Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005705.1 Hibiscus syriacus cultivar Beakdansim tig00013340_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: 75003
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:5301 original size:4 final size:4
Alignment explanation
Indices: 5292--5374 Score: 58
Period size: 4 Copynumber: 20.0 Consensus size: 4
5282 TACACCTCTT
** * * * ** *
5292 TAAA TAAA TAAA TAAA TTATT TGAAA TATA TAAA TTAA TGAA TATG GAAA
1 TAAA TAAA TAAA TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA
*
5342 TAAA TAAA TAAT TAAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA
5375 ATTACCTTCA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
4 52 0.88
5 7 0.12
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:5361 original size:17 final size:17
Alignment explanation
Indices: 5339--5376 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5329 ATGAATATGG
*
5339 AAATAAATAAATAATTA
1 AAATAAATAAATAAATA
5356 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
5373 AAAT
1 AAAT
5377 TACCTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAATAAATAAATA
Found at i:6120 original size:111 final size:109
Alignment explanation
Indices: 5928--6147 Score: 359
Period size: 111 Copynumber: 2.0 Consensus size: 109
5918 CGCGAAAATA
*
5928 AAACTTGAAATGTGATAATATATATATATTAGGTTAGACAAATTTAAACTACATCATTCTTTATA
1 AAACTTGAAATGTGATAATATATATATATTAGGTTAGACAAATTTAAACTACAGCATTCTTTATA
5993 ATATTTTCGATTACAGCTTAAAATATTACCTTCTTCATATTATT
66 ATATTTTCGATTACAGCTTAAAATATTACCTTCTTCATATTATT
*
6037 AAACTTGAAATGTGATAATATATATATATAATAGGTTAGACAAATTTAAACTATAGCATTCTTTA
1 AAACTTGAAATGTGATAATATATATATAT--TAGGTTAGACAAATTTAAACTACAGCATTCTTTA
** * **
6102 TAATATTTTTTATTACAGCTTAAAATATTATCTTCTTTTTATTATT
64 TAATATTTTCGATTACAGCTTAAAATATTACCTTCTTCATATTATT
6148 TTCGGTTGTT
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
109 29 0.28
111 73 0.72
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (109 bp):
AAACTTGAAATGTGATAATATATATATATTAGGTTAGACAAATTTAAACTACAGCATTCTTTATA
ATATTTTCGATTACAGCTTAAAATATTACCTTCTTCATATTATT
Found at i:6254 original size:25 final size:25
Alignment explanation
Indices: 6226--6304 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
6216 TCAAATTTTC
6226 AATTGCGTCCAACTTAAAATATTAT
1 AATTGCGTCCAACTTAAAATATTAT
*** * ** *
6251 AATTTTATAACATTTTCAAAT-TT-T
1 AATTGCGT-CCAACTTAAAATATTAT
6275 CAATTGCGTCCAACTTAAAATATTAT
1 -AATTGCGTCCAACTTAAAATATTAT
6301 AATT
1 AATT
6305 TTATAACATT
Statistics
Matches: 36, Mismatches: 14, Indels: 8
0.62 0.24 0.14
Matches are distributed among these distances:
24 9 0.25
25 18 0.50
26 9 0.25
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (25 bp):
AATTGCGTCCAACTTAAAATATTAT
Found at i:6291 original size:50 final size:50
Alignment explanation
Indices: 6216--6317 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
6206 ACGAAGAATG
6216 TCAAATTTTCAATTGCGTCCAACTTAAAATATTATAATTTTATAACATTT
1 TCAAATTTTCAATTGCGTCCAACTTAAAATATTATAATTTTATAACATTT
6266 TCAAATTTTCAATTGCGTCCAACTTAAAATATTATAATTTTATAACATTT
1 TCAAATTTTCAATTGCGTCCAACTTAAAATATTATAATTTTATAACATTT
6316 TC
1 TC
6318 GATCGCGCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (50 bp):
TCAAATTTTCAATTGCGTCCAACTTAAAATATTATAATTTTATAACATTT
Found at i:8603 original size:31 final size:31
Alignment explanation
Indices: 8536--8609 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
8526 TAAAACTTGT
* * * *
8536 AATATAATTCCTCAATATTTAGTCTGTTTAC
1 AATATGATCCCTCAACATTTAGTCCGTTTAC
*
8567 AATATGATCCCTCAACATTTAGTCCGTTTGC
1 AATATGATCCCTCAACATTTAGTCCGTTTAC
*
8598 AATATGGTCCCT
1 AATATGATCCCT
8610 GACGTAACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (31 bp):
