Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000815.1 Hibiscus syriacus cultivar Beakdansim tig00001575_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: 76826
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4438 original size:28 final size:28
Alignment explanation
Indices: 4406--4475 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
4396 TGAATTTAGG
* *
4406 GAAGGTAATGTGTTTCT-GGTTAATTTGA
1 GAAGGTAATGTGTTT-TAAGTTAATTTAA
4434 GAAGGTAATGTGTTTTAAGTTAATTTAA
1 GAAGGTAATGTGTTTTAAGTTAATTTAA
* *
4462 GGAGGTAATATGTT
1 GAAGGTAATGTGTT
4476 CCAGGTTGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.41
Consensus pattern (28 bp):
GAAGGTAATGTGTTTTAAGTTAATTTAA
Found at i:9191 original size:14 final size:15
Alignment explanation
Indices: 9160--9193 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
9150 ATTTGGAATT
*
9160 TAAATGATTGAAATG
1 TAAATGATTGAAAAG
9175 TAAATGA-TGAAAAG
1 TAAATGATTGAAAAG
9189 TAAAT
1 TAAAT
9194 ACATAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (15 bp):
TAAATGATTGAAAAG
Found at i:11773 original size:10 final size:10
Alignment explanation
Indices: 11760--11791 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
11750 AAAAAGACCG
11760 AAAAATAAAA
1 AAAAATAAAA
*
11770 AAAAATATAA
1 AAAAATAAAA
11780 AAAAATAAAA
1 AAAAATAAAA
11790 AA
1 AA
11792 TTGCAAACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:17780 original size:150 final size:150
Alignment explanation
Indices: 17517--17832 Score: 483
Period size: 150 Copynumber: 2.1 Consensus size: 150
17507 TTCAAGTGCC
* *
17517 TAACGTTATAAACATTACCACTTTAGGTGCCCGAACCATAACTACTGTTAAGTTTTTCCGTTAAG
1 TAACATTATAAACATTACCACTTTAGGTGCCCGAACCATAACTACTGTTAAATTTTTCCGTTAAG
*
17582 TGATACATGTCACATTCTGGTAATTTTAAAAAAAATTAAAAATTAAAAATATATATTATAATTAT
66 TGATACATGTCACATTCTGGTAATTTTAAAAAAAATTAAAAAATAAAAATATATATTATAATTAT
17647 TAAGAAACCCTAATTTATCT
131 TAAGAAACCCTAATTTATCT
*
17667 TAACATTATAAACATTACCACTTTAGGTGCTCGAACCATAACTACTGTTAAATTTTTCCGTTAAG
1 TAACATTATAAACATTACCACTTTAGGTGCCCGAACCATAACTACTGTTAAATTTTTCCGTTAAG
*
17732 TGATACATGTCACATTCTGGTAATTTTGAAAATTTTATTTTAAA-AAAAAAATTAAAAATATATA
66 TGATACATGTCACATTCTGGTAATTTT-AAAA----A----AAATTAAAAAA-TAAAAATATATA
17796 TTATAATTATTAAGAAACCCTAATTTATCT
121 TTATAATTATTAAGAAACCCTAATTTATCT
17826 TAA-ATTA
1 TAACATTA
17833 CAAAAGAAAC
Statistics
Matches: 151, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
150 89 0.59
151 4 0.03
155 1 0.01
158 9 0.06
159 48 0.32
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (150 bp):
TAACATTATAAACATTACCACTTTAGGTGCCCGAACCATAACTACTGTTAAATTTTTCCGTTAAG
TGATACATGTCACATTCTGGTAATTTTAAAAAAAATTAAAAAATAAAAATATATATTATAATTAT
TAAGAAACCCTAATTTATCT
Found at i:18215 original size:27 final size:26
Alignment explanation
Indices: 18185--18240 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
18175 GTATTTCAAA
*
18185 AATTATATT-TTTTAAAATATAATTTTT
1 AATTAT-TTATTTT-AAATAAAATTTTT
18212 AATTATTTGATTTTAAATAAAATTTTT
1 AATTATTT-ATTTTAAATAAAATTTTT
18239 AA
1 AA
18241 AATTACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 20 0.77
28 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AATTATTTATTTTAAATAAAATTTTT
Found at i:21713 original size:28 final size:25
Alignment explanation
Indices: 21670--21722 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
21660 GATAATAAAG
*
21670 ATAAACACAATAAATAATGAGAAATAT
