Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005840.1 Hibiscus syriacus cultivar Beakdansim tig00013692_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: 82286
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4392 original size:20 final size:20
Alignment explanation
Indices: 4367--4424 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
4357 TTTCTATTTC
4367 GCAAATGTGTTTATTGTTTT
1 GCAAATGTGTTTATTGTTTT
* *
4387 GCAAATGT-ATTAGTTATTTT
1 GCAAATGTGTTTA-TTGTTTT
*
4407 GCAAAAGTGTTTATTGTT
1 GCAAATGTGTTTATTGTT
4425 ACAATGGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (20 bp):
GCAAATGTGTTTATTGTTTT
Found at i:4528 original size:23 final size:25
Alignment explanation
Indices: 4501--4554 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
4491 TGGTTTGTGC
4501 TTTATTGATTTA-TGTTGA-TATTG
1 TTTATTGATTTACTGTTGATTATTG
*
4524 TTTATTGATTTACTGTTTATTATTG
1 TTTATTGATTTACTGTTGATTATTG
4549 -TTATTG
1 TTTATTG
4555 TTCTACTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 12 0.43
24 11 0.39
25 5 0.18
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (25 bp):
TTTATTGATTTACTGTTGATTATTG
Found at i:5840 original size:6 final size:6
Alignment explanation
Indices: 5829--5861 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5819 CTCTGCCACC
5829 CAACCT CAACCT CAACCT CAACCT CAACCT CAA
1 CAACCT CAACCT CAACCT CAACCT CAACCT CAA
5862 GATCCTACTT
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:0.36, C:0.48, G:0.00, T:0.15
Consensus pattern (6 bp):
CAACCT
Found at i:6506 original size:16 final size:16
Alignment explanation
Indices: 6487--6547 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
6477 TTGAAAAGAT
6487 ATAAATAATAAAAATA
1 ATAAATAATAAAAATA
* *
6503 AT-AATATTATATAATA
1 ATAAATAATA-AAAATA
* * *
6519 ATAAATATTAATAGTA
1 ATAAATAATAAAAATA
6535 ATAAAT-ATAAAAA
1 ATAAATAATAAAAA
6548 GGGGATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 10 0.27
16 20 0.54
17 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATAAATAATAAAAATA
Found at i:6594 original size:18 final size:18
Alignment explanation
Indices: 6571--6621 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
6561 AGTTTTCTTT
6571 TTAAATAAAAAATAAGAA
1 TTAAATAAAAAATAAGAA
* *
6589 TTAAATAAAAGAAAAATAA
1 TTAAATAAAA-AATAAGAA
6608 TTAAATAAACAAAT
1 TTAAATAAA-AAAT
6622 TAACGAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.36
19 17 0.61
20 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (18 bp):
TTAAATAAAAAATAAGAA
Found at i:9090 original size:10 final size:11
Alignment explanation
Indices: 9073--9120 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
9063 AAAGTTCGCT
9073 GAAAATAAAAC
1 GAAAATAAAAC
*
9084 G-AAATAAAAT
1 GAAAATAAAAC
9094 GAAAATAAAAAC
1 GAAAAT-AAAAC
* *
9106 AAAAATATAAC
1 GAAAATAAAAC
9117 GAAA
1 GAAA
9121 TGGGTTGCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
10 9 0.30
11 12 0.40
12 9 0.30
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.12
Consensus pattern (11 bp):
GAAAATAAAAC
Found at i:15433 original size:30 final size:30
Alignment explanation
Indices: 15399--15465 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
15389 TTTGACATCT
15399 TTGTTTTATTTTGCTTACCTTTTGTTGATA
1 TTGTTTTATTTTGCTTACCTTTTGTTGATA
15429 TTGTTTTATTTTGCTTACCTTTTGTTGATA
1 TTGTTTTATTTTGCTTACCTTTTGTTGATA
