Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009319.1 Hibiscus syriacus cultivar Beakdansim tig00113076_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: 93026
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2792 original size:26 final size:28
Alignment explanation
Indices: 2744--2800 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 28
2734 ATTTATGTAC
*
2744 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAG-GTTGA
*
2773 TTATT-AAAA-ATATAT-TTTAGGTTGA
1 TTATTAAAAACATATATGGTTAGGTTGA
2798 TTA
1 TTA
2801 ATCAATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 7 0.27
26 4 0.15
27 6 0.23
28 4 0.15
29 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (28 bp):
TTATTAAAAACATATATGGTTAGGTTGA
Found at i:5144 original size:27 final size:29
Alignment explanation
Indices: 5086--5144 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
5076 ATTTATGTAC
*
5086 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
5115 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
5142 TTA
1 TTA
5145 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:12281 original size:20 final size:20
Alignment explanation
Indices: 12240--12295 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
12230 TTTAACCAGT
*
12240 TTTCAACCGGTTCTGACTGG
1 TTTCAACCGGTTCTGACCGG
12260 TTTCAACCGGTTC-GAACCGG
1 TTTCAACCGGTTCTG-ACCGG
*
12280 TTT-GACCGG-TCTGACC
1 TTTCAACCGGTTCTGACC
12296 CGACCCGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.16
19 7 0.22
20 20 0.62
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (20 bp):
TTTCAACCGGTTCTGACCGG
Found at i:12329 original size:17 final size:16
Alignment explanation
Indices: 12291--12345 Score: 83
Period size: 17 Copynumber: 3.3 Consensus size: 16
12281 TTGACCGGTC
*
12291 TGACCCGACCCGACCG
1 TGACCCGACCCGACCT
12307 TGACCCGACCCGACCAT
1 TGACCCGACCCGACC-T
12324 TGACCCGACCCGACCGT
1 TGACCCGACCCGACC-T
12341 TGACC
1 TGACC
12346 GTTGACTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.11
Consensus pattern (16 bp):
TGACCCGACCCGACCT
Found at i:14472 original size:27 final size:29
Alignment explanation
Indices: 14414--14472 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
14404 ATTTATGTAC
*
14414 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
14443 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
14470 TTA
1 TTA
14473 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:28551 original size:11 final size:10
Alignment explanation
Indices: 28515--28567 Score: 65
Period size: 9 Copynumber: 5.4 Consensus size: 10
28505 CGCTGGAAAT
28515 CGGTTTTGAC
1 CGGTTTTGAC
*
28525 CGG-TTTAAC
1 CGGTTTTGAC
*
28534 CGATTTTGAAC
1 CGGTTTTG-AC
28545 CGGTTTTGAC
1 CGGTTTTGAC
28555 CGG-TTTGAC
1 CGGTTTTGAC
28564 CGGT
1 CGGT
28568 AATGACCTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 16 0.44
10 11 0.31
11 9 0.25
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (10 bp):
CGGTTTTGAC
Found at i:28661 original size:29 final size:28
Alignment explanation
Indices: 28600--28696 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 28
28590 ACCGTTGATC
* ***
28600 GGTGCTATTCTGGGAATTAATTCAATTTT
1 GGTGCTATTTTGGGAATTAATTCAA-AAG
28629 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTC-AAAAG
* * *
28658 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTA-ATTCAAAAG
28687 GGTGCTATTT
1 GGTGCTATTT
28697 GTGTAAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 55 0.93
30 4 0.07
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTAATTCAAAAG
Found at i:35767 original size:19 final size:20
Alignment explanation
Indices: 35743--35781 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
35733 GAACGCTGGA
35743 AATCGGTTTTG-ACCGGTTT
1 AATCGGTTTTGAACCGGTTT
35762 AATCGGTTTTGAACCGGTTT
1 AATCGGTTTTGAACCGGTTT
35782 GACCGGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (20 bp):
AATCGGTTTTGAACCGGTTT
Found at i:35788 original size:20 final size:19
