Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006712.1 Hibiscus syriacus cultivar Beakdansim tig00016734_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: 170398
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3423 original size:19 final size:20
Alignment explanation
Indices: 3384--3439 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
3374 GAAATCCCTT
*
3384 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
3404 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
*
3423 TGAAAATACATGCTCTT
1 TGAAAATACATGATCTT
3440 GGCCGAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:10121 original size:19 final size:20
Alignment explanation
Indices: 10097--10136 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10087 TATCCTTTCT
10097 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
10116 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
10136 T
1 T
10137 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:15654 original size:19 final size:20
Alignment explanation
Indices: 15630--15669 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
15620 TATCCTTTAT
15630 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
15649 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
15669 T
1 T
15670 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:16590 original size:16 final size:18
Alignment explanation
Indices: 16559--16591 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
16549 AAGGTAATGA
16559 AATAAGAAAGAATGAAAG
1 AATAAGAAAGAATGAAAG
16577 AATAA-AAA-AATGAAA
1 AATAAGAAAGAATGAAA
16592 TAGTAAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (18 bp):
AATAAGAAAGAATGAAAG
Found at i:16753 original size:11 final size:11
Alignment explanation
Indices: 16737--16777 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
16727 AACTTGCTTC
16737 TCTTTTCTTTT
1 TCTTTTCTTTT
**
16748 TCTTTTGATTT
1 TCTTTTCTTTT
16759 TC--TTCTTTT
1 TCTTTTCTTTT
16768 TCTTTTCTTT
1 TCTTTTCTTT
16778 CTTTTGCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
9 7 0.29
11 17 0.71
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:16779 original size:15 final size:15
Alignment explanation
Indices: 16746--16783 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
16736 CTCTTTTCTT
16746 TTTCTTTTGATTTTC
1 TTTCTTTTGATTTTC
**
16761 -TTCTTTTTCTTTTC
1 TTTCTTTTGATTTTC
16775 TTTCTTTTG
1 TTTCTTTTG
16784 CACTCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTCTTTTGATTTTC
Found at i:21639 original size:12 final size:11
Alignment explanation
Indices: 21586--21683 Score: 74
Period size: 12 Copynumber: 8.3 Consensus size: 11
21576 GATACTATTT
21586 TCATCACCATAA
1 TCATCACCAT-A
*
21598 TCCATCTCCATTA
1 T-CATCACCA-TA
*
21611 TCA-CGCCTATA
1 TCATCACC-ATA
21622 TCATCACCATA
1 TCATCACCATA
21633 GTCATCACCATTA
1 -TCATCACCA-TA
*
21646 TCA-CGCCTATA
1 TCATCACC-ATA
21657 TCATCACCATA
1 TCATCACCATA
21668 TTCCATCACCATA
1 -T-CATCACCATA
21681 TCA
1 TCA
21684 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 24 0.34
12 25 0.35
13 21 0.30
14 1 0.01
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:21650 original size:35 final size:36
Alignment explanation
Indices: 21586--21697 Score: 165
Period size: 35 Copynumber: 3.2 Consensus size: 36
21576 GATACTATTT
*
21586 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
21622 TCATCACCATAGT-CATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
21657 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
21692 ACATCA
1 TCATCA
21698 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 50 0.71
36 20 0.29
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:21712 original size:33 final size:33
Alignment explanation
Indices: 21668--21736 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
21658 CATCACCATA
*
21668 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
21701 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
21734 TTC
1 TTC
21737 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:23224 original size:158 final size:158
Alignment explanation
Indices: 22936--23251 Score: 632
Period size: 158 Copynumber: 2.0 Consensus size: 158
22926 ACTTATAAAA
22936 CTTGAAAATGTTTTGGCCAAATAATGCATGGTTATGTGGCTATTCTTTACACTTTCCTAAAGATA
1 CTTGAAAATGTTTTGGCCAAATAATGCATGGTTATGTGGCTATTCTTTACACTTTCCTAAAGATA
23001 TAATTAAAAATGCATAATTAACATGCTCAAATAAGTGTTGGTTCAGTCAAAGGTGCATTATCATG
