Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 13 of 129
Found at i:1996019 original size:21 final size:23
Alignment explanation
Indices: 1995976--1996024 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
1995966 AAAAAAAAAA
1995976 AAATCAAACGAAAATAAATCAGAT
1 AAATCAAAC-AAAATAAATCAGAT
*
1996000 AAATCAAA-AAAATTAA-CAGAT
1 AAATCAAACAAAATAAATCAGAT
1996021 AAAT
1 AAAT
1996025 TAAGATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 7 0.29
24 8 0.33
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.18
Consensus pattern (23 bp):
AAATCAAACAAAATAAATCAGAT
Found at i:1996192 original size:5 final size:5
Alignment explanation
Indices: 1996167--1996241 Score: 73
Period size: 5 Copynumber: 14.4 Consensus size: 5
1996157 ATATACATAT
* *
1996167 ATAAA ATAATA ATAAT A-AAA ATAAA ATAAA ATAAA ATGTAAA ATACA
1 ATAAA ATAA-A ATAAA ATAAA ATAAA ATAAA ATAAA A--TAAA ATAAA
1996214 A-AAA ATAAA ATAAAA ATAAAA ATAAA AT
1 ATAAA ATAAA AT-AAA AT-AAA ATAAA AT
1996242 GAAGAAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
4 6 0.10
5 33 0.55
6 16 0.27
7 5 0.08
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:1996198 original size:42 final size:41
Alignment explanation
Indices: 1996129--1996241 Score: 110
Period size: 43 Copynumber: 2.8 Consensus size: 41
1996119 ATTACCTAAG
* *
1996129 ATAAAAAATAATAAT-AAAA-GAAA-AAAAT-ATATACATAT
1 ATAAAAAATAATAATAAAAATAAAATAAAATAATATA-AAAT
*
1996167 ATAAAATAATAATAATAAAAATAAAATAAAATAAAATGTAAAAT
1 ATAAAA-AATAATAATAAAAATAAAATAAAAT--AATATAAAAT
*
1996211 ACAAAAAATAA-AATAAAAATAAAAATAAAAT
1 ATAAAAAATAATAATAAAAAT-AAAATAAAAT
1996242 GAAGAAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
38 6 0.10
39 9 0.14
40 4 0.06
41 3 0.05
42 14 0.22
43 15 0.24
44 8 0.13
45 4 0.06
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (41 bp):
ATAAAAAATAATAATAAAAATAAAATAAAATAATATAAAAT
Found at i:1996209 original size:37 final size:37
Alignment explanation
Indices: 1996133--1996242 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 37
1996123 CCTAAGATAA
* * *
1996133 AAAATAATAATAA-AAGAAA-AAAAT-ATATACATATAT
1 AAAATAATAATAATAA-AAATAAAATAAAATA-AAATGT
1996169 AAAATAATAATAATAAAAATAAAATAAAATAAAATGT
1 AAAATAATAATAATAAAAATAAAATAAAATAAAATGT
*
1996206 AAAATACA-AAAAAT-AAAATAAAAATAAAAATAAAATG
1 AAAATA-ATAATAATAAAAAT-AAAAT-AAAATAAAATG
1996243 AAGAAAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
36 21 0.33
37 27 0.42
38 16 0.25
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (37 bp):
AAAATAATAATAATAAAAATAAAATAAAATAAAATGT
Found at i:1996229 original size:6 final size:6
Alignment explanation
Indices: 1996174--1996240 Score: 59
Period size: 6 Copynumber: 11.2 Consensus size: 6
1996164 TATATAAAAT
* * *
1996174 AATAAT AATAAA AAT-AA AAT-AA AAT-AA AATGTAA AATACAA AAAATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AAT-AAA AATA-AA AATA-AA
1996222 AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA A
1996241 TGAAGAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
5 15 0.28
6 23 0.43
7 15 0.28
ACGTcount: A:0.78, C:0.01, G:0.01, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:1996252 original size:12 final size:10
Alignment explanation
Indices: 1996169--1996252 Score: 53
Period size: 11 Copynumber: 7.7 Consensus size: 10
1996159 ATACATATAT
*
1996169 AAAATAATAA
1 AAAAAAATAA
1996179 TAATAAAAATAA
1 -AA-AAAAATAA
*
1996191 AATAAAATAA
1 AAAAAAATAA
*
1996201 AATGTAAAAT-A
1 AA--AAAAATAA
*
1996212 CAAAAAATAA
1 AAAAAAATAA
1996222 AATAAAAATAA
1 AA-AAAAATAA
1996233 AAATAAAATGAA
1 AAA-AAAAT-AA
1996245 GAAAAAAA
1 -AAAAAAA
1996253 AATATAGACT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
9 5 0.08
10 12 0.20
11 21 0.35
12 19 0.32
13 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1996255 original size:31 final size:30
Alignment explanation
Indices: 1996132--1996256 Score: 112
Period size: 31 Copynumber: 4.0 Consensus size: 30
1996122 ACCTAAGATA
* * *
1996132 AAAAATAATAATAAAAGAAAAAAAT-ATAT
1 AAAAATAAAAATAAAATAAAAAAATAAAAT
* *
1996161 ACATATATAAAATAATAATAATAAAAATAAAAT
1 AAAAATA-AAAATAA-AATAA-AAAAATAAAAT
*
1996194 -AAAATAAAATGTAAAATACAAAAAATAAAAT
1 AAAAATAAAA-ATAAAATA-AAAAAATAAAAT
1996225 AAAAATAAAAATAAAATGAAGAAAAA-AAAAT
1 AAAAATAAAAATAAAAT-AA-AAAAATAAAAT
1996256 A
1 A
1996257 TAGACTTACC
Statistics
Matches: 78, Mismatches: 9, Indels: 16
0.76 0.09 0.16
Matches are distributed among these distances:
29 5 0.06
30 6 0.08
31 35 0.45
32 29 0.37
33 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (30 bp):
AAAAATAAAAATAAAATAAAAAAATAAAAT
Found at i:2000700 original size:98 final size:98
Alignment explanation
Indices: 2000531--2000727 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
2000521 AAATGGTTAT
* * * * *
2000531 TGACAATCCTGTTCTTGAACTTAGTCAATGTGGATAGACTTTACTTGGAAGAGTATGTAGTATTT
1 TGACAATCCTGTTCTCGAACTCAGTCAATGTGGATAAACTTTACTTGAAAAAGTATGTAGTATTT
*
2000596 GATAAAGAAGAAAATGATCGGAAACTTTTATTG
66 GATAAAGAAGAAAATGATCGAAAACTTTTATTG
*
2000629 TGACAATCCTGTTCTCGAACTCAGTCAATGTGGATAAACTTTGCTTGAAAAAGTATGTAGTATTT
1 TGACAATCCTGTTCTCGAACTCAGTCAATGTGGATAAACTTTACTTGAAAAAGTATGTAGTATTT
2000694 GATAAAGAAGAAAATGATCGAAAACTTTTATTG
66 GATAAAGAAGAAAATGATCGAAAACTTTTATTG
2000727 T
1 T
2000728 AATAACTTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (98 bp):
TGACAATCCTGTTCTCGAACTCAGTCAATGTGGATAAACTTTACTTGAAAAAGTATGTAGTATTT
GATAAAGAAGAAAATGATCGAAAACTTTTATTG
Found at i:2001279 original size:3 final size:3
Alignment explanation
Indices: 2001271--2001444 Score: 71
Period size: 3 Copynumber: 55.3 Consensus size: 3
2001261 TTTTATCCTG
* *
2001271 TAT TAT TAT TAT TAT TTT TTT GTAT T-T TAT GTAT T-T TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TA-T TAT
*
2001317 TAT TAT TAT TAT TAT GTAT TAA TA- TAT GTA- TAT CT-T TATT TATT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT -TAT TA-T TA-T
* *
2001361 TATT TATT TACT T-T T-T TGT TAA TAT T-T ATAT GTAT T-T TAT TCAT
1 TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT T-AT
2001405 ATAGT TAT ATATT TAT TAT TA- TAT TAT TAT TAT TAT TAT T
1 -TA-T TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2001445 TTTTGTAATA
Statistics
Matches: 141, Mismatches: 8, Indels: 44
0.73 0.04 0.23
Matches are distributed among these distances:
2 18 0.13
3 76 0.54
4 44 0.31
5 3 0.02
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2001345 original size:43 final size:40
Alignment explanation
Indices: 2001273--2001360 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 40
2001263 TTATCCTGTA
* * *
2001273 TTATTATTATTATTTTTTTGTATTTTATGTAT-TTTATTAT
1 TTATTATTATTATTATTATGTATTTTATGTATATCT-TTAT
2001313 TTATTATTATTATTATTATGTATTAATATATGTATATCTTTAT
1 TTATTATTATTATTATTATGTATT--T-TATGTATATCTTTAT
2001356 TTATT
1 TTATT
2001361 TATTTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 22 0.54
42 1 0.02
43 16 0.39
44 2 0.05
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (40 bp):
TTATTATTATTATTATTATGTATTTTATGTATATCTTTAT
Found at i:2002049 original size:20 final size:20
Alignment explanation
Indices: 2002024--2002066 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2002014 GATGAACTTC
* *
2002024 CGACGAAAAAACTCAGATTT
1 CGACGAAAAAACCCAGAATT
*
2002044 CGACGACAAAACCCAGAATT
1 CGACGAAAAAACCCAGAATT
2002064 CGA
1 CGA
2002067 TGAATTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (20 bp):
CGACGAAAAAACCCAGAATT
Found at i:2002689 original size:118 final size:118
Alignment explanation
Indices: 2002567--2002866 Score: 450
Period size: 118 Copynumber: 2.5 Consensus size: 118
2002557 TAAAAAAATC
2002567 AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
1 AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
2002632 AAAGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTA
66 AAAGATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTA
* * *
2002686 AAAAAAAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTTC---
1 AAAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA--TTTTCAAA
* * *
2002747 AAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
62 AAAAAAAGATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTA
2002804 AAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAA-TTTCAAAAAA
1 AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAAATTTTCAAAAAA
2002867 TATTTTTGGG
Statistics
Matches: 163, Mismatches: 9, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
114 4 0.02
117 32 0.20
118 61 0.37
119 58 0.36
120 3 0.02
122 5 0.03
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (118 bp):
AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
AAAGATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTA
Found at i:2002903 original size:58 final size:58
Alignment explanation
Indices: 2002565--2002899 Score: 480
Period size: 57 Copynumber: 5.7 Consensus size: 58
2002555 AATAAAAAAA
*
2002565 TCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 TCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
* **
2002623 TCAAAAAAAAAAGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 TC---AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
* * * * *
2002684 TAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTT
1 TCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA--TTT
2002745 TCAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 TCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
2002802 TCAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAA-TT
1 TCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAAATTT
**
2002859 TC-AAAAAATATTTTTGGGGAAAAGTCAAAAGTATCAATTTT
1 TCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
2002900 TCCTACACAA
Statistics
Matches: 254, Mismatches: 15, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
56 13 0.05
57 75 0.30
58 58 0.23
59 6 0.02
60 32 0.13
61 70 0.28
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
TCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
Found at i:2005620 original size:11 final size:10
Alignment explanation
Indices: 2005606--2005640 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2005596 AAAAGGTCTC
*
2005606 AAAAATGAAA
1 AAAAAAGAAA
2005616 AAAAAAGAAA
1 AAAAAAGAAA
2005626 AGAAAAAGAAA
1 A-AAAAAGAAA
2005637 AAAA
1 AAAA
2005641 TAAATGCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:2007359 original size:42 final size:42
Alignment explanation
Indices: 2007292--2007671 Score: 522
Period size: 42 Copynumber: 9.1 Consensus size: 42
2007282 ATTGTCGATA
*
2007292 AGCAATTTACTTTCT-AAAGTCGTGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
* *
2007333 AGTAATTTACTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
*
2007375 AGCAATTTAC-TTTTCAAAAGTCGTGGTGCCTCTGTTTAGATG
1 AGCAATTTACTTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAGG
* *
2007417 AGCAATTTAC-TTTTCAAAAATCATGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAGG
* *
2007459 AGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAAAGG
1 AGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
*
2007501 AGCAATTTAC-TTTTCAAAGTCATGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
2007542 AGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
* * *
2007583 AGCAATTTAGGTTTCTT-AAAGTCGTTGAGCCTCTGTTTAGAGG
1 AGCAATTTA-CTTT-TTCAAAGTCGTGGTGCCTCTGTTTAGAGG
* * *
2007626 AGCAATTTAGGTTTCTT-AAAGTCGTTGAGCCTCTGTTTAGAGG
1 AGCAATTTA-CTTT-TTCAAAGTCGTGGTGCCTCTGTTTAGAGG
2007669 AGC
1 AGC
2007672 TTTGGTCAAC
Statistics
Matches: 313, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
41 95 0.30
42 140 0.45
43 76 0.24
44 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (42 bp):
AGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGG
Found at i:2007914 original size:12 final size:13
Alignment explanation
Indices: 2007895--2007955 Score: 58
Period size: 12 Copynumber: 5.0 Consensus size: 13
2007885 TTTTCTTTTG
2007895 TATT-TTATGTAT
1 TATTATTATGTAT
*
2007907 T-TTATTATTTAT
1 TATTATTATGTAT
* *
2007919 TAATATTA-ATAT
1 TATTATTATGTAT
2007931 TATTATTATGTAT
1 TATTATTATGTAT
*
2007944 TAATA-TATGTAT
1 TATTATTATGTAT
2007956 ATCTTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
11 2 0.05
12 26 0.65
13 12 0.30
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (13 bp):
TATTATTATGTAT
Found at i:2008003 original size:21 final size:19
Alignment explanation
Indices: 2007961--2008034 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 19
2007951 TGTATATCTT
*
2007961 TATTTATTTATTTTGTTAA
1 TATTTATTTATTTTATTAA
2007980 TATTTATATGTATTTTATTTATA
1 TATTTAT-T-TATTTTA-TTA-A
* * *
2008003 TAGTTATATA-TTTATTAT
1 TATTTATTTATTTTATTAA
2008021 TATATTATTT-TTTT
1 TAT-TTATTTATTTT
2008035 TTTGTAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
18 2 0.05
19 18 0.42
20 5 0.12
21 8 0.19
22 3 0.07
23 7 0.16
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (19 bp):
TATTTATTTATTTTATTAA
Found at i:2008634 original size:20 final size:20
Alignment explanation
Indices: 2008609--2008648 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2008599 TTCGACGAAC
2008609 TTCCGACGAAAAAACCCAGA
1 TTCCGACGAAAAAACCCAGA
* *
2008629 TTCCGACGATAAAACTCAGA
1 TTCCGACGAAAAAACCCAGA
2008649 ATCTGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.15
Consensus pattern (20 bp):
TTCCGACGAAAAAACCCAGA
Found at i:2009087 original size:21 final size:22
Alignment explanation
Indices: 2009056--2009103 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
2009046 CTTTTTTATC
2009056 TTTATCTTATTTTAATTTTTGT
1 TTTATCTTATTTTAATTTTTGT
* *
2009078 TTTA-CTTATTTTTATTTTTTT
1 TTTATCTTATTTTAATTTTTGT
2009099 TTTAT
1 TTTAT
2009104 TTTCACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTATCTTATTTTAATTTTTGT
Found at i:2009118 original size:22 final size:23
Alignment explanation
Indices: 2009087--2009129 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2009077 TTTTACTTAT
* *
2009087 TTTTATTTTTTTTTTATTTTCAC
1 TTTTATTTTTGTTCTATTTTCAC
2009110 TTTTA-TTTTGTTCTATTTTC
1 TTTTATTTTTGTTCTATTTTC
2009130 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTATTTTTGTTCTATTTTCAC
Found at i:2009250 original size:120 final size:114
Alignment explanation
Indices: 2009124--2009422 Score: 338
Period size: 122 Copynumber: 2.5 Consensus size: 114
2009114 ATTTTGTTCT
* *
2009124 ATTTTCTTTAAATAA-AAAAATCAAAAAAATATTTTTGAAAAAAAATTGAAAGTATCAATTTTCC
1 ATTTTC-TTAAA-AATAAAATTCAAAAAAATATTTTTG--AAAAAGTTGAAAGTATCAATTTTCC
* *
2009188 TTGGAAATCAAAGTTTCAAAAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCA
62 TTGAAAATCAAAGTTTCAAAAAAAAAAATTTTTGGA-G-AAAGTTGAAAGTATCA
2009243 ATTTTTCTTAAAAATAAAATTTCAAAAAAA-AGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTT
1 A-TTTTCTTAAAAATAAAA-TTCAAAAAAATA---TTTTTGA--AAAAGTTGAAAGTATCAATTT
* *** *
2009307 TTCTTGAAAATCAAAGTTTTTCAAAAAAATATTTTTGGAGAAAGTTGAAAGTATCA
59 TCCTTGAAAATCAAAGTTTCAAAAAAAAAAATTTTTGGAGAAAGTTGAAAGTATCA
*
2009363 ATTTTCCTTAAAAATAAATTTTCAAAAAAATA-TTTT--AAAAGTTGAAAGTATCAATTTTCC
1 ATTTT-CTTAAAAATAAA-ATTCAAAAAAATATTTTTGAAAAAGTTGAAAGTATCAATTTTCC
2009423 AAAAAATATT
Statistics
Matches: 158, Mismatches: 11, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
113 23 0.15
117 4 0.03
118 2 0.01
119 15 0.09
120 54 0.34
121 2 0.01
122 58 0.37
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (114 bp):
ATTTTCTTAAAAATAAAATTCAAAAAAATATTTTTGAAAAAGTTGAAAGTATCAATTTTCCTTGA
AAATCAAAGTTTCAAAAAAAAAAATTTTTGGAGAAAGTTGAAAGTATCA
Found at i:2009292 original size:60 final size:58
Alignment explanation
Indices: 2009144--2009422 Score: 288
Period size: 60 Copynumber: 4.7 Consensus size: 58
2009134 AATAAAAAAA
** * ** *
2009144 TCAAAAAAATATTTTTGAAAAAAAATTGAAAGTATCAATTTTCCTTGGAAATCAAAGTT
1 TCAAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTT
* *
2009203 TCAAAAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAATT
1 TC---AAAAAAAA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTT
* *
2009264 TCAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTT
1 TCAAAAAAAA---TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAA--TTT
2009327 TCAAAAAAATATTTTT--GGAGAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTT
1 TCAAAAAAA-ATTTTTGAGGA-AAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTT
2009384 TC-AAAAAAATATTTT----AAAAGTTGAAAGTATCAATTTTCC
1 TCAAAAAAAAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
2009423 AAAAAATATT
Statistics
Matches: 196, Mismatches: 12, Indels: 30
0.82 0.05 0.13
Matches are distributed among these distances:
53 23 0.12
54 1 0.01
55 2 0.01
56 10 0.05
57 5 0.03
58 8 0.04
59 8 0.04
60 69 0.35
61 16 0.08
62 42 0.21
63 11 0.06
64 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.35
Consensus pattern (58 bp):
TCAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTT
Found at i:2009318 original size:122 final size:120
Alignment explanation
Indices: 2009155--2009392 Score: 350
Period size: 122 Copynumber: 2.0 Consensus size: 120
2009145 CAAAAAAATA
*
2009155 TTTTTGAAAAAAAATTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAAAAAAAAATTTT
1 TTTTTGAAAAAAAATTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAAAAATTTT
* *
2009220 TTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAAAGGG
66 TGGA-G-AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAGGG
** * * *** *
2009277 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTTCAAAAAAATATTTT
1 TTTTTGAAAAAAAATTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAAAAATTTT
*
2009342 TGGAGAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
66 TGGAGAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAA
2009393 TATTTTAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
120 44 0.42
121 1 0.01
122 59 0.57
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (120 bp):
TTTTTGAAAAAAAATTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAAAAATTTT
TGGAGAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAGGG
Found at i:2009427 original size:36 final size:38
Alignment explanation
Indices: 2009379--2009461 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 38
2009369 CTTAAAAATA
*
2009379 AATTTTCAAAAAAATA-TTTT-AAAAGTTGAAAGTATC
1 AATTTTCAAAAAAATATTTTTGAAAAGTCGAAAGTATC
*
2009415 AATTTTCCAAAAAATATTTTTGGGGAAAAGTCGAAAGTATC
1 AATTTTCAAAAAAATATTTTT---GAAAAGTCGAAAGTATC
2009456 AATTTT
1 AATTTT
2009462 TCCTACACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 15 0.38
37 4 0.10
41 21 0.52
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (38 bp):
AATTTTCAAAAAAATATTTTTGAAAAGTCGAAAGTATC
Found at i:2011228 original size:25 final size:24
Alignment explanation
Indices: 2011187--2011234 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2011177 AAAATCATAA
2011187 ATATTAAAATTTAAA-TTTAAAAT
1 ATATTAAAATTTAAATTTTAAAAT
2011210 ATATTAAAGATTTTAAATTTTAAAA
1 ATATTAAA-A-TTTAAATTTTAAAA
2011235 ATAATTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
24 1 0.05
25 6 0.27
26 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTAAAATTTAAATTTTAAAAT
Found at i:2011912 original size:14 final size:14
Alignment explanation
Indices: 2011893--2011920 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2011883 GCTTGGTTAG
2011893 ATACAAATCAACAT
1 ATACAAATCAACAT
2011907 ATACAAATCAACAT
1 ATACAAATCAACAT
2011921 GAATTAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
ATACAAATCAACAT
Found at i:2014173 original size:96 final size:95
Alignment explanation
Indices: 2014009--2014196 Score: 272
Period size: 96 Copynumber: 2.0 Consensus size: 95
2013999 AACTACATAA
* * * * *
2014009 AATTATTTTTGTGTTAAGATATGGACATGTTAGGTTCATAATAATAGTTTTTTCTACTATATATC
1 AATTATTTTTGTGTAAAGATAAGGAAATGTTAGGTTCATAATAATAGTTTTTTCCACCATATATC
2014074 ATGGGCATGTTCAAAAGAAATTTCACTGATC
66 ATGGGCATGTTC-AAAGAAATTTCACTGATC
* *
2014105 AATTACTTTTTGTGTAAAGA-AAGGAAAT-TTCAGGTTCATAGTAATAGTTTTTTCCACCATATT
1 AATTA-TTTTTGTGTAAAGATAAGGAAATGTT-AGGTTCATAATAATAGTTTTTTCCACCATATA
2014168 TCATGGGCATGTTCAAAGAAATTTCACTG
64 TCATGGGCATGTTCAAAGAAATTTCACTG
2014197 CAACAGCCTG
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
95 17 0.20
96 53 0.64
97 13 0.16
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (95 bp):
AATTATTTTTGTGTAAAGATAAGGAAATGTTAGGTTCATAATAATAGTTTTTTCCACCATATATC
ATGGGCATGTTCAAAGAAATTTCACTGATC
Found at i:2016641 original size:16 final size:15
Alignment explanation
Indices: 2016616--2016645 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2016606 AAAAAATTGA
2016616 TTTTATATATTTTAT
1 TTTTATATATTTTAT
2016631 TTTTAATATATTTTA
1 TTTT-ATATATTTTA
2016646 AAAATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATATATTTTAT
Found at i:2019988 original size:5 final size:5
Alignment explanation
Indices: 2019967--2020004 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
2019957 ATTTAACATA
*
2019967 AATAT GATAT AA-A- AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
2020005 TTTAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 25 0.86
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:2020000 original size:15 final size:13
Alignment explanation
Indices: 2019966--2020004 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2019956 AATTTAACAT
*
2019966 AAATATGATATAA
1 AAATATAATATAA
2019979 AAATATAATATAA
1 AAATATAATATAA
2019992 TATAATATAATAT
1 -A-AATATAATAT
2020005 TTTAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 1 0.04
15 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:2020049 original size:19 final size:23
Alignment explanation
Indices: 2019984--2020039 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
2019974 TATAAAAATA
2019984 TAAT-ATAA-TATAATATAATATTT
1 TAATAATAATTAT-ATATAA-ATTT
2020007 TAATAATAATTATATATAAA-TT
1 TAATAATAATTATATATAAATTT
2020029 TAATAA-AATTA
1 TAATAATAATTA
2020040 AAAAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.16
22 8 0.26
23 5 0.16
24 10 0.32
25 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATAATAATTATATATAAATTT
Found at i:2021590 original size:29 final size:30
