Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 156 of 203
Found at i:49633052 original size:8 final size:9
Alignment explanation
Indices: 49632994--49633062 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
49632984 TCCTAATCTG
49632994 TATTTATATA
1 TATTTA-ATA
*
49633004 AATTTAATA
1 TATTTAATA
49633013 TA-TTAATA
1 TATTTAATA
*
49633021 -ATTTGTCATA
1 TA-TT-TAATA
49633031 TAAGTTTAATA
1 T-A-TTTAATA
49633042 TATTT-ATA
1 TATTTAATA
49633050 TATTTAATA
1 TATTTAATA
49633059 TATT
1 TATT
49633063 AATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
7 1 0.02
8 14 0.29
9 15 0.31
10 10 0.21
11 5 0.10
12 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (9 bp):
TATTTAATA
Found at i:49633206 original size:9 final size:9
Alignment explanation
Indices: 49633192--49633222 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
49633182 TTTAATTAAA
49633192 TAAAAAATT
1 TAAAAAATT
49633201 TAAAAAAATT
1 T-AAAAAATT
49633211 TAAAAAATT
1 TAAAAAATT
49633220 TAA
1 TAA
49633223 CAGTTGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAAAATT
Found at i:49633208 original size:10 final size:10
Alignment explanation
Indices: 49633193--49633222 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
49633183 TTAATTAAAT
49633193 AAAAAATTTA
1 AAAAAATTTA
49633203 AAAAAATTT-
1 AAAAAATTTA
49633212 AAAAAATTTA
1 AAAAAATTTA
49633222 A
1 A
49633223 CAGTTGACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:49636757 original size:122 final size:121
Alignment explanation
Indices: 49636631--49636867 Score: 334
Period size: 122 Copynumber: 2.0 Consensus size: 121
49636621 AAATTTAAAA
* * *
49636631 TATAGATGTATGTTTAAAAATAACATGTAATAATTAATAAAAC-ATATGGTTTGAAATTAATTAA
1 TATAGATGTATATTTAAAAATAACATATAATAATTAAT-AAACTATATGGTTTGAAACTAATTAA
*
49636695 TCATAATAACACAT-AATATATGTACAATATTAAAATAAAAAATAGATTAAATTATTAT
65 TCATAATAACAAATGAA-ATATGTACAATATTAAAAT-AAAAATAGATTAAATTATTAT
* * * * *
49636753 TATAGATGTTTATTTAAAGATAACATATAATAATTAATGAACTGTATGGTTTGAAGCTAATTAAT
1 TATAGATGTATATTTAAAAATAACATATAATAATTAATAAACTATATGGTTTGAAACTAATTAAT
* *
49636818 CATAATAATAAATGAAATATGTACAATATTAAAATAAAAATATATTAAAT
66 CATAATAACAAATGAAATATGTACAATATTAAAATAAAAATAGATTAAAT
49636868 AATGAATAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
121 17 0.17
122 83 0.81
123 2 0.02
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (121 bp):
TATAGATGTATATTTAAAAATAACATATAATAATTAATAAACTATATGGTTTGAAACTAATTAAT
CATAATAACAAATGAAATATGTACAATATTAAAATAAAAATAGATTAAATTATTAT
Found at i:49643968 original size:25 final size:25
Alignment explanation
Indices: 49643888--49643968 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
49643878 GAAGCACACT
* * *
49643888 CGAGCCATATAACGGGAAACTCATG
1 CGAGCCATATAACAGGAAGCTTATG
* * * *
49643913 TGAGCCATGTAACATGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTTATG
*
49643938 CAAGCCATATAACAGGAAGCTTATG
1 CGAGCCATATAACAGGAAGCTTATG
49643963 CGAGCC
1 CGAGCC
49643969 TTTAACGGGT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTTATG
Found at i:49649819 original size:94 final size:94
Alignment explanation
Indices: 49649658--49649842 Score: 343
Period size: 94 Copynumber: 2.0 Consensus size: 94
49649648 ACAATGGTAA
* *
49649658 CCAAAGTTATTAGCTGAGTCCAAAGGCATTCAAGTTCAACACGCTTGATATGAAAATGAGATTAT
1 CCAAAGTTACTAGCTGAGTCCAAAGGCATTCAAGTTCAACACACTTGATATGAAAATGAGATTAT
49649723 GATCTTTTAAATATATAGAGTACATCTTG
66 GATCTTTTAAATATATAGAGTACATCTTG
*
49649752 CCAAAGTTACTAGTTGAGTCCAAAGGCATTCAAGTTCAACACACTTGATATGAAAATGAGATTAT
1 CCAAAGTTACTAGCTGAGTCCAAAGGCATTCAAGTTCAACACACTTGATATGAAAATGAGATTAT
49649817 GATCTTTTAAATATATAGAGTACATC
66 GATCTTTTAAATATATAGAGTACATC
49649843 CGCAATGGAT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (94 bp):
CCAAAGTTACTAGCTGAGTCCAAAGGCATTCAAGTTCAACACACTTGATATGAAAATGAGATTAT
GATCTTTTAAATATATAGAGTACATCTTG
Found at i:49653340 original size:12 final size:12
Alignment explanation
Indices: 49653323--49653387 Score: 75
Period size: 11 Copynumber: 5.8 Consensus size: 12
49653313 AACTAATCCT
49653323 CTCTCAAATTTC
1 CTCTCAAATTTC
49653335 CTCTC-AATTTC
1 CTCTCAAATTTC
*
49653346 CTCTC-AATTTG
1 CTCTCAAATTTC
*
49653357 CTATCAAA-TTC
1 CTCTCAAATTTC
*
49653368 CT-TCAAATTTT
1 CTCTCAAATTTC
49653379 CTCTCAAAT
1 CTCTCAAAT
49653388 CCATATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
10 5 0.11
11 28 0.61
12 13 0.28
ACGTcount: A:0.26, C:0.29, G:0.02, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:49653431 original size:51 final size:51
Alignment explanation
Indices: 49653349--49653446 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
49653339 CAATTTCCTC
49653349 TCAATTTGCTATCAAATTCCTTCAAATTTTCTCTCAAATCCATATTTAATT
1 TCAATTTGCTATCAAATTCCTTCAAATTTTCTCTCAAATCCATATTTAATT
* * * *
49653400 TCAATTTGCTCTCAAGTT-CTTCTTAAA-TTTCTCTTAAATCCCTATTT
1 TCAATTTGCTATCAAATTCCTTC--AAATTTTCTCTCAAATCCATATTT
49653447 TTAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 4 0.10
51 34 0.83
52 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTATCAAATTCCTTCAAATTTTCTCTCAAATCCATATTTAATT
Found at i:49655747 original size:45 final size:45
Alignment explanation
Indices: 49655698--49655813 Score: 180
Period size: 45 Copynumber: 2.6 Consensus size: 45
49655688 ATATTTTGAA
*
49655698 TATTTTGATATTATTTTATGTAATAAAATAG-AATTTGTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTT-TTTTGAGT
* *
49655743 TATTTCGATATTATTTGATATAATAAAATAGAAATTTTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTTTTTGAGT
*
49655788 TATTTTGAAATTATTTGATGTAATAA
1 TATTTTGATATTATTTGATGTAATAA
49655814 CATGAGCTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 59 0.92
46 5 0.08
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTTTTTGAGT
Found at i:49658606 original size:124 final size:125
Alignment explanation
Indices: 49658304--49658719 Score: 595
Period size: 125 Copynumber: 3.3 Consensus size: 125
49658294 CATGTTACTA
*
49658304 TAGCAAAAGCGCGTCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTAGTAGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTAGTAGAAG
* * * *
49658369 CAATTTTATACTATTTGTTCAGAAACATCAACTCGAAATTATTTCTTCCAGGACCAACTG
66 CGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTTCAGGACCAACTG
* * * * *
49658429 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATGCTTCTTA-AATAGCATCCT-GCTTGA
1 TAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCATAA-AGCATCCTAG-TAGA
* * * * * *
49658492 AGCGTTTTTATACTATTTGCTCAGAAACGTAAACTCAAAATAATTT-TTTCATGACCTACTG
64 AGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTTCAGGACCAACTG
* ** *
49658553 TAGCAAAAGCGCGTCCACGTGGGTGCGATTTAACAAATTCTTCTCATAAAGCATCCTAGTAGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTAGTAGAAG
49658618 CGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTTCAGGACCAACTG
66 CGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTTCAGGACCAACTG
* *
49658678 TAGCAAAAACGCGTCCAGGAGGGCACGATTTCACAAATTCTT
1 TAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTT
49658720 TGCGTCCACG
Statistics
Matches: 251, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
124 108 0.43
125 143 0.57
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (125 bp):
TAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTAGTAGAAG
CGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTTCAGGACCAACTG
Found at i:49659444 original size:29 final size:28
Alignment explanation
Indices: 49659398--49659474 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 28
49659388 CAATAAAAGT
49659398 TATAAAAACTA-TT-AAATTTAATATAAAA
1 TATAAAAA-TATTTAAAATTTAATAT-AAA
* * *
49659426 TATAAAAATATTTAAAATTAGAATATTAG
1 TATAAAAATATTTAAAATT-TAATATAAA
49659455 TA-AAAAATATTTTAAAATTT
1 TATAAAAATA-TTTAAAATTT
49659475 TAATTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.05
28 17 0.41
29 17 0.41
30 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (28 bp):
TATAAAAATATTTAAAATTTAATATAAA
Found at i:49659698 original size:9 final size:9
Alignment explanation
Indices: 49659684--49659853 Score: 65
Period size: 9 Copynumber: 17.3 Consensus size: 9
49659674 CTTTTAGTAC
49659684 TATAATTTT
1 TATAATTTT
49659693 TATAATTTGTTT
1 TATAA--T-TTT
*
49659705 TATGAA-ATT
1 TAT-AATTTT
*
49659714 TATATTTCTT
1 TATAATT-TT
*
49659724 TACAATTTT
1 TATAATTTT
49659733 TATAACTTTTT
1 TATAA--TTTT
49659744 TATAA-TTT
1 TATAATTTT
49659752 TATAATTTTTT
1 TATAA--TTTT
* *
49659763 TCTACATTTC
1 TATA-ATTTT
49659773 TATACATTTT
1 TATA-ATTTT
*
49659783 ATATATTTTTT
1 -TATA-ATTTT
*
49659794 TTTAATTTT
1 TATAATTTT
49659803 TAATAAATTTT
1 T-AT-AATTTT
* *
49659814 AAATATTTTT
1 -TATAATTTT
*
49659824 TATAAATTT
1 TATAATTTT
* *
49659833 AATAAATTT
1 TATAATTTT
*
49659842 TATCATTTT
1 TATAATTTT
49659851 TAT
1 TAT
49659854 CATGATATAA
Statistics
Matches: 121, Mismatches: 24, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
8 9 0.07
9 44 0.36
10 27 0.22
11 32 0.26
12 7 0.06
13 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (9 bp):
TATAATTTT
Found at i:49659743 original size:11 final size:10
Alignment explanation
Indices: 49659712--49659828 Score: 57
Period size: 10 Copynumber: 11.7 Consensus size: 10
49659702 TTTTATGAAA
49659712 TTTAT-ATTT
1 TTTATAATTT
*
49659721 CTTTACAA-TT
1 -TTTATAATTT
49659731 TTTATAACTTT
1 TTTATAA-TTT
49659742 TTTATAA--T
1 TTTATAATTT
49659750 TTTATAATTTT
1 TTTATAA-TTT
*
49659761 TTTCTACA-TT
1 TTTATA-ATTT
*
49659771 TCTATACATTT
1 TTTATA-ATTT
* *
49659782 TATATATTTT
1 TTTATAATTT
*
49659792 TTTTTAATTT
1 TTTATAATTT
* *
49659802 TTAATAA-AT
1 TTTATAATTT
*
49659811 TTTAAATATTT
1 TTTATA-ATTT
49659822 TTTATAA
1 TTTATAA
49659829 ATTTAATAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
8 8 0.10
9 11 0.14
10 31 0.39
11 29 0.36
12 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTATAATTT
Found at i:49659752 original size:19 final size:19
Alignment explanation
Indices: 49659684--49659853 Score: 96
Period size: 19 Copynumber: 8.6 Consensus size: 19
49659674 CTTTTAGTAC
49659684 TATAATTTTTATAATTTGTTT
1 TATAATTTTTATAA-TT-TTT
*
49659705 TATGAA-ATTTAT-ATTTCTT
1 TAT-AATTTTTATAATTT-TT
*
49659724 TACAATTTTTATAACTTTTT
