Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001024.1 Hibiscus syriacus cultivar Beakdansim tig00002040_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: 57480
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2304 original size:2 final size:2
Alignment explanation
Indices: 2299--2333 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2289 AAGTTGTGTG
2299 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 T
2334 GATTAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5588 original size:36 final size:36
Alignment explanation
Indices: 5548--5623 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
5538 TTCGATGTCT
* * * *
5548 AAAACGATATCATTTTGGACATCAATAATCTTCGTC
1 AAAACGATATCATTTTGAACATCAACAAGCGTCGTC
**
5584 AAAACGATATTGTTTTGAACATCAACAAGCGTCGTC
1 AAAACGATATCATTTTGAACATCAACAAGCGTCGTC
5620 AAAA
1 AAAA
5624 TGTCATCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (36 bp):
AAAACGATATCATTTTGAACATCAACAAGCGTCGTC
Found at i:7845 original size:30 final size:31
Alignment explanation
Indices: 7786--7868 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
7776 TTCGATAATA
* *
7786 TAATAATAATTTTATAGTATTTAGATAAA-T
1 TAATAATAATTTTATAATTTTTAGATAAATT
* *
7816 TATTAATAATTTTATAATCTTTTA-TTAAATT
1 TAATAATAATTTTATAAT-TTTTAGATAAATT
7847 TAATAAGT-ATTTTATAATTTTT
1 TAATAA-TAATTTTATAATTTTT
7869 TAAACTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 24 0.53
31 20 0.44
32 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (31 bp):
TAATAATAATTTTATAATTTTTAGATAAATT
Found at i:9007 original size:5 final size:5
Alignment explanation
Indices: 8997--9029 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
8987 GATCGATCCA
8997 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
9030 AACAACACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:11251 original size:49 final size:50
Alignment explanation
Indices: 11154--11252 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
11144 TTACAATATT
*
11154 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
11204 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
11253 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:11297 original size:32 final size:30
Alignment explanation
Indices: 11231--11299 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
11221 ATTTATTATT
*
11231 AAATATT-ATTTTTATAATTTTATTAATAA
1 AAATATTAATTTTTATAATTTTATAAATAA
*
11260 AAATATTAATTTTTGTATATTTTAGTGAAAT-A
1 AAATATTAATTTTTATA-ATTTTA-T-AAATAA
11292 AAATATTA
1 AAATATTA
11300 TAAATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 8 0.24
31 6 0.18
32 10 0.29
33 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATATTAATTTTTATAATTTTATAAATAA
Found at i:11385 original size:23 final size:21
Alignment explanation
Indices: 11337--11385 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
11327 AATAATGTTA
11337 TATTATATTTTTAAAAATATT
1 TATTATATTTTTAAAAATATT
* * *
11358 AATTAGTATATTTTAAATATCTT
1 TATTA-TAT-TTTTAAAAATATT
11381 TATTA
1 TATTA
11386 AAATATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTATATTTTTAAAAATATT
Found at i:11428 original size:28 final size:29
Alignment explanation
Indices: 11388--11558 Score: 104
Period size: 29 Copynumber: 5.8 Consensus size: 29
11378 CTTTATTAAA
11388 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTA-TTAAATATATAAATAATTATTAT
*
11417 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAATAA-TTATTAT
* *
