Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016193.1 Corchorus olitorius cultivar O-4 contig16226, 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, 926
Length: 1544
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:654 original size:320 final size:319
Alignment explanation
Indices: 1--859 Score: 1300
Period size: 320 Copynumber: 2.7 Consensus size: 319
1 ATGATCGAAAAAAACAAATCCTTATATCCAATATTGCAGAGCATTGGTTCGATGAATATAGATAT
1 ATGATCG-AAAAAACAAATCCTTATATCCAATATTGCAGAGCATTGGTTCGATGAATATAGATAT
66 TTCACGGAATCTTTACACCAGAAATCATGCAAAATTGAGACGGGGCCCCGGAACGCGTTTTTAGC
65 TTCACGGAATCTTTACACCAGAAATCATGCAAAATTGAGACGGGGCCCCGGAACGCGTTTTTAGC
*
131 AAAAACGTGATGGTTACTTCACGATTTCGACCAAAAACTGACCCGAAAAGTATTTTATCAATTTT
130 AAAAACGTGATGGTTACTTCACGATTTCGGCCAAAAACTGACCCGAAAAGTATTTTATCAATTTT
* *
196 TTCCACAATACTCAG-AAAAATATACAATTCAACGCCAAAAAGATTGACAAGCTTTTCACACTTC
195 TTCCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAAGATTGACAAGCTTTTCACACTTC
*
260 TAATATCGTTTTTCCATTTATTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAG
260 TAATATCGTTTTTCCATTTATATCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAG
* * * * * * *
320 ATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAG-ATTTGATTTGATGAATATAGATAT
1 ATGATCGAAAAAACAAATCCTTATATCCAATATTGCAGAGCA-TTGGTTCGATGAATATAGATAT
* * *** * * * * *
384 TTCAAGGAGTCTTTGTGCTAAAAATCATGTAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGC
65 TTCACGGAATCTTTACACCAGAAATCATGCAAAATTGAGACGGGGCCCCGGAACGCGTTTTTAG-
* * * *
449 CAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAA-T-TTTATACTCAA
129 CAAAAA-CGTGATGGTTACTTCACGATTTCGGCCAAAAACTGACCCGAAAAGTATTT-TA-TCAA
* * **
511 TTTTTTGCCACAATACACAGAAAAAATATATAATTCTACGCAAAAAATG-TTGACGGGCTTTTCA
191 TTTTTT-CCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAA-GATTGACAAGCTTTTCA
* * *
575 CGCTTCTAATATCGTTTTTCCATTT-TATCCGAATTAATTTCTAATTAAATCGAAACAAGATTGA
254 CACTTCTAATATCGTTTTTCCATTTATATCCGAATTAATTTCTAATTAAATCGAAACAAAATTCA
639 G
319 G
640 ATGATCGAAAAAACAAATCCTTATATCCAATATTGCAGAGCATTGGTTCGATGAATATAGATATT
1 ATGATCGAAAAAACAAATCCTTATATCCAATATTGCAGAGCATTGGTTCGATGAATATAGATATT
*
705 TCACGGAATCTTTACACCAGAAATCATGCAAAATTGAGACGGGGCCCCAGAACGCGTTTTTAGCA
66 TCACGGAATCTTTACACCAGAAATCATGCAAAATTGAGACGGGGCCCCGGAACGCGTTTTTAGCA
770 AAAACGTGATGGTTACTTCACGATTTCGGCCAAAAACTGACCCGAAAAGTATTTTATCAATTTTT
131 AAAACGTGATGGTTACTTCACGATTTCGGCCAAAAACTGACCCGAAAAGTATTTTATCAATTTTT
835 TCCACAATACTCAGAAAAAATATAT
196 TCCACAATACTCAGAAAAAATATAT
860 CCAATGTGGC
Statistics
Matches: 473, Mismatches: 55, Indels: 25
0.86 0.10 0.05
Matches are distributed among these distances:
317 4 0.01
318 165 0.35
319 44 0.09
320 195 0.41
321 64 0.14
322 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (319 bp):
