Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 73 of 106
Found at i:27907277 original size:38 final size:37
Alignment explanation
Indices: 27907216--27907313 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 37
27907206 CTCTTTTTCT
* *
27907216 TTCCTTTCTTCTTTTTCTTTCTCTCATTATCCTTCAA
1 TTCCTTTCTCCTTTTTCTTTCTCTCATTATACTTCAA
* * **
27907253 TTCCTTTCTCCTTTATTCTTTCTCTTATTCTACTTCCT
1 TTCCTTTCTCCTTT-TTCTTTCTCTCATTATACTTCAA
27907291 TTCCTTTCTCCTTTCTTCTTTCT
1 TTCCTTTCTCCTTT-TTCTTTCT
27907314 TTTTCTTTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 13 0.25
38 40 0.75
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (37 bp):
TTCCTTTCTCCTTTTTCTTTCTCTCATTATACTTCAA
Found at i:27907321 original size:24 final size:24
Alignment explanation
Indices: 27907263--27907323 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
27907253 TTCCTTTCTC
*
27907263 CTTTATTCTTTCTCTTATTCTACTT
1 CTTT-TTCTTTCTCCTATTCTACTT
* * *
27907288 CCTTTCCTTTCTCCT-TTCTTCTTT
1 CTTTTTCTTTCTCCTATTCTAC-TT
27907312 CTTTTTCTTTCT
1 CTTTTTCTTTCT
27907324 TTCTCCTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 5 0.17
24 21 0.72
25 3 0.10
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.66
Consensus pattern (24 bp):
CTTTTTCTTTCTCCTATTCTACTT
Found at i:27908592 original size:13 final size:13
Alignment explanation
Indices: 27908574--27908599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27908564 TTCCTGAAAA
27908574 TTTATAAAATCAT
1 TTTATAAAATCAT
27908587 TTTATAAAATCAT
1 TTTATAAAATCAT
27908600 AATTTTTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:27910315 original size:13 final size:13
Alignment explanation
Indices: 27910297--27910321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27910287 ACTCGCTTCC
27910297 TCTTTCTTCTTTA
1 TCTTTCTTCTTTA
27910310 TCTTTCTTCTTT
1 TCTTTCTTCTTT
27910322 GACTGGCCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TCTTTCTTCTTTA
Found at i:27911901 original size:165 final size:165
Alignment explanation
Indices: 27911671--27912417 Score: 953
Period size: 165 Copynumber: 4.5 Consensus size: 165
27911661 TAGTAAAAGA
* * * *
27911671 TCTCACAATCGACAAGGTGTCTAAGCACTTTATCATGACTTACCATGTCATGTGTTCAGTGATTT
1 TCTCACCATCAACAAGGTGTCTAAGCACTCTATCATAACTTACCATGTCATGTGTTCAGTGATTT
* * * * * *
27911736 TTGTTGACATGTAAAGTGTCATGGTGCACACCAACTTGAATGATCAACATGATTGACCAAACTAT
66 TTGCTAACATGTAAAGTGTCATGGTCCACACCAACTTGGATGATCAACATTACTGACCAAACTAT
* * *
27911801 TCAAAAGAACTAAAACTAGCAAAAGACTAATTAGT
131 CCAAAAGAACTGAAACTAGCAAAAGACTGATTAGT
* * *
27911836 TCTCACCATCAACAAGATGTCTAAGCACTCTATTATAACTTACCATGTCATGTGTTTAGTGATTT
1 TCTCACCATCAACAAGGTGTCTAAGCACTCTATCATAACTTACCATGTCATGTGTTCAGTGATTT
*
27911901 TTGCTAACATGTAAAGTGTCATGGTCCACACCAA-TATGGATGATCAACGTTACTGACCAAACTA
66 TTGCTAACATGTAAAGTGTCATGGTCCACACCAACT-TGGATGATCAACATTACTGACCAAACTA
* *
27911965 TCCAAAGGAACTGAAACTAGTAAAAGACTGATTAGT
130 TCCAAAAGAACTGAAACTAGCAAAAGACTGATTAGT
* *
27912001 GCTCACCATCAACAAGGTGTCTAAGCACTCTATCATAACTTACCATGTCATATGTTCAGTGATTT
1 TCTCACCATCAACAAGGTGTCTAAGCACTCTATCATAACTTACCATGTCATGTGTTCAGTGATTT
* * * * * ** * *
27912066 TTTC-ATACATGTAAAGTGTCATGGTCCATACCAACCTGGATAATCAACATTATTGATAAAATTG
66 TTGCTA-ACATGTAAAGTGTCATGGTCCACACCAACTTGGATGATCAACATTACTGACCAAACTA
* *
27912130 TCCAAAAGAATTGAAA-TCAGCTAAAGACTGATTAGT
130 TCCAAAAGAACTGAAACT-AGCAAAAGACTGATTAGT
* * * * *
27912166 TCTCACCATTAACAAGGTGTCTAAGAATTCTATCATAACTTACCATGTCTTGTGTT-TGATGATT
1 TCTCACCATCAACAAGGTGTCTAAGCACTCTATCATAACTTACCATGTCATGTGTTCAG-TGATT
** *
27912230 TTTGCTAACATGTAAAGTGTCATTATCCACACCAACTTGGATGATCAACATTACTGACCAAACTG
65 TTTGCTAACATGTAAAGTGTCATGGTCCACACCAACTTGGATGATCAACATTACTGACCAAACTA
* * * *
27912295 TCCAAAAAGAATTGAAACCAGTAAAAGATTGATTAGT
130 TCC-AAAAGAACTGAAACTAGCAAAAGACTGATTAGT
* * * * * * *
27912332 TATCACCATTAACAAAGTGTCTAAGCACTTTATCATAACTTACCATGTCATGTGTTCATTTACTT
1 TCTCACCATCAACAAGGTGTCTAAGCACTCTATCATAACTTACCATGTCATGTGTTCAGTGATTT
*
27912397 TTGCTGACATGTAAAGTGTCA
66 TTGCTAACATGTAAAGTGTCA
27912418 CGATCCATCT
Statistics
Matches: 503, Mismatches: 70, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
164 4 0.01
165 396 0.79
166 103 0.20
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (165 bp):
TCTCACCATCAACAAGGTGTCTAAGCACTCTATCATAACTTACCATGTCATGTGTTCAGTGATTT
TTGCTAACATGTAAAGTGTCATGGTCCACACCAACTTGGATGATCAACATTACTGACCAAACTAT
CCAAAAGAACTGAAACTAGCAAAAGACTGATTAGT
Found at i:27913300 original size:30 final size:28
Alignment explanation
Indices: 27913229--27913301 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
27913219 GAAGGATAAT
* *
27913229 TTAAATAAATTTTTGTTTTTTATTATAC
1 TTAAATAAATTTTTATTTTTTATTAAAC
* *
27913257 TTAATTAAGTTTTTATATTTTTATTTTAAAC
1 TTAAATAAATTTTTAT-TTTTTA--TTAAAC
27913288 -TAAATAAATTTTTA
1 TTAAATAAATTTTTA
27913302 CAATTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 13 0.36
29 6 0.17
30 12 0.33
31 5 0.14
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TTAAATAAATTTTTATTTTTTATTAAAC
Found at i:27916853 original size:30 final size:30
Alignment explanation
Indices: 27916807--27916868 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
27916797 GAATCACGCC
*
27916807 AATACGGTTCAAGGTATGCTGGCCTAGAGA
1 AATACGGTTAAAGGTATGCTGGCCTAGAGA
* *
27916837 AATATGGTTAAAGGTATGGTGGCCTAGAGA
1 AATACGGTTAAAGGTATGCTGGCCTAGAGA
27916867 AA
1 AA
27916869 AGCTCATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.24
Consensus pattern (30 bp):
AATACGGTTAAAGGTATGCTGGCCTAGAGA
Found at i:27918319 original size:22 final size:22
Alignment explanation
Indices: 27918294--27918470 Score: 142
Period size: 22 Copynumber: 8.0 Consensus size: 22
27918284 AGTTTTGGTG
27918294 GTTTTTAGGCATTGCGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
* *
27918316 GTTTTT-GGACATTACCTGACTA
1 GTTTTTAGG-CATTGCGTGACTA
* * *
27918338 GTTTTTAGGCATTGTGTTATTA
1 GTTTTTAGGCATTGCGTGACTA
* *
27918360 -ATTTTAGGCATTGCGTGATTA
1 GTTTTTAGGCATTGCGTGACTA
* * * *
27918381 ATTTTTAGGTATTACGTGACTG
1 GTTTTTAGGCATTGCGTGACTA
** * * *
27918403 GTTGATATGACATTGCTTGACTG
1 GTTTTTA-GGCATTGCGTGACTA
* *
27918426 GTTAATAAGGCATTGCGTGACTA
1 GTT-TTTAGGCATTGCGTGACTA
*
27918449 GTTTTAAGGCATTGCGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
27918471 TCAATCATGT
Statistics
Matches: 121, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
21 20 0.17
22 69 0.57
23 31 0.26
24 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (22 bp):
GTTTTTAGGCATTGCGTGACTA
Found at i:27918427 original size:23 final size:23
Alignment explanation
Indices: 27918395--27918469 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
27918385 TTAGGTATTA
* *
27918395 CGTGACTGGTTGATATGACATTG
1 CGTGACTGGTTAATAAGACATTG
* *
27918418 CTTGACTGGTTAATAAGGCATTG
1 CGTGACTGGTTAATAAGACATTG
* * *
27918441 CGTGACTAGTT-TTAAGGCATTG
1 CGTGACTGGTTAATAAGACATTG
27918463 CGTGACT
1 CGTGACT
27918470 ATCAATCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 17 0.38
23 28 0.62
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.35
Consensus pattern (23 bp):
CGTGACTGGTTAATAAGACATTG
Found at i:27918525 original size:21 final size:22
Alignment explanation
Indices: 27918470--27918526 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
27918460 TTGCGTGACT
*
27918470 ATCAATCATGTATTGCCTAAAA
1 ATCAATCATGTAATGCCTAAAA
* * * *
27918492 AACAGTCACGTAATGTCT-AAA
1 ATCAATCATGTAATGCCTAAAA
27918513 ATCAATCATGTAAT
1 ATCAATCATGTAAT
27918527 AATTAAGTCA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCAATCATGTAATGCCTAAAA
Found at i:27918710 original size:32 final size:32
Alignment explanation
Indices: 27918669--27918729 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
27918659 AGTTATACAA
* *
27918669 TTTTCTAATTTACAAATATGTTTAATCAACAG
1 TTTTCTAATTTACAAATATATCTAATCAACAG
27918701 TTTTCTAATTTACAAATATATCTAATCAA
1 TTTTCTAATTTACAAATATATCTAATCAA
27918730 TTTCTACCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.44
Consensus pattern (32 bp):
TTTTCTAATTTACAAATATATCTAATCAACAG
Found at i:27919175 original size:19 final size:19
Alignment explanation
Indices: 27919148--27919184 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27919138 TACACGATAT
*
27919148 AATATGATTAACATGTTTG
1 AATACGATTAACATGTTTG
*
27919167 AATACGATTAACTTGTTT
1 AATACGATTAACATGTTT
27919185 AGACATGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (19 bp):
AATACGATTAACATGTTTG
Found at i:27924885 original size:43 final size:43
Alignment explanation
Indices: 27924828--27924989 Score: 207
Period size: 43 Copynumber: 3.8 Consensus size: 43
27924818 GTAATGATAT
* * *
27924828 TGACTCGGCTATGTGTGAGTAGGGAGTGCGCATAAGCAGATGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCAGGTGA
* *
27924871 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCAGGTGA
* * * * *
27924914 TAACCCGGTTATGTGCAAGTAGGGAGTGCGCATAACCTGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCAGGTGA
** *
27924957 TGACCTAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
27924990 GAGCTGGGAA
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCAGGTGA
Found at i:27927398 original size:161 final size:162
Alignment explanation
Indices: 27927117--27927442 Score: 593
Period size: 161 Copynumber: 2.0 Consensus size: 162
27927107 GATGATTTTC
*
27927117 ATGTTTTAGGGGCAAAATGGTCACTTTTGTCACTTGAGGATAAAATAGAAATTTTTGAAATTTTA
1 ATGTTTTAGGGGCAAAATGGTCAATTTTGTCACTTGAGGATAAAATAGAAATTTTTGAAATTTTA
*
27927182 CACCACCCTAACACTTGTCAAGCCCATGGATTTCAGCCATTAACATTTTACATTATGGATAATTG
66 CACCACCCTAACACTTGTCAAGCCCATGGATTTCAACCATTAACATTTTACATTATGGATAATTG
27927247 AAACATTTTATGAGGTGGAGAAAGATTGCTTA
131 AAACATTTTATGAGGTGGAGAAAGATTGCTTA
27927279 ATNGTTTTAGGGGCAAAATGGT-AATTTTGTCACTTGAGGATAAAATAGAAATTTTTGAAATTTT
1 AT-GTTTTAGGGGCAAAATGGTCAATTTTGTCACTTGAGGATAAAATAGAAATTTTTGAAATTTT
*
27927343 ACACCA-CCTAACACTTGTCATGCCCATGGATTTCAACCATTAACATTTTACATTATGGATAATT
65 ACACCACCCTAACACTTGTCAAGCCCATGGATTTCAACCATTAACATTTTACATTATGGATAATT
