Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001166.1 Hibiscus syriacus cultivar Beakdansim tig00002326_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: 74128
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:724 original size:38 final size:33
Alignment explanation
Indices: 643--727 Score: 107
Period size: 33 Copynumber: 2.4 Consensus size: 33
633 GATCAAATGT
*
643 TTACCCCTAATTTATTTATTTACTTATTATTAA
1 TTACCCCTAATTTATTTATTTACTTATTATAAA
*
676 TTACCCCTAATTTATTTATTTATTTATTTGAAAATAAA
1 TTACCCCTAATTTATTTATTTACTTA-TT----ATAAA
714 TTACCCCTAATTTA
1 TTACCCCTAATTTA
728 AGAATAATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
33 25 0.56
34 2 0.04
38 18 0.40
ACGTcount: A:0.33, C:0.15, G:0.01, T:0.51
Consensus pattern (33 bp):
TTACCCCTAATTTATTTATTTACTTATTATAAA
Found at i:1447 original size:22 final size:21
Alignment explanation
Indices: 1421--1490 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
1411 ACACTAAAAT
*
1421 TAAAAGAGACAAAATGAATAAC
1 TAAAA-AGAAAAAATGAATAAC
*
1443 TAAAATA-AAAAAATGCTAA-AAT
1 TAAAA-AGAAAAAATG--AATAAC
1465 TAAAAAGGAAAAAATGAATAAC
1 TAAAAA-GAAAAAATGAATAAC
1487 TAAA
1 TAAA
1491 TTGAAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
21 10 0.26
22 19 0.49
23 10 0.26
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.17
Consensus pattern (21 bp):
TAAAAAGAAAAAATGAATAAC
Found at i:1467 original size:44 final size:45
Alignment explanation
Indices: 1400--1490 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 45
1390 TAAGAAAAAT
*
1400 AAATAAAAAATACACTAAAATT-AAAAGAGACAAAATGAATAACTA
1 AAATAAAAAATACACTAAAATTAAAAAG-GAAAAAATGAATAACTA
**
1445 AAATAAAAAA-ATGCTAAAATTAAAAAGGAAAAAATGAATAACTA
1 AAATAAAAAATACACTAAAATTAAAAAGGAAAAAATGAATAACTA
1489 AA
1 AA
1491 TTGAAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 27 0.64
45 15 0.36
ACGTcount: A:0.68, C:0.07, G:0.08, T:0.18
Consensus pattern (45 bp):
AAATAAAAAATACACTAAAATTAAAAAGGAAAAAATGAATAACTA
Found at i:1496 original size:21 final size:21
Alignment explanation
Indices: 1431--1501 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
1421 TAAAAGAGAC
*
1431 AAAATGAATAACTAAAATAAA
1 AAAATGAATAACTAAAATGAA
* *
1452 AAAATGCTAA-AATTAAAAAGGAA
1 AAAATG--AATAACT-AAAATGAA
*
1475 AAAATGAATAACTAAATTGAA
1 AAAATGAATAACTAAAATGAA
1496 ATAAAT
1 A-AAAT
1502 TAAAATTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
21 15 0.38
22 10 0.26
23 14 0.36
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAATGAATAACTAAAATGAA
Found at i:2683 original size:21 final size:21
Alignment explanation
Indices: 2658--2704 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2648 GGGCCTACAA
* *
2658 AATAATTATAGTATATAAAT-T
1 AATAATAATAATA-ATAAATAT
2679 AATAATAATAATAATAAATAT
1 AATAATAATAATAATAAATAT
2700 AATAA
1 AATAA
2705 AATGTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATAATAATAATAATAAATAT
Found at i:4249 original size:34 final size:34
Alignment explanation
Indices: 4210--4306 Score: 135
Period size: 32 Copynumber: 2.9 Consensus size: 34
4200 ATTCCCAAAG
*
4210 ATGCCCCAATATTCGATGTTGAATCTCAAAAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAAAA
* *
4244 ATGCCCCAACATTTGATGTTAAATCTC--AAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAAAA
*
4276 ATGCCCCAGTATTTGATGTTGAATCTTCAAA
1 ATGCCCCAATATTTGATGTTGAATC-TCAAA
4307 GATGCCCTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
32 27 0.50
33 2 0.04
34 24 0.44
35 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (34 bp):
ATGCCCCAATATTTGATGTTGAATCTCAAAAAAA
Found at i:5471 original size:14 final size:13
Alignment explanation
Indices: 5429--5481 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
5419 TTTTCTTCAA
5429 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
5441 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
5453 ATTTTCTCTTTGATT
1 -TTTTCTCTTTG-TT
5468 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
5480 TT
1 TT
