Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005597.1 Hibiscus syriacus cultivar Beakdansim tig00013021_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: 70205
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:7492 original size:291 final size:291
Alignment explanation
Indices: 6963--7544 Score: 1047
Period size: 291 Copynumber: 2.0 Consensus size: 291
6953 AGGAGATTGC
6963 GATTACAAGTGAGGTTGGAACTCAGGGGGATGTGGCAGAGTTGGTGGTTGAGCAGAAAGAGAAGG
1 GATTACAAGTGAGGTTGGAACTCAGGGGGATGTGGCAGAGTTGGTGGTTGAGCAGAAAGAGAAGG
* * *
7028 AAATGTTGAGCGGGGAGAGTGTTGTTGGCGGTGTGGCGTTGGATAAGATTGACGATGGAGGGACT
66 AAATGTTGAGCGGGGAGAGTGTTGGTGGCAGTGTGGCGATGGATAAGATTGACGATGGAGGGACT
* *
7093 GAAATGGGAGGAAAGGCTGATGAATTGAATGGTGGCCTGGAAGTACCTGAAATCAGAGGTACTGG
131 GAAATGGGAGCAAAGGCTGATGAATTGAATGGTGGCCTGGAAGTACCTGAAATCAGAGGTACCGG
* *
7158 AGAAACAGCTGTTCTGAGGGATGATGAAAAGGGAAATCTGAAGTCTGATACTGTAACTGAGATGC
196 AGAAACAGCTGTTCTGAGGGATGAGGAAAAAGGAAATCTGAAGTCTGATACTGTAACTGAGATGC
7223 CTGTAAAAGGTGATACCGATAAGGCACATGT
261 CTGTAAAAGGTGATACCGATAAGGCACATGT
* *
7254 GATTCCAAGTGAGGTTGGAACTCAGGGGGATGTGGCAGAGTTGGTGGTTGAGCAGCAAGAGAAGG
1 GATTACAAGTGAGGTTGGAACTCAGGGGGATGTGGCAGAGTTGGTGGTTGAGCAGAAAGAGAAGG
* * *
7319 AACTGTTGAGTGGGGAGAGTGTTGGTGGCAGTGTGGTGATGGATAAGATTGACGATGGAGGGACT
66 AAATGTTGAGCGGGGAGAGTGTTGGTGGCAGTGTGGCGATGGATAAGATTGACGATGGAGGGACT
*
7384 GAAATGGGAGCAAAGTCTGATGAATTGAATGGTGGCCTGGAAGTACCTGAAATCAGAGGTACCGG
131 GAAATGGGAGCAAAGGCTGATGAATTGAATGGTGGCCTGGAAGTACCTGAAATCAGAGGTACCGG
7449 AGAAACAGCTGTTCTGAGGGATGAGGAAAAAGGAAATCTGAAGTCTGATACTGTAACTGAGATGC
196 AGAAACAGCTGTTCTGAGGGATGAGGAAAAAGGAAATCTGAAGTCTGATACTGTAACTGAGATGC
7514 CTGTAAAAGGTGATACCGATAAGGCACATGT
261 CTGTAAAAGGTGATACCGATAAGGCACATGT
7545 AGAGGGAACA
Statistics
Matches: 278, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
291 278 1.00
ACGTcount: A:0.30, C:0.11, G:0.37, T:0.22
Consensus pattern (291 bp):
GATTACAAGTGAGGTTGGAACTCAGGGGGATGTGGCAGAGTTGGTGGTTGAGCAGAAAGAGAAGG
AAATGTTGAGCGGGGAGAGTGTTGGTGGCAGTGTGGCGATGGATAAGATTGACGATGGAGGGACT
GAAATGGGAGCAAAGGCTGATGAATTGAATGGTGGCCTGGAAGTACCTGAAATCAGAGGTACCGG
AGAAACAGCTGTTCTGAGGGATGAGGAAAAAGGAAATCTGAAGTCTGATACTGTAACTGAGATGC
CTGTAAAAGGTGATACCGATAAGGCACATGT
Found at i:12728 original size:8 final size:10
Alignment explanation
Indices: 12703--12750 Score: 87
Period size: 10 Copynumber: 4.8 Consensus size: 10
12693 AACACACCAT
12703 ATTCTCTCAA
1 ATTCTCTCAA
12713 ATTCTCTCAA
1 ATTCTCTCAA
12723 ATTCTCTCAA
1 ATTCTCTCAA
12733 ATTCTCTCAA
1 ATTCTCTCAA
*
12743 ATACTCTC
1 ATTCTCTC
12751 TCTATTTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTCTCTCAA
Found at i:12828 original size:17 final size:18
Alignment explanation
Indices: 12792--12832 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12782 ATATTATGTA
*
12792 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
12810 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
12827 TTTACT
1 TTTACT
12833 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:15003 original size:26 final size:24
Alignment explanation
Indices: 14932--15003 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
14922 TTATATTTGT
14932 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
14957 ATTT--TTTATTATT-TCT-TATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
