Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 43 of 206
Found at i:12300243 original size:27 final size:28
Alignment explanation
Indices: 12300195--12300251 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
12300185 ATTGAATTTT
* *
12300195 ATTTTTTATTTTTATTCAATATATAATTA
1 ATTTTTAATTTTTATT-AATATAAAATTA
12300224 ATTTTTAATTTTTATT-ATATAAAATTA
1 ATTTTTAATTTTTATTAATATAAAATTA
12300251 A
1 A
12300252 ATATTGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 11 0.42
29 15 0.58
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTTAATTTTTATTAATATAAAATTA
Found at i:12309227 original size:18 final size:17
Alignment explanation
Indices: 12309192--12309257 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 17
12309182 CTCGTCATGA
12309192 TCATCATTATCATC-ATCT
1 TCATC-TTATC-TCTATCT
12309210 TCATCTCTATCTCTATCT
1 TCATCT-TATCTCTATCT
* * *
12309228 CCAATGTTATCTTTATCT
1 TC-ATCTTATCTCTATCT
12309246 TCATCTTCATCT
1 TCATCTT-ATCT
12309258 TGTTTTTCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.18
18 29 0.74
19 3 0.08
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
TCATCTTATCTCTATCT
Found at i:12312854 original size:28 final size:28
Alignment explanation
Indices: 12312822--12312902 Score: 72
Period size: 33 Copynumber: 2.7 Consensus size: 28
12312812 CCATTTCCAG
*
12312822 TATCAGTGTGGGCTTTAGCCCAATACAA
1 TATCAGTGTGGGCTTTAGCCCAACACAA
* *
12312850 TATCAGAACAGTGTGGGCCTTAGCCCAACATAA
1 TAT-----CAGTGTGGGCTTTAGCCCAACACAA
* *
12312883 TAACAGTGTGGGCTTAAGCC
1 TATCAGTGTGGGCTTTAGCC
12312903 TGTTATAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
28 18 0.43
33 24 0.57
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (28 bp):
TATCAGTGTGGGCTTTAGCCCAACACAA
Found at i:12313109 original size:27 final size:27
Alignment explanation
Indices: 12313066--12313130 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
12313056 AGCCGAGCTG
*
12313066 CCAGT-ACAGTATATGTGGCATAGCCA
1 CCAGTAACAGTATATGTGGCAGAGCCA
12313092 CCAGTAACAGTGAT-TGTGGCAGAGCCA
1 CCAGTAACAGT-ATATGTGGCAGAGCCA
*
12313119 CCAGAAACAGTA
1 CCAGTAACAGTA
12313131 CTTCCTCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 6 0.17
27 27 0.77
28 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCAGAGCCA
Found at i:12313331 original size:27 final size:27
Alignment explanation
Indices: 12313287--12313367 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
12313277 CCGGTCAATC
*
12313287 TACCCTTCTGGAGGTATTTCAATAATTT
1 TACCCTAC-GGAGGTATTTCAATAATTT
*
12313315 TACCCTACGGAGGTATTTCGATAA-TT
1 TACCCTACGGAGGTATTTCAATAATTT
* *
12313341 TACCC-ATCGGGGGTATTTCAGTAATTT
1 TACCCTA-CGGAGGTATTTCAATAATTT
12313368 ACCTATTGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.02
26 21 0.46
27 17 0.37
28 7 0.15
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (27 bp):
TACCCTACGGAGGTATTTCAATAATTT
Found at i:12313355 original size:26 final size:26
Alignment explanation
Indices: 12313299--12313678 Score: 371
Period size: 26 Copynumber: 14.6 Consensus size: 26
12313289 CCCTTCTGGA
*
12313299 GGTATTTCAATAATTTTACCC-TACG-G
1 GGTATTTCGATAA-TTTACCCAT-CGAG
*
12313325 AGGTATTTCGATAATTTACCCATCGGG
1 -GGTATTTCGATAATTTACCCATCGAG
* *
12313352 GGTATTTC-AGTAATTTACCTATTGAG
1 GGTATTTCGA-TAATTTACCCATCGAG
* * *
12313378 AGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
12313404 GGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
* **
12313430 GGTATTTTGGCAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
*
12313456 GGT-TTTCGATAATTTACCCATTGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
12313481 GGTATTTCTG-TGATTTACCCATTGAG
1 GGTATTTC-GATAATTTACCCATCGAG
*
12313507 GGTATTTCTG-TGATTTACCCATCGAG
1 GGTATTTC-GATAATTTACCCATCGAG
*
12313533 GGTATTTCGATAATTTACCCATCGAT
1 GGTATTTCGATAATTTACCCATCGAG
* *
12313559 GGTATTTC-AGTAATTTACCTATTGAG
1 GGTATTTCGA-TAATTTACCCATCGAG
**
12313585 GGTATTTCTG-TAATTTACCCATTAAG
1 GGTATTTC-GATAATTTACCCATCGAG
* * * *
12313611 GGTATTTTGGTAATTTACACATTGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
12313637 GGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
12313663 GGTATTTTGGTAATTT
1 GGTATTTCGATAATTT
12313679 TTATCCGTGT
Statistics
Matches: 313, Mismatches: 29, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
25 25 0.08
26 273 0.87
27 15 0.05
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (26 bp):
GGTATTTCGATAATTTACCCATCGAG
Found at i:12313392 original size:52 final size:52
Alignment explanation
Indices: 12313299--12313678 Score: 428
Period size: 52 Copynumber: 7.3 Consensus size: 52
12313289 CCCTTCTGGA
* ** * * *
12313299 GGTATTTCAATAATTTTACCCTACGGA-GGTATTTCGATAATTTACCCATCGGG
1 GGTATTTCAGTAA-TTTACCC-ATTGAGGGTATTTTGGTAATTTACCCATCGAG
* *
12313352 GGTATTTCAGTAATTTACCTATTGAGAGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
** * *
12313404 GGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGCAATTTACCCATCGAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
* *
12313456 GGT-TTTC-GATAATTTACCCATTGAGGGTATTTCT-GTGATTTACCCATTGAG
1 GGTATTTCAG-TAATTTACCCATTGAGGGTATTT-TGGTAATTTACCCATCGAG
* * * * * *
12313507 GGTATTTCTGTGATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAT
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
* **
12313559 GGTATTTCAGTAATTTACCTATTGAGGGTATTTCT-GTAATTTACCCATTAAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTT-TGGTAATTTACCCATCGAG
** *
12313611 GGTATTTTGGTAATTTACACATTGAGGGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
**
12313663 GGTATTTTGGTAATTT
1 GGTATTTCAGTAATTT
12313679 TTATCCGTGT
Statistics
Matches: 278, Mismatches: 41, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.00
51 46 0.17
52 218 0.78
53 13 0.05
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (52 bp):
GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
Found at i:12313409 original size:78 final size:78
Alignment explanation
Indices: 12313299--12313678 Score: 410
Period size: 78 Copynumber: 4.9 Consensus size: 78
12313289 CCCTTCTGGA
* * *
12313299 GGTATTTCAATAATTTTACCC-TACG-GAGGTATTTCGATAATTTACCCATCGGGGGTATTTCAG
1 GGTATTTCGATAA-TTTACCCAT-CGAG-GGTATTTCGATAATTTACCCATCGAGGGTATTTCGG
* *
12313362 TAATTTACCTATTGAG
63 TAATTTACCCATCGAG
* * * * * * *
12313378 AGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGCAA
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAGGGTATTTCGGTAA
12313443 TTTACCCATCGAG
66 TTTACCCATCGAG
* * * * *
12313456 GGT-TTTCGATAATTTACCCATTGAGGGTATTTCTG-TGATTTACCCATTGAGGGTATTTCTGTG
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTC-GATAATTTACCCATCGAGGGTATTTCGGTA
12313519 ATTTACCCATCGAG
65 ATTTACCCATCGAG
* * * *
12313533 GGTATTTCGATAATTTACCCATCGATGGTATTTC-AGTAATTTACCTATTGAGGGTATTTCTGTA
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTCGA-TAATTTACCCATCGAGGGTATTTCGGTA
**
12313597 ATTTACCCATTAAG
65 ATTTACCCATCGAG
* * * * * * *
12313611 GGTATTTTGGTAATTTACACATTGAGGGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGTAA
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAGGGTATTTCGGTAA
12313676 TTT
66 TTT
12313679 TTATCCGTGT
Statistics
Matches: 253, Mismatches: 41, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
77 65 0.26
78 177 0.70
79 11 0.04
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (78 bp):
GGTATTTCGATAATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAGGGTATTTCGGTAA
TTTACCCATCGAG
Found at i:12315419 original size:25 final size:25
Alignment explanation
Indices: 12315391--12315446 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
12315381 ATTCAGGAAT
12315391 GCTCATAAGAGCACATA-AACGAGAA
1 GCTCATAAGAGC-CATATAACGAGAA
* ** *
12315416 GCTCTTCCGAGCCATATAACGGGAA
1 GCTCATAAGAGCCATATAACGAGAA
12315441 GCTCAT
1 GCTCAT
12315447 GTGAGCCAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (25 bp):
GCTCATAAGAGCCATATAACGAGAA
Found at i:12315597 original size:25 final size:25
Alignment explanation
Indices: 12315561--12315636 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
12315551 CCGGAAAGCC
12315561 ATTAATCAGGAAGCTCATAAGAGCTA
1 ATTAA-CAGGAAGCTCATAAGAGCTA
* * ** *
12315587 ATTATCGGGAAGCTCCGAAGAGCCA
1 ATTAACAGGAAGCTCATAAGAGCTA
12315612 ATTAACAGGACA-CTCATAAGAGCTA
1 ATTAACAGGA-AGCTCATAAGAGCTA
12315637 CGGTGTGTCC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
25 34 0.87
26 5 0.13
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (25 bp):
ATTAACAGGAAGCTCATAAGAGCTA
Found at i:12315598 original size:50 final size:50
Alignment explanation
Indices: 12315540--12315636 Score: 146
Period size: 50 Copynumber: 1.9 Consensus size: 50
12315530 AGAGCCTTTA
12315540 ATCGGGAAGCTCCGGAA-AGCC-ATTAATCAGGA-AGCTCATAAGAGCTAATT
1 ATCGGGAAGCTCC-GAAGAGCCAATTAA-CAGGACA-CTCATAAGAGCTAATT
12315590 ATCGGGAAGCTCCGAAGAGCCAATTAACAGGACACTCATAAGAGCTA
1 ATCGGGAAGCTCCGAAGAGCCAATTAACAGGACACTCATAAGAGCTA
12315637 CGGTGTGTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
49 3 0.07
50 35 0.80
51 6 0.14
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (50 bp):
ATCGGGAAGCTCCGAAGAGCCAATTAACAGGACACTCATAAGAGCTAATT
Found at i:12317705 original size:13 final size:13
Alignment explanation
Indices: 12317689--12317726 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
12317679 AAAATTCTTT
12317689 AAAAAA-TGTAAA
1 AAAAAATTGTAAA
12317701 AAAAAATTGTTAAA
1 AAAAAATTG-TAAA
*
12317715 TAAAAATTGTAA
1 AAAAAATTGTAA
12317727 TATTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (13 bp):
AAAAAATTGTAAA
Found at i:12323249 original size:20 final size:20
Alignment explanation
Indices: 12323207--12323249 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
12323197 AATTCGACCA
*
12323207 TCACATATTCATTTCACATT
1 TCACATATTCATTTCAAATT
*
12323227 TCACAT-TTCGTTTCAAATAT
1 TCACATATTCATTTCAAAT-T
12323247 TCA
1 TCA
12323250 TATCAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.44
Consensus pattern (20 bp):
TCACATATTCATTTCAAATT
Found at i:12327891 original size:20 final size:20
Alignment explanation
Indices: 12327849--12327891 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
12327839 AATTCAACCA
*
12327849 TCACATATTCATTTCACATT
1 TCACATATTCATTTCAAATT
*
12327869 TCACAT-TTCGTTTCAAATAT
1 TCACATATTCATTTCAAAT-T
12327889 TCA
1 TCA
12327892 TATCAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.44
Consensus pattern (20 bp):
TCACATATTCATTTCAAATT
Found at i:12330089 original size:19 final size:19
Alignment explanation
Indices: 12330065--12330102 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12330055 CCACTATCAC
