Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008519.1 Hibiscus syriacus cultivar Beakdansim tig00111386_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: 105782
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:325 original size:34 final size:34
Alignment explanation
Indices: 280--344 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
270 TCTTAATATC
*
280 ACCCCTTAACACCGAAACTTCTTTCACCACTTCA
1 ACCCCTCAACACCGAAACTTCTTTCACCACTTCA
***
314 ACCCCTCAACACCTCTACTTCTTTCACCACT
1 ACCCCTCAACACCGAAACTTCTTTCACCACT
345 CCATCTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.26, C:0.45, G:0.02, T:0.28
Consensus pattern (34 bp):
ACCCCTCAACACCGAAACTTCTTTCACCACTTCA
Found at i:408 original size:21 final size:22
Alignment explanation
Indices: 382--422 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
372 ATGCCTCTCG
382 AGTTTCTCTACGACT-TGATCA
1 AGTTTCTCTACGACTCTGATCA
*
403 AGTTTCTCTTCGACTCTGAT
1 AGTTTCTCTACGACTCTGAT
423 TGTCTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (22 bp):
AGTTTCTCTACGACTCTGATCA
Found at i:2678 original size:20 final size:19
Alignment explanation
Indices: 2633--2678 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2623 TCCGGTATCA
*
2633 TTTACCGTTTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
2652 TGATACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCAT-TT
2673 TTTACC
1 TTTACC
2679 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:2825 original size:20 final size:19
Alignment explanation
Indices: 2798--2843 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
2788 ACACTTTTAA
2798 TTTTACCGGTTTTATCAT-T
1 TTTTACCGG-TTTATCATAT
2817 TTGTTACCGGTTTATCATAT
1 TT-TTACCGGTTTATCATAT
2837 TTTTACC
1 TTTTACC
2844 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTATCATAT
Found at i:2832 original size:19 final size:19
Alignment explanation
Indices: 2800--2858 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
2790 ACTTTTAATT
2800 TTACCGGTTTTATCATTTTG
1 TTACCGG-TTTATCATTTTG
2820 TTACCGGTTTATCATATTT-
1 TTACCGGTTTATCAT-TTTG
* *
2839 TTACCTGGTATATCGTTTTG
1 TTACC-GGTTTATCATTTTG
2859 GATCGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (19 bp):
TTACCGGTTTATCATTTTG
Found at i:8067 original size:18 final size:19
Alignment explanation
Indices: 8032--8068 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
8022 CACGGAATGT
8032 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
8052 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
8069 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:14598 original size:2 final size:2
Alignment explanation
Indices: 14591--14619 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14581 ATAATACTAT
14591 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
14620 TTCAAATAAA
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:18125 original size:29 final size:29
Alignment explanation
Indices: 18044--18125 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
18034 CACACTTTTT
*
18044 CGAATTATTTACCAGAATAGCACAAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
18073 TGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
18102 CGAATTATTTACCAAAATAGCACC
1 CGAATTATTTACCAGAATAGCACC
18126 GGTCAACGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:18161 original size:13 final size:13
Alignment explanation
Indices: 18143--18191 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
18133 GGTCAACGGT
18143 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
18156 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
18169 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
