Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005788.1 Hibiscus syriacus cultivar Beakdansim tig00013565_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: 403709
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 3
Found at i:378854 original size:36 final size:35
Alignment explanation
Indices: 378712--378859 Score: 181
Period size: 36 Copynumber: 4.1 Consensus size: 35
378702 AGGGAAACTA
* *
378712 TCTCAAGAGAGACAAAACTTGTTTTAAGAGAAAATG
1 TCTCAAGAGAGACAAAATTTGTTTT-AGAGAAATTG
* * *
378748 TCTAAAGAGATACAAAATTTGTTTTACGAGAAACTG
1 TCTCAAGAGAGACAAAATTTGTTTTA-GAGAAATTG
378784 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAATTG
1 TCTCAAGAGAGACAAAATTTGTTTT-AGAGAAATTG
*
378820 TCTCAAGAGAGACAAAACTTTATTTT-GAGTAAATTAG
1 TCTCAAGAGAGACAAAA-TTTGTTTTAGAG-AAATT-G
378857 TCT
1 TCT
378860 TGGGCGAGAC
Statistics
Matches: 99, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
35 4 0.04
36 83 0.84
37 12 0.12
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (35 bp):
TCTCAAGAGAGACAAAATTTGTTTTAGAGAAATTG
Found at i:380382 original size:95 final size:95
Alignment explanation
Indices: 380173--380435 Score: 332
Period size: 95 Copynumber: 2.7 Consensus size: 95
380163 GGCTAGCTGA
* * * *
380173 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACATCTTAA--TATCATTGTATAGA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTGTAT---
* *
380236 CATTATAATCGCCTTTATCACGCTAGATGAATTTT
62 -ATTATAATCACCTTTATCACGCTAGATGAATCTT
*
380271 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAAGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* * *
380336 TAATCACCTTTATCAGGTTAGTTGAATCTT
66 TAATCACCTTTATCACGCTAGATGAATCTT
** * *
380366 ATCCATAAAGTTGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
380431 ATAAT
65 ATAAT
380436 ATTATAATGT
Statistics
Matches: 147, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
95 87 0.59
96 6 0.04
98 45 0.31
99 8 0.05
100 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCACGCTAGATGAATCTT
Found at i:382089 original size:16 final size:16
Alignment explanation
Indices: 382064--382124 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
382054 GGACCATCTT
382064 CATC-TGATCTTCTAA
1 CATCATGATCTTCTAA
*
382079 CATCATGATCTTTTAA
1 CATCATGATCTTCTAA
*
382095 CATCATGATCTTTTAA
1 CATCATGATCTTCTAA
382111 CATCATGATCTTCT
1 CATCATGATCTTCT
382125 TTGTCTTATC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
15 4 0.09
16 39 0.91
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.43
Consensus pattern (16 bp):
CATCATGATCTTCTAA
Found at i:384592 original size:15 final size:15
Alignment explanation
Indices: 384572--384602 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
384562 TAAATAAAAT
384572 AAGAAAACAAAGATA
1 AAGAAAACAAAGATA
384587 AAGAAAACAAAGATA
1 AAGAAAACAAAGATA
384602 A
1 A
384603 TATTGACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (15 bp):
AAGAAAACAAAGATA
Found at i:385834 original size:2 final size:2
Alignment explanation
Indices: 385827--385888 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
385817 CTATTTAATG
385827 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
385869 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
385889 ATAAGATTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:387235 original size:6 final size:6
Alignment explanation
Indices: 387224--387261 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
387214 CAATAAATTC
*
387224 GTGGGG GTGGGG GTGGGG GTGGGG GTGGCCG GTGGGG G
1 GTGGGG GTGGGG GTGGGG GTGGGG GTGG-GG GTGGGG G
387262 GCAATACTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.05, G:0.79, T:0.16
Consensus pattern (6 bp):
GTGGGG
Found at i:390989 original size:3 final size:3
Alignment explanation
Indices: 390981--391007 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
390971 ACTCAAGTCG
390981 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
391008 GAAGGATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:392473 original size:21 final size:21
Alignment explanation
Indices: 392447--392513 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
