Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008325.1 Corchorus olitorius cultivar O-4 contig08352, 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, 958
Length: 1598
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:131 original size:31 final size:29
Alignment explanation
Indices: 96--161 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 29
86 CCTAACGGAC
*
96 TATATCCTTGATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCG-TTTT-GTAACGT
*
127 TATATCCTTAATTGCTTGTTTTGTAACGT
1 TATATCCTTAATTGCTCGTTTTGTAACGT
156 TATATC
1 TATATC
162 TCAAATTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (29 bp):
TATATCCTTAATTGCTCGTTTTGTAACGT
Found at i:168 original size:29 final size:31
Alignment explanation
Indices: 96--170 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
86 CCTAACGGAC
**
96 TATATCCTTGATTGCTCGCTTTTCGTAACGT
1 TATATCCTAAATTGCTCGCTTTTCGTAACGT
* *
127 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTAAATTGCTCGCTTTTCGTAACGT
156 TATAT-CTCAAATTGC
1 TATATCCT-AAATTGC
171 ATTTTGCAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.05
29 18 0.45
30 4 0.10
31 16 0.40
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (31 bp):
TATATCCTAAATTGCTCGCTTTTCGTAACGT
Found at i:1089 original size:306 final size:302
Alignment explanation
Indices: 503--1240 Score: 941
Period size: 305 Copynumber: 2.4 Consensus size: 302
493 CATATTTTTT
* * * *
503 AATTAATTTCTAATTAAATCAAAACAAGATTTAAATACTCGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * *
568 ATGTCTGAGATTTGATTAGAT-AATATAGATATTTCAAGGAGTTTCGGCG-CAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAA
* * * * *
631 AACTGACCTGGGGACCGGAATACGTTTTTAGCCAAAAACCATGATGGTAAAAATGACCCGAAAGA
131 AACAGACCTGGGCACCAGAACACGTTTTTAGCCAAAAACCATGATGGTAAAAATAACCCGAAAGA
* * *
696 TTTTTCATCAATTTTTGGCAAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGA
196 TTTTTCATCAATTTTTGGCAAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGCA
* * *
761 GGACTTTTCACGCTTTTAATATCGTTTTTAATATTTTTTTATG
261 GGACTTTTCACGCTTCTAATATCGTTTTT-ACATTTTTTTACG
* *
804 AATTAATTTCTAATTAAATCGAAGCAAAATTCAGATGCAT-GTAAAAACAAATCCTTAAATCCAA
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAAATCCTTAAATCCAA
* *
868 TGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAATCTCAGCGCCAAAAATCATGCA
65 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCA
* * * *
933 AAACAGAGCC-GCGGCCCCAGAACGCGTTTTTAGTCAAAAATCATGATGGCTAAAAACTAACCCG
130 AAACAGA-CCTG-GGCACCAGAACACGTTTTTAGCCAAAAACCATGATGG-TAAAAA-TAACCCG
* * * *
997 AAACG-TTTATTC-TCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAA
191 AAA-GATTT-TTCATCAATTTTTGGCAAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
* * *
1060 GATTGACAGG-CTTTTCATGCTTCTAATATCGTTTTTCCATTTTTTTCCG
254 GATTG-CAGGACTTTTCACGCTTCTAATATCGTTTTTACATTTTTTTACG
* * * * *
1109 AATTAATTTCTAATTAAATTGAAACAAGATTCCGATGCTCGTAAAAACAAATCATTATATCCCAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * ** *
1174 GTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAA
1239 AA
131 AA
1241 TTGAGCCGGG
Statistics
Matches: 377, Mismatches: 49, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
301 76 0.20
302 25 0.07
303 20 0.05
304 33 0.09
305 130 0.34
306 86 0.23
307 7 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.31
Consensus pattern (302 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCCAAAAATCATGCAA
AACAGACCTGGGCACCAGAACACGTTTTTAGCCAAAAACCATGATGGTAAAAATAACCCGAAAGA
TTTTTCATCAATTTTTGGCAAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGCA
GGACTTTTCACGCTTCTAATATCGTTTTTACATTTTTTTACG
Done.