Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002871.1 Hibiscus syriacus cultivar Beakdansim tig00005921_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: 71680
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1969 original size:2 final size:2
Alignment explanation
Indices: 1962--1997 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1952 TCTTCTAAAA
1962 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1998 ATATTTTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5829 original size:15 final size:13
Alignment explanation
Indices: 5800--5831 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5790 GATTCCAACT
5800 AACAACACGAAAC
1 AACAACACGAAAC
5813 AACAACACGAAA-
1 AACAACACGAAAC
5825 AACAACA
1 AACAACA
5832 GGAGAATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.66, C:0.28, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAACACGAAAC
Found at i:10349 original size:195 final size:198
Alignment explanation
Indices: 10115--10518 Score: 511
Period size: 197 Copynumber: 2.1 Consensus size: 198
10105 TATTCTAAGT
* * * *
10115 GAGTTAAAAATGGTTCCAAAGCTTATTTTGTGCATGAAGAA-AAAGCTAAAATGGTTTGATAGGC
1 GAGTTCAAAACGGTTCCAAAGCTTATTTTGTGCATGAAGAAGAAA-CTAAAATGGCTTGATAGAC
* * * * * * *
10179 ATATTCGACAGA-T-TTTTCGGATAGTTAATGTG-AAATTTTCATAATTTGTAAGATTAGAGGCT
65 ATATTCGA-AGAGTATTTTCAGAAAGTTAATATGAAAATTTACATAATTTATAAGATTAAAGGCA
* *
10241 TAGTATTAGTACTTATG-TTCAAATGAGACTAGTATC-ATCAC-ACGAGACATTCTAAGCAGTGT
129 TAGTATTAGTA-ATATGTTTCAAATGAGACTAGTATCGA-CACAACAAGACATTCTAAGCAGTGT
10303 AAAAATC
192 AAAAATC
* *
10310 -ACGTTCAAAACGGTTCCAAAGCTTGGTTTT-TGCATGAAGAAGAAACTAGAATGGCTTGATAGA
1 GA-GTTCAAAACGGTTCCAAAGCTT-ATTTTGTGCATGAAGAAGAAACTAAAATGGCTTGATAGA
* *
10373 CATGTTTGAAGAGTATTTTCAGAAAGTTAATATGAAAATTTACATAATTTATAAGATTAAAGGCA
64 CATATTCGAAGAGTATTTTCAGAAAGTTAATATGAAAATTTACATAATTTATAAGATTAAAGGCA
* *
10438 TAGTATTGGTAATATGTTTCAAATGAGACTAGTATCGACACATACAAGACATTCTAAGCGGTGTA
129 TAGTATTAGTAATATGTTTCAAATGAGACTAGTATCGACACA-ACAAGACATTCTAAGCAGTGTA
10503 AAAATC
193 AAAATC
10509 GAGTTCAAAA
1 GAGTTCAAAA
10519 TGATTTGAAA
Statistics
Matches: 179, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
194 4 0.02
195 54 0.30
196 27 0.15
197 58 0.32
198 1 0.01
199 34 0.19
200 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (198 bp):
GAGTTCAAAACGGTTCCAAAGCTTATTTTGTGCATGAAGAAGAAACTAAAATGGCTTGATAGACA
TATTCGAAGAGTATTTTCAGAAAGTTAATATGAAAATTTACATAATTTATAAGATTAAAGGCATA
GTATTAGTAATATGTTTCAAATGAGACTAGTATCGACACAACAAGACATTCTAAGCAGTGTAAAA
ATC
Found at i:15107 original size:4 final size:4
Alignment explanation
Indices: 15084--15117 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
15074 ATACCCCTTA
15084 AAAT AAA- AAAT AAA- AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
15118 TATGTCTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:15109 original size:8 final size:7
Alignment explanation
Indices: 15083--15117 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
15073 CATACCCCTT
15083 AAAATAA
1 AAAATAA
15090 AAAATAA
1 AAAATAA
15097 AAAATAA
1 AAAATAA
15104 ATAAATAA
1 A-AAATAA
15112 ATAAAT
1 A-AAAT
15118 TATGTCTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.56
8 12 0.44
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:15843 original size:50 final size:50
Alignment explanation
Indices: 15768--15866 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
15758 TAAAACACTC
15768 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
1 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
* *
15818 TAGAAGCTTGTGGAAGAGTGTGGAATCTTTTGGAATATTCTGGAGATGT
1 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGT
15867 GTGGAACCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.27, C:0.08, G:0.32, T:0.32
Consensus pattern (50 bp):
TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
Found at i:15882 original size:50 final size:50
Alignment explanation
Indices: 15768--15882 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
15758 TAAAACACTC
* *
15768 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
1 TAGAACCTTATGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
* * * * *
15818 TAGAAGCTTGTGGAAGAGTGTGGAATCTTTTGGAATATTCTGGAGATGTG
1 TAGAACCTTATGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
*
15868 TGGAACCTTATGGAA
1 TAGAACCTTATGGAA
15883 TAATATAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.31
Consensus pattern (50 bp):
TAGAACCTTATGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
Found at i:20460 original size:50 final size:50
Alignment explanation
Indices: 20381--20496 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
20371 TAGAAGCTTT
* *
20381 TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAATCTTG
1 TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAACCTTA
* * * * **
