Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 164 of 187
Found at i:48299803 original size:50 final size:51
Alignment explanation
Indices: 48299705--48299815 Score: 188
Period size: 50 Copynumber: 2.2 Consensus size: 51
48299695 TCTGATTAGG
*
48299705 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGT
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGACAAGT
*
48299756 GACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGGGACAAGT
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGACAAGT
*
48299806 GATAAGTGAT
1 GACAAGTGAT
48299816 CATACGTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 37 0.65
51 20 0.35
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (51 bp):
GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGACAAGT
Found at i:48310183 original size:44 final size:44
Alignment explanation
Indices: 48310110--48310272 Score: 202
Period size: 44 Copynumber: 3.6 Consensus size: 44
48310100 TTTGAGTACT
* *
48310110 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATTAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
48310154 TTTGATTAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATTAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
48310198 TCTGATCAATGACAAGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1 TCTGAT---T----AGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
48310248 TCTAATCAGGGACAAGTGATAAGTG
1 TCTGATTAGGGACAAGTGATAAGTG
48310273 ATCATATGTA
Statistics
Matches: 104, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
43 17 0.16
44 46 0.44
47 1 0.01
50 18 0.17
51 22 0.21
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (44 bp):
TCTGATTAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:48310262 original size:50 final size:51
Alignment explanation
Indices: 48310164--48310274 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 51
48310154 TTTGATTAGG
* *
48310164 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGT
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGACAAGT
*
48310215 GACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTAATCAGGGACAAGT
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGACAAGT
*
48310265 GATAAGTGAT
1 GACAAGTGAT
48310275 CATATGTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
50 36 0.64
51 20 0.36
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGACAAGT
Found at i:48320733 original size:33 final size:33
Alignment explanation
Indices: 48320691--48320760 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
48320681 GATGCGTATA
48320691 TGTAGTGGTATACGAAAAGCAAAGTCGTTTGTG
1 TGTAGTGGTATACGAAAAGCAAAGTCGTTTGTG
48320724 TGTAGTGGTATACGAAAAGCAAAGTCGTTTGTG
1 TGTAGTGGTATACGAAAAGCAAAGTCGTTTGTG
48320757 TGTA
1 TGTA
48320761 AATGATGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.31
Consensus pattern (33 bp):
TGTAGTGGTATACGAAAAGCAAAGTCGTTTGTG
Found at i:48324900 original size:25 final size:25
Alignment explanation
Indices: 48324821--48324902 Score: 67
Period size: 31 Copynumber: 3.0 Consensus size: 25
48324811 CGTCCTATGT
* * *
48324821 ATCAATTTAACCCTTATACTATTAA
1 ATCAAATTAATCCTTTTACTATTAA
48324846 ATCAAATTAATCTCTCTATTA-TAAAAATTAA
1 ATCAAATTAATC-CT-T-TTACT----ATTAA
48324877 ATCAAATTAATCCTTTTACTATTAA
1 ATCAAATTAATCCTTTTACTATTAA
48324902 A
1 A
48324903 AAATCAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
25 16 0.35
26 2 0.04
27 2 0.04
28 5 0.11
29 2 0.04
30 2 0.04
31 17 0.37
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (25 bp):
ATCAAATTAATCCTTTTACTATTAA
Found at i:48330713 original size:24 final size:24
Alignment explanation
Indices: 48330681--48330752 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
48330671 GGAAAATATA
48330681 GGAATTCCTCAAATTTTAAGAATC
1 GGAATTCCTCAAATTTTAAGAATC
48330705 GGAATTCCTCAAATTTTAAGAATC
1 GGAATTCCTCAAATTTTAAGAATC
48330729 GGAATTCCTCAAATTTTAAGAATC
1 GGAATTCCTCAAATTTTAAGAATC
48330753 TAGTCATACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (24 bp):
GGAATTCCTCAAATTTTAAGAATC
Found at i:48336512 original size:21 final size:21
Alignment explanation
Indices: 48336488--48336527 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48336478 GCATGTATAT
* *
48336488 ATAATATATATTTTTATAAAA
1 ATAATATATAATTTAATAAAA
*
48336509 ATAATTTATAATTTAATAA
1 ATAATATATAATTTAATAA
48336528 GAAACTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATATATAATTTAATAAAA
Found at i:48348957 original size:2 final size:2
Alignment explanation
Indices: 48348950--48348976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48348940 AATTAAATTT
48348950 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 T
48348977 TTAGAAGGAA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48356848 original size:25 final size:25
Alignment explanation
Indices: 48356818--48356873 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
48356808 TTTCTAAAAT
48356818 TAAAAT-ATATTAGATA-TATTATTTC
1 TAAAATGAT-TTAGA-ACTATTATTTC
* *
48356843 TAAAATGATTTATAACTTTTATTTC
1 TAAAATGATTTAGAACTATTATTTC
48356868 TAAAAT
1 TAAAAT
48356874 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 24 0.89
26 2 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (25 bp):
TAAAATGATTTAGAACTATTATTTC
Found at i:48362540 original size:27 final size:26
Alignment explanation
Indices: 48362496--48362553 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
48362486 ACTCTAGTAC
* *
48362496 AATTTTAACGATTCTACCCCTCAATAA
1 AATTTTAACAATTATACCCCT-AATAA
* *
48362523 AATTTTGACAATTATACCCCTAGTAA
1 AATTTTAACAATTATACCCCTAATAA
48362549 AATTT
1 AATTT
48362554 CGAGAAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (26 bp):
AATTTTAACAATTATACCCCTAATAA
Found at i:48366394 original size:30 final size:30
Alignment explanation
Indices: 48366358--48366417 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
48366348 GGGTCCTTGT
48366358 AACCACTGTCACCCATCATAATAAAATTTG
1 AACCACTGTCACCCATCATAATAAAATTTG
*
48366388 AACCACTTTCACCCATCATAATAAAATTTG
1 AACCACTGTCACCCATCATAATAAAATTTG
48366418 TCCACCTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.28
Consensus pattern (30 bp):
AACCACTGTCACCCATCATAATAAAATTTG
Found at i:48367024 original size:30 final size:31
Alignment explanation
Indices: 48366985--48367044 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
48366975 AGAGGTGGGA
*
48366985 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
48367016 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
48367045 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:48367272 original size:9 final size:9
Alignment explanation
Indices: 48367258--48367294 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
48367248 TATAGTTTGA
48367258 TATTCGAAT
1 TATTCGAAT
48367267 TATTCGAAT
1 TATTCGAAT
**
48367276 TATTCGGGT
1 TATTCGAAT
48367285 TATTCGAAT
1 TATTCGAAT
48367294 T
1 T
48367295 CAAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:48368747 original size:17 final size:17
Alignment explanation
Indices: 48368721--48368758 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
48368711 AAAGAGAATC
48368721 AAAA-CCTAAACAA-ACT
1 AAAACCCTAAA-AACACT
48368737 AAAACCCTAAAAACACT
1 AAAACCCTAAAAACACT
48368754 AAAAC
1 AAAAC
48368759 ATTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.63, C:0.26, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAACCCTAAAAACACT
Found at i:48368764 original size:17 final size:17
Alignment explanation
Indices: 48368721--48368766 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
48368711 AAAGAGAATC
48368721 AAAAC-CTAAACAA-ACT
1 AAAACACTAAA-AACACT
*
48368737 AAAACCCTAAAAACACT
1 AAAACACTAAAAACACT
*
48368754 AAAACATTAAAAA
1 AAAACACTAAAAA
48368767 ATCGTGCCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.65, C:0.22, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAACACTAAAAACACT
Found at i:48375314 original size:14 final size:14
Alignment explanation
Indices: 48375295--48375334 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
48375285 TTGATTGGCA
48375295 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
48375309 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
48375323 GGAAAATGTTTT
1 GTAAAATGTTTT
48375335 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:48375481 original size:20 final size:19
Alignment explanation
Indices: 48375456--48375493 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
48375446 GCTTTTACAT
48375456 ATATTAATAAATTTATATAC
1 ATATTAATAAATTT-TATAC
48375476 ATATTAATAAATTTTATA
1 ATATTAATAAATTTTATA
48375494 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTAATAAATTTTATAC
Found at i:48378212 original size:25 final size:25
Alignment explanation
Indices: 48378184--48378233 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
48378174 AGAAGAGAAG
48378184 ATGAAGAACAGAAGAAGAAAAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
** *
48378209 ATGAAGAATGGAAGAAGAAGAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
48378234 GCCTTACCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.32, T:0.06
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGAAAAAGGA
Found at i:48379214 original size:38 final size:39
Alignment explanation
Indices: 48379172--48379249 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 39
48379162 ATAAAAAAAA
48379172 TTACGATTTTTATAAAATTTTA-C-AT-TTTTAATAATTTT
1 TTACGATTTTTAT-AAATTTTATCTATATTTTAAT-ATTTT
*
48379210 TTACGATTTTTATAAGTTTTATCTATATTTTAATATTTT
1 TTACGATTTTTATAAATTTTATCTATATTTTAATATTTT
48379249 T
1 T
48379250 ATTAAAATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 7 0.19
38 14 0.39
39 8 0.22
40 7 0.19
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (39 bp):
TTACGATTTTTATAAATTTTATCTATATTTTAATATTTT
Found at i:48379229 original size:19 final size:19
Alignment explanation
Indices: 48379172--48379229 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
48379162 ATAAAAAAAA
*
48379172 TTACGATTTTTATAAAATT
1 TTACGATTTTTATAAATTT
*
48379191 TTAC-ATTTTTAATAATTTT
1 TTACGATTTTT-ATAAATTT
*
48379210 TTACGATTTTTATAAGTTT
1 TTACGATTTTTATAAATTT
48379229 T
1 T
48379230 ATCTATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.18
19 22 0.65
20 6 0.18
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTACGATTTTTATAAATTT
Found at i:48384173 original size:27 final size:27
Alignment explanation
Indices: 48384136--48384211 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
48384126 GAAGCTCCGG
*
48384136 AGAGCCATTAATCGGGAAGCTCATGAA
1 AGAGCCTTTAATCGGGAAGCTCATGAA
48384163 AGAGCCTTTAATCGGGAAGCTCATGAA
1 AGAGCCTTTAATCGGGAAGCTCATGAA
*
48384190 GGAGCCTTTAATCGGGAAGCTC
1 AGAGCCTTTAATCGGGAAGCTC
48384212 CGAAGAGCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (27 bp):
AGAGCCTTTAATCGGGAAGCTCATGAA
Found at i:48384229 original size:52 final size:52
Alignment explanation
Indices: 48384112--48384231 Score: 129
Period size: 52 Copynumber: 2.3 Consensus size: 52
48384102 AAGCTATTTC
* * * *
