Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015418.1 Corchorus olitorius cultivar O-4 contig15451, 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: 3377
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Found at i:711 original size:333 final size:333
Alignment explanation
Indices: 1--2503 Score: 3507
Period size: 333 Copynumber: 7.5 Consensus size: 333
* *
1 AATTGAGGAAAAAATCTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
1 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
* *
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCATCAG
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAA
* * * *
131 GATTCCTTGAAATATCTATATT-ATCTAATTAAAACTTAGTCACATTTCATTTAAGGATTTGTTT
131 GACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGTTT
*
195 TTACGAGCATTTGAATCTTGTTTCGATTTCGTTAGAAATTAATTCAGG-AAAATATGAAAAACGA
196 TTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACGA
* * * * *
259 TATTAAAAGCGTGAAAATTCCTCCAATCTCTTTGGCGTTACATTTTATGTATATCATGAGTATTT
261 TATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTTTATATATTTTATGAGTATTT
*
324 CATCCAAA
326 TATCCAAA
* *
332 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAACTCGTGTACTAATCAT
1 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
* * **
397 CACGGTTTTTGGCTAAAAACGCGTTACGGGGTCCCGGCTCAGTTTTGCATTAATTTTT-ATGTCA
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCA-TGATTTTTGGCGTCA
* * * *
461 ACACTCCTTGAAATATCAATATTCATCTAATAAAAACTTGGCCACATTGAATTTAAGGATTTGTT
130 AGACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGTT
*
526 TTTACGAGCATTTTAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACG
195 TTTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACG
* * * * *
591 ATATTAAGAGCGTGAAAAGTCCTCCAATATTTATGGCGTTACATTGTATATATTTTATGATTATT
260 ATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTTTATATATTTTATGAGTATT
656 TTATCCAAA
325 TTATCCAAA
*
665 AATTGAGGAAAAATTTTTCGCGGTCACTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
1 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
* *
730 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTTGCGTCAG
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAA
* * *
795 GATTCCTTGAAATATCTATATTAATCTAATAAAAACTTAGCCACATCGCATTTAAGGATTTGTTT
131 GACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGTTT
*
860 TTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGAAAAAATATGAAAAACGA
196 TTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACGA
* * * *
925 TATTAAAAGCATGAAAAGTCCTCCATTCTTTTTGGCGTTAAATTTTATGTATTTTATGAGTATTT
261 TATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTTTATATATTTTATGAGTATTT
*
990 TAACCAAA
326 TATCCAAA
* *
998 AATTGAGGAAATATTTTTCGCAGTCATTTTTTGCAAAATTTTAGCCAAAATCGTG---------T
1 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
*
1054 -AC-----TTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAATTTTGCATGATTTTTGGCGTCAA
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAA
* * * *
1113 GACTCCATGTAATATTTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTT-ATT
131 GACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGTTT
* * * **
1177 TTCCTGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGGACAAATATGAAAAAAT
196 TTAC-GAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACG
* * * *
1242 ATATTAAAAGCGTGGAAAGTCCTTCAATCTTTTTGGCGTTACATTGTATATATTTTAGGAGTATT
260 ATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTTTATATATTTTATGAGTATT
1307 TTATCCAAA
325 TTATCCAAA
* *
1316 AATTGAGGAAAAATTTTTAG-GTGTATTTTTGGCGTTATTTTTTGCAAAATTTTAGCTAAAATCG
1 AATTGAGGAAAAATTTTTCGCG-G------T--C---ATTTTTTGCAAAATTTTAGCCAAAATCG
* * * * *
1380 TG---T-A-CATCATGGTTTTTGGCTAAAAACGCGTTACGGGGTCCCGACTCAGTTTTACATCAA
54 TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCAT-GA
