Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 39 of 352
Found at i:12396875 original size:4 final size:4
Alignment explanation
Indices: 12396861--12396928 Score: 66
Period size: 4 Copynumber: 16.2 Consensus size: 4
12396851 AATGATAAGC
* * *
12396861 AAAT GAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAGAA AAAT AAA- AAAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AA-AT AAAT AAAT AAAT
12396910 AAGAT GAAAT AAAT AAAT A
1 AA-AT -AAAT AAAT AAAT A
12396929 CTATGATAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
3 3 0.06
4 41 0.76
5 7 0.13
6 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:12397861 original size:21 final size:21
Alignment explanation
Indices: 12397848--12397885 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 21
12397838 TTAATTATAA
12397848 AATATAT-ATATTT-ATTAGT
1 AATATATGATATTTAATTAGT
*
12397867 AATATATGATATTAAATTA
1 AATATATGATATTTAATTA
12397886 ATTTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 5 0.31
21 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
AATATATGATATTTAATTAGT
Found at i:12398467 original size:20 final size:21
Alignment explanation
Indices: 12398430--12398477 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
12398420 ATATATGTAT
*
12398430 TTAATTATTAATAGATATTTA
1 TTAATTATTAAAAGATATTTA
12398451 TTAATTA-TAAAAGATATTTA
1 TTAATTATTAAAAGATATTTA
12398471 TTAATTA
1 TTAATTA
12398478 AATAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
TTAATTATTAAAAGATATTTA
Found at i:12399896 original size:40 final size:40
Alignment explanation
Indices: 12399788--12399922 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 40
12399778 GACCTCGAGT
* * *
12399788 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCACTATATTACTTCGGCTAG-TC
* ** * * * *
12399829 TGATGAGGTACT-AG-GT-ACCATTTTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCACTATATTACTTCGGCTAGTC
* *
12399866 CGATGAGACACTGGGTGTCACTATATTACTTTGAACTA-TC
1 CGATGAGACACTGGGTGTCACTATATTACTTCG-GCTAGTC
*
12399906 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
12399923 CCATTCTGGT
Statistics
Matches: 70, Mismatches: 20, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
37 9 0.13
38 16 0.23
39 4 0.06
40 29 0.41
41 12 0.17
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCACTATATTACTTCGGCTAGTC
Found at i:12402608 original size:20 final size:20
Alignment explanation
Indices: 12402552--12402608 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
12402542 TTAACAGACT
12402552 TTTATTTATTTTTGTTTTGGA
1 TTTATTTATTTTTG-TTTGGA
* *
12402573 TTT-TGTTTTTTTTGTTTGGG
1 TTTAT-TTATTTTTGTTTGGA
*
12402593 TTTATTTATTTGTGTT
1 TTTATTTATTTTTGTT
12402609 GGGCAGGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.09, C:0.00, G:0.18, T:0.74
Consensus pattern (20 bp):
TTTATTTATTTTTGTTTGGA
Found at i:12404182 original size:22 final size:21
Alignment explanation
Indices: 12404157--12404221 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
12404147 TGCGCATGGG
12404157 TTGGATAAAAGAAGTAAAAAGT
1 TTGGATAAAAGAA-TAAAAAGT
** *
12404179 TTGGATATCCA-AA-AACAAGT
1 TTGGATA-AAAGAATAAAAAGT
12404199 TTGGATAAAAGAAATAAAAAGT
1 TTGGATAAAAG-AATAAAAAGT
12404221 T
1 T
12404222 GTACTGATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 1 0.03
20 13 0.39
21 2 0.06
22 16 0.48
23 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (21 bp):
TTGGATAAAAGAATAAAAAGT
Found at i:12404647 original size:30 final size:30
Alignment explanation
Indices: 12404613--12404683 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
12404603 TAGCAAAATG
12404613 GGACCTGGTGGACCGGGAGGA-GGGCCG-GGA
1 GGACCTGGTGGACCGGGAGGATGGG--GAGGA
*
12404643 GGACCAGGTGGACCGGGAGGATGGGGAGGA
1 GGACCTGGTGGACCGGGAGGATGGGGAGGA
12404673 GGACCTGGTGG
1 GGACCTGGTGG
12404684 TTGGGGTCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.89
31 3 0.08
ACGTcount: A:0.18, C:0.17, G:0.56, T:0.08
Consensus pattern (30 bp):
GGACCTGGTGGACCGGGAGGATGGGGAGGA
Found at i:12414158 original size:14 final size:14
Alignment explanation
Indices: 12414139--12414168 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12414129 ATGTTAGCAC
12414139 TACTAAGTTTCCAT
1 TACTAAGTTTCCAT
12414153 TACTAAGTTTCCAT
1 TACTAAGTTTCCAT
12414167 TA
1 TA
12414169 AGTCTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (14 bp):
TACTAAGTTTCCAT
Found at i:12414667 original size:5 final size:5
Alignment explanation
Indices: 12414657--12414707 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
12414647 CACGTTAGTG
*
12414657 AATAA AATAA AAT-A AATATA AAT-A AATACA TATAA AATAA AGATAA
1 AATAA AATAA AATAA AATA-A AATAA AATA-A AATAA AATAA A-ATAA
12414703 AATAA
1 AATAA
12414708 TTTATATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 8 0.21
5 18 0.46
6 13 0.33
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:12425855 original size:27 final size:27
Alignment explanation
Indices: 12425825--12425890 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
12425815 TAGTCCAACA
** * *
12425825 GGACGTTAAACATTGGATTTTTCAATG
1 GGACGTTAAACAGGGGATTGTCCAATG
*
12425852 GGACGTTCAACAGGGGATTGTCCAATG
1 GGACGTTAAACAGGGGATTGTCCAATG
*
12425879 GGACATTAAACA
1 GGACGTTAAACA
12425891 CTTGATAGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (27 bp):
GGACGTTAAACAGGGGATTGTCCAATG
Found at i:12426007 original size:27 final size:27
Alignment explanation
Indices: 12425937--12425996 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
12425927 CCAATAGAAG
* *
12425937 GTTAAACAC-GGAATTGTCCGATGAGAT
1 GTTAAACACAGG-ATAGTCAGATGAGAT
*
12425964 GTTAAACACAGGATAGTCAGATGGGAT
1 GTTAAACACAGGATAGTCAGATGAGAT
12425991 GTTAAA
1 GTTAAA
12425997 TATGGGATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (27 bp):
GTTAAACACAGGATAGTCAGATGAGAT
Found at i:12430116 original size:22 final size:22
Alignment explanation
Indices: 12430074--12430119 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12430064 CTAATTAAAC
*
12430074 TCATATATTTTTCTTCTTCAAT
1 TCATATATTTTTATTCTTCAAT
*
12430096 TCATATCTTTTTATTAC-TCAAT
1 TCATATATTTTTATT-CTTCAAT
12430118 TC
1 TC
12430120 CCTATCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.57
Consensus pattern (22 bp):
TCATATATTTTTATTCTTCAAT
Found at i:12436820 original size:45 final size:45
Alignment explanation
Indices: 12436769--12436872 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
12436759 GTAACGGTAG
*
12436769 CAGTAACAGTAACAATATTCAACACACAAAGTG-CTGAATCGGTAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGTC-GAATCAGTAA
* * * * *
12436814 CGGTAACAGTAATAATATTCGACATACAAAGTGTCGAATTAGTAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCAGTAA
*
12436859 CAGTAACGGTAACA
1 CAGTAACAGTAACA
12436873 GTAACAGTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (45 bp):
CAGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCAGTAA
Found at i:12438115 original size:3 final size:3
Alignment explanation
Indices: 12438107--12438132 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12438097 TATTTAACAT
12438107 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
12438133 TCTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12439097 original size:44 final size:42
Alignment explanation
Indices: 12439013--12439107 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
12439003 TCCCAAATAG
* * *
12439013 GGTCTTACACGAAATCAAATACGATGCTATCATCCTAGACGT
1 GGTCTTACAAGAAATCAAATACGATGCTAACATCCCAGACGT
*
12439055 GGTCTTACAAGTAAATCATAAGT-CGATGCTAACGTCCCAGACGT
1 GGTCTTACAAG-AAATCA-AA-TACGATGCTAACATCCCAGACGT
12439099 GGTCTTACA
1 GGTCTTACA
12439108 CGATAACACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 10 0.22
43 6 0.13
44 29 0.63
45 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
GGTCTTACAAGAAATCAAATACGATGCTAACATCCCAGACGT
Found at i:12440137 original size:33 final size:33
Alignment explanation
Indices: 12440095--12440160 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
12440085 ATACAAATTT
12440095 TAATATCTCATAATATGAAATTCTTATGCTTAC
