Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 9 of 205
Found at i:2403549 original size:23 final size:23
Alignment explanation
Indices: 2403485--2403572 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
2403475 CCTGATCAAT
*
2403485 ATACGACTCAT-AAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
* ** *
2403506 A-ACGACGCACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
* *
2403528 ATACGACACATAAAGTGTCTGAT
1 ATACGACACATAAAGTGCCTGAA
2403551 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
2403573 TCGGCAAAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 7 0.13
21 8 0.15
22 3 0.06
23 36 0.67
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:2403926 original size:26 final size:25
Alignment explanation
Indices: 2403895--2403944 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2403885 TAGTTCAATA
2403895 ATTCAATTCAA-ACCATTTCAATTTCT
1 ATTCAATT-AACA-CATTTCAATTTCT
*
2403921 ATTCAATTATCACATTTCAATTTC
1 ATTCAATTAACACATTTCAATTTC
2403945 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTCAATTAACACATTTCAATTTCT
Found at i:2404559 original size:3 final size:3
Alignment explanation
Indices: 2404545--2404576 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2404535 ATTAGTTAAC
*
2404545 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2404577 ATATCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2418005 original size:16 final size:17
Alignment explanation
Indices: 2417975--2418014 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2417965 ATAATTATCT
*
2417975 AAAAAACTTAACTCAGTA
1 AAAAAACTT-ACTCAATA
2417993 AAAAAACTT-CTCAATA
1 AAAAAACTTACTCAATA
2418009 AAAAAA
1 AAAAAA
2418015 TATGTGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
18 9 0.43
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAAAACTTACTCAATA
Found at i:2422645 original size:16 final size:16
Alignment explanation
Indices: 2422620--2422657 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2422610 TTGATTTGCT
*
2422620 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
2422636 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
2422652 AATACA
1 ATTACA
2422658 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:2422929 original size:56 final size:56
Alignment explanation
Indices: 2422814--2422942 Score: 145
Period size: 56 Copynumber: 2.3 Consensus size: 56
2422804 AATAAAATTA
* *
2422814 TTAATATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* * *
2422872 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
2422928 TTACTAAAATCATAA
1 TTAATAAAATAATAA
2422943 TATATAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.07
56 29 0.48
57 21 0.35
58 6 0.10
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:2433604 original size:6 final size:6
Alignment explanation
Indices: 2433578--2433634 Score: 89
Period size: 6 Copynumber: 9.5 Consensus size: 6
2433568 TATAGATATC
*
2433578 TTTTC- TTTTCT TTTCTTT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTT-TCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
2433626 TTTTCT TTT
1 TTTTCT TTT
2433635 GAACATGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
5 5 0.10
6 38 0.79
7 5 0.10
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:2434636 original size:18 final size:17
Alignment explanation
Indices: 2434605--2434665 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
2434595 AAATAATTCT
2434605 AAGAAAAT-AAAAATAA
1 AAGAAAATAAAAAATAA
2434621 ACAGAAAATAAAAAATAA
1 A-AGAAAATAAAAAATAA
*
2434639 AA-AATAATAAGAAAAGAA
1 AAGAA-AATAA-AAAATAA
2434657 AAGAAAATA
1 AAGAAAATA
2434666 GACTCAATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 3 0.08
17 13 0.33
18 21 0.54
19 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.11
Consensus pattern (17 bp):
AAGAAAATAAAAAATAA
Found at i:2434641 original size:25 final size:24
Alignment explanation
Indices: 2434608--2434658 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
2434598 TAATTCTAAG
*
2434608 AAAATAAAAATAA-ACAGAAAATAA
1 AAAATAAAAATAATA-AGAAAAGAA
2434632 AAAATAAAAAATAATAAGAAAAGAA
1 AAAAT-AAAAATAATAAGAAAAGAA
2434657 AA
1 AA
2434659 GAAAATAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 18 0.75
26 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAATAAAAATAATAAGAAAAGAA
Found at i:2441755 original size:25 final size:25
Alignment explanation
Indices: 2441714--2441802 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 25
2441704 AAGCTCATAC
*
2441714 GAGCCA-ATATTGAGAAGCTCCGGA
1 GAGCCATATATCGAGAAGCTCCGGA
* * *
2441738 GAGCCATATATCGGGAAGCTCATGAAA
1 GAGCCATATATCGAGAAGCTC-CG-GA
*
2441765 GAGCC-TTTAATCGAGAAGCTCCGGA
1 GAGCCATAT-ATCGAGAAGCTCCGGA
* *
2441790 AAGTCATATATCG
1 GAGCCATATATCG
2441803 GGACGCTCAT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
24 6 0.12
25 20 0.41
26 6 0.12
27 17 0.35
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
GAGCCATATATCGAGAAGCTCCGGA
Found at i:2441791 original size:27 final size:27
Alignment explanation
Indices: 2441714--2441792 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
2441704 AAGCTCATAC
*
2441714 GAGCCA-ATATTGAGAAGCTCCGG--A
1 GAGCCATATATCGAGAAGCTCCGGAAA
* **
2441738 GAGCCATATATCGGGAAGCTCATGAAA
1 GAGCCATATATCGAGAAGCTCCGGAAA
*
2441765 GAGCC-TTTAATCGAGAAGCTCCGGAAA
1 GAGCCATAT-ATCGAGAAGCTCCGGAAA
2441792 G
1 G
2441793 TCATATATCG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
24 6 0.14
25 13 0.30
26 2 0.05
27 22 0.51
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (27 bp):
GAGCCATATATCGAGAAGCTCCGGAAA
Found at i:2441971 original size:24 final size:24
Alignment explanation
Indices: 2441918--2441972 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2441908 GGTAGATCAA
* * *
2441918 GAGAGCAAATATCGGGATGCTCAT
1 GAGAGCTAATAACGGGACGCTCAT
*
2441942 GAGAGCTAATAACGGGACGCTCTT
1 GAGAGCTAATAACGGGACGCTCAT
*
2441966 GGGAGCT
1 GAGAGCT
2441973 GTGGTATGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.20
Consensus pattern (24 bp):
GAGAGCTAATAACGGGACGCTCAT
Found at i:2450004 original size:31 final size:31
Alignment explanation
Indices: 2449966--2450034 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2449956 CCTTAACCAT
*
2449966 ATTAAATTACCACAATAGTTAGTACATCCCA
1 ATTAAATTACCACAATAGTTAGTACATCACA
* * *
2449997 ATTAAATTACCATATTAGTTAGTATATCACA
1 ATTAAATTACCACAATAGTTAGTACATCACA
2450028 ATTAAAT
1 ATTAAAT
2450035 AAAAAATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (31 bp):
ATTAAATTACCACAATAGTTAGTACATCACA
Found at i:2450977 original size:26 final size:27
Alignment explanation
Indices: 2450928--2450987 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 27
2450918 AAAAATAACT
2450928 AAAATATTATAACTTTTTTTATTTACC
1 AAAATATTATAACTTTTTTTATTTACC
2450955 AAAATATTATAA-TTTTTTTATTTACC
1 AAAATATTATAACTTTTTTTATTTACC
2450981 AAAATAT
1 AAAATAT
2450988 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (27 bp):
AAAATATTATAACTTTTTTTATTTACC
Found at i:2451079 original size:27 final size:27
Alignment explanation
Indices: 2451049--2451133 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
2451039 CCCTGGTCAG
* * *
2451049 GCCAAGGTGATTGGCGGGACCAAAGGT
1 GCCAAGGAGATTGGCGGCACCAATGGT
* ** *
2451076 GCCAAAGCCATTGGCGGCACCATTGGT
1 GCCAAGGAGATTGGCGGCACCAATGGT
2451103 GCCAAGGAGATTGGCGGCACCAATGGT
1 GCCAAGGAGATTGGCGGCACCAATGGT
2451130 GCCA
1 GCCA
2451134 TACTGATTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (27 bp):
GCCAAGGAGATTGGCGGCACCAATGGT
Found at i:2451141 original size:27 final size:27
Alignment explanation
Indices: 2451049--2451149 Score: 98
Period size: 27 Copynumber: 3.7 Consensus size: 27
2451039 CCCTGGTCAG
* * *
2451049 GCCAAGGTGATTGGCGGGACCAAAGGT
1 GCCAAGCTGATTGGCGGCACCAATGGT
* *
2451076 GCCAAAGC-CATTGGCGGCACCATTGGT
1 GCC-AAGCTGATTGGCGGCACCAATGGT
**
2451103 GCCAAGGAGATTGGCGGCACCAATGGT
1 GCCAAGCTGATTGGCGGCACCAATGGT
*
2451130 GCCATA-CTGATTGACGGCAC
1 GCCA-AGCTGATTGGCGGCAC
2451150 TACTCGTGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
26 3 0.05
27 53 0.88
28 4 0.07
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.17
Consensus pattern (27 bp):
GCCAAGCTGATTGGCGGCACCAATGGT
Found at i:2451206 original size:3 final size:3
Alignment explanation
Indices: 2451198--2451223 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2451188 GAGAAAAATC
2451198 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
2451224 GAGAGGGAAA
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:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2451265 original size:18 final size:18
Alignment explanation
Indices: 2451242--2451296 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
2451232 AAGAAAGAAA
2451242 GAAAGAAAGGAAGGAGAG
1 GAAAGAAAGGAAGGAGAG
* *
2451260 GAAAGAAAGACAAAGA-AG
1 GAAAGAAAG-GAAGGAGAG
2451278 GAAAGAAAAGGAAAGGAGA
1 GAAAG-AAAGG-AAGGAGA
2451297 AGAGGGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 16 0.55
19 12 0.41
20 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGGAAGGAGAG
Found at i:2451287 original size:23 final size:22
Alignment explanation
Indices: 2451234--2451344 Score: 80
Period size: 24 Copynumber: 4.9 Consensus size: 22
2451224 GAGAGGGAAA
*
2451234 GAAAG-AAAGAAAGAAAGGAAG
1 GAAAGAAAAGAAAGAAAAGAAG
* *
2451255 GAGAGGAAAGAAAGACAAAGAAG
1 GAAAGAAAAGAAAGA-AAAGAAG
* *
2451278 GAAAGAAAAGGAAAGGAGAAGAGG
1 GAAAGAAAA-GAAA-GAAAAGAAG
* * *
2451302 GAAAAAAAAGAAGAGGGAAGGAAG
1 GAAAGAAAAGAA-A-GAAAAGAAG
* *
2451326 GAAAAAAAAGAAAAAAAAG
1 GAAAGAAAAGAAAGAAAAG
2451345 GTAATTTTTA
Statistics
Matches: 71, Mismatches: 14, Indels: 9
0.76 0.15 0.10
Matches are distributed among these distances:
21 4 0.06
22 12 0.17
23 17 0.24
24 36 0.51
25 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (22 bp):
GAAAGAAAAGAAAGAAAAGAAG
