Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 64
Found at i:3313985 original size:19 final size:20
Alignment explanation
Indices: 3313963--3314004 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3313953 TATTTACTTT
*
3313963 TTATTTTAAT-ATTTTTATA
1 TTATTTTAATAAATTTTATA
3313982 TTATTTTAATAAATTTTATA
1 TTATTTTAATAAATTTTATA
3314002 TTA
1 TTA
3314005 ATAATCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTTAATAAATTTTATA
Found at i:3314189 original size:21 final size:21
Alignment explanation
Indices: 3314145--3314228 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3314135 TCCACTGTGG
* * * *
3314145 ATTGTCACACCAATATCGTAA
1 ATTGTCATATCAACATCATAA
*
3314166 ATTATCATATCAACATCATAA
1 ATTGTCATATCAACATCATAA
* * *
3314187 ATTGTCATATTAACACCATGA
1 ATTGTCATATCAACATCATAA
* *
3314208 ATCGTCATATCACCATCATAA
1 ATTGTCATATCAACATCATAA
3314229 TAATCAAGGA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (21 bp):
ATTGTCATATCAACATCATAA
Found at i:3319259 original size:8 final size:8
Alignment explanation
Indices: 3319249--3319281 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3319239 TTTTTTGAAT
*
3319249 ATTTTAAT
1 ATTTTAAA
3319257 ATTTTAAA
1 ATTTTAAA
3319265 ATTTTAAA
1 ATTTTAAA
3319273 A-TTTAAA
1 ATTTTAAA
3319280 AT
1 AT
3319282 AAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTTAAA
Found at i:3319940 original size:6 final size:6
Alignment explanation
Indices: 3319929--3319959 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3319919 GACACGTATT
3319929 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
3319960 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3321012 original size:21 final size:19
Alignment explanation
Indices: 3320988--3321028 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
3320978 TTAAAATTTT
3320988 ATTTGTATCTATTCATTTAAA
1 ATTTGTATCTATT--TTTAAA
*
3321009 ATTTTTATCTATTTTTAAA
1 ATTTGTATCTATTTTTAAA
3321028 A
1 A
3321029 ATATTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTGTATCTATTTTTAAA
Found at i:3321203 original size:136 final size:133
Alignment explanation
Indices: 3320971--3321223 Score: 310
Period size: 136 Copynumber: 1.9 Consensus size: 133
3320961 TACTAATAGT
* * * *** *
3320971 ATTTTTCTTAAAATTTTATTTGTATCTATTCATTTAAAATTTTTATCTATTTTTAAAAATATTTC
1 ATTTATCTTAAAATTTTATTTGTATCTATTAATTAAAAAAAATTATCTAATTTTAAAAATATTTC
* * * * *
3321036 TTCATTCATCACTGATTAAAGCCCGGAAGAAATTTAGTATGCGGGGAACAGCAAAATTTAAAATT
66 TACACTCATCACTGATTAAAGCCAGAAAGAAATTTAGTATGCGGAGAACAGCAAAATTTAAAATT
3321101 ATA
131 ATA
*
3321104 ATTTATCTTAAAATTTTATTTGTATCTATTAATTCAAACAAAAATTAT-TAAATTTTAAAATTAT
1 ATTTATCTTAAAATTTTATTTGTATCTATTAATT-AAA-AAAAATTATCT-AATTTTAAAAATAT
* * * *
3321168 TTCTAGACCTCGTCACTTATTAAAGCCAGAAAGAAATTTAGTATGTGGAGAACAGC
63 TTCTACA-CTCATCACTGATTAAAGCCAGAAAGAAATTTAGTATGCGGAGAACAGC
3321224 GAAGCCGACG
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
133 32 0.32
134 3 0.03
135 23 0.23
136 41 0.41
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (133 bp):
ATTTATCTTAAAATTTTATTTGTATCTATTAATTAAAAAAAATTATCTAATTTTAAAAATATTTC
TACACTCATCACTGATTAAAGCCAGAAAGAAATTTAGTATGCGGAGAACAGCAAAATTTAAAATT
ATA
Found at i:3326473 original size:21 final size:21
Alignment explanation
Indices: 3326359--3326501 Score: 145
Period size: 21 Copynumber: 6.8 Consensus size: 21
3326349 TTGTACCAAG
*
3326359 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
3326380 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
3326401 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
* *
3326422 GACGAGAAGGCAATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
3326443 GACGAGAAGACCTTTCAT-AA
1 GACGAGAAGACCATTCATCAA
3326463 CGACGAGAAGACC-TTCAT-AA
1 -GACGAGAAGACCATTCATCAA
3326483 CGAC-ATGAAGACCACTTCA
1 -GACGA-GAAGACCA-TTCA
3326502 CATTGGAGGT
Statistics
Matches: 110, Mismatches: 6, Indels: 11
0.87 0.05 0.09
Matches are distributed among these distances:
19 1 0.01
20 21 0.19
21 83 0.75
22 5 0.05
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:3331309 original size:36 final size:36
Alignment explanation
Indices: 3331262--3331450 Score: 229
Period size: 36 Copynumber: 5.2 Consensus size: 36
3331252 AGTCAATCCT
*
3331262 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTG
* * *
3331298 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTG
3331334 AAGCCTTCACCAGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCAGAGAATAGTGAAGCAAACCATC-TG
* * *
3331370 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTT
1 AAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTG
* * * * *
3331406 AAGTCTTCACCA-AAAAGTAGTGAAGCAGATCCATTTT
1 AAGCCTTCACCAGAGAA-TAGTGAAGCA-AACCATCTG
3331443 AAGCCTTC
1 AAGCCTTC
3331451 TCAGAAGAGT
Statistics
Matches: 137, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
35 3 0.02
36 119 0.87
37 15 0.11
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (36 bp):
AAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTG
Found at i:3331896 original size:51 final size:51
Alignment explanation
Indices: 3331820--3332186 Score: 421
Period size: 51 Copynumber: 7.1 Consensus size: 51
3331810 GTGAAGCAAA
* * *
3331820 TGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAACGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* *
3331871 TGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAAGAGCGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * * * *
3331922 TGAAGA-GATGTCTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTG
1 TGAAGATG-T-TC-GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * * *
3331975 TGAAGATATCCGAGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTC
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * *
3332026 TGAAGATGTTCGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGA
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT---T
* *
3332080 AGAAGATGTTTGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * * *
3332131 TGAAGAGATGTTCGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATT
1 TG-A-AGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
3332184 TGA
1 TGA
3332187 TGAAGATTGT
Statistics
Matches: 269, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.00
51 132 0.49
52 5 0.02
53 85 0.32
54 46 0.17
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (51 bp):
TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
Found at i:3332317 original size:161 final size:161
Alignment explanation
Indices: 3332162--3332730 Score: 803
Period size: 161 Copynumber: 3.5 Consensus size: 161
3332152 TACTCCCTAG
*
3332162 AGAAATAGGGAGC-GAACCCATTTGATGAAGATTG-TGAGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAG-ACCCA-TTGATGAAGATTGTTGAGTCTTATACTCTCTGAAGAAATAGGG
3332225 AGCAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAAT
64 AGCAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAAT
3332290 CTTTGAAGATTGTTCGGATCTTATACTCTCTGA
129 CTTTGAAGATTGTTCGGATCTTATACTCTCTGA
* *
3332323 AGAAATAGGGGGCAGATGCGATTGATGAAGATTG-TGAGTCTTATACTCTCTGAAGAAATAGGGA
1 AGAAATAGGGGGCAGA-CCCATTGATGAAGATTGTTGAGTCTTATACTCTCTGAAGAAATAGGGA
3332387 GCAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
65 GCAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
*
3332452 GTTGAAGATTGTTCGGATCTTATACTCTCTGA
130 TTTGAAGATTGTTCGGATCTTATACTCTCTGA
* *
3332484 AGAAATA-GGGGCAGACGCGATTGATGAAGATTGTTG-GTCTTATACTCTCTGAAGAAATAGGGG
1 AGAAATAGGGGGCAGAC-CCATTGATGAAGATTGTTGAGTCTTATACTCTCTGAAGAAATAGGGA
* * * * * *
3332547 GCAGACGCAATCGTTGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGA
65 GCAGACACGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA
* * *
3332612 T-TGATGAAGATT-AT-GGGTCTTATACTCTCTGA
128 TCT-TTGAAGATTGTTCGGATCTTATACTCTCTGA
* * * *
3332644 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAGAC-CCATTGATGAAGATTGTT-GAGTCTTATACTCTCTGAAGAAATAGGG
* * *
3332709 GGCAGACAAGTTTGTTGAAGAT
64 AGCAGACACGATTGTTGAAGAT
3332731 GATTCAAGTC
Statistics
Matches: 374, Mismatches: 24, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
160 94 0.25
161 188 0.50
162 49 0.13
163 43 0.11
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (161 bp):
AGAAATAGGGGGCAGACCCATTGATGAAGATTGTTGAGTCTTATACTCTCTGAAGAAATAGGGAG
CAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCT
TTGAAGATTGTTCGGATCTTATACTCTCTGA
Found at i:3332338 original size:108 final size:109
Alignment explanation
Indices: 3332183--3332715 Score: 789
Period size: 108 Copynumber: 5.0 Consensus size: 109
3332173 GCGAACCCAT
* * * * *
3332183 TTGATGAAGATTG-TGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGAT
1 TTGATGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
*
3332247 TG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA
66 TGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
* * * * * *
3332289 TCT-TTGAAGATTGTTCGGATCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAG
1 T-TGATGAAGATTGTT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAG
* * *
3332353 ATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
64 ATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
*
3332397 TTGTTGAAGATTG-TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
1 TTGATGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
*
3332461 TGTTCGGATCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGA
66 TGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
3332504 TTGATGAAGATTGTT-GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
1 TTGATGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
* * *
3332568 TGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGA
66 TGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
*
3332612 TTGATGAAGATT-ATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
1 TTGATGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
3332676 TGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
66 TGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
3332716 AAGTTTGTTG
Statistics
Matches: 389, Mismatches: 29, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
106 57 0.15
107 105 0.27
108 227 0.58
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (109 bp):
TTGATGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGAT
TGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
Found at i:3332541 original size:268 final size:271
Alignment explanation
Indices: 3332200--3332766 Score: 898
Period size: 268 Copynumber: 2.1 Consensus size: 271
3332190 AGATTGTGAG
*
3332200 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTC
1 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATGAAGATTGTGGGTCTTATACTCTC
* *
3332265 TGAAGAAATAGGGGGCAGACGCAATCTTTGAAGATTGTTCG-GATCTTATACTCTCTGAAGAAAT
66 TGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGCTCGAG-TCTTATACTCTCTGAAGAAAT
*
3332329 AGGGGGCAGATGCGATTGATGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
130 AGGGGGCAGATGCGATTGATGAAGATTATGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
* *
3332394 CGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGA
195 CAATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGA
3332457 AGATTGTTCGGA
260 AGATTGTTCGGA
* *
