Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002601.1 Hibiscus syriacus cultivar Beakdansim tig00005260_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: 129480
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1041 original size:170 final size:171
Alignment explanation
Indices: 727--1072 Score: 626
Period size: 168 Copynumber: 2.0 Consensus size: 171
717 TCCTTTCTGG
727 ATAAAGGGTGTGGATTTTATGTTTCTTGTTTCGGTTTCCAGTCCTTAATCTCGTTTACAAGTATA
1 ATAAAGGGTGTGGATTTTATG-TTCTTGTTTCGGTTTCCAGTCCTTAATCTCGTTTACAAGTATA
*
792 GCATAAGCAAACCTTGAAACTTGGAGTTGATTATCATTCATACTACAAATAGGAGTTGCATATCT
65 GCATAAGCAAACCTTGAAACTTGGAGTTGATTATCATTCATACTACAAATAGGAGTTGCATATCG
*
857 TATTCAGCTTTCTTTTAACTATGA-CTTTCAAGCACACACCT
130 TATTCAGCTTTCTTTTAACTATGATATTTCAAGCACACACCT
898 ATAAAGGGTGTGGA-TTTATG-TCTTGTTTCGGTTTCCAGTCCTTAATCTCGTTTACAAGTATAG
1 ATAAAGGGTGTGGATTTTATGTTCTTGTTTCGGTTTCCAGTCCTTAATCTCGTTTACAAGTATAG
961 CATAAGCAAACCTTGAAACTTGGAGTTGATTATTCATTCAGTACTACAAATAGGAGTTGCATATC
66 CATAAGCAAACCTTGAAACTTGGAGTTGATTA-TCATTCA-TACTACAAATAGGAGTTGCATATC
1026 GTATTCAGCTTTCTTTTAACTATGATATTTCAAGCACACACCT
129 GTATTCAGCTTTCTTTTAACTATGATATTTCAAGCACACACCT
1069 ATAA
1 ATAA
1073 TTTATGAGAT
Statistics
Matches: 170, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
168 75 0.44
169 7 0.04
170 54 0.32
171 34 0.20
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (171 bp):
ATAAAGGGTGTGGATTTTATGTTCTTGTTTCGGTTTCCAGTCCTTAATCTCGTTTACAAGTATAG
CATAAGCAAACCTTGAAACTTGGAGTTGATTATCATTCATACTACAAATAGGAGTTGCATATCGT
ATTCAGCTTTCTTTTAACTATGATATTTCAAGCACACACCT
Found at i:7556 original size:31 final size:31
Alignment explanation
Indices: 7521--7581 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
7511 TCTTTTTATT
* *
7521 ATTTAAAGAATTTAATT-GATATACTTTTCAA
1 ATTTAAA-AATTCAATTAAATATACTTTTCAA
*
7552 ATTTAAAAATTCAATTAAATATATTTTTCA
1 ATTTAAAAATTCAATTAAATATACTTTTCA
7582 CATAAAGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (31 bp):
ATTTAAAAATTCAATTAAATATACTTTTCAA
Found at i:10334 original size:17 final size:17
Alignment explanation
Indices: 10309--10342 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10299 CACACGTACT
*
10309 ACTGTTGTGCATGATGG
1 ACTGATGTGCATGATGG
10326 ACTGATGTGCATGATGG
1 ACTGATGTGCATGATGG
10343 TTGCGCCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.32
Consensus pattern (17 bp):
ACTGATGTGCATGATGG
Found at i:13937 original size:16 final size:16
Alignment explanation
Indices: 13916--13947 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13906 AGAGTGGTGT
13916 ACCACGAGCTGTCTCC
1 ACCACGAGCTGTCTCC
13932 ACCACGAGCTGTCTCC
1 ACCACGAGCTGTCTCC
13948 GATGTACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (16 bp):
ACCACGAGCTGTCTCC
Found at i:15676 original size:70 final size:71
Alignment explanation
Indices: 15543--15676 Score: 243
Period size: 71 Copynumber: 1.9 Consensus size: 71
15533 TAAAAATATA
15543 TCAACTTGAGTTTTCAAGGAGGTTTGAAGTTGAAGGTTGCAAGGGGAATGTTAGTGTAAATGAAC
1 TCAACTTGAGTTTTCAAGGAGGTTTGAAGTTGAAGGTTGCAAGGGGAATGTTAGTGTAAATGAAC
15608 ATTAGT
66 ATTAGT
* *
15614 TCAATTTGAGTTTTGAAGGAGGTTTGAAGTTGAA-GTTGCAAGGGGAATGTTAGTGTAAATGAA
1 TCAACTTGAGTTTTCAAGGAGGTTTGAAGTTGAAGGTTGCAAGGGGAATGTTAGTGTAAATGAA
15677 TGAATGAAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
70 29 0.48
71 32 0.52
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (71 bp):
TCAACTTGAGTTTTCAAGGAGGTTTGAAGTTGAAGGTTGCAAGGGGAATGTTAGTGTAAATGAAC
ATTAGT
Found at i:15742 original size:17 final size:17
Alignment explanation
Indices: 15717--15801 Score: 152
Period size: 17 Copynumber: 5.0 Consensus size: 17