Found at i:2451334 original size:24 final size:23
Alignment explanation
Indices: 2451272--2451338 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 23
2451262 AAGAAAGACA
*
2451272 AAGAAGGAAAGAAAAGGAAAGGAG
1 AAGAAGGAAA-AAAAAGAAAGGAG
*
2451296 AAGAGGGAAAAAAAAGAAGAGG-G
1 AAGAAGGAAAAAAAAGAA-AGGAG
2451319 AAGGAAGGAAAAAAAAGAAA
1 AA-GAAGGAAAAAAAAGAAA
2451339 AAAAAGGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (23 bp):
AAGAAGGAAAAAAAAGAAAGGAG
Found at i:2451600 original size:28 final size:27
Alignment explanation
Indices: 2451561--2451627 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
2451551 TGTTTTAGGA
2451561 AAATA-GTATTAAAAGTAAAATGATAAAG
1 AAATATGT-TTAAAA-TAAAATGATAAAG
* *
2451589 AAATATGTTTAAGATAAATTGATAAAG
1 AAATATGTTTAAAATAAAATGATAAAG
2451616 AAATATGTTTAA
1 AAATATGTTTAA
2451628 GAAAGCATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 24 0.67
28 10 0.28
29 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.31
Consensus pattern (27 bp):
AAATATGTTTAAAATAAAATGATAAAG
Found at i:2451612 original size:27 final size:27
Alignment explanation
Indices: 2451576--2451629 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2451566 GTATTAAAAG
2451576 TAAAATGATAAAGAAATATGTTTAAGA
1 TAAAATGATAAAGAAATATGTTTAAGA
*
2451603 TAAATTGATAAAGAAATATGTTTAAGA
1 TAAAATGATAAAGAAATATGTTTAAGA
2451630 AAGCATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (27 bp):
TAAAATGATAAAGAAATATGTTTAAGA
Found at i:2452062 original size:162 final size:160
Alignment explanation
Indices: 2451720--2452294 Score: 394
Period size: 161 Copynumber: 3.6 Consensus size: 160
2451710 AATAAATTTC
* * * * * *
2451720 AAACATAATGCATTGAAATAATGTAAAATTATAAAAT--TAAA-AATTACGATATTT-TTTAAAA
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAATACTAAATAA-TA-TATTTTTATTTAAAA
* * * * ****
2451781 TAAT-AAAATACGGATAAAAAAATATGAA-CAAATGGCGGAAGTAAGAGTGTATTACTAACTTTT
64 TAATAAAAAT-C-GAGAAAATAATA-CAAGCAAATGGCGGAAGTAAGAGTGTATTATTAACACCA
** * ** *
2451844 TTTAAAATTC-AGAACTAA-TTGATACAAAATATTTC
126 AATAAAATTCAAAAAC-AACTAAATACAAAATA-TTG
* *
2451879 AAAGAAAATGTACTGAAATAATATAAAATAATAAAATACTAGAATAATATATTTTTATTTAAAAT
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAATACTA-AATAATATATTTTTATTTAAAAT
* * * *
2451944 AATAAAAATCGAGAAAATAATACAAGCAAATGGCAGG-GGTAAGGGT-TATTTTTTTACACCAAA
65 AATAAAAATCGAGAAAATAATACAAGCAAATGGC-GGAAGTAAGAGTGTA-TTATTAACACCAAA
* *
2452007 T-TAATTTAAATAACACACTAAATTA-ATAAAT-TTG
128 TAAAATTCAAA-AACA-ACTAAA-TACA-AAATATTG
** * * * * * *
2452041 AAACATTATGCACTGAAATAATGTAAAATTATAAAAGACTAAGT-TTATGATATTT-TTTAAAAT
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAATACTAAATAATAT-ATTTTTATTTAAAAT
* *****
2452104 AAT-AAAATGCGGAGAAAAAAATACGAA-CAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTT
65 AATAAAAAT-C-GAGAAAATAATAC-AAGCAAATGGCGGAAGTAAGAGTGTATTATTAACACCAA
* * *
2452167 ATAAAATTCAAAAATAATTAAATACAAATTATTG
127 ATAAAATTCAAAAACAACTAAATACAAAATATTG
* * * *
2452201 AAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGT
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAATAC-TAAATAATATATTTTTATTTAAAAT
* *
2452266 AATAAAAATCG-GGAAATAATACGAGCAAA
65 AATAAAAATCGAGAAAATAATACAAGCAAA
2452295 GGGTAAGGAA
Statistics
Matches: 319, Mismatches: 68, Indels: 57
0.72 0.15 0.13
Matches are distributed among these distances:
159 42 0.13
160 80 0.25
161 94 0.29
162 82 0.26
163 15 0.05
164 6 0.02
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.30
Consensus pattern (160 bp):
AAACAAAATGCACTGAAATAATATAAAATAATAAAATACTAAATAATATATTTTTATTTAAAATA
ATAAAAATCGAGAAAATAATACAAGCAAATGGCGGAAGTAAGAGTGTATTATTAACACCAAATAA
AATTCAAAAACAACTAAATACAAAATATTG
Found at i:2452204 original size:160 final size:158
Alignment explanation
Indices: 2451720--2452236 Score: 451
Period size: 161 Copynumber: 3.2 Consensus size: 158
2451710 AATAAATTTC
* * * * * * *
2451720 AAACATAATGCATTGAAATAATGTAAAATTAT-AAAATTAAAAATTACGATATTTTTTAAAATAA
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAAACT-AAATTTATGATATTTTTTAAAATAA
* * * *
2451784 TAAAATACGGATAAAAAAATATGAACAAATGGCGGAAGTAAGAGTGTATTACTAACTTTTTTTAA
65 TAAAAT-CGGAGAAAAAAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAA
* * * *
2451849 AATTCAGAACTAATT-GATACAAAATATTTC
129 AATTCAAAAATAATTAAATACAAAATA-TTG
* * * *
2451879 AAAGAAAATGTACTGAAATAATATAAAATAATAAAATACTAGAATAATAT-ATTTTTATTTAAAA
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAA-ACTA-AAT-TTATGATATTT-TTTAAAA
* * * * * ***
2451943 TAATAAAAATC-GAGAAAATAATAC-AAGCAAATGGCAGG-GGTAAGGGT-TATTTTTTTACACC
62 TAAT-AAAATCGGAGAAAAAAATACGAA-CAAATGGC-GGAAGTAAGAGTGTA-TTATTAACTTT
** * * * *
2452004 AAAT-TAATTTAAATAACACACTAAATTA-ATAAAT-TTG
123 TTATAAAATTCAAA-AATA-ATTAAA-TACA-AAATATTG
** * * *
2452041 AAACATTATGCACTGAAATAATGTAAAATTATAAAAGACTAAGTTTATGATATTTTTTAAAATAA
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAA-ACTAAATTTATGATATTTTTTAAAATAA
2452106 TAAAATGCGGAGAAAAAAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAA
65 TAAAAT-CGGAGAAAAAAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAA
*
2452171 AATTCAAAAATAATTAAATACAAATTATTG
129 AATTCAAAAATAATTAAATACAAAATATTG
*
2452201 AAACAAAATGTACTGAAATAATATAAAATAATAAAA
1 AAACAAAATGCACTGAAATAATATAAAATAATAAAA
2452237 TACGAAAATA
Statistics
Matches: 272, Mismatches: 63, Indels: 45
0.72 0.17 0.12
Matches are distributed among these distances:
159 36 0.13
160 71 0.26
161 87 0.32
162 65 0.24
163 7 0.03
164 6 0.02
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (158 bp):
AAACAAAATGCACTGAAATAATATAAAATAATAAAAACTAAATTTATGATATTTTTTAAAATAAT
AAAATCGGAGAAAAAAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAAAA
TTCAAAAATAATTAAATACAAAATATTG
Found at i:2452289 original size:160 final size:159
Alignment explanation
Indices: 2451733--2452294 Score: 452
Period size: 160 Copynumber: 3.5 Consensus size: 159
2451723 CATAATGCAT
* * * *
2451733 TGAAATAATGTAAAATTATAAAAT--TAAAA-ATTACGATATTTT-TTAAAATAAT-AAAATACG
1 TGAAATAATATAAAATAATAAAATACTAAAATAATA-TAT-TTTTATTAAAATAATAAAAAT-CG
* * * * * *
2451793 GATAAAAAAATATGAACAAATGGCGGAAGTAAGAGTGTATTACTAACTTTTTTTAAAATTCAGAA
63 G--GAAATAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAAAATTCAAAA
* * * *
2451858 CTAATT-GATACAAAATATTTCAAAGAAAATGTAC
126 ATAATTAAATACAAAATA-TTGAAACAAAATGTAC
*
2451892 TGAAATAATATAAAATAATAAAATACTAGAATAATATATTTTTATTTAAAATAATAAAAATCGAG
1 TGAAATAATATAAAATAATAAAATACTAAAATAATATATTTTTA-TTAAAATAATAAAAATCG-G
* * * * * ***** * *
2451957 AAAATAATAC-AAGCAAATGGCAGG-GGTAAGGGT-TATTTTTTTACACCAAAT-TAATTTAAAT
64 GAAATAATACGAA-CAAATGGC-GGAAGTAAGAGTGTA-TTATTAACTTTTTATAAAATTCAAA-
* * ** *
2452018 AACACACTAAATTA-ATAAAT-TTGAAACATTATGCAC
125 AATA-ATTAAA-TACA-AAATATTGAAACAAAATGTAC
* * * ** *
2452054 TGAAATAATGTAAAATTATAAAAGACTAAGTTTATGATA-TTTT-TTAAAATAAT-AAAATGCGG
1 TGAAATAATATAAAATAATAAAATACTAAAATAAT-ATATTTTTATTAAAATAATAAAAAT-CGG
*
2452116 AGAAAAAAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAAAATTCAAAAA
64 -G-AAATAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAAAATTCAAAAA
*
2452181 TAATTAAATACAAATTATTGAAACAAAATGTAC
127 TAATTAAATACAAAATATTGAAACAAAATGTAC
* *
2452214 TGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATCGGG
1 TGAAATAATATAAAATAATAAAATACTAAAATAATATATTTTTATT-AAAATAATAAAAATCGGG
*
2452279 AAATAATACGAGCAAA
65 AAATAATACGAACAAA
2452295 GGGTAAGGAA
Statistics
Matches: 308, Mismatches: 66, Indels: 57
0.71 0.15 0.13
Matches are distributed among these distances:
159 36 0.12
160 93 0.30
161 74 0.24
162 83 0.27
163 16 0.05
164 6 0.02
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (159 bp):
TGAAATAATATAAAATAATAAAATACTAAAATAATATATTTTTATTAAAATAATAAAAATCGGGA
AATAATACGAACAAATGGCGGAAGTAAGAGTGTATTATTAACTTTTTATAAAATTCAAAAATAAT
TAAATACAAAATATTGAAACAAAATGTAC
Found at i:2452446 original size:27 final size:27
Alignment explanation
Indices: 2452416--2452471 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
2452406 AAAGAGGGTG
*
2452416 ATGGAGGGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
2452443 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
2452470 AT
1 AT
2452472 ATGTGGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.34, T:0.09
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAGGCGGCACCA
Found at i:2452757 original size:16 final size:15
Alignment explanation
Indices: 2452731--2452760 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2452721 GTACTGAAAT
2452731 AATATAAAATAATAA
1 AATATAAAATAATAA
2452746 AATATGAAAATAATA
1 AATAT-AAAATAATA
2452761 TATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:2455225 original size:11 final size:11
Alignment explanation
Indices: 2455209--2455235 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2455199 TTTATAACTT
2455209 AATTTGGATAC
1 AATTTGGATAC
2455220 AATTTGGATAC
1 AATTTGGATAC
2455231 AATTT
1 AATTT
2455236 AAGCATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:2457504 original size:18 final size:18
Alignment explanation
Indices: 2457481--2457525 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2457471 ATCCCAATGA
* *
2457481 TCGCCACCTCTTTCTTCT
1 TCGCCACCACATTCTTCT
2457499 TCGCCACCACATTCTTCT
1 TCGCCACCACATTCTTCT
*
2457517 TCACCACCA
1 TCGCCACCA
2457526 ACCATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.47, G:0.04, T:0.33
Consensus pattern (18 bp):
TCGCCACCACATTCTTCT
Found at i:2458325 original size:3 final size:3
Alignment explanation
Indices: 2458317--2458375 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
2458307 GCTTAATACT
2458317 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
2458365 AAC AAC AAC AA
1 AAC AAC AAC AA
2458376 TAATAATAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2458393 original size:15 final size:16
Alignment explanation
