Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004692.1 Hibiscus syriacus cultivar Beakdansim tig00010529_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: 91983
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:31619 original size:31 final size:31
Alignment explanation
Indices: 31581--31673 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
31571 AAGTGTTCTA
31581 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
31612 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
* *
31643 TACGAGCTATGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
31674 ATGCGCCATG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:31705 original size:22 final size:22
Alignment explanation
Indices: 31677--31728 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
31667 GCTTTGCATG
31677 CGCCATGCACGTC-AGAAGAGGT
1 CGCCATGCACGTCGA-AAGAGGT
31699 CGCCATGCACGTCGAAAGAGGT
1 CGCCATGCACGTCGAAAGAGGT
31721 CGCC-TGCA
1 CGCCATGCA
31729 TGCAGTGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.14
22 24 0.83
23 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (22 bp):
CGCCATGCACGTCGAAAGAGGT
Found at i:31811 original size:29 final size:29
Alignment explanation
Indices: 31774--31861 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
31764 AGGGCGCAGG
*
31774 ACAAGGTCGCCCAGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* * ** *
31803 ACTATGTCGCTTGGCGTGCATGGCAACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* * *
31832 ACAAGGTCGCCCGGAGGGCATGGTGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
31861 A
1 A
31862 TGCTGGGAAG
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.30, G:0.32, T:0.18
Consensus pattern (29 bp):
ACAAGGTCGCCCGGCGTGCATGGCGACCT
Found at i:32352 original size:125 final size:125
Alignment explanation
Indices: 32125--32370 Score: 384
Period size: 125 Copynumber: 2.0 Consensus size: 125
32115 GCTCACCTTC
* * * * *
32125 AAATCTAAATTTCTTTCTTTAAAATTTGAATTTTTTTATGTTAGTTGTTCATTCTGTTAATTGTG
1 AAATATAAATTTCTCTCTTTAAAATTCGAATTTTTTTATATTAGTTATTCATTCTGTTAATTGTG
**
32190 TCTATCCTTAAATTTTATTTATGTTCACTCAAGTACAAAAAATTTGTATTGTAGGTACAG
66 TCTATCCTTAAATTTTATTTATGACCACTCAAGTACAAAAAATTTGTATTGTAGGTACAG
* * *
32250 AAATATAAATTTCTCTCTTTAAAATTCGATTTTTTTTCTATTAGTTATTCATTTTGTTAATTGTG
1 AAATATAAATTTCTCTCTTTAAAATTCGAATTTTTTTATATTAGTTATTCATTCTGTTAATTGTG
* *
32315 TCTATCCTTAAATTTTATTTATGACCATTCAAGTACAAAAATTTTGTATTGTAGGT
66 TCTATCCTTAAATTTTATTTATGACCACTCAAGTACAAAAAATTTGTATTGTAGGT
32371 GCATAGAGTT
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
125 109 1.00
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.50
Consensus pattern (125 bp):
AAATATAAATTTCTCTCTTTAAAATTCGAATTTTTTTATATTAGTTATTCATTCTGTTAATTGTG
TCTATCCTTAAATTTTATTTATGACCACTCAAGTACAAAAAATTTGTATTGTAGGTACAG
Found at i:33737 original size:83 final size:83
Alignment explanation
Indices: 33598--33767 Score: 268
Period size: 83 Copynumber: 2.0 Consensus size: 83
33588 TGCCTTGTCC
*
33598 TCTAGCTCTGGAAAGATCATTTATCGTAAGATGCTTTTCTTGATAAGTGAGTCTAGTTATCTTTC
