Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 128 of 311
Found at i:43100766 original size:61 final size:61
Alignment explanation
Indices: 43100701--43100888 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
43100691 TTTTAATTAA
*
43100701 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
43100762 AATATATGATACT-GTAAAA-T-ATAA-AATAACATAATTATTAT-TAAATATAAT-ATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATTA-AT-ATTCTTATATGAATTTACTCA-AATCAT
43100821 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
43100882 AATATAT
1 AATATAT
43100889 GATTATAACT
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 29 0.31
60 16 0.17
61 37 0.39
62 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:43100799 original size:120 final size:120
Alignment explanation
Indices: 43100669--43100891 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
43100659 ATCATATTTA
* *
43100669 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
43100734 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
43100789 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
43100854 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGAT
43100892 TATAACTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
Found at i:43100827 original size:18 final size:17
Alignment explanation
Indices: 43100806--43100840 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43100796 TTATTATTAA
43100806 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
43100824 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
43100841 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:43100903 original size:17 final size:16
Alignment explanation
Indices: 43100881--43100927 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
43100871 ACTCAAATCA
43100881 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
43100898 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
43100912 TAAATATATGATTTAA
1 T-AATATATGATTTAA
43100928 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:43100928 original size:17 final size:17
Alignment explanation
Indices: 43100900--43100933 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43100890 ATTATAACTA
*
43100900 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
43100917 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
43100934 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:43106166 original size:15 final size:17
Alignment explanation
Indices: 43106140--43106171 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43106130 GAATTATTGA
43106140 ATAAATTTATG-TGTTT
1 ATAAATTTATGTTGTTT
43106156 ATAAA-TTATGTTGTTT
1 ATAAATTTATGTTGTTT
43106172 TCTATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
ATAAATTTATGTTGTTT
Found at i:43119573 original size:27 final size:27
Alignment explanation
Indices: 43119543--43119683 Score: 155
Period size: 27 Copynumber: 5.2 Consensus size: 27
43119533 GTGATGAAGT
43119543 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATATTGTGGCAGAGC
* *
43119570 CACCAGA-ACAGATATATGTAGTAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
* *
43119597 CACCAAAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
* *
43119624 CACCAG-GACAAATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
43119651 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
43119678 CACCAG
1 CACCAG
43119684 GACGCTTCCT
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
26 10 0.11
27 80 0.85
28 4 0.04
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:43119684 original size:54 final size:54
Alignment explanation
Indices: 43119543--43119686 Score: 218
Period size: 54 Copynumber: 2.7 Consensus size: 54
43119533 GTGATGAAGT
* * * *
43119543 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTAGTAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAAATATATGTAGCAGAGC
* *
43119597 CACCAAATCAGATAATTGTGGCATAGCCACCAGGACAAATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAAATATATGTAGCAGAGC
43119651 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
43119687 GCTTCCTCCA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.06
54 77 0.94
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAAATATATGTAGCAGAGC
Found at i:43120089 original size:8 final size:8
Alignment explanation
Indices: 43120073--43120102 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
43120063 CTCAAAATAC
43120073 CGGCTTTT
1 CGGCTTTT
*
43120081 CGGCATTT
1 CGGCTTTT
43120089 CGGCTTTT
1 CGGCTTTT
43120097 CGGCTT
1 CGGCTT
43120103 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:43121311 original size:26 final size:26
Alignment explanation
Indices: 43121281--43121336 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
43121271 TGAAATGCCC
43121281 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
43121307 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43121333 ATCA
1 ATCA
43121337 ATTTTTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43121343 original size:22 final size:23
Alignment explanation
Indices: 43121291--43121343 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
43121281 ATCATGGAAC
43121291 ATTTACCTAACCCATTATCATGGAAT
1 ATTTACCTAACCCATTATC---GAAT
43121317 ATTTACCTAACCCATTATC-AAT
1 ATTTACCTAACCCATTATCGAAT
*
43121339 TTTTA
1 ATTTA
43121344 TCAATTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 7 0.27
26 19 0.73
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTTACCTAACCCATTATCGAAT
Found at i:43139278 original size:40 final size:40
Alignment explanation
Indices: 43139221--43139410 Score: 238
Period size: 40 Copynumber: 4.8 Consensus size: 40
43139211 ATTTGAATAC
* * * *
43139221 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGA-TAT
*
43139261 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
* *
43139301 ATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGATGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
* * * *
43139341 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
* * *
43139381 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
43139411 TTGTGTTATA
Statistics
Matches: 134, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 131 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
Found at i:43139354 original size:80 final size:80
Alignment explanation
Indices: 43139221--43139429 Score: 271
Period size: 80 Copynumber: 2.6 Consensus size: 80
43139211 ATTTGAATAC
* * * *
43139221 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATT
*
43139286 TGTGCAAGTTGATAT
66 CGTGCAAGTTGATAT
*
43139301 ATCCGAGCTAAGACCCGAAGGCATTTGTGCGAGATGA-TATATCCGGGCTAAGACCCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGCAT
* *
43139365 TCGTGCGAGTTGCTAT
65 TCGTGCAAGTTGATAT
* * * **
43139381 ACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTG-TTATATCC-GGCTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAA
43139430 ATTCCAAGAA
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
78 6 0.05
79 9 0.08
80 95 0.84
81 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATT
CGTGCAAGTTGATAT
Found at i:43141152 original size:104 final size:106
Alignment explanation
Indices: 43140956--43141173 Score: 237
Period size: 104 Copynumber: 2.1 Consensus size: 106
43140946 ATCTTTTCTC
* * * * * * * **
43140956 TCTAAAGGTGAACCATCCTCGAGCGTAATTCTAAATGGTTGCCTACGAGCGTAATCCTAAAAGGT
1 TCTAAGGGTGAACCATCCTCAAACGTAATTCCAAATGGATGCCCACGAGCATAATCCTAAAAGAC
* * * *
43141021 GGCTCATTACTTATTGCTTAATCTTACATCTCTC-CAC-CT
66 GGCTCATTACTTATTACTCAATCTTACAACTCCCACACTCT
* * *
43141060 TCTAAGGGTGAACCATTCTCAAACGTAATTCCAAATGGATGCCCATGAGCATAATCCTAAATGAC
1 TCTAAGGGTGAACCATCCTCAAACGTAATTCCAAATGGATGCCCACGAGCATAATCCTAAAAGAC
*
43141125 GGCTTATTA-TGTATTACTCAA-CTTTACAACTCCCACACTCT
66 GGCTCATTACT-TATTACTCAATC-TTACAACTCCCACACTCT
43141166 TCTAAGGG
1 TCTAAGGG
43141174 ATTACTCCCT
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
103 2 0.02
104 78 0.84
105 3 0.03
106 10 0.11
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (106 bp):
TCTAAGGGTGAACCATCCTCAAACGTAATTCCAAATGGATGCCCACGAGCATAATCCTAAAAGAC
GGCTCATTACTTATTACTCAATCTTACAACTCCCACACTCT
Found at i:43145389 original size:29 final size:29
Alignment explanation
Indices: 43145357--43145415 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
43145347 ATATTGGGCT
43145357 ACACTTAGTGAAAGTGTTGAATGGATATG
1 ACACTTAGTGAAAGTGTTGAATGGATATG
43145386 ACACTTAGTGAAAGTGTTGAATGGATATG
1 ACACTTAGTGAAAGTGTTGAATGGATATG
43145415 A
1 A
43145416 TAATGTGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (29 bp):
ACACTTAGTGAAAGTGTTGAATGGATATG
Found at i:43146890 original size:47 final size:47
Alignment explanation
Indices: 43146837--43147178 Score: 540
