Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 71 of 189
Found at i:19694403 original size:13 final size:13
Alignment explanation
Indices: 19694387--19694411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19694377 GAAATAAAAG
19694387 ATAGAAACAGAGA
1 ATAGAAACAGAGA
19694400 ATAGAAACAGAG
1 ATAGAAACAGAG
19694412 GGCAAAACAA
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:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (13 bp):
ATAGAAACAGAGA
Found at i:19705253 original size:16 final size:16
Alignment explanation
Indices: 19705234--19705277 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
19705224 TATAAATATC
19705234 AAATAATTCAAACTTA
1 AAATAATTCAAACTTA
* * *
19705250 AAATAAGTAAAACTTG
1 AAATAATTCAAACTTA
*
19705266 AAATGATTCAAA
1 AAATAATTCAAA
19705278 TTCTTAATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (16 bp):
AAATAATTCAAACTTA
Found at i:19712210 original size:34 final size:34
Alignment explanation
Indices: 19712167--19712235 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
19712157 GATTTGACTT
19712167 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
1 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
19712201 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
1 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
19712235 T
1 T
19712236 GAAGAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (34 bp):
TTCACTAAATGAGTAAACAAACAAGAGTACAATA
Found at i:19727641 original size:10 final size:9
Alignment explanation
Indices: 19727628--19727797 Score: 96
Period size: 10 Copynumber: 17.8 Consensus size: 9
19727618 TTTTTAATAC
19727628 TTTATAATAT
1 TTTATAAT-T
*
19727638 TTTAAAATT
1 TTTATAATT
*
19727647 TTAATAATT
1 TTTATAATT
*
19727656 TATTAGAATT
1 T-TTATAATT
19727666 TTTATAAGTT
1 TTTATAA-TT
19727676 TTTATGAATT
1 TTTAT-AATT
*
19727686 TTTATATTTT
1 TTTATA-ATT
19727696 TTTATAA-T
1 TTTATAATT
**
19727704 TTTATTGTT
1 TTTATAATT
*
19727713 CTTATAATTTT
1 TTTATAA--TT
19727724 TTTATAATT
1 TTTATAATT
19727733 TATTAT-ATT
1 T-TTATAATT
*
19727742 TTTATGAGTT
1 TTTAT-AATT
19727752 TTTATAAAATT
1 TTTAT--AATT
19727763 TTGT-TAATAT
1 TT-TATAAT-T
*
19727773 TTT-TAAGT
1 TTTATAATT
19727781 TTTATAAGTT
1 TTTATAA-TT
*
19727791 TATATAA
1 TTTATAA
19727798 ATTTGAAAAT
Statistics
Matches: 125, Mismatches: 20, Indels: 30
0.71 0.11 0.17
Matches are distributed among these distances:
8 14 0.11
9 37 0.30
10 57 0.46
11 16 0.13
12 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (9 bp):
TTTATAATT
Found at i:19727684 original size:20 final size:19
Alignment explanation
Indices: 19727615--19727797 Score: 98
Period size: 19 Copynumber: 9.6 Consensus size: 19
19727605 AAATAAATGG
*
19727615 AGTTTTT-TAATACTTTATA
1 AGTTTTTATAAT-TTTTATA
* *
19727634 A-TATTTTAAAATTTTAATA
1 AGT-TTTTATAATTTTTATA
*
19727653 A-TTTATTAGAATTTTTATA
1 AGTTT-TTATAATTTTTATA
19727672 AGTTTTTATGAATTTTTATA
1 AGTTTTTAT-AATTTTTATA
**
19727692 TTTTTTTATAA-TTTTAT-
1 AGTTTTTATAATTTTTATA
* *
19727709 TGTTCTTATAATTTTTTTATA
1 AGTTTTTATAA--TTTTTATA
*
19727730 A-TTTATTAT-ATTTTTATG
1 AGTTT-TTATAATTTTTATA
19727748 AGTTTTTATAAAATTTTGT-TA
1 AGTTTTTAT--AATTTT-TATA
*
19727769 A-TATTTT-TAAGTTTTATA
1 AGT-TTTTATAATTTTTATA
*
19727787 AGTTTATATAA
1 AGTTTTTATAA
19727798 ATTTGAAAAT
Statistics
Matches: 129, Mismatches: 16, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
17 10 0.08
18 32 0.25
19 37 0.29
20 34 0.26
21 15 0.12
22 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (19 bp):
AGTTTTTATAATTTTTATA
Found at i:19727705 original size:39 final size:39
Alignment explanation
Indices: 19727628--19727801 Score: 148
Period size: 39 Copynumber: 4.5 Consensus size: 39
19727618 TTTTTAATAC
* *
19727628 TTTATAA-TATTTTA-AAATTTTAATAATTTATTAGAATT
1 TTTATAAGT-TTTTATAAATTTTTATAATTTATTATAATT
* * *
19727666 TTTATAAGTTTTTATGAATTTTTATATTTTTTTATAA-T
1 TTTATAAGTTTTTATAAATTTTTATAATTTATTATAATT
* * *
19727704 TTTAT-TGTTCTTATAATTTTTTTATAATTTATTAT-ATT
1 TTTATAAGTTTTTATAA-ATTTTTATAATTTATTATAATT
* *
19727742 TTTATGAGTTTTTATAAAATTTTGT-TAATATT-TT-TAAGT
1 TTTATAAGTTTTTAT-AAATTTT-TATAAT-TTATTATAATT
*
19727781 TTTATAAGTTTATATAAATTT
1 TTTATAAGTTTTTATAAATTT
19727802 GAAAATTTTG
Statistics
Matches: 110, Mismatches: 17, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
37 9 0.08
38 46 0.42
39 50 0.45
