Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004192.1 Hibiscus syriacus cultivar Beakdansim tig00009170_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: 68264
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:218 original size:87 final size:87
Alignment explanation
Indices: 111--294 Score: 314
Period size: 87 Copynumber: 2.1 Consensus size: 87
101 TCCTTCGTCA
* * *
111 TGAAGTTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAA
1 TGAAGTTGAGATCCAAGGGTTGCATTGCTACTTGTGGGCACGATATCCTTCGTCGTGAAGTTAAA
*
176 ATCGTGGATGGCTCATTCGTTG
66 ATCGTGAATGGCTCATTCGTTG
*
198 TGAAGTTGAGATCCAAGGGTTGCATTGCTACTTGTGGGCACTATATCCTTCGTCGTGAAGTTAAA
1 TGAAGTTGAGATCCAAGGGTTGCATTGCTACTTGTGGGCACGATATCCTTCGTCGTGAAGTTAAA
*
263 ATCGTTAATGGCTCATTCGTTG
66 ATCGTGAATGGCTCATTCGTTG
285 TGAAGTTGAG
1 TGAAGTTGAG
295 GTTTGAATTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (87 bp):
TGAAGTTGAGATCCAAGGGTTGCATTGCTACTTGTGGGCACGATATCCTTCGTCGTGAAGTTAAA
ATCGTGAATGGCTCATTCGTTG
Found at i:5426 original size:9 final size:9
Alignment explanation
Indices: 5408--5441 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5398 GGGCATCAAA
*
5408 AATAAAATT
1 AATAATATT
*
5417 AATAGTATT
1 AATAATATT
5426 AATAATATT
1 AATAATATT
5435 AATAATA
1 AATAATA
5442 AGTATTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
AATAATATT
Found at i:10033 original size:19 final size:20
Alignment explanation
Indices: 10009--10077 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 20
9999 GATTTGAAAT
10009 AATTTAA-TAAAATATTTAA
1 AATTTAATTAAAATATTTAA
*
10028 AATTTAATTAATAACATTT--
1 AATTTAATTAA-AATATTTAA
*
10047 ATTTTAATTGAAAATATTTAATA
1 AATTTAATT-AAAATATTT-A-A
10070 AATTTAAT
1 AATTTAAT
10078 AATATAATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 21 0.54
20 5 0.13
21 6 0.15
23 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (20 bp):
AATTTAATTAAAATATTTAA
Found at i:10631 original size:22 final size:22
Alignment explanation
Indices: 10588--10671 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
10578 CTCAACTATT
10588 CTCTCTCCTCCCCCTCTCTCCCTCC
1 CTCTC-CCT-CCCC-CTCTCCCTCC
* *
10613 CTCTCCCTCTCCCTCTCCCTCT
1 CTCTCCCTCCCCCTCTCCCTCC
* *
10635 CTCCCCCTCCCCCTCCCCCTCC
1 CTCTCCCTCCCCCTCTCCCTCC
*
10657 CCCTCCCTCCCCCTC
1 CTCTCCCTCCCCCTC
10672 CCCCGAATCG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 40 0.78
23 3 0.06
24 3 0.06
25 5 0.10
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (22 bp):
CTCTCCCTCCCCCTCTCCCTCC
Found at i:10637 original size:32 final size:32
Alignment explanation
Indices: 10594--10665 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
10584 TATTCTCTCT
* * * *
10594 CCTCCCCCTCTCTCCCTCCCTCTCCCTCTCCC
1 CCTCCCTCTCTCCCCCTCCCCCTCCCCCTCCC
*
10626 TCTCCCTCTCTCCCCCTCCCCCTCCCCCTCCC
1 CCTCCCTCTCTCCCCCTCCCCCTCCCCCTCCC
10658 CCTCCCTC
1 CCTCCCTC
10666 CCCCTCCCCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (32 bp):
CCTCCCTCTCTCCCCCTCCCCCTCCCCCTCCC
Found at i:10672 original size:6 final size:6
Alignment explanation
Indices: 10594--10675 Score: 87
Period size: 6 Copynumber: 13.3 Consensus size: 6
10584 TATTCTCTCT
* * *
10594 CCTCCC CCTCTCTC CCTCCC TCTCCC TCTCCC TCTCCC TCTCTCCC CCTCCC
1 CCTCCC CCTC-C-C CCTCCC CCTCCC CCTCCC CCTCCC -C-CTCCC CCTCCC
10646 CCTCCC CCTCCC CCT--C CCTCCC CCTCCC CC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CC
10676 GAATCGAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
4 4 0.06
6 51 0.75
7 3 0.04
8 10 0.15
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (6 bp):
CCTCCC
Found at i:22295 original size:14 final size:14
Alignment explanation
Indices: 22260--22300 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
22250 ATGAAATAAA
22260 TAATTA-TTATGAT
1 TAATTATTTATGAT
22273 TAATATATTTAT-ATT
1 TAAT-TATTTATGA-T
22288 TAATTATTTATGA
1 TAATTATTTATGA
22301 CCAATAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 10 0.42
15 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TAATTATTTATGAT
Found at i:28805 original size:5 final size:5
