Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024455.1 Corchorus olitorius cultivar O-4 contig24488, 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: 13570
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Found at i:975 original size:11 final size:11
Alignment explanation
Indices: 959--993 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
949 TAGGGTTTGC
959 TTTCTTTACTT
1 TTTCTTTACTT
*
970 TTTCTTTTCTT
1 TTTCTTTACTT
*
981 TTTATTTACTT
1 TTTCTTTACTT
992 TT
1 TT
994 CTAGTTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTACTT
Found at i:4522 original size:43 final size:42
Alignment explanation
Indices: 4461--4791 Score: 488
Period size: 43 Copynumber: 7.8 Consensus size: 42
4451 CCAATAACCA
*
4461 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTAT-TC
*
4504 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTC
*
4546 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATT-C
*
4589 AAAAGTCCTCAAACACATATATAACACAGAGGCA-C-CTATATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTAT-TC
* *
4631 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATT-C
* * *
4674 AAAGTCCTCAAACACATATATGACACAGAGGCATCTATA-TC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTC
*
4715 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATT-C
*
4758 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
4792 TTCTCCTTAT
Statistics
Matches: 261, Mismatches: 19, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
41 67 0.26
42 50 0.19
43 113 0.43
44 31 0.12
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.20
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTC
Found at i:4820 original size:84 final size:84
Alignment explanation
Indices: 4461--4791 Score: 583
Period size: 84 Copynumber: 3.9 Consensus size: 84
4451 CCAATAACCA
*
4461 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTA-TATCAAAGTCCCCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTA-CAAAGTCCTCAAACACATATAT
4525 AACACAGAGGCATCTATATTC
65 AACACAGAGGCATCTATA-TC
*
4546 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT
*
4611 AACACAGAGGCACCTATATC
65 AACACAGAGGCATCTATATC
* *
4631 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATG
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
4696 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
4715 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
4780 ACACAGAGGCAT
66 ACACAGAGGCAT
4792 TTCTCCTTAT
Statistics
Matches: 235, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
84 114 0.49
85 83 0.35
86 38 0.16
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:4820 original size:127 final size:128
Alignment explanation
Indices: 4458--4791 Score: 491
Period size: 127 Copynumber: 2.6 Consensus size: 128
4448 TACCCAATAA
4458 CCAAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATCAAAGTCCCCAAACACATAT
1 CCAAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATCAAAGTCCCCAAACACATAT
* * * * *
4523 ATAACACAGAGGCATCTATATTCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATT
66 ATAACACAGAGGCATCTCTATACAAAGTCCTC-AACACATATATAACACAGAGGCATCTATATT
* *
4587 CCAAAAGTCCTCAAACACATATATAACACAGAGGCA-C-CTATATCAAAGTCCCCAAACACATAT
1 CCAAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATCAAAGTCCCCAAACACATAT
* * *
4650 ATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATGACACAGAGGCATCTATA-T
66 ATAACACAGAGGCATCTCTA-TACAAAGTCCTC-AACACATATATAACACAGAGGCATCTATATT
*
4714 -C-AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TACAAAGTCCTCAAACACATA
1 CCAAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATAT-CAAAGTCCCCAAACACATA
4776 TATAACACAGAGGCAT
65 TATAACACAGAGGCAT
4792 TTCTCCTTAT
Statistics
Matches: 186, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
125 31 0.17
126 3 0.02
127 80 0.43
128 38 0.20
129 34 0.18
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (128 bp):
CCAAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATCAAAGTCCCCAAACACATAT
ATAACACAGAGGCATCTCTATACAAAGTCCTCAACACATATATAACACAGAGGCATCTATATT
Found at i:4864 original size:52 final size:54
Alignment explanation
Indices: 4786--4888 Score: 138
Period size: 52 Copynumber: 1.9 Consensus size: 54
4776 TATAACACAG
*
4786 AGGCATTTCTCCTTATGGCAAAGGCT-CATA-ATATACATGGGCCTTGCTATCA
1 AGGCATTTCTCCTTATGGCAAAGGCTACATATATACACATGGGCCTTGCTATCA
** *
4838 AGGCATTTCTTTTTGTGGCAAAGGCTCAACATATATACACATGGGCCTTGC
1 AGGCATTTCTCCTTATGGCAAAGGCT--ACATATATACACATGGGCCTTGC
4889 CACCAAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
52 23 0.53
55 4 0.09
56 16 0.37
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (54 bp):
AGGCATTTCTCCTTATGGCAAAGGCTACATATATACACATGGGCCTTGCTATCA
Found at i:4912 original size:2 final size:2
Alignment explanation
Indices: 4905--4931 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4895 ATTCCTATCT
4905 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4932 GTAACAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12110 original size:16 final size:15
Alignment explanation
Indices: 12089--12131 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
12079 TTACTTTGTT
12089 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
12105 TTGTTTTTCTGTTTAA
1 TTG-TTTTCTGTTTAA
12121 TTGTTTTCTGT
1 TTGTTTTCTGT
12132 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:13504 original size:16 final size:16
Alignment explanation
Indices: 13485--13528 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
13475 AAATTTTGGG
*
13485 TACCCGAACCCGAAAT
1 TACCCGAACCCGAAAC
*
13501 TACCCGAATCC-AAAC
1 TACCCGAACCCGAAAC
*
13516 GACCCGAACCCGA
1 TACCCGAACCCGA
13529 TCAACCCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.36, C:0.41, G:0.14, T:0.09
Consensus pattern (16 bp):
TACCCGAACCCGAAAC
Done.