Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007245.1 Hibiscus syriacus cultivar Beakdansim tig00019199_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: 74015
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2898 original size:17 final size:17
Alignment explanation
Indices: 2876--2945 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
2866 AATTAAGAGT
*
2876 TAGTTTGATTAATGCAC
1 TAGTTTGATTAATGAAC
* *
2893 TAGTTTAATAAATGAAC
1 TAGTTTGATTAATGAAC
2910 TAGTTTGATTAATGAAC
1 TAGTTTGATTAATGAAC
*
2927 TAACTTT-ATTAATGAAC
1 T-AGTTTGATTAATGAAC
2944 TA
1 TA
2946 AATGCATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 1 0.02
17 41 0.89
18 4 0.09
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTGATTAATGAAC
Found at i:2914 original size:34 final size:34
Alignment explanation
Indices: 2876--2945 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
2866 AATTAAGAGT
* *
2876 TAGTTTGATTAATGCACT-AGTTTAATAAATGAAC
1 TAGTTTGATTAATGAACTAACTTT-ATAAATGAAC
*
2910 TAGTTTGATTAATGAACTAACTTTATTAATGAAC
1 TAGTTTGATTAATGAACTAACTTTATAAATGAAC
2944 TA
1 TA
2946 AATGCATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (34 bp):
TAGTTTGATTAATGAACTAACTTTATAAATGAAC
Found at i:3022 original size:17 final size:17
Alignment explanation
Indices: 3002--3043 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2992 ACTACTTCCC
3002 TAAATGAAATACATGAT
1 TAAATGAAATACATGAT
* *
3019 TAAATGCAATACATGCT
1 TAAATGAAATACATGAT
*
3036 TTAATGAA
1 TAAATGAA
3044 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGAT
Found at i:5361 original size:21 final size:22
Alignment explanation
Indices: 5325--5365 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5315 ATAATTAGTA
*
5325 ATAAAAAGATATAACCTCACAG
1 ATAAAAAGATAAAACCTCACAG
5347 ATAAAAAGA-AAAACCTCAC
1 ATAAAAAGATAAAACCTCAC
5366 CAAACACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.15
Consensus pattern (22 bp):
ATAAAAAGATAAAACCTCACAG
Found at i:7039 original size:17 final size:17
Alignment explanation
Indices: 7019--7073 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
7009 TGATTGATAC
* *
7019 ACTAGTTTTATAAATGA
1 ACTAGCTTTATTAATGA
*
7036 ACTAGCTTGATTAATGA
1 ACTAGCTTTATTAATGA
*
7053 ACTAACTTTATTAATGA
1 ACTAGCTTTATTAATGA
7070 ACTA
1 ACTA
7074 AATGCATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (17 bp):
ACTAGCTTTATTAATGA
Found at i:10938 original size:19 final size:20
Alignment explanation
Indices: 10905--10943 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
10895 CTAAACTCTA
* *
10905 AAACGAAAACTCAAAGAAAG
1 AAACGAAAACACAAAAAAAG
10925 AAAC-AAAACACAAAAAAAG
1 AAACGAAAACACAAAAAAAG
10944 CTCCCAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.72, C:0.15, G:0.10, T:0.03
Consensus pattern (20 bp):
AAACGAAAACACAAAAAAAG
Found at i:11749 original size:29 final size:31
Alignment explanation
Indices: 11687--11757 Score: 101
Period size: 29 Copynumber: 2.3 Consensus size: 31
11677 CTTTAAGGTA
* *
11687 TATTTATTATATTTAATATTTTGTTAGTATTT
1 TATTTAAT-TATTTAATATTTTGTTAATATTT
11719 TATTTAATTATTTAA-ATTTT-TTAATATTT
1 TATTTAATTATTTAATATTTTGTTAATATTT
11748 TATTTAATTA
1 TATTTAATTA
11758 ATTTTTTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 18 0.49
30 5 0.14
31 7 0.19
32 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (31 bp):
TATTTAATTATTTAATATTTTGTTAATATTT
Found at i:18358 original size:43 final size:43
Alignment explanation