5482 CCTTTTTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.30
13 14 0.38
14 10 0.27
15 2 0.05
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:5475 original size:27 final size:25
Alignment explanation
Indices: 5428--5479 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
5418 TTTTTCTTCA
5428 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
5453 ATTTTCTCTTTGATTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTTTT
5480 TTCCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:12473 original size:22 final size:22
Alignment explanation
Indices: 12445--12550 Score: 185
Period size: 22 Copynumber: 4.8 Consensus size: 22
12435 CAGTATACAG
12445 AGGTCCTTCGGGACAAATGCAT
1 AGGTCCTTCGGGACAAATGCAT
*
12467 AGGTCCTTCAGGACAAATGCAT
1 AGGTCCTTCGGGACAAATGCAT
*
12489 AGGTCATTCGGGACAAATGCAT
1 AGGTCCTTCGGGACAAATGCAT
*
12511 AGGTCCTTCAGGACAAATGCAT
1 AGGTCCTTCGGGACAAATGCAT
12533 AGGTCCTTCGGGACAAAT
1 AGGTCCTTCGGGACAAAT
12551 TTCACATGCC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 78 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (22 bp):
AGGTCCTTCGGGACAAATGCAT
Found at i:12793 original size:12 final size:12
Alignment explanation
Indices: 12778--12811 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12768 ATCATGATAA
12778 TGATAATGATGT
1 TGATAATGATGT
**
12790 TGATGTTGATGT
1 TGATAATGATGT
12802 TGATAATGAT
1 TGATAATGAT
12812 AGTATATATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (12 bp):
TGATAATGATGT
Found at i:15054 original size:17 final size:17
Alignment explanation
Indices: 15029--15063 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15019 AATATCAATT
*
15029 AAATATATAAATTTATA
1 AAATATATAAAATTATA
*
15046 AAATTTATAAAATTATA
1 AAATATATAAAATTATA
15063 A
1 A
15064 CCAATTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATAAAATTATA
Found at i:15779 original size:20 final size:20
Alignment explanation
Indices: 15743--15780 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15733 ATACAACTCC
**
15743 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
15763 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
15781 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:24897 original size:67 final size:67
Alignment explanation
Indices: 24819--24953 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
24809 GAACCGTTCA
24819 ACATTCAGTACGTTTGTTTCTCACATCTAAATGATTCAGTGTTGACTGATTCAACAAAACAGTGC
1 ACATTCAGTACGTTTGTTTCTCACATCTAAATGATTCAGTGTTGACTGATTCAACAAAACAGTGC
24884 TG
66 TG
24886 ACATTCAGTACGTTTGTTTCTCACATCTAAATGATTCAGTGTTGACTGATTCAACAAAACAGTGC
1 ACATTCAGTACGTTTGTTTCTCACATCTAAATGATTCAGTGTTGACTGATTCAACAAAACAGTGC
24951 TG
66 TG
24953 A
1 A
24954 ATGATTCAGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (67 bp):
ACATTCAGTACGTTTGTTTCTCACATCTAAATGATTCAGTGTTGACTGATTCAACAAAACAGTGC
TG
Found at i:25303 original size:17 final size:17
Alignment explanation
Indices: 25283--25318 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25273 AAATATTATA
*
25283 TAATTAAAAATCAAATT
1 TAATTAAAAATAAAATT
*
25300 TAATTGAAAATAAAATT
1 TAATTAAAAATAAAATT
25317 TA
1 TA
25319 TAATTTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
TAATTAAAAATAAAATT
Found at i:26914 original size:15 final size:15
Alignment explanation
Indices: 26894--26923 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26884 AGAATTTTTT
*
26894 TTGTAAGGTTAGCTC
1 TTGTAAAGTTAGCTC
26909 TTGTAAAGTTAGCTC
1 TTGTAAAGTTAGCTC
26924 ACTACTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (15 bp):
TTGTAAAGTTAGCTC
Found at i:34226 original size:36 final size:36
Alignment explanation
Indices: 34186--34258 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
34176 TATTAAATAT
* *
34186 TTTTAT-ATTTTATATTTTGTAA-AAAAGTTATATAAA
1 TTTTATGAATTTA-ATTTTGTAAGAAAA-ATATATAAA
*
34222 TTTTATGAATTTAATTTTTTAAGAAAAATATATAAA
1 TTTTATGAATTTAATTTTGTAAGAAAAATATATAAA
34258 T
1 T
