Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004949.1 Hibiscus syriacus cultivar Beakdansim tig00011124_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: 55437
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3305 original size:19 final size:19
Alignment explanation
Indices: 3276--3340 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
3266 TTTGACCAGT
3276 TTTGAACCGGT-TCGAACCGG
1 TTTG-ACCGGTCT-GAACCGG
* *
3296 TTTGACCGGTCTAAATCGG
1 TTTGACCGGTCTGAACCGG
3315 TTTGACCGGTCTGAACCGG
1 TTTGACCGGTCTGAACCGG
*
3334 GTTGACC
1 TTTGACC
3341 CGACCCGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 34 0.87
20 5 0.13
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.28
Consensus pattern (19 bp):
TTTGACCGGTCTGAACCGG
Found at i:3356 original size:17 final size:18
Alignment explanation
Indices: 3334--3375 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3324 TCTGAACCGG
*
3334 GTTGACCCGAC-CCGACT
1 GTTGACCCGACTCCGACC
*
3351 GTTGACCCGACTTCGACC
1 GTTGACCCGACTCCGACC
3369 GTTGACC
1 GTTGACC
3376 GTTGACTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.17, C:0.38, G:0.24, T:0.21
Consensus pattern (18 bp):
GTTGACCCGACTCCGACC
Found at i:6107 original size:3 final size:3
Alignment explanation
Indices: 6099--6156 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
6089 TGACATTATC
** * *
6099 AAT AAT AAT AAT AAT AAT AAT AAT ACC AAT AAA AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6147 AAT AAT AAT A
1 AAT AAT AAT A
6157 CGAGTTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:11071 original size:36 final size:34
Alignment explanation
Indices: 10997--11078 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 34
10987 GTTATCGTCG
* **
10997 TATATATTTCTAATTTTTTCTTTTATTTTTTTATAT
1 TATATA-TT-TAATTTTTTCTTTTAGTTTTCAATAT
*
11033 TATATATTTAATTTTCTTTTTTTAGTTTTCAATAAT
1 TATATATTTAATTTT-TTCTTTTAGTTTTCAAT-AT
11069 TATATATTTA
1 TATATATTTA
11079 TGACATGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 7 0.17
35 15 0.38
36 18 0.45
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (34 bp):
TATATATTTAATTTTTTCTTTTAGTTTTCAATAT
Found at i:11107 original size:23 final size:22
Alignment explanation
Indices: 11075--11136 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
11065 TAATTATATA
11075 TTTATGACATGTTTTCTTCTATC
1 TTTATGACATGTTTTCTT-TATC
*
11098 TTTATAACATGTTTTTCTTTATC
1 TTTATGACATG-TTTTCTTTATC
* *
11121 GTTATGACACGTTTTC
1 TTTATGACATGTTTTC
11137 AGCCATTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.15
23 22 0.65
24 7 0.21
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTATGACATGTTTTCTTTATC
Found at i:11286 original size:105 final size:105
Alignment explanation
Indices: 11097--11291 Score: 275
Period size: 105 Copynumber: 1.9 Consensus size: 105
11087 TTTCTTCTAT
* * * *
11097 CTTTATAACATGTTTTTCTTTATCGTTATGACACGTTTTCAGCCATTTGGTCGTTGTTTTGTTTA
1 CTTTATAACATATTTTTCTTTATCATTATGACACGTTTACAGCCAGTTGGTCGTTGTTTTGTTTA
