Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002963.1 Hibiscus syriacus cultivar Beakdansim tig00006131_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: 90944
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3450 original size:46 final size:46
Alignment explanation
Indices: 3382--3491 Score: 186
Period size: 46 Copynumber: 2.4 Consensus size: 46
3372 GAAGATTGCT
* *
3382 TGAAGACGCCGAAAAATTGATAAATCCTGAAGTCTTCCTGATTGGCC
1 TGAAGACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTG-TTGGCC
3429 TGAA-ACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTGTTGGCC
1 TGAAGACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTGTTGGCC
3474 TGAAGACGCCGAGAAATC
1 TGAAGACGCCGAGAAATC
3492 TTGGAGTCTT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
45 10 0.17
46 46 0.77
47 4 0.07
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (46 bp):
TGAAGACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTGTTGGCC
Found at i:5707 original size:59 final size:62
Alignment explanation
Indices: 5636--5756 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
5626 GAGCATTAAG
* * *
5636 CGAACATGTTCATGAAC-A-AAAT-AACGAACATGAATACCTTC-AAAATAAATAAATGAATA
1 CGAACATGTTCATGAACAATAAATAAACAAACATAAACACCTTCAAAAATAAATAAAT-AATA
*
5695 CGAACATGTTCATGAACAATAAATAAACAAACATAAACATCTTCAAAAATAAATAAATAATA
1 CGAACATGTTCATGAACAATAAATAAACAAACATAAACACCTTCAAAAATAAATAAATAATA
5757 AATACGAACA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
59 17 0.31
60 1 0.02
61 4 0.07
62 19 0.35
63 13 0.24
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.22
Consensus pattern (62 bp):
CGAACATGTTCATGAACAATAAATAAACAAACATAAACACCTTCAAAAATAAATAAATAATA
Found at i:7223 original size:12 final size:12
Alignment explanation
Indices: 7208--7236 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
7198 CTTTACTCAC
7208 CTCCGATGGCCG
1 CTCCGATGGCCG
7220 CTCCGATGGCCG
1 CTCCGATGGCCG
7232 CTCCG
1 CTCCG
7237 GTGCCGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.45, G:0.31, T:0.17
Consensus pattern (12 bp):
CTCCGATGGCCG
Found at i:13565 original size:34 final size:34
Alignment explanation
Indices: 13527--13592 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
13517 GTTCTAAAAT
*
13527 CTTTTAATTATTTGACAATAAACGCTTAAATAAA
1 CTTTTAATTATTTGACAATAAACGCTCAAATAAA
*
13561 CTTTTAATTATTTGATAATAAACGCTCAAATA
1 CTTTTAATTATTTGACAATAAACGCTCAAATA
13593 TTTTAACAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (34 bp):
CTTTTAATTATTTGACAATAAACGCTCAAATAAA
Found at i:16446 original size:43 final size:43
Alignment explanation
Indices: 16393--16701 Score: 238
Period size: 43 Copynumber: 7.2 Consensus size: 43
16383 TGAGAACAAA
* * *
16393 AAACGCCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTGAGC
1 AAACGCCGCAAAAGGTCAATATCTA-TAGCGGCGTTTTTGGAAC
* *
16436 AAACGTCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAAC
* * * * * * *
16479 AAACGCCGCAAAAAGT-TATGATATATAGCGGCATTTCTAGAAA
1 AAACGCCGCAAAAGGTCAAT-ATCTATAGCGGCGTTTTTGGAAC
* * *
16522 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTTGATAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGA-AC
* * * * *
16565 AAACGCTGCAAAAGAG-C-AGACCAATA-CTGGCGTTTTTAGAAC
1 AAACGCCGCAAAAG-GTCAATATCTATAGC-GGCGTTTTTGGAAC
* * *
16607 AAATGCCGCAAAAGGTCAA-ACCTATAGCGGCGTTTTTTGACAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGA-AC
* * * * * *
16650 AAACGCTGTAAAAGGTC-AGACCTATAACGGCGTTTTTGAATAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGA-AC
16693 AAACGCCGC
1 AAACGCCGC
16702 TAATTACCTT
Statistics
Matches: 218, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.00
42 56 0.26
43 160 0.73
44 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAAC
Found at i:16615 original size:85 final size:84
Alignment explanation
Indices: 16419--16701 Score: 288
Period size: 85 Copynumber: 3.3 Consensus size: 84
