Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001137.1 Hibiscus syriacus cultivar Beakdansim tig00002265_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: 69055
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:6277 original size:2 final size:2
Alignment explanation
Indices: 6265--6294 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6255 TTTTAAGAAA
*
6265 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6295 TAAATAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:6550 original size:21 final size:21
Alignment explanation
Indices: 6513--6556 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
6503 GCCCTTTCTT
6513 AATATTGATAAATATATATTAA
1 AATATTGATAAATATAT-TTAA
6535 AATA-TGATTAAA-ATATTTAA
1 AATATTGA-TAAATATATTTAA
6555 AA
1 AA
6557 GTAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 7 0.33
22 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
AATATTGATAAATATATTTAA
Found at i:7987 original size:3 final size:3
Alignment explanation
Indices: 7979--8021 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
7969 TGTAATTATT
*
7979 TAA TAA TAA TAA TAA TAA -AA GAAA TAA -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
8022 TAAAAAACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:9483 original size:29 final size:29
Alignment explanation
Indices: 9421--9484 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
9411 AAACAGTAAC
* *
9421 CAAATATTATAAGTCAGGCAATCATGCTT
1 CAAATTTTATAAATCAGGCAATCATGCTT
*
9450 TAAATTTTAGTAAATCAGG-AATCA-GACTT
1 CAAATTTTA-TAAATCAGGCAATCATG-CTT
9479 CAAATT
1 CAAATT
9485 AGGTAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 20 0.69
30 8 0.28
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (29 bp):
CAAATTTTATAAATCAGGCAATCATGCTT
Found at i:9536 original size:25 final size:25
Alignment explanation
Indices: 9506--9569 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
9496 ACAGTAGTCA
**
9506 AATCAGATCAAACATTATATTTTTG
1 AATCAGAGAAAACATTATATTTTTG
9531 AATCAGAGAAAACATTATATTTTTG
1 AATCAGAGAAAACATTATATTTTTG
9556 AATCAGAGAAAACA
1 AATCAGAGAAAACA
9570 ATCATGTGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (25 bp):
AATCAGAGAAAACATTATATTTTTG
Found at i:21285 original size:31 final size:31
Alignment explanation
Indices: 21232--21313 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
21222 ATTATTTTTT
**
21232 TAATATTTTCGGTTA-TTTTTTAGTTTCTAA
1 TAATATTTTCGGTTATTTTTTTAGCGTCTAA
21262 TAATATTTTCGGTTATTTTTTTAGCGTCTAA
1 TAATATTTTCGGTTATTTTTTTAGCGTCTAA
* *
21293 TAATGTTTTCGGTCATTTTTT
1 TAATATTTTCGGTTATTTTTT
21314 ACCAGTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 15 0.32
31 32 0.68
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (31 bp):
TAATATTTTCGGTTATTTTTTTAGCGTCTAA
Found at i:21756 original size:21 final size:21
Alignment explanation
Indices: 21730--21777 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
21720 GTTTCCAGAT
21730 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
21751 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
21772 TCGCAA
1 TCGCAA
21778 TGTGATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:22755 original size:42 final size:42
Alignment explanation
Indices: 22696--22832 Score: 247
Period size: 42 Copynumber: 3.3 Consensus size: 42
22686 TGCAATTTTA
22696 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
22738 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
22780 GGCTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
22822 GACTATCGCAA
1 GACTATCGCAA
22833 ATCAGTTTTC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:22829 original size:21 final size:21
Alignment explanation
Indices: 22696--22879 Score: 116
Period size: 21 Copynumber: 8.8 Consensus size: 21
22686 TGCAATTTTA
*
22696 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
*
22715 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
*
22738 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
*
22757 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
* * * *
22780 GGCTATCGCAA--CAAATTTG
1 GACTATCGCAACGCGAACTTC
*
22799 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
** **
22822 GACTATCGCAAATC-AGTTTTC
1 GACTATCGCAACGCGA-ACTTC
22843 AGA-T-TCGCAACGCGAACTTC
1 -GACTATCGCAACGCGAACTTC
22863 GACTATCGCAACGCGAA
