Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006476.1 Hibiscus syriacus cultivar Beakdansim tig00015698_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: 116801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2728 original size:36 final size:36
Alignment explanation
Indices: 2681--2778 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
2671 CAACTAGAGT
*
2681 TTCATCTGTAATGCTCGTATCATTGGTGTCAGCAGC
1 TTCATCTGTAATGCTCGCATCATTGGTGTCAGCAGC
*
2717 TTCATCTGTAATGCTCGCATCATTGGTTTCAGCAGC
1 TTCATCTGTAATGCTCGCATCATTGGTGTCAGCAGC
*
2753 TTCATCTGTAACGCTCGCATCATTGG
1 TTCATCTGTAATGCTCGCATCATTGG
2779 CTGCTGTGGC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (36 bp):
TTCATCTGTAATGCTCGCATCATTGGTGTCAGCAGC
Found at i:4456 original size:17 final size:18
Alignment explanation
Indices: 4434--4467 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4424 CCCTCAAGCT
*
4434 TTGCATTTCGA-TTCGAA
1 TTGCATCTCGAGTTCGAA
4451 TTGCATCTCGAGTTCGA
1 TTGCATCTCGAGTTCGA
4468 GTCTTGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (18 bp):
TTGCATCTCGAGTTCGAA
Found at i:5686 original size:36 final size:36
Alignment explanation
Indices: 5645--5723 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
5635 ATGATAACAC
* *
5645 CACCTCCTCCCCT-TCCGCCGCCACATGAAACACCGT
1 CACCTCCT-CCATGTCCGCCACCACATGAAACACCGT
* * *
5681 CACCTCATCCATGTCCGCCACCGCATGCAACACCGT
1 CACCTCCTCCATGTCCGCCACCACATGAAACACCGT
5717 CACCTCC
1 CACCTCC
5724 GTCATATTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 3 0.08
36 33 0.92
ACGTcount: A:0.20, C:0.52, G:0.11, T:0.16
Consensus pattern (36 bp):
CACCTCCTCCATGTCCGCCACCACATGAAACACCGT
Found at i:6405 original size:31 final size:31
Alignment explanation
Indices: 6325--6405 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 31
6315 TAAAATAGTC
* *
6325 CTCT-AACTATAGAATATT-GTTTATTAAGT
1 CTCTCAACTATAGAAAATTACTTTATTAAGT
* * * *
6354 CTTTCGATTATAGAATATTACTTTATTAAGT
1 CTCTCAACTATAGAAAATTACTTTATTAAGT
6385 CTCTCAACTATTA-AAAATTAC
1 CTCTCAACTA-TAGAAAATTAC
6406 AAAATGATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 3 0.07
30 12 0.29
31 24 0.59
32 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (31 bp):
CTCTCAACTATAGAAAATTACTTTATTAAGT
Found at i:14533 original size:15 final size:17
Alignment explanation
Indices: 14515--14546 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
14505 ATAAAAGAAG
14515 AATTATA-AA-AAAATA
1 AATTATATAAGAAAATA
14530 AATTATATAAGAAAATA
1 AATTATATAAGAAAATA
14547 CAGAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AATTATATAAGAAAATA
Found at i:15825 original size:21 final size:23
Alignment explanation
Indices: 15790--15838 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
15780 GGTCACTAGT
15790 ATAATTTACCCTTT-AATTTTAA
1 ATAATTTACCCTTTAAATTTTAA
*
15812 ATAATTTA-CCTTTAAATTTTTA
1 ATAATTTACCCTTTAAATTTTAA
15834 ATAAT
1 ATAAT
