Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007915.1 Hibiscus syriacus cultivar Beakdansim tig00110318_pilon, 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: 1667290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1439240 original size:11 final size:11
Alignment explanation
Indices: 1439226--1439277 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1439216 AACAAAAAGT
1439226 GAAAAAAAAAA
1 GAAAAAAAAAA
1439237 GAAAAAAAAAGA
1 GAAAAAAAAA-A
*
1439249 GAAAAAACAAA
1 GAAAAAAAAAA
* **
1439260 GGAAAATTAAA
1 GAAAAAAAAAA
1439271 GAAAAAA
1 GAAAAAA
1439278 GAATACAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 24 0.71
12 10 0.29
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:1439242 original size:12 final size:12
Alignment explanation
Indices: 1439227--1439265 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1439217 ACAAAAAGTG
1439227 AAAAAAAAAAGA
1 AAAAAAAAAAGA
*
1439239 AAAAAAAAGAGA
1 AAAAAAAAAAGA
* *
1439251 AAAAACAAAGGA
1 AAAAAAAAAAGA
1439263 AAA
1 AAA
1439266 TTAAAGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1439252 original size:23 final size:23
Alignment explanation
Indices: 1439219--1439265 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1439209 CAATCAGAAC
*
1439219 AAAAAGTGAAAAAAAAAAGAAAA
1 AAAAAGAGAAAAAAAAAAGAAAA
* *
1439242 AAAAAGAGAAAAAACAAAGGAAA
1 AAAAAGAGAAAAAAAAAAGAAAA
1439265 A
1 A
1439266 TTAAAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAAAAGAAAA
Found at i:1440417 original size:32 final size:32
Alignment explanation
Indices: 1440339--1440432 Score: 118
Period size: 31 Copynumber: 2.9 Consensus size: 32
1440329 TGAGGGCATC
* *
1440339 TTTGAAGATTCAACATCAAATGTTGGGGTATTT
1 TTTG-AGATTCAACATCAAATATTGGGGCATTT
** *
1440372 TTT-TTATTTAACATCAAATATTGGGGCATTT
1 TTTGAGATTCAACATCAAATATTGGGGCATTT
*
1440403 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATATTGGGGCAT
1440433 CTTTGGAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.51
32 22 0.43
33 3 0.06
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGGCATTT
Found at i:1440445 original size:32 final size:32
Alignment explanation
Indices: 1440332--1440445 Score: 115
Period size: 32 Copynumber: 3.6 Consensus size: 32
1440322 GGAACAATGA
*
1440332 GGGCATC-TTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTTGAA-ATTCAACATCAAATATTG
* *** *
1440364 GGGTAT-TTTTTTTATTTAACATCAAATATTG
1 GGGCATCTTTTGAAATTCAACATCAAATATTG
* * *
1440395 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCATCTTTTGAAATTCAACATCAAATATTG
*
1440427 GGGCATCTTTGGAAATTCA
1 GGGCATCTTTTGAAATTCA
1440446 TGTTACATGC
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
31 21 0.32
32 44 0.68
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (32 bp):
GGGCATCTTTTGAAATTCAACATCAAATATTG
Found at i:1441037 original size:105 final size:106
Alignment explanation
Indices: 1440915--1441130 Score: 308
Period size: 105 Copynumber: 2.0 Consensus size: 106
1440905 ATATCGTGCC
* * * * *
1440915 ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGTTGGTTGTCAATAAA-ATTTTCCC
1 ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTACC
*
1440979 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* **
1441020 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTATT
1 ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTACC
* * * *
1441085 AGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1441126 ACTCG
1 ACTCG
1441131 GAACTATACA
Statistics
Matches: 97, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
105 52 0.54
106 45 0.46
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTACC
AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1441576 original size:101 final size:101
Alignment explanation
Indices: 1441470--1441709 Score: 367
Period size: 101 Copynumber: 2.4 Consensus size: 101
1441460 AAATTTTGTC
* *
1441470 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTATCTCGCT-TGGGGTAGTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTT-TCTCGCTCTGAGATAGTT
1441534 TCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
65 TCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
** * * *
1441571 TCTCTTGAAACATAAACATTGAAAACATTTCTTTTGAAATTAATTTTGTCTCTCTGAGATAGTTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTCTCGCTCTGAGATAGTTT
*
1441636 CCCTTGAAACAAAATTTTGTCTCCCTTGAGATAGTT
66 CCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
* *
1441672 TCTCTTGAAACAT-AACCTTGAAAACGTTTCCCTTGAAA
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
1441710 CACAAAATAT
Statistics
Matches: 126, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
100 26 0.21
101 100 0.79
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (101 bp):
TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTCTCGCTCTGAGATAGTTT
CCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
Found at i:1441578 original size:37 final size:37
Alignment explanation
Indices: 1441530--1441683 Score: 116
Period size: 37 Copynumber: 4.4 Consensus size: 37
1441520 CGCTTGGGGT
*
1441530 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAC
1 AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGAC
* *
1441567 AGTTTCTCTTGAAACATAAA---------CATTGAAAAC
1 AGTTTCTCTTGAAACA-AAATTTTGTCTCCCTTG-AGAC
* ** * *
1441597 A-TTTCTTTTGAAA-TTAATTTTGTCTCTC-TGAGAT
1 AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGAC
* *
1441631 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAT
1 AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGAC
1441668 AGTTTCTCTTGAAACA
1 AGTTTCTCTTGAAACA
1441684 TAACCTTGAA
Statistics
Matches: 87, Mismatches: 16, Indels: 28
0.66 0.12 0.21
Matches are distributed among these distances:
27 2 0.02
29 15 0.17
30 4 0.05
34 3 0.03
35 12 0.14
36 12 0.14
37 36 0.41
38 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (37 bp):
AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGAC
Found at i:1441583 original size:86 final size:87
Alignment explanation
Indices: 1441388--1441563 Score: 282
Period size: 86 Copynumber: 2.0 Consensus size: 87
1441378 ACAGTTTCTC
* *
1441388 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCTCT
1 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAATTTATCTCGATTGAGATAGTTTCCCT
* *
1441453 TGAAACGAAATTTTGTCTCTCT
66 TGAAACAAAATTTTGTCTCCCT
* * *
1441475 TGAAACATAAACATTGAAAACATTTCCCTTGAAAT-AAATTTATCTCGCTTGGGGTAGTTTCCCT
1 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAATTTATCTCGATTGAGATAGTTTCCCT
1441539 TGAAACAAAATTTTGTCTCCCT
66 TGAAACAAAATTTTGTCTCCCT
1441561 TGA
1 TGA
1441564 GACAGTTTCT
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 47 0.57
87 35 0.43
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (87 bp):
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAATTTATCTCGATTGAGATAGTTTCCCT
TGAAACAAAATTTTGTCTCCCT
Found at i:1441653 original size:36 final size:37
Alignment explanation
Indices: 1441612--1441683 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1441602 TTTTGAAATT
*
1441612 AATTTTGTCTCTC-TGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
*
1441648 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
1441684 TAACCTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 12 0.36
37 21 0.64
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:1441791 original size:21 final size:20
Alignment explanation
Indices: 1441761--1441822 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
1441751 GACAGTTTCC
1441761 CTTGAAACAAATCTTGTCTCT
1 CTTGAAACAAAT-TTGTCTCT
*
1441782 CTTGAGAC-AA-TT-TC-C-
1 CTTGAAACAAATTTGTCTCT
1441797 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAA-TTTGTCTCT
1441818 CTTGA
1 CTTGA
1441823 GACAGTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 2 0.06
18 4 0.12
19 2 0.06
20 3 0.09
21 12 0.36
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (20 bp):
CTTGAAACAAATTTGTCTCT
Found at i:1441796 original size:36 final size:36
Alignment explanation
Indices: 1441747--1441848 Score: 177
Period size: 36 Copynumber: 2.8 Consensus size: 36
1441737 AAAACGAGTT
1441747 TTGAGACAGTTTCCCTTGAAACAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAATCTTGTCTCTC
* *
1441783 TTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAATCTTGTCTCTC
1441819 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAAC-AAATCTT
1441849 TGAATATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 55 0.90
37 6 0.10
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (36 bp):
TTGAGACAGTTTCCCTTGAAACAAATCTTGTCTCTC
Found at i:1441879 original size:101 final size:102
Alignment explanation
Indices: 1441760--1441945 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 102
1441750 AGACAGTTTC
*
1441760 CCTTGAAACAAATCTTGTCTCTCTTGAGACAATTTCCCTTGA-AAC-AAATTTTGTCTCTCTTGA
1 CCTTGAAACAAATCTTGTCTCTCTTGAGACAATTT-CCTTGAGAACTAAATTTTATCTCTCTTGA
1441823 GACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
65 GACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * * * *
1441861 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAGTTTTATCTCTCTTGAG
1 CCTTGAAACAAATCTTGTCTCTCTTGAGACAATTTCCTTGAGAACTAAATTTTATCTCTCTTGAG
**
1441926 ACAGTTTCTTTTGAAACAAA
66 ACAGTTTCCCTTGAAACAAA
1441946 TTTTGTCCCT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 4 0.05
101 36 0.48
102 35 0.47
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (102 bp):
CCTTGAAACAAATCTTGTCTCTCTTGAGACAATTTCCTTGAGAACTAAATTTTATCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:1441920 original size:37 final size:36
Alignment explanation
Indices: 1441863--1441979 Score: 173
Period size: 36 Copynumber: 3.2 Consensus size: 36
1441853 TATCTTTTCC
1441863 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
1441899 TT-AGAACTAAGTTTTATCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
1441936 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
1441972 TTGAAACA
1 TTGAAACA
1441980 CAAAAAAAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.01
36 38 0.53
37 32 0.44
