Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001765.1 Hibiscus syriacus cultivar Beakdansim tig00003563_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: 105197
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4266 original size:19 final size:19
Alignment explanation
Indices: 4233--4290 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
4223 ATTTAGTTAT
4233 TCATTTTTTCCTTTTAATTTA
1 TCATTTTTT--TTTTAATTTA
4254 TCATTTTTTTTTTAA-TTA
1 TCATTTTTTTTTTAATTTA
* *
4272 TTATTTTTCTTTTAATTTA
1 TCATTTTTTTTTTAATTTA
4291 GTGTGTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 16 0.47
19 9 0.26
21 9 0.26
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (19 bp):
TCATTTTTTTTTTAATTTA
Found at i:4362 original size:16 final size:16
Alignment explanation
Indices: 4343--4378 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
4333 AAATCTAACA
4343 TTTTTATTT-TTATTAT
1 TTTTTATTTATTA-TAT
4359 TTTTTATTTATTATAT
1 TTTTTATTTATTATAT
4375 TTTT
1 TTTT
4379 CTTTCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTATTTATTATAT
Found at i:11742 original size:42 final size:42
Alignment explanation
Indices: 11671--11866 Score: 149
Period size: 42 Copynumber: 4.8 Consensus size: 42
11661 GAGTAGAACA
* * *
11671 ATAGCGGCGTTTTT-TTACAAACGCTGCAATAGGTGTAATAT
1 ATAGTGGCGTTTTTATAACAAACGCCGCAATAGGTGTAATAT
**
11712 ATAGTGGCGTTTTTATAACAAACGCCGCAATATATTTGT-AT-T
1 ATAGTGGCGTTTTTATAACAAACGCCGC-A-ATAGGTGTAATAT
* * * * **
11754 TTAGTGGTGTTTTTAAATAA-AAATGCCGCAAAAAAT-TAGATAT
1 ATAGTGGCGTTTTT--ATAACAAACGCCGCAATAGGTGTA-ATAT
* * *
11797 -TAATGGCG--TTTATAACAATCGCCGCAATAGGTGTACTAT
1 ATAGTGGCGTTTTTATAACAAACGCCGCAATAGGTGTAATAT
*
11836 ATAGTGGCGTTTTT-TACCAAACGCCGCAATA
1 ATAGTGGCGTTTTTATAACAAACGCCGCAATA
11867 TATTTGAATT
Statistics
Matches: 120, Mismatches: 22, Indels: 26
0.71 0.13 0.15
Matches are distributed among these distances:
38 4 0.03
39 14 0.12
40 13 0.11
41 31 0.26
42 36 0.30
43 12 0.10
44 10 0.08
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (42 bp):
ATAGTGGCGTTTTTATAACAAACGCCGCAATAGGTGTAATAT
Found at i:11933 original size:124 final size:125
Alignment explanation
Indices: 11676--11904 Score: 293
Period size: 123 Copynumber: 1.8 Consensus size: 125
11666 GAACAATAGC
* * *
11676 GGCGTTTTTTTACAAACGCTGCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCA
1 GGCGTTTATTAACAAACGCCGCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCA
* * * * * * *
11741 ATATATTTGTATTTTAGTGGTGTTTTTAAATAAAAATGCCGCAAAAAATTAGATATTAAT
66 ATATATTTGAATTTTAGCGGCGTTTCTAAACAAAAACGCCGCAAAAAATTAGACATTAAT
* * *
11801 GGCGTTTA-TAACAATCGCCGCAATAGGTGTACTATATAGTGGCGTTTTT-TACCAAACGCCGCA
1 GGCGTTTATTAACAAACGCCGCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCA
* *
11864 ATATATTTGAATTGTTA-CGGCGTTTCTAGACACAAACGCCG
66 ATATATTTGAATT-TTAGCGGCGTTTCTAAACAAAAACGCCG
11905 TAATATATAT
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
123 42 0.47
124 40 0.45
125 7 0.08
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (125 bp):
GGCGTTTATTAACAAACGCCGCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCA
ATATATTTGAATTTTAGCGGCGTTTCTAAACAAAAACGCCGCAAAAAATTAGACATTAAT
Found at i:14379 original size:2 final size:2
Alignment explanation
Indices: 14372--14397 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14362 TTGTGGTATT
14372 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
14398 CACAGTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21533 original size:21 final size:20
