Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007082.1 Hibiscus syriacus cultivar Beakdansim tig00018480_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: 59047
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6989 original size:7 final size:7
Alignment explanation
Indices: 6979--7008 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
6969 TTGACTCTTG
6979 AAAGGAA
1 AAAGGAA
6986 AAAGGAA
1 AAAGGAA
6993 AAAGGAA
1 AAAGGAA
7000 AAAGGAA
1 AAAGGAA
7007 AA
1 AA
7009 TAACTAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGGAA
Found at i:7440 original size:13 final size:12
Alignment explanation
Indices: 7422--7451 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
7412 TTATTTATTT
7422 AAAAAATTAAATA
1 AAAAAATT-AATA
7435 AAAAAATTAATA
1 AAAAAATTAATA
7447 AAAAA
1 AAAAA
7452 CAGTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAATTAATA
Found at i:9589 original size:6 final size:6
Alignment explanation
Indices: 9580--9605 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9570 TATGCCTATG
9580 TTAATA TTAATA TTAATA TTAATA TT
1 TTAATA TTAATA TTAATA TTAATA TT
9606 GGAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAATA
Found at i:13849 original size:28 final size:28
Alignment explanation
Indices: 13777--13836 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
13767 GAAGGCTAAA
13777 ATTGGGGGTGGGGGAGGAGGAGAGACAT
1 ATTGGGGGTGGGGGAGGAGGAGAGACAT
13805 ATTGGGGGTGGGGGAGGAGGAGAGACAT
1 ATTGGGGGTGGGGGAGGAGGAGAGACAT
13833 ATTG
1 ATTG
13837 TTGTTTGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.25, C:0.03, G:0.55, T:0.17
Consensus pattern (28 bp):
ATTGGGGGTGGGGGAGGAGGAGAGACAT
Found at i:24622 original size:17 final size:17
Alignment explanation
Indices: 24602--24640 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
24592 TTAATAAAGT
*
24602 GATTTTAGTAATTAAGA
1 GATTTTAGTAATCAAGA
24619 GATTTTAGTAATCAAGA
1 GATTTTAGTAATCAAGA
24636 GATTT
1 GATTT
24641 ATTATTATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
GATTTTAGTAATCAAGA
Found at i:24757 original size:15 final size:15
Alignment explanation
Indices: 24733--24775 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
24723 AAATATATAT
24733 TATA-ATTTATTAAA
1 TATATATTTATTAAA
*
24747 TATATATTTATCAAA
1 TATATATTTATTAAA
24762 TATAATATTT-TTAA
1 TAT-ATATTTATTAA
24776 TAGATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATTTATTAAA
Found at i:30704 original size:16 final size:16
Alignment explanation
Indices: 30683--30715 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30673 TAATAAATAA
30683 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
30699 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
30715 A
1 A
30716 AAAAATTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:30767 original size:10 final size:10
Alignment explanation
Indices: 30751--30804 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
30741 CATTTAAATG
30751 ATAAACGAAC
1 ATAAACGAAC
*
30761 GTAAACGAAC
1 ATAAACGAAC
*
30771 ATAAACGAATATA
1 ATAAACG-A-A-C
*
30784 ATAAATGAAC
1 ATAAACGAAC
30794 ATAAACGAAC
1 ATAAACGAAC
30804 A
1 A
30805 ACACAAACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 25 0.71
11 2 0.06
12 2 0.06
13 6 0.17
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:35434 original size:20 final size:20
Alignment explanation
Indices: 35409--35455 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
35399 ATTCCTTGAC
35409 AATCTTACATTCTC-ACTTGT
1 AATCTTACATTC-CGACTTGT
35429 AATCTTACATTCCGACTTGT
1 AATCTTACATTCCGACTTGT
35449 AATCTTA
1 AATCTTA
35456 TATTTCGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (20 bp):
AATCTTACATTCCGACTTGT
Found at i:35538 original size:14 final size:13
Alignment explanation