Indices: 2458375--2458404 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2458365 AACAACAACA
2458375 ATAATAATAA-TAAAC
1 ATAATAATAACTAAAC
2458390 ATAATAATAACTAAA
1 ATAATAATAACTAAA
2458405 ACTATCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAATAATAACTAAAC
Found at i:2458564 original size:3 final size:3
Alignment explanation
Indices: 2458556--2458581 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2458546 AGCACCTCTA
2458556 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
2458582 GATTTTTCTC
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2458668 original size:27 final size:26
Alignment explanation
Indices: 2458630--2458723 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 26
2458620 AACACGAGTA
*
2458630 GTGCCGTCAATCAGTATGGCACCATTG
1 GTGCCGCCAATCAGT-TGGCACCATTG
**
2458657 GTGCCGCCAATCTCCTTGGCACCATTG
1 GTGCCGCCAATC-AGTTGGCACCATTG
* *
2458684 GTGCCGCCAATGGC-TTTGGCACCTTTG
1 GTGCCGCCAAT--CAGTTGGCACCATTG
2458711 GTGCCGCCAATCA
1 GTGCCGCCAATCA
2458724 CCTTGGCCTG
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
25 1 0.02
27 55 0.95
28 1 0.02
29 1 0.02
ACGTcount: A:0.17, C:0.32, G:0.26, T:0.26
Consensus pattern (26 bp):
GTGCCGCCAATCAGTTGGCACCATTG
Found at i:2458729 original size:27 final size:27
Alignment explanation
Indices: 2458646--2458730 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
2458636 TCAATCAGTA
*
2458646 TGGCACCATTGGTGCCGCCAATCTCCT
1 TGGCACCATTGGTGCCGCCAATCACCT
** *
2458673 TGGCACCATTGGTGCCGCCAATGGCTT
1 TGGCACCATTGGTGCCGCCAATCACCT
*
2458700 TGGCACCTTTGGTGCCGCCAATCACCT
1 TGGCACCATTGGTGCCGCCAATCACCT
2458727 TGGC
1 TGGC
2458731 CTGACCAGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATCACCT
Found at i:2475916 original size:20 final size:20
Alignment explanation
Indices: 2475891--2475935 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2475881 TCCTATATTG
*
2475891 ATACAAGTTCACTTT-TATCC
1 ATACAAGTCCA-TTTCTATCC
2475911 ATACAAGTCCATTTCTATCC
1 ATACAAGTCCATTTCTATCC
2475931 ATACA
1 ATACA
2475936 TCTTGTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (20 bp):
ATACAAGTCCATTTCTATCC
Found at i:2479926 original size:20 final size:20
Alignment explanation
Indices: 2479901--2479945 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2479891 TCCTATATTG
* *
2479901 ATACAAGTTCACTTTTATCC
1 ATACAAGTTCACTTCTACCC
2479921 ATACAAGTTCACTTCTACCC
1 ATACAAGTTCACTTCTACCC
2479941 ATACA
1 ATACA
2479946 TCTTGTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (20 bp):
ATACAAGTTCACTTCTACCC
Found at i:2486374 original size:16 final size:17
Alignment explanation
Indices: 2486355--2486392 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2486345 AAAAACTTTT
* *
2486355 GAAATCAAAATTAAAC-
1 GAAAACAAAACTAAACA
2486371 GAAAACAAAACTAAACA
1 GAAAACAAAACTAAACA
2486388 GAAAA
1 GAAAA
2486393 GGCATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.68, C:0.13, G:0.08, T:0.11
Consensus pattern (17 bp):
GAAAACAAAACTAAACA
Found at i:2487851 original size:18 final size:19
Alignment explanation
Indices: 2487828--2487876 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2487818 TCACATGCGC
2487828 ATTTTTTTATAATTTTC-T
1 ATTTTTTTATAATTTTCAT
**
2487846 ATTTTTTT-TCCTTTTCAT
1 ATTTTTTTATAATTTTCAT
2487864 ATTTTTTTTATAA
1 A-TTTTTTTATAA
2487877 AACATATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 7 0.29
20 1 0.04
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTTTATAATTTTCAT
Found at i:2488063 original size:8 final size:8
Alignment explanation
Indices: 2488052--2488077 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2488042 ATACATATGC
2488052 ATACTTTT
1 ATACTTTT
2488060 ATACTTTT
1 ATACTTTT
2488068 ATACTTTT
1 ATACTTTT
2488076 AT
1 AT
2488078 TTTTAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (8 bp):
ATACTTTT
Found at i:2489036 original size:25 final size:25
Alignment explanation
Indices: 2488993--2489060 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 25
2488983 AAAATTAAGA
*
2488993 TTAGAACTTAGAACTTAAGTTTAGAAC
1 TTAGAA-TTAG-ATTTAAGTTTAGAAC
*
2489020 TTCGAATTAGATTTAAGTTTAGAAC
1 TTAGAATTAGATTTAAGTTTAGAAC
*
2489045 TTAGGATTAGATTTAA
1 TTAGAATTAGATTTAA
2489061 TAAGGATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 28 0.76
26 4 0.11
27 5 0.14
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (25 bp):
TTAGAATTAGATTTAAGTTTAGAAC
Found at i:2494081 original size:28 final size:29
Alignment explanation
Indices: 2494027--2494081 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
2494017 AATTGTAAAT
* *
2494027 GGTTTCTAGTTAAGCCATTAAAGCTAGAG
1 GGTTTCTAGTTAAGCCATAAAAACTAGAG
* *
2494056 GGTTT-TAGTTTAGGCATAAAAACTAG
1 GGTTTCTAGTTAAGCCATAAAAACTAG
2494082 GGGGAAGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 17 0.77
29 5 0.23
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (29 bp):
GGTTTCTAGTTAAGCCATAAAAACTAGAG
Found at i:2494510 original size:29 final size:29
Alignment explanation
Indices: 2494468--2494540 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
2494458 ATTTCTTTTT
2494468 TGGTCACCCAACTATGAAAAGTTAAAAAA
1 TGGTCACCCAACTATGAAAAGTTAAAAAA
* * *
2494497 TGGTCACCTAACTATGAGAAGTTACAAAA
1 TGGTCACCCAACTATGAAAAGTTAAAAAA
**
2494526 TAATCACCCAACTAT
1 TGGTCACCCAACTAT
2494541 TCAATATTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (29 bp):
TGGTCACCCAACTATGAAAAGTTAAAAAA
Found at i:2495456 original size:48 final size:48
Alignment explanation
Indices: 2495401--2495497 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
2495391 CTCTTTTAAC
* *
2495401 CATGCCATATCAAAACATACTTAATTTATAATAGATTAAACATTACTA
1 CATGCCATATCAAAACATACTCAATTTATAATAGATTAAACATAACTA
*
2495449 CATGCCATATCAAAACATACTCAATTTATGATAGATTAAACATAACTA
1 CATGCCATATCAAAACATACTCAATTTATAATAGATTAAACATAACTA
2495497 C
1 C
2495498 GTGATACCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (48 bp):
CATGCCATATCAAAACATACTCAATTTATAATAGATTAAACATAACTA
Found at i:2500752 original size:9 final size:9
Alignment explanation
Indices: 2500738--2500765 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2500728 TCTTGAATTC
2500738 TTGATAAGA
1 TTGATAAGA
2500747 TTGATAAGA
1 TTGATAAGA
2500756 TTGATAAGA
1 TTGATAAGA
2500765 T
1 T
2500766 AGGAGGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (9 bp):
TTGATAAGA
Found at i:2502582 original size:111 final size:111
Alignment explanation
Indices: 2502360--2502573 Score: 428
Period size: 111 Copynumber: 1.9 Consensus size: 111
2502350 AAAACTGTAA
2502360 AAAACATTATACTTGAGCTAACAAAGACAACCTTTTCCTAGAATACCTGTCCACTTATCACCATC
1 AAAACATTATACTTGAGCTAACAAAGACAACCTTTTCCTAGAATACCTGTCCACTTATCACCATC
2502425 TTCTATGAAAGCATGCAATGCATTGACACCATTTTCAAATAACTGC
66 TTCTATGAAAGCATGCAATGCATTGACACCATTTTCAAATAACTGC
2502471 AAAACATTATACTTGAGCTAACAAAGACAACCTTTTCCTAGAATACCTGTCCACTTATCACCATC
1 AAAACATTATACTTGAGCTAACAAAGACAACCTTTTCCTAGAATACCTGTCCACTTATCACCATC
2502536 TTCTATGAAAGCATGCAATGCATTGACACCATTTTCAA
66 TTCTATGAAAGCATGCAATGCATTGACACCATTTTCAA
2502574 GACACTGCAT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (111 bp):
AAAACATTATACTTGAGCTAACAAAGACAACCTTTTCCTAGAATACCTGTCCACTTATCACCATC
TTCTATGAAAGCATGCAATGCATTGACACCATTTTCAAATAACTGC
Found at i:2520203 original size:22 final size:24
Alignment explanation
Indices: 2520177--2520220 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2520167 GAAAAATATT
2520177 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
2520199 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
2520221 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:2520429 original size:16 final size:16
Alignment explanation
Indices: 2520408--2520449 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2520398 AATAATTTGA
*
2520408 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
2520424 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2520440 TAGTTTTAAT
1 TAATTTTAAT
2520450 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2524720 original size:19 final size:19
Alignment explanation
Indices: 2524670--2524707 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2524660 TAAAATAGTA
2524670 AAAAATA-TAAAATTTTAT
1 AAAAATATTAAAATTTTAT
2524688 AAAAATATTAAAATTTTAT
1 AAAAATATTAAAATTTTAT
2524707 A
1 A
2524708 TAAACTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATATTAAAATTTTAT
Found at i:2526225 original size:31 final size:31
Alignment explanation
Indices: 2526181--2526239 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2526171 TAAAATGATT
* *
2526181 ATTGAATTGTTTGAAAG-TTTTCATTTAAATC
1 ATTGAACTATTTGAAAGCTTTT-ATTTAAATC
2526212 ATTGAACTATTTGAAAGCTTTTATTTAA
1 ATTGAACTATTTGAAAGCTTTTATTTAA
2526240 GTTACTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (31 bp):
ATTGAACTATTTGAAAGCTTTTATTTAAATC
Found at i:2540807 original size:18 final size:17
Alignment explanation
Indices: 2540774--2540812 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2540764 TTTTATAAAT
2540774 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2540792 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2540809 TGTG
1 TGTG
2540813 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2541067 original size:23 final size:23
Alignment explanation
Indices: 2541041--2541090 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2541031 GTTATTGATT
*
2541041 AGTGGTAGATTCGGCTACATTTC
1 AGTGGTAGATTCGGCTACATATC
*
2541064 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGATTCGGCTACATATC
2541087 AGTG
1 AGTG
2541091 TGGCACTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (23 bp):
AGTGGTAGATTCGGCTACATATC
Found at i:2543606 original size:88 final size:88
Alignment explanation
Indices: 2543457--2543898 Score: 884
Period size: 88 Copynumber: 5.0 Consensus size: 88
2543447 GGAAAAGCAA
2543457 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
