Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000846.1 Hibiscus syriacus cultivar Beakdansim tig00001630_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: 988667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:973752 original size:145 final size:145
Alignment explanation
Indices: 973478--973740 Score: 350
Period size: 145 Copynumber: 1.8 Consensus size: 145
973468 ACAGTCTAAT
* * *
973478 GAGGTTACAGTTCATAAGATTGAAGTGTTAGATATGTTTTCAGTATAGGCAGGTAATTTAGGGGG
1 GAGGTTACAATTCATAAGATTAAAGTGTTAGATATGTTTTCAGTATAGGCAGGCAATTTAGGGGG
* * * * * *
973543 AAACAAAAGGAAAGTATTTTGACCAACTCTAGACTATTCATTTACTAATCATTAAGTAAACCTTA
66 AAACAAAAGGAAAATATTATGACCAACGCAAGACTATTCACTCACTAATCATTAAGTAAACCTTA
973608 TCTGAAAAACATAAC
131 TCTGAAAAACATAAC
* * *
973623 GAGGTTGCAATTCATAATATTAAAGTGTTAGATATGTTTTC-GATATAGGCAGGCACTTTAGGGG
1 GAGGTTACAATTCATAAGATTAAAGTGTTAGATATGTTTTCAG-TATAGGCAGGCAATTTAGGGG
* * * *
973687 GAAATAAAAGGAAAATAGTTAT-AGCAACGCAAGAGTATTCACTCATTAATCATT
65 GAAACAAAAGGAAAATA-TTATGACCAACGCAAGACTATTCACTCACTAATCATT
973741 TAATGATCCT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
144 1 0.01
145 96 0.96
146 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (145 bp):
GAGGTTACAATTCATAAGATTAAAGTGTTAGATATGTTTTCAGTATAGGCAGGCAATTTAGGGGG
AAACAAAAGGAAAATATTATGACCAACGCAAGACTATTCACTCACTAATCATTAAGTAAACCTTA
TCTGAAAAACATAAC
Found at i:974429 original size:143 final size:140
Alignment explanation
Indices: 974029--974542 Score: 612
Period size: 143 Copynumber: 3.6 Consensus size: 140
974019 TCACTCACAG
* * ** * * *
974029 GGTTACAGTTCATAACATAGATGTGTTAGATATAATTTCAATATAGGTTGGTATTATGGGAAATA
1 GGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTATTAGGGGAAATA
*
974094 AAAGGAAAATAGTTAGAGCAACAAAGAGTATTCACTCGCTAATCATTGAATAAA-CTAAGATTTG
66 AAAGGAAAATAGTTAGAGCAACAAAGAGTATTCACTCGCTAATCATTGAATAAACCTTA-A-TTG
* *
974158 AGAATGTAGCAA
129 AGAATCTAACAA
974170 GGTTACAGTTCATAACATTGAAGTG-T---TA-GTTTTCGATATAGGTAGGTATTTTAGGGTGTA
1 GGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTA--TTAGGG-G-A
** * *
974230 AA-AAAAGGAAAATAGTTAGAGCAATTTAAGAGTATTCACTCACTAATCATTCAATAAACCTTAA
62 AATAAAAGGAAAATAGTTAGAGCAA-CAAAGAGTATTCACTCGCTAATCATTGAATAAACCTTAA
*
974294 TGTGAGAATCTAACGA
126 T-TGAGAATCTAACAA
* *
974310 GGTTACAGTTCATAACATTGAAGTGTTAGGTATGTTTTCGATATGGGTAGGTATTAGGGGGAAAT
1 GGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTATTA-GGGGAAAT
* * *
974375 AAAAGGAAAATAGTTAGACCAACACAAGAGTATCCACTCGCTAATAATTGAATAAACCTTAACTT
65 AAAAGGAAAATAGTTAGAGCAACA-AAGAGTATTCACTCGCTAATCATTGAATAAACCTTAA-TT
*
974440 GAGAACCTAACAA
128 GAGAATCTAACAA
* * * *
974453 GGTTACAGTTCATAACATTTG-AGTGTTTGATATGTTTTCGATAGAGTTAGGTCCTTTAGGGGAA
1 GGTTACAGTTCATAACA-TTGAAGTGTTAGATATGTTTTCGATATAGGTAGGT--ATTAGGGGAA
*
974517 ATAAAAGGAAAATAGTTTGAGCAACA
63 ATAAAAGGAAAATAGTTAGAGCAACA
974543 GAATAGTTTT
Statistics
Matches: 321, Mismatches: 33, Indels: 35
0.83 0.08 0.09
Matches are distributed among these distances:
136 16 0.05
137 2 0.01
138 5 0.02
139 24 0.07
140 70 0.22
141 27 0.08
142 3 0.01
143 113 0.35
144 39 0.12
145 22 0.07
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (140 bp):
GGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTATTAGGGGAAATA
AAAGGAAAATAGTTAGAGCAACAAAGAGTATTCACTCGCTAATCATTGAATAAACCTTAATTGAG
AATCTAACAA
Found at i:974593 original size:144 final size:144
Alignment explanation
Indices: 974029--974614 Score: 457
Period size: 143 Copynumber: 4.1 Consensus size: 144
974019 TCACTCACAG
* * ** * * * *
974029 GGTTACAGTTCATAACA-TAGATGTGTTAGATATAATTTCAATATAGGTTGGTATTA-TGGGAAA
1 GGTTACAGTTCATAACATTTGAAGTGTTAGATATGTTTTCGATATGGGTAGGTATTAGGGGGAAA
* * * * * *
974092 TAAAAGGAAAATAGTTAGAGCAACA-AAGAGTATTCACTCGCTAATCATTGAATAAA-CTAAGAT
66 TAAAAGGAAAATAGTTAGACCAACACAAGAGTATCCACTCGCCAATAATTGAATAAACCTTA-AC
** * ** *
974155 TTGAGAATGTAGCAA
130 TCAAAAACCTAACAA
