Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold545
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: 30665
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:73 original size:32 final size:31
Alignment explanation
Indices: 20--1034 Score: 1566
Period size: 32 Copynumber: 31.6 Consensus size: 31
10 CATTCCAAAC
20 CACAAGTCGGTGGGCAACCCATTCAAAAGCCCA
1 CACAAGTCGGT-GGCAACCCATTC-AAAGCCCA
53 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
85 CACAAGTCGGTGGCAACACCATTCCAAAAGCCCA
1 CACAAGTCGGTGGCAAC-CCATT-C-AAAGCCCA
119 CACAAGTCGGTGGCAAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGC-AACCCATT-CAAAGCCCA
152 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
184 CACAAGTCAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTC-GGTGGCAACCCA-TTCAAAGCCCA
217 CACAAGTCGGTGGCAACCCATTTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TT-CAAAGCCCA
250 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
282 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
314 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
346 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
*
378 CACAAGTCGGGTGGCAACCCATTTCCAAGCCCA
1 CACAAGTC-GGTGGCAACCCA-TTCAAAGCCCA
*
411 CACAAGTCGGTGGCAAACCATTCAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTC-AAAGCCCA
443 CACAAGTCGGTGGCAA-CCATTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCAAAGCCCA
473 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
505 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
537 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
**
569 CACAAGTCGGTGGC-ACCCATTCCAAAGTTCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
*
600 CACAAGTTGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
*
632 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
664 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
696 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
*
728 CACAAGTCGGTGGCAACCCATTCCAAAACCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
760 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
792 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
824 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
856 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
888 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATT-CAAAGCCCA
* *
920 CATAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
952 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
*
984 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
** *
1016 TGCAAGTCAGTGGCAACCC
1 CACAAGTCGGTGGCAACCC
1035 TTTTCAAATC
Statistics
Matches: 941, Mismatches: 21, Indels: 41
0.94 0.02 0.04
Matches are distributed among these distances:
30 26 0.03
31 41 0.04
32 706 0.75
33 132 0.14
34 33 0.04
35 3 0.00
ACGTcount: A:0.32, C:0.35, G:0.19, T:0.15
Consensus pattern (31 bp):
CACAAGTCGGTGGCAACCCATTCAAAGCCCA
Found at i:1598 original size:20 final size:20
Alignment explanation
Indices: 1570--1644 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1560 TCATACCCTG
1570 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1590 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1610 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1630 ATGTATCGATACATT
1 ATGTATCGATACATT
1645 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1637 original size:40 final size:39
Alignment explanation
Indices: 1570--1647 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1560 TCATACCCTG
* *
1570 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1610 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1648 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:2582 original size:23 final size:23
Alignment explanation
Indices: 2555--2611 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
2545 AGCCTTTGAC
2555 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
2578 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
2601 CATGCATTTTT
1 CATGCATTTTT
2612 AACATGTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:2618 original size:20 final size:21
Alignment explanation
Indices: 2563--2618 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 21
2553 ACCATGCATT
**
2563 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
2584 TTTTTTTTATTATGTTTCATGCA
1 --TTTTTTAACATGTTTCATGCA
2607 -TTTTTAACATGT
1 TTTTTTAACATGT
2619 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 10 0.32
23 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:9463 original size:14 final size:14
Alignment explanation
Indices: 9444--9472 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9434 ACACGTTAGC
9444 TATTAAATATTTTA
1 TATTAAATATTTTA
9458 TATTAAATATTTTA
1 TATTAAATATTTTA
9472 T
1 T
9473 TTATTGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTAAATATTTTA
Found at i:10334 original size:29 final size:28
Alignment explanation
Indices: 10286--10355 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
10276 GATTTTATAA
*
10286 TTTTTTATTTT-TTTGTAATT-ATTGATT
1 TTTTTTATTTTATTTGAAATTAATT-ATT
10313 TTGATTTTATTTTATTT-AAATTAATTATT
1 TT--TTTTATTTTATTTGAAATTAATTATT
10342 TTTTTTCATTTTAT
1 TTTTTT-ATTTTAT
10356 GGAAGATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
27 6 0.16
28 7 0.19
29 18 0.49
30 6 0.16
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.71
Consensus pattern (28 bp):
TTTTTTATTTTATTTGAAATTAATTATT
Found at i:17240 original size:2 final size:2
Alignment explanation
Indices: 17227--17258 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17217 TAGACCGCCA
*
17227 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17259 TACATTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19765 original size:31 final size:31
Alignment explanation
Indices: 19727--19793 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
19717 CGTTGTCGTC
19727 GTCTTTGAATTCAGTATAGGTAATTTGATTA
1 GTCTTTGAATTCAGTATAGGTAATTTGATTA
19758 GTCTTTGAATTCAGTATAGGTAATTTGATTA
1 GTCTTTGAATTCAGTATAGGTAATTTGATTA
19789 -TCTTT
1 GTCTTT
19794 TTCTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (31 bp):
GTCTTTGAATTCAGTATAGGTAATTTGATTA
Found at i:23848 original size:16 final size:16
Alignment explanation
Indices: 23824--23865 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
23814 AAGTTGAGTC
*
23824 ATTTTGAGTTTAAGTT
1 ATTTCGAGTTTAAGTT
*
23840 ATTTCGAG-TTAGGTT
1 ATTTCGAGTTTAAGTT
*
23855 ATTTCAAGTTT
1 ATTTCGAGTTT
23866 TGAGTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (16 bp):
ATTTCGAGTTTAAGTT
Found at i:30216 original size:19 final size:18
Alignment explanation
Indices: 30173--30220 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
30163 AATTATTCAA
* *
30173 ATAATAATATTTATAAAT
1 ATAATATTATTTAAAAAT
*
30191 AT-TTATTATTTAAATAAT
1 ATAATATTATTTAAA-AAT
30209 ATAATATTATTT
1 ATAATATTATTT
30221 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 7 0.29
19 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAATATTATTTAAAAAT
Found at i:30322 original size:15 final size:15
Alignment explanation
Indices: 30286--30324 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
30276 TAAAATTAAA
30286 ATATTAAATATTTTT
1 ATATTAAATATTTTT
*
30301 ATTTTAAA-ATTTTT
1 ATATTAAATATTTTT
30315 ATAATTAAAT
1 AT-ATTAAAT
30325 GTAAATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTAAATATTTTT
Done.