Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000374.1 Hibiscus syriacus cultivar Beakdansim tig00000683_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: 72450
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:11592 original size:21 final size:21
Alignment explanation
Indices: 11543--11645 Score: 143
Period size: 21 Copynumber: 4.8 Consensus size: 21
11533 ACACCCTTGA
* *
11543 AGGGGAACCGATTCCCCCTTTGA
1 AGGGGAACCGATT-CCCC-ATGT
11566 AGGGGAACCGATTCCCCATGT
1 AGGGGAACCGATTCCCCATGT
11587 AGGGGAACCGATTCCCCATGT
1 AGGGGAACCGATTCCCCATGT
*
11608 AGGGGAACCAATTCCCCATGT
1 AGGGGAACCGATTCCCCATGT
* *
11629 AGGGGAATCGATACCCC
1 AGGGGAACCGATTCCCC
11646 CTGGGGTTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
21 57 0.77
22 4 0.05
23 13 0.18
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.18
Consensus pattern (21 bp):
AGGGGAACCGATTCCCCATGT
Found at i:16249 original size:27 final size:27
Alignment explanation
Indices: 16199--16293 Score: 163
Period size: 27 Copynumber: 3.5 Consensus size: 27
16189 AATTCCAGGG
* *
16199 TTTAGAGGTACTTTAGGTCATTTTACAC
1 TTTAGGGGTA-TTTTGGTCATTTTACAC
16227 TTTAGGGGTATTTTGGTCATTTTACAC
1 TTTAGGGGTATTTTGGTCATTTTACAC
16254 TTTAGGGGTATTTTGGTCATTTTACAC
1 TTTAGGGGTATTTTGGTCATTTTACAC
16281 TTTAGGGGTATTT
1 TTTAGGGGTATTT
16294 CTATAATTCC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 56 0.86
28 9 0.14
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.47
Consensus pattern (27 bp):
TTTAGGGGTATTTTGGTCATTTTACAC
Found at i:17651 original size:32 final size:32
Alignment explanation
Indices: 17607--17669 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
17597 TATAAATAGG
17607 TTTTTAGTATTTTAAT-TAAGTTTTAGGATATTA
1 TTTTTAGTATTTT-ATCTAAGTTTTAGG-TATTA
*
17640 TTTTTA-TATTTTATCTTAGTTTTAGGTATT
1 TTTTTAGTATTTTATCTAAGTTTTAGGTATT
17670 TTAGATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 6 0.21
32 16 0.57
33 6 0.21
ACGTcount: A:0.25, C:0.02, G:0.11, T:0.62
Consensus pattern (32 bp):
TTTTTAGTATTTTATCTAAGTTTTAGGTATTA
Found at i:17790 original size:64 final size:65
Alignment explanation
Indices: 17645--17792 Score: 173
Period size: 64 Copynumber: 2.3 Consensus size: 65
17635 TATTATTTTT
17645 ATATTTTATCTTAG-TTTTAGGTATTTTAGATGAAATAGGTTTTAGTGTTTAAATTAGGATTTAG
1 ATATTTTATCTT-GTTTTTAGGTATTTTAGATGAAATAGGTTTTAGTGTTTAAATTAGGATTTAG
17709 A
65 A
* * * *
17710 ATATTATAT-TAT-TTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGT-TTTTAATTAGGATTTA
1 ATATTTTATCT-TGTTTTTAGGTATTTTAGATGAAATAGGTTTT-AGTGTTTAAATTAGGATTTA
17771 -A
64 GA
*
17772 GATGTTTTATCTTGTTTTTAG
1 -ATATTTTATCTTGTTTTTAG
17793 TAATTTGAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
62 1 0.01
63 28 0.39
64 33 0.46
65 9 0.13
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (65 bp):
ATATTTTATCTTGTTTTTAGGTATTTTAGATGAAATAGGTTTTAGTGTTTAAATTAGGATTTAGA
Found at i:20456 original size:11 final size:11
Alignment explanation
Indices: 20402--20456 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
20392 ACCCATTTCG
*
20402 TTTTATTTTCA
1 TTTTATTTTTA
20413 TTTTA--TTTA
1 TTTTATTTTTA
*
20422 TTTCATTCCATTTA
1 TTTTATT---TTTA
20436 TTTTATTTTTA
1 TTTTATTTTTA
20447 TTTTATTTTT
1 TTTTATTTTT
20457 CTCTAAACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
9 7 0.19
11 19 0.53
14 10 0.28
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:22879 original size:22 final size:19
Alignment explanation
Indices: 22836--22880 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
22826 ATTTAATTTG
*
22836 TTTATTTAATAATTTTTCT
1 TTTATTTAATAATTTTTAT
22855 TTTATTTAATCATATTTTTTAT
1 TTTATTTAAT-A-A-TTTTTAT
22877 TTTA
1 TTTA
22881 AAAACAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 1 0.05
22 10 0.45
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTTAATAATTTTTAT
Found at i:25928 original size:11 final size:11
Alignment explanation
