Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000335.1 Hibiscus syriacus cultivar Beakdansim tig00000624_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: 66499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4299 original size:23 final size:24
Alignment explanation
Indices: 4250--4299 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
4240 TACCATATTG
* *
4250 AATTTCCTTTTAAACTTTTTTTAA
1 AATTTCCTTTTAAACTCTTCTTAA
4274 AATTT-CTTTTAAA-TCTTCTTAGA
1 AATTTCCTTTTAAACTCTTCTTA-A
4297 AAT
1 AAT
4300 CTTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 12 0.52
24 5 0.22
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (24 bp):
AATTTCCTTTTAAACTCTTCTTAA
Found at i:4801 original size:30 final size:30
Alignment explanation
Indices: 4743--4801 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4733 GTTTGGATCC
* *
4743 AAATTGAATCAAAATTTCATTGTGGTCCCT
1 AAATTGAATCAAAACTTCATTGTAGTCCCT
*
4773 AAATTTAATCAAAACTTCAATT-TAGTCCC
1 AAATTGAATCAAAACTTC-ATTGTAGTCCC
4802 CGAAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (30 bp):
AAATTGAATCAAAACTTCATTGTAGTCCCT
Found at i:4811 original size:30 final size:29
Alignment explanation
Indices: 4743--4811 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
4733 GTTTGGATCC
* * *
4743 AAATTGAATCAAAATTTCATTGTGGTCCCT
1 AAATT-AATCAAAACTTCATTGTAGTCCCG
4773 AAATTTAATCAAAACTTCAATT-TAGTCCCCG
1 AAA-TTAATCAAAACTTC-ATTGTAGT-CCCG
4804 AAATTAAT
1 AAATTAAT
4812 TTTAAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (29 bp):
AAATTAATCAAAACTTCATTGTAGTCCCG
Found at i:7122 original size:18 final size:18
Alignment explanation
Indices: 7099--7140 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
7089 GGTGATAGAA
7099 GCTAGGTTGAGACAAGTT
1 GCTAGGTTGAGACAAGTT
7117 GCTAGGTTGAGACAAGTT
1 GCTAGGTTGAGACAAGTT
*
7135 ACTAGG
1 GCTAGG
7141 ATTTCGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (18 bp):
GCTAGGTTGAGACAAGTT
Found at i:10571 original size:12 final size:12
Alignment explanation
Indices: 10556--10625 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
10546 GATACATTAC
10556 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
10568 CTGATTTCTGAT
1 CTGAATTCTGTT
**
10580 CTGGGTTCTGTT
1 CTGAATTCTGTT
* *
10592 ATG-ATATCTGAT
1 CTGAAT-TCTGTT
10604 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
10616 TTGATTTCTG
1 CTGAATTCTG
10626 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:10575 original size:48 final size:48
Alignment explanation
Indices: 10519--10623 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
10509 AAATATTTTA
* *
10519 TCTGATTTCCGA-CTTGAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTATGATATC-TGACCTGAATTCTGT
* ** *
10567 TCTGATTTCTGATCTGGGTTCTGTTATGATATCTGATCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTATGATATCTGACCTGAATTCTGT
*
10615 TTTGATTTC
1 TCTGATTTC
10624 TGATATCTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTATGATATCTGACCTGAATTCTGT
Found at i:10588 original size:24 final size:24
Alignment explanation
Indices: 10556--10627 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
10546 GATACATTAC
*
10556 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
** *
10580 CTGGGTTCTGTTATGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
*
10604 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
10628 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:12506 original size:75 final size:74
Alignment explanation
Indices: 12383--12530 Score: 251
Period size: 75 Copynumber: 2.0 Consensus size: 74
12373 AACATGACCT
* * *
12383 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTATTGTGGGTCACAATCATAGGGT
1 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGCACAACCATA-GGT
12448 GTAGCATTCC
65 GTAGCATTCC
*
12458 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGCACAGCCATAGGTG
1 CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGCACAACCATAGGTG
12523 TAGCATTC
66 TAGCATTC
12531 ATGTCTTCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 12 0.17
75 57 0.83
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.22
Consensus pattern (74 bp):
CTGATAGGAAAGTATGGAGACTTAAGACCAGGGTAGCCGAGTAGTGTGGGGCACAACCATAGGTG
TAGCATTCC
Found at i:25878 original size:2 final size:2
Alignment explanation
Indices: 25871--25915 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25861 TGGTGGTAAT
25871 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
25913 TA T
1 TA T
25916 TAATTACTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34675 original size:20 final size:20
Alignment explanation