1 TATAATTTTTATAA-TTTTT
49659744 TATAA-TTTTATAATTTTTT
1 TATAATTTTTATAA-TTTTT
* * *
49659763 TCTACATTTCTATACATTTTA
1 TATA-ATTTTTATA-ATTTTT
* *
49659784 TATATTTTTTTTTAATTTTT
1 TATA-ATTTTTATAATTTTT
* * *
49659804 AATAAATTTTAAATATTTTT
1 TATAATTTTTATA-ATTTTT
* * *
49659824 TATAAATTTAATAA-ATTT
1 TATAATTTTTATAATTTTT
*
49659842 TATCATTTTTAT
1 TATAATTTTTAT
49659854 CATGATATAA
Statistics
Matches: 114, Mismatches: 26, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
18 15 0.13
19 33 0.29
20 33 0.29
21 30 0.26
22 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (19 bp):
TATAATTTTTATAATTTTT
Found at i:49659776 original size:29 final size:28
Alignment explanation
Indices: 49659684--49659851 Score: 108
Period size: 30 Copynumber: 5.7 Consensus size: 28
49659674 CTTTTAGTAC
* *
49659684 TATAATTTTTATAATTTGTTTTATGAAATT
1 TATAAATTTTATAATTT-TTTTAT-AATTT
** *
49659714 TATATTTCTTTACAA--TTTTTATAACTTT
1 TATAAAT-TTTATAATTTTTTTATAA-TTT
* *
49659742 TTTATAATTTTATAATTTTTTTCTACATTT
1 TATA-AATTTTATAATTTTTTTATA-ATTT
* *
49659772 CTATACATTTTATATATTTTTTTTTAATTTT
1 -TATAAATTTTATA-ATTTTTTTATAA-TTT
49659803 TAATAAATTTTA-AATATTTTTTATAAATTT
1 T-ATAAATTTTATAAT-TTTTTTAT-AATTT
* *
49659833 AATAAATTTTATCATTTTT
1 TATAAATTTTATAATTTTT
49659852 ATCATGATAT
Statistics
Matches: 110, Mismatches: 15, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
27 2 0.02
28 17 0.15
29 18 0.16
30 39 0.35
31 34 0.31
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (28 bp):
TATAAATTTTATAATTTTTTTATAATTT
Found at i:49659794 original size:31 final size:29
Alignment explanation
Indices: 49659744--49659824 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 29
49659734 ATAACTTTTT
49659744 TATAATTTTATA-ATTTTTTTCTACATTTC
1 TATAATTTTATATATTTTTTTCTA-ATTTC
* *
49659773 TATACATTTTATATATTTTTTTTTAATTTT
1 TATA-ATTTTATATATTTTTTTCTAATTTC
*
49659803 TAATAAATTTTAAATATTTTTT
1 T-AT-AATTTTATATATTTTTT
49659825 ATAAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.09
30 13 0.29
31 27 0.60
32 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (29 bp):
TATAATTTTATATATTTTTTTCTAATTTC
Found at i:49665544 original size:3 final size:3
Alignment explanation
Indices: 49665526--49665581 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
49665516 TTATTTTTTC
*
49665526 TCT TC- TCT TAT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
49665573 TCT TCT TCT
1 TCT TCT TCT
49665582 ATTGCATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:49665956 original size:11 final size:11
Alignment explanation
Indices: 49665940--49665973 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
49665930 CAAAGAAAAT
49665940 ATAAAATTACA
1 ATAAAATTACA
*
49665951 ATAAAATTACT
1 ATAAAATTACA
49665962 ATAAAATTACA
1 ATAAAATTACA
49665973 A
1 A
49665974 AGTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAAAATTACA
Found at i:49668260 original size:28 final size:28
Alignment explanation
Indices: 49668206--49668261 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
49668196 TGAAAATGTG
* *
49668206 TGAAAATGGAAGCCTTTATGGTAATCTA
1 TGAAAATGGAAGCATTTATGGCAATCTA
* * *
49668234 TGAAAATGGAGGCATTTTTGGCGATCTA
1 TGAAAATGGAAGCATTTATGGCAATCTA
49668262 AGGAAAAGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (28 bp):
TGAAAATGGAAGCATTTATGGCAATCTA
Found at i:49677995 original size:16 final size:16
Alignment explanation
Indices: 49677974--49678012 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
49677964 ATTTTTGTTA
49677974 TAAGAATATTGATTAT
1 TAAGAATATTGATTAT
49677990 TAAGAATATTGATTAT
1 TAAGAATATTGATTAT
49678006 TAAGAAT
1 TAAGAAT
49678013 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (16 bp):
TAAGAATATTGATTAT
Found at i:49678159 original size:18 final size:17
Alignment explanation
Indices: 49678131--49678165 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49678121 ATTATTAAGA
*
49678131 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
49678148 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
49678166 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:49678417 original size:45 final size:44
Alignment explanation
Indices: 49678322--49678418 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
49678312 CTATTACACC
* *
49678322 TCCATTACATTCAACCAAACACAAGAATACTATTACGCTTCTAT
1 TCCATTACATTCAACCAAACACAAGAATACTATTACACCTCTAT
* *
49678366 TCCATTACATTCAACCAAACA-ATTGAATTGCTATTACACCTCTAT
1 TCCATTACATTCAACCAAACACA-AGAA-TACTATTACACCTCTAT
*
49678411 TTCATTAC
1 TCCATTAC
49678419 GCCTCTATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.52
45 21 0.46
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (44 bp):
TCCATTACATTCAACCAAACACAAGAATACTATTACACCTCTAT
Found at i:49680723 original size:100 final size:100
Alignment explanation
Indices: 49680550--49680749 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
49680540 ACAAATTCAG
49680550 AATCATTTTTTGGAGATATTAATCTAACATTTGCAGTTGTAAAATATGTCGCTGAAAATTTTTAT
1 AATCATTTTTTGGAGATATTAATCTAACATTTGCAGTTGTAAAATATGTCGCTGAAAATTTTTAT
49680615 TGTTGACATATAAAAATGTAGCATTTTTTTATTTT
66 TGTTGACATATAAAAATGTAGCATTTTTTTATTTT
49680650 AATCATTTTTTGGAGATATTAATCTAACATTTGCAGTTGTAAAATATGTCGCTGAAAATTTTTAT
1 AATCATTTTTTGGAGATATTAATCTAACATTTGCAGTTGTAAAATATGTCGCTGAAAATTTTTAT
49680715 TGTTGACATATAAAAATGTAGCATTTTTTTATTTT
66 TGTTGACATATAAAAATGTAGCATTTTTTTATTTT
49680750 GATCTGAAAG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (100 bp):
AATCATTTTTTGGAGATATTAATCTAACATTTGCAGTTGTAAAATATGTCGCTGAAAATTTTTAT
TGTTGACATATAAAAATGTAGCATTTTTTTATTTT
Found at i:49693641 original size:79 final size:82
Alignment explanation
Indices: 49693530--49693714 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
49693520 GCTACTCGTT
* *
49693530 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
49693593 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
49693610 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
49693673 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
49693690 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
49693715 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:49693714 original size:40 final size:40
Alignment explanation
Indices: 49693511--49693714 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
49693501 CGGAATTTAA
** *
49693511 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49693551 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
49693591 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49693630 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
49693670 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
49693710 CCGGA
1 CCGGA
49693715 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:49698153 original size:19 final size:19
Alignment explanation
Indices: 49698119--49698155 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49698109 CAATATATAT
*
49698119 ATATATAAAACCAAAATCA
1 ATATATAAAAACAAAATCA
*
49698138 ATATATAAAAATAAAATC
1 ATATATAAAAACAAAATC
49698156 GAATTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (19 bp):
ATATATAAAAACAAAATCA
Found at i:49703784 original size:23 final size:22
Alignment explanation
Indices: 49703732--49703784 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
49703722 TCCACGTCTT
*
49703732 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
49703754 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
49703777 TTTCTTTT
1 TTTCTTTT
49703785 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:49709569 original size:93 final size:93
Alignment explanation
Indices: 49709409--49709689 Score: 474
Period size: 93 Copynumber: 3.0 Consensus size: 93
49709399 ATTTTGGTAT
* *
49709409 CACTAAAACTTATGACATCTTACATGAGCAAATTTTTTACCTAACATGCATAAATTAGTACAAGA
1 CACTAAGACTTATGACATCTTACATGAGC-AATTTTTTACCTAACATGCATAAATTAGTACGAGA
*
49709474 AAATTTGCTCTACTTGCATTCCTTGTAAA
65 AAATTTGCTCTACTTGTATTCCTTGTAAA
*
49709503 CACTAAGACTTATGACATCTTACATGAGCAATTTTTTACCTAACATGCACAAATTAGTACGAGAA
1 CACTAAGACTTATGACATCTTACATGAGCAATTTTTTACCTAACATGCATAAATTAGTACGAGAA
49709568 AATTTGCTCTACTTGTATTCCTTGTAAA
66 AATTTGCTCTACTTGTATTCCTTGTAAA
* * *
49709596 CACTAAGGCTTATGACATCTTACATGAGCAATTTTTTACCTAACATGTATAAATTAGTA-GAGCA
1 CACTAAGACTTATGACATCTTACATGAGCAATTTTTTACCTAACATGCATAAATTAGTACGAGAA
*
49709660 AATTTGCTGTACTTGTATTCCTTGTAAA
66 AATTTGCTCTACTTGTATTCCTTGTAAA
49709688 CA
1 CA
49709690 GGATAAGTCC
Statistics
Matches: 178, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
92 33 0.19
93 117 0.66
94 28 0.16
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (93 bp):
CACTAAGACTTATGACATCTTACATGAGCAATTTTTTACCTAACATGCATAAATTAGTACGAGAA
AATTTGCTCTACTTGTATTCCTTGTAAA
Found at i:49710605 original size:73 final size:73
Alignment explanation
Indices: 49710522--49710668 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
49710512 ATTTAAATTC
49710522 ATTTTTTACTTAATAGCATAAAACAAATAATTACAAAATCCTCAAGGTTCTAAGCCTTTATGTAC
1 ATTTTTTACTTAATAGCATAAAACAAATAATTACAAAATCCTCAAGGTTCTAAGCCTTTATGTAC
49710587 ATGCCATT
66 ATGCCATT
* *
49710595 ATTTTTTACTTATTAGCATAAAACAAATAATTACAAAATCCTCAAGGTTCTAAGTCTTTATGTAC
1 ATTTTTTACTTAATAGCATAAAACAAATAATTACAAAATCCTCAAGGTTCTAAGCCTTTATGTAC
49710660 ATGCCATT
66 ATGCCATT
49710668 A
1 A
49710669 CTAACATATT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (73 bp):
ATTTTTTACTTAATAGCATAAAACAAATAATTACAAAATCCTCAAGGTTCTAAGCCTTTATGTAC
ATGCCATT
Found at i:49714710 original size:24 final size:23
Alignment explanation
Indices: 49714678--49714745 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
49714668 GTAGGAACTA
49714678 ATTCTGTATTTGACATTGCATATG
1 ATTCTGTATTTGA-ATTGCATATG
* * ** *
49714702 ATTCTGTATCTGAGGTTATATTTG
1 ATTCTGTATTTGA-ATTGCATATG
*
49714726 AATCTGTATTTGAATTGCAT
1 ATTCTGTATTTGAATTGCAT
49714746 TTGAAAACAT
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.47
Consensus pattern (23 bp):
ATTCTGTATTTGAATTGCATATG
Found at i:49719149 original size:14 final size:14
Alignment explanation
Indices: 49719130--49719156 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49719120 GTGGGAGGTG
49719130 CTACTAGAGCACTA
1 CTACTAGAGCACTA