Indices: 25874--25928 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
25864 ACCCATTTCG
*
25874 TTTTATTTTCA
1 TTTTATTTTTA
25885 TTTTA--TTTA
1 TTTTATTTTTA
*
25894 TTTCATTCCATTTA
1 TTTTATT---TTTA
25908 TTTTATTTTTA
1 TTTTATTTTTA
25919 TTTTATTTTT
1 TTTTATTTTT
25929 CTCTAAACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
9 7 0.19
11 19 0.53
14 10 0.28
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:31142 original size:97 final size:97
Alignment explanation
Indices: 30938--31155 Score: 264
Period size: 97 Copynumber: 2.2 Consensus size: 97
30928 AAAACAAAAA
* *
30938 ACCATAGTTCATAAACCAGTAAATTCCAAGATTCCGTAAATTTGGAACAATTCATATTTTCCAGT
1 ACCATAGTTCATAAACCAGTAAATTCCAAGATTCCATAAATATGGAACAATTCATATTTTCCAGT
* **
31003 GAAAACAAGACACCCGATAATACATTTCAGGT
66 GAAAACAAGACACCAGATAATACATACCAGGT
* *
31035 ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAT-GAACAATTCATAGTTTTCGA
1 ACCATAGTTCATAAACCAGTAAATTCCAAGATTCCATAAAT-ATGGAACAATTCATA-TTTTCCA
* * *
31099 -TGAAAACCAA-A-ATCAGATATTACATACCATGTT
64 GTGAAAA-CAAGACACCAGATAATACATACCA-GGT
* *
31132 GCCATGGTTCATAAACCAGTAAAT
1 ACCATAGTTCATAAACCAGTAAAT
31156 CAATACTTTC
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
96 13 0.12
97 82 0.78
98 10 0.10
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (97 bp):
ACCATAGTTCATAAACCAGTAAATTCCAAGATTCCATAAATATGGAACAATTCATATTTTCCAGT
GAAAACAAGACACCAGATAATACATACCAGGT
Found at i:32151 original size:27 final size:27
Alignment explanation
Indices: 32112--32179 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
32102 AATTCCAAGG
* *
32112 TTTAGAGGGCATTTTGGTTATTTTATAC
1 TTTAG-GGGCATTTTGGTCATTTTACAC
32140 TTTAGGGGCATTTTGGTCATTTTACAC
1 TTTAGGGGCATTTTGGTCATTTTACAC
*
32167 TTTAGGGGTATTT
1 TTTAGGGGCATTT
32180 CTATAATTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.19, C:0.09, G:0.24, T:0.49
Consensus pattern (27 bp):
TTTAGGGGCATTTTGGTCATTTTACAC
Found at i:33081 original size:19 final size:19
Alignment explanation
Indices: 33057--33096 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
33047 CGACGGTCAA
33057 CGGTTCGGTCCAGGCGGTT
1 CGGTTCGGTCCAGGCGGTT
*
33076 CGGTTCGGTCTAGGCGGTT
1 CGGTTCGGTCCAGGCGGTT
33095 CG
1 CG
33097 ATCCAGGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.25, G:0.42, T:0.28
Consensus pattern (19 bp):
CGGTTCGGTCCAGGCGGTT
Found at i:33176 original size:20 final size:20
Alignment explanation
Indices: 33151--33199 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
33141 TGGTTCAGCC
*
33151 GGTCAGCTGGTTCTCCAGGT
1 GGTCAGATGGTTCTCCAGGT
*
33171 GGTCAGATGGTTCTCCAGGC
1 GGTCAGATGGTTCTCCAGGT
*
33191 GATCAGATG
1 GGTCAGATG
33200 AAGCCCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (20 bp):
GGTCAGATGGTTCTCCAGGT
Found at i:36929 original size:46 final size:46
Alignment explanation
Indices: 36862--36953 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
36852 GTTTTCAAAG
36862 GGTTTTGGATGAATAAACATGTAACCCTTCGAAATACATGATTTTA
1 GGTTTTGGATGAATAAACATGTAACCCTTCGAAATACATGATTTTA
36908 GGTTTTGGATGAATAAACATGTAACCCTTCGAAATACATGATTTTA
1 GGTTTTGGATGAATAAACATGTAACCCTTCGAAATACATGATTTTA
36954 ATTAAAATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (46 bp):
GGTTTTGGATGAATAAACATGTAACCCTTCGAAATACATGATTTTA
Found at i:40570 original size:8 final size:10
Alignment explanation
Indices: 40565--40621 Score: 78
Period size: 10 Copynumber: 5.7 Consensus size: 10
40555 ATTTTATAAT
40565 TATATATATA
1 TATATATATA
40575 TATATATATA
1 TATATATATA
40585 TATATATATA
1 TATATATATA
*
40595 TATATATGTA
1 TATATATATA
* *
40605 TGTATGTATA
1 TATATATATA
*
40615 TGTATAT
1 TATATAT
40622 GTAGTTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (10 bp):
TATATATATA
Found at i:40574 original size:4 final size:4
Alignment explanation
Indices: 40565--40621 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
40555 ATTTTATAAT
* * *