12330065 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
12330084 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
12330103 TATTAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:12333703 original size:17 final size:18
Alignment explanation
Indices: 12333681--12333718 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12333671 TATTCTGCTA
12333681 TTTCAA-ATTTCTTTTAG
1 TTTCAACATTTCTTTTAG
* *
12333698 TTTCAACATTTTTTTTTG
1 TTTCAACATTTCTTTTAG
12333716 TTT
1 TTT
12333719 AATTACTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTCAACATTTCTTTTAG
Found at i:12336132 original size:36 final size:36
Alignment explanation
Indices: 12336092--12336170 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
12336082 GGAGCCATTA
*
12336092 GTGTGTTATCAGGTAGATT-GCTCTTATGAGCATCTG
1 GTGTGTT-TCAGATAGATTAGCTCTTATGAGCATCTG
* *
12336128 GTGTGTTTCAGATGGATTAGCTCTTATGATCATCTG
1 GTGTGTTTCAGATAGATTAGCTCTTATGAGCATCTG
12336164 GTGTGTT
1 GTGTGTT
12336171 CCAGTTGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 9 0.23
36 30 0.77
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.42
Consensus pattern (36 bp):
GTGTGTTTCAGATAGATTAGCTCTTATGAGCATCTG
Found at i:12338964 original size:43 final size:43
Alignment explanation
Indices: 12338885--12339035 Score: 205
Period size: 43 Copynumber: 3.5 Consensus size: 43
12338875 TGTCTTGTTC
* * *
12338885 TTTAGCGGCACTTTCCCCACAAACGCTGCTAAAGGTCATGACT
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
* * * *
12338928 TTTAGCGGCTCTTTTCCCGCAAATGCCGCTATAGGTCATGACC
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
*
12338971 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGATCATGACT
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
**
12339014 TTTAGCGGTGC-TTTCCCACAAA
1 TTTAGCGGCACTTTTCCCACAAA
12339036 TGCTACTATT
Statistics
Matches: 94, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 11 0.12
43 83 0.88
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
Found at i:12339065 original size:86 final size:86
Alignment explanation
Indices: 12338884--12339044 Score: 236
Period size: 86 Copynumber: 1.9 Consensus size: 86
12338874 TTGTCTTGTT
* * *
12338884 CTTTAGCGGCACTTTCCCCACAAACGCTGCTAAAGGTCATGACTTTTAGCGGCTCTTTTCCCGCA
1 CTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGATCATGACTTTTAGCGGCTCTTTTCCCACA
*
12338949 AATGCCGCTATAGGTCATGAC
66 AATGCCACTATAGGTCATGAC
* *
12338970 CTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGG-TGC-TTTCCCAC
1 CTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGATCATGACTTTTAGCGGCT-CTTTTCCCAC
*
12339033 AAATGCTACTAT
65 AAATGCCACTAT
12339045 TGTTTGGTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
85 18 0.27
86 49 0.73
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (86 bp):
CTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGATCATGACTTTTAGCGGCTCTTTTCCCACA
AATGCCACTATAGGTCATGAC
Found at i:12339783 original size:21 final size:21
Alignment explanation
Indices: 12339759--12339802 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12339749 TGTTTATATA
12339759 TAAGTT-TCTATATAAGTTATG
1 TAAGTTAT-TATATAAGTTATG
*
12339780 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTTATG
12339801 TA
1 TA
12339803 TTATGTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAGTTATTATATAAGTTATG
Found at i:12339790 original size:12 final size:12
Alignment explanation
Indices: 12339775--12339799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12339765 TCTATATAAG
12339775 TTATGTAAGTTA
1 TTATGTAAGTTA
12339787 TTATGTAAGTTA
1 TTATGTAAGTTA
12339799 T
1 T
12339800 GTATTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:12339957 original size:17 final size:18
Alignment explanation
Indices: 12339927--12339982 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
12339917 TTTGAAAAAA
*
12339927 TATATAAATTTTAAATAAG
1 TATAT-AATATTAAATAAG
12339946 TATAT-ATATTAAA-AATG
1 TATATAATATTAAATAA-G
12339963 TATATAAATATT-AATAAG
1 TATAT-AATATTAAATAAG
12339981 TA
1 TA
12339983 ATGTAAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.41
18 5 0.16
19 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TATATAATATTAAATAAG
Found at i:12340496 original size:14 final size:14
Alignment explanation
Indices: 12340477--12340506 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12340467 ATCGAAGAGC
*
12340477 AAGATGATTAACTA
1 AAGATGATCAACTA
12340491 AAGATGATCAACTA
1 AAGATGATCAACTA
12340505 AA
1 AA
12340507 AAACCTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (14 bp):
AAGATGATCAACTA
Found at i:12341512 original size:16 final size:16
Alignment explanation
Indices: 12341493--12341543 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
12341483 CTCTGACGAC
12341493 AGAGGAGTGCGACGGT
1 AGAGGAGTGCGACGGT
***
12341509 AGAGGACAACGACGGT
1 AGAGGAGTGCGACGGT
* *
12341525 TGACGAGTGCGACGGT
1 AGAGGAGTGCGACGGT
12341541 AGA
1 AGA
12341544 TGAGCAACGA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.43, T:0.12
Consensus pattern (16 bp):
AGAGGAGTGCGACGGT
Found at i:12342086 original size:41 final size:41
Alignment explanation
Indices: 12342013--12342245 Score: 360
Period size: 41 Copynumber: 5.6 Consensus size: 41
12342003 CTTTCGGGGA
12342013 TTTAGCGGCGTTTTTAAGG-AAAGCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTT--GGAAAAGCGCCGCTAATGCTCAGATC
* *
12342055 TTTAGCGGTGTTTTTGGAAAAGCGCCGCTAATGCCCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
*
12342096 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
* *
12342137 TTTAGCGGCGTTTTTGGAAAAGCGCCACTAATGGTCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
*
12342178 TTTAGCGGCGTTTTTGAAAGAAGCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAATGCTCAGATC
* *
12342220 TTTAGCGGCATTTTTGAAAAAGCGCC
1 TTTAGCGGCGTTTTTGGAAAAGCGCC
12342246 ACAAAAACAT
Statistics
Matches: 179, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
40 2 0.01
41 125 0.70
42 52 0.29
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
Found at i:12342392 original size:26 final size:26
Alignment explanation
Indices: 12342344--12342394 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
12342334 AAAATGGATA
** * *
12342344 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
12342370 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
12342395 ATTATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:12343868 original size:19 final size:19
Alignment explanation
Indices: 12343844--12343890 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
12343834 ATGGAATCTG
12343844 TTATAAATTAGAATGCCTA
1 TTATAAATTAGAATGCCTA
*
12343863 TTATAAACTAGAATGCCTA
1 TTATAAATTAGAATGCCTA
12343882 TTATAAATT
1 TTATAAATT
12343891 TTGGTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATAAATTAGAATGCCTA
Found at i:12344321 original size:8 final size:8
Alignment explanation
Indices: 12344308--12344332 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12344298 TATATCCCCT
12344308 TGGTTAAA
1 TGGTTAAA
12344316 TGGTTAAA
1 TGGTTAAA
12344324 TGGTTAAA
1 TGGTTAAA
12344332 T
1 T
12344333 TTTTTTTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (8 bp):
TGGTTAAA
Found at i:12347402 original size:43 final size:43
Alignment explanation
Indices: 12347306--12347567 Score: 263
Period size: 43 Copynumber: 6.3 Consensus size: 43
12347296 AGATTATGTT
* * * * * * *
12347306 TTTAGCGGCGTTTTTGCGAGAAGCGCCACAAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
12347348 TTTAGCGGCGTTTGTGAAAAAAGCGCGGCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
12347391 TATAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGCCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
12347433 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGATC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
12347476 TTTTGCAGCGTTTGTGATAAAAGCGCCGC-------CATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
12347512 TTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGGTT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
12347555 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
12347568 ATTTCTAAAA
Statistics
Matches: 178, Mismatches: 33, Indels: 17
0.78 0.14 0.07
Matches are distributed among these distances:
36 29 0.16
42 64 0.36
43 85 0.48
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:12347566 original size:79 final size:81
Alignment explanation
Indices: 12347346--12347567 Score: 254
Period size: 79 Copynumber: 2.7 Consensus size: 81
12347336 AAAGGTTTGT
** * * * * *
12347346 TCTTTAGCGGCGTTTGTGAAAAAAGCGCGGCTAAAGATCATGGTCTATAGCGGCGTTTGTGGGAA
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTTGTGGAAA
12347411 AGCGCCGCTAAAGGCCATGG
66 AGCGCCGC---A-GCCATGG
* * * *
12347431 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGATCTTTT-GCAGCGTTTGTGATA
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT-TTTTAGCGGCGTTTGTG-GA
12347495 AAAGCG-C-C-GCCATGG
64 AAAGCGCCGCAGCCATGG
*
12347510 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGGTTTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTT
12347568 ATTTCTAAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
78 4 0.03
79 56 0.47
84 1 0.01
85 50 0.42
86 8 0.07
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (81 bp):
TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTTGTGGAAA
AGCGCCGCAGCCATGG
Found at i:12348063 original size:48 final size:48
Alignment explanation
Indices: 12348005--12348110 Score: 187
Period size: 47 Copynumber: 2.2 Consensus size: 48
12347995 TTTTAATACA
*
12348005 TAGTTTTTTAAAGTTATATTTATAAAAATTAGATAAAATTAAAAATTT
1 TAGTTTTTTAAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
12348053 TAGTTTTTT-AAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
1 TAGTTTTTTAAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
12348100 TAGTGTTTTTA
1 TAGT-TTTTTA
12348111 TTTCATTTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
47 41 0.75
48 14 0.25
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (48 bp):
TAGTTTTTTAAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
Found at i:12348124 original size:25 final size:26
Alignment explanation
Indices: 12348096--12348148 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
12348086 AAAATTAAAA
*
12348096 ATTTTAGTGTTTTTATTTCATTT-TT
1 ATTTTAGTATTTTTATTTCATTTCTT
* *
12348121 ATTTTTGTATTTTTATTTTATTTCTT
1 ATTTTAGTATTTTTATTTCATTTCTT
12348147 AT
1 AT