1 TAATATCTCATAATATGAAATTCTTATGCTTAC
12440128 TAATATCTCATAATATGAAATTCTTATGCTTAC
1 TAATATCTCATAATATGAAATTCTTATGCTTAC
12440161 ACCGTTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (33 bp):
TAATATCTCATAATATGAAATTCTTATGCTTAC
Found at i:12441269 original size:40 final size:39
Alignment explanation
Indices: 12441220--12441348 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 39
12441210 ATTTTAAGGA
* *
12441220 AAATCCTATCCACCTTAAGTTACCATAGTGAATCAGGAAC
1 AAATCCTATCCACCTTAA-TTACTATAGTGAATCAGGAAT
* *
12441260 AAATCCTATCCA-CTTTATATATTTATAGTGAATCAGGAAT
1 AAATCCTATCCACCTTAAT-TA-CTATAGTGAATCAGGAAT
* * * * *
12441300 AAATCCAATTCACTTTAATTTCTTTTAGTGAATCAGGAAT
1 AAATCCTATCCACCTTAATTAC-TATAGTGAATCAGGAAT
12441340 AAATCCTAT
1 AAATCCTAT
12441349 TCACTTTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.01
39 6 0.08
40 62 0.85
41 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (39 bp):
AAATCCTATCCACCTTAATTACTATAGTGAATCAGGAAT
Found at i:12441351 original size:40 final size:40
Alignment explanation
Indices: 12441244--12441362 Score: 168
Period size: 40 Copynumber: 3.0 Consensus size: 40
12441234 TTAAGTTACC
* * *
12441244 ATAGTGAATCAGGAACAAATCCTATCCACTTTATATAT-TT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTA-ATTTCTT
*
12441284 ATAGTGAATCAGGAATAAATCCAATTCACTTTAATTTCTT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCTT
* *
12441324 TTAGTGAATCAGGAATAAATCCTATTCACTTTTATTTCT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCT
12441363 CGAGAAGGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
39 3 0.04
40 68 0.96
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (40 bp):
ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCTT
Found at i:12442321 original size:14 final size:13
Alignment explanation
Indices: 12442290--12442350 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
12442280 TGTTCTTCTT
*
12442290 TTTATCTTTGTTTC
1 TTTAT-TTTGTTTA
12442304 TTTATTTTGTTTTA
1 TTTATTTTG-TTTA
**
12442318 TTTATTTACTTTA
1 TTTATTTTGTTTA
* *
12442331 ATTCTTTTGTTTA
1 TTTATTTTGTTTA
*
12442344 TTCATTT
1 TTTATTT
12442351 AATAATAATA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
13 21 0.58
14 15 0.42
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTATTTTGTTTA
Found at i:12442504 original size:3 final size:3
Alignment explanation
Indices: 12442496--12442520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12442486 TTATTTTATT
12442496 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
12442521 CTAGTAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12450553 original size:27 final size:27
Alignment explanation
Indices: 12450519--12450590 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
12450509 TATAATAAAT
*
12450519 AATTAATAT-AACTTATTATTTTAAAAA
1 AATTAATATAAAATT-TTATTTTAAAAA
*
12450546 AATTAATATCAAAATTTTATTTTAATAA
1 AATTAATAT-AAAATTTTATTTTAAAAA
* *
12450574 CATTAATA-ATAATTTTA
1 AATTAATATAAAATTTTA
12450591 AAATTTAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 8 0.21
27 9 0.23
28 18 0.46
29 4 0.10
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
AATTAATATAAAATTTTATTTTAAAAA
Found at i:12451905 original size:22 final size:21
Alignment explanation
Indices: 12451879--12451925 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12451869 AATGTAAATA
12451879 AGACAAAAGAAAAACTATATGG
1 AGACAAAAG-AAAACTATATGG
** *
12451901 AGACATCAGGAAACTATATGG
1 AGACAAAAGAAAACTATATGG
12451922 AGAC
1 AGAC
12451926 GTCATCCCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (21 bp):
AGACAAAAGAAAACTATATGG
Found at i:12452120 original size:20 final size:20
Alignment explanation
Indices: 12452097--12452146 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12452087 AAATCCAAAT
*
12452097 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAAGA
*
12452117 TAAAAT-CTTGAAATTCAAGA
1 TAAAATAC-TAAAATTCAAGA
12452137 TAAGAATACT
1 TAA-AATACT
12452147 GATGTGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 4 0.16
22 1 0.04
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (20 bp):
TAAAATACTAAAATTCAAGA
Found at i:12455186 original size:16 final size:16
Alignment explanation
Indices: 12455160--12455192 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12455150 AATATCCATT
12455160 TCATGTATTTCATTAAA
1 TCATGTATTTCA-TAAA
12455177 TCAT-TATTTCATAAA
1 TCATGTATTTCATAAA
12455192 T
1 T
12455193 TTCATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (16 bp):
TCATGTATTTCATAAA
Found at i:12457428 original size:23 final size:24
Alignment explanation
Indices: 12457372--12457430 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
12457362 AAATAAATTA
* *
12457372 TTTTATAACAAGTGTACATATATC
1 TTTTATTACAAATGTACATATATC
12457396 TATTTATTACAAATGTACCA-ATAT-
1 T-TTTATTACAAATGTA-CATATATC
12457420 TTTTATTACAA
1 TTTTATTACAA
12457431 TTGTCAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 10 0.32
24 2 0.06
25 17 0.55
26 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (24 bp):
TTTTATTACAAATGTACATATATC
Found at i:12457654 original size:3 final size:3
Alignment explanation
Indices: 12457646--12457673 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12457636 TTAATTTATT
12457646 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12457674 TTAATCTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12464481 original size:52 final size:52
Alignment explanation
Indices: 12464390--12464544 Score: 159
Period size: 52 Copynumber: 3.0 Consensus size: 52
12464380 GACGGAAGAG
** * * *
12464390 ATGTGATATGTGCGCCCGCATAATACCATAGCTGGGCTATGGCATTGGTACA
1 ATGTGATATGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * * * * **
12464442 ATGTGATACGTGTTCCCGTATAAGACTATAGATGGGCTATAGCGTCGGTGTA
1 ATGTGATATGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* *
12464494 ATGTGATAATGTGATT-CCGTATAAGACCATACCTGGGATATGGCATCGGTA
1 ATGTGAT-ATGTG-TTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
12464545 GTATATGTGA
Statistics
Matches: 81, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
52 47 0.58
53 32 0.40
54 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (52 bp):
ATGTGATATGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:12469931 original size:26 final size:26
Alignment explanation
Indices: 12469885--12469951 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
12469875 CTCAAATTGT
*
12469885 ATTTCTCATTTCA-TCTTATAATATCA
1 ATTTCTCATTTCATTCTAATAAT-TCA
*
12469911 CTTTCTCATTTCATTC-AATAATTCA
1 ATTTCTCATTTCATTCTAATAATTCA
*
12469936 ATTTATCAATTTCATT
1 ATTTCTC-ATTTCATT
12469952 TTATTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 8 0.23
26 25 0.71
27 2 0.06
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTCTCATTTCATTCTAATAATTCA
Found at i:12470911 original size:21 final size:22
Alignment explanation
Indices: 12470865--12470911 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12470855 CAATCCTTTA
12470865 ATCAATTTAAATCAAAATTTCT
1 ATCAATTTAAATCAAAATTTCT
*
12470887 ATCAA-TTAAACTCATAATTTC-
1 ATCAATTTAAA-TCAAAATTTCT
12470908 ATCA
1 ATCA
12470912 TTAGTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (22 bp):
ATCAATTTAAATCAAAATTTCT
Found at i:12474797 original size:52 final size:52
Alignment explanation
Indices: 12474723--12474877 Score: 152
Period size: 52 Copynumber: 3.0 Consensus size: 52
12474713 GACGGAAGAG
** * *
12474723 ATGTGATATGTGCGCCCATATAAGACCATAGCTGGGCTATGACATCGGTACA
1 ATGTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGACATCGGTACA
* * * **
12474775 ATGTGATACGTGTTCCCGTATAAGACCATAAATGGGCTAT-AGCGTCGGTGTA
1 ATGTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGA-CATCGGTACA
* * * *
12474827 ATGTAATAATGTGATT-CCGTATAAGACCATATCTGGGATATGGCATCGGTA
1 ATGTGAT-ATGTG-TTCCCGTATAAGACCATAACTGGGCTATGACATCGGTA
12474878 GTTTATGTGA
Statistics
Matches: 82, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
51 1 0.01
52 47 0.57
53 32 0.39
54 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (52 bp):
ATGTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGACATCGGTACA
Found at i:12485192 original size:22 final size:22
Alignment explanation
Indices: 12485151--12485209 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
12485141 ATAATAAATC
* *
12485151 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
12485171 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
12485193 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
12485210 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:12494336 original size:29 final size:31
Alignment explanation
Indices: 12494282--12494339 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
12494272 AGAAATAATT
* *
12494282 TGACAAATAATATAAATTCAATAATTAAAAA
1 TGACAAAAAATATAAATTAAATAATTAAAAA
12494313 TGACAAAAAAT-TAAA-TAAATAATTAAA
1 TGACAAAAAATATAAATTAAATAATTAAA
12494340 GTGACCGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 4 0.16
31 10 0.40
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (31 bp):
TGACAAAAAATATAAATTAAATAATTAAAAA
Found at i:12503417 original size:6 final size:6
Alignment explanation
Indices: 12503408--12503443 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
12503398 TTCGATTTCA
12503408 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
12503444 GCACTACAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:12507504 original size:21 final size:21
Alignment explanation
Indices: 12507480--12507521 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12507470 AAATTTGAAT
* *
12507480 AAAATTAACATTTATTGTTTA
1 AAAAATAACATTTAATGTTTA
*
12507501 AAAAATATCATTTAATGTTTA
1 AAAAATAACATTTAATGTTTA
12507522 TCGTATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
AAAAATAACATTTAATGTTTA
Found at i:12513586 original size:42 final size:42
Alignment explanation
Indices: 12513524--12513645 Score: 118
Period size: 43 Copynumber: 2.9 Consensus size: 42
12513514 TAAGGTTAGT
* * *
12513524 TGAGATTACGTATAATACCATATCTGGGATATGACATCGATA
1 TGAGATTACGTGTAAAACCATACCTGGGATATGACATCGATA
* * * * * *
12513566 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATTGATA
1 TGAGATTACGTGTAAAACCATACCTGGGATA-TGACATCGATA
* ** *
12513609 TAAGATCCCATGTAAAACCATACCTGGGATATGACAT
1 TGAGATTACGTGTAAAACCATACCTGGGATATGACAT
12513646 TGGTATGATT
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 31 0.48
43 33 0.52
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAAACCATACCTGGGATATGACATCGATA
Found at i:12517989 original size:22 final size:23
Alignment explanation
Indices: 12517963--12518009 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
12517953 TAAAAGAAAT
12517963 AGAATAAAGAAAAGA-AACAAAA
1 AGAATAAAGAAAAGAGAACAAAA
* *
12517985 AGAATAGAGAAAAGAGAACAGAA
1 AGAATAAAGAAAAGAGAACAAAA
12518008 AG
1 AG
12518010 CATTCGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.70, C:0.04, G:0.21, T:0.04
Consensus pattern (23 bp):
AGAATAAAGAAAAGAGAACAAAA
Found at i:12517998 original size:27 final size:30
Alignment explanation
Indices: 12517954--12518008 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 30
12517944 TAAAGTAAAT
12517954 AAAAGAAATAGAATAAAGA-AA-AGAAACA
1 AAAAGAAATAGAATAAAGAGAACAGAAACA
12517982 AAAAG-AATAGAGA-AAAGAGAACAGAAA
1 AAAAGAAATAGA-ATAAAGAGAACAGAAA
12518009 GCATTCGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (30 bp):
AAAAGAAATAGAATAAAGAGAACAGAAACA
Found at i:12518619 original size:23 final size:22
Alignment explanation
Indices: 12518583--12518646 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
12518573 TTTACCGATT
* *
12518583 AGGCACTTTATGTGTCGTATTTC
1 AGGCACCTCATGTGTCGTA-TTC
*
12518606 AGGCACCTCGTGTGTCGTA-TC
1 AGGCACCTCATGTGTCGTATTC
* *
12518627 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
12518647 ACTAATTAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (22 bp):
AGGCACCTCATGTGTCGTATTC
Found at i:12528627 original size:114 final size:114
Alignment explanation
Indices: 12528492--12528726 Score: 364
Period size: 114 Copynumber: 2.1 Consensus size: 114
12528482 CTAGAAACTT
* * *
12528492 TTTTTAGGGGGGCCGGAATTAAATTGTATATTTTTACGATAGTAAAAATGCATTTTCACCATTTT
1 TTTTTAGGGGGGCCGAAATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTTT
* * *
12528557 AATATCTATATTTTTATAATTTTTAAAGGTTTAAATCAAAATTTTATCA
66 AATATCTATATCTTTATAATTTTTAAAAGATTAAATCAAAATTTTATCA
12528606 TTTTTAGGGGGGCC-AATATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTT
1 TTTTTAGGGGGGCCGAA-ATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTT
* * * *
12528670 TAATATCTATCTCTTTATGATTTTTAAAAGATTAAATTAAATTTTTATCA
65 TAATATCTATATCTTTATAATTTTTAAAAGATTAAATCAAAATTTTATCA
12528720 TTTTTAG
1 TTTTTAG
12528727 CGGGCGGGGG
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 1 0.01
114 109 0.99
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (114 bp):
TTTTTAGGGGGGCCGAAATTAAATTGTATATTCTTACGATAGTAAAAATGCAATTTCACCATTTT
AATATCTATATCTTTATAATTTTTAAAAGATTAAATCAAAATTTTATCA
Found at i:12533800 original size:3 final size:3
Alignment explanation
Indices: 12533786--12533824 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
12533776 ACGAGGTTGT
* *
12533786 TCA TCT TCA TCA TCA TCA TCA TCA TCA CCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
12533825 ACCCATTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:12539281 original size:17 final size:17
Alignment explanation
Indices: 12539261--12539308 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
12539251 AAAATCATTA
12539261 AAAAAATAAAAAATGAG
1 AAAAAATAAAAAATGAG
* * *
12539278 AAAAATTATAAAAT-AT
1 AAAAAATAAAAAATGAG
*
12539294 AAAAAATAATAAATG
1 AAAAAATAAAAAATG
12539309 TTAAATATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAAATAAAAAATGAG
Found at i:12539308 original size:33 final size:33
Alignment explanation
Indices: 12539261--12539326 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
12539251 AAAATCATTA
12539261 AAAAAATAAAAAATGAGAAAAATTATAAAATAT
1 AAAAAATAAAAAATGAGAAAAATTATAAAATAT
* ** * *
12539294 AAAAAATAATAAATGTTAAATATTTTAAAATAT
1 AAAAAATAAAAAATGAGAAAAATTATAAAATAT
12539327 TTGAAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (33 bp):
AAAAAATAAAAAATGAGAAAAATTATAAAATAT
Found at i:12539374 original size:11 final size:10
Alignment explanation
Indices: 12539358--12539402 Score: 63
Period size: 11 Copynumber: 4.2 Consensus size: 10
12539348 ATGAATTTAT
12539358 AAAAATGATAA
1 AAAAAT-ATAA
12539369 AAAAATATAA
1 AAAAATATAA
12539379 AAAAACTATAA
1 AAAAA-TATAA
12539390 AAAAATTATAA
1 AAAAA-TATAA
12539401 AA
1 AA
12539403 TTAATAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (10 bp):
AAAAATATAA
Found at i:12539402 original size:19 final size:19
Alignment explanation
Indices: 12539354--12539470 Score: 85
Period size: 21 Copynumber: 5.9 Consensus size: 19
12539344 TGATATGAAT
*
12539354 TTATAAAAATGATAAAAAAA
1 TTAT-AAAATTATAAAAAAA
* *
12539374 TATAAAAAAACTATAAAAAAA
1 T-T-ATAAAATTATAAAAAAA
*
12539395 TTATAAAATTAATAAAACATA
1 TTATAAAATT-ATAAAA-AAA
*
12539416 TT-TAAATTTTTATAAAAAAA
1 TTATAAA--ATTATAAAAAAA
** *
12539436 TT-TAAAATCCTATAAAAA
1 TTATAAAATTATAAAAAAA
12539454 TTATAAAATTATAAAAA
1 TTATAAAATTATAAAAA
12539471 GTATTAAAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
18 10 0.13
19 17 0.23
20 20 0.27
21 25 0.33
22 3 0.04
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (19 bp):
TTATAAAATTATAAAAAAA
Found at i:12539454 original size:18 final size:16
Alignment explanation
Indices: 12539431--12539481 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 16
12539421 ATTTTTATAA
12539431 AAAAATTTAAAATCCTAT
1 AAAAATTTAAAAT--TAT
12539449 AAAAATTATAAAATTAT
1 AAAAATT-TAAAATTAT
12539466 AAAAAGTATTAAAATT
1 AAAAA-T-TTAAAATT
12539482 GATATAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.27
18 15 0.50
19 7 0.23
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAAATTTAAAATTAT
Found at i:12539458 original size:9 final size:9
Alignment explanation
Indices: 12539446--12539499 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
12539436 TTTAAAATCC
12539446 TATAAAAAT
1 TATAAAAAT
12539455 TAT-AAAAT
