Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007208.1 Hibiscus syriacus cultivar Beakdansim tig00019045_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: 79159
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:8139 original size:18 final size:18
Alignment explanation
Indices: 8116--8155 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
8106 GACATTGTTT
8116 TCTTGTTTCTTGCCTAAC
1 TCTTGTTTCTTGCCTAAC
8134 TCTTGTTTCTTGCCTAAC
1 TCTTGTTTCTTGCCTAAC
8152 TCTT
1 TCTT
8156 CCAAGAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.53
Consensus pattern (18 bp):
TCTTGTTTCTTGCCTAAC
Found at i:9138 original size:22 final size:22
Alignment explanation
Indices: 9113--9158 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
9103 GTTTACAAAT
* *
9113 AGGGAATCGATTCCCCTACTAC
1 AGGGAACCGATTCCACTACTAC
*
9135 AGGGAACCGATTCCACTGCTAC
1 AGGGAACCGATTCCACTACTAC
9157 AG
1 AG
9159 TACTTCCGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCACTACTAC
Found at i:9700 original size:21 final size:21
Alignment explanation
Indices: 9651--9714 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
9641 ATATGAAATT
*
9651 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
9672 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
9694 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
9715 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:15965 original size:22 final size:22
Alignment explanation
Indices: 15940--15985 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
15930 GTTTACAAAT
15940 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTCCCCTGCTAC
15962 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTCCCCTGCTAC
15984 AG
1 AG
15986 TACTGCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (22 bp):
AGGGAATCGATTCCCCTGCTAC
Found at i:16553 original size:21 final size:21
Alignment explanation
Indices: 16504--16567 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
16494 ATATGAAATT
*
16504 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
16525 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
16547 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
16568 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:22196 original size:24 final size:25
Alignment explanation
Indices: 22146--22193 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
22136 GAAATTGGGA
*
22146 TTTTTTAAATATAATAATTTTTTAAT
1 TTTTTTAAATATAAT-ATTTTTAAAT
22172 TTTTTTAAATA-AAT-TTTTTAAA
1 TTTTTTAAATATAATATTTTTAAA
22194 ATTAATTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTTTAAATATAATATTTTTAAAT
Found at i:27779 original size:13 final size:13
Alignment explanation
Indices: 27761--27786 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27751 ATTATTTAAA
27761 TTTATTTTAAAAT
1 TTTATTTTAAAAT
27774 TTTATTTTAAAAT
1 TTTATTTTAAAAT
27787 ATGAATTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTTTAAAAT
Found at i:27802 original size:22 final size:22
Alignment explanation
Indices: 27774--28048 Score: 378
Period size: 22 Copynumber: 12.5 Consensus size: 22
27764 ATTTTAAAAT
27774 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
27796 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
**
27818 TTTATTTTAAAATATAGAA-AAA
1 TTTATTTTAAAATAT-GAATTGA
*
27840 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
*
27862 TTTATTTTAAAATATAGAA--AA
1 TTTATTTTAAAATAT-GAATTGA
27883 TTTATTTTAAAATAT-AGATTGA
1 TTTATTTTAAAATATGA-ATTGA
***
27905 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGAATTGA
27927 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
*
27949 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
***
27971 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGAATTGA
*
