Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003362.1 Hibiscus syriacus cultivar Beakdansim tig00007073_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: 66716
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5378 original size:19 final size:19
Alignment explanation
Indices: 5354--5397 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
5344 AAGGAGACAT
5354 TCCAACATAGTAATGGAAG
1 TCCAACATAGTAATGGAAG
5373 TCCAACATAGTAATGGAAG
1 TCCAACATAGTAATGGAAG
5392 TCCAAC
1 TCCAAC
5398 TAAGTCAACC
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:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
TCCAACATAGTAATGGAAG
Found at i:12631 original size:2 final size:2
Alignment explanation
Indices: 12626--12650 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12616 ATACATATAT
12626 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
12651 TAGTTCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15395 original size:22 final size:22
Alignment explanation
Indices: 15365--15409 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
15355 GGTTATAACT
15365 GTAAAGCATGGTAGTACATTTG
1 GTAAAGCATGGTAGTACATTTG
*
15387 GTAAGGCATGGTAGTACATTTG
1 GTAAAGCATGGTAGTACATTTG
15409 G
1 G
15410 ATGACATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (22 bp):
GTAAAGCATGGTAGTACATTTG
Found at i:17131 original size:18 final size:19
Alignment explanation
Indices: 17108--17143 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17098 TTCGGTTTGC
*
17108 AAAAAAATCGG-TTTTTTA
1 AAAAAAACCGGATTTTTTA
17126 AAAAAAACCGGATTTTTT
1 AAAAAAACCGGATTTTTT
17144 CGGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (19 bp):
AAAAAAACCGGATTTTTTA
Found at i:17595 original size:2 final size:2
Alignment explanation
Indices: 17588--17617 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17578 AAGGAACTTA
17588 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
17618 TGTCGGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18835 original size:199 final size:200
Alignment explanation
Indices: 18192--19087 Score: 801
Period size: 199 Copynumber: 4.5 Consensus size: 200
18182 AAAGTTTTTA
* * * * * *
18192 TAATTTATAGGATTAGAGGTGTACTATT-GGACTTTATCTTTCAGTTGAGG-TCAATATCGACAC
1 TAATTTATAAGATTAGAGGCGTAGTATTAGTAC-TTATCTTTCAATTGAGGCT-AATATCGGCAC
* * ** ** * * * **
18255 GTACAAGTTATTGCAAGTGG-GTAAAAATCACGTTGAAAAT-GATTTCAAAGCAT-ACTTTGTGC
64 ATACGAGACATTATAAGCGGTGTAAAAATCACGTTGAAAATAG-TTCCAAA-CTTGGTTTTGTGC
* * * *
18317 ATGAAGAAAAAGCTAAAATGGTTTGATAGGCATATTCGAGG-GTATTTT-TGGATAGTTAATATG
127 ATGAAGAAAAAACTAAAATGGCTTGATAGGCATATTCGAGGAGTATTTTCAGGA-AGTTAATATA
*
18380 AAAATATTCG
191 AAAATTTTCG
* * * * *
18390 TAATTTATAAGATTAGATGCATAGTATT-GTAACTTATCTTT-AAGCTGATGCTAATATCGGCGC
1 TAATTTATAAGATTAGAGGCGTAGTATTAGT-ACTTATCTTTCAA-TTGAGGCTAATATCGGCAC
* * * *
18453 ATACGAGACATTATAAGC-GTGTTAAAAGTCCCGTTGAAAATGGTTCCAAAGCTTGGTTTTATGC
64 ATACGAGACATTATAAGCGGTG-TAAAAATCACGTTGAAAATAGTTCCAAA-CTTGGTTTTGTGC
* * * * * * *
18517 ATAAAGAAGAAACTAAAATGGCTTGATAGGCATATTCAATGAGCATATTCAGGAAGTTAAGATAA
127 ATGAAGAAAAAACTAAAATGGCTTGATAGGCATATTCGAGGAGTATTTTCAGGAAGTTAATATAA
* *
18582 CAATTATCG
192 AAATTTTCG
* *
18591 TAATTTATAAGATTAGAGACGTAGTATTAGTACTTATGC-TTCAATTGAGGCTAGTATCGGCACA
1 TAATTTATAAGATTAGAGGCGTAGTATTAGTACTTAT-CTTTCAATTGAGGCTAATATCGGCACA
* * *** *
18655 TACGAGAAATTGTAAGCGGTGTAAAAATTGTGTTGAAAA-ATGTTTCAAACTT-GTTTTGTGCAT
65 TACGAGACATTATAAGCGGTGTAAAAATCACGTTGAAAATA-GTTCCAAACTTGGTTTTGTGCAT
