Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold341
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: 28519
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Found at i:515 original size:19 final size:19
Alignment explanation
Indices: 479--517 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
469 TTTTCATCAT
* *
479 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
498 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
517 A
1 A
518 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:1062 original size:28 final size:27
Alignment explanation
Indices: 979--1065 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 27
969 GTGACAGAGT
*
979 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
* *
1008 CACCAGAACAGAT-A--TATGG-AGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
1032 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
1060 CACCAG
1 CACCAG
1066 GACGCTTCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
24 17 0.35
25 5 0.10
27 4 0.08
28 15 0.31
29 7 0.15
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:1217 original size:28 final size:28
Alignment explanation
Indices: 1173--1234 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
1163 ATTAACCCTA
*
1173 GGGTATAAAGGTCATTTAGCATACATAG
1 GGGTATAAAGGTAATTTAGCATACATAG
* *
1201 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAAAGGTAATTTAGCATACATAG
1229 GGGTAT
1 GGGTAT
1235 TCTAGTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.32
Consensus pattern (28 bp):
GGGTATAAAGGTAATTTAGCATACATAG
Found at i:8881 original size:28 final size:28
Alignment explanation
Indices: 8820--8910 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 28
8810 GTGACAGAGT
* * *
8820 CACCAGATACAAATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGGGC
8849 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
* * * * **
8877 TACCAGAATAGATAACTTATGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
8905 CACCAG
1 CACCAG
8911 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
28 45 0.87
29 7 0.13
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGGGC
Found at i:9063 original size:28 final size:28
Alignment explanation
Indices: 9016--9080 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
9006 AAATTAACCC
*
9016 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
**
9044 TAGGGGTA-AAATGGTAATTTTTCATACA
1 TAGGGGTATAAA-GGTAATTTAGCATACA
9072 TAGGGGTAT
1 TAGGGGTAT
9081 TCTAGTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:17750 original size:19 final size:19
Alignment explanation
Indices: 17714--17752 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17704 TTTTCATCAT
* *
17714 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
17733 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
17752 A
1 A
17753 AAATAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:18265 original size:26 final size:27
Alignment explanation
Indices: 18190--18301 Score: 113
Period size: 26 Copynumber: 4.1 Consensus size: 27
18180 AGCATGGCTG
* * * *
18190 CCAGATACAGAAAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGTGCCA
*
18217 CCAGATACAGATATTTTGTGGCAGTGCCA
1 CCAGATACAGATA--ATGTGGCAGTGCCA
*
18246 CCAGA-ACAGATAATGTGGCAGGGCCA
1 CCAGATACAGATAATGTGGCAGTGCCA
*
18272 CCAGA-ACAGATAATTTGGCA-TAGCCA
1 CCAGATACAGATAATGTGGCAGT-GCCA
18298 CCAG
1 CCAG
18302 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 39 0.53
27 12 0.16
28 7 0.10
29 15 0.21
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGTGCCA
Found at i:18454 original size:28 final size:28
Alignment explanation
Indices: 18411--18471 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
18401 TAACCCTAGA
*
18411 GGTATAAAGGTCATTTTGCATACATAGG
1 GGTATAAAGGTAATTTTGCATACATAGG
*
18439 GGTATAATGGTAATTTTGCATACATAGG
1 GGTATAAAGGTAATTTTGCATACATAGG
18467 GGTAT
1 GGTAT
18472 TCTAGTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.34
Consensus pattern (28 bp):
GGTATAAAGGTAATTTTGCATACATAGG
Found at i:25437 original size:50 final size:50
Alignment explanation
Indices: 25328--25593 Score: 284
Period size: 50 Copynumber: 5.3 Consensus size: 50
25318 GCTAAATGAC
* * * * * *
25328 CTTGTATATTCAGCCACATAGGTATGTACATATGTGATGTTGTATTGGAT
1 CTTGTATATTCGGCCATATAGGTAAGTACATATGTGATATTATATTTGAT
* * * *
25378 CTTGAATATTCGGCCATGA-AGGTATGTACAAATTTGATATTATATTTGAAT
1 CTTGTATATTCGGCCAT-ATAGGTAAGTACATATGTGATATTATATTTG-AT
* * * *
25429 -TTGTATATTCGGCCATCTAAGTAAGTACATATGTGATGTTAAATTTGAT
1 CTTGTATATTCGGCCATATAGGTAAGTACATATGTGATATTATATTTGAT
* * * * *
25478 CTTGCATATTCGGCTATATAGTTAAGCACATATGTGATATTAAATTTGAT
1 CTTGTATATTCGGCCATATAGGTAAGTACATATGTGATATTATATTTGAT
* * *
25528 CTTGCATATTCGGCCATATAGGTAAGCACATATGTGCTATTATATTTGAT
1 CTTGTATATTCGGCCATATAGGTAAGTACATATGTGATATTATATTTGAT
* *
25578 CTTTTATATTTGGCCA
1 CTTGTATATTCGGCCA
25594 AATGAGTGAT
Statistics
Matches: 182, Mismatches: 30, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
49 2 0.01
50 177 0.97
51 3 0.02
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (50 bp):
CTTGTATATTCGGCCATATAGGTAAGTACATATGTGATATTATATTTGAT
Done.