49719144 CTACTAGAGCACT
1 CTACTAGAGCACT
49719157 TTCAAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (14 bp):
CTACTAGAGCACTA
Found at i:49722201 original size:20 final size:20
Alignment explanation
Indices: 49722159--49722220 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
49722149 TATTAATTCA
* *
49722159 TAATATAATTTATTTTAATT
1 TAATAAAATTTATTTTAACT
**
49722179 TAATAAAATTTATTTTTGCT
1 TAATAAAATTTATTTTAACT
49722199 TAA-AAAA-TTATTATTAA-T
1 TAATAAAATTTATT-TTAACT
49722217 TAAT
1 TAAT
49722221 TATGAAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 9 0.26
19 6 0.18
20 19 0.56
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATAAAATTTATTTTAACT
Found at i:49727895 original size:5 final size:5
Alignment explanation
Indices: 49727881--49727926 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
49727871 AAATGCTCAT
*
49727881 AAAA- AAAAG AAAAG -AAA- AAAAG AAAAG AAAAG AAAAA AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
49727927 AGAAGAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 10 0.27
5 27 0.73
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:49727908 original size:18 final size:17
Alignment explanation
Indices: 49727881--49727930 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 17
49727871 AAATGCTCAT
49727881 AAAAAAAAGAAAAGAAA
1 AAAAAAAAGAAAAGAAA
49727898 AAAAGAAAAGAAAAGAAA
1 AAAA-AAAAGAAAAGAAA
*
49727916 AAAAAAGA-AAAAGAA
1 AAAAAAAAGAAAAGAA
49727931 GAGAAGAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 17 0.55
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAGAAA
Found at i:49733047 original size:17 final size:17
Alignment explanation
Indices: 49733025--49733059 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
49733015 GGATGGCTGA
*
49733025 TAATTTTTTATTGTTAT
1 TAATTTGTTATTGTTAT
*
49733042 TAATTTGTTATTTTTAT
1 TAATTTGTTATTGTTAT
49733059 T
1 T
49733060 TTAGTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TAATTTGTTATTGTTAT
Found at i:49734627 original size:14 final size:14
Alignment explanation
Indices: 49734597--49734627 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
49734587 TTTGGGATCA
49734597 TTTTAGTTTTGGAT
1 TTTTAGTTTTGGAT
49734611 TTTTA-TTTTGGAT
1 TTTTAGTTTTGGAT
49734624 TTTT
1 TTTT
49734628 GGCATGACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.13, C:0.00, G:0.16, T:0.71
Consensus pattern (14 bp):
TTTTAGTTTTGGAT
Found at i:49741532 original size:6 final size:6
Alignment explanation
Indices: 49741514--49741552 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
49741504 CAAGTCTAAG
* *
49741514 AAAATA ACAATA AACATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
49741553 CAAATGGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:49746753 original size:16 final size:16
Alignment explanation
Indices: 49746728--49746758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49746718 AAATTAAACT
49746728 AGAAACAAAAATAAAA
1 AGAAACAAAAATAAAA
*
49746744 AGAAATAAAAATAAA
1 AGAAACAAAAATAAA
49746759 TGGATAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.10
Consensus pattern (16 bp):
AGAAACAAAAATAAAA
Found at i:49749978 original size:33 final size:33
Alignment explanation
Indices: 49749940--49750010 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
49749930 CCGTGTATGA
49749940 CACACAG-TCTAGGCCATTTTGGGCCGTGCGGAC
1 CACACAGCT-TAGGCCATTTTGGGCCGTGCGGAC
* * * *
49749973 TACACAGCTTAGGGCATTTTGGGCTGTGTGGAC
1 CACACAGCTTAGGCCATTTTGGGCCGTGCGGAC
49750006 CACAC
1 CACAC
49750011 GAGCATGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.24
Consensus pattern (33 bp):
CACACAGCTTAGGCCATTTTGGGCCGTGCGGAC
Found at i:49753871 original size:17 final size:18
Alignment explanation
Indices: 49753837--49753871 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
49753827 TATGAAACGT
49753837 TTCATGGTAGATGATATG
1 TTCATGGTAGATGATATG
*
49753855 TTCATGG-AGATGTTATG
1 TTCATGGTAGATGATATG
49753872 ATAATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (18 bp):
TTCATGGTAGATGATATG
Found at i:49754015 original size:22 final size:23
Alignment explanation
Indices: 49753990--49754039 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
49753980 CACTTTTGTG
*
49753990 CTCTCTT-TTCAATACTTTGATA
1 CTCTCTTGTTCAATACTTCGATA
*
49754012 CTCT-TTGTTCAGTACTTCGATA
1 CTCTCTTGTTCAATACTTCGATA
49754034 CTCTCT
1 CTCTCT
49754040 ACTTAGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 21 0.88
23 1 0.04
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.48
Consensus pattern (23 bp):
CTCTCTTGTTCAATACTTCGATA
Found at i:49756555 original size:25 final size:25
Alignment explanation
Indices: 49756521--49756573 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
49756511 TTTCTCCTCC
49756521 AAACAATAAGCTAGTTATAGCGGCT
1 AAACAATAAGCTAGTTATAGCGGCT
49756546 AAACAATAAGCTAGTTATAGCGGCT
1 AAACAATAAGCTAGTTATAGCGGCT
49756571 AAA
1 AAA
49756574 AACGTCCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (25 bp):
AAACAATAAGCTAGTTATAGCGGCT
Found at i:49763882 original size:30 final size:30
Alignment explanation
Indices: 49763833--49763904 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
49763823 TTCAATAGAT
49763833 AATCTAAA-TGAGCCTATAATCCTGTAAAAG
1 AATC-AAAGTGAGCCTATAATCCTGTAAAAG
* *
49763863 AATCAAAGTGAGTCTATAATCTTGTAAAAG
1 AATCAAAGTGAGCCTATAATCCTGTAAAAG
*
49763893 AGT-AAAGTGAGC
1 AATCAAAGTGAGC
49763905 ATTTTATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (30 bp):
AATCAAAGTGAGCCTATAATCCTGTAAAAG
Found at i:49765432 original size:62 final size:61
Alignment explanation
Indices: 49765349--49765464 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 61
49765339 CCAAAAATAA
* * *
49765349 TATTATTTTAATAGTTTAATATTAAATCTAATTTAACGTTTATCTTG-TATATAAACATTC
1 TATTATTTTAATAATTTAATATTAAATCTAATCTAACATTTATCTTGATATATAAACATTC
* *
49765409 TATTATTTTAATAAAATTTAATATTAAATTTAATCTAATATTTATCTTGATATATA
1 TATTATTTTAAT--AATTTAATATTAAATCTAATCTAACATTTATCTTGATATATA
49765465 TTATATTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 12 0.25
62 30 0.62
63 6 0.12
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (61 bp):
TATTATTTTAATAATTTAATATTAAATCTAATCTAACATTTATCTTGATATATAAACATTC
Found at i:49771031 original size:45 final size:45
Alignment explanation
Indices: 49770981--49771109 Score: 179
Period size: 45 Copynumber: 2.9 Consensus size: 45
49770971 TGTACTTTCA
* * *
49770981 CATGATTTCATAGCATTTTTCAGCCATGGTCTTACTCAT-TTCTAT
1 CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATATT-TAT
* * *
49771026 CATGATGTCATAGAATCTTTCAACTAAGGTCTTACTCATATTTAT
1 CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATATTTAT
*
49771071 CATGATGTCATAGCATCTTTCAGTTATGGTCTTACTCAT
1 CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCAT
49771110 CTTAGCGTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 71 0.97
46 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (45 bp):
CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATATTTAT
Found at i:49774489 original size:6 final size:6
Alignment explanation
Indices: 49774480--49774532 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
49774470 GAAAGTAAAA
49774480 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT
1 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT
49774528 GTGTA
1 GTGTA
49774533 ATAATATGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (6 bp):
GTGTAT
Found at i:49776317 original size:23 final size:24
Alignment explanation
Indices: 49776273--49776317 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
49776263 TATATGGGAT
*
49776273 AATAGGGAAATCAAAATCACATCA
1 AATAGGGAAATCAAAATAACATCA
* *
49776297 AATA-GGAACTCATAATAACAT
1 AATAGGGAAATCAAAATAACAT
49776318 TAAACATGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (24 bp):
AATAGGGAAATCAAAATAACATCA
Found at i:49780682 original size:2 final size:2
Alignment explanation
Indices: 49780675--49780741 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
49780665 GGTAGCCGAA
49780675 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
49780717 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
49780742 AAGGGTATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49782281 original size:55 final size:56
Alignment explanation
Indices: 49782158--49782283 Score: 150
Period size: 55 Copynumber: 2.3 Consensus size: 56
49782148 TTTTACACTA
*
49782158 GGGGAAAGCAAAAGGAAAAAAATTTGGGGGGGTTTGAGGGAAGTAAAAGTTATTTT
1 GGGGAAAGTAAAAGGAAAAAAATTTGGGGGGGTTTGAGGGAAGTAAAAGTTATTTT
** * * * *
49782214 GGGG-GGGATAAAAGGAAAAAAGTTT-TGGGGGTTTGAGGAGAAGT-AAATTTTTTTT
1 GGGGAAAG-TAAAAGGAAAAAAATTTGGGGGGGTTTGAGG-GAAGTAAAAGTTATTTT
49782269 GGGGAAAGTAAAAGG
1 GGGGAAAGTAAAAGG
49782284 GTTTGAGGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
55 33 0.57
56 25 0.43
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.25
Consensus pattern (56 bp):
GGGGAAAGTAAAAGGAAAAAAATTTGGGGGGGTTTGAGGGAAGTAAAAGTTATTTT
Found at i:49783440 original size:23 final size:22
Alignment explanation
Indices: 49783364--49783446 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 22
49783354 CCTTTTTAAA
*
49783364 TTTTAAAAATTTAATAAAA-AGTAT
1 TTTTAAAAA-TTAA-AAAATA-TTT
*
49783388 TTTTAAAAATTAAAAATTATTAAT
1 TTTTAAAAATTAAAAAATATT--T
*
49783412 TATTAAAAATATAAAAAATATTT
1 TTTTAAAAAT-TAAAAAATATTT
*
49783435 TTTTAAATATTA
1 TTTTAAAAATTA
49783447 TTAAATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
22 6 0.12
23 14 0.29
24 19 0.39
25 10 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (22 bp):
TTTTAAAAATTAAAAAATATTT
Found at i:49783441 original size:40 final size:41
Alignment explanation
Indices: 49783397--49783474 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
49783387 TTTTTAAAAA
*
49783397 TTAAAAATTATT-AATTATTAAAAATATAA-AAAATATTTTT
1 TTAAAAATTATTAAATT-TTAAAAAAATAATAAAATATTTTT
* *
49783437 TTAAATATTATTAAATTTTAAAAAAATAATTAAATATT
1 TTAAAAATTATTAAATTTTAAAAAAATAATAAAATATT
49783475 GACATGTCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (41 bp):
TTAAAAATTATTAAATTTTAAAAAAATAATAAAATATTTTT
Found at i:49786680 original size:2 final size:2
