Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007919.1 Hibiscus syriacus cultivar Beakdansim tig00110322_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: 60707
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:8318 original size:2 final size:2
Alignment explanation
Indices: 8301--8357 Score: 89
Period size: 2 Copynumber: 28.5 Consensus size: 2
8291 ATAATTTGTT
*
8301 TA TA TG TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8344 TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA T
8358 TTTATGAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12522 original size:23 final size:23
Alignment explanation
Indices: 12494--12548 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
12484 TCATAAATCA
12494 AGTATCATGTATCATGTCATAAC
1 AGTATCATGTATCATGTCATAAC
12517 AGTATCATGTATCATGTCATAAC
1 AGTATCATGTATCATGTCATAAC
*
12540 AGTAACATG
1 AGTATCATG
12549 AATTATCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (23 bp):
AGTATCATGTATCATGTCATAAC
Found at i:13303 original size:29 final size:27
Alignment explanation
Indices: 13259--13443 Score: 114
Period size: 28 Copynumber: 6.6 Consensus size: 27
13249 GATCAACAAT
*
13259 TTTACACAATTATCACCCTTTTAAGAAATA
1 TTTACA-AAATATCACCCTTTTAA-AAA-A
13289 TTTACAAAATATCACCCTTTTCAAAAAA
1 TTTACAAAATATCACCCTTTT-AAAAAA
* **
13317 -ATACTAAAATATCACTTTTTTCAAAAAA
1 TTTAC-AAAATATCACCCTTTT-AAAAAA
*
13345 TTTATGAAAATATCA--C-TTTAAAAAA
1 TTTA-CAAAATATCACCCTTTTAAAAAA
* *
13370 -TTACGAAAATAGCACCATTTTTAAAATAA
1 TTTAC-AAAATATCACC-CTTTTAAAA-AA
* *
13399 -TTACCAAATATCACCATTTTCAAAATAA
1 TTTACAAAATATCACCCTTTT-AAAA-AA
*
13427 -TTACTAAAATATTACCC
1 TTTAC-AAAATATCACCC
13444 GATCAACGGT
Statistics
Matches: 127, Mismatches: 16, Indels: 25
0.76 0.10 0.15
Matches are distributed among these distances:
24 11 0.09
25 6 0.05
26 3 0.02
27 7 0.06
28 49 0.39
29 43 0.34
30 8 0.06
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.34
Consensus pattern (27 bp):
TTTACAAAATATCACCCTTTTAAAAAA
Found at i:13337 original size:28 final size:28
Alignment explanation
Indices: 13290--13438 Score: 134
Period size: 28 Copynumber: 5.4 Consensus size: 28
13280 TAAGAAATAT
*
13290 TTAC-AAAATATCACCCTTTTCAAAAAA
1 TTACTAAAATATCACCTTTTTCAAAAAA
* *
13317 ATACTAAAATATCACTTTTTTCAAAAAA
1 TTACTAAAATATCACCTTTTTCAAAAAA
13345 TTTA-TGAAAATATCA-C--TTT-AAAAAA
1 -TTACT-AAAATATCACCTTTTTCAAAAAA
* *
13370 TTACGAAAATAGCACCATTTTT-AAAATAA
1 TTACTAAAATATCACC-TTTTTCAAAA-AA
* *
13399 TTAC-CAAATATCACCATTTTCAAAATAA
1 TTACTAAAATATCACCTTTTTCAAAA-AA
13427 TTACTAAAATAT
1 TTACTAAAATAT
13439 TACCCGATCA
Statistics
Matches: 100, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
24 11 0.11
25 7 0.07
26 3 0.03
27 7 0.07
28 49 0.49
29 23 0.23
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (28 bp):
TTACTAAAATATCACCTTTTTCAAAAAA
Found at i:20522 original size:29 final size:28
Alignment explanation
Indices: 20489--20641 Score: 126
Period size: 29 Copynumber: 5.3 Consensus size: 28
20479 TTTACACAAT
*
20489 TATCACCCTTTTAAGAAATATTTACGAAA
1 TATCACCCTTTTAA-AAATAATTACGAAA
* * *
20518 TATCAACCTTTTTAAAATAATTACCTAAA
1 TATCACCCTTTTAAAAATAATTA-CGAAA
** *
20547 TATCACTTTTTTAAAAAAAAATTACGAAAA
1 TATCACCCTTTT-AAAAATAATTACG-AAA
* * * *
20577 TAACACCATTTTTAAAATAATTACCAAA
1 TATCACCCTTTTAAAAATAATTACGAAA
* * * *
20605 TATCATCATTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTAAAAATAATTAC-GAAA
20634 TATCACCC
1 TATCACCC
20642 GGTCAACGGT
Statistics
Matches: 98, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
28 32 0.33
29 45 0.46
30 21 0.21
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (28 bp):
TATCACCCTTTTAAAAATAATTACGAAA