38 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:1443198 original size:8 final size:9
Alignment explanation
Indices: 1443179--1443358 Score: 55
Period size: 9 Copynumber: 18.7 Consensus size: 9
1443169 GTTTAGTATA
1443179 TATTTTTAT
1 TATTTTTAT
1443188 TATTTTTTTAT
1 TA--TTTTTAT
1443199 TATCAGTTTTAT
1 TAT---TTTTAT
*
1443211 TGATTTATA-
1 T-ATTTTTAT
*
1443220 TATATTTTAC
1 TAT-TTTTAT
1443230 TATTTTTTAT
1 TA-TTTTTAT
1443240 TATTTATTTAT
1 TA-TT-TTTAT
1443251 TATATATATATAT
1 TAT-T-T-T-TAT
*
1443264 TATTTTTTAC
1 TA-TTTTTAT
1443274 T-TTTTTAT
1 TATTTTTAT
*
1443282 TATTATT-T
1 TATTTTTAT
*
1443290 TATTTAT-T
1 TATTTTTAT
1443298 TATTTGTT-T
1 TATTT-TTAT
*
1443307 TATTTATAT
1 TATTTTTAT
* *
1443316 TTTTTTTCT
1 TATTTTTAT
* *
1443325 TCTTTTTCTT
1 TATTTTT-AT
*
1443335 TATTTTTTT
1 TATTTTTAT
* *
1443344 TTTTTTTTT
1 TATTTTTAT
1443353 TATTTT
1 TATTTT
1443359 ACTTACTATT
Statistics
Matches: 135, Mismatches: 18, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
8 22 0.16
9 47 0.35
10 27 0.20
11 21 0.16
12 9 0.07
13 8 0.06
14 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTTTTAT
Found at i:1443224 original size:45 final size:42
Alignment explanation
Indices: 1443175--1443300 Score: 120
Period size: 42 Copynumber: 3.0 Consensus size: 42
1443165 TTTAGTTTAG
*
1443175 TATATATTTTTATTATTTTTTTATTATCAGTTTTATTGA-TT-TA
1 TATATATTTTTATTA-TTTTTTATTAT-A-TTTTATTTATTTATA
*
1443218 TATATA-TTTTACTATTTTTTA-T-TA-TTTATTTATTATATA
1 TATATATTTTTATTATTTTTTATTATATTTTATTTATT-TATA
*
1443257 TATATATTATTTTTTACTTTTTTATTATTATTTTATTTATTTAT
1 TATATATT-TTTATTA-TTTTTTATTA-TATTTTATTTATTTAT
1443301 TTGTTTTATT
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
36 7 0.10
37 1 0.01
38 2 0.03
39 9 0.13
40 2 0.03
41 12 0.17
42 14 0.20
43 7 0.10
45 5 0.07
46 10 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (42 bp):
TATATATTTTTATTATTTTTTATTATATTTTATTTATTTATA
Found at i:1443248 original size:4 final size:4
Alignment explanation
Indices: 1443230--1443313 Score: 56
Period size: 4 Copynumber: 21.8 Consensus size: 4
1443220 TATATTTTAC
* *
1443230 TATT T-TT TA-T TATT TATT TA-T TATA TATA TATAT TATT T-TT TACTT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TA-TT
*
1443276 T-TT TA-T TA-T TATTT TATT TATT TATT TGTTT TATT TAT
1 TATT TATT TATT TA-TT TATT TATT TATT T-ATT TATT TAT
1443314 ATTTTTTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
3 21 0.32
4 33 0.50
5 12 0.18
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1443294 original size:5 final size:5
Alignment explanation
Indices: 1443276--1443439 Score: 55
Period size: 5 Copynumber: 33.6 Consensus size: 5
1443266 TTTTTTACTT
* *
1443276 TTTTA TTATTA TTTTA -TTTA -TTTA -TTTG TTTTA TTTATA TTTT- TTTTC
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA
* * * *
1443324 TTCT- TTTT- CTTTA TTTT- TTTT- TTTTT TTTTA TTTTA CTTACTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA
* * * * * * *
1443372 TCTTTG CTCT- CTTTA TCTTA TCTTTA -TTTA ATTTA TTTTT TTCTTCA
1 T-TTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TT-TT-A
1443419 TTTTA TTTTA -TTTA -TTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTT
1443440 CTAACCTTTT
Statistics
Matches: 125, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
4 44 0.35
5 53 0.42
6 24 0.19
7 4 0.03
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:1443301 original size:34 final size:34
Alignment explanation
Indices: 1443207--1443313 Score: 98
Period size: 34 Copynumber: 3.2 Consensus size: 34
1443197 ATTATCAGTT
* * *
1443207 TTATTGATTTA-TATATAT-TTTACTATTTTTTA
1 TTATTTATTTATTATATATATATATTATTTTTTA
1443239 TTATTTATTTATTATATATATATATTATTTTTTA
1 TTATTTATTTATTATATATATATATTATTTTTTA
* * * *
1443273 CTTTTTTA-TTATTAT-TTTATTTATTTATTTGTT-
1 -TTATTTATTTATTATATATATATA-TTATTTTTTA
1443306 TTATTTAT
1 TTATTTAT
1443314 ATTTTTTTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
32 16 0.26
33 13 0.21
34 27 0.44
35 6 0.10
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (34 bp):
TTATTTATTTATTATATATATATATTATTTTTTA
Found at i:1443315 original size:54 final size:51
Alignment explanation
Indices: 1443224--1443331 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 51
1443214 TTTATATATA
1443224 TTTTACTATTTTTTATTATTTATTTATTATATATATATATTATTTTT-TACTT
1 TTTTACTATTTTTTATTATTTATTTATTATATATATAT-TT-TTTTTCTACTT
* * * * *
1443276 TTTTATTATTATTTTATTTATTTATTTGTTTTATTTATATTTTTTTTCTTCTT
1 TTTTACTATT-TTTTA-TTATTTATTTATTATATATATATTTTTTTTCTACTT
1443329 TTT
1 TTT
1443332 CTTTATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
52 14 0.29
53 14 0.29
54 20 0.42
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (51 bp):
TTTTACTATTTTTTATTATTTATTTATTATATATATATTTTTTTTCTACTT
Found at i:1443316 original size:28 final size:25
Alignment explanation
Indices: 1443224--1443356 Score: 82
Period size: 27 Copynumber: 5.3 Consensus size: 25
1443214 TTTATATATA
* * * *
1443224 TTTTACTATTTTTTATTATTTATTT
1 TTTTATTATATTTTATTTTTTACTT
* *
1443249 ATTATATATATATATTATTTTTTACTT
1 -TTTTAT-TATATTTTATTTTTTACTT
*
1443276 TTTTATTATTATTTTATTTATTTATTT
1 TTTTATTA-TATTTTATTT-TTTACTT
1443303 GTTTTATTTATATTTT-TTTTCTT-CTT
1 -TTTTA-TTATATTTTATTTT-TTACTT
1443329 TTTCT-TTAT-TTTT-TTTTTT--TT
1 TTT-TATTATATTTTATTTTTTACTT
1443350 TTTTATT
1 TTTTATT
1443357 TTACTTACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
20 1 0.01
21 7 0.08
22 2 0.02
23 8 0.09
24 4 0.04
25 5 0.06
26 22 0.25
27 26 0.29
28 11 0.12
29 3 0.03
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.77
Consensus pattern (25 bp):
TTTTATTATATTTTATTTTTTACTT
Found at i:1443319 original size:41 final size:39
Alignment explanation
Indices: 1443177--1443372 Score: 125
Period size: 41 Copynumber: 4.9 Consensus size: 39
1443167 TAGTTTAGTA
* * *
1443177 TATATTTTTATTAT-TTTTTTATTATCAGTTTTATTGATT
1 TATATTTTTTTTATATTTTTTATTATTA-TTTTATTTATT
* *
1443216 TATATATATTTTACTATTTTTTATTATT-TATTTATTATATAT
1 TATATTTTTTTTA-TATTTTTTATTATTAT-TTTATT-TAT-T
*
1443258 ATATATTATTTTTTA-CTTTTTTATTATTATTTTATTTATT
1 -TATATT-TTTTTTATATTTTTTATTATTATTTTATTTATT
* * * *
1443298 TATTTGTTTTATTTATATTTTTT-TTCTTCTTTTTCTTTATT
1 TATAT-TTTT-TTTATATTTTTTATTATT-ATTTTATTTATT
* * *
1443339 T-T-TTTTTTTTTTTTTATTTTACTTACTATTTTAT
1 TATATTTTTTTTATATT-TTTTA-TTATTATTTTAT
1443373 CTTTGCTCTC
Statistics
Matches: 123, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
37 6 0.05
38 8 0.07
39 24 0.20
40 21 0.17
41 33 0.27
42 19 0.15
43 6 0.05
44 6 0.05
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (39 bp):
TATATTTTTTTTATATTTTTTATTATTATTTTATTTATT
Found at i:1443320 original size:50 final size:52
Alignment explanation
Indices: 1443224--1443357 Score: 135
Period size: 52 Copynumber: 2.7 Consensus size: 52
1443214 TTTATATATA
* *
1443224 TTTTACTATT-TTTTA-TTATTTATTTATTATATATATATATTATTTTTTACTT-
1 TTTTATTATTATTTTATTTATTTATTT-TT-T-TATTTATATTATTTTTTACTTC
1443276 TTTTATTATTATTTTATTTATTTATTTGTTTTATTTATATT-TTTTTT-CTTC
1 TTTTATTATTATTTTATTTATTTATTT-TTTTATTTATATTATTTTTTACTTC
1443327 TTTT-TCT-TTATTTT-TTT-TTT-TTTTTTTATTT
1 TTTTAT-TATTATTTTATTTATTTATTTTTTTATTT
1443358 TACTTACTAT
Statistics
Matches: 75, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
46 8 0.11
47 3 0.04
48 3 0.04
49 3 0.04
50 11 0.15
51 11 0.15
52 18 0.24
53 6 0.08
54 12 0.16
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.77
Consensus pattern (52 bp):
TTTTATTATTATTTTATTTATTTATTTTTTTATTTATATTATTTTTTACTTC
Found at i:1443336 original size:24 final size:22
Alignment explanation
Indices: 1443304--1443357 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1443294 TATTTATTTG
1443304 TTTTATTTATATTTTTTTTCTTCT
1 TTTTATTTAT-TTTTTTTT-TTCT
* *
1443328 TTTTCTTTATTTTTTTTTTTTT
1 TTTTATTTATTTTTTTTTTTCT
1443350 TTTTATTT
1 TTTTATTT
1443358 TACTTACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 10 0.37
23 8 0.30
24 9 0.33
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTATTTATTTTTTTTTTTCT
Found at i:1443358 original size:28 final size:27
Alignment explanation
Indices: 1443266--1443358 Score: 53
Period size: 31 Copynumber: 3.1 Consensus size: 27
1443256 ATATATATTA
*
1443266 TTTTTTACTTTTTTATTATTATTTTATTTAT
1 TTTTTTA-TTTTTT-TTATT-TTTT-TTTTT
* *
1443297 TTATTTGTTTTATTTATATTTTTTTTCTTCTT
1 TTTTTTATTTT-TTT-TA-TTTTTTT-TT-TT
1443329 TTTCTTTATTTTTTTT-TTTTTTTTTATT
1 TTT-TTTATTTTTTTTATTTTTTTTT-TT
1443357 TT
1 TT
1443359 ACTTACTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
28 6 0.12
29 7 0.14
30 6 0.12
31 16 0.32
32 8 0.16
33 7 0.14
ACGTcount: A:0.13, C:0.04, G:0.01, T:0.82
Consensus pattern (27 bp):
TTTTTTATTTTTTTTATTTTTTTTTTT
Found at i:1451818 original size:15 final size:15
Alignment explanation
Indices: 1451800--1451841 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1451790 AAGAACTCGT
1451800 TGCTCGTAAACTTCC
1 TGCTCGTAAACTTCC
*
1451815 TGCTCGGAAACTTCC
1 TGCTCGTAAACTTCC
* *
1451830 GGCCCGTAAACT
1 TGCTCGTAAACT
1451842 GTGGCTCGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (15 bp):
TGCTCGTAAACTTCC
Found at i:1452168 original size:3 final size:3
Alignment explanation
Indices: 1452160--1452184 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1452150 TAACGGCATC
1452160 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1452185 CAGTAGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1461436 original size:19 final size:17
Alignment explanation
Indices: 1461402--1461438 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
1461392 TGTGCATATT
1461402 TATAAATGTTATAAAAA
1 TATAAATGTTATAAAAA
1461419 TATAACATGTTCATAAAAA
1 TATAA-ATGTT-ATAAAAA
1461438 T
1 T
1461439 CGTGACAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
TATAAATGTTATAAAAA
Found at i:1461574 original size:26 final size:26
Alignment explanation
Indices: 1461545--1461608 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1461535 ATTATATATA
1461545 TAATTATAAATAATAAC-ATTAAAA-TT
1 TAATTATAAATAAT--CTATTAAAACTT
*
1461571 TAATTATAGAA-AATCTTTTAAAACTT
1 TAATTATA-AATAATCTATTAAAACTT
1461597 TAATTATAAATA
1 TAATTATAAATA
