Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold12889.1
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: 2023
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Found at i:182 original size:27 final size:27
Alignment explanation
Indices: 152--1374 Score: 795
Period size: 27 Copynumber: 47.2 Consensus size: 27
142 ATCAGGAAAG
*
152 TTACCGAAATACCCCTGTAAGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* *
179 TTACCGAAATACCCCTGTATGGTAAAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* *
206 TTACCGAAATACTCCTGTAGCGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
233 TTACCGAAATACCCCTGTAGGGTAG-A
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
259 TTATCGAAATA-CCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
** *
285 TTATTGAAATACCCCAGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
312 TTACCGAAATACCCCTATAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
339 TTACCGAAATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
366 TTACCGAAATAGCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
393 TTACCGAAAT-CCGCTTGTAGGGTAGAA
1 TTACCGAAATACC-CCTGTAGGGTAGAA
* * *
420 TTACCAAAATA-CCCTATAAGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* * *
446 TTACTGAAATACCCATGTAGGGTAAAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* *
473 TTATCGAAATACCCCTGTAGGGAAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* *
500 TTATCG-AA-ACCCCTGTAAGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* * *** *
525 TTACCAAAATACCCCTAATACCCCTA-TA
1 TTACCGAAATACCCCT-GTA-GGGTAGAA
* *
553 TGGTA--G-AATGA--TCTG-CGGCGCT-G-A
1 T--TACCGAAAT-ACCCCTGTAGG-G-TAGAA
** * *
577 TTATTCTAAAATACCCCTATATGGTAGAA
1 TTA--CCGAAATACCCCTGTAGGGTAGAA
** * * *
606 -T---GATCTGCGGCGCTG-A---T--TA
1 TTACCGAAATAC--CCCTGTAGGGTAGAA
** * *
625 TT-CTAAAATACCCCTATATGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
** * * *
651 -T---GATCTGCGGCGCTG-A---T--TA
1 TTACCGAAATAC--CCCTGTAGGGTAGAA
** * *
670 TT-CTAAAATACCCCTATATGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
** * * *
696 -T---GATCTGCGGCGCTG-A---T--TA
1 TTACCGAAATAC--CCCTGTAGGGTAGAA
** * *
715 TT-CTAAAATACCCCTATATGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
** * * *
741 -T---GATCTGCGGCGCTG-A---T--TA
1 TTACCGAAATAC--CCCTGTAGGGTAGAA
** * *
760 TT-CTAAAATACCCCTATATGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
786 -T---G-----CCCCTGTACGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
** * *
804 TTACTAAAATACCCCTATATGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
831 TTACCGAAATACCCATGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
858 TTACCAAAATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
885 TTTCCGAAATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* *
912 TTACCAAAATACCCCTGTAGGGTTGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
939 TTACCGAGATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
966 TTATCGAAATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
993 TTATCGAAATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
1020 TTACCGAAATACCCATGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
1047 TTACCGAAATATCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
** * * *
1074 TTACTAAAATACCCTTATATGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
1101 TTACCGAAATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
1128 TTACCGAAATACCCCAGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
1155 TTACCGAAATACCCCTGTACGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
** * *
1182 TTACTAAAATACCCCTATATGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
1209 TTACCGAAATACCCTTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* * *
1236 TTA-CAAAATACGCCTATAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
**
1262 TTACCGAAATACCTTTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* * * *
1289 TTGCTGAAATACCCTTATAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
*
1316 TTACTGAAATACCCCTGTAGGGTAGAA
1 TTACCGAAATACCCCTGTAGGGTAGAA
* * *
1343 TTACC-AAGATACCCTTGTGGGGTAAAA
1 TTACCGAA-ATACCCCTGTAGGGTAGAA
1370 TTACC
1 TTACC
1375 ATTTTGCCCC
Statistics
Matches: 935, Mismatches: 181, Indels: 160
0.73 0.14 0.13
Matches are distributed among these distances:
18 14 0.01
19 5 0.01
20 16 0.02
21 8 0.01
22 14 0.01
23 12 0.01
24 10 0.01
25 49 0.05
26 78 0.08
27 713 0.76
28 10 0.01
29 4 0.00
30 2 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (27 bp):
TTACCGAAATACCCCTGTAGGGTAGAA
Found at i:605 original size:45 final size:45
Alignment explanation
Indices: 541--787 Score: 494
Period size: 45 Copynumber: 5.5 Consensus size: 45
531 AAATACCCCT
541 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
586 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
631 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
676 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
721 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
766 AATACCCCTATATGGTAGAATG
1 AATACCCCTATATGGTAGAATG
788 CCCCTGTACG
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 202 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (45 bp):
AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAA
Found at i:811 original size:90 final size:89
Alignment explanation
Indices: 541--831 Score: 478
Period size: 90 Copynumber: 3.2 Consensus size: 89
531 AAATACCCCT
541 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAAAATACCCCTATATGGTAGAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAAAATACCCCTATATGGTAGAA
606 TGATCTGCGGCGCTGATTATTCTAA
66 TGATCTGCGGCGCTGATTA-TCTAA
631 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAAAATACCCCTATATGGTAGAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAAAATACCCCTATATGGTAGAA
696 TGATCTGCGGCGCTGATTATTCTAA
66 TGATCTGCGGCGCTGATTA-TCTAA
721 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAAAATACCCCTATATGGTAGAA
1 AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAAAATACCCCTATATGGTAGAA
** ** *
786 TGCCCCTG-TACGGTAGAATTA-CTAA
66 TG-ATCTGCGGCGCT-G-ATTATCTAA
811 AATACCCCTATATGGTAGAAT
1 AATACCCCTATATGGTAGAAT
832 TACCGAAATA
Statistics
Matches: 193, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
90 185 0.96
91 4 0.02
92 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (89 bp):
AATACCCCTATATGGTAGAATGATCTGCGGCGCTGATTATTCTAAAATACCCCTATATGGTAGAA
TGATCTGCGGCGCTGATTATCTAA
Found at i:1644 original size:27 final size:28
Alignment explanation
Indices: 1599--1707 Score: 127
Period size: 27 Copynumber: 4.0 Consensus size: 28
1589 GGAGGAAGCG
*
1599 TTCTGGTGGCTATGTCACAAATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
1627 TTCTGGT-GTTATGCCACAAATATCTG-
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
1653 TTCTGGTGGCTCTGCCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
* * * *
1680 ATCTGGTGACTCTGTCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
1707 T
1 T
1708 GACTGATCGA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
26 15 0.21
27 49 0.69
28 7 0.10
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACAAATATCTGT
Found at i:1702 original size:53 final size:54
Alignment explanation
Indices: 1598--1707 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 54
1588 TGGAGGAAGC
* * *
1598 GTTCTGGTGGCTATGTCACAAATATCTGTTTCTGGTGTTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGCTATGCCACAAATATCT
* * *
1652 GTTCTGGTGGCTCTGCCAC-AATATCTGTATCTGGTGACTCTGTCAC-AATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTG-CTATGCCACAAATATCT
1705 GTT
1 GTT
1708 GACTGATCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
53 26 0.53
54 23 0.47
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGCTATGCCACAAATATCT
Found at i:1827 original size:22 final size:22
Alignment explanation
Indices: 1795--1853 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1785 CCCGTTATCG
*
1795 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
*** *
1817 ATGGCTTTGTGCCATTTTGAAT
1 ATGGCTTTGTGCCAACCTAAAT
*
1839 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
1854 ACGTATTTCC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Done.