1 TCTAGCTCTGGAAAGATCATTTATCGTAAGATGCTTTTCTTGATAAATGAGTCTAGTTATCTTTC
* *
33663 TTTGCTTATCTAATTTCT
66 TTTGCTCAACTAATTTCT
* * **
33681 TCTAGCTCTGGTAAGATCATTTCTCGTAAGATGCTTTTCTTGATAAATGCTTCTAGTTATCTTTC
1 TCTAGCTCTGGAAAGATCATTTATCGTAAGATGCTTTTCTTGATAAATGAGTCTAGTTATCTTTC
*
33746 TTTGCTCAAGTAATTTCT
66 TTTGCTCAACTAATTTCT
33764 TCTA
1 TCTA
33768 AAGATCTATA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (83 bp):
TCTAGCTCTGGAAAGATCATTTATCGTAAGATGCTTTTCTTGATAAATGAGTCTAGTTATCTTTC
TTTGCTCAACTAATTTCT
Found at i:39712 original size:85 final size:84
Alignment explanation
Indices: 39617--39783 Score: 262
Period size: 85 Copynumber: 2.0 Consensus size: 84
39607 GAAAAAAATT
* * * *
39617 TAAAAGTTTATGTACTAAAACGGACCAAAACTGATAGTCTAATTAGCAAATGTGTAGTTTGCCCT
1 TAAAAATTTATGTACTAAAACGAACCAAAACTGATAGTCTAATTACCAAAT-TGTAGTTTACCCT
39682 AACGAAACACTAAATTAGGA
65 AACGAAACACTAAATTAGGA
* * *
39702 TAAAAATTTATGTATTAAAACGAACCAAAATTGATAGTCTAGTTACCAAATTGTAGTTTACCCTA
1 TAAAAATTTATGTACTAAAACGAACCAAAACTGATAGTCTAATTACCAAATTGTAGTTTACCCTA
39767 ACGAAACACTAAATTAG
66 ACGAAACACTAAATTAG
39784 AGTCACTTTC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
84 30 0.40
85 45 0.60
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.29
Consensus pattern (84 bp):
TAAAAATTTATGTACTAAAACGAACCAAAACTGATAGTCTAATTACCAAATTGTAGTTTACCCTA
ACGAAACACTAAATTAGGA
Found at i:48644 original size:66 final size:66
Alignment explanation
Indices: 48534--48676 Score: 198
Period size: 66 Copynumber: 2.2 Consensus size: 66
48524 CCTCCCACAA
* ** * * * *
48534 CCGACATTTCCAACAATGCAGCCATCGTTACCCAATCCGAGAGCTCTTCCTCCACTTCCTAGCAT
1 CCGACATTGCCAACAACACAGCCATCATTACCCAAGCCGAGAGCTCTACCTCCACTTCCAAGCAT
48599 G
66 G
*
48600 CCGACATTGCCGACAACACAGCCATCATTACCCAAGCCTG-GAGCTCTACCTCCACTTCCAAGCA
1 CCGACATTGCCAACAACACAGCCATCATTACCCAAGCC-GAGAGCTCTACCTCCACTTCCAAGCA
48664 TG
65 TG
48666 CCGACATTGCC
1 CCGACATTGCC
48677 TACCCTACCA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 67 0.99
67 1 0.01
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.21
Consensus pattern (66 bp):
CCGACATTGCCAACAACACAGCCATCATTACCCAAGCCGAGAGCTCTACCTCCACTTCCAAGCAT
G
Found at i:52987 original size:3 final size:3
Alignment explanation
Indices: 52979--53011 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
52969 GCGACTTCTG
52979 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
53012 AGCCTCCGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:58791 original size:20 final size:21
Alignment explanation
Indices: 58723--58802 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 21
58713 AATTTTTTGT
*
58723 ATAAAA-TTTAAAAATAAAAGT
1 ATAAAACTTTAAAAATAAAA-C
58744 ATATATATA-TTTAAAAATAAAAC
1 ATA-A-A-ACTTTAAAAATAAAAC
*
58767 ATAAAACTTTAGAAAT-AAAC
1 ATAAAACTTTAAAAATAAAAC
* * *
58787 GTAAAATTTTGAAAAT
1 ATAAAACTTTAAAAAT
58803 CTTTATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 17 0.35
21 12 0.24
22 2 0.04
23 4 0.08
24 14 0.29
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (21 bp):
ATAAAACTTTAAAAATAAAAC
Found at i:64300 original size:17 final size:18
Alignment explanation
