Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000665.1 Hibiscus syriacus cultivar Beakdansim tig00001294_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: 59962
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5979 original size:28 final size:28
Alignment explanation
Indices: 5939--5993 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
5929 TTTCGTTTAT
* *
5939 ATTATGTCATCGAGTCGATGTTTGAAAC
1 ATTATGTCATCGAGTCAATGCTTGAAAC
*
5967 ATTATGTCGTCGAGTCAATGCTTGAAA
1 ATTATGTCATCGAGTCAATGCTTGAAA
5994 ATAATGGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (28 bp):
ATTATGTCATCGAGTCAATGCTTGAAAC
Found at i:6248 original size:19 final size:21
Alignment explanation
Indices: 6215--6258 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
6205 ATAAAATACG
* *
6215 TAAAAAATAATATTTTTCA-A
1 TAAAAAATAACATTTATCATA
6235 TAAAAAA-AACATTTATCATA
1 TAAAAAATAACATTTATCATA
6255 TAAA
1 TAAA
6259 CCATTTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAAATAACATTTATCATA
Found at i:10325 original size:2 final size:2
Alignment explanation
Indices: 10318--10342 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10308 GATAAAATTG
10318 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 A
10343 ATTTTGATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19590 original size:21 final size:21
Alignment explanation
Indices: 19541--19583 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19531 TTTTAACTCA
*
19541 TAAAAATT-ATATTTTTATTT
1 TAAAATTTAATATTTTTATTT
19561 TAAAATTTAATATTTTTAATTT
1 TAAAATTTAATATTTTT-ATTT
19583 T
1 T
19584 CATTTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAAAATTTAATATTTTTATTT
Found at i:24572 original size:13 final size:13
Alignment explanation
Indices: 24554--24579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24544 GCGGTATATA
24554 AAGCGAGAGAGAG
1 AAGCGAGAGAGAG
24567 AAGCGAGAGAGAG
1 AAGCGAGAGAGAG
24580 GACCGGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.46, T:0.00
Consensus pattern (13 bp):
AAGCGAGAGAGAG
Found at i:24631 original size:15 final size:15
Alignment explanation
Indices: 24607--24686 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
24597 TCGCAAAATA
*
24607 AATTACTGAAATTTG
1 AATTATTGAAATTTG
24622 AATTATTGAAATTTG
1 AATTATTGAAATTTG
**
24637 AATTATTGAAAAATG
1 AATTATTGAAATTTG
* *
24652 AATTACT-AGAATTTA
1 AATTATTGA-AATTTG
**
24667 AATT-TTGAAAAATG
1 AATTATTGAAATTTG
24681 AATTAT
1 AATTAT
24687 ATTTCTGAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
14 9 0.18
15 42 0.82
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (15 bp):
AATTATTGAAATTTG
Found at i:24665 original size:45 final size:44
Alignment explanation
Indices: 24601--24686 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 44
24591 GGTTTTTCGC
* **
24601 AAAATAAATTACTGAAATTTGAATTATTGAAATTTGAATTATTGA
1 AAAATAAATTACTGAAATTTAAATT-TTGAAAAATGAATTATTGA
*
24646 AAAATGAATTACT-AGAATTTAAATTTTGAAAAATGAATTAT
1 AAAATAAATTACTGA-AATTTAAATTTTGAAAAATGAATTAT
24687 ATTTCTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 15 0.42
45 21 0.58
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (44 bp):
AAAATAAATTACTGAAATTTAAATTTTGAAAAATGAATTATTGA
Found at i:24873 original size:14 final size:14
Alignment explanation
Indices: 24854--24894 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
24844 TAAAATAATT
24854 TATTTATTATTAAA
1 TATTTATTATTAAA
24868 TATTTATT-TTATAA
1 TATTTATTATTA-AA
*
24882 T-TTTATTAATAAA
1 TATTTATTATTAAA
24895 AATATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTATTATTAAA
Found at i:24879 original size:19 final size:20
Alignment explanation
Indices: 24841--24876 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
24831 TATTTTAAAA
24841 TATTAAAATAATTTATTTAT
1 TATTAAAATAATTTATTTAT
24861 TATT-AAAT-ATTTATTT
1 TATTAAAATAATTTATTT
24877 TATAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTAAAATAATTTATTTAT
Found at i:25020 original size:23 final size:23
Alignment explanation
Indices: 24974--25037 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
24964 AGTGTTATAT
* *
24974 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAATATATTAACTAG
* *
24997 TATATTTTAAATATCTTTACTAG