1461609 TGATAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 1 0.03
25 8 0.24
26 22 0.67
27 2 0.06
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATTATAAATAATCTATTAAAACTT
Found at i:1465231 original size:16 final size:16
Alignment explanation
Indices: 1465207--1465248 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1465197 ATTTGGAATC
*
1465207 TATTTTAAAAAAACA-A
1 TATTATAAAAAAA-ATA
*
1465223 TATTATAAAAAAAATT
1 TATTATAAAAAAAATA
1465239 TATTATAAAA
1 TATTATAAAA
1465249 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TATTATAAAAAAAATA
Found at i:1465639 original size:13 final size:14
Alignment explanation
Indices: 1465611--1465637 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1465601 TTTTCTTCCA
1465611 AAGTTTTTGTTTTT
1 AAGTTTTTGTTTTT
1465625 AAGTTTTTGTTTT
1 AAGTTTTTGTTTT
1465638 AATTATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (14 bp):
AAGTTTTTGTTTTT
Found at i:1466890 original size:21 final size:21
Alignment explanation
Indices: 1466864--1466980 Score: 189
Period size: 21 Copynumber: 5.6 Consensus size: 21
1466854 GTTTCCAGAT
* *
1466864 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
1466885 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1466906 TCGCAATGCGAACTTAGACTA
1 TCGCAATGCGAACTTGGACTA
1466927 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1466948 TCGTAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1466969 TCGTAATGCGAA
1 TCGCAATGCGAA
1466981 TATGTAAATC
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 91 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1467084 original size:21 final size:21
Alignment explanation
Indices: 1466989--1467076 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
1466979 AATATGTAAA
1466989 TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCGATAGTCGAAGT
1467010 TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCGATAGTCGAAGT
*
1467031 TCGCAATACGATAGTCGAAGT
1 TCGCAATGCGATAGTCGAAGT
* *
1467052 TCGCATTGCGATAGTCAAAGT
1 TCGCAATGCGATAGTCGAAGT
1467073 TCGC
1 TCGC
1467077 GTTGCGATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGATAGTCGAAGT
Found at i:1467169 original size:21 final size:21
Alignment explanation
Indices: 1467124--1467211 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
1467114 ACTTCGACTA
* * *
1467124 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
*
1467144 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
*
1467165 TCGCATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
1467188 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
1467207 TCGCA
1 TCGCA
1467212 ATGACTGGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
19 11 0.20
20 12 0.22
21 21 0.38
23 11 0.20
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:1467169 original size:41 final size:40
Alignment explanation
Indices: 1467124--1467204 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 40
1467114 ACTTCGACTA
*
1467124 TCGCATTGCGATTTA-CATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTATCAAATTCG--TTGCGATAGTCCAAGT
1467165 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTA-T-CAAATTCGTTGCGATAGTCCAA
1467205 AATCGCAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
41 15 0.42
42 14 0.39
44 7 0.19
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (40 bp):
TCGCATTGCGATTTATCAAATTCGTTGCGATAGTCCAAGT
Found at i:1467211 original size:42 final size:40
Alignment explanation
Indices: 1467123--1467211 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 40
1467113 AACTTCGACT
* *
1467123 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 ATCGCATTGCGATTTACAAATTCG-ATTGCGATAGTCCAAA
*
1467164 TTCGCATTGCGATTTATTCCAAATTCG-TTGCGATAGTCCAAA
1 ATCGCATTGCGATTTA---CAAATTCGATTGCGATAGTCCAAA
1467206 ATCGCA
1 ATCGCA
1467212 ATGACTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 15 0.37
42 19 0.46
44 7 0.17
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (40 bp):
ATCGCATTGCGATTTACAAATTCGATTGCGATAGTCCAAA
Found at i:1467787 original size:6 final size:6
Alignment explanation
Indices: 1467778--1467809 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1467768 CGCCGCCGCC
1467778 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1467810 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:1467915 original size:19 final size:19
Alignment explanation
Indices: 1467894--1468029 Score: 137
Period size: 21 Copynumber: 6.7 Consensus size: 19
1467884 CGTTGCGATT
* *
1467894 TTGGACTATCGTAACGAAT
1 TTGGACTATCGCAACGAAC
*
1467913 TTGGAATAAATCGCAACGAAC
1 TTGGACT--ATCGCAACGAAC
1467934 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
* *
1467953 TTGGAATAAATCGCAACGAAT
1 TTGGACT--ATCGCAACGAAC
*
1467974 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
1467997 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
1468016 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1468030 TGCGATAGTC
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
19 42 0.42
21 50 0.50
23 9 0.09
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:1467930 original size:21 final size:21
Alignment explanation
Indices: 1467901--1468020 Score: 140
Period size: 21 Copynumber: 5.8 Consensus size: 21
1467891 ATTTTGGACT
* *
1467901 ATCGTAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1467922 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
1467941 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1467962 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1467983 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
1468004 ATCGCAACGAACTTGGA
1 ATCGCAACGAACTTGGA
1468021 CTATCGCAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
19 27 0.31
21 50 0.58
23 9 0.10
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1467950 original size:40 final size:40
Alignment explanation
Indices: 1467894--1468029 Score: 168
Period size: 40 Copynumber: 3.4 Consensus size: 40
1467884 CGTTGCGATT
* *
1467894 TTGGACTATCGTAACGAATTTGGAATAAATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
*
1467934 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
* * *
1467974 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
1468016 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1468030 TGCGATAGTC
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
40 50 0.60
42 24 0.29
44 10 0.12
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
Found at i:1467976 original size:61 final size:62
Alignment explanation
Indices: 1467901--1468020 Score: 206
Period size: 63 Copynumber: 1.9 Consensus size: 62
1467891 ATTTTGGACT
* *
1467901 ATCGTAACGAATTTGGAATAAATCGCAA-CGAACTTGGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACCGAACTTCGACTATCGCAACGAACTTGGAATAA
1467962 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 ATCGCAACGAATTTGGAATAAATCGCAAC-CGAACTTCGACTATCGCAACGAACTTGGA
1468021 CTATCGCAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 27 0.49
63 28 0.51
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (62 bp):
ATCGCAACGAATTTGGAATAAATCGCAACCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:1468277 original size:2 final size:2
Alignment explanation
Indices: 1468270--1468351 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
1468260 TATGTTGTTA
1468270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1468312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1468352 CCTTAAATTA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1469263 original size:18 final size:18
Alignment explanation
Indices: 1469228--1469276 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1469218 AAAAAAATCA
* * *
1469228 TAAATTTATAATTTTTTT
1 TAAATTTAAAAATATTTT
1469246 TAAATTTAAAAATATTTT
1 TAAATTTAAAAATATTTT
* *
1469264 CATATTTAAAAAT
1 TAAATTTAAAAAT
1469277 TAAAAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTTAAAAATATTTT
Found at i:1469908 original size:97 final size:102
Alignment explanation
Indices: 1469778--1469983 Score: 343
Period size: 97 Copynumber: 2.0 Consensus size: 102
1469768 TTAATCTATA
1469778 ATTG-TTAAGGTTAATGGTGATTAACTGATTACTAAATTTGATTTTTTTTGTTCGTGAATTAA-T
1 ATTGATTAAGGTTAA--GTGATTAACTGATTACTAAATTTGATTTTTTTTGTTCGTGAATTAATT
1469841 TT-TATAAACGCAGCTTGCCATGG-AAATATCC-CAATT
64 TTATATAAACGCAGCTTGCCATGGAAAATATCCACAATT
1469877 ATTGATTAAGGTTAA-TGATTAACTGATTACTAAATTTGATTTTTTTTGTTCGTGAATTAATTTT
1 ATTGATTAAGGTTAAGTGATTAACTGATTACTAAATTTGATTTTTTTTGTTCGTGAATTAATTTT
1469941 ATATAAACGCAGCTTGCCATGGAAAATATCCAACAATT
66 ATATAAACGCAGCTTGCCATGGAAAATATCC-ACAATT
1469979 ATTGA
1 ATTGA
1469984 GTTTTTTAAA
Statistics
Matches: 101, Mismatches: 0, Indels: 9
0.92 0.00 0.08
Matches are distributed among these distances:
97 45 0.45
98 3 0.03
99 25 0.25
100 18 0.18
102 10 0.10
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (102 bp):
ATTGATTAAGGTTAAGTGATTAACTGATTACTAAATTTGATTTTTTTTGTTCGTGAATTAATTTT
ATATAAACGCAGCTTGCCATGGAAAATATCCACAATT
Found at i:1475957 original size:24 final size:24
Alignment explanation
Indices: 1475930--1475978 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1475920 ACAAGGAATG
* *
1475930 GAAATTTGAAGTTTGAAATCGCCT
1 GAAATTTGAAATTTGAAAACGCCT
1475954 GAAATTTGAAATTTGAAAACGCCT
1 GAAATTTGAAATTTGAAAACGCCT
1475978 G
1 G
1475979 GTTAGAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (24 bp):
GAAATTTGAAATTTGAAAACGCCT
Found at i:1480749 original size:21 final size:22
Alignment explanation
Indices: 1480725--1480765 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1480715 CTATGTGGTC
*
1480725 TTTCGGGGTAAA-TATGTGACA
1 TTTCGGGGCAAATTATGTGACA
*
1480746 TTTCGGTGCAAATTATGTGA
1 TTTCGGGGCAAATTATGTGA
1480766 GTAGTGGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (22 bp):
TTTCGGGGCAAATTATGTGACA
Found at i:1483912 original size:22 final size:22
Alignment explanation
Indices: 1483884--1483926 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1483874 CCTCCAACCG
1483884 AACGCCATATACAGTTCCCCAT
1 AACGCCATATACAGTTCCCCAT
*
1483906 AACGCCATATGCAGTTCCCCA
1 AACGCCATATACAGTTCCCCA