12348149 AATTTGGTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.74
Consensus pattern (26 bp):
ATTTTAGTATTTTTATTTCATTTCTT
Found at i:12348894 original size:22 final size:22
Alignment explanation
Indices: 12348841--12348897 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
12348831 ACCCCTGAAA
*
12348841 CCTTAAA-CCCTAAATCTTTAAC
1 CCTTAAACCCCT-AATCTATAAC
* *
12348863 TCTT-AACCCCTAATGTATAAC
1 CCTTAAACCCCTAATCTATAAC
12348884 CCTTAAACCCCTAA
1 CCTTAAACCCCTAA
12348898 CCCCTAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (22 bp):
CCTTAAACCCCTAATCTATAAC
Found at i:12348962 original size:15 final size:14
Alignment explanation
Indices: 12348927--12348964 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
12348917 AACCCTTAAT
12348927 TAAAT-CATAATCC
1 TAAATCCATAATCC
*
12348940 TTAATCCATAATCCC
1 TAAATCCATAAT-CC
12348955 TAAATCCATA
1 TAAATCCATA
12348965 TATACTCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 6 0.29
15 11 0.52
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATCCATAATCC
Found at i:12349293 original size:16 final size:15
Alignment explanation
Indices: 12349255--12349309 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 15
12349245 TTTTCTGAAG
12349255 ATTTTAAAT-ATTCA
1 ATTTTAAATAATTCA
**
12349269 ATTAGAAATAAGTTCA
1 ATTTTAAATAA-TTCA
12349285 ATTTTAAATAATT-A
1 ATTTTAAATAATTCA
*
12349299 A-TATAAATAAT
1 ATTTTAAATAAT
12349310 AAACCAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 9 0.26
14 9 0.26
15 3 0.09
16 13 0.38
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (15 bp):
ATTTTAAATAATTCA
Found at i:12349383 original size:41 final size:40
Alignment explanation
Indices: 12349336--12349711 Score: 265
Period size: 41 Copynumber: 9.2 Consensus size: 40
12349326 AATATTTTTT
* *
12349336 GCGGCGCTTTAAAAAGAACGACTCTAAAACCCCGAGCATTA
1 GCGGCGCTTTTAAAA-AACGCCTCTAAAACCCCGAGCATTA
* * * *
12349377 GTGGCGCTTTCTCAAAAATGCCAT-TAAAACCCCGACCATTA
1 GCGGCGCTTT-TAAAAAACGCC-TCTAAAACCCCGAGCATTA
* * *
12349418 GCGGCGCTTTTTAGAAAACGCCGCTAAAACCTCGAGCATTA
1 GCGGCGC-TTTTAAAAAACGCCTCTAAAACCCCGAGCATTA
* *
12349459 GCGGCGCTTCTTAAAAAATG-CTGCTAAAACCCAGAGCATTA
1 GCGGCGCTT-TTAAAAAACGCCT-CTAAAACCCCGAGCATTA
** * * *
12349500 GTAGCGCTTTAACAAAAACGCCGCTAAAACCCAGAGCATTA
1 GCGGCGCTTTTA-AAAAACGCCTCTAAAACCCCGAGCATTA
* ** * * **
12349541 GCGACGCTTCCACAAAAACGCCGCTTAAACCTTGAGCATTA
1 GCGGCGCTTTTA-AAAAACGCCTCTAAAACCCCGAGCATTA
* * * *
12349582 GCGGCGCTTTCACAAAAACGCCGCTGAAACCCAGAGCATTA
1 GCGGCGCTTTTA-AAAAACGCCTCTAAAACCCCGAGCATTA
* ** * *
12349623 GCGGTGCTTCCACAAAAACGTCGT-TAAAA-CCAGAGCATTA
1 GCGGCGCTTTTA-AAAAACG-CCTCTAAAACCCCGAGCATTA
* * ** * *
12349663 GCGGCGCTTTATCAAAAACACAGCTAAAACTCCGATCATTA
1 GCGGCGCTTT-TAAAAAACGCCTCTAAAACCCCGAGCATTA
*
12349704 GCGACGCT
1 GCGGCGCT
12349712 AATCCAAAAA
Statistics
Matches: 271, Mismatches: 52, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
39 1 0.00
40 35 0.13
41 226 0.83
42 9 0.03
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.20
Consensus pattern (40 bp):
GCGGCGCTTTTAAAAAACGCCTCTAAAACCCCGAGCATTA
Found at i:12349476 original size:82 final size:81
Alignment explanation
Indices: 12349336--12349711 Score: 359
Period size: 82 Copynumber: 4.6 Consensus size: 81
12349326 AATATTTTTT
* * * * * * * *
12349336 GCGGCGCTTT-AAAAAGAACGACTCTAAAACCCCGAGCATTAGTGGCGCTTTCTCAAAAATGCCA
1 GCGGCGCTTTCACAAA-AACGCCGCTAAAA-CCCGAGCATTAGCGGCGCTTCCACAAAAACGCCG
* *
12349400 TTAAAACCCCGACCATTA
64 TTAAAACCCAGAGCATTA
* * * * *
12349418 GCGGCGCTTTTTA-GAAAACGCCGCTAAAACCTCGAGCATTAGCGGCGCTTCTTA-AAAAATGCT
1 GCGGCGC-TTTCACAAAAACGCCGCTAAAACC-CGAGCATTAGCGGCGCTTC-CACAAAAACGCC
*
12349481 GCTAAAACCCAGAGCATTA
63 GTTAAAACCCAGAGCATTA
** * *
12349500 GTAGCGCTTTAACAAAAACGCCGCTAAAACCCAGAGCATTAGCGACGCTTCCACAAAAACGCCGC
1 GCGGCGCTTTCACAAAAACGCCGCTAAAACCC-GAGCATTAGCGGCGCTTCCACAAAAACGCCG-
**
12349565 TT-AAACCTTGAGCATTA
64 TTAAAACCCAGAGCATTA
* * *
12349582 GCGGCGCTTTCACAAAAACGCCGCTGAAACCCAGAGCATTAGCGGTGCTTCCACAAAAACGTCGT
1 GCGGCGCTTTCACAAAAACGCCGCTAAAACCC-GAGCATTAGCGGCGCTTCCACAAAAACGCCGT
12349647 TAAAA-CCAGAGCATTA
65 TAAAACCCAGAGCATTA
* * * *
12349663 GCGGCGCTTT-ATCAAAAACACAGCTAAAACTCCGATCATTAGCGACGCT
1 GCGGCGCTTTCA-CAAAAACGCCGCTAAAAC-CCGAGCATTAGCGGCGCT
12349712 AATCCAAAAA
Statistics
Matches: 245, Mismatches: 38, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
80 1 0.00
81 57 0.23
82 180 0.73
83 6 0.02
84 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.20
Consensus pattern (81 bp):
GCGGCGCTTTCACAAAAACGCCGCTAAAACCCGAGCATTAGCGGCGCTTCCACAAAAACGCCGTT
AAAACCCAGAGCATTA
Found at i:12349559 original size:123 final size:122
Alignment explanation
Indices: 12349336--12349731 Score: 406
Period size: 123 Copynumber: 3.2 Consensus size: 122
12349326 AATATTTTTT
* * * * * * *
12349336 GCGGCGCTTT-AAAAAGAACGACTCTAAAACCCCGAGCATTAGTGGCGCTTTCTCAAAAATGCCA
1 GCGGCGCTTTCACAAA-AACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCG
* * **
12349400 TTAAAACCCCGACCATTAGCGGCGCTTTTTAGAAAACGCCGCTAAAACCTCGAGCATTA
65 TTAAAACCCAGAGCATTAGCGGCGCTTTACA-AAAACGCCGCTAAAACCTCGAGCATTA
* * * * *
12349459 GCGGCGCTTCTTA-AAAAATGCTGCTAAAACCCAGAGCATTAGTAGCGCTTTAACAAAAACGCCG
1 GCGGCGCTT-TCACAAAAACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCG
* * * * *
12349523 CTAAAACCCAGAGCATTAGCGACGCTTCCACAAAAACGCCGCTTAAACCTTGAGCATTA
65 TTAAAACCCAGAGCATTAGCGGCGCTT-TACAAAAACGCCGCTAAAACCTCGAGCATTA
* * * * *
12349582 GCGGCGCTTTCACAAAAACGCCGCTGAAACCCAGAGCATTAGCGGTGCTTCCACAAAAACGTCGT
1 GCGGCGCTTTCACAAAAACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCGT
* * *
12349647 TAAAA-CCAGAGCATTAGCGGCGCTTTATCAAAAACACAGCTAAAA-CTCCGATCATTA
66 TAAAACCCAGAGCATTAGCGGCGCTTTA-CAAAAACGCCGCTAAAACCT-CGAGCATTA
* * *
12349704 GCGACGCTAATC-CAAAAACGCCACTAAA
1 GCGGCGCT-TTCACAAAAACGCCGCTAAA
12349732 GCCATCGAAG
Statistics
Matches: 225, Mismatches: 41, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
121 3 0.01
122 63 0.28
123 153 0.68
124 5 0.02
125 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (122 bp):
GCGGCGCTTTCACAAAAACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCGT
TAAAACCCAGAGCATTAGCGGCGCTTTACAAAAACGCCGCTAAAACCTCGAGCATTA
Found at i:12361320 original size:28 final size:29
Alignment explanation
Indices: 12361296--12361350 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
12361286 TTAATTATCT
*
12361296 CAATGTTATTATCATTATCA-TATTATAC
1 CAATATTATTATCATTATCATTATTATAC
* *
12361324 CAATATTATTATTATTATTATTATTAT
1 CAATATTATTATCATTATCATTATTAT
12361351 TTATTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (29 bp):
CAATATTATTATCATTATCATTATTATAC
Found at i:12361335 original size:3 final size:3
Alignment explanation
Indices: 12361327--12361351 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12361317 ATTATACCAA
12361327 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
12361352 TATTCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12361376 original size:7 final size:7
Alignment explanation
Indices: 12361366--12361390 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12361356 CATTTATAAT
12361366 TTTTAAA
1 TTTTAAA
12361373 TTTTAAA
1 TTTTAAA
12361380 TTTTAAA
1 TTTTAAA
12361387 TTTT
1 TTTT
12361391 GTTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:12361688 original size:13 final size:15
Alignment explanation
Indices: 12361653--12361689 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12361643 TATGCTTACT
12361653 TATATATTTATATACA
1 TATAT-TTTATATACA
12361669 TATATTTTATATA-A
1 TATATTTTATATACA
12361683 TA-ATTTT
1 TATATTTT
12361690 GAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 3 0.14
15 8 0.38
16 5 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTTTATATACA
Found at i:12361747 original size:2 final size:2
Alignment explanation
Indices: 12361735--12361767 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12361725 TAATTTTATG
*
12361735 TA TA TA CA 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 TA TA T
12361768 CTTTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12362174 original size:109 final size:109
Alignment explanation
Indices: 12361978--12363074 Score: 1919
Period size: 109 Copynumber: 10.1 Consensus size: 109
12361968 TACACCTACT
*
12361978 AATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
12362043 CAAATGTGCTGGGTTTCTATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
*
12362087 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
12362152 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
12362196 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
12362261 CAAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGTCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* *
12362305 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAAGGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
*
12362370 CTAATGTGCTGGGTTTCAATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
12362414 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
12362479 CTAATGTGCTGGGTTTCGAGTTTTCTCGTTCGACAAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* **
12362523 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTAAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* * * *
12362588 CTAATATGCTGGGTTTCAATTTTTCTCGTTCAATCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* *
12362632 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAATTTTGAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
*
12362697 CAAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* *
12362741 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAATGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
12362806 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
*
12362850 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* * *
12362915 CTTATGTGCTGGGTTTCGATTTTTCTCATTTGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
*
12362959 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
*
12363024 CTAATGTGCTGGGTTTCG--GTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
12363066 AATATCCTT
1 AATATCCTT
12363075 CTAAATTTTA
Statistics
Matches: 940, Mismatches: 48, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
107 30 0.03
109 910 0.97
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (109 bp):
AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
Found at i:12367083 original size:25 final size:24
Alignment explanation
Indices: 12367037--12367083 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