15459 TTGTTTT
1 TTGTTTT
15466 TGCATATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.12, C:0.09, G:0.13, T:0.66
Consensus pattern (30 bp):
TTGTTTTATTTTGCTTACCTTTTGTTGATA
Found at i:15760 original size:2 final size:2
Alignment explanation
Indices: 15753--15789 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
15743 ATGGATTGCT
15753 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
15790 TAGTATTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15849 original size:2 final size:2
Alignment explanation
Indices: 15842--15886 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
15832 TCAATCTACA
15842 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
15884 AT A
1 AT A
15887 ATTTATGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16054 original size:85 final size:85
Alignment explanation
Indices: 15904--16071 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
15894 AAATACAATC
* * * * *
15904 ATGACACACGAATGTGTGTCATCTTTTTTAATAACGTGTGCTTCAATGACACGCAATGTGAGTCA
1 ATGACACACAAATGTGTGTCATCTTATTTAATAACGGGGGCTTCAATGACACGCAATGCGAGTCA
* *
15969 TACATGCGTGTCATAAATTT
66 TAAATGCGCGTCATAAATTT
* * * * *
15989 ATGACACACAAATGTGTTTCATCTTCATTT-ATGACGGGGGCTTCAATGACGCTCAATGCGCGTC
1 ATGACACACAAATGTGTGTCATCTT-ATTTAATAACGGGGGCTTCAATGACACGCAATGCGAGTC
16053 ATAAATGCGCGTCATAAAT
65 ATAAATGCGCGTCATAAAT
16072 GTGAGTCATA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
85 67 0.96
86 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (85 bp):
ATGACACACAAATGTGTGTCATCTTATTTAATAACGGGGGCTTCAATGACACGCAATGCGAGTCA
TAAATGCGCGTCATAAATTT
Found at i:16061 original size:13 final size:13
Alignment explanation
Indices: 16043--16107 Score: 85
Period size: 13 Copynumber: 5.0 Consensus size: 13
16033 AATGACGCTC
*
16043 AATGCGCGTCATA
1 AATGTGCGTCATA
*
16056 AATGCGCGTCATA
1 AATGTGCGTCATA
*
16069 AATGTGAGTCATA
1 AATGTGCGTCATA
* *
16082 AATGTGTGTCATC
1 AATGTGCGTCATA
16095 AATGTGCGTCATA
1 AATGTGCGTCATA
16108 GATTTATGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:19367 original size:19 final size:18
Alignment explanation
Indices: 19348--19396 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
19338 GTTGCTTTTA
19348 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
19366 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
19385 AAATAAACAAAT
1 AAATAAA-AAAT
19397 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:21664 original size:27 final size:28
Alignment explanation
Indices: 21624--21679 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
21614 CAACTCACAG
*
21624 ATAAGCTTCATGGTGAAAGTTGTAGCAA
1 ATAAGCTTCATGGTGAAAGGTGTAGCAA
*
21652 ATAAG-TTTATGGTGAAAGGTGTAGCAA
1 ATAAGCTTCATGGTGAAAGGTGTAGCAA
21679 A
1 A
21680 AAAATCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (28 bp):
ATAAGCTTCATGGTGAAAGGTGTAGCAA
Found at i:23383 original size:16 final size:16
Alignment explanation
Indices: 23364--23418 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
23354 TTCTACCATC
23364 ATGTAATAATATCATT
1 ATGTAATAATATCATT
23380 ATGTTGTAATAATATCATT
1 A---TGTAATAATATCATT
* * *
23399 ATGTTATTATATCATC
1 ATGTAATAATATCATT
23415 ATGT
1 ATGT
23419 CATATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 17 0.52
19 16 0.48
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (16 bp):
ATGTAATAATATCATT
