Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000698.1 Corchorus capsularis cultivar CVL-1 contig00698, 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, 821
Length: 1369
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Found at i:625 original size:22 final size:22
Alignment explanation
Indices: 597--893 Score: 148
Period size: 22 Copynumber: 13.3 Consensus size: 22
587 TCAATCAAAC
*
597 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
619 CAAAATTTTCATAGTG-TGGTTAAT
1 CAAAA-TTTCATAG-GAAGGTT-AT
643 -AAAATTTCATATGG-AGGTTAT
1 CAAAATTTCATA-GGAAGGTTAT
** *
664 CAAAACGTCATAGTGTA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* * * *
686 CAAAATTCCATA-CAGACGTTAC
1 CAAAATTTCATAGGA-AGGTTAT
** *
708 CAAAATTTCATAAAAATGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * ** *
730 CAAATTTTCTTAGTG-TCGTTAA
1 CAAAATTTCATAG-GAAGGTTAT
* *
752 CAAAATTTTATACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
774 CAAAATTT-ATA--ATGTTGTTAT
1 CAAAATTTCATAGGAAG--GTTAT
795 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATA-GGA---AGGTTAT
* * * *
821 CAAAGTTTCCTAGGGAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
843 CAAAATTTCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
* *
864 CAAAAATTTTAT-GGAGATGTTAT
1 C-AAAATTTCATAGGA-AGGTTAT
887 CAAAATT
1 CAAAATT
894 AAATAAAGAT
Statistics
Matches: 211, Mismatches: 40, Indels: 48
0.71 0.13 0.16
Matches are distributed among these distances:
19 2 0.01
21 25 0.12
22 143 0.68
23 19 0.09
24 3 0.01
25 3 0.01
26 15 0.07
28 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:1010 original size:45 final size:45
Alignment explanation
Indices: 922--1058 Score: 127
Period size: 45 Copynumber: 3.1 Consensus size: 45
912 TGTTTCGTTC
* * * * *
922 TCATAGGGTGATTATCGAAA-TTTAATGGTGTGGTTATCAAAATT
1 TCATAGAGAGATTATCAAAATTTTAATAGTGCGGTTATCAAAATT
* *
966 TTAT-GAAGAGATTATCAAAATTTTCATAGTGCGGTTATCAAAATT
1 TCATAG-AGAGATTATCAAAATTTTAATAGTGCGGTTATCAAAATT
* * * * * *
1011 TCATAGGGAAATTATCAAAATTTTACT-TTGTGGTTATCAAATTT
1 TCATAGAGAGATTATCAAAATTTTAATAGTGCGGTTATCAAAATT
1055 TCAT
1 TCAT
1059 GGGTTATCGA
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
43 1 0.01
44 32 0.43
45 41 0.55
46 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (45 bp):
TCATAGAGAGATTATCAAAATTTTAATAGTGCGGTTATCAAAATT
Found at i:1015 original size:22 final size:22
Alignment explanation
Indices: 933--1097 Score: 90
Period size: 22 Copynumber: 7.6 Consensus size: 22
923 CATAGGGTGA
* * * *
933 TTATCGAAATTTAATGGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
955 TTATCAAAATTTTAT-GAAGAGA
1 TTATCAAAATTTCATAG-TGAGG
*
977 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAA-TTTCATAGTGAGG
* **
1000 TTATCAAAATTTCATAGGGAAA
1 TTATCAAAATTTCATAGTGAGG
* * *
1022 TTATCAAAATTTTACT-TTGTGG
1 TTATCAAAATTTCA-TAGTGAGG
*
1044 TTATCAAATTTTC--A-TG-GG
1 TTATCAAAATTTCATAGTGAGG
* * *
1062 TTATCGAAATTTCATAATGATG
1 TTATCAAAATTTCATAGTGAGG
*
1084 TTATCAAATTTTCA
1 TTATCAAAATTTCA
1098 CATCATTATC
Statistics
Matches: 108, Mismatches: 26, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
18 13 0.12
19 2 0.02
20 1 0.01
21 3 0.03
22 71 0.66
23 17 0.16
24 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:1065 original size:18 final size:19
Alignment explanation
Indices: 1042--1097 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
1032 TTTACTTTGT
1042 GGTTATCAAATTTTCATG-
1 GGTTATCAAATTTTCATGA
*
1060 GGTTATCGAAATTTCATAATGA
1 GGTTATC-AAATTT--TCATGA
*
1082 TGTTATCAAATTTTCA
1 GGTTATCAAATTTTCA
1098 CATCATTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.23
19 8 0.26
21 10 0.32
22 6 0.19
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
GGTTATCAAATTTTCATGA
Done.