16409 CAATATCTAT
* * * * *
16419 TACGGCGTTTTTTGAGCAAACGTCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAACAAACG
1 TACGGCGTTTTTAGAACAAACGCCGCAAAAGGTC-AAATCTATAGCGGCGTTTTTTGAACAAACG
* * *
16484 CCGCAAAA-AGTTATGA-TATA
65 CTGCAAAAGAGTCA-GACCA-A
* * * * *
16504 TAGCGGCATTTCTAGAAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTTGATACAAAC
1 TA-CGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTTGA-ACAAAC
16569 GCTGCAAAAGAG-CAGACCAA
64 GCTGCAAAAGAGTCAGACCAA
* *
16589 TACTGGCGTTTTTAGAACAAATGCCGCAAAAGGTCAAACCTATAGCGGCGTTTTTTGACACAAAC
1 TAC-GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTTGA-ACAAAC
* *
16654 GCTGTAAAAG-GTCAGACCTA
64 GCTGCAAAAGAGTCAGACCAA
16674 TAACGGCGTTTTT-GAATACAAACGCCGC
1 T-ACGGCGTTTTTAG-A-ACAAACGCCGC
16702 TAATTACCTT
Statistics
Matches: 166, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
84 3 0.02
85 107 0.64
86 54 0.33
87 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (84 bp):
TACGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTTGAACAAACGC
TGCAAAAGAGTCAGACCAA
Found at i:16619 original size:128 final size:128
Alignment explanation
Indices: 16465--16698 Score: 292
Period size: 128 Copynumber: 1.8 Consensus size: 128
16455 TATCTATAGC
* * * *
16465 GGCGTTTTTGGAACAAACGCCGCAAAAAGTTATGATATATAGCGGCATTTCTAGA-AAAAACGCC
1 GGCGTTTTTAGAACAAACGCCGCAAAAAGTCA-AACATATAGCGGCATTTCTAGACAAAAACGCC
* * *
16529 GCAAAAGGTCAGATCTATAGCGGCATTTTTTG-ATACAAACGCTGCAAAAGAGCAGACCAATACT
65 GCAAAAGGTCAGACCTATAACGGC-GTTTTTGAATACAAACGCTGCAAAAGAGCAGACCAATACT
* * * * * * * *
16593 GGCGTTTTTAGAACAAATGCCGCAAAAGGTCAAACCTATAGCGGCGTTTTTTGACACAAACGCTG
1 GGCGTTTTTAGAACAAACGCCGCAAAAAGTCAAACATATAGCGGCATTTCTAGACAAAAACGCCG
*
16658 TAAAAGGTCAGACCTATAACGGCGTTTTTGAATACAAACGC
66 CAAAAGGTCAGACCTATAACGGCGTTTTTGAATACAAACGC
16699 CGCTAATTAC
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
127 22 0.25
128 66 0.75
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (128 bp):
GGCGTTTTTAGAACAAACGCCGCAAAAAGTCAAACATATAGCGGCATTTCTAGACAAAAACGCCG
CAAAAGGTCAGACCTATAACGGCGTTTTTGAATACAAACGCTGCAAAAGAGCAGACCAATACT
Found at i:19611 original size:42 final size:42
Alignment explanation
Indices: 19583--19972 Score: 330
Period size: 42 Copynumber: 9.4 Consensus size: 42
19573 TAGGTTATAT
*
19583 GACAATTGCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA
1 GACAATAGCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA
* * * *
19625 GTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGT
1 GACAATAGCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA
* * *
19667 GTCTATAGCGGCGTTTATGTA--AAAACGCCACTAAAGTACGA
1 GACAATAGCGGCGTTT-GGTATTAAAACGCCACTAAAGTACGA
* * * *
19708 -ATCTATAGCGGCATTTGGTATTAAAACGCCACAAAAGTACGT
1 GA-CAATAGCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA
* * * *
19750 GTCTATAGCGGCGTTTGGTATTAAAATGCCAC-AAACGTACGT
1 GACAATAGCGGCGTTTGGTATTAAAACGCCACTAAA-GTACGA
* * * *
19792 GTCTATAGCGGCATTTGTGTA--AAAATGCCACTAAAGTACGA
1 GACAATAGCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGA
* * * * *
19833 GTCTATAGCGGCGTTTGGTGTTAAAACGCCACAAAAGTACGT
1 GACAATAGCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA
* * * *
19875 GTCTATAGCGGCGTTT-GTA-TAAAGACGCCACTAAAATACTA
1 GACAATAGCGGCGTTTGGTATTAAA-ACGCCACTAAAGTACGA
*** * * * *
19916 GTTTATAGTGGCGTTT-GTATAAAAACGCCACAAAAGTACGT
1 GACAATAGCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA
* *
19957 GTCTATAGCGGCGTTT
1 GACAATAGCGGCGTTT
19973 TTATACAAAT
Statistics
Matches: 299, Mismatches: 37, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
40 9 0.03
41 124 0.41
42 160 0.54
43 6 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (42 bp):
GACAATAGCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA
Found at i:19705 original size:83 final size:82
Alignment explanation
Indices: 19590--19972 Score: 472