40 5 0.05
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (39 bp):
TTTATAAGTTTTTATAAATTTTTATAATTTATTATAATT
Found at i:19727985 original size:15 final size:16
Alignment explanation
Indices: 19727965--19727997 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19727955 ATATTTAATT
19727965 ATTCAAATATT-GATA
1 ATTCAAATATTGGATA
*
19727980 ATTCAATTATTGGATA
1 ATTCAAATATTGGATA
19727996 AT
1 AT
19727998 AAAGATAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTCAAATATTGGATA
Found at i:19742273 original size:13 final size:13
Alignment explanation
Indices: 19742257--19742283 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19742247 TTTAAACTAA
19742257 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
19742270 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
19742283 A
1 A
19742284 TTGCCAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:19750423 original size:64 final size:64
Alignment explanation
Indices: 19750322--19750471 Score: 273
Period size: 64 Copynumber: 2.3 Consensus size: 64
19750312 GGACTGGCAC
*
19750322 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGATTAAGAAA
1 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGAGTAAGAAA
* *
19750386 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAATATTCTTTGAGTAAGAAC
1 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGAGTAAGAAA
19750450 CATTGGATCATCACTTATTCAA
1 CATTGGATCATCACTTATTCAA
19750472 CCAATAGAAC
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (64 bp):
CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGAGTAAGAAA
Found at i:19750880 original size:14 final size:14
Alignment explanation
Indices: 19750861--19750922 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
19750851 ATTCAACGGC
*
19750861 CATATTGCAATAGT
1 CATATTGCAACAGT
* *
19750875 CATATTCCAACGGT
1 CATATTGCAACAGT
* *
19750889 CATATTGTAACTGT
1 CATATTGCAACAGT
* * *
19750903 CAAATTACAACGGT
1 CATATTGCAACAGT
19750917 CATATT
1 CATATT
19750923 TTTGCATTAC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (14 bp):
CATATTGCAACAGT
Found at i:19750892 original size:28 final size:28
Alignment explanation
Indices: 19750849--19750922 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
19750839 GTGGTCCAAA
*
19750849 AAATT-CAACGGCCATATTGCAA-TAGTC
1 AAATTACAACGGTCATATTGCAACT-GTC
* * *
19750876 ATATTCCAACGGTCATATTGTAACTGTC
1 AAATTACAACGGTCATATTGCAACTGTC
19750904 AAATTACAACGGTCATATT
1 AAATTACAACGGTCATATT
19750923 TTTGCATTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
27 4 0.10
28 35 0.88
29 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (28 bp):
AAATTACAACGGTCATATTGCAACTGTC
Found at i:19756240 original size:18 final size:18
Alignment explanation
Indices: 19756217--19756252 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19756207 ACCGTAAAAG
19756217 AATCTATGAGAAAATATA
1 AATCTATGAGAAAATATA
19756235 AATCTATGAGAAAATATA
1 AATCTATGAGAAAATATA
19756253 TTTAATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
AATCTATGAGAAAATATA
Found at i:19760447 original size:24 final size:24
Alignment explanation
Indices: 19760415--19760481 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
19760405 TCGTTCTGTG
*
19760415 GCAAAGGATTAATTGACAGTATAT
1 GCAAAGGATGAATTGACAGTATAT
* *
19760439 GCAAAGGATGAATTGATAATATAT
1 GCAAAGGATGAATTGACAGTATAT
19760463 GCAAAGGATGAATTGACAG
1 GCAAAGGATGAATTGACAG
19760482 CAAATGTACC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.25
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAGTATAT
Found at i:19760596 original size:21 final size:20
Alignment explanation
Indices: 19760559--19760602 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
19760549 TCTCACGAGC
*
19760559 TTCTGTTAACTCATATGAGT
1 TTCTGTTAACCCATATGAGT
* *
19760579 TTCTGTTTAACCCTTATGGGT
1 TTCTG-TTAACCCATATGAGT
19760600 TTC
1 TTC
19760603 CGTTCAGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (20 bp):
TTCTGTTAACCCATATGAGT
Found at i:19763640 original size:19 final size:19
Alignment explanation
Indices: 19763616--19763655 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19763606 CGTGGTGTGC
*
19763616 TTAGTTTTCTTATGACTTT
1 TTAGTTTGCTTATGACTTT
* *
19763635 TTAGTTTGCTTTTTACTTT
1 TTAGTTTGCTTATGACTTT
19763654 TT
1 TT
19763656 CGCCTTTCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.68
