Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011628.1 Corchorus olitorius cultivar O-4 contig11661, 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, 851
Length: 1419
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Found at i:809 original size:290 final size:289
Alignment explanation
Indices: 1--1319 Score: 2281
Period size: 290 Copynumber: 4.6 Consensus size: 289
* *
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATACTTACTAGAAACGAT
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
*
66 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATG-AAAAAGGGGTACAACA
66 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGGGGTGCAACA
* * *
130 CGAGGACTTCCCAGGAGATCACCCATCCTAGTACTACTCTCGCCCAAGCACCCCTAACTGCGGAG
131 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
* *
195 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCTTCAGTCTTCACATAATAAATA
196 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATCAGTCTTCGCATAATAAATA
260 TATATAAGCACATCTCATTGGATACGGTG
261 TATATAAGCACATCTCATTGGATACGGTG
289 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
*
354 TAGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGGAAAAAGGGGTAGCAA
66 T-GTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGGGGT-GCAA
* *
419 CACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTATCTGCAG
129 CACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGG
* * * *
484 AGTTCTGCTGGGAACCGGTGCATTAGTGTTGGTATGATCGCACCCATCTGTCTTCGCATAATAAA
194 AGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATCAGTCTTCGCATAATAAA
549 TATATATAAGCACATCTCATTGGATACGGTG
259 TATATATAAGCACATCTCATTGGATACGGTG
* *
580 TATTTTTGCCGACATATGATCATACACGCCATAC-TTTGTAAGACTTAATGCTTACTTGAAACGA
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTG-AAGACTTAATGCTTACTTGAAACGA
644 TTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAG-AAATAAAAATGAAAAAAGAGTGGTGCA
65 TTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAG-G-GGTGCA
* *
708 ACACGAGGACTTCACAGGAGGTCACCCATCCTAGTACTACTCTCGCCAAAGCACGCTTAACTGCG
128 ACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCG
* *
773 GAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCAATCTGTCTTCGCATAATAA
193 GAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATCAGTCTTCGCATAATAA
838 ATATATATAAGCACATCTCATTGGATACGGTG
258 ATATATATAAGCACATCTCATTGGATACGGTG
* * *
870 TATTTTTGCCGACATATGATCATACACGCCATACGTTTGAAGACATAATGCTTACTTGAAACGAT
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
935 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAAT-AAAATGAAAAAAGGGGTGCAACA
66 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGGGGTGCAACA
*
999 CGAGGACTT-CCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGAAG
131 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
*
1063 TTATGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATCAGTCTTCGCATAATAAA-A
196 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATCAGTCTTCGCATAATAAATA
*
1127 TATATAAGCACATCTCATTGGATCCGGTG
261 TATATAAGCACATCTCATTGGATACGGTG
1156 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
*
1221 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAAAC
66 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGGGGTGC-AAC
*
1286 ACGAGGACTTCCCAAGAGGTCACCCATCCTAGTA
130 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTA
1320 AGAAGAAAAG
Statistics
Matches: 982, Mismatches: 38, Indels: 21
0.94 0.04 0.02
Matches are distributed among these distances:
286 132 0.13
287 130 0.13
288 95 0.10
289 87 0.09
290 315 0.32
291 223 0.23
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (289 bp):
CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGGGGTGCAACA
CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATCAGTCTTCGCATAATAAATA
TATATAAGCACATCTCATTGGATACGGTG
Found at i:1260 original size:581 final size:581
Alignment explanation
Indices: 1--1319 Score: 2291
Period size: 581 Copynumber: 2.3 Consensus size: 581
* *
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATACTTACTAGAAACGAT
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
*
66 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATG-AAAAAG-GGGTACAAC
66 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGAGGGTGCAAC
* *
129 ACGAGGACTTCCCAGGAGATCACCCATCCTAGTACTACTCTCGCCCAAGCACCCCTAACTGCGGA
131 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCAAAGCACCCCTAACTGCGGA
**
194 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCTTCAGTCTTCACATAATAAAT
196 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCAATCAGTCTTCACATAATAAAT
259 ATATATAAGCACATCTCATTGGATACGGTGCATTGTTGCCGACATATGATCATACACGCCATACG
261 ATATATAAGCACATCTCATTGGATACGGTGCATTGTTGCCGACATATGATCATACACGCCATACG
*
324 TTTGAAGACTTAATGCTTACTTGAAACGATTAGTCTACCATAAGAAATTTCGAAAGAAGAAGAAA
326 TTTGAAGACATAATGCTTACTTGAAACGATTAGTCTACCATAAGAAATTTCGAAAGAAGAAGAAA
*
389 AGAAAATAAAAATGGAAAAAGGGGTAGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTA
391 AGAAAATAAAAATGAAAAAAGGGGTAGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTA
* * * *
454 CTACTCTCGCCCAAGCACGCTTATCTGCAGAGTTCTGCTGGGAACCGGTGCATTAGTGTTGGTAT
456 CTACTCTCGCCCAAGCACGCTTAACTGCAGAGTTATGATGGGAACCGGTGCATTAGTGCTGGTAT
*
519 GATCGCACCCATCTGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTG
521 GATCGCACCCATCAGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTG
* *
580 TATTTTTGCCGACATATGATCATACACGCCATAC-TTTGTAAGACTTAATGCTTACTTGAAACGA
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTG-AAGACTTAATGCTTACTTGAAACGA
644 TTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAG-AAATAAAAATGAAAAAAGAGTGGTGCA
65 TTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGAG-GGTGCA
* * *
708 ACACGAGGACTTCACAGGAGGTCACCCATCCTAGTACTACTCTCGCCAAAGCACGCTTAACTGCG
129 ACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCAAAGCACCCCTAACTGCG
* *
773 GAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCAATCTGTCTTCGCATAATAA
194 GAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCAATCAGTCTTCACATAATAA
* *
838 ATATATATAAGCACATCTCATTGGATACGGTGTATTTTTGCCGACATATGATCATACACGCCATA
259 ATATATATAAGCACATCTCATTGGATACGGTGCATTGTTGCCGACATATGATCATACACGCCATA
903 CGTTTGAAGACATAATGCTTACTTGAAACGATT-GTCTACCATAAGAAATTTCGAAAGAAGAAGA
324 CGTTTGAAGACATAATGCTTACTTGAAACGATTAGTCTACCATAAGAAATTTCGAAAGAAGAAGA
967 AAAGAAAAT-AAAATGAAAAAAGGGGT-GCAACACGAGGACTT-CCAGGAGGTCACCCATCCTAG
389 AAAGAAAATAAAAATGAAAAAAGGGGTAGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAG
*
1029 TACTACTCTCGCCCAAGCACGCTTAACTGC-GAAGTTATGATGGGATCCGGTGCATTAGTGCTGG
454 TACTACTCTCGCCCAAGCACGCTTAACTGCAG-AGTTATGATGGGAACCGGTGCATTAGTGCTGG
*
1093 TATGATCGCACCCATCAGTCTTCGCATAATAAA-ATATATAAGCACATCTCATTGGATCCGGTG
518 TATGATCGCACCCATCAGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTG
1156 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
1 CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
1221 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAA-AGGGTGCAAA
66 TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGAGGGTGC-AA
*
1285 CACGAGGACTTCCCAAGAGGTCACCCATCCTAGTA
130 CACGAGGACTTCCCAGGAGGTCACCCATCCTAGTA
1320 AGAAGAAAAG
Statistics
Matches: 703, Mismatches: 29, Indels: 19
0.94 0.04 0.03
Matches are distributed among these distances:
575 5 0.01
576 161 0.23
577 131 0.19
578 30 0.04
579 114 0.16
580 41 0.06
581 221 0.31
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (581 bp):
CATTGTTGCCGACATATGATCATACACGCCATACGTTTGAAGACTTAATGCTTACTTGAAACGAT
TGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGAGGGTGCAAC
ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCAAAGCACCCCTAACTGCGGA
GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCAATCAGTCTTCACATAATAAAT
ATATATAAGCACATCTCATTGGATACGGTGCATTGTTGCCGACATATGATCATACACGCCATACG
TTTGAAGACATAATGCTTACTTGAAACGATTAGTCTACCATAAGAAATTTCGAAAGAAGAAGAAA
AGAAAATAAAAATGAAAAAAGGGGTAGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTA
CTACTCTCGCCCAAGCACGCTTAACTGCAGAGTTATGATGGGAACCGGTGCATTAGTGCTGGTAT
GATCGCACCCATCAGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTG
Found at i:1382 original size:72 final size:73
Alignment explanation
Indices: 1246--1391 Score: 258
Period size: 72 Copynumber: 2.0 Consensus size: 73
1236 ATTTCGAAAG
1246 AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAAACACGAGGACTTCCCAAGAGGTCACCC
1 AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAAACACGAGGACTTCCCAAGAGGTCACCC
1311 ATCCTAGT
66 ATCCTAGT
* * *
1319 AAGAAGAAAAGAAAATAAAAATGAATAAAGGGGTGC-AACACGAGGACTTCCCAGGAGGTCACCC
1 AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAAACACGAGGACTTCCCAAGAGGTCACCC
1383 ATCCTAGT
66 ATCCTAGT
1391 A
1 A
1392 CTACTCTCGC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 36 0.51
73 34 0.49
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (73 bp):
AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAAACACGAGGACTTCCCAAGAGGTCACCC
ATCCTAGT
Done.