Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_270 ID=scaffold_270-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: 8778
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:2236 original size:40 final size:40
Alignment explanation
Indices: 2192--2435 Score: 231
Period size: 40 Copynumber: 5.8 Consensus size: 40
2182 GTTTCTTTTG
* *
2192 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGTTTCGA
**
2232 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C--TGGTTTCGA
* * ** * *
2275 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTG-
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTGGTTTC----GA
* * *
2319 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGTTTCGA
*
2359 TCTGCTCCACTACTGCTTGGGGAGATAAGATCTGGTTTCTTTTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGGTTTC----GA
2403 TCTGCTCCACTACTGCTTAGGGAGATAAGACTG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTG
2436 CTAGCTCAAT
Statistics
Matches: 164, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
39 1 0.01
40 59 0.36
41 12 0.07
43 37 0.23
44 54 0.33
45 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGTTTCGA
Found at i:2320 original size:127 final size:127
Alignment explanation
Indices: 2161--2392 Score: 414
Period size: 127 Copynumber: 1.8 Consensus size: 127
2151 ACTCTGCTGT
2161 AACTTCATGGGGATGAGATTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGG
1 AACTTCATGGGGATGAGATTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGG
2226 ATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGC
66 ATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGC
2288 AACTTCA-GGGAGAT-AGGATTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
1 AACTTCATGGG-GATGA-GATTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
* *
2351 TGATGCGATCTGCTCCACTACTGCTTGGGGAGATAAGATCTG
64 GGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
2393 GTTTCTTTTG
Statistics
Matches: 101, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
126 4 0.04
127 97 0.96
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (127 bp):
AACTTCATGGGGATGAGATTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGG
ATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGC
Found at i:2417 original size:84 final size:86
Alignment explanation
Indices: 2192--2435 Score: 297
Period size: 84 Copynumber: 2.9 Consensus size: 86
2182 GTTTCTTTTG
* *
2192 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGGATGC----GATCTGCTCCACTACTGCTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTTG-TCTGCTCCACTACTGCTTAG
* **
2252 GGAGATAAGATCTGTGGTTTTAA
65 GGAGATAAGA-CTGTGGATGCAA
* * ** *
2275 TCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TGGTTTCTTTTGTCTGCTCCACTACTGCTTAG
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTGCTTAG
*
2339 GGAGATAAGACT-T-GATGCGA
65 GGAGATAAGACTGTGGATGCAA
*
2359 TCTGCTCCACTACTGCTTGGGGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGG
2424 GAGATAAGACTG
66 GAGATAAGACTG
2436 CTAGCTCAAT
Statistics
Matches: 136, Mismatches: 17, Indels: 14
0.81 0.10 0.08
Matches are distributed among these distances:
83 25 0.18
84 77 0.57
85 1 0.01
86 2 0.01
87 30 0.22
88 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (86 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGG
GAGATAAGACTGTGGATGCAA
Found at i:2465 original size:127 final size:126
Alignment explanation
Indices: 2196--2524 Score: 297
Period size: 127 Copynumber: 2.6 Consensus size: 126
2186 CTTTTGTCTG
*
2196 CTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAG
1 CTCCACTAATGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAG
* * * * ** ** *
2261 ATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTG
66 ATCTGTGGTTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGACTGCTAGCTAATG-CTA
* * *
2323 CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTGGGGAGATAAG
1 CTCCACTAATGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAG
* ** * **
2388 ATCTG-GTTTCTTTTGTCTGCTCCACTACTGCTT-AGGGAGATAAGACTGCTAGCTCAATG-TA
