Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold255
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: 220819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:193189 original size:20 final size:20
Alignment explanation
Indices: 193164--193217 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
193154 CTACCACTGT
*
193164 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
193184 TTGTATCAATACATGATGAA
1 TTGTATCGATACATGATGAA
*
193204 TTGTATTGATACAT
1 TTGTATCGATACAT
193218 TGCTTCTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:201912 original size:19 final size:20
Alignment explanation
Indices: 201888--201942 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
201878 GTATCGATAT
**
201888 ATTGTATCGATACATGTTC-
1 ATTGTATCGATACATGGACA
*
201907 ATTGTATCGATTCATGGACA
1 ATTGTATCGATACATGGACA
201927 ATTGTATCGATACATG
1 ATTGTATCGATACATG
201943 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:201996 original size:20 final size:20
Alignment explanation
Indices: 201971--202024 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
201961 CTACCACTAT
*
201971 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
201991 TTGTATCGATAAATGATGAA
1 TTGTATCGATACATGATGAA
202011 TTGTATCGATACAT
1 TTGTATCGATACAT
202025 TGCTTCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:202959 original size:202 final size:202
Alignment explanation
Indices: 202736--203377 Score: 759
Period size: 202 Copynumber: 3.3 Consensus size: 202
202726 TTCAAAATAC
* * *
202736 TCAAAATTCGAAAAGAACCAATTCACCCCCCTCTTGGTTTA-TGAATCCTTAAGCTTTCATATAC
1 TCAAAATTCGAAAAGAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTTCATATAC
202800 ACTAAACAAGGAAGTGTCGAGGAGAAAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAAC
66 ACTAAACAAGGAAGTGTCGAGGAG-AAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAAC
202865 ACTTGTGTCAAGCTTTCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTT
130 ACTTGTGTCAAGCTTTCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTT
202930 CAAAACCT
195 CAAAACCT
*
202938 TCAAATTTCGATAAA-AACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGC--T--TAT-
1 TCAAAATTCGA-AAAGAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTTCATATA
* * * * **
202997 -ACT-AA-TAGG-A------A--AG-AGGACGTAGCTACCA-ATTTGGACCGAACCTCTATAAAT
65 CACTAAACAAGGAAGTGTCGAGGAGAAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAA-
* * * * * * * *
203048 C-TTTGTGTCGAA-CATT-TC--TTCCCTAATATTTTTATCTTTTGAATTG-TTTT-ATACCAAA
129 CACTTGTGTC-AAGCTTTCTCTTTTTCCTACTCTTTTTATC-TTCGAGTTGTTTTTGA-ATC-AA
* *
203106 CTTTTCAAAATAC-
190 TTTTTCAAAA-CCT
* * * *
203119 TCAAAATTCGAAAAGAACCAATTCACCCCCTTCTTGGTTTATT-AATCCTTGAGCTTTCATATAC
1 TCAAAATTCGAAAAGAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTTCATATAC
203183 ACTAAACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAAC
66 ACTAAACAAGGAAGTGTCGAGGAGA-AGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAAC
203248 ACTTGTGTCAAGCTTTCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTT
130 ACTTGTGTCAAGCTTTCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTT
203313 CAAAACCT
195 CAAAACCT
* *
203321 TCAAATTTCGATAAGAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTT
1 TCAAAATTCGAAAAGAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTT
203378 ATACTAATGT
Statistics
Matches: 355, Mismatches: 47, Indels: 75
0.74 0.10 0.16
Matches are distributed among these distances:
179 1 0.00
180 33 0.09
181 54 0.15
182 4 0.01
183 29 0.08
184 19 0.05
186 5 0.01
187 2 0.01
188 4 0.01
189 1 0.00
194 1 0.00
195 4 0.01
196 2 0.01
197 5 0.01
199 19 0.05
200 29 0.08
201 4 0.01
202 92 0.26
203 46 0.13
204 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (202 bp):
TCAAAATTCGAAAAGAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTTCATATAC
ACTAAACAAGGAAGTGTCGAGGAGAAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAACA
CTTGTGTCAAGCTTTCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTTC
AAAACCT
Found at i:203327 original size:383 final size:383
Alignment explanation
Indices: 202620--203385 Score: 1478
Period size: 383 Copynumber: 2.0 Consensus size: 383
202610 GAAAATGTCG
202620 AGGAAAGAGGACGTAGCTACCAATTTGGACCGAACCTCTATAAATCTTTGTGTCGAACATTTCTT
1 AGGAAAGAGGACGTAGCTACCAATTTGGACCGAACCTCTATAAATCTTTGTGTCGAACATTTCTT
202685 CCCTAATATTTTTATCTTTCGAATTGTTTTATACCAAACTTTTCAAAATACTCAAAATTCGAAAA
66 CCCTAATATTTTTATCTTTCGAATTGTTTTATACCAAACTTTTCAAAATACTCAAAATTCGAAAA
202750 GAACCAATTCACCCCCCTCTTGGTTTATGAATCCTTAAGCTTTCATATACACTAAACAAGGAAGT
131 GAACCAATTCACCCCCCTCTTGGTTTATGAATCCTTAAGCTTTCATATACACTAAACAAGGAAGT
202815 GTCGAGGAGAAAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAACACTTGTGTCAAGCTT
196 GTCGAGGAGAAAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAACACTTGTGTCAAGCTT
202880 TCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTTCAAAACCTTCAAATT
261 TCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTTCAAAACCTTCAAATT
202945 TCGATAAAAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTATACTAAT
326 TCGATAAAAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTATACTAAT
203003 AGGAAAGAGGACGTAGCTACCAATTTGGACCGAACCTCTATAAATCTTTGTGTCGAACATTTCTT
1 AGGAAAGAGGACGTAGCTACCAATTTGGACCGAACCTCTATAAATCTTTGTGTCGAACATTTCTT
*
203068 CCCTAATATTTTTATCTTTTGAATTGTTTTATACCAAACTTTTCAAAATACTCAAAATTCGAAAA
66 CCCTAATATTTTTATCTTTCGAATTGTTTTATACCAAACTTTTCAAAATACTCAAAATTCGAAAA
* * *
203133 GAACCAATTCACCCCCTTCTTGGTTTATTAATCCTTGAGCTTTCATATACACTAAACAAGGAAGT
131 GAACCAATTCACCCCCCTCTTGGTTTATGAATCCTTAAGCTTTCATATACACTAAACAAGGAAGT
*
203198 GTCGAGGAGAGAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAACACTTGTGTCAAGCTT
196 GTCGAGGAGAAAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAACACTTGTGTCAAGCTT
203263 TCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTTCAAAACCTTCAAATT
261 TCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTTCAAAACCTTCAAATT
*
203328 TCGATAAGAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTATACTAAT
326 TCGATAAAAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTATACTAAT
203386 GTATGCAATG
Statistics
Matches: 377, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
383 377 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (383 bp):
AGGAAAGAGGACGTAGCTACCAATTTGGACCGAACCTCTATAAATCTTTGTGTCGAACATTTCTT
CCCTAATATTTTTATCTTTCGAATTGTTTTATACCAAACTTTTCAAAATACTCAAAATTCGAAAA
GAACCAATTCACCCCCCTCTTGGTTTATGAATCCTTAAGCTTTCATATACACTAAACAAGGAAGT
GTCGAGGAGAAAGGACGTAGGTTCCATGTTTGGATTGAACCTCTATAAACACTTGTGTCAAGCTT
TCTCTTTTTCCTACTCTTTTTATCTTCGAGTTGTTTTTGAATCAATTTTTCAAAACCTTCAAATT
TCGATAAAAACCAATTCACCCCCCTCTTGGTTCATTCAATCATTAAGCTTATACTAAT
Found at i:208718 original size:2 final size:2
Alignment explanation
Indices: 208713--208742 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
208703 TCTCACACAA
*
208713 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
208743 GGGGGGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:209194 original size:24 final size:25
Alignment explanation
Indices: 209167--209216 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
209157 CATTACTTTC
209167 TTAATTT-GA-TTTTAAAATAATTTA
1 TTAATTTAGAGTTTT-AAATAATTTA
*
209191 TTAATTTAGAGTTTTAAATTATTTA
1 TTAATTTAGAGTTTTAAATAATTTA
209216 T
1 T
209217 AGATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 12 0.52
26 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (25 bp):
TTAATTTAGAGTTTTAAATAATTTA
Found at i:209214 original size:25 final size:24
Alignment explanation
Indices: 209158--209216 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
209148 TTGAATCTGC
*
209158 ATTACTTTCTTAATTTGATTTTAAA
1 ATTA-TTTATTAATTTGATTTTAAA
*
209183 ATAATTTATTAATTTAGAGTTTT-AA
1 ATTATTTATTAATTT-GA-TTTTAAA
209208 ATTATTTAT
1 ATTATTTAT
209217 AGATATCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.34