*
27927407 GAAACATTTTATGAGGTGGAGAGAGATTGCTTA
130 GAAACATTTTATGAGGTGGAGAAAGATTGCTTA
27927440 ATG
1 ATG
27927443 GATAAGTATT
Statistics
Matches: 159, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
160 1 0.01
161 90 0.57
162 49 0.31
163 19 0.12
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (162 bp):
ATGTTTTAGGGGCAAAATGGTCAATTTTGTCACTTGAGGATAAAATAGAAATTTTTGAAATTTTA
CACCACCCTAACACTTGTCAAGCCCATGGATTTCAACCATTAACATTTTACATTATGGATAATTG
AAACATTTTATGAGGTGGAGAAAGATTGCTTA
Found at i:27928763 original size:26 final size:26
Alignment explanation
Indices: 27928727--27928790 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
27928717 GCTGGGAATG
27928727 ATGATGATGATGATGGGATGGTGTGC
1 ATGATGATGATGATGGGATGGTGTGC
27928753 ATGATGATGATGATGGGATGGTGTGC
1 ATGATGATGATGATGGGATGGTGTGC
*
27928779 ATGTTGATGATG
1 ATGATGATGATG
27928791 GGAATATGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.23, C:0.03, G:0.41, T:0.33
Consensus pattern (26 bp):
ATGATGATGATGATGGGATGGTGTGC
Found at i:27933026 original size:43 final size:43
Alignment explanation
Indices: 27932964--27933074 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
27932954 ATTGACTCTA
* * ** *
27932964 CTATGTGCGAGTAGAGAGTGTGCATAGGCCGATGATGAACCGG
1 CTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGAACCAG
* * *
27933007 TTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAG
1 CTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGAACCAG
*
27933050 CCATGTGCGAGTAGGGAGTGCGCAT
1 CTATGTGCGAGTAGGGAGTGCGCAT
27933075 GAGCTGGTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (43 bp):
CTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGAACCAG
Found at i:27933120 original size:23 final size:23
Alignment explanation
Indices: 27933082--27933137 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
27933072 CATGAGCTGG
27933082 TGATGATGAGACGGTGTGCATGA
1 TGATGATGAGACGGTGTGCATGA
* * *
27933105 TGGTGATGGGATGGTGTGCATGA
1 TGATGATGAGACGGTGTGCATGA
27933128 TGATGATGAG
1 TGATGATGAG
27933138 TATATGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.05, G:0.43, T:0.29
Consensus pattern (23 bp):
TGATGATGAGACGGTGTGCATGA
Found at i:27941700 original size:44 final size:44
Alignment explanation
Indices: 27941644--27941829 Score: 210
Period size: 44 Copynumber: 4.4 Consensus size: 44
27941634 TCATGTGCTT
*
27941644 CCCCCATATCGCGCACATGGCATATATCATCATCATCGTGTGCA
1 CCCCCACATCGCGCACATGGCATATATCATCATCATCGTGTGCA
* *
27941688 CCCCTACATCGCGCACATGGCATATATCATCATTATCGTGTGCA
1 CCCCCACATCGCGCACATGGCATATATCATCATCATCGTGTGCA
* * *
27941732 CCCCCACATTGCGCACA--AC-TA-ATGC--CATCAT-GTACT-C-
1 CCCCCACATCGCGCACATGGCATATAT-CATCATCATCGT-GTGCA
* * *
27941769 CCCTCACATTGCGCACATGGCATATATTATCATCATCGTGTGCA
1 CCCCCACATCGCGCACATGGCATATATCATCATCATCGTGTGCA
27941813 CCCCCACATCGCGCACA
1 CCCCCACATCGCGCACA
27941830 ACTAATGCCA
Statistics
Matches: 117, Mismatches: 14, Indels: 22
0.76 0.09 0.14
Matches are distributed among these distances:
37 16 0.14
38 3 0.03
39 7 0.06
40 4 0.03
41 5 0.04
42 8 0.07
43 3 0.03
44 71 0.61
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.24
Consensus pattern (44 bp):
CCCCCACATCGCGCACATGGCATATATCATCATCATCGTGTGCA
Found at i:27941783 original size:81 final size:81
Alignment explanation
Indices: 27941688--27941883 Score: 297
Period size: 81 Copynumber: 2.4 Consensus size: 81
27941678 ATCGTGTGCA
* * *
27941688 CCCCT-ACATCGCGCACATGGCATATATCATCATTATCGTGTGCACCCCCACATTGCGCACAACT
1 CCCCTCACATTGCGCACATGGCATATATCATCATCATCGTGTGCACCCCCACATCGCGCACAACT
27941752 AATGCCATCATGTACT
66 AATGCCATCATGTACT
*
27941768 CCCCTCACATTGCGCACATGGCATATATTATCATCATCGTGTGCACCCCCACATCGCGCACAACT
1 CCCCTCACATTGCGCACATGGCATATATCATCATCATCGTGTGCACCCCCACATCGCGCACAACT
*
27941833 AATGCCATCATGTGCT
66 AATGCCATCATGTACT
* * *
27941849 CCCCCCACATTTCGCACATAGGCA-ATCTCATCATC
1 CCCCTCACATTGCGCACAT-GGCATATATCATCATC
27941884 CACACTCCCT
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
80 5 0.05
81 96 0.91
82 4 0.04
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (81 bp):
CCCCTCACATTGCGCACATGGCATATATCATCATCATCGTGTGCACCCCCACATCGCGCACAACT
AATGCCATCATGTACT
Found at i:27941822 original size:125 final size:125
Alignment explanation
Indices: 27941597--27941829 Score: 378
Period size: 125 Copynumber: 1.9 Consensus size: 125
27941587 AGTCGGAGTC
* * *
27941597 ATCGTGCGCACCCCCACATCGCGCACAATTAATGCCATCATGTGCTTCCCCCATATCGCGCACAT
1 ATCGTGCGCACCCCCACATCGCGCACAACTAATGCCATCATGTACTTCCCCCACATCGCGCACAT
*
27941662 GGCATATATCATCATCATCGTGTGCACCCCTACATCGCGCACATGGCATATATCATCATT
66 GGCATATATCATCATCATCGTGTGCACCCCCACATCGCGCACATGGCATATATCATCATT
* * *
27941722 ATCGTGTGCACCCCCACATTGCGCACAACTAATGCCATCATGTAC-TCCCCTCACATTGCGCACA
1 ATCGTGCGCACCCCCACATCGCGCACAACTAATGCCATCATGTACTTCCCC-CACATCGCGCACA
*
27941786 TGGCATATATTATCATCATCGTGTGCACCCCCACATCGCGCACA
65 TGGCATATATCATCATCATCGTGTGCACCCCCACATCGCGCACA
27941830 ACTAATGCCA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
124 5 0.05
125 94 0.95
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.24
Consensus pattern (125 bp):
ATCGTGCGCACCCCCACATCGCGCACAACTAATGCCATCATGTACTTCCCCCACATCGCGCACAT
GGCATATATCATCATCATCGTGTGCACCCCCACATCGCGCACATGGCATATATCATCATT
Found at i:27947592 original size:36 final size:36
Alignment explanation
Indices: 27947540--27947644 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
27947530 TGTATACTAG
*
27947540 TGAGTGGTTATACCTTAACCAAATTAAAAGGTAGGT
1 TGAGTGGTTATACCTTAACCAAACTAAAAGGTAGGT
*
27947576 TGAGCGGTTATACCTTAACCAAACTAAAAGGTA-GT
1 TGAGTGGTTATACCTTAACCAAACTAAAAGGTAGGT
* * *
27947611 T-ATGTGGTTTTACCTTAACCCAAGTAAAAGGTAG
1 TGA-GTGGTTATACCTTAACCAAACTAAAAGGTAG
27947645 AAGGGTTCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.02
35 29 0.48
36 31 0.51
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (36 bp):
TGAGTGGTTATACCTTAACCAAACTAAAAGGTAGGT
Found at i:27950630 original size:43 final size:43
Alignment explanation
Indices: 27950571--27950700 Score: 181
Period size: 43 Copynumber: 3.0 Consensus size: 43
27950561 TTGTGTGATA
*
27950571 ATGATGACCCAGCTATGTATGGTGTGGGAGTGCACATAATCTG
1 ATGATGACCCAGCTATGTATGGTGTGGGAGTGCACATAAGCTG
*
27950614 ATGATGACCCAGCTATGTGTGGTGTGGGAGTGCACATAAGCTG
1 ATGATGACCCAGCTATGTATGGTGTGGGAGTGCACATAAGCTG
* * * * *
27950657 ATGATGACCCGGCTATGTGTGAGT-CGAGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTATG-GTGTGGGAGTGCACATAAGCTG
27950700 A
1 A
27950701 GTATGGCGGG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 78 0.98
44 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTATGGTGTGGGAGTGCACATAAGCTG
Found at i:27953753 original size:89 final size:88
Alignment explanation
Indices: 27953602--27953780 Score: 331
Period size: 89 Copynumber: 2.0 Consensus size: 88
27953592 TTGAAGTAAT
27953602 GATGTGAACATAAGTAGAATGATCAAGATAGACAAAATTCATGATGATACTAAGTTGAAGTGGTT
1 GATGTGAACATAAGTAGAATGATCAAGATAGACAAAATTCATGATGATACTAAGTTGAAGTGGTT
27953667 AAACTATTTGAGTTAAAAGATAA
66 AAACTATTTGAGTTAAAAGATAA
* *
27953690 NGATGTGAGCATAAGTAGAATGATCAAGGTAGACAAAATTCATGATGATACTAAGTTGAAGTGGT
1 -GATGTGAACATAAGTAGAATGATCAAGATAGACAAAATTCATGATGATACTAAGTTGAAGTGGT
27953755 TAAACTATTTGAGTTAAAAGATAA
65 TAAACTATTTGAGTTAAAAGATAA
27953779 GA
1 GA
27953781 AAGATAGCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 2 0.02
89 86 0.98
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (88 bp):
GATGTGAACATAAGTAGAATGATCAAGATAGACAAAATTCATGATGATACTAAGTTGAAGTGGTT
AAACTATTTGAGTTAAAAGATAA
Found at i:27956267 original size:18 final size:18
Alignment explanation
Indices: 27956244--27956282 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
27956234 TTATTTTTGT
*
27956244 TTAATTGTGTTAAACGTG
1 TTAATTGTGTTAAACGAG
27956262 TTAATTGTGTTAAACGAG
1 TTAATTGTGTTAAACGAG
27956280 TTA
1 TTA
27956283 TTAATCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (18 bp):
TTAATTGTGTTAAACGAG
Found at i:27968287 original size:20 final size:20
Alignment explanation
Indices: 27968264--27968307 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
27968254 ATTGAGAAAC
*
27968264 AGAAAAGACTTAGTTGACTA
1 AGAAAAGACTTAGTCGACTA
* **
27968284 AGAAATGGGTTAGTCGACTA
1 AGAAAAGACTTAGTCGACTA
27968304 AGAA
1 AGAA
27968308 GCTACTGCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (20 bp):
AGAAAAGACTTAGTCGACTA
Found at i:27968940 original size:11 final size:11
Alignment explanation
Indices: 27968907--27968947 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
27968897 GGTTTTGGCT
27968907 AAGCTTGGTAA
1 AAGCTTGGTAA
27968918 AAGCCATT-GTAA
1 AAG-C-TTGGTAA
27968930 AAGCTTGGTAA
1 AAGCTTGGTAA
27968941 AAGCTTG
1 AAGCTTG
27968948 TGAATTTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 8 0.30
13 2 0.07
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (11 bp):
AAGCTTGGTAA
Found at i:27972256 original size:29 final size:27
Alignment explanation
Indices: 27972224--27972365 Score: 158
Period size: 29 Copynumber: 5.0 Consensus size: 27
27972214 GACATGTTTA
27972224 TCTTAATTTAGACAAGAAAATATATTTGG
1 TCTTAATTTAGACAAGAAAA-ATATTT-G
* *
27972253 TCTTAAGTTAGACAAGAAAATATGTTTG
1 TCTTAATTTAGACAAGAAAA-ATATTTG
*
27972281 CCTTAATTTAAGACAAGAAAAATATTTTGG
1 TCTTAATTT-AGACAAGAAAAATA-TTT-G
**
27972311 TCTTAATTTAGTGAAGAAAACATATTTG
1 TCTTAATTTAGACAAGAAAA-ATATTTG
*
27972339 TCTCAATTTAGACAAGATAAAATATTT
1 TCTTAATTTAGACAAGA-AAAATATTT
27972366 TTTTGTCTTA
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
28 31 0.32
29 54 0.56
30 12 0.12
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (27 bp):
TCTTAATTTAGACAAGAAAAATATTTG
Found at i:27972315 original size:58 final size:57
Alignment explanation
Indices: 27972225--27972366 Score: 187
Period size: 58 Copynumber: 2.5 Consensus size: 57
27972215 ACATGTTTAT
* *
27972225 CTTAATTTAGACAAG-AAAATATATTTGGTCTTAAGTTAGACAAGAAAATATGTTTGC
