Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000847.1 Corchorus olitorius cultivar O-4 contig00847, 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: 6369
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:457 original size:77 final size:77
Alignment explanation
Indices: 321--531 Score: 280
Period size: 77 Copynumber: 2.7 Consensus size: 77
311 ATGTGGCCAT
* * * * *
321 ATGCCGTATCATGGCAACCAAAATATCACAAGGCTACAAAGGTCTCCACTGCCATGTAATGGCAT
1 ATGCCGTATCACGGCAACCAAAATATCACATGGCTACAAAAGTCTCCACCGCCACGTAATGGCAT
386 AAGGATCTTCAC
66 AAGGATCTTCAC
* * * *
398 ATGCAGTATCACGACAACCAAAGTATCACATGGCTACAAAAGTCTCCACCGCTACGTAATGGCAT
1 ATGCCGTATCACGGCAACCAAAATATCACATGGCTACAAAAGTCTCCACCGCCACGTAATGGCAT
*
463 AAGGATCTTCAT
66 AAGGATCTTCAC
* * * *
475 ATGCCGTATCACGGCAACCAAAACATCACGTGGCTAC-AAAGCTCTCAACCACCACGT
1 ATGCCGTATCACGGCAACCAAAATATCACATGGCTACAAAAG-TCTCCACCGCCACGT
532 TGCATGACAG
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
76 4 0.03
77 111 0.97
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.20
Consensus pattern (77 bp):
ATGCCGTATCACGGCAACCAAAATATCACATGGCTACAAAAGTCTCCACCGCCACGTAATGGCAT
AAGGATCTTCAC
Found at i:2026 original size:156 final size:156
Alignment explanation
Indices: 1737--2085 Score: 628
Period size: 156 Copynumber: 2.2 Consensus size: 156
1727 GCTCCCCACA
*
1737 GTTAATTAAGTTGATGATCAAGGGCATTTTGGGAAGTTACAAAGAACCATAATAGGAAGATGTGA
1 GTTATTTAAGTTGATGATCAAGGGCATTTTGGGAAGTTACAAAGAACCATAATAGGAAGATGTGA
* *
1802 AAATACTAATTAACCAATCCAACTCTCTCTTCCCATGAATTGAAGAACAAAAGAGTCGAGTTATT
66 AAATACTAATTAACCAATCCAACTCTCACTTCCCATGAATTGAAGAACAAAAGAGTCGAGGTATT
1867 TAGGTAATTTCATGTTTGGTTATTTT
131 TAGGTAATTTCATGTTTGGTTATTTT
* * *
1893 GTTATTTAAGTTGATGATTAAGGGCATTTTGGGAAGTTATAATGAACCATAATAGGAAGATGTGA
1 GTTATTTAAGTTGATGATCAAGGGCATTTTGGGAAGTTACAAAGAACCATAATAGGAAGATGTGA
*
1958 AAATACTAATTAACCAATCCAACTCTCACTTCCCATGAATTGAAGAACAAAAGAGTCGGGGTATT
66 AAATACTAATTAACCAATCCAACTCTCACTTCCCATGAATTGAAGAACAAAAGAGTCGAGGTATT
2023 TAGGTAATTTCATGTTTGGTTATTTT
131 TAGGTAATTTCATGTTTGGTTATTTT
2049 GTTATTTAAG-TGATGATCAAGGGCATTTTGGGAAGTT
1 GTTATTTAAGTTGATGATCAAGGGCATTTTGGGAAGTT
2086 TGGCTAAAAA
Statistics
Matches: 185, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
155 26 0.14
156 159 0.86
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (156 bp):
GTTATTTAAGTTGATGATCAAGGGCATTTTGGGAAGTTACAAAGAACCATAATAGGAAGATGTGA
AAATACTAATTAACCAATCCAACTCTCACTTCCCATGAATTGAAGAACAAAAGAGTCGAGGTATT
TAGGTAATTTCATGTTTGGTTATTTT
Found at i:3082 original size:432 final size:432
Alignment explanation
Indices: 2228--3056 Score: 1070
Period size: 432 Copynumber: 1.9 Consensus size: 432
2218 ATTTTTTTTA
* * *
2228 TTTTTTTCTATTTGTCCAATTAAGATAATCCAAGTGTCTATTAAAATGTAATTTTATGATCTACA