Alignment explanation
Indices: 21486--21534 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
21476 AGCGAAAAAT
*
21486 GAAGCAAGAGAAGCAGAGAGA
1 GAAGC-AGAGAAGCAGAGAAA
*
21507 GCAGCAGCAGAAGCAGAGAAA
1 GAAGCAG-AGAAGCAGAGAAA
21528 GAAGCAG
1 GAAGCAG
21535 TGACAACACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.49, C:0.14, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAGCAGAGAAGCAGAGAAA
Found at i:22189 original size:43 final size:43
Alignment explanation
Indices: 22002--22190 Score: 202
Period size: 43 Copynumber: 4.4 Consensus size: 43
21992 AAATCTAAAA
* * * *
22002 ACCTACT-CGACGTTTGTAGGAAAAACGCCGCTAAAAATCATC
1 ACCTACTGCGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
* * * * * * *
22044 ACCTATTGCGGTGTTTGTGGGAAAAACGCCGCAAAATATCAAA
1 ACCTACTGCGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
* * *
22087 ACCTACTACGGCGTTTTTAAGTAAAACGCCGCTAAATC-TCAAC
1 ACCTACTGCGGCGTTTTTAGGAAAAACGCCGCTAAA-CATCAAC
* *
22130 ACATACTGCGACGTTTTTAGGAAAAACGCCGCTAAACATCAAC
1 ACCTACTGCGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
*
22173 ACCTATTGCGGCGTTTTT
1 ACCTACTGCGGCGTTTTT
22191 TAAAACTTTA
Statistics
Matches: 118, Mismatches: 26, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
42 7 0.06
43 111 0.94
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (43 bp):
ACCTACTGCGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
Found at i:22840 original size:30 final size:30
Alignment explanation
Indices: 22806--22904 Score: 123
Period size: 30 Copynumber: 3.3 Consensus size: 30
22796 ATTTAAGTGT
22806 TTAAAGTATTTTTTTAATTAAAATAAGTAC
1 TTAAAGTATTTTTTTAATTAAAATAAGTAC
*
22836 TTAAAGTTATTTTTTT-ATTAAAATATGTAC
1 TTAAAG-TATTTTTTTAATTAAAATAAGTAC
* * *
22866 CTAAAGTA-TTTTTTAATCAAAATAGGTA-
1 TTAAAGTATTTTTTTAATTAAAATAAGTAC
22894 TCTAAAGTATT
1 T-TAAAGTATT
22905 CAACTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.10
29 20 0.33
30 25 0.42
31 9 0.15
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (30 bp):
TTAAAGTATTTTTTTAATTAAAATAAGTAC
Found at i:22875 original size:29 final size:29
Alignment explanation
Indices: 22807--22904 Score: 124
Period size: 29 Copynumber: 3.3 Consensus size: 29
22797 TTTAAGTGTT
*
22807 TAAAGTATTTTTTTAATTAAAATAAGTACT
1 TAAAGTATTTTTTT-ATTAAAATAAGTACC
*
22837 TAAAGTTATTTTTTTATTAAAATATGTACC
1 TAAAG-TATTTTTTTATTAAAATAAGTACC
* * * *
22867 TAAAGTATTTTTTAATCAAAATAGGTATC
1 TAAAGTATTTTTTTATTAAAATAAGTACC
22896 TAAAGTATT
1 TAAAGTATT
22905 CAACTTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
29 29 0.48
30 23 0.38
31 9 0.15
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (29 bp):
TAAAGTATTTTTTTATTAAAATAAGTACC
Found at i:24392 original size:2 final size:2
Alignment explanation
Indices: 24385--24416 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24375 ATTATTTTAA
24385 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
24417 GCTTTTCATT
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:25121 original size:18 final size:19
Alignment explanation
Indices: 25098--25133 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
25088 AAACGAATAT
*
25098 AAAACATGT-AAAATTAAG
1 AAAACATATAAAAATTAAG
25116 AAAACATATAAAAATTAA
1 AAAACATATAAAAATTAA
25134 ATACATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAAATTAAG
Found at i:27085 original size:7 final size:7
Alignment explanation
Indices: 27067--27156 Score: 164
Period size: 7 Copynumber: 13.0 Consensus size: 7
27057 ACATGCCTGC