Consensus pattern (19 bp):
TTAGTTTGCTTATGACTTT
Found at i:19764431 original size:24 final size:24
Alignment explanation
Indices: 19764404--19764449 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19764394 GTCACTGCAT
* *
19764404 TATTAAAATTTAATTAAATAAAAA
1 TATTAAAATTAAATAAAATAAAAA
*
19764428 TATTAATATTAAATAAAATAAA
1 TATTAAAATTAAATAAAATAAA
19764450 TAAATATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATTAAAATTAAATAAAATAAAAA
Found at i:19765195 original size:31 final size:31
Alignment explanation
Indices: 19765092--19765200 Score: 86
Period size: 31 Copynumber: 3.6 Consensus size: 31
19765082 ATTGGTAATG
* *
19765092 AAGT-TTGAGTATTAAATTAATAGAATTTGT
1 AAGTATTGAGGATTAAATTAATAGAATATGT
* *
19765122 AA--ATGTGAAGGGTTAGATTTAAT-GAATTAT-T
1 AAGTAT-TG-AGGATTA-AATTAATAGAA-TATGT
* *
19765153 TAGAATT-AGGATTAAATTAATAGAATATGT
1 AAGTATTGAGGATTAAATTAATAGAATATGT
19765183 AAGTATTGAGGATTAAAT
1 AAGTATTGAGGATTAAAT
19765201 ATGTTTTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
29 10 0.17
30 19 0.32
31 20 0.33
32 9 0.15
33 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (31 bp):
AAGTATTGAGGATTAAATTAATAGAATATGT
Found at i:19765909 original size:19 final size:21
Alignment explanation
Indices: 19765885--19765923 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19765875 AAAATATATT
19765885 TTTTAT-TATTTTT-TAAATA
1 TTTTATATATTTTTATAAATA
19765904 TTTTATATATTTTTATAAAT
1 TTTTATATATTTTTATAAAT
19765924 TTAATACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATATATTTTTATAAATA
Found at i:19766176 original size:31 final size:31
Alignment explanation
Indices: 19766104--19766179 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
19766094 ATTTTAAGGT
* * *
19766104 AGAGTGATTACAATTGACAACTTATCTAACA
1 AGAGTGACTAAAATTGACAACTAATCTAACA
* * *
19766135 AAAGTAACTAAAATTGACAACTAATCTAAGA
1 AGAGTGACTAAAATTGACAACTAATCTAACA
*
19766166 GGAGTGACTAAAAT
1 AGAGTGACTAAAAT
19766180 AACAAATTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (31 bp):
AGAGTGACTAAAATTGACAACTAATCTAACA
Found at i:19770421 original size:26 final size:25
Alignment explanation
Indices: 19770392--19770474 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
19770382 GACTCGAAAT
19770392 CTAAAACCTAAAACTTAATATAAACC
1 CTAAAACCT-AAACTTAATATAAACC
** *
19770418 CTAATTCCTAAACTCAAATCATAAACC
1 CTAAAACCTAAACT-TAAT-ATAAACC
* * *
19770445 TTATAAACCCAAAC-TCATATAAACC
1 CTA-AAACCTAAACTTAATATAAACC
19770470 CTAAA
1 CTAAA
19770475 CTATAATCTC
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
24 2 0.05
25 14 0.32
26 12 0.27
27 9 0.20
28 7 0.16
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (25 bp):
CTAAAACCTAAACTTAATATAAACC
Found at i:19770857 original size:21 final size:21
Alignment explanation
Indices: 19770831--19770870 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19770821 GAGACAGGTG
19770831 ACGTGGCTC-GTTAACTAGCTA
1 ACGTGGC-CGGTTAACTAGCTA
19770852 ACGTGGCCGGTTAACTAGC
1 ACGTGGCCGGTTAACTAGC
19770871 CACGTCGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
ACGTGGCCGGTTAACTAGCTA
Found at i:19773626 original size:28 final size:28
Alignment explanation
Indices: 19773586--19773650 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
19773576 GAGCAAATTC
19773586 CACAATATGATATGGTAAAATTTAAACT
1 CACAATATGATATGGTAAAATTTAAACT
19773614 CACAATATGATATGGTAAAATTTAAACT
1 CACAATATGATATGGTAAAATTTAAACT
*
19773642 CATAATATG
1 CACAATATG
19773651 GTATAGTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (28 bp):
CACAATATGATATGGTAAAATTTAAACT
Found at i:19774168 original size:23 final size:19
Alignment explanation
Indices: 19774121--19774159 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
19774111 TATTTTTCTT
19774121 AATAAATAATTAAAAAATA
1 AATAAATAATTAAAAAATA
*
19774140 ATTAAATAGATTAATAAAAT
1 AATAAATA-ATTAA-AAAAT
19774160 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AATAAATAATTAAAAAATA
Found at i:19774256 original size:15 final size:15
Alignment explanation
Indices: 19774237--19774291 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
19774227 TATTTGATAA
19774237 ACTGAAATTTTAAGT
1 ACTGAAATTTTAAGT
* **
19774252 GCTGAAAAATTAAGT
1 ACTGAAATTTTAAGT
* *
19774267 ACTG-AATTTTTATT
1 ACTGAAATTTTAAGT
19774281 ACT-AAATTTTA
1 ACTGAAATTTTA
19774292 TAAGTGTTTA
