Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006512.1 Hibiscus syriacus cultivar Beakdansim tig00015866_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: 67117
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4043 original size:88 final size:87
Alignment explanation
Indices: 3893--4172 Score: 323
Period size: 88 Copynumber: 3.2 Consensus size: 87
3883 AACATGTTAT
* * * * *
3893 AAGAATGAAATTTAATGATGTTTATAGTCACTACATTATATGTTATTGAGCCTATTGCATTATAT
1 AAGAATGAAATTTACTGATGTTTCTGGTCACTACATTATCTGTTATTGAACCTATTGCATTATAT
* *
3958 ACTTCTCAGTCGCAGTCTAATCA
66 -CTTCTCAGTCACAGACTAATCA
* * *
3981 AAGAATGAGATTTACTGATGTTTCTGGTCACTCCATTATCTGTTATTGAACCTATTGTATTATAT
1 AAGAATGAAATTTACTGATGTTTCTGGTCACTACATTATCTGTTATTGAACCTATTGCATTATAT
* *
4046 CATTCTCAGTCACAGGCTAATAA
66 C-TTCTCAGTCACAGACTAATCA
* * **
4069 AAGAACGATATTTACT-A-GCATTTCTGGTCACTGTATTATCTGTTATT-AAGCCTATTGCATTA
1 AAGAATGAAATTTACTGATG--TTTCTGGTCACTACATTATCTGTTATTGAA-CCTATTGCATTA
*
4131 TATTCTTCTCAGTCAAAGACTAATCA
63 TA-TCTTCTCAGTCACAGACTAATCA
*
4157 AAGAATAAAATTTACT
1 AAGAATGAAATTTACT
4173 AGTTCTGATC
Statistics
Matches: 165, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 4 0.02
88 158 0.96
89 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (87 bp):
AAGAATGAAATTTACTGATGTTTCTGGTCACTACATTATCTGTTATTGAACCTATTGCATTATAT
CTTCTCAGTCACAGACTAATCA
Found at i:4367 original size:60 final size:61
Alignment explanation
Indices: 4239--4377 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 61
4229 TCCTCATTTC
* **
4239 AAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCTCAAAAACTATGAATTTCATTCT
1 AAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCTCAAAAACTATGAATACCATTCT
* * **
4300 AAATTAGTCCTTAAATTTTTGAACA-TTCTAATTTCATC-CCCAAACTATGAATACCATTCT
1 AAATTAGTCCTTAAACTTTTAAACATTTC-AATTTCATCTCAAAAACTATGAATACCATTCT
* *
4360 AATTTAGTCCCTAAACTT
1 AAATTAGTCCTTAAACTT
4378 GTGCATATTC
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 36 0.54
61 31 0.46
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (61 bp):
AAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCTCAAAAACTATGAATACCATTCT
Found at i:4376 original size:31 final size:30
Alignment explanation
Indices: 4281--4376 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
4271 TTCATCTCAA
* * *
4281 AAACTATGAATTTCATTCTAAATTAGTCCTT
1 AAACTATGAA-TACATTCTAATTTAGTCCCT
* * *
4312 AAATTTTTG-A-ACATTCTAATTTCA-TCCCC
1 AAA-CTATGAATACATTCTAATTT-AGTCCCT
4341 AAACTATGAATACCATTCTAATTTAGTCCCT
1 AAACTATGAATA-CATTCTAATTTAGTCCCT
4372 AAACT
1 AAACT
4377 TGTGCATATT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 3 0.06
29 17 0.34
30 3 0.06
31 24 0.48
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTATGAATACATTCTAATTTAGTCCCT
