Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2350
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: 8839
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Found at i:2958 original size:1 final size:1
Alignment explanation
Indices: 2948--3038 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
2938 TGGCAATTGG
* * * ** * * * **
2948 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAAACAAAACAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
3013 AAAGAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3039 GTGAAGATTT
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:2993 original size:35 final size:35
Alignment explanation
Indices: 2947--3038 Score: 154
Period size: 33 Copynumber: 2.7 Consensus size: 35
2937 ATGGCAATTG
*
2947 GAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
2982 GAAAAAAAAAAAAACAAAAC-AAAAAAAGGAAAAA
1 GAAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
3016 G-AAAAAAAAAAAACAAAA-AAAAA
1 GAAAAAAAAAAAAACAAAACAAAAA
3039 GTGAAGATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
33 21 0.38
34 15 0.27
35 19 0.35
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (35 bp):
GAAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
Found at i:3006 original size:34 final size:34
Alignment explanation
Indices: 2947--3038 Score: 152
Period size: 35 Copynumber: 2.7 Consensus size: 34
2937 ATGGCAATTG
*
2947 GAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAAACAAAAC-AAAAAAAGGAAAAA
2982 GAAAAAAAAAAAAACAAAACAAAAAAAGGAAAAA
1 GAAAAAAAAAAAAACAAAACAAAAAAAGGAAAAA
3016 G-AAAAAAAAAAAACAAAA-AAAAA
1 GAAAAAAAAAAAAACAAAACAAAAA
3039 GTGAAGATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 5 0.09
33 17 0.30
34 15 0.27
35 19 0.34
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
GAAAAAAAAAAAAACAAAACAAAAAAAGGAAAAA
Found at i:4994 original size:25 final size:24
Alignment explanation
Indices: 4956--5012 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
4946 TTTGGTAAGA
*
4956 TTGATTTTCATTTA-ACTTGATAAT
1 TTGATTTTCATTTATA-TTAATAAT
*
4980 TTGATTTTTATTTTATATTAATAAT
1 TTGATTTTCA-TTTATATTAATAAT
*
5005 TTGCTTTT
1 TTGATTTT
5013 ATTCATCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.32
25 18 0.64
26 1 0.04
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.61
Consensus pattern (24 bp):
TTGATTTTCATTTATATTAATAAT
Found at i:6480 original size:14 final size:14
Alignment explanation
Indices: 6420--6522 Score: 52
Period size: 15 Copynumber: 7.2 Consensus size: 14
6410 ACTTTTGCTA
*
6420 AAAGTACTTGT-AC
1 AAAGTACTTGTGTC
* *
6433 TAAAGCACTTGTATC
1 -AAAGTACTTGTGTC
*
6448 AAAAGTAC-TGATGTT
1 -AAAGTACTTG-TGTC
6463 AAAGTACTTGTGTC
1 AAAGTACTTGTGTC
* *
6477 AAAGGTACCTATG-C
1 AAA-GTACTTGTGTC
*
6491 TAAAGT-CTTGTGCC
1 -AAAGTACTTGTGTC
*
6505 AAAGGTACTTGTGCC
1 AAA-GTACTTGTGTC
6520 AAA
1 AAA
6523 AATACTGTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.10
14 31 0.44
15 32 0.46
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (14 bp):
AAAGTACTTGTGTC
Found at i:6501 original size:28 final size:30
Alignment explanation
Indices: 6432--6512 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
6422 AGTACTTGTA
* * *
6432 CTAAAGCACTTGTATCAAAAGTA-CTGATG
1 CTAAAGTACTTGTGTCAAAGGTACCTGATG
*
6461 TTAAAGTACTTGTGTCAAAGGTACCT-ATG
1 CTAAAGTACTTGTGTCAAAGGTACCTGATG
*
