Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_227 ID=scaffold_227-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: 9754
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.27
Warning! 575 characters in sequence are not A, C, G, or T
Found at i:1674 original size:18 final size:18
Alignment explanation
Indices: 1642--1676 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1632 CTTTTATAAA
* *
1642 TACATACATATATTTTTG
1 TACATACAAACATTTTTG
1660 TACATACAAACATTTTT
1 TACATACAAACATTTTT
1677 ATATATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
TACATACAAACATTTTTG
Found at i:3806 original size:19 final size:20
Alignment explanation
Indices: 3762--3806 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
3752 AGCGTCTCTT
*
3762 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
3781 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
3800 TATGCAT
1 TATGCAT
3807 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:6661 original size:45 final size:46
Alignment explanation
Indices: 6551--6683 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 46
6541 CTAAAAGGTG
*
6551 GGACCAAGGTGAAAGCCTGCAAAGGGCGCTTTGAGTCAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
* * * *
6597 GGGCCAAGGTTAAAGCCTACAAAGGGCTCTTTGGGTCAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
* * * *
6643 -GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAA
6684 GGAAAAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 6 0.08
45 27 0.36
46 41 0.55
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (46 bp):
GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
Found at i:8123 original size:50 final size:50
Alignment explanation
Indices: 8000--8321 Score: 202
Period size: 50 Copynumber: 6.4 Consensus size: 50
7990 GGTTGACAAG
*** * *
8000 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCA-A-TGCAGT
1 TAAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCT-G-ATATTGCAAT
** * * * *
8050 GGAATAGATTAAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
1 TAAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGATATTGCAAT
* * *** * * * **
8100 TAAAAATATTGAAGCAACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGA-TATTGCAAT
** * * * * *
8150 GGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATATTGCCAT
1 TAAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGATATTGCAAT
* *** * * * *
8200 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTT-CCTTAGCAGTGCAGT
1 TAAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGA-TATTGCAAT
** * * * *
8250 GGAATAGATTAAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
1 TAAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGATATTGCAAT
8300 TAAAAAGATTGAAGCCACAACG
1 TAAAAAGATTGAAGCCACAACG
8322 ACAGATCTTA
Statistics
Matches: 191, Mismatches: 75, Indels: 12
0.69 0.27 0.04
Matches are distributed among these distances:
48 1 0.01
49 10 0.05
50 172 0.90
51 8 0.04
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (50 bp):
TAAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGATATTGCAAT
Found at i:8413 original size:100 final size:100
Alignment explanation
Indices: 8000--8397 Score: 600
Period size: 100 Copynumber: 4.0 Consensus size: 100
7990 GGTTGACAAG
* * *
8000 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAATGCAGTGGAATAGATTAAAGC
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGC
*
8065 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
66 TACGACGGCAGATCTGGTTTCCCTGATATTGCAAT
* * * * *
8100 TAAAAATATTGAAGCAACAACGGCGGATCTTACTTCCTTAGCAGTGCAGCGGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGC
*
8165 TACGACGGCAGATCTGGTTTCCCTGATATTGCCAT
66 TACGACGGCAGATCTGGTTTCCCTGATATTGCAAT
*
8200 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTAAAGC
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGC
*
8265 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
66 TACGACGGCAGATCTGGTTTCCCTGATATTGCAAT
* * * * *