34259 ATTTTCTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 23 0.72
37 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (36 bp):
TTTTATGAATTTAATTTTGTAAGAAAAATATATAAA
Found at i:34263 original size:38 final size:36
Alignment explanation
Indices: 34179--34263 Score: 84
Period size: 37 Copynumber: 2.3 Consensus size: 36
34169 ACACTTTTAT
* *
34179 TAAATATTTTTATATTTTATATTTTGTAAAAAAGTTA
1 TAAATA-TTTTATAATTTATATTTTGTAAAAAAATTA
*
34216 TATAA-ATTTTATGAATTTA-ATTTTTTAAGAAAAATATA
1 TA-AATATTTTAT-AATTTATATTTTGTAA-AAAAAT-TA
34254 TAAATATTTT
1 TAAATATTTT
34264 CTAACTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
36 14 0.35
37 15 0.38
38 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (36 bp):
TAAATATTTTATAATTTATATTTTGTAAAAAAATTA
Found at i:35340 original size:17 final size:17
Alignment explanation
Indices: 35297--35348 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
35287 ACTACAGTAG
*
35297 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
35314 --ACTCAGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
35329 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
35346 AAA
1 AAA
35349 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:37596 original size:33 final size:33
Alignment explanation
Indices: 37555--37639 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
37545 CTTTATTTTG
* *
37555 TTCGGGTCGGATCGGATTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGAGTTTTTTAAGTGTGATA
* * *
37588 TTTGGGTCGGGTTGGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGAGTTTTTTAAGTGTGATA
37621 TTCGGGTCGGGTCGG-GTTT
1 TTCGGGTCGGGTCGGAGTTT
37640 GGGTTTAGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 4 0.09
33 41 0.91
ACGTcount: A:0.12, C:0.08, G:0.38, T:0.42
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGAGTTTTTTAAGTGTGATA
Found at i:37822 original size:37 final size:38
Alignment explanation
Indices: 37776--37848 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
37766 ATTCATATAT
*
37776 TCGGGTCGGG-TTTTTTAAGTGTGATATTTGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
37813 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCG
37849 GGTTCGAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 10 0.29
38 24 0.71
ACGTcount: A:0.12, C:0.10, G:0.37, T:0.41
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:38450 original size:16 final size:18
Alignment explanation
Indices: 38429--38473 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
38419 TATCGAATTG
38429 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
38445 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
38463 GATTCCAATTC
1 GATTCCAATTC
38474 TCTCATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:38695 original size:38 final size:38
Alignment explanation
Indices: 38631--38734 Score: 97
Period size: 38 Copynumber: 2.7 Consensus size: 38
38621 CTTAATTCTC
* * * * *
38631 AAATTATTTCATC-CTAACATTATAAATTCTTAATTTCTT
1 AAATTAATTCA-CACTAAAATTCTAAATTCTAAAGTT-TT
38670 AAA-TAATTCACTA-TAAAATTCTAAATTCTAAAGTTTT
1 AAATTAATTCAC-ACTAAAATTCTAAATTCTAAAGTTTT
* *
38707 AAATTATTTCACACTAATATTCTAAATT
1 AAATTAATTCACACTAAAATTCTAAATT
38735 ATTTCTTTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
37 7 0.13
38 44 0.81
39 3 0.06
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.44
Consensus pattern (38 bp):
AAATTAATTCACACTAAAATTCTAAATTCTAAAGTTTT
Found at i:39711 original size:2 final size:2
Alignment explanation
Indices: 39706--39754 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
39696 TTTTTTAGAT
39706 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
39748 TA TA TA T
1 TA TA TA T
39755 TATTTTTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39711 original size:24 final size:26
Alignment explanation
Indices: 39664--39714 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
39654 TACATTTTCT
*
39664 TTTTTACTTTTTTACTTTAGTATATA
1 TTTTTACTTTTTTACATTAGTATATA
*
39690 TTTTTA-TTTTTTAGATTA-TATATA
