Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_377 ID=scaffold_377-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: 7690
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:172 original size:17 final size:16
Alignment explanation
Indices: 150--185 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
140 GACTAGTTTT
150 AAATATAATTAAAAATA
1 AAATAT-ATTAAAAATA
*
167 AAATATTTTAAAAATA
1 AAATATATTAAAAATA
183 AAA
1 AAA
186 AAAATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATATATTAAAAATA
Found at i:3451 original size:40 final size:42
Alignment explanation
Indices: 3333--3893 Score: 328
Period size: 44 Copynumber: 13.2 Consensus size: 42
3323 GCAACTTCAA
* * * * *
3333 GGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTTTAATCTGCTCCACTACTGCTTAG
* * * *
3376 AGAGATAAGACTTGAT-GC---GATCTACTCTACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* **
3416 GGAGATAAGATATGTGGCTTTAATCTGCTCCACTGCAACTTTAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGC-TTAG
* *** **
3460 GGAGATATGATTGGTTTTTTTTCTCTGCTCCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTTTAATCTGCTCCACTACTGCTTAG
*
3503 GGAGATAAGACTTGAT-GC---GATCTGCTCCACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* * * * **
3543 GGAGATAAGATCTGTGGTTTTAATCAGCTCTACTGCAACTTCAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGCTT-AG
* * ** ** *
3587 AGAGATAGGATTGATTTCTTTTGTCTGCTGCACTACTGCTTAG
1 GGAGATAAGATTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
3630 GGAGATAAGACTTGAT-GC---AATCTGCTCCACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* * * **
3670 GGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGCTT-AG
* * * * * *
3714 AGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTTTAATCTGCTCCACTACTGCTTAG
*
3757 AGAGATAAGACTTGAT-GC---AATCTGCTCCACTACTGCTTAG
1 GGAGATAAGA-TTG-TGGCTTTAATCTGCTCCACTACTGCTTAG
* * * **
3797 GGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAG
1 GGAGATAAGAT-TGTGGCTTTAATCTGCTCCACTACTGCTT-AG
** *
3841 GGAGATAAGATTGGTTTCTTCT-GTCTGCTCCACTACTGCTTAG
1 GGAGATAAGATT-GTGGCTT-TAATCTGCTCCACTACTGCTTAG
*
3884 GAAGATAAGA
1 GGAGATAAGA
3894 CCTGCTATCT
Statistics
Matches: 394, Mismatches: 88, Indels: 72
0.71 0.16 0.13
Matches are distributed among these distances:
39 8 0.02
40 127 0.32
43 124 0.31
44 134 0.34
45 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
GGAGATAAGATTGTGGCTTTAATCTGCTCCACTACTGCTTAG
Found at i:3487 original size:127 final size:127
Alignment explanation
Indices: 3305--3894 Score: 869
Period size: 127 Copynumber: 4.6 Consensus size: 127
3295 ATGATTCATC
* ** *
3305 GTTTTAATCCGCTCCACTGCAACTTCA-AGGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTAC
1 GTTTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGGTTTCTTCTGTCTGCTGCACTAC
* * * *
3369 TGCTTAGAGAGATAAGACTTGATGCGATCTACTCTACTACTGCTTAGGGAGATAAGATATGTG
65 TGCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* * * * * * * * *
3432 GCTTTAATCTGCTCCACTGCAACTTTAGGGAGATATGATTGGTTTTTTTTCTCTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
* *
3497 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
66 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* * * *
3559 GTTTTAATCAGCTCTACTGCAACTTCAGAGAGATAGGATTGATTTCTTTTGTCTGCTGCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
