Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008914.1 Hibiscus syriacus cultivar Beakdansim tig00112217_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: 1601432
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:166447 original size:17 final size:17
Alignment explanation
Indices: 166422--166456 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
166412 ATTTAGTTAT
*
166422 TTGGTCTAAGTTGATGA
1 TTGGACTAAGTTGATGA
166439 TTGGACTAAGTTGATGA
1 TTGGACTAAGTTGATGA
166456 T
1 T
166457 GTCTGATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (17 bp):
TTGGACTAAGTTGATGA
Found at i:166906 original size:8 final size:8
Alignment explanation
Indices: 166893--166925 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
166883 AAGTAGTGTT
166893 AAAAAAGA
1 AAAAAAGA
166901 AAAAAAGA
1 AAAAAAGA
*
166909 AAAAAAGG
1 AAAAAAGA
166917 AAAAAAGA
1 AAAAAAGA
166925 A
1 A
166926 GAGAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:185993 original size:20 final size:20
Alignment explanation
Indices: 185948--185993 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
185938 ATATTTTTTT
*
185948 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* * *
185968 ATTAAATTTTTATTTTTCAA
1 AATAAATTTTTATCTATCAA
185988 AATAAA
1 AATAAA
185994 ATATTAAAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:194002 original size:29 final size:29
Alignment explanation
Indices: 193966--194025 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
193956 AAATATTAAC
193966 AAAGTTTTTACTAAAATAATTCCTTAAAA
1 AAAGTTTTTACTAAAATAATTCCTTAAAA
193995 AAAGTTTTTACTAAAATAATTCCTTAAAA
1 AAAGTTTTTACTAAAATAATTCCTTAAAA
194024 AA
1 AA
194026 CCTTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAGTTTTTACTAAAATAATTCCTTAAAA
Found at i:194031 original size:29 final size:29
Alignment explanation
Indices: 193970--194032 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
193960 ATTAACAAAG
*
193970 TTTTTACTAAAATAATTCCTTAAAAAAAG
1 TTTTTACTAAAATAATTCCTTAAAAAAAC
*
193999 TTTTTACTAAAATAATTCCTTAAAAAACC
1 TTTTTACTAAAATAATTCCTTAAAAAAAC
194028 TTTTT
1 TTTTT
194033 TAAGAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTTTACTAAAATAATTCCTTAAAAAAAC
Found at i:195510 original size:18 final size:18
Alignment explanation
Indices: 195487--195521 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
195477 CATATAACAC
195487 ATATGTCCCGAAGGACCA
1 ATATGTCCCGAAGGACCA
195505 ATATGTCCCGAAGGACC
1 ATATGTCCCGAAGGACC
195522 GCGTAGACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (18 bp):
ATATGTCCCGAAGGACCA
Found at i:196378 original size:24 final size:20
Alignment explanation
Indices: 196329--196386 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
196319 TTCCCATTGA
*
196329 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
196349 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
196372 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
196387 ATATCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:196485 original size:64 final size:62
Alignment explanation
Indices: 196374--196513 Score: 142
Period size: 63 Copynumber: 2.2 Consensus size: 62
196364 TCTTTAACAG
* * *
196374 GTGCATCGATGCAATATCATGCATCGATACACAATTTACATTCGATGTTTCCAT-TTTAAGGA
1 GTGCATCGATGCACTATCATGCATCGATACACAATGTACATTCGATGTTTACATATTTAA-GA
* * * **
196436 GATGCATCGATGCACTCCTCATGCTTCGATGCACCAACTGTAC-TT-GATGTTTATTTATTTAAG
1 G-TGCATCGATGCACT-ATCATGCATCGATACA-CAA-TGTACATTCGATGTTTACATATTTAAG
196499 A
62 A
196500 GTGCATCGATGCAC
1 GTGCATCGATGCAC
196514 ATTGAAGATG
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.02
63 26 0.40
64 24 0.37
65 10 0.15
66 4 0.06
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTATCATGCATCGATACACAATGTACATTCGATGTTTACATATTTAAGA
Found at i:200404 original size:20 final size:20
Alignment explanation
Indices: 200379--200416 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
200369 TTCCCATTGA
**
200379 AGTGCATCGGTGCATTCTAC
1 AGTGCATCAATGCATTCTAC
200399 AGTGCATCAATGCATTCT
1 AGTGCATCAATGCATTCT
200417 TTAACAGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCAATGCATTCTAC
Found at i:200535 original size:64 final size:62
Alignment explanation
Indices: 200424--200563 Score: 151
Period size: 63 Copynumber: 2.2 Consensus size: 62
200414 TCTTTAACAG
* * *
200424 GTGCATCGATACACTATCATGCATCGATACACAATTTACATTCGATGTTTCCAT-TTTAAGGA
1 GTGCATCGATGCACTATCATGCATCGATACACAATGTACATTCGATGTTTACATATTTAA-GA
* * **
200486 GATGCATCGATGCACTCCTCATGCATCGATGCACCAACTGTAC-TT-GATGTTTATTTATTTAAG
1 G-TGCATCGATGCACT-ATCATGCATCGATACA-CAA-TGTACATTCGATGTTTACATATTTAAG
200549 A
62 A
200550 GTGCATCGATGCAC
1 GTGCATCGATGCAC
200564 ATTGAAGATG
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.02
63 26 0.39
64 25 0.38
65 10 0.15
66 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCACTATCATGCATCGATACACAATGTACATTCGATGTTTACATATTTAAGA
Found at i:200575 original size:21 final size:21
Alignment explanation
Indices: 200546--200606 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
200536 TTATTTATTT
200546 AAGAGTGCATCGATGCACATTG
1 AAGA-TGCATCGATGCACATTG
200568 AAGATGCATCGATGCACATTG
1 AAGATGCATCGATGCACATTG
200589 AAGATGCATCGATGCACA
1 AAGATGCATCGATGCACA
200607 CAACCCAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
21 35 0.90
22 4 0.10
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (21 bp):
AAGATGCATCGATGCACATTG
Found at i:201981 original size:64 final size:65
Alignment explanation
Indices: 201904--202059 Score: 235
Period size: 65 Copynumber: 2.4 Consensus size: 65
201894 ACACCCCATT
* * * * *
201904 TCGAATGCATTTTATTCACCGATGCAC-ATCCATGCATCGATGCACTC-AGGATTTTATTGAAAC
1 TCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCTAGGATTGT-TTAAAAC
201967 A
65 A
*
201968 TCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCTAGGCTTGTTTAAAACA
1 TCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCTAGGATTGTTTAAAACA
202033 TCGAATGCATTTTATGCATCGATGCAC
1 TCGAATGCATTTTATGCATCGATGCAC
202060 CCTTAGTGTA
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
64 25 0.30
65 53 0.63
66 6 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCTAGGATTGTTTAAAACA
Found at i:204028 original size:21 final size:21
Alignment explanation
Indices: 203999--204038 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
203989 GAGAAATTAT
203999 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
204020 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
204039 AAATAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:222393 original size:106 final size:106
Alignment explanation
Indices: 222079--224118 Score: 3223
Period size: 106 Copynumber: 19.3 Consensus size: 106
222069 GCATTGTTCT
* * * * * * *
222079 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
** * * *
222144 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** * * * *
222185 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGAATCTAAAATTGAGAA-ATGTCTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
222249 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
222290 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTTTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
222355 CCAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
222397 G-GTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
222461 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
222502 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
222567 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTTCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
222608 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
222673 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
222714 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
222779 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
222820 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
222885 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
222926 GAGTCCAATATCATTCGCTGGGAATTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
222991 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * **
223032 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGACCCTGAGATTGGGAAACTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
223097 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
223138 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
223203 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
223244 GAGTCCAATATCCTTCGTTGTGAAGTCAAAATTGGCTCTGAAATTGGGAA-ATATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
223308 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
223349 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
223413 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
223454 GAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
223519 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
223560 GAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
223625 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
223666 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
223730 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
223771 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
223835 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
223876 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
223940 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