Found at i:23387 original size:19 final size:19
Alignment explanation
Indices: 23365--23403 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
23355 TCTACCATCA
23365 TGTAATAATATCATTATGT
1 TGTAATAATATCATTATGT
23384 TGTAATAATATCATTATGT
1 TGTAATAATATCATTATGT
23403 T
1 T
23404 ATTATATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (19 bp):
TGTAATAATATCATTATGT
Found at i:29306 original size:39 final size:38
Alignment explanation
Indices: 29252--29350 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 38
29242 ACTTTTCAAC
29252 ACTTATGCTCCTCCACCCAAAGCACC-ACCAAAGCCACCA
1 ACTTAT-CTCCTCCACCCAAAGCACCAACC-AAGCCACCA
* * *
29291 ACTTATCATCCTCCACCCAAGGCACCAACCAAGCTACTA
1 ACTTATC-TCCTCCACCCAAAGCACCAACCAAGCCACCA
*
29330 ACTTACGCTCCTCCACCCAAA
1 ACTTA-TCTCCTCCACCCAAA
29351 TCGCCGACCT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
38 1 0.02
39 47 0.90
40 4 0.08
ACGTcount: A:0.32, C:0.44, G:0.07, T:0.16
Consensus pattern (38 bp):
ACTTATCTCCTCCACCCAAAGCACCAACCAAGCCACCA
Found at i:38769 original size:18 final size:17
Alignment explanation
Indices: 38744--38777 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38734 TATTTATTTT
*
38744 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
38761 ATATGAAAAAATAATAT
1 ATAT-AAAAAATAATAT
38778 TATGATATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:42890 original size:60 final size:60
Alignment explanation
Indices: 42790--42936 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
42780 AAGTATAACC
* * ** *
42790 TTCATTTTAAATTGGTCTT-AAACTTTTAATTATTTCAATTTTATCTTCTAACTATGCC-
1 TTCATTTTAAATTAGTCTTCAAACTTTTAATTATTTCAATTTCATCCCCAAACTATGCCA
* *
42848 TATCATTTTAAATTAGTCTTCAAACTTTTGAA-TATTTTAATTTCATCCCCAAACTATGGCA
1 T-TCATTTTAAATTAGTCTTCAAACTTTT-AATTATTTCAATTTCATCCCCAAACTATGCCA
* **
42909 TTCATTCTAAATTAGTCCCCAAACTTTT
1 TTCATTTTAAATTAGTCTTCAAACTTTT
42937 TAAACATTCC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.01
59 17 0.23
60 54 0.72
61 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.46
Consensus pattern (60 bp):
TTCATTTTAAATTAGTCTTCAAACTTTTAATTATTTCAATTTCATCCCCAAACTATGCCA
Found at i:43119 original size:29 final size:29
Alignment explanation
Indices: 43086--43230 Score: 75
Period size: 29 Copynumber: 4.9 Consensus size: 29
43076 TTTGCGTGAA
43086 TTTGGGGATGAAATTAGAATATTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
** * * *
43115 TTTGGGGA-CCAATGTAGAAAGAGGGTC-ATAG
1 TTTGGGGATGAAAT-TAG-AATA--TTCAAAAG
*
43146 -TTGAGGGATGAAATTAGAATGTTCAAAAG
1 TTTG-GGGATGAAATTAGAATATTCAAAAG
** * * *
43175 TTTAAGGACT-AATTTAGAATGAGTCATAA-
1 TTTGGGGA-TGAAATTAGAAT-ATTCAAAAG
* *
43204 TTTGGGGATAAAATTGGAATATTCAAA
1 TTTGGGGATGAAATTAGAATATTCAAA
43231 TAAGGACCAA
Statistics
Matches: 82, Mismatches: 23, Indels: 23
0.64 0.18 0.18
Matches are distributed among these distances:
28 11 0.13
29 40 0.49
30 16 0.20
31 10 0.12
32 5 0.06
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.30
Consensus pattern (29 bp):
TTTGGGGATGAAATTAGAATATTCAAAAG
Found at i:43193 original size:60 final size:60
Alignment explanation
Indices: 43090--43267 Score: 183
Period size: 60 Copynumber: 3.1 Consensus size: 60
43080 CGTGAATTTG
** *
43090 GGGATGAAATTAGAATATTCAAAAGTTTGGGGACCAATGTAGAAAGAGGGTCATAGTTGA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGGGTCATAGTTGA
* * * *