48384112 GAGCCATATAACGAGAAGCTCCGGAGAGCCATTAATCGGGAAGCTCATGAAA
1 GAGCCATATATCGGGAAGCTCCGAAGAGCCATTAATCGGGAAGCTCACGAAA
* * *
48384164 GAGCC-TTTAATCGGGAAGCTCATGAAGGAGCCTTTAATCGGGAAGCTC-CG-AA
1 GAGCCATAT-ATCGGGAAGCTC-CGAA-GAGCCATTAATCGGGAAGCTCACGAAA
48384216 GAGCCATATATCGGGA
1 GAGCCATATATCGGGA
48384232 CGTTCATAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
51 2 0.04
52 29 0.52
53 5 0.09
54 20 0.36
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (52 bp):
GAGCCATATATCGGGAAGCTCCGAAGAGCCATTAATCGGGAAGCTCACGAAA
Found at i:48391054 original size:30 final size:29
Alignment explanation
Indices: 48391013--48391102 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
48391003 AACTATGTTG
*
48391013 CTCACATAAGCTGAATTTATATCAAGGTTA
1 CTCACACAAGCTGAATTTATAT-AAGGTTA
* *
48391043 CTCACACAAGCTGGATTTATATTAAGGTTT
1 CTCACACAAGCTGAATTTATA-TAAGGTTA
* *
48391073 CTCACACAAGCTTAATTTATATTAGGTTA
1 CTCACACAAGCTGAATTTATATAAGGTTA
48391102 C
1 C
48391103 CCGTCTAAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.13
30 44 0.85
31 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (29 bp):
CTCACACAAGCTGAATTTATATAAGGTTA
Found at i:48393546 original size:51 final size:49
Alignment explanation
Indices: 48393482--48393577 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 49
48393472 ATTTTTCAGG
* *
48393482 TCATTTTCATTTTCATTTTGGAAAAAATCACATTCATTTCCAAATGACT
1 TCATTTTCATTTTCATTTTGGAAAAAACCACAATCATTTCCAAATGACT
* * **
48393531 TCATTTATCCATTTTCGTTTTGGAGAAAACCTTAATCATTTCCAAAT
1 TCATTT-T-CATTTTCATTTTGGAAAAAACCACAATCATTTCCAAAT
48393578 ATTTTATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 6 0.15
50 1 0.03
51 32 0.82
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (49 bp):
TCATTTTCATTTTCATTTTGGAAAAAACCACAATCATTTCCAAATGACT
Found at i:48396112 original size:6 final size:6
Alignment explanation
Indices: 48396101--48396132 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
48396091 CAAATAGGTC
48396101 TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TG
1 TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TG
48396133 TGTCAGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
TGGGAA
Found at i:48398412 original size:13 final size:13
Alignment explanation
Indices: 48398394--48398420 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48398384 ATGCATTTCA
48398394 CCCCAACTTTAAC
1 CCCCAACTTTAAC
48398407 CCCCAACTTTAAC
1 CCCCAACTTTAAC
48398420 C
1 C
48398421 ACTCAACTGA
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:0.30, C:0.48, G:0.00, T:0.22
Consensus pattern (13 bp):
CCCCAACTTTAAC
Found at i:48420844 original size:21 final size:21
Alignment explanation
Indices: 48420794--48420844 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
48420784 ATTTATCATG
*
48420794 AAATTAACTAAATTATACAAT
1 AAATTAAATAAATTATACAAT
*
48420815 AAATCAAATAAAATTAATA-AAT
1 AAATTAAAT-AAATT-ATACAAT
48420837 -AATTAAAT
1 AAATTAAAT
48420845 TATATAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 14 0.56
22 8 0.32
23 3 0.12
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTAAATAAATTATACAAT
Found at i:48422018 original size:44 final size:42
Alignment explanation
Indices: 48421968--48422160 Score: 216
Period size: 44 Copynumber: 4.6 Consensus size: 42
48421958 TAAAAAGTAT
*
48421968 GAGAAAACCCCCTCTATTTAAAAAAAATATTATTTCTTTTGTTA
1 GAGAAAAACCCCTCTATTTAAAAAAAATATTA-TT-TTTTGTTA
* *
48422012 GAGAAAAGCCCCTCTATTTAAAAATAATATTA----TT-TTA
1 GAGAAAAACCCCTCTATTTAAAAAAAATATTATTTTTTGTTA
** *
48422049 GAGAAAAACCATTCTATTTAAAAAATATATTATTTTTTGTTA
1 GAGAAAAACCCCTCTATTTAAAAAAAATATTATTTTTTGTTA
* * * *
48422091 GAGAAAAGCCCCTCTATTTTAAAATATATATTATTTTTTTATTA
1 GAGAAAAACCCCTCTA-TTTAAAAAAAATATTA-TTTTTTGTTA
*
48422135 GAGAAAAACCCCTCTATTTTAAAAAA
1 GAGAAAAACCCCTCTATTTAAAAAAA
48422161 TGTATATTAT
Statistics
Matches: 126, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
37 30 0.24
38 2 0.02
41 2 0.02
42 16 0.13
43 22 0.17
44 54 0.43
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.38
Consensus pattern (42 bp):
GAGAAAAACCCCTCTATTTAAAAAAAATATTATTTTTTGTTA
Found at i:48422052 original size:37 final size:38
Alignment explanation
Indices: 48421968--48422127 Score: 151
Period size: 37 Copynumber: 4.0 Consensus size: 38
48421958 TAAAAAGTAT
* * *
48421968 GAGAAAACCCCCTCTATTTAAAAAAAATATTATTTCTTTTGTTA
1 GAGAAAAGCCCCTCTATTT---AAAAATA-TATAT-TATT-TTA
48422012 GAGAAAAGCCCCTCTATTTAAAAATA-ATATTATTTTA
1 GAGAAAAGCCCCTCTATTTAAAAATATATATTATTTTA
* ** *
48422049 GAGAAAAACCATTCTATTTAAAAAATATATTATTTTTTGTTA
1 GAGAAAAGCCCCTCTATTT-AAAAATATA-TA-TTATT-TTA
*
48422091 GAGAAAAGCCCCTCTATTTTAAAATATATATTATTTT
1 GAGAAAAGCCCCTCTATTTAAAAATATATATTATTTT
48422128 TTTATTAGAG
Statistics
Matches: 99, Mismatches: 12, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
37 19 0.19
38 12 0.12
39 8 0.08
40 4 0.04
41 19 0.19
42 19 0.19
44 18 0.18
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (38 bp):
GAGAAAAGCCCCTCTATTTAAAAATATATATTATTTTA
Found at i:48422793 original size:92 final size:92
Alignment explanation
Indices: 48422682--48422865 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 92
48422672 AATGACTCTT
48422682 TTGTTCTTTGAAGTAAAATAAGAATGAAAATTAGAGATAAACAAATAAATATTACATTTATTTTT
1 TTGTTCTTTGAAGTAAAATAAGAATGAAAATTAGAGATAAACAAATAAATATTACATTTATTTTT
48422747 CTTTTTTATCGAAAAATAAAATACAAA
66 CTTTTTTATCGAAAAATAAAATACAAA
48422774 TTGTTCTTTGAAGTAAAATAAGAATGAAAATTAGAGATAAACAAATAAATATTACATTTATTTTT
1 TTGTTCTTTGAAGTAAAATAAGAATGAAAATTAGAGATAAACAAATAAATATTACATTTATTTTT
*
48422839 CTTTTTTATCGAAAAATAAAATTCAAA
66 CTTTTTTATCGAAAAATAAAATACAAA
48422866 AAACCGTATA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (92 bp):
TTGTTCTTTGAAGTAAAATAAGAATGAAAATTAGAGATAAACAAATAAATATTACATTTATTTTT
CTTTTTTATCGAAAAATAAAATACAAA
Found at i:48440600 original size:27 final size:25
Alignment explanation
Indices: 48440570--48440642 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 25
48440560 AATTTCGAGG
*
48440570 TTTATAATTTTTAATTTTTATTAATT
1 TTTAT-ATTTTTAACTTTTATTAATT
* *
48440596 ATTTATGTTTTCTCACTTTTATTAATT
1 -TTTATATTTT-TAACTTTTATTAATT
48440623 TTTATTATTATTTAAACTTT
1 TTTA-TATT-TTT-AACTTT
48440643 CTTTATTTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 8 0.22
27 22 0.59
28 7 0.19
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (25 bp):
TTTATATTTTTAACTTTTATTAATT
Found at i:48440912 original size:43 final size:43
Alignment explanation
Indices: 48440814--48441040 Score: 294
Period size: 43 Copynumber: 5.3 Consensus size: 43
48440804 ATGATATGTT
* * * * * * *
48440814 TTTAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAAGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
48440856 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* ** *
48440899 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
** *
48440942 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATTGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
48440985 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
48441028 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
48441041 ATTTCCAAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
42 30 0.19
43 132 0.81
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:48441017 original size:129 final size:127
Alignment explanation
Indices: 48440809--48441040 Score: 349
Period size: 129 Copynumber: 1.8 Consensus size: 127
48440799 TTTGCATGAT
* * * **
48440809 ATGTTTTTAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAAGTTTGTTCTATAGCGGCGTTTGTGGG
1 ATGTTTTTAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAACATTGTTCTATAGCGGCGTTTGTGGG
48440874 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACC
66 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACC
* *
48440936 ATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATTG-TCTTTAGCGGCGTTTGT
1 ATGTT-TTTAGCGGCGTTTGTGCGAAAAGCGCCGCT-AA-AACATTGTTCTATAGCGGCGTTTGT
* *
48441000 GGGAGAAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTT
63 GGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
48441041 ATTTCCAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
127 5 0.05
128 26 0.28
129 57 0.61
130 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (127 bp):
ATGTTTTTAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAACATTGTTCTATAGCGGCGTTTGTGGG
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACC
Found at i:48441162 original size:22 final size:22
Alignment explanation
Indices: 48441134--48441176 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
48441124 TAGTGGCGCT
*
48441134 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
48441156 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
48441177 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:48444117 original size:32 final size:32
Alignment explanation
Indices: 48444072--48444290 Score: 258
Period size: 32 Copynumber: 6.7 Consensus size: 32
48444062 ATGTTTTATT
*
48444072 TATTTCCGAATTGAATTGTATATATATACTTA
1 TATTGCCGAATTGAATTGTATATATATACTTA
*
48444104 TATTGCTGAATTGAATTGTATATATATAAACTTA
1 TATTGCCGAATTGAATTGTATATATAT--ACTTA
48444138 TATTGCCGAATTGAATTGTATATATATATACTTA
1 TATTGCCGAATTGAATTG--TATATATATACTTA
* ** ***
48444172 TATTGTCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATATATACTTA
* *
48444204 TATTGCTGAATTGAATTGTATACATATACTTA
1 TATTGCCGAATTGAATTGTATATATATACTTA
** ***
48444236 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATATATACTTA
*
48444268 TATTGCCGAATTGATTTGTATAT
1 TATTGCCGAATTGAATTGTATAT
48444291 GTATTTATAT
Statistics
Matches: 159, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
32 106 0.67
34 44 0.28
36 9 0.06
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (32 bp):
TATTGCCGAATTGAATTGTATATATATACTTA
Found at i:48444305 original size:64 final size:64
Alignment explanation
Indices: 48444072--48444290 Score: 312
Period size: 64 Copynumber: 3.4 Consensus size: 64
48444062 ATGTTTTATT
* * ** *
48444072 TATTTCCGAATTGAATTGTATATATATACTTATATTGCTGAATTGAATTGTATATATATAAACTT
1 TATTGCCGAATTGAATTGTATATATATACTTATATTGCCGAATTGAATTGTATAGGTATACAC--
*
48444137 A
64 C
*
48444138 TATTGCCGAATTGAATTGTATATATATATACTTATATTGTCGAATTGAATTGTATAGGTATACAC
1 TATTGCCGAATTGAATTG--TATATATATACTTATATTGCCGAATTGAATTGTATAGGTATACAC
48444203 C
64 C
* *
48444204 TATTGCTGAATTGAATTGTATACATATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATATATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
*
48444268 TATTGCCGAATTGATTTGTATAT
1 TATTGCCGAATTGAATTGTATAT
48444291 GTATTTATAT
Statistics
Matches: 138, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
64 64 0.46
66 34 0.25
68 40 0.29
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (64 bp):
TATTGCCGAATTGAATTGTATATATATACTTATATTGCCGAATTGAATTGTATAGGTATACACC
Found at i:48446358 original size:41 final size:41
Alignment explanation
Indices: 48446307--48446493 Score: 268
Period size: 41 Copynumber: 4.6 Consensus size: 41
48446297 CATTGAATGT
