Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021336.1 Corchorus olitorius cultivar O-4 contig21369, 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: 14511
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Found at i:1408 original size:19 final size:19
Alignment explanation
Indices: 1377--1424 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1367 GGATTAGGGT
1377 TTAATTAATTAATGTTATT-A
1 TTAATT-ATTAATG-TATTCA
*
1397 TTATTTATTAATGTATTCA
1 TTAATTATTAATGTATTCA
1416 TTAATTATT
1 TTAATTATT
1425 TCCGCAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 16 0.64
20 5 0.20
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TTAATTATTAATGTATTCA
Found at i:5990 original size:24 final size:24
Alignment explanation
Indices: 5947--5995 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
5937 CAAAATAATA
5947 AATTAATTAAGAATAATT-AATTTT
1 AATTAATTAAGAAT-ATTAAATTTT
5971 AATTAAATTGAAGAAT-TTAAATTTT
1 AATT-AATT-AAGAATATTAAATTTT
5996 TATTCAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.27
25 10 0.45
26 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
AATTAATTAAGAATATTAAATTTT
Found at i:6061 original size:21 final size:21
Alignment explanation
Indices: 6036--6079 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6026 AAAAAAAATT
6036 AAAAT-GTACATTTTTTTAAAA
1 AAAATAGTA-ATTTTTTTAAAA
*
6057 AAAATATTAATTTTTTTAAAA
1 AAAATAGTAATTTTTTTAAAA
6078 AA
1 AA
6080 TAAAAGTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAATAGTAATTTTTTTAAAA
Found at i:6642 original size:19 final size:20
Alignment explanation
Indices: 6619--6670 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 20
6609 CAAAAGTGTA
6619 AAAAGGGGGCGGTGACAAGT
1 AAAAGGGGGCGGTGACAAGT
6639 -AAA-GGGGC-GTGACAAGT
1 AAAAGGGGGCGGTGACAAGT
6656 AAAAAGGGGGCGGTG
1 -AAAAGGGGGCGGTG
6671 TTTAGCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 9 0.32
18 5 0.18
19 6 0.21
20 5 0.18
21 3 0.11
ACGTcount: A:0.35, C:0.10, G:0.46, T:0.10
Consensus pattern (20 bp):
AAAAGGGGGCGGTGACAAGT
Found at i:8704 original size:697 final size:698
Alignment explanation
Indices: 7736--9137 Score: 2493
Period size: 697 Copynumber: 2.0 Consensus size: 698
7726 AGAACGACCA
7736 GAGAGTTTTGAAGGCTAATTTCATCACTTTTTCATCATCTTTTCGTGCTAAGAGCTTAGTTTAAA
1 GAGAGTTTTGAAGGCTAATTTCATCACTTTTTCATCATCTTTTCGTGCTAAGAGCTTAGTTTAAA
*
7801 CAACTTCCTAATGTTTTCACCTTGTAAGCATGCATTAGGGAGGGTTTTGGTTTGAAAGAGAGAGA
66 CAACTTCCTAATGTTTTCACCTTGTAAGCAAGCATTAGGGAGGGTTTTGGTTTGAAAGAGAGAGA
* * *
7866 GTTCCAGCCACCGGCCGTCGATCGGCGAACCTCCGGCCATCAAATCGGTATCAATAGATTCCTCT
131 GTTCCAGCCACCGGCCGTCGACCGGCGAACCTCCGACCATCAAATCGGTATCAATAGATTCCTCC
*
7931 AATCATTAGGAGTTCATAGAACTTGGAATAACTCAATTTGATTGGATGAATCAAAAGTTATGATG
196 AATCATTAGGAGTTCATAGAACTTGGAATAACTCAATTTGATTGGATGAATCAAAAGTTATGACG
** * *
7996 ATTTCAAGTTAAGAACCCTAAGTTGAAAATTGTGATCGGTGGGTCTACTTTCCTTGCCGGAGTTC
261 ATTTCAAGTTAAGAACCCTAAGTTGAAAATTGTGATCAATGGGTCTACTTTCCTTGCCGGAATCC
*
8061 AGCAAACCGGAGGCCTTTAGAGTTTAGCAGCCAAACTTATGGGGTAATTGTAGTATGATGTATGC
326 AGCAAACCGGAGGCCTTTAGAGTTTAGCAGCCAAACTTATGGGGTAATTGTAGTATGATGTAAGC
8126 TTTGTCCATTGGTACATTTCATACCTCCATAGGTGTTTTGAGGTGAGAGAATCGAAACTTCAAAG
