Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 12 of 103
Found at i:4635696 original size:35 final size:34
Alignment explanation
Indices: 4635647--4635720 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 34
4635637 ACATTTAAAT
* * *
4635647 TTAAATAATCAAAAATAAATATATCAAATATCAAC
1 TTAAATAATCAAAAATAAATAT-CCAAACAACAAC
4635682 TTAAATAA-CTAAAAATAAATATCCAAACAACAAC
1 TTAAATAATC-AAAAATAAATATCCAAACAACAAC
4635716 TTAAA
1 TTAAA
4635721 CAACATTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 15 0.43
35 20 0.57
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.26
Consensus pattern (34 bp):
TTAAATAATCAAAAATAAATATCCAAACAACAAC
Found at i:4635952 original size:13 final size:14
Alignment explanation
Indices: 4635934--4635977 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
4635924 TAAATATGTT
*
4635934 TATATAT-TTAAAG
1 TATATATATAAAAG
4635947 TATATATACTAAAAG
1 TATATATA-TAAAAG
*
4635962 TATATATATAATAG
1 TATATATATAAAAG
4635976 TA
1 TA
4635978 ATTATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 7 0.26
14 7 0.26
15 13 0.48
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (14 bp):
TATATATATAAAAG
Found at i:4635954 original size:15 final size:15
Alignment explanation
Indices: 4635934--4635970 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4635924 TAAATATGTT
*
4635934 TATATATTTAAAGTA
1 TATATATTAAAAGTA
*
4635949 TATATACTAAAAGTA
1 TATATATTAAAAGTA
4635964 TATATAT
1 TATATAT
4635971 AATAGTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (15 bp):
TATATATTAAAAGTA
Found at i:4637175 original size:14 final size:14
Alignment explanation
Indices: 4637156--4637204 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
4637146 TTATTTTTAT
*
4637156 TTAAATTTAAAATA
1 TTAAATATAAAATA
4637170 TTAAATATAAAAT-
1 TTAAATATAAAATA
4637183 TATAATATATAAAATA
1 T-TAA-ATATAAAATA
4637199 -TAAATA
1 TTAAATA
4637205 GTTAAATGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 4 0.13
14 18 0.58
15 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATATAAAATA
Found at i:4637197 original size:22 final size:21
Alignment explanation
Indices: 4637158--4637202 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
4637148 ATTTTTATTT
*
4637158 AAATTTAAAATATTAAATATA
1 AAATTTAAAATATAAAATATA
*
4637179 AAATTATAATATATAAAATATA
1 AAATT-TAAAATATAAAATATA
4637201 AA
1 AA
4637203 TAGTTAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTTAAAATATAAAATATA
Found at i:4637204 original size:15 final size:15
Alignment explanation
Indices: 4637163--4637204 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4637153 TATTTAAATT
*
4637163 TAAAATATTAA-ATA
1 TAAAATATAAATATA
4637177 TAAAAT-TATAATATA
1 TAAAATATA-AATATA
4637192 TAAAATATAAATA
1 TAAAATATAAATA
4637205 GTTAAATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 8 0.33
15 13 0.54
16 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATAAATATA
Found at i:4637210 original size:15 final size:14
Alignment explanation
Indices: 4637157--4637210 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
4637147 TATTTTTATT
4637157 TAAAT-TTAAAATA
1 TAAATATTAAAATA
4637170 TTAAATA-TAAAAT-
1 -TAAATATTAAAATA
4637183 TATAATATATAAAATA
1 TA-AATAT-TAAAATA
4637199 TAAATAGTTAAA
1 TAAATA-TTAAA
4637211 TGTGATATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.06
13 4 0.12
14 11 0.32
15 14 0.41
16 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TAAATATTAAAATA
Found at i:4637258 original size:16 final size:17
Alignment explanation
Indices: 4637237--4637270 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4637227 TTATACAATG
4637237 GTTAAAT-ATATAAATA
1 GTTAAATAATATAAATA
4637253 GTTAAATAATATAAATA
1 GTTAAATAATATAAATA
4637270 G
1 G
4637271 AAAGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
GTTAAATAATATAAATA
Found at i:4637677 original size:2 final size:2
Alignment explanation
Indices: 4637672--4637696 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4637662 GAGATCATTA
4637672 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4637697 ATAAAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4649278 original size:18 final size:20
Alignment explanation
Indices: 4649252--4649288 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4649242 ATCTAGCTGC
4649252 TGTAAC-TT-TCAATCTCAT
1 TGTAACTTTATCAATCTCAT
*
4649270 TGTATCTTTATCAATCTCA
1 TGTAACTTTATCAATCTCA
4649289 CCACATCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 2 0.12
20 9 0.56
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (20 bp):
TGTAACTTTATCAATCTCAT
Found at i:4650849 original size:2 final size:2
Alignment explanation
Indices: 4650837--4650888 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
4650827 GAATTATTAA
*
4650837 AT AT A- AT AT AT AT AT AT AT A- AT TT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4650876 AT -T AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
4650889 CATTGTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
1 5 0.12
2 38 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4650855 original size:15 final size:15
Alignment explanation
Indices: 4650837--4650888 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
4650827 GAATTATTAA
4650837 ATATAATATATATAT
1 ATATAATATATATAT
*
4650852 ATATAATTTATATAT
1 ATATAATATATATAT
*
4650867 ATATATTATATTATATT
1 ATATAATATA-TATA-T
4650884 ATATA
1 ATATA
4650889 CATTGTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 22 0.69
16 4 0.12
17 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:4650863 original size:11 final size:13
Alignment explanation
Indices: 4650831--4650882 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 13
4650821 CTTATAGAAT
*
4650831 TATTAAATATA-A
1 TATTATATATATA
4650843 TA-TATATATATA
1 TATTATATATATA
4650855 TAATTTATATATATA
1 T-A-TTATATATATA
4650870 TATTATAT-TATA
1 TATTATATATATA
4650882 T
1 T
4650883 TATATACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
11 7 0.20
12 9 0.26
13 7 0.20
14 1 0.03
15 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTATATATATA
Found at i:4650863 original size:13 final size:14
Alignment explanation
Indices: 4650837--4650887 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
4650827 GAATTATTAA
4650837 ATATAATATATATAT
1 ATATAATAT-TATAT
4650852 ATATAAT-TTATAT
1 ATATAATATTATAT
4650865 ATAT-ATATTATATT
1 ATATAATATTATA-T
*
4650879 ATATTATAT
1 ATATAATAT
4650888 ACATTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.06
13 14 0.42
14 6 0.18
15 11 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATAATATTATAT
Found at i:4650866 original size:19 final size:18
Alignment explanation
Indices: 4650838--4650888 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
4650828 AATTATTAAA
*
4650838 TATAATATATATATATAT
1 TATATTATATATATATAT
*
4650856 AAT-TTATATATATATAT
1 TATATTATATATATATAT
4650873 TATATTATAT-TATATA
1 TATATTATATATATATA
4650889 CATTGTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATATATATATAT
Found at i:4651380 original size:285 final size:286
Alignment explanation
Indices: 4650891--4651469 Score: 803
Period size: 287 Copynumber: 2.0 Consensus size: 286
4650881 ATTATATACA
*
4650891 TTGTTTATAAAAACTTATAATATATATACTTAAAAAGAAGTTGTGAGATTAGAATAGTTTTGAAA
1 TTGTTTATAAAAACTTATAATATATAAACTTAAAAAGAAGTTGTGAGATTAGAATAGTTTTGAAA
* * * * * *
4650956 CTTAGTTTTTTTTTTAAATTTACCATGTCATATGGACTAAAGTACATATAGTTATTAAATTAATT
66 CCTAGTTTTTTTTTTAAATTTA-CATATAATAAGGACTAAAGCACATATAATTATTAAATTAATT
* * * *
4651021 CATGAAATTATAATTATTAATTAACTTATAATGTCTTTAAATATATATACTTTATATACATTAGG
130 AAAGAAACTATAATTATTAATTAACTTATAATGTCTTTAAATATATATAATTTATATACATTAGG
* * *
4651086 TTAATTTATAAGTAATATAATTACTATTATATATAT-TAAAA-TACTTTTATTATATATACACTT
195 TTAATTTATAAGAAATATAATTACTATTATATATATATAAAAGTA-TTTTAGTATATATACACCT
4651149 TAAATATAAAAATATTTACTTTCTATTT
259 TAAATATAAAAATATTTACTTTCTATTT
* ** *
4651177 NTTGTTTATATAAACTTATAATATATAAA-TCTAAAGGGAAGTTGTGAGATTAGAATAGTTTTGG
1 -TTGTTTATAAAAACTTATAATATATAAACT-TAAAAAGAAGTTGTGAGATTAGAATAGTTTTGA
*
4651241 AACCTAGTTATTTTTTTT-AATTT-CATATAATTAAGGAC-AAA-CCCATATAATTAATTAAATT
64 AACCTAGTT-TTTTTTTTAAATTTACATATAA-TAAGGACTAAAGCACATATAATT-ATTAAATT
* * * *
4651302 AATTAAAGAAACTATGATTATTAATTGACTTGTAATGTCTTTTAATATATATAATTTATATACAT
126 AATTAAAGAAACTATAATTATTAATTAACTTATAATGTCTTTAAATATATATAATTTATATACAT
*
4651367 TAGGTTTATTTATAAGAAATATAATTACTATTATATATATAGTAAAAGTATTTTAGTATATATAC
191 TAGGTTAATTTATAAGAAATATAATTACTATTATATATATA-TAAAAGTATTTTAGTATATATAC
*
4651432 ACCTTAAATATAAACATATTTACTTTCTATTT
255 ACCTTAAATATAAAAATATTTACTTTCTATTT
4651464 TGTGTT
1 T-TGTT
4651470 AACATTATAA
Statistics
Matches: 259, Mismatches: 25, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
284 8 0.03
285 111 0.43
286 8 0.03
287 122 0.47
288 10 0.04
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (286 bp):
TTGTTTATAAAAACTTATAATATATAAACTTAAAAAGAAGTTGTGAGATTAGAATAGTTTTGAAA
CCTAGTTTTTTTTTTAAATTTACATATAATAAGGACTAAAGCACATATAATTATTAAATTAATTA
AAGAAACTATAATTATTAATTAACTTATAATGTCTTTAAATATATATAATTTATATACATTAGGT
TAATTTATAAGAAATATAATTACTATTATATATATATAAAAGTATTTTAGTATATATACACCTTA
AATATAAAAATATTTACTTTCTATTT
Found at i:4655415 original size:47 final size:47
Alignment explanation
Indices: 4655332--4655424 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
4655322 CTGTGGCAGG
4655332 GCAGGGTTTAAAGTTTGTGAAACAGCATGTTGGGAATGTGTGACACT
1 GCAGGGTTTAAAGTTTGTGAAACAGCATGTTGGGAATGTGTGACACT
* *
4655379 GCAGGGTTTAGAGTTTGTGACAC-GACATGGTT-GGAATGTGTGACAC
1 GCAGGGTTTAAAGTTTGTGAAACAG-CAT-GTTGGGAATGTGTGACAC
4655425 AGTTGTGACA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 1 0.02
47 38 0.90
48 3 0.07
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (47 bp):
GCAGGGTTTAAAGTTTGTGAAACAGCATGTTGGGAATGTGTGACACT
Found at i:4655464 original size:58 final size:58
Alignment explanation
Indices: 4655370--4655481 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
