Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold326
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: 1352760
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 3 of 8
Found at i:379789 original size:18 final size:18
Alignment explanation
Indices: 379768--379828 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
379758 CAAAACCAAG
379768 CTAAGTCACTACCACAAT
1 CTAAGTCACTACCACAAT
* ** **
379786 CTAAGTCTC-AAAACCAGG
1 CTAAGTCACTACCA-CAAT
379804 CTAAGTCACTACCACAAT
1 CTAAGTCACTACCACAAT
379822 CTAAGTC
1 CTAAGTC
379829 TCAAAACCAG
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (18 bp):
CTAAGTCACTACCACAAT
Found at i:379843 original size:18 final size:18
Alignment explanation
Indices: 379786--379845 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
379776 CTACCACAAT
379786 CTAAGTCTCAAAACCAGG
1 CTAAGTCTCAAAACCAGG
* * * **
379804 CTAAGTCAC-TACCACAAT
1 CTAAGTCTCAAAAC-CAGG
379822 CTAAGTCTCAAAACCAGG
1 CTAAGTCTCAAAACCAGG
379840 CTAAGT
1 CTAAGT
379846 TATTATCTCT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.20
Consensus pattern (18 bp):
CTAAGTCTCAAAACCAGG
Found at i:394512 original size:21 final size:21
Alignment explanation
Indices: 394465--394522 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
394455 AAAAATTATC
*
394465 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
394486 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
394507 CAAATGTATCGATACA
1 CAAATGTATCGATACA
394523 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:394582 original size:19 final size:19
Alignment explanation
Indices: 394558--394625 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
394548 AATTCAACAA
394558 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
394577 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
394592 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
394609 ATTGTATCAATACATAA
1 TTTGTATCGATACATAA
394626 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:394597 original size:13 final size:13
Alignment explanation
Indices: 394579--394603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
394569 ACATAAGTTT
394579 TGTATCGATACAA
1 TGTATCGATACAA
394592 TGTATCGATACA
1 TGTATCGATACA
394604 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:394601 original size:32 final size:32
Alignment explanation
Indices: 394560--394622 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
394550 TTCAACAATT
* *
394560 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
394592 TGTATCGATACATAAGTATTGTATCAATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
394623 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:394683 original size:13 final size:13
Alignment explanation
Indices: 394665--394690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
394655 CATTTTTCTG
394665 TGTATCGATACAT
1 TGTATCGATACAT
394678 TGTATCGATACAT
1 TGTATCGATACAT
394691 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:394684 original size:33 final size:33
Alignment explanation
Indices: 394645--394711 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
394635 GCCAAGGAAA
***
394645 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
394678 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
394711 T
1 T
394712 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:397249 original size:31 final size:28
Alignment explanation
Indices: 397166--397238 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
397156 CTTCACAATC
* * ***
397166 GGGGACACTCCAACCCCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGA
*
397193 GGGGATACTCTAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
397221 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
397239 ACTTTATTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Found at i:397283 original size:51 final size:51
Alignment explanation
Indices: 397221--397387 Score: 199
Period size: 52 Copynumber: 3.2 Consensus size: 51
397211 TTATTTCCGA
* ***
397221 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * *
397272 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTC-ATAATC
* * *
397324 AGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
*
397376 GAGGATACTCCA
1 GGGGATACTCCA
397388 TCCTCGTTAT
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
51 37 0.39
52 44 0.46
53 14 0.15
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:397347 original size:52 final size:51
Alignment explanation
Indices: 397046--397387 Score: 190
Period size: 51 Copynumber: 6.5 Consensus size: 51
397036 TTGAGTTTCT
* * * * *
397046 CAATTCTCCATAATCAGGGATATTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTTTCCATAATCAGGGATACTCCAACCCCGATTTTATTTCCAAAATAC
* * * * *
397097 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCCATAATCAGGGATACTCCAACCCCGATTTTATTTCC--AAAATAC
* * * * * * ****
397150 CAATTTCTTCACAATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATAC
1 CAATTT-TCCATAATCAGGGATACTCCAACCCCGATTTTAT-TTCCAAAATAC
** * * * *
397201 TCTAA--CCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATAT
1 -C-AATTTTCC-ATA-AT-C-A-GGGATACTCCAACCCCGATTTTATTTCCAAAATAC
** * * * * *
397257 TGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTTTCCATAATCAGGGATACTCCAACCCCGATTTTATTTCCAAAATAC
* *
397308 CAATTTTCCTTTAATCAGGGATACTCCAACACCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ATAATCAGGGATACTCCAACCCCGATTTTATTTCC-AAAATAC
* *
397361 CAATTTTTCACAATC-GAGGATACTCCA
1 CAATTTTCCATAATCAG-GGATACTCCA
397388 TCCTCGTTAT
Statistics
Matches: 214, Mismatches: 59, Indels: 35
0.69 0.19 0.11
Matches are distributed among these distances:
50 1 0.00
51 79 0.37
52 50 0.23
53 32 0.15
54 24 0.11
55 18 0.08
56 6 0.03
57 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
CAATTTTCCATAATCAGGGATACTCCAACCCCGATTTTATTTCCAAAATAC
Found at i:397413 original size:28 final size:28
Alignment explanation
Indices: 397373--397454 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
397363 ATTTTTCACA
* * * *
397373 ATCGAGGATACTCCATCCTCGTTATTTC
1 ATCGGGGAAACTCCAACCCCGTTATTTC
*
397401 ATCGGGGAAACTCCAACCCCGTTACTTC
1 ATCGGGGAAACTCCAACCCCGTTATTTC
397429 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGGAA-ACTCCAACCCCGTTATT
397455 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 5 0.11
28 39 0.85
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGAAACTCCAACCCCGTTATTTC
Found at i:397421 original size:211 final size:211
Alignment explanation
Indices: 397054--397449 Score: 589
Period size: 211 Copynumber: 1.9 Consensus size: 211
397044 CTCAATTCTC
* * * *
397054 CATAATCAGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CATAATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATA
* *
397119 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCG
66 CTCCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCG
* * * * *
397184 TTAATCATCGGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTC
131 TTAATCATCGGGGAAACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTC
397249 CAAAATATTGATTTTT
196 CAAAATATTGATTTTT
* * *
397265 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGAT
1 CATAATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCAGGGAT
* * * *
397330 ACTCCAACACCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCATCCTC
65 ACTCCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCC
*
397393 GTTATTTCATCGGGGAAACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
130 GTTA-ATCATCGGGGAAACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
397450 TTATTATCTC
Statistics
Matches: 164, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 26 0.16
211 104 0.63
212 34 0.21
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (211 bp):
CATAATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATA
CTCCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCG
TTAATCATCGGGGAAACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTC
CAAAATATTGATTTTT
Found at i:401212 original size:15 final size:15
Alignment explanation
Indices: 401185--401226 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
401175 TTAATTTTTT
401185 AATTT-ATTCTTTAAA
1 AATTTAATT-TTTAAA
**
401200 AATTTAATTTTTAGT
1 AATTTAATTTTTAAA
401215 AATTTAATTTTT
1 AATTTAATTTTT
401227 TTACTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTTAATTTTTAAA
Found at i:403938 original size:13 final size:13
Alignment explanation
Indices: 403920--403945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
403910 CATTATTCAA
403920 TGTATCGATACAT
1 TGTATCGATACAT
403933 TGTATCGATACAT
1 TGTATCGATACAT
403946 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:404009 original size:20 final size:19
Alignment explanation
Indices: 403984--404110 Score: 113
Period size: 20 Copynumber: 6.7 Consensus size: 19
403974 TTTACCCAGA
403984 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
404004 TGTATCGAT--A----CAT
1 TGTATCGATACATTTTCAT
* *
404017 TGTATCGATATATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
404037 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
*
404057 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
* *
404077 TGTATTGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
404097 TGTATCGATACATT
1 TGTATCGATACATT
404111 GAGGCATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
13 12 0.14
15 1 0.01
18 1 0.01
19 2 0.02
20 71 0.81
21 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:404050 original size:13 final size:13
Alignment explanation
Indices: 404001--404031 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
403991 ATACATTTTG
404001 CATTGTATCGATA
1 CATTGTATCGATA
404014 CATTGTATCGATA
1 CATTGTATCGATA
*
404027 TATTG
1 CATTG
404032 CTCATTGTAT
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:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:404072 original size:40 final size:40
Alignment explanation
Indices: 404012--404111 Score: 173
Period size: 40 Copynumber: 2.5 Consensus size: 40
404002 ATTGTATCGA
* *
404012 TACATTGTATCGATATATTGCTCATTGTATCGATACATTT
1 TACAATGTATCGATACATTGCTCATTGTATCGATACATTT
*
404052 TACAATGTATCGATACATTGCTCATTGTATTGATACATTT
1 TACAATGTATCGATACATTGCTCATTGTATCGATACATTT
404092 TACAATGTATCGATACATTG
1 TACAATGTATCGATACATTG
404112 AGGCATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (40 bp):
TACAATGTATCGATACATTGCTCATTGTATCGATACATTT
Found at i:406456 original size:51 final size:51
Alignment explanation
Indices: 406391--406559 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
406381 ATTTTTCATC
* * * * *
406391 TCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTCCATAA
* ** *
406442 TTGGGGATACTCCAACTCCGATTTTATTTTTAAAACACCTATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
* * *
406493 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAATACCGACTTTT-CACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACC-AATTTTCCATAA
**
406544 TCAAGGATACTCCAAC
1 TCGGGGATACTCCAAC
406560 CTCGTTATTT
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
51 93 0.95
52 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
Found at i:406585 original size:79 final size:79
Alignment explanation
Indices: 406495--406768 Score: 291
Period size: 79 Copynumber: 3.5 Consensus size: 79
406485 TTCCATAATC
* * * **
406495 GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCGACTTTTCACAATCAAGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATATCGATTTTTCACAATCGGGGATACTCCAAC
* **
406560 CTCGTTATTTTTTA
66 CCCGTTATTTTCAA
* * * * * * * *
406574 GGGGATACTCCAACCCCAGGTTTTAATTCTAAAACATCAATTTTTTATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCC-GATTTTATTTCCAAAATATCGATTTTTCACAATCGGGGATACTCCAA
*
406639 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCAA
* * * * *
406654 GGGAATACTCCAATCTCGATTTTATTT-CGAAATCATCGATTTTTCACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAT-ATCGATTTTTCACAATCGGGGATACTCCAA
406718 CCCCGTTATTTTCAA
65 CCCCGTTATTTTCAA
* *
406733 GGAGATACTCCAACCCCG-TTATTATCTCCAAAATAT
1 GGGGATACTCCAACCCCGATT-TTATTTCCAAAATAT
406769 TAAATTTCTC
Statistics