12367027 ACTAATATCA
* * *
12367037 CAAATCACAAATTATCATCAATGG
1 CAAAACACAAATAATCAACAATGG
12367061 CAAAACACAAAATAATCAACAAT
1 CAAAACAC-AAATAATCAACAAT
12367084 TACAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.55, C:0.21, G:0.04, T:0.19
Consensus pattern (24 bp):
CAAAACACAAATAATCAACAATGG
Found at i:12367792 original size:77 final size:77
Alignment explanation
Indices: 12367707--12368106 Score: 382
Period size: 77 Copynumber: 5.2 Consensus size: 77
12367697 AGGAATAATC
** * * *
12367707 ACTTAATACATGAAATGTTGGTGAAAACATGAAAAGATTTTTAAAAAATTAAGTAATTCGTAAAT
1 ACTTAATACATGAAATGTTACTTAAAACATGAAAAGATTTCTAAGAAATTAAGTAATTCGTAAAT
*
12367772 CAT-AAACGAATC
66 CATGAAA-GAATT
** * * *
12367784 ACTTAATACATGAAATGTTACTTAAAATGTGAAAAAAGTTTCTAAGAAATTAAATAATTCTTAAA
1 ACTTAATACATGAAATGTTACTTAAAACATGAAAAGA-TTTCTAAGAAATTAAGTAATTCGTAAA
*
12367849 TCATGTAA-AATT
65 TCATGAAAGAATT
* * * ** * * *
12367861 ACTTAAAACAT-TAACGATTA-TGTAAAACATGAAGTGGTTTCTAAGAAATTAAGTTATTCCTAA
1 ACTTAATACATGAAATG-TTACT-TAAAACATGAAAAGATTTCTAAGAAATTAAGTAATTCGTAA
12367924 ATCATGAAAGAATT
64 ATCATGAAAGAATT
* * ** * * *
12367938 ACTTAATCCATTAAATGTTACTTAAAACATGAAAAGGCTTCCAAGAAATTAATTAATTCATAAAA
1 ACTTAATACATGAAATGTTACTTAAAACATGAAAAGATTTCTAAGAAATTAAGTAATTCGT-AAA
*
12368003 TTA-GAAA-ATATT
65 TCATGAAAGA-ATT
* * * * *
12368015 ACTTAATATATAAAATTTTACTTAAAACATGAAATGATTTTTAAGAAATTAAGTAATTCCG-AAA
1 ACTTAATACATGAAATGTTACTTAAAACATGAAAAGATTTCTAAGAAATTAAGTAATT-CGTAAA
*
12368079 TCATGGAAGAATT
65 TCATGAAAGAATT
12368092 ACTTAATACATGAAA
1 ACTTAATACATGAAA
12368107 CATTACATGA
Statistics
Matches: 259, Mismatches: 52, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
76 41 0.16
77 178 0.69
78 38 0.15
79 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (77 bp):
ACTTAATACATGAAATGTTACTTAAAACATGAAAAGATTTCTAAGAAATTAAGTAATTCGTAAAT
CATGAAAGAATT
Found at i:12367942 original size:154 final size:154
Alignment explanation
Indices: 12367730--12368106 Score: 438
Period size: 154 Copynumber: 2.4 Consensus size: 154
12367720 AATGTTGGTG
* * * * *
12367730 AAAACATGAAAAGATTTTTAAAAAATTAAGTAATTCGTAAATCAT-AAACGAATCACTTAATACA
1 AAAACATGAAATGATTTCTAAGAAATTAAGTAATTCCTAAATCATGAAA-GAATTACTTAATACA
** * * * *
12367794 TGAAATGTTACTTAAAATGTGAAAAAAGTTTCTAAGAAATTAAATAATTC-TTAAATCATGTAAA
65 TGAAATGTTACTTAAAACATG-AAAAAGCTTCCAAGAAATTAAATAATTCATAAAATCA-GAAAA
* *
12367858 -ATTACTTAAAACATTAACGATTA-TGT
128 TATTACTTAAAACATAAAAGATTACT-T
* * * *
12367884 AAAACATGAAGTGGTTTCTAAGAAATTAAGTTATTCCTAAATCATGAAAGAATTACTTAATCCAT
1 AAAACATGAAATGATTTCTAAGAAATTAAGTAATTCCTAAATCATGAAAGAATTACTTAATACAT
* * * *
12367949 TAAATGTTACTTAAAACATGAAAAGGCTTCCAAGAAATTAATTAATTCATAAAATTAGAAAATAT
66 GAAATGTTACTTAAAACATGAAAAAGCTTCCAAGAAATTAAATAATTCATAAAATCAGAAAATAT
* * **
12368014 TACTTAATATATAAAATTTTACTT
131 TACTTAAAACATAAAAGATTACTT
* * *
12368038 AAAACATGAAATGATTTTTAAGAAATTAAGTAATTCCGAAATCATGGAAGAATTACTTAATACAT
1 AAAACATGAAATGATTTCTAAGAAATTAAGTAATTCCTAAATCATGAAAGAATTACTTAATACAT
12368103 GAAA
66 GAAA
12368107 CATTACATGA
Statistics
Matches: 186, Mismatches: 33, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
153 28 0.15
154 154 0.83
155 4 0.02
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (154 bp):
AAAACATGAAATGATTTCTAAGAAATTAAGTAATTCCTAAATCATGAAAGAATTACTTAATACAT
GAAATGTTACTTAAAACATGAAAAAGCTTCCAAGAAATTAAATAATTCATAAAATCAGAAAATAT
TACTTAAAACATAAAAGATTACTT
Found at i:12368049 original size:19 final size:19
Alignment explanation
Indices: 12368007--12368049 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
12367997 ATAAAATTAG
* *
12368007 AAAATATTACTTAATATAT
1 AAAATATTACTTAAAACAT
*
12368026 AAAATTTTACTTAAAACAT
1 AAAATATTACTTAAAACAT
*
12368045 GAAAT
1 AAAAT
12368050 GATTTTTAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATATTACTTAAAACAT
Found at i:12368091 original size:27 final size:27
Alignment explanation
Indices: 12368061--12368151 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 27
12368051 ATTTTTAAGA
*
12368061 AATTAAGTAATTCCGAAATCATGGAAG
1 AATTAAGTAATTCAGAAATCATGGAAG
** *
12368088 AATTACTTAATACATGAAACATTACAT-GAATG
1 AATTAAGTAATTCA-G-AA-A-T-CATGGAA-G
*
12368120 AATTAAGTAATTCATAAATCATGGAAG
1 AATTAAGTAATTCAGAAATCATGGAAG
12368147 AATTA
1 AATTA
12368152 CTTAATATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
27 19 0.39
28 5 0.10
29 3 0.06
30 3 0.06
31 4 0.08
32 15 0.31
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (27 bp):
AATTAAGTAATTCAGAAATCATGGAAG
Found at i:12368592 original size:41 final size:41
Alignment explanation
Indices: 12368494--12368638 Score: 98
Period size: 41 Copynumber: 3.5 Consensus size: 41
12368484 AGACTTCGAG
** * *
12368494 GAAGCTTGATAGGCTCAAGGCCTGATATGATACATCGGCAC
1 GAAGCTTGATAGGCTCAAGGCCAAAAATGATACACCGGCAC
* * * *
12368535 AAAGCCT-ACTAAGCTCAAGGCCCAAAAAT-ATATACCGGCAC
1 GAAGCTTGA-TAGGCTCAAGG-CCAAAAATGATACACCGGCAC
* * * ** *
12368576 GAAGCTTGATAGGCTCAAAGCCTAATACAATACGCCGGCAC
1 GAAGCTTGATAGGCTCAAGGCCAAAAATGATACACCGGCAC
* *
12368617 GAA-ATCTGCTAGGCTCAAGGCC
1 GAAGCT-TGATAGGCTCAAGGCC
12368639 TGATATGATA
Statistics
Matches: 79, Mismatches: 20, Indels: 10
0.72 0.18 0.09
Matches are distributed among these distances:
40 7 0.09
41 66 0.84
42 6 0.08
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (41 bp):
GAAGCTTGATAGGCTCAAGGCCAAAAATGATACACCGGCAC
Found at i:12372618 original size:24 final size:23
Alignment explanation
Indices: 12372562--12372720 Score: 127
Period size: 24 Copynumber: 7.0 Consensus size: 23
12372552 TATACATAAA
* *
12372562 AATAGTATATGATAGATCT-AAAT
1 AATAGTA-ATGATAAATTTAAAAT
*
12372585 AAT-G-ATATGATAAGTTTAAAAT
1 AATAGTA-ATGATAAATTTAAAAT
* *
12372607 TATAGTACATGATAAATTTCAAAT
1 AATAGTA-ATGATAAATTTAAAAT
*
12372631 TATCATGT-ATGATAAATTT-AAAT
1 AAT-A-GTAATGATAAATTTAAAAT
*
12372654 AATATTAATGAT-AATTTAAAAT
1 AATAGTAATGATAAATTTAAAAT
12372676 AATAGT-AT-ATTAAATATTAAAAT
1 AATAGTAATGA-TAAAT-TTAAAAT
*
12372699 AATACTAATGATAAATTTAAAA
1 AATAGTAATGATAAATTTAAAA
12372721 CAATGTTAAG
Statistics
Matches: 113, Mismatches: 11, Indels: 24
0.76 0.07 0.16
Matches are distributed among these distances:
20 1 0.01
21 19 0.17
22 25 0.22
23 28 0.25
24 36 0.32
25 2 0.02
26 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (23 bp):
AATAGTAATGATAAATTTAAAAT
Found at i:12372745 original size:46 final size:44
Alignment explanation
Indices: 12372643--12372751 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 44
12372633 TCATGTATGA
* *
12372643 TAAAT-TTAAATAATATTAATGATAATTTAAAATAATAGTATAT
1 TAAATATTAAATAATACTAATGATAATTTAAAACAATAGTATAT
12372686 TAAATATTAAAATAATACTAATGATAAATTTAAAACAAT-GT-TAAGCT
1 TAAATATT-AAATAATACTAATGAT-AATTTAAAACAATAGTAT-A--T
12372733 TAAATATTAAATAATACTA
1 TAAATATTAAATAATACTA
12372752 GATTTAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
43 5 0.09
44 3 0.05
45 18 0.31
46 23 0.40
47 9 0.16
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.38
Consensus pattern (44 bp):
TAAATATTAAATAATACTAATGATAATTTAAAACAATAGTATAT
Found at i:12385416 original size:18 final size:19
Alignment explanation
Indices: 12385383--12385420 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12385373 AGACTCCAGG
*
12385383 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
12385402 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
12385420 T
1 T
12385421 GCCTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:12390167 original size:30 final size:29
Alignment explanation
Indices: 12390131--12390198 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
12390121 TGAATGTAAG
*
12390131 AACTAAATTTACT-AATATAAAAAATATAAA
1 AACTAAATTTAATCAA-AT-AAAAATATAAA
* *
12390161 AACTAAAATTAATCAAATAAAAGTATAAA
1 AACTAAATTTAATCAAATAAAAATATAAA
*
12390190 AATTAAATT
1 AACTAAATT
12390199 CATAACTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 17 0.53
30 13 0.41
31 2 0.06
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.29
Consensus pattern (29 bp):
AACTAAATTTAATCAAATAAAAATATAAA
Found at i:12395469 original size:146 final size:146
Alignment explanation
Indices: 12395177--12395468 Score: 530
Period size: 146 Copynumber: 2.0 Consensus size: 146
12395167 AAATTTCCAC
12395177 CATGTCCTATTTGTAAGAGGACAAATCATGCTAAAAAGGATTGACAATTCAAGGAAAAAGACAAG
1 CATGTCCTATTTGTAAGAGGACAAATCATGCTAAAAAGGATTGACAATTCAAGGAAAAAGACAAG
*
12395242 TCCAAATTTCAGTGTATTTTTTGCCAAAAGTCTGGACATACTGAAAATTTTTGTTGGGTCAAGAA
66 TCCAAATTTCAGTGTATTTTTTGCCAAAAGTCTGGACATACTGAAAATTTTAGTTGGGTCAAGAA
12395307 GAAGCAAGCAAAAAAA
131 GAAGCAAGCAAAAAAA
* * *
12395323 CATGTCCTATTTGTAAGAGGACAAATCATGCTGAAAAGGATTGCCGATTCAAGGAAAAAGACAAG
1 CATGTCCTATTTGTAAGAGGACAAATCATGCTAAAAAGGATTGACAATTCAAGGAAAAAGACAAG
*
12395388 TCCAAATTTCAGTGTATTTTTTTGCCAAAAGTCTGGACATACTGACAATTTTAGTTGGGTCAAGA
66 TCCAAATTTCAGTGTA-TTTTTTGCCAAAAGTCTGGACATACTGAAAATTTTAGTTGGGTCAAGA
12395453 AGAAGCAAGCAAAAAA
130 AGAAGCAAGCAAAAAA
12395469 CCAAGATCAA
Statistics
Matches: 140, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
146 78 0.56
147 62 0.44
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (146 bp):
CATGTCCTATTTGTAAGAGGACAAATCATGCTAAAAAGGATTGACAATTCAAGGAAAAAGACAAG
TCCAAATTTCAGTGTATTTTTTGCCAAAAGTCTGGACATACTGAAAATTTTAGTTGGGTCAAGAA
GAAGCAAGCAAAAAAA
Found at i:12398569 original size:36 final size:35
Alignment explanation
Indices: 12398522--12398640 Score: 134
Period size: 36 Copynumber: 3.3 Consensus size: 35
12398512 ATTCCAACTA
* *
12398522 AAACACACCAGATGATCATAAGAGCTAATCCATCCG
1 AAACACACCAGATGCTCATAAGAGCTAGTCCA-CCG
*
12398558 AAACACACCAGATGCTCATAAGAGCCAGTCCACCTG
1 AAACACACCAGATGCTCATAAGAGCTAGTCCACC-G
*
12398594 ATAACATACCA-ATGGCTCCA-AAGAGCTAGTCCAACCG
1 A-AACACACCAGAT-GCT-CATAAGAGCTAGTCC-ACCG
12398631 AAACACACCA
1 AAACACACCA
12398641 AAACATAGAG
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
35 2 0.03
36 41 0.57
37 24 0.33
38 5 0.07
ACGTcount: A:0.40, C:0.31, G:0.14, T:0.14
Consensus pattern (35 bp):
AAACACACCAGATGCTCATAAGAGCTAGTCCACCG
Found at i:12401170 original size:14 final size:14
Alignment explanation
Indices: 12401151--12401179 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12401141 ATCACTAGAT
12401151 AAATCAAAATTTAA
1 AAATCAAAATTTAA
12401165 AAATCAAAATTTAA
1 AAATCAAAATTTAA
12401179 A
1 A
12401180 CTAAAGATCA
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:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATCAAAATTTAA
Found at i:12401189 original size:19 final size:18
Alignment explanation
