Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003231.1 Hibiscus syriacus cultivar Beakdansim tig00006801_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: 64097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:774 original size:20 final size:21
Alignment explanation
Indices: 751--790 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
741 ATATAGTAAC
751 TAAACTATCA-ATTTAGTACT
1 TAAACTATCAGATTTAGTACT
* *
771 TAAATTATCAGTTTTAGTAC
1 TAAACTATCAGATTTAGTAC
791 GTATTTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
TAAACTATCAGATTTAGTACT
Found at i:808 original size:32 final size:32
Alignment explanation
Indices: 761--822 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
751 TAAACTATCA
** *
761 ATTTAGTACTTAAATTATCAGTTTTAGTACGT
1 ATTTAGTACACAAATTATCAATTTTAGTACGT
793 ATTTAGTACACAAATTATCAATTTTAGTAC
1 ATTTAGTACACAAATTATCAATTTTAGTAC
823 TTAAATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (32 bp):
ATTTAGTACACAAATTATCAATTTTAGTACGT
Found at i:828 original size:53 final size:52
Alignment explanation
Indices: 739--838 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
729 AATCATTTTT
739 GTATATAGTAACTAAACTATCAATTTAGTACTTAAATTATCAGTTTTAGTAC
1 GTATATAGTAACTAAACTATCAATTTAGTACTTAAATTATCAGTTTTAGTAC
* * * *
791 GTATTTAGTACAC-AAATTATCAATTTTAGTACTTAAATTTTCATTTTT
1 GTATATAGTA-ACTAAACTATCAA-TTTAGTACTTAAATTATCAGTTTT
839 TCCAAAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 18 0.43
53 24 0.57
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (52 bp):
GTATATAGTAACTAAACTATCAATTTAGTACTTAAATTATCAGTTTTAGTAC
Found at i:1656 original size:29 final size:31
Alignment explanation
Indices: 1588--1664 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1578 TAAAATGTTA
* * * *
1588 TTTGGTCGAAATAAGTATCTAAACTTATCTT
1 TTTGGTCAAAATAGGTAACTAAACGTATCTT
1619 TTTGGTCAAAATAGGTAACTAAA-GTAT-TT
1 TTTGGTCAAAATAGGTAACTAAACGTATCTT
1648 TTTGGTCAAAATAGGTA
1 TTTGGTCAAAATAGGTA
1665 TCTAGATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 19 0.45
30 3 0.07
31 20 0.48
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (31 bp):
TTTGGTCAAAATAGGTAACTAAACGTATCTT
Found at i:1675 original size:29 final size:29
Alignment explanation
Indices: 1588--1675 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
1578 TAAAATGTTA
* *
1588 TTTGGTCGAAATAAGTATCTAAACTTATCTT
1 TTTGGTCAAAATAGGTATCTAAA-TTAT-TT
* *
1619 TTTGGTCAAAATAGGTAACTAAAGTATTT
1 TTTGGTCAAAATAGGTATCTAAATTATTT
*
1648 TTTGGTCAAAATAGGTATCTAGATTATT
1 TTTGGTCAAAATAGGTATCTAAATTATT
1676 CAATTTCTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 27 0.54
30 3 0.06
31 20 0.40
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTGGTCAAAATAGGTATCTAAATTATTT
Found at i:5136 original size:21 final size:21
Alignment explanation
Indices: 5103--5142 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5093 TATATTGTAT
* *
5103 TTAATGCATGATATTACATAG
1 TTAATGCAGGATATCACATAG
*
5124 TTAATGTAGGATATCACAT
1 TTAATGCAGGATATCACAT
5143 TACATTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
TTAATGCAGGATATCACATAG
Found at i:15705 original size:42 final size:41