1 CTTAATTTAGACAAGAAAAATAT-TTTGGTCTTAAGTTAGACAAGAAAACATATTTGC
* ** *
27972282 CTTAATTTAAGACAAGAAAAATATTTTGGTCTTAATTTAGTGAAGAAAACATATTTGT
1 CTTAATTT-AGACAAGAAAAATATTTTGGTCTTAAGTTAGACAAGAAAACATATTTGC
*
27972340 CTCAATTTAGACAAGATAAAATATTTT
1 CTTAATTTAGACAAGA-AAAATATTTT
27972367 TTTGTCTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 16 0.21
58 52 0.69
59 7 0.09
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (57 bp):
CTTAATTTAGACAAGAAAAATATTTTGGTCTTAAGTTAGACAAGAAAACATATTTGC
Found at i:27972346 original size:28 final size:29
Alignment explanation
Indices: 27972295--27972366 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
27972285 AATTTAAGAC
*
27972295 AAGAAAAATATTTTGGTCTTAATTTAGTG
1 AAGAAAAATATTTTGGTCTCAATTTAGTG
**
27972324 AAGAAAACATA-TTT-GTCTCAATTTAGAC
1 AAGAAAA-ATATTTTGGTCTCAATTTAGTG
27972352 AAGATAAAATATTTT
1 AAGA-AAAATATTTT
27972367 TTTGTCTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 18 0.49
29 16 0.43
30 3 0.08
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (29 bp):
AAGAAAAATATTTTGGTCTCAATTTAGTG
Found at i:27972552 original size:17 final size:17
Alignment explanation
Indices: 27972530--27972562 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27972520 ATAATAATAA
27972530 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
27972547 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
27972563 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:27975445 original size:14 final size:14
Alignment explanation
Indices: 27975428--27975461 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
27975418 TAAATGATGC
27975428 TTATATTCATATGA
1 TTATATTCATATGA
*
27975442 TTATATTCATATGT
1 TTATATTCATATGA
27975456 TTATAT
1 TTATAT
27975462 ATTTGTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (14 bp):
TTATATTCATATGA
Found at i:27977486 original size:42 final size:42
Alignment explanation
Indices: 27977412--27977537 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
27977402 GTAATGATAT
* * * * *
27977412 TGACCCAGCTATGTGCAAGTAGAAGTGTGCATAAGTCGATGC
1 TGACCCGGCTATGTGCAAGTGGGAGTGCGCATAAGCCGATGC
* *
27977454 TGACCTGGCTATGTGCTAGTGGGAGTGCGCATAAGCCGATGC
1 TGACCCGGCTATGTGCAAGTGGGAGTGCGCATAAGCCGATGC
*
27977496 TGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
1 TGACCCGGCTATGTGCAAGTGGGAGTGCGCATAAGCCGATGC
27977538 ATATGAGCTG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (42 bp):
TGACCCGGCTATGTGCAAGTGGGAGTGCGCATAAGCCGATGC
Found at i:27977681 original size:2 final size:2
Alignment explanation
Indices: 27977674--27977721 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
27977664 NNNNNNNNNN
*
27977674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27977716 AT AT AT
1 AT AT AT
27977722 GGTATATGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27981896 original size:6 final size:6
Alignment explanation
Indices: 27981885--27981933 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
27981875 ACTATTTTTC
*
27981885 TTAATA TTAATA TTAATA TTAATA TTAA-A -TAAT- TTATTGA TTAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAAT-A TTAATA
27981931 TTA
1 TTA
27981934 CAAAATTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 3 0.08
5 4 0.11
6 26 0.70
7 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
TTAATA
Found at i:27982800 original size:20 final size:20
Alignment explanation
Indices: 27982775--27982812 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
27982765 ATATAGGTGC
27982775 ACAACACCAAGGTTGTCTAT
1 ACAACACCAAGGTTGTCTAT
27982795 ACAACACCAAGGTTGTCT
1 ACAACACCAAGGTTGTCT
27982813 CAAGACAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
ACAACACCAAGGTTGTCTAT
Found at i:27983658 original size:35 final size:36
Alignment explanation
Indices: 27983601--27983698 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 36
27983591 AAAAATCATA
* * **
27983601 GGTTATCGCTTGATTTCATGAAAAAGCCCTTGTAAG
1 GGTTATCGCTTGATTCCGTGAAAAAGCCAGTGTAAG
* *
27983637 GGTT-TCGCTTGATCCCGTGAAAAAGCTAGTGTAAG
1 GGTTATCGCTTGATTCCGTGAAAAAGCCAGTGTAAG
* *
27983672 GGTTATCACTTGATTCCGTTAAAAAGC
1 GGTTATCGCTTGATTCCGTGAAAAAGC
27983699 AAGAATCCCT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 29 0.56
36 23 0.44
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (36 bp):
GGTTATCGCTTGATTCCGTGAAAAAGCCAGTGTAAG
Found at i:27983696 original size:36 final size:35
Alignment explanation
Indices: 27983631--27983698 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 35
27983621 AAAAAGCCCT
*
27983631 TGTAAGGGTTTCGCTTGATCCCGTGAAAAAGCTAG
1 TGTAAGGGTTTCACTTGATCCCGTGAAAAAGCTAG
* *
27983666 TGTAAGGGTTATCACTTGATTCCGTTAAAAAGC
1 TGTAAGGGTT-TCACTTGATCCCGTGAAAAAGC
27983699 AAGAATCCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 10 0.34
36 19 0.66
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (35 bp):
TGTAAGGGTTTCACTTGATCCCGTGAAAAAGCTAG
Found at i:27983737 original size:53 final size:52
Alignment explanation
Indices: 27983680--27983802 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
27983670 AGGGTTATCA
*
27983680 CTTGATTCCGTTAAAAAGCAAGAATCCCTTTATGAATTGTGTAAAGGCTATTG
1 CTTGA-TCCGTTAAAAAGCAAGAATCCCTTTATCAATTGTGTAAAGGCTATTG
* * * * *
27983733 CTTGATCCCTTTAAAAGCAAGAATCCCTTTGTCTATTGTGTAAAGGTTATTG
1 CTTGATCCGTTAAAAAGCAAGAATCCCTTTATCAATTGTGTAAAGGCTATTG
*
27983785 CTTGAGCTCGTTAAAAAG
1 CTTGATC-CGTTAAAAAG
27983803 TAAAAATTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
52 47 0.78
53 13 0.22
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (52 bp):
CTTGATCCGTTAAAAAGCAAGAATCCCTTTATCAATTGTGTAAAGGCTATTG
Found at i:27984907 original size:117 final size:117
Alignment explanation
Indices: 27984741--27984951 Score: 311
Period size: 118 Copynumber: 1.8 Consensus size: 117
27984731 AGAAAAAGAA
* * *
27984741 AAAAGAAATTAAAATAAAAAACTATATTAATAATTTAATAATAAATTATTACT-GTTTAAATTTT
1 AAAAGAAATTAAAATAAAAAACTACATTAATAATTTAATAATAAATTATTAATAGTTTAAAATTT
* *
27984805 TAATGAAAATAGAAATTCAAAGTTTAAAAAATAAAAATACTAATAGAGAAAAAT
66 TAATGAAAAT--AAATTAAAAGATTAAAAAATAAAAATACTAATAGAGAAAAAT
* *
27984859 AAAAGAAATTGAAATAAAAAA-TACATT-ATCAATTTAATAATAAATTATTAATATTTTAAAATT
1 AAAAGAAATTAAAATAAAAAACTACATTAAT-AATTTAATAATAAATTATTAATAGTTTAAAATT
27984922 TTAATGAAAATAAATTAAAAGATTAAAAAA
65 TTAATGAAAATAAATTAAAAGATTAAAAAA
27984952 GGAATAATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
116 19 0.23
117 26 0.31
118 39 0.46
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (117 bp):
AAAAGAAATTAAAATAAAAAACTACATTAATAATTTAATAATAAATTATTAATAGTTTAAAATTT
TAATGAAAATAAATTAAAAGATTAAAAAATAAAAATACTAATAGAGAAAAAT
Found at i:27994071 original size:16 final size:17
Alignment explanation
Indices: 27994041--27994092 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
27994031 ATGTAAAATA
* *
27994041 AGCACAAACTAAAGGGG
1 AGCACACACTTAAGGGG
27994058 AGCACACA-TTAAGGGGG
1 AGCACACACTTAA-GGGG
*
27994075 AGCACTCACTT-AGGGG
1 AGCACACACTTAAGGGG
27994091 AG
1 AG
27994093 AAATCCTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 9 0.30
17 19 0.63
18 2 0.07
ACGTcount: A:0.37, C:0.19, G:0.33, T:0.12
Consensus pattern (17 bp):
AGCACACACTTAAGGGG
Found at i:28002606 original size:31 final size:33
Alignment explanation
Indices: 28002571--28002631 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
28002561 CATTGTTGTT
28002571 GGTTATAACT-CACGT-AAAAGGTAGTGTTAAA
1 GGTTATAACTCCACGTGAAAAGGTAGTGTTAAA
* * *
28002602 GGTTATACCTCCTCTTGAAAAGGTAGTGTT
1 GGTTATAACTCCACGTGAAAAGGTAGTGTT
28002632 TGGTTATACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 3 0.12
33 13 0.52
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (33 bp):
GGTTATAACTCCACGTGAAAAGGTAGTGTTAAA
Found at i:28002652 original size:30 final size:32
Alignment explanation
Indices: 28002586--28002657 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 32
28002576 TAACTCACGT
*
28002586 AAAAGGTAGTGTTAAAGGTTATACCTCCTCTTG
1 AAAAGGTAGTGTT-AAGGTTATACCTCCTATTG
* *
28002619 AAAAGGTAGTGTT-TGGTTATACCT-TTATTG
1 AAAAGGTAGTGTTAAGGTTATACCTCCTATTG
28002649 AAAAGGTAG
1 AAAAGGTAG
28002658 AAAGGTTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.36
31 10 0.28
33 13 0.36
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.35
Consensus pattern (32 bp):
AAAAGGTAGTGTTAAGGTTATACCTCCTATTG
Found at i:28004364 original size:20 final size:20
Alignment explanation
Indices: 28004339--28004390 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
28004329 TTTAACAAAA
28004339 AATTAAACTAAAACAACTTG
1 AATTAAACTAAAACAACTTG
* * **
28004359 AATTAAATTGACTCAACTTG
1 AATTAAACTAAAACAACTTG
*
28004379 ATTTAAACTAAA
1 AATTAAACTAAA
28004391 TTAAGAAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (20 bp):
AATTAAACTAAAACAACTTG
Found at i:28012627 original size:11 final size:11
Alignment explanation
Indices: 28012611--28012637 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28012601 TATTCATTTT
28012611 TGATGATTAAA
1 TGATGATTAAA
28012622 TGATGATTAAA
1 TGATGATTAAA
28012633 TGATG
1 TGATG
28012638 TGGTTTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (11 bp):
TGATGATTAAA
Found at i:28015625 original size:20 final size:20
Alignment explanation
Indices: 28015599--28015644 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
28015589 AATCTTACCT
* *
28015599 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
28015620 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
28015641 TTTT
1 TTTT
28015645 TCCACCTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:28015646 original size:22 final size:22
Alignment explanation
Indices: 28015604--28015644 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28015594 TACCTTTTTT
*
28015604 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
28015626 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
28015645 TCCACCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:28020596 original size:20 final size:20