Found at i:4611 original size:59 final size:61
Alignment explanation
Indices: 4537--4675 Score: 169
Period size: 59 Copynumber: 2.3 Consensus size: 61
4527 AGTATTAAAT
* *
4537 TGAAATGTTCAAAAAGTTTAG-GGACCAATCTAGAATGAA-GGTCATAGTTTGGGGATGAAAA
1 TGAAATGTT-AAAAAGTTTAGAGGACCAATCTAGAAT-AATAGTCATAGTTTAGGGATGAAAA
* * *
4598 TGAAATGTT-AAAAGTTT-GAGGACTAATTTAGAATAATAGTCATAGTTTAGGGATGAAAT
1 TGAAATGTTAAAAAGTTTAGAGGACCAATCTAGAATAATAGTCATAGTTTAGGGATGAAAA
* *
4657 TGGAATGTTGAAAAGTTTA
1 TGAAATGTTAAAAAGTTTA
4676 AAGACTAATT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
58 3 0.04
59 48 0.71
60 8 0.12
61 9 0.13
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (61 bp):
TGAAATGTTAAAAAGTTTAGAGGACCAATCTAGAATAATAGTCATAGTTTAGGGATGAAAA
Found at i:4700 original size:60 final size:59
Alignment explanation
Indices: 4576--4710 Score: 162
Period size: 60 Copynumber: 2.3 Consensus size: 59
4566 CTAGAATGAA
* * * * *
4576 GGTCATAGTTTGGGGATGAAAATGAAATGTTAAAAGTTTGAGGACTAATTTAGAATAAT
1 GGTCATAGTTTAGGGATGAAAATGAAATGTTAAAAGTTTAAAGACTAATTTAAAATAAG
* * * *
4635 AGTCATAGTTTAGGGATGAAATTGGAATGTTGAAAAGTTTAAAGACTAATTTAAAATTAG
1 GGTCATAGTTTAGGGATGAAAATGAAATGTT-AAAAGTTTAAAGACTAATTTAAAATAAG
**
4695 GGTCATAAATTAGGGA
1 GGTCATAGTTTAGGGA
4711 CGTATGATGC
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 27 0.43
60 36 0.57
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (59 bp):
GGTCATAGTTTAGGGATGAAAATGAAATGTTAAAAGTTTAAAGACTAATTTAAAATAAG
Found at i:4821 original size:50 final size:49
Alignment explanation
Indices: 4767--4896 Score: 125
Period size: 50 Copynumber: 2.6 Consensus size: 49
4757 GTTGAGTGAA
*
4767 TTAAAGAATTAACTTATATCAATGTAAACAAGTATTGATAATTCAATAAC
1 TTAAAGAATTAATTTATA-CAATGTAAACAAGTATTGATAATTCAATAAC
** * * * * * *
4817 TTAAAGTTTTAATTTACACTAATATACACAAGTATTGATAGTTCACTAAT
1 TTAAAGAATTAATTTATAC-AATGTAAACAAGTATTGATAATTCAATAAC
*
4867 TTAAAAAATAATAATTTATACCAATGTAAA
1 TTAAAGAAT--TAATTTATA-CAATGTAAA
4897 TTAACATAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
49 1 0.02
50 45 0.74
52 14 0.23
53 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (49 bp):
TTAAAGAATTAATTTATACAATGTAAACAAGTATTGATAATTCAATAAC
Found at i:5567 original size:2 final size:2
Alignment explanation
Indices: 5554--5593 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5544 AAATTCATAA
*
5554 AT AT AA 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
5594 TAATTTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10880 original size:50 final size:50
Alignment explanation
Indices: 10791--10885 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
10781 CGGGGTTCTG
*
10791 TCCGAGCTAACGCCATGTCATGAAAGACACGGATAGCCATCCGCGCCTTA
1 TCCGAGCTAACGCCATGTCACGAAAGACACGGATAGCCATCCGCGCCTTA
