Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 14 of 433
Found at i:3766065 original size:26 final size:26
Alignment explanation
Indices: 3765886--3766066 Score: 299
Period size: 26 Copynumber: 7.0 Consensus size: 26
3765876 TGATATAAAT
*
3765886 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
3765912 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
3765938 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
3765964 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
3765990 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
3766016 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
* *
3766042 TAATAATGGGTTAGGTAAATGTTTC
1 TGATAATAGGTTAGGTAAATGTTTC
3766067 TGTAATGGCC
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 148 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:3766065 original size:78 final size:78
Alignment explanation
Indices: 3765888--3766066 Score: 331
Period size: 78 Copynumber: 2.3 Consensus size: 78
3765878 ATATAAATTG
*
3765888 ATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGG
1 ATAATAGGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGG
*
3765953 TAAATGTTTCATG
66 TAAATGTTTCATA
3765966 ATAATAGGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGG
1 ATAATAGGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGG
3766031 TAAATGTTTCATA
66 TAAATGTTTCATA
*
3766044 ATAATGGGTTAGGTAAATGTTTC
1 ATAATAGGTTAGGTAAATGTTTC
3766067 TGTAATGGCC
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 98 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (78 bp):
ATAATAGGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGG
TAAATGTTTCATA
Found at i:3784935 original size:137 final size:136
Alignment explanation
Indices: 3784689--3784974 Score: 518
Period size: 137 Copynumber: 2.1 Consensus size: 136
3784679 GAGTAGTCTC
3784689 CCCAAATGGGCTTGCATATGTTTACTGATGTTGAATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGAATGTATTTTGAAATGGGCCTATGGGCCATAC
*
3784754 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCT-GCCCAGTACC
3784819 ACTGTTA
130 ACTGTTA
*
3784826 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGAATGTATTTTGAAATGGGCCTATGGGCCATAC
*
3784891 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCAGTACCA
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGCCCAGTACCA
3784956 CTGTTA
131 CTGTTA
**
3784962 CCTGAATGGGCTT
1 CCCAAATGGGCTT
3784975 AGGCCCAATA
Statistics
Matches: 144, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 26 0.18
137 118 0.82
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGAATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGCCCAGTACCA
CTGTTA
Found at i:3795640 original size:37 final size:37
Alignment explanation
Indices: 3795599--3795679 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
3795589 TTGAAATCCT
* * *
3795599 TGGAAATGATATTTACATGATATATTGAAACGTGACA
1 TGGAAATGATATTTACATAATATATTAAAAAGTGACA
* *
3795636 TGGAAATGGTATTTACTTAATATATTAAAAAGTGACA
1 TGGAAATGATATTTACATAATATATTAAAAAGTGACA
*
3795673 TGTAAAT
1 TGGAAAT
3795680 ATGTGATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (37 bp):
TGGAAATGATATTTACATAATATATTAAAAAGTGACA
Found at i:3801582 original size:11 final size:11
Alignment explanation
Indices: 3801568--3801623 Score: 103
Period size: 11 Copynumber: 5.1 Consensus size: 11
3801558 CAATATCTAA
*
3801568 AAAATAACAAT
1 AAAATAATAAT
3801579 AAAATAATAAT
1 AAAATAATAAT
3801590 AAAATAATAAT
1 AAAATAATAAT
3801601 AAAATAATAAT
1 AAAATAATAAT
3801612 AAAATAATAAT
1 AAAATAATAAT
3801623 A
1 A
3801624 TTTTTTTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
11 44 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:3801589 original size:3 final size:3
Alignment explanation
Indices: 3801570--3801623 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
3801560 ATATCTAAAA
*
3801570 AAT AAC AAT AA- AAT AAT AAT AA- AAT AAT AAT AA- AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3801614 AAT AAT AAT A
1 AAT AAT AAT A
3801624 TTTTTTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 37 0.82
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:3802889 original size:46 final size:46
Alignment explanation
Indices: 3802839--3802931 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
3802829 ATATAAACTA
3802839 ATAGAATGAAAAGACTTGAGAGGGATAAATTTATGTAACTACACTG
1 ATAGAATGAAAAGACTTGAGAGGGATAAATTTATGTAACTACACTG
3802885 ATAGAATGAAAAGACTTGAGAGGGATAAATTTATGTAACTACACTG
1 ATAGAATGAAAAGACTTGAGAGGGATAAATTTATGTAACTACACTG
3802931 A
1 A
3802932 ATCCATTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.26
Consensus pattern (46 bp):
ATAGAATGAAAAGACTTGAGAGGGATAAATTTATGTAACTACACTG
Found at i:3806046 original size:26 final size:26
Alignment explanation
Indices: 3806010--3806067 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
3806000 TATAGGATAA
3806010 TATTTGTCATCAACTATTTATCTTTT
1 TATTTGTCATCAACTATTTATCTTTT
3806036 TATTTGTCATCAACTATTTATCTTTT
1 TATTTGTCATCAACTATTTATCTTTT
*
3806062 TCTTTG
1 TATTTG
3806068 CAGAGCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.59
Consensus pattern (26 bp):
TATTTGTCATCAACTATTTATCTTTT
Found at i:3809253 original size:22 final size:23
Alignment explanation
Indices: 3809215--3809283 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 23
3809205 TTCTTGAGAC
3809215 AAATCCGATATGTCTCGAGACTT
1 AAATCCGATATGTCTCGAGACTT
* *
3809238 AAATGCGAT-TGTCTCGAGAC-C
1 AAATCCGATATGTCTCGAGACTT
3809259 AACAT--GATATGTCTCGAGACATT
1 AA-ATCCGATATGTCTCGAGAC-TT
3809282 AA
1 AA
3809284 GCACTTGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 3 0.08
21 13 0.33
22 13 0.33
23 10 0.26
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (23 bp):
AAATCCGATATGTCTCGAGACTT
Found at i:3810479 original size:22 final size:22
Alignment explanation
Indices: 3810446--3810531 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 22
3810436 AATATCAGGT
*
3810446 ATTTGA-ATTTAATTTTTTTTA
1 ATTTGATATTTAATGTTTTTTA
* *
3810467 ATTTGATATTTAAGGTTTTTCA
1 ATTTGATATTTAATGTTTTTTA
* * *
3810489 ATTTGGTATCTAATTTTTTTTA
1 ATTTGATATTTAATGTTTTTTA
3810511 ATTT-AGTATTTAATGTTTTTT
1 ATTTGA-TATTTAATGTTTTTT
3810532 GGGTTCAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
21 6 0.12
22 46 0.88
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.63
Consensus pattern (22 bp):
ATTTGATATTTAATGTTTTTTA
Found at i:3811143 original size:36 final size:37
Alignment explanation
Indices: 3811066--3811143 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 37
3811056 TAATTACTTT
* *
3811066 TTAT-TTAAGTAAAAAGATATTTACTATTTATTATAA
1 TTATATTAAGTAAAAAGATATTTACTAATTATAATAA
* *
3811102 -T-TATTAAGTTAAAAGATATTTATTAATTA-AATAA
1 TTATATTAAGTAAAAAGATATTTACTAATTATAATAA
3811136 TTATATTA
1 TTATATTA
3811144 TAAGATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
34 5 0.14
35 25 0.71
36 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (37 bp):
TTATATTAAGTAAAAAGATATTTACTAATTATAATAA
Found at i:3811313 original size:15 final size:16
Alignment explanation
Indices: 3811293--3811325 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3811283 TTATTATTGT
3811293 TAATTTAT-TAAATTA
1 TAATTTATATAAATTA
*
3811308 TAATTTATATTAATTA
1 TAATTTATATAAATTA
3811324 TA
1 TA
3811326 TTATGAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTATATAAATTA
Found at i:3811918 original size:17 final size:18
Alignment explanation
Indices: 3811896--3811929 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3811886 TAAATGAGTT
3811896 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
3811913 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
3811930 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:3821356 original size:21 final size:21
Alignment explanation
Indices: 3821326--3821365 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3821316 TTTGTCAAAG
* *
3821326 ATGTGTATTGGATTGAATTTA
1 ATGTGAATTGGATTAAATTTA
*
3821347 ATGTGAATTGTATTAAATT
1 ATGTGAATTGGATTAAATT
3821366 GAGCTAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTTA
Found at i:3821817 original size:49 final size:50
Alignment explanation
Indices: 3821697--3821818 Score: 117
Period size: 49 Copynumber: 2.5 Consensus size: 50
3821687 CCACAACTCT
* * *
3821697 TATGAGCATTCCCGAT-ATATGGCTCTCATAAGCTTCTCAATTAATGGCTCT
1 TATGAGC-TTCCCGATAAT-TGGCTCACATAAGCTTCTCAATTAATAGCTCG
* * ** *
3821748 TTTGAGCTTCCC-A-AATTTGGCTCACATGAGCTTC-CCGTTTATAGCTCG
1 TATGAGCTTCCCGATAA-TTGGCTCACATAAGCTTCTCAATTAATAGCTCG
3821796 TATGAGCTTCCCGATAATTGGCT
1 TATGAGCTTCCCGATAATTGGCT
3821819 TGCAAGAGCT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
48 20 0.34
49 24 0.41
50 8 0.14
51 6 0.10
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (50 bp):
TATGAGCTTCCCGATAATTGGCTCACATAAGCTTCTCAATTAATAGCTCG
Found at i:3821878 original size:25 final size:25
Alignment explanation
Indices: 3821765--3821883 Score: 82
Period size: 25 Copynumber: 4.8 Consensus size: 25
3821755 TTCCCAAATT
* *
3821765 TGGCTCACATGAGCTTCCCGTT-TA
1 TGGCTCAAAAGAGCTTCCCGTTATA
* ** * *
3821789 TAGCTCGTATGAGCTTCCCGATA-A
1 TGGCTCAAAAGAGCTTCCCGTTATA
*** * *
3821813 TTGGCTTGCAAGAGCTTCCTGTTACA
1 -TGGCTCAAAAGAGCTTCCCGTTATA
*
3821839 TGGCTCACATA-AGCTTCCCGTTATA
1 TGGCTCA-AAAGAGCTTCCCGTTATA
3821864 TGGCTCAAAAGAGCTTCCCG
1 TGGCTCAAAAGAGCTTCCCG
3821884 ATTACATGTT
Statistics
Matches: 73, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
24 21 0.29
25 50 0.68
26 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (25 bp):
TGGCTCAAAAGAGCTTCCCGTTATA
Found at i:3827547 original size:29 final size:29
Alignment explanation
