Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_185 ID=scaffold_185-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: 9745
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:313 original size:33 final size:34
Alignment explanation
Indices: 275--349 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
265 TATAAATGAG
* *
275 TTATAAAAA-TATGTACGTGCATATGTATATATA
1 TTATAAAAAGTATGTACGTACATATGTATATAAA
* *
308 TTATAAAAATGTATGTATGTATATATGTATATAAA
1 TTATAAAAA-GTATGTACGTACATATGTATATAAA
343 TTATAAA
1 TTATAAA
350 GTATAAAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 9 0.25
35 27 0.75
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (34 bp):
TTATAAAAAGTATGTACGTACATATGTATATAAA
Found at i:353 original size:16 final size:17
Alignment explanation
Indices: 327--370 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
317 TGTATGTATG
*
327 TATATATGTATATAAA-T
1 TATATAAGTATA-AAAGT
344 TATA-AAGTATAAAAGT
1 TATATAAGTATAAAAGT
360 TATATAAGTAT
1 TATATAAGTAT
371 GTATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
17 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
TATATAAGTATAAAAGT
Found at i:472 original size:3 final size:3
Alignment explanation
Indices: 458--552 Score: 111
Period size: 3 Copynumber: 30.7 Consensus size: 3
448 TAAATGGGTA
* * *
458 AAT AAA AAT AAT AAT AGT AAGGT AAGT AAT AAT AAT AA- ATAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT A-AT AAT AAT
*
506 AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
553 CGGGACTAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
2 1 0.01
3 72 0.89
4 5 0.06
5 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2283 original size:44 final size:43
Alignment explanation
Indices: 2138--2677 Score: 275
Period size: 44 Copynumber: 12.6 Consensus size: 43
2128 TCATTTTAAC
* * * *
2138 CCGCTCCACTGCAACTTCAGGGAGATAGGAT-TAGTAGCTTCAGT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGTTTTA-T
* * * ***
2182 CTGCTCCACTGCAACTTCAGGGAGATAA-AACTG-GATGCGAT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAT
** * *
2223 CTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAGT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA-T
* ** *
2267 CCGCTCCACTGCAACTTCAGGGAGATAGGAT-TGATTTCTTTTGT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTG--TGGTTTTAT
** * ** * ***
2311 ATGCTCCACTACTGCTT-AGGGAGATAAGA-CT-TGATGCGAT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAT
* ** *
2351 CTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAGT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA-T
* * *
2395 CCGCTCCACTACAACTTCAGGGAGATAGGAT-TGAT-TTCTTCTAT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TGGT-TT-TAT
**** * ***
2439 CCGCTCCACTATTTCTT-AGGGAGATAAGA-CT-TGATGCGAT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAT
* * * *
2479 CTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAAT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT-AT
* * ** *
2523 CCGTTCCACTGCAACTTCAGGGAGATAGGAT-TGATTTTTTCTGT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TGGTTT-TAT
**** * ***
2567 CCGCTCCACTATTTCTT-AGGGAGATAAGA-CT-TGATGCGAT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAT
* * * *
2607 CTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAAT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT-AT
*
2651 CCGTTCCACTGCAACTTCAGGGAGATA
1 CCGCTCCACTGCAACTTCAGGGAGATA
2678 GGATTGTAGC
Statistics
Matches: 359, Mismatches: 110, Indels: 54
0.69 0.21 0.10
Matches are distributed among these distances:
40 39 0.11
41 62 0.17
42 12 0.03
43 57 0.16
44 181 0.50
45 8 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (43 bp):
CCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAT
Found at i:2382 original size:128 final size:128
Alignment explanation
Indices: 2131--2683 Score: 838
Period size: 128 Copynumber: 4.3 Consensus size: 128
2121 GGATTCATCA
* ** * * * *
2131 TTTTAACCCGCTCCACTGCAACTTCAGGGAGATAGGATT-AGTAGCTTCAGTCTGCTCCACTGCA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGA-TTTCTTCTGTCCGCTCCACTACT
* * * * *
2195 ACTTCAGGGAGATAAAACTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
65 TCTT-AGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
* * ** *
2260 TTTTAGTCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTTGTATGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCCGCTCCACTACTT
* *
2325 CTTAGGGAGATAAGACTTGATGCGATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
* * * *
2388 TTTTAGTCCGCTCCACTACAACTTCAGGGAGATAGGATTGATTTCTTCTATCCGCTCCACTATTT
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCCGCTCCACTACTT
2453 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
* * *
2516 TTTTAATCCGTTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTCTGTCCGCTCCACTATTT
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCCGCTCCACTACTT
2581 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
*
2644 TTTTAATCCGTTCCACTGCAACTTCAGGGAGATAGGATTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTG
2684 TAGCTTTACT
Statistics
Matches: 395, Mismatches: 28, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
128 338 0.86
129 56 0.14