* *
11162 TTTTTTTTCTTAGGATTAGATTTGATATATTTTTTTATAC
66 TTCTTTTTCTCAGGATTAGATTTGATATATTTTTTTATAC
* * * *
11202 CTTTATGACATATTTTTCTTTATCATTATGGCACGTTTACCGCCAGTTGGTTGTTGTTTTAGTTT
1 CTTTATAACATATTTTTCTTTATCATTATGACACGTTTACAGCCAGTTGGTCGTTGTTTT-GTTT
*
11267 A-TCTTTTTCTCAGGGTTAGATTTGA
65 ATTCTTTTTCTCAGGATTAGATTTGA
11292 ATACACAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 73 0.94
106 5 0.06
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.53
Consensus pattern (105 bp):
CTTTATAACATATTTTTCTTTATCATTATGACACGTTTACAGCCAGTTGGTCGTTGTTTTGTTTA
TTCTTTTTCTCAGGATTAGATTTGATATATTTTTTTATAC
Found at i:18293 original size:41 final size:41
Alignment explanation
Indices: 18236--18314 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
18226 ATTATTTCAT
18236 TAATATGCTTGTTGTTAAACACCCTATAAAAGTAAAAATCA
1 TAATATGCTTGTTGTTAAACACCCTATAAAAGTAAAAATCA
18277 TAATATGCTTGTTGTTAAACACCCTATAAAAGTAAAAA
1 TAATATGCTTGTTGTTAAACACCCTATAAAAGTAAAAA
18315 ATATCATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (41 bp):
TAATATGCTTGTTGTTAAACACCCTATAAAAGTAAAAATCA
Found at i:19576 original size:2 final size:2
Alignment explanation
Indices: 19569--19598 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19559 GTTTACGATA
19569 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
19599 GTGTGTGTGA
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:23431 original size:77 final size:80
Alignment explanation
Indices: 23322--23549 Score: 263
Period size: 77 Copynumber: 2.9 Consensus size: 80
23312 TAAGCGGCAG
* *
23322 TGTCAAATGGTTGAGAATCTTTTATTCTTTGAGGTATCGAGTTTGATCACCATGTATGC-AGAGG
1 TGTCAAATGGTTGAGAATCTTTTATCCTTTGAGGTCTCGAGTTTGATCACCATGTATGCAAG-GG
23386 TGTATAAGT-GTTAAA
65 TGTATAAGTCGTTAAA
* * * * * * *
23401 TGTCAAATGGTT-A-AGTCTTTTATCCCTTGAGGTCCCGGGTTCGAGT-ACTATGTATGTAAGGG
1 TGTCAAATGGTTGAGAATCTTTTATCCTTTGAGGTCTCGAGTTTGA-TCACCATGTATGCAAGGG
* *
23463 TGTGTAA-TCGTTCAA
65 TGTATAAGTCGTTAAA
* * *
23478 TGTCTAATGGTTGAGAATC-TTTATCCTTTGAGGTCTCGTGTTTGAACACCATGTATGCAAGGGT
1 TGTCAAATGGTTGAGAATCTTTTATCCTTTGAGGTCTCGAGTTTGATCACCATGTATGCAAGGGT
23542 GTATAAGT
66 GTATAAGT
23550 ATTTGAGTTT
Statistics
Matches: 121, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
76 1 0.01
77 57 0.47
78 47 0.39
79 16 0.13
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (80 bp):
TGTCAAATGGTTGAGAATCTTTTATCCTTTGAGGTCTCGAGTTTGATCACCATGTATGCAAGGGT
GTATAAGTCGTTAAA
Found at i:26229 original size:171 final size:171
Alignment explanation
Indices: 25811--26657 Score: 1079
Period size: 163 Copynumber: 5.0 Consensus size: 171
25801 CTGGCACAGG
* * *
25811 CCTTCTAACAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTAATATCGGATGATTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGATGATTCTGCAATG
*
25876 ACCTTCACTAGGCTAGGAACACTCGAATGAA-CAAGCCGTAGTCCTTGTTATAACAAATATCATA
66 ACCTTCACTAGGCTAGGAACACTCGAA-CAAGCAAGCCGTAGTCCTTGTTATAACAAATATCATA
* * * *
