Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019076.1 Corchorus olitorius cultivar O-4 contig19109, 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: 22611
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:6909 original size:332 final size:331
Alignment explanation
Indices: 5818--9284 Score: 3195
Period size: 332 Copynumber: 10.6 Consensus size: 331
5808 TCCTCATTTT
* * * * *
5818 TTTTTGGCAAAAATACTCAT-AAATATATATAATTCAACGCCAAAAGGATTGGAGGACTTTTCAT
1 TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
*
5882 GCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
66 GCTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * * * * *
5947 TGCACATAAAAACAAATCCTTGAATCCAATGTGCCTGAGATTTGATTAGATGAATAAATATATTT
131 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
* * * * * * * *
6012 GAAGGAGTCTCGGT-GCCAAAAATCATGCAAAACAGAGCTGTGGTCTTGGAACGCGTTTTTACCC
196 CAAGGAGTCTC-GTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGCC
* * * *
6076 AAAAACCGTGATGGTTAGTACACGATTTCAGCCAAAATTTTCCAAAAAATTGACCCGAAAGA-TA
260 AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAA-TGACCCGAAAAATTA
6140 TTTCCTCAA
324 -TTCCTCAA
* * * * ** ** *
6149 TTTTTGGATAAAATACTCATAAAAAATATATAATTCGACATCAAAAAGATT-AAAAAGCTTTTAA
1 TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGA-CTTTTCA
* * *
6213 CGCTTCTAATATTGTTTTTCCA-ATTTTTTATGAATTAATTTCTAATTAAATCGAAATAAGATTC
65 CGCTTTTAATATCGTTTTT-CATA-TTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * * ** * *
6277 AAATGCTCGAAAAAACAAATCCTTAAATCTAATGTTTCTGAGATTTGGTTAGATGAATATAGATT
128 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
* * * * * * *
6342 TTTCAAGGA-T-T-GCA-CGAAAAATCATGCAATACTGAGTCGGGTCTC-GGAACGCGTTTTTAG
193 TTTCAAGGAGTCTCGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAG
* * * * * *
6402 CCGAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGGAAAAATTGATCCGAAAGATT
258 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATT
* ** **
6467 TTTTGTTGA
323 ATTCCTCAA
* * * * * * *
6476 TTTCTAACGAAAATACTCATATAAA-ACATATAATTCAATGCCAAAAAAATTGAAAGACTTTTTC
1 TTTTTAGCTAAAATACTCATA-AAATATATATAATTCAACGCCAAAAAGATTGAAGGAC-TTTTC
* * * * *
6540 CCGCTTTTAATATCG-TTTTCATATTTTTTTTGAATTAATTTCTTATTAAATCGAAACAAAATTT
64 ACGCTTTTAATATCGTTTTTCATA-TTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTC
* *
6604 AGATGCTCGTAAAAACAAATCCTTCAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
128 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
** * *
6669 TTTCAAGGAGTCTCCGTAGCCAAAAATCATGCAAAACAAAGTC-GGACCCTGAAACGCGTTTTTA
193 TTTCAAGGAGTCT-CGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTA
*
6733 GCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAAT
257 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAAT
6798 TATTCCATCAA
322 TATTCC-TCAA
* * * *
6809 TTTTTGGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAATATTGGAGGACTTTTCAA
1 TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
* **
6874 GCTTTTGATATTATTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
66 GCTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * ** * * *
6939 TGCTCGTAAAAACAAATTCTTAAATCCAATTTAACTGAGATTTGATTAAATGAATATGGATATCT
131 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
* * * * *
7004 CAAAGAGTCTTGGT-GCCAAAAATCATGCAAAACTTAGCCGGGGCCCTAAAACGCGTTTTTAGTC
196 CAAGGAGTC-TCGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGCC
* * * * * *
7068 AAAAACCGTGATGATTATTACACGATTTCGATCGGCTAGAATTTTGCAAAAATTGACTCG-AAAG
260 AAAAACCGTGATGGTTAGTACACGA-TT---TCGGCTAAAATTTTGCAAAAAATGACCCGAAAAA
*
7132 TTATTTTCTCAA
321 TTA-TTCCTCAA
* * *
7144 TTTTTAGCCACAAA-ACTCATAAAA-ATTATATAATTCAACGCCAAAAAGTTTGAAGGTCTTTTC
1 TTTTTAGCTA-AAATACTCATAAAATA-TATATAATTCAACGCCAAAAAGATTGAAGGACTTTTC
* * * * *
7207 ATGCTTCTAATATCGTTTTTCCTATTATTTTCTGAATTAATTTCTAATTAAATCGAAACATGATT
64 ACGCTTTTAATATCGTTTTTCATA-T-TTTTATGAATTAATTTCTAATTAAATCGAAACAAGATT
* *** * * * *
7272 CAGATGCTTGT-TTTACAAATCCTTAAATCCAATTTGGCTGAAATTTGGTTAGATGAATGTAGAT
127 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
