Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006019.1 Hibiscus syriacus cultivar Beakdansim tig00014199_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: 38380
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:12254 original size:20 final size:20
Alignment explanation
Indices: 12229--12275 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
12219 TTTTCAACAT
12229 GAAGTATTGATCTATTCATG
1 GAAGTATTGATCTATTCATG
12249 GAAGTATTGATCTATTCATG
1 GAAGTATTGATCTATTCATG
12269 GAAGTAT
1 GAAGTAT
12276 CAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (20 bp):
GAAGTATTGATCTATTCATG
Found at i:14767 original size:207 final size:207
Alignment explanation
Indices: 14412--14822 Score: 788
Period size: 207 Copynumber: 2.0 Consensus size: 207
14402 AATACATGCC
*
14412 CCTAGATTTAAAAGTACTCTTATAAGCATAAAATTTTGATGGTGTTTTCTCTCATTGACAAGATT
1 CCTAGATTTAAAAGTACTCTTATAAGCATAAAATTTTGATGATGTTTTCTCTCATTGACAAGATT
14477 TATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCCT
66 TATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCCT
14542 CCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGATG
131 CCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGATG
14607 CAAAAGTCAGAG
196 CAAAAGTCAGAG
14619 CCTAGATTTTAAAAGTACTCTTATAAGCAT-AAATTTTGATGATGTTTTCTCTCATTGACAAGAT
1 CCTAGA-TTTAAAAGTACTCTTATAAGCATAAAATTTTGATGATGTTTTCTCTCATTGACAAGAT
14683 TTATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCC
65 TTATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCC
*
14748 TCCCATCCTAGTAATGTTAGCGATGAGTTCCTTTATAAGATATAGGTTCATAGGTATCAGTTGAT
130 TCCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGAT
14813 GCAAAAGTCA
195 GCAAAAGTCA
14823 TAGAGGTGAT
Statistics
Matches: 201, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
207 178 0.89
208 23 0.11
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (207 bp):
CCTAGATTTAAAAGTACTCTTATAAGCATAAAATTTTGATGATGTTTTCTCTCATTGACAAGATT
TATAGAAAGTGTTGTGGTGGATGGTTCCAAGTGTAGTCTTGAGGGTAGGGTTAGGAGTCGTTCCT
CCCATCCTAGTAATGTTAGCGATGAGTTCCTTCATAAGATATAGGTTCATAGGTATCAGTTGATG
CAAAAGTCAGAG
Found at i:17498 original size:2 final size:2
Alignment explanation
Indices: 17491--17519 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17481 AGTTCATTTG
17491 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17520 TATTGATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17592 original size:2 final size:2
Alignment explanation
Indices: 17585--17627 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
17575 GTGTGCATGT
17585 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
17627 T
1 T
17628 GGGTTAACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17657 original size:16 final size:16
Alignment explanation
Indices: 17631--17679 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
17621 TATATATGGG
17631 TTAACTATTAGTTATTA
1 TTAA-TATTAGTTATTA
*
17648 TTAATATTAGTTATAA
1 TTAATATTAGTTATTA
17664 TT-ATATATA-TTATTA
1 TTAATAT-TAGTTATTA
17679 T
1 T
17680 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 10 0.34
16 15 0.52
17 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (16 bp):
TTAATATTAGTTATTA
Found at i:17683 original size:10 final size:10
Alignment explanation
Indices: 17643--17696 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 10
17633 AACTATTAGT
17643 TATTATTA-A
1 TATTATTATA
17652 TATTAGTTATA
1 TATTA-TTATA
17663 -ATTA-TATA
1 TATTATTATA
17671 TATTATTATA
1 TATTATTATA
*
17681 TATT-TTA-C
1 TATTATTATA
17689 TATTATTA
1 TATTATTA
17697 ATTAAATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 8 0.21
9 15 0.38
10 15 0.38
11 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
TATTATTATA
Found at i:18604 original size:26 final size:26
Alignment explanation
Indices: 18564--18695 Score: 97
Period size: 26 Copynumber: 4.9 Consensus size: 26
18554 TTAATAATTT
18564 TCAAATAAATTTCGGTTCGATTAACGG
1 TCAAAT-AATTTCGGTTCGATTAACGG
* *
18591 TCAAATAATTTCGGTTCAATTAATGG
1 TCAAATAATTTCGGTTCGATTAACGG
* * * * ***
18617 TTAAAGAAAAAAAATTCGGTT--AATAATTT
1 -T----CAAATAATTTCGGTTCGATTAACGG
*
18646 TCAAATAAATTTCGGTTCGATTAACGA
1 TCAAAT-AATTTCGGTTCGATTAACGG
18673 TCAAATAATTTCGGTTCGATTAA
1 TCAAATAATTTCGGTTCGATTAA
18696 TGTTAAAGAA
Statistics
Matches: 82, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
24 3 0.04
25 9 0.11
26 35 0.43
27 17 0.21
28 1 0.01
29 5 0.06
31 12 0.15
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (26 bp):
TCAAATAATTTCGGTTCGATTAACGG
Found at i:18684 original size:82 final size:81
Alignment explanation
Indices: 18547--18721 Score: 323
Period size: 82 Copynumber: 2.1 Consensus size: 81
18537 TTATTCGGTT
*
18547 AATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATT
1 AATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTTCAATT
18612 AATGGTTAAAGAAAAAA
66 AAT-GTTAAAGAAAAAA
*
18629 AATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTTCGATT
1 AATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTTCAATT
18694 AATGTTAAAGAAAAAA
66 AATGTTAAAGAAAAAA
18710 AATTCGGTTAAT
1 AATTCGGTTAAT
18722 TTGGTTCGGT
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
81 25 0.27
82 66 0.73
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (81 bp):
AATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTTCAATT
AATGTTAAAGAAAAAA
Found at i:18788 original size:26 final size:27
Alignment explanation
Indices: 18740--18790 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
18730 GTTAATAATT
**
18740 TTCAAATAAATTTTGGTTTGATTAACG
1 TTCAAATAAATTTTGGTCCGATTAACG
18767 TTCAAAT-AATTTTGGTCCGATTAA
1 TTCAAATAAATTTTGGTCCGATTAA
18791 TGTTAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (27 bp):
TTCAAATAAATTTTGGTCCGATTAACG
Found at i:18794 original size:95 final size:94
