Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008416.1 Hibiscus syriacus cultivar Beakdansim tig00111194_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: 66523
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:12647 original size:36 final size:36
Alignment explanation
Indices: 12600--12682 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
12590 GGCACAAAAT
*
12600 TCAAATTATTGACGTGATGAGGAAATGGAATTTTGA
1 TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
* *
12636 TCAAATTATTGAGGTGATAAGGAAATGGGATTTTGA
1 TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
12672 TCAAATTATTG
1 TCAAATTATTG
12683 GCTAACTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (36 bp):
TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
Found at i:18528 original size:20 final size:20
Alignment explanation
Indices: 18503--18560 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
18493 TTTGGTTCAC
*
18503 GGAATGTAAGATTATTAGTG
1 GGAATGTAAGATTATCAGTG
*
18523 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTATCAGTG
*
18543 GGAATATAAGATTATCAG
1 GGAATGTAAGATTATCAG
18561 AGAATAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (20 bp):
GGAATGTAAGATTATCAGTG
Found at i:19439 original size:3 final size:3
Alignment explanation
Indices: 19431--19528 Score: 71
Period size: 3 Copynumber: 32.0 Consensus size: 3
19421 AAATTAAAAT
19431 TAA TAA TAAA TAAA TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
19478 T-T TAA TAA TAT TAAA TAT TAA -ATA TAA TAAA TAA TTAA -AA T-A TAA
1 TAA TAA TAA TAA T-AA TAA TAA TA-A TAA T-AA TAA -TAA TAA TAA TAA
19523 TAA TAA
1 TAA TAA
19529 ATAAATATAT
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
2 7 0.09
3 54 0.69
4 17 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:19453 original size:17 final size:17
Alignment explanation
Indices: 19433--19537 Score: 85
Period size: 17 Copynumber: 6.2 Consensus size: 17
19423 ATTAAAATTA
19433 ATAATAAATAAATAAAT
1 ATAATAAATAAATAAAT
19450 ATAAT-AAT-AAT-AAT
1 ATAATAAATAAATAAAT
* *
19464 AATAATAATAATAATTTAAT
1 -ATAAT-A-AATAAATAAAT
* *
19484 AATATTAAAT-ATTAAAT
1 -ATAATAAATAAATAAAT
*
19501 ATAATAAATAATTAAAAT
1 ATAATAAATAAAT-AAAT
19519 ATAAT-AATAAATAAAT
1 ATAATAAATAAATAAAT
19535 ATA
1 ATA
19538 TTAATTAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.04
15 8 0.11
16 18 0.24
17 20 0.27
18 15 0.20
19 3 0.04
20 8 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAAATAAATAAAT
Found at i:19659 original size:14 final size:13
Alignment explanation
Indices: 19613--19664 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
19603 AAATTATATG
*
19613 TATAATATATTAAA
1 TATAATATA-TAAT
*
19627 TATAATAAATAAT
1 TATAATATATAAT
19640 TAATAATATTATAAT
1 T-ATAATA-TATAAT
*
19655 TATAAAATAT
1 TATAATATAT
19665 TTTGAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 7 0.22
14 19 0.59
15 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAATATATAAT
Found at i:21974 original size:16 final size:16
Alignment explanation
Indices: 21950--22045 Score: 77
Period size: 17 Copynumber: 5.8 Consensus size: 16
21940 ATTAATTTTA
*
21950 ATTACTATATTTATTT
1 ATTATTATATTTATTT
*
21966 ATTATTATATTTTAATT
1 ATTATTATA-TTTATTT
* *
21983 AGTTATTATATTTAATA
1 A-TTATTATATTTATTT
* *
22000 ATTAATATTATTATATCT
1 ATTATTA-TATT-TATTT
22018 ATTTATTATATTTATTT
1 A-TTATTATATTTATTT
*
22035 GTTATTA-ATTT
1 ATTATTATATTT
22046 CAATTTGAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
15 4 0.06
16 19 0.29
17 22 0.34
18 15 0.23
19 5 0.08
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:22003 original size:20 final size:18
Alignment explanation
Indices: 21955--21995 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21945 TTTTAATTAC
*
21955 TATA-TTTATTTA-TTAT
1 TATATTTTAATTAGTTAT
21971 TATATTTTAATTAGTTAT
1 TATATTTTAATTAGTTAT
21989 TATATTT
1 TATATTT
21996 AATAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TATATTTTAATTAGTTAT
Found at i:22025 original size:22 final size:21
Alignment explanation
Indices: 21965--22029 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 21
21955 TATATTTATT
*
21965 TATTATTATAT-T-TTAATTA
1 TATTATTATATCTAATAATTA
* *
21984 -GTTATTATATTTAATAATTAA
1 TATTATTATATCTAATAATT-A
* *
