Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006575.1 Hibiscus syriacus cultivar Beakdansim tig00016108_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: 157965
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
File 2 of 2
Found at i:131281 original size:14 final size:14
Alignment explanation
Indices: 131262--131300 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
131252 ATAGAAACCA
131262 TAAACCCTAAATAT
1 TAAACCCTAAATAT
* *
131276 TAAACCATAAATCT
1 TAAACCCTAAATAT
131290 TAAACCCTAAA
1 TAAACCCTAAA
131301 CCCTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAATAT
Found at i:131307 original size:14 final size:14
Alignment explanation
Indices: 131256--131308 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
131246 TAGTTTATAG
*
131256 AAACCATAAACCCT
1 AAACCTTAAACCCT
** *
131270 AAATATTAAACCAT
1 AAACCTTAAACCCT
*
131284 AAATCTTAAACCCT
1 AAACCTTAAACCCT
*
131298 AAACCCTAAAC
1 AAACCTTAAAC
131309 TATATATGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:131485 original size:2 final size:2
Alignment explanation
Indices: 131473--131507 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
131463 ATAAACTATG
*
131473 TA TA GTA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
131508 CAATCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:131669 original size:16 final size:16
Alignment explanation
Indices: 131612--131669 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
131602 CTATATTATA
*
131612 TAATTTATA--AACTA
1 TAATTTATATTAACTG
*
131626 TAGTTTATATTAA-TG
1 TAATTTATATTAACTG
*
131641 TTAA-TTATCTTAACTG
1 -TAATTTATATTAACTG
131657 TAATTTATATTAA
1 TAATTTATATTAA
131670 TATAGTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 8 0.24
15 12 0.35
16 14 0.41
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (16 bp):
TAATTTATATTAACTG
Found at i:131708 original size:87 final size:88
Alignment explanation
Indices: 131581--131759 Score: 247
Period size: 87 Copynumber: 2.0 Consensus size: 88
131571 TTAGTGTACT
* * * * *
131581 ATATAGTTTATACTTTATAATCTATATTATATAATTTATAAACTATAGTTTATATTAATGTTAAT
1 ATATAGTATATACTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAATATTAAT
*
131646 TATCT-TA-ACTGTAATTTATATTA
66 T-T-TATAGACTATAATTTATATTA
*
131669 ATATAGTATATAGTTTATAAACTA-ACTATATAATTTATAAAATATAGTTTATATTAATATTAAT
1 ATATAGTATATACTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAATATTAAT
*
131733 TTTATAGACTATATTTTATATTA
66 TTTATAGACTATAATTTATATTA
131756 ATAT
1 ATAT
131760 TAATTATATA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
85 1 0.01
86 3 0.04
87 56 0.69
88 21 0.26
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (88 bp):
ATATAGTATATACTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAATATTAAT
TTTATAGACTATAATTTATATTA
Found at i:131751 original size:31 final size:31
Alignment explanation
Indices: 131676--131771 Score: 104
Period size: 31 Copynumber: 3.0 Consensus size: 31
131666 TTAATATAGT
*
131676 ATATAGTTTATAAACTAACTATATAA-TTTATAAA
1 ATATAGTTTAT--ATTAA-TAT-TAATTTTATAAA
*
131710 ATATAGTTTATATTAATATTAATTTTATAGA
1 ATATAGTTTATATTAATATTAATTTTATAAA
* * *
131741 CTATATTTTATATTAATATTAATTATATAAA
1 ATATAGTTTATATTAATATTAATTTTATAAA
131772 TATTAATTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
30 3 0.05
31 37 0.67
32 4 0.07
34 11 0.20
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (31 bp):