** * ** *
10841 TCCGAGCTGGCGCCATGTCACGACAGACGTGGATCGCCATCCGCG
1 TCCGAGCTAACGCCATGTCACGAAAGACACGGATAGCCATCCGCG
10886 TCTTCCAGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (50 bp):
TCCGAGCTAACGCCATGTCACGAAAGACACGGATAGCCATCCGCGCCTTA
Found at i:11125 original size:21 final size:21
Alignment explanation
Indices: 11087--11126 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11077 TAAGGTAAAA
* * *
11087 TTATTTTTTATTTTATTATAT
1 TTATTTTATATATGATTATAT
11108 TTATTTTATATATGATTAT
1 TTATTTTATATATGATTAT
11127 TTGAAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTATTTTATATATGATTATAT
Found at i:12381 original size:2 final size:2
Alignment explanation
Indices: 12328--12365 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12318 ACTAAAACAA
12328 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
12366 CAAAATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14784 original size:60 final size:60
Alignment explanation
Indices: 14673--14785 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
14663 AACATAAAGA
* *
14673 ATAGTCAGGTGATCATTTTGTAACTTTGAATAGTCGAAGAACTTCACAAAGCAACATTCT
1 ATAGTCAGATGATCATTTTGTAACTTTGAATAGTCGAAGAACTTAACAAAGCAACATTCT
* * *
14733 ATAGTCAGATGATCATTTTGTAACTTCT-AATAGTCGATGGACTTAATAAAGCA
1 ATAGTCAGATGATCATTTTGTAACTT-TGAATAGTCGAAGAACTTAACAAAGCA
14786 TAACCCTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (60 bp):
ATAGTCAGATGATCATTTTGTAACTTTGAATAGTCGAAGAACTTAACAAAGCAACATTCT
Found at i:14795 original size:60 final size:60
Alignment explanation
Indices: 14673--14799 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
14663 AACATAAAGA
* * **
14673 ATAGTCAGGTGATCATTTTGTAACTTTGAATAGTCGAAGAACTTCACAAAGCAACATTCT
1 ATAGTCAGATGATCATTTTGTAACTTTGAATAGTCGAAGAACTTAACAAAGCAACACCCT
* * *
14733 ATAGTCAGATGATCATTTTGTAACTTCT-AATAGTCGATGGACTTAATAAAGCATA-ACCCT
1 ATAGTCAGATGATCATTTTGTAACTT-TGAATAGTCGAAGAACTTAACAAAGCA-ACACCCT
14793 ATAGTCA
1 ATAGTCA
14800 AGGGACCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 56 0.97
61 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (60 bp):
ATAGTCAGATGATCATTTTGTAACTTTGAATAGTCGAAGAACTTAACAAAGCAACACCCT
Found at i:14810 original size:60 final size:59
Alignment explanation
Indices: 14673--14819 Score: 147
Period size: 60 Copynumber: 2.4 Consensus size: 59
14663 AACATAAAGA
* **
14673 ATAGTCAGGTGATCATTTTGTAACTTTGAATAGTCGAAGAACTTCACAAAGCAACATTCT
1 ATAGTCAGG-GATCATTTTGTAACTTTGAATAGTCGAAGAACTTAACAAAGCAACACCCT
* * * *
14733 ATAGTCAGATGATCATTTTGTAACTTCT-AATAGTCGATGGACTTAATAAAGCATA-ACCCT
1 ATAGTCAG-GGATCATTTTGTAACTT-TGAATAGTCGAAGAACTTAACAAAGCA-ACACCCT
*
14793 ATAGTCAAGGGACCATTTATGT-ACTTT
1 ATAGTC-AGGGATCATTT-TGTAACTTT
14820 ACCCTTAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
59 1 0.01
60 65 0.89