Alignment explanation
Indices: 28020570--28020615 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
28020560 AATCTTACCT
* *
28020570 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
28020591 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
28020612 TTTT
1 TTTT
28020616 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:28020617 original size:22 final size:22
Alignment explanation
Indices: 28020575--28020615 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28020565 TACCTTTTTT
*
28020575 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
28020597 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
28020616 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:28023858 original size:21 final size:19
Alignment explanation
Indices: 28023822--28023862 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
28023812 ACATGTTGAG
28023822 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
28023841 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
28023862 T
1 T
28023863 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:28025097 original size:23 final size:22
Alignment explanation
Indices: 28025071--28025131 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 22
28025061 AAATTCACAA
28025071 GCTTTCACCAAGCTTTTACAATG
1 GCTTTC-CCAAGCTTTTACAATG
*
28025094 GCTTTTCGCAAGCTTTTACAATG
1 GC-TTTCCCAAGCTTTTACAATG
*
28025117 GCTTTTCGCAAGCTT
1 GC-TTTCCCAAGCTT
28025132 AGCCACAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (22 bp):
GCTTTCCCAAGCTTTTACAATG
Found at i:28025099 original size:12 final size:12
Alignment explanation
Indices: 28025082--28025122 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
28025072 CTTTCACCAA
28025082 GCTTTTACAATG
1 GCTTTTACAATG
*
28025094 GCTTTTCGCAA--
1 GCTTTT-ACAATG
28025105 GCTTTTACAATG
1 GCTTTTACAATG
28025117 GCTTTT
1 GCTTTT
28025123 CGCAAGCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.12
11 6 0.25
12 12 0.50
13 3 0.12
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (12 bp):
GCTTTTACAATG
Found at i:28042884 original size:35 final size:35
Alignment explanation
Indices: 28042608--28042871 Score: 321
Period size: 35 Copynumber: 7.5 Consensus size: 35
28042598 TTAAGTTGTA
* *
28042608 CCTAATTAATTAAATTGTTTAATTAAATCATTGGG
1 CCTAATTAATTAAATTATTTAATTAAGTCATTGGG
*
28042643 CCTAATTAATTAAATTATTTAACTAAGTCATTGGG
1 CCTAATTAATTAAATTATTTAATTAAGTCATTGGG
*
28042678 CCTAATTAATTAAATTATTTAACTAAGTCATTGGG
1 CCTAATTAATTAAATTATTTAATTAAGTCATTGGG
*** * * *
28042713 CCTAATTAATTAAATTAAACAATTAACTTATTGGA
1 CCTAATTAATTAAATTATTTAATTAAGTCATTGGG
* *
28042748 CCTAATTGATTAAATTTGTTTAATTAAGTCATTGGG
1 CCTAATTAATTAAA-TTATTTAATTAAGTCATTGGG
* * * ** *
28042784 CCTAATTGATTAAAATTTTTTAATTAAATTGTTAGG
1 CCTAATTAATT-AAATTATTTAATTAAGTCATTGGG
* *
28042820 CTTAATTAATTAAATTATTTAATTAAGTTATTGGG
1 CCTAATTAATTAAATTATTTAATTAAGTCATTGGG
*
28042855 CCTAATTGATTAAATTA
1 CCTAATTAATTAAATTA
28042872 AACAATTAAG
Statistics
Matches: 196, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
35 143 0.73
36 50 0.26
37 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (35 bp):
CCTAATTAATTAAATTATTTAATTAAGTCATTGGG
Found at i:28045938 original size:31 final size:29
Alignment explanation
Indices: 28045869--28045939 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
28045859 GGCACTTTTT
*
28045869 CAATTAAGGGCCAAACGTTTCAATTGTAA
1 CAATTAAGGGCCAAACGTTTCAATTCTAA
* * * *
28045898 CAATCAAGGGCCAAACATTTTCGATTCCTTA
1 CAATTAAGGGCCAAAC-GTTTCAATT-CTAA
28045929 CAATTAAGGGC
1 CAATTAAGGGC
28045940 TAAGTTGACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 15 0.44
30 7 0.21
31 12 0.35
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (29 bp):
CAATTAAGGGCCAAACGTTTCAATTCTAA
Found at i:28046028 original size:27 final size:27
Alignment explanation
Indices: 28045989--28046231 Score: 188
Period size: 27 Copynumber: 9.0 Consensus size: 27
28045979 GAAAATTGCA
* * *
28045989 TTGAAAATGTAGTTGTTACATGTCATG
1 TTGAAAATTTAGTTGTTACACGCCATG
* *
28046016 TTGAAAATTTAGTTGTTAGACACCATG
1 TTGAAAATTTAGTTGTTACACGCCATG
* ** * * *
28046043 TTAAAAATACAATTGTTGCACACCATG
1 TTGAAAATTTAGTTGTTACACGCCATG
* * **
28046070 TTGAAAAATATAATTGTTACACATCATG
1 TTG-AAAATTTAGTTGTTACACGCCATG
* *
28046098 TTGAAAATTTAGTTGTAACATGCCATG
1 TTGAAAATTTAGTTGTTACACGCCATG
* * **
28046125 TTTAAAAATATAGTTGTTACACATCATG
1 -TTGAAAATTTAGTTGTTACACGCCATG
* * *
28046153 TTGAAAATTTAGTTATTATGA-GTCATG
1 TTGAAAATTTAGTTGTTA-CACGCCATG
28046180 TTGAAAAATTTAGTTGTTACACGCCATG
1 TTG-AAAATTTAGTTGTTACACGCCATG
* *
28046208 ATGAAAA---AGTTGTTACATGCCATG
1 TTGAAAATTTAGTTGTTACACGCCATG
28046232 CCATAATTTG
Statistics
Matches: 174, Mismatches: 37, Indels: 13
0.78 0.17 0.06
Matches are distributed among these distances:
24 16 0.09
27 91 0.52
28 67 0.39
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (27 bp):
TTGAAAATTTAGTTGTTACACGCCATG
Found at i:28046090 original size:82 final size:80
Alignment explanation
Indices: 28045989--28046207 Score: 244
Period size: 82 Copynumber: 2.6 Consensus size: 80
28045979 GAAAATTGCA
*
28045989 TTGAAAATGTAGTTGTTACATGTCATGTTGAAAATTTAGTTGTTAGACACCATG-TTAAAAATAC
1 TTGAAAATATAGTTGTTACA-GTCATGTTGAAAATTTAGTTGTTA-ACACCATGTTTAAAAATAC
*
28046053 AATTGTTGCACACCATG
64 AATTGTTACACACCATG
* *
28046070 TTGAAAAATATAATTGTTACACATCATGTTGAAAATTTAGTTG-TAACATGCCATGTTTAAAAAT
1 TTG-AAAATATAGTTGTTACA-GTCATGTTGAAAATTTAGTTGTTAACA--CCATGTTTAAAAAT
* * *
28046134 ATAGTTGTTACACATCATG
62 ACAATTGTTACACACCATG
* * * *
28046153 TTGAAAATTTAGTTATTATGAGTCATGTTGAAAAATTTAGTTGTTACACGCCATG
1 TTGAAAATATAGTTGTTA-CAGTCATGTTG-AAAATTTAGTTGTTA-ACACCATG
28046208 ATGAAAAAGT
Statistics
Matches: 116, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
80 3 0.03
81 5 0.04
82 60 0.52
83 44 0.38
84 2 0.02
85 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (80 bp):
TTGAAAATATAGTTGTTACAGTCATGTTGAAAATTTAGTTGTTAACACCATGTTTAAAAATACAA
TTGTTACACACCATG
Found at i:28046161 original size:55 final size:55
Alignment explanation
Indices: 28045989--28046231 Score: 244
Period size: 55 Copynumber: 4.5 Consensus size: 55
28045979 GAAAATTGCA
* * * *
28045989 TTGAAAATGTAGTTGTTACATGTCATGTTG-AAAATTTAGTTGTTAGACACCATG
1 TTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATATAGTTGTTACACACCATG
* ** * * ** * *
28046043 TTAAAAATACAATTGTTGCACACCATGTTGAAAAATATAATTGTTACACATCATG
1 TTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATATAGTTGTTACACACCATG
* * *
28046098 TTGAAAATTTAGTTGTAACATGCCATGTTTAAAAATATAGTTGTTACACATCATG
1 TTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATATAGTTGTTACACACCATG
* * * * *
28046153 TTGAAAATTTAGTTATTATGA-GTCATGTTGAAAAATTTAGTTGTTACACGCCATG
1 TTGAAAATTTAGTTGTTA-CATGCCATGTTGAAAAATATAGTTGTTACACACCATG
*
28046208 ATGAAAA---AGTTGTTACATGCCATG
1 TTGAAAATTTAGTTGTTACATGCCATG
28046232 CCATAATTTG
Statistics
Matches: 152, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
51 1 0.01
52 12 0.08
54 22 0.14
55 116 0.76
56 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (55 bp):
TTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATATAGTTGTTACACACCATG
Found at i:28047527 original size:26 final size:26
Alignment explanation
Indices: 28047400--28047534 Score: 101
Period size: 26 Copynumber: 5.1 Consensus size: 26
28047390 TTTTAATCAA
* *
28047400 GGATAATTTTGCCACCATAAGTGGAT
1 GGATAATTTTGCCACCAGAAGTAGAT
* * *
28047426 GGATAATTTTACCATCAGAATCTA-ATT
1 GGATAATTTTGCCACCAGAA-GTAGA-T
* * *
28047453 AGAATAATTTTGTCACCAGAAGTGGAT
1 -GGATAATTTTGCCACCAGAAGTAGAT
** *
28047480 AAATAATTTTGCCACCAAAAGTAGAT
1 GGATAATTTTGCCACCAGAAGTAGAT
** * *
28047506 GGATAATTTTATCATCAGAAGTTGAT
1 GGATAATTTTGCCACCAGAAGTAGAT
28047532 GGA
1 GGA
28047535 CACCTTAACC
Statistics
Matches: 83, Mismatches: 22, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
26 62 0.75
27 4 0.05
28 17 0.20
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (26 bp):
GGATAATTTTGCCACCAGAAGTAGAT
Found at i:28048053 original size:24 final size:22
Alignment explanation
Indices: 28047997--28048054 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
28047987 ATGAAGATGC
28047997 TTTAA-TATGTTCTTATTATAT
1 TTTAATTATGTTCTTATTATAT
* *
28048018 TTAAATGATATGTTCTTATTATGTGT
1 TTTAAT--TATGTTCTTATTA--TAT
28048044 TTTAATTATGT
1 TTTAATTATGT
28048055 ATTTAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.14
24 18 0.62
26 7 0.24
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (22 bp):
TTTAATTATGTTCTTATTATAT
Found at i:28053977 original size:20 final size:22
Alignment explanation
Indices: 28053944--28053983 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28053934 AACTTACCTA
28053944 GCTTATTTCCTTG-ATTTCTTC
1 GCTTATTTCCTTGAATTTCTTC
*
28053965 GCTT-TTTCTTTGAATTTCT
1 GCTTATTTCCTTGAATTTCT
28053984 ACCAAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.20, G:0.10, T:0.60
Consensus pattern (22 bp):
GCTTATTTCCTTGAATTTCTTC
Found at i:28070952 original size:17 final size:17
Alignment explanation
Indices: 28070927--28070963 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28070917 TGAAGGATTA
*
28070927 CTCCTCCTTAATATATG
1 CTCCCCCTTAATATATG
*
28070944 CTCCCCCTTAATATGTG
1 CTCCCCCTTAATATATG
28070961 CTC
1 CTC
28070964 ATAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (17 bp):
CTCCCCCTTAATATATG
Found at i:28074028 original size:36 final size:36
Alignment explanation
Indices: 28073964--28074069 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
28073954 AAGGTAGAGT
* * *
28073964 GGTTGTATTTTATCCAAAAAAAGGCATTGTATTGTAA
1 GGTTGTGTTTGATCC-ATAAAAGGCATTGTATTGTAA
*
28074001 GGTTGTGTTTGATCCATAAAAGGCATTGCATTGTAA
1 GGTTGTGTTTGATCCATAAAAGGCATTGTATTGTAA
* * *
28074037 GGTTGTGCTTGATTCATAAAAGGCATTATATTG
1 GGTTGTGTTTGATCCATAAAAGGCATTGTATTG
28074070 AACTTGATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
36 48 0.79
37 13 0.21