4655360 GTTGGGAATG
* * **
4655370 TGTGACACTGCAGGGTTTAGAGTTTGTGACACGACATGGTTGGAATGTGTGACACAGT
1 TGTGACACTACAAGGTTTAGAGTTTGTGACACGACATCATTGGAATGTGTGACACAGT
**
4655428 TGTGACACTACAAGGTTTAGAGTTTGTGACTTGACATCATTGGAATGTGTGACA
1 TGTGACACTACAAGGTTTAGAGTTTGTGACACGACATCATTGGAATGTGTGACA
4655482 TGCTAGAGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.31
Consensus pattern (58 bp):
TGTGACACTACAAGGTTTAGAGTTTGTGACACGACATCATTGGAATGTGTGACACAGT
Found at i:4655520 original size:47 final size:47
Alignment explanation
Indices: 4655477--4655642 Score: 192
Period size: 47 Copynumber: 3.5 Consensus size: 47
4655467 TTGGAATGTG
* *
4655477 TGACATGCTAGAGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
1 TGACACGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTA
* *
4655524 TGACACGCTAGCA-TTCAGAGTTTGTGATATGCCATGGAGGGAATCTA
1 TGACACGCTAG-AGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTA
* * * * * *
4655571 TGACACACCAGTGTTCATAGTTTGTGACACGCTATGGAGGGAATCTG
1 TGACACGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTA
* *
4655618 TGACACG-TCAGGGTTCAAAGTTTGT
1 TGACACGCT-AGAGTTCAGAGTTTGT
4655643 CAAACTCTCT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
47 99 0.99
48 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (47 bp):
TGACACGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTA
Found at i:4656360 original size:31 final size:31
Alignment explanation
Indices: 4656322--4656552 Score: 302
Period size: 31 Copynumber: 7.5 Consensus size: 31
4656312 TCAGCGTTGA
* *
4656322 CGTGTTACAACATTTGAC-TTGATACGCATGG
1 CGTGTTACAACATTTTACGTT-ATATGCATGG
* * * *
4656353 CGTGTTACAACATTTAATGTTACATACATGG
1 CGTGTTACAACATTTTACGTTATATGCATGG
4656384 CGTGTTACAACATTTTACGTTATATGCATGG
1 CGTGTTACAACATTTTACGTTATATGCATGG
* *
4656415 CGTGTTACAACATTTTACATTATATGCATAG
1 CGTGTTACAACATTTTACGTTATATGCATGG
* * * *
4656446 CGTGTTCCTATATTTTACGTTATATGCATGA
1 CGTGTTACAACATTTTACGTTATATGCATGG
* *
4656477 CTTGTTACAATATTTTACGTTATATGCATGG
1 CGTGTTACAACATTTTACGTTATATGCATGG
*
4656508 CGTGTTACCACATTTTACGTTATATGCATGG
1 CGTGTTACAACATTTTACGTTATATGCATGG
*
4656539 CGTGTTACCACATT
1 CGTGTTACAACATT
4656553 ATGGGTTAAC
Statistics
Matches: 175, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
31 173 0.99
32 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (31 bp):
CGTGTTACAACATTTTACGTTATATGCATGG
Found at i:4656389 original size:16 final size:15
Alignment explanation
Indices: 4656348--4656396 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
4656338 ACTTGATACG
4656348 CATGGCGTGTTACAA
1 CATGGCGTGTTACAA
****
4656363 CATTTAATGTTACATA
1 CATGGCGTGTTACA-A
4656379 CATGGCGTGTTACAA
1 CATGGCGTGTTACAA
4656394 CAT
1 CAT
4656397 TTTACGTTAT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (15 bp):
CATGGCGTGTTACAA
Found at i:4658259 original size:145 final size:144
Alignment explanation
Indices: 4657941--4658294 Score: 394
Period size: 145 Copynumber: 2.4 Consensus size: 144
4657931 TGGCAATGAA
* * *
4657941 GAGCCGGTAACGA-CGGTTCTAAAGGTTTATGTTCAACAATTCCATATGTGATTATCGAATAACA
1 GAGCCGGTAA-GATCGGTTCTAAA-GTTTGTGTTCAACAATTCCATATATGATTATTGAATAACA
* * * *
4658005 TATCTATGTTTGCAATTGGACCATGCGACGACAGCTCCACAACCACCGATAAGTTCTCCTCAGAC
64 TATCTATGTTTACAATTAGACCATGCGACGACAACTCCACAACCACCGAGAAGTTCTCCTCAGAC
*
4658070 TCACAGTGTTAACGAG
129 TCACAGTGTTAACGAC
** * *
4658086 GAGCCAATAAAGAT-GGTTATAATGGTTTGTGTTCAACAATTCCATATATGATTATTGAATAACA
1 GAGCCGGT-AAGATCGGTTCTAA-AGTTTGTGTTCAACAATTCCATATATGATTATTGAATAACA
* * * * ** *
4658150 TATCTGTGTTTACAGTTAGACCATGCGACGATAACTCCTCAACCATTGAGAGGTTCTCCTCAGA-
64 TATCTATGTTTACAATTAGACCATGCGACGACAACTCCACAACCACCGAGAAGTTCTCCTCAGAC
4658214 TGCACAGTGTTAACGATC
129 T-CACAGTGTTAACGA-C
* * * *
4658232 GA-TCGGTAAGATCGGTTCTAACAGTTTGTGTTCAAC-ATCTCCACATATGTTTATTGAGTAACA
1 GAGCCGGTAAGATCGGTTCTAA-AGTTTGTGTTCAACAAT-TCCATATATGATTATTGAATAACA
4658295 CATTAATTTC
Statistics
Matches: 174, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
144 8 0.05
145 162 0.93
146 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (144 bp):
GAGCCGGTAAGATCGGTTCTAAAGTTTGTGTTCAACAATTCCATATATGATTATTGAATAACATA
TCTATGTTTACAATTAGACCATGCGACGACAACTCCACAACCACCGAGAAGTTCTCCTCAGACTC
ACAGTGTTAACGAC
Found at i:4660564 original size:118 final size:117
Alignment explanation
Indices: 4660349--4660823 Score: 571
Period size: 118 Copynumber: 4.0 Consensus size: 117
4660339 CTGGAACAAG
* * * * * * * * *
4660349 TCAGCGTGTCACGCCAAGTATTTGGTTCCACT-AAGCGTGTCAGCAC-A-ATTGGGACCTGCTGT
1 TCAGCGTGTCATGCCAACTATCTGCTTCCACTCAA-CGTGTCACCACAAGATAGAG-CGTGCCGT
** *
4660411 GTCACCCCACAATATAGCAAGAAGTCAGTGTGTCACCACATAAATCTGCATGCAC
64 GTCACCCCACAATAT-GCAAGAAGTCAGCATGTCACCACAGAAATCTGCATGCAC
** * *
4660466 TCAGTATGTCATGCCAACTATCTACTTCCACTCAACATGTCACCACAAGATAGAGCGTGCCGTGT
1 TCAGCGTGTCATGCCAACTATCTGCTTCCACTCAACGTGTCACCACAAGATAGAGCGTGCCGTGT
* **
4660531 CACCCCACAATACTGCAAGAAGTCAACATGTCACCACAGAAATCTTTATGCAC
66 CACCCCACAATA-TGCAAGAAGTCAGCATGTCACCACAGAAATCTGCATGCAC
* * *
4660584 TCAGCGTGTCATGCCAACTATCTGTTTCCACTTAACGTGTCACCACAAGATAGGGCGTGCCGTGT
1 TCAGCGTGTCATGCCAACTATCTGCTTCCACTCAACGTGTCACCACAAGATAGAGCGTGCCGTGT
* * ** * *
4660649 TACCCCATAATATTAAAAGAAGTCAGTATGTCACCATAGAAATCTGCATGCAC
66 CACCCCACAATA-TGCAAGAAGTCAGCATGTCACCACAGAAATCTGCATGCAC
* *
4660702 TCAGCGTGTCACGCCAACTATCTGCTTCCACTCAACGTGTCACCACAAGATA-AGGCGTGTCGTG
1 TCAGCGTGTCATGCCAACTATCTGCTTCCACTCAACGTGTCACCACAAGATAGA-GCGTGCCGTG
* *
4660766 TCACCCCATAATAATGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCAC
65 TCACCCCACAAT-ATGCAAGAAGTCAGCATGTCACCACAGAAATCTGCATGCAC
4660820 TCAG
1 TCAG
4660824 TGTGCTAGCT
Statistics
Matches: 305, Mismatches: 47, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
117 34 0.11
118 265 0.87
119 6 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (117 bp):
TCAGCGTGTCATGCCAACTATCTGCTTCCACTCAACGTGTCACCACAAGATAGAGCGTGCCGTGT
CACCCCACAATATGCAAGAAGTCAGCATGTCACCACAGAAATCTGCATGCAC
Found at i:4660736 original size:236 final size:235
Alignment explanation
Indices: 4660349--4660823 Score: 643
Period size: 236 Copynumber: 2.0 Consensus size: 235
4660339 CTGGAACAAG
* * * * *
4660349 TCAGCGTGTCACGCCAAGTATTTGGTTCCACTAAGCGTGTCAGCACAATTGGGACCTGCTGTGTC
1 TCAGCGTGTCACGCCAACTATCTGGTTCCACTAAGCGTGTCACCACAATAGGGACCTGCCGTGTC
* * * * *
4660414 ACCCCACAATATAGCAAGAAGTCAGTGTGTCACCACATAAATCTGCATGCACTCAGTATGTCATG
66 ACCCCACAATATAGAAAGAAGTCAGTATGTCACCACAGAAATCTGCATGCACTCAGCATGTCACG
4660479 CCAACTATCTACTTCCACTCAACATGTCACCACAAGAT-AGAGCGTGCCGTGTCACCCCACAATA
131 CCAACTATCTACTTCCACTCAACATGTCACCACAAGATAAG-GCGTGCCGTGTCACCCCACAATA
* **
4660543 CTGCAAGAAGTCAACATGTCACCACAGAAATCTTTATGCAC
195 ATGCAAGAAGTCAACATGTCACCACAGAAATCTGCATGCAC
* * *
4660584 TCAGCGTGTCATGCCAACTATCTGTTTCCACTTAA-CGTGTCACCACAAGATAGGG-CGTGCCGT
1 TCAGCGTGTCACGCCAACTATCTGGTTCCAC-TAAGCGTGTCACCAC-A-ATAGGGACCTGCCGT
* * * *
4660647 GTTACCCCATAATATTA-AAAGAAGTCAGTATGTCACCATAGAAATCTGCATGCACTCAGCGTGT
63 GTCACCCCACAATA-TAGAAAGAAGTCAGTATGTCACCACAGAAATCTGCATGCACTCAGCATGT
* * * *
4660711 CACGCCAACTATCTGCTTCCACTCAACGTGTCACCACAAGATAAGGCGTGTCGTGTCACCCCATA
127 CACGCCAACTATCTACTTCCACTCAACATGTCACCACAAGATAAGGCGTGCCGTGTCACCCCACA
* *
4660776 ATAATGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCAC
192 ATAATGCAAGAAGTCAACATGTCACCACAGAAATCTGCATGCAC
4660820 TCAG
1 TCAG
4660824 TGTGCTAGCT
Statistics
Matches: 209, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
235 37 0.18
236 163 0.78
237 9 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (235 bp):
TCAGCGTGTCACGCCAACTATCTGGTTCCACTAAGCGTGTCACCACAATAGGGACCTGCCGTGTC
ACCCCACAATATAGAAAGAAGTCAGTATGTCACCACAGAAATCTGCATGCACTCAGCATGTCACG
CCAACTATCTACTTCCACTCAACATGTCACCACAAGATAAGGCGTGCCGTGTCACCCCACAATAA
TGCAAGAAGTCAACATGTCACCACAGAAATCTGCATGCAC
Found at i:4664654 original size:31 final size:31
Alignment explanation
Indices: 4664616--4664779 Score: 229
Period size: 31 Copynumber: 5.3 Consensus size: 31
4664606 TTTGTCAGTT
** * *
4664616 ATGTTGTAACACACCATGCTTATAATGTAAA
1 ATGTTGTAACATGCCATGCATATAACGTAAA
*
4664647 ATGTTGTAACATGCCATGCATATAACGTTAA
1 ATGTTGTAACATGCCATGCATATAACGTAAA
*
4664678 ATGTTGTAACATGCCATGCAGATAACGTAAA
1 ATGTTGTAACATGCCATGCATATAACGTAAA
*
4664709 ATGTTGTAACATTCCATGCATATAACGTAAA
1 ATGTTGTAACATGCCATGCATATAACGTAAA
* * * *
4664740 ATGTTATAACACGCCATACATATAACATAAA
1 ATGTTGTAACATGCCATGCATATAACGTAAA
4664771 ATGTTGTAA
1 ATGTTGTAA
4664780 TACGCCAACG
Statistics
Matches: 118, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 118 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (31 bp):
ATGTTGTAACATGCCATGCATATAACGTAAA
Found at i:4673016 original size:21 final size:21
Alignment explanation
Indices: 4672992--4673031 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4672982 TCTTTATCAG
*
4672992 TTTCTTTA-ATTTTTTCATTAT
1 TTTC-TTAGATTTTTCCATTAT
4673013 TTTCTTAGATTTTTCCATT
1 TTTCTTAGATTTTTCCATT
4673032 CTAACAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.17, C:0.12, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTCTTAGATTTTTCCATTAT
Found at i:4675842 original size:28 final size:28
Alignment explanation
Indices: 4675810--4675866 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
4675800 TCTGATAAAG
*
4675810 CCATTATACATTTGCAGTTTGGTTTTTT
1 CCATTATACATTTGCAGTTGGGTTTTTT
4675838 CCATTATACATTTGCAGTTGGGTTTTTT
1 CCATTATACATTTGCAGTTGGGTTTTTT
4675866 C
1 C
4675867 ACAGCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.51
Consensus pattern (28 bp):
CCATTATACATTTGCAGTTGGGTTTTTT
Found at i:4679858 original size:39 final size:36
Alignment explanation
Indices: 4679758--4679863 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
4679748 TCAGATACCA
*
4679758 ACTCAAATGCAGGAGAGCCTGGGAATGGAGAGGCCT
1 ACTCAAATGCAGGAGAGCCTGGGAATGGAGAGGCAT
*
4679794 ACTCAAATGCAGGAGAGCTTGGGAATGGAGAGGCAT
1 ACTCAAATGCAGGAGAGCCTGGGAATGGAGAGGCAT
4679830 ACTCAAATGCAGAAGGAGAGCCTGGGAATGGAGA
