Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000443.1 Hibiscus syriacus cultivar Beakdansim tig00000809_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: 50064
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:7434 original size:2 final size:2
Alignment explanation
Indices: 7427--7461 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7417 GCAATCCATA
7427 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
7462 GTAGACTTTT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:16228 original size:21 final size:22
Alignment explanation
Indices: 16204--16258 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
16194 AGACTCTATC
16204 AATCCTACCA-CCACTACTGAA
1 AATCCTACCAGCCACTACTGAA
*
16225 AATCCTA-CAGCCACTGCTGAA
1 AATCCTACCAGCCACTACTGAA
*
16246 AGTCCTA-CAGCCA
1 AATCCTACCAGCCA
16259 TTGTAATTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.35, C:0.36, G:0.11, T:0.18
Consensus pattern (22 bp):
AATCCTACCAGCCACTACTGAA
Found at i:26804 original size:59 final size:59
Alignment explanation
Indices: 26712--26829 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
26702 TTGGTCAGAA
26712 AGGTAAGGGCTTAGGACAAAGTTGAAATATTCTCTACCATTGTCAGTTCGGAGAGTATG
1 AGGTAAGGGCTTAGGACAAAGTTGAAATATTCTCTACCATTGTCAGTTCGGAGAGTATG
26771 AGGTAAGGGCTTAGGACAAAGTTGAAATATTCTCTACCATTGTCAGTTCGGAGAGTATG
1 AGGTAAGGGCTTAGGACAAAGTTGAAATATTCTCTACCATTGTCAGTTCGGAGAGTATG
26830 TATGGTAGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (59 bp):
AGGTAAGGGCTTAGGACAAAGTTGAAATATTCTCTACCATTGTCAGTTCGGAGAGTATG
Found at i:32647 original size:18 final size:18
Alignment explanation
Indices: 32623--32664 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
32613 AATTAGATAC
32623 CTGAAAGCTTTCCTGGGA
1 CTGAAAGCTTTCCTGGGA
*
32641 TTGAAAGCTTTCCTGGGA
1 CTGAAAGCTTTCCTGGGA
32659 CTGAAA
1 CTGAAA
32665 ATATTCACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (18 bp):
CTGAAAGCTTTCCTGGGA
Found at i:35150 original size:21 final size:21
Alignment explanation
Indices: 35126--35165 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35116 AAAAATATTA
*
35126 AAAAATATTAATGTTTTAAGT
1 AAAAATAATAATGTTTTAAGT
35147 AAAAATAATAATGTTTTAA
1 AAAAATAATAATGTTTTAA
35166 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAAGT
Found at i:36886 original size:20 final size:20
Alignment explanation
Indices: 36861--36937 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 20
36851 GCAATCGCAA
36861 TCGCAACGCG-ATTTCCAAAT
1 TCGCAACGCGAATTTCC-AAT
*
36881 TCGCAACACGGGAATTT-CAAT
1 TCGC-A-ACGCGAATTTCCAAT
* * *
36902 TCACAACTCG-ATTTCTGAAT
1 TCGCAACGCGAATTTC-CAAT
36922 TCGCAACGCGAATTTC
1 TCGCAACGCGAATTTC
36938 TTTTTCGCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.09
19 3 0.07
20 16 0.36
21 12 0.27
22 5 0.11
23 4 0.09
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGAATTTCCAAT
Found at i:36944 original size:20 final size:20
Alignment explanation
Indices: 36921--37036 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 20
36911 GATTTCTGAA
* * *
36921 TTCGCAACGCGAATTTCTTT
1 TTCGCAACACAAATTTCCTT
36941 TTCGCAACACAAATTTCCTT
1 TTCGCAACACAAATTTCCTT
* * *
36961 TTCGCAACA-AGATTTTCTAA
1 TTCGCAACACAAATTTCCT-T
* **
36981 ATCGCAACACAAATTTTGTT
1 TTCGCAACACAAATTTCCTT
* * * ***
37001 TTCGCAACTCGATTTTCGAA
1 TTCGCAACACAAATTTCCTT
37021 TTCGCAACACAAATTT
1 TTCGCAACACAAATTT
37037 TAATTTCGCA
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
19 7 0.09
20 60 0.81
21 7 0.09
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.35
Consensus pattern (20 bp):
TTCGCAACACAAATTTCCTT
Found at i:36978 original size:40 final size:39
Alignment explanation
Indices: 36941--37072 Score: 149
Period size: 40 Copynumber: 3.4 Consensus size: 39
36931 GAATTTCTTT
