Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011065.1 Corchorus olitorius cultivar O-4 contig11098, 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, 625
Length: 1042
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Found at i:282 original size:154 final size:154
Alignment explanation
Indices: 1--1003 Score: 1419
Period size: 154 Copynumber: 6.5 Consensus size: 154
* * *
1 ATTTGGAACACTTGTTATTTTGGGCCTATGGGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGA
1 ATTTGGAACACTTGTTATTTTGGGCCTAT-CGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGA
* * * * *
66 TTTGGCAAACCTCAATGCTATTGTTTCAATTGTTTATGGCCTAACTATAATTATTTTGGTGAGAT
65 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
* * *
131 TGGTCCACTTTGATGTTTTTAGC-A
130 TAGTCCACTGTGAAGTTTTTAGCTA
* * * *
155 CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATATTGAACCGTCTTCGA
1 -ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGA
220 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
65 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
*
285 TAGTCCACTGTGAAGTTTTTAGCTC
130 TAGTCCACTGTGAAGTTTTTAGCTA
310 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
1 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
* * *
375 TTGG-AAACCTCAAAGCTTTTCTTTCCTACTTGTTTA-GGAACTAACTATAATTATTTTGATGAG
66 TTGGCAAACCTCAATGCTTTTCTTTCC-A-TTGTTTATGG-ACTAACTATAATCATTTTGGTGAG
* *
438 ATTAGTCCATTGGGAAGTTTTTAGCTA
128 ATTAGTCCACTGTGAAGTTTTTAGCTA
* ** * * *
465 ATTTGGAACACTTGTTATTTTAGGCCT-TACGGGGCCCATTAGTGGCATGTTGAATCCTCTTCGA
1 ATTTGGAACACTTGTTATTTTGGGCCTAT-CGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGA
529 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
65 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
*
594 TAGTCCACAGTGAAGTTTTTAGCTA
130 TAGTCCACTGTGAAGTTTTTAGCTA
* *
619 ACTTGGAACACTTGTTATTTGGGGCCTATCGGGGCCCATTAGTT-CTGTTTTGAATCGTCTTCGA
1 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTAC-GTTTTGAATCGTCTTCGA
* * *
683 TTTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTAAAAT
65 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
*
748 TAGTCCACTGTGAAGTGTTTAGCTA
130 TAGTCCACTGTGAAGTTTTTAGCTA
* * *
773 ATTTGGAACACTTGTTATTTGGGGCCTATCGTGGCCCATTAGTTACGTTTTGAATAGTCTTCGAT
1 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
* * * * ** *
838 TTGG-AAACCTCAAAGTTTTTCTTT-AAGTTGTTTATGGCCTAGTTATAATCATTTTGATGAGAT
66 TTGGCAAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
* * * *
901 TAGTCTACTATGAAGTTCTTAGCTC
130 TAGTCCACTGTGAAGTTTTTAGCTA
* * *
926 ATTTGGAACACTTATTATTTTGGGCCTATCGGGTCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
1 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
991 TTGG-AAACCTCAA
66 TTGGCAAACCTCAA
1004 AGTGTTTCTT
Statistics
Matches: 763, Mismatches: 74, Indels: 24
0.89 0.09 0.03
Matches are distributed among these distances:
152 1 0.00
153 161 0.21
154 432 0.57
155 148 0.19
156 21 0.03
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (154 bp):
ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATT
AGTCCACTGTGAAGTTTTTAGCTA
Found at i:560 original size:309 final size:308
Alignment explanation
Indices: 1--1013 Score: 1452
Period size: 309 Copynumber: 3.3 Consensus size: 308
* *
1 ATTTGGAACACTTGTTATTTTGGGCCTATGGGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGA
1 ATTTGGAACACTTGTTATTTTGGGCCTAT-CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGA
* * * * *
66 TTTGGCAAACCTCAATGCTATTGTTTCAATTGTTTATGGCCTAACTATAATTATTTTGGTGAGAT
65 TTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATTATTTTGGTGAGAT
* *
131 TGGTCCACTT-TGATGTTTTTAGC-ACATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
130 TAGTCCA-TTGTGAAGTTTTTAGCTA-ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
194 TTAGTGACATATTGAA-CCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
193 TTAGTGACATATTGAATCC-TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
258 GACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
257 GACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
*
310 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGAT
1 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
*
375 TTGG-AAACCTCAAAGCTTTTCTTTCCTACTTGTTTA-GGAACTAACTATAATTATTTTGATGAG
66 TTGGCAAACCTCAAAGCTTTTCTTTCC-A-TTGTTTATGG-ACTAACTATAATTATTTTGGTGAG
* *
438 ATTAGTCCATTGGGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTAGGCCT-TACGGGGCCC
128 ATTAGTCCATTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTAT-CGGGGCCC
* *
502 ATTAGTGGCATGTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
192 ATTAGTGACATATTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* *
567 GACTAACTATAATCATTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTA
257 GACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* * *
619 ACTTGGAACACTTGTTATTTGGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGAT
1 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
* * * * *
684 TTGGCAAACCTCAATGCATTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTAAAATT
66 TTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATTATTTTGGTGAGATT
* * * *
749 AGTCCACTGTGAAGTGTTTAGCTAATTTGGAACACTTGTTATTTGGGGCCTATCGTGGCCCATTA
131 AGTCCATTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * * ** * * * *
814 GTTACGTTTTGAATAGTCTTCGATTTGG-AAACCTCAAAGTTTTTCTTT-AAGTTGTTTATGGCC
196 GTGACATATTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGAC
** * * * *
877 TAGTTATAATCATTTTGATGAGATTAGTCTACTATGAAGTTCTTAGCTC
260 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* *
926 ATTTGGAACACTTATTATTTTGGGCCTATCGGGTCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
1 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
991 TTGG-AAACCTCAAAG-TGTTTCTT
66 TTGGCAAACCTCAAAGCT-TTTCTT
1014 AGTTTTTATT
Statistics
Matches: 634, Mismatches: 58, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
306 17 0.03
307 152 0.24
308 152 0.24
309 290 0.46
310 23 0.04
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (308 bp):
ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
TTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATTATTTTGGTGAGATT
AGTCCATTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
GTGACATATTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACT
AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
Done.