Alignment explanation
Indices: 15628--15740 Score: 140
Period size: 42 Copynumber: 2.8 Consensus size: 41
15618 AATAACCAAC
* * *
15628 AAATTCGCAACGTGA-TCT-CAAATTCGCAACACAGTTTCC
1 AAATTCGCAACGCGATTTTCCAAATTCGCAACACAGTTTCA
* * *
15667 AAATTCGCAACGCGAATTTTCCAGATTCGCAACTCAGTTTTA
1 AAATTCGCAACGCG-ATTTTCCAAATTCGCAACACAGTTTCA
*
15709 AAATTCGCAACGCGATTTTCCAAATCCGCAAC
1 AAATTCGCAACGCGATTTTCCAAATTCGCAAC
15741 GCGATTTTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 13 0.21
40 1 0.02
41 18 0.29
42 31 0.49
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (41 bp):
AAATTCGCAACGCGATTTTCCAAATTCGCAACACAGTTTCA
Found at i:15738 original size:21 final size:21
Alignment explanation
Indices: 15627--15822 Score: 122
Period size: 20 Copynumber: 9.7 Consensus size: 21
15617 AAATAACCAA
* *
15627 CAAATTCGCAACGTGA-TCT-
1 CAAATTCGCAACGCGATTTTC
* *
15646 CAAATTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGATTTTC
15666 CAAATTCGCAACGCGAATTTTC
1 CAAATTCGCAACGCG-ATTTTC
* *
15688 CAGATTCGCAACTC-AGTTTT-
1 CAAATTCGCAACGCGA-TTTTC
*
15708 AAAATTCGCAACGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
*
15729 CAAATCCGCAACGCGATTTT-
1 CAAATTCGCAACGCGATTTTC
* * * ** *
15749 CTAATTCGCGATGTTA-ATTC
1 CAAATTCGCAACGCGATTTTC
* * * *
15769 CGAATTCGCGACGCTA-ATTC
1 CAAATTCGCAACGCGATTTTC
*
15789 CTAATTCGCAACGCGATTTT-
1 CAAATTCGCAACGCGATTTTC
* *
15809 CTAATTCGCGACGC
1 CAAATTCGCAACGC
15823 TAATTCCTAA
Statistics
Matches: 141, Mismatches: 27, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.01
19 16 0.11
20 82 0.58
21 25 0.18
22 17 0.12
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:15776 original size:20 final size:20
Alignment explanation
Indices: 15751--15879 Score: 114
Period size: 20 Copynumber: 6.5 Consensus size: 20
15741 GCGATTTTCT
* *
15751 AATTCGCGATGTTAATTCCG
1 AATTCGCGACGCTAATTCCG
*
15771 AATTCGCGACGCTAATTCCT
1 AATTCGCGACGCTAATTCCG
* * * * *
15791 AATTCGCAACGCGATTTTCT
1 AATTCGCGACGCTAATTCCG
*
15811 AATTCGCGACGCTAATTCCT
1 AATTCGCGACGCTAATTCCG
* * *
15831 AATCCGTGACGCTAAATCCG
1 AATTCGCGACGCTAATTCCG
** * *
15851 AATTAACAACGCTAATTCCT
1 AATTCGCGACGCTAATTCCG
15871 AATTCGCGA
1 AATTCGCGA
15880 TTCGCAACAC
Statistics
Matches: 84, Mismatches: 25, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (20 bp):
AATTCGCGACGCTAATTCCG
Found at i:15795 original size:40 final size:40
Alignment explanation
Indices: 15749--15879 Score: 145
Period size: 40 Copynumber: 3.3 Consensus size: 40
15739 ACGCGATTTT
* *
15749 CTAATTCGCGATGTTAATTCCGAATTCGCGACGCTAATTC
1 CTAATTCGCGACGCTAATTCCGAATTCGCGACGCTAATTC
* * * * *
15789 CTAATTCGCAACGCGATTTTCTAATTCGCGACGCTAATTC
1 CTAATTCGCGACGCTAATTCCGAATTCGCGACGCTAATTC
* * * ** *
15829 CTAATCCGTGACGCTAAATCCGAATTAACAACGCTAATTC
1 CTAATTCGCGACGCTAATTCCGAATTCGCGACGCTAATTC
15869 CTAATTCGCGA
1 CTAATTCGCGA
15880 TTCGCAACAC
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (40 bp):
CTAATTCGCGACGCTAATTCCGAATTCGCGACGCTAATTC
Found at i:15807 original size:60 final size:60
Alignment explanation
Indices: 15726--15880 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 60
15716 CAACGCGATT
* * *