AATATGATCCCTCAACATTTAGTCCGTTTAC
Found at i:10285 original size:31 final size:31
Alignment explanation
Indices: 10214--10291 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
10204 CTTTTAAAAC
**
10214 TTGCAATATAATCCCCCAACATTTAGTCTAT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
*
10245 TTGCAATATGGTCCCTCAACATTTAGTCTAT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
10276 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
10292 GATGTAACTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCTAT
Found at i:11022 original size:10 final size:10
Alignment explanation
Indices: 10983--11022 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
10973 TTCATCACAC
10983 CAAATTCTCT
1 CAAATTCTCT
*
10993 CAATTTCTCT
1 CAAATTCTCT
*
11003 CAACTTCTCT
1 CAAATTCTCT
*
11013 CAAATACTCT
1 CAAATTCTCT
11023 TATAATATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:11080 original size:9 final size:9
Alignment explanation
Indices: 11068--11101 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
11058 TAATATTTTG
11068 TATTTAATT
1 TATTTAATT
*
11077 TATTTAA-G
1 TATTTAATT
11085 TATTTAATT
1 TATTTAATT
11094 TATTTAAT
1 TATTTAAT
11102 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:11107 original size:17 final size:17
Alignment explanation
Indices: 11067--11105 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
11057 TTAATATTTT
11067 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
11084 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
11101 -TATTT
1 GTATTT
11106 TACTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:11112 original size:16 final size:17
Alignment explanation
Indices: 11067--11113 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
11057 TTAATATTTT
*
11067 GTATTTAATTTATTTAA
1 GTATTTAACTTATTTAA
*
11084 GTATTTAATTTATTTAA
1 GTATTTAACTTATTTAA
*
11101 -TATTTTACTTATT
1 GTATTTAACTTATT
11114 AATTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (17 bp):
GTATTTAACTTATTTAA
Found at i:13459 original size:35 final size:33
Alignment explanation
Indices: 13419--13503 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
13409 GTATTTCAGT
*
13419 TAATTTTGTT-TATTATCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
13454 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
13489 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
13504 TAAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 2 0.05
38 12 0.29
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:17753 original size:3 final size:3
Alignment explanation
Indices: 17745--17792 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
17735 ATAAACATCT
17745 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17793 TAAGTCCAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28525 original size:10 final size:11
Alignment explanation
Indices: 28510--28561 Score: 63
Period size: 10 Copynumber: 4.9 Consensus size: 11
28500 CTGGTTCACT
28510 GGTTCAATCG-
1 GGTTCAATCGC
*
28520 GGTTCAACCGC
1 GGTTCAATCGC
28531 GGTTCAATCG-
1 GGTTCAATCGC
*
28541 GGTTCAACCGC
1 GGTTCAATCGC
*
28552 GGTTGAATCG
1 GGTTCAATCG
28562 AATTTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (11 bp):
GGTTCAATCGC
Found at i:28536 original size:21 final size:21
Alignment explanation
Indices: 28510--28561 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
28500 CTGGTTCACT
28510 GGTTCAATCGGGTTCAACCGC
1 GGTTCAATCGGGTTCAACCGC
28531 GGTTCAATCGGGTTCAACCGC
1 GGTTCAATCGGGTTCAACCGC
*
28552 GGTTGAATCG
1 GGTTCAATCG
28562 AATTTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (21 bp):
GGTTCAATCGGGTTCAACCGC