40565 TATA TATA TATA TATA TATA TATA TATA TATA TATA TGTA TGTA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
40613 TATG TATA T
1 TATA TATA T
40622 GTAGTTTTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:40624 original size:6 final size:6
Alignment explanation
Indices: 40565--40621 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
40555 ATTTTATAAT
* * *
40565 TATATA TATATA TATATA TATATA TATATA TATATA TGTATG TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
40613 TATGTA TAT
1 TATATA TAT
40622 GTAGTTTTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:51188 original size:20 final size:19
Alignment explanation
Indices: 51150--51188 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
51140 AACTCTTTGG
* *
51150 AATACATTATTTTAATGAA
1 AATACATGATTTCAATGAA
51169 AATACATGAGTTTCAATGAA
1 AATACATGA-TTTCAATGAA
51189 TGTGCATGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (19 bp):
AATACATGATTTCAATGAA
Found at i:53506 original size:20 final size:20
Alignment explanation
Indices: 53457--53506 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 20
53447 ATTAAATTTG
53457 TAAAAGTAACCCAAATCCAA
1 TAAAAGTAACCCAAATCCAA
53477 T-AAA--AA---AAATCCAA
1 TAAAAGTAACCCAAATCCAA
53491 TAAAAGTAACCCAAAT
1 TAAAAGTAACCCAAAT
53507 ATAACCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
14 9 0.38
15 3 0.12
17 4 0.17
19 3 0.12
20 5 0.21
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (20 bp):
TAAAAGTAACCCAAATCCAA
Found at i:54487 original size:33 final size:33
Alignment explanation
Indices: 54441--54513 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
54431 CAATTATATA
54441 TATATATAT-ATAAACTATATAGA-TTATAAATAG
1 TATATAT-TCATAAACTATATA-ATTTATAAATAG
* *
54474 TTTATATTCATAAACTATATAATTTATACATAG
1 TATATATTCATAAACTATATAATTTATAAATAG
54507 TATATAT
1 TATATAT
54514 AACTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (33 bp):
TATATATTCATAAACTATATAATTTATAAATAG
Found at i:54576 original size:11 final size:11
Alignment explanation
Indices: 54560--54822 Score: 63
Period size: 11 Copynumber: 24.0 Consensus size: 11
54550 ACTATGTAGT
54560 TTATATATAAA
1 TTATATATAAA
*
54571 TTATATATATA
1 TTATATATAAA
54582 TTAAATATATAAA
1 TT--ATATATAAA
*
54595 CTATATAGT---
1 TTATATA-TAAA
*
54604 TTATACAT--A
1 TTATATATAAA
*
54613 GTAGTATATAAA
1 TTA-TATATAAA
*
54625 CTATATATAAA
1 TTATATATAAA
**
54636 CCATATAT--A
1 TTATATATAAA
*
54645 CTATATATAAA
1 TTATATATAAA
*
54656 CTATATATAAA
1 TTATATATAAA
*
54667 CTA-A-ATAAA
1 TTATATATAAA
*
54676 TTA-ATATATA
1 TTATATATAAA
*
54686 TATAAACTAATAAA
1 T-TATA-T-ATAAA
54700 -T-TATATAAA
1 TTATATATAAA
* *
54709 CTATATATGAA
1 TTATATATAAA
*
54720 CTATATATAAA
1 TTATATATAAA
* *
54731 CTGTATAGTTTATA
1 -T-TATA-TATAAA
*
54745 TT-TATATACTA
1 TTATATATA-AA
54756 TATATAATTATAAA
1 T-TAT-A-TATAAA
54770 TTATATAT--A
1 TTATATATAAA
* * *
54779 CTATGTATAGA
1 TTATATATAAA
**
54790 TTATATAGTTTA
1 TTATATA-TAAA
54802 TTA-ATATAAA
1 TTATATATAAA
*
54812 CTATATATAAA
1 TTATATATAAA
54823 CCATATATAC
Statistics
Matches: 194, Mismatches: 30, Indels: 56
0.69 0.11 0.20
Matches are distributed among these distances:
8 1 0.01
9 35 0.18
10 19 0.10
11 91 0.47
12 14 0.07
13 19 0.10
14 11 0.06
15 4 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (11 bp):
TTATATATAAA
Found at i:54577 original size:9 final size:9
Alignment explanation
Indices: 54563--54715 Score: 57
Period size: 9 Copynumber: 16.7 Consensus size: 9
54553 ATGTAGTTTA
54563 TATATAAAT
1 TATATAAAT
*
54572 TATATATA-
1 TATATAAAT
54580 TAT-TAAA-
1 TATATAAAT
*
54587 TATATAAAC
1 TATATAAAT
**
54596 TATATAGTT
1 TATATAAAT
* *
54605 TATACATAGTAG
1 TAT--ATA-AAT
54617 TATATAAACT
1 TATATAAA-T
*
54627 ATATATAAAC
1 -TATATAAAT
* *
54637 CATATATACT
1 TATATA-AAT
54647 ATATATAAACT
1 -TATATAAA-T
*
54658 ATATATAAAC
1 -TATATAAAT
*
54668 TAAATAAAT
1 TATATAAAT
*
54677 TA-ATATA-
1 TATATAAAT
