Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003030.1 Hibiscus syriacus cultivar Beakdansim tig00006308_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: 48575
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:535 original size:29 final size:30
Alignment explanation
Indices: 477--548 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
467 AATTTTTAGA
*
477 ATATGTATAATTAAATTAATATTAAATTTT
1 ATATGTATAATTAAATCAATATTAAATTTT
* * *
507 ATTTGTATAATTGAATCAA-ATTAAGTTTT
1 ATATGTATAATTAAATCAATATTAAATTTT
*
536 ATAAGTATAATTA
1 ATATGTATAATTA
549 TGTCAACTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (30 bp):
ATATGTATAATTAAATCAATATTAAATTTT
Found at i:2511 original size:3 final size:3
Alignment explanation
Indices: 2503--2551 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
2493 TACGTCTGTT
2503 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2550 TA
1 TA
2552 TGGGTAAACT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4367 original size:31 final size:31
Alignment explanation
Indices: 4245--4354 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
4235 GGGTCGAGGG
*
4245 TTACCTATGTTCTTCGGGACTTATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
4276 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
4307 TCACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
4338 TTACCTAGGTTCTTCGG
1 TTACCTATGTTCTTCGG
4355 AATCTATAGA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:4367 original size:62 final size:62
Alignment explanation
Indices: 4247--4367 Score: 190
Period size: 62 Copynumber: 2.0 Consensus size: 62
4237 GTCGAGGGTT
* * * *
4247 ACCTATGTTCTTCGGGACTTATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGTTC
1 ACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCGGAACATATAGACTGTTC
4309 ACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCGGAATC-TATAGACTG
1 ACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCGGAA-CATATAGACTG
4368 GTCCTTCGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 53 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (62 bp):
ACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCGGAACATATAGACTGTTC
Found at i:5378 original size:23 final size:22
Alignment explanation
Indices: 5347--5391 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
5337 TAATTTTTAG
5347 AAAATAAAA-ATAAAAATATATT
1 AAAATAAAACATAAAAA-ATATT
5369 AAAATGAAAACATAAAAAATATT
1 AAAAT-AAAACATAAAAAATATT
5392 TTCAGTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAAACATAAAAAATATT
Found at i:5683 original size:7 final size:7
Alignment explanation
Indices: 5648--5727 Score: 54
Period size: 7 Copynumber: 10.6 Consensus size: 7
5638 TACTATTTTA
5648 TTAATAAT
1 TTAAT-AT
*
5656 TTAATTT
1 TTAATAT
5663 TTAATAT
1 TTAATAT
*
5670 TTTATAT
1 TTAATAT
5677 TTAATAT
1 TTAATAT
5684 ATTAAATAT
1 -TT-AATAT
5693 CTTAATAATT
1 -TTAAT-A-T
*
5703 ATTTATAT
1 -TTAATAT
*
5711 TTTATAT
1 TTAATAT
5718 TTAA-AT
1 TTAATAT
5724 TTAA
1 TTAA
5728 ATAATTAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
6 6 0.10
7 29 0.48
8 11 0.18
9 9 0.15
10 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAATAT
Found at i:8560 original size:16 final size:16
Alignment explanation
Indices: 8539--8569 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8529 AAACTAGCAA
8539 ACACACGAGAAACTGT
1 ACACACGAGAAACTGT
*
8555 ACACACGAGCAACTG
1 ACACACGAGAAACTG
8570 CACTAGCTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.29, G:0.19, T:0.10
Consensus pattern (16 bp):
ACACACGAGAAACTGT
Found at i:13353 original size:3 final size:3
Alignment explanation
Indices: 13345--13410 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
13335 TGTTTGCTTT
* * *
13345 GAA GAA GAA GAA GAA GAAA GAA GGAA AAA GAA GAA -AA AATA GAA GAT
1 GAA GAA GAA GAA GAA G-AA GAA -GAA GAA GAA GAA GAA GA-A GAA GAA
*
13392 GTA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA G
13411 CTGCCACGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 2 0.04
3 42 0.81
4 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:21182 original size:14 final size:15
Alignment explanation
Indices: 21163--21201 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
21153 CCGGATGTTA
*
21163 CGGGTACCCGGT-TT
1 CGGGTACCCGGTAAT
