Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000210.1 Hibiscus syriacus cultivar Beakdansim tig00000373_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: 48984
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1431 original size:15 final size:14
Alignment explanation
Indices: 1382--1447 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 14
1372 CCTCATTTTT
1382 TTTTAATTTCTTAGA
1 TTTTAATTT-TTAGA
* *
1397 TTTTTTATTTTTATCCA
1 -TTTTAATTTTTA--GA
1414 TTTTAATTTCTTAGA
1 TTTTAATTT-TTAGA
1429 TTTCTAATTTTTAGA
1 TTT-TAATTTTTAGA
1444 TTTT
1 TTTT
1448 TTTAATCTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.02
15 15 0.36
16 22 0.52
17 4 0.10
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.65
Consensus pattern (14 bp):
TTTTAATTTTTAGA
Found at i:1624 original size:2 final size:2
Alignment explanation
Indices: 1612--1655 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1602 TTGATAAAAC
1612 TA TA TA T- 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
1653 TA T
1 TA T
1656 GTTAATTTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2335 original size:10 final size:9
Alignment explanation
Indices: 2305--2341 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2295 AATATTTAAA
2305 AAATA-AAT
1 AAATATAAT
*
2313 AAACATAAT
1 AAATATAAT
2322 AAATATAAT
1 AAATATAAT
2331 AAA-ATAAT
1 AAATATAAT
2339 AAA
1 AAA
2342 AATGAAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 12 0.46
9 14 0.54
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATATAAT
Found at i:2337 original size:17 final size:17
Alignment explanation
Indices: 2305--2341 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2295 AATATTTAAA
2305 AAATAAATAAACATAAT
1 AAATAAATAAACATAAT
2322 AAATATAATAAA-ATAAT
1 AAATA-AATAAACATAAT
2339 AAA
1 AAA
2342 AATGAAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAACATAAT
Found at i:2628 original size:2 final size:2
Alignment explanation
Indices: 2621--2671 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2611 AAATAAATGA
2621 AT AT AT AT AT AT AT AT AT AT AT AT -T 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
2662 AT AT AT AT AT
1 AT AT AT AT AT
2672 TATGACTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4014 original size:23 final size:23
Alignment explanation
Indices: 3988--4040 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
3978 CTGGACTGGG
*
3988 TTGGGCCTCCGGG-TCTGATGTAA
1 TTGGGCCTCCGGGAT-TAATGTAA
*
4011 TTGGG-CTCCGGGATTAATGTAT
1 TTGGGCCTCCGGGATTAATGTAA
4033 TTGGGCCT
1 TTGGGCCT
4041 GTATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.13, C:0.19, G:0.34, T:0.34
Consensus pattern (23 bp):
TTGGGCCTCCGGGATTAATGTAA
Found at i:4060 original size:3 final size:3
Alignment explanation
Indices: 4052--4102 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
4042 TATTTTTATT
4052 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4099 TAA T
1 TAA T
4103 GGAAAAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4169 original size:14 final size:14
Alignment explanation
Indices: 4150--4179 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4140 TTCTTGTGTT
4150 AACAAGAATAGAGC
1 AACAAGAATAGAGC
4164 AACAAGAATAGAGC
1 AACAAGAATAGAGC
4178 AA
1 AA
4180 AGACGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.13, G:0.20, T:0.07
Consensus pattern (14 bp):
AACAAGAATAGAGC
Found at i:4549 original size:46 final size:45
Alignment explanation
Indices: 4278--4741 Score: 757
Period size: 45 Copynumber: 10.2 Consensus size: 45
4268 GCTCAGAAGA
**
4278 CTTACAGATGACCCGAAGACTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
4323 CTTACAGATGACCCGAAGGTTTTGAAAACATCCTGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
4368 CTTACAGATGACCCGAAGGTTTTGATAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
4413 CTTATAGATGATCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
4458 CTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGTAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
4503 CTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCATTGAAGGT
1 CTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGT
*
4549 CTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTAAAGGT
1 CTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGT
