Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_339 ID=scaffold_339-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: 8068
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:456 original size:12 final size:11
Alignment explanation
Indices: 435--474 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
425 AAAGTTACAA
435 AAATAAAAATAT
1 AAAT-AAAATAT
447 AAATATAAATAT
1 AAATA-AAATAT
459 AAATAAAATA-
1 AAATAAAATAT
469 AAATAA
1 AAATAA
475 TTATTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.22
11 6 0.22
12 15 0.56
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:1996 original size:58 final size:58
Alignment explanation
Indices: 1906--2039 Score: 232
Period size: 58 Copynumber: 2.3 Consensus size: 58
1896 AAAGATGAAT
* *
1906 TTGATACGATCTACTCTATTCTTCAGTCTGCTCCACTGTAAACTCAGGGAGATAAGAC
1 TTGATGCGATCTACTCTATTCTTCAGTCTGCTCCACTGTAAACTCAGAGAGATAAGAC
*
1964 TTGATGCGATCTACTCTATTCTTCAGTCTGCTCCACTGTAACCTCAGAGAGATAAGAC
1 TTGATGCGATCTACTCTATTCTTCAGTCTGCTCCACTGTAAACTCAGAGAGATAAGAC
*
2022 TTGATGCCATCTACTCTA
1 TTGATGCGATCTACTCTA
2040 CTACAACTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 72 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (58 bp):
TTGATGCGATCTACTCTATTCTTCAGTCTGCTCCACTGTAAACTCAGAGAGATAAGAC
Found at i:2586 original size:45 final size:45
Alignment explanation
Indices: 2510--2633 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 45
2500 TTGTTTATTT
* * * *
2510 AGTCTGCCCCACTGTAATTTCAGGGGGATAAGACTTAC-TTCATTG
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCACTTTC-TTG
* * * *
2555 AGTCTGCTCCACTGCAACTTCAGGGAAATAAGGCTCGCTTTCTTG
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCACTTTCTTG
* * *
2600 GGTCTGCTCCACCGCAATTTCATGGAGATAAGAC
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGAC
2634 CCGATGTGAT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 61 0.95
46 3 0.05
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCACTTTCTTG
Found at i:2753 original size:44 final size:44
Alignment explanation
Indices: 2705--2966 Score: 217
Period size: 44 Copynumber: 6.2 Consensus size: 44
2695 ACTGCAACTT
* * * *
2705 CAGGGAGATAAGATTTGCCATCATTAACCTATTCCACTACTGTC
1 CAGGGAGATAAGATTTGCAATCTTTAACCTATTCCACTGCTGAC
* **
2749 CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGAC
1 CAGGGAGATAAGATTTGCAATCTTTAACCTATTCCACTGCTGAC
* * *
2793 CAGGGAGAT-AG---GGC--TCTTTAATCTATTCCACTGCTGCC
1 CAGGGAGATAAGATTTGCAATCTTTAACCTATTCCACTGCTGAC
* *
2831 CAGGGAGATAACATTCT-CAATCTTCAACCTATTCCACTGCTGAC
1 CAGGGAGATAAGATT-TGCAATCTTTAACCTATTCCACTGCTGAC
* * ** * * *
2875 TAGGGAGATAGGATTCACAATCTTTAACCTCTTCCACGGCTAAC
1 CAGGGAGATAAGATTTGCAATCTTTAACCTATTCCACTGCTGAC
* * *
2919 CAGAGAGAT-AG---GGC--TCTTTAATCTATTCCACTGCTGAC
1 CAGGGAGATAAGATTTGCAATCTTTAACCTATTCCACTGCTGAC
*
2957 CAAGGAGATA
1 CAGGGAGATA
2967 GGGTTAGGGT
Statistics
Matches: 173, Mismatches: 36, Indels: 23
0.75 0.16 0.10
Matches are distributed among these distances:
38 58 0.34
39 1 0.01
40 2 0.01
42 1 0.01
43 2 0.01
44 109 0.63
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
CAGGGAGATAAGATTTGCAATCTTTAACCTATTCCACTGCTGAC
Found at i:2835 original size:82 final size:82
Alignment explanation
Indices: 2728--2886 Score: 246
Period size: 82 Copynumber: 1.9 Consensus size: 82
2718 TTTGCCATCA
* ** *
2728 TTAACCTATTCCACTACTGTCCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGAC
1 TTAACCTATTCCACTACTGCCCAGGGAGATAACATTCACAATCTTCAACCTATTCCACTGCTGAC
2793 CAGGGAGATAGGGCTCT
66 CAGGGAGATAGGGCTCT
* * *
2810 TTAATCTATTCCACTGCTGCCCAGGGAGATAACATTCTCAATCTTCAACCTATTCCACTGCTGAC
1 TTAACCTATTCCACTACTGCCCAGGGAGATAACATTCACAATCTTCAACCTATTCCACTGCTGAC
*
2875 TAGGGAGATAGG
66 CAGGGAGATAGG
2887 ATTCACAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (82 bp):
TTAACCTATTCCACTACTGCCCAGGGAGATAACATTCACAATCTTCAACCTATTCCACTGCTGAC
CAGGGAGATAGGGCTCT
Found at i:2863 original size:126 final size:126
Alignment explanation
Indices: 2705--2966 Score: 393
Period size: 126 Copynumber: 2.1 Consensus size: 126
2695 ACTGCAACTT
* * *
2705 CAGGGAGATAAGATTTGCCATCATTAACCTATTCCACTACTGTCCAGGGAGATAGGATTCACAAT
1 CAGGGAGATAACATTTGCAATCATTAACCTATTCCACTACTGACCAGGGAGATAGGATTCACAAT
