Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008125.1 Hibiscus syriacus cultivar Beakdansim tig00110679_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: 75640
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1660 original size:40 final size:40
Alignment explanation
Indices: 1558--1754 Score: 218
Period size: 40 Copynumber: 4.9 Consensus size: 40
1548 TTGTAAACAC
* * *
1558 AAATGCCACTAAAGTATGAGTCTATAGCGACATTTGTATAA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTAT-A
* * *
1599 AAATTCCACTAAAGCATGAGTCTATAGCGGCGTTTGTATA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATA
* * * * *
1639 AAACGCCACTAAAGTACGAGTCTTTGGTGGCATTTGTATA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATA
* * *
1679 AAGTGCCACTAAAGTACGATTCTTTAGCGGCG-TTGTCA-A
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGT-ATA
* *
1718 AAATGCCACTAAAGTATGAGTATTTAGCAGCGTTTGT
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGT
1755 TCTAAAAACG
Statistics
Matches: 131, Mismatches: 23, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
39 32 0.24
40 64 0.49
41 35 0.27
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (40 bp):
AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATA
Found at i:1679 original size:81 final size:79
Alignment explanation
Indices: 1562--1738 Score: 212
Period size: 81 Copynumber: 2.2 Consensus size: 79
1552 AAACACAAAT
* *
1562 GCCACTAAAGTATGAGTCTATAGCGACATTTGTATAAAAATTCCACTAAAGCATGAGTCTATAGC
1 GCCACTAAAGTATGAGTCTATAGCGACATTTGTAT-AAAATGCCACTAAAGCACGAGTCTATAGC
1627 GGCGTTTGT-ATAAAAC
65 GGCG-TTGTCA-AAAAC
* * * * * * * * *
1643 GCCACTAAAGTACGAGTCTTTGGTGGCATTTGTATAAAGTGCCACTAAAGTACGATTCTTTAGCG
1 GCCACTAAAGTATGAGTCTATAGCGACATTTGTATAAAATGCCACTAAAGCACGAGTCTATAGCG
*
1708 GCGTTGTCAAAAAT
66 GCGTTGTCAAAAAC
1722 GCCACTAAAGTATGAGT
1 GCCACTAAAGTATGAGT
1739 ATTTAGCAGC
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 24 0.29
80 28 0.34
81 30 0.37
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (79 bp):
GCCACTAAAGTATGAGTCTATAGCGACATTTGTATAAAATGCCACTAAAGCACGAGTCTATAGCG
GCGTTGTCAAAAAC
Found at i:7033 original size:19 final size:17
Alignment explanation
Indices: 6996--7041 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
6986 TAAAGTTTAA
6996 AAAATTA-TAAAATATT
1 AAAATTATTAAAATATT
*
7012 AAATTTATTAAAATATTAT
1 AAAATTATTAAAATA-T-T
7031 AAAATTATTAA
1 AAAATTATTAA
7042 TAAATTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 7 0.28
18 1 0.04
19 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATTATTAAAATATT
Found at i:10142 original size:9 final size:9
Alignment explanation
Indices: 10128--10196 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
10118 GCTACTGGAA
10128 ACCGGTTTG
1 ACCGGTTTG
*
10137 ACCGGTTTCA
1 ACCGGTTT-G
*
10147 ACCGGTTCG
1 ACCGGTTTG
*
10156 AAACGGTTTG
1 -ACCGGTTTG
*
10166 ACCGGTCTG
1 ACCGGTTTG
10175 AACCGGTTTG
1 -ACCGGTTTG
*
10185 ACCGGTCTG
1 ACCGGTTTG
10194 ACC
1 ACC
10197 CGACCCGACC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 26 0.54
10 22 0.46
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:10168 original size:29 final size:30
Alignment explanation
Indices: 10125--10182 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
10115 GTGGCTACTG
*
10125 GAAACCGGTTTGACCGGTTTCAACCGGTTC
1 GAAACCGGTTTGACCGGTCTCAACCGGTTC
*
10155 GAAA-CGGTTTGACCGGTCTGAACCGGTT
1 GAAACCGGTTTGACCGGTCTCAACCGGTT
10183 TGACCGGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (30 bp):
GAAACCGGTTTGACCGGTCTCAACCGGTTC
Found at i:10169 original size:19 final size:20
Alignment explanation
Indices: 10147--10194 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
