Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006733.1 Hibiscus syriacus cultivar Beakdansim tig00016885_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: 113703
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5407 original size:2 final size:2
Alignment explanation
Indices: 5400--5435 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5390 TAAAAATTTA
5400 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
5436 TAAAAAGAAA
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:6541 original size:15 final size:15
Alignment explanation
Indices: 6474--6542 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
6464 CCTATTTTGG
6474 CTAAAGTTTAATT-CT
1 CTAAA-TTTAATTACT
* *
6489 TTTAATTTAATTACT
1 CTAAATTTAATTACT
*
6504 C-AATTTTCAAATTACT
1 CTAAATTT--AATTACT
6520 CCT-AATTTAATTACT
1 -CTAAATTTAATTACT
6535 CTAAATTT
1 CTAAATTT
6543 CATTTTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
14 13 0.31
15 17 0.40
16 7 0.17
17 5 0.12
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.49
Consensus pattern (15 bp):
CTAAATTTAATTACT
Found at i:7257 original size:2 final size:2
Alignment explanation
Indices: 7250--7340 Score: 175
Period size: 2 Copynumber: 46.0 Consensus size: 2
7240 AAGCTAAATA
7250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7334 AT A- AT AT
1 AT AT AT AT
7341 TAAATATTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 87 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8267 original size:18 final size:18
Alignment explanation
Indices: 8244--8282 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
8234 AGTTATATTG
8244 GGACACATTCGGTTGTAA
1 GGACACATTCGGTTGTAA
8262 GGACACATTCGGTTGTAA
1 GGACACATTCGGTTGTAA
8280 GGA
1 GGA
8283 TACCTAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (18 bp):
GGACACATTCGGTTGTAA
Found at i:9562 original size:49 final size:49
Alignment explanation
Indices: 9460--9572 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 49
9450 CTAGCAGATT
* * * * * **
9460 TGCATTCATCAACATTCACCCTGCTGAATAGCCCTTTAACTCTTCTATT
1 TGCATTCATCAACATTCACCATGCTCAATAGACCTTTAACGCTTCAAGA
**
9509 TGCATTCATCAACATTCACCATGCTCAAT-GATTTTCTAACGCTTCAAGA
1 TGCATTCATCAACATTCACCATGCTCAATAGACCTT-TAACGCTTCAAGA
9558 TGCATTCATCAACAT
1 TGCATTCATCAACAT
9573 CCTCAACCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 3 0.06
49 51 0.94
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (49 bp):
TGCATTCATCAACATTCACCATGCTCAATAGACCTTTAACGCTTCAAGA
Found at i:11387 original size:21 final size:21
Alignment explanation
Indices: 11361--11404 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11351 ATTCTGGGCT
* *
11361 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
11382 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
11403 AG
1 AG
11405 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:11475 original size:23 final size:22
Alignment explanation
Indices: 11431--11475 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11421 AATGTCATGG
*
11431 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
11453 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
11476 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:12221 original size:31 final size:31
Alignment explanation
Indices: 12186--12261 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
12176 GTCTTTCGAG
*
12186 ACATATGGACAGTAT-ACCTATGTTCTAAGGA
1 ACATATGGACAGT-TCACCTAGGTTCTAAGGA
**
12217 ACATATGGACAGTTCACCTAGGTTCTTCGGA
1 ACATATGGACAGTTCACCTAGGTTCTAAGGA
*
12248 ACCTATGGACAGTT
1 ACATATGGACAGTT
12262 GCCGAGGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (31 bp):
ACATATGGACAGTTCACCTAGGTTCTAAGGA
Found at i:12299 original size:30 final size:30
Alignment explanation