21177 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
21192 CGGGTACCCG
1 CGGGTACCCG
21202 ATACACGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.13, C:0.31, G:0.36, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:21963 original size:17 final size:16
Alignment explanation
Indices: 21941--21972 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
21931 CACCAATCAA
21941 CAGTCAAAGTCCAACGC
1 CAGTCAAAGT-CAACGC
21958 CAGTCAAAGTCAACG
1 CAGTCAAAGTCAACG
21973 ACGGTCAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.12
Consensus pattern (16 bp):
CAGTCAAAGTCAACGC
Found at i:21979 original size:16 final size:17
Alignment explanation
Indices: 21940--21980 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
21930 GCACCAATCA
21940 ACAGTCAAAGTCCAACG
1 ACAGTCAAAGTCCAACG
*
21957 CCAGTCAAAGT-CAACG
1 ACAGTCAAAGTCCAACG
*
21973 ACGGTCAA
1 ACAGTCAA
21981 CGGTGCGTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.39, C:0.29, G:0.20, T:0.12
Consensus pattern (17 bp):
ACAGTCAAAGTCCAACG
Found at i:24194 original size:2 final size:2
Alignment explanation
Indices: 24187--24213 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24177 ATTATAAATG
24187 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
24214 CCTTCAATGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42358 original size:31 final size:32
Alignment explanation
Indices: 42314--42383 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
42304 CAATTTCATC
* *
42314 CCTCAAA-TGATGATATAT-ATTCTAATTTGGT
1 CCTCAAACTGATGATAT-TCATTCTAAATTAGT
42345 CCTCAAACT-ATGATATTCATTCTAAATTAGT
1 CCTCAAACTGATGATATTCATTCTAAATTAGT
42376 CC-CAAACT
1 CCTCAAACT
42384 TTTTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 7 0.20
31 27 0.77
32 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (32 bp):
CCTCAAACTGATGATATTCATTCTAAATTAGT
Found at i:45203 original size:2 final size:2
Alignment explanation
Indices: 45196--45228 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
45186 ATTTTTGAGA
45196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45229 GACAGATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45266 original size:18 final size:17
Alignment explanation
Indices: 45232--45275 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
45222 ATATATAGAC
*
45232 AGATACAATCAATAAAAT
1 AGATA-AATAAATAAAAT
45250 AGATAAATAAATAAAAAT
1 AGATAAATAAAT-AAAAT
*
45268 AAATAAAT
1 AGATAAAT
45276 TTTAGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (17 bp):
AGATAAATAAATAAAAT
Found at i:47838 original size:26 final size:26
Alignment explanation
Indices: 47802--47888 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 26
47792 ATGCATTAAT
*
47802 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCATTTCATGCATTTTAGTTATG
* *
47828 GCATCATTTCATGC--CTCA---AT-
1 GCATCATTTCATGCATTTTAGTTATG
*
47848 GCAATCATTTCATGCATTTTAGTTTTG
1 GC-ATCATTTCATGCATTTTAGTTATG
*
47875 GCATCCTTTCATGC
1 GCATCATTTCATGC
47889 CTTAAGCATC
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
23 2 0.04
24 2 0.04
26 25 0.53
27 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.43
Consensus pattern (26 bp):
GCATCATTTCATGCATTTTAGTTATG
Found at i:47877 original size:47 final size:46
Alignment explanation
Indices: 47770--47917 Score: 217
Period size: 47 Copynumber: 3.2 Consensus size: 46
47760 TTATTCGTTA
* * *
47770 ATTTCAGTTATGGCCTCCTTTCATGCATTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
47816 ATTTTAGTTATGGCATCATTTCATGCCTCAATGCAATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGC-ATCCTTTCATGC
*
47863 ATTTTAGTTTTGGCATCCTTTCATGCCTTAA-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
47908 ATTTTAGTTA
1 ATTTTAGTTA
47918 GGAATTCGTT
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
45 20 0.22
46 31 0.34
47 39 0.43
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:48131 original size:31 final size:25
Alignment explanation
Indices: 48067--48114 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
48057 TTAAATAACA
48067 ATAAATGTACTCACCTGATAATCAC
1 ATAAATGTACTCACCTGATAATCAC
48092 ATAAATGTACTCACCTGATAATC
1 ATAAATGTACTCACCTGATAATC
48115 CCAACTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (25 bp):
ATAAATGTACTCACCTGATAATCAC
Done.