1 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
2543522 TCCAATGGAACACAAACAAAGTG
66 TCCAATGGAACACAAACAAAGTG
2543545 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
1 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
2543610 TCCAATGGAACACAAACAAAGTG
66 TCCAATGGAACACAAACAAAGTG
2543633 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
1 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
2543698 TCCAATGGAACACAAACAAAGTG
66 TCCAATGGAACACAAACAAAGTG
2543721 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
1 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
2543786 TCCAATGGAACACAAACAAAGTG
66 TCCAATGGAACACAAACAAAGTG
2543809 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
1 CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
2543874 TCCAATGGAACACAAACAAAGTG
66 TCCAATGGAACACAAACAAAGTG
2543897 CT
1 CT
2543899 GGGAATTTGA
Statistics
Matches: 354, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 354 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (88 bp):
CTAGAAATGTTGACCTAGTGGTGGGGTAAGTTTTTTATTATATAAACAAATTAACCAATCGGTGT
TCCAATGGAACACAAACAAAGTG
Found at i:2547632 original size:16 final size:16
Alignment explanation
Indices: 2547599--2547632 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2547589 TAGAGCTGTT
* *
2547599 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2547615 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2547631 AA
1 AA
2547633 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2552411 original size:16 final size:16
Alignment explanation
Indices: 2552378--2552411 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2552368 GGAGATTGTT
* *
2552378 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2552394 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2552410 AA
1 AA
2552412 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2554323 original size:16 final size:16
Alignment explanation
Indices: 2554290--2554326 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2554280 ATGATTTTAT
*
2554290 TCACCAATTGTTTAGA
1 TCACCAATTGTTCAGA
*
2554306 TCACCAATTGTTCGGA
1 TCACCAATTGTTCAGA
2554322 TCACC
1 TCACC
2554327 TATTAGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (16 bp):
TCACCAATTGTTCAGA
Found at i:2557937 original size:15 final size:14
Alignment explanation
Indices: 2557918--2557957 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
2557908 TTAACCTTTA
*
2557918 ATTAATTATAATTT
1 ATTAATTAAAATTT
2557932 ACTTAATTAAAATTT
1 A-TTAATTAAAATTT
2557947 GATTAATTAAA
1 -ATTAATTAAA
2557958 CATGAATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 21 0.91
16 1 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (14 bp):
ATTAATTAAAATTT
Found at i:2559721 original size:68 final size:68
Alignment explanation
Indices: 2559646--2559775 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
2559636 TACCAATCCT
*
2559646 AATTGTACAAATCACTCTCCCCCAAATACCTCACTTTACATAATTTTCCTCCATAACAAATCCCT
1 AATTGTACAAATCACTATCCCCCAAATACCTCACTTTACATAATTTTCCTCCATAACAAATCCCT
2559711 CCC
66 CCC
* * * *
2559714 AATTGTACAAATCATTATCCCCTAAATACCTCACTTTACATCATTTTCCTCCATAATAAATC
1 AATTGTACAAATCACTATCCCCCAAATACCTCACTTTACATAATTTTCCTCCATAACAAATC
2559776 TCTATACGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (68 bp):
AATTGTACAAATCACTATCCCCCAAATACCTCACTTTACATAATTTTCCTCCATAACAAATCCCT
CCC
Found at i:2560417 original size:53 final size:53
Alignment explanation
Indices: 2560337--2560455 Score: 213
Period size: 53 Copynumber: 2.3 Consensus size: 53
2560327 AGGGAGGTAT
*
2560337 TCATCAGCCCAAACAAACATCCAAGCCATCGATAACAACACTACCAAAGTTGC
1 TCATCAGCCCAAACAAACATCCAAGCCATAGATAACAACACTACCAAAGTTGC
*
2560390 TCATCAGCCCAAACAAACATCCAAGCCATAGGTAACAACACTACCAAAGTTGC
1 TCATCAGCCCAAACAAACATCCAAGCCATAGATAACAACACTACCAAAGTTGC
2560443 TCATCAG-CCAAAC
1 TCATCAGCCCAAAC
2560456 CATTCGTTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 6 0.09
53 58 0.91
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (53 bp):
TCATCAGCCCAAACAAACATCCAAGCCATAGATAACAACACTACCAAAGTTGC
Found at i:2566384 original size:14 final size:14
Alignment explanation
Indices: 2566365--2566393 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2566355 CAATAACAAC
2566365 AAAAAAATTT-ATT
1 AAAAAAATTTCATT
2566378 AAAAAAATTTCATT
1 AAAAAAATTTCATT
2566392 AA
1 AA
2566394 TTGGAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAAAAATTTCATT
Found at i:2569521 original size:25 final size:25
Alignment explanation
Indices: 2569487--2569537 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2569477 GGATACCCAA
2569487 CTTAGTTTTCTAAGTTCAATGTGGT
1 CTTAGTTTTCTAAGTTCAATGTGGT
2569512 CTTAGTTTTCTAAGTTCAATGTGGT
1 CTTAGTTTTCTAAGTTCAATGTGGT
2569537 C
1 C
2569538 AAACAAAACC
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:0.20, C:0.14, G:0.20, T:0.47
Consensus pattern (25 bp):
CTTAGTTTTCTAAGTTCAATGTGGT
Found at i:2572751 original size:21 final size:21
Alignment explanation
Indices: 2572721--2572822 Score: 60
Period size: 21 Copynumber: 4.9 Consensus size: 21
2572711 GCTAAATGAG
*
2572721 AACCCGTAAGGGTTAAACGGA
1 AACCCATAAGGGTTAAACGGA
* ** * * *
2572742 AGCTTATAAGAGCTGAACGGA
1 AACCCATAAGGGTTAAACGGA
**
2572763 AACCCATAAGGGTTAAACTTA
1 AACCCATAAGGGTTAAACGGA
* * * * * *
2572784 AGCTCAAAAGAGCTAAACTGA
1 AACCCATAAGGGTTAAACGGA
*
2572805 AACCCAGAAGGGTTAAAC
1 AACCCATAAGGGTTAAAC
2572823 TAAAACTCAT
Statistics
Matches: 55, Mismatches: 26, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
AACCCATAAGGGTTAAACGGA
Found at i:2572773 original size:42 final size:42
Alignment explanation
Indices: 2572721--2572822 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
2572711 GCTAAATGAG
* * * *
2572721 AACCCGTAAGGGTTAAACGGAAGCTTATAAGAGCTGAACGGA
1 AACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTAAACGGA
** *
2572763 AACCCATAAGGGTTAAACTTAAGCTCAAAAGAGCTAAACTGA
1 AACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTAAACGGA
*
2572805 AACCCAGAAGGGTTAAAC
1 AACCCATAAGGGTTAAAC
2572823 TAAAACTCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (42 bp):
AACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTAAACGGA
Found at i:2572866 original size:21 final size:21
Alignment explanation
Indices: 2572747--2572867 Score: 91
Period size: 21 Copynumber: 5.8 Consensus size: 21
2572737 ACGGAAGCTT
* * *
2572747 ATAAGAGCTGAACGGAAACCC
1 ATAAGAGCTAAACTGAAACTC
* * * *
2572768 ATAAGGGTTAAACTTAAGCTC
1 ATAAGAGCTAAACTGAAACTC
* *
2572789 AAAAGAGCTAAACTGAAACCC
1 ATAAGAGCTAAACTGAAACTC
* * * *
2572810 AGAAGGGTTAAACTAAAACTC
1 ATAAGAGCTAAACTGAAACTC
* * *
2572831 ATATGAG-TTAACTGAAGCTC
1 ATAAGAGCTAAACTGAAACTC
2572851 ATAAGAGCTAAACTGAA
1 ATAAGAGCTAAACTGAA
2572868 TGCAAACACG
Statistics
Matches: 73, Mismatches: 26, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
20 16 0.22
21 57 0.78
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (21 bp):
ATAAGAGCTAAACTGAAACTC
Found at i:2581220 original size:22 final size:23
Alignment explanation
Indices: 2581195--2581242 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
2581185 ACCAATTTGT
2581195 TTGA-AAAAATTACAAGTGTACA
1 TTGACAAAAATTACAAGTGTACA
2581217 TTGACGAAAAATTACAAGTGTACA
1 TTGAC-AAAAATTACAAGTGTACA
2581241 TT
1 TT
2581243 ACCCTCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
24 20 0.83
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (23 bp):
TTGACAAAAATTACAAGTGTACA
Found at i:2584636 original size:14 final size:14
Alignment explanation
Indices: 2584614--2584643 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2584604 TATTGTTTAA
*
2584614 GACTTCTTAAGAGG
1 GACTGCTTAAGAGG
2584628 GACTGCTTAAGAGG
1 GACTGCTTAAGAGG
2584642 GA
1 GA
2584644 GCTAATCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.23
Consensus pattern (14 bp):
GACTGCTTAAGAGG
Found at i:2598700 original size:13 final size:13
Alignment explanation
Indices: 2598667--2598709 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2598657 AAATATCTAT
**
2598667 TTTTTATTATTTA
1 TTTTTATTATAAA
*
2598680 TCTTTTATTTTAAA
1 T-TTTTATTATAAA
2598694 TTTTTATTATAAA
1 TTTTTATTATAAA
2598707 TTT
1 TTT
2598710 AAATTAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATTATAAA
Found at i:2608511 original size:75 final size:75
Alignment explanation
Indices: 2608388--2608652 Score: 521
Period size: 75 Copynumber: 3.5 Consensus size: 75
2608378 AATAAATTAT
2608388 TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTTAAATTATTGAGCATTTGTCCTGGAA
1 TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTTAAATTATTGAGCATTTGTCCTGGAA
2608453 ATGGAATAAA
66 ATGGAATAAA
2608463 TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTTAAATTATTGAGCATTTGTCCTGGAA
1 TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTTAAATTATTGAGCATTTGTCCTGGAA
2608528 ATGGAATAAA
66 ATGGAATAAA
2608538 TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTTAAATTATTGAGCATTTGTCCTGGAA
1 TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTTAAATTATTGAGCATTTGTCCTGGAA
2608603 ATGGAATAAA
66 ATGGAATAAA
*
2608613 TATTGAATTTAAATATTAGTTGACTCATTTTTTGGTCTTT
1 TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTT
2608653 GAAAGTTAAG
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 189 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (75 bp):
TATTGAATTTAAATATTAGTTGACTCATATTTTGGTCTTTAAATTATTGAGCATTTGTCCTGGAA
ATGGAATAAA
Found at i:2611057 original size:19 final size:20
Alignment explanation
Indices: 2611015--2611057 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2611005 TCATGCTTTC
*
2611015 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
*
2611035 -ATTCATATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
2611053 TATTC
1 TATTC
2611058 TACAATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:2611303 original size:45 final size:46