20431 TGGAAGAGTGTGGAATCCTTTGGATTATTCTGGAGATGTGTGGAACCTTA
1 TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAACCTTA
*
20481 TGGAAGAGTATGGAAT
1 TGGAAGAGTGTGGAAT
20497 AATATGGAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.29, C:0.09, G:0.30, T:0.32
Consensus pattern (50 bp):
TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAACCTTA
Found at i:21745 original size:21 final size:21
Alignment explanation
Indices: 21721--21788 Score: 59
Period size: 25 Copynumber: 3.0 Consensus size: 21
21711 TTCATCACCC
21721 ATAATTTATTATTTTTATTTT
1 ATAATTTATTATTTTTATTTT
21742 ATAATTTAAATT-TTTTTATTTATT
1 ATAATTT--ATTATTTTTA-TT-TT
21766 ATTAAAGTTTA-TATTTTTATTTT
1 A-T-AA-TTTATTATTTTTATTTT
21789 CTGTCAACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
21 7 0.18
22 6 0.15
23 7 0.18
24 6 0.15
25 8 0.21
26 2 0.05
27 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (21 bp):
ATAATTTATTATTTTTATTTT
Found at i:26209 original size:12 final size:12
Alignment explanation
Indices: 26192--26224 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
26182 AAGTGTACTT
26192 CTAAATCACCCA
1 CTAAATCACCCA
*
26204 CTAAATCACCCT
1 CTAAATCACCCA
26216 CTAAATCAC
1 CTAAATCAC
26225 ATGCAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (12 bp):
CTAAATCACCCA
Found at i:26233 original size:12 final size:12
Alignment explanation
Indices: 26218--26260 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
26208 ATCACCCTCT
26218 AAATCACATGCA
1 AAATCACATGCA
* * *
26230 AAATCGCCTGCT
1 AAATCACATGCA
26242 AAATCACATGCA
1 AAATCACATGCA
26254 AAATCAC
1 AAATCAC
26261 CTGCTAAGCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.44, C:0.28, G:0.09, T:0.19
Consensus pattern (12 bp):
AAATCACATGCA
Found at i:26233 original size:24 final size:25
Alignment explanation
Indices: 26206--26267 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
26196 ATCACCCACT
26206 AAATCACCCT-CTAAATCACATGCA
1 AAATCACCCTGCTAAATCACATGCA
*
26230 AAATC-GCCTGCTAAATCACATGCA
1 AAATCACCCTGCTAAATCACATGCA
26254 AAATCA-CCTGCTAA
1 AAATCACCCTGCTAA
26268 GCCATTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.40, C:0.31, G:0.08, T:0.21
Consensus pattern (25 bp):
AAATCACCCTGCTAAATCACATGCA
Found at i:26248 original size:48 final size:48
Alignment explanation
Indices: 26192--26297 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
26182 AAGTGTACTT
* *
26192 CTAAATCACCCACTAAATCACCCT-CTAAATCACATGCAAAATCGCCTG
1 CTAAATCACCCACAAAATCA-CCTGCTAAACCACATGCAAAATCGCCTG
*** * ** *
26240 CTAAATCACATGCAAAATCACCTGCTAAGCCATTTGCTAAATCGCCTG
1 CTAAATCACCCACAAAATCACCTGCTAAACCACATGCAAAATCGCCTG
26288 CTAAATCACC
1 CTAAATCACC
26298 TGTAGGCGCT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 3 0.06
48 44 0.94
ACGTcount: A:0.36, C:0.33, G:0.08, T:0.23
Consensus pattern (48 bp):
CTAAATCACCCACAAAATCACCTGCTAAACCACATGCAAAATCGCCTG
Found at i:27055 original size:20 final size:20
Alignment explanation
Indices: 27030--27096 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
27020 TTTTCCCAAT
27030 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
27050 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
27071 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
27091 TCGCAA
1 TCGCAA
27097 CACGAATTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:27073 original size:21 final size:21
Alignment explanation
Indices: 27047--27114 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
27037 GCGAATAAGT
27047 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
27068 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
27088 AAATCGCAACACGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
27109 AAATCG
1 AAATCG
27115 TAATGCGATA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:27137 original size:41 final size:41
Alignment explanation
Indices: 27030--27122 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
27020 TTTTCCCAAT
*
27030 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
27071 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
*
27112 TCGTAATGCGA
1 TCGCAATGCGA
27123 TACTTACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
Found at i:27201 original size:20 final size:20
Alignment explanation
Indices: 27153--27205 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
27143 TAATACAAAA
* *
27153 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
27173 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
27193 TCGCAACGCGATT
1 TCGCAACGCGATT
27206 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:27782 original size:19 final size:19
Alignment explanation
Indices: 27722--27802 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
27712 TTCGAGAATG
27722 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
27742 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
