Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000860.1 Hibiscus syriacus cultivar Beakdansim tig00001666_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: 43652
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:760 original size:19 final size:19
Alignment explanation
Indices: 715--762 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
705 GTTGGACCCT
*
715 TAGTGCAACGGTACACTGA
1 TAGTGCATCGGTACACTGA
734 TAGTGCATCGGTACACTGA
1 TAGTGCATCGGTACACTGA
753 TAGTGCATCG
1 TAGTGCATCG
763 ATGCATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (19 bp):
TAGTGCATCGGTACACTGA
Found at i:883 original size:19 final size:19
Alignment explanation
Indices: 859--904 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
849 TATATATGGA
859 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
878 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
897 GTGCATCG
1 GTGCATCG
905 GTACACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:7219 original size:14 final size:14
Alignment explanation
Indices: 7202--7233 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
7192 CCTTCACCTC
7202 CGCCGAGGCACCAA
1 CGCCGAGGCACCAA
7216 CGCCGAGGCACCAA
1 CGCCGAGGCACCAA
7230 CGCC
1 CGCC
7234 TCAAGAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.47, G:0.28, T:0.00
Consensus pattern (14 bp):
CGCCGAGGCACCAA
Found at i:8328 original size:36 final size:36
Alignment explanation
Indices: 8279--8465 Score: 259
Period size: 36 Copynumber: 5.2 Consensus size: 36
8269 AAGTTTGCAT
* * *
8279 CGATTCAAGTCGAACGGAGGGAAGCATTGGCACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
* * *
8315 CGATTCAAATCGAACGGGAGGAAGCACCGACACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
* *
8351 CGATTCAAGT-GAACGGAAGGAAGAATCGGCACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
*
8386 CGATTCAAATCGAACGGAATGAAGCATCGGCACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
* * *
8422 TGATTCAAATCGAACGGAATGAAGCATCGCCACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
8458 CGATTCAA
1 CGATTCAA
8466 GTGTTCATCT
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 30 0.23
36 103 0.77
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.19
Consensus pattern (36 bp):
CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
Found at i:8396 original size:71 final size:72
Alignment explanation
Indices: 8279--8465 Score: 268
Period size: 71 Copynumber: 2.6 Consensus size: 72
8269 AAGTTTGCAT
* * *
8279 CGATTCAAGTCGAACGGAGGGAAGCATTGGCACTTCCGATTCAAATCGAACGGGAGGAAGCACCG
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAATCGAACGGAAGGAAGCACCG
8344 ACACTTC
66 ACACTTC
* * *
8351 CGATTCAAGT-GAACGGAAGGAAGAATCGGCACTTCCGATTCAAATCGAACGGAATGAAGCATCG
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAATCGAACGGAAGGAAGCACCG
*
8415 GCACTTC
66 ACACTTC
* * * *
8422 TGATTCAAATCGAACGGAATGAAGCATCGCCACTTCCGATTCAA
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAA
8466 GTGTTCATCT
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
71 62 0.61
72 40 0.39
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.19
Consensus pattern (72 bp):
CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAATCGAACGGAAGGAAGCACCG
ACACTTC
Found at i:21372 original size:30 final size:30
Alignment explanation
Indices: 21338--21410 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
21328 CCCGAAGGAC
* *
21338 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCATAAAGATCCTCGATAA
21368 CTATCCAAAGGTCATAAAGATCCTCGATAA
1 CTATCCAAAGGTCATAAAGATCCTCGATAA
* *
21398 CTGTCCATAGGTC
1 CTATCCAAAGGTC
21411 CCGAAGAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAAAGGTCATAAAGATCCTCGATAA
Found at i:21506 original size:63 final size:62
Alignment explanation
Indices: 21397--21520 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
21387 ATCCTCGATA
* *
21397 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
21459 ACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
21521 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 1 0.02
62 24 0.43
63 31 0.55
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:21516 original size:32 final size:31
Alignment explanation
Indices: 21396--21523 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
21386 GATCCTCGAT
* * * *
21396 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
21427 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
21458 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
21490 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
21521 AAC
1 AAC
21524 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:22923 original size:21 final size:21
Alignment explanation
Indices: 22899--22943 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
22889 CCATGTTCGT
* *
22899 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
22920 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
22941 TTG
1 TTG
22944 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:27123 original size:23 final size:23
Alignment explanation
Indices: 27093--27155 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
27083 TGTACTTCTG
*
27093 TGCTGAATCATTCGGCATTGTTT
1 TGCTGAATCATTCAGCATTGTTT
27116 TGCTGAATCATTCAGCATTGTTT
1 TGCTGAATCATTCAGCATTGTTT
* *
27139 TGTTGAATCAGTCAGCA
1 TGCTGAATCATTCAGCA
27156 CTGAATCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (23 bp):
TGCTGAATCATTCAGCATTGTTT
Found at i:29267 original size:30 final size:30
Alignment explanation
Indices: 29233--29297 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
29223 AGTTTTGCAA
* * *
29233 TGAACCGGTT-AAAAACCGGTAAAATCGGTG
1 TGAACCGGTTGAAAAA-CGGCAAAACCAGTG
29263 TGAACCGGTTGAAAAACGGCAAAACCAGTG
1 TGAACCGGTTGAAAAACGGCAAAACCAGTG
29293 TGAAC
1 TGAAC
29298 TGTCAGTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.17
Consensus pattern (30 bp):
TGAACCGGTTGAAAAACGGCAAAACCAGTG
Found at i:30404 original size:34 final size:34
Alignment explanation
Indices: 30360--30426 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
30350 TTAAAATCAA
* *
30360 ATCAAATCAAATTAAAAT-TCATTAGATTTGAGTT
1 ATCAAATCAAATCAAAATCT-ATTAGATTCGAGTT
*
30394 ATCAGATCAAATCAAAATCTATTAGATTCGAGT
1 ATCAAATCAAATCAAAATCTATTAGATTCGAGT
30427 CTCGTACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (34 bp):
ATCAAATCAAATCAAAATCTATTAGATTCGAGTT
Found at i:34966 original size:3 final size:3
Alignment explanation
Indices: 34958--34995 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
34948 ACCAAAATTA
34958 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
34996 AAAGGAGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:35805 original size:21 final size:21
Alignment explanation
Indices: 35780--35822 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
35770 AAGTGAAAGA
*
35780 GGGTTTAATTGTGATTTTAGT
1 GGGTTTAATTGTGATTCTAGT
35801 GGGTTTAATTGTGATTCTAGT
1 GGGTTTAATTGTGATTCTAGT
35822 G
1 G
35823 TTTCTCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (21 bp):
GGGTTTAATTGTGATTCTAGT
Found at i:38203 original size:24 final size:24
Alignment explanation
Indices: 38171--38229 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
38161 TTATTCTTTC
38171 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
38195 GCTTCAATTGAGTTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
38219 GCTTCAATTGA
1 GCTTCAATTGA
38230 ACTTCTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:38486 original size:30 final size:30
Alignment explanation
Indices: 38450--38515 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
38440 AGTGAACCGG
*
38450 CGGTTCAAACCGATTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGATTTTGCCGATTTTCAGC
** * *
38480 CGGTTCACCCCGGTTTTTCCGATTTTCAGC
1 CGGTTCAAACCGATTTTGCCGATTTTCAGC
38510 CGGTTC
1 CGGTTC
38516 TTCCGGTTCT
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:0.12, C:0.30, G:0.23, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTGCCGATTTTCAGC
Done.