Alignment explanation
Indices: 2611234--2611425 Score: 248
Period size: 45 Copynumber: 4.3 Consensus size: 46
2611224 AATCAGTAAT
* ** * *
2611234 GGTAGCAGTAACAATAACAATATTCAACACACAAAGTGCT-GAATC
1 GGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTCGAATC
* * *
2611279 TGTAACAGTAACGGTAATAGTATTCGACACACAAAGT-ATCGAATC
1 GGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTCGAATC
* * *
2611324 GGTAACAATAACAGTAACATTATTCGACACACAAAGTG-TCGAATC
1 GGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTCGAATC
2611369 GGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGC-CGAATC
1 GGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTCGAATC
*
2611414 GGTAATAGTAAC
1 GGTAACAGTAAC
2611426 AGTAGTAGGC
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
44 1 0.01
45 126 0.99
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (46 bp):
GGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTCGAATC
Found at i:2611348 original size:90 final size:90
Alignment explanation
Indices: 2611242--2611429 Score: 279
Period size: 90 Copynumber: 2.1 Consensus size: 90
2611232 ATGGTAGCAG
* * *
2611242 TAACAATAACAATATTCAACACACAAAGTG-CTGAATCTGTAACAGTAACGGTAATAGTATTCGA
1 TAACAGTAACAATATTCAACACACAAAGTGTC-GAATCGGTAACAGTAACGGTAACAGTATTCGA
*
2611306 CACACAAAGTATCGAATCGGTAACAA
65 CACACAAAGTACCGAATCGGTAACAA
* *
2611332 TAACAGTAACATTATTCGACACACAAAGTGTCGAATCGGTAACAGTAACGGTAACAGTATTCGAC
1 TAACAGTAACAATATTCAACACACAAAGTGTCGAATCGGTAACAGTAACGGTAACAGTATTCGAC
* * *
2611397 ACACAAAGTGCCGAATCGGTAATAG
66 ACACAAAGTACCGAATCGGTAACAA
2611422 TAACAGTA
1 TAACAGTA
2611430 GTAGGCACAT
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 87 0.99
91 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (90 bp):
TAACAGTAACAATATTCAACACACAAAGTGTCGAATCGGTAACAGTAACGGTAACAGTATTCGAC
ACACAAAGTACCGAATCGGTAACAA
Found at i:2611694 original size:21 final size:21
Alignment explanation
Indices: 2611629--2611695 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
2611619 AATTTATTAT
*
2611629 TTCAGTAATTTCACAGTTCAA
1 TTCAGTAATTTCACAATTCAA
* ** *
2611650 TGCAGTACACATAACAA-T--A
1 TTCAGTA-ATTTCACAATTCAA
2611669 TTCAGTAATTTCACAATTCAA
1 TTCAGTAATTTCACAATTCAA
2611690 TTCAGT
1 TTCAGT
2611696 GCTAACACAT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
21 14 0.42
22 5 0.15
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (21 bp):
TTCAGTAATTTCACAATTCAA
Found at i:2613236 original size:8 final size:8
Alignment explanation
Indices: 2613223--2613251 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2613213 TATATATACT
2613223 AAATAATA
1 AAATAATA
2613231 AAATAATA
1 AAATAATA
2613239 AAATAATA
1 AAATAATA
2613247 AAATA
1 AAATA
2613252 TAATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:2631318 original size:42 final size:42
Alignment explanation
Indices: 2631250--2631352 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
2631240 TAGTTATATG
2631250 AACA-GCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAAT
1 AACAGGCACTAAGTGTGCGAAACTAAAATGGA-GAGGTTGAAT
* *
2631291 AA-AGGGCACTAAGTGTGCGAAATTAAAATGGAGATGTTGAAT
1 AACA-GGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAAT
*
2631333 AACAGGCACTAAATGTGCGA
1 AACAGGCACTAAGTGTGCGA
2631353 TACCGAGAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 49 0.89
43 3 0.05
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (42 bp):
AACAGGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAAT
Found at i:2642937 original size:82 final size:82
Alignment explanation
Indices: 2642800--2643854 Score: 2020
Period size: 82 Copynumber: 12.9 Consensus size: 82
2642790 CTAAGGCTAC
* * * *
2642800 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
* * *
2642865 TGATCATATAAGTATAA
66 TGATCAGATAAGTGTAG
2642882 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2642947 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2642964 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643029 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643046 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643111 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643128 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643193 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643210 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643275 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643292 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643357 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643374 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643439 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643456 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643521 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643538 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643603 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643620 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643685 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
2643702 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643767 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
* * *
2643784 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTATCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
2643849 TGATCA
66 TGATCA
2643855 AAAGTACTCA
Statistics
Matches: 963, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 963 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTGTAG
Found at i:2643816 original size:36 final size:36
Alignment explanation
Indices: 2643748--2643820 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2643738 CTAAAGCTAC
*
2643748 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
2643784 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
2643820 C
1 C
2643821 TAATGCTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:2649608 original size:11 final size:11
Alignment explanation
Indices: 2649592--2649649 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
2649582 TTATATACTA
*
2649592 AATAAAATTAT
1 AATAAAATAAT
2649603 AATAAAATAAT
1 AATAAAATAAT
*
2649614 AATAAAATATCT
1 AATAAAATA-AT
* *
2649626 CATTAAAATATT
1 -AATAAAATAAT
2649638 AATAAAATAAT
1 AATAAAATAAT
2649649 A
1 A
2649650 TTGATCTTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 29 0.74
12 2 0.05
13 8 0.21
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:2653230 original size:21 final size:21
Alignment explanation
Indices: 2653189--2653231 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2653179 TTGTTCCTGT
*
2653189 TTTATTATTCACATTATCATG
1 TTTATTATTCACATCATCATG
2653210 TTTATTATTC-CATCATGCATG
1 TTTATTATTCACATCAT-CATG
2653231 T
1 T
2653232 AAATATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTATTATTCACATCATCATG
Found at i:2653477 original size:107 final size:106
Alignment explanation
Indices: 2653274--2653669 Score: 555
Period size: 108 Copynumber: 3.7 Consensus size: 106
2653264 TCTAATTGAT
* * *
2653274 GCAATATTTAGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTTTCTCG
1 GCAATATTTTGCGTTTGGAAATTCGAGAGAACATGCCCTAAGGTGCTGGGTGTCGA--TTTCTCG
2653339 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAG
64 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAG
* * * *
2653382 GCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGTT
1 GCAATATTTTGCGTTTGGAAATTCGAGAGAACATGCCCTAAGGTGCTGGGTGTCGATTTCTCGTT
* * *
2653446 CAACCAAATGGCTTAATATCCTTTTCAAAAATCT-CAAAATATG
66 CAACCAAATAGCTAAATATCC-TTTC-AAAAT-TACAAAATAAG
*
2653489 GCAATATTTTGCGTTTGGAAATTCGAGATAACATGCCCTAAGGTGCTGGGTGTCGATCCTTCTCG
1 GCAATATTTTGCGTTTGGAAATTCGAGAGAACATGCCCTAAGGTGCTGGGTGTCGAT--TTCTCG
2653554 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAG
64 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAG
* * * * *
2653597 GCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTGCCCTAAGGTGCTGGGTTTCAATTTCTCGTT
1 GCAATATTTTGCGTTTGGAAATTCGAGAGAACATGCCCTAAGGTGCTGGGTGTCGATTTCTCGTT
*
2653661 TAACCAAAT
66 CAACCAAAT
2653670 TGCCGAATAT
Statistics
Matches: 256, Mismatches: 25, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
105 44 0.17
106 4 0.02
107 88 0.34
108 89 0.35
109 4 0.02
110 27 0.11
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (106 bp):
GCAATATTTTGCGTTTGGAAATTCGAGAGAACATGCCCTAAGGTGCTGGGTGTCGATTTCTCGTT
CAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAG
Found at i:2653645 original size:215 final size:215
Alignment explanation
Indices: 2653274--2653669 Score: 729
Period size: 215 Copynumber: 1.8 Consensus size: 215
2653264 TCTAATTGAT
**
2653274 GCAATATTTAGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTTTCTCG
1 GCAATATTTAGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATCCTTCTCG
2653339 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAAT
66 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAAT
*
2653404 TTGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGTTCAACCAAATGGCTTAATATCCTT
131 TTGAGGAACGTGCCCTAAGGTGCTGGGTTTCAATTTCTCGTTCAACCAAATGGCTTAATATCCTT
2653469 TTCAAAAATCTCAAAATATG
196 TTCAAAAATCTCAAAATATG
* * *
2653489 GCAATATTTTGCGTTTGGAAATTCGAGATAACATGCCCTAAGGTGCTGGGTGTCGATCCTTCTCG
1 GCAATATTTAGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATCCTTCTCG
2653554 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAAT
66 TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAAT
*
2653619 TTGAGGAACGTGCCCTAAGGTGCTGGGTTTCAATTTCTCGTTTAACCAAAT
131 TTGAGGAACGTGCCCTAAGGTGCTGGGTTTCAATTTCTCGTTCAACCAAAT
2653670 TGCCGAATAT
Statistics
Matches: 174, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
215 174 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (215 bp):
GCAATATTTAGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATCCTTCTCG
TTCAACCAAATAGCTAAATATCCTTTCAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAAT
TTGAGGAACGTGCCCTAAGGTGCTGGGTTTCAATTTCTCGTTCAACCAAATGGCTTAATATCCTT
TTCAAAAATCTCAAAATATG
Found at i:2659361 original size:51 final size:51
Alignment explanation
Indices: 2659280--2659444 Score: 244
Period size: 51 Copynumber: 3.3 Consensus size: 51
2659270 ACTTCTGATC
* * * * *
2659280 AGTGACAAGTGATAAATAGTAGCTTCAGCTACACTTATCTGATTAGTGACA
1 AGTGGCAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
2659331 AGTGGCAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
2659382 AGTGGCAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GACA
1 AGTGGCAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC-AGTGACA
**
2659432 AGTGATAAGTGAT
1 AGTGGCAAGTGAT
2659445 TATACGTAAG
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
50 35 0.33
51 71 0.67
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGGCAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:2660641 original size:42 final size:42
Alignment explanation
Indices: 2660594--2660683 Score: 180
Period size: 42 Copynumber: 2.1 Consensus size: 42
2660584 TTGGTTACTT
2660594 TATGTTAAAATATATGTTTGTTATATTGTGATTAAGGAATAA
1 TATGTTAAAATATATGTTTGTTATATTGTGATTAAGGAATAA
2660636 TATGTTAAAATATATGTTTGTTATATTGTGATTAAGGAATAA
1 TATGTTAAAATATATGTTTGTTATATTGTGATTAAGGAATAA
2660678 TATGTT
1 TATGTT
2660684 TAAGTTGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (42 bp):
TATGTTAAAATATATGTTTGTTATATTGTGATTAAGGAATAA
Found at i:2661860 original size:18 final size:18
Alignment explanation
Indices: 2661837--2661872 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2661827 TTATATATAT
*
2661837 TATTATTACTTATTAAAA
1 TATTATTACTTAATAAAA
2661855 TATTATTACTTAATAAAA
1 TATTATTACTTAATAAAA
2661873 ATACCATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATTACTTAATAAAA
Found at i:2663431 original size:44 final size:44
Alignment explanation
Indices: 2663367--2663507 Score: 194
Period size: 44 Copynumber: 3.2 Consensus size: 44
2663357 ACCATTGAAA
* * * **
2663367 TTCTTACCTAAACAATCAACCAAGACAATTATATTACATGACCAT
1 TTCTTACCAAAACAATCAACCAA-ACAATTATAATGCATGTTCAT
*
2663412 TTCTTACC-AAACAATCAACCAAACATTTATAATGCATGTTCAT
1 TTCTTACCAAAACAATCAACCAAACAATTATAATGCATGTTCAT
* *
2663455 TTATTACCAAAACAATCAATCAAACAATTATAATGCATGTTCAT
1 TTCTTACCAAAACAATCAACCAAACAATTATAATGCATGTTCAT
2663499 TTCTTACCA
1 TTCTTACCA
2663508 TTTAACAACT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
43 23 0.27
44 55 0.64
45 8 0.09
ACGTcount: A:0.41, C:0.23, G:0.04, T:0.32
Consensus pattern (44 bp):
TTCTTACCAAAACAATCAACCAAACAATTATAATGCATGTTCAT
Found at i:2673567 original size:16 final size:16
Alignment explanation
Indices: 2673538--2673577 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2673528 AATGAGTGAA
2673538 ATTAAAG-A-AAAAAT
1 ATTAAAGAATAAAAAT
*
2673552 ATTATAGAATAAAAAT
1 ATTAAAGAATAAAAAT
2673568 ATTAAAGAAT
1 ATTAAAGAAT
2673578 GTGTATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 6 0.27
15 1 0.05
16 15 0.68
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (16 bp):
ATTAAAGAATAAAAAT
Found at i:2683609 original size:19 final size:17
Alignment explanation
Indices: 2683571--2683610 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
2683561 TTATATATGG
*
2683571 ATTAATTATTTAGTTGA
1 ATTAATTATTTAGTTAA
2683588 ATTAATTAATTTAAGTTAA
1 ATTAATT-ATTT-AGTTAA
2683607 ATTA
1 ATTA
2683611 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
ATTAATTATTTAGTTAA
Found at i:2697856 original size:13 final size:13
Alignment explanation
Indices: 2697821--2697858 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2697811 ATTGATTGAG
*
2697821 TTTTATATTATAT
1 TTTTATATTTTAT
2697834 TTTTATATTTTAT
1 TTTTATATTTTAT
2697847 TTATTA-ATTTTA
1 TT-TTATATTTTA
2697859 ATTGATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATATTTTAT
Found at i:2697857 original size:20 final size:20
Alignment explanation
Indices: 2697821--2697858 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2697811 ATTGATTGAG
*
2697821 TTTTATATTATATTTTTATA
1 TTTTATATTATAATTTTATA
2697841 TTTTAT-TTATTAATTTTA
1 TTTTATATTA-TAATTTTA
2697859 ATTGATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATATTATAATTTTATA
Found at i:2699139 original size:31 final size:29
Alignment explanation
Indices: 2699104--2699178 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
2699094 TAACGCTCAA
* *
2699104 TGACTAAAATGTTACAATACAATAACGTAAG
1 TGACTAAAATGTAACAATAC-A-AACATAAG
* * *
2699135 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACTAAAATGTAACAATACAAACATAAG
2699164 TGACTAAAATGTAAC
1 TGACTAAAATGTAAC
2699179 CTGAGATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (29 bp):
TGACTAAAATGTAACAATACAAACATAAG
Found at i:2701468 original size:21 final size:20
Alignment explanation
Indices: 2701430--2701468 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2701420 TATAATTTAA
2701430 AATTTCAAACATTTTTTTTG
1 AATTTCAAACATTTTTTTTG
2701450 AATTTCAAAC-TTATTTTTT
1 AATTTCAAACATT-TTTTTT
2701469 AAGTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (20 bp):
AATTTCAAACATTTTTTTTG
Found at i:2717139 original size:17 final size:18
Alignment explanation
Indices: 2717105--2717150 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
2717095 CCGTTATGTC
2717105 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
2717120 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
2717137 CGCGACCGCGACCG
1 CGCGACCGCGACCG
2717151 TAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:2736345 original size:106 final size:104
Alignment explanation
Indices: 2736211--2736637 Score: 472
Period size: 104 Copynumber: 4.0 Consensus size: 104
2736201 AATAAAAACG
* *
2736211 AAAAAAAACTTTGGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTTAAAAAAAATTC
1 AAAAAAAAATTT--GGTGTTGGCCTGTCAATGGCCAGCACCCAGTACAA-TTTTAAAAAAAATTC
* ** *
2736276 -TTTTGTTTGTGTCAGTGTCAGATATCAATATACAAAAAAAT
63 TTTTTTTTTGTGTCAGAATCAGATATCAGTATACAAAAAAAT
*
2736317 AAATAAAAAATTTGAGTGTTGGCCTGTCAATGGCCAGCACCCAGTACAA-TTTAAAAAAAA--AT
1 AAA-AAAAAATTTG-GTGTTGGCCTGTCAATGGCCAGCACCCAGTACAATTTTAAAAAAAATTCT
* * * *
2736379 TTTTTTTCGTTTCAGAATCAGATATCAGTAAATGAAAAAAAT
64 TTTTTTTTGTGTCAGAATCAGATATCAGTATA-CAAAAAAAT
* * * *
2736421 AAAAAAAAATTTTGGGTGCTGGCCATTGACAA--GCCGGCACCCAGTACAATTTTAAAAAAATTT
1 AAAAAAAAA-TTT-GGTGTTGGCC--TGTCAATGGCCAGCACCCAGTACAATTTTAAAAAAA-AT
*
2736484 TCTTTATTTTATTCGTGTCAGAATCAGATATCAGTATACGAAAAAAT
61 TCTTT-TTTT-TT-GTGTCAGAATCAGATATCAGTATACAAAAAAAT
* * * *
2736531 AAAAAAAAAATTTGGTGATGGCCTGTTAATGGCCAGCACCAAGTACAA-ATTAAAAAAAATTCTT
1 -AAAAAAAAATTTGGTGTTGGCCTGTCAATGGCCAGCACCCAGTACAATTTTAAAAAAAATTCTT
*
2736595 TTTTTTTGTGTCAGAATCAGATATTAGTATACGAAAAAAAT
65 TTTTTTTGTGTCAGAATCAGATATCAGTATAC-AAAAAAAT
2736636 AA
1 AA
2736638 TTTTTTTTAA
Statistics
Matches: 272, Mismatches: 30, Indels: 40
0.80 0.09 0.12
Matches are distributed among these distances:
103 31 0.11
104 75 0.28
105 21 0.08
106 45 0.17
107 18 0.07
108 12 0.04
109 28 0.10
110 11 0.04
111 31 0.11
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (104 bp):
AAAAAAAAATTTGGTGTTGGCCTGTCAATGGCCAGCACCCAGTACAATTTTAAAAAAAATTCTTT
TTTTTTGTGTCAGAATCAGATATCAGTATACAAAAAAAT
Found at i:2738249 original size:26 final size:25
Alignment explanation
Indices: 2738220--2738279 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2738210 TGGATTAAAT
2738220 ATTTTAATAATAAAATTTAATTGATA
1 ATTTTAAT-ATAAAATTTAATTGATA
* ***
2738246 ATTTCTAATTTATTTTTTAATTGATA
1 ATTT-TAATATAAAATTTAATTGATA
2738272 ATTTTAAT
1 ATTTTAAT
2738280 CAAAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.14
26 21 0.72
27 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (25 bp):
ATTTTAATATAAAATTTAATTGATA
Found at i:2741458 original size:18 final size:17
Alignment explanation
Indices: 2741435--2741470 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2741425 TTCTTCTCCT
*
2741435 TATATTTTATTATTTTTA
1 TATATTTT-TTAATTTTA
2741453 TATATTTTTTAATTTTA
1 TATATTTTTTAATTTTA
2741470 T
1 T
2741471 TCAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TATATTTTTTAATTTTA
Found at i:2749143 original size:73 final size:73
Alignment explanation
Indices: 2749049--2749198 Score: 282
Period size: 73 Copynumber: 2.1 Consensus size: 73
2749039 AGAAGACTTC
* *
2749049 CATTTTTAGGCATCAACATCATTCCTTTGATAATCTCATCTTTCACTTTGATTTTTTTTGAACAC
1 CATTTTTAGGCATCAACATCATTCCTTTGATAATCTCATCTTTCACTTTGATTGTTTTTAAACAC
2749114 ATGGTTTT
66 ATGGTTTT
2749122 CATTTTTAGGCATCAACATCATTCCTTTGATAATCTCATCTTTCACTTTGATTGTTTTTAAACAC
1 CATTTTTAGGCATCAACATCATTCCTTTGATAATCTCATCTTTCACTTTGATTGTTTTTAAACAC
2749187 ATGGTTTT
66 ATGGTTTT
2749195 CATT
1 CATT
2749199 AATTGATGTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.47
Consensus pattern (73 bp):
CATTTTTAGGCATCAACATCATTCCTTTGATAATCTCATCTTTCACTTTGATTGTTTTTAAACAC
ATGGTTTT
Found at i:2750790 original size:24 final size:24
Alignment explanation
Indices: 2750758--2750843 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 24
2750748 ACGAAGTGTG
2750758 CCTTTACATATAATCGTAACCTTT
1 CCTTTACATATAATCGTAACCTTT
* *
2750782 CCTTTACAT-CAAT-GCTCAAACAATGTGT
1 CCTTTACATATAATCG-T--AAC-CT-T-T
*
2750810 GTCTTTACATATAATCGTAACCTTT
1 -CCTTTACATATAATCGTAACCTTT
2750835 CCTTTACAT
1 CCTTTACAT
2750844 CAATGCTCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 18
0.66 0.08 0.25
Matches are distributed among these distances:
22 1 0.02
23 4 0.09
24 17 0.36
25 4 0.09
26 2 0.04
27 2 0.04
28 4 0.09
29 8 0.17
30 4 0.09
31 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (24 bp):
CCTTTACATATAATCGTAACCTTT
Found at i:2763071 original size:19 final size:20
Alignment explanation
Indices: 2763047--2763087 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2763037 GAATTTAGGC
