Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006686.1 Hibiscus syriacus cultivar Beakdansim tig00016606_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: 47318
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:6038 original size:3 final size:3
Alignment explanation
Indices: 6032--6066 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
6022 CATCATCATC
*
6032 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6067 CTGATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7417 original size:191 final size:194
Alignment explanation
Indices: 7055--7447 Score: 731
Period size: 191 Copynumber: 2.0 Consensus size: 194
7045 TTTGGATTTC
*
7055 TTTTTATGTTTTATTTATGAGCCAAATTATTTATCCGTTTTGATTTGATGGTATGTATGTATATA
1 TTTTTAAGTTTTATTTATGAGCCAAATTATTTATCCGTTTTGATTTGATGGTATGTATGTATATA
7120 TGTATCATGAGCGGATGCACCAGGCCCCCTAGGAGTCAAGTGCATCCCCATTATTTAGGAAAAAA
66 TGTATCATGAGCGGATGCACCAGGCCCCCTAGGAGTCAAGTGCATCCCCATTATTTAGGAAAAAA
7185 ATTGAAATTTAGTATAATATATCAAAGAAAAATGAAAAAAAATAAAAAATTTTGCACCCCATTA
131 ATTGAAATTTAGTATAATATATCAAAGAAAAATGAAAAAAAATAAAAAATTTTGCACCCCATTA
7249 TTTTTAAGTTTTATTTATGAGCCAAATTATTTATCCGTTTTTGATTTGATGGTATGTATGTATAT
1 TTTTTAAGTTTTATTTATGAGCCAAATTATTTATCCG-TTTTGATTTGATGGTATGTATGTATAT
*
7314 ATGTATCATGAGCGGATGTACCAGG-CCCCTA-G-GTCAAGTGCATCCCCATTATTTAGG-AAAA
65 ATGTATCATGAGCGGATGCACCAGGCCCCCTAGGAGTCAAGTGCATCCCCATTATTTAGGAAAAA
7375 AATTGAAATTTAGTATAATATATCAAAGAAAAATGAAAAAAAATAAAAAATTTTGCACCCCATTA
130 AATTGAAATTTAGTATAATATATCAAAGAAAAATGAAAAAAAATAAAAAATTTTGCACCCCATTA
7440 TTTTTAAG
1 TTTTTAAG
7448 AAAAGAATAT
Statistics
Matches: 196, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
191 77 0.39
192 25 0.13
193 1 0.01
194 42 0.21
195 51 0.26
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (194 bp):
TTTTTAAGTTTTATTTATGAGCCAAATTATTTATCCGTTTTGATTTGATGGTATGTATGTATATA
TGTATCATGAGCGGATGCACCAGGCCCCCTAGGAGTCAAGTGCATCCCCATTATTTAGGAAAAAA
ATTGAAATTTAGTATAATATATCAAAGAAAAATGAAAAAAAATAAAAAATTTTGCACCCCATTA
Found at i:7497 original size:2 final size:2
Alignment explanation
Indices: 7490--7559 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
7480 AAATTTATGG
7490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7560 GAACATATGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17607 original size:43 final size:43
Alignment explanation
Indices: 17526--17609 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
17516 TTAATAATAT
* *
17526 TTTTAATATGTTAGTTTGATGTATTTGTGGATTATTACTTTGG
1 TTTTAATATGTTAATTTGATGTATTTGTAGATTATTACTTTGG
* * * *
17569 TTTTCATATGTTAATTTGGTGTATTTGTAGTTTGTTACTTT
1 TTTTAATATGTTAATTTGATGTATTTGTAGATTATTACTTT
17610 AGAGTTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.19, C:0.04, G:0.19, T:0.58
Consensus pattern (43 bp):
TTTTAATATGTTAATTTGATGTATTTGTAGATTATTACTTTGG
Found at i:18589 original size:33 final size:31
Alignment explanation
Indices: 18496--18569 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
18486 TATTTTTAGA
*
18496 AAAAGTT-GAGTATTTAATTGCACCAAAAAAT
1 AAAAGTTGGA-TACTTAATTGCACCAAAAAAT
* * *
18527 GAAATTTGGATACTTAAATGCACCAAAAAAT
1 AAAAGTTGGATACTTAATTGCACCAAAAAAT
18558 AAAAGTTGGATA
1 AAAAGTTGGATA
18570 GAGCTAATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (31 bp):
AAAAGTTGGATACTTAATTGCACCAAAAAAT
Found at i:18635 original size:17 final size:17
Alignment explanation
Indices: 18613--18664 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 17
18603 AATGAACCAT
18613 TAAAAAAGTTATGTACC
1 TAAAAAAGTTATGTACC
* *
18630 T-AAAAAG--A-CTA-T
1 TAAAAAAGTTATGTACC
18642 TAAAAAAGTTATGTACC
1 TAAAAAAGTTATGTACC
18659 TAAAAA
