Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2141
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: 16364
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Found at i:12490 original size:63 final size:63
Alignment explanation
Indices: 12013--13257 Score: 1397
Period size: 63 Copynumber: 20.6 Consensus size: 63
12003 GTTCATCCCT
* * **
12013 TTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAAC-CCATTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
12071 TTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * * * * * *
12127 TTCAAAG-CC-TACAAGTCAGTGGC-ACTCTTTTCAAAG-CC-CACAA-TCAGTGGC-ACTCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * * *
12183 TTTAAAG-CC-CACAAGTCAGTGGC-ACTCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAAC-CCATTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * * * *
12241 TTCAAAGCCCACA-AA-TCAGTGGC-ACTCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
** * * * *
12298 TTCAAAG-CC-CACAA--CCATGGC-ATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * * ** *
12352 TTCAAAG-CC-CACAAGCCAGTGGCAA--CTTTTC-AAG-CC-CACAAGTTAGTGGC-ACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12407 TTC-AAG-CC-CACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12467 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12530 TTCAAAGCCCACACAAGTCGGTGGCAACCCA-TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12592 TTCCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TT-CAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12656 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAG-CC-CACAAGTCGGTGGCAACCCA
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12717 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 -TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
12781 TTCCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TT-CAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12845 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12908 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 -TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12972 TTCCAAAGCCCACACAA-TCGGTGGCAACCCA-TTCCAAGCCCACA-ACAGTCGGTGGCAACCCA
1 TT-CAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACA-AGTCGGTGGCAACCCA
*
13034 TT-TAAG--C-CACAAGTC-GTGGCAA-CCA-TT-AAAGCCCA-ACAAGTCGGTGGCAACCCA
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
13088 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 -TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
13152 TTCCAAAGCCCACACAAAGTCGGT-GCAACCTCATTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 TT-CAAAGCCCACAC-AAGTCGGTGGCAACC-CATTTCAAAGCCCACACAAGTCGGTGGCAACCC
13216 A
63 A
* ** * *
13217 TTTAAAAAGCCCATGCAAGTTCAGTGGCAACCCTTTTCAAA
1 -TT-CAAAGCCCACACAAG-TCGGTGGCAACCCATTTCAAA
13258 TCACCCATAT
Statistics
Matches: 1090, Mismatches: 47, Indels: 92
0.89 0.04 0.07
Matches are distributed among these distances:
54 78 0.07
55 47 0.04
56 106 0.10
57 73 0.07
58 75 0.07
59 24 0.02
60 19 0.02
61 27 0.02
62 105 0.10
63 237 0.22
64 226 0.21
65 44 0.04
66 23 0.02
67 6 0.01
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.17
Consensus pattern (63 bp):
TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:13219 original size:32 final size:32
Alignment explanation
Indices: 12012--13257 Score: 1439
Period size: 32 Copynumber: 41.2 Consensus size: 32
12002 TGTTCATCCC
*
12012 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
12041 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12070 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12098 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * * *
12126 TTTCAAAG-CC-TACAAGTCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
12155 TTTCAAAG-CC-CACAA-TCAGTGGC-ACTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
12182 TTTTAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
*
12211 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
12240 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12269 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
** *
12297 TTTCAAAG-CC-CACAA--CCATGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
12323 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
12351 TTTCAAAG-CC-CACAAGCCAGTGGCAA--CT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
**
12379 TTTC-AAG-CC-CACAAGTTAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12406 TTTC-AAG-CC-CACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12435 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12467 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12498 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12530 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12561 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12592 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12624 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12656 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12687 TTCCAAAG-CC-CACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12717 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12749 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12781 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12813 TTCCAAAGCCCACACAAGTCGGTGGCAACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12844 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12876 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
12908 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12940 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
12972 TTCCAAAGCCCACACAA-TCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
13003 -TTCCAAGCCCACA-ACAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACA-AGTCGGTGGCAACCCA
13034 TTT--AAG--C-CACAAGTC-GTGGCAA-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
13059 -TT-AAAGCCCA-ACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
13088 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
13120 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
13152 TTCCAAAGCCCACACAAAGTCGGT-GCAACCTCA
1 TTTCAAAGCCCACAC-AAGTCGGTGGCAACC-CA
13185 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** * *
13217 TTTAAAAAGCCCATGCAAGTTCAGTGGCAACCCT
1 TTT-CAAAGCCCACACAAG-TCGGTGGCAACCCA
13251 TTTCAAA
1 TTTCAAA
13258 TCACCCATAT
Statistics
Matches: 1124, Mismatches: 45, Indels: 92
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.00
25 6 0.01
26 31 0.03
27 71 0.06
28 149 0.13
29 125 0.11
30 55 0.05
31 197 0.18
32 428 0.38
33 45 0.04
34 15 0.01
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.17
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:13830 original size:20 final size:21
Alignment explanation
Indices: 13784--13831 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
13774 TCATACCCTG
* *
13784 ATGTATC-GATACATTTTTCA
1 ATGTATCGGATACATGTATCA
*
13804 ATATATCGGATACATGTAT-A
1 ATGTATCGGATACATGTATCA
13824 ATGTATCG
1 ATGTATCG
13832 ATATATTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (21 bp):
ATGTATCGGATACATGTATCA
Done.