1 TATAAAAAT
*
12539463 TATAAAAAG
1 TATAAAAAT
*
12539472 TATTAAAAT
1 TATAAAAAT
*
12539481 TGATATAAACT
1 T-ATA-AAAAT
12539492 TATAAAAA
1 TATAAAAA
12539500 AATCATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 8 0.22
9 18 0.50
10 5 0.14
11 5 0.14
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (9 bp):
TATAAAAAT
Found at i:12539980 original size:20 final size:17
Alignment explanation
Indices: 12539941--12539989 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
12539931 AGTTTCTATC
*
12539941 AATTTTAATATTTTTAA
1 AATTTTTATATTTTTAA
12539958 AATTTTTATAATTCTTTACA
1 AATTTTTAT-ATT-TTTA-A
12539978 AATTTTT-TATTT
1 AATTTTTATATTT
12539990 ATTTAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 9 0.32
18 6 0.21
19 5 0.18
20 8 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTATATTTTTAA
Found at i:12539994 original size:19 final size:19
Alignment explanation
Indices: 12539912--12540000 Score: 60
Period size: 20 Copynumber: 4.6 Consensus size: 19
12539902 GTTTTTAAGT
12539912 TTATTTAATAATTTTTATAA
1 TTATTTAA-AATTTTTATAA
* * *
12539932 GTT-TCTATCAATTTTAAT-A
1 -TTATTTA-AAATTTTTATAA
12539951 TT-TTTAAAATTTTTATAA
1 TTATTTAAAATTTTTATAA
* *
12539969 TTCTTTACAAATTTTT-TAT
1 TTATTTA-AAATTTTTATAA
12539988 TTATTTAAGAATT
1 TTATTTAA-AATT
12540001 CTAATACCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.15
18 9 0.16
19 17 0.31
20 19 0.35
21 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATTTAAAATTTTTATAA
Found at i:12541047 original size:5 final size:5
Alignment explanation
Indices: 12541039--12541063 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12541029 TTGCAAGTGA
12541039 GGGGT GGGGT GGGGT GGGGT GGGGT
1 GGGGT GGGGT GGGGT GGGGT GGGGT
12541064 AGGGATGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
GGGGT
Found at i:12541073 original size:15 final size:15
Alignment explanation
Indices: 12541039--12541072 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12541029 TTGCAAGTGA
*
12541039 GGGGTGGGGTGGGGT
1 GGGGTGGGGTGGGAT
12541054 GGGGTGGGGTAGGGAT
1 GGGGTGGGGT-GGGAT
12541070 GGG
1 GGG
12541073 TTCGAAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.00, G:0.76, T:0.18
Consensus pattern (15 bp):
GGGGTGGGGTGGGAT
Found at i:12557554 original size:3 final size:3
Alignment explanation
Indices: 12557546--12557572 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12557536 AGTGCGCTTA
12557546 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
12557573 TTGTTTAGCC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12558890 original size:30 final size:30
Alignment explanation
Indices: 12558856--12558926 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
12558846 TTAATAAAGG
* *
12558856 TAAAATTATACATTGACTCC-TTCAAAATGA
1 TAAAATTATA-ATTGAATCCTTTAAAAATGA
*
12558886 TAAAACTT-TAATTTAATCCTTTAAAAATGA
1 TAAAA-TTATAATTGAATCCTTTAAAAATGA
*
12558916 TAAAAATATAA
1 TAAAATTATAA
12558927 GTTCATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 8 0.24
30 24 0.71
31 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.35
Consensus pattern (30 bp):
TAAAATTATAATTGAATCCTTTAAAAATGA
Found at i:12570141 original size:23 final size:22
Alignment explanation
Indices: 12570089--12570141 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
12570079 TCCACGTCTT
*
12570089 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
12570111 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
12570134 TTTCTTTT
1 TTTCTTTT
12570142 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:12577639 original size:26 final size:27
Alignment explanation
Indices: 12577582--12577648 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
12577572 ACATTGGTTG
* *
12577582 AATTCAAAATTAATCTTTAAATCAATTG
1 AATTCAAAATTAA-CTATAAATCAATTA
*
12577610 AATTCAAAATTAA-TATAAATTAATTA
1 AATTCAAAATTAACTATAAATCAATTA
12577636 AATT-AATAATTAA
1 AATTCAA-AATTAA
12577649 ATTAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.06
26 20 0.57
28 13 0.37
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (27 bp):
AATTCAAAATTAACTATAAATCAATTA
Found at i:12577647 original size:12 final size:12
Alignment explanation
Indices: 12577630--12577654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12577620 TAATATAAAT
12577630 TAATTAAATTAA
1 TAATTAAATTAA
12577642 TAATTAAATTAA
1 TAATTAAATTAA
12577654 T
1 T
12577655 TTTTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTAAATTAA
Found at i:12577655 original size:9 final size:10
Alignment explanation
Indices: 12577616--12577654 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
12577606 ATTGAATTCA
12577616 AAATTAATAT
1 AAATTAATAT
12577626 AAATTAAT-T
1 AAATTAATAT
12577635 AAATTAATAATT
1 AAATTAAT-A-T
12577647 AAATTAAT
1 AAATTAAT
12577655 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.35
10 8 0.31
12 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTAATAT
Found at i:12578448 original size:19 final size:19
Alignment explanation
Indices: 12578421--12578457 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12578411 TCAATATTAA
*
12578421 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
12578440 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
12578458 ACTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:12582288 original size:25 final size:26
Alignment explanation
Indices: 12582259--12582315 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
12582249 GCAAAACTTT
* *
12582259 TTTTTATATTAAAATATT-TTTTTTG
1 TTTTTAAAATAAAATATTATTTTTTG
12582284 TTTTTAAAATAAAATATTATTTTTTG
1 TTTTTAAAATAAAATATTATTTTTTG
12582310 TCTTTT
1 T-TTTT
12582316 TTTTATAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 16 0.57
26 8 0.29
27 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTTAAAATAAAATATTATTTTTTG
Found at i:12583010 original size:60 final size:58
Alignment explanation
Indices: 12582938--12583060 Score: 219
Period size: 60 Copynumber: 2.1 Consensus size: 58
12582928 ATACTAAACT
12582938 AAACATAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
1 AAACATAACAATTTATAACATAATCCTAAATTACTAA-AAATTAATTTTAAAATAATTA
*
12582997 CAAACATAACAATTTATAACATAATCCTAAATTACTAACAATTAATTTTAAAATAATTA
1 -AAACATAACAATTTATAACATAATCCTAAATTACTAAAAATTAATTTTAAAATAATTA
12583056 AAACA
1 AAACA
12583061 ATATTTTTAG
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 5 0.08
59 20 0.32
60 37 0.60
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACATAACAATTTATAACATAATCCTAAATTACTAAAAATTAATTTTAAAATAATTA
Found at i:12598645 original size:22 final size:24
Alignment explanation
Indices: 12598615--12598659 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12598605 TTACTTTTGA
*
12598615 TCTCTTTAATT-TTTTATTTCTAC
1 TCTCTTTAATTATTTAATTTCTAC
12598638 TCTC-TTAATTATTTAATTTCTA
1 TCTCTTTAATTATTTAATTTCTA
12598660 GACATTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (24 bp):
TCTCTTTAATTATTTAATTTCTAC
Found at i:12611273 original size:5 final size:5
Alignment explanation
Indices: 12611265--12611294 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
12611255 ATTTATGTTT
12611265 TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA
12611295 ACTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:12612926 original size:28 final size:28
Alignment explanation
Indices: 12612891--12612957 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
12612881 AAAAATAATA
12612891 AATAAATTAACAAAATACTGGTATTAGT
1 AATAAATTAACAAAATACTGGTATTAGT
*
12612919 AATAAATTAACAAAATACTGTTATTAGT
1 AATAAATTAACAAAATACTGGTATTAGT
12612947 AATAAATTAAC
1 AATAAATTAAC
12612958 TTTAAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (28 bp):
AATAAATTAACAAAATACTGGTATTAGT
Found at i:12613923 original size:6 final size:6
Alignment explanation
Indices: 12613914--12613941 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12613904 TGTTATTTTT
12613914 ATAATG ATAATG ATAATG ATAATG ATAA
1 ATAATG ATAATG ATAATG ATAATG ATAA
12613942 CAAAATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (6 bp):
ATAATG