1 TAAAAA
18665 GACTTAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 1 0.04
13 8 0.31
14 1 0.04
15 1 0.04
16 8 0.31
17 7 0.27
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (17 bp):
TAAAAAAGTTATGTACC
Found at i:18636 original size:16 final size:16
Alignment explanation
Indices: 18615--18665 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
18605 TGAACCATTA
18615 AAAAAGTTATGTACCT
1 AAAAAGTTATGTACCT
*
18631 AAAAAGACTAT-TA---
1 AAAAAG-TTATGTACCT
18644 AAAAAGTTATGTACCT
1 AAAAAGTTATGTACCT
18660 AAAAAG
1 AAAAAG
18666 ACTTAAATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
16 14 0.50
17 3 0.11
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (16 bp):
AAAAAGTTATGTACCT
Found at i:18668 original size:29 final size:29
Alignment explanation
Indices: 18585--18668 Score: 118
Period size: 29 Copynumber: 2.9 Consensus size: 29
18575 AATTGCAACA
* *
18585 AAAAAAGTTA-GATACCT-AAATGAACCATT
1 AAAAAAGTTATG-TACCTAAAAAG-ACTATT
18614 AAAAAAGTTATGTACCTAAAAAGACTATT
1 AAAAAAGTTATGTACCTAAAAAGACTATT
18643 AAAAAAGTTATGTACCTAAAAAGACT
1 AAAAAAGTTATGTACCTAAAAAGACT
18669 TAAATGCACC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.25
Consensus pattern (29 bp):
AAAAAAGTTATGTACCTAAAAAGACTATT
Found at i:24473 original size:5 final size:5
Alignment explanation
Indices: 24463--24493 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
24453 TGACTTAGAA
*
24463 ACCCG ACCCG ACCTG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
24494 AATAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.55, G:0.19, T:0.03
Consensus pattern (5 bp):
ACCCG
Found at i:28676 original size:30 final size:30
Alignment explanation
Indices: 28640--28698 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
28630 AGATCTAATA
* *
28640 CTAATTTGACCTTAAACTTTACATAAAATG
1 CTAATTTAACCCTAAACTTTACATAAAATG
* *
28670 CTAATTTAACCCTAAATTTTAGATAAAAT
1 CTAATTTAACCCTAAACTTTACATAAAAT
28699 ATTAGTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.37
Consensus pattern (30 bp):
CTAATTTAACCCTAAACTTTACATAAAATG
Found at i:31954 original size:20 final size:20
Alignment explanation
Indices: 31929--31966 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31919 TTTAGCTCTC
*
31929 GGAATATAATATTACCAGTG
1 GGAATATAACATTACCAGTG
31949 GGAATATAACATTACCAG
1 GGAATATAACATTACCAG
31967 GAATATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
GGAATATAACATTACCAGTG
Found at i:31971 original size:17 final size:18
Alignment explanation
Indices: 31929--31972 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
31919 TTTAGCTCTC
*
31929 GGAATATAATATTACCAGTG
1 GGAATATAACATTACCA--G
31949 GGAATATAACATTACCA-
1 GGAATATAACATTACCAG
31966 GGAATAT
1 GGAATAT
31973 GATTACTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
20 16 0.70
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.27
Consensus pattern (18 bp):
GGAATATAACATTACCAG
Found at i:33417 original size:18 final size:17
Alignment explanation
Indices: 33389--33424 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
33379 CTTTAAAAAT
33389 TTTAAATTTTTATATAA
1 TTTAAATTTTTATATAA
*
33406 TTTAAATATTTTTTATAA
1 TTTAAAT-TTTTATATAA
33424 T
1 T
33425 ATTTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAATTTTTATATAA
Found at i:35437 original size:16 final size:16
Alignment explanation
Indices: 35416--35502 Score: 58
Period size: 16 Copynumber: 5.4 Consensus size: 16
35406 TTTAAAAATA
35416 ATTTTAAATATATATT
1 ATTTTAAATATATATT
*
35432 ATTTT--ATAGTCATTTT
1 ATTTTAAATA-T-ATATT
35448 ACTTTATTAAAATATATATT
1 A--TT-TT-AAATATATATT
35468 A-TTTAAATAT-TATT
1 ATTTTAAATATATATT
**
35482 -TTAAAAATATATATT