223981 GAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
224046 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
224087 GAGT-CAAGATCCTTCGTTGAGAAGTTGAAATT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
224119 TACTCTCGAG
Statistics
Matches: 1807, Mismatches: 122, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
105 630 0.35
106 1174 0.65
107 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:231758 original size:15 final size:15
Alignment explanation
Indices: 231738--231767 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
231728 ATAATTATTA
231738 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
231753 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
231768 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:232989 original size:3 final size:3
Alignment explanation
Indices: 232981--233059 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
232971 ATATATATAT
* *
232981 ATA ATA ATA ATAA ATA ATA ATA ATA AT- ATT ATA TTA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
233026 TTT ATA ATA ATA ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
233060 ACGAAAAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:234353 original size:28 final size:28
Alignment explanation
Indices: 234300--234356 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
234290 TCGTCATTGC
* *
234300 TTTCAAGCATTGATTCGACAATATAATG
1 TTTCAAGCATTGACTCGACAACATAATG
**
234328 TTTCAAGCATTGACTCGATGACATAATG
1 TTTCAAGCATTGACTCGACAACATAATG
234356 T
1 T
234357 AAAAAGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (28 bp):
TTTCAAGCATTGACTCGACAACATAATG
Found at i:238860 original size:2 final size:2
Alignment explanation
Indices: 238853--238881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
238843 TAGTAATCAG
238853 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
238882 TAGGCACAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:240816 original size:16 final size:17
Alignment explanation
Indices: 240795--240831 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
240785 CGACCCGAAA
*
240795 TAATAAAAA-AATTATT
1 TAATAAAAACAATGATT
240811 TAATAAAAACAATGATT
1 TAATAAAAACAATGATT
240828 TAAT
1 TAAT
240832 TGAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
TAATAAAAACAATGATT
Found at i:241750 original size:16 final size:16
Alignment explanation
Indices: 241729--241769 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
241719 TCAGAGTCTC
241729 TGAATCATTCAACATT
1 TGAATCATTCAACATT
*
241745 TGAATCATTTAACATT
1 TGAATCATTCAACATT
241761 T-AATCATTC
1 TGAATCATTC
241770 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:251191 original size:4 final size:4
Alignment explanation
Indices: 251182--251231 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
251172 TGTTAGATAA
* * *
251182 AAAT AAAT AAAT AAAT -ATT AAAT AAAT CAA- AAAT AAAT AAAT TAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
251228 AAAT
1 AAAT
251232 CAAAAGGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 4 0.11
4 34 0.89
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:251205 original size:15 final size:15
Alignment explanation
Indices: 251178--251229 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
251168 AAAATGTTAG
251178 ATAAA-AATAAATAA
1 ATAAATAATAAATAA
*
251192 ATAAATATTAAATAA
1 ATAAATAATAAATAA
251207 ATCAAA-AATAAATAA
1 AT-AAATAATAAATAA
*
251222 ATTAATAA
1 ATAAATAA
251230 ATCAAAAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 7 0.22
15 22 0.69
16 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAATAATAAATAA
Found at i:251228 original size:23 final size:26
Alignment explanation
Indices: 251186--251236 Score: 81
Period size: 23 Copynumber: 2.1 Consensus size: 26
251176 AGATAAAAAT
251186 AAATAAATAAATATTAAATAAATCAA
1 AAATAAATAAATATTAAATAAATCAA
251212 AAATAAAT-AA-ATT-AATAAATCAA
1 AAATAAATAAATATTAAATAAATCAA
251235 AA
1 AA
251237 GGAAAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 12 0.48
24 3 0.12
25 2 0.08
26 8 0.32
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (26 bp):
AAATAAATAAATATTAAATAAATCAA
Found at i:251279 original size:36 final size:36
Alignment explanation
Indices: 251211--251280 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
251201 AAATAAATCA
* * *
251211 AAAATAAATAAATTAATAAATCAAAAGGAAAAAGAG
1 AAAATAAATAAAATAAAAAATCAAAAGAAAAAAGAG
*
251247 AAAATAAATAAAAATAAAAAAT-AATAGAAAAAAG
1 AAAATAAAT-AAAATAAAAAATCAAAAGAAAAAAG
251281 TCAAAGGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (36 bp):
AAAATAAATAAAATAAAAAATCAAAAGAAAAAAGAG
Found at i:251296 original size:24 final size:24
Alignment explanation
Indices: 251263--251327 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
251253 AATAAAAATA
251263 AAAAATAATAGAA-AAAAGTCAAAG-G
1 AAAAA-AATA-AATAAAA-TCAAAGAG
*
251288 AAAAAAATAAATAAAATTAAAGAG
1 AAAAAAATAAATAAAATCAAAGAG
251312 AAAAAAATAAATAAAA
1 AAAAAAATAAATAAAA
251328 AAGAATAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 7 0.19
24 25 0.68
25 5 0.14
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (24 bp):
AAAAAAATAAATAAAATCAAAGAG
Found at i:251328 original size:34 final size:35
Alignment explanation
Indices: 251312--251378 Score: 68
Period size: 34 Copynumber: 1.9 Consensus size: 35
251302 AATTAAAGAG
*
251312 AAAA-AAATAAATAAAAA-AGAAT-AAGTCAAAGGA
1 AAAATAAATAAATAAAAATA-AATAAAATCAAAGGA
*
251345 AAAATAAATAAATAAAAATAGATCAAAATGCAAA
1 AAAATAAATAAATAAAAATAAAT-AAAAT-CAAA
251379 AATTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
33 4 0.15
34 15 0.56
35 1 0.04
36 3 0.11
37 4 0.15
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (35 bp):
AAAATAAATAAATAAAAATAAATAAAATCAAAGGA
Found at i:251332 original size:19 final size:21
Alignment explanation
Indices: 251225--251332 Score: 53
Period size: 24 Copynumber: 5.0 Consensus size: 21
251215 TAAATAAATT
**
251225 AATAAATCAAAAGGAAAAAGAGA
1 AATAAAT-AAAATAAAAAAGA-A
*
251248 AAATAAATAAAAATAAAAAATAA
1 AA-TAAAT-AAAATAAAAAAGAA
* * *
251271 TAGAAA-AAAGTCAAAGGAAA-AA
1 AATAAATAAAAT-AAA--AAAGAA
* *
251293 AATAAATAAAATTAAAGAGAA
1 AATAAATAAAATAAAAAAGAA
251314 AA-AAAT-AAATAAAAAAGAA
1 AATAAATAAAATAAAAAAGAA
251333 TAAGTCAAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
19 11 0.17
20 10 0.15
21 7 0.11
22 11 0.17
23 11 0.17
24 15 0.23
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (21 bp):
AATAAATAAAATAAAAAAGAA
Found at i:251682 original size:20 final size:19
Alignment explanation
Indices: 251655--251708 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
251645 TATTTATACC
*
251655 CCTTCAACCATCCCAAATGG
1 CCTTCAACC-TCCCAAATAG
* *
251675 CGTTCAACCGGCCCAAATAG
1 CCTTCAACC-TCCCAAATAG
251695 CCTTCAACCTCCCA
1 CCTTCAACCTCCCA
251709 TTTGTGCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.28, C:0.43, G:0.11, T:0.19
Consensus pattern (19 bp):
CCTTCAACCTCCCAAATAG
Found at i:252514 original size:4 final size:4
Alignment explanation
Indices: 252505--252536 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
252495 CCCTGAACAA
252505 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
252537 CATAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:252550 original size:3 final size:3
Alignment explanation
Indices: 252538--252584 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
252528 TAAATAAATC
252538 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
252585 TAAACTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:252876 original size:147 final size:144
Alignment explanation
Indices: 252619--252979 Score: 439
Period size: 147 Copynumber: 2.5 Consensus size: 144
252609 AAATATTTTT
*
252619 AAACTATATATTATATATTTTT-AAAAATATTTTCAAAATTATATATTATAT-AGTTTTCAAAAA
1 AAACTATATATTATATATTTTTCAAAAATATTTTCAAAACTATATATTATATAAGTTTTC-AAAA
* * * *
252682 TGTTTTAAAACTGTATATTATATATATTTTGAAAAATGTTTTTAAAACCATATATTATATATGTT
65 TGTTTCAAAACTATATATTATATATATTTTGAAAAATGTTTTCAAAACCATATATTATATAAGTT
252747 TTCAAAAAAAAAATT-A
130 TT--AAAAAAAAATTAA
*
252763 AAACTATATATTATATATGTTTTCAAAAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAA
1 AAACTATATATTATATAT-TTTTCAAAAATATTTTCAAAACTATATATTATATAAGTTTTCAAAA
** *
252828 TGATTTCAAAACTATATATTATATA-AGTTTTTCAAAAT-TATTTCAAAACTATATATTATATAA
65 TG-TTTCAAAACTATATATTATATATA-TTTTGAAAAATGT-TTTCAAAACCATATATTATATAA
* ****
252891 GTTTTTAAAATGTTTTCAA
127 GTTTTAAAAAAAAATT-AA
*
252910 AAACTATATATTATATATATATTC-AAAATATTTTCAAAAACTATATATTATATATA-TTTTCAA
1 AAACTATATATTATATAT-TTTTCAAAAATATTTTC-AAAACTATATATTATATA-AGTTTTCAA
252973 AATGTTT
63 AATGTTT
252980 TCTAAAAAAA
Statistics
Matches: 190, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
144 18 0.09
145 10 0.05
146 48 0.25
147 113 0.59
148 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (144 bp):
AAACTATATATTATATATTTTTCAAAAATATTTTCAAAACTATATATTATATAAGTTTTCAAAAT
GTTTCAAAACTATATATTATATATATTTTGAAAAATGTTTTCAAAACCATATATTATATAAGTTT
TAAAAAAAAATTAA
Found at i:252954 original size:26 final size:26
Alignment explanation
Indices: 252925--252974 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
252915 ATATATTATA
252925 TATATATTCA-AAATATTTTCAAAAAC
1 TATATATT-ATAAATATTTTCAAAAAC
*
252951 TATATATTATATATATTTTCAAAA
1 TATATATTATAAATATTTTCAAAA
252975 TGTTTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (26 bp):
TATATATTATAAATATTTTCAAAAAC
Found at i:252981 original size:37 final size:36
Alignment explanation
Indices: 252586--252986 Score: 419
