Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007798.1 Hibiscus syriacus cultivar Beakdansim tig00110108_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: 471074
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:274592 original size:19 final size:20
Alignment explanation
Indices: 274555--274592 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
274545 GCTATTTTTA
* *
274555 AATTTATTTTTATATTTAAT
1 AATTTATTTTTAAAGTTAAT
274575 AATTT-TTTTTAAAGTTAA
1 AATTTATTTTTAAAGTTAA
274593 AAGTGTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTATTTTTAAAGTTAAT
Found at i:277698 original size:24 final size:25
Alignment explanation
Indices: 277644--277698 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
277634 GAAGACAATA
277644 AAAATACAATTCATAAAATAATTTT
1 AAAATACAATTCATAAAATAATTTT
** *
277669 TTAATA-AATT-ATAAATTTAATTTT
1 AAAATACAATTCATAAA-ATAATTTT
277693 AAAATA
1 AAAATA
277699 TAAAAGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 5 0.21
24 15 0.62
25 4 0.17
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAATACAATTCATAAAATAATTTT
Found at i:286134 original size:18 final size:18
Alignment explanation
Indices: 286111--286163 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
286101 AAATTGTCCT
*
286111 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
286129 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
286146 TATTTATATATTT-TAAAA
1 TA-TTATATATTTGTAAAA
286164 AAAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 10 0.33
18 17 0.57
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:286707 original size:4 final size:4
Alignment explanation
Indices: 286700--286724 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
286690 ATATATATAT
286700 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
286725 ATATAGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:303359 original size:13 final size:14
Alignment explanation
Indices: 303331--303363 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
303321 AATTTTCTCC
303331 ATTTATAATATATA
1 ATTTATAATATATA
*
303345 ATTTA-AATATTTA
1 ATTTATAATATATA
303358 ATTTAT
1 ATTTAT
303364 TCAAAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTATAATATATA
Found at i:304202 original size:14 final size:14
Alignment explanation
Indices: 304167--304206 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
304157 TGTTTTTTGT
304167 ATTTGTGTT-GTTC
1 ATTTGTGTTCGTTC
* *
304180 GTTTATGTTCGTTC
1 ATTTGTGTTCGTTC
304194 ATTTGTGTTCGTT
1 ATTTGTGTTCGTT
304207 TATCATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (14 bp):
ATTTGTGTTCGTTC
Found at i:313839 original size:35 final size:35
Alignment explanation
Indices: 313791--313868 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
313781 CAACACAATC
*
313791 TTCAATTTCATTCTAAACCCTAAATTTCAAAATAA
1 TTCAATTTCATTCTAAACCCCAAATTTCAAAATAA
* *
313826 TTCAATTAT-ATTCTAAACCCCAAATTTTAAAATAC
1 TTCAATT-TCATTCTAAACCCCAAATTTCAAAATAA
*
313861 TTTAATTT
1 TTCAATTT
313869 AGAGTTTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 36 0.95
36 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (35 bp):
TTCAATTTCATTCTAAACCCCAAATTTCAAAATAA
Found at i:313903 original size:35 final size:35
Alignment explanation
Indices: 313864--313938 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
313854 AAAATACTTT
313864 AATTT-AGAGTTTAGAATGTAATTAAAGTATTTTGG
1 AATTTGAG-GTTTAGAATGTAATTAAAGTATTTTGG
* *
313899 AATTTGAGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTGAGGTTTAGAATGTAATTAAAGTATTTTGG
313934 AATTT
1 AATTT
313939 TGAACATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
AATTTGAGGTTTAGAATGTAATTAAAGTATTTTGG
Found at i:319900 original size:18 final size:18
Alignment explanation
Indices: 319872--319913 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
319862 CAGTTGTTGT
*
319872 ATATCATTTTATTTTATAA
1 ATAT-ATTTTATATTATAA
319891 ATATATTTTATATTATAA
1 ATATATTTTATATTATAA
*
319909 TTATA
1 ATATA
319914 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATTTTATATTATAA
Found at i:320935 original size:20 final size:20
Alignment explanation
Indices: 320890--321139 Score: 258
Period size: 20 Copynumber: 12.5 Consensus size: 20
320880 GCGAATATGA
* *
320890 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
320910 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
320930 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
320950 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
320970 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
320990 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
321010 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
321030 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
321050 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
321070 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
321090 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
321110 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
321130 AAATCACAAC
1 AAATCGCAAC
321140 ACTGAAATTT
Statistics
Matches: 196, Mismatches: 25, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
20 195 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:320953 original size:40 final size:40
Alignment explanation
Indices: 320909--321139 Score: 329
Period size: 40 Copynumber: 5.8 Consensus size: 40
320899 CGCGAACACA
* * *
320909 TAAATCGCAACGTGTATCCGTATATCGCAACGCGT-ATCCG
1 TAAATCGCAACGAGTATCCGTAAATCGCAACG-ATAATCCG
* *
320949 TAAATCGCAATGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCG
*
320989 TAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCG
* *
321029 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCG
* *
321069 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCG
* * *
321109 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGAGTATCCGTAAATCGCAAC
321140 ACTGAAATTT
Statistics
Matches: 181, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.01
40 180 0.99
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCG
Found at i:321861 original size:24 final size:24
Alignment explanation
Indices: 321822--321868 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
321812 AAATTTGGTC
321822 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
321846 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
