Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009675.1 Corchorus olitorius cultivar O-4 contig09707, 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: 9974
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Found at i:173 original size:17 final size:17
Alignment explanation
Indices: 151--184 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
141 TAAAGGTAAT
151 CTACTAAAACTAAATGC
1 CTACTAAAACTAAATGC
168 CTACTAAAACTAAATGC
1 CTACTAAAACTAAATGC
185 TAACGTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (17 bp):
CTACTAAAACTAAATGC
Found at i:612 original size:50 final size:50
Alignment explanation
Indices: 491--681 Score: 274
Period size: 50 Copynumber: 3.8 Consensus size: 50
481 TCGAAATGGG
*
491 TCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAAGGA
1 TCGTCTCCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTT--AAAAGGA
* * * *
543 CCGTCTTCCGCTTATCCTTTGAACTGTCTTCCCATTCAATCTTGAAAGGA
1 TCGTCTCCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGA
*
593 TCGTCTCCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGAA
1 TCGTCTCCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGA
* * * *
643 ACGTCTCCCGCTAATCCTTTGAATTGTCTTCCAACTCAA
1 TCGTCTCCCGCTTATCCTTTGAACTGTCTTCCAATTCAA
682 CGTCGAGAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 86 0.68
52 41 0.32
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (50 bp):
TCGTCTCCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGA
Found at i:1040 original size:64 final size:64
Alignment explanation
Indices: 914--1596 Score: 879
Period size: 64 Copynumber: 10.6 Consensus size: 64
904 CCGACGCATC
* * *
914 TCTTAACAAGATCGTCTTCCGATCAAT-TTCTGAAACCTT-TTCGAGAAACTATCTTCTGGTGTA
1 TCTTGACAAGATCGTCTTCCGATC-ATCTTCTGAAA-ATTCTT-GAGAAACCATCTTCTGGTGTA
977 CT
63 CT
* * *
979 TCTTGACTAGATTGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
** * * * *
1043 TCTTGGTAAGATCGTTTTTCGATCAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
* *
1107 TCTTGACAAGATTGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
* * * * *
1171 TCTTGACAAGATTGTCTTCCGATCAACTTCTGAAAA-CCTTGAGAAACCATCTTCTGGTATGCT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
* * * * * *
1234 TCTTGACAAGAACGTCTTTCGATTAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGTATACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
* * * *
1298 TCTTGACAAGATCGTCTTCTGATCAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
* * *
1362 TCCTGAAAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
* * * * * * *
1426 TCTTGACAAGATCGTCTTCTGATCAACTTTTGAAAACTT-TTTAAAAACCATCTTCTAGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAA-TTCTTGAGAAACCATCTTCTGGTGTACT
* * * * * *
1490 TCTTTGACAAGATCGCCTTCCGATCAACTTCTGAAAACTCTTAAGACACCATCTTCTGGCGTACT
1 TC-TTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
1555 TCTTCGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTT
1 TCTT-GACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTT
1597 TCTAGCAAAC
Statistics
Matches: 544, Mismatches: 67, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
63 54 0.10
64 369 0.68
65 121 0.22
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.36
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACT
Found at i:1350 original size:255 final size:254
Alignment explanation
Indices: 914--1596 Score: 940
Period size: 255 Copynumber: 2.7 Consensus size: 254
904 CCGACGCATC
* * * *
914 TCTTAACAAGATCGTCTTCCGATCAATTTCTG-AAACCTTTTCGAGAAACTATCTTCTGGTGTAC
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACC--TT-GAGAAACCATCTTCTGGTAT-C
* * * * *
978 TTCTTGACTAGATTGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
62 TTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
** * *
1043 TCTTGGTAAGATCGT-TTTTCGATCAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
127 TCTTGACAAGATCGTCTTCT-GATCAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGCGTACT
* * *
1107 TCTTGACAAGATTGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
191 TCCTGAAAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
*
1171 TCTTGACAAGATTGTCTTCCGATCAACTTCTGAAAACCTTGAGAAACCATCTTCTGGTATGCTTC
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACCTTGAGAAACCATCTTCTGGTAT-CTTC
