Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000984.1 Hibiscus syriacus cultivar Beakdansim tig00001969_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: 53315
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:9918 original size:403 final size:405
Alignment explanation
Indices: 9136--9922 Score: 1061
Period size: 403 Copynumber: 1.9 Consensus size: 405
9126 CGCCACAAGT
*
9136 ATAGGAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATTAACTCACAA
1 ATAGGAACTATACGTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATTAACTCACAA
* *
9201 GAGTAATTTTAATATATGAGATGAGATGATTACAAATGATGGCAAGTCACTCTATTTATAAGAAT
66 GAGTAATTTTAATATAAGAGAT-AGATGAGTACAAATGATGGCAAGTCACTCTATTTATAAGAAT
* * * *
9266 GAGAGGGCTTGGCCGAATGGTTACATGATGCTTCGGCTAGATACATGACTTTATAAAGATACATA
130 GAGAGGGCATGGCCGAATGGTTACATGATGCTTCAGCTAGATACATGACTCTAGAAAGATACATA
** * * ** * *
9331 ATTCTTTAAAATGAAAGATTAAGTCATTTGGTCTTGTGATGGTTCGGCTAACCCTTCATAAAGGG
195 ACGCTTCAAAATAAAAGAACAAGTCATTAGGTCTTGTGATGGTTCAGCTAACCCTTCATAAAGGG
* * * *
9396 GCTTGATGATTCGGCTAAGTATGGGAAGGCATCTCCCTTGGCCGAATGGGCATGCTTTTTCATCT
260 ACTTGATAATTCGGCTAAGGATGGGAAGGCATCTCCCTTGGCCGAATGGGCATGCTTGTTCATCT
** * * * *
9461 TGGCACCATTTTCTCCCCATGGCCAAATGGTGATGTGCCTTCTCATTTTTGGCGCCAAAAGGTTC
325 TGGCACCAAATACTCCCCATGGCCAAATGGTGATGTACCTCCTCATTGTTGGCGCCAAAAGGTTC
9526 TCATGTGTGTGGCCAA
390 TCATGTGTGTGGCCAA
*
9542 ATAGGAACTATACGTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATTAACTCATAA
1 ATAGGAACTATACGTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATTAACTCACAA
* *
9607 GAGTATATTTTTATATAAGAGAT-GATGAGTACAAATGATGGCAAGTC-C-CTATTTATAGGAAA
66 GAGTA-ATTTTAATATAAGAGATAGATGAGTACAAATGATGGCAAGTCACTCTATTTATAAG-AA
* * * *
9669 TGAGA-GGCATGGCCGAATGGTTACATGATGTTTCAGCTAGATACATGTCTCTAGGAAGGTACAT
129 TGAGAGGGCATGGCCGAATGGTTACATGATGCTTCAGCTAGATACATGACTCTAGAAAGATACAT
* * *
9733 AACGCTTCAAAATAAAAGAACATGTC-TATAGG-CTTGTTGTTGGTTTAGCTAACCCTTCATAAA
194 AACGCTTCAAAATAAAAGAACAAGTCAT-TAGGTCTTG-TGATGGTTCAGCTAACCCTTCATAAA
*
9796 GGGACTTGATAATTTGGCTAAGGATGGGAAGGCATCTCCCTTGGCCGAATGGTG-ATGCTTGTTC
257 GGGACTTGATAATTCGGCTAAGGATGGGAAGGCATCTCCCTTGGCCGAATGG-GCATGCTTGTTC
* * ** * *
9860 ATCTTGG-AGTCAAATACTTCTCTTTGGCCGAATGGTGATGTACCTCCTTA-TGTTGGCGCCAAA
321 ATCTTGGCA-CCAAATAC-TCCCCATGGCCAAATGGTGATGTACCTCCTCATTGTTGGCGCCAAA
9923 TGCTCTCATG
Statistics
Matches: 332, Mismatches: 42, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
402 6 0.02
403 186 0.56
404 34 0.10
405 23 0.07
406 68 0.20
407 15 0.05
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (405 bp):
ATAGGAACTATACGTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATTAACTCACAA
GAGTAATTTTAATATAAGAGATAGATGAGTACAAATGATGGCAAGTCACTCTATTTATAAGAATG
AGAGGGCATGGCCGAATGGTTACATGATGCTTCAGCTAGATACATGACTCTAGAAAGATACATAA
CGCTTCAAAATAAAAGAACAAGTCATTAGGTCTTGTGATGGTTCAGCTAACCCTTCATAAAGGGA
CTTGATAATTCGGCTAAGGATGGGAAGGCATCTCCCTTGGCCGAATGGGCATGCTTGTTCATCTT
GGCACCAAATACTCCCCATGGCCAAATGGTGATGTACCTCCTCATTGTTGGCGCCAAAAGGTTCT
CATGTGTGTGGCCAA
Found at i:11892 original size:19 final size:18
Alignment explanation
Indices: 11870--11916 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
11860 AGTGAATAAT
11870 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
11889 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
11908 AATA-AAGAA
1 AATATAAGAA
11917 AAGGGATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:12359 original size:19 final size:20
Alignment explanation
Indices: 12318--12368 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12308 GAAACCCCTT
*
12318 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
12338 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
12357 TGAAGATACATG
1 TGAAAATACATG
12369 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:13296 original size:30 final size:31
Alignment explanation
Indices: 13257--13316 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
13247 ACATGCTGCC
**
13257 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
13288 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
13317 TAAATCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:15934 original size:11 final size:11
Alignment explanation
Indices: 15921--15971 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
15911 GAATTTGTCT
15921 TTTTC-TTTTC
1 TTTTCTTTTTC
15931 TTTTCTTCTTT-
1 TTTTCTT-TTTC
*
15942 TCTTCTTTTTC
1 TTTTCTTTTTC
*
15953 TCTTCTTTTTC
1 TTTTCTTTTTC
15964 -TTTCTTTT
1 TTTTCTTTT
15972 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 15 0.42
11 18 0.50