10137 ACCGGTTTCA
10147 ACCGGTTC-GAAACGGTTTG
1 ACCGGTTCTGAAACGGTTTG
*
10166 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAAACGGTTTG
10185 ACCGG-TCTGA
1 ACCGGTTCTGA
10195 CCCGACCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (20 bp):
ACCGGTTCTGAAACGGTTTG
Found at i:10214 original size:17 final size:17
Alignment explanation
Indices: 10192--10247 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
10182 TTGACCGGTC
*
10192 TGACCCGACCCGACCGG
1 TGACCCGACCCGACCGT
10209 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
10226 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
10243 TGACC
1 TGACC
10248 GTTGACTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.18, C:0.46, G:0.25, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:17317 original size:9 final size:9
Alignment explanation
Indices: 17300--17330 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17290 CCCTGGAGGA
*
17300 CGCCTCACG
1 CGCCACACG
17309 CGCCACACG
1 CGCCACACG
17318 CGCCACACG
1 CGCCACACG
17327 CGCC
1 CGCC
17331 GCCGCAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.16, C:0.58, G:0.23, T:0.03
Consensus pattern (9 bp):
CGCCACACG
Found at i:17380 original size:11 final size:11
Alignment explanation
Indices: 17364--17413 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
17354 AAACCGATTT
17364 AACCGGTTTTC
1 AACCGGTTTTC
*
17375 AACCGGTTCT-
1 AACCGGTTTTC
*
17385 GACCGG-TTTC
1 AACCGGTTTTC
*
17395 AACCGG-TTTG
1 AACCGGTTTTC
17405 AACCGGTTT
1 AACCGGTTT
17414 GACCGGTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 19 0.59
11 11 0.34
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (11 bp):
AACCGGTTTTC
Found at i:17391 original size:10 final size:9
Alignment explanation
Indices: 17376--17437 Score: 70
Period size: 10 Copynumber: 6.4 Consensus size: 9
17366 CCGGTTTTCA
17376 ACCGGTTCTG
1 ACCGGTT-TG
*
17386 ACCGGTTTCA
1 ACCGGTTT-G
17396 ACCGGTTTG
1 ACCGGTTTG
17405 AACCGGTTTG
1 -ACCGGTTTG
*
17415 ACCGGTCTG
1 ACCGGTTTG
17424 AACCGGTTTG
1 -ACCGGTTTG
17434 ACCG
1 ACCG
17438 ATCTGACCCG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
9 13 0.29
10 32 0.71
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:17394 original size:20 final size:21
Alignment explanation
Indices: 17364--17432 Score: 92
Period size: 20 Copynumber: 3.4 Consensus size: 21
17354 AAACCGATTT
17364 AACCGGTTTTCAACCGGTTCTG
1 AACCGG-TTTCAACCGGTTCTG
17386 -ACCGGTTTCAACCGGTT-TG
1 AACCGGTTTCAACCGGTTCTG
*
17405 AACCGGTTT-GACCGG-TCTG
1 AACCGGTTTCAACCGGTTCTG
17424 AACCGGTTT
1 AACCGGTTT
17433 GACCGATCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
18 1 0.02
19 18 0.41
20 20 0.45
21 5 0.11
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
AACCGGTTTCAACCGGTTCTG
Found at i:17420 original size:19 final size:19
Alignment explanation
Indices: 17376--17437 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
17366 CCGGTTTTCA
*
17376 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTT-TGAACCGGTTT-G
17396 ACCGGTTTGAACCGGTTTG
1 ACCGGTTTGAACCGGTTTG
*
17415 ACCGGTCTGAACCGGTTTG
1 ACCGGTTTGAACCGGTTTG
17434 ACCG
1 ACCG
17438 ATCTGACCCG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 24 0.62
20 15 0.38
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGAACCGGTTTG
Found at i:17442 original size:19 final size:19
Alignment explanation
Indices: 17403--17443 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
17393 TCAACCGGTT
*
17403 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGATC
17422 TGAACCGGTTTGACCGATC
1 TGAACCGGTTTGACCGATC
17441 TGA
1 TGA
17444 CCCGACCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (19 bp):