Indices: 12401162--12401201 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12401152 AATCAAAATT
12401162 TAAAAATCAAAATTTAAAC
1 TAAAAATC-AAATTTAAAC
* *
12401181 TAAAGATCAATTTTAAAC
1 TAAAAATCAAATTTAAAC
12401199 TAA
1 TAA
12401202 TTACAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (18 bp):
TAAAAATCAAATTTAAAC
Found at i:12402705 original size:21 final size:21
Alignment explanation
Indices: 12402668--12402710 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12402658 TTTCTTTTAT
*
12402668 ATTCAACATAAATTAAACTGA
1 ATTCAAAATAAATTAAACTGA
*
12402689 ATTCAAAATTAAA-TAAATTGA
1 ATTCAAAA-TAAATTAAACTGA
12402710 A
1 A
12402711 ATAACTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (21 bp):
ATTCAAAATAAATTAAACTGA
Found at i:12404645 original size:19 final size:19
Alignment explanation
Indices: 12404621--12404658 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12404611 AAAGTTAATA
12404621 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
12404640 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
12404659 GCGACAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:12411770 original size:18 final size:18
Alignment explanation
Indices: 12411718--12411770 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
12411708 ATTCACCTAA
12411718 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCAAACCCAAGT
* * * *
12411737 ATCCAACCGAAGCCAATT
1 ACCCAACCAAACCCAAGT
*
12411755 ACCCAACCCAACCCAA
1 ACCCAACCAAACCCAA
12411771 CCATAAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.42, C:0.43, G:0.06, T:0.09
Consensus pattern (18 bp):
ACCCAACCAAACCCAAGT
Found at i:12413131 original size:9 final size:9
Alignment explanation
Indices: 12413102--12413159 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
12413092 GTAGTGATTC
12413102 AATTCGGTT
1 AATTCGGTT
* **
12413111 AATTTGAAT
1 AATTCGGTT
*
12413120 AATTCAGTT
1 AATTCGGTT
12413129 AATTCGGTT
1 AATTCGGTT
*
12413138 AATTCGGGT
1 AATTCGGTT
12413147 AATTCGGTT
1 AATTCGGTT
12413156 AATT
1 AATT
12413160 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:12413134 original size:27 final size:27
Alignment explanation
Indices: 12413102--12413159 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
12413092 GTAGTGATTC
*
12413102 AATTCGGTTAATTTGAATAATTCAGTT
1 AATTCGGTTAATTCGAATAATTCAGTT
** *
12413129 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGAATAATTCAGTT
12413156 AATT
1 AATT
12413160 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (27 bp):
AATTCGGTTAATTCGAATAATTCAGTT
Found at i:12415608 original size:16 final size:16
Alignment explanation
Indices: 12415587--12415618 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12415577 TGTCACTCTT
12415587 AATAGGGCCACCAACA
1 AATAGGGCCACCAACA
12415603 AATAGGGCCACCAACA
1 AATAGGGCCACCAACA
12415619 CAATTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.31, G:0.19, T:0.06
Consensus pattern (16 bp):
AATAGGGCCACCAACA
Found at i:12418706 original size:25 final size:26
Alignment explanation
Indices: 12418677--12418732 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 26
12418667 TTCTCATCCC
*
12418677 AAAATCATGACAATTTTA-CCCTGGT
1 AAAATCATGACAATTTTACCCCGGGT
12418702 AAAATCATGACAATTTTACCCCGGGT
1 AAAATCATGACAATTTTACCCCGGGT
12418728 AAAAT
1 AAAAT
12418733 TTTGAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (26 bp):
AAAATCATGACAATTTTACCCCGGGT
Found at i:12420030 original size:41 final size:41
Alignment explanation
Indices: 12419973--12420082 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
12419963 TTTACTTTCA
* *
12419973 GTATCATATCAGGCCTTGAGTCTAGTAGGCTTCGTGCCGGT
1 GTATCATATTAGGCCTTGAGCCTAGTAGGCTTCGTGCCGGT
* * *
12420014 GTATCATATTAGGCCTTGCGCCTAGCAGGTTTCGTGCCGGT
1 GTATCATATTAGGCCTTGAGCCTAGTAGGCTTCGTGCCGGT
12420055 GTATCATATTAGGCCTTGAGCCTA-TAGG
1 GTATCATATTAGGCCTTGAGCCTAGTAGG
12420083 TATATATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 3 0.05
41 59 0.95
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (41 bp):
GTATCATATTAGGCCTTGAGCCTAGTAGGCTTCGTGCCGGT
Found at i:12420569 original size:19 final size:19
Alignment explanation
Indices: 12420545--12420581 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
12420535 TTAGACACCA
12420545 TTTCATG-ATTCAAGTAATG
1 TTTCATGTATT-AAGTAATG
12420564 TTTCATGTATTAAGTAAT
1 TTTCATGTATTAAGTAAT
12420582 TCTTCCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (19 bp):
TTTCATGTATTAAGTAATG
Found at i:12420601 original size:77 final size:77
Alignment explanation
Indices: 12420393--12420618 Score: 253
Period size: 77 Copynumber: 3.0 Consensus size: 77
12420383 AAGAATATTC
* * * * ** ** * * * *
12420393 TTTCATGTTTCCAGTAATATATCATGTATTAAGTTTTTCTTCTGTAATTTAGAAATTATTTAATT
1 TTTCATGATTCAAGTAATGTTTCATGTATTAAGTAATTCTTCCATGATTTTGGAATTACTTAATT
12420458 TCTTAGAAACCA
66 TCTTAGAAACCA
* * *
12420470 TTTCATGATGCAAGT--TGTTTCATATATTAAATAATTCTTCCATGATTTAT-GAATTACTTAA-
1 TTTCATGATTCAAGTAATGTTTCATGTATTAAGTAATTCTTCCATGATTT-TGGAATTACTTAAT
*
12420531 TTCTTTAGACACCA
65 TTC-TTAGAAACCA
12420545 TTTCATGATTCAAGTAATGTTTCATGTATTAAGTAATTCTTCCATGATTTTGGAATTACTTAATT
1 TTTCATGATTCAAGTAATGTTTCATGTATTAAGTAATTCTTCCATGATTTTGGAATTACTTAATT
*
12420610 TCATAGAAA
66 TCTTAGAAA
12420619 ATACGAATTA
Statistics
Matches: 122, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
74 3 0.02
75 56 0.46
76 1 0.01
77 59 0.48
78 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (77 bp):
TTTCATGATTCAAGTAATGTTTCATGTATTAAGTAATTCTTCCATGATTTTGGAATTACTTAATT
TCTTAGAAACCA
Found at i:12420629 original size:26 final size:25
Alignment explanation
Indices: 12420597--12420645 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
12420587 CATGATTTTG
12420597 GAATTACTTAATTTCATAGAAAATAC
1 GAATTACTTAATTTCATA-AAAATAC
*
12420623 GAATTACTTAATTTCTTAAAAAT
1 GAATTACTTAATTTCATAAAAAT
12420646 CATTTCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (25 bp):
GAATTACTTAATTTCATAAAAATAC
Found at i:12420894 original size:16 final size:16
Alignment explanation
Indices: 12420873--12420905 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12420863 AATATATATA
12420873 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
12420889 TTAAGTTTTTTATGTT
1 TTAAGTTTTTTATGTT
12420905 T
1 T
12420906 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (16 bp):
TTAAGTTTTTTATGTT
Found at i:12421028 original size:13 final size:14
Alignment explanation
Indices: 12421005--12421035 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
12420995 TATTTATTTA
12421005 TTTTTATGTTTAAG
1 TTTTTATGTTTAAG
12421019 TTTTTA-GTTTAAG
1 TTTTTATGTTTAAG
12421032 TTTT
1 TTTT
12421036 CAATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (14 bp):
TTTTTATGTTTAAG
Found at i:12421270 original size:19 final size:18
Alignment explanation
Indices: 12421227--12421271 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
12421217 CTTATTTGTT
12421227 TACAAAAATATTTGATAA
1 TACAAAAATATTTGATAA
12421245 TACAAAAATATTTGATAA
1 TACAAAAATATTTGATAA
12421263 TACAAAAAT
1 TACAAAAAT
12421272 GTAAACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (18 bp):
TACAAAAATATTTGATAA
Found at i:12421323 original size:16 final size:16
Alignment explanation
Indices: 12421302--12421340 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12421292 ATTTTGTTAC
*
12421302 AACAATTAATATAATT
1 AACAATTAATACAATT
12421318 AACAATTAATACAATT
1 AACAATTAATACAATT
*
12421334 AATAATT
1 AACAATT
12421341 TGATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:12421435 original size:22 final size:23
Alignment explanation
Indices: 12421410--12421459 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
12421400 AATAATTTGA
* * *
12421410 TAATTTTA-CTAACAATTAGTTT
1 TAATTTTATCAAAAAATTAATTT
12421432 TAATTTTATCAAAAAATTAATTT
1 TAATTTTATCAAAAAATTAATTT
12421455 TAATT
1 TAATT
12421460 AAAAACGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATTTTATCAAAAAATTAATTT
Found at i:12421450 original size:66 final size:68
Alignment explanation
Indices: 12421319--12421452 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 68
12421309 AATATAATTA
* *
12421319 ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGATTTTATCACAAAAATT
12421384 AAT
66 AAT
*
12421387 ACAATT-A-ACAATTAATAATTTGATAATTTTACTAA-CAATTAGTTTTA-ATTTTATCA-AAAA
1 ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAA--A-TGTTAGATTTTATCACAAAA
12421447 ATTAAT
63 ATTAAT
12421453 TTTAATTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
65 3 0.05
66 37 0.62
67 10 0.17
68 10 0.17
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGATTTTATCACAAAAATT
AAT
Found at i:12421734 original size:77 final size:76
Alignment explanation
Indices: 12421639--12421963 Score: 314
Period size: 77 Copynumber: 4.2 Consensus size: 76
12421629 ACTTTCTAAT
* * * *
12421639 TTTATGAATTACTTAATTTCTTGGAAACCTTTTCATGTTTTAAGTAACATTTAATGGATTAAGTA
1 TTTAAGAATTACTTAATTTCTTAGAAACCTTTTCATGTTTTAAGTAACATTTCATGTATTAAGTA
12421704 ATTCTCTCATGA
66 ATTCT-TCATGA
* * ** * * *
12421716 TTTAGGAATAACTTAATTTCTTAGAAACCACTTCATGTTATACA-TAATCGTTT-ATGTTTTAAG
1 TTTAAGAATTACTTAATTTCTTAGAAACCTTTTCATGTTTTA-AGTAA-CATTTCATGTATTAAG
12421779 TAATT-TTACATGA
64 TAATTCTT-CATGA
* *
12421792 TTTAAGAATTATTTAATTTCTTAGAAACCTTTTTCACGTTTTAAGTAACATTTCATGTATTAAGT
1 TTTAAGAATTACTTAATTTCTTAGAAACC-TTTTCATGTTTTAAGTAACATTTCATGTATTAAGT
* *
12421857 GATTCGTTTATGA
65 AATTC-TTCATGA
* * * * * * ** *
12421870 TTTACGAATTGCTTAATTTTTTAAAAATCTTTTCATGTTTTCACCAACATTTCATGTATTAAATA
1 TTTAAGAATTACTTAATTTCTTAGAAACCTTTTCATGTTTTAAGTAACATTTCATGTATTAAGTA
* *
12421935 ATTATTCCTTGA
66 ATTCTT-CATGA
*
12421947 TTTAAGTAATTTCTTAA
1 TTTAAG-AATTACTTAA
12421964 AAAAAATCAT
Statistics
Matches: 201, Mismatches: 37, Indels: 19
0.78 0.14 0.07
Matches are distributed among these distances:
75 1 0.00
76 39 0.19
77 118 0.59
78 41 0.20
79 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (76 bp):
TTTAAGAATTACTTAATTTCTTAGAAACCTTTTCATGTTTTAAGTAACATTTCATGTATTAAGTA
ATTCTTCATGA
Found at i:12421937 original size:154 final size:154
Alignment explanation
Indices: 12421639--12421963 Score: 361
Period size: 154 Copynumber: 2.1 Consensus size: 154
12421629 ACTTTCTAAT
* * *
12421639 TTTATGAATTACTTAATTTCTTGGAAACCTTTTCATGTTTTAAGTAACATTTAATGGATTAAGTA
1 TTTAAGAATTACTTAATTTCTTAGAAACCTTTTCACGTTTTAAGTAACATTTAATGGATTAAGTA
* * * *
12421704 ATTCTCTCATGATTTAGGAATAACTTAATTTCTTAGAAACCACTTCATGTTATACATAATCGTTT
66 ATTCTCTCATGATTTACGAATAACTTAATTTCTTAAAAACCACTTCATGTTATACACAATCATTT
* *
12421769 ATGTTTTAAGTAATT-TTACATGA