Matches: 155, Mismatches: 36, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
78 5 0.03
79 84 0.54
80 66 0.43
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATATCGATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCAA
Found at i:413031 original size:62 final size:62
Alignment explanation
Indices: 412917--413121 Score: 317
Period size: 62 Copynumber: 3.3 Consensus size: 62
412907 TATCCCTTCC
*
412917 AGTCCTCAAAGAGCAGGACGTCTTTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGTC--TTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
412981 AGTCCTCAAAGAGCAGGACGTCTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGTCTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * **
413043 AGTCCTCAAAGAGCAGGAC-AC-CTTTT-TTTTTAAAGCCCACACAAGTTGGTGGCACCTCCC
1 AGTCCTCAAAGAGCAGGACGTCTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCT-TT
413103 AGTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
413122 ACACTCTCCT
Statistics
Matches: 135, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
59 31 0.23
60 23 0.17
61 1 0.01
62 58 0.43
64 22 0.16
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (62 bp):
AGTCCTCAAAGAGCAGGACGTCTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:413201 original size:55 final size:55
Alignment explanation
Indices: 413137--413445 Score: 426
Period size: 55 Copynumber: 5.5 Consensus size: 55
413127 CTCCTTTCAC
413137 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
413191 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
413246 CCTTTCAATCCTCAAAGAGCAGGACGCCTTTCAAAGCCTACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
413301 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
413356 CCTTTTAGTCCT-AAAAATGCAAGGACACTCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGA-GC-AGGACGC-C-TTTC-----AAAGCCCACACAAGTTGGTGGCA
* *
413419 -CTTCCCAGTCCTCAAAGAGCAGAACGC
1 CCTT-TCAGTCCTCAAAGAGCAGGACGC
413446 TCTCTTCTTT
Statistics
Matches: 227, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
54 9 0.04
55 165 0.73
56 6 0.03
57 1 0.00
58 3 0.01
62 8 0.04
63 31 0.14
64 4 0.02
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:413279 original size:26 final size:26
Alignment explanation
Indices: 413246--413331 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
413236 GTTGGTGGCA
413246 CCTTTCAATCCTCAAAGAGCAGGACG
1 CCTTTCAATCCTCAAAGAGCAGGACG
* * ** *
413272 CCTTTCAAAGCCTACACAAGTTGGTGG-CA
1 CCTTTC-AATCCT-CA-AAG-AGCAGGACG
*
413301 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAATCCTCAAAGAGCAGGACG
413327 CCTTT
1 CCTTT
413332 TAAAGCCCAC
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
25 3 0.07
26 15 0.34
27 7 0.16
28 6 0.14
29 10 0.23
30 3 0.07
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (26 bp):
CCTTTCAATCCTCAAAGAGCAGGACG
Found at i:413498 original size:157 final size:155
Alignment explanation
Indices: 413301--413595 Score: 427
Period size: 157 Copynumber: 1.9 Consensus size: 155
413291 GTTGGTGGCA
413301 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT-AGT
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA--TTTTCAGT
* ** *
413365 CCT-AAAAATGCAAGGACACTCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGT
64 CCTCAAAAA-GC-AGGACACT-TTCTCTTTGCAAAGCCCACACAAGCTGGTGGCACCTT-CCAGT
413428 CCTCAAAGAGCAGAACGCTCTCTTCTTTCGC
125 CCTCAAAGAGCAGAACGCTCTCTTCTTTCGC
413459 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGTC
* ** *
413523 CTCAAAAAGCATGATGCTTTCTCTTTGCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCA
65 CTCAAAAAGCAGGACACTTTCTCTTTGCAAAGCCCACACAAGCTGGTGGCACCTTCCAGTCCTCA
413588 AAGAGCAG
130 AAGAGCAG
413596 GATGTCTTTC
Statistics
Matches: 125, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
155 50 0.40
156 8 0.06
157 57 0.46
158 10 0.08
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (155 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCC
TCAAAAAGCAGGACACTTTCTCTTTGCAAAGCCCACACAAGCTGGTGGCACCTTCCAGTCCTCAA
AGAGCAGAACGCTCTCTTCTTTCGC
Found at i:413585 original size:61 final size:60
Alignment explanation
Indices: 413459--413661 Score: 242
Period size: 61 Copynumber: 3.5 Consensus size: 60
413449 CTTCTTTCGC
* *
413459 CCTTT-AGTCCTCAAAGAGCAGGA--C--GCCTTT-TAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * *
413513 -TTTTCCAGTCCTCAAAAAGCATGATGCTTTCTCTTTGCAAAGCCCACACAAGCTGGTGGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGATGCTTTC-CTTTGCAAAGCCCACACAAGTTGGTGGCA
*
413574 CCTTTCAGTCCTCAAAGAGCAGGATGTCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATG-CTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
*
413635 CC-TCCTAGTCCTCAAAGAGCAGGATGC
1 CCTTTC-AGTCCTCAAAGAGCAGGATGC
413662 ACTTTATTCC
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
53 3 0.02
55 16 0.13
57 1 0.01
59 1 0.01
60 7 0.06
61 90 0.71
62 8 0.06
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (60 bp):
CCTTTCAGTCCTCAAAGAGCAGGATGCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
Found at i:413827 original size:61 final size:60
Alignment explanation
Indices: 413710--413953 Score: 305
Period size: 60 Copynumber: 4.0 Consensus size: 60
413700 TCATTTTCGC
* * *
413710 CTTTTTCTTTTAAAGCCCACATAAGTTGGTGGCACTTCTTT-AGTCCTAAAAAAGCAGGACG
1 CTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC--CTTTCAGTCCTCAAAGAGCAGGACG
* *
413771 CTTTTTCCTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
1 CTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
* * * * * * *
413832 CCTTCTCTTTCT-AAGCCCACACAAGTTGGTGGCACCCTCCAATCCTCAAAGAGTAGGATG
1 CTTTTTCTTT-TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
*
413892 CCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACG
1 -CTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
413952 CT
1 CT
413954 CACTCCTTTC
Statistics
Matches: 160, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
59 2 0.01
60 69 0.43
61 60 0.38
62 29 0.18
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (60 bp):
CTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:413963 original size:121 final size:122
Alignment explanation
Indices: 413722--413952 Score: 315
Period size: 121 Copynumber: 1.9 Consensus size: 122
413712 TTTTCTTTTA
* * ** *
413722 AAGCCCACATAAGTTGGTGGCACTTCTTTAGTCCTAAAAAAGCAGGACGCTTTTTCCTTTTAAAG
1 AAGCCCACACAAGTTGGTGGCACTCCTCCAATCCTAAAAAAGCAGGACGCTTTTTCCTTTTAAAG
* * * *
413787 CCCACATAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCTTTCT
66 CCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCCTCTCTTTCT
* * * *
413844 AAGCCCACACAAGTTGGTGGCAC-CCTCCAATCCTCAAAGAGTAGGATGCCTTTTT-CTTTTAAA
1 AAGCCCACACAAGTTGGTGGCACTCCTCCAATCCTAAAAAAGCAGGACG-CTTTTTCCTTTTAAA
413907 GCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGC
65 GCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
413953 TCACTCCTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
120 23 0.24
121 45 0.47
122 28 0.29
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (122 bp):
AAGCCCACACAAGTTGGTGGCACTCCTCCAATCCTAAAAAAGCAGGACGCTTTTTCCTTTTAAAG
CCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCCTCTCTTTCT
Found at i:414222 original size:61 final size:61
Alignment explanation
Indices: 413992--414218 Score: 318
Period size: 61 Copynumber: 3.8 Consensus size: 61
413982 AGCAGGATAC
* * *
413992 CTTTT-AAAGCCCACACAAGCTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCCTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCATGATGCCTTTT
* *
414051 CTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCATGATG-C-TTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCATGATGCCTTTT
* * * * *
414110 CTTTTTGCAAATCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCATGACGCCTTTT
1 C-TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCATGATGCCTTTT
414173 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAG
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAG
414219 GGCAGGACAC
Statistics
Matches: 148, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
59 9 0.06
60 28 0.19
61 102 0.69
62 5 0.03
63 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (61 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCATGATGCCTTTT
Found at i:415246 original size:20 final size:20
Alignment explanation
Indices: 415221--415266 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
415211 CTAGGAAGTT
*
415221 TACATTTTGCATTGTATTGA
1 TACATTTTGCATTGTATCGA
415241 TACATTTTGCATTGTATCGA
1 TACATTTTGCATTGTATCGA
415261 TACATT
1 TACATT
415267 GTATCGATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (20 bp):
TACATTTTGCATTGTATCGA
Found at i:415268 original size:13 final size:13
Alignment explanation
Indices: 415250--415313 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 13
415240 ATACATTTTG
415250 CATTGTATCGATA
1 CATTGTATCGATA
415263 CATTGTATCGATA
1 CATTGTATCGATA
415276 CATTG---C--T-
1 CATTGTATCGATA
415283 CATTGTATCGATA
1 CATTGTATCGATA
*
415296 CATTGTATTGATA
1 CATTGTATCGATA
415309 CATTG
1 CATTG
415314 CTCATTGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
7 5 0.11
8 1 0.02
10 2 0.05
12 1 0.02
13 35 0.80
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:415276 original size:33 final size:33
Alignment explanation
Indices: 415230--415328 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
415220 TTACATTTTG
*
415230 CATTGTATTGATACATT-TTGCATTGTATCGATA
1 CATTGTATTGATACATTGCT-CATTGTATCGATA
*
415263 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATTGATACATTGCTCATTGTATCGATA
415296 CATTGTATTGATACATTGCTCATTGTATCGATA
1 CATTGTATTGATACATTGCTCATTGTATCGATA
415329 AATTTTACAA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
33 61 0.98
34 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
CATTGTATTGATACATTGCTCATTGTATCGATA
Found at i:415288 original size:20 final size:20
Alignment explanation
Indices: 415263--415352 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
415253 TGTATCGATA
415263 CATTGTATCGATACATTGCT
1 CATTGTATCGATACATTGCT
415283 CATTGTATCGATACATTG-T
1 CATTGTATCGATACATTGCT
415302 -A---T-T-GATACATTGCT
1 CATTGTATCGATACATTGCT
* *
415316 CATTGTATCGATAAATT-TT
1 CATTGTATCGATACATTGCT
*
415335 ACAATGTATCGATACATT
1 -CATTGTATCGATACATT
415353 CAAGCATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.16
14 2 0.03
15 2 0.03
18 2 0.03
19 3 0.05
20 40 0.69
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (20 bp):
CATTGTATCGATACATTGCT
Found at i:423802 original size:22 final size:22
Alignment explanation
Indices: 423776--423826 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
423766 ATTTTGGCTA
423776 TTTTCTTCCTACTTCAGGTCAT
1 TTTTCTTCCTACTTCAGGTCAT
**
423798 TTTTCTTCCTACTTTGGGTCAT
1 TTTTCTTCCTACTTCAGGTCAT
*
423820 TTCTCTT
1 TTTTCTT
423827 TTGCTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.25, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTTCTTCCTACTTCAGGTCAT
Found at i:424833 original size:13 final size:13
Alignment explanation
Indices: 424815--424841 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
424805 AAGGTGAGCA
424815 CATAGTGGGGTTT
1 CATAGTGGGGTTT
424828 CATAGTGGGGTTT
1 CATAGTGGGGTTT
424841 C
1 C
424842 TCTATGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.11, G:0.37, T:0.37
Consensus pattern (13 bp):
CATAGTGGGGTTT
Found at i:426944 original size:14 final size:15
Alignment explanation
Indices: 426925--426957 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
426915 GTTAAAATTT
426925 TAAATATGAT-TATA
1 TAAATATGATATATA
426939 TAAATATGATATATA
1 TAAATATGATATATA
426954 TAAA
1 TAAA
426958 ATATAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
TAAATATGATATATA
Found at i:427555 original size:16 final size:16
Alignment explanation
Indices: 427500--427556 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
427490 CTAGTTAATA
* *
427500 TAAATAAAAATATTTA
1 TAAATAATAATATTTT
* *
427516 AAAATAATATTATATTCT
1 TAAATAATA--ATATTTT
*
427534 TGAATAATAATATTTT
1 TAAATAATAATATTTT
427550 TAAATAA
1 TAAATAA
427557 AACTTTTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 19 0.61
18 12 0.39
