Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1205
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: 37904
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:7927 original size:40 final size:40
Alignment explanation
Indices: 7777--7970 Score: 214
Period size: 40 Copynumber: 4.8 Consensus size: 40
7767 TTCGAATGAT
* * * *
7777 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
7818 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
* * * *
7858 TTCCGGGCTAAG-CCCGAAGCCATTGGTGCGAGTTCCTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
7897 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * *
7938 A-CTGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
7971 AGCTATATCC
Statistics
Matches: 128, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 32 0.25
40 68 0.53
41 27 0.21
42 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:7945 original size:79 final size:79
Alignment explanation
Indices: 7835--7996 Score: 193
Period size: 79 Copynumber: 2.1 Consensus size: 79
7825 CTAAGATCCA
* * *
7835 AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAG-CCCGAAGCCATTGGTGCGAGTTCCTAAAT
1 AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGTCCCGAAGCCATTGGAGCGAGTACCTAAAT
*
7899 CCGGGTTAAGTCCCG
66 CC-GGTTAAATCCCG
* * * * * *
7914 AAGGCATTTGTGCGAGTTACT-ATAACTGGGCTATGTCCCGAAGGCATTTGAGCGAGTAGCTATA
1 AAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAGTCCCGAAGCCATTGGAGCGAGTACCTAAA
*
7978 TCCGGTTAAATTCCG
65 TCCGGTTAAATCCCG
7993 AAGG
1 AAGG
7997 TATGTGATTC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 2 0.03
79 43 0.61
80 25 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGTCCCGAAGCCATTGGAGCGAGTACCTAAAT
CCGGTTAAATCCCG
Found at i:16707 original size:46 final size:47
Alignment explanation
Indices: 16656--16786 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 47
16646 ATGGTTGAGC
16656 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTATGGATG-GAACTAG
* * *
16703 -TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGA--GATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGGAACTA-G
16748 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTATGG
16787 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 29 0.41
47 29 0.41
48 2 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (47 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGGAACTAG
Found at i:16772 original size:47 final size:46
Alignment explanation
Indices: 16654--16779 Score: 152
Period size: 47 Copynumber: 2.7 Consensus size: 46
16644 GGATGGTTGA
* *
16654 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GGATGCGAAT
*
16702 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGA-GATG-TAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGCGAA-T
16745 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCG
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCG
16780 CTTATGGGCG
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 29 0.41
47 30 0.43
48 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGCGAAT
Found at i:26315 original size:23 final size:23
Alignment explanation
Indices: 26273--26316 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
26263 TATTAAGTGA
*
26273 AAGAATTTATTGATCAGAAGCGT
1 AAGAATTTATTGAGCAGAAGCGT
* *
26296 AAGAATTTCTTGAGCTGAAGC
1 AAGAATTTATTGAGCAGAAGC
26317 AAGGTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (23 bp):
AAGAATTTATTGAGCAGAAGCGT
Found at i:31884 original size:16 final size:17
Alignment explanation
Indices: 31844--31884 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
31834 AGCAAATTAA
31844 ATTATTTATACTTTTGC
1 ATTATTTATACTTTTGC
31861 ATTA-TTATA-TTTTG-
1 ATTATTTATACTTTTGC
31875 ATGTATTTAT
1 AT-TATTTAT
31885 CATTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 7 0.32
16 9 0.41
17 4 0.18
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (17 bp):
ATTATTTATACTTTTGC
Done.