Period size: 47 Copynumber: 7.3 Consensus size: 47
43146827 ACAAGATATG
43146837 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
43146884 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
43146931 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
43146978 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
43147025 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * *
43147072 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
43147119 TATATGTGATAAGGCTGAATGGCCAATGTGATGGATGTGAAAGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
43147166 TAAATGTGATAAG
1 TATATGTGATAAG
43147179 TCCCGAAGGG
Statistics
Matches: 269, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 269 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:43147178 original size:94 final size:94
Alignment explanation
Indices: 43146837--43147174 Score: 595
Period size: 94 Copynumber: 3.6 Consensus size: 94
43146827 ACAAGATATG
43146837 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
43146902 ATGGCCGATGTGATGAATGTGAAAGTGTA
66 ATGGCCGATGTGATGAATGTGAAAGTGTA
43146931 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
43146996 ATGGCCGATGTGATGAATGTGAAAGTGTA
66 ATGGCCGATGTGATGAATGTGAAAGTGTA
* * *
43147025 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
* *
43147090 ATGGCCGATGTGATGGATGTGAAGGTGTA
66 ATGGCCGATGTGATGAATGTGAAAGTGTA
* * * *
43147119 TATATGTGATAAGGCTGAATGGCCAATGTGATGGATGTGAAAGTATATAAATGTGA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGA
43147175 TAAGTCCCGA
Statistics
Matches: 234, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 234 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (94 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
ATGGCCGATGTGATGAATGTGAAAGTGTA
Found at i:43151049 original size:46 final size:46
Alignment explanation
Indices: 43150999--43151174 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
43150989 TGGTTGAGCA
43150999 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
43151045 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
43151090 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
43151138 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43151175 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:43151155 original size:93 final size:93
Alignment explanation
Indices: 43150996--43151167 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
43150986 GGATGGTTGA
* *
43150996 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
43151061 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
43151089 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
43151154 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
43151168 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:43158727 original size:45 final size:46
Alignment explanation
Indices: 43158564--43158738 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
43158554 TGGTTGAGCA
*
43158564 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
43158610 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
43158655 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
43158703 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43158739 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 37 0.33
46 29 0.26
47 29 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:43160591 original size:28 final size:29
Alignment explanation
Indices: 43160527--43160590 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
43160517 CCTACAGGGC
*
43160527 CCAAAACATACATTCAGGGTGGGGTTCGGC
1 CCAAAACATACATTCAGGGT-GGGTTCGGA
43160557 CCAAAACATACATTCAGGGT-GGTTCGGGA
1 CCAAAACATACATTCAGGGTGGGTTC-GGA
43160586 CCAAA
1 CCAAA
43160591 CCGTAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 5 0.16
29 7 0.22
30 20 0.62
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (29 bp):
CCAAAACATACATTCAGGGTGGGTTCGGA
Found at i:43161373 original size:42 final size:42
Alignment explanation
Indices: 43161310--43161434 Score: 143
Period size: 40 Copynumber: 3.0 Consensus size: 42
43161300 CTTTGTTTTC
** * *
43161310 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
43161353 T-GATGCCATAGCCCAGCTATGGTCTT--ACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
*
43161392 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
43161433 TC
1 TC
43161435 TCACTGATGC
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
39 2 0.03
40 34 0.48
41 8 0.11
42 25 0.35
43 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:43161460 original size:46 final size:47
Alignment explanation
Indices: 43161391--43161512 Score: 142
Period size: 46 Copynumber: 2.6 Consensus size: 47
43161381 ATATTCATAT
* * * *
43161391 ATCGATGCCATAGCCTAGCTATGGTCTTACACGAATCA-CATATCTCAC
1 ATCGATGCCATATCCCAGATATGGTCTTACAC-AAT-AGCATATATCAC
* *
43161439 -T-GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCAC
1 ATCGATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCAC
*
43161484 ATCAATGCCATATCCCAGATATGGTCTTA
1 ATCGATGCCATATCCCAGATATGGTCTTA
43161513 TATGGAAATC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 11 0.17
46 26 0.41
47 26 0.41
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (47 bp):
ATCGATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCAC
Found at i:43161576 original size:31 final size:31
Alignment explanation
Indices: 43161541--43161620 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
43161531 CTTGTCACTT
*
43161541 GTAGCCGAAGCTACCACTATTCACTAATCAG
1 GTAGCCGGAGCTACCACTATTCACTAATCAG
* * *
43161572 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTATTCACTAATCAG
*
43161603 GTAGCCGGAGCTATCACT
1 GTAGCCGGAGCTACCACT
43161621 TATCACTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTATTCACTAATCAG
Found at i:43161765 original size:14 final size:15
Alignment explanation
Indices: 43161746--43161774 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43161736 TTTTATCATC
43161746 AATACAT-ATGAAAT
1 AATACATCATGAAAT
43161760 AATACATCATGAAAT
1 AATACATCATGAAAT
43161775 TCATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (15 bp):
AATACATCATGAAAT
Found at i:43165580 original size:27 final size:25
Alignment explanation
Indices: 43165531--43165580 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
43165521 GATCATTTTG
*
43165531 ATAAAAAAATTGAGTGACCGAATTA
1 ATAAAAAAATTGAGTGACAGAATTA
43165556 ATAAAAAAATTGAGATGATCAGAAT
1 ATAAAAAAATTGAG-TGA-CAGAAT
43165581 AAAAACAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
26 3 0.14
27 5 0.23
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.24
Consensus pattern (25 bp):
ATAAAAAAATTGAGTGACAGAATTA
Found at i:43166743 original size:15 final size:15
Alignment explanation
Indices: 43166691--43166743 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
43166681 ATTTAGAAAT
*
43166691 TAAATTAAAGTATTA
1 TAAATTAAATTATTA
43166706 TAAATTACAATATTTATTA
1 TAAATT--AA-A-TTATTA
*
43166725 TAAATTAAATTAATA
1 TAAATTAAATTATTA
43166740 TAAA
1 TAAA
43166744 GTAGCATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 15 0.47
16 1 0.03
17 4 0.12
18 1 0.03
19 11 0.34
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
TAAATTAAATTATTA
Found at i:43174763 original size:15 final size:15
Alignment explanation
Indices: 43174743--43174774 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43174733 TTCTTGTCCC
43174743 TTTCCTTTATTTCTT
1 TTTCCTTTATTTCTT
*
43174758 TTTCCTTTCTTTCTT
1 TTTCCTTTATTTCTT
43174773 TT
1 TT
43174775 CGGTTTGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCCTTTATTTCTT
Found at i:43175913 original size:18 final size:18
Alignment explanation
Indices: 43175892--43175931 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43175882 TTTCTGGACT
*
43175892 TTTTGGGATTGCTTTTGG
1 TTTTGGGATTGATTTTGG
* *
43175910 TTTTGGGTTTTATTTTGG
1 TTTTGGGATTGATTTTGG
43175928 TTTT
1 TTTT
43175932 CTAGGCATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.03, G:0.28, T:0.65
Consensus pattern (18 bp):
TTTTGGGATTGATTTTGG
Found at i:43183369 original size:52 final size:52
Alignment explanation
Indices: 43183311--43183417 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
43183301 CTTGGATAGT
*
43183311 TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCGAGTGAGCTTGGA
1 TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCAAGTGAGCTTGGA
*
43183363 TTGATTCAATACTGGGAATGGACTGGCTGGTTAAACACCAAGTGAGCTTGGA
1 TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCAAGTGAGCTTGGA
43183415 TTG
1 TTG
43183418 TTCTACTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (52 bp):
TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCAAGTGAGCTTGGA
Found at i:43192482 original size:30 final size:30
Alignment explanation
