Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011080.1 Corchorus olitorius cultivar O-4 contig11113, 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: 1718
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Found at i:282 original size:154 final size:154
Alignment explanation
Indices: 2--1718 Score: 2502
Period size: 154 Copynumber: 11.2 Consensus size: 154
1 A
* * ** *
2 TTGAGGTTTACCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAAGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
*
67 CAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
132 CCATAAACAATGGAAAGAAAGGCT
131 CCATAAACAATGGAAAGAAAAGCT
*
156 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
*
221 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* *
286 CCATGAACAACT-TAAAGAAAAGCT
131 CCATAAACAA-TGGAAAGAAAAGCT
* * * ** *
310 TTGACGTTTGCCAAATCGAAAATGATTCAAAACGTCACTAATGGG-CCAGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
374 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCGAAAATGATTATAGTTA-
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAATGATTATAGTTAG
*
438 G-CAT-AAC-AT-G-AAG-AAAGCA
130 GCCATAAACAATGGAAAGAAAAGCT
* *
457 TTGAGGTTTGCCAAATCGAAGACGATTTAATAC-GACACTAATAGGGCCCCGAATAGGCCC-AAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAAT-GGGCCCCG-ATAGGCCCAAAA
* *
520 T-ACAAGTTTTCC-AATAAGCT-AAAA-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
63 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
581 AGGCCATAAACAATAGG-AAGAAAAGCT
128 AGGCCATAAACAAT-GGAAAGAAAAGCT
* * *
608 TTGAGGTTTGCCAAATCGAAGACGATTCAAACCGGAACTAATGGGTCTCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
*
673 CAAGTGTTCCAAATGAGCTAAAAACTTACACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
66 CAAGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
738 GCCATAAACAATGGAAAGAAAAGCT
130 GCCATAAACAATGGAAAGAAAAGCT
* * ** *
763 TTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGCCCCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* *
828 CAAGTGTTGCAAATGAGCTAAAAACTTCACAGTGGACTAAAT-TCACCAAAATGATAATAGTTAG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTAG
* *
892 GGCATAAACAATGGAAAGAAAAGCA
130 GCCATAAACAATGGAAAGAAAAGCT
* * ** *
917 TTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGCCCCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * *
982 CAAGTGTTCCAAATGAGTTAAAAACTTCACAGCGGACTAATCTCACCAAAATAATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1047 CCATAAACAATGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCT
* * *
1071 TTGAGGGTTGCCAAATCGAAGACAATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* *
1136 CAAGTGTTCCAAATGAGCTAAAAACTTCACGGTGGTCTAATCTCACCAAAATGATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1201 CCATAAACAATGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCT
* ** * *
1225 TTGAGGTTTGCCAATTCGAAGACGATTCAAAATAGAACTAATGGGCCTCGATAGGCCCAAAATAC
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * * *
1290 CAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTACAATTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* *
1355 CCATAAACAATGGAAATAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCT
* * *** * *
1379 TTGAGGTTTGCCAAATCGAAGAAGATTCAATACATTACTAATGGGCCCTGATAGGTCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * * * * * *
1444 CAAGTTTTCCAAATAAGCTAAAAAGTTCACAATGGACTAATCTGACCAAATTGATTATGGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1509 CCATAAACAATGGAAAGAAAAGCT
131 CCATAAACAATGGAAAGAAAAGCT
1533 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGG-CCAAAATA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA-GGCCCAAAATA
* * *
1597 ACAAGTGTTCCAAATGAGCAAAAAAACTTCAGAGTGGACTAATCTCACTAAAATGATTATAGTTA
65 ACAAGTGTTCCAAATGAGC-TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
1662 GGCCATAAACAATGG-AAGAAAAGCT
129 GGCCATAAACAATGGAAAGAAAAGCT
1687 TTGAGG-TTGCCAAATCGAAGACGATTCAAAAC
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
Statistics
Matches: 1416, Mismatches: 122, Indels: 51
0.89 0.08 0.03
Matches are distributed among these distances:
144 16 0.01
145 23 0.02
146 7 0.00
147 49 0.03
148 18 0.01
149 16 0.01
150 23 0.02
151 54 0.04
152 12 0.01
153 97 0.07
154 902 0.64
155 199 0.14
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (154 bp):
TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAGAAAAGCT
Done.