1483927 GAACTGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.37, G:0.12, T:0.21
Consensus pattern (22 bp):
AACGCCATATACAGTTCCCCAT
Found at i:1483989 original size:31 final size:31
Alignment explanation
Indices: 1483954--1484037 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 31
1483944 GGAGTACCTT
* * *
1483954 GGGGCCTGAGAGCCTACCCAAGACAATTCTC
1 GGGGCCAGAGAGCCTACCCAAGAAAAATCTC
*
1483985 GGGGCCACG-GAGGCTTACCCAAGAAAAATCTC
1 GGGGCCA-GAGA-GCCTACCCAAGAAAAATCTC
* *
1484017 GGGGCCACAAAGCCTACCCAA
1 GGGGCCAGAGAGCCTACCCAA
1484038 TGGTCGCCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
31 17 0.40
32 26 0.60
ACGTcount: A:0.30, C:0.32, G:0.26, T:0.12
Consensus pattern (31 bp):
GGGGCCAGAGAGCCTACCCAAGAAAAATCTC
Found at i:1484873 original size:19 final size:19
Alignment explanation
Indices: 1484849--1484893 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1484839 TAACTTTTCG
*
1484849 GGTCAAAATCAACGGGTCA
1 GGTCAAAATCAACGAGTCA
* *
1484868 GGTCAAAGTCAACGAGTCG
1 GGTCAAAATCAACGAGTCA
1484887 GGTCAAA
1 GGTCAAA
1484894 CAGGTCAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.29, T:0.16
Consensus pattern (19 bp):
GGTCAAAATCAACGAGTCA
Found at i:1489499 original size:55 final size:58
Alignment explanation
Indices: 1489431--1489541 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 58
1489421 TAAAATAGTG
* *
1489431 TTAATTATAAATTGAATAG-T-A-TGATTATGCATACAGTTACATCAATTCACATCCT
1 TTAATTATAAATTGAAGAGATAAGTGATTATGCATACAGTCACATCAATTCACATCCT
*
1489486 TTAATTA-AGAATTGAAGAGTATAATGTGATTATGCATATAGTCACATCAATTCACA
1 TTAATTATA-AATTGAAGAG-ATAA-GTGATTATGCATACAGTCACATCAATTCACA
1489542 ACTATATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
54 1 0.02
55 16 0.34
57 1 0.02
58 1 0.02
60 28 0.60
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (58 bp):
TTAATTATAAATTGAAGAGATAAGTGATTATGCATACAGTCACATCAATTCACATCCT
Found at i:1493136 original size:25 final size:25
Alignment explanation
Indices: 1493108--1493161 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1493098 TATTTTGTTA
1493108 ATTTGGTTGGA-TTTTT-TTAAAATTT
1 ATTTGGTTGGACTTTTTGTT--AATTT
*
1493133 ATTTTGTTGGACTTTTTGTTAATTT
1 ATTTGGTTGGACTTTTTGTTAATTT
1493158 ATTT
1 ATTT
1493162 TGATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 19 0.73
26 5 0.19
27 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (25 bp):
ATTTGGTTGGACTTTTTGTTAATTT
Found at i:1493785 original size:21 final size:21
Alignment explanation
Indices: 1493738--1493778 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1493728 GACGGGTATG
1493738 CGAGCAAGCTGCTATCACATA
1 CGAGCAAGCTGCTATCACATA
* *
1493759 CAAGCAAGCTGCTATTACAT
1 CGAGCAAGCTGCTATCACAT
1493779 GTGAGCATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (21 bp):
CGAGCAAGCTGCTATCACATA
Found at i:1498065 original size:33 final size:32
Alignment explanation
Indices: 1498025--1498096 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1498015 TCGGATTGAA
1498025 TTTTTTTTAAAATAAAATTCAGGATCGGGTCGG
1 TTTTTTTTAAAA-AAAATTCAGGATCGGGTCGG
* ** * *
1498058 TTTTTTTTTAAAAACTTTCGGGTTCGGGTCGG
1 TTTTTTTTAAAAAAAATTCAGGATCGGGTCGG
*
1498090 GTTTTTT
1 TTTTTTT
1498097 AAGTTTTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.21, C:0.10, G:0.22, T:0.47
Consensus pattern (32 bp):
TTTTTTTTAAAAAAAATTCAGGATCGGGTCGG
Found at i:1498124 original size:37 final size:38
Alignment explanation
Indices: 1498075--1498146 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 38
1498065 TTAAAAACTT
* * *
1498075 TCGGGTTCGGGTCGGGTTTTTTAAGTTTTATATTCAGA
1 TCGGGTTCGGGTCAGGTTTTTTAAGTGTGATATTCAGA
1498113 TCGGGTT-GGGTCAGGTTTTTTAAGTGTGATATTC
1 TCGGGTTCGGGTCAGGTTTTTTAAGTGTGATATTC
1498147 GGGTCGGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.44
Consensus pattern (38 bp):
TCGGGTTCGGGTCAGGTTTTTTAAGTGTGATATTCAGA
Found at i:1498697 original size:16 final size:16
Alignment explanation
Indices: 1498676--1498755 Score: 142
Period size: 16 Copynumber: 5.0 Consensus size: 16
1498666 CCAAACAGGT
*
1498676 TTCAGATTCCAATTCC
1 TTCAGATTCTAATTCC
1498692 TTCAGATTCTAATTCC
1 TTCAGATTCTAATTCC
1498708 TTCAGATTCTAATTCC
1 TTCAGATTCTAATTCC
*
1498724 TTCAGATTCCAATTCC
1 TTCAGATTCTAATTCC
1498740 TTCAGATTCTAATTCC
1 TTCAGATTCTAATTCC
1498756 CTCATAAACA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 61 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (16 bp):
TTCAGATTCTAATTCC
Found at i:1499848 original size:30 final size:31
Alignment explanation
Indices: 1499813--1499874 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1499803 TTAATGAAAA
* *
1499813 GATGTTA-TTTTTTTACTTTTAGGGTTTTTG
1 GATGTTAGGTTTTTTACTTTTAAGGTTTTTG
1499843 GATGTTAGGTTTTTTACTTTTAAGGTTTTTG
1 GATGTTAGGTTTTTTACTTTTAAGGTTTTTG
1499874 G
1 G
1499875 GACCTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.15, C:0.03, G:0.23, T:0.60
Consensus pattern (31 bp):
GATGTTAGGTTTTTTACTTTTAAGGTTTTTG
Found at i:1499868 original size:16 final size:16
Alignment explanation
Indices: 1499821--1499872 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1499811 AAGATGTTAT
*
1499821 TTTTTTACTTTTAGGG
1 TTTTTTACTTTTAAGG
* *
1499837 TTTTTGGA-TGTT-AGG
1 TTTTT-TACTTTTAAGG
1499852 TTTTTTACTTTTAAGG
1 TTTTTTACTTTTAAGG
1499868 TTTTT
1 TTTTT
1499873 GGGACCTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
14 1 0.04
15 10 0.36
16 16 0.57
17 1 0.04
ACGTcount: A:0.13, C:0.04, G:0.19, T:0.63
Consensus pattern (16 bp):
TTTTTTACTTTTAAGG
Found at i:1500112 original size:10 final size:10
Alignment explanation
Indices: 1500097--1500155 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
1500087 CATTTAATAA
1500097 ATAAACGAAC
1 ATAAACGAAC
1500107 ATAAACGAAC
1 ATAAACGAAC
1500117 ----ACGAAC
1 ATAAACGAAC
1500123 ATAAACGAAC
1 ATAAACGAAC
1500133 ----ACGAAC
1 ATAAACGAAC
*
1500139 ATGAACGAAC
1 ATAAACGAAC
1500149 ATAAACG
1 ATAAACG
1500156 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 1, Indels: 16
0.70 0.02 0.28
Matches are distributed among these distances:
6 12 0.30
10 28 0.70
ACGTcount: A:0.56, C:0.22, G:0.14, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1500122 original size:16 final size:16
Alignment explanation
Indices: 1500101--1500149 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
1500091 TAATAAATAA
1500101 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1500117 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1500133 ACGAACATGAACGAAC
1 ACGAACATAAACGAAC
1500149 A
1 A
1500150 TAAACGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.55, C:0.24, G:0.14, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1500369 original size:11 final size:11
Alignment explanation
Indices: 1500338--1500389 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1500328 TCGAGACTCG
*
1500338 AGCTCGATTGA
1 AGCTCGATTCA
*
1500349 AGCTCTATTCA
1 AGCTCGATTCA
* *
1500360 AACTCGATTCTG
1 AGCTCGATTC-A
1500372 AGCTCGATTCA
1 AGCTCGATTCA
1500383 AGCTCGA
1 AGCTCGA
1500390 CATTGCCCCA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:1500380 original size:34 final size:35
Alignment explanation
Indices: 1500314--1500389 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
1500304 AAAATTTAAG
*
1500314 AGCTCGATTAAAACTCGAGACTCGAGCTCGATTGA
1 AGCTCGATTAAAACTCGAGACTCGAGCTCGATTCA
* * **
1500349 AGCTCTATTCAAACTCGATTCT-GAGCTCGATTCA
1 AGCTCGATTAAAACTCGAGACTCGAGCTCGATTCA
1500383 AGCTCGA
1 AGCTCGA
1500390 CATTGCCCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 17 0.49
35 18 0.51
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (35 bp):
AGCTCGATTAAAACTCGAGACTCGAGCTCGATTCA
Found at i:1501276 original size:14 final size:14
Alignment explanation
Indices: 1501259--1501304 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
1501249 AATGAACATA
*
1501259 AACGAACATAACTG
1 AACGAACATAACCG
*
1501273 AACGAACATAACCA
1 AACGAACATAACCG
*
1501287 AATGAACATAACCG
1 AACGAACATAACCG
1501301 AACG
1 AACG
1501305 TTCACGAACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.52, C:0.24, G:0.13, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1502598 original size:19 final size:17
Alignment explanation
Indices: 1502552--1502612 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 17
1502542 AGTAGAGAAT
1502552 AAAAATAAAAAGGAA-ATA
1 AAAAATAAAAA--AATATA
1502570 AATAAATAAATAAAATATA
1 AA-AAATAAA-AAAATATA
*
1502589 AAAAAGTAAAAACATATCA
1 AAAAA-TAAAAAAATAT-A
1502608 AAAAA
1 AAAAA
1502613 AGTGCAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 13 0.35
19 22 0.59
20 2 0.05
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAAAATATA
Found at i:1502649 original size:27 final size:23
Alignment explanation
Indices: 1502628--1502674 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 23
1502618 AAAATAGAAT
1502628 AATAATAATAATA-ATAATAAATAG
1 AATAAT-ATAATATA-AATAAATAG
1502652 --TAATATAATATAAATAAATAG
1 AATAATATAATATAAATAAATAG
1502673 AA
1 AA
1502675 CCAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAATATAATATAAATAAATAG
Found at i:1502721 original size:2 final size:2
Alignment explanation
Indices: 1502714--1502749 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1502704 GTAATTAAAC
1502714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1502750 TAATAAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1504485 original size:37 final size:36
Alignment explanation
Indices: 1504439--1504607 Score: 149
Period size: 37 Copynumber: 4.8 Consensus size: 36
1504429 GCTTCAAGAA
*
1504439 AAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGG
1 AAACAGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGG
* * * *
1504476 AAACAGTCTCAAGGGAGACGAAATTTGTTTTAAGGA
1 AAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
* *
1504512 AAACAGAT-TC-A-A-AG----ATTTTGTTTTAAGGG
1 AAACAG-TCTCAAGAGAGACAAAATTTGTTTCAAGGG
1504541 AAA-ATGTCTCAAGAGAGACAAAACTTTGTTTCAAGGG
1 AAACA-GTCTCAAGAGAGACAAAA-TTTGTTTCAAGGG
* * *
1504578 AAACTGTCTCAAGGGAGACGAAATTTGTTT
1 AAACAGTCTCAAGAGAGACAAAATTTGTTT
1504608 TAAAGATTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