43150 GGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGA--GTCATAATTTG-
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGGGTCAT-AGTTGA
* * * *
43208 GGGATAAAATTGGAATATTC-AAA---TAAGGACCAATTTA-AAATGAGGGTTATAGTTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAA-GAGGGTCATAGTTGA
43264 GGGA
1 GGGA
43268 CTCATGATGC
Statistics
Matches: 98, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
53 2 0.02
54 15 0.15
55 3 0.03
56 8 0.08
57 3 0.03
58 22 0.22
59 4 0.04
60 41 0.42
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.29
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGGGTCATAGTTGA
Found at i:46550 original size:80 final size:80
Alignment explanation
Indices: 46412--46572 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
46402 TCCTATTAGA
*
46412 ATTATTTAACATTGTTAATATGAATGATTTATTTTACTATAAGAAAGGAGTAAGTATAATATATA
1 ATTACTTAACATTGTTAATATGAATGATTTATTTTACTATAAGAAAGGAGTAAGTATAATATATA
46477 TTTAAAAATAACTCT
66 TTTAAAAATAACTCT
*
46492 ATTACTTAACATTGTTAATATGAATGATTTATTTTACTATAAGAAAGGAGTAAGTATAATATATG
1 ATTACTTAACATTGTTAATATGAATGATTTATTTTACTATAAGAAAGGAGTAAGTATAATATATA
46557 TTTAAAAATAACTCT
66 TTTAAAAATAACTCT
46572 A
1 A
46573 AAACATTTAA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (80 bp):
ATTACTTAACATTGTTAATATGAATGATTTATTTTACTATAAGAAAGGAGTAAGTATAATATATA
TTTAAAAATAACTCT
Found at i:52124 original size:307 final size:307
Alignment explanation
Indices: 51570--52188 Score: 1168
Period size: 307 Copynumber: 2.0 Consensus size: 307
51560 ATCAAAATGC
*
51570 GAAGTGACAACCAATCCGACATAAGTATAGCTGAAAATCCAGTACACCATGAAAGAACCAAGCAT
1 GAAGTGACAACCAATCCGACATAAGTATAGCTAAAAATCCAGTACACCATGAAAGAACCAAGCAT
51635 GTGGAGATTGACAGACATTTCAGTTTAGAGATCAACAATGGGATAGTTCAACTAAGTTACATTAC
66 GTGGAGATTGACAGACATTTCAGTTTAGAGATCAACAATGGGATAGTTCAACTAAGTTACATTAC
* *
51700 CACTCAACTACAACTTGCTGACATCATCACCAAAGCTCTCCCAAGAACCAACTTCGATGAATTCA
131 CACTCAACTACAACTTGCTAACATCATCACCAAAGCTCTCACAAGAACCAACTTCGATGAATTCA
51765 AGTCCAAGCTCGGTTTGTGTAACATATGCACCCAACTTGAGGGGAGTATAGAAAGAAGCCGGTTT
196 AGTCCAAGCTCGGTTTGTGTAACATATGCACCCAACTTGAGGGGAGTATAGAAAGAAGCCGGTTT
51830 TAGAAGTCCTTTTTCTTTAATTTTGTTGTTTTATTACAAATCTGTTA
261 TAGAAGTCCTTTTTCTTTAATTTTGTTGTTTTATTACAAATCTGTTA
* *
51877 GAAGTGACAACCAATCCG-CAATAAGTATAGCTAAAAATCTAGTACACCATGATAGAACCAAGCA
1 GAAGTGACAACCAATCCGAC-ATAAGTATAGCTAAAAATCCAGTACACCATGAAAGAACCAAGCA
*
51941 TGTGGAGATTGACAGACATTTCATTTTAGAGATCAACAATGGGATAGTTCAACTAAGTTACATTA
65 TGTGGAGATTGACAGACATTTCAGTTTAGAGATCAACAATGGGATAGTTCAACTAAGTTACATTA
52006 CCACTCAACTACAACTTGCTAACATCATCACCAAAGCTCTCACAAGAACCAACTTCGATGAATTC
130 CCACTCAACTACAACTTGCTAACATCATCACCAAAGCTCTCACAAGAACCAACTTCGATGAATTC
52071 AAGTCCAAGCTCGGTTTGTGTAACATATGCACCCAACTTGAGGGGAGTATAGAAAGAAGCCGGTT
195 AAGTCCAAGCTCGGTTTGTGTAACATATGCACCCAACTTGAGGGGAGTATAGAAAGAAGCCGGTT
52136 TTAGAAGTCCTTTTTCTTTAATTTTGTTGTTTTATTACAAATCTGTTA
260 TTAGAAGTCCTTTTTCTTTAATTTTGTTGTTTTATTACAAATCTGTTA
52184 GAAGT
1 GAAGT
52189 CTTTTTATTT
Statistics
Matches: 305, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
306 1 0.00
307 304 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (307 bp):
GAAGTGACAACCAATCCGACATAAGTATAGCTAAAAATCCAGTACACCATGAAAGAACCAAGCAT
GTGGAGATTGACAGACATTTCAGTTTAGAGATCAACAATGGGATAGTTCAACTAAGTTACATTAC
CACTCAACTACAACTTGCTAACATCATCACCAAAGCTCTCACAAGAACCAACTTCGATGAATTCA