Found at i:20557 original size:28 final size:28
Alignment explanation
Indices: 20515--20639 Score: 119
Period size: 28 Copynumber: 4.3 Consensus size: 28
20505 AATATTTACG
*
20515 AAATATCAACCTTTTTAAAATAATTACCT
1 AAATATC-ACATTTTTAAAATAATTACCT
* * **
20544 AAATATCACTTTTTTAAAAAAAAATTACGA
1 AAATATCACATTTTT--AAAATAATTACCT
*
20574 AAATAACACCATTTTTAAAATAATTACC-
1 AAATATCA-CATTTTTAAAATAATTACCT
*
20602 AAATATCATCATTTTCAAAATAATTA-CT
1 AAATATCA-CATTTTTAAAATAATTACCT
20630 AAAATATCAC
1 -AAATATCAC
20640 CCGGTCAACG
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.01
28 31 0.39
29 25 0.31
30 17 0.21
31 6 0.08
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (28 bp):
AAATATCACATTTTTAAAATAATTACCT
Found at i:21641 original size:2 final size:2
Alignment explanation
Indices: 21634--21680 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
21624 CCATCTTTTA
21634 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
21676 AT AT A
1 AT AT A
21681 CAAATAAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23785 original size:30 final size:31
Alignment explanation
Indices: 23727--23796 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 31
23717 ATCGGGCCGG
23727 ATATATATATTTAAATTAAATATATAAATATT
1 ATATATATATTTAAATTAAATATATAAAT-TT
* * *
23759 ATATATATTTTTTAATTTAAT-T-TAAATTT
1 ATATATATATTTAAATTAAATATATAAATTT
23788 AT-TA-ATATT
1 ATATATATATT
23797 ATATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 4 0.12
30 5 0.15
31 1 0.03
32 18 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATATATATATTTAAATTAAATATATAAATTT
Found at i:29337 original size:6 final size:6
Alignment explanation
Indices: 29326--29351 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29316 CGAAGACGAC
29326 GAAGAT GAAGAT GAAGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GA
29352 GACGAAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAGAT
Found at i:35269 original size:8 final size:8
Alignment explanation
Indices: 35258--35291 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
35248 ATATTTTATA
35258 TATTTAAT
1 TATTTAAT
*
35266 TATTCAAT
1 TATTTAAT
*
35274 TATTTAAC
1 TATTTAAT
35282 TATTTAAT
1 TATTTAAT
35290 TA
1 TA
35292 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:35648 original size:55 final size:54
Alignment explanation
Indices: 35557--35714 Score: 178
Period size: 55 Copynumber: 2.9 Consensus size: 54
35547 ATATTCGGAA
* * *
35557 AACGAGCTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCACTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
*
35610 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCACTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* ** * * *
35666 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
35715 ATCAATCGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
53 18 0.20
54 24 0.27
55 47 0.52
56 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (54 bp):
AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:35769 original size:55 final size:55
Alignment explanation
Indices: 35621--36210 Score: 769
Period size: 55 Copynumber: 10.7 Consensus size: 55
35611 AACGAGTTCA
* * * * *
35621 CTCCCTCTTTCTTCGGGGAGTAT-AGAACTCGAACAATCTTCTGTCAA-CGGGT-TCG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTC-ATCAATCGTGTCT-G
* * * ** * *
35676 TTCCCTCTTTCTT-AGGGAGTAGGA-ACTTGAAGAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * * *
35729 CTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAATCTTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATC-AATCGTGTCTG
* *
35785 CTCCCTATTTCTTCAGAGAGTATAAGACCCAAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
