Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2255
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: 10843
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Found at i:1199 original size:19 final size:19
Alignment explanation
Indices: 1163--1201 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1153 TTTTCATCAT
* *
1163 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
1182 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
1201 A
1 A
1202 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:1721 original size:27 final size:28
Alignment explanation
Indices: 1652--1752 Score: 132
Period size: 27 Copynumber: 3.6 Consensus size: 28
1642 GATACAAAAA
* * *
1652 TGTGACAGAGTCACCAGATACAGATATTT
1 TGTGGCAGAGCCACCAGA-ACAGATAATT
*
1681 TGTGGCAGTGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGATAATT
*
1709 T-TGGCAGGGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGATAATT
*
1736 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
1753 GACGCTTCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
27 26 0.41
28 23 0.36
29 15 0.23
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (28 bp):
TGTGGCAGAGCCACCAGAACAGATAATT
Found at i:1905 original size:28 final size:28
Alignment explanation
Indices: 1858--1925 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
1848 AAATTAACCC
* *
1858 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
1886 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
1914 TAGGGGTATAAT
1 TAGGGGTATAAT
1926 AAATCTAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:2167 original size:16 final size:15
Alignment explanation
Indices: 2146--2176 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2136 CCAAAATACC
2146 GCTTTTCGGCATTTTG
1 GCTTTTCGGC-TTTTG
2162 GCTTTTCGGCTTTTG
1 GCTTTTCGGCTTTTG
2177 CCGATCTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.03, C:0.19, G:0.26, T:0.52
Consensus pattern (15 bp):
GCTTTTCGGCTTTTG
Found at i:9019 original size:19 final size:19
Alignment explanation
Indices: 8983--9021 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
8973 TTTTCATCAT
* *
8983 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
9002 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
9021 A
1 A
9022 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:9490 original size:27 final size:27
Alignment explanation
Indices: 9457--9521 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
9447 GCAGCATGCT
9457 CCAGATACAGAAAATGTGACAGAGTCA
1 CCAGATACAGAAAATGTGACAGAGTCA
9484 CCAGATACAGAAAATGTGACAGAGTCA
1 CCAGATACAGAAAATGTGACAGAGTCA
9511 CCAGATACAGA
1 CCAGATACAGA
9522 TATTTTGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (27 bp):
CCAGATACAGAAAATGTGACAGAGTCA
Found at i:9549 original size:55 final size:56
Alignment explanation
Indices: 9482--9598 Score: 141
Period size: 55 Copynumber: 2.1 Consensus size: 56
9472 GTGACAGAGT
* * *
9482 CACCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GC
1 CACCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGC
* * *
9538 CACCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGC
9593 CACCAG
1 CACCAG
9599 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.55
56 23 0.43
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CACCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGC
Found at i:9595 original size:28 final size:27
Alignment explanation
Indices: 9509--9598 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
9499 GTGACAGAGT
*
9509 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
9538 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
9565 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
9593 CACCAG
1 CACCAG
9599 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:9750 original size:27 final size:27
Alignment explanation
Indices: 9707--9763 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
9697 TTAACCCTAG
*
9707 GGGTATAAAGGTCATTTTGCATACATA
1 GGGTATAAAGGTAATTTTGCATACATA
*
9734 GGGTATAATGGTAATTTTGCATACATA
1 GGGTATAAAGGTAATTTTGCATACATA
9761 GGG
1 GGG
9764 GTATTCTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (27 bp):
GGGTATAAAGGTAATTTTGCATACATA
Done.