3332469 TCTTATACTCTCTGAAGAAATAGGG-GCAGACGCGATTGATGAAGATTGTTGGTCTTATACTCTC
1 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATGAAGATTGTGGGTCTTATACTCTC
3332533 TGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATA
66 TGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATA
* * *
3332598 GGGGGCAGATGCGATTGATGAAGATTATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGC
131 GGGGGCAGATGCGATTGATGAAGATTATGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
*
3332663 AATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTTTGTTG
196 AATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TCGTTG
*
3332726 AAGA-TGATTC-AA
259 AAGATTG-TTCGGA
* *
3332738 GTCTTATACCCTCTGAAAAAATAGGGAGC
1 -TCTTATACTCTCTGAAGAAATAGGGAGC
3332767 GAACCCATTT
Statistics
Matches: 275, Mismatches: 15, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
268 174 0.63
269 30 0.11
270 69 0.25
271 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (271 bp):
TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATGAAGATTGTGGGTCTTATACTCTC
TGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATA
GGGGGCAGATGCGATTGATGAAGATTATGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
AATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAA
GATTGTTCGGA
Found at i:3332726 original size:55 final size:54
Alignment explanation
Indices: 3332187--3332763 Score: 658
Period size: 53 Copynumber: 10.7 Consensus size: 54
3332177 ACCCATTTGA
* * *
3332187 TGAAGATTG-TGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGATTGT
*
3332240 TGAAGATTG-TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCA-ATCT-T
1 TGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC-AAGAT-TGT
* *** *
3332293 TGAAGATTGTTCGGATCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGA
1 TGAAGATTGTT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGATTGT
* * *
3332348 TGAAGATTG-TGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGATTGT
* *
3332401 TGAAGATTG-TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCA-ATCGT
1 TGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC-AAGATTGT
* ** *
3332454 TGAAGATTGTTCGGATCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATTGA
1 TGAAGATTGTT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGATTGT
* *
3332508 TGAAGATTGTT-GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCA-ATCGT
1 TGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC-AAGATTGT
* * *** *
3332561 TGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGA
1 TGAAGATTG-TTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGATTGT
* * *
3332616 TGAAGATT-ATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCA-ATCGT
1 TGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC-AAGATTGT
*
3332669 TGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTGT
1 TGAAGATTGTT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGATTGT
** * *
3332724 TGAAGA-TGATTCAAGTCTTATACCCTCTGAAAAAATAGGG
1 TGAAGATTG-TT-GGGTCTTATACTCTCTGAAGAAATAGGG
3332764 AGCGAACCCA
Statistics
Matches: 451, Mismatches: 53, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
52 23 0.05
53 213 0.47
54 33 0.07
55 182 0.40
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (54 bp):
TGAAGATTGTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGATTGT
Found at i:3337548 original size:2 final size:2
Alignment explanation
Indices: 3337541--3337566 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3337531 ACTAACAAAT
3337541 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3337567 AAATACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3337797 original size:23 final size:22
Alignment explanation
Indices: 3337770--3337812 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3337760 ATTTTTTAGA
3337770 AAAATAT-AAATCATTTTAAATTG
1 AAAATATGAAAT-A-TTTAAATTG
3337793 AAAATATGAAATATTTAAAT
1 AAAATATGAAATATTTAAAT
3337813 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAATATGAAATATTTAAATTG
Found at i:3337916 original size:20 final size:22
Alignment explanation
Indices: 3337879--3337923 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
3337869 TTAAAATACT
3337879 AAAAATACTATTAAAAATT-TA
1 AAAAATACTATTAAAAATTATA
3337900 AAAAATA-TA-TAACAAATTATA
1 AAAAATACTATTAA-AAATTATA
3337921 AAA
1 AAA
3337924 TCATAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 7 0.32
21 12 0.55
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATACTATTAAAAATTATA
Found at i:3337982 original size:37 final size:37
Alignment explanation
Indices: 3337940--3338017 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
3337930 AGGAAAACTG
3337940 TTATTGCTCATCTCTTATAAGCTTTACACGCATCCTT
1 TTATTGCTCATCTCTTATAAGCTTTACACGCATCCTT
* *
3337977 TTATTGCTCATCTCTTATAAGCTTTAGATGCATCCTT
1 TTATTGCTCATCTCTTATAAGCTTTACACGCATCCTT
3338014 TTAT
1 TTAT
3338018 AGGCTTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.22, C:0.23, G:0.09, T:0.46
Consensus pattern (37 bp):
TTATTGCTCATCTCTTATAAGCTTTACACGCATCCTT
Found at i:3338230 original size:17 final size:17
Alignment explanation
Indices: 3338208--3338248 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3338198 AATCATTGAG
3338208 GGACAAAACCCAATGAA
1 GGACAAAACCCAATGAA
*
3338225 GGACAAAATCCAATGAA
1 GGACAAAACCCAATGAA
3338242 GGA-AAAA
1 GGACAAAA
3338249 AGAGTAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.56, C:0.17, G:0.20, T:0.07
Consensus pattern (17 bp):
GGACAAAACCCAATGAA
Found at i:3340508 original size:16 final size:16
Alignment explanation
Indices: 3340471--3340509 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3340461 ATTCATTCCA
*
3340471 ACTTATTTATTTTTTC
1 ACTTATTTATTTTCTC
*
3340487 AGTTATTTATTTTCTC
1 ACTTATTTATTTTCTC
*
3340503 CCTTATT
1 ACTTATT
3340510 ATTGGGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (16 bp):
ACTTATTTATTTTCTC
Found at i:3340915 original size:16 final size:16
Alignment explanation
Indices: 3340868--3340916 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
3340858 TAATAAATAA
*
3340868 ACGAACATAAACGAAA
1 ACGAACATAAACGAAC
*
3340884 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
3340900 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3340916 A
1 A
3340917 AATTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3340915 original size:26 final size:26
Alignment explanation
Indices: 3340864--3340916 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3340854 CATTTAATAA
* *
3340864 ATAAACGAACATAAACGAAAATGAAC
1 ATAAACGAACACAAACGAAAACGAAC
*
3340890 ATAAACGAACACGAAC-ATAAACGAAC
1 ATAAACGAACACAAACGA-AAACGAAC
3340916 A
1 A
3340917 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.60, C:0.19, G:0.11, T:0.09
Consensus pattern (26 bp):
ATAAACGAACACAAACGAAAACGAAC
Found at i:3340963 original size:31 final size:31
Alignment explanation
Indices: 3340925--3341005 Score: 162
Period size: 31 Copynumber: 2.6 Consensus size: 31
3340915 CAAATTTTTT
3340925 TTGTTCATGTTCGTTCATTAAGGAATATAGC
1 TTGTTCATGTTCGTTCATTAAGGAATATAGC
3340956 TTGTTCATGTTCGTTCATTAAGGAATATAGC
1 TTGTTCATGTTCGTTCATTAAGGAATATAGC
3340987 TTGTTCATGTTCGTTCATT
1 TTGTTCATGTTCGTTCATT
3341006 TAATAAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (31 bp):
TTGTTCATGTTCGTTCATTAAGGAATATAGC
Found at i:3341027 original size:10 final size:10
Alignment explanation
Indices: 3341012--3341086 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
3341002 CATTTAATAA
3341012 ATAAACGAAC
1 ATAAACGAAC
3341022 ATAAACGAAC
1 ATAAACGAAC
3341032 ----ACGAAC
1 ATAAACGAAC
3341038 ATAAACGAAC
1 ATAAACGAAC
** *
3341048 ACGAAC-ATAA
1 ATAAACGA-AC
3341058 ATGAACACGAAC
1 AT-AA-ACGAAC
3341070 ATAAACGAAC
1 ATAAACGAAC
3341080 ATAAACG
1 ATAAACG
3341087 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3341037 original size:16 final size:16
Alignment explanation
Indices: 3341016--3341080 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
3341006 TAATAAATAA
3341016 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3341032 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
3341048 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
3341064 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3341080 A
1 A
3341081 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3342602 original size:37 final size:37
Alignment explanation
Indices: 3342547--3342618 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
3342537 ATGAAATGTC
3342547 TTTGTAGGAAAATATGAAAAATGTGCTCGTAATTTCA
1 TTTGTAGGAAAATATGAAAAATGTGCTCGTAATTTCA
* * *
3342584 TTTGTAGGAAAATCTGAAAATTGTTCTCGTAATTT
1 TTTGTAGGAAAATATGAAAAATGTGCTCGTAATTT
3342619 AATTAACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (37 bp):
TTTGTAGGAAAATATGAAAAATGTGCTCGTAATTTCA
Found at i:3345133 original size:19 final size:19
Alignment explanation
Indices: 3345109--3345145 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3345099 TGAAAATGAT
*
3345109 TTGATTTTGAAATTCAAAG
1 TTGATTTTGAAAATCAAAG
3345128 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAATCAAA
3345146 ATGAAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (19 bp):
TTGATTTTGAAAATCAAAG
Found at i:3348646 original size:32 final size:31
Alignment explanation
Indices: 3348595--3348660 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
3348585 AAATAAGAGT
3348595 CTAACGTTTTCACTGTTACACTTTTAGGTGC
1 CTAACGTTTTCACTGTTACACTTTTAGGTGC
* * * *
3348626 CTAATGTTTTCTCTCGTTACATTTTTAGGTTC
1 CTAACGTTTTCACT-GTTACACTTTTAGGTGC
3348658 CTA
1 CTA
3348661 CGTAGTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.47
Consensus pattern (31 bp):
CTAACGTTTTCACTGTTACACTTTTAGGTGC
Found at i:3348902 original size:13 final size:13
Alignment explanation
Indices: 3348884--3348908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3348874 TTTATATATT
3348884 TTTTTAAAAAATA
1 TTTTTAAAAAATA
3348897 TTTTTAAAAAAT
1 TTTTTAAAAAAT
3348909 TAATAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:3349399 original size:29 final size:29
Alignment explanation
Indices: 3349361--3349429 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
3349351 CGTCAAAATG
*
3349361 TTAGACACCTATTTTTAACGAAAAATTAT
1 TTAGACACCTATTTTTAACAAAAAATTAT
3349390 TTAGACACCTATTTTTAACAAAAAATTAT
1 TTAGACACCTATTTTTAACAAAAAATTAT
*
3349419 TTAGGCACCTA
1 TTAGACACCTA
3349430 AAGTTAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (29 bp):
TTAGACACCTATTTTTAACAAAAAATTAT
Found at i:3349436 original size:29 final size:29
Alignment explanation
Indices: 3349361--3349437 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
3349351 CGTCAAAATG
*** *
3349361 TTAGACACCTATTTTTAACGAAAAATTAT
1 TTAGACACCTAAAGTTAACAAAAAATTAT
***
3349390 TTAGACACCTATTTTTAACAAAAAATTAT
1 TTAGACACCTAAAGTTAACAAAAAATTAT
*
3349419 TTAGGCACCTAAAGTTAAC
1 TTAGACACCTAAAGTTAAC
3349438 TTAAGGTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (29 bp):
TTAGACACCTAAAGTTAACAAAAAATTAT
Found at i:3352767 original size:13 final size:13
Alignment explanation
Indices: 3352745--3352789 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
3352735 GTCATAAATC
3352745 TATGACGCGCATT
1 TATGACGCGCATT
*
3352758 TATGATGCGCATT
1 TATGACGCGCATT
*
3352771 TATGACGCGCATG
1 TATGACGCGCATT