25940 TCATTATTATGTAGTTCCACATTTTGGCATGCTTAAAGTAG--
130 TCATTCTTACGTAGTTCAACATTTTGGCATACTT-AAGTAGTT
* * ** * * * *
25981 -----T--TAGGCTAGGAACGCTAGTTTGTGTCACAAACTTGTACTATCGAATGACTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGATGATTCTGCAATG
* * * *
26039 ACCTTCACTAGGCTAGGAACACTTGCACAAGCAAGCCGTAGTCCTTGTCATGACAAATATCATAT
66 ACCTTCACTAGGCTAGGAACACTCGAACAAGCAAGCCGTAGTCCTTGTTATAACAAATATCATAT
*
26104 CGTTCTTACGTAGTTCAACATTTTGGCATACTTAAGTAGTT
131 CATTCTTACGTAGTTCAACATTTTGGCATACTTAAGTAGTT
*
26145 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGATGATTCTGCAATG
*
26210 ACCTTCACTAGGCTAGGAACACTCGAATGAA-CAAGCCGTAGTCCTTGTTATAACAAATATCATA
66 ACCTTCACTAGGCTAGGAACACTCGAA-CAAGCAAGCCGTAGTCCTTGTTATAACAAATATCATA
* * * *
26274 TCATTATTATGTAGTTCCACATTTTGGCATGCTTAAAGTAG--
130 TCATTCTTACGTAGTTCAACATTTTGGCATACTT-AAGTAGTT
* * * * * * *
26315 -----T--TAGACTAGGAACGCTAGTTTGTGTCACGAACTTGTACTATCGGATGACTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGATGATTCTGCAATG
* * * * *
26373 ACCTTCACTAGGCTAGGAACACTTGCACGAGCAAGCCGTAGTCCTTGTCATGACAAATATCATAT
66 ACCTTCACTAGGCTAGGAACACTCGAACAAGCAAGCCGTAGTCCTTGTTATAACAAATATCATAT
26438 CATTCTTACGTAGTTCAACATTTTGGCATACTTAAGTAGTT
131 CATTCTTACGTAGTTCAACATTTTGGCATACTTAAGTAGTT
*
26479 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGATGATTCTGCAATG
*
26544 ACCTTCACTAGGCTAGGAACACTCGGAACGAGCAAGCCGTAGTCCTTGTTATAACAAATATCATA
66 ACCTTCACTAGGCTAGGAACACTC-GAACAAGCAAGCCGTAGTCCTTGTTATAACAAATATCATA
* * * * *
26609 TCATTCTTAAGTAGTTCATCAGTTTGGCA-AGCTCAAGTATTT
130 TCATTCTTACGTAGTTCAACATTTTGGCATA-CTTAAGTAGTT
26651 CCTTCTG
1 CCTTCTG
26658 TCTGCTATTC
Statistics
Matches: 579, Mismatches: 74, Indels: 46
0.83 0.11 0.07
Matches are distributed among these distances:
162 15 0.03
163 267 0.46
165 2 0.00
169 2 0.00
171 206 0.36
172 87 0.15
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (171 bp):
CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGATGATTCTGCAATG
ACCTTCACTAGGCTAGGAACACTCGAACAAGCAAGCCGTAGTCCTTGTTATAACAAATATCATAT
CATTCTTACGTAGTTCAACATTTTGGCATACTTAAGTAGTT
Found at i:26429 original size:334 final size:334
Alignment explanation
Indices: 25811--26625 Score: 1504
Period size: 334 Copynumber: 2.4 Consensus size: 334
25801 CTGGCACAGG
* * * *
25811 CCTTCTAACAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTAATATCGGATGATTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
25876 ACCTTCACTAGGCTAGGAACACTCGAATGAACAAGCCGTAGTCCTTGTTATAACAAATATCATAT
66 ACCTTCACTAGGCTAGGAACACTCGAATGAACAAGCCGTAGTCCTTGTTATAACAAATATCATAT
*
25941 CATTATTATGTAGTTCCACATTTTGGCATGCTTAAAGTAGTTAGGCTAGGAACGCTAGTTTGTGT
131 CATTATTATGTAGTTCCACATTTTGGCATGCTTAAAGTAGTTAGACTAGGAACGCTAGTTTGTGT
26006 CACAAACTTGTACTATCGAATGACTCTGCAATGACCTTCACTAGGCTAGGAACACTTGCACAAGC
196 CACAAACTTGTACTATCGAATGACTCTGCAATGACCTTCACTAGGCTAGGAACACTTGCACAAGC
*
26071 AAGCCGTAGTCCTTGTCATGACAAATATCATATCGTTCTTACGTAGTTCAACATTTTGGCATACT
261 AAGCCGTAGTCCTTGTCATGACAAATATCATATCATTCTTACGTAGTTCAACATTTTGGCATACT