27758 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
27775 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
27794 AAAATCGCA
1 AAAATCGCA
27803 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:27845 original size:20 final size:19
Alignment explanation
Indices: 27798--27929 Score: 132
Period size: 20 Copynumber: 7.1 Consensus size: 19
27788 GAAACCAAAA
*
27798 TCGCATTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
*
27816 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
27835 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
27855 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
27869 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
27889 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
27908 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
27928 TC
1 TC
27930 AACCAAAAGA
Statistics
Matches: 95, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.11
16 2 0.02
17 3 0.03
18 15 0.16
19 16 0.17
20 49 0.52
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:27887 original size:33 final size:34
Alignment explanation
Indices: 27840--27904 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
27830 TTATTTCGCG
**
27840 GTTGCGATTTTCA-TTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
27873 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
27905 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (34 bp):
GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
Found at i:29989 original size:42 final size:42
Alignment explanation
Indices: 29929--30021 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
29919 GCCCGACTCG
* * *
29929 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
29971 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
30013 ACTGTCATC
1 CCTATCATC
30022 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:31336 original size:14 final size:14
Alignment explanation
Indices: 31316--31352 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
31306 TATTGTTTAA
31316 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
31329 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
31344 TTGATTTGT
1 TTGATTTGT
31353 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:31552 original size:19 final size:19
Alignment explanation
Indices: 31530--31680 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
31520 CGAAATTAAA
31530 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
31549 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
31564 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
31582 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
31596 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
31615 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
31630 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
31648 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
31667 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
31681 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:31576 original size:33 final size:32
Alignment explanation
Indices: 31534--31660 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
31524 ATTAAATTCG
31534 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
31567 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
31600 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
31633 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
31661 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:31623 original size:66 final size:66
Alignment explanation
Indices: 31527--31659 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
31517 ACGCGAAATT
*
31527 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
31592 G
66 G
*
31593 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
31658 G
66 G
31659 A
1 A
31660 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:35417 original size:20 final size:20
Alignment explanation
Indices: 35392--35449 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
35382 ATTCATTTGA
35392 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
35412 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
35432 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
35450 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:35509 original size:19 final size:19
Alignment explanation
Indices: 35468--35535 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
35458 GAAATGAAAA
35468 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
35484 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
35501 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
35520 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
35536 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:37588 original size:20 final size:19
Alignment explanation
