Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006196.1 Hibiscus syriacus cultivar Beakdansim tig00014748_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: 68807
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:11310 original size:19 final size:19
Alignment explanation
Indices: 11286--11324 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11276 ATCGTCTCGA
11286 TGAGAATTGAACCCGATTT
1 TGAGAATTGAACCCGATTT
11305 TGAGAATTGAACCCGATTT
1 TGAGAATTGAACCCGATTT
11324 T
1 T
11325 AGTTTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (19 bp):
TGAGAATTGAACCCGATTT
Found at i:16132 original size:21 final size:21
Alignment explanation
Indices: 16107--16149 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16097 AAACTATGAG
16107 TTTGTAATAATACTCCTTGAC
1 TTTGTAATAATACTCCTTGAC
*
16128 TTTGTAATAATGCTCCTTGAC
1 TTTGTAATAATACTCCTTGAC
16149 T
1 T
16150 CTTAACAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTGTAATAATACTCCTTGAC
Found at i:16161 original size:21 final size:21
Alignment explanation
Indices: 16109--16161 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
16099 ACTATGAGTT
* * *
16109 TGTAATAATACTCCTTGACTT
1 TGTAACAATGCTCCTTGACTC
*
16130 TGTAATAATGCTCCTTGACTC
1 TGTAACAATGCTCCTTGACTC
16151 T-TAACAGATGC
1 TGTAACA-ATGC
16162 GGAATGTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTAACAATGCTCCTTGACTC
Found at i:19627 original size:21 final size:20
Alignment explanation
Indices: 19590--19667 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
19580 GCAAAACATT
* *
19590 AAAGGGATCAATTCTTTCTTG
1 AAAGGGATCGATCCTTT-TTG
*
19611 AAAGGGATCGATCCTTTTTC
1 AAAGGGATCGATCCTTTTTG
**
19631 ACGGGGATCGATCC-TTTTG
1 AAAGGGATCGATCCTTTTTG
*
19650 AAAATGGATCGAT-CTTTT
1 -AAAGGGATCGATCCTTTT
19668 GCAAAATGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.11
20 26 0.57
21 15 0.33
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (20 bp):
AAAGGGATCGATCCTTTTTG
Found at i:19666 original size:19 final size:21
Alignment explanation
Indices: 19635--19675 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
19625 TTTTTCACGG
19635 GGATCGATCCTTTTG-AAAAT
1 GGATCGATCCTTTTGCAAAAT
19655 GGATCGAT-CTTTTGCAAAAT
1 GGATCGATCCTTTTGCAAAAT
19675 G
1 G
19676 AAACTTTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (21 bp):
GGATCGATCCTTTTGCAAAAT
Found at i:21475 original size:11 final size:11
Alignment explanation
Indices: 21440--21469 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21430 AAAAATGCTC
*
21440 CCAAACGCTCA
1 CCAAACACTCA
21451 CCAAACACTCA
1 CCAAACACTCA
21462 CCAAACAC
1 CCAAACAC
21470 CAACCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.47, G:0.03, T:0.07
Consensus pattern (11 bp):
CCAAACACTCA
Found at i:28852 original size:20 final size:20
Alignment explanation
Indices: 28814--28853 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28804 TTTTTTAGTA
*
28814 TTATTACATTATATCTTATT
1 TTATTACATTATATATTATT
28834 TTATTATCATTA-ATATTATT
1 TTATTA-CATTATATATTATT
28854 AATATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTACATTATATATTATT
Found at i:29142 original size:14 final size:14
Alignment explanation
Indices: 29125--29152 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29115 TTGGCATAAT
29125 TCTATATTTGGTCC
1 TCTATATTTGGTCC
29139 TCTATATTTGGTCC
1 TCTATATTTGGTCC
29153 CTCCAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
TCTATATTTGGTCC
Found at i:30274 original size:20 final size:20
Alignment explanation
Indices: 30242--30280 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30232 AAAGATTTTT
30242 ATTTTATAATGTTAAAATAG
1 ATTTTATAATGTTAAAATAG
*
30262 ATTTT-TAATTGTTACAATA
1 ATTTTATAA-TGTTAAAATA
