Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 173 of 202
Found at i:53952385 original size:33 final size:32
Alignment explanation
Indices: 53952328--53952399 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
53952318 GTTGAGTGAG
*
53952328 GAAGGCTAGTGGCCGAAGGCGAAGCAAGCAAT
1 GAAGGCTAGGGGCCGAAGGCGAAGCAAGCAAT
* *
53952360 GAAGGCTAAGGGGCCGGAGGTGAAGCAAGCAAT
1 GAAGGCT-AGGGGCCGAAGGCGAAGCAAGCAAT
*
53952393 GGAGGCT
1 GAAGGCT
53952400 GGATAAGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.32, C:0.17, G:0.42, T:0.10
Consensus pattern (32 bp):
GAAGGCTAGGGGCCGAAGGCGAAGCAAGCAAT
Found at i:53958115 original size:27 final size:26
Alignment explanation
Indices: 53958059--53958125 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
53958049 TGGGTTAATG
*
53958059 ATTTAATATAAATAA-AATATATATT
1 ATTTAATATATATAATAATATATATT
53958084 ATTTAATATATATAATTAATATGAT-TT
1 ATTTAATATATATAA-TAATAT-ATATT
*
53958111 -TTTTATA-ATATAATA
1 ATTTAATATATATAATA
53958126 CATTCGAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
24 2 0.05
25 20 0.54
26 6 0.16
27 7 0.19
28 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
ATTTAATATATATAATAATATATATT
Found at i:53964376 original size:24 final size:24
Alignment explanation
Indices: 53964361--53964412 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53964351 AATCAAAGTC
53964361 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
53964385 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
53964409 AAAT
1 AAAT
53964413 CTTCTAGAAA
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:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:53968808 original size:24 final size:24
Alignment explanation
Indices: 53968781--53968834 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
53968771 AATCAAAGTC
* *
53968781 AAATATATTATGCT-ACTAAATGTT
1 AAATATATTATACTCA-TAAATATT
53968805 AAATATATTATACTCATAAATATT
1 AAATATATTATACTCATAAATATT
53968829 AAATAT
1 AAATAT
53968835 TCTAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATATTATACTCATAAATATT
Found at i:53969032 original size:19 final size:20
Alignment explanation
Indices: 53968990--53969033 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
53968980 TTCAAAAAAT
53968990 AATTTCTGGTAAATAGATTA
1 AATTTCTGGTAAATAGATTA
*
53969010 AATTTTTGGTATAAT-GA-TA
1 AATTTCTGGTA-AATAGATTA
53969029 AATTT
1 AATTT
53969034 AGCTCTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 12 0.55
21 3 0.14
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (20 bp):
AATTTCTGGTAAATAGATTA
Found at i:53970419 original size:67 final size:66
Alignment explanation
Indices: 53970348--53970480 Score: 185
Period size: 67 Copynumber: 2.0 Consensus size: 66
53970338 CAAATTTTCC
* * ** *
53970348 CTATATTTTATGCTTAGAGTTCTATTCAACTAATAAATTTATTTTAAAATTAGCACAACTTTTTT
1 CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAA-TTTTTT
53970413 TT
65 TT
* * *
53970415 CTATATTTTATACTTAGAATTCTATTCAAGTAATAAACATACTTTAAAATTTGTACAATTTTTTT
1 CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAATTTTTTT
53970480 T
66 T
53970481 ACATTAAACT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
66 8 0.14
67 50 0.86
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (66 bp):
CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAATTTTTTT
T
Found at i:53977802 original size:9 final size:9
Alignment explanation
Indices: 53977785--53977821 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53977775 TAAGTTTTCG
53977785 AATTCGAAT
1 AATTCGAAT
*
53977794 AACTCGAAT
1 AATTCGAAT
53977803 AATTCGAAT
1 AATTCGAAT
53977812 AATTCGAAT
1 AATTCGAAT
53977821 A
1 A
53977822 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53978824 original size:6 final size:6
Alignment explanation
Indices: 53978813--53978840 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53978803 GCAGCTTGGG
53978813 TTCACT TTCACT TTCACT TTCACT TTCA
1 TTCACT TTCACT TTCACT TTCACT TTCA
53978841 ACTTGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCACT
Found at i:53982492 original size:19 final size:20
Alignment explanation
Indices: 53982450--53982492 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
53982440 TCATGCTTTC
*
53982450 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
53982470 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
53982488 TATTC
1 TATTC
53982493 TACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:53982731 original size:45 final size:45
Alignment explanation
Indices: 53982658--53982767 Score: 166
Period size: 45 Copynumber: 2.4 Consensus size: 45
53982648 CCTAAACAGT
* * *
53982658 AATCAGTAACGGTAGCAGTAACAATATTCAACACACAAAGTGCCA
1 AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
* * *
53982703 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
53982748 AATCGGTAACAGTAACAGTA
1 AATCGGTAACAGTAACAGTA
53982768 GTCGGCATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (45 bp):
AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
Found at i:53985180 original size:23 final size:23
Alignment explanation
Indices: 53985154--53985202 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
53985144 TTTTCAGAAG
53985154 TTTAATTAAATTAGAAGTTTGTT
1 TTTAATTAAATTAGAAGTTTGTT
*
53985177 TTTAATTAAATTAGAATTTTGTT
1 TTTAATTAAATTAGAAGTTTGTT
53985200 TTT
1 TTT
53985203 CATTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (23 bp):
TTTAATTAAATTAGAAGTTTGTT
Found at i:53987121 original size:3 final size:3
Alignment explanation
Indices: 53987113--53987204 Score: 184
Period size: 3 Copynumber: 30.7 Consensus size: 3
53987103 TTGCACCATG
53987113 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53987161 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53987205 GTCATTCACC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:53989978 original size:24 final size:24
Alignment explanation
Indices: 53989930--53989976 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53989920 ACTGGTCATA
*
53989930 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
53989954 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
53989977 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:53990689 original size:27 final size:27
Alignment explanation
Indices: 53990650--53990761 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
53990640 AGAGGTCGAT
* ** *
53990650 AAATGATCAAAATACCCTTACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
53990677 AAATGATCGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
53990704 AAATGATTGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
53990731 AAATGA-CTGAAATACCCCCATAGGGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
53990758 AAAT
1 AAAT
53990762 AACTGTTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:53990766 original size:27 final size:27
Alignment explanation
Indices: 53990671--53990775 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
53990661 ATACCCTTAC
53990671 AGGGTAAAATGA-TCGAAATACCCCCGT
1 AGGGTAAAATGACT-GAAATACCCCCGT
*
53990698 AGGGTAAAATGATTGAAATACCCCCGT
1 AGGGTAAAATGACTGAAATACCCCCGT
*
53990725 AGGGTAAAATGACTGAAATACCCCCAT
1 AGGGTAAAATGACTGAAATACCCCCGT
* **
53990752 AGGGTAAAATAACTGTTATACCCC
1 AGGGTAAAATGACTGAAATACCCC
53990776 TAGGAGATGA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 71 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (27 bp):
AGGGTAAAATGACTGAAATACCCCCGT
Found at i:53993717 original size:26 final size:26
Alignment explanation
Indices: 53993677--53993735 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
53993667 AGTTTGACAG
*
53993677 AATCATTTTAGACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
53993703 AATCATTTTACACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
53993729 AATCATT
1 AATCATT
53993736 AACATGTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (26 bp):
AATCATTTTACACCAATCTAGTCCTT
Found at i:53997348 original size:20 final size:21
Alignment explanation
Indices: 53997303--53997350 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
53997293 TCCAAATCAG
* **
53997303 TTTCCCGAAATCCCTTATTTT
1 TTTCCCCAAATCCCTTATAAT
53997324 TTTCCCCAAATCCCTTA-AAT
1 TTTCCCCAAATCCCTTATAAT
53997344 TTTCCCC
1 TTTCCCC
53997351 GATCGTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTCCCCAAATCCCTTATAAT
Found at i:54000803 original size:3 final size:3
Alignment explanation
Indices: 54000797--54000834 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54000787 ATTAAACACA
54000797 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54000835 CCAAGTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54001157 original size:49 final size:48
Alignment explanation
Indices: 54001097--54001328 Score: 216
Period size: 49 Copynumber: 4.7 Consensus size: 48
54001087 GATAATAACA
* * *
54001097 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTTCATGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGT-TCTCATAT-CG
* * *
54001146 AGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-GTTCTCATATC-G
* * * *
54001196 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGGCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGG-TTCTCATATC-G
* ** * *
54001245 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-GTTCTCATATC-G
* * *
54001295 TACCAACGCCATGTCCCAAACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
