Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 180 of 230
Found at i:53931555 original size:38 final size:38
Alignment explanation
Indices: 53931513--53931614 Score: 123
Period size: 38 Copynumber: 2.7 Consensus size: 38
53931503 TTATGGTGTA
* *
53931513 TTGGTGAATCCCGTGTGGCATATTCTATAATGGCATAT
1 TTGGTGAAGCCCATGTGGCATATTCTATAATGGCATAT
* **
53931551 TTGGTGAGGCCCATGTGGTGTATTCTATAATGGCATAT
1 TTGGTGAAGCCCATGTGGCATATTCTATAATGGCATAT
* * * *
53931589 TCGATAAAGCCCATGTGGCGTATTCT
1 TTGGTGAAGCCCATGTGGCATATTCT
53931615 GTGATAATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (38 bp):
TTGGTGAAGCCCATGTGGCATATTCTATAATGGCATAT
Found at i:53934733 original size:23 final size:23
Alignment explanation
Indices: 53934702--53935110 Score: 287
Period size: 23 Copynumber: 17.5 Consensus size: 23
53934692 ACACCAAAAT
* *
53934702 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
53934725 TTGGGCAGCATATATACAACAAAA
1 TTGGGCAGCATATATACAAC-AAA
* * * *
53934749 TTGAGCAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
*
53934774 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
53934797 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
53934820 TTGAGCAACATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* * *
53934844 TTTGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
* *
53934867 TTAGGCAGCATATATATAACAAA
1 TTGGGCAGCATATATACAACAAA
* ** * * *
53934890 TTGAGCAATATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* * *
53934914 TTTGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
* * *
53934937 TTAGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
53934960 TTGAGCAACATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
53934984 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
* * *
53935007 TTAGGAAGCATATATATAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * * **
53935030 TTGAGCAACATTTTTACTTCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* * *
53935054 TTGGACAGCATATATATAACAAT
1 TTGGGCAGCATATATACAACAAA
* *
53935077 TTAGGCAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
53935100 TTGGGCAGCAT
1 TTGGGCAGCAT
53935111 TTAAGCATCA
Statistics
Matches: 282, Mismatches: 97, Indels: 14
0.72 0.25 0.04
Matches are distributed among these distances:
23 184 0.65
24 80 0.28
25 17 0.06
26 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.28
Consensus pattern (23 bp):
TTGGGCAGCATATATACAACAAA
Found at i:53935066 original size:47 final size:47
Alignment explanation
Indices: 53934710--53935110 Score: 200
Period size: 47 Copynumber: 8.6 Consensus size: 47
53934700 ATTTGGACAG
* * * *
53934710 CATATATACAAC-AATTTGGGCAGCATATATACAACAAAATTGAGCAG
1 CATATATACAACAAAATTGGACAGCATATATATAAC-AAATTGAGCAA
* * * * * *
53934757 CATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAG
1 CATATATACAAC-AAAATTGGACAGCATATATATAACAAATTGAGCAA
* * * * * * * *
53934805 CATATATA-TACCAAATT-GAGCAACATTTTTACATCAAAATTTGA-CAG
1 CATATATACAACAAAATTGGA-CAGCATATATATAAC-AAA-TTGAGCAA
*
53934852 CATATATACAAC-AATTTAGG-CAGCATATATATAACAAATTGAGCAA
1 CATATATACAACAAAATT-GGACAGCATATATATAACAAATTGAGCAA
* * * * * * * *
53934898 TATTTTTACATCAAAATTTGACAGCATATATACAAC-AATTTAGGCAG
1 CATATATACAACAAAATTGGACAGCATATATATAACAAATTGA-GCAA
* * * * * * * *
53934945 CATATATA-TACCAAATT-GAGCAACATTTTTACATCAAAATTG-GACAG
1 CATATATACAACAAAATTGGA-CAGCATATATATAAC-AAATTGAG-CAA
*
53934992 CATATATACAAC-AATTTAGGA-AGCATATATATAACAAATTGAGCAA
1 CATATATACAACAAAATT-GGACAGCATATATATAACAAATTGAGCAA
* * ** * *
53935038 CATTTTTACTTCAAAATTGGACAGCATATATATAAC-AATTTAGGCAG
1 CATATATACAACAAAATTGGACAGCATATATATAACAAATTGA-GCAA
* *
53935085 CATAAATACAAC-AAATTGGGCAGCAT
1 CATATATACAACAAAATTGGACAGCAT
53935111 TTAAGCATCA
Statistics
Matches: 266, Mismatches: 65, Indels: 47
0.70 0.17 0.12
Matches are distributed among these distances:
45 8 0.03
46 90 0.34
47 117 0.44
48 27 0.10
49 24 0.09
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (47 bp):
CATATATACAACAAAATTGGACAGCATATATATAACAAATTGAGCAA
Found at i:53935124 original size:70 final size:70
Alignment explanation
Indices: 53934685--53935112 Score: 649
Period size: 70 Copynumber: 6.1 Consensus size: 70
53934675 AACTAGACAG
* * * *
53934685 CATTTTCACACCAAAATTTGGACAGCATATATACAACAATTTGGGCAGCATATATACAACAAAAT
1 CATTTTTACATCAAAA-TTGGACAGCATATATACAACAATTTAGGCAGCATATATATAAC-AAAT
*
53934750 TGAGCAG
64 TGAGCAA
* * * *
53934757 CATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATT
1 CATTTTTACATC-AAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATT
53934822 GAGCAA
65 GAGCAA
*
53934828 CATTTTTACATCAAAATTTGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
53934893 AGCAA
66 AGCAA
* * *
53934898 TATTTTTACATCAAAATTTGACAGCATATATACAACAATTTAGGCAGCATATATATACCAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
53934963 AGCAA
66 AGCAA
*
53934968 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGAAGCATATATATAACAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
53935033 AGCAA
66 AGCAA
* * * *
53935038 CATTTTTACTTCAAAATTGGACAGCATATATATAACAATTTAGGCAGCATAAATACAACAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
* *
53935103 GGCAG
66 AGCAA
53935108 CATTT
1 CATTT
53935113 AAGCATCAAA
Statistics
Matches: 332, Mismatches: 23, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
70 256 0.77
71 21 0.06
72 51 0.15
73 4 0.01
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (70 bp):
CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
AGCAA
Found at i:53935869 original size:28 final size:28
Alignment explanation
Indices: 53935834--53935902 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
53935824 AACAAGTTCT
* *
53935834 CACACTTAGTGCTTAATAATCAATCTCG
1 CACACTTAGTGCTTAACAATCAAACTCG
* *
53935862 CACACTTAGTGCTTTACAATTAAACTCG
1 CACACTTAGTGCTTAACAATCAAACTCG
*
53935890 CACACTGAGTGCT
1 CACACTTAGTGCT
53935903 AATCTCATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (28 bp):
CACACTTAGTGCTTAACAATCAAACTCG
Found at i:53935988 original size:14 final size:15
Alignment explanation
Indices: 53935957--53935995 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
53935947 AAGTCAACAA
53935957 TTCAATACATCTTAT
1 TTCAATACATCTTAT
*
53935972 TTCAATA-ATCTTTT
1 TTCAATACATCTTAT
*
53935986 TTCACTACAT
1 TTCAATACAT
53935996 GTATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.49
Consensus pattern (15 bp):
TTCAATACATCTTAT
Found at i:53937189 original size:30 final size:30
Alignment explanation
Indices: 53937146--53937212 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
53937136 ATTTCAGGGG
* *
53937146 TCACACACTCGTGTGGCCAAGCCGTGTGCC
1 TCACACGCCCGTGTGGCCAAGCCGTGTGCC
*
53937176 TCACACGCCCGTGTGGCCAAGTCGTGTGCC
1 TCACACGCCCGTGTGGCCAAGCCGTGTGCC
53937206 TCACACG
1 TCACACG
53937213 ATTGAGACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.16, C:0.37, G:0.27, T:0.19
Consensus pattern (30 bp):
TCACACGCCCGTGTGGCCAAGCCGTGTGCC
Found at i:53938217 original size:18 final size:18
Alignment explanation
Indices: 53938191--53938264 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
53938181 ATTTCATATT
*
53938191 TCATATCTCATCTCATAA
1 TCATTTCTCATCTCATAA
53938209 TCATTTCTCATATTTCTCATTTCAA
1 TCATTTCTC--A--TCTCA--T-AA
53938234 T-ATTTTCTCATCTCATAA
1 TCA-TTTCTCATCTCATAA
53938252 TCATTTCTCATCT
1 TCATTTCTCATCT
53938265 TTTCCATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 18
0.71 0.02 0.28
Matches are distributed among these distances:
18 21 0.46
19 2 0.04
20 1 0.02
21 5 0.11
22 5 0.11
23 1 0.02
24 2 0.04
25 9 0.20
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
TCATTTCTCATCTCATAA
Found at i:53938249 original size:43 final size:43
Alignment explanation
Indices: 53938196--53938279 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
53938186 ATATTTCATA
53938196 TCTCATCTCATAATCATTTCTCATA-TTTCTCATTTCAATATTT
1 TCTCATCTCATAATCATTTCTCATATTTTC-CATTTCAATATTT
* *
53938239 TCTCATCTCATAATCATTTCTCATCTTTTCCATTTCGATAT
1 TCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
53938280 CAATCACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 34 0.89
44 4 0.11
ACGTcount: A:0.24, C:0.25, G:0.01, T:0.50
Consensus pattern (43 bp):
TCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATATTT
Found at i:53943290 original size:6 final size:6
Alignment explanation
Indices: 53943279--53943340 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
53943269 CGTCGATTAG
*
53943279 TTATTT TTA--T TTAGTT TTATGTT TTA--T TTATTT TTATTT TTA-TT
1 TTATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT TTATTT TTATTT
*
53943323 TTATTT TTATTG TTATTT
1 TTATTT TTATTT TTATTT
53943341 GTTTTTCTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 8 0.17
5 5 0.11
6 29 0.62
7 5 0.11
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:53943305 original size:17 final size:16
Alignment explanation
Indices: 53943279--53943345 Score: 82
Period size: 17 Copynumber: 4.1 Consensus size: 16
53943269 CGTCGATTAG
53943279 TTATTTTTATTTAGTT
1 TTATTTTTATTTAGTT
*
53943295 TTATGTTTTATTTATTT
1 TTAT-TTTTATTTAGTT
*
53943312 TTATTTTTATTTTATTT
1 TTATTTTTA-TTTAGTT
*
53943329 TTATTGTTATTT-GTT
1 TTATTTTTATTTAGTT
53943344 TT
1 TT
53943346 TCTTTTTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.09
16 12 0.26
17 30 0.65
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