*
54684 TATATAAAC
1 TATATAAAT
54693 TA-ATAAAT
1 TATATAAAT
*
54701 TATATAAAC
1 TATATAAAT
54710 TATATA
1 TATATA
54716 TGAACTATAT
Statistics
Matches: 108, Mismatches: 23, Indels: 26
0.69 0.15 0.17
Matches are distributed among these distances:
7 8 0.07
8 22 0.20
9 44 0.41
10 5 0.05
11 26 0.24
12 3 0.03
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.39
Consensus pattern (9 bp):
TATATAAAT
Found at i:54674 original size:20 final size:20
Alignment explanation
Indices: 54620--54732 Score: 82
Period size: 20 Copynumber: 5.9 Consensus size: 20
54610 ATAGTAGTAT
* *
54620 ATAAACTATATATAAACCAT
1 ATAAACTATATATAAACTAA
*
54640 ATATACTATATATAAACTATA
1 ATAAACTATATATAAACTA-A
*
54661 TATAAACTA-A-ATAAA-TTA
1 -ATAAACTATATATAAACTAA
54679 AT--A-TATATATAAACT-A
1 ATAAACTATATATAAACTAA
54695 ATAAA-T-TATATAAACTATA
1 ATAAACTATATATAAACTA-A
*
54714 TATGAACTATATATAAACT
1 -ATAAACTATATATAAACT
54733 GTATAGTTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
14 2 0.03
15 2 0.03
16 8 0.11
17 13 0.17
18 3 0.04
19 2 0.03
20 26 0.35
21 2 0.03
22 17 0.23
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (20 bp):
ATAAACTATATATAAACTAA
Found at i:54689 original size:25 final size:23
Alignment explanation
Indices: 54657--54706 Score: 82
Period size: 25 Copynumber: 2.1 Consensus size: 23
54647 ATATATAAAC
54657 TATATATAAACTAAATAAATTAATA
1 TATATATAAACT-AATAAATT-ATA
54682 TATATATAAACTAATAAATTATA
1 TATATATAAACTAATAAATTATA
54705 TA
1 TA
54707 AACTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 5 0.20
24 8 0.32
25 12 0.48
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TATATATAAACTAATAAATTATA
Found at i:54690 original size:16 final size:17
Alignment explanation
Indices: 54648--54711 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
54638 ATATATACTA
*
54648 TATATAAACTATATATAAAC
1 TATATAAAC--TA-ATAAAT
* * *
54668 TAAATAAATTAATATA-
1 TATATAAACTAATAAAT
54684 TATATAAACTAATAAAT
1 TATATAAACTAATAAAT
54701 TATATAAACTA
1 TATATAAACTA
54712 TATATGAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.35
17 15 0.41
18 2 0.05
20 7 0.19
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TATATAAACTAATAAAT
Found at i:54828 original size:20 final size:20
Alignment explanation
Indices: 54805--54843 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54795 TAGTTTATTA
54805 ATATAAACTATATATAAACC
1 ATATAAACTATATATAAACC
* *
54825 ATATATACTATATGTAAAC
1 ATATAAACTATATATAAAC
54844 TGTAAGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (20 bp):
ATATAAACTATATATAAACC
Found at i:59327 original size:2 final size:2
Alignment explanation
Indices: 59320--59850 Score: 102
Period size: 2 Copynumber: 271.0 Consensus size: 2
59310 CATAAACTAC
*
59320 AT AT AT AT AT AT AT AT AGT -T CAC AT AT GA- AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT -AT AT AT -AT AT AT AT AT AT AT
* * * *
59360 AA ACT AT AT -T TT AT AT AT AA ACT AT AT AT -T AT AGT TT AT AT
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
* * * * *
59401 TT AT AT AG AT AT AT AT AT TT AT AT TT AT AT AT -T TT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
59441 AT AGT TT AT AT TT AT AT AT AT AT AT AT AT AT A- AT AT A- AGT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
59483 ACT CT AT ACT -T AT A- AGT AT AT A- AT AT A- AGT AT AT A- AGC AT
1 A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT
* * * * * * *
59523 AC AT -T AT A- AGT AT AT AT AT -T TT AA AT GT AC AT GT AT -T GT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
59562 AC AT AT AT GT AA ACT -T AT AT AT ACT -T AT AT AC AT AT AT -T GT
1 AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
59603 AT AT A- AT AT A- AGT AT AT AT AT AT AT AT A- AGT AT AT AA AC A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
59643 AT AC AT -T AT A- AGT AT AT A- AT AT AT AT AC AT AT AT A- AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