6490 CTAAAGT-CTTGTGCCAAAGGTAC
1 CTAAAGTACTTGTGTCAAAGGTAC
6513 TTGTGCCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 15 0.33
29 28 0.62
30 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (30 bp):
CTAAAGTACTTGTGTCAAAGGTACCTGATG
Found at i:6517 original size:15 final size:15
Alignment explanation
Indices: 6466--6538 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
6456 TGATGTTAAA
*
6466 GTACTTGTGTCAAAG
1 GTACTTGTGCCAAAG
* * *
6481 GTACCTATGCTAAA-
1 GTACTTGTGCCAAAG
6495 GT-CTTGTGCCAAAG
1 GTACTTGTGCCAAAG
*
6509 GTACTTGTGCCAAAA
1 GTACTTGTGCCAAAG
*
6524 ATACTGTGTGCCAAA
1 GTACT-TGTGCCAAA
6539 AAGTATATGT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 8 0.17
14 4 0.09
15 25 0.54
16 9 0.20
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (15 bp):
GTACTTGTGCCAAAG
Found at i:6535 original size:16 final size:15
Alignment explanation
Indices: 6497--6611 Score: 67
Period size: 15 Copynumber: 7.5 Consensus size: 15
6487 ATGCTAAAGT
**
6497 CTTGTGCCAAAGGTA
1 CTTGTGCCAAAAATA
6512 CTTGTGCCAAAAATA
1 CTTGTGCCAAAAATA
6527 CTGTGTGCCAAAAAGTA
1 CT-TGTGCCAAAAA-TA
*
6544 -TATGTGCC-AAAGTA
1 CT-TGTGCCAAAAATA
* *
6558 -TCTGTGCCGAAAGTAA
1 CT-TGTGCCAAAAAT-A
*
6574 C-TGTACCAAAAAATA
1 CTTGTGCC-AAAAATA
* * *
6589 CTTATACCAAAAGTA
1 CTTGTGCCAAAAATA
6604 CTTGTGCC
1 CTTGTGCC
6612 TAGGTACCTA
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
14 9 0.11
15 42 0.52
16 28 0.35
17 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (15 bp):
CTTGTGCCAAAAATA
Found at i:6572 original size:15 final size:14
Alignment explanation
Indices: 6538--6583 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
6528 TGTGTGCCAA
*
6538 AAAGTATATGTGCC
1 AAAGTATCTGTGCC
6552 AAAGTATCTGTGCC
1 AAAGTATCTGTGCC
* *
6566 GAAAGTAACTGTACC
1 -AAAGTATCTGTGCC
6581 AAA
1 AAA
6584 AAATACTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (14 bp):
AAAGTATCTGTGCC
Found at i:7230 original size:68 final size:67
Alignment explanation
Indices: 7137--7433 Score: 191
Period size: 66 Copynumber: 4.5 Consensus size: 67
7127 TGTATTAGGA
* ** * *
7137 AGAAT-ACAAAAGTAACGCACAGGACCACAACAGTCGACTTTTCCATTGGAAGAACTTGTATATG
1 AGAATGACAAAAGTGACGCATGGGACCACAA-AGTCGACTTCTCCATTGGAAGAACTTGTAAATG
*
7201 GGG
65 GAG
** * * ** *
7204 AGAATGACAAAAGTGGTGCATGGGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAAT-
1 AGAATGACAAAAGTGACGCATGGGACCACAAAG-TCGACTTCTCCATTGGAAGAACTTGTAAATG
7268 GAG
65 GAG
* *** * *
7271 AGAGTGACGGGAGTGACGCATGAGACCAC-AAGATCGACTTCTCCATTGGAAGAACTTGTACATG
1 AGAATGACAAAAGTGACGCATGGGACCACAAAG-TCGACTTCTCCATTGGAAGAACTTGTAAATG
*
7335 GAT
65 GAG
* * * * * *
7338 AGAGTGATAGAAGTG--GCATGAGACCGCAATGGTCGACTTCTCCATT--AAGATTACTTGTAAA
1 AGAATGACAAAAGTGACGCATGGGACCACAA-AGTCGACTTCTCCATTGGAAGA--ACTTGTAAA
7399 T-GA-
63 TGGAG
* * * *
7402 A-AAGTGACAGAAGTGGCACATGAGACCACAAA
1 AGAA-TGACAAAAGTGACGCATGGGACCACAAA
7434 CGGCCAACTT
Statistics
Matches: 182, Mismatches: 38, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
63 1 0.01
64 15 0.08
65 13 0.07
66 64 0.35
67 45 0.25
68 44 0.24
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (67 bp):
AGAATGACAAAAGTGACGCATGGGACCACAAAGTCGACTTCTCCATTGGAAGAACTTGTAAATGG
AG
Found at i:7328 original size:66 final size:68
Alignment explanation
Indices: 7170--7432 Score: 263
Period size: 66 Copynumber: 4.0 Consensus size: 68
