Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold154
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: 1945843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 156 characters in sequence are not A, C, G, or T
File 4 of 12
Found at i:450373 original size:29 final size:29
Alignment explanation
Indices: 450336--450409 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
450326 TTATTTTTGA
450336 TTTGATTATTAATTAAAGAATTAAAAAAT
1 TTTGATTATTAATTAAAGAATTAAAAAAT
450365 TTTGATTATTAATTAAAGAATTAAAAAAT
1 TTTGATTATTAATTAAAGAATTAAAAAAT
450394 TTTGATTATTAATTAA
1 TTTGATTATTAATTAA
450410 TTTGATTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.45
Consensus pattern (29 bp):
TTTGATTATTAATTAAAGAATTAAAAAAT
Found at i:451697 original size:7 final size:7
Alignment explanation
Indices: 451685--451764 Score: 71
Period size: 7 Copynumber: 11.9 Consensus size: 7
451675 TTTCTATTTT
451685 TTATATA
1 TTATATA
451692 TTATATA
1 TTATATA
451699 TTATA-A
1 TTATATA
451705 TTATAT-
1 TTATATA
*
451711 TTAAATA
1 TTATATA
451718 TTAT-TA
1 TTATATA
451724 TTTATATA
1 -TTATATA
* *
451732 ATATAAA
1 TTATATA
451739 TTATAT-
1 TTATATA
*
451745 TAATA-A
1 TTATATA
451751 TTTATATA
1 -TTATATA
451759 TTATAT
1 TTATAT
451765 TATGTTTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
6 17 0.29
7 38 0.66
8 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TTATATA
Found at i:451710 original size:20 final size:19
Alignment explanation
Indices: 451685--451767 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 19
451675 TTTCTATTTT
451685 TTATATATTATATATTATAA
1 TTATATATTATATATTAT-A
*
451705 TTATAT-TTAAATATTATTA
1 TTATATATTATATATTA-TA
* *
451724 TTTATATAATATAAATTATA
1 -TTATATATTATATATTATA
451744 TTA-ATAATTTATATATTATA
1 TTATAT-A-TTATATATTATA
451764 TTAT
1 TTAT
451768 GTTTAAATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.04
19 14 0.27
20 28 0.55
21 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATATATTATATATTATA
Found at i:451742 original size:40 final size:41
Alignment explanation
Indices: 451679--451762 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 41
451669 GTCATGTTTC
* * *
451679 TATTTTTTATATATTATATATTATAATT-AT-ATTTAAATAT
1 TATTATTTATATAATATAAATTAT-ATTAATAATTTAAATAT
*
451719 TATTATTTATATAATATAAATTATATTAATAATTTATATAT
1 TATTATTTATATAATATAAATTATATTAATAATTTAAATAT
451760 TAT
1 TAT
451763 ATTATGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 3 0.08
40 23 0.61
41 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (41 bp):
TATTATTTATATAATATAAATTATATTAATAATTTAAATAT
Found at i:452283 original size:10 final size:10
Alignment explanation
Indices: 452268--452296 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
452258 CAATGTTTGA
452268 TGTAATATAG
1 TGTAATATAG
452278 TGTAATATAG
1 TGTAATATAG
452288 TGTAATATA
1 TGTAATATA
452297 ATATTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (10 bp):
TGTAATATAG
Found at i:454276 original size:28 final size:29
Alignment explanation
Indices: 454245--454306 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
454235 AAATTAAAAT
* **
454245 ATTAAAAATATATATTAATATATTTA-TA
1 ATTAAAAATAAATAAAAATATATTTATTA
* *
454273 ATTAAATATAAATAAAAATATTTTTATTA
1 ATTAAAAATAAATAAAAATATATTTATTA
454302 ATTAA
1 ATTAA
454307 CTAATCATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTAAAAATAAATAAAAATATATTTATTA
Found at i:455835 original size:13 final size:13
Alignment explanation
Indices: 455817--455843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
455807 CATTTAAATC
455817 ACATCATATAATT
1 ACATCATATAATT
455830 ACATCATATAATT
1 ACATCATATAATT
455843 A
1 A
455844 GAATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ACATCATATAATT
Found at i:457369 original size:10 final size:11
Alignment explanation
Indices: 457318--457371 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
457308 TTTAAGCTAG
457318 ATAATTATTTA
1 ATAATTATTTA
*
457329 TAGTAA--ATTAA
1 -A-TAATTATTTA
*
457340 ATAATTATTTG
1 ATAATTATTTA
457351 ATAATTATTTA
1 ATAATTATTTA
457362 AT-ATTATTTA
1 ATAATTATTTA
457372 TATGAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 3 0.09
10 9 0.26
11 19 0.54
12 1 0.03
13 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (11 bp):
ATAATTATTTA
Found at i:459677 original size:22 final size:21
Alignment explanation
Indices: 459650--459701 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 21
459640 ACATCTTATG
459650 TGTCTTATATTGGTTCGAGGAA
1 TGTCTTAT-TTGGTTCGAGGAA
459672 TGTCTTAGTTTGGTTCGAGGAA
1 TGTCTTA-TTTGGTTCGAGGAA
459694 TGTCTTAT
1 TGTCTTAT
459702 GTGTCTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (21 bp):
TGTCTTATTTGGTTCGAGGAA
Found at i:460304 original size:31 final size:31
Alignment explanation
Indices: 460266--460341 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
460256 ACTAGTTAAA
*
460266 AATAGTGGTTTTTGCCTTGCCACCGAATAAG
1 AATAGTGGTTTTTGCCGTGCCACCGAATAAG
*
460297 AATAGTGGTTTTTACCGTGCCACCGAATAAG
1 AATAGTGGTTTTTGCCGTGCCACCGAATAAG
*
460328 AATAGTGATTTTTG
1 AATAGTGGTTTTTG
460342 TTTCAACTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (31 bp):
AATAGTGGTTTTTGCCGTGCCACCGAATAAG
Found at i:460404 original size:37 final size:38
Alignment explanation
Indices: 460310--460423 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 38
460300 AGTGGTTTTT
*
460310 ACCGTGCCACCGAATAAGAATAGTGATTTTTGTT-TCA
1 ACCGTGCCACCGGATAAGAATAGTGATTTTTGTTCTCA
* * *
460347 ACTTGTGCCACC-GATAAGAATAGTGATTTTTATTCT-G
1 AC-CGTGCCACCGGATAAGAATAGTGATTTTTGTTCTCA
* * * *
460384 ACCGTGCTACCGGATTAGAATAATGGTTTTTGTTCT-A
1 ACCGTGCCACCGGATAAGAATAGTGATTTTTGTTCTCA
460421 ACC
1 ACC
460424 TATGCCACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
36 7 0.11
37 47 0.75
38 9 0.14
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (38 bp):
ACCGTGCCACCGGATAAGAATAGTGATTTTTGTTCTCA
Found at i:461992 original size:160 final size:159
Alignment explanation
Indices: 461589--462071 Score: 630
Period size: 160 Copynumber: 3.0 Consensus size: 159
461579 GATAAGGAAT
* * * * *
461589 GTAAAACCTTTTGCCAAATATGAGTAAACTAGCCGTAATCAAAAAATAAATGGTTCATGCATTCC
1 GTAAGACCTTTTGCCAAATATGAGTAGACTAGCTGCAATCAAAAAATAAATGGTTCATGTATTCC
*
461654 TTCTCCTCCTAGCATAATAGCCA-T-TGTAGACCACACATGAATGCCCGAAGATCTTAGCTTGGT
66 TTCTCCTCTTAGCATAATAGCCATTGTGTAGACCACACATGAATGCCC-AAGATCTTAGCTTGGT
* * * *
461717 TAAGGTGTTTAACTCATCAAGAATAATCAA
130 TAAGGTGCTTAACTAATCAAGAATAGTTAA
* * * * * *
461747 CTAAGACTTTTTGCCAAATATGAGTAGACAAGCTGCAAGCAAAATATAAATGGTTCAAGTATTCC
1 GTAAGACCTTTTGCCAAATATGAGTAGACTAGCTGCAATCAAAAAATAAATGGTTCATGTATTCC
* * * *
461812 -TCTTCCTCTTATCATAATAGCCATTGTGTAGATCACAAATGAATGCCCAAGATCTTAGCTTGCT
66 TTC-TCCTCTTAGCATAATAGCCATTGTGTAGACCACACATGAATGCCCAAGATCTTAGCTTGGT
* *
461876 TAAGGTACTTAACTAATCAAGAACAGTTAA
130 TAAGGTGCTTAACTAATCAAGAATAGTTAA
* * *
461906 GTAAGACCTTTTGCAAAATATGAGTAGACTAGCTGCAATTAAAAAAATTAATGGTTCATGTATTC
1 GTAAGACCTTTTGCCAAATATGAGTAGACTAGCTGCAA-TCAAAAAATAAATGGTTCATGTATTC
* * * *
461971 CTTCTCCTCTTGGCATAATAGCCATTGTGTAGACCATACATAAATGCCTCAAGATTTTAGCTTGG
65 CTTCTCCTCTTAGCATAATAGCCATTGTGTAGACCACACATGAATGCC-CAAGATCTTAGCTTGG
*
462036 TTAAGGTGCTTAACTTATCAAGAATAGTTAA
129 TTAAGGTGCTTAACTAATCAAGAATAGTTAA
*
462067 ATAAG
1 GTAAG
462072 CTATAAATGA
Statistics
Matches: 276, Mismatches: 43, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
157 2 0.01
158 72 0.26
159 74 0.27
160 80 0.29
161 48 0.17
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (159 bp):
GTAAGACCTTTTGCCAAATATGAGTAGACTAGCTGCAATCAAAAAATAAATGGTTCATGTATTCC
TTCTCCTCTTAGCATAATAGCCATTGTGTAGACCACACATGAATGCCCAAGATCTTAGCTTGGTT
AAGGTGCTTAACTAATCAAGAATAGTTAA
Found at i:467646 original size:55 final size:54
Alignment explanation
Indices: 467577--467815 Score: 329
Period size: 55 Copynumber: 4.4 Consensus size: 54
467567 TCTTTTCACC
*
467577 CTTT-AGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
467630 CCTTTCAGTCTTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
467685 TTTTTTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
467740 TTTTCCAATCCTCAAAGAGCAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
467795 CTTCCTAGTCCTCAAAGAGCA
1 CTTTC-AGTCCTCAAAGAGCA
467816 AGATGCTCTC
Statistics
Matches: 164, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
54 9 0.05
55 153 0.93
56 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (54 bp):
CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:467872 original size:204 final size:208
Alignment explanation
Indices: 467630--468041 Score: 591
Period size: 204 Copynumber: 2.0 Consensus size: 208
467620 GTTGGTGGCA
* * *
467630 CCTTTCAGTCTTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTC
1 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAATC
467695 CTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTCAAAGAGC
66 CTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTCAAAGAGC
*
467760 AGGACGC-CT-C-TTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAAGATG
131 AGGACGCTCTCCTTTAAAGACCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGAGCAAGATG
467821 CTCTCTCCTTTCGC
195 CTCTCTCCTTTCGC
* *
467835 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAATC
1 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAATC
* * * * * *
467899 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTTCAGTCCTCAAAGAGT
66 CTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTCAAAGAGC
* * * *
467964 AGGATGCTTTCTCCTTTTAAAGACCACTCAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGA
131 AGGACGC--TCTCC-TTTAAAGACCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGA
* *
468029 TGCTTTCTTCTTT
193 TGCTCTCTCCTTT
468042 TAAAGACCAT
Statistics
Matches: 182, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
204 119 0.65
205 5 0.03
207 2 0.01
208 1 0.01
210 52 0.29
211 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (208 bp):
CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAATC
CTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTCAAAGAGC
AGGACGCTCTCCTTTAAAGACCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGATGC
TCTCTCCTTTCGC
Found at i:467958 original size:149 final size:149
Alignment explanation
Indices: 467688--467980 Score: 464
Period size: 149 Copynumber: 2.0 Consensus size: 149
467678 GGTGGCATTT
467688 TTTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTC
1 TTTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTC
467753 AAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAAG
66 AAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAAG
467818 ATGCTCTCTCCTTTCGCCC
131 ATGCTCTCTCCTTTCGCCC
* * * *
467837 TTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAATCCTC
1 TTTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTC
* ** *
467902 AAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGTA-TTTTTCAGTCCTCAAAGAGTA
66 AAAGAGCAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCACTTCCT-AGTCCTCAAAGAGCA
* *
467965 GGATGCTTTCTCCTTT
129 AGATGCTCTCTCCTTT
467981 TAAAGACCAC
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
148 5 0.04
149 127 0.96
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (149 bp):
TTTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAATCCTC
AAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAAG
ATGCTCTCTCCTTTCGCCC
Found at i:468157 original size:61 final size:59
Alignment explanation
Indices: 467837--468163 Score: 300
Period size: 61 Copynumber: 5.6 Consensus size: 59
467827 CCTTTCGCCC
* *
467837 TTTAGTCCTCAAAGAGCAGGACGC----CTTTTAAAGCCCACACAAGTTGGTGGCA-TT
1 TTTAGTCCTCAAAGAGCAGGACCCTTTTCTTTTAAAGCCCATACAAGTTGGTGGCACTT
* * *
467891 TTTCAATCCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACAAGTTGGTGGTA-TT
1 TTT-AGTCCTCAAAGAGCAGGAC-CCTTTTCTTTTAAAGCCCATACAAGTTGGTGGCACTT
* ** * *
467946 TTTCAGTCCTCAAAGAGTAGGATGCTTTCTCCTTTTAAAGACCACT-CAAGTTGGTGGCACCT
1 TTT-AGTCCTCAAAGAGCAGGACCCTTT-T-CTTTTAAAGCCCA-TACAAGTTGGTGGCACTT
* * * * *
468008 TTTAGTCCTCAAAGAGCAGGATGCTTTCTTCTTTTAAAGACCATTCGAGTTGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGA-CCCTT-TTCTTTTAAAGCCCATACAAGTTGGTGGCACTT
** * *
468069 TCCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGA-CCCTTTTCTTTT-AAAGCCCATACAAGTTGGTGGCACTT
468130 TTTAGTCCTCAAAGAGCAGGACACCTTTTCTTTT
1 TTTAGTCCTCAAAGAGCAGGAC-CCTTTTCTTTT
468164 TCTCCTTTAT
Statistics
Matches: 229, Mismatches: 25, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
54 4 0.02
55 64 0.28
56 2 0.01
57 1 0.00
59 1 0.00
60 8 0.03
61 141 0.62
62 7 0.03
63 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (59 bp):
TTTAGTCCTCAAAGAGCAGGACCCTTTTCTTTTAAAGCCCATACAAGTTGGTGGCACTT
Found at i:468230 original size:45 final size:45
Alignment explanation
Indices: 468157--468301 Score: 140
Period size: 42 Copynumber: 3.3 Consensus size: 45
468147 AGGACACCTT
* * * *
468157 TTCTTTTTCTCCTTTATCCTTAAA-AGCAGGACACACTTCATTTCC
1 TTCTTTTTC-CTTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCC
*
468202 TTCTTTTTCCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
1 TTCTTTTTCCTTTTGTCCTCAAAGAGCAGGACGCACTTCA-TTTCC
* * * *
468248 -TC--TTT-CTTTTGTCCTCGAAGAGCATGACGCATTTCGTTTTCC
1 TTCTTTTTCCTTTTGTCCTCAAAGAGCAGGACGCACTTC-ATTTCC
468290 TT-TTTTTCCTTT
1 TTCTTTTTCCTTT
468302 ATCCTCGAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
42 31 0.37
43 4 0.05
44 14 0.17
45 29 0.35
46 5 0.06
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (45 bp):
TTCTTTTTCCTTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCC
Found at i:468369 original size:41 final size:39
Alignment explanation
Indices: 468324--468425 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 39
468314 CAAGATGTAC
*
468324 TCTTTTTCACTTTGTCCTCAAGAAGCAAGACACT-TTCCTTT
1 TCTTTTTC-CTTTGTCCTCAAGAAGCAAGAC-CTATTCC-AT
* * * *
468365 TCTTTTCTCCATTGTCCTCAAGGAGTAAGACCTATTTCAT
1 TCTTTT-TCCTTTGTCCTCAAGAAGCAAGACCTATTCCAT
468405 TCTCTTTTCCTTTGTCCTCAA
1 TCT-TTTTCCTTTGTCCTCAA
468426 AAAGTGGGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 19 0.37
41 31 0.60
42 2 0.04
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.43
Consensus pattern (39 bp):
TCTTTTTCCTTTGTCCTCAAGAAGCAAGACCTATTCCAT
Found at i:474781 original size:79 final size:79
Alignment explanation
Indices: 474649--474868 Score: 244
Period size: 79 Copynumber: 2.8 Consensus size: 79
474639 TCATCTCGAG
** * * * * ** * * *
474649 GATACTCCAACCCCGGTTTTTTTTCCAAAATATCAATTTTTTATAATCGGGGATACTCCAATCCC
1 GATACTCCAACCCCAATTTTATTCCCAAAACACCAATTTTCCACAATCAGGGATACTCCAACCCC
*
474714 GTTAGTTT-CGAGGA
66 GTCA-TTTCCGAGGA
* * *
474728 GATACTCTAACCCCAATTTTATTCCCAAAACACCAATTTTTCACAATTAGGGATACTCCAACCCC
1 GATACTCCAACCCCAATTTTATTCCCAAAACACCAATTTTCCACAATCAGGGATACTCCAACCCC
*
474793 GTCATTTCCGAGGG
66 GTCATTTCCGAGGA
* * * *
474807 GATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAAC
1 GATACTCCAACCCCAATTTTATTCCCAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
474869 TCCGATTTTA
Statistics
Matches: 119, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
78 3 0.03
79 116 0.97
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (79 bp):
GATACTCCAACCCCAATTTTATTCCCAAAACACCAATTTTCCACAATCAGGGATACTCCAACCCC
GTCATTTCCGAGGA
Found at i:474878 original size:51 final size:51
Alignment explanation
Indices: 474804--474922 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
474794 TCATTTCCGA
* *
474804 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTCCACAATC
1 GGGGATACTCCAACCCCAGTTTTAGTTCCAAAACACCAATTTTCCACAATC
* * *
474855 GGGGATACTCCAACTCC-GATTTTAGTTCCAAAACGCCAATTTTTCACAATC
1 GGGGATACTCCAACCCCAG-TTTTAGTTCCAAAACACCAATTTTCCACAATC
474906 GGGGATACT-CAACCCCA
1 GGGGATACTCCAACCCCA
474923 TTATTTCATC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 7 0.12
51 53 0.88
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.27
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGTTTTAGTTCCAAAACACCAATTTTCCACAATC
Found at i:474957 original size:28 final size:29
Alignment explanation
Indices: 474903--474977 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
474893 ATTTTTCACA
*
474903 ATCGGGGATACT-CAACCCCATTATTT-C
1 ATCGGGGATACTCCAACCCCATCATTTCC
* *
474930 ATCGGGGATACTCCAACTCCGTCATTTCC
1 ATCGGGGATACTCCAACCCCATCATTTCC
*
474959 A-AGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
474978 GGCTTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.29
28 27 0.66
29 2 0.05
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCATCATTTCC
Found at i:475026 original size:51 final size:51
Alignment explanation
Indices: 474961--475080 Score: 186
Period size: 51 Copynumber: 2.4 Consensus size: 51
474951 TCATTTCCAA
*
474961 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATC
* * * * *
475012 GGGGATACTTCAACCCCGGCCTTATTTCTAAATTATTGATTTTTCAGAATC
1 GGGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATC
475063 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
475081 TTATTTTTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATC
Found at i:475063 original size:157 final size:158
Alignment explanation
Indices: 474777--475108 Score: 384
Period size: 157 Copynumber: 2.1 Consensus size: 158
474767 TTCACAATTA
* * *
474777 GGGATACTCCAACCCCGTCATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCA
1 GGGATACTCCAACCCCGTCATTTCCAAGGGGATACTCCAACCCCAGCTTTATTTCCAAAACACCA
* ** *
474842 ATTTTCCACAATCGGGGATACTCCAACTCCGATTTTAGTTCCAAAACGCCAATTTTTCACAATCG
66 ATTTTCCACAATCGGGGATACTCCAACCCCGACCTTAGTTCCAAAACACCAATTTTTCACAATCG
474907 GGGATACT-CAACCCCATTATTTCATCG
131 GGGATACTCCAACCCCATTATTTCATCG
* * * ***
474934 GGGATACTCCAACTCCGTCATTTCCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTG
1 GGGATACTCCAACCCCGTCATTTCCAAGGGGATACTCCAACCCCAGCTTTATTTCCAAAACACCA
* * * * ** *** *
474999 A-TTTCTCACAATCGGGGATACTTCAACCCCGGCCTTATTTCTAAATTATTGATTTTTCAGAATC
66 ATTTTC-CACAATCGGGGATACTCCAACCCCGACCTTAGTTCCAAAACACCAATTTTTCACAATC
* *
475063 GGGGATACTCCAACCCCGTTATTT--TTG
130 GGGGATACTCCAACCCCATTATTTCATCG
475090 AGGGAATACTCCAACCCCG
1 -GGG-ATACTCCAACCCCG
475109 ATTTTATTTT
Statistics
Matches: 145, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
156 6 0.04
157 113 0.78
158 26 0.18
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (158 bp):
GGGATACTCCAACCCCGTCATTTCCAAGGGGATACTCCAACCCCAGCTTTATTTCCAAAACACCA
ATTTTCCACAATCGGGGATACTCCAACCCCGACCTTAGTTCCAAAACACCAATTTTTCACAATCG
GGGATACTCCAACCCCATTATTTCATCG
Found at i:475147 original size:79 final size:78
Alignment explanation
Indices: 475064--475240 Score: 237
Period size: 79 Copynumber: 2.2 Consensus size: 78
475054 TTCAGAATCG
*** * *
475064 GGGATACTCCAACCCCGTTATTTTTGAGGGAATACTCCAACCCCGATTTTATTTTCAAAATACTG
1 GGGATACTCCAACCCCGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAACACTG
*
475129 ATTTTCTATAATTA
66 ATTTTCCATAA-TA
* * *
475143 GGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAGAACACTG
1 GGGATACTCCAACCCCGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAACACTG
*
475208 ATTTTCCATAATC
66 ATTTTCCATAATA
*
475221 GAGGATACTCCACCCCCGTT
1 G-GGATACTCCAACCCCGTT
475241 GTTATCTCCA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 2 0.02
79 83 0.98
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAACACTG
ATTTTCCATAATA
Found at i:478187 original size:28 final size:26
Alignment explanation
Indices: 478135--478210 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 26
478125 ATTTTTCACA
*
478135 ATCGGGGATACTCAACCCCGTTATTT
1 ATCGGGGATACTTAACCCCGTTATTT
478161 CATCGGGGATACTGTAACCCCGTTATTT
1 -ATCGGGGATACT-TAACCCCGTTATTT
478189 -TCGAGGGGATACTCTAACCCCG
1 ATC--GGGGATACT-TAACCCCG
478211 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 2 0.05
27 12 0.27
28 30 0.68
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (26 bp):
ATCGGGGATACTTAACCCCGTTATTT
Found at i:478262 original size:54 final size:54
Alignment explanation
Indices: 478193--478301 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
478183 TTATTTTCGA
*
478193 GGGGATACTCTAACCCCGACTTTATTTCCAAAAT-ATTGATTTCTCACAATCGGG
1 GGGGATACTCTAACCCCGACCTTATTT-CAAAATCATTGATTTCTCACAATCGGG
* * *
478247 GGGGATACT-TCAACCCCGGCCTTATTTCTAAATCATTGATTTTTCACAATCGGG
1 GGGGATACTCT-AACCCCGACCTTATTTCAAAATCATTGATTTCTCACAATCGGG
