Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 68 of 126
Found at i:19793556 original size:10 final size:10
Alignment explanation
Indices: 19793541--19793634 Score: 64
Period size: 10 Copynumber: 8.5 Consensus size: 10
19793531 TGAAATATTC
19793541 ATGTGATTAA
1 ATGTGATTAA
*
19793551 ATGTGACTAA
1 ATGTGATTAA
19793561 ATGTGATTAA
1 ATGTGATTAA
19793571 TATGTGATGTGATCA
1 -ATGTGAT-T-A--A
*
19793586 ATGTTGAAATAA
1 ATG-TG-ATTAA
*
19793598 TCATGTGACT-A
1 --ATGTGATTAA
19793609 ATGTGATTAA
1 ATGTGATTAA
19793619 ATGTGATTAA
1 ATGTGATTAA
19793629 TATGTG
1 -ATGTG
19793635 TTGTGTTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 21
0.72 0.05 0.22
Matches are distributed among these distances:
9 7 0.10
10 29 0.43
11 13 0.19
12 4 0.06
13 3 0.04
14 7 0.10
15 4 0.06
16 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:19793621 original size:58 final size:58
Alignment explanation
Indices: 19793518--19793679 Score: 195
Period size: 58 Copynumber: 2.8 Consensus size: 58
19793508 TTAAATATTA
* * *
19793518 ATGTGATAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTG
1 ATGTGATAAATGTTGAAATAATCATGTGATT-AATGTGATTAAATGTGATTAATATGTG
* *
19793577 ATGTGATCAATGTTGAAATAATCATGTGACTAATGTGATTAAATGTGATTAATATGTG
1 ATGTGATAAATGTTGAAATAATCATGTGATTAATGTGATTAAATGTGATTAATATGTG
* * * * *
19793635 TTGTG-TTAATGCTT-AAGTACTCATGTGATTAATGCGATT-AATGTG
1 ATGTGATAAATG-TTGAAATAATCATGTGATTAATGTGATTAAATGTG
19793680 TAAAAGAATG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
56 6 0.07
57 26 0.29
58 32 0.35
59 27 0.30
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (58 bp):
ATGTGATAAATGTTGAAATAATCATGTGATTAATGTGATTAAATGTGATTAATATGTG
Found at i:19798253 original size:17 final size:17
Alignment explanation
Indices: 19798228--19798270 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
19798218 ATGCATCCGA
19798228 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* *
19798245 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
*
19798262 TTTACTTGT
1 TTTAATTGT
19798271 TAGTTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:19799414 original size:27 final size:25
Alignment explanation
Indices: 19799384--19799433 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
19799374 AGTGCTGGAA
19799384 AACATGCAAAGATGCAGCCACAAATTT
1 AACATG-AAA-ATGCAGCCACAAATTT
* *
19799411 AACATGGAATTGCAGCCACAAAT
1 AACATGAAAATGCAGCCACAAAT
19799434 GTCACCGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 2 0.10
27 6 0.29
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (25 bp):
AACATGAAAATGCAGCCACAAATTT
Found at i:19807157 original size:26 final size:26
Alignment explanation
Indices: 19807102--19807157 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
19807092 ACACAGCTCC
* *
19807102 TGTGTGTCGCGACATCGACTCCTGGT
1 TGTGTGTCGCGACATCGACTCCTAGA
*
19807128 TGTGTGTCGCGACATCGATTCCTAGA
1 TGTGTGTCGCGACATCGACTCCTAGA
19807154 TGTG
1 TGTG
19807158 AATTTGATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.32
Consensus pattern (26 bp):
TGTGTGTCGCGACATCGACTCCTAGA
Found at i:19812913 original size:24 final size:23
Alignment explanation
Indices: 19812886--19812932 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
19812876 AAGAGTTAAT
19812886 TTGTCA-ACGAAAATATAAAATAAA
1 TTGTCAGA-GAAAAT-TAAAATAAA
*
19812910 TTGTCAGAGAAAATTAAGATAAA
1 TTGTCAGAGAAAATTAAAATAAA
19812933 AATGAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (23 bp):
TTGTCAGAGAAAATTAAAATAAA
Found at i:19813959 original size:19 final size:19
Alignment explanation
Indices: 19813935--19813974 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19813925 GCCGCAATTC
19813935 CAGGTTAACTTTGTAGCTG
1 CAGGTTAACTTTGTAGCTG
*
19813954 CAGGTTAACTTTGTGGCTG
1 CAGGTTAACTTTGTAGCTG
19813973 CA
1 CA
19813975 TCTTTGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (19 bp):
CAGGTTAACTTTGTAGCTG
Found at i:19814508 original size:10 final size:10
Alignment explanation
Indices: 19814493--19814547 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
19814483 ATAATATATA
19814493 TTCTTTCTTT
1 TTCTTTCTTT
19814503 TTCTTTCTTTT
1 TTCTTTC-TTT
*
19814514 TGTCAATT-TTT
1 T-TC-TTTCTTT
19814525 TTCTTTCTTT
1 TTCTTTCTTT
19814535 TTC--TCTTT
1 TTCTTTCTTT
19814543 TTCTT
1 TTCTT
19814548 ATGTGACTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
8 8 0.22
9 2 0.05
10 15 0.41
11 8 0.22
12 2 0.05
13 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:19824636 original size:16 final size:16
Alignment explanation
Indices: 19824598--19824640 Score: 79
Period size: 15 Copynumber: 2.8 Consensus size: 16
19824588 ATTAGAAATG
19824598 TCACCACAATCTTTAT
1 TCACCACAATCTTTAT
19824614 TCA-CACAATCTTTAT
1 TCACCACAATCTTTAT
19824629 TCACCACAATCT
1 TCACCACAATCT
19824641 CTAAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (16 bp):
TCACCACAATCTTTAT
Found at i:19838532 original size:21 final size:21
Alignment explanation
Indices: 19838506--19838562 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
19838496 TATATTTTTA
19838506 GCATTTTTTAACTTAGTTATT
1 GCATTTTTTAACTTAGTTATT
19838527 GCATTTTTTAACTTAGTTATT
1 GCATTTTTTAACTTAGTTATT
*
19838548 GCATTTTCTAACTTA
1 GCATTTTTTAACTTA
19838563 ATGGAACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (21 bp):
GCATTTTTTAACTTAGTTATT
Found at i:19838721 original size:26 final size:26
Alignment explanation
Indices: 19838670--19838727 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
19838660 GAACTTGTTC
* * *
19838670 AGAATTATCGTTGCGTGACTATGTCT
1 AGAATTATCGCTGCATGACTAGGTCT
*
19838696 AGAATTATCGCTGCATGAGTAGGTCT
1 AGAATTATCGCTGCATGACTAGGTCT
19838722 AGAATT
1 AGAATT
19838728 GCGCCCAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (26 bp):
AGAATTATCGCTGCATGACTAGGTCT
Found at i:19847461 original size:17 final size:17
Alignment explanation
Indices: 19847417--19847478 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
19847407 ATTCTCACTA
*
19847417 TCATTGTATTTTAATTG
1 TCATTGTATTTTCATTG
* * *
19847434 TCACTGCATTTGCATTG
1 TCATTGTATTTTCATTG
19847451 TCATTGTATTTTCAATTG
1 TCATTGTATTTTC-ATTG
*
19847469 TCAGTGTATT
1 TCATTGTATT
19847479 GGGGACAATG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 23 0.64
18 13 0.36
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.52
Consensus pattern (17 bp):
TCATTGTATTTTCATTG
Found at i:19853139 original size:38 final size:38
Alignment explanation
Indices: 19853088--19853178 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
19853078 ACCACTCCGA
**
19853088 CCACCCTGCACACCACAATTGGGCTATGGTAGACTTAT
1 CCACCCTGCACACCACAAAAGGGCTATGGTAGACTTAT
* * *
19853126 CCACCCTGCACACCACAAAAGGGCTTTGGTGGGCTTAT
1 CCACCCTGCACACCACAAAAGGGCTATGGTAGACTTAT
*
19853164 CCACCCTACACACCA
1 CCACCCTGCACACCA
19853179 TGATAATGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (38 bp):
CCACCCTGCACACCACAAAAGGGCTATGGTAGACTTAT
Found at i:19854272 original size:14 final size:14
Alignment explanation
Indices: 19854253--19854286 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
19854243 CTTCCTAAAG
19854253 AAATTTTGTCCCCA
1 AAATTTTGTCCCCA
*
19854267 AAATTTTGTCCTCA
1 AAATTTTGTCCCCA
19854281 AAATTT
1 AAATTT
19854287 CCTACTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (14 bp):
AAATTTTGTCCCCA
Found at i:19856295 original size:19 final size:19
Alignment explanation
Indices: 19856255--19856294 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
19856245 ACATAATGTC
*
19856255 AATCAATTCAGATATGCAA
1 AATCAATTCAGACATGCAA
*
19856274 AATCAATATCAGACATTCAA
1 AATCAAT-TCAGACATGCAA
19856294 A
1 A
19856295 TATTTCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.25
Consensus pattern (19 bp):
AATCAATTCAGACATGCAA
Found at i:19858232 original size:19 final size:19
Alignment explanation
Indices: 19858208--19858263 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
19858198 ATATTACATG
*
19858208 CACACATGATTCCACTAAC
1 CACACACGATTCCACTAAC
* *
19858227 CACACACGGTTCCACTAAT
1 CACACACGATTCCACTAAC
* * *
19858246 TAGACACAATTCCACTAA
1 CACACACGATTCCACTAA
19858264 TCAAATACCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.21
Consensus pattern (19 bp):
CACACACGATTCCACTAAC
Found at i:19862949 original size:16 final size:16
Alignment explanation
Indices: 19862930--19862960 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19862920 TTGAAAAAAT
19862930 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
19862946 TTTCAAATTTATATG
1 TTTCAAATATATATG
19862961 CACTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:19863632 original size:15 final size:15
Alignment explanation
Indices: 19863614--19863643 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19863604 ATTTTTATTT
19863614 TTAAAATTTAATTAC
1 TTAAAATTTAATTAC
*
19863629 TTAAAATTTGATTAC
1 TTAAAATTTAATTAC
19863644 AAATGTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAAATTTAATTAC
Found at i:19867185 original size:16 final size:15
Alignment explanation
Indices: 19867150--19867201 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
19867140 TCAAAGAAAC
19867150 ATAAAAAAAATTAT-
1 ATAAAAAAAATTATA
19867164 AT--AAAAAATTATAA
1 ATAAAAAAAATTAT-A
*
19867178 ATAAAAAAAATAATA
1 ATAAAAAAAATTATA
19867193 TATAAAAAA
1 -ATAAAAAA
19867202 CAAACCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 10 0.31
14 4 0.12
15 1 0.03
16 17 0.53
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAAAAAAAATTATA
Found at i:19867733 original size:156 final size:157
Alignment explanation
Indices: 19867483--19867795 Score: 619
Period size: 156 Copynumber: 2.0 Consensus size: 157
19867473 AAATTATCAA
19867483 AAATTTTATATTATGATTTTGAAATTAAAAATATAAAAAAATTTAGAAAAACACAACCAAAATGA
1 AAATTTTATATTATGATTTTGAAATTAAAAATATAAAAAAATTTAGAAAAACACAACCAAAATGA
19867548 ATTTGGATAAAATGACCACAAAGATCATTTAAATCTGGATATCCATTTGTCCATTTCATTTTTTC
