Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_247 ID=scaffold_247-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: 9099
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.32
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:295 original size:113 final size:115
Alignment explanation
Indices: 89--297 Score: 316
Period size: 113 Copynumber: 1.8 Consensus size: 115
79 TTATAATTTT
* * * * ***
89 TTTATTTTTTTCGGCGTTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGATATTATTT
1 TTTATTTTTTGCGGCGTTTGTATAGAAAACACCGCTATTGCTTATCTTTTGCGAAAATATTATTT
154 CATTTTCAACAAAATGACGCCGTTTTGCTATTTTGTTTTCTATAAATTGA
66 CATTTTCAACAAAATGACGCCGTTTTGCTATTTTGTTTTCTATAAATTGA
204 TTTA-TTTTTGCGGCGTTTGTATAGAAAACACCGCTATTTG-TTATCTTTTGC-AAAATATTATT
1 TTTATTTTTTGCGGCGTTTGTATAGAAAACACCGCTA-TTGCTTATCTTTTGCGAAAATATTATT
*
266 TCATTTTGAACAAAATGACGCCGTTTTGCTAT
65 TCATTTTCAACAAAATGACGCCGTTTTGCTAT
298 GCTAATTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
113 39 0.46
114 39 0.46
115 7 0.08
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.46
Consensus pattern (115 bp):
TTTATTTTTTGCGGCGTTTGTATAGAAAACACCGCTATTGCTTATCTTTTGCGAAAATATTATTT
CATTTTCAACAAAATGACGCCGTTTTGCTATTTTGTTTTCTATAAATTGA
Found at i:606 original size:15 final size:14
Alignment explanation
Indices: 583--660 Score: 54
Period size: 14 Copynumber: 5.4 Consensus size: 14
573 TTAACTCGAC
583 CCTTGAATCCCTAAA
1 CCTT-AATCCCTAAA
598 CCTTAAATCCCT-AA
1 CCTT-AATCCCTAAA
*
612 CTCTTAACCCCT-AA
1 C-CTTAATCCCTAAA
* *
626 CGTCTAACCCCTAAA
1 CCT-TAATCCCTAAA
*
641 CCTTGAATCCC-AAC
1 CCTT-AATCCCTAAA
655 CCTTAA
1 CCTTAA
661 ACCATAGTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 3 0.06
14 27 0.51
15 23 0.43
ACGTcount: A:0.32, C:0.38, G:0.04, T:0.26
Consensus pattern (14 bp):
CCTTAATCCCTAAA
Found at i:987 original size:14 final size:15
Alignment explanation
Indices: 945--1012 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
935 ACCCCTGAAT
*
945 CCCTAAA-CTCTAAAT
1 CCCTAAACCTCT-AAC
960 CCCT-AA-CTCTTAAC
1 CCCTAAACCTC-TAAC
*
974 CCC-AAACGTCTAAC
1 CCCTAAACCTCTAAC
*
988 CCCTAACCCTCTAAC
1 CCCTAAACCTCTAAC
1003 CCCTAAACCT
1 CCCTAAACCT
1013 TAAATCTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
14 19 0.43
15 25 0.57
ACGTcount: A:0.32, C:0.44, G:0.01, T:0.22
Consensus pattern (15 bp):
CCCTAAACCTCTAAC
Found at i:1048 original size:14 final size:14
Alignment explanation
Indices: 1031--1057 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1021 AACCCTTAAA
1031 CCATAATCCCTAAT
1 CCATAATCCCTAAT
1045 CCATAATCCCTAA
1 CCATAATCCCTAA
1058 ACCCATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:1434 original size:115 final size:114
Alignment explanation
Indices: 1153--2054 Score: 1100
Period size: 115 Copynumber: 7.9 Consensus size: 114
1143 TGTTTTTTTT
* * * *
1153 GCGGCGCTTTCCTAAAAAACGCCGCTAAATCCCCCAAAAGCTCAGAAAACGGCGTCGTTGGTCTT
1 GCGGCGCTTTCCTAAAAAACGCCACTAAAT-CCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* * *
1218 ATGTCTTTTTGC-GCGCTTTCTCACAAACGCCGCTAAAGCCCTGAGCATTA
65 A-GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * *
1268 GCAGTGC-TTCCTAAAAAACGCCACTAAATCCGCAAAAGCTCAGAAAACGGCGTCTTTGGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
*
1332 GTTTATTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
66 GTTT-TTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
** * **
1382 GCGGCGCTTTATTAAGAAACGCCACTAAATCTACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * * *
1447 TGTCTTTTTGCGGCGCTTTCTCACAAACGCCGCTAAATCCCTGAGCATTA
66 -GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * *
1497 GCGGCGC-TTCATAAAAAACGCCACTGAATCCGCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* *
1561 GTTTATTTTGCGGCGCTTCCTCAAAAACGCCGTTAAAGCCCTCAGCATTA
66 GTTT-TTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * ** * **
1611 GCGACGCTGTATTAAGAAACGCCACTAAATCTACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * *
1676 GTTTATTTTGTGGCGCTTTATCAAAAACGCCG-TAAAAGCCCTGAGCATTA
66 GTTT-TTTTGCGGCGCTTTCTCAAAAACGCCGCT-AAAGCCCTCAGCATTA
* * * * * *
1726 GCGGCGC-TTCCTGAAAAATGCCACTAAATTCGTGAATGCTCAGAAAACGGCGTCGTTAGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* *