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
TAAATAATAATATTTT
Found at i:433045 original size:15 final size:15
Alignment explanation
Indices: 433025--433083 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
433015 TTAAATTATA
*
433025 TTAAATTTTAATTTT
1 TTAAATTTGAATTTT
**
433040 TTAAATTT-ATATAACT
1 TTAAATTTGA-AT-TTT
433056 TTAAATTTGAATTTT
1 TTAAATTTGAATTTT
433071 TTAAATTTGAATT
1 TTAAATTTGAATT
433084 CGGACAAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 1 0.03
15 24 0.65
16 11 0.30
17 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (15 bp):
TTAAATTTGAATTTT
Found at i:433047 original size:31 final size:31
Alignment explanation
Indices: 433012--433083 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
433002 GATTATTTCG
*
433012 AATTTAAATTA-TATTAAATTTTAATTTTTTA
1 AATTTAAATTACT-TTAAATTTGAATTTTTTA
* *
433043 AATTTATATAACTTTAAATTTGAATTTTTTA
1 AATTTAAATTACTTTAAATTTGAATTTTTTA
*
433074 AATTTGAATT
1 AATTTAAATT
433084 CGGACAAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (31 bp):
AATTTAAATTACTTTAAATTTGAATTTTTTA
Found at i:433062 original size:25 final size:25
Alignment explanation
Indices: 433014--433063 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
433004 TTATTTCGAA
*
433014 TTTAAATTATATTAAATTTTAATTT
1 TTTAAATTATATTAAATTTAAATTT
*
433039 TTTAAATT-TATATAACTTTAAATTT
1 TTTAAATTATAT-TAAATTTAAATTT
433064 GAATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAAATTATATTAAATTTAAATTT
Found at i:436210 original size:20 final size:21
Alignment explanation
Indices: 436163--436215 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
436153 GCCAATGACC
**
436163 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
436184 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
436204 TGTATCGATACA
1 TGTATCGATACA
436216 ATGTATCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:444870 original size:13 final size:13
Alignment explanation
Indices: 444852--444876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
444842 CATTTTATGG
444852 TGTATCGATACAA
1 TGTATCGATACAA
444865 TGTATCGATACA
1 TGTATCGATACA
444877 TGCTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:444975 original size:20 final size:21
Alignment explanation
Indices: 444928--444980 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
444918 GCCAATGACC
**
444928 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
444949 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
444969 TGTATCGATACA
1 TGTATCGATACA
444981 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:444986 original size:13 final size:13
Alignment explanation
Indices: 444968--444992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
444958 ACATTTGGTC
444968 ATGTATCGATACA
1 ATGTATCGATACA
444981 ATGTATCGATAC
1 ATGTATCGATAC
444993 TATGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:445534 original size:17 final size:17
Alignment explanation
Indices: 445512--445546 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
445502 GTGATTATCT
445512 CTAAGAAT-AAGAATTCA
1 CTAAGAATGAA-AATTCA
445529 CTAAGAATGAAAATTCA
1 CTAAGAATGAAAATTCA
445546 C
1 C
445547 ATACAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.23
Consensus pattern (17 bp):
CTAAGAATGAAAATTCA
Found at i:446502 original size:61 final size:60
Alignment explanation
Indices: 446413--446529 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 60
446403 ATTTTAGTAA
* *
446413 TTTTTATTATTTTAAGGCTATTTAGGTTATTTGACATATTCTAAAGTCATTTTAAACTTT
1 TTTTTATTATTTTAAGACTATTTAGGTTATTTGACATAATCTAAAGTCATTTTAAACTTT
* * * * *
446473 TTTTTTTTCATTTTATGACTATTTAGGTTATTTTATATAATCTAAGGTCATTTTAAA
1 TTTTTATT-ATTTTAAGACTATTTAGGTTATTTGACATAATCTAAAGTCATTTTAAA
446530 AATTTTCATC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 7 0.14
61 42 0.86
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (60 bp):
TTTTTATTATTTTAAGACTATTTAGGTTATTTGACATAATCTAAAGTCATTTTAAACTTT
Found at i:446810 original size:2 final size:2
Alignment explanation
Indices: 446803--446834 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
446793 TTTAATGATG
446803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
446835 CCATTATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:447034 original size:78 final size:78
Alignment explanation
Indices: 446827--447090 Score: 221
Period size: 78 Copynumber: 3.4 Consensus size: 78
446817 ATATATATAT
* * * * * * *
446827 ATATATATCCATTATGGTTATTTAAGTAAT-GATACAATAAAACCAAGTCACTAAGGTCATGT--
1 ATATATGTCCATTAGGGTCATTTAAGTAATAG-CACATTAAAACCAAGTCTCTAAGGTCATCTAA
* *
446889 GCATGCTTTCATGTTG
65 GTAT--TTTCATGTCG
* * *
446905 ATATATGTCCACTAGGGTCGTTTAAGTAATAGTACATTAAAACCAAGTCTCTAAGGTCATCTAAG
1 ATATATGTCCATTAGGGTCATTTAAGTAATAGCACATTAAAACCAAGTCTCTAAGGTCATCTAAG
*
446970 TATTTTCATGTCA
66 TATTTTCATGTCG
* * * ** * * * *
446983 ATATATATCCATTAGGGTCATTTCAGTAATGGCACATTAAAAATGAA-TCTCTAGGGTCTTTTTA
1 ATATATGTCCATTAGGGTCATTTAAGTAATAGCACATT-AAAACCAAGTCTCTAAGGTCATCTAA
*
447047 GTATTTTCATATCG
65 GTATTTTCATGTCG
* * * *
447061 ATACATGTCCATTAAGGTCACTTAGGTAAT
1 ATATATGTCCATTAGGGTCATTTAAGTAAT
447091 GGTGTGTCAA
Statistics
Matches: 151, Mismatches: 31, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
78 141 0.93
79 7 0.05
80 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (78 bp):
ATATATGTCCATTAGGGTCATTTAAGTAATAGCACATTAAAACCAAGTCTCTAAGGTCATCTAAG
TATTTTCATGTCG
Found at i:451751 original size:51 final size:51
Alignment explanation
Indices: 451696--451792 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
451686 CAAACCTGGC
* **
451696 TTTATTTCTAAAATATTAATTTCTCACAATCAGGGATACTCCAACCCCTAT
1 TTTATTTCTAAAACACCAATTTCTCACAATCAGGGATACTCCAACCCCTAT
* * * *
451747 TTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCTAACC
1 TTTATTTCTAAAACACCAATTTCTCACAATCAGGGATACTCCAACC
451793 TTGTTATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (51 bp):
TTTATTTCTAAAACACCAATTTCTCACAATCAGGGATACTCCAACCCCTAT
Found at i:451811 original size:79 final size:79
Alignment explanation
Indices: 451728--451947 Score: 250
Period size: 79 Copynumber: 2.8 Consensus size: 79
451718 CTCACAATCA
* * *
451728 GGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCTAA-C
1 GGGATACTCCAACCCCTATTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAATC
* * *
451792 CTTGTTATTTTTGCG
66 C-CGTTATTTTCGAG
*** * * *
451807 GGGATACTCCAA-CCCTGGCCTTATTTCTGAAGCATCGATTTTTCACAATCGGGGATACTCCAAT
1 GGGATACTCCAACCCCT-ATTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAAT
451871 CCCGTTATTTTCGAG
65 CCCGTTATTTTCGAG
* *
451886 GGGATACTCCAACCTCGATTTTATTT-TCAAAACATCGA-TTTTCTATAATCGGGGATACTCCA
1 GGGATACTCCAACCCCTATTTTATTTCT-AAAACATCGATTTTTC-ATAATCGGGGATACTCCA
451948 GCTGCATCCC
Statistics
Matches: 116, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
78 10 0.09
79 102 0.88
80 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (79 bp):
GGGATACTCCAACCCCTATTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAATC
CCGTTATTTTCGAG
Found at i:451853 original size:130 final size:129
Alignment explanation
Indices: 451467--451869 Score: 535
Period size: 130 Copynumber: 3.1 Consensus size: 129
451457 TTTCATCTCG
* * * *
451467 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCATAATTGGGGATACTCTAATC
1 GGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCTAAT-
* *
451532 CCT-TTATTTTCGAGGAGATACTCCAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAATC
65 CCTGTTATTTTTGAGGGGATACTCCAACCT-GGCTTTATTTCTAAAATATTGATTTCTCACAATC
451596 A
129 A
* * *
451597 GGGATACTCCAA-CCCTAATTTTATTTCTAAAAGACCAATCTTTTCACAATCAGGGATACT-TCA
1 GGGATACTCCAACCCCT-ATTTTATTTCTAAAACACCAAT-TTTTCATAATCGGGGATACTCT-A
* *
451660 ATCCTGTTATTTCTGAGGGGATACTCCAAACCTGGCTTTATTTCTAAAATATTAATTTCTCACAA
63 ATCCTGTTATTTTTGAGGGGATACTCC-AACCTGGCTTTATTTCTAAAATATTGATTTCTCACAA
451725 TCA
127 TCA
451728 GGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCTAA-C
1 GGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCTAATC
* * * ** * *
451792 CTTGTTATTTTTGCGGGGATACTCCAACCCTGGCCTTATTTCTGAAGCATCGATTTTTCACAATC
66 C-TGTTATTTTTGAGGGGATACTCCAA-CCTGGCTTTATTTCTAAAATATTGATTTCTCACAATC
*
451857 G
129 A
451858 GGGATACTCCAA
1 GGGATACTCCAA
451870 TCCCGTTATT
Statistics
Matches: 240, Mismatches: 24, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
129 7 0.03
130 118 0.49
131 106 0.44
132 9 0.04
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (129 bp):
GGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCTAATC
CTGTTATTTTTGAGGGGATACTCCAACCTGGCTTTATTTCTAAAATATTGATTTCTCACAATCA
Found at i:456198 original size:13 final size:13
Alignment explanation
Indices: 456158--456210 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
456148 CCGTTACAAG
456158 CAATGTATCGATA
1 CAATGTATCGATA
456171 C-AT-T-TC-AT-
1 CAATGTATCGATA
456179 C-ATGTATCGATA
1 CAATGTATCGATA
456191 CAATGTATCGATA
1 CAATGTATCGATA
*
456204 CATTGTA
1 CAATGTA
456211 CCATGTATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 3 0.09
9 3 0.09
10 4 0.12
11 3 0.09
12 3 0.09
13 18 0.53
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:456198 original size:33 final size:33
Alignment explanation
Indices: 456158--456226 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
456148 CCGTTACAAG
*
456158 CAATGTATCGATACATT-TCATCATGTATCGATA
1 CAATGTATCGATACATTGT-ACCATGTATCGATA
456191 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
456224 CAA
1 CAA
456227 ACAGTAGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGATA
Found at i:456302 original size:19 final size:20
Alignment explanation
Indices: 456255--456305 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
456245 CTGCCAATCT
***
456255 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTAAA
*
456275 CATGCATCGATACAA-TAAA
1 CATGTATCGATACAATTAAA
456294 CATGTATCGATA
1 CATGTATCGATA
456306 TACAAAGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:456859 original size:21 final size:21
Alignment explanation
Indices: 456834--456906 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
456824 AGTTTTCATT
* *
456834 TTTCTCCCCATAATTAAAGAA
1 TTTCTCCCCTTAATAAAAGAA
* *
456855 TTTCTCTCCTTTAA-AAAAAAA
1 TTTCTC-CCCTTAATAAAAGAA
* *
456876 TTTCTCCCCCTTAATCAAAGCA
1 TTTCT-CCCCTTAATAAAAGAA
456898 TTTCTCCCC
1 TTTCTCCCC
456907 CATTGTCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
21 26 0.63
22 15 0.37
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.36
Consensus pattern (21 bp):
TTTCTCCCCTTAATAAAAGAA
Found at i:465007 original size:13 final size:12
Alignment explanation
Indices: 464969--465012 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 12
464959 GTTACAAGCA
464969 ATGTATCGATAC
1 ATGTATCGATAC
464981 AT-T-TC-AT-C
1 ATGTATCGATAC
464989 ATGTATCGATAC
1 ATGTATCGATAC
465001 AATGTATCGATA
1 -ATGTATCGATA
465013 TATTGTACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
8 3 0.11
9 3 0.11
10 4 0.15
11 3 0.11
12 3 0.11
13 11 0.41
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:465007 original size:33 final size:33
Alignment explanation
Indices: 464967--465035 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
464957 CCGTTACAAG
*
464967 CAATGTATCGATACATT-TCATCATGTATCGATA
1 CAATGTATCGATACATTGT-ACCATGTATCGATA
*
465000 CAATGTATCGATATATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
465033 CAA
1 CAA
465036 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGATA
Found at i:465108 original size:19 final size:19
Alignment explanation
Indices: 465064--465119 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
465054 CTGCCAATCT
**
465064 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
465084 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
465103 CATGTATCGATACAATG
1 CATGTATCGATACAATG
465120 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:465122 original size:13 final size:13
Alignment explanation
Indices: 465104--465130 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
465094 TACAATGAAC
465104 ATGTATCGATACA
1 ATGTATCGATACA
465117 ATGTATCGATACA
1 ATGTATCGATACA
465130 A
1 A
