Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3283
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: 46095
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Found at i:9550 original size:12 final size:13
Alignment explanation
Indices: 9533--9561 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
9523 AGATGGACAA
9533 AATTTGGC-TTTT
1 AATTTGGCTTTTT
9545 AATTTGGCTTTTT
1 AATTTGGCTTTTT
9558 AATT
1 AATT
9562 CATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (13 bp):
AATTTGGCTTTTT
Found at i:14771 original size:47 final size:47
Alignment explanation
Indices: 14717--15052 Score: 438
Period size: 47 Copynumber: 7.1 Consensus size: 47
14707 TTAAGATTTT
** * *
14717 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
* *
14764 ATGTGATGAATGTGAACCTGTATATATATGCATGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--CATATATG-A-GATAAGGCCGAATGGCCA
* * * *
14815 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGACA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
* * *
14862 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
* * **
14909 ATGTGATGAATGTGAACATGCGTATGTGTTATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
*
14956 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
* * * *
15003 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
15050 ATG
1 ATG
15053 CGAAATGTGT
Statistics
Matches: 264, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
47 214 0.81
49 13 0.05
50 1 0.00
51 36 0.14
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
Found at i:14844 original size:25 final size:25
Alignment explanation
Indices: 14816--14893 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
14806 GAATGGCCAA
14816 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
* * **
14841 TGTGAT-AAGGCCG-A-ATG-G-ACAA
1 TGTGATGAATG-TGAACATGCGTA-TG
14863 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
14888 TGTGAT
1 TGTGAT
14894 AAGGCCGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
21 1 0.03
22 8 0.21
23 7 0.18
24 7 0.18
25 14 0.37
26 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.32, T:0.29
Consensus pattern (25 bp):
TGTGATGAATGTGAACATGCGTATG
Found at i:15162 original size:46 final size:46
Alignment explanation
Indices: 15026--15162 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
15016 GAACATGTAT
* * *
15026 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATGG
* *
15072 ATATGAGGTAAAGCCGAATGGCTAATGTGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATGG
* * *
15118 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATG
15163 TGTATATATA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATGTGTATGAGATGG
Found at i:26033 original size:44 final size:43
Alignment explanation
Indices: 25965--26113 Score: 133
Period size: 42 Copynumber: 3.5 Consensus size: 43
25955 GATACTGATC
* ** * *
25965 TGAGATATCGTGTAAGACTGTGTCTGGGACACAGGCCTCAATT
1 TGAGATTTCGTGTAAGACCATGTCTGGGACAAAGGCATCAATT
* * * *
26008 TGAGATTTACGTGTAAGACCATGTCTGGGACATAGGCAACGTATC
1 TGAGATTT-CGTGTAAGACCATGTCTGGGACAAAGGCATC-AATT
* *
26053 T-AG-TTTCGTGTAAGACCCTGTCTGGGACAAAGGCATCGATAT
1 TGAGATTTCGTGTAAGACCATGTCTGGGACAAAGGCATCAAT-T
* *
26095 TGA-ATTACATGTAAGACCA
1 TGAGATTTCGTGTAAGACCA
26114 CATCCAGGAC
Statistics
Matches: 85, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 29 0.34
43 23 0.27
44 28 0.33
45 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
TGAGATTTCGTGTAAGACCATGTCTGGGACAAAGGCATCAATT
Found at i:32167 original size:28 final size:28
Alignment explanation
Indices: 32135--32218 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
32125 AACTTCGATC
32135 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
32163 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
32185 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
32213 ACGTGT
1 ACGTGT
32219 ACCGAATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:32208 original size:50 final size:48
Alignment explanation
Indices: 32087--32262 Score: 217
Period size: 50 Copynumber: 3.5 Consensus size: 48
32077 TGAGGTCGCA
* * *
32087 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGATAA-TT-GGTCACG
* **
32138 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGATAATT-GGTCACG
* *
32188 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCG-ATAATTGGTCACG
*
32237 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
32263 TGCGTACCAG
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 32 0.29
50 44 0.40
51 34 0.31
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATTGGTCACG
Found at i:38358 original size:39 final size:39
Alignment explanation
Indices: 38314--38587 Score: 471
Period size: 39 Copynumber: 7.1 Consensus size: 39
38304 ATGCAAGACA
38314 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
38353 CTGGAAATGTATCCGGGCTAAAGT-CC-CAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
38390 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
38429 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
38468 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
38507 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
38546 CTGGAAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
38585 CTG
1 CTG
38588 ATAATATAAT
Statistics
Matches: 223, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
37 33 0.15
38 4 0.02
39 186 0.83
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:44235 original size:39 final size:39
Alignment explanation
Indices: 44191--44464 Score: 471
Period size: 39 Copynumber: 7.1 Consensus size: 39
44181 ATGCAAGACA
44191 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
44230 CTGGAAATGTATCCGGGCTAAAGT-CC-CAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
44267 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
44306 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
44345 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
44384 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
44423 CTGGAAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
44462 CTG
1 CTG
44465 ATAATATAAT
Statistics
Matches: 223, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
37 33 0.15
38 4 0.02
39 186 0.83
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Done.