321869 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:322060 original size:12 final size:12
Alignment explanation
Indices: 322043--322067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
322033 ATATAATCCT
322043 GAAGAAGAAAAA
1 GAAGAAGAAAAA
322055 GAAGAAGAAAAA
1 GAAGAAGAAAAA
322067 G
1 G
322068 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:324438 original size:19 final size:19
Alignment explanation
Indices: 324398--324495 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
324388 GATTCTCTCG
324398 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
324418 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
324437 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
324451 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
324470 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
324489 TTGCGAT
1 TTGCGAT
324496 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:324492 original size:52 final size:53
Alignment explanation
Indices: 324379--324495 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
324369 GAAATGAAAA
324379 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
324432 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
324484 TCGCATTGCGAT
1 TCGCATTGCGAT
324496 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:324608 original size:33 final size:33
Alignment explanation
Indices: 324554--324713 Score: 139
Period size: 33 Copynumber: 4.7 Consensus size: 33
324544 CCATTACATT
*
324554 TCGCAATGCGGAAATGCAAATCGCAACGAGATAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGATAA
* *
324588 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGATAA
* * * *
324620 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CGAGAT--AA
*
324658 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGATAA
*
324691 TCGCAATGCGAAAT-TAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
324714 TTGCGATTCT
Statistics
Matches: 101, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
31 7 0.07
32 15 0.15
33 42 0.42
34 9 0.09
35 6 0.06
37 8 0.08
38 7 0.07
39 7 0.07
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGATAA
Found at i:324643 original size:14 final size:15
Alignment explanation
Indices: 324624--324701 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
324614 GCGAAATGAA
324624 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
324638 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
*
324655 AAATCGCAATGCGAAATGAA
1 -AATCGCAA-GCG--A-GAG
324675 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
324689 AATCGCAATGCGA
1 AATCGCAA-GCGA
324702 AATTAAATCG
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.14
17 3 0.06
18 12 0.24
19 8 0.16
20 1 0.02
21 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:324680 original size:51 final size:51
Alignment explanation
Indices: 324554--324719 Score: 278
Period size: 51 Copynumber: 3.2 Consensus size: 51
324544 CCATTACATT
* *
324554 TCGCAATGCGGAAATGCAAATCGCAACGAGATAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAA
324607 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
324658 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
324709 TCGCATTGCGA
1 TCGCAATGCGA
324720 TTCTCCCATT
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
51 63 0.58
52 37 0.34
53 9 0.08
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (51 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:324768 original size:19 final size:19
Alignment explanation
Indices: 324726--324825 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
324716 GCGATTCTCC
324726 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
324746 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
324765 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
324781 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
324798 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
324817 CATTGCGAT
1 CATTGCGAT
324826 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:324822 original size:52 final size:53
Alignment explanation
Indices: 324709--324825 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
324699 CGAAATTAAA
324709 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
324762 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
324814 TCGCATTGCGAT
1 TCGCATTGCGAT
324826 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:324950 original size:14 final size:14
Alignment explanation
Indices: 324931--324967 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
324921 CATCAATTAC
324931 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
324945 ACAAATCATCTTTT
1 ACAAATCAACTTTT
324959 ACAAATCAA
1 ACAAATCAA
324968 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:326963 original size:14 final size:14
Alignment explanation
Indices: 326944--327000 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
326934 GCGAAATGAA
*
326944 AATCGCAACGACAG
1 AATCGCAACGAAAG
326958 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
326975 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
326991 AATCGCAACG
1 AATCGCAACG
327001 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:326971 original size:33 final size:33
Alignment explanation
Indices: 326925--327017 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
326915 GCGAAACCAA
*
326925 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
326958 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
326991 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
327018 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:326982 original size:19 final size:19
Alignment explanation
Indices: 326888--327022 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
326878 TAGTTTACTT
* *
326888 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
326908 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
326927 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
326946 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
326960 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
326979 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
326993 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
327012 TCGCAATGCGA
1 TCGCAACGCGA
327023 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:327040 original size:19 final size:19
Alignment explanation