48446307 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCATTGATCGAA
** * *
48446348 AATTGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAG
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCATTGATCGAA
* *
48446389 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATAGAA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCATTGATCGAA
* * * *
48446430 AAGGGGTTGCTAAATGCT-GATTCCCTGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTG-TAGATTCCCCGAATCATTGATCGAA
48446471 AAGGGGTTGCTAAGTGTAGATTC
1 AAGGGGTTGCTAAGTGTAGATTC
48446494 TCTGAGGGGT
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 128 0.99
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGTAGATTCCCCGAATCATTGATCGAA
Found at i:48446590 original size:43 final size:41
Alignment explanation
Indices: 48446498--48446613 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 41
48446488 AGATTCTCTG
* *** *
48446498 AGGGGTTGCTAAGTGTTGATTCCCTAAATTATTGATTCTAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTCTAA
* *
48446539 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTCT-AA
*
48446583 AGGGGTTGCTATGTGCTGATTCCCCGTATCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCA
48446614 CTGAATATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.05
42 26 0.41
43 29 0.46
44 5 0.08
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTCTAA
Found at i:48469286 original size:93 final size:93
Alignment explanation
Indices: 48469126--48469316 Score: 330
Period size: 93 Copynumber: 2.1 Consensus size: 93
48469116 CCAACAAACT
* * *
48469126 AAACTAATTGGACTAGACTAAAACTCACATATGATGTAATTTGGAGACCCAAGTATAGAATTTCA
1 AAACTAATTGGACTAGACTAAAACTCACACATGATGTAACTTGGAGACCCAAGTATAGAATTGCA
*
48469191 CATGATAAATCTCAAATCTAAGTGCTTA
66 CATGATAAATCTCAAATCTAAGTACTTA
48469219 AAACTCAA-TGGACTAGACTAAAACTCACACATGATGTAACTTGGAGACCCAAGTATAGAATTGC
1 AAACT-AATTGGACTAGACTAAAACTCACACATGATGTAACTTGGAGACCCAAGTATAGAATTGC
48469283 ACATGATAAATCTCAAATCTAAGTACTTA
65 ACATGATAAATCTCAAATCTAAGTACTTA
48469312 AAACT
1 AAACT
48469317 GAATACCTTC
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
93 91 0.98
94 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (93 bp):
AAACTAATTGGACTAGACTAAAACTCACACATGATGTAACTTGGAGACCCAAGTATAGAATTGCA
CATGATAAATCTCAAATCTAAGTACTTA
Found at i:48472495 original size:21 final size:21
Alignment explanation
Indices: 48472453--48472506 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
48472443 AAATAAATAA
* * *
48472453 ATTGTAAAGGTGGGCAACTCG
1 ATTGTAAAGGTAGACAAATCG
*
48472474 ATTGTAAAGGTAGATAAATCG
1 ATTGTAAAGGTAGACAAATCG
*
48472495 ATTATAAAGGTA
1 ATTGTAAAGGTA
48472507 TATATATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (21 bp):
ATTGTAAAGGTAGACAAATCG
Found at i:48482145 original size:27 final size:27
Alignment explanation
Indices: 48482107--48482168 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
48482097 TGAGGCGATC
* * *
48482107 CTTTCATAATTCGTCACAAACG-TTTTT
1 CTTTCATGATTCGCCACAAA-GACTTTT
48482134 CTTTCATGATTCGCCACAAAGACTTTT
1 CTTTCATGATTCGCCACAAAGACTTTT
48482161 CTTTCATG
1 CTTTCATG
48482169 GCGTGTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (27 bp):
CTTTCATGATTCGCCACAAAGACTTTT
Found at i:48486661 original size:21 final size:19
Alignment explanation
Indices: 48486627--48486669 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
48486617 AAAAATATTC
*
48486627 AAACTTATTAATTTAAATA
1 AAACTTATTAATTTAAAAA
48486646 AAACTATATTGAATTTAAAAA
1 AAACT-TATT-AATTTAAAAA
48486667 AAA
1 AAA
48486670 AAACCCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 12 0.57
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (19 bp):
AAACTTATTAATTTAAAAA
Found at i:48486668 original size:20 final size:19
Alignment explanation
Indices: 48486627--48486668 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
48486617 AAAAATATTC
48486627 AAACTTATTAATTTAAATA
1 AAACTTATTAATTTAAATA
48486646 AAACTATATTGAATTTAAA-A
1 AAACT-TATT-AATTTAAATA
48486666 AAA
1 AAA
48486669 AAAACCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (19 bp):
AAACTTATTAATTTAAATA
Found at i:48494435 original size:43 final size:43
Alignment explanation
Indices: 48494377--48494577 Score: 278
Period size: 43 Copynumber: 4.7 Consensus size: 43
48494367 AATATTGGCG
* *
48494377 CACATAGTGCATCATCGGATAAACTGAAGTATCTATACTAGCA
1 CACACAGTGCATCATCGGATAAACCGAAGTATCTATACTAGCA
* *
48494420 CATACAGTGCATCATC-GACTAAACCGAAGTATCTATACTGGCA
1 CACACAGTGCATCATCGGA-TAAACCGAAGTATCTATACTAGCA
* *
48494463 CGCATAGTGCATCATCGGATAAACCGAAGTATCTATACTAGCA
1 CACACAGTGCATCATCGGATAAACCGAAGTATCTATACTAGCA
* * * * *
48494506 GACACAGTGCATTATCGGATAAACCAAAATATATATACTAGCA
1 CACACAGTGCATCATCGGATAAACCGAAGTATCTATACTAGCA
*
48494549 CATACAGTGCATCATCGGATAAACCGAAG
1 CACACAGTGCATCATCGGATAAACCGAAG
48494578 CCTAATCGTA
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 2 0.01
43 132 0.97
44 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (43 bp):
CACACAGTGCATCATCGGATAAACCGAAGTATCTATACTAGCA
Found at i:48502022 original size:25 final size:25
Alignment explanation
Indices: 48501981--48502030 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
48501971 AGTTGAAGAG
48501981 AGAAAATTCTCTAAAGAGATTATTTC
1 AGAAAATTCTCTAAAGAGATT-TTTC
*
48502007 AGAAAATT-TCTAAAGATATTTTTC
1 AGAAAATTCTCTAAAGAGATTTTTC
48502031 TTATCTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 11 0.48
26 8 0.35
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (25 bp):
AGAAAATTCTCTAAAGAGATTTTTC
Found at i:48503435 original size:15 final size:15
Alignment explanation
Indices: 48503415--48503450 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
48503405 TGTTTTTTTT
48503415 TCTTTTCCTTCTTTC
1 TCTTTTCCTTCTTTC
* *
48503430 TCTTTTCTTTCTTTT
1 TCTTTTCCTTCTTTC
48503445 TCTTTT
1 TCTTTT
48503451 TCCCTTTCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TCTTTTCCTTCTTTC
Found at i:48503435 original size:24 final size:23
Alignment explanation
Indices: 48503408--48503457 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
48503398 AACGTTCTGT
* *
48503408 TTTTTTTTCTTTTCCTTCTTTCTC
1 TTTTCTTTCTTTTCCTT-TTTCCC
*
48503432 TTTTCTTTCTTTTTCTTTTTCCC
1 TTTTCTTTCTTTTCCTTTTTCCC
48503455 TTT
1 TTT
48503458 CGTTTTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTCTTTCTTTTCCTTTTTCCC
Found at i:48503464 original size:24 final size:23
Alignment explanation
Indices: 48503409--48503457 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
48503399 ACGTTCTGTT
* *
48503409 TTTTTTTCTTTTCCTTCTTTCTC
1 TTTTTTTCTTTTTCTTCTTTCCC
48503432 TTTTCTTTCTTTTTCTT-TTTCCC
1 TTTT-TTTCTTTTTCTTCTTTCCC
48503455 TTT
1 TTT
48503458 CGTTTTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTTCTTTTTCTTCTTTCCC
Found at i:48505619 original size:28 final size:28
Alignment explanation
Indices: 48505566--48505620 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
48505556 TTAGAATAAA
* *
48505566 TTTGTCAATATGGTATTTGTATTTTTAG
1 TTTGTCAATATGGTATCTATATTTTTAG
*
48505594 TTTGTCTAATATGTTATCTATATTTTT
1 TTTGTC-AATATGGTATCTATATTTTT
48505621 GTTCTGCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.22, C:0.05, G:0.13, T:0.60
Consensus pattern (28 bp):
TTTGTCAATATGGTATCTATATTTTTAG
Found at i:48506518 original size:19 final size:19
Alignment explanation
Indices: 48506485--48506523 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
48506475 AAATAATTGA
* *
48506485 AAATATTTTTTAAAAATCC
1 AAATATTTATAAAAAATCC
*
48506504 AAATATTTATAAAAATTCC
1 AAATATTTATAAAAAATCC
48506523 A
1 A
48506524 CAATTTATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATTTATAAAAAATCC
Found at i:48523330 original size:20 final size:20
Alignment explanation
Indices: 48523305--48523345 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
48523295 ACTAGGATAT
*
48523305 TCACTTTCTTCTTTACTTAC
1 TCACTTACTTCTTTACTTAC
*
48523325 TCACTTACTTGTTTACTTAC
1 TCACTTACTTCTTTACTTAC
48523345 T
1 T
48523346 TGCTTGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.27, G:0.02, T:0.54
Consensus pattern (20 bp):
TCACTTACTTCTTTACTTAC
Found at i:48523676 original size:50 final size:50
Alignment explanation
Indices: 48523608--48523799 Score: 231
Period size: 50 Copynumber: 3.8 Consensus size: 50
48523598 TTTCCTGTAC
* * * ** *
48523608 TGCCAATGCCATATCCCAGATATGGTCTTACATTGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
48523658 TGCCCATGCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * * *
48523708 AGTCAATGCCATGTACCAGACATGGTCTTACATGGGACCTATTATCTTGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
48523758 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
48523800 TTATCCAAAT
Statistics
Matches: 118, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 118 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:48524170 original size:30 final size:30
Alignment explanation
Indices: 48524136--48524194 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
48524126 TACTTGACTC
48524136 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
48524166 AAACTTTTGCATAATTACACTTTTTCCCC
1 AAACTTTTGAAAAATTACAATTTTGCCCC
48524195 AAAGCTCGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:48528327 original size:22 final size:22
Alignment explanation
Indices: 48528299--48528364 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
48528289 ATACACCAGT
48528299 ATATGAGAGCCCTTTATGGGAC
1 ATATGAGAGCCCTTTATGGGAC
* * * *
48528321 ATTTGAGTGCCCCTTGTGGGAC
1 ATATGAGAGCCCTTTATGGGAC
*
48528343 ATATGAGATCCCTTTTATGGGA
1 ATATGAGAGCCC-TTTATGGGA
48528365 TGTATGAATG
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (22 bp):
ATATGAGAGCCCTTTATGGGAC
Found at i:48528443 original size:28 final size:28
Alignment explanation
Indices: 48528412--48528495 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
48528402 CATAAATGTC
* *
48528412 GAAGTCCGTCAAGATTATCGTATGTGTA
1 GAAGTCCGTCAAGACTATCTTATGTGTA
* * * *
48528440 GAAGTCTGCCAAGACTATCTTATATGTG
1 GAAGTCCGTCAAGACTATCTTATGTGTA
* *
48528468 GAAGTTCGTCAGGACTATCTTATGTGTA
1 GAAGTCCGTCAAGACTATCTTATGTGTA
48528496 TGATATTACA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (28 bp):
GAAGTCCGTCAAGACTATCTTATGTGTA
Found at i:48530878 original size:31 final size:32
Alignment explanation
Indices: 48530842--48530906 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
48530832 CTTAGATAAT
48530842 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
48530873 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
48530905 TT
1 TT
48530907 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:48531557 original size:13 final size:12
Alignment explanation
Indices: 48531526--48531556 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
48531516 CAAAAAGCAC
48531526 AAAAAAACCGCA
1 AAAAAAACCGCA
48531538 AAAAAAACCGCA
1 AAAAAAACCGCA
48531550 AAAAAAA
1 AAAAAAA
48531557 AGTTGTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.19, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAACCGCA
Found at i:48537349 original size:31 final size:32
Alignment explanation
Indices: 48537313--48537377 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
48537303 CTTAGATAAT
48537313 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
48537344 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
48537376 TT
1 TT
48537378 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:48538320 original size:19 final size:19
Alignment explanation
Indices: 48538285--48538325 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
48538275 ACTTTAAAAT
* *
48538285 CAAGTTAAAATTATTTTCA
1 CAAGTTAAAAATATTTTAA
*
48538304 CAAGTTAAAAATCTTTTAA
1 CAAGTTAAAAATATTTTAA
48538323 CAA
1 CAA
48538326 ATCAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (19 bp):
CAAGTTAAAAATATTTTAA
Found at i:48545555 original size:17 final size:18
Alignment explanation
Indices: 48545524--48545558 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48545514 TAAAGAAACA
48545524 TTTTTAAAATCTTTTGTAT
1 TTTTTAAAA-CTTTTGTAT
48545543 TTTTTAAAA-TTTTGTA
1 TTTTTAAAACTTTTGTA
48545559 GATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTTAAAACTTTTGTAT
Found at i:48546372 original size:17 final size:18
Alignment explanation
Indices: 48546339--48546374 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
48546329 TAATAAAATG
48546339 TGTATAATAAAATTAAAA
1 TGTATAATAAAATTAAAA
*
48546357 TGTATAAT-ATATTAAAA
1 TGTATAATAAAATTAAAA
48546374 T
1 T
48546375 AAAATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
TGTATAATAAAATTAAAA
Found at i:48547072 original size:14 final size:14
Alignment explanation
Indices: 48547053--48547098 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
48547043 ACATTAACGA
48547053 ATAAATATATAAAT
1 ATAAATATATAAAT
*
48547067 ATAAATAAATAAAT
1 ATAAATATATAAAT
**
48547081 ATTTATATATAAA-
1 ATAAATATATAAAT
48547094 ATAAA
1 ATAAA
48547099 ATAAATTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 3 0.12
14 23 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAAATATATAAAT
Found at i:48547117 original size:28 final size:30
Alignment explanation
Indices: 48547057--48547117 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
48547047 TAACGAATAA
*
48547057 ATATATAAATATAAATAAATAAATATTTAT
1 ATATATAAATATAAATAAATAAATAATTAT
*
48547087 ATATA-AAATA-AAATAAATTGAATAATT-T
1 ATATATAAATATAAATAAA-TAAATAATTAT
48547115 ATA
1 ATA
48547118 CTTAAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 11 0.39
29 12 0.43
30 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
ATATATAAATATAAATAAATAAATAATTAT
Found at i:48548171 original size:11 final size:11
Alignment explanation
Indices: 48548155--48548210 Score: 52
Period size: 9 Copynumber: 5.5 Consensus size: 11
48548145 AATTGAACCA
48548155 TTTTTCCTTCT
1 TTTTTCCTTCT
48548166 TTTTTCC-T-T
1 TTTTTCCTTCT
48548175 TTTTT--TTCT
1 TTTTTCCTTCT
*
48548184 TTTTTTC-T-T
1 TTTTTCCTTCT
48548193 TTTTTCCTCTCT
1 TTTTTCCT-TCT
48548205 TTTTTC
1 TTTTTC
48548211 TTTTTCTCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
8 1 0.03
9 19 0.51
10 2 0.05
11 8 0.22
12 7 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCCTTCT
Found at i:48548183 original size:18 final size:18
Alignment explanation
Indices: 48548155--48548215 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 18
48548145 AATTGAACCA
*
48548155 TTTTTCCTTCTTTTTTCCT
1 TTTTTTCTTCTTTTTT-CT
48548174 TTTTTT-TTCTTTTTTTCT
1 TTTTTTCTTC-TTTTTTCT
48548192 TTTTTTCCTCTCTTTTTTCT
1 TTTTTT-CT-TCTTTTTTCT
48548212 TTTT
1 TTTT
48548216 CTCCTGGGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 11 0.30
19 11 0.30
20 13 0.35
21 2 0.05
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTCTTTTTTCT
Found at i:48548216 original size:18 final size:17
Alignment explanation
Indices: 48548155--48548216 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
48548145 AATTGAACCA
48548155 TTTTTCCTTCTTTTTTCC
1 TTTTTCCTTCTTTTTT-C
**
48548173 TTTTTTTTTCTTTTTTTC
1 TTTTTCCTTC-TTTTTTC
48548191 TTTTTTTCCTCTCTTTTTTC
1 --TTTTTCCT-TCTTTTTTC
48548211 TTTTTC
1 TTTTTC
48548217 TCCTGGGCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 15 0.42
19 6 0.17
20 13 0.36
21 2 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCCTTCTTTTTTC
Found at i:48548220 original size:20 final size:19
Alignment explanation
Indices: 48548155--48548220 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
48548145 AATTGAACCA
48548155 TTTTTCCT-TCTTTTTTCCT
1 TTTTTCCTCTCTTTTTT-CT
**
48548174 TTTTTTTTCT-TTTTTTCTT
1 TTTTTCCTCTCTTTTTTC-T
48548193 TTTTTCCTCTCTTTTTTCT
1 TTTTTCCTCTCTTTTTTCT
48548212 TTTTCTCCT
1 TTTT-TCCT
48548221 GGGCTAGCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 26 0.67
20 12 0.31
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTCCTCTCTTTTTTCT
Found at i:48548480 original size:9 final size:9
Alignment explanation
Indices: 48548442--48548488 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
48548432 TAATTTATTT
*
48548442 TTCTATTTC
1 TTCTTTTTC
48548451 TT-TTTTTC
1 TTCTTTTTC
48548459 TT-TTTTTC
1 TTCTTTTTC
48548467 TTTCTTTTTC
1 -TTCTTTTTC
*
48548477 TTCTTCTTC
1 TTCTTTTTC
48548486 TTC
1 TTC
48548489 CTCCTTCTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 13 0.38
9 15 0.44
10 6 0.18
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:48548486 original size:19 final size:19
Alignment explanation
Indices: 48548453--48548505 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
48548443 TCTATTTCTT
* *
48548453 TTTTTCTT-TTTTTCTTTC
1 TTTTTCTTCTTCTTCTTCC
48548471 TTTTTCTTCTTCTTCTTCC
1 TTTTTCTTCTTCTTCTTCC
**
48548490 TCCTTCTTCTTCTTCT
1 TTTTTCTTCTTCTTCT
48548506 AGCCGCGCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTCTTCTTCTTCTTCC
Found at i:48548995 original size:59 final size:59
Alignment explanation
Indices: 48548867--48548996 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 59
48548857 TTCTGGGCCG
* *
48548867 AAATGTAATTTTGAAAAATTTTAGGGTCAAAATATAATTTCAAGAAATTTTAGGAGTCA
1 AAATGTAATTTTGAAAAATTTTAGGGTCAAAATATAATTTCAAGAAAGTTGAGGAGTCA
* * *
48548926 AAATGCAATTTT-AAAAATTTTAGGGGTCAAAATGA-AATTTTAA-AAAGTTGAGGGGTCA
1 AAATGTAATTTTGAAAAATTTTA-GGGTCAAAAT-ATAATTTCAAGAAAGTTGAGGAGTCA
48548984 AAATGTAAATTTT
1 AAATGT-AATTTT
48548997 TTATAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 27 0.44
59 34 0.55
60 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.35
Consensus pattern (59 bp):
AAATGTAATTTTGAAAAATTTTAGGGTCAAAATATAATTTCAAGAAAGTTGAGGAGTCA
Found at i:48548996 original size:30 final size:29
Alignment explanation
Indices: 48548867--48548996 Score: 163
Period size: 29 Copynumber: 4.4 Consensus size: 29
48548857 TTCTGGGCCG
48548867 AAATGTAATTTTGAAAAATTTTA-GGGTCA
1 AAATGTAATTTT-AAAAATTTTAGGGGTCA
* * *
48548896 AAATATAATTTCAAGAAATTTTAGGAGTCA
1 AAATGTAATTTTAA-AAATTTTAGGGGTCA
*
48548926 AAATGCAATTTTAAAAATTTTAGGGGTCA
1 AAATGTAATTTTAAAAATTTTAGGGGTCA
* * *
48548955 AAATGAAATTTTAAAAAGTTGAGGGGTCA
1 AAATGTAATTTTAAAAATTTTAGGGGTCA
48548984 AAATGTAAATTTT
1 AAATGT-AATTTT
48548997 TTATAAAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
28 2 0.02
29 63 0.72
30 22 0.25
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.35
Consensus pattern (29 bp):
AAATGTAATTTTAAAAATTTTAGGGGTCA
Found at i:48549509 original size:78 final size:77
Alignment explanation
Indices: 48549396--48551316 Score: 2007
Period size: 78 Copynumber: 24.9 Consensus size: 77
48549386 GAAATTTAAA
* * *
48549396 AAAAAAATACCTCAGC--GTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTCATTTTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT
48549459 GAAAAACAGAAATT
64 GAAAAACAGAAATT
48549473 -AAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
48549537 AAAACAGAAATTT
66 AAAACAGAAA-TT
* * * *
48549550 AAAAGAAATACATCGGCATGTG-TCCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-
*
48549614 AAAAAAACAGAAATT
64 -GAAAAACAGAAATT
* * * *
48549629 --AAAAATACCTCAGC--GTGGCCCGAGGCTCAACTCACTTCTCGCATTATGAGGTTGATTTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA-GTTGA----TT
*
48549690 TTTGAAAAATAGAAATT
61 TTTGAAAAACAGAAATT
* * * *
48549707 AAAAAAGATACCTCAGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
1 AAAAAA-ATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
48549772 AAAAACAGAAATTT
65 AAAAACAGAAA-TT
* ** * **
48549786 AAAAGAAATACCTCGGCATGTG-TCTAAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTAA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
*
48549849 AAAAACATAAATT
65 AAAAACAGAAATT
* * * *
48549862 --GAAACTACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT
*
48549923 GAAAAACAAAAATT
64 GAAAAACAGAAATT
* *
48549937 AAAAAAATA-CTCCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
1 AAAAAAATACCT-CGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
*
48550001 TGAAAAACAAAAATT
63 TGAAAAACAGAAATT
* *
48550016 AAAAAAATA-CTCCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG
1 AAAAAAATACCT-CGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
*
48550080 TAAAACAGAAATTT
65 AAAAACAGAAA-TT
* * ***
48550094 AAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATTAGTTGATTTAAA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
48550158 AAAAACAGAAATT
65 AAAAACAGAAATT
* * * *
48550171 --AAAAATACCTCAGC--GTGACCCAAGGCTCAACTCACCTCTCGCATTTTGAGTTGATATTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG--A----T
*
48550232 TTTTGAAGAACAGAAATTT
60 TTTTGAAAAACAGAAA-TT
* * * * * * **
48550251 AAAAGAAATACCTCGGCATGTG-TCCGAGGCTCCACTCTCCTCTTGCAATATGAGTTCATTCTAA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
48550315 AAAAACAGAAATT
65 AAAAACAGAAATT
* * * * *
48550328 --TAAAATACCTCAGCA--TGACCCGAGGCTCTACTCACCTCTCACATTATGAGTTGATTTTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTT
*
48550389 TGAAAAACAAAAATT
63 TGAAAAACAGAAATT
* * * *
48550404 AAAAAAAAATATCTCGGCGTGTG-CCCGTGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTT
1 --AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
48550468 GAAAAACAGAAATTT
64 GAAAAACAGAAA-TT
* * * **
48550483 AAAAGAAATACCTCGGCATGTG-TCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTAA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
48550547 AAAAACAGAAATT
65 AAAAACAGAAATT
* * * *
48550560 --GAAAATACCTCAGC--GTGACCCGGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT
48550621 GAAAAACAGAAATT
64 GAAAAACAGAAATT
* * * * *
48550635 AGAAAAATACTTCAGCGTGTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
*
48550700 AAAATAGAAATTT
66 AAAACAGAAA-TT
* * **
48550713 AAAAGAAATACTTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TT
*
48550777 AAAAAACAGAAATT
64 GAAAAACAGAAATT
* * * *
48550791 --GAAACTACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT
48550852 GAAAAACAGAAATT
64 GAAAAACAGAAATT
* *
48550866 -AAAAAATACCCCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
48550930 AAAACAGAAATTT
66 AAAACAGAAA-TT
* * * **
48550943 AAAAGAAATACATCGGCATGTG-TCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
*