Found at i:12623128 original size:13 final size:13
Alignment explanation
Indices: 12623110--12623135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12623100 CTTTCTGACC
12623110 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
12623123 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
12623136 TTAAGACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:12640275 original size:7 final size:7
Alignment explanation
Indices: 12640265--12640289 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12640255 ATCAAAGTCG
12640265 GAGTACT
1 GAGTACT
12640272 GAGTACT
1 GAGTACT
12640279 GAGTACT
1 GAGTACT
12640286 GAGT
1 GAGT
12640290 TAAGGAGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (7 bp):
GAGTACT
Found at i:12648618 original size:12 final size:13
Alignment explanation
Indices: 12648599--12648629 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12648589 AAATTAGTGG
*
12648599 GTTTTTTTTTTTT
1 GTTTTTTTTTCTT
12648612 GTTTTTTTTTCTT
1 GTTTTTTTTTCTT
12648625 GTTTT
1 GTTTT
12648630 CCTTTTATTT
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:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (13 bp):
GTTTTTTTTTCTT
Found at i:12654529 original size:6 final size:7
Alignment explanation
Indices: 12654500--12654527 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12654490 AATATTGAAT
12654500 ATTAAAA
1 ATTAAAA
12654507 ATTAAAA
1 ATTAAAA
12654514 ATTAAAA
1 ATTAAAA
12654521 ATTAAAA
1 ATTAAAA
12654528 TTGATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATTAAAA
Found at i:12654573 original size:26 final size:26
Alignment explanation
Indices: 12654509--12654573 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
12654499 TATTAAAAAT
*
12654509 TAAAAAT-TAAAAATTAAAATTGATA
1 TAAAAATATAAAAATTAAAAGTGATA
** * *
12654534 TAAACTTATTAAAATTATAAGT-ATTA
1 TAAAAATATAAAAATTAAAAGTGA-TA
12654560 TAAAAATATAAAAA
1 TAAAAATATAAAAA
12654574 AATCTAATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (26 bp):
TAAAAATATAAAAATTAAAAGTGATA
Found at i:12655079 original size:9 final size:9
Alignment explanation
Indices: 12655065--12655185 Score: 73
Period size: 10 Copynumber: 12.6 Consensus size: 9
12655055 TTATGAATTT
12655065 TTTTTATAA
1 TTTTTATAA
*
12655074 TTTTTATTAG
1 TTTTTA-TAA
*
12655084 TTTATATTAA
1 TTTTTA-TAA
* *
12655094 TTTTAATACT
1 TTTTTATA-A
12655104 TTTTTATAA
1 TTTTTATAA
12655113 TTTTTATAA
1 TTTTTATAA
*
12655122 TTTCTATAGA
1 TTTTTATA-A
* * *
12655132 ATTTAATACG
1 TTTTTATA-A
12655142 TTTTTATAA
1 TTTTTATAA
*
12655151 TATTTTAAATA
1 T-TTTTATA-A
12655162 TGTTTTATTAA
1 T-TTTTA-TAA
12655173 -TTTTATAA
1 TTTTTATAA
12655181 TTTTT
1 TTTTT
12655186 TCTTTTTTTA
Statistics
Matches: 85, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
8 3 0.04
9 34 0.40
10 39 0.46
11 8 0.09
12 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12655137 original size:38 final size:39
Alignment explanation
Indices: 12655064--12655157 Score: 120
Period size: 38 Copynumber: 2.4 Consensus size: 39
12655054 TTTATGAATT
* *
12655064 TTTTTTATAATTTTTATTAGTTTATATTAATTTTAATAC
1 TTTTTTATAATTTTTATTAATTTATATTAAATTTAATAC
*
12655103 TTTTTTATAATTTTTA-TAATTTCTA-TAGAATTTAATAC
1 TTTTTTATAATTTTTATTAATTTATATTA-AATTTAATAC
*
12655141 GTTTTTATAATATTTTA
1 TTTTTTATAAT-TTTTA
12655158 AATATGTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
37 2 0.04
38 26 0.53
39 21 0.43
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (39 bp):
TTTTTTATAATTTTTATTAATTTATATTAAATTTAATAC
Found at i:12655155 original size:20 final size:18
Alignment explanation
Indices: 12655065--12655151 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 18
12655055 TTATGAATTT
*
12655065 TTTTTATAATTTTTATTAG
1 TTTTTATAA-TTTTAATAG
* *
12655084 TTTATATTAATTTTAATACT
1 TTTTTA-TAATTTTAATA-G
* *
12655104 TTTTTATAATTTTTATAA
1 TTTTTATAATTTTAATAG
* *
12655122 TTTCTATAGAATTTAATACG
1 TTTTTATA-ATTTTAATA-G
12655142 TTTTTATAAT
1 TTTTTATAAT
12655152 ATTTTAAATA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
18 7 0.13
19 30 0.58
20 15 0.29
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTTAATAG
Found at i:12661567 original size:2 final size:2
Alignment explanation
Indices: 12661560--12661587 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12661550 TTAGACAAAG
12661560 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12661588 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12663345 original size:22 final size:20
Alignment explanation
Indices: 12663300--12663347 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
12663290 TAAACGAGTC
*
12663300 TCTTTTTTTAGCTCCCTTTA
1 TCTTCTTTTAGCTCCCTTTA
*
12663320 TCTTCTTTTAGCTCTCTTT-
1 TCTTCTTTTAGCTCCCTTTA
*
12663339 TATTCTTTT
1 TCTTCTTTT
12663348 CACCATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.08, C:0.23, G:0.04, T:0.65
Consensus pattern (20 bp):
TCTTCTTTTAGCTCCCTTTA
Found at i:12669619 original size:20 final size:19
Alignment explanation
Indices: 12669596--12669642 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
12669586 TATTTCTTAA
12669596 AATTAAAACTCAATTCTACC
1 AATTAAAACTCAATTC-ACC
* *
12669616 AATTCAAAACTCCATTCAGC
1 AATT-AAAACTCAATTCACC
12669636 AATTAAA
1 AATTAAA
12669643 CATGAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (19 bp):
AATTAAAACTCAATTCACC
Found at i:12671695 original size:40 final size:40
Alignment explanation
Indices: 12671651--12671733 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
12671641 CTTAGTAATC
12671651 ATATAGTAAAAGAATTAATATTGTAATTGACTTAAATTTA
1 ATATAGTAAAAGAATTAATATTGTAATTGACTTAAATTTA
12671691 ATATAGTAAAAGAATTAATATTGTAATTGACTTAAATTTA
1 ATATAGTAAAAGAATTAATATTGTAATTGACTTAAATTTA
12671731 ATA
1 ATA
12671734 AAGAAATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (40 bp):
ATATAGTAAAAGAATTAATATTGTAATTGACTTAAATTTA
Found at i:12675066 original size:21 final size:20
Alignment explanation
Indices: 12675034--12675080 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
12675024 AAAACAAATT
*
12675034 TAAAATATTTAAAATTTTATA
1 TAAAATATTTAAAATTCTA-A
12675055 TAAACATA-TTAAAATTCTAA
1 TAAA-ATATTTAAAATTCTAA
12675075 TAAAAT
1 TAAAAT
12675081 CATATAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 5 0.21
21 14 0.58
22 3 0.12
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAATATTTAAAATTCTAA
Found at i:12675088 original size:21 final size:20
Alignment explanation
Indices: 12675034--12675147 Score: 53
Period size: 21 Copynumber: 5.8 Consensus size: 20
12675024 AAAACAAATT
* *
12675034 TAAAAT-ATTTAAAATTTTA
1 TAAAATCATATAAAATTTAA
12675053 TATAAA-CATATTAAAATTCTAA
1 TA-AAATCATA-TAAAATT-TAA
*
12675075 TAAAATCATAT-AAA-TTACT
1 TAAAATCATATAAAATTTA-A
** *
12675094 TAAAA--ATATAAAAAGTAT
1 TAAAATCATATAAAATTTAA
*
12675112 TAAAATTGATATAAAATTATAA
1 TAAAA-TCATATAAAATT-TAA
*
12675134 AAAAATCATA-AAAA
1 TAAAATCATATAAAA
12675148 CTTGAACTGG
Statistics
Matches: 74, Mismatches: 9, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
17 4 0.05
18 11 0.15
19 10 0.14
20 12 0.16
21 23 0.31
22 14 0.19
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAATCATATAAAATTTAA
Found at i:12675578 original size:20 final size:21
Alignment explanation
Indices: 12675532--12675580 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
12675522 CCGGTTCAGT
* *
12675532 TCAAGTTTTTATAATTCTTTTA
1 TCAA-TTTTTATAAGTCTTATA
12675554 T-AATTTTTATAAGT-TTATA
1 TCAATTTTTATAAGTCTTATA
12675573 TCAATTTT
1 TCAATTTT
12675581 AATTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 16 0.67
21 2 0.08
22 1 0.04
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (21 bp):
TCAATTTTTATAAGTCTTATA
Found at i:12675596 original size:11 final size:11
Alignment explanation
Indices: 12675582--12675624 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
12675572 ATCAATTTTA
12675582 ATTTTTTTAAT
1 ATTTTTTTAAT
*
12675593 ATTTCTTT-AT
1 ATTTTTTTAAT
12675603 ACTTTTTTTATAT
1 A-TTTTTTTA-AT
12675616 ATTTTTTTA
1 ATTTTTTTA
12675625 CAACTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.11
