Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007998.1 Hibiscus syriacus cultivar Beakdansim tig00110449_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: 89262
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6388 original size:21 final size:19
Alignment explanation
Indices: 6350--6398 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
6340 ATACTTGTAA
* *
6350 TTTTATAATTTTATTTTAT
1 TTTTATATTTTTATTTTAC
6369 TTTTATATTTTTAAATTTTAC
1 TTTTATATTTTT--ATTTTAC
*
6390 TTTTCTATT
1 TTTTATATT
6399 ATATAACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.44
21 14 0.56
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATATTTTTATTTTAC
Found at i:9141 original size:31 final size:31
Alignment explanation
Indices: 9103--9166 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
9093 AATATATAAT
* *
9103 ATGTGATCATTTTCGTTTTTAGTTCATTAAG
1 ATGTGATCATGTTCGTTATTAGTTCATTAAG
* *
9134 ATGTGATCATGTTCGTTATTATTTTATTAAG
1 ATGTGATCATGTTCGTTATTAGTTCATTAAG
9165 AT
1 AT
9167 ATATGGTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.52
Consensus pattern (31 bp):
ATGTGATCATGTTCGTTATTAGTTCATTAAG
Found at i:20111 original size:11 final size:11
Alignment explanation
Indices: 20097--20152 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 11
20087 TATTTTTGAA
20097 TTCTTTTTCTT
1 TTCTTTTTCTT
20108 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
20121 TTCTTCTTCTT
1 TTCTTTTTCTT
20132 TT-TGTCTTTCTCT
1 TTCT-T-TTTCT-T
20145 TTCTTTTT
1 TTCTTTTT
20153 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 1 0.03
11 11 0.30
12 12 0.32
13 12 0.32
14 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:20124 original size:18 final size:18
Alignment explanation
Indices: 20101--20153 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
20091 TTTGAATTCT
20101 TTTTCTTTTCTTTTCT-TC
1 TTTTCTTTTCTTTT-TGTC
20119 TTTTCTTCTTCTTTTTGTC
1 TTTTCTT-TTCTTTTTGTC
20138 -TTTCTCTTTCTTTTTG
1 TTTTCT-TTTCTTTTTG
20154 CACTCCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 22 0.69
19 10 0.31
ACGTcount: A:0.00, C:0.21, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGTC
Found at i:20456 original size:23 final size:22
Alignment explanation
Indices: 20413--20462 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
20403 AATAAAGGGT
*
20413 AATAATATAAGTAATGAAAATA
1 AATAATATAAGAAATGAAAATA
20435 AATAATAATAATGAAATG-AAATA
1 AATAAT-ATAA-GAAATGAAAATA
20458 AATAA
1 AATAA
20463 AAAGATAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 14 0.56
24 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (22 bp):
AATAATATAAGAAATGAAAATA
Found at i:20917 original size:19 final size:20
Alignment explanation
Indices: 20876--20926 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
20866 GAAACCCCTT
*
20876 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
20896 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
20915 TGAAGATACATG
1 TGAAAATACATG
20927 CTCTTGACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:25062 original size:19 final size:17
Alignment explanation
Indices: 25019--25062 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
25009 TATCCTTTAT
*
25019 TTATTTTTATTTCATTC
1 TTATATTTATTTCATTC
25036 TTATTATTTATTTTCATTAC
1 TTA-TATTTA-TTTCATT-C
25056 TTATATT
1 TTATATT
25063 ATTATTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 5 0.22
19 11 0.48
20 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTTATTTCATTC
Found at i:30007 original size:13 final size:13
Alignment explanation
Indices: 29985--30014 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29975 ACTAAACACC
29985 TTTC-ACATACCT
1 TTTCAACATACCT
29997 TTTCAACATACCT
1 TTTCAACATACCT
30010 TTTCA
1 TTTCA
30015 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:47392 original size:11 final size:11
Alignment explanation
Indices: 47371--47412 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
47361 GTGCTGGAAT
47371 CAAGATAAAAA
1 CAAGATAAAAA
* *
47382 TAAGATTAAAA
1 CAAGATAAAAA
47393 CAAGATAAAGAA
1 CAAGATAAA-AA
47405 -AAGATAAA
1 CAAGATAAA
47413 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:51803 original size:11 final size:11
Alignment explanation