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (15 bp):
ACTGAAATTTTAAGT
Found at i:19781441 original size:7 final size:6
Alignment explanation
Indices: 19781411--19781440 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
19781401 GATTTTCTCA
19781411 AAATGG AAATGG AAATGG AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATG-G AAATG
19781441 ATTCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:19785630 original size:16 final size:16
Alignment explanation
Indices: 19785606--19785658 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
19785596 AGAGTGGAAA
19785606 AAAAATTGAA-ATGATG
1 AAAAATTGAAGA-GATG
*
19785622 AAAATTTGAAGAGATG
1 AAAAATTGAAGAGATG
*
19785638 AAAAACTAGAAGA-ATG
1 AAAAA-TTGAAGAGATG
19785654 AAAAA
1 AAAAA
19785659 AAAATTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 25 0.78
17 7 0.22
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAAATTGAAGAGATG
Found at i:19788356 original size:26 final size:26
Alignment explanation
Indices: 19788327--19788385 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
19788317 TATTTTCTTG
19788327 AAATTTTAAT-AGGGGCAAAATCGTCA
1 AAATTTT-ATCAGGGGCAAAATCGTCA
* *
19788353 AAATTTTATCGGGGGTAAAATCGTCA
1 AAATTTTATCAGGGGCAAAATCGTCA
19788379 AAATTTT
1 AAATTTT
19788386 GCTGAGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 28 0.93
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (26 bp):
AAATTTTATCAGGGGCAAAATCGTCA
Found at i:19793599 original size:119 final size:120
Alignment explanation
Indices: 19793423--19793645 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
19793413 TACTCGTTCA
* * * *
19793423 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAGCCCGGAT
*
19793488 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
19793543 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAGCCCGG
* * *
19793605 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
19793646 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAGCCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:19793645 original size:40 final size:40
Alignment explanation
Indices: 19793402--19793645 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
19793392 CGGAATTTAA
** *
19793402 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19793442 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19793482 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19793522 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19793561 CCGGA-ATTAGTAACTCGCACAAATACCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
19793601 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
19793641 CCGGA
1 CCGGA
19793646 CATCATTCAA
Statistics
Matches: 178, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.18
40 132 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:19801709 original size:119 final size:120
Alignment explanation
Indices: 19801533--19801755 Score: 310
Period size: 119 Copynumber: 1.9 Consensus size: 120
19801523 TACTCGTTCA
* * *
19801533 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
*
19801598 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
19801653 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* * *
19801715 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
19801756 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
118 4 0.04
119 67 0.74
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:19801755 original size:40 final size:40
Alignment explanation
Indices: 19801512--19801755 Score: 300
Period size: 40 Copynumber: 6.1 Consensus size: 40
19801502 CGGAATTTAA
** *
19801512 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19801552 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19801592 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19801632 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
19801671 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
19801711 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
19801751 CCGGA
1 CCGGA
19801756 CATCATTCAA
Statistics
Matches: 180, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.18
40 133 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:19810259 original size:7 final size:7
Alignment explanation
Indices: 19810247--19810271 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19810237 TATCTTTGTA