TTATTTTTATTTAGTT
Found at i:53943317 original size:27 final size:26
Alignment explanation
Indices: 53943279--53943333 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 26
53943269 CGTCGATTAG
53943279 TTATTTTTA-TTTAGTTTTATGTTTTAT
1 TTATTTTTATTTTA-TTTTAT-TTTTAT
53943306 TTATTTTTATTTTTATTTTATTTTTAT
1 TTATTTTTA-TTTTATTTTATTTTTAT
53943333 T
1 T
53943334 GTTATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.62
28 6 0.23
29 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (26 bp):
TTATTTTTATTTTATTTTATTTTTAT
Found at i:53943321 original size:33 final size:33
Alignment explanation
Indices: 53943279--53943352 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
53943269 CGTCGATTAG
*
53943279 TTATTTTTA-TTTAGTTTTATGTTTTATTTATTT
1 TTATTTTTATTTTAGTTTTAT-TGTTATTTATTT
* *
53943312 TTATTTTTATTTTATTTTTATTGTTATTTGTTT
1 TTATTTTTATTTTAGTTTTATTGTTATTTATTT
*
53943345 TTCTTTTT
1 TTATTTTT
53943353 TGGATTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 26 0.72
34 10 0.28
ACGTcount: A:0.15, C:0.01, G:0.05, T:0.78
Consensus pattern (33 bp):
TTATTTTTATTTTAGTTTTATTGTTATTTATTT
Found at i:53943331 original size:23 final size:24
Alignment explanation
Indices: 53943279--53943340 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
53943269 CGTCGATTAG
*
53943279 TTATTTTTA--TTTAGTTTTATGT
1 TTATTTTTATTTTTATTTTTATGT
*
53943301 TT-TATTTATTTTTATTTTTAT-T
1 TTATTTTTATTTTTATTTTTATGT
*
53943323 TTATTTTTATTGTTATTT
1 TTATTTTTATTTTTATTT
53943341 GTTTTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
23 23 0.70
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (24 bp):
TTATTTTTATTTTTATTTTTATGT
Found at i:53944320 original size:14 final size:15
Alignment explanation
Indices: 53944301--53944338 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
53944291 TTTCTCTTTT
53944301 AAAAAAAACAC-AAA
1 AAAAAAAACACTAAA
*
53944315 AAAAAAAACTCTAAA
1 AAAAAAAACACTAAA
53944330 AAAATAAAA
1 AAAA-AAAA
53944339 AAAATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 7 0.33
16 4 0.19
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAAAAAACACTAAA
Found at i:53947000 original size:31 final size:31
Alignment explanation
Indices: 53946955--53947025 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
53946945 TAGTAAAAAT
*
53946955 AAAATTATATTTTAAATCTTTCT-AAAATAATA
1 AAAATTATAATTT-AAT-TTTCTAAAAATAATA
* *
53946987 AAAATT-TAATTTAATTTTTTAAAAATTATA
1 AAAATTATAATTTAATTTTCTAAAAATAATA
53947017 AAAA-TATAA
1 AAAATTATAA
53947026 ACTAAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 5 0.15
30 18 0.53
31 5 0.15
32 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATTATAATTTAATTTTCTAAAAATAATA
Found at i:53947502 original size:6 final size:6
Alignment explanation
Indices: 53947491--53947517 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53947481 TGAGACATTG
53947491 GGATTT GGATTT GGATTT GGATTT GGA
1 GGATTT GGATTT GGATTT GGATTT GGA
53947518 AGAGACATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (6 bp):
GGATTT
Found at i:53957635 original size:19 final size:20
Alignment explanation
Indices: 53957597--53957632 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
53957587 TAGTTTACAG
53957597 ATTTATAAAGAGAAATAATC
1 ATTTATAAAGAGAAATAATC
53957617 ATTT-TAAAG-GAAATAA
1 ATTTATAAAGAGAAATAA
53957633 ATCCTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (20 bp):
ATTTATAAAGAGAAATAATC
Found at i:53969898 original size:33 final size:33
Alignment explanation
Indices: 53969763--53969901 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
53969753 ATTTGATGGG
* * * *
53969763 GAGGATGATGTTGAATGGGTAGAAGCTGCTGGA
1 GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
* * *
53969796 AAGGGTGATGTTG-AAGGTGTAGAAGCTACTGGG
1 GAGGGTGATGTTGAAAGG-GTAGAAGCTACTAGA
* * * ** *
53969829 GAAGGTGATGTTGAAGGGGTAAAAGCTTTTAAA
1 GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
* *
53969862 GAGGGTGATGTTTAAAGGGTAGAAGCTAATAGA
1 GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
53969895 GAGGGTG
1 GAGGGTG
53969902 TGACTACTGC
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
32 3 0.04
33 77 0.93
34 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.40, T:0.24
Consensus pattern (33 bp):
GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
Found at i:53978777 original size:21 final size:21
Alignment explanation
Indices: 53978716--53978779 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
53978706 TTCGGGTGCA
*
53978716 TCAGCT-TTTGTGAGCTTCTAT
1 TCAGCTCTTT-TGAGCTTCTGT
* *
53978737 TAAGCTCTTGTGAGCTTCTGT
1 TCAGCTCTTTTGAGCTTCTGT
53978758 TCAGCTCTTTTGAGCTTCTGT
1 TCAGCTCTTTTGAGCTTCTGT
53978779 T
1 T
53978780 AGCGTGTTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (21 bp):
TCAGCTCTTTTGAGCTTCTGT
Found at i:53992216 original size:23 final size:24
Alignment explanation
Indices: 53992172--53992216 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53992162 ATCCACCATA
53992172 AAACCCTAATATGAAGTTAATTAC
1 AAACCCTAATATGAAGTTAATTAC
53992196 AAACCCTGAA-ATG-AGTTAATT
1 AAACCCT-AATATGAAGTTAATT
53992217 TTCCTGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 10 0.50
25 2 0.10
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (24 bp):
AAACCCTAATATGAAGTTAATTAC
Found at i:54001981 original size:91 final size:91
Alignment explanation
Indices: 54001845--54002026 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
54001835 TTTCGAGTTG
54001845 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
1 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
54001910 TTGATTGAAAGGACTATAATGGTCGT
66 TTGATTGAAAGGACTATAATGGTCGT
54001936 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
1 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
54002001 TTGATTGAAAGGACTATAATGGTCGT
66 TTGATTGAAAGGACTATAATGGTCGT
54002027 GAACAACAAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (91 bp):
TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
TTGATTGAAAGGACTATAATGGTCGT
Found at i:54013901 original size:20 final size:20
Alignment explanation
Indices: 54013867--54013921 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
54013857 AATAACAAAC
** * *
54013867 TAAAAATTATCAAAATTTAT
1 TAAAAATTAAAAAAAATTAA
54013887 TAAAAATTAAAAAAAATTAA
1 TAAAAATTAAAAAAAATTAA
54013907 TAAAGAATTTAAAAA
1 TAAA-AA-TTAAAAA
54013922 TTATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 20 0.69
21 2 0.07
22 7 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAATTAAAAAAAATTAA
Found at i:54013940 original size:17 final size:18
Alignment explanation
Indices: 54013898--54013944 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
54013888 AAAAATTAAA
54013898 AAAAATTAATAAAGAATTT
1 AAAAATT-ATAAAGAATTT
54013917 AAAAATTATAAA-AATGTT
1 AAAAATTATAAAGAAT-TT
54013935 -AAAATTATAA
1 AAAAATTATAA
54013945 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.48
18 7 0.26
19 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAAATTATAAAGAATTT
Found at i:54014078 original size:14 final size:14
Alignment explanation
Indices: 54014059--54014085 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54014049 AATATTATTC
54014059 AAATAATTAATTTA
1 AAATAATTAATTTA
54014073 AAATAATTAATTT
1 AAATAATTAATTT
54014086 TCGCCCAGGC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATAATTAATTTA
Found at i:54031389 original size:3 final size:3
Alignment explanation
Indices: 54031381--54031423 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
54031371 AAAAAACCCT
*
54031381 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
54031424 AAGCTAAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:54042761 original size:41 final size:40
Alignment explanation
Indices: 54042658--54042776 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 40
54042648 CCTCATCGGA
* * *
54042658 TAATTTGAAGTAATAAATTGACACCCAGTGTCTCATCGGC
1 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAGAC
* * * * *
54042698 TAAACCGAAG---TAAATTGGCACCCAGTGCCTCATAGAAT
1 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAG-AC
*
54042736 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATCGAC
1 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAGAC
54042776 T
1 T
54042777 CAAAGTCGAA
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
37 22 0.36
38 8 0.13
40 9 0.15
41 22 0.36
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (40 bp):
TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAGAC
Found at i:54043329 original size:15 final size:16
Alignment explanation
Indices: 54043309--54043339 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54043299 CTTAAGTCCC
54043309 TAAATTTC-AAATTTT
1 TAAATTTCAAAATTTT
54043324 TAAATTTCAAAATTTT
1 TAAATTTCAAAATTTT
54043340 CATAATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTTCAAAATTTT
Found at i:54049392 original size:28 final size:28
Alignment explanation
Indices: 54049311--54049392 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
54049301 GTGCAGAGGT
* * ** *
54049311 CACACGGCCAAGTCACATGCCCGTGCGA
1 CACACGGCTAAGACACACACCCGTGTGA
54049339 CACACGGCTAAGACACACACCCGTGTGA
1 CACACGGCTAAGACACACACCCGTGTGA
54049367 CACACGGCTAAGACACACACCCGTGT
1 CACACGGCTAAGACACACACCCGTGT
54049393 CTCTGCCTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.29, C:0.38, G:0.22, T:0.11