27993 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
*
28015 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
28037 TTTATTTTAAAA
1 TTTATTTTAAAA
28049 AAATTATTAT
Statistics
Matches: 223, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.00
20 1 0.00
21 18 0.08
22 197 0.88
23 6 0.03
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGAATTGA
Found at i:28129 original size:31 final size:31
Alignment explanation
Indices: 28072--28130 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28062 AGTTGTATGG
* *
28072 ATTATTTAAATTTTAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
28103 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
28131 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:28380 original size:41 final size:41
Alignment explanation
Indices: 28323--28416 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
28313 GATCTGGGTG
*
28323 GCAAAAATAATTGAACTGACATGCACATTCCTGCCCAAAAA
1 GCAAACATAATTGAACTGACATGCACATTCCTGCCCAAAAA
*
28364 GCAAACATAATTGAACTGACATGCACATTCCTGCCCTAAAA
1 GCAAACATAATTGAACTGACATGCACATTCCTGCCCAAAAA
28405 GCAAACATAATT
1 GCAAACATAATT
28417 TAAACACCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (41 bp):
GCAAACATAATTGAACTGACATGCACATTCCTGCCCAAAAA
Found at i:31678 original size:2 final size:2
Alignment explanation
Indices: 31671--31697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31661 TAAGTTTGTA
31671 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 A
31698 ATTGTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34270 original size:23 final size:23
Alignment explanation
Indices: 34244--34288 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
34234 TTATGCTTTC
34244 ATCTCTTA-TCATAAAAAATCACT
1 ATCTCTTACT-ATAAAAAATCACT
*
34267 ATCTCTTACTATAGAAAATCAC
1 ATCTCTTACTATAAAAAATCAC
34289 CAACCGACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.33
Consensus pattern (23 bp):
ATCTCTTACTATAAAAAATCACT
Found at i:35697 original size:16 final size:18
Alignment explanation
Indices: 35676--35720 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
35666 AACATTCCCA
35676 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
35692 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
35712 GTAATCTTA
1 GTAATCTTA
35721 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:35714 original size:20 final size:20
Alignment explanation
Indices: 35689--35726 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
35679 ATCTTATTCC
35689 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
35709 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
35727 GTGAACCAAA
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:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:36534 original size:23 final size:23
Alignment explanation
Indices: 36506--36563 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
36496 AAATTAATAA
36506 TATATTATGTAAAATGTTTCAAT
1 TATATTATGTAAAATGTTTCAAT
*
36529 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCAAT
36552 TATA--ATGTAAAA
1 TATATTATGTAAAA
36564 ATTATAACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 8 0.24
23 26 0.76
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCAAT
Found at i:36606 original size:13 final size:13
Alignment explanation
Indices: 36577--36611 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
36567 ATAACTAATA
*
36577 ATATTAAAT-ATT
1 ATATTAAATAAAT
36589 ATATTAAATAAAT
1 ATATTAAATAAAT
36602 ATATTAAATA
1 ATATTAAATA
36612 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:39617 original size:8 final size:8
Alignment explanation
Indices: 39604--39644 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
39594 CTCATTTTCA
39604 GAGAATTT
1 GAGAATTT
39612 GAGAATTT
1 GAGAATTT
*
39620 -AGAGTTT
1 GAGAATTT
*
