Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005752.1 Hibiscus syriacus cultivar Beakdansim tig00013456_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: 53773
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:3026 original size:17 final size:16
Alignment explanation
Indices: 2993--3042 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
2983 TAAACAATAA
*
2993 AAAAATAGAG-AAAAT
1 AAAAATAAAGTAAAAT
3008 AAAAATAAAGTAAAGAT
1 AAAAATAAAGTAAA-AT
*
3025 AAAAATGAA-TAAAAT
1 AAAAATAAAGTAAAAT
3040 AAA
1 AAA
3043 TAAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.45
16 7 0.23
17 10 0.32
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAAATAAAGTAAAAT
Found at i:3027 original size:41 final size:39
Alignment explanation
Indices: 2975--3056 Score: 94
Period size: 41 Copynumber: 2.1 Consensus size: 39
2965 TAAAAAACGA
*
2975 AAAGAAAATAAACAAT-AAAAAAATAGAGAAAATAAAAAT
1 AAAGAAAATAAA-AATGAAAAAAATAAAGAAAATAAAAAT
* * *
3014 AAAGTAAAGATAAAAATGAATAAAATAAATAAAATGAAAAT
1 AAAG-AAA-ATAAAAATGAAAAAAATAAAGAAAATAAAAAT
3055 AA
1 AA
3057 TAATAATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 4 0.11
40 6 0.17
41 26 0.72
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (39 bp):
AAAGAAAATAAAAATGAAAAAAATAAAGAAAATAAAAAT
Found at i:3047 original size:18 final size:19
Alignment explanation
Indices: 3026--3076 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
3016 AGTAAAGATA
3026 AAAATGAATAA-AATAAAT
1 AAAATGAATAAGAATAAAT
*
3044 AAAATGAA-AATAAT-AAT
1 AAAATGAATAAGAATAAAT
3061 AATAA-GAATAAGAATA
1 AA-AATGAATAAGAATA
3077 TATACACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAATGAATAAGAATAAAT
Found at i:3070 original size:15 final size:14
Alignment explanation
Indices: 3003--3076 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 14
2993 AAAAATAGAG
*
3003 AAAATAAAAATAAAGT
1 AAAATAATAAT-AA-T
*
3019 AAAGATAAAAATGAAT
1 AAA-ATAATAAT-AAT
3035 AAAATAAATAA-AAT
1 AAAAT-AATAATAAT
3049 GAAAATAATAATAAT
1 -AAAATAATAATAAT
*
3064 AAGAATAAGAATA
1 AA-AATAATAATA
3077 TATACACATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
14 10 0.20
15 19 0.38
16 11 0.22
17 10 0.20
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:3289 original size:8 final size:8
Alignment explanation
Indices: 3273--3321 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
3263 AGGTAATAAA
*
3273 ATAAGAAT
1 ATAAAAAT
3281 ATAAAAAT
1 ATAAAAAT
3289 ATAAAAAT
1 ATAAAAAT
3297 ATAAAAA-
1 ATAAAAAT
* *
3304 GTAATAAT
1 ATAAAAAT
3312 ATTAAAAAT
1 A-TAAAAAT
3321 A
1 A
3322 ATAATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
7 5 0.15
8 22 0.65
9 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (8 bp):
ATAAAAAT
Found at i:3312 original size:15 final size:14
Alignment explanation
Indices: 3270--3327 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
3260 ACAAGGTAAT
*
3270 AAAATAAGAATATAA
1 AAAATAATAATAT-A
*
3285 AAATATAAAAATATA
1 AAA-ATAATAATATA
3300 AAAAGTAATAATATTA
1 AAAA-TAATAATA-TA
3316 AAAATAATAATA
1 AAAATAATAATA
3328 ATAACGGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.03
15 22 0.58
16 15 0.39
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAATAATAATATA
Found at i:10520 original size:29 final size:29
Alignment explanation
Indices: 10456--10521 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
10446 GTTCTTCATT
* * * *
10456 AATTTTCCAAAATTTACGAATTTATCCCC
1 AATTTTTCAAAACTTACGAAATAATCCCC
*
10485 AACTTTTCAAAACTTACGAAATAATCCCC
1 AATTTTTCAAAACTTACGAAATAATCCCC
*
10514 CATTTTTC
1 AATTTTTC
10522 TGAGGCTTGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AATTTTTCAAAACTTACGAAATAATCCCC
Found at i:13697 original size:59 final size:59
Alignment explanation
Indices: 13605--13725 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 59
13595 AATAGATGAA
*
13605 TAAGTGTCCTATCGAACCCTCCCAGTCGCAATGAAAAGGA-AAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCACAGTCGCAATGAAAA-GACAAACTCGATAATATGGCTC
* *
13664 TAAGTGTCTTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCACAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
13723 TAA
1 TAA
