Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004278.1 Hibiscus syriacus cultivar Beakdansim tig00009376_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: 61652
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:15412 original size:23 final size:22
Alignment explanation
Indices: 15374--15431 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
15364 CAAATAATTT
15374 AAAAAT-AATATTATTTCAAATA
1 AAAAATAAATATTATTTCAAA-A
*
15396 AAAAATAAAT-TTGATTTTAAAA
1 AAAAATAAATATT-ATTTCAAAA
15418 AATAAATAAATATT
1 AA-AAATAAATATT
15432 TTTTATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 11 0.35
23 18 0.58
24 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAATAAATATTATTTCAAAA
Found at i:16348 original size:23 final size:23
Alignment explanation
Indices: 16322--16375 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
16312 TCTCCACTCT
16322 TGGTCACTGATTTCAACAAGATA
1 TGGTCACTGATTTCAACAAGATA
*
16345 TGGTCATTGATTTCAACAAGATA
1 TGGTCACTGATTTCAACAAGATA
*
16368 TGATCACT
1 TGGTCACT
16376 TTCGTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (23 bp):
TGGTCACTGATTTCAACAAGATA
Found at i:16573 original size:27 final size:27
Alignment explanation
Indices: 16524--16615 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 27
16514 TAAATTATAA
* ** *
16524 ATTTTTAAATGAAAATAAAAATAAAAT
1 ATTTTTAAATTAAGTTAATAATAAAAT
16551 ATTTTTAAATTAAGTTAATAATAAAAT
1 ATTTTTAAATTAAGTTAATAATAAAAT
*
16578 ATATTT-AA-TAAGTTAAT-ATAAAAAT
1 ATTTTTAAATTAAGTTAATAAT-AAAAT
16603 ATTTTTAAATTAA
1 ATTTTTAAATTAA
16616 TATATATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.04
25 19 0.34
26 4 0.07
27 31 0.55
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTTTTAAATTAAGTTAATAATAAAAT
Found at i:16595 original size:25 final size:27
Alignment explanation
Indices: 16543--16615 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 27
16533 TGAAAATAAA
*
16543 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
16570 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
*
16595 -ATAAAAATATTTTTAAATTAA
1 AAT-AAAATATATTTAAATTAA
16616 TATATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.05
25 19 0.46
26 4 0.10
27 16 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
AATAAAATATATTTAAATTAAGTTAAT
Found at i:16626 original size:22 final size:23
Alignment explanation
Indices: 16569--16626 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
16559 ATTAAGTTAA
*
16569 TAATA-AAATATATTTAATAAGT
1 TAATATAAATATATTTAATAAAT
* *
16591 TAATATAAAAATATTT-TTAAAT
1 TAATATAAATATATTTAATAAAT
*
16613 TAATATATATATAT
1 TAATATAAATATAT
16627 AATTATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATATAAATATATTTAATAAAT
Found at i:16627 original size:30 final size:29
Alignment explanation
Indices: 16546--16628 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 29
16536 AAATAAAAAT
16546 AAAATATTTTTAAATTAAGTTA-ATA-AT-
1 AAAATATTTTTAAATTAA-TTATATATATA
* *
16573 AAAATATATTT-AA-TAAGT-TA-ATATA
1 AAAATATTTTTAAATTAATTATATATATA
16598 AAAATATTTTTAAATTAATATATATATATA
1 AAAATATTTTTAAATTAAT-TATATATATA
16628 A
1 A
16629 TTATATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
23 1 0.02
24 4 0.09
25 13 0.30
26 4 0.09
27 13 0.30
28 1 0.02
29 2 0.05
30 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
AAAATATTTTTAAATTAATTATATATATA
Found at i:17437 original size:31 final size:31
Alignment explanation
Indices: 17391--17466 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
17381 GTTAACTCAG
* *
17391 GTGACCACATGTTAATTAAATAAAAACAAAA
1 GTGACCATATCTTAATTAAATAAAAACAAAA
* * *
17422 GTGACTATATCTTAATTAAATAAGAACGAAA
1 GTGACCATATCTTAATTAAATAAAAACAAAA
17453 GTGACCATATCTTA
1 GTGACCATATCTTA
17467 TTTTTTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (31 bp):
GTGACCATATCTTAATTAAATAAAAACAAAA
Found at i:20252 original size:2 final size:2
Alignment explanation
Indices: 20245--20274 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20235 TCATATAAAG
20245 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