Indices: 51782--51823 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
51772 GTGCTGGAAT
51782 CAAGATAAAAA
1 CAAGATAAAAA
* *
51793 TAAGATTAAAA
1 CAAGATAAAAA
51804 CAAGATAAAGAA
1 CAAGATAAA-AA
51816 -AAGATAAA
1 CAAGATAAA
51824 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:57594 original size:8 final size:8
Alignment explanation
Indices: 57581--57625 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
57571 ATCTTTTTCT
57581 TTTTCTTC
1 TTTTCTTC
57589 TTTTCTTC
1 TTTTCTTC
57597 TTTTCTTC
1 TTTTCTTC
57605 TTTT-TGTC
1 TTTTCT-TC
57613 TTTTCTTTC
1 TTTTC-TTC
57622 TTTT
1 TTTT
57626 TGCACTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 26 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:57627 original size:17 final size:16
Alignment explanation
Indices: 57572--57627 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
57562 CTTTTTGAAA
*
57572 TCTTTTTCT-TTTTCT
1 TCTTTTTGTCTTTTCT
57587 TCTTTTCT-TCTTTTCT
1 TCTTTT-TGTCTTTTCT
57603 TCTTTTTGTCTTTTCTT
1 TCTTTTTGTCTTTTC-T
57620 TCTTTTTG
1 TCTTTTTG
57628 CACTCCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.22
16 20 0.54
17 9 0.24
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.77
Consensus pattern (16 bp):
TCTTTTTGTCTTTTCT
Found at i:60372 original size:21 final size:21
Alignment explanation
Indices: 60333--60372 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
60323 AAGGAAGATT
*
60333 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
60354 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
60373 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:60421 original size:22 final size:21
Alignment explanation
Indices: 60395--60435 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
60385 GCTACAGAAT
60395 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
60417 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
60436 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:63632 original size:28 final size:22
Alignment explanation
Indices: 63576--63629 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
63566 AGGATGCTTA
63576 AATGGTGATGAAATGATAAGGG
1 AATGGTGATGAAATGATAAGGG
63598 AATGGTGATGAAATGATAAGGG
1 AATGGTGATGAAATGATAAGGG
*
63620 AACGGTGATG
1 AATGGTGATG
63630 GTGTAGGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.37, T:0.22
Consensus pattern (22 bp):
AATGGTGATGAAATGATAAGGG
Found at i:68381 original size:47 final size:47
Alignment explanation
Indices: 68328--68421 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
68318 AATATAAGAT
*
68328 AGGGTAAGAAAGAACTCCCTTAGAATCAACAATGAAAAACATCCATG
1 AGGGTAAGAAAGAACTACCTTAGAATCAACAATGAAAAACATCCATG
*
68375 AGGGTAAGAAAGAACTACCTTAGAATCAGCAATGAAAAACATCCATG
1 AGGGTAAGAAAGAACTACCTTAGAATCAACAATGAAAAACATCCATG
68422 TTGTGATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (47 bp):
AGGGTAAGAAAGAACTACCTTAGAATCAACAATGAAAAACATCCATG
Found at i:70327 original size:2 final size:2
Alignment explanation
Indices: 70315--70375 Score: 99
Period size: 2 Copynumber: 31.0 Consensus size: 2
70305 TTTCATATGT
70315 TA TA CTA 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
70358 TA TA TA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
70376 ACTTATTCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 52 0.93
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:71998 original size:18 final size:17
Alignment explanation
Indices: 71981--72040 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
71971 GTACATAAAG
71981 AAAAGAAAATAC-AAAA
1 AAAAGAAAATACAAAAA
* * *
71997 AGAAGAAAAATTCAGAAA
1 AAAAG-AAAATACAAAAA
*
72015 AAAAGAAAAGA-AAAAA
1 AAAAGAAAATACAAAAA
72031 AAGAAGAAAA
1 AA-AAGAAAA
72041 AGTCAAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
16 10 0.29
17 17 0.50
18 7 0.21
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.05
Consensus pattern (17 bp):
AAAAGAAAATACAAAAA
Found at i:72026 original size:13 final size:12
Alignment explanation
Indices: 71981--72041 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
71971 GTACATAAAG
*
71981 AAAAGAAAATACA
1 AAAAGAAAA-AAA
71994 AAAAGAAGAAAAA
1 AAAAGAA-AAAAA
***
72007 TTCAGAAAAAAA
1 AAAAGAAAAAAA
72019 GAAAAGAAAAAAA
1 -AAAAGAAAAAAA
*
72032 AGAAGAAAAA