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (36 bp):
GGTTGTGTTTGATCCATAAAAGGCATTGTATTGTAA
Found at i:28074820 original size:2 final size:2
Alignment explanation
Indices: 28074813--28074839 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28074803 TTAAATTGCA
28074813 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28074840 ATTTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28075588 original size:18 final size:18
Alignment explanation
Indices: 28075547--28075588 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
28075537 ATTGAAAAGA
*
28075547 AAAAAATGACAAATGAAT
1 AAAAAATGACAAATAAAT
*
28075565 AGAAAAT-ACAAGATAAAT
1 AAAAAATGACAA-ATAAAT
28075583 AAAAAA
1 AAAAAA
28075589 AGTACCAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (18 bp):
AAAAAATGACAAATAAAT
Found at i:28075704 original size:31 final size:32
Alignment explanation
Indices: 28075668--28075729 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
28075658 TTTCAACAAA
*
28075668 AAATGAATCGAAAAGAAAA-ACAAAAAATAAC
1 AAATGAATAGAAAAGAAAAGACAAAAAATAAC
* *
28075699 AAATGAATAGAAAATAAAAGACAAATAATAA
1 AAATGAATAGAAAAGAAAAGACAAAAAATAA
28075730 AAGTACCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (32 bp):
AAATGAATAGAAAAGAAAAGACAAAAAATAAC
Found at i:28086662 original size:52 final size:52
Alignment explanation
Indices: 28086508--28086662 Score: 283
Period size: 52 Copynumber: 3.0 Consensus size: 52
28086498 ACATGACGAT
* * *
28086508 GATAGTGGTGTGCTATGTGAGTGCACACACTGATGATTTATGCCATGTGCAC
1 GATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCGC
28086560 GATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCGC
1 GATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCGC
28086612 GATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCG
1 GATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCG
28086663 ATGTGAGAGT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 100 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (52 bp):
GATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCGC
Found at i:28086708 original size:35 final size:37
Alignment explanation
Indices: 28086637--28086712 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
28086627 TGTGAGTGCA
*
28086637 CACACTGATGATATATGCCATGTGCGATGTGAGAGTG
1 CACACTGATGATATATGCCATGTGCGATGGGAGAGTG
* * *
28086674 CACA-TGATGATAT-TGCCTTGTGCGGTGGGGGAGTG
1 CACACTGATGATATATGCCATGTGCGATGGGAGAGTG
28086709 CACA
1 CACA
28086713 AAATGATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 22 0.63
36 9 0.26
37 4 0.11
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (37 bp):
CACACTGATGATATATGCCATGTGCGATGGGAGAGTG
Found at i:28087197 original size:22 final size:22
Alignment explanation
Indices: 28087167--28087209 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28087157 TCGTTATAGC
28087167 TGCAACGAGAATGGTTTTTCGT
1 TGCAACGAGAATGGTTTTTCGT
*
28087189 TGCAGCGAGAATGGTTTTTCG
1 TGCAACGAGAATGGTTTTTCG
28087210 CTGTAGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (22 bp):
TGCAACGAGAATGGTTTTTCGT
Found at i:28103571 original size:23 final size:24
Alignment explanation
Indices: 28103526--28103587 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
28103516 TTCATTTCAC
*
28103526 CAGCGATGCAGCCTT-GCTCTCCT
1 CAGCGCTGCAGCCTTGGCTCTCCT
28103549 CAGCGCTGCAGCCTTGGCT-TCCT
1 CAGCGCTGCAGCCTTGGCTCTCCT
* * *
28103572 TAGTGCTGTAGCCTTG
1 CAGCGCTGCAGCCTTG
28103588 AGCAACTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 31 0.91
24 3 0.09
ACGTcount: A:0.11, C:0.34, G:0.26, T:0.29
Consensus pattern (24 bp):
CAGCGCTGCAGCCTTGGCTCTCCT
Found at i:28115347 original size:42 final size:42
Alignment explanation
Indices: 28115285--28115410 Score: 207
Period size: 42 Copynumber: 3.0 Consensus size: 42
28115275 GTAATGATAT
* * *
28115285 TGACCCGGCTATGTGCGAGTAGAAGTGTGCATAAGCCGATGC
1 TGACCCGGCTATGTGTGAGTAGGAGTGCGCATAAGCCGATGC
28115327 TGACCCGGCTATGTGTGAGTAGGAGTGCGCATAAGCCGATGC
1 TGACCCGGCTATGTGTGAGTAGGAGTGCGCATAAGCCGATGC
* *
28115369 TGACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGATGC
1 TGACCCGGCTATGTGTGAGTAGGAGTGCGCATAAGCCGATGC
28115411 ATATGAGCTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.21
Consensus pattern (42 bp):
TGACCCGGCTATGTGTGAGTAGGAGTGCGCATAAGCCGATGC
Found at i:28115458 original size:2 final size:2
Alignment explanation
Indices: 28115451--28115480 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28115441 ATGATGATTG
*
28115451 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28115481 GGTACATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28117849 original size:43 final size:43
Alignment explanation
Indices: 28117776--28117894 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
28117766 GTAATTATAT
* * *
28117776 TGACTTGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCTGGCTATGTGCGAGTAGGGAATGCGCATAACCCG-GTGA
*
28117819 TGACCTGGTTATGTGCGAGTAGGGAATGCGCATAACCCGGTGA
1 TGACCTGGCTATGTGCGAGTAGGGAATGCGCATAACCCGGTGA
*** * * *
28117862 TGACCCAACCATGCGCGAGTAGGGAGTGCGCAT
1 TGACCTGGCTATGTGCGAGTAGGGAATGCGCAT
28117895 GAGCTGGTGA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (43 bp):
TGACCTGGCTATGTGCGAGTAGGGAATGCGCATAACCCGGTGA
Found at i:28118094 original size:179 final size:163
Alignment explanation
Indices: 28117901--28118242 Score: 531
Period size: 179 Copynumber: 2.0 Consensus size: 163
28117891 GCATGAGCTG
28117901 GTGATGATGATGATGGGTATATGCGTATATATATATACATATGTAAATATGTGTGTTATAGGAAA
1 GTGATGATGATGATGGGTATATGCGTATATATATATACATATGTAAATATGTGTGTTATAGGAAA
28117966 TTGATGGATAATGGTTTATGGTTGTAATGCATGTGAAACTTGACATGTTAAACCTTGAGAAATTG
66 TTGATGGATAATGGTTTATGGTTGTAATGCATGTGAAACTTGACATGTTAAACCTTGAGAAATTG
*
28118031 TTATGTGTTTCATATTGGTTTTGAACATTTCAA
131 TTATGTGTTTCATATTAGTTTTGAACATTTCAA
28118064 NNNNNNNNNNNNNNNNGTGATGATGATGATGGGTATATGCGTATATATATATACATATGTAAATA
1 ----------------GTGATGATGATGATGGGTATATGCGTATATATATATACATATGTAAATA
28118129 TGTGTGTTATAGGAAATTGATGGATAATGGTTTATGGTTGTAATGCATGTGAAACTTGACATGTT
50 TGTGTGTTATAGGAAATTGATGGATAATGGTTTATGGTTGTAATGCATGTGAAACTTGACATGTT
28118194 AAACCTTGAGAAATTGTTATGTGTTTCATATTAGTTTTGAACATTTCAA
115 AAACCTTGAGAAATTGTTATGTGTTTCATATTAGTTTTGAACATTTCAA
28118243 ACAGGGTGGT
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 162 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.38
Consensus pattern (163 bp):
GTGATGATGATGATGGGTATATGCGTATATATATATACATATGTAAATATGTGTGTTATAGGAAA
TTGATGGATAATGGTTTATGGTTGTAATGCATGTGAAACTTGACATGTTAAACCTTGAGAAATTG
TTATGTGTTTCATATTAGTTTTGAACATTTCAA
Found at i:28122598 original size:52 final size:52
Alignment explanation
Indices: 28122520--28122623 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
28122510 GTGATAATAT
* *
28122520 TGACCCGGCTATGTGTGAGTAGGGAGTGCGCATAAGCTGATGATGATGATGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGATGATGA
*
28122572 TGACCTGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGATGATGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGATGATGA
28122624 CCCGACTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.24
Consensus pattern (52 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGATGATGA
Found at i:28127276 original size:23 final size:23
Alignment explanation
Indices: 28127250--28127295 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28127240 TCATTTCACT
28127250 AGTGGTGCAGCCTT-GCTCTCCTC
1 AGTGGTGCAGCCTTAGCT-TCCTC
*
28127273 AGTGTTGCAGCCTTAGCTTCCTC
1 AGTGGTGCAGCCTTAGCTTCCTC
28127296 GACGTTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.11, C:0.33, G:0.24, T:0.33
Consensus pattern (23 bp):
AGTGGTGCAGCCTTAGCTTCCTC
Found at i:28127571 original size:21 final size:20
Alignment explanation
Indices: 28127547--28127585 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28127537 ACCTAGAGAA
28127547 AAAATAAATTAAAATTAAACT
1 AAAATAAATT-AAATTAAACT
*
28127568 AAAATAACTTAAATTAAA
1 AAAATAAATTAAATTAAA
28127586 TACTTAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAAATTAAATTAAACT
Found at i:28129384 original size:11 final size:11
Alignment explanation
Indices: 28129364--28129397 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28129354 ACTGGTGAAA
28129364 TTCA-CAAGCT
1 TTCACCAAGCT
28129374 TTCACCAAGCT
1 TTCACCAAGCT
*
28129385 TTCACTAAGCT
1 TTCACCAAGCT
28129396 TT
1 TT
28129398 ACAATGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.35
Consensus pattern (11 bp):
TTCACCAAGCT
Found at i:28131562 original size:316 final size:314
Alignment explanation
Indices: 28131067--28131699 Score: 1086
Period size: 316 Copynumber: 2.0 Consensus size: 314
28131057 CCAATGGAAT
* * *
28131067 TTAATTACTAATTTGAATTTTGTATGAATATAAACTTATCTAGATTATCTACTGTCTCGGTGAGA
1 TTAATTACTAATTTGAATTTTGCATGAATATAAACTTATCTAGATTATATACTGTCTAGGTGAGA
*** *
28131132 AGATTGTGTACACAAATGAAAATTCACTTAATGATAAGCTTGCATTTGAATTGAGACATGAACTT
66 AGATTGCACACACAAACGAAAATTCACTTAATGATAAGCTTGCATTTGAATTGAGACATGAACTT
*
28131197 GAATAATATTTGTATGTGGATTAGAGTTATGAATATGGAGTAACTTCTGAACATATTAAAGGTAA
131 GAATAATATTTGTATGTGGATTAAAGTTATGAATATGGAGTAACTTCTGAACATATTAAAGGTAA
*
28131262 TTAATAAAATGGTGCAATTAAGCTCTAGTTAAAAGTTTTCATGTTTAAGTTATTGTATTTAGTTT
196 TTAATAAAATGGTGCAATTAAGCTCTAGTTAAAAGTTTTCATATTTAAGTTATTGTATTTAGTTT
* * *
28131327 TTTGTTTTGCTCGAGGACTAGCAAAATCTTAAGTTTGGGGGTATGATAACTCTA
261 TTTATTTTGCTCGAGAACTAGCAAAATCTTAAGTTTGGGGATATGATAACTCTA
28131381 TTAATTACTAATTTGAATTTTGCATGAATATAAACTTATCTAGATTATATACTGTCTAGGTGAGA
1 TTAATTACTAATTTGAATTTTGCATGAATATAAACTTATCTAGATTATATACTGTCTAGGTGAGA
28131446 AGATTGCACACACACACACGAAAATTCACTTAATGATAAGCTTGCATTTGAATTGAGACATGAAC
66 AGATTGCACACACA-A-ACGAAAATTCACTTAATGATAAGCTTGCATTTGAATTGAGACATGAAC
*
28131511 TTGAATAATATTTGTATGTGGATTAAAGTTATGAATATGGAGTAACTTCTGAAGATATTAAAGGT
129 TTGAATAATATTTGTATGTGGATTAAAGTTATGAATATGGAGTAACTTCTGAACATATTAAAGGT
* * *
28131576 AATTAATGAAATGGTGCAATTGAGCTCTAGTTAAAAGTTTTCATATTTACGTTATTGTATTTAGT