Alignment explanation
Indices: 2021549--2021619 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
2021539 TTTCACACCG
* * *
2021549 TTATATATATAATACT-TTTTTTCATAAAAT
1 TTAT-TATTTAATACTCTTTTCTCACAAAAT
* * *
2021579 TTATTTTTTAATCCTCTTTTCTCACGAAAT
1 TTATTATTTAATACTCTTTTCTCACAAAAT
2021609 TTATTATTTAA
1 TTATTATTTAA
2021620 CCCCTCTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.32, C:0.11, G:0.01, T:0.55
Consensus pattern (30 bp):
TTATTATTTAATACTCTTTTCTCACAAAAT
Found at i:2021626 original size:31 final size:30
Alignment explanation
Indices: 2021575--2021632 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2021565 TTTTTTCATA
* * *
2021575 AAATTTATTTTTTAATCCTCTTTTCTCACG
1 AAATTTATTATTTAACCCTCTTCTCTCACG
2021605 AAATTTATTATTTAACCCCTCTTCTCTC
1 AAATTTATTATTTAA-CCCTCTTCTCTC
2021633 TATACCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50
Consensus pattern (30 bp):
AAATTTATTATTTAACCCTCTTCTCTCACG
Found at i:2026621 original size:52 final size:52
Alignment explanation
Indices: 2026534--2026690 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
2026524 TGGACAAGAA
* * *
2026534 GACTTGCAAAAGAAGAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAA-AGGATTCTTAATAGGCAAGTTT
* *
2026586 GACTTGCAAGAGAAGAATTCTAAAAGGAAATGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAAGGATTCTTAATAGGCAAGTTT
* * * *
2026638 GACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAAT-GAGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAAGGATTCTTAATAG-GCAAGTTT
2026690 G
1 G
2026691 TATGGTTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 88 0.95
53 4 0.04
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAAGGATTCTTAATAGGCAAGTTT
Found at i:2029558 original size:315 final size:312
Alignment explanation
Indices: 2028971--2029600 Score: 1179
Period size: 315 Copynumber: 2.0 Consensus size: 312
2028961 ACCCCACCCG
2028971 CATATTGCACACAGCTCATCACTGCTTAGCATAAATTTCTACGCTGGAATGAAAACAATCAGTAC
1 CATATTGCACACAGCTCATCACTGCTTAGCATAAATTTCTACGCTGGAATGAAAACAATCAGTAC
2029036 CAACACATTTTTCAACCAAATGTAACAAGGAAAGTATTTGCTTATACAAGTCACAAAAACAAAAC
66 CAACACATTTTTCAACCAAATGTAACAAGGAAAGTATTTGCTTATACAAGTCACAAAAACAAAAC
* *
2029101 TCCATTCGAACGAGCCCCAATTGCACCACTACAGCTTACGGTTAACTAAGTCTCACGTGTAGCCT
131 TCCATTCGAACGAGCCCCAATTGCACCACTACAGCTTACAGTTAACTAAGTCTCACGTATAGCCT
*
2029166 TGTTTGTAGCGTCTAAATATGTCCTCAGTTTTGGCATTCCTAAAGGCACAACATCCTATCAAATA
196 TCTTTGTAGCGTCTAAATATGTCCTCAGTTTTGGCATTCCTAAAGGCACAACATCCTATCAAATA
2029231 TACACATATCAAAGCAATAAGAGTTATAAGCAGTATTATGTCAGCTTTTCTC
261 TACACATATCAAAGCAATAAGAGTTATAAGCAGTATTATGTCAGCTTTTCTC
2029283 CATATTGCACACAGCTCATCACTGCTTAGCATAAATTTCTACGCTGGAATGAAAACAATCAGTAC
1 CATATTGCACACAGCTCATCACTGCTTAGCATAAATTTCTACGCTGGAATGAAAACAATCAGTAC
2029348 CAACACATTTTTCAACCAAATGTAACAAGGAAAAGTATTTGCTTATACAAAGTCACAAAAACAAA
66 CAACACATTTTTCAACCAAATGTAACAAGG-AAAGTATTTGCTTATAC-AAGTCACAAAAACAAA
* * *
2029413 ACTCCATTCGAACGAGCCCCAATTGCACCACTACCAGCTTACAGTTAACTGATTCTCAGGTATAG
129 ACTCCATTCGAACGAGCCCCAATTGCACCACTA-CAGCTTACAGTTAACTAAGTCTCACGTATAG
2029478 CCTTCTTTGTAGCGTCTAAATATGTCCTCAGTTTTGGCATTCCTAAAGGCACAACATCCTATCAA
193 CCTTCTTTGTAGCGTCTAAATATGTCCTCAGTTTTGGCATTCCTAAAGGCACAACATCCTATCAA
2029543 ATATACACATATCAAAGCAATAAGAGTTATAAGCAGTATTATGTCAGCTTTTCTC
258 ATATACACATATCAAAGCAATAAGAGTTATAAGCAGTATTATGTCAGCTTTTCTC
2029598 CAT
1 CAT
2029601 TCCTGCTTCA
Statistics
Matches: 309, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
312 95 0.31
313 17 0.06
314 49 0.16
315 148 0.48
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (312 bp):
CATATTGCACACAGCTCATCACTGCTTAGCATAAATTTCTACGCTGGAATGAAAACAATCAGTAC
CAACACATTTTTCAACCAAATGTAACAAGGAAAGTATTTGCTTATACAAGTCACAAAAACAAAAC
TCCATTCGAACGAGCCCCAATTGCACCACTACAGCTTACAGTTAACTAAGTCTCACGTATAGCCT
TCTTTGTAGCGTCTAAATATGTCCTCAGTTTTGGCATTCCTAAAGGCACAACATCCTATCAAATA
TACACATATCAAAGCAATAAGAGTTATAAGCAGTATTATGTCAGCTTTTCTC
Found at i:2034258 original size:18 final size:18
Alignment explanation
Indices: 2034235--2034270 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2034225 ATCTTTATTT
2034235 TTTATTTTT-TATATTATA
1 TTTATTTTTGTAT-TTATA
2034253 TTTATTTTTGTATTTATA
1 TTTATTTTTGTATTTATA
2034271 ATTTCAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTTTGTATTTATA
Found at i:2034449 original size:19 final size:19
Alignment explanation
Indices: 2034415--2034467 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2034405 TATTAATTTT
2034415 AATTAATTTA--AAAT-AA
1 AATTAATTTATTAAATAAA
*
2034431 AATTTATATTATTAAATAAA
1 AATTAAT-TTATTAAATAAA
2034451 AATTAATTTATTAAATA
1 AATTAATTTATTAAATA
2034468 TATAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 6 0.19
17 3 0.10
19 14 0.45
20 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAATTTATTAAATAAA
Found at i:2042424 original size:2 final size:2
Alignment explanation
Indices: 2042401--2042442 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2042391 AGTCATGAAC
* *
2042401 TA TA -A TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2042442 T
1 T
2042443 TTCAACAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2045992 original size:62 final size:62
Alignment explanation
Indices: 2045895--2046019 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
2045885 AACAAAGCTA
2045895 TAAACATCCATCGTTATTCAAAAGGACAGGGACTTCTTTCTTTTATTTGAATTTGCAAAGTT
1 TAAACATCCATCGTTATTCAAAAGGACAGGGACTTCTTTCTTTTATTTGAATTTGCAAAGTT
2045957 TAAACATCCATCGTTATTCAAAAGGACAGGGACTTCTTTCTTTTATTTGAATTTGCAAAGTT
1 TAAACATCCATCGTTATTCAAAAGGACAGGGACTTCTTTCTTTTATTTGAATTTGCAAAGTT
2046019 T
1 T
2046020 CACATAGAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (62 bp):
TAAACATCCATCGTTATTCAAAAGGACAGGGACTTCTTTCTTTTATTTGAATTTGCAAAGTT
Found at i:2047982 original size:76 final size:77
Alignment explanation
Indices: 2047890--2048044 Score: 285
Period size: 76 Copynumber: 2.0 Consensus size: 77
2047880 AAATACAGAG
*
2047890 TGAATTCTGCTTGTGCATACAAACTGGTTTGCAGTATGTATATTATA-ATCTACCAATATTCCAT
1 TGAATTCTGCTTGTGCATACAAACTGGTTTGCAGTATGTATATCATACATCTACCAATATTCCAT
2047954 CTGTTTACATTA
66 CTGTTTACATTA
*
2047966 TGAATTCTGCTTGTGCATACAAACTGGTTTGCAGTATGTATATCATACATCTACCAATATTTCAT
1 TGAATTCTGCTTGTGCATACAAACTGGTTTGCAGTATGTATATCATACATCTACCAATATTCCAT
2048031 CTGTTTACATTA
66 CTGTTTACATTA
2048043 TG
1 TG
2048045 TGAGCAGATG
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
76 46 0.61
77 30 0.39
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (77 bp):
TGAATTCTGCTTGTGCATACAAACTGGTTTGCAGTATGTATATCATACATCTACCAATATTCCAT
CTGTTTACATTA
Found at i:2050436 original size:20 final size:20
Alignment explanation
Indices: 2050411--2050452 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2050401 TATGCCAGTT
2050411 TATTGTAGAAGATCAAAGCC
1 TATTGTAGAAGATCAAAGCC
2050431 TATTGTAGAAGATCAAAGCC
1 TATTGTAGAAGATCAAAGCC
2050451 TA
1 TA
2050453 GCAAGCGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (20 bp):
TATTGTAGAAGATCAAAGCC
Found at i:2053574 original size:24 final size:24
Alignment explanation
Indices: 2053547--2053624 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
2053537 ATTTTTATCC
* *
2053547 TGTATAATTATTATTTTTTTCTTT-
1 TGTAT-ATTATTATTTTATTATTTA
*
2053571 TGTATTTTATGTATTTTATTATTTA
1 TGTATATTAT-TATTTTATTATTTA
2053596 T-TATTATTATTATTATTATTA-TTA
1 TGTA-TATTATTATT-TTATTATTTA
2053620 TGTAT
1 TGTAT
2053625 TAATATATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 4 0.09
24 27 0.60
25 14 0.31
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (24 bp):
TGTATATTATTATTTTATTATTTA
Found at i:2053585 original size:9 final size:8
Alignment explanation
Indices: 2053554--2053762 Score: 67
Period size: 9 Copynumber: 24.2 Consensus size: 8
2053544 TCCTGTATAA
2053554 TTATTATT
1 TTATTATT
* *
2053562 TTTTTCTT
1 TTATTATT
*
2053570 TT-GTATT
1 TTATTATT
2053577 TTATGTATT
1 TTAT-TATT
2053586 TTATTA-T
1 TTATTATT
2053593 TTATTATT
1 TTATTATT
2053601 ATTATTATT
1 -TTATTATT
2053610 ATTATTATT
1 -TTATTATT
2053619 ATGTATTAATAT
1 -T-TATT-AT-T
2053631 ATGTA-TATCT
1 -T-TATTAT-T
2053641 TTATT-TAT
1 TTATTAT-T
2053649 TTATT-TT
1 TTATTATT
*
2053656 GTTAATATT
1 -TTATTATT
2053665 TATATGTATT
1 T-TAT-TATT
2053675 TTATTTATAT
1 TTA-TTAT-T
2053685 AGTTA-TATAT
1 --TTATTAT-T
2053695 TTATTATT
1 TTATTATT
*
2053703 ATATTATT
1 TTATTATT
*
2053711 TT-TTTTT
1 TTATTATT
*
2053718 TGTAATATAT
1 T-TATTAT-T
2053728 TT-TTAGGTT
1 TTATTA--TT
*
2053737 TATCTTATT
1 T-TATTATT
2053746 TTATT-TT
1 TTATTATT
2053753 TTATTATT
1 TTATTATT
2053761 TT
1 TT
2053763 TTAAAATTAT
Statistics
Matches: 160, Mismatches: 16, Indels: 50
0.71 0.07 0.22
Matches are distributed among these distances:
7 25 0.16
8 48 0.30
9 49 0.31
10 23 0.14
11 6 0.04
12 9 0.06
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (8 bp):
TTATTATT
Found at i:2053595 original size:16 final size:16
Alignment explanation
Indices: 2053576--2053711 Score: 79
Period size: 15 Copynumber: 8.2 Consensus size: 16
2053566 TCTTTTGTAT
2053576 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
2053592 TTTATTATTATTATTA
1 TTTATTATTATTATTA
2053608 -TTATTATTATTATGTA
1 TTTATTATTATTAT-TA
* *
2053624 TTAATATATGTATATCTTTA
1 TTTAT-TAT-TAT-T-ATTA
* *
2053644 TTTATTTATTTTGTTAATA
1 TTTA-TTA--TTATTATTA
2053663 TTTA-TATGTATT-TTA
1 TTTATTAT-TATTATTA
2053678 TTTA-TA-TAGTTATATA
1 TTTATTATTA-TTAT-TA
2053694 TTTATTATTA-TATTA
1 TTTATTATTATTATTA
2053709 TTT
1 TTT
2053712 TTTTTTTGTA
Statistics
Matches: 96, Mismatches: 8, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
13 2 0.02
14 2 0.02
15 32 0.33
16 25 0.26
17 7 0.07
18 5 0.05
19 9 0.09
20 9 0.09
21 4 0.04
22 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:2053599 original size:3 final size:3
Alignment explanation
Indices: 2053573--2053626 Score: 67
Period size: 3 Copynumber: 17.7 Consensus size: 3
2053563 TTTTCTTTTG
2053573 TAT T-T TAT GTAT T-T TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
2053618 TAT GTAT TA
1 TAT -TAT TA
2053627 ATATATGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.09
3 33 0.72
4 9 0.20
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2053684 original size:21 final size:19
Alignment explanation
Indices: 2053642--2053715 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 19
2053632 TGTATATCTT
*
2053642 TATTTATTTATTTTGTTAA
1 TATTTATTTATTTTATTAA
2053661 TATTTATATGTATTTTATTTATA
1 TATTTAT-T-TATTTTA-TTA-A
* * *
2053684 TAGTTATATA-TTTATTAT
1 TATTTATTTATTTTATTAA
2053702 TATATTATTT-TTTT
1 TAT-TTATTTATTTT
2053716 TTTGTAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
18 2 0.05
19 18 0.42
20 5 0.12
21 8 0.19
22 3 0.07
23 7 0.16
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (19 bp):
TATTTATTTATTTTATTAA
Found at i:2053711 original size:46 final size:49
Alignment explanation
Indices: 2053599--2053711 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 49
2053589 TTATTTATTA
** *
2053599 TTATTATTATTATTA-TTATTATGTATTAATATATGTATATCTTTATTTAT