Alignment explanation
Indices: 49786673--49786710 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
49786663 GGTTTTACAC
49786673 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
49786711 TACTTCAACT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:49789554 original size:19 final size:20
Alignment explanation
Indices: 49789509--49789555 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
49789499 ATTATATTTA
**
49789509 ATTAAAAATAAAAATTTATT
1 ATTAAAAATAAAAATCAATT
49789529 -TTAAAAAATAAAAA-CAATT
1 ATT-AAAAATAAAAATCAATT
49789548 ATTAAAAA
1 ATTAAAAA
49789556 AACAATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTAAAAATAAAAATCAATT
Found at i:49789773 original size:23 final size:24
Alignment explanation
Indices: 49789746--49789795 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
49789736 GCCCGAAAAA
49789746 TTTT-AAATATATATA-TATTTTAT
1 TTTTAAAATATA-ATAGTATTTTAT
*
49789769 TTTTAAAATATAATAGTTTTTTAT
1 TTTTAAAATATAATAGTATTTTAT
49789793 TTT
1 TTT
49789796 AAGTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTAAAATATAATAGTATTTTAT
Found at i:49789790 original size:24 final size:23
Alignment explanation
Indices: 49789746--49789795 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
49789736 GCCCGAAAAA
49789746 TTTTAAATATATATATATTTTAT
1 TTTTAAATATATATATATTTTAT
*
49789769 TTTTAAA-ATATAATAGTTTTTTAT
1 TTTTAAATATAT-ATA-TATTTTAT
49789793 TTT
1 TTT
49789796 AAGTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 10 0.42
24 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTAAATATATATATATTTTAT
Found at i:49789889 original size:59 final size:59
Alignment explanation
Indices: 49789826--49789994 Score: 152
Period size: 59 Copynumber: 2.7 Consensus size: 59
49789816 CCTTGACTAG
49789826 TGTTACAA-AATAATAATA-ATAATACATCAAGTTTG-T-TTTACTAATCAAATGTTAGATTT
1 TGTTACAACAATAATAATACA-AATA-AT-AA-TTTGATATTTACTAATCAAATGTTAGATTT
*
49789885 TGTTACAACAAT--TAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTT
1 TGTTACAACAATAATAATACAAATAATAATTTGAT--ATTTACTAATCAAATGTTAGATTT
* *
49789944 TATTACAACAATTAATACAATTAACAATTAATAATTTGATAATTTTACTAA
1 TGTTACAACAA-TAAT--AA-T-ACAAATAATAATTTGAT-A-TTTACTAA
49789995 CAATTAATTT
Statistics
Matches: 94, Mismatches: 2, Indels: 21
0.80 0.02 0.18
Matches are distributed among these distances:
55 4 0.04
56 3 0.03
57 2 0.02
58 8 0.09
59 42 0.45
60 4 0.04
62 1 0.01
64 2 0.02
65 3 0.03
66 25 0.27
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (59 bp):
TGTTACAACAATAATAATACAAATAATAATTTGATATTTACTAATCAAATGTTAGATTT
Found at i:49790004 original size:16 final size:16
Alignment explanation
Indices: 49789983--49790024 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
49789973 AATAATTTGA
*
49789983 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
49789999 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
49790015 TAGTTTTAAT
1 TAATTTTAAT
49790025 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:49790008 original size:22 final size:23
Alignment explanation
Indices: 49789998--49790053 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
49789988 TTACTAACAA
* * *
49789998 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
49790020 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
49790043 TTAATTTTAAT
1 TTAATTTTAAT
49790054 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:49790789 original size:6 final size:6
Alignment explanation
Indices: 49790778--49790841 Score: 62
Period size: 6 Copynumber: 10.7 Consensus size: 6
49790768 AAGGTAGTTG
*
49790778 TTTTAT TTTTAT TTTTAT TTTTAT TTTT-T TCGTTT-T TATTT-T TTTTAC
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T--TTTAT T-TTTAT TTTTAT
*
49790826 TTTTAC TTTTAT TTTT
1 TTTTAT TTTTAT TTTT
49790842 TAAAGCAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.10
6 42 0.81
7 5 0.10
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:49790829 original size:15 final size:15
Alignment explanation
Indices: 49790778--49790840 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
49790768 AAGGTAGTTG
49790778 TTTTATTTTTA---T
1 TTTTATTTTTATTTT
49790790 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
**
49790805 TTTCGTTTTTATTTT
1 TTTTATTTTTATTTT
*
49790820 TTTTACTTTTACTTTT
1 TTTTATTTTTA-TTTT
49790836 ATTTT
1 -TTTT
49790841 TTAAAGCAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 11 0.27
15 22 0.54
16 4 0.10
17 4 0.10
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTATTTTTATTTT
Found at i:49790835 original size:21 final size:20
Alignment explanation
Indices: 49790778--49790842 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
49790768 AAGGTAGTTG
*
49790778 TTTTATTTTTATTTTTATTTT
1 TTTTA-TTTTACTTTTATTTT
49790799 TATTT-TTTT-CGTTTTTATTTT
1 T-TTTATTTTAC--TTTTATTTT
49790820 TTTTACTTTTACTTTTATTTT
1 TTTTA-TTTTACTTTTATTTT
49790841 TT
1 TT
49790843 AAAGCAGAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
20 7 0.19
21 22 0.59
22 7 0.19
23 1 0.03
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTATTTTACTTTTATTTT
Found at i:49791978 original size:16 final size:17
Alignment explanation
Indices: 49791959--49791991 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49791949 TGTGCGGTCC
49791959 CTATTTT-CATTTTATT
1 CTATTTTACATTTTATT
*
49791975 CTATTTTACGTTTTATT
1 CTATTTTACATTTTATT
49791992 GTTACAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (17 bp):
CTATTTTACATTTTATT
Found at i:49796637 original size:193 final size:193
Alignment explanation
Indices: 49796306--49796692 Score: 738
Period size: 193 Copynumber: 2.0 Consensus size: 193
49796296 AGAAAATTCT
* *
49796306 GGTAAAGTTGATGTTGTAGAATATTACAGCGATAGTGAACTTCTAGTCGCTTCTGTCAATAATTC
1 GGTAAAGCTGATGTTGTAGAATATTACAGCGATAGTAAACTTCTAGTCGCTTCTGTCAATAATTC
*
49796371 TAAAGCGAGCGAGGAGTGGATTCTTGATTCGGGTTGTACCTTCCACATGAGTCCCAATCGGGATT
66 TAAAGCGAGCGAAGAGTGGATTCTTGATTCGGGTTGTACCTTCCACATGAGTCCCAATCGGGATT
*
49796436 GGTTTACAACTTACGAAACAATGTCTGAAGGTATTGTGTTGATGGGAAATAATGCTTCACGTA
131 GATTTACAACTTACGAAACAATGTCTGAAGGTATTGTGTTGATGGGAAATAATGCTTCACGTA
49796499 GGTAAAGCTGATGTTGTAGAATATTACAGCGATAGTAAACTTCTAGTCGCTTCTGTCAATAATTC
1 GGTAAAGCTGATGTTGTAGAATATTACAGCGATAGTAAACTTCTAGTCGCTTCTGTCAATAATTC
49796564 TAAAGCGAGCGAAGAGTGGATTCTTGATTCGGGTTGTACCTTCCACATGAGTCCCAATCGGGATT
66 TAAAGCGAGCGAAGAGTGGATTCTTGATTCGGGTTGTACCTTCCACATGAGTCCCAATCGGGATT
49796629 GATTTACAACTTACGAAACAATGTCTGAAGGTATTGTGTTGATGGGAAATAATGCTTCACGTA
131 GATTTACAACTTACGAAACAATGTCTGAAGGTATTGTGTTGATGGGAAATAATGCTTCACGTA
49796692 G
1 G
49796693 AATTGCAGGT
Statistics
Matches: 190, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 190 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (193 bp):
GGTAAAGCTGATGTTGTAGAATATTACAGCGATAGTAAACTTCTAGTCGCTTCTGTCAATAATTC
TAAAGCGAGCGAAGAGTGGATTCTTGATTCGGGTTGTACCTTCCACATGAGTCCCAATCGGGATT
GATTTACAACTTACGAAACAATGTCTGAAGGTATTGTGTTGATGGGAAATAATGCTTCACGTA
Found at i:49798703 original size:36 final size:36
Alignment explanation
Indices: 49798656--49798728 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
49798646 CATGTAAGCC
49798656 ATGGTTTGTTCACGTCCAGATTTATCATATGCAGTT
1 ATGGTTTGTTCACGTCCAGATTTATCATATGCAGTT
*
49798692 ATGGTTTGTTCATGTCCAGATTTATCATATGCAGTT
1 ATGGTTTGTTCACGTCCAGATTTATCATATGCAGTT
49798728 A
1 A
49798729 GTGTAGTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (36 bp):
ATGGTTTGTTCACGTCCAGATTTATCATATGCAGTT
Found at i:49801773 original size:50 final size:50
Alignment explanation
Indices: 49801664--49801776 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 50
49801654 AATTGATCCA
* * * * *
49801664 AGGTCTAGAGACAAAAGAACATCAAAGTTAAATAGGTTTTGCCTTGCTTT
1 AGGTCTCGAGATAAAAGAACATCAAAGCTAAATAGGTTTTACCCTGCTTT
** *
49801714 AGGTCTCGAGATAAAAGAACATTGAAGCTCAATAGGTTTTACCCTG-TTT
1 AGGTCTCGAGATAAAAGAACATCAAAGCTAAATAGGTTTTACCCTGCTTT
49801763 CAGG-CTTCGAGATA
1 -AGGTC-TCGAGATA
49801777 GGAACCTCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 4 0.08
50 49 0.92
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (50 bp):
AGGTCTCGAGATAAAAGAACATCAAAGCTAAATAGGTTTTACCCTGCTTT
Found at i:49802418 original size:19 final size:19
Alignment explanation
Indices: 49802396--49802449 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
49802386 TAAACATGAT
49802396 TAAAAATCATAAAAAATAA
1 TAAAAATCATAAAAAATAA
* * * *
49802415 TAAAAATGATATAAACTTA
1 TAAAAATCATAAAAAATAA
* *
49802434 TTAAAATTATAAAAAA
1 TAAAAATCATAAAAAA
49802450 ATATAAATAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAAAATCATAAAAAATAA
Found at i:49802558 original size:8 final size:9
Alignment explanation
Indices: 49802535--49802598 Score: 56
Period size: 10 Copynumber: 6.7 Consensus size: 9
49802525 TTATAATTCT
*
49802535 TAAAAATAA
1 TAAAAATTA
49802544 TAAAAAATTA
1 T-AAAAATTA
49802554 TAAAAATTA
1 TAAAAATTA
*
49802563 TAAAAATACA
1 TAAAAAT-TA
*
49802573 TTAAAATTGA
1 TAAAAATT-A
*
49802583 TATAAACTTA
1 TA-AAAATTA
49802593 TAAAAA
1 TAAAAA
49802599 ATTGAACTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
9 19 0.43
10 20 0.45
11 5 0.11
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:49803002 original size:10 final size:10
Alignment explanation
Indices: 49802989--49803149 Score: 58
Period size: 10 Copynumber: 16.7 Consensus size: 10
49802979 GTTTTTATCT
49802989 ATTTTTAATA
1 ATTTTTAATA
49802999 ATTTTT-ATA
1 ATTTTTAATA
* * *
49803008 AGTTTAAATC
1 ATTTTTAATA
* *
49803018 ACTTTGAATA
1 ATTTTTAATA
*
49803028 CTTTTT-ATA
1 ATTTTTAATA
* * *
49803037 TTTTTTTCATG
1 -ATTTTTAATA
*
49803048 ATTTTTATTGA
1 ATTTTTAAT-A
*
49803059 A-TTTTAGTA
1 ATTTTTAATA
49803068 CATTTTTAA-A
1 -ATTTTTAATA
*
49803078 A-TTTAAAT-
1 ATTTTTAATA
*
49803086 ATGTTTTATTA
1 AT-TTTTAATA
49803097 A-TTTT-ATA
1 ATTTTTAATA
*
49803105 ATTTATT-A-G
1 ATTT-TTAATA
49803114 ATTTTT-ATA
1 ATTTTTAATA
49803123 ATTTTT-ATA
1 ATTTTTAATA
49803132 ACTTTTTAATA
1 A-TTTTTAATA
49803143 ATTTTTA
1 ATTTTTA
49803150 TAAGTTCATA
Statistics
Matches: 113, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
8 12 0.11
9 32 0.28
10 56 0.50
11 13 0.12
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:49803128 original size:9 final size:9