1 ACTCAAATGC---AGGAGAGCCTGGGAATGGAGA
4679864 TGCCAACTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
36 44 0.69
39 20 0.31
ACGTcount: A:0.34, C:0.16, G:0.36, T:0.14
Consensus pattern (36 bp):
ACTCAAATGCAGGAGAGCCTGGGAATGGAGAGGCAT
Found at i:4681443 original size:25 final size:25
Alignment explanation
Indices: 4681382--4681447 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
4681372 TGGTGGCTTC
4681382 TTATTAGGCTCATGCT-AAGCAGTT
1 TTATTAGGCTCATGCTAAAGCAGTT
** *
4681406 TTATGGGGTTCATGCTAAAGCAGTT
1 TTATTAGGCTCATGCTAAAGCAGTT
4681431 TTATTAGGCTCATGCTA
1 TTATTAGGCTCATGCTA
4681448 CTCCTAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 13 0.37
25 22 0.63
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (25 bp):
TTATTAGGCTCATGCTAAAGCAGTT
Found at i:4688922 original size:2 final size:2
Alignment explanation
Indices: 4688915--4688946 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4688905 GTGTTAATAA
4688915 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
4688947 TCTTACTTGA
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:4693329 original size:72 final size:72
Alignment explanation
Indices: 4693242--4693622 Score: 287
Period size: 81 Copynumber: 5.1 Consensus size: 72
4693232 TATTTAAAAA
* *
4693242 ATTCAAATAAGTCTTTTTTCTCATTTTTTAACAAATGTCTATAGCTTTTATGAAGAAATATGCTC
1 ATTCAAAAAAGTCTTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTC
4693307 CTAAATT
66 CTAAATT
* *
4693314 ATTCAAAAAAGTCTTTTTACTCATTTTTTAGCAAAAGTCTATAGCTTTTATGAAGAAATATGCTC
1 ATTCAAAAAAGTCTTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTC
4693379 CTAAATTATT
66 CT-AA--ATT
* * ** ** * * **
4693389 CAAAAATTCAAATAAAATCTATTTTCTTGTTTTTTAACAATGGCCAATAGC--TCCT----AAAT
1 -----ATTCAAA-AAAGTCTTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAAT
**
4693448 AT--T--TAAAAA
60 ATGCTCCTAAATT
* * *
4693457 ATTCAAAGAAGTCAATTTTTTTTTCATTTTTTAACAAAAGTCTACAGCTTTTATGAAGAAATATG
1 ATTCAAAAAAGTC---TTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATG
*
4693522 CTTCTTAACTATT
63 C-TCCTAA--ATT
* * *
4693535 CAGAAAATTCAAATAAGTCTTTTTTCTCGTTTTTAAACAAAAGTCTATAGCTTTTATGAAGAAAT
1 ------ATTCAAAAAAGTCTTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAAT
*
4693600 ATGCTTCTAAATT
60 ATGCTCCTAAATT
4693613 ATTCAAAAAA
1 ATTCAAAAAA
4693623 TTCAAATAAG
Statistics
Matches: 237, Mismatches: 41, Indels: 62
0.70 0.12 0.18
Matches are distributed among these distances:
62 4 0.02
63 7 0.03
65 23 0.10
67 2 0.01
68 1 0.00
70 2 0.01
71 7 0.03
72 72 0.30
73 3 0.01
74 1 0.00
75 9 0.04
76 3 0.01
78 4 0.02
79 2 0.01
80 11 0.05
81 74 0.31
84 12 0.05
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (72 bp):
ATTCAAAAAAGTCTTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTC
CTAAATT
Found at i:4693574 original size:81 final size:81
Alignment explanation
Indices: 4693434--4693649 Score: 292
Period size: 81 Copynumber: 2.7 Consensus size: 81
4693424 AACAATGGCC
* * * * * *
4693434 AATA-GCTCCTAAA-TATTTAAAAAATTCAAAGAAGTCAATTTTTTTTTCATTTTTTAACAAAAG
1 AATATGCTTCTAAACTATTCAAAAAATTCAAATAAGTC---TTTTTTCTCGTTTTTAAACAAAAG
4693497 TCTACAGCTTTTATGAAGA
63 TCTACAGCTTTTATGAAGA
* *
4693516 AATATGCTTCTTAACTATTCAGAAAATTCAAATAAGTCTTTTTTCTCGTTTTTAAACAAAAGTCT
1 AATATGCTTCTAAACTATTCAAAAAATTCAAATAAGTCTTTTTTCTCGTTTTTAAACAAAAGTCT
*
4693581 ATAGCTTTTATGAAGA
66 ACAGCTTTTATGAAGA
* *
4693597 AATATGCTTCTAAATTATTCAAAAAATTCAAATAAGTCCTTTTTCTCGTTTTT
1 AATATGCTTCTAAACTATTCAAAAAATTCAAATAAGTCTTTTTTCTCGTTTTT
4693650 TAGCATAGTC
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
81 88 0.74
82 4 0.03
83 7 0.06
84 20 0.17
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.41
Consensus pattern (81 bp):
AATATGCTTCTAAACTATTCAAAAAATTCAAATAAGTCTTTTTTCTCGTTTTTAAACAAAAGTCT
ACAGCTTTTATGAAGA
Found at i:4693650 original size:227 final size:224
Alignment explanation
Indices: 4693227--4693797 Score: 758
Period size: 227 Copynumber: 2.6 Consensus size: 224
4693217 TAAAAATTCT
* * *
4693227 TAAATTATTTAAAAAATTCAAATAAGTCTTTTTTCTCATTTTTTAACAAATGTCTATAGCTTTTA
1 TAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTTCATTTTTTAACAAAAGTCTACAGCTTTTA
* * * * *
4693292 TGAAGAAATATGC-TCCTAA--ATT------ATTCAAAAAAGTCTTTTTACTCATTTTTTAGCAA
66 TGAAGAAATATGCTTCTTAACTATTCAGAAAATTCAAATAAGTCTTTTTTCTCATTTTTAAACAA
4693348 AAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAAATTCAAATAAAATCTATTT
131 AAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAAATTCAAATAAAATCTATTT
* *
4693413 TCTTGTTTTTTAACAATGGCCAATAGCTCC
196 TCTCGTTTTTTAAC-ATAGCCAATAGCTCC
*
4693443 TAAA-TATTTAAAAAATTCAAAGAAGTCAATTTTTTTTTCATTTTTTAACAAAAGTCTACAGCTT
1 TAAATTATTTAAAAAATTCAAATAAGTC---TTTTTTTTCATTTTTTAACAAAAGTCTACAGCTT
*
4693507 TTATGAAGAAATATGCTTCTTAACTATTCAGAAAATTCAAATAAGTCTTTTTTCTCGTTTTTAAA
63 TTATGAAGAAATATGCTTCTTAACTATTCAGAAAATTCAAATAAGTCTTTTTTCTCATTTTTAAA
* *
4693572 CAAAAGTCTATAGCTTTTATGAAGAAATATGCTTCTAAATTATTCAAAAAATTCAAAT-AAGTCC
128 CAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTC-AAAAATTCAAATAAAAT-C
* * * *
4693636 T-TTTTCTCGTTTTTTAGCATAGTCTATAGCTCT
191 TATTTTCTCGTTTTTTAACATAGCCAATAGCTCC
* *
4693669 TAAATTATTTAAAAAATTCAAATAAG-CTATTTTTTCGTTTTTTAACAAAAGTCTACAGCTTTTA
1 TAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTTCATTTTTTAACAAAAGTCTACAGCTTTTA
* *
4693733 TGAAGAAATATGCTCCTAAACTATTCAGAAAATTCAAATACA-T-TTTTTTCTCATTATTTACAA
66 TGAAGAAATATGCTTCTTAACTATTCAGAAAATTCAAATA-AGTCTTTTTTCTCATT-TTTA-AA
4693796 CA
128 CA
4693798 GTCTACATCT
Statistics
Matches: 313, Mismatches: 24, Indels: 28
0.86 0.07 0.08
Matches are distributed among these distances:
215 22 0.07
216 4 0.01
218 47 0.15
219 5 0.02
221 3 0.01
222 11 0.04
223 78 0.25
224 5 0.02
226 16 0.05
227 108 0.35
228 14 0.04
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (224 bp):
TAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTTCATTTTTTAACAAAAGTCTACAGCTTTTA
TGAAGAAATATGCTTCTTAACTATTCAGAAAATTCAAATAAGTCTTTTTTCTCATTTTTAAACAA
AAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAAATTCAAATAAAATCTATTT
TCTCGTTTTTTAACATAGCCAATAGCTCC
Found at i:4693710 original size:142 final size:142
Alignment explanation
Indices: 4693538--4693843 Score: 422
Period size: 142 Copynumber: 2.1 Consensus size: 142
4693528 AACTATTCAG
*
4693538 AAAATTCAAATAAGTCTTTTTTCTCGTTTTTAAACAAAAGTCTATAGCTTTTATGAAGAAATATG
1 AAAATTCAAATAAG-CTTTTTTCTCGTTTTTAAACAAAAGTCTACAGCTTTTATGAAGAAATATG
* * * * * *
4693603 CTTCTAAATTATTCAAAAAATTCAAATA-AGTCCTTTTTCTCGTTTTTTAGC-ATAGTCTATAGC
65 CTCCTAAACTATTCAAAAAATTCAAATACA-T-CTTTTTCTCATTATTTA-CAACAGTCTACAGC
*
4693666 TCTTAAATTA-TTTAA
127 TCCTAAATTATTTTAA
*
4693681 AAAATTCAAATAAGCTATTTTT-TCGTTTTTTAACAAAAGTCTACAGCTTTTATGAAGAAATATG
1 AAAATTCAAATAAGCT-TTTTTCTCGTTTTTAAACAAAAGTCTACAGCTTTTATGAAGAAATATG
* * *
4693745 CTCCTAAACTATTCAGAAAATTCAAATACATTTTTTTCTCATTATTTACAACAGTCTACATCTCC
65 CTCCTAAACTATTCAAAAAATTCAAATACATCTTTTTCTCATTATTTACAACAGTCTACAGCTCC
4693810 TAAATTATTTTTAA
130 TAAATTA-TTTTAA
4693824 AAAATTCAAATAAGCTTTTT
1 AAAATTCAAATAAGCTTTTT
4693844 ATGAAGAAAT
Statistics
Matches: 146, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
140 1 0.01
141 32 0.22
142 72 0.49
143 41 0.28
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (142 bp):
AAAATTCAAATAAGCTTTTTTCTCGTTTTTAAACAAAAGTCTACAGCTTTTATGAAGAAATATGC
TCCTAAACTATTCAAAAAATTCAAATACATCTTTTTCTCATTATTTACAACAGTCTACAGCTCCT
AAATTATTTTAA
Found at i:4693722 original size:62 final size:61
Alignment explanation
Indices: 4693607--4693728 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 61
4693597 AATATGCTTC
* * *
4693607 TAAATTATTCAAAAAATTCAAATAAGTCCTTTTTCTCGTTTTTTAGCATAGTCTATAGCTCT
1 TAAATTATTCAAAAAATTCAAATAAG-CCTTTTTCTCGTTTTTTAACAAAGTCTACAGCTCT
* *
4693669 TAAATTATTTAAAAAATTCAAATAAG-CTATTTTTTCGTTTTTTAACAAAAGTCTACAGCT
1 TAAATTATTCAAAAAATTCAAATAAGCCT-TTTTCTCGTTTTTTAAC-AAAGTCTACAGCT
4693729 TTTATGAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
60 2 0.04
61 15 0.28
62 36 0.68
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (61 bp):
TAAATTATTCAAAAAATTCAAATAAGCCTTTTTCTCGTTTTTTAACAAAGTCTACAGCTCT
Found at i:4694162 original size:82 final size:84
Alignment explanation
Indices: 4694068--4694230 Score: 233
Period size: 82 Copynumber: 2.0 Consensus size: 84
4694058 AAAACTCTTA
* * * *
4694068 AATTATTTAAAAAATTAAAATAAAT-TCTTGTATTTTTATTTTATAC-AAATTAGCCCTTATCA-
1 AATTATTCAAAAAATTAAAATAAATCT-TTATATTTTTATTTTAAACTAAATTAGCCCCTATCAT
*
4694130 TATTTTAAACCAAATTAGTT
65 TATTTTAAACAAAATTAGTT
* *
4694150 AATTATTCAAAAAATTCAAATAAATCTTTATATTTTTATTTTAAACTAAATTAGCCCCTATGATT
1 AATTATTCAAAAAATTAAAATAAATCTTTATATTTTTATTTTAAACTAAATTAGCCCCTATCATT
4694215 ATTTTAAACAAAATTA
66 ATTTTAAACAAAATTA
4694231 ATCCTTATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
82 40 0.56
83 15 0.21
84 16 0.23
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (84 bp):
AATTATTCAAAAAATTAAAATAAATCTTTATATTTTTATTTTAAACTAAATTAGCCCCTATCATT
ATTTTAAACAAAATTAGTT
Found at i:4694511 original size:28 final size:29
Alignment explanation
Indices: 4694479--4694533 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
4694469 AAAAAACTCA
*
4694479 TAAATTATTCAAAA-AAATTCAAATAACC
1 TAAATCATTCAAAAGAAATTCAAATAACC
* *
4694507 TAAATCATTTAAAAGAAGTTCAAATAA
1 TAAATCATTCAAAAGAAATTCAAATAA
4694534 GCCTTTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (29 bp):
TAAATCATTCAAAAGAAATTCAAATAACC
Found at i:4698429 original size:10 final size:10
Alignment explanation
Indices: 4698411--4698463 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
4698401 AAATAATAAT
*
4698411 AATAAAAATA
1 AATATAAATA
4698421 AATATAAATTA
1 AATATAAA-TA
4698432 AATA-AAATA
1 AATATAAATA
4698441 AA-ATAAATA
1 AATATAAATA
*
4698450 AAAATAAATA
1 AATATAAATA
4698460 AATA
1 AATA
4698464 AAAAAATCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 1 0.03
9 11 0.29
10 20 0.53