11447 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAATA-ATTAT-TAT
* * *
11476 ATATTATTATA-ATATAATTGATTATTTTAT
1 ATATTATTAAATATATAAATAATTA--TTAT
* * *
11506 ATAATATTAAAAATATTATATTATATTATTAT
1 ATATTATTAAATATA-TA-AATA-ATTATTAT
* *
11538 A-AATATT-AATAAATAAATAAT
1 ATATTATTAAATATATAAATAAT
11559 ATTTTGATAA
Statistics
Matches: 114, Mismatches: 15, Indels: 28
0.73 0.10 0.18
Matches are distributed among these distances:
27 2 0.02
28 22 0.19
29 34 0.30
30 32 0.28
31 10 0.09
32 7 0.06
33 3 0.03
34 4 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
ATATTATTAAATATATAAATAATTATTAT
Found at i:11432 original size:19 final size:20
Alignment explanation
Indices: 11380--11432 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
11370 TTAAATATCT
11380 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
11399 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
11420 TTATTAAATATAT
1 TTATTAAATATAT
11433 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:11433 original size:30 final size:25
Alignment explanation
Indices: 11389--11452 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 25
11379 TTTATTAAAA
*
11389 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAA-ATATAAAAAAT-TTAT
11417 TCATTATTAAATATATAAAAAATTTAT
1 T-ATTATTAAA-ATATAAAAAATTTAT
11444 TATATATTA
1 TAT-TATTA
11453 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 2 0.06
27 10 0.30
28 17 0.52
29 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTATTAAAATATAAAAAATTTAT
Found at i:11826 original size:38 final size:38
Alignment explanation
Indices: 11740--11815 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
11730 ACCAATTATG
11740 TGAAACAAACACGGGAAAAACATTTTCCGAAAAACGAA
1 TGAAACAAACACGGGAAAAACATTTTCCGAAAAACGAA
11778 TGAAACAAACAC-GGAAAAACATTTTCCGAAAAACGAA
1 TGAAACAAACACGGGAAAAACATTTTCCGAAAAACGAA
11815 T
1 T
11816 TACGTGAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 26 0.68
38 12 0.32
ACGTcount: A:0.53, C:0.18, G:0.14, T:0.14
Consensus pattern (38 bp):
TGAAACAAACACGGGAAAAACATTTTCCGAAAAACGAA
Found at i:12138 original size:14 final size:14
Alignment explanation
Indices: 12119--12146 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12109 CGTATTTTGG
12119 TATTTTTAAAAAAA
1 TATTTTTAAAAAAA
12133 TATTTTTAAAAAAA
1 TATTTTTAAAAAAA
12147 CTGAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTTTTAAAAAAA
Found at i:22179 original size:16 final size:16
Alignment explanation
Indices: 22131--22179 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
22121 ATTTAATTAA
22131 AGTTAGGAATAAAAAG
1 AGTTAGGAATAAAAAG
* *
22147 A-TT--TAATAAAAAA
1 AGTTAGGAATAAAAAG
*
22160 AGTTAGGAATAGAAAG
1 AGTTAGGAATAAAAAG
22176 AGTT
1 AGTT
22180 CTTTTCTCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
13 9 0.36
14 2 0.08
15 2 0.08
16 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.24
Consensus pattern (16 bp):
AGTTAGGAATAAAAAG
Found at i:25688 original size:15 final size:16
Alignment explanation
Indices: 25668--25698 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25658 AATTTTCTTT
25668 TAAAATA-ATTTTTAA
1 TAAAATATATTTTTAA
25683 TAAAATATATTTTTAA
1 TAAAATATATTTTTAA
25699 AAGATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATATTTTTAA
Found at i:26472 original size:18 final size:19
Alignment explanation
Indices: 26449--26484 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
26439 ATTAAAATAA
26449 GACAAAA-TGTAAATAAAT
1 GACAAAATTGTAAATAAAT