Period size: 83 Copynumber: 4.6 Consensus size: 82
19580 TATGACAATT
* *
19590 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGC
1 GCGGCGTTTGTGTA--AAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTA-TAAAACGC
19654 CACAAAAGTACGTGTCTATA
63 CACAAAAGTACGTGTCTATA
* * ** *
19674 GCGGCGTTTATGTAAAAACGCCACTAAAGTACGAATCTATAGCGGCATTTGGTATTAAAACGCCA
1 GCGGCGTTTGTGTAAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTA-TAAAACGCCA
19739 CAAAAGTACGTGTCTATA
65 CAAAAGTACGTGTCTATA
* * * *
19757 GCGGCGTTTG-GTATTAAAATGCCACAAACGTACGTGTCTATAGCGGCATTTGTGTA-AAAATGC
1 GCGGCGTTTGTGTA--AAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTG-GTATAAAACGC
* *
19820 CACTAAAGTACGAGTCTATA
63 CACAAAAGTACGTGTCTATA
*
19840 GCGGCGTTTGGTGTTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTT-GTATAAAGACGCC
1 GCGGCGTTT-GTGTAAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTATAAA-ACGCC
*
19904 ACTAAAA-TAC-TAGTTTATA
64 AC-AAAAGTACGT-GTCTATA
* *
19923 GTGGCGTTTGTATAAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTT
1 GCGGCGTTTGTGTAAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTT
19973 TTATACAAAT
Statistics
Matches: 266, Mismatches: 23, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
81 3 0.01
82 45 0.17
83 165 0.62
84 45 0.17
85 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (82 bp):
GCGGCGTTTGTGTAAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTATAAAACGCCAC
AAAAGTACGTGTCTATA
Found at i:19734 original size:125 final size:125
Alignment explanation
Indices: 19590--19972 Score: 576
Period size: 125 Copynumber: 3.1 Consensus size: 125
19580 TATGACAATT
* *
19590 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCC
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTATTAAAACGCC
* *
19655 ACAAAAGTACGTGTCTATAGCGGCGTTTATGTAAAAACGCCACTAAAGTACGAATCTATA
66 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATA
* *
19715 GCGGCATTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTATTAAAATGCC
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTATTAAAACGCC
* * *
19780 ACAAACGTACGTGTCTATAGCGGCATTTGTGTAAAAATGCCACTAAAGTACGAGTCTATA
66 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATA
*
19840 GCGGCGTTTGGTGTTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTT-GTA-TAAAGACGC
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTATTAAA-ACGC
* * * * *
19903 CACTAAAA-TAC-TAGTTTATAGTGGCGTTTGTATAAAAACGCCACAAAAGTACGTGTCTATA
65 CAC-AAAAGTACGT-GTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATA
19964 GCGGCGTTT
1 GCGGCGTTT
19973 TTATACAAAT
Statistics
Matches: 235, Mismatches: 20, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
123 5 0.02
124 62 0.26
125 168 0.71
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (125 bp):
GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGGTATTAAAACGCC
ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATA
Found at i:21396 original size:36 final size:36
Alignment explanation
Indices: 21349--21556 Score: 301
Period size: 36 Copynumber: 5.8 Consensus size: 36
21339 ATCAAAAGTT
* * *
21349 CACTTCTGATTCAAGTAGAACGGAAGAAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* * *
21385 CACTTCCGATTCAAGTCAAACGGAGGGAAGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
21421 CACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* *
21457 CACTTCTGATTCAAGTCGAACGGAAAGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* *
21493 CACTTTCGATTCAAGTCGAACGGAAGGAAGCATCAG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
21529 CACTTCCGATTCATA-TCGAACGGAAGGA
1 CACTTCCGATTCA-AGTCGAACGGAAGGA
21557 TGTGTCTTAC
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
36 154 0.99
37 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (36 bp):
CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
Found at i:22030 original size:21 final size:21
