Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004498.1 Hibiscus syriacus cultivar Beakdansim tig00009921_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: 58071
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3070 original size:18 final size:18
Alignment explanation
Indices: 3047--3170 Score: 178
Period size: 18 Copynumber: 6.9 Consensus size: 18
3037 GCGTAGAACT
*
3047 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
3065 TGTCCCGAAAGACCACTG
1 TGTCCCGAAGGACCACTA
* * *
3083 TATCCCGAATGACCACTG
1 TGTCCCGAAGGACCACTA
3101 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3119 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3137 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3155 TGT-CCGAAGGACCACT
1 TGTCCCGAAGGACCACT
3171 GATAAACCTT
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
17 12 0.12
18 84 0.88
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:7175 original size:18 final size:18
Alignment explanation
Indices: 7146--7253 Score: 135
Period size: 18 Copynumber: 6.0 Consensus size: 18
7136 GCGTAAAACT
* *
7146 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTG
*
7164 TATCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
* *
7182 TATCCCGAATGACCACTG
1 TGTCCCGAAGGACCACTG
*
7200 TGTCCCGAAAGACCACTG
1 TGTCCCGAAGGACCACTG
*
7218 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTG
* *
7236 TGTACCAAAGGACCACTG
1 TGTCCCGAAGGACCACTG
7254 ATAATCCTTC
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 79 1.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:11338 original size:18 final size:18
Alignment explanation
Indices: 11315--11395 Score: 117
Period size: 18 Copynumber: 4.5 Consensus size: 18
11305 TTTGTCTCGT
* *
11315 AGGACCATTATGTCCTGA
1 AGGACCACTATGTCCCGA
* *
11333 ATGACCACTATGTTCCGA
1 AGGACCACTATGTCCCGA
11351 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
11369 AGAACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
11387 AGGACCACT
1 AGGACCACT
11396 GATAATCCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:12047 original size:14 final size:14
Alignment explanation
Indices: 12025--12058 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
12015 CTTTCGATCG
*
12025 ATGTCTACACAATC
1 ATGTATACACAATC
12039 ATGTATACACAATC
1 ATGTATACACAATC
12053 ATGTAT
1 ATGTAT
12059 TTATATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (14 bp):
ATGTATACACAATC
Found at i:13686 original size:13 final size:15
Alignment explanation
Indices: 13668--13701 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
13658 TTGACTGGAA
13668 AAATAAATAA-GA-T
1 AAATAAATAAGGACT
13681 AAATAAATAAGGACT
1 AAATAAATAAGGACT
13696 AAATAA
1 AAATAA
13702 CTTTATTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 2 0.11
15 7 0.37
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (15 bp):
AAATAAATAAGGACT
Found at i:16492 original size:19 final size:19
Alignment explanation
Indices: 16470--16525 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
16460 ATAAACTTAT
16470 TTATTTAAGTTTTCTAATA
1 TTATTTAAGTTTTCTAATA
16489 TTA-TT---TTTT-T-AT-
1 TTATTTAAGTTTTCTAATA
16501 TTATTTAAGTTTTCTAATA
1 TTATTTAAGTTTTCTAATA
16520 TTATTT
1 TTATTT
16526 TTTATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
12 3 0.10
13 4 0.13
14 1 0.03
15 4 0.13
16 4 0.13
17 1 0.03
18 4 0.13
19 9 0.30
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (19 bp):
TTATTTAAGTTTTCTAATA
Found at i:16529 original size:30 final size:30
Alignment explanation
Indices: 16466--16566 Score: 175
Period size: 30 Copynumber: 3.3 Consensus size: 30
16456 TGTAATAAAC
16466 TTATTTATTTAAGTTTTCTAATATTATTTTT
1 TTATTTATTTAAGTTTTCTAATATTA-TTTT
16497 TTATTTATTTAAGTTTTCTAATATTATTTT
1 TTATTTATTTAAGTTTTCTAATATTATTTT
* *
16527 TTATTTATTTAAGTTATCTAATATTATTAT
1 TTATTTATTTAAGTTTTCTAATATTATTTT
16557 TTATTTATTT
1 TTATTTATTT
16567 TTAATTGTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 42 0.62
31 26 0.38
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (30 bp):
TTATTTATTTAAGTTTTCTAATATTATTTT
Found at i:24341 original size:130 final size:130
Alignment explanation
Indices: 24200--24447 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
24190 TATTTATATA
*
24200 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
24265 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
24330 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
24395 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
24448 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:24478 original size:130 final size:129
Alignment explanation
Indices: 24214--24478 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
24204 ATTTGGTCCT
* *
24214 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