11 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AATATAAATA
Found at i:4698458 original size:14 final size:14
Alignment explanation
Indices: 4698401--4698467 Score: 73
Period size: 14 Copynumber: 4.6 Consensus size: 14
4698391 CATAAATTAA
* *
4698401 AAATAATAATAATAA
1 AAATAAAAATAA-AT
*
4698416 AAATAAATATAAATT
1 AAATAAAAATAAA-T
4698431 AAAT-AAAATAAAAT
1 AAATAAAAAT-AAAT
4698445 AAATAAAAATAAAT
1 AAATAAAAATAAAT
4698459 AAATAAAAA
1 AAATAAAAA
4698468 AATCGGGATG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
14 23 0.51
15 22 0.49
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:4713085 original size:178 final size:178
Alignment explanation
Indices: 4712624--4713150 Score: 646
Period size: 171 Copynumber: 3.0 Consensus size: 178
4712614 TATGATTATC
* * ** *
4712624 ATCTTCTCACGAAGGTCGAATCGAAAGCCCAACTCTTGCCCAGAAAAAGAGTTTCAAATATATTT
1 ATCTTCTCACGAAAGTCGAATC-AAGGCCCAACTCTTGCCCAGAAAAAGAGCCTCAAATGTATTT
* * * * * *
4712689 GAAAAAGCAGCCCAATCACTTTTGGTTGGACATGAATCATTTCATACATATGTCAAAATCAAAAA
65 GAAAAAGCGGCCCGATCACTCTTGGTTGGATATGAATCATTTCATACGTATGTCAAAATCCAAAA
*
4712754 ATGATAATTCAAT-TTAAATCATAATCCATCAAG------TATATATA-T
130 ATGAAAATTCAATCTT-AATCATAATCCATCAAGTATATATATATATATT
* *
4712796 ATCTTCACAC-AAAGGTCGAATAAAGGCCCAACTCTTGCCCAGAAAAAGAGCCTCAAATGTATTT
1 ATCTTCTCACGAAA-GTCGAATCAAGGCCCAACTCTTGCCCAGAAAAAGAGCCTCAAATGTATTT
* * * * * * *
4712860 GAACAAGCGGTCTGATCACTCTTGGTTAGATGTGAATCTTTTCATACGTATGTC-CAATCCCAAA
65 GAAAAAGCGGCCCGATCACTCTTGGTTGGATATGAATCATTTCATACGTATGTCAAAAT-CCAAA
* * * *
4712924 AGTAAAAACTCAATCTTAATCACAATCCATCAAGTATATATATATATATT
129 AATGAAAATTCAATCTTAATCATAATCCATCAAGTATATATATATATATT
* * *
4712974 ATCTTCTCACGAAAGTAGAATCAAGGCCCAACTCTTGCCAAGAAAAA-AACCTCAAATGTATTTG
1 ATCTTCTCACGAAAGTCGAATCAAGGCCCAACTCTTGCCCAGAAAAAGAGCCTCAAATGTATTTG
* *
4713038 AAAAAGCGGCCGGATCACTCTTGGTTGGATAT-ATAGTCATTTCATACGTATGTCTAAATCCAAA
66 AAAAAGCGGCCCGATCACTCTTGGTTGGATATGA-A-TCATTTCATACGTATGTCAAAATCCAAA
4713102 AATGAAAATTCAATCTTAATCATAATCCATCAAGTATATATATATATAT
129 AATGAAAATTCAATCTTAATCATAATCCATCAAGTATATATATATATAT
4713151 ATATATATAC
Statistics
Matches: 300, Mismatches: 41, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
170 3 0.01
171 113 0.38
172 18 0.06
176 1 0.00
177 52 0.17
178 107 0.36
179 6 0.02
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (178 bp):
ATCTTCTCACGAAAGTCGAATCAAGGCCCAACTCTTGCCCAGAAAAAGAGCCTCAAATGTATTTG
AAAAAGCGGCCCGATCACTCTTGGTTGGATATGAATCATTTCATACGTATGTCAAAATCCAAAAA
TGAAAATTCAATCTTAATCATAATCCATCAAGTATATATATATATATT
Found at i:4713143 original size:2 final size:2
Alignment explanation
Indices: 4713136--4713168 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
4713126 ATCCATCAAG
4713136 TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
4713169 AATAACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4713249 original size:2 final size:2
Alignment explanation
Indices: 4713242--4713282 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4713232 CCAACCCAAN
4713242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4713283 TAAATTTCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4729015 original size:24 final size:23
Alignment explanation
Indices: 4728968--4729019 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
4728958 TTAAAATATT
* * *
4728968 TTTTATTATAAATATTAATAAAA
1 TTTTATTATAAAAAATAAGAAAA
4728991 TTTTATTATAAAAAATAAGATAAA
1 TTTTATTATAAAAAATAAGA-AAA
4729015 TTTTA
1 TTTTA
4729020 CAAACCAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTTATTATAAAAAATAAGAAAA
Found at i:4735869 original size:30 final size:31
Alignment explanation
Indices: 4735828--4735901 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
4735818 ATATATATAA
*
4735828 TTTTAAAAATTTTATATGAGAAATAA-AATT
1 TTTTTAAAATTTTATATGAGAAATAATAATT
* **
4735858 TTTTTAAAATTTTATATGATAAATAATTTTT
1 TTTTTAAAATTTTATATGAGAAATAATAATT
*
4735889 TTTTTTAAATTTT
1 TTTTTAAAATTTT
4735902 GAGGGCTGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 24 0.63
31 14 0.37
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (31 bp):
TTTTTAAAATTTTATATGAGAAATAATAATT
Found at i:4737877 original size:13 final size:13
Alignment explanation
Indices: 4737852--4737885 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4737842 TATGTCAAAC
4737852 TTGTTTT-TTTTA
1 TTGTTTTATTTTA
*
4737864 TTTTTTTATTTTA
1 TTGTTTTATTTTA
4737877 TTGTTTTAT
1 TTGTTTTAT
4737886 GACAACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (13 bp):
TTGTTTTATTTTA
Found at i:4754833 original size:19 final size:21
Alignment explanation
Indices: 4754801--4754839 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4754791 GTAGTTAACT
*
4754801 ATTTTTAGTATTAT-TATTTA
1 ATTTTTACTATTATATATTTA
4754821 ATTTTTACT-TTATATATTT
1 ATTTTTACTATTATATATTT
4754840 TTTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
ATTTTTACTATTATATATTTA
Found at i:4754845 original size:7 final size:7
Alignment explanation
Indices: 4754811--4754901 Score: 60
Period size: 7 Copynumber: 12.7 Consensus size: 7
4754801 ATTTTTAGTA
*
4754811 TTATTAT
1 TTATTTT
*
4754818 TTAATTT
1 TTATTTT
4754825 TTACTTTAT
1 TTA-TTT-T
*
4754834 ATATTTT
1 TTATTTT
4754841 TTATTATT
1 TTATT-TT
*
4754849 ATATTTT
1 TTATTTT
*
4754856 CTA-TTT
1 TTATTTT
4754862 TTATTTT
1 TTATTTT
*
4754869 TTA-TTA
1 TTATTTT
4754875 TTATTTT
1 TTATTTT
**
4754882 TTACATT
1 TTATTTT
4754889 TTATATTT
1 TTAT-TTT
4754897 TTATT
1 TTATT
4754902 CTAAGTTTCT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
6 10 0.16
7 34 0.53
8 17 0.27
9 3 0.05
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTT
Found at i:4754866 original size:13 final size:13
Alignment explanation
Indices: 4754811--4754901 Score: 74
Period size: 15 Copynumber: 6.4 Consensus size: 13
4754801 ATTTTTAGTA
*
4754811 TTATTATTTAATTT
1 TTATT-TTTATTTT
4754825 TTACTTTATATATTTT
1 TTA-TTT-T-TATTTT
4754841 TTATTATTATATTTT
1 TTATT-TT-TATTTT
*
4754856 CTATTTTTATTTT
1 TTATTTTTATTTT
*
4754869 TTATTATTATTTT
1 TTATTTTTATTTT
*
4754882 TTACATTTTATATTT
1 TTA-TTTTTAT-TTT
4754897 TTATT
1 TTATT
4754902 CTAAGTTTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
13 20 0.31
14 12 0.19
15 23 0.36
16 9 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:4754901 original size:28 final size:29
Alignment explanation
Indices: 4754811--4754898 Score: 110
Period size: 28 Copynumber: 3.0 Consensus size: 29
4754801 ATTTTTAGTA
*
4754811 TTATTATTTAATTTTTAC-TTTATATATTTT
1 TTATTA-TTATTTTTTACATTT-TATATTTT
*
4754841 TTATTATTATATTTT-CTATTTT-TATTTT
1 TTATTATTATTTTTTAC-ATTTTATATTTT
4754869 TTATTATTATTTTTTACATTTTATATTTT
1 TTATTATTATTTTTTACATTTTATATTTT
4754898 T
1 T
4754899 ATTCTAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
28 26 0.51
29 16 0.31
30 9 0.18
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (29 bp):
TTATTATTATTTTTTACATTTTATATTTT
Found at i:4756394 original size:57 final size:58
Alignment explanation
Indices: 4756297--4756427 Score: 219
Period size: 57 Copynumber: 2.3 Consensus size: 58
4756287 AGATCAGTCT
* *
4756297 TCCCTCTTTCGCTCTCTCTCTCTCTGGTCGCCGACCCCTCTCTCAAATCCGATTGGTCC
1 TCCCTC-TTCGCTCTCTCTCTCTCTGGTCGCCGACCCCTCTCTCAAATCCAATCGGTCC
*
4756356 TCCCTCTTCGCTCTCTCTCTCT-TGGTCGTCGACCCCTCTCTCAAATCCAATCGGTCC
1 TCCCTCTTCGCTCTCTCTCTCTCTGGTCGCCGACCCCTCTCTCAAATCCAATCGGTCC
4756413 TCCCTCTTCGCTCTC
1 TCCCTCTTCGCTCTC
4756428 ACTACACAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
57 47 0.68
58 16 0.23
59 6 0.09
ACGTcount: A:0.08, C:0.45, G:0.12, T:0.34
Consensus pattern (58 bp):
TCCCTCTTCGCTCTCTCTCTCTCTGGTCGCCGACCCCTCTCTCAAATCCAATCGGTCC
Found at i:4756459 original size:10 final size:10
Alignment explanation
Indices: 4756446--4756489 Score: 51
Period size: 8 Copynumber: 4.7 Consensus size: 10
4756436 AGTTTTTTTC
4756446 TTTTTTGGTA
1 TTTTTTGGTA
4756456 --TTTTGGATA
1 TTTTTTGG-TA
4756465 TTTTTTGGTA
1 TTTTTTGGTA
4756475 TTTTTT-G-A
1 TTTTTTGGTA
4756483 TTTTTTG
1 TTTTTTG
4756490 TGGATTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
8 13 0.43
9 3 0.10
10 8 0.27
11 6 0.20
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.70
Consensus pattern (10 bp):
TTTTTTGGTA
Found at i:4756824 original size:6 final size:6
Alignment explanation
Indices: 4756803--4756839 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
4756793 CTTTTCTCTG
4756803 TTTTA- TTTTA- TTTTAT TTTTAT TTTTATT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TT
4756840 GTTGTTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.33
6 14 0.47
7 6 0.20
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:4756893 original size:11 final size:11
Alignment explanation
Indices: 4756804--4756893 Score: 51
Period size: 11 Copynumber: 8.0 Consensus size: 11
4756794 TTTTCTCTGT
*
4756804 TTTATTTTAT-
1 TTTATTTTTTA
*
4756814 TTTATTTTTATT
1 TTTATTTTT-TA
4756826 TTTATTTTTTA
1 TTTATTTTTTA
* *
4756837 TTTGTTGTTTA
1 TTTATTTTTTA
*
4756848 TCTT-TTGTTTAA
1 T-TTATT-TTTTA
4756860 TATTATTTTTTA
1 T-TTATTTTTTA
* *
4756872 -TCATATATTTA
1 TTTAT-TTTTTA
4756883 TTTATTTTTTA
1 TTTATTTTTTA
4756894 AATACAAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
10 11 0.18
11 24 0.39
12 24 0.39
13 2 0.03
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:4757139 original size:38 final size:37
Alignment explanation
Indices: 4757017--4757464 Score: 524
Period size: 37 Copynumber: 11.9 Consensus size: 37
4757007 TTTTTTAATG
* * * *
4757017 AACTTCTCAAAATTGAGACAATAAAACTTTAAAAATA
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
*
4757054 AACTCCTCAAAATTGAGGCAATGAAACTTT-AAAATA
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
* * * * * * *
4757090 AATTCCTCAAAATTTAGGTAACGACATTTTTAAAACTA
1 AACTCCTCAAAATTGAGGCAATGAGA-CTTTAAAAATA
* * *
4757128 AACTCCTCAAAATTAAGGCAA-GAAAACTTTAAGAATA
1 AACTCCTCAAAATTGAGGCAATG-AGACTTTAAAAATA
4757165 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