*
3624 GCTTAGGGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
66 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* ** *
3686 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
3751 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
66 GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
* * *
3813 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
3878 GCTTAG-GAAGATAAGAC
66 GCTTAGAG-AGATAAGAC
3895 CTGCTATCTT
Statistics
Matches: 417, Mismatches: 44, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
126 1 0.00
127 416 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (127 bp):
GTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTGCACTACT
GCTTAGAGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
Found at i:3759 original size:43 final size:41
Alignment explanation
Indices: 3334--3893 Score: 249
Period size: 40 Copynumber: 13.2 Consensus size: 41
3324 CAACTTCAAG
* * *
3334 GAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAGA
1 GAGATAAGATT-GTAG-TTCAATCTGCTCCACTACTGCTTAGA
* * * * *
3377 GAGATAAGACTTG-A-TGCGATCTACTCTACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * ** *
3417 GAGATAAGATATGTGGCTTTAATCTGCTCCACTGCAACTTTAGG
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGC-TTAGA
* ** *** *
3461 GAGATATGATTGGTTTTTTTTCTCTGCTCCACTACTGCTTAGG
1 GAGATAAGATT-G-TAGTTCAATCTGCTCCACTACTGCTTAGA
* * *
3504 GAGATAAGACTTG-A-TGCGATCTGCTCCACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * * * **
3544 GAGATAAGATCTGTGGTTTTAATCAGCTCTACTGCAACTTCAGA
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGCTT-AGA
* * ** * *
3588 GAGATAGGATTG-ATTTCTTTTGTCTGCTGCACTACTGCTTAGG
1 GAGATAAGATTGTAGTTC---AATCTGCTCCACTACTGCTTAGA
* *
3631 GAGATAAGACTTG-A-TGCAATCTGCTCCACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * * **
3671 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGA
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGCTT-AGA
* * *
3715 GAGATAGGATTAGTAGCTTCAGTCTGCTGCACTACTGCTTAGA
1 GAGATAAGATT-GTAG-TTCAATCTGCTCCACTACTGCTTAGA
* *
3758 GAGATAAGACTTG-A-TGCAATCTGCTCCACTACTGCTTAGG
1 GAGATAAGA-TTGTAGTTCAATCTGCTCCACTACTGCTTAGA
* * * * ** *
3798 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
1 GAGATAAGAT-TGTAG-TTCAATCTGCTCCACTACTGCTT-AGA
** **
3842 GAGATAAGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAG-
1 GAGATAAGATT-G-TAGTTCAATCTGCTCCACTACTGCTTAGA
3884 GAAGATAAGA
1 G-AGATAAGA
3894 CCTGCTATCT
Statistics
Matches: 386, Mismatches: 98, Indels: 66
0.70 0.18 0.12
Matches are distributed among these distances:
39 4 0.01
40 127 0.33
41 2 0.01
42 3 0.01
43 124 0.32
44 124 0.32
45 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
GAGATAAGATTGTAGTTCAATCTGCTCCACTACTGCTTAGA
Found at i:3871 original size:87 final size:86
Alignment explanation
Indices: 3522--3893 Score: 278
Period size: 87 Copynumber: 4.4 Consensus size: 86
3512 ACTTGATGCG
* * * *
3522 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCAGCTCTACTGCAACTTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTT-AG
* * **
3587 AGAGATAGGATTGATTTCTTTT
65 AGAGATAAGATTGGTTTCTTCA
* * * * ** *
3609 GTCTGCTGCACTACTGCTTAGGGAGATAAGA-CT-T-GATGCAATCTGCTCCACTACTGCTTAGG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTTAGA
*
3671 GAGATAAGATCTGTGGTT-TT-A
