Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019292.1 Corchorus olitorius cultivar O-4 contig19325, 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: 2273
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Found at i:379 original size:154 final size:150
Alignment explanation
Indices: 3--435 Score: 695
Period size: 150 Copynumber: 2.9 Consensus size: 150
1 AA
* * * * *
3 GCCATAAACGATGGAAAGAAAAGCATGGAGGGTTTCCATATCGAAAATGATTCAAACCGGAACTA
1 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAATGATTCAAAACGGAACTA
* * *
68 ATGAGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAA
66 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
133 TCTCACCAAAATGATTATAG
131 TCTCACCAAAATGATTATAG
* *
153 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTA
1 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAATGATTCAAAACGGAACTA
* *
218 ATGGGCCCCTATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
66 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
283 TCTCACCAAAATGATTATAGTTAG
131 TCTCACCAAAATGA-T-TA--TAG
*
307 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAATAATTCAAAACGGAACTA
1 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAATGATTCAAAACGGAACTA
* *
372 ATGGGCCCCGATAGGCCCAAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTA
66 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
436 GACCATAAAC
Statistics
Matches: 260, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
150 132 0.51
151 1 0.00
152 2 0.01
154 125 0.48
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (150 bp):
GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAATGATTCAAAACGGAACTA
ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATAG
Found at i:541 original size:130 final size:130
Alignment explanation
Indices: 308--565 Score: 408
Period size: 130 Copynumber: 2.0 Consensus size: 130
298 TATAGTTAGG
* *
308 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAATAATTCAAAACGGAACTAA
1 CCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAAACAATTCAAAACGGAACTAA
* *
373 TGGGCCCCGATAGGCCCAAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAGA
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAGA
* * * * **
438 CCATAAACAATGGAAATAAAAACATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGTCACTAA
1 CCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAAACAATTCAAAACGGAACTAA
* *
503 TGGGTCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGATCTAAAAACTTCACAGTGGACTA
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
566 ATCTTACCAA
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 116 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (130 bp):
CCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAAACAATTCAAAACGGAACTAA
TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAGA
Found at i:718 original size:154 final size:154
Alignment explanation
Indices: 438--1804 Score: 2042
Period size: 154 Copynumber: 8.9 Consensus size: 154
428 GTGGACTAGA
* * * *
438 CCATAAACAATGGAAATAAAAACATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
* *
503 TGGGTCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGATCTAAAAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
*
568 CTTACCAAAATGATTATAGTTAGG
131 CTCACCAAAATGATTATAGTTAGG
* * * **
592 CCATAAACAATGGAACGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAATCGGAACTAA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
* * *
657 TGGGCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
*
722 CTCACCAAAATGATTATAGGTAGG
131 CTCACCAAAATGATTATAGTTAGG
* * * * ** * **
746 CAATAAAAAATGGAAAGAAAGGCATCGAAGG-TTGCCAAATCGAAGATAATTCAAAGCGGAACTA
1 CCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
* * *
810 ATGGTCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
65 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
875 -CATCACCAAAATGATAATAGTTAGG
130 TC-TCACCAAAATGATTATAGTTAGG
* *
900 CCATAAACAATGGAAAGAAAGGCATCGAAGG-TTGCCAAATCGAAGACGATTCAAAACGTCACTA
1 CCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
* * * *
964 TTGGGCCTCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAA
65 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
1029 TCTCACCAAAATGATTATAGTTAGG
130 TCTCACCAAAATGATTATAGTTAGG
*
1054 CCATAAACAAAGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
* *
1119 TGGTCCCCGATAGGCCCAAAATCACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
1184 CTCACCAAAATGATTATAGTTAGG
131 CTCACCAAAATGATTATAGTTAGG
* *
1208 CCATAAACAAGTAGGAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGAC-AATCAAAACGTCAC
1 CCATAAACAA-T-GG-AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* *
1272 TAATGGTCCCCGATAGGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
63 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
*
1337 AATCTCACCAAAATGATTATTGTTAGG
128 AATCTCACCAAAATGATTATAGTTAGG
* * * ** **
1364 CCATAAATAATGGAAAGAAAAGTATTGAGGGTTGGGAAATCGAAGACGATTCAAAACGGAACTAA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
* * * * *
1429 TGGTCCTCAATATGCCCAAAATAACGAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
1494 CTCACCAAAATGATTATAGTTAGG
131 CTCACCAAAATGATTATAGTTAGG
* * *
1518 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCCAATCGAAGACGATTCAAAATGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
*
1583 TCGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
66 T-GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
1648 TCTCACCAAAATGATTATAGTTAGG
130 TCTCACCAAAATGATTATAGTTAGG
* * * **
1673 CCATAAACAATGGAAAGAAAAGCAATGAGCTTTGCCAAATCGAAGGA-TATTCAAAACGGAACTA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA-GACGATTCAAAACGTCACTA
*
1737 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAA
65 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
1802 TCT
130 TCT
1805 TGATACGAAT
Statistics
Matches: 1110, Mismatches: 93, Indels: 20
0.91 0.08 0.02
Matches are distributed among these distances:
153 33 0.03
154 786 0.71
155 143 0.13
156 115 0.10
157 33 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
CTCACCAAAATGATTATAGTTAGG
Done.