TGAACCGGTTTGACCGATC
Found at i:17444 original size:9 final size:9
Alignment explanation
Indices: 17376--17445 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
17366 CCGGTTTTCA
17376 ACCGGTTCTG
1 ACCGG-TCTG
* *
17386 ACCGGTTTCA
1 ACCGGTCT-G
*
17396 ACCGGTTTG
1 ACCGGTCTG
*
17405 AACCGGTTTG
1 -ACCGGTCTG
17415 ACCGGTCTG
1 ACCGGTCTG
*
17424 AACCGGTTTG
1 -ACCGGTCTG
*
17434 ACCGATCTG
1 ACCGGTCTG
17443 ACC
1 ACC
17446 CGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 20 0.40
10 30 0.60
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:20684 original size:2 final size:2
Alignment explanation
Indices: 20677--20746 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
20667 GGTAGGAGTT
20677 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
20719 T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20747 TCTTACCTAA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20928 original size:23 final size:24
Alignment explanation
Indices: 20894--20999 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 24
20884 GTTTTTATAT
20894 AAAATATATTTTTAAATTAAAAT-A
1 AAAATAT-TTTTTAAATTAAAATAA
20918 AAAATATTTTTTAAATTAAGTTAATAA
1 AAAATATTTTTTAAATTAA---AATAA
** * **
20945 AAAATATTTAATAAGTTAATGT-A
1 AAAATATTTTTTAAATTAAAATAA
* *
20968 AAAATATTTTTTAAGTTAATATAA
1 AAAATATTTTTTAAATTAAAATAA
20992 AAAATATT
1 AAAATATT
21000 ATGAATTTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
23 32 0.46
24 17 0.25
26 3 0.04
27 17 0.25
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AAAATATTTTTTAAATTAAAATAA
Found at i:21302 original size:40 final size:40
Alignment explanation
Indices: 21247--21324 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
21237 CTGATGTGGC
*
21247 GCCACGCAGGGTAAGGCGCGATGCATGGGTCGCACCTTAT
1 GCCACGCAGGGTAAGGCGCGATGCATGGGCCGCACCTTAT
* * * *
21287 GCCACGTAGGGTAAGGTGCGGTGCATGGGCCGCGCCTT
1 GCCACGCAGGGTAAGGCGCGATGCATGGGCCGCACCTT
21325 TCTGCCAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.38, T:0.18
Consensus pattern (40 bp):
GCCACGCAGGGTAAGGCGCGATGCATGGGCCGCACCTTAT
Found at i:21596 original size:21 final size:21
Alignment explanation
Indices: 21510--21589 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
21500 AGGTATATTT
*
21510 TATTCTATTTAATATTTTGTTAG
1 TATTTTATTTAA-ATTTT-TTAG
*
21533 TATTTTATTT-AA--TTATA-
1 TATTTTATTTAAATTTTTTAG
*
21550 TA-ATTATTTAAATTTTTTAG
1 TATTTTATTTAAATTTTTTAG
21570 TATTTTATTT-AATTTATTTA
1 TATTTTATTTAAATTT-TTTA
21590 TTTTTTTGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
16 6 0.13
17 4 0.09
18 2 0.04
19 6 0.13
20 7 0.15
21 11 0.24
22 1 0.02
23 9 0.20
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (21 bp):
TATTTTATTTAAATTTTTTAG
Found at i:27596 original size:29 final size:29
Alignment explanation
Indices: 27526--27598 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
27516 TCGGGTGATA
* * *
27526 TTTACGGGTTGAAAGGTTTGTTGTGTGAT
1 TTTACGGGTTGAGAGGATTGTTGTGTAAT
*
27555 TTTTCGGGTTGAGAGGATTGTTGTG-AAT
1 TTTACGGGTTGAGAGGATTGTTGTGTAAT
27583 GTTTACGGGTTGAGAG
1 -TTTACGGGTTGAGAG
27599 TGTATTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.18, C:0.04, G:0.37, T:0.41
Consensus pattern (29 bp):
TTTACGGGTTGAGAGGATTGTTGTGTAAT
Found at i:27755 original size:40 final size:40
Alignment explanation
Indices: 27704--27781 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
27694 AGTTGGCAGA
*
27704 AAGGCGCGACTCATGCACCGCGCCTTACCCTACGTGGCAT
1 AAGGCGCGACTCATGCACCGCACCTTACCCTACGTGGCAT
* *
27744 AAGGCGTGACTCATGCACCGCACCTTACCCTGCGTGGC
1 AAGGCGCGACTCATGCACCGCACCTTACCCTACGTGGC