* *
974170 GGTTACAGTTCATAACA-TTGAAGTG-T---TA-GTTTTCGATATAGGTAGGTATTTTAGGGTGT
1 GGTTACAGTTCATAACATTTGAAGTGTTAGATATGTTTTCGATATGGGTAGGTA--TTAGGG-GG
* *** * * * * *
974229 AAA-AAAAGGAAAATAGTTAGAGCAATTTAAGAGTATTCACTCACTAATCATTCAATAAACCTTA
63 AAATAAAAGGAAAATAGTTAGACCAACACAAGAGTATCCACTCGCCAATAATTGAATAAACCTTA
** * * *
974293 A-TGTGAGAATCTAACGA
128 ACT-CAAAAACCTAACAA
*
974310 GGTTACAGTTCATAACA-TTGAAGTGTTAGGTATGTTTTCGATATGGGTAGGTATTAGGGGGAAA
1 GGTTACAGTTCATAACATTTGAAGTGTTAGATATGTTTTCGATATGGGTAGGTATTAGGGGGAAA
*
974374 TAAAAGGAAAATAGTTAGACCAACACAAGAGTATCCACTCGCTAATAATTGAATAAACCTTAACT
66 TAAAAGGAAAATAGTTAGACCAACACAAGAGTATCCACTCGCCAATAATTGAATAAACCTTAACT
** *
974439 TGAGAACCTAACAA
131 CAAAAACCTAACAA
* * *
974453 GGTTACAGTTCATAACATTTG-AGTGTTTGATATGTTTTCGATA-GAGTTAGGTCCTTTA-GGGG
1 GGTTACAGTTCATAACATTTGAAGTGTTAGATATGTTTTCGATATG-GGTAGGT--ATTAGGGGG
* * * * * * * * ** ** *
974515 AAATAAAAGGAAAATAGTTTGAGCAACAGAATAGTTTTCATTCTCCGTTTGTTGAATAAACCTTG
63 AAATAAAAGGAAAATAGTTAGACCAACACAAGAGTATCCACTCGCCAATAATTGAATAAACCTTA
974580 ACTCAAAAACCTAACAA
128 ACTCAAAAACCTAACAA
**
974597 GGTTGTAGTTCATAACAT
1 GGTTACAGTTCATAACAT
974615 CTTGGTATTG
Statistics
Matches: 376, Mismatches: 51, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
136 16 0.04
137 2 0.01
138 3 0.01
139 24 0.06
140 71 0.19
141 27 0.07
142 5 0.01
143 115 0.31
144 91 0.24
145 22 0.06
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (144 bp):
GGTTACAGTTCATAACATTTGAAGTGTTAGATATGTTTTCGATATGGGTAGGTATTAGGGGGAAA
TAAAAGGAAAATAGTTAGACCAACACAAGAGTATCCACTCGCCAATAATTGAATAAACCTTAACT
CAAAAACCTAACAA
Found at i:977780 original size:48 final size:47
Alignment explanation
Indices: 977709--977803 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 47
977699 ATGTTAAGAA
*
977709 ATCGATGCTCACTTAAACTAGATAGTAACCTACTGATTGGGATATAGC
1 ATCGATGCCCACTTAAACTAGATAGTAACCTACTGATT-GGATATAGC
* *
977757 ATCGATGCCCATTTAAACTAGATAGTAACCTACTGATTGTATATAGC
1 ATCGATGCCCACTTAAACTAGATAGTAACCTACTGATTGGATATAGC
977804 CAAATATGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 8 0.18
48 36 0.82
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (47 bp):
ATCGATGCCCACTTAAACTAGATAGTAACCTACTGATTGGATATAGC
Found at i:979479 original size:51 final size:50
Alignment explanation
Indices: 979369--979532 Score: 260
Period size: 51 Copynumber: 3.3 Consensus size: 50
979359 AGGATTAGAT
979369 TTATTATTTTATTAGGAATTAGGATAGAGTT-AAAATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAATTAGGATAGAGTTAAAAATTATCTTTAGTTTA
979418 TTATTATTTTATTAGGAATTAGGATAGAGTTAAAATATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAATTAGGATAGAGTTAAAA-ATTATCTTTAGTTTA
* * *
979469 TTATTATTTTATTAGGAATTAGGATAGAATCAAAACATTATCATTT-GTTGA
1 TTATTATTTTATTAGGAATTAGGATAGAGTTAAAA-ATTATC-TTTAGTTTA
979520 TTATTATTTTATT
1 TTATTATTTTATT
979533 CATTAGTTAC
Statistics
Matches: 108, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
49 31 0.29
50 3 0.03
51 71 0.66
52 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (50 bp):
TTATTATTTTATTAGGAATTAGGATAGAGTTAAAAATTATCTTTAGTTTA
Found at i:981289 original size:18 final size:18
Alignment explanation
Indices: 981234--981280 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
981224 CCAAACCTCT
981234 TTGACCTGACCTGTTGAC
1 TTGACCTGACCTGTTGAC
981252 TTGACCTGACCTGTTGAC
1 TTGACCTGACCTGTTGAC
981270 TTGACCTGACC
1 TTGACCTGACC
981281 CTTTAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (18 bp):
TTGACCTGACCTGTTGAC
Found at i:987970 original size:19 final size:20
Alignment explanation
Indices: 987946--987988 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
987936 AGCATTTATC
*
987946 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
987965 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
987985 TTCA
1 TTCA
987989 AAGGGTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Done.