15839 ACACATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATTTACCCTTTAAATTTTAA
Found at i:20905 original size:23 final size:22
Alignment explanation
Indices: 20853--20893 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
20843 TATAGACTCG
20853 ATTATATTAGATATAATATAAA
1 ATTATATTAGATATAATATAAA
20875 ATTATATT-GATATAATATA
1 ATTATATTAGATATAATATA
20894 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTATATTAGATATAATATAAA
Found at i:21587 original size:59 final size:59
Alignment explanation
Indices: 21479--21632 Score: 227
Period size: 59 Copynumber: 2.6 Consensus size: 59
21469 TCAAGTGACT
* * * * * *
21479 ATTTTGTAACTTTTAATAGTTGAGGAACTCAATAAAGCAACACCTAATAGTCAGGGAATC
1 ATTTTGTAACTTTTAATAGTCG-GAAACTCAACAAAACAACACCTAATAGTCAAGAAATC
*
21539 ATTTTGTAACTTTTAATAGTCGGAAACTCAACAAAACAACACCTAATAGTCAATAAATC
1 ATTTTGTAACTTTTAATAGTCGGAAACTCAACAAAACAACACCTAATAGTCAAGAAATC
*
21598 ATTTTGTAACTTTTAATAGTCGGAGACTCAACAAA
1 ATTTTGTAACTTTTAATAGTCGGAAACTCAACAAA
21633 TTAGTAACAT
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 65 0.76
60 21 0.24
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCGGAAACTCAACAAAACAACACCTAATAGTCAAGAAATC
Found at i:23321 original size:492 final size:493
Alignment explanation
Indices: 22397--23367 Score: 1827
Period size: 492 Copynumber: 2.0 Consensus size: 493
22387 GGCTGCAGGA
* *
22397 GGTGTTCTGCGCAACTCTGAGGGAGAATGGATTTTTTGTTTCACGCGTAGCCTAGGAAGGTGTTC
1 GGTGTTCTACGCAACTCTGAGGGAGAATGGATTTTTGGTTTCACGCGTAGCCTAGGAAGGTGTTC
*
22462 GATTCTTACCGCTGAGTTGTGGGGTGTTCATGATCTCTTGTTGCATGCTTGGAGGTTAGGAATTC
66 GATTCTTACCGCTGAGTTGTGGGGTGTTCATGATCTCTTGTTGCATGCTTGGAGGCTAGGAATTC
*
22527 AAAAAATTGAACTGGAAACCGATAATCTAGAGGTTATGAAGATCTGCACTTTTTCTTCGGCTGCG
131 AAAAAATTGAACTGGAAACCGATAATCTAGAGGTTATGAAGATCTGCACTTTTTCTTCGACTGCG
22592 CTTGTGGGGAGTGCTTTGGTTACTAAAATCCATGAGCTGCTCGAACTTGAGTGGATCATAAAGGT
196 CTTGTGGGGAGTGCTTTGGTTACTAAAATCCATGAGCTGCTCGAACTTGAGTGGATCATAAAGGT
22657 ATCACATGTATTTAGGGAGCAAAATATGGTTGCGGATAGGCTGGCTGCTTTGAGTTGAGGAGCCC
261 ATCACATGTATTTAGGGAGCAAAATATGGTTGCGGATAGGCTGGCTGCTTTGAGTTGAGGAGCCC
* *
22722 CCATTGCTGCTATTGCTTTCTTAGAGCCACCTTCAGAGTTATCTTCCACGCTGCTGCGAGATCTT
326 CCATTACTGCTACTGCTTTCTTAGAGCCACCTTCAGAGTTATCTTCCACGCTGCTGCGAGATCTT
*
22787 CAAACCTCCAGCTAATTCTTGTCTTATTGTTATATCAAAAAAAATGGATAAAGAG-AAAATGTTA
391 CAAACCTCCAGCTAATTCTTGTCTTATTGTTATATCAAAAAAAAAGGATAAAGAGAAAAATGTTA
22851 ACTTTAATGAACGATATATTATTACCGCTGAGTTGTGG
456 ACTTTAATGAACGATATATTATTACCGCTGAGTTGTGG
22889 GGTGTTCTACGCAACTCTGAGGGAGAATGGATTTTTGGTTTCACGCGTAGCCTAGGAAGGTGTTC
1 GGTGTTCTACGCAACTCTGAGGGAGAATGGATTTTTGGTTTCACGCGTAGCCTAGGAAGGTGTTC
22954 GATTCTTACCGCTGAGTTGTGGGGTGTTCATGATCTCTTGTTGCATGCTTGGAGGCTAGGAATTC
66 GATTCTTACCGCTGAGTTGTGGGGTGTTCATGATCTCTTGTTGCATGCTTGGAGGCTAGGAATTC
*
23019 GAAAAATTGAACTGGAAACCGATAATCTAGAGGTTATGAAGATCTGCACTTTTTCTTCGACTGCG
131 AAAAAATTGAACTGGAAACCGATAATCTAGAGGTTATGAAGATCTGCACTTTTTCTTCGACTGCG