478301 G
1 G
478302 ATACTCCAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 6 0.12
54 43 0.88
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (54 bp):
GGGGATACTCTAACCCCGACCTTATTTCAAAATCATTGATTTCTCACAATCGGG
Found at i:478445 original size:79 final size:79
Alignment explanation
Indices: 478294--478447 Score: 218
Period size: 79 Copynumber: 1.9 Consensus size: 79
478284 GATTTTTCAC
* * * *
478294 AATCGGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTTATTTTCAAAA
1 AATCAGGGATACTCCAACCCTGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAA
* *
478359 TATCGATTTTCTAT
66 CACCGATTTTCTAT
* ** *
478373 AATCAGGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCTTGATTTTATTTCCAGAA
1 AATCAGGGATACTCCAACCCTGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAA
478438 CACCGATTTT
66 CACCGATTTT
478448 TCGTAACCGA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (79 bp):
AATCAGGGATACTCCAACCCTGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAA
CACCGATTTTCTAT
Found at i:478463 original size:79 final size:79
Alignment explanation
Indices: 478301--478475 Score: 201
Period size: 79 Copynumber: 2.2 Consensus size: 79
478291 CACAATCGGG
* * * * *
478301 GATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTTATTTTCAAAATATCGAT
1 GATACTCCAACCCTGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAACACCGAT
* *
478366 TTTCTATAATCAGG
66 TTTCTATAACCAGA
* ** *
478380 GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCTTGATTTTATTTCCAGAACACCGAT
1 GATACTCCAACCCTGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAACACCGAT
*
478445 TTT-TCGTAACC-GAA
66 TTTCT-ATAACCAG-A
*
478459 GATACTCCACCCCTGTT
1 GATACTCCAACCCTGTT
478476 GTTATCTCCA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 2 0.02
79 79 0.98
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.33
Consensus pattern (79 bp):
GATACTCCAACCCTGTTATTTCCAAGGGAATACTCCAACCCCGATTTTATTTCCAAAACACCGAT
TTTCTATAACCAGA
Found at i:479562 original size:61 final size:62
Alignment explanation
Indices: 479497--479653 Score: 196
Period size: 61 Copynumber: 2.5 Consensus size: 62
479487 TTGTGGACAT
* *
479497 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTACTGCA-AAGTTGTGGGCTTTG-AAAAGA
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTAC--CAGAAGTTGTAGGCTTTGAAAAAGA
* *
479559 AAAAAGGTGCCACAGAGTTGTGGACTTGAAA-GGTACCATGTAGTTGTAGGCTTTGAAAAAG-
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCA-GAAGTTGTAGGCTTTGAAAAAGA
* * *
479620 GAATAGGTGCCACAAAGTTGTGGACTTAAAAGGG
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGG
479654 AAAAATGTGC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
59 2 0.02
61 45 0.54
62 36 0.43
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.23
Consensus pattern (62 bp):
AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCAGAAGTTGTAGGCTTTGAAAAAGA
Found at i:479693 original size:27 final size:27
Alignment explanation
Indices: 479654--479933 Score: 256
Period size: 27 Copynumber: 10.1 Consensus size: 27
479644 CTTAAAAGGG
* *
479654 AAAAATGTGCCACGGAGTTGTGGACTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
*
479681 AAAAAGGTACCACGGAGTTATGGACTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
* * *
479708 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
479735 -AAAAGGTGCCACGGAGTTATGGACTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
* * **
479761 AAAAGGGTACCATAGAGTTATGGACTTAAAT
1 AAAAAGGTGCCACGGAGTTATGGAC-T---T
479792 GGGAAAAAGGTGCCACGGAGTTATGGACTT
1 ---AAAAAGGTGCCACGGAGTTATGGACTT
* * * *
479822 AAAAAGGTGCTACAGAGTTGTGGATTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
* * * * *
479849 AAAAGGGTACTACGAAGTTGTGGACTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
* * * *
479876 AGAAGGGTGCTACAGAGTTATGGACTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
* * *
479903 AAAAGGGTGCCACGGAGTTGTGGATTT
1 AAAAAGGTGCCACGGAGTTATGGACTT
479930 AAAA
1 AAAA
479934 GAGAAAAGAG
Statistics
Matches: 208, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
26 23 0.11
27 160 0.77
28 1 0.00
30 1 0.00
31 1 0.00
33 1 0.00
34 21 0.10
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (27 bp):
AAAAAGGTGCCACGGAGTTATGGACTT
Found at i:479824 original size:114 final size:115
Alignment explanation
Indices: 479681--479905 Score: 335
Period size: 114 Copynumber: 2.0 Consensus size: 115
479671 TTGTGGACTT
* *
479681 AAAAAGGTACCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA-GGTGCC
1 AAAAAGGTACCACGGAGTTATGGACTTAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTACC
* *
479745 ACGGAGTTATGGACTTAAAAGGGTACCATAGAGTTATGGACTTAAATGGG
66 ACGAAGTTATGGACTTAAAAGGGTACCACAGAGTTATGGACTTAAATGGG
* * * *
479795 AAAAAGGTGCCACGGAGTTATGGACTTAAAAAGGTGCTACAGAGTTGTGGATTTAAAAGGGTACT
1 AAAAAGGTACCACGGAGTTATGGACTTAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTACC
* * * *
479860 ACGAAGTTGTGGACTTAGAAGGGTGCTACAGAGTTATGGACTTAAA
66 ACGAAGTTATGGACTTAAAAGGGTACCACAGAGTTATGGACTTAAA
479906 AGGGTGCCAC
Statistics
Matches: 98, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
114 54 0.55
115 44 0.45
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.24
Consensus pattern (115 bp):
AAAAAGGTACCACGGAGTTATGGACTTAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTACC
ACGAAGTTATGGACTTAAAAGGGTACCACAGAGTTATGGACTTAAATGGG
Found at i:479826 original size:141 final size:142
Alignment explanation
Indices: 479629--479969 Score: 445
Period size: 141 Copynumber: 2.4 Consensus size: 142
479619 GGAATAGGTG
* *
479629 CCACAAAGTTGTGGACTTAAAAGGGAAAAATGTGCCACGGAGTTGTGGACTTAAAAAGGTACCAC
1 CCACAGAGTTGTGGACTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGGTACCAC
* * *
479694 GGAGTTATGGACTTAAAAGGGTGCCAC-AGAGTTGTGGACTTA-AAAGGTGCCACGGAGTTATGG
66 AGAGTTATGGACTTAAAAGGGTACCACGA-AGTTGTGGACTTAGAAAGGTGCCACAGAGTTATGG
479757 ACTTAAAAGGGTA
130 ACTTAAAAGGGTA
* * * * * *
479770 CCATAGAGTTATGGACTTAAATGGGAAAAAGGTGCCACGGAGTTATGGACTTAAAAAGGTGCTAC
1 CCACAGAGTTGTGGACTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGGTACCAC
* * * * *
479835 AGAGTTGTGGATTTAAAAGGGTACTACGAAGTTGTGGACTTAGAAGGGTGCTACAGAGTTATGGA
66 AGAGTTATGGACTTAAAAGGGTACCACGAAGTTGTGGACTTAGAAAGGTGCCACAGAGTTATGGA
*
479900 CTTAAAAGGGTG
131 CTTAAAAGGGTA
* * * * *
479912 CCACGGAGTTGTGGATTTAAAAGAG-AAAAGAGTGTCACGGAGTTGTGAACTTAAAAAG
1 CCACAGAGTTGTGGACTTAAAAGGGAAAAAG-GTGCCACGGAGTTGTGGACTTAAAAAG
479970 AAAAAGGTGC
Statistics
Matches: 171, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
141 97 0.57
142 74 0.43
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.23
Consensus pattern (142 bp):
CCACAGAGTTGTGGACTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGGTACCAC
AGAGTTATGGACTTAAAAGGGTACCACGAAGTTGTGGACTTAGAAAGGTGCCACAGAGTTATGGA
CTTAAAAGGGTA
Found at i:479951 original size:34 final size:34
Alignment explanation
Indices: 479903--480102 Score: 195
Period size: 34 Copynumber: 6.0 Consensus size: 34
479893 TTATGGACTT
* *
479903 AAAAGGGTGCCACGGAGTTGTGGATTTAAAAGAG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGAG
* *
479937 AAAAGAGTGTCACGGAGTTGTGAACTTAAAA-AG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGAG
* *
479970 AAAA-AGGTGCCACAGAGTTGTGGACTTAAAATA-
1 AAAAGA-GTGCCACGGAGTTGTGGACTTAAAAGAG
* *
480003 AAAGGA-TGCCACAGAGTTGTGGACTTAAAAG-G
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGAG
*
480035 AAAAAGAATGCCACGGAGTTGTGGACTT----G-G
1 -AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGAG
*
480065 AAAAGAGATGCCACTGAGTTGTGGACTTGGAAAAGAG
1 AAAAGAG-TGCCACGGAGTTGTGGACTT--AAAAGAG
480102 A
1 A
480103 TGCCACTGAG
Statistics
Matches: 139, Mismatches: 13, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
29 6 0.04
30 21 0.15
32 25 0.18
33 36 0.26
34 48 0.35
36 1 0.01
37 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGAG
Found at i:480099 original size:66 final size:63
Alignment explanation
Indices: 479935--480092 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 63
479925 GATTTAAAAG
* * * * *
479935 AGAAAAGAG-TGTCACGGAGTTGTGAACTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
1 AGAAAAGAGATGCCACAGAGTTGTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTT
* * *
479997 AAAATAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAATGCCACGGAGTTGTGGACT
1 AGAA-AAGA-GATGCCACAGAGTTGTGGACTTAAAAGGAAAAAG-ATGCCACAGAGTTGTGGACT
480062 T
63 T
* *
480063 GGAAAAGAGATGCCACTGAGTTGTGGACTT
1 AGAAAAGAGATGCCACAGAGTTGTGGACTT
480093 GGAAAAGAGA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 22 0.28
65 31 0.39
66 21 0.26
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (63 bp):
AGAAAAGAGATGCCACAGAGTTGTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTT
Found at i:481435 original size:6 final size:6
Alignment explanation
Indices: 481426--481458 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
481416 ACTTTTTTAA
481426 TTTTT- TTTTT- TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
481459 TTAACTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (6 bp):
TTTTTG
Found at i:482297 original size:80 final size:80
Alignment explanation
Indices: 482164--482319 Score: 294
Period size: 80 Copynumber: 1.9 Consensus size: 80
482154 AAACAGGCAA
*
482164 GAAAAATGCAAGGATTTCCAACAATGACTCCATCATCAAAAGCTAACTCTGATGGATGGAGAAGG
1 GAAAAATGCAAGGATTTCCAACAATGACTCCATCATCAAAAGCCAACTCTGATGGATGGAGAAGG
*
482229 GTTCTTTTGCTGCCT
66 GTTCGTTTGCTGCCT
482244 GAAAAATGCAAGGATTTCCAACAATGACTCCATCATCAAAAGCCAACTCTGATGGATGGAGAAGG
1 GAAAAATGCAAGGATTTCCAACAATGACTCCATCATCAAAAGCCAACTCTGATGGATGGAGAAGG
482309 GTTCGTTTGCT
66 GTTCGTTTGCT
482320 TCAAGACTGA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (80 bp):
GAAAAATGCAAGGATTTCCAACAATGACTCCATCATCAAAAGCCAACTCTGATGGATGGAGAAGG
GTTCGTTTGCTGCCT
Found at i:482958 original size:13 final size:13
Alignment explanation
Indices: 482940--482964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
482930 ATTACTCAAA
482940 TGTATCGATACAT
1 TGTATCGATACAT
482953 TGTATCGATACA
1 TGTATCGATACA
482965 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:489928 original size:15 final size:16
