Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold587
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: 26919
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:5084 original size:52 final size:51
Alignment explanation
Indices: 5006--5154 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
4996 CGAAATATGA
5006 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTAGGC
* * *
5058 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTAGGC
**
5110 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
5155 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTAGGC
Found at i:5161 original size:13 final size:13
Alignment explanation
Indices: 5143--5167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5133 CAAAGATCAG
5143 TGTATCGATACAA
1 TGTATCGATACAA
5156 TGTATCGATACA
1 TGTATCGATACA
5168 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5246 original size:13 final size:13
Alignment explanation
Indices: 5228--5252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5218 TACAAAAAAA
5228 TGTATCGATACAT
1 TGTATCGATACAT
5241 TGTATCGATACA
1 TGTATCGATACA
5253 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13236 original size:79 final size:77
Alignment explanation
Indices: 13143--13357 Score: 220
Period size: 78 Copynumber: 2.8 Consensus size: 77
13133 ACCCCGATGG
* * * *
13143 TGAAAA-TTTAATATTTTAGAAATAAAAATGAGGTT-AGAGTAT-CCCTTCGAAAATGATGGGGT
1 TGAAAATTTTAATATTTT-GAAATAAAAATAAGGTTGA-AGTATCCCCTTAG-AAATAATGAGGT
*
13205 TGAAGCATCATTGAGA
63 TGAAGCATC-CTGAGA
* *
13221 TGAAAATTTTGATATTTTGGAGATAAAAATAAGGTTGAAGTATCCCCTTAGAAATAATGAGGTTG
1 TGAAAATTTTAATATTTT-GAAATAAAAATAAGGTTGAAGTATCCCCTTAGAAATAATGAGGTTG
* *
13286 GAGTATCCTGAGA
65 AAGCATCCTGAGA
* * * * * *
13299 TGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCTCTCAGAGATAATG
1 TGAAAATTTTAATATTTTG-AAATAAAAATAAGGTTGAAGTATCCCCTTAGAAATAATG
13358 GGATTAGAGT
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
77 1 0.01
78 60 0.52
79 47 0.41
80 7 0.06
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (77 bp):
TGAAAATTTTAATATTTTGAAATAAAAATAAGGTTGAAGTATCCCCTTAGAAATAATGAGGTTGA
AGCATCCTGAGA
Found at i:13263 original size:158 final size:157
Alignment explanation
Indices: 12970--13327 Score: 365
Period size: 158 Copynumber: 2.3 Consensus size: 157
12960 ATCAGAGTTA
* * * * * *
12970 GAGTATCCCCGAGATGAAAATTTTAATATTTTTGAAGTAAAAATGGGGCTGGAGTATCCCTTTGG
1 GAGTAACCCCGAGATGAAAATTTTAATA-TTTTGAAATAAAAATGAGGCTAGAGTATCCCTTCGA
* *
13035 AAATGAATGGGTTGGAGTGTCTCCAATGGTGAAAATTCGATATTTTGGCAGTAAACACAAGGTTA
65 AAATGAATGGGTTGGAGAGTCTCCAATGGTGAAAATTCGATATTTTGGCAGTAAAAACAAGGTTA
* * * *
13100 GAGTATTCTCTCAAAAATGATGGGGTTG
130 GAGTATCCCCTCAAAAATAATGAGGTTG
* *
13128 GAGTAACCCCGATGGTGAAAA-TTTAATATTTTAGAAATAAAAATGAGGTTAGAGTATCCCTTCG
1 GAGTAACCCCGA-GATGAAAATTTTAATATTTT-GAAATAAAAATGAGGCTAGAGTATCCCTTCG
* * *
13192 AAAATG-ATGGGGTT-GA-AG-CAT-CATTGAGATGAAAATTTTGATATTTTGG-AGATAAAAAT
64 AAAATGAAT-GGGTTGGAGAGTC-TCCAATG-G-TGAAAA-TTCGATATTTTGGCAG-TAAAAAC
* *
13251 AAGGTT-GAAGTATCCCCTTAGAAATAATGAGGTTG
123 AAGGTTAG-AGTATCCCCTCAAAAATAATGAGGTTG
* *
13286 GAGT-ATCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAA
1 GAGTAACCCCGAGATGAAAATTTTAATATTTTG-AAATAAAAA
13328 CAGGGTTGGA
Statistics
Matches: 167, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
155 5 0.03
156 11 0.07
157 42 0.25
158 102 0.61
159 7 0.04