Indices: 43192441--43192498 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
43192431 AAAATCATAT
***
43192441 TTTGACAAAATTATGTTTTTGCCCCTAAAC
1 TTTGACAAAATTACACTTTTGCCCCTAAAC
*
43192471 TTTGTCAAAATTACACTTTTGCCCCTAA
1 TTTGACAAAATTACACTTTTGCCCCTAA
43192499 GCTCGTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (30 bp):
TTTGACAAAATTACACTTTTGCCCCTAAAC
Found at i:43198932 original size:6 final size:7
Alignment explanation
Indices: 43198915--43198939 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43198905 TTTTGGATTG
43198915 TTTTTGC
1 TTTTTGC
43198922 TTTTTGC
1 TTTTTGC
43198929 TTTTTGC
1 TTTTTGC
43198936 TTTT
1 TTTT
43198940 ATTTTAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTTGC
Found at i:43201777 original size:32 final size:32
Alignment explanation
Indices: 43201741--43201805 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
43201731 ACAAAAGATA
43201741 TAAATGTTAAGGGAAAAATTTATCACTTTTCT
1 TAAATGTTAAGGGAAAAATTTATCACTTTTCT
* *
43201773 TAAATGTTAAGGGCAAAATTTATCATTTTTCT
1 TAAATGTTAAGGGAAAAATTTATCACTTTTCT
43201805 T
1 T
43201806 TTTCCCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (32 bp):
TAAATGTTAAGGGAAAAATTTATCACTTTTCT
Found at i:43206099 original size:39 final size:40
Alignment explanation
Indices: 43206056--43206264 Score: 246
Period size: 39 Copynumber: 5.3 Consensus size: 40
43206046 TCCTCATTCA
* * * *
43206056 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
43206095 AATGCCTTCGGGACATAACCCGGATTTAACAAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAA-TAACTCGCACG
* *
43206136 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
43206176 AATGCC-TCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * * *
43206215 AATGCCTGC-GG-CGTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGAC-ATAACCCGGATTTAATAACTCGCACG
*
43206254 AAGGCCTTCGG
1 AATGCCTTCGG
43206265 ATCTTAATCC
Statistics
Matches: 150, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 97 0.65
40 25 0.17
41 27 0.18
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:43206158 original size:80 final size:80
Alignment explanation
Indices: 43206056--43206264 Score: 264
Period size: 80 Copynumber: 2.6 Consensus size: 80
43206046 TCCTCATTCA
* * * *
43206056 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACATAACCCGGAT
43206120 TTAACAAACTCGCACG
66 TTAA-AAACTCGCACG
* * * *
43206136 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCC-TCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACATAACCCGGAT
*
43206200 TTAATAACTCGCACG
66 TTAAAAACTCGCACG
* * *
43206215 AATGCCTGC-GG-CGTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGG
1 AATGCCTTCGGGAC-TTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGG
43206265 ATCTTAATCC
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
78 30 0.27
79 21 0.19
80 54 0.48
81 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACATAACCCGGAT
TTAAAAACTCGCACG
Found at i:43213634 original size:40 final size:40
Alignment explanation
Indices: 43213536--43213798 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
43213526 TCCTCGTTCA
* * * * *
43213536 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
43213575 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
43213615 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43213655 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
43213695 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
43213735 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
43213775 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
43213799 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:43230807 original size:26 final size:28
Alignment explanation
Indices: 43230762--43230820 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
43230752 AATATTCAAA
* *
43230762 AATTTTCATTTATACCATAAT-TCTTTC
1 AATTTTAATTTATACAATAATGTCTTTC
*
43230789 AATTTTAATTTATA-AATAATGTCTTTT
1 AATTTTAATTTATACAATAATGTCTTTC
43230816 AATTT
1 AATTT
43230821 AGACCTACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (28 bp):
AATTTTAATTTATACAATAATGTCTTTC
Found at i:43236826 original size:34 final size:35
Alignment explanation
Indices: 43236760--43236826 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
43236750 CAAACACCAG
*
43236760 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
43236795 AAAATATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
43236827 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43240061 original size:16 final size:17
Alignment explanation
Indices: 43240040--43240073 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43240030 AAAATTTAAT
43240040 TATTTT-ATTGAAATAA
1 TATTTTAATTGAAATAA
*
43240056 TATTTTAATTGAGATAA
1 TATTTTAATTGAAATAA
43240073 T
1 T
43240074 TTTCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (17 bp):
TATTTTAATTGAAATAA
Found at i:43241594 original size:12 final size:12
Alignment explanation
Indices: 43241577--43241601 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43241567 ATAGGTAAAA
43241577 TGGTTTAATTTT
1 TGGTTTAATTTT
43241589 TGGTTTAATTTT
1 TGGTTTAATTTT
43241601 T
1 T
43241602 TTTATACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TGGTTTAATTTT
Found at i:43244933 original size:13 final size:14
Alignment explanation
Indices: 43244915--43244944 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
43244905 TTGATTTGAT
43244915 TTGATTATGTAA-A
1 TTGATTATGTAATA
43244928 TTGATTATGTAATA
1 TTGATTATGTAATA
43244942 TTG
1 TTG
43244945 TAAATCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TTGATTATGTAATA
Found at i:43250005 original size:24 final size:24
Alignment explanation
Indices: 43249978--43250026 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
43249968 ATACTAAAAA
43249978 GAAAGCTTATTTGCGTAATATGGT
1 GAAAGCTTATTTGCGTAATATGGT
*
43250002 GAAAGCTTATTTGCGTAATGTGGT
1 GAAAGCTTATTTGCGTAATATGGT
43250026 G
1 G
43250027 CCTGTGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.37
Consensus pattern (24 bp):
GAAAGCTTATTTGCGTAATATGGT
Found at i:43266253 original size:48 final size:49
Alignment explanation
Indices: 43266108--43266258 Score: 270
Period size: 49 Copynumber: 3.1 Consensus size: 49
43266098 ACTTTAAATG
43266108 TTTA-GGCCATTATGTTAAGAAAATCAATAGTAAGTAACTTTTCCATCT
1 TTTATGGCCATTATGTTAAGAAAATCAATAGTAAGTAACTTTTCCATCT
43266156 TTTATGGCCATTATGTTAAGAAAATCAATAGTAAGTAACTTTTCCATCT
1 TTTATGGCCATTATGTTAAGAAAATCAATAGTAAGTAACTTTTCCATCT
* *
43266205 TTTATGGCCATTATGTTAAG-AAATTAATAGTAAATAACTTTTCCATCT
1 TTTATGGCCATTATGTTAAGAAAATCAATAGTAAGTAACTTTTCCATCT
43266253 TTTATG
1 TTTATG
43266259 ATTTAGTCCT
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
48 36 0.36
49 64 0.64
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (49 bp):
TTTATGGCCATTATGTTAAGAAAATCAATAGTAAGTAACTTTTCCATCT
Found at i:43269490 original size:46 final size:46
Alignment explanation
Indices: 43269440--43269615 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
43269430 TGGTTGAGCA
43269440 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
43269486 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
43269531 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
43269579 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43269616 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:43269596 original size:93 final size:93
Alignment explanation
Indices: 43269437--43269608 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
43269427 GGATGGTTGA
* *
43269437 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
43269502 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
43269530 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
43269595 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
43269609 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:43272925 original size:2 final size:2
Alignment explanation
Indices: 43272918--43272950 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43272908 TGTTTCCAGT
43272918 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
43272951 GGTCTCATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:43277048 original size:14 final size:14
Alignment explanation
Indices: 43277029--43277058 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43277019 GATTCCCTCT
43277029 TTTATAGTATATGA
1 TTTATAGTATATGA
*
43277043 TTTATAGTTTATGA
1 TTTATAGTATATGA
43277057 TT
1 TT
43277059 CAAGGGTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (14 bp):
TTTATAGTATATGA
Found at i:43278158 original size:5 final size:5
Alignment explanation
Indices: 43278148--43278174 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
43278138 AAAGATTAGA
43278148 GGTCG GGTCG GGTCG GGTCG GGTCG GG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GG
