Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008865.1 Hibiscus syriacus cultivar Beakdansim tig00112099_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: 59806
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:148 original size:16 final size:16
Alignment explanation
Indices: 127--184 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
117 GTCTCCAACG
*
127 TTATGTTCGTGTTCAT
1 TTATGTTCGTGTTCGT
143 TTATGTTCGTGTTCGT
1 TTATGTTCGTGTTCGT
*
159 TTATGTTCGTGTTTGT
1 TTATGTTCGTGTTCGT
175 TTATGTTCGT
1 TTATGTTCGT
185 TATTTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.09, C:0.10, G:0.22, T:0.59
Consensus pattern (16 bp):
TTATGTTCGTGTTCGT
Found at i:2594 original size:6 final size:7
Alignment explanation
Indices: 2569--2593 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2559 TTTTTTTGTT
2569 GGGGGAG
1 GGGGGAG
2576 GGGGGAG
1 GGGGGAG
2583 GGGGGAG
1 GGGGGAG
2590 GGGG
1 GGGG
2594 ATTTTCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.88, T:0.00
Consensus pattern (7 bp):
GGGGGAG
Found at i:2966 original size:35 final size:36
Alignment explanation
Indices: 2924--2998 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
2914 AAGGAAAATA
*
2924 TTGTCATCTTGTATAAA-TTGGATATGTTGTCATAT
1 TTGTCATCTTGTATAAATTTAGATATGTTGTCATAT
* *
2959 TTGTCATCTTTTATAAATTTAGATGTGTTGTCATAT
1 TTGTCATCTTGTATAAATTTAGATATGTTGTCATAT
2995 TTGT
1 TTGT
2999 AAACTTTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 16 0.44
36 20 0.56
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (36 bp):
TTGTCATCTTGTATAAATTTAGATATGTTGTCATAT
Found at i:19817 original size:22 final size:22
Alignment explanation
Indices: 19792--19844 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
19782 TCATTTCTTT
19792 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
19814 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
19836 AGGCGCTTG
1 AGGC-CTTG
19845 AGGTGAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (22 bp):
AGGCCTTGTTGAATAAATGTTC
Found at i:29378 original size:16 final size:15
Alignment explanation
Indices: 29323--29375 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
29313 TTTTAAAAAA
*
29323 ATAATAATATAATAAT
1 ATAATAA-AAAATAAT
*
29339 AATGAATAAAAAATGAAA
1 -AT-AATAAAAAAT-AAT
29357 ATAATAAAAAATAAT
1 ATAATAAAAAATAAT
29372 ATAA
1 ATAA
29376 ATATATAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.19
16 10 0.32
17 8 0.26
18 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
ATAATAAAAAATAAT
Found at i:29646 original size:18 final size:17
Alignment explanation
Indices: 29623--29665 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
29613 ATATATACAT
29623 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
29641 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
29658 ATAA-AATA
1 ATAATAATA
29666 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:30956 original size:105 final size:104
Alignment explanation
Indices: 30656--31211 Score: 721
Period size: 105 Copynumber: 5.3 Consensus size: 104
30646 GCATTGTTCC
* * ** *
30656 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTT-TTTGTTGACA
* * *
30720 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 AGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
30761 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAA-ATTTTGTTGACAA
1 -GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAA
* *
30821 GCAACGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCT
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
30861 GTAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAA
1 G-AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAA
*
30926 GCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
30966 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAA
1 -GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAA
*
31031 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
** * * *
31071 AGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
1 -GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAA
* *
31136 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-T
* * *
31177 GAGTAGCACGATATCCTCCGTTGTGGAGTTGAAAT
1 GAGT--C-CAATATCCTTCGTTGTGAAGTTGAAAT
31212 CGTGGATGTT
Statistics
Matches: 402, Mismatches: 35, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
99 2 0.00
100 81 0.20
101 2 0.00
102 4 0.01
104 3 0.01
105 250 0.62
106 37 0.09
107 1 0.00
108 22 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:42948 original size:24 final size:24
Alignment explanation
Indices: 42894--42944 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42884 ACTTATAAGT