Indices: 12248--12319 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
12238 GTTCTTCGGA
* * *
12248 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
12278 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
12308 ACCTCTGGATAG
1 ACCTCTGGATAG
12320 GTCCTGCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:21019 original size:13 final size:13
Alignment explanation
Indices: 21001--21025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20991 ACTGAGGTTG
21001 CTTAGTTTGTTCT
1 CTTAGTTTGTTCT
21014 CTTAGTTTGTTC
1 CTTAGTTTGTTC
21026 GTCATTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (13 bp):
CTTAGTTTGTTCT
Found at i:21113 original size:20 final size:20
Alignment explanation
Indices: 21088--21133 Score: 78
Period size: 18 Copynumber: 2.4 Consensus size: 20
21078 TGCACAACAA
21088 TTTCTACTCGAAATTACACT
1 TTTCTACTCGAAATTACACT
21108 TTTCTA--CGAAATTACACT
1 TTTCTACTCGAAATTACACT
21126 TTTCTACT
1 TTTCTACT
21134 GTGTCTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 18 0.75
20 6 0.25
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTCTACTCGAAATTACACT
Found at i:22669 original size:21 final size:21
Alignment explanation
Indices: 22643--22696 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
22633 GTTTCCAGAT
22643 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
22664 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
22685 TCGCAATGCGAA
1 TCGCAATGCGAA
22697 TATGTAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:22866 original size:6 final size:6
Alignment explanation
Indices: 22855--22886 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
22845 GACACGTATT
22855 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
22887 CGAGACGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:23411 original size:6 final size:6
Alignment explanation
Indices: 23390--23426 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
23380 TCTCGTCTGG
23390 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
23427 ATTGCATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:26629 original size:30 final size:31
Alignment explanation
Indices: 26593--26655 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
26583 AAAACATAAA
** *
26593 ATATGATAATTTTC-TTTTTATTTAATTAAG
1 ATATGATAACATTCGTTTTTATATAATTAAG
*
26623 ATATGATCACATTCGTTTTTATATAATTAAG
1 ATATGATAACATTCGTTTTTATATAATTAAG
26654 AT
1 AT
26656 GTTATTGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (31 bp):
ATATGATAACATTCGTTTTTATATAATTAAG
Found at i:26823 original size:27 final size:26
Alignment explanation
Indices: 26792--26854 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
26782 CATAAAGTAT
26792 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAATGAAAATAAAAAT-AA
* **
26819 ATATTTTTAAATTAAGTTAAAAATAA
1 ATATTTTTAAATGAAAATAAAAATAA
26845 ATATTTTTAA
1 ATATTTTTAA
26855 TAAGTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
ATATTTTTAAATGAAAATAAAAATAA
Found at i:26840 original size:26 final size:26
Alignment explanation
Indices: 26792--26877 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
26782 CATAAAGTAT
* * *
26792 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAAT-TAAGTTAAAATAAA
26819 ATATTTTTAAATTAAGTTAAAA-ATAA
1 ATATTTTTAAATTAAGTTAAAATA-AA
*
26845 ATATTTTT-AA-TAAGTTAATATAAAA
1 ATATTTTTAAATTAAGTTAAAAT-AAA
26870 ATATTTTT
1 ATATTTTT
26878 TTAAGTTAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
24 9 0.17
25 13 0.25
26 18 0.35
27 12 0.23
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
ATATTTTTAAATTAAGTTAAAATAAA
Found at i:26872 original size:29 final size:27
Alignment explanation
Indices: 26792--26872 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
26782 CATAAAGTAT
* *
26792 ATATTTTTAAATGAA-AATAAAAATAAA
