Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003793.1 Hibiscus syriacus cultivar Beakdansim tig00008116_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: 59429
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:9459 original size:2 final size:2
Alignment explanation
Indices: 9454--9483 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9444 GAAGAGAGGT
9454 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
9484 CACACACGAG
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):
TA
Found at i:10053 original size:26 final size:26
Alignment explanation
Indices: 10020--10097 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
10010 TTTATCCTTC
10020 TTCTTCCTCTTCGTTTTCTTCTTCTT
1 TTCTTCCTCTTCGTTTTCTTCTTCTT
* *
10046 TTCTTCCT-TCTCGTTGTCTTTCTTCAT
1 TTCTTCCTCT-TCGTTTTC-TTCTTCTT
* *
10073 TTCGGT-CTCTTCGTTTTCATCTTCT
1 TTC-TTCCTCTTCGTTTTCTTCTTCT
10098 AGTCGTGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
25 1 0.02
26 20 0.48
27 19 0.45
28 2 0.05
ACGTcount: A:0.03, C:0.29, G:0.08, T:0.60
Consensus pattern (26 bp):
TTCTTCCTCTTCGTTTTCTTCTTCTT
Found at i:10468 original size:21 final size:21
Alignment explanation
Indices: 10430--10470 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10420 TTTATCTTTG
*
10430 TCTTCATGCTTATCCTCTCCT
1 TCTTCATGCTTATACTCTCCT
10451 TCTTCATGCTTCA-ACTCTCC
1 TCTTCATGCTT-ATACTCTCC
10471 CGTCTGTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.39, G:0.05, T:0.44
Consensus pattern (21 bp):
TCTTCATGCTTATACTCTCCT
Found at i:22526 original size:29 final size:29
Alignment explanation
Indices: 22493--22570 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
22483 AAAAAATTTG
22493 ATTAATTTGGTTCGATTAATAATTTTCAA
1 ATTAATTTGGTTCGATTAATAATTTTCAA
* * *
22522 ATTAATTCGATTCG-GTAATAATTTTCAA
1 ATTAATTTGGTTCGATTAATAATTTTCAA
* *
22550 ATAAATTTTGGTTCAATTAAT
1 ATTAA-TTTGGTTCGATTAAT
22571 CGGACCGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 17 0.44
29 18 0.46
30 4 0.10
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (29 bp):
ATTAATTTGGTTCGATTAATAATTTTCAA
Found at i:22670 original size:24 final size:24
Alignment explanation
Indices: 22643--22688 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
22633 ATTCGGTTCA
* *
22643 GTTAATAATTTTTAAATTAATTCG
1 GTTAATAATTTTCAAATAAATTCG
22667 GTTAATAATTTTCAAATAAATT
1 GTTAATAATTTTCAAATAAATT
22689 TTGGTTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
GTTAATAATTTTCAAATAAATTCG
Found at i:22917 original size:29 final size:29
Alignment explanation
Indices: 22873--22936 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
22863 AAAAAATTGG
* *
22873 TTAATTTGGTTTAGTT-ATAAATTTTCAAA
1 TTAATTCGGTTCAGTTAAT-AATTTTCAAA
22902 TTAATTCGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
22931 TAAATT
1 TTAATT
22937 TTGGTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (29 bp):
TTAATTCGGTTCAGTTAATAATTTTCAAA
Found at i:23069 original size:67 final size:68
Alignment explanation
Indices: 22945--23091 Score: 233
Period size: 67 Copynumber: 2.2 Consensus size: 68
22935 TTTTGGTTTG
* * *
22945 ATTAACCGAACCGAATTAACCGATTTTTTTCTTTAATCGTTAATCGAACTAAAATTTATTTGAAA
1 ATTAACCGAACCGAATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAA
23010 ATT
66 ATT
* *
23013 ATTAACCGAACCGAATTAACCGA-TTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTTAAA
1 ATTAACCGAACCGAATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAA
23077 ATT
66 ATT
*
23080 ATTAACCAAACC
1 ATTAACCGAACC
23092 AAACAATATC
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 50 0.68
68 23 0.32
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (68 bp):
ATTAACCGAACCGAATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAA
ATT
Found at i:24961 original size:30 final size:29
Alignment explanation
Indices: 24926--24983 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
24916 ATTAACAGCT
24926 GGTGGTTTGATTGAATT-AATTAAATAGTTG
1 GGTGGTTTGATTG-ATTCAATTAAA-AGTTG
24956 GGTGGTTTGATTGATTCAATTAAAAGTT
1 GGTGGTTTGATTGATTCAATTAAAAGTT
24984 CGATAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (29 bp):
GGTGGTTTGATTGATTCAATTAAAAGTTG
Found at i:25229 original size:34 final size:33