3352784 TATGAC
1 TATGAC
3352790 TTACATTGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:3352874 original size:85 final size:85
Alignment explanation
Indices: 3352768--3353066 Score: 476
Period size: 85 Copynumber: 3.5 Consensus size: 85
3352758 TATGATGCGC
*
3352768 ATTTATGACGCGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGA
3352833 CACACATTTGTGCGTCATAA
66 CACACATTTGTGCGTCATAA
* *
3352853 ATTTATGACACGCATGTATGACTTATATTGCGCGTCATTGAAGCCCTCGTCATAAATTAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGA
3352918 CACACATTTGTGCGTCATAA
66 CACACATTTGTGCGTCATAA
* * *
3352938 ATTTATGACACGCATGCATGACTTACATTGCACGTCATTGAAGCCCCCGTCATAAATCT--GCTT
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAAT-TAAG-AT
* *
3353001 GACATACATTTGTGTGTCATAA
64 GACACACATTTGTGCGTCATAA
* *
3353023 ATTTATGACACGCATATATGACTTACATTGCGTGTCATTGAAGC
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGC
3353067 ACACATCATT
Statistics
Matches: 198, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
84 1 0.01
85 196 0.99
86 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGA
CACACATTTGTGCGTCATAA
Found at i:3353490 original size:86 final size:86
Alignment explanation
Indices: 3353335--3353506 Score: 312
Period size: 86 Copynumber: 2.0 Consensus size: 86
3353325 TCTTTGCGAA
3353335 TATCATCAATGTCATCATCCGTATATTCTTCTTTCCCATCGCCAACCTAAGTAAAAATATGAAAT
1 TATCATCAATGTCATCATCCGTATATTCTTCTTTCCCATCGCCAACCTAAGTAAAAATATGAAAT
3353400 AGTATATAATTTATACTTATTT
66 AGTATATAATTTA-ACTTATTT
3353422 TATCATCAA-GTCATCATCCGTATATTCTTCTTTCCCATCGCCAACCTAAGTAAAAATATG-AAT
1 TATCATCAATGTCATCATCCGTATATTCTTCTTTCCCATCGCCAACCTAAGTAAAAATATGAAAT
3353485 AAGTATATAATTTAACTTATTT
66 -AGTATATAATTTAACTTATTT
3353507 AAAGTGAAGC
Statistics
Matches: 84, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
85 11 0.13
86 64 0.76
87 9 0.11
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (86 bp):
TATCATCAATGTCATCATCCGTATATTCTTCTTTCCCATCGCCAACCTAAGTAAAAATATGAAAT
AGTATATAATTTAACTTATTT
Found at i:3362708 original size:35 final size:35
Alignment explanation
Indices: 3362663--3362738 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
3362653 TTCATGTTCA
3362663 AAATTACAAAACACTTCAATTACATTATAAACCTC
1 AAATTACAAAACACTTCAATTACATTATAAACCTC
* * * * * *
3362698 AAATTCCAAAATACTTTAATTATATTCTAAACCTT
1 AAATTACAAAACACTTCAATTACATTATAAACCTC
3362733 AAATTA
1 AAATTA
3362739 AAGTATTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (35 bp):
AAATTACAAAACACTTCAATTACATTATAAACCTC
Found at i:3364830 original size:17 final size:17
Alignment explanation
Indices: 3364803--3364851 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3364793 TAAAAATTAA
3364803 AATATTATTTTTAATATT
1 AATA-TATTTTTAATATT
*
3364821 TATATATTTTT-AT-TT
1 AATATATTTTTAATATT
3364836 AATATATTTTTTAATA
1 AATATA-TTTTTAATA
3364852 AAAAGATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 9 0.35
18 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATATATTTTTAATATT
Found at i:3364834 original size:14 final size:15
Alignment explanation
Indices: 3364817--3364846 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3364807 TTATTTTTAA
3364817 TATTT-ATATATTTT
1 TATTTAATATATTTT
3364831 TATTTAATATATTTT
1 TATTTAATATATTTT
3364846 T
1 T
3364847 TAATAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTAATATATTTT
Found at i:3366109 original size:14 final size:15
Alignment explanation
Indices: 3366090--3366118 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3366080 CCCTTTGGAC
3366090 AAAAATAT-TAAATA
1 AAAAATATATAAATA
3366104 AAAAATATATAAATA
1 AAAAATATATAAATA
3366119 TTAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAATATATAAATA
Found at i:3367900 original size:16 final size:15
Alignment explanation
Indices: 3367879--3367921 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3367869 TGTCATTTGC
3367879 TTATTTTTTATGTAGG
1 TTATTTTTTATG-AGG
*
3367895 TTATTTATTTATGGGG
1 TTATTT-TTTATGAGG
*
3367911 TTATTTGTTAT
1 TTATTTTTTAT
3367922 TTAGTCATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 14 0.58
17 6 0.25
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (15 bp):
TTATTTTTTATGAGG
Found at i:3371048 original size:4 final size:4
Alignment explanation
Indices: 3371041--3371103 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
3371031 TAGAGAGAGA
* * *
3371041 ATAC ATAC ATAC AT-- ATAC ACAC ATAT ATAC ATAC AT-- ATAC ACAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
3371085 ACAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATA
3371104 TATTTCTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
4 43 0.91
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:3371064 original size:10 final size:10
Alignment explanation
Indices: 3371045--3371099 Score: 56
Period size: 10 Copynumber: 5.1 Consensus size: 10
3371035 GAGAGAATAC
3371045 ATACATACAT
1 ATACATACAT
*
3371055 ATACACACATAT
1 ATACATAC--AT
3371067 ATACATACAT
1 ATACATACAT
*
3371077 ATACACACACAT
1 AT--ACATACAT
3371089 ATACATACAT
1 ATACATACAT
3371099 A
1 A
3371100 CATATATTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 19 0.51
12 18 0.49
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (10 bp):
ATACATACAT
Found at i:3371070 original size:12 final size:12
Alignment explanation
Indices: 3371053--3371106 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
3371043 ACATACATAC
3371053 ATATACACACAT
1 ATATACACACAT
*
3371065 ATATACATACAT
1 ATATACACACAT
*
3371077 ATACACACACAT
1 ATATACACACAT
*
3371089 ATACATACATACAT
1 AT--ATACACACAT
3371103 ATAT
1 ATAT
3371107 TTCTATATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 25 0.71
14 10 0.29
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (12 bp):
ATATACACACAT
Found at i:3371071 original size:22 final size:22
Alignment explanation
Indices: 3371045--3371099 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3371035 GAGAGAATAC
*
3371045 ATACATACATATACACACATAT
1 ATACATACATATACACACACAT
3371067 ATACATACATATACACACACAT
1 ATACATACATATACACACACAT
3371089 ATACATACATA
1 ATACATACATA
3371100 CATATATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (22 bp):
ATACATACATATACACACACAT
Found at i:3371071 original size:26 final size:24
Alignment explanation
Indices: 3371041--3371105 Score: 98
Period size: 24 Copynumber: 2.7 Consensus size: 24
3371031 TAGAGAGAGA
3371041 ATACATACATACATATACACACAT
1 ATACATACATACATATACACACAT
3371065 AT--ATACATACATATACACACACAT
1 ATACATACATACATAT--ACACACAT
3371089 ATACATACATACATATA
1 ATACATACATACATATA
3371106 TTTCTATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
22 12 0.32
24 13 0.35
26 12 0.32
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (24 bp):
ATACATACATACATATACACACAT
Found at i:3375297 original size:17 final size:17
Alignment explanation
Indices: 3375272--3375305 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3375262 AATGAGATAA
*
3375272 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
3375289 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
3375306 TGGGATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:3376025 original size:85 final size:82
Alignment explanation
Indices: 3375923--3376106 Score: 235
Period size: 85 Copynumber: 2.2 Consensus size: 82
3375913 AGATAATTCC
* *
3375923 TAAAATAACATCTTAAATCCAAATTAAAATACTTAA-AACTATTTAAACTAAAATACCTAAAACA
1 TAAAATAATATCCTAAATCCAAATTAAAATAC-TAACAACTATTTAAACTAAAATACCTAAAACA
*
3375987 AAGATAAAATAAAATACTATT
65 AAGATAAAAT---ATAATATT
** * * *
3376008 TAAAATAATATCCTAAATCCTTATTTAAATACTAACATCTATTTAAACTAAAATATCTAAAACAA
1 TAAAATAATATCCTAAATCCAAATTAAAATACTAACAACTATTTAAACTAAAATACCTAAAACAA
*
3376073 AGATAAAATATAATGTT
66 AGATAAAATATAATATT
*
3376090 TAAAATATTATCCTAAA
1 TAAAATAATATCCTAAA
3376107 ACTTGTGTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
82 22 0.25
84 3 0.03
85 63 0.72
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (82 bp):
TAAAATAATATCCTAAATCCAAATTAAAATACTAACAACTATTTAAACTAAAATACCTAAAACAA
AGATAAAATATAATATT
Found at i:3377083 original size:29 final size:25
Alignment explanation
Indices: 3377023--3377074 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
3377013 TTTTATTTTT
* *
3377023 ATTTTTTTGTTGTTCGAAACAGTGA
1 ATTTTTTTGTTGTTCAAAACAATGA
3377048 ATTTTTTCTGTTGTTCAAAACAATGA
1 ATTTTTT-TGTTGTTCAAAACAATGA
3377074 A
1 A
3377075 CAATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (25 bp):
ATTTTTTTGTTGTTCAAAACAATGA
Found at i:3378045 original size:14 final size:14
Alignment explanation
Indices: 3378026--3378052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3378016 AACTGCACTG
3378026 TTATTTTTTTACAA
1 TTATTTTTTTACAA
3378040 TTATTTTTTTACA
1 TTATTTTTTTACA
3378053 CTGCACTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTTTTTACAA
Found at i:3378256 original size:29 final size:28
Alignment explanation
Indices: 3378213--3378288 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 28
3378203 ATGTTCGAAC
* * *
3378213 TTTTCTGCACAGTTCGAACCAAGTCTATT
1 TTTTCTGCACTGTTCGAACCAAAT-TAGT
* *
3378242 TTTTATGCACTGTTCAAACCAAATTAGT
1 TTTTCTGCACTGTTCGAACCAAATTAGT
*
3378270 TTTTCTGCACTGTCCGAAC
1 TTTTCTGCACTGTTCGAAC
3378289 AGTGTATTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 19 0.49
29 20 0.51
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (28 bp):
TTTTCTGCACTGTTCGAACCAAATTAGT
Found at i:3378477 original size:13 final size:13
Alignment explanation
Indices: 3378459--3378535 Score: 66
Period size: 13 Copynumber: 5.6 Consensus size: 13
3378449 CGGGTACTTG
3378459 AAAAATAAAATAA
1 AAAAATAAAATAA
*
3378472 AAAAAT-AAATCAG
1 AAAAATAAAAT-AA
*
3378485 AAAAATAAAATTA
1 AAAAATAAAATAA
*
3378498 AAAATTAAAATTAA
1 AAAAATAAAA-TAA
*
3378512 ACAAACAGAAAATAA
1 A-AAA-ATAAAATAA
3378527 AAATAATAA
1 AAA-AATAA
3378536 TGGGTTGTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.08
13 22 0.44
14 12 0.24
15 8 0.16
16 4 0.08
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:3382514 original size:21 final size:21
Alignment explanation
Indices: 3382484--3382533 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3382474 GCTTTGGAAT
* **
3382484 TTTTCCTGGGATGCAATGAAC
1 TTTTCTTGGGATGCAACCAAC
*
3382505 TTTTCTTGGGATGTAACCAAC
1 TTTTCTTGGGATGCAACCAAC
3382526 TTTTCTTG
1 TTTTCTTG
3382534 TGAAATTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (21 bp):
TTTTCTTGGGATGCAACCAAC
Found at i:3384079 original size:17 final size:17
Alignment explanation
Indices: 3384054--3384087 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3384044 AATGTGATAA
*
3384054 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
3384071 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
3384088 TTGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:3384851 original size:85 final size:83
Alignment explanation
Indices: 3384717--3384887 Score: 229
Period size: 85 Copynumber: 2.0 Consensus size: 83
3384707 ATAACATATT
*
3384717 AAATCCTAATTAAAATACTTAAAACAATTTAAACTAAAATACCTTAAACAAAGATAAAATAAAAT
1 AAATCCTAATTAAAATACTTAAAACAATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAAT
3384782 ACTATTTAAAATAATATCC-A
66 --T-TTTAAAATAATATCCTA
* * * * *
3384802 AAATCCTAATTGAAATAC-TAACATATATTTAAACTAAAATATCTAAAACAAAGATAAAATATAA