15707 CACACGTACT
15717 ACTGCTGTGCATGATGG
1 ACTGCTGTGCATGATGG
*
15734 ACTGTTGTGCATGATGG
1 ACTGCTGTGCATGATGG
*
15751 ACTGCTTTGCATGATGG
1 ACTGCTGTGCATGATGG
15768 ACTGCTGTGCATGATGG
1 ACTGCTGTGCATGATGG
15785 ACTGCTGTGCATGATGG
1 ACTGCTGTGCATGATGG
15802 TTGTGCCTAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 64 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (17 bp):
ACTGCTGTGCATGATGG
Found at i:16160 original size:12 final size:12
Alignment explanation
Indices: 16143--16187 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
16133 TATGTTGAAG
16143 TTAGTTACATCA
1 TTAGTTACATCA
16155 TTAGTTACATCA
1 TTAGTTACATCA
16167 TTAGTTACATCA
1 TTAGTTACATCA
16179 TTAGTTACA
1 TTAGTTACA
16188 GCTATAGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (12 bp):
TTAGTTACATCA
Found at i:48090 original size:82 final size:82
Alignment explanation
Indices: 47976--48185 Score: 201
Period size: 82 Copynumber: 2.5 Consensus size: 82
47966 AGGTGAATAT
* * * * ** * *
47976 TATTGTGGCGTTTTTATAAAAACGCCATTAAAGTACTAATTTATTGTGGCGTTTGTCGAAAAAAC
1 TATTGCGGAGTTTATATAAAAACGACGCTAAAGTACTAATCTATTGTGGCATTTGTCGAAAAAAC
*
48041 G-CTACTATAGAT-TGACC
66 GTC-ACTACAGATGT-ACC
* * * * *
48058 TATTGCGGAGTTTGTATAAAAACGACGCTAAAGTATTACTCTGTTGTGGCATTTGTGGAAAAAAC
1 TATTGCGGAGTTTATATAAAAACGACGCTAAAGTACTAATCTATTGTGGCATTTGTCGAAAAAAC
*
48123 GTCACTACATATGTACC
66 GTCACTACAGATGTACC
* * *
48140 TATTGCGGCA-TTTATATAAAAACGGCGTCAAAAGTACTACTCTATT
1 TATTGCGG-AGTTTATATAAAAACGACG-CTAAAGTACTAATCTATT
48186 ACAGCGTTTA
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
82 87 0.83
83 18 0.17
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (82 bp):
TATTGCGGAGTTTATATAAAAACGACGCTAAAGTACTAATCTATTGTGGCATTTGTCGAAAAAAC
GTCACTACAGATGTACC
Found at i:48113 original size:41 final size:41
Alignment explanation
Indices: 48057--48218 Score: 107
Period size: 42 Copynumber: 3.9 Consensus size: 41
48047 ATAGATTGAC
48057 CTATTGCGG-AGTTTGTATAAAAACGACGCTAAAGTATTACT
1 CTATTGCGGCA-TTTGTATAAAAACGACGCTAAAGTATTACT
* * * * *
48098 CTGTTGTGGCATTTGTGGA-AAAAACGTCACTACA-TATGTAC-
1 CTATTGCGGCATTTGT--ATAAAAACGACGCTAAAGTAT-TACT
* * * *
48139 CTATTGCGGCATTTATATAAAAACGGCGTCAAAAGTACTACT
1 CTATTGCGGCATTTGTATAAAAACGACG-CTAAAGTATTACT
* * * * * *
48181 CTATTACAGCGTTTATTTAAAAAACGTCGCTAAAGTAT
1 CTATTGCGGCATTTGTAT-AAAAACGACGCTAAAGTAT
48219 CATTTTGTGA
Statistics
Matches: 92, Mismatches: 20, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
39 1 0.01
40 8 0.09
41 34 0.37
42 39 0.42
43 10 0.11
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (41 bp):
CTATTGCGGCATTTGTATAAAAACGACGCTAAAGTATTACT
Found at i:49267 original size:23 final size:23
Alignment explanation
Indices: 49244--49286 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49234 TTAGAATATA
*
49244 AAACTT-TAAAATTTTGACAAAT
1 AAACTTATAAAATTTTAACAAAT
*
49266 AAATTTATAAAATTTTAACAA
1 AAACTTATAAAATTTTAACAA
49287 TGAGAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (23 bp):
AAACTTATAAAATTTTAACAAAT
Found at i:55081 original size:19 final size:21
Alignment explanation
Indices: 55043--55087 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
55033 AAAATATTCG
55043 TTTTAGATAATAAAATTAATA
1 TTTTAGATAATAAAATTAATA
*
55064 TTTTTGATAA-AAAA-TAATA
1 TTTTAGATAATAAAATTAATA
55083 TTTTA
1 TTTTA
55088 AATAGTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTTAGATAATAAAATTAATA
Found at i:55624 original size:36 final size:33
Alignment explanation
Indices: 55560--55625 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
55550 GGTAAAAAAA
* * *
55560 ATTATTTTTATGTTAGTATTTTTTTAAATAGTT