43278175 ACTTAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.63, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:43280073 original size:66 final size:66
Alignment explanation
Indices: 43279967--43280137 Score: 195
Period size: 66 Copynumber: 2.6 Consensus size: 66
43279957 GTTCAAGAAC
* * * * ** *
43279967 TTGAGAAGACCCGATATCTTGTTT-AGGAGCTTGAGAAGACTCGATATCTTGTTCAAGATCTTGG
1 TTGAGAAGACCTGATAT-TTCTTTCAGGAGCTTGGGAAGACTCAATATCGAGTTCAAGAGCTTGG
43280031 GA
65 GA
* *
43280033 TTGAGAAGACCTGATATTTCTTTCAGGAGCTTGGGAAGACTTAATATCGAGTTCAGGAGCTTGGG
1 TTGAGAAGACCTGATATTTCTTTCAGGAGCTTGGGAAGACTCAATATCGAGTTCAAGAGCTTGGG
43280098 A
66 A
* *
43280099 TTGAGAAGA-CTGA-ATATCTAGTCCAGGAGCTTGGGAAGA
1 TTGAGAAGACCTGATATTTCT--TTCAGGAGCTTGGGAAGA
43280138 TATGATATTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 5 0.05
65 9 0.10
66 77 0.85
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (66 bp):
TTGAGAAGACCTGATATTTCTTTCAGGAGCTTGGGAAGACTCAATATCGAGTTCAAGAGCTTGGG
A
Found at i:43280503 original size:21 final size:21
Alignment explanation
Indices: 43280477--43280529 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
43280467 AGTGTTGCCA
43280477 CCTTACAAGAGGAAGATAATT
1 CCTTACAAGAGGAAGATAATT
*
43280498 CCTTACGAGAGGAAGATAATT
1 CCTTACAAGAGGAAGATAATT
43280519 CCTTAGCAAGA
1 CCTTA-CAAGA
43280530 CATACAGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (21 bp):
CCTTACAAGAGGAAGATAATT
Found at i:43282309 original size:30 final size:31
Alignment explanation
Indices: 43282275--43282336 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
43282265 GATTCATCCA
*
43282275 TGGAAAAT-AAAATAAAGAAAATGATGA-AAT
1 TGGAAAATGAAAAAAAAGAAAA-GATGATAAT
* *
43282305 TGGAAAGTGAAAAAAAATAAAAGATGATAAT
1 TGGAAAATGAAAAAAAAGAAAAGATGATAAT
43282336 T
1 T
43282337 AATTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (31 bp):
TGGAAAATGAAAAAAAAGAAAAGATGATAAT
Found at i:43287864 original size:46 final size:45
Alignment explanation
Indices: 43287797--43287962 Score: 154
Period size: 46 Copynumber: 3.6 Consensus size: 45
43287787 TTTGTGTGCT
43287797 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCACAATATGAGAGCC
* * *
43287843 AGTGTAAGACATGTCTGGGACATGCTTCGGCCTCGAGATATTTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCAC-A-ATA-TGAGAGCC
* * * * ** * * * *
43287891 GGTATAATACATGTTTGGGACATGCATCGGTATTAAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGCCA-CAATATGAGAGCC
43287937 AGTGTAAGACATGTCTGGGACATGCA
1 AGTGTAAGACATGTCTGGGACATGCA
43287963 CCACCCTCGT
Statistics
Matches: 94, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
45 1 0.01
46 58 0.62
47 3 0.03
48 30 0.32
49 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCCACAATATGAGAGCC
Found at i:43288079 original size:49 final size:48
Alignment explanation
Indices: 43288026--43288152 Score: 148
Period size: 49 Copynumber: 2.6 Consensus size: 48
43288016 CTTGTTGTGT
43288026 GTCAGTGTAAGACCTGTCTAGGACATGGCATCGGCAC-CAATAGATGAGA
1 GTCAGTGTAAGACCTGTCTAGGACATGGCATCGGC-CTCAATAGATGA-A
* * * * ** *
43288075 GTCAGTGTAAGACCTATCTGGGATATGTCATCGGCCTCGCTATATGAA
1 GTCAGTGTAAGACCTGTCTAGGACATGGCATCGGCCTCAATAGATGAA
*
43288123 GCCAGTGTAAGACCATGTCTAGGACATGGC
1 GTCAGTGTAAGACC-TGTCTAGGACATGGC
43288153 GTTGGCATCT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 15 0.23
49 49 0.77
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (48 bp):
GTCAGTGTAAGACCTGTCTAGGACATGGCATCGGCCTCAATAGATGAA
Found at i:43292078 original size:32 final size:32
Alignment explanation
Indices: 43292006--43292087 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
43291996 TCGATTATAT
* *
43292006 TACCG-TAGCTGATGGCTATGTGCCGAACTTAT
1 TACCGCTA-CTGATGGCTTTGTGCCGAACTTAA
* *
43292038 TACAGCTACTGATGGCTTTGTGCC-AATTGTAA
1 TACCGCTACTGATGGCTTTGTGCCGAACT-TAA
*
43292070 TACCGCTACTGAAGGCTT
1 TACCGCTACTGATGGCTT
43292088 AAAGCTGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 3 0.07
32 37 0.88
33 2 0.05
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (32 bp):
TACCGCTACTGATGGCTTTGTGCCGAACTTAA
Found at i:43294346 original size:31 final size:31
Alignment explanation
Indices: 43294311--43294378 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
43294301 TTAACAGCCT
*
43294311 AGTGACTTAAA-CAAAAGCTTTTAAATATTTC
1 AGTGACTTAAATCAAAA-CTTTTAAATAGTTC
* * *
43294342 AGTGATTTAAATGAAAACTTTTGAATAGTTC
1 AGTGACTTAAATCAAAACTTTTAAATAGTTC
*
43294373 AATGAC
1 AGTGAC
43294379 CAATTGTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
AGTGACTTAAATCAAAACTTTTAAATAGTTC
Found at i:43296527 original size:24 final size:24
Alignment explanation
Indices: 43296491--43296540 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
43296481 GTATAATAAT
43296491 TTTTTAGAATTTTAAATATT-TTTA
1 TTTTTAGAATTTTAAA-ATTATTTA
* *
43296515 TTTTTATATTTTTAAAATTATTTA
1 TTTTTAGAATTTTAAAATTATTTA
43296539 TT
1 TT
43296541 GATATGACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTTAGAATTTTAAAATTATTTA
Found at i:43301262 original size:40 final size:40
Alignment explanation
Indices: 43301019--43301251 Score: 337
Period size: 40 Copynumber: 5.8 Consensus size: 40
43301009 CGGATGATAA
* *
43301019 CCGGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
43301059 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
43301099 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
* *
43301139 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
* *
43301179 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTAAT-T
*
43301219 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTG
43301252 GCTATATCCG
Statistics
Matches: 180, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.02
40 174 0.97
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
Found at i:43309162 original size:40 final size:40
Alignment explanation
Indices: 43309107--43309350 Score: 366
Period size: 40 Copynumber: 6.1 Consensus size: 40
43309097 CGGATGATAA
* *
43309107 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
43309147 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
43309187 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
43309227 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * **
43309267 CCGGGATAAGTCCCGAAGGCATTTATGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * **
43309307 CCGAGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
43309347 CCGG
1 CCGG
43309351 TTGAAGACCG
Statistics
Matches: 188, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 187 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:43315541 original size:30 final size:29
Alignment explanation
Indices: 43315484--43315541 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
43315474 ATTTTCGAGC
**
43315484 ATAGGGGAAAATGGTCATTTTGTCAAAGT
1 ATAGGGGAAAATGGTCATTTTACCAAAGT
*
43315513 ATAGGGGCAAAATGGTCGTTTTACCAAAG
1 ATAGGGG-AAAATGGTCATTTTACCAAAG
43315542 ATATGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (29 bp):
ATAGGGGAAAATGGTCATTTTACCAAAGT
Found at i:43316062 original size:46 final size:46
Alignment explanation
Indices: 43315880--43316062 Score: 176
Period size: 46 Copynumber: 3.9 Consensus size: 46
43315870 TCACTTGTGT
* * * *
43315880 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GACGA
* * *
43315926 GAGCCAGTGTAAGACCATGTCTGGGACATGGAATCAGC-ATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGACGA
* ** * *
43315974 GTGTTAGTGTAAGACATGTCTGGGACATGCTTTGGCCT-CGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGACG-A
43316021 -AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGA
43316063 TGTGTAGTGT
Statistics
Matches: 110, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
45 2 0.02
46 56 0.51
47 31 0.28
48 20 0.18
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGA
Found at i:43317963 original size:55 final size:53
Alignment explanation
Indices: 43317776--43318026 Score: 208
Period size: 55 Copynumber: 4.7 Consensus size: 53
43317766 CGGGTACCTT
* * * * * * *
43317776 ACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT---TT-TAAACTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
* * * *
43317825 ACCATTTCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATGAACTC
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
* *
43317878 ACCAATGCCATGTCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTC
* * ** * *
43317933 ATCAATGCCATGTTTTGACATGGTCTTACATGATATTCTTGCCTTA-GAAACCTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTC
* * *
43317987 ACCAATAGCCATGCCTTGGCATGGTCTTACATGGTATCCT
1 ACCAAT-GCCATGTCTTGACATGGTCTTACATGGGATCCT
43318027 GAAACCCTAA
Statistics
Matches: 166, Mismatches: 26, Indels: 14
0.81 0.13 0.07