18182 C-GGTCGGGTC
1 CGGGTCGGGTC
18192 GTGACCGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 9 0.25
13 27 0.75
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:25331 original size:29 final size:29
Alignment explanation
Indices: 25290--25372 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
25280 CACACTTTTT
*
25290 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAAAATAGCACCAAAAC
* *
25319 TGAATTATTTACCATAATAGCACCAAAAC
1 CGAATTATTTACCAAAATAGCACCAAAAC
25348 CGAATTATTTACCAAAATAGCACCA
1 CGAATTATTTACCAAAATAGCACCA
25373 GTCAACGGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (29 bp):
CGAATTATTTACCAAAATAGCACCAAAAC
Found at i:25401 original size:17 final size:17
Alignment explanation
Indices: 25379--25446 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
25369 ACCAGTCAAC
25379 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
25396 GGTCAA----CGGGTCG
1 GGTCAACGGTCGGGTCG
25409 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
**
25426 GGTCAACTATCGGGTCG
1 GGTCAACGGTCGGGTCG
25443 GGTC
1 GGTC
25447 GTGACCGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 13 0.29
17 32 0.71
ACGTcount: A:0.13, C:0.24, G:0.44, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:25421 original size:12 final size:13
Alignment explanation
Indices: 25389--25424 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
25379 GGTCAACGGT
25389 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
25402 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
25415 C-GGTCGGGTC
1 CGGGTCGGGTC
25425 GGGTCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.11, C:0.25, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:31690 original size:37 final size:38
Alignment explanation
Indices: 31637--31782 Score: 163
Period size: 37 Copynumber: 3.9 Consensus size: 38
31627 CGAAATTACA
* * *
31637 ATATTC-TATTCTAATTGAATATATATTCGT-CATAAT
1 ATATTCGTATTCTAATTGAATATAAATTCATAAATAAT
* *
31673 ATATTCGTATTTTAATTGAATATAAATTCATAAATACT
1 ATATTCGTATTCTAATTGAATATAAATTCATAAATAAT
* ** * *
31711 ATATTTGTATT-TAATCAAATATAAATTTATAAATTAT
1 ATATTCGTATTCTAATTGAATATAAATTCATAAATAAT
* *
31748 ATATTCATATTCTAATTGAATATAAATTCGTAAAT
1 ATATTCGTATTCTAATTGAATATAAATTCATAAAT
31783 CCTTAAATAA
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
36 6 0.07
37 51 0.57
38 33 0.37
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.46
Consensus pattern (38 bp):
ATATTCGTATTCTAATTGAATATAAATTCATAAATAAT
Found at i:32035 original size:58 final size:58
Alignment explanation
Indices: 31971--32083 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 58
31961 TATCAAAAAC
*
31971 ATTTTGACTCGATATAGTCATAGATTCTATGAACAATAGTTGCATAGGATAAGTAGGT
1 ATTTTGACTCGATATAGTCATAGATTCTATGAACAATAGATGCATAGGATAAGTAGGT
* * * *
32029 ATTTTGACTTGATATAGTGATATATTCTATTAACAATAGATGCATAGGATAAGTA
1 ATTTTGACTCGATATAGTCATAGATTCTATGAACAATAGATGCATAGGATAAGTA
32084 TGTGTCTACC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (58 bp):
ATTTTGACTCGATATAGTCATAGATTCTATGAACAATAGATGCATAGGATAAGTAGGT
Found at i:34089 original size:117 final size:117
Alignment explanation
Indices: 33883--34116 Score: 396
Period size: 117 Copynumber: 2.0 Consensus size: 117
33873 CCAGACCTAT
** * *
33883 CCCATGTCTGTTTTTGTCAGTCATGTATGTATAGTCCCATCATTTCAGTATGTCAGATGTGTTAA
1 CCCATGTCCATTTGTGTCAGTCATGTATGTATAATCCCATCATTTCAGTATGTCAGATGTGTTAA
* **
33948 AGCTTGGCTTGAAGGCTATGTGAGACCAAACCAATGTTTCAGTTTGTGTGGG
66 AGCTTGACTTGAAGGCTATGTGAGACCAAACCAATACTTCAGTTTGTGTGGG
34000 CCCATGTCCATTTGTGTCAGTCATGTATGTATAATCCCATCATTTCAGTATGTCAGATGTGTTAA