30281 TATATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (20 bp):
ATTTTATAATGTTAAAATAG
Found at i:35611 original size:28 final size:28
Alignment explanation
Indices: 35532--35685 Score: 166
Period size: 29 Copynumber: 5.4 Consensus size: 28
35522 CATTTTACAG
** * *
35532 AAATAGCACCATTTTTAAAATAATTACCA
1 AAATAGCACC-TTTTCGAATTAATTCCCA
* * *
35561 AAATAGTACATTTTCAAATTAAATTCCCA
1 AAATAGCACCTTTTCGAATT-AATTCCCA
35590 AAATAGCA-CTTTTCGAATTAAATTCCCA
1 AAATAGCACCTTTTCGAATT-AATTCCCA
35618 AAATAGCATCCTTTTCGAATTAATTCCCA
1 AAATAGCA-CCTTTTCGAATTAATTCCCA
* *
35647 AAATAGCACCCATTTCGAAATAATTCCCA
1 AAATAGCA-CCTTTTCGAATTAATTCCCA
*
35676 AAATATCACC
1 AAATAGCACC
35686 CGGTCAACTG
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
28 36 0.33
29 63 0.57
30 11 0.10
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.31
Consensus pattern (28 bp):
AAATAGCACCTTTTCGAATTAATTCCCA
Found at i:35623 original size:57 final size:57
Alignment explanation
Indices: 35532--35680 Score: 176
Period size: 57 Copynumber: 2.6 Consensus size: 57
35522 CATTTTACAG
** * *
35532 AAATAGCACCATTTTTAAAATAATTACCAAAATAGTA-CATTTTCAAATTAAATTCCCA
1 AAATAGCACCA-TTTCGAAATAATTCCCAAAATAGCATCATTTTCAAATT-AATTCCCA
* * * *
35590 AAATAGCA-CTTTTCGAATTAAATTCCCAAAATAGCATCCTTTTCGAATTAATTCCCA
1 AAATAGCACCATTTCGAAAT-AATTCCCAAAATAGCATCATTTTCAAATTAATTCCCA
35647 AAATAGCACCCATTTCGAAATAATTCCCAAAATA
1 AAATAGCA-CCATTTCGAAATAATTCCCAAAATA
35681 TCACCCGGTC
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
56 6 0.08
57 31 0.40
58 31 0.40
59 9 0.12
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (57 bp):
AAATAGCACCATTTCGAAATAATTCCCAAAATAGCATCATTTTCAAATTAATTCCCA
Found at i:35709 original size:17 final size:17
Alignment explanation
Indices: 35687--35724 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35677 AATATCACCC
* *
35687 GGTCAACTGTCGGGTCG
1 GGTCAACAGTCGGATCG
35704 GGTCAACAGTCGGATCG
1 GGTCAACAGTCGGATCG
35721 GGTC
1 GGTC
35725 GGGTCTGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.39, T:0.21
Consensus pattern (17 bp):
GGTCAACAGTCGGATCG
Found at i:40277 original size:8 final size:8
Alignment explanation
Indices: 40264--40336 Score: 56
Period size: 8 Copynumber: 10.1 Consensus size: 8
40254 AACTTAGTTG
40264 TAATTTTA
1 TAATTTTA
40272 TAATTTTA
1 TAATTTTA
40280 T--TTTTA
1 TAATTTTA
40286 T-ATCTTTA
1 TAAT-TTTA
40294 T-ATTTTA
1 TAATTTTA
40301 T--TTTTA
1 TAATTTTA
*
40307 -GATTTTA
1 TAATTTTA
40314 TAA-TTT-
1 TAATTTTA
40320 TAATTTTA
1 TAATTTTA
*
40328 TAAATTTA
1 TAATTTTA
40336 T
1 T
40337 GTTATGTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
6 14 0.25
7 17 0.30
8 25 0.45
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (8 bp):
TAATTTTA
Found at i:40286 original size:6 final size:7
Alignment explanation
Indices: 40266--40329 Score: 71
Period size: 8 Copynumber: 9.1 Consensus size: 7
40256 CTTAGTTGTA
40266 ATTTTAT
1 ATTTTAT
40273 AATTTTAT
1 -ATTTTAT
40281 -TTTTAT
1 ATTTTAT
40287 ATCTTTAT
1 AT-TTTAT
40295 ATTTTAT
1 ATTTTAT
*
40302 -TTTTAG
1 ATTTTAT
40308 ATTTTAT
1 ATTTTAT
40315 AATTTTA-
1 -ATTTTAT
40322 ATTTTAT
1 ATTTTAT
40329 A
1 A
40330 AATTTATGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
6 17 0.35
7 12 0.24
8 20 0.41
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (7 bp):
ATTTTAT
Found at i:40286 original size:14 final size:14
Alignment explanation
Indices: 40267--40336 Score: 65
Period size: 14 Copynumber: 5.0 Consensus size: 14
40257 TTAGTTGTAA
40267 TTTTATAATTTTAT
1 TTTTATAATTTTAT
40281 TTTTAT-ATCTTTAT
1 TTTTATAAT-TTTAT
*
40295 ATTTTAT--TTTTAGA
1 -TTTTATAATTTTA-T
*
40309 TTTTATAATTTTAA
1 TTTTATAATTTTAT
*
40323 TTTTATAAATTTAT
1 TTTTATAATTTTAT
