Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_394 ID=scaffold_394-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: 7767
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.31
Warning! 225 characters in sequence are not A, C, G, or T
Found at i:594 original size:26 final size:25
Alignment explanation
Indices: 563--628 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
553 TATAAAATAT
563 AAAAATATATATATGT-ACATATAAGA
1 AAAAATATATATATGTGA-ATA-AAGA
* *
589 AAAAATATATGTATGTGAATAAATA
1 AAAAATATATATATGTGAATAAAGA
614 AATAAATATATATAT
1 AA-AAATATATATAT
629 AAAAATATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.14
26 29 0.83
27 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAAATATATATATGTGAATAAAGA
Found at i:2492 original size:89 final size:89
Alignment explanation
Indices: 2367--2572 Score: 204
Period size: 89 Copynumber: 2.3 Consensus size: 89
2357 ATCCTCAATT
** * * * ** * *
2367 TGCTACACTGCAACTTCAGAGAGATAAGGTTTGCTATTTTTAGTTTGCTCCACTTCAACTTCAGG
1 TGCTACACTGCAACTTCAGAGAGATAAGACTCGCTATCTTCAACTTGCCCCACTGCAACTTCAGG
2432 GAGAT-AGGATTAGTAGCTTCAGTC
66 GAGATAAGG-TTAGTAGCTTCAGTC
* *
2456 TGCTCCACTGTAACTTCA-ATGAGATAAGACTCGCTATCTTCAACTTGCCCCACTGCAACTTCAG
1 TGCTACACTGCAACTTCAGA-GAGATAAGACTCGCTATCTTCAACTTGCCCCACTGCAACTTCAG
* * **
2520 GGGGATAAGGTTAGT-GATTTCAACC
65 GGAGATAAGGTTAGTAG-CTTCAGTC
*
2545 TGCT-CTACTACAACTTCAGAGAGATAAG
1 TGCTAC-ACTGCAACTTCAGAGAGATAAG
2573 GTTTGATATG
Statistics
Matches: 95, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
88 3 0.03
89 88 0.93
90 4 0.04
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (89 bp):
TGCTACACTGCAACTTCAGAGAGATAAGACTCGCTATCTTCAACTTGCCCCACTGCAACTTCAGG
GAGATAAGGTTAGTAGCTTCAGTC
Found at i:2686 original size:50 final size:48
Alignment explanation
Indices: 2626--3196 Score: 327
Period size: 50 Copynumber: 11.4 Consensus size: 48
2616 CGGTAATTTA
*
2626 TAGCTTCAATCTTCTCCACTGCAGCTTCAAGGAAGTAAGATTCGCTGTTG
1 TAGCTTCAATCTT-TCCACTGCA-CTTCAGGGAAGTAAGATTCGCTGTTG
* * ** *
2676 TAGCTTCAATCTGTTCCATTACACCACTAGGGAAGTAAGATTCGTTGTTG
1 TAGCTTCAATCT-TTCCACTGCACTTC-AGGGAAGTAAGATTCGCTGTTG
** * * * **
2726 TAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTACTGTTG
1 TAGCTTCAATC-TTTCCACTGCACT-TCAGGGAAGTAAGATTCGCTGTTG
* * ** * *
2776 TAGCTTCAATCTGTTCTACTGTACCGCCAGAGAAGTAAGATTCGCCGTTG
1 TAGCTTCAATCT-TTCCACTGCA-CTTCAGGGAAGTAAGATTCGCTGTTG
* ** * * ** *
2826 TGGCTTCAATCTTTTTAATTGCAGTGTTGGGGAAGCAAGATTCG-TCGTTG
1 TAGCTTCAATC-TTTCCACTGCACT-TCAGGGAAGTAAGATTCGCT-GTTG
* ** *
2876 TAGCTTCAATATGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
1 TAGCTTCAATCT-TTCCACTGCA-CTTCAGGGAAGTAAGATTCGCTGTTG
* * ** * * * * * *
2926 TGGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTG
1 TAGCTTCAATC-TTTCCACTGCACT-TCAGGGAAGTAAGATTCGCTGTTG
* * * * *
2976 CAACTTCAATTTGTTCCACTGTACTGCCAGGGAAGTAAGATTCGCTGTTG
1 TAGCTTCAATCT-TTCCACTGCACT-TCAGGGAAGTAAGATTCGCTGTTG
* * * ** * *
3026 TGGCCTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG
1 TAGCTTCAATCT-TTCCACTGCA-CTTCAGGGAAGTAAGATTCGCTGTTG
* * * * *
3076 TAGCTTTAATCTAATT-AACTGCAATATTAGGGAAGTAAGATTCACTGTTG
1 TAGCTTCAATCT--TTCCACTGCACT-TCAGGGAAGTAAGATTCGCTGTTG
* ** *
3126 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTG
1 TAGCTTCAATCT-TTCCACTGCA-CTTCAGGGAAGTAAGATTCGCTGTTG
