Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005564.1 Hibiscus syriacus cultivar Beakdansim tig00012905_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: 74249
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10436 original size:22 final size:22
Alignment explanation
Indices: 10411--10480 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 22
10401 CTTTATTTTA
10411 TAATTAAAAATTATACTTAAAT
1 TAATTAAAAATTATACTTAAAT
** *
10433 TAATT--GTATTCTA--T-AAT
1 TAATTAAAAATTATACTTAAAT
*
10450 TAA--AAAAATTATACTTAAAA
1 TAATTAAAAATTATACTTAAAT
10470 TAATTAAAAAT
1 TAATTAAAAAT
10481 ATATTATCCA
Statistics
Matches: 34, Mismatches: 7, Indels: 14
0.62 0.13 0.25
Matches are distributed among these distances:
17 11 0.32
18 1 0.03
19 1 0.03
20 10 0.29
22 11 0.32
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (22 bp):
TAATTAAAAATTATACTTAAAT
Found at i:10455 original size:35 final size:36
Alignment explanation
Indices: 10404--10474 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
10394 AACTCGACTT
* *
10404 TATTTTATAATT-AAAAATTATACTTAAATTAATTG
1 TATTCTATAATTAAAAAATTATACTTAAAATAATTG
10439 TATTCTATAATTAAAAAAATTATACTTAAAATAATT
1 TATTCTATAATT-AAAAAATTATACTTAAAATAATT
10475 AAAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 11 0.34
37 21 0.66
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
TATTCTATAATTAAAAAATTATACTTAAAATAATTG
Found at i:15517 original size:20 final size:20
Alignment explanation
Indices: 15494--15543 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
15484 AAAGTAAAAA
15494 AGGCAAAAGAATTTCATTAC
1 AGGCAAAAGAATTTCATTAC
15514 AGGCAAAAGAATTTCATTAC
1 AGGCAAAAGAATTTCATTAC
*
15534 AGTCAAAAGA
1 AGGCAAAAGA
15544 TCTCCCCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (20 bp):
AGGCAAAAGAATTTCATTAC
Found at i:15962 original size:2 final size:2
Alignment explanation
Indices: 15955--15984 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15945 GAGAAAGGAT
15955 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
15985 TAAATGTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17533 original size:16 final size:16
Alignment explanation
Indices: 17512--17546 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17502 AAATTCCTGG
*
17512 TTATTTTTTTAAATTA
1 TTATTTCTTTAAATTA
*
17528 TTATTTCTTTGAATTA
1 TTATTTCTTTAAATTA
17544 TTA
1 TTA
17547 GTTGTTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
TTATTTCTTTAAATTA
Found at i:28207 original size:44 final size:42
Alignment explanation
Indices: 28060--28634 Score: 280
Period size: 43 Copynumber: 13.5 Consensus size: 42
28050 TTACAGAACG
* * *
28060 AAAGTGAGATTGAAAAAATTAAGGGCCTCAATTATAAAGGTGA
1 AAAGTGAGATTAAAAAAATTAGGGGCCTC-ATTATAAAGGTAA
* ** * * * *
28103 AAATTGAGATTAAAAAAATTAGGGGATTCAGCTACAAAGATAG
1 AAAGTGAGATTAAAAAAATTAGGGGCCTCA-TTATAAAGGTAA
* *
28146 ATAGTGAGATCAAAAAAAATTAGGGGCCTCGATTATAAAGGTAAA
1 AAAGTGAGAT-TAAAAAAATTAGGGGCCTC-ATTATAAAGGT-AA
* * ** **
28191 AAAGTGGGATTGAAAAAATTAGGGGCCTCAACATAAATATAA
1 AAAGTGAGATTAAAAAAATTAGGGGCCTCATTATAAAGGTAA
***** * *
28233 AAAGTGAGA-TAATTTTTTTAGGAGCTTCAATTATAAAGGTAAAAACTAA
1 AAAGTGAGATTAAAAAAATTAGGGGCCTC-ATTATAAAGG-------TAA
* ** * * **
28282 AAAGTGAGATTGAAAATTTTAGGAGCCTCAATTTTAATTGTAA
1 AAAGTGAGATTAAAAAAATTAGGGGCCTC-ATTATAAAGGTAA
* * * * * *
28325 AAAGTGAGATTAAAAAAATCA-AGGCTTTAATTGTAAAGGTAG
1 AAAGTGAGATTAAAAAAATTAGGGGC-CTCATTATAAAGGTAA
* * * ** *
28367 AAACTGAGATTAGAAAAAGTAGGGATCTCAATTATAAAAGTAA
1 AAAGTGAGATTAAAAAAATTAGGGGCCTC-ATTATAAAGGTAA
*