61 7 0.10
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (59 bp):
ATAGTCAGGGATCATTTTGTAACTTTGAATAGTCGAAGAACTTAACAAAGCAACACCCT
Found at i:17994 original size:2 final size:2
Alignment explanation
Indices: 17987--18022 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17977 AGAAAGATCC
*
17987 AG AG AG AG AG AG AC 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
18023 TCTTCTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19944 original size:44 final size:44
Alignment explanation
Indices: 19894--19981 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
19884 AGTGACCAAA
19894 ATGTGGGAGATAGAGTAAAGTTTAGTGACAAAAAAAGGTTCAAT
1 ATGTGGGAGATAGAGTAAAGTTTAGTGACAAAAAAAGGTTCAAT
19938 ATGTGGGAGATAGAGTAAAGTTTAGTGACAAAAAAAGGTTCAAT
1 ATGTGGGAGATAGAGTAAAGTTTAGTGACAAAAAAAGGTTCAAT
19982 GTATTAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.25
Consensus pattern (44 bp):
ATGTGGGAGATAGAGTAAAGTTTAGTGACAAAAAAAGGTTCAAT
Found at i:24599 original size:18 final size:18
Alignment explanation
Indices: 24578--24638 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
24568 TTAACTGTAA
24578 GTGCTTCGACTCTCAGAG
1 GTGCTTCGACTCTCAGAG
*
24596 GTGCTTC-ATTAC-CAGTAG
1 GTGCTTCGACT-CTCAG-AG
*
24614 GTGCTTCGACGCTCAGAG
1 GTGCTTCGACTCTCAGAG
*
24632 GTACTTC
1 GTGCTTC
24639 CTTACCAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 5 0.14
18 26 0.74
19 4 0.11
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (18 bp):
GTGCTTCGACTCTCAGAG
Found at i:24618 original size:36 final size:36
Alignment explanation
Indices: 24562--24659 Score: 142
Period size: 36 Copynumber: 2.7 Consensus size: 36
24552 AACATTATCA
* * * *
24562 ACTTCATTAACTGTAAGTGCTTCGACTCTCAGAGGT
1 ACTTCATTACCAGTAGGTGCTTCGACGCTCAGAGGT
*
24598 GCTTCATTACCAGTAGGTGCTTCGACGCTCAGAGGT
1 ACTTCATTACCAGTAGGTGCTTCGACGCTCAGAGGT
*
24634 ACTTCCTTACCAGTAGGTGCTTCGAC
1 ACTTCATTACCAGTAGGTGCTTCGAC
24660 ACCTGCAGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (36 bp):
ACTTCATTACCAGTAGGTGCTTCGACGCTCAGAGGT
Found at i:24748 original size:207 final size:207
Alignment explanation
Indices: 24403--24780 Score: 488
Period size: 207 Copynumber: 1.8 Consensus size: 207
24393 TTCATTAGTC
* ** ** **
24403 GTAGGTGCTTCGACACTCAGAGTTGTTTCATTACTGGTAGGCGCTTCGGTACCCACAGGTCCTTT
1 GTAGGTGCTTCGACACTCAGAGGTACTTCATTACCAGTAGGCGCTTCGACACCCACAGGTCCTTT
* * * * *
24468 TGGGCAAGCAGAAGAAATATGGCCCTTTTGTCCACACACGTAGCACGTCCGTCTCCTCAACTTAC
66 AGGGCAAGCAGAAGAAATATGACCCTTCTCTCCACACACGTAACACGTCCGTCTCCTCAACTTAC
* *
24533 CACTGCTAACACTCAAGCCAACATTATCAACTTCATTAACTGTAAGTGCTTCGACTCTCAGAGGT
131 CACTGCTAACACTCAAACCAACATTATCAACTTCACTAACTGTAAGTGCTTCGACTCTCAGAGGT
24598 GCTTCATTACCA
196 GCTTCATTACCA
* * * **
24610 GTAGGTGCTTCGACGCTCAGAGGTACTTCCTTACCAGTAGGTGCTTCGACACCTGCAGGTCCTTT
