Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002679.1 Hibiscus syriacus cultivar Beakdansim tig00005542_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: 55576
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:334 original size:2 final size:2
Alignment explanation
Indices: 327--375 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
317 CACGTGTAGT
327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
367 TA TA TA TA T
1 TA TA TA TA T
376 TATCCTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4681 original size:12 final size:12
Alignment explanation
Indices: 4664--4688 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4654 TTTGATGTTT
4664 TCTCTTTGATTC
1 TCTCTTTGATTC
4676 TCTCTTTGATTC
1 TCTCTTTGATTC
4688 T
1 T
4689 TGTTTCTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTCTTTGATTC
Found at i:4996 original size:64 final size:65
Alignment explanation
Indices: 4921--5125 Score: 170
Period size: 65 Copynumber: 3.2 Consensus size: 65
4911 TGCATTGGGG
* *
4921 TGTGCATCGGTGCACAAATAT-ACTTCGATGATTCAA-AATAGC-CGGGGTGCATCGATGCATTG
1 TGTGCATCGGTGCACAAA-ATCAATTCGATGATTCAATAATA-CACGGAGTGCATCGATGCA-TG
4983 CT-
63 CTA
* * * * *
4985 TGTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATGGTA
1 TGTGCATCGGTGCACAAAATCAATTCGATGATTCAATAATACACGGAGTGCATCGATGCATGCTA
* * * * * * ** *
5050 TGTGCATCGGTACATAAAAACCATTTGATG-TTCAATTAAAACAATG-GTGCATCGATGCATTGA
1 TGTGCATCGGTGCACAAAATCAATTCGATGATTCAA-TAATACACGGAGTGCATCGATGCA-TGC
5113 TA
64 TA
*
5115 TATGCATCGGT
1 TGTGCATCGGT
5126 ACACTTACCT
Statistics
Matches: 118, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
63 2 0.02
64 50 0.42
65 66 0.56
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (65 bp):
TGTGCATCGGTGCACAAAATCAATTCGATGATTCAATAATACACGGAGTGCATCGATGCATGCTA
Found at i:5045 original size:65 final size:65
Alignment explanation
Indices: 4966--5128 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 65
4956 AAATAGCCGG
* * * * *
4966 GGTGCATCGATGCATTGCT-TGTGCATCGGTGCATAAAATCAATTCGATGTTTTAA-TAATAC-A
1 GGTGCATCGATGCATTGATATGTGCATCGGTACATAAAAACAATTCGATG-TTCAATTAAAACAA
5028 T
65 T
* * *
5029 GGAGTGCATCGATGCA-TGGTATGTGCATCGGTACATAAAAACCATTTGATGTTCAATTAAAACA
1 -G-GTGCATCGATGCATTGATATGTGCATCGGTACATAAAAACAATTCGATGTTCAATTAAAACA
5093 AT
64 AT
*
5095 GGTGCATCGATGCATTGATATATGCATCGGTACA
1 GGTGCATCGATGCATTGATATGTGCATCGGTACA
5129 CTTACCTGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
64 21 0.25
65 62 0.73
66 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (65 bp):
GGTGCATCGATGCATTGATATGTGCATCGGTACATAAAAACAATTCGATGTTCAATTAAAACAAT
Found at i:5798 original size:15 final size:17
Alignment explanation
Indices: 5761--5798 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
5751 CCAAAACATA
5761 AATCCAAACATATAAAC
1 AATCCAAACATATAAAC
5778 -ATCCAAA-ATA-AAAC
1 AATCCAAACATATAAAC
5792 AATCCAA
1 AATCCAA
5799 TAACATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.16
Consensus pattern (17 bp):
AATCCAAACATATAAAC
Found at i:7551 original size:19 final size:19
Alignment explanation
Indices: 7524--7570 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
7514 ATGTTGTTTT
7524 GCACGATTTAATGATTAAA
1 GCACGATTTAATGATTAAA
* *
7543 GCTCGATTTAATGATTGAA
1 GCACGATTTAATGATTAAA
7562 GCACGATTT
1 GCACGATTT
7571 GTAGTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (19 bp):
GCACGATTTAATGATTAAA
Found at i:7652 original size:18 final size:18
Alignment explanation
Indices: 7629--7664 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7619 GCAGTTTTGA
*
7629 GAGTGGTGAGAGAGAGAG
1 GAGTGGCGAGAGAGAGAG
*
7647 GAGTGGCGATAGAGAGAG
1 GAGTGGCGAGAGAGAGAG
7665 TTTTAGGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.53, T:0.11
Consensus pattern (18 bp):
GAGTGGCGAGAGAGAGAG
Found at i:7840 original size:44 final size:43
Alignment explanation
Indices: 7751--7847 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 43
7741 GGCAGTGTGC
*
7751 ATCAATGCACATTCAAGGAGTGCATCGGTGCATATTTATTATGT
1 ATCAATGCACATTCAAGGAGTGCATCGATGCATATTTA-TATGT
* *
7795 ATCGATGCACATTCAAAGGCA-TGCATCGATGCACTATTTA-GTGT
1 ATCAATGCACATTC-AAGG-AGTGCATCGATGCA-TATTTATATGT