1 ATATTTTTAAATTAAGTATAAAAAT-AA
26819 ATATTTTTAAATTAAGT-TAAAAATAA
1 ATATTTTTAAATTAAGTATAAAAATAA
26845 ATATTTTTAATAAGTTAA-TATAAAAATA
1 ATATTTTT-A-AA-TTAAGTATAAAAATA
26873 TTTTTTTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
26 10 0.21
27 22 0.47
28 3 0.06
29 12 0.26
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
ATATTTTTAAATTAAGTATAAAAATAA
Found at i:26897 original size:27 final size:25
Alignment explanation
Indices: 26816--26901 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 25
26806 AAATAAAAAT
26816 AAAATATTTTTAAATTAAGTTAA-A-A
1 AAAATATTTTT-AA-TAAGTTAATATA
26841 ATAAATATTTTTAATAAGTTAATATA
1 A-AAATATTTTTAATAAGTTAATATA
*
26867 AAAATATTTTT-TTAAGTTAGTATATA
1 AAAATATTTTTAATAAGTTA--ATATA
26893 TAAAATATT
1 -AAAATATT
26902 GTGAATTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
24 15 0.28
25 14 0.26
26 17 0.31
27 8 0.15
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (25 bp):
AAAATATTTTTAATAAGTTAATATA
Found at i:33721 original size:20 final size:20
Alignment explanation
Indices: 33684--33723 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33674 TTTAATTTTT
**
33684 AATATTTATAAATTAAAAAA
1 AATATTTATAAAAGAAAAAA
*
33704 AATATTTTTAAAAGAAAAAA
1 AATATTTATAAAAGAAAAAA
33724 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AATATTTATAAAAGAAAAAA
Found at i:34656 original size:2 final size:2
Alignment explanation
Indices: 34649--34674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34639 TCGGTTAGTT
34649 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
34675 ATGGATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34688 original size:16 final size:16
Alignment explanation
Indices: 34669--34700 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34659 TATATATATA
34669 TATATAATGGATTATT
1 TATATAATGGATTATT
*
34685 TATATTATGGATTATT
1 TATATAATGGATTATT
34701 AGATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TATATAATGGATTATT
Found at i:36542 original size:60 final size:58
Alignment explanation
Indices: 36476--36602 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 58
36466 AATAATCGAG
* ** *
36476 TGATCATTTTATAACTTTTAATATTTTAGAGACTTAACAAAACAACATTCTATAGTCAAA
1 TGATCATTTT-TAACTTTTAATAATCGAGAGACTTAA-AAAACAACAATCTATAGTCAAA
* *
36536 TGATCATATTTTAACTTTTAATAATCGAGAGACTTAAAAAATAATAATCTATAGTCAAA
1 TGATCAT-TTTTAACTTTTAATAATCGAGAGACTTAAAAAACAACAATCTATAGTCAAA
36595 -GATCATTT
1 TGATCATTT
36603 GTGTAATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
57 2 0.03
58 6 0.10
59 19 0.32
60 30 0.50
61 3 0.05
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.38
Consensus pattern (58 bp):
TGATCATTTTTAACTTTTAATAATCGAGAGACTTAAAAAACAACAATCTATAGTCAAA
Found at i:36740 original size:20 final size:20
Alignment explanation
Indices: 36715--36765 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
36705 TAAAAAAGCT
36715 TAATTTATTTATAGAAAA-CC
1 TAATTTATTTATA-AAAATCC
*
36735 TAATTTATTTATAAAAATCT
1 TAATTTATTTATAAAAATCC
*
36755 TAATTAATTTA
1 TAATTTATTTA
36766 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTTATTTATAAAAATCC
Found at i:37187 original size:16 final size:16
Alignment explanation
Indices: 37171--37205 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
37161 GATATTATAA
37171 TATATATATATATTAAT
1 TATAT-TATATATTAAT
37188 TATATTATATATT-AT
1 TATATTATATATTAAT
37203 TAT
1 TAT
37206 TCAACTCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 8 0.44
17 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTATATATTAAT
Found at i:38160 original size:56 final size:56
Alignment explanation
Indices: 38088--38200 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
38078 CACACTTCCA
38088 CTCGATAGCACCACGGGGATGTGGTCAGAAACTGAACGGATCATAGCACCAGCATC