Indices: 3827505--3827564 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3827495 GTTCTGCAAC
3827505 TTATAGCACTCAGATTTAATGTGCCCTTT
1 TTATAGCACTCAGATTTAATGTGCCCTTT
3827534 TTATAGCACTCAGATTTAATGTGCCCTTT
1 TTATAGCACTCAGATTTAATGTGCCCTTT
3827563 TT
1 TT
3827565 TTTTTTACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.43
Consensus pattern (29 bp):
TTATAGCACTCAGATTTAATGTGCCCTTT
Found at i:3829759 original size:14 final size:14
Alignment explanation
Indices: 3829740--3829767 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3829730 TACAATATCC
3829740 AAATGATAACAATA
1 AAATGATAACAATA
3829754 AAATGATAACAATA
1 AAATGATAACAATA
3829768 TAATAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATGATAACAATA
Found at i:3829789 original size:11 final size:11
Alignment explanation
Indices: 3829775--3829817 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3829765 ATATAATAGT
3829775 AAAATAACAAC
1 AAAATAACAAC
* **
3829786 AAAACAATGAC
1 AAAATAACAAC
*
3829797 AAAAAAACAAC
1 AAAATAACAAC
3829808 AAAATAACAA
1 AAAATAACAA
3829818 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.74, C:0.16, G:0.02, T:0.07
Consensus pattern (11 bp):
AAAATAACAAC
Found at i:3838558 original size:6 final size:6
Alignment explanation
Indices: 3838547--3838587 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
3838537 CGGCACTTAA
* * *
3838547 GGGAAG GGGAAG GGGAAG GTGAAG GGGAAA GGGAAA GGGAA
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAA
3838588 TTAGAGGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02
Consensus pattern (6 bp):
GGGAAG
Found at i:3839031 original size:21 final size:21
Alignment explanation
Indices: 3838963--3839033 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
3838953 TGGTATTTGA
3838963 ATTTAATTTTTTTTAATTTAGT
1 ATTTAA-TTTTTTTAATTTAGT
* * ** *
3838985 ATTAAAATTTGTTCCATTTGGT
1 ATT-TAATTTTTTTAATTTAGT
3839007 ATTTAATTTTTTTAATTTAGT
1 ATTTAATTTTTTTAATTTAGT
3839028 ATTTAA
1 ATTTAA
3839034 GTCTTTTGGA
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
21 19 0.50
22 17 0.45
23 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.61
Consensus pattern (21 bp):
ATTTAATTTTTTTAATTTAGT
Found at i:3839471 original size:27 final size:26
Alignment explanation
Indices: 3839415--3839511 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 26
3839405 GTTTGGGTAC
* *
3839415 CAAATTAAAAAAA-AAACTTAAAT-T
1 CAAATTAAAAAAACAAATTTAAATAA
**
3839439 CTAAATTAAAAAAATCAAATTTTGATAA
1 C-AAATTAAAAAAA-CAAATTTAAATAA
* * *
3839467 CAAATTAGATAAAAGAAATTTAAATAC
1 CAAATTA-AAAAAACAAATTTAAATAA
3839494 CAAATTAAAAAAA-AAATT
1 CAAATTAAAAAAACAAATT
3839512 AATATCATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
24 1 0.02
25 17 0.29
26 5 0.09
27 29 0.50
28 6 0.10
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (26 bp):
CAAATTAAAAAAACAAATTTAAATAA
Found at i:3846153 original size:35 final size:36
Alignment explanation
Indices: 3846090--3846162 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 36
3846080 TGCCTGCGTG
3846090 AATGCCCAAATAGAGAGGGAGAGTCTATCATACGTC
1 AATGCCCAAATAGAGAGGGAGAGTCTATCATACGTC
3846126 AATGCCCAAATAGAGA-GGAGAGTCTATCATACGTC
1 AATGCCCAAATAGAGAGGGAGAGTCTATCATACGTC
3846161 AA
1 AA
3846163 GTATAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 21 0.57
36 16 0.43
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (36 bp):
AATGCCCAAATAGAGAGGGAGAGTCTATCATACGTC
Found at i:3846714 original size:25 final size:25
Alignment explanation
Indices: 3846686--3846736 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3846676 TATGTTACGT
3846686 CACTGAATCCATTTTTCCACATCTC
1 CACTGAATCCATTTTTCCACATCTC
*
3846711 CACTGAATCCATTTTTCCATATCTC
1 CACTGAATCCATTTTTCCACATCTC
3846736 C
1 C
3846737 TGTTTGTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.35, G:0.04, T:0.37
Consensus pattern (25 bp):
CACTGAATCCATTTTTCCACATCTC
Found at i:3855040 original size:3 final size:3
Alignment explanation
Indices: 3855032--3855139 Score: 53
Period size: 3 Copynumber: 34.7 Consensus size: 3
3855022 ATTAGTGTTC
* **
3855032 TAT TAT TAT TAT T-T TAT T-T GAT GCT TAT ATAT ATAT ATAT ATAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TAT -TAT TAT
* * * *
3855078 TAT TAT ATAG TAT TAT TAA TAGCT T-T TAA TAT TAT TAT TAT TAC TAT
1 TAT TAT -TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT TAT
3855125 TAT TAT TAT ATAT TA
1 TAT TAT TAT -TAT TA
3855140 GTGTATATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 18
0.74 0.11 0.16
Matches are distributed among these distances:
2 7 0.08
3 56 0.67
4 20 0.24
5 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:3855091 original size:10 final size:9
Alignment explanation
Indices: 3855056--3855191 Score: 51
Period size: 10 Copynumber: 15.1 Consensus size: 9
3855046 TATTTGATGC
3855056 TTATATATA
1 TTATATATA
3855065 -TATATATA
1 TTATATATA
3855073 -TAT-TATA
1 TTATATATA
3855080 TTATATAGTA
1 TTATATA-TA
3855090 TTAT-TAATA
1 TTATAT-ATA
*
3855099 GCTTTTA-ATA
1 --TTATATATA
3855109 TTAT-TATTA
1 TTATATA-TA
3855118 TTACTAT-TA
1 TTA-TATATA
3855127 TTATTATATA
1 TTA-TATATA
*
3855137 TTAGTGTATA
1 TTA-TATATA
3855147 TT-T-T-TA
1 TTATATATA
* *
3855153 TGTACATACA
1 T-TATATATA
*
3855163 CGTATATATA
1 -TTATATATA
3855173 TATATATATA
1 T-TATATATA
3855183 TT-TATATA
1 TTATATATA
3855191 T
1 T
3855192 GGCATTGCTT
Statistics
Matches: 98, Mismatches: 11, Indels: 37
0.67 0.08 0.25
Matches are distributed among these distances:
6 3 0.03
7 6 0.06
8 26 0.27
9 20 0.20
10 39 0.40
11 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (9 bp):
TTATATATA
Found at i:3855255 original size:3 final size:3
Alignment explanation
Indices: 3855247--3855285 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
3855237 TGTATTTCTA
* *
3855247 TAT TAT TAT TAT AAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3855286 ATAGTAGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3857669 original size:26 final size:24
Alignment explanation
Indices: 3857629--3857706 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 24
3857619 TTATTTTATT
* * *
3857629 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAAAATAA
3857653 TAAATCAAATATATTTAAAAAAATAA
1 -AAAT-AAATATATTTAAAAAAATAA
3857679 AAAT-AA-ATA-TTAAAACAAATAA
1 AAATAAATATATTTAAAA-AAATAA
3857701 AAATAA
1 AAATAA
3857707 TACTAAAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 6 0.13
22 13 0.28
23 3 0.06
25 8 0.17
26 17 0.36
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATAAATATATTTAAAAAAATAA
Found at i:3857698 original size:22 final size:22
Alignment explanation
Indices: 3857659--3857717 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
3857649 ATAATAAATC
*
3857659 AAATATAT-TTAAAA-AAATAA
1 AAATAAATATTAAAACAAATAA
3857679 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
3857701 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
3857718 TTCTTAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 7 0.20
21 18 0.51
22 10 0.29
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:3878952 original size:20 final size:20
Alignment explanation
Indices: 3878913--3878950 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3878903 AAATGTTTCG
3878913 AATTTTATTAATTATTTTTT
1 AATTTTATTAATTATTTTTT
3878933 AATTTT-TTAATT-TTTTTT
1 AATTTTATTAATTATTTTTT
3878951 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
AATTTTATTAATTATTTTTT
Found at i:3880779 original size:148 final size:150
Alignment explanation
Indices: 3880591--3880976 Score: 611
Period size: 148 Copynumber: 2.6 Consensus size: 150
3880581 TGGGAAAAAA
* *
3880591 AAAACCAAAAA-TGCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCCTGCGCT
1 AAAAGCAAAAAGT-CGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCT
* *
3880655 CTACCGACTGAGCTAGACGGGCCAGTTAAT-TTTATTTGTGTAAATTTCTTACAAATTCAAAACT
65 CTACCGACTGAGCTAGACGGGCCAATTAATGTTGA-TTGTGTAAATTTCTTACAAA-TCAAAACT
3880719 AATAGTTA-CAGTTGCTCGG-A-
128 AATAGTTACCAGTTGCTCGGAAC
*
3880739 AAAAGTAAAAAGTCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTC
1 AAAAGCAAAAAGTCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTC
* * *
3880804 TACCGACTGAGCTAGACGGGCCAATTGATGTTGATTGTGTAAATTTTTTACAAATCAAAACTTAT
66 TACCGACTGAGCTAGACGGGCCAATTAATGTTGATTGTGTAAATTTCTTACAAATCAAAACTAAT
*
3880869 AGTTATCCAGTTGCTTGGAAC
131 AGTTA-CCAGTTGCTCGGAAC
3880890 TAAAAGCAAAAAGTCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCT
1 -AAAAGCAAAAAGTCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCT
3880955 CTACCGACTGAGCTAGACGGGC
65 CTACCGACTGAGCTAGACGGGC
3880977 TTCCTGTTGC
Statistics
Matches: 221, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
147 15 0.07
148 106 0.48
149 14 0.06
150 1 0.00
152 85 0.38
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (150 bp):
AAAAGCAAAAAGTCGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCTC
TACCGACTGAGCTAGACGGGCCAATTAATGTTGATTGTGTAAATTTCTTACAAATCAAAACTAAT
AGTTACCAGTTGCTCGGAAC
Found at i:3886407 original size:92 final size:92
Alignment explanation
Indices: 3886296--3886465 Score: 313
Period size: 92 Copynumber: 1.8 Consensus size: 92
3886286 GCCCATAAGC
* *
3886296 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3886361 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
3886388 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3886453 CGAGTTCGGATGC
66 CGAGTTCGGATGC
3886466 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:3886462 original size:46 final size:46
Alignment explanation
Indices: 3886288--3886462 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