22005 TATTATTATATCTATTTATTA
1 TATTATTATATCTAATAATTA
22026 TATT
1 TATT
22030 TATTTGTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.25
19 1 0.03
20 5 0.14
21 6 0.17
22 15 0.42
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTATTATATCTAATAATTA
Found at i:27624 original size:37 final size:37
Alignment explanation
Indices: 27526--27663 Score: 159
Period size: 37 Copynumber: 3.7 Consensus size: 37
27516 TTCGTCATAC
* * *
27526 TAGGATTCAAACTCTTAAAAATAGAATATAATTTTGT
1 TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
**
27563 TAAAATTTAAACTCCTAAAAATAGGATATAATTTTGT
1 TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
* * * **
27600 TAGGATTTAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
** *
27637 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGATTTAAACTCCTAAAAATAGGAT
27664 CCACAAGCAT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 86 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (37 bp):
TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
Found at i:28046 original size:17 final size:17
Alignment explanation
Indices: 28026--28058 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28016 TTTTGAACCC
28026 TAATTCATTTTTTATTT
1 TAATTCATTTTTTATTT
*
28043 TAATTTATTTTTTATT
1 TAATTCATTTTTTATT
28059 ATTTATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TAATTCATTTTTTATTT
Found at i:28108 original size:23 final size:24
Alignment explanation
Indices: 28080--28127 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
28070 TATATGTATA
28080 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
28103 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
28127 T
1 T
28128 TTCTTTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:28221 original size:100 final size:100
Alignment explanation
Indices: 28037--28231 Score: 215
Period size: 100 Copynumber: 1.9 Consensus size: 100
28027 AATTCATTTT
* *
28037 TTATTTTAATTTATTTTTTATTATTTATATGTATATATGTATATATTTAATTATATTTTATTTAT
1 TTATTTTAATTTATTTTCTATTATTTATA-GTATATATATATATATTTAATTATATTTTATTTAT
* *
28102 TTATTTATTATAATTTTTTTTCAT-TTTTCTTTGCA
65 TTACTTATTATAATATTTTTTCATATTTTCTTTGCA
28137 TTATTTT-ATATTATTTTCCTATTA-TTATA-TATATATATATATA-TT-ATTATTATTTTATCT
1 TTATTTTAAT-TTATTTT-CTATTATTTATAGTATATATATATATATTTAATTA-TATTTTAT-T
* *
28197 ATGTTTACTTATT-TACTATATTTTTTTATATTTTC
62 -TATTTACTTATTATA--ATATTTTTTCATATTTTC
28232 CTAACGTTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
96 4 0.05
97 10 0.12
98 16 0.20
99 12 0.15
100 29 0.36
101 10 0.12
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (100 bp):
TTATTTTAATTTATTTTCTATTATTTATAGTATATATATATATATTTAATTATATTTTATTTATT
TACTTATTATAATATTTTTTCATATTTTCTTTGCA
Found at i:28375 original size:21 final size:20
Alignment explanation
Indices: 28351--28403 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
28341 ACTATTTAGT
28351 ATTTTATTATATTATACATAA
1 ATTTT-TTATATTATACATAA
* * *
28372 A-TTTTTATATTTTATATAT
1 ATTTTTTATATTATACATAA
28391 ATTTTTT-TATTAT
1 ATTTTTTATATTAT
28404 TATTTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 18 0.67
20 8 0.30
21 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTTATATTATACATAA
Found at i:28381 original size:19 final size:19
Alignment explanation
Indices: 28357--28403 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
28347 TAGTATTTTA
28357 TTATATTATACATAAATTT
1 TTATATTATACATAAATTT
* * *
28376 TTATATTTTATATATATTT
1 TTATATTATACATAAATTT
*
28395 TTTTATTAT
1 TTATATTAT
28404 TATTTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTATACATAAATTT
Found at i:28403 original size:24 final size:24
Alignment explanation
Indices: 28376--28432 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
28366 ACATAAATTT
28376 TTATATTTTATATATATTT-TTTT-A
1 TTATATTTTAT-T-TATTTATTTTCA
28400 TTAT-TATTTATTTATTTATTTTCA
1 TTATAT-TTTATTTATTTATTTTCA
28424 TTATATTTT
1 TTATATTTT
28433 TAGTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 5 0.17
23 6 0.21
24 17 0.59
25 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TTATATTTTATTTATTTATTTTCA
Found at i:29581 original size:3 final size:3
Alignment explanation
Indices: 29575--29609 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
29565 ATATGCTGCT
*