Alignment explanation
Indices: 489913--489994 Score: 87
Period size: 15 Copynumber: 4.9 Consensus size: 16
489903 AGTGATGAAA
489913 AAAAACACAAAAAAAAC
1 AAAAACAC-AAAAAAAC
489930 AAAAACAAACAAAAAAAC
1 AAAAAC--ACAAAAAAAC
*
489948 AAAAA-ACAAAAAAAG
1 AAAAACACAAAAAAAC
*
489963 AAAAACAACACAAAAA-
1 AAAAAC-ACAAAAAAAC
489979 AAAAACACAGAAAAAA
1 AAAAACACA-AAAAAA
489995 GGTGCAAAGG
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
15 17 0.30
16 11 0.19
17 14 0.25
18 13 0.23
19 2 0.04
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAACACAAAAAAAC
Found at i:489993 original size:33 final size:32
Alignment explanation
Indices: 489910--489995 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 32
489900 AAAAGTGATG
*
489910 AAAAAAAACACAAAAAAAACAAAAACAAACAAA
1 AAAAAAAACAC-AAAAAAAGAAAAACAAACAAA
*
489943 AAAACAAAAAACAAAAAAAGAAAAAC-AACACAA
1 AAAA-AAAACACAAAAAAAGAAAAACAAACA-AA
489976 AAAAAAAACACAGAAAAAAG
1 AAAAAAAACACA-AAAAAAG
489996 GTGCAAAGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.23
33 30 0.64
34 6 0.13
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (32 bp):
AAAAAAAACACAAAAAAAGAAAAACAAACAAA
Found at i:490256 original size:21 final size:20
Alignment explanation
Indices: 490232--490285 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
490222 GTTCTTTTCC
490232 AAAAA-AGAAACAACACAAAAA
1 AAAAACAGAAA-AACA-AAAAA
* *
490253 AAAAAGAGAAAAAGAAAAAA
1 AAAAACAGAAAAACAAAAAA
490273 ACAAAACAGAAAA
1 A-AAAACAGAAAA
490286 TCTCGGCGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.21
21 18 0.62
22 5 0.17
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAACAGAAAAACAAAAAA
Found at i:490270 original size:15 final size:14
Alignment explanation
Indices: 490233--490285 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
490223 TTCTTTTCCA
*
490233 AAAAAGAAACAACAC
1 AAAAAGAAA-AAAAC
* *
490248 AAAAA-AAAAAGAG
1 AAAAAGAAAAAAAC
490261 AAAAAGAAAAAAAC
1 AAAAAGAAAAAAAC
490275 AAAACAGAAAA
1 AAAA-AGAAAA
490286 TCTCGGCGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 8 0.25
14 13 0.41
15 11 0.34
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAC
Found at i:490352 original size:14 final size:15
Alignment explanation
Indices: 490335--490365 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
490325 ACAAAAAAAG
490335 AAAC-AAAAAAGAAA
1 AAACAAAAAAAGAAA
490349 AAACAAAAAAAGAAA
1 AAACAAAAAAAGAAA
490364 AA
1 AA
490366 CCTCTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (15 bp):
AAACAAAAAAAGAAA
Found at i:490366 original size:14 final size:14
Alignment explanation
Indices: 490325--490366 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
490315 CCTAATCTTC
490325 ACAAAAAAAG--AA
1 ACAAAAAAAGAAAA
490337 AC-AAAAAAGAAAAA
1 ACAAAAAAAG-AAAA
490351 ACAAAAAAAGAAAA
1 ACAAAAAAAGAAAA
490365 AC
1 AC
490367 CTCTTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.27
12 2 0.08
14 10 0.38
15 7 0.27
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (14 bp):
ACAAAAAAAGAAAA
Found at i:491394 original size:23 final size:23
Alignment explanation
Indices: 491364--491409 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
491354 GCATCTTGTC
*
491364 TCAAAGTCCACGACTCAGTGGCA
1 TCAAAGTCCACAACTCAGTGGCA
*
491387 TCAAAGTCCACAACTCCGTGGCA
1 TCAAAGTCCACAACTCAGTGGCA
491410 CTCTTTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (23 bp):
TCAAAGTCCACAACTCAGTGGCA
Found at i:491495 original size:67 final size:66
Alignment explanation
Indices: 491389--491848 Score: 422
Period size: 67 Copynumber: 6.8 Consensus size: 66
491379 CAGTGGCATC
* *
491389 AAAGTCCACAACTCCGTGGCACTCTTTTTCCTTCTTAAAGTCCACGACTCCGTGGCACC-TTCTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTTCCTT-TTAAAGCCCACAACTCCGTGGCACCTTTCTT
*
491453 TTC
64 TTT
* * * *
491456 AAAGCCCATAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACTCCATGGCACCTTGTTC
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAAGCCCACAACTCCGTGGCACC-T-TTC
*
491521 CTTTT
62 TTTTT
* * * *
491526 -AAGTCCACGACTCTGTGGTACC---TT-CTTTTCAAAGCTCACAACTCCGTGGCACCTTTTTCT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-AAAGCCCACAACTCCGTGGCACC--TTTCT
491586 TTTT
63 TTTT
* *
491590 TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACC--TTTCTT
491655 TTT
64 TTT
* * *
491658 AAAGCCCACAACTTCATGGCACCTTTTT-CTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-AAAGCCCACAACTCCGTGGCAC-C--TTT-
*
491722 CCTTTT
61 CTTTTT
*
491728 AAAGTCCACGACTCCGTGGCACC---TT-CTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-AAAGCCCACAACTCCGTGGCAC-C--TTT-
*
491789 CCTTTT
61 CTTTTT
* * * * *
491795 AAAGCCCACAACTCCGTGGCACCTTGTT-CTTTTTAAGTCCACAACTTCGTGGCA
1 AAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCA
491849 TTTTTCACCA
Statistics
Matches: 341, Mismatches: 35, Indels: 32
0.84 0.09 0.08
Matches are distributed among these distances:
63 5 0.01
64 27 0.08
65 23 0.07
67 119 0.35
68 86 0.25
69 44 0.13
70 37 0.11
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (66 bp):
AAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCTTTCTTTT
T
Found at i:491600 original size:34 final size:34
Alignment explanation
Indices: 491389--491848 Score: 503
Period size: 34 Copynumber: 13.6 Consensus size: 34
491379 CAGTGGCATC
*
491389 AAAGTCCACAACTCCGTGGCACTCTTTTTCCTTCTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* *
491425 AAAGTCCACGACTCCGTGGCACC---TTCTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* * *
491456 AAAGCCCATAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* * *
491492 AAAGTCCACAACTCCATGGCACCTTGTTCCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * *
491526 -AAGTCCACGACTCTGTGGTACC---TTCTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
491556 AAAG-CTCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGTC-CACAACTCCGTGGCACCTTTTTCTTTTT
*
491590 TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
*
491624 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * *
491658 AAAGCCCACAACTTCATGGCACCTTTTTCTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
491692 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* *
491728 AAAGTCCACGACTCCGTGGCACC---TTCTTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
491759 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* *
491795 AAAGCCCACAACTCCGTGGCACCTTGTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
*
491829 -AAGTCCACAACTTCGTGGCA
1 AAAGTCCACAACTCCGTGGCA
491849 TTTTTCACCA
Statistics
Matches: 362, Mismatches: 44, Indels: 39
0.81 0.10 0.09
Matches are distributed among these distances:
30 7 0.02
31 64 0.18
32 6 0.02
33 36 0.10
34 132 0.36
35 23 0.06
36 94 0.26
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
Found at i:492001 original size:32 final size:33
Alignment explanation
Indices: 491861--492284 Score: 659
Period size: 32 Copynumber: 13.0 Consensus size: 33
491851 TTTCACCATT
*
491861 TCTAAAGCCCACACAAGTCGGTGGCAAACCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
491894 TCTAAAGCCCACACAAGTCGGTGGCAAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGC-AACCCTTC
491928 TCTAAAGCCCACACAAGTCGGTGGCAA-CCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
491960 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
491994 TC-AAAGCCCACACAAGTCGGTGGCAACCC-TC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
492025 TCTAAAGCCCACACAAGTCGATGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
492058 TC-AAAGCCCACACAAGTCGGTGGCAATCC-TC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
* * *
492089 TCTAAAGCCCATACAAGTCAGTGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
* *
492122 TCTAAAGCCCACACAAGTCGATGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
492155 TCTAAAGCCCACACAAGTTGGTGGCAATCCC--C
1 TCTAAAGCCCACACAAGTCGGTGGCAA-CCCTTC
492187 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
492220 TC-AAAGCCCACACAAGTCAGTGGCAACCC-TC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
492251 TCTAAAGCCCACACAAGTCGATGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
492284 T
1 T
492285 AAGCCCAATA
Statistics
Matches: 361, Mismatches: 18, Indels: 24
0.90 0.04 0.06
Matches are distributed among these distances:
31 15 0.04
32 184 0.51
33 123 0.34
34 39 0.11
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.18
Consensus pattern (33 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
Found at i:492149 original size:194 final size:195
Alignment explanation
Indices: 491860--492291 Score: 666
Period size: 194 Copynumber: 2.2 Consensus size: 195
491850 TTTTCACCAT
*
491860 TTCT-AAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACC
1 TTCTCAAAGCCCACACAAGTCGGTGGCAAACC-TCTCTAAAGCCCACACAAGTCAGTGGCAAACC
* *
491924 CTTCTCTAAAGCCCACACAAGTCGGTGGCAACC-TTCTTCTAAAGCCCACACAAGTCGGTGGCAA
65 ATTCTCTAAAGCCCACACAAGTCGATGGCAACCATTC-TCTAAAGCCCACACAAGTCGGTGGCAA
*
491988 -CCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCC-TCTCTAAAGCCCACACAAGTC-GATGGC
129 TCCCCTCT-AAAGCCCACACAAGTCGGTGGCAACCCTTCTC-AAAGCCCACACAAGTCAG-TGGC
492050 AACCC
191 AACCC
* *
492055 TTCTCAAAGCCCACACAAGTCGGTGGCAATCCTCTCTAAAGCCCATACAAGTCAGTGGC-AACCA
1 TTCTCAAAGCCCACACAAGTCGGTGGCAAACCTCTCTAAAGCCCACACAAGTCAGTGGCAAACCA
*
492119 TTCTCTAAAGCCCACACAAGTCGATGGCAACCATTCTCTAAAGCCCACACAAGTTGGTGGCAATC
66 TTCTCTAAAGCCCACACAAGTCGATGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAATC
492184 CCCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCAGTGGCAACCC
131 CCCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCAGTGGCAACCC
* *
492249 -TCTCTAAAGCCCACACAAGTCGATGGCAACCCT-TCT-AAGCCCA
1 TTCTC-AAAGCCCACACAAGTCGGTGGCAAACCTCTCTAAAGCCCA
492292 ATATCGCTAG
Statistics
Matches: 222, Mismatches: 9, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
192 7 0.03
193 7 0.03
194 139 0.63
195 43 0.19
196 26 0.12
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.18
Consensus pattern (195 bp):
TTCTCAAAGCCCACACAAGTCGGTGGCAAACCTCTCTAAAGCCCACACAAGTCAGTGGCAAACCA
TTCTCTAAAGCCCACACAAGTCGATGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAATC
CCCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCAGTGGCAACCC
Found at i:492446 original size:92 final size:92
Alignment explanation
Indices: 492279--493306 Score: 1564
Period size: 92 Copynumber: 11.1 Consensus size: 92
492269 CGATGGCAAC
* * *
492279 CCTTCTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
492344 TAACTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
492372 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
492437 AGCTCGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
492464 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTCACCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
* *
492529 TGCTGGCCTTGAATCAGCATATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
492556 CCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
* * * *
492615 CAATATTGCTGGCCTTGAATCAGTATATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
492648 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
492713 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
492746 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
492811 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
492838 CATTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
492903 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
492930 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
492995 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
493022 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
493087 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
493114 CCTTTAAGTCCAATATTGCTAGCCTTGAATAAGCATATTGGCACCTTCTTCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
493179 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
493206 CCTTTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTTAAGTCCAA
* *
493271 TATAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
493301 TCCTTT
1 -CCTTT
493307 TTCTCATCTT
Statistics
Matches: 877, Mismatches: 42, Indels: 29
0.93 0.04 0.03
Matches are distributed among these distances:
92 743 0.85
93 4 0.00
94 4 0.00
95 42 0.05
96 7 0.01
98 77 0.09
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:492543 original size:141 final size:140
Alignment explanation
Indices: 492330--493306 Score: 1270
Period size: 141 Copynumber: 7.0 Consensus size: 140
492320 GCACCTTCAT
* * *
492330 CTTTAAGTCCAATGTAACTGGCCTTGAATCAGCACATTGG-----CACCTTTAAGTCCAATATAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCACCTTTAAGTCCAATATAG
* *
492390 CTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGCTCGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
492455 ACATTGGCAC
131 ACATTGGCAC
*
492465 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTCACCTTTAAGTCCAATATT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-TTCACCTTTAAGTCCAATATA
*
492530 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAG
65 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
492595 CACATTGGCAC
130 CACATTGGCAC
* * * *
492606 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGTATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTCACCTTTAAGTCCAATATA
492671 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
65 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
492736 CACATTGGCAC
130 CACATTGGCAC
** *
492747 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTCACCTTTAAGTCCAATATA
* *
492812 GCTGGCCTTGAATCAGCACATTGGCA----CA--TTTAAGTCCAATATAGCTGGCCTTGAATCAG
65 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
*
492871 CATATTGGCACCTTC
130 CACATTGGCA----C
* *
492886 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CACCTTTAAGTCCAATAT
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCACCTTTAAGTCCAATAT
*
492946 CGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCA
64 AGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCA
493011 GCACATTGGCAC
129 GCACATTGGCAC
* * *
493023 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTCACCTTTAAGTCCAATATA
* * * * *
493088 GCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATTGCTAGCCTTGAATAAG
65 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
*
493147 CATATTGGCACCTTC
130 CACATTGGCA----C
*
493162 TTCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-----CACCTTTAAGTCCAATAT
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCACCTTTAAGTCCAATAT
* * * *
493222 AGCTGGCCTTAAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATATAGCTGGCCTTGAA
64 AGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAA
*
493287 TCAGCACATTGACATC
126 TCAGCACATTGGCA-C
493303 CTTT
1 CTTT
493307 TTCTCATCTT
Statistics
Matches: 751, Mismatches: 51, Indels: 76
0.86 0.06 0.09
Matches are distributed among these distances:
135 231 0.31
137 4 0.01
139 8 0.01
141 470 0.63
142 2 0.00
144 36 0.05
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (140 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCACCTTTAAGTCCAATATAG
CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
ACATTGGCAC
Found at i:493231 original size:22 final size:22
Alignment explanation
Indices: 493164--493231 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
493154 GCACCTTCTT
493164 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* * *
493186 CTTGAA-TCAGCACAT-TGGC--AC
1 CTTTAAGTC--CA-ATATAGCTGGC
493207 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
493229 CTT
1 CTT
493232 AAATCAGCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:493336 original size:55 final size:52
Alignment explanation
Indices: 493207--493344 Score: 168
Period size: 52 Copynumber: 2.6 Consensus size: 52
493197 ACATTGGCAC
* * *
493207 CTTTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACATTTTCCAT
* *
493259 CTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA--CATTTTC-CAT
* * * *
493314 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
493345 ACATATTAGC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 38 0.52
54 6 0.08
55 29 0.40
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACATTTTCCAT
Found at i:493708 original size:10 final size:10
Alignment explanation
Indices: 493693--493726 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
493683 CCTTCCAAAC
493693 TCTACACCAA
1 TCTACACCAA
493703 TCTACACCAA
1 TCTACACCAA
*
493713 TCTACACCTA
1 TCTACACCAA
493723 TCTA
1 TCTA
493727 AGGAGGTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (10 bp):
TCTACACCAA
Found at i:494202 original size:19 final size:19
Alignment explanation
Indices: 494157--494241 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
494147 ATTTCAACGA
*
494157 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACAT-AAGT
*
494177 GTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
494196 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
494211 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
494228 TTTGTATCGATACA
1 TTTGTATCGATACA
494242 ATTTAAGCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 27 0.48
20 14 0.25
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:494216 original size:13 final size:13
Alignment explanation
Indices: 494198--494222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
494188 ACATAAGTTT
494198 TGTATCGATACAA
1 TGTATCGATACAA
494211 TGTATCGATACA
1 TGTATCGATACA
494223 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:494218 original size:32 final size:32
Alignment explanation
Indices: 494179--494243 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
494169 CATAAAATGT
494179 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
494211 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
494243 T
1 T
494244 TTAAGCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:494302 original size:13 final size:13
Alignment explanation
Indices: 494284--494308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
494274 ATTACTCAAA
494284 TGTATCGATACAT
1 TGTATCGATACAT
494297 TGTATCGATACA
1 TGTATCGATACA
494309 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:494373 original size:52 final size:52
Alignment explanation
Indices: 494317--494441 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
494307 CACTGATCTT
* *
494317 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
494369 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
494421 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
494442 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:504895 original size:19 final size:18
Alignment explanation
Indices: 504869--504936 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
504859 TATATATGTG
504869 TAAA-TATTAAAAATATGT
1 TAAATTATTAAAAATAT-T
*
504887 TAAATTATT-CAAAT-TT
1 TAAATTATTAAAAATATT
*
504903 TAAAATTTAATAAAAATA-T
1 T-AAA-TTATTAAAAATATT
*
504922 TAAATTACTAAAAAT
1 TAAATTATTAAAAAT
504937 TAAATTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.05
17 14 0.34
18 15 0.37
19 10 0.24
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (18 bp):
TAAATTATTAAAAATATT
Found at i:504948 original size:15 final size:15
Alignment explanation
Indices: 504915--504966 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
504905 AAATTTAATA
**
504915 AAAATATTAAATTACT
1 AAAA-ATTAAATTTTT
504931 AAAAATTAAATTTTT
1 AAAAATTAAATTTTT
* *
504946 AAAAAATATATTTTTT
1 AAAAATTA-AATTTTT
504962 AAAAA
1 AAAAA
504967 ATAATATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 16 0.52
16 15 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATTAAATTTTT
Found at i:504950 original size:16 final size:16
Alignment explanation
Indices: 504913--504968 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
504903 TAAAATTTAA
**
504913 TAAAAATATTAAATTAC
1 TAAAAA-ATTAAATTTT
504930 T-AAAAATTAAATTTT
1 TAAAAAATTAAATTTT
*
504945 TAAAAAA-TATATTTTT
1 TAAAAAATTA-AATTTT
504961 TAAAAAAT
1 TAAAAAAT
504969 AATATGATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 11 0.33
16 21 0.64
17 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAAAATTAAATTTT
Found at i:505150 original size:16 final size:16
Alignment explanation
Indices: 505126--505156 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
