Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012226.1 Corchorus olitorius cultivar O-4 contig12259, 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: 3115
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Found at i:1324 original size:21 final size:21
Alignment explanation
Indices: 1300--1412 Score: 147
Period size: 21 Copynumber: 5.4 Consensus size: 21
1290 CTTAGGCAAT
*
1300 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
* * *
1321 TCCAATGAACTTGGAACCTCC
1 TCCAATGAGCTTGGAACTTGC
*
1342 TCTAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
*
1363 TCCAATGAGATTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
*
1384 TCCAATGAGCTAGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
1405 TCCAATGA
1 TCCAATGA
1413 ACTTCTAGCA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 2 0.03
21 78 0.98
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:1799 original size:154 final size:154
Alignment explanation
Indices: 1513--3111 Score: 2416
Period size: 154 Copynumber: 10.4 Consensus size: 154
1503 GCATCATTTA
* ** * *
1513 CCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATAGGCCAAAAAGAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* * * *
1578 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGGTAGGCCATAAAGAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
1643 TGGAAAGAAAAGCATTGAGGTTTG
131 TGGAAAGAAAAGCATTGAGGTTTG
* * ** **
1667 CCTAATCGAATACGATTCAAAACGGAACTAATGGGCCTAGATAGGCCCAAAATAA-AATGTGTTC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA-GTGTTC
*
1731 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAGTATAGTTAGGCCATAAACA
65 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * *
1796 ATGGAGAGAAAGGCATTGAGGGTTG
130 ATGGAAAGAAAAGCATTGAGGTTTG
* *
1821 CCAAATCGAAGACGATTCAAAACATCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* *
1886 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGTTTATAGTTAGGCCATAAACAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
1951 TGGAAAGAAAAGCATTG-GGTTTTG
131 TGGAAAGAAAAGCATTGAGG-TTTG
* *
1975 CCAAATCGAAGACGATTCAAAACATCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* * *
2040 AAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTACACAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
2105 TGGAAAGAAAAGCATTGAGGTTTG
131 TGGAAAGAAAAGCATTGAGGTTTG
* * * * *
2129 TCAAATCGAAGACAATTCAAAACAG-AACTAATGGGCCTCGATAGGGCCTAAAATAACAAGTGTT
1 CCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGATA-GGCCCAAAATAACAAGTGTT
2193 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
64 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
2258 AATGGAAAGAAAAGCATTGAGGTTTG
129 AATGGAAAGAAAAGCATTGAGGTTTG
** *
2284 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* * *
2349 AAAGGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGCCCATAAACAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
*
2414 TGGAAAGAAAAGCATTGAGGTTTT
131 TGGAAAGAAAAGCATTGAGGTTTG
* *
2438 CCAAATCGAAGACGATTCAAAACGTCACTAATGGTCTCCGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
2503 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * * *
2568 TGGATAGAAAGGCACTAAGGATTG
131 TGGAAAGAAAAGCATTGAGGTTTG
*
2592 CCAAATCGAAGACGATTCAAATCGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGATTC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG-TTC
* *
2657 CAAATGAGCTAAAAACATCACATTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
65 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
2722 ATGGAAAGAAAAGCATTGAGGTTTG
130 ATGGAAAGAAAAGCATTGAGGTTTG
* ** * * **
2747 CCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAAGCCCAAAATAACAAGTGTTGA
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* *
2812 AAATGAGGTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG-CATAAACAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* *
2876 TGGAAAGAAAAGCATTGAGGGTTA
131 TGGAAAGAAAAGCATTGAGGTTTG
* * ** * * *
2900 CCAAATCAAAGACGAATCAAAACGGAACTAATGGGCCCCAATAGGCTCAAAATAACAGGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* * *
2965 AAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATAATTATAGTTGGGCCATAAA-AA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * *
3029 TTGGAAAGAAAGGCATTGTGGGTTG
131 -TGGAAAGAAAAGCATTGAGGTTTG
* * *
3054 CCAAATCAAAGACGATTCAAAACGTCACTAATAGGCCCCCATAGGCCCAAAATAACAA
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA
3112 TTGT
Statistics
Matches: 1322, Mismatches: 113, Indels: 20
0.91 0.08 0.01
Matches are distributed among these distances:
153 142 0.11
154 889 0.67
155 291 0.22
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
TGGAAAGAAAAGCATTGAGGTTTG
Found at i:2377 original size:463 final size:461
Alignment explanation
Indices: 1513--3111 Score: 2434
Period size: 463 Copynumber: 3.5 Consensus size: 461
1503 GCATCATTTA
* ** * *
1513 CCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATAGGCCAAAAAGAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* * * *
1578 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGGTAGGCCATAAAGAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * **
1643 TGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAATACGATTCAAAACGGAACTAATGGGCCTAGA
131 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGA
1708 TAGGCCCAAAATAA-AATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
196 TAGGCCCAAAATAACAA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* * * *
1772 ATGAGTATAGTTAGGCCATAAACAATGGAGAGAAAGGCATTGAGGGTTGCCAAATCGAAGACGAT
260 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
*** *
1837 TCAAAACATCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
325 TCAAAACGGAACTAATGG-GCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
* *
1902 TCACAGTGGACTAATCTCACCAAAAGGTTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
389 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
1967 G-GGTTTT
454 GAGGTTTT
* *
1974 GCCAAATCGAAGACGATTCAAAACATCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTC
1 -CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
* * *
2039 CAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTACACA
65 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * *
2104 ATGGAAAGAAAAGCATTGAGGTTTGTCAAATCGAAGACAATTCAAAACAG-AACTAATGGGCCTC
130 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTAACTAATGGGCCCC
*
2168 GATAGGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
194 GATA-GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
2233 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
258 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
*
2298 ATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAAGGAGCTAAAAA
323 ATTCAAAACGGAACTAATGGGCC-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
* *
2363 CTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCA
387 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
2428 TTGAGGTTTT
452 TTGAGGTTTT
* *
2438 CCAAATCGAAGACGATTCAAAACGTCACTAATGGTCTCCGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
2503 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * * * * *
2568 TGGATAGAAAGGCACTAAGGATTGCCAAATCGAAGACGATTCAAATCGTCACTAATGGGCCCCGA
131 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGA
* *
2633 TAGGCCCAAAATAACAAGTGATTCCAAATGAGCTAAAAACATCACATTGGACTAATCTCACCAAA
196 TAGGCCCAAAATAACAAGTG-TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
*
2698 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGAT
260 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
* ** * *
2763 TCAAAACGGAACTAATGGGCCCAGATAAGCCCAAAATAACAAGTGTTGAAAATGAGGTAAAAACA
325 TCAAAACGGAACTAATGGGCCC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
2828 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG-CATAAACAATGGAAAGAAAAGCATT
389 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
* *
2892 GAGGGTTA
454 GAGGTTTT
* * ** * * *
2900 CCAAATCAAAGACGAATCAAAACGGAACTAATGGGCCCCAATAGGCTCAAAATAACAGGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* * *
2965 AAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATAATTATAGTTGGGCCATAAA-AA
66 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * * * * *
3029 TTGGAAAGAAAGGCATTGTGGGTTGCCAAATCAAAGACGATTCAAAACGTCACTAATAGGCCCCC
131 -TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCG
3094 ATAGGCCCAAAATAACAA
195 ATAGGCCCAAAATAACAA
3112 TTGT
Statistics
Matches: 1045, Mismatches: 83, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
461 2 0.00
462 416 0.40
463 619 0.59
464 8 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (461 bp):
CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGA
TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
CAAAACGGAACTAATGGGCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
GGTTTT
Done.