1 ATTATTTTTATATTAATATTTTTGTAAATAGTT
55593 ATTATATTTTATATTAATATATTTATGTAAATA
1 ATTAT-TTTTATATTAATAT-TTT-TGTAAATA
55626 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 5 0.19
34 12 0.44
35 3 0.11
36 7 0.26
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (33 bp):
ATTATTTTTATATTAATATTTTTGTAAATAGTT
Found at i:55648 original size:14 final size:15
Alignment explanation
Indices: 55608--55664 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
55598 ATTTTATATT
55608 AATA-TATTTATGTAA
1 AATATTATTTAT-TAA
*
55623 ATATATTTTTTATTAA
1 A-ATATTATTTATTAA
55639 AATA-TATTTA-TAA
1 AATATTATTTATTAA
*
55652 ATTATTATTTATT
1 AATATTATTTATT
55665 TAGAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 6 0.17
14 11 0.31
15 5 0.14
16 7 0.20
17 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
AATATTATTTATTAA
Found at i:55652 original size:29 final size:28
Alignment explanation
Indices: 55595--55664 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
55585 AAATAGTTAT
*
55595 TATATTTTATATTAATATATTTATGTAAA
1 TATATTTTTTATTAATATATTTA-GTAAA
55624 TATATTTTTTATTAAAATATATTTA-TAAA
1 TATATTTTTTATT--AATATATTTAGTAAA
*
55653 T-TATTATTTATT
1 TATATTTTTTATT
55665 TAGAATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 10 0.27
29 17 0.46
31 10 0.27
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
TATATTTTTTATTAATATATTTAGTAAA
Found at i:55674 original size:28 final size:29
Alignment explanation
Indices: 55608--55664 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 29
55598 ATTTTATATT
*
55608 AATATATTTATGTAAATATATTTTTTATTAA
1 AATATATTTA--TAAATATATTATTTATTAA
55639 AATATATTTATAAAT-TATTATTTATT
1 AATATATTTATAAATATATTATTTATT
55665 TAGAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 5 0.20
31 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
AATATATTTATAAATATATTATTTATTAA
Found at i:55829 original size:17 final size:17
Alignment explanation
Indices: 55807--55860 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
55797 AATGTTAATA
55807 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
55824 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
55841 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
55858 TTT
1 TTT
55861 TTTATAATGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:57420 original size:21 final size:21
Alignment explanation
Indices: 57396--57458 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
57386 GTACATGCAC
* *
57396 AGCCCTCCACTTCATATGCCA
1 AGCCCACCAGTTCATATGCCA
57417 AGCCCACCAGTTCATATGCCA
1 AGCCCACCAGTTCATATGCCA
57438 AGCCCACCAGTTCATATGCCA
1 AGCCCACCAGTTCATATGCCA
57459 TCTCCGTAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.40, G:0.13, T:0.21
Consensus pattern (21 bp):
AGCCCACCAGTTCATATGCCA
Found at i:57492 original size:21 final size:20
Alignment explanation
Indices: 57466--57534 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 20
57456 CCATCTCCGT
57466 AGGGTTACATTCTGAGCCCGC
1 AGGGTTACATTCT-AGCCCGC
57487 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATT-CTAGCCCG-C
*
57509 A-GGTTACATGCCTAGCCCGC
1 AGGGTTACAT-TCTAGCCCGC
57529 AGGGTT
1 AGGGTT
57535 TTATACCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
20 2 0.05
21 37 0.86
22 4 0.09
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
AGGGTTACATTCTAGCCCGC
Found at i:58160 original size:34 final size:34
Alignment explanation
Indices: 58055--58161 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
58045 ATAAATGTTT
*
58055 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
58089 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