66 TAATTAAAAATGCATAATTAACATGCTCAAATAAGTGTTGGTTCAGTCAAAGGTGCATTATCATG
23066 TCTCTTGGCTGATCAGCACTTGTGCCCC
131 TCTCTTGGCTGATCAGCACTTGTGCCCC
23094 CTTGAAAATGTTTTGGCCAAATAATGCATGGTTATGTGGCTATTCTTTACACTTTCCTAAAGATA
1 CTTGAAAATGTTTTGGCCAAATAATGCATGGTTATGTGGCTATTCTTTACACTTTCCTAAAGATA
23159 TAATTAAAAATGCATAATTAACATGCTCAAATAAGTGTTGGTTCAGTCAAAGGTGCATTATCATG
66 TAATTAAAAATGCATAATTAACATGCTCAAATAAGTGTTGGTTCAGTCAAAGGTGCATTATCATG
23224 TCTCTTGGCTGATCAGCACTTGTGCCCC
131 TCTCTTGGCTGATCAGCACTTGTGCCCC
23252 TTCAAGTTTG
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 158 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (158 bp):
CTTGAAAATGTTTTGGCCAAATAATGCATGGTTATGTGGCTATTCTTTACACTTTCCTAAAGATA
TAATTAAAAATGCATAATTAACATGCTCAAATAAGTGTTGGTTCAGTCAAAGGTGCATTATCATG
TCTCTTGGCTGATCAGCACTTGTGCCCC
Found at i:23350 original size:47 final size:47
Alignment explanation
Indices: 23269--23361 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
23259 TTGGTGCTTA
* * * *
23269 AGTGAAGACAAGCACCTTGCTTTGCTGGTTACGCACATGGGTTGTTT
1 AGTGAAGACAAGCACCTTGCCTTGCCGGTCACGCACATGGGATGTTT
* *
23316 AGTGGAGACAAGCATCTTGCCTTGCCGGTCACGCACATGGGATGTT
1 AGTGAAGACAAGCACCTTGCCTTGCCGGTCACGCACATGGGATGTT
23362 CTTTGAGTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (47 bp):
AGTGAAGACAAGCACCTTGCCTTGCCGGTCACGCACATGGGATGTTT
Found at i:26397 original size:37 final size:37
Alignment explanation
Indices: 26347--26421 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
26337 TGCATCATTC
26347 AATGTATCCGATTTGTCACCATTTGAAGATGGAAATG
1 AATGTATCCGATTTGTCACCATTTGAAGATGGAAATG
26384 AATGTATCCGATTTGTCACCATTTGAAGATGGAAATG
1 AATGTATCCGATTTGTCACCATTTGAAGATGGAAATG
26421 A
1 A
26422 TTTGGGGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (37 bp):
AATGTATCCGATTTGTCACCATTTGAAGATGGAAATG
Found at i:29020 original size:23 final size:23
Alignment explanation
Indices: 28992--29046 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
28982 GTGATGGAAT
28992 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
29015 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
29038 ATGGTGATG
1 ATGGTGATG
29047 GACAGATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:33583 original size:23 final size:23
Alignment explanation
Indices: 33555--33609 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
33545 GTGATGGAAT
33555 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
33578 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
33601 ATGGTGATG
1 ATGGTGATG
33610 GACAGATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:38130 original size:35 final size:36
Alignment explanation
Indices: 38083--38150 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
38073 ATTTATAAGT
*
38083 TGGTGATAATATATGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
38118 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
38151 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:43751 original size:13 final size:12
Alignment explanation
Indices: 43732--43817 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
43722 ATATAGGCGT
43732 GATATGGTGATG
1 GATATGGTGATG
43744 GAATATGGTGAT-
1 G-ATATGGTGATG
*
43756 GATATAGGCG-T-
1 GATAT-GGTGATG
43767 GATAATGGTGATG
1 GAT-ATGGTGATG
43780 GACTATGGTGAT-
1 GA-TATGGTGATG
*
43792 GATATAGGCG-T-
1 GATAT-GGTGATG
43803 GATAATGGTGATG
1 GAT-ATGGTGATG
43816 GA
1 GA
43818 CAGGTTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:43787 original size:36 final size:36
Alignment explanation
Indices: 43714--43818 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
43704 ATTTATAAGT
* *
43714 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
43749 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
43785 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
43819 AGGTTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:49470 original size:13 final size:12
Alignment explanation
Indices: 49451--49536 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
49441 ATATAGGCGT
49451 GATATGGTGATG
1 GATATGGTGATG
49463 GAATATGGTGAT-
1 G-ATATGGTGATG
*
49475 GATATAGGCG-T-
1 GATAT-GGTGATG
49486 GATAATGGTGATG
1 GAT-ATGGTGATG
49499 GACTATGGTGAT-
1 GA-TATGGTGATG
*
49511 GATATAGGCG-T-
1 GATAT-GGTGATG
49522 GATAATGGTGATG
1 GAT-ATGGTGATG
49535 GA
1 GA
49537 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:49506 original size:36 final size:36