131 ATGTATTAAATAATTATTACATGA
* * *
12421792 TTTAAGAATTATTTAATTTCTTAGAAACCTTTTTCACGTTTTAAGTAACATTTCATGTATTAAGT
1 TTTAAGAATTACTTAATTTCTTAGAAACC-TTTTCACGTTTTAAGTAACATTTAATGGATTAAGT
* * ** * * ** *
12421857 GATTCGT-TTATGATTTACGAATTGCTTAATTTTTTAAAAATCTTTTCATGTT-TTCACCAA-CA
65 AATTC-TCTCATGATTTACGAATAACTTAATTTCTTAAAAACCACTTCATGTTATACA-CAATCA
* *
12421919 TTTCATGTATTAAATAATTATTCCTTGA
128 TTT-ATGTATTAAATAATTATTACATGA
*
12421947 TTTAAGTAATTTCTTAA
1 TTTAAG-AATTACTTAA
12421964 AAAAAATCAT
Statistics
Matches: 141, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
153 33 0.23
154 87 0.62
155 13 0.09
156 8 0.06
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (154 bp):
TTTAAGAATTACTTAATTTCTTAGAAACCTTTTCACGTTTTAAGTAACATTTAATGGATTAAGTA
ATTCTCTCATGATTTACGAATAACTTAATTTCTTAAAAACCACTTCATGTTATACACAATCATTT
ATGTATTAAATAATTATTACATGA
Found at i:12423426 original size:12 final size:12
Alignment explanation
Indices: 12423402--12423439 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12423392 ATTTTCATTA
12423402 TTAAATAAA-ATT
1 TTAAA-AAATATT
12423414 TTAAAAAATATT
1 TTAAAAAATATT
*
12423426 TTATAAAATATT
1 TTAAAAAATATT
12423438 TT
1 TT
12423440 CTTACGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:12425283 original size:14 final size:14
Alignment explanation
Indices: 12425261--12425314 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
12425251 TTAATTATCA
12425261 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
* *
12425275 TTATGGTTTAAGGT
1 TTATAGTTTAGGGT
*
12425289 ATATAGTTTAGGGT
1 TTATAGTTTAGGGT
12425303 TTA-AGGTTTAGG
1 TTATA-GTTTAGG
12425315 AGTTACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 1 0.03
14 32 0.97
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:12435011 original size:10 final size:9
Alignment explanation
Indices: 12434982--12435022 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
12434972 TTTAGAACAA
12434982 AAAGA-TTG
1 AAAGAGTTG
*
12434990 AGAGAGTTG
1 AAAGAGTTG
12434999 AAAGAGTTTG
1 AAAGAG-TTG
12435009 AAAGAGTTG
1 AAAGAGTTG
12435018 AAAGA
1 AAAGA
12435023 ATGATGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 4 0.14
9 16 0.55
10 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (9 bp):
AAAGAGTTG
Found at i:12435960 original size:24 final size:24
Alignment explanation
Indices: 12435897--12435948 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12435887 TTTATAGAAG
* * *
12435897 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
12435921 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
12435945 ATTT
1 ATTT
12435949 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:12440040 original size:497 final size:497
Alignment explanation
Indices: 12439107--12440212 Score: 2079
Period size: 497 Copynumber: 2.2 Consensus size: 497
12439097 ATATCTTCAT
12439107 TCATGCTTTACTACTTTTAATACATAAGCAATTTATGCTTTAAAATTTAAACATATCAATATTAT
1 TCATGCTTTACTACTTTTAATACATAAGCAATTTATGCTTTAAAATTTAAACATATCAATATTAT
12439172 TTACTT-ATCACCTATTCGACCCAATTAATATACATCATATCATAATATTTACTATATACTTAAT
66 TTACTTAATCACCTATTCGACCCAATTAATATACATCATATCATAATATTTACTATATACTTAAT
12439236 CACCTATTCGACCCAATTAATATTTACTATATGAAAACACATTTTCAAATGTTTGGAATCATCAT
131 CACCTATTCGACCCAATTAATATTTACTATATGAAAACACATTTTCAAATGTTTGGAATCATCAT
*
12439301 ACTATCGCAATATAAGAATATGGCATGTATAGCTAGACTCACACGCACTACGTTAGTCCTAGAAT
196 ACTATCGCAATATAAGAATATGGCATGTATAGCTAGACTCACACACACTACGTTAGTCCTAGAAT
**
12439366 CGACTAAACCATAGCTCTGGTACCAATCAAATGTAACACCCCTAGCCCATATCCGTTGCCGGATT
261 CGACTAAACCATAGCTCTGGTACCAATCAAATGTAACACCCCTAGCCCATATCCGTCACCGGATT
12439431 AGGGTCACAAGGCATTACCGACCAAAACACAACTCAGAACAGTCTTTCATTTTAAATTATGCACA
326 AGGGTCACAAGGCATTACCGACCAAAACACAACTCAGAACAGTCTTTCATTTTAAATTATGCACA
12439496 AATTATATTAATTCAATCACGAAAATTTTAAACTCAAATAGTAACTAGCAGTTAAATCATATAAA
391 AATTATATTAATTCAATCACGAAAATTTTAAACTCAAATAGTAACTAGCAGTTAAATCATATAAA
12439561 TCACATTCGCACATATAGATTACTTAACCAACTAAAAACCAG
456 TCACATTCGCACATATAGATTACTTAACCAACTAAAAACCAG
* * *
12439603 TCATGCTTTAATACTTTTTATACATAATCAATTTATGCTTTAAAATTTAAACATATCAATATTAT
1 TCATGCTTTACTACTTTTAATACATAAGCAATTTATGCTTTAAAATTTAAACATATCAATATTAT
*
12439668 TTACTTAATCACCTATTCGACCCAATTAATATACATCATATCATAATATTTACTATCTACTTAAT
66 TTACTTAATCACCTATTCGACCCAATTAATATACATCATATCATAATATTTACTATATACTTAAT
*
12439733 CACCTATTCGACCCAGTTAATATTTACTATATGAAAACACATTTTCAAATGTTTGGAATCATCAT
131 CACCTATTCGACCCAATTAATATTTACTATATGAAAACACATTTTCAAATGTTTGGAATCATCAT
12439798 ACTATCGCAATATAAGAATATGGCATGTATAGCTAGACTCACACACACTACGTTAGTCCTAGAAT
196 ACTATCGCAATATAAGAATATGGCATGTATAGCTAGACTCACACACACTACGTTAGTCCTAGAAT
*
12439863 CGACTAAACCATAGCTCTGGTACCAATCAAATGTAACACCCCTAGCCCGTATCCGTCACCGGATT
261 CGACTAAACCATAGCTCTGGTACCAATCAAATGTAACACCCCTAGCCCATATCCGTCACCGGATT
* *
12439928 AGGGTCACGAGGCATTACCGACCAAAACACAACTTAGAACAGTCTTTCATTTTAAATTATGCACA
326 AGGGTCACAAGGCATTACCGACCAAAACACAACTCAGAACAGTCTTTCATTTTAAATTATGCACA
12439993 AATTATATTAATTCAATCACGAAAATTTTAAACTCAAATAGTAACTAGCAGTTAAATCATATAAA
391 AATTATATTAATTCAATCACGAAAATTTTAAACTCAAATAGTAACTAGCAGTTAAATCATATAAA
*
12440058 TCACATTCGCACATATAGATTACTTAACCAACTAAAAACTAG
456 TCACATTCGCACATATAGATTACTTAACCAACTAAAAACCAG
*
12440100 TCTTGCTTTACTACTTTTAATACATAAGCAATTTATGCTTTAAAATTTAAACATATCAATATTAT
1 TCATGCTTTACTACTTTTAATACATAAGCAATTTATGCTTTAAAATTTAAACATATCAATATTAT
*
12440165 TTACTTAATCACCTATTCGACCCAAATAATATACATCATATCATAATA
66 TTACTTAATCACCTATTCGACCCAATTAATATACATCATATCATAATA
12440213 CATATACTAT
Statistics
Matches: 592, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
496 68 0.11
497 524 0.89
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (497 bp):
TCATGCTTTACTACTTTTAATACATAAGCAATTTATGCTTTAAAATTTAAACATATCAATATTAT
TTACTTAATCACCTATTCGACCCAATTAATATACATCATATCATAATATTTACTATATACTTAAT
CACCTATTCGACCCAATTAATATTTACTATATGAAAACACATTTTCAAATGTTTGGAATCATCAT
ACTATCGCAATATAAGAATATGGCATGTATAGCTAGACTCACACACACTACGTTAGTCCTAGAAT
CGACTAAACCATAGCTCTGGTACCAATCAAATGTAACACCCCTAGCCCATATCCGTCACCGGATT
AGGGTCACAAGGCATTACCGACCAAAACACAACTCAGAACAGTCTTTCATTTTAAATTATGCACA
AATTATATTAATTCAATCACGAAAATTTTAAACTCAAATAGTAACTAGCAGTTAAATCATATAAA
TCACATTCGCACATATAGATTACTTAACCAACTAAAAACCAG
Found at i:12441985 original size:42 final size:43
Alignment explanation
Indices: 12441896--12442042 Score: 126
Period size: 42 Copynumber: 3.4 Consensus size: 43
12441886 CACATTCAAT
* * *
12441896 CCAGAC-GTGGTCTTACA--TATAATCAAATATCGATGCCACTGCC
1 CCAGACAG-GGTCTTACACGTA-AATCATATA-CGATGCCAATGTC
*
12441939 CCAGACAGGGTCTTACACG-AAGTCATATACGATGCCAATGTC
1 CCAGACAGGGTCTTACACGTAAATCATATACGATGCCAATGTC
* * * *
12441981 CCAGACATGGTCTTACATGTAAATC-TAGAGTCGATGCCAACGTC
1 CCAGACAGGGTCTTACACGTAAATCATATA--CGATGCCAATGTC
12442025 CCAGAC-GTGGTCTTACAC
1 CCAGACAG-GGTCTTACAC
12442043 AAAATCACAT
Statistics
Matches: 86, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
42 31 0.36
43 26 0.30
44 29 0.34
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (43 bp):
CCAGACAGGGTCTTACACGTAAATCATATACGATGCCAATGTC
Found at i:12446336 original size:24 final size:24
Alignment explanation
Indices: 12446302--12446350 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
12446292 TTTCTAGAAG
* *
12446302 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
12446326 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
12446350 A
1 A
12446351 GTTGACTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:12449358 original size:19 final size:17
Alignment explanation
Indices: 12449332--12449374 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
12449322 AAAATAACAT
12449332 TTTGAAATTGAATAATGA
1 TTTGAAA-TGAATAATGA
*
12449350 TTTGTAAATGAATAATGT
1 TTTG-AAATGAATAATGA
12449368 TTTGAAA
1 TTTGAAA
12449375 ACGAACGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (17 bp):
TTTGAAATGAATAATGA
Found at i:12459457 original size:40 final size:40
Alignment explanation
Indices: 12459403--12459525 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 40
12459393 CGTTTAGACA
*
12459403 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAT-
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT-TG
**
12459443 AAAAACGCCGCTAAAGGTCAAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
* * *
12459483 GAAAGCGCCGCTAAAAAT-AAGCATTAGCGGCGTTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
12459522 AAAA
1 AAAA
12459526 GCACCACAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
39 24 0.33
40 49 0.67
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
Found at i:12459587 original size:41 final size:41
Alignment explanation
Indices: 12459543--12459823 Score: 449
Period size: 41 Copynumber: 6.9 Consensus size: 41
12459533 AAAAAGTTGG
*
12459543 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
*
12459584 GGCCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
12459625 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
12459666 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
* * *
12459707 GGCCTTTAGCGGCCTTTGTGAAGAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
** * *
12459748 TTCCTTTAGCGGCGTTTTT-AAAGAAACGCCGCTAGTGCTC-
1 GGCCTTTAGCGGCGTTTTTGAAA-AAGCGCCGCTAATGCTCT
*
12459788 GACCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
12459824 AATAATAAAA
Statistics
Matches: 221, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
40 30 0.14
41 191 0.86
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (41 bp):
GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
Found at i:12460615 original size:18 final size:20
Alignment explanation
Indices: 12460572--12460615 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
12460562 TAGTTTAGGG
12460572 TTTAATATATATGGTTTAGA
1 TTTAATATATATGGTTTAGA
*
12460592 -GT-ATATATATGG-TTA-A
1 TTTAATATATATGGTTTAGA
12460608 TTTAATAT
1 TTTAATAT
12460616 TTAGGGTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 6
0.71 0.07 0.21
Matches are distributed among these distances:
16 1 0.05
17 4 0.20
18 14 0.70
19 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTAATATATATGGTTTAGA
Found at i:12460727 original size:14 final size:14
Alignment explanation
Indices: 12460710--12460739 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12460700 TGTGATTTAA
12460710 GGTTTATGGGTTAG
1 GGTTTATGGGTTAG
12460724 GGTTTATGGGTTAG
1 GGTTTATGGGTTAG
12460738 GG
1 GG
12460740 GTTAGAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.40
Consensus pattern (14 bp):
GGTTTATGGGTTAG
Found at i:12460750 original size:14 final size:14
Alignment explanation