59682 A- AGT AT AC AT -T AT ACT -T AT A- AGT AT AT A- AT AT AT A- AGT
1 AT A-T AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT A-T
* * * * * * * *
59720 AT AG AGT AC GT AT AC AT AGG ACT AA AT -T A- AA AA AGT AT A- AT
1 AT AT A-T AT AT AT AT AT A-T A-T AT AT AT AT AT AT A-T AT AT AT
*
59761 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AA AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
59803 AA AGT AT -T AA AGT AC A- AT AT -T AGT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
59843 AT AT AT AT
1 AT AT AT AT
59851 GCGTAGTACT
Statistics
Matches: 382, Mismatches: 75, Indels: 144
0.64 0.12 0.24
Matches are distributed among these distances:
1 42 0.11
2 310 0.81
3 30 0.08
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:59405 original size:51 final size:51
Alignment explanation
Indices: 59350--59477 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 51
59340 CACATATGAA
*
59350 TTATATATATAAACTATATTT-TATATATAAACTATATATTATAGTTTATAT
1 TTATATATATAAA-TATATTTATATATATAAACTATATAATATAGTTTATAT
* * * * * *
59401 TTATATAGATATATATATTTATATTTATATATTTTATAATATAGTTTATAT
1 TTATATATATAAATATATTTATATATATAAACTATATAATATAGTTTATAT
* *
59452 TTATATATATATATATATATA-ATATA
1 TTATATATATAAATATATTTATATATA
59478 AGTATACTCT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
50 11 0.17
51 55 0.83
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (51 bp):
TTATATATATAAATATATTTATATATATAAACTATATAATATAGTTTATAT
Found at i:59483 original size:13 final size:13
Alignment explanation
Indices: 59453--59518 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
59443 AGTTTATATT
59453 TATATATATATATA-
1 TATATA-ATATA-AG
59467 TATATAATATAAG
1 TATATAATATAAG
59480 TATACTCTATACTTATAAG
1 TATA---TA-A--TATAAG
59499 TATATAATATAAG
1 TATATAATATAAG
59512 TATATAA
1 TATATAA
59519 GCATACATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
12 1 0.02
13 22 0.49
14 6 0.13
15 1 0.02
16 4 0.09
17 1 0.02
19 10 0.22
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (13 bp):
TATATAATATAAG
Found at i:60197 original size:21 final size:21
Alignment explanation
Indices: 60171--60210 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60161 TGCTCTTCAT
* *
60171 TTGTTCTTCCAATAAAAAAGC
1 TTGTTCATCCAAAAAAAAAGC
60192 TTGTTCATCCAAAAAAAAA
1 TTGTTCATCCAAAAAAAAA
60211 ACTTTCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (21 bp):
TTGTTCATCCAAAAAAAAAGC
Found at i:60954 original size:25 final size:23
Alignment explanation
Indices: 60916--60994 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 23
60906 AAAATTTCTT
60916 TTTTGTTTTTTTTGTTTTT-TATA
1 TTTTGTTTTTTTTGTTTTTGT-TA
60939 TTTTGTTTTGTATTTGTTTTTGTTA
1 TTTTGTTTT-T-TTTGTTTTTGTTA
* *
60964 -TTTG--TTTTATGTTTTTATTA
1 TTTTGTTTTTTTTGTTTTTGTTA
60984 -TTTGTTTTTTT
1 TTTTGTTTTTTT
60995 ATTTCTTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 15 0.31
21 1 0.02
22 6 0.12
23 9 0.19
24 5 0.10
25 11 0.23
26 1 0.02
ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80
Consensus pattern (23 bp):
TTTTGTTTTTTTTGTTTTTGTTA
Found at i:60955 original size:34 final size:33
Alignment explanation
Indices: 60917--61003 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 33
60907 AAATTTCTTT
* *
60917 TTTGTTTTTTTTGTTT-TTTATAT-TTTGTTTTGTA
1 TTTGTTTTTTTTATTTGTTT-TATGTTT-TTAT-TA
*
60951 TTTGTTTTTGTTATTTGTTTTATGTTTTTATTA
1 TTTGTTTTTTTTATTTGTTTTATGTTTTTATTA
*
60984 TTTG-TTTTTTTATTTCTTTT
1 TTTGTTTTTTTTATTTGTTTT
61004 CGTTTTCTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
32 14 0.30
33 6 0.13
34 20 0.43
35 6 0.13
ACGTcount: A:0.09, C:0.01, G:0.10, T:0.79
Consensus pattern (33 bp):
TTTGTTTTTTTTATTTGTTTTATGTTTTTATTA
Found at i:60996 original size:12 final size:12
Alignment explanation
Indices: 60921--61003 Score: 63
Period size: 12 Copynumber: 7.2 Consensus size: 12
