Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000147.1 Hibiscus syriacus cultivar Beakdansim tig00000262_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: 36328
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Found at i:1084 original size:23 final size:20
Alignment explanation
Indices: 1038--1111 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
1028 TGTCAAAGTA
* **
1038 CATCCATGCACCCTGCAGTG
1 CATCCATGCACCATATAGTG
1058 CATCCATGCACC-TGCCACTAGTG
1 CATCCATGCACCAT---A-TAGTG
*
1081 CATCGATGCACCATATAGTG
1 CATCCATGCACCATATAGTG
1101 CATCCATGCAC
1 CATCCATGCAC
1112 TCCATTTCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.02
20 27 0.60
21 1 0.02
23 15 0.33
24 1 0.02
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (20 bp):
CATCCATGCACCATATAGTG
Found at i:1162 original size:20 final size:20
Alignment explanation
Indices: 1131--1183 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1121 AATTCAATTA
* *
1131 GTGCATCGATGCATCTTGCT
1 GTGCATCCATGCATCCTGCT
*
1151 GTGCGTCCATGCATCCTGCT
1 GTGCATCCATGCATCCTGCT
1171 GTGCATCCATGCA
1 GTGCATCCATGCA
1184 CCAAGGCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.30, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGCATCCATGCATCCTGCT
Found at i:2587 original size:13 final size:14
Alignment explanation
Indices: 2562--2590 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2552 GATGATGGTG
2562 AAGGAAGATGAAGA
1 AAGGAAGATGAAGA
2576 AAGGAAGA-GAAGA
1 AAGGAAGATGAAGA
2589 AA
1 AA
2591 AACAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (14 bp):
AAGGAAGATGAAGA
Found at i:4243 original size:21 final size:21
Alignment explanation
Indices: 4217--4256 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4207 AAACAATTGG
*
4217 TAACAATTGATATCATTTTGT
1 TAACAATTAATATCATTTTGT
*
4238 TAACAATTAATATCTTTTT
1 TAACAATTAATATCATTTT
4257 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
TAACAATTAATATCATTTTGT
Found at i:13488 original size:32 final size:32
Alignment explanation
Indices: 13451--13514 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
13441 TCACTCTTAA
13451 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
1 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
13483 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
1 TTTCCCCATCTAACATCCTATGCCTGCTTCCC
13515 CATAAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.44, G:0.06, T:0.34
Consensus pattern (32 bp):
TTTCCCCATCTAACATCCTATGCCTGCTTCCC
Found at i:26532 original size:42 final size:42
Alignment explanation
Indices: 26472--26562 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
26462 CCGAAATCAT
*
26472 GTGTTTGTTTCATATAATTCGTTTTCCAGAAAATGTTTTCTC-
1 GTGTTTGTTTCACATAATTCGTTTTCCAGAAAATGTTTTC-CA
* * *
26514 GTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTCCA
1 GTGTTTGTTTCACATAATTCGTTTTCCAGAAAATGTTTTCCA
26556 GTGTTTG
1 GTGTTTG
26563 GTTAGAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (42 bp):
GTGTTTGTTTCACATAATTCGTTTTCCAGAAAATGTTTTCCA
Found at i:26821 original size:26 final size:24
Alignment explanation
Indices: 26759--26821 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
26749 CATTTTCGTC
26759 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
26783 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
26806 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
26822 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:26823 original size:22 final size:23
Alignment explanation
Indices: 26793--26839 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
26783 AAAATATATT
26793 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
26816 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
26838 TA
1 TA
26840 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:26853 original size:32 final size:32
Alignment explanation
Indices: 26787--26856 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
26777 ATATTTAAAA
* *
26787 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
26819 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
26851 TATATT
1 TATATT
26857 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 13 0.38
31 6 0.18
32 15 0.44
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:26866 original size:53 final size:54
Alignment explanation
Indices: 26798--26978 Score: 151
Period size: 53 Copynumber: 3.3 Consensus size: 54
26788 ATATTTATTA
*
26798 ATATTTCTAATAATATAATATTATATTTTTAATATTATAATA-AAATAATCAATT
1 ATATTT-TAAAAATATAATATTATATTTTTAATATTATAATATAAATAATCAATT
* * * *
26852 ATATTATAAAAATATAAGATATTAT-TTTTT-ATTTTAATAATATATAATAAATTATTT
1 ATATTTTAAAAATAT-A-ATATTATATTTTTAATATT-ATAATATA-AAT-AATCAATT
* * *
26909 ATATATTTAATAATGATAATATT-TATATTTAATA-T-TAATATAAA-AATCTAATA
1 ATAT-TTTAAAAAT-ATAATATTATATTTTTAATATTATAATATAAATAATC-AATT
26962 ATATTTTAATAAATATA
1 ATATTTTAA-AAATATA
26979 TTTAAAATAT
Statistics
Matches: 102, Mismatches: 13, Indels: 26
0.72 0.09 0.18
Matches are distributed among these distances:
52 11 0.11
53 21 0.21
54 19 0.19
55 15 0.15
56 4 0.04
57 20 0.20
58 10 0.10
59 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (54 bp):
ATATTTTAAAAATATAATATTATATTTTTAATATTATAATATAAATAATCAATT
Found at i:26906 original size:30 final size:30
Alignment explanation
Indices: 26851--26922 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
26841 AATAATCAAT
*
26851 TATATTATAA-AA-ATATAAGATATTATTT-
1 TATATT-TAATAATATATAAGAAATTATTTA
* *
26879 TTTATTTTAATAATATATAATAAATTATTTA
1 TATA-TTTAATAATATATAAGAAATTATTTA