29575 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29610 TCATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:35127 original size:22 final size:22
Alignment explanation
Indices: 35110--35176 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
35100 CTCGTATAAA
35110 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
35132 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
35154 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
35176 T
1 T
35177 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:35510 original size:29 final size:29
Alignment explanation
Indices: 35468--35539 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
35458 TTTTCTGCAT
**
35468 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
35497 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
35526 ATTCATGTCATGTA
1 ATTCATGTCATGTA
35540 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:35970 original size:70 final size:70
Alignment explanation
Indices: 35856--35995 Score: 194
Period size: 70 Copynumber: 2.0 Consensus size: 70
35846 GGAATCGGTT
* * *
35856 CCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATGAGGGGGTATCGGT
1 CCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATGAAGGGGTATCGGT
35921 TCCCC
66 TCCCC
* * *
35926 CCCCCCCTGGGGGTACCGATT-CCCTCT-AGCATTCTGGAAATCATATTCGTTGAAGGGGTATCG
1 CCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGATGAAGGGGTATCG
35989 GTTCCCC
64 GTTCCCC
35996 TTGAATGGGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
70 50 0.81
71 12 0.19
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (70 bp):
CCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATGAAGGGGTATCGGT
TCCCC
Found at i:36005 original size:21 final size:21
Alignment explanation
Indices: 35975--36017 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35965 ATCATATTCG
* *
35975 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
35996 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
36017 T
1 T
36018 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:42061 original size:22 final size:22
Alignment explanation
Indices: 42044--42110 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
42034 CTCGTATAAA
42044 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
42066 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
42088 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
42110 T
1 T
42111 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:42444 original size:29 final size:29
Alignment explanation
Indices: 42402--42473 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
42392 TTTTCTGCAT
**
42402 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
42431 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
42460 ATTCATGTCATGTA
1 ATTCATGTCATGTA
42474 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:42895 original size:68 final size:67
Alignment explanation
Indices: 42778--42928 Score: 207
Period size: 68 Copynumber: 2.3 Consensus size: 67
42768 TTTTTCTCAT
* * *
42778 GGGGGAATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGAT
1 GGGGGTATCGGTTCCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGAT
42842 GA
66 GA
* *
42844 GGGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCG
1 GGGGGTATCGGTTCCCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACG
*
42908 TTGA
64 ATGA
*
42912 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
42929 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 12 0.16
67 8 0.11
68 54 0.72
69 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGAT
GA
Found at i:42938 original size:21 final size:21
Alignment explanation
Indices: 42908--42950 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42898 ATCATATTCG
* *
42908 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
42929 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
42950 T
1 T
42951 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:56045 original size:2 final size:2
Alignment explanation
Indices: 56038--56064 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56028 TTTATTCTGC
56038 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 T
56065 TAAAGCTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.