58123 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
58157 TTAAA
1 TTAAA
58162 TTTCAACTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:58785 original size:128 final size:128
Alignment explanation
Indices: 58557--59163 Score: 1070
Period size: 128 Copynumber: 4.7 Consensus size: 128
58547 ACAATCCATC
58557 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
58622 GGAAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
58685 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
58750 GGAAGCCGCGCCCCCGAGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
58813 TAGTGTCCCTGAGGGACATGAGTGACATAATATGGCAATGATAACATATTATCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
58878 GGAAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTAAGAAATAATAGGTACTTATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
58941 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATTATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
59006 GGAAGGCGCGCTCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
59069 TAGTGCCCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTATCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
59134 GGAAGGCGCGCCCACGGGAACGCGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
59164 TGTGAATAGT
Statistics
Matches: 452, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 452 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:60108 original size:23 final size:23
Alignment explanation
Indices: 60082--60128 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
60072 TATTTAAATA
*
60082 AATGTTTTTG-TTTATAATAATTT
1 AATGTTATTGATTTAT-ATAATTT
60105 AATGTTATTGCATTTATATAATTT
1 AATGTTATTG-ATTTATATAATTT
60129 GTCAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 7 0.33
25 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (23 bp):
AATGTTATTGATTTATATAATTT
Found at i:61910 original size:3 final size:3
Alignment explanation
Indices: 61904--61940 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
61894 GGAGGAGGAG
*
61904 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
61941 AACCGAAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:67027 original size:15 final size:15
Alignment explanation
Indices: 67007--67036 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
66997 GCTTTTAAAT
67007 AAACGCTGCAATAGA
1 AAACGCTGCAATAGA
67022 AAACGCTGCAATAGA
1 AAACGCTGCAATAGA
67037 GTAGTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (15 bp):
AAACGCTGCAATAGA
Found at i:68712 original size:2 final size:2
Alignment explanation
Indices: 68707--68751 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
68697 CATATGAGAG
68707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68748 AT AT
1 AT AT
68752 TATTTTAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:78125 original size:43 final size:43
Alignment explanation
Indices: 78066--78157 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
78056 TTTTACATTA
* * * *
78066 ACAAACGTCGTAAAAAGTTAGGTTATTTAGTGACATTTTGGAG
1 ACAAACGCCGCAAAAAGTCAGGTTATTTAGCGACATTTTGGAG
* ** *
78109 ACAAACGCCGCAAAAAGTCATGTTATTTAGCGATGTTTTGGAT
1 ACAAACGCCGCAAAAAGTCAGGTTATTTAGCGACATTTTGGAG
78152 ACAAAC
1 ACAAAC
78158 ACCACTAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (43 bp):
ACAAACGCCGCAAAAAGTCAGGTTATTTAGCGACATTTTGGAG
Found at i:84071 original size:31 final size:31
Alignment explanation
Indices: 84036--84208 Score: 97
Period size: 31 Copynumber: 5.4 Consensus size: 31
84026 GCTTTAAGTA
*
84036 ACGAGTCGAACAACAAATTTTTTTAATGAGC
1 ACGAGTCGAGCAACAAATTTTTTTAATGAGC
* *
84067 ACGAGTTGAGC-A-AAA---TTTTAATGAGTA
