Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_424 ID=scaffold_424-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: 9224
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.25
Warning! 2057 characters in sequence are not A, C, G, or T
Found at i:7176 original size:7 final size:7
Alignment explanation
Indices: 7164--7210 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
7154 TCTGAGTCAA
7164 AAAAATG
1 AAAAATG
7171 AAAAATG
1 AAAAATG
*
7178 -AGAATG
1 AAAAATG
7184 AAAAATG
1 AAAAATG
*
7191 ATAAATG
1 AAAAATG
7198 -AAAATG
1 AAAAATG
7204 AAAAATG
1 AAAAATG
7211 GAGAGGCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 10 0.29
7 24 0.71
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (7 bp):
AAAAATG
Found at i:7185 original size:13 final size:14
Alignment explanation
Indices: 7166--7210 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
7156 TGAGTCAAAA
7166 AAATGAAAAATGA-
1 AAATGAAAAATGAT
*
7179 GAATGAAAAATGAT
1 AAATGAAAAATGAT
*
7193 AAATG-AAAATGAA
1 AAATGAAAAATGAT
7206 AAATG
1 AAATG
7211 GAGAGGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 24 0.86
14 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (14 bp):
AAATGAAAAATGAT
Found at i:7187 original size:20 final size:20
Alignment explanation
Indices: 7164--7210 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
7154 TCTGAGTCAA
*
7164 AAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAATG
*
7184 AAAAATGATAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
7204 AAAAATG
1 AAAAATG
7211 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:8517 original size:44 final size:44
Alignment explanation
Indices: 8451--9168 Score: 351
Period size: 44 Copynumber: 16.8 Consensus size: 44
8441 AAGAATTTCA
*
8451 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* *
8495 GATCTTATCTCCCTGAGATTACAGTGGAGGAGATTGAAGCTAGT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * * *** *
8539 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * * * *
8583 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTA-TCAG-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGT
* * *
8625 G-TCTTATCTCCCCGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * * ***
8668 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-GAAGCCAGT
* ** * * * *
8712 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGT
* * *
8754 G-TCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGA
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * ** * *
8797 GATCTTATCTCCCTAAGATTACAGCGGAGTAGATCCAAGACACT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * ** ** *
8841 -ATCCTA--T--C---GATTATAGCGGAGCAGATCCAATACACT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * ***
8877 -ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAG-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-GAAGCCAGT
* * * * * *
8920 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTA-TCAG-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGT
* * *
8962 G-TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * * * * ***
9005 AATCCTATCTCACTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-GAAGCCAGT
* * * * * * * *
9049 AATCTTATCTCTCTGA-AGTTACAGTAGAGTATATCGTA-TCAG-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGT
* * * *
9091 G-TCTTATCTCCCTGAGATGACAGCGGAGCAGATTGAAACTAGT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
* * *
9134 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT
9169 AAAATAAAGG
Statistics
Matches: 508, Mismatches: 135, Indels: 62
0.72 0.19 0.09
Matches are distributed among these distances:
36 31 0.06
38 1 0.00
39 1 0.00
40 1 0.00
41 110 0.22
42 22 0.04
43 27 0.05
44 307 0.60
45 8 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
Found at i:8684 original size:129 final size:129
Alignment explanation
Indices: 8451--8825 Score: 536
Period size: 129 Copynumber: 2.9 Consensus size: 129
8441 AAGAATTTCA
* * * * * *
8451 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGTGATCTTATCTCCCTGAGATTA
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAA-TCAG-G-TCTTATCTCCCTGAGATTA
*
8516 CAGTGGAGGAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAA
63 CAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAA
*
8581 AT
128 AG
* *
8583 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCCGAGATTACAG
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
*
8648 CGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
66 TGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
* * * *
8712 GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTACAG
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
* * * *
8777 TGGAGCAGATTGAAGCCAG-AGATCTTATCTCCCTAAGATTACAGCGGAG
66 TGGAGCAGATTGAAGCTAGTA-ATCCTATCTCCCTGAGATTACAGTGGAG
8826 TAGATCCAAG
Statistics
Matches: 221, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.00
129 184 0.83
130 1 0.00
131 3 0.01
132 32 0.14
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (129 bp):
GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
TGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
Found at i:8762 original size:85 final size:85
Alignment explanation
Indices: 8451--9124 Score: 267
Period size: 85 Copynumber: 7.9 Consensus size: 85
8441 AAGAATTTCA
* * * * *
8451 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGTGATCTTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAAGTTACAGCGGAGTAGATCGAA-TCAG-G-TCTTATCTCCCTGAGATTA
* * *
8516 CAGTGGAGGAGATT-GAA-GCTAG
63 CAGTGGAGCAGATTAAAATAC-AG
* * * ** ** * * *
8538 TAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGA-AG
1 -GATCTTATCTCCCTGAAG-TTACAGCGGAGTAGA-TCGAAT-CA-GGTCTTATCTCCCTGAGA-
* * ***
8601 TTACAGTAGAGTAGA-TCGTAT-CAG
60 TTACAGTGGAGCAGATTAAAATACAG
* * * * * *
8625 G-TCTTATCTCCCCG-AGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 GATCTTATCTCCCTGAAG-TTACAGCGGAGTAGATCGAATC-AG--GTCTTATCTCCCTGAGATT
* *
8688 ACAGTGGAGCGGATTAAAATAAAG
62 ACAGTGGAGCAGATTAAAATACAG
* * * * *
8712 GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTACAG
1 GATCTTATCTCCCTGAAGTTACAGCGGAGTAGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
* **
8777 TGGAGCAGATT-GAAGCCAG
66 TGGAGCAGATTAAAATACAG
* * ** *
8796 AGATCTTATCTCCCT-AAGATTACAGCGGAGTAGATCCAAGACA---C-TATC-CTAT-CGATTA
1 -GATCTTATCTCCCTGAAG-TTACAGCGGAGTAGATCGAA-TCAGGTCTTATCTCCCTGAGATTA
* * ** *
8854 TAGCGGAGCAGA-TCCAATACAC
63 CAGTGGAGCAGATTAAAATACAG
* * * ** ** * *
8876 TATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTT
1 GATCTTATCTCCCTGAAGTTACAGCGGAGTAGA-TCGAAT-CAGG-TCTTATCTCCCTGAGA-TT
* * ***
8940 ACAGTAGAGTAGA-TCGTAT-CAG
62 ACAGTGGAGCAGATTAAAATACAG
* * * * *
8962 G-TCTTATCTCCCTG-AGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCACTGAGATT
1 GATCTTATCTCCCTGAAG-TTACAGCGGAGTAGATCGAATC-AG--GTCTTATCTCCCTGAGATT
* *
9025 ACAGTGGAGCGGATTAAAATAAAG
62 ACAGTGGAGCAGATTAAAATACAG
* * ** * * *
9049 AATCTTATCTCTCTGAAGTTACAGTAGAGTATATCGTATCAGGTCTTATCTCCCTGAGATGACAG
1 GATCTTATCTCCCTGAAGTTACAGCGGAGTAGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
*
9114 CGGAGCAGATT
66 TGGAGCAGATT
9125 GAAACTAGTA
Statistics
Matches: 434, Mismatches: 113, Indels: 81
0.69 0.18 0.13
Matches are distributed among these distances:
79 25 0.06
80 25 0.06
81 2 0.00
82 4 0.01
83 2 0.00
84 19 0.04
85 191 0.44
86 16 0.04
87 29 0.07
88 112 0.26
89 8 0.02
90 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (85 bp):
GATCTTATCTCCCTGAAGTTACAGCGGAGTAGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
TGGAGCAGATTAAAATACAG
Found at i:8860 original size:36 final size:36
Alignment explanation
Indices: 8813--8884 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
8803 ATCTCCCTAA
*
8813 GATTACAGCGGAGTAGATCCAAGACACTATCCTATC
1 GATTACAGCGGAGCAGATCCAAGACACTATCCTATC
* *
8849 GATTATAGCGGAGCAGATCCAATACACTATCCTATC
1 GATTACAGCGGAGCAGATCCAAGACACTATCCTATC
8885 TCCCTGAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (36 bp):
GATTACAGCGGAGCAGATCCAAGACACTATCCTATC
Found at i:9038 original size:129 final size:129
Alignment explanation
Indices: 8877--9218 Score: 614
Period size: 129 Copynumber: 2.7 Consensus size: 129
8867 CCAATACACT
8877 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
1 ATCCTATCTCCCTGAGA-TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
* * *
8941 CAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTA
65 CAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATGACAGCGGAGCAGATTGAAACTAGTA
