Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_182 ID=scaffold_182-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: 10371
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.29
Warning! 564 characters in sequence are not A, C, G, or T
Found at i:1257 original size:10 final size:10
Alignment explanation
Indices: 1242--1280 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1232 AGAAACTAAA
1242 AAAATATAAT
1 AAAATATAAT
1252 AAAATATAAT
1 AAAATATAAT
*
1262 AAAATCTAAT
1 AAAATATAAT
*
1272 AAAAAATAA
1 AAAATATAA
1281 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATATAAT
Found at i:1292 original size:20 final size:21
Alignment explanation
Indices: 1240--1292 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1230 GTAGAAACTA
*
1240 AAAAAATATAATAAAATATAAT
1 AAAAAA-ATAATAAAATAAAAT
*
1262 AAAATCTAATAA-AAAATAAAAT
1 AAAA--AAATAATAAAATAAAAT
1284 AAAAAAATA
1 AAAAAAATA
1293 CAAGAACTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.15
22 17 0.65
23 4 0.15
24 1 0.04
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAAATAATAAAATAAAAT
Found at i:2248 original size:44 final size:44
Alignment explanation
Indices: 2095--2475 Score: 172
Period size: 44 Copynumber: 8.8 Consensus size: 44
2085 TGGATTCATC
* * * * *
2095 GTTTTAATCCGCTCCGCTACAACTTTAGGGAGATAGGAT-TAGTA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTT
** * * * *
2139 ACTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG-GCTG--
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTT
* *** ** * *
2180 GGTGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTT
* * *
2224 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTT
* * *** * * * * * *
2268 GCTTCAATCTTTTTCGCAGCAACTTCAGGG-GTATAAAAT-TCATC
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAG-ATAAGATCT-GTT
* * *
2312 ATTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGAT-TAGCTT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCT-G-TT
* * * * * *
2357 CTTCT-GTCCACTCCACTGCAACTTCAGGGGGATAAG-GCTG--
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTT
* *** ** * * *
2397 GATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTG
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTT
*
2441 GTTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
2476 GGAATGGCTT
Statistics
Matches: 242, Mismatches: 82, Indels: 26
0.69 0.23 0.07
Matches are distributed among these distances:
40 1 0.00
41 55 0.23
42 6 0.02
43 4 0.02
44 171 0.71
45 5 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (44 bp):
GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTGTT
Found at i:2373 original size:217 final size:217
Alignment explanation
Indices: 2088--2478 Score: 631
Period size: 217 Copynumber: 1.8 Consensus size: 217
2078 AAGGTATTGG
* * * * **
2088 ATTCATCGTTTTAATCCGCTCCGCTACAACTTTAGGGAGATAGGATTAGTAACTTCAATCTGCTC
1 ATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGACAGGATTAGTAACTTCAATCCACTC
* *
2153 CACTGTAACTTCAGGGAGATAAGGCTGGGTGCGATCTACTCTACTGCAACTTCAGAGAGATAAGA
66 CACTGCAACTTCAGGGAGATAAGGCTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGA
*
2218 TCTGTTGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAGCTTCAATCTTTTTC
131 TCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAGCTTCAATCTTTTTC
2283 GCAGCAACTTCAGGGGTATAAA
196 GCAGCAACTTCAGGGGTATAAA
* * **
2305 ATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTAGCT-TCTTCTGTCCACT
1 ATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGACAGGATTAG-TAACTTCAATCCACT
*
2369 CCACTGCAACTTCAGGGGGATAAGGCTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAG
65 CCACTGCAACTTCAGGGAGATAAGGCTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAG
*
2434 ATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGA
130 ATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
2479 ATGGCTTATT
Statistics
Matches: 158, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
217 157 0.99
218 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (217 bp):
ATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGACAGGATTAGTAACTTCAATCCACTC
CACTGCAACTTCAGGGAGATAAGGCTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGA
TCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAGCTTCAATCTTTTTC
GCAGCAACTTCAGGGGTATAAA
Found at i:2378 original size:88 final size:88
Alignment explanation
Indices: 2225--2391 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
2215 AGATCTGTTG
* * *** * *
2225 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAGCTTCAATCTTTTTCGCAGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTAGTAGCTTCAATCCACTCCACAGCAA
*
2290 CTTCAGGGGTATAAAATTCATCA
66 CTTCAGGGGGATAAAATTCATCA
* ** *
2313 TTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTAGCT-TCTTCTGTCCACTCCACTGCA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTAG-TAGCTTCAATCCACTCCACAGCA
2377 ACTTCAGGGGGATAA
65 ACTTCAGGGGGATAA
2392 GGCTGGATGC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
88 65 0.98
89 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (88 bp):
TTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTAGTAGCTTCAATCCACTCCACAGCAA
CTTCAGGGGGATAAAATTCATCA
Found at i:2494 original size:44 final size:44
Alignment explanation
Indices: 2317--2495 Score: 118
Period size: 44 Copynumber: 4.1 Consensus size: 44
2307 TCATCATTTT
* * * * *
2317 AATCCGCTCCACTGCAACTTCAGGGAGACAGGATTAGCTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGAATGGCTTATTC
** ** * * *
2361 TGTCCACTCCACTGCAACTTCAGGGGGAT---AA-GGCTGGATGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGAATGGCT-TATTC
* * * * * * *
2402 GATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTT-TT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA-ATG-GCTTATTC
2446 AATCTGCTCCACTGCAACTTCAGGGAGATAGGAATGGCTTATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGAATGGCTTATTC
2490 AATCTG
1 AATCTG
2496 TTTAACTGCA
Statistics
Matches: 99, Mismatches: 27, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
40 3 0.03
41 26 0.26
42 3 0.03
43 4 0.04
44 59 0.60
45 1 0.01
46 1 0.01
47 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAGGAATGGCTTATTC
Found at i:2593 original size:51 final size:49
Alignment explanation
Indices: 2515--2697 Score: 150
Period size: 51 Copynumber: 3.7 Consensus size: 49
2505 AATGTCGGAG
* * * *
2515 AAGTAAGATTCGCCATCGTAGCTTCAATCTATTCCACTACACCGTCAGGGA
1 AAGTAAGATTCGCCGTTGTAGCCTCAATCT-TTCAACTACACCGTC-GGGA
* * * * * ** *
2566 AAGTAAGATTCGTCGTTGTGGCCTCAATCTTTTAATTGCAATGTCGGGG
1 AAGTAAGATTCGCCGTTGTAGCCTCAATCTTTCAACTACACCGTCGGGA