23084 CTTGTGGGGAGTGCTTTGGTTACTAAAATCCATGAGCTGCTCGAACTTGAGTGGATCATAAAGGT
196 CTTGTGGGGAGTGCTTTGGTTACTAAAATCCATGAGCTGCTCGAACTTGAGTGGATCATAAAGGT
*
23149 ATCACATGTATTTAGGGAGCAAAATATGGTTGCGGATAGGCTGGCTGTTTTGAGTTGAGGAGCCC
261 ATCACATGTATTTAGGGAGCAAAATATGGTTGCGGATAGGCTGGCTGCTTTGAGTTGAGGAGCCC
* *
23214 CCATTACTGCTACTGTTTTCTTAGAGCCACCTTCGGAGTTATCTTCCACGCTGCTGCGAGATCTT
326 CCATTACTGCTACTGCTTTCTTAGAGCCACCTTCAGAGTTATCTTCCACGCTGCTGCGAGATCTT
*
23279 CAAACCTCCAGCTAATTCTTGTCTTATTGTTATATCAAAAAAAAAGGATAAAGAGAAAAATTTTA
391 CAAACCTCCAGCTAATTCTTGTCTTATTGTTATATCAAAAAAAAAGGATAAAGAGAAAAATGTTA
23344 ACTTTAATGAACGATATATTATTA
456 ACTTTAATGAACGATATATTATTA
23368 TTATTATCGG
Statistics
Matches: 466, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
492 434 0.93
493 32 0.07
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (493 bp):
GGTGTTCTACGCAACTCTGAGGGAGAATGGATTTTTGGTTTCACGCGTAGCCTAGGAAGGTGTTC
GATTCTTACCGCTGAGTTGTGGGGTGTTCATGATCTCTTGTTGCATGCTTGGAGGCTAGGAATTC
AAAAAATTGAACTGGAAACCGATAATCTAGAGGTTATGAAGATCTGCACTTTTTCTTCGACTGCG
CTTGTGGGGAGTGCTTTGGTTACTAAAATCCATGAGCTGCTCGAACTTGAGTGGATCATAAAGGT
ATCACATGTATTTAGGGAGCAAAATATGGTTGCGGATAGGCTGGCTGCTTTGAGTTGAGGAGCCC
CCATTACTGCTACTGCTTTCTTAGAGCCACCTTCAGAGTTATCTTCCACGCTGCTGCGAGATCTT
CAAACCTCCAGCTAATTCTTGTCTTATTGTTATATCAAAAAAAAAGGATAAAGAGAAAAATGTTA
ACTTTAATGAACGATATATTATTACCGCTGAGTTGTGG
Found at i:24359 original size:60 final size:61
Alignment explanation
Indices: 24246--24365 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 61
24236 TGCACATTAT
* *
24246 GTCTAGAAAACTGTTGCTTGCTCGTACTTTTTGTGTACCTAAAATTACTAAAAACCTGCTAA
1 GTCTAGAAAACTGTTGCTTGCTCATAC-TTTTGTGTACCTAAAATTACAAAAAACCTGCTAA
*
24308 GTCTAGAAAACTGTTGCTTGCTCATGC-TTTGTGTACCTAAAATTACAAAAAACCTGCT
1 GTCTAGAAAACTGTTGCTTGCTCATACTTTTGTGTACCTAAAATTACAAAAAACCTGCT
24366 GTCAGTTTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 30 0.55
62 25 0.45
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (61 bp):
GTCTAGAAAACTGTTGCTTGCTCATACTTTTGTGTACCTAAAATTACAAAAAACCTGCTAA
Found at i:27777 original size:31 final size:32
Alignment explanation
Indices: 27735--27808 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
27725 CAAAAGTAAG
* *
27735 AAATTGATCACTGATATTATCGATTTGTAACA
1 AAATTGATCACTAATATTATCGATATGTAACA
27767 AAATT-ATCACTAATATTATCGATATGTAACA
1 AAATTGATCACTAATATTATCGATATGTAACA
*
27798 AAA-CGATCACT
1 AAATTGATCACT
27809 TCACCATCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 33 0.87
32 5 0.13
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (32 bp):
AAATTGATCACTAATATTATCGATATGTAACA
Found at i:32761 original size:24 final size:25
Alignment explanation
Indices: 32655--32763 Score: 80
Period size: 26 Copynumber: 4.3 Consensus size: 25
32645 GTATTTAATA
*
32655 TTAATATAATATT-TTAATATTATT
1 TTAATATAATATTATTAATATTTTT
* * * *
32679 TTAATCAAAATATTAATTATTATAATAT
1 TTAAT-ATAATATT-ATTAATAT-TTTT