19810247 ATACTCC
1 ATACTCC
19810254 ATACTCC
1 ATACTCC
19810261 ATACTCC
1 ATACTCC
19810268 ATAC
1 ATAC
19810272 ATCATCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTCC
Found at i:19813053 original size:34 final size:33
Alignment explanation
Indices: 19812977--19813059 Score: 109
Period size: 34 Copynumber: 2.5 Consensus size: 33
19812967 CAATTCAATA
*
19812977 ACAGT-TCAGT-TCAGTTGGGCCTTTGCCCATT
1 ACAGTATCAGTATCAGTTGGGCCTTAGCCCATT
19813008 ACAGTATCAGTATCAGTGTGGGCCTTAGCCCATT
1 ACAGTATCAGTATCAGT-TGGGCCTTAGCCCATT
*
19813042 ACAGTGA-CAGTAACAGTT
1 ACAGT-ATCAGTATCAGTT
19813060 CAAACATGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
31 5 0.11
32 5 0.11
33 6 0.13
34 29 0.63
35 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (33 bp):
ACAGTATCAGTATCAGTTGGGCCTTAGCCCATT
Found at i:19813364 original size:27 final size:27
Alignment explanation
Indices: 19813325--19813395 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
19813315 ATAAGGTAAA
*
19813325 GCAT-ACAGTCATTTTATTACATAAGG
1 GCATAACAGTCATTTTATCACATAAGG
* * *
19813351 GCATAACAGTCATTTTACCACGTGAGG
1 GCATAACAGTCATTTTATCACATAAGG
* *
19813378 CCATAACATTCATTTTAT
1 GCATAACAGTCATTTTAT
19813396 ATCAGTTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (27 bp):
GCATAACAGTCATTTTATCACATAAGG
Found at i:19823785 original size:10 final size:10
Alignment explanation
Indices: 19823768--19823797 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
19823758 AACATAACCT
19823768 AAAAATGAAA
1 AAAAATGAAA
*
19823778 AGAAATGAAA
1 AAAAATGAAA
19823788 AAAAATGAAA
1 AAAAATGAAA
19823798 CCTAACCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:19824553 original size:8 final size:8
Alignment explanation
Indices: 19824505--19824561 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
19824495 GGCATAAGTG
19824505 TATATATAT
1 TATA-ATAT
19824514 TATAAATAT
1 TAT-AATAT
19824523 T-TAA-AGT
1 TATAATA-T
*
19824530 TAAAATA-
1 TATAATAT
19824537 TAT-ATAT
1 TATAATAT
19824544 TATAATAT
1 TATAATAT
19824552 TATAATAT
1 TATAATAT
19824560 TA
1 TA
19824562 AACTAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
6 4 0.10
7 9 0.22
8 17 0.43
9 9 0.22
10 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
TATAATAT
Found at i:19824659 original size:29 final size:30
Alignment explanation
Indices: 19824603--19824703 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 30
19824593 TTATAATGAT
*
19824603 AAAGTAAAAGAAAAAGAAATAGAAAAGGAATG
1 AAAG-AAAAG-AAAAGAAATAGAAAAGGAAAG
* *
19824635 AGAG-AAAGAAACGAAATA-AAGAAGGAAAG
1 AAAGAAAAGAAAAGAAATAGAA-AAGGAAAG
* *
19824664 AAAGAAAAGAAAAAAAAAAGAAAA-GAAAG
1 AAAGAAAAGAAAAGAAATAGAAAAGGAAAG
19824693 AAGGAGAAAAG
1 AA--AGAAAAG
19824704 TTAAGGTTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.04
29 26 0.46
30 17 0.30
31 9 0.16
32 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04
Consensus pattern (30 bp):
AAAGAAAAGAAAAGAAATAGAAAAGGAAAG
Found at i:19824668 original size:4 final size:4
Alignment explanation
Indices: 19824637--19824694 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
19824627 AAGGAATGAG
* * *
19824637 AGAA AGAA ACGAA ATAA AGAA GGAA AGAA AGAAA AGAA A-AA AAAA AGAAA
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AG-AA
19824687 AGAA AGAA
1 AGAA AGAA
19824695 GGAGAAAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
3 3 0.07
4 30 0.67
5 12 0.27
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:19824668 original size:25 final size:25
Alignment explanation
Indices: 19824637--19824694 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
19824627 AAGGAATGAG
* * * *
19824637 AGAAAGAAACGAAATAAAGAAGGAA
1 AGAAAGAAAAGAAAAAAAAAAGAAA
19824662 AGAAAGAAAAGAAAAAAAAAAGAAA
1 AGAAAGAAAAGAAAAAAAAAAGAAA
19824687 AGAAAGAA
1 AGAAAGAA
19824695 GGAGAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAAGAAAAAAAAAAGAAA
Found at i:19824674 original size:9 final size:9
Alignment explanation
Indices: 19824637--19824694 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
19824627 AAGGAATGAG
19824637 AGAAAGAAA
1 AGAAAGAAA
* *
19824646 CGAAA-TAA
1 AGAAAGAAA
*
19824654 AG-AAGGAA
1 AGAAAGAAA
19824662 AGAAAGAAA
1 AGAAAGAAA
19824671 AGAAA-AAA
1 AGAAAGAAA
19824679 A-AAAGAAA
1 AGAAAGAAA
19824687 AGAAAGAA
1 AGAAAGAA
19824695 GGAGAAAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