28410 AAAGTG-GAATTGAAAAAAAATTA-GGGCCTCAATTATAAATGTAA
1 AAAGTGAG-ATT--AAAAAAATTAGGGGCCTC-ATTATAAAGGTAA
* * * *
28454 AAAGTGATATT-AAAAAATT-GAGGCTTCAATTATAAAAG-AA
1 AAAGTGAGATTAAAAAAATTAGGGGCCTC-ATTATAAAGGTAA
* * * * *
28494 GAAAGTGAG-GTAGAAAAATTATGGGCCTAAATTATAAATGTAA
1 -AAAGTGAGATTAAAAAAATTAGGGGCCT-CATTATAAAGGTAA
* *
28537 AAAGTAAGATTAAAAAAATTA-GGG-C-C--T-TAAATGTAA
1 AAAGTGAGATTAAAAAAATTAGGGGCCTCATTATAAAGGTAA
* **
28573 AAA-TAGATATTAAAAAAATTAGGAACCTCAATTATAAAGGTAA
1 AAAGT-GAGATTAAAAAAATTAGGGGCCTC-ATTATAAAGGTAA
*
28616 AAAGTGAAATTAAAAAAAT
1 AAAGTGAGATTAAAAAAAT
28635 AATAGGCCTT
Statistics
Matches: 396, Mismatches: 100, Indels: 72
0.70 0.18 0.13
Matches are distributed among these distances:
35 1 0.00
36 26 0.07
37 2 0.01
38 1 0.00
39 1 0.00
40 3 0.01
41 49 0.12
42 71 0.18
43 122 0.31
44 68 0.17
45 18 0.05
49 12 0.03
50 22 0.06
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (42 bp):
AAAGTGAGATTAAAAAAATTAGGGGCCTCATTATAAAGGTAA
Found at i:28239 original size:87 final size:87
Alignment explanation
Indices: 28072--28634 Score: 255
Period size: 87 Copynumber: 6.6 Consensus size: 87
28062 AGTGAGATTG
* * * *
28072 AAAAAATTAAGGGCCTCAATTATAAAGGTGAAAATTGAGATTAAAAAAATTAGGGGATTCAGCTA
1 AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGACTCAACTA
* *
28137 CAAAGATAGATAGTGAGATCAA
66 CAAAGATAAAAAGTGAGATCAA
* * * * *
28159 AAAAAATTAGGGGCCTCGATTATAAAGGTAAAAAAGTGGGATTGAAAAAATTAGGGGCCTCAAC-
1 AAAAAATTAAGGGCCTCAATTATAAAGGT-AAAAAGTGAGATTAAAAAAATTAGGGGACTCAACT
* *
28223 ATAAATATAAAAAGTGAGAT---
65 ACAAAGATAAAAAGTGAGATCAA
**** * * * ** * *
28243 AATTTTTTTAGGAGCTTCAATTATAAAGGTAAAAACTAAAAAGTGAGATTGAAAATTTTAGGAGC
1 AAAAAATTAAGG-GCCTCAATTATAAAGG-------TAAAAAGTGAGATTAAAAAAATTAGGGGA
* ** * *
28308 CTCAATTTTAATTG-TAAAAAGTGAGAT-TA
58 CTCAACTACAA-AGATAAAAAGTGAGATCAA
* * * * * * * * *
28337 AAAAAATCAA-GGCTTTAATTGTAAAGGTAGAAACTGAGATTAGAAAAAGTA-GGGATCTCAATT
1 AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGA-CTCAACT
* *
28400 ATAAA-AGTAAAAAGTG-GAATTGAA
65 ACAAAGA-TAAAAAGTGAG-A-TCAA
* * * *
28424 AAAAAATT-AGGGCCTCAATTATAAATGTAAAAAGTGATATT-AAAAAATT-GAGG-CTTCAATT
1 AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGAC-TCAACT
* * *
28485 ATAAAAGA-AGAAAGTGAGGT--A
65 A-CAAAGATAAAAAGTGAGATCAA
* * * * * *
28506 GAAAAATTATGGGCCTAAATTATAAATGTAAAAAGTAAGATTAAAAAAATTA-GGG-C-C--TTA
1 AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGACTCAACTA
*
28566 -AATG-TAAAAA-T-AGAT-ATTA
66 CAAAGATAAAAAGTGAGATCA--A
* *
28585 AAAAAATT-AGGAACCTCAATTATAAAGGTAAAAAGTGAAATTAAAAAAAT
1 AAAAAATTAAGG-GCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAAT
28635 AATAGGCCTT
Statistics
Matches: 364, Mismatches: 79, Indels: 74
0.70 0.15 0.14
Matches are distributed among these distances:
76 3 0.01
77 1 0.00
78 9 0.02
79 41 0.11
80 3 0.01
82 9 0.02
83 29 0.08
84 22 0.06
85 65 0.18
86 14 0.04
87 76 0.21
88 27 0.07
91 29 0.08
92 31 0.09
93 1 0.00
94 4 0.01
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (87 bp):
AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGACTCAACTA
CAAAGATAAAAAGTGAGATCAA
Found at i:28469 original size:43 final size:42
Alignment explanation
Indices: 28279--28634 Score: 286
Period size: 43 Copynumber: 8.5 Consensus size: 42
28269 AGGTAAAAAC
* ** * *
28279 TAAAAAGTGAGATTGAAAATTTTAGGAGCCTCAATTTTAATTG
1 TAAAAAGTGAGATTAAAAAAATTAGG-GCCTCAATTATAAATG
* * * * * *
28322 TAAAAAGTGAGATTAAAAAAATCAAGGCTTTAATTGTAAAGG
1 TAAAAAGTGAGATTAAAAAAATTAGGGCCTCAATTATAAATG
* * * * * *
28364 TAGAAACTGAGATTAGAAAAAGTAGGGATCTCAATTATAAAAG