392437 AGAGTTTTAC
392447 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
* * * *
392468 TAGGA-T-ATAGT--T-ATAC
1 TAGGATTCAAACTCCTAAAAA
392484 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
392505 TAGGATTCA
1 TAGGATTCA
392514 GAAACATTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
16 7 0.21
17 2 0.06
18 3 0.09
19 3 0.09
20 2 0.06
21 16 0.48
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (21 bp):
TAGGATTCAAACTCCTAAAAA
Found at i:392508 original size:37 final size:37
Alignment explanation
Indices: 392399--392510 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
392389 AACATAAAGT
*
392399 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGAA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
392436 AAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
392473 TATAGTTATACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
392510 T
1 T
392511 TCAGAAACAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:392828 original size:24 final size:22
Alignment explanation
Indices: 392801--392870 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
392791 ATGCATTTTC
*
392801 TTTTTTACTTTAGTATATATATA
1 TTTTTTACATTA-TATATATATA
*
392824 TTTTTTAGATTATATATATATA
1 TTTTTTACATTATATATATATA
* * *
392846 TATATATATATATATATATATATA
1 T-TTTTTACAT-TATATATATATA
392870 T
1 T
392871 ATATGTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 11 0.28
23 16 0.40
24 13 0.32
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTTTTACATTATATATATATA
Found at i:392839 original size:2 final size:2
Alignment explanation
Indices: 392834--392874 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
392824 TTTTTTAGAT
392834 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
392875 GTTAATTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:392941 original size:9 final size:9
Alignment explanation
Indices: 392917--392994 Score: 59
Period size: 9 Copynumber: 8.1 Consensus size: 9
392907 ATATATTTAC
392917 TATTTT-TT
1 TATTTTATT
*
392925 TTTTTTATT
1 TATTTTATT
392934 TATTTTATAT
1 TATTTTAT-T
**
392944 ATATAATATT
1 -TATTTTATT
*
392954 ATCATTTTGTT
1 -T-ATTTTATT
392965 TATCTTATATT
1 TAT-TT-TATT
392976 TATTTTATT
1 TATTTTATT
392985 TATTTTATT
1 TATTTTATT
392994 T
1 T
392995 TATATTTTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
8 5 0.09
9 25 0.45
10 9 0.16
11 17 0.30
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (9 bp):
TATTTTATT
Found at i:393135 original size:16 final size:15
Alignment explanation
Indices: 393107--393150 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
393097 TTTTTATGTC
393107 TTTTATTTATTTATT
1 TTTTATTTATTTATT
*
393122 TTTTCATTTCTTTA-T
1 TTTT-ATTTATTTATT
393137 TTTTATTTAATTTA
1 TTTTATTT-ATTTA
393151 CTTGTTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 13 0.52
16 8 0.32
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTTATTTATT
Found at i:396341 original size:27 final size:26
Alignment explanation
Indices: 396310--396362 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
396300 CAATCAGAAC
* *
396310 AAAAAGGGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAACAAAG-GAAAAT
396337 AAAAAGAGAAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAAACAAAGGAAAAT
396363 TGAAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:396342 original size:13 final size:14
Alignment explanation
Indices: 396312--396362 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
396302 ATCAGAACAA
*
396312 AAAGGGAAAA-AAGC
1 AAAGAGAAAATAA-C
396326 AAAGAGAAAATAA-
1 AAAGAGAAAATAAC
*
396339 AAAGAGAAAAAAAC
1 AAAGAGAAAATAAC
396353 AAAG-GAAAAT
1 AAAGAGAAAAT
396363 TGAAGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 17 0.53
14 13 0.41
15 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.20, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAATAAC
Found at i:397527 original size:32 final size:32
Alignment explanation
Indices: 397490--397592 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 32
397480 AGGAACAATG
* *
397490 AGGGCA-TCTTTGAAGATTCAACATCAGATGTT