66 ATTTGGATAAAATGACCACAAAGATCATTTAAATCTGGATATCCATTTGTCCATTTCATTTTTTC
19867613 ATAAATTTATATATTTTTAACTAATGC
131 ATAAATTTATATATTTTTAACTAATGC
19867640 AAATTTTATATTATGATTTTGAAATTAAAAATATAAAAAAATTTA-AAAAACACAACCAAAATGA
1 AAATTTTATATTATGATTTTGAAATTAAAAATATAAAAAAATTTAGAAAAACACAACCAAAATGA
19867704 ATTTGGATAAAATGACCACAAAGATCATTTAAATCTGGATATCCATTTGTCCATTTCATTTTTTC
66 ATTTGGATAAAATGACCACAAAGATCATTTAAATCTGGATATCCATTTGTCCATTTCATTTTTTC
19867769 ATAAATTTATATATTTTTAACTAATGC
131 ATAAATTTATATATTTTTAACTAATGC
19867796 TTGTCAAGTA
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 111 0.71
157 45 0.29
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (157 bp):
AAATTTTATATTATGATTTTGAAATTAAAAATATAAAAAAATTTAGAAAAACACAACCAAAATGA
ATTTGGATAAAATGACCACAAAGATCATTTAAATCTGGATATCCATTTGTCCATTTCATTTTTTC
ATAAATTTATATATTTTTAACTAATGC
Found at i:19873319 original size:16 final size:16
Alignment explanation
Indices: 19873298--19873333 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19873288 TGTTTTAGTT
19873298 ATTTTGAGCTTGAATA
1 ATTTTGAGCTTGAATA
* *
19873314 ATTTTGTGCTTGTATA
1 ATTTTGAGCTTGAATA
19873330 ATTT
1 ATTT
19873334 CCGGTTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.53
Consensus pattern (16 bp):
ATTTTGAGCTTGAATA
Found at i:19884900 original size:3 final size:3
Alignment explanation
Indices: 19884892--19884925 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
19884882 AATGAATCAT
*
19884892 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
19884926 GTTTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:19885958 original size:30 final size:30
Alignment explanation
Indices: 19885922--19886218 Score: 149
Period size: 30 Copynumber: 10.1 Consensus size: 30
19885912 AGAAATTTTA
*
19885922 TTTTGACCCCAAACTTCTCCAAAATTATAT
1 TTTTGACCCCAAACTTCTCCAAAATTACAT
** * *
19885952 TTTTGACTCTAAAACTTCT-AAAAATTATAT
1 TTTTGAC-CCCAAACTTCTCCAAAATTACAT
*
19885982 TTTT-ACCCCCGAAC-T-TCCAAAATTACAT
1 TTTTGA-CCCCAAACTTCTCCAAAATTACAT
**
19886010 TTTTGACCCCAAAACTT-TTGAAAATTACAT
1 TTTTGACCCC-AAACTTCTCCAAAATTACAT
* *
19886040 TTTTG-CTCCTAAACTTC-CAAAAATTACAT
1 TTTTGAC-CCCAAACTTCTCCAAAATTACAT
* ** *
19886069 TTTTAAACCTGAAACTT-TCGAAAA-TACAT
1 TTTT-GACCCCAAACTTCTCCAAAATTACAT
* * *
19886098 TTTTTACCCCTCAAACTTC-CAAAAACTACA-
1 TTTTGA-CCC-CAAACTTCTCCAAAATTACAT
** * *
19886128 TTTTGACCTTAAAATT-TCCAAAAATTATAT
1 TTTTGACCCCAAACTTCTCC-AAAATTACAT
* * * *
19886158 TTTT-CCCCCGAACTTCT-AAAAATTCCA-
1 TTTTGACCCCAAACTTCTCCAAAATTACAT
* *
19886185 TTTTAACCCCAAAACTTC-CAAAAATTACCAT
1 TTTTGACCCC-AAACTTCTCCAAAATTA-CAT
19886216 TTT
1 TTT
19886219 ACCCCCGAAT
Statistics
Matches: 203, Mismatches: 40, Indels: 47
0.70 0.14 0.16
Matches are distributed among these distances:
27 5 0.02
28 36 0.18
29 69 0.34
30 76 0.37
31 17 0.08
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTTGACCCCAAACTTCTCCAAAATTACAT
Found at i:19886024 original size:58 final size:58
Alignment explanation
Indices: 19885939--19886236 Score: 250
Period size: 58 Copynumber: 5.1 Consensus size: 58
19885929 CCCAAACTTC
* * *
19885939 TCCAAAATTATATTTTTGACTCTAAAACTTCTAAAAATTATATTTTTACCCCCGAACT
1 TCCAAAATTACATTTTTGACCCTAAAACTTCTAAAAATTACATTTTTACCCCCGAACT
* * * * * **
19885997 TCCAAAATTACATTTTTGACCCCAAAACTTTTGAAAATTACATTTTTGCTCCTAAACT
1 TCCAAAATTACATTTTTGACCCTAAAACTTCTAAAAATTACATTTTTACCCCCGAACT
* * * * *
19886055 TCCAAAAATTACATTTTTAAACCTGAAACTT-TCGAAAA-TACATTTTTTACCCCTCAAACT
1 TCC-AAAATTACATTTTTGACCCTAAAACTTCT-AAAAATTACA-TTTTTACCCC-CGAACT
* * * * *
19886115 TCCAAAAACTACA-TTTTGACCTTAAAATTTCCAAAAATTATATTTTT-CCCCCGAACT
1 TCC-AAAATTACATTTTTGACCCTAAAACTTCTAAAAATTACATTTTTACCCCCGAACT
* * * * *
19886172 TCTAAAAATTCCA-TTTTAACCCCAAAACTTCCAAAAATTACCA-TTTTACCCCCGAA-T
1 TC-CAAAATTACATTTTTGACCCTAAAACTTCTAAAAATTA-CATTTTTACCCCCGAACT
19886229 GTCCAAAA
1 -TCCAAAA
19886237 ATTTTGTTTT
Statistics
Matches: 194, Mismatches: 36, Indels: 21
0.77 0.14 0.08
Matches are distributed among these distances:
57 46 0.24
58 71 0.37
59 57 0.29
60 20 0.10
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (58 bp):
TCCAAAATTACATTTTTGACCCTAAAACTTCTAAAAATTACATTTTTACCCCCGAACT
Found at i:19886092 original size:59 final size:60
Alignment explanation
Indices: 19885981--19886131 Score: 184
Period size: 59 Copynumber: 2.6 Consensus size: 60
19885971 AAAAATTATA
* * * *
19885981 TTTTTACCCC-CGAACTTCC-AAAATTACATTTTTGACCCCAAAACTTTTGAAAATTACA-
1 TTTTTACCCCTCAAACTTCCAAAAATTACATTTTTAAACCCAAAACTTTCGAAAA-TACAT
* * **
19886039 TTTTTGCTCCT-AAACTTCCAAAAATTACATTTTTAAACCTGAAACTTTCGAAAATACAT
1 TTTTTACCCCTCAAACTTCCAAAAATTACATTTTTAAACCCAAAACTTTCGAAAATACAT
*
19886098 TTTTTACCCCTCAAACTTCCAAAAACTACATTTT
1 TTTTTACCCCTCAAACTTCCAAAAATTACATTTT
19886132 GACCTTAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 19 0.24
59 38 0.49
60 21 0.27
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
TTTTTACCCCTCAAACTTCCAAAAATTACATTTTTAAACCCAAAACTTTCGAAAATACAT
Found at i:19886219 original size:30 final size:29
Alignment explanation
Indices: 19885921--19886224 Score: 175
Period size: 29 Copynumber: 10.4 Consensus size: 29
19885911 CAGAAATTTT
* * *
19885921 ATTTTGACCCC-AAACTTCTCCAAAATTAT
1 ATTTTAACCCCAAAACTTC-CAAAAATTAC
* * * * *
19885950 ATTTTTGACTCTAAAACTTCTAAAAATTAT
1 A-TTTTAACCCCAAAACTTCCAAAAATTAC
* **
19885980 ATTTTTACCCCCGAACTTCC-AAAATTAC
1 ATTTTAACCCCAAAACTTCCAAAAATTAC
* ***
19886008 ATTTTTGACCCCAAAACTTTTGAAAATTAC
1 A-TTTTAACCCCAAAACTTCCAAAAATTAC
** * *
19886038 ATTTTTGCTCCTAAACTTCCAAAAATTAC
1 ATTTTAACCCCAAAACTTCCAAAAATTAC
* ** * *
19886067 ATTTTTAAACCTGAAACTTTCGAAAA-TAC
1 A-TTTTAACCCCAAAACTTCCAAAAATTAC
* * *
19886096 ATTTTTTACCCCTCAAACTTCCAAAAACTAC
1 A-TTTTAACCCC-AAAACTTCCAAAAATTAC
* ** * *
19886127 ATTTTGACCTTAAAATTTCCAAAAATTAT
1 ATTTTAACCCCAAAACTTCCAAAAATTAC
* ** * *
19886156 ATTTT-TCCCCCGAACTTCTAAAAATTCC
1 ATTTTAACCCCAAAACTTCCAAAAATTAC
19886184 ATTTTAACCCCAAAACTTCCAAAAATTACC
1 ATTTTAACCCCAAAACTTCCAAAAATTA-C
*
19886214 ATTTTACCCCC
1 ATTTTAACCCC
19886225 GAATGTCCAA
Statistics
Matches: 207, Mismatches: 59, Indels: 17
0.73 0.21 0.06
Matches are distributed among these distances:
28 27 0.13
29 98 0.47
30 71 0.34
31 11 0.05
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTTAACCCCAAAACTTCCAAAAATTAC
Found at i:19886389 original size:29 final size:28
Alignment explanation
Indices: 19886320--19886392 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
19886310 CCAAATTTTC
* *
19886320 CCAAAATTACCATTTTGCCCCCGAGAGT
1 CCAAAAGTATCATTTTGCCCCCGAGAGT
* *
19886348 CCAAAATTATCATTTTGCCCCCGGGTA-T
1 CCAAAAGTATCATTTTGCCCCCGAG-AGT
*
19886376 CCAAAAAGTCTCATTTT
1 CC-AAAAGTATCATTTT
19886393 CAACCCCGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 26 0.67
29 13 0.33
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (28 bp):
CCAAAAGTATCATTTTGCCCCCGAGAGT
Found at i:19886692 original size:20 final size:20
Alignment explanation
Indices: 19886667--19886707 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
19886657 AATTTTTCTT
19886667 CAAATCGAAATAATTGAATA
1 CAAATCGAAATAATTGAATA
19886687 CAAATCGAAATAATTGAATA
1 CAAATCGAAATAATTGAATA
19886707 C
1 C
19886708 CCTTAATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (20 bp):
CAAATCGAAATAATTGAATA
Found at i:19891827 original size:24 final size:24
Alignment explanation
Indices: 19891797--19891907 Score: 156
Period size: 24 Copynumber: 4.6 Consensus size: 24
19891787 TGAATAAAAG
19891797 AAAAGAAAAAGAAAAAAGAAGAAA
1 AAAAGAAAAAGAAAAAAGAAGAAA
*
19891821 AAAAGAAAAA-AAGAAA-AAGAAA
1 AAAAGAAAAAGAAAAAAGAAGAAA
*
19891843 AAAAGAAAGAA-AAAGAAGAAGAAA
1 AAAAGAAA-AAGAAAAAAGAAGAAA
19891867 AAAAGAGAAAAGAAAAAAGAGAGAAA
1 AAAAGA-AAAAGAAAAAAGA-AGAAA
19891893 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
19891908 GGAGAGGTCG
Statistics
Matches: 78, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
22 14 0.18
23 11 0.14
24 24 0.31
25 18 0.23
26 11 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
AAAAGAAAAAGAAAAAAGAAGAAA
Found at i:19891831 original size:26 final size:26
Alignment explanation
Indices: 19891802--19891902 Score: 109
Period size: 27 Copynumber: 3.8 Consensus size: 26
19891792 AAAAGAAAAG
19891802 AAAAAGAAAAAAGAAGAAAAAAAGAA
1 AAAAAGAAAAAAGAAGAAAAAAAGAA
*
19891828 AAAAAG-AAAAAGAAAAAAAGAAAGAA
1 AAAAAGAAAAAAGAAGAAAA-AAAGAA
* *
19891854 AAAGAAGAAGAAAAAAAG-AGAAAAGAA
1 AAA-AAGAA-AAAAGAAGAAAAAAAGAA
19891881 AAAAGAGAGAAAAA-AAGAAAAA
1 AAAA-AGA-AAAAAGAAGAAAAA
19891903 GAAAAGGAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
25 12 0.19
26 19 0.30
27 22 0.35
28 4 0.06
29 6 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAAGAAGAAAAAAAGAA
Found at i:19891859 original size:40 final size:40
Alignment explanation
Indices: 19891795--19891907 Score: 139
Period size: 38 Copynumber: 2.9 Consensus size: 40
19891785 AATGAATAAA
19891795 AGAAAAG-AAAAAGAAA-AAAGAAGAAAAAAAGAAAAAAAG
1 AGAAAAGAAAAAAGAAAGAAA-AAGAAAAAAAGAAAAAAAG
*
19891834 A-AAAAGAAAAAAAGAAAGAAAAAG--AAGAAGAAAAAAAG
1 AGAAAAG-AAAAAAGAAAGAAAAAGAAAAAAAGAAAAAAAG
*
19891872 AGAAAAGAAAAAAGAGAGAAAAA-AAGAAAAAGAAAA
1 AGAAAAGAAAAAAGAAAGAAAAAGAA-AAAAAGAAAA
19891908 GGAGAGGTCG
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
38 34 0.53
39 6 0.09
40 21 0.33
41 3 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (40 bp):
AGAAAAGAAAAAAGAAAGAAAAAGAAAAAAAGAAAAAAAG
Found at i:19891864 original size:46 final size:42
Alignment explanation
Indices: 19891792--19891905 Score: 131
Period size: 46 Copynumber: 2.6 Consensus size: 42
19891782 TTCAATGAAT
*
19891792 AAAAGAAAAGAAAAAGAAAAAAGAAGAAAAAAAGAAAAAA-AGA
1 AAAAGAAAAAAAAAAG-AAAAAGAAGAAAAAAAGAAAAAAGA-A
*
19891835 AAAAGAAAAAAAGAAAGAAAAAGAAGAAGAAAAAAAGAGAAAAGAA
1 AAAAGAAAAAAA-AAAG--AAA-AAGAAGAAAAAAAGAAAAAAGAA
*
19891881 AAAAGAGAGAAAAAAAGAAAAAGAA
1 AAAAGA-AAAAAAAAAGAAAAAGAA
19891906 AAGGAGAGGT