8300 TAAAAAGATTGAAGCCACAACGACAGATCTTACTT-CTCTAACGGTGCGGTGGAACAGATTGAAG
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCT-TAGCAGTGCAGTGGAACAGATTAAAG
* * *
8364 CCACGACGGCAGATCTGGTTTCCCCGACATTGCA
65 CTACGACGGCAGATCTGGTTTCCCTGATATTGCA
8398 GTTGAGCAAA
Statistics
Matches: 271, Mismatches: 26, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
99 2 0.01
100 269 0.99
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (100 bp):
TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGC
TACGACGGCAGATCTGGTTTCCCTGATATTGCAAT
Found at i:8413 original size:200 final size:200
Alignment explanation
Indices: 8000--8396 Score: 661
Period size: 200 Copynumber: 2.0 Consensus size: 200
7990 GGTTGACAAG
*
8000 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAATGCAGTGGAATAGATTAAAGC
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAATGCAGTGGAATAGATTAAAGC
* * *
8065 TACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAATATTGAAGCAACAACGGCGGATCT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCAACAACGACAGATCT
* * * *
8130 TACTTCCTTAGCAGTGCAGCGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATATT
131 TACTTCCTTAACAGTGCAGCGGAACAGATTGAAGCCACGACGGCAGATCTGGTTTCCCCGACATT
8195 GCCAT
196 GCCAT
*
8200 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTAAAGC
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAATGCAGTGGAATAGATTAAAGC
*
8265 TACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGACAGATCT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCAACAACGACAGATCT
* * *
8330 TACTT-CTCTAACGGTGCGGTGGAACAGATTGAAGCCACGACGGCAGATCTGGTTTCCCCGACAT
131 TACTTCCT-TAACAGTGCAGCGGAACAGATTGAAGCCACGACGGCAGATCTGGTTTCCCCGACAT
8394 TGC
195 TGC
8397 AGTTGAGCAA
Statistics
Matches: 183, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
199 2 0.01
200 181 0.99
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (200 bp):
TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAATGCAGTGGAATAGATTAAAGC
TACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCAACAACGACAGATCT
TACTTCCTTAACAGTGCAGCGGAACAGATTGAAGCCACGACGGCAGATCTGGTTTCCCCGACATT
GCCAT
Found at i:8719 original size:89 final size:89
Alignment explanation
Indices: 8550--8723 Score: 197
Period size: 89 Copynumber: 2.0 Consensus size: 89
8540 TTGAAAAAGC
* * * *
8550 AGATCTTGTCCTCATATATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTCCCCATACTG
1 AGATCTTATCCTCATATACTGGCGTGAAGTAGATCAAAGAAAGCAGATCCTGTCTCCCCATACTG
* * *
8615 GTGGTGGAGTAGATCGAATAAAAT
66 GTAGCGAAGTAGATCGAATAAAAT
* * * * * * *
8639 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGTAGGTCCTGTCTTCCTATA-TC
1 AGATCTTATCCTCATATACTGGCGTGAAGTAGATCAAAGAAAGCAGATCCTGTCTCCCCATACT-
*
8703 GGTAGCGAAGTGGATCGAATA
65 GGTAGCGAAGTAGATCGAATA
8724 TACATATTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
88 1 0.01
89 68 0.99
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (89 bp):
AGATCTTATCCTCATATACTGGCGTGAAGTAGATCAAAGAAAGCAGATCCTGTCTCCCCATACTG
GTAGCGAAGTAGATCGAATAAAAT
Found at i:8780 original size:44 final size:44
Alignment explanation
Indices: 8573--8781 Score: 131
Period size: 44 Copynumber: 4.7 Consensus size: 44
8563 ATATATTGGC
* * * *
8573 GTGAAGTAGATCGAAGAAAGC-AGATCTTGTCTCCCCATACTGGTG
1 GTGAAGTAGATCGAATATA-CAAG-TCTTATCTTCCCATACTGGTG
* * *** *
8618 GTGGAGTAGATCGAATA-AAATAGATCTTATCTTCATGTACTGG-C
1 GTGAAGTAGATCGAATATACA-AG-TCTTATCTTCCCATACTGGTG
* * * * * * * *
8662 GTGAAGTAGATCAAAGATAGTAGGTCCTGTCTTCCTATA-TCGGTA
1 GTGAAGTAGATCGAATATA-CAAGTCTTATCTTCCCATACT-GGTG
* * *
8707 GCGAAGTGGATCGAATATACATA-TTTTATCTTCCCATACTGGTG
1 GTGAAGTAGATCGAATATACA-AGTCTTATCTTCCCATACTGGTG
8751 GTGAAGTAGATCGAATATACAAGTCTTATCT
1 GTGAAGTAGATCGAATATACAAGTCTTATCT
8782 CCCTGAAGTT
Statistics
Matches: 122, Mismatches: 33, Indels: 19
0.70 0.19 0.11
Matches are distributed among these distances:
43 2 0.02
44 69 0.57
45 50 0.41
46 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (44 bp):
GTGAAGTAGATCGAATATACAAGTCTTATCTTCCCATACTGGTG
Done.