15726 TTCCAAATCCGCAACGCGATTTTCTAATTCGCGATGTTAATTCCGAATTCGCGACGCTAA
1 TTCCAAATTCGCAACGCGATTTTCTAATTCGCGATGCTAATTCCGAATCCGCGACGCTAA
* * * *
15786 TTCCTAATTCGCAACGCGATTTTCTAATTCGCGACGCTAATTCCTAATCCGTGACGCTAA
1 TTCCAAATTCGCAACGCGATTTTCTAATTCGCGATGCTAATTCCGAATCCGCGACGCTAA
* * ** * * *
15846 ATCCGAATTAACAACGCTAATTCCTAATTCGCGAT
1 TTCCAAATTCGCAACGCGATTTTCTAATTCGCGAT
15881 TCGCAACACG
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (60 bp):
TTCCAAATTCGCAACGCGATTTTCTAATTCGCGATGCTAATTCCGAATCCGCGACGCTAA
Found at i:15921 original size:20 final size:20
Alignment explanation
Indices: 15898--15961 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
15888 ACGATTTTGT
15898 AATTCGGAATTAGCGTCGCG
1 AATTCGGAATTAGCGTCGCG
* *
15918 AATTTGGAATTAGTGTCGCG
1 AATTCGGAATTAGCGTCGCG
*
15938 AATTAC-GAATTAGCATCGCG
1 AATT-CGGAATTAGCGTCGCG
15958 AATT
1 AATT
15962 AGAAAATCGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (20 bp):
AATTCGGAATTAGCGTCGCG
Found at i:29584 original size:119 final size:119
Alignment explanation
Indices: 29373--29613 Score: 482
Period size: 119 Copynumber: 2.0 Consensus size: 119
29363 CCCCAAAACA
29373 ATACTAATAAATCATTAATTTCACATATTCAGCTGTAAAAAGAGAAACAGGAGCTGTTTTGGAAG
1 ATACTAATAAATCATTAATTTCACATATTCAGCTGTAAAAAGAGAAACAGGAGCTGTTTTGGAAG
29438 GATGAAAAGAGCTACATACTTTGTCTGCATTAAGAATGCATGATTTTTCATTTT
66 GATGAAAAGAGCTACATACTTTGTCTGCATTAAGAATGCATGATTTTTCATTTT
29492 ATACTAATAAATCATTAATTTCACATATTCAGCTGTAAAAAGAGAAACAGGAGCTGTTTTGGAAG
1 ATACTAATAAATCATTAATTTCACATATTCAGCTGTAAAAAGAGAAACAGGAGCTGTTTTGGAAG
29557 GATGAAAAGAGCTACATACTTTGTCTGCATTAAGAATGCATGATTTTTCATTTT
66 GATGAAAAGAGCTACATACTTTGTCTGCATTAAGAATGCATGATTTTTCATTTT
29611 ATA
1 ATA
29614 TCAACGAATA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 122 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (119 bp):
ATACTAATAAATCATTAATTTCACATATTCAGCTGTAAAAAGAGAAACAGGAGCTGTTTTGGAAG
GATGAAAAGAGCTACATACTTTGTCTGCATTAAGAATGCATGATTTTTCATTTT
Found at i:32292 original size:50 final size:50
Alignment explanation
Indices: 32232--32328 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
32222 CATTATTAAT
* * * *
32232 TCGTTTGATTTTAGTCCCTCGTTCGTTAACTTTTGTTTGATTTTAGTCTC
1 TCGTTCGATTTTAGTCCCTCGTTCGTTAACTCTCGTTTAATTTTAGTCTC
*
32282 TCGTTCGATTTTAGTCTCTCGTTCGTTAACTCTCGTTTAATTTTAGT
1 TCGTTCGATTTTAGTCCCTCGTTCGTTAACTCTCGTTTAATTTTAGT
32329 TCTTCAAGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.13, C:0.19, G:0.15, T:0.53
Consensus pattern (50 bp):
TCGTTCGATTTTAGTCCCTCGTTCGTTAACTCTCGTTTAATTTTAGTCTC
Found at i:32293 original size:18 final size:18
Alignment explanation
Indices: 32270--32306 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
32260 ACTTTTGTTT
32270 GATTTTAGTCTCTCGTTC
1 GATTTTAGTCTCTCGTTC
32288 GATTTTAGTCTCTCGTTC
1 GATTTTAGTCTCTCGTTC
32306 G
1 G
32307 TTAACTCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (18 bp):
GATTTTAGTCTCTCGTTC
Found at i:34301 original size:2 final size:2
Alignment explanation
Indices: 34294--34334 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
34284 ATTATCATTC
34294 TA TA TA TA TA 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 TA TA TA TA TA T