24279 TGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
24344 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
24409 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
24473 -A
128 CA
24474 AAATT
1 AAATT
24479 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:24803 original size:28 final size:27
Alignment explanation
Indices: 24772--24834 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
24762 AGTTGATACA
*
24772 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
24800 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
24828 ATATTTT
1 ATATTTT
24835 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:24940 original size:17 final size:17
Alignment explanation
Indices: 24914--24946 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24904 ATTTCTTATT
24914 AAAAATAAAT-ATTCAA
1 AAAAATAAATGATTCAA
24930 AAAATATAAATGATTCA
1 AAAA-ATAAATGATTCA
24947 TACATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAATGATTCAA
Found at i:25091 original size:21 final size:21
Alignment explanation
Indices: 25067--25109 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
25057 TATTACCTTA
25067 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
25088 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
25109 A
1 A
25110 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:25127 original size:35 final size:35
Alignment explanation
Indices: 25078--25163 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
25068 ATTGAAGTAT
** * *
25078 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
25113 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
25148 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
25164 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:28198 original size:19 final size:19
Alignment explanation
Indices: 28174--28226 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
28164 ATAATGTTTA
28174 AAAGTATCGATACTTATAT
1 AAAGTATCGATACTTATAT
* * *
28193 AAAGTATCGAAACTTTTGT
1 AAAGTATCGATACTTATAT
*
28212 ACGAGTATCGATACT
1 A-AAGTATCGATACT
28227 CTTAGGGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (19 bp):
AAAGTATCGATACTTATAT
Found at i:37872 original size:181 final size:184
Alignment explanation
Indices: 37554--37938 Score: 622
Period size: 181 Copynumber: 2.1 Consensus size: 184
37544 TTTTCTAATT
* * *
37554 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
* *
37618 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTTATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
37683 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCACATAT-TCTA
131 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCACATATGT-TA
37737 TATAT-ATATA-TTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
*
37799 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
37863 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCTCATATGTTA
130 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCACATATGTTA
37918 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
37939 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
180 2 0.01
181 100 0.53
182 70 0.37
183 16 0.09
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCACATATGTTA
Found at i:38291 original size:36 final size:36
Alignment explanation
Indices: 38223--38325 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
38213 CCAATTTAGG
*
38223 TTTCATAAGAAATTTGGGTATTTTTTCTTATTAAAGA
1 TTTCATAAGAAATTTGAGTA-TTTTTCTTATTAAAGA
*
38260 TTTCATAAGAAATTTGAGTATTTTTCTTATTAAAGG
1 TTTCATAAGAAATTTGAGTATTTTTCTTATTAAAGA
*
38296 TTTCATAAGAAATTTGTGTA-TTTTCTTATT
1 TTTCATAAGAAATTTGAGTATTTTTCTTATT
38326 GAATATTAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.16
36 34 0.54
37 19 0.30
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (36 bp):
TTTCATAAGAAATTTGAGTATTTTTCTTATTAAAGA
Found at i:41570 original size:31 final size:30
Alignment explanation
Indices: 41495--41577 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
41485 AGAAACCTAC
* * *
41495 CACAAC-AAACCAAAGAAAACAAAAACTCT
1 CACAACAAAAACAAAGGAAACAAAAACCCT
* * * *
41524 CACAGCAGAAGCAAAGGAAACAAAAGCCCTT
1 CACAACAAAAACAAAGGAAACAAAAACCC-T
41555 CACAACAAAAACAAA-GAAACAAA
1 CACAACAAAAACAAAGGAAACAAA
41578 TATAGGGGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
29 5 0.12
30 25 0.58
31 13 0.30
ACGTcount: A:0.60, C:0.25, G:0.10, T:0.05
Consensus pattern (30 bp):
CACAACAAAAACAAAGGAAACAAAAACCCT
Found at i:51587 original size:62 final size:63
Alignment explanation
Indices: 51516--51638 Score: 221
Period size: 63 Copynumber: 2.0 Consensus size: 63
51506 CTATCTATTT
*
51516 AGGTTATTTCTGTTTATATA-TTAAATTTCTATGTTATTTTGATTTAATAAGTATTACTTTTA
1 AGGTTATTTCTGTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTTTA
*
51578 AGGTTATTTCTTTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTT
1 AGGTTATTTCTGTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTT
51639 AATAAAAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 19 0.33
63 39 0.67
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (63 bp):
AGGTTATTTCTGTTTATATATTTAAATTTCTATGTTATTTTAATTTAATAAGTATTACTTTTA
Found at i:51617 original size:31 final size:31
Alignment explanation
Indices: 51518--51617 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 31
51508 ATCTATTTAG
*
51518 GTTATTTCTGTTTATATA-TTAAATTTCTAT
1 GTTATTTCTATTTATATATTTAAATTTCTAT
* *
51548 GTTATTT-TGATTTA-ATAAGTATT-ACTTT-TAAG
1 GTTATTTCT-ATTTATAT-A-T-TTAAATTTCT-AT
*
51580 GTTATTTCTTTTTATATATTTAAATTTCTAT
1 GTTATTTCTATTTATATATTTAAATTTCTAT
51611 GTTATTT
1 GTTATTT
51618 TAATTTAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 19
0.68 0.08 0.24
Matches are distributed among these distances:
29 3 0.06
30 14 0.26
31 14 0.26
32 18 0.33
33 5 0.09
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.60
Consensus pattern (31 bp):
GTTATTTCTATTTATATATTTAAATTTCTAT
Found at i:55301 original size:197 final size:196
Alignment explanation
Indices: 54928--55680 Score: 792
Period size: 197 Copynumber: 3.8 Consensus size: 196
54918 CGTTATTTAC
* * ** * *
54928 AAGTATCGACACAAATCTAA-AACGTGTCGATACACTATGTTCACCTATTTTCTCATAAAACCGG
1 AAGTATCGACACAAAT-TAACAA-GTGTCGACACATTATGTAGACCTATTCTCACATAAAA-CGG
* * * * * * * *
54992 TACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTAT-CAGTTTTGGTGTTTT
63 TATATTTATACCGGTTACATTATAAAATTACCTATTACATTATATTTATGGA-TTTCGATGTTTC
* * *
55056 TGGGATCGATACTTTTTATAAATGTATCGCCA-CTTATGCGTTCACCCTTTTGGGCATTCATTAC
127 TGGGATCGATAC-TTTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCATTCATTAG
55120 GACAAA
191 GACAAA
*
55126 AAGTATCGACACAACATTAACAAGTGTCAACACATTATGTAGACCTATTCTCACATAAAACGGTA
1 AAGTATCGACACAA-ATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACGGTA
* * *
55191 TATTTATACCGGTTATATTACAAAATTGCCTATTACA-TATATTTATGGATTTCGATGTTTCTGG
65 TATTTATACCGGTTACATTATAAAATTACCTATTACATTATATTTATGGATTTCGATGTTTCTGG
* * * *** * *
55255 GATCGATACTGTTGAAAAATGTATCGACACCTTATGGGTGCACCCTTTTGGATTTTCCTTGTGGA
130 GATCGATACT-TTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCATTCATT-AGGA
*
55320 CCAA
193 CAAA
* * * * * * * *
55324 AAGTATCGACACAAATTCTACAAGTGTCGATACATTA--TATATCTATTTTCTAAAAAAAATGGT
1 AAGTATCGACACAAATT-AACAAGTGTCGACACATTATGTAGACCTATTCTC-ACATAAAACGGT
* * * * * *
55387 TTATTTAAACCGGTTACATTGTAAATTTACCTATTACATTATA-AT-TGG-TTTCGATGTTTTTG
64 ATATTTATACCGGTTACATTATAAAATTACCTATTACATTATATTTATGGATTTCGATGTTTCTG
* * * * *
55449 GGATCGATACTTTTATAATTGTATCGATACTTTATGCGTTCACCCTTTTGGGCATTCATAATGGA
129 GGATCGATACTTTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCATTCATTA-GGA
55514 -AAA
193 CAAA
*
55517 AAGTATCGACACAACATTAACAAGTGTCGACACATTATGTAGACCTATTCT--CATAAAACAGTA
1 AAGTATCGACACAA-ATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACGGTA
* * * * *
55580 TATTTATACCGGTTATATTATAAAATTACCTATTACATTATATTTTTTGATTTTGATGTTTCTGA
65 TATTTATACCGGTTACATTATAAAATTACCTATTACATTATATTTATGGATTTCGATGTTTCTGG
* *
55645 GATCGATACATTTTAAAACTGTATCGACACTTTATG
130 GATCGATAC-TTTTAAAAATGTATCGACACCTTATG
55681 GGAAACTTTA
Statistics
Matches: 454, Mismatches: 84, Indels: 36
0.79 0.15 0.06
Matches are distributed among these distances:
192 45 0.10
193 34 0.07
194 45 0.10
195 55 0.12
196 80 0.18
197 105 0.23
198 86 0.19
199 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (196 bp):
AAGTATCGACACAAATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACGGTAT
ATTTATACCGGTTACATTATAAAATTACCTATTACATTATATTTATGGATTTCGATGTTTCTGGG
ATCGATACTTTTAAAAATGTATCGACACCTTATGCGTTCACCCTTTTGGGCATTCATTAGGACAA
A
Found at i:55701 original size:15 final size:15
Alignment explanation
Indices: 55681--55720 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
55671 ACACTTTATG
*
55681 GGAAACTTTAAGTTT
1 GGAAACTTTAAGTAT
*
55696 GGAAACTTTATGTAT
1 GGAAACTTTAAGTAT
*
55711 GAAAACTTTA
1 GGAAACTTTA
55721 TTGTGGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (15 bp):
GGAAACTTTAAGTAT
Found at i:56017 original size:10 final size:11
Alignment explanation
Indices: 55988--56047 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
55978 TATACATAAC
55988 AATGTTCAAAT
1 AATGTTCAAAT
55999 AATGTTCAAAT
1 AATGTTCAAAT
56010 AA-GTTC-AAT
1 AATGTTCAAAT
*
56019 AAT-TATACATAAC
1 AATGT-T-CA-AAT
56032 AATGTTCAAAT
1 AATGTTCAAAT
56043 AATGT
1 AATGT
56048 AACCACAACG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 6 0.15
10 5 0.12
11 21 0.51
12 2 0.05
13 6 0.15
14 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (11 bp):
AATGTTCAAAT
Done.