* *
32707 TTAAAAT-ATATTTATTAATATTTATA
1 TTAATATAATA-TTATTAATATTT-TT
*
32733 ATAATATAATATTATT-ATATTTTT
1 TTAATATAATATTATTAATATTTTT
32757 TTAATAT
1 TTAATAT
32764 TATAATAATA
Statistics
Matches: 63, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
24 12 0.19
25 14 0.22
26 20 0.32
27 12 0.19
28 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAATATAATATTATTAATATTTTT
Found at i:33384 original size:12 final size:12
Alignment explanation
Indices: 33367--33406 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
33357 ACTTGACCAT
33367 TAAAAATATATA
1 TAAAAATATATA
*
33379 TAAAAATGTATA
1 TAAAAATATATA
33391 TAAATAATTATATA
1 TAAA-AA-TATATA
33405 TA
1 TA
33407 GTGAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 15 0.62
13 2 0.08
14 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
TAAAAATATATA
Found at i:33471 original size:19 final size:19
Alignment explanation
Indices: 33447--33487 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
33437 CATAGCATAA
*
33447 TAAATAATTAAATTAAATT
1 TAAATAAATAAATTAAATT
* *
33466 TAAATAAATATATTTAATT
1 TAAATAAATAAATTAAATT
33485 TAA
1 TAA
33488 CTCTATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATAAATAAATTAAATT
Found at i:36830 original size:21 final size:20
Alignment explanation
Indices: 36806--36853 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
36796 CCCCTAAATT
36806 ATAAACACTAATCAT-TAAAAC
1 ATAAACAC-AA-CATCTAAAAC
*
36827 ATAACACACAACATCTAAATC
1 ATAA-ACACAACATCTAAAAC
36848 ATAAAC
1 ATAAAC
36854 CTTAAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.21
21 15 0.62
22 4 0.17
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (20 bp):
ATAAACACAACATCTAAAAC
Found at i:40772 original size:24 final size:24
Alignment explanation
Indices: 40744--40790 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40734 TTTTTATATA
*
40744 TAATAATATTATATATTTAATTAT
1 TAATAATATTATATATTAAATTAT
*
40768 TAATAATTTTATATATTAAATTA
1 TAATAATATTATATATTAAATTA
40791 AACTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATAATATTATATATTAAATTAT
Found at i:42572 original size:16 final size:17
Alignment explanation
Indices: 42551--42586 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42541 TAGTACGTTA
42551 ATTTATCAT-TTTTTAT
1 ATTTATCATATTTTTAT
*
42567 ATTTATCGTATTTTTAT
1 ATTTATCATATTTTTAT
42584 ATT
1 ATT
42587 AATTTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTATCATATTTTTAT
Found at i:50201 original size:3 final size:3
Alignment explanation
Indices: 50188--50221 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
50178 AAATTATTTG
50188 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
50222 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:50226 original size:3 final size:3
Alignment explanation
Indices: 50220--50266 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
50210 AATAATAATA
* * *
