Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007739.1 Hibiscus syriacus cultivar Beakdansim tig00109999_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: 642700
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:347448 original size:17 final size:17
Alignment explanation
Indices: 347406--347461 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
347396 TAAATAAATA
347406 AATAA-ATAATAATAAT
1 AATAATATAATAATAAT
**
347422 -ATTTTATAATAATAAT
1 AATAATATAATAATAAT
347438 AATAATATAATAATAAT
1 AATAATATAATAATAAT
347455 AATAATA
1 AATAATA
347462 ATTGAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 2 0.06
16 11 0.32
17 21 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAATATAATAATAAT
Found at i:347449 original size:8 final size:8
Alignment explanation
Indices: 347389--347461 Score: 55
Period size: 8 Copynumber: 9.0 Consensus size: 8
347379 CTCGAGTTTG
347389 TAATAA-A
1 TAATAATA
347396 TAAATAA-A
1 T-AATAATA
347404 TAAATAA-A
1 T-AATAATA
347412 TAATAATA
1 TAATAATA
**
347420 -ATATTTTA
1 TA-ATAATA
347428 TAATAATAA
1 TAATAAT-A
347437 TAATAATA
1 TAATAATA
347445 TAATAATAA
1 TAATAAT-A
347454 TAATAATA
1 TAATAATA
347462 ATTGAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
7 7 0.12
8 32 0.57
9 17 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAATAATA
Found at i:347734 original size:40 final size:41
Alignment explanation
Indices: 347685--347789 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 41
347675 TCAAAAATGC
* * * *
347685 TGATCCAACTCCTTATGTGATGGGT-AACCTATGGTGA-TGT
1 TGATTCAACTCCTTATGTGATGGATGAACC-AAGGTCAGTGT
* *
347725 TGATTCAACTCTTTATGTGATGGATGAGCCAAGGTCAGTGT
1 TGATTCAACTCCTTATGTGATGGATGAACCAAGGTCAGTGT
347766 TG-TTCCAACTCCTTATGTGATGGA
1 TGATT-CAACTCCTTATGTGATGGA
347790 ATTAGACAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
40 29 0.53
41 26 0.47
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
TGATTCAACTCCTTATGTGATGGATGAACCAAGGTCAGTGT
Found at i:347776 original size:41 final size:41
Alignment explanation
Indices: 347688--347789 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
347678 AAAATGCTGA
* * *
347688 TCCAACTCCTTATGTGATGGGTAACCTATGGTGATGTTGAT
1 TCCAACTCCTTATGTGATGGATAACCTAAGGTCATGTTGAT
* *
347729 T-CAACTCTTTATGTGATGGATGAGCC-AAGGTCAGTGTTG-T
1 TCCAACTCCTTATGTGATGGAT-AACCTAAGGTCA-TGTTGAT
347769 TCCAACTCCTTATGTGATGGA
1 TCCAACTCCTTATGTGATGGA
347790 ATTAGACAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
40 25 0.48
41 27 0.52
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
TCCAACTCCTTATGTGATGGATAACCTAAGGTCATGTTGAT
Found at i:348068 original size:40 final size:41
Alignment explanation
Indices: 348006--348107 Score: 100
Period size: 40 Copynumber: 2.5 Consensus size: 41
347996 TGAGAATGTC
* * ** *
348006 GATCCAATTCCTTCTGCAATGGATGA-CCTAAGGT-GATGCT
1 GATCCAACTCCTTATGTGATGGATGAGCC-AAGGTCGATGAT
*
348046 GATCCAACTCCTTATGTGATGGATGAGCCAAGGTCGGTGAT
1 GATCCAACTCCTTATGTGATGGATGAGCCAAGGTCGATGAT
** *
348087 TTTCCAACTCCTTTTGTGATG
1 GATCCAACTCCTTATGTGATG
348108 AAATCAAGCA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 27 0.53
41 24 0.47
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (41 bp):
GATCCAACTCCTTATGTGATGGATGAGCCAAGGTCGATGAT
Found at i:348222 original size:40 final size:41
Alignment explanation
Indices: 348162--348267 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 41
348152 ATCGGGAACT
* * * * *
348162 TTGATCTAACTCTTTCTGTGATGGATGA-CCTAAGGT-GACG
1 TTGATCCAACTCCTTATGTGATAGATGAGCC-AAGGTCAACG
* *
348202 TTGATCCAACTCCTTATGTGATAGATTAGCCAAGGTCAATG
1 TTGATCCAACTCCTTATGTGATAGATGAGCCAAGGTCAACG
*
348243 TTGTTCCAACTCCTTATGTGATAGA
1 TTGATCCAACTCCTTATGTGATAGA
348268 ATCAAGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 28 0.50
41 28 0.50
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (41 bp):
TTGATCCAACTCCTTATGTGATAGATGAGCCAAGGTCAACG
Found at i:348339 original size:319 final size:318
Alignment explanation
Indices: 347686--348699 Score: 1392
Period size: 319 Copynumber: 3.2 Consensus size: 318
347676 CAAAAATGCT
** * * * * * *
347686 GATCCAACTCCTTATGTGATGGGTAACCTATGGTGATGTTGATTCAACTCTTTATGTGATGGATG
1 GATCCAACTCCTTATGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATGTGATGGATG
* * *
347751 AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAAT-TAGACAAATGTTGAGCAAGCTCT
66 AGCCAAGGTCGGTGTTGTTCCAACTCCTTATGTGATGGAATCAAG-CAAATATTGAGCAAG---T
* * * * * *
347815 TCTCATTACGAACTTCTCTTATCGGGAA-TATCGATATAACTCATTCTGAGATGGATTACCTAAG
127 TCTTATTAAGAACTTCTCCTATCGGGAACT-TTGATCTAACTCATTCTGAGATGGATGACCTAAG
* * * * *
347879 GTGAGGC-CATCCAACTCCTTATGTGATAGATGGGCCAAGCTTAGTGTTGTTCCAACT-CTTATA
191 GTGACGCTGATCCAACTCCTTATGTGATAGATGAGCCAAG-GTAGTGTTGTTCCAACTCCTTATG
* * *
347942 TGATGGAATCAAGAAAATGTTGAGCAAGTTCTTCTCATTAAAAACTTTTCCTATTGAGAATGTC
255 TGATGGAATCAAGAAAATGTTGAGCAAGTTCTTCTCATTACAAACTTCTCCTATTGGGAATGTC
* *
348006 GATCCAATTCCTTCTGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATGTGATGGATG
1 GATCCAACTCCTTATGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATGTGATGGATG
* *
348071 AGCCAAGGTCGGTGATT-TTCCAACTCCTTTTGTGATGAAATCAAGCAAATATTGAGCAAGTTCT
66 AGCCAAGGTCGGTG-TTGTTCCAACTCCTTATGTGATGGAATCAAGCAAATATTGAGCAAGTTCT
* * *
348135 TATTAAGGACTTCTCCTATCGGGAACTTTGATCTAACTCTTTCTGTGATGGATGACCTAAGGTGA
130 TATTAAGAACTTCTCCTATCGGGAACTTTGATCTAACTCATTCTGAGATGGATGACCTAAGGTGA
* * *
348200 CGTTGATCCAACTCCTTATGTGATAGATTAGCCAAGGTCAATGTTGTTCCAACTCCTTATGTGAT
195 CGCTGATCCAACTCCTTATGTGATAGATGAGCCAAGGT-AGTGTTGTTCCAACTCCTTATGTGAT
*
348265 AGAATCAAGAAAATGTTGAGCAAGTTCTTCTCATTACAAACTTCTCCTATTGGGAATGTC
259 GGAATCAAGAAAATGTTGAGCAAGTTCTTCTCATTACAAACTTCTCCTATTGGGAATGTC
* * **
348325 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACACTGATCCAACTCCTTATGTGATGGATG
1 GATCCAACTCCTTATGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATGTGATGGATG
* *
348390 AGCCAAGGTCGGTGTTGTTCCAACACCTTATGTGATGGAATCAAGCAAATATTGAGCAAGTTATC
66 AGCCAAGGTCGGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGCAAATATTGAGCAAGTTCT-
** ** * * *
348455 T-TTCTGAACTTCTCCTATCTAGAACTTTGATCCAACTCCTTCTGCGATGGATGACCTAAGGTGA
130 TATTAAGAACTTCTCCTATCGGGAACTTTGATCTAACTCATTCTGAGATGGATGACCTAAGGTGA
* *
348519 CACTGATCCAACTCCTTATGTGATAGATGAGCCAAGGATGGTGTTGTTCCAACTCCTTATGTGAT
195 CGCTGATCCAACTCCTTATGTGATAGATGAGCCAAGG-TAGTGTTGTTCCAACTCCTTATGTGAT
348584 GGAATCAAGAAAATGTTGAGCAAGTTCTTCTCATTACAAACTTCTCCTATTGGGAATGTC
259 GGAATCAAGAAAATGTTGAGCAAGTTCTTCTCATTACAAACTTCTCCTATTGGGAATGTC
* * * * *
348644 AATCCAACACCTTATGCAATGGATGACTTAAGGTGAAGCTGATTCAACTCCTTATG
1 GATCCAACTCCTTATGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATG
348700 AGATAGAATA
Statistics
Matches: 619, Mismatches: 66, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
317 60 0.10
318 46 0.07
319 403 0.65
320 106 0.17
321 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (318 bp):
GATCCAACTCCTTATGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATGTGATGGATG
AGCCAAGGTCGGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGCAAATATTGAGCAAGTTCTT
ATTAAGAACTTCTCCTATCGGGAACTTTGATCTAACTCATTCTGAGATGGATGACCTAAGGTGAC
GCTGATCCAACTCCTTATGTGATAGATGAGCCAAGGTAGTGTTGTTCCAACTCCTTATGTGATGG
AATCAAGAAAATGTTGAGCAAGTTCTTCTCATTACAAACTTCTCCTATTGGGAATGTC
Found at i:348381 original size:161 final size:161
Alignment explanation
Indices: 347686--348706 Score: 1237
Period size: 161 Copynumber: 6.4 Consensus size: 161
347676 CAAAAATGCT
* * * * * * * * * *
347686 GATCCAACTCCTTATGTGATGGGTAACCTATGGTGATGTTGATTCAACTCTTTATGTGATGGATG
1 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGATG
* *
347751 AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAAT-TAGACAAATGTTGAGCAAGCTCT
66 AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGA-AAATGTTGAGCAAGTTCT
* * * *
347815 TCTCATTACGAACTTCTCTTATCGGGAATATC
130 TCTCATTACAAACTTCTCCTATTGGGAATGTC
** * * * * *
347847 GATATAACTCATTCTGAGATGGATTACCTAAGGTGAGGC-CATCCAACTCCTTATGTGATAGATG
1 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGATG
* * * *
347911 GGCCAAGCTTAGTGTTGTTCCAACT-CTTATATGATGGAATCAAGAAAATGTTGAGCAAGTTCTT
66 AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCTT
* * *
347975 CTCATTAAAAACTTTTCCTATTGAGAATGTC
131 CTCATTACAAACTTCTCCTATTGGGAATGTC
* * * *
348006 GATCCAATTCCTTCTGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATGTGATGGATG
1 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGATG
* * * * *
348071 AGCCAAGGTCGGTGATT-TTCCAACTCCTTTTGTGATGAAATCAAGCAAATATTGAGCAAGTTC-
66 AGCCAAGGTCAGTG-TTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCT
* * *
348134 T-T-ATTA-AGGACTTCTCCTATCGGGAACT-TT
130 TCTCATTACA-AACTTCTCCTATTGGGAA-TGTC
* * * * *
348164 GATCTAACTCTTTCTGTGATGGATGACCTAAGGTGACGTTGATCCAACTCCTTATGTGATAGATT
1 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGATG
* *
348229 AGCCAAGGTCAATGTTGTTCCAACTCCTTATGTGATAGAATCAAGAAAATGTTGAGCAAGTTCTT
66 AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCTT
348294 CTCATTACAAACTTCTCCTATTGGGAATGTC
131 CTCATTACAAACTTCTCCTATTGGGAATGTC
* *
348325 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACACTGATCCAACTCCTTATGTGATGGATG
1 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGATG
* * * * *
348390 AGCCAAGGTCGGTGTTGTTCCAACACCTTATGTGATGGAATCAAGCAAATATTGAGCAAGTT-AT
66 AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCTT
* * *
348454 CT--TT-CTGAACTTCTCCTATCT-AGAACT-TT
131 CTCATTAC-AAACTTCTCCTAT-TGGGAA-TGTC
*
348483 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACACTGATCCAACTCCTTATGTGATAGATG
1 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGATG
*
348548 AGCCAAGGAT-GGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCT
66 AGCCAAGG-TCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCT
348612 TCTCATTACAAACTTCTCCTATTGGGAATGTC
130 TCTCATTACAAACTTCTCCTATTGGGAATGTC
* * * * * * * *
348644 AATCCAACACCTTATGCAATGGATGACTTAAGGTGAAGCTGATTCAACTCCTTATGAGATAGA
1 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGA
348707 ATAAAGTGTA
Statistics
Matches: 734, Mismatches: 104, Indels: 44
0.83 0.12 0.05
Matches are distributed among these distances:
157 4 0.01
158 267 0.36
159 96 0.13
160 95 0.13
161 270 0.37
162 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (161 bp):
GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACGCTGATCCAACTCCTTATGTGATAGATG
AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCTT
CTCATTACAAACTTCTCCTATTGGGAATGTC
Found at i:348548 original size:40 final size:41
Alignment explanation
Indices: 348482--348583 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 41
348472 TCTAGAACTT
* * *
348482 TGATCCAACTCCTTCTGCGATGGATGA-CCTAAGG-TGACAC
1 TGATCCAACTCCTTATGTGATAGATGAGCC-AAGGATGACAC
****
348522 TGATCCAACTCCTTATGTGATAGATGAGCCAAGGATGGTGT
1 TGATCCAACTCCTTATGTGATAGATGAGCCAAGGATGACAC
*
348563 TGTTCCAACTCCTTATGTGAT
1 TGATCCAACTCCTTATGTGAT
348584 GGAATCAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
