Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_258 ID=scaffold_258-JGI_221_v2.0
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: 8985
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:2228 original size:87 final size:87
Alignment explanation
Indices: 2065--2599 Score: 797
Period size: 87 Copynumber: 6.2 Consensus size: 87
2055 ACTAGTGCTT
*** * * * *
2065 AGGAAGGCAAGATCTGCTATCTTTAGTTAGCTCTATTACAACCGATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTCATTTT
* * *
2130 CAATCTACTTCGTTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* * *
2152 AGAAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCATTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTCATTTT
2217 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* *
2239 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAATGCTT-AGTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTCA-TTT
2303 T-GATCTGCTTCGCTGTTAATGC
65 TCGATCTGCTTCGCTGTTAATGC
* * *
2325 AGGAAGGCAAGATCTACTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGATTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTCATTTT
* *
2390 TGACCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* * *
2412 AGGAAGGCAAGATCTACT-TCTTTAACCAGCTCCACTGCAATCGATGGAGGCAAGGCTTCATTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTCATTTT
2476 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* * *
2498 AGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAAGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTCATTTT
*
2563 CGATCTACTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
2585 AGGAAGGCAAGATCT
1 AGGAAGGCAAGATCT
2600 ACTTCTTCAC
Statistics
Matches: 407, Mismatches: 37, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
86 159 0.39
87 248 0.61
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTCATTTT
CGATCTGCTTCGCTGTTAATGC
Found at i:2351 original size:173 final size:174
Alignment explanation
Indices: 2065--2599 Score: 815
Period size: 173 Copynumber: 3.1 Consensus size: 174
2055 ACTAGTGCTT
*** * * * *
2065 AGGAAGGCAAGATCTGCTATCTTTAGTTAGCTCTATTACAACCGATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTAGTTTT
* * * * *
2130 CAATCTACTTCGTTGTTAATGCAGAAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACC
66 CGATCTGCTTCGCTGTTAATGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCAATGCAACC
*
2195 GATGGAGGCAAGGCTTCATTTTCGATCTGCTTCGCTGTTAATGC
131 GATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGC
* *
2239 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAATGCTTAGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTAGTTTT
* *
2304 -GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTATCTTTAACCAGCTCCAATGCAACC
66 CGATCTGCTTCGCTGTTAATGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCAATGCAACC
* * *
2368 GATGGAGGCAAGGATTCGTTTTTGACCTGCTTCGCTGTTAATGC
131 GATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGC
* * *
2412 AGGAAGGCAAGATCTACT-TCTTTAACCAGCTCCACTGCAATCGATGGAGGCAAGGCTTCA-TTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTT-AGTTT
2475 TCGATCTGCTTCGCTGTTAATGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCAATGCAAC
65 TCGATCTGCTTCGCTGTTAATGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCAATGCAAC
* *
2540 CGATGGAGGCAAAGCTTCGTTTTCGATCTACTTCGCTGTTAATGC
130 CGATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGC
2585 AGGAAGGCAAGATCT
1 AGGAAGGCAAGATCT
2600 ACTTCTTCAC
Statistics
Matches: 327, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
172 41 0.13
173 230 0.70
174 56 0.17
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (174 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTAGTTTT
CGATCTGCTTCGCTGTTAATGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCAATGCAACC
GATGGAGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGC
Found at i:2422 original size:43 final size:42
Alignment explanation
Indices: 2373--2504 Score: 101
Period size: 43 Copynumber: 3.1 Consensus size: 42
2363 CAACCGATGG
2373 AGGCAAGGATTCGTTTTTGACCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGATTC-TTTTTGACCTGCTTCGCTGTTAATGCAGGA
* * * * *
2416 AGGCAA-GATCTACTTCTTTAACCAGCTCCACTG-CAAT-CGATGG-
1 AGGCAAGGAT-T-CTT-TTTGACCTGCTTCGCTGTTAATGC-A-GGA
* * *
2459 AGGCAAGGCTTCATTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGATTC-TTTTTGACCTGCTTCGCTGTTAATGCAGGA
2502 AGG
1 AGG
2505 TAAGATCTGC
Statistics
Matches: 66, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
42 18 0.27
43 29 0.44
44 19 0.29
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (42 bp):
AGGCAAGGATTCTTTTTGACCTGCTTCGCTGTTAATGCAGGA
Found at i:4279 original size:39 final size:39
Alignment explanation
Indices: 4235--4355 Score: 118
Period size: 39 Copynumber: 3.3 Consensus size: 39
4225 TTCATTCTTC
4235 TTTCTTTTTCTCATTTTCATTTTGATCTTGATTTTGATT
1 TTTCTTTTTCTCATTTTCATTTTGATCTTGATTTTGATT
* *
4274 TTTCTTCTTTGT--TGTT--TTTT--T-TT-ATTTTGATT
1 TTTCTT-TTTCTCATTTTCATTTTGATCTTGATTTTGATT
*
4306 TTTGATTTTT-TCATTTTCATTTTGA-CTTTGATTTTGATT
1 TTT-CTTTTTCTCATTTTCATTTTGATC-TTGATTTTGATT
4345 TTTCTTTTTCT
1 TTTCTTTTTCT
4356 TCCCTTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
31 1 0.02
32 15 0.23
33 7 0.11
34 1 0.02
35 4 0.06
36 4 0.06
38 10 0.15
39 19 0.29
40 4 0.06
ACGTcount: A:0.11, C:0.10, G:0.08, T:0.71
Consensus pattern (39 bp):
TTTCTTTTTCTCATTTTCATTTTGATCTTGATTTTGATT
Done.