Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011991.1 Corchorus olitorius cultivar O-4 contig12024, 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: 18877
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:656 original size:18 final size:18
Alignment explanation
Indices: 633--667 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
623 ACAAAAATTG
633 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
651 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
668 TATAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:808 original size:16 final size:16
Alignment explanation
Indices: 787--818 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
777 ATTATTATTT
787 TTATTAATAATATATA
1 TTATTAATAATATATA
*
803 TTATTATTAATATATA
1 TTATTAATAATATATA
819 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:808 original size:25 final size:27
Alignment explanation
Indices: 761--810 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
751 AATTTAAATA
761 TATTAGATAATAGAATATTATTATTTT
1 TATTAGATAATAGAATATTATTATTTT
*
788 TATTA-ATAATA-TATATTATTATT
1 TATTAGATAATAGAATATTATTATT
811 AATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 6 0.27
27 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TATTAGATAATAGAATATTATTATTTT
Found at i:809 original size:19 final size:19
Alignment explanation
Indices: 782--834 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
772 AGAATATTAT
*
782 TATTTTTATTAATAATATA
1 TATTATTATTAATAATATA
801 TATTATTATTAAT-ATATA
1 TATTATTATTAATAATATA
* *
819 AATAATTATATAATAA
1 TATTATTAT-TAATAA
835 ACGAACACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 12 0.41
19 16 0.55
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATTATTAATAATATA
Found at i:876 original size:35 final size:35
Alignment explanation
Indices: 837--911 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
827 TATAATAAAC
*
837 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
872 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
907 GAACA
1 GAACA
912 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:9862 original size:89 final size:89
Alignment explanation
Indices: 9744--10033 Score: 492
Period size: 89 Copynumber: 3.3 Consensus size: 89
9734 CCTGTTGGCT
*
9744 GTTTATGGCTATACCAACGCC-CCCTGCTGTTGGTATACATTCTATAGCAACGGAAGCCGTAGGT
1 GTTTATGGCTATACCAACGCCACCC-GCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGT
* *
9808 TTATCTCCAATCATACTATTTTTTG
65 ATATCTCCAATCATACCATTTTTTG
*
9833 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTACAGCAACGTAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
9898 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
* * *
9922 GTTTGTGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGTAACGTAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
9987 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
*
10011 GTTTACGGCTATACCAACGCCAC
1 GTTTATGGCTATACCAACGCCAC
10034 ACGCCGTTTG
Statistics
Matches: 189, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
89 186 0.98
90 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (89 bp):
GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
TATCTCCAATCATACCATTTTTTG
Found at i:10221 original size:40 final size:40
Alignment explanation
Indices: 10176--10252 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
10166 GTCATTCACA
* * *
10176 TTAAAAATATAATCCAAAACAATTTGTTCTAATCCACACC
1 TTAAAAATAAAATCAAAAACAATTTATTCTAATCCACACC
*
10216 TTAAAAATAAAATTAAAAACAATTTATTCTAATCCAC
1 TTAAAAATAAAATCAAAAACAATTTATTCTAATCCAC
10253 TCATGTAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.31
Consensus pattern (40 bp):
TTAAAAATAAAATCAAAAACAATTTATTCTAATCCACACC
Found at i:10478 original size:22 final size:22
Alignment explanation
Indices: 10453--10494 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10443 CAGTGGGCCA
* *
10453 TGAAGAAAAGAAGAAAAAAAAT
1 TGAAAAAAACAAGAAAAAAAAT
*
10475 TGAAAAAAACAAGAAGAAAA
1 TGAAAAAAACAAGAAAAAAA
