Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009864.1 Corchorus olitorius cultivar O-4 contig09896, 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: 3784
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:941 original size:22 final size:22
Alignment explanation
Indices: 724--1260 Score: 131
Period size: 22 Copynumber: 24.5 Consensus size: 22
714 ACAATCAAAC
* *
724 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * * * * *
746 TAATATTTCATA-GTATAGCTAC
1 CAAAATTTCATAGGGA-GGTTAT
*
768 CAAAATTTCATATGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
790 CAACACTTT-ATTGTGTA-GTTAT
1 CAA-AATTTCATAG-GGAGGTTAT
* * ***
812 CAAAATTTTACACAAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*** **
834 CAAAATTTCATAAAAACTTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
856 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGGGAGGTTAT
* * * *
878 CAAAATCTCATACGAATGTTAT
1 CAAAATTTCATAGGGAGGTTAT
** * * *
900 TGAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*
922 CGAAATTTCATAGGGAGGTTAATT
1 CAAAATTTCATAGGGAGGTT-A-T
*
946 AACAAAATTTCATATGGAGGTTAT
1 --CAAAATTTCATAGGGAGGTTAT
* *
970 GAAAATTTTAT-GGAGAGGTTAT
1 CAAAATTTCATAGG-GAGGTTAT
** *
992 CAAAGAGGAT-ATCA--CA-GTT-T
1 CAAA-A-TTTCAT-AGGGAGGTTAT
* * *
1012 ---TATTCTCATAAGAAGGTTAT
1 CAAAATT-TCATAGGGAGGTTAT
* * *
1032 CGAAATTTCAT-GGTGTGTTTAT
1 CAAAATTTCATAGG-GAGGTTAT
* * *
1054 CATAATTT-TTTGAGGAGGTTAT
1 CAAAATTTCATAG-GGAGGTTAT
* * **
1076 CAAAATTTTCATTGTGTTGTTA-
1 CAAAA-TTTCATAGGGAGGTTAT
* * * *
1098 C-CAACTTCATA-GTATGATTAT
1 CAAAATTTCATAGGGA-GGTTAT
* *
1119 CAAAATATCATTGGG-GGATTAT
1 CAAAATTTCATAGGGAGG-TTAT
**
1141 CAAAATTTCATACTGAGAG-TAT
1 CAAAATTTCATAGGGAG-GTTAT
* *
1163 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
1185 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
1207 CAAATTTTCATAGGGAAGTTAT
1 CAAAATTTCATAGGGAGGTTAT
** **
1229 TGAAATTTCATAATGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*
1251 CAAATTTTCA
1 CAAAATTTCA
1261 GTTTGGTTAT
Statistics
Matches: 363, Mismatches: 115, Indels: 74
0.66 0.21 0.13
Matches are distributed among these distances:
16 3 0.01
17 2 0.01
18 1 0.00
19 3 0.01
20 10 0.03
21 18 0.05
22 274 0.75
23 26 0.07
24 7 0.02
25 1 0.00
26 18 0.05
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAT
Found at i:1185 original size:66 final size:66
Alignment explanation
Indices: 1103--1254 Score: 164
Period size: 66 Copynumber: 2.3 Consensus size: 66
1093 TGTTACCAAC
* * * *
1103 TTCATAGTATGATTATCAAAATATCATTG-GGGGATTATCAAAATTTCATACTGAGAG-TATCAA
1 TTCATAGTGTGGTTATCAAAATATCATAGTGGGG-TTATCAAAATTTCATACGGA-AGTTATCAA
1166 AAT
64 AAT
* * * * **
1169 TTCATAGTGTGGTTATCAAAATTTCATAGTGTGGTTATCAAATTTTCATAGGGAAGTTATTGAAA
1 TTCATAGTGTGGTTATCAAAATATCATAGTGGGGTTATCAAAATTTCATACGGAAGTTATCAAAA
1234 T
66 T
* *
1235 TTCATAATGAGGTTATCAAA
1 TTCATAGTGTGGTTATCAAA
1255 TTTTCAGTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
65 2 0.03
66 67 0.93
67 3 0.04
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (66 bp):
TTCATAGTGTGGTTATCAAAATATCATAGTGGGGTTATCAAAATTTCATACGGAAGTTATCAAAA
T
Found at i:1208 original size:44 final size:44
Alignment explanation
Indices: 1025--1273 Score: 172
Period size: 44 Copynumber: 5.7 Consensus size: 44
1015 TCTCATAAGA
* * * * **
1025 AGGTTATCGAAATTTCATGGTGTGTTTATCATAATTTTTTGAG-G
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAT-AGTG
* * * *
1069 AGGTTATCAAAATTTTCATTGTGTTGTTA-C-CAACTTCATAGT-
1 AGGTTATCAAAA-TTTCATAGTGTGGTTATCAAAATTTCATAGTG
* * * * *
1111 ATGATTATCAAAATATCATTG-GGGGATTATCAAAATTTCATACTG
1 A-GGTTATCAAAATTTCATAGTGTGG-TTATCAAAATTTCATAGTG
1156 AGAG-TATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTG
1 AG-GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTG
* * * ** ** *
1200 TGGTTATCAAATTTTCATAGGGAAGTTATTGAAATTTCATAATG
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTG
* *
1244 AGGTTATCAAATTTTC--AGTTTGGTTATCAA
1 AGGTTATCAAAATTTCATAGTGTGGTTATCAA
1274 TAGTTCTATG
Statistics
Matches: 160, Mismatches: 35, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
41 2 0.01
42 21 0.13
43 17 0.11
44 103 0.64
45 17 0.11
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTG
Done.