Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000858.1 Hibiscus syriacus cultivar Beakdansim tig00001663_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: 346567
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:292294 original size:23 final size:23
Alignment explanation
Indices: 292220--292298 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
292210 ATATATAATT
*
292220 TATTAATGCATGCATG-TATGTA
1 TATTAATGCATGTATGATATGTA
* *
292242 TAATATGTATGCATATATGTATAAT-T-
1 T-AT-T-AATGCATGTATG-AT-ATGTA
292268 TATTAATGCATGTATGATATGTA
1 TATTAATGCATGTATGATATGTA
292291 TATTAATG
1 TATTAATG
292299 TAATATGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
21 2 0.05
22 4 0.09
23 20 0.45
24 2 0.05
25 11 0.25
26 1 0.02
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.44
Consensus pattern (23 bp):
TATTAATGCATGTATGATATGTA
Found at i:292491 original size:20 final size:20
Alignment explanation
Indices: 292448--292504 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
292438 TAGTTTATAG
*
292448 AAACCCTAAACCCTAAACTCT
1 AAACCATAAACCCT-AACTCT
* * *
292469 AAATCATATACCCTAACTTT
1 AAACCATAAACCCTAACTCT
292489 AAACCATAAACCCTAA
1 AAACCATAAACCCTAA
292505 ATCAAAAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.23
Consensus pattern (20 bp):
AAACCATAAACCCTAACTCT
Found at i:292499 original size:34 final size:34
Alignment explanation
Indices: 292454--292518 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
292444 ATAGAAACCC
* * * *
292454 TAAACCCTAAACTCTAAATCATATACCCTAACTT
1 TAAACCATAAACCCTAAATCAAAAACCCTAACTT
292488 TAAACCATAAACCCTAAATCAAAAACCCTAA
1 TAAACCATAAACCCTAAATCAAAAACCCTAA
292519 TATAAATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (34 bp):
TAAACCATAAACCCTAAATCAAAAACCCTAACTT
Found at i:300168 original size:2 final size:2
Alignment explanation
Indices: 300161--300219 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
300151 AAAGAAGAGT
300161 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
300203 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
300220 TTTTAAATGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:314468 original size:10 final size:10
Alignment explanation
Indices: 314453--314480 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
314443 AACTGAGATC
314453 GAAACTTGTT
1 GAAACTTGTT
314463 GAAACTTGTT
1 GAAACTTGTT
314473 GAAACTTG
1 GAAACTTG
314481 GCAAGAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (10 bp):
GAAACTTGTT
Found at i:318232 original size:211 final size:210
Alignment explanation
Indices: 317843--318233 Score: 525
Period size: 211 Copynumber: 1.9 Consensus size: 210
317833 AAGAGTTAAA
* * * *
317843 GGCCATACTATTACCAGGCCATCAGTCTATTTAGGTCCACGTCCTAAGCATTTTCAACAAAAGCA
1 GGCCATACTATTACCAGGCCATCAATCTATTTAGGTCCACATCCTAAGAATTCTCAACAAAAGCA
* * *
317908 ACACTTTCACAACTTCAACCCATGTTTTCTTTTCCCTTTCCCTCCCATTGACACAATGAAAGAAC
66 ACACTTTCACAACTTCAACCCATGTCTTCTTTTCCCTTTCCCTCCCATCGACACAATGAAAGAAA
* * *
317973 ATGATATTTTTAAACCCAAATATTATATTGTCTATATTGAATGAATTACTCACTTTGTCAGATAG
131 ATAATATTTTTAAACCCAAATATAATATTGTCTATATTGAAGGAATTACTCACTTTGTCAGATAG
318038 ACTATATGGGTTCAG
196 ACTATATGGGTTCAG
* * ** ** *
318053 GGCCATGCTATTACCAGG-CGTCAATCTATTTAGGTCCTTATTTTAAGAATTCTCAGCAAAAGCA
1 GGCCATACTATTACCAGGCCATCAATCTATTTAGGTCCACATCCTAAGAATTCTCAACAAAAGCA
* * * * *
318117 ACATCCTTTCACAGCTTTAACCCATGTCTTCTTTTCCCTTTCCCTCCCCTCGACACGATGTAAGA
66 ACA--CTTTCACAACTTCAACCCATGTCTTCTTTTCCCTTTCCCTCCCATCGACACAATGAAAGA
* *
318182 AAATAATATTTTTAAACCTC-TATATAATATTGTCTATATTGTAGGAATTACT
129 AAATAATATTTTTAAACC-CAAATATAATATTGTCTATATTGAAGGAATTACT
318234 GCAGACATTT
Statistics
Matches: 154, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
209 39 0.25
210 17 0.11
211 97 0.63
212 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (210 bp):
GGCCATACTATTACCAGGCCATCAATCTATTTAGGTCCACATCCTAAGAATTCTCAACAAAAGCA
ACACTTTCACAACTTCAACCCATGTCTTCTTTTCCCTTTCCCTCCCATCGACACAATGAAAGAAA
ATAATATTTTTAAACCCAAATATAATATTGTCTATATTGAAGGAATTACTCACTTTGTCAGATAG
ACTATATGGGTTCAG
Found at i:320412 original size:18 final size:18
Alignment explanation
