Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006528.1 Hibiscus syriacus cultivar Beakdansim tig00015909_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: 59178
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2405 original size:27 final size:26
Alignment explanation
Indices: 2367--2419 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 26
2357 TCACATTACA
2367 TATACAACAAGCAAGCGTTTTATCAGG
1 TATACAACAAGCAAGCG-TTTATCAGG
2394 TATACAACAAGCAAGCGTTTATCAGG
1 TATACAACAAGCAAGCGTTTATCAGG
2420 AAAAGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (26 bp):
TATACAACAAGCAAGCGTTTATCAGG
Found at i:6167 original size:12 final size:12
Alignment explanation
Indices: 6150--6176 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6140 TGATATACAT
6150 ATATATTTTTTC
1 ATATATTTTTTC
6162 ATATATTTTTTC
1 ATATATTTTTTC
6174 ATA
1 ATA
6177 CGCAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATATTTTTTC
Found at i:7168 original size:2 final size:2
Alignment explanation
Indices: 7161--7189 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7151 CTATTTCGAC
7161 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 C
7190 GTCGAGCTAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:9112 original size:6 final size:6
Alignment explanation
Indices: 9101--9132 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
9091 GCAGCTATTG
9101 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CA
9133 TGCTATGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:16666 original size:71 final size:72
Alignment explanation
Indices: 16548--16695 Score: 208
Period size: 71 Copynumber: 2.1 Consensus size: 72
16538 TCTTAAGACC
* * * * *
16548 CCTAAAAATTTATGTTCAGGGACTTATTTGGGAAGTGTTTCCAAGTTCGAGGACTCAACATCATA
1 CCTAAAAATTCATGTTCAGGGACCTATTTGAGAAGTGGTTCCAAGTTCAAGGACTCAACATCATA
*
16613 AAACAAA
66 AAAAAAA
* * *
16620 TCTAAAAA-TCATGTTCATGGACCTATTTGAGAGGTGGTTCCAAGTTCAAGGACTCAACATCATA
1 CCTAAAAATTCATGTTCAGGGACCTATTTGAGAAGTGGTTCCAAGTTCAAGGACTCAACATCATA
16684 AAAAAAA
66 AAAAAAA
16691 CCTAA
1 CCTAA
16696 TATTTAGTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
71 59 0.89
72 7 0.11
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (72 bp):
CCTAAAAATTCATGTTCAGGGACCTATTTGAGAAGTGGTTCCAAGTTCAAGGACTCAACATCATA
AAAAAAA
Found at i:18653 original size:30 final size:30
Alignment explanation
Indices: 18617--18774 Score: 219
Period size: 30 Copynumber: 5.2 Consensus size: 30
18607 CAAACCAGGA
*
18617 TTCAGCCGGATTCTGAAAAACGAAACTGGT
1 TTCAGCCAGATTCTGAAAAACGAAACTGGT
* **
18647 TTCAGCCAGATTCTAAAAAAAAAGAACTGGT
1 TTCAGCCAGATTCTGAAAAACGA-AACTGGT
**
18678 TTCAGCCAGATTCT-AAAAAAAAGAACTGGT
1 TTCAGCCAGATTCTGAAAAACGA-AACTGGT
*
18708 TTCAGCCGGATTCTGAAAAACGAAACTGGT
1 TTCAGCCAGATTCTGAAAAACGAAACTGGT
*
18738 TTCAGCCAAATTCTGAAAAACGAAACTGGT
1 TTCAGCCAGATTCTGAAAAACGAAACTGGT
18768 TTCAGCC
1 TTCAGCC
18775 GAAATCTCAA
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 90 0.77
31 27 0.23
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (30 bp):
TTCAGCCAGATTCTGAAAAACGAAACTGGT
Found at i:18739 original size:60 final size:61
Alignment explanation
Indices: 18617--18775 Score: 223
Period size: 61 Copynumber: 2.6 Consensus size: 61
18607 CAAACCAGGA
* *
18617 TTCAGCCGGATTCTGAAAAACGAAACTGGTTTCAGCCAGATTCTAAAAAAAAAGAACTGGT
1 TTCAGCCAGATTCTGAAAAACGAAACTGGTTTCAGCCGGATTCTAAAAAAAAAGAACTGGT
** * **
18678 TTCAGCCAGATTCT-AAAAAAAAGAACTGGTTTCAGCCGGATTCTGAAAAACGA-AACTGGT
1 TTCAGCCAGATTCTGAAAAACGA-AACTGGTTTCAGCCGGATTCTAAAAAAAAAGAACTGGT
*
18738 TTCAGCCAAATTCTGAAAAACGAAACTGGTTTCAGCCG
1 TTCAGCCAGATTCTGAAAAACGAAACTGGTTTCAGCCG
18776 AAATCTCAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
60 41 0.48
61 45 0.52
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (61 bp):
TTCAGCCAGATTCTGAAAAACGAAACTGGTTTCAGCCGGATTCTAAAAAAAAAGAACTGGT
Found at i:21424 original size:9 final size:9
Alignment explanation
Indices: 21410--21441 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
21400 TTTAGCGCCA
21410 ATTGAAATC
1 ATTGAAATC
21419 ATTGAAATC
1 ATTGAAATC
21428 ATTGAAATC
1 ATTGAAATC
21437 ATTGA
1 ATTGA
21442 CAGCTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (9 bp):