1 TATATTTTAAATATATTAACTAG
25020 TATATGTTTTAAATATAT
1 TATA--TTTTAAATATAT
25038 AAATAATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 23 0.68
25 11 0.32
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (23 bp):
TATATTTTAAATATATTAACTAG
Found at i:25060 original size:28 final size:28
Alignment explanation
Indices: 25028--25086 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
25018 AGTATATGTT
* *
25028 TTAAATATATAAATAATATTATTCAT-TA
1 TTAAATATATAAAAAAAATTATT-ATATA
25056 TTAAATATATAAAAAAAATTATTATATA
1 TTAAATATATAAAAAAAATTATTATATA
25084 TTA
1 TTA
25087 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TTAAATATATAAAAAAAATTATTATATA
Found at i:25087 original size:31 final size:30
Alignment explanation
Indices: 25020--25116 Score: 82
Period size: 30 Copynumber: 3.3 Consensus size: 30
25010 TCTTTACTAG
* *
25020 TATATGTT-TTAAATATAT--AAATAATAT
1 TATATATTATTAAATATATAAAAAAAATAT
25047 TAT-TCATTATTAAATATATAAAAAAAATTAT
1 TATAT-ATTATTAAATATATAAAAAAAA-TAT
25078 TATATATTATTAAA-ATA-AAAAATATAATAT
1 TATATATTATTAAATATATAAAAA-A-AATAT
25108 CT-TATATTA
1 -TATATATTA
25117 ATATAATTGA
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
26 1 0.02
27 5 0.08
28 10 0.17
29 5 0.08
30 19 0.32
31 18 0.31
32 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (30 bp):
TATATATTATTAAATATATAAAAAAAATAT
Found at i:25169 original size:22 final size:20
Alignment explanation
Indices: 25144--25192 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
25134 ATTAAACTAA
*
25144 AAATATAATATTATATTATTAT
1 AAATATAATA-AATA-TATTAT
*
25166 AAATATTAATAAATATATTTT
1 AAATA-TAATAAATATATTAT
25187 AAATAT
1 AAATAT
25193 TTTAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 8 0.33
23 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATAATAAATATATTAT
Found at i:25180 original size:27 final size:27
Alignment explanation
Indices: 25111--25181 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
25101 ATAATATCTT
25111 ATATTAATATAATTGATTATATTATTAAA
1 ATATTAATATAA-T-ATTATATTATTAAA
* **
25140 CTAAAAATATAATATTATATTATTATAA
1 ATATTAATATAATATTATATTATTA-AA
25168 ATATTAATA-AATAT
1 ATATTAATATAATAT
25182 ATTTTAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 17 0.49
28 9 0.26
29 9 0.26
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
ATATTAATATAATATTATATTATTAAA
Found at i:25441 original size:42 final size:42
Alignment explanation
Indices: 25382--25500 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
25372 ATGAATTACG
25382 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
25424 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* * *
25466 TTCCGAAAAACGAATTACATGAAACAAATACGGGA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGA
25501 TTTCAGGGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:25793 original size:20 final size:21
Alignment explanation
Indices: 25768--25857 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 21
25758 TTTTCCCAAT
*
25768 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
25788 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* **
25809 TCGCAATGCG-A-TACTGACTA
1 TCGCAATGCGAATTA-AGAAAA
*
25829 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCGA-ATTAAGAAAA
25850 TCGCAATG
1 TCGCAATG
25858 AGATACTTAC
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.02
20 25 0.47
21 24 0.45
22 1 0.02
23 2 0.04
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:25832 original size:41 final size:41
Alignment explanation
Indices: 25805--25882 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
25795 GCGAATTGGG
* *
25805 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAA
* *
25846 AAAATCGCAATGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATA
25883 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAA
Found at i:25875 original size:20 final size:20
Alignment explanation
Indices: 25850--25902 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
25840 TAATAAAAAA
* *
25850 TCGCAATGAGATACTTACTT
1 TCGCAACGAGATACTGACTT
*
25870 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
*
25890 TCGCAACGCGATA
1 TCGCAACGAGATA
25903 ATACATAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:26118 original size:22 final size:22