7 5 0.12
8 15 0.38
9 20 0.50
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (9 bp):
AGAAAGAAA
Found at i:19824702 original size:20 final size:19
Alignment explanation
Indices: 19824652--19824703 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 19
19824642 GAAACGAAAT
19824652 AAAGAAGGAAAGAAAGAAAAG
1 AAAGAAGG-AA-AAAGAAAAG
19824673 AAA-AA--AAAAAGAAAAG
1 AAAGAAGGAAAAAGAAAAG
19824689 AAAGAAGGAGAAAAG
1 AAAGAAGGA-AAAAG
19824704 TTAAGGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
16 12 0.44
17 4 0.15
19 1 0.04
20 7 0.26
21 3 0.11
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (19 bp):
AAAGAAGGAAAAAGAAAAG
Found at i:19831037 original size:15 final size:15
Alignment explanation
Indices: 19831014--19831050 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
19831004 TTTTTATTAT
19831014 TATTCATTTTTGTTCA
1 TATT-ATTTTTGTTCA
19831030 TATTATTTTTGTTCA
1 TATTATTTTTGTTCA
*
19831045 CATTAT
1 TATTAT
19831051 CATATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (15 bp):
TATTATTTTTGTTCA
Found at i:19831310 original size:109 final size:109
Alignment explanation
Indices: 19831099--19831430 Score: 438
Period size: 109 Copynumber: 3.1 Consensus size: 109
19831089 TCAAAAAAGG
* * * *
19831099 AAAATTTTTCAAAGTAAGGCAATATTTTGCGATTGGAAATTGGAGAAAACGTGCCCTAATGTGCT
1 AAAA-TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTT
* * *
19831164 GGGTTTTGATTTTTCTCCTTCAACCAAAAAGCTAAATATCCTTTT
65 GGGTTTCGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTT
* *
19831209 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACGTGCCCTAATGTGTTG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTG
* * *
19831274 GGTTTCGATTTTTCTCGTTCGATCAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTT
* * * * * *
19831318 AAAA-TTTCGAAATAAGACAATATTTTACGTTTAGAAATTCGAGGAAATGTGCCCTAATGTGTTG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTG
* * *
19831382 GGTTTCGA--TTTCTCCTTTAACCAAATAGACAAATATCCTCTT
66 GGTTTCGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTT
19831424 -AAATTTT
1 AAAATTTT
19831431 AATACATGTC
Statistics
Matches: 195, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
105 3 0.02
106 31 0.16
108 60 0.31
109 97 0.50
110 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (109 bp):
AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTG
GGTTTCGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTT
Found at i:19838322 original size:83 final size:83
Alignment explanation
Indices: 19838183--19838343 Score: 304
Period size: 83 Copynumber: 1.9 Consensus size: 83
19838173 AAAATCAATA
19838183 ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
1 ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
19838248 AGAGGTAGGTTGAATTGT
66 AGAGGTAGGTTGAATTGT
* *
19838266 ACTTCCTTTTCTTCCGAGCCATTGAAAACATCCTTTGAAGAGTGGCCGACGAGCTTATCTCTCCA
1 ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
19838331 AGAGGTAGGTTGA
66 AGAGGTAGGTTGA
19838344 TCTGAGGACA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (83 bp):
ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
AGAGGTAGGTTGAATTGT
Found at i:19840986 original size:19 final size:17
Alignment explanation
Indices: 19840963--19841003 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
19840953 AACATAAATA
*
19840963 TTTATTATTAATTA-TT
1 TTTATTATTAATAATTT
19840979 TTTATTATTAATAATTT
1 TTTATTATTAATAATTT
19840996 TTTATTAT
1 TTTATTAT
19841004 AATCATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTATTAATAATTT
Found at i:19842616 original size:41 final size:41
Alignment explanation
Indices: 19842566--19842652 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
19842556 TCAAACAAAT
* * *
19842566 TACAACACTTGAAATAATGAAAGGAAATTAGACTCTGAGTG
1 TACATCACTTGAAATAATGAAAGAAAATTAAACTCTGAGTG
19842607 TACATCACTTGAAATAATGAAAGAAAATTAAACTCTGAGTG
1 TACATCACTTGAAATAATGAAAGAAAATTAAACTCTGAGTG
19842648 TACAT
1 TACAT
19842653 AAGTGTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (41 bp):
TACATCACTTGAAATAATGAAAGAAAATTAAACTCTGAGTG
Found at i:19852574 original size:20 final size:19
Alignment explanation
Indices: 19852551--19852596 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
19852541 ATCTTAATTC
*
19852551 TAAAAATTTTAAAAATACAT
1 TAAAAATTTCAAAAAT-CAT
*
19852571 TAAAAA-TTCAAAAATTAT