13726 CCAACCCTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 2 0.03
59 56 0.97
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (59 bp):
TAAGTGTCCTATCGAACCCTCACAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
Found at i:17160 original size:15 final size:15
Alignment explanation
Indices: 17112--17177 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
17102 TATTATTATA
*
17112 TGAATATGTTCTACG
1 TGAATATGTTCTATG
* * *
17127 TGAAAATATTTTATG
1 TGAATATGTTCTATG
*
17142 TGAATATGTTCTATT
1 TGAATATGTTCTATG
* *
17157 TGAACATGGTCTATG
1 TGAATATGTTCTATG
17172 TGAATA
1 TGAATA
17178 AATGATGCTT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (15 bp):
TGAATATGTTCTATG
Found at i:22751 original size:18 final size:18
Alignment explanation
Indices: 22728--22764 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
22718 ATATAATACA
*
22728 TATATCCCGAATGACCAC
1 TATATCCCGAAGGACCAC
22746 TATATCCCGAAGGACCAC
1 TATATCCCGAAGGACCAC
22764 T
1 T
22765 CCTTAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (18 bp):
TATATCCCGAAGGACCAC
Found at i:23099 original size:18 final size:16
Alignment explanation
Indices: 23061--23141 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
23051 TTACAATGAC
*
23061 TTATATCATATATTCA
1 TTATATCACATATTCA
23077 TTATATCACATATTCA
1 TTATATCACATATTCA
* * *
23093 TCATATAATTCACATTCA
1 TTATATCA--CATATTCA
23111 TTATATCACATGA--C-
1 TTATATCACAT-ATTCA
*
23125 TTATATCATATATTCA
1 TTATATCACATATTCA
23141 T
1 T
23142 ATAGACGCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 2 0.04
16 24 0.47
17 1 0.02
18 13 0.25
ACGTcount: A:0.37, C:0.17, G:0.01, T:0.44
Consensus pattern (16 bp):
TTATATCACATATTCA
Found at i:27731 original size:21 final size:21
Alignment explanation
Indices: 27677--27732 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
27667 ATAAGTGTAT
* * *
27677 CAAAGTACCACATATATGTTC
1 CAAAGGACCACATATATATCC
**
27698 CAAAGGATTACATATATATCC
1 CAAAGGACCACATATATATCC
*
27719 CGAAGGACCACATA
1 CAAAGGACCACATA
27733 GAACCCTCGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
CAAAGGACCACATATATATCC
Found at i:37399 original size:28 final size:29
Alignment explanation
Indices: 37363--37421 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
37353 AAATATGATT
* *
37363 AACATAAACTTGAGG-ACTAAAATAGCAA
1 AACAAAAACTTAAGGAACTAAAATAGCAA
37391 AACAAAAACTTAAGGAACTAAAATAGCAA
1 AACAAAAACTTAAGGAACTAAAATAGCAA
37420 AA
1 AA
37422 ATAGACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.15
Consensus pattern (29 bp):
AACAAAAACTTAAGGAACTAAAATAGCAA
Found at i:38849 original size:3 final size:3
Alignment explanation
Indices: 38834--38884 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
38824 TGTGATAGGT
* *
38834 ATA ATA TTA ATA ATA A-A AGTA ATA ATA ATA AAA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
38878 A-A ATA AT
1 ATA ATA AT
38885 TTTTTTGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 6 0.15
3 32 0.80
4 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:38861 original size:15 final size:14
Alignment explanation
Indices: 38836--38884 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
38826 TGATAGGTAT
*
38836 AATATTAATAATAA
1 AATAATAATAATAA
38850 AAGTAATAATAATAAA
1 AA-TAATAATAAT-AA
38866 AATAA-AATAATAA
1 AATAATAATAATAA
38879 AATAAT
1 AATAAT
38885 TTTTTTGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 7 0.23
14 8 0.26
15 12 0.39
16 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:39350 original size:55 final size:55
Alignment explanation
Indices: 39282--39697 Score: 606
Period size: 55 Copynumber: 7.6 Consensus size: 55
39272 TGCGTGCAAT
39282 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
* * * * **
39337 -TAAAGAAATTCATAATAAGTTGATTAATTTTCGTATGGGCATTGTGTGTGGAAAA
1 CT-AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
* * *
39392 CTATA-AAATTCATAATAAGTTTATGACTTTCTGTATGGGCACTGTGTGTGCAAAA
1 CTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
*
39447 CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTACAAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
* * *