Alignment explanation
Indices: 26090--26133 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
26080 CACTCTCTCA
26090 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
26112 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
26134 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Found at i:26421 original size:20 final size:20
Alignment explanation
Indices: 26367--26440 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
26357 AAATCGCAAC
*
26367 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** *
26386 GCGATAGTCGA-ATTCGCGTT
1 GCGATTTTC-ATTTTCGCGTT
*
26406 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
26426 GCGATTTTCATTTTC
1 GCGATTTTCATTTTC
26441 AGAAACTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.16
20 37 0.82
21 1 0.02
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.46
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:27704 original size:14 final size:14
Alignment explanation
Indices: 27685--27717 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
27675 CACGGAAGCC
27685 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
27699 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
27713 ATTTT
1 ATTTT
27718 CATTTCGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.55
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:27732 original size:19 final size:19
Alignment explanation
Indices: 27717--27772 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
27707 GTTGCGATTT
27717 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
*
27736 CCATTTC-CACGTTGCGATAG
1 TCATTTCGCA--TTGCGATAG
*
27756 TCATTTCGCGTTGCGAT
1 TCATTTCGCATTGCGAT
27773 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 15 0.48
21 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:29415 original size:21 final size:21
Alignment explanation
Indices: 29349--29415 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
29339 GTGAATCGGG
*
29349 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
29369 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
29391 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
29412 CTCT
1 CTCT
29416 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:29434 original size:42 final size:41
Alignment explanation
Indices: 29349--29471 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
29339 GTGAATCGGG
* * * * *
29349 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
29391 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * * *
29433 CTCTTCAACGATAGGAGTGGACACTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
29472 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:31613 original size:19 final size:19
Alignment explanation
Indices: 31473--31619 Score: 133
Period size: 20 Copynumber: 7.8 Consensus size: 19
31463 TCTTTTGGTT
*
31473 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
31492 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
31512 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** * *
31532 GAAATGACTATAGCGAC-C
1 GAAATGAAAATCGCAACGC
* *
31550 ---A-GACAATCACAACGC
1 GAAATGAAAATCGCAACGC
31565 GAAATGAAAATCGCAATCGC
1 GAAATGAAAATCGCAA-CGC
*
31585 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
31604 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
31620 TGCGGTTTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.08
15 2 0.02
18 2 0.02
19 44 0.42
20 48 0.45
21 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:31656 original size:19 final size:19
Alignment explanation
Indices: 31620--31661 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
31610 AAAATCGCAA
*
31620 TGCGGTTTTTGTTTCGCGT
1 TGCGGTTTTTATTTCGCGT
*
31639 TGCGTTTTTTATTTCGCGT
1 TGCGGTTTTTATTTCGCGT
31658 TGCG
1 TGCG
31662 ATTATCTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.17, G:0.29, T:0.52
Consensus pattern (19 bp):
TGCGGTTTTTATTTCGCGT
Found at i:32283 original size:21 final size:20
Alignment explanation
Indices: 32259--32310 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
32249 TTTTGTATTA
*
32259 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