4757202 GAACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
1 -AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
*
4757240 GAACTCCTCAAAATTGAGACAATGAGACTTTAAAAATA
1 -AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
*
4757278 AACTCCTCAAAATTGAGGCAATGAGACTTTTTAAAAAATT
1 AACTCCTCAAAATTGAGGCAATGAGAC--TTT-AAAAATA
*
4757318 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATG
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
** ** *
4757355 AACTCCTCAAAGCTGAGGCAACAAGACTTTTAAAAATG
1 AACTCCTCAAAATTGAGGCAATGAGAC-TTTAAAAATA
* * * *
4757393 AACTCCTCAAAACTGAGGCAACGAAACTTCT-ATAATA
1 AACTCCTCAAAATTGAGGCAATGAGACTT-TAAAAATA
* * *
4757430 AACTCCTCAAAACTGAGGCAATGGGACTTTTAAAA
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAA
4757465 GTCTTGAAAC
Statistics
Matches: 363, Mismatches: 37, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
36 28 0.08
37 161 0.44
38 138 0.38
39 3 0.01
40 33 0.09
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (37 bp):
AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA
Found at i:4757211 original size:75 final size:74
Alignment explanation
Indices: 4757017--4757464 Score: 524
Period size: 75 Copynumber: 6.0 Consensus size: 74
4757007 TTTTTTAATG
* * * * *
4757017 AACTTCTCAAAATTGAGACAATAAAACTTTAAAAATAAACTCCTCAAAATTGAGGCAATGAAACT
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATAAACTCCTCAAAATTGAGGCAATGAGACT
4757082 TT-AAAATA
66 TTAAAAATA
* * * * * * * * *
4757090 AATTCCTCAAAATTTAGGTAACGACATTTTTAAAACTAAACTCCTCAAAATTAAGGCAA-GAAAA
1 AACTCCTCAAAATTGAGGCAATGAGA-CTTTAAAAATAAACTCCTCAAAATTGAGGCAATG-AGA
*
4757154 CTTTAAGAATA
64 CTTTAAAAATA
4757165 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATAGAACTCCTCAAAATTGAGGCAATGAGAC
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATA-AACTCCTCAAAATTGAGGCAATGAGAC
4757230 TTTAAAAATA
65 TTTAAAAATA
*
4757240 GAACTCCTCAAAATTGAGACAATGAGACTTTAAAAATAAACTCCTCAAAATTGAGGCAATGAGAC
1 -AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATAAACTCCTCAAAATTGAGGCAATGAGAC
*
4757305 TTTTTAAAAAATT
65 --TTT-AAAAATA
* ** **
4757318 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATGAACTCCTCAAAGCTGAGGCAACAAGACT
1 AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATAAACTCCTCAAAATTGAGGCAATGAGAC-
*
4757383 TTTAAAAATG
65 TTTAAAAATA
* * * * * *
4757393 AACTCCTCAAAACTGAGGCAACGAAACTTCT-ATAATAAACTCCTCAAAACTGAGGCAATGGGAC
1 AACTCCTCAAAATTGAGGCAATGAGACTT-TAAAAATAAACTCCTCAAAATTGAGGCAATGAGAC
*
4757457 TTTTAAAA
65 TTTAAAAA
4757465 GTCTTGAAAC
Statistics
Matches: 324, Mismatches: 41, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
73 19 0.06
74 52 0.16
75 144 0.44
76 42 0.13
77 61 0.19
78 6 0.02
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (74 bp):
AACTCCTCAAAATTGAGGCAATGAGACTTTAAAAATAAACTCCTCAAAATTGAGGCAATGAGACT
TTAAAAATA
Found at i:4757535 original size:26 final size:26
Alignment explanation
Indices: 4757506--4757583 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 26
4757496 AGATGCACTT
*
4757506 GGAGGATTTAAGAGAATAATGTGTCC
1 GGAGGATTTAAGAGAATAATGTGCCC
* * *
4757532 GGAGGACTT--CAG---AATGTACCC
1 GGAGGATTTAAGAGAATAATGTGCCC
4757553 GGAGGATTTAAGAGAATAATGTGCCC
1 GGAGGATTTAAGAGAATAATGTGCCC
4757579 GGAGG
1 GGAGG
4757584 TCTTCAGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
21 15 0.38
23 2 0.05
24 2 0.05
26 21 0.52
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (26 bp):
GGAGGATTTAAGAGAATAATGTGCCC
Found at i:4757575 original size:47 final size:47
Alignment explanation
Indices: 4757506--4757609 Score: 181
Period size: 47 Copynumber: 2.2 Consensus size: 47
4757496 AGATGCACTT
*
4757506 GGAGGATTTAAGAGAATAATGTGTCCGGAGGACTTCAGAATGTACCC
1 GGAGGATTTAAGAGAATAATGTGCCCGGAGGACTTCAGAATGTACCC
*
4757553 GGAGGATTTAAGAGAATAATGTGCCCGGAGGTCTTCAGAATGTACCC
1 GGAGGATTTAAGAGAATAATGTGCCCGGAGGACTTCAGAATGTACCC
*
4757600 GGAAGATTTA
1 GGAGGATTTA
4757610 GGAAATGTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (47 bp):
GGAGGATTTAAGAGAATAATGTGCCCGGAGGACTTCAGAATGTACCC
Found at i:4769724 original size:15 final size:13
Alignment explanation
Indices: 4769715--4769801 Score: 75
Period size: 14 Copynumber: 6.2 Consensus size: 13
4769705 CTATTTTTAG
*
4769715 TATTATTATTTAAT
1 TATTATTATTT-TT
*
4769729 TATTATTTTATTTT
1 TATTATTAT-TTTT
4769743 TACTTTATATATTTTT
1 TA--TTAT-TATTTTT
4769759 TATTATTATATTTT
1 TATTATTAT-TTTT
* *
4769773 CTATTTTTATTTCT
1 -TATTATTATTTTT
4769787 TATTATTATTTTT
1 TATTATTATTTTT
4769800 TA
1 TA
4769802 CATTTTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
13 16 0.27
14 22 0.37
15 10 0.17
16 10 0.17
17 2 0.03
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTATTTTT
Found at i:4769732 original size:11 final size:11
Alignment explanation
Indices: 4769715--4769767 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
4769705 CTATTTTTAG
4769715 TATTATTATTT
1 TATTATTATTT
*
4769726 AATTATTATTT
1 TATTATTATTT
* *
4769737 TATTTTTACTT
1 TATTATTATTT
4769748 TATATATT-TTT
1 TAT-TATTATTT
4769759 TATTATTAT
1 TATTATTAT
4769768 ATTTTCTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 4 0.12
11 27 0.79
12 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTATTT
Found at i:4769777 original size:7 final size:6
Alignment explanation
Indices: 4769706--4769818 Score: 57
Period size: 7 Copynumber: 16.7 Consensus size: 6
4769696 TNCAGTTAAC
* * *
4769706 TATTTT TAGTAT TATTATT TAATTAT TA-TTT TATTTT TACTTTAT ATATTTTT
1 TATTTT TATTTT TATT-TT T-ATTTT TATTTT TATTTT TA-TTT-T -TA-TTTT
*
4769759 TATTATT ATATTTT CTATTTT TATTTCT TATTAT TATTTTT TACATTTT
1 TATT-TT -TATTTT -TATTTT TATTT-T TATTTT TA-TTTT T--ATTTT
4769808 ATATTTT TATT
1 -TATTTT TATT
4769819 CTAAGTTTCA
Statistics
Matches: 84, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
5 4 0.05
6 27 0.32
7 33 0.39
8 13 0.15
9 7 0.08
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.71
Consensus pattern (6 bp):
TATTTT
Found at i:4769784 original size:28 final size:29
Alignment explanation
Indices: 4769728--4769815 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 29
4769718 TATTATTTAA
*
4769728 TTATTATTTTATTTT-TACTTTATATATTTT
1 TTATTATTATATTTTCTA-TTT-TATATTTT
*
4769758 TTATTATTATATTTTCTATTTT-TATTTC
1 TTATTATTATATTTTCTATTTTATATTTT
*
4769786 TTATTATTATTTTTTAC-ATTTTATATTTT
1 TTATTATTATATTTT-CTATTTTATATTTT
4769815 T
1 T
4769816 ATTCTAAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
28 24 0.47
29 8 0.16
30 17 0.33
31 2 0.04
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (29 bp):
TTATTATTATATTTTCTATTTTATATTTT
Found at i:4771294 original size:58 final size:62
Alignment explanation
Indices: 4771187--4771330 Score: 224
Period size: 59 Copynumber: 2.4 Consensus size: 62
4771177 CCTTGGCTTG
*
4771187 ATCGGTCCTCCCTCTTTCGCTCTCTCTCTCTCTCTCTGGCCGTCGACCCCTCTCTCAAAT-CG
1 ATCGGTCCTCCCTCTTT-GCTCTCTCTCTCTCTCTCTGGCCGTCGACCCCTCTCTCAAATCCA
*
4771249 ATTGGTCCTCCCTCTTTGCTCTCTCTCT-T-TCT-TGGCCGTCGACCCCTCTCTCAAATCCA
1 ATCGGTCCTCCCTCTTTGCTCTCTCTCTCTCTCTCTGGCCGTCGACCCCTCTCTCAAATCCA
*
4771308 ATCGGTCCTCCCTCTTCGCTCTC
1 ATCGGTCCTCCCTCTTTGCTCTC
4771331 ACTGCACAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
58 24 0.31
59 25 0.32
60 1 0.01
61 11 0.14
62 16 0.21
ACGTcount: A:0.08, C:0.44, G:0.12, T:0.35
Consensus pattern (62 bp):
ATCGGTCCTCCCTCTTTGCTCTCTCTCTCTCTCTCTGGCCGTCGACCCCTCTCTCAAATCCA
Found at i:4771720 original size:10 final size:10
Alignment explanation
Indices: 4771707--4771733 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4771697 TTTTTCTCTT
4771707 TTTTTTTTTA
1 TTTTTTTTTA
4771717 TTTTTTTTTA
1 TTTTTTTTTA
4771727 TTTTTTT
1 TTTTTTT
4771734 GTTTGTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:4776362 original size:33 final size:33
Alignment explanation
Indices: 4776308--4776382 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
4776298 TCTTTCAATG
* *
4776308 TAAAGAGTTGTTTCTTCTCATAATATAAATATT
1 TAAAGAGTTGTTTCCTATCATAATATAAATATT
* *
4776341 TAAACAGTTGTTTCCTATCATAATATAACTATT
1 TAAAGAGTTGTTTCCTATCATAATATAAATATT
*
4776374 CAAAGAGTT
1 TAAAGAGTT
4776383 ATATTTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (33 bp):
TAAAGAGTTGTTTCCTATCATAATATAAATATT
Found at i:4785977 original size:2 final size:2
Alignment explanation
Indices: 4785970--4786035 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
4785960 ATAATATTAC
4785970 AT AT AT AT AT 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 AT AT AT AT AT
*
4786012 -T AT -T NT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4786036 GTATTGTGCT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
1 2 0.03
2 59 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4792630 original size:22 final size:23
Alignment explanation
Indices: 4792597--4792639 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
4792587 TCAAATAAAA
4792597 AAAAGAAAAAAATCTCAACATTT
1 AAAAGAAAAAAATCTCAACATTT
4792620 AAAA-AAAAAAATCTCAACAT
1 AAAAGAAAAAAATCTCAACAT
4792640 GAGATCTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (23 bp):
AAAAGAAAAAAATCTCAACATTT
Found at i:4799452 original size:21 final size:21
Alignment explanation
Indices: 4799428--4799467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4799418 TAGTTACGAG
* *
4799428 AATCAATTCATTTTCTTCCAC
1 AATCAAATCAGTTTCTTCCAC
4799449 AATCAAATCAGTTTCTTCC
1 AATCAAATCAGTTTCTTCC
4799468 TTTCTCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.40
Consensus pattern (21 bp):
AATCAAATCAGTTTCTTCCAC
Found at i:4808619 original size:14 final size:14
Alignment explanation
Indices: 4808602--4808628 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4808592 CAAAATTTAT
4808602 TAATTAACTAAAAC
1 TAATTAACTAAAAC
4808616 TAATTAACTAAAA
1 TAATTAACTAAAA
4808629 TTAAAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:4809744 original size:25 final size:26
Alignment explanation
Indices: 4809707--4809761 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
