Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024168.1 Corchorus olitorius cultivar O-4 contig24201, 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: 12269
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:908 original size:69 final size:69
Alignment explanation
Indices: 625--1002 Score: 512
Period size: 69 Copynumber: 5.4 Consensus size: 69
615 TGGCTCAATC
* * * *
625 AGTTTGGCTTGTGGAAAAGCCTCTGCT-GCTTGGATGGAACCAAGGC-TAAACTGAGTCGTGTGG
1 AGTTTGGCTTGTGGAAAAGCCTATG-TGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGG
688 AAACG
65 AAACG
* * *
693 AGTTTGGCTTGTAGAAAAGCCTCTGCT-GTTTGGATGGAACCAAGGCTTTGAACTGACTCGTATG
1 AGTTTGGCTTGTGGAAAAGCCTATG-TGGCTTGGATGGAACCAAGGC-TTGAACTGACTCGTATG
757 GAAACG
64 GAAACG
** * *
763 AGTTTGGCTTGTGGAAAAGCCCCTG-GATGCTTGGATGGAACCAAAGCAAAATCTTGAAATGACT
1 AGTTTGGCTTGTGGAAAAGCCTATGTG--GCTTGGATGGAACC-AAG-----GCTTGAACTGACT
827 CGTATGGAAACG
58 CGTATGGAAACG
*
839 AGTTTGGCTTGTGGAAAATCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
1 AGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
904 AACG
66 AACG
908 AGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
1 AGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
*
973 AACA
66 AACG
977 AGTTTGGCTTGTGGAAAAGCCTATGT
1 AGTTTGGCTTGTGGAAAAGCCTATGT
1003 TGATAATTGA
Statistics
Matches: 281, Mismatches: 17, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
68 44 0.16
69 116 0.41
70 42 0.15
71 13 0.05
72 3 0.01
74 3 0.01
75 14 0.05
76 44 0.16
77 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (69 bp):
AGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
AACG
Found at i:1014 original size:50 final size:50
Alignment explanation
Indices: 960--1246 Score: 468
Period size: 50 Copynumber: 5.8 Consensus size: 50
950 AGGCTTGAAC
*
960 TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
1010 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
1060 TGACTCGTATGGAAACAAGTTTGGTTTGTGGAAAA-ACTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
1109 TGACTCGTATGGAAACGAGTTTGGCTTGTGGGAAAGCCTATGTCGATAAC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
1159 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTCGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
1209 TGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1247 AAAGCATTCA
Statistics
Matches: 220, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
49 45 0.20
50 175 0.80
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:1133 original size:99 final size:100
Alignment explanation
Indices: 957--1246 Score: 483
Period size: 99 Copynumber: 2.9 Consensus size: 100
947 CCAAGGCTTG
957 AACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGG
1 AACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGG
* *
1022 AAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGAT
66 AAACGAGTTTGGCTTGTGGAAAAGCCTATGTCGAT
* * *
1057 AATTGACTCGTATGGAAACAAGTTTGGTTTGTGGAAAA-ACTATGTTGATAATTGACTCGTATGG
1 AACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGG
*
1121 AAACGAGTTTGGCTTGTGGGAAAGCCTATGTCGAT
66 AAACGAGTTTGGCTTGTGGAAAAGCCTATGTCGAT
* *
1156 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTCGATAATTGACTCGTATGG
1 AACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGG
* *
1221 AAACGAGTTTGACTTATGGAAAAGCC
66 AAACGAGTTTGGCTTGTGGAAAAGCC
1247 AAAGCATTCA
Statistics
Matches: 175, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
99 92 0.53
100 83 0.47
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (100 bp):
AACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGG
AAACGAGTTTGGCTTGTGGAAAAGCCTATGTCGAT
Found at i:1157 original size:149 final size:149
Alignment explanation
Indices: 960--1231 Score: 481
Period size: 149 Copynumber: 1.8 Consensus size: 149
950 AGGCTTGAAC
* *
960 TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTCGATAACTGACTCGTATGGAAA
*
1025 CGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACAAGTTTGGTTTGTG
66 CGAGCTTGGCTTGTGGAAAAGCCTATGTCGATAATTGACTCGTATGGAAACAAGTTTGGTTTGTG
1090 GAAAAACTATGTTGATAAT
131 GAAAAACTATGTTGATAAT
* *
1109 TGACTCGTATGGAAACGAGTTTGGCTTGTGGGAAAGCCTATGTCGATAACTGACTCGTATGGAAA
1 TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTCGATAACTGACTCGTATGGAAA
* *
1174 CGAGTTTGGCTTGTGGAAAAGCCTATGTCGATAATTGACTCGTATGGAAACGAGTTTG
66 CGAGCTTGGCTTGTGGAAAAGCCTATGTCGATAATTGACTCGTATGGAAACAAGTTTG
1232 ACTTATGGAA
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
149 116 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.31
Consensus pattern (149 bp):
TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTATGTCGATAACTGACTCGTATGGAAA
CGAGCTTGGCTTGTGGAAAAGCCTATGTCGATAATTGACTCGTATGGAAACAAGTTTGGTTTGTG
GAAAAACTATGTTGATAAT
Found at i:2546 original size:6 final size:6
Alignment explanation
Indices: 2535--2570 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2525 ATCCATTCTC
2535 TTTTGA TTTTGA TTTTGA -TTTGA TTTT-A TTTT-A TTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTT
2571 CATTTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 14 0.48
6 15 0.52
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (6 bp):
TTTTGA
Found at i:2570 original size:10 final size:10
Alignment explanation
Indices: 2535--2595 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
2525 ATCCATTCTC
2535 TTTTGATTTTGA
1 TTTT-ATTTT-A
*
2547 TTTTGATTTGA
1 TTTT-ATTTTA
2558 TTTTATTTTA
1 TTTTATTTTA
*
2568 TTTCATTTT-
1 TTTTATTTTA
* *
2577 TTTGATTTTT
1 TTTTATTTTA
2587 TTTTATTTT
1 TTTTATTTT
2596 TTATTTTCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 8 0.19
10 21 0.49
11 5 0.12
12 9 0.21
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:2634 original size:20 final size:19
Alignment explanation
Indices: 2582--2630 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2572 ATTTTTTTGA
*
2582 TTTTTTTTT-ATTTTTTAT
1 TTTTTTTTTGATTTATTAT
*
2600 TTTCTCTTTTGATTTATTAT
1 TTT-TTTTTTGATTTATTAT
2620 TTTTTTTTTGA
1 TTTTTTTTTGA
2631 ATTTCTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 3 0.12
19 12 0.46
20 11 0.42
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTGATTTATTAT
Found at i:7376 original size:22 final size:22
Alignment explanation
Indices: 7332--7383 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
7322 GGTCTTGCGC
* * *
7332 GGCATGTCTTGGCCTGGTACGG
1 GGCATGGCTCGGCCTGGCACGG
* *
7354 GGCGTGGCTCGGCCTGGCGCGG
1 GGCATGGCTCGGCCTGGCACGG
7376 GGCATGGC
1 GGCATGGC
7384 CGAGTCATGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.06, C:0.27, G:0.48, T:0.19
Consensus pattern (22 bp):
GGCATGGCTCGGCCTGGCACGG
Done.