60911 TTCTTTTTTG
60921 TTTTT-TTTGTT
1 TTTTTATTTGTT
60932 TTTTATATTT-TGT
1 TTTT-TATTTGT-T
*
60945 TTTGTATTTGTT
1 TTTTTATTTGTT
60957 TTTGTTATTTG--
1 TTT-TTATTTGTT
60968 -TTTTA--TGTT
1 TTTTTATTTGTT
60977 TTTATTATTTGTT
1 TTT-TTATTTGTT
*
60990 TTTTTATTTCTT
1 TTTTTATTTGTT
61002 TT
1 TT
61004 CGTTTTCTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 21
0.71 0.04 0.26
Matches are distributed among these distances:
7 2 0.03
9 3 0.05
10 4 0.07
11 7 0.12
12 21 0.36
13 21 0.36
ACGTcount: A:0.10, C:0.01, G:0.10, T:0.80
Consensus pattern (12 bp):
TTTTTATTTGTT
Found at i:60998 original size:45 final size:44
Alignment explanation
Indices: 60931--61016 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 44
60921 TTTTTTTTGT
* *
60931 TTTTTATATTTTGTTTTGTATTTGTTTTTGTTATT-TGTTTTATG
1 TTTTTATATTTTGTTTTGTATTTCTTTTCGTT-TTCTGTTTTATG
*
60975 TTTTTAT-TATTTGTTTTTTTATTTCTTTTCGTTTTCTGTTTT
1 TTTTTATAT-TTTG-TTTTGTATTTCTTTTCGTTTTCTGTTTT
61017 TTAGTAGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 1 0.03
44 13 0.36
45 22 0.61
ACGTcount: A:0.09, C:0.03, G:0.10, T:0.77
Consensus pattern (44 bp):
TTTTTATATTTTGTTTTGTATTTCTTTTCGTTTTCTGTTTTATG
Found at i:61926 original size:14 final size:14
Alignment explanation
Indices: 61882--61949 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 14
61872 GTTTTATATG
61882 TTTTTATTTTCT-T
1 TTTTTATTTTCTGT
*
61895 TTTTTAATATTATATGT
1 TTTTT-AT-TT-TCTGT
61912 TTTTTATTTTCTGT
1 TTTTTATTTTCTGT
* *
61926 TTTTCTGTTTTGTGT
1 TTTT-TATTTTCTGT
61941 TTTTTATTT
1 TTTTTATTT
61950 GTTTTCTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
13 5 0.11
14 14 0.31
15 16 0.36
16 4 0.09
17 6 0.13
ACGTcount: A:0.12, C:0.04, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTATTTTCTGT
Found at i:62001 original size:22 final size:22
Alignment explanation
Indices: 61971--62033 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
61961 ACGTTATATG
61971 TTTTTATTTTATTT-TTTCTAT
1 TTTTTATTTTATTTATTTCTAT
*
61992 TTTTCTATTTTATTTATTTTTAT
1 TTTT-TATTTTATTTATTTCTAT
*
62015 TTTTTGTTTTATATTATTT
1 TTTTTATTTTAT-TTATTT
62034 TTAAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.11
22 17 0.46
23 16 0.43
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTATTTATTTCTAT
Found at i:62002 original size:17 final size:17
Alignment explanation
Indices: 61980--62012 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
61970 GTTTTTATTT
61980 TATTTT-TTCTATTTTTC
1 TATTTTATT-TATTTTTC
61997 TATTTTATTTATTTTT
1 TATTTTATTTATTTTT
62013 ATTTTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
TATTTTATTTATTTTTC
Found at i:62031 original size:23 final size:22
Alignment explanation
Indices: 61971--62036 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
61961 ACGTTATATG
*
61971 TTTTTATTTTATTT-TTTCTAT
1 TTTTTATTTTATTTATTTTTAT
61992 TTTTCTATTTTATTTATTTTTAT
1 TTTT-TATTTTATTTATTTTTAT
*
62015 TTTTTGTTTTATATTATTTTTA
1 TTTTTATTTTAT-TTATTTTTA
62037 AAATTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.10
22 17 0.43
23 19 0.47
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTATTTATTTTTAT
Found at i:62047 original size:23 final size:23
Alignment explanation
Indices: 61997--62052 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
61987 TCTATTTTTC
***
61997 TATTTTAT-TTATTTTTATTTTT
1 TATTTTATATTATTTTTAAAATT
*
62019 TGTTTTATATTATTTTTAAAATT
1 TATTTTATATTATTTTTAAAATT
*
62042 TATTTTCTATT
1 TATTTTATATT
62053 TTTATAAGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTTTATATTATTTTTAAAATT
Found at i:62088 original size:14 final size:15
Alignment explanation
Indices: 62071--62138 Score: 57
Period size: 17 Copynumber: 4.3 Consensus size: 15
62061 TTCAATCTTA
62071 TTTTCTGTTTTTATTT
1 TTTTCTGTTTTTA-TT
* *
62087 TTATTTTGTTTTTAAT
1 TT-TTCTGTTTTTATT
*
62103 TATT-TGTTTTGTATT
1 TTTTCTGTTTT-TATT
62118 AGTTTTCTGTTTTTATT
1 --TTTTCTGTTTTTATT