40 28 0.54
41 24 0.46
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
TGATCCAACTCCTTATGTGATAGATGAGCCAAGGATGACAC
Found at i:348722 original size:158 final size:159
Alignment explanation
Indices: 347686--348706 Score: 1090
Period size: 158 Copynumber: 6.4 Consensus size: 159
347676 CAAAAATGCT
* ** * * * * * * * *
347686 GATCCAACTCCTTATGTGATGGGTAACCTATGGTGATGTTGATTCAACTCTTTATGTGATGGATG
1 GATCCAACTCCTTCTGCAATGGATGACCTAAGGTGAAGCTGATCCAACTCCTTATGTGATAGATG
* *
347751 AGCCAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAAT-TAGACAAATGTTGAGCAAGCTCT
66 A--CAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGA-AAATGTTGAGCAAGTTCT
* * * *
347815 TCTCATTACGAACTTCTCTTATCGGGAATATC
128 TCTCATTACAAACTTCTCCTATTGGGAATGTC
** * * * *
347847 GATATAACTCATTCTG-AGATGGATTACCTAAGGTGAGGC-CATCCAACTCCTTATGTGATAGAT
1 GATCCAACTCCTTCTGCA-ATGGATGACCTAAGGTGAAGCTGATCCAACTCCTTATGTGATAGAT
* * * *
347910 GGGCCAAGCTTAGTGTTGTTCCAACT-CTTATATGATGGAATCAAGAAAATGTTGAGCAAGTTCT
65 --GACAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCT
* * *
347974 TCTCATTAAAAACTTTTCCTATTGAGAATGTC
128 TCTCATTACAAACTTCTCCTATTGGGAATGTC
* * *
348006 GATCCAATTCCTTCTGCAATGGATGACCTAAGGTGATGCTGATCCAACTCCTTATGTGATGGATG
1 GATCCAACTCCTTCTGCAATGGATGACCTAAGGTGAAGCTGATCCAACTCCTTATGTGATAGATG
* * * * *
348071 AGCCAAGGTCGGTGATT-TTCCAACTCCTTTTGTGATGAAATCAAGCAAATATTGAGCAAGTTC-
66 A--CAAGGTCAGTG-TTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCT
* * *
348134 T-T-ATTA-AGGACTTCTCCTATCGGGAACT-TT
128 TCTCATTACA-AACTTCTCCTATTGGGAA-TGTC
* * ** * *
348164 GATCTAACTCTTTCTGTGATGGATGACCTAAGGTGACGTTGATCCAACTCCTTATGTGATAGATT
1 GATCCAACTCCTTCTGCAATGGATGACCTAAGGTGAAGCTGATCCAACTCCTTATGTGATAGA-T
* * *
348229 AGCCAAGGTCAATGTTGTTCCAACTCCTTATGTGATAGAATCAAGAAAATGTTGAGCAAGTTCTT
65 -GACAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCTT
348294 CTCATTACAAACTTCTCCTATTGGGAATGTC
129 CTCATTACAAACTTCTCCTATTGGGAATGTC
* *
348325 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACA-CTGATCCAACTCCTTATGTGATGGAT
1 GATCCAACTCCTTCTGCAATGGATGACCTAAGGTGA-AGCTGATCCAACTCCTTATGTGATAGAT
* * * * *
348389 GAGCCAAGGTCGGTGTTGTTCCAACACCTTATGTGATGGAATCAAGCAAATATTGAGCAAGTT-A
65 GA--CAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCT
* * *
348453 TCT--TT-CTGAACTTCTCCTATCT-AGAACT-TT
128 TCTCATTAC-AAACTTCTCCTAT-TGGGAA-TGTC
*
348483 GATCCAACTCCTTCTGCGATGGATGACCTAAGGTGACA-CTGATCCAACTCCTTATGTGATAGAT
1 GATCCAACTCCTTCTGCAATGGATGACCTAAGGTGA-AGCTGATCCAACTCCTTATGTGATAGAT
*
348547 GAGCCAAGGAT-GGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTC
65 GA--CAAGG-TCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTC
348611 TTCTCATTACAAACTTCTCCTATTGGGAATGTC
127 TTCTCATTACAAACTTCTCCTATTGGGAATGTC
* * * * * *
348644 AATCCAACACCTTATGCAATGGATGACTTAAGGTGAAGCTGATTCAACTCCTTATGAGATAGA
1 GATCCAACTCCTTCTGCAATGGATGACCTAAGGTGAAGCTGATCCAACTCCTTATGTGATAGA
348707 ATAAAGTGTA
Statistics
Matches: 726, Mismatches: 100, Indels: 68
0.81 0.11 0.08
Matches are distributed among these distances:
157 4 0.01
158 264 0.36
159 98 0.13
160 93 0.13
161 264 0.36
162 3 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (159 bp):
GATCCAACTCCTTCTGCAATGGATGACCTAAGGTGAAGCTGATCCAACTCCTTATGTGATAGATG
ACAAGGTCAGTGTTGTTCCAACTCCTTATGTGATGGAATCAAGAAAATGTTGAGCAAGTTCTTCT
CATTACAAACTTCTCCTATTGGGAATGTC
Found at i:352120 original size:181 final size:181
Alignment explanation
Indices: 351816--352357 Score: 1021
Period size: 181 Copynumber: 3.0 Consensus size: 181
351806 GTGAATTTCT
*
351816 TTCTTAGGTAATAAATGGCTCTCTCCTTTCTTCCTGACTCATCATGTTGTCCTAAAACACACCCC
1 TTCTTAGGTAATAAATGGCTCTCTCCTTTCTTCCTGACTCATCATGTTGTCCTAACACACACCCC
351881 ATTGAATTCTTGAAAATTGTTAAGTAAAGAATTAACGGCCTACCAGGCATTGGTGCTACTAGGAT
66 ATTGAATTCTTGAAAATTGTTAAGTAAAGAATTAACGGCCTACCAGGCATTGGTGCTACTAGGAT
*
351946 TGCATCATTGGACTTGTATTTCATGATAATCTCCAAAATCTCATGGTATCA
131 TGCATCATTGGACATGTATTTCATGATAATCTCCAAAATCTCATGGTATCA
*
351997 TTCTTAGGTAATAAATGGCTCTCTCCTTTCTTCCTGACTCATCATGTTTTCCTAACACACACCCC
1 TTCTTAGGTAATAAATGGCTCTCTCCTTTCTTCCTGACTCATCATGTTGTCCTAACACACACCCC
352062 ATTGAATTCTTGAAAATTGTTAAGTAAAGAATTAACGGCCTACCAGGCATTGGTGCTACTAGGAT
66 ATTGAATTCTTGAAAATTGTTAAGTAAAGAATTAACGGCCTACCAGGCATTGGTGCTACTAGGAT
*
352127 TGCATCATTGGACATGTATTTCATGATAATCTCCAAAGTCTCATGGTATCA
131 TGCATCATTGGACATGTATTTCATGATAATCTCCAAAATCTCATGGTATCA
352178 TTCTTAGGTAATAAATGGCTCTCTCCTTTCTTCCTGACTCATCATGTTGTCCTAACACACACCCC
1 TTCTTAGGTAATAAATGGCTCTCTCCTTTCTTCCTGACTCATCATGTTGTCCTAACACACACCCC
*
352243 ATTTAATTCTTGAAAATTGTTAAGTAAAGAATTAACGGCCTACCAGGCATTGGTGCTACTAGGAT
66 ATTGAATTCTTGAAAATTGTTAAGTAAAGAATTAACGGCCTACCAGGCATTGGTGCTACTAGGAT
*
352308 TGCATCATTGGACATGTATTTCATGATAATCTCCAAAAGTATCATGGTAT
131 TGCATCATTGGACATGTATTTCATGATAATCTCCAAAA-TCTCATGGTAT
352358 TTCTCATTCT
Statistics
Matches: 352, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
181 342 0.97
182 10 0.03
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (181 bp):
TTCTTAGGTAATAAATGGCTCTCTCCTTTCTTCCTGACTCATCATGTTGTCCTAACACACACCCC
ATTGAATTCTTGAAAATTGTTAAGTAAAGAATTAACGGCCTACCAGGCATTGGTGCTACTAGGAT
TGCATCATTGGACATGTATTTCATGATAATCTCCAAAATCTCATGGTATCA
Found at i:358130 original size:16 final size:16
Alignment explanation
Indices: 358093--358124 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
358083 TGCATAGCTC
*
358093 GCTTCTTTTCTTACTT
1 GCTTCTTCTCTTACTT
358109 GCTTCTTCTCTTACTT
1 GCTTCTTCTCTTACTT
358125 CTTTCTACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.28, G:0.06, T:0.59
Consensus pattern (16 bp):
GCTTCTTCTCTTACTT
Found at i:365143 original size:21 final size:21
Alignment explanation
Indices: 365119--365164 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
365109 ATAACCAGAA
*
365119 CCCTGGGGGGGGTATCGATTC
1 CCCTGGGGGGGGAATCGATTC
** *
365140 CCCTTTGGGGGGAATCGGTTC
1 CCCTGGGGGGGGAATCGATTC
365161 CCCT
1 CCCT
365165 TCAAAGGGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (21 bp):
CCCTGGGGGGGGAATCGATTC
Found at i:365165 original size:21 final size:22
Alignment explanation
Indices: 365125--365185 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
365115 AGAACCCTGG
* * *
365125 GGGGGGTATCGATTCCCCTT-T
1 GGGGGGAATCGGTTCCCCTTAA
365146 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTT-AA
*
365169 AGGGGGAATCGGTTCCC
1 GGGGGGAATCGGTTCCC
365186 TCATGGGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGGTTCCCCTTAA
Found at i:365199 original size:20 final size:21
Alignment explanation
Indices: 365145--365207 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
365135 GATTCCCCTT
365145 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
365169 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
365189 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
365208 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:369143 original size:7 final size:7
Alignment explanation
Indices: 369131--369156 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
369121 TCTTCAAGAT
369131 TTTCAAA
1 TTTCAAA
369138 TTTCAAA
1 TTTCAAA
369145 TTTCAAA
1 TTTCAAA
369152 TTTCA
1 TTTCA
369157 TTTCTAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTCAAA
Found at i:373076 original size:3 final size:3
Alignment explanation
Indices: 373063--373096 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
373053 CCCGGGTTTG
373063 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
373097 CGTTTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:377941 original size:22 final size:22
Alignment explanation
Indices: 377913--377962 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
377903 AGGTTTGATC
*
377913 GACGGCAATAACAATAAATAGA
1 GACGGCAACAACAATAAATAGA
* *
377935 GACGGCAACAACGATAAATAGC
1 GACGGCAACAACAATAAATAGA
377957 GACGGC
1 GACGGC
377963 GGGCGTGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (22 bp):
GACGGCAACAACAATAAATAGA
Found at i:378884 original size:30 final size:29
Alignment explanation
Indices: 378826--378881 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
378816 AAACTTATAC
*
378826 ATTCTATAAATTTATCTTAATTTAAAATA
1 ATTCAATAAATTTATCTTAATTTAAAATA
378855 ATTCAATAAATTTAATCTT-ATTTAAAA
1 ATTCAATAAATTT-ATCTTAATTTAAAA
378882 ATATATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTCAATAAATTTATCTTAATTTAAAATA
Found at i:382163 original size:20 final size:20
Alignment explanation
Indices: 382125--382164 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
382115 AACTCGGACC
*
382125 GAACCGAGTTAACCCGAACT
1 GAACCGAGTTAACACGAACT
* *
382145 GAACTGAGTTAACATGAACT
1 GAACCGAGTTAACACGAACT
382165 AAGTCAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
GAACCGAGTTAACACGAACT
Found at i:383161 original size:25 final size:25
Alignment explanation
Indices: 383100--383161 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
383090 TCTAATGTTC
* *
383100 AAATGATCAAAATACCTTGAACTCT
1 AAATAATCAGAATACCTTGAACTCT
* *
383125 AAAGAATTAGAATACCTTGAAGC-CT
1 AAATAATCAGAATACCTTGAA-CTCT
*
383150 AAATTATCAGAA
1 AAATAATCAGAA
383162 GTAATGCCAC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (25 bp):
AAATAATCAGAATACCTTGAACTCT
Found at i:384513 original size:22 final size:22
Alignment explanation
Indices: 384485--384535 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
384475 TGTCCCGAAG
384485 GAAGGACCACTAGATACATCCC
1 GAAGGACCACTAGATACATCCC
* *
384507 GAAGGACCACTGGATACGTCCC
1 GAAGGACCACTAGATACATCCC
384529 GAAGGAC
1 GAAGGAC
384536 TAATATACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.29, G:0.25, T:0.12
Consensus pattern (22 bp):
GAAGGACCACTAGATACATCCC
Found at i:391407 original size:22 final size:22
Alignment explanation
Indices: 391378--391477 Score: 137
Period size: 22 Copynumber: 4.5 Consensus size: 22
391368 TTCAGTATTT
391378 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
391400 ATCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*** * *
391422 GTTTTGAAGAACCACTGAATAC
1 GTCCCGAAGGACCACTGGATAC
*
391444 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAC
391466 GTCCCGAAGGAC
1 GTCCCGAAGGAC
391478 TAATATATCC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:394098 original size:3 final size:3
Alignment explanation
Indices: 394090--394115 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
394080 CTTAAATCTC
394090 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
394116 CATTAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:394338 original size:2 final size:2
Alignment explanation
Indices: 394331--394361 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
394321 TTTTAATCTT
394331 TA TA TA TA T- 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
394362 CATGTTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:395833 original size:5 final size:5
Alignment explanation
Indices: 395823--395850 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
395813 CATATTAATA