14979 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
15004 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:18741 original size:34 final size:34
Alignment explanation
Indices: 18698--18763 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
18688 GAAAAAACGC
18698 CCGTTAATCGTAGTTTACCCTGATAATTAAATGG
1 CCGTTAATCGTAGTTTACCCTGATAATTAAATGG
18732 CCGTTAATCGTAGTTTACCCTGATAATTAAAT
1 CCGTTAATCGTAGTTTACCCTGATAATTAAAT
18764 ACTGCGTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (34 bp):
CCGTTAATCGTAGTTTACCCTGATAATTAAATGG
Found at i:33411 original size:4 final size:4
Alignment explanation
Indices: 33402--33430 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
33392 TTCGAAACTG
33402 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
33431 GAGATTCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:35492 original size:3 final size:3
Alignment explanation
Indices: 35484--35508 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35474 CCTTTGTAAC
35484 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
35509 TATACCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35928 original size:20 final size:20
Alignment explanation
Indices: 35884--36171 Score: 275
Period size: 20 Copynumber: 14.2 Consensus size: 20
35874 AATGACCAAC
*
35884 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
35903 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
35923 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
35943 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
35963 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
35984 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
36005 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
36026 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
*
36047 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
36067 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
36087 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
36107 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
36127 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
36149 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
36167 AAAAT
1 AAAAT
36172 GAGTAAATTT
Statistics
Matches: 226, Mismatches: 28, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.01
19 15 0.07
20 164 0.73
21 14 0.06
22 30 0.13
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:35976 original size:60 final size:63
Alignment explanation
Indices: 35903--36171 Score: 303
Period size: 60 Copynumber: 4.4 Consensus size: 63
35893 ACGCGAAATA
* * * *
35903 AAAATCGCAACGCGATTTAGAAAATCGCAACGTTGA-AAAGAAAATCGCAACG-G-TC-AAAAG
1 AAAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTAAGAAAATCGCAACGCGATCTACAAG
* * * *
35963 AAAATCGCAACGCGATATTCCA-AGAATCGCAATGCGATTAAGAGAATCGCAACGCGATCTTCCA
1 AAAATCGCAACGCG--ATT-CAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATC-TACA
36027 AG
62 AG
* *
36029 --AATCGCAATGCGATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGAT-T--AAG
1 AAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTACAAG
*
36087 AAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGAT-TCCAAG
1 AAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTACAAG
36149 --AATCGCAACGCGATTCAGAAAAT