1 CTCGATAGCACCACGGGGATGTGGTCAGAAACTGAACGGATCATAGCACCAGCATC
*
38144 CTCGGTAGCACCACGGGGATGTGGTCAGAAACTGAACGGATCATAGCACCAGCATC
1 CTCGATAGCACCACGGGGATGTGGTCAGAAACTGAACGGATCATAGCACCAGCATC
38200 C
1 C
38201 ATTTATCATC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (56 bp):
CTCGATAGCACCACGGGGATGTGGTCAGAAACTGAACGGATCATAGCACCAGCATC
Found at i:39772 original size:31 final size:31
Alignment explanation
Indices: 39734--39810 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
39724 AAAAATTGAA
39734 AGTTTAGGTACTAAAACAAACCAAAACCGAT
1 AGTTTAGGTACTAAAACAAACCAAAACCGAT
39765 AGTTTAGGTACTAAAACAAACCAAAACCGAT
1 AGTTTAGGTACTAAAACAAACCAAAACCGAT
39796 AGTTTAGGTACTAAA
1 AGTTTAGGTACTAAA
39811 CACATAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (31 bp):
AGTTTAGGTACTAAAACAAACCAAAACCGAT
Found at i:52239 original size:20 final size:20
Alignment explanation
Indices: 52214--52263 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
52204 TAAGTTTAAA
52214 TGAAACTTAAAATAAAAAAT
1 TGAAACTTAAAATAAAAAAT
52234 TGAAACTTAAAATAAAAAAT
1 TGAAACTTAAAATAAAAAAT
52254 TGAAACTTAA
1 TGAAACTTAA
52264 TTCGAGCTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (20 bp):
TGAAACTTAAAATAAAAAAT
Found at i:52411 original size:28 final size:28
Alignment explanation
Indices: 52351--52408 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
52341 ACTCGAATTC
* *
52351 AAACTCGAACTTAGACTTTAAATATGTA
1 AAACTCAAACTTAGACTTTAAATATATA
*
52379 AAACTCAAACTT-GGCTTTAAATATATA
1 AAACTCAAACTTAGACTTTAAATATATA
52406 AAA
1 AAA
52409 ACTTATACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (28 bp):
AAACTCAAACTTAGACTTTAAATATATA
Found at i:64488 original size:31 final size:30
Alignment explanation
Indices: 64449--64545 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
64439 AAAAAAGTTG
64449 AAAT-TTAATTTCAACCCTAAATTTTATATA
1 AAATATTAATTT-AACCCTAAATTTTATATA
* * *
64479 AAATATTAATTTAATCCTAAATTTTATGTT
1 AAATATTAATTTAACCCTAAATTTTATATA
* * * * *
64509 AAATTTTAATCTAACCCCTGAATTTTAGATG
1 AAATATTAATTTAA-CCCTAAATTTTATATA
64540 AAATAT
1 AAATAT
64546 CAATCTGATA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
30 31 0.57
31 23 0.43
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATATTAATTTAACCCTAAATTTTATATA
Found at i:65207 original size:31 final size:31
Alignment explanation
Indices: 65169--65324 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
65159 CCCGAAGGAC
* * *
65169 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
65200 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
65231 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
65262 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
65293 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
65324 C
1 C
65325 CCTCGACCCT
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 120 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:65895 original size:19 final size:21
Alignment explanation
Indices: 65853--65895 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
65843 TTCATAATCA
65853 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
65874 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
65893 CAT
1 CAT
65896 CATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:65904 original size:22 final size:20
Alignment explanation
Indices: 65859--65905 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
65849 ATCACATATT
*
65859 CATATAGTTTATTATCATAT
1 CATATAGTTTATTATCATAA
*
65879 CATATGGTTTATATCATCATAA
1 CATATAGTTTAT-T-ATCATAA
65901 CATAT
1 CATAT
65906 CACACATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATATAGTTTATTATCATAA
Found at i:66357 original size:21 final size:21
Alignment explanation
Indices: 66333--66377 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