395823 TTATT TTATT TTATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTA
395851 CATATTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:396548 original size:23 final size:23
Alignment explanation
Indices: 396518--396562 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
396508 AGAGGAGGGA
396518 GAAAAGAAAGTGAAGGCGGGGGG
1 GAAAAGAAAGTGAAGGCGGGGGG
396541 GAAAAGAAAGTGAAGGCGGGGG
1 GAAAAGAAAGTGAAGGCGGGGG
396563 AGTGAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.51, T:0.04
Consensus pattern (23 bp):
GAAAAGAAAGTGAAGGCGGGGGG
Found at i:399322 original size:16 final size:15
Alignment explanation
Indices: 399301--399364 Score: 83
Period size: 16 Copynumber: 4.1 Consensus size: 15
399291 TGTACAAACA
*
399301 TATTTTGTTTTATGTT
1 TATTTTATTTTAT-TT
399317 TATTTTATGTTTATTT
1 TATTTTAT-TTTATTT
*
399333 TATTTTGGTTTTATTT
1 TATTTT-ATTTTATTT
399349 TATTTTATTTTATTT
1 TATTTTATTTTATTT
399364 T
1 T
399365 CTTGCACTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 9 0.21
16 28 0.65
17 6 0.14
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.77
Consensus pattern (15 bp):
TATTTTATTTTATTT
Found at i:399324 original size:11 final size:10
Alignment explanation
Indices: 399301--399364 Score: 83
Period size: 11 Copynumber: 6.1 Consensus size: 10
399291 TGTACAAACA
*
399301 TATTTTGTTT
1 TATTTTATTT
399311 TATGTTTATTT
1 TAT-TTTATTT
399322 TATGTTTATTT
1 TAT-TTTATTT
*
399333 TATTTTGGTTT
1 TATTTT-ATTT
399344 TATTTTATTT
1 TATTTTATTT
399354 TATTTTATTT
1 TATTTTATTT
399364 T
1 T
399365 CTTGCACTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
10 20 0.41
11 29 0.59
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.77
Consensus pattern (10 bp):
TATTTTATTT
Found at i:399329 original size:6 final size:5
Alignment explanation
Indices: 399301--399364 Score: 83
Period size: 5 Copynumber: 12.2 Consensus size: 5
399291 TGTACAAACA
* *
399301 TATTT TGTTT TATGTT TATTT TATGTT TATTT TATTT TGGTTT TATTT
1 TATTT TATTT TAT-TT TATTT TAT-TT TATTT TATTT T-ATTT TATTT
399349 TATTT TATTT TATTT T
1 TATTT TATTT TATTT T
399365 CTTGCACTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
5 38 0.73
6 14 0.27
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:400754 original size:14 final size:14
Alignment explanation
Indices: 400735--400762 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
400725 ACATAAAGGG
400735 AATGATTGAAATAA
1 AATGATTGAAATAA
400749 AATGATTGAAATAA
1 AATGATTGAAATAA
400763 TTCTATCATG
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:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (14 bp):
AATGATTGAAATAA
Found at i:402751 original size:18 final size:19
Alignment explanation
Indices: 402704--402752 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
402694 TTTGTAACCC
*
402704 TTATATGTTTTCATATATT
1 TTATATTTTTTCATATATT
402723 TTACTAATTTTTT-ATAT-TT
1 TTA-T-ATTTTTTCATATATT
402742 TTATATTTTTT
1 TTATATTTTTT
402753 ACCCCATGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.26
18 1 0.04
19 8 0.30
20 5 0.19
21 6 0.22
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
TTATATTTTTTCATATATT
Found at i:403850 original size:41 final size:41
Alignment explanation
Indices: 403804--403928 Score: 175
Period size: 41 Copynumber: 3.0 Consensus size: 41
403794 TATTTAAAAA
403804 AAGTCTTTTTACATAGAAAATTTTTAGTTAAGATGATTCCT
1 AAGTCTTTTTACATAGAAAATTTTTAGTTAAGATGATTCCT
**
403845 AAGTCTTTTTATGTAG-AAATATTTTAGTTAAGATGATTCCT
1 AAGTCTTTTTACATAGAAAAT-TTTTAGTTAAGATGATTCCT
*
403886 AAGT-TCTTTTACATAGGAAAA-TTTTAGTAAAGATGATTCCT
1 AAGTCT-TTTTACATA-GAAAATTTTTAGTTAAGATGATTCCT
403927 AA
1 AA
403929 AATAACTCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
40 5 0.07
41 66 0.88
42 1 0.01
43 3 0.04
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (41 bp):
AAGTCTTTTTACATAGAAAATTTTTAGTTAAGATGATTCCT
Found at i:404694 original size:87 final size:86
Alignment explanation
Indices: 404564--404771 Score: 195
Period size: 86 Copynumber: 2.4 Consensus size: 86
404554 TGAGTTTTAG
* * * * * * *
404564 CTCTTAAAGGATTCATAGCCC-AGATTTTTGGTGATTCTAGTGAGGAGGACTTGATGAATCCACT
1 CTCTTAATGAATTCATAGCCCAAGA-TTTGGGTGGTCCTAGTGAGAAGGA-TTAATGAATCCACT
*
404628 AACGT-GAAAGGATGACCTTTACA
64 AAC-TCGAAAGGATGAACTTTACA
* * *
404651 CTCTTAATGAATTCATAGCCCAAGATTTGGGTGGTCCTTGTGAGAAGGATTAATGAATTCACTGA
1 CTCTTAATGAATTCATAGCCCAAGATTTGGGTGGTCCTAGTGAGAAGGATTAATGAATCCACTAA
* * * * * *
404716 CTCTAGATGTTGAATTTTATA
66 CTCGAAAGGATGAACTTTACA
* * *
404737 CTCTTAATGAGTTCATAGCCTAGGATTTGGGTGGT
1 CTCTTAATGAATTCATAGCCCAAGATTTGGGTGGT
404772 GTCACACCCC
Statistics
Matches: 99, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
85 1 0.01
86 57 0.58
87 38 0.38
88 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (86 bp):
CTCTTAATGAATTCATAGCCCAAGATTTGGGTGGTCCTAGTGAGAAGGATTAATGAATCCACTAA
CTCGAAAGGATGAACTTTACA
Found at i:416818 original size:21 final size:21
Alignment explanation
Indices: 416792--416837 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
416782 GATTTCTGGG
* *
416792 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
416813 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
416834 CAAG
1 CAAG
416838 CGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:416908 original size:23 final size:22
Alignment explanation
Indices: 416864--416908 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
416854 AATGTCATGG
*
416864 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
416886 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
416909 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:418284 original size:31 final size:31
Alignment explanation
Indices: 418211--418343 Score: 146
Period size: 31 Copynumber: 4.3 Consensus size: 31
418201 AGAGTCGAGG
*
418211 GTTTACCTATGTTCTACGAAACATATGGACA
1 GTTTACCTATGTTCTACGAGACATATGGACA
*
418242 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTC-TACGAGACATATGGACA
* *
418274 GTATACCTATGTTCTAAG-GAACATATGGACA
1 GTTTACCTATGTTCTACGAG-ACATATGGACA
* * * *
418305 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGAGACATATGGACA
418336 G-TTACCTA
1 GTTTACCTA
418344 GGATCTTTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
30 8 0.09
31 50 0.57
32 29 0.33
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGAGACATATGGACA
Found at i:418358 original size:30 final size:30
Alignment explanation
Indices: 418297--418393 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
418287 CTAAGGAACA
* ***
418297 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCTAGGATCTTTATGACC
418328 TATGGACAGTTACCTAGGATCTTTATGACC
1 TATGGACAGTTACCTAGGATCTTTATGACC
* * * *
418358 TCTGGATAGTTACCGAGGATCTTTATAACC
1 TATGGACAGTTACCTAGGATCTTTATGACC
*
418388 TCTGGA
1 TATGGA
418394 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 49 0.84
31 9 0.16
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCTAGGATCTTTATGACC
Found at i:418394 original size:30 final size:30
Alignment explanation
Indices: 418325--418396 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
418315 GTTCTTCGGG
* * * *
418325 ACCTATGGACAGTTACCTAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
418355 ACCTCTGGATAGTTACCGAGGATCTTTATA
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
418385 ACCTCTGGATAG
1 ACCTCTGGATAG
418397 GTCCTTCAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATA
Found at i:421840 original size:21 final size:21
Alignment explanation
Indices: 421814--421859 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
421804 GATTTCTGGG
* *
421814 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
421835 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
421856 CAAG
1 CAAG
421860 CGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:421930 original size:23 final size:22
Alignment explanation
Indices: 421886--421930 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
421876 AATGTCATGG
*
421886 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
421908 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
421931 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:423306 original size:31 final size:31
Alignment explanation
Indices: 423233--423360 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
423223 AGAGTCGAGG
*
423233 GTTTACCTATGTTCTACGAAACATATGGACA
1 GTTTACCTATGTTCTACGAGACATATGGACA
*
423264 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTC-TACGAGACATATGGACA
* *
423296 GTATACCTATGTTCTAAG-GAACATATGGACA
1 GTTTACCTATGTTCTACGAG-ACATATGGACA
* * * *
423327 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGAGACATATGGACA
423358 GTT
1 GTT
423361 ATCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.01
31 52 0.63
32 29 0.35
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGAGACATATGGACA
Found at i:423391 original size:30 final size:30
Alignment explanation
Indices: 423346--423418 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
423336 GGTTCTTCGG
* * *
423346 GACCTATGGACAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
423376 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
423406 GACCTCTGGATAG
1 GACCTCTGGATAG
423419 GTCCTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:443120 original size:13 final size:13
Alignment explanation
Indices: 443102--443131 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
443092 ATAAATGAAC
*
443102 ATATATGAAAATG
1 ATATATCAAAATG
443115 ATATATCAAAATG
1 ATATATCAAAATG
443128 ATAT
1 ATAT
443132 TAAAAGTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.33
Consensus pattern (13 bp):
ATATATCAAAATG
Found at i:454623 original size:14 final size:14
Alignment explanation
Indices: 454604--454645 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
454594 ATCTACTTTA
454604 CTTTTTCACTTCAC
1 CTTTTTCACTTCAC
*
454618 CTTTTTCACTTTAC
1 CTTTTTCACTTCAC
454632 CTTATTTCATCTTC
1 CTT-TTTCA-CTTC
454646 TTCTTCCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 16 0.67
15 5 0.21
16 3 0.12
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (14 bp):
CTTTTTCACTTCAC
Found at i:456697 original size:6 final size:6
Alignment explanation
Indices: 456683--456711 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
456673 CCCATATAAA
456683 AAAAT- AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG
456712 GATGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:457316 original size:20 final size:20
Alignment explanation
Indices: 457291--457333 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
457281 TCTAAGAGCC
457291 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
457311 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
457331 CAT
1 CAT
457334 GTGGTGGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:458860 original size:18 final size:18
Alignment explanation
Indices: 458824--458865 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
458814 CGATATTTCC
*