27067 TTCTTC-
1 TTCTTCT
27073 TTCTTCT
1 TTCTTCT
27080 TTCTTCT
1 TTCTTCT
27087 TTCTTCT
1 TTCTTCT
27094 TTCTTCT
1 TTCTTCT
27101 TTCTTCT
1 TTCTTCT
27108 TTCTTCT
1 TTCTTCT
27115 TTCTTCT
1 TTCTTCT
27122 TTCTTCT
1 TTCTTCT
27129 TTCTTCT
1 TTCTTCT
27136 TTCTTCT
1 TTCTTCT
*
27143 TTCTTCA
1 TTCTTCT
27150 TTCTTCT
1 TTCTTCT
27157 ACTTCCACGC
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
6 6 0.07
7 75 0.93
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (7 bp):
TTCTTCT
Found at i:28125 original size:42 final size:42
Alignment explanation
Indices: 28076--28205 Score: 154
Period size: 42 Copynumber: 3.1 Consensus size: 42
28066 TTTTTCTCTA
28076 AAACGCCACAGTATG-TGTTAATGTTTTGCGACGTTTTCCCAC
1 AAACGCCACAGTA-GATGTTAATGTTTTGCGACGTTTTCCCAC
* *
28118 AAACGCCACAGTAGATGTTGATGTTTTGCGGCGTTTTCCCAC
1 AAACGCCACAGTAGATGTTAATGTTTTGCGACGTTTTCCCAC
* * * * * * *
28160 AAACGTCGCAGTAGATTTTGATGTTTTGTGGCGTTTTTCTCAC
1 AAACGCCACAGTAGATGTTAATGTTTTGCGACG-TTTTCCCAC
28203 AAA
1 AAA
28206 TGCCGCAATA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.01
42 67 0.85
43 11 0.14
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
AAACGCCACAGTAGATGTTAATGTTTTGCGACGTTTTCCCAC
Found at i:28224 original size:43 final size:43
Alignment explanation
Indices: 27904--28240 Score: 261
Period size: 43 Copynumber: 7.9 Consensus size: 43
27894 TTTAAACAAA
* * * *
27904 AAACGCCGCAATAGGTATTGATATATAGCGGCGTTTGTCACAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTCAC
* * ** *
27947 AAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAGAA
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTCAC
* *
27990 AAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT-T-AGTT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTCA--C
**
28033 AAACGCCGCAATAGGTAATGATATTTAGCGGCGTTTTTCTCTA-
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTC-AC
* * * * * * * *
28076 AAACGCCACAGTATGTGTTAATGTTTTGCGACG-TTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTCAC
* * * * * *
28118 AAACGCCACAGTAGATGTTGATGTTTTGCGGCG-TTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTCAC
* * * * * * *
28160 AAACGTCGCAGTAGATTTTGATGTTTTGTGGCGTTTTTCTCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTCAC
* * * * *
28203 AAATGCCGCAATAGGTATTGATTTTTTGCGGCATTTTT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
28241 GCTAAAAACA
Statistics
Matches: 249, Mismatches: 38, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
41 2 0.01
42 73 0.29
43 172 0.69
44 1 0.00
46 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCTCAC
Found at i:28711 original size:21 final size:21
Alignment explanation
Indices: 28653--28722 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
28643 GCTGATATGT
* *
28653 TGCTTCTCTTTGTGCTACCTC
1 TGCTTCTCTTTGTGCTGCCGC
* * *
28674 TGCTTCTCTCTATGCTGCCGG
1 TGCTTCTCTTTGTGCTGCCGC
* *
28695 TGCTTCTCTTTGTGCTGCTGT
1 TGCTTCTCTTTGTGCTGCCGC
28716 TGCTTCT
1 TGCTTCT
28723 TTCTCTACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.30, G:0.20, T:0.47
Consensus pattern (21 bp):
TGCTTCTCTTTGTGCTGCCGC
Found at i:28916 original size:15 final size:15
Alignment explanation
Indices: 28871--28909 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
28861 GAAGATCGAG
28871 ACTGTGATGACATGT
1 ACTGTGATGACATGT
28886 ACTGTGATGACATGT
1 ACTGTGATGACATGT
28901 ACTGTGATG
1 ACTGTGATG
28910 TACTGTATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (15 bp):
ACTGTGATGACATGT
Found at i:31216 original size:9 final size:10