39627 GGGAATTT
1 GAGAATTT
39635 GAGAATTT
1 GAGAATTT
39643 GA
1 GA
39645 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:39937 original size:126 final size:127
Alignment explanation
Indices: 39712--39953 Score: 477
Period size: 126 Copynumber: 1.9 Consensus size: 127
39702 CTATAATCGG
39712 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
39777 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATA-TATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATTATCAGTACCTATTAT
39838 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
39903 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATTATCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATTATCA
39954 TTAATTATAA
Statistics
Matches: 115, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 110 0.96
127 5 0.04
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (127 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATTATCAGTACCTATTAT
Found at i:40129 original size:34 final size:32
Alignment explanation
Indices: 40084--40172 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
40074 TTAATAATTC
40084 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAATAATTATATAAATA-TA--TTAATA
* * *
40120 -ATAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTATATAAATATATTAATA
* *
40151 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
40173 AAATACTAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 6 0.14
32 16 0.36
33 2 0.05
34 18 0.41
35 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTATATAAATATATTAATA
Found at i:40153 original size:14 final size:15
Alignment explanation
Indices: 40087--40159 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
40077 ATAATTCTAA
40087 ATAAATAATAATT-AT
1 ATAAATAAT-ATTAAT
*
40102 ATAAATATTATTTTAAT
1 ATAAATA--ATATTAAT
* *
40119 AATAAAATAATATTTAC
1 -AT-AAATAATATTAAT
40136 ATAAAT-ATATTAAT
1 ATAAATAATATTAAT
*
40150 ATAAAAAATA
1 ATAAATAATA
40160 ATAACTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 11 0.24
15 14 0.31
16 4 0.09
17 9 0.20
18 2 0.04
19 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAATATTAAT
Found at i:41098 original size:14 final size:15
Alignment explanation
Indices: 41069--41142 Score: 59
Period size: 14 Copynumber: 5.3 Consensus size: 15
41059 AAATAATTAA
41069 AATAATATATTTTAT
1 AATAATATATTTTAT
41084 AATAATATA-TTTAT
1 AATAATATATTTTAT
* *
41098 AATCAT-TATTATAT
1 AATAATATATTTTAT
** *
41112 TTTAA-AT-TATTA-
1 AATAATATATTTTAT
*
41124 AAAAATATATTTTAT
1 AATAATATATTTTAT
41139 AATA
1 AATA
41143 TTTTTAATAA
Statistics
Matches: 42, Mismatches: 12, Indels: 10
0.66 0.19 0.16
Matches are distributed among these distances:
12 2 0.05
13 7 0.17
14 21 0.50
15 12 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:41156 original size:32 final size:33
Alignment explanation
Indices: 41103--41168 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
41093 TTTATAATCA
* * *
41103 TTATTATATTTTAAATTATTAAA-AAATATATT
1 TTATAATATTTTAAATAATTAAATAAAAATATT
*
41135 TTATAATATTTTTAATAATTAAATAAAAATATT
1 TTATAATATTTTAAATAATTAAATAAAAATATT
41168 T
1 T
41169 AAAATCTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TTATAATATTTTAAATAATTAAATAAAAATATT
Found at i:41167 original size:55 final size:56
Alignment explanation
Indices: 41051--41173 Score: 137
Period size: 55 Copynumber: 2.2 Consensus size: 56
41041 TGAATATATC
* * *
41051 AATATTTTAAATAATTAAAATAATATATTTTATAATAATATATTTATAATCATTAT
1 AATATTTTAAATAATTAAAATAATATATTTTATAATAATATATTTATAATAATAAA
* *
41107 TATATTTTAAATTATTAAAA-AATATATTTTATAAT-AT-T-TTTAATAATTAAATAAA
1 AATATTTTAAATAATTAAAATAATATATTTTATAATAATATATTT-ATAA-T-AATAAA
*
41162 AATATTTAAAAT
1 AATATTTTAAAT
41174 CTTAAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
52 3 0.05
53 5 0.09
