Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011380.1 Corchorus olitorius cultivar O-4 contig11413, 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: 2068
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1169 original size:331 final size:330
Alignment explanation
Indices: 1--1401 Score: 2441
Period size: 331 Copynumber: 4.2 Consensus size: 330
1 GGTCAATTTTTTCAAAATTTTAGCCGAAATCGTTGTACTAACCATCACGGTTTTTTGGCTAAAAA
1 GGTCAATTTTTTCAAAATTTTAGCCGAAATCG-TGTACTAACCATCACGG-TTTTTGGCT-AAAA
* *
66 ACGCATTCTGGGACCCCGACTCAGTTTCACATGTTTTTTTGTCGCCCAGACTCCTTGAAATATGT
63 ACGCATTCTGGGACCCCGACTCAGTTTCGCATG-TTTTTTGTCGCCCAGACTCCTTGAAATATCT
* *
131 TTATTCATCCAGCCAAATCTCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATC
127 ATATTCATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATC
* *
196 TTGTTTCGATTTAAATAGATATTAATTTTAAAAAATATTAAAAAAATGATATTAGAAGCGTGGAA
192 TTGTTTCGATTTAAATAGAAATTAATTCTAAAAAATATT-AAAAAATGATATTAGAAGCGTGGAA
* *
261 AACACTTCAATCTTTTTGGCATTTAATTATATATTTTTTAT-A-T-TTGGCCAGAAAATGAGGAA
256 AACACTTCAATCTTTTTGGCATTGAATTATATAATTTTTATAAGTATTGGCCAGAAAATGAGGAA
323 AAAACATTCG
321 AAAACATTCG
333 GGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
1 GGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
398 CATTCTGGGACCCCGACTCAGTTTCGCATGTTTTTTGTCGCCCAGACTCCTTGAAATATCTATAT
66 CATTCTGGGACCCCGACTCAGTTTCGCATGTTTTTTGTCGCCCAGACTCCTTGAAATATCTATAT
463 TCATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATCTTGT
131 TCATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATCTTGT
*
528 TTCGATTTAAATAGAAATTAATTCTAAAAAATATTAAAAAATGATATTAGAAGCGTGGAAAGCAC
196 TTCGATTTAAATAGAAATTAATTCTAAAAAATATTAAAAAATGATATTAGAAGCGTGGAAAACAC
*
593 TTCAATCTTTTTGGCATTGAATTATATAATTTTTATAAGTATT-GCCAGAAAATGAGGAAAAAGC
261 TTCAATCTTTTTGGCATTGAATTATATAATTTTTATAAGTATTGGCCAGAAAATGAGGAAAAAAC
657 ATTCG
326 ATTCG
* *
662 GGTCAATTTTTTTCAAAACTTTAGCCGAAATCGTGTACTAACCATCACGGTCTTTGGCTAAAAAC
1 GGTCAA-TTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
*
727 GCATTCCGGGACCCCGACTCAGTTTCGCATGTTTTTTGTCGCCCAGACTCCTTGAAATATCTATA
65 GCATTCTGGGACCCCGACTCAGTTTCGCATGTTTTTTGTCGCCCAGACTCCTTGAAATATCTATA
* *
792 TTCATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTAGGAGTATCTGAATCTTA
130 TTCATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATCTTG
857 TTTCGATTTAAATAGAAATTAATTCTAAAAAATATTAAAAAATGATATTAGAAGCGTGGAAAACA
195 TTTCGATTTAAATAGAAATTAATTCTAAAAAATATTAAAAAATGATATTAGAAGCGTGGAAAACA
* *
922 CTTCAATCTTTATGGCATTGAATTATATAATTTTTATAAGTATTTGGCCCGAAAATGAGGAAAAA
260 CTTCAATCTTTTTGGCATTGAATTATATAATTTTTATAAGTA-TTGGCCAGAAAATGAGGAAAAA
987 ACATTCG
324 ACATTCG
994 GGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
1 GGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
* *
1059 CATTCCGGGACCCCGACTCAGTTTCGCATGTTTTTTGTCGCCCAGACTCCTTCAAATATCTATAT
66 CATTCTGGGACCCCGACTCAGTTTCGCATGTTTTTTGTCGCCCAGACTCCTTGAAATATCTATAT
*
1124 TAATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATCTTGT
131 TCATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATCTTGT
* *
1189 TTCGATTTAAGTAGAAATTAATTCTAAAAAATATTTAAAAAATGATATTAGAAGCGTGGAAAGCA
196 TTCGATTTAAATAGAAATTAATTCTAAAAAATA-TTAAAAAATGATATTAGAAGCGTGGAAAACA
* * *
1254 CTTCAATCATTTTGGCATTGAATTATATAATTTTTATAAGTATTAGCCATAAAATGAGGAAAAAA
260 CTTCAATCTTTTTGGCATTGAATTATATAATTTTTATAAGTATTGGCCAGAAAATGAGGAAAAAA
1319 CATTCG
325 CATTCG
* * * *
1325 GGTCTATTTTTTCAAAATTTTAGCCGAAATCGTGTTCTAACCATCACGGTTTTTGACAAAAAACG
1 GGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
1390 CATTCTGGGACC
66 CATTCTGGGACC
1402 TTGATCAGAC
Statistics
Matches: 1025, Mismatches: 37, Indels: 15
0.95 0.03 0.01
Matches are distributed among these distances:
327 63 0.06
328 131 0.13
329 68 0.07
330 299 0.29
331 332 0.32
332 132 0.13
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (330 bp):
GGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACG
CATTCTGGGACCCCGACTCAGTTTCGCATGTTTTTTGTCGCCCAGACTCCTTGAAATATCTATAT
TCATCCAGCCAAATCCCATCCACATTGGATTCAAGTATTTGATTTTACGAGTATCTGAATCTTGT
TTCGATTTAAATAGAAATTAATTCTAAAAAATATTAAAAAATGATATTAGAAGCGTGGAAAACAC
TTCAATCTTTTTGGCATTGAATTATATAATTTTTATAAGTATTGGCCAGAAAATGAGGAAAAAAC
ATTCG
Found at i:1881 original size:21 final size:21
Alignment explanation
Indices: 1838--1882 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1828 GTGACACTGC
* * *
1838 CCACCTGGGTTCTCAAGTAAA
1 CCACATGGGTGCTCAAGGAAA
*
1859 CCACATGGGTGCTCAAGGCAA
1 CCACATGGGTGCTCAAGGAAA
1880 CCA
1 CCA
1883 TGTGGGCGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGGAAA
Done.