Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_600 ID=scaffold_600-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: 5347
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Found at i:25 original size:19 final size:19
Alignment explanation
Indices: 1--48 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
*
1 ATTGCATATCATATCTAGG
1 ATTGCATATCATATCTAAG
20 ATTGCATATCATATCTAAG
1 ATTGCATATCATATCTAAG
39 ATTGCATATC
1 ATTGCATATC
49 CTCAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (19 bp):
ATTGCATATCATATCTAAG
Found at i:517 original size:132 final size:131
Alignment explanation
Indices: 277--818 Score: 809
Period size: 132 Copynumber: 4.1 Consensus size: 131
267 CTGCAACTGC
* * * *
277 AGGGAGATAAGA-CTTACAATCTTCAACCTATTCCACTGCTGACCAGGG-AGATAGGATTACTGG
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTG-TTACCAGGGAAG-TAGAATTACTGG
* * *
340 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTTGATCTACTCCACTACT
63 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACT
405 GCTT
128 GCTT
**
409 AGGGAGATAAGATCTGAAATCTGAAATCTATTCCACTGTTACCTAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTACC-AGGGAAGTAGAATTACTGGCT
* * * * *
474 CCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTTC
65 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGC
539 TT
130 TT
*
541 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT-ACCAGGGAAGTAGAATTACTGGCT
* *
606 TCAATGTACTCCACTATAACCATAGGGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGC
65 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGC
671 TT
130 TT
* *
673 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT-ACCAGGGAAGTAGAATTACTGGCT
* * *
738 TCAATGTACTCCACTATAACCATAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTGC
65 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGC
803 TT
130 TT
*
805 ATGGAGATAAGATC
1 AGGGAGATAAGATC
819 GGTTTTAACC
Statistics
Matches: 378, Mismatches: 28, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
131 4 0.01
132 367 0.97
133 7 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (131 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTACCAGGGAAGTAGAATTACTGGCTT
CAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCT
T
Found at i:576 original size:44 final size:44
Alignment explanation
Indices: 515--709 Score: 109
Period size: 44 Copynumber: 4.4 Consensus size: 44
505 AAAATCCGCC
* *
515 ATCTTCGATCTGCTCCACTACTTCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTACTTCTTAGGGAGATAAGATCTGAA
* * **
559 ATCTTCAATCTATTCCACT-GTTGCCCAGGGA-AGT-AGAATTACTG--
1 ATCTTCAATCTACTCCACTACTT-CTTAGGGAGA-TAAG-A-T-CTGAA
* * * * * * *
603 -GCTTCAATGTACTCCACTA-TAACCATAGGGAGGTAAAATCT-ACC
1 ATCTTCAATCTACTCCACTACT--TCTTAGGGAGATAAGATCTGA-A
* * *
647 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTACTTCTTAGGGAGATAAGATCTGAA
*
691 ATCTTCAATCTATTCCACT
1 ATCTTCAATCTACTCCACT
710 GTTGTCCAGG
Statistics
Matches: 109, Mismatches: 26, Indels: 32
0.65 0.16 0.19
Matches are distributed among these distances:
42 2 0.02
43 22 0.20
44 63 0.58
45 18 0.17
46 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTACTTCTTAGGGAGATAAGATCTGAA
Found at i:879 original size:44 final size:44
Alignment explanation
Indices: 831--1117 Score: 204
Period size: 44 Copynumber: 6.7 Consensus size: 44
821 TTTTAACCCA
*
831 CTCCACTGCAACTTCAGGGAGATATGATTATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
* * * * ** *
875 CTCCACTGCAACTTTAGAGAGATAAGA-T-TCGCCATCTTGGGTATG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGC-T-TT-AATCTG
* ** *
920 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTAC-TTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGA-TTATTGGCTTTAATCTG
* ** * * *
964 CTCCACTGCAACTTCAAGGAGATAAGACCA---GATGTGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
* * * *
1005 CT-CTCTGCAACTTCAGAGAGATAAGATCA---ACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
* *
1045 CTCCACAGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
1089 CTCCACTGCAACTGT-AGGGAGATAAGATT
1 CTCCACTGCAACT-TCAGGGAGATAAGATT
1118 TGCCATCTTC
Statistics
Matches: 188, Mismatches: 39, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
40 32 0.17
41 29 0.15
42 3 0.02
43 2 0.01
44 89 0.47
45 30 0.16
47 1 0.01
48 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
Found at i:1044 original size:40 final size:41
Alignment explanation
Indices: 960--1068 Score: 125
Period size: 40 Copynumber: 2.7 Consensus size: 41
950 GTTTACTTAG
*
960 TCTGCTCCACTGCAACTTCA-AGGAGATAAGACCAGATGTGA
1 TCTGCTCCACTGCAACTTCAGA-GAGATAAGACCAGATGTAA
* * *
1001 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCA-ACTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGA-TGTAA
* *
1041 TCTGCTCCACAGCAACTTCAGGGAGATA
1 TCTGCTCCACTGCAACTTCAGAGAGATA
1069 GGATTATTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.02
40 32 0.55
41 25 0.43
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGATGTAA
Done.