Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015339.1 Corchorus olitorius cultivar O-4 contig15372, 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: 9857
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6803 original size:331 final size:330
Alignment explanation
Indices: 5940--7052 Score: 1384
Period size: 330 Copynumber: 3.4 Consensus size: 330
5930 TGTAAAAATC
* * * * * *
5940 AGCCGAAATCGTGTACATTCTATCACAGTTTTAAGC-AAAAAAAGTGTTTCGGGGCCCCGATTCA
1 AGCCGAAATCGTGTACTTTCCATCACAGTTTTAAGCTAAAAACA-CGTTTCGAGGCCCCGACTCA
* * * * * * *
6004 GTTTTGCATTATTTTTAGCAAGAAGACTTCTTGAAATATTTATATTTATCTAACCAAATCTCAG-
65 GTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCAGC
* * *
6068 -ACATTGGATTTAAGGATTTGCTTTTACGACCATCTGAATCATGTTTC-GATTTTATTTGAAATT
130 CACTTTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATCATGTTTCTG-TTTAATTTGAAATT
* * * *
6131 AATTCAGAAAAAATTGGAAAACGATATTAGTAGCGTGAAAAACCTTT-AATCTTTTTGCCTTTGA
194 AATTCAGAAAAAATTGGAAAACGATATTAGAAGCCTGAAAAACCTTTCAATATTTTTGTCTTTGA
* * * *
6195 ATTATATATATTTTATGAGAGTTGTGACCTAAAATTGAGGAAAAATTTTCCGGATCAATTTTTTC
259 ATTATATAT-TTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAATTTTTGC
6260 AAAATTTT
323 AAAATTTT
* * * * * *
6268 AGCAGAAATCGTATACTTTCCATCACGGCTTTAAGCTAAAAACACGTTTCG-GGACACCGACTTA
1 AGCCGAAATCGTGTACTTTCCATCACAGTTTTAAGCTAAAAACACGTTTCGAGG-CCCCGACTCA
* ** * * * *
6332 GTTTTGTATGATTTTTTTCACAAAGACTCCTTAAAATATTTATATTCATCTGATCAAATCTCAGC
65 GTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCAGC
* * * * **
6397 CACTTTGGATTTAAGGATTTGCTTTTACGAGCGTTTGTATCATGTTTCTATTTAATTCAAAATTA
130 CACTTTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATCATGTTTCTGTTTAATTTGAAATTA
* * *
6462 A-TCAAGAAAAAAATTGGAAAAACAATATTAAAAGCCTGAAAAACCTTTCAAGATTTTTGTCTTT
195 ATTC-AG-AAAAAATTGG-AAAACGATATTAGAAGCCTGAAAAACCTTTCAATATTTTTGTCTTT
*
6526 GAATTATATATTTTCTATGAAAATTGTGGCC-AAAATTGAGGAAAAATTTTCCGGATCCAA-TTT
257 GAATTATATATTTT-TATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGAT-CAATTTT
6589 TGCAAAATTTT
320 TGCAAAATTTT
* * * * *
6600 AGCCGAAATCGTGTACTGTCCATTACGGTTTTAAGCTAAAAACGCGTTTCGAGGCTCCGACTCAG
1 AGCCGAAATCGTGTACTTTCCATCACAGTTTTAAGCTAAAAACACGTTTCGAGGCCCCGACTCAG
* *
6665 TTTTGCATGATTTTTGGCACGAAGAGTCCTTG-AATATCTATATTCATCTGACCAAAT-TTAGGC
66 TTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCA-GC
* * **
6728 CACTTTTGTTTTAAGGATTTATTTTTACGAGCATCTGAATCATGTTTCTGTTTAATTTGAAATTA
130 CACTTTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATCATGTTTCTGTTTAATTTGAAATTA
* * * * * *
6793 ATTCAGAAAAAATTGGGAAAACGATATTAGAAGTCTTAAAAGCCCTTCAATTTTTTTGTCATTGA
195 ATTCAGAAAAAATT-GGAAAACGATATTAGAAGCCTGAAAAACCTTTCAATATTTTTGTCTTTGA
* * *
6858 ATTATATATTTTTATGAGAATTTTGGCCAAAAAGTGAGGAAAAATTTTCCGAATCAATTTTTGCA
259 ATTATATATTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAATTTTTGCA
6923 AAATTTT
324 AAATTTT
* * * *
6930 AGTCGAAATCGTGTACTTTTCATTACAGTTTTAAGCTAAAAACACGTTTCGAGGCCCCGGCTCAG
1 AGCCGAAATCGTGTACTTTCCATCACAGTTTTAAGCTAAAAACACGTTTCGAGGCCCCGACTCAG
* * *
6995 TTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTACATTCATATGAACAAAT
66 TTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATATTCATCTGACCAAAT
7053 TTTTTTGGCT
Statistics
Matches: 674, Mismatches: 93, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
327 2 0.00
328 96 0.14
329 25 0.04
330 244 0.36
331 117 0.17
332 149 0.22
333 41 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (330 bp):
AGCCGAAATCGTGTACTTTCCATCACAGTTTTAAGCTAAAAACACGTTTCGAGGCCCCGACTCAG
TTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTCAGCC
ACTTTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATCATGTTTCTGTTTAATTTGAAATTAA
TTCAGAAAAAATTGGAAAACGATATTAGAAGCCTGAAAAACCTTTCAATATTTTTGTCTTTGAAT
TATATATTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGATCAATTTTTGCAAA
ATTTT
Found at i:8575 original size:332 final size:329
Alignment explanation
Indices: 7096--8895 Score: 2322
Period size: 334 Copynumber: 5.4 Consensus size: 329
7086 GAGTTGTGCC
** * * * * * * *
7096 AAAAATTTTCCAAATCAATTTTTGTAAAATGTTAGACGAAATCATATACTTTCCATCAAGATTTT
1 AAAAATTTTCCGGATCAA-TTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTT
* * * * * * *
7161 AAGCTAGAAATGTGTTTTG-GGACACCGACTCAGTTTTGCATGATTTTTTGCACAAAGAATCCTT
65 AAGCTAAAAACGCGTTTCGAGG-C-CCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTT
* * *
7225 GAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGTTTTGTTTTTACGAGC
128 GAAATATCTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGC
* * * * * * *
7290 ATTTGTATCATGTTTCTATTCAATTCAAAATTAATTCTGAAAAAATTGGAAAAATGATATTAAAA
193 ATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAA
* * * *
7355 GCCTGAAAAACCCTTCAAGCTTTTTTTCTTTGAACTATATATTGTCTATGAGAATTGTGGCCAAA
258 GCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATT-TTTATGAGAATTGTGGCCAAA
7420 AATTGAGG
322 AATTGAGG
* * **
7428 AAAAATTTTCCGGATCATTTTTGCAAAATTTTAGCCGAAATCGTGCACTATT-CATCACAATTTT
1 AAAAATTTTCCGGATCAATTTTGCAAAATTTTAGCCGAAATCGTGTACT-TTCCATCACGGTTTT
* * * *
7492 ATGCTAAAAACGTGTTTCGAGGCCTCGGCTCAGTTTTGCATGAGTTTTGGCACGAAGACTCCTTG
65 AAGCTAAAAACGCGTTTCGAGGCC-CGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTG
* * * * *
7557 AACTATCTATATTCATCTGACCAAATCTCTGACACTTTGGATTTAAAGATTTGTTTTTACGAGCA
129 AAATATCTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCA
7622 TCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTTGGAAAAACGATATTAGA
194 TCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAG-AAAAAA-TTGGAAAAACGATATTAGA
*
7687 AGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTTTTTTATGAGAATTGTGGTC
257 AGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATA---TTTTTATGAGAATTGTGGCC
7752 AAAAATTGAGG
319 AAAAATTGAGG
* * * * *
7763 AAAAGTCTTT-CGGATCAATTTAGCAAAATTTCAACCGAAATCGTGTA-TTTCCATCACAGTTTT
1 AAAAAT-TTTCCGGATCAATTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTT
* * * *
7826 AAGCTAAAAAAGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTTG
65 AAGCTAAAAACGCGTTTCGAGGCCC-GACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTG
* * * * * *
7891 AAATATTTATATTTATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGACCA
129 AAATATCTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCA
* * * * *
7956 TCTGAATCATGTATCGATTTTATTTGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGTAG
194 TCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAG
* * * *
8021 CGTGAAAAACCCTTTCAATCTTTTTGCCTTTGAATTATATATATTTTATGAGAGTTGTGGCCTAA
259 CCTGAAAAACCC-TTCAATCTTTTTGTCTTTGAATTATATAT-TTTTATGAGAATTGTGGCCAAA
8086 AATTGAGG
322 AATTGAGG
* * * *
8094 AAAAATTTCCCGGATCAATTTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACGGCTT
1 AAAAATTTTCCGGATCAA--TTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTT
* * * * *
8159 TAAGCTAAAAACACGTTTTG-GGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCT
64 TAAGCTAAAAACGCGTTTCGAGG-C-CCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCT
*
8223 TGAAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAG
127 TGAAATATCTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAG
* * * * * * *
8288 CGTTTGTATCATGTTTCTATTTAATTCAAAATTAATTAAGAAAAAAATTGGAAAAACAATATTAA
192 CATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAG-AAAAAATTGGAAAAACGATATTAG
* ** *
8353 AAGCCTGAAAAACCTTTCAAGATTTTTGTCTTTGAATTATATATTTTCTATGAAAATTGTGGCC-
256 AAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTT-TATGAGAATTGTGGCCA
*
8417 AAAATTGAGC
320 AAAATTGAGG
*
8427 AAAAATTTTCCGGATCAAATTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTT
1 AAAAATTTTCCGGATC-AATTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTT
* *
8492 AAGCTAAAAACGCGTTTCGAGGCTCCGACTCAGTTTTGCATGATTTTTGGCACGAAGAGTCCATG
65 AAGCTAAAAACGCGTTTCGAGGC-CCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTG
* * *
8557 AAATATCTATATTCATCTGACCAAAT-TAAAGCCACTTTTGTTTTAAGGATTT-ATTTTTACGAG
129 AAATATCTATATTCATCTGACCAAATCT-CAGCCACTTTGGATTTAAGGATTTGA-TTTTACGAG
* *
8620 CATCTGAATCATGTTTCTGTTTAATTCGAAATTAATTCAGAACAAATTGGAAAAAACGATATTAG
192 CATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAATTGG-AAAAACGATATTAG
* * *
8685 AAGCCTTAAAAGCCCTTCAATCTTTTTGTCTTTGAATTATATATTTTT-TGAGAATTTTGGCCAA
256 AAGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTTTATGAGAATTGTGGCCAA
*
8749 AAAGTGAGG
321 AAATTGAGG
* * *
8758 AAAAATTTTCCGAATCAATTTTGCAAAATTTTAGTCGAAATCGTGTACTTTTCATCACGGTTTTA
1 AAAAATTTTCCGGATCAATTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTA
* * *
8823 AGCTTAAAACACGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGA
66 AGCTAAAAACGCGTTTCGAGG-CCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGA
8888 AATATCTA
130 AATATCTA
8896 CATTGATATG
Statistics
Matches: 1281, Mismatches: 159, Indels: 58
0.86 0.11 0.04
Matches are distributed among these distances:
330 128 0.10
331 254 0.20
332 295 0.23
333 147 0.11
334 352 0.27
335 100 0.08
336 5 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (329 bp):
AAAAATTTTCCGGATCAATTTTGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACGGTTTTA
AGCTAAAAACGCGTTTCGAGGCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAA
ATATCTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATC
TGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCC
TGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATATTTTTATGAGAATTGTGGCCAAAAATT