26136 TAAGTAGTT
326 TAAGTAGTT
26145 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
26210 ACCTTCACTAGGCTAGGAACACTCGAATGAACAAGCCGTAGTCCTTGTTATAACAAATATCATAT
66 ACCTTCACTAGGCTAGGAACACTCGAATGAACAAGCCGTAGTCCTTGTTATAACAAATATCATAT
26275 CATTATTATGTAGTTCCACATTTTGGCATGCTTAAAGTAGTTAGACTAGGAACGCTAGTTTGTGT
131 CATTATTATGTAGTTCCACATTTTGGCATGCTTAAAGTAGTTAGACTAGGAACGCTAGTTTGTGT
* * *
26340 CACGAACTTGTACTATCGGATGACTCTGCAATGACCTTCACTAGGCTAGGAACACTTGCACGAGC
196 CACAAACTTGTACTATCGAATGACTCTGCAATGACCTTCACTAGGCTAGGAACACTTGCACAAGC
26405 AAGCCGTAGTCCTTGTCATGACAAATATCATATCATTCTTACGTAGTTCAACATTTTGGCATACT
261 AAGCCGTAGTCCTTGTCATGACAAATATCATATCATTCTTACGTAGTTCAACATTTTGGCATACT
26470 TAAGTAGTT
326 TAAGTAGTT
26479 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
1 CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
* *
26544 ACCTTCACTAGGCTAGGAACACTCGGAACGAGCAAGCCGTAGTCCTTGTTATAACAAATATCATA
66 ACCTTCACTAGGCTAGGAACACTC-GAATGAACAAGCCGTAGTCCTTGTTATAACAAATATCATA
* *
26609 TCATTCTTAAGTAGTTC
130 TCATTATTATGTAGTTC
26626 ATCAGTTTGG
Statistics
Matches: 467, Mismatches: 13, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
334 414 0.89
335 53 0.11
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (334 bp):
CCTTCTGATAGGCTAGGAACACTAGTTGGTGTCATGAGCTCGTACTATCGGACGATTCTGCAATG
ACCTTCACTAGGCTAGGAACACTCGAATGAACAAGCCGTAGTCCTTGTTATAACAAATATCATAT
CATTATTATGTAGTTCCACATTTTGGCATGCTTAAAGTAGTTAGACTAGGAACGCTAGTTTGTGT
CACAAACTTGTACTATCGAATGACTCTGCAATGACCTTCACTAGGCTAGGAACACTTGCACAAGC
AAGCCGTAGTCCTTGTCATGACAAATATCATATCATTCTTACGTAGTTCAACATTTTGGCATACT
TAAGTAGTT
Found at i:27981 original size:27 final size:27
Alignment explanation
Indices: 27939--28005 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
27929 GATAATGGCT
**
27939 CTGAATCATTCAGAATGTACTTTTGTG
1 CTGAATCATTCAGAATGTACTTCAGTG
*
27966 CTGAATCATTCGGAATGTACTTCAGTG
1 CTGAATCATTCAGAATGTACTTCAGTG
27993 CTGAATCATTCAG
1 CTGAATCATTCAG
28006 CACTGTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCAGTG
Found at i:39508 original size:32 final size:33
Alignment explanation
Indices: 39467--39529 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
39457 TTTTTTGGTC
39467 AACCCGACCC-AAAAATATACACCCTCCACCCG
1 AACCCGACCCGAAAAATATACACCCTCCACCCG
* *
39499 AACCCGACCCGAAAAATATATACTCTCCACC
1 AACCCGACCCGAAAAATATACACCCTCCACC
39530 GACTACGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.38, C:0.43, G:0.06, T:0.13
Consensus pattern (33 bp):
AACCCGACCCGAAAAATATACACCCTCCACCCG
Found at i:39539 original size:32 final size:33
Alignment explanation
Indices: 39471--39541 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
39461 TTGGTCAACC
*
39471 CGACCC-AAAAATATACACCCTCCACCCGAACC
1 CGACCCGAAAAATATACACCCTCCACCCGAACA
* *
39503 CGACCCGAAAAATATATACTCTCCA-CCG-ACTA
1 CGACCCGAAAAATATACACCCTCCACCCGAAC-A
39535 CGACCCG
1 CGACCCG
39542 GCCCAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 2 0.06