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
43 16 0.25
44 7 0.11
45 4 0.06
46 30 0.48
47 6 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (42 bp):
AAAAGAAAAAAAAAAGAAAAAGAAGAAAAAAAGAAAAAAGAA
Found at i:19891865 original size:56 final size:55
Alignment explanation
Indices: 19891793--19891906 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 55
19891783 TCAATGAATA
*
19891793 AAAGAAAAGAAAAAGAAAAAAGAAGAAAAAAAGAAAAAA-AGA-AAAAGAA-AAAAAG
1 AAAGAAAAGAAAAAG-AAAAA-AAG-AAAAAAGAAAAAAGAGAGAAAAAAAGAAAAAG
* *
19891848 AAAGAAAAAGAAGAAGAAAAAAAGAGAAAAGAAAAAAGAGAGAAAAAAAGAAAAAG
1 AAAG-AAAAGAAAAAGAAAAAAAGAAAAAAGAAAAAAGAGAGAAAAAAAGAAAAAG
19891904 AAA
1 AAA
19891907 AGGAGAGGTC
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
53 12 0.23
54 6 0.12
55 15 0.29
56 19 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (55 bp):
AAAGAAAAGAAAAAGAAAAAAAGAAAAAAGAAAAAAGAGAGAAAAAAAGAAAAAG
Found at i:19891903 original size:32 final size:30
Alignment explanation
Indices: 19891797--19891907 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 30
19891787 TGAATAAAAG
19891797 AAAAGAAAAAGAAAAAAGAAGAAAAAAAGAAA
1 AAAAGAAAAAGAAAAAAG-A-AAAAAAAGAAA
19891829 AAAAGAAAAAGAAAAAAAGAAAGAAAAAGAAGA
1 AAAAGAAAAAG-AAAAAAGAAA-AAAAAGAA-A
* *
19891862 AGAA-AAAAAGAGAAAAGAAAAAAGAGAGAAA
1 AAAAGAAAAAGAAAAAAGAAAAAA-A-AGAAA
19891893 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
19891908 GGAGAGGTCG
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
30 3 0.04
31 16 0.23
32 39 0.57
33 11 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (30 bp):
AAAAGAAAAAGAAAAAAGAAAAAAAAGAAA
Found at i:19893208 original size:101 final size:101
Alignment explanation
Indices: 19893033--19893377 Score: 408
Period size: 101 Copynumber: 3.4 Consensus size: 101
19893023 GCACCATGAA
* * * * *
19893033 ACACGACGGGAAAGATCTAAGACTGCAACGGCGGATCCAGTACTGCAAAGATACAAAAGGGAAAG
1 ACACGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGTAAAAAGACAAAAGGGAAAG
* *
19893098 GTCTAAGTCGCAATGGCAAACCGTGTACCTCAAAAG
66 GTCTAAGTCGCAACGGCAAACCGTGTACCTCAGAAG
* *
19893134 ACACGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGTAAAAAGAGAAAAGGGAAAG
1 ACACGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGTAAAAAGACAAAAGGGAAAG
* * *
19893199 GTCTAAGTCGCAACGGTAGATCGTGTACCTCAGAAG
66 GTCTAAGTCGCAACGGCAAACCGTGTACCTCAGAAG
* * ** * * *
19893235 ACACGAAGGGAAAGATCTAAGACCGTAACGGCAGATCCAGTACTACAAAGATACAGAAGGGAAAG
1 ACACGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGTAAAAAGACAAAAGGGAAAG
* * * * * *
19893300 ATCTAAGATCGCAACAGCGGATCC-AGTACCAC-GAAG
66 GTCTAAG-TCGCAACGGC-AAACCGTGTACCTCAGAAG
* *
19893336 ACATGAAGGGAAAGATCTAAG-CAGCAACGGCGGATCCAGTAC
1 ACACGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC
19893378 ATGAACATGA
Statistics
Matches: 210, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
100 18 0.09
101 177 0.84
102 14 0.07
103 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.27, T:0.13
Consensus pattern (101 bp):
ACACGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGTAAAAAGACAAAAGGGAAAG
GTCTAAGTCGCAACGGCAAACCGTGTACCTCAGAAG
Found at i:19893376 original size:49 final size:49
Alignment explanation
Indices: 19893040--19893493 Score: 346
Period size: 51 Copynumber: 9.1 Consensus size: 49
19893030 GAAACACGAC
* ** * *
19893040 GGGAAAGATCTAAGACTGCAACGGCGGATCCAGTACTGCAAAGATACA-AAA
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAG--ACATGAA
* * * * * * * * * *
19893091 GGGAAAGGTCTAAGTCGCAATGGC-AAACCGTGTACCTCAAAAGACACGAC
1 GGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACCAC-GAAGACATGAA
* ** * *
19893141 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGTAAAAAGAGA-AAA
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTAC--CACGAAGACATGAA
* * ** ** * *
19893192 GGGAAAGGTCTAAGTCGCAACGGTAGATCGTGTACCTCAGAAGACACGAA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC-GAAGACATGAA
* * * *
19893242 GGGAAAGATCTAAGACCGTAACGGCAGATCCAGTACTACAAAGATACA-GAA
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAG--ACATGAA
* *
19893293 GGGAAAGATCTAAGATCGCAACAGCGGATCCAGTACCACGAAGACATGAA
1 GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAGACATGAA
* *
19893343 GGGAAAGATCTAAGCAGCAACGGCGGATCCAGTA-CATG-A-ACATGAA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACATGAA
* * * *
19893389 GAGAAAGATCTAAGCCGCAACGGCGGATCCAATACCATGAAGACATCAA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACATGAA
* * **
19893438 AGGAAAGATCTAAGCTGCAACGGCGGATCCAGTACCACGAAGATTTGAA
1 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACATGAA
19893487 GGGAAAG
1 GGGAAAG
19893494 GTTTAAATCG
Statistics
Matches: 320, Mismatches: 67, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
46 38 0.12
47 5 0.02
48 4 0.01
49 84 0.26
50 77 0.24
51 100 0.31
52 12 0.04
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.13
Consensus pattern (49 bp):
GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACATGAA
Found at i:19893431 original size:95 final size:97
Alignment explanation
Indices: 19893231--19893472 Score: 301
Period size: 95 Copynumber: 2.5 Consensus size: 97
19893221 GTGTACCTCA
* * * * *
19893231 GAAGACACGAAGGGAAAGATCTAAGACCGTAACGGCAGATCCAGTACTACAAAGATACAGAAGGG
1 GAAGACATGAAGGGAAAGATCTAAG-CAGCAACGGCGGATCCAG---TACAAAGATACAGAAGAG
* *
19893296 AAAGATCTAAGATCGCAACAGCGGATCCAGTACCAC
62 AAAGATCTAAGACCGCAACAGCGGATCCAATACCAC
*
19893332 GAAGACATGAAGGGAAAGATCTAAGCAGCAACGGCGGATCCAGTAC-ATGA-ACATGAAGAGAAA
1 GAAGACATGAAGGGAAAGATCTAAGCAGCAACGGCGGATCCAGTACAAAGATACA-GAAGAGAAA
* *
19893395 GATCTAAG-CCGCAACGGCGGATCCAATACCAT
65 GATCTAAGACCGCAACAGCGGATCCAATACCAC
* * *
19893427 GAAGACATCAAAGGAAAGATCTAAGCTGCAACGGCGGATCCAGTAC
1 GAAGACATGAAGGGAAAGATCTAAGCAGCAACGGCGGATCCAGTAC
19893473 CACGAAGATT
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
95 66 0.52
96 19 0.15
97 3 0.02
100 15 0.12
101 24 0.19
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.12
Consensus pattern (97 bp):
GAAGACATGAAGGGAAAGATCTAAGCAGCAACGGCGGATCCAGTACAAAGATACAGAAGAGAAAG
ATCTAAGACCGCAACAGCGGATCCAATACCAC
Found at i:19893509 original size:49 final size:49
Alignment explanation
Indices: 19893131--19893511 Score: 304
Period size: 49 Copynumber: 7.7 Consensus size: 49
19893121 TGTACCTCAA
* * * **
19893131 AAGACACGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGTAAA
1 AAGACATGAAGGGAAAGATCTAA-ACCGCAACGGCGGATCCAGTAC--CACG
* * * ** ** ** *
19893183 AAGAGA-AAAGGGAAAGGTCTAAGTCGCAACGGTAGATCGTGTACCTCAG
1 AAGACATGAAGGGAAAGATCTAAACCGCAACGGCGGATCCAGTACCAC-G
* * * * *
19893232 AAGACACGAAGGGAAAGATCTAAGACCGTAACGGCAGATCCAGTACTACA
1 AAGACATGAAGGGAAAGATCTAA-ACCGCAACGGCGGATCCAGTACCACG
* *
19893282 AAGATACA-GAAGGGAAAGATCTAAGATCGCAACAGCGGATCCAGTACCACG
1 AAG--ACATGAAGGGAAAGATCTAA-ACCGCAACGGCGGATCCAGTACCACG
* * *
19893333 AAGACATGAAGGGAAAGATCTAAGCAGCAACGGCGGATCCAGTA-CATG
1 AAGACATGAAGGGAAAGATCTAAACCGCAACGGCGGATCCAGTACCACG
* * * *
19893381 -A-ACATGAAGAGAAAGATCTAAGCCGCAACGGCGGATCCAATACCATG
1 AAGACATGAAGGGAAAGATCTAAACCGCAACGGCGGATCCAGTACCACG
* * * *
19893428 AAGACATCAAAGGAAAGATCTAAGCTGCAACGGCGGATCCAGTACCACG
1 AAGACATGAAGGGAAAGATCTAAACCGCAACGGCGGATCCAGTACCACG
** * * * *
19893477 AAGATTTGAAGGGAAAGGTTTAAATCGTAACGGCG
1 AAGACATGAAGGGAAAGATCTAAACCGCAACGGCG
19893512 AACTCGATAC
Statistics
Matches: 264, Mismatches: 56, Indels: 21
0.77 0.16 0.06
Matches are distributed among these distances:
46 38 0.14
47 5 0.02
48 4 0.02
49 90 0.34
50 49 0.19
51 70 0.27
52 8 0.03
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (49 bp):
AAGACATGAAGGGAAAGATCTAAACCGCAACGGCGGATCCAGTACCACG
Found at i:19894263 original size:206 final size:206
Alignment explanation
Indices: 19893887--19894733 Score: 1123
Period size: 206 Copynumber: 4.1 Consensus size: 206
19893877 AACCTGGGGC
* * * * * * *
19893887 AGATACTGAGAAGTAGACCAAATTAAACCCATGCTCGATGTGAGCAAATATTCGAACCTCAGCTT
1 AGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGCTT
* ** * *
19893952 CCTAATGAGATACTGAGAAGTGGGTCGAAGCAATATAAAATGGTTAGCTTCCTGATGAGTTACTG
66 CCTGATGAGATACTGAGAAGCAGGTCGAAGC-A-ATAAAATGGTTAGCTTCCTAATGAGATACTG
19894017 AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGT
129 AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGT
*
19894082 CATCTTCCTGATG
194 CATCTTCCTAATG
* * *
19894095 AGATACTGAGAAGAAGACCAAATCAAACTCACGCACGATATGAGTAAATCTTCGGACCCCAGCTT
1 AGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGCTT
*
19894160 CCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTACCTAATGAGATACTGAG
66 CCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAG
* *
19894225 AAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAAACGATGCGGTCA
131 AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGTCA
*
19894290 TCTTCCTGATG
196 TCTTCCTAATG
* * *
19894301 AGATACTAAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAGCCCTAGCTT
1 AGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGCTT
*
19894366 CCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAG
66 CCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAG
* * ** *
19894431 AAGTGGACCAAATTCGTCTTCCTGATGAGATACTGAGAAGCGAATTGAAACAAGTGAGGCGGTCA
131 AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGTCA
*
19894496 TCTTCTTAATG
196 TCTTCCTAATG
* * * * **
19894507 AGATA-T-A-TAGAAG----TATGCCAACTCGACGCTCTATGCGAGCAAATCTTCGAACCCCAGC
1 AGATACTGAGAAGAAGACCAAAT-CAAACTC-ACGCTCGATATGAGCAAATCTTCGAACCCCAGC
* * * * *
19894565 TTCTTGATGAAATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAGCTTCCTGATGAGATACAG
64 TTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTG
* * * * * * ** ** *
19894630 AGAAGTGAACCAAATCCGTCTTCCTGTTGAAACACAGAGAAGTGGATCAAAACAAGTGACGCGGT
129 AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGT
19894695 CATCTTCCTAATG
194 CATCTTCCTAATG
* *
19894708 AGATACTGAGAAGAAGGCCAAGTCAA