1 ATAAACAAAATAAATAA-G-GAAATAT
21697 ATAAACAAAGATAAATAAGGAAATAT
1 ATAAACAAA-ATAAATAAGGAAATAT
21723 GATTTGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 9 0.38
28 8 0.33
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (25 bp):
ATAAACAAAATAAATAAGGAAATAT
Found at i:22699 original size:19 final size:19
Alignment explanation
Indices: 22675--22718 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
22665 CAAATCCCCT
22675 AAATCAAGGAATTATAACC
1 AAATCAAGGAATTATAACC
22694 AAATCAAGGAATTATAACC
1 AAATCAAGGAATTATAACC
22713 AAATCA
1 AAATCA
22719 TACCTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (19 bp):
AAATCAAGGAATTATAACC
Found at i:27831 original size:12 final size:15
Alignment explanation
Indices: 27783--27821 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
27773 ATTTTAAAGA
27783 AATTTTGTTGATGCG
1 AATTTTGTTGATGCG
27798 AATTTTGTTGATGCG
1 AATTTTGTTGATGCG
27813 AATTTTGTT
1 AATTTTGTT
27822 AGCGATTTTG
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:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (15 bp):
AATTTTGTTGATGCG
Found at i:30292 original size:4 final size:4
Alignment explanation
Indices: 30277--30307 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
30267 TAAAAGGGGA
*
30277 AAAT AGAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
30308 ATATAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:32066 original size:84 final size:84
Alignment explanation
Indices: 31965--32422 Score: 514
Period size: 84 Copynumber: 5.5 Consensus size: 84
31955 GTTTGCCTCT
* * * *
31965 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
32030 CTGCAAATGATATGTCTTG
66 CTGCAAATGATATGCCTTG
* * * * *
32049 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
32114 CTGCAAATGATATGCCTTG
66 CTGCAAATGATATGCCTTG
* * *
32133 GAGTTGAGCGTAGTCGAATTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
32198 CTGCAAATGATATGCCTTG
66 CTGCAAATGATATGCCTTG
* * ** * * *
32217 GAGCTGAGCGGAGTTGAACTCGAAGGTCTTTTGG-TCACAAATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
* * *
32281 ACTGTAAATGATATGCCCTCG
65 GCTGCAAATGATATG-CCTTG
* * * * * ** * * *
32302 AAGCTGAGTGCAATCAAACTCGGGGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
32363 CTGCAAATGATGTGCCATT-
66 CTGCAAATGATATGCC-TTG
* * *
32382 GAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
32423 CACTCCTTCT
Statistics
Matches: 308, Mismatches: 59, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
80 25 0.08
81 34 0.11
84 220 0.71
85 29 0.09
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
CTGCAAATGATATGCCTTG
Found at i:32176 original size:168 final size:169
Alignment explanation
Indices: 31966--32432 Score: 606
Period size: 168 Copynumber: 2.8 Consensus size: 169
31956 TTTGCCTCTG
* *
31966 AGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
32031 TGCAAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCC
66 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCC
* * *
32096 TTCTAGACTTAAGTTGTACTGCAAATGATATG-CCTTGG
131 TTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGA
* * * *
32134 AGTTGAGCGTAGTCGAATTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* * * * ** * *
32199 TGCAAATGATATGCCTTGGAGCTGAGCGGAGTTGAACTCGAAGGTCTTTTGGTCACAAATAACCC
66 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCC
* * *
32264 TTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGA
131 TTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGA
* * ** * *
32303 AGCTGAGTGCAATCAAACTCGGGGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* *
32364 TGCAAATGATGTGCCATT-GAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGAC-ACT
66 TGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAAC-
32427 CCTTCT
129 CCTTCT
32433 TTGAGTTGGA
Statistics
Matches: 255, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
164 2 0.01
165 79 0.31
166 2 0.01
168 144 0.56
169 28 0.11
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (169 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCC
TTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGA
Found at i:32922 original size:94 final size:94
Alignment explanation
Indices: 32756--33529 Score: 1149
Period size: 94 Copynumber: 8.1 Consensus size: 94
32746 AAATTGGCTC
* * * * * *
32756 TGAAATTGGGAAGTTGTTTGTTGA-AAGTCAGCCG-CCACTTCG-CTGCGAAGTTGAGCTTGTGT
1 TGAAATTGGGAAATTGTTTGTTGACAA-CCAGCGGTCC-CTTCGTC-GTGAAGTTGAACTTGCGT
*
32818 TGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
63 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
32850 TGAAATTGGGAAATTGTTTGTTGACAACCTGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
32915 CTGGAGTCCAATGTCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
32944 TGAAATTGGGAAATTATTTGTTGACAACCATCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
**
33009 CTGGAGTCCAATGCCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
*
33038 TGAAATTGGGAAATTGTTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
33103 CTGGAGTCCAATGTCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
33132 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
33197 CTGGAGTCCAATGTCATTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
33226 TAAAATTTGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
33291 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
33320 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
33385 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
**
33414 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGTAGTCCCTTCGTCGTGAAGTTG
1 TGAAATT-G----G-----GA-AA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* *
33479 AACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
33520 TGAAATTGGG
1 TGAAATTGGG
33530 TCTAAAATTG
Statistics
Matches: 628, Mismatches: 37, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
94 533 0.85
95 6 0.01
96 1 0.00
99 1 0.00
101 1 0.00
104 2 0.00
105 3 0.00
106 81 0.13
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:33556 original size:106 final size:106
Alignment explanation
Indices: 33322--33557 Score: 373
Period size: 106 Copynumber: 2.2 Consensus size: 106
33312 TGTGAAGTTG
* * * * *
33322 AAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGTGTTGTCT
1 AAATTGGGAAGTTGTTTGTTGACAACCAGCAGTCCCCTCGTCGTGAAGTTGAACATGCGTTGTCT
* *
33387 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTA
* * *
33428 AAATTGAGAAGTTGTTTGTTGACAACCAGTAGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCT
1 AAATTGGGAAGTTGTTTGTTGACAACCAGCAGTCCCCTCGTCGTGAAGTTGAACATGCGTTGTCT
*
33493 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGGTCTA
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTA
33534 AAATTGGGAAGTTGTTTGTTGACA
1 AAATTGGGAAGTTGTTTGTTGACA
33558 GACAACTTTT