40337 GTTATGTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.25
14 25 0.52
15 11 0.23
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (14 bp):
TTTTATAATTTTAT
Found at i:40300 original size:21 final size:21
Alignment explanation
Indices: 40266--40329 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
40256 CTTAGTTGTA
40266 ATTTTATAATTTTATTTTTAT
1 ATTTTATAATTTTATTTTTAT
*
40287 ATCTTTAT-ATTTTATTTTTAG
1 AT-TTTATAATTTTATTTTTAT
*
40308 ATTTTATAATTTTAATTTTAT
1 ATTTTATAATTTTATTTTTAT
40329 A
1 A
40330 AATTTATGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 5 0.13
21 28 0.74
22 5 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTATAATTTTATTTTTAT
Found at i:44159 original size:18 final size:18
Alignment explanation
Indices: 44130--44207 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 18
44120 AATTCTAAAT
*
44130 ATTTACAGTTATCAGATG
1 ATTTACAATTATCAGATG
* *
44148 ATTTTCAATTATCATATG
1 ATTTACAATTATCAGATG
* *
44166 ATTTACAGTAATCAGAT-
1 ATTTACAATTATCAGATG
* *
44183 AATTACAAATATCAGATG
1 ATTTACAATTATCAGATG
*
44201 TTTTACA
1 ATTTACA
44208 TGTATTAGAT
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
17 13 0.28
18 33 0.72
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (18 bp):
ATTTACAATTATCAGATG
Found at i:45917 original size:55 final size:54
Alignment explanation
Indices: 45784--45924 Score: 194
Period size: 54 Copynumber: 2.6 Consensus size: 54
45774 AGAAATGGAA
* * * * * *
45784 AGGGTATTGATAAACTCATCAGTGTATCAATACACAAATAACATTCGATGTTTT
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATATTTT
45838 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAGA-ATTCGATATTTT
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATA-ACATTCGATATTTT
*
45892 GCGGGTATCGATACACTCCTCAGTGTACCGATA
1 -AGGGTATCGATACACTCCTCAGTGTACCGATA
45925 AACACTCATA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
54 46 0.59
55 32 0.41
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (54 bp):
AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATATTTT
Found at i:52777 original size:55 final size:55
Alignment explanation
Indices: 52718--52863 Score: 247
Period size: 55 Copynumber: 2.7 Consensus size: 55
52708 CGAAATGGCA
* * *
52718 AGGGTATCGATATACTCCTCAATGTACCGATACACAAATAACATTTGATGTTTTG
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATGTTTTG
*
52773 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACATTCGATGTTTTG
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATGTTTTG
*
52828 CGGGTATCGATACACTCCTCAGTGTACCGATACACA
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACA
52864 CTCATACAAT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 86 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (55 bp):
AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATGTTTTG
Found at i:58195 original size:20 final size:20
Alignment explanation
Indices: 58172--58211 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
58162 AGTTTTATAT
*
58172 TTAATACAGATGGAACAATA
1 TTAATACAGAAGGAACAATA
58192 TTAATACAGAAGGAACAATA
1 TTAATACAGAAGGAACAATA
58212 CCTGCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
TTAATACAGAAGGAACAATA
Found at i:68241 original size:37 final size:38
Alignment explanation
Indices: 68168--68241 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
68158 GACCCGATAT
* * *
68168 CACACTTAAAAAAACCCGACCAGACTCGACCCAAATAC
1 CACACTTAAAAAAACCCGACCAGACCCGAACAAAATAC
*
68206 CACACTTAAAAAAA-CCGACCCGACCCGAACAAAATA
1 CACACTTAAAAAAACCCGACCAGACCCGAACAAAATA
68242 AAGTTTCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 18 0.56
38 14 0.44
ACGTcount: A:0.47, C:0.35, G:0.08, T:0.09
Consensus pattern (38 bp):
CACACTTAAAAAAACCCGACCAGACCCGAACAAAATAC
Done.