Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020781.1 Corchorus olitorius cultivar O-4 contig20814, 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: 7759
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:5426 original size:5 final size:5
Alignment explanation
Indices: 5377--5441 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
5367 ATAAATAATT
* * *
5377 TTATT TTATC TTATT TTATC TTA-C -TATC TTA-C TATCTC ATTATC TTATC
1 TTATC TTATC TTATC TTATC TTATC TTATC TTATC T-TATC -TTATC TTATC
5426 TTA-C -TATC TTATC TTA
1 TTATC TTATC TTATC TTA
5442 CTACTATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
3 4 0.08
4 6 0.12
5 33 0.69
6 4 0.08
7 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATC
Found at i:5433 original size:13 final size:13
Alignment explanation
Indices: 5392--5444 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
5382 TTATCTTATT
5392 TTATCTTACTATC
1 TTATCTTACTATC
* *
5405 TTACTATCTCATTATC
1 -T--TATCTTACTATC
5421 TTATCTTACTATC
1 TTATCTTACTATC
5434 TTATCTTACTA
1 TTATCTTACTA
5445 CTATATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 21 0.64
14 1 0.03
15 1 0.03
16 10 0.30
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATCTTACTATC
Found at i:6787 original size:322 final size:321
Alignment explanation
Indices: 6268--7080 Score: 967
Period size: 322 Copynumber: 2.5 Consensus size: 321
6258 TTTTTTTTGT
* * * * **
6268 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* * * * * *
6333 ACATT--TA-AA-TATTTATTTTTACGAGCATCTGAATTTTGTTTCAATTTAATTATAATTTAAT
65 ACATTGATATAAGGATTTGTTTTTACGAGCATCTGAA-ATTGTTTCGATTTAATTAGAAATTAAT
* * * * *
6394 TCGGAAAATAAATGGAATAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA
129 TCGGAAAATAATTGGAA-AATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTGAA
* * *
6459 TTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCCGATCAGTTTTTAGC
193 TTATATATTTTTTATGAGTATTGTGGCAAAAAATTAAGAAAAAAAAATTCCGATCAGTTTTTAGC
* * *
6524 CG-AAATCGTGTACTAATCATCACAGTTTTT-TGCTAAAAACGCG-TTCCCGAGCCCCGACTCAA
258 CGAAAATCATG-ACTAACCATCACAGTTTTTGGGCTAAAAACGCGTTTCCCGAGCCCCGACTCAA
* *
6586 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAACA
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
*
6651 ACATTGGATATAAGGATTTGTTTTTACGAGCAGCTGAAACTTGTTTCGATTTAATTAGAAATTAA
65 ACATT-GATATAAGGATTTGTTTTTACGAGCATCTGAAA-TTGTTTCGATTTAATTAGAAATTAA
*
6716 TTCGGAAAATAATTGGAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAA
128 TTCGGAAAATAATTGGAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTGAA
* *
6781 TTATATATTTTTTATGAGTATTGTGGCAAAAAATTAAGAAAAAAAAATTCGGGTCAGTTTTTAGC
193 TTATATATTTTTTATGAGTATTGTGGCAAAAAATTAAGAAAAAAAAATTCCGATCAGTTTTTAGC
* ** ** * * *
6846 CGAAAATCATGCCTAACCATCATTGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGGCTCAG
258 CGAAAATCATGACTAACCATCACAGTTTTTGGGCTAAAAACGCGTTTCCCGAGCCCCGACTCAA
* * *
6910 TTTTGCATGATTTTTGGCAGAAAGACTCATTAAAATATCTATATTCATCTAACCAATATGAGGCT
1 TTTTGCATGATTTTTGGC-GAAAGACTCCTTGAAATATCTATATTCATCAAACCAA-AT---G--
* * * *
6975 CTCAGCCACATTAGATTTACGGATTTGTTTTTACGAGAATTTGAATATTGTTTCGATTTAATTAG
59 -TCAGCCACATT-GATATAAGGATTTGTTTTTACGAGCATCTGAA-ATTGTTTCGATTTAATTAG
* * * *
7040 AAA-TAGATTCGGAAAAAAAATAGAAAAATGATATTTAAAGC
121 AAATTA-ATTCGG-AAAATAATTGGAAAATGATATTAAAAGC
7081 TAGAAAAATA
