Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022636.1 Corchorus olitorius cultivar O-4 contig22669, 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: 8267
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:682 original size:26 final size:27
Alignment explanation
Indices: 636--740 Score: 99
Period size: 26 Copynumber: 3.9 Consensus size: 27
626 TTAAGAGTGG
* **
636 ACTT-AAAATGACCAACGTGCCCCTGA
1 ACTTGAAAATGACTAAAATGCCCCTGA
662 ACTT-AAAATGACTAAAATGCCCCT-A
1 ACTTGAAAATGACTAAAATGCCCCTGA
* *
687 AATGTGCAAATGACTAAAATGCCCCTAGA
1 ACT-TGAAAATGACTAAAATGCCCCT-GA
** *
716 TTTTGAAAATGACTGAAATGCCCCT
1 ACTTGAAAATGACTAAAATGCCCCT
741 AGTTGATCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
25 3 0.05
26 22 0.33
27 19 0.29
28 20 0.30
29 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (27 bp):
ACTTGAAAATGACTAAAATGCCCCTGA
Found at i:734 original size:28 final size:28
Alignment explanation
Indices: 666--742 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
656 CCCTGAACTT
666 AAAATGACTAAAATGCCCCTA-AATGTG
1 AAAATGACTAAAATGCCCCTAGAATGTG
* * *
693 CAAATGACTAAAATGCCCCTAGATTTTG
1 AAAATGACTAAAATGCCCCTAGAATGTG
*
721 AAAATGACTGAAATGCCCCTAG
1 AAAATGACTAAAATGCCCCTAG
743 TTGATCCTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 20 0.45
28 24 0.55
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAATGACTAAAATGCCCCTAGAATGTG
Found at i:1036 original size:35 final size:35
Alignment explanation
Indices: 993--1505 Score: 741
Period size: 35 Copynumber: 14.7 Consensus size: 35
983 TAAGTCCATA
*
993 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
* *
1028 TCGAAGATGCTACACTGAGTCATCT-GAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCATCT
* * * *
1063 TTGAAAATGCTACACCGAGTCATTTGAATTTATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
*
1098 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
* *
1133 TTGAAGATGCTGCACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
1168 TTGAAGATGCTACACCGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGGATTC-ATCT
*
1203 TCGAAGATGCTACACCGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGGATTC-ATCT
*
1238 TCGAAGATGCTACACCGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGGATTC-ATCT
*
1273 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
* *
1308 TTGAAGATGCTACACCGAGTCATCTAGATTCAGCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
* *
1343 TTGAAGATGCTACACCGAGTCATCTGAATAT-AGCT
1 TTGAAGATGCTACACCGAGTCATCTGGAT-TCATCT
* *
1378 TTGAAGATGCTACACCGAGTCATCTGAATAT-AACT
1 TTGAAGATGCTACACCGAGTCATCTGGAT-TCATCT
*
1413 TTGAAGATGCTACACTGAGTCATCTGGATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
*
1448 TTGAAGATGCTACACCGAGTCATCTGGATTGATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
1483 TTGAAGATGCTACACCGAGTCAT
1 TTGAAGATGCTACACCGAGTCAT
1506 TTGAGAAGAT
Statistics
Matches: 443, Mismatches: 29, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
34 5 0.01
35 434 0.98
36 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
Found at i:1615 original size:50 final size:50
Alignment explanation
Indices: 1528--1759 Score: 374
Period size: 50 Copynumber: 4.6 Consensus size: 50
1518 TAATGTATCA
* * *
1528 TATGGAAACGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTGACTCG
1 TATGGAAACG-AGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCG
* * *
1579 TATGGAAACGAGTTTGCCTTGTGGAAAAGTCTATGTTGATAATTGACTCG
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCG
* *
1629 TATGGAAACGAGTTCGGCTTGTGGAAAAGCCCATGTTGATATTTGACTCG
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCG
*
1679 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCG
1729 TATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1760 GAAACATTCG
Statistics
Matches: 167, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
50 157 0.94
51 10 0.06
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCG
Found at i:1975 original size:79 final size:79
Alignment explanation
Indices: 1844--2130 Score: 475
Period size: 79 Copynumber: 3.6 Consensus size: 79
1834 ATACCTTTGG
* * * **
1844 AAAATAACTCTGAATCTGATGCTGTAACTGAAAACTTCTTGATTGATGATGAAAAAAGACCAATG
1 AAAATAACTATGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGGACCAATG
1909 TGCGGTCAACTTGA
66 TGCGGTCAACTTGA
*
1923 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGGACCAATG
1 AAAATAACTATGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGGACCAATG
1988 TGCGGTCAACTTGA
66 TGCGGTCAACTTGA
*
2002 AAAATAACTATGAGTCTGATGTTGTAACTGAAAGCTTCTTGATTGATGATGAAAAGGGACCAATG
1 AAAATAACTATGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGGACCAATG
2067 TGCGGTCAACTTGA
66 TGCGGTCAACTTGA
* * * *
2081 AAAATAACTATGCGTCTGATGTTATGATTGAAAACTTCTTGATTGATGAT
1 AAAATAACTATGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGAT
2131 TCGAATCTTT
Statistics
Matches: 197, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 197 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (79 bp):
AAAATAACTATGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGGACCAATG
TGCGGTCAACTTGA
Found at i:2580 original size:50 final size:50
Alignment explanation
Indices: 2522--2762 Score: 365
Period size: 50 Copynumber: 4.8 Consensus size: 50
2512 TTAAATGCCC
* * * * * *
2522 TTTGAAAAGCAAATTTTTATCTTGGACTCACAACTGGAATGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTAT
* * *
2572 TTTGAAAAGCGAATTTTAATCTTGAACTCATAAACGGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTAT
**
2622 TTTGAAAAGCGAATTTTGATCTTGAACTCTTAAATGGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTAT
*
2672 TTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTAT
*
2722 TTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAG
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAG
2763 AAATCTTGTT
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 177 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTAT
Found at i:3366 original size:6 final size:6
Alignment explanation
Indices: 3355--3398 Score: 58
Period size: 5 Copynumber: 7.7 Consensus size: 6
3345 ATCAATTCTC
3355 TTTTGA TTTTGA -TTTGA -TTTGA TTTTTGA TTTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA TTTT
3399 TTTATTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.43
6 15 0.43
7 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:7697 original size:16 final size:16
Alignment explanation
Indices: 7676--7706 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7666 GAGATTGCGT
7676 TTTATTTTTATTTTTC
1 TTTATTTTTATTTTTC
*
7692 TTTATTTTTCTTTTT
1 TTTATTTTTATTTTT
7707 TTAATTTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTATTTTTATTTTTC
Done.