26910 TATATTTAATAAT
1 TATATTTAATAAT
26923 GATAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 6 0.17
29 4 0.11
30 23 0.64
31 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TATATTTAATAATATATAAGAAATTATTTA
Found at i:26994 original size:23 final size:23
Alignment explanation
Indices: 26968--27012 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
26958 AATAATATTT
26968 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
26991 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
27013 ATATCACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:26994 original size:34 final size:32
Alignment explanation
Indices: 26949--27012 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 32
26939 AATATTAATA
26949 TAAAAATCTAA-TAATATTTTAATAAATATATT
1 TAAAAATCTAATTAATATTTTAA-AAATATATT
*
26981 TAAAATATACTAATTAATATTTTTAAAATATA
1 TAAAA-AT-CTAATTAATATTTTAAAAATATA
27013 ATATCACACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 5 0.18
33 2 0.07
34 11 0.39
35 10 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (32 bp):
TAAAAATCTAATTAATATTTTAAAAATATATT
Found at i:27328 original size:14 final size:14
Alignment explanation
Indices: 27318--27357 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
27308 TCATTTTACA
27318 GAAAACATTTTCCG
1 GAAAACATTTTCCG
*
27332 GAAAACGTTTTCCG
1 GAAAACATTTTCCG
*
27346 GAAAACGTTTTC
1 GAAAACATTTTC
27358 TAGAAATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (14 bp):
GAAAACATTTTCCG
Found at i:27363 original size:14 final size:14
Alignment explanation
Indices: 27311--27363 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
27301 ATATAATTCA
* *
27311 TTTTACAGAAAACA
1 TTTTCCAGAAAACG
*
27325 TTTTCCGGAAAACG
1 TTTTCCAGAAAACG
*
27339 TTTTCCGGAAAACG
1 TTTTCCAGAAAACG
*
27353 TTTTCTAGAAA
1 TTTTCCAGAAA
27364 TGTAATTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (14 bp):
TTTTCCAGAAAACG
Found at i:27386 original size:14 final size:14
Alignment explanation
Indices: 27367--27425 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
27357 CTAGAAATGT
*
27367 AATTCATTTTCCAG
1 AATTCAATTTCCAG
* * *
27381 AATTCAAATTGCATT
1 AATTCAATTTCCA-G
*
27396 AATTCATTTTCCAG
1 AATTCAATTTCCAG
27410 AATTCAATTTCCAG
1 AATTCAATTTCCAG
27424 AA
1 AA
27426 AACCAATTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:29167 original size:36 final size:36
Alignment explanation
Indices: 29126--29265 Score: 217
Period size: 36 Copynumber: 3.9 Consensus size: 36
29116 ATTTATCCAT
*
29126 TATCAGCTTTGATACATTCATGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
29162 TATCAGCTTTGATACATTCGTGTATCATTGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* * *
29198 TATCAACTTTGGTACATCCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
29234 TATCAGTTTTGGTACATTCGTGTATCAATGTT
1 TATCAGCTTTGATACATTCGTGTATCAATGTT
29266 CAGCACCGTT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
Found at i:29891 original size:14 final size:14
Alignment explanation
Indices: 29872--29904 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29862 TAGAACTATT
29872 TTAGTTTA-TTTTA
1 TTAGTTTAGTTTTA
29885 CTTAGTTTAGTTTTA
1 -TTAGTTTAGTTTTA
29900 TTAGT
1 TTAGT
29905 ATATATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (14 bp):
TTAGTTTAGTTTTA
Found at i:32738 original size:16 final size:16
Alignment explanation
Indices: 32717--32749 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
32707 TAATAAATAG
32717 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
32733 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
32749 A
1 A
32750 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:32830 original size:10 final size:10
Alignment explanation
Indices: 32815--32889 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
32805 CATTTAATAA
32815 ATAAACGAAC
1 ATAAACGAAC
32825 ATAAACGAAC
1 ATAAACGAAC
32835 ----ACGAAC
1 ATAAACGAAC
32841 ATAAACGAAC
1 ATAAACGAAC
** *
32851 ACGAAC-ATAA
1 ATAAACGA-AC
32861 ATGAACACGAAC
1 AT-AA-ACGAAC
32873 ATAAACGAAC
1 ATAAACGAAC
32883 ATAAACG
1 ATAAACG
32890 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:32840 original size:16 final size:16
Alignment explanation
Indices: 32819--32883 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
32809 TAATAAATAA
32819 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
32835 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
32851 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
32867 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
32883 A
1 A
32884 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:33652 original size:14 final size:14
Alignment explanation
Indices: 33635--33690 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
33625 AATGAACATA
33635 AACGAACATAATCG
1 AACGAACATAATCG
33649 AACGAACAT-A---
1 AACGAACATAATCG
* *
33659 AACAAACATAACCG
1 AACGAACATAATCG
*
33673 AACGAAGATAATCG
1 AACGAACATAATCG
33687 AACG
1 AACG
33691 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 24 0.71
ACGTcount: A:0.54, C:0.21, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:33655 original size:24 final size:24
Alignment explanation
Indices: 33615--33689 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
33605 GATTGAGTTA
*
33615 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
33639 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* * *
33663 AACATAACCGAACGAAGATAATCG
1 AACATAATCGAACGAACATAAACG
33687 AAC
1 AAC
33690 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Done.