Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023264.1 Corchorus olitorius cultivar O-4 contig23297, 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: 19740
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:580 original size:2 final size:2
Alignment explanation
Indices: 573--636 Score: 85
Period size: 2 Copynumber: 31.5 Consensus size: 2
563 TAACTAGTAC
*
573 AT AT AT AT AT AT AT AT AT AT AT AT TT GAT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
*
615 AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT A
637 AAAGTACGAG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 1 0.02
2 51 0.93
3 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:692 original size:31 final size:31
Alignment explanation
Indices: 654--715 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
644 GAGTTTTGTA
**
654 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTAACATACCCTTATT
*
685 AAACTTTTGAATCGCCTAACATACCCTTATT
1 AAACTTTTGAATCACCTAACATACCCTTATT
716 TTTTCGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (31 bp):
AAACTTTTGAATCACCTAACATACCCTTATT
Found at i:857 original size:84 final size:85
Alignment explanation
Indices: 752--921 Score: 288
Period size: 84 Copynumber: 2.0 Consensus size: 85
742 TTGTTTAAAT
*
752 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATT-AATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
816 TTTTATTTTTACCATTTTAC
66 TTTTATTTTTACCATATTAC
* *
836 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
901 TTTTATTTTTACGATATTAC
66 TTTTATTTTTACCATATTAC
921 T
1 T
922 AATTTAATTA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 42 0.52
85 38 0.47
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.52
Consensus pattern (85 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTAC
Found at i:2427 original size:2 final size:2
Alignment explanation
Indices: 2420--2457 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2410 TGAAAACTAG
*
2420 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2458 GAGAGTAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9290 original size:12 final size:12
Alignment explanation
Indices: 9275--9306 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
9265 TTGTAAGGTG
9275 ATTTTTTTAATA
1 ATTTTTTTAATA
9287 ATTTTTTTAATA
1 ATTTTTTTAATA
9299 ATTTTTTT
1 ATTTTTTT
9307 CTTTATAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTTTTAATA
Found at i:9371 original size:15 final size:15
Alignment explanation
Indices: 9342--9384 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
9332 TTAAGATAGA
9342 TTTTTTAATAA--TT
1 TTTTTTAATAATTTT
9355 TTTTTTAATAATTTT
1 TTTTTTAATAATTTT
9370 TTTCTTT-ATAATTTT
1 TTT-TTTAATAATTTT
9385 CGTTTCCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.41
15 13 0.48
16 3 0.11
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTAATAATTTT
Found at i:9384 original size:13 final size:13
Alignment explanation
Indices: 9342--9372 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
9332 TTAAGATAGA
9342 TTTTTTAATAATT
1 TTTTTTAATAATT
9355 TTTTTTAATAATT
1 TTTTTTAATAATT
9368 TTTTT
1 TTTTT
9373 CTTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTAATAATT
Found at i:10758 original size:13 final size:12
Alignment explanation
Indices: 10742--10774 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