Consensus pattern (28 bp):
CACACGGCTAAGACACACACCCGTGTGA
Found at i:54050130 original size:14 final size:16
Alignment explanation
Indices: 54050100--54050131 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
54050090 CATTCAATTC
54050100 ATCACTTCATAAACAT
1 ATCACTTCATAAACAT
54050116 ATCA-TTCAT-AACAT
1 ATCACTTCATAAACAT
54050130 AT
1 AT
54050132 TCAATTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (16 bp):
ATCACTTCATAAACAT
Found at i:54050156 original size:22 final size:21
Alignment explanation
Indices: 54050131--54050173 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
54050121 TCATAACATA
*
54050131 TTCAATTCTCATCACTTGCTAT
1 TTCAAGTCTCAT-ACTTGCTAT
54050153 TTCAAGTCTCATACTTGCTAT
1 TTCAAGTCTCATACTTGCTAT
54050174 CAAATAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.26, G:0.07, T:0.44
Consensus pattern (21 bp):
TTCAAGTCTCATACTTGCTAT
Found at i:54050433 original size:37 final size:38
Alignment explanation
Indices: 54050337--54050433 Score: 97
Period size: 40 Copynumber: 2.5 Consensus size: 38
54050327 AACACACCAG
* * **
54050337 ATTGGTACCCAGTACCTCATCGGATAATTCGAAGTAATAA
1 ATTGGCACCCAGTACCTCATCAGATAAACCGAAG--ATAA
* ** *
54050377 ATTGACACCCAGTGTCTCATCAGCTAAACCGAAG-TAA
1 ATTGGCACCCAGTACCTCATCAGATAAACCGAAGATAA
54050414 ATTGGCACCCAGTACCTCAT
1 ATTGGCACCCAGTACCTCAT
54050434 AAAATTAATC
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
37 20 0.43
40 26 0.57
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (38 bp):
ATTGGCACCCAGTACCTCATCAGATAAACCGAAGATAA
Found at i:54059450 original size:14 final size:14
Alignment explanation
Indices: 54059431--54059462 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
54059421 GGTAGGCAAC
*
54059431 TTTTTTTTTGCGGT
1 TTTTTTTTTGCGCT
54059445 TTTTTTTTTGCGCT
1 TTTTTTTTTGCGCT
54059459 TTTT
1 TTTT
54059463 GCTTCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.16, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTGCGCT
Found at i:54069701 original size:46 final size:45
Alignment explanation
Indices: 54069634--54069958 Score: 359
Period size: 46 Copynumber: 7.6 Consensus size: 45
54069624 TTTGAATACT
*
54069634 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
54069680 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
54069716 TTTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
54069762 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
54069798 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
54069844 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACTCTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
54069890 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
54069934 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
54069959 ATCATATGTA
Statistics
Matches: 241, Mismatches: 18, Indels: 44
0.80 0.06 0.15
Matches are distributed among these distances:
36 57 0.24
37 2 0.01
38 1 0.00
39 1 0.00
40 5 0.02
41 1 0.00
42 19 0.08
43 4 0.02
44 18 0.07
45 3 0.01
46 130 0.54
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:54069711 original size:36 final size:36
Alignment explanation
Indices: 54069670--54069824 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
54069660 GGTAGCATTA
54069670 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
54069706 GCTACACTTATTTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
54069751 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
54069788 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
54069824 G
1 G
54069825 TTAGCCTTAG
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 64 0.63
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 29 0.29
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:54069739 original size:82 final size:81
Alignment explanation
Indices: 54069634--54069958 Score: 431
Period size: 82 Copynumber: 3.9 Consensus size: 81
54069624 TTTGAATACT
*
54069634 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAAAAAGT
54069699 GATAAGTGCTACACTTA
65 GATAAGTGCTACACTTA
* *
54069716 TTTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
54069781 GATAAGTGCTATACTTA
65 GATAAGTGCTACACTTA
* *
54069798 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAAGTGAAAAAGT
54069863 GATAAGTGGTAGCCTTAGCTACTCTTA
65 GATAA---GT-G-C-TA-C-A--CTTA
* * *
54069890 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CAGCTACACTTATCTGATC-AG-GGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
54069952 ATAAGTG
66 ATAAGTG
54069959 ATCATATGTA
Statistics
Matches: 217, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
82 141 0.65
83 1 0.00
84 1 0.00
85 4 0.02
86 1 0.00
87 1 0.00
88 12 0.06
89 2 0.01
90 19 0.09
91 1 0.00
92 34 0.16
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (81 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
ATAAGTGCTACACTTA
Found at i:54075535 original size:17 final size:17
Alignment explanation
Indices: 54075515--54075561 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
54075505 AAAAAATTAA
54075515 AAATCCTTTAAAAGTAT
1 AAATCCTTTAAAAGTAT
*
54075532 AAATCAATTTAAAAAGTAT
1 AAATC-CTTT-AAAAGTAT
*
54075551 -AATTCTTTAAA
1 AAATCCTTTAAA
54075562 CATATTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 8 0.32
18 6 0.24
19 8 0.32
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (17 bp):
AAATCCTTTAAAAGTAT
Found at i:54077294 original size:17 final size:18
Alignment explanation
Indices: 54077254--54077294 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
54077244 CTTTTTTCAG
54077254 TTTAGGAGGTTGAATAACAA
1 TTTAGGAGGTTGAAT-A-AA
54077274 TTTAGGAGGTTGAAT-AA
1 TTTAGGAGGTTGAATAAA
54077291 TTTA
1 TTTA
54077295 TAAAGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
20 15 0.71
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (18 bp):
TTTAGGAGGTTGAATAAA
Found at i:54080597 original size:15 final size:15
Alignment explanation
Indices: 54080579--54080614 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
54080569 TGGCCCCGAA
54080579 ACCACTATTTTCAAC
1 ACCACTATTTTCAAC
54080594 ACCACTATTTTCAAC
1 ACCACTATTTTCAAC
54080609 ACCACT
1 ACCACT
54080615 TAAAAACGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (15 bp):
ACCACTATTTTCAAC
Found at i:54083944 original size:20 final size:20
Alignment explanation
Indices: 54083919--54083961 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
54083909 TTAAGCTAGT
*
54083919 TAAAGTCTGTTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
54083939 TAAAGTCTGGTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
54083959 TAA
1 TAA
54083962 CATTGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
TAAAGTCTGGTTTAGTATAA
Found at i:54086655 original size:21 final size:22
Alignment explanation
Indices: 54086637--54086678 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54086627 AACAAATATA
*
54086637 TACATATAGATAAA-AAATAAT
1 TACATATAAATAAATAAATAAT
54086658 TACATATAAATAAATAAATAA
1 TACATATAAATAAATAAATAA
54086679 AAAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TACATATAAATAAATAAATAAT
Found at i:54086729 original size:21 final size:21
Alignment explanation
Indices: 54086703--54086743 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54086693 ATACTACAAA
*
54086703 AAAAATAAATATGCATATATG
1 AAAAATAAATATACATATATG
*
54086724 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
54086744 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:54088280 original size:44 final size:43
Alignment explanation
Indices: 54088218--54088328 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 43
54088208 GATCTGCTCT
* *
54088218 CTGCAACTTCA-GAGAGATAAGATC-CAAGGTTTTAATCCACTCCA
1 CTGCAACTTTAGGA-AGATAAGATCAC-A-GCTTTAATCCACTCCA
* * *
54088262 CTGCAACTTTAGGAAGATAGGATTATCAGCTTTAATCTACTCCA
1 CTGCAACTTTAGGAAGATAAGATCA-CAGCTTTAATCCACTCCA
* *
54088306 CTGTAACTTTAGGGAGATAAGAT
1 CTGCAACTTTAGGAAGATAAGAT
54088329 TTGCCATCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
44 52 0.93
45 3 0.05
46 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (43 bp):
CTGCAACTTTAGGAAGATAAGATCACAGCTTTAATCCACTCCA
Found at i:54088698 original size:218 final size:218
Alignment explanation
Indices: 54088164--54088993 Score: 1286
Period size: 218 Copynumber: 3.8 Consensus size: 218
54088154 TCAACTTGAT
** * *
54088164 TTAGTCTGCTCCTGGTGTAACTTCAGGAAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCA
1 TTAGTCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCA
* *
54088229 GAGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTTAGGAAGATAGGATTATCAGCTT
65 GAGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTT
* *
54088294 TAATCTACTCCACTGTAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACT
130 TAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACT
**
54088359 TCAGGAGGATAAGACTTGC-CCAC
195 TCAGGAGGATAAGACTTGCTTTAC
*
54088382 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
** * * * *
54088447 AGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGTCGGCTTT
66 AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
*
54088512 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTT
131 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
54088577 CAGGAGGATAAGACTTGCTTTAC
196 CAGGAGGATAAGACTTGCTTTAC
*
54088600 TTAGTCTGCTCCAGTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
*