Alignment explanation
Indices: 31193--31219 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31183 TAATTGCTCC
31193 AAAAAGCAAG
1 AAAAAGCAAG
31203 AAAAAGCAAG
1 AAAAAGCAAG
31213 AAAAAGC
1 AAAAAGC
31220 TATGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.11, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAGCAAG
Found at i:33212 original size:42 final size:41
Alignment explanation
Indices: 33118--33214 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 41
33108 AAGGGACACA
* *
33118 CTATTGCGGCGTTTATTACAAAAAGCCACTAAATTACAACT
1 CTATTGCGGCGTTTATTACAAAAAACCACTAAAGTACAACT
*
33159 CTATTGTGGCGTTTATGT-CAAAAACACCACTAAAGTACAACT
1 CTATTGCGGCGTTTAT-TACAAAAA-ACCACTAAAGTACAACT
*
33201 -TTTTAGCGGCGTTT
1 CTATT-GCGGCGTTT
33215 TGATAACAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
41 24 0.50
42 24 0.50
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (41 bp):
CTATTGCGGCGTTTATTACAAAAAACCACTAAAGTACAACT
Found at i:33231 original size:42 final size:42
Alignment explanation
Indices: 33118--33234 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 42
33108 AAGGGACACA
*
33118 CTATTGCGGCGTTTAT-TACAAAAA-GCCACTAAATTACAACT
1 CTATTGCGGCGTTTATGT-CAAAAACGCCACTAAAGTACAACT
* *
33159 CTATTGTGGCGTTTATGTCAAAAACACCACTAAAGTACAACT
1 CTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACT
*
33201 -TTTTAGCGGCGTTT-TGAT-AACAAACGCCACTAAA
1 CTATT-GCGGCGTTTATG-TCAA-AAACGCCACTAAA
33235 TTTAGAGTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
41 28 0.43
42 37 0.57
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (42 bp):
CTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACT
Found at i:33401 original size:135 final size:135
Alignment explanation
Indices: 33152--33427 Score: 374
Period size: 135 Copynumber: 2.0 Consensus size: 135
33142 GCCACTAAAT
**
33152 TACAACTCTATTGTGGCGTTTATGTCAAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTTG
1 TACAACTCTATTACGGCGTTTATGTCAAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTTG
* * ** *
33217 ATAACAAACGCCACTAAATTTAGAGTATTTTATGGCGTTTTCTTAAAAAATGCCATTATAAATAA
66 ATAACAAACGCCACTAAATTAAGAGTATTTTACGGCGTTTGATTAAAAAATGCCACTATAAATAA
33282 CAATA
131 CAATA
* **
33287 TACAACTCTATTACGGCGTTTATGTCAAAAAACGCCTTTAAAGTACAACTTTTTAGCGGCG-TTT
1 TACAACTCTATTACGGCGTTTATGTC-AAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTT
* * * * * * *
33351 GTTACCAAACGCTACTAAATTAAGAGTATTTTGCGGCGTTTGATTGAAAAATGCCGCTATAAATT
65 GATAACAAACGCCACTAAATTAAGAGTATTTTACGGCGTTTGATTAAAAAATGCCACTATAAATA
33416 ACAATA
130 ACAATA
*
33422 TGCAAC
1 TACAAC
33428 CATTTTGCAG
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
135 91 0.75
136 31 0.25
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (135 bp):
TACAACTCTATTACGGCGTTTATGTCAAAAACACCACTAAAGTACAACTTTTTAGCGGCGTTTTG
ATAACAAACGCCACTAAATTAAGAGTATTTTACGGCGTTTGATTAAAAAATGCCACTATAAATAA
CAATA
Found at i:34860 original size:41 final size:40
Alignment explanation
Indices: 34772--34953 Score: 199
Period size: 41 Copynumber: 4.5 Consensus size: 40
34762 GACTATATAT
* *
34772 TTAACA-TTTTGCGGCGTTTATAAAAAACGCCACTATTGA
1 TTAACACTATTGCGGCGTTTTTAAAAAACGCCACTATTGA
** *
34811 TT-ACACTATTATGGCGTTTGTTAAAAAACGCCATTATTGA
1 TTAACACTATTGCGGCGTTT-TTAAAAAACGCCACTATTGA
* * * * *
34851 TTAAAACTATTGCGGTGTTTTTCTAAAAATGCCACTAGTGA
1 TTAACACTATTGCGGCGTTTTT-AAAAAACGCCACTATTGA
*
34892 TTAACACTATTGCGGCGTTTGTCT-AAAAACGCCACTATTTA
1 TTAACACTATTGCGGCGTTT-T-TAAAAAACGCCACTATTGA
*
34933 TTATCACTATTGCGGCGTTTT