Alignment explanation
Indices: 35746--35788 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
35736 CGCTGGAAAT
*
35746 CGGTTTTGACCGGTTTAAT
1 CGGTTTTGACCGGTTTAAC
*
35765 CGGTTTTGAACCGGTTTGAC
1 CGGTTTTG-ACCGGTTTAAC
35785 CGGT
1 CGGT
35789 CATGACCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.14, C:0.19, G:0.30, T:0.37
Consensus pattern (19 bp):
CGGTTTTGACCGGTTTAAC
Found at i:35806 original size:23 final size:23
Alignment explanation
Indices: 35780--35834 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
35770 TTGAACCGGT
35780 TTGACCGGTCATGACCCGACCCG
1 TTGACCGGTCATGACCCGACCCG
* * *
35803 TTGACCCGACCTGACCCGACCCG
1 TTGACCGGTCATGACCCGACCCG
35826 TTGACCGGT
1 TTGACCGGT
35835 GCTATTCTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.40, G:0.25, T:0.18
Consensus pattern (23 bp):
TTGACCGGTCATGACCCGACCCG
Found at i:35809 original size:13 final size:13
Alignment explanation
Indices: 35791--35831 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
35781 TGACCGGTCA
35791 TGACCCGACCCGT
1 TGACCCGACCCGT
35804 TGACCCGA-CC--
1 TGACCCGACCCGT
35814 TGACCCGACCCGT
1 TGACCCGACCCGT
35827 TGACC
1 TGACC
35832 GGTGCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.32
11 2 0.08
12 2 0.08
13 13 0.52
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:35917 original size:29 final size:29
Alignment explanation
Indices: 35861--35928 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
35851 ATTCGGTTTT
* *
35861 GGTGTTATTTTGGGAATTAATTCGAAAAA
1 GGTGCTATTTTGGGAATTAATTCAAAAAA
* * * *
35890 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAA
35919 GGTGCTATTT
1 GGTGCTATTT
35929 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAA
Found at i:40222 original size:27 final size:29
Alignment explanation
Indices: 40164--40222 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
40154 ATTTATGTAC
*
40164 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
40193 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
40220 TTA
1 TTA
40223 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:42540 original size:27 final size:29
Alignment explanation
Indices: 42482--42540 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
42472 ATTTATGTAC
*
42482 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* *
42511 TTATTTAAAACATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
42538 TTA
1 TTA
42541 ATCAATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.47
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:44959 original size:13 final size:13
Alignment explanation
Indices: 44939--44995 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
44929 TAACCCGACC
44939 TGACCCGACCCTT
1 TGACCCGACCCTT
* *
44952 TTACCCGA-CCTGC
1 TGACCCGACCCT-T
*
44965 TGACCCGACCCGT
1 TGACCCGACCCTT
*
44978 TGACCCGACCCGT
1 TGACCCGACCCTT
44991 TGACC
1 TGACC
44996 GTTGACCGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 3 0.08
13 32 0.86
14 2 0.05
ACGTcount: A:0.16, C:0.46, G:0.19, T:0.19
Consensus pattern (13 bp):
TGACCCGACCCTT
Found at i:44973 original size:26 final size:26
Alignment explanation
Indices: 44938--44987 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
44928 ATAACCCGAC
* *
44938 CTGACCCGACCCTTTTACCCGACCTG
1 CTGACCCGACCCGTTGACCCGACCTG
44964 CTGACCCGACCCGTTGACCCGACC
1 CTGACCCGACCCGTTGACCCGACC
44988 CGTTGACCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.48, G:0.18, T:0.18
Consensus pattern (26 bp):
CTGACCCGACCCGTTGACCCGACCTG
Found at i:44994 original size:26 final size:26
Alignment explanation
Indices: 44938--44995 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
44928 ATAACCCGAC
* * *
44938 CTGACCCGACCCTTTTACCCGACCTG
1 CTGACCCGACCCGTTGACCCGACCCG
44964 CTGACCCGACCCGTTGACCCGACCCG
1 CTGACCCGACCCGTTGACCCGACCCG
*
44990 TTGACC
1 CTGACC
44996 GTTGACCGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.19
Consensus pattern (26 bp):