* *
42894 AAAATATTAAAAAAATATATATAT
1 AAAATAATAAAAAAATATATATAA
* *
42918 ATAATAATAATAAAATATA-ATAA
1 AAAATAATAAAAAAATATATATAA
42941 AAAA
1 AAAA
42945 ATAAATGAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAATAATAAAAAAATATATATAA
Found at i:42959 original size:37 final size:36
Alignment explanation
Indices: 42888--42959 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 36
42878 TATTAGACTT
* *
42888 ATAAGTAAAATATTAAAAAAATATATATATATAATA
1 ATAAGTAAAATATTAAAAAAATAAATATAAATAATA
42924 ATAA-TAAAATATAATAAAAAAATAAATGA-AAATAAT
1 ATAAGTAAAATAT--TAAAAAAATAAAT-ATAAATAAT
42960 TTAATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 8 0.26
36 4 0.13
37 18 0.58
38 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (36 bp):
ATAAGTAAAATATTAAAAAAATAAATATAAATAATA
Found at i:43004 original size:18 final size:17
Alignment explanation
Indices: 42918--43025 Score: 61
Period size: 18 Copynumber: 6.5 Consensus size: 17
42908 ATATATATAT
*
42918 ATAATAATAATAAA-AT
1 ATAATAATAATAAATAA
42934 ATAATAA-AA-AAATAA
1 ATAATAATAATAAATAA
* *
42949 ATGAA-AATAATTTAATAT
1 AT-AATAATAA-TAAATAA
*
42967 AT-AT-AT-ATATATACA
1 ATAATAATAATAAATA-A
*
42982 TATAATAATAATAACATGA
1 -ATAATAATAATAA-ATAA
*
43001 ATAATAAAAATAAATAA
1 ATAATAATAATAAATAA
43018 ATAA-AATA
1 ATAATAATA
43026 TCCATATAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
14 7 0.10
15 8 0.12
16 19 0.28
17 9 0.13
18 20 0.29
19 4 0.06
20 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:43011 original size:55 final size:55
Alignment explanation
Indices: 42907--43013 Score: 130
Period size: 55 Copynumber: 1.9 Consensus size: 55
42897 ATATTAAAAA
*
42907 AATATATATATATAATAATAATAAAATATAATAAAAAAATAAATGAAAATAATTT
1 AATATATATATATAATAATAATAAAATATAATAAAAAAATAAATAAAAATAATTT
* **
42962 AATATATATATAT-AT-ATACATATAATAATAATAACATGAAT-AATAAAAATAA
1 AATATATATATATAATAATA-ATAAAAT-ATAATAA-AAAAATAAATAAAAATAA
43014 ATAAATAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 3 0.07
54 8 0.18
55 30 0.67
56 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (55 bp):
AATATATATATATAATAATAATAAAATATAATAAAAAAATAAATAAAAATAATTT
Found at i:43464 original size:37 final size:37
Alignment explanation
Indices: 43382--43483 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
43372 GTGCTTGTGG
* * * * * *
43382 ATCTTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
43419 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
43456 ATCTTATTTTTAGGAGTTTGAATCCTAG
1 ATCTTATTTTTAGGAGTTTGAATCCTAG
43484 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (37 bp):
ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:43601 original size:2 final size:2
Alignment explanation
Indices: 43594--43632 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
43584 TCATTCCTCT
43594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43633 GAGTGAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56449 original size:20 final size:20
Alignment explanation
Indices: 56424--56475 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
56414 CGCAACGATC
56424 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
56444 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
56464 CCAAAATCGCAA
1 CCAGAATCGCAA
56476 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:56590 original size:20 final size:20
Alignment explanation
Indices: 56528--56720 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
56518 CGATTTTCCA
* ** *
56528 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
56548 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
56568 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
56588 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
56608 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
56628 AAATCGCAATGCGTA-CCGT
1 AAATCGCAACGCGTATCCGT
*
56647 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
56667 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
56687 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
56708 AAATCGCAACGCG
1 AAATCGCAACGCG
56721 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.12
20 109 0.76
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:56617 original size:80 final size:80
Alignment explanation
Indices: 56527--56721 Score: 241
Period size: 80 Copynumber: 2.4 Consensus size: 80
56517 GCGATTTTCC
* * *
56527 AAAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAAT
1 AAAATCGCAACGCGTATACGTAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGTAAAT
* * *
56592 CGCAACG-TGTATCCGT
65 CGCAACGAT-AATACAT