* * * * *
1236 TTGACAAGAACGTCTTTCGATTAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGTATACTTCT
65 TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCT
1301 TGACAAGATCGTCTTCTGATCAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGCGTACTTCCT
130 TGACAAGATCGTCTTCTGATCAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGCGTACTTCCT
1366 GAAAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
195 GAAAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
* * * * *
1426 TCTTGACAAGATCGTCTTCTGATCAACTTTTGAAAACTTTTTAAAAACCATCTTCTAGCGTA-CT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAAC-CTTGAGAAACCATCTTCT-G-GTATCT
* * * *
1490 TCTTTGACAAGATCGCCTTCCGATCAACTTCTGAAAACTCTTAAGACACCATCTTCTGGCGTACT
63 TC-TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * *
1555 TCTTCGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTT
127 TCTT-GACAAGATCGTCTTCTGATCAGCTTCTGAAAACTCTT
1597 TCTAGCAAAC
Statistics
Matches: 379, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
255 226 0.60
256 24 0.06
257 87 0.23
258 42 0.11
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.36
Consensus pattern (254 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACCTTGAGAAACCATCTTCTGGTATCTTCT
TGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTT
GACAAGATCGTCTTCTGATCAGCTTCTGAAAACTCTTGAGAAACCATCTTCTGGCGTACTTCCTG
AAAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
Found at i:1658 original size:67 final size:67
Alignment explanation
Indices: 1564--1822 Score: 270
Period size: 67 Copynumber: 3.7 Consensus size: 67
1554 TTCTTCGACA
* * * * * *
1564 AGATCGTCTTCCGATCATC-TTCTGAAAATTCTTTCTAGCAAACCATTTTTCGATTTGTTTCTTA
1 AGATTGTCTTCCAATCAACATT-TGAAAATTCTTTCTAGCAAACCATCTTCCGATTTATTTCTTA
1628 ATG
65 ATG
* * * * *
1631 AGATTGTCTTCCAATCAACATTTGAAAATTATTTCTAGCAAACCGTCTTCCGGTGTATTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCATCTTCCGATTTATTTCTTAA
1696 TG
66 TG
* * * *
1698 AGATTGTCATCCAATCAACATTT-AAAATTCTTTCTAGCAAACCGTCTTCCAATATTCTTCTAAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCATCTTCCGAT-TTATT-T---
*
1762 AAACCTTAACG
61 ----CTTAATG
1773 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCATCTTC
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCATCTTC
1823 TGGTGTATCA
Statistics
Matches: 160, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
66 27 0.17
67 78 0.49
68 2 0.01
75 28 0.17
76 25 0.16
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (67 bp):
AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCATCTTCCGATTTATTTCTTAA
TG
Found at i:1836 original size:43 final size:43
Alignment explanation
Indices: 1786--1871 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1776 TTGTCTTCCA
*
1786 ATCAACATTTGAAAATTCTTTCTAGCAAACCATCTTCTGGTGT
1 ATCAACATTTGAAAATTCTTTCTAACAAACCATCTTCTGGTGT
1829 ATCAACATTTGAAAATTCTTTCTAACAAACCATCTTCTGGTGT
1 ATCAACATTTGAAAATTCTTTCTAACAAACCATCTTCTGGTGT
1872 TCTTCTAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.37
Consensus pattern (43 bp):
ATCAACATTTGAAAATTCTTTCTAACAAACCATCTTCTGGTGT
Found at i:4624 original size:12 final size:12
Alignment explanation
Indices: 4607--4645 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
4597 TCTTAAAAGA
4607 TTCAAAACCTTT
1 TTCAAAACCTTT
4619 TTCAAAACCTATTT
1 TTCAAAACC--TTT
*
4633 TTGAAAACCTTT
1 TTCAAAACCTTT
4645 T
1 T
4646 CTTGAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (12 bp):
TTCAAAACCTTT
Found at i:4639 original size:14 final size:13
Alignment explanation
Indices: 4610--4653 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
4600 TAAAAGATTC
*
4610 AAAACC-TTTTTC
1 AAAACCTTTTTTG
4622 AAAACCTATTTTTG
1 AAAACCT-TTTTTG
4636 AAAACCTTTTCTTG
1 AAAACCTTTT-TTG
4650 AAAA
1 AAAA
4654 ACATGTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 3 0.11
14 19 0.68
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:8021 original size:9 final size:9
Alignment explanation
Indices: 8007--8033 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
7997 GCTTCAGGGC
8007 CAAATTGGA
1 CAAATTGGA
8016 CAAATTGGA
1 CAAATTGGA
8025 CAAATTGGA
1 CAAATTGGA
8034 AGGTCTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (9 bp):
CAAATTGGA
Done.