27782 GCCACATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.19, C:0.37, G:0.26, T:0.18
Consensus pattern (40 bp):
AAGGCGCGACTCATGCACCGCACCTTACCCTACGTGGCAT
Found at i:34273 original size:21 final size:21
Alignment explanation
Indices: 34229--34274 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
34219 GATTTCTGGG
* * *
34229 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
34250 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
34271 CAAG
1 CAAG
34275 CGAACCAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:34346 original size:23 final size:22
Alignment explanation
Indices: 34298--34346 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
34288 ATAGAATGTC
34298 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
34319 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
34342 AAGGA
1 AAGGA
34347 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:34743 original size:20 final size:22
Alignment explanation
Indices: 34703--34759 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
34693 TGAATATGTG
*
34703 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
34725 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
34745 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
34760 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:37711 original size:2 final size:2
Alignment explanation
Indices: 37704--37754 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
37694 TTTATCTATG
37704 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
37746 TA TA TA TA T
1 TA TA TA TA T
37755 GTAATCACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38241 original size:52 final size:52
Alignment explanation
Indices: 38172--38567 Score: 668
Period size: 52 Copynumber: 7.6 Consensus size: 52
38162 TCACTCTCTA
* * * *
38172 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
38224 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
38276 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
38328 TTTCTTCAGGGAGTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
38380 TTTCTTCAAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* **
38432 TTTCTTCAGGGACTAGAACTCGAACAA-AATCTTCCTACGAGAATGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
38483 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
38535 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
38568 CCAACGATCG
Statistics
Matches: 321, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
51 48 0.15
52 273 0.85
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
Found at i:38516 original size:28 final size:28
Alignment explanation
Indices: 38434--38517 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 28
38424 TGCCCAATTT
38434 TCTTCAGGGACTAGAACTCGAACAA-AA
1 TCTTCAGGGACTAGAACTCGAACAATAA
** * ** **
38461 TCTTC--CTACGAGAA-T-GCCCAATTT
1 TCTTCAGGGACTAGAACTCGAACAATAA
38485 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTCAGGGACTAGAACTCGAACAATAA
38513 TCTTC
1 TCTTC
38518 CTACGGGTCT
Statistics
Matches: 38, Mismatches: 14, Indels: 9
0.62 0.23 0.15
Matches are distributed among these distances:
23 4 0.11
24 6 0.16
25 6 0.16
26 6 0.16
27 6 0.16
28 10 0.26
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (28 bp):
TCTTCAGGGACTAGAACTCGAACAATAA
Found at i:38622 original size:55 final size:55
Alignment explanation
Indices: 38563--38842 Score: 474
Period size: 55 Copynumber: 5.1 Consensus size: 55
38553 CTCGAACAAT
*
38563 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
38618 AATCTTCAACAATCGCGTCTGCCCCTTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
38673 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
