Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004519.1 Hibiscus syriacus cultivar Beakdansim tig00009967_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: 51930
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1880 original size:40 final size:40
Alignment explanation
Indices: 1794--1908 Score: 223
Period size: 40 Copynumber: 2.9 Consensus size: 40
1784 GCAGTATAGT
1794 TATGAAAGTGTACAACGTACTTTGTTAGGGG-ACTAGTAG
1 TATGAAAGTGTACAACGTACTTTGTTAGGGGAACTAGTAG
1833 TATGAAAGTGTACAACGTACTTTGTTAGGGGAACTAGTAG
1 TATGAAAGTGTACAACGTACTTTGTTAGGGGAACTAGTAG
1873 TATGAAAGTGTACAACGTACTTTGTTAGGGGAACTA
1 TATGAAAGTGTACAACGTACTTTGTTAGGGGAACTA
1909 TCTCCTTGGT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
39 31 0.41
40 44 0.59
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.30
Consensus pattern (40 bp):
TATGAAAGTGTACAACGTACTTTGTTAGGGGAACTAGTAG
Found at i:2839 original size:35 final size:36
Alignment explanation
Indices: 2748--2847 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 36
2738 AAATAATCTA
*
2748 AATAATAATTATTAAT-TTA-TT-ATAAATAATAAT
1 AATAATAATTAATAATATTATTTAATAAATAATAAT
2781 AATAATAAGTTAACTAATCTATTATTTAATAAATAA-AAT
1 AATAATAA-TTAA-TAA--TATTATTTAATAAATAATAAT
* *
2820 ATTAGTAATTAATAATATTATTTTAATA
1 AATAATAATTAATAATATTA-TTTAATA
2848 CAAAAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
33 8 0.14
34 3 0.05
35 8 0.14
36 7 0.12
37 4 0.07
38 7 0.12
39 11 0.20
40 8 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (36 bp):
AATAATAATTAATAATATTATTTAATAAATAATAAT
Found at i:3959 original size:20 final size:21
Alignment explanation
Indices: 3919--3960 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3909 AACAGAATGT
3919 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
3940 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
3961 TGTTTAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:14933 original size:17 final size:19
Alignment explanation
Indices: 14899--14935 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
14889 TGCTGACATG
14899 TCTTGCTCTTCTTCGCTTC
1 TCTTGCTCTTCTTCGCTTC
14918 TCTT-CTCTTC-TCGCTTC
1 TCTTGCTCTTCTTCGCTTC
14935 T
1 T
14936 TTAACCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.00, C:0.38, G:0.08, T:0.54
Consensus pattern (19 bp):
TCTTGCTCTTCTTCGCTTC
Found at i:15918 original size:2 final size:2
Alignment explanation
Indices: 15911--15942 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15901 ACTCATAGTC
15911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15943 GTAGACACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16095 original size:40 final size:40
Alignment explanation
Indices: 15985--16110 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
15975 ATATATAGTA
* *
15985 ATATAATATA-TTTTTT-GAAAATGATTTTGAAAA-ATAT
1 ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAATATAT
** * **
16022 A-AT-ATATAGTTTTCAAAAAAACGGTTTCCGAAAATATAT
1 ATATAATATAGTTTTTTAAAAAA-TGTTTTTGAAAATATAT
16061 ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAACT-TAT
1 ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAA-TATAT
*
16101 ATACAATATA
1 ATATAATATA
16111 CAAGTTTTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
35 5 0.07
36 6 0.09
37 5 0.07
38 8 0.12
39 5 0.07
40 23 0.33
41 17 0.25
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (40 bp):
ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAATATAT
Found at i:16211 original size:73 final size:68
Alignment explanation
Indices: 16115--16323 Score: 230
Period size: 73 Copynumber: 3.0 Consensus size: 68
16105 AATATACAAG
* * *
16115 TTTT-AAAACA-TTTTGAAAGTTATATAATATATGGTTTTGAAATCATTTTGAAAATATAATGTA
1 TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAAAATATAAT-TA
16178 TAGT
65 TAGT
*
16182 TTTTAAAAAAACATTTTTGAAAAATTTATATAATATATAGTTTTAAAAACATTTTGAAAA-ACTT
1 TTTT--AAAAACATTTTTG-AAAA-TTATATAATATATAGTTTTGAAAACATTTTGAAAATA--T
16246 ATATTATA-T
60 A-ATTATAGT
* * * *
16255 TTTTAAAATCATTTTTGAAAACTATATAATATATAGTTTTGAAAACATTTT-TAAGTATAATATA
1 TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAAAATATAAT-TA
16319 TAGT
65 TAGT
16323 T
1 T
16324 CAAAAAATAT
Statistics