1 TTATTATTA-TATTATTTATTATGTATT-ATATATGTATATAGTTATATAT
* * *
2053649 TTATT-TTGTTAATATTTA-TATGTATT-T-TATTTATATAGTTATATAT
1 TTATTATT-ATATTATTTATTATGTATTATATATGTATATAGTTATATAT
2053695 TTATTATTATATTATTT
1 TTATTATTATATTATTT
2053712 TTTTTTTGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
46 27 0.52
47 3 0.06
49 14 0.27
50 8 0.15
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (49 bp):
TTATTATTATATTATTTATTATGTATTATATATGTATATAGTTATATAT
Found at i:2054315 original size:20 final size:20
Alignment explanation
Indices: 2054290--2054329 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2054280 TTCGACGAAC
2054290 TTCCGACGAAAAAACCCAGA
1 TTCCGACGAAAAAACCCAGA
* *
2054310 TTCCGACGATAAAACTCAGA
1 TTCCGACGAAAAAACCCAGA
2054330 ATCTGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.15
Consensus pattern (20 bp):
TTCCGACGAAAAAACCCAGA
Found at i:2054656 original size:23 final size:23
Alignment explanation
Indices: 2054613--2054658 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2054603 AGCCGAGCCG
* *
2054613 TTTCAGATTTTTTTTTCTTTTTT
1 TTTCAGATTTATTTATCTTTTTT
2054636 TTTCAGAATTTATTTAT-TTTTTT
1 TTTCAG-ATTTATTTATCTTTTTT
2054659 ATTTATTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTCAGATTTATTTATCTTTTTT
Found at i:2054846 original size:61 final size:60
Alignment explanation
Indices: 2054781--2055010 Score: 315
Period size: 61 Copynumber: 3.8 Consensus size: 60
2054771 ATAAAAAAAT
* *
2054781 AAAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTC
1 AAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTC
* * *
2054841 AAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAATTTTC
1 -AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTC
**
2054901 -AAAAAACGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAG--TTTC
* *
2054962 AAAAAAAA-ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAA
2055011 AATTAAATTT
Statistics
Matches: 151, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
58 46 0.30
59 3 0.02
60 7 0.05
61 88 0.58
62 7 0.05
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (60 bp):
AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTC
Found at i:2054905 original size:119 final size:118
Alignment explanation
Indices: 2054782--2055010 Score: 354
Period size: 119 Copynumber: 1.9 Consensus size: 118
2054772 TAAAAAAATA
* *
2054782 AAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAG-TTTCAAAA
1 AAAAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTC-AAA
2054845 AAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
64 AAAAA-ATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
* *
2054901 AAAAAACGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTTCAAAA
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAG-TTTTCAAAA
**
2054966 AAAAATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
65 AAAAATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
2055011 AATTAAATTT
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
119 88 0.87
120 9 0.09
121 4 0.04
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (118 bp):
AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTCAAAAA
AAAATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
Found at i:2057747 original size:30 final size:30
Alignment explanation
Indices: 2057713--2057803 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
2057703 GATAAGATAA
2057713 AATAACTTTTATTAAATGGTAATGCACTTT
1 AATAACTTTTATTAAATGGTAATGCACTTT
*
2057743 AATAACTTTTATTAAATTGTAATGCACTTT
1 AATAACTTTTATTAAATGGTAATGCACTTT
*
2057773 AATAACTTTTATTAAATGGCAATGCACTTT
1 AATAACTTTTATTAAATGGTAATGCACTTT
2057803 A
1 A
2057804 CTTTCCAAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (30 bp):
AATAACTTTTATTAAATGGTAATGCACTTT
Found at i:2059702 original size:11 final size:11
Alignment explanation
Indices: 2059688--2059714 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2059678 TAAATCAATT
2059688 TAAAATATTAC
1 TAAAATATTAC
2059699 TAAAATATTAC
1 TAAAATATTAC
2059710 TAAAA
1 TAAAA
2059715 CAATATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATATTAC
Found at i:2062701 original size:2 final size:2
Alignment explanation
Indices: 2062694--2062736 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2062684 ACCACACTCA
2062694 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2062736 T
1 T
2062737 ACCTTTTTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2065937 original size:2 final size:2
Alignment explanation
Indices: 2065930--2065964 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2065920 CTTCAAAGCA
2065930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2065965 AAATTTACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2067969 original size:52 final size:52
Alignment explanation
Indices: 2067883--2068039 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
2067873 TATAACCATA
* * * *
2067883 CAAACTTGCCCATTAAGAATCTCA-CTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATC-CATTTTCTCTTAGAATTCTTCTCCTGCAAGT
* *
2067935 CAAACTTGCCTATTAAGAATCCATTTTCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCATTTTCTCTTAGAATTCTTCTCCTGCAAGT
* **
2067987 CAAACTTACCTATTAAGAATCC-TCTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCAT-TTTCTCTTAGAATTCTTCTCCTGCAAGT
2068039 C
1 C
2068040 TTTTTGTCCA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 3 0.03
52 91 0.97
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCATTTTCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:2069519 original size:2 final size:2
Alignment explanation
Indices: 2069514--2069543 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2069504 AGCGTGTGTG
2069514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2069544 ATGAAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2070392 original size:12 final size:12
Alignment explanation
Indices: 2070375--2070401 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2070365 AATTTGATGC
2070375 ATTTTAAAAATA
1 ATTTTAAAAATA
2070387 ATTTTAAAAATA
1 ATTTTAAAAATA
2070399 ATT
1 ATT
2070402 AAATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTTTAAAAATA
Found at i:2116476 original size:2 final size:2
Alignment explanation
Indices: 2116469--2116502 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2116459 ATTCACGCAA
2116469 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2116503 TCACCCGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2117003 original size:5 final size:5
Alignment explanation
Indices: 2116995--2117020 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2116985 TATAATAACG
2116995 TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA T
2117021 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:2117031 original size:23 final size:24
Alignment explanation
Indices: 2117005--2117078 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 24
2116995 TAATATAATA
2117005 TAATATAATATAATATTA-AAATT
1 TAATATAATATAATATTATAAATT
*
2117028 TAATATAA-ATTATA-TATAAATT
1 TAATATAATATAATATTATAAATT
* *
2117050 TAATAAAAT-TAAAATTATAAATT
1 TAATATAATATAATATTATAAATT
*
2117073 TTATAT
1 TAATAT
2117079 TTTTACAATG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.05
22 20 0.48
23 20 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATAATATAATATTATAAATT
Found at i:2117183 original size:17 final size:17
Alignment explanation
Indices: 2117156--2117194 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2117146 TTATGTAATA
**
2117156 TAAAT-TATTAAATTAT
1 TAAATCTATTAAAAAAT
2117172 TAAATCTATTAAAAAAT
1 TAAATCTATTAAAAAAT
2117189 TAAATC
1 TAAATC
2117195 AAAGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATCTATTAAAAAAT
Found at i:2117559 original size:6 final size:6
Alignment explanation
Indices: 2117541--2117572 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2117531 CCACTACCAG
*
2117541 CCAAAC CCGAAC CCAAAC CCAAAC CCAAAC CC
1 CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CC
2117573 GACCCCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.44, C:0.53, G:0.03, T:0.00
Consensus pattern (6 bp):
CCAAAC
Found at i:2134995 original size:59 final size:61
Alignment explanation
Indices: 2134901--2135019 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 61
2134891 TAGCGACTAT
* * *
2134901 GATTTTAATTTACGGTACGTGCCAAATATTCTC-TTTTTAAAATTCTTATTTTTATTTTAA
1 GATTTTAATTTACGATACATGCCAAATATTATCTTTTTTAAAATTCTTATTTTTATTTTAA
* * *
2134961 GATTTT-ATTTACGATACATGCCAAATATTATCTTTTTTTAAATTCTTGTTTTTTTTTTA
1 GATTTTAATTTACGATACATGCCAAATATTATCTTTTTTAAAATTCTTATTTTTATTTTA
2135020 TCTTTTAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 23 0.44
60 29 0.56
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.55
Consensus pattern (61 bp):
GATTTTAATTTACGATACATGCCAAATATTATCTTTTTTAAAATTCTTATTTTTATTTTAA
Found at i:2142548 original size:2 final size:2
Alignment explanation
Indices: 2142541--2142567 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2142531 AGTTTACATG
2142541 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2142568 CCGCTTACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2146088 original size:61 final size:61
Alignment explanation
Indices: 2145985--2146106 Score: 165
Period size: 63 Copynumber: 2.0 Consensus size: 61
2145975 ATCAAATCTA
* * *
2145985 TTAAAAGTCTTACATTTATAAATTGATAATGTTTAATTTTTATTCATATAAAATAAAATCG
1 TTAAAAGTCTTACATTTATAAATTAATAATATTTAATTTATATTCATATAAAATAAAATCG
* *
2146046 TTAAAAGT-TATACATTGTTATAAGTTAATAATATTTAATTTATATTCATATTAAATAAAAT
1 TTAAAAGTCT-TACA-T-TTATAAATTAATAATATTTAATTTATATTCATATAAAATAAAAT
2146107 ATTTAATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
60 1 0.02
61 12 0.23
62 1 0.02
63 39 0.74
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (61 bp):
TTAAAAGTCTTACATTTATAAATTAATAATATTTAATTTATATTCATATAAAATAAAATCG
Found at i:2148720 original size:181 final size:181
Alignment explanation
Indices: 2148385--2148748 Score: 667
Period size: 181 Copynumber: 2.0 Consensus size: 181
2148375 CAGTATCTAT
2148385 CATGGCAAAAATAGGGGAAAAAAAGAAAAAAAAATGATGCCTTTGAAAGATATTCCATTTGTCTC
1 CATGGCAAAAATAGGGGAAAAAAAGAAAAAAAAATGATGCCTTTGAAAGATATTCCATTTG-CTC
*
2148450 TTATTTCCTTGAGATTCAACCCCTTCTGTCCTGATGGTCTTGTCTTTAAATTTCCTCTTGCTCTT
65 TTATTTCCTTGAGATTCAACCCCTTCTGTCCTGATGGTCTTGTCTTAAAATTTCCTCTTGCTCTT
* *
2148515 CCTGCAGAAATGAAAGGTAACTTTTTAGCCATTGAGCTAGCTGATACTGATG
130 CCTGCAGAAATGAAAAGAAACTTTTTAGCCATTGAGCTAGCTGATACTGATG
*
2148567 CATGGCAAAAATAGGGGAAAAAAGGAAAAAAAAATGATGCCTTTGAAAGATATTCCATTTG-TCT
1 CATGGCAAAAATAGGGGAAAAAAAGAAAAAAAAATGATGCCTTTGAAAGATATTCCATTTGCTCT
2148631 TATTTCCTTGAGATTCAACCCCTTCTGTCCTGATGGTCTTGTCTTAAAAATTTCCTCTTGCTCTT
66 TATTTCCTTGAGATTCAACCCCTTCTGTCCTGATGGTCTTGTCTT-AAAATTTCCTCTTGCTCTT
2148696 CCTGCAGAAATGAAAAGAAACTTTTTAGCCATTGAGCTAGCTGATACTGATG
130 CCTGCAGAAATGAAAAGAAACTTTTTAGCCATTGAGCTAGCTGATACTGATG
2148748 C
1 C
2148749 TTGATACCTA
Statistics
Matches: 177, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
180 48 0.27