Statistics
Matches: 422, Mismatches: 53, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
318 61 0.14
321 2 0.00
322 121 0.29
323 79 0.19
324 65 0.15
325 3 0.01
328 1 0.00
330 2 0.00
331 63 0.15
332 25 0.06
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (321 bp):
TTTTGCATGATTTTTGGCGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCA
CATTGATATAAGGATTTGTTTTTACGAGCATCTGAAATTGTTTCGATTTAATTAGAAATTAATTC
GGAAAATAATTGGAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTGAATTA
TATATTTTTTATGAGTATTGTGGCAAAAAATTAAGAAAAAAAAATTCCGATCAGTTTTTAGCCGA
AAATCATGACTAACCATCACAGTTTTTGGGCTAAAAACGCGTTTCCCGAGCCCCGACTCAA
Found at i:7614 original size:852 final size:863
Alignment explanation
Indices: 5993--7759 Score: 2571
Period size: 879 Copynumber: 2.0 Consensus size: 863
5983 TATATATTTT
* *
5993 TTTTTGAGTAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCAGAAAGACT
1 TTTTTGGGTAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACT
* * *
6058 CCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAGCCACATTAGATTTAAGGATTTG
66 CATTAAAATATCTATATTCATCTAACCAATATCAGGCTCTCAGCCACATTAGATTTAAGGATTTG
*
6123 TTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAAAAAAAAAGAAAAA
131 TTTTTACGAGAATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAAAAAAAAAGAAAAA
*
6188 TGATATTTAAAGCGAGAAATATATTTCAATTTTTTTTTTGCGTTGAATTGTGTATTTTTTGCCGA
196 TGATATTTAAAGCGAGAAAAATATTTCAA--TTTTTTTTGCGTTGAATTGTGTATTTTTTGCCGA
*
6253 AAATATTTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCG
259 AAATATTTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTCC-----ATATCTAAATTCATCG
*
6318 AACAAAATCCCAGCCACATTTAAATATTTATTTTTACGAGCATCTGAATTTTGTTTCAATTTAAT
319 AACAAAATCCCAGCCACATTTAAATATTTATTTTTACGAGCATCTGAATATTGTTTCAATTTAAT
* *
6383 TATAATTTAATTCGGAAAATAAATGGAATAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTT
384 TAAAAATTAATTCGGAAAATAAATGGAATAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTT
* *
6448 TTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCCGAT
449 TTGGCGTTAAATTATATATTTTTTCTGAGTATTGGGGCAAAAAATTGAGAAAAAAAATTTCCGAT
6513 CAGTTTTTAGCCGAAATCGTGTACTAATCATCACAGTTTTTTGCTAAAAACGCGTTCCCGAGCCC
514 CAGTTTTTAGCCGAAATC-TGTACTAA-CAT-AC-------TG---AAAACGCGTTCCCGAGCCC
* * *
6578 CGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAA
566 CGACTCAATTTTCCATGATTTTTGGCGAAAAGACTCCTTGAAATATCTATATTCAACAAACCAAA
6643 TGTCAACAACATTGGATATAAGGATTTGTTTTTACGAGCAGCTGAAACTTGTTTCGATTTAATTA
631 TGTCAACAACATTGGATATAAGGATTTGTTTTTACGAGCAGCTGAAACTTGTTTCGATTTAATTA
*
6708 GAAATTAATTCGGAAAATAATTGGAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTG
696 GAAATTAATTCGGAAAAAAATTGGAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTG
*
6773 GTGTTGAATTATATA-TTTTTTATGAGTATT-GT-GGCAAAAAATTAAG-AAAA-AAAAATTCGG
761 GTGTTGAATTATATATTTTTTTA-GAGTATTAGTCGGAAAAAAATTAAGTAAAAGAAAAA-TCGG
* *
6833 GTCAGTTTTTAG-CCGAAAATCATG-CCTAACCATCATTG
824 GTCAGTTTTTAGCCCGAAAATCATGTACTAACCATCATGG
6871 TTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
1 TTTTTGGG-TAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
* *
6936 TCATTAAAATATCTATATTCATCTAACCAATATGAGGCTCTCAGCCACATTAGATTTACGGATTT
65 TCATTAAAATATCTATATTCATCTAACCAATATCAGGCTCTCAGCCACATTAGATTTAAGGATTT
*
7001 GTTTTTACGAGAATTTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAAAAAAAATAGAAA
130 GTTTTTACGAGAATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAAAAAAAA-AGAAA
* *
7066 AATGATATTTAAAGCTAGAAAAATATTTCAA-TTTTTTTGCGTTGATTTGTGTA-TTTTTGCCGA
194 AATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAATTGTGTATTTTTTGCCG-
*
7129 AAAATATTTTTTTTTTGTTTTTGCATGATTTTTGACGTAATTACTCC-T-TC-AAATTCATCGAA
258 AAAATA--TTTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTCCATATCTAAATTCATCGAA
* * * * *
7191 CAAAATCCCAGCCACGTTCGATTTAAGTATTTGTTTTTATGAGCATGTGAATATTGTTTTAATTT
321 CAAAATCCCAGCCA----C-ATTTAAATATTTATTTTTACGAGCATCTGAATATTGTTTCAATTT
7256 AATTAAAAATTAATTCGGAAAA-AAATGGAA-AACGATATTAGAAGCGTGAAACA-CCCGTCAAT
381 AATTAAAAATTAATTCGGAAAATAAATGGAATAACGATATTAGAAGCGTGAAA-AGCCCGTCAAT
*
7318 CTTTTTGGCGTTAAATTATAT-TTTTTT-T-AGTATTGGGGCAAAAAATTGAGAAAAAAACTTTT
445 CTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGGGGCAAAAAATTGAGAAAAAAA-ATTT
* **
7380 CCGATCAGTTTTTAGCCGAAAT-TGT-GTAA-AT-C-G-AAAC-TTTTCCCGAGCCCCGACTCAA
509 CCGATCAGTTTTTAGCCGAAATCTGTACTAACATACTGAAAACGCGTTCCCGAGCCCCGACTCAA
* * *
7438 TTTTCCATGATTTTTGGCGAAAAGACTCCTTGGAATATCTATATTCAACAAACCAAATGTTAGGC
574 TTTTCCATGATTTTTGGCGAAAAGACTCCTTGAAATATCTATATTCAACAAACCAAATGTCA-AC
* **
7503 -ACATTGGATATAAGGATTT-TTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTA
638 AACATTGGATATAAGGATTTGTTTTTACGAGCAGCTGAAACTTGTTTCGATTTAATTAGAAATTA
* *
7566 CTTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAATGACCATCAATCTTTTTGGTGTTG
703 ATTCGGAAAAAAATTGG-AAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTG
* *
7631 AATTATATATTTTTTTCAGAGTATTAGTCGGAAAAAAATTCAGTAAAAGAAAAATCGGGTCTGTT
767 AATTATATATTTTTTT-AGAGTATTAGTCGGAAAAAAATTAAGTAAAAGAAAAATCGGGTCAGTT
*
7696 TTTAGCCCGAAAATCGTGTACTAACCATCATGG
831 TTTAGCCCGAAAATCATGTACTAACCATCATGG
* *
7729 TTTCTGAGGTAAAAACGTGTTTCGGGGGCCC
1 TTTTTG-GGTAAAAACGCGTTTCGGGGGCCC
Statistics
Matches: 818, Mismatches: 48, Indels: 66
0.88 0.05 0.07
Matches are distributed among these distances:
851 56 0.07
852 150 0.18
853 18 0.02
854 3 0.00
855 12 0.01
856 19 0.02
857 17 0.02
858 38 0.05
859 2 0.00
865 1 0.00
867 2 0.00
869 3 0.00
870 3 0.00
871 53 0.06
872 28 0.03
873 7 0.01
874 50 0.06
875 10 0.01
876 68 0.08
877 27 0.03
878 7 0.01
879 210 0.26
880 34 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (863 bp):
TTTTTGGGTAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACT
CATTAAAATATCTATATTCATCTAACCAATATCAGGCTCTCAGCCACATTAGATTTAAGGATTTG
TTTTTACGAGAATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAAAAAAAAAGAAAAA
TGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAATTGTGTATTTTTTGCCGAAA
ATATTTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTCCATATCTAAATTCATCGAACAAAA
TCCCAGCCACATTTAAATATTTATTTTTACGAGCATCTGAATATTGTTTCAATTTAATTAAAAAT
TAATTCGGAAAATAAATGGAATAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGT
TAAATTATATATTTTTTCTGAGTATTGGGGCAAAAAATTGAGAAAAAAAATTTCCGATCAGTTTT
TAGCCGAAATCTGTACTAACATACTGAAAACGCGTTCCCGAGCCCCGACTCAATTTTCCATGATT
TTTGGCGAAAAGACTCCTTGAAATATCTATATTCAACAAACCAAATGTCAACAACATTGGATATA
AGGATTTGTTTTTACGAGCAGCTGAAACTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA
TTGGAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTT
TTAGAGTATTAGTCGGAAAAAAATTAAGTAAAAGAAAAATCGGGTCAGTTTTTAGCCCGAAAATC
ATGTACTAACCATCATGG
Done.