Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008951.1 Hibiscus syriacus cultivar Beakdansim tig00112277_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: 153195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:142518 original size:60 final size:60
Alignment explanation
Indices: 142453--142683 Score: 300
Period size: 60 Copynumber: 3.8 Consensus size: 60
142443 CTTTTTAACG
* * * *
142453 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * * *
142513 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * * * *
142573 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAGATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTC-TC-A-ATCGCATTGCGATTCTCTCAATCGCA
* *
142636 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATT
142684 TTCTTCTAAA
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
60 94 0.64
61 3 0.02
62 3 0.02
63 48 0.32
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (60 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:142743 original size:20 final size:20
Alignment explanation
Indices: 142718--142771 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
142708 TGGAAGCTCG
*
142718 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
142738 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
*
142758 CATTGCGATTTTCT
1 CGTTGCGATTTTCT
142772 AAATCGCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:142798 original size:19 final size:20
Alignment explanation
Indices: 142760--142808 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
142750 CTTTTTAACA
*
142760 TTGCGATTTTCTAAATCGCG
1 TTGCGATTTTCGAAATCGCG
*
142780 TTGCGATTTT-GATATCGCG
1 TTGCGATTTTCGAAATCGCG
142799 TTGCGATTTT
1 TTGCGATTTT
142809 ATTGGTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTCGAAATCGCG
Found at i:142930 original size:20 final size:20
Alignment explanation
Indices: 142905--142944 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
142895 AATTTTTATC
142905 TCAAAATAAA-ATATTAATTA
1 TCAAAATAAATAT-TTAATTA
142925 TCAAAATAAATATTTAATTA
1 TCAAAATAAATATTTAATTA
142945 AATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TCAAAATAAATATTTAATTA
Found at i:148600 original size:23 final size:23
Alignment explanation
Indices: 148574--148625 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
148564 AATAACATAT
**
148574 TAGGTAGCGCCTATATAATGTAA
1 TAGGTAGCGCCTATATAATAAAA
*
148597 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCCTATATAATAAAA
148620 TAGGTA
1 TAGGTA
148626 TTTAATCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (23 bp):
TAGGTAGCGCCTATATAATAAAA
Found at i:148684 original size:87 final size:87
Alignment explanation
Indices: 148538--148699 Score: 306
Period size: 87 Copynumber: 1.9 Consensus size: 87
148528 ATGTTATATC
148538 ATTTAATCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCCTATATAATGTAATAGGTA
1 ATTTAATCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCCTATATAATGTAATAGGTA
148603 GCGCTTATATAATAAAATAGGT
66 GCGCTTATATAATAAAATAGGT
* *
148625 ATTTAATCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAATCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCCTATATAATGTAATAGGTA
148690 GCGCTTATAT
66 GCGCTTATAT
148700 TGACATATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
ATTTAATCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCCTATATAATGTAATAGGTA
GCGCTTATATAATAAAATAGGT
Found at i:149143 original size:201 final size:196
Alignment explanation
Indices: 148694--149181 Score: 583
Period size: 197 Copynumber: 2.5 Consensus size: 196
148684 TAGGTAGCGC
* * * * *
148694 TTATATTGACATATTTTCTAACT-AAACCGATATAATTATACCGGTAACATTGCAAATTTACCTA
1 TTATGTTGACATATTTTCTCA-TAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTA
* * * *
148758 TTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTAGGATCGATACAATTTTAAATATATCAACACTTT
* *
148823 ATGTGTGTACCTCGTTGGGCATTCATTCTGAAAAAAGTATCGACACAAACTTAAAACATGTCGAT
130 ATGTGTGCACCTCGTTGGACATTCATTCTGAAAAAAGTATCGACAC-AACTTAAAACATGTCGAT
148888 ACA
194 ACA
* * * *
148891 TTATGTAGACCTATTTTCTCATAAAACC-AGTATATTTCTACCGGGTACATTGTAAATTTACCTA
1 TTATGTTGACATATTTTCTCATAAAACCGA-TATATTTATACCGGTTACATTGTAAATTTACCTA
* * *
148955 TTACATTGTAATTATCGGTTTCGATGTTTTTAGGATCGATAC-TTTTAATAAATATGTCAACACT
65 TTACATTATAATTATCGGTTTCGATGTTTTTAGGATCGATACAATTT--TAAATATATCAACACT
* * * * ** * **
149019 TTATGCT-TGCACTTTCGTTTGACATTCATTTTGGACAAAATGTATCGACAC-TTTTTAAATTTG
128 TTATG-TGTGCAC-CTCGTTGGACATTCATTCT-GA-AAAAAGTATCGACACAACTTAAAACATG
149082 TTTCGATACA
189 --TCGATACA
*
149092 TTATGTTGACATATTATCTCATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
1 TTATGTTGACATATTTTCTCATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
149157 TACATTAT-ATTATCGGTTTCGATGT
66 TACATTATAATTATCGGTTTCGATGT
149182 AACATATGCG
Statistics
Matches: 247, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
196 5 0.02
197 90 0.36
198 22 0.09
199 23 0.09
200 19 0.08
201 87 0.35
202 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (196 bp):
TTATGTTGACATATTTTCTCATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTAGGATCGATACAATTTTAAATATATCAACACTTTA
TGTGTGCACCTCGTTGGACATTCATTCTGAAAAAAGTATCGACACAACTTAAAACATGTCGATAC
A
Found at i:149288 original size:16 final size:16
Alignment explanation
Indices: 149267--149313 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
149257 ATTATTCTTA
149267 TTATAATAAATATAAT
1 TTATAATAAATATAAT
* *
149283 TTATAAT-AATTTTAT
1 TTATAATAAATATAAT
149298 TT-TAATAAAATATAAT
1 TTATAAT-AAATATAAT
149314 AATCATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATAATAAATATAAT
Found at i:149312 original size:31 final size:30
Alignment explanation
Indices: 149264--149356 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
149254 TATATTATTC
* *
149264 TTATTATAAT-AAATATAATTTATAATAATT
1 TTATTTTAATAAAATATAA-TAATAATAATT
*
149294 TTATTTTAATAAAATATAATAATCATAATT
1 TTATTTTAATAAAATATAATAATAATAATT
*
149324 TT-TTATTTATAAAATTATAGAT-ATAAT-ATT
1 TTATT-TTAATAAAA-TATA-ATAATAATAATT
149354 TTA
1 TTA
149357 ATAATAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
29 2 0.04
30 33 0.62
31 16 0.30
32 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TTATTTTAATAAAATATAATAATAATAATT
Found at i:149363 original size:14 final size:14
Alignment explanation
Indices: 149281--149367 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
149271 AATAAATATA
**
149281 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
149296 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
149309 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
149323 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
149337 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
149351 ATTTTAATAATAAT
1 ATTTTAATAATAAT
149365 ATT
1 ATT
149368 GACATAAATA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:149363 original size:28 final size:28
Alignment explanation
Indices: 149295--149363 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
149285 ATAATAATTT
*
149295 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
149322 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
149350 TATTTTAATAATAA
1 TATTTTAATAATAA
149364 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:149707 original size:30 final size:32
Alignment explanation
Indices: 149647--149718 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
149637 TTATACACAA
149647 CAATAACAAAACAGGTACCACAATTTTTTAGC
1 CAATAACAAAACAGGTACCACAATTTTTTAGC
* * *
149679 TAATAACAAAACTGGTACCGC-A-TTTTTAGC
1 CAATAACAAAACAGGTACCACAATTTTTTAGC
149709 CAATAACAAA
1 CAATAACAAA
149719 TCGATACCGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 17 0.47
31 1 0.03
32 18 0.50
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (32 bp):
CAATAACAAAACAGGTACCACAATTTTTTAGC
Found at i:149727 original size:29 final size:30
Alignment explanation
Indices: 149647--149734 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
149637 TTATACACAA
* * *
149647 CAATAACAAAACAGGTACCACAATTTTTTAGC
1 CAATAACAAAACTGATACCGC-A-TTTTTAGC
* *
149679 TAATAACAAAACTGGTACCGCATTTTTAGC
1 CAATAACAAAACTGATACCGCATTTTTAGC
* *
149709 CAATAACAAATC-GATACCGCTTTTTT
1 CAATAACAAAACTGATACCGCATTTTT
149735 CTAGCTGTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.24
30 18 0.37
31 1 0.02
32 18 0.37
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.30
Consensus pattern (30 bp):
CAATAACAAAACTGATACCGCATTTTTAGC
Found at i:150321 original size:19 final size:19
Alignment explanation
Indices: 150307--150352 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
150297 TGATTTTGAA
150307 CAAAACATGTAATTTTGTC
1 CAAAACATGTAATTTTGTC
150326 CAAAACATGTAATTTTGTC
1 CAAAACATGTAATTTTGTC
150345 CAAAACAT
1 CAAAACAT
150353 AACCACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (19 bp):
CAAAACATGTAATTTTGTC
Found at i:150485 original size:17 final size:17
Alignment explanation
Indices: 150463--150496 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
150453 GAGACAAAAC
150463 GTCACCAAAAATACCTT
1 GTCACCAAAAATACCTT
150480 GTCACCAAAAATACCTT
1 GTCACCAAAAATACCTT
150497 ATGATACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (17 bp):
GTCACCAAAAATACCTT
Done.