66 ATCTGTG-GT-TTTAATCCGCTCCACTACAACTTCAGGGAGATAAGACTGCTAGCT-AATGCTA
* * *** * * *
2449 CTCCACTGTAAT-CTTAGGGAGGTAAAATCCACCATCTTCGATTTGCTCCATTACTGCTTAGGGA
1 CTCCAC--TAATGCTTAGGGAGATAAGA--CTGGA--TGCGATCTGCTCCACTACTGCTTAGGGA
2513 GATAAGATCTGT
60 GATAAGATCTGT
2525 AATCTTCAAT
Statistics
Matches: 165, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
126 8 0.05
127 98 0.59
128 22 0.13
129 2 0.01
131 35 0.21
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (126 bp):
CTCCACTAATGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAG
ATCTGTGGTTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGACTGCTAGCTAATGCTA
Found at i:2530 original size:44 final size:43
Alignment explanation
Indices: 2192--2787 Score: 246
Period size: 44 Copynumber: 13.8 Consensus size: 43
2182 GTTTCTTTTG
* *
2192 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGGA--TGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATCTTCGA
* **
2232 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-ATCTTCGA
* * ** * * *
2275 TCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TGGTTTCTTTTG-
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGATCT-GTATC-TTCGA
*
2319 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGA--TGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-ATCTTCGA
* * *
2359 TCTGCTCCACTACTGCTTGGGGAGATAAGATCTGGTTTCTTTTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTATC-TTCGA
* *
2403 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGCTAGC-TCAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-TATCTTCGA
* * * * * ***
2445 TGTACTCCACTGTAAT-CTTAGGGAGGTAAAATCCACCATCTTCGA
1 TCTGCTCCAC--TACTGCTTAGGGAGATAAGAT-CTGTATCTTCGA
* * *
2490 TTTGCTCCATTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-ATCTTCGA
** * ** * * *
2534 TCTATTCCACTCCTGCCCAGGGAGAT-AGAGCT-AATGGCTTCAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAT--CTTCGA
* * * * * * **
2577 TGTACTCCACTA-TAATCTCAGGGAGGTAAAATCCTCCATCTTCGA
1 TCTGCTCCACTACT--GCTTAGGGAGATAAGAT-CTGTATCTTCGA
* * *
2622 TCTGCTCCACTA-TGCTTAAGGAGATAAGATATGTAATCTTCAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-ATCTTCGA
** * ** * * *
2665 TCTATTCCACTGCTGCCCAGGGAGAT-AGAACT-AATGGCTTCAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAT--CTTCGA
* * * * * * *
2708 TGTACTCCACTGTAAT-CTCAGGGAGGTAAAAT-TCGCCATCTTCGA
1 TCTGCTCCAC--TACTGCTTAGGGAGATAAGATCT-G-TATCTTCGA
*
2753 TCTGCCCCACTACTGCTTAGGGAGATAAGATCTGT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
2788 GGTTTTAATC
Statistics
Matches: 406, Mismatches: 106, Indels: 85
0.68 0.18 0.14
Matches are distributed among these distances:
39 2 0.00
40 59 0.15
41 11 0.03
42 11 0.03
43 121 0.30
44 145 0.36
45 51 0.13
46 2 0.00
47 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATCTTCGA
Found at i:2620 original size:132 final size:132
Alignment explanation
Indices: 2356--2787 Score: 593
Period size: 131 Copynumber: 3.3 Consensus size: 132
2346 AGACTTGATG
* * *** ** * *
2356 CGATCTGCTCCACTACTGCTTGGGGAGATAAGATCTGGT-TTCTTTTGTCTGCTCCACTACTGCT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAATCTATTCCACTCCTGCC
* ** * *
2420 TAGGGAGATA-AGACTGCTAGC-TCAATGTACTCCACTGTAATCTTAGGGAGGTAAAATCCACCA
65 CAGGGAGATAGA-ACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCA
2483 TCTT
129 TCTT
* *
2487 CGATTTGCTCCATTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTCCTGCCC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTCCTGCCC
* * *
2552 AGGGAGATAGAGCTAATGGCTTCAATGTACTCCACTATAATCTCAGGGAGGTAAAATCCTCCATC
66 AGGGAGATAGAACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCATC
2617 TT
131 TT
* * *
2619 CGATCTGCTCCACTA-TGCTTAAGGAGATAAGATATGTAATCTTCAATCTATTCCACTGCTGCCC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTCCTGCCC
* *
2683 AGGGAGATAGAACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATTCGCCATC
66 AGGGAGATAGAACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCATC
2748 TT
131 TT
*