* * * *
2770 CTTTAACCTATTCCACTGCTGACCAGGGAGATAGGGCTCTTTAATCTATTCCACTGCTGCC
66 CTTTAACCTATTCCACGGCTAACCAGAGAGATAGGGCTCTTTAATCTATTCCACTGCTGAC
* *
2831 CAGGGAGATAACATTCT-CAATC-TTCAACCTATTCCACTGCTGACTAGGGAGATAGGATTCACA
1 CAGGGAGATAACATT-TGCAATCATT-AACCTATTCCACTACTGACCAGGGAGATAGGATTCACA
*
2894 ATCTTTAACCTCTTCCACGGCTAACCAGAGAGATAGGGCTCTTTAATCTATTCCACTGCTGAC
64 ATCTTTAACCTATTCCACGGCTAACCAGAGAGATAGGGCTCTTTAATCTATTCCACTGCTGAC
*
2957 CAAGGAGATA
1 CAGGGAGATA
2967 GGGTTAGGGT
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
125 2 0.02
126 120 0.98
127 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (126 bp):
CAGGGAGATAACATTTGCAATCATTAACCTATTCCACTACTGACCAGGGAGATAGGATTCACAAT
CTTTAACCTATTCCACGGCTAACCAGAGAGATAGGGCTCTTTAATCTATTCCACTGCTGAC
Found at i:3096 original size:88 final size:88
Alignment explanation
Indices: 2979--3378 Score: 683
Period size: 88 Copynumber: 4.5 Consensus size: 88
2969 GTTAGGGTCA
* * *
2979 TCGATCTACTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
3044 TCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
3067 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAT
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* *
3132 CCAGGGAAGCAAGGCTGGTGTTT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
3155 TCGATCTGCTTCACTGTCGGTGCAGGAAAGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
3220 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
3243 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
3308 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
3331 TCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATCTGCTATTTTTA
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
3379 CCCATCTGTT
Statistics
Matches: 294, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 294 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:3098 original size:44 final size:44
Alignment explanation
Indices: 2979--3364 Score: 190
Period size: 44 Copynumber: 8.8 Consensus size: 44
2969 GTTAGGGTCA
* * * * * *
2979 TCGATCTACTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTT
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG-GCTGGTGTTT
** * * * * *
3024 TTAACCTGCTCCGCTGT-AACT-CAGGGAGGCAAGGCTGGTGTCT
1 TCGATCTGCTTCGCTGTCGA-TGCAGGAAGGCAAGGCTGGTGTTT
* * * *
3067 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTT
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG-GCTGGTGTTT
** * * * *
3112 TTAACCTGCTCCGCTG-CAATCCAGGGAA-GCAAGGCTGGTGTTT
1 TCGATCTGCTTCGCTGTCGATGCA-GGAAGGCAAGGCTGGTGTTT
* * * * * * *
3155 TCGATCTGCTTCACTGTCGGTGCAGGAAAGTAAGATCTGCTATTT
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG-GCTGGTGTTT
** * * * ** * *
3200 TTAACCTGCTCCGCTG-CAACCCAGGGAGGCAAGGCTGGTGTCT
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGGCTGGTGTTT
* * * * *
3243 TCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTT
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG-GCTGGTGTTT
** * * * ** * *
3288 TTAACCTGCTCCGCTG-CAACCCAGGGAGGCAAGGCTGGTGTCT
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGGCTGGTGTTT
*
3331 TCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAG
1 TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAG
3365 ATCTGCTATT
Statistics
Matches: 231, Mismatches: 99, Indels: 23
0.65 0.28 0.07
Matches are distributed among these distances:
43 77 0.33
44 85 0.37
45 69 0.30
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.27
Consensus pattern (44 bp):
TCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGGCTGGTGTTT
Found at i:5282 original size:63 final size:63
Alignment explanation
Indices: 5204--5330 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
5194 TTCTTTGTAG
5204 AGTAAGATCTGTTTCTCGACTTGTTCTACCATCCTTAACAAGTCCGGAAATAGGCTACAATCT
1 AGTAAGATCTGTTTCTCGACTTGTTCTACCATCCTTAACAAGTCCGGAAATAGGCTACAATCT
5267 AGTAAGATCTGTTTCTCGACTTGTTCTACCATCCTTAACAAGTCCGGAAATAGGCTACAATCT
1 AGTAAGATCTGTTTCTCGACTTGTTCTACCATCCTTAACAAGTCCGGAAATAGGCTACAATCT
5330 A
1 A
5331 TGTCATCTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (63 bp):
AGTAAGATCTGTTTCTCGACTTGTTCTACCATCCTTAACAAGTCCGGAAATAGGCTACAATCT
Done.