505116 AATTATAATA
505126 TGATATTATAATTTTG
1 TGATATTATAATTTTG
*
505142 TGATCTTATAATTTT
1 TGATATTATAATTTT
505157 ATTTTTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (16 bp):
TGATATTATAATTTTG
Found at i:505529 original size:16 final size:17
Alignment explanation
Indices: 505502--505552 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
505492 TTAAAAAAGT
505502 TTTAAATAAAAAATAAA
1 TTTAAATAAAAAATAAA
505519 TTTAAAT-AAAAATAAA
1 TTTAAATAAAAAATAAA
* **
505535 TATATTTAAAAAATAAA
1 TTTAAATAAAAAATAAA
505552 T
1 T
505553 CAAGCATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTAAATAAAAAATAAA
Found at i:505618 original size:7 final size:7
Alignment explanation
Indices: 505606--505694 Score: 53
Period size: 7 Copynumber: 13.0 Consensus size: 7
505596 TTTTTTAAAT
505606 TATATAA
1 TATATAA
505613 TATAT-A
1 TATATAA
*
505619 TCATAT-T
1 T-ATATAA
*
505626 TATAT-T
1 TATATAA
*
505632 TATATAT
1 TATATAA
505639 TATATAA
1 TATATAA
* *
505646 TTTATAT
1 TATATAA
505653 TATATAA
1 TATATAA
* *
505660 AAAATAAA
1 TATAT-AA
505668 TATATAA
1 TATATAA
505675 TATTATAA
1 TA-TATAA
505683 TATA-AA
1 TATATAA
505689 TA-ATAA
1 TATATAA
505695 AAAATATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
5 1 0.01
6 18 0.27
7 36 0.54
8 12 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:505638 original size:21 final size:21
Alignment explanation
Indices: 505605--505658 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
505595 ATTTTTTAAA
*
505605 TTATATAATATA-TATCAT-AT
1 TTATATTATATATTAT-ATAAT
505625 TTATATTTATATATTATATAAT
1 TTATA-TTATATATTATATAAT
505647 TTATATTATATA
1 TTATATTATATA
505659 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 15 0.50
22 10 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATATTATATATTATATAAT
Found at i:505653 original size:14 final size:15
Alignment explanation
Indices: 505603--505659 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 15
505593 CTATTTTTTA
*
505603 AATTATATAATATAT
1 AATTATATATTATAT
*
505618 -ATCATAT-TTATAT
1 AATTATATATTATAT
505631 --TTATATATTATAT
1 AATTATATATTATAT
505644 AATT-TATATTATAT
1 AATTATATATTATAT
505658 AA
1 AA
505660 AAAATAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.14
13 11 0.31
14 18 0.50
15 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTATATATTATAT
Found at i:505694 original size:28 final size:28
Alignment explanation
Indices: 505639--505695 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
505629 ATTTATATAT
505639 TATATAATTTATATTATATAAAAAATAAA
1 TATATAATTTATA-TATATAAAAAATAAA
*
505668 TATATAATATTATA-ATATAAATAATAAA
1 TATATAAT-TTATATATATAAAAAATAAA
505696 AAATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 8 0.31
30 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TATATAATTTATATATATAAAAAATAAA
Found at i:505703 original size:31 final size:30
Alignment explanation
Indices: 505639--505711 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
505629 ATTTATATAT
* *
505639 TATATAAT-TTATATTATATAAAAAATAAA
1 TATATAATATTATAATATATAAAAAAAAAA
505668 TATATAATATTATAATATA-AATAATAAAAAA
1 TATATAATATTATAATATATAA-AA-AAAAAA
505699 TATATTAA-ATTAT
1 TATA-TAATATTAT
505712 CTATTATTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 10 0.26
30 11 0.29
31 14 0.37
32 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TATATAATATTATAATATATAAAAAAAAAA
Found at i:506104 original size:24 final size:23
Alignment explanation
Indices: 506070--506125 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
506060 GAATATGTAT
* *
506070 ATATTAAATTTTTATATATTTAAA
1 ATATTATATTTATATATATTT-AA
506094 ATATTATATTTATATATATTTAA
1 ATATTATATTTATATATATTTAA
506117 ATA-TATATT
1 ATATTATATT
506126 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 6 0.20
23 5 0.17
24 19 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTATATTTATATATATTTAA
Found at i:506108 original size:22 final size:22
Alignment explanation
Indices: 506080--506125 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
506070 ATATTAAATT
506080 TTTATATAT-TTAAAATATTATA
1 TTTATATATATTAAAATA-TATA
*
506102 TTTATATATATTTAAATATATA
1 TTTATATATATTAAAATATATA
506124 TT
1 TT
506126 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATATATATTAAAATATATA
Found at i:506601 original size:21 final size:21
Alignment explanation
Indices: 506568--506607 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
506558 ACACTCACTT
*
506568 ATTTAATAAATTTATATTTAA
1 ATTTAACAAATTTATATTTAA
* *
506589 ATTTAACATATTTTTATTT
1 ATTTAACAAATTTATATTT
506608 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAACAAATTTATATTTAA
Found at i:506638 original size:3 final size:3
Alignment explanation
Indices: 506630--506656 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
506620 TCTATTGTAA
506630 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
506657 CAATCCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:507079 original size:27 final size:26
Alignment explanation
Indices: 507017--507079 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
507007 ATTAATCTAG
*
507017 ATTTATATAAAAAATAATTCTTATTAA
1 ATTTATAT-AAAAATAATTCTTATAAA
* *
507044 A-TTATTATAAATATAATTTTTTATAAA
1 ATTTA-TATAAAAATAA-TTCTTATAAA
507071 ATTTATATA
1 ATTTATATA
507080 GTAATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 10 0.33
27 17 0.57
28 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTATATAAAAATAATTCTTATAAA
Found at i:507892 original size:28 final size:26
Alignment explanation
Indices: 507858--507911 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
507848 TTAAATTATT
507858 ATTTAATTAATA-AAAAAGTTTTATATAA
1 ATTTAATT-ATACAAAAA-TTTTA-ATAA
507886 ATTTAATTATACAAAAATTTTAATAA
1 ATTTAATTATACAAAAATTTTAATAA
507912 TAATATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.16
27 8 0.32
28 13 0.52
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTAATTATACAAAAATTTTAATAA
Found at i:508342 original size:2 final size:2
Alignment explanation
Indices: 508335--508371 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
508325 GAAGCTTCTT
*
508335 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
508372 ATATAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:509297 original size:63 final size:63
Alignment explanation
Indices: 509071--509303 Score: 315
Period size: 63 Copynumber: 3.7 Consensus size: 63
509061 GTCTCCCGGA
** *
509071 CATCATGGCCCTGTTGTTGAACCTCCCAAAGCATCATTTCCAGGACCTGCTCACTCTCCAAAG
1 CATCATGGCCCTGTTGTTGAACCTCCCAAAGCATCATCACCAGGACCTGCTCACTCTCCTAAG
* * * *
509134 CATCATGGCCCGGTTGTTGAACCTCCCAAAGGATC-TTATCCAGGACCTGCTCACCCTCCTAAG
1 CATCATGGCCCTGTTGTTGAACCTCCCAAAGCATCATCA-CCAGGACCTGCTCACTCTCCTAAG
* * *
509197 CATCATGGCCCTGTTGTTGAACCTCCCAAATCATCATCACCAGGCCCTGCTTACTCTCCTAAG
1 CATCATGGCCCTGTTGTTGAACCTCCCAAAGCATCATCACCAGGACCTGCTCACTCTCCTAAG
* *** *
509260 CACCATGGCCCTGTTGCAAAACCTCCCAAATCATCATCACCAGG
1 CATCATGGCCCTGTTGTTGAACCTCCCAAAGCATCATCACCAGG
509304 GCCAGGTTTA
Statistics
Matches: 152, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
62 2 0.01
63 148 0.97
64 2 0.01
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (63 bp):
CATCATGGCCCTGTTGTTGAACCTCCCAAAGCATCATCACCAGGACCTGCTCACTCTCCTAAG
Found at i:509319 original size:63 final size:63
Alignment explanation
Indices: 509189--509320 Score: 176
Period size: 63 Copynumber: 2.1 Consensus size: 63
509179 CCTGCTCACC
* *** ** *
509189 CTCCTAAGCATCATGGCCCTGTTGTTGAACCTCCCAAATCATCATCACCAGGCCCTGCTTACT
1 CTCCTAAGCACCATGGCCCTGTTGCAAAACCTCCCAAATCATCATCACCAGGCCAGGCTTACG
*
509252 CTCCTAAGCACCATGGCCCTGTTGCAAAACCTCCCAAATCATCATCACCAGGGCCAGGTTTA-G
1 CTCCTAAGCACCATGGCCCTGTTGCAAAACCTCCCAAATCATCATCACCA-GGCCAGGCTTACG
509315 CTCCTA
1 CTCCTA
509321 TAGTGGCCGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 52 0.87
64 8 0.13
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24
Consensus pattern (63 bp):
CTCCTAAGCACCATGGCCCTGTTGCAAAACCTCCCAAATCATCATCACCAGGCCAGGCTTACG
Found at i:511744 original size:16 final size:17
Alignment explanation
Indices: 511713--511747 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
511703 TTTATATTTA
511713 ATAATAATAAACATAAT
1 ATAATAATAAACATAAT
*
511730 ATAAT-ATAAATATAAT
1 ATAATAATAAACATAAT
511746 AT
1 AT
511748 GTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAAACATAAT
Found at i:511813 original size:21 final size:21
Alignment explanation
Indices: 511779--511833 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
511769 ATGTTTAATA
*
511779 ATATATTT-AT-ATTATGTTG
1 ATATATTTAATAATTATATTG
*
511798 ATATATTTAATAATTATATTT
1 ATATATTTAATAATTATATTG
*
511819 ATATTTTTAA-AATTA
1 ATATATTTAATAATTA
511834 AATATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
21 16 0.52
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
ATATATTTAATAATTATATTG
Found at i:512170 original size:10 final size:10
Alignment explanation
Indices: 512080--512162 Score: 64
Period size: 10 Copynumber: 8.2 Consensus size: 10
512070 AAAAGTCAAA
512080 AAATTAATTT
1 AAATTAATTT
* *
512090 AATTTAATAT
1 AAATTAATTT
512100 AAA-TAATTT
1 AAATTAATTT
*
512109 -AATTTATATT
1 AAATTAAT-TT
512119 AAATTAAATTT
1 AAATT-AATTT
512130 AAATATAATATT
1 AAAT-TAAT-TT
* *
512142 TAA-TGATTT
1 AAATTAATTT
512151 AAATTAATTT
1 AAATTAATTT
512161 AA
1 AA
512163 TTTCATTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
8 2 0.04
9 12 0.21
10 22 0.39
11 13 0.23
12 7 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (10 bp):
AAATTAATTT
Found at i:512187 original size:22 final size:21
Alignment explanation
Indices: 512148--512193 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
512138 TATTTAATGA
512148 TTTAAATTAATTTAATTTCAT
1 TTTAAATTAATTTAATTTCAT
* * *
512169 TTTAAGTTATATTTTATTTGAT
1 TTTAAATTA-ATTTAATTTCAT
512191 TTT
1 TTT
512194 GTTTAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTAAATTAATTTAATTTCAT
Found at i:513105 original size:8 final size:8
Alignment explanation
Indices: 513092--513230 Score: 58
Period size: 8 Copynumber: 17.1 Consensus size: 8
513082 TTATTTATAT
513092 TATATTTA
1 TATATTTA