28 2 0.02
29 19 0.18
30 1 0.01
31 1 0.01
32 2 0.02
33 2 0.02
35 1 0.01
36 27 0.25
37 52 0.49
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (36 bp):
AAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
Found at i:1504620 original size:50 final size:48
Alignment explanation
Indices: 1504565--1504658 Score: 134
Period size: 50 Copynumber: 1.9 Consensus size: 48
1504555 GAGACAAAAC
* *
1504565 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTTAAAGAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAAAC-AAATTT-TTTTAAAGAT
**
1504615 TTTGTTTCAAGGGAAGTTGTCTCAAGAGAAACAAATTTTTTTAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAATTTTTTTAA
1504659 GACAAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 6 0.15
49 6 0.15
50 28 0.70
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (48 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAATTTTTTTAAAGAT
Found at i:1504636 original size:87 final size:84
Alignment explanation
Indices: 1504522--1504695 Score: 231
Period size: 84 Copynumber: 2.0 Consensus size: 84
1504512 AAACAGATTC
* * ** *
1504522 AAAGATTTTGTTTTAAGGGAAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCT
1 AAAGATTTTGTTTCAAGGGAAAATGTCTCAAGAGAAAC-AAA-TTT-TTTCAAGACAAAATGTCT
* *
1504587 CAAGGGAGACGAAATTTGTTTT
63 CAAGAGAGACAAAATTTGTTTT
** *
1504609 AAAGATTTTGTTTCAAGGGAAGTTGTCTCAAGAGAAACAAATTTTTTTAAGACAAAATGTCTCAA
1 AAAGATTTTGTTTCAAGGGAAAATGTCTCAAGAGAAACAAATTTTTTCAAGACAAAATGTCTCAA
1504674 GAGAGACAAAATTTGTTTT
66 GAGAGACAAAATTTGTTTT
1504693 AAA
1 AAA
1504696 AGAAACTGTC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
84 37 0.48
85 3 0.04
86 3 0.04
87 34 0.44
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (84 bp):
AAAGATTTTGTTTCAAGGGAAAATGTCTCAAGAGAAACAAATTTTTTCAAGACAAAATGTCTCAA
GAGAGACAAAATTTGTTTT
Found at i:1504670 original size:34 final size:36
Alignment explanation
Indices: 1504632--1504731 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
1504622 CAAGGGAAGT
*
1504632 TGTCTCAAGAGAAAC-AAATTT-TTTTAAGACAAAA
1 TGTCTCAAGAGAAACAAAATTTGTTTTAAAACAAAA
* * *
1504666 TGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAC
1 TGTCTCAAGAGAAACAAAATTTGTTTTAAAACAAAA
*
1504702 TGTCTCAAG-GAAGACGAAATTTGTTTTAAA
1 TGTCTCAAGAGAA-ACAAAATTTGTTTTAAA
1504732 GATTTTGTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 14 0.25
35 8 0.14
36 35 0.61
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (36 bp):
TGTCTCAAGAGAAACAAAATTTGTTTTAAAACAAAA
Found at i:1504746 original size:120 final size:122
Alignment explanation
Indices: 1504528--1504813 Score: 452
Period size: 120 Copynumber: 2.4 Consensus size: 122
1504518 ATTCAAAGAT
** * ** *
1504528 TTTGTTTTAAGGGAAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGGG
1 TTTGTTTTAAGACAAAATGTCTCAAGAGAGACAAAA-TTTGTTTTAAAAGAAACTGTCTCAAGGA
**
1504593 AGACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAGTTGTCTCAAGAGAAAC-AAA
65 AGACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAA
1504650 TTT-TTTTAAGACAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGAA
1 TTTGTTTTAAGACAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGAA
*
1504714 GACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
66 GACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAA
*
1504771 TTTGTTTTAAGACAAAATGTCTCAAGAGAAAC-AAATTTGTTTT
1 TTTGTTTTAAGACAAAATGTCTCAAGAGAGACAAAATTTGTTTT
1504814 GAGTAAATTA
Statistics
Matches: 152, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
120 75 0.49
121 47 0.31
122 30 0.20
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (122 bp):
TTTGTTTTAAGACAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGAA
GACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAA
Found at i:1504776 original size:36 final size:35
Alignment explanation
Indices: 1504735--1504812 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
1504725 TTTTAAAGAT
** * *
1504735 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGACAAAATGTCTCAAGAGAAAC-AAA
*
1504771 TTTGTTTTAAGACAAAATGTCTCAAGAGAAACAAA
1 TTTGTTTCAAGACAAAATGTCTCAAGAGAAACAAA
1504806 TTTGTTT
1 TTTGTTT
1504813 TGAGTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 10 0.27
36 27 0.73
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (35 bp):
TTTGTTTCAAGACAAAATGTCTCAAGAGAAACAAA
Found at i:1506515 original size:17 final size:18
Alignment explanation
Indices: 1506493--1506551 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
1506483 AAAAGTAGAG
*
1506493 AATAAAAATAAAAAGA-A
1 AATAAAAATAAAAAAATA
1506510 AATAAAAAATACAAATAAATA
1 AAT-AAAAATA-AAA-AAATA
*
1506531 AATAAAATATAAAAAAGTA
1 AATAAAA-ATAAAAAAATA
1506550 AA
1 AA
1506552 AACATATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 3 0.09
18 7 0.20
19 9 0.26
20 9 0.26
21 7 0.20
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (18 bp):
AATAAAAATAAAAAAATA
Found at i:1506595 original size:21 final size:21
Alignment explanation
Indices: 1506571--1506620 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1506561 AAAAAGAGCA
*
1506571 AAATAGAAAAATGATA-ATAAT
1 AAATAGAAAAATAATATA-AAT
* *
1506592 AAATAGTAATATAATATAAAT
1 AAATAGAAAAATAATATAAAT
1506613 AAATAGAA
1 AAATAGAA
1506621 CCAAAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (21 bp):
AAATAGAAAAATAATATAAAT
Found at i:1506667 original size:2 final size:2
Alignment explanation
Indices: 1506660--1506698 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1506650 ATAATTAAAC
1506660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1506699 CTAAGGATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1509069 original size:20 final size:21
Alignment explanation
Indices: 1509044--1509083 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1509034 AATATTAATA
*
1509044 TTTAC-AATAATTATAAAATT
1 TTTACAAATAATTACAAAATT
1509064 TTTACAGAATAATTACAAAA
1 TTTACA-AATAATTACAAAA
1509084 AAAAAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (21 bp):
TTTACAAATAATTACAAAATT
Found at i:1509921 original size:3 final size:3
Alignment explanation
Indices: 1509913--1509958 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1509903 TTTTCATTTG
1509913 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1509959 CTAAATAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1515749 original size:18 final size:19
Alignment explanation
Indices: 1515714--1515752 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1515704 TAGTCAAGGG
1515714 GTATCGATACCTAGAAGGGTA
1 GTATCGATACC-A-AAGGGTA
1515735 GTATCGATACC-AAGGGTA
1 GTATCGATACCAAAGGGTA
1515753 CCGATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (19 bp):
GTATCGATACCAAAGGGTA
Found at i:1517394 original size:509 final size:516
Alignment explanation
Indices: 1516462--1517418 Score: 1601
Period size: 509 Copynumber: 1.9 Consensus size: 516
1516452 CAATAAAAAT
1516462 AATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATGTCTGT
1 AATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATGTC--T
1516527 ATGCCGATATGAGAAAGTGAACTAAGTTAAATGATATTGAATTTGTGAATATAAGAGATTAAAAC
64 ATGCCGATATGAGAAAGTGAACTAAGTTAAATGATATTGAATTTGTGAATATAAGAGATTAAAAC
*
1516592 ATAAACTATATGAAAAGATATAAGCCATATGATATGACATTTGTGAACATATGAGAAGGTTATAG
129 ATAAACTATATGAAAAGATATAAGCCATATGATATGAAATTTGTGAACATAT-AGAAGG-TATAG
1516657 GTGTTATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCATGTGAAATTATTATGTGATAT
192 GTGTTATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCATGTGAAATTATTATGTGATAT
*
1516722 AAGTATATGACATTACTATATGGATTATATGAAAGAATATATATGACTACATGTGTAAGCTTATA
257 AAGTATATGACATTAC-ATATGGATTATATGAAAAAATATATATGACTACATGTGTAAGCTTATA
* * *
1516787 TGGTATTGATAGGATATATAAGATTATATGCATGTATGATGATATGTGAAAGTGAACTAAGTTCA
321 TGGTATTGATAGGACATATAAGATTATATGCACGTATGATGATATGAGAAAGTGAACTAAGTTCA
*
1516852 ATGTTATTGAATTATGTGAATATAAGAGATTAAAACATAAACTATATGAAAAAATATAGACATAA
386 ATGATATTGAATTATGTGAATATAAGAGATTAAAACATAAACTATATGAAAAAATATAGACATAA
1516917 GATATAGTCATGTGAAATTATTATGTGATATAAGTATATGACATTACTATATGGATTATATGAAA
451 GATATAGTCATGTGAAATTATTATGTGATATAAGTATATGACATTACTATATGGATTATATGAAA
1516982 G
516 G
*
1516983 AATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGATATATAAGATTATATG-C-AT
1 AATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATGTCTAT
* * * * *
1517046 GCATGATATGTGAATGTGAACTAAGTTCAATGTTATTGAATTATGTGAATATAAGAGATTAAAAC
66 GC-CGATATGAGAAAGTGAACTAAGTTAAATGATATTGAATT-TGTGAATATAAGAGATTAAAAC
1517111 ATAAACTATATGAAAA-ATATAAGCCATATGATATGAAATTTGTGAACATAT-G-A-G-AT-GGT
129 ATAAACTATATGAAAAGATATAAGCCATATGATATGAAATTTGTGAACATATAGAAGGTATAGGT
* *
1517170 GTTATATGATTTGAGCAGGGAAATGGACATAAGATATAGTCA-GATGAAATTATTATGTGATATA
194 GTTATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCATG-TGAAATTATTATGTGATATA
*
1517234 AGTATATGACATTAC-TATGGATTGTATGAAAAAATATATATGACTACATGTGTAAGCTTATATG
258 AGTATATGACATTACATATGGATTATATGAAAAAATATATATGACTACATGTGTAAGCTTATATG
* * *
1517298 GTATTGATAGGACATTTAAGATTATATGCCCGTATGATGATATGAGAAAGTGAACTAAGTTTAAT
323 GTATTGATAGGACATATAAGATTATATGCACGTATGATGATATGAGAAAGTGAACTAAGTTCAAT
*
1517363 GATATTGAATTATGTGAATATAAGAGATTAAAACATAAACTATATGAAAAGATATA
388 GATATTGAATTATGTGAATATAAGAGATTAAAACATAAACTATATGAAAAAATATA
1517419 AGCCATATGA
Statistics
Matches: 414, Mismatches: 19, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
509 160 0.39
510 1 0.00
511 78 0.19
512 2 0.00
514 1 0.00
515 1 0.00
516 1 0.00
517 4 0.01
518 68 0.16
519 38 0.09
520 1 0.00
521 59 0.14
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (516 bp):
AATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATGTCTAT
GCCGATATGAGAAAGTGAACTAAGTTAAATGATATTGAATTTGTGAATATAAGAGATTAAAACAT
AAACTATATGAAAAGATATAAGCCATATGATATGAAATTTGTGAACATATAGAAGGTATAGGTGT
TATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCATGTGAAATTATTATGTGATATAAGT
ATATGACATTACATATGGATTATATGAAAAAATATATATGACTACATGTGTAAGCTTATATGGTA
TTGATAGGACATATAAGATTATATGCACGTATGATGATATGAGAAAGTGAACTAAGTTCAATGAT
ATTGAATTATGTGAATATAAGAGATTAAAACATAAACTATATGAAAAAATATAGACATAAGATAT
AGTCATGTGAAATTATTATGTGATATAAGTATATGACATTACTATATGGATTATATGAAAG