ATTGAAATC
Found at i:22634 original size:18 final size:18
Alignment explanation
Indices: 22611--22646 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
22601 ATACCTAATC
22611 ATATGAATCAA-CACACCT
1 ATATGAAT-AATCACACCT
22629 ATATGAATAATCACACCT
1 ATATGAATAATCACACCT
22647 CTTAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (18 bp):
ATATGAATAATCACACCT
Found at i:23471 original size:26 final size:26
Alignment explanation
Indices: 23422--23471 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
23412 TTTACTCTTC
*
23422 AAATTCAAGCACCTTCATATATTTAT
1 AAATTCAAGCACCTTCATAGATTTAT
23448 AAATTCAAGCACCTTTCA-AGATTT
1 AAATTCAAGCACC-TTCATAGATTT
23472 TCGAGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (26 bp):
AAATTCAAGCACCTTCATAGATTTAT
Found at i:25465 original size:31 final size:30
Alignment explanation
Indices: 25430--25527 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
25420 GACAGACTCT
25430 AAAAAGCAAACCAGGATTCAGCCGGATTCTG
1 AAAAA-CAAACCAGGATTCAGCCGGATTCTG
* * * * *
25461 AAAAACGAAGCTGGTTTCAGTCGGATTCTG
1 AAAAACAAACCAGGATTCAGCCGGATTCTG
** * * *
25491 AAAAACGAAA-CTTGTTTCAGCCGGACTCTA
1 AAAAAC-AAACCAGGATTCAGCCGGATTCTG
25521 AAAAACA
1 AAAAACA
25528 GAACTGCTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 1 0.02
30 48 0.86
31 7 0.12
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (30 bp):
AAAAACAAACCAGGATTCAGCCGGATTCTG
Found at i:25480 original size:30 final size:30
Alignment explanation
Indices: 25446--25579 Score: 153
Period size: 30 Copynumber: 4.5 Consensus size: 30
25436 CAAACCAGGA
*
25446 TTCAGCCGGATTCTGAAAAACGAAGCTGGT
1 TTCAGCCGGATTCTGAAAAACGAAACTGGT
* *
25476 TTCAGTCGGATTCTGAAAAACGAAACTTGT
1 TTCAGCCGGATTCTGAAAAACGAAACTGGT
* * *
25506 TTCAGCCGGACTCTAAAAAAC-AGAACTGCT
1 TTCAGCCGGATTCTGAAAAACGA-AACTGGT
** * *
25536 TTCAGCAAGATTCTGAAAAAAGAAACTTGT
1 TTCAGCCGGATTCTGAAAAACGAAACTGGT
*
25566 TTCAGCCGAATTCT
1 TTCAGCCGGATTCT
25580 ACGAAAGCAT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
29 1 0.01
30 82 0.98
31 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (30 bp):
TTCAGCCGGATTCTGAAAAACGAAACTGGT
Found at i:25525 original size:60 final size:60
Alignment explanation
Indices: 25446--25573 Score: 179
Period size: 60 Copynumber: 2.1 Consensus size: 60
25436 CAAACCAGGA
* * * * *
25446 TTCAGCCGGATTCTGAAAAAC-GAAGCTGGTTTCAGTC-GGATTCTGAAAAACGAAACTTGT
1 TTCAGCCGGACTCTAAAAAACAGAA-CTGCTTTCAG-CAAGATTCTGAAAAAAGAAACTTGT
25506 TTCAGCCGGACTCTAAAAAACAGAACTGCTTTCAGCAAGATTCTGAAAAAAGAAACTTGT
1 TTCAGCCGGACTCTAAAAAACAGAACTGCTTTCAGCAAGATTCTGAAAAAAGAAACTTGT
25566 TTCAGCCG
1 TTCAGCCG
25574 AATTCTACGA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 1 0.02
60 57 0.93
61 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
TTCAGCCGGACTCTAAAAAACAGAACTGCTTTCAGCAAGATTCTGAAAAAAGAAACTTGT
Found at i:26042 original size:26 final size:26
Alignment explanation
Indices: 25993--26042 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
25983 TTTACTCTTC
*
25993 AAATTCAAGCACCTTCATATATTTAT
1 AAATTCAAGCACCTTCATAGATTTAT
26019 AAATTCAAGCACCTTTCA-AGATTT
1 AAATTCAAGCACC-TTCATAGATTT
26043 TCGAGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (26 bp):
AAATTCAAGCACCTTCATAGATTTAT
Found at i:27336 original size:2 final size:2
Alignment explanation
Indices: 27329--27357 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27319 CCTAAACTAA
27329 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
27358 GTTTGAATAC
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:30503 original size:2 final size:2
Alignment explanation
Indices: 30496--30521 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30486 GCCCCTGGTT
30496 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
30522 ATGATTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30565 original size:16 final size:18
Alignment explanation
Indices: 30536--30568 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
30526 TTATCTATTT
30536 TTTTTTGAAGTATTTTAG
1 TTTTTTGAAGTATTTTAG
30554 TTTTTT-AA-TATTTTA
1 TTTTTTGAAGTATTTTA
30569 TTTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (18 bp):
TTTTTTGAAGTATTTTAG