Indices: 12460713--12460743 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12460703 GATTTAAGGT
*
12460713 TTATGGGTTAGGGT
1 TTATGGGTTAGGGG
12460727 TTATGGGTTAGGGG
1 TTATGGGTTAGGGG
12460741 TTA
1 TTA
12460744 GAGGTTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (14 bp):
TTATGGGTTAGGGG
Found at i:12461978 original size:23 final size:23
Alignment explanation
Indices: 12461951--12462018 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
12461941 ACAAAAAATA
12461951 ATTTTATTTTAAAAAATAATGCC
1 ATTTTATTTTAAAAAATAATGCC
* *** * *
12461974 ATTTTATATGCCAAAATACTGTC
1 ATTTTATTTTAAAAAATAATGCC
12461997 ATTTTATTTTAAATAAAATAAT
1 ATTTTATTTT-AA-AAAATAAT
12462019 TTTTTACGGC
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
23 25 0.78
25 7 0.22
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTTTATTTTAAAAAATAATGCC
Found at i:12462083 original size:106 final size:105
Alignment explanation
Indices: 12461887--12462074 Score: 258
Period size: 107 Copynumber: 1.8 Consensus size: 105
12461877 ACATAGCATG
** *
12461887 TGTCATTTTATTCCAAATAAATTTTTTTTTGCGGCGTTATTTTTAAAAAACGCCACAAAAAATAA
1 TGTCATTTTATTCCAAATAAATAATTTTTTACGGCGTTATTTTTAAAAAACGCCAC-AAAAATAA
* *
12461952 TTTTATTTTAAAAAATAATGCCATTTTATATGCCAAAATAC
65 GTTTACTTTAAAAAATAATGCCATTTTATATGCCAAAATAC
**
12461993 TGTCATTTTATTTTAAATAAAATAATTTTTTACGGCGTT-TTTTTATAAAAACGCCAC-AAAA-A
1 TGTCATTTTATTCCAAAT-AAATAATTTTTTACGGCGTTATTTTTA-AAAAACGCCACAAAAATA
12462055 AGTTTACTTTAAAAAA-AATG
64 AGTTTACTTTAAAAAATAATG
12462075 GCGCCATTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
103 4 0.05
104 15 0.21
105 4 0.05
106 22 0.30
107 28 0.38
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (105 bp):
TGTCATTTTATTCCAAATAAATAATTTTTTACGGCGTTATTTTTAAAAAACGCCACAAAAATAAG
TTTACTTTAAAAAATAATGCCATTTTATATGCCAAAATAC
Found at i:12466237 original size:23 final size:22
Alignment explanation
Indices: 12466207--12466250 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
12466197 CCCGTATAAT
*
12466207 GAAATTTATTTATTTATTGTTAG
1 GAAATTTAATTATTTA-TGTTAG
*
12466230 GAAATTTAATTGTTTATGTTA
1 GAAATTTAATTATTTATGTTA
12466251 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
GAAATTTAATTATTTATGTTAG
Found at i:12466470 original size:43 final size:43
Alignment explanation
Indices: 12466401--12466795 Score: 504
Period size: 43 Copynumber: 9.2 Consensus size: 43
12466391 GACACTTTTC
** * * **
12466401 GCGGCGTTTGTGAAAAAAGAGCCGCTAAAAGTTATGATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
* * * * *
12466444 GCGGCATTCGTGAGAGAAGCGTCGCTAAAGGTCCTGATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
* * * *
12466487 GCGGCGTTTATGGGAAAAGCGTCACTAAAGGTCTTGATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
* * *
12466530 GCGGTGTTTGTGGGAAAAGCGCCGTTAAAGGTCTTGATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
* * * *
12466573 GCGGCGTTTGTAGAAAAAGCGTCGCTAAAGGTCCTAATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
* *
12466616 GCGGCATTTGTGGGAAAAGCGTCGCTAAAGGTCCTGATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
* * *
12466659 GTGGCGTTTGTGGGAAAAGTGCCGCTAAAGATCCTGATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
*
12466702 GCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGATCTATA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
* * *
12466744 GTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCCTGATCTTTA
1 GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
12466787 GCGGCGTTT
1 GCGGCGTTT
12466796 ATTTCTAAAA
Statistics
Matches: 305, Mismatches: 46, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 37 0.12
43 268 0.88
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (43 bp):
GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATA
Found at i:12466956 original size:49 final size:49
Alignment explanation
Indices: 12466898--12466994 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
12466888 AAAAAGCGCT
12466898 GCTAAAGGTCTAAAAAAGCGCCGCTAAAAGCCTGTTTTGGTGTAGTGAC
1 GCTAAAGGTCTAAAAAAGCGCCGCTAAAAGCCTGTTTTGGTGTAGTGAC
12466947 GCTAAAGGTCTAAAAAAGCGCCGCTAAAAGCCTGTTTTGGTGTAGTGA
1 GCTAAAGGTCTAAAAAAGCGCCGCTAAAAGCCTGTTTTGGTGTAGTGA
12466995 ATTTGATAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (49 bp):
GCTAAAGGTCTAAAAAAGCGCCGCTAAAAGCCTGTTTTGGTGTAGTGAC
Found at i:12471258 original size:12 final size:13
Alignment explanation
Indices: 12471227--12471259 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12471217 TTTGCAAATT
12471227 TACTTGTATATTA
1 TACTTGTATATTA
12471240 TACTTGTATA-TA
1 TACTTGTATATTA
*
12471252 TATTTGTA
1 TACTTGTA
12471260 AATGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (13 bp):
TACTTGTATATTA
Found at i:12486365 original size:41 final size:41
Alignment explanation
Indices: 12486177--12486441 Score: 443
Period size: 40 Copynumber: 6.5 Consensus size: 41
12486167 GACTTTATGT
12486177 CTAGCAGGCTAAGTGCCGGTGATC-GAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTG-AATCAGGTTATAAAC
12486218 CTAGCAGGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
12486258 CTAGCAGGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
12486298 CTAGCAAGG-T-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGC-AGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
12486338 CTAGCTGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
12486379 CTAGCAGGCTAAGTGCCGGTGATCTGAATCA-GTCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT-TATAAAC
12486420 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
12486442 ATATGTTAAA
Statistics
Matches: 216, Mismatches: 3, Indels: 10
0.94 0.01 0.04
Matches are distributed among these distances:
39 2 0.01
40 112 0.52
41 102 0.47
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:12493088 original size:2 final size:2
Alignment explanation
Indices: 12493081--12493118 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12493071 TAATAATTCA
12493081 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
12493119 TTGTGTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12494290 original size:40 final size:41
Alignment explanation
Indices: 12494178--12494402 Score: 375
Period size: 41 Copynumber: 5.5 Consensus size: 41
12494168 GACTTTATGT
12494178 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
12494219 CTAGCAGGCTAAGTGTCGGTGATATGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
12494260 CTAGCAGGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
12494300 CTAGCAAGCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
**
12494340 CTAGCAGGCTAAGTGCCGGTGATCTGAATCA-GTCTATATGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT-TATAAAC
12494381 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
12494403 ATATGTTAAA
Statistics
Matches: 174, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
40 78 0.45
41 96 0.55
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:12499571 original size:22 final size:22
Alignment explanation
Indices: 12499545--12499589 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12499535 ATTATGAGTA
12499545 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
12499567 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
12499589 T
1 T
12499590 AGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:12516823 original size:33 final size:33
Alignment explanation
Indices: 12516780--12516964 Score: 166
Period size: 33 Copynumber: 5.5 Consensus size: 33
12516770 ATATAAAGGG
12516780 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * * * *
12516813 GGTTGATAAGTGCTGATTCTACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTC-CCCG-A--AT-CAT-T---GGT
*
12516855 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
12516882 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGC
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
12516915 GGTTGTTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
12516948 TGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
12516965 CCCACCATAT
Statistics
Matches: 123, Mismatches: 14, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
27 22 0.18
28 2 0.02
31 2 0.02
32 2 0.02
33 65 0.53
34 3 0.02
35 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
41 2 0.02
42 20 0.16
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:12516864 original size:75 final size:75
Alignment explanation
Indices: 12516775--12517122 Score: 384
Period size: 75 Copynumber: 4.8 Consensus size: 75
12516765 ATTGAATATA
* * *
12516775 AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGATAAGTGCTGATTCTACCGTAT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
12516840 TTTAAATGTG
66 TTTAAATGTG
*
12516850 AAGGGGGTTGCTAAGTGCTGATTCCCC----CA-AGG-GGTTGCTAAGTGCTGATTCC-CCG-A-
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
* *
12516906 -AT-CAT-T-
66 TTTAAATGTG
* * * * * *
12516912 --GGCGGTTGTTAAGTGCTGATTCCCCGAATCATTGGTTGTTGCTAAGTGCTGATCCCACCATAT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
12516975 TTTAAATGTG
66 TTTAAATGTG
* * * *
12516985 AAAGGGGTTGCTAAGTGTTGATTCCTCGATTCACTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTA-
*
12517050 TTTTGAATGTG
65 TTTTAAATGTG
* * * * *
12517061 AAAGGGGTTGCTAAGTCCTGATTCCCCAAATCACTGGTGGTTACTAAGTGCTGAATCCACCG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCG
12517123 ATAATGGACA
Statistics
Matches: 226, Mismatches: 31, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
60 23 0.10
63 1 0.00
64 4 0.02
65 3 0.01
66 18 0.08
67 3 0.01
68 4 0.02
69 18 0.08
70 3 0.01
71 4 0.02
72 1 0.00
75 79 0.35
76 65 0.29
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (75 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
TTTAAATGTG
Found at i:12517084 original size:76 final size:75
Alignment explanation
Indices: 12516915--12517122 Score: 290
Period size: 76 Copynumber: 2.8 Consensus size: 75
12516905 AATCATTGGC
* * * * *
12516915 GGTTGTTAAGTGCTGATTCCCCGAATCATTGGTTGTTGCTAAGTGCTGATCCCACCATATTTTAA
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAA
12516980 ATGTGAAAGG
66 ATGTGAAAGG
* * * *
12516990 GGTTGCTAAGTGTTGATTCCTCGATTCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTTG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTA-TTTTA
12517055 AATGTGAAAGG
65 AATGTGAAAGG
* * * *
12517066 GGTTGCTAAGTCCTGATTCCCCAAATCACTGGTGGTTACTAAGTGCTGAATCCACCG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCG
12517123 ATAATGGACA
Statistics
Matches: 116, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 51 0.44