Alignment explanation
Indices: 49433--49537 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
49423 ATTTATAAGT
* *
49433 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
49468 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
49504 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
49538 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:50664 original size:30 final size:29
Alignment explanation
Indices: 50620--50680 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
50610 GAAAGCTTTT
*
50620 ATAAGCTATGTTTGGGGATGTATTCTTAA
1 ATAAGCTATGTTTGGGGATGCATTCTTAA
*
50649 ATAATCTATTGTTTGGGGATGCATTCTTAA
1 ATAAGCTA-TGTTTGGGGATGCATTCTTAA
50679 AT
1 AT
50681 GATTCAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (29 bp):
ATAAGCTATGTTTGGGGATGCATTCTTAA
Found at i:56148 original size:12 final size:11
Alignment explanation
Indices: 56133--56176 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
56123 TAAATTTTAA
56133 CTTTTTTTTTG
1 CTTTTTTTTTG
56144 CCTTTTTTTTTG
1 -CTTTTTTTTTG
*
56156 TTTCCTTTTTTTG
1 CTT--TTTTTTTG
56169 CTTTTTTT
1 CTTTTTTT
56177 GTTTTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 7 0.25
12 11 0.39
13 10 0.36
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (11 bp):
CTTTTTTTTTG
Found at i:56152 original size:15 final size:15
Alignment explanation
Indices: 56134--56167 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56124 AAATTTTAAC
*
56134 TTTTTTT-TTGCCTT
1 TTTTTTTGTTTCCTT
56148 TTTTTTTGTTTCCTT
1 TTTTTTTGTTTCCTT
56163 TTTTT
1 TTTTT
56168 GCTTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTTTGTTTCCTT
Found at i:56181 original size:8 final size:9
Alignment explanation
Indices: 56136--56186 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
56126 ATTTTAACTT
56136 TTTTTTTGC
1 TTTTTTTGC
*
56145 CTTTTTT--
1 TTTTTTTGC
* *
56152 TTTGTTTCC
1 TTTTTTTGC
56161 TTTTTTTGC
1 TTTTTTTGC
*
56170 TTTTTTTGT
1 TTTTTTTGC
56179 TTTTTTTG
1 TTTTTTTG
56187 AAAAAAATAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 5 0.15
9 29 0.85
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:57031 original size:45 final size:45
Alignment explanation
Indices: 56954--57055 Score: 104
Period size: 50 Copynumber: 2.2 Consensus size: 45
56944 ATAACTAATG
56954 AATAAAATAATAATAAACTAAACATATATTAA-C-TC-TAATTCCT
1 AATAAAAT-ATAATAAACTAAACATATATTAACCATCTTAATTCCT
*
56997 AATAAAATATAAT-AACTAAAGATAATATTTTTAACCCAATCTTAATTCCT
1 AATAAAATATAATAAACTAAACAT-ATA---TTAA-CC-ATCTTAATTCCT
57047 AATAAAATA
1 AATAAAATA
57056 ATAAATCTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
41 9 0.18
42 8 0.16
43 8 0.16
45 4 0.08
47 1 0.02
49 2 0.04
50 17 0.35
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (45 bp):
AATAAAATATAATAAACTAAACATATATTAACCATCTTAATTCCT
Found at i:57063 original size:25 final size:22
Alignment explanation
Indices: 57034--57079 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
57024 TTTTTAACCC
57034 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
57059 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
57080 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:60632 original size:12 final size:12
Alignment explanation
Indices: 60611--60652 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
60601 TTTTTTGAAA
60611 TTTTGACTTTTT
1 TTTTGACTTTTT
*
60623 TTTTGCCTTTTT
1 TTTTGACTTTTT
*
60635 TTTTTACTTTTT
1 TTTTGACTTTTT
60647 TTTTGA
1 TTTTGA
60653 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTGACTTTTT
Found at i:61419 original size:25 final size:22
Alignment explanation
Indices: 61390--61435 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
61380 TTTTTAACCT
61390 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
61415 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
61436 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:67494 original size:13 final size:13
Alignment explanation
Indices: 67476--67501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67466 TGGCCAAAGA
67476 TGAAAAGGTATGT
1 TGAAAAGGTATGT
67489 TGAAAAGGTATGT
1 TGAAAAGGTATGT
67502 GAGAGGTGTT
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:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:72307 original size:30 final size:31
Alignment explanation
Indices: 72255--72314 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
72245 CTTAGCTTTA