Found at i:32793 original size:571 final size:571
Alignment explanation
Indices: 31711--32852 Score: 2266
Period size: 571 Copynumber: 2.0 Consensus size: 571
31701 AAAATAATAA
31711 GACAGAAATATGATTAATAATGGGTTTAAGAAATGAATAATAATATAAGTAATGGAATGAAAGAA
1 GACAGAAATATGATTAATAATGGGTTTAAGAAATGAATAATAATATAAGTAATGGAATGAAAGAA
31776 TAAGAATAGAGATGGCTGCGGAATTGATGGATTGATGGGTGTTGTTGATGATGGAAATGACGAAA
66 TAAGAATAGAGATGGCTGCGGAATTGATGGATTGATGGGTGTTGTTGATGATGGAAATGACGAAA
31841 TGGAGATGGTGGTGATAGTATCCCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
131 TGGAGATGGTGGTGATAGTATCCCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
31906 GGTCTTTACAAACTTGCTTGAGGGGTGGTGATCGTGTCTTCAACCCACTAGATAACAATCTAGGA
196 GGTCTTTACAAACTTGCTTGAGGGGTGGTGATCGTGTCTTCAACCCACTAGATAACAATCTAGGA
*
31971 ATTTAGGAATCAAAATGGAAGGAATGACGCCACAAGTATAGGAACTACACTTGTTTAATCGATAA
261 ATTTAGGAATCAAAATGGAAGGAATGACGCCACAAGTATAGGAACTACACTTGTTTAATCAATAA
32036 AGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTAATTTTATATATGAGATGAGATGAC
326 AGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTAATTTTATATATGAGATGAGATGAC
32101 TACAAATGATGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATGATTACAAGTT
391 TACAAATGATGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATGATTACAAGTT
32166 GTTTCGGCTAGATACATGTCTCTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTG
456 GTTTCGGCTAGATACATGTCTCTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTG
32231 GGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCT
521 GGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCT
32282 GACAGAAATATGATTAATAATGGGTTTAAGAAATGAATAATAATATAAGTAATGGAATGAAAGAA
1 GACAGAAATATGATTAATAATGGGTTTAAGAAATGAATAATAATATAAGTAATGGAATGAAAGAA
32347 TAAGAATAGAGATGGCTGCGGAATTGATGGATTGATGGGTGTTGTTGATGATGGAAATGACGAAA
66 TAAGAATAGAGATGGCTGCGGAATTGATGGATTGATGGGTGTTGTTGATGATGGAAATGACGAAA
*
32412 TGGAGATGGTGGTGATAGTATCCCAAACACGCCAAAGAGGAGACTATGCTATGAAGCACAATCCC
131 TGGAGATGGTGGTGATAGTATCCCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
32477 GGTCTTTACAAACTTGCTTGAGGGGTGGTGATCGTGTCTTCAACCCACTAGATAACAATCTAGGA
196 GGTCTTTACAAACTTGCTTGAGGGGTGGTGATCGTGTCTTCAACCCACTAGATAACAATCTAGGA
32542 ATTTAGGAATCAAAATGGAAGGAATGACGCCACAAGTATAGGAACTACACTTGTTTAATCAATAA
261 ATTTAGGAATCAAAATGGAAGGAATGACGCCACAAGTATAGGAACTACACTTGTTTAATCAATAA
32607 AGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTAATTTTATATATGAGATGAGATGAC
326 AGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTAATTTTATATATGAGATGAGATGAC
32672 TACAAATGATGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATGATTACAAGTT
391 TACAAATGATGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATGATTACAAGTT
32737 GTTTCGGCTAGATACATGTCTCTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTG
456 GTTTCGGCTAGATACATGTCTCTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTG
32802 GGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCT
521 GGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCT
32853 AAGGATGGGA
Statistics
Matches: 569, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
571 569 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (571 bp):
GACAGAAATATGATTAATAATGGGTTTAAGAAATGAATAATAATATAAGTAATGGAATGAAAGAA
TAAGAATAGAGATGGCTGCGGAATTGATGGATTGATGGGTGTTGTTGATGATGGAAATGACGAAA
TGGAGATGGTGGTGATAGTATCCCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
GGTCTTTACAAACTTGCTTGAGGGGTGGTGATCGTGTCTTCAACCCACTAGATAACAATCTAGGA
ATTTAGGAATCAAAATGGAAGGAATGACGCCACAAGTATAGGAACTACACTTGTTTAATCAATAA
AGTTCACAAAGAACTTTGAAGAGAAATAACTCACAAGAGTAATTTTATATATGAGATGAGATGAC
TACAAATGATGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATGATTACAAGTT
GTTTCGGCTAGATACATGTCTCTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTG
GGCTTGTGATGGTTCGGCTAACTCTTCATGAAAGGCCTTAATGATTCGGCT
Found at i:33128 original size:163 final size:163
Alignment explanation
Indices: 32858--33184 Score: 654
Period size: 163 Copynumber: 2.0 Consensus size: 163
32848 CGGCTAAGGA
32858 TGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCTCCCTTTG
1 TGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCTCCCTTTG
32923 GCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAGGCTCTCATGTGTATGGCATGTGATGT
66 GCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAGGCTCTCATGTGTATGGCATGTGATGT
32988 GGCCGAATAGGCATGGAGCCTCTAGCTCATGTT
131 GGCCGAATAGGCATGGAGCCTCTAGCTCATGTT
33021 TGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCTCCCTTTG
1 TGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCTCCCTTTG
33086 GCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAGGCTCTCATGTGTATGGCATGTGATGT
66 GCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAGGCTCTCATGTGTATGGCATGTGATGT
33151 GGCCGAATAGGCATGGAGCCTCTAGCTCATGTT
131 GGCCGAATAGGCATGGAGCCTCTAGCTCATGTT
33184 T
1 T
33185 CTTGATGATT
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.33
Consensus pattern (163 bp):
TGGGAAGACATCTCCCTTGGCCGAATATGTATGTTGGTTCATCTTGGCGCCATTTTCTCCCTTTG
GCCGAATGGTGGTGTGTCTCTTCATGCTTGGCGCCAAAGGCTCTCATGTGTATGGCATGTGATGT
GGCCGAATAGGCATGGAGCCTCTAGCTCATGTT
Found at i:34536 original size:30 final size:30
Alignment explanation
Indices: 34501--34566 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
34491 AGTGAACCGG
*
34501 CGGTTCAAACCGGTTTTACCGGTTTTCAAC
1 CGGTTCAAACCGGTTTTACCAGTTTTCAAC
** * *
34531 CGGTTCACCCCGGTTTTACTAGTTTTCATC
1 CGGTTCAAACCGGTTTTACCAGTTTTCAAC
34561 CGGTTC
1 CGGTTC
34567 TACCGATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.15, C:0.29, G:0.20, T:0.36
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTACCAGTTTTCAAC
Found at i:42901 original size:2 final size:2
Alignment explanation
Indices: 42894--42932 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
42884 TCACTGTTCT
42894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42933 ACATTCCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:45486 original size:27 final size:24
Alignment explanation
Indices: 45466--45511 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
45456 TAATGAGAAT
45466 TCTAAAAAAAATACCCTTAATAAA
1 TCTAAAAAAAATACCCTTAATAAA
**
45490 TCTTGAAAAAATACCCTTAATA
1 TCTAAAAAAAATACCCTTAATA
45512 CTTTAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.28
Consensus pattern (24 bp):
TCTAAAAAAAATACCCTTAATAAA
Found at i:74472 original size:21 final size:21
Alignment explanation
Indices: 74447--74520 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
74437 TTTGGAATTA
74447 GCGTCGCGAATCTGGGTGATC
1 GCGTCGCGAATCTGGGTGATC
74468 GCGTCGCGAATCTGGGTGATC
1 GCGTCGCGAATCTGGGTGATC
** * *
74489 GTATCGCGAATATGGGTGAAC
1 GCGTCGCGAATCTGGGTGATC
*
74510 GCGTCACGAAT
1 GCGTCGCGAAT
74521 TCGAGTTCGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.23
Consensus pattern (21 bp):
GCGTCGCGAATCTGGGTGATC
Found at i:74580 original size:21 final size:21
Alignment explanation
Indices: 74556--74623 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
74546 ATCACGTCGT
74556 GAATTTAGAGAATCGCGTTGC
1 GAATTTAGAGAATCGCGTTGC
74577 GAATTTAGAGAATCGCGTTGC
1 GAATTTAGAGAATCGCGTTGC
* * * *
74598 GAAATTGGAG-TTTGCGTTGC
1 GAATTTAGAGAATCGCGTTGC
74618 GAATTT
1 GAATTT
74624 GTTGGTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 13 0.31
21 29 0.69
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (21 bp):
GAATTTAGAGAATCGCGTTGC
Done.