25 15 0.52
26 4 0.14
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (24 bp):
ATTATTTATTAATTTGATTTTAAA
Found at i:212977 original size:18 final size:19
Alignment explanation
Indices: 212949--212986 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
212939 TTTTTATGAT
212949 TTTTTATAAATATATTTAA
1 TTTTTATAAATATATTTAA
*
212968 TTTTTA-AAATATTTTTAA
1 TTTTTATAAATATATTTAA
212986 T
1 T
212987 CATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTATAAATATATTTAA
Found at i:213795 original size:20 final size:20
Alignment explanation
Indices: 213764--213810 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
213754 AAATTAAAAT
*
213764 ATTTAT-AAAATTTACTATTA
1 ATTTATAAAAATTTA-TATAA
213784 A-TTATAAAAATTTATATAA
1 ATTTATAAAAATTTATATAA
213803 ATTTATAA
1 ATTTATAA
213811 TATTTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATAAAAATTTATATAA
Found at i:213804 original size:10 final size:10
Alignment explanation
Indices: 213764--213809 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
213754 AAATTAAAAT
213764 ATTTATA-AA
1 ATTTATATAA
*
213773 ATTTACTATTA
1 ATTTA-TATAA
*
213784 A-TTATAAAA
1 ATTTATATAA
213793 ATTTATATAA
1 ATTTATATAA
213803 ATTTATA
1 ATTTATA
213810 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
9 9 0.30
10 19 0.63
11 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTTATATAA
Found at i:213817 original size:20 final size:20
Alignment explanation
Indices: 213764--213815 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
213754 AAATTAAAAT
*
213764 ATTTATAAAATTTACTATTA
1 ATTTATAAAATTTACTATAA
213784 A-TTATAAAAATTTA-TATAA
1 ATTTAT-AAAATTTACTATAA
*
213803 ATTTATAATATTT
1 ATTTATAAAATTT
213816 TAAACATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTATAAAATTTACTATAA
Found at i:214358 original size:16 final size:16
Alignment explanation
Indices: 214337--214367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
214327 GATTGCTTCT
214337 GTTTTAAGTCATTTTG
1 GTTTTAAGTCATTTTG
*
214353 GTTTTAAGTTATTTT
1 GTTTTAAGTCATTTT
214368 TGATTAGGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.03, G:0.16, T:0.61
Consensus pattern (16 bp):
GTTTTAAGTCATTTTG
Found at i:215037 original size:16 final size:15
Alignment explanation
Indices: 215016--215084 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
215006 TTTGAAATTA
*
215016 AAAATAGTTCAAACT
1 AAAATAATTCAAACT
215031 CAAAATAATTCAAAACT
1 -AAAATAATTC-AAACT
* * *
215048 GAAGTAACTTAAAACT
1 AAAATAA-TTCAAACT
215064 AAAATAATTCAAACT
1 AAAATAATTCAAACT
215079 CAAAAT
1 -AAAAT
215085 TACATAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 7 0.16
16 29 0.67
17 7 0.16
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.25
Consensus pattern (15 bp):
AAAATAATTCAAACT
Found at i:215093 original size:32 final size:33
Alignment explanation
Indices: 215026--215093 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
215016 AAAATAGTTC
* * *
215026 AAACTCAAAATAATTCAAAACTGAAGTAACTTA
1 AAACTCAAAATAATTCAAAACTAAAATAACATA
*
215059 AAACT-AAAATAATTC-AAACTCAAAATTACATA
1 AAACTCAAAATAATTCAAAACT-AAAATAACATA
215091 AAA
1 AAA
215094 ATTTACTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 5 0.17
32 20 0.67
33 5 0.17
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (33 bp):
AAACTCAAAATAATTCAAAACTAAAATAACATA
Found at i:215763 original size:19 final size:18
Alignment explanation
Indices: 215714--215784 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
215704 TTATTTTTAA
*
215714 TTTAATATTATAAAAATAT
1 TTTAATA-TATAAATATAT
* *
215733 ATT-ATTTATAAATATAAT
1 TTTAATATATAAATAT-AT
*
215751 TTTAATATATAAA-ATTT
1 TTTAATATATAAATATAT
*
215768 TTTAGTATATATAATAT
1 TTTAATATATA-AATAT
215785 GCATATAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
17 19 0.46
18 10 0.24
19 12 0.29
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
TTTAATATATAAATATAT
Done.