**
36941 TTCGCAACACAAATTTCCTTTTCGCAACAAGATTTTCTAA
1 TTCGCAACACAAATTTTATTTTCGCAAC-AGATTTTCTAA
* * * *
36981 ATCGCAACACAAATTTTGTTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACAAATTTTATTTTCGCAAC-AGATTTTCTAA
* * * *
37021 TTCGCAACACAAATTTTAATTTCGCAACAGCTTTTAT-T
1 TTCGCAACACAAATTTTATTTTCGCAACAGATTTTCTAA
37059 TTCGCAACACAAAT
1 TTCGCAACACAAAT
37073 GTTTTGGGTA
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 14 0.18
39 5 0.06
40 59 0.76
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (39 bp):
TTCGCAACACAAATTTTATTTTCGCAACAGATTTTCTAA
Found at i:37044 original size:20 final size:20
Alignment explanation
Indices: 36940--37072 Score: 82
Period size: 20 Copynumber: 6.8 Consensus size: 20
36930 CGAATTTCTT
***
36940 TTTCGCAACACAAATTTCCT
1 TTTCGCAACACAAATTTTAA
*
36960 TTTCGCAACA-AGATTTTCTAA
1 TTTCGCAACACA-AATTT-TAA
* **
36981 -ATCGCAACACAAATTTTGT
1 TTTCGCAACACAAATTTTAA
* *
37000 TTTCGCAACTC-GATTTTCGAA
1 TTTCGCAACACAAATTTT--AA
37021 -TTCGCAACACAAATTTTAA
1 TTTCGCAACACAAATTTTAA
*
37040 TTTCGCAACAGC---TTTTAT
1 TTTCGCAACA-CAAATTTTAA
37058 TTTCGCAACACAAAT
1 TTTCGCAACACAAAT
37073 GTTTTGGGTA
Statistics
Matches: 85, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
17 1 0.01
18 15 0.18
19 9 0.11
20 53 0.62
21 7 0.08
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.35
Consensus pattern (20 bp):
TTTCGCAACACAAATTTTAA
Found at i:37241 original size:16 final size:15
Alignment explanation
Indices: 37206--37244 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
37196 TCCCCATCTC
*
37206 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
37221 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
37237 TAATTTTT
1 TAATTTTT
37245 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:37274 original size:7 final size:7
Alignment explanation
Indices: 37262--37286 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37252 TTCTCTCCCA
37262 AACTATC
1 AACTATC
37269 AACTATC
1 AACTATC
37276 AACTATC
1 AACTATC
37283 AACT
1 AACT
37287 TAATTAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (7 bp):
AACTATC
Found at i:37868 original size:12 final size:12
Alignment explanation
Indices: 37847--37880 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37837 ACCACATTTC
*
37847 CAATACCAAACA
1 CAATATCAAACA
37859 CAATATCAAACA
1 CAATATCAAACA
*
37871 CAATCTCAAA
1 CAATATCAAA
37881 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:38039 original size:24 final size:24
Alignment explanation
Indices: 38007--38052 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
37997 TATTCGAAAT
*
38007 TTGATCTTGGTTAATACCCGGACA
1 TTGATCTTGGTCAATACCCGGACA
*
38031 TTGATCTTGGTCAATACTCGGA
1 TTGATCTTGGTCAATACCCGGA
38053 TTTTGATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (24 bp):
TTGATCTTGGTCAATACCCGGACA
Found at i:38058 original size:24 final size:24
Alignment explanation
Indices: 38006--38059 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
37996 GTATTCGAAA
*
38006 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
38030 ATTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
38054 TTTGAT
1 TTTGAT
38060 GTTCAGAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:40687 original size:20 final size:20
Alignment explanation
Indices: 40636--40693 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
40626 TCGTAACGCG
* *
40636 AATTTGACTTCCGCGTTGTG
1 AATTTGACTTTCGCGTTGTA
40656 AATTTGACTTTCGCGTTGTA
1 AATTTGACTTTCGCGTTGTA
* *
40676 AATTTGATTTTCGTGTTG
1 AATTTGACTTTCGCGTTG
40694 CGAAAGTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGTA
Found at i:42221 original size:42 final size:42
Alignment explanation
Indices: 42158--42247 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
