Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014979.1 Corchorus olitorius cultivar O-4 contig15012, 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: 15729
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Found at i:397 original size:123 final size:127
Alignment explanation
Indices: 155--409 Score: 392
Period size: 131 Copynumber: 2.0 Consensus size: 127
145 ATTTAAGAAA
*
155 TATATTTAAAAAATTCTAATGTATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---A
* *
220 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
285 G
127 G
* *
286 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
*
349 TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
409 T
1 T
410 TTAAGTAATG
Statistics
Matches: 118, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 55 0.47
124 2 0.02
125 2 0.02
127 1 0.01
131 58 0.49
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:435 original size:123 final size:127
Alignment explanation
Indices: 161--417 Score: 335
Period size: 123 Copynumber: 2.0 Consensus size: 127
151 GAAATATATT
* *
161 TAAAAAATTCTAATG-TATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAATAGGT
1 TAAAAAATTCTAA-GAAATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---ACA-GT
*
225 ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATA
61 ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATA
**
290 TT
126 AG
* * * *
292 TAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-TA-AA-
1 TAAAAAATTCTAAGAAATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAGTATAAG
* *
353 GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAG
66 GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAG
415 TAA
1 TAA
418 TGGCATTTAA
Statistics
Matches: 116, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
123 60 0.52
124 2 0.02
125 2 0.02
127 1 0.01
131 51 0.44
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (127 bp):
TAAAAAATTCTAAGAAATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAGTATAAG
GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAG
Found at i:719 original size:56 final size:56
Alignment explanation
Indices: 633--741 Score: 200
Period size: 56 Copynumber: 1.9 Consensus size: 56
623 AGATTCCAAT
*
633 TTTGAAATATATTCATTAACTTAAAGTGAAAAATCTCAATCCAAGACTATATACTA
1 TTTGAAACATATTCATTAACTTAAAGTGAAAAATCTCAATCCAAGACTATATACTA
*
689 TTTGAAACATATTCATTAACTTAAAGTGAAAAATCTTAATCCAAGACTATATA
1 TTTGAAACATATTCATTAACTTAAAGTGAAAAATCTCAATCCAAGACTATATA
742 ATACAATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (56 bp):
TTTGAAACATATTCATTAACTTAAAGTGAAAAATCTCAATCCAAGACTATATACTA
Found at i:8578 original size:83 final size:84
Alignment explanation
Indices: 8474--8641 Score: 329
Period size: 83 Copynumber: 2.0 Consensus size: 84
8464 CTAACATCGT
8474 TTTTCCATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
1 TTTTCCATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
8539 CAAATCCTTAAATCCAATG
66 CAAATCCTTAAATCCAATG
8558 TTTTCCA-TTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
1 TTTTCCATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
8622 CAAATCCTTAAATCCAATG
66 CAAATCCTTAAATCCAATG
8641 T
1 T
8642 GGCTGATATT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 77 0.92
84 7 0.08
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (84 bp):
TTTTCCATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
CAAATCCTTAAATCCAATG
Found at i:14227 original size:43 final size:42
Alignment explanation
Indices: 14180--14509 Score: 461
Period size: 41 Copynumber: 7.8 Consensus size: 42
14170 ATAAGGAGAA
* *
14180 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-AATAGAG
14223 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGA-ATAGAG
* *
14264 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-AATAGAG
* *
14307 GTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
* * *
14348 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-AATAGAG
* *
14391 GTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGAATACAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
* *
