Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1052 ID=scaffold_1052-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, 747
Length: 1245
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Found at i:244 original size:132 final size:132
Alignment explanation
Indices: 7--804 Score: 1141
Period size: 132 Copynumber: 6.1 Consensus size: 132
1 TCTTTT
* *
7 ATCTGCTCCACTACCGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAG
*
72 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTT
66 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
*
137 TG
131 CG
* * *
139 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAG
* * * *
204 GG-AGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCATAGAGAGGTAAAATCTGTCATCT
66 GGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCT
268 TCG
130 TCG
* * *
271 ATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTAACCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAG
*
336 GG-AGATAGAATTAC-GGCTTCAATGTACTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATC
66 GGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATCTGCCATC
398 TTCG
129 TTCG
* * * * * *
402 ATCTGCTTCGCTGTCTA-TGC--AGGAAGGTAAGATCTAAAATCTTCAATCCATTCCACTGCTGT
1 ATCTGC-TC-C--ACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGA
*
464 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCTGCCA
62 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
* *
529 TTTTTG
127 TCTTCG
* *
535 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAG
600 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTA-AGGGAGGTAAAATCTGCCATCT
66 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC-ACAGGGAGGTAAAATCTGCCATCT
664 TCG
130 TCG
* * * **
667 ATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAACCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAG
*
732 GG-AGATAGAATTAC-GGCTTCAATGTACTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATC
66 GGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATCTGCCATC
794 TTCG
129 TTCG
798 ATCTGCT
1 ATCTGCT
805 TCGCTGTCTA
Statistics
Matches: 601, Mismatches: 49, Indels: 33
0.88 0.07 0.05
Matches are distributed among these distances:
129 3 0.00
130 6 0.01
131 110 0.18
132 419 0.70
133 56 0.09
134 4 0.01
135 3 0.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (132 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAG
GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
CG
Found at i:325 original size:44 final size:44
Alignment explanation
Indices: 139--326 Score: 116
Period size: 44 Copynumber: 4.3 Consensus size: 44
129 GCCATTTTTG
* * * * *
139 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCA
1 ATCTACTCCACTAATGCCTAGGGAGATAAAATCTGAAATCTTCA
* * ** * *
183 ATCTATTCCGCTGCTGCCCAGGGAGATAAAATTACTG---GCTTCA
1 ATCTACTCCACTAATGCCTAGGGAGATAAAA-T-CTGAAATCTTCA
* * * ** *
226 ATGTACTCCACTGTAA--CCATAGAGAGGTAAAATCTGTCATCTTCG
1 ATCTACTCCAC--TAATGCC-TAGGGAGATAAAATCTGAAATCTTCA
* *
271 ATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCA
1 ATCTACTCCACTAATGCCTAGGGAGATAAAATCTGAAATCTTCA
*
315 ATCTATTCCACT
1 ATCTACTCCACT
327 GCTAACCAGG
Statistics
Matches: 105, Mismatches: 29, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
42 3 0.03
43 19 0.18
44 63 0.60
45 17 0.16
46 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
ATCTACTCCACTAATGCCTAGGGAGATAAAATCTGAAATCTTCA
Found at i:676 original size:45 final size:43
Alignment explanation
Indices: 617--801 Score: 124
Period size: 44 Copynumber: 4.2 Consensus size: 43
607 GAATTACTGG
* *
617 CTTCAATGTACTCCACTGTAACCTAAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAACC--AGGGAGATAAAATCTGCCAT
* * * * **
662 CTTCGATCTACTCCACTACT-GCCTAGGGAGATAAGATCTGTAAT
1 CTTCAATCTACTCCACT-GTAACC-AGGGAGATAAAATCTGCCAT
* * * * **
706 CTTCAATCTATTCCACTGCCAACCAGGGAGATAGAAT-T-ACGG
1 CTTCAATCTACTCCACTG-TAACCAGGGAGATAAAATCTGCCAT
* * *
748 CTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGTAACCA-G-GGAGATAAAATCTGCCAT
*
793 CTTCGATCT
1 CTTCAATCT
802 GCTTCGCTGT
Statistics
Matches: 102, Mismatches: 31, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
41 5 0.05
42 17 0.17
43 10 0.10
44 42 0.41
45 27 0.26
46 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
CTTCAATCTACTCCACTGTAACCAGGGAGATAAAATCTGCCAT
Found at i:765 original size:396 final size:396
Alignment explanation
Indices: 33--834 Score: 1455
Period size: 396 Copynumber: 2.0 Consensus size: 396
23 CTTAGGGAGA
* *
33 TAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
1 TAAGATCTAAAATCTTCAATCCATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
*
98 ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTGATCTGCTCCACTACTGCTTAGGGA
66 ACTCCACTGCAACCACAGGGAGGTAAAATCTGCCATTTTTGATCTGCTCCACTACTGCTTAGGGA
*
163 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAGATAAAATTACTGGCTTCAAT
131 GACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAAATTACTGGCTTCAAT
* *
228 GTACTCCACTGTAACCATAGAGAGGTAAAATCTGTCATCTTCGATCTGCTCCACTAATGCCTAGG
196 GTACTCCACTGTAACCATAGAGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGG
*
293 GAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTACGGCTTCAA
261 GAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAA
358 TGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGTCTATGCA
326 TGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGTCTATGCA
423 GGAAGG
391 GGAAGG
*
429 TAAGATCTAAAATCTTCAATCCATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGT
1 TAAGATCTAAAATCTTCAATCCATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
494 ACTCCACTGCAACCACAGGGAGGTAAAATCTGCCATTTTTGATCTGCTCCACTACTGCTTAGGGA
66 ACTCCACTGCAACCACAGGGAGGTAAAATCTGCCATTTTTGATCTGCTCCACTACTGCTTAGGGA
* *
559 GACAAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGA-AGTAGAATTACTGGCTTCAA
131 GACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGA-TAAAATTACTGGCTTCAA
* *
623 TGTACTCCACTGTAACC-TAAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTGCCTA
195 TGTACTCCACTGTAACCAT-AGAGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTA
*
687 GGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTC
259 GGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTC
752 AATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGTCTATG
324 AATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGTCTATG
817 CAGGAAGG
389 CAGGAAGG
825 TAAGATCTAA
1 TAAGATCTAA
835 CATTTTCACT
Statistics
Matches: 391, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
395 2 0.01
396 389 0.99
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (396 bp):
TAAGATCTAAAATCTTCAATCCATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
ACTCCACTGCAACCACAGGGAGGTAAAATCTGCCATTTTTGATCTGCTCCACTACTGCTTAGGGA
GACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAAATTACTGGCTTCAAT
GTACTCCACTGTAACCATAGAGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGG
GAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAA
TGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGTCTATGCA
GGAAGG
Done.