3886278 TGTAACCCGC
* * * *
3886288 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3886334 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3886384 -C-TCA--GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3886426 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3886463 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 2 0.02
44 2 0.02
46 92 0.83
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3889365 original size:45 final size:45
Alignment explanation
Indices: 3889254--3889369 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
3889244 ATCATACCAG
* * *
3889254 AAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCACGATTC
1 AAATGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACGATTC
* * **
3889299 AGACGAGTAAGACCATAGTTGAAAGACGCTATGGCATTGCGATTC
1 AAATGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACGATTC
* *
3889344 AAATGTGTAAGACCATGGTTGAAAGA
1 AAATGAGTAAGACCATAGTTGAAAGA
3889370 TACCATGGCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACGATTC
Found at i:3889378 original size:45 final size:45
Alignment explanation
Indices: 3889254--3889520 Score: 185
Period size: 46 Copynumber: 5.9 Consensus size: 45
3889244 ATCATACCAG
* * * *
3889254 AAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCACGATTC
1 AAATGAGTAAGACCATAGTTGAAAGATACCATGGCATCACGATTC
* * ** * **
3889299 AGACGAGTAAGACCATAGTTGAAAGACGCTATGGCATTGCGATTC
1 AAATGAGTAAGACCATAGTTGAAAGATACCATGGCATCACGATTC
* * * * **
3889344 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAGG
1 AAATGAGTAAGACCATAGTTGAAAGATACCATGGCATCACGAT-TC
* * * * ***
3889390 AAATGTA-TAAGATCATGGTTGAAAGATACCATGGCAACATGACAGG
1 AAATG-AGTAAGACCATAGTTGAAAGATACCATGGCATCACGA-TTC
* * * * * * ***
3889436 AAATGAATAAGACTATGGTTGAAAGATACCCTGGCAACATGACAGA
1 AAATGAGTAAGACCATAGTTGAAAGATACCATGGCATCACGA-TTC
*
3889482 AAATGAGTAAGACCATAGTTGAAAGATACTATGGCATCA
1 AAATGAGTAAGACCATAGTTGAAAGATACCATGGCATCA
3889521 TGTCGAAGAT
Statistics
Matches: 185, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
45 71 0.38
46 114 0.62
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGTTGAAAGATACCATGGCATCACGATTC
Found at i:3889407 original size:46 final size:46
Alignment explanation
Indices: 3889344--3889522 Score: 252
Period size: 46 Copynumber: 3.9 Consensus size: 46
3889334 ATTGCGATTC
* *
3889344 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAGG
1 AAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG
*
3889390 AAATGTATAAGATCATGGTTGAAAGATACCATGGCAACATGACAGG
1 AAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG
* * * *
3889436 AAATGAATAAGACTATGGTTGAAAGATACCCTGGCAACATGACAGA
1 AAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG
* * *
3889482 AAATG-AGTAAGACCATAGTTGAAAGATACTATGGCATCATG
1 AAATGTA-TAAGACCATGGTTGAAAGATACCATGGCAACATG
3889523 TCGAAGATAA
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 118 0.99
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
AAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG
Found at i:3889458 original size:92 final size:92
Alignment explanation
Indices: 3889351--3889544 Score: 259
Period size: 92 Copynumber: 2.1 Consensus size: 92
3889341 TTCAAATGTG
* * * *
3889351 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGTA-TAAGATCATGGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATG-AGTAAGACCATAGTTGAAAG
3889415 ATACCATGGCAACATGACAGGAAATGAA
65 ATACCATGGCAACATGACAGGAAATGAA
* *
3889443 TAAGACTATGGTTGAAAGATACCCTGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGA
* * * *
3889508 TACTATGGCATCATGTC--GAAGATAAA
66 TACCATGGCAACATGACAGGAA-ATGAA
3889534 TAAGACCATGG
1 TAAGACCATGG
3889545 ATGGGAGACG
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
90 3 0.03
91 15 0.17
92 71 0.80
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGA
TACCATGGCAACATGACAGGAAATGAA
Found at i:3896984 original size:15 final size:14
Alignment explanation
Indices: 3896954--3896988 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3896944 TTTTTGGAAG
*
3896954 AGGAAAAAAGAGAA
1 AGGAAAAAAAAGAA
3896968 AGGAAAAGAAAAGAA
1 AGGAAAA-AAAAGAA
3896983 AGGAAA
1 AGGAAA
3896989 GGGTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AGGAAAAAAAAGAA
Found at i:3902152 original size:21 final size:21
Alignment explanation
Indices: 3902126--3902166 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3902116 AGACGAGCGA
* *
3902126 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3902147 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3902167 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3904809 original size:13 final size:13
Alignment explanation
Indices: 3904791--3904819 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3904781 TTTCAGTAAC
3904791 TACCTTTATAATT
1 TACCTTTATAATT
3904804 TACCTTTATAATT
1 TACCTTTATAATT
3904817 TAC
1 TAC
3904820 TATGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (13 bp):
TACCTTTATAATT
Found at i:3905815 original size:10 final size:10
Alignment explanation
Indices: 3905800--3905859 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
3905790 TACATTATGG
3905800 AATTATAAAA
1 AATTATAAAA
3905810 AATTAT-AAA
1 AATTATAAAA
3905819 AA-TATTAAAA
1 AATTA-TAAAA
* *
3905829 AATTATTATA
1 AATTATAAAA
*
3905839 AATTAATTAAA
1 AATT-ATAAAA
*
3905850 AATGATAAAA
1 AATTATAAAA
3905860 TGATTTACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 2 0.05
9 6 0.15
10 23 0.56
11 10 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AATTATAAAA
Found at i:3905825 original size:11 final size:11
Alignment explanation
Indices: 3905801--3905840 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
3905791 ACATTATGGA
3905801 ATTATAAAAA-
1 ATTATAAAAAT
3905811 ATTATAAAAAT
1 ATTATAAAAAT
3905822 ATTA-AAAAATT
1 ATTATAAAAA-T
3905833 ATTATAAA
1 ATTATAAA
3905841 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.56
11 9 0.33
12 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTATAAAAAT
Found at i:3905847 original size:11 final size:10
Alignment explanation
Indices: 3905800--3905852 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
3905790 TACATTATGG
*
3905800 AATTATAAAA
1 AATTATTAAA
3905810 AATTA-TAAA
1 AATTATTAAA
3905819 AA-TATTAAAA
1 AATTATT-AAA
*
3905829 AATTATTATA
1 AATTATTAAA
3905839 AATTAATTAAA
1 AATT-ATTAAA
3905850 AAT
1 AAT
3905853 GATAAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
8 2 0.06
9 6 0.17
10 16 0.44
11 12 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATTATTAAA
Found at i:3906029 original size:16 final size:16
Alignment explanation
Indices: 3906004--3906041 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
3905994 ATTTGTATGG
3906004 TTTTTAATAAATTGTTA
1 TTTTTAATAAATT-TTA
3906021 TTTTT-ATAAATTTTA
1 TTTTTAATAAATTTTA
3906036 TGTTTT
1 T-TTTT
3906042 TTAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTTTAATAAATTTTA
Found at i:3906042 original size:17 final size:18
Alignment explanation
Indices: 3906003--3906042 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
3905993 TATTTGTATG
3906003 GTTTTTAATAAATTGTTA
1 GTTTTTAATAAATTGTTA
3906021 -TTTTT-ATAAATT-TTA
1 GTTTTTAATAAATTGTTA
3906036 TGTTTTT
1 -GTTTTT
3906043 TAATTAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.15
16 7 0.35
17 10 0.50
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (18 bp):
GTTTTTAATAAATTGTTA
Found at i:3906061 original size:18 final size:18
Alignment explanation
Indices: 3906040--3906075 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3906030 ATTTTATGTT
3906040 TTTTAATTAATTCTAATA
1 TTTTAATTAATTCTAATA
* *
3906058 TTTTTATTAATTTTAATA
1 TTTTAATTAATTCTAATA
3906076 AAATTTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAATTAATTCTAATA
Found at i:3906063 original size:37 final size:35
Alignment explanation
Indices: 3905994--3906072 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
3905984 AAAATATATT
*
3905994 ATTTGTATGGTTTTTAATAAATTGTTATTTTTATAA
1 ATTT-TATGGTTTTTAATAAATTCTTATTTTTATAA
* * *
3906030 ATTTTATGTTTTTTAATTAATTCTAATATTTTTATTA
1 ATTTTATGGTTTTTAATAAATTCT--TATTTTTATAA
3906067 ATTTTA
1 ATTTTA
3906073 ATAAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 17 0.46
36 4 0.11
37 16 0.43
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (35 bp):
ATTTTATGGTTTTTAATAAATTCTTATTTTTATAA
Found at i:3906071 original size:28 final size:28
Alignment explanation
Indices: 3906040--3906099 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
3906030 ATTTTATGTT
* *
3906040 TTTTAAT-TAATTCTAAT-ATTTTTATTAA
1 TTTTAATAAAATT-TAATGATTTTT-CTAA
3906068 TTTTAATAAAATTTAATGATTTTTCTAA
1 TTTTAATAAAATTTAATGATTTTTCTAA
3906096 TTTT
1 TTTT
3906100 TTAGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTAATAAAATTTAATGATTTTTCTAA
Found at i:3907407 original size:17 final size:17
Alignment explanation
Indices: 3907387--3907426 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3907377 TATGTGTTAT
3907387 AAATTACATAATATAAA
1 AAATTACATAATATAAA
*
3907404 AAATAACATAATATAAA
1 AAATTACATAATATAAA
*
3907421 ATATTA
1 AAATTA
3907427 TAAACTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTACATAATATAAA
Found at i:3907833 original size:14 final size:15
Alignment explanation
Indices: 3907814--3907847 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3907804 TTTTAAATTG
*
3907814 ATTTTACATA-TTTT
1 ATTTTAAATATTTTT
3907828 ATTTTAAATATTTTT
1 ATTTTAAATATTTTT
3907843 ATTTT
1 ATTTT
3907848 TATAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTAAATATTTTT
Found at i:3912913 original size:3 final size:3
Alignment explanation
