Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016489.1 Corchorus olitorius cultivar O-4 contig16522, 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: 36087
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:603 original size:320 final size:321
Alignment explanation
Indices: 5--1557 Score: 1573
Period size: 320 Copynumber: 4.9 Consensus size: 321
1 ATTG
* *
5 GAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCGGAGTATTGTGGAA
1 GAAGCGTGAAAATCCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTAGGAGTATTGTGGAA
*
70 AAAAATTGTGAAAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGATT
66 AAAAATTGTGAAAAAAAGTTTTCGGGTCAAGTTTTAGCCGAAATCGTGTACTAACCATCACGA--
* * * * * *
135 TTTGCTTTTTGGCTAAAAACGCGTTTCGGGGCCCC-GATTCAGTTTTGCATTATTTTCGGCAGAA
129 ------TTTTGGCTAAAAACGCGTTCCGGAGCCCCAG-CTCAGTTTTGCATGATTTTTGGCACAA
* ** *
199 AAACTCCTTGAAATATCTATATTTATTAAACCAAATCACAACCAAATTGGATTTAAGGATTTGTT
187 AGACTCCTTGAAATATCTATATTTATCGAACCAAATCACAACCAAATTGGATATAAGGATTTGTT
* * *
264 TTTACGAGCATTTGAATCTTGTTTCAATTTAATTAAAAATAAATTCGGAAAAAAATGAAAAACGA
252 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGAAAAACGA
329 TATTA
317 TATTA
* * * *
334 GAAGCGTGAAAAAT-TCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGT
1 GAAGCGTG-AAAATCCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTAGGAGTATTGTGGA
* * * *
398 AAAAAATTGTGGAAAGAAA-TTTTCGGGT-TAGTTTTAGCCGAAATCATGTACTACCCATCACGA
65 AAAAAATTGT-GAAAAAAAGTTTTCGGGTCAAGTTTTAGCCGAAATCGTGTACTAACCATCACGA
* * * *
461 TTTTGGCTAAAAACTCGTTCCGGAGCCCCGGCTCTA-TTTTGCATGATTTTTGGCACAAATACTA
129 TTTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTC-AGTTTTGCATGATTTTTGGCACAAAGACTC
* * * * * *
525 CTCGAAATATCTATATTTATCGAATCAAATCTCTACCACATTAGATATAAGGATTTGTTTTTACG
193 CTTGAAATATCTATATTTATCGAACCAAATCACAACCAAATTGGATATAAGGATTTGTTTTTACG
* * * *
590 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAAAACAATACTG
258 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATG-AAAAACGATATTA
* * * *
655 GAAGCGTGAAAATCCCATCAATATTTTT----TTGAATTATATATTTTTTCGGGGTATTGTGGAA
1 GAAGCGTGAAAATCCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTAGGAGTATTGTGGAA
* * * * *
716 AAAAATTCTGAAAAAAAGTTTTCGGGTCAATTTTTAGCCGTAATCGTGTACTAACCATCATAGTT
66 AAAAATTGTGAAAAAAAGTTTTCGGGTCAAGTTTTAGCCGAAATCGTGTACTAACCATCA-CGAT
* * * * * *
781 TTTGGCTAAAAACGCATTTCGGGGCCCCAGCTCAGTTTCGCATGATTTTTGGTAGAAAGACTCCT
130 TTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAGTTTTGCATGATTTTTGGCACAAAGACTCCT
* * * *
846 TGAAATAACTAT-TTTCATCTAACCAAATCACAGCCAAATTGGATTTAAGGATTTG-TTTTACGA
195 TGAAATATCTATATTT-ATCGAACCAAATCACAACCAAATTGGATATAAGGATTTGTTTTTACGA
* * *
909 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGGAAAAAATGGAAAACGATATTA
259 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAAATGAAAAACGATATTA
* * * ** *
973 GAAGCGTGAAAAACCCTTTAA-TTTTTTGGAATTGAATTATATATTTTTTATGAGTATTGTGG--
1 GAAGCGTGAAAATCCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTAGGAGTATTGTGGAA
* * *
1035 -CAAA----G-----AA-TTTTCGGGTC-AGTTTTAGCCAAAATCGTG---T-ACCATCACGGTT