1 GTAGGTGCTTCGACACTCAGAGGTACTTCATTACCAGTAGGCGCTTCGACACCCACAGGTCCTTT
* * * * *
24675 AGTGCAAGCAGAAGAAATATGACCCTTCTCTCCGCAC-TGATAACACGTCCTTCTCCTCAGCTTA
66 AGGGCAAGCAGAAGAAATATGACCCTTCTCTCCACACACG-TAACACGTCCGTCTCCTCAACTTA
* ** *
24739 CCACTGCTAACGCTCAAACCTCCGTTATCAACTTCACTAACT
130 CCACTGCTAACACTCAAACCAACATTATCAACTTCACTAACT
24781 TGAGGGGCTT
Statistics
Matches: 142, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
206 1 0.01
207 141 0.99
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (207 bp):
GTAGGTGCTTCGACACTCAGAGGTACTTCATTACCAGTAGGCGCTTCGACACCCACAGGTCCTTT
AGGGCAAGCAGAAGAAATATGACCCTTCTCTCCACACACGTAACACGTCCGTCTCCTCAACTTAC
CACTGCTAACACTCAAACCAACATTATCAACTTCACTAACTGTAAGTGCTTCGACTCTCAGAGGT
GCTTCATTACCA
Found at i:26450 original size:423 final size:423
Alignment explanation
Indices: 25664--26508 Score: 1663
Period size: 423 Copynumber: 2.0 Consensus size: 423
25654 TAACAATAGC
25664 GATAAACTACAAGAAGACTTTACTTATTTCAAGCATATATATATATATATATGCATGAAATATCC
1 GATAAACTACAAGAAGACTTTACTTATTTCAAGCATATATATATATATATATGCATGAAATATCC
25729 ATTTTCAAAGAACAAATAGAGCCAACTCCGATGCAAAGAATAGTGTTAGAATACTTCAGCTTCTG
66 ATTTTCAAAGAACAAATAGAGCCAACTCCGATGCAAAGAATAGTGTTAGAATACTTCAGCTTCTG
*
25794 CTCCTTCCAACTTTAGTAATAACTAGCTTATCATAGCAATAACGATTAATACACCGGATGATACT
131 CTCCTTCCAACTTTAGTAATAACTAGCTTATCATAGCAATAACGATTAACACACCGGATGATACT
*
25859 AATATGAATAAACTGATCCACCTCGAATTAGTAAAGCATTTATAAGTGTGTACAAGCAAGCATCA
196 AATATGAATAAACTGATCCACCTAGAATTAGTAAAGCATTTATAAGTGTGTACAAGCAAGCATCA
25924 TGGATAATTACCTCGAAACTAACAATTGCAATTCCTCTGAACTTCCCAGTGTCGGGAAACTTCAT
261 TGGATAATTACCTCGAAACTAACAATTGCAATTCCTCTGAACTTCCCAGTGTCGGGAAACTTCAT
*
25989 ACAATCAATATCAGTTATGGTGCCACAATTTTCAAAATAATATCGAATATCATCCTCGGAATAGC
326 ACAATCAATATCAGTTATGGTGCCACAACTTTCAAAATAATATCGAATATCATCCTCGGAATAGC
26054 GATATGGAATCCCTCCAACGTATACTTTTGTGA
391 GATATGGAATCCCTCCAACGTATACTTTTGTGA
26087 GATAAACTACAAGAAGACTTTACTTATTTCAAGCATATATATATATATATATGCATGAAATATCC
1 GATAAACTACAAGAAGACTTTACTTATTTCAAGCATATATATATATATATATGCATGAAATATCC
26152 ATTTTCAAAGAACAAATAGAGCCAACTCCGATGCAAAGAATAGTGTTAGAATACTTCAGCTTCTG
66 ATTTTCAAAGAACAAATAGAGCCAACTCCGATGCAAAGAATAGTGTTAGAATACTTCAGCTTCTG
26217 CTCCTTCCAACTTTAGTAATAACTAGCTTATCATAGCAATAACGATTAACACACCGGATGATACT
131 CTCCTTCCAACTTTAGTAATAACTAGCTTATCATAGCAATAACGATTAACACACCGGATGATACT
26282 AATATGAATAAACTGATCCACCTAGAATTAGTAAAGCATTTATAAGTGTGTACAAGCAAGCATCA
196 AATATGAATAAACTGATCCACCTAGAATTAGTAAAGCATTTATAAGTGTGTACAAGCAAGCATCA
26347 TGGATAATTACCTCGAAACTAACAATTGCAATTCCTCTGAACTTCCCAGTGTCGGGAAACTTCAT
261 TGGATAATTACCTCGAAACTAACAATTGCAATTCCTCTGAACTTCCCAGTGTCGGGAAACTTCAT
26412 ACAATCAATATCAGTTATGGTGCCACAACTTTCAAAATAATATCGAATATCATCCTCGGAATAGC
326 ACAATCAATATCAGTTATGGTGCCACAACTTTCAAAATAATATCGAATATCATCCTCGGAATAGC