1 AAAATCGCAACGCGATTCAGAAAAT
36172 GAGTAAATTT
Statistics
Matches: 181, Mismatches: 15, Indels: 26
0.82 0.07 0.12
Matches are distributed among these distances:
58 3 0.02
60 91 0.50
61 4 0.02
62 65 0.36
63 2 0.01
64 13 0.07
66 3 0.02
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (63 bp):
AAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTACAAG
Found at i:36277 original size:6 final size:6
Alignment explanation
Indices: 36266--36305 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
36256 AGACACGTAT
36266 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
36306 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:36817 original size:6 final size:6
Alignment explanation
Indices: 36806--36880 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
36796 TCTCGTCTCG
36806 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
36854 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
36881 AATGGTAATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:37014 original size:20 final size:20
Alignment explanation
Indices: 36989--37384 Score: 368
Period size: 20 Copynumber: 19.6 Consensus size: 20
36979 AATTTACTCA
36989 GCGTTGCGATTTTCTGAATC
1 GCGTTGCGATTTTCTGAATC
*
37009 GCGTTGCGATTCTT-GGAATC
1 GCGTTGCGATT-TTCTGAATC
*
37029 GCGTTGCGATTCTT-GGAATC
1 GCGTTGCGATT-TTCTGAATC
37049 GCGTTGCGATTTTCTGAATC
1 GCGTTGCGATTTTCTGAATC
*
37069 GCGTTGCGATTCTT-GGAATC
1 GCGTTGCGATT-TTCTGAATC
*
37089 GCGTTGCGATTTTCTTAATC
1 GCGTTGCGATTTTCTGAATC
*
37109 GCGTTGCGATTCTT-GGAATC
1 GCGTTGCGATT-TTCTGAATC
*
37129 GCGTTGCGATTTTCTTAATC
1 GCGTTGCGATTTTCTGAATC
*
37149 GCGTTGCGATTCTT-GGAATC
1 GCGTTGCGATT-TTCTGAATC
37169 GCGTTGCGATTTTCTGAATC
1 GCGTTGCGATTTTCTGAATC
* *
37189 GCATTGCGATTCTT-GGAAGATC
1 GCGTTGCGATT-TTCTG-A-ATC
* *
37211 GCGTTGCGATTCTCTTAATC
1 GCGTTGCGATTTTCTGAATC
* *
37231 GCATTGCGATTCTT-GGAATATC
1 GCGTTGCGATT-TTCTG-A-ATC
37253 GCGTTGCGATTTTCTTTTG-A-C
1 GCGTTGCGATTTTC---TGAATC
**
37274 -CGTTGCGATTTTCT-TTTC
1 GCGTTGCGATTTTCTGAATC
* *
37292 AACGTTGCGATTTTCTAAATC
1 -GCGTTGCGATTTTCTGAATC
* *
37313 ACGTTGCGATTTTCTAAATC
1 GCGTTGCGATTTTCTGAATC
*
37333 GCGTTGCGATTTTCTAAATC
1 GCGTTGCGATTTTCTGAATC
*
37353 GCGTTGCGATTTT-T-ATTTC
1 GCGTTGCGATTTTCTGA-ATC
37372 GCGTTGCGATTTT
1 GCGTTGCGATTTT
37385 GTTGGTCATT
Statistics
Matches: 322, Mismatches: 29, Indels: 51
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 24 0.07
20 247 0.77
21 20 0.06
22 27 0.08
25 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
GCGTTGCGATTTTCTGAATC
Found at i:46457 original size:20 final size:22
Alignment explanation
Indices: 46418--46459 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
46408 TTATTCGGTA
*
46418 CATTGCGAATCCAGGTAAAGAG
1 CATTGCGAATACAGGTAAAGAG
46440 CATTG-GAATACA-GTAAAGAG
1 CATTGCGAATACAGGTAAAGAG
46460 GATCTTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.19
Consensus pattern (22 bp):
CATTGCGAATACAGGTAAAGAG
Found at i:49976 original size:19 final size:20
Alignment explanation
Indices: 49935--49980 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
49925 ATTATATATA
*
49935 TTGAAAAAAACACATAAATT
1 TTGAAAAAAACACATAAACT
* *
49955 TTGAAATAAAC-CCTAAACT
1 TTGAAAAAAACACATAAACT
49974 TTGAAAA
1 TTGAAAA
49981 CCTTCATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (20 bp):