2763047 AAATATTGAATA-AAAATTG
1 AAATATTGAATATAAAATTG
* *
2763066 AAATATTTAATATGAAATTG
1 AAATATTGAATATAAAATTG
2763086 AA
1 AA
2763088 TTCTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (20 bp):
AAATATTGAATATAAAATTG
Found at i:2764682 original size:16 final size:17
Alignment explanation
Indices: 2764661--2764693 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2764651 ATGTCTAGGT
2764661 AAATT-ATTAATTGAGA
1 AAATTAATTAATTGAGA
2764677 AAATTAGATTAATTGAG
1 AAATTA-ATTAATTGAG
2764694 GGGTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
AAATTAATTAATTGAGA
Found at i:2766272 original size:178 final size:178
Alignment explanation
Indices: 2765973--2766326 Score: 699
Period size: 178 Copynumber: 2.0 Consensus size: 178
2765963 TGAATTATAC
2765973 AATGTATGATGAAATGTATTCATTTTTGAAATGAGAATAAAATAAAAATGTGAAAAAAATCGAAT
1 AATGTATGATGAAATGTATTCATTTTTGAAATGAGAATAAAATAAAAATGTGAAAAAAATCGAAT
2766038 AAATGATCAAATTAAGTGGAACGCCGGATTTGAGTACTTCTGATCAAGAGATAAAGTGATAAGTG
66 AAATGATCAAATTAAGTGGAACGCCGGATTTGAGTACTTCTGATCAAGAGATAAAGTGATAAGTG
2766103 GTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
131 GTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
2766151 AATGTATGATGAAATGTATTCATTTTTGAAATGAGAATAAAATAAAAATGTGAAAAAAATCGAAT
1 AATGTATGATGAAATGTATTCATTTTTGAAATGAGAATAAAATAAAAATGTGAAAAAAATCGAAT
2766216 AAATGATCAAATTAAGTGGAACGCCGGATTTGAGTACTTCTGATCAAGAGATAAAGTGATAAGTG
66 AAATGATCAAATTAAGTGGAACGCCGGATTTGAGTACTTCTGATCAAGAGATAAAGTGATAAGTG
*
2766281 GTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
131 GTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
2766327 GTAGCCTAGC
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 175 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (178 bp):
AATGTATGATGAAATGTATTCATTTTTGAAATGAGAATAAAATAAAAATGTGAAAAAAATCGAAT
AAATGATCAAATTAAGTGGAACGCCGGATTTGAGTACTTCTGATCAAGAGATAAAGTGATAAGTG
GTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCT
Found at i:2766352 original size:45 final size:46
Alignment explanation
Indices: 2766254--2766369 Score: 175
Period size: 46 Copynumber: 2.6 Consensus size: 46
2766244 TTTGAGTACT
* *
2766254 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
*
2766300 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
*
2766345 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
2766370 ATCATACGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
43 12 0.18
44 5 0.08
45 19 0.29
46 30 0.45
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
Found at i:2768892 original size:78 final size:78
Alignment explanation
Indices: 2768763--2768919 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
2768753 CTTAAGAGGG
2768763 ACCAATTTACTCAATTTCAAAATTAAGAACTGGAGAGGTTTTTTTACCTTTTTTATGCTATATTG
1 ACCAATTTACTCAATTTCAAAATTAAGAACTGGAGAGGTTTTTTTACCTTTTTTATGCTATATTG
2768828 TGGTGATGTTAAT
66 TGGTGATGTTAAT
2768841 ACCAATTTACTCAATTTCAAAATTAAGAACTGGAGAGGTTTTTTTACCTTTTTTATGCTATATTG
1 ACCAATTTACTCAATTTCAAAATTAAGAACTGGAGAGGTTTTTTTACCTTTTTTATGCTATATTG
2768906 TGGTGATGTTAAT
66 TGGTGATGTTAAT
2768919 A
1 A
2768920 TGAAAATTTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (78 bp):
ACCAATTTACTCAATTTCAAAATTAAGAACTGGAGAGGTTTTTTTACCTTTTTTATGCTATATTG
TGGTGATGTTAAT
Found at i:2769123 original size:19 final size:21
Alignment explanation
Indices: 2769085--2769123 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
2769075 AAAACTTATA
*
2769085 TATAAATAATAATATAACATT
1 TATAAATAAAAATATAACATT
2769106 TATAAA-AAAAAT-TAACAT
1 TATAAATAAAAATATAACAT
2769124 CCATTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAATAAAAATATAACATT
Found at i:2773210 original size:7 final size:7
Alignment explanation
Indices: 2773198--2773231 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2773188 AGGTAATTTG
2773198 ATTAAAA
1 ATTAAAA
2773205 ATTAAAA
1 ATTAAAA
2773212 ATTAAAA
1 ATTAAAA
2773219 ATTAAAA
1 ATTAAAA
2773226 ATTAAA
1 ATTAAA
2773232 GGTCGACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATTAAAA
Found at i:2780026 original size:35 final size:35
Alignment explanation
Indices: 2779979--2780248 Score: 193
Period size: 35 Copynumber: 7.4 Consensus size: 35
2779969 TAATTAGTGA
*
2779979 GCCCAGCTCTAGTTGGATATACCAACGATATTTGC
1 GCCCAGCGCTAGTTGGATATACCAACGATATTTGC
* * **
2780014 GCCTAGCGCTAGTTGGATAAACTGACGAATAATTAGTGAC
1 GCCCAGCGCTAGTTGGATATACCAACG-AT-ATT--TG-C
*
2780054 -CCCAGCTCTAGTTGGATATACCAACGATATTTGC
1 GCCCAGCGCTAGTTGGATATACCAACGATATTTGC
* * **
2780088 GCCTAGCGCTAGTTGGATAAACTGACGAATAATTAGTGAC
1 GCCCAGCGCTAGTTGGATATACCAACG-AT-ATT--TG-C
* *
2780128 -CCCAGCTCTAGTTGGATATACCAACGATATTTGT
1 GCCCAGCGCTAGTTGGATATACCAACGATATTTGC
* * * * *
2780162 GCCCAGCGCTAGTCGTATAAACCAACGAATAAATAGTGA
1 GCCCAGCGCTAGTTGGATATACCAACG-AT--AT-TTGC
* * * *
2780201 GCCTAGCTCTAGTTGGATTTACCAACAATATTTGC
1 GCCCAGCGCTAGTTGGATATACCAACGATATTTGC
* *
2780236 GCCGAGCACTAGT
1 GCCCAGCGCTAGT
2780249 CTGATAAACC
Statistics
Matches: 181, Mismatches: 38, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
34 1 0.01
35 82 0.45
36 8 0.04
37 12 0.07
38 8 0.04
39 68 0.38
40 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (35 bp):
GCCCAGCGCTAGTTGGATATACCAACGATATTTGC
Found at i:2780058 original size:74 final size:74
Alignment explanation
Indices: 2779936--2780272 Score: 478
Period size: 74 Copynumber: 4.6 Consensus size: 74
2779926 CTGACGAAAG
* * ** *
2779936 TTGCGCCTAGCGCTAGTCGGTTAAACCGAAAAATAATTAGTGAGCCCAGCTCTAGTTGGATATAC
1 TTGCGCCTAGCGCTAGTTGGATAAACCGACGAATAATTAGTGACCCCAGCTCTAGTTGGATATAC
2780001 CAACGATAT
66 CAACGATAT
*
2780010 TTGCGCCTAGCGCTAGTTGGATAAACTGACGAATAATTAGTGACCCCAGCTCTAGTTGGATATAC
1 TTGCGCCTAGCGCTAGTTGGATAAACCGACGAATAATTAGTGACCCCAGCTCTAGTTGGATATAC
2780075 CAACGATAT
66 CAACGATAT
*
2780084 TTGCGCCTAGCGCTAGTTGGATAAACTGACGAATAATTAGTGACCCCAGCTCTAGTTGGATATAC
1 TTGCGCCTAGCGCTAGTTGGATAAACCGACGAATAATTAGTGACCCCAGCTCTAGTTGGATATAC
2780149 CAACGATAT
66 CAACGATAT
* * * * * * * * *
2780158 TTGTGCCCAGCGCTAGTCGTATAAACCAACGAATAAATAGTGAGCCTAGCTCTAGTTGGATTTAC
1 TTGCGCCTAGCGCTAGTTGGATAAACCGACGAATAATTAGTGACCCCAGCTCTAGTTGGATATAC
*
2780223 CAACAATAT
66 CAACGATAT
* * *
2780232 TTGCGCCGAGCACTAGTCT-GATAAACCGACGAATAAATAGT
1 TTGCGCCTAGCGCTAGT-TGGATAAACCGACGAATAATTAGT
2780273 TATTTATTTT
Statistics
Matches: 239, Mismatches: 23, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
74 239 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (74 bp):
TTGCGCCTAGCGCTAGTTGGATAAACCGACGAATAATTAGTGACCCCAGCTCTAGTTGGATATAC
CAACGATAT
Found at i:2782592 original size:13 final size:13
Alignment explanation
Indices: 2782574--2782598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2782564 AATATAACTC
2782574 TAAAAATATTTAA
1 TAAAAATATTTAA
2782587 TAAAAATATTTA
1 TAAAAATATTTA
2782599 TGAGTCTAGT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAAATATTTAA
Found at i:2784164 original size:14 final size:14
Alignment explanation
Indices: 2784145--2784172 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2784135 GATTTTCGGG
2784145 TTGGGTTAGGGTTA
1 TTGGGTTAGGGTTA
2784159 TTGGGTTAGGGTTA
1 TTGGGTTAGGGTTA
2784173 GTAGGTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (14 bp):
TTGGGTTAGGGTTA
Found at i:2786715 original size:15 final size:16
Alignment explanation
Indices: 2786687--2786716 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2786677 TTAATTGGCC
2786687 AATAAAAATCGAGAGA
1 AATAAAAATCGAGAGA
2786703 AATAAAAAT-GAGAG
1 AATAAAAATCGAGAG
2786717 TCTTGTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.13
Consensus pattern (16 bp):
AATAAAAATCGAGAGA
Found at i:2787261 original size:28 final size:28
Alignment explanation
Indices: 2787229--2788041 Score: 1626
Period size: 28 Copynumber: 29.0 Consensus size: 28
2787219 AGGCTACCAC
2787229 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787257 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787285 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787313 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787341 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787369 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787397 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787425 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787453 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787481 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787509 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787537 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787565 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787593 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787621 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787649 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787677 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787705 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787733 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787761 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787789 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787817 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787845 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787873 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787901 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787929 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787957 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2787985 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2788013 TTATCACTTTGTCACTTGATCAGATAAG
1 TTATCACTTTGTCACTTGATCAGATAAG
2788041 T
1 T
2788042 GTAGCTAAAG
Statistics
Matches: 785, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 785 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (28 bp):
TTATCACTTTGTCACTTGATCAGATAAG