458824 ATCCATTTTGCCACGACAT
1 ATCCA-TTTGCCACCACAT
*
458843 ATCCATTTGCTACCACAT
1 ATCCATTTGCCACCACAT
458861 A-CCAT
1 ATCCAT
458866 CATTCCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.07, T:0.31
Consensus pattern (18 bp):
ATCCATTTGCCACCACAT
Found at i:461585 original size:19 final size:20
Alignment explanation
Indices: 461551--461598 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
461541 GCTCAAAATC
* *
461551 ATTTTTCAAAGCTTCATTTT
1 ATTTTTCAAAGATTCAATTT
461571 ATTTTTCAAA-ATTCAATTT
1 ATTTTTCAAAGATTCAATTT
*
461590 ATCTTTCAA
1 ATTTTTCAA
461599 GAAAAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTTCAAAGATTCAATTT
Found at i:464091 original size:20 final size:20
Alignment explanation
Indices: 464055--464143 Score: 62
Period size: 20 Copynumber: 4.6 Consensus size: 20
464045 TTTATAGTTT
*
464055 AATATTTATTATATTTTTAA
1 AATATTTAATATATTTTTAA
* *
464075 AATATTTAATAGTTTTTTTAG
1 AATATTTAATA-TATTTTTAA
* * *
464096 TAT-TTTAATATATATATATA
1 AATATTTAATATATTTTTA-A
*
464116 TATATTTAAT-T-TTTTT--
1 AATATTTAATATATTTTTAA
464132 AATATTTAATAT
1 AATATTTAATAT
464144 TTAATTTTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
16 9 0.17
17 1 0.02
19 8 0.15
20 21 0.39
21 15 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATATTTAATATATTTTTAA
Found at i:464145 original size:23 final size:23
Alignment explanation
Indices: 464117--464175 Score: 93
Period size: 23 Copynumber: 2.5 Consensus size: 23
464107 ATATATATAT
464117 ATATTTAATTTTTTTAATATTT-A
1 ATATTTAATTTTTTT-ATATTTGA
464140 ATATTTAATTTTTTTATATTTGA
1 ATATTTAATTTTTTTATATTTGA
464163 ATATTTATATTTT
1 ATATTTA-ATTTT
464176 CAATAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.18
23 23 0.68
24 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
ATATTTAATTTTTTTATATTTGA
Found at i:464148 original size:14 final size:13
Alignment explanation
Indices: 464099--464174 Score: 51
Period size: 14 Copynumber: 6.2 Consensus size: 13
464089 TTTTTAGTAT
*
464099 TTTAATATATATA
1 TTTAATATTTATA
*
464112 TATATATATTTA-A
1 TTTA-ATATTTATA
464125 TTT--T-TTTAATA
1 TTTAATATTT-ATA
464136 TTTAATATTTA-A
1 TTTAATATTTATA
464148 TTT--T-TTTATA
1 TTTAATATTTATA
464158 TTTGAATATTTATA
1 TTT-AATATTTATA
464172 TTT
1 TTT
464175 TCAATAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 21
0.67 0.04 0.29
Matches are distributed among these distances:
9 7 0.14
10 7 0.14
11 4 0.08
12 4 0.08
13 9 0.18
14 18 0.37
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:464158 original size:22 final size:22
Alignment explanation
Indices: 464108--464175 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 22
464098 TTTTAATATA
*
464108 TATATATATATATTTAATTTTTT
1 TATATTTA-ATATTTAATTTTTT
464131 TAATATTTAATATTTAATTTTTT
1 T-ATATTTAATATTTAATTTTTT
464154 TATATTTGAATATTTATATTTT
1 TATATTT-AATATTTA-ATTTT
464176 CAATAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 6 0.15
23 24 0.59
24 11 0.27
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (22 bp):
TATATTTAATATTTAATTTTTT
Found at i:467000 original size:3 final size:3
Alignment explanation
Indices: 466992--467025 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
466982 TTAATCTAAA
466992 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
467026 GCCAACATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:473984 original size:31 final size:31
Alignment explanation
Indices: 473949--474007 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
473939 AATTATACAA
473949 ATGAAAGTTTGAATTTGATTCAGTTGTACCC
1 ATGAAAGTTTGAATTTGATTCAGTTGTACCC
*
473980 ATGAAAGTTTGATTTTGATTCAGTTGTA
1 ATGAAAGTTTGAATTTGATTCAGTTGTA
474008 GACATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (31 bp):
ATGAAAGTTTGAATTTGATTCAGTTGTACCC
Found at i:475415 original size:21 final size:21
Alignment explanation
Indices: 475391--475435 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
475381 TCGATAAAAA
*
475391 TTTATTTAAAATATTATTATT
1 TTTATTTAAAATATTAATATT
475412 TTTATTTAAAATATTAATATT
1 TTTATTTAAAATATTAATATT
475433 TTT
1 TTT
475436 TAACATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTTAAAATATTAATATT
Found at i:475560 original size:21 final size:21
Alignment explanation
Indices: 475458--475551 Score: 161
Period size: 21 Copynumber: 4.5 Consensus size: 21
475448 TAAAGTACCT
*
475458 AATAATAATAAAATCGGTAAA
1 AATAATAATAAAATCGGTAGA
*
475479 AAAAATAATAAAATCGGTAGA
1 AATAATAATAAAATCGGTAGA
*
475500 AAAAATAATAAAATCGGTAGA
1 AATAATAATAAAATCGGTAGA
475521 AATAATAATAAAATCGGTAGA
1 AATAATAATAAAATCGGTAGA
475542 AATAATAATA
1 AATAATAATA
475552 TTTTCGGTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.22
Consensus pattern (21 bp):
AATAATAATAAAATCGGTAGA
Found at i:478944 original size:15 final size:13
Alignment explanation
Indices: 478910--478949 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
478900 CTAGTCGAGA
478910 TGAGTCAACTCAC
1 TGAGTCAACTCAC
*
478923 TGAGTCAACTCGAG
1 TGAGTCAACTC-AC
478937 TGGAGTCAACTCA
1 T-GAGTCAACTCA
478950 TTGACCGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 11 0.46
14 3 0.12
15 10 0.42
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (13 bp):
TGAGTCAACTCAC
Found at i:487945 original size:28 final size:27
Alignment explanation
Indices: 487914--487970 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
487904 TATTTTATAT
* *
487914 TTTATAATTAATAAAA-AGTATTATATTA
1 TTTAAAATCAATAAAATA-TATTA-ATTA
*
487942 TTTAAAATCATTAAAATATATTAATTA
1 TTTAAAATCAATAAAATATATTAATTA
487969 TT
1 TT
487971 CTGACAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 6 0.24
28 18 0.72
29 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTAAAATCAATAAAATATATTAATTA
Found at i:492899 original size:45 final size:45
Alignment explanation
Indices: 492848--493002 Score: 181
Period size: 45 Copynumber: 3.5 Consensus size: 45
492838 TTGAATTTGC
492848 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTG
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTG
* ** * * * ** *
492893 TTCCACTATTCTTTTGTGGAG-TTCAGA-TTT-ATGATTGAATTTG
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGA-AAAATCTG
492936 CTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTG
1 -TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTG
*
492982 TTCCACTACTCTTTCGTGGAG
1 TTCCACTACTCTTCCGTGGAG
493003 CTCAGACTTT
Statistics
Matches: 86, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
42 3 0.03
43 8 0.09
44 22 0.26
45 42 0.49
46 8 0.09
47 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (45 bp):
TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTG
Found at i:492956 original size:44 final size:46
Alignment explanation
Indices: 492838--493013 Score: 139
Period size: 45 Copynumber: 3.9 Consensus size: 46
492828 AAATTCAAAG
* * *
492838 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGA
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAG-TTCAGACTTTGATGA
** * * **
492885 -AAAATCTG-TTCCACTATTCTTTTGTGGAGTTCAGA-TTT-ATGA
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTCAGACTTTGATGA
* * *
492927 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGA
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAG-TTCAGACTTTGATGA
** * * *
492974 -AAAATCTG-TTCCACTACTCTTTCGTGGAGCTCAGACTTTG
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTCAGACTTTG
493014 GTCTTGTTCT
Statistics
Matches: 99, Mismatches: 25, Indels: 13
0.72 0.18 0.09
Matches are distributed among these distances:
42 3 0.03
43 8 0.08
44 30 0.30
45 42 0.42
46 13 0.13
47 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (46 bp):
TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTCAGACTTTGATGA
Found at i:492989 original size:89 final size:89
Alignment explanation
Indices: 492838--493008 Score: 315
Period size: 89 Copynumber: 1.9 Consensus size: 89
492828 AAATTCAAAG
*
492838 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTGTTCCACTATT
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTGTTCCACTACT
* *
492903 CTTTTGTGGAGTTCAGATTTATGA
66 CTTTCGTGGAGCTCAGATTTATGA
492927 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTGTTCCACTACT
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTGTTCCACTACT
492992 CTTTCGTGGAGCTCAGA
66 CTTTCGTGGAGCTCAGA
493009 CTTTGGTCTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (89 bp):
TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTGTTCCACTACT
CTTTCGTGGAGCTCAGATTTATGA
Found at i:493635 original size:22 final size:22
Alignment explanation
Indices: 493610--493664 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
493600 AAAGCTTTGG
*
493610 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTACCA
*
493632 TCTTTAAAAAGAGAATCTACCA
1 TCTTTGAAAAGAGAATCTACCA
*
493654 TCCTTGTAAAA
1 TCTTTG-AAAA
493665 TGTAGATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTACCA
Found at i:499071 original size:16 final size:16
Alignment explanation
Indices: 499050--499080 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
499040 AACTTTGACC
499050 GAAAAGTCAAATTTTT
1 GAAAAGTCAAATTTTT
*
499066 GAAAAGTCATATTTT
1 GAAAAGTCAAATTTT
499081 ATGTTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (16 bp):
GAAAAGTCAAATTTTT
Found at i:501370 original size:24 final size:24
Alignment explanation
Indices: 501331--501392 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
501321 ATATTTTATC
* *
501331 TGATTTCCGATTTGAAATATGTTA
1 TGATTTCTGATATGAAATATGTTA
* * *
501355 TGATTTCTGATATGAATTCTGTTC
1 TGATTTCTGATATGAAATATGTTA
*
501379 TGATTTTTGATATG
1 TGATTTCTGATATG
501393 GATTCTGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (24 bp):
TGATTTCTGATATGAAATATGTTA
Found at i:501397 original size:24 final size:24
Alignment explanation
Indices: 501350--501439 Score: 117
Period size: 24 Copynumber: 3.8 Consensus size: 24
501340 ATTTGAAATA
* *
501350 TGTTATGATTTCTGATATGAATTC
1 TGTTCTGATTTTTGATATGAATTC
*
501374 TGTTCTGATTTTTGATATGGATTC
1 TGTTCTGATTTTTGATATGAATTC
* *
501398 TGTTCTGATATATGATATGAATTC
1 TGTTCTGATTTTTGATATGAATTC
* *
501422 TGTTTTGATTTTTAATAT
1 TGTTCTGATTTTTGATAT
501440 CTCTGTTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (24 bp):
TGTTCTGATTTTTGATATGAATTC
Found at i:501739 original size:154 final size:153
Alignment explanation
Indices: 501457--501740 Score: 419
Period size: 154 Copynumber: 1.8 Consensus size: 153
501447 TATTGATGAA
* *
501457 AAATGTTTTATTTGGGGGTATTGTTGGAGGAAGAATATATGTAGGCTCCTCAGCTTTGTGCTCAG
1 AAATGTTTTATTTGGGGGTATTGTTGGAGGAAGAATATATGAAGGCTCCTCAGCTGTGTGCTCAG
* * * * * *
501522 GGCTTAACTGTTGTGTCGGGGTTGTATTGTTCTGGGGAACCTACACATTATGATGTGTTCGGTTG
66 GGCTTAACTGTTGTGCCGGAGTTGTATGGTTATGGGGAACCTACACATTATGACGTGTGCGGTTG
501587 GGGAATTTACTATGGTTTTTTAT
131 GGGAATTTACTATGGTTTTTTAT
**
501610 AAATGTTTTATTTGGGGGTTATTGTTGGAGGAAGAATATATGAAGGCTCCTTGGCTGTGTGCTCA
1 AAATGTTTTATTTGGGGG-TATTGTTGGAGGAAGAATATATGAAGGCTCCTCAGCTGTGTGCTCA
* *