* *
9006 ATCCTATCTCACTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
*
9071 AGTAGAGTATATCGTATCAGGTCTTATCTCCCTGAGATGACAGCGGAGCAGATTGAAACTAGTA
66 AGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATGACAGCGGAGCAGATTGAAACTAGTA
9135 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
9200 AGTAGAGTAGATCGTATCA
66 AGTAGAGTAGATCGTATCA
9219 AGCCTT
Statistics
Matches: 203, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
129 202 1.00
130 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (129 bp):
ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
AGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATGACAGCGGAGCAGATTGAAACTAGTA
Found at i:9155 original size:337 final size:337
Alignment explanation
Indices: 8540--9162 Score: 1061
Period size: 337 Copynumber: 1.8 Consensus size: 337
8530 GAAGCTAGTA
*
8540 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
8605 AGTAGAGTAGATCGTATCAGGTCTTATCTCCCCGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
66 AGTAGAGTAGATCGTATCAGGTCTTATCTCCCCGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
* *
8670 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACA
131 TCCTATCTCACTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTTACA
* * * *
8735 GCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGAGAT
196 GCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGATGACAGCGGAGCAGATTGAAACCAGAGAT
*
8800 CTTATCTCCCTAAGATTACAGCGGAGTAGATCCAAGACACTATCCTATCGATTATAGCGGAGCAG
261 CCTATCTCCCTAAGATTACAGCGGAGTAGATCCAAGACACTATCCTATCGATTATAGCGGAGCAG
8865 ATCCAATACACT
326 ATCCAATACACT
8877 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
1 ATCCTATCTCCCTGAGA-TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
* *
8941 CAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTA
65 CAGTAGAGTAGATCGTATCAGGTCTTATCTCCCCGAGATTACAGCGGAGCAGATTGAAGCTAGTA
9006 ATCCTATCTCACTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTTAC
130 ATCCTATCTCACTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTTAC
* * * * *
9071 AGTAGAGTATATCGTATCAGGTCTTATCTCCCTGAGATGACAGCGGAGCAGATTGAAACTAGTA-
195 AGCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGATGACAGCGGAGCAGATTGAAACCAG-AG
* *
9135 ATCCTATCTCCCTGAGATTACAGTGGAG
259 ATCCTATCTCCCTAAGATTACAGCGGAG
9163 CGGATTAAAA
Statistics
Matches: 267, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
336 1 0.00
337 265 0.99
338 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (337 bp):
ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
AGTAGAGTAGATCGTATCAGGTCTTATCTCCCCGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
TCCTATCTCACTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTTACA
GCAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGATGACAGCGGAGCAGATTGAAACCAGAGAT
CCTATCTCCCTAAGATTACAGCGGAGTAGATCCAAGACACTATCCTATCGATTATAGCGGAGCAG
ATCCAATACACT
Found at i:9187 original size:44 final size:44
Alignment explanation
Indices: 8881--9211 Score: 177
Period size: 44 Copynumber: 7.7 Consensus size: 44
8871 TACACTATCC
* *
8881 TATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATACAGGATCT
* * * ***
8925 TATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGTAT-CAGG-TCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATACAGGATCT
* * * * * *
8966 TATCTCCCTGAGATTACAGCGGAGTAGATT-GAA-GCTAGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAC-AG-GATCT
* * * *
9010 TATCTCACTGAGATTACAGTGGAGCGGATTAAAATAAAGAATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATACAGGATCT
* * * * ***
9054 TATCTCTCTGA-AGTTACAGTAGAGTATA-TCGTAT-CAGG-TCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATACAGGATCT
* * * * *
9095 TATCTCCCTGAGATGACAGCGGAGCAGATT-GAA-ACTAGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAC-AG-GATCT
* *
9139 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATACAGGATCT
* * *
9183 TATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGAT
9212 CGTATCAAGC
Statistics
Matches: 217, Mismatches: 52, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
41 55 0.25
42 13 0.06
43 8 0.04
44 132 0.61
45 8 0.04
46 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATACAGGATCT
Done.