48551006 AAAAATAGAAATT
65 AAAAACAGAAATT
* * * *
48551019 ---TAAATACCTCAGCA--TGACCCGAGGCTTAACTCACCTCTCGCATTATGAGTTGATTTTTTT
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TT
*
48551079 TTTGAAAAATAGAAATT
61 TTTGAAAAACAGAAATT
* *
48551096 AAAAAAGATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTG
1 AAAAAA-ATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
48551161 AAAAACAGAAATTT
65 AAAAACAGAAA-TT
* * ***
48551175 AAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTAAA
1 AAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
48551239 AAAAACAGAAATT
65 AAAAACAGAAATT
* * * *
48551252 --GAAACTACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGA
1 AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
48551313 AAAA
66 AAAA
48551317 AACGGAAATT
Statistics
Matches: 1565, Mismatches: 187, Indels: 188
0.81 0.10 0.10
Matches are distributed among these distances:
70 2 0.00
71 35 0.02
72 53 0.03
73 144 0.09
74 82 0.05
75 86 0.05
76 99 0.06
77 110 0.07
78 467 0.30
79 279 0.18
80 41 0.03
81 50 0.03
82 10 0.01
83 77 0.05
84 27 0.02
85 3 0.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (77 bp):
AAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
AAAACAGAAATT
Found at i:48550501 original size:232 final size:229
Alignment explanation
Indices: 48549140--48551310 Score: 2945
Period size: 230 Copynumber: 9.3 Consensus size: 229
48549130 TTTTTCTTTG
* * *
48549140 AAAAACAGAAATTGAAAATACCTCGACGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTATGAG
1 AAAAACAGAAATTGAAAATACCTC-A-GCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
* * ** *
48549205 TTGA--TTTTTGAAAAACAGAAATTTAAAAGATACCTCGGTATGTGACCTGAGGCTCAACTCACC
64 TTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACC
* *
48549268 TCTCGCAATATGAGTTGATTTTAGAAAAAACTGAAATTTAAAAGAAATACCTCGGCATGTGTCCG
129 TCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCG
48549333 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCTTTATA
193 AGGCTCAACTCACCTCTCGCAATATGAGTTGA------TTTA-A
* * * *
48549377 TGAAAAATAGAAATTTAAAAAAAAAATACCTCAGCGTGACCCGAGGCTTAACTCACCTCTCGCAA
1 --AAAAACAGAAA-TT-----GAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAT
* *
48549442 TATGAGTTCATTTTTTTGAAAAACAGAAATT-AAAAAATACCTCGGCATGTGACCCGAGGCTCAA
58 TATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAA
*
48549506 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACATCGGCATGT
123 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGT
* *
48549571 GTCCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTAAA
188 GTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT-AA
* * *
48549616 AAAAACAGAAATTAAAAATACCTCAGCGTGGCCCGAGGCTCAACTCACTTCTCGCATTATGAGGT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA-GT
* * * *
48549681 TGATTTTTTTTTGAAAAATAGAAATTAAAAAAGATACCTCAGCGTGTGATCTGAGGCTCAACTCA
65 TGA--TTTTTTTGAAAAACAGAAATTAAAAAA-ATACCTCGGCGTGTGACCCGAGGCTCAACTCA
*
48549746 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCT
127 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCC
* *
48549811 AAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTAA
192 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAA
* *
48549849 AAAAACATAAATTGAAACTACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
*
48549914 GATTTTTTTGAAAAACAAAAATTAAAAAAATA-CTCCGGCGTGTGACCCGAGGCTCAACTCACCT
66 GATTTTTTTGAAAAACAGAAATTAAAAAAATACCT-CGGCGTGTGACCCGAGGCTCAACTCACCT
* * * *
48549978 CTCGCATTATGAGTTGATTTTTTTGAAAAACA-AAAATTAAAA-AAATA-CTCCGGCGTGTGACC
130 CTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAGAAATACCT-CGGCATGTG-TC
**
48550040 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG
191 CGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTAA
* * * * *
48550080 TAAAACAGAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATA
1 AAAAACAGAAA-TT--GA-AAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTA
* *** * *
48550144 TTAGTTGA--TTTAAAAAAAACAGAAATT--AAAAATACCTCAGC--GTGACCCAAGGCTCAACT
60 TGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACT
* * *
48550203 CACCTCTCGCATTTTGAGTTGATATTTTTTTTTGAAGAACAGAAATTTAAAAGAAATACCTCGGC
125 CACCTCTCGCAATATGAGTTG--A----TTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGC
* * * *
48550268 ATGTGTCCGAGGCTCCACTCTCCTCTTGCAATATGAGTTCATTCTAA
184 ATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TAA
* * * *
48550315 AAAAACAGAAATTTAAAATACCTCAGCATGACCCGAGGCTCTACTCACCTCTCACATTATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
* * *
48550380 GATTTTTTTTGAAAAACAAAAATTAAAAAAAAATATCTCGGCGTGTG-CCCGTGGCTCAACTCAC
66 GA-TTTTTTTGAAAAACAGAAATT--AAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCAC
* *
48550444 CTCTAGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCTG
128 CTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCG
*
48550509 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTAA
193 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAA
*
48550547 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGGGGCTCAACTCACCTCTCGCATTATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
* * * *
48550612 GATTTTTTTGAAAAACAGAAATTAGAAAAATACTTCAGCGTGTGACCCGAGGCTTAACTCACCTC
66 GATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTC
* *
48550677 TCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAAATACTTCGGCATGTGTCCGAGG
131 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGG
48550742 CTCAACTCACCTCTCGCAATATGAGTTGATTTAAAA
196 CTCAACTCACCTCTCGCAATATGAGTTGATTT--AA
*
48550778 AAAAACAGAAATTGAAACTACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
* * *
48550843 GATTTTTTTGAAAAACAGAAATT-AAAAAATACCCCAGCATGTGACCCGAGGCTCAACTCACCTC
66 GATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTC
* *
48550907 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACATCGGCATGTGTCCAAGG
131 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGG
48550972 CTCAACTCACCTCTCGCAATATGAGTTGATTTAA
196 CTCAACTCACCTCTCGCAATATGAGTTGATTTAA
* * * *
48551006 AAAAATAGAAATT-TAAATACCTCAGCATGACCCGAGGCTTAACTCACCTCTCGCATTATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
*
48551070 GATTTTTTTTTTGAAAAATAGAAATTAAAAAAGATACCTCGGCGTGTGACCCGAGGCTCAACTCA
66 GA---TTTTTTTGAAAAACAGAAATTAAAAAA-ATACCTCGGCGTGTGACCCGAGGCTCAACTCA
*
48551135 CCTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCC
127 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCC
*
48551200 GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTAAA
192 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-AA
*
48551239 AAAAACAGAAATTGAAACTACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
48551304 GATTTTT
66 GATTTTT
48551311 GAAAAAAACG
Statistics
Matches: 1730, Mismatches: 146, Indels: 120
0.87 0.07 0.06
Matches are distributed among these distances:
227 49 0.03
228 18 0.01
229 80 0.05
230 390 0.23
231 200 0.12
232 287 0.17
233 92 0.05
234 107 0.06
235 65 0.04
236 171 0.10
237 27 0.02
238 30 0.02
239 18 0.01
240 3 0.00
243 104 0.06
244 60 0.03
245 29 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (229 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
GATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGG
CTCAACTCACCTCTCGCAATATGAGTTGATTTAA
Found at i:48551318 original size:78 final size:79
Alignment explanation
Indices: 48549140--48551318 Score: 1490
Period size: 78 Copynumber: 28.0 Consensus size: 79
48549130 TTTTTCTTTG
* * * * *
48549140 AAAAACAGAAATTGAAAATACCTCGACGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTATGAG
1 AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
48549205 TTGATTTTTG-----
65 TTGATTTTTGAAAAA
* * * *
48549215 AAAAACAGAAATTTAAAAGATACCTCGGTATGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
1 AAAAATAGAAA-TTGAAA-ATACCTCGG-CTGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
*
48549280 AGTTGATTTTAGAAAAA
63 AGTTGATTTTTGAAAAA
* ** * *
48549297 ACTGAAATTTAAA-AG-AAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATG
1 A--AAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
* * **
48549359 AGTTGATTTTTCTTTATATG
63 AGTTGA--TTT-TTGAAAAA
* * *
48549379 AAAAATAGAAATTTAAAAAAAAAATACCTCAGC-GTGACCCGAGGCTTAACTCACCTCTCGCAAT
1 AAAAATAGAAA-TT-----GAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAAT
* ***
48549443 ATGAGTTCATTTTT---TTG
60 ATGAGTTGATTTTTGAAAAA
* *
48549460 AAAAACAGAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAATAGAAATT-GAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48549525 GTTGATTTTTGAAAAA
64 GTTGATTTTTGAAAAA
* ** * * * * *
48549541 CAGAAATTTAAA-AG-AAATACATCGGCATGTG-TCCAAGGCTCAACTCACCTCTCGCAATATAA
1 -AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48549603 GTTGATTTTT---AAA
64 GTTGATTTTTGAAAAA
* * * * * *
48549616 AAAAACAGAAATTAAAAATACCTCAGC-GTGGCCCGAGGCTCAACTCACTTCTCGCATTATGAGG
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA-G
*****
48549680 TTGATTTTT-TTTTG
65 TTGATTTTTGAAAAA
* * * *
48549694 AAAAATAGAAATTAAAAAAGATACCTCAGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAATAGAAATT--GAAA-ATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
48549759 GAGTTGATTTTTGAAAAA
62 GAGTTGATTTTTGAAAAA
* ** * * ** *
48549777 CAGAAATTTAAA-AG-AAATACCTCGGCATGTG-TCTAAGGCTCAACTCACCTCTCGTAATATGA
1 -AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48549839 GTTGA--TTT--AAAA
64 GTTGATTTTTGAAAAA
* * * *
48549851 AAACAT--AAATTGAAACTACCTCAGC-GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGT
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
48549913 TGATTTTTTTGAAAAA
66 TGA--TTTTTGAAAAA
* *
48549929 CAAAAAT-TAAA---AAAATA-CTCCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 -AAAAATAGAAATTGAAAATACCT-CGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
48549989 AGTTGATTTTTTTGAAAAA
63 AGTTGA--TTTTTGAAAAA
*
48550008 CAAAAAT-TAAA---AAAATA-CTCCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
1 -AAAAATAGAAATTGAAAATACCT-CGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
* *
48550068 AGTTGAATTTTGTAAAAC
63 AGTTGATTTTTG-AAAAA
* ** * * *
48550086 AGAAATTTAAA-AG-AAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATTAG
1 AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
48550148 TTGA--TTT---AAA
65 TTGATTTTTGAAAAA
* * * * * *
48550158 AAAAACAGAAATTAAAAATACCTCAGC-GTGACCCAAGGCTCAACTCACCTCTCGCATTTTGAGT
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
*
48550222 TGATATTTTTTTTTGAAGAAC
66 TG--A----TTTTTGAA-AAA
* ** * * * * *
48550243 AGAAATTTAAA-AG-AAATACCTCGGCATGTG-TCCGAGGCTCCACTCTCCTCTTGCAATATGAG
1 AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
* *
48550305 TTCA-TTCT----AA
65 TTGATTTTTGAAAAA
* * * * * * *
48550315 AAAAACAGAAATTTAAAATACCTCAGC-ATGACCCGAGGCTCTACTCACCTCTCACATTATGAGT
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
48550379 TGATTTTTTTTGAAAAA
66 TGA---TTTTTGAAAAA
* * * *
48550396 CAAAAATTA-AAA--AAAAATATCTCGGCGTGTG-CCCGTGGCTCAACTCACCTCTAGCAATATG
1 -AAAAA-TAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