Found at i:30670 original size:12 final size:12
Alignment explanation
Indices: 30647--30681 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
30637 TGTCACATCA
*
30647 TAAAAATATTTT
1 TAAATATATTTT
30659 TAAAT-TATTTT
1 TAAATATATTTT
30670 TAAATATATTTT
1 TAAATATATTTT
30682 GTTAAGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAAATATATTTT
Found at i:31544 original size:19 final size:19
Alignment explanation
Indices: 31520--31558 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31510 TCGAATGCAT
*
31520 TCCATGCACCGATGCACTC
1 TCCATGCACCGACGCACTC
*
31539 TCCATGCATCGACGCACTC
1 TCCATGCACCGACGCACTC
31558 T
1 T
31559 GATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.41, G:0.15, T:0.23
Consensus pattern (19 bp):
TCCATGCACCGACGCACTC
Found at i:31582 original size:64 final size:64
Alignment explanation
Indices: 31500--31667 Score: 191
Period size: 64 Copynumber: 2.6 Consensus size: 64
31490 TCAATGAATA
* * *
31500 AATTGAAACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGACGCACTC-TG-ATT
1 AATTAAAACATCGAATGCATT-CATGCATCGATGCACTCTCCATGCATCGACGCAC-CAGGCATT
31563 T
64 T
* ** *
31564 AATTAAAACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTCCATGCATCGACGCACCAGGC-ATT
31629 T
64 T
*
31630 --TTCAAACATCGAATGCACTTCATGCATCGATGCACTCT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCT
31668 TAGTGCACCG
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 81 0.92
65 2 0.02
66 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (64 bp):
AATTAAAACATCGAATGCATTCATGCATCGATGCACTCTCCATGCATCGACGCACCAGGCATTT
Found at i:31664 original size:17 final size:19
Alignment explanation
Indices: 31636--31684 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
31626 ATTTTTCAAA
31636 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
31654 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
31673 CACCGATGCACT
1 CATCGATGCACT
31685 AGGAATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:40745 original size:19 final size:19
Alignment explanation
Indices: 40702--40754 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
40692 AAATGATCAA
* * *
40702 CAAATTCGCAACGCGATCT
1 CAAATTCACAACACGAACT
40721 CAAATTCACAACACGAACT
1 CAAATTCACAACACGAACT
*
40740 CCAATTTCACAACAC
1 -CAAATTCACAACAC
40755 AGTTTCCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.40, C:0.34, G:0.08, T:0.19
Consensus pattern (19 bp):
CAAATTCACAACACGAACT
Found at i:40791 original size:20 final size:20
Alignment explanation
Indices: 40766--40804 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40756 GTTTCCAAAT
*
40766 TCGCAATGCAAATATGTAAA
1 TCGCAACGCAAATATGTAAA
*
40786 TCGCAACGCAAATTTGTAA
1 TCGCAACGCAAATATGTAA
40805 TTCGTAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (20 bp):
TCGCAACGCAAATATGTAAA
Found at i:40889 original size:20 final size:19
Alignment explanation
Indices: 40864--40911 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
40854 CTGAATTTCA
*
40864 AATTCGCAACTCGATTTTT
1 AATTCGCAACTCGAATTTT
40883 GAATTCGCAACTCGAATTTT
1 -AATTCGCAACTCGAATTTT
40903 AATTTCGCA
1 AA-TTCGCA
40912 GCAGGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
AATTCGCAACTCGAATTTT
Found at i:41874 original size:24 final size:24
Alignment explanation
Indices: 41847--41929 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
41837 GTATTCGAAA
*
41847 TTTGATCTTGGTCAATACCTGGAC
1 TTTGATCTTGGTCAATACCCGGAC
41871 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
41895 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCCGGAC
41919 TTTGATCTTGG
1 TTTGATCTTGG
41930 ACAGACCCTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:45983 original size:21 final size:20
Alignment explanation
Indices: 45957--46032 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
45947 GTGAATCGGG
*
45957 CTCTTGAACAATGGGAGGGAC
1 CTCTTGAACGATGGGAGGG-C
**
45978 CTCTTGAACGATGACATGGGC
1 CTCTTGAACGATGGGA-GGGC
* *
45999 CTCTTGAATGGTGGGAGGGGC
1 CTCTTGAACGATGGGA-GGGC
46020 CTCTTGAACGATG
1 CTCTTGAACGATG
46033 ACTGGTAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 41 0.93
22 3 0.07
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGATGGGAGGGC
Found at i:46209 original size:4 final size:4
Alignment explanation
Indices: 46177--46230 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
46167 AGGCCGCTAA
* * * *
46177 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
46225 AAAT AA
1 AAAT AA
46231 TTCCGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:48430 original size:22 final size:22
Alignment explanation
Indices: 48400--48457 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
48390 GATGGAGATA
*
48400 GACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
48422 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
48444 GACAGATGTCGCCG
1 GACGGATTTCGCCG
48458 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.21, G:0.40, T:0.17
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:48583 original size:19 final size:20
Alignment explanation
Indices: 48561--48598 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48551 AATATTGTGT
48561 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
*
48580 TTCGCATTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
48599 TGCGCTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:48608 original size:19 final size:20
Alignment explanation
Indices: 48569--48608 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
48559 GTTTCGAATT
*
48569 CGAAAATAAAATTCGCATTG
1 CGAAAATAAAATGCGCATTG
*
48589 CGAAAAT-AAATGCGCTTTG
1 CGAAAATAAAATGCGCATTG
48608 C
1 C
48609 AAATTTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (20 bp):
CGAAAATAAAATGCGCATTG
Found at i:48633 original size:20 final size:20
Alignment explanation
Indices: 48605--48674 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
48595 TAAATGCGCT
***
48605 TTGCAAATTTGACTTCTGTG
1 TTGCAAATTTGAAAACTGTG
*
48625 TTGCTAATTTGAAAACTGTG
1 TTGCAAATTTGAAAACTGTG
* *
48645 TTGCGAATTTGGAAACTGTG
1 TTGCAAATTTGAAAACTGTG
48665 TTGCGAAATT
1 TTGC-AAATT
48675 GGAGTTCGCG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 38 0.90
21 4 0.10
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCAAATTTGAAAACTGTG
Found at i:48676 original size:20 final size:20
Alignment explanation
Indices: 48620--48677 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
48610 AATTTGACTT
* *
48620 CTGTGTTGCTAATTTGAAAA
1 CTGTGTTGCGAATTTGGAAA
48640 CTGTGTTGCGAATTTGGAAA
1 CTGTGTTGCGAATTTGGAAA
*
48660 CTGTGTTGCGAAATTGGA
1 CTGTGTTGCGAATTTGGA
48678 GTTCGCGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (20 bp):
CTGTGTTGCGAATTTGGAAA
Found at i:51770 original size:17 final size:18
Alignment explanation
Indices: 51738--51771 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
51728 CCCTGCTTGA
*
51738 TTAAATATTTAATATTTT
1 TTAAATATTAAATATTTT
51756 TTAAAT-TTAAATATTT
1 TTAAATATTAAATATTT
51772 ATTTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATATTAAATATTTT
Found at i:52558 original size:31 final size:31
Alignment explanation
Indices: 52523--52598 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
52513 TTAAAAAAAC
*
52523 ATAAGATGTGATCACTCTCGTTTTTATTTAA
1 ATAAGATGTGATCACTCTCATTTTTATTTAA
* * * *
52554 ATAAGATATGGTCACTTTTATTTTTATTTAA
1 ATAAGATGTGATCACTCTCATTTTTATTTAA
* *
52585 TTAAGACGTGATCA
1 ATAAGATGTGATCA
52599 TCACAGGTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (31 bp):
ATAAGATGTGATCACTCTCATTTTTATTTAA
Found at i:52740 original size:20 final size:19
Alignment explanation
Indices: 52715--52770 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
52705 TTTTAACAAA
* *
52715 TTTTAACATAAAATATATAT
1 TTTTAA-ATAAAATAGATAC
52735 TTTTAAATGAAAATAAGATAC
1 TTTTAAAT-AAAAT-AGATAC
52756 TTTTAAATAAAATAG
1 TTTTAAATAAAATAG
52771 TATCCCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.12
20 16 0.50
21 12 0.38
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (19 bp):
TTTTAAATAAAATAGATAC
Found at i:53784 original size:18 final size:18
Alignment explanation
Indices: 53727--53788 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
53717 CTTGGGATTA
53727 TCTTTAGGTATTTTATTT
1 TCTTTAGGTATTTTATTT
* * * *
53745 T-TATAGGTCTTTTAATC
1 TCTTTAGGTATTTTATTT
* *
53762 CCTTTAGCTATTTTATTT
1 TCTTTAGGTATTTTATTT
53780 TCTTTAGGT
1 TCTTTAGGT
53789 TTTCTAAGTT