1 AGATACTGAGAAGAAGACCAAATCAA
19894734 TAAAACCAGA
Statistics
Matches: 565, Mismatches: 65, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
199 2 0.00
200 6 0.01
201 158 0.28
202 1 0.00
203 6 0.01
204 6 0.01
205 1 0.00
206 298 0.53
207 3 0.01
208 84 0.15
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
AGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAGCTT
CCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAG
AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGTCA
TCTTCCTAATG
Found at i:19894671 original size:407 final size:411
Alignment explanation
Indices: 19893887--19894733 Score: 1159
Period size: 407 Copynumber: 2.1 Consensus size: 411
19893877 AACCTGGGGC
* * * *
19893887 AGATACTGAGAAGTAGACCAAATTAAACCCATGCTCGATGTGAGCAAATATTCGAACCTCAGCTT
1 AGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATATTCGAACCTCAGCTT
* * *
19893952 CCTAATGAGATACTGAGAAGTGGGTCGAAGCAATATAAAATGGTTAGCTTCCTGATGAGTTACTG
66 CCTAATGAGATACTGAGAAGTAGGTCGAAGCAATATAAAATGGTTAGCTTCCTAATGAGATACTG
* *
19894017 AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGGT
131 AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGAGGCGGT
* * *
19894082 CATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCACGATATGAGTAAATCTT
196 CATCTTCCTAATGAGATACTGAGAAGAAG---AAATCAAACTCACGCACGATACGAGCAAATCTT
* *
19894147 CGGACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTACCTA
258 CGAACCCCAGCTTCCTGATGAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTACCTA
* * * * * * **
19894212 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGTGGATTGAAACA
323 ATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGTGGATCAAAACA
* *
19894277 AACGATGCGGTCATCTTCCTGATG
388 AACGACGCGGTCATCTTCCTAATG
* * * *
19894301 AGATACTAAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAGCC-CTAGCT
1 AGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATATTCGAACCTC-AGCT
*
19894365 TCCTGATGAGATACTGAGAAGTAGGTCGAAGC-A-ATAAAATGGTTAGCTTCCTAATGAGATACT
65 TCCTAATGAGATACTGAGAAGTAGGTCGAAGCAATATAAAATGGTTAGCTTCCTAATGAGATACT
* **
19894428 GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACTGAGAAGCGAATTGAAACAAGTGAGGCGG
130 GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGAGGCGG
* * * * * * *
19894493 TCATCTTCTTAATGAGATA-T-A-TAGAAG-TATGCCAACTCGACGCTCTATGCGAGCAAATCTT
195 TCATCTTCCTAATGAGATACTGAGAAGAAGAAAT-CAAACTC-ACGCACGATACGAGCAAATCTT
* * * *
19894554 CGAACCCCAGCTTCTTGATGAAATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAGCTTCCTG
258 CGAACCCCAGCTTCCTGATGAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTACCTA
*
19894619 ATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGTTGAAACACAGAGAAGTGGATCAAAACA
323 ATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGTGGATCAAAACA
**
19894684 AGTGACGCGGTCATCTTCCTAATG
388 AACGACGCGGTCATCTTCCTAATG
* *
19894708 AGATACTGAGAAGAAGGCCAAGTCAA
1 AGATACTGAGAAGAAGACCAAATCAA
19894734 TAAAACCAGA
Statistics
Matches: 381, Mismatches: 49, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
405 2 0.01
406 6 0.02
407 175 0.46
409 5 0.01
410 1 0.00
411 1 0.00
412 105 0.28
413 2 0.01
414 84 0.22
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (411 bp):
AGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATATTCGAACCTCAGCTT
CCTAATGAGATACTGAGAAGTAGGTCGAAGCAATATAAAATGGTTAGCTTCCTAATGAGATACTG
AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGAGGCGGT
CATCTTCCTAATGAGATACTGAGAAGAAGAAATCAAACTCACGCACGATACGAGCAAATCTTCGA
ACCCCAGCTTCCTGATGAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTACCTAATG
AGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGTGGATCAAAACAAAC
GACGCGGTCATCTTCCTAATG
Found at i:19895102 original size:6 final size:6
Alignment explanation
Indices: 19895082--19895181 Score: 64
Period size: 6 Copynumber: 17.0 Consensus size: 6
19895072 TAAGTTGGGT
* * * **
19895082 TTTAAA TTT-AT TTTAAG TTTAAA TTTAAA TTCATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
19895129 TTT-AT TTTAAA TTTAGT TTTAAA TTTGAAA --TAAT TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTT-AAA TTTAAA
*
19895176 ATTAAA
1 TTTAAA
19895182 AGCCCAAAAT
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
4 2 0.03
5 9 0.13
6 51 0.73
7 8 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:19895126 original size:24 final size:23
Alignment explanation
Indices: 19895082--19895181 Score: 76
Period size: 23 Copynumber: 4.3 Consensus size: 23
19895072 TAAGTTGGGT
* *
19895082 TTTAAATTTATTTTAAGTTTAAA
1 TTTAAATTCATTTTAAATTTAAA
19895105 TTTAAATTCATTTTTAAATTTAAA
1 TTTAAATTCA-TTTTAAATTTAAA
** * * **
19895129 TTTATTTTAAATTTAGTTTTAAA
1 TTTAAATTCATTTTAAATTTAAA
*
19895152 TTTGAAA-TAATTTTAAAATTTAAA
1 TTT-AAATTCATTTT-AAATTTAAA
*
19895176 ATTAAA
1 TTTAAA
19895182 AGCCCAAAAT
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
23 31 0.52
24 29 0.48
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTAAATTCATTTTAAATTTAAA
Found at i:19895137 original size:29 final size:29
Alignment explanation
Indices: 19895105--19895168 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
19895095 TAAGTTTAAA
* *
19895105 TTTAAATTCATTTTTAAATTT-AAATTTAT
1 TTTAAATTCAGTTTTAAATTTGAAA-TAAT
*
19895134 TTTAAATTTAGTTTTAAATTTGAAATAAT
1 TTTAAATTCAGTTTTAAATTTGAAATAAT
19895163 TTTAAA
1 TTTAAA
19895169 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTAAATTCAGTTTTAAATTTGAAATAAT
Found at i:19895149 original size:17 final size:17
Alignment explanation
Indices: 19895081--19895143 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
19895071 TTAAGTTGGG
*
19895081 TTTTAAATTT-ATTTTAA
1 TTTTAAATTTAAATTT-A
* *
19895098 GTTTAAATTTAAATTCA
1 TTTTAAATTTAAATTTA
19895115 TTTTTAAATTTAAATTTA
1 -TTTTAAATTTAAATTTA
19895133 TTTTAAATTTA
1 TTTTAAATTTA
19895144 GTTTTAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 21 0.54
18 18 0.46
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:19897136 original size:88 final size:86
Alignment explanation
Indices: 19896981--19897168 Score: 216
Period size: 88 Copynumber: 2.1 Consensus size: 86
19896971 CTGGAGGTCT
* * *
19896981 CTAAACTGTCCAAAAAATTATATTTTGACCCCAAACTTCTCCAAAATTACTTTTTGACCTCAAAA
1 CTAAACT-TCC-AAAAATTACATTTTAACCCCAAACTTCT-CAAAATTACTTTTTGACCCCAAAA
* *
19897046 CTTCTAAAAATTACATTTTTACCC
63 CTTCCAAAAATTACATTTTAACCC
* * * *
19897070 CTAAACTTCCAAAAGTTACATTTTAACCCGAAACTTCT-AAAATTACATTTTTTTATCCCCCAAA
1 CTAAACTTCCAAAAATTACATTTTAACCCCAAACTTCTCAAAATTAC--TTTTTGA-CCCCAAAA
19897134 CTTCCAAAAATTACATTTTAACCC
63 CTTCCAAAAATTACATTTTAACCC
* *
19897158 CAAAAATTCCA
1 CTAAACTTCCA
19897169 TTTTCCCCTC
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
85 8 0.09
87 30 0.35
88 40 0.47
89 7 0.08
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.34
Consensus pattern (86 bp):
CTAAACTTCCAAAAATTACATTTTAACCCCAAACTTCTCAAAATTACTTTTTGACCCCAAAACTT
CCAAAAATTACATTTTAACCC
Found at i:19897148 original size:59 final size:57
Alignment explanation
Indices: 19896993--19897260 Score: 211
Period size: 59 Copynumber: 4.8 Consensus size: 57
19896983 AAACTGTCCA
* * * * *
19896993 AAAAATTATATTTTGA-CCCCAAACTTCTCCAAAATTACTTTTTGACCTCAAAACTTCT
1 AAAAATTACATTTTTACCCCCAAACTTC-CAAAAATTACATTTTAACC-CAAAACTTCT
* * *
19897051 AAAAATTACATTTTTACCCCTAAACTTCCAAAAGTTACATTTTAACCCGAAACTTCT
1 AAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACATTTTAACCCAAAACTTCT
19897108 -AAAATTACATTTTTTTATCCCCCAAACTTCCAAAAATTACATTTTAA-CC----C--C-
1 AAAAATTACA--TTTTTA-CCCCCAAACTTCCAAAAATTACATTTTAACCCAAAACTTCT
* * * **
19897159 AAAAATTCCA-TTTT-CCCCTCGAACTTTCCAAAAATTCCATTTTAATCCTGAAACTTCT
1 AAAAATTACATTTTTACCCC-CAAAC-TTCCAAAAATTACATTTTAA-CCCAAAACTTCT
** *
19897217 AAAAATTACCGTTTTACCCCCAAA-TATCCAAAAAATTCCATTTT
1 AAAAATTACATTTTTACCCCCAAACT-TCC-AAAAATTACATTTT
19897261 TGATCCTGAT
Statistics
Matches: 173, Mismatches: 17, Indels: 39
0.76 0.07 0.17
Matches are distributed among these distances:
47 4 0.02
48 4 0.02
49 23 0.13
51 1 0.01
52 9 0.05
54 1 0.01
55 1 0.01
56 9 0.05
57 11 0.06
58 48 0.28
59 58 0.34
60 4 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACATTTTAACCCAAAACTTCT
Found at i:19897167 original size:29 final size:29
Alignment explanation
Indices: 19896983--19897168 Score: 162
Period size: 29 Copynumber: 6.3 Consensus size: 29
19896973 GGAGGTCTCT
* *
19896983 AAACTGTCCAAAAAATTATATTTTGACCCC-
1 AAACT-TCC-AAAAATTACATTTTAACCCCA
* * * *
19897013 AAACTTCTCCAAAATTACTTTTTGACCTCA
1 AAACTTC-CAAAAATTACATTTTAACCCCA
* * *
19897043 AAACTTCTAAAAATTACATTTTTACCCCT
1 AAACTTCCAAAAATTACATTTTAACCCCA
* *
19897072 AAACTTCCAAAAGTTACATTTTAA-CCCG
1 AAACTTCCAAAAATTACATTTTAACCCCA
* * *
19897100 AAACTT-CTAAAATTACATTTTTTTATCCCCC
1 AAACTTCCAAAAATTACA---TTTTAACCCCA
19897131 AAACTTCCAAAAATTACATTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTAACCCCA
*
19897160 AAAATTCCA
1 AAACTTCCA
19897169 TTTTCCCCTC
Statistics
Matches: 127, Mismatches: 22, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
27 9 0.07
28 9 0.07
29 72 0.57
30 18 0.14
31 9 0.07
32 10 0.08
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTAACCCCA
Found at i:19897232 original size:108 final size:107
Alignment explanation
Indices: 19897051--19897260 Score: 250
Period size: 108 Copynumber: 1.9 Consensus size: 107
19897041 CAAAACTTCT
*
19897051 AAAAATTACATTTTTACCCCTAAACTTCCAAAAGTTACATTTTAACCCGAAACTTCTAAAATTAC
1 AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTAACCCGAAACTTCTAAAATTAC
**
19897116 ATTTTTTTATCCCCCAAACT-TCC-AAAAATTACATTTTAACCCC
66 A-CGTTTTA-CCCCCAAA-TATCCAAAAAATTACATTTTAACCCC
* * * *
19897159 AAAAATTCCA-TTTT-CCCCTCGAACTTTCCAAAAATTCCATTTTAATCCTGAAACTTCTAAAAA
1 AAAAATTACATTTTTACCCCT-AAAC-TTCCAAAAATTACATTTTAA-CCCGAAACTTCT-AAAA
*
19897222 TTAC-CGTTTTACCCCCAAATATCCAAAAAATTCCATTTT
62 TTACACGTTTTACCCCCAAATATCCAAAAAATTACATTTT
19897261 TGATCCTGAT
Statistics