54088665 AGAGATAAGATCCAAGGTTTTAATCTACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
66 AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
* * *
54088730 AATCTGCTCCATTCCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
131 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
54088795 TAGGAGGATAAGACTTGCTTTAC
196 CAGGAGGATAAGACTTGCTTTAC
* * * *
54088818 TTAGTCTGCTCTACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGTAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
* ** ** * * *
54088883 AGAGATAAGATCTAAGGTTTTAATCCGTTTTACTGCAACTTCAGGGAGATATGATTGTCGGCTTT
66 AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
* *
54088948 AATCTGCTCCTCTGCAA-TTTCAGGGAGATAAGATTTTCCATCTTCA
131 AATCTGCTCCACTGCAACTTT-AGGGAGATAAGATTTGCCATCTTCA
54088994 CTGATATGCT
Statistics
Matches: 559, Mismatches: 51, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
217 187 0.33
218 372 0.67
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (218 bp):
TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
CAGGAGGATAAGACTTGCTTTAC
Found at i:54088853 original size:45 final size:44
Alignment explanation
Indices: 54088301--54088854 Score: 314
Period size: 44 Copynumber: 12.7 Consensus size: 44
54088291 CTTTAATCTA
* * * *
54088301 CTCCACTGTAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTT-AGTCTG
*
54088346 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCCCA-CTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTG-CTATCTTAGTCTG
* *
54088390 CTCCACTGCAACTTCAGGGAGATAAGACTAG--ATGC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT-CTTAGTCTG
* * * * * *
54088431 CT-CTCTGCAACTTCAGAGAGATAAGATCTGAGGT-T-TTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTATCTTAGTCTG
* * ** *
54088474 CTCCACTGTAACTTCAGGGAGATAGGA-TTG-TCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCT-ATC-TTAGTCTG
* * *
54088518 CTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTT-AGTCTG
* *
54088563 C-CTCACTGTAACTTCA-GGAGGATAAGACTTGCTTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTAT-CTTAGTCTG
* ** *
54088608 CTCCAGTGCAACTTCAGGGAGATAAGAC-T-AAATGC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT-CTTAGTCTG
* * * * * * *
54088649 CT-CTCTGCAACTTCAGAGAGATAAGA--TCCAAGGTTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTA--TCTTAGTCTG
* * * *
54088692 CTCCACTGCAACTTCAGGAAGATAGGATTATCGGC--T-TTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTATCTTAGTCTG
* * * *
54088736 CTCCATTCCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTT-AGTCTG
* *
54088781 C-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTAT-CTTAGTCTG
*
54088826 CTCTACTGCAACTTCAGGGAGATAAGACT
1 CTCCACTGCAACTTCAGGGAGATAAGACT
54088855 AGATGCGATC
Statistics
Matches: 402, Mismatches: 61, Indels: 92
0.72 0.11 0.17
Matches are distributed among these distances:
39 1 0.00
40 46 0.11
41 18 0.04
42 8 0.02
43 16 0.04
44 150 0.37
45 144 0.36
46 17 0.04
47 1 0.00
49 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTAGTCTG
Found at i:54101090 original size:22 final size:22
Alignment explanation
Indices: 54101049--54101091 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
54101039 AAATAAAAAA
* * *
54101049 TAAAAAAATATATTTTTTCATT
1 TAAAAAAATAAATATGTTCATT
54101071 TAAAAAAATAAATATGTTCAT
1 TAAAAAAATAAATATGTTCAT
54101092 ATATATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAAAAATAAATATGTTCATT
Found at i:54101173 original size:21 final size:22
Alignment explanation
Indices: 54101155--54101196 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54101145 AACAAATATA
*
54101155 TACATATAGATAAA-AAATAAT
1 TACATATAAATAAATAAATAAT
54101176 TACATATAAATAAATAAATAA
1 TACATATAAATAAATAAATAA
54101197 AAAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TACATATAAATAAATAAATAAT
Found at i:54101246 original size:21 final size:21
Alignment explanation
Indices: 54101220--54101260 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54101210 TATACTACAA
*
54101220 AAAAATATATATGCATATATG
1 AAAAATATATATACATATATG
54101241 AAAAATATATATACATATAT
1 AAAAATATATATACATATAT
54101261 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAAATATATATACATATATG
Found at i:54103777 original size:20 final size:20
Alignment explanation
Indices: 54103752--54103794 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
54103742 TTAAGCTAGT
*
54103752 TAAAGTCTGTTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
54103772 TAAAGTCTGGTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
54103792 TAA
1 TAA
54103795 CATTGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
TAAAGTCTGGTTTAGTATAA
Found at i:54106487 original size:21 final size:22
Alignment explanation
Indices: 54106469--54106510 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54106459 AACAAATATA
*
54106469 TACATATAGATAAA-AAATAAT
1 TACATATAAATAAATAAATAAT
54106490 TACATATAAATAAATAAATAA
1 TACATATAAATAAATAAATAA
54106511 AATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TACATATAAATAAATAAATAAT
Found at i:54110027 original size:31 final size:31
Alignment explanation
Indices: 54109989--54110050 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
54109979 ATGGCTATTG
* **
54109989 AACTATTCGAAAGCTTTCATTGAAATCATTA
1 AACTATTCAAAAAATTTCATTGAAATCATTA
* *
54110020 AACTATTCAAAAAATTTTATTGAAGTCATTA
1 AACTATTCAAAAAATTTCATTGAAATCATTA
54110051 GACTGTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (31 bp):
AACTATTCAAAAAATTTCATTGAAATCATTA
Found at i:54114139 original size:23 final size:23
Alignment explanation
Indices: 54114111--54114204 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
54114101 ATGTGTGTAT
* *
54114111 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
54114134 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
54114157 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
54114180 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
54114203 CT
1 CT
54114205 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:54123019 original size:16 final size:15
Alignment explanation
Indices: 54122972--54123020 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
54122962 TTTTAAGATT
*
54122972 TTTAAAATGTTAATA
1 TTTAAAATGTTATTA
* *
54122987 TTTTAAATTTTATTTA
1 TTTAAAATGTTA-TTA
54123003 TTTAAAATGTTAGTTA
1 TTTAAAATGTTA-TTA
54123019 TT
1 TT
54123021 GTAATTGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTAAAATGTTATTA
Found at i:54123088 original size:16 final size:17
Alignment explanation
Indices: 54123050--54123096 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
54123040 TTAAAATTTT
54123050 ATAA-ATTATAAAATAAG
1 ATAATATTA-AAAATAAG
*
54123067 AAAATATTAAAAATAA-
1 ATAATATTAAAAATAAG
*
54123083 ATAATATAAAAAAT
1 ATAATATTAAAAAT
54123097 TTAAAATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 10 0.38
18 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
ATAATATTAAAAATAAG
Found at i:54127569 original size:25 final size:25
Alignment explanation
Indices: 54127536--54127614 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
54127526 ATACGAAGCG
* *
54127536 TATCTTATCGTATCATAGCATATCA
1 TATCATATCGAATCATAGCATATCA
*
54127561 TATCATATCGAATCATAGCATTTCA
1 TATCATATCGAATCATAGCATATCA
* * *
54127586 TAATGA-ATCAAACCATAGCATATCA
1 T-ATCATATCGAATCATAGCATATCA
54127611 TATC
1 TATC
54127615 GAATCACAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
24 2 0.04
25 40 0.89
26 3 0.07
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (25 bp):
TATCATATCGAATCATAGCATATCA
Found at i:54127577 original size:20 final size:20
Alignment explanation
Indices: 54127554--54127609 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
54127544 CGTATCATAG
*
54127554 CATATCATATCATATCGAAT
1 CATACCATATCATATCGAAT
* *
54127574 CATAGCATTTCATAAT-GAAT
1 CATACCATATCAT-ATCGAAT
* *
54127594 CAAACCATAGCATATC
1 CATACCATATCATATC
54127610 ATATCGAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.30
Consensus pattern (20 bp):
CATACCATATCATATCGAAT
Found at i:54127618 original size:25 final size:24
Alignment explanation
Indices: 54127549--54127638 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 24
54127539 CTTATCGTAT
*
54127549 CATAGCATATCATATC-ATATCGAAT
1 CATAGCATATCATATCGA-ATC-AAA
*
54127574 CATAGCATTTCATAAT-GAATCAAA
1 CATAGCATATCAT-ATCGAATCAAA
54127598 CCATAGCATATCATATCGAATCACAA
1 -CATAGCATATCATATCGAATCA-AA
54127624 CAT-GACATATCATAT
1 CATAG-CATATCATAT
54127639 TACGTCCTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
24 5 0.09
25 46 0.82
26 5 0.09
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (24 bp):
CATAGCATATCATATCGAATCAAA
Found at i:54138917 original size:20 final size:20
Alignment explanation
Indices: 54138888--54138927 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
54138878 TCACTTTTGC
*
54138888 CTTGATTAAACCCGTTTGGA
1 CTTGAATAAACCCGTTTGGA
54138908 CTTGAATAAACCCGTTTGGA
1 CTTGAATAAACCCGTTTGGA
54138928 ATAGGGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
CTTGAATAAACCCGTTTGGA
Found at i:54139055 original size:21 final size:21
Alignment explanation
Indices: 54139027--54139082 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
54139017 AATAGCGGTG
*
54139027 GCAGTGAGATTAGTTACTGTA
1 GCAGTGAGATTAGATACTGTA
* *
54139048 GCGGTGAGATTGGATACTGTA
1 GCAGTGAGATTAGATACTGTA
54139069 GCAGTGAGATTAGA