181 69 0.39
182 60 0.34
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (181 bp):
CATGGCAAAAATAGGGGAAAAAAAGAAAAAAAAATGATGCCTTTGAAAGATATTCCATTTGCTCT
TATTTCCTTGAGATTCAACCCCTTCTGTCCTGATGGTCTTGTCTTAAAATTTCCTCTTGCTCTTC
CTGCAGAAATGAAAAGAAACTTTTTAGCCATTGAGCTAGCTGATACTGATG
Found at i:2150357 original size:151 final size:152
Alignment explanation
Indices: 2150144--2150419 Score: 387
Period size: 151 Copynumber: 1.8 Consensus size: 152
2150134 AGTGAACGAT
* * *
2150144 ATAAATACTTTTATAAATTTTAAAAAATAACAAATTTACCTTTAAATTTTTAGCATTTTTTATTT
1 ATAAATACTCTTATAAATTTTAAAAAATAACAAATTTACCTTTAAATTTCTAACATTTTTTATTT
* * * ** *
2150209 ATGTATTAGAGATTATTTTTCATTAAATATATAAC-ATTTATT-AGTTAATTATTTAAATTAATC
66 ATGTAATAAAAATTATTTACCATTAAATAGATAACTATTTATTCA-TTAATTATTTAAATTAATC
2150272 TAAAAGTGTTAAAAGTGAATAGC
130 TAAAAGTGTTAAAAGTGAATAGC
*
2150295 ATAAATACTCTTAT-AATTTTAAAAAATAACAAATTTATCTTTAAATTTCTAACATTTATTTATT
1 ATAAATACTCTTATAAATTTTAAAAAATAACAAATTTACCTTTAAATTTCTAACATTT-TTTATT
* * * *
2150359 TATTTAATAAAAATTATTTACCATTAAATAGATAGCTTTTTATTCATTAGTTATTTAAATT
65 TATGTAATAAAAATTATTTACCATTAAATAGATAACTATTTATTCATTAATTATTTAAATT
2150420 GAAATCAATT
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
150 40 0.37
151 47 0.44
152 20 0.19
153 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (152 bp):
ATAAATACTCTTATAAATTTTAAAAAATAACAAATTTACCTTTAAATTTCTAACATTTTTTATTT
ATGTAATAAAAATTATTTACCATTAAATAGATAACTATTTATTCATTAATTATTTAAATTAATCT
AAAAGTGTTAAAAGTGAATAGC
Found at i:2150749 original size:150 final size:154
Alignment explanation
Indices: 2150541--2150843 Score: 438
Period size: 151 Copynumber: 2.0 Consensus size: 154
2150531 TGTGAACTCT
* *
2150541 AAAACTATTAAAAGTGAATGATATAAATACCCTTATAAATTTTTAAAAATAACAAATTTACCTTT
1 AAAACTATTAAAAGTGAATGACATAAATACCCTTATAAATTTTAAAAAATAACAAATTTACCTTT
* * **
2150606 AAATTTCTAGCATTT-TTTGTTTATATATTAAAGATTATTTTTCATTAAATATATAGC-ATTTAT
66 AAATTTCTAGCATTTATTTATTTATATAATAAAGATTATTTGCCATTAAATATATAGCTATTTAT
2150669 T-AGTTAATTATTTAAA-TTAATCC
131 TCA-TTAATTATTTAAATTTAATCC
* *
2150692 AAAAGTATTAAAAGTTAAT-AGCATAAATACCCTTAT-AATTTTAAAAAATAACAAATTTACCTT
1 AAAACTATTAAAAGTGAATGA-CATAAATACCCTTATAAATTTTAAAAAATAACAAATTTACCTT
* * *
2150755 TAAATTTTTAGCATTTATTTATTTATTTAATAAAGATTATTTGCCATTAAATATATAGCTTTTTA
65 TAAATTTCTAGCATTTATTTATTTATATAATAAAGATTATTTGCCATTAAATATATAGCTATTTA
*
2150820 TTCATTAGTTATTTAAATTTAATC
130 TTCATTAATTATTTAAATTTAATC
2150844 AATTAAAAAT
Statistics
Matches: 135, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
150 42 0.31
151 68 0.50
152 18 0.13
153 7 0.05
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (154 bp):
AAAACTATTAAAAGTGAATGACATAAATACCCTTATAAATTTTAAAAAATAACAAATTTACCTTT
AAATTTCTAGCATTTATTTATTTATATAATAAAGATTATTTGCCATTAAATATATAGCTATTTAT
TCATTAATTATTTAAATTTAATCC
Found at i:2153205 original size:22 final size:21
Alignment explanation
Indices: 2153180--2153294 Score: 97
Period size: 22 Copynumber: 5.3 Consensus size: 21
2153170 AATTTAGACA
*
2153180 AAATCAATAATAACTTTATACT
1 AAAT-AATAATAACTTTATAAT
* * *
2153202 AAATTAATGATCACTGTATAAT
1 AAA-TAATAATAACTTTATAAT
* *
2153224 AAATTATAGATAACTTAATAAT
1 AAATAATA-ATAACTTTATAAT
* *
2153246 AAAATAATAATAACTTAATAGT
1 -AAATAATAATAACTTTATAAT
*
2153268 AAATAAAAATAA-TTTAATAAT
1 AAATAATAATAACTTT-ATAAT
2153289 AAATAA
1 AAATAA
2153295 ATGATAAAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 24 0.32
22 41 0.55
23 8 0.11
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (21 bp):
AAATAATAATAACTTTATAAT
Found at i:2153247 original size:11 final size:11
Alignment explanation
Indices: 2153185--2153290 Score: 65
Period size: 11 Copynumber: 9.7 Consensus size: 11
2153175 AGACAAAATC
2153185 AATAATAACTT
1 AATAATAACTT
* * *
2153196 TATACTAAATT
1 AATAATAACTT
* *
2153207 AATGATCACTGT
1 AATAATAACT-T
*
2153219 -ATAATAAATT
1 AATAATAACTT
2153229 -ATAGATAACTT
1 AATA-ATAACTT
**
2153240 AATAATAAAAT
1 AATAATAACTT
2153251 AATAATAACTT
1 AATAATAACTT
* *
2153262 AATAGTAA-AT
1 AATAATAACTT
* *
2153272 AAAAATAATTT
1 AATAATAACTT
2153283 AATAATAA
1 AATAATAA
2153291 ATAAATGATA
Statistics
Matches: 69, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
10 11 0.16
11 54 0.78
12 4 0.06
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (11 bp):
AATAATAACTT
Found at i:2153479 original size:11 final size:11
Alignment explanation
Indices: 2153463--2153519 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
2153453 GGTTAATTAT
2153463 TAATAACTTAA
1 TAATAACTTAA
* *
2153474 TAATAAATCAA
1 TAATAACTTAA
*
2153485 TGATAACTTAA
1 TAATAACTTAA
* *
2153496 TAGTAAATTAA
1 TAATAACTTAA
*
2153507 TGATAACTTAA
1 TAATAACTTAA
2153518 TA
1 TA
2153520 GTAAATAAGA
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (11 bp):
TAATAACTTAA
Found at i:2153490 original size:22 final size:22
Alignment explanation
Indices: 2153408--2153525 Score: 139
Period size: 22 Copynumber: 5.4 Consensus size: 22
2153398 TAACACATAT
*
2153408 TAGTAAATTAAGGATAACTTAA
1 TAGTAAATTAATGATAACTTAA
* *
2153430 TA-AAAAGTAAGTGATAACTTAA
1 TAGTAAATTAA-TGATAACTTAA
* * * *
2153452 TGGTTAATTATTAATAACTTAA
1 TAGTAAATTAATGATAACTTAA
* *
2153474 TAATAAATCAATGATAACTTAA
1 TAGTAAATTAATGATAACTTAA
2153496 TAGTAAATTAATGATAACTTAA
1 TAGTAAATTAATGATAACTTAA
2153518 TAGTAAAT
1 TAGTAAAT
2153526 AAGATTCAGT
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
21 6 0.08
22 67 0.87
23 4 0.05
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (22 bp):
TAGTAAATTAATGATAACTTAA
Found at i:2153904 original size:22 final size:22
Alignment explanation
Indices: 2153855--2153904 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
2153845 CTTAGTAATA
2153855 AATTAA-TGATAATCTAATAGT
1 AATTAATTGATAATCTAATAGT
*
2153876 AGA-TAATTTATAA-CTAAGTAGT
1 A-ATTAATTGATAATCTAA-TAGT
2153898 AATTAAT
1 AATTAAT
2153905 AATTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (22 bp):
AATTAATTGATAATCTAATAGT
Found at i:2154080 original size:44 final size:44
Alignment explanation
Indices: 2154032--2154134 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 44
2154022 AATTTAGTAG
* * *
2154032 TAAATTAGTAATAATATAATAGTCAAA-GCATAATAACTTAATAA
1 TAAATTAATAATAACATAATAGT-AAATGCATAATAACATAATAA
* * * * **
2154076 TAAATCAATTATAACGTAATTGTAAATGCATAATAACATAATTG
1 TAAATTAATAATAACATAATAGTAAATGCATAATAACATAATAA
2154120 TAAATTAATAATAAC
1 TAAATTAATAATAAC
2154135 TTCATAAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
43 3 0.06
44 44 0.94
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (44 bp):
TAAATTAATAATAACATAATAGTAAATGCATAATAACATAATAA
Found at i:2154124 original size:22 final size:22
Alignment explanation
Indices: 2154040--2154134 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 22
2154030 AGTAAATTAG
*
2154040 TAATAATATAATAGTCAAA-GCA
1 TAATAACATAATAGT-AAATGCA
* *
2154062 TAATAACTTAATAATAAAT-CAA
1 TAATAACATAATAGTAAATGC-A
* * *
2154084 TTATAACGTAATTGTAAATGCA
1 TAATAACATAATAGTAAATGCA
* **
2154106 TAATAACATAATTGTAAATTAA
1 TAATAACATAATAGTAAATGCA
2154128 TAATAAC
1 TAATAAC
2154135 TTCATAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.07
22 54 0.92
23 1 0.02
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (22 bp):
TAATAACATAATAGTAAATGCA
Found at i:2154386 original size:22 final size:22
Alignment explanation
Indices: 2154361--2154499 Score: 102
Period size: 22 Copynumber: 6.3 Consensus size: 22
2154351 AGTATAATAG
*
2154361 TAAATTATTAATAATTTAGTTA
1 TAAATTATTGATAATTTAGTTA
* *
2154383 TAAATTATCGATAACTTAG-TA
1 TAAATTATTGATAATTTAGTTA
* * * ** *
2154404 GTAAATCACTAATAACGTA-ATA
1 -TAAATTATTGATAATTTAGTTA
* *
2154426 GTAAAATATTGATAATTTAGTTG
1 -TAAATTATTGATAATTTAGTTA
** * *
2154449 TAAAACACTGATAATTTATTTA
1 TAAATTATTGATAATTTAGTTA
*
2154471 TAAATTAATGATAATTTAGTTA
1 TAAATTATTGATAATTTAGTTA
2154493 TAAATTA
1 TAAATTA
2154500 ATTAATTATT
Statistics
Matches: 90, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
21 2 0.02
22 87 0.97
23 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
TAAATTATTGATAATTTAGTTA
Found at i:2154397 original size:66 final size:66
Alignment explanation
Indices: 2154326--2154452 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 66
2154316 GTAAATCAAT
** *
2154326 GATAACAAAGTAGCAAATGCA-TAACAGTATAATAGTAAATTATTAATAATTTAGTTATAAATTA
1 GATAACAAAGTAGCAAAT-CACTAACAACATAATAGTAAAATATTAATAATTTAGTTATAAATTA
2154390 TC
65 TC
** * * * * *
2154392 GATAACTTAGTAGTAAATCACTAATAACGTAATAGTAAAATATTGATAATTTAGTTGTAAA
1 GATAACAAAGTAGCAAATCACTAACAACATAATAGTAAAATATTAATAATTTAGTTATAAA
2154453 ACACTGATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 2 0.04
66 48 0.96
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (66 bp):
GATAACAAAGTAGCAAATCACTAACAACATAATAGTAAAATATTAATAATTTAGTTATAAATTAT
C
Found at i:2154406 original size:44 final size:43
Alignment explanation
Indices: 2154358--2154677 Score: 157
Period size: 44 Copynumber: 7.2 Consensus size: 43
2154348 AACAGTATAA
* *
2154358 TAGTAAATTATTAATAATTTAGTTATAAATTATCGATAACTTAG
1 TAGTAAATTATTAATAACTTA-TTATAAATTATTGATAACTTAG
* * * * * *
2154402 TAGTAAATCACTAATAACGTAATAGTAAAATATTGATAATTTAG
1 TAGTAAATTATTAATAACTTATTA-TAAATTATTGATAACTTAG
* ** * * * * *
2154446 TTGTAAAACACTGATAATTTATTTATAAATTAATGATAATTTAG
1 TAGTAAATTATTAATAACTTA-TTATAAATTATTGATAACTTAG
* * * **
2154490 TTATAAATTAATTAATTATTAATAACTTTATTGTAAATCATCAATAACTTTA-
1 ---T--AGT-A--AATTATTAATAAC-TTATTATAAATTATTGATAAC-TTAG
* ** * *
2154542 TAGTAAATTAGTAATAACATTAAAATAAATTATTAATAACTTAA
1 TAGTAAATTATTAATAAC-TTATTATAAATTATTGATAACTTAG
* * * *
2154586 TAGTAAATTATTAATAACTTAGTAATAAATCATTTATAACTTAA
1 TAGTAAATTATTAATAACTTA-TTATAAATTATTGATAACTTAG
* *
2154630 TAGTAAATCATCT-ATAACTTAGTGAT-AATTA-TGATAA-TTA-
1 TAGTAAATTAT-TAATAACTTA-TTATAAATTATTGATAACTTAG
2154670 TAGTAAAT
1 TAGTAAAT
2154678 CAGTGATAAC
Statistics
Matches: 216, Mismatches: 45, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
40 8 0.04
41 3 0.01
42 5 0.02
43 12 0.06
44 152 0.70
45 3 0.01
46 1 0.00
47 3 0.01
49 2 0.01
50 1 0.00
52 20 0.09
53 6 0.03
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (43 bp):
TAGTAAATTATTAATAACTTATTATAAATTATTGATAACTTAG
Found at i:2154538 original size:22 final size:22
Alignment explanation
Indices: 2154507--2154649 Score: 137
Period size: 22 Copynumber: 6.5 Consensus size: 22
2154497 TTAATTAATT
*
2154507 ATTAATAACTTTATTGTAAATC
1 ATTAATAACTTTATAGTAAATC
* *
2154529 ATCAATAACTTTATAGTAAATT
1 ATTAATAACTTTATAGTAAATC
* * * * *
2154551 AGTAATAACATTAAAATAAATT
1 ATTAATAACTTTATAGTAAATC
* *
2154573 ATTAATAACTTAATAGTAAATT
1 ATTAATAACTTTATAGTAAATC
*
2154595 ATTAATAAC-TTAGTAATAAATC
1 ATTAATAACTTTA-TAGTAAATC
* *
2154617 ATTTATAACTTAATAGTAAATC
1 ATTAATAACTTTATAGTAAATC
2154639 ATCT-ATAACTT
1 AT-TAATAACTT
2154650 AGTGATAATT
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
21 2 0.02
22 94 0.95
23 3 0.03
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (22 bp):
ATTAATAACTTTATAGTAAATC
Found at i:2154625 original size:66 final size:65
Alignment explanation