66 GAGATAAGAT-TG-GTTTCTTCA
* * ** * * * * * * **
3692 ATCCGCTCCACTGCAACTTCAGAGAGATAGGAT-TAGTAGCTTCAGTCTGCTGCACTACTGCTTA
1 ATCTGCTCCACTACTGCTT-AGGGAGATAAGATCT-GTGGTTTCAATCTGCTCCACTACAACTTA
* *
3756 GAGAGATAAGACTT-G---ATGCA
64 GAGAGATAAGA-TTGGTTTCTTCA
* * *
3776 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTT-AG
* *
3841 GGAGATAAGATTGGTTTCTTCT
65 AGAGATAAGATTGGTTTCTTCA
* *
3863 GTCTGCTCCACTACTGCTTAGGAAGATAAGA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGA
3894 CCTGCTATCT
Statistics
Matches: 219, Mismatches: 50, Indels: 32
0.73 0.17 0.11
Matches are distributed among these distances:
83 57 0.26
84 61 0.28
85 4 0.02
86 3 0.01
87 93 0.42
88 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (86 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCAATCTGCTCCACTACAACTTAGA
GAGATAAGATTGGTTTCTTCA
Found at i:3933 original size:45 final size:46
Alignment explanation
Indices: 3882--4270 Score: 432
Period size: 45 Copynumber: 8.7 Consensus size: 46
3872 ACTACTGCTT
* * * * * *
3882 AGGAAGATAAGACCTGCTATCTTTGA-TCTACTTCGCTACCAATAT
1 AGGAAGACAAGACTTGCTATCTTTCAGTCTACTTCACTGCCAATAC
*
3927 AGGAAGACAAGACTTGCTATC-TTCAGTCTACTTCGCTGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTTCAGTCTACTTCACTGCCAATAC
* *
3972 AGGAAGACAA-ACTTGCTATC-TTC-GATCTACTTAACAGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTTCAG-TCTACTTCACTGCCAATAC
* * *
4016 AGGAAGATAAGA-TCTGCTATC-TTCAGTCTACTTCATTGTCAATAC
1 AGGAAGACAAGACT-TGCTATCTTTCAGTCTACTTCACTGCCAATAC
**
4061 AGGAAGATTAGACTTGCTATC-TTCAGTCTACTTCACTGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTTCAGTCTACTTCACTGCCAATAC
4106 AGGAAGACAAGACTTGCTAT-TTTC-GATCTACTTCACTGCCAATAC
1 AGGAAGACAAGACTTGCTATCTTTCAG-TCTACTTCACTGCCAATAC
* *
4151 AGGAAAACAAGA-TCTGCTATC-TTCAGTCTACTTCGCTGCCAATAC
1 AGGAAGACAAGACT-TGCTATCTTTCAGTCTACTTCACTGCCAATAC
* *
4196 AGGAAGACAAGACTTGCTATC-TTC-GATCTACTTTACTACCAATAC
1 AGGAAGACAAGACTTGCTATCTTTCAG-TCTACTTCACTGCCAATAC
* *
4241 AGGAAGATAAGA-TCTGTTATC-TTCAGTCTA
1 AGGAAGACAAGACT-TGCTATCTTTCAGTCTA
4271 ATTAATTACA
Statistics
Matches: 303, Mismatches: 26, Indels: 30
0.84 0.07 0.08
Matches are distributed among these distances:
43 1 0.00
44 46 0.15
45 251 0.83
46 5 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (46 bp):
AGGAAGACAAGACTTGCTATCTTTCAGTCTACTTCACTGCCAATAC
Found at i:4111 original size:90 final size:90
Alignment explanation
Indices: 3882--4270 Score: 479
Period size: 90 Copynumber: 4.3 Consensus size: 90
3872 ACTACTGCTT
* * * * *
3882 AGGAAGATAAGACCTGCTATCTT-TGATCTACTTCGCTACCAATATAGGAAGACAAGACTTGCTA
1 AGGAAGATAAGACTTGCTATCTTCAG-TCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTA
*
3946 TCTTC-AGTCTACTTCGCTGCCAATAC
65 TCTTCGA-TCTACTTCACTGCCAATAC
* * * *
3972 AGGAAGACAA-ACTTGCTATCTTC-GATCTACTTAACAGCCAATACAGGAAGATAAGA-TCTGCT
1 AGGAAGATAAGACTTGCTATCTTCAG-TCTACTTCACTGCCAATACAGGAAGACAAGACT-TGCT
* *
4034 ATCTTC-AGTCTACTTCATTGTCAATAC
64 ATCTTCGA-TCTACTTCACTGCCAATAC
*
4061 AGGAAGATTAGACTTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTAT
1 AGGAAGATAAGACTTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTAT
*
4126 TTTCGATCTACTTCACTGCCAATAC
66 CTTCGATCTACTTCACTGCCAATAC
* * *
4151 AGGAAAACAAGA-TCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCTA
1 AGGAAGATAAGACT-TGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTA
* *
4215 TCTTCGATCTACTTTACTACCAATAC
65 TCTTCGATCTACTTCACTGCCAATAC
*
4241 AGGAAGATAAGA-TCTGTTATCTTCAGTCTA
1 AGGAAGATAAGACT-TGCTATCTTCAGTCTA
4271 ATTAATTACA
Statistics
Matches: 263, Mismatches: 29, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
88 1 0.00
89 75 0.29
90 184 0.70
91 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (90 bp):
AGGAAGATAAGACTTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTAT
CTTCGATCTACTTCACTGCCAATAC
Found at i:4183 original size:135 final size:135
Alignment explanation
Indices: 3890--4936 Score: 532
Period size: 135 Copynumber: 7.7 Consensus size: 135
3880 TTAGGAAGAT
* * * * *
3890 AAGACCTGCTATCTT-TGATCTACTTCGCTACCAATATAGGAAGACAAGACTTGCTATCTTCAGT
1 AAGATCTGCTATCTTCAG-TCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAGT
*
3954 CTACTTCGCTGCCAATACAGGAAGACAA-ACTTGCTATCTTCGATCTACTTAACAGCCAATACAG
65 CTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCGATCTACTTAACAGCCAATACAG
* *
4018 GAAGAT
130 GAAAAC
* * **
4024 AAGATCTGCTATCTTCAGTCTACTTCATTGTCAATACAGGAAGATTAGACTTGCTATCTTCAGTC
1 AAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAGTC
* * *
4089 TACTTCACTGCCAATACAGGAAGACAAGACTTGCTATTTTCGATCTACTTCACTGCCAATACAGG
66 TACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCGATCTACTTAACAGCCAATACAGG
4154 AAAAC
131 AAAAC
*
4159 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCTATCTTC-GAT
1 AAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAG-T
* * * * * * *
4223 CTACTTTACTACCAATACAGGAAGATAAGA-TCTGTTATCTTC-AGTCTAATTAATTA--CAGTG
65 CTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATCTTCGA-TCTACTTAA-CAGCCAAT-
* **
4284 TC-GGGGAAC
126 ACAGGAAAAC
* * * ** * * *
4293 AAGATTCACCGTTG-TAGCTTCAATCT-GTTCCACTGTACC--GCCAGAGAAG-TAGGATTTGCA
1 AAGA-T---C--TGCTATCTTCAGTCTACTT-CACTG--CCAATACAG-GAAGACAAGACTTGC-
* * ** * * *
4353 GTTACGGCTTCAATCTTTTTAATTG-CAATGTA-ATGGAAG-CAAGA-TTCGTCATTGTAGCTTC
55 --TA--TCTTCAGTCTACTTCACTGCCAA--TACA-GGAAGACAAGACTT-G-C----TATCTTC
* * * *** * **
4414 AATCTA-TTCCACTG-CACCGCTTGGAAAGT
107 GATCTACTT-AACAGCCAATAC-AGGAAAAC
* * ** * * *
4443 AAGATTCATTG-T-T-TTCGATTTGCTCCACCACTG-C--T-TAGG--GATAAGA-TCTGCAATC
1 AAGA-TC--TGCTATCTTC-A-GT-CTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATC
** * *** * * * * * *
4498 TTCAACCTAC-TCAATGCTGCT-CAGGGAGATAAGGCTGGTGC--T-TTCGATCTGCTTTACTGC
59 TTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACT--TGCTATCTTCGATCTACTTAACAGC
* * *
4558 CAGTATAGGAAGAC
122 CAATACAGGAAAAC
* *
4572 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACTTGCTATCTT-TGAT
1 AAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAG-T
* * * * ** * *
4636 CTACTTCGCTGCCAATACAGAAAGAAAAGA-TCTGCTATCTTCGATCCACTTTGCTGCCAATATA
65 CTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATCTTCGATCTACTTAACAGCCAATACA
*
4700 GGAAGAC
129 GGAAAAC
** * *
4707 AAGATCTGCTATCTTC-GATCTACTTCGGTGCCAATACAGGAAGACAAGA-TCTACTATCTTTAG
1 AAGATCTGCTATCTTCAG-TCTACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATCTTCAG
* * ** *
4770 TCTACTTCGCTGCCAATATAGGAAGACAAGACTTGCTATCTTCGATCTACTTCGCTGCCAATACA
64 TCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCGATCTACTTAACAGCCAATACA
*
4835 GGAAGAC
129 GGAAAAC
* *