Alignment explanation
Indices: 49803089--49803188 Score: 75
Period size: 9 Copynumber: 11.0 Consensus size: 9
49803079 TTTAAATATG
49803089 TTTTATTAA-
1 TTTTA-TAAT
49803098 TTTTATAAT
1 TTTTATAAT
*
49803107 TTATTA-GAT
1 TT-TTATAAT
49803116 TTTTATAAT
1 TTTTATAAT
49803125 TTTTATAACT
1 TTTTATAA-T
49803135 TTTTAATAAT
1 TTTT-ATAAT
49803145 TTTTATAAGT
1 TTTTATAA-T
**
49803155 TCATATCAAT
1 TTTTAT-AAT
*
49803165 TTTCAT-AT
1 TTTTATAAT
49803173 TTTTA-AAT
1 TTTTATAAT
49803181 TTTT-TAAT
1 TTTTATAAT
49803189 ATTAAAAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
8 21 0.28
9 25 0.34
10 22 0.30
11 6 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:49803138 original size:20 final size:20
Alignment explanation
Indices: 49803115--49803152 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
49803105 ATTTATTAGA
49803115 TTTTT-ATAATTTTTATAAC
1 TTTTTAATAATTTTTATAAC
49803134 TTTTTAATAATTTTTATAA
1 TTTTTAATAATTTTTATAA
49803153 GTTCATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAATAATTTTTATAAC
Found at i:49804070 original size:21 final size:21
Alignment explanation
Indices: 49804044--49804085 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
49804034 TATATGGTGA
49804044 TTTATAAAGGATGTAACAACC
1 TTTATAAAGGATGTAACAACC
49804065 TTTATAAAGGATGTAACAACC
1 TTTATAAAGGATGTAACAACC
49804086 ACCATTAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
TTTATAAAGGATGTAACAACC
Found at i:49807799 original size:43 final size:44
Alignment explanation
Indices: 49807738--49807894 Score: 157
Period size: 43 Copynumber: 3.7 Consensus size: 44
49807728 AAAACTCGTA
*
49807738 CAATGCCAA-TGTCCCAGACGTGGTCTTACATGTAATCATATAT
1 CAATGCCAACTATCCCAGACGTGGTCTTACATGTAATCATATAT
* *
49807781 CAATGCC-ACTATCTCAGACAG-GGTCTTACATG-AATCAAATA-
1 CAATGCCAACTATCCCAGAC-GTGGTCTTACATGTAATCATATAT
* * * * * *
49807822 CAATGCCGA-TGTCCCAGACATGGTCTTACACGTAAACATAAAT
1 CAATGCCAACTATCCCAGACGTGGTCTTACATGTAATCATATAT
* *
49807865 CGATGCCAAC-ATCCCAGATGTGGTCTTACA
1 CAATGCCAACTATCCCAGACGTGGTCTTACA
49807895 CGAAAACACG
Statistics
Matches: 92, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
41 25 0.27
42 16 0.17
43 50 0.54
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (44 bp):
CAATGCCAACTATCCCAGACGTGGTCTTACATGTAATCATATAT
Found at i:49807840 original size:41 final size:41
Alignment explanation
Indices: 49807736--49807856 Score: 138
Period size: 41 Copynumber: 2.9 Consensus size: 41
49807726 AGAAAACTCG
*
49807736 TACAATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCATA
1 TACAATGCC-ATGTCCCAGACAG-GGTCTTACATGTAATCAAA
* *
49807778 TATCAATGCCACTATCTCAGACAGGGTCTTACATG-AATCAAA
1 TA-CAATGCCA-TGTCCCAGACAGGGTCTTACATGTAATCAAA
* *
49807820 TACAATGCCGATGTCCCAGACATGGTCTTACACGTAA
1 TACAATGCC-ATGTCCCAGACAGGGTCTTACATGTAA
49807857 ACATAAATCG
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
41 26 0.39
42 14 0.21
43 26 0.39
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (41 bp):
TACAATGCCATGTCCCAGACAGGGTCTTACATGTAATCAAA
Found at i:49809060 original size:91 final size:90
Alignment explanation
Indices: 49808896--49809073 Score: 261
Period size: 91 Copynumber: 2.0 Consensus size: 90
49808886 CATAATTTAA
* *
49808896 AGTCATTCAGACCACATTTATTGACATCTAAACAACAATTTTCTGCTGCATTAATACACCAAACA
1 AGTCATTCAGACAACATTAATTGACATCTAAACAACAATTTTCTGCTGCATTAATACACCAAACA
*
49808961 GCAGCCCTTAAAACAATATAAATAC
66 GCAGCCCTTAAAACAACATAAATAC
* *
49808986 AGTCACTT-AGACAACATTAATTGACGA-CTAAACAAGAATTTTTTTGCTGCATTAATACACCAA
1 AGTCA-TTCAGACAACATTAATTGAC-ATCTAAACAACAA-TTTTCTGCTGCATTAATACACCAA
*
49809049 ACATCAGCCCTTAAAACAACATAAA
63 ACAGCAGCCCTTAAAACAACATAAA
49809074 CAGTGTCACT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
90 30 0.38
91 49 0.62
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.26
Consensus pattern (90 bp):
AGTCATTCAGACAACATTAATTGACATCTAAACAACAATTTTCTGCTGCATTAATACACCAAACA
GCAGCCCTTAAAACAACATAAATAC
Found at i:49817425 original size:6 final size:6
Alignment explanation
Indices: 49817414--49817443 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
49817404 ATTATATGTT
49817414 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
49817444 AATTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
TTTTAG
Found at i:49817461 original size:12 final size:12
Alignment explanation
Indices: 49817413--49817460 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
49817403 AATTATATGT
49817413 TTTTTAGTTTTA
1 TTTTTAGTTTTA
*
49817425 GTTTTAGTTTTA
1 TTTTTAGTTTTA
*
49817437 GTTTTAGAATTTTA
1 TTTTTAG--TTTTA
49817451 TTTTTA-TTTT
1 TTTTTAGTTTT
49817461 TTAAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 4 0.12
12 18 0.56
14 10 0.31
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTTTAGTTTTA
Found at i:49817500 original size:13 final size:13
Alignment explanation
Indices: 49817484--49817508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49817474 AATTTTTATG
49817484 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
49817497 ATTGGGTTGGGT
1 ATTGGGTTGGGT
49817509 TGAATACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:49819367 original size:15 final size:16
Alignment explanation
Indices: 49819349--49819379 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49819339 TGTAGTATAT
49819349 AATA-TTAAAAAAATA
1 AATATTTAAAAAAATA
49819364 AATATTTAAAAAAATA
1 AATATTTAAAAAAATA
49819380 GACACATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATTTAAAAAAATA
Found at i:49821100 original size:35 final size:35
Alignment explanation
Indices: 49821059--49821152 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 35
49821049 ACTGAAGACT
* *
49821059 TAAAATTTCCATTAATAAAACCAAAATCAAAGAAG
1 TAAAATTTCCATTAATAAAACCAAAAACAAAGAAC
* * ** *
49821094 TAAAATTTCCATGAATAAAACGAAAAAGGAAGACC
1 TAAAATTTCCATTAATAAAACCAAAAACAAAGAAC
* *
49821129 TAAATTTTCCATTAATAAAGCCAA
1 TAAAATTTCCATTAATAAAACCAA
49821153 GTGAAGACTA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.23
Consensus pattern (35 bp):
TAAAATTTCCATTAATAAAACCAAAAACAAAGAAC
Found at i:49821734 original size:25 final size:28
Alignment explanation
Indices: 49821699--49821784 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 28
49821689 CATATTTATG
*
49821699 GAAAGCCAAAGATATGGGTATCAA-A-T
1 GAAAGTCAAAGATATGGGTATCAATATT
*
49821725 -AAAGTCAAAGATATGGGTATAAAATATT
1 GAAAGTCAAAGATATGGGTAT-CAATATT
49821753 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-A-ATATT
49821784 G
1 G
49821785 GCATAAGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 19 0.38
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.44
31 5 0.10
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.24
Consensus pattern (28 bp):
GAAAGTCAAAGATATGGGTATCAATATT
Found at i:49821761 original size:30 final size:27
Alignment explanation
Indices: 49821696--49821774 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 27
49821686 ATCCATATTT
* *
49821696 ATGGAAAGCCAAAGATATGGGTATCAA
1 ATGGAAAGTCAAAGATATGGGTATAAA
49821723 AT--AAAGTCAAAGATATGGGTATAAAA
1 ATGGAAAGTCAAAGATATGGGTAT-AAA
49821749 TATTGGAAAGTCAAAGATATGGGTAT
1 -A-TGGAAAGTCAAAGATATGGGTAT
49821775 CGAGATATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 19 0.42
26 2 0.04
27 3 0.07
28 1 0.02
30 20 0.44
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24
Consensus pattern (27 bp):
ATGGAAAGTCAAAGATATGGGTATAAA
Found at i:49829946 original size:44 final size:45
Alignment explanation
Indices: 49829896--49830277 Score: 267
Period size: 44 Copynumber: 8.7 Consensus size: 45
49829886 GATTGGCTTT
** *
49829896 AATCTGCTCCACTGCAACCTCAGTAAGATAGGA-TTATCGTCTTC
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGTCTTC
* *
49829940 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATCATCTT-
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGTCTTC
* * * * ** *
49829984 AGATCTGCCCCACTGCAACATCAGGGGGAGAAGACCT-TCTTAC-TC
1 A-ATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGT-CTTC
* * * *
49830029 AGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGATC--C
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGA-TTTAT-CG-TCTTC
* * *
49830075 -A-CT--T-TACTGCAACTTCAGAGAGATAAGATTTAT--TACGTT-
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGT-C-TTC
* * * *
49830114 AATCCGCTCCACTACAACTTCAGGGAGATAGGA-TTATCGTCTTC
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGTCTTC
*
49830158 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCATCTTC
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGTCTTC
* * * * ** * *
49830203 GATCTGCCCCACTGCAACCTCTGGGGGATAAGACCT-GCTTAC-TC
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGT-CTTC
* *
49830247 AGTCTGCTCCACTGCAACCTCACGGAGATAA
1 AATCTGCTCCACTGCAACCTCAGGGAGATAA
49830278 AACCTGATGC
Statistics
Matches: 264, Mismatches: 52, Indels: 44
0.73 0.14 0.12
Matches are distributed among these distances:
36 1 0.00
37 1 0.00
40 4 0.02
41 21 0.08
42 1 0.00
43 7 0.03
44 141 0.53
45 83 0.31
46 2 0.01
47 2 0.01
48 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTATCGTCTTC
Found at i:49830285 original size:218 final size:218
Alignment explanation
Indices: 49829892--49830603 Score: 894
Period size: 218 Copynumber: 3.2 Consensus size: 218
49829882 GGGGGATTGG
* * * ** *
49829892 CTTTAATCTGCTCCACTGCAACCTCAGTAAGATAGGATTATCGTCTTCAATCTGCTCCACTGCAA
1 CTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTATCGTCTTCAATCTGCTCCACTGCAA
* * * * * *
49829957 CTTCAGGGAGATAAGATTTATCATCTTAGATCTGCCCCACTGCAACATCAGGGGGAGAAGACCTT
66 CCTCAGGGAGATAAGATTTATCATCTTCGATCTGCCCCACTGCAACCTCTGGGGGATAAGACCTG
*
49830022 CTTACTCAGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGATCCACTTTACTGCAA
131 CTTACTCAGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGATCCACTCTACTGCAA
*
49830087 CTTCAGAGAGATAAGATTTATTA
196 CTTCAGAGAGATAAGATCTATTA
* *
49830110 CGTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGTCTTCAATCTGCTCCACTGCAA
1 CTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTATCGTCTTCAATCTGCTCCACTGCAA
49830175 CCTCAGGGAGATAAGATTTATCATCTTCGATCTGCCCCACTGCAACCTCTGGGGGATAAGACCTG