* * ** *
18718 GAAGAAAAAAACTAAAATGGTTTGATAGGCATATTCGA-GAGTTTTTTTGGGTAGTTAATATAAA
129 GAAG-AAAAAACTAAAATGGCTTGATAGGCATATTCGAGGAGTATTTTCAGGAAGTTAATATAAA
18782 AATTTTCG
193 AATTTTCG
* *
18790 TAATTTATAAGATTAGAGGCCTAGTATT-GTAACTTATCTTTCAATTGAAGCTAATATCGGCACA
1 TAATTTATAAGATTAGAGGCGTAGTATTAGT-ACTTATCTTTCAATTGAGGCTAATATCGGCACA
* *
18854 T--GAGACATTATAAGCGGGGTAAAAATCACGTTGAAAATAGTTCCAAAACTTGGTTTTGTGCGT
65 TACGAGACATTATAAGCGGTGTAAAAATCACGTTGAAAATAGTTCC-AAACTTGGTTTTGTGCAT
* * * * *
18917 GATG---AAGCT-AAATGGCTTGATAAGCATGTTCGAGGAGTATTTTCAGGAAGTTAATATGAAA
129 GAAGAAAAAACTAAAATGGCTTGATAGGCATATTCGAGGAGTATTTTCAGGAAGTTAATATAAAA
18978 ATTTT-G
194 ATTTTCG
* * * * * * * * * * *
18984 TAATTGACAAGATTAGATGTGTTGTATTGGTACTTATGTTTCAATTGAGGCTAGTATTGACAGAT
1 TAATTTATAAGATTAGAGGCGTAGTATTAGTACTTATCTTTCAATTGAGGCTAATATCGGCACAT
* * *** *
19049 ACAAGACATTGTAAGCAACGTAAAAATCATGTTGAAAAT
66 ACGAGACATTATAAGCGGTGTAAAAATCACGTTGAAAAT
19088 GATTTGAAAC
Statistics
Matches: 566, Mismatches: 108, Indels: 50
0.78 0.15 0.07
Matches are distributed among these distances:
194 72 0.13
195 33 0.06
196 31 0.05
197 36 0.06
198 67 0.12
199 136 0.24
200 75 0.13
201 105 0.19
202 11 0.02
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (200 bp):
TAATTTATAAGATTAGAGGCGTAGTATTAGTACTTATCTTTCAATTGAGGCTAATATCGGCACAT
ACGAGACATTATAAGCGGTGTAAAAATCACGTTGAAAATAGTTCCAAACTTGGTTTTGTGCATGA
AGAAAAAACTAAAATGGCTTGATAGGCATATTCGAGGAGTATTTTCAGGAAGTTAATATAAAAAT
TTTCG
Found at i:21874 original size:21 final size:21
Alignment explanation
Indices: 21848--21891 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21838 AGCATCTACG
21848 ACCATCTAGAGAAAAGAACAA
1 ACCATCTAGAGAAAAGAACAA
21869 ACCATCTAGAGAAAAGAACAA
1 ACCATCTAGAGAAAAGAACAA
21890 AC
1 AC
21892 ATTGGATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.20, G:0.14, T:0.09
Consensus pattern (21 bp):
ACCATCTAGAGAAAAGAACAA
Found at i:22395 original size:15 final size:15
Alignment explanation
Indices: 22354--22396 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
22344 CTGAAAAGAC
* *
22354 AATAACATAAAATAT
1 AATAACATAAATTAA
*
22369 AATACCATAAATTAA
1 AATAACATAAATTAA
22384 AATAACATAAATT
1 AATAACATAAATT
22397 TCAATATCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAACATAAATTAA
Found at i:24244 original size:26 final size:27
Alignment explanation
Indices: 24206--24261 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
24196 ATGAACTCGG
* * *
24206 TTATTCGATATAAATAAGTAATA-TTT
1 TTATTCAAAATAAATAAATAATAGTTT
24232 TTATTCAAAATAAATAAATAATAGTTT
1 TTATTCAAAATAAATAAATAATAGTTT
24259 TTA
1 TTA
24262 ATTTTGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (27 bp):
TTATTCAAAATAAATAAATAATAGTTT
Found at i:25060 original size:34 final size:33
Alignment explanation
Indices: 25017--25122 Score: 140
Period size: 34 Copynumber: 3.1 Consensus size: 33
25007 GGGGAGCCAC
* * *
25017 ATATATTTCTTGTGGTTGCTCTTATTCAGTCAGT
1 ATATGTTTCTTGTGCTCGCTCTTATTC-GTCAGT
* *
25051 ATATGTTTCTTGTGCTCGCTGTTATTTGGTCAGT
1 ATATGTTTCTTGTGCTCGCTCTTA-TTCGTCAGT
25085 ATATGTTTCTTGTGCTCGCTCTTATTCGATCAGT
1 ATATGTTTCTTGTGCTCGCTCTTATTCG-TCAGT
25119 ATAT
1 ATAT
25123 ATGCTTCATA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
33 3 0.05
34 58 0.92
35 2 0.03
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (33 bp):
ATATGTTTCTTGTGCTCGCTCTTATTCGTCAGT
Found at i:26757 original size:14 final size:14
Alignment explanation