38726 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
38781 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
38836 AATCTTC
1 AATCTTC
38843 TTTTGCTTCA
Statistics
Matches: 208, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
53 48 0.23
54 4 0.02
55 156 0.75
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:38773 original size:108 final size:110
Alignment explanation
Indices: 38563--38842 Score: 492
Period size: 108 Copynumber: 2.6 Consensus size: 110
38553 CTCGAACAAT
*
38563 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
*
38628 AATCGCGTCTGCCCCTTATTTATTCAGAGAGTATAAGACTCGAAC
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* *
38673 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
38736 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
38781 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
38843 TTTTGCTTCA
Statistics
Matches: 161, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
108 101 0.63
109 4 0.02
110 56 0.35
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (110 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:40152 original size:15 final size:14
Alignment explanation
Indices: 40134--40165 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
40124 TTATTTTTTG
40134 TTTTTTTCTTCTTCT
1 TTTTTTTCTTCTT-T
40149 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
40163 TTT
1 TTT
40166 CCATTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTCTTCTTT
Found at i:40157 original size:9 final size:9
Alignment explanation
Indices: 40122--40232 Score: 62
Period size: 9 Copynumber: 11.4 Consensus size: 9
40112 TGAACCCCCC
*
40122 TTTTATTTT
1 TTTTCTTTT
*
40131 TTGTTTTTTT
1 TT-TTCTTTT
40141 CTTCTTCTTTT
1 -TT-TTCTTTT
40152 TTTTCTTCTT
1 TTTTCTT-TT
**
40162 TTTTCCATT
1 TTTTCTTTT
40171 TTTTCTATTT
1 TTTTCT-TTT
*
40181 TTCTATTTTTT
1 TT-T-TCTTTT
*
40192 TATTTC-ATT
1 T-TTTCTTTT
*
40201 TTTTCATTT
1 TTTTCTTTT
*
40210 TTTTCATTT
1 TTTTCTTTT
40219 TTTTCATTTT
1 TTTTC-TTTT
40229 TTTT
1 TTTT
40233 ATCTTTAAGC
Statistics
Matches: 81, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
8 4 0.05
9 33 0.41
10 27 0.33
11 14 0.17
12 3 0.04
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.79
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:40165 original size:12 final size:12
Alignment explanation
Indices: 40127--40165 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
40117 CCCCCTTTTA
*
40127 TTTTTTGTT-TT
1 TTTTTTCTTCTT
*
40138 TTTCTTCTTCTT
1 TTTTTTCTTCTT
40150 TTTTTTCTTCTT
1 TTTTTTCTTCTT
40162 TTTT
1 TTTT
40166 CCATTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTCTT
Found at i:40172 original size:17 final size:16
Alignment explanation
Indices: 40152--40221 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 16
40142 TTCTTCTTTT
40152 TTTTCTTCTTTTTTCCA
1 TTTT-TTCTTTTTTCCA
*
40169 TTTTTTCTATTTTTCTA
1 TTTTTTCT-TTTTTCCA
*
40186 -TTTTT-TTATTT-CA
1 TTTTTTCTTTTTTCCA
*
40199 TTTTTTCATTTTTTTCA
1 TTTTTTC-TTTTTTCCA
40216 TTTTTT
1 TTTTTT
40222 TCATTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 1 0.02
14 9 0.20
15 1 0.02
16 14 0.32
17 19 0.43
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTCTTTTTTCCA
Found at i:40190 original size:38 final size:38
Alignment explanation
Indices: 40148--40232 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 38
40138 TTTCTTCTTC
40148 TTTTTTTTCTTC-TTTTTTCCA-TTTTTTCTATTTTTCT-A
1 TTTTTTTT-TTCATTTTTT-CATTTTTTTC-ATTTTTCTCA
*
40186 TTTTTTTATTTCATTTTTTCATTTTTTTCATTTTTTTCA
1 TTTTTTT-TTTCATTTTTTCATTTTTTTCATTTTTCTCA
40225 TTTTTTTT
1 TTTTTTTT
40233 ATCTTTAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