66 CCTCAGGGAGATAAGATTTATCATCTTCGATCTGCCCCACTGCAACCTCTGGGGGATAAGACCTG
* *
49830240 CTTACTCAGTCTGCTCCACTGCAACCTCACGGAGATAAAACCTGATGCGATCCACTCTACTGCAA
131 CTTACTCAGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGATCCACTCTACTGCAA
*
49830305 CTTCAAAGAGATAAGATCTATTA
196 CTTCAGAGAGATAAGATCTATTA
** * *
49830328 CTTTAATCTTCTCCACTACAACTTCAGGAAGATAGGAGAGATAAGATTTATCATCTTCGATCTGC
1 CTTTAATCCGCTCCACTACAACTTC--------AGG-GAGATAAGA-TTATCGTCTTCAATCTGC
* * ** * * * * * *
49830393 CCCACTGCAACCTCAAGGG-GATAACACCT-GCTTAC-TC-AGTCTACTCCGCTGTAACCT-TAG
56 TCCACTGCAACCTC-AGGGAGATAAGATTTATCAT-CTTCGA-TCTGCCCCACTGCAACCTCT-G
* * * * * *
49830453 GGAGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGGTAAGACCTGATGCGAT
117 GGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGAT
*
49830518 CCACTCTACTGCAGCTTCAGAGAGATAAGATCTATTA
182 CCACTCTACTGCAACTTCAGAGAGATAAGATCTATTA
*
49830555 CTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTATCGGCTTCA
1 CTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTATCGTCTTCA
49830604 CCGATCTGTT
Statistics
Matches: 433, Mismatches: 47, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
217 9 0.02
218 232 0.54
219 3 0.01
226 5 0.01
227 143 0.33
228 37 0.09
229 4 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (218 bp):
CTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTATCGTCTTCAATCTGCTCCACTGCAA
CCTCAGGGAGATAAGATTTATCATCTTCGATCTGCCCCACTGCAACCTCTGGGGGATAAGACCTG
CTTACTCAGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGATCCACTCTACTGCAA
CTTCAGAGAGATAAGATCTATTA
Found at i:49830460 original size:44 final size:44
Alignment explanation
Indices: 49830394--49830510 Score: 137
Period size: 44 Copynumber: 2.7 Consensus size: 44
49830384 TCGATCTGCC
*
49830394 CCACTGCAACCTCAAGGG-GATAACACCTGCTTACTCAGTCTACT
1 CCACTGCAACCTC-AGGGAGATAAGACCTGCTTACTCAGTCTACT
* * * * * * *
49830438 CCGCTGTAACCTTAGGGAGATAAGACTTGTTTTCTCAGTCTGCT
1 CCACTGCAACCTCAGGGAGATAAGACCTGCTTACTCAGTCTACT
*
49830482 CCACTGCAACCTCAGGGAGGTAAGACCTG
1 CCACTGCAACCTCAGGGAGATAAGACCTG
49830511 ATGCGATCCA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
43 4 0.07
44 55 0.93
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (44 bp):
CCACTGCAACCTCAGGGAGATAAGACCTGCTTACTCAGTCTACT
Found at i:49832690 original size:15 final size:15
Alignment explanation
Indices: 49832670--49832714 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
49832660 CCTTGGCCTC
49832670 TCCTTTTTTTCTTTT
1 TCCTTTTTTTCTTTT
*
49832685 TCC-TTTTTTCATTT
1 TCCTTTTTTTCTTTT
*
49832699 TCATTTTTTTACTTTT
1 TCCTTTTTTT-CTTTT
49832715 ATTTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TCCTTTTTTTCTTTT
Found at i:49840877 original size:114 final size:113
Alignment explanation
Indices: 49840658--49840948 Score: 302
Period size: 114 Copynumber: 2.5 Consensus size: 113
49840648 ACCGCAATAT
* * * *
49840658 GCAAGAATTATCGGCG-TTTGGTCATAAACGCCGCAAAAACTGTTAAGAAAAACGTTGCCGTTTT
1 GCAAGAATTAGCGGCGCTTT-ATCATAAGCGCCGC-AAAACTGTTAAG-AAAACGTTGCCATTTT
** * * * *
49840722 TAGTTTAGGTTTTGGGGACTTTAGTGGCGCTTAATGAAAAACGCCGCTA-TA
63 TAGTTTACCTTTTCGAGACGTTAGTGGCGATTAATGAAAAACGCCG-TAGTA
49840773 GTCAAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAAACTGTTAAGAAAACGTTGCCATTTTTC
1 G-CAAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAAACTGTTAAGAAAACGTTGCCATTTTT-
* *
49840838 A-TTTACCTTTTCGAGACGTTAGTGGCGATT-TTCGGAAAACGCCGTAGTA
64 AGTTTACCTTTTCGAGACGTTAGTGGCGATTAAT-GAAAAACGCCGTAGTA
** * * * * * *
49840887 GCGAAGCTTTAGTGGCGCTTTATCAGAAGTGCCGCAAAACTATTAAGAAAACGATGTCATTT
1 GC-AAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAAACTGTTAAGAAAACGTTGCCATTT
49840949 CCAATTTAGG
Statistics
Matches: 150, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
113 4 0.03
114 103 0.69
115 14 0.09
116 26 0.17
117 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (113 bp):
GCAAGAATTAGCGGCGCTTTATCATAAGCGCCGCAAAACTGTTAAGAAAACGTTGCCATTTTTAG
TTTACCTTTTCGAGACGTTAGTGGCGATTAATGAAAAACGCCGTAGTA
Found at i:49841672 original size:13 final size:13
Alignment explanation
Indices: 49841656--49841704 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
49841646 TGGATATGGT
*
49841656 TTAAGGATTGGGG
1 TTAAGGGTTGGGG
*
49841669 TTAAGGGTTAAGGG
1 TTAAGGGTT-GGGG
*
49841683 TTAAGGGCTGGGG
1 TTAAGGGTTGGGG
*
49841696 TTAGGGGTT
1 TTAAGGGTT
49841705 TAGGGCTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.31
Consensus pattern (13 bp):
TTAAGGGTTGGGG
Found at i:49841686 original size:27 final size:27
Alignment explanation
Indices: 49841656--49841709 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
49841646 TGGATATGGT
*
49841656 TTAAGGATTGGGGTTAAGGGTTAAGGG
1 TTAAGGACTGGGGTTAAGGGTTAAGGG
* * *
49841683 TTAAGGGCTGGGGTTAGGGGTTTAGGG
1 TTAAGGACTGGGGTTAAGGGTTAAGGG
49841710 CTTTATAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.02, G:0.48, T:0.30
Consensus pattern (27 bp):
TTAAGGACTGGGGTTAAGGGTTAAGGG
Found at i:49841696 original size:20 final size:20
Alignment explanation
Indices: 49841673--49841711 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49841663 TTGGGGTTAA
49841673 GGGTTAAGGGTTAAGGGCTG
1 GGGTTAAGGGTTAAGGGCTG
* *
49841693 GGGTTAGGGGTTTAGGGCT
1 GGGTTAAGGGTTAAGGGCT
49841712 TTATAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.51, T:0.28
Consensus pattern (20 bp):
GGGTTAAGGGTTAAGGGCTG
Found at i:49841910 original size:8 final size:7
Alignment explanation
Indices: 49841877--49841947 Score: 56
Period size: 7 Copynumber: 9.9 Consensus size: 7
49841867 TATGGATTAT
*
49841877 GGTTTAA
1 GGTTTAG
*
49841884 GGTTTGG
1 GGTTTAG
*
49841891 GGTTAAG
1 GGTTTAG
49841898 GGTTTATG
1 GGTTTA-G
49841906 GGTTTAG
1 GGTTTAG
49841913 GG-TTAG
1 GGTTTAG
49841919 AGG-TTAG
1 -GGTTTAG
*
49841926 GGGTTATG
1 GGTTTA-G
49841934 GGTTTAGG
1 GGTTTA-G
49841942 GGTTTA
1 GGTTTA
49841948 TAGTTAACGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
6 6 0.11
7 27 0.51
8 20 0.38
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (7 bp):
GGTTTAG
Found at i:49841940 original size:28 final size:28
Alignment explanation
Indices: 49841855--49841942 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 28
49841845 TAAGAGATAT
*
49841855 GGGTTAGAGGCTTATGGATTAT-GGTTTA
1 GGGTTAGAGG-TTAGGGATTATGGGTTTA
* * * *
49841883 AGGTTTGGGGTTAAGGGTTTATGGGTTTA
1 GGGTTAGAGGTT-AGGGATTATGGGTTTA
*
49841912 GGGTTAGAGGTTAGGGGTTATGGGTTTA
1 GGGTTAGAGGTTAGGGATTATGGGTTTA
49841940 GGG
1 GGG
49841943 GTTTATAGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.04
28 32 0.65
29 15 0.31
ACGTcount: A:0.18, C:0.01, G:0.43, T:0.38
Consensus pattern (28 bp):
GGGTTAGAGGTTAGGGATTATGGGTTTA
Found at i:49844705 original size:17 final size:17
Alignment explanation
Indices: 49844685--49844734 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
49844675 TTAATATCTA
49844685 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
49844702 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
49844716 -ATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
49844732 TAT
1 TAT
49844735 TTGTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
16 2 0.07
17 14 0.48
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:49844721 original size:13 final size:13
Alignment explanation
Indices: 49844703--49844730 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49844693 TTCTAAATTT
49844703 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
49844716 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
49844729 AT
1 AT
49844731 TTATTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAAGTTTTCTAA
Found at i:49844761 original size:15 final size:15
Alignment explanation
Indices: 49844726--49844764 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
49844716 ATAAGTTTTC
*
49844726 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
49844741 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
49844757 TAAATTTA
1 TAAATTTA
49844765 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:49844807 original size:62 final size:61
Alignment explanation
Indices: 49844696--49844844 Score: 174
Period size: 62 Copynumber: 2.4 Consensus size: 61
49844686 ATAAGTTTTC
* *** * *
49844696 TAAATTTATAAGTTTTCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTAT-TAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGT-GTAT
** *
49844757 TAAATTTACTTCGTTTTCTAAATAAGTGTTCTAAATTTGGGAGAAATAAAATTTATGTGTAT
1 TAAATTTA-TAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
* *
49844819 TAAGTTTATAAGTTTTCTACATAAGT
1 TAAATTTATAAGTTTTCTAAATAAGT
49844845 TACATAATAC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
61 23 0.32
62 49 0.67
63 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
Found at i:49844952 original size:31 final size:31
Alignment explanation
Indices: 49844917--49845060 Score: 118
Period size: 31 Copynumber: 4.6 Consensus size: 31
49844907 TGCATAACTT
*
49844917 ACATAATAAATTACATAGCTTATATATAATA
1 ACATAATAAATTACATAACTTATATATAATA
*
49844948 ACATAATAAATTACATAATACTTTATGTTATAAT-
1 ACATAATAAATTACAT-A-AC-TTAT-ATATAATA
* ** * *
49844982 ACATAACT---TGTATATAAGCTTGCATA-ACTT
1 ACATAA-TAAAT-TACATAA-CTTATATATAATA
*
49845012 ACATAATAATTTACATAACTTATATATAATA
1 ACATAATAAATTACATAACTTATATATAATA
49845043 ACATAATAAATTACATAA
1 ACATAATAAATTACATAA
49845061 TACTTTATGT
Statistics
Matches: 88, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
29 3 0.03
30 14 0.16
31 44 0.50
32 5 0.06
33 5 0.06
34 10 0.11
35 7 0.08
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (31 bp):
ACATAATAAATTACATAACTTATATATAATA
Found at i:49844983 original size:95 final size:95
Alignment explanation
Indices: 49844881--49845074 Score: 352
Period size: 95 Copynumber: 2.0 Consensus size: 95
49844871 ACAAAACTTA
* *
49844881 TATAATACATAACTTATATTTAAGCTTGCATAACTTACATAATAAATTACATAGCTTATATATAA
1 TATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAAATTACATAACTTATATATAA
49844946 TAACATAATAAATTACATAATACTTTATGT
66 TAACATAATAAATTACATAATACTTTATGT
* *
49844976 TATAATACATAACTTGTATATAAGCTTGCATAACTTACATAATAATTTACATAACTTATATATAA
1 TATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAAATTACATAACTTATATATAA
49845041 TAACATAATAAATTACATAATACTTTATGT
66 TAACATAATAAATTACATAATACTTTATGT
49845071 TATA
1 TATA
49845075 TAACTTACAT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (95 bp):
TATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAAATTACATAACTTATATATAA
TAACATAATAAATTACATAATACTTTATGT
Found at i:49845088 original size:9 final size:9
Alignment explanation
Indices: 49845074--49845291 Score: 220
Period size: 9 Copynumber: 24.7 Consensus size: 9
49845064 TTTATGTTAT
49845074 ATAACTTAC
1 ATAACTTAC
49845083 ATAACTTAC
1 ATAACTTAC
* *
49845092 ATAAATTAA
1 ATAACTTAC
49845101 ATAACTTAC
1 ATAACTTAC
49845110 ATAACTTAC
1 ATAACTTAC
* *
49845119 ATAAATTAA
1 ATAACTTAC
*
49845128 ATATCTTAC
1 ATAACTTAC
49845137 ATAACTTAC
1 ATAACTTAC
*
49845146 ATAAATTA-
1 ATAACTTAC
49845154 AGTAACTTAC
1 A-TAACTTAC
49845164 ATAACTTAC
1 ATAACTTAC
* *
49845173 ATAAATTAA
1 ATAACTTAC
49845182 ATAACTTAC
1 ATAACTTAC
49845191 ATAACTTAC
1 ATAACTTAC
*
49845200 ATAAATGTA-
1 ATAACT-TAC
*
49845209 GTAACTTAC
1 ATAACTTAC
49845218 ATAACTTAC
1 ATAACTTAC
*
49845227 ATAAATGTA-
1 ATAACT-TAC
*
49845236 GTAACTTAC
1 ATAACTTAC
49845245 ATAACTTAC
1 ATAACTTAC
49845254 AGT-ACTTAC
1 A-TAACTTAC
49845263 AGT-ACTTAC
1 A-TAACTTAC
49845272 ATAA--TAC
1 ATAACTTAC
49845279 ATAA--TAC
1 ATAACTTAC
49845286 ATAACT
1 ATAACT
49845292 GGCGTTTTAG
Statistics
Matches: 175, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
7 14 0.08
8 6 0.03
9 149 0.85
10 6 0.03
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:49845108 original size:27 final size:27
Alignment explanation
Indices: 49845074--49845254 Score: 294
Period size: 27 Copynumber: 6.7 Consensus size: 27
49845064 TTTATGTTAT
49845074 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
49845101 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
*
49845128 ATATCTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
*
49845155 GTAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
49845182 ATAACTTACATAACTTACATAAATGT-A
1 ATAACTTACATAACTTACATAAAT-TAA
*
49845209 GTAACTTACATAACTTACATAAATGT-A
1 ATAACTTACATAACTTACATAAAT-TAA
*
49845236 GTAACTTACATAACTTACA
1 ATAACTTACATAACTTACA
49845255 GTACTTACAG
Statistics
Matches: 148, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
27 147 0.99
28 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (27 bp):
ATAACTTACATAACTTACATAAATTAA
Found at i:49845269 original size:27 final size:27
Alignment explanation
Indices: 49845075--49845282 Score: 293
Period size: 27 Copynumber: 7.8 Consensus size: 27
49845065 TTATGTTATA
*
49845075 TAACTTACATAACTTACATAAATTAAA
1 TAACTTACATAACTTACATAAATTAAG
*
49845102 TAACTTACATAACTTACATAAATTAAA
1 TAACTTACATAACTTACATAAATTAAG
*
49845129 TATCTTACATAACTTACATAAATTAAG
1 TAACTTACATAACTTACATAAATTAAG
*
49845156 TAACTTACATAACTTACATAAATTAAA
1 TAACTTACATAACTTACATAAATTAAG
49845183 TAACTTACATAACTTACATAAATGT-AG
1 TAACTTACATAACTTACATAAAT-TAAG
49845210 TAACTTACATAACTTACATAAATGT-AG
1 TAACTTACATAACTTACATAAAT-TAAG
*
49845237 TAACTTACATAACTTACAGT-ACTTACAG
1 TAACTTACATAACTTACA-TAAATTA-AG
49845265 T-ACTTACATAA--TACATAA
1 TAACTTACATAACTTACATAA
49845283 TACATAACTG
Statistics
Matches: 170, Mismatches: 6, Indels: 12
0.90 0.03 0.06
Matches are distributed among these distances:
24 1 0.01
25 5 0.03
26 1 0.01
27 158 0.93
28 5 0.03
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (27 bp):
TAACTTACATAACTTACATAAATTAAG
Found at i:49850816 original size:21 final size:21
Alignment explanation
Indices: 49850790--49850831 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
49850780 AACAAATGCG
49850790 GCAGCGAAAGAAGCAGAGGTT
1 GCAGCGAAAGAAGCAGAGGTT
*
49850811 GCAGCGAGAGAAGCAGAGGTT
1 GCAGCGAAAGAAGCAGAGGTT
49850832 CAAAAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.40, T:0.10
Consensus pattern (21 bp):
GCAGCGAAAGAAGCAGAGGTT
Found at i:49851218 original size:778 final size:745
Alignment explanation
Indices: 49850086--49851613 Score: 2274
Period size: 778 Copynumber: 2.0 Consensus size: 745
49850076 CACAGCCGGG
* * *
49850086 TCGAGAAGTTTTGCATGTGTAGCTGAGGCGGAGCTATTTTTAATTTTTTAATATTGTCAAATATG
1 TCGAAAAGTTTTGCATATGTAGCCGAGGCGGAGCTATTTTTAATTTTTTAATATTGTCAAATATG
*
49850151 TATAACTTTCCATTAAATAATATTTTTACTACTATATTGTAGAAACTGTCGTCCGGTCAAAAAGT
66 TATAACTATCCATTAAATAATATTTTTACTACTATATTGTAGAAACTGTCGTCCGGTCAAAAAGT
*
49850216 TGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATAGATCTCCCATGACTCTTGAAG
131 TGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATAGATCTCCCATGACTCCTGAAG
*
49850281 CCGGTGAAATAATGGTACGTTTACTTAATACGATTTAACTTGTTTTAGTTATTTATAGTGTTTAT
196 CCAGTGAAATAATGGTACGTTTACTTAATACGATTTAACTTGTTTTAGTTATTTATAGTGTTTAT
49850346 TTTCTAATGGTTTAATTCATTGCTTGTAATGCGACTATTGTTATGTTGCATATGTTTTTTAATAT
261 TTTCTAATGGTTTAATTCATTGCTTGTAATGCGACTATTGTTATGTTGCATATGTTTTTTAATAT
49850411 ATATTGCGTTCCTAACAATGCGATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTAC
326 ATATTGCGTTCCTAACAATGCGATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTAC
* * * * *
49850476 GAAGCGATTGCTTCTAGTGATAGTTCTGTT-TTTTGTAGGCGAGGTTTGCTTTAGAGGTTTCGGA
391 GAAGCGATTGCTTCTAGTGATAGTTCTGTTATCTTGAAGAC-A---TTG--ATA-A-----CCGA
* *
49850540 TGCTTATGTAAAGAAGTCATTGGG-AAAAAG-ATGG-AGAGACAATAAAAGTACTTTGAA-GAAA
444 --ATTAT-TAAAGAAGT-ATTGGGCAAAAAGTATGGTAG-G---AT--AAG-A-TTTCAATG--A
*
49850601 AATTATTATAAGACAAAAACAACCCTCGATGAGAAATTGCAAAATGTTTCGCAGCAATACATGGC
495 AATT-TTATAAGACAAAAACAA-CAT-GATG-G--A-T-C-AAA---TTCGCAGCAATACATGGC
49850666 TTCGGAGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATGACTCAGATGCAAGTGA
548 TTCGGAGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATGACTCAGATGCAAGTGA
49850731 CCACAACTGAGGTTCAAAGGAAATATGAAGAACTCCAGCTACTACTTAAAACAAATGCGGCAGCG
613 CCACAACTGAGGTTCAAAGGAAATATGAAGAACTCCAGCTACTACTTAAAACAAATGCGGCAGCG
49850796 AAAGAAGCAGAGGTTGCAGCGAGAGAAGCAGAGGTTCAAAAGAAATATGAAGAACTGCAGCTAAA
678 AAAGAAGCAGAGGTTGCAGCGAGAGAAGCAGAGGTTCAAAAGAAATATGAAGAACTGCAGCTAAA
49850861 ACT
743 ACT
* *
49850864 TCGAAAAGTTTTGCATATGTAGCCGAGGCGGAGGTATTTTTAATTTTTTAATATTTTCAAATATG
1 TCGAAAAGTTTTGCATATGTAGCCGAGGCGGAGCTATTTTTAATTTTTTAATATTGTCAAATATG
49850929 TATAACTATCCATTAAATAATATTTTTACTACTATATTGTAGAAACTGTCGTCCGGTCAAAAAGT
66 TATAACTATCCATTAAATAATATTTTTACTACTATATTGTAGAAACTGTCGTCCGGTCAAAAAGT
*
49850994 TGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATGGATCTCCCATGACTCCTGAAG
131 TGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATAGATCTCCCATGACTCCTGAAG
*
49851059 CCAGTGAAATAATGGTACGTTTACTTAATACGATTTGACTTGTTTTAGTTATTTATAGTGTTTAT
196 CCAGTGAAATAATGGTACGTTTACTTAATACGATTTAACTTGTTTTAGTTATTTATAGTGTTTAT
49851124 TTTCTAATGGTTTAATTCATTGCTTGTAATGCGACTATTGTTATGTTGCATATGTTTTTTAATAT
261 TTTCTAATGGTTTAATTCATTGCTTGTAATGCGACTATTGTTATGTTGCATATGTTTTTTAATAT
* *
49851189 ATATTGCTTTCCTAACTATGCGATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTAC
326 ATATTGCGTTCCTAACAATGCGATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTAC
* **
49851254 GAAGTGATTGCTTCTAGTGATAGTTCTGTTCATCTTGAAGACATTGATAACCGAATTATTACTGA
391 GAAGCGATTGCTTCTAGTGATAGTTCTGTT-ATCTTGAAGACATTGATAACCGAATTATTAAAGA
* * * * ** ** * * * * ** *
49851319 AGTTTTGGGTCCTGAAAAGTATGGTCGGGTTCGATTTCAATGATCTTTTGTTAGCCCAACCCAAT
455 AGTATTGGG--C-AAAAAGTATGGTAGGATAAGATTTCAATGAAATTTTATAAGACAAAAACAAC
** *
49851384 ATTTTGGATCCAATTCGCAGCAATACATGGCTTCGGAGAGTCAGGCTCAAGCTGAAGTTCAGAGG
517 ATGATGGATCAAATTCGCAGCAATACATGGCTTCGGAGAGTCAGGCTCAAGCTGAAGTTCAGAGG
49851449 TTAAAAGACCAGATGACTCAGATGCAAGTGACCACAACTGAGGTTCAAAGGAAATATGAAGAACT
582 TTAAAAGACCAGATGACTCAGATGCAAGTGACCACAACTGAGGTTCAAAGGAAATATGAAGAACT
49851514 CCAGCTACTACTTAAAACAAATGCGGCAGCGAAAGAAGCAGAGGTTGCAGCGAGAGAAGCAGAGG
647 CCAGCTACTACTTAAAACAAATGCGGCAGCGAAAGAAGCAGAGGTTGCAGCGAGAGAAGCAGAGG
49851579 TTCAAAAGAAATATGAAGAACTGCAGCTAAAACT
712 TTCAAAAGAAATATGAAGAACTGCAGCTAAAACT
49851613 T
1 T
49851614 AAAACAGAGG
Statistics
Matches: 700, Mismatches: 41, Indels: 47
0.89 0.05 0.06
Matches are distributed among these distances:
749 217 0.31
752 2 0.00
753 1 0.00
754 1 0.00
755 1 0.00
757 1 0.00
758 2 0.00
759 1 0.00
760 11 0.02
761 3 0.00
762 5 0.01
763 2 0.00
764 6 0.01
765 7 0.01
766 5 0.01
768 8 0.01
769 5 0.01
770 1 0.00
773 1 0.00
774 2 0.00
776 3 0.00
778 407 0.58
779 1 0.00
780 7 0.01
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (745 bp):
TCGAAAAGTTTTGCATATGTAGCCGAGGCGGAGCTATTTTTAATTTTTTAATATTGTCAAATATG
TATAACTATCCATTAAATAATATTTTTACTACTATATTGTAGAAACTGTCGTCCGGTCAAAAAGT
TGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATAGATCTCCCATGACTCCTGAAG
CCAGTGAAATAATGGTACGTTTACTTAATACGATTTAACTTGTTTTAGTTATTTATAGTGTTTAT
TTTCTAATGGTTTAATTCATTGCTTGTAATGCGACTATTGTTATGTTGCATATGTTTTTTAATAT
ATATTGCGTTCCTAACAATGCGATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTAC
GAAGCGATTGCTTCTAGTGATAGTTCTGTTATCTTGAAGACATTGATAACCGAATTATTAAAGAA
GTATTGGGCAAAAAGTATGGTAGGATAAGATTTCAATGAAATTTTATAAGACAAAAACAACATGA
TGGATCAAATTCGCAGCAATACATGGCTTCGGAGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAA
AAGACCAGATGACTCAGATGCAAGTGACCACAACTGAGGTTCAAAGGAAATATGAAGAACTCCAG
CTACTACTTAAAACAAATGCGGCAGCGAAAGAAGCAGAGGTTGCAGCGAGAGAAGCAGAGGTTCA
AAAGAAATATGAAGAACTGCAGCTAAAACT
Found at i:49851565 original size:21 final size:21
Alignment explanation
Indices: 49851539--49851580 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
49851529 AACAAATGCG
49851539 GCAGCGAAAGAAGCAGAGGTT
1 GCAGCGAAAGAAGCAGAGGTT
*
49851560 GCAGCGAGAGAAGCAGAGGTT
1 GCAGCGAAAGAAGCAGAGGTT
49851581 CAAAAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.40, T:0.10
Consensus pattern (21 bp):
GCAGCGAAAGAAGCAGAGGTT
Found at i:49852030 original size:42 final size:41
Alignment explanation
Indices: 49851959--49852297 Score: 376
Period size: 42 Copynumber: 8.1 Consensus size: 41
49851949 GTTTTTGTAA
* *
49851959 CGGCGCTCAAAGAAAAAGCGCCGCTAAAGAACATGTTTTTTAG
1 CGGCGCT-TAAGAAAAA-CGCCGCTAAAGAACATGTTCTTTAG
* *
49852002 CGGCGCTCATAA-AAAAATGCCACTAAAGAACATGTTCTTTAG
1 CGGCGCT--TAAGAAAAACGCCGCTAAAGAACATGTTCTTTAG
* *
49852044 AGGCGCTTAA-AAAATCGCCGCTAAAGAACATGTTCTTTAG
1 CGGCGCTTAAGAAAAACGCCGCTAAAGAACATGTTCTTTAG