54 3 0.05
55 28 0.49
56 18 0.32
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (56 bp):
AATATTTTAAATAATTAAAATAATATATTTTATAATAATATATTTATAATAATAAA
Found at i:41693 original size:17 final size:17
Alignment explanation
Indices: 41671--41709 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
41661 TGATCACTGT
41671 AACAATTACACTACTTA
1 AACAATTACACTACTTA
41688 AACAATTACACTACTTA
1 AACAATTACACTACTTA
41705 AACAA
1 AACAA
41710 ATAATTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (17 bp):
AACAATTACACTACTTA
Found at i:47900 original size:15 final size:15
Alignment explanation
Indices: 47880--47920 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
47870 CGTGCGATTA
47880 CAACATGGGTGCCTT
1 CAACATGGGTGCCTT
* *
47895 CAACATTGGTGTCTT
1 CAACATGGGTGCCTT
47910 CAACATGGGTG
1 CAACATGGGTG
47921 GCATTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (15 bp):
CAACATGGGTGCCTT
Found at i:51621 original size:59 final size:60
Alignment explanation
Indices: 51554--51666 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
51544 TAAAGTACAC
* * * *
51554 AAATGATCCCCT-ATTATAGGATATTATTTTGTTGAGTC-CCCTGACTATTAAAAGTTGTA
1 AAATGATCCCATGATTATAGGAAATTACTTTGTTGAGTCACTC-GACTATTAAAAGTTGTA
* *
51613 AAATGATCCCATGGTTATAGGAAATTGCTTTGTTGAGTCACTCGACTATTAAAA
1 AAATGATCCCATGATTATAGGAAATTACTTTGTTGAGTCACTCGACTATTAAAA
51667 TTTACAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 11 0.24
60 33 0.72
61 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (60 bp):
AAATGATCCCATGATTATAGGAAATTACTTTGTTGAGTCACTCGACTATTAAAAGTTGTA
Found at i:51676 original size:60 final size:59
Alignment explanation
Indices: 51545--51676 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
51535 GATTTAGGGT
* * *
51545 AAAG-TACACAAATGATCCCCTATTATAGGATATTATTTTGTTGAGTCCCCTGACTATTA
1 AAAGTTACA-AAATGATCCCATATTATAGGAAATTACTTTGTTGAGTCCCCTGACTATTA
** * * *
51604 AAAGTTGTAAAATGATCCCATGGTTATAGGAAATTGCTTTGTTGAGT-CACTCGACTATTA
1 AAAGTTACAAAATGATCCCAT-ATTATAGGAAATTACTTTGTTGAGTCCCCT-GACTATTA
*
51664 AAATTTACAAAAT
1 AAAGTTACAAAAT
51677 AGTCATCAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
59 18 0.31
60 41 0.69
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (59 bp):
AAAGTTACAAAATGATCCCATATTATAGGAAATTACTTTGTTGAGTCCCCTGACTATTA
Found at i:53280 original size:8 final size:9
Alignment explanation
Indices: 53259--53283 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53249 ATGTTTACAT
53259 TTTTTTATA
1 TTTTTTATA
53268 TTTTTTATA
1 TTTTTTATA
53277 TTTTTTA
1 TTTTTTA
53284 AGACTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTATA
Found at i:55588 original size:20 final size:20
Alignment explanation
Indices: 55560--55599 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55550 GAACATCCTA
*
55560 GAACCAGTTCGAATCAACTC
1 GAACAAGTTCGAATCAACTC
* *
55580 GAACAAGTTTGAGTCAACTC
1 GAACAAGTTCGAATCAACTC
55600 AAACCAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (20 bp):
GAACAAGTTCGAATCAACTC
Found at i:55632 original size:20 final size:20
Alignment explanation
Indices: 55609--55664 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
55599 CAAACCAAAT
*
55609 TGAGTCAACTCAAATCGGCC
1 TGAGTCAACCCAAATCGGCC
55629 TGAGTCAACCCAAATCGGCC
1 TGAGTCAACCCAAATCGGCC
*
55649 TGAGTAAACCCAAATC
1 TGAGTCAACCCAAATC
55665 AGTTTGACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (20 bp):
TGAGTCAACCCAAATCGGCC
Found at i:55703 original size:19 final size:19
Alignment explanation
Indices: 55693--55756 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
55683 TGACATGAAC
*
55693 CGTTGACTTTGACACAAAT
1 CGTTAACTTTGACACAAAT
55712 CGTTAACTTTGACACAAAT
1 CGTTAACTTTGACACAAAT
55731 CGTTAACTTTGACACAAAT
1 CGTTAACTTTGACACAAAT
55750 CGTTAAC
1 CGTTAAC