1 CCCATGTCCATTTGTGTCAGTCATGTATGTATAATCCCATCATTTCAGTATGTCAGATGTGTTAA
*
34065 AGCTTGACTTGAAGGCTATGTGAGACCAATCCAATACTTCAGTTTGTGTGGG
66 AGCTTGACTTGAAGGCTATGTGAGACCAAACCAATACTTCAGTTTGTGTGGG
34117 AATTGTATCA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 109 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (117 bp):
CCCATGTCCATTTGTGTCAGTCATGTATGTATAATCCCATCATTTCAGTATGTCAGATGTGTTAA
AGCTTGACTTGAAGGCTATGTGAGACCAAACCAATACTTCAGTTTGTGTGGG
Found at i:34325 original size:31 final size:31
Alignment explanation
Indices: 34290--34370 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
34280 ACTAATTAGA
* **
34290 TTTGTACTCAGATAATGCGTAATATATCAGG
1 TTTGTATTCAGATAATGCACAATATATCAGG
* * *
34321 TTTGTATTTAGATAATGCACAATATGTGAGG
1 TTTGTATTCAGATAATGCACAATATATCAGG
34352 TTTGTATTCAGATAATGCA
1 TTTGTATTCAGATAATGCA
34371 TATGGGTATC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (31 bp):
TTTGTATTCAGATAATGCACAATATATCAGG
Found at i:37672 original size:8 final size:8
Alignment explanation
Indices: 37659--37688 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
37649 TTAATTTGAA
37659 AATAAAAT
1 AATAAAAT
37667 AATAAAAT
1 AATAAAAT
37675 AATAATAAT
1 AATAA-AAT
37684 AATAA
1 AATAA
37689 TATTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATAAAAT
Found at i:37678 original size:3 final size:3
Alignment explanation
Indices: 37659--37690 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
37649 TTAATTTGAA
37659 AAT AA- AAT AAT AA- AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
37691 TTTAAATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:37934 original size:30 final size:30
Alignment explanation
Indices: 37899--37972 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
37889 TCTCTCCCAT
* * ** *
37899 AATTTTTAAAAATTCTCATTTGGTCTCTCA
1 AATTTTAAAAAATTCTCATTAGACCTATCA
37929 AATTTTAAAAAATTCTCATTAGACCTATCA
1 AATTTTAAAAAATTCTCATTAGACCTATCA
*
37959 AATTTTCAAAAATT
1 AATTTTAAAAAATT
37973 TTAGTTAGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTTTAAAAAATTCTCATTAGACCTATCA
Found at i:38197 original size:38 final size:38
Alignment explanation
Indices: 38128--38300 Score: 190
Period size: 38 Copynumber: 4.6 Consensus size: 38
38118 TATAATATTG
* * *
38128 TATTCTAATCGAATATAAATTCGT-AATAATATATTTA
1 TATTTTAATCAAATATAAATTCATAAATAATATATTTA
** * *
38165 TATTTTAATTGAATATAATTTCATAAATAATATATTTT
1 TATTTTAATCAAATATAAATTCATAAATAATATATTTA
* * *
38203 TA-TTTAATAAAATATAAATTTATAAATAAATATATTCA
1 TATTTTAATCAAATATAAATTCATAAAT-AATATATTTA
* *
38241 TATTATAATCAAATATAAATTCGTAAATAATATATTTGA
1 TATTTTAATCAAATATAAATTCATAAATAATATATTT-A
*
38280 -ATTTTAATTAAATATAAATTC
1 TATTTTAATCAAATATAAATTC
38301 TTTAATATTC
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
37 41 0.36
38 51 0.45
39 22 0.19
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (38 bp):
TATTTTAATCAAATATAAATTCATAAATAATATATTTA
Found at i:38218 original size:20 final size:19
Alignment explanation
Indices: 38193--38257 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
38183 TTTCATAAAT
38193 AATATATTTTTATTTAATAA
1 AATATATTTTTATTTAAT-A
** *
38213 AATATAAATTTA-TAAATA
1 AATATATTTTTATTTAATA
**
38231 AATATATTCATATTATAATCA
1 AATATATTTTTATT-TAAT-A
38252 AATATA
1 AATATA
38258 AATTCGTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
18 9 0.26
19 5 0.15
20 13 0.38
21 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATATTTTTATTTAATA
Found at i:40378 original size:2 final size:2
Alignment explanation
Indices: 40371--40401 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40361 TCAATTAGGC
40371 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 A