ATGATCGAAAAAACAAATCCTTATATCCAATATTGCAGAGCATTGGTTCGATGAATATAGATATT
TCACGGAATCTTTACACCAGAAATCATGCAAAATTGAGACGGGGCCCCGGAACGCGTTTTTAGCA
AAAACGTGATGGTTACTTCACGATTTCGGCCAAAAACTGACCCGAAAAGTATTTTATCAATTTTT
TCCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAAGATTGACAAGCTTTTCACACTTCT
AATATCGTTTTTCCATTTATATCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAG
Found at i:1494 original size:320 final size:320
Alignment explanation
Indices: 855--1544 Score: 989
Period size: 320 Copynumber: 2.1 Consensus size: 320
845 TCAGAAAAAA
* * * * * * * *
855 TATATCCAATGTGGCTGAGATTTGATTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCTAAA
1 TATATCCAATATGGC-AATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCAAA
* * *
920 AATCATGTAAAAATGAGTCGAGGCTCCGGAATGCGATTTTAGCCAAAAACCGTGATAGTTAGTAC
65 AATCATGCAAAAATGAGACGAGGCCCCGGAATGCGATTTTAGCCAAAAACCGTGATAGTTAGTAC
985 ACGATTTCGGCTAAAAACTGACCCGAAAATGTTATACTCAATTTTTTGCCACAATACACAGAAAA
130 ACGATTTCGGCTAAAAACTGACCCGAAAATGTTATACTCAATTTTTTGCCACAATACACAGAAAA
* * *
1050 AATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATTGTTTTTCCAATT
195 AATATATAATTCAAAGCCAAAAAGATAGACGGGCTTTTCACACTTCTAATATCGTTTTTCCAATT
1115 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCT
260 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCT
* *
1176 TATATCCAATATTGC-ATAGCTTTGGTTCGATGAATATAGATATTTCATGGAGTCTTTACACCAA
1 TATATCCAATATGGCAATA--TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCAA
* *
1240 AAATCATGCAAAATTGAGACGGGGCCCCGGAATGC-ATTTTTAG-CAAAAACCGTGAT-GTTTAG
64 AAATCATGCAAAAATGAGACGAGGCCCCGGAATGCGA-TTTTAGCCAAAAACCGTGATAG-TTAG
* ** *
1302 TACACGATTTCGGAC-AAAAACTGACCCGAAAA-GTATTTTGTCAATTTTTTGCCACAATACTCA
127 TACACGATTTCGG-CTAAAAACTGACCCGAAAATGT-TATACTCAATTTTTTGCCACAATACACA
* * * *
1365 TAAATAATATATAATTCAAATCCAAAAAGATAGACGGGCTTTTCACGCTTCTAATATCGTTTTTC
190 GAAAAAATATATAATTCAAAGCCAAAAAGATAGACGGGCTTTTCACACTTCTAATATCGTTTTTC
*
1430 C-ATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAAGCAAATC
255 CAATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAA-CAAATC
1494 CT
319 CT
* *
1496 TATATCCATTATGGCTAATATTTGGTTCAATGAATATAGATATTTCAAG
1 TATATCCAATATGGC-AATATTTGGTTCGATGAATATAGATATTTCAAG
Statistics
Matches: 330, Mismatches: 30, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
319 60 0.18
320 179 0.54
321 88 0.27
322 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (320 bp):
TATATCCAATATGGCAATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAA
ATCATGCAAAAATGAGACGAGGCCCCGGAATGCGATTTTAGCCAAAAACCGTGATAGTTAGTACA
CGATTTCGGCTAAAAACTGACCCGAAAATGTTATACTCAATTTTTTGCCACAATACACAGAAAAA
ATATATAATTCAAAGCCAAAAAGATAGACGGGCTTTTCACACTTCTAATATCGTTTTTCCAATTT
TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCT
Done.