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (18 bp):
TCTTTAGGTATTTTATTT
Found at i:54253 original size:21 final size:21
Alignment explanation
Indices: 54202--54254 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
54192 ATTATGACTA
54202 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
54223 TCGCGTTGCGATTTTCCCAATT
1 TCGCAATGCGATTTT-CCAATT
54245 T-GCAATGCGA
1 TCGCAATGCGA
54255 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:54271 original size:20 final size:20
Alignment explanation
Indices: 54246--54378 Score: 151
Period size: 20 Copynumber: 6.5 Consensus size: 20
54236 TTCCCAATTT
54246 GCAATGCGAATAAGTAAATC
1 GCAATGCGAATAAGTAAATC
* * *
54266 GCAATGTGATACTCA-TAATTC
1 GCAATGCGA-A-TAAGTAAATC
*
54287 GCAATGCGAATACGTAAATC
1 GCAATGCGAATAAGTAAATC
* *
54307 GCAACGCGATTAAGTAAATC
1 GCAATGCGAATAAGTAAATC
* *
54327 GCAATGCGAATTAGGAAAATC
1 GCAATGCGAA-TAAGTAAATC
*
54348 GCAATGCGAATACGTAAATC
1 GCAATGCGAATAAGTAAATC
54368 GCAATGCGAAT
1 GCAATGCGAAT
54379 CTTACTATAG
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.01
20 58 0.62
21 32 0.34
22 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (20 bp):
GCAATGCGAATAAGTAAATC
Found at i:54295 original size:41 final size:40
Alignment explanation
Indices: 54241--54378 Score: 131
Period size: 41 Copynumber: 3.4 Consensus size: 40
54231 CGATTTTCCC
* *
54241 AATTTGCAATGCGAATAAGTAAATCGCAATGTGATACTCAT
1 AATTCGCAATGCGAATAAGTAAATCGCAATGCGATACT-AT
* *
54282 AATTCGCAATGCGAATACGTAAATCGCAACGCGAT--TAAGT
1 AATTCGCAATGCGAATAAGTAAATCGCAATGCGATACT-A-T
* * *
54322 AAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTA-
1 AATTCGCAATGCGAA-TAAGTAAATCGCAATGCG-ATAC-TAT
54364 AA-TCGCAATGCGAAT
1 AATTCGCAATGCGAAT
54379 CTTACTATAG
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
39 2 0.02
40 16 0.20
41 58 0.71
42 4 0.05
44 1 0.01
45 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (40 bp):
AATTCGCAATGCGAATAAGTAAATCGCAATGCGATACTAT
Found at i:54988 original size:19 final size:19
Alignment explanation
Indices: 54949--54993 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
54939 GCAACGAGAT
**
54949 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
*
54968 AATCTCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
54987 AATCGCA
1 AATCGCA
54994 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.27, G:0.16, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:55011 original size:19 final size:19
Alignment explanation
Indices: 54989--55144 Score: 80
Period size: 19 Copynumber: 9.1 Consensus size: 19
54979 GAAACCAAAA
*
54989 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
55008 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
55022 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
55041 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
55055 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
55072 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
55086 T--CGTTGCAATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
55103 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
55123 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
55143 TC
1 TC
55145 AACTAAAAGA
Statistics
Matches: 104, Mismatches: 12, Indels: 42
0.66 0.08 0.27
Matches are distributed among these distances:
12 15 0.14
14 16 0.15
16 3 0.03
17 10 0.10
19 30 0.29
20 29 0.28
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:55060 original size:31 final size:31
Alignment explanation
Indices: 54994--55119 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
54984 CAAAATCGCA
**
54994 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGA-T-TCTCG
**
55027 TTGCGATTTTCATTTCGCGTTGCGATTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCG
55058 TTGCGATAGTCATTTCGCGTTGCGATTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCG
*
55089 TTGCAATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
55120 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
31 48 0.54
32 16 0.18
33 25 0.28
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (31 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCG
Found at i:55121 original size:20 final size:20
