Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011307.1 Corchorus olitorius cultivar O-4 contig11340, 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: 38123
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3270 original size:32 final size:32
Alignment explanation
Indices: 3234--3303 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
3224 CCTTTATTCC
*
3234 TTGATTTGAAT-TATTCGTTATG-TTTCTATGCT
1 TTGATTTGAATCT-TT-ATTATGATTTCTATGCT
*
3266 TTGATTTGGATCTTTATTATGATTTCTATGCT
1 TTGATTTGAATCTTTATTATGATTTCTATGCT
*
3298 ATGATT
1 TTGATT
3304 GTTATGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 5 0.15
32 27 0.82
33 1 0.03
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.56
Consensus pattern (32 bp):
TTGATTTGAATCTTTATTATGATTTCTATGCT
Found at i:4691 original size:32 final size:32
Alignment explanation
Indices: 4668--4806 Score: 197
Period size: 32 Copynumber: 4.3 Consensus size: 32
4658 ACTACTTTAA
4668 GGCGTTTTCTTCAGTAGACGCCACTAAATAGG
1 GGCGTTTTCTTCAGTAGACGCCACTAAATAGG
* * *
4700 GGCGTTTTGTTCAGTAGACGCCGCTAGATAGG
1 GGCGTTTTCTTCAGTAGACGCCACTAAATAGG
*
4732 GGCGTTTTCTTCAGTAGACGCTACTAAATAGG
1 GGCGTTTTCTTCAGTAGACGCCACTAAATAGG
* * * * *
4764 GACGTTTTCTTCAATAGACGTCGCTAAATCGG
1 GGCGTTTTCTTCAGTAGACGCCACTAAATAGG
4796 GGCGTTTTCTT
1 GGCGTTTTCTT
4807 TTCATAGACG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 93 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (32 bp):
GGCGTTTTCTTCAGTAGACGCCACTAAATAGG
Found at i:4825 original size:32 final size:31
Alignment explanation
Indices: 4668--4829 Score: 182
Period size: 32 Copynumber: 5.0 Consensus size: 31
4658 ACTACTTTAA
4668 GGCGTTTTCTTCAGTAGACGCCACTAAATAGG
1 GGCGTTTTCTTCAGTAGACGCC-CTAAATAGG
* *
4700 GGCGTTTTGTTCAGTAGACGCCGCTAGATAGG
1 GGCGTTTTCTTCAGTAGACGCC-CTAAATAGG
*
4732 GGCGTTTTCTTCAGTAGACGCTACTAAATAGG
1 GGCGTTTTCTTCAGTAGACGC-CCTAAATAGG
* * * *
4764 GACGTTTTCTTCAATAGACGTCGCTAAATCGG
1 GGCGTTTTCTTCAGTAGACG-CCCTAAATAGG
*
4796 GGCGTTTTCTTTTCA-TAGACGCCCCAAATCAGG
1 GGCGTTTTC--TTCAGTAGACGCCCTAAAT-AGG
4829 G
1 G
4830 CTTTTATTTA
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
32 97 0.87
33 10 0.09
34 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (31 bp):
GGCGTTTTCTTCAGTAGACGCCCTAAATAGG
Found at i:5187 original size:12 final size:12
Alignment explanation
Indices: 5170--5202 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5160 AAAGTTACCA
5170 CCATCGCCAGCT
1 CCATCGCCAGCT
5182 CCATCGCCAGCT
1 CCATCGCCAGCT
5194 CCATCGCCA
1 CCATCGCCA
5203 CCGCAACTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.52, G:0.15, T:0.15
Consensus pattern (12 bp):
CCATCGCCAGCT
Found at i:7779 original size:13 final size:13
Alignment explanation
Indices: 7761--7790 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
7751 TTGGTTTGCA
*
7761 AAAAGTGCTTTTT
1 AAAAGTGCTTTTG
7774 AAAAGTGCTTTTG
1 AAAAGTGCTTTTG
7787 AAAA
1 AAAA
7791 TAGCTGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (13 bp):
AAAAGTGCTTTTG
Found at i:15024 original size:14 final size:13
Alignment explanation
Indices: 14982--15078 Score: 52
Period size: 14 Copynumber: 6.9 Consensus size: 13
14972 GAAATTAAAA
14982 TTAGAAAATAATAT
1 TTAG-AAATAATAT
* *
14996 TTATAAATTATAT
1 TTAGAAATAATAT
15009 TTAGAAAGTAATAT
1 TTAGAAA-TAATAT
*
15023 TT-GCAAATTATAAAT
1 TTAG-AAA-TA-ATAT
* * *
15038 GTCATGAAATTACAT
1 -TTA-GAAATAATAT