54001329 TGACCTCTCA
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
48 2 0.01
49 80 0.51
50 75 0.48
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.26
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGTTCTCATATCG
Found at i:54001221 original size:50 final size:50
Alignment explanation
Indices: 54001097--54001339 Score: 253
Period size: 50 Copynumber: 4.9 Consensus size: 50
54001087 GATAATAACA
* * * *
54001097 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGG-GTGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATCT-CGG
* * * * * *
54001146 AGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
* * *
54001196 TGCCCATGCCATGTCCCAGACATGGTCTTAC--GGGGGCCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATCTCGG
* *
54001245 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
* * * *
54001295 TACCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT
54001340 GATCTCAAGG
Statistics
Matches: 165, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
48 5 0.03
49 77 0.47
50 80 0.48
51 3 0.02
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
Found at i:54001250 original size:99 final size:99
Alignment explanation
Indices: 54001099--54001326 Score: 262
Period size: 99 Copynumber: 2.3 Consensus size: 99
54001089 TAATAACATG
* * ** * * *
54001099 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTTCATGTACAGCCAATGCCATATCCCA
1 CCAACGCCATGTCCCAGACATGGTCTTACAGGGGGCCTCTCATCTACAGCCAACGCCATATCCCA
* ** *
54001164 GATATGGTCTTACATGGGAGTTCTCATATCGGTG
66 GACATGGTCTTACATGGGACCTCTCATATCGGTA
* * * *
54001198 CCCATGCCATGTCCCAGACATGGTCTTAC-GGGGGCCTCTCATCT-CGGTGCCAACGCCATGTCC
1 CCAACGCCATGTCCCAGACATGGTCTTACAGGGGGCCTCTCATCTAC--AGCCAACGCCATATCC
* *
54001261 CAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
64 CAGACATGGTCTTACATGGGACCTCTCATATCGGTA
*
54001297 CCAACGCCATGTCCCAAACATGGTCTTACA
1 CCAACGCCATGTCCCAGACATGGTCTTACA
54001327 TGTGACCTCT
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
97 1 0.01
98 10 0.09
99 96 0.90
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.25
Consensus pattern (99 bp):
CCAACGCCATGTCCCAGACATGGTCTTACAGGGGGCCTCTCATCTACAGCCAACGCCATATCCCA
GACATGGTCTTACATGGGACCTCTCATATCGGTA
Found at i:54001363 original size:56 final size:50
Alignment explanation
Indices: 54001099--54001375 Score: 236
Period size: 50 Copynumber: 5.5 Consensus size: 50
54001089 TAATAACATG
* *** * * * *
54001099 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTTCATGTACAG--
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCT-CGGTA
* * * ** * * *
54001148 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
* * * * * *
54001198 CCCATGCCATGTCCCAGACATGGTCTTAC-GGGGGCCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
54001247 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
* *
54001297 CCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTCATGATCTCAAGGATA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TCTC--GG-TA
* *
54001353 CCAATGCCATGTCCTAGACATGG
1 CCAACGCCATGTCCCAGACATGG
54001376 AATCTCTTTA
Statistics
Matches: 191, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
48 2 0.01
49 79 0.41
50 81 0.42
52 1 0.01
53 4 0.02
55 2 0.01
56 22 0.12
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
Found at i:54002967 original size:50 final size:51
Alignment explanation
Indices: 54002799--54002980 Score: 206
Period size: 51 Copynumber: 3.6 Consensus size: 51
54002789 TGTCTGCGAA
* * * ****
54002799 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAAATAACGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAGCTTGGT
* * *
54002850 CACGTGTGTAGTACTAAGTGCAAGCTACTATGTGAACC-AGAAGGCCTTGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAG-CTTGGT
* * *
54002901 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCGA-AAAGCTTGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAGCTTGGT
* *
54002951 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
54002981 TGTGTATCAA
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
50 37 0.33
51 74 0.66
52 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAGCTTGGT
Found at i:54004388 original size:2 final size:2
Alignment explanation
Indices: 54004381--54004423 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54004371 TAATAGTAAG
54004381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54004423 T
1 T
54004424 TAATTATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54006296 original size:25 final size:25
Alignment explanation
Indices: 54006262--54006348 Score: 156
Period size: 25 Copynumber: 3.5 Consensus size: 25
54006252 TACGAGCACT
54006262 TAACGGGAAGCTCATGTGAGCTGTA
1 TAACGGGAAGCTCATGTGAGCTGTA
*
54006287 TAACGGGAAGCTCATGTGAGCCGTA
1 TAACGGGAAGCTCATGTGAGCTGTA
*
54006312 TAACGGGAAGCTCATGTGAGCTCTA
1 TAACGGGAAGCTCATGTGAGCTGTA
54006337 TAACGGGAAGCT
1 TAACGGGAAGCT
54006349 TATCCAGGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (25 bp):
TAACGGGAAGCTCATGTGAGCTGTA
Found at i:54006372 original size:50 final size:50
Alignment explanation
Indices: 54006268--54006376 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
54006258 CACTTAACGG
* ** **
54006268 GAAGCTCATGTGAGCTGTATAACGGGAAGCTCATGTGAGCCGTATAACGG
1 GAAGCTCATGTGAGCTCTATAACGGGAAGCTCATCAGAGCCGTATAACAA
* **
54006318 GAAGCTCATGTGAGCTCTATAACGGGAAGCTTATCCAG-GTTGTATAACAA
1 GAAGCTCATGTGAGCTCTATAACGGGAAGCTCAT-CAGAGCCGTATAACAA
54006368 GAAGCTCAT
1 GAAGCTCAT
54006377 AAGAGCCATA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (50 bp):
GAAGCTCATGTGAGCTCTATAACGGGAAGCTCATCAGAGCCGTATAACAA
Found at i:54010854 original size:2 final size:2
Alignment explanation
Indices: 54010841--54010872 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
54010831 AAAATTTATC
54010841 AT AT AT -T A- 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
54010873 TTACAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54029079 original size:20 final size:19
Alignment explanation
Indices: 54029035--54029073 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54029025 GCTCTTGAAC
54029035 TATACTCATTTTTCTATAT
1 TATACTCATTTTTCTATAT
54029054 TATACTCATTTTTCTATAT
1 TATACTCATTTTTCTATAT
54029073 T
1 T
54029074 GGTACTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (19 bp):
TATACTCATTTTTCTATAT
Found at i:54031913 original size:10 final size:10
Alignment explanation
Indices: 54031885--54031918 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
54031875 TTTCATATTA
54031885 AAATTAAAAT
1 AAATTAAAAT
*
54031895 ATA-TAAAAT
1 AAATTAAAAT
54031904 AAATTAAAAT
1 AAATTAAAAT
54031914 AAATT
1 AAATT
54031919 TTTGGTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:54036462 original size:23 final size:23
Alignment explanation
Indices: 54036436--54036534 Score: 164
Period size: 23 Copynumber: 4.3 Consensus size: 23
54036426 ATAAGTGCCA
54036436 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54036459 CACT-ATTATGTAGCCGAAGCTAC
1 CACTGA-TATGTAGCCGAAGCTAC
*
54036482 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54036505 CACTGATATGTAGCCGAAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
54036528 CACTGAT
1 CACTGAT
54036535 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
22 1 0.01
23 69 0.97
24 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54038975 original size:31 final size:31
Alignment explanation
Indices: 54038938--54038996 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
54038928 ATTTAACTAA
54038938 ATTTGTTATTATTATTTTCAATTTATATGTT
1 ATTTGTTATTATTATTTTCAATTTATATGTT
54038969 ATTTGTTATTATTATTTTCAATTTATAT
1 ATTTGTTATTATTATTTTCAATTTATAT
54038997 ATATTTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.64
Consensus pattern (31 bp):
ATTTGTTATTATTATTTTCAATTTATATGTT
Found at i:54038994 original size:17 final size:17
Alignment explanation
Indices: 54038943--54039003 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
54038933 ACTAAATTTG
54038943 TTATTATTATTTTCAAT
1 TTATTATTATTTTCAAT
* *
54038960 TTATATGTTA-TTT---G
1 TTAT-TATTATTTTCAAT
54038974 TTATTATTATTTTCAAT
1 TTATTATTATTTTCAAT
54038991 TTA-TATATATTTT
1 TTATTAT-TATTTT
54039004 GGAGTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 4 0.12
14 7 0.21
16 3 0.09
17 16 0.47
18 4 0.12
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATTATTATTTTCAAT
Found at i:54049530 original size:58 final size:58
Alignment explanation
Indices: 54049389--54049535 Score: 159
Period size: 58 Copynumber: 2.5 Consensus size: 58
54049379 GTACGTAGTG
* * * * * *
54049389 TAAGACCATGGATGAAAGATGTTATGGTAGCATGGTACAAGGTAAAATGTATATAGCG
1 TAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATACAGCA
* ** * * * *
54049447 TAAGACCATGGAAGAAAGACACTATGGCGGCACGGTACAAGGTATAAGGTATACGGTA
1 TAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATACAGCA
* *
54049505 TAAGACCATAGATGAAAGATGCTATGACAGC
1 TAAGACCATGGATGAAAGATGCTATGGCAGC
54049536 CAGGCATGAT
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (58 bp):
TAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATACAGCA
Found at i:54049622 original size:32 final size:32
Alignment explanation
Indices: 54049585--54049646 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
54049575 GCATCCACAG
54049585 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
