Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022338.1 Corchorus olitorius cultivar O-4 contig22371, 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: 1884
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Found at i:297 original size:154 final size:153
Alignment explanation
Indices: 1--1884 Score: 2748
Period size: 154 Copynumber: 12.3 Consensus size: 153
*
1 AAGACGATTCCAAAACGTCACTAATGGTCCC-GATAGG-CC-AAAT-ACAAGT-TTCCAAATGAG
1 AAGACGATT-CAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * *
61 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGGTTATAGTTAGGCCATACACAATGGAATG
65 CTAAAAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCATAAACAATGGAAAG
*
126 AAAAGCATTGAGCTTTGCCAAATCG
129 AAAAGCATTGAGGTTTGCCAAATCG
* * * * *
151 AAGACAATTCAAAACATCACTAATGGTCCCCGATAGGCGCAAAATAACAAGTGTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
216 TAAAAACTTCACACTGGACTAATCTCACCAAATGATTATAGTTTGGCCATAAATAATGGAAAGAA
66 TAAAAACTTCACAGTGGACTAATCTCACCAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
281 AAGCATCGAAGGTTTG-CAAATCG
131 AAGCATTG-AGGTTTGCCAAATCG
* ** * * * *
304 AAGACTATTCAAAACGGAACTAATGGGCCCCGATAGGGCCAAAATAAAAAGTGTTCCAAATGAGT
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
369 TAAAAATTTCACAGTGGATTAATCTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-
66 TAAAAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCATAAACAATGGAAAGA
*
433 AAAGACATCGAAGG-TTGCCAAATCG
130 AAAG-CATTG-AGGTTTGCCAAATCG
* * *
458 AAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTCTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* *
523 TAAAACCTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
66 TAAAAACTTCACAGTGGACTAATCTCAC-CAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
*
588 AACGCATTGAGGTTTGCCAAATCG
130 AAAGCATTGAGGTTTGCCAAATCG
* *
612 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGACCAAAATAACAGGTGTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* *
677 TAAAAACTTCACAGTGGACTGATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
66 TAAAAACTTCACAGTGGACTAATCTCAC-CAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* *
742 AAAGCATCGAGGGTTGCCAAATCG
130 AAAGCATTGAGGTTTGCCAAATCG
** * * * *
766 AAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACATGTGTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* *
831 TAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATACTTAGGCCATAAACAATGGAAAGA
66 TAAAAACTTCACAGTGGACTAATCTCAC-CAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
896 AAAGCATTGAGGTTTGCCAAATCG
130 AAAGCATTGAGGTTTGCCAAATCG
*
920 AAGACGATTCAAAACGTCAGTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
*
985 TAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
66 TAAAAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCATAAACAATGGAAAGA
*
1050 AACGCATTGAGGTTTGCCAAATCG
130 AAAGCATTGAGGTTTGCCAAATCG
1074 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
1139 TAAAAACTTCACAGTGG-CTGATCTCACTAAAATGATTATAGTTAGACCATAAACAATGGAAAGA
66 TAAAAACTTCACAGTGGACTAATCTCAC-CAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* *
1203 AAAGCATCGAGGGTTGCCAAATCG
130 AAAGCATTGAGGTTTGCCAAATCG
* ** * * * * *
1227 AAGAAGATTCAAAACGGAACTAATGGACCCCGAAAGGCAC-AAATAACAAGTGTTCCAAATTAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* ** *
1291 TAAAACCTTCACAGTGGACTAGCCTCACTAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
66 TAAAAACTTCACAGTGGACTAATCTCACCAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * *
1356 ACGCATTGAAGTTTGCGAAATCA
131 AAGCATTGAGGTTTGCCAAATCG
* *
1379 AAGATGATTACAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAGGTGTTCCAAATGAG
1 AAGACGATT-CAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
* *
1444 CTAAAAACTTTACAGTGGACT-ATCTTACCAAAATG-TATATAGTTAGGCCATAAACAATGGAAA
65 CTAAAAACTTCACAGTGGACTAATCTCACC-AAATGAT-TATAGTTAGGCCATAAACAATGGAAA
* *
1507 GAAACGCATTGAGGTTTGCCAAATCA
128 GAAAAGCATTGAGGTTTGCCAAATCG
* * *
1533 AAGACGATTCAAAACGCCACTAATGGACCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
1598 TAAAAACTTTACAGTGGACTAATCTCGCCAAAATGATTATAGTTAGGCCATAAACGATGGAAAGA
66 TAAAAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCATAAACAATGGAAAGA
*
1663 AACGCATTGAGGTTTGCCAAATCG
130 AAAGCATTGAGGTTTGCCAAATCG
* *
1687 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAATAGGTGTTCCAAATGAGC
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* *
1752 TAAAAACTTCACAGTGGACTGATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
66 TAAAAACTTCACAGTGGACTAATCTCAC-CAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
1817 AAAGCATTGAGGTTTGCCAAATCG
130 AAAGCATTGAGGTTTGCCAAATCG
**
1841 AAGACGATTCAAAACGGAACTAATGGGCCCTGATAGGCCCAAAA
1 AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAA
Statistics
Matches: 1572, Mismatches: 140, Indels: 40
0.90 0.08 0.02
Matches are distributed among these distances:
149 20 0.01
150 14 0.01
151 1 0.00
152 103 0.07
153 348 0.22
154 1082 0.69
155 4 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (153 bp):
AAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
TAAAAACTTCACAGTGGACTAATCTCACCAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTTTGCCAAATCG
Done.