Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022905.1 Corchorus olitorius cultivar O-4 contig22938, 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: 22219
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:714 original size:27 final size:28
Alignment explanation
Indices: 646--750 Score: 122
Period size: 28 Copynumber: 3.8 Consensus size: 28
636 AAAATGAGCT
* *
646 TAAAATGACCGAAATGCCCTTGAATGTG
1 TAAAATGACCAAAATGCCCCTGAATGTG
674 TAAAATGACCAAAATGCCCCTGAATGTG
1 TAAAATGACCAAAATGCCCCTGAATGTG
* * * * *
702 -CAAATGACTAAAATGCCCCTAGATTCTT
1 TAAAATGACCAAAATGCCCCT-GAATGTG
*
730 TAGAATGACCAAAATGCCCCT
1 TAAAATGACCAAAATGCCCCT
751 AGTTGATCCT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 18 0.28
28 30 0.46
29 17 0.26
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (28 bp):
TAAAATGACCAAAATGCCCCTGAATGTG
Found at i:5670 original size:19 final size:18
Alignment explanation
Indices: 5637--5673 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5627 TTGAAATAAT
5637 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
5655 TCTTCGAATTATCTTCAAA
1 TCTTC-AATGATCTTCAAA
5674 CCCGAACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7897 original size:26 final size:27
Alignment explanation
Indices: 7837--7909 Score: 103
Period size: 26 Copynumber: 2.7 Consensus size: 27
7827 TCAATTAAGA
* *
7837 AAATTACCAAAATACCCCTAAATGTAC
1 AAATGACCAAAATACCCCCAAATGTAC
*
7864 AAATGACCAAAATACCCCCGAAT-TAC
1 AAATGACCAAAATACCCCCAAATGTAC
*
7890 AAATGACCAAAATGCCCCCA
1 AAATGACCAAAATACCCCCA
7910 GGACACCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.47, C:0.30, G:0.07, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCAAATGTAC
Found at i:18446 original size:11 final size:11
Alignment explanation
Indices: 18430--18475 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
18420 AAAGAAAAAA
18430 AGCTAGGAAGG
1 AGCTAGGAAGG
18441 AGCTAGGAAGG
1 AGCTAGGAAGG
*
18452 ACCCTAGGAAGG
1 A-GCTAGGAAGG
18464 AGCTAGGAAGG
1 AGCTAGGAAGG
18475 A
1 A
18476 CTTAGTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.37, C:0.13, G:0.41, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:18458 original size:23 final size:23
Alignment explanation
Indices: 18432--18476 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
18422 AGAAAAAAAG
18432 CTAGGAAGGAGCTAGGAAGGACC
1 CTAGGAAGGAGCTAGGAAGGACC
18455 CTAGGAAGGAGCTAGGAAGGAC
1 CTAGGAAGGAGCTAGGAAGGAC
18477 TTAGTCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.40, T:0.09
Consensus pattern (23 bp):
CTAGGAAGGAGCTAGGAAGGACC
Found at i:18819 original size:21 final size:21
Alignment explanation
Indices: 18795--18907 Score: 167
Period size: 21 Copynumber: 5.4 Consensus size: 21
18785 CTTAGGCAAT
*
18795 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
18816 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
18837 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
18858 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
18879 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
18900 TCCAATGA
1 TCCAATGA
18908 ACTTCTAGCA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 84 0.97
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:19433 original size:154 final size:154
Alignment explanation
Indices: 19013--20168 Score: 1859
Period size: 154 Copynumber: 7.5 Consensus size: 154
19003 TTGGCGCATC
* * * * *
19013 AGTTAGGCCGTACACAATGGAAAGAAAAACATTGAAGTCTGCCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
* *
19078 TCACTAATGGTCTCCGATAGGCCCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTCACAGTG
66 TCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
19143 GACTAATCTCACCAAAATGATTAT
131 GACTAATCTCACCAAAATGATTAT
19167 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-GGTTTGCCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
** * * * * *
19231 GAACTAAGGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGAGCTCAAAACTTCACAGTG
66 TCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
19296 GACTAATCTCACCAAAATGATTAT
131 GACTAATCTCACCAAAATGATTAT
* *
19320 AGTTAGGCCGTACACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
*
19385 TCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTCACAGTG
66 TCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
19450 GACTAATCTCACCAAAATGATTAT
131 GACTAATCTCACCAAAATGATTAT
* * * * *
19474 AGTTAGGCCGTACACAATGGAAAGAAAGGCATCGAAGG-TTACCAAATCGAAGACGATTCAAAAC
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAAC
* *
19538 GTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
65 GTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
19603 GGACTAATCTCACCAAAATGATTAT
130 GGACTAATCTCACCAAAATGATTAT
*
19628 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
** * * * * *
19693 GAACTAATGGGCCTCGATTGGCACAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
66 TCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
19758 GACTAATCTCACCAAAATGATTAT
131 GACTAATCTCACCAAAATGATTAT
* *
19782 AGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGG-TTGCCAAATCGAAGACGATTCAAAAC
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAAC
*
19846 GTCACTAATGGTCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
65 GTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
19911 GGACTAATCTCACCAAAATGATTAT
130 GGACTAATCTCACCAAAATGATTAT
* * *
19936 AGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGGTTTGTCAAAATCGAAGACGATTCAAAA
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTG-CCAAATCGAAGACGATTCAAAA
* *
20001 CGTCACTAATGTTCTCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAAGCTAAAAACTTCACA
64 CGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG-AGCTAAAAACTTCACA
*
20066 GTGAACTAATCTCACCAAAATGATTAT
128 GTGGACTAATCTCACCAAAATGATTAT
* *
20093 AGTTAGGCCATAAACAATTGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
20158 TCACTAATGGT
66 TCACTAATGGT
20169 GATGCGCCAA
Statistics
Matches: 932, Mismatches: 63, Indels: 13
0.92 0.06 0.01
Matches are distributed among these distances:
153 143 0.15
154 602 0.65
155 42 0.05
156 73 0.08
157 72 0.08
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (154 bp):
AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
TCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
GACTAATCTCACCAAAATGATTAT
Done.