*
4595 CTTACAGATGACCCAAAGGTTTTCGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTT-GAAAACATCATGCACTGAAGGT
4641 CTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGT
* * *
4687 CTTACAAATAACCCCAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
4732 ATTACAGATG
1 CTTACAGATG
4742 TGGGAAATAG
Statistics
Matches: 390, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
45 223 0.57
46 163 0.42
47 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (45 bp):
CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
Found at i:5468 original size:22 final size:22
Alignment explanation
Indices: 5426--5468 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5416 TTGAAAAGCG
5426 AATCTATCATCTTTGAAGAATA
1 AATCTATCATCTTTGAAGAATA
5448 AATCTATCATCTTTGAAGAAT
1 AATCTATCATCTTTGAAGAAT
5469 GTAGATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAATA
Found at i:5909 original size:54 final size:53
Alignment explanation
Indices: 5827--5980 Score: 227
Period size: 54 Copynumber: 2.9 Consensus size: 53
5817 AAAATCGTTG
*
5827 GTTCGTAAAACACTTGACAACACATTCATCATTTCTTGTGGCTTCTACATAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTAC-TAGAT
** *
5881 GTTCGTAAAACATTTGACAACACATTCATTTTTTCTTATGGCTTCTTACTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTC-TACTAGAT
* * *
5935 GTTCGTAAAATATTTGACAACCCATTCATCCTTTCTTGTGGCTTCT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCT
5981 GCCAAGATTT
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 86 0.96
55 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTACTAGAT
Found at i:14231 original size:152 final size:146
Alignment explanation
Indices: 13900--14272 Score: 380
Period size: 152 Copynumber: 2.5 Consensus size: 146
13890 AATTAAAGTA
** * * * * *
13900 TTTATTTATTAAAAATATTAGAAAATGACATCTAGTTGCTTTAAGACATCCCATTTCTTTAATAT
1 TTTATTT-TTAAAAATACCAGAATAGGACATCTAGTTGCATTAAGACAACCCCTTTCTTTAATAT
* *
13965 TAAAAAATAAATAAACATTAATAAGAATATAATAAAATAATAAAAATGAAGTAAATATATGTTTT
65 TAAAAAATAAATAAACATAAAAAAGAATATAATAAAATAATAAAAATGAAGTAAATATATGTTTT
*
14030 TATAAACATGATATTTG
130 TATAAACATGATATTCG
* *
14047 TTTATTTTTTAAAATACCAGAATAGGACATCTAGTTGCGTTAAGACAACCCCTTTCTTTAATATT
1 TTTATTTTTAAAAATACCAGAATAGGACATCTAGTTGCATTAAGACAACCCCTTTCTTTAATATT
* * * * *
14112 AAAAAATAAGATAATTTTACCTAAAAAATAATTTAAATAAAACTAA-AAAATAT-ATA-TATATT
66 AAAAAATAA-ATAA----ACATAAAAAAGAATAT-AATAAAA-TAATAAAA-ATGA-AGTAAATA
* *
14174 TTTGTTTTTATAAGCA-GAATATTCG
122 TATGTTTTTATAAACATG-ATATTCG
* ** * *
14199 TTTATTTTTAAAAATACCAGAATAGGATATCTAGTTATATTATGACTA-CCCTTTC-TTAATATT
1 TTTATTTTTAAAAATACCAGAATAGGACATCTAGTTGCATTAAGACAACCCCTTTCTTTAATATT
*
14262 TAAAAATAAAT
66 AAAAAATAAAT
14273 GAATATTATT
Statistics
Matches: 190, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
146 59 0.31
147 11 0.06
149 2 0.01
150 16 0.08
151 19 0.10
152 77 0.41
153 6 0.03
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.39
Consensus pattern (146 bp):
TTTATTTTTAAAAATACCAGAATAGGACATCTAGTTGCATTAAGACAACCCCTTTCTTTAATATT
AAAAAATAAATAAACATAAAAAAGAATATAATAAAATAATAAAAATGAAGTAAATATATGTTTTT
ATAAACATGATATTCG
Found at i:14296 original size:2 final size:2
Alignment explanation
Indices: 14289--14342 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
14279 TATTATTTAA
14289 AT AT AT 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
14331 AT AT AT AT AT AT
1 AT AT AT AT AT AT
14343 TTATGACTAA
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):
AT
Found at i:15808 original size:2 final size:2
Alignment explanation
Indices: 15803--15831 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15793 TTATTTAATA
15803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15832 AATGGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16578 original size:19 final size:19
Alignment explanation
Indices: 16556--16644 Score: 103
Period size: 19 Copynumber: 4.6 Consensus size: 19
16546 TGGAGTGCAA
16556 GCTGGGGTGGGGTGGGCAG
1 GCTGGGGTGGGGTGGGCAG
16575 GCTGGGGTGGGGTGGGCAG
1 GCTGGGGTGGGGTGGGCAG
16594 GCTGGGGCTGGGGCT-GG--G
1 GCTGGGG-TGGGG-TGGGCAG
* *
16612 GCTGCGGTTGAGGTGGGCAG
1 GCTG-GGGTGGGGTGGGCAG
16632 GCTGGGGTTGGGG
1 GCTGGGG-TGGGG
16645 CATGTAGACA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