7839 ATCAATGCA
1 ATCAATGCA
7848 TTATGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 24 0.52
45 15 0.33
46 7 0.15
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (43 bp):
ATCAATGCACATTCAAGGAGTGCATCGATGCATATTTATATGT
Found at i:11703 original size:22 final size:21
Alignment explanation
Indices: 11661--11700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11651 AAGACTATTT
11661 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
11682 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
11701 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:13729 original size:64 final size:65
Alignment explanation
Indices: 13638--13762 Score: 148
Period size: 64 Copynumber: 1.9 Consensus size: 65
13628 TGCACTGGGG
* *
13638 TGTGCATCAGTGCACAAATATACTTCGATGATTCAA-AATAGC-CGGGGTGCATCGATGCATTGC
1 TGTGCATCAGTGCACAAATATAATTCGATGATTCAATAATA-CACGGAGTGCATCGATGCATTGC
13701 T
65 T
* * * * *
13702 TGTGCATCGGTGCATAAA-ATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCAT
1 TGTGCATCAGTGCACAAATAT-AATTCGATGATTCAATAATACACGGAGTGCATCGATGCAT
13763 GGTATGTGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.04
64 29 0.57
65 20 0.39
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
TGTGCATCAGTGCACAAATATAATTCGATGATTCAATAATACACGGAGTGCATCGATGCATTGCT
Found at i:13845 original size:65 final size:64
Alignment explanation
Indices: 13682--13845 Score: 172
Period size: 65 Copynumber: 2.5 Consensus size: 64
13672 AAAATAGCCG
* * * *
13682 GGGTGCATCGATGCATTGCTTGTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACAT
1 GGGTGCATCGATGCATTGTTTGTGCATCGGTACATAAAAGCAATTCAATGTTTTAATAATACAT
* * * * *
13746 GGAGTGCATCGATGCATGGTATGTGAATCAGTACATAAAAGCCATTCAATGTTCAATTAA-AATA
1 GG-GTGCATCGATGCATTGTTTGTGCATCGGTACATAAAAGCAATTCAATGTT---TTAATAATA
13810 -A-
62 CAT
*
13811 GGGTGCATCGATGCATTGATTTATGCATCGGTACA
1 GGGTGCATCGATGCATTG-TTTGTGCATCGGTACA
13846 CTTACCTGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
64 17 0.21
65 55 0.68
66 1 0.01
67 4 0.05
68 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (64 bp):
GGGTGCATCGATGCATTGTTTGTGCATCGGTACATAAAAGCAATTCAATGTTTTAATAATACAT
Found at i:15727 original size:18 final size:18
Alignment explanation
Indices: 15701--15789 Score: 151
Period size: 18 Copynumber: 4.9 Consensus size: 18
15691 ACTGAATATT
*
15701 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
15719 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
15737 TGTCCCGAAGGACCTCTA
1 TGTCCCGAAGGACCACTA
15755 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
15773 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
15790 GTAAATCCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:17033 original size:2 final size:2
Alignment explanation
Indices: 17026--17057 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17016 CGTGTAGCTA
17026 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
17058 CTCCTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23819 original size:31 final size:31
Alignment explanation
Indices: 23784--23844 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
23774 TGACCATATC
23784 TATTTTTCACAATAGTATTTGTTTATATTTA
1 TATTTTTCACAATAGTATTTGTTTATATTTA
23815 TATTTTTCACAATAGTATTTGTTTATATTT
1 TATTTTTCACAATAGTATTTGTTTATATTT
23845 CTCTATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (31 bp):
TATTTTTCACAATAGTATTTGTTTATATTTA
Found at i:23854 original size:31 final size:31
Alignment explanation
Indices: 23788--23854 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
23778 CATATCTATT
*
23788 TTTCACAATAGTATTTGTTTATATTTATATT
1 TTTCACAATAGTATTTGTTTATATTTATATA
* *
23819 TTTCACAATAGTATTTGTTTATATTTCTCTA
1 TTTCACAATAGTATTTGTTTATATTTATATA
23850 TTTCA
1 TTTCA
23855 AGTTGTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (31 bp):
TTTCACAATAGTATTTGTTTATATTTATATA
Found at i:25061 original size:13 final size:13
Alignment explanation
Indices: 25043--25072 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
25033 AACCCGACCC
25043 GACCCGACCCGTT
1 GACCCGACCCGTT
25056 GACCCGACCCGTT
1 GACCCGACCCGTT
25069 GACC
1 GACC
