Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_232 ID=scaffold_232-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: 10037
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.26
Warning! 893 characters in sequence are not A, C, G, or T
Found at i:315 original size:109 final size:110
Alignment explanation
Indices: 91--384 Score: 416
Period size: 108 Copynumber: 2.7 Consensus size: 110
81 TCAAAAAAGG
* * *
91 AAAATATTTCTAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAAT-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* * * * *
156 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATACCCTTCTA
*
202 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATG-CCTAAGGTGCTG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
266 GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATACCCCTTC-A
66 GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATA-CCCTTCTA
* * * *
311 AAAA-TTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAG-GAACGTGTCCTAAGGTGCTG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
374 GGTTTCGATTT
66 GGTGTCGATTT
385 CTCGTTTATC
Statistics
Matches: 167, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
107 5 0.03
108 59 0.35
109 50 0.30
110 48 0.29
111 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (110 bp):
AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATACCCTTCTA
Found at i:4236 original size:18 final size:18
Alignment explanation
Indices: 4227--4261 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4217 AAAAAGAAGA
4227 AAAAAGAAAAATAAAAAT
1 AAAAAGAAAAATAAAAAT
4245 AAAAAGAAAAATAAAAA
1 AAAAAGAAAAATAAAAA
4262 GGAGAGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAAAGAAAAATAAAAAT
Found at i:4242 original size:6 final size:6
Alignment explanation
Indices: 4227--4261 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4217 AAAAAGAAGA
* *
4227 AAAAAG AAAAAT AAAAAT AAAAAG AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
4262 GGAGAGGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.09
Consensus pattern (6 bp):
AAAAAT
Found at i:7570 original size:125 final size:125
Alignment explanation
Indices: 7346--7745 Score: 712
Period size: 125 Copynumber: 3.2 Consensus size: 125
7336 TCATATTCCC
*
7346 ACAACAGCGAATCTTACG-CCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTT
1 ACAACAGCGAATCTTACGCCCCAAGCAATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTT
7410 GTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACCTCGGTGAATCTTGATTAAAGCT
66 GTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACCTCGGTGAATCTTGATTAAAGCT
*
7470 ACGACAGCGAATCTTACGCCCCAAGCAATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTT
1 ACAACAGCGAATCTTACGCCCCAAGCAATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTT
* * *
7535 GTTTCTCCGACATTGTAGTTAAAAAAATTAAAGCCACATCGGTGAATCTTGATTAAAGCT
66 GTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACCTCGGTGAATCTTGATTAAAGCT
* * * *
7595 ACAACAGGGAATCTTATGCCCAAAACAATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTT
1 ACAACAGCGAATCTTACGCCCCAAGCAATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTT
7660 GTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACCTCGGTGAATCTTGATTAAAGCT
66 GTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACCTCGGTGAATCTTGATTAAAGCT
7720 ACAACAGCGAATCTTACGCCCCAAGC
1 ACAACAGCGAATCTTACGCCCCAAGC
7746 GANNNNNNNN
Statistics
Matches: 258, Mismatches: 17, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
124 17 0.07
125 241 0.93
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (125 bp):
ACAACAGCGAATCTTACGCCCCAAGCAATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTT
GTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACCTCGGTGAATCTTGATTAAAGCT
Found at i:7606 original size:25 final size:25
Alignment explanation
Indices: 7561--7609 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
7551 AGTTAAAAAA
*
7561 ATTAAAGCCACATCGGTGAATCTTG
1 ATTAAAGCCACAACGGTGAATCTTG
*
7586 ATTAAAGCTACAACAGG-GAATCTT
1 ATTAAAGCCACAAC-GGTGAATCTT
7610 ATGCCCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (25 bp):
ATTAAAGCCACAACGGTGAATCTTG
Found at i:8106 original size:25 final size:25
Alignment explanation
Indices: 8060--8109 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
8050 CAGTTAAAAA
* * *
8060 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
8085 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
8110 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:8213 original size:25 final size:25
Alignment explanation
Indices: 8185--8234 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
8175 CAGTTAAAAA
* *
8185 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGTGAATCTT
*
8210 GATTAAAGCTACAACAGTGAATCTT
1 GATTAAAGCCACAACAGTGAATCTT
8235 ACGCCTCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (25 bp):
GATTAAAGCCACAACAGTGAATCTT
Found at i:8356 original size:25 final size:25
Alignment explanation
Indices: 8310--8359 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
8300 CAGTTAAAAA
* * *
8310 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
8335 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
8360 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:8459 original size:125 final size:125
Alignment explanation
Indices: 8024--8443 Score: 795
Period size: 125 Copynumber: 3.4 Consensus size: 125
8014 NNNNNNNNNN
8024 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATT
1 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATT
*
8089 AAAGCTACAACAGCGAATCTTACGCCCCAAGCAATGCAGTGGAATAGATTAAAGCCAAAT
66 AAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAAT
8149 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATT
1 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATT
* * *
8214 AAAGCTACAACAGTGAATCTTACGCCTCAAGCGATGCAGTGGAATACATTAAAGCCAAAT
66 AAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAAT
8274 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATT
1 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATT
*
8339 AAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAACCAAAT
66 AAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAAT
8399 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGC
1 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGC
8444 TTCAATGACG
Statistics
Matches: 287, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 287 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (125 bp):
TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATT
AAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAAT
Done.