1 TAAAAAGTGAGATTAAAAAAATTAGGG-CCTCAATTATAAATG
28407 TAAAAAGTG-GAATTGAAAAAAAATTAGGGCCTCAATTATAAATG
1 TAAAAAGTGAG-ATT--AAAAAAATTAGGGCCTCAATTATAAATG
* * *
28451 TAAAAAGTGATATT-AAAAAATT-GAGGCTTCAATTATAAAAG
1 TAAAAAGTGAGATTAAAAAAATTAG-GGCCTCAATTATAAATG
* * *
28492 -AAGAAAGTGAG-GTAGAAAAATTATGGGCCTAAATTATAAATG
1 TAA-AAAGTGAGATTAAAAAAATTA-GGGCCTCAATTATAAATG
*
28534 TAAAAAGTAAGATTAAAAAAATTAGGG-C-C---T-TAAATG
1 TAAAAAGTGAGATTAAAAAAATTAGGGCCTCAATTATAAATG
* * *
28570 TAAAAA-TAGATATTAAAAAAATTAGGAACCTCAATTATAAAGG
1 TAAAAAGT-GAGATTAAAAAAATTAGG-GCCTCAATTATAAATG
*
28613 TAAAAAGTGAAATTAAAAAAAT
1 TAAAAAGTGAGATTAAAAAAAT
28635 AATAGGCCTT
Statistics
Matches: 247, Mismatches: 45, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
35 1 0.00
36 28 0.11
37 1 0.00
38 1 0.00
39 1 0.00
40 4 0.02
41 38 0.15
42 58 0.23
43 78 0.32
44 26 0.11
45 11 0.04
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (42 bp):
TAAAAAGTGAGATTAAAAAAATTAGGGCCTCAATTATAAATG
Found at i:33177 original size:2 final size:2
Alignment explanation
Indices: 33170--33197 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33160 GATTAAAATC
33170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33198 TTAAGACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37145 original size:14 final size:14
Alignment explanation
Indices: 37126--37155 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
37116 CTCAATGTTA
37126 TTATTTGATTTTAT
1 TTATTTGATTTTAT
37140 TTATTTGATTTTAT
1 TTATTTGATTTTAT
37154 TT
1 TT
37156 CAATCACGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTATTTGATTTTAT
Found at i:41340 original size:4 final size:4
Alignment explanation
Indices: 41331--41357 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41321 CTTTTTATAG
41331 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
41358 CTTTCAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:42459 original size:16 final size:17
Alignment explanation
Indices: 42423--42456 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
42413 GTGTATGCGC
42423 GTGTGTATAAAATGTTTT
1 GTGTGTATAAAATG-TTT
42441 GTGTGTATAAAATGTT
1 GTGTGTATAAAATGTT
42457 GTGCAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (17 bp):
GTGTGTATAAAATGTTT
Found at i:45327 original size:24 final size:23
Alignment explanation
Indices: 45281--45332 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
45271 GTTGTTGTGA
45281 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
45304 TTTATGTTCATTCGT-TTGTGTTCG
1 TTTATGTTCATT--TATTGTGTTCG
45328 TTTAT
1 TTTAT
45333 TATGTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 12 0.44
24 14 0.52
25 1 0.04
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (23 bp):
TTTATGTTCATTTATTGTGTTCG
Found at i:45355 original size:14 final size:12
Alignment explanation
Indices: 45322--45383 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 12
45312 CATTCGTTTG
45322 TGTTCGTTTATTA
1 TGTTCGTTTA-TA
45335 TGTTCGTTTATA
1 TGTTCGTTTATA
*
45347 TCCGTTCGTTTATGTT
1 T--GTTCGTTTA--TA
45363 TGTTCG-TT-TA
1 TGTTCGTTTATA
45373 TGTTCGTTTAT
1 TGTTCGTTTAT
45384 CATTTAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 7 0.17
11 2 0.05
12 4 0.10
13 12 0.29
14 14 0.34
16 2 0.05
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (12 bp):
TGTTCGTTTATA
Found at i:45355 original size:37 final size:37
Alignment explanation
Indices: 45281--45383 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 37
45271 GTTGTTGTGA
* * * *
45281 TTTATGTTCATTTATTGTGTTCGTTTATGTTCATTCG