Found at i:1517476 original size:7 final size:7
Alignment explanation
Indices: 1517465--1517504 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1517455 GATAAGAGAT
1517465 ATATATG
1 ATATATG
*
1517472 TTATATG
1 ATATATG
1517479 ATATATG
1 ATATATG
1517486 ATATATG
1 ATATATG
*
1517493 -TATGTG
1 ATATATG
1517499 ATATAT
1 ATATAT
1517505 AAGAAACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (7 bp):
ATATATG
Found at i:1517745 original size:31 final size:29
Alignment explanation
Indices: 1517705--1517794 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
1517695 ATGCCAAGAG
1517705 AGTTACCTATGTCCTTCGGATATATGGAC
1 AGTTACCTATGTCCTTCGGATATATGGAC
* * *
1517734 ATGATTACCTATGTCCTTTGGGACATATAGAC
1 A-G-TTACCTATGTCC-TTCGGATATATGGAC
* *
1517766 AGGTACCTATGTTCTTCGGAATATATGGA
1 AGTTACCTATGTCCTTCGG-ATATATGGA
1517795 TAGGTCTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
29 5 0.10
30 18 0.37
31 13 0.27
32 13 0.27
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (29 bp):
AGTTACCTATGTCCTTCGGATATATGGAC
Found at i:1519036 original size:208 final size:204
Alignment explanation
Indices: 1518647--1519036 Score: 618
Period size: 205 Copynumber: 1.9 Consensus size: 204
1518637 AAATAAAACA
* * *
1518647 AAATGAGTGTTCAAAATAAAAAGATTTGGAGTCTTTTTCAGTGACCGAAATACAAGAATAACAAG
1 AAATGAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTCAGTAACCGAAATACAAGAATAACAAG
1518712 ATTTAAAACTCAAAATATAAACTCAAAATTGCATTAAGTGACTAAAATGAAATATACAAACATTG
66 ATTTAAAACTCAAAATATAAACTCAAAATTGCATTAAGTGACTAAAATGAAATATACAAACATTG
* *
1518777 AGGAACCAACAAGGGTTTACCCAAGCGCTGAATATATATCCACCCTTCCCTAGAATACAACAAAA
131 AGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCTAGAATACAACAAAA
1518842 TGGAAATAC
196 TGGAAATAC
*
1518851 AAATCGAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTCAGTAACTGAAATACAAGAATAACAA
1 AAAT-GAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTCAGTAACCGAAATACAAGAATAACAA
* ** * * * *
1518916 GATTTGAAACTTGAAATATAAACTTGAAATTTTCATTAAGTGACTAAAATGGAATACTACAAAAC
65 GATTTAAAACTCAAAATATAAAC-TCAAAATTGCATTAAGTGACTAAAATGAAATA-TAC-AAAC
*
1518981 CTTGAGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCTA
127 ATTGAGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCTA
1519037 AAACGACGTC
Statistics
Matches: 168, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
204 4 0.02
205 76 0.45
206 28 0.17
207 3 0.02
208 57 0.34
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (204 bp):
AAATGAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTCAGTAACCGAAATACAAGAATAACAAG
ATTTAAAACTCAAAATATAAACTCAAAATTGCATTAAGTGACTAAAATGAAATATACAAACATTG
AGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCTAGAATACAACAAAA
TGGAAATAC
Found at i:1524203 original size:24 final size:24
Alignment explanation
Indices: 1524133--1524203 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 24
1524123 AGTAAGAGAG
*
1524133 AGAGAAAAAGTAAAAGTTAACATGAA
1 AGAGAAAAA-AAAAAGTTAA-ATGAA
* * *
1524159 AGAGAGAAAAAAATGAATAAA-GAA
1 AGAGAAAAAAAAAAG-TTAAATGAA
1524183 AGAGAAAAGAAAAAAGTTAAA
1 AGAGAAAA-AAAAAAGTTAAA
1524204 AATTTGGGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
24 14 0.39
25 11 0.31
26 11 0.31
ACGTcount: A:0.68, C:0.01, G:0.20, T:0.11
Consensus pattern (24 bp):
AGAGAAAAAAAAAAGTTAAATGAA
Found at i:1531094 original size:24 final size:24
Alignment explanation
Indices: 1531050--1531099 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1531040 ATAAAGAACC
*
1531050 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1531074 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
1531098 AA
1 AA
1531100 TCAACAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1531966 original size:3 final size:3
Alignment explanation
Indices: 1531960--1531992 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1531950 TAAATAAAAA
1531960 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1531993 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1532565 original size:139 final size:139
Alignment explanation
Indices: 1532384--1533136 Score: 832
Period size: 139 Copynumber: 5.4 Consensus size: 139
1532374 TATTTGGGTT
* * * *
1532384 ATTTGGAGACAACACGGTTCCTTCACATTGAGGAAGTCTGATTGTCTAAGGATAACACTGCTCCT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
* * * * * *
1532449 TCACATTGAGGAGATCTGGCCGGTGGATGACATTGTTCCTTCGTGTTGAGGACGTATAGCCGTAT
66 TCGCGTTAAGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGTTGAGGACGTATAGCCGTAT
1532514 TTGGAGATA
131 TTGGAGATA
* * * * *
1532523 ATTTGGAGACAACACAGTTCCTTCGCATTGAGGAATTTTGATTGTCTGAGGATGACATTGCTCCT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
* * * * * *
1532588 TCGCGTTGAA-GAGATCTTGTCGGTAGACGACATTGTTCCTTCGTGTTAAGGACGTATAACCATA
66 TCGCGTT-AAGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGTTGAGGACGTATAGCCGTA
*
1532652 TTTAGAGATA
130 TTTGGAGATA
* * ** * * *
1532662 ATTTGGAGACAATATAGTTTATTCACATTAAGGAAGTCTAATTGTCTGATGATGACACTGCTCAT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
* * * * * * *
1532727 TCGCGTT-AGTGAGATGTGGTCGATGGACGACATTGTTCATTCGTGATGAGGATGTTTAACCGTC
66 TCGCGTTAAG-GAGATCTGGTCGGTGGACGACATTGTTCATTCGTGTTGAGGACGTATAGCCGTA
1532791 TTTGG-GATA
130 TTTGGAGATA
* * * * *
1532800 ATTTGGAGACAACA-TGATTCTTTCACGTTGAGGAAGTCTGATTATCTGAGGATGACATTGCTCA
1 ATTTGGAGACAACACAG-TTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCA
* * * * * * *
1532864 TTCGCTTTAAGGAGATGTGGTCGGTGGATGACATTATTCTTTCGTGTTGAGGACGTCTAGTCGTA
65 TTCGCGTTAAGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGTTGAGGACGTATAGCCGTA
1532929 TTTGGAGATA
130 TTTGGAGATA
** * *
1532939 ATTTGGAGAGC-ACACAGTTCCTTCGTATTGAGGAAGTCTGATTGTATGAGGATGACACTGCTCT
1 ATTTGGAGA-CAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCA
* * * * ** * *
1533003 TTTGCGTTAAAGAGATCCGGTCGGTGGACGACATTGTTCATTCGTGATGAGGATATCTAGCCGTC
65 TTCGCGTTAAGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGTTGAGGACGTATAGCCGTA
*
1533068 TTTGGGGGATA
130 TTT-GGAGATA
* * * * *
1533079 ATTTGGAGATAACACAATTTCTTCACGTTGAGGAAGTCTGATTGTCCGAGGATGACAC
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACAC
1533137 CACTCCTTCA
Statistics
Matches: 510, Mismatches: 94, Indels: 19
0.82 0.15 0.03
Matches are distributed among these distances:
137 2 0.00
138 112 0.22
139 338 0.66
140 58 0.11
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (139 bp):
ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
TCGCGTTAAGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGTTGAGGACGTATAGCCGTAT
TTGGAGATA
Found at i:1532919 original size:277 final size:275
Alignment explanation
Indices: 1532384--1533135 Score: 846
Period size: 277 Copynumber: 2.7 Consensus size: 275
1532374 TATTTGGGTT
* * * * *
1532384 ATTTGGAGA-CAACACGGTTCCTTCACATTGAGGAAGTCTGATTGTCTAAGGATAACACTGCTCC
1 ATTTGGAGAGC-ACACAGTTCATTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCA
* * * * * * * *
1532448 TTCACATTGAGGAGATCTGGCCGGTGGATGACATTGTTCCTTCGTGTTGAGGACGTATAGCCGTA
65 TTCGCGTT-AGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGATGTATAGCCGTC
* * * * * *
1532513 TTTGGAGATAATTTGGAGACAACACAGTTCCTTCGCATTGAGGAATTTTGATTGTCTGAGGATGA
129 TTTGG-GATAATTTGGAGACAACA-AATTCTTTCACGTTGAGGAAGTCTGATTGTCTGAGGATGA
* * *
1532578 CATTGCTCCTTCGCGTTGAAGAGATCTTGTCGGTAGACGACATTGTTCCTTCGTGTTAAGGACGT
192 CATTGCTCATTCGCGTTGAAGAGATCTGGTCGGTAGACGACATTATTCCTTCGTGTTAAGGACGT
1532643 ATAACCATATTTAGAGATA
257 ATAACCATATTTAGAGATA
* * * * * *
1532662 ATTTGGAGA-CAATATAGTTTATTCACATTAAGGAAGTCTAATTGTCTGATGATGACACTGCTCA
1 ATTTGGAGAGC-ACACAGTTCATTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCA
* * * *
1532726 TTCGCGTTAGTGAGATGTGGTCGATGGACGACATTGTTCATTCGTGATGAGGATGTTTAACCGTC
65 TTCGCGTTAG-GAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGATGTATAGCCGTC
* *
1532791 TTTGGGATAATTTGGAGACAACATGATTCTTTCACGTTGAGGAAGTCTGATTATCTGAGGATGAC
129 TTTGGGATAATTTGGAGACAACA-AATTCTTTCACGTTGAGGAAGTCTGATTGTCTGAGGATGAC
* * * * * *
1532856 ATTGCTCATTCGC-TTTAAGGAGATGTGGTCGGTGGATGACATTATTCTTTCGTGTTGAGGACGT
193 ATTGCTCATTCGCGTTGAA-GAGATCTGGTCGGTAGACGACATTATTCCTTCGTGTTAAGGACGT
* ** * *
1532920 CTAGTCGTATTTGGAGATA
257 ATAACCATATTTAGAGATA
* ** * *
1532939 ATTTGGAGAGCACACAGTTCCTTCGTATTGAGGAAGTCTGATTGTATGAGGATGACACTGCTCTT
1 ATTTGGAGAGCACACAGTTCATTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
* * * * *
1533004 TTGCGTTAAAGAGATCCGGTCGGTGGACGACATTGTTCATTCGTGATGAGGATATCTAGCCGTCT
66 TCGCGTT-AGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGATGTATAGCCGTCT
* *
1533069 TTGGGGGATAATTTGGAGATAACACAATT-TCTTCACGTTGAGGAAGTCTGATTGTCCGAGGATG
130 TT--GGGATAATTTGGAGACAACA-AATTCT-TTCACGTTGAGGAAGTCTGATTGTCTGAGGATG
1533133 ACA
191 ACA
1533136 CCACTCCTTC
Statistics
Matches: 397, Mismatches: 70, Indels: 13
0.83 0.15 0.03
Matches are distributed among these distances:
276 4 0.01
277 226 0.57
278 111 0.28
279 56 0.14
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (275 bp):
ATTTGGAGAGCACACAGTTCATTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
TCGCGTTAGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGATGTATAGCCGTCTT
TGGGATAATTTGGAGACAACAAATTCTTTCACGTTGAGGAAGTCTGATTGTCTGAGGATGACATT
GCTCATTCGCGTTGAAGAGATCTGGTCGGTAGACGACATTATTCCTTCGTGTTAAGGACGTATAA
CCATATTTAGAGATA
Found at i:1533630 original size:67 final size:67
Alignment explanation
Indices: 1533552--1533724 Score: 210
Period size: 67 Copynumber: 2.6 Consensus size: 67
1533542 GAAAACTTTA
* * * *
1533552 TCAAGCGAGATGAAATT-TGTTTTTGAGAGAAATAATCTCAAAGGCTTATGTTTCAAAAGAAAAT
1 TCAAGGGAGATGAAATTAT-ATTTGGAGAGAAACAATCTCAAAGGCTTATGTTTCAAAAGAAAAT
1533616 GTC
65 GTC
* * *
1533619 TCAAGGGAGATGAAATTATATTTGGAGATAAACAATCTCAAAGGTTTATGTTTCAAGAGAAAATG
1 TCAAGGGAGATGAAATTATATTTGGAGAGAAACAATCTCAAAGGCTTATGTTTCAAAAGAAAATG
1533684 TC
66 TC
* * *
1533686 TCAAGGGAGA-CACAATTTTGTTTGG-GA-AAACAATCTCAA
1 TCAAGGGAGATGA-AATTATATTTGGAGAGAAACAATCTCAA
1533725 GTGAGATCAA
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
65 12 0.13
66 3 0.03
67 78 0.83
68 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (67 bp):