66 AAAAATTGTGAAAAAAAGTTTTCGGGTCAAGTTTTAGCCGAAATCGTGTACTAACCATCAC-G-A
** * * *
1084 TTTTTACTAAAAACACGTTCCGGAG-CCCAGCTCAATTTTGCATGATTTTTGGCACAAAGAGTCC
129 TTTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAGTTTTGCATGATTTTTGGCACAAAGACTCC
* * * *
1148 TTGAAATATCTTTATTCATCGAACCAAATCCCAACCACATTGGATATAAGGATTTGTTTTTACGA
194 TTGAAATATCTATATTTATCGAACCAAATCACAACCAAATTGGATATAAGGATTTGTTTTTACGA
* * *
1213 GCATCTGAATCTTGTTTCGA-TTATTTAGAAATAAATTC--AATAAAAATGGAAAAACGGTATTT
259 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAA-AAAAAT-GAAAAACGATATTA
* * *
1275 GAAGCGTGAGAATCCCGTCAATCTTTTTT-GCGTTGAATTATATATTTTTTCA-GAGTGTTGTAG
1 GAAGCGTGAAAATCCCGTCAAT-TTTTTTGGCGTTGAATTATATATTTTTT-AGGAGTATTGTGG
* * * * * * *
1338 CAAAAAATTGAGAAAAAAAAAGTATTCTGGTCAATTTTTAGCCAAAATCGTGTACT----GT---
64 AAAAAAATTGTG--AAAAAAAGTTTTCGGGTCAAGTTTTAGCCGAAATCGTGTACTAACCATCAC
* * * * * * * * *
1396 -TTTTTTGTTAAAAACGCGTTTCGG-GGCCCGGCTCAGTTTTGCTTTG-TTTTTGGCAGAAACAC
127 GATTTTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAGTTTTGC-ATGATTTTTGGCACAAAGAC
* ** * * * *
1458 TCATTGAAATATCTATATTCGTCAAACCAAATCTCAGA-CAAATTGGATTTAATGATTTG-TTTT
191 TCCTTGAAATATCTATATTTATCGAACCAAATCACA-ACCAAATTGGATATAAGGATTTGTTTTT
1521 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
255 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
1558 TACTCCTTCC
Statistics
Matches: 1030, Mismatches: 146, Indels: 112
0.80 0.11 0.09
Matches are distributed among these distances:
300 1 0.00
301 6 0.01
302 28 0.03
303 131 0.13
304 58 0.06
306 3 0.00
307 16 0.02
308 10 0.01
309 2 0.00
310 1 0.00
312 29 0.03
313 107 0.10
314 4 0.00
316 7 0.01
317 53 0.05
318 116 0.11
319 125 0.12
320 159 0.15
321 59 0.06
322 1 0.00
328 31 0.03
329 71 0.07
330 12 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (321 bp):
GAAGCGTGAAAATCCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTAGGAGTATTGTGGAA
AAAAATTGTGAAAAAAAGTTTTCGGGTCAAGTTTTAGCCGAAATCGTGTACTAACCATCACGATT
TTGGCTAAAAACGCGTTCCGGAGCCCCAGCTCAGTTTTGCATGATTTTTGGCACAAAGACTCCTT
GAAATATCTATATTTATCGAACCAAATCACAACCAAATTGGATATAAGGATTTGTTTTTACGAGC
ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGAAAAACGATATTA
Found at i:2449 original size:330 final size:329
Alignment explanation
Indices: 1843--2944 Score: 1159
Period size: 330 Copynumber: 3.4 Consensus size: 329
1833 TAATTTGGAA
* * *
1843 AAAAAAATGGAAAAACCATATTAAAAGCGTGAAAAGCCCGTCAA-TTTTGTTGGCGTTGAATTAT
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAACTTTT-TTGGCGTTGAATTAT
* *** *
1907 ATATTTTTT-TAGAGTATTGTGGCAAAAAATTGATAAAAAAAAATT---TCAG---AT---AAGT
65 ATATTTTTTCT-GAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTGGGTCAGTTTTTGCAAAG-
* * * * * * * * *
1962 TTTTAGGCGAAATCGTGTACGT----TGC-GGTTTTTTTGTCTAAGAACGCGTTTCGGGGCCCCT
128 TTTTAGCCAAAATCGTGTAC-TACCAT-CACG-ATTTTTGACTAAAAACGCCTTCCGGAGCCCC-
** ** * * ** * * * ** *
2022 G-CTCTGTTTTGCATGGTTTTTTGCATAAAGACTCCTCGAAGTATCTATAATCATCTAACCGAAT
189 GACTCAATTTTATATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATGGAACCAAAT
* *
2086 CTCAGCCACATTGGACT-TAAGGGTTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA
254 CTCAGCCACATTGGA-TATAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
*
2150 GAAATAAATTCGG
317 GAAATTAATTCGG
* * * * *
2163 AAAAAAAAGGGAAAACGATATTAGAAGCGTGAAAAACCCTTAAACTTTTTTGGTGTTGAATTATA
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAACTTTTTTGGCGTTGAATTATA
* *
2228 TATTTTTTCTGAGTATTGTGGCAAAAGATGGAGAAAAAACTATTTGGGTCAGTTTTTGCAAAAG-
66 TATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACT-TTTGGGTCAGTTTTTGC-AAAGT
* ** * ** *
2292 TTTAGCCAAAATCGTGTACT-CCATCACGGTTTTTGGTTAAAAACGCGTTCTTGAGTCCCGACTC
129 TTTAGCCAAAATCGTGTACTACCATCACGATTTTTGACTAAAAACGCCTTCCGGAGCCCCGACTC
* *
2356 AATTTTGTATGATTTTTGGTGCAAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAG
194 AATTTTATATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAG
* * *
2421 CCACATTGGATATACAGATATGTTTTTACGTGCATCTGAATATTGTTTCGATTTAATTAGAAATT
259 CCACATTGGATATA-AGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
2486 AATTCGG
323 AATTCGG
*** *
2493 AAAAAAATGGAAAAACGATATTAGAAGTAAGAAAATCCCGTCAA-TCTTTTTGGCGTTGAATTAT
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAACT-TTTTTGGCGTTGAATTAT
* * * * *
2557 ATTTTTTTTCTAAGTATTGTGGCAAAAAATTGAGGAAAAATTTTTGGGTTAGTTTTTGCAAAGTT
65 ATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTGGGTCAGTTTTTGCAAAGTT
* * * *
2622 TTAGCCGAAATCTTGTACTAACCATCACGATTTTTGACTAAAAATGCCTTCCGGAGCCCCGGCTC
130 TTAGCCAAAATCGTGTACT-ACCATCACGATTTTTGACTAAAAACGCCTTCCGGAGCCCCGACTC
* * *
2687 AATTTTATATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATTTTTATGGAACCAAATCTCAA
194 AATTTTATATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAG
* *
2752 CCACATTGGATATAGGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGACATT
259 CCACATTGGATATA-AGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
2817 AATTCGG
323 AATTCGG
** * * * *
2824 -AAAATGTGGTAAAACGATATTAGAAGCGTGAAAAGCCCGCCAACATTTTTGGCGTTGAATTATA
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAACTTTTTTGGCGTTGAATTATA
* ** * * *
2888 TGTTTTCACTGAGTATTGTGGAAAAAAATTGAGAATAGACTTTTCGGGTCAGTTTTT
66 TATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTT-GGGTCAGTTTTT
2945 AGCCGAAATC
Statistics
Matches: 652, Mismatches: 104, Indels: 41
0.82 0.13 0.05
Matches are distributed among these distances:
320 86 0.13
321 7 0.01
324 4 0.01
327 1 0.00
328 5 0.01
329 54 0.08
330 317 0.49
331 178 0.27
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (329 bp):
AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAACTTTTTTGGCGTTGAATTATA
TATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTGGGTCAGTTTTTGCAAAGTTT
TAGCCAAAATCGTGTACTACCATCACGATTTTTGACTAAAAACGCCTTCCGGAGCCCCGACTCAA
TTTTATATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAGCC
ACATTGGATATAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
TCGG
Found at i:2789 original size:331 final size:330
Alignment explanation
Indices: 2048--2944 Score: 1160
Period size: 330 Copynumber: 2.7 Consensus size: 330
2038 TTTTTTGCAT
* * * ** *
2048 AAAGACTCCTCGAAGTATCTATAATCATCTAACCGAATCTCAGCCACATTGGACT-TAAGGG-TT
1 AAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAGCCACATTGGA-TAT-AGGGATT
