Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_652 ID=scaffold_652-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: 4921
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1348 original size:100 final size:100
Alignment explanation
Indices: 1125--1414 Score: 397
Period size: 100 Copynumber: 2.9 Consensus size: 100
1115 CGCCATCGTG
* * ** * *
1125 GCTTTAATCTTTTCAACTGTAATGTCGGGGAAG-CATGATTCACTGTTGTGGCTTTAATCTACTT
1 GCTTTAATCTTTTTAACTGCAATGTTAGGGAGGCCA-GATTCACTGTTGTGGCTTTAATCT-GTT
* *
1189 CGCA--ACACTGCCTGGGAATGTAAGATTCACTGCTGTA
64 C-CACTGCACTGCCTGGG-AGGTAAGATTCACTGCTGTA
* * *
1226 GCTTTAATCTTTTTAACCGCAATGTTAGGGAGGCCAGATTCACCGTTGTGGCTTAAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTTAGGGAGGCCAGATTCACTGTTGTGGCTTTAATCTGTTCC
*
1291 ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
66 ACTGCACTGCCTGGGAGGTAAGATTCACTGCTGTA
*
1326 GCTTTAATCTTTTTAACTGCAATGTTAGGGAGGCAAGATTCACTGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTTAGGGAGGCCAGATTCACTGTTGTGGCTTTAATCTGTTCC
*
1391 ACTGCACTGCCTGTGAGGTAAGAT
66 ACTGCACTGCCTGGGAGGTAAGAT
1415 CTGTAATTCT
Statistics
Matches: 169, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
99 2 0.01
100 105 0.62
101 60 0.36
102 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTTAGGGAGGCCAGATTCACTGTTGTGGCTTTAATCTGTTCC
ACTGCACTGCCTGGGAGGTAAGATTCACTGCTGTA
Found at i:1395 original size:50 final size:49
Alignment explanation
Indices: 1122--1396 Score: 210
Period size: 50 Copynumber: 5.5 Consensus size: 49
1112 ATTCGCCATC
* * * *
1122 GTGGCTTTAATCTTTTCAACTGTAATGTCGGGGAAGCATGATTCACTGTT
1 GTGGCTTTAATCTTTTCAACTGCAATGT-TGGGAGGCAAGATTCACTGTT
* * ** * * * * *
1172 GTGGCTTTAATCTACTTC-GCAACACTGCCTGGGAATGTAAGATTCACTGCT
1 GTGGCTTTAATCT-TTTCAACTGCAATG-TTGGG-AGGCAAGATTCACTGTT
* * * * *
1223 GTAGCTTTAATCTTTTTAACCGCAATGTTAGGGAGGCCAGATTCACCGTT
1 GTGGCTTTAATCTTTTCAACTGCAATGTT-GGGAGGCAAGATTCACTGTT
* * * * * * * *
1273 GTGGCTTAAATCTGTTCCACTGCACTGCCTGGGAGGTAAGATTCGCTGCT
1 GTGGCTTTAATCTTTTCAACTGCAATG-TTGGGAGGCAAGATTCACTGTT
* *
1323 GTAGCTTTAATCTTTTTAACTGCAATGTTAGGGAGGCAAGATTCACTGTT
1 GTGGCTTTAATCTTTTCAACTGCAATGTT-GGGAGGCAAGATTCACTGTT
* *
1373 GTGGCTTTAATCTGTTCCACTGCA
1 GTGGCTTTAATCTTTTCAACTGCA
1397 CTGCCTGTGA
Statistics
Matches: 166, Mismatches: 52, Indels: 14
0.72 0.22 0.06
Matches are distributed among these distances:
49 1 0.01
50 128 0.77
51 37 0.22
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (49 bp):
GTGGCTTTAATCTTTTCAACTGCAATGTTGGGAGGCAAGATTCACTGTT
Found at i:1723 original size:142 final size:142
Alignment explanation
Indices: 1464--1887 Score: 715
Period size: 142 Copynumber: 3.0 Consensus size: 142
1454 ATAAAACCTA
*
1464 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTCTATTTTAATCCGCTCCACTGTAA
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* * *
1529 TCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTTCGCTGTAATCTTAGGGAGATAAAATTTCT
66 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAAATTTCT
*
1594 GGTTTTAATCTG
131 GGCTTTAATCTG
* *
1606 ATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAA
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* *
1671 TCTCAGGGAGATAGGATTACTAGCTTCCACCTGCTCCGCTGTAATCTCAGGGAGATAAAATTTCT