1 TTTTTTTCTATTTGTCCAATTAAGATAATCCAAGTGTCTATTAAAAGGTAATTTCACGATCTACA
* * * * * *
2293 CCTTTTATTAAAGACTCAAAAGCCAATTTTTATGTTTCAGTTAACAAAAATGCTTTCCGAAATTT
66 ACTCTCATGAAAGACTCAAAAGCCAATTTTCATGTTTCAGTTAACAAAAATGCTTTCCAAAATTT
* * * * * *
2358 GGTGGTTTCGATTGTCTGTCTATGTAATATCATGCAATTTTCGATCTACATGCCCGATTAAAGTT
131 GGTCGTTTCGAGTGACTGTCTATGTAATACCATACAATTTTCGATCCACATGCCCGATTAAAGTT
* * ** ** *
2423 ATTCAAGTGTCGGTGAAATGGTTATTGCATTATCTATGACTTTCATGAAGGGTCCGAAAGCTCAA
196 ATTCAAGTGTCGGTAAAATGGTTATTGCATGATCTACAACTTTCATGAAGACTCCGAAAGCTAAA
* * * * * * *
2488 TTTTATCTACGAGTTTCGTGAATGGCTCAAAAGAGAATTTTTATGTTTTAGGATCTTCATCAATA
261 TTTAATCTACGAGTTTCATGAATGGCTCAAAAGAGAATATTTATGTTTCAAGATCTCCATCAACA
* * * *
2553 AACAATTTCTATTTTGGATTATTTTTTCAAATGATCCTCATTTTTTTTCTACTTTATACTACTTA
326 AACAATTTCTATTTTGGATTATTTTATCAAATGACCCTCA-TTATTTTCTACATTATACTACTTA
*
2618 GTCCTTTACTAATTTTATCTTCATCGATTTAACACTTCAGTTT
390 CTCCTTTACTAATTTTATCTTCATCGATTTAACACTTCAGTTT
* * *
2661 TTTTTTTCTATTTGTCCGAA-TAAGGTAATTCAGGTGTCTATTAAAAGGTAATTTCACGATCTAC
1 TTTTTTTCTATTTGTCC-AATTAAGATAATCCAAGTGTCTATTAAAAGGTAATTTCACGATCTAC
* *
2725 AACTCTCATGAAGGACTCAAAAGCCAATTTTCATGTTTCAGTTCTA-AAAAATGC-TTCCAAAAT
65 AACTCTCATGAAAGACTCAAAAGCCAATTTTCATGTTTCAGTT-AACAAAAATGCTTTCCAAAAT
* * * *
2788 TTGGTCGTTTCGAGTGAC-GATTTATTTAATACCATATAATTTTCGATCCACATGTCCGATTAAA
129 TTGGTCGTTTCGAGTGACTG-TCTATGTAATACCATACAATTTTCGATCCACATGCCCGATTAAA
*
2852 GTTATTCAAGTGTTGGTTAAAAT-GTTATTGCATGATCTACAACTTTCATGAAAGACT-CGAAAG
193 GTTATTCAAGTGTCGG-TAAAATGGTTATTGCATGATCTACAACTTTCATG-AAGACTCCGAAAG
* *
2915 CTAAATTTAATTTACGATTTTCATGAATGGCTCAAAAG-GAAATATTTATG-TTCAAGATCTCCA
256 CTAAATTTAATCTACGAGTTTCATGAATGGCTCAAAAGAG-AATATTTATGTTTCAAGATCTCCA
2978 TCAACAAACATAATTT-TA-TTTGGATTA-TTTATCAAATGACCCTCA-TATTTTCTACATTATA
320 TCAACAAAC--AATTTCTATTTTGGATTATTTTATCAAATGACCCTCATTATTTTCTACATTATA
*
3039 CTATTTACTCCTTTACTA
383 CTACTTACTCCTTTACTA
3057 TTGTTAATTT
Statistics
Matches: 341, Mismatches: 47, Indels: 21
0.83 0.11 0.05
Matches are distributed among these distances:
428 30 0.09
430 16 0.05
431 29 0.09
432 149 0.44
433 114 0.33
434 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.41
Consensus pattern (432 bp):
TTTTTTTCTATTTGTCCAATTAAGATAATCCAAGTGTCTATTAAAAGGTAATTTCACGATCTACA
ACTCTCATGAAAGACTCAAAAGCCAATTTTCATGTTTCAGTTAACAAAAATGCTTTCCAAAATTT
GGTCGTTTCGAGTGACTGTCTATGTAATACCATACAATTTTCGATCCACATGCCCGATTAAAGTT
ATTCAAGTGTCGGTAAAATGGTTATTGCATGATCTACAACTTTCATGAAGACTCCGAAAGCTAAA
TTTAATCTACGAGTTTCATGAATGGCTCAAAAGAGAATATTTATGTTTCAAGATCTCCATCAACA
AACAATTTCTATTTTGGATTATTTTATCAAATGACCCTCATTATTTTCTACATTATACTACTTAC
TCCTTTACTAATTTTATCTTCATCGATTTAACACTTCAGTTT
Found at i:3369 original size:29 final size:29
Alignment explanation
Indices: 3321--3564 Score: 338