50220 ATT ATT ATT ATT ATT ATA ATA ATT ATT ATT ATT ATT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
50267 GGGAGTGGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:50238 original size:21 final size:21
Alignment explanation
Indices: 50214--50257 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
50204 AATAATAATA
50214 ATAATAATTATTATTATTATT
1 ATAATAATTATTATTATTATT
50235 ATAATAATTATTATTATTATT
1 ATAATAATTATTATTATTATT
50256 AT
1 AT
50258 TATTTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAATAATTATTATTATTATT
Found at i:52112 original size:12 final size:13
Alignment explanation
Indices: 52089--52117 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52079 AGTTCGTGCG
52089 ATTTTCGTTATAA
1 ATTTTCGTTATAA
52102 ATTTT-GTTATAA
1 ATTTTCGTTATAA
52114 ATTT
1 ATTT
52118 GAGAGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (13 bp):
ATTTTCGTTATAA
Found at i:56031 original size:20 final size:21
Alignment explanation
Indices: 56001--56058 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
55991 TTCTCTGACT
56001 CAAAA-GATCGATCCCTTAG-
1 CAAAAGGATCGATCCCTTAGA
* *
56020 CAAAAGGATCGATCCGTTTGA
1 CAAAAGGATCGATCCCTTAGA
*
56041 CCAAAGGATCGATCCCTT
1 CAAAAGGATCGATCCCTT
56059 GAACAACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.15
20 12 0.36
21 16 0.48
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (21 bp):
CAAAAGGATCGATCCCTTAGA
Found at i:70010 original size:51 final size:51
Alignment explanation
Indices: 69955--70076 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
69945 AAGTTCCGAT
* * * * *
69955 CCATCACCCCGGTTCCATGAAGCAAATAACCTGCATTCTGGTGATATTCGA
1 CCATCACCTCAGTTCCATGAAGCAAATAACCAGCATTCTGGTAATATTCCA
*
70006 CCATCACCTCATTTCCATGAAGCAAATAACCAGCATTCTGGTAATATTCCA
1 CCATCACCTCAGTTCCATGAAGCAAATAACCAGCATTCTGGTAATATTCCA
70057 CCATCACCTCAGTTCCATGA
1 CCATCACCTCAGTTCCATGA
70077 TAAGATCGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (51 bp):
CCATCACCTCAGTTCCATGAAGCAAATAACCAGCATTCTGGTAATATTCCA
Found at i:72061 original size:106 final size:106
Alignment explanation
Indices: 71753--72072 Score: 498
Period size: 107 Copynumber: 3.0 Consensus size: 106
71743 ACATCGTTTT
* **
71753 GCTGAAAATTTTATTTTTCTAAAACGACGTCATTTTAACGAA-GTTAGATATTTAACGGCTAAGT
1 GCTGAAAA-TTTATTTTTCTAAAATGACGTCA-TTTAA--AACGTTAGATATTTAATAGCTAAGT
* * * * *
71817 GACCAAAAATATTAATTGTATTAAATTCAGCGATAAAATTGAATG
62 GACAAAAAATACTAATTGTATTAATTTCAGTGAGAAAATTGAATG
*
71862 GCTGAAATTTTATTTTTCTAAAATGACGTCATTTAAAACCGTTAGATATTTAATAGCTAAGTGAC
1 GCTGAAAATTTATTTTTCTAAAATGACGTCATTTAAAA-CGTTAGATATTTAATAGCTAAGTGAC
71927 AAAAAATACTAATTGTATTAATTTCAGTGAGAAAATTGAATG
65 AAAAAATACTAATTGTATTAATTTCAGTGAGAAAATTGAATG
*
71969 GCTGAAAATTTATTTTTCTAAAATGACGTCATTTAAAACGTTAGATATTTAATAGCTAAGTGATA
1 GCTGAAAATTTATTTTTCTAAAATGACGTCATTTAAAACGTTAGATATTTAATAGCTAAGTGACA
72034 AAAAATACTAATTGTATTAATTTCAGTGAGAAAATTGAA