1 ATTTTAAATATATATT
35497 ATTTTA
1 ATTTTA
35503 TAGTCGTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 22
0.66 0.07 0.27
Matches are distributed among these distances:
14 14 0.26
15 11 0.20
16 15 0.28
17 1 0.02
18 2 0.04
19 2 0.04
20 5 0.09
21 1 0.02
22 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
ATTTTAAATATATATT
Found at i:35467 original size:36 final size:35
Alignment explanation
Indices: 35421--35524 Score: 112
Period size: 36 Copynumber: 3.0 Consensus size: 35
35411 AAATAATTTT
35421 AAATATATATTATTTTATAGTCATTTTACTTTATTA
1 AAATATATATTATTTTATAGTCATTTTA-TTTATTA
* *
35457 AAATATATATTA-TTTA-A---ATATTATTT-TAA
1 AAATATATATTATTTTATAGTCATTTTATTTATTA
35486 AAATATATATTATTTTATAGTCGTATTTTATATTATTA
1 AAATATATATTATTTTATAGTC--ATTTTAT-TTATTA
35524 A
1 A
35525 TATCTAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
29 14 0.25
30 7 0.13
31 6 0.11
34 1 0.02
35 4 0.07
36 18 0.33
37 2 0.04
38 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (35 bp):
AAATATATATTATTTTATAGTCATTTTATTTATTA
Found at i:35475 original size:15 final size:15
Alignment explanation
Indices: 35451--35499 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
35441 TCATTTTACT
35451 TTATTAAAATATATA
1 TTATTAAAATATATA
*
35466 TTATTTAAATAT-TA
1 TTATTAAAATATATA
35480 TT-TTAAAAATATATA
1 TTATT-AAAATATATA
35495 TTATT
1 TTATT
35500 TTATAGTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 10 0.34
15 15 0.52
16 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTAAAATATATA
Found at i:35513 original size:31 final size:30
Alignment explanation
Indices: 35421--35515 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 30
35411 AAATAATTTT
*
35421 AAATATATATTATTTTATAGTCATTTTACTTTATTA
1 AAATATATATTATTTTATAGTC----TA-TTT-TAA
*
35457 AAATATATATTATTTAAATA-T-TATTTTAA
1 AAATATATATTATTT-TATAGTCTATTTTAA
35486 AAATATATATTATTTTATAGTCGTATTTTA
1 AAATATATATTATTTTATAGTC-TATTTTA
35516 TATTATTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 3 0.06
29 18 0.35
30 3 0.06
31 9 0.17
36 16 0.31
37 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (30 bp):
AAATATATATTATTTTATAGTCTATTTTAA
Found at i:35527 original size:65 final size:62
Alignment explanation
Indices: 35404--35524 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 62
35394 ATATTATTAA
35404 TATTTAAAAATAATTTTAAATATATATTATTTTATAGTCATTTTACTTTATTAAAATATATAT
1 TATTTAAAAATAATTTTAAATATATATTATTTTATAGTCATTTTACTTTATT-AAATATATAT
* *
35467 TATTTAAATATTATTTTAAAAATATATATTATTTTATAGTCGTATTTTA-TATTATTAA
1 TATTTAAAAATAATTTT--AAATATATATTATTTTATAGTC--ATTTTACT-TTATTAA
35525 TATCTAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
63 15 0.29
65 22 0.43
66 3 0.06
67 11 0.22
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (62 bp):
TATTTAAAAATAATTTTAAATATATATTATTTTATAGTCATTTTACTTTATTAAATATATAT
Found at i:37814 original size:15 final size:15
Alignment explanation
Indices: 37794--37830 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
37784 CTCTTATTCT
37794 TTTTTTAATATTTTA
1 TTTTTTAATATTTTA
*
37809 TTTTTTAATGTTTTA
1 TTTTTTAATATTTTA
*
37824 ATTTTTA
1 TTTTTTA
37831 TTTAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTTTAATATTTTA
Found at i:40354 original size:29 final size:29
Alignment explanation
Indices: 40297--40354 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
40287 AGAAATGTCT
* *
40297 CATTTTGAAAACACAATTCTTTTTAAGAA
1 CATTTTGAAAACACAACTCTTTTCAAGAA
*
40326 CATTTTGAAAACACAACTCTTTTCGAGAA
1 CATTTTGAAAACACAACTCTTTTCAAGAA
40355 TTTATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (29 bp):
CATTTTGAAAACACAACTCTTTTCAAGAA
Done.