Matches are distributed among these distances:
49 35 0.21
52 4 0.02
53 47 0.28
54 9 0.05
55 70 0.42
56 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (53 bp):
ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
Found at i:43321088 original size:25 final size:25
Alignment explanation
Indices: 43321054--43321103 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
43321044 TAAAGCATAC
43321054 TTGGAATGGTAAAAAAATTCTCATT
1 TTGGAATGGTAAAAAAATTCTCATT
43321079 TTGGAATGGTAAAAAAATTCTCATT
1 TTGGAATGGTAAAAAAATTCTCATT
43321104 CATAATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (25 bp):
TTGGAATGGTAAAAAAATTCTCATT
Found at i:43322316 original size:14 final size:15
Alignment explanation
Indices: 43322278--43322326 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
43322268 ATGATTAATG
*
43322278 TTTAGTTAATTAAGA
1 TTTAATTAATTAAGA
*
43322293 TTTAATTAATTAA-T
1 TTTAATTAATTAAGA
*
43322307 TTTGATTAATTAAGA
1 TTTAATTAATTAAGA
43322322 TTTAA
1 TTTAA
43322327 ACTAAGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (15 bp):
TTTAATTAATTAAGA
Found at i:43338576 original size:48 final size:48
Alignment explanation
Indices: 43338309--43338583 Score: 381
Period size: 48 Copynumber: 5.7 Consensus size: 48
43338299 TAAAATACCA
* * * **
43338309 ATGCCATGTCCCCGACATGGTCTTACATGAATC-CACATATCATTTCCG
1 ATGCCATGTCCCAGACATGGTCTTACA-CAAGCACACATATCATCGCCG
***
43338357 ATGCCATGTCCCAGACATGGTCTTACATTGGCACACATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
* * * *
43338405 ATGCCATGTCCTAGACATGGTCTTACACTAGCACAAATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
**
43338453 ATGCCATGTCCCAGACATGGTCTTACACGGGCACACATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
* *
43338501 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCTCTG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
*
43338549 ATGCCATGTCCCAGACATGGTCTTACACAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACA
43338584 TTTAGCATGG
Statistics
Matches: 204, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
47 1 0.00
48 203 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
Found at i:43346132 original size:12 final size:13
Alignment explanation
Indices: 43346115--43346152 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
43346105 ATCCTGGAAT
43346115 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
43346127 ATTAAGAACACATA
1 ATTAAGAACA-AGA
43346141 ATTAAGAACAAG
1 ATTAAGAACAAG
43346153 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:43354415 original size:12 final size:13
Alignment explanation
Indices: 43354398--43354435 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
43354388 ATCCTAGAAT
43354398 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
43354410 ATTAAGAACACATA
1 ATTAAGAACA-AGA
43354424 ATTAAGAACAAG
1 ATTAAGAACAAG
43354436 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:43354847 original size:15 final size:13
Alignment explanation
Indices: 43354792--43354844 Score: 97
Period size: 13 Copynumber: 4.1 Consensus size: 13
43354782 GCTCGACAGG
*
43354792 GACACGCCCGTGT
1 GACATGCCCGTGT
43354805 GACATGCCCGTGT
1 GACATGCCCGTGT
43354818 GACATGCCCGTGT
1 GACATGCCCGTGT
43354831 GACATGCCCGTGT
1 GACATGCCCGTGT
43354844 G
1 G
43354845 TGATTGCTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (13 bp):
GACATGCCCGTGT
Found at i:43355235 original size:22 final size:22
Alignment explanation
Indices: 43355200--43355241 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43355190 TAAGTTAGTA
* *
43355200 ATGTTTTAGTTATGGAAATGGT
1 ATGTTTTAGGTATGAAAATGGT
*
43355222 ATGTTTTTGGTATGAAAATG
1 ATGTTTTAGGTATGAAAATG
43355242 AATGTGAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (22 bp):
ATGTTTTAGGTATGAAAATGGT
Found at i:43368904 original size:57 final size:58
Alignment explanation
Indices: 43368776--43368912 Score: 195
Period size: 57 Copynumber: 2.4 Consensus size: 58
43368766 GCTGATGAAG
* * **
43368776 TTTAGCCTAGACTGGTAATCCTAATATAATCTCTCCTGAGCATATGTTACAATTAGGA
1 TTTAGCCTAGACTGGTAATCCTAATATAAGCTCTCCTGAGCATATATTACAAAAAGGA
* * * *
43368834 TTTAGCCTGGACTGGTAATCCTAAT-TGAGCTCTTCTGAGCATATATTTCAAAAAGGA
1 TTTAGCCTAGACTGGTAATCCTAATATAAGCTCTCCTGAGCATATATTACAAAAAGGA
43368891 TTTAGCCTAGACTGGTAATCCT
1 TTTAGCCTAGACTGGTAATCCT
43368913 GTTATATGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
57 46 0.66
58 24 0.34
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (58 bp):
TTTAGCCTAGACTGGTAATCCTAATATAAGCTCTCCTGAGCATATATTACAAAAAGGA
Found at i:43374474 original size:19 final size:20
Alignment explanation
Indices: 43374437--43374474 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
43374427 CTTACAATTT
*
43374437 AATTTTGCTTTTATTTACTA
1 AATTTTGCTTTTATCTACTA
*
43374457 AATTTT-CTTTTCTCTACT
1 AATTTTGCTTTTATCTACT
43374475 TCTGACAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.21, C:0.16, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTGCTTTTATCTACTA
Found at i:43379844 original size:6 final size:6
Alignment explanation
Indices: 43379835--43379922 Score: 72
Period size: 6 Copynumber: 14.3 Consensus size: 6
43379825 AAGAAACATT
* * * *
43379835 ATCAGA ATCAGA GTCAGA ATCAGA ATCAAA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
43379884 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
43379923 GGGAATGCAA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
5 3 0.05
6 54 0.84
7 5 0.08
8 2 0.03
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:43379886 original size:31 final size:31
Alignment explanation
Indices: 43379843--43379922 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
43379833 TTATCAGAAT
* * *
43379843 CAGAGTCAGAATCAGAATCAAAATTAGGTGA
1 CAGAATCAGAATCAGAATCAAAATCAGGTAA
**
43379874 CAGAATCAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAAAATCAGGTAA
*
43379905 CAGAATCAAAATCAGAAT
1 CAGAATCAGAATCAGAAT
43379923 GGGAATGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGAATCAGAATCAGAATCAAAATCAGGTAA
Found at i:43380547 original size:27 final size:27
Alignment explanation
Indices: 43380323--43380600 Score: 299
Period size: 27 Copynumber: 10.3 Consensus size: 27
43380313 AGGGGCAAAA
* * ** *
43380323 TGGTAATTTTACCCCACAATGGTATCT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
43380350 CGGTAATTCCACCCTACAGGGCTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
43380377 TAGTAATTCTACCCTACAGGGCTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
43380404 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
43380431 CGGTAATTCTAACCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
43380458 CGGTAATTCTACCCTACAGAGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
43380485 CGGTAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
43380512 TGGTAATTTTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* ** *
43380539 TGGTAATTTTA-CAAATTAGGGGTATTT
1 TGGTAATTCTACCCTA-CAGGGGTATTT
* **
43380566 TGGTAATTTTA-CAAACTAGGGGTATTT
1 TGGTAATTCTACCCTAC-AGGGGTATTT
43380593 TGGTAATT
1 TGGTAATT
43380601 TTGTAAACCA
Statistics
Matches: 223, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 2 0.01
27 221 0.99
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (27 bp):
TGGTAATTCTACCCTACAGGGGTATTT
Found at i:43380601 original size:27 final size:27
Alignment explanation
Indices: 43380501--43380629 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
43380491 TTCTACCCTA
**
43380501 TAGGGGTATTTTGGTAATTTTACCCTAC
1 TAGGGGTATTTTGGTAATTTTA-CAAAC
*
43380529 -AGGGGTATTTTGGTAATTTTACAAAT
1 TAGGGGTATTTTGGTAATTTTACAAAC
43380555 TAGGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
**
43380582 TAGGGGTATTTTGGTAATTTTGTAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
* * * *
43380609 CAAGGGTAGTTTAGTAATTTT
1 TAGGGGTATTTTGGTAATTTT
43380630 GTAAATCGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.02
27 88 0.98
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (27 bp):
TAGGGGTATTTTGGTAATTTTACAAAC
Found at i:43380616 original size:54 final size:54
Alignment explanation
Indices: 43380394--43380629 Score: 158
Period size: 54 Copynumber: 4.4 Consensus size: 54
43380384 TCTACCCTAC
* * ** * * **
43380394 AGGGCTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAACCTA-CA
1 AGGG-TATTTTGGTAATTTTACCAAACAGGGGTATTTTGGTAATT-TTACAAACCA
* * * ** * * *
43380449 GGGGTATTTCGGTAATTCTACCCTACAGAGGTATTTCGGTAATTCTAC---CCTA
1 AGGGTATTTTGGTAATTTTACCAAACAGGGGTATTTTGGTAATTTTACAAACC-A
** **
43380501 TAGGGGTATTTTGGTAATTTTACCCTACAGGGGTATTTTGGTAATTTTACAAATTA
1 -A-GGGTATTTTGGTAATTTTACCAAACAGGGGTATTTTGGTAATTTTACAAACCA
* **
43380557 GGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTACCAAAC-AGGGGTATTTTGGTAATTTTACAAACCA
* *
43380611 AGGGTAGTTTAGTAATTTT
1 AGGGTATTTTGGTAATTTT