501675 GGGCCTT-ACTGTTGTGCCGGAGTTGTATGGTTAT-GGGAACTTACACATTTTGGACGTGTGCGG
65 GGG-CTTAACTGTTGTGCCGGAGTTGTATGGTTATGGGGAACCTACACATTAT-GACGTGTGCGG
501738 TTG
128 TTG
501741 AGACAATTAC
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
153 33 0.28
154 80 0.69
155 3 0.03
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (153 bp):
AAATGTTTTATTTGGGGGTATTGTTGGAGGAAGAATATATGAAGGCTCCTCAGCTGTGTGCTCAG
GGCTTAACTGTTGTGCCGGAGTTGTATGGTTATGGGGAACCTACACATTATGACGTGTGCGGTTG
GGGAATTTACTATGGTTTTTTAT
Found at i:506967 original size:24 final size:24
Alignment explanation
Indices: 506916--506998 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
506906 ATATTTTATC
* * * * *
506916 TGATTACTGATCTAAATTATGCTC
1 TGATTTCTGATCTGAATTCTGTTA
506940 TGATTTCTGATCTGAATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTTA
* * * * *
506964 TGATATATGATATGAATTCTATTT
1 TGATTTCTGATCTGAATTCTGTTA
506988 TGATTTCTGAT
1 TGATTTCTGAT
506999 ATCTCTATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTA
Found at i:506999 original size:24 final size:24
Alignment explanation
Indices: 506940--507000 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
506930 AATTATGCTC
* *
506940 TGATTTCTGATCTGAATTCTGTTA
1 TGATTTCTGATATGAATTCTATTA
* * *
506964 TGATATATGATATGAATTCTATTT
1 TGATTTCTGATATGAATTCTATTA
506988 TGATTTCTGATAT
1 TGATTTCTGATAT
507001 CTCTATTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (24 bp):
TGATTTCTGATATGAATTCTATTA
Found at i:510146 original size:10 final size:11
Alignment explanation
Indices: 510129--510161 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
510119 TAAAATTATT
510129 GACCGTTGACC
1 GACCGTTGACC
510140 G-CCGTTGACC
1 GACCGTTGACC
*
510150 GACTGTTGACC
1 GACCGTTGACC
510161 G
1 G
510162 TTGACTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.21
Consensus pattern (11 bp):
GACCGTTGACC
Found at i:512697 original size:24 final size:24
Alignment explanation
Indices: 512649--512757 Score: 96
Period size: 24 Copynumber: 4.5 Consensus size: 24
512639 GAATATTTTA
* * * *
512649 TCTGATTTCCGATTTGAAATATGT
1 TCTGATTTCTGATCTGAATTCTGT
512673 TCTGATTTCTGATCT-AATTTCTGT
1 TCTGATTTCTGATCTGAA-TTCTGT
* *
512697 TTTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
512721 TCTGA-TACATGATATGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
* *
512745 TTTGATTTTTGAT
1 TCTGATTTCTGAT
512758 ATCTCCATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
23 4 0.06
24 62 0.91
25 2 0.03
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:512979 original size:155 final size:154
Alignment explanation
Indices: 512781--513079 Score: 460
Period size: 155 Copynumber: 1.9 Consensus size: 154
512771 GACGAATTTT
*
512781 TTTTATTTGGGGGTATTGTTGGAGGAAGAATATATGCAAGCTCCTCGGCTTTGTGCTCAGGGCCT
1 TTTTATTTGGGGGTATTGTTGGAGGAAGAATATATGCAAGCTCCTCGGCTGTGTGCTCAGGGCCT
* * * *
512846 AACTGTTGTGCCGGGGTTGTATGGTTCTGGGGAACCTACACATTAT-GATGTGTTCGGTTG-TGG
66 AACTGTTGTGCCGGGGTTGTATGGTTATGGGGAACCTACACATTATGGACGTGTGCGGTTGAGGG
512909 AATTTACTATGATTTTTTATAAATG
131 AA-TTACTATGATTTTTTATAAATG
*
512934 TTTTATTTGGGGTGTAATTGTTGGAGGAATAATATATG-AAGGCTCCTCGGCTGTGTGCTCAGGG
1 TTTTATTTGGGG-GT-ATTGTTGGAGGAAGAATATATGCAA-GCTCCTCGGCTGTGTGCTCAGGG
* *
512998 CCTTACTGTTGTGCTGGGGTTGTATGGTTATGGGGAACCTACACATTATGGACGTGTGCGGTTGA
63 CCTAACTGTTGTGCCGGGGTTGTATGGTTATGGGGAACCTACACATTATGGACGTGTGCGGTTGA
*
513063 GGGAATTGCTATGATTT
128 GGGAATTACTATGATTT
513080 CTAAATGTTT
Statistics
Matches: 132, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
153 12 0.09
154 4 0.03
155 89 0.67
156 23 0.17
157 4 0.03
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.37
Consensus pattern (154 bp):
TTTTATTTGGGGGTATTGTTGGAGGAAGAATATATGCAAGCTCCTCGGCTGTGTGCTCAGGGCCT
AACTGTTGTGCCGGGGTTGTATGGTTATGGGGAACCTACACATTATGGACGTGTGCGGTTGAGGG
AATTACTATGATTTTTTATAAATG
Found at i:520788 original size:23 final size:23
Alignment explanation
Indices: 520754--520803 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
520744 ATCAACTAAG
520754 AAGAGCTAATGTTAGGTCATGGA
1 AAGAGCTAATGTTAGGTCATGGA
*
520777 AAGAGCTGATGTTAGGTCATGGA
1 AAGAGCTAATGTTAGGTCATGGA
520800 AAGA
1 AAGA
520804 TCTGGCCAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (23 bp):
AAGAGCTAATGTTAGGTCATGGA
Found at i:528613 original size:21 final size:21
Alignment explanation
Indices: 528587--528626 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
528577 CAGAACCCCA
*
528587 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
528608 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
528627 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:529037 original size:21 final size:22
Alignment explanation
Indices: 528997--529037 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
528987 CTAAAGGTTT
* *
528997 TGTAAAGATATCCGCTAATTGG
1 TGTAAAGATATCCACAAATTGG
529019 TGTAAAG-TATCCACAAATT
1 TGTAAAGATATCCACAAATT
529038 CTAAAACTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (22 bp):
TGTAAAGATATCCACAAATTGG
Found at i:534508 original size:3 final size:3
Alignment explanation
Indices: 534493--534561 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
534483 AAAAACATAC
* * * *
534493 ATA ATA TTA ATA ATA ATA ATA AT- ATG GTA ATT ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
534540 AT- ATA ATA ATT ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
534562 TTTATAACCC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
2 6 0.11
3 48 0.89
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:534549 original size:26 final size:26
Alignment explanation
Indices: 534500--534561 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
534490 TACATAATAT
**
534500 TAATAATAATAATAATATGGTAATTA
1 TAATAATAATAATAATATAATAATTA
534526 TAATAATAATAATAATATAATAATTA
1 TAATAATAATAATAATATAATAATTA
534552 TAAT-ATAATA
1 TAATAATAATA
534562 TTTATAACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 6 0.18
26 28 0.82
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
TAATAATAATAATAATATAATAATTA
Found at i:534558 original size:14 final size:14
Alignment explanation
Indices: 534502--534568 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
534492 CATAATATTA
*
534502 ATAATAATAATAAT
1 ATAATAATTATAAT
**
534516 ATGGTAATTAT-A-
1 ATAATAATTATAAT
*
534528 ATAATAATAATAAT
1 ATAATAATTATAAT
534542 ATAATAATTATAAT
1 ATAATAATTATAAT
*
534556 ATAATATTTATAA
1 ATAATAATTATAA
534569 CCCGGACAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 8 0.19
13 2 0.05
14 33 0.77
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (14 bp):
ATAATAATTATAAT
Found at i:534812 original size:54 final size:54
Alignment explanation
Indices: 534738--535537 Score: 879
Period size: 54 Copynumber: 14.8 Consensus size: 54
534728 CAACCAGCGA
* * *
534738 GTTCACTCTCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCGTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* ** * * * ** *
534792 GTTCCCTCCCTCTTTTTTCAGGGAGTGGGAACTTGAACAATCTTCTACAAACGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * * * *
534846 GTTCGTTCCTTCTTTCTTTCAAGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGC-TTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* *
534901 GTTTGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTATGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * * *
534955 GTTTGCTCCATCTTACTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * * *
535009 GTTCACTCCCTCTTGCTTCAGAGAGTAAGAACTCGAACAATCCTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * * *
535063 GTTTGCTCTCTCTTGCTTCAGGGAGTAGGAACTCAAACAATCTTCTGCCTACGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * * * **
535117 GTTCACTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATGTTTTGCTTATAG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * *
535171 GTTTGCTCTCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTTTGGCCTATCGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCT-GCCTA-CGG
* *
535227 GTTCACTCCCTCTTGCTTCAGGGAGTAGGAACTC-AAAAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * *
535280 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTC-AAAAATATTCTGCTTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * * * * **
535333 GTTCGCTCTCTCTTTCTTTAGGGAGTAAGAACTCGAACAATCTTCTACGAACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
** * *
535387 GTTTTCTTCCTCTTGCTTCAGGGAGTTTA-GAACTCGAACAATCTTCTGCCAACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAG--TAGGAACTCGAACAATCTTCTGCCTACGG
** * * * * **** *
535442 GTTCAATCTCTCTTGCTTCAGGGATTA-GAACTCGAACAATTTTTTAAGAATGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* * * *
535495 GTTCGCTCCCTCTTTCTTCACGGAGTATAGAACTCAAACAATC
1 GTTCGCTCCCTCTTGCTTCAGGGAGTA-GGAACTCGAACAATC
535538 ATGATTTGCT
Statistics
Matches: 626, Mismatches: 112, Indels: 15
0.83 0.15 0.02
Matches are distributed among these distances:
53 126 0.20
54 356 0.57
55 110 0.18
56 34 0.05
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (54 bp):
GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
Found at i:535580 original size:37 final size:37
Alignment explanation
Indices: 535538--535623 Score: 122
Period size: 37 Copynumber: 2.3 Consensus size: 37
535528 TCAAACAATC
535538 ATGATTTGCTTCACTACT-TTTCTGTGAAGGCTTATAG-
1 ATGATTTGCTTCACTACTCTTTC-GTGAAGGCTTA-AGT
*
535575 ATGATTTGCTGCACTACTCTTTCGTGAAGGCTTAAGT
1 ATGATTTGCTTCACTACTCTTTCGTGAAGGCTTAAGT
*
535612 TTGATTTGCTTC
1 ATGATTTGCTTC
535624 GAAGGTCGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 2 0.05
37 38 0.86
38 4 0.09
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (37 bp):
ATGATTTGCTTCACTACTCTTTCGTGAAGGCTTAAGT
Found at i:536683 original size:15 final size:15
Alignment explanation
Indices: 536663--536692 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
536653 TTGAGATCTT
536663 TTGTTTCCCATTCTC
1 TTGTTTCCCATTCTC
536678 TTGTTTCCCATTCTC
1 TTGTTTCCCATTCTC
536693 CTCTGAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.53
Consensus pattern (15 bp):
TTGTTTCCCATTCTC
Found at i:538008 original size:2 final size:2
Alignment explanation
Indices: 538001--538205 Score: 259
Period size: 2 Copynumber: 103.0 Consensus size: 2
537991 ACAGAAGAGA
* * * *
538001 AT AT AT AT GT AC AT AT AT AT AC AT AT AT AT AT AC 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
*
538043 AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
* * * * *
538085 GT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT AC AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
538127 AT AT AT AT GT AT AT AT AC AT GT -T AT AT AT GT 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
* *
538168 AT AT AT AT AT AT AC AT AT AT AT AC 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
538206 GGGAGAATCG
Statistics
Matches: 171, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
1 1 0.01
2 170 0.99
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:539926 original size:24 final size:23