62135 TTTT
1 TTTT
62139 TATTAGCTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
14 6 0.14
15 9 0.21
16 4 0.10
17 17 0.40
18 6 0.14
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (15 bp):
TTTTCTGTTTTTATT
Found at i:62137 original size:25 final size:25
Alignment explanation
Indices: 62071--62144 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
62061 TTCAATCTTA
*
62071 TTTTCTGTTTTTATTTTTAT-TTTG
1 TTTTCTGTTTTTATTTTTATATTAG
* * *
62095 TTTT-TAATTATTT-GTTTTGTATTAG
1 TTTTCT-GTT-TTTATTTTTATATTAG
*
62120 TTTTCTGTTTTTATTTTTTTATTAG
1 TTTTCTGTTTTTATTTTTATATTAG
62145 CTGATTCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
23 1 0.03
24 14 0.37
25 22 0.58
26 1 0.03
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (25 bp):
TTTTCTGTTTTTATTTTTATATTAG
Found at i:62225 original size:82 final size:83
Alignment explanation
Indices: 62139--62320 Score: 251
Period size: 83 Copynumber: 2.2 Consensus size: 83
62129 TTTATTTTTT
* ** *
62139 TATTAGCTGATTCTTATA-TTGTTTTATGTTTTTATTAGTTGATGTGAAGGATATCAGTTGATTC
1 TATTAGCTTATTCTTATATTTGTTTTATGTTTTTATTAGTT-ATGTGAAGGATATCAACTGATTA
62203 TT-ATGTTAATGTGAAGGA
65 TTAATGTTAATGTGAAGGA
* * * * *
62221 TATTAGCTTATTCTTATATTTTTTTTCTGTTTTTATTTGTTATGTGGAGGATATTAACTGATTAT
1 TATTAGCTTATTCTTATATTTGTTTTATGTTTTTATTAGTTATGTGAAGGATATCAACTGATTAT
*
62286 TAATGTTAATGTGAAGGC
66 TAATGTTAATGTGAAGGA
62304 TATTAGCTTATTCTTAT
1 TATTAGCTTATTCTTAT
62321 GTTAATGTGA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
82 37 0.42
83 51 0.58
ACGTcount: A:0.25, C:0.06, G:0.18, T:0.52
Consensus pattern (83 bp):
TATTAGCTTATTCTTATATTTGTTTTATGTTTTTATTAGTTATGTGAAGGATATCAACTGATTAT
TAATGTTAATGTGAAGGA
Found at i:62298 original size:32 final size:31
Alignment explanation
Indices: 62253--62334 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 31
62243 TTTTCTGTTT
*
62253 TTATT-TGTT-ATGTGGAGGATATTAACTGA
1 TTATTATGTTAATGTGAAGGATATTAACTGA
* * *
62282 TTATTAATGTTAATGTGAAGGCTATTAGCTTA
1 TTATT-ATGTTAATGTGAAGGATATTAACTGA
*
62314 TTCTTATGTTAATGTGAAGGA
1 TTATTATGTTAATGTGAAGGA
62335 CTTTGAATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 5 0.11
31 19 0.43
32 20 0.45
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (31 bp):
TTATTATGTTAATGTGAAGGATATTAACTGA
Found at i:62375 original size:7 final size:7
Alignment explanation
Indices: 62363--62472 Score: 86
Period size: 7 Copynumber: 15.9 Consensus size: 7
62353 TTATATTGTT
62363 TTTTTTA
1 TTTTTTA
62370 TTTTTTA
1 TTTTTTA
*
62377 -TTTGT-
1 TTTTTTA
62382 TTTTTTA
1 TTTTTTA
* *
62389 TTTTATG
1 TTTTTTA
62396 TTTTTTA
1 TTTTTTA
62403 TTTTATGTA
1 TTTT-T-TA
62412 -TTTTTA
1 TTTTTTA
*
62418 TTATTTA
1 TTTTTTA
* *
62425 GTTTCTA
1 TTTTTTA
62432 -TTTTTA
1 TTTTTTA
62438 TTTGTTT-
1 TTT-TTTA
*
62445 TTTGTTA
1 TTTTTTA
62452 TTTATTTA
1 TTT-TTTA
62460 TTTTTTA
1 TTTTTTA
62467 TTTTTT
1 TTTTTT
62473 GATATTTATT
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
6 17 0.21
7 49 0.60
8 13 0.16
9 2 0.02
ACGTcount: A:0.15, C:0.01, G:0.05, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:62387 original size:14 final size:14
Alignment explanation
Indices: 62370--62497 Score: 80
Period size: 15 Copynumber: 8.4 Consensus size: 14
62360 GTTTTTTTTA
62370 TTTTTTATTTGTTT
1 TTTTTTATTTGTTT
62384 TTTTATT-TTATGTTT
1 TTTT-TTATT-TGTTT
*
62399 TTTATTT-TATGTATT
1 TTT-TTTATTTGT-TT
*
62414 TTTATTATTTAGTTT
1 TTTTTTATTT-GTTT
62429 CTATTTTTATTTGTTT
1 -T-TTTTTATTTGTTT
* *
62445 TTTGTTATTTATTT
1 TTTTTTATTTGTTT
*
62459 ATTTTTTATTTTTTGAT
1 -TTTTTTATTTGTT--T
62476 ATTTATTTATTTGTTGT
1 -TTT-TTTATTTGTT-T
62493 TTTTT
1 TTTTT
62498 GTTTAGATTT
Statistics
Matches: 92, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.24
15 36 0.39
16 11 0.12
17 14 0.15
18 9 0.10
ACGTcount: A:0.15, C:0.01, G:0.07, T:0.77
Consensus pattern (14 bp):
TTTTTTATTTGTTT
Found at i:62445 original size:29 final size:30