1 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
* *
54049617 AGATAAGTCTGCTGGGACAGTAAACACAGA
1 AGATAAGCCTGCTGAGACAGTAAACACAGA
54049647 TGAATTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (32 bp):
AGATAAGCCTGCTGAGACAGTAAACACAGAAT
Found at i:54051151 original size:22 final size:22
Alignment explanation
Indices: 54051126--54051169 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54051116 TCAAAAATAC
*
54051126 AGGAGCACATAAA-TGCTAAATT
1 AGGAGAAC-TAAAGTGCTAAATT
*
54051148 AGGAGAACTAAAGTGTTAAATT
1 AGGAGAACTAAAGTGCTAAATT
54051170 GATTGCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (22 bp):
AGGAGAACTAAAGTGCTAAATT
Found at i:54056862 original size:13 final size:13
Alignment explanation
Indices: 54056844--54056868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54056834 ATAAGGGGAT
54056844 TTAAAATTAAAAA
1 TTAAAATTAAAAA
54056857 TTAAAATTAAAA
1 TTAAAATTAAAA
54056869 CAAATTAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:54068253 original size:27 final size:27
Alignment explanation
Indices: 54068223--54068290 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
54068213 GTCTATCTCA
54068223 GAGGCGCCAATGGTGGTGCC-TATCTGG
1 GAGGCGCCAATGGTGGTGCCATA-CTGG
* **
54068250 GAGGCGCCATTATTGGTGCCATACTGG
1 GAGGCGCCAATGGTGGTGCCATACTGG
54068277 GAGGCGCCAATGGT
1 GAGGCGCCAATGGT
54068291 CTGATTTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.38, T:0.22
Consensus pattern (27 bp):
GAGGCGCCAATGGTGGTGCCATACTGG
Found at i:54068380 original size:18 final size:18
Alignment explanation
Indices: 54068344--54068395 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
54068334 ACTAGAGAAA
54068344 CAGAAGAAATAAGAAGGAAG
1 CAGAAGAAA-AA-AAGGAAG
54068364 CAGAAGAAAAAAAGGAAG
1 CAGAAGAAAAAAAGGAAG
* *
54068382 GAAAAGAAGAAAAA
1 CAGAAGAA-AAAAA
54068396 AATGTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 13 0.45
19 7 0.24
20 9 0.31
ACGTcount: A:0.67, C:0.04, G:0.27, T:0.02
Consensus pattern (18 bp):
CAGAAGAAAAAAAGGAAG
Found at i:54068396 original size:20 final size:19
Alignment explanation
Indices: 54068340--54068396 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
54068330 TTTTACTAGA
*
54068340 GAAACAGAAGAAATAAGAAG
1 GAAA-AGAAGAAAAAAGAAG
*
54068360 GAAGCAGAAGAAAAAAAGGAAG
1 GAA-AAGAAG-AAAAAA-GAAG
54068382 GAAAAGAAGAAAAAA
1 GAAAAGAAGAAAAAA
54068397 ATGTATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.45
21 10 0.32
22 7 0.23
ACGTcount: A:0.68, C:0.04, G:0.26, T:0.02
Consensus pattern (19 bp):
GAAAAGAAGAAAAAAGAAG
Found at i:54071750 original size:6 final size:6
Alignment explanation
Indices: 54071742--54071773 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
54071732 GTCTCTAGCA
*
54071742 CTGGCA CTGGCT CTGGCT CTGGCT CTGGCT CT
1 CTGGCT CTGGCT CTGGCT CTGGCT CTGGCT CT
54071774 AGTGCATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.34, G:0.31, T:0.31
Consensus pattern (6 bp):
CTGGCT
Found at i:54073427 original size:16 final size:15
Alignment explanation
Indices: 54073396--54073439 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
54073386 ACAAAATCAA
54073396 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
54073411 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
54073427 ATAAAAATTAAAT
1 AT-AAAATTAAAT
54073440 GAGTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:54073516 original size:37 final size:37
Alignment explanation
Indices: 54073474--54073549 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
54073464 AAAAAGTCAG
54073474 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
54073511 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
54073548 TT
1 TT
54073550 TTATAAACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (37 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTT
Found at i:54073773 original size:19 final size:19
Alignment explanation
Indices: 54073749--54074010 Score: 107
Period size: 19 Copynumber: 13.2 Consensus size: 19
54073739 ATATCCCGAC
54073749 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
54073768 ATTACAATATCACAATATTCATACAAA
1 ATTAC-A-AT----AT--TCATACAAA
54073795 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATAC---AAA
* *
54073817 ATTGCAATATTCATATAAA
1 ATTACAATATTCATACAAA
* *
54073836 ATTATAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
54073852 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
54073866 ATTACAATATTCATATAAAAA
1 ATTACAATATTC--ATACAAA
54073887 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
* * *
54073906 A-TACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
54073926 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
54073948 ATTACAATATTCATAAAAA
1 ATTACAATATTCATACAAA
54073967 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATAC---AAA
* *
54073989 ATTAGAATATTCATAAAAA
1 ATTACAATATTCATACAAA
54074008 ATT
1 ATT
54074011 CTAATCCAAA
Statistics
Matches: 189, Mismatches: 20, Indels: 68
0.68 0.07 0.25
Matches are distributed among these distances:
14 9 0.05
15 1 0.01
16 10 0.05
17 3 0.02
18 9 0.05
19 54 0.29
20 15 0.08
21 23 0.12
22 39 0.21
23 5 0.03
25 6 0.03
26 1 0.01
27 14 0.07
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:54073785 original size:27 final size:27
Alignment explanation
Indices: 54073752--54073804 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
54073742 TCCCGACATT
54073752 ACAATATTCATACAAAATTACAATATC
1 ACAATATTCATACAAAATTACAATATC
54073779 ACAATATTCATACAAAATTACAATAT
1 ACAATATTCATACAAAATTACAATAT
54073805 TCATACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (27 bp):
ACAATATTCATACAAAATTACAATATC
Found at i:54073830 original size:41 final size:41
Alignment explanation
Indices: 54073749--54074010 Score: 214
Period size: 49 Copynumber: 6.1 Consensus size: 41
54073739 ATATCCCGAC
*
54073749 ATTACAATATTCATACAAAATTACAATATCACAATATTCATACAAA
1 ATTACAATATTCATACAAAA--A-AAT-T-ACAATATTCATAAAAA
*
54073795 ATTACAATATTCATACAAAAAAATTGCAATATTCATATAAAATTATAA
1 ATTACAATATTCATACAAAAAAATTACAATATTC--AT--AA--A-AA
54073843 TATTACAATATTCATACAAAAAAATTACAATATTCATATAAAAA
1 -ATTACAATATTCATACAAAAAAATTACAATATTC--ATAAAAA
* *
54073887 ATTACAATATTCATAC---AAAA-TACTA-ATCCA-AAACTATA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATAAA--A-A
* * * *
54073925 AATACAA-ATTTAATTATAAAATAATTACAATATTCATAAAAA
1 ATTACAATA-TTCA-TACAAAAAAATTACAATATTCATAAAAA
*
54073967 ATTACAATATTCATACAAAAAAATTAGAATATTCATAAAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATAAAAA
54074008 ATT
1 ATT
54074011 CTAATCCAAA
Statistics
Matches: 180, Mismatches: 16, Indels: 45
0.75 0.07 0.19
Matches are distributed among these distances:
35 3 0.02
36 1 0.01
37 2 0.01
38 13 0.07
39 6 0.03
40 4 0.02
41 36 0.20
42 14 0.08
43 27 0.15
44 7 0.04
45 5 0.03
46 20 0.11
47 3 0.02
48 2 0.01
49 37 0.21
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAAATTACAATATTCATAAAAA
Found at i:54073837 original size:68 final size:68
Alignment explanation
Indices: 54073749--54073907 Score: 239
Period size: 68 Copynumber: 2.3 Consensus size: 68
54073739 ATATCCCGAC
54073749 ATTACAATATTCATACAAAATTACAATATCACAATATTCATAC-AAAATTACAATATTCATACAA
1 ATTACAATATTCATACAAAATTACAATATCACAATATTCATACAAAAATTACAATATTCATA-AA
54073813 AAAA
65 AAAA
* * * * *
54073817 ATTGCAATATTCATATAAAATTATAATATTACAATATTCATACAAAAAAATTACAATATTCATAT
1 ATTACAATATTCATACAAAATTACAATATCACAATATTCATAC--AAAAATTACAATATTCATAA
54073882 AAAAA
64 AAAAA
54073887 ATTACAATATTCATACAAAAT
1 ATTACAATATTCATACAAAAT
54073908 ACTAATCCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
68 39 0.48
70 24 0.30
71 18 0.22
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (68 bp):
ATTACAATATTCATACAAAATTACAATATCACAATATTCATACAAAAATTACAATATTCATAAAA
AAA
Found at i:54073930 original size:70 final size:71
Alignment explanation
Indices: 54073792--54073932 Score: 171
Period size: 70 Copynumber: 2.0 Consensus size: 71
54073782 ATATTCATAC
* * ** * **
54073792 AAAATTACAATATTCATACAAAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCA
1 AAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTATAATACCAAAATATAAA
54073857 TACAAA
66 TACAAA
*
54073863 AAAATTACAATATTCATA-TAAAAAATTACAATATTCATACAAAA-TACTAAT-CCAAAACTATA
1 AAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTA-TAATACCAAAA-TATA
54073925 AATACAAA
64 AATACAAA
54073933 TTTAATTATA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
69 5 0.08
70 37 0.62
71 18 0.30
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.30
Consensus pattern (71 bp):
AAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTATAATACCAAAATATAAA
TACAAA
Found at i:54073987 original size:22 final size:21
Alignment explanation
Indices: 54073942--54074008 Score: 93
Period size: 22 Copynumber: 3.2 Consensus size: 21
54073932 ATTTAATTAT
*
54073942 AAAATAATTACAATATTCAT-
1 AAAAAAATTACAATATTCATA
54073962 -AAAAAATTACAATATTCATA
1 AAAAAAATTACAATATTCATA
*
54073982 CAAAAAAATTAGAATATTCATA
1 -AAAAAAATTACAATATTCATA
54074004 AAAAA
1 AAAAA
54074009 TTCTAATCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 18 0.43
21 5 0.12
22 19 0.45
ACGTcount: A:0.61, C:0.09, G:0.01, T:0.28
Consensus pattern (21 bp):
AAAAAAATTACAATATTCATA
Found at i:54074052 original size:102 final size:102
Alignment explanation