**
72255 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
72285 TATTATGTTTGCATGTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
72315 GGCAACATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:74663 original size:24 final size:25
Alignment explanation
Indices: 74607--74668 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
74597 TCTTTCTTTT
*
74607 CTTTGCTTTTC-TTCTTTTTGAGTG
1 CTTTGTTTTTCTTTCTTTTTGAGTG
*
74631 C-TGGATTTTTCTTTC-TTTTGAGTG
1 CTTTG-TTTTTCTTTCTTTTTGAGTG
74655 CTTTGTTTTTCTTT
1 CTTTGTTTTTCTTT
74669 GCTAGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.06
24 25 0.78
25 5 0.16
ACGTcount: A:0.05, C:0.15, G:0.16, T:0.65
Consensus pattern (25 bp):
CTTTGTTTTTCTTTCTTTTTGAGTG
Found at i:78008 original size:23 final size:24
Alignment explanation
Indices: 77981--78034 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
77971 GAAATCCAGC
77981 AAAGAAAATCAAAGCACTC-AAAA
1 AAAGAAAATCAAAGCACTCGAAAA
* * *
78004 GAAGAAATTGAAAGCACTCGAAAA
1 AAAGAAAATCAAAGCACTCGAAAA
78028 AAAGAAA
1 AAAGAAA
78035 CAGAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.63, C:0.13, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAGAAAATCAAAGCACTCGAAAA
Found at i:78040 original size:24 final size:23
Alignment explanation
Indices: 77991--78041 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
77981 AAAGAAAATC
* **
77991 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAAAAGAAACAG
78014 AAAGCACTCGAAAAAAAGAAACAG
1 AAAGCACTC-AAAAAAAGAAACAG
78038 AAAG
1 AAAG
78042 AAAGAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.61, C:0.14, G:0.18, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAAAAGAAACAG
Found at i:79330 original size:24 final size:25
Alignment explanation
Indices: 79284--79336 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
79274 ACAGTTATGC
*
79284 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
79308 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
79333 CACT
1 CACT
79337 GAGGCTCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:82106 original size:22 final size:21
Alignment explanation
Indices: 82078--82130 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
82068 TAAAGGTAAT
82078 AATAATATAAGTAATGAAA-ATA
1 AATAATATAA-TAATGAAATA-A
82100 AATAATAATAATAATGAAATAA
1 AATAAT-ATAATAATGAAATAA
82122 AATAA-ATAA
1 AATAATATAA
82131 ATGATAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.14
22 20 0.69
23 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (21 bp):
AATAATATAATAATGAAATAA
Found at i:82123 original size:26 final size:25
Alignment explanation
Indices: 82075--82130 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
82065 TAATAAAGGT
*
82075 AATAATAATATAAGTAATGAAAATA
1 AATAATAATATAAGAAATGAAAATA
82100 AATAATAATAATAATGAAAT-AAAATA
1 AATAATAAT-ATAA-GAAATGAAAATA
82126 AATAA
1 AATAA
82131 ATGATAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 9 0.32
26 15 0.54
27 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (25 bp):
AATAATAATATAAGAAATGAAAATA
Found at i:82580 original size:19 final size:20
Alignment explanation
Indices: 82539--82589 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
82529 GAAACCCCTT
*
82539 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
82559 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
82578 TGAAGATACATG
1 TGAAAATACATG
82590 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:85627 original size:30 final size:30
Alignment explanation
Indices: 85593--85707 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
85583 GTTGGGACAG
85593 CTTGGTGGAGCATTTGGAAGACATATACAA
1 CTTGGTGGAGCATTTGGAAGACATATACAA
* *
85623 CTTGGTGGAGCATTTGGAAGACATATATAG
1 CTTGGTGGAGCATTTGGAAGACATATACAA
*
85653 CTTAGTGGAGCATTTGGAAGACATATACAA
1 CTTGGTGGAGCATTTGGAAGACATATACAA
* *
85683 CTTGGTGGATCATTTGGGAGACATA
1 CTTGGTGGAGCATTTGGAAGACATA
85708 AACTGATGTA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (30 bp):
CTTGGTGGAGCATTTGGAAGACATATACAA
Found at i:85661 original size:60 final size:60
Alignment explanation
Indices: 85591--85707 Score: 207
Period size: 60 Copynumber: 1.9 Consensus size: 60
85581 ACGTTGGGAC
*
85591 AGCTTGGTGGAGCATTTGGAAGACATATACAACTTGGTGGAGCATTTGGAAGACATATAT
1 AGCTTAGTGGAGCATTTGGAAGACATATACAACTTGGTGGAGCATTTGGAAGACATATAT
* *
85651 AGCTTAGTGGAGCATTTGGAAGACATATACAACTTGGTGGATCATTTGGGAGACATA