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 118 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (106 bp):
AAATTGGGAAGTTGTTTGTTGACAACCAGCAGTCCCCTCGTCGTGAAGTTGAACATGCGTTGTCT
GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTA
Found at i:40562 original size:2 final size:2
Alignment explanation
Indices: 40555--40619 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
40545 CTGCTAGTGA
40555 AT AT AT AT AT 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 AT AT AT AT AT
40597 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
40620 ATCCTCAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43193 original size:2 final size:2
Alignment explanation
Indices: 43186--43257 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
43176 ATTTAACTTG
43186 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
43228 TA TA 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 TA TA
43258 CATCTCAAAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43852 original size:25 final size:25
Alignment explanation
Indices: 43824--43882 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
43814 TTTTTCAAGC
43824 TTGAGTCAAGCTTCAGTTTTTTATT
1 TTGAGTCAAGCTTCAGTTTTTTATT
*
43849 TTGAGTCAAGCTTCATTTTTTTATT
1 TTGAGTCAAGCTTCAGTTTTTTATT
43874 TTGAGTCAA
1 TTGAGTCAA
43883 ACTTGAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (25 bp):
TTGAGTCAAGCTTCAGTTTTTTATT
Found at i:43895 original size:25 final size:25
Alignment explanation
Indices: 43824--43896 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
43814 TTTTTCAAGC
* ***
43824 TTGAGTCAAGCTTCAGTTTTTTATT
1 TTGAGTCAAACTTCAAAATTTTATT
* ***
43849 TTGAGTCAAGCTTCATTTTTTTATT
1 TTGAGTCAAACTTCAAAATTTTATT
*
43874 TTGAGTCAAACTTGAAAATTTTA
1 TTGAGTCAAACTTCAAAATTTTA
43897 AGCTTTTGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (25 bp):
TTGAGTCAAACTTCAAAATTTTATT
Found at i:44277 original size:27 final size:26
Alignment explanation
Indices: 44209--44284 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
44199 ATATTAATTT
*
44209 AATTTAAATAAATGAATATAAAATATATA
1 AATTTAAATAAAT-AA-ATAAAACATA-A
* * *
44238 ATTTTAAACAAATAAATAGAACATAA
1 AATTTAAATAAATAAATAAAACATAA
44264 AATTTAAAATAAATAAATAAA
1 AATTT-AAATAAATAAATAAA
44285 GAATGGAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 5 0.13
27 21 0.54
28 2 0.05
29 11 0.28
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (26 bp):
AATTTAAATAAATAAATAAAACATAA
Found at i:44968 original size:2 final size:2
Alignment explanation
Indices: 44961--44988 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44951 ACCCTTCAAG
44961 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
44989 TTACTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47216 original size:107 final size:107
Alignment explanation
Indices: 47024--47299 Score: 455
Period size: 107 Copynumber: 2.6 Consensus size: 107
47014 TAGAAAATCT
* * * * *
47024 CCAAGTATAAATTTCACTGTGTATAGAAAATCTCTATAGATCATATAGCATATACTTCAGAACTG
1 CCAACTATAAATTTCACTGTCTATAGAAAATCTCCATGGATCATATAGCATATACTTCAGAACTC
47089 GATTCCCTTTGACCTCAATGTCAAATTAGAGTTAATTAACCC
66 GATTCCCTTTGACCTCAATGTCAAATTAGAGTTAATTAACCC
* *
47131 CTAACTATAAATTTCACTGTCTATAGAAAATCTCCATGGATCATATAGCATATACTTCATAACTC
1 CCAACTATAAATTTCACTGTCTATAGAAAATCTCCATGGATCATATAGCATATACTTCAGAACTC
47196 GATTCCCTTTGACC-CTAATGTCAAATTAGAGTTAATTAACCC
66 GATTCCCTTTGACCTC-AATGTCAAATTAGAGTTAATTAACCC
* *
