Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1823
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: 39353
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:18339 original size:24 final size:24
Alignment explanation
Indices: 18315--18361 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
18305 AAACTACTTC
18315 TAAAGAAAACTCAAGAGAGAATTCT
1 TAAAGAAAACTCAA-AGAGAATTCT
**
18340 TGGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAGAGAATT
18362 TCTACTCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAGAGAATTCT
Found at i:26202 original size:15 final size:16
Alignment explanation
Indices: 26163--26203 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
26153 AACAACACTC
26163 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
26179 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
26193 CTTTCTTTTTC
1 CTTTCTTTTTC
26204 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:26398 original size:17 final size:15
Alignment explanation
Indices: 26361--26399 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
26351 TATCTCCCAC
26361 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
26377 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
26394 TCATTT
1 TCATTT
26400 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:27331 original size:26 final size:27
Alignment explanation
Indices: 27302--27363 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
27292 ATCACTCTTT
* *
27302 TTTTTTTTCAATTTC-GATTTTTTTTC
1 TTTTTTTTCAATTCCAAATTTTTTTTC
*
27328 TTTTTTTTTAATTCCAAATTTTTTTTC
1 TTTTTTTTCAATTCCAAATTTTTTTTC
27355 TTCTTTTTT
1 TT-TTTTTT
27364 TCTTCAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 13 0.42
27 12 0.39
28 6 0.19
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTTTTTTCAATTCCAAATTTTTTTTC
Found at i:27348 original size:27 final size:27
Alignment explanation
Indices: 27301--27365 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
27291 AATCACTCTT
* *
27301 TTTTTTTTTCAATTTCGATTTTTTTTC
1 TTTTTTTTTCAATTCCAATTTTTTTTC
27328 TTTTTTTTT-AATTCCAAATTTTTTTTC
1 TTTTTTTTTCAATTCC-AATTTTTTTTC
27355 TTCTTTTTTTC
1 TT-TTTTTTTC
27366 TTCAATACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 5 0.15
27 21 0.64
28 7 0.21
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTTTTTTTCAATTCCAATTTTTTTTC
Found at i:27427 original size:13 final size:12
Alignment explanation
Indices: 27410--27467 Score: 107
Period size: 12 Copynumber: 4.8 Consensus size: 12
27400 AATACAAACT
27410 TTTTTTTTTGAA
1 TTTTTTTTTGAA
27422 TTTTTTTTTGAAA
1 TTTTTTTTTG-AA
27435 TTTTTTTTTGAA
1 TTTTTTTTTGAA
27447 TTTTTTTTTGAA
1 TTTTTTTTTGAA
27459 TTTTTTTTT
1 TTTTTTTTT
27468 ACAATACCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
12 33 0.73
13 12 0.27
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:27438 original size:25 final size:24
Alignment explanation
Indices: 27410--27467 Score: 107
Period size: 25 Copynumber: 2.4 Consensus size: 24
27400 AATACAAACT
27410 TTTTTTTTTGAATTTTTTTTTGAAA
1 TTTTTTTTTGAATTTTTTTTTG-AA
27435 TTTTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTTTGAATTTTTTTTTGAA
27459 TTTTTTTTT
1 TTTTTTTTT
27468 ACAATACCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 11 0.33
25 22 0.67
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTTTTTTGAATTTTTTTTTGAA
Found at i:37460 original size:20 final size:20
Alignment explanation
Indices: 37437--37501 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
37427 AAGCTCAAAC
37437 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTAAGCTAAATT
37457 GAGCTCAAACG--AGCTAAATT
1 GAGCT-AAA-GTAAGCTAAATT
* * * *
37477 AAGCTTATGTAAGCTAAATC
1 GAGCTAAAGTAAGCTAAATT
37497 GAGCT
1 GAGCT
37502 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGCTAAAGTAAGCTAAATT
Found at i:37500 original size:30 final size:29
Alignment explanation
Indices: 37427--37501 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
37417 AACTTAAGCC
37427 AAGCTCAAACGAGCTAAAGTAAGCTAAATT
1 AAGCT-AAACGAGCTAAAGTAAGCTAAATT
* * *
37457 GAGCTCAAACGAGCTAAATTAAGCT-TATGT
1 AAGCT-AAACGAGCTAAAGTAAGCTAAAT-T
37487 AAGCTAAATCGAGCT
1 AAGCTAAA-CGAGCT
37502 GGGAAAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (29 bp):
AAGCTAAACGAGCTAAAGTAAGCTAAATT
Done.