10495 TCATAAATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (22 bp):
TGAAAAAAACAAGAAAAAAAAT
Found at i:13543 original size:62 final size:61
Alignment explanation
Indices: 13442--13557 Score: 205
Period size: 62 Copynumber: 1.9 Consensus size: 61
13432 ACAAGGAACC
*
13442 TTATACTATCAGTGTCATATATATACTACCCTCATATTATCCATACAAATTTTCATCACCA
1 TTATACTATCAGTCTCATATATATACTACCCTCATATTATCCATACAAATTTTCATCACCA
*
13503 TTATCACTATTAGTCTCATATATATACTACCCTCATATTATCCATACAAATTTTC
1 TTAT-ACTATCAGTCTCATATATATACTACCCTCATATTATCCATACAAATTTTC
13558 TTTTCTTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
61 4 0.08
62 48 0.92
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (61 bp):
TTATACTATCAGTCTCATATATATACTACCCTCATATTATCCATACAAATTTTCATCACCA
Found at i:14192 original size:16 final size:16
Alignment explanation
Indices: 14171--14221 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
14161 CGGCAAAGCA
14171 GAGAAGAGGAGTGGCG
1 GAGAAGAGGAGTGGCG
*
14187 GAGAAGAGGAGGGGCG
1 GAGAAGAGGAGTGGCG
14203 GAGAAGAGGAGTGGCG
1 GAGAAGAGGAGTGGCG
14219 GAG
1 GAG
14222 TGAATGAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.59, T:0.04
Consensus pattern (16 bp):
GAGAAGAGGAGTGGCG
Found at i:14743 original size:125 final size:125
Alignment explanation
Indices: 14521--14770 Score: 455
Period size: 125 Copynumber: 2.0 Consensus size: 125
14511 ATTTTCATTT
* * *
14521 AGGTCTATAGCTACGGGAAACATTATGTGCGTTGGTATATTACACTACTATACCTACAGCAATTA
1 AGGTCTATAGCTACGGGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAACAATTA
*
14586 CAACACTGTTAGAATAGCCTTAATCTATACCAATAGATGCCACAGGCTTTGGTATATGTC
66 CAACACTGTTAGAATAGCCTTAATCTATACCAATAGATGCCACAGGCGTTGGTATATGTC
14646 AGGTCTATAGCTACGGGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAACAATTA
1 AGGTCTATAGCTACGGGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAACAATTA
*
14711 CAACACTGTTAGAATAGCCTTAATCTATACCAATAGATGCCACGGGCGTTGGTATATGTC
66 CAACACTGTTAGAATAGCCTTAATCTATACCAATAGATGCCACAGGCGTTGGTATATGTC
14771 TTATATATAC
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (125 bp):
AGGTCTATAGCTACGGGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAACAATTA
CAACACTGTTAGAATAGCCTTAATCTATACCAATAGATGCCACAGGCGTTGGTATATGTC
Found at i:16229 original size:4 final size:4
Alignment explanation
Indices: 16222--16247 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16212 GTATTTTTTT
16222 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
16248 TATTCAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:17375 original size:13 final size:13
Alignment explanation
Indices: 17359--17426 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
17349 CCCAAAATTG
* *
17359 AAACCGAAAATCA
1 AAACCCAAAACCA
17372 AAACCCAAAACCA
1 AAACCCAAAACCA
* *
17385 AAATCCAAATCCA
1 AAACCCAAAACCA
*
17398 AAA-TCAAAACCTA
1 AAACCCAAAACC-A
*
17411 AAA-TCAAAACCCA
1 AAACCCAAAA-CCA
17424 AAA
1 AAA
17427 GTGTCTTCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 6 0.13
13 39 0.83
14 2 0.04
ACGTcount: A:0.62, C:0.28, G:0.01, T:0.09
Consensus pattern (13 bp):
AAACCCAAAACCA
Found at i:17382 original size:7 final size:6
Alignment explanation
Indices: 17359--17426 Score: 55
Period size: 6 Copynumber: 10.5 Consensus size: 6
17349 CCCAAAATTG
* * *
17359 AAACCGA AAATCA AAACCCA AAACCA AAATCCA AATCCA AAATCA AAACCTA
1 AAACC-A AAACCA AAA-CCA AAACCA AAA-CCA AAACCA AAACCA AAACC-A
*
17411 AAATCA AAACCCA AAA
1 AAACCA AAA-CCA AAA
17427 GTGTCTTCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 25 0.51
7 24 0.49
ACGTcount: A:0.62, C:0.28, G:0.01, T:0.09
Consensus pattern (6 bp):
AAACCA
Found at i:17386 original size:32 final size:32
Alignment explanation
Indices: 17365--17425 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
17355 ATTGAAACCG
17365 AAAATCAAAACCCAAAACCAAAATCCAAATCC
1 AAAATCAAAACCCAAAACCAAAATCCAAATCC
* * *
17397 AAAATCAAAACCTAAAATCAAAACCCAAA
1 AAAATCAAAACCCAAAACCAAAATCCAAA
17426 AGTGTCTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (32 bp):
AAAATCAAAACCCAAAACCAAAATCCAAATCC
Done.