48550457 AGTTGATTTTTGAAAAA
63 AGTTGATTTTTGAAAAA
* ** * * * *
48550474 CAGAAATTTAAA-AG-AAATACCTCGGCATGTG-TCTGAGGCTCAACTCACCTCTTGCAATATGA
1 -AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48550536 GTTGA-TTTT----AA
64 GTTGATTTTTGAAAAA
* * * *
48550547 AAAAACAGAAATTGAAAATACCTCAGC-GTGACCCGGGGCTCAACTCACCTCTCGCATTATGAGT
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
***
48550611 TGATTTTT---TTG
66 TGATTTTTGAAAAA
* * * *
48550622 AAAAACAGAAATTAGAAAAATACTTCAGCGTGTGACCCGAGGCTTAACTCACCTCTCGCAATATG
1 AAAAATAGAAATT-G-AAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
48550687 AGTTGATTTTTGAAAAA
63 AGTTGATTTTTGAAAAA
* ** * * *
48550704 TAGAAATTTAAA-AG-AAATACTTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGA
1 -AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48550766 GTTGA--TTT--AAAA
64 GTTGATTTTTGAAAAA
* * * *
48550778 AAAAACAGAAATTGAAACTACCTCAGC-GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGT
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
***
48550842 TGATTTTT---TTG
66 TGATTTTTGAAAAA
* * * *
48550853 AAAAACAGAAATTAAAAAATACCCCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAATAGAAATT-GAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48550918 GTTGATTTTTGAAAAA
64 GTTGATTTTTGAAAAA
* ** * * * *
48550934 CAGAAATTTAAA-AG-AAATACATCGGCATGTG-TCCAAGGCTCAACTCACCTCTCGCAATATGA
1 -AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48550996 GTTGA--TTT----AA
64 GTTGATTTTTGAAAAA
* * * * *
48551006 AAAAATAGAAATT-TAAATACCTCAGC-ATGACCCGAGGCTTAACTCACCTCTCGCATTATGAGT
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
******
48551069 TGATTTTTTTTTTG
66 TGATTTTTGAAAAA
* *
48551083 AAAAATAGAAATTAAAAAAGATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATAT
1 AAAAATAGAAATT--GAAA-ATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
48551148 GAGTTGATTTTTGAAAAA
62 GAGTTGATTTTTGAAAAA
* ** * * *
48551166 CAGAAATTTAAA-AG-AAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATAA
1 -AAAAATAGAAATTGAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
48551228 GTTGA--TTT---AAA
64 GTTGATTTTTGAAAAA
* * * *
48551239 AAAAACAGAAATTGAAACTACCTCAGC-GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGT
1 AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
48551303 TGATTTTTGAAAAA
66 TGATTTTTGAAAAA
48551317 AA
1 AA
48551319 CGGAAATTGA
Statistics
Matches: 1685, Mismatches: 275, Indels: 285
0.75 0.12 0.13
Matches are distributed among these distances:
70 2 0.00
71 46 0.03
72 86 0.05
73 157 0.09
74 100 0.06
75 79 0.05
76 74 0.04
77 104 0.06
78 389 0.23
79 284 0.17
80 48 0.03
81 73 0.04
82 40 0.02
83 90 0.05
84 51 0.03
85 15 0.01
86 3 0.00
87 33 0.02
88 11 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (79 bp):
AAAAATAGAAATTGAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTGAAAAA
Found at i:48551924 original size:21 final size:20
Alignment explanation
Indices: 48551887--48551944 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
48551877 TTTCATCTTA
*
48551887 ATTTTTTTCTT-TTTTTTTT
1 ATTTTTTTTTTGTTTTTTTT
48551906 ATTTTTGTTTTTG-TTTTTTT
1 ATTTTT-TTTTTGTTTTTTTT
* *
48551926 GTTTTTTTTTTGTGTTTTT
1 ATTTTTTTTTTGTTTTTTT
48551945 AGGCATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.03, C:0.02, G:0.09, T:0.86
Consensus pattern (20 bp):
ATTTTTTTTTTGTTTTTTTT
Found at i:48551935 original size:19 final size:19
Alignment explanation
Indices: 48551887--48551945 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
48551877 TTTCATCTTA
48551887 ATTTTTTTCTTT-TTTTTTT
1 ATTTTTTT-TTTGTTTTTTT
48551906 ATTTTTGTTTTTGTTTTTTT
1 ATTTTT-TTTTTGTTTTTTT
* *
48551926 GTTTTTTTTTTGTGTTTTT
1 ATTTTTTTTTTGTTTTTTT
48551945 A
1 A
48551946 GGCATAATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.05, C:0.02, G:0.08, T:0.85
Consensus pattern (19 bp):
ATTTTTTTTTTGTTTTTTT
Found at i:48551937 original size:11 final size:11
Alignment explanation
Indices: 48551888--48551944 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
48551878 TTCATCTTAA
*
48551888 TTTTTTTCTTT
1 TTTTTTTGTTT
*
48551899 TTTTTTTATTT
1 TTTTTTTGTTT
48551910 TTGTTTTTGTTT
1 TT-TTTTTGTTT
*
48551922 TTTTGTT-TTT
1 TTTTTTTGTTT
*
48551932 TTTTTGTGTTT
1 TTTTTTTGTTT
48551943 TT
1 TT
48551945 AGGCATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 8 0.21
11 21 0.54
12 10 0.26
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:48551944 original size:1 final size:1
Alignment explanation
Indices: 48551888--48551936 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
48551878 TTCATCTTAA
* * * * *
48551888 TTTTTTTCTTTTTTTTTTATTTTTGTTTTTGTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
48551937 GTGTTTTTAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.02, C:0.02, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:48557959 original size:40 final size:40
Alignment explanation
Indices: 48557910--48558004 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
48557900 AGAACACCGT
*
48557910 CATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCGG
1 CATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCAG
* * *
48557950 TATTAAGCCTACTAGACATTAAGTCTGAATATTTCACCAG
1 CATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCAG
48557990 CATTAAGCCTGCTAG
1 CATTAAGCCTGCTAG
48558005 GTACAAAACC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (40 bp):
CATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCAG
Found at i:48562976 original size:21 final size:20
Alignment explanation
Indices: 48562951--48563012 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
48562941 AATTAAACCA
48562951 TTTTTCCTTCTTTTTTCCTTT
1 TTTTTCCTTCTTTTTT-CTTT
48562972 TTTTT-CTT-TTTTTTCTTT
1 TTTTTCCTTCTTTTTTCTTT
*
48562990 TTTTCCCTCTCTTTTTTCTTT
1 TTTTTCCT-TCTTTTTTCTTT
48563011 TT
1 TT
48563013 CTACTAGGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 4 0.11
21 17 0.46
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCCTTCTTTTTTCTTT
Found at i:48562981 original size:8 final size:9
Alignment explanation
Indices: 48562951--48563012 Score: 61
Period size: 9 Copynumber: 6.3 Consensus size: 9
48562941 AATTAAACCA
*
48562951 TTTTTCCTT
1 TTTTTTCTT
48562960 CTTTTTTCCTT
1 -TTTTTT-CTT
48562971 TTTTTTCTT
1 TTTTTTCTT
48562980 TTTTTTCTT
1 TTTTTTCTT
*
48562989 TTTTTCCCTCTC
1 TTTTT---TCTT
48563001 TTTTTTCTT
1 TTTTTTCTT
48563010 TTT
1 TTT
48563013 CTACTAGGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 23 0.51
10 11 0.24
11 3 0.07
12 8 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:48563192 original size:16 final size:15
Alignment explanation
Indices: 48563157--48563191 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
48563147 GTTTTTTTTC
48563157 TTTTTCTGCTTTGTT
1 TTTTTCTGCTTTGTT
48563172 TTTTTCTGCTTTGTT
1 TTTTTCTGCTTTGTT
48563187 TTTTT
1 TTTTT
48563192 TTGGGCCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (15 bp):
TTTTTCTGCTTTGTT
Found at i:48563306 original size:8 final size:8
Alignment explanation
Indices: 48563288--48563325 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
48563278 ATATAATTTA
48563288 TTTTTTCT
1 TTTTTTCT
*
48563296 TTTTCT-T
1 TTTTTTCT
48563303 TTTTTTCT
1 TTTTTTCT
48563311 TTTTTTCT
1 TTTTTTCT
48563319 TTCTTTT
1 TT-TTTT
48563326 TCTTCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 16 0.62
9 4 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTCT
Found at i:48563309 original size:9 final size:9
Alignment explanation
Indices: 48563295--48563329 Score: 54
Period size: 8 Copynumber: 3.9 Consensus size: 9
48563285 TTATTTTTTC
48563295 TTTTTCTTT
1 TTTTTCTTT
48563304 TTTTTC-TT
1 TTTTTCTTT
48563312 TTTTTCTTT
1 TTTTTCTTT
48563321 CTTTTTCTT
1 -TTTTTCTT
48563330 CTTCTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 8 0.33
10 8 0.33
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:48563331 original size:3 final size:3
Alignment explanation
Indices: 48563292--48563356 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
48563282 AATTTATTTT
* * * * *
48563292 TTC TTT TTC TTT TTT TTC TT- TTT TTC TTTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
48563337 TTC TTCC TTC TTC TTC TTC T
1 TTC TT-C TTC TTC TTC TTC T
48563357 AGCGGCGCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:48563331 original size:9 final size:9
Alignment explanation
Indices: 48563288--48563356 Score: 70
Period size: 9 Copynumber: 7.7 Consensus size: 9
48563278 ATATAATTTA
48563288 TTTT-TTCT
1 TTTTCTTCT
*
48563296 TTTTCTTTT
1 TTTTCTTCT
48563305 TTTTCTT-T
1 TTTTCTTCT
48563313 TTTTCTTTCT
1 TTTTC-TTCT
48563323 TTTTCTTCT
1 TTTTCTTCT
*
48563332 TCTTCTTCT
1 TTTTCTTCT
*
48563341 TCCTTCTTCT
1 T-TTTCTTCT
*
48563351 TCTTCT
1 TTTTCT
48563357 AGCGGCGCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
8 10 0.18
9 30 0.55
10 15 0.27
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:48563442 original size:17 final size:19
Alignment explanation
Indices: 48563420--48563468 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
48563410 CCACCGGTAC
48563420 TCTTTCT-TTTT-TCCTCA
1 TCTTTCTCTTTTCTCCTCA
*
48563437 TCTTTCTCTTTTCTCCTCT
1 TCTTTCTCTTTTCTCCTCA
*
48563456 TTTCTTCTCTTTT
1 TCT-TTCTCTTTT
48563469 TTTGGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 4 0.15
19 7 0.26
20 9 0.33
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTTTCTCTTTTCTCCTCA
Found at i:48563794 original size:59 final size:58
Alignment explanation
Indices: 48563719--48563884 Score: 188
Period size: 59 Copynumber: 2.8 Consensus size: 58
48563709 TTCTGGGCTG
* * *
48563719 AAATGTAAATTTAAAAAAATTTTAGGGTCAAAATATAATTTTAAAAAGTTTAGGGGTTA
1 AAATGT-AATTTAAAAAAATTTAAGGGTCAAAATATAATTTTAAAAAGTTTAGAGGTCA
* * *
48563778 AAATGTAATTTCAAAAAAGTTTAAGGGTCACAATGTAATTTTAAAAAGTTTAGAGGTCA
1 AAATGTAATTT-AAAAAAATTTAAGGGTCAAAATATAATTTTAAAAAGTTTAGAGGTCA
* * * * * *
48563837 AAATGAAATTTTAAAAAGTTGAGGGGTCAAAATGTAAATTTTTAAAAA
1 AAATGTAATTTAAAAAAATTTAAGGGTCAAAATAT-AA-TTTTAAAAA
48563885 AAACATGAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 25 0.27
59 59 0.63
60 9 0.10
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (58 bp):
AAATGTAATTTAAAAAAATTTAAGGGTCAAAATATAATTTTAAAAAGTTTAGAGGTCA
Found at i:48563870 original size:29 final size:29
Alignment explanation
Indices: 48563719--48563884 Score: 174
Period size: 29 Copynumber: 5.6 Consensus size: 29
48563709 TTCTGGGCTG
* *
48563719 AAATGTAAATTTAAAAAAATTTTA-GGGTCA
1 AAATG-AAATTT-TAAAAAGTTTAGGGGTCA
*
48563749 AAAT-ATAATTTTAAAAAGTTTAGGGGTTA
1 AAATGA-AATTTTAAAAAGTTTAGGGGTCA
* * *
48563778 AAATGTAATTTCAAAAAAGTTTAAGGGTCA
1 AAATGAAATTT-TAAAAAGTTTAGGGGTCA
* * *
48563808 CAATGTAATTTTAAAAAGTTTAGAGGTCA
1 AAATGAAATTTTAAAAAGTTTAGGGGTCA
*
48563837 AAATGAAATTTTAAAAAGTTGAGGGGTCA
1 AAATGAAATTTTAAAAAGTTTAGGGGTCA
48563866 AAATGTAAATTTTTAAAAA
1 AAATG-AAA-TTTTAAAAA
48563885 AAACATGAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
28 10 0.09
29 64 0.56
30 32 0.28
31 9 0.08