130 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (128 bp):
TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCCGCTCCACTACTT
CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATGG
Found at i:9011 original size:139 final size:142
Alignment explanation
Indices: 8847--9115 Score: 472
Period size: 139 Copynumber: 1.9 Consensus size: 142
8837 ATTGCCTTTA
8847 TTTGATTAAAATAGATGTGTATATATATATATATATATTATAAAAAGTATGTATATATATAAATG
1 TTTGATTAAAATAGATGTGTATATATATATATATATATTATAAAAAGTATGTATATATATAAATG
* *
8912 AGTTATAAAAATATGTACGTGC-ATG-AGA-ATATATATATATTGTAAAAATGTATGTATGTATG
66 AGTTATAAAAATATGTACGTGCAATGTAGATATATATATATATTATAAAAATGTATATATGTATG
8974 TATGTATGAGTT
131 TATGTATGAGTT
*
8986 TTTGATTAAAATAGGTGTGTATATATATATATATATATTATAAAAAGTATGTATATATATAAATG
1 TTTGATTAAAATAGATGTGTATATATATATATATATATTATAAAAAGTATGTATATATATAAATG
*
9051 AGTTATAAAAATATGTACGTGCATATGTATATATATATATATATTATAAAAATGTATATATGTAT
66 AGTTATAAAAATATGTACGTGCA-ATGTAGATATATATATATATTATAAAAATGTATATATGTAT
9116 ATAAATTATA
Statistics
Matches: 122, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
139 86 0.70
141 3 0.02
142 2 0.02
143 31 0.25
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.42
Consensus pattern (142 bp):
TTTGATTAAAATAGATGTGTATATATATATATATATATTATAAAAAGTATGTATATATATAAATG
AGTTATAAAAATATGTACGTGCAATGTAGATATATATATATATTATAAAAATGTATATATGTATG
TATGTATGAGTT
Found at i:9085 original size:2 final size:2
Alignment explanation
Indices: 9073--9210 Score: 70
Period size: 2 Copynumber: 69.5 Consensus size: 2
9063 ATGTACGTGC
* * * * *
9073 AT AT GT AT AT AT AT AT AT AT AT -T AT AA AA AT GT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
9114 AT AT AA AT -T AT AA AGT AT A- AA AGT -T AT AT A- AGT AT GT AT
1 AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT A-T AT AT AT
* * * * * *
9153 AT AT AT AT AT AT AT AT AT AT AT AA AT CAA AG GT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
9196 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
9211 ACAAAATCTA
Statistics
Matches: 101, Mismatches: 26, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
1 5 0.05
2 93 0.92
3 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.43
Consensus pattern (2 bp):
AT
Found at i:9109 original size:27 final size:27
Alignment explanation
Indices: 9075--9127 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
9065 GTACGTGCAT
*
9075 ATGTATATATATATATATATTATAAAA
1 ATGTATATATATATATAAATTATAAAA
*
9102 ATGTATATATGTATATAAATTATAAA
1 ATGTATATATATATATAAATTATAAA
9128 GTATAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (27 bp):
ATGTATATATATATATAAATTATAAAA
Found at i:9140 original size:16 final size:17
Alignment explanation
Indices: 9077--9148 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
9067 ACGTGCATAT
*
9077 GTATATATA-TATATATA
1 GTATATAAATTATATA-A
* * *
9094 TTATAAAAATGTATATAT
1 GTATATAAAT-TATATAA
9112 GTATATAAATTATA-AA
1 GTATATAAATTATATAA
9128 GTATA-AAAGTTATATAA
1 GTATATAAA-TTATATAA
9145 GTAT
1 GTAT
9149 GTATATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
15 3 0.07
16 11 0.25
17 16 0.36
18 8 0.18
19 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
GTATATAAATTATATAA
Found at i:9154 original size:139 final size:136
Alignment explanation
Indices: 8866--9167 Score: 369
Period size: 139 Copynumber: 2.2 Consensus size: 136
8856 AATAGATGTG
8866 TATATATATATATATATATTATAAAAAGTATGTATATATATAAATGAGTTATAAAAATATGTACG
1 TATATATATATATATATATTATAAAAAGTATGTATATATATAAATGAGTTATAAAAATATGTACG
* * * * ** *
8931 TGCATGAGAATATATATATATTGTAAAAATGTATGTATGTATGTATGTATGAGTTTTTGATTAAA
66 TGCATGAGAATATATATATATTATAAAAATGTA-GTA-GTATGTA-GTATAAATTATAAAGTAAA
* *
8996 ATAGGTGTG
128 ATAGGTATA
9005 TATATATATATATATATATTATAAAAAGTATGTATATATATAAATGAGTTATAAAAATATGTACG
1 TATATATATATATATATATTATAAAAAGTATGTATATATATAAATGAGTTATAAAAATATGTACG
*
9070 TGCATATGTATATATATATATATATTATAAAAATGTA-TA-TATGTA-TATAAATTATAAAGTAT
66 TGC--ATG-AGA-ATATATATATATTATAAAAATGTAGTAGTATGTAGTATAAATTATAAAGTA-
*
9132 AAA-AGTTATA
126 AAATAGGTATA
*
9142 TAAGTATGTATATATATATATATATA
1 T-A-TATATATATATATATAT-TATA
9168 TATATATAAA
Statistics
Matches: 143, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
137 15 0.10
138 4 0.03
139 90 0.63
140 4 0.03
141 5 0.03
142 2 0.01
143 23 0.16
ACGTcount: A:0.45, C:0.01, G:0.12, T:0.41
Consensus pattern (136 bp):
TATATATATATATATATATTATAAAAAGTATGTATATATATAAATGAGTTATAAAAATATGTACG
TGCATGAGAATATATATATATTATAAAAATGTAGTAGTATGTAGTATAAATTATAAAGTAAAATA
GGTATA
Found at i:9254 original size:3 final size:3
Alignment explanation
Indices: 9240--9360 Score: 72
Period size: 3 Copynumber: 39.7 Consensus size: 3
9230 TAAATGGGTA
* * *
9240 AAT AAA AAT AAT AAT AGT AAGGT AAGT AAT AAT AAT AA- ATAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT A-AT AAT AAT
* * * * *
9288 AAT GAT AAT AAT AA- ATAT AAT AAT GAT AA- AACT AATT AGT -TT GAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT
9333 AAT AAT AAT AAT AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9361 CGAGACTATA
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
2 7 0.07
3 74 0.79
4 10 0.11
5 3 0.03
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Done.