Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019173.1 Corchorus olitorius cultivar O-4 contig19206, 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: 11681
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:8710 original size:35 final size:35
Alignment explanation
Indices: 8546--8949 Score: 431
Period size: 35 Copynumber: 11.3 Consensus size: 35
8536 TTCTGAAGAG
*
8546 TTATTTCAGTTGATCCAGGGCGATCTGTAT-TTCAGT
1 TTATTTCAGTTGATCCAGGGCGATCT-T-TCTTCAAT
* * *
8582 TTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAAT
1 TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAAT
* * * * **
8617 TCATTTTAATGGATCCAGGGCGATCTTTTCTTCAGC
1 TTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAAT
* * *
8653 TTACTTGACCCAGTTGCTCCAGGGTGATCTTTCTTCAGA-
1 TTA-TT---TCAGTTGATCCAGGGCGATCTTTCTTCA-AT
* * *
8692 ATATTTCAGTTGACCCAGGGCCG-TCTCTCTTCAAT
1 TTATTTCAGTTGATCCAGGG-CGATCTTTCTTCAAT
* * * *
8727 TTATTCCAGTTGACCCAGGGTGGTCTTTCTTCAAT
1 TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAAT
* *
8762 TTACTTCAGTTGATCCAGGGCGATCTTTTCTACAAT
1 TTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAAT
*
8798 CTATTT-AGTTGATCCAGGGCGATCTTTTCTTCAAT
1 TTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAAT
8833 TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAAT
1 TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAAT
8868 TTATTTCAGTTGATCCAGGGC-AGTCTTTCTTCAAT
1 TTATTTCAGTTGATCCAGGGCGA-TCTTTCTTCAAT
* *
8903 TTATTTCAGTTGATCCAGGGCGATCTTTTCTGCAGT
1 TTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAAT
8939 TTATTTCAGTT
1 TTATTTCAGTT
8950 TACCGCAAAT
Statistics
Matches: 310, Mismatches: 43, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
34 4 0.01
35 194 0.63
36 84 0.27
37 2 0.01
38 2 0.01
39 10 0.03
40 14 0.05
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (35 bp):
TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAAT
Found at i:8754 original size:70 final size:70
Alignment explanation
Indices: 8546--8949 Score: 406
Period size: 71 Copynumber: 5.7 Consensus size: 70
8536 TTCTGAAGAG
* * * *
8546 TTATTTCAGTTGATCCAGGGCGATCTGTAT-TTCAGTTTATTTCAGTTGACCCAGGGCGGTCCTT
1 TTATTTCAGTTGATCCAGGGCGATCT-T-TCTTCAATTTATTCCAGTTGACCCAGGGCGATCTTT
8610 CTTCAAT
64 CTTCAAT
* * * * ** *
8617 TCATTTTAATGGATCCAGGGCGATCTTTTCTTCAGCTTACTTGACCCAGTTG-CTCCAGGGTGAT
1 TTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAATTTA-TT---CCAGTTGAC-CCAGGGCGAT
8681 CTTTCTTCAGA-
60 CTTTCTTCA-AT
* * * * *
8692 ATATTTCAGTTGACCCAGGGCCG-TCTCTCTTCAATTTATTCCAGTTGACCCAGGGTGGTCTTTC
1 TTATTTCAGTTGATCCAGGG-CGATCTTTCTTCAATTTATTCCAGTTGACCCAGGGCGATCTTTC
8756 TTCAAT
65 TTCAAT
* * * * *
8762 TTACTTCAGTTGATCCAGGGCGATCTTTTCTACAATCTATT-TAGTTGATCCAGGGCGATCTTTT
1 TTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAATTTATTCCAGTTGACCCAGGGCGATC-TTT
8826 CTTCAAT
64 CTTCAAT
* *
8833 TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTATTTCAGTTGATCCAGGGC-AGTCTTTC
1 TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTATTCCAGTTGACCCAGGGCGA-TCTTTC
8897 TTCAAT
65 TTCAAT
* * *
8903 TTATTTCAGTTGATCCAGGGCGATCTTTTCTGCAGTTTATTTCAGTT
1 TTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAATTTATTCCAGTT
8950 TACCGCAAAT
Statistics
Matches: 281, Mismatches: 35, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
69 3 0.01
70 109 0.39
71 112 0.40
72 3 0.01
73 2 0.01
74 11 0.04
75 38 0.14
76 3 0.01
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (70 bp):
TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTATTCCAGTTGACCCAGGGCGATCTTTCT
TCAAT
Found at i:8851 original size:106 final size:105
Alignment explanation
Indices: 8550--8949 Score: 432
Period size: 106 Copynumber: 3.7 Consensus size: 105
8540 GAAGAGTTAT
* * *
8550 TTCAGTTGATCCAGGGCGATCTGTAT-TTCAGTTTATTTCAGTTGACCCAGGGCGGTCCTTCTTC
1 TTCAGTTGATCCAGGGCGATCT-T-TCTTCAATTTATTTCAGTTGACCCAGGGCGATCTTTCTTC
* * * * **
8614 AATTCATTTTAATGGATCCAGGGCGATCTTTTCTTCAGCTTAC
64 AATTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAATTTAC
* * * *
8657 TTGACCCAGTTGCTCCAGGGTGATCTTTCTTCAGA-ATATTTCAGTTGACCCAGGGCCG-TCTCT
1 TT----CAGTTGATCCAGGGCGATCTTTCTTCA-ATTTATTTCAGTTGACCCAGGG-CGATCTTT
* * * *
8720 CTTCAATTTATTCCAGTTGACCCAGGGTGGTCTTTCTTCAATTTAC
