances:
9 2 0.02
10 12 0.11
11 46 0.42
12 2 0.02
13 28 0.26
14 17 0.16
15 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:6585 original size:21 final size:21
Alignment explanation
Indices: 6561--6604 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
6551 ATATATTTCA
*
6561 ACCACTATGCTCTGCCATTCC
1 ACCACTATGCTCTGCCATCCC
* * *
6582 ACCAGTTTGCTCTTCCATCCC
1 ACCACTATGCTCTGCCATCCC
6603 AC
1 AC
6605 TTGGAAACGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.18, C:0.43, G:0.09, T:0.30
Consensus pattern (21 bp):
ACCACTATGCTCTGCCATCCC
Found at i:7571 original size:2 final size:2
Alignment explanation
Indices: 7564--7588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7554 TATAACATTA
7564 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7589 GGTATGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7928 original size:19 final size:19
Alignment explanation
Indices: 7904--7954 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
7894 CCTCGACTGA
7904 GGTATCGGTACCCTCCCTG
1 GGTATCGGTACCCTCCCTG
7923 GGTATCGGTACCCTCCCTG
1 GGTATCGGTACCCTCCCTG
*
7942 GGTATCGATACCC
1 GGTATCGGTACCC
7955 CTATTGTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.14, C:0.35, G:0.25, T:0.25
Consensus pattern (19 bp):
GGTATCGGTACCCTCCCTG
Found at i:9492 original size:16 final size:16
Alignment explanation
Indices: 9467--9498 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9457 TGTTACAGTA
9467 ATCATAACTAAATCAT
1 ATCATAACTAAATCAT
*
9483 ATCATTACTAAATCAT
1 ATCATAACTAAATCAT
9499 TAAATATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (16 bp):
ATCATAACTAAATCAT
Found at i:14961 original size:37 final size:37
Alignment explanation
Indices: 14888--14962 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
14878 GTTGGAAAAT
*
14888 ATTTATATATTTTCTTTAAAAAACTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAACTTAAAATCATAAA
* *
14925 ATTTATATAATTTTTTTTATAAAA-TTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAACTT-AAAATCATAAA
14962 A
1 A
14963 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAACTTAAAATCATAAA
Found at i:15270 original size:6 final size:6
Alignment explanation
Indices: 15259--15284 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15249 TTCAATATTT
15259 AAACCG AAACCG AAACCG AAACCG AA
1 AAACCG AAACCG AAACCG AAACCG AA
15285 TAGTTAAAAA
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:0.54, C:0.31, G:0.15, T:0.00
Consensus pattern (6 bp):
AAACCG
Found at i:22553 original size:24 final size:24
Alignment explanation
Indices: 22526--22571 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
22516 TTAATTTGTC
22526 TATCTCATTTTAACTGTTTGAATT
1 TATCTCATTTTAACTGTTTGAATT
22550 TATCTCATTTTAACTGTTTGAA
1 TATCTCATTTTAACTGTTTGAA
22572 GCGATCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (24 bp):
TATCTCATTTTAACTGTTTGAATT
Found at i:23145 original size:3 final size:3
Alignment explanation
Indices: 23128--23160 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
23118 CTACAAAAAA
*
23128 TAT TAT TAA TA- TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
23161 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:38010 original size:29 final size:28
Alignment explanation
Indices: 37978--38069 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
37968 ATTTTCGTTC
*
37978 TCTAGAATTTTATAAATTTATATTAATCT
1 TCTAAAATTTTATAAATTTA-ATTAATCT
* *
38007 TCTAAAATTTTATAATTTTAAGTTTATCT
1 TCTAAAATTTTATAAATTTAA-TTAATCT
* *
38036 CCT-TAATTTTATAAATTTAAATTAATCT
1 TCTAAAATTTTATAAATTT-AATTAATCT
*
38064 CCTAAA
1 TCTAAA
38070 GTTAAGTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 23 0.44
29 29 0.56
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (28 bp):
TCTAAAATTTTATAAATTTAATTAATCT
Found at i:38043 original size:28 final size:28
Alignment explanation
Indices: 37983--38066 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
37973 CGTTCTCTAG
* * *
37983 AATTTTATAAATTTATATTAATCTTCTAA
1 AATTTTATAAATTTAAATTAATCTCCT-T
* * *
38012 AATTTTATAATTTTAAGTTTATCTCCTT
1 AATTTTATAAATTTAAATTAATCTCCTT
38040 AATTTTATAAATTTAAATTAATCTCCT
1 AATTTTATAAATTTAAATTAATCTCCT
38067 AAAGTTAAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 24 0.52
29 22 0.48
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (28 bp):
AATTTTATAAATTTAAATTAATCTCCTT
Found at i:38281 original size:18 final size:18
Alignment explanation
Indices: 38260--38294 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38250 TAAAATATAT
38260 TAAACCATTTTAATATTG
1 TAAACCATTTTAATATTG
*