Indices: 3912905--3912949 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3912895 ATTCATTTGA
3912905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3912950 TAAATTTAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3913133 original size:9 final size:9
Alignment explanation
Indices: 3913121--3913163 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3913111 AAAAAACAAA
3913121 AAAAAAATT
1 AAAAAAATT
*
3913130 AAAATAATCT
1 AAAAAAAT-T
3913140 AAAAAAATT
1 AAAAAAATT
* *
3913149 CATAAAATT
1 AAAAAAATT
3913158 AAAAAA
1 AAAAAA
3913164 TTTATATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAAAATT
Found at i:3913155 original size:28 final size:28
Alignment explanation
Indices: 3913124--3913183 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
3913114 AAACAAAAAA
3913124 AAAATTAAAATAATCTA-AAAAAATTCAT
1 AAAATTAAAA-AATCTATAAAAAATTCAT
* * *
3913152 AAAATTAAAAAATTTATATAAAATTCTT
1 AAAATTAAAAAATCTATAAAAAATTCAT
3913180 AAAA
1 AAAA
3913184 ATGATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAATTAAAAAATCTATAAAAAATTCAT
Found at i:3917737 original size:26 final size:26
Alignment explanation
Indices: 3917708--3917758 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3917698 CCTGATATAT
3917708 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* * *
3917734 GGCTTTTTGTGAGCTTCCTGATTAA
1 GGCTCTTCGTGAGCTTCCCGATTAA
3917759 TGATTCTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:3917768 original size:26 final size:27
Alignment explanation
Indices: 3917711--3917780 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
3917701 GATATATGGC
* *
3917711 TCTTCGTGAGCTTCCCGATTAAAGGCT
1 TCTTTGTGAGCTTCCCGATTAAAGGAT
* *
3917738 T-TTTGTGAGCTTCCTGATT-AATGAT
1 TCTTTGTGAGCTTCCCGATTAAAGGAT
*
3917763 TCTTTG-GAGCTTCTCGAT
1 TCTTTGTGAGCTTCCCGAT
3917781 ATGGCTCACT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 15 0.42
26 20 0.56
27 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.41
Consensus pattern (27 bp):
TCTTTGTGAGCTTCCCGATTAAAGGAT
Found at i:3920044 original size:17 final size:19
Alignment explanation
Indices: 3920017--3920054 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3920007 CGTAGCCTCC
3920017 CATGATCAGCAC-CCCACA
1 CATGATCAGCACGCCCACA
3920035 CATG-TCAGCACGCCCACA
1 CATGATCAGCACGCCCACA
3920053 CA
1 CA
3920055 CGATTCCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.32, C:0.45, G:0.13, T:0.11
Consensus pattern (19 bp):
CATGATCAGCACGCCCACA
Found at i:3921265 original size:30 final size:29
Alignment explanation
Indices: 3921201--3921269 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
3921191 TTCATATTAT
*
3921201 TTTATGTA-AATATTTTCTTTTAAATTTA
1 TTTATGTATAATATTTTCTTTAAAATTTA
3921229 -TTATGTATATATATTTTCTTTAAAATTTA
1 TTTATGTATA-ATATTTTCTTTAAAATTTA
3921258 TTTATGTATAAT
1 TTTATGTATAAT
3921270 TTGGCTTTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 7 0.19
28 1 0.03
29 20 0.54
30 9 0.24
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.59
Consensus pattern (29 bp):
TTTATGTATAATATTTTCTTTAAAATTTA
Found at i:3921277 original size:28 final size:29
Alignment explanation
Indices: 3921217--3921277 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3921207 TAAATATTTT
* **
3921217 CTTTTAAATTTATTATGTATATATATTTT
1 CTTTAAAATTTATTATGTATATATATTGG
3921246 CTTTAAAATTTATTTATGTATA-AT-TTGG
1 CTTTAAAATTTA-TTATGTATATATATTGG
3921274 CTTT
1 CTTT
3921278 CTTTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 13 0.46
30 9 0.32
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (29 bp):
CTTTAAAATTTATTATGTATATATATTGG
Found at i:3924072 original size:19 final size:18
Alignment explanation
Indices: 3924048--3924092 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3924038 GGTAAAAATC
*
3924048 TTATTTTTTTATTCTTTTT
1 TTATTTTTTTATT-TTATT
*
3924067 TTATTTTGTTATTTTATT
1 TTATTTTTTTATTTTATT
*
3924085 GTATTTTT
1 TTATTTTT
3924093 GATAAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (18 bp):
TTATTTTTTTATTTTATT
Found at i:3926275 original size:36 final size:36
Alignment explanation
Indices: 3926228--3926306 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
3926218 TTCTAACAGA
*
3926228 TTTTTACTATGTCATTATTTGCCTTTATTTTCTAAC
1 TTTTAACTATGTCATTATTTGCCTTTATTTTCTAAC
3926264 TTTTAACTATGTCATTATTTGCCTTTATTTTCTAAC
1 TTTTAACTATGTCATTATTTGCCTTTATTTTCTAAC
3926300 TTTTAAC
1 TTTTAAC
3926307 CCTCCTAGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57
Consensus pattern (36 bp):
TTTTAACTATGTCATTATTTGCCTTTATTTTCTAAC
Found at i:3931883 original size:32 final size:33
Alignment explanation
Indices: 3931810--3931905 Score: 133
Period size: 35 Copynumber: 2.8 Consensus size: 33
3931800 CTAACCCAAA
3931810 AAAATAAAAGAAGAAAAAAGAAAAACCTAACCCC
1 AAAA-AAAAGAAGAAAAAAGAAAAACCTAACCCC
3931844 AAAAAAAAAAGAAGAAAAAAGAAAAACCTAACCCC
1 --AAAAAAAAGAAGAAAAAAGAAAAACCTAACCCC
*
3931879 AAAAAAAA-AAGAAACTAA-AAAAACCTA
1 AAAAAAAAGAAGAAA-AAAGAAAAACCTA
3931906 GCCACCTAAC
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
32 15 0.26
33 10 0.17
35 29 0.50
36 4 0.07
ACGTcount: A:0.72, C:0.16, G:0.07, T:0.05
Consensus pattern (33 bp):
AAAAAAAAGAAGAAAAAAGAAAAACCTAACCCC
Found at i:3931899 original size:36 final size:35
Alignment explanation
Indices: 3931794--3931891 Score: 169
Period size: 35 Copynumber: 2.8 Consensus size: 35
3931784 AGCCCCCCCA
* *
3931794 AAAAAACTAACCCAAAAAAATAAAAGAAGAAAAAAG
1 AAAAACCTAACCCCAAAAAA-AAAAGAAGAAAAAAG
3931830 AAAAACCTAACCCCAAAAAAAAAAGAAGAAAAAAG
1 AAAAACCTAACCCCAAAAAAAAAAGAAGAAAAAAG
3931865 AAAAACCTAACCCCAAAAAAAAAAGAA
1 AAAAACCTAACCCCAAAAAAAAAAGAA
3931892 ACTAAAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 42 0.70
36 18 0.30
ACGTcount: A:0.72, C:0.16, G:0.07, T:0.04
Consensus pattern (35 bp):
AAAAACCTAACCCCAAAAAAAAAAGAAGAAAAAAG
Found at i:3932709 original size:3 final size:3
Alignment explanation
Indices: 3932655--3932695 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3932645 TTATTGTAGA
3932655 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3932696 CATACTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3939351 original size:46 final size:46
Alignment explanation
Indices: 3939299--3939474 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
3939289 TGGTTGAGCA
*
3939299 TCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
3939345 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
3939390 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
3939438 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3939475 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3939455 original size:93 final size:93
Alignment explanation
Indices: 3939296--3939466 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
3939286 GGATGGTTGA
* **
3939296 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3939361 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
3939389 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3939454 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3939467 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3941200 original size:46 final size:46
Alignment explanation
Indices: 3941148--3941323 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
3941138 TGGTTGAGCA
*
3941148 TCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
3941194 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
3941239 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
3941287 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3941324 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3941304 original size:93 final size:93
Alignment explanation
Indices: 3941145--3941315 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
3941135 GGATGGTTGA
* **
3941145 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3941210 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
3941238 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3941303 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3941316 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3943981 original size:46 final size:45
Alignment explanation
Indices: 3943824--3944035 Score: 202
Period size: 44 Copynumber: 4.7 Consensus size: 45
3943814 AGATTTGTGT
* * * *
3943824 GCCAGTGTAAGACCATGTAT-GGACATGGCATCGGCATTGAGACG-A
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA
* * * * *
3943869 GGGCTAGTGTAAGTCATGTCTGGGACATGCATCAGCCAC-AG-TGAGA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-TA
*
3943915 GCCACTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-TA
* *
3943961 GCCAGTGTCAGACATGTCTGGGACATGCGTCGG-CTACGAGATGT-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTA
*
3944005 GCTAGTGTAAGACATGTCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
3944036 AGCACGGTTA
Statistics
Matches: 138, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
44 61 0.44
45 7 0.05
46 54 0.39
47 16 0.12
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA
Found at i:3947502 original size:46 final size:46
Alignment explanation
Indices: 3947450--3947625 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
3947440 TGGTTGAGCA
*
3947450 TCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
3947496 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
3947541 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
3947589 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3947626 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3947606 original size:93 final size:93
Alignment explanation
Indices: 3947447--3947617 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