12 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:19611 original size:13 final size:13
Alignment explanation
Indices: 19589--19618 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19579 ACTAAAAACC
19589 TTTC-ACATACCT
1 TTTCAACATACCT
19601 TTTCAACATACCT
1 TTTCAACATACCT
19614 TTTCA
1 TTTCA
19619 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:22425 original size:30 final size:31
Alignment explanation
Indices: 22389--22448 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
22379 CTTAGTTTTA
22389 TATTATGTTTACATAT-GTTTTAGAT-TCATT
1 TATTATGTTTACATATCG-TTTAGATATCATT
*
22419 TATTATGTTTGCATATCGTTTAGATATCAT
1 TATTATGTTTACATATCGTTTAGATATCAT
22449 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCGTTTAGATATCATT
Found at i:23831 original size:19 final size:20
Alignment explanation
Indices: 23807--23846 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
23797 TATCCTTTCT
23807 TTATTTCATTTCATTA-TTA
1 TTATTTCATTTCATTACTTA
*
23826 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
23846 T
1 T
23847 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:24134 original size:11 final size:10
Alignment explanation
Indices: 24114--24157 Score: 61
Period size: 11 Copynumber: 4.2 Consensus size: 10
24104 ACTGGAGTGC
24114 AAAAAGAAAA
1 AAAAAGAAAA
*
24124 GAAAAGAAAA
1 AAAAAGAAAA
24134 AAAGAAGAAAA
1 AAA-AAGAAAA
24145 AAAGAAGAAAA
1 AAA-AAGAAAA
24156 AA
1 AA
24158 TTCAGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 11 0.35
11 20 0.65
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:25951 original size:11 final size:11
Alignment explanation
Indices: 25930--25959 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
25920 ATTTTTTTCA
25930 AAAACAAAAAAC
1 AAAA-AAAAAAC
25942 AAAAAAAAAAC
1 AAAAAAAAAAC
25953 AAAAAAA
1 AAAAAAA
25960 CCAAAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:35756 original size:19 final size:20
Alignment explanation
Indices: 35732--35771 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
35722 TATCCTTTCT
*
35732 TTATTTCATTTGATT-CTTA
1 TTATTTCATTTCATTACTTA
*
35751 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
35771 T
1 T
35772 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:42520 original size:19 final size:20
Alignment explanation
Indices: 42482--42521 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42472 GAATAATAAG
*
42482 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATCAAAAGAAATA
*
42502 ATAAG-AATCAAATGAAATA
1 ATAAGTAATCAAAAGAAATA
42521 A
1 A
42522 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (20 bp):
ATAAGTAATCAAAAGAAATA
Found at i:46678 original size:16 final size:16
Alignment explanation
Indices: 46657--46692 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
46647 GCTTGCCTTG
46657 TTTTGAATTCTTTTTC
1 TTTTGAATTCTTTTTC
46673 TTTTGAATTCTTTTTC
1 TTTTGAATTCTTTTTC
46689 TTTT
1 TTTT
46693 CTTCTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (16 bp):
TTTTGAATTCTTTTTC
Found at i:46708 original size:22 final size:23
Alignment explanation
Indices: 46683--46736 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
46673 TTTTGAATTC
46683 TTTTTCTTTTCTTCTTTTCTG-A
1 TTTTTCTTTTCTTCTTTTCTGTA
* * *
46705 TTTTTCTCTTCTTCTTTTTTGTC
1 TTTTTCTTTTCTTCTTTTCTGTA
46728 TTTTTCTTT
1 TTTTTCTTT
46737 CCTTTTGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTCTTTTCTTCTTTTCTGTA
Found at i:46967 original size:19 final size:19
Alignment explanation
Indices: 46932--46970 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
46922 GAATAATAAT
46932 ATAAGTAATGAAAGAAATA
1 ATAAGTAATGAAAGAAATA
46951 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAA-GAAATA
46970 A
1 A
46971 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (19 bp):
ATAAGTAATGAAAGAAATA
Found at i:49096 original size:23 final size:23
Alignment explanation
Indices: 49040--49097 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
49030 AAAATCAGCA
*
49040 AAGAAATA-AAAGCACTCAAAAG
1 AAGAAATAGAAAGCACTAAAAAG
* *
49062 AAGAAATTGAAAGCACTAAAAAT
1 AAGAAATAGAAAGCACTAAAAAG
*
49085 AAGAAAAAGAAAG
1 AAGAAATAGAAAG
49098 AAACAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.23
23 23 0.77
ACGTcount: A:0.66, C:0.09, G:0.16, T:0.10
Consensus pattern (23 bp):
AAGAAATAGAAAGCACTAAAAAG
Found at i:51841 original size:13 final size:12
Alignment explanation
Indices: 51823--51852 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
51813 TGGCTAAAGA
51823 TGAAAAGGTATG
1 TGAAAAGGTATG
51835 TTGAAAAGGTATG
1 -TGAAAAGGTATG
51848 TGAAA
1 TGAAA
51853 TGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAAAGGTATG
Done.