60 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTAC
* * *
8766 TTCAGTTGATCCAGGGCGATCTTTTCTACAATCTATTT-AGTTGATCCAGGGCGATCTTTTCTTC
1 TTCAGTTGATCCAGGGCGATC-TTTCTTCAATTTATTTCAGTTGACCCAGGGCGATC-TTTCTTC
*
8830 AATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTAT
64 AATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTAC
* *
8872 TTCAGTTGATCCAGGGC-AGTCTTTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTGC
1 TTCAGTTGATCCAGGGCGA-TCTTTCTTCAATTTATTTCAGTTGACCCAGGGCGATC-TTTCTTC
*
8936 AGTTTATTTCAGTT
64 AATTTATTTCAGTT
8950 TACCGCAAAT
Statistics
Matches: 249, Mismatches: 31, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
104 2 0.01
105 47 0.19
106 112 0.45
107 2 0.01
109 15 0.06
110 51 0.20
111 20 0.08
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (105 bp):
TTCAGTTGATCCAGGGCGATCTTTCTTCAATTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAA
TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTAC
Found at i:8878 original size:141 final size:142
Alignment explanation
Indices: 8546--8933 Score: 482
Period size: 141 Copynumber: 2.7 Consensus size: 142
8536 TTCTGAAGAG
* *
8546 TTATTTCAGTTGATCCAGGGCGATCTGTAT-TTCAGTTTATTTCAGTTGACCCAGGGCGGTCCTT
1 TTATTTCAGTTGATCCAGGGCGATCT-T-TCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTT
* * * * * *
8610 CTTCAATTCATTTTAATGGATCCAGGGCGATCTTTTCTTCAGCTTACTTGACCCAGTTGCTCCAG
64 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTACAGCTTACTT---CCAGTTGATCCAG
*
8675 GGTGATCTTTCTTCAGA
126 GGCGATCTTTCTTCAGA
* * * * *
8692 ATATTTCAGTTGACCCAGGGCCG-TCTCTCTTCAATTTATTCCAGTTGACCCAGGGTGGTCTTTC
1 TTATTTCAGTTGATCCAGGG-CGATCTTTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTTC
* * *
8756 TTCAATTTACTTCAGTTGATCCAGGGCGATCTTTTCTACA-ATCTA-TT-TAGTTGATCCAGGGC
65 TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTACAGCT-TACTTCCAGTTGATCCAGGGC
8818 GATCTTTTCTTCA-A
129 GATC-TTTCTTCAGA
* *
8832 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTATTTCAGTTGATCCAGGGCAGTCTTTC
1 -TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTTC
8897 TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCT
65 TTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCT
8934 GCAGTTTATT
Statistics
Matches: 211, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
140 19 0.09
141 98 0.46
144 4 0.02
145 67 0.32
146 21 0.10
147 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (142 bp):
TTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTATTTCAGTTGACCCAGGGCGGTCTTTCT
TCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTACAGCTTACTTCCAGTTGATCCAGGGCGA
TCTTTCTTCAGA
Found at i:9532 original size:169 final size:169
Alignment explanation
Indices: 9253--9613 Score: 623
Period size: 169 Copynumber: 2.1 Consensus size: 169
9243 AACTTATTTC
* * * *
9253 CAATTGATAAAACCTCCGGGTACCATTTGATTTCATTAAGTTTTTCATCAAAAGTTCATGTTTAA
1 CAATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAA
* * *
9318 GTTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTTCGGACACAAATT
66 GTTAAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGACACAAATT
* *
9383 CAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGG
131 CAGAAACCTCCGGGTATTAATTCCGATAAGTCCTCAGGG
9422 CAATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAA
1 CAATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAA
*
9487 GTTAAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATT
66 GTTAAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGACACAAATT
9552 CAGAAACCTCCGGGTATTAATTCCGATAAGTCCTCAGGG
131 CAGAAACCTCCGGGTATTAATTCCGATAAGTCCTCAGGG
*
9591 CAATTAATAAAACCTCCGGGTAT
1 CAATTGATAAAACCTCCGGGTAT
9614 TAATTCTGAT
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
169 181 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (169 bp):
CAATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAA
GTTAAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGACACAAATT
CAGAAACCTCCGGGTATTAATTCCGATAAGTCCTCAGGG
Found at i:9573 original size:22 final size:22
Alignment explanation
Indices: 9548--9619 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
9538 TCCGGGCACA
9548 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
* * *