Alignment explanation
Indices: 21997--22040 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
21987 AATAAATTGC
* *
21997 AAGTTAACCAATTAATGATAA
1 AAGTTAACAAATTAATGAAAA
* *
22018 AAGTTATCAAATTATTGAAAA
1 AAGTTAACAAATTAATGAAAA
22039 AA
1 AA
22041 TCAAATAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.30
Consensus pattern (21 bp):
AAGTTAACAAATTAATGAAAA
Found at i:27375 original size:2 final size:2
Alignment explanation
Indices: 27368--27402 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27358 CATCCTAAAT
27368 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
27403 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27407 original size:2 final size:2
Alignment explanation
Indices: 27402--27462 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
27392 ACACACACAC
27402 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
27444 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
27463 AAACTTAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39406 original size:117 final size:117
Alignment explanation
Indices: 39285--39534 Score: 383
Period size: 117 Copynumber: 2.1 Consensus size: 117
39275 TGCCCAAACA
*
39285 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGATCCA
1 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
* * * * *
39350 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGTACCAATG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
** * *
39402 AAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
* *
39467 TTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
*
39519 AAGTAAAGCTCGGTGC
1 AAGCAAAGCTCGGTGC
39535 GAAAGCTAAG
Statistics
Matches: 117, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (117 bp):
AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
Found at i:39562 original size:117 final size:116
Alignment explanation
Indices: 39285--39596 Score: 333
Period size: 117 Copynumber: 2.7 Consensus size: 116
39275 TGCCCAAACA
* * * * * *
39285 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGATCCA
1 AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* * * * *
39350 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGTACCAATG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
** * * *
39402 AAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* *
39467 TTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
* * *
39519 AAGTAAAGCTCGGTG-CGAAAGCTAAG-GGCCAAGCTGAA-GAGCCGAGGGTAAATAAGCGAGAG
1 AAGCAAAGCTCGGTGAC-AAAGC-AAGTGGCCAAGC--AACAAGCCGAGGGTAAAGAAGCGAGAG
* * *
39581 CAACTGGAGTGTTTCC
62 CCATTGAAGTGTTTCC
39597 GGTGCAAAGG
Statistics
Matches: 168, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
116 1 0.01
117 163 0.97
118 2 0.01
119 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (116 bp):
AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAACAAGCCGAGGGTAAAGAAGCGAGAGCCAT
TGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
Found at i:40223 original size:15 final size:15
Alignment explanation
Indices: 40203--40237 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40193 AGCAAGGCTC
40203 TTCGAGTGAAGCTTG
1 TTCGAGTGAAGCTTG
*
40218 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
40233 TTCGA
1 TTCGA
40238 ATGGTGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.37
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:47454 original size:23 final size:23
Alignment explanation
Indices: 47428--47478 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
47418 TTAAACGAAT
47428 ATGTTCGCGAATATAAAATGAAC
1 ATGTTCGCGAATATAAAATGAAC
* **
47451 ATGTTCGCGAGTATTCAATGAAC
1 ATGTTCGCGAATATAAAATGAAC
*
47474 TTGTT
1 ATGTT
47479 AACCTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (23 bp):
ATGTTCGCGAATATAAAATGAAC
Found at i:50532 original size:18 final size:20
Alignment explanation
