Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008682.1 Hibiscus syriacus cultivar Beakdansim tig00111704_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: 58793
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6299 original size:26 final size:26
Alignment explanation
Indices: 6267--6316 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
6257 TGATAGTACG
*
6267 TTGATAGTTATGATATCCTTAAACGT
1 TTGATAGTTATGATAACCTTAAACGT
6293 TTGATAGTTATGATAACCTTAAAC
1 TTGATAGTTATGATAACCTTAAAC
6317 TTAGCATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (26 bp):
TTGATAGTTATGATAACCTTAAACGT
Found at i:8112 original size:21 final size:22
Alignment explanation
Indices: 8085--8134 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
8075 ATTTTTTAAA
8085 ATATATTAACTTAAAATATTTT
1 ATATATTAACTTAAAATATTTT
* * *
8107 -TATATTAATTTAATATGTTTT
1 ATATATTAACTTAAAATATTTT
8128 ATATATT
1 ATATATT
8135 TATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTAACTTAAAATATTTT
Found at i:11981 original size:32 final size:31
Alignment explanation
Indices: 11920--11982 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
11910 TTAATAATTT
* * *
11920 GATTATGTAAAAAATTATTCTTTGATATATA
1 GATTATATAAAAAAATATTCATTGATATATA
11951 GATTATATAAAAAAATATTACATT-ATTATATA
1 GATTATATAAAAAAATATT-CATTGA-TATATA
11983 TTTTAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (31 bp):
GATTATATAAAAAAATATTCATTGATATATA
Found at i:12104 original size:9 final size:9
Alignment explanation
Indices: 12090--12115 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12080 CTTAAAGTAC
12090 AAAATTTAT
1 AAAATTTAT
12099 AAAATTTAT
1 AAAATTTAT
12108 AAAATTTA
1 AAAATTTA
12116 CGTAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATTTAT
Found at i:21543 original size:17 final size:17
Alignment explanation
Indices: 21521--21553 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21511 TAAGAGGGAG
21521 GAAAAATAAT-AATAATA
1 GAAAAA-AATAAATAATA
21538 GAAAAAAATAAATAAT
1 GAAAAAAATAAATAAT
21554 GTAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
GAAAAAAATAAATAATA
Found at i:21834 original size:193 final size:183
Alignment explanation
Indices: 21550--21928 Score: 525
Period size: 193 Copynumber: 2.0 Consensus size: 183
21540 AAAAAATAAA
*
21550 TAATGTAAATAAATACTTTAATAAAGAAGTAAAAAAGGGTAAAATACAAAATGTGTACATATATA
1 TAATGTAAATAAATACTATAATAAAGAAGTAAAAAAGGGTAAAATACAAAATGTGTACATATATA
*
21615 TATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAATGTAT-AAA
66 TATATAATATAACATATAAATGAAATAATAATATACTAATAATAAA--TATACGAATGTATAAAA
** *
21679 AAACTAATA-ATAGTATAAATATAT-ATATATTATAATGTAATATAAAAATAATTAAAAC
129 AAAAAAATATATA-TA-AAATATATAAAATATTATAATGT-A-AT-AAAATAATTAAAAC
21737 TAATGTAAATAAATA-TAATAATAAAGAAGTAAACAAATAGGGTAAAATAC-AAATGTGTACATA
1 TAATGTAAATAAATACT-ATAATAAAGAAGT-AA-AAA-AGGGTAAAATACAAAATGTGTAC--A
*
21800 TACATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATACGAATGT
60 T--ATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATACGAATGT
*
21865 GTAAAAAAAAAAATATATATAAAATATATAAAATATTATAATGTAATAAAATAATTAAAAC
123 ATAAAAAAAAAAATATATATAAAATATATAAAATATTATAATGTAATAAAATAATTAAAAC
21926 TAA
1 TAA
21929 ATCCCGAGAA
Statistics
Matches: 174, Mismatches: 7, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
186 1 0.01
187 27 0.16
188 2 0.01
189 30 0.17
190 14 0.08
191 23 0.13
192 25 0.14
193 52 0.30
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (183 bp):
TAATGTAAATAAATACTATAATAAAGAAGTAAAAAAGGGTAAAATACAAAATGTGTACATATATA
TATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATACGAATGTATAAAAAA
AAAAATATATATAAAATATATAAAATATTATAATGTAATAAAATAATTAAAAC
Found at i:22912 original size:3 final size:3
Alignment explanation
Indices: 22904--22938 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
22894 GTAAAGAGAA
22904 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22939 CAAATAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23607 original size:105 final size:105
Alignment explanation
Indices: 23407--24178 Score: 1345
Period size: 105 Copynumber: 7.4 Consensus size: 105
23397 ATATTGTTCC
* ** * *
23407 GAGTCCAATATCCTCCGCCGTGAAGTCGAAATTGGCTCTGAAATTGAG--ATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
23470 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
23510 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
23575 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
23615 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
23680 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
23720 GAGTCAAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
23785 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
23825 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
23890 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
23930 GAGTCC-A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
23993 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
24033 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
24098 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
24138 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
24179 GTAAAACATA
Statistics
Matches: 642, Mismatches: 23, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
103 145 0.23
104 2 0.00
105 495 0.77
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:24914 original size:1 final size:1
Alignment explanation
Indices: 24910--24944 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
24900 TTTTTCTCCC
24910 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24945 CAACTTAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35956 original size:8 final size:8
Alignment explanation