Indices: 18304--18512 Score: 162
Period size: 43 Copynumber: 5.0 Consensus size: 43
18294 AGAGAACAAA
**
18304 AAACGCCGCAAATTATCGAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
18347 AGACGCCGCAAAAGGA-CGGGATCTTTAGCGACAG-TTTTGGAAC
1 AAACGCCGCAAAA-GATCGAGATCTATAGCGGC-GTTTTTGGAAC
* * *
18390 AAACGCAGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAAC
* * * * * **
18432 AAATGCGGCAAAATATCGAGAACTACAGCAACGTTTTTCGG-AC
1 AAACGCCGCAAAAGATCGAGATCTATAGCGGCGTTTTT-GGAAC
* * * *
18475 AAATGTCGTAAAAGGTC---ATCTATAGCGGCGTTTTTGGA
1 AAACGCCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGA
18513 TACGAATGCC
Statistics
Matches: 128, Mismatches: 31, Indels: 17
0.73 0.18 0.10
Matches are distributed among these distances:
39 2 0.02
40 14 0.11
41 1 0.01
42 33 0.26
43 74 0.58
44 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:22480 original size:30 final size:32
Alignment explanation
Indices: 22411--22481 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
22401 GAATTTTGAT
*
22411 AAATTTAATTATCATTTTAGAACACTTTGATA
1 AAATTTAATTATCATTTTAGAACACTTGGATA
* *
22443 AATTTTAATTAAT-ATTTTATAA-A-TTGGATA
1 AAATTTAATT-ATCATTTTAGAACACTTGGATA
22473 AAATTTAAT
1 AAATTTAAT
22482 AATTATTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 14 0.41
31 1 0.03
32 17 0.50
33 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (32 bp):
AAATTTAATTATCATTTTAGAACACTTGGATA
Found at i:27333 original size:2 final size:2
Alignment explanation
Indices: 27328--27358 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27318 AAAAATAAAT
27328 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 T
27359 TAAATTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27670 original size:20 final size:20
Alignment explanation
Indices: 27641--27678 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27631 TTTTAAATAT
* *
27641 AATTTTAAAAATATATTTAA
1 AATTTCAAAAATAAATTTAA
27661 AATTTCAAAAATAAATTT
1 AATTTCAAAAATAAATTT
27679 TGAAAATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTCAAAAATAAATTTAA
Found at i:28606 original size:2 final size:2
Alignment explanation
Indices: 28599--28626 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28589 TCAACAATTA
28599 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
28627 TATTTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42755 original size:17 final size:17
Alignment explanation
Indices: 42733--42769 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42723 AACGATCAAC
*
42733 GGTCAACGGTCGGGTTG
1 GGTCAACGGTCGGGTCG
*
42750 GGTCAACGGTTGGGTCG
1 GGTCAACGGTCGGGTCG
42767 GGT
1 GGT
42770 AGGTTGGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:42776 original size:14 final size:14
Alignment explanation
Indices: 42757--42797 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
42747 TTGGGTCAAC
42757 GGTTGGGTCGGGTA
1 GGTTGGGTCGGGTA
*
42771 GGTTGGGTCGGGTT
1 GGTTGGGTCGGGTA
*
42785 GGTCGGGTCGGGT
1 GGTTGGGTCGGGT
42798 CGGGTCAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.02, C:0.10, G:0.59, T:0.29
Consensus pattern (14 bp):
GGTTGGGTCGGGTA
Found at i:42821 original size:9 final size:9
Alignment explanation
Indices: 42809--42879 Score: 61
Period size: 10 Copynumber: 7.3 Consensus size: 9
42799 GGGTCAGACT
42809 GGTCAAACC
1 GGTCAAACC
*
42818 GGTCAAAAC
1 GGTCAAACC
*
42827 GGTTCGAACC
1 GG-TCAAACC
42837 GGTCGAAACC
1 GGTC-AAACC
42847 GGTCAAAACC
1 GGTC-AAACC
* *
42857 AGTTGAAAACC
