Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014887.1 Corchorus olitorius cultivar O-4 contig14920, 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: 7401
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:1009 original size:68 final size:68
Alignment explanation
Indices: 898--1383 Score: 733
Period size: 68 Copynumber: 7.1 Consensus size: 68
888 CTCATTGAAC
* * * * * *
898 TTGGCTTATGGAAAAGCCCCTGAATGCTTGGATGAAACCAAGGCTAAACTGACTCGTATGTAAAC
1 TTGGCTTGTGGAAAAGCCCCTG-CTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
*
963 GAGC
65 GAGT
* * * *
967 CTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
1032 AGT
66 AGT
* *
1035 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
1100 AGT
66 AGT
* *
1103 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAAACAAGGCTTAATTGGCTCGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
1168 AGT
66 AGT
1171 TTGGCTTGTGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
1 TTGGCTTGTG-GAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
*
1236 GAAT
65 GAGT
*
1240 TTGGCTTG-CGAGAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
1 TTGGCTTGTGGA-AAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
1304 GAGT
65 GAGT
* * *
1308 TTGGCTTG-CGAGAAAGCCCTTGCTGTTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
1 TTGGCTTGTGGA-AAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
1372 GAGT
65 GAGT
*
1376 TTGACTTG
1 TTGGCTTG
1384 GAAAAGTCAA
Statistics
Matches: 394, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
67 2 0.01
68 310 0.79
69 82 0.21
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
AGT
Found at i:1258 original size:205 final size:204
Alignment explanation
Indices: 898--1383 Score: 726
Period size: 205 Copynumber: 2.4 Consensus size: 204
888 CTCATTGAAC
* * * * *
898 TTGGCTTATGGAAAAGCCCCTGAATGCTTGGAT-GAAACCAAGGCTAAACTGACTCGTATGTAAA
1 TTGGCTTGTGGAAAAGCCCCTG-CTGCTTGGATGGAAA-CAAGGCTTAACTGGCTCGTATGGAAA
** *
962 CGAGCCTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGG
64 CGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGG
* *
1027 AAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTA
129 AAACGAATTTGGCTTGCGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTA
1092 TGGAAACGAGT
194 TGGAAACGAGT
*
1103 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAAACAAGGCTTAATTGGCTCGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAAACAAGGCTTAACTGGCTCGTATGGAAACG
* *
1168 AGTTTGGCTTGTGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGA
66 AGTTTGGCTTGTG-GAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGA
* *
1233 AACGAATTTGGCTTGC-GAGAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTA
130 AACGAATTTGGCTTGCGGA-AAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTA
1297 TGGAAACGAGT
194 TGGAAACGAGT
* * * *
1308 TTGGCTTG-CGAGAAAGCCCTTGCTGTTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
1 TTGGCTTGTGGA-AAAGCCCCTGCTGCTTGGATGGAAACAAGGCTTAACTGGCTCGTATGGAAAC
*
1372 GAGTTTGACTTG
65 GAGTTTGGCTTG
1384 GAAAAGTCAA
Statistics
Matches: 256, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
204 48 0.19
205 208 0.81
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (204 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAAACAAGGCTTAACTGGCTCGTATGGAAACG
AGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAA
ACGAATTTGGCTTGCGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATG
GAAACGAGT
Found at i:2156 original size:50 final size:50
Alignment explanation
Indices: 2051--2149 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
2041 GAAATGCCCT
* **
2051 TTGAAAAGCGAATTTTGATTTTGGACTCACAAATGGAATGCAATCTTATC
1 TTGAAAAGCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTATC
*
2101 TTGAAAATCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTAT
1 TTGAAAAGCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTAT
2150 TATGAAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (50 bp):
TTGAAAAGCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTATC
Found at i:2467 original size:15 final size:15
Alignment explanation
Indices: 2434--2480 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 15
2424 TCTTTTCTTC
*
2434 TTTTCTTCATTTTCA
1 TTTTTTTCATTTTCA
2449 -TTTTTTCA-TTTCA
1 TTTTTTTCATTTTCA
2462 TTTTTTTCATTTTCA
1 TTTTTTTCATTTTCA
2477 TTTT
1 TTTT
2481 CATCATCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 5 0.17
14 15 0.52
15 9 0.31
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTTCATTTTCA
Found at i:2493 original size:28 final size:27
Alignment explanation
Indices: 2434--2495 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
2424 TCTTTTCTTC
* *
2434 TTTTCTTCATTTTCATTTTTTCATTTCA
1 TTTTTTTCATTTTCA-TTTTTCATATCA
2462 TTTTTTTCATTTTCA-TTTTCATCATCA
1 TTTTTTTCATTTTCATTTTTCAT-ATCA
2489 TTTTTTT
1 TTTTTTT
2496 ATGCACTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.23
27 10 0.32
28 14 0.45
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTTTCATTTTCATTTTTCATATCA
Found at i:2847 original size:11 final size:11
Alignment explanation
Indices: 2833--2861 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2823 TTTTCACTTC
2833 TTTTTTGTATT
1 TTTTTTGTATT
2844 TTTTTTGTATT
1 TTTTTTGTATT
2855 TTTTTTG
1 TTTTTTG
2862 CATCTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (11 bp):
TTTTTTGTATT
Found at i:3840 original size:75 final size:75
Alignment explanation
Indices: 3698--3846 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
3688 TGGATTCAGT
* * * * **
3698 CACCTTGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAGAACTCATTTTT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATTAAAACTCATCATT
3763 CCTTTGCTCA
66 CCTTTGCTCA
*
3773 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATTAAAATTCATCATT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATTAAAACTCATCATT
3838 CCTTTGCTC
66 CCTTTGCTC
3847 CCAGTCCAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (75 bp):
CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATTAAAACTCATCATT
CCTTTGCTCA
Done.