* * * * * *
2615 AAGCAAAATTTGCCGTTGTAGCTTCAATCTGTTCTACTACACCGCTTGGGA
1 AAGTAAGATTCGCCGTTGTAGCCTCAATCT-TTCAACTACACCG-TCGGGA
* *
2666 AAGTAAGATTTGCCGTTGTGGCCTCAATCTTT
1 AAGTAAGATTCGCCGTTGTAGCCTCAATCTTT
2698 TAAATTGCAA
Statistics
Matches: 100, Mismatches: 30, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
49 27 0.27
50 18 0.18
51 55 0.55
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (49 bp):
AAGTAAGATTCGCCGTTGTAGCCTCAATCTTTCAACTACACCGTCGGGA
Found at i:2636 original size:100 final size:99
Alignment explanation
Indices: 2488--2969 Score: 450
Period size: 100 Copynumber: 4.8 Consensus size: 99
2478 AATGGCTTAT
* * * * *
2488 TCAATCTGTTTAACTGCAATGTCGGAGAAGTAAGATTCGCCATCGTAGCTTCAATCTATTCCACT
1 TCAATCT-TTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACT
*
2553 ACACCGTCAGGGAAAGTAAGATTCGTCGTTGTGGCC
65 ACACCG-CAGGGAAAGTAAGATTCGCCGTTGTGGCC
* * * *
2589 TCAATCTTTTAATTGCAATGTCGGGGAAGCAAAATTTGCCGTTGTAGCTTCAATCTGTTCTACTA
1 TCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTA
* *
2654 CACCGCTTGGGAAAGTAAGATTTGCCGTTGTGGCC
66 CACCGC-AGGGAAAGTAAGATTCGCCGTTGTGGCC
* * * * * **
2689 TCAATCTTTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCATAGCTTCAATTTGTTCTGCT
1 TCAATCTTTT-AATTGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACT
* * * *
2754 GCACTAC-CTGGG-AAGTAAGATTCACCGTTGTGGCT
65 ACAC--CGCAGGGAAAGTAAGATTCGCCGTTGTGGCC
* * * * * *
2789 TCAATCTTTTAAATTACAATGTCAGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTATTCCATT
1 TCAATCTTTT-AATTGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACT
* * ** * *
2854 ATATCAC-CAGGG-AAGTGAGATTCGCTATTGTAGCT
65 ACA-C-CGCAGGGAAAGTAAGATTCGCCGTTGTGGCC
* * * * * *
2889 TCAATCTATTTGACTGCAAATGTCGAGGAAGCGAGATTTGCCATCGTAGCTTCAATCTGTTCCAC
1 TCAATCT-TTTAATTGC-AATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCAC
*
2954 TGCACCGCTAGGGAAA
64 TACACCGC-AGGGAAA
2970 TGAGATTGCT
Statistics
Matches: 315, Mismatches: 56, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
99 2 0.01
100 200 0.63
101 109 0.35
102 3 0.01
103 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (99 bp):
TCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTA
CACCGCAGGGAAAGTAAGATTCGCCGTTGTGGCC
Found at i:2817 original size:50 final size:50
Alignment explanation
Indices: 2487--2957 Score: 240
Period size: 50 Copynumber: 9.4 Consensus size: 50
2477 GAATGGCTTA
* *
2487 TTCAATCTGTTT-AACTGCAATGTC-GGAGAAGTAAGATTCGCCATCGTAGC
1 TTCAATCT-TTTCAACTGCAATGTCAGG-GAAGTAAGATTCGCCGTTGTAGC
* * * ** * *
2537 TTCAATCTATTCCACTACACCGTCAGGGAAAGTAAGATTCGTCGTTGTGGC
1 TTCAATCTTTTCAACTGCAATGTCAGGG-AAGTAAGATTCGCCGTTGTAGC
* * * * * *
2588 CTCAATCTTTT-AATTGCAATGTCGGGGAAGCAAAATTTGCCGTTGTAGC
1 TTCAATCTTTTCAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGC
* * * ** * * *
2637 TTCAATCTGTTCTACTACACCG-CTTGGGAAAGTAAGATTTGCCGTTGTGGC
1 TTCAATCTTTTCAACTGCAATGTC-AGGG-AAGTAAGATTCGCCGTTGTAGC
* * * * * * **
2688 CTCAATCTTTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCATAGC
1 TTCAATCTTTTCAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGC
** * ** * * *
2738 TTCAAT-TTGTTCTGCTGCACTACCTGGGAAGTAAGATTCACCGTTGTGGC
1 TTCAATCTT-TTCAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGC
* * * **
2788 TTCAATCTTTTAAATTACAATGTCAGGGAAGCGAGATTCGCCGTTGTAGC