Alignment explanation
Indices: 539882--539926 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 23
539872 TCACGGGACT
539882 CCTAATGTTTAGGTTAGGCTCGA
1 CCTAATGTTTAGGTTAGGCTCGA
539905 CCTAA-GTTTAGGCTCTAGGCTC
1 CCTAATGTTTAGG-T-TAGGCTC
539927 ACTATATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 7 0.35
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (23 bp):
CCTAATGTTTAGGTTAGGCTCGA
Found at i:541447 original size:54 final size:54
Alignment explanation
Indices: 541370--542333 Score: 950
Period size: 54 Copynumber: 17.8 Consensus size: 54
541360 CAACCAGCGA
* * **
541370 GTTCACTCCTTCTTGCTTCAGGGAGTAAGAACTTAAACAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * * * * * * * ** *
541424 GTTTGCTCCCTCTTTCTTTAGGGAGTAGGACCTCGAACAATTTTTTACAAAAGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* ** * ** * * *
541478 GTTCGTTCATTCTTTCTTTCAATGAGTAAGAACTCAAACAATCTTCAGCCTACGA
1 GTTCGCTCCCTCTTGC-TTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * * * * *
541533 GTTCGCTTCCTCTTACTTCAGGG-GGAAGGAACTCGAACAATCTTTTGCCAACGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAA-GAACTCGAACAATCTTCTGCCTACGG
** * *
541587 GTTTTCTCTCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * * *
541641 GTTCGCTCCCTCTTGTTTCAGGGAGTAAGAACTCGAATAAACTTTTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * * *
541695 GTTCACTCCTTTTTGCTTTAGGGAGT-AGAAACTCGAACAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAG-AACTCGAACAATCTTCTGCCTACGG
** * * *
541749 GTTTACTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTACCTACAG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * *
541803 GTTCACT--CTCTTACTTCAGGGAGTAGGAACTCGAACAATCTTCTGGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCT-GCCTACGG
* * *
541856 GTTCGCTCCCTCTTGCTTCAGGGAGTAGGAATTCGAACAATCTTCTGCCTATGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * *
541910 GTTTGCTCCCTCTTGCTTCAGGGAGTAGGAACTCGAACAATATTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * * * * *
541964 GTTCGCTCTCTCTTTCTTCAAGGAGTACGAACTTGAACAATCTTCTGCCTATGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * * **
542018 GTTCACTCCCTTTTGCTTCAGGGAGT-AGAAACTCGAACAATCTTCTGCTTACTA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAG-AACTCGAACAATCTTCTGCCTACGG
* * * **** * *
542072 GTTCGCTCTCTCTTGTTTCAGGGAGTAGGAACTCGAACAATCTTCTATGAATGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * * * * **
542126 GTTTGTTTCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTGTGCCAATAG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTA-AGAACTCGAACAATCTTCTGCCTACGG
*** * * * ** *
542181 GTTTAATCTCTCTTGCTTCAGGGA-TTAGAACTCAAACAATCTTCTGCGAATGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
* * *
542234 GTTCGTTCCCTCTTACTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTA-AGAACTCGAACAATCTTCTGCCTACGG
*
542289 GTTCTCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTT
1 GTTCGCTCCCTCTTGCTTCAGGGAGTA-AGAACTCGAACAATCTT
542334 GATTTGCTTC
Statistics
Matches: 744, Mismatches: 153, Indels: 25
0.81 0.17 0.03
Matches are distributed among these distances:
52 36 0.05
53 60 0.08
54 468 0.63
55 180 0.24
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (54 bp):
GTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGCCTACGG
Found at i:542411 original size:37 final size:37
Alignment explanation
Indices: 542332--542417 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
542322 TCGAACAATC
* * *
542332 TTGATTTGCTTCACTATTTTTTTGTGAAGGCTTATAG
1 TTGATTTGCTTCACTACTCTTTCGTGAAGGCTTATAG
* *
542369 ATGATTTACTTCACTACTCTTTCGTGAAGGCTTA-AG
1 TTGATTTGCTTCACTACTCTTTCGTGAAGGCTTATAG
542405 TTTGATTTGCTTC
1 -TTGATTTGCTTC
542418 GAAGATCGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 39 0.95
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (37 bp):
TTGATTTGCTTCACTACTCTTTCGTGAAGGCTTATAG
Found at i:543668 original size:10 final size:10
Alignment explanation
Indices: 543653--543745 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 10
543643 TTTCCCTCTC
543653 TTTTTTTCC-
1 TTTTTTTCCT
543662 TTTTTTT-CT
1 TTTTTTTCCT
*
543671 ATTCTTTTTCAT
1 -TT-TTTTTCCT
* *
543683 TTTCTTTCAT
1 TTTTTTTCCT
*
543693 TTTCTTT-C-
1 TTTTTTTCCT
* *
543701 ATTTTTTCAT
1 TTTTTTTCCT
* *
543711 TTTCTTTCAT
1 TTTTTTTCCT
543721 TTTTTTTCCT
1 TTTTTTTCCT
**
543731 TTTTCCTCCT
1 TTTTTTTCCT
543741 TTTTT
1 TTTTT
543746 CCTTTTCTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
8 6 0.09
9 7 0.11
10 44 0.68
11 7 0.11
12 1 0.02
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:543678 original size:20 final size:18
Alignment explanation
Indices: 543653--543726 Score: 87
Period size: 20 Copynumber: 3.9 Consensus size: 18
543643 TTTCCCTCTC
*
543653 TTTTTTTCCTTTTTTTCTA
1 TTTTTTTCATTTTTTTC-A
543672 TTCTTTTTCATTTTCTTTCA
1 TT-TTTTTCATTTT-TTTCA
543692 TTTTCTTTCA-TTTTTTCA
1 TTTT-TTTCATTTTTTTCA
543710 TTTTCTTTCATTTTTTT
1 TTTT-TTTCATTTTTTT
543727 TCCTTTTTCC
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
18 15 0.30
19 13 0.26
20 18 0.36
21 4 0.08
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTCATTTTTTTCA
Found at i:543695 original size:28 final size:28
Alignment explanation
Indices: 543664--543735 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
543654 TTTTTTCCTT
543664 TTTTTCTATTC-TTTTTCATTTTCTTTCA
1 TTTTTCT-TTCATTTTTCATTTTCTTTCA
543692 -TTTTCTTTCATTTTTTCATTTTCTTTCA
1 TTTTTCTTTCA-TTTTTCATTTTCTTTCA
*
543720 TTTTT-TTTCCTTTTTC
1 TTTTTCTTTCATTTTTC
543736 CTCCTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 3 0.08
27 12 0.30
28 21 0.52
29 4 0.10
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTCTTTCATTTTTCATTTTCTTTCA
Found at i:543710 original size:18 final size:18
Alignment explanation
Indices: 543663--543725 Score: 83
Period size: 18 Copynumber: 3.3 Consensus size: 18
543653 TTTTTTTCCT
543663 TTTTTTCTATTCTT-TTTCA
1 TTTTTTC-ATT-TTCTTTCA
543682 TTTTCTTTCATTTTCTTTCA
1 -TTT-TTTCATTTTCTTTCA
543702 TTTTTTCATTTTCTTTCA
1 TTTTTTCATTTTCTTTCA
543720 TTTTTT
1 TTTTTT
543726 TTCCTTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 21 0.51
19 5 0.12
20 11 0.27
21 4 0.10
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTCATTTTCTTTCA
Found at i:543744 original size:38 final size:36
Alignment explanation
Indices: 543655--543754 Score: 96
Period size: 38 Copynumber: 2.7 Consensus size: 36
543645 TCCCTCTCTT
543655 TTTTTCCT-TTTTTTCTATTCTT-TTTCATTTTCTTTC
1 TTTTTCCTCTTTTTTC-ATT-TTCTTTCATTTTCTTTC
* * *
543691 ATTTTCTTTCATTTTTTCATTTTCTTTCATTTTTTTTCC
1 TTTTTC-CTC-TTTTTTCATTTTCTTTCATTTTCTTT-C
*
543730 TTTTTCCTCCTTTTTTCCTTTTCTT
1 TTTTTCCT-CTTTTTTCATTTTCTT
543755 ATTCAAGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
36 5 0.10
37 3 0.06
38 30 0.58
39 14 0.27
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (36 bp):
TTTTTCCTCTTTTTTCATTTTCTTTCATTTTCTTTC
Found at i:552988 original size:18 final size:17
Alignment explanation
Indices: 552965--552998 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
552955 CAGGGCTTAA
*
552965 TTTTAATGGTTTCAAAAC
1 TTTTAAGGGTTT-AAAAC
552983 TTTTAAGGGTTTAAAA
1 TTTTAAGGGTTTAAAA
552999 TACAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TTTTAAGGGTTTAAAAC
Found at i:555039 original size:31 final size:31
Alignment explanation
Indices: 555001--555064 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
554991 TTTTTATTTT
* *
555001 TTATTAAAGTTTTCTATTAAGGTCTTTTTCA
1 TTATTAAAGTTTTCTATTAAAGTATTTTTCA
* *
555032 TTATTAAAGTTTTTTGTTAAAGTATTTTTCA
1 TTATTAAAGTTTTCTATTAAAGTATTTTTCA
555063 TT
1 TT
555065 TATTTCTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (31 bp):
TTATTAAAGTTTTCTATTAAAGTATTTTTCA
Found at i:560414 original size:6 final size:5
Alignment explanation
Indices: 560393--560592 Score: 71
Period size: 5 Copynumber: 40.8 Consensus size: 5
560383 TTGAAAAATA
* * *
560393 AAAAG -AAAG GAAA- AAATG AAAAG AAAGGG AAAAATG AAAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG -AAAA-G AA-AAG AAAAG
560440 AAAA- AAGAA- AAAAG AAAA- AAGAA- AAAAG AAAA- AAGAA- AAAAG
1 AAAAG AA-AAG AAAAG AAAAG AA-AAG AAAAG AAAAG AA-AAG AAAAG
*
560482 AAAA- AAGAA- AAAAG AAAA- AAGAA- AAAAG AAAA- AAAA- AAAGAA
1 AAAAG AA-AAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAA-AG
*
560524 AAAAGG AAAA- AGAA- AAAAG AAAA- AAGAA- AAAAG AAAAAG AAAA-
1 AAAA-G AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG -AAAAG AAAAG
560567 AAGAA- AAAAG AAAAAG AAAATG AAAA
1 AA-AAG AAAAG -AAAAG AAAA-G AAAA
560593 AAAGAGAGAA
Statistics
Matches: 160, Mismatches: 8, Indels: 53
0.72 0.04 0.24
Matches are distributed among these distances:
4 47 0.29
5 79 0.49
6 28 0.17
7 6 0.04
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:560593 original size:7 final size:7
Alignment explanation
Indices: 560347--560586 Score: 278
Period size: 7 Copynumber: 33.6 Consensus size: 7
560337 AAAAAATGAA
560347 AAAAAGAG
1 AAAAA-AG
560355 AAAAAATG
1 AAAAAA-G
*
560363 AAAAAAT
1 AAAAAAG
*
560370 AAAAAGG
1 AAAAAAG
560377 AAAAAATTG
1 AAAAAA--G
*
560386 AAAAATAA
1 AAAAA-AG
560394 AAAGAAAGG
1 AAA-AAA-G
560403 AAAAAATG
1 AAAAAA-G
560411 AAAAGAAAGGG
1 -AAA-AAA--G
*
560422 AAAAATG
1 AAAAAAG
560429 -AAAAAG
1 AAAAAAG
560435 --AAAAG
1 AAAAAAG
560440 AAAAAAG
1 AAAAAAG
560447 AAAAAAG
1 AAAAAAG
560454 AAAAAAG
1 AAAAAAG
560461 AAAAAAG
1 AAAAAAG
560468 AAAAAAG
1 AAAAAAG
560475 AAAAAAG
1 AAAAAAG
560482 AAAAAAG
1 AAAAAAG
560489 AAAAAAG
1 AAAAAAG
560496 AAAAAAG
1 AAAAAAG
560503 AAAAAAG
1 AAAAAAG
560510 -AAAAA-
1 AAAAAAG
560515 AAAAAAG
1 AAAAAAG
560522 AAAAAAG
1 AAAAAAG
*
560529 GAAAAAG
1 AAAAAAG
560536 AAAAAAG
1 AAAAAAG
560543 AAAAAAG
1 AAAAAAG
560550 AAAAAAG
1 AAAAAAG
560557 -AAAAAG
1 AAAAAAG
560563 AAAAAAG
1 AAAAAAG
560570 AAAAAAG
1 AAAAAAG
560577 -AAAAAG
1 AAAAAAG
560583 AAAA
1 AAAA
560587 TGAAAAAAAG
Statistics
Matches: 205, Mismatches: 12, Indels: 31
0.83 0.05 0.12
Matches are distributed among these distances:
5 5 0.02
6 27 0.13
7 129 0.63
8 20 0.10
9 16 0.08
10 7 0.03
11 1 0.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:560595 original size:40 final size:40
Alignment explanation
Indices: 560330--560597 Score: 204
Period size: 40 Copynumber: 6.6 Consensus size: 40
560320 ATTTTGCTTG
560330 AAGAAGAAA-AAAATGAAAAAAAG----AGAAAAAATGAAAA
1 AAGAA-AAAGAAAATGAAAAAAAGAAAAAGAAAAAA-GAAAA
* *
560367 AATAAAAAGGAAAAAATTGAAAAATAAAAAGAAAGGAAAAAATG--AA
1 AAGAAAAA-G--AAAA-TGAAAAA-AAGAA-AAA-GAAAAAA-GAAAA
**
560413 AAGAAAGGGAAAAATG--AAAAAG-AAAAGAAAAAAGAAAA
1 AAGAAAAAG-AAAATGAAAAAAAGAAAAAGAAAAAAGAAAA
*
560451 AAGAAAAAAGAAAA-AAGAAAAAAGAAAAAAGAAAAAAGAAAA
1 AAG-AAAAAGAAAATGA-AAAAAAG-AAAAAGAAAAAAGAAAA
* *
560493 AAGAAAAAAGAAAA--AAGAAAAAAAAAAAGAAAAAAGGAAA
1 AAG-AAAAAGAAAATGAA-AAAAAGAAAAAGAAAAAAGAAAA
*
560533 AAGAAAAAAGAAAA-AAGAAAAAAGAAAAAGAAAAAAGAAAA
1 AAG-AAAAAGAAAATGA-AAAAAAGAAAAAGAAAAAAGAAAA
560574 AAGAAAAAGAAAATGAAAAAAAGA
1 AAGAAAAAGAAAATGAAAAAAAGA