1 ACGAGTCGAGCAACAAATTTTTTTAATGAG-C
* * * *
84094 ACAACTCGAGCAACAAATTTTCTTAACGAGC
1 ACGAGTCGAGCAACAAATTTTTTTAATGAGC
* *
84125 ACGAGTCGAGCAA-AATTTTAATTAGCTTAACGAGCAAC
1 ACGAGTCGAGCAACAAATTT--TT---TTAATGAG---C
* *
84163 GAGTCGAGTCGAGCAATAAATTTTTTTAACGAGC
1 -A--CGAGTCGAGCAACAAATTTTTTTAATGAGC
84197 ACGAGTCGAGCA
1 ACGAGTCGAGCA
84209 CTGCTCAACT
Statistics
Matches: 110, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
26 10 0.09
27 8 0.07
28 1 0.01
29 6 0.05
30 6 0.05
31 31 0.28
32 9 0.08
33 1 0.01
34 1 0.01
35 8 0.07
37 8 0.07
38 1 0.01
39 1 0.01
40 2 0.02
41 12 0.11
42 5 0.05
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (31 bp):
ACGAGTCGAGCAACAAATTTTTTTAATGAGC
Found at i:84090 original size:26 final size:26
Alignment explanation
Indices: 84056--84146 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 26
84046 CAACAAATTT
*
84056 TTTTAATGAGCACGAGTTGAGCAAAA
1 TTTTAATGAGCACGAGTCGAGCAAAA
* * *
84082 TTTTAATGAGTAACAACTCGAGCAACAAA
1 TTTTAATGAG-CACGAGTCGAGC-A-AAA
*
84111 TTTTCTTAACGAGCACGAGTCGAGCAAAA
1 --TT-TTAATGAGCACGAGTCGAGCAAAA
84140 TTTTAAT
1 TTTTAAT
84147 TAGCTTAACG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
26 14 0.28
27 10 0.20
28 1 0.02
29 6 0.12
30 1 0.02
31 11 0.22
32 7 0.14
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (26 bp):
TTTTAATGAGCACGAGTCGAGCAAAA
Found at i:84108 original size:58 final size:58
Alignment explanation
Indices: 84032--84146 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
84022 ATGAGCTTTA
* * * * *
84032 AGTAACGAGTCGAACAACAAATTTTTTTAATGAGCACGAGTTGAGCAAAATTTTAATG
1 AGTAACAACTCGAACAACAAATTTTCTTAACGAGCACGAGTCGAGCAAAATTTTAATG
*
84090 AGTAACAACTCGAGCAACAAATTTTCTTAACGAGCACGAGTCGAGCAAAATTTTAAT
1 AGTAACAACTCGAACAACAAATTTTCTTAACGAGCACGAGTCGAGCAAAATTTTAAT
84147 TAGCTTAACG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (58 bp):
AGTAACAACTCGAACAACAAATTTTCTTAACGAGCACGAGTCGAGCAAAATTTTAATG
Found at i:84264 original size:21 final size:21
Alignment explanation
Indices: 84238--84286 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
84228 CTCGCTCGAT
*
84238 AAGCACCCTAGAAAATATCAA
1 AAGCACCCTAGAAAATACCAA
84259 AAGCACCCTAGAAAATACCAA
1 AAGCACCCTAGAAAATACCAA
84280 AAGCACC
1 AAGCACC
84287 AAACTTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.29, G:0.10, T:0.10
Consensus pattern (21 bp):
AAGCACCCTAGAAAATACCAA
Found at i:93163 original size:18 final size:16
Alignment explanation
Indices: 93124--93178 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
93114 CATGTCTTTT
93124 TTTTTTCTTTCGAACAG
1 TTTTTT-TTTCGAACAG
*
93141 TTTTTTTTTCGAACTG
1 TTTTTTTTTCGAACAG
93157 CTATTTTTTTTC-AACA-
1 -T-TTTTTTTTCGAACAG
93173 TTTTTT
1 TTTTTT
93179 GTGATGGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 5 0.15
15 1 0.03
16 9 0.26
17 10 0.29
18 9 0.26
ACGTcount: A:0.16, C:0.15, G:0.07, T:0.62
Consensus pattern (16 bp):
TTTTTTTTTCGAACAG
Found at i:104573 original size:16 final size:17
Alignment explanation
Indices: 104552--104592 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
104542 AGCAATTAGG
104552 TGAGCAACGAACTT-AA
1 TGAGCAACGAACTTAAA
* *
104568 TGAGCAATGAGCTTAAA
1 TGAGCAACGAACTTAAA
104585 TGAGCAAC
1 TGAGCAAC
104593 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (17 bp):
TGAGCAACGAACTTAAA
Found at i:104800 original size:30 final size:31
Alignment explanation
Indices: 104764--104826 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
104754 TTCTTTAGTA
*
104764 AATTATTAAATTTAGTT-TA-TATTATAAAAT
1 AATTATTAAATTTA-TTAAATTATTATAAAAT
104794 AATTATTAAATTTATTAAATTATTATAAAAT
1 AATTATTAAATTTATTAAATTATTATAAAAT