66 AAAAATACTAATTGTATTAATTTCAGTGAGAAAATTGAA
72073 CGGATTTAAA
Statistics
Matches: 198, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
105 2 0.01
106 65 0.33
107 102 0.52
108 22 0.11
109 7 0.04
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (106 bp):
GCTGAAAATTTATTTTTCTAAAATGACGTCATTTAAAACGTTAGATATTTAATAGCTAAGTGACA
AAAAATACTAATTGTATTAATTTCAGTGAGAAAATTGAATG
Found at i:73842 original size:60 final size:60
Alignment explanation
Indices: 73771--73926 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 60
73761 TGAATTCGAT
* * *
73771 GTCCCTAAACTTTTGATTATTCTAATTTCATCCTCAAACTATAATACTCACTCTAAATTA
1 GTCCTTAAACTTTTGAATATTCTAATTTCATCCTCAAACTATAACACTCACTCTAAATTA
* * * * * *
73831 GTTCTTAAACTTTTGAATATT-TCAATTTTATCTTCAAACTATGACACTCATTCTAAATTG
1 GTCCTTAAACTTTTGAATATTCT-AATTTCATCCTCAAACTATAACACTCACTCTAAATTA
* * * *
73891 GTCCTCAAACTTTTAAATCTTCCAATTTCAT-CTCAA
1 GTCCTTAAACTTTTGAATATTCTAATTTCATCCTCAA
73927 GTTCATTCAA
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
59 5 0.06
60 73 0.94
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (60 bp):
GTCCTTAAACTTTTGAATATTCTAATTTCATCCTCAAACTATAACACTCACTCTAAATTA
Found at i:84877 original size:2 final size:2
Alignment explanation
Indices: 84870--84905 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
84860 AGACAGAAAG
84870 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
84906 GCATATAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89276 original size:23 final size:24
Alignment explanation
Indices: 89231--89278 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
89221 GAATTTAGAG
*
89231 AATTTGAGTTTTTAAAAAATATAAT
1 AATTTAAGTTTTT-AAAAATATAAT
89256 AATTTAAGTTTTT-AAAATATAAT
1 AATTTAAGTTTTTAAAAATATAAT
89279 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
25 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
AATTTAAGTTTTTAAAAATATAAT
Found at i:89897 original size:24 final size:24
Alignment explanation
Indices: 89870--89942 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
89860 AACATATTAT
89870 ATTATTTTGTTAGGTTAGTAAAAA
1 ATTATTTTGTTAGGTTAGTAAAAA
89894 ATTATTTTGTTAGGTTAGTAAAAA
1 ATTATTTTGTTAGGTTAGTAAAAA
*
89918 ATAATTTTGTTAGGTTAGTAAAAA
1 ATTATTTTGTTAGGTTAGTAAAAA
89942 A
1 A
89943 CAATGAGAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (24 bp):
ATTATTTTGTTAGGTTAGTAAAAA
Found at i:92802 original size:28 final size:27
Alignment explanation
Indices: 92750--92802 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
92740 AACAACCCCG
* *
92750 TCTTTTTTATTGAGTGATCAAAAATAA
1 TCTTTTATATTGAGTGACCAAAAATAA
*
92777 TCTTTTATAGTTGAGTGACCAGAAAT
1 TCTTTTATA-TTGAGTGACCAAAAAT
92803 GAAACTTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (27 bp):
TCTTTTATATTGAGTGACCAAAAATAA
Found at i:94475 original size:11 final size:11
Alignment explanation
Indices: 94459--94492 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
94449 GTTTCGTATA