4842 AAGATCTGTTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAATC
1 AAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAGTC
** *
4907 TACTTTGCTGCCAAATACAGGAAGATAAGA
66 TACTTCACTGCC-AATACAGGAAGACAAGA
4937 TCTGTAATGT
Statistics
Matches: 700, Mismatches: 139, Indels: 146
0.71 0.14 0.15
Matches are distributed among these distances:
126 9 0.01
127 3 0.00
128 4 0.01
129 23 0.03
130 7 0.01
132 21 0.03
133 8 0.01
134 111 0.16
135 356 0.51
136 25 0.04
137 9 0.01
138 4 0.01
139 25 0.04
140 6 0.01
141 4 0.01
142 9 0.01
143 5 0.01
144 20 0.03
145 11 0.02
146 1 0.00
147 6 0.01
148 10 0.01
149 13 0.02
150 10 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (135 bp):
AAGATCTGCTATCTTCAGTCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAGTC
TACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCGATCTACTTAACAGCCAATACAGG
AAAAC
Found at i:4618 original size:45 final size:46
Alignment explanation
Indices: 4554--4940 Score: 517
Period size: 45 Copynumber: 8.6 Consensus size: 46
4544 ATCTGCTTTA
* *
4554 CTGCCAGTATAGGAAGACAAGATCTGCTATCTTCAG-TCTACTTCG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGATCTACTTCG
*
4599 CTGCCAATACAGGAAGACAAGA-CTTGCTATCTT-TGATCTACTTCG
1 CTGCCAATACAGGAAGACAAGATC-TGCTATCTTCAGATCTACTTCG
* * * *
4644 CTGCCAATACAGAAAGAAAAGATCTGCTATCTTC-GATCCACTTTG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGATCTACTTCG
*
4689 CTGCCAATATAGGAAGACAAGATCTGCTATCTTC-GATCTACTTCG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGATCTACTTCG
* * *
4734 GTGCCAATACAGGAAGACAAGATCTACTATCTTTAG-TCTACTTCG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGATCTACTTCG
*
4779 CTGCCAATATAGGAAGACAAGA-CTTGCTATCTTC-GATCTACTTCG
1 CTGCCAATACAGGAAGACAAGATC-TGCTATCTTCAGATCTACTTCG
* *
4824 CTGCCAATACAGGAAGACAAGATCTGTTATCTTCAG-TCTACTTCA
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGATCTACTTCG
*
4869 CTGCCAATACAGGAAGACAAGA-CTTGCTATCTTCA-ATCTACTTTG
1 CTGCCAATACAGGAAGACAAGATC-TGCTATCTTCAGATCTACTTCG
*
4914 CTGCCAAATACAGGAAGATAAGATCTG
1 CTGCC-AATACAGGAAGACAAGATCTG
4941 TAATGTATAG
Statistics
Matches: 302, Mismatches: 27, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
44 5 0.02
45 274 0.91
46 22 0.07
47 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (46 bp):
CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGATCTACTTCG
Found at i:4667 original size:90 final size:90
Alignment explanation
Indices: 4540--4940 Score: 581
Period size: 90 Copynumber: 4.4 Consensus size: 90
4530 GGCTGGTGCT
* ** * *
4540 TTCGATCTGCTTTACTGCCAGTATAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCA
4605 ATACAGGAAGACAAGACTTGCTATC
66 ATACAGGAAGACAAGACTTGCTATC
* * * * *
4630 TTTGATCTACTTCGCTGCCAATACAGAAAGAAAAGATCTGCTATCTTC-GATCCACTTTGCTGCC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG-TCTACTTCGCTGCC
*
4694 AATATAGGAAGACAAGA-TCTGCTATC
65 AATACAGGAAGACAAGACT-TGCTATC
* * *
4720 TTCGATCTACTTCGGTGCCAATACAGGAAGACAAGATCTACTATCTTTAGTCTACTTCGCTGCCA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCA
*
4785 ATATAGGAAGACAAGACTTGCTATC
66 ATACAGGAAGACAAGACTTGCTATC
* *
4810 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCAGTCTACTTCACTGCCA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCA
4875 ATACAGGAAGACAAGACTTGCTATC
66 ATACAGGAAGACAAGACTTGCTATC
* * *
4900 TTCAATCTACTTTGCTGCCAAATACAGGAAGATAAGATCTG