560598 GAGAAAAATT
Statistics
Matches: 193, Mismatches: 14, Indels: 45
0.77 0.06 0.18
Matches are distributed among these distances:
36 4 0.02
37 11 0.06
38 12 0.06
39 5 0.03
40 61 0.32
41 42 0.22
42 33 0.17
43 2 0.01
44 5 0.03
45 1 0.01
46 7 0.04
47 1 0.01
48 9 0.05
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (40 bp):
AAGAAAAAGAAAATGAAAAAAAGAAAAAGAAAAAAGAAAA
Found at i:560605 original size:1 final size:1
Alignment explanation
Indices: 560429--560586 Score: 109
Period size: 1 Copynumber: 158.0 Consensus size: 1
560419 GGGAAAAATG
* * * * * * * * *
560429 AAAAAGAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** * * * *
560494 AGAAAAAAGAAAAAAGAAAAAAAAAAAGAAAAAAGGAAAAAGAAAAAAGAAAAAAGAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
560559 AAAGAAAAAAGAAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
560587 TGAAAAAAAG
Statistics
Matches: 113, Mismatches: 44, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 113 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (1 bp):
A
Found at i:561879 original size:37 final size:36
Alignment explanation
Indices: 561824--561908 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
561814 TCGACCTTCG
* * *
561824 AAGCAAATCAAACTTAAGCCTTCACGAAAGAGTAGTA
1 AAGCAAATC-ATCTTAAGCCTTCACAAAAAAGTAGTA
*
561861 AAGCAAATCATCTATAAGCCTTCACAAAAAAGTAGTG
1 AAGCAAATCATCT-TAAGCCTTCACAAAAAAGTAGTA
561898 AAGCAAATCAT
1 AAGCAAATCAT
561909 GATTGTTCGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 3 0.07
37 40 0.93
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (36 bp):
AAGCAAATCATCTTAAGCCTTCACAAAAAAGTAGTA
Found at i:562017 original size:54 final size:54
Alignment explanation
Indices: 561909--562388 Score: 696
Period size: 54 Copynumber: 8.9 Consensus size: 54
561899 AGCAAATCAT
** * * *
561909 GATTGTTCGAGTTCTGCCTCCCTGAAGAAAGAGGGAGCGAACCCGTAGGTAGAA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
* * * *
561963 GATTATTCCCA-TTCTTACTCCCTGAAGTAAGAGAGAGCGAACCCATAGGCAGAA
1 GATTGTT-CGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
* * *
562017 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAACGAACCCATAGGCATAA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
* *
562071 GATTGTTCGAGTTC-TACTCCCTGAAGCAAGAGAGAGCGAACTCGTAGGCAAAA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
** * *
562124 GATTGTTCGAGTTCTTACTCCCTGAAGTTAGAGAGAGAGAACCCATAGGCAGAA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
* * * *
562178 TATTATCCGAGTTC-TACTCCTTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
562231 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
* * *
562285 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCAAACCCATACGCAGAA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
*
562339 GATTGTTCGACTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
562389 GTTGCAGAAG
Statistics
Matches: 380, Mismatches: 42, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
53 96 0.25
54 282 0.74
55 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.21
Consensus pattern (54 bp):
GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
Found at i:562132 original size:107 final size:108
Alignment explanation
Indices: 561909--562388 Score: 696
Period size: 107 Copynumber: 4.5 Consensus size: 108
561899 AGCAAATCAT
** * * * *
561909 GATTGTTCGAGTTCTGCCTCCCTGAAGAAAGAGGGAGCGAACCCGTAGGTAGAAGATTATTCCCA
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTATT-CGA
*
561974 -TTCTTACTCCCTGAAGTAAGAGAGAGCGAACCCATAGGCAGAA
65 GTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCATAGGCAGAA
* * * *
562017 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAACGAACCCATAGGCATAAGATTGTTCGAG
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTATTCGAG
* * *
562082 TTC-TACTCCCTGAAGCAAGAGAGAGCGAACTCGTAGGCAAAA
66 TTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCATAGGCAGAA
** * * * *
562124 GATTGTTCGAGTTCTTACTCCCTGAAGTTAGAGAGAGAGAACCCATAGGCAGAATATTATCCGAG
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTATTCGAG
* *
562189 TTC-TACTCCTTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
66 TTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCATAGGCAGAA
*
562231 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGAG
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTATTCGAG
* *
562296 TTCTTACTCCCTGAAGCAAGAGAGAGCAAACCCATACGCAGAA
66 TTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCATAGGCAGAA
*
562339 GATTGTTCGACTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
1 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
562389 GTTGCAGAAG
Statistics
Matches: 333, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
107 194 0.58
108 139 0.42
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.21
Consensus pattern (108 bp):
GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTATTCGAG
TTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCATAGGCAGAA
Found at i:562175 original size:161 final size:161
Alignment explanation
Indices: 561909--562388 Score: 723
Period size: 161 Copynumber: 3.0 Consensus size: 161
561899 AGCAAATCAT
* * * * * *
561909 GATTGTTCGAGTTCTGCCTCCCTGAAGAAAGAGGGAGCGAACCCGTAGGTAGAAGATTATTCCCA
1 GATTGTTCGAGTTCT-ACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTT-CGA
*
561974 -TTCTTACTCCCTGAAGTAAGAGAGAGCGAACCCATAGGCAGAAGATTGTTCGAGTTCTTACTCC
64 GTTCTTACTCCCTGAAGTAAGAGAGAGAGAACCCATAGGCAGAAGATTGTTCGAGTTCTTACTCC
* * *
562038 CTGAAGCAAGAGAGAACGAACCCATAGGCATAA
129 CTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
* *
562071 GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACTCGTAGGCAAAAGATTGTTCGAGT
1 GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGAGT
* * * * *
562136 TCTTACTCCCTGAAGTTAGAGAGAGAGAACCCATAGGCAGAATATTATCCGAGTTC-TACTCCTT
66 TCTTACTCCCTGAAGTAAGAGAGAGAGAACCCATAGGCAGAAGATTGTTCGAGTTCTTACTCCCT
562200 GAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
131 GAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
562231 GATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGAG
1 GATTGTTCGAGTTC-TACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGAG
* * *
562296 TTCTTACTCCCTGAAGCAAGAGAGAGCA-AACCCATACGCAGAAGATTGTTCGACTTCTTACTCC
65 TTCTTACTCCCTGAAGTAAGAGAGAG-AGAACCCATAGGCAGAAGATTGTTCGAGTTCTTACTCC
562360 CTGAAGCAAGAGAGAGCGAACCCGTAGGC
129 CTGAAGCAAGAGAGAGCGAACCCGTAGGC
562389 GTTGCAGAAG
Statistics
Matches: 287, Mismatches: 27, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
160 51 0.18
161 186 0.65
162 50 0.17
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.21
Consensus pattern (161 bp):
GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGAGT
TCTTACTCCCTGAAGTAAGAGAGAGAGAACCCATAGGCAGAAGATTGTTCGAGTTCTTACTCCCT
GAAGCAAGAGAGAGCGAACCCGTAGGCAGAA
Found at i:562742 original size:27 final size:27
Alignment explanation
Indices: 562700--562763 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
562690 TTTATGTTAT
*
562700 TTATATAATAATTATTATTATTATA-A
1 TTATATAATAATTATTATTAATATATA
562726 TTATAATAATAATTATTATTAATATATA
1 TTAT-ATAATAATTATTATTAATATATA
*
562754 TTATTTAATA
1 TTATATAATA
562764 TTACAAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 25 0.74
28 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATATAATAATTATTATTAATATATA
Found at i:568648 original size:15 final size:15
Alignment explanation
Indices: 568628--568659 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
568618 ATCAATACCT
568628 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
568643 TTTTGCATACATTCA
1 TTTTGCATACATGCA
568658 TT
1 TT
568660 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:575992 original size:4 final size:4
Alignment explanation
Indices: 575983--576051 Score: 60
Period size: 4 Copynumber: 18.5 Consensus size: 4
575973 ATTATGCTTG
* *
575983 AAGA AAGA AA-A AAAA AAGG AA-A AA-A AAGA AA-A AAGA AAGAA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AAGA
*
576028 AAGA AA-A AAAA AAGA AA-A AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
576052 AAGAAAAAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
3 17 0.31
4 34 0.62
5 4 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:575996 original size:1 final size:1
Alignment explanation
Indices: 575990--576059 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
575980 TTGAAGAAAG
** * * * * * * * *
575990 AAAAAAAAAAGGAAAAAAAAGAAAAAAGAAAGAAAAGAAAGAAAAAAAAAAGAAAAAAGAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
576055 AAAAA
1 AAAAA
576060 GGGGAGTCAA
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:576007 original size:9 final size:8
Alignment explanation
Indices: 575983--576053 Score: 69
Period size: 8 Copynumber: 9.0 Consensus size: 8
575973 ATTATGCTTG
575983 AAGAAAGAA
1 AAGAAA-AA
575992 AA-AAAAA
1 AAGAAAAA
*
575999 AGGAAAAA
1 AAGAAAAA
576007 AA-AGAAAA
1 AAGA-AAAA
576015 AAGAAAGAA
1 AAGAAA-AA
*
576024 AAGAAAGA
1 AAGAAAAA
576032 AA-AAAAA
1 AAGAAAAA
576039 AAG-AAAA
1 AAGAAAAA
576046 AAGAAAAA
1 AAGAAAAA
576054 GAAAAAGGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
7 17 0.33
8 24 0.46
9 11 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:576016 original size:20 final size:20
Alignment explanation
Indices: 575986--576061 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
575976 ATGCTTGAAG
575986 AAAGAAAAAAAAAAGGAAAAA
1 AAAG-AAAAAAAAAGGAAAAA
*
576007 AAAGAAAAAAGAAA-GAAAAG
1 AAAGAAAAAA-AAAGGAAAAA
*
576027 AAAGAAAAAAAAAAGAAAAA
1 AAAGAAAAAAAAAGGAAAAA
*
576047 AGAA-AAAGAAAAAGG
1 A-AAGAAAAAAAAAGG
576062 GGAGTCAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.06
20 36 0.75
21 9 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAAAAGGAAAAA
Found at i:576035 original size:37 final size:37
Alignment explanation
Indices: 575986--576057 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
575976 ATGCTTGAAG
**
575986 AAAGAAAAAAAAAAGGAA-AAAAAAGAAAAAAGAAAGA
1 AAAGAAAAAAAAAAAAAAGAAAAAAG-AAAAAGAAAGA
*
576023 AAAGAAAGAAAAAAAAAAGAAAAAAGAAAAAGAAA
1 AAAGAAAAAAAAAAAAAAGAAAAAAGAAAAAGAAA
576058 AAGGGGAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (37 bp):
AAAGAAAAAAAAAAAAAAGAAAAAAGAAAAAGAAAGA
Found at i:576043 original size:24 final size:22
Alignment explanation
Indices: 576002--576059 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
575992 AAAAAAAAGG
576002 AAAAAAAAG-AAAAAAGAAAGAA
1 AAAAAAAAGAAAAAAAGAAA-AA
576024 AAGAAAGAAA-AAAAAAAG-AAAA
1 AA-AAA-AAAGAAAAAAAGAAAAA
*
576046 AAGAAAAAGAAAAA
1 AAAAAAAAGAAAAA
576060 GGGGAGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.10
21 7 0.23
22 6 0.19
23 5 0.16
24 10 0.32
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAAAAAAAGAAAAA
Found at i:577483 original size:83 final size:83
Alignment explanation
Indices: 577195--577671 Score: 697
Period size: 83 Copynumber: 5.6 Consensus size: 83
577185 AACAAATGCC
* * * *