Alignment explanation
Indices: 28797--28824 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28787 ACGTATATAC
28797 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
28825 TATGATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:30871 original size:20 final size:19
Alignment explanation
Indices: 30834--30883 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
30824 CTCAAAATCA
***
30834 TTTTTCAAAATTTCAATTT
1 TTTTTCAAAATCAAAATTT
30853 GTTTTTCAAAATCAAAATTT
1 -TTTTTCAAAATCAAAATTT
*
30873 TCTTTCAAAAT
1 TTTTTCAAAAT
30884 TAAATCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTTCAAAATCAAAATTT
Found at i:36529 original size:5 final size:5
Alignment explanation
Indices: 36285--36522 Score: 368
Period size: 5 Copynumber: 48.4 Consensus size: 5
36275 TTTTTATTTT
36285 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
36335 T-ATA TAA-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA T-A-A
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
36381 TAATA TAATA TAATA TAATA TAATATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA T-A-ATA TAATA TAATA TAATA TAATA TAATA
36433 TAATA T-ATA TAATA TAATA T-ATA TAATA T-ATA T-ATA TAATA T-ATAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT-A
36479 TATATA TAATA TAATA TAATA TAATA TATATA TAATA TAATA TA
1 TA-ATA TAATA TAATA TAATA TAATA TA-ATA TAATA TAATA TA
36523 TAATATATAA
Statistics
Matches: 220, Mismatches: 0, Indels: 26
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.01
4 28 0.13
5 174 0.79
6 10 0.05
7 6 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:39356 original size:21 final size:21
Alignment explanation
Indices: 39327--39371 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
39317 GTTTACCGTG
* *
39327 ATTGTGGCCGTCGCGGGCGCT
1 ATTGCGGCCATCGCGGGCGCT
39348 ATTGCGGCCATCGCGGGCGCT
1 ATTGCGGCCATCGCGGGCGCT
39369 ATT
1 ATT
39372 ACGGATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (21 bp):
ATTGCGGCCATCGCGGGCGCT
Found at i:43601 original size:31 final size:31
Alignment explanation
Indices: 43578--43656 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
43568 CATAGATTCT
* *
43578 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
43609 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
43640 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
43657 CCCTCGACCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:44652 original size:21 final size:21
Alignment explanation
Indices: 44610--44654 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
44600 TTTTGTTCGT
* *
44610 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
44631 TTGAATGGGTACCGATTGCCC
1 TTGAAGGGGTACCGATTCCCC
44652 TTG
1 TTG
44655 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:47797 original size:31 final size:31
Alignment explanation
Indices: 47759--47852 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
47749 CCCGAAGGAC
* * *
47759 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
47790 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
47821 CAGTCCATATGTCCCGAAGAACATAGATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
47852 C
1 C
47853 CCTCGACCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 55 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:48853 original size:21 final size:21
Alignment explanation
Indices: 48811--48855 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48801 TTTTGTTTGT
* *
48811 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
48832 TTGAATGGGTACCGATTGCCC
1 TTGAAGGGGTACCGATTCCCC
48853 TTG
1 TTG
48856 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:51885 original size:31 final size:31
Alignment explanation
Indices: 51847--51940 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
51837 CCCGAAGAAC
* * *
51847 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
51878 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
51909 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
51940 C
1 C