465131 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:474164 original size:11 final size:11
Alignment explanation
Indices: 474148--474172 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
474138 CCCACCTTTT
474148 AAAAAAAAACA
1 AAAAAAAAACA
474159 AAAAAAAAACA
1 AAAAAAAAACA
474170 AAA
1 AAA
474173 CAAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:474172 original size:16 final size:16
Alignment explanation
Indices: 474148--474182 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
474138 CCCACCTTTT
474148 AAAAAAAAACAAA-AA
1 AAAAAAAAACAAAGAA
474163 AAAAACAAAACAAAGAA
1 AAAAA-AAAACAAAGAA
474180 AAA
1 AAA
474183 GGAGAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 8 0.44
17 5 0.28
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAGAA
Found at i:475532 original size:62 final size:61
Alignment explanation
Indices: 475286--476202 Score: 1034
Period size: 61 Copynumber: 15.1 Consensus size: 61
475276 GAGCAGGATG
* * * * * * *
475286 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTTCAAGGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * * * * *
475347 CCTTTTAAAACCTACACAAGTTGGTGGTACTTTCCAGTCCTTAAAGACCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * *
475408 CCTTTTAAAGCCTACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGTAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * * * *
475468 CCTTTTAAATCCCGCATAAGTTGCTGGCACTTTGCTAGTCCTCAAAGAGTAGGATGTCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CTAGTCCTCAAAGAGCAGGATGCCTTTT
* * *
475530 CCTTTTAAAGCCCATACAAGTTGGTGGCACTTTTCTAATCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
475592 CCTTTCAAAGCCCACATAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * **
475653 CCTTTTAAAGCCTACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* *
475715 CCTTTAAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAAGATG-CTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
475775 -C----AAAGCCCACACAAGTTGGTGGCACATTC-AGTCCTCAAAGAGCAGAACGTCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
*
475830 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGGAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
475892 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGAATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTT-T
* * * *
475953 CCTTTTAAAGACCACACAAGTTGATGGCACTTT-TCAGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCT-AGTCCTCAAAGAGCAGGATGCCTTTT
** * * * *
476014 CCTTTTAAAGCTTACACAAGTTGGTGGTACCTTCCAGTCCTCAAAGAGCAAGATG-C-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * * * **
476073 CTCTTTGCAAAGGCCACACAAGTTGGTGGCACCTTCTAGTCCTTAAAGAGTAGGACACCTTTT
1 C-CTTT-TAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
** * * * *
476136 -CTTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTAGTCCTTAAAGAACAGGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
476197 CCTTTT
1 CCTTTT
476203 CTCCTTTGTC
Statistics
Matches: 730, Mismatches: 103, Indels: 45
0.83 0.12 0.05
Matches are distributed among these distances:
54 21 0.03
55 28 0.04
56 1 0.00
59 4 0.01
60 87 0.12
61 363 0.50
62 219 0.30
63 7 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
Found at i:476255 original size:44 final size:42
Alignment explanation
Indices: 476198--476427 Score: 144
Period size: 44 Copynumber: 5.5 Consensus size: 42
476188 ACGCCTTTTC
*
476198 CTTTTCTCCTTTGTCCTCAAAGACAGGACATATTTCATTTCCTT
1 CTTTTC-CCTTTGTCCTCAAAGACAGGACACA-TTCATTTCCTT
* * * *
476242 CTTTTCCCTTTTGTCCTCAAAG--AGCA-AGATGCCTTT--TT
1 CTTTTCCC-TTTGTCCTCAAAGACAGGACACATTCATTTCCTT
* *
476280 -TTTTCCCTTTATCCTCAAAGTGCAGGACACACTTCATTTCCTT
1 CTTTTCCCTTTGTCCTCAAAG-ACAGGACACA-TTCATTTCCTT
* *
476323 CTTTTCCCTTCTGTTCTCAAAGAGCAGGATGCAC-TTTA-TTCTCTT
1 CTTTTCCCTT-TGTCCTCAAAGA-CAGGA--CACATTCATTTC-CTT
* * *
476368 -TTTT-CCTTTGTCTTCAAAAAGCAGGACACATTTAATTTCC-T
1 CTTTTCCCTTTGTCCTCAAAGA-CAGGACACA-TTCATTTCCTT
*
476409 -TTTT-CCTTTGTCTTCAAAG
1 CTTTTCCCTTTGTCCTCAAAG
476428 GGTATGATGC
Statistics
Matches: 151, Mismatches: 18, Indels: 37
0.73 0.09 0.18
Matches are distributed among these distances:
36 12 0.08
37 7 0.05
38 2 0.01
39 3 0.02
40 10 0.07
41 26 0.17
42 22 0.15
43 11 0.07
44 35 0.23
45 20 0.13
47 3 0.02
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.43
Consensus pattern (42 bp):
CTTTTCCCTTTGTCCTCAAAGACAGGACACATTCATTTCCTT
Found at i:476316 original size:81 final size:82
Alignment explanation
Indices: 476167--476409 Score: 256
Period size: 81 Copynumber: 2.9 Consensus size: 82
476157 TGGTGGCACT
* * * * * *
476167 TTTTAGTCCTTAAAGAACAGGACGCCTTTTCCTTTTCTCCTTTGTCCTCAAAGACAGGACATATT
1 TTTT-GTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCTCCTTTATCCTCAAAGACAGGACACACT
476232 TCATTTCCTTCTTTTCCC
65 TCATTTCCTTCTTTTCCC
* * *
476250 TTTTGTCCTCAAAGAGCAAGATGCCTTTT-TTTTTC-CCTTTATCCTCAAAGTGCAGGACACACT
1 TTTTGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCTCCTTTATCCTCAAAG-ACAGGACACACT
476313 TCATTTCCTTCTTTTCCC
65 TCATTTCCTTCTTTTCCC
* * * * * *
476331 TTCTGTTCTCAAAGAGCAGGATGCACTTTATTCTCTTTTTTCCTTTGTCTTCAAAAAGCAGGACA
1 TTTTGTCCTCAAAGAGCAGGATGC-C-TT-TTC-CTTTTCTCCTTTATCCTCAAAGA-CAGGACA
* *
476396 CATTTAATTTCCTT
61 CACTTCATTTCCTT
476410 TTTCCTTTGT
Statistics
Matches: 132, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
80 14 0.11
81 53 0.40
82 22 0.17
83 6 0.05
84 2 0.02
86 4 0.03
87 31 0.23
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (82 bp):
TTTTGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCTCCTTTATCCTCAAAGACAGGACACACTT
CATTTCCTTCTTTTCCC
Found at i:476344 original size:45 final size:43
Alignment explanation
Indices: 476278--476427 Score: 132
Period size: 45 Copynumber: 3.5 Consensus size: 43
476268 AGATGCCTTT
* * * *
476278 TTTTTTCCCTTTATCCTCAAAGTGCAGGACACACTTCATTTCC
1 TTTTTTCCCTTTGTTCTCAAAGAGCAGGACACACTTAATTTCC
** *
476321 TTCTTTTCCCTTCTGTTCTCAAAGAGCAGGATGCACTTTA-TTCTC
1 TT-TTTTCCCTT-TGTTCTCAAAGAGCAGGACACACTTAATTTC-C
* *
476366 TTTTTT-CCTTTG-TCTTCAAAAAGCAGGACACATTTAATTTCC
1 TTTTTTCCCTTTGTTC-TCAAAGAGCAGGACACACTTAATTTCC
476408 -TTTTT-CCTTTG-TCTTCAAAG
1 TTTTTTCCCTTTGTTC-TCAAAG
476428 GGTATGATGC
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
41 21 0.23
42 20 0.22
43 9 0.10
44 16 0.18
45 24 0.27
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (43 bp):
TTTTTTCCCTTTGTTCTCAAAGAGCAGGACACACTTAATTTCC
Found at i:476424 original size:41 final size:41
Alignment explanation
Indices: 476194--476517 Score: 186
Period size: 41 Copynumber: 7.8 Consensus size: 41
476184 CAGGACGCCT
* *
476194 TTTCCTTTTCTCCTTTGTCCTCAAAGA-CAGGACATATTTCA
1 TTTCCTTTT-TCCTTTGTCTTCAAAGAGCAGGACACATTTCA
* * ** *
476235 TTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAAGATGC-CTT--
1 TTTCC-T-TTTT-CC-TTTGTCTTCAAAGAGCAGGACACATTTCA
* * * * *
476277 TTT--TTTTCCCTTTATCCTCAAAGTGCAGGACACACTTCA
1 TTTCCTTTTTCCTTTGTCTTCAAAGAGCAGGACACATTTCA
476316 TTTCCTTCTTTTCCCTTCTGT-TCTCAAAGAGCAGGATGCAC-TTT-A
1 TTTCC-T-TTTT-CCTT-TGTCT-TCAAAGAGCAGGA--CACATTTCA
* * *
476361 TTCTCTTTTTTCCTTTGTCTTCAAAAAGCAGGACACATTTAA
1 TT-TCCTTTTTCCTTTGTCTTCAAAGAGCAGGACACATTTCA
* * * ** *
476403 TTTCCTTTTTCCTTTGTCTTCAAAGGGTATGATGCATTTTA
1 TTTCCTTTTTCCTTTGTCTTCAAAGAGCAGGACACATTTCA
* * *
476444 TTTCTTTTTTCCTTTGTCCTT-AAGGAGCAGGACCCATTTCA
1 TTTCCTTTTTCCTTTGT-CTTCAAAGAGCAGGACACATTTCA
* *
476485 TTCTCC-TTTT-CTTTAATCCTCAAAGAGCAGGAC
1 TT-TCCTTTTTCCTTT-GTCTTCAAAGAGCAGGAC
476518 GCCCCCTTTT
Statistics
Matches: 220, Mismatches: 38, Indels: 50
0.71 0.12 0.16
Matches are distributed among these distances:
36 18 0.08
37 5 0.02
38 3 0.01
39 4 0.02
40 9 0.04
41 86 0.39
42 29 0.13
43 13 0.06
44 24 0.11
45 22 0.10
46 4 0.02
47 3 0.01
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (41 bp):
TTTCCTTTTTCCTTTGTCTTCAAAGAGCAGGACACATTTCA
Found at i:476473 original size:82 final size:85
Alignment explanation
Indices: 476278--476494 Score: 237
Period size: 82 Copynumber: 2.5 Consensus size: 85
476268 AGATGCCTTT
* * * *
476278 TTTTTTCCCTTTATCCTCAAAGTGCAGGACACACTTCATTTCCTTCTTTTCCCTTCTGTTCTCAA
1 TTTTTT-CCTTTGTCCTTAAAGAGCAGGACACATTTCATTTCC-T-TTTTCCCTTCTGTTCTCAA
476343 AGAGCAGGATGCACTTTATTCTC
63 AGAGCAGGATGCACTTTATTCTC
* *
476366 TTTTTTCCTTTGT-CTTCAAAAAGCAGGACACATTTAATTTCCTTTTT-CCTT-TG-TCTTCAAA
1 TTTTTTCCTTTGTCCTT-AAAGAGCAGGACACATTTCATTTCCTTTTTCCCTTCTGTTC-TCAAA
* * * *
476427 GGGTATGATGCATTTTATT-TC
64 GAGCAGGATGCACTTTATTCTC
* *
476448 TTTTTTCCTTTGTCCTTAAGGAGCAGGACCCATTTCATTCTCCTTTT
1 TTTTTTCCTTTGTCCTTAAAGAGCAGGACACATTTCATT-TCCTTTT
476495 CTTTAATCCT
Statistics
Matches: 111, Mismatches: 14, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
82 35 0.32
83 32 0.29
84 4 0.04
85 4 0.04
86 3 0.03
87 27 0.24
88 6 0.05
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (85 bp):
TTTTTTCCTTTGTCCTTAAAGAGCAGGACACATTTCATTTCCTTTTTCCCTTCTGTTCTCAAAGA
GCAGGATGCACTTTATTCTC
Found at i:477126 original size:13 final size:13
Alignment explanation
Indices: 477108--477135 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
477098 ACATTGTTCT
477108 TTGTATCGATACA
1 TTGTATCGATACA
477121 TTGTATCGATACA
1 TTGTATCGATACA
477134 TT
1 TT
477136 CTGGGTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:477175 original size:62 final size:63
Alignment explanation
Indices: 477056--477183 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 63
477046 ATACATTATT
* * * **
477056 CATTTTATCGACACATTTTGGGTTTTACCCAGATGTATCGATACATTGTTCTTTGTATCGATA
1 CATTGTATCGACACATTCTGGGTTTTACCCAGATATATCGATACATTGTTCAATGTATCGATA
* * * *
477119 CATTGTATCGATACATTCTGGG-TTTACCTAGATATATTGATACATTTTTCAATGTATCGATA
1 CATTGTATCGACACATTCTGGGTTTTACCCAGATATATCGATACATTGTTCAATGTATCGATA
477181 CAT
1 CAT
477184 CCAGGCATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
62 37 0.66
63 19 0.34
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (63 bp):
CATTGTATCGACACATTCTGGGTTTTACCCAGATATATCGATACATTGTTCAATGTATCGATA
Found at i:479819 original size:79 final size:79
Alignment explanation
Indices: 479736--479885 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
479726 TCTCACAGTC
*
479736 GGGGATACTCTAACCCC-TATTTTATTTCTAAAACACCAAATTTTC-ACAATCGAGGATATTCCA
1 GGGGATACTCTAACCCCGT-TTTTATTTCTAAAACACC-AATTTTCTACAATCGAGGATACTCCA
479799 ACCCCGTTATTTTCGA
64 ACCCCGTTATTTTCGA
* * * * *
479815 GGGGATACTCTAACCCCGTTTTTATTTTTAAAACACCGATTTTCTATAATCGGGGATACTCCAGC
1 GGGGATACTCTAACCCCGTTTTTATTTCTAAAACACCAATTTTCTACAATCGAGGATACTCCAAC
479880 CCCGTT
66 CCCGTT
479886 GTTATCCCCA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
78 6 0.10
79 56 0.89
80 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCTAACCCCGTTTTTATTTCTAAAACACCAATTTTCTACAATCGAGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:479840 original size:130 final size:130
Alignment explanation
Indices: 479478--479877 Score: 477
Period size: 130 Copynumber: 3.1 Consensus size: 130
479468 TTCATCTCGA
* * * * * * *
479478 GGATACTCCAACCTCGATTTTTTTTCCAAAACATCAATTTTTTATAATCG-GGATACTCTAATCC
1 GGATACTCCAACCTCTATTTTATTTCTAAAACACCAAATTTTTACAATCGAGGATACTCCAA-CC
* * *
479542 CC-TTATTTTCAAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATCG
65 CCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTTTAAAATATTGATTTCTCACAATCG
479606 G
130 G
* * *
479607 GGAAACTCCAA-CTCTAATTTTATTTCTAAAAAACCAATCTTTTTACAATCGAGGATACTCCAAC
1 GGATACTCCAACCTCT-ATTTTATTTCTAAAACACCAA-ATTTTTACAATCGAGGATACTCCAAC
* * *
479671 CCTGTTA-TTTCTGAGGGGATACTCCAACCCCGACTTTATTTTTGAAATATTGATTTCTCACAGT
64 CCCGTTATTTTC-GAGGGGATACTCCAACCCCGACTTTATTTTTAAAATATTGATTTCTCACAAT
479735 CGG
128 CGG
* * * *
479738 GGATACTCTAACCCCTATTTTATTTCTAAAACACCAAATTTTCACAATCGAGGATATTCCAACCC
1 GGATACTCCAACCTCTATTTTATTTCTAAAACACCAAATTTTTACAATCGAGGATACTCCAACCC
* ** * ** *
479803 CGTTATTTTCGAGGGGATACTCTAACCCCGTTTTTATTTTTAAAACACCGATTT-TCTATAATCG
66 CGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTTTAAAATATTGATTTCTC-ACAATCG
479867 G
130 G
479868 GGATACTCCA
1 GGATACTCCA
479878 GCCCCGTTGT
Statistics
Matches: 230, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
128 3 0.01
129 29 0.13
130 99 0.43
131 96 0.42
132 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (130 bp):