32 16 0.47
33 16 0.47
ACGTcount: A:0.35, C:0.42, G:0.10, T:0.13
Consensus pattern (33 bp):
CGACCCGAAAAATATACACCCTCCACCCGAACA
Found at i:42552 original size:24 final size:24
Alignment explanation
Indices: 42517--42602 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
42507 TCGTGAATGC
*
42517 TAAACGAACACGTTCGTGAACATA
1 TAAATGAACACGTTCGTGAACATA
* **
42541 TAAATGAGCACGTTCACGAACAT-
1 TAAATGAACACGTTCGTGAACATA
** *
42564 TAAGCGAACATGTTCGTGAACAATAAA
1 TAAATGAACACGTTCGTGAAC-AT--A
42591 TAAATGAACACG
1 TAAATGAACACG
42603 AACACCTTCA
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
23 15 0.33
24 21 0.47
27 9 0.20
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (24 bp):
TAAATGAACACGTTCGTGAACATA
Found at i:42584 original size:23 final size:23
Alignment explanation
Indices: 42517--42590 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
42507 TCGTGAATGC
42517 TAAACGAACACGTTCGTGAACAT
1 TAAACGAACACGTTCGTGAACAT
* * **
42540 ATAAATGAGCACGTTCACGAACAT
1 -TAAACGAACACGTTCGTGAACAT
* * *
42564 TAAGCGAACATGTTCGTGAACAA
1 TAAACGAACACGTTCGTGAACAT
42587 TAAA
1 TAAA
42591 TAAATGAACA
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (23 bp):
TAAACGAACACGTTCGTGAACAT
Found at i:46734 original size:105 final size:105
Alignment explanation
Indices: 46624--47211 Score: 1014
Period size: 105 Copynumber: 5.6 Consensus size: 105
46614 TTTGTCGGAT
* * * * *
46624 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
46689 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
46729 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTTTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
** *
46794 GGAACATACTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
46834 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTTCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
46899 GGAACAGGCTCTTTTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
46939 GAGTTCTTCTCATTATGAACTCTTCTGAAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
47004 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
47044 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
47109 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
47149 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGGTCACCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGA
47212 TTGTTGTTGA
Statistics
Matches: 460, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 460 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:48141 original size:8 final size:8
Alignment explanation
Indices: 48130--48202 Score: 96
Period size: 8 Copynumber: 9.0 Consensus size: 8
48120 CTTTTTTTTC
48130 TTTTCATT
1 TTTTCATT
48138 TTTTCATT
1 TTTTCATT
48146 TTTTCATTT
1 TTTTCA-TT
48155 TTTTCATT
1 TTTTCATT
48163 TTTTCATTTT
1 TTTTCA--TT
48173 TTTTCATT
1 TTTTCATT
48181 TTTTC--T
1 TTTTCATT
*
48187 TTTTCACT
1 TTTTCATT
48195 TTTTCATT
1 TTTTCATT
48203 CATTCTTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