51941 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:52975 original size:21 final size:23
Alignment explanation
Indices: 52949--52994 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
52939 GCCCTTGCCC
52949 AAAAATCA-T-ATTTTTAGCTCA
1 AAAAATCATTCATTTTTAGCTCA
52970 AAAAATCATTTCATTTTTAGCTCA
1 AAAAATCA-TTCATTTTTAGCTCA
52994 A
1 A
52995 CACTTCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.36
23 1 0.05
24 13 0.59
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39
Consensus pattern (23 bp):
AAAAATCATTCATTTTTAGCTCA
Found at i:55384 original size:174 final size:176
Alignment explanation
Indices: 55076--55394 Score: 498
Period size: 174 Copynumber: 1.8 Consensus size: 176
55066 TTTTTATTCC
* * * * *
55076 TCGTTTGAAATCAATTTAGATATTTTAGATTCGGATCATAGTTAAGTATTATCTTTTTATCTGAT
1 TCGTTTGAAATCAAATTAGAGATTTTAGATTCGGATCATAGTTAAGAAGTATCTTTTTATATGAT
* *
55141 TTTTTTATTAAGCTAAAGTGATTACAAAGTAGTGTCTATTCTAAATACTATTACTCATTTGACAA
66 TTTTTTATTAAGATAAAGTGATTACAAAGTAGTGTCTATTCTAAATACTATCACTCATTTGACAA
55206 TGAACACTCAATCACATTGCTGTCAAATTTCCTATGCTTCTTGGAA
131 TGAACACTCAATCACATTGCTGTCAAATTTCCTATGCTTCTTGGAA
*
55252 TCGTTTGAAATCAAATTAGAGATTTTAGATTCGGATCATATTTAAGAAGTATCTTTTTATAT-A-
1 TCGTTTGAAATCAAATTAGAGATTTTAGATTCGGATCATAGTTAAGAAGTATCTTTTTATATGAT
* * * * *
55315 TTTTTTATTAAGATAAGGTGATTACAAAGTATTGTTTGTTCTAATTACTATCACTCATTTGACAA
66 TTTTTTATTAAGATAAAGTGATTACAAAGTAGTGTCTATTCTAAATACTATCACTCATTTGACAA
*
55380 TGAACATTCAATCAC
131 TGAACACTCAATCAC
55395 CTTGTTGCAG
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
174 72 0.56
175 1 0.01
176 56 0.43
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (176 bp):
TCGTTTGAAATCAAATTAGAGATTTTAGATTCGGATCATAGTTAAGAAGTATCTTTTTATATGAT
TTTTTTATTAAGATAAAGTGATTACAAAGTAGTGTCTATTCTAAATACTATCACTCATTTGACAA
TGAACACTCAATCACATTGCTGTCAAATTTCCTATGCTTCTTGGAA
Found at i:56453 original size:43 final size:43
Alignment explanation
Indices: 56392--56592 Score: 160
Period size: 43 Copynumber: 4.7 Consensus size: 43
56382 CCTCAATTAA
* * *
56392 TATAAAGGTAGAACGTGAGATT-AAAAAAGTAAAGGACCTCAAT
1 TATAAATGTAAAAAGTGAGATTGAAAAAA-TAAAGGACCTCAAT
* * *
56435 TATAAA-GATAAAAAGTGAGAAT-AAAAAA-AATTAGTAGTCTCAAT
1 TATAAATG-TAAAAAGTGAGATTGAAAAAATAA--AGGA-CCTCAAT
* * * *
56479 TATAAATGTAAAAAGTGGGATTGAAAAAAT-AGGGGCTTCAAT
1 TATAAATGTAAAAAGTGAGATTGAAAAAATAAAGGACCTCAAT
* * * * * *
56521 TATAAATGTAAAAAGTTAGATTGAAAAAATTAGGGGCCTTAGT
1 TATAAATGTAAAAAGTGAGATTGAAAAAATAAAGGACCTCAAT
* *
56564 TATAAATGTAAAATGTGAGATTCAAAAAA
1 TATAAATGTAAAAAGTGAGATTGAAAAAA
56593 AATGTAGGGG
Statistics
Matches: 130, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.02
42 34 0.26
43 62 0.48
44 24 0.18
45 8 0.06
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (43 bp):
TATAAATGTAAAAAGTGAGATTGAAAAAATAAAGGACCTCAAT
Found at i:56521 original size:42 final size:44
Alignment explanation
Indices: 56430--56610 Score: 192
Period size: 42 Copynumber: 4.1 Consensus size: 44
56420 GTAAAGGACC
** ** *
56430 TCAATTATAAA-GATAAAAAGTGAGAATAAAAAAAATTAGTAGTC-
1 TCAATTATAAATG-TAAAAAGTGAG-ATTGAAAAAATTAGGGGCCT
*
56474 TCAATTATAAATGTAAAAAGTGGGATTGAAAAAA-TAGGGG-CT
1 TCAATTATAAATGTAAAAAGTGAGATTGAAAAAATTAGGGGCCT
*
56516 TCAATTATAAATGTAAAAAGTTAGATTGAAAAAATTAGGGGCCT
1 TCAATTATAAATGTAAAAAGTGAGATTGAAAAAATTAGGGGCCT
* * *
56560 T-AGTTATAAATGTAAAATGTGAGATTCAAAAAAAATGTAGGGGCCT
1 TCAATTATAAATGTAAAAAGTGAGATT--GAAAAAAT-TAGGGGCCT
56606 TCAAT
1 TCAAT
56611 GAAATCATTT
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
41 1 0.01
42 36 0.31
43 36 0.31
44 24 0.21
45 8 0.07
46 10 0.09
47 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.28
Consensus pattern (44 bp):
TCAATTATAAATGTAAAAAGTGAGATTGAAAAAATTAGGGGCCT
Found at i:59105 original size:6 final size:6
Alignment explanation
Indices: 59094--59122 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
59084 GGATCCACAA
59094 GGGAAT GGGAAT GGGAAT GGGAAT GGGAA
1 GGGAAT GGGAAT GGGAAT GGGAAT GGGAA
59123 GGAAGCTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.52, T:0.14
Consensus pattern (6 bp):
GGGAAT
Done.