42148 AATCGGGCTC
* * *
42158 TTGAATGGTGGGAGTGACCTCTTGCACGATGAGAGGGGCCTA
1 TTGAACGGTGGGAGAGACCTCTTGAACGATGAGAGGGGCCTA
* * *
42200 TTGAACGGTGGGAGAGGCCTCTTGAACGATGAGAGGGTCCTC
1 TTGAACGGTGGGAGAGACCTCTTGAACGATGAGAGGGGCCTA
42242 TTGAAC
1 TTGAAC
42248 AATAGGAGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (42 bp):
TTGAACGGTGGGAGAGACCTCTTGAACGATGAGAGGGGCCTA
Found at i:42224 original size:21 final size:20
Alignment explanation
Indices: 42175--42273 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
42165 GTGGGAGTGA
*
42175 CCTCTTGCACGATGAGAGGGG
1 CCTCTTGAACGATGAGA-GGG
* * *
42196 CCTATTGAACGGTGGGAGAGG
1 CCTCTTGAACGATGAGAG-GG
42217 CCTCTTGAACGATGAGAGGG
1 CCTCTTGAACGATGAGAGGG
*
42237 TCCTCTTGAACAAT-AGGAGGGG
1 -CCTCTTGAACGATGA-GA-GGG
*
42259 CCTATTGAACGATGA
1 CCTCTTGAACGATGA
42274 CAGGTGAATC
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
20 4 0.06
21 55 0.87
22 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.21
Consensus pattern (20 bp):
CCTCTTGAACGATGAGAGGG
Found at i:42261 original size:42 final size:42
Alignment explanation
Indices: 42175--42273 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
42165 GTGGGAGTGA
* ** *
42175 CCTCTTGCACGATGAGAGGGGCCTATTGAACGGTGGGAGAGG
1 CCTCTTGAACGATGAGAGGGGCCTATTGAACAATAGGAGAGG
* * *
42217 CCTCTTGAACGATGAGAGGGTCCTCTTGAACAATAGGAGGGG
1 CCTCTTGAACGATGAGAGGGGCCTATTGAACAATAGGAGAGG
*
42259 CCTATTGAACGATGA
1 CCTCTTGAACGATGA
42274 CAGGTGAATC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.21
Consensus pattern (42 bp):
CCTCTTGAACGATGAGAGGGGCCTATTGAACAATAGGAGAGG
Found at i:42576 original size:21 final size:21
Alignment explanation
Indices: 42552--42593 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42542 TGAAACAATC
*
42552 TCACGTAGAGT-GACTACCTCA
1 TCACGTAAAGTAGA-TACCTCA
42573 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGTAGATACCTCA
42594 CCACATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
TCACGTAAAGTAGATACCTCA
Found at i:42705 original size:21 final size:21
Alignment explanation
Indices: 42679--42725 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
42669 ATTATCGTCG
*
42679 CGTAAAGTACCGACCTCATCA
1 CGTAAAGCACCGACCTCATCA
*
42700 CGTAAAGCACTGACCTCATCA
1 CGTAAAGCACCGACCTCATCA
42721 CGTAA
1 CGTAA
42726 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.19
Consensus pattern (21 bp):
CGTAAAGCACCGACCTCATCA
Found at i:42725 original size:42 final size:41
Alignment explanation
Indices: 42626--42725 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
42616 CGTAAAACAT
* *
42626 CTACCTCACCACGTAAAGACCGTACCTCATCACGCCAAGCA
1 CTACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
** * * *
42667 CTATTATCGTCGCGTAAAGTACCG-ACCTCATCACGTAAAGCA
1 CTA-CCTCATCACGTAAAG-ACCGTACCTCATCACGCAAAGCA
42709 CTGACCTCATCACGTAA
1 CT-ACCTCATCACGTAA
42726 CTCCCCTAAC
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
41 3 0.07
42 37 0.82
43 5 0.11
ACGTcount: A:0.31, C:0.35, G:0.14, T:0.20
Consensus pattern (41 bp):
CTACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
Found at i:43507 original size:20 final size:20
Alignment explanation
Indices: 43455--43498 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
43445 TGTTCCATGC
*
43455 ATTTGACTTCCGCGCTGCGA
1 ATTTGACTTTCGCGCTGCGA
*
43475 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGCTGCGA
43495 ATTT
1 ATTT
43499 TATTATCGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTGACTTTCGCGCTGCGA
Found at i:43548 original size:20 final size:20
Alignment explanation
Indices: 43523--43562 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43513 GAAAATCGTA
43523 ATGCAAATTTAACTTTCGCG
1 ATGCAAATTTAACTTTCGCG
* *
43543 ATGCAAATTTGATTTTCGCG
1 ATGCAAATTTAACTTTCGCG