1 AAATCCTAATTAAAATACTTAAAACA-ATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
*
3384866 TTTTTAAAATATTATCCTA
65 TTTTTAAAATAATATCCTA
3384885 AAA
1 AAA
3384888 CTTGAGTTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
82 14 0.18
83 5 0.06
84 5 0.06
85 53 0.69
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (83 bp):
AAATCCTAATTAAAATACTTAAAACAATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAAT
TTTTAAAATAATATCCTA
Found at i:3386222 original size:24 final size:24
Alignment explanation
Indices: 3386182--3386238 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
3386172 CATTTGGGAC
* *
3386182 ATTTCTATGTGGAACTTCGGTGCA
1 ATTTCTATGTCGAACTTCAGTGCA
*
3386206 ATTTCTATG-CGACACTTTAGTGCA
1 ATTTCTATGTCGA-ACTTCAGTGCA
*
3386230 ATTTATATG
1 ATTTCTATG
3386239 AGCTGTGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTTCTATGTCGAACTTCAGTGCA
Found at i:3389125 original size:973 final size:974
Alignment explanation
Indices: 3387447--3389387 Score: 3731
Period size: 973 Copynumber: 2.0 Consensus size: 974
3387437 TTTAAGGTTG
3387447 GAATCTGACCATGTTTCCATGGAGAAGAACTGAACAATTGGACTACATAGGATCTTTCTATAGTT
1 GAATCTGACCATGTTTCCATGGAGAAGAACTGAACAATTGGACTACATAGGATCTTTCTATAGTT
3387512 TTAGACCAAATTTAGAGTAATAATAGGAACTAACCCTTATGCTTTTGCCCGCGAGTATTAAAGAA
66 TTAGACCAAATTTAGAGTAATAATAGGAACTAACCCTTATGCTTTTGCCCGCGAGTATTAAAGAA
*
3387577 TCTTTTTGTAAGGGATGCTATATCAATTCTACTTTTTTTTTATGTAATTAAATATGTTTTCTTGC
131 TCTTTTTGTAAGGGATGATATATCAATTCTAC-TTTTTTTTATGTAATTAAATATGTTTTCTTGC
3387642 ATTTCTTAAGTGGAAATCATTTATACATTTTACATTCTCTATCATTTTTACATTATTTTTTACAT
195 ATTTCTTAAGTGGAAATCATTTATACATTTTACATTCTCTATCATTTTTACATTATTTTTTACAT
3387707 TTTGTATTCTTTCATTCATTCCACAACACATTTATTTTTCGTCCCAAATGTATATATTCATTCCA
260 TTTGTATTCTTTCATTCATTCCACAACACATTTATTTTTCGTCCCAAATGTATATATTCATTCCA
3387772 AATTTTCTTTACATGTGTCTCAATCATTAATAGTATGAATGTTTTTGAATTTAATTATAAATAAA
325 AATTTTCTTTACATGTGTCTCAATCATTAATAGTATGAATGTTTTTGAATTTAATTATAAATAAA
3387837 TTTTTAGCGACCCATGTGACTAAAAGAAGTCGATGAGTGTGAGAATGAGGTGGAATATGATGTTC
390 TTTTTAGCGACCCATGTGACTAAAAGAAGTCGATGAGTGTGAGAATGAGGTGGAATATGATGTTC
*
3387902 CTAATGAATTATTAAGGTTGGTGGGAAAGGTGGACAAACAAATCTTACCTCACAAAGAAGAAGTT
455 CTAACGAATTATTAAGGTTGGTGGGAAAGGTGGACAAACAAATCTTACCTCACAAAGAAGAAGTT
* *
3387967 GAGATTTTGAATTTGGGGATGGATGAAGAAAGAAGAGGGGTGAATATTGCCATTACTTTGTCACA
520 GAGATTCTAAATTTGGGGATGGATGAAGAAAGAAGAGGGGTGAATATTGCCATTACTTTGTCACA
*
3388032 TGAAACAAGACAAGAGTTGACAGAGTTGTTTCAAGATTTCAAAGACATCTTTTCCTTGTCTTATC
585 TGAAACAAGACAAGAGATGACAGAGTTGTTTCAAGATTTCAAAGACATCTTTTCCTTGTCTTATC
3388097 AAGATATGCTAGGATTGAATACAAATATAGTAGTGCACAAGTTTCTCATAAGGCTTGATCGTAAA
650 AAGATATGCTAGGATTGAATACAAATATAGTAGTGCACAAGTTTCTCATAAGGCTTGATCGTAAA
*
3388162 CCAATTTGGCAAACACTGAAAAGAATGAGGCCAAAATGTTGTTACAGAGGAAGAAGATTGACACA
715 CCAATTTGGCAAACACTGAAAAGAATGAGGCAAAAATGTTGTTACAGAGGAAGAAGATTGACACA
3388227 GGATTCCTCTAGGCTGCCAATTATTTAGAGTAGGTAGTCAATATAGTCCATGTGCCAAAGAGATA
780 GGATTCCTCTAGGCTGCCAATTATTTAGAGTAGGTAGTCAATATAGTCCATGTGCCAAAGAGATA
* *
3388292 TTGAGAAGCGAAATTGTGTATAGACTACAAATATCTCAATAGAGCAAGCCCAAAAGACAAATTTT
845 TTGAGAAGCAAAATTGTGTATAGACTACAAAGATCTCAATAGAGCAAGCCCAAAAGACAAATTTT
3388357 CTCTACCACATATTGATACACTAGTGGACAACACTGCGGGTCATTCTTGATTCTCTTTCGTAGAT
910 CTCTACCACATATTGATACACTAGTGGACAACACTGCGGGTCATTCTTGATTCTCTTTCGTAGAT
*
3388422 GAATCTGACCGTGTTTCCATGGAGAAGAACTGAACAATTGGACTACATAGGATCTTTCTATAGTT
1 GAATCTGACCATGTTTCCATGGAGAAGAACTGAACAATTGGACTACATAGGATCTTTCTATAGTT
*
3388487 TTAGACCAAATTTAGAGTAATAATAGGAACTAACCCTTATGCTTTTGCCCGTGAGTATTAAAGAA
66 TTAGACCAAATTTAGAGTAATAATAGGAACTAACCCTTATGCTTTTGCCCGCGAGTATTAAAGAA
3388552 TCTTTTTGTAAGGGATGATATATCAATTCTAC-TTTTTTTATGTAATTAAATATGTTTTCTTGCA
131 TCTTTTTGTAAGGGATGATATATCAATTCTACTTTTTTTTATGTAATTAAATATGTTTTCTTGCA
3388616 TTTCTTAAGTGGAAATCATTTATACATTTTACATTCTCTATCATTTTTACATTATTTTTTACATT
196 TTTCTTAAGTGGAAATCATTTATACATTTTACATTCTCTATCATTTTTACATTATTTTTTACATT
3388681 TTGTATTCTTTCATTCATTCCACAACACATTTATTTTTCGTCCCAAATGTATATATTCATTCCAA
261 TTGTATTCTTTCATTCATTCCACAACACATTTATTTTTCGTCCCAAATGTATATATTCATTCCAA
3388746 ATTTTCTTTACATGTGTCTCAATCATTAATAGTATGAATGTTTTTGAATTTAATTATAAATAAAT
326 ATTTTCTTTACATGTGTCTCAATCATTAATAGTATGAATGTTTTTGAATTTAATTATAAATAAAT
*
3388811 TTTTAGCGACCCATGTGACTAATAGAAGTCGATGAGTGTGAGAATGAGGTGGAATATGATGTTCC
391 TTTTAGCGACCCATGTGACTAAAAGAAGTCGATGAGTGTGAGAATGAGGTGGAATATGATGTTCC
*
3388876 TAACGAATTATTAAGGTTGGTGGGAAAGGTGGACAAACAAATCTTACCTCACAACGAAGAAGTTG
456 TAACGAATTATTAAGGTTGGTGGGAAAGGTGGACAAACAAATCTTACCTCACAAAGAAGAAGTTG
3388941 AGATTCTAAATTTGGGGATGGATGAAGAAAGAAGAGGGGTGAATATTGCCATTACTTTGTCACAT
521 AGATTCTAAATTTGGGGATGGATGAAGAAAGAAGAGGGGTGAATATTGCCATTACTTTGTCACAT
3389006 GAAACAAGACAAGAGATGACAGAGTTGTTTCAAGATTTCAAAGACATCTTTTCCTTGTCTTATCA
586 GAAACAAGACAAGAGATGACAGAGTTGTTTCAAGATTTCAAAGACATCTTTTCCTTGTCTTATCA
3389071 AGATATGCTAGGATTGAATACAAATATAGTAGTGCACAAGTTTCTCATAAGGCTTGATCGTAAAC
651 AGATATGCTAGGATTGAATACAAATATAGTAGTGCACAAGTTTCTCATAAGGCTTGATCGTAAAC
* *
3389136 CAATTTGGCAAACACTGAAAAGAATGAGGCAAAAATGTTGTTACAGAGGAAGCAGATTGACACGG
716 CAATTTGGCAAACACTGAAAAGAATGAGGCAAAAATGTTGTTACAGAGGAAGAAGATTGACACAG
*
3389201 GATTCCTCTAGGCTGCCAATTATTTAGAGTAGGTAGTCAATATAGTCCATGTTCCAAAGAGATAT
781 GATTCCTCTAGGCTGCCAATTATTTAGAGTAGGTAGTCAATATAGTCCATGTGCCAAAGAGATAT
3389266 TGAGAAGCAAAATTGTGTATAGACTACAAAGATCTCAATAGAGCAAGCCCAAAAGACAAATTTTC
846 TGAGAAGCAAAATTGTGTATAGACTACAAAGATCTCAATAGAGCAAGCCCAAAAGACAAATTTTC
3389331 TCTACCACATATTGATACACTAGTGGACAACACTGCGGGTCATTCTTGATTCTCTTT
911 TCTACCACATATTGATACACTAGTGGACAACACTGCGGGTCATTCTTGATTCTCTTT
3389388 ATTAAATGGT
Statistics
Matches: 951, Mismatches: 15, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
973 792 0.83
975 159 0.17
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (974 bp):
GAATCTGACCATGTTTCCATGGAGAAGAACTGAACAATTGGACTACATAGGATCTTTCTATAGTT
TTAGACCAAATTTAGAGTAATAATAGGAACTAACCCTTATGCTTTTGCCCGCGAGTATTAAAGAA
TCTTTTTGTAAGGGATGATATATCAATTCTACTTTTTTTTATGTAATTAAATATGTTTTCTTGCA
TTTCTTAAGTGGAAATCATTTATACATTTTACATTCTCTATCATTTTTACATTATTTTTTACATT
TTGTATTCTTTCATTCATTCCACAACACATTTATTTTTCGTCCCAAATGTATATATTCATTCCAA
ATTTTCTTTACATGTGTCTCAATCATTAATAGTATGAATGTTTTTGAATTTAATTATAAATAAAT
TTTTAGCGACCCATGTGACTAAAAGAAGTCGATGAGTGTGAGAATGAGGTGGAATATGATGTTCC
TAACGAATTATTAAGGTTGGTGGGAAAGGTGGACAAACAAATCTTACCTCACAAAGAAGAAGTTG
AGATTCTAAATTTGGGGATGGATGAAGAAAGAAGAGGGGTGAATATTGCCATTACTTTGTCACAT
GAAACAAGACAAGAGATGACAGAGTTGTTTCAAGATTTCAAAGACATCTTTTCCTTGTCTTATCA
AGATATGCTAGGATTGAATACAAATATAGTAGTGCACAAGTTTCTCATAAGGCTTGATCGTAAAC
CAATTTGGCAAACACTGAAAAGAATGAGGCAAAAATGTTGTTACAGAGGAAGAAGATTGACACAG
GATTCCTCTAGGCTGCCAATTATTTAGAGTAGGTAGTCAATATAGTCCATGTGCCAAAGAGATAT
TGAGAAGCAAAATTGTGTATAGACTACAAAGATCTCAATAGAGCAAGCCCAAAAGACAAATTTTC
TCTACCACATATTGATACACTAGTGGACAACACTGCGGGTCATTCTTGATTCTCTTTCGTAGAT
Found at i:3391202 original size:15 final size:14
Alignment explanation
Indices: 3391165--3391225 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3391155 TTGAAAAAAT
3391165 AAAAAAGAAAA---
1 AAAAAAGAAAAGGG
3391176 AAAAAAGAAAAGGG
1 AAAAAAGAAAAGGG
3391190 AAAAAAGATAAA-GG
1 AAAAAAGA-AAAGGG
** *
3391204 AGGAAA-AAAAGAG
1 AAAAAAGAAAAGGG
3391217 AAAAAAGAA
1 AAAAAAGAA
3391226 TAGAAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 11 0.28
12 3 0.08
13 6 0.15
14 16 0.41
15 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAGGG
Found at i:3391237 original size:22 final size:22
Alignment explanation
Indices: 3391206--3391247 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3391196 GATAAAGGAG
3391206 GAAAAAAAGAGAAAA-AAGAATA
1 GAAAAAAAGA-AAAAGAAGAATA
*
3391228 GAAAATAAGAAAAAGAAGAA
1 GAAAAAAAGAAAAAGAAGAA
3391248 ATAAAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (22 bp):
GAAAAAAAGAAAAAGAAGAATA
Found at i:3397600 original size:256 final size:255
Alignment explanation
Indices: 3397154--3397614 Score: 744
Period size: 256 Copynumber: 1.8 Consensus size: 255
3397144 AACACAACCC
* * * *
3397154 TGAGCCTCAGTCATGGAGAACAACGTGTTAGTAGACGAATCCTCGGACAGGGAGGAAGTCGAATG
1 TGAGCCTCAGTCATGGAGAACAACATGTTAGTAGACGAACCCTCAGACAGGGAGGAAGTCAAATG
* * * *
3397219 TAACTCAGAGTCTCAGTCATGGATGACACCCCGTTAGTAGGTGAACCTTTAGCCATGGAGAAAGC
66 TAACTCAGAGCCTCAGTCATGAACGACACCCCGTTAGTAGGTGAACCTTCAGCCATGGAGAAAGC
*
3397284 CAAACGTCACTTTGAACCTCAGTCATAGAGGATACCCAGTTAGTAGATGAACCCTCAGCCATGGA
131 CAAACGTCACTTTGAACCTCAGTCATAGAGGACACCCAGTTAGTAGATGAACCCTCAGCCATGGA
3397349 GGAAGTCAAACACAGTCCTGAGCCTTAGCCATGGAGGAAGTCAAACACCAAACACAGGCT
196 GGAAGTCAAACACAGTCCTGAGCCTTAGCCATGGAGGAAGTCAAACACCAAACACAGGCT
* * *
3397409 TGAGCCTCAGT-ATTGTAGGACAACATGTTAGTAGACGAACCCTCAGACATGGAGGAAGTCAAAT
1 TGAGCCTCAGTCA-TGGAGAACAACATGTTAGTAGACGAACCCTCAGACAGGGAGGAAGTCAAAT
*
3397473 GTAACTCAGAGCCTCAGTCATGAACGACACCCACGTTAGTAGGTGAACCTTCAGCCATGGAGGAA
65 GTAACTCAGAGCCTCAGTCATGAACGACACCC-CGTTAGTAGGTGAACCTTCAGCCATGGAGAAA
* * * *
3397538 GTCAAACGTCACTTTGAACCTTATTCATGGAGGACACCCAGTTAGTAGATGAACCCTCAGCCATG
129 GCCAAACGTCACTTTGAACCTCAGTCATAGAGGACACCCAGTTAGTAGATGAACCCTCAGCCATG
3397603 GAGGAAGTCAAA
194 GAGGAAGTCAAA
3397615 AGCAATCTCG
Statistics
Matches: 187, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
254 1 0.01
255 84 0.45
256 102 0.55
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (255 bp):
TGAGCCTCAGTCATGGAGAACAACATGTTAGTAGACGAACCCTCAGACAGGGAGGAAGTCAAATG
TAACTCAGAGCCTCAGTCATGAACGACACCCCGTTAGTAGGTGAACCTTCAGCCATGGAGAAAGC
CAAACGTCACTTTGAACCTCAGTCATAGAGGACACCCAGTTAGTAGATGAACCCTCAGCCATGGA
GGAAGTCAAACACAGTCCTGAGCCTTAGCCATGGAGGAAGTCAAACACCAAACACAGGCT
Found at i:3397608 original size:71 final size:70
Alignment explanation
Indices: 3397435--3398177 Score: 495
Period size: 71 Copynumber: 10.5 Consensus size: 70
3397425 AGGACAACAT
* * * * * *
3397435 GTTAGTAGACGAACCCTCAGACATGGAGGAAGTCAAATGTAACTCAGAGCCTCAGTCAT-GAACG
1 GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACG-CACTCTGAGCCTCAATCATAG-AGG
3397499 ACACCCA
64 ACACCCA
** * * * * * *
3397506 CGTTAGTAGGTGAACCTTCAGCCATGGAGGAAGTCAAACGTCACTTTGAACCTTATTCATGGAGG
1 -GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACG-CACTCTGAGCCTCAATCATAGAGG
3397571 ACACCCA
64 ACACCCA
* * * * * *
3397578 GTTAGTAGATGAACCCTCAGCCATGGAGGAAGTCAAAAGCAATCTCGAGCCTCAGTCATGGAAGA
1 GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACGCACTCT-GAGCCTCAATCATAGAGGA
*
3397643 CACCTA
65 CACCCA
* * * * ** * ** *
3397649 GTTAGTAGATGAACCCTCAACCAT-TAGGGAAGTCGAACAAAACCCCAAGCCTTAATCATAGAGG
1 GTTAGTAGACGAACCCTCAGCCATGGA-GGAAGTCAAAC-GCACTCTGAGCCTCAATCATAGAGG
3397713 ACACCTC-
64 ACACC-CA
* * * * * * * *
3397720 GTTAGTAAATGGACCCTCAGCTATGGAGGAAGTTAAACGCAATCTCGAGCCTCATTCATGGAGGA
1 GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACGCACTCT-GAGCCTCAATCATAGAGGA
3397785 CACCTCA
65 CACC-CA
* * ** * * * *
3397792 -TTAATAGACGAACCATC-GACCATGGAGGAAGTTGAACGCAACCCTAAGCCTCAATCATGGATG
1 GTTAGTAGACGAACCCTCAG-CCATGGAGGAAGTCAAACGC-ACTCTGAGCCTCAATCATAGAGG
3397855 ACACCTC-
64 ACACC-CA
* * * * * * *
3397862 GCTAGTAGATGAACCCTCAACCTTGGAGGAAGTCGAACGCAATCCAGAGCCTCAATCATAGAGGA
1 GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACGCACT-CTGAGCCTCAATCATAGAGGA
*
3397927 CACCCC
65 CACCCA
* * * * * * * *
3397933 GTTACTAGACGAACCCTTAGCCTTGGAGAAAGTCGAGCGCAATCTTGAGCCTCAGTCATAGAGGA