Indices: 26738--26766 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26728 AAGTTTAGCT
26738 ATTAAAATGGACTA
1 ATTAAAATGGACTA
26752 ATTAAAATGGACTA
1 ATTAAAATGGACTA
26766 A
1 A
26767 AACTGGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATTAAAATGGACTA
Found at i:29167 original size:199 final size:199
Alignment explanation
Indices: 28840--29224 Score: 673
Period size: 199 Copynumber: 1.9 Consensus size: 199
28830 GCCGAATGAC
* * *
28840 AGTGGCGCGCGAGAAGCTCCCTTGTTTTCTATCACTCAACAAGGGAATAGAGAATGTAAACATTA
1 AGTGGCGCGCGAGAAGCTCCCTTATTTTCTATCACTCAACAAGAGAATAGAAAATGTAAACATTA
28905 AATATCCAATCACAATGTATTTCCCACTCAACGTGGGATTGAGCATTACCAATAAAAGAGAGCAC
66 AATATCCAATCACAATGTATTTCCCACTCAACGTGGGATTGAGCATTACCAATAAAAGAGAGCAC
28970 CAACATCAAGATCCTGATCCACATGAGGAAAGTGCTTCTGCGGAAGAGGATCATCTCGAGCCGAA
131 CAACATCAAGATCCTGATCCACATGAGGAAAGTGCTTCTGCGGAAGAGGATCATCTCGAGCCGAA
29035 CGGT
196 CGGT
* *
29039 AGTGGCGCGCGAGAAG-TCCCCTTATTTTCTATCACTCAACAAGAGAGTAGAAAATGTGAACATT
1 AGTGGCGCGCGAGAAGCT-CCCTTATTTTCTATCACTCAACAAGAGAATAGAAAATGTAAACATT
*
29103 AAATATTCAATCACAATGTATTTCCCACTCAACGTGGGATTGAGCATTACCAATAAAAGAGAGCA
65 AAATATCCAATCACAATGTATTTCCCACTCAACGTGGGATTGAGCATTACCAATAAAAGAGAGCA
* * *
29168 CCAGCATCAAGATCCTGATGCACATGAGGAAAGTGCTTCTGGGGAAGAGGATCATCT
130 CCAACATCAAGATCCTGATCCACATGAGGAAAGTGCTTCTGCGGAAGAGGATCATCT
29225 TCTCCACCTA
Statistics
Matches: 176, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
198 1 0.01
199 175 0.99
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (199 bp):
AGTGGCGCGCGAGAAGCTCCCTTATTTTCTATCACTCAACAAGAGAATAGAAAATGTAAACATTA
AATATCCAATCACAATGTATTTCCCACTCAACGTGGGATTGAGCATTACCAATAAAAGAGAGCAC
CAACATCAAGATCCTGATCCACATGAGGAAAGTGCTTCTGCGGAAGAGGATCATCTCGAGCCGAA
CGGT
Found at i:31534 original size:31 final size:31
Alignment explanation
Indices: 31498--31599 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 31
31488 TTTAAAAATC
* *
31498 ATACCTAATATTTATTTTTTGTTTCATTTTA
1 ATACCTAATATTAACTTTTTGTTTCATTTTA
* * *
31529 ATACCTGATGTTAACTTTTTGCTTCATTTTA
1 ATACCTAATATTAACTTTTTGTTTCATTTTA
** *
31560 ATACCTCACCATTAACTTTTTGTTTGATTTTA
1 ATACCT-AATATTAACTTTTTGTTTCATTTTA
*
31592 GTACCTAA
1 ATACCTAA
31600 ATTTTTAGCG
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 33 0.58
32 24 0.42
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (31 bp):
ATACCTAATATTAACTTTTTGTTTCATTTTA
Found at i:31575 original size:32 final size:31
Alignment explanation
Indices: 31513--31597 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 31
31503 TAATATTTAT
* **
31513 TTTTTGTTTCATTTTAATACCTGATGTTAAC
1 TTTTTGTTTCATTTTAATACCTCACATTAAC
*
31544 TTTTTGCTTCATTTTAATACCTCACCATTAAC
1 TTTTTGTTTCATTTTAATACCTCA-CATTAAC
* *
31576 TTTTTGTTTGATTTTAGTACCT
1 TTTTTGTTTCATTTTAATACCT
31598 AAATTTTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 22 0.48
32 24 0.52
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.54
Consensus pattern (31 bp):
TTTTTGTTTCATTTTAATACCTCACATTAAC
Found at i:32017 original size:3 final size:3
Alignment explanation
Indices: 32009--32034 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31999 CAACTTACAC
32009 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
32035 TAATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:33306 original size:30 final size:29
Alignment explanation
Indices: 33267--33330 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
33257 ATTTTTCCCT
* *
33267 CCTAAAA-TTTATAAGTTCAAGTTCGTCTCC
1 CCTAAAATTTTAAAAATTCAAGTTCG-C-CC