Indices: 37553--37619 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
37543 GAAACTTAAA
37553 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
37572 ATCGTAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * **
37592 ATTGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
37611 ATCGCAACG
1 ATCGCAACG
37620 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:37627 original size:14 final size:14
Alignment explanation
Indices: 37608--37665 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
37598 ATGCGAAATG
37608 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
37622 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
37638 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
37654 AAAATCGCAACG
1 AAAATCGCAACG
37666 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:37650 original size:32 final size:33
Alignment explanation
Indices: 37595--37670 Score: 136
Period size: 32 Copynumber: 2.3 Consensus size: 33
37585 AATGGCTATT
*
37595 GCAATGCGAAATGAAAATCGCAACGACAAAATC
1 GCAACGCGAAATGAAAATCGCAACGACAAAATC
37628 GCAACGCGAAATG-AAATCGCAACGACAAAATC
1 GCAACGCGAAATGAAAATCGCAACGACAAAATC
37660 GCAACGCGAAA
1 GCAACGCGAAA
37671 CACAAATCGC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 30 0.71
33 12 0.29
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (33 bp):
GCAACGCGAAATGAAAATCGCAACGACAAAATC
Found at i:37718 original size:14 final size:14
Alignment explanation
Indices: 37699--37756 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
37689 TTTCATTTCG
37699 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
37713 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
*
37729 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
37745 CGTTGCGATTTT
1 CGTTGCGATTTT
37757 CATTTCGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:37763 original size:33 final size:33
Alignment explanation
Indices: 37682--37772 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
37672 ACAAATCGCA
* *
37682 TTGCGATTTTCATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
37715 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
37747 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
37773 AGCCATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:37808 original size:20 final size:20
Alignment explanation
Indices: 37759--37811 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
37749 GCGATTTTCA
*
37759 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
37779 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
37799 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
37812 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:38313 original size:18 final size:18
Alignment explanation
Indices: 38287--38331 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
38277 GTCGATCAGA
*
38287 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
38305 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
38323 TGATGGCTC
1 TGATGGCTC
38332 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:39976 original size:22 final size:22
Alignment explanation
Indices: 39951--39994 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39941 GATTTAGATA
39951 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
39973 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
39995 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:40208 original size:20 final size:20
Alignment explanation
Indices: 40183--40276 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
40173 GATTATGTAT
40183 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
40203 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
40223 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
40244 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
40264 TATCGCATTGCGA
1 TATCGCGTTGCGA
40277 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:40248 original size:41 final size:41
Alignment explanation
Indices: 40203--40280 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
40193 CGAAAGTCAG
* * *
40203 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
40244 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
40281 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:40277 original size:20 final size:20
Alignment explanation
Indices: 40163--40277 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
40153 CGCTTTGAAA
*
40163 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
40184 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
40204 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
40224 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
40245 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
40265 ATCGCATTGCGAT
1 ATCGCATTGCGAT
40278 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:40296 original size:41 final size:41
Alignment explanation