4809697 TACAAAAAAT
4809707 ATAAAAATCAATAA-ATAATAACTAAA
1 ATAAAAATCAATAACATAA-AACTAAA
* *
4809733 ATAAAAA-GAATAACATAAAATTAAA
1 ATAAAAATCAATAACATAAAACTAAA
4809758 ATAA
1 ATAA
4809762 CTCACTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (26 bp):
ATAAAAATCAATAACATAAAACTAAA
Found at i:4809772 original size:20 final size:18
Alignment explanation
Indices: 4809741--4809791 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
4809731 AAATAAAAAG
*
4809741 AATAA-CAT-AAAATTAA
1 AATAATCATAAAAACTAA
4809757 AATAACTCACTAAAAACTAA
1 AATAA-TCA-TAAAAACTAA
*
4809777 CATAATCATAAAAAC
1 AATAATCATAAAAAC
4809792 AACTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 5 0.17
18 9 0.31
19 4 0.14
20 11 0.38
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.22
Consensus pattern (18 bp):
AATAATCATAAAAACTAA
Found at i:4817067 original size:14 final size:14
Alignment explanation
Indices: 4817048--4817074 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4817038 CAAAATTTAT
4817048 TAATTAACTAAAAC
1 TAATTAACTAAAAC
4817062 TAATTAACTAAAA
1 TAATTAACTAAAA
4817075 TTAAAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:4830891 original size:57 final size:57
Alignment explanation
Indices: 4830801--4830926 Score: 180
Period size: 57 Copynumber: 2.2 Consensus size: 57
4830791 AGTGTGTGAG
* * * * * *
4830801 AAGATGGAAAATGGGTGTAGATGGGGGGTTCATGTCCATCATATTGTTGTAGCGAGA
1 AAGATGGAAAATAGGTATAGATGGAGGGCTCATGCCCATCATATTATTGTAGCGAGA
* *
4830858 AAGATGGCAAATAGGTATAGATGGAGGGCTCATGCCCATCATATTATTGTAGGGAGA
1 AAGATGGAAAATAGGTATAGATGGAGGGCTCATGCCCATCATATTATTGTAGCGAGA
4830915 AAGATGGAAAAT
1 AAGATGGAAAAT
4830927 GTGTGTAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (57 bp):
AAGATGGAAAATAGGTATAGATGGAGGGCTCATGCCCATCATATTATTGTAGCGAGA
Found at i:4830961 original size:57 final size:57
Alignment explanation
Indices: 4830831--4830961 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 57
4830821 ATGGGGGGTT
* * * * * * *
4830831 CATGTCCATCATATTGTTGTAGCGAGAAAGATGGCAAATAGGTATAGATGGAGGGCT
1 CATGTCCCTCATATTATTGTAGCGAGAAAGATGGAAAATAGGTATAAATAGAAGGCC
* *
4830888 CATG-CCCATCATATTATTGTAGGGAGAAAGATGGAAAAT-GTGTGTAAATAGAAGGCC
1 CATGTCCC-TCATATTATTGTAGCGAGAAAGATGGAAAATAG-GTATAAATAGAAGGCC
*
4830945 CATGTCCCTCAAATTAT
1 CATGTCCCTCATATTAT
4830962 GCTATGAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
56 3 0.05
57 55 0.90
58 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (57 bp):
CATGTCCCTCATATTATTGTAGCGAGAAAGATGGAAAATAGGTATAAATAGAAGGCC
Found at i:4831294 original size:21 final size:22
Alignment explanation
Indices: 4831254--4831295 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4831244 TCTAGGTTTT
*
4831254 ATGAATGAACTATAGATACTTC
1 ATGAATGAAATATAGATACTTC
*
4831276 ATGAAT-AAATATTGATACTT
1 ATGAATGAAATATAGATACTT
4831296 AAGAAGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
ATGAATGAAATATAGATACTTC
Found at i:4833158 original size:2 final size:2
Alignment explanation
Indices: 4833151--4833177 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4833141 AATAAAACAA
4833151 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
4833178 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4833182 original size:2 final size:2
Alignment explanation
Indices: 4833177--4833222 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4833167 ACACACACAC
4833177 AT AT AT AT AT 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 AT AT AT AT AT
4833219 AT AT
1 AT AT
4833223 TAGACACATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4834047 original size:2 final size:2
Alignment explanation
Indices: 4834040--4834074 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4834030 NNTATAATAC
4834040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4834075 TATGTTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4834444 original size:21 final size:21
Alignment explanation
Indices: 4834418--4834457 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4834408 TGGTATGGCT
4834418 ATCTATCAATAGATTTCATGA
1 ATCTATCAATAGATTTCATGA
*
4834439 ATCTATTAATAGATTTCAT
1 ATCTATCAATAGATTTCAT
4834458 CCAGATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
ATCTATCAATAGATTTCATGA
Found at i:4837077 original size:52 final size:52
Alignment explanation
Indices: 4837015--4837117 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
4837005 TTTCTGAGAT
*
4837015 AGTCTTGTCAAAAAGGATTCAATCTTACAAAAATCTTAAACAAATCGTTTGA
1 AGTCTTGTCAAAAAGGATGCAATCTTACAAAAATCTTAAACAAATCGTTTGA
* * * *
4837067 AGTCTTGTCAAAAGGGATGCAATGTTACAAAAGTCTTACACAAATCGTTTG
1 AGTCTTGTCAAAAAGGATGCAATCTTACAAAAATCTTAAACAAATCGTTTG
4837118 TAGTATTTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (52 bp):
AGTCTTGTCAAAAAGGATGCAATCTTACAAAAATCTTAAACAAATCGTTTGA
Found at i:4839205 original size:42 final size:42
Alignment explanation
Indices: 4839144--4839310 Score: 208
Period size: 42 Copynumber: 4.0 Consensus size: 42
4839134 TGTTGATGTG
* *
4839144 GACCCGGCTATGTGGGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
*
4839186 GACCCGACTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* * * *
4839228 GACCCGATTATGTGTGAGTGGGAGTGCACATAAGCCATTGCT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
** * * * * *
4839270 GACCCGGTTATATGCAAGTGGGAGTACGCATAAGCCGTTGC
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
4839311 ATATGAGATG
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 110 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.23
Consensus pattern (42 bp):
GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:4839358 original size:2 final size:2
Alignment explanation
Indices: 4839351--4839463 Score: 208
Period size: 2 Copynumber: 56.0 Consensus size: 2
4839341 ATGATGATTG
4839351 AT AT AT AT AT 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 AT AT AT AT AT
4839393 AT AT AT AT AT ANT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4839436 AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4839464 GGTATATGGT
Statistics
Matches: 108, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 106 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4842236 original size:21 final size:21
Alignment explanation
Indices: 4842212--4842251 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4842202 CTTACATTTT
*
4842212 GTGACTAAGGTATTGATACAA
1 GTGAATAAGGTATTGATACAA
4842233 GTGAATAAGGTATTGATAC
1 GTGAATAAGGTATTGATAC
4842252 TTGCTGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGAATAAGGTATTGATACAA
Found at i:4842424 original size:101 final size:101
Alignment explanation
Indices: 4842248--4842456 Score: 292
Period size: 101 Copynumber: 2.1 Consensus size: 101
4842238 TAAGGTATTG
* * *
4842248 ATACTTGCTGCCCATAATACTTTTAAAAGGAAATTGGAAGAACAAATACCGATACTTTCTTCAAA
1 ATACTTGCTACACATAATACTTTTAAAAGGAAATTGGAAGAACAAATACCAATACTTTCTTCAAA
* * *
4842313 GGTATTGATACTCAAAAGCCAAAACTAAAAGTATCA
66 GATATCGATACTCAAAACCCAAAACTAAAAGTATCA
* * * *
4842349 ATACTTGCTACACATAATACTTTTAAAAGGGAATTTGAAGAACAAGTATCAATACTTTCTTCAAA
1 ATACTTGCTACACATAATACTTTTAAAAGGAAATTGGAAGAACAAATACCAATACTTTCTTCAAA
** * *
4842414 GATATCGATACTTGAAACCCAGAACTAAAAGTATCT
66 GATATCGATACTCAAAACCCAAAACTAAAAGTATCA
4842450 ATACTTG
1 ATACTTG
4842457 AGCCCTAGTA
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (101 bp):
ATACTTGCTACACATAATACTTTTAAAAGGAAATTGGAAGAACAAATACCAATACTTTCTTCAAA
GATATCGATACTCAAAACCCAAAACTAAAAGTATCA
Found at i:4847847 original size:2 final size:2
Alignment explanation
Indices: 4847840--4847865 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4847830 TTCTCACAAT
4847840 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4847866 TAGTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4847923 original size:2 final size:2
Alignment explanation
Indices: 4847916--4847942 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4847906 TAGTTTTAGN
4847916 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
4847943 TCTTTTTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4850369 original size:17 final size:16
Alignment explanation
Indices: 4850325--4850369 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
4850315 AATCCTTAAA
*
4850325 GAGTTTAAATAATTAT
1 GAGTTTAAATAATGAT
4850341 GAGATTTAAATAACTGAT
1 GAG-TTTAAATAA-TGAT
*
4850359 GAGTTTCAATA
1 GAGTTTAAATA
4850370 GTTTTTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (16 bp):
GAGTTTAAATAATGAT
Found at i:4872637 original size:28 final size:27
Alignment explanation
Indices: 4872598--4872650 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
4872588 ATATCCTGGT
*
4872598 GGTGGAAAATTACAATTTTGCCCTTGG
1 GGTGGAAAATTACAATTTTACCCTTGG
*
4872625 GGTGGCAAAATTACCATTTTACCCTT
1 GGTGG-AAAATTACAATTTTACCCTT
4872651 TTACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCTTGG
Found at i:4872718 original size:20 final size:20
Alignment explanation
Indices: 4872695--4872740 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
4872685 CTTCTAAACC
4872695 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
4872715 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
4872735 TCAAAT
1 TCAAAT
4872741 GGGTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:4880758 original size:20 final size:20
Alignment explanation
Indices: 4880733--4880772 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4880723 CTTCTAAACC
4880733 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
4880753 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
4880773 ACAATTGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:4882724 original size:17 final size:17
Alignment explanation
Indices: 4882678--4882724 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
4882668 CTTTCTTTAA
*
4882678 GTATATATATTATAA-G
1 GTATATATATAATAATG
*
4882694 AT-TATATA-AATAATG
1 GTATATATATAATAATG