Indices: 35943--35980 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
35933 ACAAAATGTG
35943 TACATATA
1 TACATATA
35951 TACATATA
1 TACATATA
*
35959 TATATATA
1 TACATATA
35967 TA-ATATA
1 TACATATA
35974 -ACATATA
1 TACATATA
35981 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:35992 original size:203 final size:195
Alignment explanation
Indices: 35691--36091 Score: 626
Period size: 204 Copynumber: 2.0 Consensus size: 195
35681 GAAAAAATAA
*
35691 TAATGTAAATAAATACTTTAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
1 TAATGTAAATAAATACTATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
* *
35756 TATATATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACG-ATGTAT
66 TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATGTAT
* * *
35820 AAAAAATAATAATAGTATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
131 AAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
35885 TAATGTAAATAAATA-TAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATA
1 TAATGTAAATAAATACT-ATAATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTG------
*
35949 TATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATAT
58 --TACATATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATAT
*
36014 ACGAATGTGTAAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGA
121 ACGAATGTATAAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGA
36079 TAATTAAAAC
186 TAATTAAAAC
36089 TAA
1 TAA
36092 AATCCCGAGA
Statistics
Matches: 188, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
193 1 0.01
194 30 0.16
195 24 0.13
203 63 0.34
204 70 0.37
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (195 bp):
TAATGTAAATAAATACTATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATGTAT
AAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
Found at i:37078 original size:3 final size:3
Alignment explanation
Indices: 37070--37104 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
37060 GTAAAGAGAA
37070 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37105 CAAATAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42329 original size:2 final size:2
Alignment explanation
Indices: 42322--42353 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42312 AACGCGGGAG
42322 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42354 ATCGTTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42770 original size:33 final size:35
Alignment explanation
Indices: 42706--42771 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 35
42696 AAAATATTTA
*
42706 TATATTTTCTTTAAAAAAATTAAATTAATAAAATT
1 TATATTTTCTTTAAAAAAATTAAAATAATAAAATT
*
42741 TATATTTT-TTT-ACAAAATTCAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAAATT-AAAATAATAAAA
42772 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 8 0.29
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (35 bp):
TATATTTTCTTTAAAAAAATTAAAATAATAAAATT
Found at i:45600 original size:18 final size:18
Alignment explanation
Indices: 45577--45612 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45567 ACTGAGATTT
* *
45577 ATTATTTTTTATTAGTAA
1 ATTATTTTATAATAGTAA
45595 ATTATTTTATAATAGTAA
1 ATTATTTTATAATAGTAA
45613 TGATAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTATTTTATAATAGTAA
Found at i:47371 original size:22 final size:20
Alignment explanation
Indices: 47332--47372 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
47322 TCACCACCTA
*
47332 TTACTTAATTTATGTTTTTG
1 TTACTTAATTTATATTTTTG
47352 TTACTTAACTATTATATTTTT
1 TTACTTAA-T-TTATATTTTT
47373 TAAATCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (20 bp):
TTACTTAATTTATATTTTTG
Found at i:48505 original size:2 final size:2
Alignment explanation
Indices: 48498--48558 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
48488 CATTCGACTT
48498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48540 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
48559 CTTTACTTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57061 original size:101 final size:101
Alignment explanation
Indices: 56886--57080 Score: 257
Period size: 101 Copynumber: 1.9 Consensus size: 101
56876 GTGAAGTGAT
* ** * * *
56886 TGATATGCCATGGTGTTATTGGTGGGTACACTAGTATATTTTCGATATGACTGCACTTTATGTGC
1 TGATATACCATGGTGTTACCGGTAGGTACACTAATATATTTTAGATATGACTGCACTTTATGTGC
*
56951 ATATATGATTCTGATGTGATACCACTGTGGTGCTTA
66 ATATATGATTCTGATATGATACCACTGTGGTGCTTA
* ** * *
56987 TGATATACGATGGTGTTACCGGTAGGTACACTAATATATTTTAGATA-GGTTGTACTTTGTGTGC
1 TGATATACCATGGTGTTACCGGTAGGTACACTAATATATTTTAGATATGACTGCACTTTATGTGC
*
57051 ATATTATGATTCTGATATGATAGCACTGTG
66 ATA-TATGATTCTGATATGATACCACTGTG
57081 TTTGCTAATA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
100 16 0.20
101 64 0.80
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (101 bp):
TGATATACCATGGTGTTACCGGTAGGTACACTAATATATTTTAGATATGACTGCACTTTATGTGC
ATATATGATTCTGATATGATACCACTGTGGTGCTTA
Found at i:58306 original size:47 final size:47
Alignment explanation
Indices: 58247--58379 Score: 197
Period size: 47 Copynumber: 3.0 Consensus size: 47
58237 CACACATTAT
* *
58247 TTTGGAGGGTAAGTCTATCAAACAAGATTTGCTACATACACAAAAAA
1 TTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAAA
*
58294 TTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAAT
1 TTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAAA
58341 TTTGGAA-G---G-CTCTCAAACAAGATTTGCTA-ATACACAAAA
1 TTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAA
58380 TTCAAACTTA
Statistics
Matches: 83, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
41 10 0.12
42 20 0.24
43 1 0.01
46 1 0.01
47 51 0.61
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (47 bp):
TTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAAA
Done.