AGTCCAAGCTCGGTTTGTGTAACATATGCACCCAACTTGAGGGGAGTATAGAAAGAAGCCGGTTT
TAGAAGTCCTTTTTCTTTAATTTTGTTGTTTTATTACAAATCTGTTA
Found at i:54876 original size:37 final size:38
Alignment explanation
Indices: 54795--54945 Score: 241
Period size: 38 Copynumber: 4.0 Consensus size: 38
54785 AAAATCGAAG
*
54795 TAAAAAAAAGAATTGGTTGTGCTACAACGTGCAACTGT
1 TAAAAAAAAGAATTGGTTGTGCTACAACATGCAACTGT
*
54833 TAAAAAAAGGAATTGGTTGTGCTACAACATGCAACTGT
1 TAAAAAAAAGAATTGGTTGTGCTACAACATGCAACTGT
*
54871 T-AAAAAAAGAATTGGTTGTGCCACAACATGCAACTGT
1 TAAAAAAAAGAATTGGTTGTGCTACAACATGCAACTGT
* *
54908 TAAAAAAAAAGAATTGTTTGCGCTACAACATGCAACTG
1 T-AAAAAAAAGAATTGGTTGTGCTACAACATGCAACTG
54946 AAGAATTGTT
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
37 35 0.34
38 37 0.36
39 32 0.31
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (38 bp):
TAAAAAAAAGAATTGGTTGTGCTACAACATGCAACTGT
Found at i:54877 original size:75 final size:76
Alignment explanation
Indices: 54797--54945 Score: 246
Period size: 75 Copynumber: 2.0 Consensus size: 76
54787 AATCGAAGTA
* * * *
54797 AAAAAAAGAATTGGTTGTGCTACAACGTGCAACTGTT-AAAAAAAGGAATTGGTTGTGCTACAAC
1 AAAAAAAGAATTGGTTGTGCCACAACATGCAACTGTTAAAAAAAAAGAATTGGTTGCGCTACAAC
54861 ATGCAACTGTT
66 ATGCAACTGTT
*
54872 AAAAAAAGAATTGGTTGTGCCACAACATGCAACTGTTAAAAAAAAAGAATTGTTTGCGCTACAAC
1 AAAAAAAGAATTGGTTGTGCCACAACATGCAACTGTTAAAAAAAAAGAATTGGTTGCGCTACAAC
54937 ATGCAACTG
66 ATGCAACTG
54946 AAGAATTGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 35 0.51
76 33 0.49
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (76 bp):
AAAAAAAGAATTGGTTGTGCCACAACATGCAACTGTTAAAAAAAAAGAATTGGTTGCGCTACAAC
ATGCAACTGTT
Found at i:56640 original size:20 final size:21
Alignment explanation
Indices: 56615--56655 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
56605 TTGTTTGGCT
56615 CTGAATG-GAACCATTCAGCG
1 CTGAATGTGAACCATTCAGCG
*
56635 CTGAATGTTGAACCGTTCAGC
1 CTGAATG-TGAACCATTCAGC
56656 ATTCAGACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
CTGAATGTGAACCATTCAGCG
Found at i:59534 original size:165 final size:165
Alignment explanation
Indices: 59234--59547 Score: 461
Period size: 165 Copynumber: 1.9 Consensus size: 165
59224 CCACTTTATT
* * ** *
59234 GCCAAAAGCATTAATTAACTCAGAGAACTCCGAGAATGAAAGCTTTCCATCTTCATCATAGTCCT
1 GCCAAAAGCATTAATTAACTCAGAAAACACAAAGAATGAAAGCTTTCCATCTTCATCATAGTCCA
* ** *
59299 GAATACATAATCATATATAATGACAGCTTTAATACATGAACTAGAAAGTTGCATGAAAAGTCCAC
66 GAATACATAATCACATATAACAACAGCTTTAATACATGAACTAGAAAGTTGAATGAAAAGTCCAC
59364 AAGATCATGTCATAAGAACAAGATGACAATCTATC
131 AAGATCATGTCATAAGAACAAGATGACAATCTATC
* *
59399 GCCAAAAGCATTAATTAATTCAGAAAACACAAAGAATGAAAGCTTTCGATCTTCATCATAGTCCA
1 GCCAAAAGCATTAATTAACTCAGAAAACACAAAGAATGAAAGCTTTCCATCTTCATCATAGTCCA
* *
59464 GAATACATAATCACATATAACAACAGGGTTTTAATATATGAACTAGAAAGTTGAATGAAAAGT-C
66 GAATACATAATCACATATAACAACA--GCTTTAATACATGAACTAGAAAGTTGAATGAAAAGTCC
* *
59528 -CAAGATCTTTTCATAAGAAC
129 ACAAGATCATGTCATAAGAAC
59548 TAAAGCAATA
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
165 98 0.74
166 1 0.01
167 33 0.25
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (165 bp):
GCCAAAAGCATTAATTAACTCAGAAAACACAAAGAATGAAAGCTTTCCATCTTCATCATAGTCCA
GAATACATAATCACATATAACAACAGCTTTAATACATGAACTAGAAAGTTGAATGAAAAGTCCAC
AAGATCATGTCATAAGAACAAGATGACAATCTATC
