Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1620
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: 32352
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:1325 original size:50 final size:50
Alignment explanation
Indices: 1211--1346 Score: 155
Period size: 50 Copynumber: 2.7 Consensus size: 50
1201 CTACCATCAA
* * * *
1211 ATCTCTAAGAATATAATATCATATCTTCTAAGATTACATATCTTAGATAAG
1 ATCTCTAAGATTATAATATCATATCTTATAAGA-TCCATATCATAGATAAG
* * * * * **
1262 ATATGTAATATTATAAAATAATATCTTATAAGATCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTATAAGATCCATATCATAGATAAG
*
1312 ATCTCTAAGATTATAATATCATATCTTTTAAGATC
1 ATCTCTAAGATTATAATATCATATCTTATAAGATC
1347 ATGTTTCCAT
Statistics
Matches: 68, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
50 42 0.62
51 26 0.38
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (50 bp):
ATCTCTAAGATTATAATATCATATCTTATAAGATCCATATCATAGATAAG
Found at i:2442 original size:93 final size:95
Alignment explanation
Indices: 2245--2524 Score: 378
Period size: 91 Copynumber: 3.0 Consensus size: 95
2235 CGCTTCTTTT
*
2245 TGCTCCTCTTTAGCCCTC-TGGCTTGGGCTTTACCCTTGCTCGAACCAAGCTTCTT-GGCTCCTT
1 TGCTCCTCTTT-GCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
*
2308 GT-TGCTCCATCGTT-CCTTTGATGACAGAC
65 GTCTGCTCCATCGTTCCCTTCGATGACAGAC
2337 TTGCTCCTCTTTGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
1 -TGCTCCTCTTTGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
2402 GTCTGCTCCATCGTTCCCTTCGATGACAGAC
65 GTCTGCTCCATCGTTCCCTTCGATGACAGAC
* ** * * *
2433 TGCT-C-CTTTGTCC-CTT-GCTTCGATTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCTCCGTA
1 TGCTCCTCTTTGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTG
* * * *
2494 TCTGCTCGATCATTCCCATCGATAACAGAC
66 TCTGCTCCATCGTTCCCTTCGATGACAGAC
2524 T
1 T
2525 TCCTCGGACA
Statistics
Matches: 171, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
91 67 0.39
92 9 0.05
93 54 0.32
94 11 0.06
95 16 0.09
96 14 0.08
ACGTcount: A:0.12, C:0.34, G:0.18, T:0.36
Consensus pattern (95 bp):
TGCTCCTCTTTGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTG
TCTGCTCCATCGTTCCCTTCGATGACAGAC
Found at i:5270 original size:104 final size:103
Alignment explanation
Indices: 5090--5312 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
5080 TGTATATAAA
** * *
5090 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
5155 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
* *
5194 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
5258 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
5297 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
5313 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 21 0.19
104 90 0.80
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:5362 original size:69 final size:71
Alignment explanation
Indices: 5232--5381 Score: 232
Period size: 71 Copynumber: 2.1 Consensus size: 71
5222 TCATTGGTGG
* *
5232 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAA-GTGAAAAGGGGTTGCTATGTGCTGATTCCCCC
5296 GAGGGGT
65 GAGGGGT
***
5303 TGCTAAGTGCGATATCCATTGTATATTTGAAA-TGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
5367 AGGGGT
66 AGGGGT
5373 TGCTAAGTG
1 TGCTAAGTG
5382 ATGATTCCCC
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 25 0.34
70 20 0.27
71 28 0.38
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:5386 original size:27 final size:27
Alignment explanation
Indices: 5340--5391 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5330 TGAAATGAAA
* *
5340 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGATGATTCCCCCG
5367 AGGGGTTGCTAAGTGATGATTCCCC
1 AGGGGTTGCTAAGTGATGATTCCCC
5392 GATTCAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGATGATTCCCCCG
Found at i:12819 original size:104 final size:104
Alignment explanation
Indices: 12639--12862 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
12629 TGTATATAAA
** * *
12639 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
12704 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
12743 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
12807 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
12847 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
12863 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:12914 original size:71 final size:72
Alignment explanation
Indices: 12781--12932 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
12771 TCATTGGTGG
* *
12781 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
12846 GAGGGGT
66 GAGGGGT
***
12853 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
12917 GAGGGGT
66 GAGGGGT
12924 TGCTAAGTG
1 TGCTAAGTG
12933 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:14577 original size:51 final size:51
Alignment explanation
Indices: 14505--14637 Score: 158
Period size: 51 Copynumber: 2.6 Consensus size: 51
14495 CCATCAAATC
* * *
14505 TCTAAGAATATAATATCATATCTTCTAAGATTACATATCTTAGATAAGATA
1 TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
* * * * * ** *
14556 TGTAATATTATAAAATAATATCTTATAAGATTCCATATCATATCTAAGATC
1 TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
*
14607 TCTAAGATTATAATATCATATCTTTTAAGAT
1 TCTAAGATTATAATATCATATCTTATAAGAT
14638 CATGTTTCCA
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (51 bp):
TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
Found at i:17737 original size:46 final size:46
Alignment explanation
Indices: 17670--17842 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
17660 AACCCGCCCT
* *
17670 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* *
17716 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG---GAC--GTTCGCATCCA
* * *
17764 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
*
17809 TAGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
17843 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 1 0.01
46 60 0.56
47 27 0.25
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:17782 original size:93 final size:93
Alignment explanation
Indices: 17675--17845 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
17665 GCCCTTAAGT
* *
17675 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
17740 CGAGTTCGAATGCCTAGTTACATCTCAC
66 CGAGTTCGAATGCCTAGTTACATCTCAC
* *
17768 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
17833 CGAGTTCGGATGC
66 CGAGTTCGAATGC
17846 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGAATGCCTAGTTACATCTCAC
Found at i:18299 original size:30 final size:30
Alignment explanation
Indices: 18265--18324 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
18255 ATTTAATACG
18265 AACTTTTGAAAAATTACACTTTTGCCCCTA
1 AACTTTTGAAAAATTACACTTTTGCCCCTA
* *
18295 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTGAAAAATTACACTTTTGCCCCTA
18325 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTTGAAAAATTACACTTTTGCCCCTA
Found at i:20809 original size:46 final size:47
Alignment explanation
Indices: 20739--21001 Score: 358
Period size: 46 Copynumber: 5.7 Consensus size: 47
20729 GTGTGCTCTC
* *
20739 TGATATGAAATGTGTATGACCATGGTTGAAAGATACCATGACAACCA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCA
* *
20786 T-TTATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCC-
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCA
*
20831 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCC-
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCA
* *
20877 TGATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGC-AGCA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCA
* **
20923 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA-CA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCA
* * *
20969 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 TGATATG-AAATGTGTAAGACCATGGTTGAAAGA
21002 CATATGGCAT
Statistics
Matches: 198, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
45 3 0.02
46 193 0.97
47 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (47 bp):
TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCA
Done.