Indices: 2154503--2154629 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 65
2154493 TAAATTAATT
* * * *
2154503 AATTATTAATAACTTTATTGTAAATCATCAATAACTTTATAGTAAATTAGTAATAACATTAAAAT
1 AATTATTAATAACTTAATAGTAAATCATCAATAACTTTATAATAAATCAGTAATAAC-TTAAAAT
2154568 A
65 A
* * * *
2154569 AATTATTAATAACTTAATAGTAAATTATTAATAAC-TTAGTAATAAATCATTTATAACTTAA
1 AATTATTAATAACTTAATAGTAAATCATCAATAACTTTA-TAATAAATCAGTAATAACTTAA
2154630 TAGTAAATCA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
65 7 0.13
66 45 0.87
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (65 bp):
AATTATTAATAACTTAATAGTAAATCATCAATAACTTTATAATAAATCAGTAATAACTTAAAATA
Found at i:2154962 original size:22 final size:22
Alignment explanation
Indices: 2154937--2155013 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
2154927 TCTATCATAA
*
2154937 ATAACTTAGTAGCAATTTAA-TG
1 ATAACTTAGTAGCAA-ATAATTG
* *
2154959 ATAATTTAGTAGTAAATAATTG
1 ATAACTTAGTAGCAAATAATTG
* *
2154981 ATAACTTAATAGCTAACT-ATTG
1 ATAACTTAGTAGC-AAATAATTG
*
2155003 AAAACTTAGTA
1 ATAACTTAGTA
2155014 ATAAATCAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 3 0.07
22 38 0.86
23 3 0.07
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (22 bp):
ATAACTTAGTAGCAAATAATTG
Found at i:2155166 original size:22 final size:21
Alignment explanation
Indices: 2155141--2155312 Score: 125
Period size: 22 Copynumber: 7.9 Consensus size: 21
2155131 AATGTTGTAG
*
2155141 TAAATCATTGATAACTTCATAA
1 TAAATCATTAATAACTT-ATAA
*
2155163 TAAATTAGTT-ATAACTTTATAA
1 TAAATCA-TTAATAAC-TTATAA
* *
2155185 -AAATTTATTAATAACTTAGTAT
1 TAAA-TCATTAATAACTTA-TAA
**
2155207 TAAATCATCGATAACTTAGTAA
1 TAAATCATTAATAACTTA-TAA
* *
2155229 TAAATCATTCATAACTTAATAG
1 TAAATCATTAATAACTT-ATAA
*
2155251 TAAATCATTAATAATTTAATAA
1 TAAATCATTAATAACTT-ATAA
* *
2155273 TAAATCACTGATAA-TATAGTAA
1 TAAATCATTAATAACT-TA-TAA
*
2155295 TAAATCAGTAATAACTTA
1 TAAATCATTAATAACTTA
2155313 ATTGTTAATC
Statistics
Matches: 124, Mismatches: 16, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
21 10 0.08
22 105 0.85
23 9 0.07
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (21 bp):
TAAATCATTAATAACTTATAA
Found at i:2155211 original size:66 final size:66
Alignment explanation
Indices: 2155141--2155314 Score: 194
Period size: 66 Copynumber: 2.6 Consensus size: 66
2155131 AATGTTGTAG
* * * *
2155141 TAAATCATTGATAACTTCA-TAATAAATTAGTTATAACTTTATA-AAAATTTATTAATAACTTAG
1 TAAATCATTGATAACTT-AGTAATAAATCAGTTATAACTTAATAGAAAA-TCATTAATAACTTAA
*
2155204 TAT
64 TAA
* * *
2155207 TAAATCATCGATAACTTAGTAATAAATCA-TTCATAACTTAATAGTAAATCATTAATAATTTAAT
1 TAAATCATTGATAACTTAGTAATAAATCAGTT-ATAACTTAATAGAAAATCATTAATAACTTAAT
2155271 AA
65 AA
* *
2155273 TAAATCACTGATAA-TATAGTAATAAATCAGTAATAACTTAAT
1 TAAATCATTGATAACT-TAGTAATAAATCAGTTATAACTTAAT
2155315 TGTTAATCAA
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
65 4 0.04
66 84 0.91
67 4 0.04
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (66 bp):
TAAATCATTGATAACTTAGTAATAAATCAGTTATAACTTAATAGAAAATCATTAATAACTTAATA
A
Found at i:2155578 original size:22 final size:22
Alignment explanation
Indices: 2155510--2155578 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
2155500 TAAATCAATG
*
2155510 ATAACTTATTAGTAAATTAGTTT
1 ATAACTTAATAGTAAATTA-TTT
** * * * *
2155533 -TAGTTTAGTAGTAAAATCTGT
1 ATAACTTAATAGTAAATTATTT
2155554 ATAACTTAATAGTAAATTATTT
1 ATAACTTAATAGTAAATTATTT
2155576 ATA
1 ATA
2155579 TTTTGATAAT
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTATTT
Found at i:2157895 original size:87 final size:84
Alignment explanation
Indices: 2157755--2157917 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 84
2157745 TTTCACAATA
* * *
2157755 AAAAAGTAAATGAGCACCTTAAATAAGTAATAACTAAATGAATAGGATCTGATATGATTAAAAAA
1 AAAAAGTAAATGAACACCTTAAATAAATAATAAATAAATGAATAGGATCTGATATGATTAAAAAA
2157820 TTCATGATAAATAAGTATG
66 TTCATGATAAATAAGTATG
2157839 AAAAAGTAAATGAACACCTTAAATAAATATGAATAAATAAATGAATAGGATCTGATATGATTAAA
1 AAAAAGTAAATGAACACCTTAAAT-AA-AT-AATAAATAAATGAATAGGATCTGATATGATTAAA
* *
2157904 GAGTTCATGATAAA
63 AAATTCATGATAAA
2157918 AACATTAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
84 23 0.32
85 2 0.03
86 1 0.01
87 45 0.63
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (84 bp):
AAAAAGTAAATGAACACCTTAAATAAATAATAAATAAATGAATAGGATCTGATATGATTAAAAAA
TTCATGATAAATAAGTATG
Found at i:2157917 original size:42 final size:42
Alignment explanation
Indices: 2157784--2157917 Score: 105
Period size: 42 Copynumber: 3.1 Consensus size: 42
2157774 TAAATAAGTA
*
2157784 ATAACTAAATGAATAGGATCTGATATGATTAAAAAATTCATG
1 ATAAATAAATGAATAGGATCTGATATGATTAAAAAATTCATG
* * ** *
2157826 ATAAATAAGTATGAAAAAGTAAATGA-A-CACCTTAAATAAA-T-ATG
1 ATAAATAA--ATG-AATAGGATCTGATATGA--TTAAA-AAATTCATG
* *
2157870 AATAAATAAATGAATAGGATCTGATATGATTAAAGAGTTCATG
1 -ATAAATAAATGAATAGGATCTGATATGATTAAAAAATTCATG
2157913 ATAAA
1 ATAAA
2157918 AACATTAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
41 1 0.01
42 26 0.38
43 8 0.12
44 8 0.12
45 22 0.32
46 3 0.04
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.28
Consensus pattern (42 bp):
ATAAATAAATGAATAGGATCTGATATGATTAAAAAATTCATG
Found at i:2162544 original size:18 final size:20
Alignment explanation
Indices: 2162510--2162547 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2162500 TCAGATAAGG
2162510 ATAATAGAATAAAAAATAGA
1 ATAATAGAATAAAAAATAGA
2162530 ATAATA-AAT-AAAAATAGA
1 ATAATAGAATAAAAAATAGA
2162548 GTTTCGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
ATAATAGAATAAAAAATAGA
Found at i:2163561 original size:57 final size:57
Alignment explanation
Indices: 2163466--2163882 Score: 439
Period size: 57 Copynumber: 7.1 Consensus size: 57
2163456 TTTTCAATGA
* * *
2163466 TTTTCTT-AAAATAAAAATTTGAAAAAGAAAATACTTTAAGAAAAAGTTGAAAATATCAAT
1 TTTTCTTGAAAAT-AAAATTT--CAAA-AAAATATTTTAAGAAAAAGTTGAAAGTATCAAT
* ** * * *
2163526 TTTCCTTGAAAATCCAATTTCAAAGAAATAATTTAAGAAAAATTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAAATTTCAAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAAT
* * * * *
2163583 TTTTCTAGAAGATCAAATTTCAAAAAAATACTTTAAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAAATTTCAAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAAT
*
2163640 TTTTCTTGAAAAAAAAGATTTCAAAAGAAAATTATTTTAA-AGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAA-ATTTC-AAA-AAAA-TATTTTAAGA-AAAAGTTGAAAGTATCAAT
* *
2163701 TTTTCTTGAAAATAAAAATTTCAAAAAAATATTTTTGAAG-AAAAGTTTAAAATATCAAT
1 TTTTCTTGAAAAT-AAAATTTCAAAAAAATA-TTTT-AAGAAAAAGTTGAAAGTATCAAT
* * *
2163760 TTTTCTTGAAAATAATATTTTCAAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAA-AATTTCAAAAAAA-TA-TTTTAAGAAAAAGTTGAAAGTATCAAT
* *
2163820 TTTTCTT-AAAATAAAAATTTCAAAAAAAATTTTTTAAGGAAAAGTTG-AAGATATCAAT
1 TTTTCTTGAAAAT-AAAATTTC-AAAAAAATATTTTAAGAAAAAGTTGAAAG-TATCAAT
2163878 TTTTC
1 TTTTC
2163883 GAAAAAAAAT
Statistics
Matches: 309, Mismatches: 32, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
57 93 0.30
58 39 0.13
59 66 0.21
60 60 0.19
61 48 0.16
62 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (57 bp):
TTTTCTTGAAAATAAAATTTCAAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAAT
Found at i:2163874 original size:118 final size:115
Alignment explanation
Indices: 2163466--2163882 Score: 479
Period size: 118 Copynumber: 3.5 Consensus size: 115
2163456 TTTTCAATGA
* * *
2163466 TTTTCTTAAAATAAAAATTTGAAAAAGAAAATACTTTAAGAAAAAGTTGAAAATATCAATTTTCC
1 TTTTCTTAAAATAAAAATTT-CAAAA-AAAATACTTTAAGGAAAAGTTGAAAATATCAATTTTTC
* * * * *
2163531 TTGAAAATCCAATTTCAAAGAAATA-ATTTAAGAAAAATTTGAAAGTATCAAT
64 TTGAAAAT-AAATTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAAT
* *
2163583 TTTTC-TAGAAGAT-CAAATTTC-AAAAAAATACTTTAAGGAAAAGTTGAAAGTATCAATTTTTC
1 TTTTCTTA-AA-ATAAAAATTTCAAAAAAAATACTTTAAGGAAAAGTTGAAAATATCAATTTTTC
* *
2163645 TTGAAAAAAAAGATTTCAAAAGAAA-ATTATTTTAAAGAAAAGTTGAAAGTATCAAT
64 TTG-AAAATAA-ATTTCAAAA-AAATA-T-TTTTAAGGAAAAGTTGAAAGTATCAAT
* *
2163701 TTTTCTTGAAAATAAAAATTTC-AAAAAAATATTTTTGAA-GAAAAGTTTAAAATATCAATTTTT
1 TTTTCTT-AAAATAAAAATTTCAAAAAAAATA-CTTT-AAGGAAAAGTTGAAAATATCAATTTTT
*
2163764 CTTGAAAATAATATTTTCAAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAAT
63 CTTGAAAATAA-A-TTTCAAAAAAA-TATTTTTAAGGAAAAGTTGAAAGTATCAAT
** *
2163820 TTTTCTTAAAATAAAAATTTCAAAAAAAATTTTTTAAGGAAAAGTTGAAGATATCAATTTTTC
1 TTTTCTTAAAATAAAAATTTCAAAAAAAATACTTTAAGGAAAAGTTGAAAATATCAATTTTTC
2163883 GAAAAAAAAT
Statistics
Matches: 259, Mismatches: 23, Indels: 35
0.82 0.07 0.11
Matches are distributed among these distances:
114 39 0.15
115 16 0.06
116 5 0.02
117 15 0.06
118 73 0.28
119 69 0.27
120 39 0.15
121 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (115 bp):
TTTTCTTAAAATAAAAATTTCAAAAAAAATACTTTAAGGAAAAGTTGAAAATATCAATTTTTCTT
GAAAATAAATTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAAT
Found at i:2163924 original size:42 final size:42
Alignment explanation
Indices: 2163837--2163923 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 42
2163827 AAAATAAAAA
* * * *
2163837 TTTCAAAAAAAATTTTTTAAGGAAAAGTTGAAGATATCAATT
1 TTTCAAAAAAAATATTTTAAGAAAAAATTAAAGATATCAATT
2163879 TTTCGAAAAAAAATATTTTAAGAAAAAATTAAA-AGTATCAATT
1 TTTC-AAAAAAAATATTTTAAGAAAAAATTAAAGA-TATCAATT
2163922 TT
1 TT
2163924 CCTTAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 5 0.13
43 34 0.87
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.36
Consensus pattern (42 bp):
TTTCAAAAAAAATATTTTAAGAAAAAATTAAAGATATCAATT
Found at i:2163984 original size:27 final size:27
Alignment explanation
Indices: 2163901--2163985 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
2163891 ATATTTTAAG
* * *
2163901 AAAAAATTAAAAGTATCAATTTTCCTT
1 AAAAAATTGAAAGTATAAATTTTTCTT
* * *
2163928 -AAAAATTGAAA-AAAAAATTTTT-TGAG
1 AAAAAATTGAAAGTATAAATTTTTCT--T
*
2163954 AAAAAATTGAAAGTATTAATTTTTCTT
1 AAAAAATTGAAAGTATAAATTTTTCTT
2163981 AAAAA
1 AAAAA
2163986 TAAAAATTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
24 1 0.02
25 7 0.16
26 10 0.23
27 16 0.37
28 8 0.19
29 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (27 bp):
AAAAAATTGAAAGTATAAATTTTTCTT
Found at i:2164032 original size:55 final size:53
Alignment explanation
Indices: 2163884--2164035 Score: 173
Period size: 53 Copynumber: 2.8 Consensus size: 53
2163874 CAATTTTTCG
** * *
2163884 AAAAAAAATATTTTAAGAAAAAATTAAAAGTATCAATTTTCCTTAAAAATTGA
1 AAAAAAAATGCTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATTGA
** * *
2163937 AAAAAAAATTTTTTGAGAAAAAATTGAAAGTATTAATTTTTCTTAAAAA-T-A
1 AAAAAAAATGCTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATTGA
*
2163988 AAAATTTCAAAATGCTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAA----AAAATGCTTTAAGAAAAAATTGAAAGTATCAATTTTTCTT
2164036 GAATAAAGGC
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 5 0.06
52 1 0.01
53 44 0.52
55 35 0.41
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (53 bp):
AAAAAAAATGCTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATTGA
Found at i:2169888 original size:15 final size:15