43380630 GTAAATCGAG
Statistics
Matches: 151, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
51 1 0.01
52 1 0.01
53 5 0.03
54 140 0.93
55 3 0.02
56 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACCAAACAGGGGTATTTTGGTAATTTTACAAACCA
Found at i:43380630 original size:27 final size:27
Alignment explanation
Indices: 43380531--43380643 Score: 109
Period size: 27 Copynumber: 4.2 Consensus size: 27
43380521 TACCCTACAG
** ** *
43380531 GGGTATTTTGGTAATTTTACAAATTAG
1 GGGTATTTTGGTAATTTTGTAAACCAA
** * *
43380558 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTGTAAACCAA
43380585 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTGTAAACCAA
* * * *
43380612 GGGTAGTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTGTAAACCAA
43380639 GGGTA
1 GGGTA
43380644 AAATGGTAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTGTAAACCAA
Found at i:43380651 original size:54 final size:54
Alignment explanation
Indices: 43380593--43380712 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 54
43380583 AGGGGTATTT
* * *** * *
43380593 TGGTAATTTTGTAAACCAAGGGTAGTTTAGTAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTCTATAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGAGTAAAA
* * *
43380647 TGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGAGTAAAA
1 TGGTAATTCTATAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGAGTAAAA
43380701 TGGTAATTCTAT
1 TGGTAATTCTAT
43380713 CTTATTTCGG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.34
Consensus pattern (54 bp):
TGGTAATTCTATAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGAGTAAAA
Found at i:43380652 original size:27 final size:27
Alignment explanation
Indices: 43380622--43380710 Score: 151
Period size: 27 Copynumber: 3.3 Consensus size: 27
43380612 GGGTAGTTTA
*
43380622 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
43380649 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
43380676 GTAATTCTGTAAATCGAGAGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
43380703 GTAATTCT
1 GTAATTCT
43380711 ATCTTATTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:43380745 original size:27 final size:27
Alignment explanation
Indices: 43380715--43380801 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
43380705 AATTCTATCT
*
43380715 TATTTCGGTAATTTTACAAATCGAGGA
1 TATTTCGGTAATTTTACAAATCGAGGG
* * *
43380742 TATTTGGGTAATTTTATAAATCGGGGG
1 TATTTCGGTAATTTTACAAATCGAGGG
*
43380769 TACTTT-GGTAATTTTACAAGTCGAGGG
1 TA-TTTCGGTAATTTTACAAATCGAGGG
43380796 TATTTC
1 TATTTC
43380802 AATAATTTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
26 3 0.06
27 45 0.88
28 3 0.06
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (27 bp):
TATTTCGGTAATTTTACAAATCGAGGG
Found at i:43393730 original size:43 final size:42
Alignment explanation
Indices: 43393664--43393766 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 42
43393654 AGCTCGTACA
* * * *
43393664 ATGCCAATGTCCTAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAATATCCTAGACAGGGTCTTACACGAAATCAAATA-CG
*
43393707 ATGCCACTATCCTAGACAGGGTCTTACACGAAATCAAATACG
1 ATGCCAATATCCTAGACAGGGTCTTACACGAAATCAAATACG
* * *
43393749 ATGTCAATGTCCCAGACA
1 ATGCCAATATCCTAGACA
43393767 TGACCTTACA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
42 16 0.31
43 35 0.69
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (42 bp):
ATGCCAATATCCTAGACAGGGTCTTACACGAAATCAAATACG
Found at i:43394263 original size:9 final size:8
Alignment explanation
Indices: 43394232--43394265 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
43394222 AGTCCCTAAT
43394232 TCACAAAA
1 TCACAAAA
43394240 TCACAAAA
1 TCACAAAA
43394248 TCACAAAA
1 TCACAAAA
43394256 TACACAAAA
1 T-CACAAAA
43394265 T
1 T
43394266 TTCTATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.15
Consensus pattern (8 bp):
TCACAAAA
Found at i:43399788 original size:32 final size:32
Alignment explanation
Indices: 43399752--43399817 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
43399742 TATACCTCTG
43399752 AGAATTTTCTGCGTCTTTTTAATATTTTTCCA
1 AGAATTTTCTGCGTCTTTTTAATATTTTTCCA
43399784 AGAATTTTCTGCGTCTTTTTAATATTTTTCCA
1 AGAATTTTCTGCGTCTTTTTAATATTTTTCCA
43399816 AG
1 AG
43399818 GTGTAGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.52
Consensus pattern (32 bp):
AGAATTTTCTGCGTCTTTTTAATATTTTTCCA
Found at i:43399854 original size:22 final size:22
Alignment explanation
Indices: 43399829--43399884 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
43399819 TGTAGGGTTC
**
43399829 ACATGCCCGTGTTTTCCAAGGG
1 ACATGCCCGTGTTGACCAAGGG
**
43399851 ACATGCCCGTG-TGACCCTGGG
1 ACATGCCCGTGTTGACCAAGGG
43399872 ACATGCCCGTGTT
1 ACATGCCCGTGTT
43399885 AGAGACTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.16, C:0.30, G:0.29, T:0.25
Consensus pattern (22 bp):
ACATGCCCGTGTTGACCAAGGG
Found at i:43406053 original size:15 final size:15
Alignment explanation
Indices: 43406033--43406063 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43406023 AAATATGAAA
43406033 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
43406048 GATATGTTTTGTATT
1 GATATGTTTTGGATT
43406063 G
1 G
43406064 GAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:43407018 original size:18 final size:19
Alignment explanation
Indices: 43406984--43407027 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
43406974 GATACAAATT
43406984 ATATATGATGCAAATGAAA
1 ATATATGATGCAAATGAAA
*
43407003 ATATATG-TGCATATGAAA
1 ATATATGATGCAAATGAAA
43407021 AGTATAT
1 A-TATAT
43407028 TCGGCAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
ATATATGATGCAAATGAAA
Found at i:43419772 original size:53 final size:53
Alignment explanation
Indices: 43419703--43419909 Score: 157
Period size: 53 Copynumber: 3.8 Consensus size: 53
43419693 TTCCTTTTTA
* * *
43419703 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
* * * * *
43419756 AACTCACCATTGCCATGCCTTGGCATGATCTTACATAGG-ATCTTTGCCTTAGCG
1 AACTTACCATTGCCATGCCTTGACATGGTCTTACAT-GGTATCCTTGCCTTA-TG
** * * * * * * * * *
43419810 TAGTTTATCAATGCTATGTCTTAACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
* * *
43419865 AACTTACCAATT-CCATGCCTTGGCATGGTCTTACTTGGTGTCCTT
1 AACTTACC-ATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
43419910 AAACCCTAAT
Statistics
Matches: 113, Mismatches: 35, Indels: 11
0.71 0.22 0.07
Matches are distributed among these distances:
53 41 0.36
54 35 0.31
55 37 0.33
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (53 bp):
AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:43421866 original size:28 final size:28
Alignment explanation
Indices: 43421834--43421894 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
43421824 ACGGGTGACG
*
43421834 CACGGATGTGTCTAGACCGTGTAAATGA
1 CACGGACGTGTCTAGACCGTGTAAATGA
43421862 CACGGACGTGTCTAGACCGTGTAAATGA
1 CACGGACGTGTCTAGACCGTGTAAATGA
43421890 CACGG
1 CACGG
43421895 GCTAGGGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (28 bp):
CACGGACGTGTCTAGACCGTGTAAATGA
Found at i:43430841 original size:11 final size:11
Alignment explanation
Indices: 43430825--43430866 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
43430815 TAAATAATCA
43430825 TATGATTAATG
1 TATGATTAATG
43430836 TATGATTAATG
1 TATGATTAATG
*
43430847 T-TGCTT-AT-
1 TATGATTAATG
43430855 TATGATTAATG
1 TATGATTAATG
43430866 T
1 T
43430867 TGCTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.04
9 6 0.23
10 6 0.23
11 13 0.50
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (11 bp):
TATGATTAATG
Found at i:43430860 original size:19 final size:19
Alignment explanation
Indices: 43430836--43430876 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
43430826 ATGATTAATG
43430836 TATGATTAATGTTGCTTAT
1 TATGATTAATGTTGCTTAT
43430855 TATGATTAATGTTGCTTAT
1 TATGATTAATGTTGCTTAT
43430874 TAT
1 TAT
43430877 TTGCATGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (19 bp):
TATGATTAATGTTGCTTAT
Found at i:43434836 original size:18 final size:18
Alignment explanation
Indices: 43434808--43434844 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43434798 TAGTAGACAA
43434808 AGCTTGCAAAGA-AAAAG
1 AGCTTGCAAAGAGAAAAG
43434825 AGCTTAGCAAAGAGAAAAG
1 AGCTT-GCAAAGAGAAAAG
43434844 A
1 A
43434845 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.54, C:0.11, G:0.24, T:0.11
Consensus pattern (18 bp):
AGCTTGCAAAGAGAAAAG
Found at i:43437133 original size:67 final size:65
Alignment explanation
Indices: 43436934--43437140 Score: 167
Period size: 67 Copynumber: 3.2 Consensus size: 65
43436924 CATAATTTTG
* * * * * * *
43436934 GCTCTCTTGTAC-ACATGGTG-AACACTTAGTACCACCGATGTGACCTAGC--CAGTTTATCTCG
1 GCTCTCTTGT-CTACATGGTGCTACACATAGAACCACCCATGCGACCTAGCTACA-TATATCTCC