ATATAGTTTATATTAATATTAATTTTATAAA
Found at i:131774 original size:21 final size:20
Alignment explanation
Indices: 131750--131790 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
131740 ACTATATTTT
131750 ATATTAA-TATTAATTATATAA
1 ATATTAATTA-TAA-TATATAA
131771 ATATTAATTATAATATATAA
1 ATATTAATTATAATATATAA
131791 TTTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 10 0.53
22 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTAATTATAATATATAA
Found at i:131787 original size:87 final size:87
Alignment explanation
Indices: 131608--131796 Score: 222
Period size: 87 Copynumber: 2.1 Consensus size: 87
131598 TAATCTATAT
* * *
131608 TATATAATTTATAAACTATAGTTTATATTAATGTTAATTATCTTAACTGTAATTTATATTAATAT
1 TATATAATTTATAAAATATAGTTTATATTAATATTAATTATCTTAACTATAATTTATATTAATAT
** *
131673 AGTATATAGTTTATAAACTAAC
66 AGTATATAGAATATAAACTAAA
*
131695 TATATAATTTATAAAATATAGTTTATATTAATATTAATT-T-TATAGACTATATTTTATATTAAT
1 TATATAATTTATAAAATATAGTTTATATTAATATTAATTATCT-TA-ACTATAATTTATATTAAT
* * *
131758 ATTAATTATATA-AATATTAATTATAA
64 A-T-AGTATATAGAATATAAACTA-AA
131784 TATATAATTTATA
1 TATATAATTTATA
131797 TTAAGGGCGT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
85 1 0.01
86 3 0.03
87 54 0.62
88 8 0.09
89 21 0.24
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (87 bp):
TATATAATTTATAAAATATAGTTTATATTAATATTAATTATCTTAACTATAATTTATATTAATAT
AGTATATAGAATATAAACTAAA
Found at i:140763 original size:336 final size:336
Alignment explanation
Indices: 140138--140775 Score: 1134
Period size: 336 Copynumber: 1.9 Consensus size: 336
140128 GATCCTGAAT
140138 TAATATGTGTTATATGTTTGAAGAAAATTTCTAAAGATTTATCCATTCATCAGGATGTTTGATTA
1 TAATATGTGTTATATGTTTGAAGAAAATTTCTAAAGATTTATCCATTCATCAGGATGTTTGATTA
*
140203 GTTTGTATTCCTTAAATATAAATTTCTAATTAGTTATAACGTATGGATAAAACCTCTAATAATTA
66 GTTTGTATTCCTTAAATATAAATTTCTAATTAGTTATAACGTATGGATAAAACCTCTAATAAGTA
*
140268 AGTCACTCGAAAAGTCCATGTGAATCGTCAGAATAAAATTTAAAATATGATTATCAAATTTACTT
131 AGTCACTCGAAAAGTCCATGTGAATCGTCAGAATAAAATTTAAAATATAATTATCAAATTTACTT
140333 AATTTGTTGAACTATAAAAAGTCATGATAACCCTATGTACTACGGTTAACGCACTCATTAAAAAT
196 AATTTGTTGAACTATAAAAAGTCATGATAACCCTATGTACTACGGTTAACGCACTCATTAAAAAT
*
140398 CACTATAAATGCTCCATTCGCAGTTGAACAAGGAGATGAATTTTTTTTTTCATAAACATGGCTTT
261 CACTATAAATGCTCCATTCGCAATTGAACAAGGAGATGAATTTTTTTTTTCATAAACATGGCTTT
140463 CCCTTGAATGA
326 CCCTTGAATGA
140474 TAATATGTGTTATATGTTTGAAGAAAATTTCTAAAGATTTATCCATTCATCAGGATGTTTGATTA
1 TAATATGTGTTATATGTTTGAAGAAAATTTCTAAAGATTTATCCATTCATCAGGATGTTTGATTA
* *
140539 GTTTGTATTCCTTAAATATAAATTTCTAATTAGTTATAATGTATGGATAAGACCTCTAATAAGTA
66 GTTTGTATTCCTTAAATATAAATTTCTAATTAGTTATAACGTATGGATAAAACCTCTAATAAGTA
* * *
140604 AGTCACTCGAATAGTTCATGTGAATCGTCAGAATAAAATTTAAAATATAATTATCAAATTTATTT
131 AGTCACTCGAAAAGTCCATGTGAATCGTCAGAATAAAATTTAAAATATAATTATCAAATTTACTT
* * * **
140669 AATTTGTTGAACTATAAAAAGTCATGATGATCCTATAG-ACTACGGTTATCGTGCTCATTAAAAA
196 AATTTGTTGAACTATAAAAAGTCATGATAACCCTAT-GTACTACGGTTAACGCACTCATTAAAAA
*
140733 TCACTATAAATGCTCCCTTCGCAATTGAACAAGGAGATGAATT
260 TCACTATAAATGCTCCATTCGCAATTGAACAAGGAGATGAATT
140776 GACGGTAACC
Statistics
Matches: 287, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
336 286 1.00
337 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (336 bp):
TAATATGTGTTATATGTTTGAAGAAAATTTCTAAAGATTTATCCATTCATCAGGATGTTTGATTA
GTTTGTATTCCTTAAATATAAATTTCTAATTAGTTATAACGTATGGATAAAACCTCTAATAAGTA