Indices: 34638--34676 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34628 TTTCAATATG
*
34638 CATATATATATATTTCATGA
1 CATATATATATATGTCATGA
34658 CATATATA-ATCATGTCATG
1 CATATATATAT-ATGTCATG
34677 CACACATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (20 bp):
CATATATATATATGTCATGA
Found at i:35209 original size:14 final size:15
Alignment explanation
Indices: 35182--35210 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35172 ATATCATATA
35182 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
35197 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
35211 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:37287 original size:26 final size:27
Alignment explanation
Indices: 37228--37287 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
37218 CATAAGACCT
37228 TATAATACCATTAATGCTTATTATGAAA
1 TATAATACCATTAATGCTTATTAT-AAA
*
37256 TCATAATACTATTAATGCTTATTAT-AA
1 T-ATAATACCATTAATGCTTATTATAAA
37283 TATAA
1 TATAA
37288 AATTTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 3 0.10
28 1 0.03
29 22 0.73
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (27 bp):
TATAATACCATTAATGCTTATTATAAA
Found at i:39988 original size:14 final size:13
Alignment explanation
Indices: 39966--40041 Score: 50
Period size: 14 Copynumber: 5.8 Consensus size: 13
39956 GAGATTGGGT
*
39966 TGAATATAAACGAA
1 TGAACATAAAC-AA
*
39980 TGAACATAAATAAA
1 TGAACATAAA-CAA
39994 TGAACATAAACAGA
1 TGAACATAAACA-A
*
40008 TGTAC--AAA-AA
1 TGAACATAAACAA
* *
40018 CGAACATAAGCGAA
1 TGAACATAAAC-AA
40032 TGAACATAAA
1 TGAACATAAA
40042 TGAACATATT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
10 4 0.09
11 1 0.02
12 5 0.11
13 1 0.02
14 36 0.77
ACGTcount: A:0.58, C:0.12, G:0.13, T:0.17
Consensus pattern (13 bp):
TGAACATAAACAA
Found at i:40046 original size:24 final size:24
Alignment explanation
Indices: 39989--40049 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
39979 ATGAACATAA
*
39989 ATAAATGAACATAAACAGATGTAC
1 ATAAATGAACATAAACAGATGAAC
* * *
40013 AAAAACGAACATAAGC-GAATGAAC
1 ATAAATGAACATAAACAG-ATGAAC
40037 ATAAATGAACATA
1 ATAAATGAACATA
40050 TTACTGAACG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.16
Consensus pattern (24 bp):
ATAAATGAACATAAACAGATGAAC
Found at i:47877 original size:36 final size:36
Alignment explanation
Indices: 47830--47901 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
47820 GCATGGTTAC
47830 ATGGATTTTGCACTTATCTGTTTTAAATAAGGTGAT
1 ATGGATTTTGCACTTATCTGTTTTAAATAAGGTGAT
47866 ATGGATTTTGCACTTATCTGTTTTAAATAAGGTGAT
1 ATGGATTTTGCACTTATCTGTTTTAAATAAGGTGAT
47902 TTTTTGTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.44
Consensus pattern (36 bp):
ATGGATTTTGCACTTATCTGTTTTAAATAAGGTGAT
Found at i:48053 original size:23 final size:21
Alignment explanation
Indices: 48032--48074 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
48022 TTAAATTGAT
48032 AATTAAATATATTTAAATTTG
1 AATTAAATATATTTAAATTTG
*
48053 AATTATAATAATATTAAAATTT
1 AATTA-AAT-ATATTTAAATTT
48075 ACATAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATTAAATATATTTAAATTTG
Found at i:49506 original size:28 final size:28
Alignment explanation
Indices: 49470--49527 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
49460 AAAAACAAAC
49470 ATCATGAGAAAATTATCTACGAATACAA
1 ATCATGAGAAAATTATCTACGAATACAA
49498 ATCATGAGAAAATTATCTACGAATACAA
1 ATCATGAGAAAATTATCTACGAATACAA
49526 AT
1 AT
49528 AATTTATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (28 bp):
ATCATGAGAAAATTATCTACGAATACAA
Found at i:57704 original size:31 final size:32
Alignment explanation
Indices: 57635--57710 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
57625 TCTTTTGGTA
** **
57635 TTCGGGTCGGATTTTATTTTCAAAATTTTCGGG
1 TTCGGGTCGGA-TTTATTTAAAAAAAATTCGGG
*
57668 ATCGGGTCGGATTT-TTTAAAAAAAATTCGGG
1 TTCGGGTCGGATTTATTTAAAAAAAATTCGGG
57699 TTCGGGTCGGAT
1 TTCGGGTCGGAT
57711 CGAGTTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 24 0.65
32 3 0.08
33 10 0.27
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (32 bp):
TTCGGGTCGGATTTATTTAAAAAAAATTCGGG
Found at i:57753 original size:27 final size:29
Alignment explanation
Indices: 57705--57773 Score: 97
Period size: 27 Copynumber: 2.4 Consensus size: 29
57695 CGGGTTCGGG
*
57705 TCGGATCGAGTTCTTTTTAAGTTTGATAT
1 TCGGATCGAGTTCTTTTTAAGTGTGATAT
57734 TCGGATCGA-TT-TTTTTAAGTGTGATAT
1 TCGGATCGAGTTCTTTTTAAGTGTGATAT
* *
57761 TCGGGTCGGGTTC
1 TCGGATCGAGTTC
57774 GGGTTTAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.63
28 4 0.11
29 9 0.26
ACGTcount: A:0.17, C:0.12, G:0.26, T:0.45
Consensus pattern (29 bp):
TCGGATCGAGTTCTTTTTAAGTGTGATAT
Done.