Matches: 121, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
66 2 0.02
67 10 0.08
68 4 0.03
69 29 0.24
70 10 0.08
71 17 0.14
72 4 0.03
73 37 0.31
74 6 0.05
75 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (68 bp):
TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAAAATATAATTAT
AGT
Found at i:16240 original size:108 final size:109
Alignment explanation
Indices: 16051--16299 Score: 276
Period size: 110 Copynumber: 2.3 Consensus size: 109
16041 AACGGTTTCC
* * ** *
16051 GAAAATATATATATAATATAGTTTTTTAAAAAATGTTTTTGAAAACTTATATACAATATACAAGT
1 GAAAACATATA-AT-ATATAGTTTTTAAAAAAACATTTTTGAAAAATTATATACAATATACAAGT
* *
16116 TTTAAAACATTTTG-AAAGTTATATAATATATGGTTTTGAAATCA-TTTT
64 TTTAAAACATTTTGAAAACTTATAT--TATAT--TTTTAAAATCATTTTT
* * *
16164 G-AAA-ATATAATGTATAGTTTTTAAAAAAACATTTTTGAAAAATT-TATATAATATA-TAGTTT
1 GAAAACATATAATATATAGTTTTTAAAAAAACATTTTTGAAAAATTATATACAATATACAAGTTT
16225 TAAAAACATTTTGAAAAACTTATATTATATTTTTAAAATCATTTTT
66 T-AAAACATTTTG-AAAACTTATATTATATTTTTAAAATCATTTTT
*
16271 GAAAACTATATAATATATAGTTTTGAAAA
1 GAAAAC-ATATAATATATAGTTTTTAAAA
16300 CATTTTTAAG
Statistics
Matches: 118, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
106 10 0.08
107 11 0.09
108 29 0.25
109 28 0.24
110 31 0.26
111 5 0.04
112 3 0.03
113 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (109 bp):
GAAAACATATAATATATAGTTTTTAAAAAAACATTTTTGAAAAATTATATACAATATACAAGTTT
TAAAACATTTTGAAAACTTATATTATATTTTTAAAATCATTTTT
Found at i:16336 original size:31 final size:31
Alignment explanation
Indices: 16279--16337 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
16269 TTGAAAACTA
***
16279 TATAATATATAGTTTTGAAAACATTTTTAAG
1 TATAATATATAGTTCAAAAAACATTTTTAAG
*
16310 TATAATATATAGTTCAAAAAATATTTTT
1 TATAATATATAGTTCAAAAAACATTTTT
16338 TTATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (31 bp):
TATAATATATAGTTCAAAAAACATTTTTAAG
Found at i:18794 original size:28 final size:30
Alignment explanation
Indices: 18763--18818 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
18753 CAAAAATAAC
*
18763 ATACAGAAGA-AA-ACACACTCCTACAAAA
1 ATACAGAAGACAAGAAACACTCCTACAAAA
**
18791 ATACTTAAGACAAGAAACACTCCTACAA
1 ATACAGAAGACAAGAAACACTCCTACAA
18819 TACCTCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 2 0.09
30 13 0.57
ACGTcount: A:0.54, C:0.25, G:0.07, T:0.14
Consensus pattern (30 bp):
ATACAGAAGACAAGAAACACTCCTACAAAA
Found at i:39768 original size:31 final size:30
Alignment explanation
Indices: 39730--39789 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
39720 TTATATAAGC
39730 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
39761 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
39790 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:44344 original size:60 final size:60
Alignment explanation
Indices: 44300--44448 Score: 228
Period size: 59 Copynumber: 2.5 Consensus size: 60
44290 AACCACTGTA
* *
44300 TAACTTTTAATAGCCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCGTTATG
1 TAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCATTATG
* * *
44360 TAAC-TTTAATAGTCGAGAGAGTCAACGAAACAACTCCCTATAGTCGGGAGACCATTATG
1 TAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCATTATG
**
44419 TAACTTTTAATAGTCGAGGGGTTCAACAAA
1 TAACTTTTAATAGTCGAGGGACTCAACAAA
44449 GCAATATCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 54 0.68
60 25 0.32
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
TAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCATTATG
Found at i:45675 original size:2 final size:2
Alignment explanation
Indices: 45668--45700 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
45658 AAACTGTTAT
45668 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 T
45701 GTTCTTTCTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51288 original size:21 final size:22
Alignment explanation
Indices: 51249--51291 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
51239 TAAACACCCG
*
51249 AAATGCCACTAAAATACCATTA
1 AAATGCCACTAAAACACCATTA
*
51271 AAAT-CCACTCAAACACCATTA
1 AAATGCCACTAAAACACCATTA
51292 TTCGGGCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.21
Consensus pattern (22 bp):
AAATGCCACTAAAACACCATTA
Done.