Found at i:68955 original size:9 final size:9
Alignment explanation
Indices: 68943--68987 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
68933 AAATTTTGGC
68943 TTTTTTGTT-
1 TTTTTT-TTG
68952 TTTTTTTTG
1 TTTTTTTTG
*
68961 CCTTTTTTTG
1 -TTTTTTTTG
68971 TTTTTTTTG
1 TTTTTTTTG
68980 TTTTTTTT
1 TTTTTTTT
68988 TAAAAAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 2 0.06
9 22 0.69
10 8 0.25
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:70964 original size:94 final size:95
Alignment explanation
Indices: 70802--70982 Score: 285
Period size: 94 Copynumber: 1.9 Consensus size: 95
70792 GATACCAAAA
* * *
70802 AGGAAAGTATCGATATCATGGATTCTAGAATGTCGAAATGGTATCGATACTGAATGGGAGTATTG
1 AGGAAAGTATCGATACCATGGATACTAGAATGTAGAAATGGTATCGATACTGAATGGGAGTATTG
* *
70867 GTACCATAGTATAGAAGTATCGGTACTAGG
66 GTACCACAATATAGAAGTATCGGTACTAGG
*
70897 AGGAAAGTATCGATACCATGGATAC-ATAATGTAGAAATGGTATCGATACTGCAA-GGGAGTATT
1 AGGAAAGTATCGATACCATGGATACTAGAATGTAGAAATGGTATCGATACTG-AATGGGAGTATT
70960 GGTACCACAATATAGAAGTATCG
65 GGTACCACAATATAGAAGTATCG
70983 ATACCATGGT
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 54 0.68
95 25 0.32
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.27
Consensus pattern (95 bp):
AGGAAAGTATCGATACCATGGATACTAGAATGTAGAAATGGTATCGATACTGAATGGGAGTATTG
GTACCACAATATAGAAGTATCGGTACTAGG
Found at i:71005 original size:94 final size:94
Alignment explanation
Indices: 70787--71006 Score: 248
Period size: 94 Copynumber: 2.3 Consensus size: 94
70777 TACTGATAGG
** * * * *
70787 GTATCGATACCAAAAAGGAAAGTATCGATATCATGGATTCTAGAATGTCGAAATGGTATCGATAC
1 GTATCGATACC-AGGAGG-AAGTACCGATACCATGGATACTAGAATGTAGAAATGGTATCGATAC
* *
70852 TGAATGGGAGTATTGGTACCATAGTATAGAA
64 TGAATGGGAGTATTGGTACCACAATATAGAA
* * * *
70883 GTATCGGTACTAGGAGGAAAGTATCGATACCATGGATAC-ATAATGTAGAAATGGTATCGATACT
1 GTATCGATACCAGGAGG-AAGTACCGATACCATGGATACTAGAATGTAGAAATGGTATCGATACT
70947 GCAA-GGGAGTATTGGTACCACAATATAGAA
65 G-AATGGGAGTATTGGTACCACAATATAGAA
*
70977 GTATCGATACCATGGTAGG-GGTACCGATAC
1 GTATCGATACCA-GG-AGGAAGTACCGATAC
71007 TATTTAGCCA
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
94 67 0.63
95 28 0.26
96 12 0.11
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (94 bp):
GTATCGATACCAGGAGGAAGTACCGATACCATGGATACTAGAATGTAGAAATGGTATCGATACTG
AATGGGAGTATTGGTACCACAATATAGAA
Found at i:71525 original size:81 final size:81
Alignment explanation
Indices: 71390--72028 Score: 882
Period size: 81 Copynumber: 7.9 Consensus size: 81
71380 TGTTTTAAAA
* * * * * *
71390 TAAAAGATTAATTGCTTAGTTGTGCATTTGATAAAAATGTGTCAATCATGCCAGTTAGATGAAAG
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
71455 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
71471 TAAAAGACTAATTGCCTAGTTATGCATTTGACAGAAAGGTGTCAACCATGCCAGTTAGATGAAAT
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
71536 GTTGAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * **
71552 TAAAAGACTAATTGCCTAGCTGTCCATTTGACATAAAGGTGTCAATCATGTTAGTTAGATGAAAG
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
71617 GTTAAATACCTCTGAG
66 GTTAAATACCTTTGAG
* * * *
71633 TAAAAGATTAATTGCCTAGTTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
71698 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
71714 TAAAAGATTAATTGTCTAGCTGTGCATTTGATAGAAAGGTGCCAATCATGTCAATTACATGAAAG
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