1 GCAGTGAGATTAGA
54139083 AACAATGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCAGTGAGATTAGATACTGTA
Found at i:54143949 original size:21 final size:22
Alignment explanation
Indices: 54143913--54143997 Score: 120
Period size: 21 Copynumber: 4.0 Consensus size: 22
54143903 CCAAGAACAA
*
54143913 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAATGAGGGGAGAAACC
* *
54143935 AGCAAAAACGA-GGGAGAAACT
1 AGCAAAAATGAGGGGAGAAACC
*
54143956 AGCAAGAATGA-GGGAGAAACC
1 AGCAAAAATGAGGGGAGAAACC
54143977 AGCAAAAATGAGGGGAGAAAC
1 AGCAAAAATGAGGGGAGAAAC
54143998 GGCTGTTTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 37 0.66
22 19 0.34
ACGTcount: A:0.52, C:0.13, G:0.32, T:0.04
Consensus pattern (22 bp):
AGCAAAAATGAGGGGAGAAACC
Found at i:54147007 original size:17 final size:18
Alignment explanation
Indices: 54146986--54147029 Score: 81
Period size: 17 Copynumber: 2.5 Consensus size: 18
54146976 CTAATGTGTT
54146986 TTTTTATTTGTATTTGTA
1 TTTTTATTTGTATTTGTA
54147004 -TTTTATTTGTATTTGTA
1 TTTTTATTTGTATTTGTA
54147021 TTTTTATTT
1 TTTTTATTT
54147030 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (18 bp):
TTTTTATTTGTATTTGTA
Found at i:54147031 original size:6 final size:6
Alignment explanation
Indices: 54146990--54147029 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
54146980 TGTGTTTTTT
*
54146990 TATTTG TATTTG TATTT- TATTTG TATTTG TATTTT TATTT
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTT
54147030 TTTTTCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (6 bp):
TATTTG
Found at i:54152843 original size:22 final size:22
Alignment explanation
Indices: 54152818--54152865 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
54152808 GAAGGTTAGA
54152818 TTCTTTGAGGAGATCATACGCT
1 TTCTTTGAGGAGATCATACGCT
54152840 TTCTTTGAGGAGATCATACGCT
1 TTCTTTGAGGAGATCATACGCT
54152862 TTCT
1 TTCT
54152866 CGAGTTCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (22 bp):
TTCTTTGAGGAGATCATACGCT
Found at i:54155518 original size:28 final size:28
Alignment explanation
Indices: 54155478--54155534 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
54155468 TCAATACACG
54155478 AAAGAGTGCAACTTTCCTTTCTGAACTT
1 AAAGAGTGCAACTTTCCTTTCTGAACTT
54155506 AAAGAGTGCAACTTTCCTTTCTGAACTT
1 AAAGAGTGCAACTTTCCTTTCTGAACTT
54155534 A
1 A
54155535 GTCGAGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (28 bp):
AAAGAGTGCAACTTTCCTTTCTGAACTT
Found at i:54158833 original size:29 final size:29
Alignment explanation
Indices: 54158791--54158852 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
54158781 TGTTCAAATT
54158791 TTAATAATTCACATTAATTTTATACTAAC
1 TTAATAATTCACATTAATTTTATACTAAC
*
54158820 TTAATAATTCACATTAATTTTATTCTAAC
1 TTAATAATTCACATTAATTTTATACTAAC
54158849 TTAA
1 TTAA
54158853 GGAACTAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAATAATTCACATTAATTTTATACTAAC
Found at i:54160487 original size:68 final size:68
Alignment explanation
Indices: 54160383--54160554 Score: 215
Period size: 68 Copynumber: 2.5 Consensus size: 68
54160373 CTTTATTTCA
* * *
54160383 TGCCATAGTCGAGTTATGGTCTTACATAATATAACCCCATGTTTATGGTCCTGGC-GAACTCTA-
1 TGCCATAGTCGAGCTATGTTCTTACACAATA-AACCCCATGTTTATGGTCCTGGCAG-ACTCTAT
54160446 TTTGT
64 TTTGT
*
54160451 TGCCATAGTCGAGCTATGTTCTTACACAATACAACCCCATGTTTATGGTCTTGGCAGACTCTATT
1 TGCCATAGTCGAGCTATGTTCTTACACAATA-AACCCCATGTTTATGGTCCTGGCAGACTCTATT
*
54160516 TTTT
65 TTGT
** *
54160520 TATCATAGTTGAGCTATGGTT-TTACACAATAAACC
1 TGCCATAGTCGAGCTAT-GTTCTTACACAATAAACC
54160555 TTTTTCGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
68 60 0.65
69 29 0.32
70 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (68 bp):
TGCCATAGTCGAGCTATGTTCTTACACAATAAACCCCATGTTTATGGTCCTGGCAGACTCTATTT
TGT
Found at i:54162653 original size:76 final size:76
Alignment explanation
Indices: 54162527--54162672 Score: 265
Period size: 76 Copynumber: 1.9 Consensus size: 76
54162517 GTAAAATTTA
*
54162527 AAAATTTTGAAAATAGGGGTCACACGGCCGTGTGACATAACTCAAGCCATGTGGGTATTTGAAGT
1 AAAATTTTGAAAACAGGGGTCACACGGCCGTGTGACATAACTCAAGCCATGTGGGTATTTGAAGT
54162592 TTAGTCGCACG
66 TTAGTCGCACG
* *
54162603 AAAATTTTGAAAACAGGGGTCACACGGCCGTGTGACATAACTCACGCCATGTGGTTATTTGAAGT
1 AAAATTTTGAAAACAGGGGTCACACGGCCGTGTGACATAACTCAAGCCATGTGGGTATTTGAAGT
54162668 TTAGT
66 TTAGT
54162673 TACATGGCTA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (76 bp):
AAAATTTTGAAAACAGGGGTCACACGGCCGTGTGACATAACTCAAGCCATGTGGGTATTTGAAGT
TTAGTCGCACG
Found at i:54163802 original size:18 final size:17
Alignment explanation
Indices: 54163779--54163813 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
54163769 ATTTAGGGTT
54163779 TATATATCATCCATTACA
1 TATATAT-ATCCATTACA
*
54163797 TATATATATTCATTACA
1 TATATATATCCATTACA
54163814 CATTTTTCTC
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:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATATATCCATTACA
Found at i:54164125 original size:41 final size:41
Alignment explanation
Indices: 54164058--54164186 Score: 170
Period size: 41 Copynumber: 3.1 Consensus size: 41
54164048 ACTACCTAAA
*
54164058 ACAATACACGGGCACGAAGCCTGCTAGGCTCAAGGCTTGAT
1 ACAATACACCGGCACGAAGCCTGCTAGGCTCAAGGCTTGAT
* * * *
54164099 ACAACACACCGGCACGAAGCTTGCTAGGCTTAAGGCCTGAT
1 ACAATACACCGGCACGAAGCCTGCTAGGCTCAAGGCTTGAT
* * *
54164140 ACAATACACTGGCACAAAGCCTACTAGGCTCAAGG-TCTGAT
1 ACAATACACCGGCACGAAGCCTGCTAGGCTCAAGGCT-TGAT
54164181 ACAATA
1 ACAATA
54164187 GACTAGCAAG
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (41 bp):
ACAATACACCGGCACGAAGCCTGCTAGGCTCAAGGCTTGAT
Found at i:54164201 original size:41 final size:40
Alignment explanation
Indices: 54164058--54164213 Score: 152
Period size: 41 Copynumber: 3.8 Consensus size: 40
54164048 ACTACCTAAA
* * *
54164058 ACAATACACGGGCACGAAGCCTGCTAGGCTCAAGGCTTGAT
1 ACAATACACTGGCAAGAAGCCTACTAGGCTCAAGGC-TGAT
* * * * * *
54164099 ACAACACACCGGCACGAAGCTTGCTAGGCTTAAGGCCTGAT
1 ACAATACACTGGCAAGAAGCCTACTAGGCTCAAGG-CTGAT
54164140 ACAATACACTGGCACA-AAGCCTACTAGGCTCAAGGTCTGAT
1 ACAATACACTGGCA-AGAAGCCTACTAGGCTCAAGG-CTGAT
* * * *
54164181 ACAATAGACTAGCAAGAAGCCTAGTACGCTCAA
1 ACAATACACTGGCAAGAAGCCTACTAGGCTCAA
54164214 AGCCTGTTCT
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.01
41 95 0.98
42 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.17
Consensus pattern (40 bp):
ACAATACACTGGCAAGAAGCCTACTAGGCTCAAGGCTGAT
Found at i:54164219 original size:82 final size:82
Alignment explanation
Indices: 54164058--54164219 Score: 184
Period size: 82 Copynumber: 2.0 Consensus size: 82
54164048 ACTACCTAAA
* * * * *
54164058 ACAATACACGGGCACGAAGCCTGCTAGGCTCAAGGCTTGATACAACACACCGGCACGAAGCTTGC
1 ACAATACACGGGCACAAAGCCTACTAGGCTCAAGGCTTGATACAACACACCAGCAAGAAGCTAGC
* * *
54164123 TAGGCTTAAGGCCTGAT
66 TACGCTCAAAGCCTGAT
* * * *
54164140 ACAATACACTGGCACAAAGCCTACTAGGCTCAAGG-TCTGATACAATAGACTAGCAAGAAGCCTA
1 ACAATACACGGGCACAAAGCCTACTAGGCTCAAGGCT-TGATACAACACACCAGCAAGAAG-CTA
54164204 G-TACGCTCAAAGCCTG
64 GCTACGCTCAAAGCCTG
54164220 TTCTGGTACA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
81 1 0.02
82 62 0.94
83 3 0.05
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (82 bp):
ACAATACACGGGCACAAAGCCTACTAGGCTCAAGGCTTGATACAACACACCAGCAAGAAGCTAGC
TACGCTCAAAGCCTGAT
Found at i:54166776 original size:5 final size:5
Alignment explanation
Indices: 54166754--54166811 Score: 66
Period size: 5 Copynumber: 11.8 Consensus size: 5
54166744 CGACATAAGA
* **
54166754 AAAAT AAAAG AAGCT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA- AATAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT
54166803 AAAAT AAAA
1 AAAAT AAAA
54166812 CAAAGAAGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:54166801 original size:7 final size:7
Alignment explanation
Indices: 54166774--54166811 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
54166764 AAGCTAAAAT
54166774 AAAATAA
1 AAAATAA
54166781 AATAA-AA
1 AA-AATAA
54166788 TAAAATAA
1 -AAAATAA
54166796 AAAATAA
1 AAAATAA
54166803 AAAATAA
1 AAAATAA
54166810 AA
1 AA
54166812 CAAAGAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:54168012 original size:21 final size:21
Alignment explanation
Indices: 54167988--54168027 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54167978 GCCTAAGATG
*
54167988 TGAATTGGATTGAATTGAATA
1 TGAATTGGATTAAATTGAATA
*
54168009 TGAATTGTATTAAATTGAA
1 TGAATTGGATTAAATTGAA
54168028 CTAAATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (21 bp):
TGAATTGGATTAAATTGAATA
Found at i:54179223 original size:44 final size:45
Alignment explanation
Indices: 54178989--54179240 Score: 140
Period size: 44 Copynumber: 5.6 Consensus size: 45
54178979 TTTTAGTCTA
* * *
54178989 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAA-CTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATC-TG
* * ** * * *
54179033 CTCTACTGCAACTTAAGGGAGATAAGGTTTGATA---T-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
** * ** *
54179074 CTTTACTGCAACTTCAGAGAGATAAGATCTACAATTTATAGCTTCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-C----GCTAGCTTCAATCTG
* * * * * *
54179125 TTCAACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
* * * * *
54179170 CTTCGCTGCAACTTCAGGGAGATAAGGCT-GGTGGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
*
54179214 CTCCACTGCAACTTCAGAGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