Indices: 50509--50555 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
50499 AATGCAATAA
* *
50509 AATATTTTTGTA-TAT-ATT
1 AATATTTTTATATTATGAAT
50527 AATATTATTTATATTATGAAT
1 AATATT-TTTATATTATGAAT
50548 AATATTTT
1 AATATTTT
50556 AGTTTTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 5 0.21
20 5 0.21
21 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
AATATTTTTATATTATGAAT
Found at i:52469 original size:21 final size:21
Alignment explanation
Indices: 52439--52516 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
52429 GATTTACATA
*
52439 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
52460 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
52481 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
52502 TT--CGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
52517 GAAGACACGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.22
21 38 0.78
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:52491 original size:42 final size:40
Alignment explanation
Indices: 52439--52520 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 40
52429 GATTTACATA
*
52439 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAATT--CGTTGCGATAGTCGAAG
* **
52481 TTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAATTCGTTGCGATAGTCGAAG
52521 ACACGTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 17 0.47
42 19 0.53
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (40 bp):
TTCGCATTGCGATAGTCCAAATTCGTTGCGATAGTCGAAG
Found at i:53827 original size:25 final size:25
Alignment explanation
Indices: 53799--53853 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
53789 CATTTCCTCT
53799 GTGTTATCATTGACCGTGATTTTAG
1 GTGTTATCATTGACCGTGATTTTAG
53824 GTGTTATCATTGACCGTGATTTTAG
1 GTGTTATCATTGACCGTGATTTTAG
53849 GTGTT
1 GTGTT
53854 CTCAGATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (25 bp):
GTGTTATCATTGACCGTGATTTTAG
Found at i:56331 original size:8 final size:8
Alignment explanation
Indices: 56318--56348 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
56308 GTATCAGCCA
56318 GGAAAATT
1 GGAAAATT
56326 GGAAAATT
1 GGAAAATT
56334 GGAAAATT
1 GGAAAATT
56342 GGAAAAT
1 GGAAAAT
56349 AGCCTCGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.23
Consensus pattern (8 bp):
GGAAAATT
Found at i:57064 original size:23 final size:22
Alignment explanation
Indices: 57028--57077 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
57018 GATAATTTAA
*
57028 AAATAAAATTATTTCAAATAAAT
1 AAATAAAATGATTTCAAA-AAAT
* * *
57051 AAATAAGATGATTTTACAAAAT
1 AAATAAAATGATTTCAAAAAAT
57073 AAATA
1 AAATA
57078 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (22 bp):
AAATAAAATGATTTCAAAAAAT
Found at i:58472 original size:56 final size:56
Alignment explanation
Indices: 58381--58501 Score: 188
Period size: 56 Copynumber: 2.2 Consensus size: 56
58371 AAATAAGGTC
* *
58381 GTATATCTATCAGTTGTTACCATTAAGAAGTATAAAAATAGGGGCCCCGAAATTGA
1 GTATATCTATCAGTTGTTACCATTAAGAAGCATAAAAATAGGGGCCCCGAAATCGA
* * *
58437 GTATATCTATCAGTTGTTGCCATTAAGAAGCATAAAAATAGGGGCTCCGGAATCGA
1 GTATATCTATCAGTTGTTACCATTAAGAAGCATAAAAATAGGGGCCCCGAAATCGA
*
58493 ATATATCTA
1 GTATATCTA
58502 GAAAATAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (56 bp):
GTATATCTATCAGTTGTTACCATTAAGAAGCATAAAAATAGGGGCCCCGAAATCGA
Found at i:66638 original size:27 final size:30
Alignment explanation
Indices: 66599--66653 Score: 80
Period size: 27 Copynumber: 1.9 Consensus size: 30
66589 AAACACTCAA
66599 AACATTATTATTTTATAT-A-TTTAATATT
1 AACATTATTATTTTATATCATTTTAATATT
*
66627 AACA-TATTATTTTGTATCATTTTAATA
1 AACATTATTATTTTATATCATTTTAATA
66654 AAATATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 5 0.21
29 7 0.29
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (30 bp):
AACATTATTATTTTATATCATTTTAATATT
Found at i:68609 original size:6 final size:6
Alignment explanation
