Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016515.1 Corchorus olitorius cultivar O-4 contig16548, 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: 7781
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2670 original size:43 final size:44
Alignment explanation
Indices: 2587--2671 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
2577 TCACTCAGCC
2587 AATCGACCTTCTAATTATTGATTTTTTCCTTTATACATGTAGGT
1 AATCGACCTTCTAATTATTGATTTTTTCCTTTATACATGTAGGT
2631 AATCGACCTTCTAATTATTGATTTTTTCC-TTATACATGTAG
1 AATCGACCTTCTAATTATTGATTTTTTCCTTTATACATGTAG
2672 CTTAAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 12 0.29
44 29 0.71
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (44 bp):
AATCGACCTTCTAATTATTGATTTTTTCCTTTATACATGTAGGT
Found at i:3604 original size:17 final size:17
Alignment explanation
Indices: 3582--3620 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3572 ATCGTTGCTG
*
3582 ATCCTCCGAATACTTGT
1 ATCCTCCAAATACTTGT
3599 ATCCTCCAAATACTTGT
1 ATCCTCCAAATACTTGT
3616 ATCCT
1 ATCCT
3621 TGCTGCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.08, T:0.36
Consensus pattern (17 bp):
ATCCTCCAAATACTTGT
Found at i:7063 original size:297 final size:302
Alignment explanation
Indices: 6516--7703 Score: 984
Period size: 322 Copynumber: 3.8 Consensus size: 302
6506 AACTGACCTG
* *
6516 AAAATTTTTTACTCAATTTGC-TGCCACAATACTTAGAAAAAATATATAATTCTACGCCAA-ACA
1 AAAATTTTTT-CTCAATTT-CTTGCCACAATACTCATAAAAAATATATAATTC-ACGCCAAGA-A
* * * * *
6579 AATTGAAGGGGTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCAGAATTTATTTCTATTTAA
62 AATTGAA-GGGTTTTCACACTTCTAATATCGTATTTCCATTTTTTCA-AATTAATTTCTAATTAA
* *
6644 ATCG-AAGTAAGATTCAGATGCTCAGAA-AAACAAATCCCTTTATTCCAATGTGGCTGAGATTTG
125 ATCGAAAG-AAGATTCAGATGCTCA-AAGAAACAAAT-CC-TTAATCCAATGTGGCAGAGATTTG
* *
6707 GTTAGATGATTATAGATATTTCAAGGAGTCTTTATGCCATAAACCATGCAAAACTGAGTCGAGAC
186 GTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGAC
* * *
6772 -TGCGAA-ACGCATTT-T-T-A-G-C-CAATTTCGGCTAAAAAATGATCCAA
251 ATCCAAACACGCATTTATATAAGGACACAATTTCGGCTAAAAAATGACCCAA
* * * * *
6816 AAAACTTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATAAAATTCAGTGCCAAGAATAT
1 AAAATTTTTTCTCAATTTCTTGCCACAATACTCATAAAAAATATATAATTCA-CGCCAAGAAAAT
* * *
6881 TGAAGGGATTTCACACTTCTAATATCGTATTACCATTTTTTTAACATTAATTTCTAATTAAATCG
65 TGAAGGGTTTTCACACTTCTAATATCGTATTTCCATTTTTTCAA-ATTAATTTCTAATTAAATCG
6946 AAAGAAGATTCAGATGCTCAAAGAAACAAATCCTTAAGTCCAATGTGGCAGAGATTTGGTTAGAT
129 AAAGAAGATTCAGATGCTCAAAGAAACAAATCCTTAA-TCCAATGTGGCAGAGATTTGGTTAGAT
* * * * *
7011 AAATACAGATATTTCAATGAGTCTTTATGCCAAAAATCATGCAAAACTGAGTCGAGGCATCCAAA
193 GAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGACATCCAAA
** *
7076 CACGTTTTTAGTCAAAAACCGTAAAGGTTGGTACACAATTTCGGCTAAAAACTGACCCGAA
258 CACGCATTTA-T-----A---T-AA----GG-ACACAATTTCGGCTAAAAAATGACCC-AA
*** *
7137 ATTTTTTTTTTCTCAATTTCTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAGAAGA
1 A-AAATTTTTTCTCAATTTCTTGCCACAATACTCATAAAAAATATATAATTC-ACGCCAAGAAAA
* * *
7202 TTGAAGGGTTTTTCA-AGATTCTAATATCG-ATTTTCCATTTTTTCGAATTAATTTATAATTAAA
64 TTGAAGGG-TTTTCACA-CTTCTAATATCGTA-TTTCCATTTTTTCAAATTAATTTCTAATTAAA
* * ** * * *
7265 TCAAAACAAGATTCAGATGCTCGTAGAAACAAAT-CTTATATCAAATATGG-ATGGGATTTGGTT
126 TCGAAAGAAGATTCAGATGCTCAAAGAAACAAATCCTTA-ATCCAATGTGGCA-GAGATTTGGTT
* * * *
7328 TGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAATCTGAGTCAAGGC--C
189 AGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGACATC
** * * * * *
7391 CTAAAACACGTTTTTAGAAAAAAAACTGTGATGGCTAGTACACGATTTCGGCTAAACACTAACCC
254 C--AAACACGCATTT----ATATAA--G-GA---C----ACA--ATTTCGGCTAAAAAATGACCC
7456 GAA
301 -AA
*** * * * * *
7459 AGTTTTTTTTCTCAATTTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAGGACAAAAAAA
1 AAAATTTTTTCTCAA-TTTCTTGCCACAATACTCATAAAAAATATATAATTC-ACGCCAAGAAAA
* * * *
7524 TTGAAGGGTTTTTTACGA-TTCTAATATCGTTTTTCCATGTTTTATGAAA-AAATTTCTAATTAA
64 TTGAAGGG-TTTTCAC-ACTTCTAATATCGTATTTCCAT-TTTT-TCAAATTAATTTCTAATTAA
* * *
7587 ATCGAAACAAAATTCAGAT-CGT--AA-AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT
125 ATCGAAAGAAGATTCAGATGC-TCAAAGAAACAAATCCTT-AATCCAATGTGGCAGAGATTTGGT
* * *
7648 TTGATGATTATAGATATTTCAAGGAGTTTTTATGCCAAAAACCATGCAAAACTGAG
188 TAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAG
7704 CTGAGGCCCA
Statistics
Matches: 738, Mismatches: 86, Indels: 107
0.79 0.09 0.11
Matches are distributed among these distances:
296 3 0.00
297 82 0.11
298 80 0.11
299 57 0.08
300 10 0.01
301 1 0.00
310 1 0.00
312 1 0.00
313 3 0.00
314 1 0.00
315 2 0.00
316 1 0.00
317 1 0.00
319 4 0.01
320 33 0.04
321 180 0.24
322 210 0.28
323 63 0.09
324 4 0.01
325 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (302 bp):
AAAATTTTTTCTCAATTTCTTGCCACAATACTCATAAAAAATATATAATTCACGCCAAGAAAATT
GAAGGGTTTTCACACTTCTAATATCGTATTTCCATTTTTTCAAATTAATTTCTAATTAAATCGAA
AGAAGATTCAGATGCTCAAAGAAACAAATCCTTAATCCAATGTGGCAGAGATTTGGTTAGATGAA
TATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGACATCCAAACAC
GCATTTATATAAGGACACAATTTCGGCTAAAAAATGACCCAA
Found at i:7441 original size:322 final size:317
Alignment explanation
Indices: 6821--7779 Score: 1180
Period size: 322 Copynumber: 3.0 Consensus size: 317
6811 TCCAAAAAAC
* ** *
6821 TTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATAAAATTCAGTGCCAAGAATATTGAAG
1 TTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAGAAAATTGAAG
* * * *
6886 GG-ATTTCACA-CTTCTAATATCGTATTACCATTTTTTTAACATTAATTTCTAATTAAATCGAAA
