Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_967 ID=scaffold_967-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: 2865
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.17
Warning! 1015 characters in sequence are not A, C, G, or T
Found at i:248 original size:132 final size:132
Alignment explanation
Indices: 9--536 Score: 698
Period size: 132 Copynumber: 3.9 Consensus size: 132
1 CCATAAAT
* * * *
9 CCTTGTCTCTCTGAGCAGCAGCGGAGAAGTTTGAGGATTGTATATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
* * *
74 TGGAGCAGATCAAAGATGGT-AAATCTTATATTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAA
66 TGGAGCAGATCAAAGAT-GTCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACA
138 AAG
130 AAG
* * * *
141 CATTGTCTCTTTGAGCAGCAGCGGAGCAGGTTGAAGATTATAGATCTTCTCTCCCTAAGCAGTAG
1 CCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
*
206 TGGAGCAGATCAAAGATGTCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCACAA
66 TGGAGCAGATCAAAGATGTCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAA
271 AG
131 AG
* * *
273 CCTTATCTCTCTGAGTAACAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
* *
338 TGGGGCAGACTACAAACCGTACGGTACTAAATCCTTTAGTCTTTCCAAGATAGTGGGAAGCAGAT
66 TGGAGCAGA-T-CAAA--G-A-TGT-C-AAAT-C-TTA-TCTTTCCAAGATAGTGGGAAGCAGAT
* *
403 TTAGGCCACCAAG
120 TTAAGCCACAAAG
* * * * *
416 CCTTGTCTCCCTGAGCAGTAACGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
* * *
481 TGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATATTGGGAAGCAGATTT
66 TGGAGCAGATCAAAGATGTCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTT
537 NNNNNNNNNN
Statistics
Matches: 348, Mismatches: 36, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
131 2 0.01
132 210 0.60
133 4 0.01
134 5 0.01
135 4 0.01
136 2 0.01
137 2 0.01
138 3 0.01
139 2 0.01
140 4 0.01
141 5 0.01
142 4 0.01
143 101 0.29
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (132 bp):
CCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCAAAGATGTCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAA
AG
Found at i:494 original size:275 final size:264
Alignment explanation
Indices: 9--536 Score: 723
Period size: 275 Copynumber: 2.0 Consensus size: 264
1 CCATAAAT
* * * * * *
9 CCTTGTCTCTCTGAGCAGCAGCGGAGAAGTTTGAGGATTGTATATCTTATCTCCCTAAGCAGTAG
1 CCTTATCTCTCTGAGCAACAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
*
74 TGGAGCAGATCAAAGATGGTAAATCTTATATTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAA
66 TGGAGCAGATCAAAGACGGTAAATCTTATATTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAA
** * *
139 AGCATTGTCTCTTTGAGCAGCAGCGGAGCAGGTTGAAGATTATAGATCTTCTCTCCCTAAGCAGT
131 AGCATTGTCTCCCTGAGCAGCAACGGAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGT
* *
204 AGTGGAGCAGATCAAAGATGTCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCAC
196 AGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCAC
269 AAAG
261 AAAG
*
273 CCTTATCTCTCTGAGTAACAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
1 CCTTATCTCTCTGAGCAACAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
* * *
338 TGGGGCAGACTACAAACCGTACGGTACTAAATCCTTTAGTCTTTCCAAGATAGTGGGAAGCAGAT
66 TGGAGCAGA-T-CAAA--G-ACGG---TAAAT-C-TTA-TATTTCCAAGATAGTGGAAAGCAGAT
* ** * * * *
403 TTAGGCCACCAAGCCTTGTCTCCCTGAGCAGTAACGGAGTAGGTTGAAGATTGTAGATCTTATCT
120 TTAAGCCAAAAAGCATTGTCTCCCTGAGCAGCAACGGAGCAGGTTGAAGATTATAGATCTTATCT
* *
468 CCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATATTGGGAAGCAG
185 CCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAA
533 ATTT
250 ATTT
537 NNNNNNNNNN
Statistics
Matches: 227, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
264 66 0.29
265 1 0.00
266 4 0.02
268 1 0.00
269 3 0.01
272 5 0.02
273 1 0.00
274 3 0.01
275 143 0.63
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (264 bp):
CCTTATCTCTCTGAGCAACAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCAAAGACGGTAAATCTTATATTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAA
AGCATTGTCTCCCTGAGCAGCAACGGAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCAC
AAAG
Found at i:1794 original size:132 final size:132
Alignment explanation
Indices: 1552--2837 Score: 2055
Period size: 132 Copynumber: 9.8 Consensus size: 132
1542 NNNNNNNNNN
* *
1552 GATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACGAAGCCTTGTCTCTCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
*
1617 TAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1682 AA
131 AA
* * * *
1684 GATGTCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGTCACAAAGGCTTGTCTCTCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
* * * *
1749 GAGTACCAGCGGAGAAGGTTGAAGATTGTCGATCTTATCTACCTAAGCAGTAGTGGAGCAGATCA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1814 AA