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (29 bp):
AAATGAAATTTTAAAAAGTTTAGGGGTCA
Found at i:48566938 original size:83 final size:83
Alignment explanation
Indices: 48566762--48567378 Score: 503
Period size: 83 Copynumber: 7.5 Consensus size: 83
48566752 CCCTTGGATT
* * * * *
48566762 TGTTAAACGGCAGGATTAAATCCTGAAACAAAATTATTTAATTAAATCTT-GTTTGGAAACAAAA
1 TGTTAAACGGCGGGAATAAATCCCGAAACAAATTTATTTAATTTAATCTTCGTTTGGAAACAAAA
48566826 TC--AA---AATAAAATC
66 TCAAAATCGAATAAAATC
* * *
48566839 TGTTAAACGGTGGGAATAAATCCCGAAACAAAATTATTTGA-TTAAGTCTTCGTTTGGAAACAAA
1 TGTTAAACGGCGGGAATAAATCCCGAAACAAATTTATTTAATTTAA-TCTTCGTTTGGAAACAAA
*
48566903 ATCAAGATCGAATAAAGA-C
65 ATCAAAATCGAATAAA-ATC
* * * *
48566922 TGTTAAACGGCGGGAATATATCTCGAAACAGATTTATTTGA-TTAAGTCTTCGTTTGGAAACAAA
1 TGTTAAACGGCGGGAATAAATCCCGAAACAAATTTATTTAATTTAA-TCTTCGTTTGGAAACAAA
* *
48566986 ATCAAGATCGAATACAGAT-
65 ATCAAAATCGAATA-AAATC
* ** * * **
48567005 TGTTAAATGGTAGGAATAAATCCTGAAA-AAGA-TTATTCAATTTAAT-TCTAATTTGGAAACAA
1 TGTTAAACGGCGGGAATAAATCCCGAAACAA-ATTTATTTAATTTAATCT-TCGTTTGGAAACAA
*
48567067 AATTAAAATCGAATAAAATC
64 AATCAAAATCGAATAAAATC
* * * ** * *
48567087 TGTTAAACAGCCGGAATAAATCCCAAAACAGGTTTTATTTAATTTTAATTTCTCGTTTGGCAACA
1 TGTTAAACGGCGGGAATAAATCCCGAAACA-AATTTATTTAA-TTTAATCT-TCGTTTGGAAACA
*
48567152 AAATCAAAAATAGAATAAAATC
63 AAATC-AAAATCGAATAAAATC
* * * * *
48567174 TGTTGAATGGTGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATGC-TCATTTGGAAACA
1 TGTTAAACGGCGGGAATAAATCCCGAAACA-AATTTATTTAA-TTTAAT-CTTCGTTTGGAAACA
48567238 AAAT---AA---AAT---A--
63 AAATCAAAATCGAATAAAATC
*
48567248 TGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAATAC-TCGTTTGGAAACA
1 TGTTAAACGGCGGGAATAAATCCCGAAACAAA-TTTATTTAA-TTTAAT-CTTCGTTTGGAAACA
* *
48567312 AAATAAAAAATGGAATAAAATC
63 AAAT-CAAAATCGAATAAAATC
* * * *
48567334 TATTGAACGGCGGGAATAAATCCCAAAACAAATTTTATTCAATTT
1 TGTTAAACGGCGGGAATAAATCCCGAAACAAA-TTTATTTAATTT
48567379 TTATTTTTAT
Statistics
Matches: 447, Mismatches: 59, Indels: 60
0.79 0.10 0.11
Matches are distributed among these distances:
73 1 0.00
74 61 0.14
76 4 0.01
77 40 0.09
78 18 0.04
79 3 0.01
80 1 0.00
81 7 0.02
82 57 0.13
83 109 0.24
84 10 0.02
85 9 0.02
86 70 0.16
87 57 0.13
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (83 bp):
TGTTAAACGGCGGGAATAAATCCCGAAACAAATTTATTTAATTTAATCTTCGTTTGGAAACAAAA
TCAAAATCGAATAAAATC
Found at i:48567252 original size:74 final size:74
Alignment explanation
Indices: 48567165--48567319 Score: 256
Period size: 74 Copynumber: 2.1 Consensus size: 74
48567155 TCAAAAATAG
* * * * *
48567165 AATAAAATCTGTTGAATGGTGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATGCTCATT
1 AATAAAATATGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAATACTCATT
48567230 TGGAAACAA
66 TGGAAACAA
*
48567239 AATAAAATATGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAATACTCGTT
1 AATAAAATATGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAATACTCATT
48567304 TGGAAACAA
66 TGGAAACAA
48567313 AATAAAA
1 AATAAAA
48567320 AATGGAATAA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (74 bp):
AATAAAATATGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAATACTCATT
TGGAAACAA
Found at i:48567353 original size:160 final size:161
Alignment explanation
Indices: 48567078--48567379 Score: 444
Period size: 160 Copynumber: 1.9 Consensus size: 161
48567068 ATTAAAATCG
* ** *
48567078 AATAAAATCTGTTAAACAGCCGGAATAAATCCCAAAACAGGTTTTATTTAATTTTAATTTCTCGT
1 AATAAAATATGTTAAACAGCCGGAATAAATCCCAAAACAAATTTTATTTAATTTTAATTACTCGT
* * * * * * *
48567143 TTGGCAACAAAATCAAAAATAGAATAAAATCTGTTGAATGGTGGGAATAAATCCCGAAACAGATT
66 TTGGAAACAAAATAAAAAATAGAATAAAATCTATTGAACGGCGGGAATAAATCCCAAAACAAATT
*
48567208 TTATTTAATTTTAATGCTCATTTGGAAACAA
131 TTATTCAATTTTAATGCTCATTTGGAAACAA
* * * *
48567239 AATAAAATATGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAA-TACTCGT
1 AATAAAATATGTTAAACAGCCGGAATAAATCCCAAAACAAATTTTATTTAATTTTAATTACTCGT
*
48567303 TTGGAAACAAAATAAAAAATGGAATAAAATCTATTGAACGGCGGGAATAAATCCCAAAACAAATT
66 TTGGAAACAAAATAAAAAATAGAATAAAATCTATTGAACGGCGGGAATAAATCCCAAAACAAATT
48567368 TTATTCAATTTT
131 TTATTCAATTTT
48567380 TATTTTTATT
Statistics
Matches: 124, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
160 74 0.60
161 50 0.40
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (161 bp):
AATAAAATATGTTAAACAGCCGGAATAAATCCCAAAACAAATTTTATTTAATTTTAATTACTCGT
TTGGAAACAAAATAAAAAATAGAATAAAATCTATTGAACGGCGGGAATAAATCCCAAAACAAATT
TTATTCAATTTTAATGCTCATTTGGAAACAA
Found at i:48567531 original size:22 final size:23
Alignment explanation
Indices: 48567505--48567548 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
48567495 GTTAGCGATA
48567505 AAATATATAAATAT-AAATAAAC
1 AAATATATAAATATAAAATAAAC
* *
48567527 AAATATTTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
48567549 ATAAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAC
Found at i:48567550 original size:28 final size:31
Alignment explanation
Indices: 48567507--48567577 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
48567497 TAGCGATAAA
48567507 ATATAT-AAATATAAATAAA-CAAAT-ATTT
1 ATATATAAAATATAAATAAATCAAATAATTT
**
48567535 ATATATAAAATA-AAATAAATTGAATAATTT
1 ATATATAAAATATAAATAAATCAAATAATTT
*
48567565 ATATTTAAAATAT
1 ATATATAAAATAT
48567578 CATATACGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.36
29 8 0.22
30 15 0.42
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (31 bp):
ATATATAAAATATAAATAAATCAAATAATTT
Found at i:48568001 original size:20 final size:20
Alignment explanation
Indices: 48567978--48568018 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
48567968 TTAAATCAAT
*
48567978 TTGATTAAAATCAAATTAAA
1 TTGATTAAAATCAAATAAAA
**
48567998 TTGATTGGAATCAAATAAAA
1 TTGATTAAAATCAAATAAAA
48568018 T
1 T
48568019 CAGGATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (20 bp):
TTGATTAAAATCAAATAAAA
Found at i:48569608 original size:16 final size:17
Alignment explanation
Indices: 48569587--48569623 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
48569577 AGACTTTTTT
48569587 TTATAAAAGTTATA-TA
1 TTATAAAAGTTATATTA
*
48569603 TTATAAAATTTATATTA
1 TTATAAAAGTTATATTA
48569620 TTAT
1 TTAT
48569624 TTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATAAAAGTTATATTA
Found at i:48571272 original size:23 final size:26
Alignment explanation
Indices: 48571217--48571277 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 26
48571207 GAGCTATGAT
48571217 CGGTAAGCTCATTCCGAGCTGAAGAA
1 CGGTAAGCTCATTCCGAGCTGAAGAA
*
48571243 CGATAAGCTC-TAT-CGAGCTG-A-AA
1 CGGTAAGCTCAT-TCCGAGCTGAAGAA
48571266 CGGTAAGCTCAT
1 CGGTAAGCTCAT
48571278 ACGAGATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 11 0.35
24 2 0.06
25 8 0.26
26 10 0.32
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (26 bp):
CGGTAAGCTCATTCCGAGCTGAAGAA
Found at i:48576275 original size:21 final size:21
Alignment explanation
Indices: 48576251--48576313 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
48576241 ATTTGGTTTT
48576251 AATTTTTGTTACTTAATGAGA
1 AATTTTTGTTACTTAATGAGA
* *
48576272 AA-TTAT-TT--TT-ATGGGTA
1 AATTTTTGTTACTTAATGAG-A
48576289 AATTTTTGTTACTTAATGAGA
1 AATTTTTGTTACTTAATGAGA
48576310 AATT
1 AATT
48576314 ATTTTTATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 4 0.12
17 5 0.16
18 3 0.09
19 4 0.12
20 3 0.09
21 9 0.28
22 4 0.12
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.49
Consensus pattern (21 bp):
AATTTTTGTTACTTAATGAGA
Found at i:48576295 original size:38 final size:38
Alignment explanation
Indices: 48576251--48576328 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
48576241 ATTTGGTTTT
48576251 AATTTTTGTTACTTAATGAGAAATTATTTTTATGGGTA
1 AATTTTTGTTACTTAATGAGAAATTATTTTTATGGGTA
48576289 AATTTTTGTTACTTAATGAGAAATTATTTTTATGGGTA
1 AATTTTTGTTACTTAATGAGAAATTATTTTTATGGGTA
48576327 AA
1 AA
48576329 CTATCAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (38 bp):
AATTTTTGTTACTTAATGAGAAATTATTTTTATGGGTA
Found at i:48576373 original size:31 final size:29
Alignment explanation
Indices: 48576338--48576407 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
48576328 ACTATCAAAA
* *
48576338 TAGTCACTTTTGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGA--AAGGTTACATTT
*
48576369 TAGTCACTTATGTTTGAAATGTTACATTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
48576398 TAGTCACTTA
1 TAGTCACTTA
48576408 CGTTATCGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 20 0.56
31 16 0.44
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:48577622 original size:14 final size:14
Alignment explanation
Indices: 48577586--48577619 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
48577576 TCATCATTTG
48577586 CCTATAACCAAAAC
1 CCTATAACCAAAAC
48577600 CCTATAACCAAAAC
1 CCTATAACCAAAAC
48577614 CC-ATAA
1 CCTATAA
48577620 ACCCATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:48578376 original size:22 final size:22
Alignment explanation
Indices: 48578340--48578398 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
48578330 GGTCTGGCTC
48578340 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATACCAAAA
***
48578362 ATTTATTTTAAAAATTTTAAAA
1 ATTTATTTTAAAAATACCAAAA
*
48578384 A-GTATTTTAAAAATA
1 ATTTATTTTAAAAATA
48578399 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 12 0.39
22 13 0.42
23 6 0.19
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTATTTTAAAAATACCAAAA
Found at i:48578400 original size:11 final size:11
Alignment explanation
Indices: 48578365--48578536 Score: 133
Period size: 11 Copynumber: 16.9 Consensus size: 11
48578355 ACCAAAAATT
48578365 TATTTT-AAAA
1 TATTTTAAAAA
48578375 -ATTTTAAAAA
1 TATTTTAAAAA
48578385 GTATTTTAAAAA
1 -TATTTTAAAAA
48578397 TATTTTAAAAA
1 TATTTTAAAAA
48578408 TATTTT--AAA
1 TATTTTAAAAA
*
48578417 -A-TTAAAAAA
1 TATTTTAAAAA
*
48578426 AATTTT-AAAA
1 TATTTTAAAAA
*
48578436 TATTTTAAAAT
1 TATTTTAAAAA
48578447 TATTTT--AAA
1 TATTTTAAAAA
48578456 -A--TTAAAAA
1 TATTTTAAAAA
* *
48578464 AAATTTAAAAA
1 TATTTTAAAAA
48578475 TATTTTAAAAA
1 TATTTTAAAAA
48578486 TATTTT--AAA
1 TATTTTAAAAA
*
48578495 -A-TTAAAAAA
1 TATTTTAAAAA
* **
48578504 TAATAAAAAAA
1 TATTTTAAAAA
48578515 GTATTTTAAAAA
1 -TATTTTAAAAA
48578527 TATTTTAAAA
1 TATTTTAAAA
48578537 TTAAAAAAAT
Statistics
Matches: 132, Mismatches: 12, Indels: 35
0.74 0.07 0.20
Matches are distributed among these distances:
6 2 0.02
7 4 0.03
8 6 0.05
9 20 0.15
10 15 0.11
11 67 0.51
12 18 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:48578435 original size:8 final size:9
Alignment explanation
Indices: 48578366--48578497 Score: 77
Period size: 10 Copynumber: 13.3 Consensus size: 9
48578356 CCAAAAATTT
48578366 ATTTTAAAA
1 ATTTTAAAA
48578375 ATTTTAAAAA
1 ATTTT-AAAA
48578385 GTATTTTAAAAA
1 --ATTTT-AAAA
48578397 TATTTTAAAA
1 -ATTTTAAAA
*
48578407 ATATTTTAAA
1 AT-TTTAAAA
**
48578417 ATTAAAAAAA
1 ATT-TTAAAA
48578427 ATTTTAAAA
1 ATTTTAAAA
48578436 TATTTTAAAA
1 -ATTTTAAAA
48578446 TTATTTT-AAA
1 --ATTTTAAAA