Indices: 54073844--54074044 Score: 280
Period size: 102 Copynumber: 1.9 Consensus size: 102
54073834 AAATTATAAT
* *
54073844 ATTACAATATTCATACAAAAAAATTACAATATTCATATAAAAAATTACAATATTCATACAAAATA
1 ATTACAATATTCAT--AAAAAAATTACAATATTCATAAAAAAAATTACAATATTCATAAAAAATA
* * *
54073909 CTAATCCAAAACTATAAATACAAATTTAATTATAAAATA
64 CTAATCCAAAACTATAAACACAAATATAATAATAAAATA
* *
54073948 ATTACAATATTCAT-AAAAAATTACAATATTCATACAAAAAAATTAGAATATTCATAAAAAATTC
1 ATTACAATATTCATAAAAAAATTACAATATTCATA-AAAAAAATTACAATATTCATAAAAAATAC
54074012 TAATCC-AAACTATAAACACTAAATATAGATAAT
65 TAATCCAAAACTATAAACAC-AAATATA-ATAAT
54074045 TTATAATTGA
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
101 32 0.37
102 37 0.43
103 4 0.05
104 14 0.16
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.30
Consensus pattern (102 bp):
ATTACAATATTCATAAAAAAATTACAATATTCATAAAAAAAATTACAATATTCATAAAAAATACT
AATCCAAAACTATAAACACAAATATAATAATAAAATA
Found at i:54074174 original size:3 final size:3
Alignment explanation
Indices: 54074168--54074219 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
54074158 TTTTTTTTCT
*
54074168 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC -TC TTC TTC TCC TTC -TC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54074213 TTC TTC T
1 TTC TTC T
54074220 CCTTTCTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:54074186 original size:11 final size:11
Alignment explanation
Indices: 54074172--54074216 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
54074162 TTTTCTTTCT
54074172 TCTTCTTCTTC
1 TCTTCTTCTTC
54074183 TCTTCTTCTTC
1 TCTTCTTCTTC
54074194 T-TCTCTTCTTC
1 TCT-TCTTCTTC
54074205 TCCTTC-TCTTC
1 T-CTTCTTCTTC
54074216 T
1 T
54074217 TCTCCTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 27 0.87
12 2 0.06
13 1 0.03
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:54074188 original size:14 final size:14
Alignment explanation
Indices: 54074164--54074219 Score: 96
Period size: 14 Copynumber: 4.1 Consensus size: 14
54074154 CCTTTTTTTT
54074164 TTCTT-TCTTCTTC
1 TTCTTCTCTTCTTC
54074177 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
54074191 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
*
54074205 TCCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
54074219 T
1 T
54074220 CCTTTCTCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
13 5 0.12
14 36 0.88
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:54074219 original size:17 final size:17
Alignment explanation
Indices: 54074164--54074216 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
54074154 CCTTTTTTTT
54074164 TTCT-TTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
54074180 TTCTCTTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
*
54074197 -TCTTCTTCTCCTTC-TC
1 TTC-TCTTCTTCTTCTTC
54074213 TTCT
1 TTCT
54074217 TCTCCTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCTCTTCTTCTTCTTC
Found at i:54074229 original size:17 final size:16
Alignment explanation
Indices: 54074163--54074231 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 16
54074153 ACCTTTTTTT
*
54074163 TTTCTTTCTTCTTCTTC
1 TTTC-TTCTTCTTCTCC
*
54074180 -TTC-TCTTCTTCTTC
1 TTTCTTCTTCTTCTCC
54074194 -TTC-TCTTCTTCTCC
1 TTTCTTCTTCTTCTCC
54074208 -TTC-TCTTCTTCTCC
1 TTTCTTCTTCTTCTCC
54074222 TTTCTCTCTT
1 TTTCT-TCTT
54074232 TTTTTTTTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
14 38 0.79
15 3 0.06
16 3 0.06
17 4 0.08
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCTTCTTCTTCTCC
Found at i:54074231 original size:14 final size:14
Alignment explanation
Indices: 54074169--54074228 Score: 93
Period size: 14 Copynumber: 4.2 Consensus size: 14
54074159 TTTTTTTCTT
*
54074169 TCTTCTTCTTCTTC
1 TCTTCTTCTCCTTC
*
54074183 TCTTCTTCTTCTTC
1 TCTTCTTCTCCTTC
54074197 TCTTCTTCTCCTTC
1 TCTTCTTCTCCTTC
54074211 TCTTCTTCTCCTTTC
1 TCTTCTTCTCC-TTC
54074226 TCT
1 TCT
54074229 CTTTTTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
14 38 0.86
15 6 0.14
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTCTTCTCCTTC
Found at i:54075427 original size:26 final size:26
Alignment explanation
Indices: 54075369--54075429 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
54075359 TAAATTTATC
* * *
54075369 AAAAATATTTTTCAAAAGTACTTTTC
1 AAAAACATTTTTCAAAAGTACTTCTA
* * *
54075395 CATAACATTTTTTAAAAGTACTTCTA
1 AAAAACATTTTTCAAAAGTACTTCTA
54075421 AAAAACATT
1 AAAAACATT
54075430 GCTACTAGCC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39
Consensus pattern (26 bp):
AAAAACATTTTTCAAAAGTACTTCTA
Found at i:54088824 original size:14 final size:13
Alignment explanation
Indices: 54088797--54088835 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
54088787 CCCTCCTTTC
*
54088797 TTTCTTTCTTTTT
1 TTTCTTTGTTTTT
54088810 TTT-TTTGGTTTTT
1 TTTCTTT-GTTTTT
54088823 TTTCTTTGTTTTT
1 TTTCTTTGTTTTT
54088836 GTTGCAGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTCTTTGTTTTT
Found at i:54089832 original size:14 final size:15
Alignment explanation
Indices: 54089813--54089844 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
54089803 ATATTAAAAG
54089813 ATAATAATATT-ATT
1 ATAATAATATTAATT
54089827 ATAATAATATTAATT
1 ATAATAATATTAATT
54089842 ATA
1 ATA
54089845 TTTTAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATAATATTAATT
Found at i:54092845 original size:32 final size:31
Alignment explanation
Indices: 54092764--54092846 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
54092754 CATAACTTTT
* * * **
54092764 TTGAAAATTTCAATTAGGCTCTTCCAAATATT
1 TTGAAAA-TTCAATTAAGCTCTTCAAAAAAAA
*
54092796 TTAGAAAATTCTCATTAAGCTCTTCAAAAAAAA
1 TT-GAAAATTC-AATTAAGCTCTTCAAAAAAAA
54092829 TTGAAAAGTTCAATTAAG
1 TTGAAAA-TTCAATTAAG
54092847 TCCCCAAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
32 16 0.39
33 25 0.61
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (31 bp):
TTGAAAATTCAATTAAGCTCTTCAAAAAAAA
Found at i:54093132 original size:91 final size:88
Alignment explanation
Indices: 54092993--54093164 Score: 218
Period size: 91 Copynumber: 1.9 Consensus size: 88
54092983 AAAAAAAAAG
* * * * * *
54092993 AAAAACAAAGTAATTAAGCTCCTCTTTTTTTCACTCAATTGAGCACTTGAACTTTTAAAATGCAT
1 AAAAAAAAAGCAATTAAACTCCTCTTTTTTTCACTCAATTGAGCACTTGAACTTTCAAAATACAC
* *
54093058 CAAAAAGGCTCTCAAACTTCTTC
66 CAAAAAGACCCTCAAACTTCTTC
* * *
54093081 AAAAAAAAAGCAATTAAACTCCTACTTTTTTTTTCACTTAATTGGGTACTTGAACTTTCAAAATA
1 AAAAAAAAAGCAATTAAACTCCT-C--TTTTTTTCACTCAATTGAGCACTTGAACTTTCAAAATA
54093146 CACCAAAAAGACCCTCAAA
63 CACCAAAAAGACCCTCAAA
54093165 ATTTTTAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
88 20 0.29
89 1 0.01
91 49 0.70
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (88 bp):
AAAAAAAAAGCAATTAAACTCCTCTTTTTTTCACTCAATTGAGCACTTGAACTTTCAAAATACAC
CAAAAAGACCCTCAAACTTCTTC
Found at i:54093547 original size:19 final size:18
Alignment explanation
Indices: 54093525--54093660 Score: 80
Period size: 19 Copynumber: 7.3 Consensus size: 18
54093515 GAATTAGTAT
54093525 TTTTTTACATTTTGTATAA
1 TTTTTTACATTTT-TATAA
* *
54093544 TTTTCTTACGACTTTATAAAA
1 TTTT-TTAC-A-TTTTTATAA
*
54093565 TTTTATA-ATTTTT-T-A
1 TTTTTTACATTTTTATAA
* * *
54093580 TATTCTATATATTTTATAA
1 TTTTTTACAT-TTTTATAA
54093599 TTTTTTACGATTTTTATACA
1 TTTTTTAC-ATTTTTATA-A
* *
54093619 ATTTTTATATTTTTATACA
1 TTTTTTACATTTTTATA-A
* * *
54093638 ATTTTTATATTTTTCTAA
1 TTTTTTACATTTTTATAA
54093656 TTTTT
1 TTTTT
54093661 AATAAATTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
15 6 0.06
16 2 0.02
17 8 0.09
18 7 0.07
19 44 0.47
20 15 0.16
21 9 0.10
22 3 0.03
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTTACATTTTTATAA
Found at i:54093603 original size:9 final size:9
Alignment explanation
Indices: 54093565--54093731 Score: 71
Period size: 9 Copynumber: 17.6 Consensus size: 9
54093555 CTTTATAAAA
54093565 TTTTATAAT
1 TTTTATAAT
54093574 TTTT-T-AT
1 TTTTATAAT
*
54093581 ATTCTAT-AT
1 -TTTTATAAT
54093590 ATTTTATAAT
1 -TTTTATAAT
54093600 TTTT-TACGAT
1 TTTTATA--AT
54093610 TTTTATACAAT
1 TTTTAT--AAT
54093621 TTTTAT-AT
1 TTTTATAAT
54093629 TTTTATACAAT
1 TTTTAT--AAT
54093640 TTTTAT-AT
1 TTTTATAAT
*
54093648 TTTTCTAAT
1 TTTTATAAT
54093657 TTTTAATAAAT
1 TTTT-AT-AAT
*
54093668 TTTTAATATT
1 TTTT-ATAAT
*
54093678 TTTTTTAAT
1 TTTTATAAT
54093687 TAAAATTTAATAAT
1 T----TTT-ATAAT
*
54093701 ATTTATAGA-
1 TTTTATA-AT
*
54093710 TTTTA-ATT
1 TTTTATAAT
54093718 TTTTATAAT
1 TTTTATAAT
54093727 TTTTA
1 TTTTA
54093732 ATAAAAGCAG
Statistics
Matches: 124, Mismatches: 12, Indels: 44
0.69 0.07 0.24
Matches are distributed among these distances:
7 2 0.02
8 27 0.22
9 41 0.33
10 19 0.15
11 27 0.22
13 4 0.03
14 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:54093622 original size:11 final size:11
Alignment explanation
Indices: 54093597--54093646 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
54093587 TATATTTTAT
54093597 AATTTTT-TAC
1 AATTTTTATAC
*
54093607 GATTTTTATAC
1 AATTTTTATAC
54093618 AATTTTTAT--
1 AATTTTTATAC
54093627 -ATTTTTATAC
1 AATTTTTATAC
54093637 AATTTTTATA
1 AATTTTTATA
54093647 TTTTTCTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.24
10 6 0.18
11 20 0.59
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (11 bp):
AATTTTTATAC
Found at i:54093651 original size:28 final size:28
Alignment explanation
Indices: 54093585--54093681 Score: 92