Alignment explanation
Indices: 2169868--2169897 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2169858 GAATCAGGCG
2169868 TACGTATCCCATAAT
1 TACGTATCCCATAAT
2169883 TACGTATCCCATAAT
1 TACGTATCCCATAAT
2169898 GTATCTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
TACGTATCCCATAAT
Found at i:2175653 original size:85 final size:85
Alignment explanation
Indices: 2175507--2176207 Score: 512
Period size: 85 Copynumber: 8.2 Consensus size: 85
2175497 GGCTTAGTTT
* * * * *
2175507 AAGTTATTCTTTTCAGACTTCGA-TTCTATCCAAGTCATTTCATTTTGAACTTTAG-CTTATGCT
1 AAGTTATTCTTTTCAGACTTCGATTTC-ATCCAGGTCATTTCATTTTGGA-TTTCGACCTATGCC
2175570 AGATCTTTCTTCGACTTAGTCC
64 AGATCTTTCTTCGACTTAGTCC
* * * * *
2175592 AGGTTATTCTTTTTAGACTTCAATTTCATTCAGGTCATTTCGTTTTGGATTTCGACCTATGCCAG
1 AAGTTATTCTTTTCAGACTTCGATTTCATCCAGGTCATTTCATTTTGGATTTCGACCTATGCCAG
2175657 ATCTTTCTTCGACTTAGTCC
66 ATCTTTCTTCGACTTAGTCC
* * * * * * ***
2175677 AAGTTATTCTTTTTAGACTTCGGTTCCATTCAGGTCATTTCATTTTAGATTTCAACCTATAATAA
1 AAGTTATTCTTTTCAGACTTCGATTTCATCCAGGTCATTTCATTTTGGATTTCGACCTAT-GCCA
* * * *
2175742 GATCTTTATTTGGCTCAGTCC
65 GATCTTTCTTCGACTTAGTCC
* * *
2175763 AAGTTATT-TGGTTT-AAACTT--ATATTCAGTCCAGTTCATTTTATTTTGGATTTCGACCTATG
1 AAGTTATTCT--TTTCAGACTTCGAT-TTCA-TCCAGGTCATTTCATTTTGGATTTCGACCTATG
* ** * *
2175824 CCAGATCCTTCTTTTA-TTCAATCT
62 CCAGATCTTTCTTCGACTT-AGTCC
* * * ** * * * * *
2175848 AAGTGATT-TATTTCAAACTTTGATTAAATCTTA-GTCATTTCATTTTGTATTTTGGCCTATGTC
1 AAGTTATTCT-TTTCAGACTTCGATTTCATC-CAGGTCATTTCATTTTGGATTTCGACCTATGCC
*
2175911 AGATCTTTTTTCTG-CTTAGTCC
64 AGATCTTTCTTC-GACTTAGTCC
* * * * * ** *
2175933 AAGTTATTCTTTTCATACTTTGGTTTCATCCAAGTCATTTCGTTTTAAATTTTGACCTATGCCAG
1 AAGTTATTCTTTTCAGACTTCGATTTCATCCAGGTCATTTCATTTTGGATTTCGACCTATGCCAG
*
2175998 ATCCTTCTTC-AGCTTAGTCC
66 ATCTTTCTTCGA-CTTAGTCC
* * * * * * **
2176018 AAATTATTCTTTTTAGACTTTGGTTTCATCCAGGTCATTTCGTTTTGGATTTTGGTCTATGCCAG
1 AAGTTATTCTTTTCAGACTTCGATTTCATCCAGGTCATTTCATTTTGGATTTCGACCTATGCCAG
* * * *
2176083 ATCCTTCTTCGGCTCAGTCT
66 ATCTTTCTTCGACTTAGTCC
* ** * *
2176103 AAGTTATT-TAGTTCAGACTTCGA-TTCAGTCCAGGTCATTTTGTTTTAGATTTCAACCTATGCC
1 AAGTTATTCT-TTTCAGACTTCGATTTCA-TCCAGGTCATTTCATTTTGGATTTCGACCTATGCC
* * * * *
2176166 AGATTTTTTTTTG-TTTAATCC
64 AGATCTTTCTTCGACTTAGTCC
*
2176187 AAGTTATTCATTTCAGACTTC
1 AAGTTATTCTTTTCAGACTTC
2176208 AGTCAGTCCA
Statistics
Matches: 490, Mismatches: 104, Indels: 45
0.77 0.16 0.07
Matches are distributed among these distances:
84 37 0.08
85 381 0.78
86 67 0.14
87 5 0.01
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (85 bp):
AAGTTATTCTTTTCAGACTTCGATTTCATCCAGGTCATTTCATTTTGGATTTCGACCTATGCCAG
ATCTTTCTTCGACTTAGTCC
Found at i:2176142 original size:255 final size:256
Alignment explanation
Indices: 2175621--2176245 Score: 622
Period size: 255 Copynumber: 2.4 Consensus size: 256
2175611 TCAATTTCAT
*
2175621 TCAGGTCATTTCGTTTTGGATTTCGACCTATGCCAGATCTTTCTTC-GACTTAGTCCAAGTTATT
1 TCAGGTCATTTCGTTTT-GATTTCGACCTATGCCAGATCTTTTTTCTG-CTTAGTCCAAGTTATT
* * * * * * *
2175685 CTTTTTAGACTTCGGTTCCATTCAGGTCATTTCATTTTAGATTTCAACCTATAATAAGATCTTTA
64 CTTTTCAGACTTCGGTTTCATCCAAGTCATTTCGTTTTAGATTTCAACCTATAACAAGATCCTTA
** * * *
2175750 TTTGGCTCAGTCCAAGTTATTTGGTTTAAACTTATATTCAGTCCAGTTCATTTTATTTTGGATTT
129 TTCAGCTCAGTCCAAATTATTTGGTTTAAACTTATATTCAGTCCAGGTCATTTCATTTTGGATTT
** * * *
2175815 CGACCTATGCCAGATCCTTCTTTTATTCAATCTAAGTGATTTATTTCAAACTTTGATTAAATC
194 CGACCTATGCCAGATCCTTCTTCGACTCAATCTAAGTGATTTAGTTCAAACTTCGATTAAATC
* * * * *
2175878 TTA-GTCATTTCATTTTGTATTTTGGCCTATGTCAGATCTTTTTTCTGCTTAGTCCAAGTTATTC
1 TCAGGTCATTTCGTTTTG-ATTTCGACCTATGCCAGATCTTTTTTCTGCTTAGTCCAAGTTATTC
* * * ** * * *
2175942 TTTTCATACTTTGGTTTCATCCAAGTCATTTCGTTTTAAATTTTGACCTAT-GCCAGATCCTTCT
65 TTTTCAGACTTCGGTTTCATCCAAGTCATTTCGTTTTAGATTTCAACCTATAACAAGATCCTTAT
* * * * *
2176006 TCAGCTTAGTCCAAATTATTCT-TTTTAGACTT-TGGTTTCA-TCCAGGTCATTTCGTTTTGGAT
130 TCAGCTCAGTCCAAATTATT-TGGTTTAAACTTAT--ATTCAGTCCAGGTCATTTCATTTTGGAT
* ** * * * * * *
2176068 TTTGGTCTATGCCAGATCCTTCTTCGGCTCAGTCTAAGTTATTTAGTTCAGACTTCGATTCAGTC
192 TTCGACCTATGCCAGATCCTTCTTCGACTCAATCTAAGTGATTTAGTTCAAACTTCGATTAAATC
* * * * *
2176133 -CAGGTCATTTTGTTTTAGATTTCAACCTATGCCAGAT-TTTTTTTTGTTTAATCCAAGTTATTC
1 TCAGGTCATTTCGTTTT-GATTTCGACCTATGCCAGATCTTTTTTCTGCTTAGTCCAAGTTATTC
* * * *
2176196 ATTTCAGACTTCAG--TCAGTCCAAGTCATTTTGTTTTAGATTTCACCCTAT
65 TTTTCAGACTTCGGTTTCA-TCCAAGTCATTTCGTTTTAGATTTCAACCTAT
2176246 GCCGAATTTT
Statistics
Matches: 296, Mismatches: 64, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
252 3 0.01
253 27 0.09
254 35 0.12
255 129 0.44
256 99 0.33
257 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (256 bp):
TCAGGTCATTTCGTTTTGATTTCGACCTATGCCAGATCTTTTTTCTGCTTAGTCCAAGTTATTCT
TTTCAGACTTCGGTTTCATCCAAGTCATTTCGTTTTAGATTTCAACCTATAACAAGATCCTTATT
CAGCTCAGTCCAAATTATTTGGTTTAAACTTATATTCAGTCCAGGTCATTTCATTTTGGATTTCG
ACCTATGCCAGATCCTTCTTCGACTCAATCTAAGTGATTTAGTTCAAACTTCGATTAAATC
Found at i:2176231 original size:83 final size:83
Alignment explanation
Indices: 2176103--2176256 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 83
2176093 GGCTCAGTCT
* * *
2176103 AAGTTATTTAGTTCAGACTTCGATTCAGTCCAGGTCATTTTGTTTTAGATTTCAACCTATGCCAG
1 AAGTTATTCAGTTCAGACTTCGAGTCAGTCCAAGTCATTTTGTTTTAGATTTCAACCTATGCC-G
*
2176168 ATTTTTTTTTGTTTAATCC
65 AATTTTTTTTGTTTAATCC
* *
2176187 AAGTTATTCATTTCAGACTTC-AGTCAGTCCAAGTCATTTTGTTTTAGATTTCACCCTATGCCGA
1 AAGTTATTCAGTTCAGACTTCGAGTCAGTCCAAGTCATTTTGTTTTAGATTTCAACCTATGCCGA
2176251 ATTTTT
66 ATTTTT
2176257 CTTGGGTTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
82 7 0.11
83 38 0.59
84 19 0.30
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (83 bp):
AAGTTATTCAGTTCAGACTTCGAGTCAGTCCAAGTCATTTTGTTTTAGATTTCAACCTATGCCGA
ATTTTTTTTGTTTAATCC
Found at i:2177763 original size:60 final size:59
Alignment explanation
Indices: 2177487--2178076 Score: 491
Period size: 59 Copynumber: 10.1 Consensus size: 59
2177477 TTTTCAATGA
* * * * * *
2177487 TTTTCTT-AAAAT-AAAATTTTCAAAAAGAAAATACTTTAAGGAAAACTTAAAAATATCAAT
1 TTTTCTTAAAAATAAAAATTTT-AAAAA-AATAT-TTTTAAGAAAAAGTTGAAAGTATCAAT
* * * * * *
2177547 TTTCCTTGAAGAT-CAAATTTTAAAAAAATA-CTTTAAGGAAAAA-TTGAAAGTATTAAT
1 TTTTCTTAAAAATAAAAATTTTAAAAAAATATTTTTAA-GAAAAAGTTGAAAGTATCAAT
* * * * *
2177604 TTTTCTTTAAAATAAAGATTTCAAAAAAAATATATTTTAAGGAAAAGTTGAGAGTATCAAT
1 TTTTCTTAAAAATAAAAATTT-TAAAAAAATAT-TTTTAAGAAAAAGTTGAAAGTATCAAT
** * *
2177665 TTTTCTTAAAAATAAAAATTTTTTAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAAT
1 TTTTCTTAAAAATAAAAATTTTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
*
2177724 TTTTCTTAAAAATAAAAATTTTAAAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAAAATTTTAAAAAAA-TATTTTTAAGAAAAAGTTGAAAGTATCAAT
* *
2177784 TTTTCTT-AAAAT-AAAATTTTCAAAAAAA-ATGTTTTAAGGAAAAGTTG-AAGATATCTAT
1 TTTTCTTAAAAATAAAAATTTT-AAAAAAATAT-TTTTAAGAAAAAGTTGAAAG-TATCAAT
* * * * *
2177842 TTTTCTAAAAAAAAAAAAAATTTT-TAAAAATA-TTTTAAGAAAAAATTGAAAGTATTAAT
1 TTTTCT--TAAAAATAAAAATTTTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
* *
2177901 TTTTCTTAAAAAT-AAAATTTT--CAAAATA-CTTTAAGGAAAAA-TTGAATA-TATCAA-
1 TTTTCTTAAAAATAAAAATTTTAAAAAAATATTTTTAA-GAAAAAGTTGAA-AGTATCAAT
* ** *
2177955 TTTTCTTTAAAAACAAAAATTTTTTTTAAAAATATTTTTCA-AAAAAGTTGAAAGTATCAAT
1 TTTTC-TTAAAAATAAAAA--TTTTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
* ** * * * * * *
2178016 TTTTCTTGAAAATAAAAATTCGAAAGATAT-TTTTTGAGAAAAAATTAAAAATATCAAT
1 TTTTCTTAAAAATAAAAATTTTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
2178074 TTT
1 TTT
2178077 CGTTGAATAA
Statistics
Matches: 439, Mismatches: 61, Indels: 62
0.78 0.11 0.11
Matches are distributed among these distances:
54 5 0.01
55 28 0.06
56 19 0.04
57 43 0.10
58 74 0.17
59 105 0.24
60 96 0.22
61 61 0.14
62 8 0.02
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.37
Consensus pattern (59 bp):
TTTTCTTAAAAATAAAAATTTTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
Found at i:2178058 original size:59 final size:58
Alignment explanation
Indices: 2177578--2178076 Score: 387
Period size: 60 Copynumber: 8.5 Consensus size: 58
2177568 AAAAAAATAC
* * * * *
2177578 TTTAAGGAAAAA-TTGAAAGTATTAATTTTTCTTTAAAATAAAGATTTCAAAAAAAATATAT
1 TTTAA-GAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-AATTC--TAAAAATATTT
* * *
2177639 TTTAAGGAAAAGTTGAGAGTATCAATTTTTCTTAAAAATAAAAATTTTTTAAAAATA-TT
1 TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAA--TTCTAAAAATATTT
* * * *
2177698 TTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTTAAAAAAAGTATT
1 TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTCTAAAAATA-T-TT
* * * * *
2177758 TTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAAATTTTCAAAAAAAATGT
1 TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAA-ATTCTAAAAATATTT
* * * * *
2177816 TTTAAGGAAAAGTTG-AAGATATCTATTTTTCTAAAAAAAAAAAAAATTTTTAAAAATA--T
1 TTTAAGAAAAAGTTGAAAG-TATCAATTTTTCT--TAAAAATAAAAA-TTCTAAAAATATTT
* * * * *
2177875 TTTAAGAAAAAATTGAAAGTATTAATTTTTCTTAAAAAT-AAAATTTTCAAAATA--C
1 TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTCTAAAAATATTT
* *
2177930 TTTAAGGAAAAA-TTGAATA-TATCAA-TTTTCTTTAAAAACAAAAATTTTTTTTAAAAATA-TT
1 TTTAA-GAAAAAGTTGAA-AGTATCAATTTTTC-TTAAAAATAAAAA----TTCTAAAAATATTT
* * * *
2177991 TTTCA-AAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTCGAAAGATATTT
1 TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTCTAAAAATATTT
* * * *
2178048 TTTGAGAAAAAATTAAAAATATCAATTTT
1 TTTAAGAAAAAGTTGAAAGTATCAATTTT
2178077 CGTTGAATAA
Statistics
Matches: 362, Mismatches: 49, Indels: 57
0.77 0.10 0.12
Matches are distributed among these distances:
54 5 0.01
55 32 0.09
56 23 0.06
57 24 0.07
58 46 0.13
59 82 0.23
60 91 0.25
61 57 0.16
62 2 0.01
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.38
Consensus pattern (58 bp):
TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTCTAAAAATATTT
Found at i:2180208 original size:23 final size:22
Alignment explanation
Indices: 2180154--2180216 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
2180144 AATAGAGCCA
*
2180154 TATTTT-TTTGGTATTTTTTAT
1 TATTTTGTTTAGTATTTTTTAT
*
2180175 TATTTTGTTTATTTATTTTTTAT
1 TATTTTGTTTA-GTATTTTTTAT
*
2180198 GTGTTTT-TTTAGTATTTTT
1 -TATTTTGTTTAGTATTTTT
2180217 GCATGATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.17
22 10 0.29
23 14 0.40
24 5 0.14
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (22 bp):
TATTTTGTTTAGTATTTTTTAT
Found at i:2180886 original size:58 final size:55
Alignment explanation
Indices: 2180801--2181007 Score: 190
Period size: 57 Copynumber: 3.7 Consensus size: 55
2180791 TTTTCTTTCC
* *
2180801 AAAAAAAA-ATTTCTAAATAGACTCAAATGGTGAAAAATTTAGAAATTTTGAAAAAA
1 AAAAAAAATATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAA-TTT-AAAAAA
* * *
2180857 AAAAGAAAATATTTTTAAATTGACCCAAATGGTGAAAAATTTAGAGA-TAAAAAAA
1 AAAA-AAAATATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAATTTAAAAAA
* * * *
2180912 TTAAAAAAAATAATTTTTAAATAGGCCCAAATGGTGAAAATTTTA-AAAATT--CAAA