194 AATTAATAAAATGGTGCAATTAAGCTCTAGTTAAAAGTTTTCATATTTAAGTTATTGTATTTAGT
* *
28131641 TTTTTATTTTGCTCGAGAACTAGCAAAATTTTAAGTTTGGGGATGTGATAACTCTA
259 TTTTTATTTTGCTCGAGAACTAGCAAAATCTTAAGTTTGGGGATATGATAACTCTA
28131697 TTA
1 TTA
28131700 TATAGAGTTA
Statistics
Matches: 299, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
314 73 0.24
315 1 0.00
316 225 0.75
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (314 bp):
TTAATTACTAATTTGAATTTTGCATGAATATAAACTTATCTAGATTATATACTGTCTAGGTGAGA
AGATTGCACACACAAACGAAAATTCACTTAATGATAAGCTTGCATTTGAATTGAGACATGAACTT
GAATAATATTTGTATGTGGATTAAAGTTATGAATATGGAGTAACTTCTGAACATATTAAAGGTAA
TTAATAAAATGGTGCAATTAAGCTCTAGTTAAAAGTTTTCATATTTAAGTTATTGTATTTAGTTT
TTTATTTTGCTCGAGAACTAGCAAAATCTTAAGTTTGGGGATATGATAACTCTA
Found at i:28133877 original size:18 final size:18
Alignment explanation
Indices: 28133854--28133888 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28133844 TTCACCAAAA
28133854 TTTTCAATCA-CAATTTCT
1 TTTTCAA-CATCAATTTCT
28133872 TTTTCAACATCAATTTC
1 TTTTCAACATCAATTTC
28133889 AACCTTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTCAACATCAATTTCT
Found at i:28134384 original size:21 final size:19
Alignment explanation
Indices: 28134348--28134388 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
28134338 ACATGTTGAG
28134348 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
28134367 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
28134388 T
1 T
28134389 GTTTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:28134397 original size:21 final size:21
Alignment explanation
Indices: 28134351--28134397 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
28134341 TGTTGAGTAG
28134351 TTAA-TTTAAGTTATTTTAGT
1 TTAATTTTAAGTTATTTTAGT
* *
28134371 TAAATTTTATGTTATTTT-GTT
1 TTAATTTTAAGTTATTTTAG-T
28134392 TTAATT
1 TTAATT
28134398 ACTTTAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (21 bp):
TTAATTTTAAGTTATTTTAGT
Found at i:28135845 original size:14 final size:14
Alignment explanation
Indices: 28135806--28135836 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28135796 ATAAATTTTG
28135806 GTTAATTAATTTCA
1 GTTAATTAATTTCA
28135820 GTTAATTAATTT-A
1 GTTAATTAATTTCA
28135833 GTTA
1 GTTA
28135837 TTTGAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (14 bp):
GTTAATTAATTTCA
Found at i:28143842 original size:92 final size:92
Alignment explanation
Indices: 28143692--28143886 Score: 363
Period size: 92 Copynumber: 2.1 Consensus size: 92
28143682 ACAAAGCTAT
28143692 AATCGATCTTAGAGCAAAGCTAATCAATCCAAAGACAAAATGGATGAGAAATAATGAAGGATCAA
1 AATCGATCTTAGAGCAAAGCTAATCAATCCAAAGACAAAATGGATGAGAAATAATGAAGGATCAA
*
28143757 AGTTTTAGTCGATCCTAGAGAAGCTTC
66 AGTTTTAGTCAATCCTAGAGAAGCTTC
*
28143784 AATCGATCTTAGAGCAAAGCTAATCAATCCAAAGACAGAATGGATGAGAAATAATGAAGGATCAA
1 AATCGATCTTAGAGCAAAGCTAATCAATCCAAAGACAAAATGGATGAGAAATAATGAAGGATCAA
28143849 AGTTTTAGTCAATCCTAGAGAAGCTTC
66 AGTTTTAGTCAATCCTAGAGAAGCTTC
*
28143876 AATTGATCTTA
1 AATCGATCTTA
28143887 TGACAAAACG
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 100 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (92 bp):
AATCGATCTTAGAGCAAAGCTAATCAATCCAAAGACAAAATGGATGAGAAATAATGAAGGATCAA
AGTTTTAGTCAATCCTAGAGAAGCTTC
Found at i:28146428 original size:37 final size:37
Alignment explanation
Indices: 28146387--28146489 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
28146377 AATATCATCA
*
28146387 TCCCTACTCGCACACTTCAACATCATCATGTGTACAC
1 TCCCTACTCGCACACTTCAACATCATCACGTGTACAC
* *
28146424 TCCCTACTCGCACAC-TCTATCATCATCACGTGTGCAC
1 TCCCTACTCGCACACTTC-AACATCATCACGTGTACAC
*
28146461 TCCCTACTCGCACAGTTCAACATCATCAC
1 TCCCTACTCGCACACTTCAACATCATCAC
28146490 ACAACATCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
36 2 0.03
37 55 0.93
38 2 0.03
ACGTcount: A:0.25, C:0.40, G:0.09, T:0.26
Consensus pattern (37 bp):
TCCCTACTCGCACACTTCAACATCATCACGTGTACAC
Found at i:28149498 original size:73 final size:73
Alignment explanation
Indices: 28149374--28149597 Score: 385
Period size: 73 Copynumber: 3.1 Consensus size: 73
28149364 TAATTGGGCG
* *
28149374 TGTGTGGTGTGGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
1 TGTGCGGTGTAGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
28149439 ATATGCTA
66 ATATGCTA
28149447 TGTGCGGTGTAGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
1 TGTGCGGTGTAGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
28149512 ATATGCTA
66 ATATGCTA
* * * *
28149520 TGTGTGGTGTAAGAGTGCATATGATGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
1 TGTGCGGTGTAGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
*
28149585 ATATGCCA
66 ATATGCTA
28149593 TGTGC
1 TGTGC
28149598 AATGGGAGAG
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 143 1.00
ACGTcount: A:0.21, C:0.12, G:0.36, T:0.30
Consensus pattern (73 bp):
TGTGCGGTGTAGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
ATATGCTA
Found at i:28149585 original size:34 final size:35
Alignment explanation
Indices: 28149375--28149585 Score: 148
Period size: 34 Copynumber: 5.9 Consensus size: 35
28149365 AATTGGGCGT
* * * *
28149375 GTGTGGTGTGGGAGTGCACATGAC-GGTGATAGTG
1 GTGTGCTGTGTGAGTGCACATCACTGATGATAGTG
*
28149409 GTGTGCTGTGTGAGTGCACA-CACTGATGATATATG
1 GTGTGCTGTGTGAGTGCACATCACTGATGATA-GTG
* * * *
28149444 CTATGTGCGGTGTAGGAGTGCACATGAC-GGTGATAGTG
1 --GTGTGCTGTGT--GAGTGCACATCACTGATGATAGTG
*
28149482 GTGTGCTGTGTGAGTGCACA-CACTGATGATATATG
1 GTGTGCTGTGTGAGTGCACATCACTGATGATA-GTG
* * * *
28149517 CTATGTG-TGGTGTAAGAGTGCATATGA-TGGTGATAGTG
1 --GTGTGCT-GTGT--GAGTGCACATCACTGATGATAGTG
28149555 GTGTGCTGTGTGAGTGCACA-CACTGATGATA
1 GTGTGCTGTGTGAGTGCACATCACTGATGATA
28149586 TATGCCATGT
Statistics
Matches: 136, Mismatches: 24, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
33 5 0.04
34 54 0.40
35 4 0.03
36 18 0.13
37 18 0.13
38 4 0.03
39 30 0.22
40 3 0.02
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.30
Consensus pattern (35 bp):
GTGTGCTGTGTGAGTGCACATCACTGATGATAGTG
Found at i:28150448 original size:22 final size:23
Alignment explanation
Indices: 28150423--28150466 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28150413 ATCATCTTCT
28150423 AGCAGCTTCTTC-TCATTTTTTC
1 AGCAGCTTCTTCTTCATTTTTTC
* *
28150445 AGCAGTTTCTTCTTCTTTTTTT
1 AGCAGCTTCTTCTTCATTTTTT
28150467 TTCCTCCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.11, C:0.23, G:0.09, T:0.57
Consensus pattern (23 bp):
AGCAGCTTCTTCTTCATTTTTTC
Found at i:28153510 original size:2 final size:2
Alignment explanation
Indices: 28153505--28153530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28153495 TATATATATA
28153505 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
28153531 AATAGGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28162214 original size:18 final size:18
Alignment explanation
Indices: 28162193--28162228 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28162183 TAATTTTAAT
28162193 TTTAATTTTATTTATTTA
1 TTTAATTTTATTTATTTA
* *
28162211 TTTATTTTTATTTTTTTA
1 TTTAATTTTATTTATTTA
28162229 GACCCAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTAATTTTATTTATTTA
Found at i:28162806 original size:8 final size:8
Alignment explanation
Indices: 28162793--28162879 Score: 50
Period size: 8 Copynumber: 10.1 Consensus size: 8
28162783 TTCTCTTCTC
28162793 TCTTTTTCT
1 TCTTTTT-T
*
28162802 TTTTTTTT
1 TCTTTTTT
28162810 TCTTTTTT
1 TCTTTTTT
*
28162818 T-TTATTT
1 TCTTTTTT
* * *
28162825 CCTTCCTTC
1 TCTT-TTTT
28162834 TCTTTTTCTT
1 TC-TTTT-TT
28162844 TCTTTTTCT
1 TCTTTTT-T
*
28162853 CTCCTTTCTT
1 -T-CTTTTTT
28162863 TCTTTTTT
1 TCTTTTTT
28162871 TCTTTTTT
1 TCTTTTTT
28162879 T
1 T
28162880 ATTTCCTTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
7 5 0.08
8 27 0.45
9 16 0.27
10 7 0.12
11 5 0.08
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (8 bp):
TCTTTTTT
Found at i:28162808 original size:10 final size:11
Alignment explanation
Indices: 28162795--28162884 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 11
28162785 CTCTTCTCTC
28162795 TTTTTCTTTTT
1 TTTTTCTTTTT
28162806 TTTTTCTTTTT
1 TTTTTCTTTTT
**
28162817 TTTTAT-TTCCT
1 TTTT-TCTTTTT
**
28162828 TCCTTCTCTTTT
1 TTTTTCT-TTTT
*
28162840 TCTTTCTTTTT
1 TTTTTCTTTTT
28162851 CTCTCCTTTCTTTCTT
1 -T-T--TTTCTTT-TT
28162867 TTTTTCTTTTT
1 TTTTTCTTTTT
28162878 TTATTTC
1 TT-TTTC
28162885 CTTCCTTCTC
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
10 1 0.02
11 29 0.47
12 21 0.34
14 1 0.02
15 8 0.13
16 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:28162842 original size:30 final size:30
Alignment explanation
Indices: 28162806--28162899 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
28162796 TTTTCTTTTT
28162806 TTTTTCTTTTTTTTTATTTCCTTCCTTCTC
1 TTTTTCTTTTTTTTTATTTCCTTCCTTCTC
* * * *
28162836 TTTTTCTTTCTTTTTCTCTCCTTTCTT-TC
1 TTTTTCTTTTTTTTTATTTCCTTCCTTCTC
28162865 TTTTT-TTCTTTTTTTATTTCCTTCCTTCTC
1 TTTTTCTT-TTTTTTTATTTCCTTCCTTCTC
28162895 TTTTT
1 TTTTT
28162900 TCTTCCTCTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.04
29 22 0.41
30 30 0.56
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTTTCTTTTTTTTTATTTCCTTCCTTCTC
Found at i:28162845 original size:20 final size:20
Alignment explanation
Indices: 28162816--28162899 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
28162806 TTTTTCTTTT
28162816 TTTTTATTTCCTTCCTTCTC
1 TTTTTATTTCCTTCCTTCTC
* *
28162836 TTTTTCTTT-CTT-TTTCTC
1 TTTTTATTTCCTTCCTTCTC
* * * ** *
28162854 TCCTTTCTTTCTTTTTTTCTT
1 T-TTTTATTTCCTTCCTTCTC
28162875 TTTTTATTTCCTTCCTTCTC
1 TTTTTATTTCCTTCCTTCTC
28162895 TTTTT
1 TTTTT
28162900 TCTTCCTCTC
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
18 6 0.12
19 10 0.20
20 28 0.56
21 6 0.12
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTATTTCCTTCCTTCTC
Found at i:28162905 original size:20 final size:19
Alignment explanation