Period size: 28 Copynumber: 3.4 Consensus size: 28
54093575 TTTTATATTC
* *
54093585 TATATATTTTATAATTTTT-TACGATTTT
1 TATATTTTTTAT-ATTTTTATACAATTTT
*
54093613 TATACAATTTTTATATTTTTATACAATTTT
1 TAT--ATTTTTTATATTTTTATACAATTTT
54093643 TATATTTTTCTA-ATTTTTAATA-AATTTT
1 TATATTTTT-TATATTTTT-ATACAATTTT
54093671 TAATATTTTTT
1 T-ATATTTTTT
54093682 TTAATTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
28 22 0.37
29 19 0.32
30 18 0.31
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (28 bp):
TATATTTTTTATATTTTTATACAATTTT
Found at i:54093659 original size:17 final size:18
Alignment explanation
Indices: 54093556--54093661 Score: 92
Period size: 19 Copynumber: 5.8 Consensus size: 18
54093546 TTCTTACGAC
*
54093556 TTTATAAAATTTTATAATT
1 TTTATAAATTTTTAT-ATT
* *
54093575 TTT-TATA-TTCTATATAT
1 TTTATAAATTTTTATAT-T
* *
54093592 TTTATAATTTTTTACGATT
1 TTTATAAATTTTTA-TATT
54093611 TTTATACAATTTTTATATT
1 TTTATA-AATTTTTATATT
54093630 TTTATACAATTTTTATATT
1 TTTATA-AATTTTTATATT
*
54093649 TTTCT-AATTTTTA
1 TTTATAAATTTTTA
54093662 ATAAATTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
16 2 0.03
17 17 0.23
18 5 0.07
19 40 0.55
20 9 0.12
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (18 bp):
TTTATAAATTTTTATATT
Found at i:54093686 original size:23 final size:26
Alignment explanation
Indices: 54093656--54093704 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
54093646 ATTTTTCTAA
*
54093656 TTTTTAA-T-AAATTT-TTAATATTT
1 TTTTTAATTAAAATTTAATAATATTT
54093679 TTTTTAATTAAAATTTAATAATATTT
1 TTTTTAATTAAAATTTAATAATATTT
54093705 ATAGATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 1 0.05
25 6 0.27
26 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTAATTAAAATTTAATAATATTT
Found at i:54093885 original size:89 final size:88
Alignment explanation
Indices: 54093746--54093939 Score: 259
Period size: 89 Copynumber: 2.2 Consensus size: 88
54093736 AAGCAGGGGT
* *
54093746 TTAATTGTTTTTTTTTTAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA-CCAAAT
1 TTAATTGTTTTTTTTTAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCCAAA-
*
54093810 TGAGTGCAAAAAAAAAGTAGGGAA-
65 TGAGTGCAAAAAAAAAGTA-AGAAC
* *
54093834 TTAATTGTTTTTTTTTAAAAGGTTTGA-GGTCTTTTTTATGTATTTTAAAAGTTCAAGTACCCAA
1 TTAATTGTTTTTTTTT-AAA-GTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCCAA
*
54093898 ATGAGTGCGAAAAAAAAGTAAGAAC
64 ATGAGTGCAAAAAAAAAGTAAGAAC
*
54093923 TTAATTACTTTTTTTTT
1 TTAATT-GTTTTTTTTT
54093940 TTTAAAATTG
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
88 19 0.20
89 55 0.59
90 20 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (88 bp):
TTAATTGTTTTTTTTTAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCCAAAT
GAGTGCAAAAAAAAAGTAAGAAC
Found at i:54093959 original size:89 final size:85
Alignment explanation
Indices: 54093746--54093961 Score: 229
Period size: 89 Copynumber: 2.4 Consensus size: 85
54093736 AAGCAGGGGT
** *
54093746 TTAATTGTTTTTTTTTTAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCAAATT
1 TTAATT-TTTTTTTTTTAAAATTGA-GGTCTTTTT-ATGCATTTTAAAAGTTCAAGTACCAAATT
*
54093811 GAGTGCAAAAAAAAAGTAGGGAA
63 GAGTGCAAAAAAAAAGTAGAGAA
* *
54093834 TTAATTGTTTTTTTTTAAAAGGTTTGAGGTCTTTTTTATGTATTTTAAAAGTTCAAGTACCCAAA
1 TTAATTTTTTTTTTTTAAAA---TTGAGGTC-TTTTTATGCATTTTAAAAGTTCAAGTA-CCAAA
*
54093899 -TGAGTGCGAAAAAAAAGTA-AGAA
61 TTGAGTGCAAAAAAAAAGTAGAGAA
*
54093922 CTTAATTACTTTTTTTTTTTTAAAATTGAGGACTTTTTAT
1 -TT-A--A-TTTTTTTTTTTTAAAATTGAGGTCTTTTTAT
54093962 CCACTTAAAC
Statistics
Matches: 109, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
87 11 0.10
88 9 0.08
89 51 0.47
90 22 0.20
92 1 0.01
93 15 0.14
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.44
Consensus pattern (85 bp):
TTAATTTTTTTTTTTTAAAATTGAGGTCTTTTTATGCATTTTAAAAGTTCAAGTACCAAATTGAG
TGCAAAAAAAAAGTAGAGAA
Found at i:54098266 original size:2 final size:2
Alignment explanation
Indices: 54098259--54098295 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54098249 TGCATATTTA
54098259 AT AT AT AT AT 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 AT AT AT AT AT A
54098296 ATTTGAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54099983 original size:3 final size:3
Alignment explanation
Indices: 54099975--54100019 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
54099965 ATAAATTTCA
*
54099975 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54100020 AATTGCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54100186 original size:13 final size:13
Alignment explanation
Indices: 54100165--54100194 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54100155 CATCTTTAAA
*
54100165 ATATTTATTTTAT
1 ATATGTATTTTAT
54100178 ATATGTATTTTAT
1 ATATGTATTTTAT
54100191 ATAT
1 ATAT
54100195 TATGATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
ATATGTATTTTAT
Found at i:54102773 original size:30 final size:30
Alignment explanation
Indices: 54102733--54103018 Score: 320
Period size: 30 Copynumber: 9.3 Consensus size: 30
54102723 ATATATGTAA
* *
54102733 ACATATACAAATCATTTCGGCAATATATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54102763 ACATGTACAAATCCATTCGGCAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54102793 CCATATAAAAATCAATTCGGCAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* **
54102823 ACATATACAAATCAATTTGATAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* * *
54102853 CCATATACAAATCAATTCGGCTATGCATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54102883 CCATATACAAATCAATTCGGCAATATATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
54102913 ATCCATATACAAATCAATTCGACAATATATATGT
1 A--CATATACAAATCAATTCGGCAATGTATA--T
* * *
54102947 AAACATATACAAATCATTTCGACAATATATAT
1 --ACATATACAAATCAATTCGGCAATGTATAT
* *
54102979 ACATGTACAAATCAATTCGGCAATGTATAAA
1 ACATATACAAATCAATTCGGCAATGTAT-AT
54103010 ACATATACA
1 ACATATACA
54103019 TTTGAATTCA
Statistics
Matches: 218, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
30 152 0.70
31 9 0.04
32 28 0.13
34 28 0.13
36 1 0.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (30 bp):
ACATATACAAATCAATTCGGCAATGTATAT
Found at i:54107652 original size:30 final size:30
Alignment explanation
Indices: 54107618--54107677 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
54107608 TATTTTATTA
54107618 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
54107648 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
54107678 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:54117198 original size:13 final size:13
Alignment explanation
Indices: 54117180--54117207 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54117170 TGAACCCGAG
54117180 AACCAAAACCCAA
1 AACCAAAACCCAA
54117193 AACCAAAACCCAA
1 AACCAAAACCCAA
54117206 AA
1 AA
54117208 ACTGGTTGAA
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:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (13 bp):
AACCAAAACCCAA
Found at i:54139158 original size:23 final size:23
Alignment explanation
Indices: 54139114--54139158 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
54139104 CGAAAACCCT
*
54139114 TAAAACAAAAACCCTAATCCTAA
1 TAAAACAAAAACCCTAACCCTAA
* **
54139137 TAAAATAAAAACTTTAACCCTA
1 TAAAACAAAAACCCTAACCCTA
54139159 GGAGAGAACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (23 bp):
TAAAACAAAAACCCTAACCCTAA
Found at i:54143999 original size:2 final size:2
Alignment explanation
Indices: 54143992--54144016 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54143982 ACTTATATTA
54143992 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
54144017 AAAAGCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54145271 original size:10 final size:9
Alignment explanation
Indices: 54145257--54145364 Score: 87
Period size: 9 Copynumber: 11.7 Consensus size: 9
54145247 ACATATGGCA
54145257 AAAAATTAT
1 AAAAATTAT
54145266 AAAAA--AT
1 AAAAATTAT
*
54145273 AAAAGTTAT
1 AAAAATTAT
54145282 AAAAATTAT
1 AAAAATTAT
*
54145291 -TAAATTAT
1 AAAAATTAT
54145299 AAAAAAATTAT
1 --AAAAATTAT
*
54145310 AAAAATCAT
1 AAAAATTAT
*
54145319 AAAAATATAAA
1 AAAAAT-T-AT
54145330 AAAATATTAT
1 AAAA-ATTAT
*
54145340 AAAATTTTAT
1 AAAA-ATTAT
*
54145350 AAAAATCAT
1 AAAAATTAT
54145359 AAAAAT
1 AAAAAT
54145365 AGATATAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.08
8 7 0.09
9 38 0.47
10 14 0.17
11 13 0.16
12 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:54145281 original size:16 final size:15
Alignment explanation
Indices: 54145258--54145332 Score: 59
Period size: 17 Copynumber: 4.9 Consensus size: 15
54145248 CATATGGCAA
54145258 AAAATTATAAAAAAT
1 AAAATTATAAAAAAT
54145273 AAAAGTTATAAAAATTAT
1 AAAA-TTATAAAAA--AT
*
54145291 TAAATTAT---AAA-
1 AAAATTATAAAAAAT
54145302 AAAATTATAAAAATCAT
1 AAAATTATAAAAA--AT
*
54145319 AAAAATATAAAAAA
1 AAAATTATAAAAAA
54145333 ATATTATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
11 7 0.15
12 1 0.02
14 4 0.08
15 5 0.10
16 10 0.21
17 16 0.33
18 5 0.10
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (15 bp):
AAAATTATAAAAAAT
Found at i:54145304 original size:19 final size:20
Alignment explanation
Indices: 54145282--54145384 Score: 72
Period size: 20 Copynumber: 5.2 Consensus size: 20
54145272 TAAAAGTTAT
* *
54145282 AAAAATTAT-TAAATTATAA
1 AAAAATTATAAAAATCATAA