GGATACTCCAACCTCTATTTTATTTCTAAAACACCAAATTTTTACAATCGAGGATACTCCAACCC
CGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTTTAAAATATTGATTTCTCACAATCGG
Found at i:493236 original size:21 final size:20
Alignment explanation
Indices: 493215--493254 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
493205 TCTAGAATGA
493215 AAATATATCAATACATTTTG
1 AAATATATCAATACATTTTG
* * *
493235 AATTGTATCGATACATTTTG
1 AAATATATCAATACATTTTG
493255 GGTTTTGACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (20 bp):
AAATATATCAATACATTTTG
Found at i:493300 original size:51 final size:51
Alignment explanation
Indices: 493215--493334 Score: 136
Period size: 51 Copynumber: 2.3 Consensus size: 51
493205 TCTAGAATGA
* * *
493215 AAATATATCAATACATTTTGAATTGTATCGATACATT-TTGGGTTTTG-ACC
1 AAATGTATC-ATACATTCTGAATTATATCGATACATTCTTGGGTTTTGAACC
* * *
493265 TAAATGTATCACTACATTCTGCATTATATCTATACATTCTTGGTTTTTGAACC
1 -AAATGTATCA-TACATTCTGAATTATATCGATACATTCTTGGGTTTTGAACC
493318 AAATGTATCGATACATT
1 AAATGTATC-ATACATT
493335 GAAATGCATC
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
50 1 0.02
51 30 0.51
52 24 0.41
53 4 0.07
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (51 bp):
AAATGTATCATACATTCTGAATTATATCGATACATTCTTGGGTTTTGAACC
Found at i:495712 original size:27 final size:27
Alignment explanation
Indices: 495681--495751 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
495671 TTTGTCCATC
495681 GGGGATACTCCAACCCCTTTTTCTGAA
1 GGGGATACTCCAACCCCTTTTTCTGAA
*
495708 GGGGATACTCCAACCCTTTTTTCTGAA
1 GGGGATACTCCAACCCCTTTTTCTGAA
495735 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
495752 ACTTTTAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.27
Consensus pattern (27 bp):
GGGGATACTCCAACCCCTTTTTCTGAA
Found at i:498825 original size:79 final size:79
Alignment explanation
Indices: 498707--499062 Score: 346
Period size: 79 Copynumber: 4.5 Consensus size: 79
498697 ACGGAGTTGA
** * * * *
498707 AGTATCCCTAATGGT-GAAAATTAGTGTTTTAAAAATAAAATCGGGGTTAGAGTATCCCCTTGGA
1 AGTATCCCCGATGGTGGAAAATCAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTAGA
498771 AATAACGAGATTAG
66 AATAACGAGATTAG
* * * * * *
498785 AGTATCTCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCGGGGTTGGAGTGTCCCCTCATA
1 AGTATCCCCGATGGTGGAAAATCAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTAGA
*
498850 AATAAC-AGGATTTG
66 AATAACGA-GATTAG
* * * * *
498864 AGTATCCCCGATAGTGGAAAATCAATGTTTTAGAAATAAAATTGGGTTTGAAGTAT-CCCTTCAG
1 AGTATCCCCGATGGTGGAAAATCAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTT-AG
*
498928 AAATAACGAGGTT-G
65 AAATAACGAGATTAG
* * * * * *
498942 AAGTATCCCCGATGGTGGAAAATCAATGCTTTAGAAATAAAA-CTGAGGTTGGAGCAT-CCTTTT
1 -AGTATCCCCGATGGTGGAAAATCAGTGTTTTAGAAATAAAATC-GGGGTTGGAGTATCCCCTTA
* * *
499005 GAAAATAATGGGGTTAG
64 G-AAATAACGAGATTAG
** *
499022 AGTATCCCCGATGGTGGAAAATTGGTGTTCTAGAAATAAAA
1 AGTATCCCCGATGGTGGAAAATCAGTGTTTTAGAAATAAAA
499063 CATCAATGAA
Statistics
Matches: 229, Mismatches: 41, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
78 19 0.08
79 208 0.91
80 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (79 bp):
AGTATCCCCGATGGTGGAAAATCAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTAGA
AATAACGAGATTAG
Found at i:499011 original size:158 final size:156
Alignment explanation
Indices: 498690--499062 Score: 403
Period size: 158 Copynumber: 2.4 Consensus size: 156
498680 CTATCCTATC
* ** *
498690 GAAAATAACGGAGTTGAAGTATCCCTAATGGT-GAAAATTAGTGTTTTAAAAATAAAATCGGGGT
1 GAAAATAACGGATTTG-AGTATCCCCGATGGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGGT
* * * *
498754 TAGAGTATCCCCTTGGAAATAACGAGATTAGAGTATCTCCGATGGTGAAAAATCAGTGTTTTAGA
65 TAGAGTATCCCCTTAGAAATAACGAGATTAGAGTATCCCCGATGGTGAAAAATCAATGCTTTAGA
* **
498819 AATAAAACCGGGGTTGGAGTGTCCCCT
130 AATAAAACCGAGGTTGGAGCATCCCCT
* * * * *
498846 CATAAATAACAGGATTTGAGTATCCCCGATAGTGGAAAATCAATGTTTTAGAAATAAAAT-TGGG
1 GA-AAATAAC-GGATTTGAGTATCCCCGATGGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGG
* * *
498910 TTTGAAGTAT-CCCTTCAGAAATAACGAGGTT-GAAGTATCCCCGATGGTGGAAAATCAATGCTT
64 TTAG-AGTATCCCCTT-AGAAATAACGAGATTAG-AGTATCCCCGATGGTGAAAAATCAATGCTT
* **
498973 TAGAAATAAAACTGAGGTTGGAGCATCCTTTT
126 TAGAAATAAAACCGAGGTTGGAGCATCC-CCT
* * * * *
499005 GAAAATAATGGGGTTAGAGTATCCCCGATGGTGGAAAATTGGTGTTCTAGAAATAAAA
1 GAAAATAA-CGGATTTGAGTATCCCCGATGGTGGAAAATTAGTGTTTTAGAAATAAAA
499063 CATCAATGAA
Statistics
Matches: 178, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
156 1 0.01
157 31 0.17
158 144 0.81
159 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (156 bp):
GAAAATAACGGATTTGAGTATCCCCGATGGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTT
AGAGTATCCCCTTAGAAATAACGAGATTAGAGTATCCCCGATGGTGAAAAATCAATGCTTTAGAA
ATAAAACCGAGGTTGGAGCATCCCCT
Found at i:501560 original size:20 final size:21
Alignment explanation
Indices: 501535--501581 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
501525 GGCATGTAAT
501535 GATACATTCACT-TATATATC
1 GATACATTCACTGTATATATC
* * *
501555 GATACATTTACTGTTTGTATC
1 GATACATTCACTGTATATATC
501576 GATACA
1 GATACA
501582 AAATGTAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (21 bp):
GATACATTCACTGTATATATC
Found at i:502320 original size:42 final size:41
Alignment explanation
Indices: 502273--502670 Score: 226
Period size: 42 Copynumber: 9.5 Consensus size: 41
502263 TTGCTTTTCA
502273 AGGACAAAGGAAAAAGGAGAATGAAATAG-GTCCTGCTCTTTG
1 AGGACAAAGGAAAAAGGA-AATGAAAT-GCGTCCTGCTCTTTG
* * * * *
502315 AGGACAAAGGAAAAAAAGAAAAAGAAAAGTGTCTTGCTAC-TTG
1 AGGACAAAGG--AAAAAGGAAATGAAATGCGTCCTGCT-CTTTG
* * * *
502358 AGGGCAAAGGGAAAAGG--A-G---TACGTCTTGCT-TTTCG
1 AGGACAAAGGAAAAAGGAAATGAAATGCGTCCTGCTCTTT-G
* * * * * *
502393 ATGACAAAGGAAGAAAGAAAATGAAGTGC-TCTTACTTTTTG
1 AGGACAAAGGAA-AAAGGAAATGAAATGCGTCCTGCTCTTTG
* * * *
502434 AGGATAAAGGGAAAAGAAGGAAATGAAGTGCATCTTGCTCTTTG
1 AGGACAAA-GG-AAA-AAGGAAATGAAATGCGTCCTGCTCTTTG
* * **
502478 AGGACAAAAGGAAAATAAGGAAATAAAATACGTTGTGCTCTTTG
1 AGGAC-AAAGG-AAA-AAGGAAATGAAATGCGTCCTGCTCTTTG
* * *
502522 AGGACAAAAGAAAAAGGAAA-CAAAGTGCGTCCTGATCTTTG
1 AGGACAAAGGAAAAAGGAAATGAAA-TGCGTCCTGCTCTTTG
* * * *
502563 AGGACAAAAGAGAAAAGGAAA-CAAAGTGCGTCCTGCTATTTT
1 AGGACAAAGGA-AAAAGGAAATGAAA-TGCGTCCTGCTCTTTG
* *
502605 AGGACAAAAGGAAAAAGAAGGAAATGAAGTGTGTCCTGCTCTTTG
1 AGGAC-AAAGG--AAA-AAGGAAATGAAATGCGTCCTGCTCTTTG
*
502650 AGGATAAAGGAAATAAGGAAA
1 AGGACAAAGGAAA-AAGGAAA
502671 GTGTCCTGCT
Statistics
Matches: 284, Mismatches: 46, Indels: 52
0.74 0.12 0.14
Matches are distributed among these distances:
34 2 0.01
35 18 0.06
36 4 0.01
38 2 0.01
39 2 0.01
40 3 0.01
41 48 0.17
42 64 0.23
43 49 0.17
44 62 0.22
45 28 0.10
46 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (41 bp):
AGGACAAAGGAAAAAGGAAATGAAATGCGTCCTGCTCTTTG
Found at i:502431 original size:41 final size:44
Alignment explanation
Indices: 502381--502501 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 44
502371 AAGGAGTACG
* * *
502381 TCTTGCTTTTCGATGACAAA-GGAAGA-AAGAAAATGAAGTGC-
1 TCTTACTTTTCGAGGACAAAGGGAAAAGAAGAAAATGAAGTGCA
* * *
502422 TCTTACTTTTTGAGGATAAAGGGAAAAGAAGGAAATGAAGTGCA
1 TCTTACTTTTCGAGGACAAAGGGAAAAGAAGAAAATGAAGTGCA
* * * *
502466 TCTTGCTCTTT-GAGGACAAAAGGAAAATAAGGAAAT
1 TCTTACT-TTTCGAGGACAAAGGGAAAAGAAGAAAAT
502502 AAAATACGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
41 16 0.24
42 5 0.08
43 14 0.21
44 28 0.42
45 3 0.05
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (44 bp):
TCTTACTTTTCGAGGACAAAGGGAAAAGAAGAAAATGAAGTGCA
Found at i:502478 original size:44 final size:43
Alignment explanation
Indices: 502395--502670 Score: 222
Period size: 44 Copynumber: 6.5 Consensus size: 43
502385 GCTTTTCGAT
* * * * * *
502395 GACAAA-GGAAGAAAGAAAATGAAGTGC-TCTTACTTTTTGAG
1 GACAAAGGGAAAAAAGGAAATAAAGTGCGTCCTGCTCTTTGAG
* * * *
502436 GATAAAGGGAAAAGAAGGAAATGAAGTGCATCTTGCTCTTTGAG
1 GACAAAGGGAAAA-AAGGAAATAAAGTGCGTCCTGCTCTTTGAG
* * * **
502480 GACAAAAGGAAAATAAGGAAATAAAATACGTTGTGCTCTTTGAG
1 GACAAAGGGAAAA-AAGGAAATAAAGTGCGTCCTGCTCTTTGAG
* * *
502524 GACAAA-AG-AAAAAGGAAACAAAGTGCGTCCTGATCTTTGAG
1 GACAAAGGGAAAAAAGGAAATAAAGTGCGTCCTGCTCTTTGAG
* * * * *
502565 GACAAA-AGAGAAAAGGAAACAAAGTGCGTCCTGCTATTTTAG
1 GACAAAGGGAAAAAAGGAAATAAAGTGCGTCCTGCTCTTTGAG
* * *
502607 GACAAAAGGAAAAAGAAGGAAATGAAGTGTGTCCTGCTCTTTGAG
1 GAC-AAAGGGAAAA-AAGGAAATAAAGTGCGTCCTGCTCTTTGAG
* *
502652 GATAAA-GGAAATAAGGAAA
1 GACAAAGGGAAAAAAGGAAA
502671 GTGTCCTGCT
Statistics
Matches: 192, Mismatches: 36, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
41 37 0.19
42 47 0.24
43 22 0.11
44 59 0.31
45 27 0.14
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (43 bp):
GACAAAGGGAAAAAAGGAAATAAAGTGCGTCCTGCTCTTTGAG
Found at i:502561 original size:41 final size:42
Alignment explanation
Indices: 502450--502696 Score: 213
Period size: 42 Copynumber: 5.9 Consensus size: 42
502440 AAGGGAAAAG
** * *
502450 AAGGAAATGAAGTGCATCTTGCTCTTTGAGGACAAAAGGAAAAT
1 AAGGAAACAAAGTGCGTCCTGCTCTTTGAGGACAAAA-G-AAAT
* * * **
502494 AAGGAAATAAAATACGTTGTGCTCTTTGAGGACAAAAGAAA-
1 AAGGAAACAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAT
*
502535 AAGGAAACAAAGTGCGTCCTGATCTTTGAGGACAAAAGAGAA-
1 AAGGAAACAAAGTGCGTCCTGCTCTTTGAGGACAAAAGA-AAT
* * *
502577 AAGGAAACAAAGTGCGTCCTGCTATTTTAGGACAAAAGGAAAAAG
1 AAGGAAACAAAGTGCGTCCTGCTCTTTGAGGACAAAA-G--AAAT
** * * *
502622 AAGGAAATGAAGTGTGTCCTGCTCTTTGAGGATAAAGGAAAT
1 AAGGAAACAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAT
502664 AAGG----AAAGT--GTCCTGCTCTTTGAGGACTAAAAG
1 AAGGAAACAAAGTGCGTCCTGCTCTTTGAGGAC-AAAAG
502697 GTGCCACCAA
Statistics
Matches: 171, Mismatches: 26, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
36 17 0.10
37 4 0.02
38 4 0.02
41 33 0.19
42 46 0.27
43 2 0.01
44 34 0.20
45 31 0.18
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (42 bp):
AAGGAAACAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAT
Found at i:502641 original size:87 final size:86
Alignment explanation
Indices: 502430--502670 Score: 265
Period size: 87 Copynumber: 2.8 Consensus size: 86
502420 GCTCTTACTT
* * * *
502430 TTTGAGGATAAAGGGAAAAGAAGGAAATGAAGTGCATCTTGCTCTTTGAGGACAAAAGGAAAATA
1 TTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAA-G-AAATA
* ** *
502495 AGGAAATAAAATACGTTGTGCTC
64 AGGAAACAAAATACGTCCTGCTA
** *
502518 TTTGAGGACAAAA-G-AAA-AAGGAAACAAAGTGCGTCCTGATCTTTGAGGACAAAAGAGAA-AA
1 TTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGA-AATAA
* *
502579 GGAAACAAAGTGCGTCCTGCTA
65 GGAAACAAAATACGTCCTGCTA
* * * *
502601 TTTTAGGACAAAAGGAAAAAGAAGGAAATGAAGTGTGTCCTGCTCTTTGAGGATAAAGGAAATAA
1 TTTGAGGACAAAAGG-AAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAATAA
502666 GGAAA
65 GGAAA
502671 GTGTCCTGCT
Statistics
Matches: 127, Mismatches: 20, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
83 31 0.24
84 4 0.03
85 32 0.25
86 8 0.06
87 41 0.32
88 11 0.09
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.20
Consensus pattern (86 bp):
TTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAATAAG
GAAACAAAATACGTCCTGCTA
Found at i:502770 original size:62 final size:62
Alignment explanation
Indices: 502673--503530 Score: 632
Period size: 62 Copynumber: 14.4 Consensus size: 62
502663 TAAGGAAAGT
* **
502673 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAATTC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
502735 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * * * * *
502797 GTCTTGCTATTTGAGGACTAAAGGGTGCCACCAATTCGTGTGGGCTTTAAAAGGGAAAAGAC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * ** * **
502859 GTCCTGCTCTTTGAGGACT-AA------C-TC--GT-GTG-GGCTTTAAAAAAGAAAAGACATC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAA-A-GGC
* * ** * ** * * * ** * *
502911 TTGCT-CT-TTTAGGATTA--AAGGGTGCCACCAAC-TCGT-GTG-AGCTTTGAAAAG--AAAAG
1 GTCCTGCTCTTT--GAGGACTAAAGG-G-TGCCACCAAC-TCGTGTGGGCTTTAAAAAGAAAAAG
502967 GC
61 GC
* * * * * *
502969 GTCCTACTCTTTAAGGACTAAAGGGTGCCACCAAATCATGTGGGCTTTGAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * * * * * *
503031 GTCCTACTCTTTAAGGACTAAAGGTTGCCACCAACTCGTGTGGACTTTGAAAACAAAAATGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * * * *
503093 ATCCTGCTTTTTTAGGACTAAAAGGTG---------CGTGTGGGCTTCAAAAAGAAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * *
503146 ATCTTGCTCTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * * * * *
503208 AT-TTGCTCTTTGAAGACTAAAGGGTGCCACCAACTCGTGTAGGCTTTAGAAAGGAAAA-G-
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * * * * *
503267 GT-AT-C-C--TAAAGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGT
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * * * *
503324 ATCCTACTCTTTGAGGACTAAAGGGTGTCACCAACTCGTATGGGCTTT-GAAA-AAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * *
503384 ATCCTGCTCTTTGAGGA-TAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAG-AAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * * * * *
503444 GTCCTACTCTTTGAGGACTAAAGGTTGCCACCAACTCGTGTGAG-TTTTAAAAGGAAAAGAC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
* * *
503505 ATCATGCTCTTTGAGGACTAGAGGGT
1 GTCCTGCTCTTTGAGGACTAAAGGGT
503531 AAAAAGGGTG
Statistics
Matches: 638, Mismatches: 113, Indels: 91
0.76 0.13 0.11
Matches are distributed among these distances:
50 15 0.02
51 7 0.01
52 8 0.01
53 43 0.07
54 1 0.00
55 43 0.07
56 1 0.00
57 2 0.00
58 13 0.02
59 37 0.06
60 75 0.12
61 106 0.17
62 287 0.45
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (62 bp):
GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
Found at i:502918 original size:173 final size:171
Alignment explanation
Indices: 502705--503051 Score: 500
Period size: 172 Copynumber: 2.0 Consensus size: 171
502695 AGGTGCCACC
*
502705 AACTCGTGTGGGCTTTAAAAAGAAAAATTCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAAC
1 AACTCGTGTGGGCTTTAAAAAGAAAAA-TCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAAC
* * * * * *
502770 TCGTGTGGGCTTTAAAAAGAAAAAGGCGTCTTGCTATTTGAGGACTAAAGGGTGCCACCAATTCG
65 TCGTGTGAGCTTTAAAAAG-AAAAGGCGTCCTACTATTTAAGGACTAAAGGGTGCCACCAAATCA
* *
502835 TGTGGGCTTT-AAAAGGGAAAAGACGTCCTGCTCTTTGAGGACT
129 TGTGGGCTTTGAAAA-GGAAAAGACGTCCTACTCTTTAAGGACT
* * *
502878 AACTCGTGTGGGCTTTAAAAAAGAAAAGA-CATCTTGCTCTTTTAGGATTAAAGGGTGCCACCAA
1 AACTCGTGTGGGCTTT-AAAAAGAAAA-ATCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAA
* *
502942 CTCGTGTGAGCTTTGAAAAGAAAAGGCGTCCTACTCTTTAAGGACTAAAGGGTGCCACCAAATCA
64 CTCGTGTGAGCTTTAAAAAGAAAAGGCGTCCTACTATTTAAGGACTAAAGGGTGCCACCAAATCA
*
503007 TGTGGGCTTTGAAAAGGAAAAGGCGTCCTACTCTTTAAGGACT
129 TGTGGGCTTTGAAAAGGAAAAGACGTCCTACTCTTTAAGGACT
503050 AA
1 AA
503052 AGGTTGCCAC
Statistics
Matches: 156, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
172 76 0.49
173 69 0.44
174 10 0.06
175 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (171 bp):
AACTCGTGTGGGCTTTAAAAAGAAAAATCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACT
CGTGTGAGCTTTAAAAAGAAAAGGCGTCCTACTATTTAAGGACTAAAGGGTGCCACCAAATCATG
TGGGCTTTGAAAAGGAAAAGACGTCCTACTCTTTAAGGACT
Found at i:502979 original size:61 final size:61
Alignment explanation
Indices: 502878--503530 Score: 662
Period size: 62 Copynumber: 10.9 Consensus size: 61
502868 TTTGAGGACT
* * * * * *
502878 AACTCGTGTGGGCTTTAAAAAAGAAAAGACATCTTGCTCTTTTAGGATTAAAGGGTGCCACC
1 AACTCGTGTGGGCTTT-GAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* * *
502940 AACTCGTGTGAGCTTTGAAAAGAAAAGGCGTCCTACTCTTTAAGGACTAAAGGGTGCCACC
1 AACTCGTGTGGGCTTTGAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* * * * *
503001 AAATCATGTGGGCTTTGAAAAGGAAAAGGCGTCCTACTCTTTAAGGACTAAAGGTTGCCACC
1 AACTCGTGTGGGCTTTGAAAA-GAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* * * * * * *
503063 AACTCGTGTGGACTTTGAAAACAAAAATGCATCCTGCTTTTTTAGGACTAAAAGGTG-----
1 AACTCGTGTGGGCTTTGAAAA-GAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
** * * *
503120 ----CGTGTGGGCTTCAAAAAGAAAAAGGCATCTTGCTCTTTGAGGACTAAAGAGTGCCACC
1 AACTCGTGTGGGCTTTGAAAAG-AAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* * * *
503178 AACTCGTGTGGGCTTTAAAAAGAAAAAGGCAT-TTGCTCTTTGAAGACTAAAGGGTGCCACC
1 AACTCGTGTGGGCTTTGAAAAG-AAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* * * * *
503239 AACTCGTGTAGGCTTTAGAAAGGAAAAGGTATCCTA-------AAGACTAAAAGGTGCCACC
1 AACTCGTGTGGGCTTT-GAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* *
503294 AACTCGTGTGGGCTTTGAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAGGGTGTCACC
1 AACTCGTGTGGGCTTTGAAAAG-AAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* *
503356 AACTCGTATGGGCTTTGAAAA-AAAAGGCATCCTGCTCTTTGAGGA-TAAAGGGTGCCACC
1 AACTCGTGTGGGCTTTGAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* * *
503415 AACTCGTGTAGGCTTTGAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAAAGGTTGCCACC
1 AACTCGTGTGGGCTTTGAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
* * * * * *
503476 AACTCGTGTGAG-TTTTAAAAGGAAAAGACATCATGCTCTTTGAGGACTAGAGGGT
1 AACTCGTGTGGGCTTTGAAAA-GAAAAGGCATCCTACTCTTTGAGGACTAAAGGGT
503531 AAAAAGGGTG
Statistics
Matches: 500, Mismatches: 67, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
53 42 0.08
54 5 0.01
55 46 0.09
59 32 0.06
60 51 0.10
61 157 0.31
62 167 0.33
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (61 bp):
AACTCGTGTGGGCTTTGAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACC
Found at i:503236 original size:238 final size:232
Alignment explanation
Indices: 502677--503502 Score: 890
Period size: 238 Copynumber: 3.5 Consensus size: 232
502667 GAAAGTGTCC
** *
502677 TGCTCTTTGAGGACTAAA-AGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAATTCGTCCTG
1 TGCTCTTTGAGGACTAAAGA-GTGCCACCAACTCGTGTGGGCTTTAAAAAG-AAAAGGCGTCCTA
* * * *
502741 CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGCGTCTTGCTA
64 CTCTTTGAAGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAAAAGGCGTC-TACTC
* * * *
502806 TTTGAGGACTAAAGGGTGCCACCAATTCGTGTGGGCTTT-AAAAGGGAAAAGACGTCCTGCTCTT
127 TTTAAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAG-CATCCTGCTCTT
* *
502870 TGAGGACT--AA-CT-CGTGTGGGCTTTAAAAAAGAAAAGACATCT
189 TGAGGACTAAAAGGTGCGTGTGGGC-TTAAAAAA-AAAAGGCATCT
* * * * *
502912 TGCTCTTTTAGGATTAAAGGGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAGGCGTCCTACT
1 TGCTCTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAGGCGTCCTACT
* *
502977 CTTT-AAGGACTAAAGGGTGCCACCAAATCATGTGGGCTTTGAAAAGGAAAAGGCGTCCTACTCT
66 CTTTGAA-GACTAAAGGGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAAAAGGCGT-CTACTCT
* * * *
503041 TTAAGGACTAAAGGTTGCCACCAACTCGTGTGGACTTTGAAAACAAAAATGCATCCTGCTTTTTT
128 TTAAGGACTAAAGG-TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA-GCATCCTGCTCTTTG
503106 AGGACTAAAAGGTGCGTGTGGGCTTCAAAAAGAAAAAGGCATCT
191 AGGACTAAAAGGTGCGTGTGGGCTT-AAAAA-AAAAAGGCATCT
* * *
503150 TGCTCTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGCAT-TTGC
1 TGCTCTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAG-AAAAGGCGTCCTAC
* *
503214 TCTTTGAAGACTAAAGGGTGCCACCAACTCGTGTAGGCTTTAGAAAGGAAAA-G-G--TA-TC-C
65 TCTTTGAAGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTA-AAAGGAAAAGGCGTCTACTCTT
* * *
503273 TAAAGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGTATCCTACTCTTTGA
129 TAAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA-GCATCCTGCTCTTTGA
* * ** *
503338 GGACTAAAGGGTGTCACCAACTCGTATGGGCTTTGAAAAAAAAGGCATCC
192 GGACTAAAAGGTG---------CGTGTGGGCTTAAAAAAAAAAGGCATCT
* * *
503388 TGCTCTTTGAGGA-TAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAGGCGTCCTACT
1 TGCTCTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAGGCGTCCTACT
* * * *
503452 CTTTGAGGACTAAAGGTTGCCACCAACTCGTGTGAGTTTTAAAAGGAAAAG
66 CTTTGAAGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAG
503503 ACATCATGCT
Statistics
Matches: 503, Mismatches: 61, Indels: 52
0.82 0.10 0.08
Matches are distributed among these distances:
231 63 0.13
232 7 0.01
233 5 0.01
234 118 0.23
235 50 0.10
236 20 0.04
237 77 0.15
238 139 0.28
239 14 0.03
240 10 0.02
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (232 bp):
TGCTCTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAGGCGTCCTACT
CTTTGAAGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAGGCGTCTACTCTTTA
AGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGAC
TAAAAGGTGCGTGTGGGCTTAAAAAAAAAAGGCATCT
Found at i:503289 original size:55 final size:55
Alignment explanation
Indices: 503161--503329 Score: 198
Period size: 55 Copynumber: 3.0 Consensus size: 55
503151 GCTCTTTGAG
* * *
503161 GACT-AAAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGCATTTGCTCTTTGAA
1 GACTAAAAG-GTGCCACCAACTCGTGTGGGCTTTAGAAAGAAAAAGG--TAT-C-C--TAAA
* * *
503222 GACTAAAGGGTGCCACCAACTCGTGTAGGCTTTAGAAAGGAAAAGGTATCCTAAA
1 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAGAAAGAAAAAGGTATCCTAAA
503277 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-GAAAAGAAAAAGGTATCCTA
1 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAG-AAAGAAAAAGGTATCCTA
503330 CTCTTTGAGG
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
54 1 0.01
55 51 0.53
57 1 0.01
58 1 0.01
59 2 0.02
61 38 0.39
62 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (55 bp):
GACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAGAAAGAAAAAGGTATCCTAAA
Found at i:503604 original size:30 final size:30
Alignment explanation
Indices: 503552--503667 Score: 108
Period size: 30 Copynumber: 3.8 Consensus size: 30
503542 CATGGAGTCA
**
503552 TGGACTTTGAAGAAGGGATGCCACTTAGTTG
1 TGGACTTTGAA-AAAAGATGCCACTTAGTTG
* * **
503583 TGAACTTTGAAAAAAGATGCCACTAAGTCA
1 TGGACTTTGAAAAAAGATGCCACTTAGTTG
* * *
503613 TGGACTTTGATGAAAAGATACCACTGAG-TG
1 TGGACTTTGA-AAAAAGATGCCACTTAGTTG
* *
503643 TGGACTTTAAAAAAAAATGCCACTT
1 TGGACTTTGAAAAAAGATGCCACTT
503668 TACTGGGGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 11 0.16
30 32 0.48
31 24 0.36
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (30 bp):
TGGACTTTGAAAAAAGATGCCACTTAGTTG
Found at i:503637 original size:61 final size:60
Alignment explanation
Indices: 503547--503666 Score: 159
Period size: 61 Copynumber: 2.0 Consensus size: 60
503537 GGTGCCATGG
** * * * *
503547 AGTCATGGACTTTGAAGAAGGGATGCCACTTAGTTGTGAACTTTGAAAAAAGATGCCACTA
1 AGTCATGGACTTTGAAGAAAAGATACCACTGAG-TGTGAACTTTAAAAAAAAATGCCACTA
* *
503608 AGTCATGGACTTTGATGAAAAGATACCACTGAGTGTGGACTTTAAAAAAAAATGCCACT
1 AGTCATGGACTTTGAAGAAAAGATACCACTGAGTGTGAACTTTAAAAAAAAATGCCACT
503667 TTACTGGGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 23 0.45
61 28 0.55
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (60 bp):
AGTCATGGACTTTGAAGAAAAGATACCACTGAGTGTGAACTTTAAAAAAAAATGCCACTA
Found at i:504881 original size:11 final size:10
Alignment explanation
Indices: 504863--504897 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
504853 TTTTTTTTGA
504863 TTTTTGTTTC
1 TTTTTGTTTC
504873 TTTTGTGTTTC
1 TTTT-TGTTTC
504884 TTTTTGTTTC
1 TTTTTGTTTC
504894 TTTT
1 TTTT
504898 AAAAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (10 bp):
TTTTTGTTTC
Found at i:509063 original size:20 final size:20
Alignment explanation
Indices: 509040--509112 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
509030 ACAATTCAAA
509040 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
509060 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
509081 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
509101 GTATCGATACAT
1 GTATCGATACAT
509113 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:509084 original size:21 final size:21
Alignment explanation
Indices: 509058--509133 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
509048 ACATGTTGCA
509058 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
509079 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
509099 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
509120 ATGTATCGATACAT
1 ATGTATCGATACAT
509134 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:509091 original size:41 final size:41
Alignment explanation
Indices: 509040--509133 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
509030 ACAATTCAAA
*
509040 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
