Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001822.1 Hibiscus syriacus cultivar Beakdansim tig00003689_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: 61644
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1212 original size:23 final size:23
Alignment explanation
Indices: 1154--1214 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1144 TTGGTGCAGA
1154 GGGAATCGATA-CCCC-TTGAAG
1 GGGAATCGATACCCCCTTTGAAG
* *
1175 GGGAA-CTGATTCCCCCTTTGTAG
1 GGGAATC-GATACCCCCTTTGAAG
1198 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
1215 GGTTTGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 8 0.24
22 4 0.12
23 19 0.58
24 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (23 bp):
GGGAATCGATACCCCCTTTGAAG
Found at i:2812 original size:18 final size:18
Alignment explanation
Indices: 2777--2814 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2767 GGAGCAGCAC
*
2777 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCACCACCA
*
2795 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
2813 GA
1 GA
2815 AGATCAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.26, T:0.03
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:4935 original size:17 final size:15
Alignment explanation
Indices: 4913--4960 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
4903 AGTGACGTTT
4913 TTATATAATATATATTA
1 TTATATAA-AT-TATTA
4930 TTATATAAATTATTA
1 TTATATAAATTATTA
* *
4945 TAATAT-TATTATTA
1 TTATATAAATTATTA
4959 TT
1 TT
4961 TACAAAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.29
15 10 0.36
16 2 0.07
17 8 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATAAATTATTA
Found at i:4941 original size:12 final size:12
Alignment explanation
Indices: 4920--4956 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4910 TTTTTATATA
4920 ATATATATTATT
1 ATATATATTATT
*
4932 ATATAAATTATT
1 ATATATATTATT
4944 ATA-ATATTATT
1 ATATATATTATT
4955 AT
1 AT
4957 TATTTACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATATATTATT
Found at i:6316 original size:18 final size:19
Alignment explanation
Indices: 6293--6331 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6283 AATAACATAT
* *
6293 TATTTTGAT-ATTTTTTTA
1 TATTTTAATCATTATTTTA
6311 TATTTTAATCATTATTTTA
1 TATTTTAATCATTATTTTA
6330 TA
1 TA
6332 CATATGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TATTTTAATCATTATTTTA
Found at i:6383 original size:29 final size:29
Alignment explanation
Indices: 6325--6384 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
6315 TTAATCATTA
*
6325 TTTTATACATATGTATTTAAATTATATTC
1 TTTTATACATATGTAATTAAATTATATTC
*
6354 TTTTATACA-ATAGATAATTAAA-TATTTTC
1 TTTTATACATAT-G-TAATTAAATTATATTC
6383 TT
1 TT
6385 AATAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 18 0.67
30 7 0.26
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (29 bp):
TTTTATACATATGTAATTAAATTATATTC
Found at i:13520 original size:20 final size:20
Alignment explanation
Indices: 13495--13641 Score: 242
Period size: 20 Copynumber: 7.3 Consensus size: 20
13485 TATTTCCACA
*
13495 CATTTGTAAAGCCTCCAGGT
1 CATTTGTAAAGCCTCCGGGT
13515 CATTTGTAAAGCCTCCGGGT
1 CATTTGTAAAGCCTCCGGGT
13535 CATTTGTAAAGCCTCCGGGT
1 CATTTGTAAAGCCTCCGGGT
*
13555 CATTTGTAAAGCCTCCGAGT
1 CATTTGTAAAGCCTCCGGGT
*
13575 CATTTGTAAAGACTCCGGGT
1 CATTTGTAAAGCCTCCGGGT
13595 CATTTGTAAAGCCAT-CGGGT
1 CATTTGTAAAGCC-TCCGGGT
*
13615 CATTTGTAAAGCCTCTGGGT
1 CATTTGTAAAGCCTCCGGGT
13635 CATTTGT
1 CATTTGT
13642 CAATCTTTCG
Statistics
Matches: 119, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
19 1 0.01
20 117 0.98
21 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (20 bp):
CATTTGTAAAGCCTCCGGGT
Found at i:14229 original size:17 final size:15
Alignment explanation