*
26467 GACAAAATTGTGAATAAA
1 GACAAAATTGTAAATAAA
26485 CCAAACATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (19 bp):
GACAAAATTGTAAATAAAT
Found at i:29151 original size:35 final size:35
Alignment explanation
Indices: 29100--29174 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
29090 AATTGCATAC
* *
29100 TCAAAATCCAACATCATTATTAGTTAGTAAAACAA
1 TCAAAATCCAAAATCATTATTAATTAGTAAAACAA
*
29135 TCAAAATCCAAAATCATTATTAATTAGTATAACAA
1 TCAAAATCCAAAATCATTATTAATTAGTAAAACAA
*
29170 ACAAA
1 TCAAA
29175 TCTCCTTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (35 bp):
TCAAAATCCAAAATCATTATTAATTAGTAAAACAA
Found at i:34996 original size:17 final size:17
Alignment explanation
Indices: 34974--35007 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34964 ATCTGATTGT
*
34974 AGTTAAGAATTGAAAGA
1 AGTTAAGAATAGAAAGA
34991 AGTTAAGAATAGAAAGA
1 AGTTAAGAATAGAAAGA
35008 GTTCTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.21
Consensus pattern (17 bp):
AGTTAAGAATAGAAAGA
Found at i:37625 original size:169 final size:170
Alignment explanation
Indices: 37345--37684 Score: 655
Period size: 169 Copynumber: 2.0 Consensus size: 170
37335 ATAGCTATTG
*
37345 ACATGTTCCATAGCAATTCTAATACAACAAAACAGACTCAAAATCCAACTTTATTTATCTCAACT
1 ACATGTTCCATAGCAATTCTAATACAACAAAACAAACTCAAAATCCAACTTTATTTATCTCAACT
37410 ATCACTTAAAGAACAAACAATGATTTTCCAACAAGCACTTTGGCTGCAACTTAAGTCCATCCTTG
66 ATCACTTAAAGAACAAACAATGATTTTCCAACAAGCACTTTGGCTGCAACTTAAGTCCATCCTTG
37475 TGGCGGCACCTTAGATAACTGCAATTTAATTAAACAAGGA
131 TGGCGGCACCTTAGATAACTGCAATTTAATTAAACAAGGA
37515 ACATGTTCCATAGCAATTCTAATACAACAAAACAAACTCAAAATCCAAC-TTATTTATCTCAACT
1 ACATGTTCCATAGCAATTCTAATACAACAAAACAAACTCAAAATCCAACTTTATTTATCTCAACT
37579 ATCACTTAAAGAACAAACAATGATTTTCCAACAAGCACTTTGGCTGCAACTTAAGTCCATCCTTG
66 ATCACTTAAAGAACAAACAATGATTTTCCAACAAGCACTTTGGCTGCAACTTAAGTCCATCCTTG
*
37644 TGGCGTCACCTTAGATAACTGCAATTTAATTAAACAAGGA
131 TGGCGGCACCTTAGATAACTGCAATTTAATTAAACAAGGA
37684 A
1 A
37685 ATCTCTTAAG
Statistics
Matches: 168, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
169 120 0.71
170 48 0.29
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (170 bp):
ACATGTTCCATAGCAATTCTAATACAACAAAACAAACTCAAAATCCAACTTTATTTATCTCAACT
ATCACTTAAAGAACAAACAATGATTTTCCAACAAGCACTTTGGCTGCAACTTAAGTCCATCCTTG
TGGCGGCACCTTAGATAACTGCAATTTAATTAAACAAGGA
Found at i:42732 original size:34 final size:32
Alignment explanation
Indices: 42679--42748 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
42669 ACCTTACAAC
*
42679 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
42711 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
42745 TCCC
1 TCCC
42749 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:43058 original size:21 final size:21
Alignment explanation
Indices: 43032--43073 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43022 CCAGAATGGG
* *
43032 GGGAATCGGTATCCCTTCATA
1 GGGAATCGATACCCCTTCATA
43053 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
43074 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:43209 original size:19 final size:19
Alignment explanation
Indices: 43165--43209 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
43155 ATACTGGAAT
*
43165 TTATTCAAATAGTAATTTA
1 TTATTCAAATAGTAAATTA
* *
43184 CTGTTCAAATAGTAAATTA
1 TTATTCAAATAGTAAATTA
43203 TTATTCA
1 TTATTCA
43210 TAAAAACATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (19 bp):
TTATTCAAATAGTAAATTA