Matches: 88, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
106 6 0.07
107 18 0.20
108 45 0.51
109 11 0.12
110 8 0.09
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.34
Consensus pattern (107 bp):
AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTAACCCGAAACTTCTAAAATTAC
ACGTTTTACCCCCAAATATCCAAAAAATTACATTTTAACCCC
Found at i:19897311 original size:59 final size:58
Alignment explanation
Indices: 19897248--19897378 Score: 133
Period size: 59 Copynumber: 2.2 Consensus size: 58
19897238 AAATATCCAA
* * * * *
19897248 AAAATTCCATTTTTGATCCTGATTTTTGTCTAAAAATTACCGTTTTAACCTCGA-A-TGCT
1 AAAATTCCATTTTTAACCCTAAATTTT-TCTAAAAATTACCATTTT-ACCTCGAGAGT-CT
* *
19897307 AAAATAT-CATTTTTAACCCTAAATTTTTCTCAAAATTACCATTTTCCCTCGAGAGTCT
1 AAAAT-TCCATTTTTAACCCTAAATTTTTCTAAAAATTACCATTTTACCTCGAGAGTCT
19897365 AAAATTACCATTTT
1 AAAATT-CCATTTT
19897379 ACCCCCGAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
57 7 0.12
58 24 0.40
59 28 0.47
60 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCTAAATTTTTCTAAAAATTACCATTTTACCTCGAGAGTCT
Found at i:19898584 original size:17 final size:17
Alignment explanation
Indices: 19898564--19898601 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
19898554 TGATTTTGAT
19898564 TTTA-TTTTATTTATTTA
1 TTTATTTTTA-TTATTTA
*
19898581 TTTATTTTTATTCTTTA
1 TTTATTTTTATTATTTA
19898598 TTTA
1 TTTA
19898602 CTAACTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTATTATTTA
Found at i:19909616 original size:14 final size:16
Alignment explanation
Indices: 19909599--19909632 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19909589 TATTTTAAAT
19909599 TTTTTA-TTATTTC-C
1 TTTTTAGTTATTTCAC
19909613 TTTTTAGTTATTTCAC
1 TTTTTAGTTATTTCAC
19909629 TTTT
1 TTTT
19909633 CATCGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 7 0.39
16 5 0.28
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTAGTTATTTCAC
Found at i:19921518 original size:5 final size:5
Alignment explanation
Indices: 19921503--19921536 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
19921493 TAAATACTTC
* *
19921503 TCTTT TTTTT TCTTT TCTTT TCTTA TCTTT TCTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTT
19921537 CTTTTTTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:19921523 original size:15 final size:15
Alignment explanation
Indices: 19921503--19921543 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
19921493 TAAATACTTC
19921503 TCTTTTTTTTTCTTT
1 TCTTTTTTTTTCTTT
* *
19921518 TCTTTTCTTATCTTT
1 TCTTTTTTTTTCTTT
19921533 TCTTCTTTTTT
1 TCTT-TTTTTT
19921544 ATGTGATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTTTTTTCTTT
Found at i:19929209 original size:37 final size:38
Alignment explanation
Indices: 19929168--19929261 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
19929158 ATGTTCATGT
*
19929168 AGCGACATTCTTGGGTGCAA-TTGAAGAAAACTTATGC
1 AGCGATATTCTTGGGTGCAATTTGAAGAAAACTTATGC
** * * *
19929205 AGCGATAGTT-TTGATTACAATTTGAAGAATATTTATGC
1 AGCGATA-TTCTTGGGTGCAATTTGAAGAAAACTTATGC
*
19929243 AGCGATAGTCTTGGGTGCA
1 AGCGATATTCTTGGGTGCA
19929262 TTCCGAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
37 14 0.32
38 30 0.68
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
AGCGATATTCTTGGGTGCAATTTGAAGAAAACTTATGC
Found at i:19953008 original size:26 final size:28
Alignment explanation
Indices: 19952970--19953033 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
19952960 GACCTTTCTC
* *
19952970 TTATAATTCACC-AAAAAATAGCTCATT
1 TTATTATTCACCAAAAAAAAAGCTCATT
*
19952997 TTATTATT-ACCAAGAAAAAAAATCTCATT
1 TTATTATTCACC-A-AAAAAAAAGCTCATT
19953026 TTATTATT
1 TTATTATT
19953034 TTAATATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 7 0.23
29 21 0.68
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (28 bp):
TTATTATTCACCAAAAAAAAAGCTCATT
Found at i:19957292 original size:21 final size:21
Alignment explanation
Indices: 19957251--19957289 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19957241 TTTATGTGAA
* *
19957251 TTGATGTTTGATCTGGTAATT
1 TTGATGATTGATCTGCTAATT
19957272 TTGATGATTGAT-TGCTAA
1 TTGATGATTGATCTGCTAA
19957290 ATTGAGGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (21 bp):
TTGATGATTGATCTGCTAATT
Found at i:19958846 original size:55 final size:54
Alignment explanation
Indices: 19958755--19958878 Score: 151
Period size: 55 Copynumber: 2.3 Consensus size: 54
19958745 ATTCTGTTTC
* * * *
19958755 TGGCTCGAAAGAGCGTTATTCTAGACTCTAGCTCATAAGAGCGATACTCTATTTT
1 TGGCTCGAAAGAGCATTATTATAGACTCTAGATCATAAGAGCGACACTCTA-TTT
* * * *
19958810 TGGCTTGAAAGAGCATTATTATGGACTCTGGATCATAAGAGCGACATTCTATTT
1 TGGCTCGAAAGAGCATTATTATAGACTCTAGATCATAAGAGCGACACTCTATTT
19958864 TGGCTC-ATAAGAGCA
1 TGGCTCGA-AAGAGCA
19958879 ATACTCTATT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.02
54 15 0.25
55 43 0.73
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (54 bp):
TGGCTCGAAAGAGCATTATTATAGACTCTAGATCATAAGAGCGACACTCTATTT
Found at i:19958873 original size:26 final size:27
Alignment explanation
Indices: 19958842--19958905 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
19958832 GGACTCTGGA
* *
19958842 TCATAAGAGCGACATTCTA-TTTTGGC
1 TCATAAGAGCAACACTCTATTTTTGGC
*
19958868 TCATAAGAGCAATACTCTATTTTTGGC
1 TCATAAGAGCAACACTCTATTTTTGGC
19958895 TCGA-AAGAGCA
1 TC-ATAAGAGCA
19958906 TTACTCTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.48
27 16 0.48
28 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (27 bp):
TCATAAGAGCAACACTCTATTTTTGGC
Found at i:19958902 original size:27 final size:26
Alignment explanation
Indices: 19958857--19958931 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
19958847 AGAGCGACAT
19958857 TCTATTTTGGCTC-ATAAGAGCAATAC
1 TCTATTTTGGCTCGA-AAGAGCAATAC
*
19958883 TCTATTTTTGGCTCGAAAGAGCATTAC
1 TCTA-TTTTGGCTCGAAAGAGCAATAC
* *
19958910 TCTAGACTTTGGTTCGAAAGAG
1 TCT--ATTTTGGCTCGAAAGAG
19958932 TGTTTATTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.10
27 22 0.52
28 15 0.36
29 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTATTTTGGCTCGAAAGAGCAATAC
Found at i:19958931 original size:81 final size:82
Alignment explanation
Indices: 19958785--19958959 Score: 219
Period size: 81 Copynumber: 2.1 Consensus size: 82
19958775 CTAGACTCTA
* * * *
19958785 GCTCATAAGAGCGATACTCTATTTTTGGCTTGAAAGAGCATTATTATGGACTCTGGATCATAAGA
1 GCTCATAAGAGCAATACTCTATTTTTGGCTCGAAAGAGCATTACTATAGACTCTGGATCATAAGA
*
19958850 GCG-ACATTCTATTTTG
66 GCGTACATTCTATTTGG
* * *
19958866 GCTCATAAGAGCAATACTCTATTTTTGGCTCGAAAGAGCATTACTCTAGACTTTGGTTCGA-AAG
1 GCTCATAAGAGCAATACTCTATTTTTGGCTCGAAAGAGCATTACTATAGACTCTGGATC-ATAAG
* ** *
19958930 AGTGTTTATTCTGTTTGG
65 AGCGTACATTCTATTTGG
19958948 GCTCATAAGAGC
1 GCTCATAAGAGC
19958960 TAAACTCCGT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 58 0.73
82 22 0.28
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (82 bp):
GCTCATAAGAGCAATACTCTATTTTTGGCTCGAAAGAGCATTACTATAGACTCTGGATCATAAGA
GCGTACATTCTATTTGG
Found at i:19958975 original size:26 final size:26
Alignment explanation
Indices: 19958939--19959045 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
19958929 GAGTGTTTAT
*
19958939 TCTGTTTGGGCTCATAAGAGCTAAAC
1 TCTGTCTGGGCTCATAAGAGCTAAAC
*
19958965 TCCGTCTGGGCTCATAAGAGCTAAAC
1 TCTGTCTGGGCTCATAAGAGCTAAAC
* * * *
19958991 TCTGTCTGGGCTCGTATGAGTTAAAT
1 TCTGTCTGGGCTCATAAGAGCTAAAC
*
19959017 TCTGTCTGGGCTCGTAAGAGCTAAAC
1 TCTGTCTGGGCTCATAAGAGCTAAAC
19959043 TCT
1 TCT
19959046 ATTCTGGACT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (26 bp):
TCTGTCTGGGCTCATAAGAGCTAAAC
Found at i:19960079 original size:43 final size:43
Alignment explanation
Indices: 19959975--19960069 Score: 190
Period size: 43 Copynumber: 2.2 Consensus size: 43
19959965 CATGGTCTAG
19959975 CACACGGCTACACACACGGGTGTGTGAGGTAAATTCGCATACT
1 CACACGGCTACACACACGGGTGTGTGAGGTAAATTCGCATACT
19960018 CACACGGCTACACACACGGGTGTGTGAGGTAAATTCGCATACT
1 CACACGGCTACACACACGGGTGTGTGAGGTAAATTCGCATACT
19960061 CACACGGCT
1 CACACGGCT
19960070 TGTCACACGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (43 bp):
CACACGGCTACACACACGGGTGTGTGAGGTAAATTCGCATACT
Found at i:19961398 original size:4 final size:4
Alignment explanation
Indices: 19961391--19961432 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
19961381 TATATATATA
* *
19961391 TATG TATG TATG TATG TATG TATG TATG CATG TATG TGTG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
19961433 GGTGTGTGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:19963984 original size:19 final size:19
Alignment explanation
Indices: 19963960--19964005 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
19963950 AGAATTAAAT
19963960 TAATTAGTC-ATTGTAATTA
1 TAATTAGTCAATTG-AATTA
*
19963979 TAATTAGGCAATTGAATTA
1 TAATTAGTCAATTGAATTA
*
19963998 AAATTAGT
1 TAATTAGT
19964006 AGTAGATTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (19 bp):
TAATTAGTCAATTGAATTA
Found at i:19973251 original size:17 final size:17
Alignment explanation
Indices: 19973202--19973273 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
19973192 ATGGATGTTC
19973202 AACCTTCCATCTT-TCTT
1 AACCTTCCATCTTCT-TT
**
19973219 AACC-TCACATGATCTTT
1 AACCTTC-CATCTTCTTT
19973236 AACCTTCCATCTTCTTT
1 AACCTTCCATCTTCTTT
* *
19973253 AACCTTTCATATTCTTGT
1 AACCTTCCATCTTCTT-T
19973271 AAC
1 AAC
19973274 TACTTTTTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
16 2 0.04
17 36 0.80
18 7 0.16
ACGTcount: A:0.24, C:0.31, G:0.03, T:0.43
Consensus pattern (17 bp):
AACCTTCCATCTTCTTT
Found at i:19978594 original size:17 final size:17
Alignment explanation
Indices: 19978572--19978630 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
19978562 CCCTTGACTT
*
19978572 TTAACCTTCCATCTTTC
1 TTAACCTTCCATCTTCC
19978589 TTAACC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