GAGG
Found at i:9598 original size:333 final size:328
Alignment explanation
Indices: 8953--9855 Score: 1070
Period size: 333 Copynumber: 2.7 Consensus size: 328
8943 GAGTTGTGCC
* * * *
8953 AAAAATTTTCTGAATCAATTTTTGTAAAATGTTAGCCGAAATCGTATACT-TTCCATCAA-GATT
1 AAAAATTTTCCGAATCAATTTTTG-AAAATTTTAGCCGAAATCGT-GACTATT-CAT-AACAATT
* * * * *
9016 TTAAGCTAGAAATGCGTTTTGGGACACCGACTCAGTTTTGCATGATTTTTGGCACGAAA-AATCC
62 TTAAGCTAAAAAAGCGTTTCGGG-CCCCGACTCAGTTTTGCATGA-TTTTGGCAC-AAAGACTCC
* *
9080 TTGGAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGTTTTGTTTTTGCGA
124 TT-GAATATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGA
* * * * * *
9145 GCATTTGTATCATGTTTCTATTCAATTCAAAATTAATTCAGAAAAAAATTGGAAAAATGTTATTA
188 GCATCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTA
* *
9210 AAAGCCTGAAAAACCCTTCAAGCTTTTTTTCTTTGAACTATAAATTGTCTATGAGAATTGTGGCC
253 AAAGCCTGAAAAACCCTTCAAGCTTTTTGTCTTTGAACTATAAATTGTCTATGAGAATTGTGGCA
9275 AAAAATTGAGG
318 AAAAATTGAGG
*
9286 AAAAATTTTCCGAATCAATTTTTGCAAAATTTTAGACGAAATCGTGCACTATTCATAACAATTTT
1 AAAAATTTTCCGAATCAATTTTTG-AAAATTTTAGCCGAAATCGTG-ACTATTCATAACAATTTT
* * * *
9351 AAGCCAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGAGTTTTGACACAAAGACTCCTTG
64 AAGCTAAAAAAGCGTTTCG-GGCCCCGACTCAGTTTTGCATGA-TTTTGGCACAAAGACTCCTTG
* * *
9416 AACTATCTATATTCATCTGACCAAATCTCAGACACTTAGGATTTAAGGATTTGTTTTTACGAGCA
127 AA-TATTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCA
* *
9481 TCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGAGAAAAATTTGGAAAAACGATATTAGA
191 TCTGAATCATGTTTCTATTTAATTCGAAATTAATTCAGA-AAAAAATTGGAAAAACGATATTAAA
* * * * *
9546 AGCCTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTAT-ATTTTTTTATGAGAATTGTGGCAAA
255 AGCCTGAAAAACCCTTCAAGCTTTTTGTCTTTGAACTATAAATTGTCTATGAGAATTGTGGCAAA
9610 AAATTGAGG
320 AAATTGAGG
* * * * * * *
9619 AAAAGTCTTT-CGGATCAA-TTTAGAAAATTTCAGCCGAAATCGTG--TATCCATCACAGTTTTA
1 AAAAAT-TTTCCGAATCAATTTTTGAAAATTTTAGCCGAAATCGTGACTATTCATAACAATTTTA
*
9680 AGCTAAAAAAGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTGGCA-AGAAGACTTCTTGA
65 AGCTAAAAAAGCGTTTC-GGGCCCCGACTCAGTTTTGCATGATTTTGGCACA-AAGACTCCTTG-
* * *
9744 AATATTTATATTTATCTAACCAAATCTCAGCCACATTTGGATTTAAAGATTTTGCTTTTTA-GAC
127 AATATTTATATTCATCTGACCAAATCTCAGCCAC-TTTGGATTTAAGGA-TTTG-TTTTTACGA-
* * * * *
9808 CCATCTGAATCATGTATCGATTTTAATTTTGAAATTAATTCNGAAAAA
188 GCATCTGAATCATGTTTCTA-TTTAA-TTCGAAATTAATTCAGAAAAA
9856 TA
Statistics
Matches: 494, Mismatches: 59, Indels: 36
0.84 0.10 0.06
Matches are distributed among these distances:
326 1 0.00
327 45 0.09
328 65 0.13
329 7 0.01
330 23 0.05
331 28 0.06
332 27 0.05
333 234 0.47
334 64 0.13
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (328 bp):
AAAAATTTTCCGAATCAATTTTTGAAAATTTTAGCCGAAATCGTGACTATTCATAACAATTTTAA
GCTAAAAAAGCGTTTCGGGCCCCGACTCAGTTTTGCATGATTTTGGCACAAAGACTCCTTGAATA
TTTATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
ATCATGTTTCTATTTAATTCGAAATTAATTCAGAAAAAAATTGGAAAAACGATATTAAAAGCCTG
AAAAACCCTTCAAGCTTTTTGTCTTTGAACTATAAATTGTCTATGAGAATTGTGGCAAAAAATTG
AGG
Done.