Found at i:49981 original size:334 final size:335
Alignment explanation
Indices: 49372--50045 Score: 1300
Period size: 334 Copynumber: 2.0 Consensus size: 335
49362 GTTATTAATT
49372 TCAAACAATATAATGTTCCCATGAATGACATGTTCAATAGCAATGCTGATACAATAAGTTACAGA
1 TCAAACAATATAATGTTCCCATGAATGACATGTTCAATAGCAATGCTGATACAATAAGTTACAGA
49437 CGCAAAATCCAACATTATTAGTAATACAACAAACAAGTCGCCTTGTATGATCTAAGCCTCTCAAA
66 CGCAAAATCCAACATTATTAGTAATACAACAAACAAGTCGCCTTGTATGATCTAAGCCTCTCAAA
49502 GTTTCATCCTTATGAACCTTAGGTACCTGCAGCAGGAAAATCTTTTTACTTCTTCCTATTGTATG
131 GTTTCATCCTTATGAACCTTAGGTACCTGCAGCAGGAAAATCTTTTTACTTCTTCCTATTGTATG
49567 AATGCAACATTTATTGAAAAAGTAGTGGAAATAAACCTTAAAGGCTTTGCTTGATATGAAGGATG
196 AATGCAACATTTATTGAAAAAGTAGTGGAAATAAACCTTAAAGGCTTTGCTTGATATGAAGGATG
*
49632 AAAAAAAGGAAAGATGAATTTTAATCATTTGATTAACAATTTTTTATCCTTCCTCATTTCCATCC
261 AAAAAAAGGAAAGATGAATTTTAATCATTTGATTAACAAATTTTTATCCTTCCTCATTTCCATCC
49697 TTTATA-CAA
326 TTTATACCAA
49706 TCAAACAATATAATGTTCCCATGAATGACATGTTCAATAGCAATGCTGATACAATAAGTTACAGA
1 TCAAACAATATAATGTTCCCATGAATGACATGTTCAATAGCAATGCTGATACAATAAGTTACAGA
49771 CGCAAAATCCAACATTATTAGTAATACAACAAACAAGTCGCCTTGTATGATCTAAGCCTCTCAAA
66 CGCAAAATCCAACATTATTAGTAATACAACAAACAAGTCGCCTTGTATGATCTAAGCCTCTC-AA
49836 AG-TTCATCCTTATGAAACCTTAGGTACCTGCAGCAGGAAAATCTTTTTACTTCTTCCTATTGTA
130 AGTTTCATCCTTATG-AACCTTAGGTACCTGCAGCAGGAAAATCTTTTTACTTCTTCCTATTGTA
49900 TGAATGCAACATTTATTGAAAAAGTAGTGGAAATAAACCTTAAAGGC-TTGCTTGATATGAAGGA
194 TGAATGCAACATTTATTGAAAAAGTAGTGGAAATAAACCTTAAAGGCTTTGCTTGATATGAAGGA
49964 TGAAAAAAAGGAAAGATGAATTTTAATCATTTGATTAACAAATTTTTATCCTTCCTCATTTCCAT
259 TGAAAAAAAGGAAAGATGAATTTTAATCATTTGATTAACAAATTTTTATCCTTCCTCATTTCCAT
50029 CCTTTATACCAA
324 CCTTTATACCAA
50041 TCAAA
1 TCAAA
50046 GCCTAAGTGA
Statistics
Matches: 336, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
334 228 0.68
335 108 0.32
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (335 bp):
TCAAACAATATAATGTTCCCATGAATGACATGTTCAATAGCAATGCTGATACAATAAGTTACAGA
CGCAAAATCCAACATTATTAGTAATACAACAAACAAGTCGCCTTGTATGATCTAAGCCTCTCAAA
GTTTCATCCTTATGAACCTTAGGTACCTGCAGCAGGAAAATCTTTTTACTTCTTCCTATTGTATG
AATGCAACATTTATTGAAAAAGTAGTGGAAATAAACCTTAAAGGCTTTGCTTGATATGAAGGATG
AAAAAAAGGAAAGATGAATTTTAATCATTTGATTAACAAATTTTTATCCTTCCTCATTTCCATCC
TTTATACCAA
Found at i:55008 original size:14 final size:14
Alignment explanation
Indices: 54964--55007 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
54954 TTTTTATTTA
* *
54964 TTTAATTTCAGTCT
1 TTTAATTTCACTAT
*
54978 TTTAATTTCATTAT
1 TTTAATTTCACTAT
54992 TTTAATTT-ACTAT
1 TTTAATTTCACTAT
55005 TTT
1 TTT
55008 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (14 bp):
TTTAATTTCACTAT
Found at i:55078 original size:17 final size:17
Alignment explanation
Indices: 55052--55085 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55042 ATTTTTAGTA
55052 TTTTAATTTTAGTATTT
1 TTTTAATTTTAGTATTT
* *
55069 TTTTATTTTTTGTATTT
1 TTTTAATTTTAGTATTT
55086 AATATTTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTAATTTTAGTATTT
Found at i:55103 original size:30 final size:31
Alignment explanation
Indices: 55042--55103 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
55032 TTTACCCTTC
**
55042 ATTTTTAGTATTTTAATTTTAGTATTTTTTT
1 ATTTTTAGTATTTTAATTTTAGTATCCTTTT
*
55073 ATTTTTTGTA-TTTAATATTT-GTATCCTTTT
1 ATTTTTAGTATTTTAAT-TTTAGTATCCTTTT
55103 A
1 A
55104 ATTTAGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (31 bp):
ATTTTTAGTATTTTAATTTTAGTATCCTTTT
Done.