3947437 GGATGGTTGA
* **
3947447 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3947512 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
3947540 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3947605 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3947618 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3950111 original size:715 final size:715
Alignment explanation
Indices: 3948741--3950171 Score: 2727
Period size: 715 Copynumber: 2.0 Consensus size: 715
3948731 TGTGAGTATG
*
3948741 TAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGTAGTATTAGTCATGTAAATTGGC
1 TAATATTATGATTTAGCCAAAGGCATTGCCTTGTTATTAAGGTAGTATTAGTCATGTAAATTGGC
3948806 CTATGTCGGCTAATGACATTATGGGCCCATATGATTAATCTTATGCATGTATGTTATTATCTCTT
66 CTATGTCGGCTAATGACATTATGGGCCCATATGATTAATCTTATGCATGTATGTTATTATCTCTT
3948871 GTGATGTGGCTTACAACATGTATGCCTAGAGATTGAATTGAGATTCATTGATGAGCTAGTAACTA
131 GTGATGTGGCTTACAACATGTATGCCTAGAGATTGAATTGAGATTCATTGATGAGCTAGTAACTA
3948936 ATGCAGGATTAAGTGATTGGTAAATAGTTAATAATGCTTCATGAATGGTTTGTGATGTAATGATA
196 ATGCAGGATTAAGTGATTGGTAAATAGTTAATAATGCTTCATGAATGGTTTGTGATGTAATGATA
3949001 GTTATGTCTAGTATGTGGTAATGATATGGGCAAATTCTATAATATTTATTACATAAGAAAATAAC
261 GTTATGTCTAGTATGTGGTAATGATATGGGCAAATTCTATAATATTTATTACATAAGAAAATAAC
3949066 TCGAGCATAACATGTTTGTAGATGTTTAAGAGCTCATTTATGCCACGTTGTATGTTATTGGATAA
326 TCGAGCATAACATGTTTGTAGATGTTTAAGAGCTCATTTATGCCACGTTGTATGTTATTGGATAA
3949131 GTATGTATCTATGCATGTGGTGTGAGAGTGACAAAAGGCTTGATAATTAGACTATTTCTGGCCAC
391 GTATGTATCTATGCATGTGGTGTGAGAGTGACAAAAGGCTTGATAATTAGACTATTTCTGGCCAC
*
3949196 ACGGCCTGAGCACATGGGTGTGTGAAGCCTTAACGCAAGAGATTTTTCTAAGTTTTTCATGAGTT
456 ACGGCCTGAGCACATGGGCGTGTGAAGCCTTAACGCAAGAGATTTTTCTAAGTTTTTCATGAGTT
* *
3949261 CTCGATTGGGTTCCGAACCGCCCCGAATGCATGTATTGGGCCTTGTAAGCTCGCATAAGGGACAA
521 CTCGATTGGGTCCCGAACCGCCCCGAATGCATGTATTGGGCCTCGTAAGCTCGCATAAGGGACAA
3949326 ATTGCATGTGAAAAGAAAAGTTTTTAATTATTTGAGATTTCATGGCCCTGTTTAGTATGGAAGTG
586 ATTGCATGTGAAAAGAAAAGTTTTTAATTATTTGAGATTTCATGGCCCTGTTTAGTATGGAAGTG
*
3949391 TTAGTAAAAGTCAGGTAGCACCTCGAACCCTGTCCCAACGTCGGATGCGGGCGAGGGGTGTTACA
651 TTAGTAAAAGTCAGGTAGCACCTCGAACCCCGTCCCAACGTCGGATGCGGGCGAGGGGTGTTACA
3949456 TAATATTATGATTTAGCCAAAGGCATTGCCTTGTTATTAAGGTAGTATTAGTCATGTAAATTGGC
1 TAATATTATGATTTAGCCAAAGGCATTGCCTTGTTATTAAGGTAGTATTAGTCATGTAAATTGGC
* * * *
3949521 CTATGTCGGCTAATGACGTTATGGGCCCATATGATTATTCTTATGCATTTATGTTATTATTTCTT
66 CTATGTCGGCTAATGACATTATGGGCCCATATGATTAATCTTATGCATGTATGTTATTATCTCTT
3949586 GTGATGTGGCTTACAACATGTATGCCTAGAGATTGAATTGAGATTCATTGATGAGCTAGTAACTA
131 GTGATGTGGCTTACAACATGTATGCCTAGAGATTGAATTGAGATTCATTGATGAGCTAGTAACTA
3949651 ATGCAGGATTAAGTGATTGGTAAATAGTTAATAATGCTTCATGAATGGTTTGTGATGTAATGATA
196 ATGCAGGATTAAGTGATTGGTAAATAGTTAATAATGCTTCATGAATGGTTTGTGATGTAATGATA
3949716 GTTATGTCTAGTATGTGGTAATGATATGGGCAAATTCTATAATATTTATTACATAAGAAAATAAC
261 GTTATGTCTAGTATGTGGTAATGATATGGGCAAATTCTATAATATTTATTACATAAGAAAATAAC
* *
3949781 TTGAGCATATCATGTTTGTAGATGTTTAAGAGCTCATTTATGCCACGTTGTATGTTATTGGATAA
326 TCGAGCATAACATGTTTGTAGATGTTTAAGAGCTCATTTATGCCACGTTGTATGTTATTGGATAA
*
3949846 GTATGTATCTATGCATGTGGTGTGAGAGTGACAAAAGGCTTGATAATTAGACTATTTCTGGCTAC
391 GTATGTATCTATGCATGTGGTGTGAGAGTGACAAAAGGCTTGATAATTAGACTATTTCTGGCCAC
*
3949911 ACGGCCTGAGCACATGGGCGTTTGAAGCCTTAACGCAAGAGATTTTTCTAAGTTTTTCATGAGTT
456 ACGGCCTGAGCACATGGGCGTGTGAAGCCTTAACGCAAGAGATTTTTCTAAGTTTTTCATGAGTT
3949976 CTCGATTGGGTCCCGAACCGCCCCGAATGCATGTATTGGGCCTCGTAAGCTCGCATAAGGGACAA
521 CTCGATTGGGTCCCGAACCGCCCCGAATGCATGTATTGGGCCTCGTAAGCTCGCATAAGGGACAA
3950041 ATTGCATGTGAAAAGAAAAGTTTTTAATTATTTGAGATTTCATGGCCCTGTTTAGTATGGAAGTG
586 ATTGCATGTGAAAAGAAAAGTTTTTAATTATTTGAGATTTCATGGCCCTGTTTAGTATGGAAGTG
**
3950106 TTAGTAAAAGTCAGGTAGCACCTCGAACCCCGTCCCGGCGTCGGATGCGGGCGAGGGGTGTTACA
651 TTAGTAAAAGTCAGGTAGCACCTCGAACCCCGTCCCAACGTCGGATGCGGGCGAGGGGTGTTACA
3950171 T
1 T
3950172 TCTCACAACA
Statistics
Matches: 701, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
715 701 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (715 bp):
TAATATTATGATTTAGCCAAAGGCATTGCCTTGTTATTAAGGTAGTATTAGTCATGTAAATTGGC
CTATGTCGGCTAATGACATTATGGGCCCATATGATTAATCTTATGCATGTATGTTATTATCTCTT
GTGATGTGGCTTACAACATGTATGCCTAGAGATTGAATTGAGATTCATTGATGAGCTAGTAACTA
ATGCAGGATTAAGTGATTGGTAAATAGTTAATAATGCTTCATGAATGGTTTGTGATGTAATGATA
GTTATGTCTAGTATGTGGTAATGATATGGGCAAATTCTATAATATTTATTACATAAGAAAATAAC
TCGAGCATAACATGTTTGTAGATGTTTAAGAGCTCATTTATGCCACGTTGTATGTTATTGGATAA
GTATGTATCTATGCATGTGGTGTGAGAGTGACAAAAGGCTTGATAATTAGACTATTTCTGGCCAC
ACGGCCTGAGCACATGGGCGTGTGAAGCCTTAACGCAAGAGATTTTTCTAAGTTTTTCATGAGTT
CTCGATTGGGTCCCGAACCGCCCCGAATGCATGTATTGGGCCTCGTAAGCTCGCATAAGGGACAA
ATTGCATGTGAAAAGAAAAGTTTTTAATTATTTGAGATTTCATGGCCCTGTTTAGTATGGAAGTG
TTAGTAAAAGTCAGGTAGCACCTCGAACCCCGTCCCAACGTCGGATGCGGGCGAGGGGTGTTACA
Found at i:3950727 original size:78 final size:78
Alignment explanation
Indices: 3950626--3950784 Score: 291
Period size: 78 Copynumber: 2.0 Consensus size: 78
3950616 TTTCCAGTTG
3950626 TACACTCGAGGTGTACGTTTCTTTCCAAGTGGTACACATAAAGTATACCTTTCCTTTTCAAATGG
1 TACACTCGAGGTGTACGTTTCTTTCCAAGTGGTACACATAAAGTATACCTTTCCTTTTCAAATGG
3950691 TATACAAAAAGTA
66 TATACAAAAAGTA
* *
3950704 TACACTTGAGGTGTACGTTTCTTTCCGAGTGGTACACATAAAGTATACCTTTCCTTTTCAAATGG
1 TACACTCGAGGTGTACGTTTCTTTCCAAGTGGTACACATAAAGTATACCTTTCCTTTTCAAATGG
*
3950769 TATACACAAAGTA
66 TATACAAAAAGTA
3950782 TAC
1 TAC
3950785 CTAACCTTTC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (78 bp):
TACACTCGAGGTGTACGTTTCTTTCCAAGTGGTACACATAAAGTATACCTTTCCTTTTCAAATGG
TATACAAAAAGTA
Found at i:3950770 original size:33 final size:33
Alignment explanation
Indices: 3950733--3950893 Score: 175
Period size: 33 Copynumber: 4.9 Consensus size: 33
3950723 TCTTTCCGAG
*
3950733 TGGTACACATAAAGTATACCTTTCCTTTTCAAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAAA
* ** * *
3950766 TGGTATACACAAAGTATACCTAACCTTTCCAAG
1 TGGTACACACAAAGTATACCTTTCCTTTTCAAA
* * ** *
3950799 T-GTACACACAAAGTGTACATCACCTTTTCCAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAAA
*
3950831 TGAATACACA-AAA-TATACCTTTCCTTTTCAAA
1 TG-GTACACACAAAGTATACCTTTCCTTTTCAAA
*
3950863 TGGTATACACAAAGTATACCTTTCCTTTTCA
1 TGGTACACACAAAGTATACCTTTCCTTTTCA
3950894 CATTCGATAT
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
31 5 0.05
32 44 0.43
33 48 0.47
34 6 0.06
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (33 bp):
TGGTACACACAAAGTATACCTTTCCTTTTCAAA
Found at i:3950840 original size:32 final size:32
Alignment explanation
Indices: 3950756--3950881 Score: 119
Period size: 32 Copynumber: 3.9 Consensus size: 32
3950746 GTATACCTTT
* *
3950756 CCTTTTCAAATGGTATACACAAAGTATACCTAA
1 CCTTTTCCAAT-GTATACACAAAGTATACATAA
* * *
3950789 CC-TTTCCAAGTGTACACACAAAGTGTACATCA
1 CCTTTTCCAA-TGTATACACAAAGTATACATAA
* * * **
3950821 CCTTTTCCAATGAATACACAAAATATACCTTT
1 CCTTTTCCAATGTATACACAAAGTATACATAA
*
3950853 CCTTTTCAAATGGTATACACAAAGTATAC
1 CCTTTTCCAAT-GTATACACAAAGTATAC
3950882 CTTTCCTTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
32 50 0.67
33 25 0.33
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (32 bp):
CCTTTTCCAATGTATACACAAAGTATACATAA
Found at i:3950890 original size:65 final size:66
Alignment explanation
Indices: 3950724--3950893 Score: 191
Period size: 65 Copynumber: 2.6 Consensus size: 66
3950714 GTGTACGTTT
* * * * *
3950724 CTTTCCGAGTGGTACACATAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATACCTAA
1 CTTTCCAAATGGTACACACAAAGTATACCTTTCCTTTTCAAATGGAATACACAAAATATACCTAA
3950789 C
66 C
* * * ** * **
3950790 CTTTCCAAGT-GTACACACAAAGTGTACATCACCTTTTCCAAT-GAATACACAAAATATACCTTT
1 CTTTCCAAATGGTACACACAAAGTATACCTTTCCTTTTCAAATGGAATACACAAAATATACCTAA
3950853 C
66 C
* *
3950854 CTTTTCAAATGGTATACACAAAGTATACCTTTCCTTTTCA
1 CTTTCCAAATGGTACACACAAAGTATACCTTTCCTTTTCA
3950894 CATTCGATAT
Statistics
Matches: 84, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
64 26 0.31
65 49 0.58
66 9 0.11
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (66 bp):
CTTTCCAAATGGTACACACAAAGTATACCTTTCCTTTTCAAATGGAATACACAAAATATACCTAA
C
Found at i:3950928 original size:29 final size:29
Alignment explanation
Indices: 3950886--3951158 Score: 447
Period size: 29 Copynumber: 9.4 Consensus size: 29
3950876 GTATACCTTT
*
3950886 CCTTTTCACATTCGATATCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
3950915 CCTTTTCACATTCGATAGCTGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
3950944 CTTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
* *
3950973 CATTTTTACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
3951002 CCTTTTCACATTCGATAGCTGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
* *
3951031 CCTTTTCACATTCGAAAGCCGAAACTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
* *
3951060 CATTTTTACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
3951089 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
3951118 CCTTTTCATATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
3951147 CCTTTTCACATT
1 CCTTTTCACATT
3951159 GTACACACAA
Statistics
Matches: 224, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 224 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.34
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:3955530 original size:23 final size:23
Alignment explanation
Indices: 3955504--3955548 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3955494 TGGGTATGTG
* *
3955504 ATGACGTTATCTTATAAATATGC
1 ATGAAGTTATCTTAAAAATATGC
*
3955527 ATGAATTTATCTTAAAAATATG
1 ATGAAGTTATCTTAAAAATATG
3955549 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTAAAAATATGC
Found at i:3957664 original size:13 final size:13