9570 AATTCCGATAAGTCCTCAGGGCAATT
1 AATTCAGA-AA--CCTCCGGG-TATT
9596 AA-T-A-AAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
9615 AATTC
1 AATTC
9620 TGATAAGTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 13
0.67 0.11 0.23
Matches are distributed among these distances:
19 5 0.13
20 8 0.21
22 9 0.24
23 3 0.08
25 8 0.21
26 5 0.13
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (22 bp):
AATTCAGAAACCTCCGGGTATT
Found at i:9929 original size:30 final size:30
Alignment explanation
Indices: 9890--10577 Score: 643
Period size: 30 Copynumber: 23.6 Consensus size: 30
9880 TTACTTTGGA
9890 CCTGGTTGAGGATCATTGCTTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* *
9920 CCTGTTTGAGGATCGTTGCTTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
*
9950 CCTGGTTAAGGATCATTGCTTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* *
9980 CCTGGTTGAGGAT-ATTTGCATCATTTTAAT
1 CCTGGTTGAGGATCA-TTGCTTTATTTTAAT
* *
10010 CCTGTTTGAGGATCTTTGCTTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* * *
10040 CCTGCTTGAGGATCTTTGCTCTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* * *
10070 CTTGTTTGAGGATCATCGCTTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* * *
10100 CTTGTTTGAGGATCATTGCTTTACTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* ** *
10130 CCTGTTTGAGGATTTTTGCTTTGTTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
*
10160 CCTGATTGAGGATC---G--TTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* * *
10185 CTTGTTTGAGGATCATTGCCTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
** ** *
10215 CCTTTTTGAGGATCGCTACTTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* *
10245 CCTGGTTGAGGATCGTTACTTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
*
10275 CCTGGTTGA-GA--A-T-CGTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* * *
10300 CTTGGTTGAGGAT-ATTTGCATCATTTTAAT
1 CCTGGTTGAGGATCA-TTGCTTTATTTTAAT
*
10330 CCTGGTTGA-GA--A-T-CGTTATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* *
10355 CCTGGTTGAGGAT-ATTTGCATCATTTTAAT
1 CCTGGTTGAGGATCA-TTGCTTTATTTTAAT
* * ** *
10385 CCTGGTTGAGGATCGTTACTCCATTTTCAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
* *
10415 CCTGGTTGAGGAT-ATTTGCATCATTTTAAT
1 CCTGGTTGAGGATCA-TTGCTTTATTTTAAT
* * * **
10445 CCTGGTTGAGAATCGTTACTCCATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
** * **
10475 CCTGGTTGAGGATTGTTACTCCATTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
*
10505 CCTGGTTGAGGATCA-TGCTTTATTTCAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
*
10534 CCTGGTTTAGGATCATTG-----TTTTAAT
1 CCTGGTTGAGGATCATTGCTTTATTTTAAT
*
10559 CCTGGTTTAGGATCATTGC
1 CCTGGTTGAGGATCATTGC
10578 CTCATCAGAT
Statistics
Matches: 561, Mismatches: 75, Indels: 48
0.82 0.11 0.07
Matches are distributed among these distances:
25 83 0.15
26 6 0.01
27 3 0.01
28 2 0.00
29 31 0.06
30 436 0.78
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (30 bp):
CCTGGTTGAGGATCATTGCTTTATTTTAAT
Found at i:10565 original size:25 final size:25
Alignment explanation
Indices: 10498--10576 Score: 104
Period size: 25 Copynumber: 3.0 Consensus size: 25
10488 TGTTACTCCA
* *
10498 TTTTAATCCTGGTTGAGGATCATGCTT
1 TTTTAATCCTGGTTTAGGATCAT--TG
10525 TATTTCAATCCTGGTTTAGGATCATTG
1 T-TTT-AATCCTGGTTTAGGATCATTG
10552 TTTTAATCCTGGTTTAGGATCATTG
1 TTTTAATCCTGGTTTAGGATCATTG
10577 CCTCATCAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
25 21 0.44
26 3 0.06
27 3 0.06
28 3 0.06
29 18 0.38
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (25 bp):
TTTTAATCCTGGTTTAGGATCATTG
Found at i:11172 original size:26 final size:27
Alignment explanation
Indices: 11083--11179 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
11073 GGTCATCTAT
* * *
11083 GGGCATTTTAGTCATTTGCACGTTTAG
1 GGGCATTTTGGTCATTTGCACATTCAG
* *
11110 GGGCATTTCGGTCATTTGCACATTCTG
1 GGGCATTTTGGTCATTTGCACATTCAG
*
11137 GGGCATTTTGGTCATTTGTAC-TTCAG
1 GGGCATTTTGGTCATTTGCACATTCAG
*
11163 GGGGATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
11180 TTCTTTCTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 20 0.33
27 41 0.67
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.41
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTGCACATTCAG
Done.