Alignment explanation
Indices: 55098--55144 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
55088 GTTGCAATAG
55098 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
55118 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
55138 TCATTTC
1 TCATTTC
55145 AACTAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:57297 original size:42 final size:42
Alignment explanation
Indices: 57221--57309 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
57211 GACTCGCCTG
* * *
57221 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
57263 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
57305 TCATC
1 TCATC
57310 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:58684 original size:14 final size:14
Alignment explanation
Indices: 58665--58700 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
58655 ATTGTTTAAT
58665 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
58679 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
58693 TGATTTGT
1 TGATTTGT
58701 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:58828 original size:19 final size:19
Alignment explanation
Indices: 58804--58862 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
58794 CAAAAGTACT
58804 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
58823 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
58837 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
58856 ATCGCAA
1 ATCGCAA
58863 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:58849 original size:33 final size:33
Alignment explanation
Indices: 58804--58883 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
58794 CAAAAGTACT
* * * *
58804 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
58837 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
58870 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
58884 CTAAATCGCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:58916 original size:19 final size:19
Alignment explanation
Indices: 58889--59017 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
58879 CGAAACTAAA
*
58889 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
58908 TCGCATTGCGA--TTC-CT
1 TCGCATTGCGATTTTCATT
58924 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
58941 TCGCATTGCGAAATTCA--
1 TCGCATTGCGATTTTCATT
58958 -CG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
58974 TCGTATTGCGA---TC-TC
1 TCGCATTGCGATTTTCATT
58989 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
59006 TCGCATTGCGAT
1 TCGCATTGCGAT
59018 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 9, Indels: 32
0.67 0.07 0.25
Matches are distributed among these distances:
13 6 0.07
14 16 0.19
15 4 0.05
16 13 0.15
17 13 0.15
19 33 0.39
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:58929 original size:33 final size:32
Alignment explanation
Indices: 58892--59017 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
58882 AACTAAATCG
58892 CGTTGCGATTTTCATTTCGCATTGCGATTCCTT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CTT
*
58925 CGTTGCGATTTTCATTTCGCATTGCGAAATTC-A
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCTT
*
58958 CGTTGCGATTTTCATTTCGTATTGCGA-TCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCT-T
58990 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
59018 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
30 2 0.02
31 1 0.01
32 26 0.31
33 51 0.61
34 1 0.01
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTT
Found at i:59015 original size:65 final size:66
Alignment explanation
Indices: 58892--59016 Score: 218
Period size: 65 Copynumber: 1.9 Consensus size: 66
58882 AACTAAATCG
58892 CGTTGCGATTTTCATTTCGCATTGCGATTCCTTCGTTGCGATTTTCATTTCGCATTGCGAAATTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCTTCGTTGCGATTTTCATTTCGCATTGCGAAATTC
58957 A
66 A
*
58958 CGTTGCGATTTTCATTTCGTATTGCGA-T-CTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCT-TCGTTGCGATTTTCATTTCGCATTGCGA
59017 TAGTAATTTC
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
64 2 0.04
65 29 0.51
66 26 0.46
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCTTCGTTGCGATTTTCATTTCGCATTGCGAAATTC
A
Done.