Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1406
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: 28119
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:446 original size:46 final size:46
Alignment explanation
Indices: 294--468 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
284 TAACCACCGC
* * * *
294 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--GTGTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCAT
* *
339 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGA---C-ATTTGCAT
*
390 -C-TCA--GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
432 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
469 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
42 6 0.06
43 2 0.02
44 2 0.02
45 30 0.28
46 39 0.36
47 23 0.21
49 2 0.02
50 1 0.01
51 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:460 original size:93 final size:91
Alignment explanation
Indices: 302--471 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 91
292 GCCCATAAGC
*
302 GAACTCGGACTCAACTCAACGAGCTCGGGTGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
367 GAGCTTCGGATGCCTAGTTACATCTCA
66 GAG-TTCGGATGCCTAGTTACATCTCA
* *
394 GAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGG--ATGTCGCATCCATAAGTGAACTCGGACTCAACTCA
458 ACGAGTTCGGATGC
64 ACGAGTTCGGATGC
472 TCAACCATCC
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
92 36 0.49
93 36 0.49
94 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA
Found at i:5877 original size:93 final size:93
Alignment explanation
Indices: 5765--5936 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
5755 CGCCCATAAG
***
5765 CGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCACATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
5830 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* **
5858 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
5923 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
5937 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:5880 original size:47 final size:49
Alignment explanation
Indices: 5758--5936 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 49
5748 TGTAACCCGC
* *
5758 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G--TGTTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTT-ACAT
*
5804 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACAT
* * *
5854 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
*
5897 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
5937 TCAACCATCC
Statistics
Matches: 113, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 63 0.56
47 29 0.26
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
Found at i:9035 original size:46 final size:45
Alignment explanation
Indices: 8968--9142 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
8958 TGTAACCCGC
* *
8968 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCAT
* * *
9014 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCAT
* * *
9064 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCAT
* *
9107 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
9143 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.55
47 27 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCAT
Found at i:9088 original size:93 final size:93
Alignment explanation
Indices: 8975--9146 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
8965 CGCCCATAAG
* * *
8975 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
*
9040 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * *
9068 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGAACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
9133 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
9147 TCAACCATCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:12574 original size:27 final size:27
Alignment explanation
Indices: 12544--12809 Score: 170
Period size: 27 Copynumber: 10.0 Consensus size: 27
12534 ACATGCTAGA
* *
12544 AAATGTAAGCCTTTGTAGAAATCTATG
1 AAATGGAAGCCTTTGTGGAAATCTATG
* * **
12571 AAATGAAAGTCTTTGTGGCGTATC--TG
1 AAATGGAAGCCTTTGTGG-AAATCTATG
* *
12597 AAATGGAAGCCTTTATGGAAATATATG
1 AAATGGAAGCCTTTGTGGAAATCTATG
*
12624 AAATGGAAGCCTTTGTGGCAATCTATG
1 AAATGGAAGCCTTTGTGGAAATCTATG
* ** * *
12651 AAATGGAAACCTTTACAGCATATC--TG
1 AAATGGAAGCCTTT-GTGGAAATCTATG
** **
12677 AAATGGAAGTATTTGTGGCGTATC--TG
1 AAATGGAAGCCTTTGTGG-AAATCTATG
* *
12703 AAATGGAAGCCTTTGTGGCAATCTGTG
1 AAATGGAAGCCTTTGTGGAAATCTATG
* *
12730 AAATAGAAGCCTTTGTGGCATATCTA--
1 AAATGGAAGCCTTTGTGG-AAATCTATG
** * **
12756 AAATGGAAGAATTTTTGTCAATCTATG
1 AAATGGAAGCCTTTGTGGAAATCTATG
* **
12783 AAATTGAAGCCTTTGTGGTGATCTATG
1 AAATGGAAGCCTTTGTGGAAATCTATG
12810 GAAAGGATTG
Statistics
Matches: 180, Mismatches: 49, Indels: 20
0.72 0.20 0.08
Matches are distributed among these distances:
25 11 0.06
26 65 0.36
27 93 0.52
28 11 0.06