* ** * * * * * ** * *
7336 ATCT-AAGGAGTCTCGGCGCAAAAAATCATGCAACATTGAACCTGGGCCAAGGAACGAGTTTTTA
192 ATTTCAAGGAGTCTCGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTA
* * * * * *
7400 GCCAAAAACCGTGATTTCGACTAACGTACACGATATCAGCTAATATTTTGC-AAAAATAGACCAG
257 GCCAAAAACCGTGA--T-G-GTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAAAT-GACCCG
* * *
7464 AAATATTTTTTCTCAA
316 AAAAATTATTCCTCAA
* * * * * * * *
7480 CTTTTATCTGAAATACTTATAAAATATATATAATTCAACTCAAAAAAGATTGGAGAACTTTTCAC
1 TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
* * * * *
7545 GCTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAACCGAAACAATATTCATA
66 GCTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * * * * *
7610 TGCACGTAAAAACAAATCCTTAAATGCAATATGGATGATACTTGATTAGATGAATATAGATATTT
131 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
* * * *
7675 CAAGGAGTCTC-AACGCCAAAAATCATGCAAAACTGAACCGGGGCCCCGAAACACGTTTTTAGCA
196 CAAGGAGTCTCGTA-GCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGC-
* * * * *
7739 AAGAAAACCGTGATGGTTAGTACACTATTTCAGCTAAAAATTTGC-AAAAATGACCAGAAAAAAT
259 CA-AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCG-AAAAAT
7803 T-TTCCTCAA
322 TATTCCTCAA
* * * * *
7812 TTTTTAGCCACAATA-TCATAAAAAAATATATAATTCAACGCTAAAAAGATTGAAGGGCTTTTCA
1 TTTTTAGCTAAAATACTCAT-AAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
* * * *
7876 CGCTTCTAATATCGTTTTTCCTATTTTT-TCGGAATTAATTTCTAATTAAAACGAAACATGATTC
65 CGCTTTTAATATCGTTTTTCATATTTTTAT--GAATTAATTTCTAATTAAATCGAAACAAGATTC
** * * *
7940 AGATG-T--T---------T-C-TAAAAACAA--TGGCTGGGATTTGGTTAGATGAATACAGATA
128 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
* * ** * * * * *
7989 TTCCAAGGAGTCGCGGCGCCAAAAATCATTCAAAATTGAACC-GGGCCCTGGAACACGTTTTTAG
193 TTTCAAGGAGTCTCGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAG
* * * * * ** * *
8053 CCAAAAAACCCTAATGATTATTACACGATTTCGGTTAAAATTTTTTAAAAATTGACCCGAAAGA-
258 CC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAAT
8117 TATATCCTCAA
322 TAT-TCCTCAA
* * * * * *
8128 TTTTTAGCCATAATACTTATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCAC
1 TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
* **
8193 GCTTTTAATAACGTTTTTCATATTTTTTTTAAAAAATTAATTTCTAATTAAATCGAAACAAGATT
66 GCTTTTAATATCGTTTTTCATA---TTTTT-ATGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * * *
8258 TAGATGCTCGTAAAAAGAAATCCTTAAATGCAATGTGGCTAAGATTTTATCAGATGAATATAGAT
127 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
* * *
8323 ATTTCAAGGAGAGC-CG-ACGCCAAAAACCATGCAAAACTGAGCCGGGGCCCTGAAACACG-TTT
192 ATTTCAAGGAG-TCTCGTA-GCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTT
* *
8385 TAGCCAAAAAAACCGTGATGGGTTAGTACACGATTTTGGCTAAAATTTTGCACAAAAA-AACCCG
255 TAGCC--AAAAACCGTGAT-GGTTAGTACACGATTTCGGCTAAAATTTTGCA-AAAAATGACCCG
8449 -AAAA-TATTTCGCT-AA
316 AAAAATTA-TTC-CTCAA
* ** * * *
8464 TTTTTTA-TTAAAATACTCATAAAATATATATAATTTGACGCCAAGAAGATTGGAGGGCTTTTCA
1 -TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
* *
8528 TGCTTTTAATATCGTTTTTCATA-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
65 CGCTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
* * *
8592 ATGCTTGTACAAACAAAT-CTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATAT-GCATAT
130 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG-ATAT
* * ** ** ** *
8655 CTCAAGGAGTCTTGGCGTAAAAAATCATGCAAAACTGAGCCGGGG-CCAAAAACGCTTTTTTAGC
194 TTCAAGGAGTCTCGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGC
* * * * * * ** *
8719 CAAAAACTGTGATAGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTAACTTGAACGATAT
259 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAA--AAAT
8784 T-TT-CTCAA
322 TATTCCTCAA
* * *
8792 TTTTTGGCTAAAATACTCATAAAAACATATATAATTCAACACCAAAAAGATTGAAGG--------
1 TTTTTAGCTAAAATACTCAT-AAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
* * *
8849 -GC--TT--T-T-G--------A-TGTT-T-AATTAATTTCTAATTTAATCGAAACAAGATTCAA
65 CGCTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
* * *
8896 ATGCTCGTAAAAACATATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATTAATATAGATATT
130 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT
* * * * * * *
8961 TCAAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAGTCGGGTCCC-CAGAACGCATTTTTAGC
195 TCAAGGAGTCTCGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGA-AACGCGTTTTTAGC
* * *
9025 CAAAAACCGTCATGGTTTGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACAC-AAAA
259 CAAAAACCGTGAT-G---GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAA
9089 GATT-TATCCTCAA
320 -ATTAT-TCCTCAA
** ** * *
9102 TTTTTAATTAAAATACAGATAAAA-ATATATAATTCAACGCCAAAAAGATTTGAGGGA-TTTTTA
1 TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGA-TTGAAGGACTTTTCA
* * * *
9165 CTCTTTTAATATCGTATTTCTTATTTTTACTAAATTAATTTCTAATTAAATCGAAACAAGATTCA
65 CGCTTTTAATATCGTTTTTCATATTTTTA-TGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * * *
9230 GATGCTCGTAAAAGCAAATTCTTAAATCCAATGTTGCTGAGATTTGGTTAGATGA
129 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
9285 TGTAAAGTAT
Statistics
Matches: 2562, Mismatches: 439, Indels: 266
0.78 0.13 0.08
Matches are distributed among these distances:
304 47 0.02
305 78 0.03
306 31 0.01
307 1 0.00
308 27 0.01
309 13 0.01
310 57 0.02
314 2 0.00
315 38 0.01
316 116 0.05
317 64 0.02
318 2 0.00
319 48 0.02
320 4 0.00
321 2 0.00
322 2 0.00
323 1 0.00
326 6 0.00
327 197 0.08
328 109 0.04
329 64 0.02
330 86 0.03
331 104 0.04
332 404 0.16
333 233 0.09
334 48 0.02
335 335 0.13
336 325 0.13
337 93 0.04
338 15 0.01
339 3 0.00
340 7 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (331 bp):
TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
GCTTTTAATATCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
CAAGGAGTCTCGTAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGCCA
AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTATT
CCTCAA
Found at i:9957 original size:13 final size:13
Alignment explanation
Indices: 9909--9944 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
9899 TTTTATATAG
*
9909 TAGTAAGATAAGA
1 TAGTAAGATAAAA
*
9922 TAGTAAAATAAAA
1 TAGTAAGATAAAA
9935 TAGTAAGATA
1 TAGTAAGATA
9945 GTAAGATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (13 bp):
TAGTAAGATAAAA
Found at i:22327 original size:3 final size:3
Alignment explanation
Indices: 22319--22359 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
22309 TCTCTGATGC
22319 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
22360 AGAATTTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22449 original size:3 final size:3
Alignment explanation
Indices: 22441--22481 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
22431 TCTCTGATGC
22441 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
22482 AGAATTTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22456 original size:122 final size:122
Alignment explanation
Indices: 22239--22566 Score: 611
Period size: 122 Copynumber: 2.7 Consensus size: 122
22229 TTTCTTATTT
22239 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
1 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
22304 ATCGATCTCTGATGCAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAA
66 ATCGATCTCTGATGCAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAA
*
22361 GAATTTACTAAAAAAACTACAAGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
1 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
22426 ATCGATCTCTGATGCAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAA
66 ATCGATCTCTGATGCAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAA
* * *
22483 GAATTTACTAAAAAACCTACAGGGCTATTAAGAACAAAGTTAAATATTAATCAATTAAGAAGGTT
1 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
*
22548 ATCGATCTCTGATGAAAGA
66 ATCGATCTCTGATGCAAGA
22567 TGATTATCAA
Statistics
Matches: 200, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 200 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (122 bp):
GAATTTACTAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
ATCGATCTCTGATGCAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAA
Done.