Indices: 28162823--28162906 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 19
28162813 TTTTTTTTAT
28162823 TTCCTTCCTTCTC-TTTTTC
1 TTCCTT-CTTCTCTTTTTTC
* * **
28162842 TTTCTTTTTCTCTCCTTTC
1 TTCCTTCTTCTCTTTTTTC
* * * *
28162861 TTTCTTTTTTTCTTTTTTTAT
1 TTCCTTCTTCTC-TTTTTT-C
28162882 TTCCTTCCTTCTCTTTTTTC
1 TTCCTT-CTTCTCTTTTTTC
28162902 TTCCT
1 TTCCT
28162907 CTCTCCTCCG
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
18 5 0.10
19 20 0.41
20 9 0.18
21 11 0.22
22 4 0.08
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (19 bp):
TTCCTTCTTCTCTTTTTTC
Found at i:28162960 original size:14 final size:14
Alignment explanation
Indices: 28162943--28162984 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
28162933 CATTCTTTTC
*
28162943 TCTTTTTTTCTCTT
1 TCTTTCTTTCTCTT
*
28162957 TCTTTCCTTCTCTT
1 TCTTTCTTTCTCTT
*
28162971 T-GTTCTTTCTCTT
1 TCTTTCTTTCTCTT
28162984 T
1 T
28162985 TTCGATGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.71
Consensus pattern (14 bp):
TCTTTCTTTCTCTT
Found at i:28163202 original size:18 final size:19
Alignment explanation
Indices: 28163180--28163223 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
28163170 TTTCTTCTTC
28163180 CTTCTCCATCTCTTTCTCT
1 CTTCTCCATCTCTTTCTCT
* * *
28163199 -TTCTTCTTCTCTTTTTCT
1 CTTCTCCATCTCTTTCTCT
28163217 CTTCTCC
1 CTTCTCC
28163224 TCCGGACGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (19 bp):
CTTCTCCATCTCTTTCTCT
Found at i:28163384 original size:21 final size:22
Alignment explanation
Indices: 28163345--28163386 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28163335 CCATTTCCTT
*
28163345 TTTTTTTGTTTTCTTTTTGGTA
1 TTTTTTTGTTTTCCTTTTGGTA
28163367 TTTTTTTG-TTTCCTTTTGGT
1 TTTTTTTGTTTTCCTTTTGGT
28163387 TGTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.02, C:0.07, G:0.14, T:0.76
Consensus pattern (22 bp):
TTTTTTTGTTTTCCTTTTGGTA
Found at i:28163797 original size:17 final size:16
Alignment explanation
Indices: 28163777--28163823 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
28163767 TTCTCTCTTT
28163777 TTATATTTTAATTTTTA
1 TTATATTTT-ATTTTTA
* *
28163794 TTATATTGTATTATTA
1 TTATATTTTATTTTTA
28163810 TT-TATTTTTATTTT
1 TTATA-TTTTATTTT
28163824 AGTTGATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 8 0.32
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATATTTTATTTTTA
Found at i:28164209 original size:58 final size:58
Alignment explanation
Indices: 28164071--28164707 Score: 724
Period size: 58 Copynumber: 10.9 Consensus size: 58
28164061 GGGTTCGATA
* * * * * * * *
28164071 AAATTCCTAAACTTAATCTAGGCTCGATCTATCTAAAAATAGATTCGATTTAAAAATTG
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTT-AAAATTG
* * * * *
28164130 AAATT-TCAAGACTTGATCTAGGCTCGACCTACATTAGAACAGGTTCGATTTAAAATTA
1 AAATTCT-TAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
* * * *
28164188 AAATTCTTAGACTTAATCTAGGCTCGGCCTATATCAAAACAGATTCAATTTAAAATTG
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
* * *
28164246 AAATTCCTAGA-TTAATCTAGGCTCGACCTATATCAGAACAGATTCGATTTAAAAAATTA
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTT--AAAATTG
* * * ** * * *
28164305 AAATTCCTAGACTTAATCTAGGCTTGATCTATATTGGAACAAGTTTGATTTAAAAATG
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
* *
28164363 AAATTCCTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAGAATTG
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
* * * * * *
28164421 AAATTCCTAGACTTAATCTAGGCTCGATCTATATCAGAATAGGTTCAATTAAAAATTA
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
*
28164479 AAATTCTTAGA-TTAAATCTAGGCTCGACCTATATCAGAACATGTTCGATTTAAAAAATTG
1 AAATTCTTAGACTT-AATCTAGGCTCGACCTATATCAGAACAGGTTCGATTT--AAAATTG
*
28164539 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAAATTA
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTT-AAAATTG
* * * * * *
28164598 AAATTCTTAGATTTAATCTA-GCTCAACTTATATCACAACAGGTTAGATTAAAAATTG
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
* ** * * *
28164655 AAATTCTTAGACTTAATTTAGGCAAGACCTATCTCACAATAGGTTCGATTTAA
1 AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAA
28164708 TTCTCTAATG
Statistics
Matches: 493, Mismatches: 75, Indels: 21
0.84 0.13 0.04
Matches are distributed among these distances:
57 62 0.13
58 261 0.53
59 83 0.17
60 85 0.17
61 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (58 bp):
AAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
Found at i:28164528 original size:234 final size:233
Alignment explanation
Indices: 28164069--28164700 Score: 822
Period size: 234 Copynumber: 2.7 Consensus size: 233
28164059 ATGGGTTCGA
* * * *
28164069 TAAAATTCCTAAACTTAATCTAGGCTCGATCTAT-CTAAAAATAGATTCGATTTAAAAATTGAAA
1 TAAAATTCCTAGACTTAATCTAGGCTCGATCTATATTGAACA-AG-TTCGATTTAAAAATTGAAA
* * * * * *
28164133 TTTCAAGACTTGATCTAGGCTCGACCTACATTAGAACAGGTTCGATTTAAAATTAAAATTCTTAG
64 TTCCTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTGAAATTCTTAG
* * * * *
28164198 ACTTAATCTAGGCTCGGCCTATATCAAAACAGATTCAATTTAAAATTGAAATTCCTAGATTAATC
129 ACTTAATCTAGGCTCGACCTATATCAAAATAGGTTCAATTAAAAATTAAAATTCCTAGATTAATC
28164263 TAGGCTCGACCTATATCAGAACAGATTCGATTTAAAAAAT
194 TAGGCTCGACCTATATCAGAACAGATTCGATTTAAAAAAT
* *
28164303 TAAAATTCCTAGACTTAATCTAGGCTTGATCTATATTGGAACAAGTTTGATTTAAAAA-TGAAAT
1 TAAAATTCCTAGACTTAATCTAGGCTCGATCTATATT-GAACAAGTTCGATTTAAAAATTGAAAT
* *
28164367 TCCTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAGAATTGAAATTCCTAGA
65 TCCTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTGAAATTCTTAGA
* * *
28164432 CTTAATCTAGGCTCGATCTATATCAGAATAGGTTCAATTAAAAATTAAAATTCTTAGATTAAATC
130 CTTAATCTAGGCTCGACCTATATCAAAATAGGTTCAATTAAAAATTAAAATTCCTAGATT-AATC
28164497 TAGGCTCGACCTATATCAGAACATG-TTCGATTTAAAAAAT
194 TAGGCTCGACCTATATCAGAACA-GATTCGATTTAAAAAAT
* * * * * *
28164537 TGAAATTCTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAAATTAAAAT
1 TAAAATTCCTAGACTTAATCTAGGCTCGATCTATAT-TGAACAAGTTCGATTTAAAAATTGAAAT
* * * * * * *
28164602 TCTTAGATTTAATCTA-GCTCAACTTATATCACAACAGGTTAGATTAAAAATTGAAATTCTTAGA
65 TCCTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTGAAATTCTTAGA
* ** * *
28164666 CTTAATTTAGGCAAGACCTATCTCACAATAGGTTC
130 CTTAATCTAGGCTCGACCTATATCAAAATAGGTTC
28164701 GATTTAATTC
Statistics
Matches: 347, Mismatches: 45, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
233 115 0.33
234 206 0.59
235 23 0.07
236 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (233 bp):
TAAAATTCCTAGACTTAATCTAGGCTCGATCTATATTGAACAAGTTCGATTTAAAAATTGAAATT
CCTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTGAAATTCTTAGAC
TTAATCTAGGCTCGACCTATATCAAAATAGGTTCAATTAAAAATTAAAATTCCTAGATTAATCTA
GGCTCGACCTATATCAGAACAGATTCGATTTAAAAAAT
Found at i:28164560 original size:176 final size:176
Alignment explanation
Indices: 28164071--28164707 Score: 761
Period size: 176 Copynumber: 3.6 Consensus size: 176
28164061 GGGTTCGATA
* * * * * * *
28164071 AAATTCCTAAACTTAATCTAGGCTCGATCTATCTAAAAATAGATTCGATTTAAAAATTGAAATT-
1 AAATTCCTAGACTTAATCTAGGCTCGATCTATATCAGAACAGATTCGAATTAAAAATTAAAATTC
* * * * *
28164135 TCAAGACTTGATCTAGGCTCGACCTACATTAGAACAGGTTCGATTT-AAAATTAAAATTCTTAGA
66 T-TAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAAATTGAAATTCTTAGA
* * * *
28164199 CTTAATCTAGGCTCGGCCTATATCAAAACAGATTCAATTTAAAATTG
130 CTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
* *
28164246 AAATTCCTAGA-TTAATCTAGGCTCGACCTATATCAGAACAGATTCGATTTAAAAAATTAAAATT
1 AAATTCCTAGACTTAATCTAGGCTCGATCTATATCAGAACAGATTCGAATT-AAAAATTAAAATT
* * * ** * * *
28164310 CCTAGACTTAATCTAGGCTTGATCTATATTGGAACAAGTTTGATTTAAAAA-TGAAATTCCTAGA
65 CTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAAATTGAAATTCTTAGA
*
28164374 CTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAGAATTG
130 CTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
* *
28164421 AAATTCCTAGACTTAATCTAGGCTCGATCTATATCAGAATAGGTTC-AATTAAAAATTAAAATTC
1 AAATTCCTAGACTTAATCTAGGCTCGATCTATATCAGAACAGATTCGAATTAAAAATTAAAATTC
*
28164485 TTAGA-TTAAATCTAGGCTCGACCTATATCAGAACATGTTCGATTTAAAAAATTGAAATTCTTAG
66 TTAGACTT-AATCTAGGCTCGACCTATATCAGAACAGGTTCGATTT-AAAAATTGAAATTCTTAG
*
28164549 ACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAAATTA
129 ACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTT-AAAATTG
* * * * * * *
28164598 AAATTCTTAGATTTAATCTA-GCTC-AACTTATATCACAACAGGTTAG-ATTAAAAATTGAAATT
1 AAATTCCTAGACTTAATCTAGGCTCGATC-TATATCAGAACAGATTCGAATTAAAAATTAAAATT
* ** * * *
28164660 CTTAGACTTAATTTAGGCAAGACCTATCTCACAATAGGTTCGATTTAA
65 CTTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAA
28164708 TTCTCTAATG
Statistics
Matches: 400, Mismatches: 51, Indels: 22
0.85 0.11 0.05
Matches are distributed among these distances:
173 2 0.00
174 83 0.21
175 134 0.34
176 156 0.39
177 25 0.06
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (176 bp):
AAATTCCTAGACTTAATCTAGGCTCGATCTATATCAGAACAGATTCGAATTAAAAATTAAAATTC
TTAGACTTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAAATTGAAATTCTTAGAC
TTAATCTAGGCTCGACCTATATCAGAACAGGTTCGATTTAAAATTG
Found at i:28165661 original size:18 final size:18
Alignment explanation
Indices: 28165638--28165678 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28165628 ACCCCTTTAA
28165638 TTTTTGTTTTTAATTTTC
1 TTTTTGTTTTTAATTTTC
* *
28165656 TTTTTGTTTTTGATTTTG
1 TTTTTGTTTTTAATTTTC
28165674 TTTTT
1 TTTTT
28165679 TTTAAGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.02, G:0.10, T:0.80
Consensus pattern (18 bp):
TTTTTGTTTTTAATTTTC
Found at i:28172608 original size:21 final size:21
Alignment explanation
Indices: 28172548--28172615 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
28172538 GTTTATGCAA
* * *
28172548 TTCATGATAAAGAATGAGGCC
1 TTCATGACAAAGACTGATGCC
* *
28172569 TTCATAACAAAGACAGATGCC
1 TTCATGACAAAGACTGATGCC
*
28172590 TTCATGACAATGACTGATGCC
1 TTCATGACAAAGACTGATGCC
*
28172611 ATCAT
1 TTCAT