131 AA
* * * *
1816 GACGACAAATCTTATCTTCCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
* * *
1881 GAGCAGTAGCGGAGGAGGGTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1946 AA
131 AA
* * *
1948 GATGGCAAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
*
2013 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCTGTAGTGGAGCAGATCA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
2078 AA
131 AA
*
2080 GATGGCAAATCTTATCTTTCCAA-ATAGT-GGAAGCAGATTTAAGCCACAAAGCC-TGTCTCTCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
* *
2142 TAGGCAGCAGCGGAGAA-GTTGAAGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATC
66 GA-GCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
2206 AAA
130 AAA
*
2209 GATGACAAATCTTATCTTTCCTAGATAGTGGGAAGCAGATTTAAGCCACAAAGCC-TGTCTCTCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
* * *
2273 GAGTAGCAGCGCAGAAGGTTGAATATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
2338 AA
131 AA
* * * *
2340 GACGACAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAAGCCTTGTCTCCCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
* * * *
2405 GGGCAGCAGCAGAGTAGGTTG-AGATTGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
2469 AA
131 AA
*
2471 GATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
* *
2536 GAGTAGCAGCGGAGAAGGATGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
2601 AA
131 AA
* * * *
2603 GACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTATGCCACCAAGCCTTGTCTCCCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
* * *
2668 GAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAATGGAGCAGATTA
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
2733 AA
131 AA
* * *
2735 GACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCT
1 GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
*
2800 GAGCAGCAGCGGAGTAGGTTG-AGATTGTAGATCTTATC
66 GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATC
2838 ACCGTAGGCA
Statistics
Matches: 1066, Mismatches: 82, Indels: 13
0.92 0.07 0.01
Matches are distributed among these distances:
129 79 0.07
130 54 0.05
131 275 0.26
132 658 0.62
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
GATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCT
GAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
AA
Found at i:1950 original size:44 final size:44
Alignment explanation
Indices: 1779--2096 Score: 116
Period size: 44 Copynumber: 7.2 Consensus size: 44
1769 GAAGATTGTC
* * *
1779 GATCTTATCTACCTAAGCAGTAGTGGAGCAGATCAAAGACGACA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCA
* ** ****
1823 AATCTTATCTTCCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA
1 GATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGCA
* * * * * * * * *
1867 -AGCCTTGTCTCCCTGAGCAGTAGCGGAGGAGGGT-GAAGATTGTA
1 GA-TCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGATGGCA
1911 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCA
* * ** ***
1955 AATCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTTAAGCCA-AAAA
1 GATCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATCAAAG--ATGGCA
* * * * * * * * ** * *
2000 G-CCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCA
*
2043 GATCTTATCTCCCTAAGCTGTAGTGGAGCAGATCAAAGATGGCA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCA
*
2087 AATCTTATCT
1 GATCTTATCT
2097 TTCCAAATAG
Statistics
Matches: 191, Mismatches: 63, Indels: 40
0.65 0.21 0.14
Matches are distributed among these distances:
42 11 0.06
43 15 0.08
44 143 0.75
45 14 0.07
46 8 0.04
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (44 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCA
Found at i:2483 original size:44 final size:44
Alignment explanation
Indices: 2433--2619 Score: 116
Period size: 44 Copynumber: 4.2 Consensus size: 44
2423 TTGAGATTGT
* *
2433 AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
1 AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
* ** *
2477 AAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCAC
1 AAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGACGAC
* * * * * * * * * * *
2520 AAAGCCTTGTCTCTCTGAGTAGCAGCGGAGAAGGAT-GAAGATTG-T
1 AAA-TCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGA-CGAC
*
2565 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
1 AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
2609 AAATCTTATCT
1 AAATCTTATCT
2620 TTCCAAGATA
Statistics
Matches: 100, Mismatches: 31, Indels: 24
0.65 0.20 0.15
Matches are distributed among these distances:
42 4 0.04
43 13 0.13
44 70 0.70
45 11 0.11
46 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (44 bp):
AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
Done.