Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014977.1 Corchorus olitorius cultivar O-4 contig15010, 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: 10899
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1038 original size:334 final size:328
Alignment explanation
Indices: 9--1210 Score: 1165
Period size: 334 Copynumber: 3.6 Consensus size: 328
1 TATATATA
* * * *
9 TTATAAGTATTGTGGCTAAAAATT-ATGGAAAAATATTTCGCGTCAATTTTTGCAAAATTTTAGC
1 TTATGAGTATTTTAGCTAAAAATTGA-GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGC
* * * * *
73 CGAAATCG-TGT-AGCATCACGGTTTTTTGGCTAAAAATGCGTTTCGGGGCCCTAAGTCAGTTTT
65 CGAAATTGTTCTAACCATCACGG-TTTTTGGCTAAAAACGCGTTTCGGGGCCC--GGTCAGTTTT
* * * * *
136 GCATGATTTTTTGTGGCAAAACTCCATGAAATATCTATATTCATCTAATCAAATCTTAGCCACAT
127 GCATGATTTTTTGTGCCAAAACTCCTTAAAATATCTATATTCATCAAACCAAATC-TAGCCACAT
* * *
201 TGGATTTAAGGATTTGTTTTT-CGAGCATTTAAATCATGTTTCGATTTAATTAGAAATTAATTTG
191 TGGATTTAAGGATTT-TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCG
* * *
265 --AAAAATATAGGAAAAACGATATTAGAAGC-ATAAGAAAACCTTCAATATTTTTGGCGTTGAAT
255 AAAAAAATATAGGAAAAACAATATTAGAAGCGTTAA-AAGACCTTCAATATTTTTGGCGTTGAAT
327 TATATATTTTT
319 TATATA-TTTT
* * * **
338 TTATGAGTATTGTGGCTAAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAATC
1 TTATGAGTATTTTAGCTAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * ***** *
403 GAAATTGTGTTTAATCAATGTTTTTTTTTGGCTAAAAACGCGTTTCGGGCCCCCGGGTCAGTTTT
66 GAAATTGT-TCTAA-CCATCACGGTTTTTGGCTAAAAACGCGTTTCGGG-GCCC-GGTCAGTTTT
* * * * * *
468 GAATGATTTTTTGCGCCAAGACTACTTAAAATATATCTATATTTATCCAACCAAATCTCAGCCAC
127 GCATGATTTTTTGTGCCAAAACTCCTT-AAA-ATATCTATATTCATCAAACCAAATCT-AGCCAC
* * * * * * *
533 ATTGTATTTAAAGAAATGTTTTTCATGA-CTATCAAAATCTTGTTTCGATTTAATCAGAAATTAA
189 ATTGGATTT-AAG-GATTTTTTTTACGAGC-ATCTAAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * *
597 TTTCGAAATAAA-ATAGGAAAAACTATATTAGAAGCGTGAAAAAGACTTTCAATTTTTTTGGCGT
251 -TTCGAAAAAAATATAGGAAAAACAATATTAGAAGCGT-TAAAAGACCTTCAATATTTTTGGCGT
661 TGAATTATATATTTT
314 TGAATTATATATTTT
* ** *
676 TTATGAGTATTTTCA-CTAGATTTTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
1 TTATGAGTATTTT-AGCTAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGC
** * *
740 CGAAATTGTATACTAACCATCACGGTTTTCAGCTAAAAACGCGTTCCGGGGCCCGGCTCTGTTTT
65 CGAAATTGT-T-CTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGG-TCAGTTTT
* * * *
805 GCATGATTTTTGGTGTCAAAATTCCTTAAAATATCTATATTCATCAAACCAAATAGTAGCCACAT
127 GCATGATTTTTTGTGCCAAAACTCCTTAAAATATCTATATTCATCAAACCAAAT-CTAGCCACAT
* *
870 TGGATTTAAGGATTTTTTTTAAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA
191 TGGATTTAAGGATTTTTTTT-ACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC-
* * ** *
935 GAAAAAAATATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGTCGAAT
254 GAAAAAAATATAGGAAAAACAATATTAGAAGCGTTAAAAGACCTTCAATATTTTTGGCGTTGAAT
*
1000 GATATCA-TTT
319 TATAT-ATTTT
* * * *
1010 TTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCAGGTCAATTTTTGCAAAATTTTAGCC
1 TTATGAGTATTTTAGCTAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * * ** * * *
1075 GAAATCG-TGT-ACCATCACGATTTTTGATTAAAAACGTGTTTCGGGGCCACGACTCTA-TTTTA
66 GAAATTGTTCTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCC-CG-GTC-AGTTTTG
* * * ** * * * * * *
1137 CATAATTTTTGGCGCTGAGACTCCTTTAAATATCTATATT-ATCTAATCAAATCTCAGGCATATT
128 CATGATTTTTTGTGCCAAAACTCCTTAAAATATCTATATTCATCAAACCAAATCT-AGCCACATT
1201 GGATTTAAGG
192 GGATTTAAGG
1211 TTCTTTTAAA
Statistics
Matches: 715, Mismatches: 126, Indels: 63