1 TTTTTACTTTTTTACATTAGTATATA
39714 T
1 T
39715 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 10 0.43
26 6 0.26
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (26 bp):
TTTTTACTTTTTTACATTAGTATATA
Found at i:39787 original size:49 final size:43
Alignment explanation
Indices: 39734--39868 Score: 145
Period size: 47 Copynumber: 3.1 Consensus size: 43
39724 TATATATATA
39734 TATATATATATATATATATATTATTTTTTTATTATCAGTTTTATTAAT
1 TATATATATATATATATATATTATTTTTTTA-T-T---TTTTATTAAT
*
39782 T-TATATATATATATACTAT-TTACTATTTTTTATTTTTTATTTAT
1 TATATATATATATATA-TATATTA-T-TTTTTTATTTTTTATTAAT
*
39826 TATATATATATATATATATATTA--TTTTTACTTTTTATT-AT
1 TATATATATATATATATATATTATTTTTTTATTTTTTATTAAT
39866 TAT
1 TAT
39869 TTTATTTATT
Statistics
Matches: 80, Mismatches: 2, Indels: 18
0.80 0.02 0.18
Matches are distributed among these distances:
40 5 0.06
41 14 0.17
44 13 0.16
45 17 0.21
47 18 0.22
48 6 0.08
49 7 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (43 bp):
TATATATATATATATATATATTATTTTTTTATTTTTTATTAAT
Found at i:39826 original size:4 final size:4
Alignment explanation
Indices: 39805--39934 Score: 53
Period size: 4 Copynumber: 33.2 Consensus size: 4
39795 TACTATTTAC
* * * * *
39805 TATT T-TT TATT T-TT TATT TATT ATATA TATA TATA TATA TATT ATTTT
1 TATT TATT TATT TATT TATT TATT -TATT TATT TATT TATT TATT -TATT
* * *
39853 TACT T-TT TA-T TA-T TATTT TATT TATT TGTTT TATT TATA TATT T-TT
1 TATT TATT TATT TATT TA-TT TATT TATT T-ATT TATT TATT TATT TATT
* *
39899 T-TCT T-TT TCTT TATT T-TT TATT TTTT ATATT TATT T
1 TAT-T TATT TATT TATT TATT TATT TATT -TATT TATT T
39935 TACTTACTAT
Statistics
Matches: 101, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
3 23 0.23
4 63 0.62
5 15 0.15
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:39869 original size:43 final size:43
Alignment explanation
Indices: 39736--39869 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 43
39726 TATATATATA
* * *
39736 TATATATATATATATATATTATTTTTTTATTATCAGTTTTATTAAT-T
1 TATATATATATATATATA-TA-TTATTT-TTA-C-TTTTTATTATTAT
* * *
39783 TATATATATATATACTATTTACTATTTTTTATTTTTTA-T-TTAT
1 TATATATATATATA-TATATATTA-TTTTTACTTTTTATTATTAT
39826 TATATATATATATATATATATTATTTTTACTTTTTATTATTAT
1 TATATATATATATATATATATTATTTTTACTTTTTATTATTAT
39869 T
1 T
39870 TTATTTATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
41 12 0.16
42 9 0.12
43 21 0.29
44 5 0.07
46 4 0.05
47 19 0.26
48 3 0.04
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (43 bp):
TATATATATATATATATATATTATTTTTACTTTTTATTATTAT
Found at i:39890 original size:25 final size:24
Alignment explanation
Indices: 39857--39947 Score: 85
Period size: 25 Copynumber: 3.7 Consensus size: 24
39847 TATTTTTACT
*
39857 TTTTA-TTATTATTTTATTTATTTG
1 TTTTATTTATTATTTT-TTTATTTA
* *
39881 TTTTATTTATATATTTTTTTCTTTT
1 TTTTATTTAT-TATTTTTTTATTTA
*
39906 TCTTTATTTTTTATTTTTTATATTTA
1 T-TTTATTTATTATTTTTT-TATTTA
* *
39932 TTTTACTTACTATTTT
1 TTTTATTTATTATTTT
39948 ATCTTTGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
24 5 0.09
25 31 0.56
26 19 0.35
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTATTTATTATTTTTTTATTTA
Found at i:43088 original size:13 final size:13
Alignment explanation
Indices: 43068--43102 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
43058 GCAAAAAGAG
43068 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
43080 AACAAAGAGAAAAT
1 AA-AAAGAGAAAAT
43094 AAAAAGAGA
1 AAAAAGAGA
43103 CACATACGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:43393 original size:106 final size:107
Alignment explanation
Indices: 43268--43589 Score: 445
Period size: 106 Copynumber: 3.0 Consensus size: 107
43258 ATATCGTGCC
* * * *
43268 ACTC-GAGACAACACAAGTTCAACTCCACAACGAAGGGACGACTGATTATCAACAAACAATTTCC
1 ACTCTGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
43332 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