47238 CCAACTATAAATTTCTCTATCTATAGAAAATCTCCATGGATCATATAGCATATACTTCAGAA
1 CCAACTATAAATTTCACTGTCTATAGAAAATCTCCATGGATCATATAGCATATACTTCAGAA
47300 TTACTATAAA
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
106 1 0.01
107 156 0.99
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (107 bp):
CCAACTATAAATTTCACTGTCTATAGAAAATCTCCATGGATCATATAGCATATACTTCAGAACTC
GATTCCCTTTGACCTCAATGTCAAATTAGAGTTAATTAACCC
Found at i:47342 original size:61 final size:61
Alignment explanation
Indices: 47241--47360 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
47231 TTAACCCCCA
* * * * *
47241 ACTATAAATTTCTCTATCTATAGAAAATCTCCATGGATCATATAGCATATACTTCAGAATT
1 ACTATAAAATTCACTATCTATAGAAAATCTCCATGAATCATATAACACATACTTCAGAATT
* * *
47302 ACTATAAAATTCACTGTCTATAGAAAATCTCTATGAATCATATAACACATATTTCAGAA
1 ACTATAAAATTCACTATCTATAGAAAATCTCCATGAATCATATAACACATACTTCAGAA
47361 CTCGATTCCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (61 bp):
ACTATAAAATTCACTATCTATAGAAAATCTCCATGAATCATATAACACATACTTCAGAATT
Found at i:48662 original size:23 final size:24
Alignment explanation
Indices: 48632--48686 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 24
48622 ATGAATTTAA
*
48632 ATTTTTTAAA-AATATATATAAAT
1 ATTTTTTAAAGAAAATATATAAAT
48655 ATTTTTTAAAGAAAATATATAAAT
1 ATTTTTTAAAGAAAATATATAAAT
48679 -TTTTTTAA
1 ATTTTTTAA
48687 CTTGTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTTTTAAAGAAAATATATAAAT
Found at i:48672 original size:22 final size:23
Alignment explanation
Indices: 48629--48683 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 23
48619 TTTATGAATT
48629 TAAATTTTTTAAAAATATATATA
1 TAAATTTTTTAAAAATATATATA
48652 -AATATTTTTTAAAGAA-A-ATATA
1 TAA-ATTTTTTAAA-AATATATATA
48674 TAAATTTTTT
1 TAAATTTTTT
48684 TAACTTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 14 0.48
23 13 0.45
24 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAATTTTTTAAAAATATATATA
Found at i:55062 original size:156 final size:156
Alignment explanation
Indices: 54778--55064 Score: 376
Period size: 156 Copynumber: 1.8 Consensus size: 156
54768 AACAGTCTTG
* * * * * * * * * *
54778 TTCTCTTTGACCAGCCAAAATAGGGTGTTTTCTTGTCCAAGAGAGACTTCATATTACACTCGGGA
1 TTCTCCTTAACCAGACAAAATAGAGTGCTTTCTTGCCCAAGAGAGACATCAAACTACACTCGAGA
**
54843 GCTTGAAGCTTAACAACCTTGATTCCACGAAAAAGAAAGTCCCAATAAATGAGAAGAAAATATTT
66 GCTCAAAGCTTAACAACCTTGATTCCACGAAAAAGAAAGTCCCAATAAATGAGAAGAAAATATTT
54908 GGGTAGAGTCAAGTGTTTAACAATCT
131 GGGTAGAGTCAAGTGTTTAACAATCT
* **
54934 TTCTCCTTAACCAGACAAAATAGAGTGCTTTCTTGCCCAAGAGAGGCATCAAACTGTACTCGAGA
1 TTCTCCTTAACCAGACAAAATAGAGTGCTTTCTTGCCCAAGAGAGACATCAAACTACACTCGAGA
* * * * * * *
54999 GCTCAAAGCTTAACGACCTTGCTTCCACTAAAAATAAAGTCCCAATAAATTAGAATAACATATTT
66 GCTCAAAGCTTAACAACCTTGATTCCACGAAAAAGAAAGTCCCAATAAATGAGAAGAAAATATTT
55064 G
131 G
55065 TTTACGGAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
156 109 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (156 bp):
TTCTCCTTAACCAGACAAAATAGAGTGCTTTCTTGCCCAAGAGAGACATCAAACTACACTCGAGA
GCTCAAAGCTTAACAACCTTGATTCCACGAAAAAGAAAGTCCCAATAAATGAGAAGAAAATATTT
GGGTAGAGTCAAGTGTTTAACAATCT
Found at i:64714 original size:120 final size:123
Alignment explanation
Indices: 64451--64764 Score: 377
Period size: 120 Copynumber: 2.6 Consensus size: 123
64441 TATTACTCGG
* * * ** *
64451 CCTTGTGGTGACCAAATCCT-AGATAAGATCCATATTATTATAATTCGGACTCTGTTAACCACT-
