Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014109.1 Corchorus olitorius cultivar O-4 contig14142, 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: 71799
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:3991 original size:20 final size:21
Alignment explanation
Indices: 3951--3992 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3941 TTGATCCTTC
3951 GATTATTACCAACAGATATAAA
1 GATTATTACCAACA-ATATAAA
*
3973 GATTATTACCGAC-ATATAAA
1 GATTATTACCAACAATATAAA
3993 AAAGGACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
GATTATTACCAACAATATAAA
Found at i:36375 original size:13 final size:13
Alignment explanation
Indices: 36353--36383 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
36343 AAACGGAAAA
36353 TTCAGAAGTGTTT
1 TTCAGAAGTGTTT
*
36366 TTCAGGAGTGTTT
1 TTCAGAAGTGTTT
36379 TTCAG
1 TTCAG
36384 TTGTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (13 bp):
TTCAGAAGTGTTT
Found at i:37143 original size:7 final size:7
Alignment explanation
Indices: 37131--37155 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37121 TAATTAGAAA
37131 AAAAAAG
1 AAAAAAG
37138 AAAAAAG
1 AAAAAAG
37145 AAAAAAG
1 AAAAAAG
37152 AAAA
1 AAAA
37156 TGGCAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:42205 original size:23 final size:22
Alignment explanation
Indices: 42179--42224 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
42169 TTTAATTGAA
*
42179 TTGCTAAATATCGTCCCCCCTTT
1 TTGCTAAATACCG-CCCCCCTTT
**
42202 TTGCTAGTTACCGCCCCCCTTT
1 TTGCTAAATACCGCCCCCCTTT
42224 T
1 T
42225 GACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.13, C:0.37, G:0.11, T:0.39
Consensus pattern (22 bp):
TTGCTAAATACCGCCCCCCTTT
Found at i:55806 original size:6 final size:6
Alignment explanation
Indices: 55795--55853 Score: 100
Period size: 6 Copynumber: 9.7 Consensus size: 6
55785 GTGGGGAATT
*
55795 AGATTA AGATTA GGATTA AGATTA AGATTA AGATTA AGATTA AGATTAA
1 AGATTA AGATTA AGATTA AGATTA AGATTA AGATTA AGATTA AGATT-A
55844 AGATTA AGAT
1 AGATTA AGAT
55854 GAAGCCTAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
6 44 0.88
7 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (6 bp):
AGATTA
Found at i:62422 original size:21 final size:19
Alignment explanation
Indices: 62395--62453 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
62385 CGCTGTTTTA
62395 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
* * * *
62414 ACATGATCTAATTTGTATAGT
1 --ATAATCTCATCTGTACAGT
62435 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
62454 TGTCAAACAG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:70144 original size:161 final size:161
Alignment explanation
Indices: 69852--70171 Score: 446
Period size: 161 Copynumber: 2.0 Consensus size: 161
69842 TCGTAAAAAC
** * * *
69852 AAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTTTGGG
1 AAATCCTTAAATCCAATGTGAATGAGATTTGGTTAGACGAATATAGATATTTCAAGGAGTTTGAG
* * * *
69917 AGGCAAAAATCATGCAAAACAAAGCCGAGGACTCGTAACGTGTTATTAGCAAAATACTATGATGG
66 AGCCAAAAATCATGAAAAACAAAGCCGAGGACTCGTAACGCGTTATTAGCAAAATACTACGATGG
69982 TTAAGTACACGATTTCGGCTAAGATTTTGCAA
131 TT-AGTACACGATTTCGGCTAAGATTTTGCAA
*
70014 AAATCCTTAAATCTAATGTGAATGAGATTTGGTTAGACGAA-ATAGATATTTCAAGGAGTTTGAG
1 AAATCCTTAAATCCAATGTGAATGAGATTTGGTTAGACGAATATAGATATTTCAAGGAGTTTGAG
* ** * * * *
70078 AGCCAGAAATCATGAAAAACTCAGTCGGGGCCTCGTAACGCGTTTTTAGCCAAAAT-CTACGATG
66 AGCCAAAAATCATGAAAAACAAAGCCGAGGACTCGTAACGCGTTATTAG-CAAAATACTACGATG
*
70142 GTTAGTACACGATTTTGGCTAAGATTTTGC
130 GTTAGTACACGATTTCGGCTAAGATTTTGC
70172 GCAAACTGAC
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
160 26 0.19
161 70 0.50
162 43 0.31
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (161 bp):
AAATCCTTAAATCCAATGTGAATGAGATTTGGTTAGACGAATATAGATATTTCAAGGAGTTTGAG
AGCCAAAAATCATGAAAAACAAAGCCGAGGACTCGTAACGCGTTATTAGCAAAATACTACGATGG