1 GACTATCGCAACGCGAA
22880 TATGTAGATC
Statistics
Matches: 123, Mismatches: 25, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
19 22 0.18
20 12 0.10
21 60 0.49
22 2 0.02
23 27 0.22
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:22893 original size:41 final size:40
Alignment explanation
Indices: 22696--22875 Score: 204
Period size: 42 Copynumber: 4.3 Consensus size: 40
22686 TGCAATTTTA
22696 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAA-TTGG-ATAAATCGCAACGCGAACTTC
22738 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAA-TTGG-ATAAATCGCAACGCGAACTTC
* *
22780 GGCTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAA-TTGG-ATAAATCGCAACGCGAACTTC
* * *
22822 GACTATCGCAAATC-AGTT--TTCAGATTCGCAACGCGAACTTC
1 GACTATCGC-AA-CGAATTGGAT-A-AATCGCAACGCGAACTTC
22863 GACTATCGCAACG
1 GACTATCGCAACG
22876 CGAATATGTA
Statistics
Matches: 126, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
39 2 0.02
40 3 0.02
41 26 0.21
42 91 0.72
43 3 0.02
44 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (40 bp):
GACTATCGCAACGAATTGGATAAATCGCAACGCGAACTTC
Found at i:26208 original size:137 final size:137
Alignment explanation
Indices: 25892--26208 Score: 384
Period size: 138 Copynumber: 2.3 Consensus size: 137
25882 ACTAAGGTTT
* * *
25892 AATTTATTAGGGTTTAATATTAGAGTCTACACTTTAGGTTTATTTTTATTTTAGTCCCTAATTTT
1 AATTTATTAGGGTTTAATATTAGAGCCTA-ACTTTAGGTTTAATTTCATTTTAGTCCCTAATTTT
* * * * *
25957 AGGGGAATATTTAAAATGGTCCCTGCCAATACTCGAGGTTTCATTTTAATTATTCGGCAGAACAG
65 AGGGGAATATGTAAAAGGGTCCCTGCCAATACTCGAGGTTCCATCTTAATTATTCGACAGAACAG
*
26022 ACTTGTAA
130 AATTGTAA
* * * *
26030 AATTTATTATGGTTTAATATTAGAGCCTGCACTTTATGTTTAATTTCATTTTAGTCCCTACTTTT
1 AATTTATTAGGGTTTAATATTAGAGCCT-AACTTTAGGTTTAATTTCATTTTAGTCCCTAATTTT
* * * * * ** * *
26095 AGGGGAATATGTAAAAGGGTCCC-GTCAATGCTTGGGGTTCCATCTTAATTATTTGATTGAATAT
65 AGGGGAATATGTAAAAGGGTCCCTGCCAATACTCGAGGTTCCATCTTAATTATTCGACAGAACAG
*
26159 AATTTTAA
130 AATTGTAA
*
26167 AATTTATTAGGGTTTAATATTAGAGCCTAAATTATAGGTTTA
1 AATTTATTAGGGTTTAATATTAGAGCCTAACTT-TAGGTTTA
26209 GTTCTATTAA
Statistics
Matches: 150, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
136 3 0.02
137 69 0.46
138 78 0.52
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (137 bp):
AATTTATTAGGGTTTAATATTAGAGCCTAACTTTAGGTTTAATTTCATTTTAGTCCCTAATTTTA
GGGGAATATGTAAAAGGGTCCCTGCCAATACTCGAGGTTCCATCTTAATTATTCGACAGAACAGA
ATTGTAA
Found at i:28580 original size:19 final size:19
Alignment explanation
Indices: 28556--28626 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 19
28546 GACCCGATTT
28556 AAAATAATATATTTA-TTAA
1 AAAATAATAT-TTTACTTAA
*
28575 AAAATAATACTTTTATTTAATA
1 AAAATAATA-TTTTACTT-A-A
* *
28597 AAAATAGATATTTAACTGAA
1 AAAATA-ATATTTTACTTAA
28617 AAAATAATAT
1 AAAATAATAT
28627 ATATAAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 17 0.39
20 10 0.23
21 2 0.05
22 12 0.27
23 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTTACTTAA
Found at i:29376 original size:15 final size:16
Alignment explanation
Indices: 29346--29395 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
29336 AATATTAAAA
29346 ATAATTATTATATATAT
1 ATAA-TATTATATATAT
29363 ATAATATT-TATATAT
1 ATAATATTATATATAT
* *
29378 TTAAT-TTAAATATAT
1 ATAATATTATATATAT
29393 ATA
1 ATA
29396 TTCAGCCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 19 0.66
16 4 0.14
17 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAATATTATATATAT
Found at i:44475 original size:32 final size:32
Alignment explanation
Indices: 44401--44588 Score: 288
Period size: 32 Copynumber: 5.8 Consensus size: 32
44391 GAGTCGATGG
* * *
44401 TTACCAATGTCCTTT-GAGACATATGGACAGATT
1 TTACCTATGT-CTTTCGGGACATATGGACAG-TA
44434 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
*
44466 TTACCTATGTCTTTCGGGACATATGGATAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
44498 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
* * *
44530 TTACCTATGTATTTCAGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
44562 TTACCTATGTCTTTCGGGACATATGGA
1 TTACCTATGTCTTTCGGGACATATGGA
44589 TAGTTACATA
Statistics
Matches: 144, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
32 121 0.84
33 23 0.16
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGTA
Found at i:49988 original size:18 final size:20