43436995 TA
64 TA
* * * *
43436997 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATC-CC
1 GCTCTCTTGTCTACATGGTG--CTACACATAGAACCACCCATGCGACCTAGCTACATATATCTCC
43437061 GTA
64 -TA
* *
43437064 GCTCTCTTGTCTACATGGTG-TACACATAGTATCACCCATGC-ACCTAGCTACATCATAATTTCT
1 GCTCTCTTGTCTACATGGTGCTACACATAGAACCACCCATGCGACCTAGCTACAT-AT-A--TCT
43437127 CCTA
62 CCTA
43437131 GCTCTCTTGT
1 GCTCTCTTGT
43437141 ACACATGATG
Statistics
Matches: 116, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
62 1 0.01
63 30 0.26
64 17 0.15
65 1 0.01
66 22 0.19
67 41 0.35
68 4 0.03
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.31
Consensus pattern (65 bp):
GCTCTCTTGTCTACATGGTGCTACACATAGAACCACCCATGCGACCTAGCTACATATATCTCCTA
Found at i:43449666 original size:6 final size:6
Alignment explanation
Indices: 43449657--43449758 Score: 91
Period size: 6 Copynumber: 16.7 Consensus size: 6
43449647 AAGAAAGATT
* *
43449657 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAAA ATCAAA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * *
43449705 ATTAG- GTGACAAA ATCAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA
1 ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
43449755 ATCA
1 ATCA
43449759 AAATGGGAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
5 3 0.04
6 70 0.89
7 4 0.05
8 2 0.03
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:43449724 original size:31 final size:31
Alignment explanation
Indices: 43449657--43449762 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 31
43449647 AAGAAAGATT
* * *
43449657 ATCAGAATCAGAATCAGAATCA-G-AATCAGA
1 ATCAGAATCAAAATCAAAATCAGGTAA-CAAA
* *
43449687 ATCAGAATCAAAATCAAAATTAGGTGACAAA
1 ATCAGAATCAAAATCAAAATCAGGTAACAAA
* ** *
43449718 ATCAGAATCAGAATCAGTATCAGGTAACAGA
1 ATCAGAATCAAAATCAAAATCAGGTAACAAA
*
43449749 ATCAAAATCAAAAT
1 ATCAGAATCAAAAT
43449763 GGGAATGCAA
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
30 19 0.31
31 41 0.67
32 1 0.02
ACGTcount: A:0.52, C:0.15, G:0.14, T:0.19
Consensus pattern (31 bp):
ATCAGAATCAAAATCAAAATCAGGTAACAAA
Found at i:43450193 original size:27 final size:27
Alignment explanation
Indices: 43450163--43450358 Score: 257
Period size: 27 Copynumber: 7.3 Consensus size: 27
43450153 AGGGCAAAAT
* * * *
43450163 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
43450190 GGTAATTCCACCCTACATGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
43450217 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
43450244 GGTAATTCTACCATACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
43450271 AATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
43450298 GCTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
43450325 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
43450352 GGTAATT
1 GGTAATT
43450359 TCACAAATTA
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:43450419 original size:27 final size:27
Alignment explanation
Indices: 43450340--43450446 Score: 115
Period size: 27 Copynumber: 4.0 Consensus size: 27
43450330 TTCTACCCTA
* * *
43450340 CAGGGGTATTTTGGTAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTATAAAC
* *
43450367 TAGGGGTATTTTGGTAAATTTATAAAC
1 CAGGGGTATTTTGGTAATTTTATAAAC
*
43450394 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTATAAAC
** ** *
43450421 CAATGGTATTTCAGTAATTTTGTAAA
1 CAGGGGTATTTTGGTAATTTTATAAA
43450447 TCGAGGGTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.40
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTATAAAC
Found at i:43450464 original size:27 final size:27
Alignment explanation
Indices: 43450434--43450522 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
43450424 TGGTATTTCA
* *
43450434 GTAATTTTGTAAATCGAGGGTCAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
43450461 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
43450488 ATAATTCTGTAAATCGAGAGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
43450515 GTAATTCT
1 GTAATTCT
43450523 ATCTTTTTCG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.31
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:43450606 original size:26 final size:27
Alignment explanation
Indices: 43450532--43450610 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
43450522 TATCTTTTTC
*
43450532 GGTAATTTTACAAATCGAGGATATTTG
1 GGTAATTTTACAAATCGAGGGTATTTG
* *
43450559 GGTAATTTTATAAATCGGGGGTACTTT-
1 GGTAATTTTACAAATCGAGGGTA-TTTG
*
43450586 GGTAA-TTTACAAGTCGAGGGTATTT
1 GGTAATTTTACAAATCGAGGGTATTT
43450611 CAATAATTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.07
26 14 0.31
27 25 0.56
28 3 0.07
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (27 bp):
GGTAATTTTACAAATCGAGGGTATTTG
Found at i:43464135 original size:9 final size:8
Alignment explanation
Indices: 43464104--43464137 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
43464094 AGTCCCTAAT
43464104 TCACAAAA
1 TCACAAAA
43464112 TCACAAAA
1 TCACAAAA
43464120 TCACAAAA
1 TCACAAAA
43464128 TACACAAAA
1 T-CACAAAA
43464137 T
1 T
43464138 TTCTATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.15
Consensus pattern (8 bp):
TCACAAAA
Found at i:43467026 original size:28 final size:28
Alignment explanation
Indices: 43466994--43467058 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
43466984 ATTTACTAGA
*
43466994 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
43467022 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
43467050 ATACCCCTA
1 ATACCCCTA
43467059 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:43467205 original size:28 final size:27
Alignment explanation
Indices: 43467164--43467253 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
43467154 AGGAAGCGTC
43467164 CTGGTGGCTA-TGCCAAAAATTATCTGTT
1 CTGGTGGC-ACTGCCAAAAA-TATCTGTT
* ***
43467192 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCAAAAATATCTGTT
*
43467219 CTGGTGGCACTGCCACAAAATATCTATAT
1 CTGGTGGCACTGCCA-AAAATATCTGT-T
43467248 CTGGTG
1 CTGGTG
43467254 ACTCTGTCAC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 22 0.44
28 21 0.42
29 7 0.14
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCAAAAATATCTGTT
Found at i:43467264 original size:29 final size:28
Alignment explanation
Indices: 43467174--43467264 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 28
43467164 CTGGTGGCTA
* * *
43467174 TGCCA-AAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAA-TATCTATTCTGGTGACAC
** * *
43467202 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTATTCTGGTGACAC
*
43467229 TGCCACAAAATATCTATATCTGGTGACTC
1 TGCCACAAAATATCTAT-TCTGGTGACAC
*
43467258 TGTCACA
1 TGCCACA
43467265 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 23 0.45
28 13 0.25
29 15 0.29
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTATTCTGGTGACAC
Found at i:43467740 original size:19 final size:19
Alignment explanation
Indices: 43467718--43467756 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
43467708 TTTAATTATT
* *
43467718 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
43467737 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
43467756 T
1 T
43467757 ATGATGAAAA
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:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:43473503 original size:15 final size:15
Alignment explanation
Indices: 43473483--43473513 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43473473 AAATATTAAA
43473483 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
43473498 GATATGTTTTGTATT
1 GATATGTTTTGGATT
43473513 G
1 G
43473514 GAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:43474185 original size:56 final size:55
Alignment explanation
Indices: 43474123--43474233 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 55
43474113 GACCATGGCA
* *
43474123 TCGATATATGTATGCGAGGAATACCATGTTTA-ATACATTGGCATCGATATGTGATT
1 TCGATATATGTATGCGAGGAAGACCATGTTTAGATAC--TGACATCGATATGTGATT
* * *
43474179 TCGATATATGTGTGCGAGTAAGACCTTGTTTAGGATACTGACATCGATATGTGAT
1 TCGATATATGTATGCGAGGAAGACCATGTTTA-GATACTGACATCGATATGTGAT
43474234 AACATGTAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 44 0.92
58 4 0.08
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (55 bp):
TCGATATATGTATGCGAGGAAGACCATGTTTAGATACTGACATCGATATGTGATT
Found at i:43474459 original size:19 final size:18
Alignment explanation
Indices: 43474435--43474478 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
43474425 GATACAAATT
43474435 ATATATGATGCAAATGAAA
1 ATATATG-TGCAAATGAAA
* *
43474454 ATATATGTGTATATGAAA
1 ATATATGTGCAAATGAAA
43474472 AGTATAT
1 A-TATAT
43474479 TCGGCAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (18 bp):
ATATATGTGCAAATGAAA
Found at i:43488429 original size:28 final size:28