28172616 TCAAAGTCAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGACTGATGCC
Found at i:28174522 original size:16 final size:18
Alignment explanation
Indices: 28174498--28174536 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
28174488 TGTGAAGTTG
28174498 TGAAAAAAAAAA-TGTGT
1 TGAAAAAAAAAAGTGTGT
28174515 TGAAAAAAAAAAGTGTGT
1 TGAAAAAAAAAAGTGTGT
28174533 TGAA
1 TGAA
28174537 TGAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (18 bp):
TGAAAAAAAAAAGTGTGT
Found at i:28174523 original size:18 final size:18
Alignment explanation
Indices: 28174500--28174536 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28174490 TGAAGTTGTG
28174500 AAAAAAAAAATGTGTTGA
1 AAAAAAAAAATGTGTTGA
*
28174518 AAAAAAAAAGTGTGTTGA
1 AAAAAAAAAATGTGTTGA
28174536 A
1 A
28174537 TGAAAGAAAA
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:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (18 bp):
AAAAAAAAAATGTGTTGA
Found at i:28184455 original size:17 final size:17
Alignment explanation
Indices: 28184433--28184469 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
28184423 ATGGTACGTG
28184433 ATGCACTTATAATTCTA
1 ATGCACTTATAATTCTA
28184450 ATGCACTTATAATTCTA
1 ATGCACTTATAATTCTA
28184467 ATG
1 ATG
28184470 TTTGTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (17 bp):
ATGCACTTATAATTCTA
Found at i:28185619 original size:28 final size:28
Alignment explanation
Indices: 28185588--28185680 Score: 97
Period size: 27 Copynumber: 3.4 Consensus size: 28
28185578 TCTCTTTTTT
28185588 TTTCTTTTTTTCTCTATCATTCCTTCTC
1 TTTCTTTTTTTCTCTATCATTCCTTCTC
**
28185616 TTTCTCCTTTTCTC-AT--TTCCTTCTCTC
1 TTTCTTTTTTTCTCTATCATTCC-T-TCTC
*
28185643 TTTCTTTTTTTCT-T-CCATTCCTTCTC
1 TTTCTTTTTTTCTCTATCATTCCTTCTC
28185669 TTTCTTCTTTTT
1 TTTCTT-TTTTT
28185681 TCTCCTCCGG
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 4 0.07
26 11 0.20
27 23 0.43
28 16 0.30
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTCTTTTTTTCTCTATCATTCCTTCTC
Found at i:28185641 original size:25 final size:26
Alignment explanation
Indices: 28185605--28185679 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 26
28185595 TTTTCTCTAT
*
28185605 CATTCCTTCTCTTTCTCCTTTTC-T-
1 CATTCCTTCTCTTTCTTCTTTTCTTC
*
28185629 CATTTCCTTCTCTCTTTCTTTTTTTCTTC
1 CA-TTCC-T-TCTCTTTCTTCTTTTCTTC
28185658 CATTCCTTCTCTTTCTTCTTTT
1 CATTCCTTCTCTTTCTTCTTTT
28185680 TTCTCCTCCG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 15 0.35
27 15 0.35
28 5 0.12
29 2 0.05
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.63
Consensus pattern (26 bp):
CATTCCTTCTCTTTCTTCTTTTCTTC
Found at i:28185681 original size:28 final size:27
Alignment explanation
Indices: 28185588--28185683 Score: 94
Period size: 28 Copynumber: 3.6 Consensus size: 27
28185578 TCTCTTTTTT
28185588 TTTCTT-TTTTTCTCTATCATTCCTTCTC
1 TTTCTTCTTTTT-TCT-TCATTCCTTCTC
*
28185616 TTTC-TC-CTTTTC-TCATTTCCTTCTC
1 TTTCTTCTTTTTTCTTCA-TTCCTTCTC
*
28185641 TCT-TTCTTTTTTTCTTCCATTCCTTCTC
1 TTTCTTC-TTTTTTCTT-CATTCCTTCTC
28185669 TTTCTTCTTTTTTCT
1 TTTCTTCTTTTTTCT
28185684 CCTCCGGTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
24 3 0.05
25 13 0.23
26 2 0.04
27 9 0.16
28 24 0.43
29 5 0.09
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTCTTCTTTTTTCTTCATTCCTTCTC
Found at i:28185805 original size:17 final size:16
Alignment explanation
Indices: 28185766--28185807 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
28185756 TGCTGACGTC
28185766 TTCTTTCTCTTTTTTT
1 TTCTTTCTCTTTTTTT
*
28185782 TT-ATTCTCTTTTTTT
1 TTCTTTCTCTTTTTTT
28185797 TTCCTTTCTCT
1 TT-CTTTCTCT
28185808 CATTCCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 14 0.64
16 2 0.09
17 6 0.27
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTCTCTTTTTTT
Found at i:28185826 original size:37 final size:36
Alignment explanation
Indices: 28185785--28185877 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 36
28185775 TTTTTTTTTA
*
28185785 TTCTCTTTTTTTTTCCTTTCTCTCATTCCCTTTCTTC
1 TTCTCTTTTTTTTTCCTTTCTCTCATTCAC-TTCTTC
* * * * *
28185822 TTCTCTTTTCTTTCTCCCTT-TGTCGTTGACTTCTTC
1 TTCTCTTTT-TTTTTCCTTTCTCTCATTCACTTCTTC
*
28185858 -TCTCTTTTTTTTTTCTTTCT
1 TTCTCTTTTTTTTTCCTTTCT
28185878 TTCCTTCTCC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
34 7 0.16
35 9 0.20
36 6 0.13
37 15 0.33
38 8 0.18
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (36 bp):
TTCTCTTTTTTTTTCCTTTCTCTCATTCACTTCTTC
Found at i:28186046 original size:34 final size:34
Alignment explanation
Indices: 28185981--28186046 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
28185971 TTTTCTTTCT
* *
28185981 TCTCTCTTTCTCTCCTCCTCCGATTGGCCTTCAC
1 TCTCTCTTTCTCTCCTCCTCCGACTGACCTTCAC
*
28186015 TCTCTCTTTCTCTTCT-CTACCGACTGACCTTC
1 TCTCTCTTTCTCTCCTCCT-CCGACTGACCTTC
28186047 CCTTTCTCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.08, C:0.42, G:0.08, T:0.42
Consensus pattern (34 bp):
TCTCTCTTTCTCTCCTCCTCCGACTGACCTTCAC
Found at i:28188230 original size:16 final size:16
Alignment explanation
Indices: 28188209--28188239 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28188199 CAACTTTTAA
28188209 TAAAATATTAATATTT
1 TAAAATATTAATATTT
28188225 TAAAATATTAATATT
1 TAAAATATTAATATT
28188240 AAATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:28188346 original size:16 final size:17
Alignment explanation
Indices: 28188310--28188346 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
28188300 TTATTCCTAT
28188310 TTAAAATATAAAATAAA
1 TTAAAATATAAAATAAA
28188327 TTAAAA-AT-AAATAAA
1 TTAAAATATAAAATAAA
28188342 CTTAA
1 -TTAA
28188347 TATCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAATATAAAATAAA
Found at i:28188436 original size:113 final size:113
Alignment explanation
Indices: 28188238--28188452 Score: 260
Period size: 113 Copynumber: 1.9 Consensus size: 113
28188228 AATATTAATA
* * * *
28188238 TTAAATTATAAAATAAAATATTAATATTTAAATTATCAATTTTTAATAAAATAAATTATAAATTA
1 TTAAATTATAAAATAAAATATTAATAATTAAATCATCAATTATTAATAAAACAAATTATAAATTA
** *
28188303 TTCCTATTTAAAATATAAAATAAATTAAAAATAAATAAACTTAATATCAT
66 TTAATATTT-AAATATAAAATAAA-AAAAAATAAATAAACTTAATATCAT
*
28188353 TTAAATTAT-ATA-AAAATATTAATAATTAAATCATCAATTATTAATATTTTAAACAAATTATAA
1 TTAAATTATAAAATAAAATATTAATAATTAAATCATCAATTATTAATA----AAACAAATTATAA
*
28188416 ATTATTAATATTT-AA-A-AAAATAAAAAAAAATAGATAA
62 ATTATTAATATTTAAATATAAAATAAAAAAAAATAAATAA
28188453 TCATGTATTA
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
112 11 0.13
113 39 0.45
114 3 0.03
115 11 0.13
117 23 0.26
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (113 bp):
TTAAATTATAAAATAAAATATTAATAATTAAATCATCAATTATTAATAAAACAAATTATAAATTA
TTAATATTTAAATATAAAATAAAAAAAAATAAATAAACTTAATATCAT
Found at i:28190415 original size:55 final size:55
Alignment explanation
Indices: 28190330--28190487 Score: 226
Period size: 55 Copynumber: 2.9 Consensus size: 55
28190320 AACATGTATA
*
28190330 CAACCACTGGCTCATCAACTTATGTGCACTCCCACACCGCACATAGCTAAAATCAT
1 CAACCACTGG-TCATCAACTCATGTGCACTCCCACACCGCACATAGCTAAAATCAT
* * *
28190386 CAACCACTGGTCATCATCTCATGTGCACTCCCACACCGCACATAACTAGAATCAT
1 CAACCACTGGTCATCAACTCATGTGCACTCCCACACCGCACATAGCTAAAATCAT
* ** * *
28190441 CATCCACAAGTCATCAGCTCATGTGTACTCCCACACCGCACATAGCT
1 CAACCACTGGTCATCAACTCATGTGCACTCCCACACCGCACATAGCT
28190488 GGAATCACCC
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 82 0.89
56 10 0.11
ACGTcount: A:0.30, C:0.37, G:0.11, T:0.22
Consensus pattern (55 bp):
CAACCACTGGTCATCAACTCATGTGCACTCCCACACCGCACATAGCTAAAATCAT
Found at i:28191794 original size:2 final size:2
Alignment explanation
Indices: 28191726--28191786 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
28191716 ACATATTTAC
*
28191726 AT AT GT 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
28191768 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
28191787 CGTATATACC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28191856 original size:20 final size:20
Alignment explanation
Indices: 28191799--28191861 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
28191789 TATATACCCA
*
28191799 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
28191818 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
28191838 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
28191858 TCAT
1 TCAT
28191862 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:28191908 original size:43 final size:43
Alignment explanation
Indices: 28191860--28191978 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
28191850 TCACCAGCTC
** *
28191860 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGATT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGATT
*
28191903 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGATT
* * *
28191946 ATGCACACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
28191979 ACATAATTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGATT
Found at i:28199724 original size:20 final size:20
Alignment explanation
Indices: 28199667--28199729 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
28199657 TATATACCCA
*
28199667 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
28199686 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
28199706 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
28199726 TCAT
1 TCAT
28199730 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:28199776 original size:43 final size:43
Alignment explanation
Indices: 28199728--28199846 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
28199718 TCACCAGCTC
** *
28199728 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGATT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGATT
*
28199771 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGATT
* * *
28199814 ATGCACACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
28199847 ACATAATTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGATT
Done.