11 13 0.48
12 8 0.30
13 3 0.11
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTTAAT
Found at i:12675617 original size:23 final size:24
Alignment explanation
Indices: 12675583--12675638 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
12675573 TCAATTTTAA
*
12675583 TTTTTTTA-ATATTTCTTTA-TAC
1 TTTTTTTATATATTTCTTTACAAC
*
12675605 TTTTTTTATATATTTTTTTACAAC
1 TTTTTTTATATATTTCTTTACAAC
12675629 TTTTTATTAT
1 TTTTT-TTAT
12675639 TTTTTAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.28
23 10 0.34
24 7 0.24
25 4 0.14
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTTATATATTTCTTTACAAC
Found at i:12675711 original size:10 final size:9
Alignment explanation
Indices: 12675692--12675837 Score: 78
Period size: 9 Copynumber: 16.4 Consensus size: 9
12675682 AAAAAATTAT
12675692 TAATTTTTA
1 TAATTTTTA
12675701 TAATTTATTA
1 TAATTT-TTA
12675711 T-ATTTATTA
1 TAATTT-TTA
12675720 T-A-TTTTA
1 TAATTTTTA
*
12675727 TAATATTTA
1 TAATTTTTA
12675736 TAAGTTTTTA
1 TAA-TTTTTA
*
12675746 TAATTTTAA
1 TAATTTTTA
*
12675755 TAAGTTTATA
1 TAA-TTTTTA
*
12675765 TCAATTTTAA
1 T-AATTTTTA
12675775 T-A-TTTT-
1 TAATTTTTA
*
12675781 TAATATTTA
1 TAATTTTTA
12675790 -ATATTTTTA
1 TA-ATTTTTA
12675799 T--TTTTATA
1 TAATTTT-TA
**
12675807 TCTTTTTTTA
1 T-AATTTTTA
*
12675817 TAATTTTTC
1 TAATTTTTA
12675826 TAATTTTT-
1 TAATTTTTA
12675834 TAAT
1 TAAT
12675838 ATCTTCATGG
Statistics
Matches: 109, Mismatches: 13, Indels: 31
0.71 0.08 0.20
Matches are distributed among these distances:
6 1 0.01
7 12 0.11
8 15 0.14
9 50 0.46
10 25 0.23
11 6 0.06
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
TAATTTTTA
Found at i:12675726 original size:19 final size:19
Alignment explanation
Indices: 12675688--12675736 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
12675678 TTTTAAAAAA
12675688 TTATTA-ATTT-TTATAAT
1 TTATTATATTTATTATAAT
*
12675705 TTATTATATTTATTATATT
1 TTATTATATTTATTATAAT
*
12675724 TTATAATATTTAT
1 TTATTATATTTAT
12675737 AAGTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.21
18 4 0.14
19 18 0.64
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATATTTATTATAAT
Found at i:12675744 original size:19 final size:19
Alignment explanation
Indices: 12675704--12675789 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
12675694 ATTTTTATAA
* *
12675704 TTTATTATATTTATTATAT
1 TTTATAATATTTATAATAT
12675723 TTTATAATATTTATAAGT-T
1 TTTATAATATTTATAA-TAT
12675742 TTTATAAT-TTTAATAAGT-T
1 TTTATAATATTT-ATAA-TAT
* *
12675761 TATATCA-ATTT-TAATAT
1 TTTATAATATTTATAATAT
12675778 TTT-TAATATTTA
1 TTTATAATATTTA
12675790 ATATTTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
16 3 0.05
17 10 0.18
18 3 0.05
19 38 0.69
20 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTATAATATTTATAATAT
Found at i:12675773 original size:20 final size:19
Alignment explanation
Indices: 12675725--12675776 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
12675715 TATTATATTT
*
12675725 TATAATATTT-ATAAGTTTT
1 TATAAT-TTTAATAAGTTTA
12675744 TATAATTTTAATAAGTTTA
1 TATAATTTTAATAAGTTTA
12675763 TATCAATTTTAATA
1 TAT-AATTTTAATA
12675777 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 3 0.10
19 17 0.57
20 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TATAATTTTAATAAGTTTA
Found at i:12677051 original size:149 final size:149
Alignment explanation
Indices: 12676773--12677076 Score: 464
Period size: 149 Copynumber: 2.0 Consensus size: 149
12676763 ATCAAGTCAA
* * * * *
12676773 GATGAATGACAAGATTTATCCCGTCTGTGACATCCTCGTCTAATAGAAAACACCCCCTCCTACAT
1 GATGAATGACAAGATCTATCCCATCTCTGACATCCTCGTCCAATAGAAAACACCCCCTCCCACAT
** * *
12676838 GTTCTGTAATGATGATTAAATGGCAAGCCTAACATGTTAACACCATCTTACATAGGACCATCACC
66 GTTCTGTAATGATGATTAAATGGCAAGCCTAACACATTAACACCATCTTACACAGAACCATCACC
12676903 TATAAATATCTCCAAGAAC
131 TATAAATATCTCCAAGAAC
* * *
12676922 GATGAATGACAGGATCTATCCCATCTCTGACATTCTCGTCCAATAGAAAACACCCCTTCCCACAT
1 GATGAATGACAAGATCTATCCCATCTCTGACATCCTCGTCCAATAGAAAACACCCCCTCCCACAT
* * *
12676987 GTTCTTTAATGATGATTAAATGGCAAGTCTAACACATTAACACCATCTTACACAGAACCCTCACC
66 GTTCTGTAATGATGATTAAATGGCAAGCCTAACACATTAACACCATCTTACACAGAACCATCACC
*
12677052 TATAAATATCTCTAAGAAC
131 TATAAATATCTCCAAGAAC
12677071 GATGAA
1 GATGAA
12677077 AAAAGGACTA
Statistics
Matches: 139, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
149 139 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (149 bp):
GATGAATGACAAGATCTATCCCATCTCTGACATCCTCGTCCAATAGAAAACACCCCCTCCCACAT
GTTCTGTAATGATGATTAAATGGCAAGCCTAACACATTAACACCATCTTACACAGAACCATCACC
TATAAATATCTCCAAGAAC
Found at i:12683072 original size:40 final size:40
Alignment explanation
Indices: 12683011--12683148 Score: 186
Period size: 40 Copynumber: 3.5 Consensus size: 40
12683001 CTCGAGAATA
* * *
12683011 TAAAGTGGATAGGATTCGTTCCTGATTCACTATGATACCT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
* * *
12683051 CAAAGTGGATAGGATTTGTTCCTGATTCACTGTGGTAATT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
* *
12683091 TAAAGTGAATAGGATTTATTCCTGATTCACTATGGTAACT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
* *
12683131 TAAGGCGGATAGGATTTG
1 TAAAGTGGATAGGATTTG
12683149 ACCTGAAAAG
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (40 bp):
TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
Found at i:12683204 original size:78 final size:78
Alignment explanation
Indices: 12683113--12683264 Score: 250
Period size: 78 Copynumber: 1.9 Consensus size: 78
12683103 GATTTATTCC
* **
12683113 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGATAATCCTGATTTGCTACA
1 TGATTCACTATGGTAACCTAAGGCGGATAGGATTTGACCTGAAAAGATAATCCTGATTCACTACA
12683178 GTTACATGATATA
66 GTTACATGATATA
* * *
12683191 TGATTCATTATGGTAACCTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTACA
1 TGATTCACTATGGTAACCTAAGGCGGATAGGATTTGACCTGAAAAGATAATCCTGATTCACTACA
12683256 GTTACATGA
66 GTTACATGA
12683265 GATGTGACTC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (78 bp):
TGATTCACTATGGTAACCTAAGGCGGATAGGATTTGACCTGAAAAGATAATCCTGATTCACTACA
GTTACATGATATA
Found at i:12689065 original size:25 final size:25
Alignment explanation
Indices: 12689037--12689085 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
12689027 TTTGATTCAA
12689037 TTGTCGATCTATATAATAATTTAAC
1 TTGTCGATCTATATAATAATTTAAC
12689062 TTGTCGATCTATATAATAATTTAA
1 TTGTCGATCTATATAATAATTTAA
12689086 TTCAATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (25 bp):
TTGTCGATCTATATAATAATTTAAC
Found at i:12690666 original size:25 final size:25
Alignment explanation
Indices: 12690632--12690682 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12690622 GATTTATACC
12690632 ATAGTTTCCATAATTTTAATTTTAA
1 ATAGTTTCCATAATTTTAATTTTAA
12690657 ATAGTTTCCATAATTTTAATTTTAA
1 ATAGTTTCCATAATTTTAATTTTAA
12690682 A
1 A
12690683 CCCTTGACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (25 bp):
ATAGTTTCCATAATTTTAATTTTAA
Found at i:12691064 original size:18 final size:18
Alignment explanation
Indices: 12691041--12691084 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12691031 TTTATTGGCC
*
12691041 GATTGGTTTGATTAATAT
1 GATTGGTTTGATCAATAT
*
12691059 GATTGGTTTGATCAATCT
1 GATTGGTTTGATCAATAT
*
12691077 GTTTGGTT
1 GATTGGTT
12691085 CTATTAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (18 bp):
GATTGGTTTGATCAATAT
Found at i:12692677 original size:9 final size:9
Alignment explanation
Indices: 12692663--12692688 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12692653 TGCACACCAA
12692663 CATTTACAT
1 CATTTACAT
12692672 CATTTACAT
1 CATTTACAT
12692681 CATTTACA
1 CATTTACA
12692689 AGCCAACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (9 bp):
CATTTACAT
Found at i:12696079 original size:46 final size:46
Alignment explanation
Indices: 12696004--12696277 Score: 415
Period size: 46 Copynumber: 6.0 Consensus size: 46
12695994 AGTGTGCTCT
* *
12696004 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGAAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
12696050 CTTATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