** * * * *
56608 -AAATCGCAACGCGTATGGGTAAATCGCAATGCGTACCGTATATCGCAACGCGTATCCGTAAATC
1 AAAATCGCAACGCGTATACGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTAAATC
56672 GCAACGATAATACAT
66 GCAACGATAATACAT
*
56687 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AAAATCGCAACGCGTATACGTAAATCGCAACGCGA
56722 TATTTAAAGC
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 36 0.37
80 61 0.63
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (80 bp):
AAAATCGCAACGCGTATACGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTAAATC
GCAACGATAATACAT
Found at i:57134 original size:33 final size:33
Alignment explanation
Indices: 57095--57165 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
57085 TTCACTTAGA
*
57095 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
57128 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
57161 TTTCA
1 TTTCA
57166 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:57304 original size:14 final size:14
Alignment explanation
Indices: 57285--57337 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
57275 AGAATGACTG
57285 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
57299 TCGCAACGCGAAATGAAA
1 TCGCAA--CGAGA-G-AA
57317 TCGC-ACGAGAGAA
1 TCGCAACGAGAGAA
57330 TCGCAACG
1 TCGCAACG
57338 CGAAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 6 0.19
14 10 0.31
15 4 0.12
16 4 0.12
17 2 0.06
18 6 0.19
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:57350 original size:32 final size:31
Alignment explanation
Indices: 57285--57353 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
57275 AGAATGACTG
**
57285 TCGCAACGAGAGAATCGCAACGCGAAATGAAA
1 TCGC-ACGAGAGAATCGCAACGCGAAACAAAA
57317 TCGCACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCACGAGAGAATCGCAACGCGAAA-CAAAA
57349 TCGCA
1 TCGCA
57354 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.42, C:0.26, G:0.23, T:0.09
Consensus pattern (31 bp):
TCGCACGAGAGAATCGCAACGCGAAACAAAA
Found at i:57438 original size:19 final size:18
Alignment explanation
Indices: 57349--57459 Score: 86
Period size: 14 Copynumber: 6.8 Consensus size: 18
57339 GAAACCAAAA
* *
57349 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
57368 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
57384 T--CG-TGCGATTTCATT
1 TCGCGTTGCGATTTCATC
57399 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
57415 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
57432 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
57448 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
57460 TCATTTCAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
13 5 0.06
14 21 0.27
15 5 0.06
16 9 0.12
17 13 0.17
18 6 0.08
19 18 0.23
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:57441 original size:33 final size:33
Alignment explanation
Indices: 57354--57466 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
57344 CAAAATCGCA
57354 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
57387 -TGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
57418 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
57451 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
57467 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
31 26 0.35
32 10 0.14
33 38 0.51
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:59399 original size:90 final size:92
Alignment explanation
Indices: 59132--59503 Score: 668
Period size: 90 Copynumber: 4.1 Consensus size: 92
59122 CTAGATGCTT
*
59132 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
59197 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
59225 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATA-TA-
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
59288 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
59315 AGT-AATTTGTTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
59378 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
59405 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAC-GTGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
59469 TTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
59495 AGTAAATTT
1 AGTAAATTT
59504 ATCCATTCAA
Statistics
Matches: 273, Mismatches: 1, Indels: 13
0.95 0.00 0.05
Matches are distributed among these distances:
88 6 0.02
89 50 0.18
90 109 0.40
91 42 0.15
92 35 0.13
93 31 0.11
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:59475 original size:181 final size:181
Alignment explanation
Indices: 59136--59505 Score: 674
Period size: 181 Copynumber: 2.0 Consensus size: 181
59126 ATGCTTAGTA
59136 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