Indices: 327018--327146 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
327008 AAAATCGCAA
327018 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
327037 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
327051 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
327070 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
** *
327084 TGCGATTTTCATTTCGTGT
1 TGCGATTTTGGTTTCGCGT
327103 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
327122 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
327142 TGCGA
1 TGCGA
327147 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:327060 original size:33 final size:33
Alignment explanation
Indices: 327018--327109 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
327008 AAAATCGCAA
327018 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
327051 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
327084 TGCGATTTTCATTTCGTGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
327110 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:327349 original size:93 final size:93
Alignment explanation
Indices: 327190--327475 Score: 531
Period size: 93 Copynumber: 3.1 Consensus size: 93
327180 TTGAATGGAT
327190 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
327255 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
327283 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
327348 AGTTTAGCAGAATTAGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
327376 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT--CAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
327439 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
327467 AAATTTACT
1 AAATTTACT
327476 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
91 52 0.28
93 136 0.72
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:328412 original size:33 final size:33
Alignment explanation
Indices: 328367--328480 Score: 210
Period size: 33 Copynumber: 3.5 Consensus size: 33
328357 TCTTTTGGTT
328367 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
328400 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
328433 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
328466 GAAATGAAAATCGCA
1 GAAATGAAAATCGCA
328481 CTCGTTGCGC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:328413 original size:19 final size:18
Alignment explanation
Indices: 328374--328480 Score: 85
Period size: 14 Copynumber: 6.4 Consensus size: 18
328364 GTTGAAATGA
328374 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
328389 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
328406 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
328422 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
328439 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
328455 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
328472 AAAATCGCA
1 -AAATCGCA
328481 CTCGTTGCGC
Statistics
Matches: 74, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
14 24 0.32
16 15 0.20
17 12 0.16
19 23 0.31
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:328552 original size:21 final size:21
Alignment explanation
Indices: 328481--328552 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
328471 GAAAATCGCA
*
328481 CTCGTTGCGCTTTTCATTTCT
1 CTCGTTGCGATTTTCATTTCT
***
328502 CTCGTTGCGACAGTCA-TTCT
1 CTCGTTGCGATTTTCATTTCT
*
328522 CTCGTTGCGATTTTCATTTAT
1 CTCGTTGCGATTTTCATTTCT
328543 CTCGTTGCGA
1 CTCGTTGCGA
328553 CTCTTCTGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.11, C:0.26, G:0.18, T:0.44
Consensus pattern (21 bp):
CTCGTTGCGATTTTCATTTCT
Found at i:328679 original size:33 final size:33
Alignment explanation
Indices: 328632--328702 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
328622 AATACAAACT
* *
328632 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
328665 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
328698 TGAAA
1 TGAAA
328703 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:328936 original size:22 final size:22
Alignment explanation
Indices: 328884--328938 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
328874 TGGTTGTGAG
**
328884 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
328906 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
328928 GGATTTCTTCG
1 GGATTTCTTCG
328939 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:329110 original size:20 final size:20
Alignment explanation
Indices: 329085--329278 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
329075 CTTTAAATAT
329085 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
329105 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
329127 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
329146 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
329166 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
329186 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
329206 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
329226 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
329246 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
329266 CGCGTTGCGATTT
1 CGCGTTGCGATTT
329279 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:329272 original size:60 final size:60
Alignment explanation
Indices: 329085--329278 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
329075 CTTTAAATAT
**
329085 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
329146 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
329206 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
329266 CGCGTTGCGATTT
1 CGCGTTGCGATTT
329279 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:329304 original size:41 final size:41
Alignment explanation
Indices: 329251--329367 Score: 153
Period size: 41 Copynumber: 2.8 Consensus size: 41
329241 GTGTTCGCGT
329251 TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
1 TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
* ** ** *
329292 TGCGATTTTCATATTCGCGTTGCGAATTTATACTATCGCAT
1 TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
* *
329333 TGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAA
1 TGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAA
329368 TTGATTTGCG
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
41 45 0.73
42 17 0.27
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (41 bp):
TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
Found at i:329320 original size:21 final size:20
Alignment explanation
Indices: 329226--329362 Score: 116
Period size: 20 Copynumber: 6.7 Consensus size: 20
329216 TTTACGGATA
* *
329226 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
329246 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
* * *
329266 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT-CATATT
**
329287 CGCAATGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
*
329307 CGCGTTGCGAATTT-ATACTAT
1 CGCGTTGCGATTTTCATA-T-T
* * *
329328 CGCATTGCGATTTTCAAGAAT
1 CGCGTTGCGATTTTC-ATATT
329349 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
329363 GGAAATTGAT
Statistics
Matches: 93, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.04
20 45 0.48
21 42 0.45
23 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:329377 original size:41 final size:40
Alignment explanation
Indices: 329245--329402 Score: 138
Period size: 41 Copynumber: 3.9 Consensus size: 40
329235 ATTTATGTGT
* * *
329245 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTCAGAATCGCGTTGCGATTTTGG-AAA
* * * * ** *
329286 TCGCAATGCGATTTTCATATTCGCGTTGCGAATTTATACTA
1 TCGCATTGCGATTTTCAGAATCGCGTTGCGATTTTGGA-AA
329327 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTC-AGAATCGCGTTGCGATTTTGGAAA
* * ** *
329368 TTG-ATTTGCGATTCTGGGGATCGCGTTGCGATTTT
1 TCGCA-TTGCGATTTTCAGAATCGCGTTGCGATTTT
329403 TATTTCGCGT
Statistics
Matches: 96, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
40 19 0.20
41 60 0.62
42 17 0.18
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (40 bp):
TCGCATTGCGATTTTCAGAATCGCGTTGCGATTTTGGAAA
Found at i:354205 original size:21 final size:21
Alignment explanation
Indices: 354176--354222 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
354166 CTTAAACTAA
*
354176 ATTCAAGATTCAATTCCGCGT
1 ATTCTAGATTCAATTCCGCGT
354197 ATTCTAGATTCAATTCCGCGT
1 ATTCTAGATTCAATTCCGCGT
354218 ATTCT
1 ATTCT
354223 TTTAACAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (21 bp):
ATTCTAGATTCAATTCCGCGT
Found at i:356209 original size:21 final size:21
Alignment explanation
Indices: 356183--356402 Score: 239
Period size: 21 Copynumber: 10.5 Consensus size: 21
356173 ATTTTGTTGT
356183 ATTAATTTATTCTTAAATTAA
1 ATTAATTTATTCTTAAATTAA
* * *
356204 ATTAATATAATTC-AAGAATTAT
1 ATTAAT-TTATTCTTA-AATTAA
356226 ATTAATTTATTCTTAAATTAA
1 ATTAATTTATTCTTAAATTAA
* * *
356247 AATAATGTATT-TTTAATTAA
1 ATTAATTTATTCTTAAATTAA
*
356267 ATTAATTTATTCTTAAATTAT
1 ATTAATTTATTCTTAAATTAA
* * * *
356288 ATTAGTGTATTCTTGAATTAT
1 ATTAATTTATTCTTAAATTAA
* *
356309 ATTAATTTATTCTTGAATTAT
1 ATTAATTTATTCTTAAATTAA
*
356330 ATTAATTTATT-TTTAATTAA
1 ATTAATTTATTCTTAAATTAA
*
356350 ATTAATTTATTCTTAAATTAT
1 ATTAATTTATTCTTAAATTAA
* *
356371 ATTAGTGTATTCTTAAATTAA
1 ATTAATTTATTCTTAAATTAA
*
356392 ATTAATATATT
1 ATTAATTTATT
356403 TATATAGTTT
Statistics
Matches: 167, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
20 35 0.21
21 115 0.69
22 17 0.10
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
ATTAATTTATTCTTAAATTAA
Found at i:356321 original size:83 final size:83
Alignment explanation
Indices: 356183--356402 Score: 323
Period size: 83 Copynumber: 2.6 Consensus size: 83
356173 ATTTTGTTGT
* * * **
356183 ATTAATTTATTCTTAAATTAAATTAATATAATTCAAGAATTATATTAATTTATTCTTAAATTAAA
1 ATTAATTTATTCTTAAATTATATTAGTGT-ATTCTTGAATTATATTAATTTATTCTTAAATTAAA
356248 ATAATGTATTTTTAATTAA
65 ATAATGTATTTTTAATTAA
* * *
356267 ATTAATTTATTCTTAAATTATATTAGTGTATTCTTGAATTATATTAATTTATTCTTGAATTATAT
1 ATTAATTTATTCTTAAATTATATTAGTGTATTCTTGAATTATATTAATTTATTCTTAAATTAAAA
*
356332 TAATTTATTTTTAATTAA
66 TAATGTATTTTTAATTAA
* * *
356350 ATTAATTTATTCTTAAATTATATTAGTGTATTCTTAAATTAAATTAATATATT
1 ATTAATTTATTCTTAAATTATATTAGTGTATTCTTGAATTATATTAATTTATT
356403 TATATAGTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
83 98 0.79
84 26 0.21
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (83 bp):
ATTAATTTATTCTTAAATTATATTAGTGTATTCTTGAATTATATTAATTTATTCTTAAATTAAAA
TAATGTATTTTTAATTAA
Found at i:356403 original size:62 final size:63
Alignment explanation
Indices: 356182--356402 Score: 259
Period size: 62 Copynumber: 3.5 Consensus size: 63
356172 CATTTTGTTG
* *
356182 TATTAATTTATTCTTAAATTAAATTAATATAATTC-AAGAATTATATTAATTTATTCTTAAATTA
1 TATTAATGTATTCTTAAATTAAATTAATAT-ATTCTTA-AATTATATTAATTTATTCTTAAATTA
* * * * * * *
356246 AAATAATGTATT-TTTAATTAAATTAATTTATTCTTAAATTATATTAGTGTATTCTTGAATTA
1 TATTAATGTATTCTTAAATTAAATTAATATATTCTTAAATTATATTAATTTATTCTTAAATTA
* * * * * *
356308 TATTAATTTATTCTTGAATTATATTAATTTATT-TTTAATTAAATTAATTTATTCTTAAATTA
1 TATTAATGTATTCTTAAATTAAATTAATATATTCTTAAATTATATTAATTTATTCTTAAATTA
*
356370 TATTAGTGTATTCTTAAATTAAATTAATATATT
1 TATTAATGTATTCTTAAATTAAATTAATATATT
356403 TATATAGTTT
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
62 88 0.67
63 34 0.26
64 9 0.07
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (63 bp):
TATTAATGTATTCTTAAATTAAATTAATATATTCTTAAATTATATTAATTTATTCTTAAATTA
Found at i:359794 original size:804 final size:806
Alignment explanation
Indices: 358049--360055 Score: 3600
Period size: 804 Copynumber: 2.5 Consensus size: 806
358039 ATTCATAACC
358049 CTTTTAACAGTAAATTTATTTTTGTTTCTCCTCGATTTAAAGTGTATAAAGATGGTTGATGCCGC
1 CTTTTAACAGTAAATTTATTTTTGTTTCTCCTCGATTTAAAGTGTATAAAGATGGTTGATGCCGC
* *
358114 GAGAAGTTGGGAGAGGTCGCCGGCTGGGTCAGCGCGACTGTGGTCTCAGCCTTCTTCTCATCCCT
66 GAGAAGTTGGGAGAGGTCGCCGGCTGGGTCAGCGCCACTGTGGTCTCGGCCTTCTTCTCATCCC-
*
358179 GGAGCGTTTCTCCTGTGTCAACCTCTCCACCAACGATCCTGACGATGACGACAATTCCGATGAGG
130 ---GC--TTCTCCTGTGTCAACCTCTCCACCAACGATCCTGACGATGACGACAATTCCGACGAGG
358244 CTAGGGACCGCCCCCTCACCTACTCTTAAACATCCTCTCCACTCCCTGCCAAAATTGGTACTTGC
190 CTAGGGACCGCCCCCTCACCTACTCTTAAACATCCTCTCCACTCCCTGCCAAAATTGGTACTTGC
*
358309 CCATGGCATATATTTTCTGTCTTTCTTGATTTAGTGTCTTGTTTACAGGAAAAAAAAGAAAGAAA
255 CCATGGCATATATTTTCGGTCTTTCTTGATTTAGTGTCTTGTTTACAGG-AAAAAAAGAAAGAAA
*
358374 GAAGAGAACTTTATATGTTATAAATTTGTTGCTGCTTCTTATTGAAAATGAATGTGTTATGTAAT
319 GAAGAGAACTTTATATGTTATAAATTTGTTGCTGCTTCTTATTGAAAATGGATGTGTTATGTAAT
358439 AACGTGTCTCTATTTGACATGCCTGCTTTAATAAGGCCCTCTTGACTTTTGCATCACATATAGCA
384 AAC--GTCTCTATTTGACATGCCTGCTTTAATAAGGCCCTCTTGACTTTTGCATCACATATAGCA
358504 GCTGTCCATATTATAGCCATCCCAGAAACTTTCATGCCAAATTGTATAGTTTTTATTTTTTGAAT