391 TTTGTCCATTGGTACATTTCATACCTCCATAGGTGTTTTGAGGTGAGAGAATCGAAACTTCAAAG
* *
8191 ATGCTTCGTCGATGGGATAAATCTGGAATTTTCAGATTTGTTCATGGAGAAGATGAACAGTAACT
456 ATGCTTCATCGATGGGATAAATATGGAATTTTCAGATTTGTTCATGGAGAAGATGAACAGTAACT
*
8256 GGCGATGCCCAGTCTCGGCCAGAAATTGAATCGGAGAGTGTAGTTCACCCCTAGGTCGTTTTAGA
521 GGCGATGCCCAGTCTCGACCAGAAATTGAATCGGAGAGTGTAGTTCACCCCTAGGTCGTTTTAGA
* *
8321 GTGAAATTTGGGGGATTTGCTCAACAAAGCATTTCTGATTTTCTGGAATTTTTTTATAATTTTTC
586 GTGAAATTTGGGGGATTTGCTCAACAAAGCATTTCTGATTTTCTGAAATTTTTATATAATTTTTC
*
8386 AGATTACAAATTATTTTATATAAATTATTC-TTTGGAAAAATGATTGG
651 AGATTACAAATTATTTTATATAAAGTATTCTTTTGGAAAAATGATTGG
8433 GAGAGTTTTGAAGGCTAATTTCATCACTTTTTCATCATCTTTTCGTGCTAAGAGCTTAGTTTAAA
1 GAGAGTTTTGAAGGCTAATTTCATCACTTTTTCATCATCTTTTCGTGCTAAGAGCTTAGTTTAAA
8498 CAACTTCCTAATGTTTTCACCTTGTAAGCAAGCATTAGGGAGGGTTTTGGTTTGAAAGAGAGAGA
66 CAACTTCCTAATGTTTTCACCTTGTAAGCAAGCATTAGGGAGGGTTTTGGTTTGAAAGAGAGAGA
* * *
8563 GTTCCAGCCACCGGCTGTCGACCGTC-AAGCCTCCGACCATCAAATTGGTATCAATAGATTCCTC
131 GTTCCAGCCACCGGCCGTCGACCGGCGAA-CCTCCGACCATCAAATCGGTATCAATAGATTCCTC
8627 CAATCATTAGGAGTTCATAGAACTTGGAATAACTCAATTTGATTGGATGAATCAAAAGTTATGAC
195 CAATCATTAGGAGTTCATAGAACTTGGAATAACTCAATTTGATTGGATGAATCAAAAGTTATGAC
* *
8692 GATTTTAAGTTAAGAACCCTAAGTTGAAAATTGTGATCAATGGGTCTGCTTTCCTTGCCGGAATC
260 GATTTCAAGTTAAGAACCCTAAGTTGAAAATTGTGATCAATGGGTCTACTTTCCTTGCCGGAATC
*
8757 CAGCAAACCGGAGGCCTTTAGAGTTTAGCGGCCAAACTTATGGGGTAATTGTAGTATGATGTAAG
325 CAGCAAACCGGAGGCCTTTAGAGTTTAGCAGCCAAACTTATGGGGTAATTGTAGTATGATGTAAG
*
8822 CTTTGTCCATTGGTACATTTCATACCTCCATAGGTGTTTTGAGGTGAGAGAATCGAAGCTTCAAA
390 CTTTGTCCATTGGTACATTTCATACCTCCATAGGTGTTTTGAGGTGAGAGAATCGAAACTTCAAA
* * *
8887 GATGCTTCATCGATGGGATAAATATGGACTTTTCAGATTTGTTCATGGAGATGATGAATAGTAAC
455 GATGCTTCATCGATGGGATAAATATGGAATTTTCAGATTTGTTCATGGAGAAGATGAACAGTAAC
* *
8952 TGGCGATGCCTAGTCTCGACCAGAAATTGAATCGGAGAGTGTAGTTCACCCCTAGGTTGTTTTAG
520 TGGCGATGCCCAGTCTCGACCAGAAATTGAATCGGAGAGTGTAGTTCACCCCTAGGTCGTTTTAG
* *
9017 AGTGAAATTTGGGGGATTTGCTCAACAAAGTATTTTTGATTTTCTGAAATTTTTATATAATTTTT
585 AGTGAAATTTGGGGGATTTGCTCAACAAAGCATTTCTGATTTTCTGAAATTTTTATATAATTTTT
*
9082 TAGATTACAAATTATTTTATATAAAGTATTCTTTTTGGAAAAATGATTGG
650 CAGATTACAAATTATTTTATATAAAGTATTC-TTTTGGAAAAATGATTGG
9132 GAGAGT
1 GAGAGT
9138 GTGGCTTAAT
Statistics
Matches: 671, Mismatches: 31, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
696 2 0.00
697 646 0.96
699 23 0.03
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (698 bp):
GAGAGTTTTGAAGGCTAATTTCATCACTTTTTCATCATCTTTTCGTGCTAAGAGCTTAGTTTAAA
CAACTTCCTAATGTTTTCACCTTGTAAGCAAGCATTAGGGAGGGTTTTGGTTTGAAAGAGAGAGA
GTTCCAGCCACCGGCCGTCGACCGGCGAACCTCCGACCATCAAATCGGTATCAATAGATTCCTCC
AATCATTAGGAGTTCATAGAACTTGGAATAACTCAATTTGATTGGATGAATCAAAAGTTATGACG
ATTTCAAGTTAAGAACCCTAAGTTGAAAATTGTGATCAATGGGTCTACTTTCCTTGCCGGAATCC
AGCAAACCGGAGGCCTTTAGAGTTTAGCAGCCAAACTTATGGGGTAATTGTAGTATGATGTAAGC
TTTGTCCATTGGTACATTTCATACCTCCATAGGTGTTTTGAGGTGAGAGAATCGAAACTTCAAAG
ATGCTTCATCGATGGGATAAATATGGAATTTTCAGATTTGTTCATGGAGAAGATGAACAGTAACT
GGCGATGCCCAGTCTCGACCAGAAATTGAATCGGAGAGTGTAGTTCACCCCTAGGTCGTTTTAGA
GTGAAATTTGGGGGATTTGCTCAACAAAGCATTTCTGATTTTCTGAAATTTTTATATAATTTTTC
AGATTACAAATTATTTTATATAAAGTATTCTTTTGGAAAAATGATTGG
Done.