19978605 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
19978623 TTAACCTT
1 TTAACCTT
19978631 TCATATTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 3 0.09
16 4 0.11
17 20 0.57
18 5 0.14
20 3 0.09
ACGTcount: A:0.19, C:0.37, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:19978598 original size:34 final size:34
Alignment explanation
Indices: 19978560--19978629 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
19978550 AACCTTTCAT
* *
19978560 CTCCCTTGACTTTTAACCTTCCATCTTTCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
19978594 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
19978628 CT
1 CT
19978630 TTCATATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.17, C:0.39, G:0.03, T:0.41
Consensus pattern (34 bp):
CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
Found at i:19987191 original size:26 final size:27
Alignment explanation
Indices: 19987144--19987196 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
19987134 TGTCGGTTTT
19987144 TCAGAAACTTGGGAGCGGAGATCTCAA
1 TCAGAAACTTGGGAGCGGAGATCTCAA
19987171 TCAGAAACTT-GGAGCGGAGATCTCAA
1 TCAGAAACTTGGGAGCGGAGATCTCAA
19987197 AAATACCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (27 bp):
TCAGAAACTTGGGAGCGGAGATCTCAA
Found at i:19988146 original size:27 final size:31
Alignment explanation
Indices: 19988088--19988147 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 31
19988078 AACACTTATA
*
19988088 ACTCTCATCTACAACACATAAACTCTATAAT
1 ACTCTCATCTACAACACATAAACTCTACAAT
*
19988119 ACTCTCAT-TAC-AC-CAT-AACTCTCCAAT
1 ACTCTCATCTACAACACATAAACTCTACAAT
19988146 AC
1 AC
19988148 CTCTAAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 11 0.41
28 3 0.11
29 2 0.07
30 3 0.11
31 8 0.30
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.28
Consensus pattern (31 bp):
ACTCTCATCTACAACACATAAACTCTACAAT
Found at i:20011941 original size:17 final size:18
Alignment explanation
Indices: 20011919--20011958 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20011909 AGATTGCATA
20011919 CATTTT-TATTGTCATCG
1 CATTTTATATTGTCATCG
* *
20011936 CATTTTATTTTGTCATTG
1 CATTTTATATTGTCATCG
20011954 CATTT
1 CATTT
20011959 CTTTTGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (18 bp):
CATTTTATATTGTCATCG
Found at i:20012567 original size:6 final size:6
Alignment explanation
Indices: 20012556--20012598 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
20012546 TTATTGAATG
*
20012556 AGAAAA AG-AAA AGAAAA AGAGAAA AGAGAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA A
20012599 TTACTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:20012579 original size:19 final size:20
Alignment explanation
Indices: 20012555--20012598 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
20012545 ATTATTGAAT
20012555 GAGAAAAAGA-AAAGAAAAA
1 GAGAAAAAGAGAAAGAAAAA
20012574 GAG-AAAAGAGAAAGAAAAA
1 GAGAAAAAGAGAAAGAAAAA
20012593 GA-AAAA
1 GAGAAAA
20012599 TTACTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
GAGAAAAAGAGAAAGAAAAA
Found at i:20017193 original size:17 final size:17
Alignment explanation
Indices: 20017173--20017207 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20017163 AAATGAACTA
*
20017173 ACAAGTAAAATGCAATG
1 ACAACTAAAATGCAATG
20017190 ACAACTAAAATGCAATG
1 ACAACTAAAATGCAATG
20017207 A
1 A
20017208 AAATTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.17
Consensus pattern (17 bp):
ACAACTAAAATGCAATG
Found at i:20017215 original size:17 final size:17
Alignment explanation
Indices: 20017178--20017215 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20017168 AACTAACAAG
*
20017178 TAAAATGCAATGACAAC
1 TAAAATGCAATGAAAAC
*
20017195 TAAAATGCAATGAAAAT
1 TAAAATGCAATGAAAAC
20017212 TAAA
1 TAAA
20017216 TGAGATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (17 bp):
TAAAATGCAATGAAAAC
Found at i:20027418 original size:53 final size:53
Alignment explanation
Indices: 20027338--20027577 Score: 293
Period size: 53 Copynumber: 4.5 Consensus size: 53
20027328 TTGTTCCAAA
* *
20027338 GATTAAAGGTCCGATGACTTTATGTCATCATGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCATG
*
20027391 GATTAAAGGTCCAATGACTCTGTGTCATCATGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCATG
* * * * * *
20027444 GATTAAATGTCCGATGACTATGTGTCATCGTGAGTTATATAAATCCTATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCATG
* * * * * ** * * *
20027497 AATTAAGGGTCCGATGACTTTGTGTTATCATAAAATACACGAATCC-ATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCATG
*
20027549 GATTAAAGGTTCGATGACTCTGTGTCATC
1 GATTAAAGGTCCGATGACTCTGTGTCATC
20027578 GCAAGTTATC
Statistics
Matches: 159, Mismatches: 28, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
52 29 0.18
53 130 0.82
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCATG
Found at i:20035170 original size:13 final size:13
Alignment explanation
Indices: 20035152--20035177 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20035142 ATAGGATGAG
20035152 ATGGACAACTTGT
1 ATGGACAACTTGT
20035165 ATGGACAACTTGT
1 ATGGACAACTTGT
20035178 CTAAGTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
ATGGACAACTTGT
Found at i:20037036 original size:24 final size:24
Alignment explanation
Indices: 20037008--20037070 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
20036998 AGAAATAATC
20037008 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* * *
20037032 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
20037056 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
20037071 TATTAGTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:20039022 original size:24 final size:24
Alignment explanation
Indices: 20038995--20039049 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
20038985 AATCTTTCAG
*
20038995 TTAAACTCTA-TTTAATTGTTCCAA
1 TTAAACTC-ACTTTAATTATTCCAA
* *
20039019 TTAAACTCACTTTATTTATTTCAA
1 TTAAACTCACTTTAATTATTCCAA
20039043 TTAAACT
1 TTAAACT
20039050 GTTTATTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (24 bp):
TTAAACTCACTTTAATTATTCCAA
Found at i:20041015 original size:24 final size:24
Alignment explanation
Indices: 20040987--20041061 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
20040977 AGAAATAATC
* *
20040987 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
20041011 TTTCAACTAAACT-TAGTTTATTTG
1 TTTCAATTAAACTCT-GTTTATTTG
20041035 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
20041059 TTT
1 TTT
20041062 GAGTAAAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 43 0.96
25 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:20043449 original size:12 final size:12
Alignment explanation
Indices: 20043432--20043461 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20043422 ATCATTAATA
*
20043432 AATAAAAGAGTC
1 AATAAAAGAGCC
20043444 AATAAAAGAGCC
1 AATAAAAGAGCC
20043456 AATAAA
1 AATAAA
20043462 TAAGCTTATT
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:0.63, C:0.10, G:0.13, T:0.13
Consensus pattern (12 bp):
AATAAAAGAGCC
Found at i:20049229 original size:14 final size:14
Alignment explanation
Indices: 20049210--20049254 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
20049200 TTGCATCAAG
20049210 ATTTATTTTAGTTT
1 ATTTATTTTAGTTT
*
20049224 ATTTATTTTATTTTT
1 ATTTATTTTA-GTTT
*
20049239 GTTCTATTTTAGTTT
1 ATT-TATTTTAGTTT
20049254 A
1 A
20049255 ACATTTTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 10 0.40
15 8 0.32
16 7 0.28
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (14 bp):
ATTTATTTTAGTTT
Found at i:20056618 original size:26 final size:26
Alignment explanation
Indices: 20056588--20056649 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
20056578 CAGCACACTG
20056588 ATTTAGTTTTTATTTTTTAGCACTTA
1 ATTTAGTTTTTATTTTTTAGCACTTA
20056614 ATTTAGTTTTTATTTTTTAGCACTTA
1 ATTTAGTTTTTATTTTTTAGCACTTA
20056640 ATTTAGTTTT
1 ATTTAGTTTT
20056650 CATGCATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (26 bp):
ATTTAGTTTTTATTTTTTAGCACTTA
Found at i:20061158 original size:6 final size:5
Alignment explanation
Indices: 20061121--20061161 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
20061111 GCAACCCAAA
20061121 TTAAT TTAAT TTAAT TTAAT TTCAAAT TTAATT TTAAT TTA
1 TTAAT TTAAT TTAAT TTAAT TT--AAT TTAA-T TTAAT TTA
20061162 GGATGAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 23 0.70
6 5 0.15
7 5 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:20098931 original size:24 final size:23
Alignment explanation
Indices: 20098900--20098964 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
20098890 CAACAAAAAT
* *
20098900 TTCTTCCTTCTCTCCTTCTTTTCC
1 TTCTTCCTTCTCTCCTCCTTCT-C
*
20098924 TTCTTCCTTTTCCTCCTCCTTCTC
1 TTCTTCCTTCT-CTCCTCCTTCTC
*
20098948 TTCTTCTTTCTCTCCTC
1 TTCTTCCTTCTCTCCTC
20098965 AATACCCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 6 0.17
24 20 0.57
25 9 0.26
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (23 bp):
TTCTTCCTTCTCTCCTCCTTCTC
Found at i:20101947 original size:17 final size:18
Alignment explanation
Indices: 20101926--20101967 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
20101916 TATAAGAATG
20101926 GAAATGCAACT-AC-AAT
1 GAAATGCAACTAACAAAT
20101942 GCAAATGC-ACTAACAAAT
1 G-AAATGCAACTAACAAAT
20101960 GAAATGCA
1 GAAATGCA
20101968 GTGACAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (18 bp):
GAAATGCAACTAACAAAT
Found at i:20114078 original size:21 final size:22
Alignment explanation
Indices: 20114036--20114078 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
20114026 CATTTTTCTG
*
20114036 CTTTTCTCTTCTTCTTTGTTTT
1 CTTTTCTCTTCTTCTTTATTTT
20114058 CTTTT-TCTTCTT-TTCTATTTT
1 CTTTTCTCTTCTTCTT-TATTTT
20114079 TGTACGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 12 0.63
22 5 0.26
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (22 bp):
CTTTTCTCTTCTTCTTTATTTT