25073 GGAGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:26465 original size:43 final size:41
Alignment explanation
Indices: 26386--26480 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 41
26376 GGACTGAAAC
* * *
26386 AAATAATGATATT-GAATTAATAATAAGATCGGATGGAGGTAA
1 AAAT-ATGAAATTGGAATTAATAATAAGACCGAATGGAGG-AA
26428 AAGATAT-AAATTGGAATTAAATAATAAGACCGAATGGAGGAA
1 AA-ATATGAAATTGGAATT-AATAATAAGACCGAATGGAGGAA
26470 AAATATGAAAT
1 AAATATGAAAT
26481 ACCGTGGATC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
41 8 0.17
42 17 0.37
43 21 0.46
ACGTcount: A:0.52, C:0.03, G:0.20, T:0.25
Consensus pattern (41 bp):
AAATATGAAATTGGAATTAATAATAAGACCGAATGGAGGAA
Found at i:27639 original size:23 final size:24
Alignment explanation
Indices: 27592--27682 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
27582 TCCGACTTGA
* * *
27592 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
27616 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
27639 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
27663 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
27683 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:27652 original size:47 final size:48
Alignment explanation
Indices: 27592--27682 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
27582 TCCGACTTGA
* * *
27592 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
27639 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
27683 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:29886 original size:13 final size:13
Alignment explanation
Indices: 29867--29922 Score: 103
Period size: 13 Copynumber: 4.3 Consensus size: 13
29857 AACCCGACCC
29867 GACCCGACCCGTT
1 GACCCGACCCGTT
*
29880 TACCCGACCCGTT
1 GACCCGACCCGTT
29893 GACCCGACCCGTT
1 GACCCGACCCGTT
29906 GACCCGACCCGTT
1 GACCCGACCCGTT
29919 GACC
1 GACC
29923 GGAGTTGACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.16, C:0.46, G:0.21, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:32492 original size:23 final size:24
Alignment explanation
Indices: 32445--32535 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
32435 TCCGACTTGA
* * *
32445 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
32469 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
32492 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
32516 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
32536 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:32505 original size:47 final size:48
Alignment explanation
Indices: 32445--32535 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
32435 TCCGACTTGA
* * *
32445 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
32492 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
32536 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:34564 original size:31 final size:31
Alignment explanation
Indices: 34528--34591 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
34518 CGCTGATTGG
34528 TTTATCGCCGTGAATGAGGACTGGGATTTTC
1 TTTATCGCCGTGAATGAGGACTGGGATTTTC
34559 TTTATCGCCGTGAATGAGGACTGGGATTTTC
1 TTTATCGCCGTGAATGAGGACTGGGATTTTC
34590 TT
1 TT
34592 GTAAACCGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.38
Consensus pattern (31 bp):
TTTATCGCCGTGAATGAGGACTGGGATTTTC
Found at i:35810 original size:16 final size:16
Alignment explanation
Indices: 35789--35819 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35779 TTTAATATAT
35789 TTTTTAATATTTAATC
1 TTTTTAATATTTAATC
*
35805 TTTTTAATCTTTAAT
1 TTTTTAATATTTAAT
35820 ATTTCAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAATATTTAATC
Found at i:39495 original size:22 final size:21
Alignment explanation
Indices: 39447--39487 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39437 AAATAAATAA
*
39447 TAAATAAATAATATGTATATAT
1 TAAA-AAATAATATGTATATAG
39469 TAAAAAA-AATATGTATATA
1 TAAAAAATAATATGTATATA
39488 CAGTAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.63
21 3 0.16
22 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
TAAAAAATAATATGTATATAG
Found at i:41107 original size:105 final size:105
Alignment explanation
Indices: 40933--41707 Score: 1469