Period size: 37 Copynumber: 11.1 Consensus size: 36
252576 ATAATAATAT
* * *
252586 AAACTATATA--ATATATATTTTAAAAATATTTT-T
1 AAACTATATATTATATATATTTTCAAAATGTTTTCA
* *
252619 AAACTATATATTATATAT-TTTTAAAAATATTTTCA
1 AAACTATATATTATATATATTTTCAAAATGTTTTCA
* *
252654 AAATTATATATTATATA-GTTTTCAAAAATGTTTT-A
1 AAACTATATATTATATATATTTTC-AAAATGTTTTCA
* * *
252689 AAACTGTATATTATATATATTTTGAAAAATGTTTTTA
1 AAACTATATATTATATATATTTT-CAAAATGTTTTCA
* * ****
252726 AAACCATATATTATATATGTTTTCAAAAAAAAAATT-A
1 AAACTATATATTATATATATTTTC--AAAATGTTTTCA
*
252763 AAACTATATATTATATATGTTTTCAAAAATGTTTTCA
1 AAACTATATATTATATATATTTTC-AAAATGTTTTCA
*
252800 AAACTATATATTATATA-AGTTTTCAAAATGATTTCA
1 AAACTATATATTATATATA-TTTTCAAAATGTTTTCA
252836 AAACTATATATTATATA-AGTTTTTCAAAAT-TATTTCA
1 AAACTATATATTATATATA--TTTTCAAAATGT-TTTCA
*
252873 AAACTATATATTATATA-AGTTTTTAAAATGTTTTCAA
1 AAACTATATATTATATATA-TTTTCAAAATGTTTTC-A
* *
252910 AAACTATATATTATATATATATTCAAAATATTTTCAA
1 AAACTATATATTATATATATTTTCAAAATGTTTTC-A
252947 AAACTATATATTATATATATTTTCAAAATGTTTTCTA
1 AAACTATATATTATATATATTTTCAAAATGTTTTC-A
252984 AAA
1 AAA
252987 AAATATTTTC
Statistics
Matches: 318, Mismatches: 33, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
33 10 0.03
34 15 0.05
35 42 0.13
36 72 0.23
37 172 0.54
38 7 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
AAACTATATATTATATATATTTTCAAAATGTTTTCA
Found at i:254736 original size:28 final size:28
Alignment explanation
Indices: 254704--254769 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
254694 AGGATCGGAC
254704 ATAAAATTTTATGTTAGATAATAAATTT
1 ATAAAATTTTATGTTAGATAATAAATTT
254732 ATAAAATTTTATGTTAGATAATAAATTT
1 ATAAAATTTTATGTTAGATAATAAATTT
254760 ATAAAATTTT
1 ATAAAATTTT
254770 TGAGATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (28 bp):
ATAAAATTTTATGTTAGATAATAAATTT
Found at i:254782 original size:28 final size:28
Alignment explanation
Indices: 254704--254786 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
254694 AGGATCGGAC
** *
254704 ATAAAATTTTATGTTAGATAATAAATTT
1 ATAAAATTTTATGAGAGAAAATAAATTT
** *
254732 ATAAAATTTTATGTTAGATAATAAATTT
1 ATAAAATTTTATGAGAGAAAATAAATTT
254760 ATAAAATTTT-TGAGATGAAAATAAATT
1 ATAAAATTTTATGAGA-GAAAATAAATT
254787 ATTAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
27 3 0.06
28 48 0.94
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43
Consensus pattern (28 bp):
ATAAAATTTTATGAGAGAAAATAAATTT
Found at i:255162 original size:3 final size:3
Alignment explanation
Indices: 255124--255202 Score: 94
Period size: 3 Copynumber: 26.3 Consensus size: 3
255114 TTTACAAAAA
255124 TAT T-T TAT TA- TAT TA- TATT TATT TATT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TA-T TAT TAT TAT TAT TAT
255170 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
255203 TTTACAGGCC
Statistics
Matches: 71, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
2 8 0.11
3 49 0.69
4 14 0.20
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:255293 original size:33 final size:33
Alignment explanation
Indices: 255256--255324 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
255246 AAAAATAAAT
* * * *
255256 CAACGTATTTGAGTCTTATTGAAACACTAAAAC
1 CAACGTATTTAAATCATATTAAAACACTAAAAC
255289 CAACGTATTTAAATCATATTAAAACACTAAAAC
1 CAACGTATTTAAATCATATTAAAACACTAAAAC
255322 CAA
1 CAA
255325 ATCATTTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (33 bp):
CAACGTATTTAAATCATATTAAAACACTAAAAC
Found at i:258768 original size:17 final size:18
Alignment explanation
Indices: 258746--258784 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
258736 AACGGTCAAC
*
258746 GGTCAAC-GATTGGGTCG
1 GGTCAACGGATCGGGTCG
*
258763 GGTCAACGGGTCGGGTCG
1 GGTCAACGGATCGGGTCG
258781 GGTC
1 GGTC
258785 GGGTCAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.13, C:0.21, G:0.46, T:0.21
Consensus pattern (18 bp):
GGTCAACGGATCGGGTCG
Found at i:258787 original size:23 final size:23
Alignment explanation
Indices: 258757--258803 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
258747 GTCAACGATT
258757 GGGTCGGGTCAACGGGTCGGGTC
1 GGGTCGGGTCAACGGGTCGGGTC
*
258780 GGGTCGGGTCAATGGGTCGGGTC
1 GGGTCGGGTCAACGGGTCGGGTC
258803 G
1 G
258804 TGATCGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.19, G:0.53, T:0.19
Consensus pattern (23 bp):
GGGTCGGGTCAACGGGTCGGGTC
Found at i:258812 original size:23 final size:23
Alignment explanation
Indices: 258760--258814 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
258750 AACGATTGGG
*
258760 TCGGGTCAACGGGTCGGGTCGGG
1 TCGGGTCAACGGGTCGGGTCGGA
*
258783 TCGGGTCAATGGGTCGGGTCGTGA
1 TCGGGTCAACGGGTCGGGTCG-GA
258807 TC-GGTCAA
1 TCGGGTCAA
258815 ACCGGTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.13, C:0.20, G:0.45, T:0.22
Consensus pattern (23 bp):
TCGGGTCAACGGGTCGGGTCGGA
Found at i:266144 original size:29 final size:29
Alignment explanation
Indices: 266112--266214 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 29
266102 CTTTTTAAAA
* * **
266112 TAATTACCAAAATAACACCTATTTCGAAT
1 TAATTACCAGAATAGCACCTAAATCGAAT
*
266141 TAATTACCAGAATAGCACCTAAACCGAAT
1 TAATTACCAGAATAGCACCTAAATCGAAT
* * *
266170 TATTTACCATAATAGCACCAAAATCGAAT
1 TAATTACCAGAATAGCACCTAAATCGAAT
*
266199 TATTTACCAGAATAGC
1 TAATTACCAGAATAGC
266215 GTCGGTCAAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (29 bp):
TAATTACCAGAATAGCACCTAAATCGAAT
Found at i:266256 original size:13 final size:13
Alignment explanation
Indices: 266235--266279 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
266225 GGTCAACGAT
*
266235 CGGGACGGGTCAA
1 CGGGTCGGGTCAA
266248 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
266261 CGGGTCAGGTCAA
1 CGGGTCGGGTCAA
266274 CGGGTC
1 CGGGTC
266280 AAACCGGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.44, T:0.13
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:269624 original size:43 final size:43
Alignment explanation
Indices: 269563--269665 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
269553 AGAGTCAATT
269563 TCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGC
1 TCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGC
269606 TCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGC
1 TCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGC
*
269649 TCAACTTCACAACGAAG
1 TCAACTTCACAGCGAAG
269666 AGGCGACTGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (43 bp):
TCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGC
Found at i:269851 original size:109 final size:111
Alignment explanation
Indices: 269606--269865 Score: 407
Period size: 109 Copynumber: 2.4 Consensus size: 111
269596 CAACACAAGC
* *
269606 TCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAACGAAGAGGCG
1 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACAAAGAGGCG
** * * *
269671 ACTGACTGTCAACTTCATAACTTCTCAGTTTCATTCAGAGTCAATT
66 ACTGACTGTCAACTAAACAACTTCCCAGTTTCATTCAGAGCCAATT
*
269717 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCAAAG-GGCG
1 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACAAAGAGGCG
*
269781 ACTGACTGTGAAC-AAACAACTTCCCAGTTTCATTCAGAGCCAATT
66 ACTGACTGTCAACTAAACAACTTCCCAGTTTCATTCAGAGCCAATT
* *
269826 TCAACTTCACAGCGAAGGATATTGGACTTGAAACAACACA
1 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
269866 TACTTGGATT
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
109 65 0.47
110 16 0.12
111 57 0.41
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (111 bp):
TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACAAAGAGGCG
ACTGACTGTCAACTAAACAACTTCCCAGTTTCATTCAGAGCCAATT
Found at i:270745 original size:36 final size:36
Alignment explanation
Indices: 270646--270802 Score: 210
Period size: 37 Copynumber: 4.3 Consensus size: 36
270636 TTGAATATGT
*
270646 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
270681 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACGG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
270718 TTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
270754 TTTAC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTT-CTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
270791 TTTCTCTTGAAA
1 TTTCTCTTGAAA
270803 AAAACCTTTA
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
35 4 0.04
36 40 0.38
37 62 0.58
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:270772 original size:73 final size:73
Alignment explanation
Indices: 270646--270802 Score: 228
Period size: 73 Copynumber: 2.2 Consensus size: 73
270636 TTGAATATGT
* * * *
270646 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAGTTTTGTCTCTCT
*
270710 TGAGACGG
66 TGAGACAG
* *
270718 TTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAATTTAC-CTTGAAACAAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTT-CTCTTGAAACAAAGTTTTGTCTCTC
270782 TTGAGACAG
65 TTGAGACAG
270791 TTTCTCTTGAAA
1 TTTCTCTTGAAA
270803 AAAACCTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
72 4 0.05
73 70 0.93
74 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:270975 original size:84 final size:84
Alignment explanation
Indices: 270832--271060 Score: 343
Period size: 85 Copynumber: 2.7 Consensus size: 84
270822 CTCTTGAAAC
* * * * **
270832 ACCAAAGACCTTTGAGTTCGACTACTCTCAGCTGCAAGGCACTTCATTTTCAGTTTAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTT-AGCATAGCTTAAGT
*
270897 CGAGAA-GGGCTATCTGTCA
65 CGAGAATGGGCTATCTGCCA
* *