40402 GTTTACATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48667 original size:21 final size:21
Alignment explanation
Indices: 48619--48680 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
48609 ATTCCCCTGT
48619 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTT-CCC-TCAA
48642 AGGGGGAATCGGTTCCCTCAA
1 AGGGGGAATCGGTTCCCTCAA
* * *
48663 GGGGGGGATCGATTCCCT
1 AGGGGGAATCGGTTCCCT
48681 TTGCACCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.53
22 3 0.08
23 14 0.39
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCTCAA
Found at i:52379 original size:21 final size:20
Alignment explanation
Indices: 52337--52380 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
52327 TCAAAAGAAG
*
52337 TTTTAAGATCATCAATTTTC
1 TTTTAAGATCATCAATTATC
52357 TTTTAATGATCATC-ATTGATC
1 TTTTAA-GATCATCAATT-ATC
52378 TTT
1 TTT
52381 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTAAGATCATCAATTATC
Found at i:52538 original size:20 final size:20
Alignment explanation
Indices: 52496--52538 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
52486 TTGTTTTCAT
* *
52496 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
52516 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
52536 TTT
1 TTT
52539 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:55716 original size:20 final size:20
Alignment explanation
Indices: 55693--55732 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55683 TATTTAAAAT
55693 TTGATGTATTTATTAGATAA
1 TTGATGTATTTATTAGATAA
55713 TTGATGTATTTATTAGATAA
1 TTGATGTATTTATTAGATAA
55733 CTTATTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (20 bp):
TTGATGTATTTATTAGATAA
Found at i:57226 original size:17 final size:16
Alignment explanation
Indices: 57200--57233 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
57190 AATTTGGGAC
*
57200 AGAGAATTATTATTTT
1 AGAGAATTATTAATTT
57216 AGAGAAATTATTAATTT
1 AGAG-AATTATTAATTT
57233 A
1 A
57234 TCAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
AGAGAATTATTAATTT
Found at i:58042 original size:10 final size:11
Alignment explanation
Indices: 58022--58046 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58012 TAGATGTACT
58022 AAAAACAAAAA
1 AAAAACAAAAA
58033 AAAAACAAAAA
1 AAAAACAAAAA
58044 AAA
1 AAA
58047 TAAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:62330 original size:23 final size:25
Alignment explanation
Indices: 62299--62364 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 25
62289 TAATTAATAG
* *
62299 TATTGTTATATAT-AACTTTTTA-A
1 TATTTTTATATATAAAATTTTTATA
*
62322 TATTTTTATATTTAAAATTTTTATA
1 TATTTTTATATATAAAATTTTTATA
*
62347 TATTTTT-TATAAAAAATT
1 TATTTTTATATATAAAATT
62365 AAATAAGCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.31
24 17 0.47
25 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTTTTATATATAAAATTTTTATA
Found at i:62335 original size:15 final size:15
Alignment explanation
Indices: 62317--62347 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62307 TATATAACTT
*
62317 TTTAATATTTTTATA
1 TTTAAAATTTTTATA
62332 TTTAAAATTTTTATA
1 TTTAAAATTTTTATA
62347 T
1 T
62348 ATTTTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAAAATTTTTATA
Found at i:63555 original size:60 final size:60
Alignment explanation
Indices: 63465--63630 Score: 147
Period size: 60 Copynumber: 2.8 Consensus size: 60
63455 ATCTCTCTCC
* * * ** * *
63465 AAACTATAACACTAATTTTAAATTTATCCTTAAACTTTTGAATATTCTAATTTTACTC-T
1 AAACTATAACACTCATTCTGAATAGATCCTTAAACTTTTGAATATTCTAATTTGAATCGT
* * * * * *
63524 CAAATTATAACCCTCATTCTGAATA-AGTCCTTACACTATTGAACATTCTACTTTGAATCGT