54179241 TCTGCCATAA
Statistics
Matches: 156, Mismatches: 40, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
41 26 0.17
42 3 0.02
44 61 0.39
45 34 0.22
47 3 0.02
49 1 0.01
50 2 0.01
51 26 0.17
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
Found at i:54179460 original size:142 final size:143
Alignment explanation
Indices: 54179069--54179480 Score: 507
Period size: 142 Copynumber: 2.9 Consensus size: 143
54179059 GTTTGATATG
** * * * * *
54179069 ATCTGCTTTACTGCAACTTCAGAGAGATAAGATCT---ACAATTTATAGCTTCAATCTATTCAAC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAC
** * * * *
54179131 TGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTTCGCTGCAACTTCAGGGAGATAAG
66 TGCAACGCCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAG
54179196 GCTGGTGGCTTCA
131 GCTGGTGGCTTCA
*
54179209 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAC
* * * * * * *
54179274 TGCTACGCC-AGAGAAATAAGATTTGTTGTATTCAGTTTGTTCCACTGCAACTTCAAGGAGATAA
66 TGCAACGCCAAG-GAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAA
54179338 GGCTGGT-GCTTCA
130 GGCTGGTGGCTTCA
*
54179351 ATCTGCTCCACTGCAACTTCA-AGAAGATAAGATCTGCCATAATTTGTAGTTTTAATCTGTTCCA
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCA
* * *
54179415 CTGCAACGCCAAGGAAATAAGGTTCGACT-TCTTCAATCTACTCCACTGCAACTTC-AGGAAGAT
65 CTGCAACGCCAAGGAAATAAGATTCG-CTATCTTCAGTCTGCTCCACTGCAACTTCAAGG-AGAT
54179478 AAG
128 AAG
54179481 ATTCGCCATA
Statistics
Matches: 232, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
140 33 0.14
141 5 0.02
142 114 0.49
143 80 0.34
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (143 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAC
TGCAACGCCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAG
GCTGGTGGCTTCA
Found at i:54179480 original size:99 final size:98
Alignment explanation
Indices: 54179311--54179579 Score: 326
Period size: 99 Copynumber: 2.7 Consensus size: 98
54179301 GTATTCAGTT
** * * * * *
54179311 TGTTCCACTGCAACTTCAAGGAGATAAGGCT-GGTGCTTCAATCTGCTCCACTGCAACTTCAAGA
1 TGTTCCACTGCAACGCCAAGGAAATAAGGTTCGCTTCTTCAATCTGCTCCACTGCAACTTCAGGA
*
54179375 AGATAAGA-TCTGCCATAATTTGTAGTTTTAATC
66 AGATAAGATTC-GCCATAATTTGTAGCTTTAATC
*
54179408 TGTTCCACTGCAACGCCAAGGAAATAAGGTTCGACTTCTTCAATCTACTCCACTGCAACTTCAGG
1 TGTTCCACTGCAACGCCAAGGAAATAAGGTTCG-CTTCTTCAATCTGCTCCACTGCAACTTCAGG
54179473 AAGATAAGATTCGCCATAATTTGTAGCTTTAATC
65 AAGATAAGATTCGCCATAATTTGTAGCTTTAATC
* * * * * * * * *
54179507 TATTCCACTGTAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTTCGCTGTAACTTCAGG
1 TGTTCCACTGCAACGCCAAGGAAATAAGGTTCGCT-TCTTCAATCTGCTCCACTGCAACTTCAGG
*
54179572 GAGATAAG
65 AAGATAAG
54179580 GTTGGTGACT
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
97 27 0.18
98 3 0.02
99 116 0.78
100 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (98 bp):
TGTTCCACTGCAACGCCAAGGAAATAAGGTTCGCTTCTTCAATCTGCTCCACTGCAACTTCAGGA
AGATAAGATTCGCCATAATTTGTAGCTTTAATC
Found at i:54179499 original size:241 final size:242
Alignment explanation
Indices: 54179204--54179677 Score: 697
Period size: 241 Copynumber: 2.0 Consensus size: 242
54179194 AGGCTGGTGG
* *
54179204 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
1 CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTAT
* * * *
54179269 TCCATTGCT-ACGCCAGAGAAATAAGATTTGTTGTATTCAGTTTG-TTCCACTGCAACTTCAAGG
66 TCCACTG-TAACGCCAGAGAAATAAGATTCGCTGTATTCAGTCTGCTT-CACTGCAACTTCAAGG
**
54179332 AGATAAGGCTGGTG-CTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATAATTT
129 AGATAAGGCTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTT
* *
54179396 GTAGTTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGGTTCGACTT
194 GTAGCTTTAATCTGTTCCACTACAACGCCAAGGAAATAAGGTTCGACTT
54179445 CTTCAATCTACTCCACTGCAACTTCAG-GAAGATAAGAT-TCGCCATAATTTGTAGCTTTAATCT
1 CTTCAATCTACTCCACTGCAACTTCAGAG-AGATAAGATCT-GCCATAATTTGTAGCTTTAATCT
* * * * * *
54179508 ATTCCACTGTAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTTCGCTGTAACTTCAGGG
64 ATTCCACTGTAACGCCAGAGAAATAAGATTCGCTGTATTCAGTCTGCTTCACTGCAACTTCAAGG
*
54179573 AGATAAGGTTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTT
129 AGATAAGGCTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTT
* * *
54179638 GTAGCTTTAATCTGTTCTACTACAACGCTAGGGAAATAAG
194 GTAGCTTTAATCTGTTCCACTACAACGCCAAGGAAATAAG
54179678 ATTAGTTGTC
Statistics
Matches: 208, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
240 3 0.01
241 120 0.58
242 85 0.41
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (242 bp):
CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTAT
TCCACTGTAACGCCAGAGAAATAAGATTCGCTGTATTCAGTCTGCTTCACTGCAACTTCAAGGAG
ATAAGGCTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTTGT
AGCTTTAATCTGTTCCACTACAACGCCAAGGAAATAAGGTTCGACTT
Found at i:54179579 original size:45 final size:44
Alignment explanation
Indices: 54179524--54179625 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
54179514 CTGTAACGCT
* * * * * *
54179524 AGGGAAATAAGATTCGCTGTCTTCAGTCTGCTTCGCTGTAACTTC
1 AGGGAGATAAGATT-GCTGACTTCAATCTGCTCCACTGCAACTTC
* *
54179569 AGGGAGATAAGGTTGGTGACTTCAATCTGCTCCACTGCAACTTC
1 AGGGAGATAAGATTGCTGACTTCAATCTGCTCCACTGCAACTTC
* *
54179613 AAGAAGATAAGAT
1 AGGGAGATAAGAT
54179626 CCACCATAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
44 34 0.74
45 12 0.26
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
AGGGAGATAAGATTGCTGACTTCAATCTGCTCCACTGCAACTTC
Found at i:54179710 original size:143 final size:143
Alignment explanation
Indices: 54179445--54179921 Score: 634
Period size: 143 Copynumber: 3.3 Consensus size: 143
54179435 GGTTCGACTT
* * *
54179445 CTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
** * *
54179510 TCCACTGTAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCT-TCGCTGTAACTTCAGGGA
66 TCCACTACAACGCTAGGGAAATAAGATTAGCTGTCTTCAGTCTGCTCT-GCTGCAACTTCAGGGA
*
54179574 GATAAGGTTGGTGA
130 GATAAGGTTGGTGG
* *
54179588 CTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTTGTAGCTTTAATCTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
* * * *
54179653 TCTACTACAACGCTAGGGAAATAAGATTAGTTGTCTTCAGTCTGCTCTGTTGCAACTTCAAGGAG
66 TCCACTACAACGCTAGGGAAATAAGATTAGCTGTCTTCAGTCTGCTCTGCTGCAACTTCAGGGAG
*
54179718 ATAAGGCTGGTGG
131 ATAAGGTTGGTGG
* * * **** *
54179731 CTTCAATCTGTTCCACTGCGACTTCAGGAAGATAAAATCTTTTATAATTAGTAGCTTTAATCTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
* * ** * **
54179796 TCCATTACAACG-TCAGGGAAATAAGATTTGCAATCTTCAGTCTACTCCACTGCAACTTCAGGGA
66 TCCACTACAACGCT-AGGGAAATAAGATTAGCTGTCTTCAGTCTGCTCTGCTGCAACTTCAGGGA
54179860 GATAAGGTTGGTGG
130 GATAAGGTTGGTGG
* *
54179874 CTTCAATCTGCTCCATTGCAACTTCAGGAAGATAAGATTCGCCATAAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAAT
54179922 GACTTTAATC
Statistics
Matches: 287, Mismatches: 45, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
142 1 0.00
143 285 0.99
144 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (143 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
TCCACTACAACGCTAGGGAAATAAGATTAGCTGTCTTCAGTCTGCTCTGCTGCAACTTCAGGGAG
ATAAGGTTGGTGG
Found at i:54180810 original size:6 final size:6
Alignment explanation
Indices: 54180801--54180872 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
54180791 TTGGCCTCTC
** * * *
54180801 CTTTTT CTTTTT CTTCTTT -TGCTT CTTCTT CTATTT CTTTTT CCTTTT
1 CTTTTT CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
54180849 CTTTTT CTATTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT
54180873 TTTAATTGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
5 2 0.04
6 49 0.91
7 3 0.06
ACGTcount: A:0.03, C:0.21, G:0.01, T:0.75
Consensus pattern (6 bp):
CTTTTT
Found at i:54180850 original size:24 final size:24
Alignment explanation
Indices: 54180823--54180872 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
54180813 CTTCTTTTGC
54180823 TTCTTCTTCTATTTCTTTTTCCTT
1 TTCTTCTTCTATTTCTTTTTCCTT
* *
54180847 TTCTTTTTCTATTTCTTTTTCTTT
1 TTCTTCTTCTATTTCTTTTTCCTT
54180871 TT
1 TT
54180873 TTTAATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCTTCTTCTATTTCTTTTTCCTT
Found at i:54185051 original size:40 final size:40
Alignment explanation
Indices: 54184968--54185153 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
54184958 TTGAATGATG
* * * *
54184968 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
54185008 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54185048 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54185088 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54185129 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54185154 AACGAGTAGC
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 122 0.92
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54185160 original size:80 final size:79
Alignment explanation
Indices: 54185021--54185186 Score: 228
Period size: 80 Copynumber: 2.1 Consensus size: 79
54185011 GGACTAAGAT
* **
54185021 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT
*
54185085 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAATC
*
54185101 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT
* *
54185165 ATATCCGGTTAAATT
65 AAATCCGGTTAAATC
54185180 CCGAAGG
1 CCGAAGG
54185187 TACGTGATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
79 16 0.21
80 59 0.77
81 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAATC
Found at i:54193035 original size:76 final size:79
Alignment explanation
Indices: 54192901--54193080 Score: 210
Period size: 76 Copynumber: 2.3 Consensus size: 79
54192891 TGAATGATGT
* *
54192901 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCTGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-TT
54192965 GTGCGAGTTAC-TAA
65 GTGCGAGTTACATAA
* * * * **
54192979 TC-GG-TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
54193040 GTGCGAGTTACTATAA
65 GTGCGAGTTAC-ATAA
*
54193056 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54193081 AACGAGTAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
75 14 0.16
76 38 0.44
77 13 0.15
78 3 0.03
79 18 0.21
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTG
TGCGAGTTACATAA
Found at i:54193038 original size:40 final size:40
Alignment explanation
Indices: 54192900--54193080 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
54192890 TTGAATGATG
* * * *
54192900 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
54192940 TCCGGACTAAGAT-CTGAAGGCATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
54192979 T-C-GG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54193016 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54193056 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54193081 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
35 1 0.01
36 27 0.22
37 4 0.03
38 2 0.02
39 38 0.31
40 42 0.34
41 8 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54193060 original size:39 final size:39
Alignment explanation
Indices: 54192901--54193078 Score: 179
Period size: 39 Copynumber: 4.6 Consensus size: 39
54192891 TGAATGATGT
* * * * *
54192901 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGC-GAGTTACTATAA
* *
54192941 CCGGACTAAGAT-CTGAAGGCATTTGTGCGAGTTAC--TAA
1 CCGGGCTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTATAA
*
54192979 TC-GG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAA
*
54193016 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAA
*
54193056 CCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
54193079 TGAACGAGTA
Statistics
Matches: 117, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
35 1 0.01
36 26 0.22
37 3 0.03
38 4 0.03
39 38 0.32
40 38 0.32
41 7 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAA
Found at i:54193087 original size:79 final size:75
Alignment explanation
Indices: 54192955--54193113 Score: 187
Period size: 79 Copynumber: 2.1 Consensus size: 75
54192945 ACTAAGATCT
* **
54192955 GAAGGCATTTGTGCGAGTTACTAATCGGTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAATCC
1 GAAGGCATTTGTGCGAGTTACTAACCGGTAAGTCCCGAAGGCATTTGAACGAG-TAGCTAAATCC
*
54193019 GGGTTAAGTCCC
65 -GGTTAAATCCC
* *
54193031 GAAGGCA-TTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATA
1 GAAGGCATTTGTGCGAGTTAC--TAACC-GG-TAAGTCCCGAAGGCATTTGAACGAGTAGCTAAA
*
54193095 TCCGGTTAAATTCC
62 TCCGGTTAAATCCC
54193109 GAAGG
1 GAAGG
54193114 TACGTGATTG
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
75 13 0.18
76 7 0.10
77 4 0.06
78 18 0.25
79 29 0.41
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (75 bp):
GAAGGCATTTGTGCGAGTTACTAACCGGTAAGTCCCGAAGGCATTTGAACGAGTAGCTAAATCCG
GTTAAATCCC
Found at i:54218529 original size:24 final size:24
Alignment explanation
Indices: 54218501--54218548 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
54218491 TTCATATTGA
54218501 ATATTGAATATTTAAATTTTTACT
1 ATATTGAATATTTAAATTTTTACT
54218525 ATATTGAATATTTAAATTTTTACT
1 ATATTGAATATTTAAATTTTTACT
54218549 CAATATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTGAATATTTAAATTTTTACT
Found at i:54218981 original size:18 final size:19
Alignment explanation
Indices: 54218958--54218995 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54218948 CGTGCGTGAC
54218958 TTTCTTT-TCTTC-TTTCTT
1 TTTCTTTCT-TTCTTTTCTT
54218976 TTTCTTTCTTTCTTTTCTT
1 TTTCTTTCTTTCTTTTCTT
54218995 T
1 T
54218996 CTAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTTCTTTCTTTTCTT
Found at i:54218992 original size:13 final size:13
Alignment explanation
Indices: 54218957--54218997 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
54218947 TCGTGCGTGA
54218957 CTTTCTTTTC-TT
1 CTTTCTTTTCTTT
54218969 CTTTCTTTTTCTTT
1 CTTTC-TTTTCTTT
54218983 CTTTCTTTTCTTT
1 CTTTCTTTTCTTT
54218996 CT
1 CT
54218998 AATTTGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.19
13 15 0.56
14 7 0.26
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTCTTTTCTTT
Found at i:54219072 original size:18 final size:18
Alignment explanation
Indices: 54219023--54219072 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
54219013 ATCTTTCTTT
*
54219023 CTTTATTTTTTTATTATA
1 CTTTAATTTTTTATTATA
*
54219041 C-TAAATTTTTTTATTATA
1 CTTTAA-TTTTTTATTATA
*
54219059 CTTTAATTTATTAT
1 CTTTAATTTTTTAT
54219073 AATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 21 0.81
19 3 0.12
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (18 bp):
CTTTAATTTTTTATTATA
Found at i:54223921 original size:9 final size:9
Alignment explanation
Indices: 54223900--54223953 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
54223890 TTTATAACCC
54223900 AAAAAATTAT
1 AAAAAATT-T
*
54223910 AAAAAGTTT
1 AAAAAATTT
54223919 AAAAAATATAT
1 AAAAAAT-T-T
*
54223930 AAAAATTTT
1 AAAAAATTT
*
54223939 AAAAAATAT
1 AAAAAATTT
54223948 AAAAAA
1 AAAAAA
54223954 AACCTAAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
9 21 0.57
10 9 0.24
11 7 0.19
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAAATTT
Found at i:54223928 original size:18 final size:19
Alignment explanation
Indices: 54223900--54223952 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
54223890 TTTATAACCC
*
54223900 AAAAAATTATAAAAAGTTT
1 AAAAAAATATAAAAAGTTT
54223919 AAAAAATATATAAAAA-TTT
1 AAAAAA-ATATAAAAAGTTT
*
54223938 TAAAAAATATAAAAA
1 AAAAAAATATAAAAA
54223953 AAACCTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 9 0.29
19 14 0.45
20 8 0.26
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAAAATATAAAAAGTTT
Found at i:54223954 original size:20 final size:20
Alignment explanation
Indices: 54223900--54223953 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
54223890 TTTATAACCC
54223900 AAAAAAT-TATAAAAAGTTT
1 AAAAAATATATAAAAAGTTT
*
54223919 AAAAAATATATAAAAATTTT
1 AAAAAATATATAAAAAGTTT
54223939 AAAAAATATA-AAAAA
1 AAAAAATATATAAAAA
54223954 AACCTAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAATATATAAAAAGTTT
Found at i:54223961 original size:20 final size:20
Alignment explanation
Indices: 54223918--54223961 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
54223908 ATAAAAAGTT
* ***
54223918 TAAAAAATATATAAAAATTT
1 TAAAAAATATAAAAAAAACC
54223938 TAAAAAATATAAAAAAAACC
1 TAAAAAATATAAAAAAAACC
54223958 TAAA
1 TAAA
54223962 CTCTAAACTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAAAAATATAAAAAAAACC
Found at i:54224186 original size:12 final size:12
Alignment explanation
Indices: 54224169--54224193 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54224159 ATTTAATTAT
54224169 TTTCTAAGTCAA
1 TTTCTAAGTCAA
54224181 TTTCTAAGTCAA
1 TTTCTAAGTCAA
54224193 T
1 T
54224194 CTCCCTTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTCTAAGTCAA
Found at i:54227442 original size:10 final size:10
Alignment explanation
Indices: 54227423--54227454 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
54227413 GCTGTCATAC
*
54227423 TGCTGATTAA
1 TGCTGTTTAA
54227433 TGCTGTTTAA
1 TGCTGTTTAA
54227443 TGCTGTTTAA
1 TGCTGTTTAA
54227453 TG
1 TG
54227455 ATTTTGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (10 bp):
TGCTGTTTAA
Found at i:54238250 original size:26 final size:25
Alignment explanation
Indices: 54238218--54238266 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
54238208 AAATGTTCTA
*
54238218 AAAATAAAATAATTTATAAAATTAAG
1 AAAATAAAA-AAGTTATAAAATTAAG
*
54238244 AAAATAAAAAAGTTCTAAAATTA
1 AAAATAAAAAAGTTATAAAATTA
54238267 TTGGGGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAATAAAAAAGTTATAAAATTAAG
Found at i:54238375 original size:19 final size:18
Alignment explanation
Indices: 54238353--54238394 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54238343 ATTTTTTCAA
54238353 AATTTTGGAAATATTTATT
1 AATTTTGG-AATATTTATT
* *
54238372 AATTTTTGAATGTTTATT
1 AATTTTGGAATATTTATT
54238390 -ATTTT
1 AATTTT
54238395 TTATATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (18 bp):
AATTTTGGAATATTTATT
Found at i:54240181 original size:22 final size:21
Alignment explanation
Indices: 54240145--54240193 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
54240135 TATAAAAATA
*
54240145 TTTA-AAAATTAAAAAATATTTT
1 TTTATAAAATT-AAAAAT-TGTT
54240167 TTTATAAAATT-AAAATTGTT
1 TTTATAAAATTAAAAATTGTT
54240187 TTTATAA
1 TTTATAA
54240194 TGTTTCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 10 0.40
21 5 0.20
22 4 0.16
23 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTATAAAATTAAAAATTGTT
Found at i:54256381 original size:13 final size:13
Alignment explanation
Indices: 54256363--54256396 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
54256353 TAGCATCGTC
54256363 AATATTTAATAAA
1 AATATTTAATAAA
54256376 AATATTTAATAAA
1 AATATTTAATAAA
54256389 AATATTTA
1 AATATTTA
