Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3499
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: 31626
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:67 original size:1 final size:1
Alignment explanation
Indices: 57--152 Score: 183
Period size: 1 Copynumber: 96.0 Consensus size: 1
47 ATGGAAAGAG
*
57 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
122 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
153 TGAGGAAAGG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
1 93 1.00
ACGTcount: A:0.99, C:0.00, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:4652 original size:14 final size:14
Alignment explanation
Indices: 4631--4666 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4621 GCATACCTAC
4631 TCAGCCTCAGAAAT
1 TCAGCCTCAGAAAT
*
4645 TTAGCCTCAGAAAT
1 TCAGCCTCAGAAAT
4659 TCAGCCTC
1 TCAGCCTC
4667 GTACTCAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.25
Consensus pattern (14 bp):
TCAGCCTCAGAAAT
Found at i:6499 original size:55 final size:56
Alignment explanation
Indices: 6434--6548 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
6424 AGCATGGCTG
* * *
6434 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
6490 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
6545 CCAG
1 CCAG
6549 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:6545 original size:28 final size:27
Alignment explanation
Indices: 6459--6548 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
6449 GTGACAGAGT
*
6459 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
6488 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
6515 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
6543 CACCAG
1 CACCAG
6549 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:6698 original size:28 final size:28
Alignment explanation
Indices: 6651--6715 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
6641 AAATTAACCC
*
6651 TAGGGGTATAAAGGTCATTTTGCACACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
* *
6679 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
6707 TAGGGGTAT
1 TAGGGGTAT
6716 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCACACA
Found at i:13634 original size:29 final size:29
Alignment explanation
Indices: 13613--13696 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
13603 GACTATTGAC
13613 TATGAAAAGGGATGGTTCCGACCATCGAA
1 TATGAAAAGGGATGGTTCCGACCATCGAA
** *
13642 TATGAAAAGGGATGGTAACAACCATCGAA
1 TATGAAAAGGGATGGTTCCGACCATCGAA
* * * * *
13671 TTTAAAAAGAGATGGTTACAACCATC
1 TATGAAAAGGGATGGTTCCGACCATC
13697 ATTTAGTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (29 bp):
TATGAAAAGGGATGGTTCCGACCATCGAA
Found at i:22015 original size:27 final size:27
Alignment explanation
Indices: 21985--22162 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21975 ATATTGAGTC
* * * *
21985 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
22012 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
22039 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
22067 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
22094 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
22121 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
22148 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22163 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:22124 original size:82 final size:81
Alignment explanation
Indices: 22006--22161 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21996 TGCTATATAA
* *
22006 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
22071 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
22088 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
22152 CACTTAGTGC
65 CACTTAGTGC
22162 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:30632 original size:24 final size:24
Alignment explanation
Indices: 30581--30637 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
30571 TTGCATAGCG
* * **
30581 GATAAGCGATAGGATTTAGGAGTT
1 GATAAGGGATACGATTTAGGAGCA
*
30605 GATACGGGATACGATTTAGGAGCA
1 GATAAGGGATACGATTTAGGAGCA
30629 GATAAGGGA
1 GATAAGGGA
30638 GGAAATTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (24 bp):
GATAAGGGATACGATTTAGGAGCA
Done.