Indices: 14197--14228 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
14187 ACATTTTTTA
14197 TATAATATATATTAT
1 TATAATATATATTAT
14212 TATAATAT-TATTAT
1 TATAATATATATTAT
14226 TAT
1 TAT
14229 TTACAAAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATATATATTAT
Found at i:16467 original size:18 final size:18
Alignment explanation
Indices: 16444--16484 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
16434 GTGTTTACTC
*
16444 AACTCAAAAGGAGAAACG
1 AACTCAAAAGGAGAAACA
16462 AACTCAAAAGGAGAAACA
1 AACTCAAAAGGAGAAACA
16480 AACTC
1 AACTC
16485 TAAATGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.20, G:0.17, T:0.07
Consensus pattern (18 bp):
AACTCAAAAGGAGAAACA
Found at i:19444 original size:22 final size:22
Alignment explanation
Indices: 19392--19608 Score: 262
Period size: 22 Copynumber: 9.9 Consensus size: 22
19382 ATCAAGATCG
**
19392 ATCCATATTTTAAAAT-AATTT
1 ATCCATATTTTAAAATAAATCA
* * *
19413 TTTCATATTTTAAAATAAATAA
1 ATCCATATTTTAAAATAAATCA
**
19435 ATCCATATTTTAAAATAAAATTTT
1 ATCCATATTTTAAAAT-AAA-TCA
19459 AT--ATATTTTAAAATAAATCA
1 ATCCATATTTTAAAATAAATCA
*
19479 ATCCATATTTTAAAATAAAAT-T
1 ATCCATATTTTAAAAT-AAATCA
* *
19501 TTTCATATTTTAAAATAAATCA
1 ATCCATATTTTAAAATAAATCA
*
19523 ATCTATATTTTAAAATAAATCA
1 ATCCATATTTTAAAATAAATCA
19545 ATCCATATTTTAAAATAAATCA
1 ATCCATATTTTAAAATAAATCA
*
19567 ATCTATATTTTAAAATAAATCA
1 ATCCATATTTTAAAATAAATCA
*
19589 ATCTATATTTTAAAATAAAT
1 ATCCATATTTTAAAATAAAT
19609 TTTAAAATAG
Statistics
Matches: 170, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
20 3 0.02
21 21 0.12
22 136 0.80
23 7 0.04
24 3 0.02
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (22 bp):
ATCCATATTTTAAAATAAATCA
Found at i:19482 original size:44 final size:44
Alignment explanation
Indices: 19392--19608 Score: 291
Period size: 44 Copynumber: 5.0 Consensus size: 44
19382 ATCAAGATCG
* *
19392 ATCCATATTTTAAAAT-AATTTTTTCATATTTTAAAATAAATAA
1 ATCCATATTTTAAAATAAATTTTATCATATTTTAAAATAAATCA
19435 ATCCATATTTTAAAATAAAATTTTAT-ATATTTTAAAATAAATCA
1 ATCCATATTTTAAAAT-AAATTTTATCATATTTTAAAATAAATCA
19479 ATCCATATTTTAAAATAAAATTTT-TCATATTTTAAAATAAATCA
1 ATCCATATTTTAAAAT-AAATTTTATCATATTTTAAAATAAATCA
* **
19523 ATCTATATTTTAAAATAAA-TCAATCCATATTTTAAAATAAATCA
1 ATCCATATTTTAAAATAAATTTTAT-CATATTTTAAAATAAATCA
* **
19567 ATCTATATTTTAAAATAAA-TCAATCTATATTTTAAAATAAAT
1 ATCCATATTTTAAAATAAATTTTATC-ATATTTTAAAATAAAT
19609 TTTAAAATAG
Statistics
Matches: 163, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
42 1 0.01
43 22 0.13
44 133 0.82
45 7 0.04
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (44 bp):
ATCCATATTTTAAAATAAATTTTATCATATTTTAAAATAAATCA
Found at i:20242 original size:2 final size:2
Alignment explanation
Indices: 20230--20275 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
20220 ATGGAACATA
*
20230 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20272 AT AT
1 AT AT
20276 GGTTGTCCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21415 original size:23 final size:23
Alignment explanation
Indices: 21352--21407 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
21342 AGAAAGAAAA
**
21352 AAACGT-TCTACAAAGGTAAAGAT
1 AAACGTGTC-ACAAAGACAAAGAT
21375 AAACGTGTCACAAAGACAAAGAT
1 AAACGTGTCACAAAGACAAAGAT
21398 AAACGTGTCA
1 AAACGTGTCA
21408 TGAAGACAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAACGTGTCACAAAGACAAAGAT
Found at i:24869 original size:39 final size:39
Alignment explanation
Indices: 24764--24891 Score: 157
Period size: 39 Copynumber: 3.3 Consensus size: 39
24754 CTATGACTTG
* * ** *
24764 TAAGACCTTATCGTAGGCTCCTCTATTTTCTACACAGGA
1 TAAGCCCTTACCGTAGGCTCCTCTGCTTTGTACACAGGA
*
24803 TAAGCCCTTACCGAAGGCTCCTCTGCTTTGTACACAGGA
1 TAAGCCCTTACCGTAGGCTCCTCTGCTTTGTACACAGGA
* * * *
24842 TAAGCCCTTACCGTAGGCTCCTTTGCTTTGTGCATAGGG