Indices: 68598--68628 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
68588 GACACGTATT
68598 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
68629 GCCGTGCCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:68694 original size:5 final size:5
Alignment explanation
Indices: 68629--68692 Score: 119
Period size: 5 Copynumber: 12.8 Consensus size: 5
68619 ACGACCACGA
68629 GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT
1 GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT
*
68679 GCCGT GCCGA GCCG
1 GCCGT GCCGT GCCG
68693 AGACGAGACG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.02, C:0.41, G:0.41, T:0.17
Consensus pattern (5 bp):
GCCGT
Found at i:69587 original size:2 final size:2
Alignment explanation
Indices: 69566--69616 Score: 75
Period size: 2 Copynumber: 24.0 Consensus size: 2
69556 ACTTGAAGGG
69566 TA TA TA TCA TCA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
69609 TA TA TA TA
1 TA TA TA TA
69617 ATTAAGAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 40 0.85
3 7 0.15
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:72424 original size:17 final size:17
Alignment explanation
Indices: 72402--72458 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
72392 AAAATGAAAC
72402 TAAAAGATACAATATAG
1 TAAAAGATACAATATAG
* * * *
72419 TAAAAGATATAGTAAAT
1 TAAAAGATACAATATAG
*
72436 TAAAAGATACATTATAG
1 TAAAAGATACAATATAG
*
72453 TGAAAG
1 TAAAAG
72459 GAACAATACA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (17 bp):
TAAAAGATACAATATAG
Found at i:75239 original size:2 final size:2
Alignment explanation
Indices: 75234--75272 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
75224 TCATCTCTCA
75234 AT AT AT AT AT 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 AT AT AT AT AT A
75273 CTAACTAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83494 original size:2 final size:2
Alignment explanation
Indices: 83470--83515 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
83460 AAGCATCTAG
* * *
83470 AT AT GT AT AT AT GT AT -T AA 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
83511 AT AT A
1 AT AT A
83516 CTTAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88514 original size:20 final size:20
Alignment explanation
Indices: 88489--88640 Score: 100
Period size: 20 Copynumber: 7.7 Consensus size: 20
88479 AAATGACCAA
88489 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
88509 CAAATTCGCAATGCG-AACT
1 CAAATTCGCAACGCGAAAGT
* * ***
88528 CCAATTTCGCAAC-CCAGTTT
1 -CAAATTCGCAACGCGAAAGT
*
88548 CCAATTTCGCAACGCG-AA-T
1 -CAAATTCGCAACGCGAAAGT
* *
88567 CTATAAATCGCAACAC-AGAA-T
1 C-A-AATTCGCAACGCGA-AAGT
* *
88588 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAAAGT
*
88608 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
88628 CAAATTCGCAACG
1 CAAATTCGCAACG
88641 TGAATAATAA
Statistics
Matches: 105, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.01
19 19 0.18
20 80 0.76
21 5 0.05
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:88664 original size:21 final size:21
Alignment explanation
Indices: 88634--88681 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
88624 TAGTCAAATT
88634 CGCAACGTGAATAATAAAAAG
1 CGCAACGTGAATAATAAAAAG
* * *
88655 CGCAATGTGAATAGT-AAAAT
1 CGCAACGTGAATAATAAAAAG
88675 CGCAACG
1 CGCAACG
88682 AATCTATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (21 bp):
CGCAACGTGAATAATAAAAAG
Found at i:89065 original size:20 final size:20
Alignment explanation
Indices: 89042--89090 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
89032 AAATTCGCGT
89042 TGCGATTTTACTATTCACGC
1 TGCGATTTTACTATTCACGC
89062 TGCGATTTTACTATTCACGC
1 TGCGATTTTACTATTCACGC
*
89082 TACGATTTT
1 TGCGATTTT
89091 GGAAACTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.43
Consensus pattern (20 bp):
TGCGATTTTACTATTCACGC
Done.