Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_294 ID=scaffold_294-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: 9072
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.31
Warning! 552 characters in sequence are not A, C, G, or T
Found at i:265 original size:27 final size:26
Alignment explanation
Indices: 232--282 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
222 CGAATAGAAT
* *
232 GCGATAAATGATAATATACAACATAGA
1 GCGATAAATCATAA-ATAAAACATAGA
*
259 GCGATAATTCATAAATAAAACATA
1 GCGATAAATCATAAATAAAACATA
283 CACTAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (26 bp):
GCGATAAATCATAAATAAAACATAGA
Found at i:1243 original size:19 final size:19
Alignment explanation
Indices: 1217--1274 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
1207 AATCATATCT
1217 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
1236 TTTAAGATTGCATATATCAAA
1 TCTAAGATTGC--ATATCATA
*
1257 TCTAAGATTACATATCAT
1 TCTAAGATTGCATATCAT
1275 TGAAGATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1254 original size:21 final size:21
Alignment explanation
Indices: 1217--1271 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1207 AATCATATCT
*
1217 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCAAA
*
1236 TTTAAGATTGCATATATCAAA
1 TCTAAGATTGCATATATCAAA
*
1257 TCTAAGATTACATAT
1 TCTAAGATTGCATAT
1272 CATTGAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 10 0.33
21 20 0.67
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCAAA
Found at i:1893 original size:44 final size:44
Alignment explanation
Indices: 1831--2160 Score: 164
Period size: 44 Copynumber: 7.6 Consensus size: 44
1821 GATCTACTCT
* * *
1831 ACTGTAACTTCAGAGAGATAAGA-T-TTGCGGTTTAAATCCCCTCC
1 ACTGCAACTTCAGGGAGATAAGATTATTG-GCTTT-AATCCCCTCC
* **
1875 ACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCCCCTCC
* * **** * * *
1919 ACTGCAACTTCAAGGAGATAATATTCACCATCTTCATTCTGCCT-C
1 ACTGCAACTTCAGGGAGATAAGATT-ATTGGCTTTAATC-CCCTCC
* * * ** *
1964 ACTACAACTTCA-GGAGGATAAGACTTGATT-AC-TTAGTCTGCTCT
1 ACTGCAACTTCAGGGA-GATAAGA-TT-ATTGGCTTTAATCCCCTCC
* * * *
2008 ACTGCAACTTCAGGGAGATAAGACTAGAT-GCGATT--T--GCT-C
1 ACTGCAACTTCAGGGAGATAAGATTA-TTGGC-TTTAATCCCCTCC
* * * ** * *
2048 TCTGCAACTTCAGAGAGATAAGATCT-GTGATTTTAATCCGCTCT
1 ACTGCAACTTCAGGGAGATAAGAT-TATTGGCTTTAATCCCCTCC
* **
2092 ACTGCAACTTCAGGGAGATAAAATTATTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCCCCTCC
2136 ACTGCAACTTCAGGGAGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
2161 CGCCATCTTC
Statistics
Matches: 217, Mismatches: 50, Indels: 38
0.71 0.16 0.12
Matches are distributed among these distances:
39 3 0.01
40 21 0.10
41 5 0.02
42 1 0.00
43 10 0.05
44 133 0.61
45 36 0.17
46 8 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCCCCTCC
Found at i:2098 original size:217 final size:219
Alignment explanation
Indices: 1737--2171 Score: 631
Period size: 217 Copynumber: 2.0 Consensus size: 219
1727 GTTTATTTAG
* * * * *
1737 TCTGCCCCACTGCAATTTCAGGGGGATAAGACTTGCTTTCTTGAGTCTACTCCACTGCAACTTCA
1 TCTGCCCCACTACAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGCAACTTCA
* * * * *
1802 GGGAGATAAGACCCGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATTTGCGGTTTAAA
66 GGGAGATAAGACCAGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGCGATTTAAA
**
1867 TCCCCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAA
131 TCCCCTCCACTGCAACTTCAGGGAGATAAAATTATTGGCTTTAATCTGCTCCACTGCAACTTCAA
*
1932 GGAGATAATATTCACCATCTTCAT
196 GGAGATAAGATTCACCATCTTCAT
* * *
1956 TCTGCCTCACTACAACTTCAGGAGGATAAGACTTGATTACTT-AGTCTGCTCTACTGCAACTTCA
1 TCTGCCCCACTACAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGCAACTTCA
* * * * *
2020 GGGAGATAAGACTAGATGCGATTTGCTCT-CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
66 GGGAGATAAGACCAGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGCGATTTAAA
* * *
2084 TCCGCTCTACTGCAACTTCAGGGAGATAAAATTATTGGCTTTAATCTGCTCCACTGCAACTTCAG
131 TCCCCTCCACTGCAACTTCAGGGAGATAAAATTATTGGCTTTAATCTGCTCCACTGCAACTTCAA
*
2149 GGAGATAAGATTCGCCATCTTCA
196 GGAGATAAGATTCACCATCTTCA
2172 GTCTTTTAAT
Statistics
Matches: 191, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
217 111 0.58
218 44 0.23
219 36 0.19
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (219 bp):
TCTGCCCCACTACAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGCAACTTCA
GGGAGATAAGACCAGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGCGATTTAAA
TCCCCTCCACTGCAACTTCAGGGAGATAAAATTATTGGCTTTAATCTGCTCCACTGCAACTTCAA
GGAGATAAGATTCACCATCTTCAT
Found at i:2245 original size:95 final size:97
Alignment explanation
Indices: 2119--2356 Score: 243
Period size: 100 Copynumber: 2.4 Consensus size: 97
2109 ATAAAATTAT
* * * * ** *
2119 TGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCC-AT-CTTCAGTC-TTTTAA
1 TGGCTTCAATCTGTTCCACTACACCGCCAGGGAGATAAGATTCGCCGATGCTTCAATCTTTTTAA
**
2181 TTTGCAATGTTGGGGAAACAAGATTTGCCATCG
66 -TTGCAATGTTGGGGAAACAAGATTCACCATCG
*
2214 TGGCTTCAATCTGTTCCACTACACCGCCAGGGA-AGTAAGATTCGCCGTTGCGGCTTCAATCTTT
1 TGGCTTCAATCTGTTCCACTACACCGCCAGGGAGA-TAAGATTCGCCGAT---GCTTCAATCTTT
* *
2278 TTAATTGCAATGTTGGTGAAACAAGATTCACTATCG
62 TTAATTGCAATGTTGGGGAAACAAGATTCACCATCG
* * * *
2314 TAGCTTCAATTTGTTCCATTACACTGCCAGAGGAGA-AAGATTC
1 TGGCTTCAATCTGTTCCACTACACCGCCAG-GGAGATAAGATTC
2357 ACCGTCGTGG
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
94 1 0.01
95 38 0.32
96 1 0.01
100 68 0.58
101 9 0.08
102 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (97 bp):
TGGCTTCAATCTGTTCCACTACACCGCCAGGGAGATAAGATTCGCCGATGCTTCAATCTTTTTAA
TTGCAATGTTGGGGAAACAAGATTCACCATCG
Found at i:2314 original size:100 final size:100
Alignment explanation
Indices: 2167--2361 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 100
2157 GATTCGCCAT
* ** *
2167 CTTCAGTCTTTTAATTTGCAATGTTGGGGAAACAAGATTTGCCATCGTGGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAATTTGCAATGTTGGGGAAACAAGATTCACCATCGTAGCTTCAATCTGTTCCA
* *
2232 CTACACCGCCAG-GGAAGTAAGATTCGCCGTTGCGG
66 CTACACCGCCAGAGG-AGAAAGATTCACCGTTGCGG
* * *
2267 CTTCAATCTTTTTAA-TTGCAATGTTGGTGAAACAAGATTCACTATCGTAGCTTCAATTTGTTCC
1 CTTCAATC-TTTTAATTTGCAATGTTGGGGAAACAAGATTCACCATCGTAGCTTCAATCTGTTCC
* *
2331 ATTACACTGCCAGAGGAGAAAGATTCACCGT
65 ACTACACCGCCAGAGGAGAAAGATTCACCGT
2362 CGTGGTTTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
100 74 0.90
101 8 0.10
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (100 bp):
CTTCAATCTTTTAATTTGCAATGTTGGGGAAACAAGATTCACCATCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGAGGAGAAAGATTCACCGTTGCGG
Found at i:2446 original size:45 final size:45
Alignment explanation
Indices: 2395--2536 Score: 196
Period size: 45 Copynumber: 3.2 Consensus size: 45
2385 TAATGCCAAA
* * * *
2395 GAGATAGGACTTTGTGATTTTCAGCCTATTCTACTACTAACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
**** *
2440 GAGATAGGA-TTCACAATCTTCAACCTATTCCACTGCTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
2484 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
2529 GAGATAGG
1 GAGATAGG
2537 GCTGGGGTCA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
44 35 0.43
45 47 0.57
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (45 bp):
GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
Found at i:2652 original size:88 final size:88
Alignment explanation
Indices: 2536--3123 Score: 870
Period size: 88 Copynumber: 6.7 Consensus size: 88
2526 AGGGAGATAG
* * * * *
2536 GGCTGGGGTCATCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * *
2601 TTCGTTGCAACCCAGGGAGGTAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
2624 GGCTGGTGTCTTCGATTTGCTTCACTGTCGCTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
2689 TCCACTGCAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
2712 GGCTGGTGTCTTCGATCTACTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTAC
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
2777 TCTGCTGTAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
2800 GGCTTGTGTCTTCGATTTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGT
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
2865 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
*
2888 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTTAACCTG
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTTAACCTG
* *
2953 CTCCGCTGCAACACAAGGAGGCAA
65 CTCCGCTGCAACCCAGGGAGGCAA
* * *
2977 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGTAGGAATGCAAGATTTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
3042 CCCGCTGCAACTCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
3065 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
3124 CTGATCTGCT
Statistics
Matches: 451, Mismatches: 48, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
88 370 0.82
89 81 0.18
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGGAGGCAA
Done.