2750 CGATCTGCCCCACTACTGCTTAGGGAGATAAGATCTGT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
2788 GGTTTTAATC
Statistics
Matches: 266, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
130 2 0.01
131 187 0.70
132 77 0.29
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTCCTGCCC
AGGGAGATAGAACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCATC
TT
Found at i:3082 original size:44 final size:43
Alignment explanation
Indices: 3024--3422 Score: 363
Period size: 44 Copynumber: 9.1 Consensus size: 43
3014 AGATCTGTTT
* * *
3024 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * * * *
3068 TTTTCGATCCACTTCCTACCAATATAGGAAGA-TAGAACCTGCTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAG-ATCTGC-A
* * * * *
3112 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* *
3156 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * * *
3200 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * * *
3244 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
* * * * *
3287 TCTTCGATCCACTTCCTACCAATATAGGAAGAC-AGAACCTACTG
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAG-ATCTGC-A
* * * * * *
3331 TCTAT-GATCTACTTCACGCCAATACATGAAGACAAGATCTTCTT
1 TCT-TCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
*
3375 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
3419 TCTT
1 TCTT
3423 TAACTAGCTC
Statistics
Matches: 280, Mismatches: 64, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
42 3 0.01
43 74 0.26
44 156 0.56
45 47 0.17
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (43 bp):
TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
Found at i:3250 original size:132 final size:132
Alignment explanation
Indices: 3013--3320 Score: 512
Period size: 132 Copynumber: 2.3 Consensus size: 132
3003 TCAGAGAGAT
* * *
3013 AAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCATTTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCC
*
3078 ACTTCCTACCAATATAGGAAGATAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
3143 AC
131 AC
3145 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCC
*
3210 ACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
3275 AC
131 AC
* * * * *
3277 AAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACA
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACA
3321 GAACCTACTG
Statistics
Matches: 166, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
130 16 0.10
131 14 0.08
132 136 0.82
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (132 bp):
AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCC
ACTTCCTACCAATATAGGAAGACAGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
AC
Found at i:3303 original size:87 final size:89
Alignment explanation
Indices: 3013--3422 Score: 356
Period size: 87 Copynumber: 4.7 Consensus size: 89
3003 TCAGAGAGAT
* * * * * * * * * *
3013 AAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGC-ATTTTCGATC
1 AAGATCTGCTATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGACCTGCTATCTTCGATC
* * * *
3077 CACTTC-CTACCAATATAGGAAGA-
66 TACTTCAC-GCCAATACATGAAGAC
* * * * * * * *
3100 TAGAACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTTCGAT
1 AAG-ATCTGCTATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGACCTGCTATCTTCGAT
* * * ***
3164 CTACTTCGCCACCAGTATGGGAAGAC
65 CTACTTC-ACGCCAATACATGAAGAC
*
3190 AAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTATCTTCGATC
1 AAGATCTGCTATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGACCTGCTATCTTCGATC
3253 TACTTCACGCCAATACATGAAGAC
66 TACTTCACGCCAATACATGAAGAC
* *
3277 AAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGAC-AGAACCTACTGTCTAT-GA
1 AAGATCTGCTATCTTCGATCCACTTCACTACCAATATAGGAAGACAAG-ACCTGCTATCT-TCGA
3338 TCTACTTCACGCCAATACATGAAGAC
64 TCTACTTCACGCCAATACATGAAGAC
* * * * * * *
3364 AAGATCTTCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTT
1 AAGATCTGCTATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGACCTGCTATCTT
3423 TAACTAGCTC
Statistics
Matches: 270, Mismatches: 42, Indels: 22
0.81 0.13 0.07