1 TTCGATCTACTTCGCTGCC-AATACAGGAAGACAAGATCTG
4941 TAATGTATAG
Statistics
Matches: 278, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
89 2 0.01
90 254 0.91
91 22 0.08
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (90 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCA
ATACAGGAAGACAAGACTTGCTATC
Found at i:5317 original size:100 final size:100
Alignment explanation
Indices: 4960--5327 Score: 468
Period size: 100 Copynumber: 3.7 Consensus size: 100
4950 GCTTTAAACT
* * * ** * *
4960 TTTTAAATTGCGATGTCGGGGAAGCAAGATCCACTGTTGTAGCTACAATCTG-TCCCATTACACC
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCT-CCACTACATC
* * * *
5024 ACCAGAGAAGTAAGATTCGCCGTTGCGGCCTCAATC
65 GCCATAGAAGTAAGATTCACCGTTGCGGCTTCAATC
* * ** * *
5060 TTTTAAATTGCAATATCGGGGAAGTAAGATTCGTCGTTGTAACTTTAATCTGCTCCATTACATCG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTACATCG
*
5125 CCATGGAAGTAAGATTCACCGTTGCGGCTTCAATC
66 CCATAGAAGTAAGATTCACCGTTGCGGCTTCAATC
* * **
5160 TTTTAAATTACAATGTCGGGGAAGCAAGATTTACCGTTGTAGCTTTAATCTGCTCCACTGTATCG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTACATCG
* *
5225 CCATAGAAGTAAGATTCACTGTCGCGGCTTCAATC
66 CCATAGAAGTAAGATTCACCGTTGCGGCTTCAATC
* * * *
5260 TTTTAAATTGCAATGTCGGGGAAGGAAGATTCACCGTTGTAGCTTTAATCTGTTCCACTGCATTG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTACATCG
5325 CCA
66 CCA
5328 GGGAAGGTAA
Statistics
Matches: 232, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
100 231 1.00
101 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (100 bp):
TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTACATCG
CCATAGAAGTAAGATTCACCGTTGCGGCTTCAATC
Found at i:5334 original size:50 final size:50
Alignment explanation
Indices: 5078--5333 Score: 170
Period size: 50 Copynumber: 5.1 Consensus size: 50
5068 TGCAATATCG
** * * * *
5078 GGGAAGTAAGATTCGTCGTTGTAACTTTAATCTGCTCCATTACATCGCCA
1 GGGAAGTAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCATTGCCA
* ** * * ** * * * *
5128 TGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTAAATTACAATGTCG
1 GGGAAGTAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCATTGCCA
* * * * * *
5178 GGGAAGCAAGATTTACCGTTGTAGCTTTAATCTGCTCCACTGTATCGCCA
1 GGGAAGTAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCATTGCCA
** * * ** * * ** * * *
5228 TAGAAGTAAGATTCACTGTCGCGGCTTCAATCTTTTAAATTGCAATGTCG
1 GGGAAGTAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCATTGCCA
* *
5278 GGGAAGGAAGATTCACCGTTGTAGCTTTAATCTGTTCCACTGCATTGCCA
1 GGGAAGTAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCATTGCCA
5328 GGGAAG
1 GGGAAG
5334 GTAACTTCAT
Statistics
Matches: 140, Mismatches: 66, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
50 140 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (50 bp):
GGGAAGTAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCATTGCCA
Found at i:7073 original size:28 final size:26
Alignment explanation
Indices: 7033--7092 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
7023 CCAGTAGAGG
*
7033 TTTTTTATTTTTTTGTCTTTTTTGTT
1 TTTTTTATTTTTTTGTCTTTTTGGTT
* *
7059 CTTTTTTTTTGTTTTTGTGTTTTTGGTT
1 -TTTTTTATT-TTTTTGTCTTTTTGGTT
7087 TTTTTT
1 TTTTTT
7093 GCCTCCACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (26 bp):
TTTTTTATTTTTTTGTCTTTTTGGTT
Done.