Found at i:2800168 original size:39 final size:40
Alignment explanation
Indices: 2800124--2800219 Score: 95
Period size: 45 Copynumber: 2.3 Consensus size: 40
2800114 AACGGTAGCA
* *
2800124 GTAACAGTAACAA-TATTCAACACACAAAGTGTTGAATCT
1 GTAACAGTAACAAGTATTCAACACACAAAGTGTCGAATCG
* * *
2800163 GTAACAATAACGGTAATGGTATTCGACACACAAATTGTCGAATCG
1 GTAACAGTAAC---AA--GTATTCAACACACAAAGTGTCGAATCG
2800208 GTAACAGTAACA
1 GTAACAGTAACA
2800220 GTAGTCGGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
39 10 0.22
42 3 0.07
45 32 0.71
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24
Consensus pattern (40 bp):
GTAACAGTAACAAGTATTCAACACACAAAGTGTCGAATCG
Found at i:2801153 original size:5 final size:5
Alignment explanation
Indices: 2801143--2801172 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2801133 TTACCTATTT
2801143 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
2801173 TAATAATCTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:2802257 original size:32 final size:31
Alignment explanation
Indices: 2802217--2802284 Score: 118
Period size: 32 Copynumber: 2.2 Consensus size: 31
2802207 TCGACATTAG
*
2802217 GGGGAGAGAAATAATAACTTGTAATGAGTTAA
1 GGGGAGAGAAATAATAACTTATAATGAGTT-A
2802249 GGGGAGAGAAATAATAACTTATAATGAGTTA
1 GGGGAGAGAAATAATAACTTATAATGAGTTA
2802280 GGGGA
1 GGGGA
2802285 AGAGTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 6 0.17
32 29 0.83
ACGTcount: A:0.43, C:0.03, G:0.31, T:0.24
Consensus pattern (31 bp):
GGGGAGAGAAATAATAACTTATAATGAGTTA
Found at i:2804909 original size:16 final size:16
Alignment explanation
Indices: 2804871--2804909 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
2804861 CAAAAAATAT
*
2804871 AAATAAAATATTCAAA
1 AAATAAAACATTCAAA
2804887 AATATAAAACATTCAAA
1 AA-ATAAAACATTCAAA
2804904 AAATAA
1 AAATAA
2804910 TCAATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAACATTCAAA
Found at i:2812059 original size:23 final size:21
Alignment explanation
Indices: 2812032--2812087 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
2812022 TATTACATAG
2812032 ATTATTTTATTATATGATATTATT
1 ATTATTTT-TT-TATG-TATTATT
*
2812056 -TTATGTTTTTATGTATTATT
1 ATTATTTTTTTATGTATTATT
2812076 ACTTATTTTTTT
1 A-TTATTTTTTT
2812088 TTGCACAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 7 0.25
21 4 0.14
22 11 0.39
23 6 0.21
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTATTTTTTTATGTATTATT
Found at i:2812508 original size:53 final size:53
Alignment explanation
Indices: 2812428--2812534 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
2812418 TAAATTAATA
* *
2812428 ACTTTTGAATGTTGATGTTGATAGTGGCATAATGCATGACTAGAGTTATTGTT
1 ACTTTTGAATGTTGACGTTGATAGTGGCATAATGCATGACTAGAGCTATTGTT
* *
2812481 ACTTTTGAATGTTGACGTTGATAGTGGCATAATGCATGATTGGAGCTATTGTT
1 ACTTTTGAATGTTGACGTTGATAGTGGCATAATGCATGACTAGAGCTATTGTT
2812534 A
1 A
2812535 TTGTATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.40
Consensus pattern (53 bp):
ACTTTTGAATGTTGACGTTGATAGTGGCATAATGCATGACTAGAGCTATTGTT
Found at i:2816710 original size:12 final size:12
Alignment explanation
Indices: 2816695--2816737 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2816685 AAGAAGAAGG
*
2816695 AAAAGGAAAATC
1 AAAATGAAAATC
* *
2816707 AAAATCAAAGTC
1 AAAATGAAAATC
*
2816719 AAAATGAAAATA
1 AAAATGAAAATC
2816731 AAAATGA
1 AAAATGA
2816738 GAGAAGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.07, G:0.12, T:0.14
Consensus pattern (12 bp):
AAAATGAAAATC
Found at i:2819216 original size:128 final size:128
Alignment explanation
Indices: 2818892--2820042 Score: 1709
Period size: 128 Copynumber: 9.0 Consensus size: 128
2818882 TCGGTGAAAT
* *
2818892 CACAAGTCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * *
2818957 CAGTAGTGGAGCAGATCGAAGACAGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
*
2819020 CACAAGT-CTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAATTTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
** * * * *
2819084 CAGTAGCGGAGCAGATTAAAGATGGCGAATTTTATCTTCAAGGGTAAGGAAGTAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
*
2819147 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* *
2819212 CAGTAGCGGAGCAGATCGGAAG-CGACAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATC-GAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
** * *
2819275 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTAGAAATTACAAATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * *
2819340 CAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGT
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * * ** *
2819403 CACAAGTCCTATCTCCCTGGCCAGCAGTGGAATAAGTTAAAAATTATAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
*
2819468 CAGTAGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
** * * *
2819531 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTAGAAATTACAAATATTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* *
2819596 CAGTAGCGGAGCAGATCGGAAG-CGACAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATC-GAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
** * *
2819659 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTAGAAATTACAAATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
2819724 CAGTAGCGGAGCAGATTGAAGACGGTGAATCTTATCTTCAAGGGTAAGGAAGTAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* *
2819787 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGA-CATTGTTTCCCTAA
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATC-TTGTCTCCCTAA
* * * *
2819851 GCAGTAGCGGAGCAGATTGAAGACGGTGAATCTTATCTTCAAGGGTAAGGAAGTAGATTTAAGC
65 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* *
2819915 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGA-CATTGTTTCCCTAA
1 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATC-TTGTCTCCCTAA
* * * * * *
2819979 GCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATATTCAAGTGTAAGGGAGTAGATTGAAGC
65 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
2820043 TCCTATAGGG
Statistics
Matches: 945, Mismatches: 72, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
127 124 0.13
128 814 0.86
129 7 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (128 bp):
CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
Found at i:2820177 original size:44 final size:43
Alignment explanation
Indices: 2820114--2820487 Score: 192
Period size: 44 Copynumber: 8.7 Consensus size: 43
2820104 CCGATAATCC
2820114 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAG-AATAGATCT
* * * * * *
2820158 TATCTCTCTGAAGTTGTAGTAGAGTGGA-T--CGCATCAGGTCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGAAT-AGATCT
* *
2820199 TATCTCCCTGAAGTTGTAGTGGAGCAGATTGAGAA-AACA-AGTCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATT-A-AAGAATAGA-TCT
* **** * * *** * *
2820243 TATCCCCCTGAAGGCACAGTGGGGCAGACCGAAGAAGCAAATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGAA-TAGATCT
* * ** * *
2820287 TATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGTCGATA-ATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAG--AATAGATCT
* *
2820331 TATCTCCCTGAAGTTGTAGCGGAGCGGATTAAAGTAACAGATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAG-AATAGATCT
** * * ** ** *
2820375 TATCTCTTTGAAGTTGCAGTAGAATGG---ACCGCATCAGATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGAAT-AGATCT
** *
2820416 TATCTCCCT-AAGCAGTAGTGGAGCAGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAG-AATAGATCT
* * *
2820459 TATCTCTCTGAAGTTGCAGTAGAGCGGAT
1 TATCTCCCTGAAGTTGTAGTGGAGCGGAT
2820488 CGCATCAAGT
Statistics
Matches: 239, Mismatches: 72, Indels: 38
0.68 0.21 0.11
Matches are distributed among these distances:
40 13 0.05
41 45 0.19
42 3 0.01
43 21 0.09
44 153 0.64
45 3 0.01
46 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGAATAGATCT
Found at i:2820457 original size:84 final size:85
Alignment explanation
Indices: 2820327--2820481 Score: 249
Period size: 84 Copynumber: 1.8 Consensus size: 85
2820317 GAAGTCGATA
** * *
2820327 ATCTTATCTCCCTGAAGTTGTAGCGGAGCGGATTAAAGTAACAGATCTTATCTCTTTGAAGTTGC
1 ATCTTATCTCCCTGAAGCAGTAGCGGAGCAGATTAAAGTAACAGATCTTATCTCTCTGAAGTTGC
2820392 AGTAGAATGGACCGCATCAG
66 AGTAGAATGGACCGCATCAG
* *
2820412 ATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGC
1 ATCTTATCTCCCTGAAGCAGTAGCGGAGCAGATTAAAGTAACAGATCTTATCTCTCTGAAGTTGC
2820476 AGTAGA
66 AGTAGA
2820482 GCGGATCGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
84 51 0.80
85 13 0.20
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (85 bp):
ATCTTATCTCCCTGAAGCAGTAGCGGAGCAGATTAAAGTAACAGATCTTATCTCTCTGAAGTTGC
AGTAGAATGGACCGCATCAG
Found at i:2824166 original size:33 final size:33
Alignment explanation
Indices: 2824104--2824166 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
2824094 CCATTTATAA
* * **
2824104 ATCTATACACTATATGCTATAAATTAATTATGT
1 ATCTATAAACTATATACTATAAACGAATTATGT
*
2824137 ATCTATAAACTATATATTATAAACGAATTA
1 ATCTATAAACTATATACTATAAACGAATTA
2824167 CAAGGTAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (33 bp):
ATCTATAAACTATATACTATAAACGAATTATGT
Found at i:2825789 original size:60 final size:60
Alignment explanation
Indices: 2825664--2825789 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
2825654 GAAATAAGTA
* * * * * ***
2825664 AATGATGATCTTTGTAAGAATAGATATATGTAGTGAACACTTCAATGAAGGGGTTCATTTG
1 AATGATGAACTTTGAAAGAATAGATATA-GTAATGAACACTCCAATGAAGGGATTCACCCG
* *
2825725 AATGATTGAACTTTGAAAGAATAGATATA-TAATGAACTCTCCGATGAAGGGATTCACCCG
1 AATGA-TGAACTTTGAAAGAATAGATATAGTAATGAACACTCCAATGAAGGGATTCACCCG
2825785 AATGA
1 AATGA
2825790 GTTGTTGGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
60 28 0.52
61 5 0.09
62 21 0.39
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (60 bp):
AATGATGAACTTTGAAAGAATAGATATAGTAATGAACACTCCAATGAAGGGATTCACCCG
Done.