12696096 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
12696142 CTTATATGAAATGTGTAAGATCATGGTTGAAAGATACCATAGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
12696188 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
12696234 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
12696278 TCATGTCAAA
Statistics
Matches: 209, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 208 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:12696511 original size:19 final size:19
Alignment explanation
Indices: 12696458--12696498 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
12696448 AATTATGAAG
12696458 ATAGATAAATGAAATAAGA
1 ATAGATAAATGAAATAAGA
12696477 ATAGATAAATGAAATAAGA
1 ATAGATAAATGAAATAAGA
12696496 ATA
1 ATA
12696499 AGTACATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (19 bp):
ATAGATAAATGAAATAAGA
Found at i:12696603 original size:16 final size:17
Alignment explanation
Indices: 12696582--12696614 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12696572 ATGATGGAGC
12696582 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
12696598 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
12696615 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:12702823 original size:8 final size:7
Alignment explanation
Indices: 12702793--12702842 Score: 82
Period size: 7 Copynumber: 6.9 Consensus size: 7
12702783 GGTTTTGACT
12702793 GGGTTTA
1 GGGTTTA
12702800 GGGTTTA
1 GGGTTTA
12702807 GGGTTTA
1 GGGTTTA
12702814 GGGTTTTA
1 GGG-TTTA
12702822 GGGTTTTA
1 GGG-TTTA
12702830 GGGTTTA
1 GGGTTTA
12702837 GGGTTT
1 GGGTTT
12702843 GCTCTACATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 27 0.64
8 15 0.36
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (7 bp):
GGGTTTA
Found at i:12702823 original size:15 final size:15
Alignment explanation
Indices: 12702796--12702842 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
12702786 TTTGACTGGG
12702796 TTTAGGGTTTAGGG-
1 TTTAGGGTTTAGGGT
12702810 TTTAGGGTTTTAGGGT
1 TTTAGGG-TTTAGGGT
12702826 TTTAGGGTTTAGGGT
1 TTTAGGGTTTAGGGT
12702841 TT
1 TT
12702843 GCTCTACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.23
15 17 0.55
16 7 0.23
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (15 bp):
TTTAGGGTTTAGGGT
Found at i:12709692 original size:6 final size:6
Alignment explanation
Indices: 12709681--12709721 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
12709671 GCCATCATCA
* *
12709681 CCACCT CCACCT CCACCT CCACCT CCACCA CCCCCT CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
12709722 GCCTCCTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.71, G:0.00, T:0.12
Consensus pattern (6 bp):
CCACCT
Found at i:12718022 original size:6 final size:6
Alignment explanation
Indices: 12718013--12718039 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12718003 ATCGCAACCA
12718013 CAGCCG CAGCCG CAGCCG CAGCCG CAG
1 CAGCCG CAGCCG CAGCCG CAGCCG CAG
12718040 TAACAGCCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.33, T:0.00
Consensus pattern (6 bp):
CAGCCG
Found at i:12718026 original size:18 final size:18
Alignment explanation
Indices: 12718005--12718039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12717995 TCCTCGCAAT
12718005 CGCAACCACAGCCGCAGC
1 CGCAACCACAGCCGCAGC
* *
12718023 CGCAGCCGCAGCCGCAG
1 CGCAACCACAGCCGCAG
12718040 TAACAGCCGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.49, G:0.29, T:0.00
Consensus pattern (18 bp):
CGCAACCACAGCCGCAGC
Found at i:12720481 original size:130 final size:130
Alignment explanation
Indices: 12720184--12720575 Score: 525
Period size: 130 Copynumber: 3.0 Consensus size: 130
12720174 ATTTGGAGAA
* * * * * *
12720184 CATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAAC-AAAAGATAGTAACCCAGCAC
1 CATGACTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAA-ATCGCAACCCAGCAC
** * * *
12720248 GATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTTGTTTTGGAGAGTTTTTTTT
65 GATAGGGCACGATT-CCCGAATTGCCAAACATCGAGTATTGCCTTCGTTTTGGAGA---ATTTTT
*
12720313 TAAAG
126 AAAAG
* * * *
12720318 CATGAGTGAAATCCCAAAGAAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCTAGCACG
1 CATGACTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* *
12720383 ATAGGGCACGATTCCCAAATTGCCAAACACCGAGTATTGCCTTCGTTTTGGAGAATTTTTAAAAG
66 ATAGGGCACGATTCCCGAATTGCCAAACATCGAGTATTGCCTTCGTTTTGGAGAATTTTTAAAAG
* *
12720448 CATGTCTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGGGAAATCGCAACCCAGCACG
1 CATGACTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
** *
12720513 ATAGGGCACGATTCTTGAATTGCCAAACATCGAGTATTGCCTTCGTTTTAGAGAATTTTTAAA
66 ATAGGGCACGATTCCCGAATTGCCAAACATCGAGTATTGCCTTCGTTTTGGAGAATTTTTAAA
12720576 TGAATAATTA
Statistics
Matches: 230, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
130 126 0.55
133 35 0.15
134 66 0.29
135 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (130 bp):
CATGACTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
ATAGGGCACGATTCCCGAATTGCCAAACATCGAGTATTGCCTTCGTTTTGGAGAATTTTTAAAAG
Found at i:12721572 original size:18 final size:17
Alignment explanation
Indices: 12721539--12721572 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12721529 ATCAACTTTA
12721539 ATATAAAGTATATATAT
1 ATATAAAGTATATATAT
*
12721556 ATATAATAGTGTATATA
1 ATATAA-AGTATATATA
12721573 AAAAACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
ATATAAAGTATATATAT
Found at i:12722707 original size:45 final size:45
Alignment explanation
Indices: 12722605--12722824 Score: 297
Period size: 45 Copynumber: 5.0 Consensus size: 45
12722595 CTAAATTCAT
* * * *
12722605 TCACCAGCATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
12722647 TCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATC
*
12722692 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* *
12722737 TCACCGACGTTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * *
12722782 TCACCTGCAATATAGCCTGTTAGGCTCAAAGGCCCGAATAGTA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
12722825 CTGTACGATA
Statistics
Matches: 160, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
42 10 0.06
43 14 0.09
44 10 0.06
45 125 0.78
46 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:12726077 original size:48 final size:48
Alignment explanation
Indices: 12725928--12726082 Score: 149
Period size: 48 Copynumber: 3.2 Consensus size: 48
12725918 ACTTAATTAC
* *
12725928 TTTAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAA
1 TTTAATATTAAATTAATAAAATAC-TATCAAGATAAATATTAAATTAAA
* * *
12725977 --T-CTATT-AATTAATAGAATATTTATCTAT-AAGATAAATATTAAATTGAT
1 TTTAATATTAAATTAATA-AA-A--TA-CTATCAAGATAAATATTAAATTAAA
* *
12726025 TTTAATATTAAATTAATAAAATACAATCAAGATAAGTATTAAATTAAA
1 TTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAA
12726073 TTTAAGTATT
1 TTTAA-TATT
12726083 TTTTTAAATT
Statistics
Matches: 85, Mismatches: 10, Indels: 22
0.73 0.09 0.19
Matches are distributed among these distances:
45 8 0.09
46 5 0.06
47 5 0.06
48 41 0.48
49 9 0.11
50 3 0.04
51 6 0.07
52 8 0.09
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (48 bp):
TTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAA
Found at i:12726080 original size:18 final size:18
Alignment explanation
Indices: 12726057--12726103 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
12726047 ACAATCAAGA
12726057 TAAGTATTAAATTAAATT
1 TAAGTATTAAATTAAATT
***
12726075 TAAGTATTTTTTTAAATT
1 TAAGTATTAAATTAAATT
12726093 TAA-TATTAAAT
1 TAAGTATTAAAT
12726104 CTTATTAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TAAGTATTAAATTAAATT
Found at i:12729508 original size:23 final size:23
Alignment explanation
Indices: 12729466--12729509 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12729456 ACTACCATTT
*
12729466 TCTAAATAAAATAATCATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
12729489 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
12729510 ATAATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:12729779 original size:31 final size:31