14432 GTGCCTCTGTGTTATATATGTGTTTGGGGACTTTTGGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTT-GAATAGAG
14476 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
14510 TGGTTATTGG
Statistics
Matches: 258, Mismatches: 20, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
41 109 0.42
42 7 0.03
43 106 0.41
44 36 0.14
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (42 bp):
ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
Found at i:14292 original size:84 final size:84
Alignment explanation
Indices: 14178--14509 Score: 560
Period size: 84 Copynumber: 3.9 Consensus size: 84
14168 CCATAAGGAG
14178 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
14243 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
*
14262 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
14327 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * *
14346 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
14411 TGTTTGGGGAC-TTGA-AT
66 TGTTTGGGGACTTTGATAT
* * *
14428 ACAGGTGCCTCTGTGTTATATATGTGTTTGGGGACTTTTGGAATAGAGATGCCCCTGTGTTATAT
1 A-A-ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGATGCCCCTGTGTTATAT
14493 ATGTGTTTGGGGACTTT
63 ATGTGTTTGGGGACTTT
14510 TGGTTATTGG
Statistics
Matches: 235, Mismatches: 9, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
82 3 0.01
83 4 0.02
84 186 0.79
85 40 0.17
86 2 0.01
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:15414 original size:338 final size:324
Alignment explanation
Indices: 14695--15453 Score: 904
Period size: 338 Copynumber: 2.3 Consensus size: 324
14685 GGCCCCTAAC
*
14695 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
1 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGATATTTCAAGGAG
* * **
14760 TCTTTCTACCAAAAATCATGCAAAACTGAGTCGGGGCCACGAAACACGTTTTTAGCCCAAAAACC
66 TCTTTC-GCCAAAAATCATGCAAAACTGAGCCGGGGCCACGAAACACGTTTTTAGCAAAAAAACC
* * * * *
14825 ATGATGGTTAGTACATGATTTCGGCTAAAAACTTATCCGAAAAATTTTTCTTCTGAATTTTTGCC
130 ATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAATTTTTC-TCTCAATTTTTACC
* ** * *
14890 ACAATACTCAAAAACAAAATATATAATTCAACGCCAAAAGATTGGCGGGCTTTTCACGTTTCTAA
194 ACAATACTCAAAAACAAAATATATAATTCAACGCCAAAAAATTGAAGAGCTTTTCACGTTTCAAA
*
14955 TATCGTTTTTTCCATTTTTTCCCGAATTAATTTCTAACTAAATCGAAAAAAGATTCAGATGCTCA
259 TATCGTTTTTTCCATTTTTTCCCGAATTAATTTCTAACTAAATCGAAAAAAGATTAAGATGCTCA
15020 T
324 T
* *
15021 AAAAACAAATCTTTATATCCAATGTGGCTGAGATTTGGTT-CGATGAATATAGATATTTCAAGGA
1 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAC-ATGAATATAGATATTTCAAGGA
* * * * *
15085 GACTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGTTC-CGGAACGCGTTTTTAGCAAAAAAA
65 GTCTTT-CGCCAAAAATCATGCAAAACTGAGCCGGGG-CCACGAAACACGTTTTTAGCAAAAAAA
* * *
15149 CCGTGATGGTTAGTACACGCTTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTC-CT
128 CCATGATGGTTAGTACACGATTTCGGC--------T--AAAAACTGACCCGAAAAATTTTTCTCT
15213 CAATTTTTTACCACAATACTCAATAAA-AATATATATATAATTCAACGCCAAAAAAATTGAAGAG
183 CAA-TTTTTACCACAATACTCAA-AAACAA-A-ATATATAATTCAACGCC-AAAAAATTGAAGAG
* ** * * *
15277 TTTTTCACGCTTT-AAATATCG-TTTTTCCATTTTTTTTTCGAATTTATTTTTAATTAAATC-AA
243 CTTTTCACG-TTTCAAATATCGTTTTTTCCA-TTTTTTCCCGAATTAATTTCTAACTAAATCGAA
*
15339 AACAAGATTAAGATGCTCGT
306 AA-AAGATTAAGATGCTCAT
* * *
15359 AAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAAAATAGATATTTTAAGGAG
1 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGATATTTCAAGGAG
*
15424 TCTGTAT-GCCAAAAACCATGCAAAACTGAG
66 TCT-T-TCGCCAAAAATCATGCAAAACTGAG
15454 TCGATATCCC
Statistics
Matches: 368, Mismatches: 41, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
326 135 0.37
327 2 0.01
334 5 0.01
335 20 0.05
336 25 0.07
337 29 0.08
338 146 0.40
339 5 0.01
340 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (324 bp):
AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGATATTTCAAGGAG
TCTTTCGCCAAAAATCATGCAAAACTGAGCCGGGGCCACGAAACACGTTTTTAGCAAAAAAACCA
TGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAATTTTTCTCTCAATTTTTACCAC
AATACTCAAAAACAAAATATATAATTCAACGCCAAAAAATTGAAGAGCTTTTCACGTTTCAAATA
TCGTTTTTTCCATTTTTTCCCGAATTAATTTCTAACTAAATCGAAAAAAGATTAAGATGCTCAT
Done.