59201 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTA
59266 TTCTTTAACACTGTGAAATATATTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
131 TTCTTTAACACTGTGAAATATATTGTCTTTGTTTTGTC-TTTGGTTGAAAGT
*
59318 AATTTGTTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
59382 TCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAC-GTGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTA
59445 TTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAAAGT
131 TTCTTTAACACTGTGAAATA-TA-TTGTCTTTGTTTTGTCTTTGGTTGAAAGT
59498 AAATTTAT
1 -AATTTAT
59506 CCATTCAAGT
Statistics
Matches: 183, Mismatches: 2, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
179 25 0.14
180 60 0.33
181 78 0.43
182 20 0.11
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (181 bp):
AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAACTGTGTA
TTCTTTAACACTGTGAAATATATTGTCTTTGTTTTGTCTTTGGTTGAAAGT
Found at i:59571 original size:19 final size:19
Alignment explanation
Indices: 59547--59672 Score: 98
Period size: 19 Copynumber: 7.3 Consensus size: 19
59537 TAGTTTACTT
* *
59547 TCGCAACACGAAACTTAAA
1 TCGCAACGCGAAACTAAAA
*
59566 TCGCAACGCG-AACCAAAA
1 TCGCAACGCGAAACTAAAA
59584 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
59603 TCGCAA--CG--AC--AAA
1 TCGCAACGCGAAACTAAAA
*
59616 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
59635 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACTAAAA
*
59649 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
59668 TCGCA
1 TCGCA
59673 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
13 9 0.10
14 9 0.10
15 5 0.06
16 2 0.02
17 6 0.07
18 18 0.21
19 38 0.44
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:59653 original size:14 final size:13
Alignment explanation
Indices: 59600--59656 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 13
59590 CGCGAAATGA
59600 AAATCGCAACGAC
1 AAATCGCAACGAC
59613 AAATCGCAACGCGAAACC
1 AAATCGCAA--CG--A-C
59631 AAAATCGCAACGAC
1 -AAATCGCAACGAC
59645 AAGATCGCAACG
1 AA-ATCGCAACG
59657 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.30
14 10 0.27
15 3 0.08
17 3 0.08
18 1 0.03
19 9 0.24
ACGTcount: A:0.46, C:0.30, G:0.18, T:0.07
Consensus pattern (13 bp):
AAATCGCAACGAC
Found at i:59657 original size:33 final size:32
Alignment explanation
Indices: 59581--59672 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 32
59571 ACGCGAACCA
**
59581 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
59613 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
59645 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
59673 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 32 0.56
33 25 0.44
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:59690 original size:19 final size:19
Alignment explanation
Indices: 59668--59801 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
59658 GAAACCAAAA
*
59668 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
59687 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
59703 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
59719 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
59735 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
59752 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
59771 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
59791 TCGTGTTGCGA
1 TCGCGTTGCGA
59802 AAGTA
Statistics
Matches: 97, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
14 16 0.16
15 3 0.03
16 11 0.11
17 8 0.08
18 8 0.08
19 39 0.40
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:59709 original size:14 final size:14
Alignment explanation
Indices: 59690--59745 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
59680 TTTCATTTCG
59690 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
59704 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
59720 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
59736 CGTTGCGATT
1 CGTTGCGATT
59746 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 3 0.08
16 5 0.14
17 3 0.08
18 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:59754 original size:33 final size:33
Alignment explanation
Indices: 59673--59764 Score: 168
Period size: 32 Copynumber: 2.8 Consensus size: 33
59663 CAAAATCGCA
*
59673 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
59706 TTGCGA-TTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
59738 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
59765 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.54
33 26 0.46
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Done.