Alignment explanation
Indices: 62365--62445 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 30
62355 ATATTGTTTT
*
62365 TTTTATTTTTTATTTGTTTTTTTATTTTATG
1 TTTTA-TTTTTATTTGTTTTATTATTTTATG
*
62396 TTTTTTATTTTATGTAT-TTTTATTA-TTTA-G
1 TTTTAT-TTTTAT-T-TGTTTTATTATTTTATG
62426 TTTCTATTTTTATTTGTTTT
1 TTT-TATTTTTATTTGTTTT
62446 TTGTTATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
28 1 0.02
29 5 0.12
30 11 0.26
31 16 0.38
32 8 0.19
33 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.06, T:0.78
Consensus pattern (30 bp):
TTTTATTTTTATTTGTTTTATTATTTTATG
Found at i:62462 original size:48 final size:48
Alignment explanation
Indices: 62364--62464 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
62354 TATATTGTTT
* * *
62364 TTTTTATTTTTTATTTGTTTTTTTATTTTATGTTTTTTATTTTATGTA
1 TTTTTATTATTTATTTCTATTTTTATTTTATGTTTTTTATTTTATGTA
*
62412 TTTTTATTATTTAGTTTCTATTTTTATTTGT-T-TTTTGTTA-TTTATTTA
1 TTTTTATTATTTA-TTTCTATTTTTATTT-TATGTTTT-TTATTTTATGTA
62460 TTTTT
1 TTTTT
62465 TATTTTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
48 28 0.61
49 17 0.37
50 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.06, T:0.78
Consensus pattern (48 bp):
TTTTTATTATTTATTTCTATTTTTATTTTATGTTTTTTATTTTATGTA
Found at i:62465 original size:49 final size:49
Alignment explanation
Indices: 62363--62468 Score: 121
Period size: 49 Copynumber: 2.2 Consensus size: 49
62353 TTATATTGTT
* * *
62363 TTTTTTATTTTTTATTTGTTTTTTTATTTTATGTTTTTTATTTTATGTA
1 TTTTTTATTATTTATTTCTATTTTTATTTTATGTTTTTTATTTTATGTA
*
62412 -TTTTTATTATTTAGTTTCTATTTTTATTTGT-T-TTTTGTTA-TTTATTTA
1 TTTTTTATTATTTA-TTTCTATTTTTATTT-TATGTTTT-TTATTTTATGTA
62460 TTTTTTATT
1 TTTTTTATT
62469 TTTTGATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
48 23 0.47
49 25 0.51
50 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.06, T:0.78
Consensus pattern (49 bp):
TTTTTTATTATTTATTTCTATTTTTATTTTATGTTTTTTATTTTATGTA
Found at i:62478 original size:25 final size:25
Alignment explanation
Indices: 62442--62498 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
62432 TTTTTATTTG
* *
62442 TTTTTTGTTATTTATTTATTTTTTA
1 TTTTTTGATATTTATTTATTTGTTA
*
62467 TTTTTTGATATTTATTTATTTGTTG
1 TTTTTTGATATTTATTTATTTGTTA
62492 TTTTTTG
1 TTTTTTG
62499 TTTAGATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (25 bp):
TTTTTTGATATTTATTTATTTGTTA
Found at i:65000 original size:22 final size:22
Alignment explanation
Indices: 64975--65050 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
64965 TGGATTAGTA
*
64975 TGAATGCTGACTGGACTT-GATC
1 TGAATGCTGACTGGAATTCG-TC
*
64997 TGAATGCTGATTGGAATTCGTC
1 TGAATGCTGACTGGAATTCGTC
* * * *
65019 TGAATGCTGATTAGAAATCGTT
1 TGAATGCTGACTGGAATTCGTC
65041 TGAATGCTGA
1 TGAATGCTGA
65051 TTAGTTTTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 47 0.98
23 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (22 bp):
TGAATGCTGACTGGAATTCGTC
Found at i:65051 original size:22 final size:22
Alignment explanation
Indices: 64995--65054 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
64985 CTGGACTTGA
* *
64995 TCTGAATGCTGATTGGAATTCG
1 TCTGAATGCTGATTAGAAATCG
65017 TCTGAATGCTGATTAGAAATCG
1 TCTGAATGCTGATTAGAAATCG
*
65039 TTTGAATGCTGATTAG
1 TCTGAATGCTGATTAG
65055 TTTTGGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (22 bp):
TCTGAATGCTGATTAGAAATCG
Found at i:68477 original size:33 final size:33
Alignment explanation
Indices: 68435--68500 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
68425 ATGCCTTTAA
68435 CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
1 CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
68468 CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
1 CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
68501 TAGCCCTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (33 bp):
CTCTCCTTTAAGCTTCAAGTTATATGGAAAAGC
Done.