Alignment explanation
Indices: 12729740--12729843 Score: 126
Period size: 31 Copynumber: 3.4 Consensus size: 31
12729730 AATTAGATTA
12729740 TTTT-CACTTTTGGTCCTTCAAATTTCTCAT
1 TTTTACACTTTTGGTCCTTCAAATTTCTCAT
* *
12729770 TTTTACACTTTT-ATCCCTT-AAATTT-TAAAT
1 TTTTACACTTTTGGT-CCTTCAAATTTCT-CAT
*
12729800 TATTTTCACTTTTGGTCCTTCAAATTTCTCAT
1 T-TTTACACTTTTGGTCCTTCAAATTTCTCAT
12729832 TTTTACACTTTT
1 TTTTACACTTTT
12729844 ATCCCTTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
29 1 0.02
30 14 0.23
31 35 0.57
32 10 0.16
33 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.55
Consensus pattern (31 bp):
TTTTACACTTTTGGTCCTTCAAATTTCTCAT
Found at i:12729805 original size:62 final size:62
Alignment explanation
Indices: 12729736--12729871 Score: 256
Period size: 62 Copynumber: 2.2 Consensus size: 62
12729726 ATTAAATTAG
12729736 ATTATTTTCACTTTTGGTCCTTCAAATTTCTCATTTTTACACTTTTATCCCTTAAATTTTAA
1 ATTATTTTCACTTTTGGTCCTTCAAATTTCTCATTTTTACACTTTTATCCCTTAAATTTTAA
12729798 ATTATTTTCACTTTTGGTCCTTCAAATTTCTCATTTTTACACTTTTATCCCTTAAATTTTAA
1 ATTATTTTCACTTTTGGTCCTTCAAATTTCTCATTTTTACACTTTTATCCCTTAAATTTTAA
*
12729860 A-TATTTACACTT
1 ATTATTTTCACTT
12729872 AAGCCAAAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 10 0.14
62 63 0.86
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (62 bp):
ATTATTTTCACTTTTGGTCCTTCAAATTTCTCATTTTTACACTTTTATCCCTTAAATTTTAA
Found at i:12735208 original size:18 final size:19
Alignment explanation
Indices: 12735167--12735226 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
12735157 TAACTATTAG
*
12735167 TTAAT-TAATAGTATATTATA
1 TTAATATAATATTA-ATT-TA
12735187 TTAAT-TAATTATTAA-TTA
1 TTAATATAA-TATTAATTTA
12735205 TTAATATAATATTAATTTA
1 TTAATATAATATTAATTTA
12735224 TTA
1 TTA
12735227 TTTTTAAGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 13 0.36
19 10 0.28
20 9 0.25
21 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAATATAATATTAATTTA
Found at i:12748387 original size:107 final size:107
Alignment explanation
Indices: 12748226--12748438 Score: 417
Period size: 107 Copynumber: 2.0 Consensus size: 107
12748216 TAGTTAAAAT
12748226 ATAACATAAATATCATAGCAACAGCCAAGACCCAAAAATTTTATAGTTGCATCTCTTGGAACTGA
1 ATAACATAAATATCATAGCAACAGCCAAGACCCAAAAATTTTATAGTTGCATCTCTTGGAACTGA
12748291 AGTACAAGCAAACACAAATTGCACGGAAAATTCATCAGGAGA
66 AGTACAAGCAAACACAAATTGCACGGAAAATTCATCAGGAGA
12748333 ATAACATAAATATCATAGCAACAGCCAAGACCCAAAAATTTTATAGTTGCATCTCTTGGAACTGA
1 ATAACATAAATATCATAGCAACAGCCAAGACCCAAAAATTTTATAGTTGCATCTCTTGGAACTGA
*
12748398 AGTACGAGCAAACACAAATTGCACGGAAAATTCATCAGGAG
66 AGTACAAGCAAACACAAATTGCACGGAAAATTCATCAGGAG
12748439 GTACTTGGAC
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (107 bp):
ATAACATAAATATCATAGCAACAGCCAAGACCCAAAAATTTTATAGTTGCATCTCTTGGAACTGA
AGTACAAGCAAACACAAATTGCACGGAAAATTCATCAGGAGA
Found at i:12758667 original size:19 final size:20
Alignment explanation
Indices: 12758631--12758669 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12758621 TATTTTTTTC
*
12758631 ATTTTTTTATCCCAATAACA
1 ATTTTTTTATCACAATAACA
*
12758651 ATTTTTTTATTAC-ATAACA
1 ATTTTTTTATCACAATAACA
12758670 TATTCTCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTTTTATCACAATAACA
Found at i:12763703 original size:26 final size:26
Alignment explanation
Indices: 12763653--12763704 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
12763643 GATAGAGTTT
*
12763653 AATAAAATTTAAAAAATTTTATTTTAA
1 AATAAAA-TTAAAAAAATTTATTTTAA
12763680 AATAAAA-TAAAAAAATTTAGTTTTA
1 AATAAAATTAAAAAAATTTA-TTTTA
12763705 TATGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 5 0.22
27 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
AATAAAATTAAAAAAATTTATTTTAA
Found at i:12763729 original size:16 final size:18
Alignment explanation
Indices: 12763710--12763747 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12763700 TTTTATATGA
12763710 ATTTTACT-TT-TATTTT
1 ATTTTACTATTATATTTT
12763726 ATTTTACTATTATATTTT
1 ATTTTACTATTATATTTT
12763744 ATTT
1 ATTT
12763748 AAATAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTACTATTATATTTT
Found at i:12765593 original size:26 final size:26
Alignment explanation
Indices: 12765537--12765586 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
12765527 TTAGTAATAG
* * *
12765537 TCAGTTATTCAGTATCAATCAATTGA
1 TCAGTTATCCAATAACAATCAATTGA
*
12765563 TCAGTTATCCAATAACAGTCAATT
1 TCAGTTATCCAATAACAATCAATT
12765587 ATTCAGTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (26 bp):
TCAGTTATCCAATAACAATCAATTGA
Found at i:12765602 original size:18 final size:19
Alignment explanation
Indices: 12765581--12765634 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
12765571 CCAATAACAG
12765581 TCAATTATTCAGTAA-AAA
1 TCAATTATTCAGTAACAAA
* * *
12765599 TCAAATATACAGTAACAAT
1 TCAATTATTCAGTAACAAA
*
12765618 TAAATTATTCAGTAACA
1 TCAATTATTCAGTAACA
12765635 GTTGGTCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (19 bp):
TCAATTATTCAGTAACAAA
Found at i:12765632 original size:19 final size:19
Alignment explanation
Indices: 12765583--12765634 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
12765573 AATAACAGTC
*
12765583 AATTATTCAGTAAAAATCA
1 AATTATTCAGTAACAATCA
* *
12765602 AA-TATACAGTAACAATTA
1 AATTATTCAGTAACAATCA
12765620 AATTATTCAGTAACA
1 AATTATTCAGTAACA
12765635 GTTGGTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (19 bp):
AATTATTCAGTAACAATCA
Found at i:12765840 original size:47 final size:47
Alignment explanation
Indices: 12765746--12765868 Score: 142
Period size: 47 Copynumber: 2.6 Consensus size: 47
12765736 TCGGCCGAAG
* *
12765746 CCGAAACAATAACAGTAACAGTAACAGTAAGTATCTCATCGGAACAAAT
1 CCGAAACAATAACAGT-ACAGTAACAG-AAGTACCTCATCGAAACAAAT
*
12765795 CCGGAACAATAACAGTAC-GATACACAG-AGTACCTCATCGAAACAAAT
1 CCGAAACAATAACAGTACAG-TA-ACAGAAGTACCTCATCGAAACAAAT
* *
12765842 CCGAAACAGTAACAGTAACGGTAACAG
1 CCGAAACAATAACAGT-ACAGTAACAG
12765869 TAACAATATC
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
47 37 0.57
48 8 0.12
49 20 0.31
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.15
Consensus pattern (47 bp):
CCGAAACAATAACAGTACAGTAACAGAAGTACCTCATCGAAACAAAT
Found at i:12767022 original size:15 final size:15
Alignment explanation
Indices: 12767002--12767044 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
12766992 GTTTCATCCT
12767002 TTCTTTCTT-TTTTTA
1 TTCTTT-TTCTTTTTA
12767017 TTCTTTTTCTTTTTA
1 TTCTTTTTCTTTTTA
*
12767032 TTCCTTTTACTTT
1 TT-CTTTTTCTTT
12767045 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 2 0.08
15 14 0.56
16 9 0.36
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTTCTTTTTA
Found at i:12767038 original size:16 final size:15
Alignment explanation
Indices: 12767011--12767044 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12767001 TTTCTTTCTT
*
12767011 TTTTTATTCTTTTTC
1 TTTTTATTCTTTTAC
12767026 TTTTTATTCCTTTTAC
1 TTTTTATT-CTTTTAC
12767042 TTT
1 TTT
12767045 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTCTTTTAC
Found at i:12767059 original size:12 final size:12
Alignment explanation
Indices: 12767042--12767067 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12767032 TTCCTTTTAC
12767042 TTTATATATATA
1 TTTATATATATA
12767054 TTTATATATATA
1 TTTATATATATA
12767066 TT
1 TT
12767068 ATAATAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATATATATA
Found at i:12775111 original size:39 final size:39
Alignment explanation
Indices: 12774972--12775111 Score: 217
Period size: 39 Copynumber: 3.6 Consensus size: 39
12774962 GCTCTGATGA
* *
12774972 GCTTCAGTTAGCCTTTGGGCTTTCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
12775011 GCTTCAGTTAGCTTTCGGGTTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
12775050 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCAATTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
12775089 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
12775112 AGATCACGAT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Done.