1 -GGT-CAAACC
42868 GGTCAAACC
1 GGTCAAACC
42877 GGT
1 GGT
42880 TTCCAGCAGC
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 20 0.41
10 22 0.45
11 7 0.14
ACGTcount: A:0.34, C:0.27, G:0.25, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:42856 original size:20 final size:20
Alignment explanation
Indices: 42809--42879 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
42799 GGGTCAGACT
42809 GGTCAAACCGGTC-AAAA-C
1 GGTCAAACCGGTCGAAAACC
*
42827 GGTTCGAACCGGTCG-AAACC
1 GG-TCAAACCGGTCGAAAACC
* *
42847 GGTCAAAACCAGTTGAAAACC
1 GGTC-AAACCGGTCGAAAACC
42868 GGTCAAACCGGT
1 GGTCAAACCGGT
42880 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.05
19 15 0.35
20 17 0.40
21 9 0.21
ACGTcount: A:0.34, C:0.27, G:0.25, T:0.14
Consensus pattern (20 bp):
GGTCAAACCGGTCGAAAACC
Found at i:50589 original size:62 final size:62
Alignment explanation
Indices: 50513--50640 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
50503 ATAATAAAAC
50513 TCAATACATTATATAAAAGAGAAAATGCACGAATAAAAAATGGAAACTCATTTTTCTTGACT
1 TCAATACATTATATAAAAGAGAAAATGCACGAATAAAAAATGGAAACTCATTTTTCTTGACT
50575 TCAATACATTATATAAAAGAGAAAATGCACGAATAAAAAATGGAAACTCATTTTTCTTGACT
1 TCAATACATTATATAAAAGAGAAAATGCACGAATAAAAAATGGAAACTCATTTTTCTTGACT
50637 TCAA
1 TCAA
50641 GTGTGGATAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (62 bp):
TCAATACATTATATAAAAGAGAAAATGCACGAATAAAAAATGGAAACTCATTTTTCTTGACT
Found at i:54393 original size:15 final size:15
Alignment explanation
Indices: 54373--54422 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
54363 TACACCAAAT
54373 AAATTTATAGTATAA
1 AAATTTATAGTATAA
* *
54388 AAATTTCA-ACTA-AT
1 AAATTT-ATAGTATAA
*
54402 AAATCTATAGTATAA
1 AAATTTATAGTATAA
54417 AAATTT
1 AAATTT
54423 CAACTACTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.35
15 15 0.58
16 1 0.04
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (15 bp):
AAATTTATAGTATAA
Found at i:54403 original size:29 final size:29
Alignment explanation
Indices: 54370--54433 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
54360 GCATACACCA
*
54370 AATAAATTTATAGTATAAAAATTTCAACT
1 AATAAATCTATAGTATAAAAATTTCAACT
54399 AATAAATCTATAGTATAAAAATTTCAACT
1 AATAAATCTATAGTATAAAAATTTCAACT
*
54428 ACTAAA
1 AATAAA
54434 CAAACAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (29 bp):
AATAAATCTATAGTATAAAAATTTCAACT
Found at i:56744 original size:24 final size:24
Alignment explanation
Indices: 56717--56780 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
56707 ATCATAACAT
56717 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
56741 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
56765 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
56781 TATAATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:60533 original size:18 final size:18
Alignment explanation
Indices: 60496--60569 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 18
60486 CGGTCAACGA
* *
60496 GTCGGGTCAACAGATCGG
1 GTCGGGTCAACGGGTCGG
60514 GTCGGGTCAACGGGT---
1 GTCGGGTCAACGGGTCGG
*
60529 -T-GGGTTAACGGGTCGG
1 GTCGGGTCAACGGGTCGG
** *
60545 GTCAAGTCAACGGGTTGG
1 GTCGGGTCAACGGGTCGG
60563 GTCGGGT
1 GTCGGGT
60570 TGTGACCGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
17 1 0.02
18 29 0.69
ACGTcount: A:0.16, C:0.18, G:0.45, T:0.22
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCGG
Found at i:60545 original size:31 final size:31
Alignment explanation