TTAGTACACGATTTCGGCTAAGATTTTGCAA
Found at i:71336 original size:323 final size:320
Alignment explanation
Indices: 70603--71799 Score: 1787
Period size: 323 Copynumber: 3.7 Consensus size: 320
70593 TTTTTCCCGA
*
70603 AAAAAATATATAATTCAAAGCCAAAAAAAATT-AAGGGTTTTTTACGCTTCCAATATCGTTTTTC
1 AAAAAATATATAATTCAAAGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTTTC
* *
70667 CATTTTTTTTTCCGAATTTATTTCTAATTAAATCAAAACAAAATCTAGATGCTCGTAAAAAGAAA
66 CA--TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAAGAAA
* *
70732 TCCTTAAATCCAAATTTGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGC
129 TCCTTAAATCCAAATTAGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTTTCTGC
* * * ** *
70797 CAAAAATCATGTAAAACTAAGCCGGGGCCCCGAAACATGTTTTTAGCCAAAAAAAACGTGATGGT
194 CAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGCC--AAAAACCGTGATGGT
* * * *
70862 AGTACACGATTTCTGTTAAAAATTTACCCGAAAGCTTTTTTTCACAATTTTTGCCACACTACTCT
257 AGTACACGATTTCTGCTAAAAATTGACCCGAAAAC-TTTTTTCTC-ATTTTTGCCACACTACTCT
70927 G
320 G
70928 AAAAAATATATAATTCAAAGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTTTC
1 AAAAAATATATAATTCAAAGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTTTC
*
70993 CATTTTTTT-CGAAATTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAAGAAATC
66 CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAAGAAATC
* *
71057 CTTAAATCCAAATTAGTTGAGATTTCATTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCA
131 CTTAAATCCAAATTAGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCA
* * *
71122 AAAATCATGCAAAACTGAGCCGACGCCCCGAAACGCATTTTTAGCCAAAAACCGTGACGGTTAGT
196 AAAATCATGCAAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG-TAGT
* *
71187 GCACGATTTCTGCTAAAAATTGACCCGAAAACTTTTTTCTCATTTTTAACCACACTACTCTG
260 ACACGATTTCTGCTAAAAATTGACCCGAAAACTTTTTTCTCATTTTT-GCCACACTACTCTG
*** *
71249 TTGAAATATATAATTCAAAGCCAAAAAAAATTGAAGGATTTTTCACGCTTCCAATATCGTTTTTC
1 AAAAAATATATAATTCAAAGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTTTC
* * *
71314 CAATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCATAAATAGAAAC
66 C-ATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAAGAAAT
* *
71379 CCTTAAATCCAAATTGGATGAGATTTGGA-TATATGAATATAGATATTTCAAGGAGTCTTTCTGC
130 CCTTAAATCCAAATTAGCTGAGATTT-GATTATATGAATATAGATATTTCAAGGAGTCTTTCTGC
*
71443 CAAAAATCATGCAAAACTGAGCCG-GAGCCCCGAAACGCGGTTTTAGCCAAAAACCGTGATGG-A
194 CAAAAATCATGCAAAACTGAGCCGAG-GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTA
* * *
71506 GTACACGATTTCTGCTAAAAGTTGACCCGAAAACTTTCTTCTCATTTTTTTGCCACACAACTCT-
258 GTACACGATTTCTGCTAAAAATTGACCCGAAAACTTTTTTCTCA--TTTTTGCCACACTACTCTG
* *
71570 ACAAAATATATAATTCAACGCCAAAAAAAATTGAAGGG-TTTTCACGCTTCCAATATCGTTTTTC
1 AAAAAATATATAATTCAAAGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTTTC
* *
71634 CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAACTCAGATGCTCGTAAAAAGAAATC
66 CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAAGAAATC
* * * * *
71699 CTTAAATCCAAATCAGCTGGGATTTGATTATATGAATATAGATAATTCAAGTAGTCTTTCTGCCT
131 CTTAAATCCAAATTAGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCA
* * * *
71764 AAAATCTTGCAAAATTGAGCCGGGGCCGCGAAACGC
196 AAAATCATGCAAAACTGAGCCGAGGCCCCGAAACGC
Statistics
Matches: 798, Mismatches: 63, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
318 2 0.00
319 145 0.18
320 34 0.04
321 170 0.21
322 51 0.06
323 323 0.40
324 8 0.01
325 32 0.04
326 33 0.04
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (320 bp):
AAAAAATATATAATTCAAAGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTTTC
CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAAGAAATC
CTTAAATCCAAATTAGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCA
AAAATCATGCAAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTA
CACGATTTCTGCTAAAAATTGACCCGAAAACTTTTTTCTCATTTTTGCCACACTACTCTG
Done.