TCAAGGGAGATGAAATTATATTTGGAGAGAAACAATCTCAAAGGCTTATGTTTCAAAAGAAAATG
TC
Found at i:1541434 original size:18 final size:17
Alignment explanation
Indices: 1541380--1541428 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1541370 TTGGATCCTT
* *
1541380 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1541398 TAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1541416 AGTGCATTCGATG
1 AGTGCA-TCGATG
1541429 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1541533 original size:65 final size:64
Alignment explanation
Indices: 1541374--1541559 Score: 205
Period size: 65 Copynumber: 2.9 Consensus size: 64
1541364 TAACTGTTGG
* ** *
1541374 ATCCTTAGTGCATCGGTGCACTAATAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAAT
1 ATCCTCAGTGCATCGGTGCA-TGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
* ** * *
1541438 AGCCAGAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTCAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
1541503 -
64 T
* ** *
1541503 ATCCTCAGTGCATCGGTGCATGGTATGTGCACCGATGCAAGAAATACATTCGATGTT
1 ATCCTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
1541560 CAATTTAATT
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
63 1 0.01
64 46 0.46
65 51 0.50
66 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (64 bp):
ATCCTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:1541598 original size:65 final size:63
Alignment explanation
Indices: 1541400--1541598 Score: 156
Period size: 65 Copynumber: 3.1 Consensus size: 63
1541390 TGCACTAATA
* * * * * *
1541400 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCACCGATGCAACAAATACATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
1541463 G
63 G
* * * *
1541464 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCACCGATGCAACAAATACATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
1541529 -
63 G
* **
1541529 GTGCACCGATGCAAGAAATACATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCACCGATGCAACAAATACATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
1541592 TG
62 TG
1541594 GTGCA
1 GTGCA
1541599 TCACTCTAAA
Statistics
Matches: 114, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 49 0.43
65 53 0.46
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCACCGATGCAACAAATACATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:1549356 original size:23 final size:23
Alignment explanation
Indices: 1549330--1549389 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1549320 ATGGCACTAC
1549330 GGTGCATTTCTACGCAACACTTA
1 GGTGCATTTCTACGCAACACTTA
* *** *
1549353 GGTGCAATTCTACGTGGCACTTT
1 GGTGCATTTCTACGCAACACTTA
*
1549376 GGTGCATTTATACG
1 GGTGCATTTCTACG
1549390 AGCTGTGGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (23 bp):
GGTGCATTTCTACGCAACACTTA
Found at i:1553303 original size:12 final size:13
Alignment explanation
Indices: 1553288--1553327 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
1553278 TTCGGGTTGA
1553288 TTATA-TTGGGCT
1 TTATATTTGGGCT
1553300 TTATAATTTGGGCT
1 TTAT-ATTTGGGCT
1553314 TTATAATTTGGGCT
1 TTAT-ATTTGGGCT
1553328 CCATTTAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 4 0.15
13 1 0.04
14 21 0.81
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (13 bp):
TTATATTTGGGCT
Found at i:1553312 original size:14 final size:14
Alignment explanation
Indices: 1553293--1553327 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1553283 GTTGATTATA
1553293 TTGGGCTTTATAAT
1 TTGGGCTTTATAAT
1553307 TTGGGCTTTATAAT
1 TTGGGCTTTATAAT
1553321 TTGGGCT
1 TTGGGCT
1553328 CCATTTAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.49
Consensus pattern (14 bp):
TTGGGCTTTATAAT
Found at i:1553367 original size:3 final size:3
Alignment explanation
Indices: 1553359--1553390 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1553349 TAATTAGGAT
1553359 ATA ATA ATA ATA ATA ATA ATTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
1553391 ACAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1560495 original size:19 final size:19
Alignment explanation
Indices: 1560468--1560512 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1560458 CCGGCAACGA
1560468 TTTGCTTTTGCTTTTA-GTT
1 TTTGCTTTT-CTTTTATGTT
*
1560487 TTTGTTTTTCTTTTATGTT
1 TTTGCTTTTCTTTTATGTT
1560506 TTTGCTT
1 TTTGCTT
1560513 CTTCATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.04, C:0.09, G:0.13, T:0.73
Consensus pattern (19 bp):
TTTGCTTTTCTTTTATGTT
Found at i:1564567 original size:28 final size:28
Alignment explanation
Indices: 1564525--1564581 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1564515 GTCTCTGTTT
*
1564525 ATATTATGTCATTGAATCAGTACTTAAA
1 ATATTATATCATTGAATCAGTACTTAAA
* * * *
1564553 ATATTATATCGTTGAGTTAGTGCTTAAA
1 ATATTATATCATTGAATCAGTACTTAAA
1564581 A
1 A
1564582 ACAATGGCGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (28 bp):
ATATTATATCATTGAATCAGTACTTAAA
Found at i:1565259 original size:14 final size:14
Alignment explanation
Indices: 1565240--1565270 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1565230 TGTGTGGTAA
1565240 TAAAAAATATTGTT
1 TAAAAAATATTGTT
*
1565254 TAAAAAATATTTTT
1 TAAAAAATATTGTT
1565268 TAA
1 TAA
1565271 TGGCCAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
TAAAAAATATTGTT
Found at i:1565738 original size:20 final size:20
Alignment explanation
Indices: 1565710--1565765 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1565700 AAGATTTTTT
*
1565710 TGAATAGTGAATAGTATTCG
1 TGAAAAGTGAATAGTATTCG
*
1565730 TGAAAAGTGAATATTATTCG
1 TGAAAAGTGAATAGTATTCG
* *
1565750 TGAACAGTGAACAGTA
1 TGAAAAGTGAATAGTA
1565766 ACAGTGAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (20 bp):
TGAAAAGTGAATAGTATTCG
Found at i:1565759 original size:7 final size:7
Alignment explanation
Indices: 1565749--1565778 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1565739 AATATTATTC
1565749 GTGAACA
1 GTGAACA
1565756 GTGAACA
1 GTGAACA
1565763 GT-AACA
1 GTGAACA
1565769 GTGAACA
1 GTGAACA
1565776 GTG
1 GTG
1565779 GGGGAATCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.40, C:0.13, G:0.30, T:0.17
Consensus pattern (7 bp):
GTGAACA
Found at i:1565768 original size:13 final size:13
Alignment explanation
Indices: 1565752--1565777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1565742 ATTATTCGTG
1565752 AACAGTGAACAGT
1 AACAGTGAACAGT
1565765 AACAGTGAACAGT
1 AACAGTGAACAGT
1565778 GGGGGAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (13 bp):
AACAGTGAACAGT
Found at i:1566252 original size:44 final size:44
Alignment explanation
Indices: 1566186--1566292 Score: 162
Period size: 44 Copynumber: 2.4 Consensus size: 44
1566176 GAGCAATATT
1566186 TTACCATTTAATACCATAAGCTCGTAAGATTATTTTACCAATACAC
1 TTACCATTT-AT-CCATAAGCTCGTAAGATTATTTTACCAATACAC
*
1566232 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGATTATTTTACCAATACAC
*
1566276 TTTCCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
1566293 CCATATACCA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
43 3 0.05
44 44 0.76
45 2 0.03
46 9 0.16
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAAGATTATTTTACCAATACAC
Found at i:1566314 original size:20 final size:20
Alignment explanation
Indices: 1566289--1566331 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1566279 CCATTATTCC
* *
1566289 ATAACCATATACCATAGACA
1 ATAACCATAAACAATAGACA
1566309 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
1566329 ATA
1 ATA
1566332 GCCCAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:1566433 original size:33 final size:33
Alignment explanation
Indices: 1566391--1566457 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1566381 ACCGTAGTGC
*
1566391 TAATCCGTATGACACATAATGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1566424 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1566457 T
1 T
1566458 CTGTACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACCA
Found at i:1572000 original size:82 final size:81
Alignment explanation
Indices: 1571856--1572154 Score: 375
Period size: 82 Copynumber: 3.7 Consensus size: 81
1571846 ATATCAAATT
* * *
1571856 TAGAGAATCTACACTATTCACATCCTTTAATTTTCATTGACATATCACATCAACTCAGATAAATT
1 TAGAGAATCTACACTATTCACATCATTTAATTTTCATTGACATATAACATCAACTCAGATAAACT
1571921 GAAATAATTTAGAGAA
66 GAAATAATTTAGAGAA
* ** * ** *
1571937 TATGAGAATATACACTATTCATGTCCTTTTTTTTTCATTGACATATAACATCAACTCATATAAAC
1 TA-GAGAATCTACACTATTCACATCATTTAATTTTCATTGACATATAACATCAACTCAGATAAAC
1572002 TGAAATAATTTAGAGAA
65 TGAAATAATTTAGAGAA
* * * *
1572019 TAAGAGAATCTACACTATTCACATAATTTGATTTTCATTGACATATCACATCAACTCAGATAAAG
1 T-AGAGAATCTACACTATTCACATCATTTAATTTTCATTGACATATAACATCAACTCAGATAAAC
* *
1572084 TAAAATAATTTAGAAAA
65 TGAAATAATTTAGAGAA
* * * *
1572101 TCAGAGAATCTACATTATTCACGTCATTTACTTTTCATTGAAATATCAA-ATCAA
1 T-AGAGAATCTACACTATTCACATCATTTAATTTTCATTGACATAT-AACATCAA
1572155 ATAAGAGAAA
Statistics
Matches: 187, Mismatches: 28, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
81 2 0.01
82 183 0.98
83 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (81 bp):
TAGAGAATCTACACTATTCACATCATTTAATTTTCATTGACATATAACATCAACTCAGATAAACT
GAAATAATTTAGAGAA
Found at i:1572041 original size:164 final size:164
Alignment explanation
Indices: 1571857--1572154 Score: 447
Period size: 164 Copynumber: 1.8 Consensus size: 164
1571847 TATCAAATTT
** * *
1571857 AGAGAATCTACACTATTCACATCCTTTAATTTTCATTGACATATCACATCAACTCAGATAAATTG
1 AGAGAATCTACACTATTCACATAATTTAATTTTCATTGACATATCACATCAACTCAGATAAAGTA
* * * ** *
1571922 AAATAATTTAGAGAAT-ATGAGAATATACACTATTCATGTCCTTTTTTTTTCATTGACATAT-AA
66 AAATAATTTAGAAAATCA-GAGAATATACACTATTCACGTCATTTACTTTTCATTGAAATATCAA
1571985 CATCAACTCATATAAACTGAAATAATTTAGAGAATA
130 -ATCAACTCATATAAACTGAAATAATTTAGAGAATA
*
1572021 AGAGAATCTACACTATTCACATAATTTGATTTTCATTGACATATCACATCAACTCAGATAAAGTA
1 AGAGAATCTACACTATTCACATAATTTAATTTTCATTGACATATCACATCAACTCAGATAAAGTA
* *
1572086 AAATAATTTAGAAAATCAGAGAATCTACATTATTCACGTCATTTACTTTTCATTGAAATATCAAA
66 AAATAATTTAGAAAATCAGAGAATATACACTATTCACGTCATTTACTTTTCATTGAAATATCAAA
