Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1071 ID=scaffold_1071-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: 1890
ACGTcount: A:0.18, C:0.11, G:0.14, T:0.17
Warning! 768 characters in sequence are not A, C, G, or T
Found at i:308 original size:135 final size:132
Alignment explanation
Indices: 1--311 Score: 419
Period size: 132 Copynumber: 2.3 Consensus size: 132
* * *
1 GTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGGCAGCAGTGTAATAGATTGAAG
1 GTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAG
* * *
66 ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTA
66 ATTACAAATCTTATCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTA
131 AG
131 AG
*
133 GTTACAGTGGAGTACATTGAAA-CCAGTAATTCTATCTCCCTGGGTAGCAGTGGAATAGATTAAA
1 GTTACAGTGGAGTACATT-AAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAA
* * * *
197 GATTATAAATCTTATCTCCGTAAACAGTAGTGGAGCAGATCAAGGTTGATGGCGGATTTTACCTC
65 GATTACAAATCTTATCTCCCTAAACAGTAGTGGAGCAGATCAA---AGATGGCAGATTTTACCTC
*
262 CCTGAG
127 CCTAAG
* * * *
268 GTTACAGTAGAGTACA-AATAAGTCAGTAAATCTATCTCCCTGGG
1 GTTACAGTGGAGTACATTA-AAGCCAGTAATTCTATCTCCCTGGG
312 NNNNNNNNNN
Statistics
Matches: 157, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
132 95 0.61
133 4 0.03
134 2 0.01
135 56 0.36
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (132 bp):
GTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAG
ATTACAAATCTTATCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTA
AG
Found at i:1162 original size:44 final size:43
Alignment explanation
Indices: 1085--1167 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 43
1075 NNNNNCCAAT
* * * *
1085 AAATCTATCTCCCTAGGCAGCAGTGTAGTAGATCGAAGACTAC
1 AAATCTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGACTAC
*
1128 AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
1 AAATC-TATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGA
1168 TGGTAGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 5 0.15
44 29 0.85
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (43 bp):
AAATCTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGACTAC
Found at i:1329 original size:132 final size:132
Alignment explanation
Indices: 1088--1890 Score: 1146
Period size: 132 Copynumber: 6.1 Consensus size: 132
1078 NNCCAATAAA
* * * * *
1088 TCTATCTCCCTAGGCAGCAGTGTAGTAGATCGAAGACTACAAATCTTATCTCCCTAAGCAGTAGT
1 TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
* * * *
1153 GGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTACAGTGCAATACATTGAAGCCAGTA
66 GGAGCAGATCAAGGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
1218 AT
131 AT
* * * *
1220 TCTGTCTCCCTTGGCAGCAGTGGAATAGATTGAAGATTGCAGATCCTATCTCCCTAAGCAGTAGT
1 TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
* * * *
1285 GGAGCAGATCAAGGATGGTAGATTTTACCTCCATGAGGTTACAGTGGAGTACAATGAAGGCAATA
66 GGAGCAGATCAAGGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
1350 AT
131 AT
1352 TCTATCTCCC-AGGCCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
1 TCTATCTCCCTAGG-CAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
* *
1416 TGGAGCAGATCAAGGAT-G-ACGAATTTTACCTCCTTGAGGTTAAAGTGGAGTACATTGAAGCCA
65 TGGAGCAGATCAAGGATGGTA-G-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
1479 GTAAT
128 GTAAT
* * * *
1484 TCTATCTACCTAGGCAGCAGTGGAATAGATTGAAGATTACAAATCTTATCTCCTTAAGTAGTAGT
1 TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
* * * * *
1549 GGAGCAGATCAATGATGGGAGATTTTACCTGCCTGATGTGACAGTGGAGTACATTGAAGCCAGTA
66 GGAGCAGATCAAGGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
1614 AT
131 AT
* * *
1616 TCTATCTCCCTGGGTAGCAGTGCAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTA-T
1 TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
* *
1680 GGAGCAGATCAAGGATGATAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGACAGTA
66 GGAGCAGATCAAGGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
1745 AT
131 AT
* * * *
1747 TCTATCTACCTGGGTAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGT
1 TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
** ***
1812 GGAGCAGATCAAGGTTGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGTTT
66 GGAGCAGATCAA-G--GATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
1877 GTAAT
128 GTAAT
1882 TCTATCTCC
1 TCTATCTCC
Statistics
Matches: 601, Mismatches: 60, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
130 1 0.00
131 125 0.21
132 412 0.69
133 6 0.01
134 1 0.00
135 56 0.09
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (132 bp):
TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCAAGGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
AT
Done.