Alignment explanation
Indices: 43488397--43488457 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
43488387 CACGGGTGAG
*
43488397 CACGGACGTGTCTAGACCGTTTAAATGA
1 CACGGACGTGTCTAGACCGTGTAAATGA
43488425 CACGGACGTGTCTAGACCGTGTAAATGA
1 CACGGACGTGTCTAGACCGTGTAAATGA
43488453 CACGG
1 CACGG
43488458 GCCAGGGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (28 bp):
CACGGACGTGTCTAGACCGTGTAAATGA
Found at i:43497465 original size:11 final size:11
Alignment explanation
Indices: 43497449--43497490 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
43497439 TAAATAATCA
43497449 TATGATTAATG
1 TATGATTAATG
43497460 TATGATTAATG
1 TATGATTAATG
*
43497471 T-TGCTT-AT-
1 TATGATTAATG
43497479 TATGATTAATG
1 TATGATTAATG
43497490 T
1 T
43497491 TGCTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.04
9 6 0.23
10 6 0.23
11 13 0.50
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (11 bp):
TATGATTAATG
Found at i:43497484 original size:19 final size:19
Alignment explanation
Indices: 43497460--43497500 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
43497450 ATGATTAATG
43497460 TATGATTAATGTTGCTTAT
1 TATGATTAATGTTGCTTAT
43497479 TATGATTAATGTTGCTTAT
1 TATGATTAATGTTGCTTAT
43497498 TAT
1 TAT
43497501 TTGCATGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (19 bp):
TATGATTAATGTTGCTTAT
Found at i:43510870 original size:23 final size:22
Alignment explanation
Indices: 43510831--43510887 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
43510821 TATTAGATTC
43510831 TATTATTTTATTTCTTTCTTTA
1 TATTATTTTATTTCTTTCTTTA
*
43510853 TATATATTTT-TTTCCTTTTTTTA
1 TAT-TATTTTATTT-CTTTCTTTA
*
43510876 TATTATTATATT
1 TATTATTTTATT
43510888 GTTATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTATTTTATTTCTTTCTTTA
Found at i:43511281 original size:13 final size:13
Alignment explanation
Indices: 43511259--43511295 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
43511249 TTATTATTCC
43511259 TTTA-TTATTTTA
1 TTTATTTATTTTA
*
43511271 TTTATTTATTTCA
1 TTTATTTATTTTA
43511284 TTTATTTATTTT
1 TTTATTTATTTT
43511296 GTTTTTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:43514235 original size:39 final size:39
Alignment explanation
Indices: 43514096--43514216 Score: 197
Period size: 39 Copynumber: 3.1 Consensus size: 39
43514086 GCTCTGATGA
* * *
43514096 GCTTCAGTTCGTCTTTGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
43514135 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTACGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
43514174 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
43514213 GCTT
1 GCTT
43514217 TGGCTAGATT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:43516599 original size:27 final size:27
Alignment explanation
Indices: 43516569--43516625 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
43516559 AACATAGGTA
*
43516569 AGTCCACT-GGGACATTAAAAACGGGGT
1 AGTCC-CTCGGGACATTAAAAACAGGGT
* *
43516596 AGTCCGTCGGGACATTAAAAATAGGGT
1 AGTCCCTCGGGACATTAAAAACAGGGT
43516623 AGT
1 AGT
43516626 TCGCCAGGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (27 bp):
AGTCCCTCGGGACATTAAAAACAGGGT
Found at i:43516635 original size:27 final size:27
Alignment explanation
Indices: 43516578--43516635 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
43516568 AAGTCCACTG
* * *
43516578 GGACATTAAAAACGGGGTAGTCCGTCG
1 GGACATTAAAAACAGGGTAGTCCGCCA
* *
43516605 GGACATTAAAAATAGGGTAGTTCGCCA
1 GGACATTAAAAACAGGGTAGTCCGCCA
43516632 GGAC
1 GGAC
43516636 GTGAAACATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (27 bp):
GGACATTAAAAACAGGGTAGTCCGCCA
Found at i:43517533 original size:239 final size:239
Alignment explanation
Indices: 43517114--43517577 Score: 903
Period size: 239 Copynumber: 1.9 Consensus size: 239
43517104 CAACTAATCT
43517114 TCCATGTTTTCAAGTCATTCAAACTAACATTCATCTATGCCAATACCAAGCTCAAACTATACCTT
1 TCCATGTTTTCAAGTCATTCAAACTAACATTCATCTATGCCAATACCAAGCTCAAACTATACCTT
43517179 ACCACATTCAAATAAGCCATTCAACAAGGCACACATATAAGCCTATTATATTGCCAAATCACAAT
66 ACCACATTCAAATAAGCCATTCAACAAGGCACACATATAAGCCTATTATATTGCCAAATCACAAT
*
43517244 TATGCATATATATAGACATTGACTCTCCAAAATTCAAACATAAAACAAGGTTCCCACCAAACCAT
131 TATGCATATATATAAACATTGACTCTCCAAAATTCAAACATAAAACAAGGTTCCCACCAAA-CAT
43517309 CAATTCA-TAAAATATGACATATATAAACACATATATAACATTCA
195 CAATTCATTAAAATATGACATATATAAACACATATATAACATTCA
43517353 TCCATGTTTTCAAGTCATTCAAACTAACATTCATCTATGCCAATACCAAGCTCAAACTATACCTT
1 TCCATGTTTTCAAGTCATTCAAACTAACATTCATCTATGCCAATACCAAGCTCAAACTATACCTT
43517418 ACCACATTCAAATAAGCCATTCAACAAGGCACACATATAAGCCTATTATATTGCCAAATCACAAT
66 ACCACATTCAAATAAGCCATTCAACAAGGCACACATATAAGCCTATTATATTGCCAAATCACAAT
43517483 TATGCATATATATAAACATTGACTCTCCAAAATTCAAACATAAAACAAGGTTCCCACCAAACATC
131 TATGCATATATATAAACATTGACTCTCCAAAATTCAAACATAAAACAAGGTTCCCACCAAACATC
43517548 AATTCATTAAAATATGACATATATAAACAC
196 AATTCATTAAAATATGACATATATAAACAC
43517578 CTAAGAAACG
Statistics
Matches: 223, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
238 10 0.04
239 213 0.96
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (239 bp):
TCCATGTTTTCAAGTCATTCAAACTAACATTCATCTATGCCAATACCAAGCTCAAACTATACCTT
ACCACATTCAAATAAGCCATTCAACAAGGCACACATATAAGCCTATTATATTGCCAAATCACAAT
TATGCATATATATAAACATTGACTCTCCAAAATTCAAACATAAAACAAGGTTCCCACCAAACATC
AATTCATTAAAATATGACATATATAAACACATATATAACATTCA
Found at i:43521725 original size:75 final size:75
Alignment explanation
Indices: 43521636--43521788 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
43521626 GCGTATTAAT
* * * *
43521636 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCTGTATTATATATAGTTT
1 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATACAATTT
43521701 GAATTTAAAA
66 GAATTTAAAA
*
43521711 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATGCAATTT
1 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATACAATTT
43521776 GAATTTAAAA
66 GAATTTAAAA
43521786 TTT
1 TTT
43521789 TCGTATATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.50
Consensus pattern (75 bp):
TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATACAATTT
GAATTTAAAA
Found at i:43521842 original size:90 final size:90
Alignment explanation
Indices: 43521711--43521890 Score: 261
Period size: 90 Copynumber: 2.0 Consensus size: 90
43521701 GAATTTAAAA
* *
43521711 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATGCAATTT
1 TTTACCCATCTATTTGTAGTTTGTTAGGTGTTTAAATTTAATTTAGTCCGTAATATATGCAATTT
43521776 GAATTTAAAATTTTCGTATATTAAT
66 GAATTTAAAATTTTCGTATATTAAT
* * * **
43521801 TTTACCCATCTATTTGTAGTTTGTTAGGTGTTTAAATTTAATTTAGTCTGTATTATTTGTTATTT
1 TTTACCCATCTATTTGTAGTTTGTTAGGTGTTTAAATTTAATTTAGTCCGTAATATATGCAATTT
* * * *
43521866 GAATTTTACATTTTTGTGTATTAAT
66 GAATTTAAAATTTTCGTATATTAAT
43521891 ATTCTAGAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.53
Consensus pattern (90 bp):
TTTACCCATCTATTTGTAGTTTGTTAGGTGTTTAAATTTAATTTAGTCCGTAATATATGCAATTT
GAATTTAAAATTTTCGTATATTAAT
Found at i:43524568 original size:17 final size:17
Alignment explanation
Indices: 43524511--43524569 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
43524501 TTTTATTTTC
* **
43524511 ATTTCATTTCCATTTCC
1 ATTTAATTTCCATTTAA
43524528 ATTTAATTT-CATTTAA
1 ATTTAATTTCCATTTAA
***
43524544 AAAAAATTTCCATTTAA
1 ATTTAATTTCCATTTAA
43524561 ATTTAATTT
1 ATTTAATTT
43524570 TTTCTCATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATTTCCATTTAA
Found at i:43524586 original size:16 final size:15
Alignment explanation
Indices: 43524561--43524599 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
43524551 TTCCATTTAA
43524561 ATTTAATTTTTTCTC
1 ATTTAATTTTTTCTC
*
43524576 ATTTCAATTTTTTTTC
1 ATTT-AATTTTTTCTC
43524592 ATATTAAT
1 AT-TTAAT
43524600 AACAATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTAATTTTTTCTC
Found at i:43524633 original size:17 final size:18
Alignment explanation
Indices: 43524611--43524657 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
43524601 ACAATTAGTC
43524611 TCATTTCAATTTTT-TTT
1 TCATTTCAATTTTTGTTT
*
43524628 TCATTTCAGTTTTTGTTT
1 TCATTTCAATTTTTGTTT
*
43524646 TCATTTTAATTT
1 TCATTTCAATTT
43524658 ATAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (18 bp):
TCATTTCAATTTTTGTTT
Found at i:43524718 original size:5 final size:5
Alignment explanation
Indices: 43524708--43524775 Score: 55
Period size: 5 Copynumber: 12.2 Consensus size: 5
43524698 CATTACAAAA
* *
43524708 TTCAT TTCAT TTGCATT TTCAT TACAAAT TACAT TTCAT TTCAT ATTCAT
1 TTCAT TTCAT TT-CA-T TTCAT TTC--AT TTCAT TTCAT TTCAT -TTCAT
43524758 TTAACAT TTCAT TTCAT T
1 TT--CAT TTCAT TTCAT T
43524776 ATTTTTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
5 32 0.59
6 9 0.17
7 13 0.24
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (5 bp):
TTCAT
Done.