Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022674.1 Corchorus olitorius cultivar O-4 contig22707, 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: 10854
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:144 original size:40 final size:39
Alignment explanation
Indices: 90--400 Score: 291
Period size: 40 Copynumber: 7.7 Consensus size: 39
80 GACAAAGGCA
*
90 ACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTG
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGCAATAC-G
* * ** * *
130 ACAACTCCTTCCGATGAGGAAGGGCAAGCTGAACAA-AGGCA
1 ACAACACCTCCCGATGAGGAAGGGCAAATTG-GCAATA--CG
* * *
171 ACAACACCTCCCGATAAGGAAAGGCAAATTGGTAATACTG
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGCAATAC-G
* * ** *
211 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACCAAGGCA
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGG--CAATACG
* *
252 ACACCACCTCCCGATGAGGAAGGGCAAATTGGTAATACTG
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGCAATAC-G
* * ** *
292 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACCAAGGCA
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGG--CAATACG
* *
333 ACAACACCTCCCGGTGAGGAAGGGCAAATTGGCGATACCG
1 ACAACACCTCCCGATGAGGAAGGGCAAATTGGCAATA-CG
*
373 ACAACACCTTCCGATGAGGAAGGGCAAA
1 ACAACACCTCCCGATGAGGAAGGGCAAA
401 ACATGAAGTA
Statistics
Matches: 213, Mismatches: 47, Indels: 22
0.76 0.17 0.08
Matches are distributed among these distances:
39 6 0.03
40 114 0.54
41 86 0.40
42 7 0.03
ACGTcount: A:0.36, C:0.25, G:0.26, T:0.13
Consensus pattern (39 bp):
ACAACACCTCCCGATGAGGAAGGGCAAATTGGCAATACG
Found at i:177 original size:81 final size:81
Alignment explanation
Indices: 78--400 Score: 522
Period size: 81 Copynumber: 4.0 Consensus size: 81
68 TTGGGTAAAT
*
78 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTGACAACTCCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTGACAACACCTTCCG
*
143 ATGAGGAAGGGCAAGC
66 ATGAGGAAGGGCAAAC
* * * *
159 TGAACAAAGGCAACAACACCTCCCGATAAGGAAAGGCAAATTGGTAATACTGACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTGACAACACCTTCCG
224 ATGAGGAAGGGCAAAC
66 ATGAGGAAGGGCAAAC
* * *
240 TGGACCAAGGCAACACCACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTGACAACACCTTCCG
305 ATGAGGAAGGGCAAAC
66 ATGAGGAAGGGCAAAC
* * *
321 TGGACCAAGGCAACAACACCTCCCGGTGAGGAAGGGCAAATTGGCG-ATACCGACAACACCTTCC
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGG-GAATACTGACAACACCTTCC
385 GATGAGGAAGGGCAAA
65 GATGAGGAAGGGCAAA
401 ACATGAAGTA
Statistics
Matches: 226, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
81 226 1.00
ACGTcount: A:0.36, C:0.25, G:0.26, T:0.13
Consensus pattern (81 bp):
TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTGACAACACCTTCCG
ATGAGGAAGGGCAAAC
Found at i:532 original size:50 final size:50
Alignment explanation
Indices: 417--654 Score: 328
Period size: 50 Copynumber: 4.8 Consensus size: 50
407 AGTAAACAAA
*
417 TGGGACCTTCCGACCAGGAAGGGGCATTTTT--GAAATA-A-A-AGAAAAC
1 TGGGACCTTCCGACCAGGAAGGGGCATTTTTGGGAAA-AGATATTGAAAAC
* * *
463 GGGGACCTTCCAACCAGGAAGGGGCATTTTTGGGATAAGATATTGAAAAC
1 TGGGACCTTCCGACCAGGAAGGGGCATTTTTGGGAAAAGATATTGAAAAC
*
513 TGGGACATTCCGACCAGGAAGGGGCATTTTT-GGAAAGAGATATTGAAAAC
1 TGGGACCTTCCGACCAGGAAGGGGCATTTTTGGGAAA-AGATATTGAAAAC
*
563 TGGGACCTTCCGACCATGAAGGGGCATTTTT-GGAAAGAGATATTGAAAAC
1 TGGGACCTTCCGACCAGGAAGGGGCATTTTTGGGAAA-AGATATTGAAAAC
* *