* *
3176 TAGTTTTAATCTATTCCACTG
1 TAGCTTCAATCT-TTCCACTG
3197 TAACACCAAA
Statistics
Matches: 384, Mismatches: 117, Indels: 40
0.71 0.22 0.07
Matches are distributed among these distances:
49 7 0.02
50 370 0.96
51 7 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (48 bp):
TAGCTTCAATCTTTCCACTGCACTTCAGGGAAGTAAGATTCGCTGTTG
Found at i:2926 original size:150 final size:150
Alignment explanation
Indices: 2704--3196 Score: 400
Period size: 150 Copynumber: 3.3 Consensus size: 150
2694 TTACACCACT
* * ** ** * * * *
2704 AGGGAAGTAAGATTCGTTGTTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTT
1 AGGGAAGTAAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTC
* * * * * * ***
2769 ACTGTTGTAGCTTCAATCTGTTCT-ACTGTACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
66 ACCGTTGTAGCTTTAATCT-TTCTAACTGCAACGCCAGAGAAGCAAGATTCACCGTTGCAACTTC
* * * **
2833 AATCTT-TTTAATTGCAGTGTT
130 AAT-TTGTTCAACTGCACTGCC
* * *
2854 GGGGAAGCAAGATTCGTCGTTGTAGCTTCAATATGTTCCACTGCACCGCCAGGGAAGTAAGATTC
1 AGGGAAGTAAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTC
* * * * * * * *
2919 GCCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGCAACTTCA
66 ACCGTTGTAGCTTTAATCTTTCTAACTGCAACGCCAGAGAAGCAAGATTCACCGTTGCAACTTCA
* *
2984 ATTTGTTCCACTGTACTGCC
131 ATTTGTTCAACTGCACTGCC
* * *
3004 AGGGAAGTAAGATTCG-CTGTTGTGGCCTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATT
1 AGGGAAGTAAGATTCGTC-GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATT
* **** * * * * *
3068 CACCGTTGTAGCTTTAATCTAAT-TAACTGCAATATTAGGGAAGTAAGATTCACTGTTGTAGCTT
65 CACCGTTGTAGCTTTAATCT-TTCTAACTGCAACGCCAGAGAAGCAAGATTCACCGTTGCAACTT
* * * *
3132 CAATCTGTTCCACTACACCGCC
129 CAATTTGTTCAACTGCACTGCC
* * * *
3154 AGGGAAGTAAGATTCGCCGTTGTAGTTTTAATCTATTCCACTG
1 AGGGAAGTAAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTG
3197 TAACACCAAA
Statistics
Matches: 274, Mismatches: 64, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
149 6 0.02
150 266 0.97
151 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (150 bp):
AGGGAAGTAAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTC
ACCGTTGTAGCTTTAATCTTTCTAACTGCAACGCCAGAGAAGCAAGATTCACCGTTGCAACTTCA
ATTTGTTCAACTGCACTGCC
Found at i:2985 original size:200 final size:200
Alignment explanation
Indices: 2656--3037 Score: 559
Period size: 200 Copynumber: 1.9 Consensus size: 200
2646 GCAGCTTCAA
* * * * *
2656 GGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCATTACACCACTAGGGAAGTAAGATTCGT
1 GGAAGCAAGATTCGCTGTTGTAGCTTCAATATGTTCCACTACACCACCAGGGAAGTAAGATTCGC
* * * * *
2721 TGTTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTACTGTTGTAGCTTCAAT
66 CGTTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGCAACTTCAAT
* *
2786 CTGTTCTACTGTACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAGT
131 CTGTTCCACTGTACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAGT
2851 GTTGG
196 GTTGG
* *
2856 GGAAGCAAGATTCG-TCGTTGTAGCTTCAATATGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
1 GGAAGCAAGATTCGCT-GTTGTAGCTTCAATATGTTCCACTACACCACCAGGGAAGTAAGATTCG
* * *
2920 CCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGCAACTTCAA
65 CCGTTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGCAACTTCAA
* * * *
2985 TTTGTTCCACTGTACTGCCAGGGAAGTAAGATTCGCTGTTGTGGCCTCAATCT
130 TCTGTTCCACTGTACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCCTCAATCT
3038 GCTCCACTGC
Statistics
Matches: 160, Mismatches: 21, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
199 1 0.01
200 159 0.99
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (200 bp):
GGAAGCAAGATTCGCTGTTGTAGCTTCAATATGTTCCACTACACCACCAGGGAAGTAAGATTCGC
CGTTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGCAACTTCAAT
CTGTTCCACTGTACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAGT
GTTGG
Found at i:3059 original size:100 final size:100
Alignment explanation
Indices: 2656--3081 Score: 492
Period size: 100 Copynumber: 4.3 Consensus size: 100
2646 GCAGCTTCAA
* * * * * * * * *
2656 GGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCATTACACCACTAGGGAAGTAAGATTCGT
1 GGAAGCAAGATTCACCGTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGC
*
2721 TGTTGTAGCTTCAATCTTTTTAACTGCAATGTCGG
66 TGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGG
* * * * * *
2756 GGAAGCAAGATTTACTGTTGTAGCTTCAATCTGTTCTACTGTACCGCCAGAGAAGTAAGATTCGC
1 GGAAGCAAGATTCACCGTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGC
* * * *
2821 CGTTGTGGCTTCAATCTTTTTAATTGCAGTGTTGG
66 TGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGG
** *
2856 GGAAGCAAGATTCGTCGTTGTAGCTTCAATATGTTCCACTGCACCGCCAGGGAAGTAAGATTCGC
1 GGAAGCAAGATTCACCGTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGC
* * *
2921 CGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGG
66 TGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGG
* * * *
2956 GGAAGCAAGATTCACCGTTGCAACTTCAATTTGTTCCACTGTACTGCCAGGGAAGTAAGATTCGC
1 GGAAGCAAGATTCACCGTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGC
* ** ** ** * *
3021 TGTTGTGGCCTCAATCTGCTCCACTGCACCGCCAG
66 TGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGG
*
3056 GGAAGTAAGATTCACCGTTGTAGCTT
1 GGAAGCAAGATTCACCGTTGTAGCTT
3082 TAATCTAATT
Statistics
Matches: 277, Mismatches: 49, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 277 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (100 bp):
GGAAGCAAGATTCACCGTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGC
TGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGG
Found at i:3377 original size:87 final size:87
Alignment explanation
Indices: 3268--3506 Score: 352
Period size: 87 Copynumber: 2.7 Consensus size: 87
3258 TTATTCCACA
* ** *
3268 TCTTCAGTCTTAACGCTAGGGAGATAAGATTCGCTATTTTCAGCTTTAATCTGCTCCGCTACAAT
1 TCTTCAGTCTTAACGCCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCGCTACAAC
3333 GCCAGGGAAAGAAGACTCGCAG
66 GCCAGGGAAAGAAGACTCGCAG
* * * *
3355 TCTTCGGTCTTAACGCCAGGGAGATAAGATTCTCTACCTTCAACTTTAATCTGCTTCGCTACAAC
1 TCTTCAGTCTTAACGCCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCGCTACAAC
*
3420 GCCAGGGAAAGAAGACTCGCTG
66 GCCAGGGAAAGAAGACTCGCAG
* * * * *
3442 TCTTCAGTCTTAACGTCAGGGAGATAAGATTCGTTGCCTTCAGTTTTAATCTGCTCCGTTACAAC
1 TCTTCAGTCTTAACGCCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCGCTACAAC
3507 TTTAAACATT
Statistics
Matches: 134, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 134 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (87 bp):
TCTTCAGTCTTAACGCCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCGCTACAAC
GCCAGGGAAAGAAGACTCGCAG
Done.