1 TAAGCCCTTACCGTAGGCTCCTCTGCTTTGTACACAGGA
*
24881 TAAGTCCTTAC
1 TAAGCCCTTAC
24892 TACAGCCTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (39 bp):
TAAGCCCTTACCGTAGGCTCCTCTGCTTTGTACACAGGA
Found at i:26130 original size:43 final size:43
Alignment explanation
Indices: 25997--26169 Score: 132
Period size: 43 Copynumber: 4.0 Consensus size: 43
25987 ATCCTAGAAA
* * * * * * * *
25997 AAAAATAGGACGAGAATGTTGCCCTTCATAGATGGTCTTATGC
1 AAAAATAGGACAAGGATGTTACCCTCCGTAGACGATCCTATGC
* * * * * *
26040 AAAAACAAGACATGGATGTTGCCCTCCGTAGACTATCCTATGA
1 AAAAATAGGACAAGGATGTTACCCTCCGTAGACGATCCTATGC
* * *
26083 AAAAATAGGACAAGGATGTTTCCCTCCGTATAGGAT-CTCATGC
1 AAAAATAGGACAAGGATGTTACCCTCCGTAGACGATCCT-ATGC
** * * *
26126 AAAAATAGGACGGGGATGTTACCCTCCATACATGATCCTATGC
1 AAAAATAGGACAAGGATGTTACCCTCCGTAGACGATCCTATGC
26169 A
1 A
26170 TATGACAAAA
Statistics
Matches: 102, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
42 2 0.02
43 98 0.96
44 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (43 bp):
AAAAATAGGACAAGGATGTTACCCTCCGTAGACGATCCTATGC
Found at i:26580 original size:15 final size:16
Alignment explanation
Indices: 26556--26588 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
26546 TACTTAACAT
*
26556 AACTATAATAT-AAAA
1 AACTAAAATATGAAAA
26571 AACTAAAATATGAAAA
1 AACTAAAATATGAAAA
26587 AA
1 AA
26589 ATAAGACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (16 bp):
AACTAAAATATGAAAA
Found at i:27982 original size:29 final size:28
Alignment explanation
Indices: 27873--27983 Score: 73
Period size: 29 Copynumber: 3.8 Consensus size: 28
27863 AAAAGGTCAC
* *
27873 AGTTTAAGGATTAAATTAGAATGTTTAAA
1 AGTTTAAGGATTAAATTAAAATATTT-AA
* *
27902 AGTTTAAGGATTAATTTATAATGAGAGTCTT-A
1 AGTTTAAGGATTAAATTA-AA--ATA-T-TTAA
** *
27934 A-TTTGGGGATAAAATTAAAATATTTGAA
1 AGTTTAAGGATTAAATTAAAATATTT-AA
*
27962 AGTTTAAGGATTAATTTAAAAT
1 AGTTTAAGGATTAAATTAAAAT
27984 GAGTAGTCTA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 4 0.07
29 33 0.54
30 3 0.05
31 12 0.20
32 3 0.05
33 1 0.02
34 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.17, T:0.39
Consensus pattern (28 bp):
AGTTTAAGGATTAAATTAAAATATTTAA
Found at i:28995 original size:128 final size:129
Alignment explanation
Indices: 28740--28982 Score: 335
Period size: 128 Copynumber: 1.9 Consensus size: 129
28730 TGACCGACCG
* *
28740 TTGACTTTGACCAAAAAGTCAAATTTTTCGAAAAAGTCATATTTTAAGTTTTTCAACATCCTGAG
1 TTGACTTTGACCAAAAAGTCAAAATTTTCGAAAAAGACATATTTTAAGTTTTTCAACATCCTGAG
* * *
28805 TCCAAATTCGAAGTCCGTTTTTCCAAATTCAAACCCGAAAGCCTCGAAATCCTCAGTCAAACCA
66 TCCAAATTCCAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATCCTCAGTCAAACCA
* * *
28869 TTGACTTTGACCAAAAAGTCAAAATTTTCG-AAAAGACATATTTTATGTTTTTCGACATCGTGAG
1 TTGACTTTGACCAAAAAGTCAAAATTTTCGAAAAAGACATATTTTAAGTTTTTCAACATCCTGAG
* * * * * * * *
28933 TTCGATTTCCCAGTCTGTTTTGCCAAATTCGAAGCTGAAAGCCTCCAAAT
66 TCCAAATTCCAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAAT
28983 TGGTAGTCAA
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
128 69 0.70
129 29 0.30
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (129 bp):
TTGACTTTGACCAAAAAGTCAAAATTTTCGAAAAAGACATATTTTAAGTTTTTCAACATCCTGAG
TCCAAATTCCAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATCCTCAGTCAAACCA
Found at i:30625 original size:15 final size:16
Alignment explanation
Indices: 30595--30631 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
30585 ATATTTGATC
*
30595 TAGATTAATTAATCAA
1 TAGATTAATAAATCAA
30611 TAGATTAA-AAATCAA
1 TAGATTAATAAATCAA
30626 T-GATTA
1 TAGATTA
30632 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 5 0.25
15 7 0.35
16 8 0.40
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (16 bp):
TAGATTAATAAATCAA
Found at i:30637 original size:2 final size:2
Alignment explanation