270916 ACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGTAGCATAGCTTACGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT-TAGCATAGCTTAAGT
270981 CGAGAATGGGCTATCTGCCA
65 CGAGAATGGGCTATCTGCCA
271001 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTATAGCATAGCT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT-TAGCATAGCT
271061 CAAAGAAAGA
Statistics
Matches: 132, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
84 61 0.46
85 71 0.54
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (84 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTTAGCATAGCTTAAGTC
GAGAATGGGCTATCTGCCA
Found at i:271643 original size:3 final size:3
Alignment explanation
Indices: 271619--271666 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
271609 CTACAAAAAA
271619 TAT T-T TAT TA- TAT TA- TATT TAT TAT TAT TAT TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
271660 TAT TAT T
1 TAT TAT T
271667 TTTACAGGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
2 10 0.26
3 27 0.69
4 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:271758 original size:33 final size:33
Alignment explanation
Indices: 271720--271803 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
271710 GAAAATAAAT
271720 CAACGTATTTGAGTCCAATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCAATTAAAACACTAAAAC
* *
271753 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCAATTAAAACACTAAAAC
*
271786 CGAA-GCATTTGAGTCCAA
1 C-AACGTATTTGAGTCCAA
271804 GTAGGACTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 44 0.96
34 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (33 bp):
CAACGTATTTGAGTCCAATTAAAACACTAAAAC
Found at i:273259 original size:113 final size:118
Alignment explanation
Indices: 273044--273269 Score: 291
Period size: 113 Copynumber: 1.9 Consensus size: 118
273034 AAAAGCATGA
*
273044 TTAAATTTAATTCAAAATTGAATAAATAAATAAATAAGAGAAATGGAAAAAGAGGGTAAAAAACT
1 TTAAATTTAATTCAAAATTGAATAAAT--ATAAATAAGAGAAATGGAAAAAGAGGATAAAAAACT
* * *
273109 AAACATTTTATGAAATTATAAAAATTAGGGGCCTAATTATAAGTATAAAAACTGG
64 AAACACTTTATAAAACTATAAAAATTAGGGGCCTAATTATAAGTATAAAAACTGG
* * ** * *
273164 TTAAATTTAATTCAAAATT-AATGAAT-T-AATAAGAGAAA-GGAAAAGGATTATCAAAACCTAA
1 TTAAATTTAATTCAAAATTGAATAAATATAAATAAGAGAAATGGAAAAAGAGGATAAAAAACTAA
* *
273225 A-ACTTTATAAAACTATAAAAATTAGGGTCTTAATTATAAGTATAA
66 ACACTTTATAAAACTATAAAAATTAGGGGCCTAATTATAAGTATAA
273270 TAAATTGGGA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
113 39 0.41
114 18 0.19
115 11 0.12
116 1 0.01
119 6 0.06
120 19 0.20
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (118 bp):
TTAAATTTAATTCAAAATTGAATAAATATAAATAAGAGAAATGGAAAAAGAGGATAAAAAACTAA
ACACTTTATAAAACTATAAAAATTAGGGGCCTAATTATAAGTATAAAAACTGG
Found at i:275169 original size:99 final size:105
Alignment explanation
Indices: 275001--275227 Score: 333
Period size: 100 Copynumber: 2.2 Consensus size: 105
274991 ATGAATATCA
*
275001 TTTTTTAAAA-AATTAAAAATTAAATAATTATAATATATATATATATATATATAATATCAATAGA
1 TTTTTTAAAATAATT-AAATTTAAATAATTATAATATATATATATATATATAT-ATATCAATAGA
275065 TT-AAAAATTATTAACAGAAATTATTTCATAATCATTTTAAT
64 TTAAAAAATTATTAACAGAAATTATTTCATAATCATTTTAAT
275106 TTTTTTAAAATAATTAAATTTAAATAA-T-T-ATA-ATATATATATATATAT-TATCAATAGATT
1 TTTTTTAAAATAATTAAATTTAAATAATTATAATATATATATATATATATATATATCAATAGATT
* *
275166 AAAAAATTATTAACATATATTATTTCATAATCATTTTAAT
66 AAAAAATTATTAACAGAAATTATTTCATAATCATTTTAAT
*
275206 TTTTTAAAAAAATAATTAAATT
1 TTTTT--TAAAATAATTAAATT
275228 GTCCGTTTTG
Statistics
Matches: 114, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
99 12 0.11
100 42 0.37
101 16 0.14
102 17 0.15
103 1 0.01
104 1 0.01
105 21 0.18
106 4 0.04
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (105 bp):
TTTTTTAAAATAATTAAATTTAAATAATTATAATATATATATATATATATATATATCAATAGATT
AAAAAATTATTAACAGAAATTATTTCATAATCATTTTAAT
Found at i:275643 original size:3 final size:3
Alignment explanation
Indices: 275635--275676 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
275625 TTTTATTTGT
*
275635 TTA TTA TTA TTA TTA CTA TTA -TA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
275677 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:275684 original size:10 final size:10
Alignment explanation
Indices: 275637--275684 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
275627 TTATTTGTTT
275637 ATTATTATT-
1 ATTATTATTA
*
275646 ATTACTATTA
1 ATTATTATTA
*
275656 TATTATTATTT
1 -ATTATTATTA
275667 ATTATTATTA
1 ATTATTATTA
*
275677 ATTTTTAT
1 ATTATTAT
275685 ATTACATGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTATTATTA
Found at i:277363 original size:22 final size:22
Alignment explanation
Indices: 277335--277377 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
277325 TTAATTCCTT
277335 TTATTTTAGTCATTATTTAATG
1 TTATTTTAGTCATTATTTAATG
277357 TTATTTTAGTCATTATTTAAT
1 TTATTTTAGTCATTATTTAAT
277378 ACTATATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
TTATTTTAGTCATTATTTAATG
Found at i:277504 original size:26 final size:24
Alignment explanation
Indices: 277456--277505 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
277446 ATATATATGT
*
277456 TATATAATTTATATGTTACTTATA
1 TATATAATTTATATGTCACTTATA
*
277480 TATATATATTGTATATGTCATTTATA
1 TATATA-ATT-TATATGTCACTTATA
277506 CATCCTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
TATATAATTTATATGTCACTTATA
Found at i:279421 original size:107 final size:106
Alignment explanation
Indices: 279108--279476 Score: 549
Period size: 106 Copynumber: 3.5 Consensus size: 106
279098 ACAAATGGGC
279108 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
* ** *
279173 CAACTTTACAACGAAGGGGCGACTGGTTGTCAACAAACAAC
66 CAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
* * * * *
279214 TTCCCAGTTTCAGAGCCAATTTTAACTTCATAGTGAAGGATATTGGACTCAAGACAGCACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
* *
279279 CAACTTCACAACGAAGGGGCGGCTGACTGTCAACAAATAAT
66 CAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
* *
279320 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAAGACAACACAAGC
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTC-AAGACAACACAAGC
*
279385 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAAT
65 TCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
* * * ** *
279427 TTCCCTGTTCCAGAACCAATTTCAACTTCATGGCGGAGGATATTAGACTC
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTC
279477 GGAGCAATAC
Statistics
Matches: 235, Mismatches: 27, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
106 141 0.60
107 94 0.40
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
CAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
Found at i:279958 original size:33 final size:33
Alignment explanation
Indices: 279914--279981 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
279904 TCCTTTAAAC
*
279914 AAATTTCGTCTCTCTCGAGACAGTTTCTCTTGA
1 AAATTTCGTCTCCCTCGAGACAGTTTCTCTTGA
* *
279947 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 AAATTTCGTCTCCCTCGAGACAGTTTCTCTTGA
279980 AA
1 AA
279982 CACAAAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (33 bp):
AAATTTCGTCTCCCTCGAGACAGTTTCTCTTGA
Found at i:282726 original size:17 final size:17
Alignment explanation
Indices: 282706--282769 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
282696 TTTTTAATAA
282706 ATAAATATTTTACTTTT
1 ATAAATATTTTACTTTT
*
282723 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTACTTTT
282745 AAATAAATATTTTACTTTT
1 --ATAAATATTTTACTTTT
282764 ATAAAT
1 ATAAAT
282770 TATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 7 0.18
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATATTTTACTTTT
Found at i:282735 original size:22 final size:21
Alignment explanation
Indices: 282697--282769 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
282687 TTTATGATAT
282697 TTTTAATAAATAAATATTTTAC
1 TTTT-ATAAATAAATATTTTAC
* *
282719 TTTTATAAATTATATATATTA-
1 TTTTATAAA-TAAATATTTTAC
282740 TTTT-TAAATAAATATTTTAC
1 TTTTATAAATAAATATTTTAC
282760 TTTTATAAAT
1 TTTTATAAAT
282770 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.20
20 8 0.18
21 14 0.32
22 13 0.30
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAAATAAATATTTTAC
Found at i:282750 original size:24 final size:23
Alignment explanation
Indices: 282694--282752 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
282684 CATTTTATGA
*
282694 TATTTTTAATAAA-TAAATATTT
1 TATTTTTAATAAATTAAATATAT
* *
282716 TACTTTT-ATAAATTATATATAT
1 TATTTTTAATAAATTAAATATAT
282738 TATTTTTAAATAAAT
1 TATTTTT-AATAAAT
282753 ATTTTACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.63
24 6 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTTTAATAAATTAAATATAT
Found at i:282807 original size:19 final size:19
Alignment explanation
Indices: 282783--282825 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
282773 ATATATAAAT
282783 ATATTT-TTTAATTTTTTTA
1 ATATTTATTT-ATTTTTTTA
282802 ATATTTATTTATTTTTTTA
1 ATATTTATTTATTTTTTTA
282821 ATATT
1 ATATT
282826 AAGAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATATTTATTTATTTTTTTA
Found at i:284253 original size:9 final size:9
Alignment explanation
Indices: 284239--284274 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
284229 ACTTGATCTG
284239 AATTTTAAA
1 AATTTTAAA
284248 AATTTTAAA
1 AATTTTAAA
*
284257 ATTTTTAAA
1 AATTTTAAA
*
284266 AATATTAAA
1 AATTTTAAA
284275 GACTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTTTAAA
Found at i:285591 original size:35 final size:35
Alignment explanation
Indices: 285546--285617 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
285536 TCCAAAAGGT
*
285546 AGGTGTTTACAATTTAAGCTCACAAAAACACTCTA
1 AGGTGTTTACAACTTAAGCTCACAAAAACACTCTA
*
285581 AGGTGTTTACAACTTAAGCTCACAAAAGCACTCTA
1 AGGTGTTTACAACTTAAGCTCACAAAAACACTCTA
285616 AG
1 AG
285618 TACAAGAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (35 bp):
AGGTGTTTACAACTTAAGCTCACAAAAACACTCTA
Found at i:287384 original size:19 final size:21
Alignment explanation
Indices: 287348--287391 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
287338 CTCAAAATCA
*
287348 TTTTTCAAAATTTCA-TTTTG
1 TTTTTCAAAATCTCATTTTTG
287368 TTTTTCAAAATCT-ATTTTTG
1 TTTTTCAAAATCTCATTTTTG
287388 TTTT
1 TTTT
287392 CGAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTTCAAAATCTCATTTTTG
Found at i:293606 original size:20 final size:19
Alignment explanation
Indices: 293583--293625 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
293573 AAATTATACC
*
293583 CAAAACGAAAAAATAAATCA
1 CAAAACCAAAAAAT-AATCA
*
293603 CAAACCCAAAAAATAATCA
1 CAAAACCAAAAAATAATCA
293622 CAAA
1 CAAA
293626 CCCTCATCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.67, C:0.21, G:0.02, T:0.09
Consensus pattern (19 bp):
CAAAACCAAAAAATAATCA
Found at i:293613 original size:19 final size:19
Alignment explanation
Indices: 293590--293628 Score: 69
Period size: 19 Copynumber: 2.0 Consensus size: 19
293580 ACCCAAAACG
293590 AAAAAATAAATCACAAACCC
1 AAAAAAT-AATCACAAACCC
293610 AAAAAATAATCACAAACCC
1 AAAAAATAATCACAAACCC
293629 TCATCCCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.64, C:0.26, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAAATAATCACAAACCC
Found at i:297169 original size:18 final size:20
Alignment explanation
Indices: 297134--297176 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
297124 ATTTAAAAAC
297134 TAAAAATTATTATTATTTTT
1 TAAAAATTATTATTATTTTT
297154 TAAAAA-TATT-TTATTTTT
1 TAAAAATTATTATTATTTTT
297172 TAAAA
1 TAAAA
297177 TCTTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAAAATTATTATTATTTTT
Found at i:299059 original size:14 final size:14
Alignment explanation
Indices: 299040--299068 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
299030 AAATGAATTG
299040 AAAATATTAGATAA
1 AAAATATTAGATAA
299054 AAAATATTAGATAA
1 AAAATATTAGATAA
299068 A
1 A
299069 CCCAAGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAAATATTAGATAA
Found at i:301101 original size:106 final size:106
Alignment explanation
Indices: 300909--302222 Score: 2042
Period size: 106 Copynumber: 12.4 Consensus size: 106
300899 GCATTGTTCC
* * **
300909 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAA-CCAGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTGTTGAC
* * * *
300972 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
301015 GAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
301080 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
301121 GAGTCCAATATCCTTCGCTCTGAAGTTGAAATTAGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
301186 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * * *
301227 GAGTTCAATATATTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
301292 CCAGCGGTCCATTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
301333 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * *
301398 CCAGCGGTCCCTTCGTCATGAAGTTGAACATGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
301439 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * *
301504 CCAGCGGTCCCTTCGTCGTAAAGTTGAACGTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
301545 GAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
301610 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
301651 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGCTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * *
301716 CCAGCGGTCCCTTCATCGTAAAGTTGAACGTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
301757 GAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
301822 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
301863 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGCTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
301928 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
301969 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TTGTTTGTTGACA
*
302033 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
302075 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TTGTTTGTTGACA
*
302139 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
302181 GAGTCCAATTTTCTTCGCTGCGAAGTTGAAATAGACTCTGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
302223 TAAAATTGGA
Statistics
Matches: 1123, Mismatches: 82, Indels: 6
0.93 0.07 0.00
Matches are distributed among these distances:
105 3 0.00
106 1119 1.00
107 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:302869 original size:257 final size:257
Alignment explanation
Indices: 302413--302925 Score: 963
Period size: 257 Copynumber: 2.0 Consensus size: 257
302403 TGTTGAACTG
* *
302413 GTTCTCGAACCTATCTGAAATTGGTTCTAAGATGTCAAGTCGGTTGAGGTGTAACTTCTTACTGC
1 GTTCTCGAACCTATCTGAAATTGGTTCTAAGATGTCAAGTCGATTGAGGTGTAACTTCTTACTAC
302478 CGAGTTAATCAACCACCATCCTTCTTTGAAGGCACTTGAGAATCGAACATCCTTCATCCTGAAGT
66 CGAGTTAATCAACCACCATCCTTCTTTGAAGGCACTTGAGAATCGAACATCCTTCATCCTGAAGT
* *
302543 CAAAACTTGACTTTAAAAGCTGTAAAAACGTGTATGCTAAAATGATGAATGTGATGCACCTAAGT
131 CAAAACTTGACTCTAAAAGCTGCAAAAACGTGTATGCTAAAATGATGAATGTGATGCACCTAAGT
*
302608 ATGTCTAAGATGCACGCAATATGAATGAATTATGTGTTATCTCCTGGATGGAGCCTCGTGCA
196 ATGTCTAAGATGCACGCAATATGAATGAATTATGTGTTATCTCCTAGATGGAGCCTCGTGCA
*
302670 GTTCTCGAACCTATCTGAAATTGGTTCTAAGATGTCAAGTCGATTGAGGTGTAGCTTCTTACTAC
1 GTTCTCGAACCTATCTGAAATTGGTTCTAAGATGTCAAGTCGATTGAGGTGTAACTTCTTACTAC
*
302735 CGAGTTAATCAACCACCATCCTTCTTTGAAGGCACTTGAGAATCGAATATCCTTCATCCTGAAGT
66 CGAGTTAATCAACCACCATCCTTCTTTGAAGGCACTTGAGAATCGAACATCCTTCATCCTGAAGT
302800 CAAAACTTGACTCTAAAAGCTGCAAAAACGTGTATGCTAAAATGATGAATGTGATGCACCTAAGT
131 CAAAACTTGACTCTAAAAGCTGCAAAAACGTGTATGCTAAAATGATGAATGTGATGCACCTAAGT
302865 ATGTCTAAGATGCACGCAATATGAATGAATTATGTGTTATCTCCTAGATGGAGCCTCGTGC
196 ATGTCTAAGATGCACGCAATATGAATGAATTATGTGTTATCTCCTAGATGGAGCCTCGTGC
302926 TTTGTCTGTC
Statistics
Matches: 249, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
257 249 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (257 bp):
GTTCTCGAACCTATCTGAAATTGGTTCTAAGATGTCAAGTCGATTGAGGTGTAACTTCTTACTAC
CGAGTTAATCAACCACCATCCTTCTTTGAAGGCACTTGAGAATCGAACATCCTTCATCCTGAAGT
CAAAACTTGACTCTAAAAGCTGCAAAAACGTGTATGCTAAAATGATGAATGTGATGCACCTAAGT
ATGTCTAAGATGCACGCAATATGAATGAATTATGTGTTATCTCCTAGATGGAGCCTCGTGCA
Found at i:306423 original size:14 final size:14
Alignment explanation
Indices: 306404--306432 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
306394 AAATGAATCG
306404 AAAATATTAGATAA
1 AAAATATTAGATAA
306418 AAAATATTAGATAA
1 AAAATATTAGATAA
306432 A
1 A
306433 CCCAAGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAAATATTAGATAA
Found at i:313889 original size:35 final size:35
Alignment explanation
Indices: 313848--313922 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
313838 TTCATGTTCA
313848 AAATTCCAAAACACTTCAATTATATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTATATTCTAAACCCC
* * *
313883 AAATTCCAAAATACTTTAATTATATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTATATTCTAAACCCC
313918 AAATT
1 AAATT
313923 AAAGTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTATATTCTAAACCCC
Found at i:313955 original size:34 final size:34
Alignment explanation
Indices: 313917--313993 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
313907 TTCTAAACCC
*
313917 TAAATTAAAGTATTTTAGACTTTAGGGTTTAAAA
1 TAAATTAAAGTATTTTAGAATTTAGGGTTTAAAA
* * * *
313951 TAAATTGAATTATTTTGGAATTTGGGGTTTAAAA
1 TAAATTAAAGTATTTTAGAATTTAGGGTTTAAAA
313985 TGAAATTAA
1 T-AAATTAA
313994 GGATTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 30 0.83
35 6 0.17
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.42
Consensus pattern (34 bp):
TAAATTAAAGTATTTTAGAATTTAGGGTTTAAAA
Found at i:319867 original size:54 final size:54
Alignment explanation
Indices: 319763--319867 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
319753 TGATACCTGC
* * *
319763 TCTATAGACATGTAAATATCTTTTGGTTGAAATCTTTTGAGTGGTCCGAGTAAT
1 TCTATAGACATGTAAATATCTTTTGGTTGAAACCTTCTGAGTGATCCGAGTAAT
*
319817 TCTATAGACATGTAAATATCTTTTGGTTGAAACCTTCTGAGTGATTCGAGT
1 TCTATAGACATGTAAATATCTTTTGGTTGAAACCTTCTGAGTGATCCGAGT
319868 TGTTAAGTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (54 bp):
TCTATAGACATGTAAATATCTTTTGGTTGAAACCTTCTGAGTGATCCGAGTAAT
Found at i:322345 original size:42 final size:42
Alignment explanation
Indices: 322284--322466 Score: 163
Period size: 42 Copynumber: 4.4 Consensus size: 42
322274 ATCTGGTCAG
* ***
322284 AAGAATAACTCACATGGCTTTCCCATTAAGGGGAGTCATTGA
1 AAGAATATCTCACATGGCTTTCCCGCGAAGGGGAGTCATTGA
* ** * * *
322326 AAGAATATCTCACACGGCTTTCTTGCGAAGGGGACTCATCGG
1 AAGAATATCTCACATGGCTTTCCCGCGAAGGGGAGTCATTGA
* * *
322368 AAGAATATCTCACAAGGCTTTCTCGCGAAGGGGAGTAATTTGA
1 AAGAATATCTCACATGGCTTTCCCGCGAAGGGGAGTCA-TTGA
* * ** **
322411 AA-AATATCTCACTTGGCTTTCCCGGGAAGATGAGTCATTCT
1 AAGAATATCTCACATGGCTTTCCCGCGAAGGGGAGTCATTGA
*
322452 AA-AATATTTCACATG
1 AAGAATATCTCACATG
322467 ACTTAGACCT
Statistics