Indices: 35520--35544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35510 ATGCGTATCT
35520 TTTTTTATTTGTA
1 TTTTTTATTTGTA
35533 TTTTTTATTTGT
1 TTTTTTATTTGT
35545 CTAATAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTTATTTGTA
Found at i:35892 original size:60 final size:60
Alignment explanation
Indices: 35747--35915 Score: 243
Period size: 60 Copynumber: 2.8 Consensus size: 60
35737 CCCAAAATAT
* * *
35747 AAGACATTGTTTTATTGAGT-ATTCTAACTATTAAAAGTTACAAAAT-ATCTCTCAATCAG
1 AAGATATTGTTTTATTGAGTCATTC-AACTATTAAAAGTTACAAAATGATCCCTAAATCAG
* *
35806 AAGATGTTGTTTTATTGAGTCATTCAACTATTAAAAGTTACAAAATGATCCCTAAATCAT
1 AAGATATTGTTTTATTGAGTCATTCAACTATTAAAAGTTACAAAATGATCCCTAAATCAG
* * *
35866 AGGATATTGTTTTATTGAGTCCTTCAACTATTATAAGTTACAAAATGATC
1 AAGATATTGTTTTATTGAGTCATTCAACTATTAAAAGTTACAAAATGATC
35916 ATTTGACTAT
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 39 0.39
60 60 0.61
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (60 bp):
AAGATATTGTTTTATTGAGTCATTCAACTATTAAAAGTTACAAAATGATCCCTAAATCAG
Found at i:36835 original size:74 final size:74
Alignment explanation
Indices: 36732--36954 Score: 437
Period size: 74 Copynumber: 3.0 Consensus size: 74
36722 TTTTATTATT
36732 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
1 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
36797 TAATCGCAA
66 TAATCGCAA
36806 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
1 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
36871 TAATCGCAA
66 TAATCGCAA
36880 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
1 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
*
36945 TAGTCGCAA
66 TAATCGCAA
36954 T
1 T
36955 AAAAATAAAA
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 148 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (74 bp):
TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
TAATCGCAA
Found at i:38249 original size:25 final size:25
Alignment explanation
Indices: 38221--38270 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
38211 ACTTACTCCA
38221 CCAGATTAATAAATAAATATATAAT
1 CCAGATTAATAAATAAATATATAAT
38246 CCAGATTAATAAATAAATATATAAT
1 CCAGATTAATAAATAAATATATAAT
38271 TAAAATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (25 bp):
CCAGATTAATAAATAAATATATAAT
Found at i:40087 original size:120 final size:122
Alignment explanation
Indices: 39784--40089 Score: 386
Period size: 122 Copynumber: 2.5 Consensus size: 122
39774 TAATGCTAAG
* * *
39784 TTTTGAAAAAAATTGAAAGTTTATGA-ACTAAAACATATTAAAACTGATAGTTTATGTACTAAAT
1 TTTTTAAAAAAATTAAAAGTTTA-GATACTAAAACATATCAAAACTGATAGTTTATGTACTAAAT
** * *
39848 GCGTTAAGTTTTTAACGGATGTTACTAAAATGAAACAAAAACTAAATGTTAAATATAA
65 GCGTTAAGTTTTTAACAAAAGTTACTAAAATGAAACAAAAACTAAACGTTAAATATAA
** * * *
39906 TTTTTTTAAAAATTAAAAGTTTAGGTACTAAAACATATCAAAACTAATAGTTTATGCACTAAATG
1 TTTTTAAAAAAATTAAAAGTTTAGATACTAAAACATATCAAAACTGATAGTTTATGTACTAAATG
* * *
39971 TGTTTAA-TTTTTAATAAAAG-TACTAAAATGAAACAAAAACTAAACGTTAAATATGA
66 CG-TTAAGTTTTTAACAAAAGTTACTAAAATGAAACAAAAACTAAACGTTAAATATAA
* * * * *
40027 -TTTTAAAAAAATTAAAAATTTAGATACTAAAATAAATCAAAACTGATATTTTAAGTACTAAAT
1 TTTTTAAAAAAATTAAAAGTTTAGATACTAAAACATATCAAAACTGATAGTTTATGTACTAAAT
40090 ATTTAATTTA
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
120 53 0.34
121 35 0.22
122 65 0.41
123 4 0.03
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (122 bp):
TTTTTAAAAAAATTAAAAGTTTAGATACTAAAACATATCAAAACTGATAGTTTATGTACTAAATG
CGTTAAGTTTTTAACAAAAGTTACTAAAATGAAACAAAAACTAAACGTTAAATATAA
Found at i:40108 original size:121 final size:120
Alignment explanation
Indices: 39870--40098 Score: 318
Period size: 120 Copynumber: 1.9 Consensus size: 120
39860 TAACGGATGT
* ** * *
39870 TACTAAAATGAAACAAAAACTAAATGTTAAATATAATTTTTTTAAAAATTAAAAGTTTAGGTACT