*
513100 TATATTTTT
1 TATA-TTTA
513109 TATATATTA
1 TATAT-TTA
513118 TA-A-TTA
1 TATATTTA
*
513124 -ATATTAA
1 TATATTTA
* *
513131 AATA-ATA
1 TATATTTA
513138 TATATTTA
1 TATATTTA
*
513146 TATAATTTTT
1 TAT-A-TTTA
*
513156 TATAAATTA
1 TAT-ATTTA
513165 -ATAATTTA
1 TAT-ATTTA
513173 TAT-TTTA
1 TATATTTA
*
513180 TAAAATTTAA
1 T-ATATTT-A
*
513190 AATATTTA
1 TATATTTA
513198 TATATTTA
1 TATATTTA
*
513206 TATAATTTT
1 TAT-ATTTA
513215 TATA-TTA
1 TATATTTA
*
513222 TATTTTTA
1 TATATTTA
513230 T
1 T
513231 TTTATGTTAA
Statistics
Matches: 99, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
5 1 0.01
6 4 0.04
7 16 0.16
8 38 0.38
9 31 0.31
10 9 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:513150 original size:15 final size:14
Alignment explanation
Indices: 513090--513175 Score: 52
Period size: 15 Copynumber: 5.9 Consensus size: 14
513080 TTTTATTTAT
513090 ATTATATTTATATA
1 ATTATATTTATATA
* * *
513104 TTTTTTATATATTATA
1 -ATTATATTTA-TATA
* *
513120 ATTAATATTAAAATA
1 ATT-ATATTTATATA
513135 ATATATATTTATATA
1 AT-TATATTTATATA
513150 ATT-T-TTTATA-A
1 ATTATATTTATATA
513161 ATTAATAATTTATAT
1 ATT-AT-ATTTATAT
513176 TTTATAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
11 4 0.08
12 6 0.11
13 2 0.04
14 1 0.02
15 31 0.58
16 9 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATATTTATATA
Found at i:513168 original size:33 final size:31
Alignment explanation
Indices: 513131--513215 Score: 88
Period size: 33 Copynumber: 2.8 Consensus size: 31
513121 TTAATATTAA
513131 AATAATATATATTTATATAATTTTTTATAAATT
1 AATAATATATATTTATATAATTTTTTA-AAA-T
* **
513164 AATAATTTATATTT-TATAA-AATTTAAAAT
1 AATAATATATATTTATATAATTTTTTAAAAT
*
513193 -AT-TTATATATTTATATAATTTTT
1 AATAATATATATTTATATAATTTTT
513216 ATATTATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
27 8 0.19
28 7 0.16
29 3 0.07
30 3 0.07
31 4 0.09
32 5 0.12
33 13 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
AATAATATATATTTATATAATTTTTTAAAAT
Found at i:513174 original size:25 final size:26
Alignment explanation
Indices: 513146--513210 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 26
513136 TATATATTTA
* *
513146 TATAATTTTTTATAAA-TTAATA-ATT
1 TATAATTTTATA-AAATTTAAAATATT
513171 TAT-ATTTTATAAAATTTAAAATATT
1 TATAATTTTATAAAATTTAAAATATT
513196 TATATATTTATATAA
1 TATA-ATTT-TATAA
513211 TTTTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 3 0.09
24 12 0.36
25 9 0.27
27 4 0.12
28 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TATAATTTTATAAAATTTAAAATATT
Found at i:513228 original size:13 final size:13
Alignment explanation
Indices: 513195--513235 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
513185 TTTAAAATAT
*
513195 TTATATATTTATA
1 TTATATTTTTATA
513208 -TA-ATTTTTATA
1 TTATATTTTTATA
*
513219 TTATATTTTTATT
1 TTATATTTTTATA
513232 TTAT
1 TTAT
513236 GTTAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 12 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:513635 original size:17 final size:18
Alignment explanation
Indices: 513610--513656 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
513600 ATTTTAAAAA
*
513610 TAATTAAATATA-TTAAT
1 TAATAAAATATACTTAAT
513627 TAATAAAATATTACTTTAAT
1 TAATAAAATA-TAC-TTAAT
513647 TAA-AAAATAT
1 TAATAAAATAT
513657 CATAAAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.35
18 3 0.12
19 6 0.23
20 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAAATATACTTAAT
Found at i:513916 original size:25 final size:28
Alignment explanation
Indices: 513888--513954 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
513878 CTGTTATGTT
513888 TTTATTTTAATTATA-T-TA-TTTTATA
1 TTTATTTTAATTATATTATATTTTTATA
*
513913 TTTA--TTAAATATATTATATTTTTATA
1 TTTATTTTAATTATATTATATTTTTATA
513939 TTATATTTTAAATTAT
1 TT-TATTTT-AATTAT
513955 TAAATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
23 8 0.24
24 1 0.03
25 6 0.18
26 9 0.27
27 2 0.06
29 2 0.06
30 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTATTTTAATTATATTATATTTTTATA
Found at i:513930 original size:5 final size:5
Alignment explanation
Indices: 513897--513945 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
513887 TTTTATTTTA
* *
513897 ATTAT ATTAT TTTAT ATT-T ATTA- AATAT ATTAT ATT-T -TTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
513943 ATT
1 ATT
513946 TTAAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
3 2 0.06
4 9 0.25
5 25 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
ATTAT
Found at i:513931 original size:18 final size:18
Alignment explanation
Indices: 513908--513969 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
513898 TTATATTATT
513908 TTATATTTATTAAATATA
1 TTATATTTATTAAATATA
*
513926 TTATATTT-TTATATTATA
1 TTATATTTATTA-AATATA
* *
513944 TTTTAAATTATTAAATATA
1 TTAT-ATTTATTAAATATA
513963 TTTATAT
1 -TTATAT
513970 AAAAATATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
17 3 0.09
18 16 0.47
19 9 0.26
20 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTATTAAATATA
Found at i:513936 original size:20 final size:19
Alignment explanation
Indices: 513890--513937 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
513880 GTTATGTTTT
* * *
513890 TATTTTAATTATATTATTT
1 TATTTTTATTAAATTATTA
*
513909 TATATTTATTAAATATATTA
1 TATTTTTATTAAAT-TATTA
513929 TATTTTTAT
1 TATTTTTAT
513938 ATTATATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATTAAATTATTA
Found at i:513938 original size:13 final size:13
Alignment explanation
Indices: 513892--513947 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
513882 TATGTTTTTA
513892 TTTTA-ATTATATT
1 TTTTATATTATA-T
513905 ATTTTATATT-TAT
1 -TTTTATATTATAT
**
513918 TAAATATATTATAT
1 T-TTTATATTATAT
513932 TTTTATATTATAT
1 TTTTATATTATAT
513945 TTT
1 TTT
513948 AAATTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
12 1 0.03
13 20 0.57
14 11 0.31
15 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTATATTATAT
Found at i:514159 original size:14 final size:13
Alignment explanation
Indices: 514140--514200 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
514130 ACTAACATAA
514140 ATTTTTATTTAATT
1 ATTTTTATTTAA-T
514154 ATTTTTTATTTAA-
1 A-TTTTTATTTAAT
* *
514167 ATTTAATTA-TAAAA
1 ATTT--TTATTTAAT
514181 ATTTTTATTTAAT
1 ATTTTTATTTAAT
514194 ATTTTTA
1 ATTTTTA
514201 AATAATAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
12 6 0.15
13 14 0.36
14 8 0.21
15 11 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTATTTAAT
Found at i:514167 original size:27 final size:27
Alignment explanation
Indices: 514137--514200 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
514127 TTAACTAACA
* *
514137 TAAATTTTTATT-TAATTATTTTTTATT
1 TAAATTTTTATTATAA-AAATTTTTATT
*
514164 TAAA-TTTAATTATAAAAATTTTTATT
1 TAAATTTTTATTATAAAAATTTTTATT
514190 TAATATTTTTA
1 TAA-ATTTTTA
514201 AATAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 18 0.60
27 8 0.27
28 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TAAATTTTTATTATAAAAATTTTTATT
Found at i:514671 original size:28 final size:26
Alignment explanation
Indices: 514606--514701 Score: 92
Period size: 28 Copynumber: 3.7 Consensus size: 26
514596 TCATATCATC
* *
514606 TATTATTTTATATTAAAATCATATTT
1 TATTATTTTATATTAAAATAATAGTT
* *
514632 TATTAATATATATTAAAATAATAAAGTT
1 TATTATTTTATATTAAAATAAT--AGTT
*
514660 TATTATTTTATATTAAAATTATA--T
1 TATTATTTTATATTAAAATAATAGTT
514684 TA-TATATTTATA-TAAAAT
1 TATTAT-TTTATATTAAAAT
514702 TTTATATATT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.15
24 9 0.15
26 20 0.33
28 22 0.37
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTATTTTATATTAAAATAATAGTT
Found at i:514689 original size:18 final size:18
Alignment explanation
Indices: 514609--514731 Score: 65
Period size: 20 Copynumber: 6.6 Consensus size: 18
514599 TATCATCTAT
* *
514609 TATTTTATATTAAAATCA
1 TATTATATATTAAAATTA
*
514627 TATT-T-TATTAATA-TA
1 TATTATATATTAAAATTA
* * *
514642 TATTAAAATAATAAAGTTTA
1 TATT-ATATATTAAA-ATTA
*
514662 TTATTTTATATTAAAATTA
1 -TATTATATATTAAAATTA
*
514681 TATTATATATTTATATAA-AA
1 TATTATATA-TTA-A-AATTA
*
514701 TTTTATATATTAATAATTTA
1 TATTATATATTAA-AA-TTA
514721 TATTATATATT
1 TATTATATATT
514732 TCTATACGAG
Statistics
Matches: 79, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
15 5 0.06
16 7 0.09
17 1 0.01
18 21 0.27
19 9 0.11
20 30 0.38
21 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TATTATATATTAAAATTA
Found at i:514726 original size:20 final size:19
Alignment explanation
Indices: 514663--514731 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
514653 TAAAGTTTAT
*
514663 TATTTTATATTAA-AATTA
1 TATTATATATTAATAATTA
*
514681 TATTATATATTTATATAA-AA
1 TATTATATA-TTA-ATAATTA
*
514701 TTTTATATATTAATAATTTA
1 TATTATATATTAATAA-TTA
514721 TATTATATATT
1 TATTATATATT
514732 TCTATACGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 12 0.29
19 6 0.15
20 21 0.51
21 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATATATTAATAATTA
Found at i:515200 original size:15 final size:16
Alignment explanation
Indices: 515182--515212 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
515172 ATATTTAATA
515182 TTAAAATAT-AATTTT
1 TTAAAATATAAATTTT
515197 TTAAAATATAAATTTT
1 TTAAAATATAAATTTT
515213 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAATATAAATTTT
Found at i:515209 original size:21 final size:21
Alignment explanation
Indices: 515178--515233 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
515168 ATTTATATTT
*
515178 AATATTAAAATATAATTTTTTAA
1 AATATT-AAATATAA-TTTTAAA
* *
515201 AATA-TAAATTTTATTTTAAA
1 AATATTAAATATAATTTTAAA
515221 AATATTAAATATA
1 AATATTAAATATA
515234 TTTATATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 1 0.04
23 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATTAAATATAATTTTAAA
Found at i:515235 original size:20 final size:20
Alignment explanation
Indices: 515178--515236 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
515168 ATTTATATTT
*
515178 AATATTAAAATATAATTTTTTAA
1 AATATT-AAATAT-A-TTTTAAA
*
515201 AATA-TAAATTTTATTTTAAA
1 AATATTAAA-TATATTTTAAA
515221 AATATTAAATATATTT
1 AATATTAAATATATTT