1790 GTTTATTTTGCGGTGC-TTCATCAAAAACGCCGCTAAAGCCCTCAGTATTA
66 GTTT-TTTTGCGGCGCTTTC-TCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * **
1840 GCGGCGTTTTCCTAAAAAACG-CAGCTAAGTCCCCGAAAGCTCAGAAAACGGCACCGTTGGGCTT
1 GCGGCGCTTTCCTAAAAAACGCCA-CTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* * * * *
1904 ATGTCTTTTTGCGGCGCTTTCTCAAAATCGCCGCTAAAAGTCCTAACCATTA
65 A-GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT-AAAGCCCTCAGCATTA
* * * *
1956 GCGACGCTTT-CTAAAAAACGCCACTAAATCTGCGAAAGCTCAGAATACGACGTCGTTGGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* *
2020 GTTTTTTTGCGGCGCTTTCTGAAAAACGCTGCTAA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
2055 TGCTTATTTT
Statistics
Matches: 673, Mismatches: 99, Indels: 32
0.84 0.12 0.04
Matches are distributed among these distances:
112 3 0.00
113 45 0.07
114 280 0.42
115 314 0.47
116 31 0.05
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCCTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
Found at i:1558 original size:229 final size:230
Alignment explanation
Indices: 1153--2054 Score: 1244
Period size: 229 Copynumber: 3.9 Consensus size: 230
1143 TGTTTTTTTT
* * * * *
1153 GCGGCGCTTTCCTAAAAAACGCCGCTAAATCCCCCAAAAGCTCAGAAAACGGCGTCGTTGGTCTT
1 GCGGCGCTTTACTAAAAAACGCCACTAAAT-CCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* *
1218 ATGTCTTTTTGC-GCGCTTTCTCACAAACGCCGCT-AAAGCCCTGAGCATTAGCAGTGCTTCCTA
65 ATGTCTTTTTGCGGCGCTTTCTCACAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTCCTA
*
1281 AAAAACGCCACTAAATCCGCAAAAGCTCAGAAAACGGCGTCTTTGGGCTTAGTTTATTTTGCGGC
130 AAAAACGCCACTAAATCCGCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGC
1346 GCTTCCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
195 GCTTCCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * *
1382 GCGGCGCTTTATTAAGAAACGCCACTAAATCTACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTACTAAAAAACGCCACTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* *
1447 TGTCTTTTTGCGGCGCTTTCTCACAAACGCCGCT-AAATCCCTGAGCATTAGCGGCGCTTCATAA
66 TGTCTTTTTGCGGCGCTTTCTCACAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTCCTAA
*
1511 AAAACGCCACTGAATCCGCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGCG
131 AAAACGCCACTAAATCCGCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGCG
*
1576 CTTCCTCAAAAACGCCGTTAAAGCCCTCAGCATTA
196 CTTCCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * * *
1611 GCGACGCTGTATTAAGAAACGCCACTAAATCTACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTACTAAAAAACGCCACTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * * * *
1676 -GTTTATTTTGTGGCGCTTTATCAAAAACGCCG-TAAAAGCCCTGAGCATTAGCGGCGCTTCCTG
66 TGTCT-TTTTGCGGCGCTTTCTCACAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTCCTA
* * ** * * *
1739 AAAAATGCCACTAAATTCGTGAATGCTCAGAAAACGGCGTCGTTAGGCTTAGTTTATTTTGCGGT
130 AAAAACGCCACTAAATCCGCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGC
* *
1804 GCTTCATCAAAAACGCCGCTAAAGCCCTCAGTATTA
195 GCTTCCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * * **
1840 GCGGCGTTTTCCTAAAAAACG-CAGCTAAGTCCCCGAAAGCTCAGAAAACGGCACCGTTGGGCTT
1 GCGGCGCTTTACTAAAAAACGCCA-CTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* * * * *
1904 ATGTCTTTTTGCGGCGCTTTCTCA-AAATCGCCGCTAAAAGTCCTAACCATTAGCGACGCTTTCT
65 ATGTCTTTTTGCGGCGCTTTCTCACAAA-CGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTCCT
* * * *
1968 AAAAAACGCCACTAAATCTGCGAAAGCTCAGAATACGACGTCGTTGGGCTTAGTTT-TTTTGCGG
129 AAAAAACGCCACTAAATCCGCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGG
* * *
2032 CGCTTTCTGAAAAACGCTGCTAA
194 CGCTTCCTCAAAAACGCCGCTAA
2055 TGCTTATTTT
Statistics
Matches: 598, Mismatches: 68, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
228 51 0.09
229 472 0.79
230 75 0.13
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (230 bp):
GCGGCGCTTTACTAAAAAACGCCACTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
TGTCTTTTTGCGGCGCTTTCTCACAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTCCTAA
AAAACGCCACTAAATCCGCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGCG
CTTCCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
Done.