34335 TTAATCATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35079 original size:195 final size:195
Alignment explanation
Indices: 34736--35117 Score: 570
Period size: 195 Copynumber: 2.0 Consensus size: 195
34726 TTTTCATGTC
* * * *
34736 AATGAGTGTTCGTACGAGTGGTTGGGATTTATAAATTTGAATTTGTAAGAGCAAGTTTGAATCCT
1 AATGAGTGTTCGTACGAGTGGTTGGGATTCAGAAATTTAAATTTGTAAGAGCAAGTTTAAATCCT
* * *
34801 ATTAATGTCACTCTTGGTGGACAATTTGTAAATTATTATGTAAATCTCAATTGTGTCTCAAGTAT
66 ATTAATGTCACTCTTGGTGGACAATTTGTAAATTACTATGTAAATCTCAATTGTATCTCAAATAT
* * *
34866 GCCCTGACCTTGGATTAAGGGAGTCACCTCTGTCCTAAATTTTAATGTACCAAAAAATATTTTTT
131 GCCCTGACCTTAGATTAAGGGAGTCACATCTGGCCTAAATTTTAATGTACCAAAAAATATTTTTT
* * * *
34931 AATGAGTGTTGGTCCGAGTGGTTGGGATTCAGGAATTTAAATTTGTAAGGGCAAGTTTAAATCCT
1 AATGAGTGTTCGTACGAGTGGTTGGGATTCAGAAATTTAAATTTGTAAGAGCAAGTTTAAATCCT
* *
34996 ATTACCAT-T-ACTCTTGGTGGACAATTTGTAAATTCCTATGTAAATCTCAATTGTATCTTAAAT
66 ATTA--ATGTCACTCTTGGTGGACAATTTGTAAATTACTATGTAAATCTCAATTGTATCTCAAAT
* *
35059 ATGCCCTGGCCTTAGATTAAGGGAGTCACATTTGGCCTAAATTTTAATGTACCAAAAAA
129 ATGCCCTGACCTTAGATTAAGGGAGTCACATCTGGCCTAAATTTTAATGTACCAAAAAA
35118 ATATATATAT
Statistics
Matches: 167, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
195 164 0.98
196 1 0.01
197 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (195 bp):
AATGAGTGTTCGTACGAGTGGTTGGGATTCAGAAATTTAAATTTGTAAGAGCAAGTTTAAATCCT
ATTAATGTCACTCTTGGTGGACAATTTGTAAATTACTATGTAAATCTCAATTGTATCTCAAATAT
GCCCTGACCTTAGATTAAGGGAGTCACATCTGGCCTAAATTTTAATGTACCAAAAAATATTTTTT
Found at i:35622 original size:19 final size:20
Alignment explanation
Indices: 35554--35628 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 20
35544 ATACTCCTTT
35554 ATATATTATTTCCTTTCAATTAA
1 ATATATTATTT--TTTCAA-TAA
*
35577 ATATA-TATTTTTATCGAAGAA
1 ATATATTATTTTT-TC-AATAA
*
35598 AAATATTATTTTTT-AATAA
1 ATATATTATTTTTTCAATAA
35617 ATATATTATTTT
1 ATATATTATTTT
35629 GGGTCGGATC
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
19 15 0.33
20 2 0.04
21 9 0.20
22 14 0.31
23 5 0.11
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (20 bp):
ATATATTATTTTTTCAATAA
Found at i:37035 original size:23 final size:21
Alignment explanation
Indices: 36998--37061 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
36988 CAAACAACCG
*
36998 AAAACGTATCA-AAAGATAGAGA
1 AAAACGTGTCATAAAGATA-A-A
* *
37020 GAAACGTGTTATAAAGATAAA
1 AAAACGTGTCATAAAGATAAA
*
37041 AAAACGTGTCATAAAAATAAA
1 AAAACGTGTCATAAAGATAAA
37062 TATAAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 19 0.54
22 9 0.26
23 7 0.20
ACGTcount: A:0.58, C:0.08, G:0.16, T:0.19
Consensus pattern (21 bp):
AAAACGTGTCATAAAGATAAA
Found at i:37440 original size:10 final size:10
Alignment explanation
Indices: 37425--37503 Score: 50
Period size: 10 Copynumber: 7.2 Consensus size: 10
37415 AACACAAATG
37425 AACGAACATA
1 AACGAACATA
**
37435 AACGAATGTA
1 AACGAACATA
*
37445 AACAGACACAAATG
1 AAC-GA-AC--ATA
*
37459 AACGAACGTA
1 AACGAACATA
37469 AACGAACACAATA
1 AACG-A-AC-ATA
*
37482 AACGAACGTA
1 AACGAACATA
37492 AACGAACATA
1 AACGAACATA
37502 AA
1 AA