1 TAAAAATTTCAAAAATCAT
19852589 TAAAAATT
1 TAAAAATT
19852597 ATATAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATTTCAAAAATCAT
Found at i:19852593 original size:10 final size:10
Alignment explanation
Indices: 19852551--19852604 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
19852541 ATCTTAATTC
19852551 TAAAAATT-T
1 TAAAAATTAT
*
19852560 TAAAAATACAT
1 TAAAAAT-TAT
19852571 TAAAAA-T-T
1 TAAAAATTAT
*
19852579 CAAAAATTAT
1 TAAAAATTAT
19852589 TAAAAATTAT
1 TAAAAATTAT
19852599 ATAAAA
1 -TAAAA
19852605 TGATATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
8 6 0.17
9 8 0.22
10 10 0.28
11 12 0.33
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:19853560 original size:94 final size:92
Alignment explanation
Indices: 19853419--19853598 Score: 270
Period size: 94 Copynumber: 1.9 Consensus size: 92
19853409 AAATCTAAAA
* * *
19853419 CTTTCTTTTAGAAAATATTCAATTTCACTATTAGACTTTATTTTAAAATATTTTTTTCATTCTTG
1 CTTTCTTTTAGAAAATAGTCAATTTCACTATTAGACTTTATTCTAAAATA--TTTTTCATTCCTG
* *
19853484 TTAAATATTTAGAAAAAATAAATATGAAT
64 TTAAACATTGAGAAAAAATAAATATGAAT
* *
19853513 CTTTCTTTTAGAAAATAGTCAATTTCACTTTTAGACTTTCTTCTAAAATATTTTTCATTCCTGTT
1 CTTTCTTTTAGAAAATAGTCAATTTCACTATTAGACTTTATTCTAAAATATTTTTCATTCCTGTT
*
19853578 AAACATTGAGAACAAATAAAT
66 AAACATTGAGAAAAAATAAAT
19853599 CTAAGCTTCA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 32 0.41
94 46 0.59
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (92 bp):
CTTTCTTTTAGAAAATAGTCAATTTCACTATTAGACTTTATTCTAAAATATTTTTCATTCCTGTT
AAACATTGAGAAAAAATAAATATGAAT
Found at i:19861837 original size:23 final size:23
Alignment explanation
Indices: 19861805--19861848 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19861795 TAACATTCTA
*
19861805 TAAAGCCTTTATGGCGTATTAAG
1 TAAAGCCTTTATGGCATATTAAG
*
19861828 TAAAGGCTTTATGGCATATTA
1 TAAAGCCTTTATGGCATATTA
19861849 TGTGATGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (23 bp):
TAAAGCCTTTATGGCATATTAAG
Found at i:19867305 original size:215 final size:216
Alignment explanation
Indices: 19866911--19867332 Score: 476
Period size: 215 Copynumber: 2.0 Consensus size: 216
19866901 CTTCTTGAGT
* * * * * *
19866911 AGTAAGCTGGTATTTACCAATGGTTTTTTTACTAGCTATAGGAAACCTTCCTCGTCTTCTGTAAT
1 AGTAAGCTGGTATTTAACAAGGGTGTTTTGACTAGCTACAGGAAACCTTCCTCGTCTTCTCTAAT
** * * *
19866976 GAACATACATTAAAAATTTTTAAAGACTCAGAAAAGAGGGTAAAAAAAAATAAGGGTGAAACATG
66 GAACATACATTAAAAATTTCCAAAGACTCAGAAAAGAAGGTAAAAAAAAACAAAGGTGAAACATG
* * * * * * *
19867041 TCGACTATCAGCATCCTTATGTAGCACAGACAACATGAATAATGCTTAGTGTGAGGGTTAAAAAA
131 TCGACTATCAACATCCTTATATAGCACAGACAACATGAACAAAGCTTAGTGGGAAGATTAAAAAA
*
19867106 -CCCATTATAGCATAGACAAC
196 CCCCACTATAGCATAGACAAC
* *
19867126 AGTAAGTTGGTATTTAATAAGGGTGTTTTGACTAGCTACAGGAAACCTTCCTCGTCTTCTCTAAC
1 AGTAAGCTGGTATTTAACAAGGGTGTTTTGACTAGCTACAGGAAACCTTCCTCGTCTTCTCTAA-
* * * * * * * *
19867191 TG-AGATATC-TTAAAACTTTCCAAAGACTTAGAAAATAATGTAGAGAAAAACAAATGTGAAACA
65 TGAACATA-CATTAAAAATTTCCAAAGACTCAGAAAAGAAGGTAAAAAAAAACAAAGGTGAAACA
* * * *
19867254 TGTCGACTATCAACATCCTTATATTGCATAGA-AA-GTGGGGACAAAGCTTAGTGGGAAGATTAA
129 TGTCGACTATCAACATCCTTATATAGCACAGACAACAT--GAACAAAGCTTAGTGGGAAGATTAA
19867317 AAAACCCCACTATAGC
192 AAAACCCCACTATAGC
19867333 CCTAAAACCC
Statistics
Matches: 169, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
213 1 0.01
214 2 0.01
215 153 0.91
216 13 0.08
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (216 bp):
AGTAAGCTGGTATTTAACAAGGGTGTTTTGACTAGCTACAGGAAACCTTCCTCGTCTTCTCTAAT
GAACATACATTAAAAATTTCCAAAGACTCAGAAAAGAAGGTAAAAAAAAACAAAGGTGAAACATG
TCGACTATCAACATCCTTATATAGCACAGACAACATGAACAAAGCTTAGTGGGAAGATTAAAAAA
CCCCACTATAGCATAGACAAC
Found at i:19868239 original size:28 final size:29
Alignment explanation
Indices: 19868168--19868250 Score: 123
Period size: 30 Copynumber: 2.9 Consensus size: 29
19868158 AGCAATACAA
*
19868168 TGTGGGCCTTAGCCCATTACAGTAACAGTG
1 TGTGGGCCTTAGCCCAATACAGTAACAG-G
19868198 TGTGGGCCTTAGCCCAATACAGTAACA-G
1 TGTGGGCCTTAGCCCAATACAGTAACAGG
* *
19868226 TGTGAGCCTCAGCCCAATACAGTAA
1 TGTGGGCCTTAGCCCAATACAGTAA
19868251 TAGTATAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
28 24 0.48
30 26 0.52
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (29 bp):
TGTGGGCCTTAGCCCAATACAGTAACAGG
Found at i:19868390 original size:26 final size:26