Indices: 30630--30683 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
30620 AATCAATGAT
30630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30672 TA TA TA TA TA TA
1 TA TA TA TA TA TA
30684 CACTTTTTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32181 original size:46 final size:44
Alignment explanation
Indices: 32108--32193 Score: 109
Period size: 46 Copynumber: 1.9 Consensus size: 44
32098 TTATTAAAAA
* **
32108 TATTAATTTACTAATAAATAATTAAAAAGATGATAAATTATTAATC
1 TATTAATTTACTAATAAACAAGAAAAAAGAT--TAAATTATTAATC
* *
32154 TATTAATTTTCTAATAAACAAGAAAAAATATTAAATTATT
1 TATTAATTTACTAATAAACAAGAAAAAAGATTAAATTATT
32194 GATTAATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 9 0.26
46 26 0.74
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (44 bp):
TATTAATTTACTAATAAACAAGAAAAAAGATTAAATTATTAATC
Found at i:34582 original size:23 final size:23
Alignment explanation
Indices: 34552--34600 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
34542 TGGTGGTTGG
*
34552 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
34575 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
34598 TTT
1 TTT
34601 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:44803 original size:23 final size:23
Alignment explanation
Indices: 44773--44821 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
44763 TGGTGGTTGG
*
44773 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
44796 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
44819 TTT
1 TTT
44822 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:49944 original size:13 final size:13
Alignment explanation
Indices: 49926--49955 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49916 GGTCAACGCC
*
49926 GGTCAACGGGTCG
1 GGTCAACGGATCG
49939 GGTCAACGGATCG
1 GGTCAACGGATCG
49952 GGTC
1 GGTC
49956 TGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGATCG
Found at i:49953 original size:18 final size:18
Alignment explanation
Indices: 49932--49972 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
49922 CGCCGGTCAA
49932 CGGGTCGGGTCAACGGAT
1 CGGGTCGGGTCAACGGAT
* *
49950 CGGGTCTGGTCAACGGGT
1 CGGGTCGGGTCAACGGAT
49968 CGGGT
1 CGGGT
49973 TATGATCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.22, G:0.46, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGAT
Found at i:52058 original size:32 final size:31
Alignment explanation
Indices: 52013--52088 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
52003 GGTGCCGTGA
** *
52013 GGCCTACTGAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCCAAGAA-ACATCTCAGGGCCGCAG
**
52045 GGCCTACCCAAGAATGATCTCAGGGCCGCAG
1 GGCCTACCCAAGAAACATCTCAGGGCCGCAG
* *
52076 AGCCTACCTAAGA
1 GGCCTACCCAAGA
52089 GTCACATTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 25 0.68
32 12 0.32
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCCAAGAAACATCTCAGGGCCGCAG
Found at i:52073 original size:31 final size:31
Alignment explanation
Indices: 52030--52088 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
52020 TGAAGAACAC
* *
52030 ATCTTAGGGCCGCAGGGCCTACCCAAGAATG
1 ATCTCAGGGCCGCAGAGCCTACCCAAGAATG
*
52061 ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTCAGGGCCGCAGAGCCTACCCAAGA
52089 GTCACATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (31 bp):
ATCTCAGGGCCGCAGAGCCTACCCAAGAATG
Found at i:56442 original size:26 final size:26
Alignment explanation
Indices: 56398--56448 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
56388 TTGATCGTTA
* * *
56398 ACTTTGATCGTTGATTTTTTTTGTTG
1 ACTTTGACCGTTGACTTTTTCTGTTG
*
56424 ACTTTGACCGTTTACTTTTTCTGTT
1 ACTTTGACCGTTGACTTTTTCTGTT
56449 CAATTTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.59
Consensus pattern (26 bp):
ACTTTGACCGTTGACTTTTTCTGTTG
Done.