Found at i:20121374 original size:18 final size:18
Alignment explanation
Indices: 20121343--20121382 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20121333 TTATATGAAT
*
20121343 GCATTTGATTATGTGATC
1 GCATTTGATCATGTGATC
*
20121361 GCATTTGGTCATGTGATC
1 GCATTTGATCATGTGATC
20121379 GCAT
1 GCAT
20121383 ATTATCTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (18 bp):
GCATTTGATCATGTGATC
Found at i:20125448 original size:13 final size:14
Alignment explanation
Indices: 20125430--20125459 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20125420 GTCAGCATAA
20125430 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
20125443 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
20125457 TCA
1 TCA
20125460 ATATACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:20129939 original size:20 final size:21
Alignment explanation
Indices: 20129914--20129952 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
20129904 GCAAGTAATT
20129914 TGAAACAAA-AAAAGTAAAAG
1 TGAAACAAATAAAAGTAAAAG
20129934 TGAAACAAATAAAAGTAAA
1 TGAAACAAATAAAAGTAAA
20129953 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.69, C:0.05, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAATAAAAGTAAAAG
Found at i:20135763 original size:13 final size:14
Alignment explanation
Indices: 20135745--20135774 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20135735 GTCAGCGTAA
20135745 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
20135758 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
20135772 TCA
1 TCA
20135775 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:20136675 original size:76 final size:75
Alignment explanation
Indices: 20136550--20136701 Score: 259
Period size: 76 Copynumber: 2.0 Consensus size: 75
20136540 AGCATCTGGC
* *
20136550 ACTCCTCGTCAAGAGTTGCTGCTCGTTGGCTCAATCAGCTCTCCGGTCTCCAGTAATAAATTCAA
1 ACTCCTCATCAAGAGTTGCTGCTCGTTGGCTCAATCAGCTCTCCGGTCTCCAGCAATAAATTCAA
20136615 AAGAACACAA
66 AAGAACACAA
* *
20136625 ACTCCTCATCAAGAGTTTTCTGCTCGTTGGCTCAATTAGCTCTCCGGTCTCCAGCAATAAATTCA
1 ACTCCTCATCAAGAG-TTGCTGCTCGTTGGCTCAATCAGCTCTCCGGTCTCCAGCAATAAATTCA
20136690 AAAGAACACAA
65 AAAGAACACAA
20136701 A
1 A
20136702 GTAATTTGCA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
75 14 0.19
76 58 0.81
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (75 bp):
ACTCCTCATCAAGAGTTGCTGCTCGTTGGCTCAATCAGCTCTCCGGTCTCCAGCAATAAATTCAA
AAGAACACAA
Found at i:20143620 original size:14 final size:14
Alignment explanation
Indices: 20143578--20143635 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
20143568 TCATAAACCA
20143578 AAATAAAATAAAAAGT
1 AAATAAAAT-AAAA-T
* *
20143594 AAAGAAAACAAAAT
1 AAATAAAATAAAAT
*
20143608 ATGA-AAAATAAAAT
1 A-AATAAAATAAAAT
20143622 AAATAAAATAAAAT
1 AAATAAAATAAAAT
20143636 CGTATCTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.03
14 22 0.63
15 5 0.14
16 7 0.20
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:20149804 original size:20 final size:21
Alignment explanation
Indices: 20149779--20149821 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20149769 TTGAAATACT
*
20149779 TTAGGAACGG-TTTGAGAGAG
1 TTAGGAAAGGATTTGAGAGAG
*
20149799 TTAGGAAAGGATTTTAGAGAG
1 TTAGGAAAGGATTTGAGAGAG
20149820 TT
1 TT
20149822 TAAGTGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (21 bp):
TTAGGAAAGGATTTGAGAGAG
Found at i:20151392 original size:15 final size:15
Alignment explanation
Indices: 20151361--20151408 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
20151351 GGATCTCCTA
20151361 ATCTTCATAGA-ACTC
1 ATCTTCATAGATA-TC
20151376 ATCTTCATAGATATC
1 ATCTTCATAGATATC
* * *
20151391 ATCATCAGAGATGTC
1 ATCTTCATAGATATC
20151406 ATC
1 ATC
20151409 ATCGTAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 28 0.97
16 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (15 bp):
ATCTTCATAGATATC
Found at i:20166839 original size:17 final size:17
Alignment explanation
Indices: 20166806--20166856 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
20166796 CATTGCATTC
20166806 TTACATTTATGTT-TTTTT
1 TTAC-TTTAT-TTCTTTTT
20166824 TTACTTTATTTCTTTTT
1 TTACTTTATTTCTTTTT
* *
20166841 TTA-TCTGTTTCTTTTT
1 TTACTTTATTTCTTTTT
20166857 AGATTCTACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 13 0.43
17 13 0.43
18 4 0.13
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.75
Consensus pattern (17 bp):
TTACTTTATTTCTTTTT
Found at i:20168700 original size:21 final size:21
Alignment explanation
Indices: 20168676--20168729 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20168666 GGAACTTGAG
* *
20168676 GAGAAGAAGGAAAATGAGGAA
1 GAGAAGAAGGAAAAAGAAGAA
*
20168697 GAGAAGAAAGAAAAAGAAGAA
1 GAGAAGAAGGAAAAAGAAGAA
20168718 GA-AGAGAAGGAA
1 GAGA-AGAAGGAA
20168730 GATGTCCCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (21 bp):
GAGAAGAAGGAAAAAGAAGAA
Found at i:20175060 original size:15 final size:15
Alignment explanation
Indices: 20175037--20175076 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
20175027 CCCACTTCAT
*
20175037 AGATATCATCATCAG
1 AGATGTCATCATCAG
*
20175052 AGATGTCATCATCAT
1 AGATGTCATCATCAG
*
20175067 AAATGTCATC
1 AGATGTCATC
20175077 TGAACAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (15 bp):
AGATGTCATCATCAG
Found at i:20185090 original size:24 final size:24
Alignment explanation
Indices: 20185045--20185090 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
20185035 ACGACAAAGT
**
20185045 TTTCTTCTTTCTCATCTTCCTTTC
1 TTTCTTCTTTCTCATCGGCCTTTC
* *
20185069 TTTCTTCTTTTTCTTCGGCCTT
1 TTTCTTCTTTCTCATCGGCCTT
20185091 CTCCTCCACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.02, C:0.30, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTCTTCTTTCTCATCGGCCTTTC
Found at i:20187801 original size:62 final size:63
Alignment explanation
Indices: 20187703--20187823 Score: 192
Period size: 62 Copynumber: 1.9 Consensus size: 63
20187693 ACCATCCGGA
* * *
20187703 CGGTTATTCCCTCACTTTTGGTAAGAGAGTTCTATGCCAACTTAGTGGATTCTGAACAGTAGC
1 CGGTTATTCCCTCACTTTTGGTAAGAGAATTCTATGCCAACTTAGTAGATTCTAAACAGTAGC
20187766 CGGTTATTTCCC-CAC-TTTGGTAAGAGAATTCTATGCCAACTTAGTAGATTCTAAACAG
1 CGGTTA-TTCCCTCACTTTTGGTAAGAGAATTCTATGCCAACTTAGTAGATTCTAAACAG
20187824 GAGCTTGTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
62 40 0.74
63 9 0.17
64 5 0.09
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (63 bp):
CGGTTATTCCCTCACTTTTGGTAAGAGAATTCTATGCCAACTTAGTAGATTCTAAACAGTAGC
Found at i:20189412 original size:18 final size:18
Alignment explanation
Indices: 20189377--20189412 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20189367 ATGCATAGCA
* *
20189377 TTTAGTTGTCATTGCATT
1 TTTAGTTGTCACTACATT
20189395 TTTAGTTGTCACTACATT
1 TTTAGTTGTCACTACATT
20189413 GTATGTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (18 bp):
TTTAGTTGTCACTACATT
Found at i:20201519 original size:16 final size:17
Alignment explanation
Indices: 20201498--20201542 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
20201488 GCGATCGCAG
20201498 AACCAGATGCAGTC-AT
1 AACCAGATGCAGTCTAT
20201514 AACCAGATGCAGTCTTAT
1 AACCAGATGCAGTC-TAT
*
20201532 AATCAGATGCA
1 AACCAGATGCA
20201543 ACCACAAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 14 0.54
18 12 0.46
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (17 bp):
AACCAGATGCAGTCTAT
Found at i:20205907 original size:24 final size:23
Alignment explanation
Indices: 20205872--20205923 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
20205862 TGTCATTGTA
*
20205872 ATTTTCTGTT-AATTTTTGTCTTTT
1 ATTTTCTGTTAAATTGTT-TC-TTT
20205896 ATTTTACT-TTAAATTGTTTCTTT
1 ATTTT-CTGTTAAATTGTTTCTTT
20205919 ATTTT
1 ATTTT
20205924 TTGTAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.32
24 9 0.36
25 8 0.32
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (23 bp):
ATTTTCTGTTAAATTGTTTCTTT
Found at i:20208036 original size:17 final size:17
Alignment explanation
Indices: 20208014--20208051 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20208004 TTTTCTCTAG
*
20208014 TTGTCATTACATTTTAA
1 TTGTCACTACATTTTAA
*
20208031 TTGTCACTGCATTTTAA
1 TTGTCACTACATTTTAA
20208048 TTGT
1 TTGT
20208052 TTTCACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53
Consensus pattern (17 bp):
TTGTCACTACATTTTAA
Found at i:20216549 original size:32 final size:33
Alignment explanation
Indices: 20216491--20216554 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
20216481 GCATGACTAT
* *
20216491 TAGATACATCTTCTCTAAATACATTCATTAAAC
1 TAGATACATATACTCTAAATACATTCATTAAAC
20216524 TAGATACATATACTCT-AATACATTCATTAAA
1 TAGATACATATACTCTAAATACATTCATTAAA
20216555 TATAAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (33 bp):
TAGATACATATACTCTAAATACATTCATTAAAC
Found at i:20218013 original size:19 final size:19
Alignment explanation
Indices: 20217989--20218026 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20217979 CAAATTTGAG
20217989 AGATAATCTCTCAATAAAC
1 AGATAATCTCTCAATAAAC
20218008 AGATAATCTCTCAATAAAC
1 AGATAATCTCTCAATAAAC
20218027 TCTATTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (19 bp):
AGATAATCTCTCAATAAAC
Found at i:20229012 original size:37 final size:37
Alignment explanation
Indices: 20228962--20229139 Score: 234
Period size: 37 Copynumber: 4.8 Consensus size: 37
20228952 CTAAGAATTC
*
20228962 GGGCTATGTGCCTAGCAGGATTTGTGCC-AGTGTATTA
1 GGGCTATGTGCCTAGCAGGCTTTGTGCCGA-TGTATTA
20228999 GGGCTATGTGCCTAGCAGGCTTTGTGCCGATGTATTCA
1 GGGCTATGTGCCTAGCAGGCTTTGTGCCGATGTATT-A
* * * *
20229037 -GGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTGTTC
1 GGGCTATGTGCCTAGCAGGCTTTGTGCCGATGTATTA
* * *
20229073 GGACTATGTGCCTAGCAGGCTTCGTGCCGATGTATTC
1 GGGCTATGTGCCTAGCAGGCTTTGTGCCGATGTATTA
*
20229110 GGGCTTTGTGCCTAGCAGGCCTTTGTGCCG
1 GGGCTATGTGCCTAGCAGG-CTTTGTGCCG
20229140 GTGATCCAAG
