Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005574.1 Hibiscus syriacus cultivar Beakdansim tig00012935_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: 24832
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:946 original size:69 final size:64
Alignment explanation
Indices: 868--1125 Score: 217
Period size: 67 Copynumber: 3.9 Consensus size: 64
858 GTTTTAAAAG
* *
868 AAAACATTTTGAAAAATATGGGTAATATAGTTTTTTAAATATTTTTTGAAAACTATATAACATAT
1 AAAACATTTTGAAAAATAT--ATAATATAG-TTTTTAAATA-TTTTTAAAAACTATATAA-ATAT
933 TTTT
61 TTTT
*
937 AAAACATTTT-AGAAAATATAAAAATATAG-TTTTAAATCA-TTTTAAAAACTTATATAATATAG
1 AAAACATTTTGA-AAAATAT-ATAATATAGTTTTTAAAT-ATTTTTAAAAAC-TATATAA-ATA-
*
999 TTTTA
60 TTTTT
*
1004 AAAACATTTTGAATAAATATATAATATA-TAGTTTTAAAAACGTTTTTAAAAACT-TATATAATA
1 AAAACATTTTGAA-AAATATATAATATAGT--TTTTAAATA--TTTTTAAAAACTATATA-AATA
1067 TTTTT
60 TTTTT
* * *
1072 -AAACATTTTGAAGACTATATAATATAGTTTTGAAA-ACTTTTTAAATAA-TATATA
1 AAAACATTTTGAAAAATATATAATATAGTTTTTAAATA-TTTTTAAA-AACTATATA
1126 GTTTAAAAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 37
0.76 0.06 0.18
Matches are distributed among these distances:
63 9 0.06
64 7 0.04
65 15 0.09
66 30 0.19
67 36 0.22
68 20 0.12
69 31 0.19
70 2 0.01
71 10 0.06
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (64 bp):
AAAACATTTTGAAAAATATATAATATAGTTTTTAAATATTTTTAAAAACTATATAAATATTTTT
Found at i:952 original size:33 final size:33
Alignment explanation
Indices: 868--1114 Score: 170
Period size: 33 Copynumber: 7.3 Consensus size: 33
858 GTTTTAAAAG
* *
868 AAAACATTTT-GAAAAATATGGGTAATATAGTTTTT
1 AAAACATTTTAGAAAACTAT--ATAATATA-TTTTT
* * * *
903 TAAATATTTTTTGAAAACTATATAACATATTTTT
1 AAAACA-TTTTAGAAAACTATATAATATATTTTT
* *
937 AAAACATTTTAGAAAA-TATAAAAATATAGTTTT
1 AAAACATTTTAGAAAACTAT-ATAATATATTTTT
* *
970 AAATCATTTTA-AAAACTTATATAATATAGTTTTA
1 AAAACATTTTAGAAAAC-TATATAATATA-TTTTT
*
1004 AAAACATTTT-GAATAAATATATAATATATAGTTTT
1 AAAACATTTTAGAA-AACTATATAATATAT--TTTT
*
1039 AAAAACGTTTTTA-AAAACT-TAT-ATAATATTTTT
1 -AAAAC-ATTTTAGAAAACTATATAAT-ATATTTTT
* *
1072 -AAACATTTT-GAAGACTATATAATATAGTTTTG
1 AAAACATTTTAGAAAACTATATAATATA-TTTTT
*
1104 AAAACTTTTTA
1 AAAACATTTTA
1115 AATAATATAT
Statistics
Matches: 168, Mismatches: 24, Indels: 41
0.72 0.10 0.18
Matches are distributed among these distances:
30 9 0.05
31 10 0.06
32 13 0.08
33 49 0.29
34 39 0.23
35 22 0.13
36 12 0.07
37 14 0.08
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (33 bp):
AAAACATTTTAGAAAACTATATAATATATTTTT
Found at i:1225 original size:15 final size:14
Alignment explanation
Indices: 1190--1218 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1180 TTATTATTAT
1190 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
1204 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
1218 T
1 T
1219 GTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTCTTTTTA
Found at i:2769 original size:20 final size:19
Alignment explanation
Indices: 2746--2799 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
2736 AATTTAATCC
2746 TTTTATCTTTATTATTATTA
1 TTTTATCTTTATT-TTATTA
*
2766 TTTTATTTTTATTTTATT-
1 TTTTATCTTTATTTTATTA
*
2784 TCTTAT-TTT-TTTTATT
1 TTTTATCTTTATTTTATT
2800 TATACGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 5 0.16
19 5 0.16
20 12 0.38
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATCTTTATTTTATTA
Found at i:2777 original size:11 final size:11
Alignment explanation
Indices: 2757--2800 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
2747 TTTATCTTTA
*
2757 TTATTATTATT
1 TTATTTTTATT
2768 TTATTTTTATT
1 TTATTTTTATT
2779 TTATTTCTTA-T
1 TTATTT-TTATT
2790 TT-TTTTTATT
1 TTATTTTTATT
2800 T
1 T
2801 ATACGATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 3 0.10
10 5 0.17
11 19 0.63
12 3 0.10
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:2860 original size:8 final size:8
Alignment explanation
Indices: 2829--2892 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
2819 ATATATATTA
2829 TATTTTAT
1 TATTTTAT
2837 T-TTTTAAAT
1 TATTTT--AT
*
2846 CATTTTAT
1 TATTTTAT
2854 TATTTTAT
1 TATTTTAT
2862 T-TCTTTA-
1 TAT-TTTAT
2869 T-TTTTAT
1 TATTTTAT
2876 TATTTTAT
1 TATTTTAT
*
2884 TCTTTTAT
1 TATTTTAT
2892 T
1 T
2893 TCTATTACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
6 4 0.09
7 8 0.17
8 29 0.62
9 2 0.04
10 4 0.09
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (8 bp):
TATTTTAT
Found at i:2873 original size:22 final size:22
Alignment explanation
Indices: 2848--2899 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2838 TTTTAAATCA
2848 TTTTATTATTTTATT-TCTTTAT
1 TTTTATTATTTTATTCT-TTTAT
2870 TTTTATTATTTTATTCTTTTAT
1 TTTTATTATTTTATTCTTTTAT
*
2892 TTCTATTA
1 TTTTATTA
2900 CTTTGTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTATTATTTTATTCTTTTAT
Found at i:2921 original size:2 final size:2
Alignment explanation
Indices: 2916--2966 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2906 TATACGTGTG