*
15053 TTAGAAAATAGTAT
1 TTAG-AAATAATAT
15067 TTAGAAATAATA
1 TTAGAAATAATA
15079 AATGTAATCA
Statistics
Matches: 62, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
13 23 0.37
14 27 0.44
15 6 0.10
16 2 0.03
17 3 0.05
18 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.38
Consensus pattern (13 bp):
TTAGAAATAATAT
Found at i:15030 original size:27 final size:27
Alignment explanation
Indices: 14973--15035 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
14963 ATATGTAATG
* *
14973 AAATTAAAATTAGAAAATAATATTTAT
1 AAATTATAATTAGAAAATAATATTTAC
* * *
15000 AAATTATATTTAGAAAGTAATATTTGC
1 AAATTATAATTAGAAAATAATATTTAC
15027 AAATTATAA
1 AAATTATAA
15036 ATGTCATGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (27 bp):
AAATTATAATTAGAAAATAATATTTAC
Found at i:15138 original size:46 final size:45
Alignment explanation
Indices: 15000--15157 Score: 205
Period size: 44 Copynumber: 3.5 Consensus size: 45
14990 TAATATTTAT
* * * * *
15000 AAATTATATTTAGAAAGTAATATT-T-GCAAATTATAAATGTCATG
1 AAATTACATTTAGAAAATAGTATTATAG-AAATAATAAATGTAATG
*
15044 AAATTACATTTAGAAAATAGTATT-TAGAAATAATAAATGTAATC
1 AAATTACATTTAGAAAATAGTATTATAGAAATAATAAATGTAATG
15088 AAATTACATTTAGAAAATAGTATATATAGAAATAATAAATGTAATG
1 AAATTACATTTAGAAAATAGTAT-TATAGAAATAATAAATGTAATG
* *
15134 AAATTACATTTACAAAATAATATT
1 AAATTACATTTAGAAAATAGTATT
15158 TATAAATTAT
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
44 59 0.58
45 3 0.03
46 40 0.39
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.35
Consensus pattern (45 bp):
AAATTACATTTAGAAAATAGTATTATAGAAATAATAAATGTAATG
Found at i:15158 original size:14 final size:14
Alignment explanation
Indices: 15141--15190 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
15131 ATGAAATTAC
15141 ATTTACAAAATAAT
1 ATTTACAAAATAAT
* *
15155 ATTTA-TAAATTAT
1 ATTTACAAAATAAT
*
15168 ATTTAGAAAATAAT
1 ATTTACAAAATAAT
*
15182 ATTTGCAAA
1 ATTTACAAA
15191 TTATAAATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (14 bp):
ATTTACAAAATAAT
Found at i:15169 original size:13 final size:14
Alignment explanation
Indices: 15134--15195 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 14
15124 AAATGTAATG
*
15134 AAATTACATTTACA
1 AAATTATATTTACA
* *
15148 AAATAATATTTA-T
1 AAATTATATTTACA
*
15161 AAATTATATTTAGA
1 AAATTATATTTACA
* *
15175 AAATAATATTTGC-
1 AAATTATATTTACA
15188 AAATTATA
1 AAATTATA
15196 AATGTAAACA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
13 18 0.47
14 20 0.53
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (14 bp):
AAATTATATTTACA
Found at i:15191 original size:27 final size:27
Alignment explanation
Indices: 15134--15195 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
15124 AAATGTAATG
* *
15134 AAATTACATTTACAAAATAATATTTAT
1 AAATTATATTTACAAAATAATATTTAC
* *
15161 AAATTATATTTAGAAAATAATATTTGC
1 AAATTATATTTACAAAATAATATTTAC
15188 AAATTATA
1 AAATTATA
15196 AATGTAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (27 bp):
AAATTATATTTACAAAATAATATTTAC
Found at i:15212 original size:37 final size:37
Alignment explanation
Indices: 15168--15239 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
15158 TATAAATTAT
*
15168 ATTTAGAAAATAATATTT-GCAAATTATAAATGTAAAC
1 ATTTAGAAAATAATATTTAG-AAATAATAAATGTAAAC
*
15205 ATTTAGAAAATAGTATTTAGAAATAATAAATGTAA
1 ATTTAGAAAATAATATTTAGAAATAATAAATGTAA