Indices: 64280--64313 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64270 ATTTTTCTTA
64280 AAATT-ATAAAAATAATT
1 AAATTAATAAAAATAATT
*
64297 AAATTAATAAAAGTAAT
1 AAATTAATAAAAATAAT
64314 ACTTAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAATTAATAAAAATAATT
Found at i:66024 original size:18 final size:18
Alignment explanation
Indices: 66001--66035 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65991 ACATCATGAC
66001 TGAGATT-TGATAGTCATT
1 TGAGATTATGATA-TCATT
66019 TGAGATTATGATATCAT
1 TGAGATTATGATATCAT
66036 ATTTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (18 bp):
TGAGATTATGATATCATT
Found at i:66230 original size:59 final size:59
Alignment explanation
Indices: 66140--66284 Score: 245
Period size: 59 Copynumber: 2.4 Consensus size: 59
66130 GAGTGACCAA
*
66140 TTTATATATTTTAATATTTAAGAGACTCAACAAAGTAACTCCCTATGGTTAGAGGATAAT
1 TTTATA-ATTTTAATATTTAAGAGACTCAACAAAGTAACTCCCTATAGTTAGAGGATAAT
66200 TTTATAATTTTAATATTTAAGAGACTCAACAAAGTAACTCCCTATAGTTAGAGGATAAT
1 TTTATAATTTTAATATTTAAGAGACTCAACAAAGTAACTCCCTATAGTTAGAGGATAAT
* * *
66259 TTTGTAATTTTAATAGTTAAGGGACT
1 TTTATAATTTTAATATTTAAGAGACT
66285 TAATAAAGCA
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 75 0.93
60 6 0.07
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (59 bp):
TTTATAATTTTAATATTTAAGAGACTCAACAAAGTAACTCCCTATAGTTAGAGGATAAT
Found at i:66305 original size:59 final size:59
Alignment explanation
Indices: 66140--66305 Score: 190
Period size: 59 Copynumber: 2.8 Consensus size: 59
66130 GAGTGACCAA
* * * * *
66140 TTTATATATTTTAATATTTAAGAGACTCAACAAAGTAACTCCCTATGGTTAGAGGATAAT
1 TTTATA-ATTTTAATAGTTAAGAGACTCAACAAAGAAAATCCATATAGTTAGAGGATAAT
* * * *
66200 TTTATAATTTTAATATTTAAGAGACTCAACAAAGTAACTCCCTATAGTTAGAGGATAAT
1 TTTATAATTTTAATAGTTAAGAGACTCAACAAAGAAAATCCATATAGTTAGAGGATAAT
* * * *
66259 TTTGTAATTTTAATAGTTAAGGGACTTAATAAAGCAAAAT-CATATAG
1 TTTATAATTTTAATAGTTAAGAGACTCAACAAAG-AAAATCCATATAG
66306 GCAGGGGACC
Statistics
Matches: 96, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 87 0.91
60 9 0.09
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (59 bp):
TTTATAATTTTAATAGTTAAGAGACTCAACAAAGAAAATCCATATAGTTAGAGGATAAT
Found at i:86492 original size:31 final size:28
Alignment explanation
Indices: 86448--86520 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 28
86438 CAGTTACGTC
*
86448 GGGGACC-ATTGCAAAACGGACTAAATGTT
1 GGGGACCTATTGCAAAACGAACT--ATGTT
86477 GGGGACCTTATTGC-AAACGAACTATGTT
1 GGGGACC-TATTGCAAAACGAACTATGTT
86505 GGGGACCGTATTGCAA
1 GGGGACC-TATTGCAA
86521 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 18 0.46
29 8 0.21
30 8 0.21
31 5 0.13
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (28 bp):
GGGGACCTATTGCAAAACGAACTATGTT
Found at i:89293 original size:13 final size:14
Alignment explanation
Indices: 89275--89303 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
89265 ATCTTTCTTA
89275 ACTATTAGC-ATAC
1 ACTATTAGCAATAC
89288 ACTATTAGCAATAC
1 ACTATTAGCAATAC
89302 AC
1 AC
89304 ACCTACAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (14 bp):
ACTATTAGCAATAC
Done.