CTGACCCGACCCGTTGACCCGACCCG
Found at i:47471 original size:48 final size:47
Alignment explanation
Indices: 47414--47529 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 47
47404 TTCGATTTGA
*
47414 ATTCTGATCTGATACTTGACATGGATTCTGATCTGATATCTGACATGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATGATATCTGACAT-G
* * * * * *
47462 ATTCAGATCTAATACTTGACTTGGATTCTGATATGTTATTTGACCTG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATGATATCTGACATG
*
47509 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
47530 CTAATTTATG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 2 0.04
48 55 0.96
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (47 bp):
ATTCTGATCTGATACTTGACATGGATTCTGATATGATATCTGACATG
Found at i:47531 original size:24 final size:24
Alignment explanation
Indices: 47414--47529 Score: 128
Period size: 24 Copynumber: 4.8 Consensus size: 24
47404 TTCGATTTGA
47414 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
47438 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* * *
47462 ATTCAGATCTAATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * * *
47486 ATTCTGATATGTTATTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
47509 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
47530 CTAATTTATG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.04
24 74 0.95
25 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:47536 original size:24 final size:24
Alignment explanation
Indices: 47487--47536 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
47477 TTGACTTGGA
* * *
47487 TTCTGATATGTTATTTGACCTGAT
1 TTCTGATATGATACTTGACCTAAT
47511 TTCTGATATGATACTTGACCTAAT
1 TTCTGATATGATACTTGACCTAAT
47535 TT
1 TT
47537 ATGTTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (24 bp):
TTCTGATATGATACTTGACCTAAT
Found at i:49655 original size:18 final size:20
Alignment explanation
Indices: 49611--49659 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
49601 ACCGGTCATA
49611 ACCCGACCTGACCTGACCCGTTT
1 ACCCGACCTGA-CTGACCCG--T
49634 ACCCGACCTG-CTGACCCG-
1 ACCCGACCTGACTGACCCGT
49652 ACCCGACC
1 ACCCGACC
49660 CGTTGACCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.31
21 8 0.31
23 10 0.38
ACGTcount: A:0.18, C:0.49, G:0.18, T:0.14
Consensus pattern (20 bp):
ACCCGACCTGACTGACCCGT
Found at i:51829 original size:29 final size:29
Alignment explanation
Indices: 51792--51937 Score: 143
Period size: 29 Copynumber: 5.1 Consensus size: 29
51782 ATCAACCATT
* *
51792 TTACGAAAATAGCATCATTTTCAAAATAA
1 TTACCAAAATAGCACCATTTTCAAAATAA
*
51821 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACCAAAATAGCACCATTTTCAAAATAA
* ** ** **
51850 TTACTAAAATATTA-TTTTTTTTAAA-AA
1 TTACCAAAATAGCACCATTTTCAAAATAA
* * *
51877 TAACAAAAATAGCACCCTTTTCAAAATAA
1 TTACCAAAATAGCACCATTTTCAAAATAA
* *
51906 TTACCAGAATACCACCATTTTCAAAATAA
1 TTACCAAAATAGCACCATTTTCAAAATAA
51935 TTA
1 TTA
51938 TCAACGGGTC
Statistics
Matches: 93, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
27 12 0.13
28 14 0.15
29 67 0.72
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (29 bp):
TTACCAAAATAGCACCATTTTCAAAATAA
Found at i:51961 original size:18 final size:18
Alignment explanation
Indices: 51938--52016 Score: 77
Period size: 18 Copynumber: 4.1 Consensus size: 18
51928 AAAATAATTA
51938 TCAACGGGTCGGGTCAGG
1 TCAACGGGTCGGGTCAGG
51956 TCAACGGGTCGGGTCGAGTCTAG
1 TCAACGGGTCGGGTC-AG----G
* *
51979 TCAACGGGTCTGGTCGGG
1 TCAACGGGTCGGGTCAGG
* *
51997 TTAACGGGTCGAGTCAGG
1 TCAACGGGTCGGGTCAGG
52015 TC
1 TC
52017 GTAACCGGTC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
18 31 0.63
19 2 0.04
22 1 0.02
23 15 0.31
ACGTcount: A:0.16, C:0.22, G:0.41, T:0.22
Consensus pattern (18 bp):
TCAACGGGTCGGGTCAGG
Found at i:51981 original size:23 final size:23
Alignment explanation
Indices: 51942--51994 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
51932 TAATTATCAA
*
51942 CGGGTCGGGTCAGGTCAACGGGT
