Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_766 ID=scaffold_766-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: 4540
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.29
Warning! 626 characters in sequence are not A, C, G, or T
Found at i:2432 original size:44 final size:44
Alignment explanation
Indices: 2377--2488 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 44
2367 AATCTGCTTT
* *
2377 CTACAACTTCAGAGAGATAAGATCTATT-ACTTTAATCCACTCCA
1 CTACAACTTCAGGGAGATAAGAT-TATTGACTTTAATCCACCCCA
* * * **
2421 CTACAAATTCAGGGAGATAGGATTATTGGCTTTAATCTGCCCCA
1 CTACAACTTCAGGGAGATAAGATTATTGACTTTAATCCACCCCA
2465 CTACAACTTCAGGGAGATAAGATT
1 CTACAACTTCAGGGAGATAAGATT
2489 CGCCATCTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 4 0.07
44 54 0.93
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (44 bp):
CTACAACTTCAGGGAGATAAGATTATTGACTTTAATCCACCCCA
Found at i:2455 original size:174 final size:173
Alignment explanation
Indices: 2163--2533 Score: 494
Period size: 174 Copynumber: 2.1 Consensus size: 173
2153 ATCTACTCCT
* * * *
2163 CTGCAACTTTAGTG-AGATGAGACCAGATGCGATCTGCTCTCTGAAACTTCAGAGAGATAAGATC
1 CTGCAACTTTAG-GAAGATAAGACTAGACGCAATCTGCTCTCTGAAACTTCAGAGAGATAAGATC
* ** * * ** * *
2227 TGTGGTTTTAATCCGCTCCACTGCACCTTTAGGGAGATAGGATTATCAGCTTTAATCTGCTCCAC
65 TATGACTTTAATCCACTCCACTACAAATTCAGGGAGATAGGATTATCAGCTTTAATCTGCCCCAC
* * *
2292 TGCAACTTCAAGGAGATAAGATTTGTCATCTTTCAGTCTGCCTCA
130 TACAACTTCAAGGAGATAAGATTCGCCATC-TTCAGTCTGCCTCA
* *
2337 CTGCAACTTCAGGAAGATAAGACTAGACGCAATCTGCTTTCT-ACAACTTCAGAGAGATAAGATC
1 CTGCAACTTTAGGAAGATAAGACTAGACGCAATCTGCTCTCTGA-AACTTCAGAGAGATAAGATC
* **
2401 TATTACTTTAATCCACTCCACTACAAATTCAGGGAGATAGGATTATTGGCTTTAATCTGCCCCAC
65 TATGACTTTAATCCACTCCACTACAAATTCAGGGAGATAGGATTATCAGCTTTAATCTGCCCCAC
*
2466 TACAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCA
130 TACAACTTCAAGGAGATAAGATTCGCCATCTTCAGTCTGCCTCA
*
2510 CTGCAACTTTAGGAGGATAAGACT
1 CTGCAACTTTAGGAAGATAAGACT
2534 TGCTTACATA
Statistics
Matches: 171, Mismatches: 24, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
173 38 0.22
174 133 0.78
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (173 bp):
CTGCAACTTTAGGAAGATAAGACTAGACGCAATCTGCTCTCTGAAACTTCAGAGAGATAAGATCT
ATGACTTTAATCCACTCCACTACAAATTCAGGGAGATAGGATTATCAGCTTTAATCTGCCCCACT
ACAACTTCAAGGAGATAAGATTCGCCATCTTCAGTCTGCCTCA
Found at i:2518 original size:45 final size:44
Alignment explanation
Indices: 2456--2576 Score: 115
Period size: 45 Copynumber: 2.7 Consensus size: 44
2446 TTGGCTTTAA
* * *
2456 TCTGCCCCACTACAACTTCAGGGAGATAAGA-TTCGCCAT-CTTCAG
1 TCTGCCTCACTGCAACTTCAGGGAGATAAGACTT-G-CATACAT-AG
* *
2501 TCTGCCTCACTGCAACTTTA-GGAGGATAAGACTTGCTTACATAG
1 TCTGCCTCACTGCAACTTCAGGGA-GATAAGACTTGCATACATAG
*
2545 TCT-ACTCGACTGCAACTTCAGGGAGATAAGAC
1 TCTGCCTC-ACTGCAACTTCAGGGAGATAAGAC
2577 CTGATATCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
45 30 0.47
46 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (44 bp):
TCTGCCTCACTGCAACTTCAGGGAGATAAGACTTGCATACATAG
Found at i:2672 original size:49 final size:49
Alignment explanation
Indices: 2611--2773 Score: 130
Period size: 50 Copynumber: 3.3 Consensus size: 49
2601 GGAATGTCGG
* *
2611 GGAAGCAAGATTCGCCGTCGTAACTTCAATCTGTTCCACTAACCACCAA
1 GGAAGTAAGATTCGCCGTCGTAACTTCAATCTGTTCCACTAACCGCCAA
* * ** * ** * * ***
2660 GGAAGTAAGATTCACCGTTGCGACTTCAATCTTTTAAATTGCAA-TGTTGA
1 GGAAGTAAGATTCGCCGTCGTAACTTCAATCTGTTCCACT--AACCGCCAA
* * * *
2710 GCAAATAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTATACCGCCAG
1 GGAAGTAAGATTCGCCGTCGTAACTTCAATCTGTTCCACTA-ACCGCCAA
2760 GGAAGTAAGATTCG
