Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_304 ID=scaffold_304-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: 8490
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:118 original size:44 final size:45
Alignment explanation
Indices: 47--336 Score: 197
Period size: 44 Copynumber: 6.6 Consensus size: 45
37 ACTTTATGCG
* ** * *
47 ATCTGCTCTACTGGAACTTCAGAGAGATAAGATCT-ATTACTTTA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATCTGATTACTTCA
** * * **
91 ATCCACTCCACTACAACTTTAGGGAGATAGGAT-T-ATCGGCTTCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATCTGAT-TACTTCA
** * * * *
135 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTGCTT-CTTCG
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATCTGATTACTTCA
* * *
179 ATCTGCCCCACTACAACTTCAGGGGGATAAG-TCCTGCTTAC-TCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGAT-CTGATTACTTCA
* * * * * *
223 GTCTGCTCCACTGCAACCTCAGGGAGAAAAGACCTG---A-TGCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATCTGATTACTTCA
** * * * *
264 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCT-ATTACTTTA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATCTGATTACTTCA
308 ATCTGCTCCACTACAACTTCAGGGAGATA
1 ATCTGCTCCACTACAACTTCAGGGAGATA
337 GGATTATCGG
Statistics
Matches: 184, Mismatches: 51, Indels: 22
0.72 0.20 0.09
Matches are distributed among these distances:
41 30 0.16
43 5 0.03
44 146 0.79
45 2 0.01
46 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (45 bp):
ATCTGCTCCACTACAACTTCAGGGAGATAAGATCTGATTACTTCA
Found at i:696 original size:128 final size:128
Alignment explanation
Indices: 326--731 Score: 584
Period size: 128 Copynumber: 3.1 Consensus size: 128
316 CACTACAACT
* * * *
326 TCAGGGAGATAGGA-TTATCGGCTTCAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCT
1 TCAGGGACATAGGACTTGT-GGCTTCAATCTGCTTTCTTACACTTGAAGATAAGATTCTCCGTCT
390 TCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
65 TCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* * * *
454 TCAGGGACATAGGACTTGTGGCTTAAATCTG-TTTCCCTACTCCTGGGGAAGATAAGATTCGT-C
1 TCAGGGACATAGGACTTGTGGCTTCAATCTGCTTT-CTTAC-ACT--TGAAGATAAGATTC-TCC
* * * *
517 GTCTTCGATCTGCTCTGCTACTGCCTAGGGAGACAAGATCTGCAATCTCCAACCTATTCCACTAC
61 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGC
582 TGG
126 TGG
* *
585 TCAGGGACATAGGACTTGTGGCTTCAATCTGCTTTCTTACACTTGAAGATAAGATTTTCCATCTT
1 TCAGGGACATAGGACTTGTGGCTTCAATCTGCTTTCTTACACTTGAAGATAAGATTCTCCGTCTT
650 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* * *
713 CCCGGGATATAGGACTTGT
1 TCAGGGACATAGGACTTGT
732 AATCTTCGAT
Statistics
Matches: 245, Mismatches: 25, Indels: 16
0.86 0.09 0.06
Matches are distributed among these distances:
127 3 0.01
128 120 0.49
129 5 0.02
130 2 0.01
131 112 0.46
132 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (128 bp):
TCAGGGACATAGGACTTGTGGCTTCAATCTGCTTTCTTACACTTGAAGATAAGATTCTCCGTCTT
CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
Found at i:1057 original size:86 final size:87
Alignment explanation
Indices: 736--1090 Score: 604
Period size: 87 Copynumber: 4.1 Consensus size: 87
726 ACTTGTAATC
* * * *
736 TTCGATCTGCTTCACTGTCGACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
801 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
** * **
823 TTCGATCTGCTTAACTGTCAATACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTATAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
888 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
910 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
975 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
997 TTTGAT-TGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1061 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
1083 TTCGATCT
1 TTCGATCT
1091 TCACTAATCT
Statistics
Matches: 252, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
86 84 0.33
87 168 0.67
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:2307 original size:6 final size:6
Alignment explanation
Indices: 2298--2339 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
2288 CGTTTTTACT
2298 TTTTCA TTTTCA TTTTCA TTTTTCA TTTTCA TTCTTCA TTTT
1 TTTTCA TTTTCA TTTTCA -TTTTCA TTTTCA TT-TTCA TTTT
2340 TCACCCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 22 0.65
7 12 0.35
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCA
Found at i:2313 original size:13 final size:13
Alignment explanation
Indices: 2298--2339 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2288 CGTTTTTACT
2298 TTTTCA-TTTTCA
1 TTTTCATTTTTCA
2310 TTTTCATTTTTCA
1 TTTTCATTTTTCA
*
2323 TTTTCATTCTTCA
1 TTTTCATTTTTCA
2336 TTTT
1 TTTT
2340 TCACCCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 6 0.21
13 22 0.79
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:3323 original size:12 final size:12
Alignment explanation
Indices: 3283--3316 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3273 TTCCTTTTCT
*
3283 TTTTTGTTTTTG
1 TTTTTGATTTTG
3295 TTTTTGATTTTG
1 TTTTTGATTTTG
*
3307 ATTTTGATTT
1 TTTTTGATTT
3317 ATTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (12 bp):
TTTTTGATTTTG
Done.