94459 TATATTATTAT
1 TATATTATTAT
94470 TATATTATTAT
1 TATATTATTAT
*
94481 TATATTTTTAT
1 TATATTATTAT
94492 T
1 T
94493 TGATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTATTAT
Found at i:107982 original size:24 final size:24
Alignment explanation
Indices: 107952--108015 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
107942 ATAGTTGAAA
*
107952 TAATATATTTTATAATAATATA-TT
1 TAATATATTTTATAATAAT-TACAT
* *
107976 TATTATATTTTA-AACAATTACAT
1 TAATATATTTTATAATAATTACAT
107999 TAATATATTTTATAATA
1 TAATATATTTTATAATA
108016 TTTATAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 2 0.06
23 17 0.52
24 14 0.42
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATATATTTTATAATAATTACAT
Found at i:108035 original size:32 final size:32
Alignment explanation
Indices: 107965--108045 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
107955 TATATTTTAT
*
107965 AATAATATATTTATTATATTTTAAACAATTAC
1 AATAATATATTTATAATATTTTAAACAATTAC
* *
107997 ATTAATATATTTTATAATA-TTTATAATAATTA-
1 AATAATATA-TTTATAATATTTTA-AACAATTAC
*
108029 AATAATATTATTAATAA
1 AATAATA-TATTTATAA
108046 AATAAAATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
32 24 0.59
33 17 0.41
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
AATAATATATTTATAATATTTTAAACAATTAC
Found at i:108091 original size:65 final size:65
Alignment explanation
Indices: 108021--108149 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
108011 TAATATTTAT
*
108021 AATAATTAAATAATATTATTAATAAAAT-AAAATCAAAAATTCTTAAAATATTAAATATAGTAAA
1 AATAATTAAATAATATTATTAATAAAATAAAAAT-AAAAATTCTTAAAATATTAAATATAATAAA
108085 A
65 A
*
108086 AATAATTAAATAATATTATTAATAAAATAAAAATAAATATTCTTAAAATATTAAATATAATAAA
1 AATAATTAAATAATATTATTAATAAAATAAAAATAAAAATTCTTAAAATATTAAATATAATAAA
108150 TATAATAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 56 0.92
66 5 0.08
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (65 bp):
AATAATTAAATAATATTATTAATAAAATAAAAATAAAAATTCTTAAAATATTAAATATAATAAAA
Found at i:108126 original size:21 final size:21
Alignment explanation
Indices: 108028--108135 Score: 53
Period size: 21 Copynumber: 5.0 Consensus size: 21
108018 TATAATAATT
108028 AAATAATATTATTAATAAAAT-A
1 AAATAA-A-TATTAATAAAATAA
* ** *
108050 AAATCAAAAATTCTTAAAATATT
1 AAAT-AAATATTAATAAAATA-A
*
108073 AAAT--ATAGTAA-AAAATAA
1 AAATAAATATTAATAAAATAA
108091 TTAAATAATATTATTAATAAAATAA
1 --AAATAA-A-TATTAATAAAATAA
**
108116 AAATAAATATTCTTAAAATA
1 AAATAAATATTAATAAAATA
108136 TTAAATATAA
Statistics
Matches: 64, Mismatches: 12, Indels: 21
0.66 0.12 0.22
Matches are distributed among these distances:
19 6 0.09
20 7 0.11
21 20 0.31
22 6 0.09
23 13 0.20
24 5 0.08
25 7 0.11
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (21 bp):
AAATAAATATTAATAAAATAA
Found at i:108131 original size:24 final size:24
Alignment explanation
Indices: 108021--108131 Score: 62