6 6 0.10
8 37 0.63
9 8 0.14
10 8 0.14
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCATT
Found at i:48156 original size:17 final size:17
Alignment explanation
Indices: 48130--48202 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
48120 CTTTTTTTTC
48130 TTTTCA-TTTTTTCATT
1 TTTTCATTTTTTTCATT
48146 TTTTCATTTTTTTCATT
1 TTTTCATTTTTTTCATT
48163 TTTTCATTTTTTTTCATT
1 TTTTCA-TTTTTTTCATT
*
48181 TTTTC---TTTTTCACT
1 TTTTCATTTTTTTCATT
48195 TTTTCATT
1 TTTTCATT
48203 CATTCTTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
14 13 0.25
16 6 0.12
17 16 0.31
18 16 0.31
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCATTTTTTTCATT
Found at i:48158 original size:25 final size:25
Alignment explanation
Indices: 48130--48202 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
48120 CTTTTTTTTC
48130 TTTTCATTTTTTCATTTTTTCATTT
1 TTTTCATTTTTTCATTTTTTCATTT
48155 TTTTCATTTTTTCATTTTTTTTCA-TT
1 TTTTCATTTTTTCA--TTTTTTCATTT
*
48181 TTTTC--TTTTTCACTTTTTCATT
1 TTTTCATTTTTTCATTTTTTCATT
48203 CATTCTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
22 7 0.16
23 1 0.02
24 7 0.16
25 14 0.32
26 7 0.16
27 8 0.18
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTCATTTTTTCATTTTTTCATTT
Found at i:48198 original size:26 final size:24
Alignment explanation
Indices: 48165--48218 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
48155 TTTTCATTTT
48165 TTCATTTTTTTTCATTTTTTCTTT
1 TTCATTTTTTTTCATTTTTTCTTT
*
48189 TTCACTTTTTCATTCATTCTTTT-TTT
1 TTCA-TTTTT-TTTCATT-TTTTCTTT
48215 TTCA
1 TTCA
48219 AGCATAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 4 0.15
25 5 0.19
26 13 0.50
27 4 0.15
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (24 bp):
TTCATTTTTTTTCATTTTTTCTTT
Found at i:48215 original size:32 final size:31
Alignment explanation
Indices: 48130--48217 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 31
48120 CTTTTTTTTC
* *
48130 TTTTCATTTT-TTCATTTTTTCATTTTTTTCATT
1 TTTTCATTTTCTTTATTTTTTC---TTTTTCACT
*
48163 TTTTCATTTTTTTTCATTTTTTCTTTTTCACT
1 TTTTCATTTTCTTT-ATTTTTTCTTTTTCACT
48195 TTTTCATTCATTCTTT-TTTTTTC
1 TTTTCATT--TTCTTTATTTTTTC
48218 AAGCATAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
32 23 0.48
33 10 0.21
34 7 0.15
35 8 0.17
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTCATTTTCTTTATTTTTTCTTTTTCACT
Found at i:48217 original size:18 final size:18
Alignment explanation
Indices: 48136--48218 Score: 87
Period size: 18 Copynumber: 4.4 Consensus size: 18
48126 TTTCTTTTCA
*
48136 TTTTTTCATTTTTTC-AT
1 TTTTTTCATTTTTTCTTT
*
48153 TTTTTTCATTTTTTCATT
1 TTTTTTCATTTTTTCTTT
48171 TTTTTTCATTTTTTCTTTT
1 TTTTTTCATTTTTTC-TTT
**
48190 TCACTTTTTCATTCATTCTTT
1 T---TTTTTCATTTTTTCTTT
48211 TTTTTTCA
1 TTTTTTCA
48219 AGCATAGTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
17 15 0.26
18 23 0.40
19 3 0.05
21 4 0.07
22 12 0.21
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTCATTTTTTCTTT
Done.