**
48578456 ATTAAAAAAA
1 ATT-TTAAAA
*
48578466 ATTTAAAAA
1 ATTTTAAAA
48578475 TATTTTAAAA
1 -ATTTTAAAA
*
48578485 ATATTTTAAA
1 AT-TTTAAAA
48578495 ATT
1 ATT
48578498 AAAAAATAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 22
0.75 0.08 0.16
Matches are distributed among these distances:
8 3 0.03
9 20 0.20
10 56 0.55
11 12 0.12
12 10 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:48578451 original size:39 final size:39
Alignment explanation
Indices: 48578389--48578555 Score: 273
Period size: 39 Copynumber: 4.3 Consensus size: 39
48578379 TAAAAAGTAT
48578389 TTTAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAA
1 TTTAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAA
* *
48578428 TTTTAAAATATTTTAAAATTATTTTAAAATTAAAAAAAA
1 TTTAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAA
48578467 TTTAAAAATATTTTAAAAATATTTTAAAATTAAAAAATAA
1 TTTAAAAATATTTTAAAAATATTTTAAAATTAAAAAA-AA
**
48578507 TAAAAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAAA
1 TTTAAAAA-TATTTTAAAAATATTTTAAAATTAAAAAAAA
48578546 TTTAAAAATA
1 TTTAAAAATA
48578556 AATATATTTA
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.02
39 80 0.68
40 13 0.11
41 23 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (39 bp):
TTTAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAA
Found at i:48578496 original size:50 final size:50
Alignment explanation
Indices: 48578366--48578536 Score: 163
Period size: 50 Copynumber: 3.4 Consensus size: 50
48578356 CCAAAAATTT
* * * ***
48578366 ATTTTAAAA-ATTTTAAAAAGTATTTTAAAAATATTTTAAAAATATTTTAAA
1 ATTTAAAAATATTTTAAAAA-TATTTTAAAATTATTTTAAAATTA-AAAAAA
* *
48578417 ATTAAAAAAAATTTT-AAAATATTTTAAAATTATTTTAAAATTAAAAAAA
1 ATTTAAAAATATTTTAAAAATATTTTAAAATTATTTTAAAATTAAAAAAA
*
48578466 ATTTAAAAATATTTTAAAAATATTTTAAAATTA---AAAAATAATAAAAAAA
1 ATTTAAAAATATTTTAAAAATATTTTAAAATTATTTTAAAAT--TAAAAAAA
48578515 GTATTTTAAAAATATTTTAAAA
1 --A-TTTAAAAATATTTTAAAA
48578537 TTAAAAAAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
47 5 0.05
49 24 0.23
50 39 0.38
51 12 0.12
52 23 0.22
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (50 bp):
ATTTAAAAATATTTTAAAAATATTTTAAAATTATTTTAAAATTAAAAAAA
Found at i:48578542 original size:17 final size:17
Alignment explanation
Indices: 48578520--48578564 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
48578510 AAAAAGTATT
48578520 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
48578537 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
48578553 ATAAATATATTT
1 TTAAAAATATTT
48578565 ATTATATCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:48581703 original size:8 final size:7
Alignment explanation
Indices: 48581669--48581702 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
48581659 TAATTGAGTT
48581669 TATTTTA
1 TATTTTA
48581676 TA-TTTA
1 TATTTTA
48581682 TAATTTTA
1 T-ATTTTA
48581690 TATTTTA
1 TATTTTA
48581697 TATTTT
1 TATTTT
48581703 TTTTTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.20
7 15 0.60
8 5 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTTTA
Found at i:48591804 original size:32 final size:32
Alignment explanation
Indices: 48591768--48591830 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
48591758 AAAATTCTAA
*
48591768 TAGTCTTCCGCATTCTCCACTCCCTGTAATTG
1 TAGTCTTCCACATTCTCCACTCCCTGTAATTG
* * *
48591800 TAGTCTTCCACATTTTTCACTCCTTGTAATT
1 TAGTCTTCCACATTCTCCACTCCCTGTAATT
48591831 AGTATCAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.43
Consensus pattern (32 bp):
TAGTCTTCCACATTCTCCACTCCCTGTAATTG
Found at i:48594269 original size:43 final size:42
Alignment explanation
Indices: 48594234--48594347 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 42
48594224 CGACACTACT
48594234 GTCCCAGACAAGGTCTTACACGAAAACATAAATCGATGCCAAC
1 GTCCCAGACAAGGTCTTACACGAAAACATAAATCGA-GCCAAC
* ** * *
48594277 GTCCTAGACGTGGTCTTACACGAAAACATAAATCGATGGCAAT
1 GTCCCAGACAAGGTCTTACACGAAAACATAAATCGA-GCCAAC
* * *
48594320 GTCCCATACGTA-GTCTTACATGAAAACA
1 GTCCCAGAC-AAGGTCTTACACGAAAACA
48594348 CATATCGGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
GTCCCAGACAAGGTCTTACACGAAAACATAAATCGAGCCAAC
Found at i:48601774 original size:108 final size:108
Alignment explanation
Indices: 48601585--48601782 Score: 308
Period size: 108 Copynumber: 1.8 Consensus size: 108
48601575 GACAGGTGCA
* * *
48601585 ACTGTTTTGGAGAAGGATAATGAAAAAAATTCTGCTGAAACTGAACCGGCAGATAATGTACTTGC
1 ACTGTTTTGGAGAAGGATAATGAAAAAAAATCTGCTGAAACTGAACCAGCAGATAATGTACATGC
*
48601650 AGAACCTGATAGGAGCCCCAAGATATCTAATTTGAAAGATGCG
66 AGAACCTGATAAGAGCCCCAAGATATCTAATTTGAAAGATGCG
* * *
48601693 ACTGTTCTT-GAGAAGTATAATGAAAAAAAATCTGCTGAAACTGAACCAGCTGATGATGTACATG
1 ACTGTT-TTGGAGAAGGATAATGAAAAAAAATCTGCTGAAACTGAACCAGCAGATAATGTACATG
*
48601757 CAGAACCTGATAAGAGCCTCAAGATA
65 CAGAACCTGATAAGAGCCCCAAGATA
48601783 CACCCTCGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 79 0.98
109 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (108 bp):
ACTGTTTTGGAGAAGGATAATGAAAAAAAATCTGCTGAAACTGAACCAGCAGATAATGTACATGC
AGAACCTGATAAGAGCCCCAAGATATCTAATTTGAAAGATGCG
Found at i:48611377 original size:30 final size:31
Alignment explanation
Indices: 48611308--48611382 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
48611298 GATTATCAGC
* **
48611308 TAATGAAAAGGGATAGCCTCGGTTATCAAAA
1 TAATGAAAAGGGATAACCTCGACTATCAAAA
48611339 TAATGAAAAGGGATAACCTCGACTATC-AAA
1 TAATGAAAAGGGATAACCTCGACTATCAAAA
*
48611369 TTATGAAAAGGGAT
1 TAATGAAAAGGGAT
48611383 GGTGATGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 16 0.40
31 24 0.60
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (31 bp):
TAATGAAAAGGGATAACCTCGACTATCAAAA
Found at i:48611412 original size:29 final size:29
Alignment explanation
Indices: 48611371--48611527 Score: 174
Period size: 29 Copynumber: 5.3 Consensus size: 29
48611361 CTATCAAATT
* * *
48611371 ATGAAAAGGGATGGTGATGATCATCAAAA
1 ATGAAAAGGGATGGTGACGACCATCAATA
48611400 ATGAAAAGGGATGGTGACGACCATCGAATA
1 ATGAAAAGGGATGGTGACGACCATC-AATA
* * * *
48611430 ACGAAAAGGGATAGCT-TC-AGCTATCAATTA
1 ATGAAAAGGGAT-GGTGACGA-CCATCAA-TA
*
48611460 ATGAAAAGGGATGGTGACGACCATTAATA
1 ATGAAAAGGGATGGTGACGACCATCAATA
*
48611489 ATGAAAAGGGATGGTGACGACTATCAAATA
1 ATGAAAAGGGATGGTGACGACCATC-AATA
48611519 ATGAAAAGG
1 ATGAAAAGG
48611528 AATAGCTTTG
Statistics
Matches: 107, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
29 53 0.50
30 51 0.48
31 3 0.03
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.20
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCAATA
Found at i:48611437 original size:59 final size:58
Alignment explanation
Indices: 48611373--48611527 Score: 181
Period size: 59 Copynumber: 2.6 Consensus size: 58
48611363 ATCAAATTAT
48611373 GAAAAGGGATGGTGATGA-TCATCAAAAATGAAAAGGGATGGTGACGACCATCGAATAAC
1 GAAAAGGGATGGTGATGACT-ATCAAAAATGAAAAGGGATGGTGACGACCAT-GAATAAC
* * * * *
48611432 GAAAAGGGATAGCT--TCAGCTATCAATTAATGAAAAGGGATGGTGACGACCATTAATAAT
1 GAAAAGGGAT-GGTGATGA-CTATCAA-AAATGAAAAGGGATGGTGACGACCATGAATAAC
*
48611491 GAAAAGGGATGGTGACGACTATCAAATAATGAAAAGG
1 GAAAAGGGATGGTGATGACTATCAAA-AATGAAAAGG
48611528 AATAGCTTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
58 4 0.05
59 47 0.59
60 29 0.36
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (58 bp):
GAAAAGGGATGGTGATGACTATCAAAAATGAAAAGGGATGGTGACGACCATGAATAAC
Found at i:48611542 original size:89 final size:89
Alignment explanation
Indices: 48611331--48611543 Score: 284
Period size: 89 Copynumber: 2.4 Consensus size: 89
48611321 TAGCCTCGGT
* * * * *
48611331 TATCAAAATAATGAAAAGGGATAACCTCGACTATCAAATTATGAAAAGGGATGGTGATGATCATC
1 TATC-AAATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATC
48611396 AAAAATGAAAAGGGATGGTGACGAC
65 AAAAATGAAAAGGGATGGTGACGAC
* * * * *
48611421 CATCGAATAACGAAAAGGGATAGCTTCAGCTATC-AATTAATGAAAAGGGATGGTGACGACCATT
1 TATCAAATAATGAAAAGGGATAGCTTCGGCTATCAAATT-ATGAAAAGGGATGGTGACGACCATC
*
48611485 AATAATGAAAAGGGATGGTGACGAC
65 AAAAATGAAAAGGGATGGTGACGAC
* *
48611510 TATCAAATAATGAAAAGGAATAGCTTTGGCTATC
1 TATCAAATAATGAAAAGGGATAGCTTCGGCTATC
48611544 GAGCTGCGAA
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
88 4 0.04
89 98 0.93
90 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (89 bp):
TATCAAATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCA
AAAATGAAAAGGGATGGTGACGAC
Found at i:48611588 original size:30 final size:30
Alignment explanation
Indices: 48611519--48611588 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
48611509 CTATCAAATA
* * *
48611519 ATGAAAAGGAATAGCTTTGGCTATCGAGCT
1 ATGAAAAGGGATAGCTTCGGCTATCAAGCT
**
48611549 GCGAAAAGGGATAGCTTCGGCTATCAAGCT
1 ATGAAAAGGGATAGCTTCGGCTATCAAGCT
48611579 ATGAAAAGGG
1 ATGAAAAGGG
48611589 TTGGGACAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.21
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAGCT
Found at i:48613314 original size:69 final size:67
Alignment explanation
Indices: 48613196--48613324 Score: 188
Period size: 69 Copynumber: 1.9 Consensus size: 67
48613186 AATAATATTA
* *
48613196 ATTTAATATATTTAATACTTATCTTAAAAGTATTTTATTAATTTAATATTAAAGTGATTATCTTA
1 ATTTAATATATTTAATACTTATCTTAAAAGTATTATATTAATTTAATATTAAAATGATTATCTTA
48613261 AT
66 AT
* *
48613263 ATTTAATTTAATTTAATATTTATCTTGATAAA-TATTATATTAATTTAATATTAAAATGATTA
1 ATTTAATAT-ATTTAATACTTATCTT-A-AAAGTATTATATTAATTTAATATTAAAATGATTA
48613325 AGTTTAATCA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
67 8 0.15
68 15 0.27
69 29 0.53
70 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (67 bp):
ATTTAATATATTTAATACTTATCTTAAAAGTATTATATTAATTTAATATTAAAATGATTATCTTA
AT
Found at i:48615828 original size:21 final size:21
Alignment explanation
Indices: 48615802--48615841 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
48615792 TTCATTTAAG
48615802 AAAAAAAAAGAAATTGCCAAA
1 AAAAAAAAAGAAATTGCCAAA
48615823 AAAAAAAAAGAAATTGCCA
1 AAAAAAAAAGAAATTGCCA
48615842 TCCCTATCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.10, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAAAAAAGAAATTGCCAAA
Found at i:48619762 original size:12 final size:12
Alignment explanation
Indices: 48619745--48619777 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
48619735 CGTTTTTACC
48619745 TAATTTCTTCAA
1 TAATTTCTTCAA
48619757 TAATTTCTTCAA
1 TAATTTCTTCAA
48619769 TAATTTCTT
1 TAATTTCTT
48619778 TTTCTAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATTTCTTCAA
Found at i:48624684 original size:38 final size:38
Alignment explanation
Indices: 48624642--48624715 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
48624632 TCTAGCTTTC
48624642 ATATACATTATATTATATA-TATTCTCTTTTTATTTTGT
1 ATATACA-TATATTATATAGTATTCTCTTTTTATTTTGT
* * *
48624680 ATATACATATATTTTCTAGTATTTTCTTTTTATTTT
1 ATATACATATATTATATAGTATTCTCTTTTTATTTT
48624716 CAACTTTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 9 0.28
38 23 0.72
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (38 bp):
ATATACATATATTATATAGTATTCTCTTTTTATTTTGT
Done.