17 1 0.02
18 11 0.19
19 30 0.51
20 16 0.27
21 1 0.02
ACGTcount: A:0.04, C:0.12, G:0.65, T:0.18
Consensus pattern (19 bp):
GCTGGGGTGGGGTGGGCAG
Found at i:16826 original size:31 final size:29
Alignment explanation
Indices: 16791--16850 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
16781 ATACAATAGA
*
16791 TTAAAAGATAAAAAATGAATATATAATATCT
1 TTAAAA-ATAAAAAATCAA-ATATAATATCT
* *
16822 TTAAAATTAAAAATTCAAATATAATATCT
1 TTAAAAATAAAAAATCAAATATAATATCT
16851 GAATAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 9 0.35
31 6 0.23
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (29 bp):
TTAAAAATAAAAAATCAAATATAATATCT
Found at i:17565 original size:2 final size:2
Alignment explanation
Indices: 17558--17603 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
17548 CTCCCCCTCC
17558 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17600 CT CT
1 CT CT
17604 ATATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18657 original size:14 final size:14
Alignment explanation
Indices: 18638--18666 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18628 CAACCAAAAC
18638 GATCATTTTAGTAA
1 GATCATTTTAGTAA
18652 GATCATTTTAGTAA
1 GATCATTTTAGTAA
18666 G
1 G
18667 TGTTGAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (14 bp):
GATCATTTTAGTAA
Found at i:22640 original size:19 final size:20
Alignment explanation
Indices: 22616--22666 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
22606 AATGACCAAT
22616 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
22635 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
22655 AAAATCGCAACG
1 AAAATCGCAACG
22667 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:22660 original size:20 final size:20
Alignment explanation
Indices: 22616--22893 Score: 162
Period size: 20 Copynumber: 13.6 Consensus size: 20
22606 AATGACCAAT
* *
22616 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
22635 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
22655 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
** ***
22675 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
* **
22695 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
22716 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* *
22739 AAAATCGCAACGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
22759 AGAATCGCAATGCGATTAAT
1 AAAATCGCAACGCGATTTAG
* * *
22779 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
22799 AGATTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
22822 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
22842 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
22862 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
22882 AAAATCGCAACG
1 AAAATCGCAACG
22894 TTAAAAAGAA
Statistics
Matches: 210, Mismatches: 41, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
19 17 0.08
20 150 0.71
21 13 0.06
23 30 0.14
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:22828 original size:63 final size:63
Alignment explanation
Indices: 22741--22883 Score: 204
Period size: 63 Copynumber: 2.3 Consensus size: 63
22731 TTTAGAAGAA
* * *
22741 AATCGCAACGCGA-TT-GATAG--AATCGCAATGCGATTAATAGAATCGCAATGCGATTGAGAG
1 AATCGCAACGCGATTTAGA-AGAAAATCGCAATGCGACTAAGAGAATCGCAATGCGACTGAGAG
* *
22801 ATTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTAAGAGAATCGCAATGCGACTGAGAG
22864 AATCGCAACGCGATTTAGAA
1 AATCGCAACGCGATTTAGAA
22884 AATCGCAACG
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
60 12 0.16
61 4 0.05
62 2 0.03
63 55 0.75
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (63 bp):
AATCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTAAGAGAATCGCAATGCGACTGAGAG
Found at i:22831 original size:83 final size:83
Alignment explanation
Indices: 22719--22893 Score: 260
Period size: 83 Copynumber: 2.1 Consensus size: 83
22709 AGCTTCCAAG
* * * *
22719 TTCGCAACGCGATTTAGAAGAAAATCGCAACGCGATTGATAGAATCGCAATGCGATTAATAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAACGCGACTGAGAGAATCGCAATGCGACTAAGAGAAT
* *
22784 CGCAATGCGATTGAGAGA
66 CGCAACGCGATTGAGAAA
* *
22802 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAACGCGACTGAGAGAATCGCAATGCGACTAAGAGAAT
*
22867 CGCAACGCGATTTAGAAA
66 CGCAACGCGATTGAGAAA
*
22885 ATCGCAACG
