Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005920.1 Hibiscus syriacus cultivar Beakdansim tig00013898_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: 68407
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1424 original size:33 final size:32
Alignment explanation
Indices: 1378--1465 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 32
1368 TAAACATGAG
* * *
1378 AAAAGAATAAAAAAATATAATATATA-ATATTAA
1 AAAACAATGAAAAAATA-AATAAATATATA-TAA
1411 TAAAA-AATGAAAAAATAAATAAATATATATAA
1 -AAAACAATGAAAAAATAAATAAATATATATAA
* *
1443 AAAACAATGTAAAAAGAAATAAA
1 AAAACAATGAAAAAATAAATAAA
1466 AATTATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 4 0.08
32 26 0.54
33 14 0.29
34 4 0.08
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.23
Consensus pattern (32 bp):
AAAACAATGAAAAAATAAATAAATATATATAA
Found at i:1476 original size:32 final size:30
Alignment explanation
Indices: 1403--1476 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 30
1393 TATAATATAT
*
1403 AATATTAATAAAAAATGAAAAAATAAATAAA
1 AATATTAA-AAAAAATGAAAAAAGAAATAAA
* *
1434 TATATATAAAAAACAATGTAAAAAGAAATAAA
1 AATAT-TAAAAAA-AATGAAAAAAGAAATAAA
1466 AATTATTAAAA
1 AA-TATTAAAA
1477 TTAGGAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 8 0.22
32 25 0.69
33 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (30 bp):
AATATTAAAAAAAATGAAAAAAGAAATAAA
Found at i:1833 original size:33 final size:32
Alignment explanation
Indices: 1796--1881 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 32
1786 AGTCCTACTT
1796 GGACTCAAATGCTTTGGTTTTAGTGTTTCAATA
1 GGACTCAAAT-CTTTGGTTTTAGTGTTTCAATA
* *
1829 GGACTTAAATATGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATCT-TTGGTTTTAGTGTTTCAATA
*
1862 GGACTCAAATACGTTGGTTT
1 GGACTCAAAT-CTTTGGTTT
1882 ATTTTCTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.02
33 45 0.98
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (32 bp):
GGACTCAAATCTTTGGTTTTAGTGTTTCAATA
Found at i:1974 original size:12 final size:11
Alignment explanation
Indices: 1930--1992 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 11
1920 GGGCATGCAA
1930 AAATAATAAAAT
1 AAATAAT-AAAT
1942 AAA-AATATAAT
1 AAATAATA-AAT
1953 AATAATAATAAAT
1 -A-AATAATAAAT
1966 AAATAAATAAAT
1 AAAT-AATAAAT
*
1978 ATATAATATAAT
1 AAATAATA-AAT
1990 AAA
1 AAA
1993 ATGTTTTTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 1 0.02
11 13 0.30
12 20 0.47
13 5 0.12
14 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:1974 original size:32 final size:31
Alignment explanation
Indices: 1930--1991 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
1920 GGGCATGCAA
1930 AAATAATAAAATAAAAATATAATAATAATAAT
1 AAATAATAAAATAAAAATATAAT-ATAATAAT
*
1962 AAATAA-ATAAATAAATATATAATATAATAA
1 AAATAATA-AAATAAAAATATAATATAATAA
1992 AATGTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (31 bp):
AAATAATAAAATAAAAATATAATATAATAAT
Found at i:2765 original size:23 final size:22
Alignment explanation
Indices: 2734--2779 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2724 AAAAAATTAA
2734 AAAATTAAAAATATT-TAAATAT
1 AAAATT-AAAATATTATAAATAT
*
2756 AAAATATAAAATATTATTAATAT
1 AAAAT-TAAAATATTATAAATAT
2779 A
1 A
2780 TTTAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATTAAAATATTATAAATAT
Found at i:4723 original size:31 final size:31
Alignment explanation
Indices: 4670--4755 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 31
4660 TTTAATTTAA
*
4670 TTTTATAAAATTTTATTTTTATCATGAATAT-T
1 TTTTATTAAA-TTT-TTTTTATCATGAATATGT
*
4702 TTTTATTAAACTTTTTTTTATCATGAATGTGT
1 TTTTATTAAA-TTTTTTTTATCATGAATATGT
*
4734 TTTTAATTTAAATTTTATTTAT
1 TTTT-A-TTAAATTTTTTTTAT
4756 TTAACATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 15 0.32
32 17 0.36
33 10 0.21
34 5 0.11
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTTATTAAATTTTTTTTATCATGAATATGT
Found at i:7906 original size:29 final size:30
Alignment explanation
Indices: 7864--7928 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
7854 TTTTATGTTA
* * *
7864 GGAGACGAATTTGACCTTATAAAATTTTAG
1 GGAGACGAACTTGAACTTATAAAATTCTAG
*
7894 GGAG-CGAACTTGAACTTATAGAATTCTAG
1 GGAGACGAACTTGAACTTATAAAATTCTAG
7923 GGAGAC
1 GGAGAC
7929 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (30 bp):
GGAGACGAACTTGAACTTATAAAATTCTAG
Found at i:11352 original size:18 final size:18
