Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_669 ID=scaffold_669-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: 4762
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:195 original size:27 final size:26
Alignment explanation
Indices: 139--236 Score: 65
Period size: 27 Copynumber: 3.6 Consensus size: 26
129 AAAAGGGTAC
* *
139 AAAATATATACATGTACATATAATAA
1 AAAATATATACATATACATAGAATAA
*
165 AAAATTATATACATATATATAGATTATAA
1 AAAA-TATATACATATACATAGA--ATAA
* * *
194 AAAAGATAATTACATATATATA-AACAA
1 AAAATAT-A-TACATATACATAGAATAA
*
221 ATAATA-ATTACATATA
1 AAAATATA-TACATATA
237 TTAAAATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
25 10 0.17
26 4 0.07
27 22 0.37
28 2 0.03
29 10 0.17
30 12 0.20
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (26 bp):
AAAATATATACATATACATAGAATAA
Found at i:213 original size:21 final size:23
Alignment explanation
Indices: 189--252 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
179 ATATATAGAT
*
189 TATAAAAAA-GATAATTACATATA
1 TATAAAAAATAATAATTACA-ATA
212 TATAAACAAATAATAATTAC-ATA
1 TATAAA-AAATAATAATTACAATA
* *
235 TATTAAAATTAATTAATT
1 TATAAAAAATAA-TAATT
253 TAGAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 5 0.14
23 19 0.54
24 3 0.09
25 8 0.23
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (23 bp):
TATAAAAAATAATAATTACAATA
Found at i:216 original size:23 final size:24
Alignment explanation
Indices: 139--242 Score: 79
Period size: 25 Copynumber: 4.1 Consensus size: 24
129 AAAAGGGTAC
139 AAAATATATACATGTACATATA-ATAA
1 AAAATA-ATA-AT-TACATATATATAA
* *
165 AAAATTATATACATATATATAGATTATAA
1 AAAA-TA-ATA-AT-TACATATA-TATAA
*
194 AAAA-GATAATTACATATATATAA
1 AAAATAATAATTACATATATATAA
217 ACAAATAATAATTACATATAT-TAA
1 A-AAATAATAATTACATATATATAA
241 AA
1 AA
243 TTAATTAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
23 7 0.11
24 13 0.20
25 16 0.24
26 7 0.11
27 15 0.23
29 8 0.12
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.33
Consensus pattern (24 bp):
AAAATAATAATTACATATATATAA
Found at i:360 original size:33 final size:32
Alignment explanation
Indices: 323--397 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 32
313 CATATTTATC
323 AAAGTAAAAAATATATAAAA-GTATATGCATATA
1 AAAGTAAAAAATA-A-AAAATGTATATGCATATA
** *
356 AAAGTTAGGAAATAAAAAATGTATATGTATATA
1 AAAG-TAAAAAATAAAAAATGTATATGCATATA
389 AAATGTAAA
1 AAA-GTAAA
398 TGTATATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
32 4 0.12
33 22 0.65
34 8 0.24
ACGTcount: A:0.59, C:0.01, G:0.12, T:0.28
Consensus pattern (32 bp):
AAAGTAAAAAATAAAAAATGTATATGCATATA
Found at i:554 original size:3 final size:3
Alignment explanation
Indices: 546--587 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
536 GTATATATAG
* *
546 TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
588 GTTAATAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:901 original size:22 final size:21
Alignment explanation
Indices: 876--944 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
866 TACAAATTAA
876 ATCTCTAAGATTAGAAAATCAT
1 ATCTCTAAGATT-GAAAATCAT
* *
898 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTGAAAATCAT
*
920 A--TCTAAGATTGCATATATCAT
1 ATCTCTAAGATTG-A-AAATCAT
941 ATCT
1 ATCT
945 AAGATCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 11 0.28
23 10 0.26
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
ATCTCTAAGATTGAAAATCAT
Found at i:909 original size:23 final size:22
Alignment explanation
Indices: 879--923 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
869 AAATTAAATC
879 TCTAAGATTAGAAAATCATATCT
1 TCTAAGATT-GAAAATCATATCT
* *
902 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGAAAATCATATCT
924 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TCTAAGATTGAAAATCATATCT
Found at i:926 original size:19 final size:20
Alignment explanation
Indices: 902--949 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
892 AATCATATCT
902 TCTAAGATTGC-ATATCATA
1 TCTAAGATTGCAATATCATA
921 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
942 TCTAAGAT
1 TCTAAGAT
950 CATATCTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.41
21 16 0.59
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:969 original size:14 final size:12
Alignment explanation
Indices: 936--961 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
926 GATTGCATAT
936 ATCATATCTAAG
1 ATCATATCTAAG
948 ATCATATCTAAG
1 ATCATATCTAAG
960 AT
1 AT
962 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:1791 original size:44 final size:44
Alignment explanation
Indices: 1742--1951 Score: 262
Period size: 44 Copynumber: 4.8 Consensus size: 44
1732 ATCTGCTATT
* * *
1742 TTCAACCTACTCCACTGCTG-CTGAGGGAGATAGGATTCATAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