1 TACTAAAATGAAACAAAAACTAAACGTTAAATATAATTTTTAAAAAAATTAAAAATTTAGATACT
* * *
39935 AAAACATATCAAAACTAATAGTTTATGCACTAAATGTGTTTAATTTTTAATAAAAG
66 AAAACAAATCAAAACTAATAGTTTAAGCACTAAA-GTATTTAATTTTTAATAAAAG
*
39991 TACTAAAATGAAACAAAAACTAAACGTTAAATATGA-TTTTAAAAAAATTAAAAATTTAGATACT
1 TACTAAAATGAAACAAAAACTAAACGTTAAATATAATTTTTAAAAAAATTAAAAATTTAGATACT
* * * *
40055 AAAATAAATCAAAACTGATATTTTAAGTACTAAA-TATTTAATTT
66 AAAACAAATCAAAACTAATAGTTTAAGCACTAAAGTATTTAATTT
40099 ATCCTAATAA
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
118 9 0.09
120 52 0.55
121 34 0.36
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (120 bp):
TACTAAAATGAAACAAAAACTAAACGTTAAATATAATTTTTAAAAAAATTAAAAATTTAGATACT
AAAACAAATCAAAACTAATAGTTTAAGCACTAAAGTATTTAATTTTTAATAAAAG
Found at i:47281 original size:29 final size:29
Alignment explanation
Indices: 47249--47318 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
47239 CGCCATGCCT
* *
47249 TCCAGGCGACTTTGTAGGTCG-CGATACAC
1 TCCAGGCGACCTTCTAGGTCGTC-ATACAC
*
47278 TCCAGGCGACCTTCTAGGTCGTCATGCAC
1 TCCAGGCGACCTTCTAGGTCGTCATACAC
*
47307 TCCGGGCGACCT
1 TCCAGGCGACCT
47319 ACCCTTACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (29 bp):
TCCAGGCGACCTTCTAGGTCGTCATACAC
Found at i:47410 original size:29 final size:29
Alignment explanation
Indices: 47377--47461 Score: 136
Period size: 29 Copynumber: 2.9 Consensus size: 29
47367 TCCCAACACA
*
47377 TAGGTCGCCATGCCCTCCGGGAGACCTTG
1 TAGGTCGCCATGCACTCCGGGAGACCTTG
47406 TAGGTCGCCATGCACTCC-GGACGACCTTG
1 TAGGTCGCCATGCACTCCGGGA-GACCTTG
*
47435 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGAGACCT
47462 ACCCTCGCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 3 0.06
29 47 0.90
30 2 0.04
ACGTcount: A:0.15, C:0.35, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGAGACCTTG
Found at i:47508 original size:23 final size:23
Alignment explanation
Indices: 47479--47537 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
47469 CTCGACTGCC
*
47479 CTCGGAT-TCCCTCGCATAGCTCG
1 CTCGGATGT-CCTCGCATAACTCG
47502 CTCGGATGTCCTCGCATAACTCG
1 CTCGGATGTCCTCGCATAACTCG
* *
47525 TTCGGATGGCCTC
1 CTCGGATGTCCTC
47538 AGATGCTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.14, C:0.36, G:0.24, T:0.27
Consensus pattern (23 bp):
CTCGGATGTCCTCGCATAACTCG
Found at i:47551 original size:20 final size:20
Alignment explanation
Indices: 47526--47577 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
47516 CATAACTCGT
47526 TCGGATGGCCTCAGATGCTC
1 TCGGATGGCCTCAGATGCTC
*
47546 TCGGATGGCCTCTGATGCTC
1 TCGGATGGCCTCAGATGCTC
*
47566 TCGGATAGCCTC
1 TCGGATGGCCTC
47578 GGTCGGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.31, G:0.29, T:0.27
Consensus pattern (20 bp):
TCGGATGGCCTCAGATGCTC
Found at i:49387 original size:21 final size:21
Alignment explanation
Indices: 49361--49539 Score: 193
Period size: 21 Copynumber: 8.6 Consensus size: 21
49351 GTTTTCAGAT
* *
49361 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
49382 TCGCAATACGAGCTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
49403 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
49424 TCGCAATACGAATTTGGACTA
1 TCGCAATGCGAACTTGGACTA
49445 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
49466 TCACAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * * *
49486 TCGCATTACGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
49507 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
49528 TCGCAATGCGAA
1 TCGCAATGCGAA
49540 TATGTAAATC
Statistics
Matches: 128, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
20 13 0.10
21 115 0.90
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:49514 original size:62 final size:62
Alignment explanation
Indices: 49375--49565 Score: 253