1 AGGGCATTTTTTG-AGATTCAACATCAAATGTT
* * *
397522 GGGGCATTTTTTGATATTTAACATCAAATGTT
1 AGGGCATTTTTTGAGATTCAACATCAAATGTT
** *
397554 AGGGCATTTTTTGAGATTCAACATTGAATATT
1 AGGGCATTTTTTGAGATTCAACATCAAATGTT
397586 AGGGCAT
1 AGGGCAT
397593 CTTTGGGAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 54 0.92
33 5 0.08
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (32 bp):
AGGGCATTTTTTGAGATTCAACATCAAATGTT
Found at i:398865 original size:36 final size:36
Alignment explanation
Indices: 398790--398886 Score: 124
Period size: 36 Copynumber: 2.7 Consensus size: 36
398780 TTTCGTCTTC
* *
398790 CTTGAGACAGTTTCTTTT-ATAACTAAGTTTTGTCTCT
1 CTTGAGACAGTTTCTTTTGA-AAC-AAATTTTGTCCCT
* *
398827 CTTGAGATAGTTTTTTTTGAAACAAATTTTGTCCCT
1 CTTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCT
*
398863 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCTTTTGAAACA
398887 CAAAAAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 32 0.62
37 19 0.37
38 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.44
Consensus pattern (36 bp):
CTTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCT
Found at i:398929 original size:31 final size:30
Alignment explanation
Indices: 398891--398950 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
398881 GAAACACAAA
398891 AAAAAAACCCTCAAAATTGTTTCTCTTGAAG
1 AAAAAAACCCTCAAAA-TGTTTCTCTTGAAG
** *
398922 AAAAAAACTTTGAAAATGTTTCTCTTGAA
1 AAAAAAACCCTCAAAATGTTTCTCTTGAA
398951 ACACAAAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (30 bp):
AAAAAAACCCTCAAAATGTTTCTCTTGAAG
Found at i:399224 original size:84 final size:85
Alignment explanation
Indices: 399087--399242 Score: 201
Period size: 84 Copynumber: 1.8 Consensus size: 85
399077 TGCAGTATAA
* * *
399087 CTCAAGGCAAGAAGGGTTATCAGTCATCAAAGACCTTCGAGTTCGATTACATTCAACTCAGAGGA
1 CTCAAGGCAAGAAGGGCTATCAGCCAACAAAGACCTTCGAGTTCGATTACATTCAACTC-GAGGA
399152 -AAATCAAATTTACAGCATAG
65 CAAATCAAATTTACAGCATAG
* * * * *
399172 CTCAAGGCAAGAAGGGCTATCTGCCAACAAA-A-TTATCGAGTTCGATTCCATTCAGCTCGATGA
1 CTCAAGGCAAGAAGGGCTATCAGCCAACAAAGACCT-TCGAGTTCGATTACATTCAACTCGAGGA
399235 CAAATCAA
65 CAAATCAA
399243 TCACACTACT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
83 5 0.08
84 29 0.48
85 27 0.44
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (85 bp):
CTCAAGGCAAGAAGGGCTATCAGCCAACAAAGACCTTCGAGTTCGATTACATTCAACTCGAGGAC
AAATCAAATTTACAGCATAG
Found at i:399745 original size:37 final size:36
Alignment explanation
Indices: 399704--399809 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 36
399694 ACATAGCGTT
*
399704 AGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 AGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
399740 CAGAGTTTTAATAGGATTCAAACTCTTAAAAATAGGA
1 -AGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
399777 TGAAGTTCTACTATGATTCAAACTCCTAAAAAT
1 AG-AGTTTTACTAGGATTCAAACTCCTAAAAAT
399810 TGGATCCAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 1 0.02
37 59 0.98
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (36 bp):
AGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:400093 original size:23 final size:23
Alignment explanation
Indices: 400067--400111 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
400057 TTGTTATTTT
*
400067 TTTTCATGTAATTT-TTTTTTACA
1 TTTT-ATGCAATTTCTTTTTTACA
*
400090 TTTTATGCATTTTCTTTTTTAC
1 TTTTATGCAATTTCTTTTTTAC
400112 TTTAGTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.18, C:0.11, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATGCAATTTCTTTTTTACA
Found at i:403587 original size:23 final size:23
Alignment explanation
Indices: 403545--403613 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
403535 GAAAAAAACG
* **
403545 AACGAACACAATGAGCGAACATA
1 AACGAACACAATAAATGAACATA
*
403568 AACGAACACAATAAATGAACGTA
1 AACGAACACAATAAATGAACATA
*
403591 AAC-TA-AC-ATAAATGAACATA
1 AACGAACACAATAAATGAACATA
403611 AAC
1 AAC
403614 CACAAAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.38
21 2 0.05
22 1 0.03
23 22 0.55
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.13
Consensus pattern (23 bp):
AACGAACACAATAAATGAACATA
Done.