1 CCTTGTGGTGACCAAAT-CTGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTA
* *
64514 AATTTTTAATTTAATTTAATTTATTTTATTTTTATATATTCGTTTGCATTATTCGATTCGA
65 AATTTTTAATTTAATTTAA--TATTTTATTTTTATACATTCGTTTGCATTATTCGATTCAA
* ** *
64575 CCTTGTAGTGACCCGATCTGGGGTAAGATCCACATTATTATGGTTCGGACTCCGCTAACCACTAA
1 CCTTGTGGTGACCAAATCTGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTAA
* * *
64640 ATTTTTTATTTTATTT-A-ATTTTATTTTTATACATT-TTTTGCATTATTCGATTCAA
66 ATTTTTAATTTAATTTAATATTTTATTTTTATACATTCGTTTGCATTATTCGATTCAA
* * * * *
64695 TCTTGTGGTGACCTAATCTGGGGTAAGATCGACATTATTATGGTTCGAACTCTGCTAACAACTAA
1 CCTTGTGGTGACCAAATCTGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTAA
*
64760 CTTTT
66 ATTTT
64765 CTAACTTACG
Statistics
Matches: 164, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
120 79 0.48
121 17 0.10
123 2 0.01
124 51 0.31
125 15 0.09
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (123 bp):
CCTTGTGGTGACCAAATCTGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTAA
ATTTTTAATTTAATTTAATATTTTATTTTTATACATTCGTTTGCATTATTCGATTCAA
Found at i:69682 original size:10 final size:10
Alignment explanation
Indices: 69667--69691 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
69657 TTGGTTTGCC
69667 TCAATTTTCA
1 TCAATTTTCA
69677 TCAATTTTCA
1 TCAATTTTCA
69687 TCAAT
1 TCAAT
69692 CATTGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (10 bp):
TCAATTTTCA
Found at i:71109 original size:16 final size:16
Alignment explanation
Indices: 71088--71120 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
71078 TAATAAATAA
71088 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
71104 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
71120 A
1 A
71121 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:71564 original size:14 final size:14
Alignment explanation
Indices: 71545--71572 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
71535 GAACATAAAT
71545 GAACATAAATGAAC
1 GAACATAAATGAAC
71559 GAACATAAATGAAC
1 GAACATAAATGAAC
71573 ATATAAGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:75432 original size:20 final size:21
Alignment explanation
Indices: 75402--75441 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
75392 TAGCCATTGG
*
75402 GCCTGATGGTATTGATACTAA
1 GCCTGATGGTATCGATACTAA
75423 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
75442 CTATATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAA
Found at i:76062 original size:20 final size:20
Alignment explanation
Indices: 76039--76106 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
76029 TATGTCAGTA
*
76039 GTATTGATACTGACCATTGG
1 GTATCGATACTGACCATTGG
76059 GTATCGATACTGACCATTGG
1 GTATCGATACTGACCATTGG
* *
76079 GTATCGATACTCACCA--GA
1 GTATCGATACTGACCATTGG
76097 GTATCGATAC
1 GTATCGATAC
76107 CTAAAATAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 11 0.24
20 34 0.76
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (20 bp):
GTATCGATACTGACCATTGG
Found at i:76182 original size:18 final size:19
Alignment explanation
Indices: 76139--76183 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
76129 AAAATGGCTC
*
76139 AGTATCGATACTTCTATGGGG
1 AGTATCGATACTCCTAT--GG
76160 AGTATCGATACTCCTAT-G
1 AGTATCGATACTCCTATGG
76178 AGTATC
1 AGTATC
76184 AGTTCCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
21 16 0.70
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (19 bp):
AGTATCGATACTCCTATGG
Done.