54145301 AAAAATTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
* *
54145321 AAATA-TAAAAAAAT-ATTATA
1 AAAAATTATAAAAATCA-TA-A
**
54145341 AAATTTTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
54145361 AAATAGA-TAT-AAAATGCATAA
1 AAA-A-ATTATAAAAAT-CATAA
54145382 AAA
1 AAA
54145385 TGACCTTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
18 1 0.01
19 19 0.28
20 26 0.38
21 21 0.31
22 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAATCATAA
Found at i:54145339 original size:30 final size:29
Alignment explanation
Indices: 54145268--54145385 Score: 98
Period size: 30 Copynumber: 3.9 Consensus size: 29
54145258 AAAATTATAA
* * *
54145268 AAAATAAAAGTTATAAAAATTATTAAATTAT
1 AAAA-AAAA-TTATAAAAATCATAAAAATAT
54145299 -AAAAAAATTATAAAAATCATAAAAATAT
1 AAAAAAAATTATAAAAATCATAAAAATAT
* *
54145327 AAAAAAATATTATAAAATTTTATAAAAATCAT
1 AAAAAAA-ATTATAAAA-ATCATAAAAAT-AT
*
54145359 AAAAATAGA-TAT-AAAATGCATAAAAAT
1 AAAAA-AAATTATAAAAAT-CATAAAAAT
54145386 GACCTTTAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
28 18 0.25
29 11 0.15
30 23 0.32
31 12 0.16
32 8 0.11
33 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAAAAATTATAAAAATCATAAAAATAT
Found at i:54145354 original size:11 final size:11
Alignment explanation
Indices: 54145294--54145355 Score: 60
Period size: 10 Copynumber: 6.0 Consensus size: 11
54145284 AAATTATTAA
*
54145294 ATTATAAAAAA
1 ATTATAAAAAT
54145305 ATTAT-AAAA-
1 ATTATAAAAAT
*
54145314 ATCATAAAAAT
1 ATTATAAAAAT
*
54145325 A-TAAAAAAAT
1 ATTATAAAAAT
54145335 ATTAT-AAAAT
1 ATTATAAAAAT
*
54145345 TTTATAAAAAT
1 ATTATAAAAAT
54145356 CATAAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 4 0.10
10 25 0.60
11 13 0.31
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTATAAAAAT
Found at i:54145371 original size:21 final size:19
Alignment explanation
Indices: 54145301--54145385 Score: 84
Period size: 21 Copynumber: 4.3 Consensus size: 19
54145291 TAAATTATAA
54145301 AAAAAT-TATAAAAATCAT
1 AAAAATATATAAAAATCAT
*
54145319 AAAAATATAAAAAAAT-ATT
1 AAAAATATATAAAAATCA-T
*
54145338 ATAAAATTTTATAAAAATCAT
1 A-AAAA-TATATAAAAATCAT
*
54145359 AAAAATAGATATAAAATGCAT
1 AAAAATATATA-AAAAT-CAT
54145380 AAAAAT
1 AAAAAT
54145386 GACCTTTAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
18 7 0.13
19 14 0.25
20 13 0.24
21 20 0.36
22 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAATATATAAAAATCAT
Found at i:54145372 original size:31 final size:31
Alignment explanation
Indices: 54145273--54145375 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 31
54145263 TATAAAAAAT
* * *
54145273 AAAAG-TTATAAAA-ATTATTAAATTAT-AA
1 AAAAGATTATAAAATTTTATAAAAATATAAA
* *
54145301 AAAA-ATTATAAAA-ATCATAAAAATATAAA
1 AAAAGATTATAAAATTTTATAAAAATATAAA
*
54145330 AAAATATTATAAAATTTTATAAAAATCATAAA
1 AAAAGATTATAAAATTTTATAAAAAT-ATAAA
*
54145362 AATAGA-TATAAAAT
1 AAAAGATTATAAAAT
54145376 GCATAAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 22 0.35
29 6 0.10
30 9 0.14
31 17 0.27
32 9 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (31 bp):
AAAAGATTATAAAATTTTATAAAAATATAAA
Found at i:54145382 original size:40 final size:40
Alignment explanation
Indices: 54145306--54145383 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
54145296 TATAAAAAAA
* **
54145306 TTATAAAAATCATAAAAATATAAAAAAATATTATAAAATT
1 TTATAAAAATCATAAAAATAGAAAAAAATAGCATAAAATT
*
54145346 TTATAAAAATCATAAAAATAGATATAAAAT-GCATAAAA
1 TTATAAAAATCATAAAAATAGA-AAAAAATAGCATAAAA
54145384 ATGACCTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 27 0.82
41 6 0.18
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (40 bp):
TTATAAAAATCATAAAAATAGAAAAAAATAGCATAAAATT
Found at i:54145573 original size:9 final size:9
Alignment explanation
Indices: 54145554--54145746 Score: 53
Period size: 9 Copynumber: 21.2 Consensus size: 9
54145544 TTTTGGTACG
54145554 ATAATTTTTT
1 ATAA-TTTTT
54145564 ATAATTTTT
1 ATAATTTTT
*
54145573 ACGAA-TTTT
1 A-TAATTTTT
*
54145582 AT--TCTTT
1 ATAATTTTT
* *
54145589 ACATTTTTT
1 ATAATTTTT
54145598 ATAATTTTCTT
1 ATAA-TTT-TT
*
54145609 ATGA-TTTT
1 ATAATTTTT
**
54145617 ATAA-AATT
1 ATAATTTTT
54145625 ATAATTTTT
1 ATAATTTTT
* **
54145634 CTATATTTAC
1 ATA-ATTTTT
*
54145644 ATAAATTTT
1 ATAATTTTT
54145653 ATAA---TT
1 ATAATTTTT
* *
54145659 ACAAATTTT
1 ATAATTTTT
*
54145668 ATAAAATTTT
1 AT-AATTTTT
*
54145678 ACAATTTTTT
1 ATAA-TTTTT
54145688 ATAATTTTT
1 ATAATTTTT
54145697 A-ATATTTTT
1 ATA-ATTTTT
*
54145706 ATATTCTTTT
1 ATAAT-TTTT
* *
54145716 ATTAAAATTTA
1 A-T-AATTTTT
54145727 ATAATTTTT
1 ATAATTTTT
*
54145736 ATAACTTTT
1 ATAATTTTT
54145745 AT
1 AT
54145747 TGATTTTATT
Statistics
Matches: 133, Mismatches: 32, Indels: 37
0.66 0.16 0.18
Matches are distributed among these distances:
6 5 0.04
7 4 0.03
8 12 0.09
9 64 0.48
10 37 0.28
11 10 0.08
12 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (9 bp):
ATAATTTTT
Found at i:54145647 original size:27 final size:29
Alignment explanation
Indices: 54145596--54145658 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
54145586 TTTACATTTT
*
54145596 TTATAA-TTTTCTTATGATTTTATAAA-A
1 TTATAATTTTTCTTATGATTTCATAAATA
*
54145623 TTATAATTTTTC-TAT-ATTTACATAAATT
1 TTATAATTTTTCTTATGATTT-CATAAATA
54145651 TTATAATT
1 TTATAATT
54145659 ACAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.13
27 14 0.45
28 13 0.42
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATAATTTTTCTTATGATTTCATAAATA
Found at i:54145675 original size:17 final size:17
Alignment explanation
Indices: 54145612--54145675 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
54145602 TTTTCTTATG
*
54145612 ATTTTATAAAATTATAA
1 ATTTTATAAAATTACAA
* * * *
54145629 TTTTTCTATATTTACATAA
1 ATTTTATAAAATTAC--AA
54145648 ATTTTAT--AATTACAA
1 ATTTTATAAAATTACAA
54145663 ATTTTATAAAATT
1 ATTTTATAAAATT
54145676 TTACAATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
15 9 0.26
17 19 0.54
19 7 0.20
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTATAAAATTACAA
Found at i:54145754 original size:48 final size:49
Alignment explanation
Indices: 54145663--54145764 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 49
54145653 ATAATTACAA
* *
54145663 ATTTTATAAAATTTTACAATTTTTTATAATTTTTAATATTTTTA-TATT
1 ATTTTATAAAATTTAACAATTTTTTATAACTTTTAATATTTTTATTATT
* * *
54145711 CTTTTATTAAAATTTAATAA-TTTTTATAACTTTTATTGA-TTTTATTATT
1 ATTTTA-TAAAATTTAACAATTTTTTATAACTTTTAAT-ATTTTTATTATT
54145760 ATTTT
1 ATTTT
54145765 TTGCCACATG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
48 25 0.56
49 20 0.44
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (49 bp):
ATTTTATAAAATTTAACAATTTTTTATAACTTTTAATATTTTTATTATT
Found at i:54146086 original size:16 final size:17
Alignment explanation
Indices: 54146052--54146086 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54146042 AAAGTTAGAG
*
54146052 AGCCTTTTATACCATTA
1 AGCCTTTTATACAATTA
54146069 AGCCTTTTATA-AATTA
1 AGCCTTTTATACAATTA
54146085 AG
1 AG
54146087 TGTTTAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (17 bp):
AGCCTTTTATACAATTA
Found at i:54153626 original size:41 final size:41
Alignment explanation
Indices: 54153579--54153718 Score: 210
Period size: 41 Copynumber: 3.4 Consensus size: 41
54153569 TATATGATTG
* *
54153579 GCACTAAGTGTGCGAAATTAAATAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
54153620 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
* * * *
54153661 ACACTAAGTGTGCGAAACCAAGTAATTATGTT-AATAACGG
1 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
*
54153701 GCACTAAGTGTGCAAAAC
1 GCACTAAGTGTGCGAAAC
54153719 CGAGATCAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 23 0.25
41 68 0.75
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (41 bp):
GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
Found at i:54157736 original size:264 final size:265
Alignment explanation
Indices: 54157239--54157746 Score: 874
Period size: 265 Copynumber: 1.9 Consensus size: 265
54157229 TTCTCCCACT
54157239 CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
1 CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
* * * *
54157304 CTAGTGGCATTCTTACCTAATTTACATGTCATGCTTCCAGTATATGCATGACATGTTATGAAAAT
66 CTAGTAGCATTCTTACCTAATCTACATGACATGCTTCCAGTATATGCATGACATGCTATGAAAAT
**
54157369 TTTATAATATTCACATTCATTCATTCAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
131 TTTATAATATTCACATTCATTCATGAAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
*
54157434 CTCCACAATTTTTCGTTTAAGGGAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCTC
196 CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCTC
54157499 TTACA
261 TTACA
*
54157504 CAATATTTTAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
1 CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
* * * *
54157569 CTAGTAGCATTCTTACCTAATCTATATGACATGCTTTCAGTATATGCATGACATGCTATGATAGT
66 CTAGTAGCATTCTTACCTAATCTACATGACATGCTTCCAGTATATGCATGACATGCTATGAAAAT
* *
54157634 TTTATAATATTCACATTCATTTA-GAAGAAGAATCAATCAACCATAAAAACAAACAATTTTGATT
131 TTTATAATATTCACATTCATTCATGAAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
*
54157698 CTCCACAATTTTTCGTTTAAGGAAAAAACCGAAGAAGTGAATGTGAACA
196 CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACA
54157747 GTGCACCAGG
Statistics
Matches: 228, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
264 85 0.37
265 143 0.63