AGTCACTCGAAAAGTCCATGTGAATCGTCAGAATAAAATTTAAAATATAATTATCAAATTTACTT
AATTTGTTGAACTATAAAAAGTCATGATAACCCTATGTACTACGGTTAACGCACTCATTAAAAAT
CACTATAAATGCTCCATTCGCAATTGAACAAGGAGATGAATTTTTTTTTTCATAAACATGGCTTT
CCCTTGAATGA
Found at i:144110 original size:9 final size:9
Alignment explanation
Indices: 144096--144152 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
144086 TCTTTTTTAT
144096 TTATTACTA
1 TTATTACTA
144105 TTATTACTA
1 TTATTACTA
*
144114 TTTTTA-TA
1 TTATTACTA
144122 TT-TTA-T-
1 TTATTACTA
*
144128 TTAAATACTTA
1 TT-ATTAC-TA
144139 TTATTACTA
1 TTATTACTA
144148 TTATT
1 TTATT
144153 TTTATACCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
6 2 0.05
7 4 0.10
8 6 0.15
9 21 0.52
10 5 0.12
11 2 0.05
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (9 bp):
TTATTACTA
Found at i:144190 original size:12 final size:12
Alignment explanation
Indices: 144175--144208 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
144165 TTATAAGTTA
*
144175 TTATATATATAT
1 TTATTTATATAT
*
144187 TTATTTATTTAT
1 TTATTTATATAT
144199 TTATTTATAT
1 TTATTTATAT
144209 GACTATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTTATATAT
Found at i:149701 original size:44 final size:46
Alignment explanation
Indices: 149651--149760 Score: 143
Period size: 47 Copynumber: 2.4 Consensus size: 46
149641 GTAACCATGC
* *
149651 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAGTATATTGGAA
* * * *
149695 AAATAAGCTTACGAGCTTATAGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTACAGAA-TTAAATGGCAAGTATATTGGAA
149742 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
149761 TGGGATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 21 0.37
46 1 0.02
47 35 0.61
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAGTATATTGGAA
Found at i:157452 original size:11 final size:11
Alignment explanation
Indices: 157436--157471 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
157426 GAAGAAAGAA
157436 AAAACAAAAAG
1 AAAACAAAAAG
157447 AAAAC-AAAA-
1 AAAACAAAAAG
157456 AAAACAAAAAG
1 AAAACAAAAAG
157467 AAAAC
1 AAAAC
157472 GTTTAGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.22
10 8 0.35
11 10 0.43
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAG
Found at i:157459 original size:20 final size:20
Alignment explanation
Indices: 157434--157471 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
157424 TCGAAGAAAG
157434 AAAAAACAAAAAGAAAACAA
1 AAAAAACAAAAAGAAAACAA
157454 AAAAAACAAAAAGAAAAC
1 AAAAAACAAAAAGAAAAC
157472 GTTTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAACAAAAAGAAAACAA
Found at i:157530 original size:19 final size:19
Alignment explanation
Indices: 157508--157553 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
157498 ACCTAAATTG
*
157508 AAAAAAGAGAA-AAAGAGA
1 AAAAAAAAGAAGAAAGAGA
157526 AAAAAAAAGAAGAAAGAGA
1 AAAAAAAAGAAGAAAGAGA
157545 AAAGAAAAA
1 AAA-AAAAA
157554 TAAGGTGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
19 10 0.40
20 5 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAGAAAGAGA
Found at i:157532 original size:21 final size:19
Alignment explanation
Indices: 157508--157553 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
157498 ACCTAAATTG
157508 AAAAAAGAGAAAAAGAGAAA
1 AAAAAAGA-AAAAAGAGAAA
*
157528 AAAAAAGAAGAAAGAGAAA
1 AAAAAAGAAAAAAGAGAAA
157547 AGAAAAA
1 A-AAAAA
157554 TAAGGTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAGAAA
Done.