Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011938.1 Corchorus olitorius cultivar O-4 contig11971, 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: 20973
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:590 original size:22 final size:22
Alignment explanation
Indices: 565--632 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
555 TATAAAAAAC
565 ATTATACCATCAGGATGGAGAA
1 ATTATACCATCAGGATGGAGAA
* * *
587 ATTAGT-TC-TGATGG-TCTGAGAA
1 ATTA-TACCATCA-GGAT-GGAGAA
609 ATTTATACCATCAGGATGGAGAA
1 A-TTATACCATCAGGATGGAGAA
632 A
1 A
633 ATAGTTCTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
21 3 0.09
22 14 0.42
23 13 0.39
24 3 0.09
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (22 bp):
ATTATACCATCAGGATGGAGAA
Found at i:672 original size:46 final size:46
Alignment explanation
Indices: 566--1130 Score: 746
Period size: 46 Copynumber: 12.4 Consensus size: 46
556 ATAAAAAACA
*
566 TTATACCATCAGGATGGAG-AAATTAGTTCTGATGGTCTG-AGAAAT
1 TTATACCATCAGGATGGAGAAAATT-GTTCTGATGGTGTGAAGAAAT
*
611 TTATACCATCAGGATGGAGAAAATAGTTCTGATGGTGTGAAGAAAT
1 TTATACCATCAGGATGGAGAAAATTGTTCTGATGGTGTGAAGAAAT
*
657 TTATACCATCAGGATGAAG-AAATTGGTTCTGATGGTGTG-AGAAAT
1 TTATACCATCAGGATGGAGAAAATT-GTTCTGATGGTGTGAAGAAAT
702 TTATACCATCAGGATGGAG--AATTAGTTCTGATGGTGTG-AGAAAT
1 TTATACCATCAGGATGGAGAAAATT-GTTCTGATGGTGTGAAGAAAT
*
746 TTATACCATCAGGATGGAG-AAATTGATCTTGATGGTGTGAA-AAAT
1 TTATACCATCAGGATGGAGAAAATTGTTC-TGATGGTGTGAAGAAAT
*
791 TTATACCATCAGGATGGAGAAAATTGATCTTGATGGTGTGAAGAAAT
1 TTATACCATCAGGATGGAGAAAATTGTTC-TGATGGTGTGAAGAAAT
* * *
838 TTATACCATCAGGATGAAG-AAATTGATCTTGATGGTATGAAGAAAT
1 TTATACCATCAGGATGGAGAAAATTGTTC-TGATGGTGTGAAGAAAT
*
884 TTATACCATCAGGATGGAG-AAATTGATCTTGATGGTGTGAAGAAAT
1 TTATACCATCAGGATGGAGAAAATTGTTC-TGATGGTGTGAAGAAAT
* * *
930 TTATACCATCACGATGGAG-AAATTGATCTTGATGGTGTGAAAAAAT
1 TTATACCATCAGGATGGAGAAAATTGTTC-TGATGGTGTGAAGAAAT
* *
976 TTATACCATCTGGATGGA-AAAATTGGTCCTGATGGTGTGAAGAAAT
1 TTATACCATCAGGATGGAGAAAATT-GTTCTGATGGTGTGAAGAAAT
* *
1022 TTATACCATCTGGATGGAG-AAATTGGTTTTGATGGTGTGAAGAAAT
1 TTATACCATCAGGATGGAGAAAATT-GTTCTGATGGTGTGAAGAAAT
* * *
1068 TTATACCATCTGGATGGA-AAAATTGGTCCTGATGGTGTGGAGAAAT
1 TTATACCATCAGGATGGAGAAAATT-GTTCTGATGGTGTGAAGAAAT
*
1114 TTGTACCATCAGGATGG
1 TTATACCATCAGGATGG
1131 GTGACGTTGC
Statistics
Matches: 483, Mismatches: 25, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
44 46 0.10
45 97 0.20
46 316 0.65
47 24 0.05
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.31
Consensus pattern (46 bp):
TTATACCATCAGGATGGAGAAAATTGTTCTGATGGTGTGAAGAAAT
Found at i:674 original size:23 final size:23
Alignment explanation
Indices: 648--953 Score: 106
Period size: 23 Copynumber: 13.4 Consensus size: 23
638 TCTGATGGTG
648 TGAAGAAATTTATACCATCAGGA
1 TGAAGAAATTTATACCATCAGGA
** * *
671 TGAAGAAATTGGT-TC-TGATGG-
1 TGAAGAAATTTATACCATCA-GGA
*
692 TGTGAGAAATTTATACCATCAGGA
1 TG-AAGAAATTTATACCATCAGGA
* * *
716 TGGAG-AA-TTAGT-TC-TGATGG-
1 TGAAGAAATTTA-TACCATCA-GGA
*
736 TGTGAGAAATTTATACCATCAGGA
1 TG-AAGAAATTTATACCATCAGGA
* * * * *
760 TGGAGAAATTGAT--CTTGATGGTG
1 TGAAGAAATTTATACCATCA-GG-A
783 TGAA-AAATTTATACCATCAGGA
1 TGAAGAAATTTATACCATCAGGA
* * * * *
805 TGGAGAAAATTGAT--CTTGATGGTG
1 TGAAG-AAATTTATACCATCA-GG-A
829 TGAAGAAATTTATACCATCAGGA
1 TGAAGAAATTTATACCATCAGGA
* * *
852 TGAAGAAATTGAT--CTTGATGGTA
1 TGAAGAAATTTATACCATCA-GG-A
875 TGAAGAAATTTATACCATCAGGA
1 TGAAGAAATTTATACCATCAGGA
* * * * *
898 TGGAGAAATTGAT--CTTGATGGTG
1 TGAAGAAATTTATACCATCA-GG-A
*
921 TGAAGAAATTTATACCATCACGA
1 TGAAGAAATTTATACCATCAGGA
*
944 TGGAGAAATT
1 TGAAGAAATT
954 GATCTTGATG
Statistics
Matches: 202, Mismatches: 50, Indels: 62
0.64 0.16 0.20
Matches are distributed among these distances:
20 4 0.02
21 22 0.11
22 36 0.18
23 104 0.51
24 27 0.13
25 9 0.04
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (23 bp):
TGAAGAAATTTATACCATCAGGA
Found at i:996 original size:23 final size:23
Alignment explanation
Indices: 970--1091 Score: 69
Period size: 23 Copynumber: 5.3 Consensus size: 23
960 GATGGTGTGA
970 AAAAATTTATACCATCTGGATGG
1 AAAAATTTATACCATCTGGATGG
** *
993 AAAAATTGGT-CC-TGATGG-TGTG
1 AAAAATTTATACCAT-CTGGATG-G
1015 AAGAAATTTATACCATCTGGATGG
1 AA-AAATTTATACCATCTGGATGG
* ***
1039 AGAAATTGGT-TTTGA--TGG-TGTG
1 AAAAATT--TATACCATCTGGATG-G
1061 AAGAAATTTATACCATCTGGATGG
1 AA-AAATTTATACCATCTGGATGG
1085 AAAAATT
1 AAAAATT
1092 GGTCCTGATG
Statistics
Matches: 71, Mismatches: 14, Indels: 28
0.63 0.12 0.25
Matches are distributed among these distances:
21 6 0.08
22 15 0.21
23 29 0.41
24 15 0.21
25 6 0.08
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (23 bp):
AAAAATTTATACCATCTGGATGG
Found at i:2603 original size:2 final size:2
Alignment explanation
Indices: 2596--2626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2586 ATGCCATTTC
2596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2627 AAATCAGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.