509081 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
509122 GTATCGATACAT
1 GTATCGATACAT
509134 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:509190 original size:13 final size:13
Alignment explanation
Indices: 509172--509197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
509162 TACAGAAAGT
509172 ATGTATCGATACA
1 ATGTATCGATACA
509185 ATGTATCGATACA
1 ATGTATCGATACA
509198 CAAAAATTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:509195 original size:32 final size:32
Alignment explanation
Indices: 509154--509216 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
509144 TAGCCAAACT
* *
509154 TGTATCGATACA-GAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAT-TGTATCGATACAA
509186 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
509217 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:509719 original size:34 final size:35
Alignment explanation
Indices: 509656--509722 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
509646 CTAAGTGATT
509656 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
509692 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
509723 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:512743 original size:13 final size:13
Alignment explanation
Indices: 512725--512749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
512715 TTTTCCAGAT
512725 TGTATCGATACAA
1 TGTATCGATACAA
512738 TGTATCGATACA
1 TGTATCGATACA
512750 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:514458 original size:20 final size:20
Alignment explanation
Indices: 514435--514507 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
514425 ACAATTCAAA
514435 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
514455 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
514476 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
514496 GTATCGATACAT
1 GTATCGATACAT
514508 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:514479 original size:21 final size:21
Alignment explanation
Indices: 514453--514528 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
514443 ACATGTTGCA
514453 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
514474 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
514494 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
514515 ATGTATCGATACAT
1 ATGTATCGATACAT
514529 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:514486 original size:41 final size:41
Alignment explanation
Indices: 514435--514528 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
514425 ACAATTCAAA
*
514435 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
514476 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
514517 GTATCGATACAT
1 GTATCGATACAT
514529 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:514585 original size:13 final size:13
Alignment explanation
Indices: 514567--514592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514557 TACAGAAAGT
514567 ATGTATCGATACA
1 ATGTATCGATACA
514580 ATGTATCGATACA
1 ATGTATCGATACA
514593 CAAAAATTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:514590 original size:32 final size:32
Alignment explanation
Indices: 514549--514611 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
514539 TAGCCAAACT
* *
514549 TGTATCGATACA-GAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAT-TGTATCGATACAA
514581 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
514612 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:515114 original size:34 final size:35
Alignment explanation
Indices: 515051--515117 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
515041 CTAAGTGATT
515051 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
515087 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
515118 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:516033 original size:39 final size:40
Alignment explanation
Indices: 515986--516067 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 40
515976 AAAACAGAAA
** *
515986 ATAACGAATAAATTTATGCAAAATAACACA-CAAAAATAC
1 ATAACGAATAAATACACGCAAAATAACACACCAAAAATAC
516025 ATAACGAATAAATACACGCAAAATAACACACCCAAAAATAC
1 ATAACGAATAAATACACGCAAAATAACACA-CCAAAAATAC
516066 AT
1 AT
516068 TAAAAATAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 27 0.71
41 11 0.29
ACGTcount: A:0.59, C:0.20, G:0.05, T:0.17
Consensus pattern (40 bp):
ATAACGAATAAATACACGCAAAATAACACACCAAAAATAC
Found at i:516480 original size:98 final size:99
Alignment explanation
Indices: 516316--516494 Score: 238
Period size: 98 Copynumber: 1.8 Consensus size: 99
516306 TGCAAATGGG
* * *
516316 GTTGGAGTATCCCCGATGATGAAAAATCGATATTTTGGAAATAAAATCAAGGTTGGAGCATCCCC
1 GTTGGAGTATCCCCGATGATGAAAAATCGATATTTTAGAAATAAAATCAAGGATGGAACATCCCC
516381 TC-GAAAATAATGGGGTAGGACTATCCCTTCAGAA
66 TCAG-AAATAATGGGGTAGGACTATCCCTTCAGAA
* * * * * *
516415 GTTGGAGTATCCTCGATGGTG-AAAATTGGTGTTTTAGAAATAAAAT-AGAGGATGGAATATCCC
1 GTTGGAGTATCCCCGATGATGAAAAATCGATATTTTAGAAATAAAATCA-AGGATGGAACATCCC
516478 CTCAGAAATAATGGGGT
65 CTCAGAAATAATGGGGT
516495 TAGAGCATTC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
97 1 0.01
98 48 0.70
99 20 0.29
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (99 bp):
GTTGGAGTATCCCCGATGATGAAAAATCGATATTTTAGAAATAAAATCAAGGATGGAACATCCCC
TCAGAAATAATGGGGTAGGACTATCCCTTCAGAA
Found at i:516629 original size:78 final size:78
Alignment explanation
Indices: 516415--516774 Score: 313
Period size: 78 Copynumber: 4.6 Consensus size: 78
516405 CCCTTCAGAA
* * * * *
516415 GTTGGAGTATCCTCGATGGT-GAAAATTGGTGTTTTAGAAATAAAATAGAGGATGGAATATCCCC
1 GTTGGAGTAT-CTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATTGAGGTTGGAGTATCCCC
*
516479 TCAGAAATAATGGG
65 TCAGAAATAATAGG
* * **
516493 GTTAGAGCAT-TCCTGATGGT-GAAAATCGATGTTTTAGAAATAAAATTGATTTTGGAGTATCCC
1 GTTGGAGTATCT-C-GATGGTGGAAAATCGATGTTTTAGAAATAAAATTGAGGTTGGAGTATCCC
516556 CTCAGAAATAATAGG
64 CTCAGAAATAATAGG
* * * * *
516571 ATTGGAGTATCTCAATGGTGGAAAATCGATGTTTTAGAAATAAAATTGGGGTTAGAGTATCCCTT
1 GTTGGAGTATCTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATTGAGGTTGGAGTATCCCCT
*
516636 C-GAAAATAACAGG
66 CAG-AAATAATAGG
* * * * ** * * *
516649 GGTGGAATATCCCCGATGGTGAAAAAATTC-ATACTATAGAAATAAAA-TCAGGGTTGGAGCATC
1 GTTGGAGTAT-CTCGATGGTG-GAAAA-TCGATGTTTTAGAAATAAAATTGA-GGTTGGAGTATC
*
516712 CCCTCAGAAATAA-CGAG
62 CCCTCAGAAATAATAG-G
* *
516729 GTTGTAATATCTTCGATGGTGGAAAATC-AGTGTTTTAGAAATAAAA
1 GTTGGAGTATC-TCGATGGTGGAAAATCGA-TGTTTTAGAAATAAAA
516775 CATCAATGAA
Statistics
Matches: 227, Mismatches: 42, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
76 1 0.00
77 7 0.03
78 132 0.58
79 29 0.13
80 55 0.24
81 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (78 bp):
GTTGGAGTATCTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATTGAGGTTGGAGTATCCCCT
CAGAAATAATAGG
Found at i:516643 original size:156 final size:157
Alignment explanation
Indices: 516415--516774 Score: 358
Period size: 156 Copynumber: 2.3 Consensus size: 157
516405 CCCTTCAGAA
* * *
516415 GTTGGAGTATCCTCGATGGT-GAAAATTGGTGTTTTAGAAATAAAATAGAGGATGGAATATCCCC
1 GTTGGAGTAT-CTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATAGAGGATAGAATATCCCC
* * * * ** * *
516479 TCAGAAATAA-TGGGGTTAGAGCATTCCTGATGGTG-AAAA-TCGATGTTTTAGAAATAAAAT-T
65 TCAGAAATAACAGGGG-TAGAACATCCCCGATGGTGAAAAATTC-ATACTATAGAAATAAAATCA
** * *
516540 GATTTTGGAGTATCCCCTCAGAAATAA-TAG
128 G-GGTTGGAGCATCCCCTCAGAAATAACGAG
* * * * * *
516570 GATTGGAGTATCTCAATGGTGGAAAATCGATGTTTTAGAAATAAAATTGGGGTTAGAGTATCCCT
1 G-TTGGAGTATCTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATAGAGGATAGAATATCCCC
* *
516635 TC-GAAAATAACAGGGGTGGAATATCCCCGATGGTGAAAAAATTCATACTATAGAAATAAAATCA
65 TCAG-AAATAACAGGGGTAGAACATCCCCGATGGTG-AAAAATTCATACTATAGAAATAAAATCA
516699 GGGTTGGAGCATCCCCTCAGAAATAACGAG
128 GGGTTGGAGCATCCCCTCAGAAATAACGAG
* *
516729 GTTGTAATATCTTCGATGGTGGAAAATC-AGTGTTTTAGAAATAAAA
1 GTTGGAGTATC-TCGATGGTGGAAAATCGA-TGTTTTAGAAATAAAA
516775 CATCAATGAA
Statistics
Matches: 168, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
155 10 0.06
156 67 0.40
157 4 0.02
158 50 0.30
159 37 0.22
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (157 bp):
GTTGGAGTATCTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATAGAGGATAGAATATCCCCT
CAGAAATAACAGGGGTAGAACATCCCCGATGGTGAAAAATTCATACTATAGAAATAAAATCAGGG
TTGGAGCATCCCCTCAGAAATAACGAG
Found at i:519302 original size:21 final size:20
Alignment explanation
Indices: 519252--519305 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
519242 CATTTTAAGC
519252 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
* *
519272 ATGCATCGATACATTTACTAT
1 ATGTATCGATACATTCACT-T
*
519293 TTGTATCGATACA
1 ATGTATCGATACA
519306 AATTGTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:522644 original size:80 final size:79
Alignment explanation
Indices: 522419--522745 Score: 251
Period size: 80 Copynumber: 4.1 Consensus size: 79
522409 ATAAAAATGG
* * * * * * *
522419 GGTTGAAGTATCCTCGATGGTG-GAAAATCGATGTTTT-GGAAATAAAAC-CAGAGTTGGAGTAT
1 GGTTGGAGTATCCCCGATGGTGCAAAAATCGATGTTTTAAG-AATAAAACTGAG-GTTAGAGTGT
* *
522481 CTCCTCGAAAATAA-AG
64 C-CCTCAAAAATAACAA
* * ** * * * * *
522497 GGTTAGAGTATCCTCGATTATG-GAAAATCGATGTTTTAGGAATAAAA-TCGGGGTTGGAGTATC
1 GGTTGGAGTATCCCCGATGGTGCAAAAATCGATGTTTTAAGAATAAAACT-GAGGTTAGAGTGT-
522560 CCCTCAAAAATAAC-A
64 CCCTCAAAAATAACAA
* * *
522575 GATTTGGAGTATCCCCGAT-G-GCAAAAATTGATTTTTTTTTAA-AATAAAACTGAGGTTAGAGT
1 G-GTTGGAGTATCCCCGATGGTGCAAAAATCGA---TGTTTTAAGAATAAAACTGAGGTTAGAGT
522637 GTACCCTCAAAAATAACAA
62 GT-CCCTCAAAAATAACAA
* * *
522656 GGTTGGAGTATCCCCGATGGTGGAAAAATCGATGTTTTAAGAATAAAACTGGGGTTGGAGTGTCC
1 GGTTGGAGTATCCCCGATGGTGCAAAAATCGATGTTTTAAGAATAAAACTGAGGTTAGAGTGTCC
**
522721 TCTCAAAAATAACGG
66 -CTCAAAAATAACAA
522736 GGTTGGAGTA
1 GGTTGGAGTA
522746 ACCTCAATGG
Statistics
Matches: 205, Mismatches: 28, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
77 1 0.00
78 69 0.34
79 27 0.13
80 89 0.43
81 10 0.05
82 9 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATGGTGCAAAAATCGATGTTTTAAGAATAAAACTGAGGTTAGAGTGTCC
CTCAAAAATAACAA
Found at i:522756 original size:80 final size:80
Alignment explanation
Indices: 522418--522831 Score: 350
Period size: 78 Copynumber: 5.2 Consensus size: 80
522408 GATAAAAATG
* * ** * *
522418 GGGTTGAAGTATCCTCGATGGTGG-AAAATCGATGTTTT-GGAAATAAAACCAGAGTTGGAGTAT
1 GGGTTGGAGTATCCTCGATGGTGGAAAAATCGATGTTTTAAG-AATAAAACTGGGGTTGGAGTGT
*
522481 -CTCCTCGAAAATAA-A
65 CCT-CTCAAAAATAACA
* ** * *
522496 GGGTTAGAGTATCCTCGATTATGG-AAAATCGATGTTTTAGGAATAAAA-TCGGGGTTGGAGTAT
1 GGGTTGGAGTATCCTCGATGGTGGAAAAATCGATGTTTTAAGAATAAAACT-GGGGTTGGAGTGT
*
522559 CCCCTCAAAAATAACA
65 CCTCTCAAAAATAACA
** * * * * * *
522575 GATTTGGAGTATCCCCGAT-G-GCAAAAATTGATTTTTTTTTAA-AATAAAACTGAGGTTAGAGT
1 GGGTTGGAGTATCCTCGATGGTGGAAAAATCGA---TGTTTTAAGAATAAAACTGGGGTTGGAGT
522637 GTACC-CTCAAAAATAACA
63 GT-CCTCTCAAAAATAACA
* *
522655 AGGTTGGAGTATCCCCGATGGTGGAAAAATCGATGTTTTAAGAATAAAACTGGGGTTGGAGTGTC
1 GGGTTGGAGTATCCTCGATGGTGGAAAAATCGATGTTTTAAGAATAAAACTGGGGTTGGAGTGTC
*
522720 CTCTCAAAAATAACG
66 CTCTCAAAAATAACA
* * * * * * *
522735 GGGTTGGAGTAACCTCAATGGT-GAAAATTTGGTATTTTAAAAAT-AAACTGGGGTTGGAGTGTT
1 GGGTTGGAGTATCCTCGATGGTGGAAAAATCGATGTTTTAAGAATAAAACTGGGGTTGGAGTG-T
** * *
522798 CCT-TCGGAAAGAACG
65 CCTCTCAAAAATAACA
522813 GGGTTGGAGTATCCTCGAT
1 GGGTTGGAGTATCCTCGAT
522832 AGTAAAAAAC
Statistics
Matches: 277, Mismatches: 44, Indels: 30
0.79 0.13 0.09
Matches are distributed among these distances:
77 1 0.00
78 112 0.40
79 49 0.18
80 96 0.35
81 10 0.04
82 9 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (80 bp):
GGGTTGGAGTATCCTCGATGGTGGAAAAATCGATGTTTTAAGAATAAAACTGGGGTTGGAGTGTC
CTCTCAAAAATAACA
Found at i:525335 original size:377 final size:378
Alignment explanation
Indices: 524682--525432 Score: 1441
Period size: 377 Copynumber: 2.0 Consensus size: 378
524672 TGGTTTTGGG
524682 AGCTACGCGAATGGGGTTTTTTGGGCAATGGAATAGTGTTTTCTAAATGTTTTTTTTGAATGAGT
1 AGCTACGCGAATGGGGTTTTTTGGGCAATGGAATAGTGTTTTCTAAATGTTTTTTTTGAATGAGT
524747 ATCAAGGTTTTTTTTTTGCTGCTAGAACTTTTTTTTTGCTGCCCAAAGATCTCCTTTGCTGAGCC