TTGAAAAAAACACATAAACT
Found at i:51254 original size:13 final size:13
Alignment explanation
Indices: 51218--51293 Score: 73
Period size: 13 Copynumber: 5.9 Consensus size: 13
51208 GAAATAGCTG
*
51218 ATAATTGATTTCA
1 ATAATTGATTTGA
* *
51231 ATAGTTTATTTGA
1 ATAATTGATTTGA
*
51244 CTAATTGATTTGA
1 ATAATTGATTTGA
* *
51257 TTAGTTGATTTGA
1 ATAATTGATTTGA
*
51270 AAAATTGATTTGA
1 ATAATTGATTTGA
*
51283 TTAATTG-TTTG
1 ATAATTGATTTG
51294 GTAAAATTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
12 4 0.08
13 46 0.92
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.50
Consensus pattern (13 bp):
ATAATTGATTTGA
Found at i:51261 original size:26 final size:26
Alignment explanation
Indices: 51218--51293 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
51208 GAAATAGCTG
* * *
51218 ATAATTGATTTCAATAGTTTATTTGA
1 ATAATTGATTTGATTAGTTGATTTGA
*
51244 CTAATTGATTTGATTAGTTGATTTGA
1 ATAATTGATTTGATTAGTTGATTTGA
* *
51270 AAAATTGATTTGATTAATTG-TTTG
1 ATAATTGATTTGATTAGTTGATTTG
51294 GTAAAATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 4 0.09
26 39 0.91
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.50
Consensus pattern (26 bp):
ATAATTGATTTGATTAGTTGATTTGA
Found at i:51308 original size:26 final size:26
Alignment explanation
Indices: 51246--51309 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
51236 TTATTTGACT
* *
51246 AATTGATTTGATTAGTTGATTTGAAA
1 AATTGAGTTGATTAATTGATTTGAAA
* *
51272 AATTGATTTGATTAATTG-TTTGGTAA
1 AATTGAGTTGATTAATTGATTT-GAAA
*
51298 AATTTAGTTGAT
1 AATTGAGTTGAT
51310 AGTTGATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 3 0.09
26 30 0.91
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (26 bp):
AATTGAGTTGATTAATTGATTTGAAA
Found at i:53150 original size:44 final size:44
Alignment explanation
Indices: 53097--53182 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
53087 CAACTCGTAA
*
53097 TTTGCACCGAAATGCCACATAATTGTCCCGAATGACCACATAGG
1 TTTGCACCGAAATGCCACATAATTGTCCCGAAGGACCACATAGG
* * *
53141 TTTGCACCGAAGTGCCACATATTTGTCCCGAAGGACTACATA
1 TTTGCACCGAAATGCCACATAATTGTCCCGAAGGACCACATA
53183 ATTATCCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
TTTGCACCGAAATGCCACATAATTGTCCCGAAGGACCACATAGG
Found at i:53173 original size:21 final size:22
Alignment explanation
Indices: 53103--53204 Score: 90
Period size: 21 Copynumber: 4.8 Consensus size: 22
53093 GTAATTTGCA
*
53103 CCGAAATG-CCACATAATTGTC
1 CCGAAGTGACCACATAATTGTC
*
53124 CCGAA-TGACCACATAGGTT-TGC
1 CCGAAGTGACCACATA-ATTGT-C
*
53146 ACCGAAGTG-CCACATATTTGTC
1 -CCGAAGTGACCACATAATTGTC
* *
53168 CCGAAG-GACTACATAATTATC
1 CCGAAGTGACCACATAATTGTC
53189 CCGAAG-GACCACATAA
1 CCGAAGTGACCACATAA
53205 AACCCTCGAC
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
20 3 0.04
21 44 0.65
22 6 0.09
23 13 0.19
24 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (22 bp):
CCGAAGTGACCACATAATTGTC
Found at i:53291 original size:13 final size:15
Alignment explanation
Indices: 53263--53294 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
53253 TACTTTGGGC
53263 TATTAATCACATCAT
1 TATTAATCACATCAT
53278 TATT-ATCA-ATCAT
1 TATTAATCACATCAT
53291 TATT
1 TATT
53295 CGAAGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAATCACATCAT
Found at i:53871 original size:20 final size:20
Alignment explanation