Indices: 60487--60565 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
60477 GCCAGTCAAC
* * *
60487 GGTCAACGAGTCGGGTCAACAGATCGGGTCG
1 GGTCAACGGGTTGGGTCAACAGATCGGGTCA
* * *
60518 GGTCAACGGGTTGGGTTAACGGGTCGGGTCA
1 GGTCAACGGGTTGGGTCAACAGATCGGGTCA
*
60549 AGTCAACGGGTTGGGTC
1 GGTCAACGGGTTGGGTC
60566 GGGTTGTGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.20
Consensus pattern (31 bp):
GGTCAACGGGTTGGGTCAACAGATCGGGTCA
Found at i:65253 original size:20 final size:19
Alignment explanation
Indices: 65207--65255 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
65197 ATGACCAACA
* * *
65207 AATTCGCAACGCAATCTCG
1 AATTCGCAACGCAAACACC
65226 AATTCGCAACGCAAACACC
1 AATTCGCAACGCAAACACC
65245 AATTTCGCAAC
1 AA-TTCGCAAC
65256 ACAGTTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.18
Consensus pattern (19 bp):
AATTCGCAACGCAAACACC
Found at i:65266 original size:20 final size:20
Alignment explanation
Indices: 65243--65282 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
65233 AACGCAAACA
*
65243 CCAATTTCGCAACACAGTTT
1 CCAAATTCGCAACACAGTTT
* *
65263 CCAAATTCGTAACTCAGTTT
1 CCAAATTCGCAACACAGTTT
65283 TTGCAATCGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (20 bp):
CCAAATTCGCAACACAGTTT
Found at i:65364 original size:20 final size:20
Alignment explanation
Indices: 65328--65414 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
65318 AAGTTTCCTT
* *
65328 TTCGCAACAAGATTTTTTAA
1 TTCGCAACACGAATTTTTAA
* *
65348 ATCGCAACACGAA-TTTTATT
1 TTCGCAACACGAATTTTTA-A
* *
65368 TTCGCAACTCG-ATTTTCGAA
1 TTCGCAACACGAATTTT-TAA
65388 TTCGCAACACGAA-TTTTAA
1 TTCGCAACACGAATTTTTAA
65407 TTTCGCAA
1 -TTCGCAA
65415 TAGCTTTTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
19 8 0.15
20 42 0.81
21 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (20 bp):
TTCGCAACACGAATTTTTAA
Found at i:65382 original size:40 final size:40
Alignment explanation
Indices: 65309--65414 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
65299 AATTTCTTTT
** **
65309 TCGCAACAC-AAGTTTCCTTTTCGCAACAAGATTTTTTAAA
1 TCGCAACACGAA-TTTTATTTTCGCAACAAGATTTTCGAAA
** *
65349 TCGCAACACGAATTTTATTTTCGCAACTCGATTTTCGAAT
1 TCGCAACACGAATTTTATTTTCGCAACAAGATTTTCGAAA
*
65389 TCGCAACACGAATTTTAATTTCGCAA
1 TCGCAACACGAATTTTATTTTCGCAA
65415 TAGCTTTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 55 0.96
41 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (40 bp):
TCGCAACACGAATTTTATTTTCGCAACAAGATTTTCGAAA
Found at i:66372 original size:24 final size:24
Alignment explanation
Indices: 66345--66398 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
66335 GTATTCGAAA
66345 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
66369 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
66393 TTTGAT
1 TTTGAT
66399 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:68975 original size:20 final size:20
Alignment explanation
Indices: 68932--68996 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
68922 TGCGATTGTT
* **
68932 GCGAAAGTCAAATTCAAAAC
1 GCGAAAGTAAAATTCGCAAC
*
68952 GCGAAAGTAAAATTCGCAAT
1 GCGAAAGTAAAATTCGCAAC
*
68972 GCGAAAATCAAAA-TCGCAAC
1 GCGAAAGT-AAAATTCGCAAC
68992 GCGAA
1 GCGAA
68997 TTTGACTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 34 0.89
21 4 0.11
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (20 bp):
GCGAAAGTAAAATTCGCAAC
Found at i:69108 original size:16 final size:16
Alignment explanation