Period size: 105 Copynumber: 7.4 Consensus size: 105
40923 GTGTTGTTTC
40933 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
40998 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* ** *
41038 GAGTCCAATATCCCTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
41103 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
41143 GAGTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
41208 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
41248 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
41313 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
41353 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
41418 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
41458 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
41523 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
41563 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
41628 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
41668 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
41708 GGTAAAACCT
Statistics
Matches: 656, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 656 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:42510 original size:48 final size:48
Alignment explanation
Indices: 42452--42544 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
42442 CTTTTTCCTC
* * * *
42452 TTTTTCTTTTTTAATTTAGGGCGCCCTT-TCGGGTTTTCACCCTAAACG
1 TTTTTCTTTTTCAACTTAGGAC-ACCTTCTCGGGTTTTCACCCTAAACG
* *
42500 TTTTTTTTTTTCAACTTAGGACACCTTCTCGGGTTTTCATCCTAA
1 TTTTTCTTTTTCAACTTAGGACACCTTCTCGGGTTTTCACCCTAA
42545 GCGAAGTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 4 0.11
48 34 0.89
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.47
Consensus pattern (48 bp):
TTTTTCTTTTTCAACTTAGGACACCTTCTCGGGTTTTCACCCTAAACG
Found at i:50987 original size:20 final size:21
Alignment explanation
Indices: 50962--51003 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
50952 TAATAAATTA
50962 CCTAGAGGTGAATA-GTGGTG
1 CCTAGAGGTGAATAGGTGGTG
50982 CCTAGAGGTGAATAGGTGGTG
1 CCTAGAGGTGAATAGGTGGTG
51003 C
1 C
51004 TGAAACGGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (21 bp):
CCTAGAGGTGAATAGGTGGTG
Found at i:54413 original size:7 final size:7
Alignment explanation
Indices: 54410--54443 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
54400 TAAATATAAT
54410 ATATATA
1 ATATATA
54417 TATATATA
1 -ATATATA
54425 ATATATA
1 ATATATA
*
54432 TTATATA
1 ATATATA
54439 ATATA
1 ATATA
54444 ATTTACACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATATATA
Found at i:54415 original size:2 final size:2
Alignment explanation
Indices: 54403--54443 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
54393 TAATTAATAA
54403 AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT AT -T AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54441 AT A
1 AT A
54444 ATTTACACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:54415 original size:9 final size:9
Alignment explanation
Indices: 54397--54445 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
54387 ATGTAATAAT
*
54397 TAATAAATA
1 TAATATATA
54406 TAATATATA
1 TAATATATA
54415 T-ATATATA
1 TAATATATA
54423 TAATATATA
1 TAATATATA
*
54432 TTATATAATA
1 TAATAT-ATA
54442 TAAT
1 TAAT
54446 TTACACTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 8 0.23
9 21 0.60
10 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATATATA
Found at i:54432 original size:19 final size:19
Alignment explanation
Indices: 54402--54445 Score: 74
Period size: 17 Copynumber: 2.4 Consensus size: 19
54392 ATAATTAATA
54402 AATATAATATATA-TATAT
1 AATATAATATATATTATAT
54420 -ATATAATATATATTATAT
1 AATATAATATATATTATAT
54438 AATATAAT
1 AATATAAT
54446 TTACACTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATAATATATATTATAT
Found at i:55156 original size:20 final size:20
Alignment explanation
Indices: 55133--55170 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55123 AAATTATGAT
55133 AAAAATATTTTATTAAAATA
1 AAAAATATTTTATTAAAATA
55153 AAAAATATTTTATTAAAA
1 AAAAATATTTTATTAAAA
55171 AACTTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATATTTTATTAAAATA
Done.