2916 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
2958 TA TA TA TA T
1 TA TA TA TA T
2967 TTTTTTCCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3041 original size:23 final size:21
Alignment explanation
Indices: 3011--3067 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
3001 CTCTCTTTTA
3011 TTTA-TTTAATTTATTTAATTT
1 TTTATTTTAATTTATTT-ATTT
* *
3032 TTTATCTTTAGTGTATTTATTT
1 TTTAT-TTTAATTTATTTATTT
3054 TTTATTTCTAATTT
1 TTTATTT-TAATTT
3068 CTAGTTTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 6 0.21
22 13 0.45
23 10 0.34
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTATTTTAATTTATTTATTT
Found at i:3099 original size:11 final size:10
Alignment explanation
Indices: 3079--3121 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
3069 TAGTTTCTAG
3079 TTTTTATTTT
1 TTTTTATTTT
*
3089 TTTTTACTTT
1 TTTTTATTTT
3099 TTTTTATTATAT
1 TTTTTATT-T-T
*
3111 ATTTTATTTT
1 TTTTTATTTT
3121 T
1 T
3122 CCCTTGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 17 0.63
11 2 0.07
12 8 0.30
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:3197 original size:5 final size:5
Alignment explanation
Indices: 3187--3278 Score: 80
Period size: 5 Copynumber: 18.0 Consensus size: 5
3177 ATTTAAATTC
* * * *
3187 ATTTT ATTTT ATTTT ATTTT ATTTT -CTTT ATCTT ATCTT ATCTT A-TTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
* *
3235 ATTTC ATTTGT TTTTT AATAGTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTT-T ATTTT -AT--TTT ATTTT ATTTT ATTTT ATTTT
3279 TTTCATTACT
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
4 6 0.08
5 58 0.79
6 4 0.05
7 2 0.03
8 3 0.04
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (5 bp):
ATTTT
Found at i:3235 original size:19 final size:19
Alignment explanation
Indices: 3194--3236 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3184 TTCATTTTAT
* * * *
3194 TTTATTTTATTTTATTTTC
1 TTTATCTTATCTTATCTTA
3213 TTTATCTTATCTTATCTTA
1 TTTATCTTATCTTATCTTA
3232 TTTAT
1 TTTAT
3237 TTCATTTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATCTTATCTTATCTTA
Found at i:13497 original size:181 final size:181
Alignment explanation
Indices: 13161--13633 Score: 646
Period size: 181 Copynumber: 2.6 Consensus size: 181
13151 GATCCAAATT
* * * *
13161 AAAAATATGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCAGTATTG-AAATAAT
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAA-CAGTA-TGAAAATGAT
* * * * * *
13225 AAAACCGGTAAAGCGCTACCAGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTC
64 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTC
* *
13290 CGTGAATTTAAAAGAGAAGCAGTTTTAAG-TCCTATAAAGTGTCGATACTTTTA
129 CGTGAATTTAAAAGAGAAGCAGTTTT-AGCGCCTATAAAGTGTCGATACTTTAA
* * * *
13343 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATGAAACATGTAAGAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACA-GTATGAAAATGATA
* **
13408 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTCC
*
13472 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * * *
13524 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAA-CAGTATGAAAATGATA
* *
13589 AAACCGGTAAAATGATACCGAATATATTGAAAGTGTCGATACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
13634 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
180 2 0.01
181 163 0.63
182 92 0.36
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (181 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACAGTATGAAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTCCG
TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:13602 original size:17 final size:19
Alignment explanation
Indices: 13563--13605 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
13553 ATGTAAAAAT
13563 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
13583 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
13600 ATGATA
1 ATGATA
13606 CCGAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:14043 original size:23 final size:23
Alignment explanation
Indices: 14012--14084 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
14002 ATAGGTAAAA
*
14012 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
14035 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
14058 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
14081 ATAT
1 ATAT
14085 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:24242 original size:37 final size:38
Alignment explanation
Indices: 24186--24268 Score: 150
Period size: 37 Copynumber: 2.2 Consensus size: 38
24176 ATTTATCTCG
*
24186 ATTTCTATAGTTTTACTGATTTTGTGCTACCTAACTTC
1 ATTTCAATAGTTTTACTGATTTTGTGCTACCTAACTTC
24224 A-TTCAATAGTTTTACTGATTTTGTGCTACCTAACTTC
1 ATTTCAATAGTTTTACTGATTTTGTGCTACCTAACTTC
24261 ATTTCAAT
1 ATTTCAAT
24269 TTGATATATC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 36 0.84
38 7 0.16
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (38 bp):
ATTTCAATAGTTTTACTGATTTTGTGCTACCTAACTTC
Done.