Alignment explanation
Indices: 18631--18843 Score: 354
Period size: 95 Copynumber: 2.3 Consensus size: 94
18621 AGAAAAAAAA
*
18631 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTCCGATTAA
18696 TGTTAAAGAAAAAAAATTCGGTTAATTTGG
66 TGTTAAAG-AAAAAAATTCGGTTAATTTGG
* * * *
18726 TTCGGTTAATAATTTTCAAATAAATTTTGGTTTGATTAACGTTCAAATAATTTTGGTCCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTCCGATTAA
*
18791 TGTTAAAGAAAAAAATTCGGTTAATTTTG
66 TGTTAAAGAAAAAAATTCGGTTAATTTGG
*
18820 TTTGGTTAATAATTTTCAAATAAA
1 TTCGGTTAATAATTTTCAAATAAA
18844 ATATTTTTTC
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 43 0.39
95 68 0.61
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.41
Consensus pattern (94 bp):
TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATCAAATAATTTCGGTCCGATTAA
TGTTAAAGAAAAAAATTCGGTTAATTTGG
Found at i:18910 original size:32 final size:32
Alignment explanation
Indices: 18842--18910 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
18832 TTTTCAAATA
* * * *
18842 AAATATTTTTTCTTTAACCGTTAATCGAACCG
1 AAATTTTTTTTCTGTAACCATTAATCAAACCG
* *
18874 -AATTTTTTTTCTGTAACTATTAATCAAACTG
1 AAATTTTTTTTCTGTAACCATTAATCAAACCG
18905 AAATTT
1 AAATTT
18911 ATTTAACCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (32 bp):
AAATTTTTTTTCTGTAACCATTAATCAAACCG
Found at i:19597 original size:12 final size:12
Alignment explanation
Indices: 19582--19628 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
19572 CCGGTTTTTT
*
19582 AACCGGATAAAA
1 AACCGGTTAAAA
19594 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
19609 AACCGGTTAAAA
1 AACCGGTTAAAA
19621 AACCGGTT
1 AACCGGTT
19629 TTTATCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:21939 original size:21 final size:21
Alignment explanation
Indices: 21915--21954 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21905 TTTATTTTAT
21915 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
21936 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
21955 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:22002 original size:33 final size:33
Alignment explanation
Indices: 21949--22047 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
21939 TTTGTTTCAA
21949 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
21981 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
22014 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
22047 T
1 T
22048 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:22076 original size:13 final size:13
Alignment explanation
Indices: 22033--22087 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
22023 TTGGAAGTAT
22033 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
22046 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
22060 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
22073 TTAAGTATTTGAA
1 TTAAGTATTTCAA
22086 TT
1 TT
22088 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:22508 original size:15 final size:15
Alignment explanation
Indices: 22483--22538 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
22473 ATCTGGAATA
*
22483 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
22498 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
22513 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
22530 TTAAAACCG
1 TTAAAACCG
22539 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:22547 original size:21 final size:18
Alignment explanation
Indices: 22502--22535 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22492 GTTTTTTTAT
22502 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
22519 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
22536 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:24156 original size:3 final size:3
Alignment explanation
Indices: 24148--24207 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
24138 CCATATTGAT
* *
24148 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA -TA TCA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24194 TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA
24208 AATATATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 5 0.10
3 45 0.90
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:24214 original size:34 final size:34
Alignment explanation
Indices: 24149--24214 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
24139 CATATTGATT
*
24149 TATTATTATTATTATTATAATTATTATTATATCA
1 TATTATTATTATTATTATAATTATTAATATATCA
*
24183 TATTATTATTATTA-TATTATTATTAAATATAT
1 TATTATTATTATTATTATAATTATT-AATATAT
24215 TAAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 9 0.31
34 20 0.69
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (34 bp):
TATTATTATTATTATTATAATTATTAATATATCA
Found at i:25770 original size:3 final size:3
Alignment explanation
Indices: 25762--25821 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
25752 CCATATTGAT
* *
25762 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25810 TTA TTA TTA TTA
1 TTA TTA TTA TTA
25822 AATATATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:31283 original size:15 final size:15
Alignment explanation
Indices: 31263--31294 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31253 ATCAATACCT
31263 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
31278 TTTTGCATACATTCA
1 TTTTGCATACATGCA
31293 TT
1 TT
31295 ATCATTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:33175 original size:13 final size:13
Alignment explanation
Indices: 33157--33183 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33147 GTCCTGAGTT
33157 AGGGATTTGGTGC
1 AGGGATTTGGTGC
33170 AGGGATTTGGTGC
1 AGGGATTTGGTGC
33183 A
1 A
33184 AAATTGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.07, G:0.44, T:0.30
Consensus pattern (13 bp):
AGGGATTTGGTGC
Done.