32280 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
32300 TCGCATTGCGA
1 TCGCATTGCGA
32311 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:32381 original size:21 final size:21
Alignment explanation
Indices: 32341--32381 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
32331 ATTGTATACC
**
32341 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
32362 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
32382 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:32664 original size:16 final size:16
Alignment explanation
Indices: 32639--32679 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
32629 CTAAGGGGTT
32639 TTAA-AAATAATATTAA
1 TTAATAAATAA-ATTAA
*
32655 TT-ATAAATAAATTTA
1 TTAATAAATAAATTAA
32670 TTAATAAATA
1 TTAATAAATA
32680 TTTTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATAAATAAATTAA
Found at i:34317 original size:42 final size:42
Alignment explanation
Indices: 34270--34361 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
34260 TCTCGAAATC
* *
34270 CCGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
34312 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
*
34354 -AGTGTTTG
1 CCGTGTTTG
34362 GTTAGAGGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 7 0.15
42 40 0.85
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
Found at i:34601 original size:21 final size:20
Alignment explanation
Indices: 34575--34642 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
34565 TAATTATTAA
34575 AATATTTAAAATATATTTATT
1 AATATTT-AAATATATTTATT
*
34596 AATATTT-ATTATATTT-TT
1 AATATTTAAATATATTTATT
34614 AATATTTATAATAATATTATATT
1 AATATTTA-AAT-ATATT-TATT
34637 -ATATTT
1 AATATTT
34643 TTAATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 9 0.22
19 8 0.20
20 2 0.05
21 12 0.30
22 7 0.17
23 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTTAAATATATTTATT
Found at i:34610 original size:30 final size:31
Alignment explanation
Indices: 34576--34657 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
34566 AATTATTAAA
*
34576 ATATTTAAAATATATT-TATTAATATT-TATT
1 ATATTTAAAATAT-TTATAATAATATTATATT
**
34606 ATATTTTTAATATTTATAATAATATTATATT
1 ATATTTAAAATATTTATAATAATATTATATT
**
34637 ATATTTTTAATA-TTATAATAA
1 ATATTTAAAATATTTATAATAA
34658 AATAATCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
29 2 0.04
30 29 0.62
31 16 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
ATATTTAAAATATTTATAATAATATTATATT
Found at i:34611 original size:9 final size:9
Alignment explanation
Indices: 34586--34641 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
34576 ATATTTAAAA
34586 TATATTTAT
1 TATATTTAT
34595 TAATATTTAT
1 T-ATATTTAT
34605 TATATTT-T
1 TATATTTAT
34613 TAATATTTAT
1 T-ATATTTAT
* *
34623 AATA-ATAT
1 TATATTTAT
34631 TATATTATAT
1 TATATT-TAT
34641 T
1 T
34642 TTTAATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 8 0.21
9 16 0.42
10 14 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TATATTTAT
Found at i:34653 original size:19 final size:18
Alignment explanation
Indices: 34586--34650 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
34576 ATATTTAAAA
34586 TATATTTATTAATATTTAT
1 TATATTT-TTAATATTTAT
34605 TATATTTTTAATATTTA-
1 TATATTTTTAATATTTAT
34622 TA-A----TAATATTATAT
1 TATATTTTTAATATT-TAT
34636 TATATTTTTAATATT
1 TATATTTTTAATATT
34651 ATAATAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
12 7 0.18
13 2 0.05
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 10 0.26
19 14 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTTAATATTTAT
Found at i:34656 original size:39 final size:39
Alignment explanation
Indices: 34562--34656 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 39
34552 TTCATCAAAA
*
34562 TATTAATTATTAAAATATTTAAAATATATTTATTAATATT
1 TATTAA-TATTATAATATTTAAAATATATTTATTAATATT
* *
34602 TATT-ATATTTTTAATATTTATAATAATATTATATT-ATATT
1 TATTAATA-TTATAATATTTAAAAT-ATATT-TATTAATATT
34642 T-TTAATATTATAATA
1 TATTAATATTATAATA
34657 AAATAATCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
38 2 0.04
39 23 0.49
40 18 0.38
41 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (39 bp):
TATTAATATTATAATATTTAAAATATATTTATTAATATT
Found at i:34679 original size:31 final size:31