55757 CGTTGACCAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (19 bp):
CGTTAACTTTGACACAAAT
Found at i:55779 original size:39 final size:38
Alignment explanation
Indices: 55693--55782 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 38
55683 TGACATGAAC
*
55693 CGTTGACTTTGACACAAATCGTTAACTTTGACACAAAT
1 CGTTGACTTTGACACAAATCGTTAACGTTGACACAAAT
*
55731 CGTTAACTTTGACACAAATCGTTAACCGTTGAC-CAGACA-
1 CGTTGACTTTGACACAAATCGTTAA-CGTTGACACA-A-AT
55770 CGTTGACTTTGAC
1 CGTTGACTTTGAC
55783 TGGTTTGACC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
38 26 0.57
39 19 0.41
40 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (38 bp):
CGTTGACTTTGACACAAATCGTTAACGTTGACACAAAT
Found at i:55952 original size:13 final size:14
Alignment explanation
Indices: 55934--55962 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55924 CATGTGTAAT
55934 TTAAGTG-ATTTAA
1 TTAAGTGCATTTAA
55947 TTAAGTGCATTTAA
1 TTAAGTGCATTTAA
55961 TT
1 TT
55963 TAATTTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (14 bp):
TTAAGTGCATTTAA
Found at i:68485 original size:29 final size:29
Alignment explanation
Indices: 68452--68542 Score: 173
Period size: 29 Copynumber: 3.1 Consensus size: 29
68442 ACAGAGAAAG
68452 AAACAAATTATTAACTCAACTAAAAATTA
1 AAACAAATTATTAACTCAACTAAAAATTA
68481 AAACAAATTATTAACTCAACTAAAAATTA
1 AAACAAATTATTAACTCAACTAAAAATTA
*
68510 AAACAAATTATTAACACAACTAAAAATTA
1 AAACAAATTATTAACTCAACTAAAAATTA
68539 AAAC
1 AAAC
68543 CTTCTATCTC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.25
Consensus pattern (29 bp):
AAACAAATTATTAACTCAACTAAAAATTA
Found at i:68799 original size:37 final size:37
Alignment explanation
Indices: 68758--68832 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
68748 GTAGAAAAAT
*
68758 ATTTATATA-TTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTTCTTTAAAAAATTGAAATT-ATAAA
* *
68795 ATTTATATATTTTTTTTTATAAAATTGAAATTATAAA
1 ATTTATATATTTTTCTTTAAAAAATTGAAATTATAAA
68832 A
1 A
68833 AGGTTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 15 0.44
38 19 0.56
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (37 bp):
ATTTATATATTTTTCTTTAAAAAATTGAAATTATAAA
Found at i:71442 original size:16 final size:16
Alignment explanation
Indices: 71421--71454 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
71411 TTACTATTCA
*
71421 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
71437 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
71453 CG
1 CG
71455 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:75985 original size:22 final size:22
Alignment explanation
Indices: 75960--76003 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
75950 CTTGTGACGG
*
75960 TAGGTAATGGTTAATTAATGTT
1 TAGGTAATGGTTAATAAATGTT
* *
75982 TAGGTTATGTTTAATAAATGTT
1 TAGGTAATGGTTAATAAATGTT
76004 GAAATTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (22 bp):
TAGGTAATGGTTAATAAATGTT
Found at i:78888 original size:22 final size:22
Alignment explanation
Indices: 78863--78912 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
78853 TCACTCTCTA
* * *
78863 CGACGACATCCGTCCCCATCTT
1 CGACGACATCAGTCCCCATATC
78885 CGACGACATCAGTCCCCATATC
1 CGACGACATCAGTCCCCATATC
78907 CGACGA
1 CGACGA
78913 TCTCCCTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.42, G:0.16, T:0.18
Consensus pattern (22 bp):
CGACGACATCAGTCCCCATATC
Found at i:79015 original size:14 final size:15
Alignment explanation
Indices: 78993--79029 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
78983 CGAGGGTTAA
78993 TTTTT-TTTT-AATT
1 TTTTTATTTTAAATT
79006 TTTTTATTTTAAATT
1 TTTTTATTTTAAATT
79021 TTTTGTATT
1 TTTT-TATT
79030 ATTATTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 4 0.19
15 8 0.38
16 4 0.19
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTTATTTTAAATT
Done.