Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000796.1 Corchorus olitorius cultivar O-4 contig00796, 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: 2963
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Found at i:1020 original size:7 final size:7
Alignment explanation
Indices: 1010--1055 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
1000 AAAGTGAATG
1010 TGAAAAT
1 TGAAAAT
1017 TGAAAAT
1 TGAAAAT
*
1024 TG-AAAG
1 TGAAAAT
1030 TG--AAT
1 TGAAAAT
1035 GTGAAAAT
1 -TGAAAAT
1043 TGAAAAT
1 TGAAAAT
1050 TGAAAA
1 TGAAAA
1056 AAGCATAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 2 0.06
6 7 0.21
7 22 0.65
8 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (7 bp):
TGAAAAT
Found at i:1024 original size:26 final size:26
Alignment explanation
Indices: 991--1054 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
981 GAAAAAGAAG
991 TGAAAATTGAAAGTGAATGTGAAAAT
1 TGAAAATTGAAAGTGAATGTGAAAAT
1017 TGAAAATTGAAAGTGAATGTGAAAAT
1 TGAAAATTGAAAGTGAATGTGAAAAT
1043 TGAAAATTGAAA
1 TGAAAATTGAAA
1055 AAAGCATAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.27
Consensus pattern (26 bp):
TGAAAATTGAAAGTGAATGTGAAAAT
Found at i:1701 original size:8 final size:8
Alignment explanation
Indices: 1684--1719 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
1674 GATGATTTTC
1684 AAAAAA-A
1 AAAAAAGA
1691 AAAAAAG-
1 AAAAAAGA
1698 AAAAAAGA
1 AAAAAAGA
1706 AAAAAAGA
1 AAAAAAGA
1714 AAAAAA
1 AAAAAA
1720 AGAGAGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1708 original size:15 final size:14
Alignment explanation
Indices: 1684--1720 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
1674 GATGATTTTC
1684 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
1698 AAAAAAGAAAAAAAG
1 AAAAAA-AAAAAAAG
1713 AAAAAAAA
1 AAAAAAAA
1721 GAGAGACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:2848 original size:138 final size:139
Alignment explanation
Indices: 2305--2963 Score: 1097
Period size: 138 Copynumber: 4.7 Consensus size: 139
2295 GAAGACAAAA
2305 TTCATTTCATCAAGGTTTTAATCAAAGCTGCGTTTAAAATTTCAAAAACCTTGCTCAAGGTTGAG
1 TTCATTTCATCAA-GTTTTAATCAAAGCTGCGTTT-AAATTTCAAAAACCTTGCTCAAGGTTGAG
2370 TTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCT
64 TTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCT
*
2435 TCGGGTATCAT
129 CCGGGTATCAT
*
2446 TTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGT
1 TTCATTTCATCAAG-TTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGT
2511 TTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTC
65 TTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTC
2576 CGGGTATCAT
130 CGGGTATCAT
* * ** *
2586 CTCATTTCATCATGTTGTTAATCAAATTTGCGTTTAAATTTCAAATAAACCTTGCTCAAGGTCGA
1 TTCATTTCATCAAGTT-TTAATCAAAGCTGCGTTTAAATTTC-AA-AAACCTTGCTCAAGGTTGA
* * *
2651 GTTTGCATTTGTGAGACCACCAGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
63 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
2716 TCCGGGTATCAT
128 TCCGGGTATCAT
* *
2728 TTCATTTCATCAAGTTTTAATCAAAGCTGTGTTTAAATTTC-AAAACCTGGCTCAAGGTTGAGTT
1 TTCATTTCATCAAGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTT
* * *
2792 TGCATTTGTAAGACCTCCGGGCATAATTTCAGAAACCTCCGGGTATTAATTATGATAAATCCCCC
66 TGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCC
2857 GGGTATCAT
131 GGGTATCAT
* *
2866 TTCATTTCTTCATGTTTTAATCAAAGCTGCGTTTAAATTTC-AAAACCTTGCTCAAGGTTGAGTT
1 TTCATTTCATCAAGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTT
2930 TGCATTTGTAAGACCTCCGGGCACAATTTCAGAA
66 TGCATTTGTAAGACCTCCGGGCACAATTTCAGAA
Statistics
Matches: 485, Mismatches: 29, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
138 181 0.37
139 3 0.01
140 139 0.29
141 56 0.12
142 106 0.22
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (139 bp):
TTCATTTCATCAAGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTT
TGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCC
GGGTATCAT
Found at i:2850 original size:280 final size:279
Alignment explanation
Indices: 2306--2963 Score: 1124
Period size: 280 Copynumber: 2.4 Consensus size: 279
2296 AAGACAAAAT
*
2306 TCATTTCATCAAGGTTTTAATCAAAGCTGCGTTTAAAATTTCAAAAACCTTGCTCAAGGTTGAGT
1 TCATTTCATC-ATGTTTTAATCAAAGCTGCGTTT-AAATTTCAAAAACCTTGCTCAAGGTTGAGT
*
2371 TTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTT
64 TTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTC
*
2436 CGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAATTTCAAAAACCTTGCTC
129 CGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAATTTCAAAAACCTGGCTC
*
2501 AAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTG
194 AAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTATG
*
2566 ATAAATCCTCCGGGTATCATC
259 ATAAATCCCCCGGGTATCATC
** *
2587 TCATTTCATCATGTTGTTAATCAAATTTGCGTTTAAATTTCAAATAAACCTTGCTCAAGGTCGAG
1 TCATTTCATCATGTT-TTAATCAAAGCTGCGTTTAAATTTC-AA-AAACCTTGCTCAAGGTTGAG
* * *
2652 TTTGCATTTGTGAGACCACCAGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCT
63 TTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCT
2717 CCGGGTATCATTTCATTTCATCAAG-TTTTAATCAAAGCTGTGTTTAAATTTC-AAAACCTGGCT
128 CCGGGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAATTTCAAAAACCTGGCT
*
2780 CAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCATAATTTCAGAAACCTCCGGGTATTAATTAT
193 CAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTAT
*
2845 GATAAATCCCCCGGGTATCATT
258 GATAAATCCCCCGGGTATCATC
*
2867 TCATTTCTTCATGTTTTAATCAAAGCTGCGTTTAAATTTC-AAAACCTTGCTCAAGGTTGAGTTT
1 TCATTTCATCATGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTT
2931 GCATTTGTAAGACCTCCGGGCACAATTTCAGAA
66 GCATTTGTAAGACCTCCGGGCACAATTTCAGAA
Statistics
Matches: 354, Mismatches: 20, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
276 52 0.15
277 1 0.00
279 23 0.06
280 118 0.33
281 55 0.16
282 105 0.30
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (279 bp):
TCATTTCATCATGTTTTAATCAAAGCTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTT
GCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCG
GGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGTGTTTAAATTTCAAAAACCTGGCTCAA
GGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTATGAT
AAATCCCCCGGGTATCATC
Done.