Indices: 40203--40298 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
40193 CGAAAGTCAG
* * * ** *
40203 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
40244 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
40286 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
40299 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:41479 original size:21 final size:21
Alignment explanation
Indices: 41453--41496 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41443 CTTTTGTCTC
41453 AATTAGCCTTAGAATTAAGTT
1 AATTAGCCTTAGAATTAAGTT
41474 AATTAGCCTTAGAATTAAGTT
1 AATTAGCCTTAGAATTAAGTT
41495 AA
1 AA
41497 GTGTATAAAT
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:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (21 bp):
AATTAGCCTTAGAATTAAGTT
Found at i:41990 original size:29 final size:29
Alignment explanation
Indices: 41941--41996 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
41931 AAAATATCAT
*
41941 TCAAAAGTTTACAAATAAAATTGGAATGC
1 TCAAAAGTTTACAAATAAAATTAGAATGC
* * *
41970 TCAAAAGTTTAGAGATGAAATTAGAAT
1 TCAAAAGTTTACAAATAAAATTAGAAT
41997 AATTAAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (29 bp):
TCAAAAGTTTACAAATAAAATTAGAATGC
Found at i:44547 original size:3 final size:3
Alignment explanation
Indices: 44539--44616 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
44529 ACTTAAGTTC
44539 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44587 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44617 CTTACTATAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:47721 original size:40 final size:40
Alignment explanation
Indices: 47677--47758 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
47667 CCAAGTGCAT
*
47677 CTATTCTTTTGCTATGTTTAAATTAGAATTATTTAATTAA
1 CTATTATTTTGCTATGTTTAAATTAGAATTATTTAATTAA
47717 CTATTATTTTGCTATGTTTAAATTAGAATTATTTAATTAA
1 CTATTATTTTGCTATGTTTAAATTAGAATTATTTAATTAA
47757 CT
1 CT
47759 TAATATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (40 bp):
CTATTATTTTGCTATGTTTAAATTAGAATTATTTAATTAA
Found at i:49759 original size:30 final size:29
Alignment explanation
Indices: 49720--49805 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 29
49710 GATCATTACG
49720 TTATCATTTGTTACAAAATAGTCACTAACA
1 TTATCATTTGTTACAAAATA-TCACTAACA
* * *
49750 TTATTATTTGTGACAAAATTATCACTAACG
1 TTATCATTTGTTACAAAA-TATCACTAACA
*
49780 TTATCGTTTGTTACAAAATGATCACT
1 TTATCATTTGTTACAAAAT-ATCACT
49806 CGTCGTTAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.94
31 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (29 bp):
TTATCATTTGTTACAAAATATCACTAACA
Found at i:50690 original size:30 final size:30
Alignment explanation
Indices: 50653--50830 Score: 286
Period size: 30 Copynumber: 6.0 Consensus size: 30
50643 ACAATGAGTT
* *
50653 ACCATTTTGTAGCAAACGATAATGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
**
50683 ATTATTTTGTAAC-AACGATAACGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
50712 ACCATTTTGTAACAAACGATAACGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
50742 ACCATTTTGTAACAAACGATAACGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
*
50772 ACCATTTTGTAACAAACGATAAAGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
* *
50802 ATCATTTTGTAACAAACGATAATGTTAGT
1 ACCATTTTGTAACAAACGATAACGTTAGT
50831 AACAATTTGT
Statistics
Matches: 138, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
29 26 0.19
30 112 0.81
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (30 bp):
ACCATTTTGTAACAAACGATAACGTTAGTG
Found at i:57845 original size:31 final size:31
Alignment explanation
Indices: 57810--57886 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
57800 TTATGAGCAA
* *
57810 ACACTTTGATCTGACCCGACATGATAAGTAT
1 ACACTATGATCCGACCCGACATGATAAGTAT
57841 ACACTATGATCCGACCCGACATGATAAGTAT
1 ACACTATGATCCGACCCGACATGATAAGTAT
57872 ACACTATGATCCGAC
1 ACACTATGATCCGAC
57887 TCGATCCAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (31 bp):
ACACTATGATCCGACCCGACATGATAAGTAT
Found at i:64038 original size:25 final size:26
Alignment explanation
Indices: 64010--64060 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
64000 TCTTAAATCA
64010 TTTGATTTTTT-TTCTT-ATATACTTT
1 TTTGATTTTTTCTTCTTCATA-ACTTT
*
64035 TTTGTTTTTTTCTTCTTCATAACTTT
1 TTTGATTTTTTCTTCTTCATAACTTT
64061 CTCATTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 10 0.43
26 10 0.43
27 3 0.13
ACGTcount: A:0.14, C:0.12, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTGATTTTTTCTTCTTCATAACTTT
Found at i:67738 original size:13 final size:13
Alignment explanation
Indices: 67720--67744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67710 ATTTTAGGGA
67720 TTTCTCTTCTCCT
1 TTTCTCTTCTCCT
67733 TTTCTCTTCTCC
1 TTTCTCTTCTCC
67745 GCAACAGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCTCTTCTCCT
Done.