26477 GATATGGAATCCCTCCAACGTATACTTTTGTG
391 GATATGGAATCCCTCCAACGTATACTTTTGTG
26509 GCAACATCCT
Statistics
Matches: 419, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
423 419 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (423 bp):
GATAAACTACAAGAAGACTTTACTTATTTCAAGCATATATATATATATATATGCATGAAATATCC
ATTTTCAAAGAACAAATAGAGCCAACTCCGATGCAAAGAATAGTGTTAGAATACTTCAGCTTCTG
CTCCTTCCAACTTTAGTAATAACTAGCTTATCATAGCAATAACGATTAACACACCGGATGATACT
AATATGAATAAACTGATCCACCTAGAATTAGTAAAGCATTTATAAGTGTGTACAAGCAAGCATCA
TGGATAATTACCTCGAAACTAACAATTGCAATTCCTCTGAACTTCCCAGTGTCGGGAAACTTCAT
ACAATCAATATCAGTTATGGTGCCACAACTTTCAAAATAATATCGAATATCATCCTCGGAATAGC
GATATGGAATCCCTCCAACGTATACTTTTGTGA
Found at i:28988 original size:27 final size:27
Alignment explanation
Indices: 28950--29001 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
28940 TAATTTGGGG
28950 AGTAAGGACTAATTTGAATAACATTGT
1 AGTAAGGACTAATTTGAATAACATTGT
28977 AGTAAGGACTAATTTGAATAACATT
1 AGTAAGGACTAATTTGAATAACATT
29002 TAATCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (27 bp):
AGTAAGGACTAATTTGAATAACATTGT
Found at i:35218 original size:21 final size:20
Alignment explanation
Indices: 35194--35240 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
35184 AGATGTGATA
*
35194 TTTTTTAAATTTTCATTCTTT
1 TTTTTTAAATTTT-ATTCATT
*
35215 TTTTATTGAATTTTATTCATT
1 TTTT-TTAAATTTTATTCATT
35236 TTTTT
1 TTTTT
35241 CTTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTTAAATTTTATTCATT
Found at i:35245 original size:30 final size:30
Alignment explanation
Indices: 35213--35269 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
35203 TTTTCATTCT
*
35213 TTTTTTATTGAAT-TTTATTCATTTTTTTC
1 TTTTTTATTGAATACTTATTCATTTTTTTC
* *
35242 TTTTTTATTGTATACTTATTGATTTTTT
1 TTTTTTATTGAATACTTATTCATTTTTT
35270 AAAAAAGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (30 bp):
TTTTTTATTGAATACTTATTCATTTTTTTC
Found at i:35781 original size:22 final size:22
Alignment explanation
Indices: 35751--35792 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35741 GACTAGGACT
* * *
35751 ATAAGACACGTCTCAGTTTTTA
1 ATAACACACGCCTCACTTTTTA
35773 ATAACACACGCCTCACTTTT
1 ATAACACACGCCTCACTTTT
35793 GATCTCTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (22 bp):
ATAACACACGCCTCACTTTTTA
Found at i:44293 original size:57 final size:57
Alignment explanation
Indices: 44223--44353 Score: 226
Period size: 57 Copynumber: 2.3 Consensus size: 57
44213 CTAAAAGGGC
* *
44223 ATAGATGCCAACCTAAGAGAGCACCTTATGTCCATAAGGTATTGCCTTAGCCGAAGT
1 ATAGGTGCCAACCTAAGAGAGCACCTTATGTCCATAAGGTATTACCTTAGCCGAAGT
44280 ATAGGTGCCAACCTAAGAGAGCACCTTATGTCCATAAGGTATTACCTTAGCCGAAGT
1 ATAGGTGCCAACCTAAGAGAGCACCTTATGTCCATAAGGTATTACCTTAGCCGAAGT
* *
44337 GTAGGTGCCCACCTAAG