Period size: 62 Copynumber: 3.1 Consensus size: 62
49365 AACGCGAACT
* * *
49375 TCGACTATCGCAATACGAGCTTGGACTATCGCAATGCGAACT-TCG-ACTATCGCAATACGA-AT
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TAT-GTA-AATCGCAATACGATA-
*
49437 T
62 G
* * *
49438 TGGACTATCGCAATGCGAACTTGGACTATCACAATGCGAATATGTAAATCGCATTACGATAG
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATACGATAG
*
49500 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATACGATAG
49562 TCGA
1 TCGA
49566 AGTTCGCATT
Statistics
Matches: 114, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
62 75 0.66
63 39 0.34
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (62 bp):
TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATACGATAG
Found at i:49573 original size:62 final size:62
Alignment explanation
Indices: 49445--49705 Score: 217
Period size: 62 Copynumber: 4.1 Consensus size: 62
49435 ATTTGGACTA
* * * *
49445 TCGCAATGCGAACTTGGACTATCACAATGCGAATATGTAAATCGCATTACGATAGTCG-ACT
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
49506 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
1 -TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
* * * * * ** * * *
49569 TCGCATTGCGATAGTCGAAGT-TCGCGTTGCG-ATA-GTCCAAGTTCGCATTGCAATAGTCGACT
1 TCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGT--AA-ATCGCAATGCGATAGTCGA--
49631 ATCGCAT
60 A--G--T
* *
49638 T-GCGATTTACAGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
1 TCGC-A-ATGC-GAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
49702 TCGC
1 TCGC
49706 GTTGCGATAG
Statistics
Matches: 157, Mismatches: 24, Indels: 33
0.73 0.11 0.15
Matches are distributed among these distances:
60 2 0.01
61 3 0.02
62 75 0.48
63 23 0.15
64 2 0.01
65 3 0.02
66 1 0.01
67 1 0.01
68 3 0.02
69 3 0.02
70 24 0.15
71 12 0.08
72 3 0.02
73 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (62 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
Found at i:49578 original size:21 final size:21
Alignment explanation
Indices: 49548--49755 Score: 154
Period size: 21 Copynumber: 9.6 Consensus size: 21
49538 AATATGTAAA
*
49548 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
49569 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
49590 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
49611 TCGCATTGCAATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
* *
49631 ATCGCATTGCGAT-TTACAGAACT
1 -TCGCATTGCGATAGT-C-GAAGT
* * *
49654 TGGACTATCGCAAT-G-CGAATATGT
1 TCG-C-ATTGCGATAGTCG-A-A-GT
*
49678 AAATCGCAATGCGATAGTCGAAGT
1 ---TCGCATTGCGATAGTCGAAGT
* *
49702 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
49723 TCGCATCGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
49744 TCGCGTTGCGAT
1 TCGCATTGCGAT
49756 TTATTCCAAA
Statistics
Matches: 147, Mismatches: 26, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
20 3 0.02
21 112 0.76
22 5 0.03
23 5 0.03
24 9 0.06
25 6 0.04
26 3 0.02
27 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:49776 original size:42 final size:41
Alignment explanation
Indices: 49687--49780 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 41
49677 TAAATCGCAA
*
49687 TGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCG-AT
* *
49729 CGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG-T
1 TGCGATAGTCGAAGTTCGCGTTGCGA--TAGTCCAAATTCGAT
49771 TGCGATAGTC
1 TGCGATAGTC
49781 CAAAATCGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 35 0.76
44 11 0.24
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (41 bp):
TGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCGAT
Found at i:50399 original size:6 final size:6
Alignment explanation
Indices: 50377--50413 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
50367 TCTCGTCTCG
