Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold937
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: 4074
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.32
Warning! 256 characters in sequence are not A, C, G, or T
Found at i:629 original size:87 final size:87
Alignment explanation
Indices: 500--1085 Score: 1014
Period size: 87 Copynumber: 6.7 Consensus size: 87
490 CGGTCTACTC
* * * *
500 CACTACTGCTTAGGGAGATAAGA-TC-TACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGAT
1 CACTACTGCTTAGGAAGATGAGATTCGT-C-GTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
*
563 AGGACTGGTGGCTTAAATCTGCTT
64 AGGACTGGAGGCTTAAATCTGCTT
* * *
587 CACTACTGTTTAGGAAGGTGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
1 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
652 GACTGGAGGCTTAAATCTGCTT
66 GACTGGAGGCTTAAATCTGCTT
674 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
1 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
739 GACTGGAGGCTTAAATCTGCTT
66 GACTGGAGGCTTAAATCTGCTT
761 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
1 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
826 GACTGGAGGCTTAAATCTGCTT
66 GACTGGAGGCTTAAATCTGCTT
848 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
1 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
913 GACTGGAGGCTTAAATCTGCTT
66 GACTGGAGGCTTAAATCTGCTT
* *
935 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGGTAG
1 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
*
1000 GACTGGTGGCTTAAATCTGCTT
66 GACTGGAGGCTTAAATCTGCTT
* * *
1022 CACTACTGCTTAGGAATATGAGATTCGCCGTATTCGATCTGCTCCACTACTGCTTAGGGAGATA
1 CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATA
1086 AGATCTAACA
Statistics
Matches: 478, Mismatches: 19, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
87 475 0.99
88 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (87 bp):
CACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAG
GACTGGAGGCTTAAATCTGCTT
Found at i:1149 original size:87 final size:87
Alignment explanation
Indices: 1058--1237 Score: 245
Period size: 87 Copynumber: 2.1 Consensus size: 87
1048 GCCGTATTCG
* *
1058 ATCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTAACATCTTTGACCTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATTC-AACATCTTCGACCTGCTCCACTACTGCTTA
*
1122 GGGAGATAGGACTGGTGGCTTAA
65 GGGAGATAGGACTGGTGACTTAA
* * ** * *
1145 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATTCAACATCTTCGACCTGCTCCACTACTGCTTAG
* *
1210 GGATATAGGACTGGTGACTTTA
66 GGAGATAGGACTGGTGACTTAA
1232 ATCTGC
1 ATCTGC
1238 ANNNNNNNNN
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
87 79 0.98
88 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (87 bp):
ATCTGCTCCACTACTGCTTAGGAAGATAAGATTCAACATCTTCGACCTGCTCCACTACTGCTTAG
GGAGATAGGACTGGTGACTTAA
Found at i:1151 original size:261 final size:261
Alignment explanation
Indices: 532--1171 Score: 908
Period size: 261 Copynumber: 2.5 Consensus size: 261
522 ATCTACAATC
* * *** * * *
532 TTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGTT
1 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTGAAAGCTTAAACCTGCTCCACTACTGCT
* * * * **
597 TAGGAAGGTGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGACTGGAGGC
66 TAGGAAGATGAGACTCGTCGGCTTAAATCTGCTCCACTACTGCTTAGGGAGATAGGACTGGAGGC
662 TTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGC
131 TTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGC
* *
727 TTAGGGAGATAGGACTGGAGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGT
196 TTAAGGAGATAGGACTGGAGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGT
*
792 C
261 A
* * * * *
793 TTCGATCTGCTCCACTACTGCTTAGGGAGATAGGACTGGAGGCTTAAATCTGCTTCACTACTGCT
1 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTGAAAGCTTAAACCTGCTCCACTACTGCT
* * **
858 TAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGACTGGAGGC
66 TAGGAAGATGAGACTCGTCGGCTTAAATCTGCTCCACTACTGCTTAGGGAGATAGGACTGGAGGC
923 TTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGC
131 TTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGC
* * *
988 TTAAGGAGGTAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAATATGAGATTCGCCGT
196 TTAAGGAGATAGGACTGGAGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGT
1053 A
261 A
* **
1054 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-AACATCTTTGACCTGCTCCACTACTG
1 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGAA-AGCTTAAACCTGCTCCACTACTG
* * * *
1118 CTTAGGGAGAT-AGGACTGGT-GGCTTAAATCTGCTTCACTACTGCTTAGGAAGAT
64 CTTAGGAAGATGA-GACTCGTCGGCTTAAATCTGCTCCACTACTGCTTAGGGAGAT
1172 GAGATTCGCC
Statistics
Matches: 349, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
261 315 0.90
262 34 0.10
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (261 bp):
TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTGAAAGCTTAAACCTGCTCCACTACTGCT
TAGGAAGATGAGACTCGTCGGCTTAAATCTGCTCCACTACTGCTTAGGGAGATAGGACTGGAGGC
TTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGC
TTAAGGAGATAGGACTGGAGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGT
A
Found at i:1211 original size:131 final size:131
Alignment explanation
Indices: 666--1212 Score: 674
Period size: 131 Copynumber: 4.2 Consensus size: 131
656 GGAGGCTTAA
* * *
666 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAG
* *
731 GGAGATAGGACTGGAGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTC
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCTTC
796 G
131 G
* * ** * ** *
797 ATCTGCTCCACTACTGCTTAGGGAGATAGGACT-GGAGGCTTAAATCTGCTTCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAG
* * * * ** * * * ** *
861 GAAGAT-GAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT-AGGACT-GGAGGC
66 GGAGATAG-GACTGGT-GGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGA-GATTCGCCGTC
**
923 TTAA
128 TTCG
* * * *
927 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAG
* * *
992 GGAGGTAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAATATGAGATTCGCCGTATTC
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCTTC
1057 G
131 G
* * *
1058 ATCTGCTCCACTACTGCTTAGGGAGATAAGA-TC-TAACATCTTTGACCTGCTCCACTACTGCTT
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGT--CGTCTTCGATCTGCTCCACTACTGCTT
1121 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCT
64 AGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCT
1186 TCG
129 TCG
1189 ATCTGCTCCACTACTGCTTAGGGA
1 ATCTGCTCCACTACTGCTTAGGGA
1213 TATAGGACTG
Statistics
Matches: 342, Mismatches: 65, Indels: 18
0.80 0.15 0.04
Matches are distributed among these distances:
129 2 0.01
130 101 0.30
131 238 0.70
132 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (131 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAG
GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCTTC
G
Found at i:2759 original size:13 final size:15
Alignment explanation
Indices: 2731--2764 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
2721 TTAGCCTCTC
2731 CATTTTTACTATTTT
1 CATTTTTACTATTTT
2746 CATTTTT-C-ATTTT
1 CATTTTTACTATTTT
2759 CATTTT
1 CATTTT
2765 CGTTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 1 0.05
15 7 0.37
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (15 bp):
CATTTTTACTATTTT
Done.