Alignment explanation
Indices: 34602--34673 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
34592 TATTAATATT
* *
34602 TATTATATTTTTAATATTTATAATAATATTA
1 TATTATATTTTTAATATTTATAATAAAATAA
34633 TATTATATTTTTAATA-TTATAATAAAATAA
1 TATTATATTTTTAATATTTATAATAAAATAA
34663 TCAATTATATT
1 T--ATTATATT
34674 ATAATAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 13 0.35
31 16 0.43
32 8 0.22
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
TATTATATTTTTAATATTTATAATAAAATAA
Found at i:34739 original size:27 final size:28
Alignment explanation
Indices: 34709--34773 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
34699 TATTTTAATA
34709 AATATATAATAA-ACTT-TTTATATATTT
1 AATATATAATAATA-TTATTTATATATTT
34736 AATA-ATGAATAATATTATTTATATATTT
1 AATATAT-AATAATATTATTTATATATTT
34764 AATAT-TAATA
1 AATATATAATA
34774 TAATAATCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 2 0.06
27 15 0.44
28 17 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
AATATATAATAATATTATTTATATATTT
Found at i:34796 original size:19 final size:18
Alignment explanation
Indices: 34728--34798 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
34718 TAAACTTTTT
*
34728 ATATATTTAATAATGAATA
1 ATAT-TTTAATAATTAATA
*
34747 ATATTATTTATATATTTAATA
1 ATA-T-TTTA-ATAATTAATA
* * *
34768 TTAATATAATAATCTAATA
1 ATATTTTAATAAT-TAATA
34787 ATATTTTAATAA
1 ATATTTTAATAA
34799 AGATATTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 4 0.10
19 20 0.50
20 6 0.15
21 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATATTTTAATAATTAATA
Found at i:34819 original size:23 final size:23
Alignment explanation
Indices: 34793--34837 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34783 AATAATATTT
34793 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
34816 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
34838 ATACAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:45777 original size:2 final size:2
Alignment explanation
Indices: 45770--45803 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
45760 TTTTCGAATA
45770 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
45804 CGAAATTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46184 original size:19 final size:20
Alignment explanation
Indices: 46157--46201 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
46147 AAACAACGGA
*
46157 TAAA-AAAAACAAAAGATTT
1 TAAACAAAACCAAAAGATTT
**
46176 TAAACAAAACCCGAAGATTT
1 TAAACAAAACCAAAAGATTT
46196 TAAACA
1 TAAACA
46202 GATCCACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (20 bp):
TAAACAAAACCAAAAGATTT
Found at i:47849 original size:18 final size:20
Alignment explanation
Indices: 47826--47862 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47816 TCAAAAGATC
47826 CTCATT-AA-GTTGTTTGAT
1 CTCATTCAACGTTGTTTGAT
47844 CTCATTCAACGTTGTTTGA
1 CTCATTCAACGTTGTTTGA
47863 GGTTAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (20 bp):
CTCATTCAACGTTGTTTGAT
Found at i:55948 original size:23 final size:22
Alignment explanation
Indices: 55917--55985 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
55907 CACCACAGCT
*
55917 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCT-AGTGCCA
* * * *
55940 CTTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACC-TAGTGCCA
55963 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACC-TAGTGCCA
55986 TATAATAATG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
CGTAGAATTGCACCTAGTGCCA
Found at i:56727 original size:19 final size:20
Alignment explanation
Indices: 56690--56727 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56680 TTTTTTATTA
*
56690 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
56710 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
56728 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:56779 original size:21 final size:21
Alignment explanation
Indices: 56755--56797 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
56745 TCATATTCGT
*
56755 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
56776 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
56797 T
1 T
56798 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Done.