1 GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACGCACTC-TGAGCCTCAATCATAGAGGA
*
3397998 CACCCC
65 CACCCA
* * * * * * *
3398004 GTTACTAGACGGACCCTCAGCCATGAAGGAAGTTAAA--CA--C-AACCCTTAATCATAGAGGAC
1 GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACGCACTCTGAGCCTCAATCATAGAGGAC
3398064 ACCCCA
66 A-CCCA
* * * * * *
3398070 -TCAGTA-AGCGAACCCTCAGCCATGGAGGAAGCCGAACGTAACCCTGAGCCTCAATCATAGAGA
1 GTTAGTAGA-CGAACCCTCAGCCATGGAGGAAGTCAAACG-CACTCTGAGCCTCAATCATAGAGG
3398133 ACACCCA
64 ACACCCA
* * * * *
3398140 GTTAGTAGACAAACCCTTATCCATAGAGGAAGCCAAAC
1 GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAAC
3398178 ACAACCCCGA
Statistics
Matches: 528, Mismatches: 118, Indels: 51
0.76 0.17 0.07
Matches are distributed among these distances:
64 1 0.00
65 44 0.08
66 3 0.01
67 1 0.00
68 1 0.00
69 2 0.00
70 16 0.03
71 395 0.75
72 64 0.12
73 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (70 bp):
GTTAGTAGACGAACCCTCAGCCATGGAGGAAGTCAAACGCACTCTGAGCCTCAATCATAGAGGAC
ACCCA
Found at i:3397788 original size:213 final size:213
Alignment explanation
Indices: 3397517--3398049 Score: 578
Period size: 213 Copynumber: 2.5 Consensus size: 213
3397507 GTTAGTAGGT
* * * * *
3397517 GAACCTTCAGCCATGGAGGAAGTCAAACGTCACT-TTGAACCTTATTCATGGAGGACACCCAGTT
1 GAACCCTCAGCTATGGAGGAAGTCAAACG-CAATCTTGAGCCTCATTCATGGAGGACACCCAGTT
* * * * *
3397581 AGTAGATGAACCCTCAGCCATGGAGGAAGTCAAAAGCAA-TCTCGAGCCTCAGTCATGGAAGACA
65 AATAGACGAACCCTCAGCCATGGAGGAAGTCAAAAGCAACCCT-AAGCCTCAATCATGGAAGACA
* *
3397645 CCTAGTTAGTAGATGAACCCTCAACCATTAG-GGAAGTCGAACAAAACCCCA-AGCCTTAATCAT
129 CCTAGCTAGTAGATGAACCCTCAACC-TTAGAGGAAGTCGAACAAAA-CCCAGAGCCTCAATCAT
* * *
3397708 AGAGGACACCTCGTTAGTAAAT
192 AGAGGACACCCCGTTACTAAAC
* * *
3397730 GGACCCTCAGCTATGGAGGAAGTTAAACGCAATCTCGAGCCTCATTCATGGAGGACACCTCA-TT
1 GAACCCTCAGCTATGGAGGAAGTCAAACGCAATCTTGAGCCTCATTCATGGAGGACACC-CAGTT
* ** * *
3397794 AATAGACGAACCATC-GACCATGGAGGAAGTTGAACGCAACCCTAAGCCTCAATCATGGATGACA
65 AATAGACGAACCCTCAG-CCATGGAGGAAGTCAAAAGCAACCCTAAGCCTCAATCATGGAAGACA
* * ** *
3397858 CCTCGCTAGTAGATGAACCCTCAACCTTGGAGGAAGTCGAACGCAATCCAGAGCCTCAATCATAG
129 CCTAGCTAGTAGATGAACCCTCAACCTTAGAGGAAGTCGAACAAAACCCAGAGCCTCAATCATAG
*
3397923 AGGACACCCCGTTACTAGAC
194 AGGACACCCCGTTACTAAAC
* * * * * * *
3397943 GAACCCTTAGCCT-TGGAGAAAGTCGAGCGCAATCTTGAGCCTCAGTCATAGAGGACACCCCGTT
1 GAACCCTCAG-CTATGGAGGAAGTCAAACGCAATCTTGAGCCTCATTCATGGAGGACACCCAGTT
* * * *
3398007 ACTAGACGGACCCTCAGCCATGAAGGAAGTTAAACA-CAACCCT
65 AATAGACGAACCCTCAGCCATGGAGGAAGTCAAA-AGCAACCCT
3398050 TAATCATAGA
Statistics
Matches: 265, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
212 11 0.04
213 247 0.93
214 7 0.03
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.19
Consensus pattern (213 bp):
GAACCCTCAGCTATGGAGGAAGTCAAACGCAATCTTGAGCCTCATTCATGGAGGACACCCAGTTA
ATAGACGAACCCTCAGCCATGGAGGAAGTCAAAAGCAACCCTAAGCCTCAATCATGGAAGACACC
TAGCTAGTAGATGAACCCTCAACCTTAGAGGAAGTCGAACAAAACCCAGAGCCTCAATCATAGAG
GACACCCCGTTACTAAAC
Found at i:3398118 original size:136 final size:136
Alignment explanation
Indices: 3397915--3398184 Score: 319
Period size: 136 Copynumber: 2.0 Consensus size: 136
3397905 CCAGAGCCTC
* * * * * * * *
3397915 AATCATAGAGGACACCCCGTTACTAGACGAACCCTTAGCCTTGGAGAAAGTCGAGCGCAATCTTG
1 AATCATAGAGGACACCCCATCACTAGACGAACCCTCAGCCATGGAGAAAGCCGAACGCAACCCTG
* * * ** **
3397980 AGCCTCAGTCATAGAGGACACCCCGTTACTAGACGGACCCTCAGCCAT-GAAGGAAGTTAAACAC
66 AGCCTCAATCATAGAGAACACCCAGTTACTAGACAAACCCTCAGCCATAG-AGGAAGCCAAACAC
3398044 AACCCTT
130 AACCCTT
* * *
3398051 AATCATAGAGGACACCCCATCAGTA-AGCGAACCCTCAGCCATGGAGGAAGCCGAACGTAACCCT
1 AATCATAGAGGACACCCCATCACTAGA-CGAACCCTCAGCCATGGAGAAAGCCGAACGCAACCCT
* * *
3398115 GAGCCTCAATCATAGAGAACACCCAGTTAGTAGACAAACCCTTATCCATAGAGGAAGCCAAACAC
65 GAGCCTCAATCATAGAGAACACCCAGTTACTAGACAAACCCTCAGCCATAGAGGAAGCCAAACAC
3398180 AACCC
130 AACCC
3398185 CGAGCTTAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
135 1 0.01
136 109 0.98
137 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (136 bp):
AATCATAGAGGACACCCCATCACTAGACGAACCCTCAGCCATGGAGAAAGCCGAACGCAACCCTG
AGCCTCAATCATAGAGAACACCCAGTTACTAGACAAACCCTCAGCCATAGAGGAAGCCAAACACA
ACCCTT
Found at i:3399080 original size:359 final size:354
Alignment explanation
Indices: 3398392--3399106 Score: 1353
Period size: 359 Copynumber: 2.0 Consensus size: 354
3398382 CCCTCAGCCA
3398392 TGGAGTAAGTTGAACGCAACCCCAAGCCTTAGCCATGAGTGACACCCCGCTAGTAGGCAAACTAT
1 TGGAGTAAGTTGAACGCAACCCCAAGCCTTAGCCATGAGTGACACCCCGCTAGTAGGCAAACTAT
3398457 TATCCATGAAAGAAGCCGAATGCACCCTGAGACTCAGTCATAAAGGATACCCACTAATAGATGAA
66 TATCCATGAAAGAAGCCGAATGCACCCTGAGACTCAGTCATAAAGGATACCCACTAATAGATGAA
3398522 CCCTCAACCATAGAGAAAGTCAAAACGTAACCCTGAGCCTTAATCATAAAGGATGCCTATAGTAG
131 CCCTCAACCATAGAGAAAGTCAAAACGTAACCCTGAGCCTTAATCATAAAGGATGCCTATAGTAG
3398587 GCGAACCCTTAGCAGGGAGGAGCCGAACACAAAATTAAAAGCCTCAATCATGAGGATATCAAGAT
196 GCGAACCCTTAGCAGGGAGGAGCCGAACACAAAATTAAAAGCCTCAATCATGAGGATATCAAGAT
3398652 TCAAAAAATGAACCCCAGTCGTGCAGGACATTAGATTAAACTTAGATTGGATATCAAACGAAAAC
261 TCAAAAAATGAACCCCAGTCGTGCAGGACATTAGATTAAACTTAGATTGGATATCAAACGAAAAC
3398717 TTATATCTTTTTCGTCTTTGTCCAATTCT
326 TTATATCTTTTTCGTCTTTGTCCAATTCT
3398746 TGGAGTAAGTTGAACGCAACCCCAAGCCTTAGCCATGAGTGACACCCCGCTAGTAGGCAAACTAT
1 TGGAGTAAGTTGAACGCAACCCCAAGCCTTAGCCATGAGTGACACCCCGCTAGTAGGCAAACTAT
3398811 TATCCATGAAAGAAGCCGAATGCAACCCTGAGACTCAGTCATAAAGGATACCCCACTAATAGATG
66 TATCCATGAAAGAAGCCGAATGC-ACCCTGAGACTCAGTCATAAAGGATA-CCCACTAATAGATG
3398876 AACCCTCAACCATAGAGAAAGTC-AAACGTAACCCTGAGCCTTAATCATAAAGGATGCCCTATTA
129 AACCCTCAACCATAGAGAAAGTCAAAACGTAACCCTGAGCCTTAATCATAAAGGATG-CCTA-TA
3398940 GTAGGCGAACCCTTAGCAGCGGAGGAAGCCGAACACAAAATTAAAAGCCTCAATCATGGAGGATA
192 GTAGGCGAACCCTTAGCAG-GGAGG-AGCCGAACACAAAATTAAAAGCCTCAATCAT-GAGGATA
3399005 TCAAGATTCAAAAAATGAA-CCCAGTCGTGCAGGACATTAGATTAAACTTAGATTGGATATCAAA
254 TCAAGATTCAAAAAATGAACCCCAGTCGTGCAGGACATTAGATTAAACTTAGATTGGATATCAAA
3399069 CGAAAACTTATATCTTTTTCGTCTTTGTCCAATTCT
319 CGAAAACTTATATCTTTTTCGTCTTTGTCCAATTCT
3399105 TG
1 TG
3399107 TGACACGACA
Statistics
Matches: 354, Mismatches: 0, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
354 88 0.25
355 59 0.17
356 41 0.12
357 21 0.06
358 5 0.01
359 114 0.32
360 26 0.07
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (354 bp):
TGGAGTAAGTTGAACGCAACCCCAAGCCTTAGCCATGAGTGACACCCCGCTAGTAGGCAAACTAT
TATCCATGAAAGAAGCCGAATGCACCCTGAGACTCAGTCATAAAGGATACCCACTAATAGATGAA
CCCTCAACCATAGAGAAAGTCAAAACGTAACCCTGAGCCTTAATCATAAAGGATGCCTATAGTAG
GCGAACCCTTAGCAGGGAGGAGCCGAACACAAAATTAAAAGCCTCAATCATGAGGATATCAAGAT
TCAAAAAATGAACCCCAGTCGTGCAGGACATTAGATTAAACTTAGATTGGATATCAAACGAAAAC
TTATATCTTTTTCGTCTTTGTCCAATTCT
Found at i:3399192 original size:10 final size:10
Alignment explanation
Indices: 3399159--3399203 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
3399149 TTTCATTTGG
3399159 ATTATTAATA
1 ATTATTAATA
*
3399169 A-TAATAAT-
1 ATTATTAATA
*
3399177 ATTATTATTA
1 ATTATTAATA
3399187 ATTATTAATA
1 ATTATTAATA
3399197 ATTATTA
1 ATTATTA
3399204 GATATCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 1 0.03
9 11 0.38
10 17 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTATTAATA
Found at i:3400783 original size:2 final size:2
Alignment explanation
Indices: 3400776--3400818 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3400766 CTAAATGTGT
* *
3400776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3400818 T
1 T
3400819 GTTTCTGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3402813 original size:10 final size:10
Alignment explanation
Indices: 3402787--3402821 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
3402777 CTTTTAAAAT
3402787 TTTAATTTTTAA
1 TTTAA-TTTT-A
3402799 TTTAATTTTA
1 TTTAATTTTA
3402809 TTTAATTTTA
1 TTTAATTTTA
3402819 TTT
1 TTT
3402822 TTTCCCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.61
11 4 0.17
12 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:3403448 original size:2 final size:2
Alignment explanation
Indices: 3403441--3403478 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3403431 TTGATTTTTA
3403441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3403479 ATCATGAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3411346 original size:41 final size:41
Alignment explanation
Indices: 3411289--3411370 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3411279 ATCGAATTCA
3411289 CTTTACTAGAGTGTATGTGAGTCACTATGCTCAGTTAAAAG
1 CTTTACTAGAGTGTATGTGAGTCACTATGCTCAGTTAAAAG
3411330 CTTTACTAGAGTGTATGTGAGTCACTATGCTCAGTTAAAAG
1 CTTTACTAGAGTGTATGTGAGTCACTATGCTCAGTTAAAAG
3411371 TATGAAGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (41 bp):
CTTTACTAGAGTGTATGTGAGTCACTATGCTCAGTTAAAAG
Found at i:3414753 original size:14 final size:16
Alignment explanation
Indices: 3414715--3414754 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
3414705 AAATTTTAGT
3414715 ACTA-TAATTTCTACC
1 ACTATTAATTTCTACC
*
3414730 ACTTTTAATTTCTA-C
1 ACTATTAATTTCTACC
3414745 AC-ATTAATTT
1 ACTATTAATTT
3414755 TCAGCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 9 0.41
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (16 bp):
ACTATTAATTTCTACC
Found at i:3415644 original size:32 final size:31
Alignment explanation
Indices: 3415580--3415703 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
3415570 TTGTAAAAAG
* * *
3415580 ATTTATAAACATTTATTCAAATAGAAATAAT
1 ATTTACAAACACTTGTTCAAATAGAAATAAT
*
3415611 ATTTACAAACACTTGTTCAAATTTGAAATAAT
1 ATTTACAAACACTTGTTCAAA-TAGAAATAAT
3415643 ATTTACAAACACTTGTTCAAATAGAAATAAT
1 ATTTACAAACACTTGTTCAAATAGAAATAAT
*
3415674 ATTTACAAACACTCGTTCAAATAGAAATAA
1 ATTTACAAACACTTGTTCAAATAGAAATAA
3415704 GAGTAAACTA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 56 0.65
32 30 0.35
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (31 bp):
ATTTACAAACACTTGTTCAAATAGAAATAAT
Found at i:3415679 original size:63 final size:62
Alignment explanation
Indices: 3415580--3415703 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 62
3415570 TTGTAAAAAG
* * * *
3415580 ATTTATAAACATTTATTCAAATAGAAATAATATTTACAAACACTTGTTCAAATTTGAAATAAT
1 ATTTACAAACACTTATTCAAATAGAAATAATATTTACAAACACTCGTTCAAA-TAGAAATAAT
*
3415643 ATTTACAAACACTTGTTCAAATAGAAATAATATTTACAAACACTCGTTCAAATAGAAATAA
1 ATTTACAAACACTTATTCAAATAGAAATAATATTTACAAACACTCGTTCAAATAGAAATAA
3415704 GAGTAAACTA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 8 0.14
63 48 0.86
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (62 bp):
ATTTACAAACACTTATTCAAATAGAAATAATATTTACAAACACTCGTTCAAATAGAAATAAT
Found at i:3417231 original size:31 final size:31
Alignment explanation
Indices: 3417193--3417263 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
3417183 TAATTTACTC
*
3417193 TAGAAATAGTATATGCAAACACTCGTTCAAA
1 TAGAAATAGTATATGCAAACACTCATTCAAA
* * *
3417224 TAGAAATAATATTTGCAAACATTCATTCAAA
1 TAGAAATAGTATATGCAAACACTCATTCAAA
*
3417255 TATAAATAG
1 TAGAAATAG
3417264 GATTTACATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (31 bp):
TAGAAATAGTATATGCAAACACTCATTCAAA
Found at i:3421159 original size:16 final size:17
Alignment explanation
Indices: 3421116--3421162 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