66 GGTTTTTCA-AGATTCTAATATCGT-TTTCCA-TTTTTTGA-ATTAATTTCTAATTAAATCGAAA
* ** * *
6949 GAAGATTCAGATGCTCAAAGAAACAAATCCTTAAGTCCAATGTGGCA-GAGATTTGGTTAGATAA
127 CAAGATTCAGATGCTCGTAGAAACAAATCCTTAA-TCCAATGTGG-ATGAGATTTGGTTTGATGA
* * *
7013 ATACAGATATTTCAATGAGTCTTTATGCCAAAAATCATGCAAAACTGAGTCGAGGCATCC-AAAC
190 ATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGC--CCAAAAC
* * * * * * *
7077 ACGTTTTTAGTCAAAAACCGTAAAGGTTGGTACACAATTTCGGCTAAAAACTGACCCGAAATTTT
253 ACGTTTTTAGACAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA-GTT
7142 T
317 T
* *
7143 TTTTTCTCAATTTCTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAGAAGATTGAAG
1 TTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAGAAAATTGAAG
* *
7208 GGTTTTTCAAGATTCTAATATCGATTTTCCATTTTTTCGAATTAATTTATAATTAAATCAAAACA
66 GGTTTTTCAAGATTCTAATATCG-TTTTCCATTTTTT-GAATTAATTTCTAATTAAATCGAAACA
* * *
7273 AGATTCAGATGCTCGTAGAAACAAAT-CTTATATCAAATATGGATGGGATTTGGTTTGATGAATA
129 AGATTCAGATGCTCGTAGAAACAAATCCTTA-ATCCAATGTGGATGAGATTTGGTTTGATGAATA
* *
7337 TAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAATCTGAGTCAAGGCCCTAAAACACGT
193 TAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCC-AAAACACGT
* * * *
7402 TTTTAGAAAAAAAACTGTGATGGCTAGTACACGATTTCGGCTAAACACTAACCCGAAAGTTT
257 TTTTAG-ACAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAGTTT
* * * *
7464 TTTTTCTCAATTTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAGGACAAAAAAATTGAA
1 TTTTTCTCAA-TTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAGAAAATTGAA
* * **
7529 GGGTTTTTTACGATTCTAATATCGTTTTTCCATGTTTTATGAAAAAATTTCTAATTAAATCGAAA
65 GGGTTTTTCAAGATTCTAATATCG-TTTTCCAT-TTTT-TGAATTAATTTCTAATTAAATCGAAA
* * * *
7594 CAAAATTCAGA---TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTGATGAT
127 CAAGATTCAGATGCTCGTAGAAACAAATCCTT-AATCCAATGTGGATGAGATTTGGTTTGATGAA
* *
7656 TATAGATATTTCAAGGAGTTTTTATGCCAAAAACCATGCAAAACTGAG-CTGAGGCCCAAAAACG
191 TATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTC-GAGGCCC-AAAACA
* * * *
7720 CGTTTTTAGCCAAAAATTGTGATGGTTAGTACACGATTTCGGCTAAATATTGACCCGAAA
254 CGTTTTTAGACAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
7780 AC
Statistics
Matches: 555, Mismatches: 67, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
319 2 0.00
320 59 0.11
321 199 0.36
322 236 0.43
323 57 0.10
324 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (317 bp):
TTTTTCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAAGAAAATTGAAG
GGTTTTTCAAGATTCTAATATCGTTTTCCATTTTTTGAATTAATTTCTAATTAAATCGAAACAAG
ATTCAGATGCTCGTAGAAACAAATCCTTAATCCAATGTGGATGAGATTTGGTTTGATGAATATAG
ATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCAAAACACGTTTTT
AGACAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAGTTT
Done.