* *
49852084 CGACGCTTAAGGAAAAACGCCGCTAAAGAACATGATCTTTAG
1 CGGCGCTTAA-GAAAAACGCCGCTAAAGAACATGTTCTTTAG
*
49852126 CGGCGCTTAAGGAAAAACGCCGCTAAAGAACATGATCTTTAG
1 CGGCGCTTAA-GAAAAACGCCGCTAAAGAACATGTTCTTTAG
*
49852168 CGGCGCTTAAGGAAAAACGCCGCTAAAGAACATGATCTTTAG
1 CGGCGCTTAA-GAAAAACGCCGCTAAAGAACATGTTCTTTAG
** * * *
49852210 CTACGCTTAAGGGAAAACGCCGCTAAAGATCATGTTTTTTAG
1 CGGCGCTTAA-GAAAAACGCCGCTAAAGAACATGTTCTTTAG
* ** ** * * *
49852252 CGGCGTTTTTCGTTAAGCGCCGCTAAAGATCATGTTCTTTAA
1 CGGCG-CTTAAGAAAAACGCCGCTAAAGAACATGTTCTTTAG
49852294 CGGC
1 CGGC
49852298 ATTTTTAGTT
Statistics
Matches: 262, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
40 38 0.15
42 208 0.79
43 14 0.05
44 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
CGGCGCTTAAGAAAAACGCCGCTAAAGAACATGTTCTTTAG
Found at i:49852237 original size:126 final size:123
Alignment explanation
Indices: 49851970--49852256 Score: 414
Period size: 126 Copynumber: 2.3 Consensus size: 123
49851960 GGCGCTCAAA
*
49851970 GAAAAAGCGCCGCTAAAGAACATGTTTTTTAGCGGCGCTCATAAAAAAATGCCACTAAAGAACAT
1 GAAAAA-CGCCGCTAAAGAACATGTTTTTTAGCGGCGCT-ATAAAAAAACGCCACTAAAGAACAT
* * *
49852035 GTTCTTTAGAGGCGCTTAAAAAATCGCCGCTAAAGAACATGTTCTTTAGCGACGCTTAAG
64 GATCTTTAGAGGCGCTTAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTAAG
* * *
49852095 GAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCT-TAAGGAAAAACGCCGCTAAAGAACAT
1 GAAAAACGCCGCTAAAGAACATGTTTTTTAGCGGCGCTATAA--AAAAACGCCACTAAAGAACAT
* *
49852159 GATCTTTAGCGGCGCTTAAGGAAAAACGCCGCTAAAGAACATGATCTTTAGCTACGCTTAAG
64 GATCTTTAGAGGCGCTTAA--AAAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTAAG
* *
49852221 GGAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCG
1 GAAAAACGCCGCTAAAGAACATGTTTTTTAGCGGCG
49852257 TTTTTCGTTA
Statistics
Matches: 145, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
122 3 0.02
124 66 0.46
125 6 0.04
126 70 0.48
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (123 bp):
GAAAAACGCCGCTAAAGAACATGTTTTTTAGCGGCGCTATAAAAAAACGCCACTAAAGAACATGA
TCTTTAGAGGCGCTTAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTAAG
Found at i:49855812 original size:17 final size:17
Alignment explanation
Indices: 49855785--49855824 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
49855775 CTTTATTTTT
*
49855785 GTGTGGTGTCATCGTTG
1 GTGTTGTGTCATCGTTG
* *
49855802 TTGTTGTGTCATCTTTG
1 GTGTTGTGTCATCGTTG
49855819 GTGTTG
1 GTGTTG
49855825 GGTATCGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.10, G:0.35, T:0.50
Consensus pattern (17 bp):
GTGTTGTGTCATCGTTG
Found at i:49856549 original size:21 final size:19
Alignment explanation
Indices: 49856525--49856567 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
49856515 TAAACTCTCC
49856525 TTAAAGTTCTGTTAAAAGTTT
1 TTAAAGTTCTGTT--AAGTTT
* *
49856546 TTAAGGTTTTGTTAAGTTT
1 TTAAAGTTCTGTTAAGTTT
49856565 TTA
1 TTA
49856568 TGATAAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (19 bp):
TTAAAGTTCTGTTAAGTTT
Found at i:49862656 original size:17 final size:17
Alignment explanation
Indices: 49862623--49862657 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
49862613 ATGTGGCTCG
* *
49862623 ATAATGATTTTATTAAT
1 ATAATGATTTAAGTAAT
49862640 ATAATGATTTAAGTAAT
1 ATAATGATTTAAGTAAT
49862657 A
1 A
49862658 GTATATCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (17 bp):
ATAATGATTTAAGTAAT
Found at i:49864122 original size:24 final size:25
Alignment explanation
Indices: 49864095--49864154 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
49864085 ATTTTTTAAA
*
49864095 TTATAATGTATTTTTATTAT-AAGT
1 TTATAATGTATTATTATTATAAAGT
* * * *
49864119 TTATTACGTATTATTATTTTAAATT
1 TTATAATGTATTATTATTATAAAGT
*
49864144 TTATCATGTAT
1 TTATAATGTAT
49864155 CACTACTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (25 bp):
TTATAATGTATTATTATTATAAAGT
Found at i:49865570 original size:15 final size:14
Alignment explanation
Indices: 49865538--49865567 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49865528 TAAATTTTAG
49865538 TTATGAAATTATTT
1 TTATGAAATTATTT
*
49865552 TTATTAAATTATTT
1 TTATGAAATTATTT
49865566 TT
1 TT
49865568 TATATATTTT
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:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTATGAAATTATTT
Found at i:49865577 original size:11 final size:10
Alignment explanation
Indices: 49865563--49865596 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
49865553 TATTAAATTA
49865563 TTTTTTATAT
1 TTTTTTATAT
49865573 ATTTTTTA-AT
1 -TTTTTTATAT
49865583 TTTTTTATAT
1 TTTTTTATAT
49865593 TTTT
1 TTTT
49865597 ATCTTAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 8 0.36
11 7 0.32
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:49868617 original size:16 final size:16
Alignment explanation
Indices: 49868596--49868649 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
49868586 TTTGGTTCGC
49868596 TGTAATGGAATAGAAG
1 TGTAATGGAATAGAAG
*
49868612 TGTAATAGAATAG-AG
1 TGTAATGGAATAGAAG
*
49868627 CTGTAATGGAATAGAGG
1 -TGTAATGGAATAGAAG
49868644 TGTAAT
1 TGTAAT
49868650 AGTAATTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 30 0.91
17 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAAG
Found at i:49868999 original size:120 final size:123
Alignment explanation
Indices: 49868862--49869112 Score: 384
Period size: 120 Copynumber: 2.0 Consensus size: 123
49868852 TTAATCATAT
*
49868862 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAG-T-A
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTTAA
49868925 -T-TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 CTATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
49868982 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAG--TT
*
49869047 AAAAACTAGATAAATATTCTTATATGAATTTACTAAAATCATATTATATAATACTATAAAAATAA
64 ---AACT--ATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
49869112 T
1 T
49869113 ATATAATCTA
Statistics
Matches: 118, Mismatches: 2, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
120 60 0.51
123 1 0.01
127 1 0.01
128 1 0.01
130 5 0.04
131 50 0.42
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (123 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTTAA
CTATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
Found at i:49870573 original size:49 final size:49
Alignment explanation
Indices: 49870502--49870605 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
49870492 GAAAAAAATC
*
49870502 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTCAACACTTTATA
*
49870551 AAATTAAAATTAA-TTTCAATATCATGAATCAAAAGTTCAACACTTTATA
1 AAATTAAAATTAAGTTT-AATATCATGAATCAAAAGGTCAACACTTTATA
49870600 AAATTA
1 AAATTA
49870606 TAACACATGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
48 3 0.06
49 49 0.94
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.34
Consensus pattern (49 bp):
AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTCAACACTTTATA
Found at i:49871487 original size:29 final size:29
Alignment explanation
Indices: 49871445--49871531 Score: 174
Period size: 29 Copynumber: 3.0 Consensus size: 29
49871435 TTGTTGCTAT
49871445 GTTTATCAACTGTTGGAACCCTAATCTTG
1 GTTTATCAACTGTTGGAACCCTAATCTTG
49871474 GTTTATCAACTGTTGGAACCCTAATCTTG
1 GTTTATCAACTGTTGGAACCCTAATCTTG
49871503 GTTTATCAACTGTTGGAACCCTAATCTTG
1 GTTTATCAACTGTTGGAACCCTAATCTTG
49871532 ATGTGGGTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (29 bp):
GTTTATCAACTGTTGGAACCCTAATCTTG
Found at i:49876630 original size:18 final size:18
Alignment explanation
Indices: 49876607--49876667 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
49876597 CAAGGTCACG
49876607 ATCAATAGTGTCACTATC
1 ATCAATAGTGTCACTATC
** * *
49876625 ATCAATAGCATGACTAGC
1 ATCAATAGTGTCACTATC
*
49876643 ATCAATA-TCGTCACTGTC
1 ATCAATAGT-GTCACTATC
49876661 ATCAATA
1 ATCAATA
49876668 TTGATATCAC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (18 bp):
ATCAATAGTGTCACTATC
Found at i:49880028 original size:34 final size:32
Alignment explanation
Indices: 49879985--49880073 Score: 123
Period size: 34 Copynumber: 2.8 Consensus size: 32
49879975 TTAATATAAC
49879985 ATTTGGTACCTAAACTTGACAATTTTTTTTTCTA
1 ATTTGGTACCTAAACTTGAC-ATTTTTTTTT-TA
*
49880019 ATTTGGTACCCAAACTTGACA---TTTTTTTA
1 ATTTGGTACCTAAACTTGACATTTTTTTTTTA
49880048 ATTT-GTACCTAAACTTGACATTTTTT
1 ATTTGGTACCTAAACTTGACATTTTTT
49880074 CTTAAGTTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
28 15 0.30
29 6 0.12
30 6 0.12
31 3 0.06
33 1 0.02
34 19 0.38
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (32 bp):
ATTTGGTACCTAAACTTGACATTTTTTTTTTA
Found at i:49880056 original size:28 final size:30
Alignment explanation
Indices: 49879985--49880075 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 30
49879975 TTAATATAAC
*
49879985 ATTTGGTACCTAAACTTGACAATTTTTTTTTCTA
1 ATTTGGTACCCAAACTTGAC-A---TTTTTTCTA
49880019 ATTTGGTACCCAAACTTGACATTTTTT-TA
1 ATTTGGTACCCAAACTTGACATTTTTTCTA
*
49880048 ATTT-GTACCTAAACTTGACATTTTTTCT
1 ATTTGGTACCCAAACTTGACATTTTTTCT
49880076 TAAGTTGATA
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
28 21 0.39
29 7 0.13
30 6 0.11
33 1 0.02
34 19 0.35
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.48
Consensus pattern (30 bp):
ATTTGGTACCCAAACTTGACATTTTTTCTA
Found at i:49880329 original size:24 final size:21
Alignment explanation
Indices: 49880265--49880318 Score: 85
Period size: 19 Copynumber: 2.7 Consensus size: 21
49880255 TCTTCAAGGA
*
49880265 TATGTAATCTTAGATATGA--
1 TATGCAATCTTAGATATGATT
49880284 TATGCAATCTTAGATATGATT
1 TATGCAATCTTAGATATGATT
49880305 TATGCAATCTTAGA
1 TATGCAATCTTAGA
49880319 AGATATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.56
21 14 0.44
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (21 bp):
TATGCAATCTTAGATATGATT
Found at i:49880667 original size:3 final size:3
Alignment explanation
Indices: 49880659--49880694 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
49880649 TGTTATTAAG
* *
49880659 TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49880695 CTATATATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Done.