447 GCTGTCCATATTATAGCCATCCCAGAAACTTTCATGCCAAATTGTATAGTTTTTATTTTTTGAAT
* * *
358569 TTCGGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTATATTAAATCAATTGTTATTATTA
512 TTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATCAACTGTTATTATTA
358634 TTTTTCATGATTGCTCGGTTGTCAAAGAGAAGCATGCAGGGAAAAATATATTACGGTGGTATAGT
577 TTTTTCATGATTGCTCGGTTGTCAAAGAGAAGCATGCAGGGAAAAATATATTACGGTGGTATAGT
358699 ATTTTTTCAGATAAAGGTTAGCGTATTCTTTCAAACATATTACGGTGATACAGTGATTCAACCAA
642 ATTTTTTCAGATAAAGGTTAGCGTATTCTTTCAAACATATTACGGTGATACAGTGATTCAACCAA
*
358764 CGTCTCCCAACGGCTATATTCCAAGAAAATAAATTCATATCCCTTTTACCAAAATCCTTCAGGTA
707 CGTCTCCCAACGGCTATATTCCAAGAAAATAAATTCATAACCCTTTTACCAAAATCCTTCAGGTA
358829 ACCTAAACTACATTCAAGATTCAATTCCGCGTATT
772 ACCTAAACTACATTCAAGATTCAATTCCGCGTATT
*
358864 CTTTTAACAGTAAATTTATTTTTGTTTCTCCTCGAATTTAAAGTGTATAAAGATGTTTGATGCCG
1 CTTTTAACAGTAAATTTATTTTTGTTTCTCCTCG-ATTTAAAGTGTATAAAGATGGTTGATGCCG
* *
358929 CGAGAAGTTGGGAGAGGTCGTCGGCTGGGTCAGCGCCACTGTGGTCTCGGCATTC-TCTCAT-CC
65 CGAGAAGTTGGGAGAGGTCGCCGGCTGGGTCAGCGCCACTGTGGTCTCGGCCTTCTTCTCATCCC
358992 -C-TCTCCTGTGTCAACCTCTCCACCAACGATCCTGACGATGACGACAATTCCGACGAGGCTAGG
130 GCTTCTCCTGTGTCAACCTCTCCACCAACGATCCTGACGATGACGACAATTCCGACGAGGCTAGG
359055 GACCGCCCCCTCACCTACTCTTAAACATCCTCTCCACTCCCTGCCAAAATTGGTACTTGCCCATG
195 GACCGCCCCCTCACCTACTCTTAAACATCCTCTCCACTCCCTGCCAAAATTGGTACTTGCCCATG
359120 GCATATATTTTCGGTCTTTCTTGATTTAGTGTCTTGTTTACAGGAAAAGAAAGAAAGAAAGAAGA
260 GCATATATTTTCGGTCTTTCTTGATTTAGTGTCTTGTTTACAGGAAAA-AAAGAAAGAAAGAAGA
359185 GAACTTTATATGTTATAAATTTGTTGCTGCTTCTTATTGAAAATGGATGTGTTATGTAATAACGT
324 GAACTTTATATGTTATAAATTTGTTGCTGCTTCTTATTGAAAATGGATGTGTTATGTAATAACGT
359250 CTCTATTTGACATGCCTGCTTTAATAAGGCCCTCTTGACTTTTGCATCACATATAGCAGCTGTCC
389 CTCTATTTGACATGCCTGCTTTAATAAGGCCCTCTTGACTTTTGCATCACATATAGCAGCTGTCC
* *
359315 ATATTATAGCCATCCCAGAAACTTTCATGCCAAATTGTATTGTTTTTATTTTTTGTATTTCAGTA
454 ATATTATAGCCATCCCAGAAACTTTCATGCCAAATTGTATAGTTTTTATTTTTTGAATTTCAGTA
359380 CAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATCAACTGTTATTATTATTTTTCA
519 CAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATCAACTGTTATTATTATTTTTCA
*
359445 TGATTGCTCGGTTGTCAAAGAGAAGCATGCTGGGAAAAATATATTACGGTGGTATAGTATTTTTT
584 TGATTGCTCGGTTGTCAAAGAGAAGCATGCAGGGAAAAATATATTACGGTGGTATAGTATTTTTT
*
359510 CAGATAAAGGTTAGCGTATTCTTTCAAACATATTACGGTGATATAGTGATTCAACCAACGTCTCC
649 CAGATAAAGGTTAGCGTATTCTTTCAAACATATTACGGTGATACAGTGATTCAACCAACGTCTCC
359575 CAACGGCTATATTCCAAGAAAATAAATTCATAACCCTTTTACCAAAATCCTTCAGGTAACCTAAA
714 CAACGGCTATATTCCAAGAAAATAAATTCATAACCCTTTTACCAAAATCCTTCAGGTAACCTAAA
359640 CTACATTCAAGATTCAATTCCGCGTATT
779 CTACATTCAAGATTCAATTCCGCGTATT
*
359668 CTTTTAACAGTAAATTTATTTTTGTTTCTCCTCGATTTAAAGTGTATAAAGATGGTTGATACCGC
1 CTTTTAACAGTAAATTTATTTTTGTTTCTCCTCGATTTAAAGTGTATAAAGATGGTTGATGCCGC
*
359733 GAGAAGTTGGGAGAGGTCGCCGGCTGGGTCAGCGCCACTGTGGTTTCGGCCTTCTTCTCATCCCT
66 GAGAAGTTGGGAGAGGTCGCCGGCTGGGTCAGCGCCACTGTGGTCTCGGCCTTCTTCTCATCCC-
*
359798 GGAGCGTTTCTCCTGTGTCAACCTCTCCACCAACGATCCTGATGATGACGACAATTCCGACGAGG
130 ---GC--TTCTCCTGTGTCAACCTCTCCACCAACGATCCTGACGATGACGACAATTCCGACGAGG
* *
359863 CTTGGGACCGCCCCCTCACCTACTC-T-AACATCCTCTCCACTCCCTGCCAAAATTGGTACTTAC
190 CTAGGGACCGCCCCCTCACCTACTCTTAAACATCCTCTCCACTCCCTGCCAAAATTGGTACTTGC
359926 CCATGGCATATATTTTCGGTCTTTCTTGATTTAGTGTCTTGTTTACAGG---AAAAGAAAGAAAG
255 CCATGGCATATATTTTCGGTCTTTCTTGATTTAGTGTCTTGTTTACAGGAAAAAAAGAAAGAAAG
*
359988 AAGAGAACTTTATATGTTATAAATTTGTTGCTACTTCTTATTGAAAATGGATGTGTTATGTAATA
320 AAGAGAACTTTATATGTTATAAATTTGTTGCTGCTTCTTATTGAAAATGGATGTGTTATGTAATA
360053 ACG
385 ACG
360056 ACTGATTTTG
Statistics
Matches: 1155, Mismatches: 25, Indels: 32
0.95 0.02 0.03
Matches are distributed among these distances:
803 80 0.07
804 452 0.39
805 6 0.01
806 247 0.21
807 79 0.07
808 1 0.00
809 1 0.00
810 1 0.00
811 85 0.07
812 1 0.00
813 80 0.07
814 2 0.00
815 40 0.03
816 80 0.07
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (806 bp):
CTTTTAACAGTAAATTTATTTTTGTTTCTCCTCGATTTAAAGTGTATAAAGATGGTTGATGCCGC
GAGAAGTTGGGAGAGGTCGCCGGCTGGGTCAGCGCCACTGTGGTCTCGGCCTTCTTCTCATCCCG
CTTCTCCTGTGTCAACCTCTCCACCAACGATCCTGACGATGACGACAATTCCGACGAGGCTAGGG
ACCGCCCCCTCACCTACTCTTAAACATCCTCTCCACTCCCTGCCAAAATTGGTACTTGCCCATGG
CATATATTTTCGGTCTTTCTTGATTTAGTGTCTTGTTTACAGGAAAAAAAGAAAGAAAGAAGAGA
ACTTTATATGTTATAAATTTGTTGCTGCTTCTTATTGAAAATGGATGTGTTATGTAATAACGTCT
CTATTTGACATGCCTGCTTTAATAAGGCCCTCTTGACTTTTGCATCACATATAGCAGCTGTCCAT
ATTATAGCCATCCCAGAAACTTTCATGCCAAATTGTATAGTTTTTATTTTTTGAATTTCAGTACA
AAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATCAACTGTTATTATTATTTTTCATG
ATTGCTCGGTTGTCAAAGAGAAGCATGCAGGGAAAAATATATTACGGTGGTATAGTATTTTTTCA
GATAAAGGTTAGCGTATTCTTTCAAACATATTACGGTGATACAGTGATTCAACCAACGTCTCCCA
ACGGCTATATTCCAAGAAAATAAATTCATAACCCTTTTACCAAAATCCTTCAGGTAACCTAAACT
ACATTCAAGATTCAATTCCGCGTATT
Found at i:363701 original size:47 final size:47
Alignment explanation
Indices: 363630--363729 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 47
363620 TAATGTTTCA
*
363630 AAAATTATGTATATATGTAAACACGTGTATACATATAAAATCTAGGT
1 AAAATTATGTATATATGTAAACACGTGCATACATATAAAATCTAGGT
* *
363677 AAAATTATGTATATATGTATACACGTGCATATATATAAAATCTAGGT
1 AAAATTATGTATATATGTAAACACGTGCATACATATAAAATCTAGGT
363724 AAAATT
1 AAAATT
363730 TTCAGAGTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (47 bp):
AAAATTATGTATATATGTAAACACGTGCATACATATAAAATCTAGGT
Found at i:370370 original size:683 final size:687
Alignment explanation
Indices: 368421--370478 Score: 3969
Period size: 679 Copynumber: 3.0 Consensus size: 687
368411 ATCAAAGCCT
368421 TATATCTTTTCTCTTTCATTATTGAGACTTATTGGCTAAACTTTTTTTCATGCTGAACTTGTAGC
1 TATATCTTTTCTCTTTCATTATTGAGACTTATTGGCTAAACTTTTTTTCATGCTGAACTTGTAGC
368486 CCACTGGAAGATTCACTTCTTTATGTTGAGATGGACATTGAGAAATGCCATCACACAGACTCTGT
66 CCACTGGAAGATTCACTTCTTTATGTTGAGATGGACATTGAGAAATGCCATCACACAGACTCTGT
368551 AAGAAATTCTTTCATCTCAATTTTTCTCGTGCATGCTTCCAGCCTATTTAATGTTTATATGATTT
131 AAGAAATTCTTTCATCTCAATTTTTCTCGTGCATGCTTCCAGCCTATTTAATGTTTATATGATTT
368616 TTATTTTTATAGAAATAATTTTAAAAAATGTGCTCTTAGTAGTGTTATTCCTTATTTGTTCGTAC
196 TTA-TTTTATAGAAATAATTTTAAAAAATGTGCTCTTAGTAGTGTTATTCCTTATTTGTTCGTAC
368681 ACAGAAAGAGTTTGGATCCTCCATATTCTTTTATTTTCAGTGTCAATTCTTCCTATCCAATCAAT
260 ACAGAAAGAGTTTGGATCCTCCATATTCTTTTATTTTCAGTGTCAATTCTTCCTATCCAATCAAT
368746 TTGGGGTAACCCCATAGCAATTCTTTTTAGGAAACTTAGTCGATATGGTAAATGAAAAATTATTT