Matches: 113, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
41 15 0.13
42 94 0.83
43 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
AAGAATATCTCACATGGCTTTCCCGCGAAGGGGAGTCATTGA
Found at i:323966 original size:104 final size:104
Alignment explanation
Indices: 323891--324082 Score: 260
Period size: 104 Copynumber: 1.8 Consensus size: 104
323881 TTCCCCATTT
*
323891 TTTTTCTATATT-TTTTTCTCCTTGAATTTCCCCCATTTTCTTTTTAAATTTAATTTTAATTATT
1 TTTTTCCATATTGTTTTTC-CCTTGAATTT-CCCCATTTTCTTTTTAAATTTAATTTTAATTATT
*** *
323955 CCCTTATTTATTTCCTTCAGGATTATAACGTTTTCTCTCTC
64 CCCTTATTTATTTCCTTCTTAATTATAACGTTTTCCCTCTC
* * * * *
323996 TTTTTCCATGTTGTTTTTCCCTTTAATTTCCTCATTTTCTTTTTAAATTTAGTTTTAATTATTCT
1 TTTTTCCATATTGTTTTTCCCTTGAATTTCCCCATTTTCTTTTTAAATTTAATTTTAATTATTCC
*
324061 CTTATATATTTCCTTCTTAATT
66 CTTATTTATTTCCTTCTTAATT
324083 TATTTTTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
104 51 0.67
105 19 0.25
106 6 0.08
ACGTcount: A:0.19, C:0.18, G:0.04, T:0.59
Consensus pattern (104 bp):
TTTTTCCATATTGTTTTTCCCTTGAATTTCCCCATTTTCTTTTTAAATTTAATTTTAATTATTCC
CTTATTTATTTCCTTCTTAATTATAACGTTTTCCCTCTC
Found at i:338326 original size:51 final size:52
Alignment explanation
Indices: 338160--338688 Score: 446
Period size: 55 Copynumber: 9.9 Consensus size: 52
338150 TGGCGGGTCT
** * * ** * *
338160 GCTCCCTATTGTTTCAGGGAGTATAAGACCCAAACAATCTTCGGCAAGCGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGA--C-TACAATCTTCAACAAACGTGTCC
** * * * *
338215 GCTCCCTATTCAGTCAGGGAGTATAAGACTTGAATAATCTTAAACAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGAC-T--ACAATCTTCAACAAACGTGTCC
*
338270 GCTCCCTATTCCTTCAGAGAGTATAAGACT-CAATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTACAATCTTCAACAAACGTGTCC
* * **
338321 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTTAACAAACGTGTTT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTACAATCTTCAACAAACGTGTCC
*
338372 GCTCCCTATTCCTTCAGAGAGTAT-AGAACTCGAGCAATCTTCATA-AAACGAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACT--A-CAATCTTCA-ACAAACGTGTCC
* * *
338427 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATATTCAACAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACT---ACAATCTTCAACAAACGTGTCC
* ** *
338482 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCATGAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACT---ACAATCTTCAACAAACGTGTCC
* * **
338537 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACGAATTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACT---ACAATCTTCAACAAACGTGTCC
* * * ** *
338592 ACTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAATTTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTACAATCTTCAACAAACGTGTCC
*
338643 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTACAATCTTCAACAAACG
338689 AATTTGCTTC
Statistics
Matches: 409, Mismatches: 54, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.00
51 152 0.37
53 1 0.00
54 2 0.00
55 250 0.61
56 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (52 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTACAATCTTCAACAAACGTGTCC
Found at i:338337 original size:110 final size:107
Alignment explanation
Indices: 338208--338688 Score: 504
Period size: 110 Copynumber: 4.5 Consensus size: 107
338198 CTTCGGCAAG
* ** * * * * *
338208 CGTGTCTGCTCCCTATTCAGTCAGGGAGTATA-AGACTTGAATAATCTTAAACAAACGGGTCCGC
1 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGTGTCCGC
338272 TCCCTATTCCTTCAGAGAGTATA-AGACT-CAATCTTCA-ATAAA
65 TCCCTATTCCTTCAGAGAGTATAGA-ACTACAATCTTCATA-AAA
* * **
338314 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGTGTTTGCT
1 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCT
338375 CCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAA
66 CCCTATTCCTTCAGAGAGTATAGAACT--A-CAATCTTCATAAAA
* * * *
338420 CGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATATTCAACAAACGTGTTCGCT
1 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCT
* *
338485 CTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAA
66 CCCTATTCCTTCAGAGAGTATAGAACT---ACAATCTTCATAAAA
* * * ** *
338530 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAATTTGTCCACT
1 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCT
* *
338595 CCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCA-ACGAA
66 CCCTATTCCTTCAGAGAGTATAGAACTACAATCTTCATA-AAA
** * *
338636 TTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
338689 AATTTGCTTC
Statistics
Matches: 322, Mismatches: 40, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
102 57 0.18
103 1 0.00
106 119 0.37
107 1 0.00
110 143 0.44
111 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (107 bp):
CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCT
CCCTATTCCTTCAGAGAGTATAGAACTACAATCTTCATAAAA
Found at i:338730 original size:36 final size:36
Alignment explanation
Indices: 338690--338797 Score: 144
Period size: 36 Copynumber: 3.0 Consensus size: 36
338680 CAACAAACGA
* *
338690 ATTTGCTTCACTACTCTTCCATGAAGACTTCAGATG
1 ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGATG
* *
338726 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTG
1 ATTTGCTTCACTACTCTTCCATGAAGGCTTAAG-ATG
* * *
338763 AATTGCTTCACTGCTCTTTCATGAAGGCTTAAGAT
1 ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGAT
338798 TGACCTGTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 31 0.50
37 31 0.50
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (36 bp):
ATTTGCTTCACTACTCTTCCATGAAGGCTTAAGATG
Found at i:338780 original size:37 final size:36
Alignment explanation
Indices: 338692--338800 Score: 137
Period size: 37 Copynumber: 3.0 Consensus size: 36
338682 ACAAACGAAT
* * * *
338692 TTGCTTCACTACTCTTCCATGAAGACTTCAGATGAT
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAGTTGAA
*
338728 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAG-TTGAA
* *
338765 TTGCTTCACTGCTCTTTCATGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAG-TTGA
338801 CCTGTTTTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
36 28 0.44
37 35 0.56
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCCATGAAGGCTTAAGTTGAA
Found at i:340141 original size:15 final size:16
Alignment explanation
Indices: 340121--340154 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
340111 CCATTTTCCA
340121 TTTTTTCTCTTC-TTT
1 TTTTTTCTCTTCGTTT
*
340136 TTTTTTCTTTTCGTTT
1 TTTTTTCTCTTCGTTT
340152 TTT
1 TTT
340155 CCATCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTCTCTTCGTTT
Found at i:340153 original size:28 final size:27
Alignment explanation
Indices: 340121--340199 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 27
340111 CCATTTTCCA
340121 TTTTTTCTCTTCTTTTTTT-TTCTTTTC
1 TTTTTTCTCTTCTTTTTTTCTT-TTTTC
*
340148 GTTTTTTC-CATCATTTTTTTCTTTTTTC
1 -TTTTTTCTCTTC-TTTTTTTCTTTTTTC
340176 TCATTTTT-TCTTCTTTTTCTTCTT
1 T--TTTTTCTCTTCTTTTT-TTCTT
340200 CTCATTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
27 4 0.09
28 24 0.56
29 15 0.35
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (27 bp):
TTTTTTCTCTTCTTTTTTTCTTTTTTC
Found at i:340173 original size:21 final size:18
Alignment explanation
Indices: 340143--340192 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 18
340133 TTTTTTTTTC
340143 TTTTCGTTTTTTCCATCATTT
1 TTTTC-TTTTTTCC-TCA-TT
340164 TTTTCTTTTTT-CTCATT
1 TTTTCTTTTTTCCTCATT
340181 TTTTCTTCTTTT
1 TTTTCTT-TTTT
340193 TCTTCTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 1 0.04
20 6 0.21
21 5 0.18
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTCTTTTTTCCTCATT
Found at i:340195 original size:19 final size:19
Alignment explanation
Indices: 340095--340195 Score: 63
Period size: 19 Copynumber: 5.3 Consensus size: 19
340085 TCTTTTTTCA
*
340095 TTTT-TCATTTTTTCTTCCA
1 TTTTCTCATTTTTTCTT-CT
340114 TTTTC-CATTTTTTCTCTTCT
1 TTTTCTCA-TTTTT-TCTTCT
* *
340134 TTTT-T-TTTCTTTTCGT-T
1 TTTTCTCATT-TTTTCTTCT
340151 TTTTC-CATCATTTTT-TTCTT
1 TTTTCTCAT--TTTTTCTTC-T
340171 TTTTCTCATTTTTTCTTCT
1 TTTTCTCATTTTTTCTTCT
340190 TTTTCT
1 TTTTCT
340196 TCTTCTCATT
Statistics
Matches: 64, Mismatches: 5, Indels: 26
0.67 0.05 0.27
Matches are distributed among these distances:
17 5 0.08
18 7 0.11
19 25 0.39
20 20 0.31
21 7 0.11
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTTCTCATTTTTTCTTCT
Found at i:340253 original size:16 final size:15
Alignment explanation
Indices: 340218--340255 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
340208 TATTATTATT
340218 TTTTATTCTTTTTTC
1 TTTTATTCTTTTTTC
*
340233 ATTTATTCTTTTTTCC
1 TTTTATTCTTTTTT-C
340249 TTTTATT
1 TTTTATT
340256 TCTTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTCTTTTTTC
Found at i:350013 original size:47 final size:45
Alignment explanation
Indices: 349913--350016 Score: 127
Period size: 47 Copynumber: 2.2 Consensus size: 45
349903 TTGTTATCCA
* * *
349913 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTT
1 CAAAAAAAAAACCTAACCGCATGATATCTAATTCGCATGCTTATT
*
349958 CAAAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATT
1 C-AAAAAAA-AAACCTAACCGCATGATATCTAATTCGCATGC--TTATT
*
350007 CGAAAAAAAA
1 CAAAAAAAAA
350017 CGAAAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
45 1 0.02
46 6 0.12
47 32 0.64
48 6 0.12
49 5 0.10
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (45 bp):
CAAAAAAAAAACCTAACCGCATGATATCTAATTCGCATGCTTATT
Found at i:360535 original size:26 final size:26
Alignment explanation