10732 GTAGTTTTGT
10742 TTTTTTTTTTACC
1 TTTTTTTTTT-CC
10755 TTTTTTTTTTCC
1 TTTTTTTTTTCC
10767 TTTTTTTT
1 TTTTTTTT
10775 CTTCTCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTCC
Found at i:10782 original size:15 final size:13
Alignment explanation
Indices: 10741--10774 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
10731 GGTAGTTTTG
10741 TTTTTTTTTTTACC
1 TTTTTTTTTTT-CC
10755 -TTTTTTTTTTCC
1 TTTTTTTTTTTCC
10767 TTTTTTTT
1 TTTTTTTT
10775 CTTCTCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTTCC
Found at i:12538 original size:16 final size:15
Alignment explanation
Indices: 12517--12604 Score: 86
Period size: 16 Copynumber: 5.5 Consensus size: 15
12507 GGCAATTGGG
12517 CGGGTTCGGGCTTTTT
1 CGGGTTCGGG-TTTTT
*
12533 CGGGTTTGGGTTTATT
1 CGGGTTCGGGTTT-TT
*
12549 CGGCTTCGGGTATTTT
1 CGGGTTCGGGT-TTTT
* *
12565 CGGGCTCGGGTTATAT
1 CGGGTTCGGGTT-TTT
*
12581 CGGGTTCGGCTATTTT
1 CGGGTTCGGGT-TTTT
12597 CGGGTTCG
1 CGGGTTCG
12605 ATCTCGGGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
15 4 0.07
16 52 0.88
17 3 0.05
ACGTcount: A:0.06, C:0.17, G:0.36, T:0.41
Consensus pattern (15 bp):
CGGGTTCGGGTTTTT
Found at i:12565 original size:32 final size:32
Alignment explanation
Indices: 12521--12604 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
12511 ATTGGGCGGG
*
12521 TTCGGGCT-TTTTCGGGTTTGGGTT-TATTCGGC
1 TTCGGG-TATTTTCGGGTTCGGGTTATA-TCGGC
* *
12553 TTCGGGTATTTTCGGGCTCGGGTTATATCGGG
1 TTCGGGTATTTTCGGGTTCGGGTTATATCGGC
*
12585 TTCGGCTATTTTCGGGTTCG
1 TTCGGGTATTTTCGGGTTCG
12605 ATCTCGGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
31 1 0.02
32 42 0.93
33 2 0.04
ACGTcount: A:0.06, C:0.17, G:0.35, T:0.43
Consensus pattern (32 bp):
TTCGGGTATTTTCGGGTTCGGGTTATATCGGC
Found at i:12630 original size:55 final size:55
Alignment explanation
Indices: 12563--12686 Score: 185
Period size: 55 Copynumber: 2.3 Consensus size: 55
12553 TTCGGGTATT
* * *
12563 TTCGGGCTCGGGTTATATCGGGTTCGGCTATTTTCGGGTTCGATCTCGGGTAGGG
1 TTCGGGTTCGGGTTATATCGGGTTCGACTATTTTCGGGTTCGATCTCGAGTAGGG
* *
12618 TTCGGGTTCGGGTTATATCGGGTTCGACTATTTTCGGGTTCGGTCTCGAGTAGGT
1 TTCGGGTTCGGGTTATATCGGGTTCGACTATTTTCGGGTTCGATCTCGAGTAGGG
* *
12673 TTCAGGTTCAGGTT
1 TTCGGGTTCGGGTT
12687 CGAGCTCGGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.10, C:0.17, G:0.35, T:0.37
Consensus pattern (55 bp):
TTCGGGTTCGGGTTATATCGGGTTCGACTATTTTCGGGTTCGATCTCGAGTAGGG
Found at i:13661 original size:16 final size:16
Alignment explanation
Indices: 13642--13685 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
13632 TCGGGCTGCC
*
13642 TCAGGTTCGGGTATTT
1 TCAGGTTCGGGTAATT
*
13658 TCAGGCTCGGGTAATT
1 TCAGGTTCGGGTAATT
*
13674 TCGGGTTCGGGT
1 TCAGGTTCGGGT
13686 TTAGGCGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.11, C:0.16, G:0.36, T:0.36
Consensus pattern (16 bp):
TCAGGTTCGGGTAATT
Found at i:17883 original size:26 final size:28
Alignment explanation
Indices: 17854--17908 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
17844 TATTTTTGCG
17854 TCAT-AAAAAAAAGGTTT-TTGCGTTTT
1 TCATAAAAAAAAAGGTTTCTTGCGTTTT
*
17880 TCATAAAAAAAAAGTTTTCTTGCGTTTT
1 TCATAAAAAAAAAGGTTTCTTGCGTTTT
17908 T
1 T
17909 AATTTATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 10 0.38
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.44
Consensus pattern (28 bp):
TCATAAAAAAAAAGGTTTCTTGCGTTTT
Done.