Period size: 29 Copynumber: 8.5 Consensus size: 29
3311 TATTTCTTAA
* *
3321 TTGGTCA--TTTGCACACTCAGTGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
*
3348 TTGGTCATTTTTGCATATTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
3377 TTGGTCATTTTTGCACATTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
3406 TTGGTCATTTTTGCACAATT-AGGGGCATT
1 TTGGTCATTTTTGCAC-ATTCAGGGGCATT
*
3435 TTGGTCA--TTTGCACATCCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
3462 TTGGTCATTTTTTGCACACTT-AGGGGCATT
1 TTGGTCA-TTTTTGCACA-TTCAGGGGCATT
* * *
3492 TTTGTCATTTTTGCACATTCTGTGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
**
3521 TTGGTCATTTTTGCACATTTTGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
3550 TTGGTCATTTTTGCA
1 TTGGTCATTTTTGCA
3565 TACTCTAGGT
Statistics
Matches: 196, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
26 2 0.01
27 30 0.15
28 2 0.01
29 135 0.69
30 26 0.13
31 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (29 bp):
TTGGTCATTTTTGCACATTCAGGGGCATT
Found at i:3522 original size:115 final size:114
Alignment explanation
Indices: 3321--3559 Score: 374
Period size: 115 Copynumber: 2.1 Consensus size: 114
3311 TATTTCTTAA
* *
3321 TTGGTCATTTGCACACTCAGTGGCATTTTGGTCATTTTTGCATATTCAGGGGCATTTTGGTCATT
1 TTGGTCATTTGCACACTCAGGGGCATTTTGGTCATTTTTGCACATTCAGGGGCATTTTGGTCATT
3386 TTTGCACATTCAGGGGCATTTTGGTCATTTTTGCACAATTAGGGGCATT
66 TTTGCACATTCAGGGGCATTTTGGTCATTTTTGCACAATTAGGGGCATT
*
3435 TTGGTCATTTGCACA-TCCAGGGGCATTTTGGTCATTTTTTGCACACTT-AGGGGCATTTTTGTC
1 TTGGTCATTTGCACACT-CAGGGGCATTTTGGTCA-TTTTTGCACA-TTCAGGGGCATTTTGGTC
* * * *
3498 ATTTTTGCACATTCTGTGGCATTTTGGTCATTTTTGCACATTTTGGGGCATT
63 ATTTTTGCACATTCAGGGGCATTTTGGTCATTTTTGCACAATTAGGGGCATT
3550 TTGGTCATTT
1 TTGGTCATTT
3560 TTGCATACTC
Statistics
Matches: 115, Mismatches: 7, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
113 1 0.01
114 31 0.27
115 81 0.70
116 2 0.02
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.44
Consensus pattern (114 bp):
TTGGTCATTTGCACACTCAGGGGCATTTTGGTCATTTTTGCACATTCAGGGGCATTTTGGTCATT
TTTGCACATTCAGGGGCATTTTGGTCATTTTTGCACAATTAGGGGCATT
Found at i:3561 original size:10 final size:10
Alignment explanation
Indices: 3488--3562 Score: 50
Period size: 10 Copynumber: 7.8 Consensus size: 10
3478 CACTTAGGGG
3488 CATTTTT-GT
1 CATTTTTGGT
**
3497 CATTTTTGCA
1 CATTTTTGGT
*
3507 CATTCTGTGG-
1 CATT-TTTGGT
3517 CA-TTTTGGT
1 CATTTTTGGT
**
3526 CATTTTTGCA
1 CATTTTTGGT
* *
3536 CATTTTGGGG
1 CATTTTTGGT
3546 CA-TTTTGGT
1 CATTTTTGGT
3555 CATTTTTG
1 CATTTTTG
3563 CATACTCTAG
Statistics
Matches: 49, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
8 4 0.08
9 17 0.35
10 25 0.51
11 3 0.06
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (10 bp):
CATTTTTGGT
Done.