Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000093.1 Hibiscus syriacus cultivar Beakdansim tig00000172_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: 65190
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:29683 original size:10 final size:10
Alignment explanation
Indices: 29670--29713 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
29660 AAATTTTGGA
29670 TTTTTTGTTT
1 TTTTTTGTTT
29680 TTTTTTGTTTT
1 TTTTTTG-TTT
**
29691 TTTTTTGCCT
1 TTTTTTGTTT
29701 TTTTTTGTTT
1 TTTTTTGTTT
29711 TTT
1 TTT
29714 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:29696 original size:21 final size:21
Alignment explanation
Indices: 29670--29713 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29660 AAATTTTGGA
**
29670 TTTTTTGTTTTTTTTTGTTTT
1 TTTTTTGCCTTTTTTTGTTTT
29691 TTTTTTGCCTTTTTTTGTTTT
1 TTTTTTGCCTTTTTTTGTTTT
29712 TT
1 TT
29714 ATTTAAAAAA
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:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (21 bp):
TTTTTTGCCTTTTTTTGTTTT
Found at i:33121 original size:5 final size:5
Alignment explanation
Indices: 33104--33165 Score: 71
Period size: 5 Copynumber: 13.0 Consensus size: 5
33094 TTCTTTTTGA
33104 CTTTT C-TTT -TTTT CTTTT CTTTT -TTTT CTTTT -TTTT CTTCTT -TTTGT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTTT-T
33151 CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT
33166 TGTACTCCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
4 15 0.30
5 30 0.60
6 5 0.10
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (5 bp):
CTTTT
Found at i:33128 original size:13 final size:13
Alignment explanation
Indices: 33093--33166 Score: 80
Period size: 13 Copynumber: 5.7 Consensus size: 13
33083 CTTAGCTTGC
**
33093 TTTCTTTTTGACT
1 TTTCTTTTTTTCT
33106 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
33119 TTTCTTTTTTTTCT
1 TTTC-TTTTTTTCT
*
33133 TTT-TTTTCTTCT
1 TTTCTTTTTTTCT
*
33145 TTT-TGTCTTTTCT
1 TTTCT-TTTTTTCT
33158 TTTCTTTTT
1 TTTCTTTTT
33167 GTACTCCAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
12 12 0.23
13 27 0.52
14 13 0.25
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:33167 original size:18 final size:18
Alignment explanation
Indices: 33104--33168 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
33094 TTCTTTTTGA
*
33104 CTTTTCTTTTTTTCTTTT
1 CTTTTCTTTTTGTCTTTT
33122 CTTTT-TTTTCT-T-TTTT
1 CTTTTCTTTT-TGTCTTTT
33138 -TTCTTCTTTTTGTCTTTT
1 CTT-TTCTTTTTGTCTTTT
33156 CTTTTCTTTTTGT
1 CTTTTCTTTTTGT
33169 ACTCCAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.05
16 7 0.17
17 10 0.24
18 20 0.49
19 2 0.05
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (18 bp):
CTTTTCTTTTTGTCTTTT
Found at i:34137 original size:22 final size:22
Alignment explanation
Indices: 34109--34154 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
34099 TTTTCTTTTA
*
34109 TTTTTGAGTTCTTTCAATTTCT
1 TTTTTGAGTGCTTTCAATTTCT
* *
34131 TTTTTGAGTGCTTTGATTTTCT
1 TTTTTGAGTGCTTTCAATTTCT
34153 TT
1 TT
34155 GCTGGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.65
Consensus pattern (22 bp):
TTTTTGAGTGCTTTCAATTTCT
Found at i:34851 original size:19 final size:20
Alignment explanation
Indices: 34804--34854 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
34794 GAAACCCCTT
**
34804 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
34824 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
34843 TGAAGATACATG
1 TGAAAATACATG
34855 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:38526 original size:26 final size:28
Alignment explanation
Indices: 38473--38528 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
38463 ATTTCTTCTT
* * *
38473 TTCTTCCTTTTTGAGTGCTTGATTTTTC
1 TTCTTCCTTTTGGAGTGCTTCATATTTC
38501 TTCTT-CTTTTGGAGTGCTTCA-ATTTC
1 TTCTTCCTTTTGGAGTGCTTCATATTTC
38527 TT
1 TT
38529 TTGTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.09, C:0.18, G:0.14, T:0.59
Consensus pattern (28 bp):
TTCTTCCTTTTGGAGTGCTTCATATTTC
Found at i:46454 original size:32 final size:33
Alignment explanation
Indices: 46418--46484 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