1 GGAAGTAAGATTCG
2774 TCGTTGCGGC
Statistics
Matches: 78, Mismatches: 32, Indels: 7
0.67 0.27 0.06
Matches are distributed among these distances:
48 1 0.01
49 32 0.41
50 43 0.55
51 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (49 bp):
GGAAGTAAGATTCGCCGTCGTAACTTCAATCTGTTCCACTAACCGCCAA
Found at i:2981 original size:44 final size:44
Alignment explanation
Indices: 2933--3058 Score: 189
Period size: 44 Copynumber: 2.9 Consensus size: 44
2923 TAAGATTCGT
2933 AATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
1 AATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
* * *
2977 AATCTTCAACCTATTCCACTGCTGACCACGGAGATAGAATTCAG
1 AATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
* * * *
3021 GATCTTCAACCTATTTCACTACTGTCCAGGGAGATAGG
1 AATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG
3059 GCTGGGGTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCAC
Found at i:3177 original size:88 final size:88
Alignment explanation
Indices: 3069--3547 Score: 753
Period size: 88 Copynumber: 5.4 Consensus size: 88
3059 GCTGGGGTCA
*
3069 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
3134 CCAGGGAGGCAAGGCTGGTGACT
66 CCAGGGAGGCAAGGCTGGTGACT
* * * *
3157 TCGATCTCCATCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
3222 CCAGGGAGGCAAGGCTGGTGTA-T
66 CCAGGGAGGCAAGGCTGGTG-ACT
* * *
3245 TCGATCTGCTTCGCTGTCAGTGTAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
3310 CCAGGGAGGCAAGGCTGGTGACT
66 CCAGGGAGGCAAGGCTGGTGACT
*
3333 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
3398 CCAGGGAGGCAAGGCTGGTGACT
66 CCAGGGAGGCAAGGCTGGTGACT
* * * *
3421 TTGATCCGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
*
3486 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGACT
* * * * * * *
3509 TTGATCTACTTCGCTGCCAGTACAAGAAGGTAAGATCTG
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
3548 TTATCTTCAC
Statistics
Matches: 359, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
87 1 0.00
88 357 0.99
89 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.26
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGACT
Found at i:3700 original size:6 final size:6
Alignment explanation
Indices: 3689--3819 Score: 206
Period size: 6 Copynumber: 23.2 Consensus size: 6
3679 TTTTTTAATT
3689 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
3737 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT- TATTT-
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
3783 TATTT- TATTT- TATTT- TATTT- TATTT- TATTT- TATTTA T
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA T
3820 TTATTTATTT
Statistics
Matches: 124, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
5 40 0.32
6 84 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TATTTA
Found at i:3724 original size:30 final size:29
Alignment explanation
Indices: 3687--3840 Score: 207
Period size: 30 Copynumber: 5.5 Consensus size: 29
3677 AATTTTTTAA
3687 TTTATTTATATTTATATTTATATTTATAT
1 TTTATTTATATTTATATTTATATTTATAT
3716 TTATATTTATATTTATATTTATATTTATAT
1 TT-TATTTATATTTATATTTATATTTATAT
3746 TTATATTTATATTTATATTTATATTTATAT
1 TT-TATTTATATTTATATTTATATTTATAT
3776 TTTATTT-TATTT-TATTT-TATTT-TAT
1 TTTATTTATATTTATATTTATATTTATAT
*
3801 TTTATTT-TATTT-TA-TT-TATTTATTT
1 TTTATTTATATTTATATTTATATTTATAT
*
3826 ATTTATTTATTTTTA
1 -TTTATTTATATTTA
3841 AGAATGATCC
Statistics
Matches: 118, Mismatches: 2, Indels: 11
0.90 0.02 0.08
Matches are distributed among these distances:
24 7 0.06
25 19 0.16
26 12 0.10
27 9 0.08
28 5 0.04
29 7 0.06
30 59 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTATTTATATTTATATTTATATTTATAT
Done.