37504 TGAAAATAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
10 29 0.56
11 5 0.10
12 6 0.12
13 8 0.15
14 4 0.08
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.10
Consensus pattern (10 bp):
AACGAACATA
Found at i:37454 original size:34 final size:35
Alignment explanation
Indices: 37404--37474 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 35
37394 CATTCATTTA
37404 AATGATAAACAAACACAAATGAACGAACATAAACG
1 AATGATAAACAAACACAAATGAACGAACATAAACG
* *
37439 AATG-TAAACAGACACAAATGAACGAACGTAAACG
1 AATGATAAACAAACACAAATGAACGAACATAAACG
37473 AA
1 AA
37475 CACAATAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.11
Consensus pattern (35 bp):
AATGATAAACAAACACAAATGAACGAACATAAACG
Found at i:37489 original size:23 final size:24
Alignment explanation
Indices: 37432--37504 Score: 96
Period size: 23 Copynumber: 3.1 Consensus size: 24
37422 ATGAACGAAC
*
37432 ATAAACGAATGTAAAC-AGACACAA
1 ATAAACGAACGTAAACGA-ACACAA
*
37456 ATGAACGAACGTAAACGAACAC-A
1 ATAAACGAACGTAAACGAACACAA
*
37479 ATAAACGAACGTAAACGAACATAA
1 ATAAACGAACGTAAACGAACACAA
37503 AT
1 AT
37505 GAAAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 21 0.49
24 21 0.49
25 1 0.02
ACGTcount: A:0.56, C:0.18, G:0.14, T:0.12
Consensus pattern (24 bp):
ATAAACGAACGTAAACGAACACAA
Found at i:46425 original size:60 final size:60
Alignment explanation
Indices: 46361--46477 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
46351 ACTACTACTA
* * *
46361 TCATTCTAAATTAGTCCTCAAA-ATTTTGAACATTTTAGTTTCATCTCCAAAATATATCCT
1 TCATTCTAAATTAGTCCTCAAACATTTTCAACATTTCAATTTCATC-CCAAAATATATCCT
* * * *
46421 TCATTCTAAATTGGTCTTGAAACATTTTCAACATTTCAATTTCATCCCAAATTATAT
1 TCATTCTAAATTAGTCCTCAAACATTTTCAACATTTCAATTTCATCCCAAAATATAT
46478 GTATTCACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 29 0.59
61 20 0.41
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTCAAACATTTTCAACATTTCAATTTCATCCCAAAATATATCCT
Found at i:47518 original size:15 final size:15
Alignment explanation
Indices: 47498--47528 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47488 ATGACGATCA
*
47498 TGTATTGGGTCGGAT
1 TGTATTGAGTCGGAT
47513 TGTATTGAGTCGGAT
1 TGTATTGAGTCGGAT
47528 T
1 T
47529 TTTTTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.35, T:0.42
Consensus pattern (15 bp):
TGTATTGAGTCGGAT
Found at i:49249 original size:30 final size:30
Alignment explanation
Indices: 49210--49271 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
49200 GAATGGTAAA
* * *
49210 TTATGCGTTTAGTACTTAAACTATCAATTT
1 TTATCCGTTTAGCACTTAAACTATAAATTT
*
49240 TTATCCGTTTAGCACTTAAACTTTAAATTT
1 TTATCCGTTTAGCACTTAAACTATAAATTT
49270 TT
1 TT
49272 TTCTTCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (30 bp):
TTATCCGTTTAGCACTTAAACTATAAATTT
Found at i:50728 original size:4 final size:4
Alignment explanation
Indices: 50719--50774 Score: 103
Period size: 4 Copynumber: 14.0 Consensus size: 4
50709 AAAGATCATC
50719 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
*
50767 AGGA AAGA
1 AAGA AAGA
50775 TTTGGTTGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:52640 original size:102 final size:100
Alignment explanation