Alignment explanation
Indices: 3957648--3957672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3957638 GTAAAAAAAA
3957648 ATGTAAAAGTGTT
1 ATGTAAAAGTGTT
3957661 ATGTAAAAGTGT
1 ATGTAAAAGTGT
3957673 AAAAGTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (13 bp):
ATGTAAAAGTGTT
Found at i:3957668 original size:21 final size:21
Alignment explanation
Indices: 3957644--3957685 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3957634 ATTTGTAAAA
*
3957644 AAAAATGTAAAAGTGTTATGT
1 AAAAATGTAAAAGTGATATGT
*
3957665 AAAAGTGTAAAAGTGATATGT
1 AAAAATGTAAAAGTGATATGT
3957686 GTGCATGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (21 bp):
AAAAATGTAAAAGTGATATGT
Found at i:3960124 original size:20 final size:20
Alignment explanation
Indices: 3960099--3960139 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3960089 TAGTAAGAAA
3960099 ATTTAGTTAGTTAAGTTGAG
1 ATTTAGTTAGTTAAGTTGAG
3960119 ATTTAGTTAGTTAAGTTGAG
1 ATTTAGTTAGTTAAGTTGAG
3960139 A
1 A
3960140 ATTGAACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (20 bp):
ATTTAGTTAGTTAAGTTGAG
Found at i:3965684 original size:27 final size:28
Alignment explanation
Indices: 3965630--3965684 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
3965620 TATTAAATAA
3965630 ATATATAATTTTTTAGGATATATAAAAAT
1 ATATATAATTTTTTA-GATATATAAAAAT
3965659 ATATATAATTTTTTA-ATTATATAAAA
1 ATATATAATTTTTTAGA-TATATAAAA
3965685 GAAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 1 0.04
28 9 0.36
29 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (28 bp):
ATATATAATTTTTTAGATATATAAAAAT
Found at i:3966710 original size:88 final size:91
Alignment explanation
Indices: 3966547--3966746 Score: 257
Period size: 88 Copynumber: 2.2 Consensus size: 91
3966537 TAAAAAGTCT
* * *
3966547 TCAAATTTTTTCAAAAAAAGCAATTAAGCCCCTACTCTCTTTTTTTACACTCAATTGGGTATTTG
1 TCAAACTTTTTCAAAAAAA-CAATTAAGCCCCTACTCTCTTTTTTTACACTCAATTGGGTACTTA
**
3966612 AACTTTCAAAATGCATC-AAAAGGCCC
65 AACTTTCAAAATGCATCAAAAACACCC
* * *
3966638 TCAAACCTTTTT-AAAAAAACAATTAAG-CCC-AGCT-TTTTTTTTTGCACTTAATTGGGTACTT
1 TCAAA-CTTTTTCAAAAAAACAATTAAGCCCCTA-CTCTCTTTTTTTACACTCAATTGGGTACTT
*
3966699 AAACTTTCAAAATGTATCAAAAACACCC
64 AAACTTTCAAAATGCATCAAAAACACCC
3966727 TCAAACTTTTTCAAAAAAAC
1 TCAAACTTTTTCAAAAAAAC
3966747 CCTAATTTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
88 46 0.48
89 25 0.26
90 8 0.08
91 12 0.12
92 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (91 bp):
TCAAACTTTTTCAAAAAAACAATTAAGCCCCTACTCTCTTTTTTTACACTCAATTGGGTACTTAA
ACTTTCAAAATGCATCAAAAACACCC
Found at i:3966730 original size:22 final size:22
Alignment explanation
Indices: 3966705--3966749 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3966695 ACTTAAACTT
*
3966705 TCAAAATGTATCAAAAACACCC
1 TCAAAATGTATCAAAAAAACCC
* * *
3966727 TCAAACTTTTTCAAAAAAACCC
1 TCAAAATGTATCAAAAAAACCC
3966749 T
1 T
3966750 AATTTTATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (22 bp):
TCAAAATGTATCAAAAAAACCC
Found at i:3968244 original size:27 final size:27
Alignment explanation
Indices: 3968183--3968238 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
3968173 AAATAAATTT
*
3968183 AAAATATATATATATATAAAATTTGAAAG
1 AAAATATATATATA-A-AAAATATGAAAG
*
3968212 AAAATATTTATATAAAATAATATGAAA
1 AAAATATATATATAAAA-AATATGAAA
3968239 ACAATAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 9 0.38
29 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (27 bp):
AAAATATATATATAAAAAATATGAAAG
Found at i:3970478 original size:131 final size:131
Alignment explanation
Indices: 3970027--3970637 Score: 537
Period size: 132 Copynumber: 4.6 Consensus size: 131
3970017 GTTAAATTCC
* * * * *
3970027 GAAGAGATATTCGATTATTTTGAACAAACGGGAGATTGCAACCCAGCACGATAGGGCACTATTCC
1 GAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATT-C
* * * * **
3970092 CCAAATTGCCAAACATCGGACATTTCCTTCGTTTTTAA-GAGTTTTTAGAAA-ATGTGAGTGAAA
65 CCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAATGA-TTTTTA-AAAGACATGAGTGAAA
**
3970155 TTCC
128 TTTT
* * * * * * * * * ** * *
3970159 AAAGGGATCTTCAATTGTTTCGAACCAATGAAAAAGCGCAACCCAGCATGATAGGGCACGATTCT
1 GAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTCC
* * *
3970224 CAAATTGCCAAACATTGAACATTACCTTCGTTTTAAAGTGTTTTCTTAAAAGACATGAGTGTAAA
66 CGAATTGCCAAACATCGAACATTACCTTCGTTTTAAA-TGATTT-TTAAAAGACATGAGTG-AAA
**
3970289 -CCT
128 TTTT
* * * * * ** *
3970292 AAAGGAATATTCGATTGTTTTGAGCAAATGAGAGATCACAACCCAGCACGATAGGGCATGATTCC
1 GAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTCC
* * ** * * * *
3970357 CGAATTGTCAAACACCGAGTATTACCTTGGTTTTAAATGATTTTTAGAAGACATGAATGGAATTT
66 CGAATTGCCAAACATCGAACATTACCTTCGTTTTAAATGATTTTTAAAAGACATGAGTGAAATTT
3970422 T
131 T
* * *
3970423 GAAGGGATATTCGATCATTTTAAGCAAACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCT
1 GAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTC-
* ** * * * * * *
3970488 ACGAATTGCCAAATGTCAAACCTTGCCTTCGTTTTAAA-GAGTTCTTAAAAGGCTTGAGTGAAAT
65 CCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAATGA-TTTTTAAAAGACATGAGTGAAAT
3970552 TTT
129 TTT
* * * *
3970555 GAAGGGATATTCGATTATTTTGAGCAAACGTGAAATTTCAACCCAACACGTTAGGGCACGATTCC
1 GAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTCC
*
3970620 GCGAATTGCCAAATATCG
66 -CGAATTGCCAAACATCG
3970638 GATCTCGTCT
Statistics
Matches: 383, Mismatches: 87, Indels: 18
0.78 0.18 0.04
Matches are distributed among these distances:
130 2 0.01
131 104 0.27
132 180 0.47
133 94 0.25
134 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (131 bp):
GAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTCC
CGAATTGCCAAACATCGAACATTACCTTCGTTTTAAATGATTTTTAAAAGACATGAGTGAAATTT
T
Found at i:3970650 original size:132 final size:132
Alignment explanation
Indices: 3970417--3970668 Score: 369
Period size: 132 Copynumber: 1.9 Consensus size: 132
3970407 ACATGAATGG
*
3970417 AATTTTGAAGGGATATTCGATCATTTTAAGCAAACGAGAAATTGCAACCCAGCACGTTAGGGCAC
1 AATTTTGAAGGGATATTCGATCATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCAC
* * * *
3970482 GATTCTACGAATTGCCAAATGTCAAACCTTGCCTTCGTTTTAAAGAGTTCTTAAAAGGCTTGAGT
66 GATTCCACGAATTGCCAAATATCAAACCTCGCCTTCGTTTTAAAGAATTCTTAAAAGGCTTGAGT
3970547 GA
131 GA
* * * *
3970549 AATTTTGAAGGGATATTCGATTATTTTGAGCAAACGTGAAATTTCAACCCAACACGTTAGGGCAC
1 AATTTTGAAGGGATATTCGATCATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCAC
* ** * * *
3970614 GATTCCGCGAATTGCCAAATATCGGATCTCGTCTTCGTTTTAAAGAATTTTTAAA
66 GATTCCACGAATTGCCAAATATCAAACCTCGCCTTCGTTTTAAAGAATTCTTAAA
3970669 TGAGTGCTCA
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 105 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (132 bp):
AATTTTGAAGGGATATTCGATCATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCAC
GATTCCACGAATTGCCAAATATCAAACCTCGCCTTCGTTTTAAAGAATTCTTAAAAGGCTTGAGT
GA
Found at i:3971344 original size:12 final size:12
Alignment explanation
Indices: 3971327--3971352 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3971317 TTATTGTAAG
3971327 AAAAATGAGATT
1 AAAAATGAGATT
3971339 AAAAATGAGATT
1 AAAAATGAGATT
3971351 AA
1 AA
3971353 TAATAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (12 bp):
AAAAATGAGATT
Found at i:3980686 original size:37 final size:37
Alignment explanation
Indices: 3980646--3980888 Score: 240
Period size: 37 Copynumber: 6.5 Consensus size: 37
3980636 GATATCGCTT
*
3980646 ATTTGAGCAACTTTCAGTATAATCAGTAAACATTGCT-
1 ATTTGAGC-ACTTTCAGTATAATCAGTAGACATTGCTC
* *
3980683 ATTTTGAGCA-TGTTCAGTATATTCAGTAGATATTGCTC
1 A-TTTGAGCACT-TTCAGTATAATCAGTAGACATTGCTC
* * * *
3980721 ATTTGAGCCCATTCAGTATAATCAGTGGATATTGCTC
1 ATTTGAGCACTTTCAGTATAATCAGTAGACATTGCTC
* * *
3980758 GTTTGAGCAACTTTCAGTATAATCAATAGACATTTCTC
1 ATTTGAGC-ACTTTCAGTATAATCAGTAGACATTGCTC
* * *
3980796 TTTTGAGCACGTTCAGTA-AATTCAGTAGATATTGCTC
1 ATTTGAGCACTTTCAGTATAA-TCAGTAGACATTGCTC
* * * *
3980833 GTTTGAACACATTCAGTACAATCAGTAGACATTGCTC
1 ATTTGAGCACTTTCAGTATAATCAGTAGACATTGCTC
* * *
3980870 GTTTGAGCTCATTCAGTAT
1 ATTTGAGCACTTTCAGTAT
3980889 TCCATTTTTC
Statistics
Matches: 173, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
36 3 0.02
37 130 0.75
38 40 0.23
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (37 bp):
ATTTGAGCACTTTCAGTATAATCAGTAGACATTGCTC
Found at i:3980791 original size:112 final size:112
Alignment explanation
Indices: 3980571--3980877 Score: 398
Period size: 112 Copynumber: 2.7 Consensus size: 112
3980561 ATAATACTCG
* * * * * * *
3980571 TTTGAGCATGCATTCCGTATAATCAGTGGATATAGCTCGTTTGAACCCATTCAGCAGAACCAGTG
1 TTTGAGCATG--TTCAGTATATTCAGTAGATATTGCTCGTTTGAACCCATTCAGTACAATCAGTG
* ** *
3980636 GATATCGCTTATTTGAGCAACTTTCAGTATAATCAGTAAACATTGCTAT
64 GATATTGCTCGTTTGAGCAACTTTCAGTATAATCAATAAACATTGCTAT
* * *
3980685 TTTGAGCATGTTCAGTATATTCAGTAGATATTGCTCATTTGAGCCCATTCAGTATAATCAGTGGA
1 TTTGAGCATGTTCAGTATATTCAGTAGATATTGCTCGTTTGAACCCATTCAGTACAATCAGTGGA
* * *
3980750 TATTGCTCGTTTGAGCAACTTTCAGTATAATCAATAGACATTTCTCT
66 TATTGCTCGTTTGAGCAACTTTCAGTATAATCAATAAACATTGCTAT
* * * *
3980797 TTTGAGCACGTTCAGTAAATTCAGTAGATATTGCTCGTTTGAACACATTCAGTACAATCAGTAGA
1 TTTGAGCATGTTCAGTATATTCAGTAGATATTGCTCGTTTGAACCCATTCAGTACAATCAGTGGA
*
3980862 CATTGCTCGTTTGAGC
66 TATTGCTCGTTTGAGC
3980878 TCATTCAGTA
Statistics
Matches: 169, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
112 159 0.94
114 10 0.06
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (112 bp):
TTTGAGCATGTTCAGTATATTCAGTAGATATTGCTCGTTTGAACCCATTCAGTACAATCAGTGGA
TATTGCTCGTTTGAGCAACTTTCAGTATAATCAATAAACATTGCTAT
Found at i:3980821 original size:75 final size:74
Alignment explanation
Indices: 3980571--3980888 Score: 296