66323 TTTTGTTCGT
* *
66333 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
66354 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
66375 TTG
1 TTG
66378 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:75419 original size:21 final size:22
Alignment explanation
Indices: 75395--75477 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
75385 TTGGTGCAGA
*
75395 GGGAATCGATTCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
*
75416 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
**
75439 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTTGAG
* *
75460 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
75478 GGGGTTCTGC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 35 0.67
22 1 0.02
23 16 0.31
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:75446 original size:23 final size:21
Alignment explanation
Indices: 75393--75455 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 21
75383 TTTTGGTGCA
*
75393 GAGGGAATCGATTCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
75414 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
75435 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
75456 ACAGGGGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 20 0.54
22 1 0.03
23 16 0.43
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:79173 original size:31 final size:31
Alignment explanation
Indices: 79135--79259 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
79125 CTCGAAGGAC
* * *
79135 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
79166 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
79197 CATTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
79228 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
79259 C
1 C
79260 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:79835 original size:19 final size:21
Alignment explanation
Indices: 79793--79835 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
79783 TTCATAATCA
79793 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
79814 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
79833 CAT
1 CAT
79836 CATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:79844 original size:22 final size:20
Alignment explanation
Indices: 79799--79845 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
79789 ATCACATATT
*
79799 CATATAGTTTATTATCATAT
1 CATATAGTTTATTATCATAA
*
79819 CATATGGTTTATATCATCATAA
1 CATATAGTTTAT-T-ATCATAA
79841 CATAT
1 CATAT
79846 CACACATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATATAGTTTATTATCATAA
Found at i:80293 original size:21 final size:21
Alignment explanation
Indices: 80269--80313 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
80259 TTTTGTTCGT
* *
80269 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
80290 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
80311 TTG
1 TTG
80314 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:81249 original size:13 final size:13
Alignment explanation
Indices: 81231--81255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
81221 TAAATTTCTT
81231 TAAAAATAAATAG
1 TAAAAATAAATAG
81244 TAAAAATAAATA
1 TAAAAATAAATA
81256 TGCCATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
TAAAAATAAATAG
Found at i:82086 original size:156 final size:156
Alignment explanation
Indices: 81874--82357 Score: 636
Period size: 156 Copynumber: 3.1 Consensus size: 156
81864 TTAAGTCCAT
* ** * *
81874 TTTTTATCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTTTACTTTCAATTCCT
1 TTTTTACCAAATTTGAGTCACATGCTCCTAAAACATAGTAGAATACATGTGTACTTTCAATTCCT
*
81939 CTTGTTT-ATAACAAATTTTTATTTTTCAATTTAGTCATTCAATTTTTCATAATCTCTTTATTTC
66 CTT-TTTGATAACAAATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTTC
*
