Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009234.1 Hibiscus syriacus cultivar Beakdansim tig00112856_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: 912649
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:885415 original size:3 final size:3
Alignment explanation
Indices: 885407--885479 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
885397 TTAATATATT
* * * *
885407 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TTAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
*
885453 TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
885480 ATAAATCAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 57 0.97
4 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:886517 original size:113 final size:113
Alignment explanation
Indices: 885743--886516 Score: 1140
Period size: 113 Copynumber: 6.8 Consensus size: 113
885733 TCTTGATGAG
* * *
885743 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* * *
885808 GAAAAGTTGATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
* ** *
885856 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* *
885921 GAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGTTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
** *
885969 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
*
886034 GAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
* * *
886082 TTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* *
886147 GAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAAGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
* * *
886195 TTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* * * *
886260 GAAAAGCAGATCCATTGAA-TGATGGATTTAAACATAAGGTTGAACAAA
66 GAAAAGCTGATCCA-TCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
* * *
886308 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTATCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* * * *
886373 GAAAAGCCGATCCATTGAA-TGATGGATTTAAACATAAGGTTGAACAAA
66 GAAAAGCTGATCCA-TCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
* * *
886421 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTATCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* *
886486 GAAAAGCCGATCCATTGAA-TGATGGATTTAA
66 GAAAAGCTGATCCA-TCAAGTGATGGATTTAA
886517 ATCTTTGCTA
Statistics
Matches: 625, Mismatches: 35, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
113 622 1.00
114 3 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
GAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
Found at i:887444 original size:83 final size:83
Alignment explanation
Indices: 887305--887809 Score: 866
Period size: 83 Copynumber: 6.1 Consensus size: 83
887295 CTTATTTCTA
* * * * *
887305 CTATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
887370 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
887388 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
887453 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
887471 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
887536 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * * *
887554 GTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGACAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
887619 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
887637 CTATGAGCATATTCATCTTCCAAATTCAATGTTTGATTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
887702 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
887720 CTATGAGCATATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
887785 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
887803 CTATGAG
1 CTATGAG
887810 TACATTGCAT
Statistics
Matches: 399, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 399 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CTATGAGCATATTCATCTTCCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:888989 original size:9 final size:9
Alignment explanation
Indices: 888966--889009 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
888956 CCCTCATTCA
888966 TTTTTTTTC
1 TTTTTTTTC
* *
888975 TCTTTTTCC
1 TTTTTTTTC
888984 TTTTTTTTC
1 TTTTTTTTC
*
888993 TTTTCTTTC
1 TTTTTTTTC
889002 TTTTTTTT
1 TTTTTTTT
889010 TCTCTCTCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:888989 original size:18 final size:19
Alignment explanation
Indices: 888966--889019 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
888956 CCCTCATTCA
888966 TTTTTTTTCTCTT-TTTCC
1 TTTTTTTTCTCTTCTTTCC
* *
888984 TTTTTTTTCTTTTCTTTCT
1 TTTTTTTTCTCTTCTTTCC
889003 TTTTTTTTCTCTCTCTT
1 TTTTTTTTCTCT-TCTT
889020 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 12 0.39
19 15 0.48
20 4 0.13
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTTCTCTTCTTTCC
Found at i:900398 original size:15 final size:15
Alignment explanation
Indices: 900360--900406 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
900350 TTTTCTTCGA
*
900360 TATTGAAAAATAAA-
1 TATTAAAAAATAAAT
*
900374 TATT--AAAATAATT
1 TATTAAAAAATAAAT
900387 TATTAAAAAATAAAT
1 TATTAAAAAATAAAT
900402 TATTA
1 TATTA
900407 TTTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 4 0.14
15 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TATTAAAAAATAAAT
Found at i:901308 original size:15 final size:14
Alignment explanation
Indices: 901284--901325 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
901274 CCTCGGTAAG
*
901284 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
901299 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
901313 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
901326 GCTGCGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:901316 original size:20 final size:20
Alignment explanation
Indices: 901284--901325 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
901274 CCTCGGTAAG
*
901284 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
901304 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
901324 TT
1 TT
901326 GCTGCGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:901765 original size:3 final size:3
Alignment explanation
Indices: 901757--901838 Score: 101
Period size: 3 Copynumber: 27.0 Consensus size: 3
901747 TTAATATATT
* * *
901757 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
901805 TTAT TAA TAA TAA TAA TTA CAA TAA TAA TAA TAA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
901839 ATAAATCAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 64 0.97
4 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Done.