Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007167.1 Hibiscus syriacus cultivar Beakdansim tig00018792_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: 51623
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1143 original size:19 final size:19
Alignment explanation
Indices: 1102--1143 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1092 AAAATATTAA
*
1102 TTTTTTAGATGTTTAGAGGT
1 TTTTTTAGA-GTTTAGAGAT
1122 TTTTTTAGA-TTTACGAGAT
1 TTTTTTAGAGTTTA-GAGAT
1141 TTT
1 TTT
1144 GAGAGTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.57
Consensus pattern (19 bp):
TTTTTTAGAGTTTAGAGAT
Found at i:15604 original size:17 final size:17
Alignment explanation
Indices: 15570--15605 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15560 CCTGAAAAAG
* *
15570 AAAATGAAAAAGACTAA
1 AAAATGAAAAAAAATAA
15587 AAAATGAAAAAAAATAA
1 AAAATGAAAAAAAATAA
15604 AA
1 AA
15606 GAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAATGAAAAAAAATAA
Found at i:16965 original size:110 final size:110
Alignment explanation
Indices: 16769--17316 Score: 749
Period size: 110 Copynumber: 5.0 Consensus size: 110
16759 TTCAATCCCA
16769 ATTCAATGGATCAACTCCCCAGATATGATATTCCCTTAGAAGAAGTGGAACATATCCATATCTTT
1 ATTCAATGGATCAACTCCCCAGATATGATATTCCCTTAGAAGAAGTGGAACATATCCATATCTTT
* * *
16834 TAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTTTGCCCCG
66 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCG
* *
16879 ATTCAATGGATCAACTCCCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCCATATATTT
1 ATTCAATGGATCAACTCCCCAGATATGATATTCCCTTAGAAGAAGTGGAACATATCCATATCTTT
* *
16944 CAAGATTTGATATTCCATGAGTGACAGCGGAACAAGTCTGTCCCG
66 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCG
* * * * * *
16989 ATTCAATGGATCAACTTCCCATATCTGATATTCCCTTAGAAGAAATGGAACAAATCCATAGCTTT
1 ATTCAATGGATCAACTCCCCAGATATGATATTCCCTTAGAAGAAGTGGAACATATCCATATCTTT
* *
17054 CAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGACCCG
66 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCG
* * *
17099 ATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTAAAAGAAGTGGAACATAACCATCTCTT
1 ATTCAATGGATCAACT-CCCCAGATATGATATTCCCTTAGAAGAAGTGGAACATATCCATATCTT
* * * *
17164 TCAAGATTTGGTATTCCCTGAGTGACATCGGAATAAGTCTTCCCCG
65 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCG
* * * * * * * *
17210 ATTCAATGGATCAACTCCCCCAGATTTGATATTCCCTTTTA-AATAAGCT-AAATAGACCCCTCT
1 ATTCAATGGATCAACT-CCCCAGATATGATATTCCC--TTAGAAGAAG-TGGAACATATCCATAT
* *
17273 CTTTCAAGATTTGATATTCCCTGAGTGATAGCGGAATAAGTCTG
62 CTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTG
17317 AATCAATTCA
Statistics
Matches: 392, Mismatches: 42, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
110 220 0.56
111 114 0.29
112 54 0.14
113 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (110 bp):
ATTCAATGGATCAACTCCCCAGATATGATATTCCCTTAGAAGAAGTGGAACATATCCATATCTTT
CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCG
Found at i:18817 original size:25 final size:24
Alignment explanation
Indices: 18767--18821 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
18757 GTGAATGTAC
* * *
18767 ATATATATTATATTATTTAAGTTT
1 ATATATATTATAGTATGTAAGATT
*
18791 ATATATATATATAGTATGTAGGATT
1 ATATATAT-TATAGTATGTAAGATT
18816 ATATAT
1 ATATAT
18822 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (24 bp):
ATATATATTATAGTATGTAAGATT
Found at i:18928 original size:2 final size:2
Alignment explanation
Indices: 18921--18952 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18911 TTAAATACGA
18921 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
18953 TACGTATATT
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:21235 original size:20 final size:20
Alignment explanation
Indices: 21210--21247 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21200 TTTGCAGAGA
21210 AAAACA-TCTCCAACGGCTCC
1 AAAACACTC-CCAACGGCTCC
21230 AAAACACTCCCAACGGCT
1 AAAACACTCCCAACGGCT
21248 AGAAACGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.37, C:0.39, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAACACTCCCAACGGCTCC
Found at i:21670 original size:31 final size:31
Alignment explanation
Indices: 21635--21763 Score: 134
Period size: 31 Copynumber: 4.2 Consensus size: 31
21625 GATAAAAATA
*
21635 TGTCTAATGTTTTCTTCGTTTTACTTTTAGG
1 TGTCTAATGTTTTCTCCGTTTTACTTTTAGG
21666 TGTCTAATGTTTTCTCCGTTTTACTTTTAGG
1 TGTCTAATGTTTTCTCCGTTTTACTTTTAGG
* * ** **
21697 TGTCTAACGTTTTATCCACTACACTTTTAGG
1 TGTCTAATGTTTTCTCCGTTTTACTTTTAGG
* * ** *