43374 ACT-TGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 ACTCTGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
** *
43438 CAATTTTGGAGCCAATTTCAACTTTACAGCGAAGGATATTGG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
43480 ACTCT-AGACAACACAAGCTCAATTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCT
1 ACTCTGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
* * * * *
43544 TAGTTCCAGAGCCAATTTTAACTTCACGGC-AGAGGATATTGG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGG
43586 ACTC
1 ACTC
43590 GGAACAATAC
Statistics
Matches: 192, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
105 1 0.01
106 190 0.99
107 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (107 bp):
ACTCTGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:44045 original size:87 final size:87
Alignment explanation
Indices: 43850--44025 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
43840 AGTTTCTCTA
* *
43850 GAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCCATT
1 GAAACATAAACATTAAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCCATT
* *
43915 GAAACGAAATTTTGTCTCCCTT
66 AAAACAAAATTTTGTCTCCCTT
* * * *
43937 GAAACATAAACATTAAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCCCTT
1 GAAACATAAACATTAAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCCATT
44002 AAAACAAAATTTTGTCTCCCTT
66 AAAACAAAATTTTGTCTCCCTT
44024 GA
1 GA
44026 GACAGTTTCT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (87 bp):
GAAACATAAACATTAAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCCATT
AAAACAAAATTTTGTCTCCCTT
Found at i:44050 original size:102 final size:102
Alignment explanation
Indices: 43934--44173 Score: 372
Period size: 102 Copynumber: 2.4 Consensus size: 102
43924 TTTTGTCTCC
* * *
43934 CTTGAAACATAAACATTAAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
*
43999 CTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
66 CTTAAAACAAAATTTTGTCTCCCTTGAAACAGTTTCT
* * * *
44036 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
* *
44101 CTTGAAACAAAATTTTGTCTCCCTTGAAATAGTTTCT
66 CTTAAAACAAAATTTTGTCTCCCTTGAAACAGTTTCT
* *
44138 CTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
44174 CACAAAATAT
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 125 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
CTTAAAACAAAATTTTGTCTCCCTTGAAACAGTTTCT
Found at i:44121 original size:37 final size:37
Alignment explanation
Indices: 44074--44146 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
44064 CTTTGAAATT
* *
44074 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAAATAGTTTCCCTTGAAACAA
*
44111 AATTTTGTCTCCCTTGAAATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAAATAGTTTCCCTTGAAACA
44147 TAAACCTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAAATAGTTTCCCTTGAAACAA
Found at i:44266 original size:37 final size:37
Alignment explanation
Indices: 44211--44313 Score: 163
Period size: 36 Copynumber: 2.8 Consensus size: 37
44201 AAAACGAGTT
* *
44211 TTGAGACAATTTCTCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
* *
44248 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
44284 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
44314 TGAATATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 34 0.57
37 26 0.43
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:44328 original size:100 final size:100
Alignment explanation
Indices: 44219--44408 Score: 242
Period size: 100 Copynumber: 1.9 Consensus size: 100
44209 TTTTGAGACA
*
44219 ATTTCTCTTGAAACAAAATCTT-GTCTCTCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCT
1 ATTTCTCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAGTTT-CCTTGAGAACTAAATTTTGTCT
*
44281 CTTTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
63 CTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
* ** * * *
44319 ATTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTTTTTTAGAACTAAGTTTTGTTTCTC
1 ATTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTTGTCTCTC
**
44384 TTGAGACAGTTTCTTTTGAAACAAA
66 TTGAGACAGTTTCCCTTGAAACAAA
44409 TTTTGTCCCT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
98 5 0.06
99 25 0.32
100 47 0.61
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42
Consensus pattern (100 bp):
ATTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTTGTCTCTC
TTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
Found at i:44421 original size:36 final size:36
Alignment explanation
Indices: 44326--44442 Score: 130
Period size: 36 Copynumber: 3.2 Consensus size: 36
44316 AATATTTTTC
*
44326 TTGAAACAAATTTCGTCTCC-CTTGAGACAGTTT-TT
1 TTGAAACAAATTTTGTC-CCTCTTGAGACAGTTTCTT
* * **
44361 TTTAGAACTAAGTTTTGTTTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCCCTCTTGAGACAGTTTCTT
*
44399 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTT
*
44435 CTGAAACA
1 TTGAAACA
44443 CAAAAAAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
35 3 0.04
36 36 0.54
37 23 0.34
38 5 0.07
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTT
Found at i:45719 original size:44 final size:42
Alignment explanation
Indices: 45666--45808 Score: 143
Period size: 44 Copynumber: 3.4 Consensus size: 42
45656 ATTTTTTAGA
*
45666 TTATATATATATATATATTATTTTTTATTATCAGTTTTATTAAT
1 TTATATATATATATATATTATTTTTTATTAT-A-TTTTATTTAT
* * *
45710 TTATATATATATATTTACTATTATTTATT-TA-TTTATTTA-
1 TTATATATATATATATATTATTTTTTATTATATTTTATTTAT
* * *
45749 TTATATATAT-TAT-TCTTACTTTATTATTATTATTTTATTTTT
1 TTATATATATATATATATTA-TTTTTTATTA-TATTTTATTTAT
*
45791 TTTTATATATATATATAT
1 TTATATATATATATATAT
45809 ATATATATAT
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
37 3 0.04
38 10 0.12
39 10 0.12
40 9 0.11
41 7 0.09
42 10 0.12
43 4 0.05
44 28 0.35
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (42 bp):
TTATATATATATATATATTATTTTTTATTATATTTTATTTAT
Found at i:45734 original size:40 final size:39
Alignment explanation
Indices: 45669--45806 Score: 120
Period size: 42 Copynumber: 3.4 Consensus size: 39
45659 TTTTAGATTA
* * *
45669 TATATATATATATATTATTTTTTATTATCAGTTTTATTAATT
1 TATATATATATATATTA-CTATTATTAT-A-TTTTATTTATT
45711 TATATATATATAT-TTACTATTATT-TA-TTTATTTATT
1 TATATATATATATATTACTATTATTATATTTTATTTATT
* *
45747 TATTATATATATTATTCTTACTTTATTATTATTATTTTATTTTTT
1 TA-TATATATA-TA-TATTAC--TATTATTA-TATTTTATTTATT
*
45792 TTTATATATATATAT
1 TATATATATATATAT
45807 ATATATATAT
Statistics
Matches: 81, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
36 11 0.14
37 8 0.10
38 3 0.04
39 2 0.02
40 10 0.12
41 3 0.04
42 22 0.27
43 2 0.02
44 10 0.12
45 10 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (39 bp):
TATATATATATATATTACTATTATTATATTTTATTTATT
Found at i:45799 original size:2 final size:2
Alignment explanation
Indices: 45794--45832 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
45784 TATTTTTTTT
45794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45833 TTTCCTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45925 original size:21 final size:20
Alignment explanation
Indices: 45881--45932 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
45871 TTTTACTTAC
* *
45881 TATTTTATCTTTGCTTTCTT
1 TATTTTATCTTTGATTTATT
*
45901 TATTTTATCTTTTATTTAATT
1 TATTTTATCTTTGATTT-ATT
*
45922 TATTTTTTCTT
1 TATTTTATCTT
45933 CATTTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTATCTTTGATTTATT
Found at i:45939 original size:16 final size:16
Alignment explanation
Indices: 45895--45939 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
45885 TTATCTTTGC
45895 TTTCTTTATTTTATCT
1 TTTCTTTATTTTATCT
* * *
45911 TTTATTTAATTTATTT
1 TTTCTTTATTTTATCT
*
45927 TTTCTTCATTTTA
1 TTTCTTTATTTTA
45940 ATTTAATTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTTTATTTTATCT
Found at i:55370 original size:30 final size:31
Alignment explanation
Indices: 55335--55392 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
55325 ATTCAATTAG
* *