613 TGGGACATTCCGACCAGGAAGGGGCATTTTTGGAAAAAGATA
1 TGGGACCTTCCGACCAGGAAGGGGCATTTTTGGGAAAAGATA
655 AGAAAACAAT
Statistics
Matches: 172, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
46 29 0.17
47 1 0.01
48 4 0.02
49 5 0.03
50 129 0.75
51 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (50 bp):
TGGGACCTTCCGACCAGGAAGGGGCATTTTTGGGAAAAGATATTGAAAAC
Found at i:594 original size:100 final size:99
Alignment explanation
Indices: 417--661 Score: 372
Period size: 100 Copynumber: 2.5 Consensus size: 99
407 AGTAAACAAA
* *
417 TGGGACCTTCCGACCAGGAAGGGGCATTTTT-GAAATA-A-AAGAAAACGGGGACCTTCCAACCA
1 TGGGACATTCCGACCAGGAAGGGGCATTTTTGGAAAAAGATAAGAAAACGGGGACCTTCCAACCA
*
479 GGAAGGGGCATTTTTGGGATA-AGATATTGAAAAC
66 GGAAGGGGCATTTTT-GGAAAGAGATATTGAAAAC
* * * *
513 TGGGACATTCCGACCAGGAAGGGGCATTTTTGGAAAGAGATATTGAAAACTGGGACCTTCCGACC
1 TGGGACATTCCGACCAGGAAGGGGCATTTTTGGAAAAAGATA-AGAAAACGGGGACCTTCCAACC
*
578 ATGAAGGGGCATTTTTGGAAAGAGATATTGAAAAC
65 AGGAAGGGGCATTTTTGGAAAGAGATATTGAAAAC
613 TGGGACATTCCGACCAGGAAGGGGCATTTTTGGAAAAAGATAAGAAAAC
1 TGGGACATTCCGACCAGGAAGGGGCATTTTTGGAAAAAGATAAGAAAAC
662 AATTCTTTTG
Statistics
Matches: 135, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
96 30 0.22
97 5 0.04
98 1 0.01
99 11 0.08
100 88 0.65
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.21
Consensus pattern (99 bp):
TGGGACATTCCGACCAGGAAGGGGCATTTTTGGAAAAAGATAAGAAAACGGGGACCTTCCAACCA
GGAAGGGGCATTTTTGGAAAGAGATATTGAAAAC
Found at i:1371 original size:20 final size:20
Alignment explanation
Indices: 1346--1391 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1336 CACATTATTC
1346 AAAGATTTC-ATCTTTTACTT
1 AAAGATTTCAATC-TTTACTT
1366 AAAGA-TTCAATCTTTACTT
1 AAAGATTTCAATCTTTACTT
*
1385 ACAGATT
1 AAAGATT
1392 ACCTAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
AAAGATTTCAATCTTTACTT
Found at i:1410 original size:51 final size:50
Alignment explanation
Indices: 1346--1476 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 50
1336 CACATTATTC
* *
1346 AAAGATTTCATCTTTTACTTA-AAGATTCAATCTTTACTTACAGATTACCTA
1 AAAGACTTCATCTTTTACTTACAA-ATTCAATCTTTACTTACAAATTA-CTA
* * *
1397 AAAGA-TTCAATCTTTTACTTACAAATTTAATCTTTATTTACAAATTACTT
1 AAAGACTTC-ATCTTTTACTTACAAATTCAATCTTTACTTACAAATTACTA
*
1447 AAAGACTTCATC-TTTATTTACAAA-TCAATC
1 AAAGACTTCATCTTTTACTTACAAATTCAATC
1477 AAAAATCTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
48 5 0.07
49 11 0.15
50 13 0.18
51 40 0.56
52 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (50 bp):
AAAGACTTCATCTTTTACTTACAAATTCAATCTTTACTTACAAATTACTA
Found at i:1437 original size:19 final size:20
Alignment explanation
Indices: 1405--1442 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1395 TAAAAGATTC
1405 AATCTTTTACTTACAAATTT
1 AATCTTTTACTTACAAATTT
*
1425 AATC-TTTATTTACAAATT
1 AATCTTTTACTTACAAATT
1443 ACTTAAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
AATCTTTTACTTACAAATTT
Found at i:1490 original size:30 final size:30
Alignment explanation
Indices: 1419--1491 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1409 TTTTACTTAC
* * * *
1419 AAATTTAATCTTTATTTACAAATTACTTAA
1 AAATCTAATCTTTATTTACAAATCAATCAA
* *
1449 AGA-CTTCATCTTTATTTACAAATCAATCAA
1 AAATC-TAATCTTTATTTACAAATCAATCAA
1479 AAATCTAATCTTT
1 AAATCTAATCTTT
1492 TAGTCCAAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.01, T:0.42
Consensus pattern (30 bp):
AAATCTAATCTTTATTTACAAATCAATCAA
Done.