1 -AAACTATAACACTCATTCTGAATAGA-TCCTTAAACTTTTGAATATTCTAATTTGAATCGT
* * * *
63585 AAACTATGACATTCATTTTGAATTGATCCTTAAACTTTTGAATATT
1 AAACTATAACACTCATTCTGAATAGATCCTTAAACTTTTGAATATT
63631 TGTAACACCC
Statistics
Matches: 82, Mismatches: 21, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
59 1 0.01
60 79 0.96
61 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (60 bp):
AAACTATAACACTCATTCTGAATAGATCCTTAAACTTTTGAATATTCTAATTTGAATCGT
Found at i:67714 original size:161 final size:161
Alignment explanation
Indices: 67532--67850 Score: 455
Period size: 161 Copynumber: 2.0 Consensus size: 161
67522 CACTTTGATC
* *
67532 CTTGAACTTTTCTCGAATTTCTATTTTGACCACAAAACTT-TCCAAATTTACATTTTGG-CAACT
1 CTTGAACTTTTCTCAAATTTCTACTTTGACCACAAAA-TTATCCAAATTTACATTTTGGTC-ACT
*
67595 TATAAAAATTTTGGGGTATCACAACATTCCAATTCCCTCCCCAAATTCTTCAAAATATGTAATTA
64 TATAAAAATTTTGGGGTATCACAACATTCCAATTCCATCCCCAAATTCTTCAAAATATGTAATTA
*
67660 GCTCCAACCATAGTTTAACCTAAATTTTTGGTA
129 GCTCCAACCATAGTTTAACCTAAAATTTTGGTA
* * * *
67693 CTTGAACTTTT-TCCAAATTTCTACTTTGGCCACCAAATTATCCAAGTTTACATTTTGGTCCCTT
1 CTTGAACTTTTCT-CAAATTTCTACTTTGACCACAAAATTATCCAAATTTACATTTTGGTCACTT
* * * * *
67757 ATCAAAGTTTTGGGGTATTACAATATTCCAATTCCATCCCCAAATTCTTCAAAATATTTAATTAG
65 ATAAAAATTTTGGGGTATCACAACATTCCAATTCCATCCCCAAATTCTTCAAAATATGTAATTAG
* *
67822 TTCCAACCATAGTTTAACTTAAAATTTTG
130 CTCCAACCATAGTTTAACCTAAAATTTTG
67851 TTTTTATCAA
Statistics
Matches: 140, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
160 3 0.02
161 136 0.97
162 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (161 bp):
CTTGAACTTTTCTCAAATTTCTACTTTGACCACAAAATTATCCAAATTTACATTTTGGTCACTTA
TAAAAATTTTGGGGTATCACAACATTCCAATTCCATCCCCAAATTCTTCAAAATATGTAATTAGC
TCCAACCATAGTTTAACCTAAAATTTTGGTA
Found at i:74853 original size:29 final size:29
Alignment explanation
Indices: 74811--74899 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
74801 TACCGGGGGT
*
74811 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
74840 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
74869 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
74898 AG
1 AG
74900 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:75167 original size:29 final size:29
Alignment explanation
Indices: 75106--75189 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
75096 ATGAATCCTT
** * **
75106 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
75135 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
75164 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
75190 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:85011 original size:20 final size:20
Alignment explanation
Indices: 84986--85024 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
84976 TTGTGTATTG
84986 AAACCCTACACTTG-GTTTCA
1 AAACCC-ACACTTGAGTTTCA
*
85006 AAACCCATACTTGAGTTTC
1 AAACCCACACTTGAGTTTC
85025 GACCGATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (20 bp):
AAACCCACACTTGAGTTTCA
Found at i:88194 original size:199 final size:198
Alignment explanation
Indices: 87768--88176 Score: 671
Period size: 199 Copynumber: 2.1 Consensus size: 198
87758 ATGAATAAAT
*
87768 AAATTCAAGATCGCTGTCGAATGAATTATACTGAAAATTTTATTTCAAAAGTAATAATTATATTG
1 AAATTCAAGATCGTTGTCGAATGAATTATACTGAAAATTTTATTTCAAAAGTAATAATTATATTG
87833 AAAATTTTGAGTATTATTTCTAGAGAGAGAGGTTGTAAACGAGTCGAACTGAGCTTGAGTATTGT
66 AAAATTTTGAGTATTATTTC-AGAGAGAGAGGTTGTAAACGAGTCGAACTGAGCTTGAGTATTGT
* * * *
87898 TGAGCACAACTCGAAAACTCTAAAATGGAGCTCGATTCGGCTATAAAACTCGCAAGCTTTAAATT
130 TGAGCACAACTCGAAAACTCTAAAATGAAGCTCGACTCCGCTAGAAAACTCGCAAGCTTTAAATT
*
87963 TTAAAT