38 20 0.48
39 22 0.52
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (38 bp):
TTTTTTTTTTCATTTTTTCATTTTTTTCATTTTTCTCA
Found at i:40201 original size:30 final size:31
Alignment explanation
Indices: 40167--40227 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
40157 TTCTTTTTTC
40167 CATTTTTTCTATTTTTCT-ATTTTTTT-ATTT
1 CATTTTTTC-ATTTTTCTCATTTTTTTCATTT
*
40197 CATTTTTTCATTTTTTTCATTTTTTTCATTT
1 CATTTTTTCATTTTTCTCATTTTTTTCATTT
40228 TTTTTATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.25
30 17 0.61
31 4 0.14
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.75
Consensus pattern (31 bp):
CATTTTTTCATTTTTCTCATTTTTTTCATTT
Found at i:40205 original size:8 final size:8
Alignment explanation
Indices: 40160--40230 Score: 60
Period size: 8 Copynumber: 8.8 Consensus size: 8
40150 TTTTTTCTTC
40160 TTTTTTCCA
1 TTTTTT-CA
40169 TTTTTTC-
1 TTTTTTCA
40176 TATTTTTC-
1 T-TTTTTCA
40184 TATTTTT--
1 T-TTTTTCA
*
40191 TTATTTCA
1 TTTTTTCA
40199 TTTTTTCA
1 TTTTTTCA
40207 TTTTTTTCA
1 -TTTTTTCA
40216 TTTTTTTCA
1 -TTTTTTCA
40225 TTTTTT
1 TTTTTT
40231 TTATCTTTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 27 0.48
9 23 0.41
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:48616 original size:2 final size:2
Alignment explanation
Indices: 48609--48637 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48599 TTTATCTATG
48609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48638 GTAATCACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48893 original size:31 final size:31
Alignment explanation
Indices: 48857--49105 Score: 410
Period size: 31 Copynumber: 8.0 Consensus size: 31
48847 AGGGTCGAGG
48857 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
48888 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
48919 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
48950 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
48981 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
49012 GTTTACCTATGTTATTCGTGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
49043 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
49074 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
49105 G
1 G
49106 GTCCTTCGGG
Statistics
Matches: 204, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
31 203 1.00
32 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:60493 original size:20 final size:20
Alignment explanation
Indices: 60449--60506 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
60439 ATAATAATAT
* *
60449 AATATTATTTTTATTCAATAAA
1 AATATTATTATAATT-AA-AAA
60471 AATAATTATT-TAATTAAAAA
1 AAT-ATTATTATAATTAAAAA
60491 AATATTATTATAATTA
1 AATATTATTATAATTA
60507 TTCTTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.18
20 12 0.36
21 2 0.06
22 7 0.21
23 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATTATTATAATTAAAAA
Found at i:66029 original size:61 final size:59
Alignment explanation
Indices: 65902--66038 Score: 143
Period size: 61 Copynumber: 2.3 Consensus size: 59
65892 CAATACAGAC
* ** *
65902 CAGGTCGCTCAATTATGTGTCCAGTAGTAAATGAATCACTCTTTTCTCTACAATTTAAA
1 CAGGTCACTCAATTATGTGTCCAGTAACAAATGAACCACTCTTTTCTCTACAATTTAAA
* * *
65961 CATAGGTCACTCCATTATGTGTCTAGTAACAAATGGACCACTCTTTTCTCTA-AAGGTTATAAA
1 C--AGGTCACTCAATTATGTGTCCAGTAACAAATGAACCACTCTTTTCTCTACAA--TT-TAAA
*
66024 CAGGTC-CTTAATTAT
1 CAGGTCACTCAATTAT
66039 TAAATATTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
59 1 0.02
60 9 0.14
61 47 0.73
62 2 0.03
63 5 0.08
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (59 bp):
CAGGTCACTCAATTATGTGTCCAGTAACAAATGAACCACTCTTTTCTCTACAATTTAAA
Done.