4882709 GTATATATATAATAAT
1 GTATATATATAATAAT
4882725 TAATAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 7 0.28
17 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
GTATATATATAATAATG
Found at i:4896302 original size:23 final size:23
Alignment explanation
Indices: 4896276--4896322 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
4896266 CAATCTTTTG
*
4896276 ACATGCCACATGGTAGCCTCTTA
1 ACATGCCACATGGTAACCTCTTA
4896299 ACATGCCACATGGTAACCTCTTA
1 ACATGCCACATGGTAACCTCTTA
4896322 A
1 A
4896323 AAAGCCGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (23 bp):
ACATGCCACATGGTAACCTCTTA
Found at i:4896333 original size:23 final size:23
Alignment explanation
Indices: 4896280--4896334 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
4896270 CTTTTGACAT
* * *
4896280 GCCACATGGTAGCCTCTTAACAT
1 GCCACATGGTAACCTCTTAAAAA
4896303 GCCACATGGTAACCTCTTAAAAA
1 GCCACATGGTAACCTCTTAAAAA
*
4896326 GCCGCATGG
1 GCCACATGG
4896335 CTCTGACATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (23 bp):
GCCACATGGTAACCTCTTAAAAA
Found at i:4897580 original size:13 final size:13
Alignment explanation
Indices: 4897547--4897571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4897537 TTTAAATAAA
4897547 ATAAAATTTTTTG
1 ATAAAATTTTTTG
4897560 ATAAAATTTTTT
1 ATAAAATTTTTT
4897572 TTTAAAATTA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATAAAATTTTTTG
Found at i:4912220 original size:43 final size:43
Alignment explanation
Indices: 4912167--4912319 Score: 126
Period size: 43 Copynumber: 3.6 Consensus size: 43
4912157 TTACCAGCTC
* * ** *
4912167 ATGCGCACTCCTTACTCACACATGGCTAGGTCATCACCGGGTT
1 ATGCACACTCCCTACTCACACATAACCAGGTCATCACCGGGTT
** *
4912210 ATGCACACTCCCTACTCGTACATAACCGGGTCATCACCGGGTT
1 ATGCACACTCCCTACTCACACATAACCAGGTCATCACCGGGTT
** ** * * * **
4912253 ATGTGCACTCCCTACTTGCACATAATCGGGTCATCATCGACTT
1 ATGCACACTCCCTACTCACACATAACCAGGTCATCACCGGGTT
* * *
4912296 ATGCGCACTCCTTACTCGCACATA
1 ATGCACACTCCCTACTCACACATA
4912320 GCCGAGTCAA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCACACTCCCTACTCACACATAACCAGGTCATCACCGGGTT
Found at i:4917322 original size:22 final size:22
Alignment explanation
Indices: 4917294--4917336 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4917284 CTCCCAAATT
*
4917294 GATTTTCATTGCAGCAAGAATG
1 GATTTTCATTGCAACAAGAATG
* *
4917316 GATTTTCGTTGTAACAAGAAT
1 GATTTTCATTGCAACAAGAAT
4917337 TCTTCTAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (22 bp):
GATTTTCATTGCAACAAGAATG
Found at i:4923758 original size:23 final size:23
Alignment explanation
Indices: 4923714--4923758 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4923704 ATTGTTATGC
*
4923714 ACATTGCTTGTAACATAGTGTGA
1 ACATTGCTTGTAACATACTGTGA
4923737 ACATTGCTTGTAACGA-ACTGTG
1 ACATTGCTTGTAAC-ATACTGTG
4923759 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (23 bp):
ACATTGCTTGTAACATACTGTGA
Found at i:4933785 original size:28 final size:27
Alignment explanation
Indices: 4933754--4933828 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
4933744 ATGAACTTTA
* *
4933754 TAATTTATATTTCGTTACAAGCCCTGAC
1 TAATTT-TATTTTGTTACAAGCCCTAAC
*
4933782 TAATTTTGATTTTGTTACATGCCCTAAC
1 TAATTTT-ATTTTGTTACAAGCCCTAAC
4933810 TAATTTCTATTTTGTTACA
1 TAATTT-TATTTTGTTACA
4933829 CGACATACCT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.95
29 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (27 bp):
TAATTTTATTTTGTTACAAGCCCTAAC
Found at i:4934176 original size:28 final size:27
Alignment explanation
Indices: 4934112--4934255 Score: 119
Period size: 28 Copynumber: 5.1 Consensus size: 27
4934102 AACATATTTT
*
4934112 TTTTGTTACACGCCCTGTATAATCTT-TA
1 TTTTGTTACACGCCTTG-ATAAT-TTCTA
* * *
4934140 TTTTATTACATGCACTTTATAATTTCTA
1 TTTTGTTACACGC-CTTGATAATTTCTA
* * ** *
4934168 CTTTGTTACAAGCCATAAACAATTTCTA
1 TTTTGTTACACGCC-TTGATAATTTCTA
* *
4934196 TTTTGTAACATGCCTTGACTAATTTCTA
1 TTTTGTTACACGCCTTGA-TAATTTCTA
*
4934224 TTTTCTTACACGCCTTGAGTAATTTCTA
1 TTTTGTTACACGCCTTGA-TAATTTCTA
4934252 TTTT
1 TTTT
4934256 ATAATACACC
Statistics
Matches: 92, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
27 5 0.05
28 85 0.92
29 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTGTTACACGCCTTGATAATTTCTA
Found at i:4937990 original size:18 final size:18
Alignment explanation
Indices: 4937967--4938005 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
4937957 TAATATTTCT
4937967 TTAATAATTTTTTATTCA
1 TTAATAATTTTTTATTCA
4937985 TTAATAATTTTTTATTCA
1 TTAATAATTTTTTATTCA
4938003 TTA
1 TTA
4938006 TTTTTATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATAATTTTTTATTCA
Found at i:4957166 original size:26 final size:26
Alignment explanation
Indices: 4957116--4957166 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
4957106 ATGTCTTGAT
*
4957116 GGTGGAAAATTACAATTTTGCCCCTG
1 GGTGGAAAATTACAATTTTGACCCTG
4957142 GGTGGCAAAATTATC-ATTTT-ACCCT
1 GGTGG-AAAATTA-CAATTTTGACCCT
4957167 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.41
27 12 0.55
28 1 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (26 bp):
GGTGGAAAATTACAATTTTGACCCTG
Found at i:4960164 original size:2 final size:2
Alignment explanation
Indices: 4960159--4960191 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4960149 CATATATTGT
*
4960159 TA TA TA CA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4960192 ACCTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4960313 original size:2 final size:2
Alignment explanation
Indices: 4960306--4960343 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4960296 ACCATTTTAC
4960306 AT AT AT 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 AT AT AT
4960344 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4960372 original size:2 final size:2
Alignment explanation
Indices: 4960365--4960403 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4960355 NNNNNNNNNN
4960365 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4960404 TATGTCTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4963037 original size:175 final size:173
Alignment explanation
Indices: 4962737--4963073 Score: 530
Period size: 175 Copynumber: 1.9 Consensus size: 173
4962727 GATGAAAGCT
* * *
4962737 GAAACAGAAGACCAATACTCACCATTTCAATAAAGCCTAGCATAAAATACTAAAACTCACCGTTT
1 GAAACAGAAGACCAATACTCACCATTTCAATAAAGCCTAGCATAAAAGACTAAAACCCACCATTT
* * *
4962802 CATTTAAAAATTTAAAAGTTAGTTAAGAGCTAATTATTAGTTAGTTAACAGCTGACATTTTCTCT
66 CATTTAAAAATTTAAAAGTTAATTAAGAGCTAATCATTAGTTAGTTAAAAGCTGACATTTTCTCT
*
4962867 TTCTTTAATTAACCCAATAACTATATATATATATACTGGAAAGAA
131 TTCTTAAATTAACCCAA-AACT-TATATATATATACTGGAAAGAA
* * * *
4962912 GAAATAGAGGACCAATACTCATCATTTCAATAAAGCCTAGCATAAGAGACTAAAACCCACCATTT
1 GAAACAGAAGACCAATACTCACCATTTCAATAAAGCCTAGCATAAAAGACTAAAACCCACCATTT
* *
4962977 CATTTAAAAGTTTAAAAGTTAATTAGGAGCTAATCATTAGTTAGTTAAAAGCTGACATTTTCTCT
66 CATTTAAAAATTTAAAAGTTAATTAAGAGCTAATCATTAGTTAGTTAAAAGCTGACATTTTCTCT
*
4963042 TTCTTAAATTAATCCAAAACTTATATATATAT
131 TTCTTAAATTAACCCAAAACTTATATATATAT
4963074 GCACACACAC
Statistics
Matches: 148, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
173 11 0.07
174 4 0.03
175 133 0.90
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.32
Consensus pattern (173 bp):
GAAACAGAAGACCAATACTCACCATTTCAATAAAGCCTAGCATAAAAGACTAAAACCCACCATTT
CATTTAAAAATTTAAAAGTTAATTAAGAGCTAATCATTAGTTAGTTAAAAGCTGACATTTTCTCT
TTCTTAAATTAACCCAAAACTTATATATATATACTGGAAAGAA
Found at i:4967937 original size:8 final size:8
Alignment explanation
Indices: 4967924--4967950 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4967914 TCAAAATATT
4967924 ACAGATTA
1 ACAGATTA
4967932 ACAGATTA
1 ACAGATTA
4967940 ACAGATTA
1 ACAGATTA
4967948 ACA
1 ACA
4967951 ACGATTGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (8 bp):
ACAGATTA
Found at i:4968760 original size:181 final size:178
Alignment explanation
Indices: 4968475--4968947 Score: 483
Period size: 180 Copynumber: 2.6 Consensus size: 178
4968465 GCAAGCCATG
* *** * * * * *
4968475 GTTTTGAATTTTTTTGACAACTAAAAACGTTTCCTAAAATCCTGAAAAATTACTGTGGAATTGTC
1 GTTTTGAATTTTTTTGACAGCTAAAAACACCTCCTAAAATCCTGAAAATTTATTCTGGAATAGTT
* * * *
4968540 CCATAAGTTTTCTATCAAGGAAAATTTAATTGAGAATTAAATTCCTGA-TTTTATGCCACCAAAT
66 CCATAAGTTATCTATC-AGGAAAATTTTATTG-GAATTAAATTCCTAATTTTTA-GCCA-CAAAG
* *
4968604 AGCTTCAAAA-GAAAGACAAAACCGAA-ACTGCCT-CTGCAGATAAAGGTCACA
127 AACTTCAAAATGAAACA-AAAACC-AATACTGCCTCCTGCAGATAAAGGTCACA
*
4968655 GTTTTGAATTTTTTTTGACAGCTAAAAGCACCTCCTAAAATCCTGAAAATTTATTCTGGAATAGT
1 GTTTTGAA-TTTTTTTGACAGCTAAAAACACCTCCTAAAATCCTGAAAATTTATTCTGGAATAGT
* * * * *
4968720 TACATGAGTTATCTATCAGTATAAATTTTATAAGGAATTAAATTCCTAATTTTTAGTCACAAAGA
65 TCCATAAGTTATCTATCAGGA-AAATTTTAT-TGGAATTAAATTCCTAATTTTTAGCCACAAAGA
* *** * *
4968785 ATTTCAAAATGTCTCAAAAACCAATTCTGCCTCCTGCAGATAAAGGTCACG
128 ACTTCAAAATGAAACAAAAACCAATACTGCCTCCTGCAGATAAAGGTCACA
* * * *
4968836 GTTTTTTAA-TTTTTTGA-ATGGC-CAAATCACCTCTTAAAATCCTGAAAATTTATTCTGGAATA
1 G-TTTTGAATTTTTTTGACA--GCTAAAAACACCTCCTAAAATCCTGAAAATTTATTCTGGAATA
* *
4968898 GTTCCATTAGTTATCTATCAGGAAAAATTTTATTGGAATTAAATTTCTAA
63 GTTCCATAAGTTATCTATCAGG-AAAATTTTATTGGAATTAAATTCCTAA
4968948 AGATACAGCA
Statistics
Matches: 246, Mismatches: 36, Indels: 23
0.81 0.12 0.08
Matches are distributed among these distances:
179 18 0.07
180 108 0.44
181 108 0.44
182 12 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (178 bp):
GTTTTGAATTTTTTTGACAGCTAAAAACACCTCCTAAAATCCTGAAAATTTATTCTGGAATAGTT
CCATAAGTTATCTATCAGGAAAATTTTATTGGAATTAAATTCCTAATTTTTAGCCACAAAGAACT
TCAAAATGAAACAAAAACCAATACTGCCTCCTGCAGATAAAGGTCACA
Found at i:4970299 original size:58 final size:58
Alignment explanation
Indices: 4970178--4970296 Score: 177
Period size: 58 Copynumber: 2.1 Consensus size: 58
4970168 CATAATCATC
* * **
4970178 CAAAGTAGTTTGCATGTGATAGATTTATTTTATGCAATTTAATAAATGTTATGCAATG
1 CAAAGTAGTATGCATGTGATAGATTTATTTTATACAATTTAATAAATACTATGCAATG