1 TTTATGTTCGTTTATTATGTTCGTTTATATCCATTCG
* *
45318 TTTGTGTTCGTTTATTATGTTCGTTTATATCCGTTCG
1 TTTATGTTCGTTTATTATGTTCGTTTATATCCATTCG
*
45355 TTTATGTTTGTTCGT-TTATGTTCGTTTAT
1 TTTATGTTCGTT--TATTATGTTCGTTTAT
45384 CATTTAAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 41 0.73
38 14 0.25
39 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.60
Consensus pattern (37 bp):
TTTATGTTCGTTTATTATGTTCGTTTATATCCATTCG
Found at i:45362 original size:51 final size:50
Alignment explanation
Indices: 45282--45383 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 50
45272 TTGTTGTGAT
** *
45282 TTATGTTCATTTATTGTGTTCGTTTATGTTCATTCGTTTGTGTTCGTTTA
1 TTATGTTCATTTATTCCGTTCGTTTATGTTCATTCGTTTATGTTCGTTTA
* **
45332 TTATGTTCGTTTATATCCGTTCGTTTATGTTTGTTCGTTTATGTTCGTTTA
1 TTATGTTCATTTAT-TCCGTTCGTTTATGTTCATTCGTTTATGTTCGTTTA
45383 T
1 T
45384 CATTTAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
50 13 0.29
51 32 0.71
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (50 bp):
TTATGTTCATTTATTCCGTTCGTTTATGTTCATTCGTTTATGTTCGTTTA
Found at i:52563 original size:19 final size:20
Alignment explanation
Indices: 52539--52592 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
52529 AAATGACCAA
52539 CAAATTCGCAACACGATCT-
1 CAAATTCGCAACACGATCTC
* *
52558 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACACGATCTC
*
52578 CAAATTCACAACACG
1 CAAATTCGCAACACG
52593 GAATTTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACGATCTC
Found at i:52684 original size:40 final size:40
Alignment explanation
Indices: 52623--52730 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 40
52613 AATTTATTTT
* * * *
52623 TCGCAACAC-AAGTTTCCTTTTCGCGACAATATTTTCTAAA
1 TCGCAACACGAA-TTTTCTTTTCGCAACAAGATTTTCGAAA
* ** *
52663 TCGCAACACGAATTTTGTTTTCGCAACTCGATTTTCGAAT
1 TCGCAACACGAATTTTCTTTTCGCAACAAGATTTTCGAAA
**
52703 TCGCAACACGAATTTTAATTTCGCAACA
1 TCGCAACACGAATTTTCTTTTCGCAACA
52731 GCTTTTATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 54 0.96
41 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (40 bp):
TCGCAACACGAATTTTCTTTTCGCAACAAGATTTTCGAAA
Found at i:52688 original size:20 final size:20
Alignment explanation
Indices: 52663--52730 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
52653 ATTTTCTAAA
*
52663 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTTGATT
* *
52683 TCGCAACTCG-ATTTTCGAAT
1 TCGCAACACGAATTTT-GATT
*
52703 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
52723 TCGCAACA
1 TCGCAACA
52731 GCTTTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 5 0.12
20 30 0.75
21 5 0.12
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:52906 original size:14 final size:15
Alignment explanation
Indices: 52887--52924 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
52877 TCCCCATCTC
52887 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
52901 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
52917 TAATTTTT
1 TAATTTTT
52925 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:53540 original size:12 final size:12
Alignment explanation
Indices: 53519--53552 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53509 ACCATATTTC
*
53519 CAATACCAAACA
1 CAATATCAAACA
53531 CAATATCAAACA
1 CAATATCAAACA
*
53543 CAATCTCAAA
1 CAATATCAAA
53553 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:53705 original size:24 final size:24
Alignment explanation
Indices: 53678--53731 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
53668 GTATTCGAAA
53678 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