20275 TTCATTTCCC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22675 original size:105 final size:105
Alignment explanation
Indices: 22501--22708 Score: 308
Period size: 105 Copynumber: 2.0 Consensus size: 105
22491 GGCTTGGTTA
* *
22501 AGGCTTACTTAGTTGCAGAGAAGACACAAAAGTGTCAAGAAGCGTATAAGGCCGTACATCCCGTT
1 AGGCTTACTTAGTTGCAGAGAAGACACAAAAGTGTCAAGAAGCGTATAAGGCCGTACATCCCATC
* * *
22566 AGACCTTAATTCTAATATTGCGACAGTTTGGGCTTGAAGG
66 AGACCTTAACTCTAATATTGCGACAATTTGGACTTGAAGG
* * * * * **
22606 AGGCTTACTTAGTTGTAGAGAAGACCCAGAAGTGTCAAGAAGCGTCTAAGGTCGTATGTCCCATC
1 AGGCTTACTTAGTTGCAGAGAAGACACAAAAGTGTCAAGAAGCGTATAAGGCCGTACATCCCATC
22671 AGACCTTAACTCTAATATTGCGACAATTTGGACTTGAA
66 AGACCTTAACTCTAATATTGCGACAATTTGGACTTGAA
22709 AATTATGAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 91 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (105 bp):
AGGCTTACTTAGTTGCAGAGAAGACACAAAAGTGTCAAGAAGCGTATAAGGCCGTACATCCCATC
AGACCTTAACTCTAATATTGCGACAATTTGGACTTGAAGG
Found at i:23143 original size:29 final size:30
Alignment explanation
Indices: 23091--23159 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
23081 ATATATATTT
*
23091 AATAT-TAATAGTTATAGTTATATTATT-AA
1 AATATATAATAGTTATACTTATATT-TTGAA
* *
23120 AATATATAATA-TTATACTTTTATTTTGAT
1 AATATATAATAGTTATACTTATATTTTGAA
23149 AATATATAATA
1 AATATATAATA
23160 AATTATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 28 0.80
30 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (30 bp):
AATATATAATAGTTATACTTATATTTTGAA
Found at i:23199 original size:26 final size:26
Alignment explanation
Indices: 23147--23220 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
23137 TTTTATTTTG
*
23147 ATAATATATAATAAATTA--TTAATAAA
1 ATAATAT-TATTAAATTATTTTAA-AAA
* *
23173 ATTAATATTATTTATTTATTTTAAAAA
1 A-TAATATTATTAAATTATTTTAAAAA
*
23200 ATGATATTATTAAATTATTTT
1 ATAATATTATTAAATTATTTT
23221 TTGATTAAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 25 0.64
27 10 0.26
28 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (26 bp):
ATAATATTATTAAATTATTTTAAAAA
Found at i:24474 original size:26 final size:26
Alignment explanation
Indices: 24445--24513 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
24435 ATTTACAATT
*
24445 ACCCATACGATTAATCCAGTTCTAAA
1 ACCCATACCATTAATCCAGTTCTAAA
*
24471 ACCCATACCATTAATCCATTTCTAAA
1 ACCCATACCATTAATCCAGTTCTAAA
24497 ACCCATACCATTAATCC
1 ACCCATACCATTAATCC
24514 TTTACACAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.28
Consensus pattern (26 bp):
ACCCATACCATTAATCCAGTTCTAAA
Found at i:25440 original size:33 final size:31
Alignment explanation
Indices: 25403--25473 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 31
25393 GTCAAAATCC
25403 TAAAAAATAG-CTAA-ATAGAAAAGAAAATAAATA
1 TAAAAAAT-GTCTAACAT-GAAAA-AAAAT-AATA
*
25436 TAAAAAATGTCTAACATTAAAAAAAATAATA
1 TAAAAAATGTCTAACATGAAAAAAAATAATA
25467 TAAAAAA
1 TAAAAAA
25474 AGTAAAAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 11 0.31
32 6 0.17
33 16 0.46
34 2 0.06
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (31 bp):
TAAAAAATGTCTAACATGAAAAAAAATAATA
Found at i:28618 original size:5 final size:5
Alignment explanation
Indices: 26759--28615 Score: 2371
Period size: 5 Copynumber: 372.6 Consensus size: 5
26749 AATATTTGTT
26759 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
26809 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
26859 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
26909 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
26959 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27009 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27059 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27109 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27159 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27209 TAACA TAACA TAACA TAACACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA T-A-ACA TAACA TAACA TAACA TAACA TAACA TAACA