104825 AA
1 AA
104827 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 2 0.07
30 15 0.50
31 13 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
AATTATTAAATTTATTAAATTATTATAAAAT
Found at i:104813 original size:20 final size:20
Alignment explanation
Indices: 104785--104851 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
104775 TTAGTTTATA
*
104785 TTATAAAATAATTATTAAAT
1 TTATAAAATAATTATAAAAT
* *
104805 TTATTAAATTATTATAAAA-
1 TTATAAAATAATTATAAAAT
*
104824 -TA-AAAATAA--AAAAAAT
1 TTATAAAATAATTATAAAAT
104840 TTA-AAAATAATT
1 TTATAAAATAATT
104852 TAACAACAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
15 5 0.14
17 14 0.38
18 2 0.05
20 16 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTATAAAATAATTATAAAAT
Found at i:105325 original size:31 final size:31
Alignment explanation
Indices: 105287--105354 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
105277 TTTCAAAATT
105287 TGTTTTTAATAAAGAAATTGTACATAGAATA
1 TGTTTTTAATAAAGAAATTGTACATAGAATA
105318 TGTTTTTAATAAAGAAATTGTACATAGAATA
1 TGTTTTTAATAAAGAAATTGTACATAGAATA
105349 TGTTTT
1 TGTTTT
105355 ATTATTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (31 bp):
TGTTTTTAATAAAGAAATTGTACATAGAATA
Found at i:105403 original size:17 final size:17
Alignment explanation
Indices: 105383--105421 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
105373 AGGTTCATTT
* *
105383 TTTTATATATAATTATA
1 TTTTATAAAAAATTATA
*
105400 TTTTATAAAAAATTGTA
1 TTTTATAAAAAATTATA
105417 TTTTA
1 TTTTA
105422 GATAATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTATAAAAAATTATA
Found at i:111261 original size:2 final size:2
Alignment explanation
Indices: 111254--111282 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
111244 AAGCGTACAG
111254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
111283 CAACATTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:126410 original size:20 final size:21
Alignment explanation
Indices: 126385--126439 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
126375 TTTTGAGAGT
126385 AAAGTATCGATACT-ACTCAC
1 AAAGTATCGATACTCACTCAC
*
126405 AAAGTATCGATACTCACTCAT
1 AAAGTATCGATACTCACTCAC
*
126426 AGAGTATCGATACT
1 AAAGTATCGATACT
126440 GTTGGCCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (21 bp):
AAAGTATCGATACTCACTCAC
Found at i:128963 original size:29 final size:28
Alignment explanation
Indices: 128931--128991 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
128921 AGATGAAAAC
*
128931 AAAATAAAACATGTA-AATATATAATAATA
1 AAAATAAAACATATATAATA-ATAATAA-A
* *
128960 AAAATGAAATATATATAATAATAATAAA
1 AAAATAAAACATATATAATAATAATAAA
128988 AAAA
1 AAAA
128992 CCAAAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.18
29 19 0.68
30 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (28 bp):
AAAATAAAACATATATAATAATAATAAA
Found at i:128979 original size:20 final size:23
Alignment explanation
Indices: 128933--128983 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
128923 ATGAAAACAA
128933 AATAAAACATGTAAATATATAAT
1 AATAAAACATGTAAATATATAAT
*
128956 AATAAAA-ATGAAATATATATAAT
1 AATAAAACATGTAA-ATATATAAT
128979 AATAA
1 AATAA
128984 TAAAAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
AATAAAACATGTAAATATATAAT
Found at i:129075 original size:14 final size:15
Alignment explanation
Indices: 129052--129087 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
129042 AAATGCAAGT
129052 AAATATATGTAAATA
1 AAATATATGTAAATA
*
129067 AAATA-ATGTATATA
1 AAATATATGTAAATA
129081 AAATATA
1 AAATATA
129088 ATAGAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
AAATATATGTAAATA
Done.