53702 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
53726 TTTGAT
1 TTTGAT
53732 GATGTTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:57878 original size:21 final size:21
Alignment explanation
Indices: 57816--57949 Score: 117
Period size: 21 Copynumber: 6.4 Consensus size: 21
57806 GTGAATCGGA
* * * *
57816 CTCTTGAACGGTGGGAGTGAC
1 CTCTTGAACGATGAGAGGGGC
* *
57837 CACTTGAACGATGAGAAGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
57858 CTCTTAAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
57879 CTCTTCAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
57900 CTATTCAACGATGATAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
57921 CTATTGAACAAT-AGGAGGGGC
1 CTCTTGAACGATGA-GAGGGGC
57942 CTCTTGAA
1 CTCTTGAA
57950 TAATGACAGG
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
20 1 0.01
21 91 0.99
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:58387 original size:21 final size:21
Alignment explanation
Indices: 58363--58412 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
58353 ACCATTGTCG
*
58363 TCACGTAAAGTACCGACCTTA
1 TCACGTAAAGTACCGACCTCA
* *
58384 TCACGCAAAGTACTGACCTCA
1 TCACGTAAAGTACCGACCTCA
58405 TCACGTAA
1 TCACGTAA
58413 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:59978 original size:14 final size:14
Alignment explanation
Indices: 59959--59992 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
59949 TGCGATTTTC
59959 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
59973 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
59987 AATTTC
1 ATTTTC
59993 ATTTTCGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:59996 original size:20 final size:20
Alignment explanation
Indices: 59973--60011 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
59963 TCGCGTTGCG
59973 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
59993 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
60012 AAGTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:60018 original size:20 final size:20
Alignment explanation
Indices: 59975--60018 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
59965 GCGTTGCGAT
* *
59975 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
59995 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
60015 TTTC
1 TTTC
60019 AAAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:60264 original size:22 final size:23
Alignment explanation
Indices: 60228--60270 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
60218 TTTAAATATG
*
60228 AAAAATATAATAATAATAATACA
1 AAAAATATAATAATAAAAATACA
*
60251 AAAAATTTAA-AATAAAAATA
1 AAAAATATAATAATAAAAATA
60271 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAATATAATAATAAAAATACA
Found at i:60605 original size:19 final size:20
Alignment explanation
Indices: 60558--60605 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
60548 TAAACGCGCT
60558 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
* *
60578 TTGTGAATTTGAC-TCTGTG
1 TTGCGAATTTGACTTATGTG
*
60597 TTGCAAATT
1 TTGCGAATT
60606 ACAAATTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:67430 original size:31 final size:32
Alignment explanation
Indices: 67373--67432 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
67363 AAATAAAAAT
*
67373 TAATTTGAAAGTGAGAGTGATTAAATTAAGAG
1 TAATTTGAAAGTGAGAGTAATTAAATTAAGAG
*
67405 TAATTTGAAAGTTA-AGTAATTAAATTAA
1 TAATTTGAAAGTGAGAGTAATTAAATTAA
67433 AAAAATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (32 bp):
TAATTTGAAAGTGAGAGTAATTAAATTAAGAG
Done.