Alignment explanation
Indices: 11318--11352 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11308 AAAATTGTAT
* *
11318 TCCAATGCTTCTGGCAAC
1 TCCAATGCTCCTAGCAAC
11336 TCCAATGCTCCTAGCAA
1 TCCAATGCTCCTAGCAA
11353 ACATCGAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (18 bp):
TCCAATGCTCCTAGCAAC
Found at i:17919 original size:3 final size:3
Alignment explanation
Indices: 17913--17977 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
17903 TCATTTAAGT
* ** *
17913 TTA TTA TTA ATA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17961 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
17978 AATATTACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:26916 original size:93 final size:92
Alignment explanation
Indices: 26775--26963 Score: 256
Period size: 93 Copynumber: 2.0 Consensus size: 92
26765 AGAAGACCCA
* * * * * *
26775 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGGTCTGGTTTGGTATGAAAC-CACATAATCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAACCA
26839 ATCATTGAATTT-AGAAGATGAATGTACTC
64 ATCATTGAATTTGA-AAGATGAATGTACTC
26868 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAACCAAT
* * *
26933 CATTGGATTTGAAAGATGAATTTGCTC
66 CATTGAATTTGAAAGATGAATGTACTC
26960 ATAG
1 ATAG
26964 TAGAAATAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
92 37 0.44
93 48 0.56
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (92 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAACCAAT
CATTGAATTTGAAAGATGAATGTACTC
Found at i:29326 original size:54 final size:54
Alignment explanation
Indices: 29245--29365 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 54
29235 AAAGAGCTTC
* *** *
29245 AATGTTTGA-GAACATCTGAGCAGAAGCCACAAAAAAAAATAAATGTGTTGTCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACAAAAAAAAATAAATGCACTATCA
** * *
29298 AATGTTTTACGAACATCTGAGCAGAAGCCACAGGAAAAGATGAATGCACTATCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACAAAAAAAAATAAATGCACTATCA
29352 AATGTTTTACGAAC
1 AATGTTTTACGAAC
29366 CTGCTATTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
53 8 0.14
54 50 0.86
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (54 bp):
AATGTTTTACGAACATCTGAGCAGAAGCCACAAAAAAAAATAAATGCACTATCA
Found at i:30626 original size:76 final size:76
Alignment explanation
Indices: 30498--31369 Score: 1618
Period size: 76 Copynumber: 11.5 Consensus size: 76
30488 ATATTTCCCA
* * *
30498 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAATCCTTCGGGAACTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30563 AGCCTTCGGGT
66 AGCCTTCGGGT
30574 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30639 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
30650 TATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30715 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
30726 TATCTGTAAGTCATTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30791 AGCCTTCGGGT
66 AGCCTTCGGGT
*
30802 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30867 AGCCTTCGGGT
66 AGCCTTCGGGT
30878 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30943 AGCCTTCGGGT
66 AGCCTTCGGGT
30954 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31019 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
31030 TATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31095 AGCCTTCGGGT
66 AGCCTTCGGGT
31106 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31171 AGCCTTCGGGT
66 AGCCTTCGGGT
31182 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31247 AGCCTTCGGGT
66 AGCCTTCGGGT
31258 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
31323 AAACCTTCGGGT
65 AAGCCTTCGGGT
* *
31335 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
31370 CATTTCCATC
Statistics
Matches: 777, Mismatches: 18, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
76 732 0.94
77 45 0.06
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:31505 original size:3 final size:3
Alignment explanation
Indices: 31499--31563 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
31489 TCATTTAAGT
* ** *
31499 TTA TTA TTA ATA TTA AAA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31547 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
31564 AATATTACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:31531 original size:24 final size:24
Alignment explanation