325 TTGGGGTAACCCCATAGCAATTCTTTTTAGGAAACTTAGTCGATATGGTAAATGAAAAATTATTT
368811 TACATTAGTTTGATATTCATGTTGAGCCTCTCTACCATTAGCCATGTGTTGGAAGTATGACTGTT
390 TACATTAGTTTGATATTCATGTTGAGCCTCTCTACCATTAGCCATGTGTTGGAAGTATGACTGTT
368876 CTAAAATTGCTAGGAAAAACCAAAAATACATCTGAATATAAATAGGATACTTAGGGATTATTATG
455 CTAAAATTGCTAGGAAAAACCAAAAATACATCTGAATATAAATAGGATACTTAGGGATTATTATG
368941 TACTCTTAACGTCCAATCTTTTCCATGTTGTGATTGAAGATTTTCTTGAGTTTCACGGAAGCTAA
520 TACTCTTAACGTCCAATCTTTTCCATGTTGTGATTGAAGATTTTCTTGAGTTTCACGGAAGCTAA
369006 TTTAAGTCTGAACTTTGACATTTTCATGGAATCCAATTTTATGGTATTAGTTTTCATTTTTTTTT
585 TTTAAGTCTGAACTTTGACATTTTCATGGAATCCAATTTTATGGTATTAGTTTTCATTTTTTTTT
369071 T--AAAAGCCACATTACTTTTGAAATACATACTTAGTC
650 TAAAAAAGCCACATTACTTTTGAAATACATACTTAGTC
369107 TATATCTTTTCTCTTTCATTATTGAGACTTATTGGCTAAACTTTTTTTCATGCTGAACTTGTAGC
1 TATATCTTTTCTCTTTCATTATTGAGACTTATTGGCTAAACTTTTTTTCATGCTGAACTTGTAGC
369172 CCACTGGAAGATTCACTTCTTTATGTTGAGATGGACATTGAGAAATGCCATCACACAGACTCTGT
66 CCACTGGAAGATTCACTTCTTTATGTTGAGATGGACATTGAGAAATGCCATCACACAGACTCTGT
369237 AAGAAATTC-TTCATCTCAATTTTTCTCGTGCATGCTTCCAGCCTATTTAATGTTTATATGA-TT
131 AAGAAATTCTTTCATCTCAATTTTTCTCGTGCATGCTTCCAGCCTATTTAATGTTTATATGATTT
369300 TT-TTTTATAGAAATAATTTTAAAAAATGTGCTCTTAGTAGTGTTATTCCTTATTTGTTCGTACA
196 TTATTTTATAGAAATAATTTTAAAAAATGTGCTCTTAGTAGTGTTATTCCTTATTTGTTCGTACA
369364 CAGAAAGAGTTTGGATCCTCCATATTCTTTTATTTTCAGTGTCAATTCTTCCTATCCAATCAA-T
261 CAGAAAGAGTTTGGATCCTCCATATTCTTTTATTTTCAGTGTCAATTCTTCCTATCCAATCAATT
369428 TGGGGTAACCCCATAGCAATTCTTTTTAGGAAACTTAGTCGATATGGTAAATG-AAAATTATTTT
326 TGGGGTAACCCCATAGCAATTCTTTTTAGGAAACTTAGTCGATATGGTAAATGAAAAATTATTTT
369492 ACATTAGTTTGATATTCATG-TGAGCCTCTCTACCATTAGCCATGTGTTGGAAGTATGACTGTTC
391 ACATTAGTTTGATATTCATGTTGAGCCTCTCTACCATTAGCCATGTGTTGGAAGTATGACTGTTC
369556 TAAAATTGCTAGGAAAAACCAAAAATACATCTGAATATAAATAGGATACTTAGGGATTATTATGT
456 TAAAATTGCTAGGAAAAACCAAAAATACATCTGAATATAAATAGGATACTTAGGGATTATTATGT
369621 ACTCTTAACGTCCAATCTTTTCCATGTTGTGATTGAAGATTTTCTTGAGTTTCACGGAAGCTAAT
521 ACTCTTAACGTCCAATCTTTTCCATGTTGTGATTGAAGATTTTCTTGAGTTTCACGGAAGCTAAT
*
369686 TTAAGTATGAACTTTGACATTTTCATGGAATCCAATTTTATGGTATTAGTTTTCATTTTTTTTTT
586 TTAAGTCTGAACTTTGACATTTTCATGGAATCCAATTTTATGGTATTAGTTTTCATTTTTTTTTT
369751 AAAAAAGCCACATTACTTTTGAAATACATACTTAGTC
651 AAAAAAGCCACATTACTTTTGAAATACATACTTAGTC
369788 TATATCTTTTCTCTTTCATTATTGAGACTTATTGGCT-AAC-TTTTTTCATGCTGAACTTGTAGC
1 TATATCTTTTCTCTTTCATTATTGAGACTTATTGGCTAAACTTTTTTTCATGCTGAACTTGTAGC
369851 CCACTGGAAGATTCACTTCTTTATGTTG-GATGGACATTGAGAAATGCCATCACACAGACTCTGT
66 CCACTGGAAGATTCACTTCTTTATGTTGAGATGGACATTGAGAAATGCCATCACACAGACTCTGT
369915 AAGAAATTCTTTCATCTCAATTTTTCTCGTGCATGCTTCCAGCCTATTTAATG-TTATATGATTT
131 AAGAAATTCTTTCATCTCAATTTTTCTCGTGCATGCTTCCAGCCTATTTAATGTTTATATGATTT
*
369979 TTATTTTATAGAAATAATTTTAAAAAATATGCTCTTAGTAGTGTTATTCCTTATTTGTTCGTACA
196 TTATTTTATAGAAATAATTTTAAAAAATGTGCTCTTAGTAGTGTTATTCCTTATTTGTTCGTACA
*
370044 CAGAAAGAGTTTGGATCCTCCATATTCTTTTATTTTCAGTGTCAATTCTTCTTATCCAATCAATT
261 CAGAAAGAGTTTGGATCCTCCATATTCTTTTATTTTCAGTGTCAATTCTTCCTATCCAATCAATT
370109 TGGGGTAACCCCATAGCAATTCTTTTTAGGAAACTTAGTCGATATGGTAAATGAAAAATTATTTT
326 TGGGGTAACCCCATAGCAATTCTTTTTAGGAAACTTAGTCGATATGGTAAATGAAAAATTATTTT
370174 ACATTAGTTTGATATTCATGTTGAGCCTCTCTACCATTAGCCATGTGTTGGAAGTATGACTGTTC
391 ACATTAGTTTGATATTCATGTTGAGCCTCTCTACCATTAGCCATGTGTTGGAAGTATGACTGTTC
370239 TAAAATTGCTAGGAAAAACCAAAAATACATCTGAATATAAATAGGATACTTAGGGATTATTATGT
456 TAAAATTGCTAGGAAAAACCAAAAATACATCTGAATATAAATAGGATACTTAGGGATTATTATGT
370304 ACTCTTAACGTCCAATCTTTTCCATGTTGTGATTGAAGATTTTCTTGAGTTTCACGGAAGCTAAT
521 ACTCTTAACGTCCAATCTTTTCCATGTTGTGATTGAAGATTTTCTTGAGTTTCACGGAAGCTAAT
370369 TTAAGTCTGAACTTTGACATTTTCATGGAATCCAATTTTATGGTATTAGTTTTCATTTCTTTTTT
586 TTAAGTCTGAACTTTGACATTTTCATGGAATCCAATTTTATGGTATTAGTTTTCA-TT-TTTTTT
370434 TTAAAAAAAGCCACATTACTTTTGAAATACATACTTAGTC
649 TT-AAAAAAGCCACATTACTTTTGAAATACATACTTAGTC
370474 TATAT
1 TATAT
370479 TCTGAAAATA
Statistics
Matches: 1357, Mismatches: 4, Indels: 22
0.98 0.00 0.02
Matches are distributed among these distances:
678 53 0.04
679 336 0.25
680 157 0.12
681 180 0.13
682 156 0.11
683 228 0.17
684 6 0.00
685 60 0.04
686 181 0.13
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (687 bp):
TATATCTTTTCTCTTTCATTATTGAGACTTATTGGCTAAACTTTTTTTCATGCTGAACTTGTAGC
CCACTGGAAGATTCACTTCTTTATGTTGAGATGGACATTGAGAAATGCCATCACACAGACTCTGT
AAGAAATTCTTTCATCTCAATTTTTCTCGTGCATGCTTCCAGCCTATTTAATGTTTATATGATTT
TTATTTTATAGAAATAATTTTAAAAAATGTGCTCTTAGTAGTGTTATTCCTTATTTGTTCGTACA
CAGAAAGAGTTTGGATCCTCCATATTCTTTTATTTTCAGTGTCAATTCTTCCTATCCAATCAATT
TGGGGTAACCCCATAGCAATTCTTTTTAGGAAACTTAGTCGATATGGTAAATGAAAAATTATTTT
ACATTAGTTTGATATTCATGTTGAGCCTCTCTACCATTAGCCATGTGTTGGAAGTATGACTGTTC
TAAAATTGCTAGGAAAAACCAAAAATACATCTGAATATAAATAGGATACTTAGGGATTATTATGT
ACTCTTAACGTCCAATCTTTTCCATGTTGTGATTGAAGATTTTCTTGAGTTTCACGGAAGCTAAT
TTAAGTCTGAACTTTGACATTTTCATGGAATCCAATTTTATGGTATTAGTTTTCATTTTTTTTTT
AAAAAAGCCACATTACTTTTGAAATACATACTTAGTC
Found at i:371972 original size:62 final size:63
Alignment explanation
Indices: 371870--371998 Score: 242
Period size: 62 Copynumber: 2.1 Consensus size: 63
371860 GTATACAATG
*
371870 TTTTCCCATGGAATAAAATGGCTAATATATAAACATCAAAGGGTAATCTTGAGTTTTATACGA
1 TTTTCCCATGGAATAAAATGGCTAATATATAAACATCAAAGGGTAATCTTAAGTTTTATACGA
371933 TTTT-CCATGGAATAAAATGGCTAATATATAAACATCAAAGGGTAATCTTAAGTTTTATACGA
1 TTTTCCCATGGAATAAAATGGCTAATATATAAACATCAAAGGGTAATCTTAAGTTTTATACGA
371995 TTTT
1 TTTT
371999 TCAGGCATTT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 61 0.94
63 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (63 bp):
TTTTCCCATGGAATAAAATGGCTAATATATAAACATCAAAGGGTAATCTTAAGTTTTATACGA
Found at i:398779 original size:33 final size:33
Alignment explanation
Indices: 398737--398811 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
398727 GTGCACCCAA
398737 GTGCTAATCCATATAGTCCACCGCCACAACCCG
1 GTGCTAATCCATATAGTCCACCGCCACAACCCG
398770 GTGCTAATCCATATAGTCCACCGCCACAACCCG
1 GTGCTAATCCATATAGTCCACCGCCACAACCCG
398803 GTGCTAATC
1 GTGCTAATC
398812 ATTGCGGCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.27, C:0.37, G:0.16, T:0.20
Consensus pattern (33 bp):
GTGCTAATCCATATAGTCCACCGCCACAACCCG
Found at i:399542 original size:164 final size:165
Alignment explanation
Indices: 399183--399592 Score: 402