Indices: 360504--360563 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
360494 TTGCTTTAAC
360504 TTTCTCTAATTTATCAGGGAATGTTG
1 TTTCTCTAATTTATCAGGGAATGTTG
360530 TTTCTCTAATTTATCAGGGAATGTTG
1 TTTCTCTAATTTATCAGGGAATGTTG
360556 TTTCTCTA
1 TTTCTCTA
360564 GTTCCTAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (26 bp):
TTTCTCTAATTTATCAGGGAATGTTG
Found at i:362352 original size:18 final size:18
Alignment explanation
Indices: 362307--362343 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
362297 TTCAGATGAT
362307 GCAGCAGCAGCAACAACA
1 GCAGCAGCAGCAACAACA
*
362325 GCAGCAGCAGCAGCAACA
1 GCAGCAGCAGCAACAACA
362343 G
1 G
362344 TTGCAGCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.32, G:0.27, T:0.00
Consensus pattern (18 bp):
GCAGCAGCAGCAACAACA
Found at i:363227 original size:41 final size:41
Alignment explanation
Indices: 362951--363297 Score: 299
Period size: 41 Copynumber: 8.4 Consensus size: 41
362941 CAAATTGATA
* * * * *
362951 ACTTTAGCGGCGTTTTTTATACAAAACGCCACAACAGAGTA-GT
1 ACTTTAGTGGCG-TTTTTATAC-AAACGCCGCTATAGA-CACGT
* *** *
362994 ACTTTAGTGGCGTTTTTATACAAACGCCGCAATAGGTTCAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGT
** * * *
363035 -CCATAGTGGCGTTTTTTAAACAAACGTCATGAC-ATAG-TA-GT
1 ACTTTAGTGGCG-TTTTTATACAAACG-C-CG-CTATAGACACGT
* * *
363076 ACTTTAGCGCCGTTTTTATACAAACGCCGCTATAAACACGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGT
** * * *
363117 AAGTTAGTGGCGTTTTTATACAAATGCCGTTATAGACATGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGT
* *
363158 AATTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGT
*
363199 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGT
* * * *
363240 ACTTTAGTGGCGTTTGTGTTTAAAAACGCTGCTATAGACTCGT
1 ACTTTAGTGGCGTTT-T-TATACAAACGCCGCTATAGACACGT
*
363283 ACTTTAGCGGCGTTT
1 ACTTTAGTGGCGTTT
363298 GTAAAAACAA
Statistics
Matches: 253, Mismatches: 40, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.00
39 4 0.02
40 12 0.05
41 164 0.65
42 19 0.08
43 52 0.21
44 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGT
Found at i:367751 original size:21 final size:21
Alignment explanation
Indices: 367694--367752 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
367684 TGATTTATTA
* *
367694 TTATAGATTTTAAGTATCTTG
1 TTATGGATTTTAAGTTTCTTG
* *
367715 TTATGAATTTTAAGTTTGTTG
1 TTATGGATTTTAAGTTTCTTG
*
367736 TTATGGATGTTAAGTTT
1 TTATGGATTTTAAGTTT
367753 ATTGGATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.02, G:0.19, T:0.54
Consensus pattern (21 bp):
TTATGGATTTTAAGTTTCTTG
Found at i:377414 original size:15 final size:15
Alignment explanation
Indices: 377394--377430 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
377384 ATATTTAGCT
*
377394 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
377409 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
377424 GGGCGGG
1 GGGCGGG
377431 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:378547 original size:24 final size:26
Alignment explanation
Indices: 378520--378576 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
378510 TTAGATTATT
378520 ATATTAAT-ATTA-AAT-ATTTAAATA
1 ATATTAATCATTATAATAATTT-AATA
*
378544 ATATTATTCATTATTAATAATTTAATA
1 ATATTAATCATTA-TAATAATTTAATA
378571 ATATTA
1 ATATTA
378577 TTTCTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.25
25 4 0.14
27 13 0.46
28 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTAATCATTATAATAATTTAATA
Found at i:378773 original size:24 final size:23
Alignment explanation
Indices: 378746--378791 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
378736 TTAAATATTT
378746 TAATAATT-AATATTTTGATTAAAA
1 TAAT-ATTAAATATTTT-ATTAAAA
378770 TAATATTAAAATATTTTATTAA
1 TAATATT-AAATATTTTATTAA
378792 TATTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 9 0.45
25 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATTAAATATTTTATTAAAA
Found at i:380372 original size:12 final size:12
Alignment explanation
Indices: 380355--380381 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
380345 ACTACTTCAT
380355 AGATTCAAATTA
1 AGATTCAAATTA
380367 AGATTCAAATTA
1 AGATTCAAATTA
380379 AGA
1 AGA
380382 ATACTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (12 bp):
AGATTCAAATTA
Found at i:396401 original size:22 final size:22
Alignment explanation
Indices: 396373--396414 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
396363 TACGATTATG
*
396373 AGATATTACTGGATCACGATCC
1 AGATATTACGGGATCACGATCC
*
396395 AGATATTACGGGATTACGAT
1 AGATATTACGGGATCACGAT
396415 TAAAATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (22 bp):
AGATATTACGGGATCACGATCC
Found at i:397818 original size:16 final size:16
Alignment explanation
Indices: 397799--397833 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
397789 TCAACTACCG
397799 CTTAGCACAACAACCA
1 CTTAGCACAACAACCA
397815 CTTAGCACAACAACCA
1 CTTAGCACAACAACCA
397831 CTT
1 CTT
397834 CCAATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.37, G:0.06, T:0.17
Consensus pattern (16 bp):
CTTAGCACAACAACCA
Found at i:400021 original size:25 final size:25
Alignment explanation
Indices: 399991--400054 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
399981 ATAGATATTA
399991 ATTACTGTGATTTTATTATTCTAAT
1 ATTACTGTGATTTTATTATTCTAAT
400016 ATTACTGTGATTTTATTATTCTAAT
1 ATTACTGTGATTTTATTATTCTAAT
400041 ATTACTGTGATTTT
1 ATTACTGTGATTTT
400055 TAGATATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.56
Consensus pattern (25 bp):
ATTACTGTGATTTTATTATTCTAAT
Found at i:400752 original size:17 final size:17
Alignment explanation
Indices: 400727--400760 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
400717 TTTTTATTAT
*
400727 TATATAATATAAAATAA
1 TATAAAATATAAAATAA
400744 TATAAAATATAAAATAA
1 TATAAAATATAAAATAA
400761 AAATAGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAAAATATAAAATAA
Found at i:402413 original size:25 final size:27
Alignment explanation
Indices: 402365--402415 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
402355 TTAATAATTT
402365 GTTTTTATCTTTTCTAAAATTTTATAG
1 GTTTTTATCTTTTCTAAAATTTTATAG
*
402392 GTTTTTGTC-TTT-TAAAATTTTATA
1 GTTTTTATCTTTTCTAAAATTTTATA
402416 AATTCATCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 3 0.13
27 8 0.35
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.61
Consensus pattern (27 bp):
GTTTTTATCTTTTCTAAAATTTTATAG
Found at i:404117 original size:2 final size:2
Alignment explanation
Indices: 404052--404104 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
404042 GATGTGTAAG
404052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
404094 AT AT AT AT AT A
1 AT AT AT AT AT A
404105 CAAAAGTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:414944 original size:21 final size:21
Alignment explanation
Indices: 414893--414945 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
414883 ATTATGACTA
414893 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
414914 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
414935 TCGCAATGCGA
1 TCGCAATGCGA
414946 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:414960 original size:20 final size:21
Alignment explanation
Indices: 414935--414986 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
414925 TTTTCCCAAT
*
414935 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
414955 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
414976 TCGCAATGCGA
1 TCGCAATGCGA
414987 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:415000 original size:20 final size:20
Alignment explanation
Indices: 414975--415109 Score: 137
Period size: 20 Copynumber: 6.7 Consensus size: 20
414965 AATTTGGAAA
*
414975 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
414995 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
415016 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
415036 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
415056 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * * *
415076 TTCGCAACGAGATTCTAACT
1 ATCGCAACGCGATACTGACT
*
415096 ATCGCAACGAGATA
1 ATCGCAACGCGATA
415110 ATACAGAATC
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.82
21 14 0.14
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:415048 original size:41 final size:42
Alignment explanation
Indices: 414972--415084 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 42
414962 GCGAATTTGG
*
414972 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATGAC
*
415013 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATGAC
** * *
415055 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAATGCGATACTGACTTTCGCAACG
415085 AGATTCTAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 26 0.40
41 37 0.57
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:415282 original size:12 final size:12
Alignment explanation
Indices: 415265--415296 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
415255 CTCCGGCGAC
415265 ATCCGTTCCTAT
1 ATCCGTTCCTAT
415277 ATCCGTTCCTAT
1 ATCCGTTCCTAT
415289 ATCC-TTCC
1 ATCCGTTCC
415297 CCATCCGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.16, C:0.38, G:0.06, T:0.41
Consensus pattern (12 bp):
ATCCGTTCCTAT
Found at i:415902 original size:24 final size:24
Alignment explanation
Indices: 415851--415904 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
415841 GTATTCGAAA
* *
415851 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