0.79 0.14 0.07
Matches are distributed among these distances:
329 65 0.09
330 59 0.08
331 43 0.06
332 56 0.08
333 19 0.03
334 174 0.24
335 70 0.10
336 41 0.06
337 33 0.05
338 115 0.16
339 38 0.05
340 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
TTATGAGTATTTTAGCTAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCC
GAAATTGTTCTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGTCAGTTTTGCAT
GATTTTTTGTGCCAAAACTCCTTAAAATATCTATATTCATCAAACCAAATCTAGCCACATTGGAT
TTAAGGATTTTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAA
ATATAGGAAAAACAATATTAGAAGCGTTAAAAGACCTTCAATATTTTTGGCGTTGAATTATATAT
TTT
Found at i:2474 original size:119 final size:118
Alignment explanation
Indices: 2253--2478 Score: 319
Period size: 119 Copynumber: 1.9 Consensus size: 118
2243 TAACAATTAC
* *
2253 TATATTTAATATTTATAAGATGGGTTCCCGGCATTTAAAATGCCACAAATAAAGATGTTTTGCCT
1 TATATATAATATTTATAAGATGGGTTCCCGGCATTTAAAATGCCACAAATAAAGATGTTTTGACT
* * * * *
2318 TTTTCCGGCGTTTAGATTGCCACTAATTGTAATTTTCATCACACATTTTCCAT
66 TTTCCCGGCGTTTAAATTGCCACTAACTGAAACTTTCATCACACATTTTCCAT
* * *
2371 TATATATAATATTTATAAGATGGCTTTCCTGGCATTTAAAATGCCACAACTAAAGAT-TTTTGGA
1 TATATATAATATTTATAAGATGG-GTTCCCGGCATTTAAAATGCCACAAATAAAGATGTTTT-GA
* *
2435 GTTTTCCCGGCGTTTAAATTGTCACTAACTGAAACTTTCATCAC
64 CTTTTCCCGGCGTTTAAATTGCCACTAACTGAAACTTTCATCAC
2479 TCAATTAATA
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
118 26 0.28
119 68 0.72
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (118 bp):
TATATATAATATTTATAAGATGGGTTCCCGGCATTTAAAATGCCACAAATAAAGATGTTTTGACT
TTTCCCGGCGTTTAAATTGCCACTAACTGAAACTTTCATCACACATTTTCCAT
Found at i:3164 original size:27 final size:25
Alignment explanation
Indices: 3101--3164 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
3091 TGGTAGGCTG
* *
3101 TCGGCCTAAAGCTCATATTACACCG
1 TCGGCCTAAAGTTCATATTACACCA
** *
3126 TCAACCTGAAGTTCATATTCAACACCA
1 TCGGCCTAAAGTTCATATT--ACACCA
3153 TCGGCCTAAAGT
1 TCGGCCTAAAGT
3165 GGATTGAACA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 15 0.52
27 14 0.48
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (25 bp):
TCGGCCTAAAGTTCATATTACACCA
Found at i:7106 original size:106 final size:105
Alignment explanation
Indices: 6973--7173 Score: 305
Period size: 106 Copynumber: 1.9 Consensus size: 105
6963 AACTTGTCCT
* * *
6973 CATTCTTCAACCTGCACCAGGACAACACTAATCTGCAATCATTTTTCAAACCAATGCATGTAAAT
1 CATTATTCAACCTGCACCAGAACAACACAAATCTGCAATCATTTTTCAAACCAATGCATGTAAAT
7038 TACGCTTCATTATTAAACC-ACAAAGCAATTTTAATATTTC
66 TACGCTTCATTA-TAAACCTACAAAGCAATTTTAATATTTC
* * ** *
7078 CATTATTCAAACCTGCACCAGAAGAACACAAATCTGGAATCATTTTTCACGCTAATGCATGTAAA
1 CATTATTC-AACCTGCACCAGAACAACACAAATCTGCAATCATTTTTCAAACCAATGCATGTAAA
7143 TTACGCTTCATTATAAACCTACAAAGCAATT
65 TTACGCTTCATTATAAACCTACAAAGCAATT
7174 AATGTTTCTA
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 13 0.15
106 73 0.85
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (105 bp):
CATTATTCAACCTGCACCAGAACAACACAAATCTGCAATCATTTTTCAAACCAATGCATGTAAAT
TACGCTTCATTATAAACCTACAAAGCAATTTTAATATTTC
Found at i:7846 original size:13 final size:13
Alignment explanation
Indices: 7819--7862 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
7809 TTCATCTCAT
7819 TTTTCCTTC-CT-
1 TTTTCCTTCTCTC
*
7830 TTTCCCTT-TCTC
1 TTTTCCTTCTCTC
7842 TTTTCCTTCTCTC
1 TTTTCCTTCTCTC
7855 -TTTCCTTC
1 TTTTCCTTC
7863 ACAAAATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 15 0.54
13 4 0.14
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTCCTTCTCTC
Done.