Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2049
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: 25666
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:141 original size:46 final size:45
Alignment explanation
Indices: 91--266 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
81 TGGTTGAGCA
91 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
137 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
184 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
230 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
267 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:247 original size:93 final size:93
Alignment explanation
Indices: 88--258 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
78 GGATGGTTGA
* *
88 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
153 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCAAGTTCGAGAGATGTAACTAG
* *
181 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
246 TGAGTCCAAGTTC
66 TGAGTCCAAGTTC
259 ACTTATGGGC
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:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGAGAGATGTAACTAG
Found at i:14325 original size:27 final size:27
Alignment explanation
Indices: 14295--14463 Score: 194
Period size: 27 Copynumber: 6.3 Consensus size: 27
14285 TGTAGGGTAG
* **
14295 AATTACCAAAATACCCTTGGTTTACAA
1 AATTACCAAAATACCCTTGATTTGTAA
* *
14322 AATTACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTTGATTTGTAA
* *
14349 AATTACCAAAATACCTTTGGTTTGTAA
1 AATTACCAAAATACCCTTGATTTGTAA
* * *
14376 AATTACCAAAATACCCCTAATTTGTGA
1 AATTACCAAAATACCCTTGATTTGTAA
* *
14403 AATTACCAAAATACCCTCGACTTGTAA
1 AATTACCAAAATACCCTTGATTTGTAA
* * * *
14430 AATTACCAAAGTACCCCTGATTTATAG
1 AATTACCAAAATACCCTTGATTTGTAA
14457 AATTACC
1 AATTACC
14464 GTTTTACCCT
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGATTTGTAA
Found at i:14353 original size:54 final size:54
Alignment explanation
Indices: 14295--14499 Score: 212
Period size: 54 Copynumber: 3.8 Consensus size: 54
14285 TGTAGGGTAG
* * *
14295 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCCTGATTTGTAA
* * * ** * *
14349 AATTACCAAAATACCTTTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTGA
1 AATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCCTGATTTGTAA
* ** * * *
14403 AATTACCAAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTATAG
1 AATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCCTGATTTGTAA
**** **
14457 AATTACCGTTTTACCCTCGATTTACAAAATTATTAAAATACCC
1 AATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCC
14500 TTGTAGGGTA
Statistics
Matches: 126, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 126 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (54 bp):
AATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCCTGATTTGTAA
Found at i:14514 original size:27 final size:27
Alignment explanation
Indices: 14484--14759 Score: 272
Period size: 27 Copynumber: 10.2 Consensus size: 27
14474 CGATTTACAA
*
14484 AATTATTAAAATACCCTTGTAGGGTAG
1 AATTACTAAAATACCCTTGTAGGGTAG
* * *
14511 AATTATTGAAATATCCC-TATAGGGTAG
1 AATTACTAAAATA-CCCTTGTAGGGTAG
14538 AATTACTAAAATACCCTTGTAGGGTAG
1 AATTACTAAAATACCCTTGTAGGGTAG
* *
14565 AATTACTGAAATACTCC-TGTAGCGTAG
1 AATTACTAAAATAC-CCTTGTAGGGTAG
* * *
14592 AGTTACTGAAATA-CCTCTGTAGGGTAA
1 AATTACTAAAATACCCT-TGTAGGGTAG
*
14619 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACTAAAATACCCTTGTAGGGTAG
* * *
14646 AAGTACTGAAATACCCCTGTAGGGTAG
1 AATTACTAAAATACCCTTGTAGGGTAG
* *
14673 AATTACCAAAATACCCTTGTAGGGTAA
1 AATTACTAAAATACCCTTGTAGGGTAG
* ** *
14700 AAATACCGAAATACTCC-TGTAAGGTAG
1 AATTACTAAAATAC-CCTTGTAGGGTAG
** * * *
14727 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTAAAATACCCTTGTAGGGTAG
14754 AATTAC
1 AATTAC
14760 CATTTTGCCC
Statistics
Matches: 211, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.01
26 5 0.02
27 195 0.92
28 9 0.04
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (27 bp):
AATTACTAAAATACCCTTGTAGGGTAG
Found at i:15200 original size:22 final size:22
Alignment explanation
Indices: 15148--15212 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
15138 GCCAATTATT
* *
15148 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTATGTGCCAAC
* *
15170 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTATGTGCCAAC
*
15192 CTGATTATGGCTATATGCCAA
1 CTGATTATGGCTATGTGCCAA
15213 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (22 bp):
CTGATTATGGCTATGTGCCAAC
Found at i:15601 original size:25 final size:25
Alignment explanation
Indices: 15554--15602 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
15544 TTTGATTTTG
* * *
15554 ATTCTGTTACCTGATACTGATTCTA
1 ATTCTGTCACCTAATACTAATTCTA
*
15579 ATTCTGTCACCTAATTCTAATTCT
1 ATTCTGTCACCTAATACTAATTCT
15603 GATTTTGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.45
Consensus pattern (25 bp):
ATTCTGTCACCTAATACTAATTCTA
Found at i:15605 original size:37 final size:37
Alignment explanation
Indices: 15564--15642 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
15554 ATTCTGTTAC
*
15564 CTGATACTGATTCTAATTCTGTCACCTAATTCTAATT
1 CTGATACTGATTATAATTCTGTCACCTAATTCTAATT
** * * *
15601 CTGATTTTGATTATGATTCTGTCACCTGATTCTGATT
1 CTGATACTGATTATAATTCTGTCACCTAATTCTAATT
15638 CTGAT
1 CTGAT
15643 TGTCATTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.46
Consensus pattern (37 bp):
CTGATACTGATTATAATTCTGTCACCTAATTCTAATT
Found at i:15636 original size:19 final size:19
Alignment explanation
Indices: 15570--15640 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
15560 TTACCTGATA
15570 CTGATTCTAATTCTGTCAC
1 CTGATTCTAATTCTGTCAC
* *
15589 CTAATTCTAATTCTG--ATT
1 CTGATTCTAATTCTGTCA-C
* * *
15607 TTGATTATGATTCTGTCAC
1 CTGATTCTAATTCTGTCAC
*
15626 CTGATTCTGATTCTG
1 CTGATTCTAATTCTG
15641 ATTGTCATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 1 0.03
18 11 0.28
19 27 0.68
20 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (19 bp):
CTGATTCTAATTCTGTCAC
Found at i:15643 original size:37 final size:37
Alignment explanation
Indices: 15579--15657 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
15569 ACTGATTCTA
* *
15579 ATTCTGTCACCTAATTCTAATTCTGATTTTGATTATG
1 ATTCTGTCACCTAATTCTAATTCTGATTGTCATTATG
* * *
15616 ATTCTGTCACCTGATTCTGATTCTGATTGTCATTTTG
1 ATTCTGTCACCTAATTCTAATTCTGATTGTCATTATG
15653 ATTCT
1 ATTCT
15658 AGTTCTGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (37 bp):
ATTCTGTCACCTAATTCTAATTCTGATTGTCATTATG
Found at i:20790 original size:40 final size:40
Alignment explanation
Indices: 20692--20994 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
20682 TCCTCGTTCA
* * * * *
20692 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
20731 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
20771 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20811 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20851 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
20891 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
20931 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
20971 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20995 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Done.