Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011000.1 Corchorus olitorius cultivar O-4 contig11032, 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: 2730
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Found at i:415 original size:154 final size:153
Alignment explanation
Indices: 2--759 Score: 1061
Period size: 154 Copynumber: 4.9 Consensus size: 153
1 A
* *
2 AGGCCCAAAATAAC-AGTGTTCCAAATGAGCTAAAAATTTCACAGGTGGACTAATCTAACCAAAA
1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA-GTGGACTAATCTCACCAAAA
*
66 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTGAGGTTTCCCAAATCGAAGGCGAC
65 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA-TTGAGGTTT-CCAAATCGAAGACGA-
*
131 TTCAAAACGGA-ACTAATGAGCCCCGAT
127 TTCAAAAC-GATACTAATGGGCCCCGAT
*
158 AGGCCCAAAATAACAAGTGCTCCAAAATGAGCTAAAAAACTTCACAAGTGGACTAATCTCACCAA
1 AGGCCCAAAATAACAAGTGTTCC-AAATGAGCT-AAAAACTTCAC-AGTGGACTAATCTCACC-A
* *
223 AAATGGTTATAGTTAGGCCATAAACAATGGAAACAAAAGCATTGAGGTTTCCTAAATCGAAGACG
62 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCC-AAATCGAAGACG
*
288 ATTCAGAACGATACTAATGGGCCCCGAT
126 ATTCAAAACGATACTAATGGGCCCCGAT
* * ** *
316 AGGCCCAAAATTACAAGTGTTCCGAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAAT
1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* ** * *
381 GATTACAGTTAGGCCATAAACAATGGAAAGAAAAGCATCAACGGTTGCCAAATCGATGACGATTC
66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCCAAATCGAAGACGATTC
* * **
446 AAAACGTTACTAATGGGTCTTGAT
130 AAAACGATACTAATGGGCCCCGAT
*
470 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAAT
1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* * ** *
535 GATAAGAGTTAGGCCATAATTAATGGAAAGAAACGCATTGAGGTTTCTCAAATCGAAGACGATTC
66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTC-CAAATCGAAGACGATTC
*
600 AAAACGACACTAATGGGCCCCGAT
130 AAAACGATACTAATGGGCCCCGAT
* * *
624 AGGCGCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTATTCTCACCAAAAT
1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* * * *
689 GATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTC
66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCCAAATCGAAGACGATTC
754 AAAACG
130 AAAACG
760 GAACTTAATG
Statistics
Matches: 533, Mismatches: 59, Indels: 22
0.87 0.10 0.04
Matches are distributed among these distances:
153 5 0.01
154 319 0.60
155 26 0.05
156 25 0.05
157 17 0.03
158 54 0.10
159 46 0.09
160 41 0.08
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (153 bp):
AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAGACGATTCA
AAACGATACTAATGGGCCCCGAT
Found at i:2118 original size:153 final size:154
Alignment explanation
Indices: 1701--2729 Score: 1405
Period size: 153 Copynumber: 6.7 Consensus size: 154
1691 CAATCGGGGG
* * * *
1701 TTGCCAAATCGAAAAAGATTCAAAACGGAACTAATGGGCCCCGAAAGGC-CTAAAATAACAAGTG
1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCAC-AAAATAACAAGTG
1765 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
65 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
* * *
1830 ACAATGAAAAGAAAAACATTGAGGT
130 ACAATGGAAAGAAAAGCATCGAGGT
* * ** *
1855 TTACCAAATCGAAGACGATTTAAAACGTCACTAATGGACCTTC-ATAGGCACAAAATAACAAGTG
1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACC-CCGATAGGCACAAAATAACAAGTG
*
1919 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCATAA
65 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
* *
1984 ACAATGGAAAG-AAAGCATCAAGGG
130 ACAATGGAAAGAAAAGCATCGAGGT
* *** * ** *
2008 TTGCCAAATCGATGACGATTCAAAACATCACTAATAGG-TCTTGATAGGAACAAAATAACAAGTG
1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAAT-GGACCCCGATAGGCACAAAATAACAAGTG
* * ** ** * **
2072 TTCAAAATGAGCTAAAATCTTCACAGTGTTCTAATCTCACTGAAATGACTACGGTTAGGCCATAA
65 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
* *
2137 A-AATGGAAAGAAAAGCATCGTGGA
130 ACAATGGAAAGAAAAGCATCGAGGT
* * *
2161 TTGCCAAATCGAAGACGATTCAAAACGGAACAAATGG-GCCCGAAAGGC-CTAAAATAACAAGTG
1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCAC-AAAATAACAAGTG
* *
2224 TTCCAAATGAGCTAAAAACTCCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATGA
65 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
* *
2289 ACATTGGAAAGAAAAGCATTGAGGT
130 ACAATGGAAAGAAAAGCATCGAGGT
*
2314 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGT
1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCACAAAATAACAAGTGT
*
2379 TCCAAATGAGCTAAAAACTTCACAGTGGA-TTATCTCACCAAAATGAATTATAGTTAGGCCATAA
66 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG-ATTATAGTTAGGCCATAA
*
2443 ACAAAGGAAAGAAAAGCATCGAGGT
130 ACAATGGAAAGAAAAGCATCGAGGT
** * *
2468 TT-CCAAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAACAAGTGT
1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCACAAAATAACAAGTGT
*
2532 TCCAAATGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAA
66 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* *
2597 CAATGGAAA-AAAACGAATTGAGGT
131 CAATGGAAAGAAAA-GCATCGAGGT
* * *
2621 TTGCCAAATCGAAAACAATTCAAAACGGAACTAATAGG-CCTCGATAGGCACAAAATAACAAGTG
1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAAT-GGACCCCGATAGGCACAAAATAACAAGTG
* * *
2685 TTCCAAATGAGCCAAAAACTTCACGGTGGACTTATCTCACCAAAA
65 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
2730 A
Statistics
Matches: 773, Mismatches: 88, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
151 1 0.00
152 90 0.12
153 352 0.46
154 325 0.42
155 5 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCACAAAATAACAAGTGT
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
CAATGGAAAGAAAAGCATCGAGGT
Done.