Indices: 69087--69121 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
69077 CAGATTGTCG
* *
69087 ATTAAACAACAAATCA
1 ATTAAACAAAAAAACA
69103 ATTAAACAAAAAAACA
1 ATTAAACAAAAAAACA
69119 ATT
1 ATT
69122 CTTATTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (16 bp):
ATTAAACAAAAAAACA
Found at i:69575 original size:19 final size:19
Alignment explanation
Indices: 69553--69594 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
69543 ACGTTCCAAG
69553 CACATGCATACAAGAGGAC
1 CACATGCATACAAGAGGAC
69572 CACATGCATACAAGAGGAC
1 CACATGCATACAAGAGGAC
69591 CACA
1 CACA
69595 ATCCCCTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.29, G:0.19, T:0.10
Consensus pattern (19 bp):
CACATGCATACAAGAGGAC
Found at i:70553 original size:21 final size:21
Alignment explanation
Indices: 70542--70624 Score: 130
Period size: 21 Copynumber: 4.0 Consensus size: 21
70532 TTGAATGGTG
70542 GGAGGGGCCTCTTGAACGATA
1 GGAGGGGCCTCTTGAACGATA
* *
70563 AGAGGGGCCTCTTGAACGATG
1 GGAGGGGCCTCTTGAACGATA
*
70584 GGAGGGGCCTATTGAACGATA
1 GGAGGGGCCTCTTGAACGATA
*
70605 GGAGGAGCCTCTTGAACGAT
1 GGAGGGGCCTCTTGAACGAT
70625 GTTAGGTGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.19
Consensus pattern (21 bp):
GGAGGGGCCTCTTGAACGATA
Found at i:70588 original size:42 final size:42
Alignment explanation
Indices: 70529--70625 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
70519 ATGAATCGGG
* * * *
70529 CTCTTGAATGGTGGGAGGGGCCTCTTGAACGATAAGAGGGGC
1 CTCTTGAACGATGGGAGGGGCCTATTGAACGATAAGAGGAGC
*
70571 CTCTTGAACGATGGGAGGGGCCTATTGAACGATAGGAGGAGC
1 CTCTTGAACGATGGGAGGGGCCTATTGAACGATAAGAGGAGC
70613 CTCTTGAACGATG
1 CTCTTGAACGATG
70626 TTAGGTGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATGGGAGGGGCCTATTGAACGATAAGAGGAGC
Found at i:71072 original size:21 final size:21
Alignment explanation
Indices: 71046--71095 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
71036 ACCATTGTCG
*
71046 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
71067 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
71088 TCTCGTAA
1 TCACGTAA
71096 CTCGCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:72749 original size:19 final size:19
Alignment explanation
Indices: 72725--72782 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
72715 AAACTTAAAT
*
72725 TCGCAACACGAAAATGAAA
1 TCGCAACGCGAAAATGAAA
72744 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATG-AAA
**
72764 TCTTAACGCGAAAATGAAA
1 TCGCAACGCGAAAATGAAA
72783 ATTGCAATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAAATGAAA
Found at i:72783 original size:20 final size:20
Alignment explanation
Indices: 72725--72789 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
72715 AAACTTAAAT
*
72725 TCGCAACACGAAAATG-AAA
1 TCGCAACGCGAAAATGAAAA
72744 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
**
72764 TCTTAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
72784 TTGCAA
1 TCGCAA
72790 TGCAAAACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 15 0.38
20 24 0.62
ACGTcount: A:0.49, C:0.18, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:73363 original size:19 final size:20
Alignment explanation
Indices: 73341--73379 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
73331 TAATATTGTG
*
73341 TTTCGAATT-TGAAAATAAA
1 TTTCGAATTGCGAAAATAAA
*
73360 TTTCGCATTGCGAAAATAAA
1 TTTCGAATTGCGAAAATAAA
73380 CGCGCTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
TTTCGAATTGCGAAAATAAA
Done.