82003 TTCAATTTATCATTTATTTTAAGTTTG
130 TTCAATTTGTCATTTATTTTAAGTTTG
* * *
82030 TTTTTATCAAATTTGAGTCACATGCTCCTAAAACATAGTAGAATACATATGTACTTTCAATTTCT
1 TTTTTACCAAATTTGAGTCACATGCTCCTAAAACATAGTAGAATACATGTGTACTTTCAATTCCT
* *
82095 CTTTTTGATAAC-AATTTTT-TTGTT-AATTTAGTCCTTTAATTTATT-ATAATCTCTTTATTTC
66 CTTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTTCAATTT-TTCATAATCTCTTTATTTC
* * * * *
82156 TTTAATTCGTTATTTGTTTTAAGTGCCTTT
130 TTCAATTTGTCATTTATTTTAAGT---TTG
* * *
82186 TTTTTACCAAATTTGAGTCACATGCTCTTAAATCATAGTAGAATATATGTGTACTTTCAATTCCT
1 TTTTTACCAAATTTGAGTCACATGCTCCTAAAACATAGTAGAATACATGTGTACTTTCAATTCCT
* * * *
82251 CTTTTTGATAACAAAGTTTTTATTTTTCATTTTAGTCCTTCAACTTTTCATAATCTCGTTATTCC
66 CTTTTTGATAACAAA-TTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTTC
* *
82316 TTCACTTTGTCATTTATTTTAAGTTCG
130 TTCAATTTGTCATTTATTTTAAGTTTG
82343 TTTTTTACCAAATTT
1 -TTTTTACCAAATTT
82358 AAACCACATG
Statistics
Matches: 283, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
153 51 0.18
154 6 0.02
155 10 0.04
156 140 0.49
157 3 0.01
158 19 0.07
159 6 0.02
160 48 0.17
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.50
Consensus pattern (156 bp):
TTTTTACCAAATTTGAGTCACATGCTCCTAAAACATAGTAGAATACATGTGTACTTTCAATTCCT
CTTTTTGATAACAAATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTTCT
TCAATTTGTCATTTATTTTAAGTTTG
Found at i:90188 original size:177 final size:177
Alignment explanation
Indices: 89891--90215 Score: 490
Period size: 177 Copynumber: 1.8 Consensus size: 177
89881 GGGAAATACT
* * * ** *
89891 TTGCAGACTGCAATGAATGTATCTGCTCGGCCTTGGCGAACGACGAGTCCGGGGCTAGGCGGCTG
1 TTGCAGACTGCAATGAATGTAGCTGCTCGGCCTTGGCCAACGACGAATCCGACGCTAGGAGGCTG
* * *
89956 TGGACGCAGACCCGAGCTCTGATCAGCAGAAGGTTGCAGTATCAAATCCCTACACCATCTTAGAA
66 TGGACGCAGACCCGAGCTCTGATCAGCAGAAGATTGCAGCATCAAATCACTACACCATCTTAGAA
*
90021 TGTTTCATTATTTACCATGTTTGTGTAAAATGGTAAACTTAGATTGA
131 TGTCTCATTATTTACCATGTTTGTGTAAAATGGTAAACTTAGATTGA
* * *
90068 TTGCAGACTGCAATGAATGTAGCTGCTCGGCCTTGGCCAACGATGAATCTGACGCTCGGAGGCTG
1 TTGCAGACTGCAATGAATGTAGCTGCTCGGCCTTGGCCAACGACGAATCCGACGCTAGGAGGCTG
* * *
90133 TGTATGCTGACCCGAGCTCTGATCCA-CAGAAGATTGCAGCATCAAATCACTACACCATCTTAGA
66 TGGACGCAGACCCGAGCTCTGAT-CAGCAGAAGATTGCAGCATCAAATCACTACACCATCTTAGA
90197 ATGTCTCATTATTTACCAT
130 ATGTCTCATTATTTACCAT
90216 AAATGATTAG
Statistics
Matches: 131, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
177 129 0.98
178 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (177 bp):
TTGCAGACTGCAATGAATGTAGCTGCTCGGCCTTGGCCAACGACGAATCCGACGCTAGGAGGCTG
TGGACGCAGACCCGAGCTCTGATCAGCAGAAGATTGCAGCATCAAATCACTACACCATCTTAGAA
TGTCTCATTATTTACCATGTTTGTGTAAAATGGTAAACTTAGATTGA
Found at i:96709 original size:20 final size:20
Alignment explanation
Indices: 96670--96712 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
96660 AAATGAAACA
**
96670 AAACTAATAATTTATGTATT
1 AAACTAATAATTTAAATATT
96690 AAACTAATAATTTAAATATT
1 AAACTAATAATTTAAATATT
96710 AAA
1 AAA
96713 ATGGATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
AAACTAATAATTTAAATATT
Found at i:96754 original size:51 final size:51
Alignment explanation
Indices: 96647--96744 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
96637 AAAAAATAAA
96647 AATTTAAATACTAAAATGAAACAAAACTAATAATTTATGTATTAAACTAAT
1 AATTTAAATACTAAAATGAAACAAAACTAATAATTTATGTATTAAACTAAT
* * ** * *
96698 AATTTAAATATTAAAATGGATTAGAACTAATAATTTTTGTATTAAAC
1 AATTTAAATACTAAAATGAAACAAAACTAATAATTTATGTATTAAAC
96745 GTGTTATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (51 bp):
AATTTAAATACTAAAATGAAACAAAACTAATAATTTATGTATTAAACTAAT
Found at i:97681 original size:15 final size:14
Alignment explanation
Indices: 97661--97690 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
97651 CAGTTAAAAA