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (265 bp):
CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
CTAGTAGCATTCTTACCTAATCTACATGACATGCTTCCAGTATATGCATGACATGCTATGAAAAT
TTTATAATATTCACATTCATTCATGAAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCTC
TTACA
Found at i:54160551 original size:23 final size:23
Alignment explanation
Indices: 54160521--54160568 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
54160511 TATCATCTGT
* *
54160521 TTTATGATATGAGATTAGTCTTA
1 TTTATGATATGAGATCACTCTTA
54160544 TTTATGATATGAGATCACTCTTA
1 TTTATGATATGAGATCACTCTTA
54160567 TT
1 TT
54160569 GGATTAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (23 bp):
TTTATGATATGAGATCACTCTTA
Found at i:54168238 original size:13 final size:13
Alignment explanation
Indices: 54168220--54168246 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54168210 TTTTCAAAAC
54168220 TTAGAAACATGTA
1 TTAGAAACATGTA
54168233 TTAGAAACATGTA
1 TTAGAAACATGTA
54168246 T
1 T
54168247 CAATACCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (13 bp):
TTAGAAACATGTA
Found at i:54168415 original size:19 final size:20
Alignment explanation
Indices: 54168391--54168441 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
54168381 CCAATCATAT
54168391 GTATCGATACCTT-TGTAAA
1 GTATCGATACCTTGTGTAAA
**
54168410 GTATCGATACCTTGGTGTAGG
1 GTATCGATACCTT-GTGTAAA
54168431 GTATCGATACC
1 GTATCGATACC
54168442 AAATTGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.46
21 15 0.54
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
GTATCGATACCTTGTGTAAA
Found at i:54169556 original size:21 final size:21
Alignment explanation
Indices: 54169531--54169579 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
54169521 AGCGGTGGCA
*
54169531 GTGAGATCAGTTACTGTAGCG
1 GTGAGATCAGATACTGTAGCG
**
54169552 GTGAGATTGGATACTGTAGCG
1 GTGAGATCAGATACTGTAGCG
54169573 GTGAGAT
1 GTGAGAT
54169580 TAGAAACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.37, T:0.29
Consensus pattern (21 bp):
GTGAGATCAGATACTGTAGCG
Found at i:54177192 original size:46 final size:46
Alignment explanation
Indices: 54177135--54177224 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
54177125 GGTAACACAC
*
54177135 ATATGACAAGGTCATTGGAAAAAACAGTTGGACGAATTGCTTTCGT
1 ATATGACAAGGTCATTGGAAAAAACAGTTGGACAAATTGCTTTCGT
* *
54177181 ATATGATAAGGTCATTGGAAAAAGCAGTTGGACAAATTGCTTTC
1 ATATGACAAGGTCATTGGAAAAAACAGTTGGACAAATTGCTTTC
54177225 ATAAAGAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (46 bp):
ATATGACAAGGTCATTGGAAAAAACAGTTGGACAAATTGCTTTCGT
Found at i:54179544 original size:25 final size:25
Alignment explanation
Indices: 54179479--54179534 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
54179469 AGCAAAAAAT
* *
54179479 GGTAAGCTCCTCCGAGTTGGATATC
1 GGTAAGCTCATACGAGTTGGATATC
54179504 GGTAAGCTCATACGAGTTGTGA-ATC
1 GGTAAGCTCATACGAGTTG-GATATC
54179529 GGTAAG
1 GGTAAG
54179535 TTCTGACGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (25 bp):
GGTAAGCTCATACGAGTTGGATATC
Found at i:54184573 original size:31 final size:30
Alignment explanation
Indices: 54184538--54184642 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
54184528 GATATTAAAT
* *
54184538 TTAATTTAATATTTGTCTAAATAGTATTTTA
1 TTAATTTAATATTTATCTAGATA-TATTTTA
* * * **
54184569 TTAATTTAATATTAATAT-GAGATATTAAA
1 TTAATTTAATATTTATCTAGATATATTTTA
54184598 TTTAATTTAATATTTATCTAGATAATATTTTA
1 -TTAATTTAATATTTATCTAGAT-ATATTTTA
*
54184630 TTATTTTAATATT
1 TTAATTTAATATT
54184643 AATGTGATTA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
29 5 0.09
30 18 0.31
31 29 0.50
32 6 0.10
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (30 bp):
TTAATTTAATATTTATCTAGATATATTTTA
Found at i:54184587 original size:61 final size:61
Alignment explanation
Indices: 54184516--54184645 Score: 224
Period size: 61 Copynumber: 2.1 Consensus size: 61
54184506 ATTTATCTAG
* *
54184516 ATATTAATATGAGATATTAAATTTAATTTAATATTTGTCTAAATAGTATTTTATTAATTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAATAATATTTTATTAATTTA
* *
54184577 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTATTTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAATAATATTTTATTAATTTA
54184638 ATATTAAT
1 ATATTAAT
54184646 GTGATTAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (61 bp):
ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAATAATATTTTATTAATTTA
Found at i:54190415 original size:41 final size:40
Alignment explanation
Indices: 54190370--54190531 Score: 126
Period size: 41 Copynumber: 4.0 Consensus size: 40
54190360 AGTGCCTAGA
* *
54190370 AGGCTTATTGCCAATGAGATAATTCAAACTCTATGTCTAAC
1 AGGCTTA-TGCCAATGAAACAATTCAAACTCTATGTCTAAC
* ** * *
54190411 AGGCTGGATGCCGGTGAAACAATTCAGACTCTATGTCTAGC
1 AGGCT-TATGCCAATGAAACAATTCAAACTCTATGTCTAAC
* * * * * *
54190452 AGGCTTGATACCAGTAAAACAATTCAGACTTTATGTCTAGC
1 AGGCTT-ATGCCAATGAAACAATTCAAACTCTATGTCTAAC
** * * *
54190493 AGGCTTGATGCCTGTGAAACATTTCAAACTTTAAGTCTA
1 AGGCTT-ATGCCAATGAAACAATTCAAACTCTATGTCTA
54190532 GCAAGCCAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
41 100 0.99
42 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (40 bp):
AGGCTTATGCCAATGAAACAATTCAAACTCTATGTCTAAC
Found at i:54190532 original size:41 final size:41
Alignment explanation
Indices: 54190390--54190534 Score: 182
Period size: 41 Copynumber: 3.5 Consensus size: 41
54190380 CCAATGAGAT
* * *
54190390 AATTCAAACTCTATGTCTAACAGGCTGGATGCCGGTGAAAC
1 AATTCAAACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
* * *
54190431 AATTCAGACTCTATGTCTAGCAGGCTTGATACCAGTAAAAC
1 AATTCAAACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
* * *
54190472 AATTCAGACTTTATGTCTAGCAGGCTTGATGCCTGTGAAAC
1 AATTCAAACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
* * *
54190513 ATTTCAAACTTTAAGTCTAGCA
1 AATTCAAACTCTATGTCTAGCA
54190535 AGCCAAAAGC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
AATTCAAACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
Found at i:54197048 original size:4 final size:4
Alignment explanation
Indices: 54197039--54197067 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
54197029 TGTTAGACAT
54197039 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
54197068 GTGTGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:54202571 original size:25 final size:22
Alignment explanation
Indices: 54202528--54202573 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54202518 GATGTTTAGA
*
54202528 ATTTTACTCAAATAATAACTTT
1 ATTTTACTCAAAAAATAACTTT
54202550 ATTTTACATCAATAAAATTAACTT
1 ATTTTAC-TCAA-AAAA-TAACTT
54202574 AACTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 3 0.15
25 6 0.30
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTACTCAAAAAATAACTTT
Found at i:54203734 original size:25 final size:24
Alignment explanation
Indices: 54203704--54203757 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
54203694 ACGAACGAAC
*
54203704 GAAAAAAGAGAAATAGTAGCAAAAAA
1 GAAAAAAGA-AAATAGGAG-AAAAAA
*
54203730 GAAAAAAGAAAATAGGAGAAAAAC
1 GAAAAAAGAAAATAGGAGAAAAAA
54203754 GAAA
1 GAAA
54203758 TACATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.35
25 8 0.31
26 9 0.35
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.06
Consensus pattern (24 bp):
GAAAAAAGAAAATAGGAGAAAAAA
Found at i:54205163 original size:30 final size:31
Alignment explanation
Indices: 54205123--54205188 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
54205113 CTCTTTTCAG
*
54205123 AAGAAAAATTTATTTTTAAACTTTTCTAAAA
1 AAGAAAATTTTATTTTTAAACTTTTCTAAAA
54205154 AAGAAAATTTTATTTTTAAACTTTTCTAAAA
1 AAGAAAATTTTATTTTTAAACTTTTCTAAAA
54205185 AAGA
1 AAGA
54205189 GGCAATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (31 bp):
AAGAAAATTTTATTTTTAAACTTTTCTAAAA
Found at i:54205444 original size:18 final size:19
Alignment explanation
Indices: 54205422--54205486 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
54205412 AAAATAATAA
54205422 TTTTTGAAAACACGAAGA-
1 TTTTTGAAAACACGAAGAT
* *
54205440 TTTTTG-AAACATGAAAAT
1 TTTTTGAAAACACGAAGAT
*
54205458 TTTTTGAACACACG-AGAAT
1 TTTTTGAAAACACGAAG-AT
54205477 TTTTTGAAAA
1 TTTTTGAAAA
54205487 GCCGAAAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 9 0.24
18 13 0.34
19 16 0.42
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (19 bp):
TTTTTGAAAACACGAAGAT
Found at i:54205462 original size:19 final size:18
Alignment explanation
Indices: 54205422--54205646 Score: 81
Period size: 17 Copynumber: 11.9 Consensus size: 18
54205412 AAAATAATAA
*
54205422 TTTTTGAAAACACGAAGA-
1 TTTTTG-AAACACGAAAAT
*
54205440 TTTTTGAAACATGAAAAT
1 TTTTTGAAACACGAAAAT
*
54205458 TTTTTGAACACACGAGAAT
1 TTTTTGAA-ACACGAAAAT
54205477 TTTTTGAAA-AGCCGAAAACAT
1 TTTTTGAAACA--CG-AAA-AT
*
54205498 GAAAATTTTGAAAACACGAAAA-
1 ----TTTTTG-AAACACGAAAAT
*
54205520 TTTTTGAAACACGAGAAT
1 TTTTTGAAACACGAAAAT
54205538 TTTTATGACACGAAAACACG-AAAT
1 TTTT-T-----G-AAACACGAAAAT
** **
54205562 TTTTTTTAACACGGGAA-
1 TTTTTGAAACACGAAAAT
*
54205579 TTTTTGAAAACCCGAAAA-
1 TTTTTG-AAACACGAAAAT
54205597 TTTTTGAAACAC-AAAA-
1 TTTTTGAAACACGAAAAT
* * * *
54205613 ATTTTAAAACACTAACA-
1 TTTTTGAAACACGAAAAT
*
54205630 TTTGTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
54205647 CTCTTGAAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 47
0.68 0.11 0.20