*** * *
1440 TTTTT-ATATCAACACTCCTTGAAATATCTATATTCATCTAATAAAAATTTAGCCACATTGCATT
118 TTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATT
*
1504 TAAGGATTTTTTTTTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAA
183 TAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAA
*
1569 ATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTGTATATAT
248 ATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTTTATATAT
*
1634 TTTAAGAGTATTTTATCCAAA
313 TTTATGAGTATTTTATCCAAA
* * *
1655 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAGTTTTAGTCAAAACCGTGTACTAACCAT
1 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
* * * ** *
1720 CACGGTTTATCGCTAAAAACGCGTTTCGGGGTCTCGGCTCAGTTTTATATGATTTTTGGCGTCAG
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAA
* **
1785 GA-TCCATTCAAATATCTATATTCATCTAATAAAAACTTAGTTACATTGCATTTAAGGATTTGTT
131 GACTCC-TTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGTT
* * *
1849 TTTACGAGCATTTGAATCTTGTTTCGATTTTATTAGAAATTAATTTAGAAAAAATATGAAAAACG
195 TTTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACG
* * *
1914 ATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTTA-ATTTTATGTATTTTATGAGCAT
260 ATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCG-TTACATTTTATATATTTTATGAGTAT
1978 TTTATCCAAA
324 TTTATCCAAA
* * * * *
1988 AATTGAGGAAATATTTTTCGCAGTCATTTTTTGCAAAATTTTATCCAAAATCTTGTACTAACTAT
1 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
* *
2053 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCTGACTCAGTTTTGCATGATTTTTGGCGTCAA
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAA
* *
2118 GACTCCATGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTTTTT
131 GACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGTTT
* * * **
2183 TTCCCGAGCATTTGAATCTTGTTTCGATTTAATTAGAAAATAATTCAGG-AAAATATGAAAAAAA
196 TT-ACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACG
* * * * * **
2247 ACTATTAAAAGCGTGGAAAGTCCTTCAATCTTTTTGACATGACATTTTATATATTTTGGGAGTAT
260 A-TATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTTTATATATTTTATGAGTAT
2312 TTTATCCAAA
324 TTTATCCAAA
* ** *
2322 AATTGAGGAAAACTTTTTCATGGTCATTTTTTGCAAAATTTTAGACAAAATCGTGTACTAACCAT
1 AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
* ** * *
2387 CACGGTTTTTGACTAAAAACGCGTTTCGCAGTCCCGGCTCAGTTTTTCATGATTTTTGGCGTCAG
66 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAA
* * *
2452 GATTCCTTAAAATATCTATATTCATCTAATAAAAACTTAGCTACATTGCATT
131 GACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATT
2504 GCAAGTGGAT
Statistics
Matches: 1928, Mismatches: 202, Indels: 81
0.87 0.09 0.04
Matches are distributed among these distances:
317 5 0.00
318 248 0.13
323 2 0.00
324 2 0.00
326 1 0.00
328 26 0.01
329 29 0.02
331 133 0.07
332 107 0.06
333 848 0.44
334 270 0.14
339 245 0.13
340 12 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (333 bp):
AATTGAGGAAAAATTTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAT
CACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTCAA
GACTCCTTGAAATATCTATATTCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGTTT
TTACGAGCATTTGAATCTTGTTTCGATTTCATTAGAAATTAATTCAGGAAAAATATGAAAAACGA
TATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTACATTTTATATATTTTATGAGTATTT
TATCCAAA
Found at i:3009 original size:16 final size:17
Alignment explanation
Indices: 2982--3027 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
2972 TTTGGTAGGG
2982 AGGAAA-GAAATAGA-A
1 AGGAAAGGAAATAGACA
2997 AGGAAAGGAAATA-ACA
1 AGGAAAGGAAATAGACA
3013 AGGGAAAGGAAATAG
1 A-GGAAAGGAAATAG
3028 GGAGGAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.26
16 8 0.30
17 12 0.44
ACGTcount: A:0.61, C:0.02, G:0.30, T:0.07
Consensus pattern (17 bp):
AGGAAAGGAAATAGACA
Done.