27261 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27311 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27361 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27411 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
27461 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAAC-
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * * * * * * * * * * *
27510 -AACA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * * * * * * * * * *
27559 CAGCA CAGCA CAGCA TAACA CAGCA CAACA CAGCA CAGCA CAGCA CAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * * * * * * * * *
27609 CAACA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
27659 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAAC- -AACA CAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * * *
27707 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * *
27757 CAACA CAACA CAACA CAACA GAACA TAACA TAGCA TAGCA TAGCA TAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * *
27807 TAGCA TAGCA TAGCA TAACA TAACA TAACA TAACA TAGCA TAGCA TAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * *
27857 TAGCA TAGCA TAGCA TAGCA T-ACA TAGCA TAGCA TAGCA T-ACA TAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * * *
27905 TAGCA TAGCA TAGCA TAGCA TAGCA TAGCA TAGCA TAGCA TAGCA TAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * *
27955 TAGCA TAGCA TAGCA TAGCA TAGCA TAGCA TAACA TAGCA TAACA TAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
28005 TAGCA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28055 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28105 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28155 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28205 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * * * * * *
28255 TAACA TAAC- -AACA CAACA CAGCA CAGCA CATCA CAGCA CAGCA CAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * * * * * * * * * * * * * * * * *
28303 CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAGCA CAACA CAGCA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * * *
28353 CAGCA TAACA TAGCA TAGCA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28403 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28453 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28503 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
28553 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
28603 TAACA TAATA TAA
1 TAACA TAACA TAA
28616 TATGCAATGT
Statistics
Matches: 1807, Mismatches: 35, Indels: 20
0.97 0.02 0.01
Matches are distributed among these distances:
3 9 0.00
4 6 0.00
5 1786 0.99
6 2 0.00
7 4 0.00
ACGTcount: A:0.56, C:0.23, G:0.04, T:0.17
Consensus pattern (5 bp):
TAACA
Found at i:34672 original size:67 final size:64
Alignment explanation
Indices: 34557--34712 Score: 185
Period size: 67 Copynumber: 2.4 Consensus size: 64
34547 ACTTTTCAAA
*
34557 CCTTTTACTATTCAAACTTAAAT-A-AATATTATTTTAATTTGAAATATTCAAAAGTATATAATT
1 CCTTTTAATATTCAAA-TTAAATAATAATATTATTTTAATTTGAAATATTCAAAAG-A-ATAATT
34620 AT
63 AT
*
34622 -CTTTTAATATTCAAAGTTAAATAATAAGTTATT-TTTTAATTTGATATATTCAAAAGAATAATT
1 CCTTTTAATATTCAAA-TTAAATAATAA--TATTATTTTAATTTGAAATATTCAAAAGAATAATT
34685 AT
63 AT
** *
34687 CCTACTAATATTCAAATCAAATAATA
1 CCTTTTAATATTCAAATTAAATAATA
34713 TCTTTCAATT
Statistics
Matches: 80, Mismatches: 6, Indels: 10
0.83 0.06 0.10
Matches are distributed among these distances:
64 20 0.25
65 18 0.22
66 16 0.20
67 22 0.28
68 4 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (64 bp):
CCTTTTAATATTCAAATTAAATAATAATATTATTTTAATTTGAAATATTCAAAAGAATAATTAT
Found at i:34710 original size:65 final size:68
Alignment explanation
Indices: 34583--34712 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 68
34573 CTTAAATAAA
** *
34583 TATTATTTTAATTTGAAATATTCAAAAGTATATAATTATCTTTTAATATTCAAAGTTAAATAATA
1 TATTATTTTAATTTGAAATATTCAAAAGTATATAATTATCTACTAATATTCAAAGTCAAATAATA
34648 AGT
66 AGT
*
34651 TATT-TTTTAATTTGATATATTCAAAAG-A-ATAATTATCCTACTAATATTCAAA-TCAAATAAT
1 TATTATTTTAATTTGAAATATTCAAAAGTATATAATTAT-CTACTAATATTCAAAGTCAAATAAT
34712 A
65 A
