Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_747 ID=scaffold_747-JGI_221_v2.0
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: 4186
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.23
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:48 original size:36 final size:36
Alignment explanation
Indices: 1--1027 Score: 1583
Period size: 36 Copynumber: 28.6 Consensus size: 36
*
1 TCAGCCCCCTGAACCCTAAGGAGCCGACCGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
*
37 TCAGCCCCCTGAACCCTAAGGAGCCGACCGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* *
73 TCAGCCCCCTGAACCCAAAGGAGCCGGACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* *
109 TCAGCCCCCTTGAACCCTAAGGAGCCGGACGTGGGGG
1 TCAGCCCCC-TGAACCCTAAGGAGCCGAACGCGGGGG
*
146 TCAGCCCCCTGAACCCTAAGGAGCCGACCGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* *
182 TCAGCCCCCTGAACCCTAAGGAGCCGGACGC-GGGT
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
217 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* *
253 TCAGCCCCCTGAACCCTAAGGAGCCGGACTCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
*
289 TCAGCTCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
325 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* * *
361 TCAGCCCCCTGAACCCTAATGAGCCGGACGCAGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
397 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
** *
433 TCAGCCCCCTGAATACTAAGGAGCCGGACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
** *
469 TCAGCCCCCTGAATACTAAGGAGCCGATCGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* * *
505 TCAGCCGCCTGAACCCTATGGAGCCGAACGCGGGGA
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
541 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* * * *
577 TCA-TCCCCTGAACCCCAAGGAGCCGACCGCGGGAG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* *
612 TCAG-CCCCTGAACCATAAGGAGCCGAGCGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
*
647 TCAGCCCCCTGAACCCTAAGGAGCCGACCGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* **
683 TCAGCCCCCTGAACCCTAAGGAGCCGGACTTGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
719 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
*
755 TGAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
*
791 TCATCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
*
827 TCATCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* * *
863 TCATCCCCCTGAACCCCAAGGATCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* *
899 TCAGCCCCCTGAACCCCAAGGAGCCGAACACGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* * **
935 TCATCCCCCTGAACCCCAAGGAGCCGAAATCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
* *
971 TCATCCCCCTGAACCCCAAGGAGCCGAACGCGGGGG
1 TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
*
1007 TCAGCCCCCTGAGCCCTAAGG
1 TCAGCCCCCTGAACCCTAAGG
1028 TGCTGAGGAG
Statistics
Matches: 915, Mismatches: 72, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
35 95 0.10
36 786 0.86
37 34 0.04
ACGTcount: A:0.22, C:0.36, G:0.33, T:0.10
Consensus pattern (36 bp):
TCAGCCCCCTGAACCCTAAGGAGCCGAACGCGGGGG
Found at i:3356 original size:341 final size:335