1 TTCGCAACG
22894 TTAAAAAGAA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (83 bp):
TTCGCAACGCGATTTAGAAGAAAATCGCAACGCGACTGAGAGAATCGCAATGCGACTAAGAGAAT
CGCAACGCGATTGAGAAA
Found at i:22992 original size:6 final size:6
Alignment explanation
Indices: 22981--23055 Score: 108
Period size: 6 Copynumber: 13.5 Consensus size: 6
22971 GACACGTATT
22981 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
23028 ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
23056 CGAGACGAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 30 0.43
6 39 0.57
ACGTcount: A:0.28, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:23772 original size:6 final size:6
Alignment explanation
Indices: 23761--23811 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
23751 GGGTCGGGTC
23761 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
23809 GGT
1 GGT
23812 AATTCACTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:24307 original size:38 final size:38
Alignment explanation
Indices: 24265--24363 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 38
24255 ATAACATTAT
* * *
24265 GAAAGATAAGGTTGAGGTTTCTAG-GAAAATGATCTTAA
1 GAAAGATAAGATTGAGGTTTCTAGAG-AAACGATCATAA
* *
24303 GAAAGAATAA-ATTGAGGTTTATAGAGAAACGATCATGA
1 GAAAG-ATAAGATTGAGGTTTCTAGAGAAACGATCATAA
*
24341 GAAAGATTAAGAATGAGGTTTCT
1 GAAAGA-TAAGATTGAGGTTTCT
24364 TGGGGAACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
37 1 0.02
38 34 0.68
39 15 0.30
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.27
Consensus pattern (38 bp):
GAAAGATAAGATTGAGGTTTCTAGAGAAACGATCATAA
Found at i:27429 original size:18 final size:18
Alignment explanation
Indices: 27390--27431 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
27380 AGAAAGGAAG
*
27390 AACAAAAAAACAAGTTCA
1 AACAAAAAAACAAGTGCA
*
27408 AACAAAAAATGCAAGTGC-
1 AACAAAAAA-ACAAGTGCA
27426 AACAAA
1 AACAAA
27432 GCTTCATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.64, C:0.17, G:0.10, T:0.10
Consensus pattern (18 bp):
AACAAAAAAACAAGTGCA
Found at i:32892 original size:41 final size:42
Alignment explanation
Indices: 32776--32894 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 42
32766 GTTGCGACAT
*
32776 AGTAGTATTTTAGCGGTGTTTTTATACAAATG-C-TGCAATAG
1 AGTAGTACTTTAGCGGTGTTTTTATACAAATGTCATG-AATAG
* * * * * *
32817 GGTTAAT-CTATAGTGGCGTTTTT-TCAATAAATGTCATG-ATAG
1 AG-TAGTACTTTAGCGGTGTTTTTAT--ACAAATGTCATGAATAG
32859 AGTAGTACTTTAGCGGTGTTTTTATACAAATGTCAT
1 AGTAGTACTTTAGCGGTGTTTTTATACAAATGTCAT
32895 AGTATGATTT
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
40 1 0.02
41 26 0.45
42 27 0.47
43 2 0.03
44 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (42 bp):
AGTAGTACTTTAGCGGTGTTTTTATACAAATGTCATGAATAG
Found at i:32941 original size:83 final size:83
Alignment explanation
Indices: 32776--33063 Score: 237
Period size: 83 Copynumber: 3.5 Consensus size: 83
32766 GTTGCGACAT
* *
32776 AGTAGTATTTTAGCGGTGTTTTTATACAAATGCTGCAATAGGGTTAATCTATAGTGGCGTTTTTT
1 AGTAGTACTTTAGCGGTGTTTTTATACAAATGCTGCAATAGGATTAATCTATAGTGGCGTTTTTT
*** *
32841 CAATAAATGTCATGATAG
66 CAATAAACACCACGATAG
* * *
32859 AGTAGTACTTTAGCGGTGTTTTTATACAAATG-T-CATAGTATGATTTATCTATAGTGGTGTTTT
1 AGTAGTACTTTAGCGGTGTTTTTATACAAATGCTGCA-A-TAGGATTAATCTATAGTGGCGTTTT
*
32922 TTCAATAAACACCGCGATAG
64 TTCAATAAACACCACGATAG
* * *** ** * * *
32942 AGTAGTACCTTAACGACATTTTTATACAAACT-CCACAATAAGG-TTCATCCATAGTGGC-ATTT
1 AGTAGTACTTTAGCGGTGTTTTTATACAAA-TGCTGCAAT-AGGATTAATCTATAGTGGCGTTTT
* * * *
33004 TTCAACAAACGCCGCGACAG
64 TTCAATAAACACCACGATAG
* ** * *
33024 AGTAGTACGTTAGCGGCATTTTT-TACAAACGCCGCAATAG
1 AGTAGTACTTTAGCGGTGTTTTTATACAAATGCTGCAATAG
33064 TTTGATATGT
Statistics
Matches: 169, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
80 2 0.01
81 14 0.08
82 42 0.25
83 105 0.62
84 4 0.02
85 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (83 bp):
AGTAGTACTTTAGCGGTGTTTTTATACAAATGCTGCAATAGGATTAATCTATAGTGGCGTTTTTT
CAATAAACACCACGATAG
Found at i:33809 original size:18 final size:18
Alignment explanation
Indices: 33771--33811 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
33761 ATTTTTGTTC
***
33771 ATGATTTCGTGTATTTTA
1 ATGATTTCGTGTATGAAA
33789 ATGATTTCGTGTATGAAA
1 ATGATTTCGTGTATGAAA
33807 ATGAT
1 ATGAT