54256397 CGGGCCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTTAATAAA
Found at i:54270603 original size:17 final size:18
Alignment explanation
Indices: 54270581--54270624 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
54270571 GACAAGAAAT
54270581 AATATATAAAT-TTTAAA
1 AATATATAAATATTTAAA
54270598 AATATATAAATAATTTAAA
1 AATATATAAAT-ATTTAAA
54270617 AA-ATATAA
1 AATATATAA
54270625 TAATAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 6 0.24
19 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATATAAATATTTAAA
Found at i:54270619 original size:21 final size:20
Alignment explanation
Indices: 54270581--54270636 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
54270571 GACAAGAAAT
54270581 AATATATAAAT--TTT-AAA
1 AATATATAAATAATTTAAAA
54270598 AATATATAAATAATTTAAAA
1 AATATATAAATAATTTAAAA
54270618 AATATA-ATAATAAATTTAA
1 AATATATA-AAT-AATTTAA
54270637 CTTTTATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 11 0.32
19 4 0.12
20 12 0.35
21 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATATAAATAATTTAAAA
Found at i:54291561 original size:7 final size:7
Alignment explanation
Indices: 54291550--54291602 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
54291540 TATATATTTT
*
54291550 TTTTTAT
1 TTTTTAA
*
54291557 TTTTTAT
1 TTTTTAA
54291564 TTTTTAA
1 TTTTTAA
54291571 TTTTTAA
1 TTTTTAA
54291578 TTTTTAA
1 TTTTTAA
54291585 TTTTTAA
1 TTTTTAA
54291592 TTTTTAA
1 TTTTTAA
54291599 TTTT
1 TTTT
54291603 AAAATACTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:54291660 original size:27 final size:26
Alignment explanation
Indices: 54291610--54291662 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
54291600 TTTAAAATAC
*
54291610 TTTAAAATTTTTTTTATTTTTTTATT
1 TTTAAAATTTTTTTTATTTGTTTATT
54291636 TTTAAAATATTTTTTT-TTGTGTTTATT
1 TTTAAAAT-TTTTTTTATT-TGTTTATT
54291663 AAAAATCGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (26 bp):
TTTAAAATTTTTTTTATTTGTTTATT
Found at i:54300862 original size:15 final size:15
Alignment explanation
Indices: 54300842--54300874 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54300832 GAGAGACGAC
54300842 AAAGGAGAAAAAAAG
1 AAAGGAGAAAAAAAG
*
54300857 AAAGGAGAGAAAAAG
1 AAAGGAGAAAAAAAG
54300872 AAA
1 AAA
54300875 AAAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGGAGAAAAAAAG
Found at i:54303313 original size:20 final size:21
Alignment explanation
Indices: 54303288--54303326 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54303278 ATCTTACATG
*
54303288 AAATTAAA-AATATAACTCTT
1 AAATTAAAGAAAATAACTCTT
54303308 AAATTAAAGAAAATAACTC
1 AAATTAAAGAAAATAACTC
54303327 AATAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATTAAAGAAAATAACTCTT
Found at i:54305179 original size:24 final size:24
Alignment explanation
Indices: 54305151--54305202 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54305141 TTAGTAAGTC
* *
54305151 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54305175 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54305199 AAAT
1 AAAT
54305203 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54305790 original size:9 final size:9
Alignment explanation
Indices: 54305776--54305836 Score: 86
Period size: 9 Copynumber: 6.6 Consensus size: 9
54305766 TTTGGTTAAA
54305776 AATTACCCG
1 AATTACCCG
54305785 AATTACCCG
1 AATTACCCG
*
54305794 AATCACCCG
1 AATTACCCG
*
54305803 AAAATTACCCA
1 --AATTACCCG
54305814 AATTACCCG
1 AATTACCCG
54305823 AATTACCCG
1 AATTACCCG
54305832 AATTA
1 AATTA
54305837 AATCACTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
9 39 0.85
11 7 0.15
ACGTcount: A:0.39, C:0.31, G:0.08, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:54305817 original size:29 final size:29
Alignment explanation
Indices: 54305774--54305833 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54305764 TTTTTGGTTA
*
54305774 AAAATTACCCGAATTACCCGAATCACCCG
1 AAAATTACCCAAATTACCCGAATCACCCG
*
54305803 AAAATTACCCAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATCACCCG
54305832 AA
1 AA
54305834 TTAAATCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.32, G:0.08, T:0.18
Consensus pattern (29 bp):
AAAATTACCCAAATTACCCGAATCACCCG
Found at i:54310139 original size:15 final size:16
Alignment explanation
Indices: 54310119--54310157 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
54310109 GGTGTTGTGA
54310119 AAATTGGGCT-GGATT
1 AAATTGGGCTGGGATT
*
54310134 AAATTGGGCTGGGTTT
1 AAATTGGGCTGGGATT
54310150 AAATTGGG
1 AAATTGGG
54310158 AGGGAATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.33
Consensus pattern (16 bp):
AAATTGGGCTGGGATT
Found at i:54311927 original size:24 final size:24
Alignment explanation
Indices: 54311899--54311950 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54311889 TTAGTAAGTC
* *
54311899 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54311923 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54311947 AAAT
1 AAAT
54311951 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54321097 original size:11 final size:11
Alignment explanation
Indices: 54321060--54321101 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
54321050 TAAGAAATAA
54321060 AAATCAGAATC
1 AAATCAGAATC
**
54321071 AAATCCCAA-C
1 AAATCAGAATC
54321081 -AATCAGAATC
1 AAATCAGAATC
54321091 AAATCAGAATC
1 AAATCAGAATC
54321102 TGAATCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 6 0.24
10 2 0.08
11 17 0.68
ACGTcount: A:0.52, C:0.24, G:0.07, T:0.17
Consensus pattern (11 bp):
AAATCAGAATC
Found at i:54321388 original size:151 final size:151
Alignment explanation
Indices: 54321114--54321416 Score: 597
Period size: 151 Copynumber: 2.0 Consensus size: 151
54321104 AATCAAAACC
*
54321114 TAACAAATGCTATGGTCTACTGTTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
1 TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
54321179 CATACAATGTTTAACTTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
66 CATACAATGTTTAACTTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
54321244 TCTATGACGGTTTGGTCCTCT
131 TCTATGACGGTTTGGTCCTCT
54321265 TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
1 TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
54321330 CATACAATGTTTAACTTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
66 CATACAATGTTTAACTTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
54321395 TCTATGACGGTTTGGTCCTCT
131 TCTATGACGGTTTGGTCCTCT
54321416 T
1 T
54321417 GCAGAAACGT
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (151 bp):
TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
CATACAATGTTTAACTTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
TCTATGACGGTTTGGTCCTCT
Found at i:54325339 original size:18 final size:18
Alignment explanation
Indices: 54325311--54325355 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
54325301 CGTTCGTTTC
*
54325311 CAAAACATTATTC-ATTT
1 CAAAACGTTATTCAATTT
*
54325328 ACAAATCGTTATTCAATTT
1 -CAAAACGTTATTCAATTT
54325347 CAAAACGTT
1 CAAAACGTT
54325356 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCAATTT
Found at i:54339811 original size:80 final size:79
Alignment explanation
Indices: 54339674--54339898 Score: 229
Period size: 80 Copynumber: 2.8 Consensus size: 79
54339664 TTGAATGCTG
* * * * * * * * * *
54339674 TCCGGGCTAAGTCCCGAAGTCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTG-TGAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
54339738 TGTGCGAGATATTAAA
64 TGTGCGAGATATTAAA
** * *
54339754 TCCGGGTTAAGTCCCGAAGGCATTCGTGCT-AGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT-GTG-TGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* * *
54339818 CGTGCGAGTTGTTAAA
64 TGTGCGAGATATTAAA
* *
54339834 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
54339899 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 1 0.01
79 34 0.28
80 82 0.67
81 5 0.04
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATTAAA
Found at i:54339878 original size:39 final size:40
Alignment explanation
Indices: 54339727--54339896 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
54339717 GGACTAAGAT
* * *
54339727 CCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
54339767 CCGAAGGCATTCGTGCTAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
54339807 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
54339847 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
54339886 CCGAAGGCATT
1 CCGAAGGCATT
54339897 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 34 0.29
40 84 0.71
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:54341699 original size:12 final size:12
Alignment explanation
Indices: 54341682--54341713 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
54341672 ATCTTGGTAA
54341682 GGCCAATGTGGT
1 GGCCAATGTGGT
54341694 GGCCAATGTGGT
1 GGCCAATGTGGT
*
54341706 AGCCAATG
1 GGCCAATG
54341714 CTCTTAGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.22
Consensus pattern (12 bp):
GGCCAATGTGGT
Found at i:54351042 original size:12 final size:12
Alignment explanation
Indices: 54351005--54351034 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54350995 TACATTGTTT
*
54351005 TTCTTTCTTTTC
1 TTCTTTCTTTCC
54351017 TTCTTTCTTTCC
1 TTCTTTCTTTCC
54351029 TTCTTT
1 TTCTTT
54351035 TTTGCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTTCTTTCC
Done.