Indices: 53845--53954 Score: 84
Period size: 20 Copynumber: 5.4 Consensus size: 20
53835 TCCTTCTGGC
53845 ATCGATACTACCCATACAGT
1 ATCGATACTACCCATACAGT
* * *
53865 ATTGATAC--CCCTTCAACCGGT
1 ATCGATACTACCCAT--A-CAGT
*
53886 ATCGATACTATCCATACAGT
1 ATCGATACTACCCATACAGT
*
53906 ATCGATAC--CCCTTCAACCAGT
1 ATCGATACTACCCAT--A-CAGT
*
53927 ATCGATACTACTCATACAGT
1 ATCGATACTACCCATACAGT
53947 ATCGATAC
1 ATCGATAC
53955 CCCTTCAACC
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
18 7 0.10
20 32 0.46
21 24 0.35
23 6 0.09
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (20 bp):
ATCGATACTACCCATACAGT
Found at i:53891 original size:41 final size:41
Alignment explanation
Indices: 53845--53980 Score: 227
Period size: 41 Copynumber: 3.3 Consensus size: 41
53835 TCCTTCTGGC
*
53845 ATCGATACTACCCATACAGTATTGATACCCCTTCAACCGGT
1 ATCGATACTACCCATACAGTATCGATACCCCTTCAACCGGT
* *
53886 ATCGATACTATCCATACAGTATCGATACCCCTTCAACCAGT
1 ATCGATACTACCCATACAGTATCGATACCCCTTCAACCGGT
*
53927 ATCGATACTACTCATACAGTATCGATACCCCTTCAACCGGT
1 ATCGATACTACCCATACAGTATCGATACCCCTTCAACCGGT
*
53968 ATGGATACTACCC
1 ATCGATACTACCC
53981 TTAATAATTT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.26
Consensus pattern (41 bp):
ATCGATACTACCCATACAGTATCGATACCCCTTCAACCGGT
Found at i:53892 original size:21 final size:21
Alignment explanation
Indices: 53861--53975 Score: 103
Period size: 21 Copynumber: 5.6 Consensus size: 21
53851 ACTACCCATA
*
53861 CAGTATTGATACCCCTTCAAC
1 CAGTATCGATACCCCTTCAAC
* ** *
53882 CGGTATCGATA-CTATCCATA-
1 CAGTATCGATACCCCTTCA-AC
53902 CAGTATCGATACCCCTTCAAC
1 CAGTATCGATACCCCTTCAAC
**
53923 CAGTATCGATACTAC-TCATA-
1 CAGTATCGATACCCCTTCA-AC
53943 CAGTATCGATACCCCTTCAAC
1 CAGTATCGATACCCCTTCAAC
* *
53964 CGGTATGGATAC
1 CAGTATCGATAC
53976 TACCCTTAAT
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
20 32 0.44
21 41 0.56
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (21 bp):
CAGTATCGATACCCCTTCAAC
Found at i:55581 original size:2 final size:2
Alignment explanation
Indices: 55576--55602 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55566 CACACATTGA
55576 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
55603 ACTTAATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60145 original size:15 final size:16
Alignment explanation
Indices: 60121--60156 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
60111 AACTAGAGTA
*
60121 TTTTATTAAAGTAACT
1 TTTTATTAAAATAACT
60137 TTTTA-TAAAATAACT
1 TTTTATTAAAATAACT
60152 TTTTA
1 TTTTA
60157 CTTTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTATTAAAATAACT
Found at i:60323 original size:17 final size:17
Alignment explanation
Indices: 60301--60337 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
60291 TCTCTTTGTG
* *
60301 TTTTTCCCAAAAGGGTT
1 TTTTTCACAAAAGGATT
60318 TTTTTCACAAAAGGATT
1 TTTTTCACAAAAGGATT
60335 TTT
1 TTT
60338 CACGTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (17 bp):
TTTTTCACAAAAGGATT
Found at i:62447 original size:4 final size:4
Alignment explanation
Indices: 62427--62465 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
62417 TGTGATGACA
* *
62427 ATAC AAAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
62466 TATCTCACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (4 bp):
ATAC
Done.