1 ATAGGTGCCAACCTAAG
44354 GGAAGTGCCT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 70 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (57 bp):
ATAGGTGCCAACCTAAGAGAGCACCTTATGTCCATAAGGTATTACCTTAGCCGAAGT
Found at i:48071 original size:23 final size:23
Alignment explanation
Indices: 48043--48090 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
48033 ATTGTTTCTA
*
48043 GAGGATAGTGTAGAGTCGATTAG
1 GAGGATAATGTAGAGTCGATTAG
48066 GAGGATAATGTAGAGTCGATTAG
1 GAGGATAATGTAGAGTCGATTAG
48089 GA
1 GA
48091 ACACAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.38, T:0.25
Consensus pattern (23 bp):
GAGGATAATGTAGAGTCGATTAG
Found at i:52232 original size:21 final size:21
Alignment explanation
Indices: 52189--52234 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
52179 ATTAGAAATG
*
52189 TTAAGAATATAGAGTTTTTTT
1 TTAAGAATATAGAGTTTTCTT
*
52210 TTAAGAATATATA-TATTTCTT
1 TTAAGAATATAGAGT-TTTCTT
52231 TTAA
1 TTAA
52235 AAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
TTAAGAATATAGAGTTTTCTT
Found at i:55767 original size:19 final size:19
Alignment explanation
Indices: 55727--55763 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55717 TGGAAAAGAA
*
55727 AAATGAAATGAATTAAAAT
1 AAATAAAATGAATTAAAAT
55746 AAATAAAATGAA-TAAAAT
1 AAATAAAATGAATTAAAAT
55764 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
AAATAAAATGAATTAAAAT
Found at i:55970 original size:37 final size:36
Alignment explanation
Indices: 55856--56136 Score: 242
Period size: 39 Copynumber: 7.8 Consensus size: 36
55846 AAAAAAATTC
*
55856 AAAACTATATGCTATAT-AGTTTTCAAAATG-TTTT
1 AAAACTATATACTATATAAGTTTTCAAAATGTTTTT
* *
55890 AAAA--A-ATATTATATAAGTTTTCACAAACTATTTTT
1 AAAACTATATACTATATAAGTTTTCA-AAA-TGTTTTT
* *
55925 AAAACTATATATTATATAACTTTTCAGAAATGTTTTT
1 AAAACTATATACTATATAAGTTTTCA-AAATGTTTTT
** *
55962 AAAACTATATACTATATATTTTTTCAAAAACTATTTTTT
1 AAAACTATATACTATATAAGTTTTC-AAAA-T-GTTTTT
* * *
56001 TAAACTATATATTATATAATTTTTCAAAAAATGGTTTTT
1 AAAACTATATACTATATAAGTTTTC--AAAAT-GTTTTT
* *
56040 AAAACTATATA-T-TAT-A--TTT-AAAACGTTTTA
1 AAAACTATATACTATATAAGTTTTCAAAATGTTTTT
* *
56070 AAAACTATATACTATATAAGTTTTCAAAGTGTTTTA
1 AAAACTATATACTATATAAGTTTTCAAAATGTTTTT
*
56106 AAAACTATATAGTATATAAATGTTTTCAAAA
1 AAAACTATATACTATAT-AA-GTTTTCAAAA
56137 CTACATATTA
Statistics
Matches: 206, Mismatches: 22, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
30 16 0.08
31 12 0.06
32 12 0.06
33 4 0.02
34 8 0.04
35 11 0.05
36 26 0.13
37 37 0.18
38 32 0.16
39 43 0.21
40 5 0.02
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (36 bp):
AAAACTATATACTATATAAGTTTTCAAAATGTTTTT
Found at i:56057 original size:76 final size:75
Alignment explanation
Indices: 55856--56123 Score: 251
