Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004329.1 Corchorus capsularis cultivar CVL-1 contig04337, 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, 733
Length: 1222
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1034 original size:462 final size:460
Alignment explanation
Indices: 4--1222 Score: 1894
Period size: 463 Copynumber: 2.6 Consensus size: 460
1 CGC
*
4 TCATCGAACATGTTGTTCATTCGCAG-CCATACTAAGACGTAATGCGTACATGAACCGATTGCTT
1 TCATCGAACATGTTGTTCATTCGCAGCCCATACTAAGACGTAATGCTTACATGAACCGATTGCTT
68 CCCATAAGAAATTCC-AGAAAGTAG-A-AAAATTAAAGAAAAAAATG-AAAAGGGGTGCAACAT-
66 CCCATAAGAAATTCCGA-AAAGTAGAAGAAAATTAAAGAAAAAAATGAAAAAGGGGTGCAAC-TC
* * * * *
128 GAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGGCGAAGCACGTTTAACGTGTGGAG
129 GAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCACGCCCAAGCACGCTTAAC-TGCGGAG
*
193 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAATT
193 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAATC
258 TATACAAGCCACATCTTCATTTGGATCCGGTGCTATTGTTGACCAACATATGATCGTATACGTCA
258 TATACAAGCCACATC-TCA-TTGGATCCGGTGC-ATTGTTGACCAACATATGATCGTATACGTCA
*
323 TACGTACTAAGACTTTAATACTTACTTCAGCCGATGACTACCCAAAAAGTTTTCGAAAGAAGAAG
320 TACGTACTAAGACTTTAATACTTACTTCAACCGATGACTACCCAAAAAGTTTTCGAAAGAAGAAG
* * *
388 AAAACTTTATTTCTCTTTGGAAACCTTACCGAGCGAACATTAAACGGCCTTTGTATCCAGGTTGT
385 AAAAATTTATTTCTCTTTGGAAACCTTACCGACCGAACATTAAACGGCCTTTGTATCCAGCTTGT
453 TCACGTGCCGT
450 TCACGTGCCGT
*
464 TCATCGAACTATGTTGTTCATTCGCAGACCAATACGTAAGACGTAATGCTTACATGAACCGATTG
1 TCATCGAAC-ATGTTGTTCATTCGCAG-CCCATAC-TAAGACGTAATGCTTACATGAACCGATTG
*
529 CTTCCCAT-AGAAATTCCG-AAAGTAGAAG-AAATTAAAGAAAAAAATGAAAAATGGGTGCAACT
63 CTTCCCATAAGAAATTCCGAAAAGTAGAAGAAAATTAAAGAAAAAAATGAAAAAGGGGTGCAACT
* * *
591 CGAGGACTTCCCTGGAGGTCACCCATCCTAGTACCACTCACGCCCAACCACGCTTAACTGCGGAG
128 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCACGCCCAAGCACGCTTAACTGCGGAG
* *
656 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGNACCCATTGG-CTTTAGCATGNTAAAT
193 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTT-GCATGATAAAT
720 CTATACAAGCCACAATCTCATTGGATCCCGGTGCATTGTT-AGCCAACATATGATCGTATACGTC
257 CTATACAAGCCAC-ATCTCATTGGAT-CCGGTGCATTGTTGA-CCAACATATGATCGTATACGTC
*
784 ATACGTACTAAGAC-TTAATACTTACTTCAATCGATGAACTACCCAAAAAGTTTTCGAAAGAAGA
319 ATACGTACTAAGACTTTAATACTTACTTCAACCGATG-ACTACCCAAAAAGTTTTCGAAAGAAGA
848 AGAAAAATTTATTTCTCTTTGGAAACCTTACCGACCGAACA-TAAACGGCCTTTG-ATCCAGCTT
383 AGAAAAATTTATTTCTCTTTGGAAACCTTACCGACCGAACATTAAACGGCCTTTGTATCCAGCTT
911 GTTCACGTGCCGT
448 GTTCACGTGCCGT
924 TCATCGAACATG-TGTTCATTCGCAGCCCATACTAAGACGTAATGCTTACATGAACCGATTGACT
1 TCATCGAACATGTTGTTCATTCGCAGCCCATACTAAGACGTAATGCTTACATGAACCGATTG-CT
*
988 TCCCATAAGAAATTCCGAAAAGTAGAAGAAAATTAAAGAAAAAAAAATGAAAAAGGGGTGCAACA
65 TCCCATAAGAAATTCCGAAAAGTAGAAGAAAATTAAAG--AAAAAAATGAAAAAGGGGTGCAACT
* * *
1053 CGACGGA-TTCCCCAGGAGGTCACCCAACCTAGTACTACTCTACGCCCAAGCACGCTTCACTGCA
128 CGA-GGACTT-CCCAGGAGGTCACCCATCCTAGTACTACTC-ACGCCCAAGCACGCTTAACTGCG
* *
1117 GAGTTCTGATGAGATCCGGTGCATTAGGGACTGGTATGATCGCACCCATTGGTCTTTGCATGATA
190 GAGTTCTGATGGGATCCGGTGCATTAGTG-CTGGTATGATCGCACCCATTGGTCTTTGCATGATA
* *
1182 AATCTATACAAGCCACATCTCATTGAATCTGGTGCATTGTT
254 AATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTT
Statistics
Matches: 700, Mismatches: 34, Indels: 47
0.90 0.04 0.06
Matches are distributed among these distances:
456 29 0.04
457 14 0.02
458 23 0.03
459 13 0.02
460 48 0.07
461 51 0.07
462 153 0.22
463 161 0.23
464 160 0.23
465 44 0.06
466 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (460 bp):
TCATCGAACATGTTGTTCATTCGCAGCCCATACTAAGACGTAATGCTTACATGAACCGATTGCTT
CCCATAAGAAATTCCGAAAAGTAGAAGAAAATTAAAGAAAAAAATGAAAAAGGGGTGCAACTCGA
GGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCACGCCCAAGCACGCTTAACTGCGGAGTTC
TGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAATCTAT
ACAAGCCACATCTCATTGGATCCGGTGCATTGTTGACCAACATATGATCGTATACGTCATACGTA
CTAAGACTTTAATACTTACTTCAACCGATGACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAAAT
TTATTTCTCTTTGGAAACCTTACCGACCGAACATTAAACGGCCTTTGTATCCAGCTTGTTCACGT
GCCGT
Done.