1 CGGGTCGAGTCAGGTCAACGGGT
51965 CGGGTCGAGTCTA-GTCAACGGGT
1 CGGGTCGAGTC-AGGTCAACGGGT
*
51988 CTGGTCG
1 CGGGTCG
51995 GGTTAACGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.21
Consensus pattern (23 bp):
CGGGTCGAGTCAGGTCAACGGGT
Found at i:58115 original size:42 final size:42
Alignment explanation
Indices: 58064--58185 Score: 190
Period size: 42 Copynumber: 2.9 Consensus size: 42
58054 CCTAGTAAAC
*
58064 CTGTAAGGCTTACCCTTACACACAGCAAAGGGACCTGAGAAA
1 CTGTAAGGCTTACCTTTACACACAGCAAAGGGACCTGAGAAA
* * *
58106 CTGTAAGGCTTACCTTTAAACACAACAAAGGGACCTGGGAAA
1 CTGTAAGGCTTACCTTTACACACAGCAAAGGGACCTGAGAAA
* *
58148 TTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGA
1 CTGTAAGGCTTACCTTTACACACAGCAAAGGGACCTGA
58186 TAATACTTCC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (42 bp):
CTGTAAGGCTTACCTTTACACACAGCAAAGGGACCTGAGAAA
Found at i:59193 original size:29 final size:29
Alignment explanation
Indices: 59009--59197 Score: 164
Period size: 29 Copynumber: 6.6 Consensus size: 29
58999 ATCAACCATT
* * *
59009 TTACGAAAATAGCATCATTTTCAAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
59038 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
* *** * *
59067 TTACTAAAATATCATTTTTTTAAAAAAAA
1 TTACCAAAATATCACCATTTTCAAAATAA
** * * * *
59096 TTATGAAATTATCA-CTTTTTTAAAAAAA
1 TTACCAAAATATCACCATTTTCAAAATAA
* * * *
59124 TTACAAAAATAGCTCCCTTTTCAAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
* * *
59153 TTACCAGAATACCACCATTTTCCAAATAA
1 TTACCAAAATATCACCATTTTCAAAATAA
*
59182 TTACCAAAATACCACC
1 TTACCAAAATATCACC
59198 CGATCAACGG
Statistics
Matches: 130, Mismatches: 29, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
28 21 0.16
29 109 0.84
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.33
Consensus pattern (29 bp):
TTACCAAAATATCACCATTTTCAAAATAA
Found at i:66694 original size:30 final size:30
Alignment explanation
Indices: 66660--66720 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
66650 AAATCGTTTG
66660 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
66690 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
66720 G
1 G
66721 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:69210 original size:21 final size:21
Alignment explanation
Indices: 69160--69222 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
69150 ATTCCCCTGT
69160 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
69183 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
*
69204 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
69223 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 20 0.56
22 3 0.08
23 13 0.36
ACGTcount: A:0.17, C:0.25, G:0.37, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:73075 original size:22 final size:21
Alignment explanation
Indices: 73033--73072 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
73023 GAGTTTGTTT
*
73033 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
73054 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
73073 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:75323 original size:30 final size:30
Alignment explanation
Indices: 75289--75349 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
75279 AAATCGTTTG
75289 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
75319 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
75349 G
1 G
75350 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:76617 original size:27 final size:27
Alignment explanation
Indices: 76569--76625 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
76559 ATTTTCGTAC
*
76569 TTATTAAAACATATATGGTTAGTGTTTA
1 TTATTAAAACATATATGGTTAG-GTTGA
* **
76597 TTATTTAAA-ATATATTTTTAGGTTGA
1 TTATTAAAACATATATGGTTAGGTTGA
76623 TTA
1 TTA
76626 ATCAATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.28
27 10 0.40
28 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (27 bp):
TTATTAAAACATATATGGTTAGGTTGA
Done.