3421106 AAATGTATTC
* *
3421116 ACATTTTGTTATATATAT
1 ACATTATGTTTTAT-TAT
3421134 ACATTATGTTTTATTAT
1 ACATTATGTTTTATTAT
3421151 ACA-TATGTTTTA
1 ACATTATGTTTTA
3421163 GTATTGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 12 0.44
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
ACATTATGTTTTATTAT
Found at i:3423147 original size:23 final size:23
Alignment explanation
Indices: 3423117--3423181 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
3423107 TGCACTTATA
3423117 ACAAGGCATGGGAAGTTGGCATC
1 ACAAGGCATGGGAAGTTGGCATC
3423140 ACAAGGCATGGGAAGTTGGCATC
1 ACAAGGCATGGGAAGTTGGCATC
*
3423163 GCAAGGCATGGGAAGTTGG
1 ACAAGGCATGGGAAGTTGG
3423182 TTTGCAAGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.38, T:0.17
Consensus pattern (23 bp):
ACAAGGCATGGGAAGTTGGCATC
Found at i:3423265 original size:41 final size:40
Alignment explanation
Indices: 3423215--3423316 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 40
3423205 ATATTTCGGG
*
3423215 CATGCTGAAGAC-ATGTAAAAAGCATGGAGAT-TTCACCATGC
1 CATGTTGAAGACGA-GTAAAAAGCATGGAG-TCTTCACCA-GC
* ** *
3423256 TATGTTGAAGACGAGTGGAAAGCGTGGAGTCTTCACCAGC
1 CATGTTGAAGACGAGTAAAAAGCATGGAGTCTTCACCAGC
* *
3423296 CATGTTGAAGACTAGTGAAAA
1 CATGTTGAAGACGAGTAAAAA
3423317 TAAAATGAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 21 0.41
41 29 0.57
42 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (40 bp):
CATGTTGAAGACGAGTAAAAAGCATGGAGTCTTCACCAGC
Found at i:3423595 original size:12 final size:12
Alignment explanation
Indices: 3423578--3423602 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3423568 ACAAAGCACC
3423578 ATTTGGTGCCTA
1 ATTTGGTGCCTA
3423590 ATTTGGTGCCTA
1 ATTTGGTGCCTA
3423602 A
1 A
3423603 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:3429248 original size:96 final size:96
Alignment explanation
Indices: 3429084--3429275 Score: 357
Period size: 96 Copynumber: 2.0 Consensus size: 96
3429074 TGTTTATTTT
* * *
3429084 GTTATTGATAAGTACATCTGGTATCCTGTATAGTTTCTCCATCTGTGTCTCATTCTTATTTTTTG
1 GTTATTGATAAGTACATATGATATCCTGTATAGTTTCTCCATCTGTGTCTCATTCTTATTTGTTG
3429149 TTGTCTAATATTTGTCATCCTTTTCTTCAGA
66 TTGTCTAATATTTGTCATCCTTTTCTTCAGA
3429180 GTTATTGATAAGTACATATGATATCCTGTATAGTTTCTCCATCTGTGTCTCATTCTTATTTGTTG
1 GTTATTGATAAGTACATATGATATCCTGTATAGTTTCTCCATCTGTGTCTCATTCTTATTTGTTG
3429245 TTGTCTAATATTTGTCATCCTTTTCTTCAGA
66 TTGTCTAATATTTGTCATCCTTTTCTTCAGA
3429276 TTGATTTTCT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (96 bp):
GTTATTGATAAGTACATATGATATCCTGTATAGTTTCTCCATCTGTGTCTCATTCTTATTTGTTG
TTGTCTAATATTTGTCATCCTTTTCTTCAGA
Found at i:3432534 original size:13 final size:13
Alignment explanation
Indices: 3432513--3432590 Score: 120
Period size: 13 Copynumber: 6.0 Consensus size: 13
3432503 AATGACGCGC
*
3432513 AATGAGCGTCATA
1 AATGCGCGTCATA
*
3432526 AATGTGCGTCATA
1 AATGCGCGTCATA
3432539 AATGCGCGTCATA
1 AATGCGCGTCATA
*
3432552 AATGCGCATCATA
1 AATGCGCGTCATA
*
3432565 AATGCGTGTCATA
1 AATGCGCGTCATA
3432578 AATGCGCGTCATA
1 AATGCGCGTCATA
3432591 GATTTATGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:3432537 original size:85 final size:85
Alignment explanation
Indices: 3432376--3432541 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 85
3432366 ATAAAATCAC
3432376 GACACAAGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGCAAGTCATA
1 GACACAAGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGCAAGTCATA
* *
3432441 CATACGTGTCATAAATTTAT
66 AATACGCGTCATAAATTTAT
* *
3432461 GACACACA-AATGTGTGTCAT-TTTAATTT-ATGACG-GTGGCTTCAATGACGCGCAATG-AGCG
1 GACACA-AGAATGTGTGTCATCTTT--TTTAATGACGTGT-GCTTCAATGACACGCAATGCA-AG
**
3432521 TCATAAATGTGCGTCATAAAT
61 TCATAAATACGCGTCATAAAT
3432542 GCGCGTCATA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
84 6 0.09
85 60 0.86
86 4 0.06
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (85 bp):
GACACAAGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGCAAGTCATA
AATACGCGTCATAAATTTAT
Found at i:3433901 original size:43 final size:43
Alignment explanation
Indices: 3433839--3434009 Score: 225
Period size: 43 Copynumber: 4.0 Consensus size: 43
3433829 GGCGTATTTC
* ** * *
3433839 GGATACAAACGTCACAAAAGGTCTGGTATATAGCGGCATTTTA
1 GGATACAAACGCCGTAAAAGGTATGGTACATAGCGGCATTTTA
* *
3433882 GGATACAAACGACGTAAAAGGTATGGTACATAGCGGCGTTTTA
1 GGATACAAACGCCGTAAAAGGTATGGTACATAGCGGCATTTTA
* **
3433925 GGATACAAACGCCGTAAAAGGTATGGTACATAACGGTGTTTTA
1 GGATACAAACGCCGTAAAAGGTATGGTACATAGCGGCATTTTA
* * *
3433968 AGATACAAATGCCGTAAAAGGTATGGTATATAGCGGCATTTT
1 GGATACAAACGCCGTAAAAGGTATGGTACATAGCGGCATTTT
3434010 TTTGTTACAA
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 113 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (43 bp):
GGATACAAACGCCGTAAAAGGTATGGTACATAGCGGCATTTTA
Found at i:3441101 original size:32 final size:32
Alignment explanation
Indices: 3441064--3441128 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3441054 AAGCTGTTGA
3441064 TGGACGTTACCATCCTATAAGTGATTTGATGT
1 TGGACGTTACCATCCTATAAGTGATTTGATGT
3441096 TGGACGTTACCATCCTATAAGTGATTTGATGT
1 TGGACGTTACCATCCTATAAGTGATTTGATGT
3441128 T
1 T
3441129 ACCATCCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (32 bp):
TGGACGTTACCATCCTATAAGTGATTTGATGT
Found at i:3443410 original size:22 final size:22
Alignment explanation
Indices: 3443385--3443427 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3443375 TTTTCAAACG
3443385 CTATTATTTTCCTATTCGAAAA
1 CTATTATTTTCCTATTCGAAAA
*
3443407 CTATTATTTTTCTATTCGAAA
1 CTATTATTTTCCTATTCGAAA
3443428 GCATAAAAAC
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:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (22 bp):
CTATTATTTTCCTATTCGAAAA
Found at i:3443982 original size:42 final size:41
Alignment explanation
Indices: 3443936--3444065 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 41
3443926 ATAATCGTTG
3443936 CTATATTACTACTATATAGCGGCGTTTGTGCACCAAACGCCA
1 CTATATTACTACTATATAGCGGCGTTTGTGCA-CAAACGCCA
* * * * * *
3443978 CTATA-AACAAC-ATTATTGCGGCATTTGTTTG-ATAAACGCCG
1 CTATATTACTACTA-TATAGCGGCGTTTG--TGCACAAACGCCA
* * *
3444019 CTACATTACTACTCTATAGCGGTGTTTGTGCAACAAACGCCA
1 CTATATTACTACTATATAGCGGCGTTTGTGC-ACAAACGCCA
3444061 CTATA
1 CTATA
3444066 AATAACCCTG
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
40 3 0.05
41 27 0.42
42 33 0.51
43 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (41 bp):
CTATATTACTACTATATAGCGGCGTTTGTGCACAAACGCCA
Found at i:3443987 original size:83 final size:83
Alignment explanation
Indices: 3443887--3444067 Score: 236
Period size: 83 Copynumber: 2.2 Consensus size: 83
3443877 ATTTTTCTAA
* * * * ** *
3443887 AAACACCACTATTAACAACAATATTGCGGCGTTTATAGGATAATCGTTGCTATATTACTACTATA
1 AAACGCCACTATAAACAACAATATTGCGGCATTTATAGGATAAACGCCGCTACATTACTACTATA
*
3443952 TAGCGGCGTTTGTGCACC
66 TAGCGGCGTTTGTGCAAC
* * ** *
3443970 AAACGCCACTATAAACAACATTATTGCGGCATTTGTTTGATAAACGCCGCTACATTACTACTCTA
1 AAACGCCACTATAAACAACAATATTGCGGCATTTATAGGATAAACGCCGCTACATTACTACTATA
*
3444035 TAGCGGTGTTTGTGCAAC
66 TAGCGGCGTTTGTGCAAC
3444053 AAACGCCACTATAAA
1 AAACGCCACTATAAA
3444068 TAACCCTGTA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (83 bp):
AAACGCCACTATAAACAACAATATTGCGGCATTTATAGGATAAACGCCGCTACATTACTACTATA
TAGCGGCGTTTGTGCAAC
Found at i:3461074 original size:21 final size:20
Alignment explanation
Indices: 3461050--3461088 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3461040 TTACTTTGGG
3461050 TTTTATAAAAGTTTTCTTTTA
1 TTTT-TAAAAGTTTTCTTTTA
*
3461071 TTTTTCAAAGTTTTCTTT
1 TTTTTAAAAGTTTTCTTT
3461089 GTTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTTAAAAGTTTTCTTTTA
Found at i:3469082 original size:12 final size:12
Alignment explanation
Indices: 3469065--3469090 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3469055 GTAAGAGATC
3469065 GATCCTTTTGGT
1 GATCCTTTTGGT
3469077 GATCCTTTTGGT
1 GATCCTTTTGGT
3469089 GA
1 GA
3469091 AGTGATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46
Consensus pattern (12 bp):
GATCCTTTTGGT
Found at i:3469122 original size:21 final size:20
Alignment explanation
Indices: 3469098--3469143 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
3469088 TGAAGTGATT
3469098 GATCCTTCTTCTAG-AGGGATC
1 GATCCTT-TT-TAGAAGGGATC
*
3469119 GATCCTTTTTTGAAGGGATC
1 GATCCTTTTTAGAAGGGATC
3469139 GATCC
1 GATCC
3469144 ATGGCTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 14 0.61
21 7 0.30
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
GATCCTTTTTAGAAGGGATC
Found at i:3469789 original size:28 final size:28
Alignment explanation
Indices: 3469756--3469826 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
3469746 AGTCCTACAT
*
3469756 AATATCAAATAAAACTATTCAAGATCCA
1 AATATCAAATAAAAATATTCAAGATCCA
*
3469784 AATATCAAATAAAAATATTTAAGATCCA
1 AATATCAAATAAAAATATTCAAGATCCA
*
3469812 AATATAAAATAAAAA
1 AATATCAAATAAAAA
3469827 ATAACATCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.25
Consensus pattern (28 bp):
AATATCAAATAAAAATATTCAAGATCCA
Found at i:3472860 original size:2 final size:2
Alignment explanation
Indices: 3472853--3472898 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
3472843 ATCATATTTA
* *
3472853 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3472895 AT AT
1 AT AT
3472899 TATTAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:3478756 original size:24 final size:25
Alignment explanation
Indices: 3478696--3478756 Score: 99
Period size: 24 Copynumber: 2.5 Consensus size: 25
3478686 CAATATGTAA
3478696 CATCTGATCGAATCAAATGTCGCTG
1 CATCTGATCGAATCAAATGTCGCTG
3478721 -ATCTGATCGAATCAAATGTCGCTG
1 CATCTGATCGAATCAAATGTCGCTG
*
3478745 CATCAGAT-GAAT
1 CATCTGATCGAAT
3478757 AATGGGGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (25 bp):
CATCTGATCGAATCAAATGTCGCTG
Found at i:3479558 original size:2 final size:2
Alignment explanation
Indices: 3479551--3479646 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
3479541 ATCCTTTCAA
3479551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3479593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3479635 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3479647 CCCTTGTTGT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3479948 original size:9 final size:9
Alignment explanation
Indices: 3479936--3480081 Score: 145
Period size: 9 Copynumber: 15.2 Consensus size: 9
3479926 AGGAAAAAAT
*
3479936 AAAATAGAA
1 AAAAAAGAA
3479945 AAAAAAGAA
1 AAAAAAGAA
3479954 AAAAACATGAAA
1 AAAAA-A-G-AA
3479966 AAAGAAAGGAA
1 AAA-AAA-GAA
*
3479977 ACAAAAGAA
1 AAAAAAGAA
3479986 AGGAAAAA-ATA
1 A--AAAAAGA-A
3479997 GAAAAAA-AA
1 -AAAAAAGAA
3480006 AAAAAA-AA
1 AAAAAAGAA
3480014 AAAAAAGAA
1 AAAAAAGAA
3480023 AAAAAAGAAA
1 AAAAAAG-AA
3480033 AAAAAAGAA
1 AAAAAAGAA
3480042 AAAAAAGAA
1 AAAAAAGAA
3480051 AAAAAAGAA
1 AAAAAAGAA
3480060 AAAAAAGAA
1 AAAAAAGAA
3480069 AGAAGAAAGAA
1 A-AA-AAAGAA
3480080 AA
1 AA
3480082 CCGATCAAAT
Statistics
Matches: 121, Mismatches: 4, Indels: 23
0.82 0.03 0.16
Matches are distributed among these distances:
8 14 0.12
9 57 0.47
10 23 0.19
11 17 0.14
12 8 0.07
13 2 0.02
ACGTcount: A:0.84, C:0.01, G:0.13, T:0.02
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:3479984 original size:14 final size:13