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
37 115 0.91
38 11 0.09
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.31
Consensus pattern (37 bp):
GGGCTATGTGCCTAGCAGGCTTTGTGCCGATGTATTA
Found at i:20229024 original size:16 final size:16
Alignment explanation
Indices: 20229000--20229056 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
20228990 AGTGTATTAG
20229000 GGCTATGTGCCTAGCA
1 GGCTATGTGCCTAGCA
* *
20229016 GGCTTTGTGCCGATGTATTCA
1 GGCTATGTGCC----TA-GCA
20229037 GGCTATGTGCCTAGCA
1 GGCTATGTGCCTAGCA
20229053 GGCT
1 GGCT
20229057 TCGTGCCGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 16 0.50
17 2 0.06
20 2 0.06
21 12 0.38
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.30
Consensus pattern (16 bp):
GGCTATGTGCCTAGCA
Found at i:20229084 original size:74 final size:74
Alignment explanation
Indices: 20228958--20229142 Score: 280
Period size: 74 Copynumber: 2.5 Consensus size: 74
20228948 GCATCTAAGA
* * * *
20228958 ATTCGGGCTATGTGCCTAGCAGGATTTGTGCCAGTGTATTAGGGCTATGTGCCTAGCAGGCTTTG
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGTATTAGGACTATGTGCCTAGCAGGCTTCG
20229023 TGCCGATGT
66 TGCCGATGT
* * * *
20229032 ATTCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGTGTTCGGACTATGTGCCTAGCAGGCTTCG
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGTATTAGGACTATGTGCCTAGCAGGCTTCG
20229097 TGCCGATGT
66 TGCCGATGT
*
20229106 ATTCGGGCTTTGTGCCTAGCAGGCCTTTGTGCCGGTG
1 ATTCGGGCTATGTGCCTAGCAGG-CTTTGTGCCGGTG
20229143 ATCCAAGAAG
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 87 0.88
75 12 0.12
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.31
Consensus pattern (74 bp):
ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGTATTAGGACTATGTGCCTAGCAGGCTTCG
TGCCGATGT
Found at i:20232618 original size:3 final size:3
Alignment explanation
Indices: 20232610--20232651 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
20232600 GGCTCCATCT
20232610 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
20232652 GTTGAATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:20232899 original size:22 final size:22
Alignment explanation
Indices: 20232869--20232925 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
20232859 AACAACTTCC
*
20232869 CAGCAAGTCCCATGTTAAGAAT
1 CAGCGAGTCCCATGTTAAGAAT
20232891 CAGCGAGTCCCATGTTAAGAAT
1 CAGCGAGTCCCATGTTAAGAAT
20232913 CAGCGAGTCCCAT
1 CAGCGAGTCCCAT
20232926 TTAGCTATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (22 bp):
CAGCGAGTCCCATGTTAAGAAT
Found at i:20239633 original size:27 final size:27
Alignment explanation
Indices: 20239592--20239675 Score: 150
Period size: 27 Copynumber: 3.1 Consensus size: 27
20239582 ACAAGATTTT
*
20239592 TCTAAACCCGAACCAATAGAAAACTAC
1 TCTAAACCCGGACCAATAGAAAACTAC
20239619 TCTAAACCCGGACCAATAGAAAACTAC
1 TCTAAACCCGGACCAATAGAAAACTAC
*
20239646 TCTAAACCCAGACCAATAGAAAACTAC
1 TCTAAACCCGGACCAATAGAAAACTAC
20239673 TCT
1 TCT
20239676 TGACCAACCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.45, C:0.30, G:0.08, T:0.17
Consensus pattern (27 bp):
TCTAAACCCGGACCAATAGAAAACTAC
Found at i:20240911 original size:16 final size:16
Alignment explanation
Indices: 20240890--20240921 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20240880 TTAAAAATAA
20240890 TATTATTTTTATTTTT
1 TATTATTTTTATTTTT
20240906 TATTATTTTTATTTTT
1 TATTATTTTTATTTTT
20240922 AAATTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TATTATTTTTATTTTT
Found at i:20241054 original size:17 final size:17
Alignment explanation
Indices: 20241024--20241063 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
20241014 AAATACAAAC
20241024 CTTTT-TTTTTAATT-T
1 CTTTTATTTTTAATTAT
20241039 CTTTTATTTTTGAATTAT
1 CTTTTATTTTT-AATTAT
20241057 -TTTTATT
1 CTTTTATT
20241064 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 11 0.50
18 1 0.05
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (17 bp):
CTTTTATTTTTAATTAT
Found at i:20244110 original size:18 final size:19
Alignment explanation
Indices: 20244061--20244111 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
20244051 GAAATTAATT
20244061 TAAATTTAAATAAAATATAA
1 TAAATTTAAAT-AAATATAA
* * *
20244081 GATATTTTAATAAAT-TAA
1 TAAATTTAAATAAATATAA
20244099 TAAATTTAAATAA
1 TAAATTTAAATAA
20244112 TGAAGAGCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 13 0.52
19 4 0.16
20 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAATTTAAATAAATATAA
Found at i:20253412 original size:45 final size:44
Alignment explanation
Indices: 20253316--20253410 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
20253306 GAATGAGGTT
* *
20253316 AAAAAAAGGGTCAAGATAAAAACTCGCAAAGGGCATCTTAAAAC
1 AAAAAAAGGGTCAAGATAAAAACCCGCAAAAGGCATCTTAAAAC
* * * *
20253360 AAAAAAAGGGTCGAGATGAAAACCCGCAAAAGGCATCTTGAAAT
1 AAAAAAAGGGTCAAGATAAAAACCCGCAAAAGGCATCTTAAAAC
20253404 AAAAAAA
1 AAAAAAA
20253411 AGAAAAAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.54, C:0.15, G:0.19, T:0.13
Consensus pattern (44 bp):
AAAAAAAGGGTCAAGATAAAAACCCGCAAAAGGCATCTTAAAAC
Found at i:20255680 original size:50 final size:50
Alignment explanation
Indices: 20255584--20255798 Score: 218
Period size: 50 Copynumber: 4.3 Consensus size: 50
20255574 TTTATCTCTT
* * * * * * *
20255584 TGAAATTGCAGTAGAGCAAGATTAGGCTACAAAACCAAGTCCTATACCCC
1 TGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCTTATACCCC
* * *
20255634 TGAAGTTGCAGTGGAGCAAGATGAAGCTACGACATCAAATCTTATACCCT
1 TGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCTTATACCCC
** *
20255684 TGAAGTTGCAGTGG-GTTAGATTGAAGCTACAAAATCAAATCTTAT-CTCCT
1 TGAAGTTGCAGTGGAGCAAGA-TGAAGCTACAAAATCAAATCTTATAC-CCC
* * * * * * *
20255734 TGAAGATGCAATGGAGCAGGATGAAGTTACGACATCAAATCTTATATCCC
1 TGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCTTATACCCC
20255784 TGAAGTTGCAGTGGA
1 TGAAGTTGCAGTGGA
20255799 TCAGATTAAA
Statistics
Matches: 135, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
49 5 0.04
50 127 0.94
51 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (50 bp):
TGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCTTATACCCC
Found at i:20255713 original size:100 final size:100
Alignment explanation
Indices: 20255609--20255846 Score: 318
Period size: 100 Copynumber: 2.4 Consensus size: 100
20255599 GCAAGATTAG
*
20255609 GCTACAAAACCAAGTCCTATAC-CCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACATCAAA
1 GCTACAAAACCAAGTCCTAT-CTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACATCAAA
* * *
20255673 TCTTATA-CCCTTGAAGTTGCAGTGGGTTAGATTGAA
65 TCTTATATCCC-TGAAGTTGCAGTGGATCAGATTAAA
* * * * * * *
20255709 GCTACAAAATCAAATCTTATCTCCTTGAAGATGCAATGGAGCAGGATGAAGTTACGACATCAAAT
1 GCTACAAAACCAAGTCCTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACATCAAAT
20255774 CTTATATCCCTGAAGTTGCAGTGGATCAGATTAAA
66 CTTATATCCCTGAAGTTGCAGTGGATCAGATTAAA
* * *
20255809 ACTACATAAGCAAGTCCTATCTCCTTGAAGTTGCAGTG
1 GCTACAAAACCAAGTCCTATCTCCTTGAAGTTGCAGTG
20255847 AAGTGGACAA
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
99 1 0.01
100 114 0.97
101 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (100 bp):
GCTACAAAACCAAGTCCTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACATCAAAT
CTTATATCCCTGAAGTTGCAGTGGATCAGATTAAA
Found at i:20257889 original size:19 final size:20
Alignment explanation
Indices: 20257862--20257899 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20257852 TTTATCATGA
20257862 TTGTAATTATT-TTTTTTAT
1 TTGTAATTATTATTTTTTAT
*
20257881 TTGTTATTATTATTTTTTA
1 TTGTAATTATTATTTTTTA
20257900 GCATCATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTGTAATTATTATTTTTTAT
Found at i:20259446 original size:87 final size:86
Alignment explanation
Indices: 20259353--20259586 Score: 241
Period size: 86 Copynumber: 2.7 Consensus size: 86
20259343 AACTTTAAAA
*
20259353 AAAAAAACAATTAAGTTCCTGTTTTTCTTTTT-CACTAAATTGAGTACTTGAACTATT-AAAATG
1 AAAAAAACAATTAAGTCCCTG----TCTTTTTGCACTAAATTGAGTACTTGAACT-TTCAAAATG
* **
20259416 CATCAAAAAAATTCTC-AATTTTTTC
61 CATAAAAAAAACCCTCAAATTTTTTC
* * *
20259441 AAAAAAAGCAATTAAGTCCCTGTCTTTTTGCACTTAATTGGGTGCTTGAACTTTCAAAATGCATA
1 AAAAAAA-CAATTAAGTCCCTGTCTTTTTGCACTAAATTGAGTACTTGAACTTTCAAAATGCATA
20259506 AAAAAAACCCTCAAATTTTTTC
65 AAAAAAACCCTCAAATTTTTTC
* * * * *
20259528 AAAAAAATAATTAAG-CCTCT-T-TTTTT-TACTCAATTGGGTACTTGAACTGTC-AAATGCAT
1 AAAAAAACAATTAAGTCC-CTGTCTTTTTGCACTAAATTGAGTACTTGAACTTTCAAAATGCAT
20259587 TAGAAAAGCC
Statistics
Matches: 129, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
82 8 0.06
83 21 0.16
84 5 0.04
85 12 0.09
86 47 0.36
87 16 0.12
88 7 0.05
89 13 0.10
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (86 bp):
AAAAAAACAATTAAGTCCCTGTCTTTTTGCACTAAATTGAGTACTTGAACTTTCAAAATGCATAA
AAAAAACCCTCAAATTTTTTC
Found at i:20259500 original size:86 final size:84
Alignment explanation
Indices: 20259377--20259586 Score: 250
Period size: 86 Copynumber: 2.5 Consensus size: 84
20259367 GTTCCTGTTT
* * **
20259377 TTCTTTTTCACTAAATTGAGTACTTGAACTATT-AAAATGCATCAAAAAAATTCTC-AATTTTTT
1 TTCTTTTTCACTAAATTGGGTACTTGAACT-TTCAAAATGCATAAAAAAAACCCTCAAATTTTTT
20259440 CAAAAAAAGCAATTAAGTCC-C
65 CAAAAAAA-CAATTAAG-CCTC
* *
20259461 TGTCTTTTTGCACTTAATTGGGTGCTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAATTTTT
1 T-TCTTTTT-CACTAAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAATTTTT
*
20259526 TCAAAAAAATAATTAAGCCTC
64 TCAAAAAAACAATTAAGCCTC
* * *
20259547 TT-TTTTTTACTCAATTGGGTACTTGAACTGTC-AAATGCAT
1 TTCTTTTTCACTAAATTGGGTACTTGAACTTTCAAAATGCAT
20259587 TAGAAAAGCC
Statistics
Matches: 110, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
82 8 0.07
83 21 0.19
84 6 0.05
85 12 0.11
86 47 0.43
87 16 0.15
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (84 bp):
TTCTTTTTCACTAAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAATTTTTTC
AAAAAAACAATTAAGCCTC
Done.