577195 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
577260 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
* *
577278 ATGTGCTCATAGCATCTTCTGGAAGTGTTGTTTGAGTTATCTGATCTGTTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A
* **
577343 GAACCAATTATTGAATTTGAAAGATAA
58 -AACCAATTATTGAATTTGGAAGAGGA
577370 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
577435 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
*
577453 ATGTGCT-AGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAAT
1 ATGTGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
* * **
577517 CATTGAATTTGAAAGATAA
65 TATTGAATTTGGAAGAGGA
* *
577536 ATGTTCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
577601 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
577619 ATGTGCT-AGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 ATGTGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
577672 ATATGAAACC
Statistics
Matches: 356, Mismatches: 26, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
82 2 0.01
83 274 0.77
84 2 0.01
85 2 0.01
90 2 0.01
91 1 0.00
92 73 0.21
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
ATTGAATTTGGAAGAGGA
Found at i:577489 original size:175 final size:174
Alignment explanation
Indices: 577195--577723 Score: 833
Period size: 166 Copynumber: 3.1 Consensus size: 174
577185 AACAAATGCC
* * * *
577195 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
*
577260 ATTGAATTTGGAAGAGGAATGTGCTCA-TAGCATCTTCTGGAAGTGTTGTTTGAGTTATCTGATC
66 ATTGAATTTGGAAGAGGAATGTGCT-AGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
577324 TGTTTTGGTATGAACCACAGAACCAATTATTGAATTTGAAAGATAA
130 TGGTTTGGTATGAACCACA-AACCAATCATTGAATTTGAAAGATAA
577370 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
577435 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
*
577500 GGTTTGG--T-----A-AAATCAATCATTGAATTTGAAAGATAA
131 GGTTTGGTATGAACCACAAACCAATCATTGAATTTGAAAGATAA
* *
577536 ATGTTCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
577601 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* * *
577666 GGTTTGATATGAAACCACATAACCAATCATTAAATTTGAAAGATGA
131 GGTTTGGTATG-AACCACA-AACCAATCATTGAATTTGAAAGATAA
*
577712 ATTTGCTCATAG
1 ATGTGCTCATAG
577724 TAGAAATAAG
Statistics
Matches: 327, Mismatches: 16, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
166 158 0.48
167 1 0.00
168 2 0.01
173 1 0.00
174 2 0.01
175 130 0.40
176 33 0.10
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.37
Consensus pattern (174 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATT
ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGGTATGAACCACAAACCAATCATTGAATTTGAAAGATAA
Found at i:578241 original size:52 final size:52
Alignment explanation
Indices: 578163--578267 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
578153 TATCGATATC
*
578163 TGTGAAATCATCTTGAAATATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
578215 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
578267 T
1 T
578268 TAACATGTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (52 bp):
TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:578897 original size:113 final size:113
Alignment explanation
Indices: 578565--579781 Score: 2302
Period size: 113 Copynumber: 10.8 Consensus size: 113
578555 GCAAAGATTT
578565 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
578630 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* *
578678 AAATCCATCACTTGATGGATAAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTAAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
*
578742 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTACTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
*
578790 AAATCCATCACTTGATGGATCCGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
*
578855 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTAAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
578903 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
578968 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
579016 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
579081 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
*
579129 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCCGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
*
579194 AAGGAAGAAGAAGTTCATAATGATAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* *
579242 AAATACATCACTTGATGGATCAGCTTTTCCAAAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
579307 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
579355 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
579420 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
579468 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
579533 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
*
579581 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTAAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
579645 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
579693 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
579758 AA-G-AG-A-AAGTTCATAATGAGAAGA
66 AAGGAAGAAGAAGTTCATAATGAGAAGA
579782 ACTCATCTGA
Statistics
Matches: 1082, Mismatches: 20, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
109 18 0.02
110 1 0.00
111 2 0.00
112 220 0.20
113 841 0.78
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
Found at i:579801 original size:43 final size:40
Alignment explanation
Indices: 579723--579836 Score: 191
Period size: 40 Copynumber: 3.0 Consensus size: 40
579713 CAGCTTTTCC
*
579723 AGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAA-G-
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
579761 AG-A-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
579799 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
579837 AGCTTATTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
36 31 0.44
37 2 0.03
38 4 0.06
39 1 0.01
40 33 0.46
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (40 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:580098 original size:3 final size:3
Alignment explanation
Indices: 580092--580164 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
580082 TTATATAATA
* * * * * *
580092 ATT ATT ATT ATT ATA ATT ATA ATA ATT ATT ATT ATT ATA ATT ATA ATA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
580140 ATT ATT ATT ATT AAT ATAT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT
580165 TAATATTACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:580112 original size:24 final size:24
Alignment explanation
Indices: 580085--580152 Score: 136
Period size: 24 Copynumber: 2.8 Consensus size: 24
580075 ATGTTATTTA
580085 TATAATAATTATTATTATTATAAT
1 TATAATAATTATTATTATTATAAT
580109 TATAATAATTATTATTATTATAAT
1 TATAATAATTATTATTATTATAAT
580133 TATAATAATTATTATTATTA
1 TATAATAATTATTATTATTA
580153 ATATATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAATAATTATTATTATTATAAT
Found at i:592862 original size:14 final size:16
Alignment explanation
Indices: 592828--592866 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
592818 AACAAAAACG
592828 ATAAAGATAAATTGAAA
1 ATAAAGA-AAATTGAAA
592845 ATAAAGAAAA-TG-AA
1 ATAAAGAAAATTGAAA
592859 ATAAAGAA
1 ATAAAGAA
592867 GAGATAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 2 0.09
16 3 0.14
17 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (16 bp):
ATAAAGAAAATTGAAA
Found at i:594790 original size:106 final size:106
Alignment explanation
Indices: 594595--595031 Score: 640
Period size: 106 Copynumber: 4.1 Consensus size: 106
594585 TCCAAGTAGG
* * * * * * ** *
594595 TTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTGGAATTGGTTCTGGGACTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * *
594660 GTTTGTTGACAACTAGCCATCCCTTCGTTGTGAAGTTGATC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
* *
594701 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGAAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * *
594766 GTTTGTTAACAACCAGACGTCCCTTCGTTGTGAAATTGAAC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
** *
594807 TTGTGTTGTCTCGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
*
594872 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAATTTGAAC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
* * *
594913 TTGTGTTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
*
594978 GTTTGTTGATAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
*
595019 TTGTGTTATCTCG
1 TTGTGTTGTCTCG
595032 GGTGGCGCGA
Statistics
Matches: 298, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 298 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
Found at i:595744 original size:37 final size:37
Alignment explanation
Indices: 595662--595746 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
595652 GTTTCATGAG
* * * * **
595662 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
595699 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
595735 GAAATTGTCTCA
1 -AAACTGTCTCA
595747 CGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:601077 original size:12 final size:13
Alignment explanation
Indices: 601055--601087 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
601045 AAACAGTTAG
601055 TAAAAAA-AATAA
1 TAAAAAATAATAA
601067 -AAAAAATAATAA
1 TAAAAAATAATAA
601079 TAAAAAATA
1 TAAAAAATA
601088 CATGGCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 5 0.26
13 8 0.42
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:603287 original size:105 final size:105
Alignment explanation
Indices: 603105--603455 Score: 393
Period size: 106 Copynumber: 3.3 Consensus size: 105
603095 CAAGCGATCA
* * *
603105 ATTGTTCGAGTTATTACTCCCTGAAGCAAGAGAGAGCAATCCCGTAGACAGAAGATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCAAACCCGTAGACAAAAGATTGTTCGAGT
*
603170 TCTACTCCCTGAAGCAAGAGAGAGAACCCGTAGGCAGAAT
66 TCTACTCCCTGAAGCAAGAGAGAGAACCCGTAGGCAGAAG
* * * ** *
603210 ATTGTTTGAGTTCTTACTCTCTGAAGAAAGAGAGAGCAAACATGTAGACAAAAGATTGTTTGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCAAACCCGTAGACAAAAGATTGTTCGAGT
* * * **
603275 TCTTAC-CTCTGAAGTAAGAGAGAGAGAACCCCTAGATAGAAG
66 TC-TACTCCCTGAAG-CA-AGAGAGAGAACCCGTAGGCAGAAG
* * * *
603317 ATTGTTCGAGTTC-TACTCCCTGAAGCAAGAGAGAGCGAACCCGTGGATAAAAGCTTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCAAACCCGTAGACAAAAGATTGTTCGAGT
* * * *
603381 TCCACTCCCTAAAGCAAGAGGGAGCGAACCCGTTGGCAGAAG
66 TCTACTCCCTGAAGCAAGA--GAGAGAACCCGTAGGCAGAAG
* *
603423 ATTGTTGGAGTTTTATACAT-CCTGAAGCAAGAG
1 ATTGTTCGAGTTCT-TAC-TCCCTGAAGCAAGAG
603456 GCAGCGAACC
Statistics
Matches: 201, Mismatches: 36, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
104 3 0.01
105 68 0.34
106 81 0.40
107 32 0.16
108 16 0.08
109 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (105 bp):
ATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAGCAAACCCGTAGACAAAAGATTGTTCGAGT
TCTACTCCCTGAAGCAAGAGAGAGAACCCGTAGGCAGAAG
Done.