Matches are distributed among these distances:
86 1 0.00
87 123 0.46
88 103 0.38
89 38 0.14
90 5 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (89 bp):
AAGATCTGCTATCTTCGATCCACTTCACTACCAATATAGGAAGACAAGACCTGCTATCTTCGATC
TACTTCACGCCAATACATGAAGAC
Found at i:3528 original size:87 final size:87
Alignment explanation
Indices: 3402--3647 Score: 422
Period size: 87 Copynumber: 2.8 Consensus size: 87
3392 CACCAATATG
* * *
3402 GGAAGACAAGATCTGC-ATCTTTAACTAGCTCCACTGCAACCGATGGAGGCAAGATTTTGTTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
3466 GATCTGCTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
*
3488 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTATTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
* *
3553 GATATACTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
*
3575 GGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
3640 GATCTGCT
66 GATCTGCT
3648 TCCTACCAAT
Statistics
Matches: 149, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 15 0.10
87 134 0.90
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (87 bp):
GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
GATCTGCTCCGCTGTTAATGCA
Found at i:3698 original size:43 final size:43
Alignment explanation
Indices: 3637--3887 Score: 249
Period size: 44 Copynumber: 5.7 Consensus size: 43
3627 AGGTTTTGTT
*
3637 TTCGATCTGCTTCCTACCAATATAGGAAGACAGGACCTGCATC
1 TTCGATCTACTTCCTACCAATATAGGAAGACAGGACCTGCATC
* * *
3680 TTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGATATT
1 TTCGATCTACTTCCTACCAATATAGGAAGACAGGACCTG-CATC
* * * * * *
3724 TTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTC
1 TTCGATCTACTTC-CTACCAATATAGGAAGACAGGACCTGC-ATC
* * *
3768 TTCGATCTACTCTGCC-ACCAATATGGGAAGACAAGATCTGCATC
1 TTCGATCTACT-T-CCTACCAATATAGGAAGACAGGACCTGCATC
* *
3812 TTCGATCCACTTCCTACCAATA-AGGAAGACAGGACCTACTATC
1 TTCGATCTACTTCCTACCAATATAGGAAGACAGGACCTGC-ATC
* *
3855 TTC-AGTCTACTTCGCTGCCAATACAGGAAGACA
1 TTCGA-TCTACTTC-CTACCAATATAGGAAGACA
3888 AGACTTGATG
Statistics
Matches: 173, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
42 16 0.09
43 58 0.34
44 65 0.38
45 33 0.19
46 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
TTCGATCTACTTCCTACCAATATAGGAAGACAGGACCTGCATC
Found at i:3865 original size:87 final size:88
Alignment explanation
Indices: 3637--3891 Score: 270
Period size: 87 Copynumber: 2.9 Consensus size: 88
3627 AGGTTTTGTT
* * *
3637 TTCGATCTGCTTCCTACCAATATAGGAAGACAGGACCTGC-ATCTTCGATCCACTTCCTACCAAT
1 TTCGATCTACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACTTCCTACCAAT
* * *
3701 ATAGGAAGACAGGACCTGATATT
66 ATAGGAAGACAAGACCTGACATC
* * * * *
3724 TTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCTGCC-ACC
1 TTCGATCTACTTC-CTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACT-T-CCTACC
* *
3787 AATATGGGAAGACAAGATCTG-CATC
63 AATATAGGAAGACAAGACCTGACATC
* * *
3812 TTCGATCCACTTCCTACCAATA-AGGAAGACAGGACCTACTATCTTC-AGTCTACTTCGCTGCCA
1 TTCGATCTACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGA-TCTACTTC-CTACCA
*
3875 ATACAGGAAGACAAGAC
64 ATATAGGAAGACAAGAC
3892 TTGATGTGAT
Statistics
Matches: 136, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
85 1 0.01
86 3 0.02
87 75 0.55
88 33 0.24
89 22 0.16
90 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (88 bp):
TTCGATCTACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACTTCCTACCAAT
ATAGGAAGACAAGACCTGACATC
Found at i:3875 original size:132 final size:132
Alignment explanation
Indices: 3652--3890 Score: 376
Period size: 132 Copynumber: 1.8 Consensus size: 132
3642 TCTGCTTCCT
*
3652 ACCAATATAGGAAGACAGGACCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACC
1 ACCAATATAGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACC
* *
3717 TGATATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCTG
66 TGATATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCTG
3782 CC
131 CC
* *
3784 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATA-AGGAAGACAGGACC