Alignment explanation
Indices: 3479963--3480070 Score: 74
Period size: 14 Copynumber: 8.8 Consensus size: 13
3479953 AAAAAACATG
3479963 AAAAAAGAAAGGA
1 AAAAAAGAAAGGA
3479976 AACAAAAGAAAGGA
1 AA-AAAAGAAAGGA
3479990 AAAAATAG-AA--A
1 AAAAA-AGAAAGGA
3480001 AAAAAA-AAA--A
1 AAAAAAGAAAGGA
*
3480011 AAAAAA-AAAGAA
1 AAAAAAGAAAGGA
3480023 AAAAAAG-AA--A
1 AAAAAAGAAAGGA
**
3480033 AAAAAAGAAAAAA
1 AAAAAAGAAAGGA
* *
3480046 AAGAAAAAAAAGAA
1 AA-AAAAGAAAGGA
3480060 AAAAAAGAAAG
1 AAAAAAGAAAG
3480071 AAGAAAGAAA
Statistics
Matches: 82, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
10 21 0.26
11 8 0.10
12 9 0.11
13 18 0.22
14 26 0.32
ACGTcount: A:0.85, C:0.01, G:0.13, T:0.01
Consensus pattern (13 bp):
AAAAAAGAAAGGA
Found at i:3479994 original size:60 final size:57
Alignment explanation
Indices: 3479919--3480081 Score: 181
Period size: 56 Copynumber: 2.8 Consensus size: 57
3479909 AAAAAAGATT
* * *
3479919 AAAAA-AAAGGAAAAAATAAAATAGAAAAAAAAGAAAAAAACATGAAAAAAGAAAGGAAA
1 AAAAAGAAAGGAAAAAATAAAA-AGAAAAAAAAGAAAAAAAAAAG-AAAAA-AAAGAAAA
*
3479978 CAAAAGAAAGGAAAAAATAGAAAA-AAAAAAAA-AAAAAAAAAAGAAAAAAAAGAAAA
1 AAAAAGAAAGGAAAAAATA-AAAAGAAAAAAAAGAAAAAAAAAAGAAAAAAAAGAAAA
* * * *
3480034 AAAAAGAAA-AAAAAGAAAAAAAAGAAAAAAAAGAAAGAAGAAAGAAAA
1 AAAAAGAAAGGAAAA-AATAAAAAGAAAAAAAAGAAAAAAAAAAGAAAA
3480082 CCGATCAAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
55 8 0.09
56 26 0.29
57 18 0.20
58 9 0.10
59 12 0.13
60 14 0.16
61 3 0.03
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.02
Consensus pattern (57 bp):
AAAAAGAAAGGAAAAAATAAAAAGAAAAAAAAGAAAAAAAAAAGAAAAAAAAGAAAA
Found at i:3480002 original size:1 final size:1
Alignment explanation
Indices: 3479998--3480065 Score: 91
Period size: 1 Copynumber: 68.0 Consensus size: 1
3479988 GAAAAAATAG
* * * * *
3479998 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAGAAAAAAAAGAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3480063 AAA
1 AAA
3480066 GAAAGAAGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:3480004 original size:37 final size:33
Alignment explanation
Indices: 3479920--3480069 Score: 149
Period size: 37 Copynumber: 4.3 Consensus size: 33
3479910 AAAAAGATTA
* * *
3479920 AAAAAAAGGAAAAAATAAAATAGAAAAAAAAGA
1 AAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAGA
** * *
3479953 AAAAAACATGAAAAAAGAAAGGAAACAAAAGAAAGGA
1 AAAAAA-A-GAAAAAA-AAAAAAAAGAAAA-AAAAGA
*
3479990 AAAAATAGAAAAAAAAAAAAAA-AAAAAAAAGA
1 AAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAGA
3480022 AAAAAAAGAAAAAAAAAGAAAAAAAAGAAAAAAAAGA
1 AAAAAAAG---AAAAAA-AAAAAAAAGAAAAAAAAGA
3480059 AAAAAAAGAAA
1 AAAAAAAGAAA
3480070 GAAGAAAGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 17
0.77 0.10 0.14
Matches are distributed among these distances:
32 12 0.12
33 10 0.10
34 10 0.10
35 19 0.20
36 17 0.18
37 28 0.29
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (33 bp):
AAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAGA
Found at i:3480081 original size:28 final size:28
Alignment explanation
Indices: 3479936--3480080 Score: 136
Period size: 28 Copynumber: 5.0 Consensus size: 28
3479926 AGGAAAAAAT
*
3479936 AAAATAGAAAAAAAAGAAAAAAACATGAAAA
1 AAAA-AGAAAAAAAAGAAAAAAA-A-GAAAG
* *
3479967 AAGAAAGGAAACAAAAGAAAGGAAAAA-ATAG
1 AA-AAA-GAAAAAAAAGAAA--AAAAAGAAAG
*
3479998 AAAAA-AAAAAAAAAAAAAAAAAGAAA-
1 AAAAAGAAAAAAAAGAAAAAAAAGAAAG
3480024 AAAAAGAAAAAAAAAGAAAAAAAAGAAA-
1 AAAAAG-AAAAAAAAGAAAAAAAAGAAAG
3480052 AAAAAGAAAAAAAAGAAAGAAGAAAGAAA
1 AAAAAGAAAAAAAAGAAA-AA-AAAGAAA
3480081 ACCGATCAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
26 10 0.10
27 14 0.14
28 38 0.39
29 7 0.07
30 3 0.03
31 7 0.07
32 14 0.14
33 1 0.01
34 4 0.04
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.02
Consensus pattern (28 bp):
AAAAAGAAAAAAAAGAAAAAAAAGAAAG
Found at i:3482067 original size:55 final size:56
Alignment explanation
Indices: 3482006--3482263 Score: 208
Period size: 54 Copynumber: 4.7 Consensus size: 56
3481996 GTTTGTTTAG
*
3482006 AAACTAAGTCTGATTTTCAGAAGTTTCTTAATTATTTTTAAATGAGTTTTCAAA-A
1 AAACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGTTTTCAAAGA
* * * * *
3482061 AAACTAAGTTTGATTTTCATAAGTTTCCTGATGA-TTTTAAATGAGTTTTTAAAGA
1 AAACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGTTTTCAAAGA
* * * *
3482116 AAA-TAAGTCTGATTTTC-GAAAGTTTCTTGA-TATTTTCAAATGAATTTTTTTTTAAAAA
1 AAACTAAGTCTGATTTTCAG-AAGTTTCTTGATTATTTTTAAATG-A---GTTTTCAAAGA
* * * ** * * * *
3482174 AAACTAAGCCTAATTTTTAGGGGTTTCTTGA-TGTTTTCAAATGA-ATTTGAAAG-
1 AAACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGTTTTCAAAGA
** **
3482227 AAACTAAGTCCAATTTTTGGAAGTTTCTTGATTATTT
1 AAACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTT
3482264 GAAATTTCAA
Statistics
Matches: 165, Mismatches: 28, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
53 27 0.16
54 59 0.36
55 34 0.21
58 13 0.08
59 31 0.19
60 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.44
Consensus pattern (56 bp):
AAACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGTTTTCAAAGA
Found at i:3482254 original size:53 final size:53
Alignment explanation
Indices: 3482081--3482258 Score: 137
Period size: 59 Copynumber: 3.2 Consensus size: 53
3482071 TGATTTTCAT
* * * * ** * *
3482081 AAGTTTCCTGATGATTTT-AAATGAGTTTTTAAAGAAAATAAGTCTGATTTTCGA
1 AAGTTTCTTGATG-TTTTCAAATGA-ATTTAAAAGAAACTAAGTCCAATTTTTGG
* *
3482135 AAGTTTCTTGATATTTTCAAATGAATTTTTTTTTAAAAAAAACTAAG-CCTAATTTTTAGG
1 AAGTTTCTTGATGTTTTCAAATGAA------TTTAAAAGAAACTAAGTCC-AATTTTT-GG
* *
3482195 -GGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAACTAAGTCCAATTTTTGG
1 AAGTTTCTTGATGTTTTCAAATGAATTTAAAAGAAACTAAGTCCAATTTTTGG
3482247 AAGTTTCTTGAT
1 AAGTTTCTTGAT
3482259 TATTTGAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
52 2 0.02
53 35 0.36
54 19 0.19
58 1 0.01
59 40 0.41
60 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (53 bp):
AAGTTTCTTGATGTTTTCAAATGAATTTAAAAGAAACTAAGTCCAATTTTTGG
Found at i:3482777 original size:145 final size:145
Alignment explanation
Indices: 3482507--3483225 Score: 946
Period size: 145 Copynumber: 5.0 Consensus size: 145
3482497 AGCAAGATGA
* * * * *
3482507 TAAGTCTTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAACATTTCCTTTGCTTGATT
1 TAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACATTTCATTTGCTCGATT
* * *
3482572 CACAACACTTCAAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATAGTGCTCGATTCACAA
66 CACAACACTTCGAATCAGCAACACCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
3482637 CACTTCGAATCAGCT
131 CACTTCGAATCAGCT
* * * *
3482652 TAAGTCATTCGGGCCAACCATAAAACCTTCGGGCAAGATGTTTACAACATTTCATTTGCTTGATT
1 TAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACATTTCATTTGCTCGATT
* * * *
3482717 CACAACACTTCGAATCAGCAATACCCCACCAAAGGGGTTAAAATTTCATATTGCTTGATTCACAA
66 CACAACACTTCGAATCAGCAACACCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
* **
3482782 CACTTCAAATCTTCT
131 CACTTCGAATCAGCT
* * * * ** * *
3482797 TAAGTCCTTCGGGTCATCCATAAGACCTCCAGATAAGATG-TTTCAACATTTCCTTTTCTCGATT
1 TAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACATTTCATTTGCTCGATT
* *
3482861 CACAACACTTCGAATCAGCAACGA-CCTACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACA
66 CACAACACTTCGAATCAGCAAC-ACCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACA
*
3482925 AAACTTCGAATCAGCT
130 ACACTTCGAATCAGCT
* *
3482941 TAAGTCATTCGGGCCATCCATAAGACATTCGGGCATGATGTTTTCAACATTTTC-TTTGCTCGAT
1 TAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACA-TTTCATTTGCTCGAT
* * * * * *
3483005 TCACAACCCTTCGAATCAACAACACACCACCAGAGGGGTTAATATTTCCTATTGCTCAATTCACA
65 TCACAACACTTCGAATCAGCAACACCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACA
*
3483070 ACACTTTGAATCAGCT
130 ACACTTCGAATCAGCT
* * ** *
3483086 TAAGTCCTTCGGGTCATCCATAAGACCTTCAAGCATGATGTTTTCAACATTTCATTTGCTCGATT
1 TAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACATTTCATTTGCTCGATT
* * *
3483151 CACAACACTTCGAATCAACAACGCCCCACC-GAGGGGTTAACATTT-ACT-TTGCTCGATTCATA
66 CACAACACTTCGAATCAGCAACACCCCACCAGAGGGGTTAACATTTCA-TATTGCTCGATTCACA
3483213 ACACTTCGAATCA
130 ACACTTCGAATCA
3483226 ACAACGCCCC
Statistics
Matches: 499, Mismatches: 69, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
143 24 0.05
144 140 0.28
145 331 0.66
146 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (145 bp):
TAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACATTTCATTTGCTCGATT
CACAACACTTCGAATCAGCAACACCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
CACTTCGAATCAGCT
Found at i:3483069 original size:289 final size:289
Alignment explanation
Indices: 3482507--3483225 Score: 1025
Period size: 289 Copynumber: 2.5 Consensus size: 289
3482497 AGCAAGATGA
* * * * * *
3482507 TAAGTCTTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAACATTTCCTTTGCTTGATT
1 TAAGTCCTTCGGGTCATCCATAAGACCTCCAGATA-GATGTTTTCAACATTTCCTTTGCTCGATT
* * *
3482572 CACAACACTTCAAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATAGTGCTCGATTCACAA
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAA
*
3482637 CACTTCGAATCAGCTTAAGTCATTCGGGCCAACCATAAAACCTTCGGGCAAGATGTTTACAACAT
130 CACTTCGAATCAGCTTAAGTCATTCGGGCCAACCATAAAACATTCGGGCAAGATGTTTACAACAT
* * * *
3482702 TTCATTTGCTTGATTCACAACACTTCGAATCAGCAATACCCCACCAAAGGGGTTAAAATTTCATA
195 TTCATTTGCTCGATTCACAACACTTCGAATCAACAACACACCACCAAAGGGGTTAAAATTTCATA
** **
3482767 TTGCTTGATTCACAACACTTCAAATCTTCT
260 TTGCTCAATTCACAACACTTCAAATCAGCT
*
3482797 TAAGTCCTTCGGGTCATCCATAAGACCTCCAGATAAGATG-TTTCAACATTTCCTTTTCTCGATT
1 TAAGTCCTTCGGGTCATCCATAAGACCTCCAGAT-AGATGTTTTCAACATTTCCTTTGCTCGATT
* *
3482861 CACAACACTTCGAATCAGCAACGACCTACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAA
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAA
* * * * *
3482926 AACTTCGAATCAGCTTAAGTCATTCGGGCCATCCATAAGACATTCGGGCATGATGTTTTCAACAT
130 CACTTCGAATCAGCTTAAGTCATTCGGGCCAACCATAAAACATTCGGGCAAGATGTTTACAACA-
* * * *
3482991 TTTC-TTTGCTCGATTCACAACCCTTCGAATCAACAACACACCACCAGAGGGGTTAATATTTCCT
194 TTTCATTTGCTCGATTCACAACACTTCGAATCAACAACACACCACCAAAGGGGTTAAAATTTCAT
**
3483055 ATTGCTCAATTCACAACACTTTGAATCAGCT
259 ATTGCTCAATTCACAACACTTCAAATCAGCT
* *
3483086 TAAGTCCTTCGGGTCATCCATAAGACCTTCAAGCAT-GATGTTTTCAACATTTCATTTGCTCGAT
1 TAAGTCCTTCGGGTCATCCATAAGACC-TCCAG-ATAGATGTTTTCAACATTTCCTTTGCTCGAT
* * *
3483150 TCACAACACTTCGAATCAACAACGCCCCACC-GAGGGGTTAACATTTACT-TTGCTCGATTCATA
64 TCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACA
3483213 ACACTTCGAATCA
129 ACACTTCGAATCA
3483226 ACAACGCCCC
Statistics
Matches: 383, Mismatches: 41, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
288 25 0.07
289 265 0.69
290 90 0.23
291 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (289 bp):
TAAGTCCTTCGGGTCATCCATAAGACCTCCAGATAGATGTTTTCAACATTTCCTTTGCTCGATTC
ACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAAC
ACTTCGAATCAGCTTAAGTCATTCGGGCCAACCATAAAACATTCGGGCAAGATGTTTACAACATT
TCATTTGCTCGATTCACAACACTTCGAATCAACAACACACCACCAAAGGGGTTAAAATTTCATAT
TGCTCAATTCACAACACTTCAAATCAGCT
Found at i:3483221 original size:58 final size:58
Alignment explanation
Indices: 3483131--3483285 Score: 204
Period size: 58 Copynumber: 2.6 Consensus size: 58
