Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012385.1 Corchorus olitorius cultivar O-4 contig12418, 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: 10402
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:109 original size:18 final size:18
Alignment explanation
Indices: 86--122 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
76 ACCTCTTAAA
86 ATGGAATATGCTAAATGC
1 ATGGAATATGCTAAATGC
104 ATGGAATATGCTAAATGC
1 ATGGAATATGCTAAATGC
122 A
1 A
123 ACTTAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (18 bp):
ATGGAATATGCTAAATGC
Found at i:854 original size:30 final size:30
Alignment explanation
Indices: 818--1389 Score: 747
Period size: 30 Copynumber: 19.0 Consensus size: 30
808 TTAACTGATG
*
818 AAGCAATGATCCT-AAACCAGGATAAAAATA
1 AAGCAATGATCCTCAAA-CAGGATTAAAATA
*
848 AAGCAATGATCCTCAAACAGGATTAAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * *
878 GAGCAAAT-ATCCTCAACCAGGATTAAAGATG
1 AAGC-AATGATCCTCAAACAGGATTAAA-ATA
* *
909 AAGCAAAT-ATCCTCAACCAGGATTAAAATG
1 AAGC-AATGATCCTCAAACAGGATTAAAATA
* * *
939 GAGCAAAT-ATCCTCGACCAGGATTAAAATA
1 AAGC-AATGATCCTCAAACAGGATTAAAATA
* * * *
969 AAGCAACGATCCTCAACCAGGAATAAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
999 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
1029 AAGCAATGATCCTCAAACATGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * ** *
1059 AAGCAACGATCCTCAACCAGGACGAAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* **
1089 AAGCAATGGTCCTCAAACAGGATTGGAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
1119 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* **
1149 AAGCGATGATCCTCAAACAGGATTGGAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
1179 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* **
1209 AAGCGATGATCCTCAAACAGGATTGGAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
1239 AAGCAATGATCCTCAAACAAGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
**
1269 AAGCAATGATCCTCAAACAGGATTGGAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
1299 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
1329 AAGCAATGATCCTCAAATAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * *
1359 GAGCAATGATCCTCAAATAGGATTAGAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
1389 A
1 A
1390 GACTAAAAAA
Statistics
Matches: 481, Mismatches: 57, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
29 2 0.00
30 444 0.92
31 35 0.07
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (30 bp):
AAGCAATGATCCTCAAACAGGATTAAAATA
Found at i:2206 original size:169 final size:169
Alignment explanation
Indices: 1745--2523 Score: 1089
Period size: 169 Copynumber: 4.7 Consensus size: 169
1735 CAGTTGTCTT
* * *
1745 GAGGACTTATCAATGTAAACTCTGCATAGAGACCTTCACCAAGGATTTTAAACTTAAACATGAAT
1 GAGGACTTACCAATGTAAACTCTGAATAGAGACCTTAACCAAGGATTTTAAACTTAAACATGAAT
* * * *
1810 CTTTGATGAAAAAC-T--T--AATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGAGGACTT
66 TTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTT
* *
1870 ATCAGAATTAATACCCAGAGGTTTCTGAAGTTGTGCCCG
131 ATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCG
* * * * * * *
1909 GAGGACTTATCAGTTGCAAACTTTAAATTGAGACCTTAAACAAGGA---T---CTTAAACATGAA
1 GAGGACTTACCA-ATGTAAACTCTGAATAGAGACCTTAACCAAGGATTTTAAACTTAAACATGAA
* * *
1968 -TTTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGATT
65 TTTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACT
*
2032 TATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCG
130 TATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCG
*
2072 GAGGACTTACCAATGTAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAAACATGAAT
1 GAGGACTTACCAATGTAAACTCTGAATAGAGACCTTAACCAAGGATTTTAAACTTAAACATGAAT
* * *
2137 TTTTAATGACAAACTTGATGAAATGAAATGATACCTGGAGGTTTTATCAATTGCCCGGAGGACTT
66 TTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTT
* *
2202 ATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCA
131 ATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCG
*
2241 GAGGACTTACCAATGTAAACTCTGAATAGAGACCTTAAACAAGGATTTTAAACTTAAACATGAAT
1 GAGGACTTACCAATGTAAACTCTGAATAGAGACCTTAACCAAGGATTTTAAACTTAAACATGAAT
* * *
2306 TTTTAATGACAAGCTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTT
66 TTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTT
* **
2371 ATCAGAATTAATACCCTGAGGTTTCTGAATTCATGCCCG
131 ATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCG
*** * *
2410 GAGGACTTACCAACACAAACTCTGAATAGAGACCTTGACCAAGGAATTT-AACTTAAACATGAAT
1 GAGGACTTACCAATGTAAACTCTGAATAGAGACCTTAACCAAGGATTTTAAACTTAAACATGAAT
* * *
2474 TTTTGGTGAAAAACTTGATAAAATGAAATGACACCCGGAGGTTTTATCAA
66 TTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAA
2524 ATGGAAATAA
Statistics
Matches: 550, Mismatches: 52, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
158 13 0.02
159 13 0.02
161 1 0.00
162 27 0.05
163 87 0.16
164 12 0.02
165 26 0.05
168 71 0.13
169 300 0.55
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (169 bp):
GAGGACTTACCAATGTAAACTCTGAATAGAGACCTTAACCAAGGATTTTAAACTTAAACATGAAT
TTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTT
ATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCG
Found at i:2702 original size:69 final size:70
Alignment explanation
Indices: 2565--2744 Score: 335
Period size: 69 Copynumber: 2.6 Consensus size: 70
2555 AAGTAAGGCT
* *
2565 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCCATGTGGCTTGGATGGAACCAAGGCT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCTATGTGGCTTGGATGGAACCAAAGCT
2630 TAAAC
66 TAAAC
2635 TGACTCGTATGGAAACGAGTTTGGCTTGTGG-AAAAGCCTATGTGGCTTGGATGGAACCAAAGCT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCTATGTGGCTTGGATGGAACCAAAGCT
2699 TAAAC
66 TAAAC
2704 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCTA
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCTA
2745 ATCATTCGGA
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
69 67 0.63
70 40 0.37
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (70 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCTATGTGGCTTGGATGGAACCAAAGCT
TAAAC
Found at i:4400 original size:8 final size:8
Alignment explanation
Indices: 4368--4411 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
4358 TTTATTTTGA
4368 TTTTGATT
1 TTTTGATT
*
4376 TTTTTATT
1 TTTTGATT
4384 ATTTT-ATT
1 -TTTTGATT
4392 TTTTGATT
1 TTTTGATT
4400 TTTTGATT
1 TTTTGATT
4408 TTTT
1 TTTT
4412 TTTGAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 4 0.12
8 25 0.76
9 4 0.12
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.80
Consensus pattern (8 bp):
TTTTGATT
Found at i:4420 original size:12 final size:11
Alignment explanation
Indices: 4355--4426 Score: 55
Period size: 12 Copynumber: 6.5 Consensus size: 11
4345 ATCCATTCCC
4355 TTTTTT-ATTT
1 TTTTTTGATTT
*
4365 TGATTTTGATTT
1 T-TTTTTGATTT
4377 TTTTATT-ATTTT
1 TTTT-TTGA-TTT
4389 ATTTTTTGA---
1 -TTTTTTGATTT
4398 TTTTTTGATTT
1 TTTTTTGATTT
4409 TTTTTTGAATTT
1 TTTTTTG-ATTT
4421 TTTTTT
1 TTTTTT
4427 TTTGAAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
8 8 0.16
10 1 0.02
11 14 0.28
12 22 0.44
13 5 0.10
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTGATTT
Found at i:4428 original size:19 final size:18
Alignment explanation
Indices: 4385--4429 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
4375 TTTTTTATTA
*
4385 TTTTATTTTTTGATTTTT
1 TTTTTTTTTTTGATTTTT
*
4403 TGATTTTTTTTTGAATTTTT
1 T-TTTTTTTTTTG-ATTTTT
4423 TTTTTTT
1 TTTTTTT
4430 GAAATTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.05
19 14 0.64
20 7 0.32
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTTTGATTTTT
Found at i:4842 original size:10 final size:8
Alignment explanation
Indices: 4813--4848 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
4803 TTTATTTCCA
4813 TTTTCATT
1 TTTTCATT
4821 TTTTCATT
1 TTTTCATT
4829 TTTTCATGT
1 TTTTCAT-T
4838 ATTTTCATT
1 -TTTTCATT
4847 TT
1 TT
4849 GTGGGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 17 0.65
9 2 0.08
10 7 0.27
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.72
Consensus pattern (8 bp):
TTTTCATT
Found at i:4842 original size:18 final size:16
Alignment explanation
Indices: 4813--4848 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
4803 TTTATTTCCA
4813 TTTTCATTTTTTCATT
1 TTTTCATTTTTTCATT
4829 TTTTCATGTATTTTCATT
1 TTTTCAT-T-TTTTCATT
4847 TT
1 TT
4849 GTGGGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTCATTTTTTCATT
Done.