71779 GTTAAACACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
71795 AAAAAGACTAATTTCCTAGTTGTGCATTTGATAGAAAGATGTCAATCATGCCAGTTAGATGAAAG
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
71860 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
71876 TAAAAGACTAATTGCCTAGCTATGCATTTGACAGAAAGGTATCAATCATGCCAGTTAGATGAAAG
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
71941 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * * * *
71957 TAAAATATTAATTGCCTAACTGTGCATTTGGCAGAAAGTTGCCAATAATGCAAGTTATATGAAAG
1 TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
72022 GTTAAAT
66 GTTAAAT
72029 GCCTGCCAAT
Statistics
Matches: 493, Mismatches: 65, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 493 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (81 bp):
TAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:72043 original size:36 final size:36
Alignment explanation
Indices: 71996--72068 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
71986 GGCAGAAAGT
71996 TGCCAATAATGCAAGTTATATGAAAGGTTAAATGCC
1 TGCCAATAATGCAAGTTATATGAAAGGTTAAATGCC
*
72032 TGCCAATAATGCAAGTTTTATGAAAGGTTAAATGCC
1 TGCCAATAATGCAAGTTATATGAAAGGTTAAATGCC
72068 T
1 T
72069 TTGGCATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (36 bp):
TGCCAATAATGCAAGTTATATGAAAGGTTAAATGCC
Found at i:73846 original size:12 final size:11
Alignment explanation
Indices: 73829--73897 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
73819 TATATATATA
73829 TTATTTTCATT
1 TTATTTTCATT
73840 TTCATTTTCATT
1 TT-ATTTTCATT
**
73852 TTATTTTGTTTGT
1 TTATTTT-CAT-T
*
73865 TTCTTTTC-TT
1 TTATTTTCATT
*
73875 TATATTTTTATT
1 T-TATTTTCATT
73887 TTATTTT-ATT
1 TTATTTTCATT
73897 T
1 T
73898 GTTTTCAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
10 6 0.13
11 19 0.40
12 15 0.32
13 7 0.15
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.75
Consensus pattern (11 bp):
TTATTTTCATT
Found at i:74092 original size:21 final size:21
Alignment explanation
Indices: 74067--74111 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
74057 TTAGCTACAT
*
74067 TTTTTGGTATATTTTTTTTTA
1 TTTTTGGTATATTTATTTTTA
*
74088 TTTTTGTTATATTTATTTTTA
1 TTTTTGGTATATTTATTTTTA
74109 TTT
1 TTT
74112 GTTATCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTGGTATATTTATTTTTA
Found at i:74114 original size:19 final size:18
Alignment explanation
Indices: 74069--74129 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 18
74059 AGCTACATTT
*
74069 TTTGGTATATTTTTTTTTA
1 TTTGTTATA-TTTTTTTTA
74088 TTTTTGTTATATTTATTTTTA
1 --TTTGTTATATTT-TTTTTA
* *
74109 TTTGTTATCTTTTTTTCA
1 TTTGTTATATTTTTTTTA
74127 TTT
1 TTT
74130 TTTGTATCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.22
19 11 0.31
20 3 0.08
21 14 0.39
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (18 bp):
TTTGTTATATTTTTTTTA
Found at i:76461 original size:85 final size:85
Alignment explanation
Indices: 76309--76972 Score: 931
Period size: 85 Copynumber: 7.8 Consensus size: 85
76299 TAAAGAAACT
* * * *
76309 ATTCGCAACATA-CTCAAGGCGAGAAGGACTATCCGT-AA-AAAAACCTTTGAGTTTGATTCCAT
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
*
76371 TCAGCTCAAAGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * *
76391 ATTCGCAGCATAACTCAAGGTGAGAAGGGCTATCTGTAAACAAAAACCTTTGAGTTCGATTCCAT