3483121 TGATGTTTTC
* *
3483131 AACATTTCATTTGCTCGATTCACAACACTTCGAATCAACAACGCCCCACC-GAGGGGTT
1 AACATTTC-TTTGCTCGATTCAAAACACTTCGAATCAACAACGCCCCACCAGAGGAGTT
* *
3483189 AACATTTACTTTGCTCGATTCATAACACTTCGAATCAACAACGCCCCACCAGAGGATTT
1 AACATTT-CTTTGCTCGATTCAAAACACTTCGAATCAACAACGCCCCACCAGAGGAGTT
* * *
3483248 TACATTTCCTATTGCTTGATTCAAAACACTTTGAATCA
1 AACATTT-CT-TTGCTCGATTCAAAACACTTCGAATCA
3483286 GCTAAAGTCC
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
58 47 0.55
59 15 0.17
60 24 0.28
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (58 bp):
AACATTTCTTTGCTCGATTCAAAACACTTCGAATCAACAACGCCCCACCAGAGGAGTT
Found at i:3483225 original size:203 final size:204
Alignment explanation
Indices: 3482986--3483430 Score: 631
Period size: 203 Copynumber: 2.2 Consensus size: 204
3482976 TGATGTTTTC
* * * *
3482986 AACATTTTCTTTGCTCGATTCACAACCCTTCGAATCAACAACACACCACCAGAGGGGTTAATATT
1 AACATTTACTTTGCTCGATTCACAACACTTCGAATCAACAACACACCACCAGAGGAGTTAACATT
* * *
3483051 TCCTATTGCTCAATTCACAACACTTTGAATCAGCTTAAGTCCTTCGGGTCATCCATAAGACCTTC
66 TCCTATTGCTCAATTCAAAACACTTTGAATCAGCTAAAGTCCTTCGGGCCATCCATAAGACCTTC
* *
3483116 AAGCATGATGTTTTCAACATTTCATTTGCTCGATTCACAACACTTCGAATCAACAACGCCCCA-C
131 AAGAAGGATGTTTTCAACATTTCATTTGCTCGATTCACAACACTTCGAATCAACAACGCCCCATC
*
3483180 CGAGGGGTT
196 AGAGGGGTT
* * * * *
3483189 AACATTTACTTTGCTCGATTCATAACACTTCGAATCAACAACGCCCCACCAGAGGATTTTACATT
1 AACATTTACTTTGCTCGATTCACAACACTTCGAATCAACAACACACCACCAGAGGAGTTAACATT
** * *
3483254 TCCTATTGCTTGATTCAAAACACTTTGAATCAGCTAAAGTCCTTTGGGCCATCCATAAGACCTTG
66 TCCTATTGCTCAATTCAAAACACTTTGAATCAGCTAAAGTCCTTCGGGCCATCCATAAGACCTTC
** * * *
3483319 GGGAAGGATGTTTTCAACATTTCATTTGCTCGATTCATAACACTTCGAATCAGCAACGCCCCATT
131 AAGAAGGATGTTTTCAACATTTCATTTGCTCGATTCACAACACTTCGAATCAACAACGCCCCATC
3483384 AGAGGGGTT
196 AGAGGGGTT
* **
3483393 AACATTTCCTATTAATCGATTCACAACACTTCGAATCA
1 AACATTTACT-TTGCTCGATTCACAACACTTCGAATCA
3483431 GATTAAGTCC
Statistics
Matches: 212, Mismatches: 28, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
203 171 0.81
204 17 0.08
205 24 0.11
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (204 bp):
AACATTTACTTTGCTCGATTCACAACACTTCGAATCAACAACACACCACCAGAGGAGTTAACATT
TCCTATTGCTCAATTCAAAACACTTTGAATCAGCTAAAGTCCTTCGGGCCATCCATAAGACCTTC
AAGAAGGATGTTTTCAACATTTCATTTGCTCGATTCACAACACTTCGAATCAACAACGCCCCATC
AGAGGGGTT
Found at i:3484257 original size:4 final size:4
Alignment explanation
Indices: 3484248--3484272 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3484238 GGTATTTTAA
3484248 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3484273 GTGATAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3485500 original size:16 final size:18
Alignment explanation
Indices: 3485468--3485503 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
3485458 ATTGAAATGC
3485468 TTTAATATATCATTTTAA
1 TTTAATATATCATTTTAA
3485486 TTTAA-ATAT-ATTTTAA
1 TTTAATATATCATTTTAA
3485502 TT
1 TT
3485504 AGGCATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAATATATCATTTTAA
Found at i:3488109 original size:12 final size:12
Alignment explanation
Indices: 3488078--3488131 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
3488068 ACTTGTTTTT
3488078 TTTTTCTTCATTC
1 TTTTTCTTC-TTC
*
3488091 -TTATCTTCTTC
1 TTTTTCTTCTTC
3488102 TTTTTCTTCTTC
1 TTTTTCTTCTTC
* * *
3488114 TTGTTCCTCCTC
1 TTTTTCTTCTTC
3488126 TTTTTC
1 TTTTTC
3488132 CATCAACTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 3 0.09
12 31 0.91
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:3492043 original size:10 final size:10
Alignment explanation
Indices: 3492014--3492063 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3492004 GCTGCTGGAA
3492014 AACCGGTTTG
1 AACCGGTTTG
*
3492024 -ACCAGTTTTG
1 AACC-GGTTTG
3492034 AACCGGTTTG
1 AACCGGTTTG
*
3492044 -ACCGGTCTG
1 AACCGGTTTG
*
3492053 GACCGGTTTG
1 AACCGGTTTG
3492063 A
1 A
3492064 CTGGTCTGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:3492047 original size:9 final size:9
Alignment explanation
Indices: 3492015--3492074 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
3492005 CTGCTGGAAA
3492015 ACCGGTTTG
1 ACCGGTTTG
*
3492024 ACCAGTTTTG
1 ACC-GGTTTG
3492034 AACCGGTTTG
1 -ACCGGTTTG
*
3492044 ACCGGTCTGG
1 ACCGGT-TTG
3492054 ACCGGTTTG
1 ACCGGTTTG
* *
3492063 ACTGGTCTG
1 ACCGGTTTG
3492072 ACC
1 ACC
3492075 CGACCCGACT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 20 0.49
10 18 0.44
11 3 0.07
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3492059 original size:19 final size:19
Alignment explanation
Indices: 3492014--3492072 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
3492004 GCTGCTGGAA
* *
3492014 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
3492034 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
* *
3492053 GACCGGTTTGACTGGTCTG
1 AACCGGTTTGACCGGTCTG
3492072 A
1 A
3492073 CCCGACCCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 21 0.62
20 13 0.38
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.31
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3492097 original size:22 final size:21
Alignment explanation
Indices: 3492071--3492130 Score: 74
Period size: 17 Copynumber: 3.0 Consensus size: 21
3492061 TGACTGGTCT
3492071 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC-GTTGACCC
3492093 GACCCGA--C--CGTTGACCC
1 GACCCGACCCGACGTTGACCC
3492110 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGA-CGTTGACC
3492131 GTTGACCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 15 0.45
18 1 0.03
19 1 0.03
20 1 0.03
22 15 0.45
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (21 bp):
GACCCGACCCGACGTTGACCC
Found at i:3492130 original size:17 final size:17
Alignment explanation
Indices: 3492070--3492118 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
3492060 TTGACTGGTC
*
3492070 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
3492087 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
3492104 TGACCCGACCCGACC
1 TGACCCGACCCGACC
3492119 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:3492132 original size:7 final size:7
Alignment explanation
Indices: 3492120--3492150 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3492110 GACCCGACCC
3492120 GACCGTT
1 GACCGTT
3492127 GACCGTT
1 GACCGTT
3492134 GACCGTT
1 GACCGTT
3492141 GACCGTT
1 GACCGTT
3492148 GAC
1 GAC
3492151 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:3495670 original size:29 final size:27
Alignment explanation
Indices: 3495601--3495713 Score: 112
Period size: 25 Copynumber: 4.3 Consensus size: 27
3495591 CTTTTATTTG
* *
3495601 AATATTATT-TTTTAAT-ATTA-TAAT
1 AATATTTTTATTTTAATAATAATTAAT
*
3495625 AATATTCTTATTTTAATAAGTAATTAAT
1 AATATTTTTATTTTAATAA-TAATTAAT
*
3495653 AATATTTATTATTTTAATAAT-A-TACT
1 AATATTT-TTATTTTAATAATAATTAAT
*
3495679 AATATTTTTATGTTAATAAATAATTAAT
1 AATATTTTTATTTTAAT-AATAATTAAT
3495707 AA-ATTTT
1 AATATTTT
3495714 AAAATATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
24 8 0.11
25 16 0.21
26 14 0.19
27 9 0.12
28 16 0.21
29 12 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
AATATTTTTATTTTAATAATAATTAAT
Found at i:3495683 original size:54 final size:53
Alignment explanation
Indices: 3495601--3495712 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 53
3495591 CTTTTATTTG
* * *
3495601 AATA-TTATTTTTTAATATTATAATAATATTCTTATTTTAATAAGTAATTAAT
1 AATATTTATTTTTTAATAATATAATAATATTCTTATGTTAATAAATAATTAAT
* *
3495653 AATATTTATTATTTTAATAATATACTAATATTTTTATGTTAATAAATAATTAAT
1 AATATTTATT-TTTTAATAATATAATAATATTCTTATGTTAATAAATAATTAAT
3495707 AA-ATTT
1 AATATTT
3495713 TAAAATATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 4 0.08
53 9 0.17
54 40 0.75
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (53 bp):
AATATTTATTTTTTAATAATATAATAATATTCTTATGTTAATAAATAATTAAT
Found at i:3495800 original size:15 final size:14
Alignment explanation
Indices: 3495766--3495810 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
3495756 AAAATTATAG
*
3495766 AAATAATATTTTAA-
1 AAATAATA-TTAAAT
3495780 AAATAATATTAACAT
1 AAATAATATTAA-AT
3495795 AAATAATATTAAAT
1 AAATAATATTAAAT
3495809 AA
1 AA
3495811 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 13 0.46
15 12 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:3495848 original size:22 final size:21
Alignment explanation
Indices: 3495813--3495869 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
3495803 TTAAATAATT
3495813 TATT-TTAATATTTTACAAATAA
1 TATTATTAAT-TTTTACAAA-AA
**
3495835 TATTATTAATTTTTTTTAAAAA
1 TATTATTAA-TTTTTACAAAAA
3495857 TATTATT-ATTTTT
1 TATTATTAATTTTT
3495870 CATATTCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 5 0.16
21 1 0.03
22 13 0.42
23 11 0.35
24 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTAATTTTTACAAAAA
Found at i:3498924 original size:19 final size:19
Alignment explanation
Indices: 3498892--3498938 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
3498882 AACGATCATC
*
3498892 GGGTCAGGTTAAAGTCAAT
1 GGGTCAGGTCAAAGTCAAT
* *
3498911 GGGTCGGGTCAAAGTCGAT
1 GGGTCAGGTCAAAGTCAAT
3498930 GGGTCAGGT
1 GGGTCAGGT
3498939 AGGGTTGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.40, T:0.23
Consensus pattern (19 bp):
GGGTCAGGTCAAAGTCAAT
Found at i:3498979 original size:20 final size:20
Alignment explanation
Indices: 3498942--3498980 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3498932 GTCAGGTAGG
*
3498942 GTTGACTCGATTCGGGTCAT
1 GTTGACTCGATTCAGGTCAT
* *
3498962 GTTGACTTGTTTCAGGTCA
1 GTTGACTCGATTCAGGTCA
3498981 ACAGATCCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.38
Consensus pattern (20 bp):
GTTGACTCGATTCAGGTCAT
Found at i:3501514 original size:19 final size:19
Alignment explanation
Indices: 3501473--3501515 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3501463 AAATTAGTGA
* *
3501473 TCAGAACAGATATCAAAGT
1 TCAGAACAGAAATCAAAGG
*
3501492 TCAGAACAGAAATCAGAGG
1 TCAGAACAGAAATCAAAGG
3501511 TCAGA
1 TCAGA
3501516 CTGTATTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
TCAGAACAGAAATCAAAGG
Found at i:3503181 original size:7 final size:7
Alignment explanation
Indices: 3503171--3503200 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3503161 ATGGTCAGAC
3503171 CGATCAA
1 CGATCAA
3503178 CGATCAA
1 CGATCAA
*
3503185 CAATCAA
1 CGATCAA
3503192 CGATCAA
1 CGATCAA
3503199 CG
1 CG
3503201 GGTCAGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.13
Consensus pattern (7 bp):
CGATCAA
Found at i:3507034 original size:2 final size:2
Alignment explanation
Indices: 3507029--3507100 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
3507019 TGTGTGTGCG
3507029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3507071 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3507101 GTAGTGTGGG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3507457 original size:14 final size:14
Alignment explanation
Indices: 3507438--3507465 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3507428 TTGTTCAAAA
3507438 ACCTAAAATATATT
1 ACCTAAAATATATT
3507452 ACCTAAAATATATT
1 ACCTAAAATATATT
3507466 CTCTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
ACCTAAAATATATT
Done.