Period size: 164 Copynumber: 2.5 Consensus size: 165
399173 AGGTTGTATG
* * * * * *
399183 AGCTCAAAACTATGTCGAGCCCAACTAAGATTGACCTAGTACT-ATCCCATATCTCAAATAGACA
1 AGCTCAGAAGTATGTCGAACCCAAATAGGATTGACCTAGTACTGA-CCCATATCTCGAATAGACA
* * *
399247 TTTTTAACTCGATTTTATCAATCAATTTTGACTAAGGTTGGCCTTATTAAATTTTGAATCATAGC
65 TTTTTAA--C---TTTACCAATCAACTTTGACAAAGGTTGGCCTTATTAAATTTTGAATCATAGC
* * *
399312 CCGATTTGTTGACTGAACCAACTTATCTATTATTCTCTATG
125 CCGATTTATTGACTGAACAAACTTATCTATTATTCTCTATA
* *
399353 AGCTCATAAGTATATC-AAGCCCAAATAGGATTGA-CTGAGTACTGACCCATATCTCGAATAGAC
1 AGCTCAGAAGTATGTCGAA-CCCAAATAGGATTGACCT-AGTACTGACCCATATCTCGAATAGAC
** * *
399416 ATTTTTAACTTTACCAATTGACTTTG-CAAAGGTTGGCCTT-TTCCAATTTTGACTCAT-GACCC
64 ATTTTTAACTTTACCAATCAACTTTGACAAAGGTTGGCCTTATT-AAATTTTGAATCATAG-CCC
* * *
399478 GATTTATTGATTGAATAAACTTAT-TAATTATTCTGTATA
127 GATTTATTGACTGAACAAACTTATCT-ATTATTCTCTATA
** * * * * * *
399517 AGCTTGGAAGTATGTCGAACCCAAATAGGATTGACCTTGTATTGATCCATATCTCGAACATACCT
1 AGCTCAGAAGTATGTCGAACCCAAATAGGATTGACCTAGTACTGACCCATATCTCGAATAGACAT
*
399582 TTTTAAATTTA
66 TTTTAACTTTA
399593 TTTTATCGAT
Statistics
Matches: 201, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
163 4 0.02
164 118 0.59
165 17 0.08
168 1 0.00
169 3 0.01
170 57 0.28
171 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (165 bp):
AGCTCAGAAGTATGTCGAACCCAAATAGGATTGACCTAGTACTGACCCATATCTCGAATAGACAT
TTTTAACTTTACCAATCAACTTTGACAAAGGTTGGCCTTATTAAATTTTGAATCATAGCCCGATT
TATTGACTGAACAAACTTATCTATTATTCTCTATA
Found at i:406733 original size:6 final size:6
Alignment explanation
Indices: 406722--406755 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
406712 GATACATAAA
406722 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
406756 AATGCTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (6 bp):
ATTTTG
Found at i:418810 original size:55 final size:55
Alignment explanation
Indices: 418703--418815 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 55
418693 AGTTTAACAC
**
418703 TAACTTAAAATTCAATCCATAGTTTAAGAACATCTAATGTAAATAATACGTAGTT
1 TAACTTAAAATTCAATCCATAGTTTAAGAACATCTAATACAAATAATACGTAGTT
* * *
418758 TAACTTAAAATTCGATCCATAGTTTAAGAACATCTGATACAACTAA-ACCGTAGTT
1 TAACTTAAAATTCAATCCATAGTTTAAGAACATCTAATACAAATAATA-CGTAGTT
418813 TAA
1 TAA
418816 GACTAATTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 1 0.02
55 51 0.98
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (55 bp):
TAACTTAAAATTCAATCCATAGTTTAAGAACATCTAATACAAATAATACGTAGTT
Found at i:432382 original size:29 final size:29
Alignment explanation
Indices: 432341--432414 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
432331 AATATTAATC
** *
432341 ATTAAATGTATATTAGTATTTATT-CATTT
1 ATTAAATAAATATTAATATTT-TTGCATTT
*
432370 ATTAAATAAATA-TAATATTTTTGTATTT
1 ATTAAATAAATATTAATATTTTTGCATTT
*
432398 TTTAAATAAATA-TAATA
1 ATTAAATAAATATTAATA
432415 CAAATAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.05
28 27 0.69
29 10 0.26
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (29 bp):
ATTAAATAAATATTAATATTTTTGCATTT
Found at i:432389 original size:28 final size:28
Alignment explanation
Indices: 432357--432414 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
432347 TGTATATTAG
432357 TATTTATT-CATTTATTAAATAAATATAA
1 TATTT-TTGCATTTATTAAATAAATATAA
* *
432385 TATTTTTGTATTTTTTAAATAAATATAA
1 TATTTTTGCATTTATTAAATAAATATAA
432413 TA
1 TA
432415 CAAATAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TATTTTTGCATTTATTAAATAAATATAA
Found at i:443122 original size:129 final size:132
Alignment explanation
Indices: 442892--443156 Score: 419
Period size: 129 Copynumber: 2.0 Consensus size: 132
442882 ATAACTCCAA
*
442892 TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACGACTAAAACGACAC
1 TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACAACTAAAACGACAC
442957 TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTG-T-TT-GATTTTATTGATT
66 TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTGATGTTAGATTTTATTGATT
443019 AT
131 AT
* * * * *
443021 TAATGTTTGTAACTAGTAAAAATTCAATTTATTACTGCAAGTTTAAAAGGCAACTTAAATGACAC
1 TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACAACTAAAACGACAC
** * *
443086 TCGGCACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATGGTTGATGTTATATTTTATTGATT
66 TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTGATGTTAGATTTTATTGATT
443151 AT
131 AT
443153 TAAT
1 TAAT
443157 CTACTTTTTT
Statistics
Matches: 123, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
129 102 0.83
130 1 0.01
131 2 0.02
132 18 0.15
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (132 bp):
TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACAACTAAAACGACAC
TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTGATGTTAGATTTTATTGATT
AT
Found at i:447719 original size:2 final size:2
Alignment explanation
Indices: 447706--447738 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
447696 ATTTGTTTGA
*
447706 AT AT AC 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 A
447739 ATTAGTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:456015 original size:11 final size:12
Alignment explanation
Indices: 455999--456031 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
455989 GGACGGTTAA
455999 GATTCCGATT-C
1 GATTCCGATTCC
456010 GATTCCGATTCC
1 GATTCCGATTCC
456022 GATTTCCGAT
1 GA-TTCCGAT
456032 CTTAATCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 3 0.15
13 7 0.35
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (12 bp):
GATTCCGATTCC
Found at i:456018 original size:6 final size:6
Alignment explanation
Indices: 455999--456031 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
455989 GGACGGTTAA
455999 GATTCC GATT-C GATTCC GATTCC GATTTCC GAT
1 GATTCC GATTCC GATTCC GATTCC GA-TTCC GAT
456032 CTTAATCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (6 bp):
GATTCC
Found at i:458486 original size:20 final size:20
Alignment explanation
Indices: 458463--458500 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
458453 AGTATTATCT
458463 AAAATATTAATATTTTATTG
1 AAAATATTAATATTTTATTG
*
458483 AAAATATTAATTTTTTAT
1 AAAATATTAATATTTTAT
458501 CTAATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAAATATTAATATTTTATTG
Found at i:458951 original size:17 final size:15
Alignment explanation
Indices: 458921--458956 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