66 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAAATTTCT
*
1736 GGCTTCAATCTG
131 GGCTTTAATCTG
*
1748 ATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
** *
1813 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAATGAGAT-AAGTTTCT
66 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAAATTTCT
1877 GGCTTTAATCT
131 GGCTTTAATCT
1888 TCTCCACTGT
Statistics
Matches: 263, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
141 17 0.06
142 246 0.94
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (142 bp):
ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAAATTTCT
GGCTTTAATCTG
Found at i:2104 original size:44 final size:45
Alignment explanation
Indices: 1889--2133 Score: 153
Period size: 44 Copynumber: 5.7 Consensus size: 45
1879 CTTTAATCTT
* *
1889 CTCCACTGTAACATT-AGGGAGATAAGATTTG-CTTC-TCAGTCTG
1 CTCCACTGTAAC-TTCAGGGAGATAAGACTTGATTTCTTCAGTCTG
* * * *
1932 CCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTT-AGTCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGATTTCTTCAGTCTG
* * ** * *
1976 CTCCGCTGCAACTTCAGGGAGATAAGACCCGA-TGC--GA-TCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGATTTCTTCAGTCTG
* * * * *
2017 CTCCACTACT-GCTT-AAGGAGATAAGA-TCT-ATTGT-TTTAATCTG
1 CTCCACT-GTAACTTCAGGGAGATAAGACT-TGATT-TCTTCAGTCTG
*
2060 CTCCACTGTAACTTCAGGGAGATAAGA-TTGATTTCTTCTGTCTG
1 CTCCACTGTAACTTCAGGGAGATAAGACTTGATTTCTTCAGTCTG
* *
2104 CTCCACTACT-GCTT-AGGGAGATAAGACTTG
1 CTCCACT-GTAACTTCAGGGAGATAAGACTTG
2134 TAATTTCCAA
Statistics
Matches: 154, Mismatches: 31, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
39 1 0.01
40 12 0.08
41 13 0.08
42 5 0.03
43 54 0.35
44 67 0.44
45 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (45 bp):
CTCCACTGTAACTTCAGGGAGATAAGACTTGATTTCTTCAGTCTG
Found at i:2125 original size:87 final size:85
Alignment explanation
Indices: 1880--2134 Score: 238
Period size: 87 Copynumber: 3.0 Consensus size: 85
1870 AGTTTCTGGC
* * * * *
1880 TTTAATCTTCTCCACTGTAACATT-AGGGAGATAAGATTTGCTTC-TCAGTCTGCCCCACT-GTG
1 TTTAATCTGCTCCACTGTAAC-TTCAGGGAGATAAGACTTGATTCTTC-GTCTGCTCCACTACTG
* *
1942 ACTTCAGGGGGATAAGACTTGTTT
64 -CTT-AGGGAGATAAGACTTGTGT
* * * ** *
1966 TCTTAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACCCGA---TGCGATCTGCTCCACTACTG
1 T-TTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGATTCTTCG-TCTGCTCCACTACTG
*
2028 CTTAAGGAGATAAGATCTAT-TGT
64 CTTAGGGAGATAAGA-CT-TGTGT
2051 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TTGATTTCTTCTGTCTGCTCCACTACTG
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGA-TTCTTC-GTCTGCTCCACTACTG
2115 CTTAGGGAGATAAGACTTGT
64 CTTAGGGAGATAAGACTTGT
2135 AATTTCCAAC
Statistics
Matches: 135, Mismatches: 21, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
83 2 0.01
84 43 0.32
85 20 0.15
86 9 0.07
87 60 0.44
88 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (85 bp):
TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGATTCTTCGTCTGCTCCACTACTGCT
TAGGGAGATAAGACTTGTGT
Found at i:4799 original size:2 final size:2
Alignment explanation
Indices: 4792--4816 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4782 TTAAAATTAA
4792 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4817 CATTAGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.