1 TTAACACTATTGCGGCGTTTT
34954 AAGAATAAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
38 3 0.03
39 12 0.10
40 23 0.19
41 78 0.66
42 1 0.01
43 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (40 bp):
TTAACACTATTGCGGCGTTTTTAAAAAACGCCACTATTGA
Found at i:35088 original size:41 final size:41
Alignment explanation
Indices: 34899--35088 Score: 142
Period size: 42 Copynumber: 4.6 Consensus size: 41
34889 TGATTAACAC
* * * *
34899 TATTGCGGCGTTTGT-CTAAAAACGCCACTATTTATT-ATCA
1 TATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTAAT-A
* * * * *
34939 CTATTGCGGCGTTT-TAAGAATAAATGTCACTATATGTGTAATC
1 -TATTGCGGCGTTTGT-GGTATAAACGCCACTATATGT-TAATA
* *
34982 TATTGCGGCGTTTGTGGTATAAATGCCACTA-AT-TTACCGATC
1 TATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTA---ATA
* *
35024 TATTACGACGTTT-TGGCTA-AAACGCCACTATATGTTAATA
1 TATTGCGGCGTTTGTGG-TATAAACGCCACTATATGTTAATA
35064 TATTGCGGCGTTTGTGGTATAAACG
1 TATTGCGGCGTTTGTGGTATAAACG
35089 GAAGTTTAGA
Statistics
Matches: 119, Mismatches: 17, Indels: 26
0.73 0.10 0.16
Matches are distributed among these distances:
39 2 0.02
40 17 0.14
41 36 0.30
42 57 0.48
43 5 0.04
44 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (41 bp):
TATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTAATA
Found at i:41850 original size:15 final size:16
Alignment explanation
Indices: 41824--41856 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
41814 AAACAGAGGC
*
41824 AAATATATATAAAGTA
1 AAATATATATAAAATA
41840 AAATA-ATATAAAATA
1 AAATATATATAAAATA
41855 AA
1 AA
41857 GGGGAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAATATATATAAAATA
Found at i:43493 original size:20 final size:20
Alignment explanation
Indices: 43441--43506 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 20
43431 GATGAGAAAA
*
43441 ATATGTATGTGATATATGTTAT
1 ATAT-TATGTAATATATG-TAT
43463 ATAATTA--TAATATATGTAT
1 AT-ATTATGTAATATATGTAT
*
43482 ATATTATGTAATGTA--TAT
1 ATATTATGTAATATATGTAT
43500 ATATTAT
1 ATATTAT
43507 ATACTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 14 0.36
19 5 0.13
20 14 0.36
22 4 0.10
23 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
ATATTATGTAATATATGTAT
Found at i:71828 original size:31 final size:31
Alignment explanation
Indices: 71793--71856 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
71783 ATTTAATTAA
*
71793 TTTAATCTTAATTT-TAATTTAATATAATAAT
1 TTTAATCTTAATTTAT-ATTTAATAAAATAAT
71824 TTTAATCTTAATTTATATTTAATAAAATAAT
1 TTTAATCTTAATTTATATTTAATAAAATAAT
71855 TT
1 TT
71857 AATACTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTAATCTTAATTTATATTTAATAAAATAAT
Found at i:71829 original size:25 final size:26
Alignment explanation
Indices: 71795--71848 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
71785 TTAATTAATT
*
71795 TAATCTTAATTTTAATTTA-ATATAA
1 TAATCTTAATCTTAATTTATATATAA
* *
71820 TAATTTTAATCTTAATTTATATTTAA
1 TAATCTTAATCTTAATTTATATATAA
71846 TAA
1 TAA
71849 AATAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
TAATCTTAATCTTAATTTATATATAA
Found at i:71859 original size:5 final size:5
Alignment explanation
Indices: 71783--71846 Score: 53
Period size: 5 Copynumber: 12.4 Consensus size: 5
71773 TTACTTACAT
*
71783 ATTTA A-TTA ATTTA ATCTTA ATTTTA ATTTA ATATA A--TA ATTTTA
1 ATTTA ATTTA ATTTA AT-TTA A-TTTA ATTTA ATTTA ATTTA A-TTTA
71828 ATCTTA ATTTA TATTTA AT
1 AT-TTA ATTTA -ATTTA AT
71847 AAAATAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 21 0.42
6 21 0.42