Indices: 31499--31570 Score: 99
Period size: 24 Copynumber: 2.9 Consensus size: 24
31489 TCATTTAAGT
*
31499 TTATTATTAATATTAAAATTATTA
1 TTATTATTATTATTAAAATTATTA
*
31523 TTATTATTATTATTATAATTATTA
1 TTATTATTATTATTAAAATTATTA
31547 TTATATATTATTTATTAAATATTA
1 TTAT-TATTA-TTATTAAA-ATTA
31571 CAAAGCCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 26 0.62
25 5 0.12
26 7 0.17
27 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTATTATTATTAAAATTATTA
Found at i:32349 original size:13 final size:13
Alignment explanation
Indices: 32331--32355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32321 ACCACCGTTA
32331 CGGTGGCCGACGG
1 CGGTGGCCGACGG
32344 CGGTGGCCGACG
1 CGGTGGCCGACG
32356 CCGGAACAAG
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:0.08, C:0.32, G:0.52, T:0.08
Consensus pattern (13 bp):
CGGTGGCCGACGG
Found at i:36270 original size:126 final size:126
Alignment explanation
Indices: 36045--36296 Score: 432
Period size: 126 Copynumber: 2.0 Consensus size: 126
36035 AACGACAATA
* * * * *
36045 CCCTTGTTTAATGACTTATCCAGAGGCGTAAAAGGACCCTCGAAAGCATTTACCTCGTGAGCAGC
1 CCCTTGTTTAACGACCTATCCAAAGGCGTAAAAGGACCATCGAAAGCATTTACCTCGTGAGCAAC
* * *
36110 GTCCAATGCCACTACTGAACCCACATGCGTATTATTAAATTCCTCCACCACGTTTGTATTG
66 ATCCAATGCCACTACTGAACCCACATGCGTATTATTAAATACCTCCACCAAGTTTGTATTG
36171 CCCTTGTTTAACGACCTATCCAAAGGCGTAAAAGGACCATCGAAAGCATTTACCTCGTGAGCAAC
1 CCCTTGTTTAACGACCTATCCAAAGGCGTAAAAGGACCATCGAAAGCATTTACCTCGTGAGCAAC
36236 ATCCAATGCCACTACTGAACCCACATGCGTATTATTAAATACCTCCACCAAGTTTGTATTG
66 ATCCAATGCCACTACTGAACCCACATGCGTATTATTAAATACCTCCACCAAGTTTGTATTG
36297 ATGTTCCTCT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 118 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (126 bp):
CCCTTGTTTAACGACCTATCCAAAGGCGTAAAAGGACCATCGAAAGCATTTACCTCGTGAGCAAC
ATCCAATGCCACTACTGAACCCACATGCGTATTATTAAATACCTCCACCAAGTTTGTATTG
Found at i:37678 original size:21 final size:21
Alignment explanation
Indices: 37654--37699 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
37644 AATTTGTTCC
* * *
37654 CATCTTGAATTGTTTTATGTT
1 CATCTTAAATTATTTTATGAT
37675 CATCTTAAATTATTTTATGAT
1 CATCTTAAATTATTTTATGAT
37696 CATC
1 CATC
37700 AAATACCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (21 bp):
CATCTTAAATTATTTTATGAT
Found at i:41930 original size:45 final size:45
Alignment explanation
Indices: 41871--42126 Score: 442
Period size: 45 Copynumber: 5.7 Consensus size: 45
41861 AAAATTTCTC
* * *
41871 ACCATTTATCCCATAAGCTTGTAAGCTTATTTTACCAAAATACTT
1 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
*
41916 ACCATTTATTCCATAAGCTCGTGAGCTTATTTTACCAATATACTT
1 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
41961 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
1 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
*
42006 ACTATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
1 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
42051 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
1 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
**
42096 GTCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 ACCATTTATTCCATAAGCTCGTAAGCTTATTT
42127 GCATGCTTAC
Statistics
Matches: 202, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
44 27 0.13
45 175 0.87
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT
Found at i:42081 original size:21 final size:21
Alignment explanation
Indices: 42056--42125 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
42046 TACTTACCAT
42056 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
* *
42077 TTATTTTACCAATATA-CTTGTCA--
1 TTA--TT-CC-ATA-AGCTCGTAAGC
42100 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
42121 TTATT
1 TTATT
42126 TGCATGCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
18 1 0.03
19 8 0.22
20 2 0.05
21 10 0.27
23 5 0.14
24 2 0.05
25 8 0.22
26 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (21 bp):
TTATTCCATAAGCTCGTAAGC
Found at i:56686 original size:20 final size:20
Alignment explanation
Indices: 56661--56701 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56651 ATGCACATGT
*
56661 TAAAGAATGCATCGATGCAC
1 TAAAGAATGCACCGATGCAC
56681 TAAAGAATGCACCGATGCAC
1 TAAAGAATGCACCGATGCAC
56701 T
1 T
56702 GCAATGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
TAAAGAATGCACCGATGCAC
Done.