415875 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
415899 TTTGAT
1 TTTGAT
415905 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:418930 original size:42 final size:42
Alignment explanation
Indices: 418866--418948 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
418856 AATCGGGCTC
*
418866 TTGAATGGTGGGAGGGACCTCTTCAACG-ATGACAGTGGCCTT
1 TTGAACGGTGGGAGGGACCTCTT-AACGAATGACAGTGGCCTT
* *
418908 TTGAACGGTGGGAGGGGA-CTCTTGAGGAATGACAGTGGCCT
1 TTGAACGGTGGGA-GGGACCTCTTAACGAATGACAGTGGCCT
418949 CTTCTTGCGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.06
42 30 0.83
43 4 0.11
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (42 bp):
TTGAACGGTGGGAGGGACCTCTTAACGAATGACAGTGGCCTT
Found at i:418932 original size:21 final size:21
Alignment explanation
Indices: 418863--418932 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
418853 GTGAATCGGG
*
418863 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
418883 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
*
418905 CTTTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
418926 CTCTTGA
1 CTCTTGA
418933 GGAATGACAG
Statistics
Matches: 33, Mismatches: 15, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.26
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:419414 original size:19 final size:19
Alignment explanation
Indices: 419333--419408 Score: 98
Period size: 19 Copynumber: 3.9 Consensus size: 19
419323 TCTGGAACTT
*
419333 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
419354 ACTATCGCAACACGAAATG
1 AAAATCGCAACGCGAAATG
419373 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
419392 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
419409 CCAAAAGACA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 38 0.79
21 10 0.21
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:419603 original size:94 final size:93
Alignment explanation
Indices: 419495--419776 Score: 482
Period size: 94 Copynumber: 3.1 Consensus size: 93
419485 ATGGATTGCA
*
419495 TTACTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
419560 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAATAAAT
419588 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
419653 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
*
419682 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
419743 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
419772 TTACT
1 TTACT
419777 AAGCAATCTA
Statistics
Matches: 183, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
90 42 0.23
93 23 0.13
94 118 0.64
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:421498 original size:40 final size:38
Alignment explanation
Indices: 421454--421594 Score: 140
Period size: 33 Copynumber: 3.9 Consensus size: 38
421444 TCTTTTGGTT
**
421454 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGACTATCGCAACGAGA-AATGAAAATCGCAACGC
421493 GGAAATGACTATCGCAACGAG--A-G--AATCGCAACGC
1 -GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
* *
421527 GAAATGACTATCGCAACGCGAAATGAAAATCGTAA--C
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
* *
421563 GAGA-GA--ATCGCAACGCGAAATGAAAATCGCAA
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAA
421595 TGTGATTTTG
Statistics
Matches: 90, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
33 44 0.49
34 11 0.12
35 3 0.03
36 6 0.07
37 1 0.01
38 7 0.08
40 18 0.20
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (38 bp):
GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:421541 original size:19 final size:19
Alignment explanation
Indices: 421463--421552 Score: 91
Period size: 20 Copynumber: 4.9 Consensus size: 19
421453 TGAAATGAAA
* **
421463 ATCGCAACGAGATAATGAAA
1 ATCGCAACGCGA-AATGACT
421483 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
421503 ATCGCAA--CGAGA-GA--
1 ATCGCAACGCGAAATGACT
421517 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
421536 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
421553 AAATCGTAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.12
16 6 0.10
17 5 0.08
18 1 0.02
19 17 0.29
20 21 0.36
21 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:421558 original size:19 final size:19
Alignment explanation
Indices: 421454--421594 Score: 122
Period size: 19 Copynumber: 7.8 Consensus size: 19
421444 TCTTTTGGTT
*
421454 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
421473 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
421493 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
421511 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
421527 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
421546 GAAATGAAAATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
421563 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
421579 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
421595 TGTGATTTTG
Statistics
Matches: 97, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 18 0.19
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 37 0.38
20 28 0.29
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:421568 original size:52 final size:53
Alignment explanation
Indices: 421462--421594 Score: 196
Period size: 52 Copynumber: 2.5 Consensus size: 53
421452 TTGAAATGAA
* **
421462 AATCGCAACGAGATAATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
** *
421516 AATCGCAACGCGAAATGACTATCGCAACGC-GAAATGAAAATCGTAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
421568 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
421595 TGTGATTTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 44 0.62
53 15 0.21
54 12 0.17
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
Found at i:421643 original size:33 final size:33
Alignment explanation
Indices: 421606--421687 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
421596 GTGATTTTGG
**
421606 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCA
*
421639 TTTCGCGTTGCGATTCTCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCA
*
421672 TTTCCACGTTGCGATT
1 TTT-CGCGTTGCGATT
421688 TTCATTCTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.75
34 11 0.25
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATAGTCA
Found at i:422245 original size:20 final size:20
Alignment explanation
Indices: 422220--422312 Score: 77
Period size: 20 Copynumber: 4.6 Consensus size: 20
422210 GCTATGTAAA
422220 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
*
422240 TCGCATTGCGAT--TTACGTAT
1 TCGCATTGCGATAGTCA-G-AT
** *
422260 TCGCATTGCGAATTAGGAAAAT
1 TCGCATTGCG-A-TAGTCAGAT
422282 T-GCATTGCGATAGTCAG-T
1 TCGCATTGCGATAGTCAGAT
422300 ATCGCATTGCGAT
1 -TCGCATTGCGAT
422313 GTTCCAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
18 3 0.05
19 6 0.10
20 35 0.60
21 9 0.16
22 4 0.07
24 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:422349 original size:20 final size:20
Alignment explanation
Indices: 422220--422352 Score: 76
Period size: 20 Copynumber: 6.5 Consensus size: 20
422210 GCTATGTAAA
* *
422220 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGAT-TTACAAAT
**
422240 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACAAAT
* *
422260 TCGCATTGCGAATTAGGAAAAT
1 TCGCATTGCGATTTA--CAAAT
* *
422282 T-GCATTGCGATAGT-C-AGT
1 TCGCATTGCGAT-TTACAAAT
*
422300 ATCGCATTGCGATGTTCCAAAT
1 -TCGCATTGCGAT-TTACAAAT
* **
422322 TCGTATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
422342 TCGCATTGCGA
1 TCGCATTGCGA
422353 ATTGTGAAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 55 0.64
21 21 0.24
22 6 0.07
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:422394 original size:21 final size:22
Alignment explanation
Indices: 422342--422394 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
422332 ATTTACTTAT
422342 TCGCATTGCG-AATTGTGAAAA
1 TCGCATTGCGAAATTGTGAAAA
* **
422363 ACGCAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGTGAAAA
422384 TCGCATTGCGA
1 TCGCATTGCGA
422395 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGTGAAAA
Found at i:422413 original size:82 final size:80
Alignment explanation
Indices: 422217--422414 Score: 202
Period size: 82 Copynumber: 2.4 Consensus size: 80
422207 GGCGCTATGT
* *
422217 AAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAAT
1 AAATCGCATTGCGATAGTCA-AATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAAA
* ** *
422282 TGCATTGCGATAGTCA
65 CGCAACGCGAAAGTCA
** * *
422298 GTATCGCATTGCGAT-GTTCCAAATTCGTATTGCGATTTACTTATTCGCATTGCGAATT-GTGAA
1 AAATCGCATTGCGATAG-T-CAAA-TCGCATTGCGATTTACGTATTCGCATTGCGAATTAG-GAA
* *
422361 AAACGCAACGCGAAATTGGA
62 AAACGCAACGCGAAAGT-CA
*
422381 AAATCGCATTGCGATAGTCATAATCGCGTTGCGA
1 AAATCGCATTGCGATAGTCA-AATCGCATTGCGA
422415 ATCTGGAAAC
Statistics
Matches: 94, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
80 1 0.01
81 16 0.17
82 59 0.63
83 17 0.18
84 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (80 bp):
AAATCGCATTGCGATAGTCAAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAAAC
GCAACGCGAAAGTCA
Found at i:432008 original size:23 final size:23
Alignment explanation
Indices: 431963--432008 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
431953 GGTAAAAAAA
* *
431963 TTTATTTAAAAATTTATTATTTT
1 TTTATCTAAAAATTAATTATTTT
431986 TTTATCTAAAATATTAATT-TTTT
1 TTTATCTAAAA-ATTAATTATTTT
432009 AACATTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTATCTAAAAATTAATTATTTT
Done.