76 65 0.56
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (75 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAA
ATGTGAAAGG
Found at i:12520896 original size:14 final size:14
Alignment explanation
Indices: 12520877--12520905 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12520867 ACGTCTCTCC
12520877 ATACTTTCTCCTGG
1 ATACTTTCTCCTGG
12520891 ATACTTTCTCCTGG
1 ATACTTTCTCCTGG
12520905 A
1 A
12520906 AGTAGCAAAG
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:0.17, C:0.28, G:0.14, T:0.41
Consensus pattern (14 bp):
ATACTTTCTCCTGG
Found at i:12523003 original size:41 final size:41
Alignment explanation
Indices: 12522953--12523034 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
12522943 CTCTGCACTG
12522953 TGTAGCAATGTCACTCTCTAAGTACCTCATTTTCTGGTCAT
1 TGTAGCAATGTCACTCTCTAAGTACCTCATTTTCTGGTCAT
*
12522994 TGTATCAATGTCACTCTCTAAGTACCTCATTTTCTGGTCAT
1 TGTAGCAATGTCACTCTCTAAGTACCTCATTTTCTGGTCAT
12523035 ACTTTCCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (41 bp):
TGTAGCAATGTCACTCTCTAAGTACCTCATTTTCTGGTCAT
Found at i:12524886 original size:2 final size:2
Alignment explanation
Indices: 12524879--12524905 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12524869 TTTATCTCAA
12524879 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
12524906 AATGAAATTT
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:12532177 original size:2 final size:2
Alignment explanation
Indices: 12532172--12532231 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
12532162 GGGTCATATA
12532172 TG TG TG TG TG TG TG TG 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 TG TG TG TG TG TG TG TG
12532214 TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG
12532232 AAAGGTTCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12546354 original size:4 final size:4
Alignment explanation
Indices: 12546345--12546369 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12546335 GTTTGATTAT
12546345 ACTA ACTA ACTA ACTA ACTA ACTA A
1 ACTA ACTA ACTA ACTA ACTA ACTA A
12546370 AATTTGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACTA
Found at i:12548358 original size:74 final size:72
Alignment explanation
Indices: 12548259--12548585 Score: 232
Period size: 73 Copynumber: 4.5 Consensus size: 72
12548249 TATGAGTAAG
* **
12548259 GCCAAATCCCTCAATA-GATGAAATCAAAACAAGCATTTTATGTTCCAAAAATTTGCTCTCACTT
1 GCCAAATCCCTCAA-AGGATGCAATCAAGTCAA-CATTTTAT-TTCCAAAAATTTGCTCTCACTT
* *
12548323 AATTAATAAA
63 AATTAGTAGA
** * * * * *
12548333 GCCAAATCCCTCAGGGGATGCAATCAAGTCAACAATTTGATTTCCACAGACTTGCTCTCACTCAA
1 GCCAAATCCCTCAAAGGATGCAATCAAGTCAAC-ATTTTATTTCCAAAAATTTGCTCTCACTTAA
*
12548398 TTGGTAGA
65 TTAGTAGA
* * * * *
12548406 GCTAAATCTCTTAAAGGATGCAATCAAGTCAAACATTTTGATTT-CACATAATTT-CTCCCACTT
1 GCCAAATCCCTCAAAGGATGCAATCAAGTC-AACATTTT-ATTTCCA-AAAATTTGCTCTCACTT
12548469 AATTAGTAGA
63 AATTAGTAGA
* * * * * * * *
12548479 GCCAAATCCCTTAAAGGATGTAATCAAATTAAACACTTTGACTTT-CACAAACTTGTTCTCACTT
1 GCCAAATCCCTCAAAGGATGCAATC-AAGTCAACA-TTTTA-TTTCCAAAAATTTGCTCTCACTT
*
12548543 AA-TCGATAGA
63 AATTAG-TAGA
* * * **
12548553 GCTAAATCCCTTAAGGGATATAATCAAGTCAAC
1 GCCAAATCCCTCAAAGGATGCAATCAAGTCAAC
12548586 CAATTCAGCC
Statistics
Matches: 200, Mismatches: 43, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
73 112 0.56
74 88 0.44
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (72 bp):
GCCAAATCCCTCAAAGGATGCAATCAAGTCAACATTTTATTTCCAAAAATTTGCTCTCACTTAAT
TAGTAGA
Found at i:12548413 original size:73 final size:72
Alignment explanation
Indices: 12548311--12548590 Score: 274
Period size: 73 Copynumber: 3.8 Consensus size: 72
12548301 TTCCAAAAAT
* * **
12548311 TTGCTCTCACTTAATTAATAAAGCCAAATCCCTCAGGGGATGCAATCAAGTCAACAATTTGATTT
1 TTGCTCTCACTTAATTAATAGAGCCAAATCCCTTAAAGGATGCAATCAAGTCAACAATTTGATTT
*
12548376 CCACAGAC
66 -CACAAAC
* ** * * *
12548384 TTGCTCTCACTCAATTGGTAGAGCTAAATCTCTTAAAGGATGCAATCAAGTCAAACATTTTGATT
1 TTGCTCTCACTTAATTAATAGAGCCAAATCCCTTAAAGGATGCAATCAAGTC-AACAATTTGATT
12548449 TCACATAA-
65 TCACA-AAC
* * * * * * *
12548457 TTTCTCCCACTTAATTAGTAGAGCCAAATCCCTTAAAGGATGTAATCAAATTAAACACTTTGACT
1 TTGCTCTCACTTAATTAATAGAGCCAAATCCCTTAAAGGATGCAATC-AAGTCAACAATTTGA-T
12548522 TTCACAAAC
64 TTCACAAAC
* ** * * **
12548531 TTGTTCTCACTTAATCGATAGAGCTAAATCCCTTAAGGGATATAATCAAGTCAACCAATT
1 TTGCTCTCACTTAATTAATAGAGCCAAATCCCTTAAAGGATGCAATCAAGTCAA-CAATT
12548591 CAGCCCGACA
Statistics
Matches: 168, Mismatches: 33, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
73 103 0.61
74 65 0.39
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (72 bp):
TTGCTCTCACTTAATTAATAGAGCCAAATCCCTTAAAGGATGCAATCAAGTCAACAATTTGATTT
CACAAAC
Found at i:12548539 original size:147 final size:147
Alignment explanation
Indices: 12548308--12548584 Score: 351
Period size: 147 Copynumber: 1.9 Consensus size: 147
12548298 ATGTTCCAAA
* ** *
12548308 AATTTGCTCTCACTTAATTAATAAAGCCAAATCCCTCAGGGGATGCAATCAAGTCAACAATTTGA
1 AATTTGCTCCCACTTAATTAATAAAGCCAAATCCCTCAAAGGATGCAATCAAGTAAACAATTTGA
* * * * *
12548373 TTTCCACAGACTTGCTCTCACTCAATTGGTAGAGCTAAATCTCTTAAAGGATGCAATCAAGTCAA
66 TTTCCACAAACTTGCTCTCACTCAATCGATAGAGCTAAATCCCTTAAAGGATACAATCAAGTCAA
12548438 ACATTTTGATTTCACAT
131 ACATTTTGATTTCACAT
* * * * * *
12548455 AATTT-CTCCCACTTAATTAGTAGAGCCAAATCCCTTAAAGGATGTAATCAAATTAAACACTTTG
1 AATTTGCTCCCACTTAATTAATAAAGCCAAATCCCTCAAAGGATGCAATC-AAGTAAACAATTTG
* * * *
12548519 ACTTT-CACAAACTTGTTCTCACTTAATCGATAGAGCTAAATCCCTTAAGGGATATAATCAAGTC
65 A-TTTCCACAAACTTGCTCTCACTCAATCGATAGAGCTAAATCCCTTAAAGGATACAATCAAGTC
12548583 AA
129 AA
12548585 CCAATTCAGC
Statistics
Matches: 109, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
146 37 0.34
147 69 0.63
148 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (147 bp):
AATTTGCTCCCACTTAATTAATAAAGCCAAATCCCTCAAAGGATGCAATCAAGTAAACAATTTGA
TTTCCACAAACTTGCTCTCACTCAATCGATAGAGCTAAATCCCTTAAAGGATACAATCAAGTCAA
ACATTTTGATTTCACAT
Found at i:12553336 original size:20 final size:20
Alignment explanation
Indices: 12553281--12553336 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
12553271 AAAAAAAAAG
*
12553281 AAAATAATT-TTTAAAATTC
1 AAAATATTTATTTAAAATTC
**
12553300 AAAATATTTATAAAAAATTC
1 AAAATATTTATTTAAAATTC
*
12553320 AAAATTTTTATTTAAAA
1 AAAATATTTATTTAAAA
12553337 ATTATAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATTTATTTAAAATTC
Found at i:12553363 original size:20 final size:19
Alignment explanation
Indices: 12553293--12553366 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 19
12553283 AATAATTTTT
12553293 AAAATTCAAAATATTTATAA
1 AAAATTCAAAATATTTAT-A
12553313 AAAATTCAAAAT-TTT-T-
1 AAAATTCAAAATATTTATA
*
12553329 ---ATTTAAAA-A-TTATA
1 AAAATTCAAAATATTTATA
12553343 AAAATTCTAAAATATTTATA
1 AAAATTC-AAAATATTTATA
12553363 AAAA
1 AAAA
12553367 AGTTAAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
12 2 0.05
13 8 0.19
17 3 0.07
18 5 0.12
19 4 0.09
20 21 0.49
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:12572125 original size:15 final size:15
Alignment explanation
Indices: 12572105--12572145 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
12572095 TTTATTTTTC
12572105 TGGCAAAAAAAAAAT
1 TGGCAAAAAAAAAAT
12572120 TGGC--AAAAAAAAT
1 TGGCAAAAAAAAAAT
12572133 T-GCAAAAAAAAAA
1 TGGCAAAAAAAAAA
12572146 GTAGAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 8 0.33
15 4 0.17
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.12
Consensus pattern (15 bp):
TGGCAAAAAAAAAAT
Found at i:12572129 original size:13 final size:12
Alignment explanation
Indices: 12572111--12572143 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
12572101 TTTCTGGCAA
12572111 AAAAAAAATTGGC
1 AAAAAAAATT-GC
12572124 AAAAAAAATTGC
1 AAAAAAAATTGC
12572136 AAAAAAAA
1 AAAAAAAA
12572144 AAGTAGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.73, C:0.06, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTGC
Found at i:12579906 original size:31 final size:30
Alignment explanation
Indices: 12579868--12579926 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
12579858 TATAATTTGA
* *
12579868 TCATTAAATTATTTAAAATTTTTCATTTAAG
1 TCATTAAACTATTTAAAAATTTT-ATTTAAG
12579899 TCATTAAACTATTTAAAAATTTTATTTA
1 TCATTAAACTATTTAAAAATTTTATTTA
12579927 CGTTGTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (30 bp):
TCATTAAACTATTTAAAAATTTTATTTAAG
Found at i:12584469 original size:15 final size:15
Alignment explanation
Indices: 12584434--12584485 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12584424 TTAAGAATTT
*
12584434 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12584448 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12584462 TATTTAATAATAAT-
1 TATTTAATTATAATA
12584476 TATGTTAATT
1 TAT-TTAATT
12584486 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12584592 original size:120 final size:120
Alignment explanation
Indices: 12584379--12584721 Score: 641
Period size: 120 Copynumber: 2.9 Consensus size: 120
12584369 AGCAATAACA
*
12584379 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
*
12584444 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATATTATAGT
*
12584499 ATCATATATTATGACTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
* *
12584564 TATCTTTTAATTATAATATACTTAATAATAATTATGTTAATTTATATATTATAGT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATATTATAGT
12584619 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
12584684 TATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTT
12584722 TAAATATGAT
Statistics
Matches: 215, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 215 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATATTATAGT
Found at i:12584704 original size:16 final size:16
Alignment explanation
Indices: 12584683--12584724 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12584673 TTATTAAATT
*
12584683 ATATATTTTAATTATA
1 ATATATTTTAATAATA
12584699 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
12584714 AT-TATGTTTAA
1 ATATAT-TTTAA
12584725 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:12584709 original size:15 final size:15
Alignment explanation
Indices: 12584674--12584715 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12584664 TTAAGAATTT
*
12584674 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12584688 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12584702 TATTTAATAATAAT
1 TATTTAATTATAAT
12584716 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Done.