* * * *
2111 TGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGGAA
64 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAA
* * * *
2176 AACGATATTAGAAGCGTGAAAAACCCTTAAACTTTTTTGGTGTTGAATTATATATTTTTTCTGAG
129 AACGATATTAGAAGCGTGAAAAACCCGTCAACATTTTTGGCGTTGAATTATATATTTTTTCTGAG
* *
2241 TATTGTGGCAAAAGATGGAGAAAAAACTATTTGGGTCAGTTTTTGCAAAAGTTTAGCCAAAATCG
194 TATTGTGGCAAAAAATTGAGAAAAAACTATTTGGGTCAGTTTTTGCAAAAGTTTAGCCAAAATCG
* ** * ** * *
2306 TGTACTCCATCACGGTTTTTGGTTAAAAACGCGTTCTTGAGTCCCGACTCAATTTTGTATGATTT
259 TGTACTCCATCACGATTTTTGACTAAAAACGCCTTCCGGAGCCCCGACTCAATTTTATATGATTT
*
2371 TTGGTGC
324 TTGGCGC
** *
2378 AAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAGCCACATTGGATATACAGATATG
1 AAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAGCCACATTGGATATAGGGATTTG
* *
2443 TTTTTACGTGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAA
66 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAA
*** * * *
2508 CGATATTAGAAGTAAGAAAATCCCGTCAATC-TTTTTGGCGTTGAATTATATTTTTTTTCTAAGT
131 CGATATTAGAAGCGTGAAAAACCCGTCAA-CATTTTTGGCGTTGAATTATATATTTTTTCTGAGT
* * * * *
2572 ATTGTGGCAAAAAATTGAGGAAAAA-TTTTTGGGTTAGTTTTTGC-AAAGTTTTAGCCGAAATCT
195 ATTGTGGCAAAAAATTGAGAAAAAACTATTTGGGTCAGTTTTTGCAAAAG-TTTAGCCAAAATCG
* *
2635 TGTACTAACCATCACGATTTTTGACTAAAAATGCCTTCCGGAGCCCCGGCTCAATTTTATATGAT
259 TGTACT--CCATCACGATTTTTGACTAAAAACGCCTTCCGGAGCCCCGACTCAATTTTATATGAT
2700 TTTTGGCGC
322 TTTTGGCGC
* * *
2709 AAAGACTCCTTGAAATATCTATTTTTATGGAACCAAATCTCAACCACATTGGATATAGGGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAGCCACATTGGATATAGGGATTTG
* ** *
2774 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGACATTAATTCGG-AAAATGTGGTAAAA
66 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAA
* * * **
2838 CGATATTAGAAGCGTGAAAAGCCCGCCAACATTTTTGGCGTTGAATTATATGTTTTCACTGAGTA
131 CGATATTAGAAGCGTGAAAAACCCGTCAACATTTTTGGCGTTGAATTATATATTTTTTCTGAGTA
* * *
2903 TTGTGGAAAAAAATTGAGAATAGACT-TTTCGGGTCAGTTTTT
196 TTGTGGCAAAAAATTGAGAAAAAACTATTT-GGGTCAGTTTTT
2945 AGCCGAAATC
Statistics
Matches: 490, Mismatches: 68, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
328 4 0.01
329 39 0.08
330 273 0.56
331 174 0.36
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35
Consensus pattern (330 bp):
AAAGACTCCTTGAAATATCTATATTCATGGAACCAAATCTCAGCCACATTGGATATAGGGATTTG
TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAA
CGATATTAGAAGCGTGAAAAACCCGTCAACATTTTTGGCGTTGAATTATATATTTTTTCTGAGTA
TTGTGGCAAAAAATTGAGAAAAAACTATTTGGGTCAGTTTTTGCAAAAGTTTAGCCAAAATCGTG
TACTCCATCACGATTTTTGACTAAAAACGCCTTCCGGAGCCCCGACTCAATTTTATATGATTTTT
GGCGC
Found at i:26333 original size:31 final size:31
Alignment explanation
Indices: 26298--26365 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
26288 ATATTCTAAA
* *
26298 AATAAGGGTATGATAGACGATTCAAAAGTTT
1 AATAAAGGTATAATAGACGATTCAAAAGTTT
*
26329 AATAAAGGTATAATAGGCGATTCAAAAGTTT
1 AATAAAGGTATAATAGACGATTCAAAAGTTT
*
26360 TATAAA
1 AATAAA
26366 AGTCGTACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (31 bp):
AATAAAGGTATAATAGACGATTCAAAAGTTT
Done.