Alignment explanation
Indices: 2726--3639 Score: 949
Period size: 339 Copynumber: 2.7 Consensus size: 335
2716 TTCCGCAGGT
* *
2726 TTTTAGCGTCAAAATCGAAAGTTCGCCGATCGAGCCGAAAGCAAGTTATGCCGCTTGGAAATGAC
1 TTTTAGCGTCAAAATCGAAATTTCGCCGATCGAGCCGAAAGCAAGTTAAGCCGCTTGGAAATGAC
* * * *
2791 CCACTGAGTACGATTTTCCAGTCGAAAAAGCTCCGCGAGTCCCTC-ATTTCGAGCTATCCGCTGA
66 CCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTT-GAGCTATCCGCTGA
* * * * *
2855 ACACGCTCCAGAGAAAGAGTCAAAAATTGGTCTGAAATGCTCGTGTTTGACCAGTTTTTGACTGT
130 A-ACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGAAA-ACTCGTTTTTGACCAGTTTATAACTGT
* * *
2920 TTCTCGACTCAGGAAGTCTCGCCGAGAAATGGAACCGTGTGGAATCGATTCTACGCCTCCAAAAT
193 ATCCCGACTCAGGAAGTCTCGCCGAGAAATGGAACCGTGCGGAATCGATTCTACGCCTCCAAAAT
* * * * ** *
2985 TCGTTAGATGCGACTGCAATCTTGATTTTTTTTTTATCAGTCCAAAATCGAGTAAAATCGAC-A-
258 ACGTAAGATGCGACTGAAATCCTGA----TTTTTTATCAGTCCAAAAAAGAGAAAAATCGACAAT
* * *
3048 GGCGTTACATTAACCGAA
319 GG-ATTACATCAACCAAA
* * *
3066 TTTTAAGCGTCAAAATCGAAATTTCACCGATCGAGCCGAAAGCAACTTAGGCCGCTTGGAAATGA
1 TTTT-AGCGTCAAAATCGAAATTTCGCCGATCGAGCCGAAAGCAAGTTAAGCCGCTTGGAAATGA
* * *
3131 CCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCACAAGTCCCTCGCTTTGAACTATCCGCTGA
65 CCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTTGAGCTATCCGCTGA
*
3196 AACGCTCCAGAGAAAGAGTCAAAAATTGGGCAGACAAACTCGTTTTTGACCAGTTTATAACCT-T
130 AACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGA-AAACTCGTTTTTGACCAGTTTATAA-CTGT
* * *
3260 ATCCCGGCTCAGGATA-TCTCGCC-ATG-AGTCGGGACCGTGCGGAATCGATTCTACGCCTCC-A
193 ATCCCGACTCAGGA-AGTCTCGCCGA-GAAAT-GGAACCGTGCGGAATCGATTCTACGCCTCCAA
*
3321 AATACG-AAGGATGCGACTGAAATCCTGAAATTTTTTCTCAGTCCAAAAAAGAGAAAAATCGACA
255 AATACGTAA-GATGCGACTGAAATCCTG--ATTTTTTATCAGTCCAAAAAAGAGAAAAATCGACA
* *
3385 TATGGATTACATCGACTAAA
317 -ATGGATTACATCAACCAAA
* ** * * * * ** *
3405 TTTT-TCGTTCAAAGGCG-AATGTTCGCGGATTGGGCCGAAA-CCAGGGAAGCTCGCTTGGAATT
1 TTTTAGCG-TCAAAATCGAAAT-TTCGCCGATCGAGCCGAAAGCAAGTTAAGC-CGCTTGGAAAT
* * *
3467 GACCCGCTCAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTACCTCGCTTAGAGCTATCCGCT
63 GACCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTTGAGCTATCCGC-
* ** * * *
3532 TAAAACGCTTTAGAGAACGAGTCAAAAAGTGGTCAGAAAAGCTCGTTTTTGACCAGATTT-TGAC
127 TGAAACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGAAAA-CTCGTTTTTGACCAG-TTTATAAC
* * * *
3596 TGTTTCTCGGCTTC-GGAAGTCTCGCCGAG-AATCGGAACTGTGCG
190 TGTATCCCGAC-TCAGGAAGTCTCGCCGAGAAAT-GGAACCGTGCG
3640 TTTGCGGTAT
Statistics
Matches: 484, Mismatches: 67, Indels: 47
0.81 0.11 0.08
Matches are distributed among these distances:
337 39 0.08
338 97 0.20
339 118 0.24
340 110 0.23
341 117 0.24
342 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (335 bp):
TTTTAGCGTCAAAATCGAAATTTCGCCGATCGAGCCGAAAGCAAGTTAAGCCGCTTGGAAATGAC
CCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTTGAGCTATCCGCTGAA
ACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGAAAACTCGTTTTTGACCAGTTTATAACTGTATC
CCGACTCAGGAAGTCTCGCCGAGAAATGGAACCGTGCGGAATCGATTCTACGCCTCCAAAATACG
TAAGATGCGACTGAAATCCTGATTTTTTATCAGTCCAAAAAAGAGAAAAATCGACAATGGATTAC
ATCAACCAAA
Done.