Indices: 320389--320424 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
320379 TAGAAAATTG
320389 GTGAAGAATAAAACATGT
1 GTGAAGAATAAAACATGT
320407 GTGAAGAATAAAACATGT
1 GTGAAGAATAAAACATGT
320425 TGCAAGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
GTGAAGAATAAAACATGT
Found at i:331695 original size:317 final size:314
Alignment explanation
Indices: 331123--331753 Score: 1217
Period size: 317 Copynumber: 2.0 Consensus size: 314
331113 CAGAAGGCCT
*
331123 AAATAAACCGTCGGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
1 AAATAAACCGTCAGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
331188 CTTCACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAACTAA
66 CTTCACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAACTAA
331253 AGATCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATTAAG
131 AGATCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATTAAG
331318 TCGTCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCCTTG
196 TCGTCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCCTTG
331383 GAATAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
261 GAATAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
331437 AAATAAACCGTCAGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
1 AAATAAACCGTCAGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
331502 CTCCTCCACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAAC
66 CT--T-CACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAAC
331567 TAAAGATCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATT
128 TAAAGATCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATT
*
331632 AAGTCGTCAGCAAACTGGAGATGAGTCAAATTGAAGCAGTTTTGACTCTTTCCAAAAGAAAATCC
193 AAGTCGTCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCC
331697 TTGGAATAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
258 TTGGAATAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
331754 CACGTTAAAC
Statistics
Matches: 312, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
314 66 0.21
316 1 0.00
317 245 0.79
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (314 bp):
AAATAAACCGTCAGAAAGGAACCAATAGAGCAGCCAATGTCCTTAGCCCAATTTCCAATGATGTC
CTTCACATTAATACCATAAAGTTTGCTTTTAACTAAATTAAGATGAAGCACTGTCATAAAACTAA
AGATCGTCAACACTCGTCTAACATTTTTAATTTGAGTGATGGAGGCTCGGCAAAAAATAATTAAG
TCGTCAGCAAACTGGAGATGAGTCAAATTGAAACAGTTTTGACTCTTTCCAAAAGAAAATCCTTG
GAATAAGCCCGAATCCACAACTTTAGTTAACATCATATGAAGAAGTTCACCAAC
Found at i:336639 original size:20 final size:20
Alignment explanation
Indices: 336614--336654 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
336604 GCTCTACGAT
336614 TTGGTCTTTCATTCCAGGGG
1 TTGGTCTTTCATTCCAGGGG
336634 TTGGTCTTTCATTCCAGGGG
1 TTGGTCTTTCATTCCAGGGG
336654 T
1 T
336655 CGTTCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.20, G:0.29, T:0.41
Consensus pattern (20 bp):
TTGGTCTTTCATTCCAGGGG
Found at i:336661 original size:20 final size:20
Alignment explanation
Indices: 336616--336662 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
336606 TCTACGATTT
*
336616 GGTCTTTCATTCCAGGGGTT
1 GGTCTTTCATTCCAGGGGTC
336636 GGTCTTTCATTCCAGGGGTC
1 GGTCTTTCATTCCAGGGGTC
*
336656 GTTCTTT
1 GGTCTTT
336663 GGACCACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.43
Consensus pattern (20 bp):
GGTCTTTCATTCCAGGGGTC
Found at i:337473 original size:24 final size:24
Alignment explanation
Indices: 337446--337493 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
337436 GGCTCGATTT
337446 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
337470 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
337494 ATTCCAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (24 bp):
TCTTCCAACAGTCAGACCTTTTAA
Found at i:345315 original size:12 final size:12
Alignment explanation
Indices: 345298--345327 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
345288 TTCGAGCCCA
345298 AGACCCAGATCC
1 AGACCCAGATCC
345310 AGACCCAGATCC
1 AGACCCAGATCC
345322 AGACCC
1 AGACCC
345328 GGTTACAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.43, G:0.17, T:0.07
Consensus pattern (12 bp):
AGACCCAGATCC
Done.