Indices: 52462--52853 Score: 507
Period size: 102 Copynumber: 3.9 Consensus size: 100
52452 ACCAATGCCG
* * * *
52462 CAAAATACAGCTCCGC-CTTTAGTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGTATTC
1 CAAAATACAGCTCCGCAC--CATTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTC
* * * *
52526 CGGTAGTGTTGCCACCATCTCCTCCATCCACGCGAAC
64 CAGTGGTGTTGCCACCACCTCCTCCATCCGCGCGAAC
* * * * *
52563 TCGAAATATAGCTCCGTCACCATTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGCATTC
1 -CAAAATACAGCTCCG-CACCATTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTC
52628 CAGTGGTGTTGCCACCACCTCCTCCATCCGCGCGAAAC
64 CAGTGGTGTTGCCACCACCTCCTCCATCCGCGCG-AAC
52666 CAAAATACAGCTCCGCTACCATTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTCC
1 CAAAATACAGCTCCGC-ACCATTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTCC
* * * * *
52731 ATTGGTGTTGCCACCATCTCCTCAATCCGTGCAAACC
65 AGTGGTGTTGCCACCACCTCCTCCATCCGCGCGAA-C
* *
52768 CAAAATACAGCTCCGCCACCATTCTCTATCGAAGAACATTTACCATCCTTGGCACCAAGTACTCC
1 CAAAATACAGCTCCG-CACCATTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTCC
* *
52833 ATTGGTGTTTCCACCACCTCC
65 AGTGGTGTTGCCACCACCTCC
52854 GCTCGTTCAG
Statistics
Matches: 261, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
101 3 0.01
102 252 0.97
103 5 0.02
104 1 0.00
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.26
Consensus pattern (100 bp):
CAAAATACAGCTCCGCACCATTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTCCA
GTGGTGTTGCCACCACCTCCTCCATCCGCGCGAAC
Found at i:52812 original size:204 final size:204
Alignment explanation
Indices: 52462--52853 Score: 561
Period size: 204 Copynumber: 1.9 Consensus size: 204
52452 ACCAATGCCG
** * *
52462 CAAAATACAGCTCCGCCTTTAGTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGTATTCC
1 CAAAATACAGCTCCGCCTCCAGTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTCC
* * * * * * *
52527 GGTAGTGTTGCCACCATCTCCTCCATCCACGCGAACTCGAAATATAGCTCCGTCACCATTCCCTA
66 AGTAGTGTTGCCACCATCTCCTCAATCCACGCAAACCCAAAATACAGCTCCGCCACCATTCCCTA
* * *
52592 TTGAAGAACATTTACCATCCTTGGCTCCAAGCATTCCAGTGGTGTTGCCACCACCTCCTCCATCC
131 TCGAAGAACATTTACCATCCTTGGCACCAAGCACTCCAGTGGTGTTGCCACCACCTCCTCCATCC
52657 GCGCGAAAC
196 GCGCGAAAC
*
52666 CAAAATACAGCTCCG-CTACCATTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTC
1 CAAAATACAGCTCCGCCT-CCAGTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTC
* * ** *
52730 CATTGGTGTTGCCACCATCTCCTCAATCCGTGCAAACCCAAAATACAGCTCCGCCACCATTCTCT
65 CAGTAGTGTTGCCACCATCTCCTCAATCCACGCAAACCCAAAATACAGCTCCGCCACCATTCCCT
* * *
52795 ATCGAAGAACATTTACCATCCTTGGCACCAAGTACTCCATTGGTGTTTCCACCACCTCC
130 ATCGAAGAACATTTACCATCCTTGGCACCAAGCACTCCAGTGGTGTTGCCACCACCTCC
52854 GCTCGTTCAG
Statistics
Matches: 164, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
203 2 0.01
204 162 0.99
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.26
Consensus pattern (204 bp):
CAAAATACAGCTCCGCCTCCAGTCCCTATTGAAGAACATTTACCATCCTTGGCACCAAGTACTCC
AGTAGTGTTGCCACCATCTCCTCAATCCACGCAAACCCAAAATACAGCTCCGCCACCATTCCCTA
TCGAAGAACATTTACCATCCTTGGCACCAAGCACTCCAGTGGTGTTGCCACCACCTCCTCCATCC
GCGCGAAAC
Done.