Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2352
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: 22947
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Found at i:2247 original size:138 final size:133
Alignment explanation
Indices: 1973--2262 Score: 323
Period size: 138 Copynumber: 2.1 Consensus size: 133
1963 ATTAAACATA
* * * * *
1973 TTTTGACATATTAAACATACATGCCATAAAAAATTAATAATATCAGATATCTCAAATAACATTAA
1 TTTTAACATATTAAAC--ACATACCATAAAAAATTAATAATATAAAAAATCTCAAATAACATTAA
* ** * * *
2038 GAGTATTTAAACAAGCATTCATATTAAAGAGGAATATAATCCAAAACCACGTCAAAACAAGTCTT
64 GAGTATTTAAACAAGCATTCATATTAAAAAAAAATATAATCAAAAAACACGTCAAAACAAATCTT
2103 TTTAT
129 TTTAT
* * *
2108 TTTTAACATAATAAACACATACCATAAAAAATTAATAATATAAAAAATCTTAAATAATATATTAA
1 TTTTAACATATTAAACACATACCATAAAAAATTAATAATATAAAAAATCTCAAAT-A-ACATTAA
* * *
2173 GAGGTATTTAAACGAGTATTTCATATTAAACAAAAAATATAA-CTAAAAAATACGTC-AAACTAA
64 GA-GTATTTAAACAAGCA-TTCATATTAAA-AAAAAATATAATC-AAAAAACACGTCAAAAC-AA
2236 ATCTTTTTAT
124 ATCTTTTTAT
*
2246 TTTAAACATATTAAACA
1 TTTTAACATATTAAACA
2263 TATTTTGACA
Statistics
Matches: 129, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
133 34 0.26
134 1 0.01
135 22 0.17
136 13 0.10
137 16 0.12
138 43 0.33
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (133 bp):
TTTTAACATATTAAACACATACCATAAAAAATTAATAATATAAAAAATCTCAAATAACATTAAGA
GTATTTAAACAAGCATTCATATTAAAAAAAAATATAATCAAAAAACACGTCAAAACAAATCTTTT
TAT
Found at i:3013 original size:22 final size:22
Alignment explanation
Indices: 2960--3035 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
2950 ATACTTTAAT
2960 CAAATTAAT-CTTAAAATAAAA
1 CAAATTAATACTTAAAATAAAA
* *
2981 -ATAAATCATACTTAAAATAAAA
1 CA-AATTAATACTTAAAATAAAA
*
3003 CAAATTTATACTTCTACAAATAAAA
1 CAAATTAATAC-T-TA-AAATAAAA
*
3028 TAAATTAA
1 CAAATTAA
3036 ACACATATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 5 0.12
22 19 0.44
23 2 0.05
24 2 0.05
25 14 0.33
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (22 bp):
CAAATTAATACTTAAAATAAAA
Found at i:3299 original size:15 final size:16
Alignment explanation
Indices: 3286--3315 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3276 TTTACTTTTT
3286 AATTTTTTAATTTTAA
1 AATTTTTTAATTTTAA
3302 AATTTTTT-ATTTTA
1 AATTTTTTAATTTTA
3316 TTAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTTTAATTTTAA
Found at i:12899 original size:2 final size:2
Alignment explanation
Indices: 12892--12932 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12882 CTAAGGGATA
12892 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12933 AACAGTGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18238 original size:14 final size:14
Alignment explanation
Indices: 18216--18248 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18206 GGATTTTTCC
*
18216 TTTTT-TTTATATT
1 TTTTTATTTATATA
18229 TTTTTATTTATATA
1 TTTTTATTTATATA
18243 TTTTTA
1 TTTTTA
18249 AATTCTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTATATA
Found at i:18546 original size:19 final size:20
Alignment explanation
Indices: 18522--18570 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
18512 ATAATTAAAA
18522 ATATTAAAA-TAT-TATTTTT
1 ATATTAAAATTATAT-TTTTT
18541 ATATTAATAATTATATTTTTT
1 ATATTAA-AATTATATTTTTT
18562 ATAATTAAA
1 AT-ATTAAA
18571 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.27
20 2 0.08
21 11 0.42
22 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTAAAATTATATTTTTT
Found at i:18559 original size:20 final size:19
Alignment explanation
Indices: 18522--18570 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 19
18512 ATAATTAAAA
18522 ATATTAAAATATTATTTTT
1 ATATTAAAATATTATTTTT
18541 ATATTAATAAT-TATATTTTTT
1 ATATTAA-AATAT-TA-TTTTT
18562 ATAATTAAA
1 AT-ATTAAA
18571 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.31
20 5 0.19
21 8 0.31
22 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTAAAATATTATTTTT
Found at i:18891 original size:18 final size:18
Alignment explanation
Indices: 18850--18888 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
18840 AAAGCTAAAT
*
18850 TAATTTTATATATTTTTA
1 TAATTTTATATATATTTA
18868 TAATTTTATATATGATTTA
1 TAATTTTATATAT-ATTTA
18887 TA
1 TA
18889 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATTTTATATATATTTA
Found at i:19204 original size:2 final size:2
Alignment explanation
Indices: 19197--19230 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19187 ATAGATTTCT
*
19197 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19231 AAGATCTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19428 original size:21 final size:21
Alignment explanation
Indices: 19364--19428 Score: 53
Period size: 23 Copynumber: 3.1 Consensus size: 21
19354 TTCAAGTTTC
*
19364 TTAATAAG-ATATATATTATA
1 TTAATATGCATATATATTATA
* * *
19384 TGAATATGCAAATATACTTCTA
1 TTAATATGCATATATA-TTATA
*
19406 TTATATATGTATATATATT-TA
1 TTA-ATATGCATATATATTATA
19427 TT
1 TT
19429 TGTAAATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.17
21 10 0.29
22 8 0.23
23 11 0.31
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (21 bp):
TTAATATGCATATATATTATA
Found at i:19473 original size:31 final size:30
Alignment explanation
Indices: 19438--19516 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
19428 TTGTAAATAT
*
19438 AAATTTTAAAATTATAAATATTTAA-TATCAA
1 AAATTTTAAAATTATAAATA-ATAAGTAT-AA
*
19469 AAATTTTTAAATT-TCAAATAATAAGTATAA
1 AAATTTTAAAATTAT-AAATAATAAGTATAA
*
19499 AAATATTTAAAAATATAA
1 AAAT-TTTAAAATTATAA
19517 TAAATAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
30 10 0.25
31 29 0.73
32 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATTTTAAAATTATAAATAATAAGTATAA
Found at i:22347 original size:19 final size:19
Alignment explanation
Indices: 22323--22375 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
22313 AAAATGCCTG
***
22323 AATGTATCGATACATTTTC
1 AATGTATCGATACATGAAC
22342 AATGTATCGATACATGAAC
1 AATGTATCGATACATGAAC
*
22361 AATATATCGATACAT
1 AATGTATCGATACAT
22376 CTAGGTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (19 bp):
AATGTATCGATACATGAAC
Found at i:22947 original size:20 final size:20
Alignment explanation
Indices: 22909--22947 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22899 AAATGAATTC
*
22909 ATATTATTTATATTTTTTAA
1 ATATTATTTATATTATTTAA
22929 ATATT-TTTATACTTATTTA
1 ATATTATTTATA-TTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTATTTATATTATTTAA
Done.