*
33297 CCTAGAATTTTAAAAATTCAAGTTCGCCC
1 CCTAAAATTTTAAAAATTCAAGTTCGCCC
33326 CCTAA
1 CCTAA
33331 CATAAAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 6 0.21
30 7 0.24
31 16 0.55
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (29 bp):
CCTAAAATTTTAAAAATTCAAGTTCGCCC
Found at i:34289 original size:37 final size:37
Alignment explanation
Indices: 34213--34289 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
34203 TTTTTTATAT
*
34213 TTTAATTTTGTAAAAACAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAACAATTATATAAATATTATCAA
* *
34250 TTTAATTTTTTAAAGAA-AA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AACAATTATATAAATATTAT-CAA
34287 TTT
1 TTT
34290 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAACAATTATATAAATATTATCAA
Found at i:34951 original size:11 final size:11
Alignment explanation
Indices: 34937--34962 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34927 TATATAAATT
34937 AATTATAGTAG
1 AATTATAGTAG
34948 AATTATAGTAG
1 AATTATAGTAG
34959 AATT
1 AATT
34963 CAACTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (11 bp):
AATTATAGTAG
Found at i:39085 original size:13 final size:12
Alignment explanation
Indices: 39063--39097 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
39053 TTATCACAAT
39063 AATAATAAAATA
1 AATAATAAAATA
*
39075 CATATATAAAATA
1 AATA-ATAAAATA
39088 AATAATAAAA
1 AATAATAAAA
39098 ATACCATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:44625 original size:23 final size:23
Alignment explanation
Indices: 44571--44626 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
44561 ATTTTATATA
* **
44571 AAATTTT-AAAAAATAAAATTAT
1 AAATTTTAAAAAAAGAAAAACAT
* *
44593 ATATTATAAAAAAAGAAAAACAT
1 AAATTTTAAAAAAAGAAAAACAT
44616 AAATTTTAAAA
1 AAATTTTAAAA
44627 TAACCCCTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATTTTAAAAAAAGAAAAACAT
Found at i:50231 original size:15 final size:15
Alignment explanation
Indices: 50211--50245 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
50201 TAAAAAAGCG
*
50211 TTGCTTTTGGACAGT
1 TTGCTTTTGGACAAT
50226 TTGC-TTTGGACAAT
1 TTGCTTTTGGACAAT
50240 TTGCTT
1 TTGCTT
50246 GTAATTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (15 bp):
TTGCTTTTGGACAAT
Found at i:53377 original size:17 final size:18
Alignment explanation
Indices: 53343--53383 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
53333 ATTAAATCCC
*
53343 TATTTAATAAAATAATA-
1 TATTTTATAAAATAATAT
53360 TATTTTATATAAAT-ATAT
1 TATTTTATA-AAATAATAT
53378 TATTTT
1 TATTTT
53384 GGGTTGGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTATAAAATAATAT
Found at i:56121 original size:22 final size:22
Alignment explanation
Indices: 56096--56154 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
56086 AATTCAACCG
56096 TTTGTAACTCATGCAATAAAGC
1 TTTGTAACTCATGCAATAAAGC
* * *
56118 TTTGTAAAT-ATTGTATTAAAGC
1 TTTGTAACTCA-TGCAATAAAGC
*
56140 TTTGTAACTCTTGCA
1 TTTGTAACTCATGCA
56155 TTCATTTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (22 bp):
TTTGTAACTCATGCAATAAAGC
Found at i:62917 original size:23 final size:23
Alignment explanation
Indices: 62887--62938 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
62877 CTATTCTCAA
*
62887 TGTCAATCAGATCACATCTTGTT
1 TGTCAATCAGATCACACCTTGTT
62910 TGTCAATCAGATCACACCTTGTT
1 TGTCAATCAGATCACACCTTGTT
62933 TGTCAA
1 TGTCAA
62939 ACACTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (23 bp):
TGTCAATCAGATCACACCTTGTT
Done.