43563 TTGCGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGCAAATTTAACTTTCGCG
Found at i:45057 original size:21 final size:22
Alignment explanation
Indices: 45033--45130 Score: 116
Period size: 21 Copynumber: 4.7 Consensus size: 22
45023 GTGGGAGTGA
45033 CCTCTTGAACGATGA-GAGGGG
1 CCTCTTGAACGATGAGGAGGGG
*
45054 CCTCTTG-ACGGT-AGGAGGGG
1 CCTCTTGAACGATGAGGAGGGG
*
45074 CCTCTTGAATGATGA-GAGGGG
1 CCTCTTGAACGATGAGGAGGGG
*
45095 CCTCTTGAACAAT-AGGAGGGG
1 CCTCTTGAACGATGAGGAGGGG
* *
45116 CCTATTGAATGATGA
1 CCTCTTGAACGATGA
45131 TAGGTAAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.28
21 43 0.67
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.22
Consensus pattern (22 bp):
CCTCTTGAACGATGAGGAGGGG
Found at i:45080 original size:41 final size:42
Alignment explanation
Indices: 45033--45130 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 42
45023 GTGGGAGTGA
* **
45033 CCTCTTGAACGATGAGAGGGGCCTCTTG-ACGGTAGGAGGGG
1 CCTCTTGAATGATGAGAGGGGCCTCTTGAACAATAGGAGGGG
45074 CCTCTTGAATGATGAGAGGGGCCTCTTGAACAATAGGAGGGG
1 CCTCTTGAATGATGAGAGGGGCCTCTTGAACAATAGGAGGGG
*
45116 CCTATTGAATGATGA
1 CCTCTTGAATGATGA
45131 TAGGTAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 27 0.52
42 25 0.48
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.22
Consensus pattern (42 bp):
CCTCTTGAATGATGAGAGGGGCCTCTTGAACAATAGGAGGGG
Found at i:45124 original size:42 final size:41
Alignment explanation
Indices: 45037--45130 Score: 143
Period size: 42 Copynumber: 2.3 Consensus size: 41
45027 GAGTGACCTC
* ** *
45037 TTGAACGATGAGAGGGGCCTCTTGACGGTAGGAGGGGCCTC
1 TTGAATGATGAGAGGGGCCTCTTGACAATAGGAGGGGCCTA
45078 TTGAATGATGAGAGGGGCCTCTTGAACAATAGGAGGGGCCTA
1 TTGAATGATGAGAGGGGCCTCTTG-ACAATAGGAGGGGCCTA
45120 TTGAATGATGA
1 TTGAATGATGA
45131 TAGGTAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 23 0.48
42 25 0.52
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (41 bp):
TTGAATGATGAGAGGGGCCTCTTGACAATAGGAGGGGCCTA
Found at i:45555 original size:21 final size:21
Alignment explanation
Indices: 45531--45571 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
45521 GTCGTCATGT
*
45531 AAAGTACCGACCTCATCACGC
1 AAAGCACCGACCTCATCACGC
*
45552 AAAGCACTGACCTCATCACG
1 AAAGCACCGACCTCATCACG
45572 TAACTCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.37, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAGCACCGACCTCATCACGC
Found at i:47102 original size:20 final size:20
Alignment explanation
Indices: 47077--47136 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
47067 AATCGCGTTG
*
47077 CATTTTTGTGTTGCGAATTT
1 CATTTTCGTGTTGCGAATTT
* *
47097 CATTTTCGTGTTACAAATTT
1 CATTTTCGTGTTGCGAATTT
*
47117 CATTTTCGTGTTGTGAATTT
1 CATTTTCGTGTTGCGAATTT
47137 AAGTTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (20 bp):
CATTTTCGTGTTGCGAATTT
Found at i:47692 original size:19 final size:19
Alignment explanation
Indices: 47650--47697 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
47640 TAAACGTGCT
47650 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTA-GTG
47670 TTGCGAATTTGACTCTA-TG
1 TTGCGAATTTGACT-TAGTG
47689 TTGCGAATT
1 TTGCGAATT
47698 ACAAATTCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.41
20 14 0.52
21 2 0.07
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (19 bp):
TTGCGAATTTGACTTAGTG
Found at i:47713 original size:20 final size:21
Alignment explanation
Indices: 47688--47740 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
47678 TTGACTCTAT
47688 GTTGCGAATTACAAA-TTCGC
1 GTTGCGAATTACAAATTTCGC
* * *
47708 GTTGCGATTTACAAATTTTGT
1 GTTGCGAATTACAAATTTCGC
47729 GTTGCGAATTAC
1 GTTGCGAATTAC
47741 TTGTTGGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (21 bp):
GTTGCGAATTACAAATTTCGC
Done.