Period size: 69 Copynumber: 3.7 Consensus size: 75
55846 AAAAAAATTC
** * * ** *
55856 AAAACTATATGCTATAT-AGTTTTC-AAAATG-TTTTAAAA--A-ATATTATATAAGTTTTCACA
1 AAAACTATATATTATATAACTTTTCAAAAATGTTTTTAAAACTATATACTATATATTTTTTCAAA
55915 AACTATTTTT
66 AACTATTTTT
*
55925 AAAACTATATATTATATAACTTTTCAGAAATGTTTTTAAAACTATATACTATATATTTTTTCAAA
1 AAAACTATATATTATATAACTTTTCAAAAATGTTTTTAAAACTATATACTATATATTTTTTCAAA
55990 AACTATTTTTT
66 AACTA-TTTTT
* *
56001 TAAACTATATATTATATAATTTTTCAAAAAATGGTTTTTAAAACTATATA-T-TATA---TTT--
1 AAAACTATATATTATATAACTTTTC-AAAAAT-GTTTTTAAAACTATATACTATATATTTTTTCA
* *
56059 AAAAC-GTTTTA
64 AAAACTATTTTT
* * * * *
56070 AAAACTATATACTATATAAGTTTTC-AAAGTGTTTTAAAAACTATATAGTATATA
1 AAAACTATATATTATATAACTTTTCAAAAATGTTTTTAAAACTATATACTATATA
56124 AATGTTTTCA
Statistics
Matches: 170, Mismatches: 18, Indels: 23
0.81 0.09 0.11
Matches are distributed among these distances:
66 16 0.09
67 5 0.03
68 4 0.02
69 41 0.24
70 6 0.04
71 10 0.06
72 8 0.05
73 3 0.02
74 1 0.01
75 21 0.12
76 32 0.19
77 6 0.04
78 17 0.10
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (75 bp):
AAAACTATATATTATATAACTTTTCAAAAATGTTTTTAAAACTATATACTATATATTTTTTCAAA
AACTATTTTT
Found at i:56189 original size:27 final size:27
Alignment explanation
Indices: 56105--56196 Score: 67
Period size: 32 Copynumber: 3.1 Consensus size: 27
56095 AAAGTGTTTT
*
56105 AAAAACTATATAGTATATAAATGTTTTCA
1 AAAAACTATATAATATATAAA--TTTTCA
* * * *
56134 AAACTACATATTATATTTTAAAAATATTTTCA
1 AAA-AAC-TA-TATAATAT-ATAA-ATTTTCA
*
56166 AAAAACTATATAATATATAAATTTTCG
1 AAAAACTATATAATATATAAATTTTCA
56193 AAAA
1 AAAA
56197 TCATTTTCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 10 0.20
28 3 0.06
29 9 0.18
30 4 0.08
31 4 0.08
32 15 0.31
33 3 0.06
34 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (27 bp):
AAAAACTATATAATATATAAATTTTCA
Found at i:56263 original size:2 final size:2
Alignment explanation
Indices: 56256--56318 Score: 94
Period size: 2 Copynumber: 32.0 Consensus size: 2
56246 ACTATATTAC
56256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
56296 GA TGA TA TA TA TA TA TA TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA TA
56319 AACAAAATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.04
2 53 0.93
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:60819 original size:26 final size:24
Alignment explanation
Indices: 60790--60839 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
60780 TTTTAAGTTG
60790 GGGTAAAAAGATGAGGGACCAAAAGT
1 GGGT-AAAA-ATGAGGGACCAAAAGT
*
60816 GGGTAAAACTGAGGGACCAAAAGT
1 GGGTAAAAATGAGGGACCAAAAGT
60840 ATAGTTTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.65
25 4 0.17
26 4 0.17
ACGTcount: A:0.44, C:0.10, G:0.34, T:0.12
Consensus pattern (24 bp):
GGGTAAAAATGAGGGACCAAAAGT
Done.