Period size: 75 Copynumber: 4.2 Consensus size: 74
3980561 ATAATACTCG
* * * * * * * *
3980571 TTTGAGCATGCATTCCGTATAATCAGTGGATATAGCTCGTTTGAACCCATTCAGCAGAACCAGTG
1 TTTGAGCA--CATTCAGTATAATCAGTAGATATTGCTCGTTTGAACACATTCAGTATAATCAGTA
* * *
3980636 GATATCGCTTA
64 GACATTGCTCA
* * * ** * ** *
3980647 TTTGAGCAACTTTCAGTATAATCAGTAAACATTGCTATTTTGAGCATGTTCAGTATATTCAGTAG
1 TTTGAGC-ACATTCAGTATAATCAGTAGATATTGCTCGTTTGAACACATTCAGTATAATCAGTAG
*
3980712 ATATTGCTCA
65 ACATTGCTCA
* * * * *
3980722 TTTGAGCCCATTCAGTATAATCAGTGGATATTGCTCGTTTGAGCAACTTTCAGTATAATCAATAG
1 TTTGAGCACATTCAGTATAATCAGTAGATATTGCTCGTTTGAAC-ACATTCAGTATAATCAGTAG
* *
3980787 ACATTTCTCT
65 ACATTGCTCA
* *
3980797 TTTGAGCACGTTCAGTA-AATTCAGTAGATATTGCTCGTTTGAACACATTCAGTACAATCAGTAG
1 TTTGAGCACATTCAGTATAA-TCAGTAGATATTGCTCGTTTGAACACATTCAGTATAATCAGTAG
*
3980861 ACATTGCTCG
65 ACATTGCTCA
*
3980871 TTTGAGCTCATTCAGTAT
1 TTTGAGCACATTCAGTAT
3980889 TCCATTTTTC
Statistics
Matches: 194, Mismatches: 44, Indels: 9
0.79 0.18 0.04
Matches are distributed among these distances:
74 72 0.37
75 114 0.59
76 7 0.04
77 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (74 bp):
TTTGAGCACATTCAGTATAATCAGTAGATATTGCTCGTTTGAACACATTCAGTATAATCAGTAGA
CATTGCTCA
Found at i:3985774 original size:2 final size:2
Alignment explanation
Indices: 3985758--3985797 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
3985748 ATATCCCACA
3985758 AT AT A- AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3985798 TAATTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3987345 original size:13 final size:13
Alignment explanation
Indices: 3987327--3987357 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3987317 ATTTCTTACT
3987327 TTCAAATTGATAA
1 TTCAAATTGATAA
3987340 TTCAAATTGATAA
1 TTCAAATTGATAA
3987353 -TCAAA
1 TTCAAA
3987358 CTGTTTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (13 bp):
TTCAAATTGATAA
Found at i:3987471 original size:15 final size:16
Alignment explanation
Indices: 3987445--3987480 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
3987435 TTAATGGAAA
3987445 AAAGTCTAAATTGCAT
1 AAAGTCTAAATTGCAT
3987461 AAAGT-TAAATTGCAT
1 AAAGTCTAAATTGCAT
3987476 AAAGT
1 AAAGT
3987481 GCAAACTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (16 bp):
AAAGTCTAAATTGCAT
Found at i:3989159 original size:35 final size:35
Alignment explanation
Indices: 3989113--3989182 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3989103 TAAACTTGTA
*
3989113 TCATCATAGCAAATAACCCTAGATCTCCCTGGTCC
1 TCATCATAGCAAATAACCCTAGATCTCCCAGGTCC
*
3989148 TCATCATAGCAAATAACCCTAGATTTCCCAGGTCC
1 TCATCATAGCAAATAACCCTAGATCTCCCAGGTCC
3989183 CGACTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (35 bp):
TCATCATAGCAAATAACCCTAGATCTCCCAGGTCC
Found at i:3990436 original size:15 final size:15
Alignment explanation
Indices: 3990418--3990448 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3990408 GAAAGATAAT
*
3990418 TCAAAGTGGTAATTG
1 TCAAAGTGGCAATTG
3990433 TCAAAGTGGCAATTG
1 TCAAAGTGGCAATTG
3990448 T
1 T
3990449 TGAATGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (15 bp):
TCAAAGTGGCAATTG
Found at i:3994331 original size:2 final size:2
Alignment explanation
Indices: 3994318--3994355 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3994308 TAAAATAATG
* *
3994318 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3994356 TTTAAATTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4005349 original size:14 final size:14
Alignment explanation
Indices: 4005330--4005358 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4005320 CGCTGAGGTA
4005330 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4005344 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4005358 T
1 T
4005359 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:4005408 original size:88 final size:79
Alignment explanation
Indices: 4005197--4005419 Score: 241
Period size: 88 Copynumber: 2.7 Consensus size: 79
4005187 TCTACCAAAG
*
4005197 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTTAATTTCTGT
4005262 TCAACAAAAAAAAAA
65 TCAACAAAAAAAAAA
* *
4005277 AATTAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGCTCACGCGCTGAGGTATTTTCAATTTC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACACGCTGAGGTATTTT-AATTTC
********
4005341 TGTTTTTCAATTTCTGTTCGTCAA
62 TG---TTCAA---CAAAAAAAAAA
4005365 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTT
4005420 TAGTTTTAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
79 1 0.01
80 34 0.29
81 5 0.04
82 19 0.16
85 5 0.04
86 16 0.13
88 37 0.31
89 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (79 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTAATTTCTGTT
CAACAAAAAAAAAA
Found at i:4005495 original size:53 final size:53
Alignment explanation
Indices: 4005433--4005856 Score: 208
Period size: 53 Copynumber: 7.4 Consensus size: 53
4005423 TTTTAAATTG
*
4005433 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTGTTCAAAATCA
1 ACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTGTTCAAAATCA
* * * * * ** **
4005486 ACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTT-TAGTTTTAAATTG
1 ACTCATATTGCGAGAAGTGAGTTAAGCCT---------TTTA-AT-TTTTGTTGTTCAAAATCA
* *
4005549 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTGTTCAAAATCA
1 ACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTGTTCAAAATCA
* * * * * ** **
4005602 ACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTT-TAGTTTTAAATTG
1 ACTCATATTGCGAGAAGTGAGTTAAGCCT---------TTTA-AT-TTTTGTTGTTCAAAATCA
* * *
4005665 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTCTGTTGTTCAAAATCA
1 ACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTGTTCAAAATCA
* * * * ** **
4005718 ACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTATTTT-TAGTTTTAAATTG
1 ACTCATATTGCGAGAAGTGAGTTAAGCCT---------TTTA-AT-TTTTGTTGTTCAAAATCA
* *
4005781 ACTCATATTGCGA-AAGGTGAGTTCAGCCTTTTTATTTTTGTTGTTCAAAATCA
1 ACTCATATTGCGAGAA-GTGAGTTAAGCCTTTTAATTTTTGTTGTTCAAAATCA
4005834 ACTCATATTGCGAGAAGTGAGTT
1 ACTCATATTGCGAGAAGTGAGTT
4005857 GAGCTTCAGG
Statistics
Matches: 268, Mismatches: 65, Indels: 76
0.66 0.16 0.19
Matches are distributed among these distances:
52 11 0.04
53 129 0.48
54 5 0.02
62 6 0.02
63 106 0.40
64 11 0.04
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (53 bp):
ACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTGTTCAAAATCA
Found at i:4005685 original size:63 final size:63
Alignment explanation
Indices: 4005602--4005809 Score: 208
Period size: 63 Copynumber: 3.5 Consensus size: 63
4005592 TTCAAAATCA
*
4005602 ACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
1 ACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
* ** * ** **
4005665 ACTCATATTGCGAGAGGTGAGTTAAGCCT----------T--TTTATTTCTGTTGTTCAAAATCA
1 ACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTATTT-T-TAGTTTTAAATTG
4005718 ACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
1 ACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
*
4005781 ACTCATATTGCGA-AAGGTGAGTTCAGCCT
1 ACTCATATTGCGAGAA-GTGAGTTAAGCCT
4005810 TTTTATTTTT
Statistics
Matches: 112, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
51 5 0.04
52 1 0.01
53 37 0.33
62 2 0.02
63 61 0.54
64 1 0.01
65 5 0.04
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (63 bp):
ACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
Found at i:4005873 original size:116 final size:116
Alignment explanation
Indices: 4005361--4005860 Score: 919
Period size: 116 Copynumber: 4.3 Consensus size: 116
4005351 TTTCTGTTCG
* ** *
4005361 TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAGTTT
1 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
*
4005426 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTGT
66 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTGT
4005477 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
1 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
4005542 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTGT
66 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTGT
4005593 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
1 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
*
4005658 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTCTGTTGT
66 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTGT
*
4005709 TCAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
1 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
* *
4005774 TAAATTGACTCATATTGCGAAAGGTGAGTTCAGCCTTTTTATTTTTGTTGT
66 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTGT
4005825 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
4005861 TTCAGGACAC
Statistics
Matches: 373, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 373 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (116 bp):
TCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTT
TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTGT
Found at i:4006807 original size:11 final size:11
Alignment explanation
Indices: 4006791--4006824 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
4006781 AAAAAAAAAA
4006791 AAGAGAGAGGG
1 AAGAGAGAGGG
4006802 AAGAGAGAGGG
1 AAGAGAGAGGG
4006813 -AGAGAGAAGGG
1 AAGAGAG-AGGG
4006824 A
1 A
4006825 GGGGAATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (11 bp):
AAGAGAGAGGG
Found at i:4006977 original size:35 final size:35
Alignment explanation
Indices: 4006932--4007035 Score: 172
Period size: 35 Copynumber: 3.0 Consensus size: 35
4006922 GAGTGTGTGA
*
4006932 TGGTGTTGGTGGCAGACAGCATGGGAGAATGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAATGGGAG
*
4006967 TGGTGCTGGTGGCAGACAGCATGAGAGAATGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAATGGGAG
* *
4007002 TGGTGCTGGTGGCAGACAGCATGGAAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAATGGGA
4007036 AGAGGCAAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.24, C:0.11, G:0.47, T:0.18
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAATGGGAG
Found at i:4007859 original size:3 final size:3
Alignment explanation
Indices: 4007851--4007884 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4007841 GGTCTAAGCT
4007851 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4007885 CTAATTTCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4009186 original size:13 final size:15
Alignment explanation
Indices: 4009159--4009190 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
4009149 TTAATCGTAT
4009159 TTATATATATATATA
1 TTATATATATATATA
4009174 TTATAT-TAT-TATA
1 TTATATATATATATA
4009187 TTAT
1 TTAT
4009191 GTAATAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:4012177 original size:2 final size:2
Alignment explanation
Indices: 4012170--4012207 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4012160 AGTCTCGTAA
4012170 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
4012208 TGGAGAGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4014956 original size:113 final size:113
Alignment explanation
Indices: 4014753--4014977 Score: 378
Period size: 113 Copynumber: 2.0 Consensus size: 113
4014743 TATAAAAATT
* * * *
4014753 AGATTGGATTAAGGTGGGCAAAACCCTTCTTCAATATCGTCCTTAGCTTCCACTAGTGTAAACCA
1 AGATTGGATTAAGGTGAGCAAAACCCTTCTTCAATATCGTCCTTAGCTCCCACCAATGTAAACCA
* *
4014818 TGAGTGGGTAAGATCGTTTAAGTTGGTCAGTACTTGTAATGATTGATC
66 TGAGTGAGTAAGATCGTTTAAGTTGGTCAATACTTGTAATGATTGATC
*
4014866 AGATTGGATTAAGGTGAGCAAAGCCCTTCTTCAATATCGTCCTTAGCTCCCACCAATGTAAACCA
1 AGATTGGATTAAGGTGAGCAAAACCCTTCTTCAATATCGTCCTTAGCTCCCACCAATGTAAACCA
*
4014931 TGAGTGAGTAAGATCGTTTAGGTTGGTCAATACTTGTAATGATTGAT
66 TGAGTGAGTAAGATCGTTTAAGTTGGTCAATACTTGTAATGATTGAT
4014978 TGTGATGTTA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 104 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (113 bp):
AGATTGGATTAAGGTGAGCAAAACCCTTCTTCAATATCGTCCTTAGCTCCCACCAATGTAAACCA
TGAGTGAGTAAGATCGTTTAAGTTGGTCAATACTTGTAATGATTGATC
Found at i:4015771 original size:20 final size:19
Alignment explanation
Indices: 4015742--4015799 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
4015732 TCTAATTAAA
*
4015742 TATAACAAATTTTAACAAAT
1 TATAAAAAATTTTAA-AAAT
4015762 TATAAAAAA-TTTATAAAAT
1 TATAAAAAATTTTA-AAAAT
4015781 TAATAAAAAATATTTAAAA
1 T-ATAAAAAAT-TTTAAAA
4015800 TTTTATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 9 0.27
20 17 0.52
21 3 0.09
22 4 0.12
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TATAAAAAATTTTAAAAAT
Found at i:4015779 original size:10 final size:10
Alignment explanation
Indices: 4015742--4015889 Score: 51
Period size: 10 Copynumber: 14.8 Consensus size: 10
4015732 TCTAATTAAA
4015742 TATAACAAATT
1 TATAA-AAATT
4015753 T-TAACAAA-T
1 TATAA-AAATT
4015762 TATAAAAAATT
1 TAT-AAAAATT
4015773 TAT-AAAATT
1 TATAAAAATT
*
4015782 AATAAAAAATAT
1 TAT-AAAAAT-T
*
4015794 T-TAAAATTT
1 TATAAAAATT
* *
4015803 TATTAAAATG
1 TATAAAAATT
*
4015813 TATACAAATT
1 TATAAAAATT
**
4015823 CT-TAAAAGCT
1 -TATAAAAATT
*
4015833 TATAAAAAAT
1 TATAAAAATT
*
4015843 CATTAAAAATAT
1 TA-TAAAAAT-T
4015855 T-T--AAATT
1 TATAAAAATT
* * *
4015862 GACATAAATT
1 TATAAAAATT
*
4015872 TATAAAAAAT
1 TATAAAAATT
4015882 TATAAAAA
1 TATAAAAA
4015890 CTTAAATTGT
Statistics
Matches: 100, Mismatches: 23, Indels: 29
0.66 0.15 0.19
Matches are distributed among these distances:
7 1 0.01
8 4 0.04
9 13 0.13
10 60 0.60
11 20 0.20
12 2 0.02
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (10 bp):
TATAAAAATT
Found at i:4016430 original size:20 final size:20
Alignment explanation
Indices: 4016407--4016460 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
4016397 CAGTTCATGT
*
4016407 TTTTATGATTTTTTTCATAA
1 TTTTATGATTTTTTTAATAA
*
4016427 TTTTAT-ATAATTTTTAATAA
1 TTTTATGAT-TTTTTTAATAA
4016447 TTTTATGATTTTTT
1 TTTTATGATTTTTT
4016461 ATGTTTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTATGATTTTTTTAATAA
Found at i:4016592 original size:43 final size:42
Alignment explanation
Indices: 4016504--4016600 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 42
4016494 ATTCTATTAA
* * *
4016504 TTTTATAATTTTTTAAAATTTATTTTTATAATATTTATAAGT
1 TTTTATAATTTATTAAAATTTAATTTTATAATATTTACAAGT
*
4016546 TTTTATTAATTTATTAAAATTCTTAATTTT-TAATAGTTT-CAATT
1 TTTTA-TAATTTATTAAAA-T-TTAATTTTATAATA-TTTACAAGT
*
4016590 TTTTATGATTT
1 TTTTATAATTT
4016601 TTTTAATCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
42 5 0.11
43 17 0.37
44 14 0.30
45 10 0.22
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (42 bp):
TTTTATAATTTATTAAAATTTAATTTTATAATATTTACAAGT
Found at i:4016595 original size:44 final size:43
Alignment explanation
Indices: 4016504--4016595 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 43
4016494 ATTCTATTAA
* * *
4016504 TTTTA-TAATTTTTTAAAATTTATTTTTATAATATTTATAAGT
1 TTTTATTAATTTATTAAAATTTAATTTTATAATATTTACAAGT
*
4016546 TTTTATTAATTTATTAAAATTCTTAATTTT-TAATAGTTT-CAATT
1 TTTTATTAATTTATTAAAA-T-TTAATTTTATAATA-TTTACAAGT
4016590 TTTTAT
1 TTTTAT
4016596 GATTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
42 5 0.12
43 12 0.29
44 15 0.36
45 10 0.24
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (43 bp):
TTTTATTAATTTATTAAAATTTAATTTTATAATATTTACAAGT
Found at i:4019184 original size:53 final size:53
Alignment explanation
Indices: 4019104--4019208 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
4019094 TAATAGCTAG
4019104 TTTACAAACCACATTCATATGCCATCAAAGGCCAAGTTACCTATACATGCCAA
1 TTTACAAACCACATTCATATGCCATCAAAGGCCAAGTTACCTATACATGCCAA
*
4019157 TTTACAAACTACATTCATATGCCATCAAAGGCCAAGTTACCTATACATGCCA
1 TTTACAAACCACATTCATATGCCATCAAAGGCCAAGTTACCTATACATGCCA
4019209 TTATACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.28, G:0.10, T:0.26
Consensus pattern (53 bp):
TTTACAAACCACATTCATATGCCATCAAAGGCCAAGTTACCTATACATGCCAA
Found at i:4020249 original size:88 final size:88
Alignment explanation
Indices: 4020100--4020285 Score: 363
Period size: 88 Copynumber: 2.1 Consensus size: 88
4020090 GTAGAATCAT
4020100 ATTTCATGTACAGGAAATCACATGTATCTATCGATTTTCATTATTCCAACAGAATTTACAATTTA
1 ATTTCATGTACAGGAAATCACATGTATCTATCGATTTTCATTATTCCAACAGAATTTACAATTTA
4020165 ATGAATTTTGCAATCATGTAACC
66 ATGAATTTTGCAATCATGTAACC
4020188 ATTTCATGTACAGGAAATCACATGTATCTATCGATTTTCATTATTCCAACAGAATTTACAATTTA
1 ATTTCATGTACAGGAAATCACATGTATCTATCGATTTTCATTATTCCAACAGAATTTACAATTTA
*
4020253 ATGACTTTTGCAATCATGTAACC
66 ATGAATTTTGCAATCATGTAACC
4020276 ATTTCATGTA
1 ATTTCATGTA
4020286 TTTATAACAT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 97 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (88 bp):
ATTTCATGTACAGGAAATCACATGTATCTATCGATTTTCATTATTCCAACAGAATTTACAATTTA
ATGAATTTTGCAATCATGTAACC
Found at i:4028302 original size:19 final size:19
Alignment explanation
Indices: 4028261--4028302 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
4028251 TAGACAATTC
*
4028261 TATTTTATTTTTATTTATT
1 TATTTTATTTTTATTTATA
4028280 TATTTTATTTTTGATTT-TA
1 TATTTTATTTTT-ATTTATA
4028299 TATT
1 TATT
4028303 AAATTAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TATTTTATTTTTATTTATA
Found at i:4031119 original size:25 final size:26
Alignment explanation
Indices: 4031091--4031149 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
4031081 CATGTAAACA
**
4031091 GGAAGCTCATT-CAAGCCGTATATCG
1 GGAAGCTCATTGCAAGCCAAATATCG
4031116 GGAAGCTC-TTGCAAGCCAAATATCG
1 GGAAGCTCATTGCAAGCCAAATATCG
4031141 GGAAGCTCA
1 GGAAGCTCA
4031150 AGAGAACTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (26 bp):
GGAAGCTCATTGCAAGCCAAATATCG
Found at i:4057480 original size:7 final size:7
Alignment explanation
Indices: 4057468--4057499 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
4057458 TTATTATTAA
4057468 AAAATTT
1 AAAATTT
4057475 AAAATTT
1 AAAATTT
4057482 AAAATTT
1 AAAATTT
4057489 AAAATTT
1 AAAATTT
4057496 AAAA
1 AAAA
4057500 CCATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:4063943 original size:22 final size:24
Alignment explanation
Indices: 4063891--4063945 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 24
4063881 ATTTTTATGA
4063891 TTAAATTATTGTTATTAAATATACT
1 TTAAATTATTGTTATT-AATATACT
*
4063916 TGAAATTATTG-TATT-ATAT-CTT
1 TTAAATTATTGTTATTAATATAC-T
4063938 TTAAATTA
1 TTAAATTA
4063946 AATTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 12 0.44
24 4 0.15
25 10 0.37
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (24 bp):
TTAAATTATTGTTATTAATATACT
Found at i:4064028 original size:5 final size:5
Alignment explanation
Indices: 4064018--4064048 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4064008 TGATACAATG
4064018 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT T
1 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT T
4064049 TAAAATAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (5 bp):
TGTAT
Found at i:4073723 original size:22 final size:21
Alignment explanation
Indices: 4073698--4073749 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
4073688 GATTGAATAA
* *
4073698 ATTATATTATTTTCATTCATCC
1 ATTATATTATTTT-ATGCATAC
4073720 ATTAT-TGTATTTTATGCATAC
1 ATTATAT-TATTTTATGCATAC
4073741 A-TATATTAT
1 ATTATATTAT
4073750 CCCATGCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTATATTATTTTATGCATAC
Done.