38278 TAAATCATTTTAATATT
1 TAAACCATTTTAATATT
38295 ATAGACACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (18 bp):
TAAACCATTTTAATATTG
Found at i:38751 original size:20 final size:20
Alignment explanation
Indices: 38728--38766 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38718 TGAATTAAAA
*
38728 AAATAATTTACAATTAATTT
1 AAATAATATACAATTAATTT
*
38748 AAATAATATATAATTAATT
1 AAATAATATACAATTAATT
38767 AATATTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATAATATACAATTAATTT
Found at i:39669 original size:29 final size:28
Alignment explanation
Indices: 39637--39728 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
39627 GTTTTTGTTC
*
39637 TCTAGAATTTTATAAATTTATATTAATCT
1 TCTAAAATTTTATAAATTTA-ATTAATCT
* *
39666 TCTAAAATTTTATAATTTTAAGTTTATCT
1 TCTAAAATTTTATAAATTTAA-TTAATCT
* *
39695 CCT-TAATTTTATAAATTTAAATTAATCT
1 TCTAAAATTTTATAAATTT-AATTAATCT
*
39723 CCTAAA
1 TCTAAA
39729 GTTAAGTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 23 0.44
29 29 0.56
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (28 bp):
TCTAAAATTTTATAAATTTAATTAATCT
Found at i:39702 original size:28 final size:28
Alignment explanation
Indices: 39642--39725 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
39632 TGTTCTCTAG
* * *
39642 AATTTTATAAATTTATATTAATCTTCTAA
1 AATTTTATAAATTTAAATTAATCTCCT-T
* * *
39671 AATTTTATAATTTTAAGTTTATCTCCTT
1 AATTTTATAAATTTAAATTAATCTCCTT
39699 AATTTTATAAATTTAAATTAATCTCCT
1 AATTTTATAAATTTAAATTAATCTCCT
39726 AAAGTTAAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 24 0.52
29 22 0.48
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (28 bp):
AATTTTATAAATTTAAATTAATCTCCTT
Found at i:40392 original size:20 final size:20
Alignment explanation
Indices: 40369--40407 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40359 TTAATTAAAA
*
40369 AAATAATTTACAATTAATTT
1 AAATAATATACAATTAATTT
*
40389 AAATAATATATAATTAATT
1 AAATAATATACAATTAATT
40408 AATATTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATAATATACAATTAATTT
Found at i:47845 original size:21 final size:17
Alignment explanation
Indices: 47808--47856 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 17
47798 CTACGAGGTC
47808 CTTCGGGACATAGTGGTT
1 CTTCGGGACATAGTGG-T
47826 CTTCGGGACATCTAAGTGGT
1 CTTCGGGACA--T-AGTGGT
47846 CATTCGGGACA
1 C-TTCGGGACA
47857 CATTCTACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.37
20 3 0.11
21 14 0.52
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (17 bp):
CTTCGGGACATAGTGGT
Found at i:59806 original size:29 final size:30
Alignment explanation
Indices: 59747--59806 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
59737 GTCCCGAAGG
*
59747 ACCTATCCATATGTTCCGAAGAACATAGGT
1 ACCTATCCATATGTCCCGAAGAACATAGGT
* *
59777 ACCTGTCCATATGTCCCG-AGGACATAGGT
1 ACCTATCCATATGTCCCGAAGAACATAGGT
59806 A
1 A
59807 ACCCTCGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (30 bp):
ACCTATCCATATGTCCCGAAGAACATAGGT
Found at i:60016 original size:20 final size:21
Alignment explanation
Indices: 59991--60036 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
59981 ATCAGATAGC
*
59991 ATATATCAAATCATACAA-AT
1 ATATATCAAAACATACAACAT
*
60011 ATATATCAAAACATATAACAT
1 ATATATCAAAACATACAACAT
60032 ATATA
1 ATATA
60037 ACTCATGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATATCAAAACATACAACAT
Found at i:62603 original size:29 final size:31
Alignment explanation
Indices: 62477--62603 Score: 67
Period size: 29 Copynumber: 4.1 Consensus size: 31
62467 AGAGTCTTTA
*
62477 TCTTTTTTAATATTTAA-ATATTTAATAGAT
1 TCTTTTTTAATATTTAATATAGTTAATAGAT
* *
62507 TC-TTTTTAATA--TAATGATA-TT-TTAG-G
1 TCTTTTTTAATATTTAAT-ATAGTTAATAGAT
*
62533 TC-TTTTTAATATTAAATATTAGTTAAATAGAGTCTTT
1 TCTTTTTTAATATTTAATA-TAGTT-AATAGA-----T
62570 ATCTTTTTTAATATTTAA-ATA-TTAATAGAT
1 -TCTTTTTTAATATTTAATATAGTTAATAGAT
62600 TCTT
1 TCTT
62604 ATTCTTTTGA
Statistics
Matches: 75, Mismatches: 6, Indels: 33
0.66 0.05 0.29
Matches are distributed among these distances:
26 11 0.15
27 7 0.09
28 7 0.09
29 18 0.24
30 3 0.04
31 3 0.04
35 6 0.08
36 2 0.03
37 2 0.03
38 3 0.04
39 13 0.17
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (31 bp):
TCTTTTTTAATATTTAATATAGTTAATAGAT
Found at i:63114 original size:19 final size:19
Alignment explanation
Indices: 63082--63119 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
63072 TTTAAAATAC
* *
63082 TTTAACATATAAAAATTAT
1 TTTAAAATAAAAAAATTAT
63101 TTTAAAATAAAAAAATTAT
1 TTTAAAATAAAAAAATTAT
63120 AAATGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAAAATAAAAAAATTAT
Done.