1 ACCAATATAGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACC
*
3848 T-ACTATCTTC-AGTCTACTTCGCTGCCAATACAGGAAGACAAGA
66 TGA-TATCTTCGA-TCTACTTCAC-GCCAATACAGGAAGACAAGA
3891 CTTGATGTGA
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
130 2 0.02
131 30 0.31
132 66 0.67
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (132 bp):
ACCAATATAGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACC
TGATATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCTG
CC
Found at i:4547 original size:56 final size:55
Alignment explanation
Indices: 4487--4655 Score: 120
Period size: 56 Copynumber: 3.1 Consensus size: 55
4477 GATGTATAAG
4487 ATGAAAAAGATGATCACAATAGATAAGATGGAAATTTGTTGAGAGCAAATCTCTAA
1 ATGAAAAAGAT-ATCACAATAGATAAGATGGAAATTTGTTGAGAGCAAATCTCTAA
* * * * * * * *
4543 ATGAACAA-AT-TAATC-A-AGAT-AGCA---AATTTTGCTGAGATACGAGATGTATAA
1 ATGAAAAAGATATCA-CAATAGATAAG-ATGGAAATTTGTTGAGA-GC-AAATCTCTAA
* * *
4594 GATGAAAAAGATTATCACAATGGATAATATGGAAATTTGTTGAGAGCAAAGCTCTAA
1 -ATGAAAAAGA-TATCACAATAGATAAGATGGAAATTTGTTGAGAGCAAATCTCTAA
4651 ATGAA
1 ATGAA
4656 CAAATTAAAC
Statistics
Matches: 80, Mismatches: 19, Indels: 28
0.63 0.15 0.22
Matches are distributed among these distances:
49 11 0.14
50 1 0.01
51 9 0.11
52 12 0.15
53 4 0.05
54 3 0.04
55 5 0.06
56 16 0.20
57 7 0.09
58 1 0.01
59 11 0.14
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (55 bp):
ATGAAAAAGATATCACAATAGATAAGATGGAAATTTGTTGAGAGCAAATCTCTAA
Found at i:4569 original size:108 final size:108
Alignment explanation
Indices: 4408--4680 Score: 456
Period size: 108 Copynumber: 2.5 Consensus size: 108
4398 TGGACAAAAT
** *
4408 GAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATCAAGATAGCAAATTTTGCTGAGAT
1 GAAA-TTTGTTGAGAGCAAAGCTCTAAATGAACAAATTAATCAAGATAGCAAATTTTGCTGAGAT
4473 ACGAGATGTATAAGATGAAAAAGATGATCACAATAGATAAGATG
65 ACGAGATGTATAAGATGAAAAAGATGATCACAATAGATAAGATG
*
4517 GAAATTTGTTGAGAGCAAATCTCTAAATGAACAAATTAATCAAGATAGCAAATTTTGCTGAGATA
1 GAAATTTGTTGAGAGCAAAGCTCTAAATGAACAAATTAATCAAGATAGCAAATTTTGCTGAGATA
* * *
4582 CGAGATGTATAAGATGAAAAAGATTATCACAATGGATAATATG
66 CGAGATGTATAAGATGAAAAAGATGATCACAATAGATAAGATG
* *
4625 GAAATTTGTTGAGAGCAAAGCTCTAAATGAACAAATTAAACAAGATAGAAAATTTT
1 GAAATTTGTTGAGAGCAAAGCTCTAAATGAACAAATTAATCAAGATAGCAAATTTT
4681 TCTAGAATAC
Statistics
Matches: 154, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 150 0.97
109 4 0.03
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (108 bp):
GAAATTTGTTGAGAGCAAAGCTCTAAATGAACAAATTAATCAAGATAGCAAATTTTGCTGAGATA
CGAGATGTATAAGATGAAAAAGATGATCACAATAGATAAGATG
Found at i:5505 original size:9 final size:9
Alignment explanation
Indices: 5491--5543 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
5481 CCAGTAGAGG
5491 TTTTTTGTT
1 TTTTTTGTT
*
5500 TTTTTTGTC
1 TTTTTTGTT
*
5509 TCTTTTGTT
1 TTTTTTGTT
* *
5518 CTTTTTCTT
1 TTTTTTGTT
5527 TGTTTTTGTGT
1 T-TTTTTGT-T
5538 TTTTTT
1 TTTTTT
5544 TGCCTCCACT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
9 21 0.62
10 11 0.32
11 2 0.06
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:8619 original size:106 final size:106
Alignment explanation
Indices: 8434--8644 Score: 298
Period size: 106 Copynumber: 2.0 Consensus size: 106
8424 ATGAAACCAT
* * * * *
8434 ACTTTGAAGTTTTAAGAGGGTATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCATCACGTTA
1 ACTTTGAAATTTTAAAAGGATATTTGGCTATTTAGTCAAACAAGAAATCGAAACCCATCACGTTA
*
8499 GGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTC
66 GGGCACATTTTCTCGAATTTCCAAACGCAAAATATTGCCTC
* * *
8540 ACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACAAGAAGTCGGAACCCGA-CACGTT
1 ACTTTGAAATTTTAAAAGGATATTTGGCTATTTAGTCAAACAAGAAATCGAAACCC-ATCACGTT
* * *
8604 AGGGCACATTTTCTCGATTTTCTAAACGCGAAATATTGCCT
65 AGGGCACATTTTCTCGAATTTCCAAACGCAAAATATTGCCT
8645 TATTTAGAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 91 0.99
107 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (106 bp):
ACTTTGAAATTTTAAAAGGATATTTGGCTATTTAGTCAAACAAGAAATCGAAACCCATCACGTTA
GGGCACATTTTCTCGAATTTCCAAACGCAAAATATTGCCTC
Done.