Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold445
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: 18590
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:489 original size:45 final size:45
Alignment explanation
Indices: 330--501 Score: 165
Period size: 45 Copynumber: 3.8 Consensus size: 45
320 TGTAACCCGC
* ** *
330 CCATAAGCGAACTCGGACTCAACTCAACGACCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCAT
* * *
375 CCAT-AGTGAACTC-GACTCAACTCAAACGAG-TCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTC-AACGAGTTCGGA--CATTGCAT
* ***
419 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
465 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
502 TGCCCAACAT
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
43 14 0.14
44 17 0.17
45 38 0.37
46 19 0.18
47 15 0.15
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
Found at i:4130 original size:40 final size:40
Alignment explanation
Indices: 4086--4264 Score: 286
Period size: 40 Copynumber: 4.5 Consensus size: 40
4076 TCTATATTCA
* *
4086 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATAC
1 GGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCC
4126 GGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCC
1 GGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCC
*
4166 GGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCC
1 GGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCC
* * * *
4206 GGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATACCC
1 GGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCC
*
4246 GGGTTAAGACCCGAAGGCA
1 GGGCTAAGACCCGAAGGCA
4265 ATTGAGCTTG
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 130 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (40 bp):
GGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCC
Found at i:12490 original size:40 final size:40
Alignment explanation
Indices: 12432--12614 Score: 303
Period size: 40 Copynumber: 4.6 Consensus size: 40
12422 ATTTGAATAC
12432 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
12472 ATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
12512 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
12552 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
12592 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
12615 ATTGAGCTTG
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 134 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:14220 original size:15 final size:15
Alignment explanation
Indices: 14187--14266 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
14177 CAAAGATAAC
*
14187 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
*
14201 AAGAAATCCAAAATA
1 AAGAAATCCAGAATA
* * *
14216 GAGAAACCCGGAATA
1 AAGAAATCCAGAATA
14231 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* * *
14246 AAGAGATCTAGGATA
1 AAGAAATCCAGAATA
14261 AAGAAA
1 AAGAAA
14267 CCCAAGATAC
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
14 8 0.15
15 44 0.85
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:14275 original size:15 final size:15
Alignment explanation
Indices: 14198--14275 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
14188 AGAAAACCGA
*
14198 ATAAAGAAATCCAAA
1 ATAAAGAAATCCAAG
* **
14213 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
14227 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* * *
14242 AATAAAGAGATCTAGG
1 -ATAAAGAAATCCAAG
*
14258 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
14273 ATA
1 ATA
14276 CGATACTATG
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
14 2 0.04
15 42 0.89
16 3 0.06
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:17315 original size:87 final size:86
Alignment explanation
Indices: 17171--17333 Score: 267
Period size: 87 Copynumber: 1.9 Consensus size: 86
17161 CGCCATAAGC
*
17171 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCTCCATAGTGAACTCGGACTCAACTCAACGA
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCTCCATAGTGAACTCGGACTCAACTCAACGA
17236 GTT-GGATGCCTAGTTACTCA
66 GTTCGGATGCCTAGTTACTCA
*
17256 GAACTCGGACT-AACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGC-TCCAT-AGTGAACTCGGACTCAACTCAA
17320 CGAGTTCGGATGCC
63 CGAGTTCGGATGCC
17334 CAATATCCCA
Statistics
Matches: 72, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
84 15 0.21
85 17 0.24
86 5 0.07
87 28 0.39
88 7 0.10
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (86 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCTCCATAGTGAACTCGGACTCAACTCAACGA
GTTCGGATGCCTAGTTACTCA
Found at i:17329 original size:46 final size:44
Alignment explanation
Indices: 17163--17328 Score: 184
Period size: 43 Copynumber: 3.8 Consensus size: 44
17153 CATGTAACCG
* * *
17163 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCT
17207 CCAT-AGTGAACTCGGACTCAACTCAACGAGTT-GG-A-T-GC-
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCT
* * *
17245 CTAGTTACTCAGAACTCGGACT-AACTCAACGAGTTCGGACATTCGCAT
1 CCA-TAAGT--GAACTCGGACTCAACTCAACGAGTTCGG-CATTCGC-T
17293 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
17329 ATGCCCAATA
Statistics
Matches: 102, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
38 2 0.02
39 3 0.03
40 3 0.03
41 13 0.13
42 15 0.15
43 26 0.25
44 5 0.05
45 12 0.12
46 18 0.18
47 3 0.03
48 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCT
Done.