Period size: 24 Copynumber: 4.9 Consensus size: 24
108011 TAATATTTAT
108021 AATAATTAAATAATATTATTAATAA
1 AATAA-TAAATAATATTATTAATAA
* **
108046 AAT-A-AAATCAA-A-AATTCTTAA
1 AATAATAAAT-AATATTATTAATAA
* *
108067 AAT-AT-TA-AATA-TAGTAA-AA
1 AATAATAAATAATATTATTAATAA
108086 AATAATTAAATAATATTATTAATAA
1 AATAA-TAAATAATATTATTAATAA
*
108111 AATAA-AAATAAATATTCTTAA
1 AATAATAAAT-AATATTATTAA
108132 AATATTAAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
19 7 0.11
20 4 0.06
21 12 0.18
22 6 0.09
23 10 0.15
24 16 0.25
25 10 0.15
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (24 bp):
AATAATAAATAATATTATTAATAA
Found at i:108151 original size:9 final size:9
Alignment explanation
Indices: 108137--108168 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
108127 CTTAAAATAT
108137 TAAATATAA
1 TAAATATAA
108146 TAAATATAA
1 TAAATATAA
108155 TAAATATAA
1 TAAATATAA
108164 GTAAA
1 -TAAA
108169 AAATAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAATATAA
Found at i:111885 original size:277 final size:278
Alignment explanation
Indices: 111390--111925 Score: 984
Period size: 277 Copynumber: 1.9 Consensus size: 278
111380 GATATGATAG
*
111390 CAAGATAGGAATAACCGTATGCACTGATAGCTCTATTAGCGAGGGCAAATCAGTTGCAGCAAGAA
1 CAAGATAGGAATAACCGTATGCACTGATAGCTCTAATAGCGAGGGCAAATCAGTTGCAGCAAGAA
* *
111455 CAGCTGTGCAAAGAAAAATAACAACTTGCATGAGAAGGTAAAGAAAAACTAAAATCGGCACCTGA
66 CAGCTGTGCAAAGAAAAATAACAACTTGCACGAGAAGGTAAAGAAAAACTAAAATCGGCACATGA
* * *
111520 CAAACAAAATAAAGACATACTAAAGTCGACAACAAGGTTCAGTATCAGGATGACATGAAAATATT
131 CAAAAAAAATAAAGACATAATAAAGTCGACAACAAGGCTCAGTATCAGGATGACATGAAAATATT
111585 AAAAGAAAAACAGAGCAAAATGACCACCACTTTACTAAAATCATTAATGCACCCACATAGCAACT
196 AAAAGAAAAACAGAGCAAAATGACCACCACTTTACTAAAATCATTAATGCACCCACATAGCAACT
111650 AATCAGGTGCCGACGCAC
261 AATCAGGTGCCGACGCAC
*
111668 CAAGATAGGAATAACCGTATGCACTGATAGCTCTAATAGCGAGGGCATATCAGTTGCAGCAAGAA
1 CAAGATAGGAATAACCGTATGCACTGATAGCTCTAATAGCGAGGGCAAATCAGTTGCAGCAAGAA
*
111733 CAGCTGTGCAAAG-AAAATTACAACTTGCACGAGAAGGTAAAGAAAAACTAAAATCGGCACATGA
66 CAGCTGTGCAAAGAAAAATAACAACTTGCACGAGAAGGTAAAGAAAAACTAAAATCGGCACATGA
111797 CAAAAAAAATAAAGACATAATAAAGTCGACAACAAGGCTCAGTATCAGGATGACATGAAAATATT
131 CAAAAAAAATAAAGACATAATAAAGTCGACAACAAGGCTCAGTATCAGGATGACATGAAAATATT
*
111862 AAAAGAAAAACAGAGCAAAATGACCACCACTTTACTAAAATCATTAATGCACCGACATAGCAAC
196 AAAAGAAAAACAGAGCAAAATGACCACCACTTTACTAAAATCATTAATGCACCCACATAGCAAC
111926 GGTAGACAGG
Statistics
Matches: 249, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
277 173 0.69
278 76 0.31
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.18
Consensus pattern (278 bp):
CAAGATAGGAATAACCGTATGCACTGATAGCTCTAATAGCGAGGGCAAATCAGTTGCAGCAAGAA
CAGCTGTGCAAAGAAAAATAACAACTTGCACGAGAAGGTAAAGAAAAACTAAAATCGGCACATGA
CAAAAAAAATAAAGACATAATAAAGTCGACAACAAGGCTCAGTATCAGGATGACATGAAAATATT
AAAAGAAAAACAGAGCAAAATGACCACCACTTTACTAAAATCATTAATGCACCCACATAGCAACT
AATCAGGTGCCGACGCAC
Done.