39502 CTAAGAAATTCATAATAAGTTGATGAATTTTCGTATGGGCACTATGTGTGA-AAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGT-ACAAAA
* *
39557 CTATA-AAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTATGTGTACAAAA
1 CTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
* * *
39612 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCATTGTGTGTGCAAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
39667 CTAAGAAATTCATAATAAGTTTATGAATTTC
1 CTAAGAAATTCATAATAAGTTTATGAATTTC
39698 TATATTGGTA
Statistics
Matches: 326, Mismatches: 27, Indels: 16
0.88 0.07 0.04
Matches are distributed among these distances:
54 4 0.01
55 318 0.98
56 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (55 bp):
CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
Found at i:39559 original size:165 final size:165
Alignment explanation
Indices: 39282--39696 Score: 706
Period size: 165 Copynumber: 2.5 Consensus size: 165
39272 TGCGTGCAAT
39282 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA-TAAAGAAAT
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACT-AAGAAAT
* * * *
39346 TCATAATAAGTTGATTAATTTTCGTATGGGCATTGTGTGTGGAAAACTATAAAATTCATAATAAG
65 TCATAATAAGTTGATGAATTTTCGTATGGGCACTATGTGTGAAAAACTATAAAATTCATAATAAG
* * *
39411 TTTATGACTTTCTGTATGGGCACTGTGTGTGCAAAA
130 TTTATGAATTTCTGTATGGGCACTATGTGTACAAAA
*
39447 CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
39512 CATAATAAGTTGATGAATTTTCGTATGGGCACTATGTGTGAAAAACTATAAAATTCATAATAAGT
66 CATAATAAGTTGATGAATTTTCGTATGGGCACTATGTGTGAAAAACTATAAAATTCATAATAAGT
39577 TTATGAATTTCTGTATGGGCACTATGTGTACAAAA
131 TTATGAATTTCTGTATGGGCACTATGTGTACAAAA
* * *
39612 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCATTGTGTGTGCAAAACTAAGAAATT
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
*
39677 CATAATAAGTTTATGAATTT
66 CATAATAAGTTGATGAATTT
39697 CTATATTGGT
Statistics
Matches: 236, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
165 235 1.00
166 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (165 bp):
CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
CATAATAAGTTGATGAATTTTCGTATGGGCACTATGTGTGAAAAACTATAAAATTCATAATAAGT
TTATGAATTTCTGTATGGGCACTATGTGTACAAAA
Found at i:42207 original size:2 final size:2
Alignment explanation
Indices: 42195--42234 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
42185 ATATTTATGT
42195 TA TA GTA TA TA 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 TA TA TA TA TA T
42235 TACATCATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48461 original size:55 final size:55
Alignment explanation
Indices: 48401--48660 Score: 385
Period size: 55 Copynumber: 4.7 Consensus size: 55
48391 CTATGCGTGC
*
48401 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGTA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTGTGTGTGTA
* * * * * *
48456 AAACTAAGAAATTCATAATAAGTTTATAAATTTTCATATGGGTACTGTATGTGTA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTGTGTGTGTA
* *
48511 AAACTAAGAAATTCATAATAAATTTATGAATTTCTGTATAGGCACTGTGTGTGTA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTGTGTGTGTA
* **
48566 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGACACTGTGTGTACA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTGTGTGTGTA
* *
48621 AAACTAAAAAAATTCATAATAAGTTTATGAATTTTCGTAT
1 AAACT-AAGAAATTCATAATAAGTTTATGAATTTCCGTAT
48661 TGACAGTGGG
Statistics
Matches: 184, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
55 152 0.83
56 32 0.17
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (55 bp):
AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTGTGTGTGTA
Found at i:53447 original size:26 final size:26
Alignment explanation
Indices: 53404--53468 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
53394 AAAATTTTGA
*
53404 TGATAAT-ATAAAGGAGTTGAGGAAT
1 TGATAATAAGAAAGGAGTTGAGGAAT
53429 TGATAATAAGAAAGGAGTTGAGGAAT
1 TGATAATAAGAAAGGAGTTGAGGAAT
53455 TGATAATAAGAAAG
1 TGATAATAAGAAAG
53469 AATTTGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 7 0.18
26 31 0.82
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.25
Consensus pattern (26 bp):
TGATAATAAGAAAGGAGTTGAGGAAT
Done.