458911 TTGAATATAT
458921 TATATTTTAAAATAA
1 TATATTTTAAAATAA
458936 TATATTTT-AAATAA
1 TATATTTTAAAATAA
458950 TATATTT
1 TATATTT
458957 ATAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTTTAAAATAA
Found at i:459866 original size:2 final size:2
Alignment explanation
Indices: 459859--459909 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
459849 AACAATACAA
459859 AT AT AT AT AT -T 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
459900 AT AT AT AT AT
1 AT AT AT AT AT
459910 TGTATATGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:461733 original size:20 final size:20
Alignment explanation
Indices: 461708--461831 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
461698 TTAATTATGA
*
461708 CATCCTTTCATGTCTTAATT
1 CATCCTTTCATGCCTTAATT
*
461728 CATCCTTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
*
461752 GACATCCTTTCATGCCTTAATG
1 --CATCCTTTCATGCCTTAATT
*
461774 CATCCTTTCATGCATTTAATTAT
1 CATCCTTTCATGC-CTTAA-T-T
*
461797 GGCATCCTTTCATGCCTTAATG
1 --CATCCTTTCATGCCTTAATT
461819 CATCCTTTCATGC
1 CATCCTTTCATGC
461832 ATTTTAATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
20 38 0.45
21 4 0.05
22 5 0.06
23 3 0.04
24 9 0.11
25 13 0.15
26 13 0.15
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.44
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATT
Found at i:461807 original size:45 final size:46
Alignment explanation
Indices: 461694--461857 Score: 285
Period size: 46 Copynumber: 3.6 Consensus size: 46
461684 TCCATTTATA
* *
461694 CATTTTAATTATGACATCCTTTCATGTCTTAATTCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
461740 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
*
461786 CA-TTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
*
461831 CATTTTAATTATGGCATCCTTTCATGC
1 CATTTTAATTATGACATCCTTTCATGC
461858 ATTTTACATA
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
45 44 0.39
46 70 0.61
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (46 bp):
CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:462369 original size:20 final size:19
Alignment explanation
Indices: 462344--462393 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
462334 TGAAATAAGA
462344 AAAATAAAATAAATAAAAT-G
1 AAAATAAAAT-AAT-AAATGG
462364 AAAATAATAATAATAAATGG
1 AAAATAA-AATAATAAATGG
462384 AAAATAAAAT
1 AAAATAAAAT
462394 GCTAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.25
20 18 0.64
21 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAATAAAATAATAAATGG
Found at i:462465 original size:38 final size:36
Alignment explanation
Indices: 462418--462690 Score: 153
Period size: 37 Copynumber: 7.4 Consensus size: 36
462408 GTATATATTA
*
462418 AAAAAACGTTTTTAAAAACTATATGCTATATGTTTTC
1 AAAAAACGTTTTTAAAAACTATAT-ATATATGTTTTC
* *
462455 AAAAATACGTTTTCAAAAACTATATATATACGTTTTC
1 AAAAA-ACGTTTTTAAAAACTATATATATATGTTTTC
* *
462492 AAAAGAA--ATTTTAAAAACTACATATTATATGTTTTC
1 AAAA-AACGTTTTTAAAAACTATATA-TATATGTTTTC
* * * * *
462528 --AAAATGTTGTTCTTAAAATTATACATTATATGTCTTC
1 AAAAAACGTT-TT-TAAAAACTATATA-TATATGTTTTC
* * * * * *
462565 CAAAACCGATTTAAAAAACCATATATCATATGTTTTTTT
1 AAAAAACGTTTTTAAAAACTATATAT-ATATG--TTTTC
* * * *
462604 AAAATATG-TTTTCAAAACTATATATTATACGTTTTC
1 AAAAAACGTTTTTAAAAACTATATA-TATATGTTTTC
* * **
462640 -AAAAACGTGTTTTCAAAACCATATTATATACATTTTC
1 AAAAAACGT-TTTTAAAAACTATA-TATATATGTTTTC
*
462677 AAAAACCGATTTTT
1 AAAAAACG-TTTTT
462691 TTTTAAATTT
Statistics
Matches: 181, Mismatches: 37, Indels: 35
0.72 0.15 0.14
Matches are distributed among these distances:
33 2 0.01
34 2 0.01
35 20 0.11
36 17 0.09
37 76 0.42
38 50 0.28
39 14 0.08
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.40
Consensus pattern (36 bp):
AAAAAACGTTTTTAAAAACTATATATATATGTTTTC
Found at i:462504 original size:73 final size:70
Alignment explanation
Indices: 462427--462643 Score: 190
Period size: 74 Copynumber: 2.9 Consensus size: 70
462417 AAAAAAACGT
462427 TTTTAAAAACTATATGCTATATGTTTTCAAAAATACGTTTTCAAAAACTATATA-TATACGTTTT
1 TTTTAAAAACTATAT-CTATATGTTTTC-AAAATA-GTTTTC-AAAACTATATATTATACGTTTT
*
462491 CAAAAGAAA
62 CAAAACAAA
* * *
462500 TTTTAAAAACTACATAT-TATATGTTTTCAAAAT-GTTGTTCTTAAAATTATACATTATATGTCT
1 TTTTAAAAACT--ATATCTATATGTTTTCAAAATAGTT-TTC--AAAACTATATATTATACGT-T
* **
462563 TCCAAAACCGA
60 TTCAAAACAAA
* *
462574 TTTAAAAAACCATATATC-ATATGTTTTTTTAAAATATGTTTTCAAAACTATATATTATACGTTT
1 TTTTAAAAA-C-TATATCTATATG--TTTTCAAAATA-GTTTTCAAAACTATATATTATACGTTT
462638 TCAAAA
61 TCAAAA
462644 ACGTGTTTTC
Statistics
Matches: 117, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
70 3 0.03
71 3 0.03
72 14 0.12
73 28 0.24
74 32 0.27
75 21 0.18
76 10 0.09
77 3 0.03
78 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (70 bp):
TTTTAAAAACTATATCTATATGTTTTCAAAATAGTTTTCAAAACTATATATTATACGTTTTCAAA
ACAAA
Found at i:466571 original size:10 final size:9
Alignment explanation
Indices: 466526--466596 Score: 72
Period size: 9 Copynumber: 7.6 Consensus size: 9
466516 GGCTGCTGGA
466526 AACCGGTTT
1 AACCGGTTT
466535 AACCGGTTTT
1 AACCGG-TTT
466545 CAACCGGTTT
1 -AACCGGTTT
*
466555 GACCGGTTT
1 AACCGGTTT
466564 CAACCGG-TT
1 -AACCGGTTT
*
466573 GACCGGTTT
1 AACCGGTTT
466582 CAACCGGTTT
1 -AACCGGTTT
*
466592 GACCG
1 AACCG
466597 ATCTGACCCG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
8 5 0.10
9 22 0.42
10 19 0.37
11 6 0.12
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:466576 original size:18 final size:19
Alignment explanation
Indices: 466526--466596 Score: 117
Period size: 18 Copynumber: 3.7 Consensus size: 19
466516 GGCTGCTGGA
*
466526 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TTTC
466546 AACCGGTTTGACCGGTTTC
1 AACCGGTTTGACCGGTTTC
466565 AACCGG-TTGACCGGTTTC
1 AACCGGTTTGACCGGTTTC
466583 AACCGGTTTGACCG
1 AACCGGTTTGACCG
466597 ATCTGACCCG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 18 0.37
19 17 0.35
20 14 0.29
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTC
Found at i:466622 original size:17 final size:17
Alignment explanation
Indices: 466600--466638 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
466590 TTGACCGATC
466600 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
466617 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
466634 TGACC
1 TGACC
466639 GTGACTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Done.