97661 ATTATTATTGATTTT
1 ATTATTATT-ATTTT
97676 ATTATTATTATTTT
1 ATTATTATTATTTT
97690 A
1 A
97691 ATAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
ATTATTATTATTTT
Found at i:97792 original size:21 final size:21
Alignment explanation
Indices: 97766--97810 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
97756 TCATAATTAT
*
97766 TAAAAATATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
*
97787 TAAAAATAATAATTTTTTAAA
1 TAAAAATAATAATATTTTAAA
97808 TAA
1 TAA
97811 TTTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:99542 original size:17 final size:17
Alignment explanation
Indices: 99520--99552 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
99510 TAACACCCCC
99520 AACCCGTATCCGACCTA
1 AACCCGTATCCGACCTA
99537 AACCCGTATCCGACCT
1 AACCCGTATCCGACCT
99553 GGATACGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.42, G:0.12, T:0.18
Consensus pattern (17 bp):
AACCCGTATCCGACCTA
Found at i:99991 original size:8 final size:9
Alignment explanation
Indices: 99978--100018 Score: 52
Period size: 8 Copynumber: 4.9 Consensus size: 9
99968 TAATGAATCT
99978 ATACATA-C
1 ATACATATC
99986 ATACATA-C
1 ATACATATC
*
99994 ATACAAATC
1 ATACATATC
100003 AT-CATATC
1 ATACATATC
100011 ATACATAT
1 ATACATAT
100019 ATTTGTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (9 bp):
ATACATATC
Found at i:100919 original size:20 final size:20
Alignment explanation
Indices: 100894--100951 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
100884 ATATGAAATT
*
100894 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAATGACCTATGTA
*
100914 TGTCCCGAATGACCTCTGTA
1 TGTCCCGAATGACCTATGTA
*
100934 TGTCTCGAATGACCTATG
1 TGTCCCGAATGACCTATG
100952 AACCCTCGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTCCCGAATGACCTATGTA
Found at i:101774 original size:24 final size:24
Alignment explanation
Indices: 101747--101827 Score: 162
Period size: 24 Copynumber: 3.4 Consensus size: 24
101737 TCTATAGTGT
101747 ATCGATGCATCCCTTAATGTGTGC
1 ATCGATGCATCCCTTAATGTGTGC
101771 ATCGATGCATCCCTTAATGTGTGC
1 ATCGATGCATCCCTTAATGTGTGC
101795 ATCGATGCATCCCTTAATGTGTGC
1 ATCGATGCATCCCTTAATGTGTGC
101819 ATCGATGCA
1 ATCGATGCA
101828 CTACCTATGC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (24 bp):
ATCGATGCATCCCTTAATGTGTGC
Found at i:108577 original size:14 final size:14
Alignment explanation
Indices: 108555--108607 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
108545 TCGATTATAT
*
108555 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
108569 GTTCATTTA---T-
1 GTTCATTTATGTTC
108579 GTTCATTTATGTTC
1 GTTCATTTATGTTC
108593 GTTCATTTATGTTC
1 GTTCATTTATGTTC
108607 G
1 G
108608 AACAAAGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:108587 original size:24 final size:24
Alignment explanation
Indices: 108542--108606 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 24
108532 CGTTCGTGAA
*
108542 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTT
108568 CGTTCATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCATTTATGTT
108592 CGTTCATTTATGTTC
1 CGTTCATTTATGTTC
108607 GAACAAAGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 30 0.79
25 3 0.08
26 5 0.13
ACGTcount: A:0.15, C:0.14, G:0.15, T:0.55
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTT
Found at i:113074 original size:27 final size:28
Alignment explanation
Indices: 113035--113088 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
113025 GAAGTTATAT
*
113035 ATTATTTATATTTTTTTA-ATAAAAATC
1 ATTATTTATATTTATTTATATAAAAATC
*
113062 ATTATTT-TAATTTATTTATATTAAAAT
1 ATTATTTAT-ATTTATTTATATAAAAAT
113089 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.04
27 15 0.65
28 7 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTATTTATATTTATTTATATAAAAATC
Done.