1 TTCAATCTTTTCAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGC
* * * ** * **
2838 TTCAATCTATTCCA-T-TATATCACCAGGGAAGTGAGATTCGCTATTGTAGC
1 TTCAATCTTTTCAACTGCA-AT-GTCAGGGAAGTAAGATTCGCCGTTGTAGC
* ** * * *
2888 TTCAATCTATTT-GACTGCAAATGTC-GAGGAAGCGAGATTTGCCATCGTAGC
1 TTCAATCT-TTTCAACTGC-AATGTCAG-GGAAGTAAGATTCGCCGTTGTAGC
* *
2939 TTCAATCTGTTCCACTGCA
1 TTCAATCTTTTCAACTGCA
2958 CCGCTAGGGA
Statistics
Matches: 310, Mismatches: 94, Indels: 34
0.71 0.21 0.08
Matches are distributed among these distances:
48 1 0.00
49 34 0.11
50 168 0.54
51 103 0.33
52 3 0.01
53 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (50 bp):
TTCAATCTTTTCAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGC
Found at i:2941 original size:201 final size:200
Alignment explanation
Indices: 2487--2969 Score: 488
Period size: 201 Copynumber: 2.4 Consensus size: 200
2477 GAATGGCTTA
* *
2487 TTCAATCTGTTTAACTGCAATGTCG-GAGAAGTAAGATTCGCCATCGTAGCTTCAATCTATTCCA
1 TTCAATCT-TTTAACTGCAATGTCGAG-GAAGCAAGATTCGCCATCGTAGCTTCAATCTGTTCCA
** ** * *
2551 CTACACCGTCAGGGAAAGTAAGATTCGTCGTTGTGGCCTCAATCTTTTAATTGCAATGTCGGGGA
64 CTACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTACAATGTCAGGGA
* * * * ** * *
2616 AGCAAAATTTGCCGTTGTAGCTTCAATCTGTTCTACTACACCGCTTGGGAAAGTAAGATTTGCCG
129 AGCAAAATTCGCCGTTGTAGCTTCAATCTATTCCACTACACCACCAGGGAAAGTAAGATTCGCCA
*
2681 TTGTGGC
194 TTGTAGC
* * * * * * * **
2688 CTCAATCTTTTAAATTGCAATATC-AGGGAAGCAAGATTCACCGTCATAGCTTCAATTTGTTCTG
1 TTCAATCTTTT-AACTGCAATGTCGA-GGAAGCAAGATTCGCCATCGTAGCTTCAATCTGTTCCA
* * * *
2752 CTGCACTACCTGGG-AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTACAATGTCAGGG
64 CTACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTTT-AATTACAATGTCAGGG
* * * * * * *
2816 AAGCGAGATTCGCCGTTGTAGCTTCAATCTATTCCATTATATCACCAGGG-AAGTGAGATTCGCT
128 AAGCAAAATTCGCCGTTGTAGCTTCAATCTATTCCACTACACCACCAGGGAAAGTAAGATTCGCC
2880 ATTGTAGC
193 ATTGTAGC
* * *
2888 TTCAATCTATTTGACTGCAAATGTCGAGGAAGCGAGATTTGCCATCGTAGCTTCAATCTGTTCCA
1 TTCAATCT-TTTAACTGC-AATGTCGAGGAAGCAAGATTCGCCATCGTAGCTTCAATCTGTTCCA
* * *
2953 CTGCACCGCTAGGGAAA
64 CTACACCACCAGGGAAA
2970 TGAGATTGCT
Statistics
Matches: 221, Mismatches: 53, Indels: 15
0.76 0.18 0.05
Matches are distributed among these distances:
200 61 0.28
201 156 0.71
202 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (200 bp):
TTCAATCTTTTAACTGCAATGTCGAGGAAGCAAGATTCGCCATCGTAGCTTCAATCTGTTCCACT
ACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTACAATGTCAGGGAAG
CAAAATTCGCCGTTGTAGCTTCAATCTATTCCACTACACCACCAGGGAAAGTAAGATTCGCCATT
GTAGC
Found at i:4562 original size:12 final size:13
Alignment explanation
Indices: 4540--4569 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
4530 TGGCCTCTCA
4540 TTTTTCTTTCTTT
1 TTTTTCTTTCTTT
4553 TTTTTC-TTCTTT
1 TTTTTCTTTCTTT
4565 TTTTT
1 TTTTT
4570 AATTTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:7419 original size:19 final size:20
Alignment explanation
Indices: 7390--7441 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
7380 CGTTTTGTAA
* *
7390 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
7409 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
7429 AAATG-AATGCAAA
1 AAATGTAATGCAAA
7442 AAGAGACGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Done.