66 ATCAAGGTTTTTTTTTTGCTGCTAGAACTTTTTTTTTGCTGCCCAAAGATCTCCTTTGCTGAGCC
*
524812 AATAACCCTTATTTATCCTCATGCTCAATCAATACGATTAGGGGACATACCAAGGGCATTATGGA
131 AATAACCCTTATTTATCCTCATGCTCAATCAATACGATTAGGGGACATACCAAAGGCATTATGGA
*
524877 TTTTCTCCTTTGCACAAGGAGACAACTAGCCACCAACTCAGGCTGCCCCTCATTACCATTGGTTC
196 TTTTCTCCTTTGCACAAGGAGACAACTAGCCACCAACTCAGGCTGCCCCTCATTACCATGGGTTC
524942 TGCCATGCAGTGTGATGGTCCTGAAGCTGAAGCTACCAGCATTCTG-AAAAAAAAAACTAACATG
261 TGCCATGCAGTGTGATGGTCCTGAAGCTGAAGCTACCAGCATTCTGAAAAAAAAAAACTAACATG
525006 TCCTTTGGTGGAAAATGATTTTTGGCTTTTTGCAAATTTGATCCTGAAGCTGA
326 TCCTTTGGTGGAAAATGATTTTTGGCTTTTTGCAAATTTGATCCTGAAGCTGA
525059 AGCTACGCGAATGGGGTTTTTTGGGCAATGGAATAGTGTTTTCTAAATGTTTTTTTTGAATGAGT
1 AGCTACGCGAATGGGGTTTTTTGGGCAATGGAATAGTGTTTTCTAAATGTTTTTTTTGAATGAGT
*
525124 ATCAAGGTTTTTTTTTTGCTGCTGGAACTTTTTTTTTGCTGCCCAAAGATCTCCTTTGCTGAGCC
66 ATCAAGGTTTTTTTTTTGCTGCTAGAACTTTTTTTTTGCTGCCCAAAGATCTCCTTTGCTGAGCC
525189 AATAACCCTTATTTATCCTCATGCTCAATCAATACGATTAGGGGACATACCAAAGGCATTATGGA
131 AATAACCCTTATTTATCCTCATGCTCAATCAATACGATTAGGGGACATACCAAAGGCATTATGGA
*
525254 TTTTCTCCTTTGCACAAGGAGACAACTAGCCACTAACTCAGGCTGCCCCTCATTACCATGGGTTC
196 TTTTCTCCTTTGCACAAGGAGACAACTAGCCACCAACTCAGGCTGCCCCTCATTACCATGGGTTC
525319 TGCCATGCAGTGTGATGGTCCTGAAGCTGAAGCTACCAGCATTCTGAAAAAAAAAAAACTAACAT
261 TGCCATGCAGTGTGATGGTCCTGAAGCTGAAGCTACCAGCATTCTG-AAAAAAAAAAACTAACAT
*
525384 GTCCTTTGGTGGAAAATGATTTTTGGCTTTTTGCAAATTTGATCTTGAA
325 GTCCTTTGGTGGAAAATGATTTTTGGCTTTTTGCAAATTTGATCCTGAA
525433 ACTTGTTTAA
Statistics
Matches: 367, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
377 302 0.82
379 65 0.18
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (378 bp):
AGCTACGCGAATGGGGTTTTTTGGGCAATGGAATAGTGTTTTCTAAATGTTTTTTTTGAATGAGT
ATCAAGGTTTTTTTTTTGCTGCTAGAACTTTTTTTTTGCTGCCCAAAGATCTCCTTTGCTGAGCC
AATAACCCTTATTTATCCTCATGCTCAATCAATACGATTAGGGGACATACCAAAGGCATTATGGA
TTTTCTCCTTTGCACAAGGAGACAACTAGCCACCAACTCAGGCTGCCCCTCATTACCATGGGTTC
TGCCATGCAGTGTGATGGTCCTGAAGCTGAAGCTACCAGCATTCTGAAAAAAAAAAACTAACATG
TCCTTTGGTGGAAAATGATTTTTGGCTTTTTGCAAATTTGATCCTGAAGCTGA
Found at i:525654 original size:50 final size:50
Alignment explanation
Indices: 525579--525688 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
525569 TGACTGAATT
* * *
525579 TATCGATACATCTCGGTAAAACCCAGAATATATCGATACCATGAAAAATG
1 TATCGATACATCTCGGTAAAACCCAGAATAGATCCATACAATGAAAAATG
* * **
525629 TATCGATACATCTGGGTAAAACCCAGAATGGATCCATACAATGAAGGATG
1 TATCGATACATCTCGGTAAAACCCAGAATAGATCCATACAATGAAAAATG
525679 TATCGATACA
1 TATCGATACA
525689 AATTGTGTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (50 bp):
TATCGATACATCTCGGTAAAACCCAGAATAGATCCATACAATGAAAAATG
Found at i:529426 original size:20 final size:21
Alignment explanation
Indices: 529379--529431 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
529369 CCCAATGACC
**
529379 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
529400 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
529420 TGTATCGATACA
1 TGTATCGATACA
529432 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:529437 original size:13 final size:13
Alignment explanation
Indices: 529419--529443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
529409 ACATTTGGTC
529419 ATGTATCGATACA
1 ATGTATCGATACA
529432 ATGTATCGATAC
1 ATGTATCGATAC
529444 TGTGCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:538209 original size:20 final size:21
Alignment explanation
Indices: 538162--538214 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
538152 CCCAATGACC
**
538162 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
538183 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
538203 TGTATCGATACA
1 TGTATCGATACA
538215 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:538220 original size:13 final size:13
Alignment explanation
Indices: 538202--538226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
538192 ACATTTGGTC
538202 ATGTATCGATACA
1 ATGTATCGATACA
538215 ATGTATCGATAC
1 ATGTATCGATAC
538227 TATGCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:545716 original size:28 final size:28
Alignment explanation
Indices: 545670--545847 Score: 119
Period size: 28 Copynumber: 6.3 Consensus size: 28
545660 CTAGTAAATC
*
545670 TCAAAGCCCACAAGCTAGTGGAACCCTT
1 TCAAAGCCCACAAGTTAGTGGAACCCTT
*
545698 TCAAAGCCCACGAGTTAGT-GACACCCTTT
1 TCAAAGCCCACAAGTTAGTGGA-ACCC-TT
* * *
545727 TCAAAAGCCTATAAGTTAGTGGCACCCTT
1 TC-AAAGCCCACAAGTTAGTGGAACCCTT
** * * * *
545756 TCAAAGTACATAAGTCAAT-GACACCATT
1 TCAAAGCCCACAAGTTAGTGGA-ACCCTT
* * * * *
545784 TCAAAGCTCATAAGTCAGTGGCACTCTT
1 TCAAAGCCCACAAGTTAGTGGAACCCTT
* * *
545812 TTAAAGCCCACAAGTCAAT-GATACCCTT
1 TCAAAGCCCACAAGTTAGTGGA-ACCCTT
545840 TCAAAGCC
1 TCAAAGCC
545848 TACGAGCCAG
Statistics
Matches: 117, Mismatches: 26, Indels: 14
0.75 0.17 0.09
Matches are distributed among these distances:
27 4 0.03
28 85 0.73
29 9 0.08
30 18 0.15
31 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (28 bp):
TCAAAGCCCACAAGTTAGTGGAACCCTT
Found at i:545859 original size:56 final size:56
Alignment explanation
Indices: 545670--546385 Score: 199
Period size: 56 Copynumber: 12.7 Consensus size: 56
545660 CTAGTAAATC
* * * * * *
545670 TCAAAGCCCACAAGCTAGTGGAACCCTTTCAAAGCCCACGAGTTAGTGACACCCTTT
1 TCAAAGCCTACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACACCC-TT
* ** ** * *
545727 TCAAAAGCCTATAAGTTAGTGGCACCCTTTCAAAGTACATAAGTCAATGACACCATT
1 TC-AAAGCCTACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACACCCTT
* * * * *
545784 TCAAAG-CTCATAAGTCAGTGGCACTCTTTTAAAGCCCACAAGTCAATGATACCCTT
1 TCAAAGCCT-ACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACACCCTT
* **** ** **** *
545840 TCAAAGCCTACGAGCCAGTGGCA-CGAGCCAGTGGCACC-TTTTTCAA--A-AGCC--
1 TCAAAGCCTACAAGCCAGTGGCACCCTTTCA-AAGC-CCACAAGTCAATGACACCCTT
** * * * *
545891 -C--A--C-ACAAGTTAGTGGCACCCTCTCAAAGCCTACAAGTCGATGGCATCCCTT
1 TCAAAGCCTACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACA-CCCTT
* ** * * * ** * *
545942 TCAAAGCCCACAAGTTAGTGGCACCTTTTTAAAGCTCATGAGTC-ATTAGCATCCTT
1 TCAAAGCCTACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGA-CACCCTT
* * * * ** * * * *
545998 TCAAAGCCCACGAA-TCAATGGCACCCTTTTAAAGCGTACGAGTCAGTGGCACCTTTT
1 TCAAAGCCTAC-AAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACACC-CTT
** * * * *
546055 TCAAAAGCCTACACAAATCAATGGTA-CCTTCTCAAAGCCCACAAGTTAATGGCATCCCTT
1 TC-AAAGCCT--ACAAGCCAGTGGCACCCTT-TCAAAGCCCACAAGTCAATGACA-CCCTT
* *** * ** * * * *
546115 TCAAAGCCCACAATTTATTGGCATTCTTTTAAAGCCCACAAGTTAGTGGCACCCTT
1 TCAAAGCCTACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACACCCTT
* * * * * *
546171 TCAAAACCCACAAGTCAGTGGCACCCTTTTCAAAAGCCTACATAAGTCAATGACACCATC
1 TCAAAGCCTACAAGCCAGTGGCACCC-TTTC-AAAGCC--CACAAGTCAATGACACCCTT
* ** * * * *
546231 TCAAAGCCCACAAGTAAGTGACATCCCTTTCAAAGCCCACAAGTTAGTGGCACCCTT
1 TCAAAGCCTACAAGCCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAATGACACCCTT
* ** * * * * *
546288 TCAAAG-TTCACAAGTTAATGGCACCTTTTCAAAGCCCACGAGTCAGTGTCACCCTTT
1 TCAAAGCCT-ACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACACCC-TT
* ** * *
546345 TCAAAAGCTCACACAAGTTAGTGGCACTCTCTCAAAGCCCA
1 TC-AAAGC-C-TACAAGCCAGTGGCACCCTTTCAAAGCCCA
546386 TAAATTGATG
Statistics
Matches: 491, Mismatches: 127, Indels: 79
0.70 0.18 0.11
Matches are distributed among these distances:
44 1 0.00
45 16 0.03
46 4 0.01
48 2 0.00
49 2 0.00
50 1 0.00
52 1 0.00
53 3 0.01
54 2 0.00
55 3 0.01
56 163 0.33
57 116 0.24
58 60 0.12
59 18 0.04
60 94 0.19
61 5 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (56 bp):
TCAAAGCCTACAAGCCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGACACCCTT
Found at i:545867 original size:13 final size:13
Alignment explanation
Indices: 545849--545876 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
545839 TTCAAAGCCT
545849 ACGAGCCAGTGGC
1 ACGAGCCAGTGGC
545862 ACGAGCCAGTGGC
1 ACGAGCCAGTGGC
545875 AC
1 AC
545877 CTTTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.32, G:0.36, T:0.07
Consensus pattern (13 bp):
ACGAGCCAGTGGC
Found at i:545927 original size:28 final size:28
Alignment explanation
Indices: 545869--546417 Score: 368
Period size: 28 Copynumber: 18.9 Consensus size: 28
545859 GGCACGAGCC
*
545869 AGTGGCACCTTTTTCAAAAGCCCACACAAGTT
1 AGTGGCACC-CTTTC-AAAG-CC-CACAAGTT
* *
545901 AGTGGCACCCTCTCAAAGCCTACAAG-T
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
*
545928 CGATGGCATCCCTTTCAAAGCCCACAAGTT
1 AG-TGGCA-CCCTTTCAAAGCCCACAAGTT
* * * ** *
545958 AGTGGCACCTTTTTAAAGCTCATGAGTC
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
* * * *
545986 ATTAGCATCCTTTCAAAGCCCACGAA-TC
1 AGTGGCACCCTTTCAAAGCCCAC-AAGTT
* * ** * *
546014 AATGGCACCCTTTTAAAGCGTACGAGTC
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
* * *
546042 AGTGGCACCTTTTTCAAAAGCCTACACAAATC
1 AGTGGCACC-CTTTC-AAAGCC--CACAAGTT
* *
546074 AATGGTA-CCTTCTCAAAGCCCACAAGTT
1 AGTGGCACCCTT-TCAAAGCCCACAAGTT
* *
546102 AATGGCATCCCTTTCAAAGCCCACAATTT
1 AGTGGCA-CCCTTTCAAAGCCCACAAGTT
* ** *
546131 ATTGGCATTCTTTTAAAGCCCACAAGTT
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
* *
546159 AGTGGCACCCTTTCAAAACCCACAAGTC
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
* *
546187 AGTGGCACCCTTTTCAAAAGCCTACATAAGTC
1 AGTGGCACCC-TTTC-AAAGCC--CACAAGTT
* * * * *
546219 AATGACACCATCTCAAAGCCCACAAGTA
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
*
546247 AGTGACATCCCTTTCAAAGCCCACAAGTT
1 AGTGGCA-CCCTTTCAAAGCCCACAAGTT
**
546276 AGTGGCACCCTTTCAAAGTTCACAAGTT
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
* * * *
546304 AATGGCACCTTTTCAAAGCCCACGAGTC
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
*
546332 AGTGTCACCCTTTTCAAAAGCTCACACAAGTT
1 AGTGGCACCC-TTTC-AAAGC-C-CACAAGTT
* * * *
546364 AGTGGCACTCTCTCAAAGCCCATAAATT
1 AGTGGCACCCTTTCAAAGCCCACAAGTT
*
546392 -GATGGCAACCCTCTCAAAAGCCCACA
1 AG-TGGC-ACCCTTTC-AAAGCCCACA
546418 CAAGTCGGTG
Statistics
Matches: 407, Mismatches: 86, Indels: 50
0.75 0.16 0.09
Matches are distributed among these distances:
27 4 0.01
28 201 0.49
29 89 0.22
30 53 0.13
31 13 0.03
32 47 0.12
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (28 bp):
AGTGGCACCCTTTCAAAGCCCACAAGTT
Found at i:546149 original size:145 final size:145
Alignment explanation
Indices: 545901--546417 Score: 534
Period size: 145 Copynumber: 3.6 Consensus size: 145
545891 CACACAAGTT
* * *
545901 AGTGGCACCC-TCTC-AAAGCCT--ACAAGTCGATGGCATCCCTT-TCAAAGCCCACAAGTTAGT
1 AGTGGCACCCTTTTCAAAAGCCTACACAAGTCAATGGCA--CCTTCTCAAAGCCCACAAGTTAAT
* * * ** * * *
545961 GGCA-CCTTTTTAAAGCTCATGAGTCATTAGCATCCTTTCAAAGCCCACGAA-TCAATGGCACCC
64 GGCATCCCTTTCAAAGCCCACAAGTTATTGGCATCCTTTCAAAGCCCAC-AAGTTAATGGCACCC
**
546024 TTTTAAAGCGTACGAGTC
128 TTTTAAAGCCCACGAGTC
* * *
546042 AGTGGCACCTTTTTCAAAAGCCTACACAAATCAATGGTACCTTCTCAAAGCCCACAAGTTAATGG
1 AGTGGCACCCTTTTCAAAAGCCTACACAAGTCAATGGCACCTTCTCAAAGCCCACAAGTTAATGG
* * * *
546107 CATCCCTTTCAAAGCCCACAATTTATTGGCATTCTTTTAAAGCCCACAAGTTAGTGGCACCCTTT
66 CATCCCTTTCAAAGCCCACAAGTTATTGGCATCCTTTCAAAGCCCACAAGTTAATGGCACCCTTT
* * *
546172 CAAAACCCACAAGTC
131 TAAAGCCCACGAGTC
* * *
546187 AGTGGCACCCTTTTCAAAAGCCTACATAAGTCAATGACACCATCTCAAAGCCCACAAG-TAAGTG
1 AGTGGCACCCTTTTCAAAAGCCTACACAAGTCAATGGCACCTTCTCAAAGCCCACAAGTTAA-TG
* * * **
546251 ACATCCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGTTCACAAGTTAATGGCA-CCTT
65 GCATCCCTTTCAAAGCCCACAAGTTATTGGCATCCTTTCAAAGCCCACAAGTTAATGGCACCCTT
546315 TTCAAAGCCCACGAGTC
130 TT-AAAGCCCACGAGTC
* * * * * *
546332 AGTGTCACCCTTTTCAAAAG-CTCACACAAGTTAGTGGCA-CTCTCTCAAAGCCCATAAATTGAT
1 AGTGGCACCCTTTTCAAAAGCCT-ACACAAGTCAATGGCACCT-TCTCAAAGCCCACAAGTTAAT
* *
546395 GGCAACCCTCTCAAAAGCCCACA
64 GGCATCCCTTTC-AAAGCCCACA
546418 CAAGTCGGTG
Statistics
Matches: 310, Mismatches: 53, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
141 9 0.03
142 3 0.01
143 11 0.04
144 35 0.11
145 240 0.77
146 12 0.04
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (145 bp):
AGTGGCACCCTTTTCAAAAGCCTACACAAGTCAATGGCACCTTCTCAAAGCCCACAAGTTAATGG
CATCCCTTTCAAAGCCCACAAGTTATTGGCATCCTTTCAAAGCCCACAAGTTAATGGCACCCTTT
TAAAGCCCACGAGTC
Done.