Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold595
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: 24760
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Found at i:4485 original size:40 final size:40
Alignment explanation
Indices: 4450--4632 Score: 260
Period size: 40 Copynumber: 4.6 Consensus size: 40
4440 TACTCGCTTG
* *
4450 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
4490 AATGTCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
**
4530 AATGCCTTCGATACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * * *
4570 AATGCCTTCGGGACTTAGCTCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA
*
4610 AATGCCTTTGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
4633 TTATCATCCA
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 1 0.01
40 127 0.99
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:10035 original size:68 final size:66
Alignment explanation
Indices: 9962--10133 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
9952 CATCATGTGT
* * * *
9962 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
10025 TGTAG
62 TGTAG
** * *
10030 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
10095 AG
65 AG
* * * *
10097 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
10134 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:10067 original size:64 final size:64
Alignment explanation
Indices: 9986--10169 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
9976 AGACATTATG
* * *
9986 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
10050 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
10115 AA
63 AA
* * *
10117 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
10170 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:15841 original size:27 final size:27
Alignment explanation
Indices: 15811--15865 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
15801 GACGATTTGA
*
15811 AGACGGACTCAATGAAGACATTAAAGT
1 AGACGGAATCAATGAAGACATTAAAGT
*
15838 AGACGGAATCAATGAAGTCATTAAAGT
1 AGACGGAATCAATGAAGACATTAAAGT
15865 A
1 A
15866 TTTCTGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (27 bp):
AGACGGAATCAATGAAGACATTAAAGT
Found at i:17775 original size:79 final size:81
Alignment explanation
Indices: 17639--17823 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
17629 TTGAATGATG
*
17639 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
17703 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
17718 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
17780 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
17798 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
17824 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:17837 original size:40 final size:40
Alignment explanation
Indices: 17640--17823 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
17630 TGAATGATGT
* * * *
17640 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
17680 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
17720 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
17758 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
17799 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
17824 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:17845 original size:79 final size:79
Alignment explanation
Indices: 17692--17856 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
17682 GGACTAAGAT
* **
17692 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
17757 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
17771 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
17834 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
17850 CCGAAGG
1 CCGAAGG
17857 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.