* *
4970236 CAAAGTCGTATGCATGTGATAGATTTATTTTATACGATTTAATAAATACTATGC-ATG
1 CAAAGTAGTATGCATGTGATAGATTTATTTTATACAATTTAATAAATACTATGCAATG
4970293 CAAA
1 CAAA
4970297 AGTGAGACCC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 7 0.13
58 48 0.87
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (58 bp):
CAAAGTAGTATGCATGTGATAGATTTATTTTATACAATTTAATAAATACTATGCAATG
Found at i:4972208 original size:22 final size:22
Alignment explanation
Indices: 4972183--4972228 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
4972173 TAATATGTAC
4972183 AAGTGTATTTATCTCATAGACA
1 AAGTGTATTTATCTCATAGACA
4972205 AAGTGTATTTATCTCATAGACA
1 AAGTGTATTTATCTCATAGACA
4972227 AA
1 AA
4972229 AGAAAGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
AAGTGTATTTATCTCATAGACA
Found at i:4978473 original size:22 final size:23
Alignment explanation
Indices: 4978448--4978494 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
4978438 ATTTATATGC
4978448 ATTACTATAAAAACTAAGCT-AA
1 ATTACTATAAAAACTAAGCTCAA
* * *
4978470 ATTATTATCAAAATTAAGCTCAA
1 ATTACTATAAAAACTAAGCTCAA
4978493 AT
1 AT
4978495 AACTCTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
ATTACTATAAAAACTAAGCTCAA
Found at i:4978628 original size:3 final size:3
Alignment explanation
Indices: 4978620--4978648 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4978610 CAAATATAGT
4978620 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
4978649 AAGATAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:4980324 original size:89 final size:89
Alignment explanation
Indices: 4980149--4980321 Score: 283
Period size: 89 Copynumber: 1.9 Consensus size: 89
4980139 GATTGGGTTT
* * *
4980149 GGGTAGTGGGTAGTGGGTAAATGGGCAATGGGTAGTCCAAATAGGAAAAAAAAAGAATTGGGTTT
1 GGGTAGTGGGTAATGGGAAAATGGGCAATGGGTAGTCCAAATAGAAAAAAAAAAGAATTGGGTTT
*
4980214 GGTTAGTGGGCTGCCCACAATGGA
66 GCTTAGTGGGCTGCCCACAATGGA
*
4980238 GGGTAGTGGTTAATGGGAAAATGGGCAATGGGTAGTCCAAATAGAAAAAAAAAAAAGAATTGGGT
1 GGGTAGTGGGTAATGGGAAAATGGGCAATGGGTAGTCCAAATAG--AAAAAAAAAAGAATTGGGT
4980303 TTGCTTAGTGGGCTGCCCA
64 TTGCTTAGTGGGCTGCCCA
4980322 ATGTTAGCAG
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 41 0.53
91 36 0.47
ACGTcount: A:0.34, C:0.09, G:0.35, T:0.23
Consensus pattern (89 bp):
GGGTAGTGGGTAATGGGAAAATGGGCAATGGGTAGTCCAAATAGAAAAAAAAAAGAATTGGGTTT
GCTTAGTGGGCTGCCCACAATGGA
Found at i:4985058 original size:2 final size:2
Alignment explanation
Indices: 4985051--4985094 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4985041 AATACCCATA
4985051 AT AT AT AT AT 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 AT AT AT AT AT
4985093 AT
1 AT
4985095 TATTACCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5013990 original size:83 final size:84
Alignment explanation
Indices: 5013848--5014009 Score: 195
Period size: 83 Copynumber: 1.9 Consensus size: 84
5013838 AAATTAAGAA
* * *
5013848 AAATACTTTTAATGAAAGTCATTCAATACAATTACAATTCTTATTTATAAATTGAATAAATTTTA
1 AAATACTTTTAATGAAAATCATTCAATACAATTACAATTCTTACTTATAAATTGAATAAATCTTA
5013913 CTAACT-TTTATAATGAAAG
66 CTAA-TATTTATAATGAAAG
* * * * * *
5013932 AAATATTTTTAATGAAAATCA-TCCATGCAATTAGAATTTTTACTTATAAGTT-AGATAAATCTT
1 AAATACTTTTAATGAAAATCATTCAATACAATTACAATTCTTACTTATAAATTGA-ATAAATCTT
*
5013995 ATTAATATTTATAAT
65 ACTAATATTTATAAT
5014010 AAAAATGTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
82 2 0.03
83 45 0.68
84 19 0.29
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (84 bp):
AAATACTTTTAATGAAAATCATTCAATACAATTACAATTCTTACTTATAAATTGAATAAATCTTA
CTAATATTTATAATGAAAG
Found at i:5022590 original size:10 final size:10
Alignment explanation
Indices: 5022575--5022604 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5022565 GCTTTTCCTC
5022575 TTTTATTTTT
1 TTTTATTTTT
5022585 TTTTATTTTT
1 TTTTATTTTT
*
5022595 ATTTATTTTT
1 TTTTATTTTT
5022605 GTTATTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:5026771 original size:4 final size:4
Alignment explanation
Indices: 5026764--5026788 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5026754 CATCATCTTT
5026764 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
5026789 ATATAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:5029300 original size:2 final size:2
Alignment explanation
Indices: 5029279--5029332 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
5029269 TTGTAACATC
* * *
5029279 AT AT AC AT AC AT AC 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 AT AT AT AT AT
5029321 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5029333 GCATGGATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5032579 original size:28 final size:28
Alignment explanation
Indices: 5032520--5032850 Score: 200
Period size: 28 Copynumber: 12.2 Consensus size: 28
5032510 TCAAATTATG
5032520 ACATGACGTGTAACAA-T---TTTTTCA
1 ACATGACGTGTAACAACTAAATTTTTCA
* * * *
5032544 TCACGACGTGTAATAACTAAATTTTTTA
1 ACATGACGTGTAACAACTAAATTTTTCA
* * **
5032572 ATATGACGTATAACAGTTAAA-TTTTCA
1 ACATGACGTGTAACAACTAAATTTTTCA
* *
5032599 ACATG-CTGTGTAACAATTACATTTTTCA
1 ACATGAC-GTGTAACAACTAAATTTTTCA
* * *
5032627 ATATGGCGTGTAACAACTCAA-TTTTCA
1 ACATGACGTGTAACAACTAAATTTTTCA
* * * * * *
5032654 ACATGACGTATGATAATTACATTTTTTA
1 ACATGACGTGTAACAACTAAATTTTTCA
* *
5032682 ACATGATGTGTAATAACTAAA-TTTTCA
1 ACATGACGTGTAACAACTAAATTTTTCA
* * *
5032709 ACACTG-TGTGTAACGACTAAA-TCTTCA
1 ACA-TGACGTGTAACAACTAAATTTTTCA
* * * *
5032736 ACATGAGGTATAACAATTACATTTTTCA
1 ACATGACGTGTAACAACTAAATTTTTCA
* * *
5032764 ACATGATGTATAACAATTAAA-TTTTCA
1 ACATGACGTGTAACAACTAAATTTTTCA
* * * *
5032791 ATATGACCTATAACAATTAAATTTTTCA
1 ACATGACGTGTAACAACTAAATTTTTCA
* * * * *
5032819 ACATAACATATAATAATTAAATTTTT-A
1 ACATGACGTGTAACAACTAAATTTTTCA
5032846 ACATG
1 ACATG
5032851 GCATATAACA
Statistics
Matches: 241, Mismatches: 54, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
24 13 0.05
25 1 0.00
26 3 0.01
27 107 0.44
28 116 0.48
29 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (28 bp):
ACATGACGTGTAACAACTAAATTTTTCA
Found at i:5032611 original size:55 final size:55
Alignment explanation
Indices: 5032551--5032873 Score: 235
Period size: 55 Copynumber: 5.9 Consensus size: 55
5032541 TCATCACGAC
* * * *
5032551 GTGTAATAACTAAATTTTTTAATATGACGTATAACAGTTAAATTTTCAACATGCT
1 GTGTAACAATTAAATTTTTCAATATGACGTATAACAATTAAATTTTCAACATGCT
* * * * *
5032606 GTGTAACAATTACATTTTTCAATATGGCGTGTAACAACTCAATTTTCAACATGAC-
1 GTGTAACAATTAAATTTTTCAATATGACGTATAACAATTAAATTTTCAACATG-CT
* * * * * * * * * *
5032661 GTATGATAATTACATTTTTTAACATGATGTGTAATAACTAAATTTTCAACACTG-T
1 GTGTAACAATTAAATTTTTCAATATGACGTATAACAATTAAATTTTCAACA-TGCT
* * * * * * *
5032716 GTGTAACGACTAAA-TCTTCAACATGAGGTATAACAATTACATTTTTCAACATGAT
1 GTGTAACAATTAAATTTTTCAATATGACGTATAACAATTA-AATTTTCAACATGCT
* * *
5032771 GTATAACAATTAAA-TTTTCAATATGACCTATAACAATTAAATTTTTCAACATAAC-
1 GTGTAACAATTAAATTTTTCAATATGACGTATAACAATTAAA-TTTTCAACAT-GCT
* * * * * * *
5032826 ATATAATAATTAAATTTTT-AACATGGCATATAACAATTATATTTTCAA
1 GTGTAACAATTAAATTTTTCAATATGACGTATAACAATTAAATTTTCAA
5032874 AATAATTTTC
Statistics
Matches: 213, Mismatches: 47, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
54 29 0.14
55 177 0.83
56 7 0.03
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (55 bp):
GTGTAACAATTAAATTTTTCAATATGACGTATAACAATTAAATTTTCAACATGCT
Found at i:5032612 original size:27 final size:27
Alignment explanation
Indices: 5032579--5032873 Score: 179
Period size: 27 Copynumber: 10.8 Consensus size: 27
5032569 TTAATATGAC
*
5032579 GTATAACAGTTAAATTTTCAACATGCT
1 GTATAACAATTAAATTTTCAACATGCT
* * *
5032606 GTGTAACAATTACATTTTTCAATATGGC-
1 GTATAACAATTA-AATTTTCAACAT-GCT
* * *
5032634 GTGTAACAACTCAATTTTCAACATGAC-
1 GTATAACAATTAAATTTTCAACATG-CT
* * * * *
5032661 GTATGATAATTACATTTTTTAACATGAT
1 GTATAACAATTA-AATTTTCAACATGCT
* * *
5032689 GTGTAATAACTAAATTTTCAACACTG-T
1 GTATAACAATTAAATTTTCAACA-TGCT
* * * * **
5032716 GTGTAACGACTAAATCTTCAACATGAG
1 GTATAACAATTAAATTTTCAACATGCT
* *
5032743 GTATAACAATTACATTTTTCAACATGAT
1 GTATAACAATTA-AATTTTCAACATGCT
*
5032771 GTATAACAATTAAATTTTCAATATGAC-
1 GTATAACAATTAAATTTTCAACATG-CT
* *
5032798 CTATAACAATTAAATTTTTCAACATAAC-
1 GTATAACAATTAAA-TTTTCAACAT-GCT
* * *
5032826 ATATAATAATTAAATTTTTAACATGGC-
1 GTATAACAATTAAATTTTCAACAT-GCT
* *
5032853 ATATAACAATTATATTTTCAA
1 GTATAACAATTAAATTTTCAA
5032874 AATAATTTTC
Statistics
Matches: 212, Mismatches: 45, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.01
27 119 0.56
28 88 0.42
29 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (27 bp):
GTATAACAATTAAATTTTCAACATGCT
Found at i:5032812 original size:82 final size:81
Alignment explanation
Indices: 5032550--5032873 Score: 301
Period size: 82 Copynumber: 4.0 Consensus size: 81
5032540 TTCATCACGA
* * * * * * *
5032550 CGTGTAATAACTAAATTTTTTAATATGACGTATAACAGTTA-AATTTTCAACATGCTGTGTAACA
1 CGTGTAACAACTAAA-TTTTCAACATGACGTATAACAATTACATTTTTCAACATGATGTATAACA
*
5032614 ATTACATTTTTCAATATGG
65 ATTA-AATTTTCAATAT-G
* * * * * *
5032633 CGTGTAACAACTCAATTTTCAACATGACGTATGATAATTACATTTTTTAACATGATGTGTAATAA
1 CGTGTAACAACTAAATTTTCAACATGACGTATAACAATTACATTTTTCAACATGATGTATAACAA
* *
5032698 CTAAATTTTCAACACTG
66 TTAAATTTTCAATA-TG
* * * *
5032715 TGTGTAACGACTAAATCTTCAACATGAGGTATAACAATTACATTTTTCAACATGATGTATAACAA
1 CGTGTAACAACTAAATTTTCAACATGACGTATAACAATTACATTTTTCAACATGATGTATAACAA
5032780 TTAAATTTTCAATATG
66 TTAAATTTTCAATATG
* * * * * * * ***
5032796 ACCTATAACAATTAAATTTTTCAACATAACATATAATAATTAAATTTTT-AACATGGCATATAAC
1 -CGTGTAACAACTAAA-TTTTCAACATGACGTATAACAATTACATTTTTCAACATGATGTATAAC
*
5032860 AATTATATTTTCAA
64 AATTAAATTTTCAA
5032874 AATAATTTTC
Statistics
Matches: 196, Mismatches: 41, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
81 2 0.01
82 132 0.67
83 62 0.32
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (81 bp):
CGTGTAACAACTAAATTTTCAACATGACGTATAACAATTACATTTTTCAACATGATGTATAACAA
TTAAATTTTCAATATG
Done.