46408 AGGTTAAGAA
*
46418 AAAGAATAAAGTAAT-AAA-AATAAGAAAAGATG
1 AAAGAATAAAGAAATGAAATAATAAGAAAA-ATG
* *
46450 AAAGAATAAGGAAATGAAATAGTAAGAAAAATG
1 AAAGAATAAAGAAATGAAATAATAAGAAAAATG
46483 AA
1 AA
46485 GATAACTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 13 0.43
33 8 0.27
34 9 0.30
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (33 bp):
AAAGAATAAAGAAATGAAATAATAAGAAAAATG
Found at i:46690 original size:22 final size:22
Alignment explanation
Indices: 46649--46690 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
46639 TAGGAGTCTT
*
46649 TTCTTTCTTTTTTTTATTTTTC
1 TTCTTTCTTTTTTCTATTTTTC
*
46671 TTCTTTC-TTTTTCTCTTTTT
1 TTCTTTCTTTTTTCTATTTTT
46691 ATTGCTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (22 bp):
TTCTTTCTTTTTTCTATTTTTC
Found at i:46698 original size:22 final size:22
Alignment explanation
Indices: 46649--46698 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
46639 TAGGAGTCTT
* *
46649 TTCTTTCTTTTTTTTATTTTTC
1 TTCTTTCTTTTTTCTATTTTTA
*
46671 TTCTTTC-TTTTTCTCTTTTTA
1 TTCTTTCTTTTTTCTATTTTTA
46692 TTGCTTT
1 TT-CTTT
46699 TGTTGAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (22 bp):
TTCTTTCTTTTTTCTATTTTTA
Found at i:48322 original size:22 final size:22
Alignment explanation
Indices: 48282--48323 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
48272 AAATATGTGG
*
48282 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
48304 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
48324 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:53334 original size:13 final size:12
Alignment explanation
Indices: 53317--53346 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
53307 AAAAAAAAAC
53317 AAAAAAAGGCAA
1 AAAAAAAGGCAA
53329 AGAAAAAAGGCAA
1 A-AAAAAAGGCAA
53342 AAAAA
1 AAAAA
53347 GCCAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:53334 original size:23 final size:23
Alignment explanation
Indices: 53308--53352 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
53298 ACAAAAAAAA
*
53308 AAAAAAAACAAAAAAAGGCAAAG
1 AAAAAAAACAAAAAAAGCCAAAG
**
53331 AAAAAAGGCAAAAAAAGCCAAA
1 AAAAAAAACAAAAAAAGCCAAA
53353 AAAGCTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAAAACAAAAAAAGCCAAAG
Found at i:59000 original size:19 final size:19
Alignment explanation
Indices: 58971--59033 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
58961 AAAAAGAAGA
*
58971 AGAAATGAGAGTTGAAAA-
1 AGAATTGAGAGTTGAAAAG
58989 AGACATTGAGAGTATTGAAAAG
1 AGA-ATTGAGAG--TTGAAAAG
59011 AGAATTGAGAG-TGAAAATG
1 AGAATTGAGAGTTGAAAA-G
59030 AGAA
1 AGAA
59034 CATTGAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 9 0.23
19 12 0.31
21 15 0.38
22 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.19
Consensus pattern (19 bp):
AGAATTGAGAGTTGAAAAG
Found at i:60232 original size:17 final size:17
Alignment explanation
Indices: 60210--60262 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
60200 CGAATAAAGT
60210 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
60227 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
60244 TAGTTCATTTAA-TAAAC
1 TAGTTCA-TTAATTAAAC
60261 TA
1 TA
60263 ACTCTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:63968 original size:19 final size:19
Alignment explanation
Indices: 63939--63995 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
63929 AAAAAGAAGA
*
63939 AGAAATGAGAGTTGAAAA-
1 AGAATTGAGAGTTGAAAAG
63957 AGACATTGAGAGTATTGAAAAG
1 AGA-ATTGAGAG--TTGAAAAG
63979 AGAATTGAGAG-TGAAAA
1 AGAATTGAGAGTTGAAAA
63996 TGAGCACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 9 0.26
19 7 0.21
21 15 0.44
22 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.28, T:0.19
Consensus pattern (19 bp):
AGAATTGAGAGTTGAAAAG
Found at i:63974 original size:21 final size:21
Alignment explanation
Indices: 63950--63990 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
63940 GAAATGAGAG
63950 TTGAAAA-AGACATTGAGAGTA
1 TTGAAAAGAGA-ATTGAGAGTA
63971 TTGAAAAGAGAATTGAGAGT
1 TTGAAAAGAGAATTGAGAGT
63991 GAAAATGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.24
Consensus pattern (21 bp):
TTGAAAAGAGAATTGAGAGTA
Done.