55335 TGCACAGTATG-TCAGGGTGCATTTAGGAAA
1 TGCACAGTACGTTCAGGGTACATTTAGGAAA
*
55365 TGCACAGTACGTTCAGGTTACATTTAGG
1 TGCACAGTACGTTCAGGGTACATTTAGG
55393 TAATACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (31 bp):
TGCACAGTACGTTCAGGGTACATTTAGGAAA
Found at i:59538 original size:16 final size:18
Alignment explanation
Indices: 59512--59544 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59502 CGATATGAGT
59512 GGAAGAAAATA-ATTTAG
1 GGAAGAAAATATATTTAG
59529 GGAA-AAAATATATTTA
1 GGAAGAAAATATATTTA
59545 TAAAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (18 bp):
GGAAGAAAATATATTTAG
Found at i:69260 original size:2 final size:2
Alignment explanation
Indices: 69253--69283 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69243 CACTTTAAGA
69253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69284 ATTCTGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69530 original size:11 final size:11
Alignment explanation
Indices: 69514--69554 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
69504 TTTTCTTCCT
69514 TAATTTCCTCA
1 TAATTTCCTCA
* *
69525 TAATTTCTTTCT
1 TAATTTC-CTCA
69537 TAATTTCCTCA
1 TAATTTCCTCA
69548 TAATTTC
1 TAATTTC
69555 TTTTGTGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATTTCCTCA
Found at i:69565 original size:23 final size:23
Alignment explanation
Indices: 69505--69557 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
69495 TTTTTGCTTT
*
69505 TTTCTTCCTTAATTTCCTCATAA
1 TTTCTTTCTTAATTTCCTCATAA
69528 TTTCTTTCTTAATTTCCTCATAA
1 TTTCTTTCTTAATTTCCTCATAA
69551 TTTCTTT
1 TTTCTTT
69558 TGTGATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTCTTTCTTAATTTCCTCATAA
Found at i:69800 original size:18 final size:15
Alignment explanation
Indices: 69776--69814 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
69766 TGTTACGCTG
69776 GAGAAGAAGAGAGAT
1 GAGAAGAAGAGAGAT
69791 GAGAAGAAGAGAGAT
1 GAGAAGAAGAGAGAT
69806 GAGAAGAAG
1 GAGAAGAAG
69815 TATACAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (15 bp):
GAGAAGAAGAGAGAT
Found at i:70619 original size:114 final size:114
Alignment explanation
Indices: 70419--70651 Score: 457
Period size: 114 Copynumber: 2.0 Consensus size: 114
70409 CAGAATTACA
70419 ATAAATGTTTACAATTATAATTGTAAACTAAATATATACCTAGAACATTTTTCTATAATCACTGA
1 ATAAATGTTTACAATTATAATTGTAAACTAAATATATACCTAGAACATTTTTCTATAATCACTGA
70484 CAAAAGAAATAACCATTTGAGATTGTAGAAGGACTATACAAGGAAATTG
66 CAAAAGAAATAACCATTTGAGATTGTAGAAGGACTATACAAGGAAATTG
70533 ATAAATGTTTACAATTATAATTGTAAACTAAATATATACCTAGAACATTTTTCTATAATCACTGA
1 ATAAATGTTTACAATTATAATTGTAAACTAAATATATACCTAGAACATTTTTCTATAATCACTGA
70598 CAAAAGAAATAACCATTTGAGATTGTAGAAGGACTATACAAGGAAATTG
66 CAAAAGAAATAACCATTTGAGATTGTAGAAGGACTATACAAGGAAATTG
*
70647 CTAAA
1 ATAAA
70652 AAAATCAACC
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 118 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (114 bp):
ATAAATGTTTACAATTATAATTGTAAACTAAATATATACCTAGAACATTTTTCTATAATCACTGA
CAAAAGAAATAACCATTTGAGATTGTAGAAGGACTATACAAGGAAATTG
Found at i:71934 original size:29 final size:29
Alignment explanation
Indices: 71890--71947 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
71880 AGGGAAAGGA
71890 AAACTCACATTAGGTTGAGTCTTGAACAT
1 AAACTCACATTAGGTTGAGTCTTGAACAT
* *
71919 AAACTCACCTTGGGTTGAGTCTTGAACAT
1 AAACTCACATTAGGTTGAGTCTTGAACAT
71948 TTTCAACAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (29 bp):
AAACTCACATTAGGTTGAGTCTTGAACAT
Found at i:72445 original size:18 final size:18
Alignment explanation
Indices: 72391--72447 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
72381 CTCACATAAA
* *
72391 GTATCGATACCAAGGTAGGG
1 GTATCGATACTAAGG--GTG
*
72411 GTATCAATACTACAAGGGTG
1 GTATCGATACT--AAGGGTG
72431 GTATCGATACTAAGGGT
1 GTATCGATACTAAGGGT
72448 ATTTTTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 6 0.19
20 21 0.68
22 4 0.13
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (18 bp):
GTATCGATACTAAGGGTG
Done.