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
76456 TCAGCTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * *
76476 ATTTGTAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAA-CTTTATAGTTCGATTCCA
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTT-GAGTTCGATTCCA
*
76540 TTTAGCTCAAGGGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* * * * *
76561 ATTCGTAGCATAGCTCAACGCGAGAAGGGTTATCCGTCAACAAAAACCTTCGAGTTCGATTCCAT
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
76626 TCAGCTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * * * * * *
76646 ATTTGCAGCATAGCTCAAAGTGAGAAGAGCTATCTGTCAATAAAAACCTTCGAGTTCGATTTCAT
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
*
76711 TCAACTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * *
76731 ATTCGCAGCATAGCTCAAGGAGAGAAGGGCTATCTATCAACAAAAACCTTAGAGTTCGATTCCAT
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
*
76796 TTAGCTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * * * *
76816 ATTCGCAGCATAGCTAAAAGTGAGAAGGGCTATCTGTTAACAAAAACCTTAGAGTTCGATTCCAT
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
76881 TCAGCTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
** * * * *
76901 ATTTACAGTATAGCTCAAGGCGAGAAGGGCTATCTGTCAACGAAAACTTTTGATTTCGATTCCAT
1 ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
76966 TCAGCTC
66 TCAGCTC
76973 GTTGATAGCG
Statistics
Matches: 520, Mismatches: 57, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
82 11 0.02
83 21 0.04
84 6 0.01
85 479 0.92
86 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (85 bp):
ATTCGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTCCAT
TCAGCTCAAGGGCATATCAA
Found at i:78822 original size:2 final size:2
Alignment explanation
Indices: 78815--78839 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78805 CATGTTTTAT
78815 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
78840 TATTTTCATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79040 original size:17 final size:16
Alignment explanation
Indices: 78979--79119 Score: 58
Period size: 16 Copynumber: 8.6 Consensus size: 16
78969 TTTTTTAGGG
*
78979 TTTTATATTTTATTTTG
1 TTTTAT-TTTTATTTTA
* *
78996 TTTCATTTTTATGTTAA
1 TTTTATTTTTAT-TTTA
*
79013 TTTCTTTTTTTATTTTA
1 TTT-TATTTTTATTTTA
**
79030 TTTTATCTTTTCAACTTA
1 TTTTAT-TTTT-ATTTTA
* **
79048 TCTATATTTTT-TGGTA
1 T-TTTATTTTTATTTTA
79064 TATTT-TTTTTATTTT-
1 T-TTTATTTTTATTTTA
*
79079 TGTTATTTTTATCTTTA
1 TTTTATTTTTAT-TTTA
* *
79096 -TTTGTTTTTCTTTT-
1 TTTTATTTTTATTTTA
*
79110 TTTCATTTTT
1 TTTTATTTTT
79120 TATCTTTTTT
Statistics
Matches: 91, Mismatches: 23, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
14 2 0.02
15 23 0.25
16 26 0.29
17 20 0.22
18 16 0.18
19 4 0.04
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:79078 original size:9 final size:9
Alignment explanation
Indices: 79064--79120 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
79054 TTTTTTGGTA
79064 TATTTTTTT
1 TATTTTTTT
*
79073 TATTTTTGT
1 TATTTTTTT
79082 TATTTTTATCTT
1 TA-TTTT-T-TT
79094 TATTTGTTTT
1 TATTT-TTTT
*
79104 TCTTTTTTT
1 TATTTTTTT
*
79113 CATTTTTT
1 TATTTTTT
79121 ATCTTTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
9 20 0.51
10 10 0.26
11 5 0.13
12 4 0.10
ACGTcount: A:0.11, C:0.05, G:0.04, T:0.81
Consensus pattern (9 bp):
TATTTTTTT
Done.