1 --AAAAAAAAT-ATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAATTTAAAAAA
* * * * *
2180967 AAGAAAAATATTTTTAATTTGGCCCAAATAGTGAAATAATT
1 AAAAAAAATATTTTTAAATAGACCCAAATGGTGAAA-AATT
2181008 ATATATATTT
Statistics
Matches: 128, Mismatches: 16, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
52 24 0.19
53 11 0.09
55 9 0.07
56 12 0.09
57 39 0.30
58 33 0.26
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (55 bp):
AAAAAAAATATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAATTTAAAAAA
Found at i:2180951 original size:57 final size:57
Alignment explanation
Indices: 2180801--2180974 Score: 194
Period size: 58 Copynumber: 3.1 Consensus size: 57
2180791 TTTTCTTTCC
* *
2180801 AAAAAAA-AATTTCTAAATAGACTCAAATGGTGAAAAATTTAGAAATTTTGAAAAAAAA
1 AAAAAAATAATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAA--TTGAAAAAAAA
* * *
2180859 AAGAAAAT-ATTTTTAAATTGACCCAAATGGTGAAAAATTTAGAGA-T-AAAAAAATTA
1 AAAAAAATAATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAATTGAAAAAAA--A
* * * * *
2180915 AAAAAAATAATTTTTAAATAGGCCCAAATGGTGAAAATTTTAAAAATTCAAAAAGAA
1 AAAAAAATAATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAATTGAAAAAAAA
2180972 AAA
1 AAA
2180975 TATTTTTAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
54 7 0.07
55 1 0.01
56 8 0.08
57 36 0.37
58 40 0.41
59 6 0.06
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (57 bp):
AAAAAAATAATTTTTAAATAGACCCAAATGGTGAAAAATTTAGAAATTGAAAAAAAA
Found at i:2184553 original size:23 final size:23
Alignment explanation
Indices: 2184527--2184576 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2184517 ATGTCAACAT
*
2184527 AATAGAGATAGAGTCTGCTAAAA
1 AATAGAGATAGAATCTGCTAAAA
*
2184550 AATAGGGATAGAATCTGCTAAAA
1 AATAGAGATAGAATCTGCTAAAA
2184573 AATA
1 AATA
2184577 TTATACAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (23 bp):
AATAGAGATAGAATCTGCTAAAA
Found at i:2187458 original size:12 final size:12
Alignment explanation
Indices: 2187423--2187458 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
2187413 AAAAGACAAA
2187423 TAGTTTTAATTT
1 TAGTTTTAATTT
2187435 TAGTTATT-ATTT
1 TAGTT-TTAATTT
2187447 TAGTTTTAATTT
1 TAGTTTTAATTT
2187459 AATTTTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (12 bp):
TAGTTTTAATTT
Found at i:2208294 original size:21 final size:24
Alignment explanation
Indices: 2208250--2208301 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
2208240 TTAATTTTAA
*
2208250 TTTTATATATTATTTTAATAAAAT
1 TTTTATATATTATTTAAATAAAAT
2208274 TTTTA-ATA-TATTTAAAT-AAAT
1 TTTTATATATTATTTAAATAAAAT
*
2208295 TTATATA
1 TTTTATA
2208302 CAAAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 8 0.32
22 9 0.36
23 3 0.12
24 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATATATTATTTAAATAAAAT
Found at i:2223955 original size:15 final size:16
Alignment explanation
Indices: 2223935--2223966 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2223925 CCTCCTTTAT
2223935 AAAATAAAAAAA-TAA
1 AAAATAAAAAAACTAA
2223950 AAAATAAAAAAACTAA
1 AAAATAAAAAAACTAA
2223966 A
1 A
2223967 TCTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAAACTAA
Found at i:2225697 original size:21 final size:21
Alignment explanation
Indices: 2225671--2225718 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2225661 ATTGGAGGAT
2225671 TTAGGAATGTTGAAGATGTTC
1 TTAGGAATGTTGAAGATGTTC
2225692 TTAGGAATGTTGAAGATGTTC
1 TTAGGAATGTTGAAGATGTTC
2225713 TT-GGAA
1 TTAGGAA
2225719 CTGACCAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (21 bp):
TTAGGAATGTTGAAGATGTTC
Found at i:2230174 original size:3 final size:3
Alignment explanation
Indices: 2230166--2230200 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2230156 TGAGAATCTA
2230166 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2230201 ACTATTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2231390 original size:6 final size:6
Alignment explanation
Indices: 2231379--2231405 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2231369 ATATTAATTT
2231379 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
2231406 TATTAATAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:2233801 original size:1 final size:1
Alignment explanation
Indices: 2233797--2233829 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
2233787 TCGTTTTTGT
2233797 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2233830 CCGCGTGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2234561 original size:20 final size:19
Alignment explanation
Indices: 2234519--2234567 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2234509 TGTAAAATTT
*
2234519 TTTTATCAAAATAAATAATA
1 TTTTAT-AAAATAAATAAAA
*
2234539 TTTTATAAACTAAATATAAA
1 TTTTATAAAATAAATA-AAA
2234559 TTTTCATAA
1 TTTT-ATAA
2234568 TTAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 12 0.48
21 4 0.16
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTATAAAATAAATAAAA
Found at i:2241213 original size:15 final size:14
Alignment explanation
Indices: 2241195--2241229 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2241185 AAATTTTATC
2241195 TTTTTAATTAAAAT
1 TTTTTAATTAAAAT
*
2241209 TTTTTAATTTAAAT
1 TTTTTAATTAAAAT
*
2241223 TTATTAA
1 TTTTTAA
2241230 ATACAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAATTAAAAT
Found at i:2242219 original size:19 final size:20
Alignment explanation
Indices: 2242195--2242248 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
2242185 AACTCATGAG
2242195 TTTAATTAAATTTTTAA-AT
1 TTTAATTAAATTTTTAATAT
*
2242214 TTTAA-TATA-TTTTAATTAT
1 TTTAATTAAATTTTTAA-TAT
2242233 TTTAATTAAAATTTTT
1 TTTAATT-AAATTTTT
2242249 TTTATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 6 0.21
18 3 0.11
19 12 0.43
20 1 0.04
21 2 0.07
22 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAATTAAATTTTTAATAT
Found at i:2245929 original size:14 final size:14
Alignment explanation
Indices: 2245910--2245939 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2245900 CTTGGACCCA
2245910 CGAACCTAGAACCT
1 CGAACCTAGAACCT
*
2245924 CGAACCTGGAACCT
1 CGAACCTAGAACCT
2245938 CG
1 CG
2245940 CTCTGATACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.37, G:0.20, T:0.13
Consensus pattern (14 bp):
CGAACCTAGAACCT
Found at i:2248057 original size:27 final size:27
Alignment explanation
Indices: 2248027--2248079 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2248017 AATTCATATC
*
2248027 TATAAGTA-TGATTTTTAAATATTTTTT
1 TATAAGTATTAATTTTTAAA-ATTTTTT
**
2248054 TATATTTATTAATTTTTAAAATTTTT
1 TATAAGTATTAATTTTTAAAATTTTT
2248080 ACATGAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TATAAGTATTAATTTTTAAAATTTTTT
Found at i:2253782 original size:18 final size:18
Alignment explanation
Indices: 2253716--2253785 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
2253706 AATTTATCTT
*
2253716 ATTTTAATTTAATTAAAA
1 ATTTTATTTTAATTAAAA
*
2253734 ATTTTAATATTTTATTAATAA
1 ATTTT-AT-TTTAATTAA-AA
*
2253755 ATCACGTTATTTTAATTAAAA
1 AT---TTTATTTTAATTAAAA
2253776 ATTTTATTTT
1 ATTTTATTTT
2253786 TATATCAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
18 12 0.29
19 1 0.02
20 8 0.20
21 8 0.20
22 8 0.20
23 2 0.05
24 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (18 bp):
ATTTTATTTTAATTAAAA
Found at i:2255206 original size:70 final size:70
Alignment explanation
Indices: 2255093--2255234 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
2255083 TTTAGTTTTC
* *
2255093 ATCCAAGTTTAAGATATAAAATTTCAGTCTTTTAACTTATCTATAGTGCCTATTACTGATTGAGT
1 ATCCAAGTTTAAGATATAAAATTTCAGTCTTCTAACTTATCTATAGTGCCTATTACCGATTGAGT
2255158 TGTTA
66 TGTTA
*
2255163 ATCCAAGTTTCAGATATAAAATTTCAGTCTTCTAACTTATCTATAGTGCCTATTACCGATTGAGT
1 ATCCAAGTTTAAGATATAAAATTTCAGTCTTCTAACTTATCTATAGTGCCTATTACCGATTGAGT
2255228 TGTTA
66 TGTTA
2255233 AT
1 AT
2255235 AGTATTGGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (70 bp):
ATCCAAGTTTAAGATATAAAATTTCAGTCTTCTAACTTATCTATAGTGCCTATTACCGATTGAGT
TGTTA
Found at i:2262705 original size:256 final size:255
Alignment explanation
Indices: 2262246--2262760 Score: 976
Period size: 256 Copynumber: 2.0 Consensus size: 255
2262236 AGCTCAAATC
**
2262246 ATGAGAACTGTGATCCCAAGAGCAAGGAAGAGGAGGAAGCTGAAGAAGTGCTTCATGCTTCACAA
1 ATGAGAACTGTGATCCCAAGAGCAAGGAAGAGGAGGAAGCTGAAGAAGTGCTTCATAATTCACAA
*
2262311 ATGTGAGACAGATTTTGTAACCAGTGCTTAAAAATTTTGAGTTCCTTTGTTAGTGGAATTTGTAT
66 ATGTGAGACAGATTTTGTAACCAATGCTTAAAAATTTTGAGTTCCTTTGTTAGTGGAATTTGTAT
2262376 TGGTAATGGTTACAGGAAGCAGATAAAATCGAATTTGCTGCTTCAATAAAGATTAGAGTTCCAAG
131 TGGTAATGGTTACAGGAAGCAGATAAAATCGAATTTGCTGCTTCAATAAAGATTAGAGTTCCAAG
2262441 CTTCCAATTCCAGGTCCATTCCTCGTATGTTCACCTAATATATCAATGCATAAATCTTTT
196 CTTCCAATTCCAGGTCCATTCCTCGTATGTTCACCTAATATATCAATGCATAAATCTTTT
2262501 ATGAGAACTGTGATCCCAAGAGCAAGGAAGAGGAGGAAGCTGAAGAAGTGCTTCATAATTCACAA
1 ATGAGAACTGTGATCCCAAGAGCAAGGAAGAGGAGGAAGCTGAAGAAGTGCTTCATAATTCACAA
*
2262566 ATGTGAGACAGATTTTGTAACCAATGCTTAAAAATTTTTTAGTTCCTTTGTTAGTGGAATTTGTA
66 ATGTGAGACAGATTTTGTAACCAATGCTTAAAAA-TTTTGAGTTCCTTTGTTAGTGGAATTTGTA
2262631 TTGGTAATGGTTACAGGAAGCAGATAAAATCGAATTTGCTGCTTCAATAAAGATTAGAGTTCCAA
130 TTGGTAATGGTTACAGGAAGCAGATAAAATCGAATTTGCTGCTTCAATAAAGATTAGAGTTCCAA
*
2262696 GCTTCCAATTCCAGGTCCATTCCTCGTATGTTCACCTAGTATATCAATGCATAAATCTTTT
195 GCTTCCAATTCCAGGTCCATTCCTCGTATGTTCACCTAATATATCAATGCATAAATCTTTT
2262757 ATGA
1 ATGA
2262761 ACTGCTCTAA
Statistics
Matches: 254, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
255 96 0.38
256 158 0.62
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (255 bp):
ATGAGAACTGTGATCCCAAGAGCAAGGAAGAGGAGGAAGCTGAAGAAGTGCTTCATAATTCACAA
ATGTGAGACAGATTTTGTAACCAATGCTTAAAAATTTTGAGTTCCTTTGTTAGTGGAATTTGTAT
TGGTAATGGTTACAGGAAGCAGATAAAATCGAATTTGCTGCTTCAATAAAGATTAGAGTTCCAAG
CTTCCAATTCCAGGTCCATTCCTCGTATGTTCACCTAATATATCAATGCATAAATCTTTT
Found at i:2268514 original size:76 final size:76
Alignment explanation
Indices: 2268388--2268542 Score: 265
Period size: 76 Copynumber: 2.0 Consensus size: 76
2268378 AGTGCCACTG
* * *
2268388 GGTTAAAGGTAGAGAATTTAAACTATGCATGTGGTTATGCTAATTGTCATTTGACAATGTTGTGG
1 GGTTAAAGGTAAAGAACTTAAACTATGCATGTAGTTATGCTAATTGTCATTTGACAATGTTGTGG
**
2268453 TTTATTATTGT
66 GCTATTATTGT
2268464 GGTTAAAGGTAAAGAACTTAAACTATGCATGTAGTTATGCTAATTGTCATTTGACAATGTTGTGG
1 GGTTAAAGGTAAAGAACTTAAACTATGCATGTAGTTATGCTAATTGTCATTTGACAATGTTGTGG
2268529 GCTATTATTGT
66 GCTATTATTGT
2268540 GGT
1 GGT
2268543 AATTTTTGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (76 bp):
GGTTAAAGGTAAAGAACTTAAACTATGCATGTAGTTATGCTAATTGTCATTTGACAATGTTGTGG
GCTATTATTGT
Found at i:2286363 original size:18 final size:18
Alignment explanation
Indices: 2286340--2286383 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
2286330 AGCTTTGTGT
*
2286340 TAAATGGGCCTTAAATGG
1 TAAATGAGCCTTAAATGG
2286358 TAAATGAGCCTTAAATGG
1 TAAATGAGCCTTAAATGG
2286376 TAAATGAG
1 TAAATGAG
2286384 ACTGAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (18 bp):
TAAATGAGCCTTAAATGG
Done.