15240 TGAAATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 31 0.97
38 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (37 bp):
ATTTAGAAAATAATATTTAGAAATAATAAATGTAAAC
Found at i:15340 original size:32 final size:32
Alignment explanation
Indices: 15288--15407 Score: 134
Period size: 32 Copynumber: 3.8 Consensus size: 32
15278 ATAGCAACGT
* * *
15288 TTTCTTCATTAAACACCGCTATTTAGGGGCGC
1 TTTCTTCAGTAGACGCCGCTATTTAGGGGCGC
* * *
15320 TTTATTCAGTAAACGTCGCTATTTAGGGGCGC
1 TTTCTTCAGTAGACGCCGCTATTTAGGGGCGC
** *
15352 TTTCTTC-GCTAGACGCCGCTAAATAGGGGCGT
1 TTTCTTCAG-TAGACGCCGCTATTTAGGGGCGC
*
15384 TTTCTTCAATAGACGCCGCTATTT
1 TTTCTTCAGTAGACGCCGCTATTT
15408 TGCAGCAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
31 1 0.01
32 72 0.99
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (32 bp):
TTTCTTCAGTAGACGCCGCTATTTAGGGGCGC
Found at i:20370 original size:18 final size:20
Alignment explanation
Indices: 20347--20385 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
20337 TTAAATATGT
20347 AATTTAAAT-T-TAAAATAA
1 AATTTAAATATGTAAAATAA
20365 AATTTAAATATGTAAAATAA
1 AATTTAAATATGTAAAATAA
20385 A
1 A
20386 TGTTTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 1 0.05
20 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AATTTAAATATGTAAAATAA
Found at i:28803 original size:30 final size:30
Alignment explanation
Indices: 28769--28827 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28759 AAGTTCGTGT
28769 TTGAAGACCATTTGAAG-ATAATTTGAAGAC
1 TTGAAGA-CATTTGAAGAATAATTTGAAGAC
** *
28799 TTGAAGATTTTTGAAGAATTATTTGAAGA
1 TTGAAGACATTTGAAGAATAATTTGAAGA
28828 GCAAGAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (30 bp):
TTGAAGACATTTGAAGAATAATTTGAAGAC
Found at i:28804 original size:19 final size:18
Alignment explanation
Indices: 28780--28815 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28770 TGAAGACCAT
28780 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
28799 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
28816 ATTATTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:30204 original size:15 final size:15
Alignment explanation
Indices: 30173--30214 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
30163 TTACTTTGCT
*
30173 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-TTTTAA
30189 TTGTTTTCTTTTTAA
1 TTGTTTTCTTTTTAA
30204 TTGTTCTTCTT
1 TTGTT-TTCTT
30215 AACTCTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.69
Consensus pattern (15 bp):
TTGTTTTCTTTTTAA
Found at i:31530 original size:29 final size:30
Alignment explanation
Indices: 31483--31542 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
31473 GAAGTTCGTG
* *
31483 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
31514 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
31543 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:33124 original size:40 final size:41
Alignment explanation
Indices: 33048--33124 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
33038 GTTTCTGCGT
* * *
33048 TTTTTATCTAAAAAAAAAAGTTGGTTTTGTTTTTTTTTACG
1 TTTTTATCTAAAAAAAAAAGTTGATTTTGCTGTTTTTTACG
*
33089 TTTTT-TCTAAAAAAAAATATTTGATTTT-CTGTTTTT
1 TTTTTATCTAAAAAAAAA-AGTTGATTTTGCTGTTTTT
33125 AATTTTGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
40 18 0.58
41 13 0.42
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (41 bp):
TTTTTATCTAAAAAAAAAAGTTGATTTTGCTGTTTTTTACG
Done.