35840 CTCCCCA-TTCTTTCAGAGAGTATAAGACTTGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
**
35895 CTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
35950 CTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
36005 CTCCCTATTTCTTCAGAGAGTACAAGACTCGAACAATCTTCATCCATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * *
36060 CTCCATATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
36115 CTCCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
*
36170 CTCCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTC
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
36211 GATTATCGTT
Statistics
Matches: 476, Mismatches: 51, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
52 4 0.01
53 28 0.06
54 19 0.04
55 370 0.78
56 55 0.12
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
Found at i:37234 original size:7 final size:8
Alignment explanation
Indices: 37214--37265 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
37204 GAACCCTTCT
37214 TTTTTTCCA
1 TTTTTT-CA
37223 TTTTTTCA
1 TTTTTTCA
*
37231 TTTTTTTA
1 TTTTTTCA
*
37239 TTTTTTTA
1 TTTTTTCA
37247 TTTTTTC-
1 TTTTTTCA
37254 TTTTTTCA
1 TTTTTTCA
37262 TTTT
1 TTTT
37266 CACTCATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.17
8 27 0.68
9 6 0.15
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:37242 original size:15 final size:16
Alignment explanation
Indices: 37210--37280 Score: 58
Period size: 18 Copynumber: 4.3 Consensus size: 16
37200 TCTTGAACCC
37210 TTCTTTTTTTCCATTTT
1 TTCTTTTTTT-CATTTT
37227 TTCATTTTTTT-ATTTT
1 TTC-TTTTTTTCATTTT
37243 TT-TATTTTTTC-TTTT
1 TTCT-TTTTTTCATTTT
**
37258 TTCATTTTCACTCATTTT
1 TTC-TTTT-TTTCATTTT
37276 TTCTT
1 TTCTT
37281 CTTCTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.02
15 12 0.27
16 10 0.22
17 8 0.18
18 14 0.31
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTTTCATTTT
Found at i:40789 original size:8 final size:8
Alignment explanation
Indices: 40776--40803 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40766 GAAAAAGAAG
40776 ATATATAC
1 ATATATAC
40784 ATATATAC
1 ATATATAC
40792 ATATATAC
1 ATATATAC
40800 ATAT
1 ATAT
40804 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:47275 original size:16 final size:16
Alignment explanation
Indices: 47254--47291 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
47244 AACCTTATTC
47254 ACATGATATCTACCCA
1 ACATGATATCTACCCA
47270 ACATGATATCTACCCA
1 ACATGATATCTACCCA
47286 ATCATG
1 A-CATG
47292 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:50715 original size:8 final size:8
Alignment explanation
Indices: 50704--50737 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
50694 ATATTTTATA
50704 TATTTAAT
1 TATTTAAT
*
50712 TATTCAAT
1 TATTTAAT
*
50720 TATTTAAC
1 TATTTAAT
50728 TATTTAAT
1 TATTTAAT
50736 TA
1 TA
50738 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:56231 original size:26 final size:28
Alignment explanation
Indices: 56172--56227 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
56162 CACTTTCATC
*
56172 ACCATTGCTCCCACACACCTACAATAGA
1 ACCATTGATCCCACACACCTACAATAGA
*
56200 ACCATTGATCTCACACACCTACAATAGA
1 ACCATTGATCCCACACACCTACAATAGA
56228 CATTCATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.36, G:0.07, T:0.20
Consensus pattern (28 bp):
ACCATTGATCCCACACACCTACAATAGA
Found at i:56571 original size:20 final size:20
Alignment explanation
Indices: 56534--56570 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56524 TTTTCAAACT
*
56534 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTCCATTTTGA
56554 TTTTCAAAA-TCCATTTT
1 TTTTCAAAATTCCATTTT
56571 TTGCTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGA
Done.