515237 ATATTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 16 0.52
21 8 0.26
22 3 0.10
23 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTAAATATATTTTAAA
Found at i:515253 original size:13 final size:15
Alignment explanation
Indices: 515222--515254 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
515212 TATTTTAAAA
515222 ATATTAAATATATTT
1 ATATTAAATATATTT
515237 ATATTAAATA-A-TT
1 ATATTAAATATATTT
515250 ATATT
1 ATATT
515255 CAACACCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 1 0.06
15 10 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTAAATATATTT
Found at i:520484 original size:16 final size:16
Alignment explanation
Indices: 520463--520574 Score: 127
Period size: 16 Copynumber: 7.0 Consensus size: 16
520453 TTTGAGTTAT
*
520463 TTTCGGGTTTGGGTCA
1 TTTCGGGTTCGGGTCA
*
520479 TTTCGGGTTCGAGTCA
1 TTTCGGGTTCGGGTCA
*
520495 CTTT-GGATTCGGGTCA
1 -TTTCGGGTTCGGGTCA
*
520511 TTTCGGGTTCGAGTCA
1 TTTCGGGTTCGGGTCA
* **
520527 TTTCGGCTTCGGGTTG
1 TTTCGGGTTCGGGTCA
*
520543 TTTCGGGTTCAGGTCA
1 TTTCGGGTTCGGGTCA
*
520559 TTTCGAGTTCGGGTCA
1 TTTCGGGTTCGGGTCA
520575 ATCGGGTTTA
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
15 3 0.04
16 72 0.92
17 3 0.04
ACGTcount: A:0.10, C:0.18, G:0.33, T:0.39
Consensus pattern (16 bp):
TTTCGGGTTCGGGTCA
Found at i:521654 original size:16 final size:16
Alignment explanation
Indices: 521628--521763 Score: 114
Period size: 16 Copynumber: 8.5 Consensus size: 16
521618 CGGGTTAATT
*
521628 ATTCAGGTCATTTCGG
1 ATTCGGGTCATTTCGG
* **
521644 GTTCGGGTCATTTCAA
1 ATTCGGGTCATTTCGG
*
521660 ATTCAGGTCATTTCGG
1 ATTCGGGTCATTTCGG
*
521676 ATTCGAGTCATTTCAGG
1 ATTCGGGTCATTTC-GG
*
521693 -TTGGGGTCA-TTCTGG
1 ATTCGGGTCATTTC-GG
*
521708 ATTCGGATCATTTCGG
1 ATTCGGGTCATTTCGG
* * *
521724 GTTCGAGTTATTTCGG
1 ATTCGGGTCATTTCGG
* * *
521740 GTTCAGGTCAATTCGG
1 ATTCGGGTCATTTCGG
521756 ATTCGGGT
1 ATTCGGGT
521764 TGTTGACTTT
Statistics
Matches: 92, Mismatches: 25, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
15 5 0.05
16 82 0.89
17 5 0.05
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.38
Consensus pattern (16 bp):
ATTCGGGTCATTTCGG
Found at i:521719 original size:48 final size:48
Alignment explanation
Indices: 521634--521761 Score: 134
Period size: 48 Copynumber: 2.7 Consensus size: 48
521624 AATTATTCAG
* * * **
521634 GTCATTTCGGGTTCGGGTCATTTCAAATTCAGG-TCATTTCGGATTCGA
1 GTCATTTCAGGTTCAGGTCAATTCGGATTC-GGATCATTTCGGATTCGA
** *
521682 GTCATTTCAGGTTGGGGTC-ATTCTGGATTCGGATCATTTCGGGTTCGA
1 GTCATTTCAGGTTCAGGTCAATTC-GGATTCGGATCATTTCGGATTCGA
* *
521730 GTTATTTCGGGTTCAGGTCAATTCGGATTCGG
1 GTCATTTCAGGTTCAGGTCAATTCGGATTCGG
521762 GTTGTTGACT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 5 0.07
48 58 0.87
49 4 0.06
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.38
Consensus pattern (48 bp):
GTCATTTCAGGTTCAGGTCAATTCGGATTCGGATCATTTCGGATTCGA
Found at i:530790 original size:20 final size:20
Alignment explanation
Indices: 530765--530802 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
530755 CTAAACCTCA
530765 TTCTGAAGTAATGGCTGTCC
1 TTCTGAAGTAATGGCTGTCC
530785 TTCTGAAGTAATGGCTGT
1 TTCTGAAGTAATGGCTGT
530803 ATTTCGAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (20 bp):
TTCTGAAGTAATGGCTGTCC
Found at i:534242 original size:52 final size:51
Alignment explanation
Indices: 534164--534347 Score: 199
Period size: 52 Copynumber: 3.6 Consensus size: 51
534154 TAGATGCATT
* * * * *
534164 GATACATTGAAAAATGTATCAATACATTTAGGTCAAAAACTCATAATATATC
1 GATACAATGAAAAATGTATCGATACATTT-GGTTAAAAACTCAGAATGTATC
* *
534216 GATACAATGAAAAATGTATCGATACATTTGGATTGAAAACCCAGAATGTATC
1 GATACAATGAAAAATGTATCGATACATTTGG-TTAAAAACTCAGAATGTATC
* * * *
534268 AATACAAT-AAAAATTTATTGATACATTTGAATTAAAAACTCAGAATGTATC
1 GATACAATGAAAAATGTATCGATACATTTG-GTTAAAAACTCAGAATGTATC
* * * *
534319 GATAAAATAAAAAATATATCGATGCATTT
1 GATACAATGAAAAATGTATCGATACATTT
534348 TCTTTCTAGA
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
51 45 0.41
52 66 0.59
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (51 bp):
GATACAATGAAAAATGTATCGATACATTTGGTTAAAAACTCAGAATGTATC
Found at i:535037 original size:17 final size:18
Alignment explanation
Indices: 535007--535041 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
534997 TATAATATTT
535007 TATATATTGAATATAAATC
1 TATATATT-AATATAAATC
535026 TATATATT-ATATAAAT
1 TATATATTAATATAAAT
535042 AATTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TATATATTAATATAAATC
Found at i:535493 original size:73 final size:75
Alignment explanation
Indices: 535361--535506 Score: 226
Period size: 73 Copynumber: 2.0 Consensus size: 75
535351 ATATATTACC
*
535361 AAATAAATTTCATTTAGCCAAAACATTTTAATAGAATTAGAATTATTATTTATAAATGTGATAAA
1 AAATAAATTTCATTTAACCAAAACATTTTAATAGAATTAGAATTATTATTTATAAATGTGATAAA
535426 TTTTATTATT
66 TTTTATTATT
* * *
535436 AAATAAATTT-ATTTAACTAAATC-TTTTGAATATAATTAGAATT-TTATTTATAAATGTGATAA
1 AAATAAATTTCATTTAACCAAAACATTTT-AATAGAATTAGAATTATTATTTATAAATGTGATAA
535498 ATTTTATTA
65 ATTTTATTA
535507 ATAATAAGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
73 32 0.48
74 24 0.36
75 10 0.15
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (75 bp):
AAATAAATTTCATTTAACCAAAACATTTTAATAGAATTAGAATTATTATTTATAAATGTGATAAA
TTTTATTATT
Found at i:535648 original size:2 final size:2
Alignment explanation
Indices: 535641--535671 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
535631 ACTTATAAAG
535641 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
535672 ATAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:536136 original size:25 final size:25
Alignment explanation
Indices: 536103--536151 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
536093 AAGGATTTTT
* * *
536103 AAATCAAATTAAATTATAATTTTAA
1 AAATAAAATAAAATTATAAATTTAA
536128 AAATAAAATAAAATTATAAATTTA
1 AAATAAAATAAAATTATAAATTTA
536152 GATACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
AAATAAAATAAAATTATAAATTTAA
Found at i:536506 original size:19 final size:20
Alignment explanation
Indices: 536463--536515 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
536453 CACACCCAAA
*
536463 TGTATCGATACATGCTGCTT
1 TGTATCGATACATGCTGCAT
*
536483 TGTATCGATACATG-TTCAT
1 TGTATCGATACATGCTGCAT
536502 TGTATCGATACATG
1 TGTATCGATACATG
536516 GATAAAGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATGCTGCAT
Found at i:536602 original size:13 final size:13
Alignment explanation
Indices: 536581--536611 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
536571 CGATACACAG
*
536581 TACAATGTATCGA
1 TACATTGTATCGA
536594 TACATTGTATCGA
1 TACATTGTATCGA
536607 TACAT
1 TACAT
536612 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:536607 original size:33 final size:32
Alignment explanation
Indices: 536565--536631 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
536555 CTATCATTAT
*
536565 TTGTATCGATACA-CAGTACAATGTATCGATACA
1 TTGTATCGATACAGAAG-A-AATGTATCGATACA
536598 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACA-GAAGAAATGTATCGATACA
536631 T
1 T
536632 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 28 0.90
34 1 0.03
35 2 0.06
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (32 bp):
TTGTATCGATACAGAAGAAATGTATCGATACA
Found at i:537135 original size:22 final size:22
Alignment explanation
Indices: 537109--537153 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
537099 TTAGCCTTAA
537109 AAGATAAGGATTGTAAGGTTAT
1 AAGATAAGGATTGTAAGGTTAT
537131 AAGATAAGGATTGTAAGGTTAT
1 AAGATAAGGATTGTAAGGTTAT
537153 A
1 A
537154 CCTTTGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (22 bp):
AAGATAAGGATTGTAAGGTTAT
Found at i:542431 original size:19 final size:19
Alignment explanation
Indices: 542386--542478 Score: 75
Period size: 19 Copynumber: 4.7 Consensus size: 19
542376 CTGCCAGTTT
**
542386 CATGTATCGATACAATTTGGC
1 CATGTATCGATACAA--TGAA
542407 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
542426 CATGTATCGATATCGAT--A
1 CATGTATCGATA-CAATGAA
*
542444 CATTGTATCGATACAAAGCAGA
1 CA-TGTATCGATACAATG-A-A
542466 -ATGTATCGATACA
1 CATGTATCGATACA
542479 TCTGGGTGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
18 5 0.08
19 24 0.39
20 15 0.25
21 16 0.26
22 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:542737 original size:17 final size:18
Alignment explanation
Indices: 542705--542738 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
542695 ACTTTGTTTA
542705 CGATTTTCAAACAATCTC
1 CGATTTTCAAACAATCTC
*
542723 CGATTTT-ATACAATCT
1 CGATTTTCAAACAATCT
542739 TTGTTATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (18 bp):
CGATTTTCAAACAATCTC
Found at i:544771 original size:20 final size:19
Alignment explanation
Indices: 544730--544769 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
544720 TTCTGTTGAT
544730 GATTTTGATGAAAAATGAAA
1 GATTTTGATGAAAAAT-AAA
544750 GATTTTGAAGTGAAAAATAA
1 GATTTTG-A-TGAAAAATAA
544770 GAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (19 bp):
GATTTTGATGAAAAATAAA
Found at i:544914 original size:13 final size:13
Alignment explanation
Indices: 544896--544937 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
544886 AAATAGTACC
544896 CAATGTATCGATA
1 CAATGTATCGATA
544909 CAATGTATCGATA
1 CAATGTATCGATA
544922 CAATGTATCGATA
1 CAATGTATCGATA
544935 CAA
1 CAA
544938 GGAATGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:551160 original size:18 final size:19
Alignment explanation
Indices: 551137--551176 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
551127 TAGCTACTGC
551137 CAATTT-CATGTATCGATA
1 CAATTTGCATGTATCGATA
551155 CAATTTGGCCATGTATCGATA
1 CAATTT-G-CATGTATCGATA
551176 C
1 C
551177 GATGAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (19 bp):
CAATTTGCATGTATCGATA
Found at i:552740 original size:13 final size:13
Alignment explanation
Indices: 552722--552749 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
552712 ACAACATTCC
552722 TTGTATCGATACA
1 TTGTATCGATACA
552735 TTGTATCGATACA
1 TTGTATCGATACA
552748 TT
1 TT
552750 AGGTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Done.