** *
1786 TTCAACCTATTCCACTGCTGACCAGGGAGATA-GAACCTACAACC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATC
* * * * *
1830 TTCAATCTATTCCACTGCTGCCCAGAGAGATAGAATTCTCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
1874 TTCAACCCATTCCACTACTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
1918 TTTAACCTATTCCACTGCTGACCAGGGAGATAGG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGG
1952 GCTGGGGTCA
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.02
44 133 0.96
45 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:2174 original size:44 final size:44
Alignment explanation
Indices: 2120--2713 Score: 506
Period size: 44 Copynumber: 13.5 Consensus size: 44
2110 GTCAATACAT
* *
2120 GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAATATAG
* * * *
2164 GAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAA
1 GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAATATAG
* * * * * *
2207 GAAGACAGGACCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAATATAG
* * * * *
2251 GAAGACAGGATATGCTTTCTTCGATCTACTTCGCCACTAGTATGG
1 GAAGACAAGATCTGC-TTCTTCGATCTACTTCGCCACCAATATAG
* * *
2296 GAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAG
1 GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAATATAG
** * * * *
2340 GAAGACAAGATCTGCTATCTTTTATCTACTTC-ACGCCAATACAT
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAATATAG
* * *
2384 GAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAG
1 GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAATATAG
* * * * * *
2428 GAAGACAGGATCTTCTATCTTCGATCTACTTC-ACGCCAATACAT
1 GAAGACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAATATAG
*
2472 GAAGACAAGATCTGCTTTCTTCGATCTAC-TCTGCCACCAATATCG
1 GAAGACAAGATCTGC-TTCTTCGATCTACTTC-GCCACCAATATAG
* * *
2517 GAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAG
1 GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAATATAG
* **** * *
2560 GAAGACAGGA-CTTGCTATCTTCGATCTACTT-AATGCCAATACAT
1 GAAGACAAGATC-TGCT-TCTTCGATCTACTTCGCCACCAATATAG
* * *
2604 GAAGACAAGATCTGCTTTATTCGATCTAC-TCAACCACCAATATGG
1 GAAGACAAGATCTGC-TTCTTCGATCTACTTC-GCCACCAATATAG
* * * * *
2649 GAAGACAAGATATGCATCTTCGATCCATTTC-CTACCAATATAG
1 GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAATATAG
* * *
2692 AAAGACAGGACCTGCTATCTTC
1 GAAGACAAGATCTGCT-TCTTC
2714 AATGATCTGC
Statistics
Matches: 434, Mismatches: 97, Indels: 38
0.76 0.17 0.07
Matches are distributed among these distances:
42 1 0.00
43 79 0.18
44 259 0.60
45 95 0.22
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAATATAG
Found at i:2674 original size:132 final size:132
Alignment explanation
Indices: 2112--2713 Score: 639
Period size: 132 Copynumber: 4.6 Consensus size: 132
2102 GCTCTACTGT
* * * * * * *
2112 CAATACATGAAGACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA-TC
1 CAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGACT-
* * * * *
2176 TGC-ATCTTCGATCCACTTCCTACCAATATAAGAAGACAGGACCTGCTATCTTCGATCTACTTCA
65 TGCTATCTTCGATCCACTTCATACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCA
*
2240 CGC
130 CAC
* * * * * * * * * *
2243 CAATACATGAAGACAGGATATGCTTTCTTCGATCTACTTCGCCACTAGTATGGGAAGACAAGA-T
1 CAATACAGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGACT
* * * **
2307 CTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTTATCTACTT
65 -TGCTATCTTCGATCCACTTC-ATACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTT
*
2371 CACGC
128 CACAC
*
2376 CAATACATGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCT
1 CAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGA-CT
* ** *
2441 T-CTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCTG
65 TGCTATCTTCGATCCACTTCATACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACT-T-
2505 C-CAC
128 CACAC
2509 CAATATC-GGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGACT
1 CAATA-CAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGACT
* * * * *
2572 TGCTATCTTCGATCTACTTAATGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTAC-TCA
65 TGCTATCTTCGATCCACTTCATACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-
2636 ACCAC
129 A-CAC
** * * * *
2641 CAATATGGGAAGACAAGATATGCATCTTCGATCCATTTC-CTACCAATATAGAAAGACAGGACCT
1 CAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGACTT
2705 GCTATCTTC
66 GCTATCTTC
2714 AATGATCTGC
Statistics
Matches: 422, Mismatches: 36, Indels: 25
0.87 0.07 0.05
Matches are distributed among these distances:
129 1 0.00
130 1 0.00
131 24 0.06
132 274 0.65
133 119 0.28
134 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (132 bp):
CAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGACTT
GCTATCTTCGATCCACTTCATACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
AC
Done.