Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1221
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: 15057
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Found at i:133 original size:47 final size:48
Alignment explanation
Indices: 23--159 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 48
13 TATTTGAGGT
*
23 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATC
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CC--AGACTGTGATC
* * * *
74 ACGTGTGTAGTACTAAGT-CAGGCTACTACGTGTACCAGACTGTTG-TC
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTG-TGATC
121 GCATGTGTAGTACTAAGTGCA-GCTACTATGCGTACCAGA
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
160 TACTTCGGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
47 39 0.52
48 4 0.05
49 2 0.03
50 14 0.19
51 16 0.21
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (48 bp):
GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTGTGATC
Found at i:5455 original size:49 final size:51
Alignment explanation
Indices: 5325--5468 Score: 202
Period size: 49 Copynumber: 2.9 Consensus size: 51
5315 TCTATTGTGA
*
5325 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAAAACTGT
* * * * * **
5376 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTA-T-T
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAAAACTGT
5425 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
5469 TAGCTTCGGC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 40 0.50
50 1 0.01
51 39 0.49
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAAAACTGT
Found at i:7504 original size:45 final size:48
Alignment explanation
Indices: 7431--7520 Score: 150
Period size: 45 Copynumber: 1.9 Consensus size: 48
7421 TTGTTCGAGT
7431 AGATGAATGGATAAGTCAAGCTATCCAGAAAACATA-GATGCATGATGC
1 AGATGAATGGATAAG-CAAGCTATCCAGAAAACATAGGATGCATGATGC
7479 AGATGAATGGAT-A-CAAGCTATCCAGAAAACATAGGATGCATG
1 AGATGAATGGATAAGCAAGCTATCCAGAAAACATAGGATGCATG
7521 CATAATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
45 20 0.49
46 8 0.20
47 1 0.02
48 12 0.29
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.20
Consensus pattern (48 bp):
AGATGAATGGATAAGCAAGCTATCCAGAAAACATAGGATGCATGATGC
Found at i:8517 original size:15 final size:15
Alignment explanation
Indices: 8497--8550 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
8487 TATCGTATCT
8497 TGGGTTTCTTTATTC
1 TGGGTTTCTTTATTC
8512 TGGGTTT-TTCTA-TC
1 TGGGTTTCTT-TATTC
*
8526 TTGGATTTCTTTATTC
1 -TGGGTTTCTTTATTC
*
8542 -GGTTTTCTT
1 TGGGTTTCTT
8551 GTTATCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 12 0.36
15 17 0.52
16 4 0.12
ACGTcount: A:0.07, C:0.13, G:0.19, T:0.61
Consensus pattern (15 bp):
TGGGTTTCTTTATTC
Found at i:10809 original size:49 final size:48
Alignment explanation
Indices: 10681--10824 Score: 189
Period size: 49 Copynumber: 2.9 Consensus size: 48
10671 TCTATTGTGA
*
10681 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC---AGACTGT
* * * * * *
10732 GATCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGACTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTG-T
10781 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
10825 TAGCTTCGGC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
48 5 0.06
49 39 0.49
51 35 0.44
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTGT
Found at i:13140 original size:68 final size:66
Alignment explanation
Indices: 13065--13213 Score: 176
Period size: 66 Copynumber: 2.2 Consensus size: 66
13055 CATCATGTGT
* * * *
13065 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
13128 TGTAG
62 TGTAG
** * *
13133 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGTGAAGGACACCATGTA
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
13198 G
66 G
13199 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
13214 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.34
65 5 0.07
66 28 0.40
68 13 0.19
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:13170 original size:64 final size:64
Alignment explanation
Indices: 13089--13271 Score: 210
Period size: 66 Copynumber: 2.8 Consensus size: 64
13079 AGACATTATG
* * *
13089 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
13153 ATGTAGCTAGGTCGCATGCGTGGTTCCAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
1 ATGTAGCTAGGTCGCATGGGTGGTACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGATA
13218 A
64 A
* * *
13219 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
13272 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
65 21 0.21
66 31 0.31
67 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Done.