1 AAAAGAAAAA
72042 GTCAAATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
12 14 0.37
13 22 0.58
14 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:76452 original size:13 final size:13
Alignment explanation
Indices: 76430--76459 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
76420 ACTTAACACC
76430 TTTC-ACATACCT
1 TTTCAACATACCT
76442 TTTCAACATACCT
1 TTTCAACATACCT
76455 TTTCA
1 TTTCA
76460 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:83650 original size:17 final size:17
Alignment explanation
Indices: 83628--83689 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
83618 AAAATTAGAG
83628 TACAAAAGAAAAGAAAA
1 TACAAAAGAAAAGAAAA
*
83645 TACAAAA-AGAAGAAAAA
1 TACAAAAGAAAAG-AAAA
* *
83662 TTCAAAAAAAAAAGAAAA
1 TAC-AAAAGAAAAGAAAA
* *
83680 GAAAAAAGAA
1 TACAAAAGAA
83690 GAAAAAGTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
16 4 0.11
17 19 0.54
18 8 0.23
19 4 0.11
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.06
Consensus pattern (17 bp):
TACAAAAGAAAAGAAAA
Found at i:83662 original size:40 final size:34
Alignment explanation
Indices: 83631--83703 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
83621 ATTAGAGTAC
* *
83631 AAAAGAAAAGAAAATACAAAAAGAAGAAAAATTCA
1 AAAAAAAAAGAAAAGA-AAAAAGAAGAAAAATTCA
*
83666 AAAAAAAAAGAAAAGAAAAAAGAAGAAAAAGTCA
1 AAAAAAAAAGAAAAGAAAAAAGAAGAAAAATTCA
83700 AAAA
1 AAAA
83704 TAGAAAGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 21 0.60
35 14 0.40
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.05
Consensus pattern (34 bp):
AAAAAAAAAGAAAAGAAAAAAGAAGAAAAATTCA
Found at i:83708 original size:19 final size:18
Alignment explanation
Indices: 83648--83708 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
83638 AAGAAAATAC
*
83648 AAAAAGAAGAAAAATTCA
1 AAAAAGAAGAAAAAGTCA
*
83666 AAAAA-AAAAGAAAAG--A
1 AAAAAGAAGA-AAAAGTCA
83682 AAAAAGAAGAAAAAGTCA
1 AAAAAGAAGAAAAAGTCA
83700 AAAATAGAA
1 AAAA-AGAA
83709 AGCAAGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
16 11 0.31
17 6 0.17
18 14 0.40
19 4 0.11
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (18 bp):
AAAAAGAAGAAAAAGTCA
Found at i:85044 original size:27 final size:28
Alignment explanation
Indices: 85006--85063 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
84996 TCCCAACTTT
85006 GAAGAAGTCTACT-CTACTCCTACAAAG
1 GAAGAAGTCTACTCCTACTCCTACAAAG
85033 GAAGAAGTCTACTCCTACTCCTACAAAG
1 GAAGAAGTCTACTCCTACTCCTACAAAG
85061 GAA
1 GAA
85064 AAGGCCGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.21
Consensus pattern (28 bp):
GAAGAAGTCTACTCCTACTCCTACAAAG
Found at i:87935 original size:15 final size:15
Alignment explanation
Indices: 87900--87946 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
87890 TCTTTCTATC
87900 TTTATTT-CATTTCT
1 TTTATTTCCATTTCT
87914 TTCTATTTCCATATT-T
1 TT-TATTTCCAT-TTCT
87930 TTTATTATCCATTTCT
1 TTTATT-TCCATTTCT
87946 T
1 T
87947 AAGTCCACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
16 13 0.46
17 2 0.07
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTTCCATTTCT
Found at i:88190 original size:15 final size:14
Alignment explanation
Indices: 88172--88237 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
88162 AAAATTAGAG
88172 TACATAAAAAAAAAA
1 TACA-AAAAAAAAAA
*
88187 TACAAAAAAGAAAA
1 TACAAAAAAAAAAA
*
88201 TTCAGAAAAAAGAAAA
1 TACA-AAAAAA-AAAA
*
88217 GA-AAAAAAGAAAAA
1 TACAAAAAA-AAAAA
88231 T-CAAAAA
1 TACAAAAA
88238 TAGAAAGCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 26 0.63
15 11 0.27
16 4 0.10
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.09
Consensus pattern (14 bp):
TACAAAAAAAAAAA
Found at i:88210 original size:29 final size:28
Alignment explanation
Indices: 88177--88243 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
88167 TAGAGTACAT
* *
88177 AAAAAA-AAAATACAAAAAAGAAAATTCA
1 AAAAAAGAAAAGA-AAAAAAGAAAAATCA
88205 GAAAAAAGAAAAGAAAAAAAGAAAAATCA
1 -AAAAAAGAAAAGAAAAAAAGAAAAATCA
*
88234 AAAATAGAAA
1 AAAAAAGAAA
88244 GCAAGCCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 9 0.26
29 20 0.59
30 5 0.15
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.07
Consensus pattern (28 bp):
AAAAAAGAAAAGAAAAAAAGAAAAATCA
Done.