7160 ACCACAACAG
* * * * * * *
7170 TCGACTTTTCCATTGGAAGAACTTGTATATGGGGAGAATGACAAAAGTGGTGCATGGGACCACAA
1 TCGACTTCTCCATTGGAAGAACTTGTAAATGGAGAGAGTGACAGAAGTGGCGCATGAGACCACAA
7235 TGA
66 TGA
* ** * * * *
7238 TCAACTTCTCCATTAAAAGTACTTGTAAAT-GAGAGAGTGACGGGAGTGACGCATGAGACCACAA
1 TCGACTTCTCCATTGGAAGAACTTGTAAATGGAGAGAGTGACAGAAGTGGCGCATGAGACCACAA
7302 -GA
66 TGA
* * * *
7304 TCGACTTCTCCATTGGAAGAACTTGTACATGGATAGAGTGATAGAAGT-G-GCATGAGACCGCAA
1 TCGACTTCTCCATTGGAAGAACTTGTAAATGGAGAGAGTGACAGAAGTGGCGCATGAGACCACAA
*
7367 TGG
66 TGA
* *
7370 TCGACTTCTCCATT--AAGATTACTTGTAAAT-GA-AAAGTGACAGAAGTGGCACATGAGACCAC
1 TCGACTTCTCCATTGGAAGA--ACTTGTAAATGGAGAGAGTGACAGAAGTGGCGCATGAGACCAC
7431 AA
64 AA
7433 ACGGCCAACT
Statistics
Matches: 158, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
64 16 0.10
65 16 0.10
66 63 0.40
67 39 0.25
68 24 0.15
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (68 bp):
TCGACTTCTCCATTGGAAGAACTTGTAAATGGAGAGAGTGACAGAAGTGGCGCATGAGACCACAA
TGA
Found at i:7398 original size:132 final size:134
Alignment explanation
Indices: 7159--7432 Score: 347
Period size: 132 Copynumber: 2.1 Consensus size: 134
7149 TAACGCACAG
* * *
7159 GACCACAACAGTCGACTTTTCCATTGGAAGAACTTGTATATGGGGAGAATGACAAAAGTGGTGCA
1 GACCACAACAGTCGACTTCTCCATTGGAAGAACTTGTACATGGAGAGAATGACAAAAGTGGTGCA
* * * * *
7224 TGGGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAGAGAGTGACGGGAGTGACG
66 TGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGA-AAAGTGACAGAAGTGACA
7289 CATGA
130 CATGA
* * * * *
7294 GACCACAAGA-TCGACTTCTCCATTGGAAGAACTTGTACATGGATAGAGTGATAGAAGT-G-GCA
1 GACCACAACAGTCGACTTCTCCATTGGAAGAACTTGTACATGGAGAGAATGACAAAAGTGGTGCA
* * * * * *
7356 TGAGACCGCAATGGTCGACTTCTCCATTAAGATTACTTGTAAATGAAAAGTGACAGAAGTGGCAC
66 TGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAAGTGACAGAAGTGACAC
7421 ATGA
131 ATGA
7425 GACCACAA
1 GACCACAA
7433 ACGGCCAACT
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
131 26 0.22
132 43 0.36
133 1 0.01
134 41 0.34
135 9 0.08
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (134 bp):
GACCACAACAGTCGACTTCTCCATTGGAAGAACTTGTACATGGAGAGAATGACAAAAGTGGTGCA
TGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAAGTGACAGAAGTGACAC
ATGA
Found at i:7460 original size:67 final size:65
Alignment explanation
Indices: 7203--7460 Score: 223
Period size: 66 Copynumber: 3.9 Consensus size: 65
7193 TGTATATGGG
* * * * *
7203 GAGAATGACAAAAGTGGTGCATGGGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAAT
1 GAGAGTGACAGAAGTGG-CCATGAGACCACAA-GGTCAACTTCTCCATTAAAAGTACTTGTAAAT
7268 GA
64 GA
* * * * * ** * *
7270 GAGAGTGACGGGAGTGACGCATGAGACCACAAGATCGACTTCTCCATTGGAAGAACTTGTACATG
1 GAGAGTGACAGAAGTGGC-CATGAGACCACAAGGTCAACTTCTCCATTAAAAGTACTTGTAAAT-
7335 GA
64 GA
* * * * * *
7337 TAGAGTGATAGAAGTGG-CATGAGACCGCAATGGTCGACTTCTCCATTAAGATTACTTGTAAATG
1 GAGAGTGACAGAAGTGGCCATGAGACCACAA-GGTCAACTTCTCCATTAAAAGTACTTGTAAATG
7401 A
65 A
* * *
7402 -AAAGTGACAGAAGTGGCACATGAGACCACAAACGGCCAACTTCTCTATTAAAAGTACTT
1 GAGAGTGACAGAAGTGGC-CATGAGACCAC-AA-GGTCAACTTCTCCATTAAAAGTACTT
7461 ACATTGGAAG
Statistics
Matches: 151, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
64 14 0.09
65 14 0.09
66 62 0.41
67 61 0.40
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (65 bp):
GAGAGTGACAGAAGTGGCCATGAGACCACAAGGTCAACTTCTCCATTAAAAGTACTTGTAAATGA
Done.