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGAAATCTATG
Found at i:12624 original size:53 final size:53
Alignment explanation
Indices: 12544--12764 Score: 205
Period size: 53 Copynumber: 4.2 Consensus size: 53
12534 ACATGCTAGA
* * * *
12544 AAATGTAAGCCTTTGTAGAAATCTATGAAATGAAAGTCTTTGTGGCGTATCTG
1 AAATGGAAGCCTTTATAGAAATATATGAAATGAAAGCCTTTGTGGCGTATCTG
* * *
12597 AAATGGAAGCCTTTATGGAAATATATGAAATGGAAGCCTTTGTGGC-AATCTATG
1 AAATGGAAGCCTTTATAGAAATATATGAAATGAAAGCCTTTGTGGCGTATC--TG
* * * * * **
12651 AAATGGAAACCTTTACAG-CATATCTGAAATGGAAGTATTTGTGGCGTATCTG
1 AAATGGAAGCCTTTATAGAAATATATGAAATGAAAGCCTTTGTGGCGTATCTG
* * * * * * *
12703 AAATGGAAGCCTTTGTGGCAATCTGTGAAAT-AGAAGCCTTTGTGGCATATCTA
1 AAATGGAAGCCTTTATAGAAATATATGAAATGA-AAGCCTTTGTGGCGTATCTG
12756 AAATGGAAG
1 AAATGGAAG
12765 AATTTTTGTC
Statistics
Matches: 136, Mismatches: 27, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
52 19 0.14
53 97 0.71
54 20 0.15
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (53 bp):
AAATGGAAGCCTTTATAGAAATATATGAAATGAAAGCCTTTGTGGCGTATCTG
Found at i:12732 original size:79 final size:79
Alignment explanation
Indices: 12544--12809 Score: 230
Period size: 80 Copynumber: 3.3 Consensus size: 79
12534 ACATGCTAGA
* * * * *** * * **
12544 AAATGTAAGCCTTTGTAGAAATCTATGAAAT-GAAAGTCTTTGTGGCGTATCTGAAATGGAAGCC
1 AAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAA-CCTTTACAGCATATCTAAAATGGAAGAA
* * *
12608 TTTATGGAAATATATG
65 TTTGTGGCAAT-CATG
* * *
12624 AAATGGAAGCCTTTGTGGCAATCTATGAAATGGAAACCTTTACAGCATATCTGAAATGGAAGTAT
1 AAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAACCTTTACAGCATATCTAAAATGGAAGAAT
*
12689 TTGTGGCGTATC-TG
66 TTGTGGC-AATCATG
* * ***
12703 AAATGGAAGCCTTTGTGGCAATCTGTGAAATAGAAGCCTTTGTGGCATATCTAAAATGGAAGAAT
1 AAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAACCTTTACAGCATATCTAAAATGGAAGAAT
* *
12768 TTTTGTCAATCTATG
66 TTGTGGCAATC-ATG
* **
12783 AAATTGAAGCCTTTGTGGTGATCTATG
1 AAATGGAAGCCTTTGTGGCAATCTATG
12810 GAAAGGATTG
Statistics
Matches: 153, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
78 3 0.02
79 64 0.42
80 80 0.52
81 6 0.04
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (79 bp):
AAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAACCTTTACAGCATATCTAAAATGGAAGAAT
TTGTGGCAATCATG
Found at i:12778 original size:53 final size:53
Alignment explanation
Indices: 12563--12800 Score: 180
Period size: 53 Copynumber: 4.5 Consensus size: 53
12553 CCTTTGTAGA
* * * ** * *
12563 AATCTATGAAAT-GAAAGTCTTTGTGGCGTATCTGAAATGGAAGCCTTTATGGA
1 AATCTATGAAATAG-AAGCCTTTGTGGCATATCTAAAATGGAAGAATTTGTGGC
* * * ***
12616 AATATATGAAATGGAAGCCTTTGTGGCA-ATCTATGAAATGGAA-ACCTTTACAGC
1 AATCTATGAAATAGAAGCCTTTGTGGCATATCTA--AAATGGAAGA-ATTTGTGGC
* ** * * **
12670 ATATC--TGAAATGGAAGTATTTGTGGCGTATCTGAAATGGAAGCCTTTGTGGC
1 A-ATCTATGAAATAGAAGCCTTTGTGGCATATCTAAAATGGAAGAATTTGTGGC
* * *
12722 AATCTGTGAAATAGAAGCCTTTGTGGCATATCTAAAATGGAAGAATTTTTGTC
1 AATCTATGAAATAGAAGCCTTTGTGGCATATCTAAAATGGAAGAATTTGTGGC
*
12775 AATCTATGAAATTGAAGCCTTTGTGG
1 AATCTATGAAATAGAAGCCTTTGTGG
12801 TGATCTATGG
Statistics
Matches: 148, Mismatches: 28, Indels: 18
0.76 0.14 0.09
Matches are distributed among these distances:
51 3 0.02
52 19 0.13
53 104 0.70
54 20 0.14
55 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (53 bp):
AATCTATGAAATAGAAGCCTTTGTGGCATATCTAAAATGGAAGAATTTGTGGC
Found at i:12785 original size:106 final size:106
Alignment explanation
Indices: 12563--12800 Score: 288
Period size: 106 Copynumber: 2.2 Consensus size: 106
12553 CCTTTGTAGA
*
12563 AATCTATGAAATGAAAGTCTTTGTGGCGTATCTGAAATGGAAGCCTTTATGGAAATATATGAAAT
1 AATCTATGAAATGGAAGTCTTTGTGGCGTATCTGAAATGGAAGCCTTTATGGAAATATATGAAAT
* *
12628 GGAAGCCTTTGTGGCAATCTATGAAATGGAAACCTTTACAGC
66 AGAAGCCTTTGTGGCAATCTA-GAAATGGAAACATTTACAGC
* * * * *
12670 ATATC--TGAAATGGAAGTATTTGTGGCGTATCTGAAATGGAAGCCTTTGTGGCAATCTGTGAAA
1 A-ATCTATGAAATGGAAGTCTTTGTGGCGTATCTGAAATGGAAGCCTTTATGGAAATATATGAAA
**
12733 TAGAAGCCTTTGTGGCATATCTA-AAATGGAAGA-ATTT-TTGTC
65 TAGAAGCCTTTGTGGCA-ATCTAGAAATGGAA-ACATTTACAG-C
* *
12775 AATCTATGAAATTGAAGCCTTTGTGG
1 AATCTATGAAATGGAAGTCTTTGTGG
12801 TGATCTATGG
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
104 4 0.04
105 13 0.12
106 86 0.77
107 6 0.05
108 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (106 bp):
AATCTATGAAATGGAAGTCTTTGTGGCGTATCTGAAATGGAAGCCTTTATGGAAATATATGAAAT
AGAAGCCTTTGTGGCAATCTAGAAATGGAAACATTTACAGC
Found at i:20060 original size:27 final size:27
Alignment explanation
Indices: 20030--20098 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
20020 TAAATTGTAC
* *
20030 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTACAT
*
20057 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTACAT
*
20084 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20099 GACTCGAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTACAT
Done.