Matches are distributed among these distances:
16 14 0.09
17 51 0.32
18 39 0.25
19 19 0.12
20 2 0.01
21 2 0.01
23 2 0.01
24 11 0.07
25 14 0.09
26 3 0.02
27 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (18 bp):
TTTTTGAAACACGAAAAT
Found at i:54205512 original size:17 final size:18
Alignment explanation
Indices: 54205490--54205656 Score: 96
Period size: 17 Copynumber: 9.3 Consensus size: 18
54205480 TTGAAAAGCC
*
54205490 GAAAACATGAAAA-TTTT
1 GAAAACACGAAAATTTTT
54205507 GAAAACACGAAAATTTTT
1 GAAAACACGAAAATTTTT
*
54205525 G-AAACACGAGAATTTTTAT
1 GAAAACACGA-AAATTTT-T
54205544 GACACGAAAACACG-AAATTTTT
1 -----GAAAACACGAAAATTTTT
*** **
54205566 TTTAACACGGGAATTTTT
1 GAAAACACGAAAATTTTT
*
54205584 GAAAACCCGAAAATTTTT
1 GAAAACACGAAAATTTTT
*
54205602 G-AAACAC-AAAAATTTT
1 GAAAACACGAAAATTTTT
* * *
54205618 -AAAACACTAACATTTGT
1 GAAAACACGAAAATTTTT
* *
54205635 G-AAACACGAAAACTCTT
1 GAAAACACGAAAATTTTT
54205652 GAAAA
1 GAAAA
54205657 TGTTAAAAGT
Statistics
Matches: 113, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
16 14 0.12
17 49 0.43
18 34 0.30
19 1 0.01
22 1 0.01
23 6 0.05
24 1 0.01
25 7 0.06
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (18 bp):
GAAAACACGAAAATTTTT
Found at i:54205526 original size:18 final size:18
Alignment explanation
Indices: 54205420--54205656 Score: 112
Period size: 18 Copynumber: 12.7 Consensus size: 18
54205410 ACAAAATAAT
54205420 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
54205438 GATTTTTG-AAACATGAA
1 AATTTTTGAAAACACGAA
*
54205455 AATTTTTTGAACACACGAGA
1 AA-TTTTTGAAAACACGA-A
*
54205475 ATTTTTTGAAAAGC-CGAAA
1 AATTTTTGAAAA-CACG-AA
54205494 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
54205518 AATTTTTG-AAACACGAGA
1 AATTTTTGAAAACACGA-A
*
54205536 ATTTTTATGACACGAAAACACG-A
1 AATTTT-T-----GAAAACACGAA
*** **
54205559 AATTTTTTTTAACACGGG
1 AATTTTTGAAAACACGAA
*
54205577 AATTTTTGAAAACCCGAA
1 AATTTTTGAAAACACGAA
54205595 AATTTTTG-AAACAC-AA
1 AATTTTTGAAAACACGAA
* *
54205611 AAATTTT-AAAACACTAA
1 AATTTTTGAAAACACGAA
* *
54205628 CATTTGTG-AAACACGAA
1 AATTTTTGAAAACACGAA
* *
54205645 AACTCTTGAAAA
1 AATTTTTGAAAA
54205657 TGTTAAAAGT
Statistics
Matches: 164, Mismatches: 30, Indels: 50
0.67 0.12 0.20
Matches are distributed among these distances:
16 14 0.09
17 46 0.28
18 47 0.29
19 20 0.12
20 5 0.03
22 1 0.01
23 8 0.05
24 5 0.03
25 18 0.11
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:54205573 original size:25 final size:25
Alignment explanation
Indices: 54205526--54205574 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54205516 AAAATTTTTG
*
54205526 AAACACGAGAATTTTTATGACACGA
1 AAACACGAGAATTTTTATAACACGA
*
54205551 AAACACGA-AATTTTTTTTAACACG
1 AAACACGAGAA-TTTTTATAACACG
54205575 GGAATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (25 bp):
AAACACGAGAATTTTTATAACACGA
Found at i:54205617 original size:16 final size:16
Alignment explanation
Indices: 54205593--54205646 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
54205583 TGAAAACCCG
*
54205593 AAAATTTTTGAAACAC
1 AAAAATTTTGAAACAC
*
54205609 AAAAATTTTAAAACAC
1 AAAAATTTTGAAACAC
* *
54205625 TAACATTTGTGAAACAC
1 AAAAATTT-TGAAACAC
54205642 GAAAA
1 -AAAA
54205647 CTCTTGAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 20 0.69
17 7 0.24
18 2 0.07
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (16 bp):
AAAAATTTTGAAACAC
Found at i:54205622 original size:33 final size:34
Alignment explanation
Indices: 54205580--54205656 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
54205570 ACACGGGAAT
* *
54205580 TTTTGAAAACCCGAAAATTTTTGAAACACAAAAA
1 TTTTGAAAACACGAAAATTTGTGAAACACAAAAA
* * *
54205614 TTTT-AAAACACTAACATTTGTGAAACACGAAAAC
1 TTTTGAAAACACGAAAATTTGTGAAACAC-AAAAA
*
54205648 TCTTGAAAA
1 TTTTGAAAA
54205657 TGTTAAAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
33 20 0.57
34 11 0.31
35 4 0.11
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (34 bp):
TTTTGAAAACACGAAAATTTGTGAAACACAAAAA
Found at i:54206372 original size:18 final size:18
Alignment explanation
Indices: 54206324--54206372 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
54206314 TTGGGCCTGC
*
54206324 TTTGTTCTTTTTTGCTAT
1 TTTGTTTTTTTTTGCTAT
* * *
54206342 TCTGTTTCTTTTTGCTGT
1 TTTGTTTTTTTTTGCTAT
54206360 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
54206373 TGGGGGCGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.10, G:0.12, T:0.76
Consensus pattern (18 bp):
TTTGTTTTTTTTTGCTAT
Found at i:54206501 original size:11 final size:11
Alignment explanation
Indices: 54206472--54206536 Score: 64
Period size: 11 Copynumber: 6.1 Consensus size: 11
54206462 AAAATATATA
**
54206472 TTTTTTCTTTT
1 TTTTTTCTTCC
54206483 TTTTTTCTTCC
1 TTTTTTCTTCC
*
54206494 TTTCTTC-T-C
1 TTTTTTCTTCC
*
54206503 TCTTTTC-TCC
1 TTTTTTCTTCC
54206513 TTTTTTCTTCC
1 TTTTTTCTTCC
54206524 TTTTTTCCTTCC
1 TTTTTT-CTTCC
54206536 T
1 T
54206537 CTTCGGGGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
9 7 0.16
10 8 0.18
11 24 0.53
12 6 0.13
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTTCTTCC
Found at i:54206513 original size:19 final size:19
Alignment explanation
Indices: 54206485--54206533 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
54206475 TTTCTTTTTT
54206485 TTTTCTTCCTTTCTTC-TCTC
1 TTTTC-TCCTTTCTTCTTC-C
*
54206505 TTTTCTCCTTTTTTCTTCC
1 TTTTCTCCTTTCTTCTTCC
*
54206524 TTTTTTCCTT
1 TTTTCTCCTT
54206534 CCTCTTCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTCTCCTTTCTTCTTCC
Found at i:54207218 original size:29 final size:29
Alignment explanation
Indices: 54207091--54207279 Score: 125
Period size: 30 Copynumber: 6.4 Consensus size: 29
54207081 CGAAGTTTCT
*
54207091 GGGGT-AAAAGTGTAATTTTAGCAAA--ATA
1 GGGGTCAAAA-TGTAATTTTAG-AAAGTTTA
* * * *
54207119 TGGGCCAAAATGTAATTTCTTGAGAGTTTA
1 GGGGTCAAAATGTAATTT-TAGAAAGTTTA
** * *
54207149 GGGGTCAAGGTGCAATTTTGAGAAAGTATA
1 GGGGTCAAAATGTAATTTT-AGAAAGTTTA
* * *
54207179 AGGGTCGAAATGTAATTTTAGAAAGTTTT
1 GGGGTCAAAATGTAATTTTAGAAAGTTTA
* * *
54207208 GGGGCCAAAATGTAAATTTTAGAAAATTTT
1 GGGGTCAAAATGT-AATTTTAGAAAGTTTA
*
54207238 GGGGTCAAAATGTAAATTTT-GAAAAGTATA
1 GGGGTCAAAATGT-AATTTTAG-AAAGTTTA
* *
54207268 AGGGTTAAAATG
1 GGGGTCAAAATG
54207280 CAAAAAATAA
Statistics
Matches: 124, Mismatches: 30, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
28 13 0.10
29 26 0.21
30 85 0.69
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTAGAAAGTTTA
Found at i:54209944 original size:20 final size:20
Alignment explanation
Indices: 54209883--54209952 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
54209873 ATTAGACAGA
54209883 TATTGAATTAATCAATTTTAT
1 TATTGAATTAATCAATTTT-T
* ** * *
54209904 GATT-TCTTATTGAATTTTTT
1 TATTGAATTAATCAA-TTTTT
54209924 TATTGAATTAATCAATTTTT
1 TATTGAATTAATCAATTTTT
54209944 TATTGAATT
1 TATTGAATT
54209953 TTTTATTTAC
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
20 24 0.65
21 13 0.35
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (20 bp):
TATTGAATTAATCAATTTTT
Found at i:54212926 original size:22 final size:23
Alignment explanation
Indices: 54212898--54212942 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
54212888 ATGCAATCTT
54212898 ATATATGA-TATGTAATCTTAGA
1 ATATATGATTATGTAATCTTAGA
*
54212920 ATATATGATTCTGTAATCTTAGA
1 ATATATGATTATGTAATCTTAGA
54212943 GATTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (23 bp):
ATATATGATTATGTAATCTTAGA
Found at i:54219172 original size:125 final size:125
Alignment explanation
Indices: 54218942--54219365 Score: 591
Period size: 125 Copynumber: 3.4 Consensus size: 125
54218932 ACGTGGACGC
** * * * *
54218942 GAAGAATTTGTGAAATTGCGCTCTCTTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
*
54219007 TTTCGAGTTGACATTTCTGAGAAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
66 TTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
* * * * * *
54219067 GAAGAATTTGTTAAATCACGCCCACACGGGCGCACTTTTGCTACAGTAGGTCCT-GAAAAAATTA
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
* * * *
54219131 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATT-TGA
66 TTTCGAGTTGACATTTCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGCT-TTATGA
* * * *
54219192 GAAGAATTTCTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
* *
54219257 TTTTGAGTTGACATTTCTGAGCAAATAGTTTAAAATCGCTTCTACCAGGATGCTTTATGA
66 TTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
**
54219317 GAAGAATTTGTGAAATTGCGCCCACATGGACGCGCTTTTGCTACAGTAG
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAG
54219366 CATGTTTGGG
Statistics
Matches: 256, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
124 39 0.15
125 179 0.70
126 38 0.15
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (125 bp):
GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
TTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
Found at i:54221374 original size:21 final size:21
Alignment explanation
Indices: 54221341--54221388 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
54221331 TTGTCTAGCT
* * *
54221341 TCCGGCGGCGATTGTTGTTCC
1 TCCGGTGGCGATTCTGGTTCC
* *
54221362 TCCGGTGGGGATTCTGGTTCT
1 TCCGGTGGCGATTCTGGTTCC
54221383 TCCGGT
1 TCCGGT
54221389 ACGACATCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.25, G:0.35, T:0.35
Consensus pattern (21 bp):
TCCGGTGGCGATTCTGGTTCC
Done.