7 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTTA
Found at i:75592 original size:11 final size:11
Alignment explanation
Indices: 75576--75602 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
75566 TCACAATGCC
75576 ATTTTCCTTCT
1 ATTTTCCTTCT
75587 ATTTTCCTTCT
1 ATTTTCCTTCT
75598 ATTTT
1 ATTTT
75603 ATATACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTCCTTCT
Found at i:91438 original size:20 final size:20
Alignment explanation
Indices: 91402--91439 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
91392 ATCCTATTCC
**
91402 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
91422 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
91440 GTTAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:95672 original size:22 final size:22
Alignment explanation
Indices: 95612--95673 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
95602 AAATTAATAT
* *
95612 TAAAAATATATTAATATTTTAA
1 TAAAAATATATTAATATATGAA
* *
95634 CAAAAATAT-TTAAATATATGGA
1 TAAAAATATATT-AATATATGAA
*
95656 TAAAAATATATTTATATA
1 TAAAAATATATTAATATA
95674 AATATATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAAAATATATTAATATATGAA
Found at i:95687 original size:18 final size:18
Alignment explanation
Indices: 95661--95702 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
95651 ATGGATAAAA
*
95661 ATATATTTATATAAATAT
1 ATATTTTTATATAAATAT
* *
95679 ATATTTTTATTTAAATGT
1 ATATTTTTATATAAATAT
95697 ATATTT
1 ATATTT
95703 ATTTATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATTTTTATATAAATAT
Found at i:95703 original size:16 final size:16
Alignment explanation
Indices: 95656--95712 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
95646 AATATATGGA
* *
95656 TAAAAATATATTTATA
1 TAAATATATATTTATT
95672 TAAATATATATTTTTATT
1 TAAATATATA--TTTATT
*
95690 TAAATGTATATTTATT
1 TAAATATATATTTATT
*
95706 TATATAT
1 TAAATAT
95713 TTAAATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 20 0.59
18 14 0.41
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TAAATATATATTTATT
Found at i:99422 original size:85 final size:83
Alignment explanation
Indices: 99282--99471 Score: 231
Period size: 85 Copynumber: 2.3 Consensus size: 83
99272 TGGATTAATC
* *
99282 TCAAGTTTTAGGATAATATTTT-AAACATTATATTTTATCTCTGTTTTAGATATTTTAGTTTAAA
1 TCAAGATTTAGGATATTATTTTAAAACATTATATTTTATCTCTGTTTTAGATATTTTAGTTTAAA
99346 TAGATGTT-AGTATTTCAA
66 TAG-TGTTAAGTATTTCAA
* * * *
99364 TCAAGATTTAGGATATTATTTTAAATAGTATTTTATTTTATCTTTGTTTTAGGTATTTTAGTTTA
1 TCAAGATTTAGGATATTATTTTAAA-A-CATTATATTTTATCTCTGTTTTAGATATTTTAGTTTA
* *
99429 AATAGTTTTAAGTATTTTAA
64 AATAGTGTTAAGTATTTCAA
* * * *
99449 TTAGGATTTAAGATGTTATTTTA
1 TCAAGATTTAGGATATTATTTTA
99472 GGAATTATCT
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
82 20 0.22
83 2 0.02
84 4 0.04
85 66 0.72
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (83 bp):
TCAAGATTTAGGATATTATTTTAAAACATTATATTTTATCTCTGTTTTAGATATTTTAGTTTAAA
TAGTGTTAAGTATTTCAA
Found at i:101770 original size:31 final size:31
Alignment explanation
Indices: 101735--101808 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
101725 AAAACATAAG
* * *
101735 TTTTGGTCACTTATGTTTTTGTTTTATTAAA
1 TTTTGGTCACTTATGTTATCGTTGTATTAAA
* * * *
101766 TTTTGATCATTTGTGTTATCGTTGTATTAAG
1 TTTTGGTCACTTATGTTATCGTTGTATTAAA
*
101797 GTTTGGTCACTT
1 TTTTGGTCACTT
101809 GGACGTTGAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.57
Consensus pattern (31 bp):
TTTTGGTCACTTATGTTATCGTTGTATTAAA
Done.