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (157 bp):
GAGTAACCCCGAGATGAAAATTTTAATATTTTGAAATAAAAATGAGGCTAGAGTATCCCTTCGAA
AATGAATGGGTTGGAGAGTCTCCAATGGTGAAAATTCGATATTTTGGCAGTAAAAACAAGGTTAG
AGTATCCCCTCAAAAATAATGAGGTTG
Found at i:13325 original size:78 final size:77
Alignment explanation
Indices: 12970--13372 Score: 226
Period size: 79 Copynumber: 5.1 Consensus size: 77
12960 ATCAGAGTTA
* * ** * * * *
12970 GAGTATCCCCGAGATGAAAATTTTAATATTTTTG-AAGTAAAAATGGGGCTGGAGTATCCCTTTG
1 GAGTAT-CCTGAGATGAAAATTTTAATA-TTTTGAAAATAAAAATAAGGTTGAAGTATCCCCTTA
13034 GAAATGAATGGGTTG
64 GAAAT-AATGGGTTG
* ** * ** ** * * * * * *
13049 GAGTGTCTCCAATGGTGAAAA-TTCGATATTTTGGCAGTAAACACAAGGTT-AGAGTATTCTCTC
1 GAGTATC-CTGA-GATGAAAATTTTAATATTTTGAAAATAAAAATAAGGTTGA-AGTATCCCCTT
* *
13112 AAAAATGATGGGGTTG
63 AGAAATAAT-GGGTTG
* * * *
13128 GAGTAACCCCGATGGTGAAAA-TTTAATATTTT-AGAAATAAAAATGAGGTT-AGAGTAT-CCCT
1 GAGT-ATCCTGA-GATGAAAATTTTAATATTTTGA-AAATAAAAATAAGGTTGA-AGTATCCCCT
* *
13189 TCGAAAATGATGGGGTTG
62 TAG-AAATAAT-GGGTTG
* * * * * *
13207 AAGCATCATTGAGATGAAAATTTTGATATTTTGGAGATAAAAATAAGGTTGAAGTATCCCCTTAG
1 GAGTATC-CTGAGATGAAAATTTTAATATTTTGAAAATAAAAATAAGGTTGAAGTATCCCCTTAG
13272 AAATAATGAGGTTG
65 AAATAATG-GGTTG
* * * * *
13286 GAGTATCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCTCTCAGA
1 GAGTATCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAATAAGGTTGAAGTATCCCCTTAGA
* *
13351 GATAATGGGATTA
66 AATAATGGG-TTG
13364 GAGTATCCT
1 GAGTATCCT
13373 TAATGGTAAA
Statistics
Matches: 250, Mismatches: 59, Indels: 31
0.74 0.17 0.09
Matches are distributed among these distances:
77 2 0.01
78 87 0.35
79 146 0.58
80 15 0.06
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (77 bp):
GAGTATCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAATAAGGTTGAAGTATCCCCTTAGA
AATAATGGGTTG
Found at i:15737 original size:52 final size:51
Alignment explanation
Indices: 15679--15812 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 51
15669 AGCCTACATG
* * * * ** *
15679 TATCGATACATTAAAAAATGTATCGATATATTTGAGTCAAAAACTTAGAATT
1 TATCGATACAATGAAAAATGTATCGATACATTTAAGTC-AAAACCCAGAATA
* * *
15731 TATCGATACAACGAATAATGTATCAATACATTTAAGTCAAAACCCAGAATA
1 TATCGATACAATGAAAAATGTATCGATACATTTAAGTCAAAACCCAGAATA
*
15782 TATCGATATAATGAAAAATGTATCGATACAT
1 TATCGATACAATGAAAAATGTATCGATACAT
15813 ATTCTTTTCA
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
51 37 0.54
52 31 0.46
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.31
Consensus pattern (51 bp):
TATCGATACAATGAAAAATGTATCGATACATTTAAGTCAAAACCCAGAATA
Found at i:17242 original size:42 final size:42
Alignment explanation
Indices: 17196--17278 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
17186 ATTTCTTTGT
* *
17196 ATTCAAGAAATGTTCTTCATTCCTTAAAAGTGAAAAACAAAC
1 ATTCAAGAAATGTTATTCATTCCTTAAAAGTAAAAAACAAAC
* *
17238 ATTCAAGAAATGTTATTGATTCCTTAAGAGTAAAAAACAAA
1 ATTCAAGAAATGTTATTCATTCCTTAAAAGTAAAAAACAAA
17279 TATTTTAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (42 bp):
ATTCAAGAAATGTTATTCATTCCTTAAAAGTAAAAAACAAAC
Found at i:25457 original size:15 final size:16
Alignment explanation
Indices: 25439--25477 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
25429 TAAAAAAATT
25439 ATTAAATTATTAAAA-
1 ATTAAATTATTAAAAG
25454 ATTAAATT-TTAAAAG
1 ATTAAATTATTAAAAG
*
25469 AATAAATTA
1 ATTAAATTA
25478 AAAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATTAAATTATTAAAAG
Done.