34713 TCTTTCAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
65 17 0.30
66 14 0.25
67 22 0.39
68 4 0.07
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (68 bp):
TATTATTTTAATTTGAAATATTCAAAAGTATATAATTATCTACTAATATTCAAAGTCAAATAATA
AGT
Found at i:34868 original size:2 final size:2
Alignment explanation
Indices: 34861--34889 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34851 GTATTCCTTA
34861 AT AT 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 AT AT A
34890 AAGAAACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36140 original size:3 final size:3
Alignment explanation
Indices: 36134--36168 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
36124 CTCCTCCTCA
* *
36134 TCT TCT TCT TCT TTT TCT TCT TCT TCA TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
36169 ATCATCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:36169 original size:9 final size:9
Alignment explanation
Indices: 36131--36171 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
36121 CTCCTCCTCC
36131 TCATCTTCT
1 TCATCTTCT
* *
36140 TCTTCTTTT
1 TCATCTTCT
*
36149 TCTTCTTCT
1 TCATCTTCT
36158 TCATCTTCT
1 TCATCTTCT
36167 TCATC
1 TCATC
36172 ATCATTGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (9 bp):
TCATCTTCT
Found at i:41956 original size:14 final size:14
Alignment explanation
Indices: 41922--41965 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
41912 TATTTTGTTT
41922 GTCAAAGTCAACAG
1 GTCAAAGTCAACAG
* * *
41936 GTTAAAGTTAACGG
1 GTCAAAGTCAACAG
41950 GTCAAAGTCAACAG
1 GTCAAAGTCAACAG
41964 GT
1 GT
41966 TGACTCAGAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (14 bp):
GTCAAAGTCAACAG
Found at i:44170 original size:18 final size:18
Alignment explanation
Indices: 44147--44190 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
44137 AACTTTGACT
*
44147 AAAAAGTCAACCT-TTTCG
1 AAAAAGGCAA-CTGTTTCG
44165 AAAAAGGCAACTGTTTCG
1 AAAAAGGCAACTGTTTCG
*
44183 AAGAAGGC
1 AAAAAGGC
44191 CTATTTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (18 bp):
AAAAAGGCAACTGTTTCG
Found at i:47256 original size:60 final size:59
Alignment explanation
Indices: 47070--47257 Score: 209
Period size: 60 Copynumber: 3.1 Consensus size: 59
47060 GCATCGTATG
* *
47070 TTCTCAAACTATGATCCTCATTTTAAATTAGTCCCTAAAATTTTGAATATTCTAATTTCA
1 TTCTCAAACTA-AATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
* * * *
47130 -TCATCAAACTAATATACTCATTTTAAACTAGTCCTTAAACTTTTGAACATTCTAATTTCA
1 TTC-TCAAACTAA-ATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
* * * * * *
47190 TCCTCAAACTACAACCCTTATTCTAAATTGGTCCCTAAACTTTTAAATATT-TCAATTTCA
1 TTCTCAAACTA-AATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCT-AATTTCA
47250 TTCTCAAA
1 TTCTCAAA
47258 TTTATTCAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
59 3 0.03
60 101 0.95
61 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (59 bp):
TTCTCAAACTAAATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
Found at i:53276 original size:2 final size:2
Alignment explanation
Indices: 53269--53298 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53259 AGGCTTCGTG
53269 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
53299 GTAATTAAAG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58833 original size:94 final size:94
Alignment explanation
Indices: 58707--58884 Score: 320
Period size: 94 Copynumber: 1.9 Consensus size: 94
58697 ATTTTGATTA
* * *
58707 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAATTCACTCTTCTTCTTATTCTTTTAATCGTT
1 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
58772 AGAGTTCCTTTATTGGGTGTTTCAGACTC
66 AGAGTTCCTTTATTGGGTGTTTCAGACTC
58801 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
1 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
*
58866 AGGGTTCCTTTATTGGGTG
66 AGAGTTCCTTTATTGGGTG
58885 CTTCTCGTTA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 80 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (94 bp):
TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
AGAGTTCCTTTATTGGGTGTTTCAGACTC
Done.