50377 GGTCGT -GTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
50414 AATAGTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
GGTCGT
Found at i:50421 original size:6 final size:6
Alignment explanation
Indices: 50412--50447 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
50402 CGTGGTCGTG
*
50412 GTAATA GTAATA ATAATA GTAATA GTAATA GTAATA
1 GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA
50448 CGTGTCTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (6 bp):
GTAATA
Found at i:52280 original size:23 final size:24
Alignment explanation
Indices: 52220--52283 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 24
52210 ATTTAAAGAA
52220 CTTTAAATTATTTTTATATTATATAT
1 CTTTAAA--ATTTTTATATTATATAT
* *
52246 -ATTATTAA-TTTTATATT-TATAT
1 CTTTA-AAATTTTTATATTATATAT
52268 CTTTAAAATTTTTATA
1 CTTTAAAATTTTTATA
52284 ATATCTTACC
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
22 7 0.23
23 19 0.61
24 1 0.03
25 3 0.10
26 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (24 bp):
CTTTAAAATTTTTATATTATATAT
Found at i:52528 original size:2 final size:2
Alignment explanation
Indices: 52521--52550 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52511 GACATTTTAA
52521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52551 TTTAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53261 original size:60 final size:60
Alignment explanation
Indices: 53154--53302 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
53144 ATACATATAA
* * * *
53154 TTTG-GGATGAACTTAAAATGGTCAAAAAGTTTGGGGACCAATTTAGAATGAAAATCATAG
1 TTTGAGGATGAAATTAAAAT-GTTAAAAAGTTTGAGGACCAATCTAGAATGAAAATCATAG
* * * * *
53214 TTTGAGGATGAAATTGAAATGTTAAAAAGTTTGATGACTAATCTAGAATGATAGTCATAG
1 TTTGAGGATGAAATTAAAATGTTAAAAAGTTTGAGGACCAATCTAGAATGAAAATCATAG
* * *
53274 TTTAAGGATGAAATTAAAATATTTAAAAG
1 TTTGAGGATGAAATTAAAATGTTAAAAAG
53303 CTTAGGGACT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
60 62 0.83
61 13 0.17
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTGAGGATGAAATTAAAATGTTAAAAAGTTTGAGGACCAATCTAGAATGAAAATCATAG
Found at i:53332 original size:60 final size:60
Alignment explanation
Indices: 53206--53332 Score: 130
Period size: 60 Copynumber: 2.1 Consensus size: 60
53196 TTAGAATGAA
* * * * * * * *
53206 AATCATAGTTTGAGGATGAAATTGAAATGTTAAAAAGTTTGATGACTAATCTAGAATGAT
1 AATCATAGTTTAAGGATGAAATTAAAATATTAAAAAGTTAGAGGACTAATCTAAAATAAG
* * * *
53266 AGTCATAGTTTAAGGATGAAATTAAAATATTTAAAAGCTTAG-GGACTAGTTTAAAATAAG
1 AATCATAGTTTAAGGATGAAATTAAAATATTAAAAAG-TTAGAGGACTAATCTAAAATAAG
53326 AATCATA
1 AATCATA
53333 TATAAAGGAT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
60 50 0.94
61 3 0.06
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (60 bp):
AATCATAGTTTAAGGATGAAATTAAAATATTAAAAAGTTAGAGGACTAATCTAAAATAAG
Found at i:55247 original size:13 final size:13
Alignment explanation
Indices: 55229--55255 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55219 TTACAGATGC
55229 GCATATGAAGACT
1 GCATATGAAGACT
55242 GCATATGAAGACT
1 GCATATGAAGACT
55255 G
1 G
55256 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:56486 original size:54 final size:53
Alignment explanation
Indices: 56394--56496 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
56384 CACGAAAAAC
56394 CGAATCCGAATAACATAGTTGTAATATCTCTAAAACCCGAATGACCGAACAAT
1 CGAATCCGAATAACATAGTTGTAATATCTCTAAAACCCGAATGACCGAACAAT
* * *
56447 CGAAT-CGAAATAACATAGGTTGTGATATCTCTAAGACCCGAATGGCCGAA
1 CGAATCCG-AATAACATA-GTTGTAATATCTCTAAAACCCGAATGACCGAA
56497 GTACCCATGT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 2 0.04
53 14 0.31
54 29 0.64
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.22
Consensus pattern (53 bp):
CGAATCCGAATAACATAGTTGTAATATCTCTAAAACCCGAATGACCGAACAAT
Done.