21728 TGTTTAACT-TTTTCTCTGTTACACTTTTATG
1 TGTCTAA-TGTTTTCTCCGTTTTACTTTTAGG
21759 TGTCT
1 TGTCT
21764 GGTCTGTTAC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.16, C:0.17, G:0.14, T:0.53
Consensus pattern (31 bp):
TGTCTAATGTTTTCTCCGTTTTACTTTTAGG
Found at i:21913 original size:26 final size:28
Alignment explanation
Indices: 21877--21933 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
21867 GGCCCTAATT
21877 TTTTCTAAAATAT-A-AAAAATCATAAA
1 TTTTCTAAAATATCATAAAAATCATAAA
* *
21903 TTTTCTAAAATATCATAAAATTCTTAAA
1 TTTTCTAAAATATCATAAAAATCATAAA
21931 TTT
1 TTT
21934 CATAAACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
27 1 0.04
28 13 0.48
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTTCTAAAATATCATAAAAATCATAAA
Found at i:21926 original size:18 final size:19
Alignment explanation
Indices: 21889--21939 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
21879 TTCTAAAATA
* *
21889 TAAAAAATCATAAATTTTC
1 TAAAATATCATAAATATTC
21908 TAAAATATCATAAA-ATTC
1 TAAAATATCATAAATATTC
* *
21926 TTAAATTTCATAAA
1 TAAAATATCATAAA
21940 CCCAAAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAATATCATAAATATTC
Found at i:24487 original size:20 final size:20
Alignment explanation
Indices: 24462--24502 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
24452 AGCTTTCCTA
24462 TAGCAAGAAATTATTCTATG
1 TAGCAAGAAATTATTCTATG
24482 TAGCAAGAAATTATTCTATG
1 TAGCAAGAAATTATTCTATG
24502 T
1 T
24503 CTAGGATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
TAGCAAGAAATTATTCTATG
Found at i:25489 original size:20 final size:20
Alignment explanation
Indices: 25464--25511 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
25454 TGTGTTAGAC
25464 TTGCAAGATAAAACTCGCCT
1 TTGCAAGATAAAACTCGCCT
25484 TTGCAAGATAAAACTCGCCT
1 TTGCAAGATAAAACTCGCCT
*
25504 TGGCAAGA
1 TTGCAAGA
25512 AAATTTGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
TTGCAAGATAAAACTCGCCT
Found at i:33393 original size:15 final size:15
Alignment explanation
Indices: 33373--33401 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33363 TTAATAGTGA
33373 GGTGGTGGTGGTATT
1 GGTGGTGGTGGTATT
33388 GGTGGTGGTGGTAT
1 GGTGGTGGTGGTAT
33402 GCTAGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.55, T:0.38
Consensus pattern (15 bp):
GGTGGTGGTGGTATT
Found at i:38212 original size:64 final size:63
Alignment explanation
Indices: 38097--38249 Score: 202
Period size: 64 Copynumber: 2.4 Consensus size: 63
38087 GTGCACTAAA
* *
38097 AGTGCATCGACGTATAAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGT
* * *
38160 CTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CTTGATTGCATCGATGCATGG
1 -AGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGG
38223 T
63 T
* *
38224 AGTGCATTGATGCATGAAATGCATTC
1 AGTGCATCGATGCATAAAATGCATTC
38250 AATATGGTGA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 23 0.29
64 47 0.59
65 7 0.09
66 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGT
Found at i:40527 original size:16 final size:18
Alignment explanation
Indices: 40496--40530 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
40486 TACAATTAAA
40496 TCAAAACATCAATAATTT
1 TCAAAACATCAATAATTT
40514 TCAAAA-AT-AATAATTT
1 TCAAAACATCAATAATTT
40530 T
1 T
40531 TTATTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TCAAAACATCAATAATTT
Found at i:45808 original size:84 final size:85
Alignment explanation
Indices: 45663--45831 Score: 304
Period size: 84 Copynumber: 2.0 Consensus size: 85
45653 ATACTAATTA
*
45663 TTGAGTTAATCGATCGATGAATATGGCCAAGAGGGGGGGTGAATTGGCAATTAAAAATTTCGGTG
1 TTGAGTTAATCGATCGATGAATATGGCCAAGA-GGGGGGTGAATTAGCAATTAAAAATTTCGGTG
45728 GAAGCTTTTGCAGAAAATTGG
65 GAAGCTTTTGCAGAAAATTGG
*
45749 TTGAGTTAATCGATCGATGAATATGGCCAAGA-GGGGGTGAATTAGCAATTAAAATTTTCGGTGG
1 TTGAGTTAATCGATCGATGAATATGGCCAAGAGGGGGGTGAATTAGCAATTAAAAATTTCGGTGG
45813 AAGCTTTTGCAGAAAATTG
66 AAGCTTTTGCAGAAAATTG
45832 TGCAGTTATT
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
84 49 0.60
86 32 0.40
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (85 bp):
TTGAGTTAATCGATCGATGAATATGGCCAAGAGGGGGGTGAATTAGCAATTAAAAATTTCGGTGG
AAGCTTTTGCAGAAAATTGG
Found at i:49503 original size:21 final size:21
Alignment explanation
Indices: 49479--49520 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49469 TATGAGAAAT
*
49479 TGTTTTAAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
49500 TGTTTCAAAATTGAAAAATGA
1 TGTTTCAAAATTGAAAAATGA
49521 AACAAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Done.