Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001952.1 Corchorus capsularis cultivar CVL-1 contig01954, 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, 619
Length: 1032
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:621 original size:35 final size:35
Alignment explanation
Indices: 595--844 Score: 383
Period size: 35 Copynumber: 7.1 Consensus size: 35
585 TGAGATCATT
* *
595 TCTGATTGTTGGAAACTACTAAAAATGTGATCAAC
1 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
* *
630 TCTAATCATTGGAAACTACTGAAAATGTGATCAAC
1 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
* *
665 TCTAATCATTGGAAACTACTGAAAATGTGATCAAC
1 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
* * * *
700 TCTGATCGTTGCAAAATATTGAAAATGCGATCAAC
1 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
*
735 TCTGATTGTTGGAAACTACTGAAAATGTGATCAAC
1 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
770 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
1 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
* *
805 TCTGATCGTTGGAAAATACTGAAAATGAGATCAAC
1 TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
840 TCTGA
1 TCTGA
845 CCTCTGAAAA
Statistics
Matches: 197, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 197 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (35 bp):
TCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
Found at i:856 original size:70 final size:70
Alignment explanation
Indices: 578--1020 Score: 388
Period size: 70 Copynumber: 6.3 Consensus size: 70
568 TCGCGAATTT
** * * * * * * *
578 CTTGAAATGAGATCATTTCTGATTGTTGGAAACTACTAAAAATGTGATCAACTCTAATCATTGGA
1 CTTGAAATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGATCCTTGAA
643 AACTA
66 AACTA
* * * * * *
648 C-TGAAAATGTGATCAACTCTAATCATTGGAAACTACTGAAAATGTGATCAACTCTGATCGTTGC
1 CTTG-AAATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGATCCTTG-
712 AAAA-TA
64 AAAACTA
* * * * * *
718 -TTGAAAATGCGATCAACTCTGATTGTTGGAAACTACTGAAAATGTGATCAACTCTGATCGTTGG
1 CTTG-AAATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGATCCTTGA
782 AAACTA
65 AAACTA
*
788 C-TGAAAATGTGATCAACTCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGA-CCTCTG
1 CTTG-AAATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGATCCT-TG
*
851 AAAACTT
64 AAAACTA
* * * * *
858 CTTGGAATGAGATCAACTCTGA-CCTCT-GAAAACTTCTTAGAATGAGATCAACTCTGA-CCTCT
1 CTTGAAATGAGATCAACTCTGATCGT-TGGAAAA-TACTGAAAATGAGATCAACTCTGATCCT-T
*
920 GAAAAACTT
63 G-AAAACTA
* *
929 CTTGAAATGAGATCAACTCTGA-CCTCT-GAAAACTTCTTG-AAATGAGATCAACTCTGA-CCTC
1 CTTGAAATGAGATCAACTCTGATCGT-TGGAAAA-TAC-TGAAAATGAGATCAACTCTGATCCT-
*
990 TGAAAACTT
62 TGAAAACTA
*
999 CTTGGAATGAGATCAACTCTGA
1 CTTGAAATGAGATCAACTCTGA
1021 CCTCTGAAAA
Statistics
Matches: 330, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
69 14 0.04
70 245 0.74
71 70 0.21
72 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (70 bp):
CTTGAAATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGATCCTTGAA
AACTA
Found at i:856 original size:105 final size:105
Alignment explanation
Indices: 595--985 Score: 400
Period size: 105 Copynumber: 3.7 Consensus size: 105
585 TGAGATCATT
* * * * * * * *
595 TCTGATTGTTGGAAACTACTAAAAATGTGATCAACTCTAATCAT-TGGAAACTAC-TGAAAATGT
1 TCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGA-CCTCTGAAAACTACTTG-AAATGA
*
658 GATCAACTCTAATCATTGGAAACTACTGAAAATGTGATCAAC
64 GATCAACTCTGATCATTGGAAACTACTGAAAATGTGATCAAC
* * * * * * *
700 TCTGATCGTTGCAAAATATTGAAAATGCGATCAACTCTGA-TTGTTGGAAACTAC-TGAAAATGT
1 TCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGACCT-CTGAAAACTACTTG-AAATGA
*
763 GATCAACTCTGATCGTTGGAAACTACTGAAAATGTGATCAAC
64 GATCAACTCTGATCATTGGAAACTACTGAAAATGTGATCAAC
* *
805 TCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGA
1 TCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGACCTCTGAAAACTACTTGAAATGAGA
* * * * * *
870 TCAACTCTGA-CCTCTGAAAACTTCTTAGAATGAGATCAAC
66 TCAACTCTGATCAT-TGGAAACTACTGAAAATGTGATCAAC
* * * *
910 TCTGA-CCTCTGAAAAACTTCTTG-AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATG
1 TCTGATCGT-TGGAAAA-TAC-TGAAAATGAGATCAACTCTGACCTCTGAAAACTACTTGAAATG
973 AGATCAACTCTGA
63 AGATCAACTCTGA
986 CCTCTGAAAA
Statistics
Matches: 249, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
103 1 0.00
104 4 0.02
105 185 0.74
106 57 0.23
107 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (105 bp):
TCTGATCGTTGGAAAATACTGAAAATGAGATCAACTCTGACCTCTGAAAACTACTTGAAATGAGA
TCAACTCTGATCATTGGAAACTACTGAAAATGTGATCAAC
Found at i:867 original size:35 final size:35
Alignment explanation
Indices: 828--1030 Score: 370
Period size: 35 Copynumber: 5.8 Consensus size: 35
818 AAATACTGAA
828 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
863 AATGAGATCAACTCTGACCTCTGAAAACTTCTTAG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
898 AATGAGATCAACTCTGACCTCTGAAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTG-AAAACTTCTTGG
*
934 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
969 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1004 AATGAGATCAACTCTGACCTCTGAAAA
1 AATGAGATCAACTCTGACCTCTGAAAA
1031 AC
Statistics
Matches: 163, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
35 130 0.80
36 33 0.20
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (35 bp):
AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
Found at i:949 original size:71 final size:70
Alignment explanation
Indices: 827--1030 Score: 374
Period size: 71 Copynumber: 2.9 Consensus size: 70
817 AAAATACTGA
827 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACT
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACT
892 TCTT-
66 TCTTG
*
896 AGAATGAGATCAACTCTGACCTCTGAAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAA
1 A-AATGAGATCAACTCTGACCTCTG-AAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAA
961 CTTCTTG
64 CTTCTTG
968 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAA
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAA
1031 AC
Statistics
Matches: 130, Mismatches: 2, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
69 1 0.01
70 61 0.47
71 67 0.52
72 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (70 bp):
AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACT
TCTTG
Found at i:961 original size:106 final size:106
Alignment explanation
Indices: 827--1032 Score: 394
Period size: 106 Copynumber: 1.9 Consensus size: 106
817 AAAATACTGA
*
827 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACT
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACT
892 TCTTAGAATGAGATCAACTCTGACCTCTGAAAAACTTCTTG
66 TCTTAGAATGAGATCAACTCTGACCTCTGAAAAACTTCTTG
933 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACT
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACT
*
998 TCTTGGAATGAGATCAACTCTGACCTCTGAAAAAC
66 TCTTAGAATGAGATCAACTCTGACCTCTGAAAAAC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (106 bp):
AAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACT
TCTTAGAATGAGATCAACTCTGACCTCTGAAAAACTTCTTG
Done.