Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:3067296 original size:20 final size:20
Alignment explanation
Indices: 3067222--3067310 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
3067212 TCGCGTTGCG
3067222 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3067242 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
3067255 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
3067275 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3067295 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
3067311 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3067432 original size:33 final size:33
Alignment explanation
Indices: 3067390--3067460 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3067380 AATACTAACT
*
3067390 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3067423 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3067456 TGAAA
1 TGAAA
3067461 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3067694 original size:22 final size:22
Alignment explanation
Indices: 3067642--3067696 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3067632 TGGTTGTGAG
**
3067642 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3067664 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3067686 GGATTTCTTCG
1 GGATTTCTTCG
3067697 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3067867 original size:20 final size:20
Alignment explanation
Indices: 3067842--3068034 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
3067832 CTTTAAATAT
3067842 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3067862 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3067884 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3067903 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3067923 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3067943 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3067963 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3067983 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3068003 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3068023 CGCGTTGCGATT
1 CGCGTTGCGATT
3068035 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3068029 original size:60 final size:60
Alignment explanation
Indices: 3067842--3068034 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
3067832 CTTTAAATAT
**
3067842 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3067903 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3067963 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3068023 CGCGTTGCGATT
1 CGCGTTGCGATT
3068035 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3068115 original size:20 final size:20
Alignment explanation
Indices: 3068090--3068141 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3068080 AAGAATCGCG
*
3068090 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3068110 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3068130 TTGCGATTCTGG
1 TTGCGATTCTGG
3068142 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:3068837 original size:68 final size:68
Alignment explanation
Indices: 3068708--3068838 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 68
3068698 ATATATATAA
* * * * * ** *
3068708 AATTTTTAAATAAAAAATGGTATAAATATAATTTTAGGATGGATATTATCCGTAAATTAAGTATG
1 AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATAGACATCATCAATAAAATAAGTATG
3068773 TAG
66 TAG
3068776 AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATAGACATCATCAATAAAATAAGTA
1 AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATAGACATCATCAATAAAATAAGTA
3068839 ACTAATTGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.34
Consensus pattern (68 bp):
AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATAGACATCATCAATAAAATAAGTATG
TAG
Found at i:3072602 original size:22 final size:22
Alignment explanation
Indices: 3072574--3072644 Score: 133
Period size: 22 Copynumber: 3.2 Consensus size: 22
3072564 CAAAGGGATC
3072574 CCACCGTTTGTGTGGAGTCATT
1 CCACCGTTTGTGTGGAGTCATT
3072596 CCACCGTTTGTGTGGAGTCATT
1 CCACCGTTTGTGTGGAGTCATT
*
3072618 CCACCGTTTGTGTGGAGTTATT
1 CCACCGTTTGTGTGGAGTCATT
3072640 CCACC
1 CCACC
3072645 TTCAAAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.35
Consensus pattern (22 bp):
CCACCGTTTGTGTGGAGTCATT
Found at i:3074199 original size:125 final size:125
Alignment explanation
Indices: 3073993--3074242 Score: 455
Period size: 125 Copynumber: 2.0 Consensus size: 125
3073983 TTGGTTCGCC
*
3073993 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAATGTATGTTG
1 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAACGTATGTTG
3074058 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
66 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
* **
3074118 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTGGGGTATGGAACGTATGTTG
1 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAACGTATGTTG
*
3074183 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTCTTTTTCCTCCATTTA
66 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
3074243 GGATTAAGGA
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (125 bp):
TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAACGTATGTTG
TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
Found at i:3074661 original size:14 final size:14
Alignment explanation
Indices: 3074644--3074672 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3074634 ATTATTTGCA
3074644 ATTTTAAATTTTAT
1 ATTTTAAATTTTAT
3074658 ATTTTAAATTTTAT
1 ATTTTAAATTTTAT
3074672 A
1 A
3074673 AATTAAATTA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTAAATTTTAT
Found at i:3074678 original size:14 final size:14
Alignment explanation
Indices: 3074647--3074681 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3074637 ATTTGCAATT
**
3074647 TTAAATTTTATATT
1 TTAAATTTTATAAA
3074661 TTAAATTTTATAAA
1 TTAAATTTTATAAA
3074675 TTAAATT
1 TTAAATT
3074682 AATGATACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTTTATAAA
Found at i:3077516 original size:31 final size:31
Alignment explanation
Indices: 3077459--3077541 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
3077449 TTAAAAAGTT
* * * *
3077459 AAATTCAAGTATCTAA-TAAGAGATTAAAATG
1 AAATTCAAGTATCAAATTGA-ACATTAAAATC
*
3077490 AAGATT-AAGTATCACATTGAACATTAAAATC
1 AA-ATTCAAGTATCAAATTGAACATTAAAATC
3077521 AAATTCAAGTATCAAATTGAA
1 AAATTCAAGTATCAAATTGAA
3077542 ACCAAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
30 3 0.07
31 35 0.81
32 5 0.12
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (31 bp):
AAATTCAAGTATCAAATTGAACATTAAAATC
Found at i:3077657 original size:6 final size:6
Alignment explanation
Indices: 3077646--3077673 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3077636 TATCAAAATG
3077646 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
3077674 TATGAAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:3080528 original size:24 final size:24
Alignment explanation
Indices: 3080501--3080550 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3080491 TGGTGGTTGA
*
3080501 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAAATTTATT
*
3080525 TTTAATGGTGTATTTAAATTTATT
1 TTTAATGGTGTATTGAAATTTATT
3080549 TT
1 TT
3080551 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAAATTTATT
Found at i:3087430 original size:26 final size:24
Alignment explanation
Indices: 3087379--3087457 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 24
3087369 TCCCTCTTAA
*
3087379 ACTTTTAAATTTTTCT-TTTCTCTTT
1 ACTTTT-AATTTATCTCTTTCT-TTT
*
3087404 ATTTATTAATTTATCTCTTTCATTTT
1 ACTT-TTAATTTATCTCTTTC-TTTT
* *
3087430 AACTTTTACTTTTTCTCTTTCTTTT
1 -ACTTTTAATTTATCTCTTTCTTTT
3087455 ACT
1 ACT
3087458 CATCTTCTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
24 3 0.07
25 15 0.33
26 23 0.51
27 4 0.09
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (24 bp):
ACTTTTAATTTATCTCTTTCTTTT
Found at i:3092242 original size:23 final size:24
Alignment explanation
Indices: 3092215--3092266 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3092205 AACTATGAAA
*
3092215 CAAAACAATTAAATAAAAT-TAAT
1 CAAAACAATTAAACAAAATATAAT
*
3092238 CAAAATAATTAAACAAAATATAAT
1 CAAAACAATTAAACAAAATATAAT
*
3092262 AAAAA
1 CAAAA
3092267 ACAGTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (24 bp):
CAAAACAATTAAACAAAATATAAT
Found at i:3092291 original size:15 final size:17
Alignment explanation
Indices: 3092260--3092299 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
3092250 ACAAAATATA
3092260 ATAAAAAACAGTAAAAT
1 ATAAAAAACAGTAAAAT
3092277 ATAAAAAACA-T-AAAT
1 ATAAAAAACAGTAAAAT
*
3092292 AGAAAAAA
1 ATAAAAAA
3092300 TAAACATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (17 bp):
ATAAAAAACAGTAAAAT
Done.