195 TT--AC
87969 AAATTCAAGATCGTTGTCGAATGAATTATACTGAAAATTTTATTTCAAAAGTAATAATTATATTG
1 AAATTCAAGATCGTTGTCGAATGAATTATACTGAAAATTTTATTTCAAAAGTAATAATTATATTG
*
88034 AAAATTTTGAGTATTATTTC-GAGAGAGAGGTTGTAAACGAGTCGAGCTGAGCTTGAGTATTGTT
66 AAAATTTTGAGTATTATTTCAGAGAGAGAGGTTGTAAACGAGTCGAACTGAGCTTGAGTATTGTT
* * *
88098 GAGCACGACTCGAAAACTCTAAAATGAATCTCGACTCCGCTCGAAAACTCGCAAGCTTTAAATTT
131 GAGCACAACTCGAAAACTCTAAAATGAAGCTCGACTCCGCTAGAAAACTCGCAAGCTTTAAATTT
88163 T-C
196 TAC
*
88165 AAGTTCAA-ATCG
1 AAATTCAAGATCG
88177 AATTCGAATC
Statistics
Matches: 197, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
195 4 0.02
196 7 0.04
199 102 0.52
201 84 0.43
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (198 bp):
AAATTCAAGATCGTTGTCGAATGAATTATACTGAAAATTTTATTTCAAAAGTAATAATTATATTG
AAAATTTTGAGTATTATTTCAGAGAGAGAGGTTGTAAACGAGTCGAACTGAGCTTGAGTATTGTT
GAGCACAACTCGAAAACTCTAAAATGAAGCTCGACTCCGCTAGAAAACTCGCAAGCTTTAAATTT
TAC
Found at i:92645 original size:18 final size:20
Alignment explanation
Indices: 92622--92665 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
92612 CCAGTAATCC
*
92622 TATTCCC-C-GGTAGTCTTA
1 TATTCCCACTGGTAATCTTA
92640 TATTCCCACTGGTAATCTTA
1 TATTCCCACTGGTAATCTTA
*
92660 CATTCC
1 TATTCC
92666 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 14 0.64
ACGTcount: A:0.20, C:0.30, G:0.11, T:0.39
Consensus pattern (20 bp):
TATTCCCACTGGTAATCTTA
Found at i:95884 original size:2 final size:2
Alignment explanation
Indices: 95877--95911 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
95867 GATCTAACTC
95877 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 A
95912 GAAGTTTATA
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:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:96441 original size:20 final size:20
Alignment explanation
Indices: 96416--96475 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
96406 AACTACAAGT
96416 CTTCAACACCATTATACATA
1 CTTCAACACCATTATACATA
96436 CTTCAACACCATTATACATA
1 CTTCAACACCATTATACATA
96456 CTTCAACACCATTATACATA
1 CTTCAACACCATTATACATA
96476 TTTATTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (20 bp):
CTTCAACACCATTATACATA
Found at i:103337 original size:35 final size:35
Alignment explanation
Indices: 103264--103412 Score: 144
Period size: 35 Copynumber: 4.2 Consensus size: 35
103254 TGAAAGTATT
* **
103264 AAAATGATTTTC-AAGTTTGGT-AA-CTAACTTTG
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
* *
103296 AAAAAATGGTTTTCAAAGTTTGGAAAATGTTTCTTTG
1 --AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
*
103333 AAAATAATTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
103368 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTTG
103404 AAAAATGAT
1 -AAAATGAT
103413 AATGGGATAA
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
34 11 0.11
35 42 0.43
36 16 0.16
37 28 0.29
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (35 bp):
AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:103390 original size:37 final size:37
Alignment explanation
Indices: 103291--103409 Score: 156
Period size: 37 Copynumber: 3.3 Consensus size: 37
103281 TGGTAACTAA
* *
103291 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGAAAATGTTT
1 CTTTGAAAAATA-GATTTTCAAAGTTTGGTAAATGTTT
103328 CTTTG-AAAATA-ATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
* *
103363 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
103400 -GTTGAAAAAT
1 CTTTGAAAAAT
103410 GATAATGGGA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
35 27 0.36
36 19 0.26
37 28 0.38
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
Done.