1 AGCTTAGTGGAGCATTTGGAAGACATATACAACTTGGTGGAGCATTTGGAAGACATA
85708 AACTGATGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (60 bp):
AGCTTAGTGGAGCATTTGGAAGACATATACAACTTGGTGGAGCATTTGGAAGACATATAT
Found at i:88014 original size:33 final size:33
Alignment explanation
Indices: 87972--88040 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
87962 GTTGATGAAT
*
87972 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
88005 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
88038 GAA
1 GAA
88041 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:88045 original size:13 final size:12
Alignment explanation
Indices: 88026--88090 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
88016 TTATTGGCGT
88026 GATATGGTGATG
1 GATATGGTGATG
88038 GAATATGGTGAT-
1 G-ATATGGTGATG
*
88050 GATATAGGCG-T-
1 GATAT-GGTGATG
88061 GATAATGGTGATG
1 GAT-ATGGTGATG
88074 GACTATGGTGAT-
1 GA-TATGGTGATG
88086 GATAT
1 GATAT
88091 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:88081 original size:36 final size:36
Alignment explanation
Indices: 88011--88123 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
88001 AATGGAAGGA
* *
88011 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
88046 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
88082 TGATGATATAGGCGTGATAATGGAGATAGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
88118 TGATGA
1 TGATGA
88124 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:93743 original size:33 final size:33
Alignment explanation
Indices: 93701--93769 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
93691 GTTGATGAAT
*
93701 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
93734 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
93767 GAA
1 GAA
93770 TATGGTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:93802 original size:36 final size:36
Alignment explanation
Indices: 93740--93852 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
93730 AATGGAAGGA
* *
93740 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
93775 TTATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
93811 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
93847 TGATGA
1 TGATGA
93853 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 15 0.21
36 55 0.79
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:98696 original size:11 final size:11
Alignment explanation
Indices: 98682--98726 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
98672 TCAAAAAAAC
*
98682 AAAAAAAGGCA
1 AAAAAAAGCCA
98693 AAAAAAA--CA
1 AAAAAAAGCCA
98702 AAAAAAAGCCA
1 AAAAAAAGCCA
98713 AAAAAAAGCCA
1 AAAAAAAGCCA
98724 AAA
1 AAA
98727 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.28
11 23 0.72
ACGTcount: A:0.78, C:0.13, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCCA
Found at i:98698 original size:19 final size:20
Alignment explanation
Indices: 98674--98719 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
98664 TTTATTTTTC
*
98674 AAAAAAAC-AAAAAAAGGCA
1 AAAAAAACAAAAAAAAGCCA
98693 AAAAAAACAAAAAAAAGCCA
1 AAAAAAACAAAAAAAAGCCA
98713 AAAAAAA
1 AAAAAAA
98720 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAGCCA
Found at i:98699 original size:20 final size:19
Alignment explanation
Indices: 98674--98719 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
98664 TTTATTTTTC
*
98674 AAAAAAACAAAAAAAGGCA
1 AAAAAAACAAAAAAAAGCA
98693 AAAAAAACAAAAAAAAGCCA
1 AAAAAAACAAAAAAAAG-CA
98713 AAAAAAA
1 AAAAAAA
98720 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAGCA
Found at i:109812 original size:21 final size:20
Alignment explanation
Indices: 109765--109817 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
109755 CGGCCAAGAG
*
109765 CATGTATCTTC-ATTAAAAT
1 CATGTATTTTCAATTAAAAT
109784 CATGTATTTTCAATTAAAAGT
1 CATGTATTTTCAATTAAAA-T
*
109805 CATTTATTTTCAA
1 CATGTATTTTCAA
109818 AGGGGTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.33
20 7 0.23
21 13 0.43
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCAATTAAAAT
Found at i:110261 original size:15 final size:14
Alignment explanation
Indices: 110241--110271 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
110231 GCCATCTCTC
110241 TTTCATTTCTTTCTA
1 TTTCATTTCTTT-TA
110256 TTTCATTTCTTTTA
1 TTTCATTTCTTTTA
110270 TT
1 TT
110272 ATATATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCATTTCTTTTA
Found at i:110574 original size:34 final size:31
Alignment explanation
Indices: 110532--110603 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
110522 GTACAAAAAG
*
110532 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
110566 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
110597 AAAGAAA
1 AAAGAAA
110604 GCAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:113761 original size:19 final size:21
Alignment explanation
Indices: 113737--113788 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
113727 CAGCCAAGAG
113737 CATGTATCTTT-A-TTAAAA-T
1 CATGTAT-TTTCATTTAAAAGT
113756 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
113777 CATGTATTTTCA
1 CATGTATTTTCA
113789 AAGGAGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.10
19 8 0.27
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:114233 original size:15 final size:14
Alignment explanation
Indices: 114213--114243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
114203 GCCATCTCTC
114213 TTTCATTTCTTTCTA
1 TTTCATTTCTTT-TA
114228 TTTCATTTCTTTTA
1 TTTCATTTCTTTTA
114242 TT
1 TT
114244 ATATATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCATTTCTTTTA
Found at i:122012 original size:36 final size:36
Alignment explanation
Indices: 121960--122072 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
121950 GATACTATTT
*
121960 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
121996 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
122032 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
122067 ACATCA
1 TCATCA
122073 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:122087 original size:33 final size:33
Alignment explanation
Indices: 122043--122111 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
122033 CATCACCATA
*
122043 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
122076 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
122109 TTC
1 TTC
122112 ATTCATCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:127751 original size:36 final size:36
Alignment explanation
Indices: 127692--127804 Score: 149
Period size: 36 Copynumber: 3.2 Consensus size: 36
127682 GATACTATTT
*
127692 TCATCACCATAATCTAT-ATCCATTATCACGCCTATA
1 TCATCACCATAATCCATCA-CCATTATCACGCCTATA
* *
127728 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
127764 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
127799 ACATCA
1 TCATCA
127805 TCCTTCCATT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 16 0.23
36 52 0.75
37 1 0.01
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:130146 original size:13 final size:13
Alignment explanation
Indices: 130124--130153 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
130114 ACTAAACACC
130124 TTTC-ACATACCT
1 TTTCAACATACCT
130136 TTTCAACATACCT
1 TTTCAACATACCT
130149 TTTCA
1 TTTCA
130154 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:131741 original size:16 final size:16
Alignment explanation
Indices: 131720--131752 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
131710 TAGTTAGCTC
131720 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
131736 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
131752 A
1 A
131753 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:139202 original size:19 final size:21
Alignment explanation
Indices: 139159--139210 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
139149 GAAACCCCTT
139159 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
139180 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
139199 TGAAGATACATG
1 TGAAAATACATG
139211 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:144449 original size:35 final size:36
Alignment explanation
Indices: 144402--144469 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
144392 ATTTATAAGT
144402 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
144437 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
144470 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:144860 original size:19 final size:20
Alignment explanation
Indices: 144813--144863 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
144803 GAAACCCCTT
**
144813 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
144833 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
144852 TGAAGATACATG
1 TGAAAATACATG
144864 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.