Alignment explanation
Indices: 25180--25246 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
25170 TATATGTTAT
25180 GTTTAAACTCAAAATCTTAAAAAAA-AATAATAA
1 GTTTAAACTCAAAATC-TAAAAAAATAATAATAA
*
25213 GTTTCAAACTCGAAATCTAAAAAAATAATAATAA
1 GTTT-AAACTCAAAATCTAAAAAAATAATAATAA
25247 ATTTTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.27
Consensus pattern (33 bp):
GTTTAAACTCAAAATCTAAAAAAATAATAATAA
Found at i:25515 original size:20 final size:20
Alignment explanation
Indices: 25475--25515 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25465 ACGAACGGAT
* **
25475 GTAAACGAACATAAATGAAC
1 GTAAACGAACACAAAAAAAC
25495 GTAAACGAACACAAAAAAAC
1 GTAAACGAACACAAAAAAAC
25515 G
1 G
25516 AACGCAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.17, G:0.15, T:0.10
Consensus pattern (20 bp):
GTAAACGAACACAAAAAAAC
Found at i:25526 original size:13 final size:14
Alignment explanation
Indices: 25497--25528 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25487 AAATGAACGT
25497 AAACGAACACAAAA
1 AAACGAACACAAAA
*
25511 AAACGAACGCAAAA
1 AAACGAACACAAAA
25525 AAAC
1 AAAC
25529 ACAATAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.22, G:0.09, T:0.00
Consensus pattern (14 bp):
AAACGAACACAAAA
Found at i:25547 original size:10 final size:10
Alignment explanation
Indices: 25532--25570 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
25522 AAAAAACACA
25532 ATAAATGAAC
1 ATAAATGAAC
*
25542 ATAAATAAAC
1 ATAAATGAAC
* *
25552 TTAAACGAAC
1 ATAAATGAAC
25562 ATAAATGAA
1 ATAAATGAA
25571 AATATATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.21
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:25804 original size:14 final size:14
Alignment explanation
Indices: 25740--25792 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
25730 TGCGCAAAAT
*
25740 ATAAATGAACGCAC
1 ATAAATGAACGAAC
* *
25754 ATAAACGAACAAAC
1 ATAAATGAACGAAC
25768 ATAAATGAACGAAC
1 ATAAATGAACGAAC
*
25782 ATAAACGAACG
1 ATAAATGAACG
25793 TAAATGAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.57, C:0.19, G:0.13, T:0.11
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:25839 original size:13 final size:13
Alignment explanation
Indices: 25821--25845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25811 ATTTGTTCAT
25821 CTTCGTTCATTTA
1 CTTCGTTCATTTA
25834 CTTCGTTCATTT
1 CTTCGTTCATTT
25846 GATTAAACGA
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:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
CTTCGTTCATTTA
Found at i:28715 original size:24 final size:24
Alignment explanation
Indices: 28683--28734 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
28673 TACGATCTTT
28683 GAATCATATAACAGCAAATAAGAA
1 GAATCATATAACAGCAAATAAGAA
*
28707 GAATCATATAACAGCAAATAAGAT
1 GAATCATATAACAGCAAATAAGAA
28731 GAAT
1 GAAT
28735 ATTTCTCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.12, G:0.13, T:0.19
Consensus pattern (24 bp):
GAATCATATAACAGCAAATAAGAA
Found at i:29664 original size:29 final size:28
Alignment explanation
Indices: 29602--29676 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 28
29592 ATATTGTACC
*
29602 ATTTAAT-TTATAACTCTAAACCCTAAA
1 ATTTAATCTCATAACTCTAAACCCTAAA
***
29629 GCATAATCTCATATACTCTAAACCCTAAA
1 ATTTAATCTCATA-ACTCTAAACCCTAAA
29658 ATTTAATCTC-TAACT-TAAA
1 ATTTAATCTCATAACTCTAAA
29677 ACTCTCAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 4 0.10
27 7 0.18
28 6 0.15
29 22 0.56
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (28 bp):
ATTTAATCTCATAACTCTAAACCCTAAA
Found at i:42733 original size:291 final size:291
Alignment explanation
Indices: 42204--42791 Score: 1113
Period size: 291 Copynumber: 2.0 Consensus size: 291
42194 CTTACCTCGG
*
42204 AAGCACAAATTTCTATAACTTAAGCTTTTATCTCTAAGAAGAGATAAAATTAGTAGCCAAAATTA
1 AAGCACAAATTTCTATAACTTAAGCTTTTATCTCTAAGAAGAGAGAAAATTAGTAGCCAAAATTA
42269 CTAGTTACCACAGTTTAAAGTTTGAATATTTTGCCTCGTTGCTTCTGACTCTTCATTTTACTTGA
66 CTAGTTACCACAGTTTAAAGTTTGAATATTTTGCCTCGTTGCTTCTGACTCTTCATTTTACTTGA
*
42334 GGTATTTACATAAAAATACTTGTGTTTGACATATATTTATATAGCTATATTTGACACACTTTTGT
131 GGTATTTACATAAAAATACTTGTGTTTGACATATATTTATATACCTATATTTGACACACTTTTGT
*
42399 ACGAGTAACATAGCTTCTAAGCTTCAGTAACATTAGTGGTCAATTCCTTTATCAGGCTGAAGCAA
