Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011509.1 Corchorus olitorius cultivar O-4 contig11542, 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, 925
Length: 1542
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Found at i:967 original size:52 final size:52
Alignment explanation
Indices: 907--1007 Score: 202
Period size: 52 Copynumber: 1.9 Consensus size: 52
897 AACTTCACAG
907 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAACAA
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAACAA
959 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1008 GAAAAAGCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.24
Consensus pattern (52 bp):
TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAACAA
Found at i:1110 original size:207 final size:206
Alignment explanation
Indices: 753--1162 Score: 666
Period size: 207 Copynumber: 2.0 Consensus size: 206
743 AACTTCACAG
753 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAGGGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAGGGGT
* * *
818 TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGTCCCAATAGGCCCAAAATAAAAAGTGTT
66 TACCAAATCGAAGACAATTCAAAACGGAACTAATGGGTCCCAATAGACCCAAAATAAAAAGTGTT
*
883 CCAAATGAGCTAATAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
131 CCAAATGAGCTAATAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
948 AATGGAAACAA
196 AATGGAAACAA
959 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGCATT-GAGG
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTAG-GG
* ** *
1023 TTTACCAAATCGAAGACAATTCAAAAC-GACACTAAT-GGTCACCGTTAGACCCAAAATAACAAG
64 GTTACCAAATCGAAGACAATTCAAAACGGA-ACTAATGGGTC-CCAATAGACCCAAAATAAAAAG
*
1086 TGTTCCAAATGAGCTTAA-AACTTCATACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
127 TGTTCCAAATGAGC-TAATAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
1150 TAAACAATGGAAA
191 TAAACAATGGAAA
1163 GAAAAGCATT
Statistics
Matches: 190, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
206 57 0.30
207 130 0.68
208 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.22
Consensus pattern (206 bp):
TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAGGGGT
TACCAAATCGAAGACAATTCAAAACGGAACTAATGGGTCCCAATAGACCCAAAATAAAAAGTGTT
CCAAATGAGCTAATAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
AATGGAAACAA
Found at i:1519 original size:155 final size:155
Alignment explanation
Indices: 959--1542 Score: 849
Period size: 154 Copynumber: 3.8 Consensus size: 155
949 ATGGAAACAA
*
959 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGCATTGAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATCGAGGT
* * * * * *
1024 TTACCAAATCGAAGACAATTCAAAACGACACTAATGGTCACCGTTAGACCCAAAATAACAAGTGT
65 TTGCCAAATCGAAGACGATTCAAAACGACACTAATGGTCCCCGATAGGCCCAAAATAAAAAGTGT
* *
1089 TCCAAATGAGCTTAAAACTTCATAC-
130 TCCAAATGAGCTAAAAACTTCACACG
*
1114 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGTT
* * *
1179 TGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATATGCCCAAAATAAAAAGTTTT
66 TGCCAAATCGAAGACGATTCAAAACGACACTAATGGTCCCCGATAGGCCCAAAATAAAAAGTGTT
*
1244 CCAAATGAGCTAAAATCTTCACA-G
131 CCAAATGAGCTAAAAACTTCACACG
1268 TGGACTAATCTCACC-AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCG-AGGT
* * * * *
1332 TT-CCAAATCGAAGACGATTCAAAATGGA-ACTAATGGGCCCCGATAGGGCCAGATTAAAAAGTG
65 TTGCCAAATCGAAGACGATTCAAAA-CGACACTAATGGTCCCCGATAGGCCCAAAATAAAAAGTG
1395 TTCCAAATGAGCTAAAAACTTCACACG
129 TTCCAAATGAGCTAAAAACTTCACACG
* *
1422 TGGACTAATCTCACCAAAATGATTTTAGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGG-
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCG-AGGT
* *
1486 TTGCCAAATCGAACACGTTTTCAAAACG-CACTAATGGTCCCCGGAATAGGCCCAAAA
65 TTGCCAAATCGAAGACG-ATTCAAAACGACACTAATGGTCCCC-G-ATAGGCCCAAAA
Statistics
Matches: 388, Mismatches: 31, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
153 118 0.30
154 131 0.34
155 122 0.31
156 8 0.02
157 9 0.02
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (155 bp):
TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGTT
TGCCAAATCGAAGACGATTCAAAACGACACTAATGGTCCCCGATAGGCCCAAAATAAAAAGTGTT
CCAAATGAGCTAAAAACTTCACACG
Done.