Alignment explanation
Indices: 49965--50006 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
49955 AGCATATATT
*
49965 CATACAA-ATCATAT-AACA
1 CATACAATAACATATAAACA
49983 CATACAATAACATATAAACA
1 CATACAATAACATATAAACA
50003 CATA
1 CATA
50007 TACTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (20 bp):
CATACAATAACATATAAACA
Found at i:50555 original size:62 final size:63
Alignment explanation
Indices: 50480--50615 Score: 238
Period size: 62 Copynumber: 2.2 Consensus size: 63
50470 GCTTCCCAGG
*
50480 TATCGATACCCCATGAATAATTTATAAATTTCTACCTTAT-GTATCGATACTCATCCATATGA
1 TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGATACTCATCCATATGA
* *
50542 TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGGTACTCATCCATATGG
1 TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGATACTCATCCATATGA
50605 TATCGATACCC
1 TATCGATACCC
50616 TCACTCGAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 39 0.56
63 31 0.44
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.35
Consensus pattern (63 bp):
TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGATACTCATCCATATGA
Found at i:57561 original size:3 final size:3
Alignment explanation
Indices: 57547--57592 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
57537 CTACAAAAAC
* * *
57547 ATT ATT -TT ATT ATT ATT ATC ATC ATC ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
57593 CATTTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:57579 original size:21 final size:21
Alignment explanation
Indices: 57553--57596 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
57543 AAACATTATT
57553 TTATTATTATTATCATCATCA
1 TTATTATTATTATCATCATCA
* *
57574 TTATTATTATTATTATTATCA
1 TTATTATTATTATCATCATCA
57595 TT
1 TT
57597 TATTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTATTATTATCATCATCA
Found at i:60192 original size:54 final size:53
Alignment explanation
Indices: 60129--60311 Score: 213
Period size: 54 Copynumber: 3.4 Consensus size: 53
60119 TAAAATTAAA
* * *
60129 TATTTATTGTGCCAATTTAGTTATCTACAATAAATTAAAATTATTATAACCAAG
1 TATTTATTGTACCAATTTA-TTATCTAAAATAAATTAAAATTATTATAATCAAG
* * *
60183 TACTTATTGTACCAATTTATTATTCTAAAATAAATTAAAATTATTATTATAAAG
1 TATTTATTGTACCAATTTATTA-TCTAAAATAAATTAAAATTATTATAATCAAG
** * * * * *
60237 TATTTATTGTGTCAATTTATTTATCTATAATAAATCAATATTAATATCATCAAG
1 TATTTATTGTACCAATTTA-TTATCTAAAATAAATTAAAATTATTATAATCAAG
*
60291 TATTTATTGTATCAATTTATT
1 TATTTATTGTACCAATTTATT
60312 GTGTACAATG
Statistics
Matches: 111, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.05
54 103 0.93
55 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (53 bp):
TATTTATTGTACCAATTTATTATCTAAAATAAATTAAAATTATTATAATCAAG
Found at i:64975 original size:33 final size:34
Alignment explanation
Indices: 64920--64988 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
64910 CAATAAAGAT
*
64920 TATATTTTTCCAAAATAATTTTCTCATTTAATTC
1 TATATATTTCCAAAATAATTTTCTCATTTAATTC
*
64954 TATATATTTCC-AAATATTTTTCTCATTTAATTC
1 TATATATTTCCAAAATAATTTTCTCATTTAATTC
64987 TA
1 TA
64989 AAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (34 bp):
TATATATTTCCAAAATAATTTTCTCATTTAATTC
Found at i:68571 original size:118 final size:118
Alignment explanation
Indices: 68433--68681 Score: 346
Period size: 118 Copynumber: 2.1 Consensus size: 118
68423 GTATCCTATG
*
68433 ATGTAAACTCCACCATGAATACAAATACATAATATCTTATGTATCCTAAAA-TCCATTATCTATA
1 ATGTAAACTCCACCACGAATAC-AA-AC---ATATCTTATGTATCCTAAAATTCCATTATCTATA
68497 TCAAAAC-TCGTGTATCCCAAAACA-CTCCCAACA-TCCTAT-ATATCCATCTCTACA
61 TCAAAACTTCGTGTATCCCAAAACATCTCCCAACATTCCTATAATATCCATCTCTACA
** *
68551 ATGTAAACTCCACCACGAATACAAACATATCTTATGTATCCTAAAATTCGTTTATTTATATCAAA
1 ATGTAAACTCCACCACGAATACAAACATATCTTATGTATCCTAAAATTCCATTATCTATATCAAA
* * *
68616 ACTTGGTGTATCCCAAAATATTCTCCCAACATTCCTATAATATCCATCTTTACA
66 ACTTCGTGTATCCCAAAACA-TCTCCCAACATTCCTATAATATCCATCTCTACA
68670 ATGTAAACTCCA
1 ATGTAAACTCCA
68682 AAAGTTACAG
Statistics
Matches: 118, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
113 20 0.17
114 17 0.14
115 15 0.13
116 2 0.02
117 11 0.09
118 27 0.23
119 26 0.22
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (118 bp):
ATGTAAACTCCACCACGAATACAAACATATCTTATGTATCCTAAAATTCCATTATCTATATCAAA
ACTTCGTGTATCCCAAAACATCTCCCAACATTCCTATAATATCCATCTCTACA
Done.