33812 ACTCCAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (18 bp):
ATGATTTCGTGTATGAAA
Found at i:34478 original size:13 final size:13
Alignment explanation
Indices: 34460--34506 Score: 94
Period size: 13 Copynumber: 3.6 Consensus size: 13
34450 CTTTGGTATA
34460 TGATCCTTGAATG
1 TGATCCTTGAATG
34473 TGATCCTTGAATG
1 TGATCCTTGAATG
34486 TGATCCTTGAATG
1 TGATCCTTGAATG
34499 TGATCCTT
1 TGATCCTT
34507 TTAAATGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (13 bp):
TGATCCTTGAATG
Found at i:35547 original size:42 final size:42
Alignment explanation
Indices: 35478--35807 Score: 331
Period size: 43 Copynumber: 7.8 Consensus size: 42
35468 TAATTAACGA
* *
35478 CGTTTGTATCAAAAAACGCTGCTATAGATCTTACCTTTTGCGG
1 CGTTTGT-TCCAAAAACGCCGCTATAGATCTTACCTTTTGCGG
* * * *
35521 CGCTTGTTCCAAAAGCGTCGCTATAGATCTGACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTTACCTTTTGCGG
* * * * * *
35563 TGTTTCTT-CAGGAAACGTCGCTATAGATCTGACCTTTTGCGA
1 CGTTTGTTCCA-AAAACGCCGCTATAGATCTTACCTTTTGCGG
* * *
35605 CGTTTGTTCCAAAAACGTCGCTATAGATCTTGATCTTTTGTGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTT-ACCTTTTGCGG
* * * *
35648 CATTTGTTTCAAAAATGCCGCTATAGATATTGACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTT-ACCTTTTGCGG
* * * * * * *
35691 CGTTTGTTCTAAAAATGCCGCTATAAATATCAACCTTTTACGA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCT-TACCTTTTGCGG
35734 CGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTT-ACCTTTTGCGG
* * *
35777 TGTTTGTTCC-GAAACGCCACTATAGATCTTA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTTA
35808 ACTATTGTGG
Statistics
Matches: 239, Mismatches: 43, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
41 3 0.01
42 105 0.44
43 131 0.55
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (42 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCTTACCTTTTGCGG
Found at i:37226 original size:20 final size:20
Alignment explanation
Indices: 37203--37290 Score: 115
Period size: 20 Copynumber: 4.3 Consensus size: 20
37193 GAATATGTAA
37203 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
37223 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
37243 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
37264 ATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
37284 GTCGCAA
1 ATCGCAA
37291 TGCTGAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.03
20 40 0.68
21 15 0.25
22 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:38163 original size:24 final size:24
Alignment explanation
Indices: 38112--38165 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
38102 GTATTCGAAA
*
38112 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
38136 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
38160 TTTGAT
1 TTTGAT
38166 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:38513 original size:20 final size:19
Alignment explanation
Indices: 38490--38535 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
38480 GGAAACTGAT
* *
38490 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
38510 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
38529 TTGCGAT
1 TTGCGAT
38536 TTTGTTAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:38525 original size:19 final size:19
Alignment explanation
Indices: 38501--38537 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
38491 TGCGATACTG
*
38501 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
38520 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
38538 TGTTAATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:46597 original size:19 final size:19
Alignment explanation
Indices: 46565--46607 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
46555 ATGGAGAGAG
46565 AAAAGTAAAAAAAGGAAAT
1 AAAAGTAAAAAAAGGAAAT
46584 AAAA-TAAAAGAAAGGAAAT
1 AAAAGTAAAA-AAAGGAAAT
*
46603 CAAAG
1 AAAAG
46608 AATTTTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAAGTAAAAAAAGGAAAT
Found at i:48515 original size:15 final size:15
Alignment explanation
Indices: 48495--48523 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48485 CATCACACAT
48495 TAGCTCAAATGGTGC
1 TAGCTCAAATGGTGC
48510 TAGCTCAAATGGTG
1 TAGCTCAAATGGTG
48524 ATGTCCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (15 bp):
TAGCTCAAATGGTGC
Done.