1572151 TCAA
131 TCAA
1572155 ATAAGAGAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
164 116 0.97
165 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (164 bp):
AGAGAATCTACACTATTCACATAATTTAATTTTCATTGACATATCACATCAACTCAGATAAAGTA
AAATAATTTAGAAAATCAGAGAATATACACTATTCACGTCATTTACTTTTCATTGAAATATCAAA
TCAACTCATATAAACTGAAATAATTTAGAGAATA
Found at i:1575262 original size:26 final size:28
Alignment explanation
Indices: 1575233--1575286 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1575223 CTAAGTATGT
1575233 ATATATGCATG-ATGT-TATGTTACATG
1 ATATATGCATGTATGTATATGTTACATG
* *
1575259 ATATGTGCATGTGTGTATATGTTACATG
1 ATATATGCATGTATGTATATGTTACATG
1575287 GAAGAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.42
27 3 0.12
28 11 0.46
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (28 bp):
ATATATGCATGTATGTATATGTTACATG
Found at i:1576492 original size:21 final size:21
Alignment explanation
Indices: 1576448--1576493 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1576438 TGAAGAATTG
* **
1576448 CATATATGTTCCAAAGGATTA
1 CATATATATTCCAAAGGACCA
*
1576469 CATATATATTCCGAAGGACCA
1 CATATATATTCCAAAGGACCA
1576490 CATA
1 CATA
1576494 GAACCCTCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (21 bp):
CATATATATTCCAAAGGACCA
Found at i:1578462 original size:23 final size:22
Alignment explanation
Indices: 1578404--1578519 Score: 103
Period size: 23 Copynumber: 5.2 Consensus size: 22
1578394 CACTATAACT
*
1578404 CACATA-ATTTTCACCGAAGTGA-
1 CACATAGATTGTC-CCGAA-TGAC
*
1578426 CACATA-TTTGTCCCGAATGAC
1 CACATAGATTGTCCCGAATGAC
* * *
1578447 CACATAGTTTTGTCCCAAAAGAC
1 CACATAG-ATTGTCCCGAATGAC
*
1578470 TACATAGGATTGTCCCGAATGAC
1 CACATA-GATTGTCCCGAATGAC
*
1578493 CACATAAGATTGTCCCGAAGGAC
1 CACAT-AGATTGTCCCGAATGAC
1578516 CACA
1 CACA
1578520 AAGAACCCTC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
20 3 0.04
21 11 0.14
22 10 0.13
23 53 0.67
24 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (22 bp):
CACATAGATTGTCCCGAATGAC
Found at i:1578801 original size:27 final size:27
Alignment explanation
Indices: 1578755--1578815 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
1578745 TGTTCCATAG
* *
1578755 AACATATTCACTTAGCACA-TATTCACAT
1 AACAT-TTCACATAGAACATTA-TCACAT
1578783 AACATTTCACATAGAACATTATCACAT
1 AACATTTCACATAGAACATTATCACAT
*
1578810 AGCATT
1 AACATT
1578816 GTCAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (27 bp):
AACATTTCACATAGAACATTATCACAT
Found at i:1578809 original size:15 final size:15
Alignment explanation
Indices: 1578750--1578811 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
1578740 ATTTATGTTC
1578750 CATAGAACATATTCA
1 CATAGAACATATTCA
* *
1578765 CTTAGCACATATTCA
1 CATAGAACATATTCA
1578780 CAT--AACAT-TTCA
1 CATAGAACATATTCA
1578792 CATAGAACAT-TATCA
1 CATAGAACATAT-TCA
1578807 CATAG
1 CATAG
1578812 CATTGTCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 7 0.17
13 4 0.10
14 6 0.15
15 23 0.57
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (15 bp):
CATAGAACATATTCA
Found at i:1580630 original size:29 final size:28
Alignment explanation
Indices: 1580539--1580640 Score: 66
Period size: 29 Copynumber: 3.5 Consensus size: 28
1580529 TTATGAGCTC
1580539 TATGAGATATGT-CCTATGTGATCATATGAA
1 TATGAGATATGTGCCTATGTG---ATATGAA
* * * *
1580569 AATGTGACTATGTG-CAATGTGA-AAGAA
1 TATGAGA-TATGTGCCTATGTGATATGAA
1580596 GTTATGAGATTATGTGCCTATGTGATATGAA
1 --TATGAGA-TATGTGCCTATGTGATATGAA
*
1580627 TATGTGAATATGTG
1 TATGAG-ATATGTG
1580641 ACAAACATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
27 4 0.07
28 1 0.02
29 22 0.40
30 13 0.24
31 15 0.27
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (28 bp):
TATGAGATATGTGCCTATGTGATATGAA
Found at i:1580773 original size:21 final size:21
Alignment explanation
Indices: 1580735--1580810 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
1580725 GTCCTCTAGG
* *
1580735 ACATATATGTATTCCTTTGGA
1 ACATATATGTAGTACTTTGGA
* *
1580756 ACATATATGTGGTACTTTGGT
1 ACATATATGTAGTACTTTGGA
* * *
1580777 ACACT-TATTTAGTCCATTGGA
1 ACA-TATATGTAGTACTTTGGA
* *
1580798 ATATGTATGTAGT
1 ACATATATGTAGT
1580811 CTCTAAGGAG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (21 bp):
ACATATATGTAGTACTTTGGA
Found at i:1580847 original size:21 final size:21
Alignment explanation
Indices: 1580823--1580866 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1580813 CTAAGGAGTA
* *
1580823 GTCCTTCGGGACATCTATGTG
1 GTCCTTCGAGACATATATGTG
1580844 GTCCTTCGAGACATATATGTG
1 GTCCTTCGAGACATATATGTG
1580865 GT
1 GT
1580867 TATTTGGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
GTCCTTCGAGACATATATGTG
Found at i:1580877 original size:21 final size:21
Alignment explanation
Indices: 1580827--1580877 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1580817 GGAGTAGTCC
* *
1580827 TTCGGGACATCTATGTGGTCC
1 TTCGGGACATATATGTGGTCA
* *
1580848 TTCGAGACATATATGTGGTTA
1 TTCGGGACATATATGTGGTCA
*
1580869 TTTGGGACA
1 TTCGGGACA
1580878 AATTCTATGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (21 bp):
TTCGGGACATATATGTGGTCA
Found at i:1581916 original size:20 final size:20
Alignment explanation
Indices: 1581891--1581940 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1581881 CAGACTTAAT
*
1581891 AGTATCGGTACCCCAACTAC
1 AGTATCGATACCCCAACTAC
*
1581911 AGTATCGATACTCCAACTAC
1 AGTATCGATACCCCAACTAC
1581931 AGTATCGATA
1 AGTATCGATA
1581941 TTTCTCTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (20 bp):
AGTATCGATACCCCAACTAC
Found at i:1582061 original size:20 final size:20
Alignment explanation
Indices: 1582019--1582067 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1582009 TTAATAATAA
*
1582019 TATCGATACCTTACTCTTGG
1 TATCGATACCTTACTCTTAG
1582039 TATCGATACCTTACT-TTCAG
1 TATCGATACCTTACTCTT-AG
*
1582059 TATCAATAC
1 TATCGATAC
1582068 TAATTCAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (20 bp):
TATCGATACCTTACTCTTAG
Found at i:1587247 original size:17 final size:17
Alignment explanation
Indices: 1587225--1587265 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1587215 TGTTTAAGGT
1587225 ATATTTTATTATATTTA
1 ATATTTTATTATATTTA
1587242 ATATTTTATTATATTTA
1 ATATTTTATTATATTTA
1587259 ATATTTT
1 ATATTTT
1587266 GTTTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTTTATTATATTTA
Found at i:1589709 original size:35 final size:33
Alignment explanation
Indices: 1589670--1589749 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
1589660 GTATTTTGGT
*
1589670 TAATTTTGTTCA-TTGCCATTTAATATCAGTCATTG
1 TAATTTTGTTCATTTACCATTTAATA-C--TCATTG
*
1589705 TAATTTGTGTATCATTTACCATTTAATACTTATTG
1 TAATTT-TGT-TCATTTACCATTTAATACTCATTG
1589740 TAATTTTGTT
1 TAATTTTGTT
1589750 GTATTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 1 0.03
34 3 0.08
35 17 0.43
36 3 0.08
37 4 0.10
38 12 0.30
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (33 bp):
TAATTTTGTTCATTTACCATTTAATACTCATTG
Found at i:1594069 original size:124 final size:125
Alignment explanation
Indices: 1593839--1594102 Score: 397
Period size: 124 Copynumber: 2.1 Consensus size: 125
1593829 TAAAATATAC
* * *
1593839 ATCGATTTTTTTATTGTTGTGCATAACAAAACTGGTAAAAATTATCGAAAACATCATTATTTCTA
1 ATCGATTTTGTTATTGTTGTGCATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTCTA
* *
1593904 CCGGTTTTGTTATTATTTTGGCATTTTATCGCGTTCCTTAACAAAACCAGT-AAAGGGCT
66 CCGGTTTTGTTATTATTTTGGCATTTTATCGAGTTCCTTAACAAAACCAGTAAAAGCGCT
* *
1593963 ATCGGTTTTGTTATTGTTGTGCATAACAAAACCGGTAAAATTTACCGAAAACATCATTATTTCTA
1 ATCGATTTTGTTATTGTTGTGCATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTCTA
* * *
1594028 CCGGTTTTGTTATTATTTTTGCATTTTA-CTGAGTTTCTTAACAAAACCGGTAAAAGCGCT
66 CCGGTTTTGTTATTATTTTGGCATTTTATC-GAGTTCCTTAACAAAACCAGTAAAAGCGCT
* *
1594088 ACCGTTTTTGTTATT
1 ATCGATTTTGTTATT
1594103 TTTTTTACCG
Statistics
Matches: 126, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
123 1 0.01
124 105 0.83
125 20 0.16
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (125 bp):
ATCGATTTTGTTATTGTTGTGCATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTCTA
CCGGTTTTGTTATTATTTTGGCATTTTATCGAGTTCCTTAACAAAACCAGTAAAAGCGCT
Found at i:1594690 original size:200 final size:199
Alignment explanation
Indices: 1594283--1594780 Score: 709
Period size: 200 Copynumber: 2.5 Consensus size: 199
1594273 AGATTTATAG
* * *
1594283 CGGTATATTTATACC-GGTAACATTGTAAATTTACCTATTACGTTATAATTATCGATTTCAATGT
1 CGGTATATTTATACCGGGT-ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
* *
1594347 TTTTGGGATCGATACAATTT--TAAATGTATCGATACTTTATACGTGCACCTCGTTGGGCATTCA
65 TTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATACGTGCACCTCGTTGGGCATTCA
* *
1594410 TTCTGGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACCTATTTTCTCA
129 TTCTAGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACCTATTTTATCA
1594475 TAAAAC
194 TAAAAC
* * *
1594481 CGATATATTTCTACCGGGTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTT
1 CGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* ** *
1594546 TTTGTGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGCATTCATT
66 TTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATACGTGCACCTCGTTGGGCATTCATT
* *** * *
1594611 CTAGACAAAATGTATCGACAC-TTTTTAAAATTGTGTCGATACATTATGTTGACCTATTTTATCA
131 CTAGA-AAAAAGTATCGACACAAACTTAAAA-CGTGTCGATACATTATGTAGACCTATTTTATCA
1594675 TAAAAC
194 TAAAAC
*
1594681 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
1 CGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* *
1594746 TTTGGGGTCGATACTTTTAGA-AAATGTATTGACAC
66 TTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
1594781 ATATGTTTAC
Statistics
Matches: 267, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
197 3 0.01
198 68 0.25
199 54 0.20
200 141 0.53
201 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (199 bp):
CGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
TTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATACGTGCACCTCGTTGGGCATTCATT
CTAGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACCTATTTTATCATA
AAAC
Done.