196 ACGAGTAACATAGCTTCTAAGCTTCAGTAACATTAGCGGTCAATTCCTTTATCAGGCTGAAGCAA
42464 CCATTTCAAAACTGACAGAAGAGAGGAGAAT
261 CCATTTCAAAACTGACAGAAGAGAGGAGAAT
42495 AAGCACAAATTTCTATAACTTAAGCTTTTATCTCTAAGAAGAGAGAAAATTAGTAGCCAAAATTA
1 AAGCACAAATTTCTATAACTTAAGCTTTTATCTCTAAGAAGAGAGAAAATTAGTAGCCAAAATTA
*
42560 CTAGTTACCACAGTTTAAAGTTTGAATATTTTGCCTTGTTGCTTCTGACTCTTCATTTTACTTGA
66 CTAGTTACCACAGTTTAAAGTTTGAATATTTTGCCTCGTTGCTTCTGACTCTTCATTTTACTTGA
*
42625 GGTGTTTACATAAAAATACTTGTGTTTGACATATATTTATATACCTATATTTGACACACTTTTGT
131 GGTATTTACATAAAAATACTTGTGTTTGACATATATTTATATACCTATATTTGACACACTTTTGT
*
42690 ATGAGTAACATAGCTTCTAAGCTTCAGTAACATTAGCGGTCAATTCCTTTATCAGGCTGAAGCAA
196 ACGAGTAACATAGCTTCTAAGCTTCAGTAACATTAGCGGTCAATTCCTTTATCAGGCTGAAGCAA
*
42755 CCATTTCAAAACTGACAGAAGAGAGGAGGAT
261 CCATTTCAAAACTGACAGAAGAGAGGAGAAT
42786 AAGCAC
1 AAGCAC
42792 CCGAGAACGA
Statistics
Matches: 290, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 290 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (291 bp):
AAGCACAAATTTCTATAACTTAAGCTTTTATCTCTAAGAAGAGAGAAAATTAGTAGCCAAAATTA
CTAGTTACCACAGTTTAAAGTTTGAATATTTTGCCTCGTTGCTTCTGACTCTTCATTTTACTTGA
GGTATTTACATAAAAATACTTGTGTTTGACATATATTTATATACCTATATTTGACACACTTTTGT
ACGAGTAACATAGCTTCTAAGCTTCAGTAACATTAGCGGTCAATTCCTTTATCAGGCTGAAGCAA
CCATTTCAAAACTGACAGAAGAGAGGAGAAT
Found at i:57652 original size:34 final size:35
Alignment explanation
Indices: 57568--57665 Score: 148
Period size: 35 Copynumber: 2.9 Consensus size: 35
57558 CGTCACGTCC
* *
57568 AGTAAGGCCCTGAG--CACAGCCGATGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCAGTA
*
57601 AGTAAGGCCCTGAGCACACAGCCAAGGAACCAGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCAGTA
57636 AGTAAGG-CCTGAGCACACAGCCGAGGAACC
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
57666 TCCAGGTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
33 14 0.24
34 22 0.37
35 23 0.39
ACGTcount: A:0.34, C:0.29, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCAGTA
Found at i:57765 original size:24 final size:24
Alignment explanation
Indices: 57755--57869 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
57745 CATAATTCAC
* *
57755 GTCAAGTATCATATCA-AAGTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAT
* *
57779 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
57803 GTCAAGTATCAAATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
57827 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
57851 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
57870 ATCAAATCGA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 2 0.02
24 75 0.93
25 4 0.05
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:57886 original size:48 final size:48
Alignment explanation
Indices: 57731--57886 Score: 122
Period size: 48 Copynumber: 3.2 Consensus size: 48
57721 AACGGAATAT
* * * * * * *
57731 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCA-AAGTCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAAATCAGAA-TCCAA
* * *
57779 GTCAAGTAA-CAGATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAT
1 ATC-AGAAATCAGATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAA
* * * *
57827 GTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAAATCAG-AATCCAA
57875 ATC-GAAAATCAG
1 ATCAG-AAATCAG
57887 GTAAATATTC
Statistics
Matches: 87, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
47 4 0.05
48 75 0.86
49 8 0.09
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAA
Found at i:59417 original size:30 final size:29
Alignment explanation
Indices: 59317--59417 Score: 82
Period size: 30 Copynumber: 3.3 Consensus size: 29
59307 TCAATTGCTT
59317 TCTTGAACACTCTCTGATCTTGAAACGGTTC
1 TCTT-AACACTCTCTGATCTTGAAAC-GTTC
*
59348 TCTTAACAGACT-TCTAGTATCATTCACAAC--TC
1 TCTTAAC--ACTCTCT-G-ATC-TTGA-AACGTTC
*
59380 TCCTAACACTCTCTGATCTTGAAACTGTTC
1 TCTTAACACTCTCTGATCTTGAAAC-GTTC
59410 TCTTAACA
1 TCTTAACA
59418 GACTTCTAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
27 3 0.05
28 3 0.05
29 3 0.05
30 16 0.29
31 10 0.18
32 12 0.21
33 3 0.05
34 3 0.05
35 3 0.05
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.36
Consensus pattern (29 bp):
TCTTAACACTCTCTGATCTTGAAACGTTC
Done.