Alignment explanation
Indices: 19868360--19868436 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 26
19868350 ACACCAATAT
* *
19868360 CGCAGCAAAGCTACCAGTAATAGTGA
1 CGCAGCAAAGCTACCAGTAACAGTAA
* * * *
19868386 TGCAGCAACGCTGCTAGTAACAGTAA
1 CGCAGCAAAGCTACCAGTAACAGTAA
* *
19868412 CGTAGCAAAGCTACCAATAACAGTA
1 CGCAGCAAAGCTACCAGTAACAGTA
19868437 TATGTGGCAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
CGCAGCAAAGCTACCAGTAACAGTAA
Found at i:19868631 original size:27 final size:27
Alignment explanation
Indices: 19868610--19868848 Score: 250
Period size: 27 Copynumber: 9.0 Consensus size: 27
19868600 GGGGTATAAT
*
19868610 AATCATTTTACCCTTCGAGGGTATTTC
1 AATCATTTTACCCTTCAAGGGTATTTC
* *
19868637 GATTATTTTACCCTTCAAGGGTATTTC
1 AATCATTTTACCCTTCAAGGGTATTTC
** *
19868664 GGTCATTTTACCCTTCAGGGGTATTTC
1 AATCATTTTACCCTTCAAGGGTATTTC
* *
19868691 ---GATTTTACCCTTCAAGGATATTTC
1 AATCATTTTACCCTTCAAGGGTATTTC
* * * *
19868715 AGTCATTTTTCCCTTTAAGGGTATTTT
1 AATCATTTTACCCTTCAAGGGTATTTC
* * *
19868742 GATTATTTTACCCTTCGAGGGTATTTC
1 AATCATTTTACCCTTCAAGGGTATTTC
* *
19868769 AATCATTTTACCTTTCGAGGGTATTTC
1 AATCATTTTACCCTTCAAGGGTATTTC
** * *
19868796 TGTCATTTTACCCTTCAAGAGTATTTT
1 AATCATTTTACCCTTCAAGGGTATTTC
* *
19868823 AATCATTTTACCATTCGAGGGTATTT
1 AATCATTTTACCCTTCAAGGGTATTT
19868849 TGATCGTTTT
Statistics
Matches: 174, Mismatches: 35, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
24 21 0.12
27 153 0.88
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (27 bp):
AATCATTTTACCCTTCAAGGGTATTTC
Found at i:19868660 original size:54 final size:53
Alignment explanation
Indices: 19868610--19868848 Score: 295
Period size: 54 Copynumber: 4.5 Consensus size: 53
19868600 GGGGTATAAT
19868610 AATCATTTTACCCTTCGAGGGTATTTCGATTATTTTACCCTTCAAGGGTATTTC
1 AATCATTTTACCCTTCGAGGGTATTTCG-TTATTTTACCCTTCAAGGGTATTTC
** *
19868664 GGTCATTTTACCCTTC-AGGGGTATTTCG--ATTTTACCCTTCAAGGATATTTC
1 AATCATTTTACCCTTCGA-GGGTATTTCGTTATTTTACCCTTCAAGGGTATTTC
* * ** * *
19868715 AGTCATTTTTCCCTTTAAGGGTATTTTGATTATTTTACCCTTCGAGGGTATTTC
1 AATCATTTTACCCTTCGAGGGTATTTCG-TTATTTTACCCTTCAAGGGTATTTC
* * * *
19868769 AATCATTTTACCTTTCGAGGGTATTTCTGTCATTTTACCCTTCAAGAGTATTTT
1 AATCATTTTACCCTTCGAGGGTATTTC-GTTATTTTACCCTTCAAGGGTATTTC
*
19868823 AATCATTTTACCATTCGAGGGTATTT
1 AATCATTTTACCCTTCGAGGGTATTT
19868849 TGATCGTTTT
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
51 44 0.28
52 1 0.01
53 1 0.01
54 112 0.70
55 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (53 bp):
AATCATTTTACCCTTCGAGGGTATTTCGTTATTTTACCCTTCAAGGGTATTTC
Found at i:19875903 original size:13 final size:13
Alignment explanation
Indices: 19875885--19875909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19875875 TAATTTATAT
19875885 GTGTGAAAATTTC
1 GTGTGAAAATTTC
19875898 GTGTGAAAATTT
1 GTGTGAAAATTT
19875910 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:19876898 original size:34 final size:35
Alignment explanation
Indices: 19876834--19876906 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
19876824 AAGGATTTTA
* **
19876834 AATTGTATGTATTTATTTTTTACATAGCCGAATTG
1 AATTGTATGTATGTATTAATTACATAGCCGAATTG
*
19876869 AATTGTATGTATGTA-TAATTACATTGCCGAATTG
1 AATTGTATGTATGTATTAATTACATAGCCGAATTG
19876903 AATT
1 AATT
19876907 TAGCATGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 20 0.59
35 14 0.41
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (35 bp):
AATTGTATGTATGTATTAATTACATAGCCGAATTG
Found at i:19877082 original size:44 final size:43
Alignment explanation
Indices: 19877016--19877144 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 43
19877006 ATAGGATTCT
*
19877016 GATATGTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
1 GATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
* * *
19877059 G--ATTTGATATTTACGTGTAAGACC-CTGTCTAGGAAAG-TGGCATT
1 GATATTTG--ATTT-CGTGTAAGACCAC-GTCT-GGGACGTTGGCATC
*
19877103 GATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
19877145 TGTACGATCT
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
41 4 0.06
42 4 0.06
43 26 0.37
44 27 0.39
45 4 0.06
46 5 0.07
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
GATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:19877143 original size:43 final size:43
Alignment explanation
Indices: 19877015--19877146 Score: 146
Period size: 43 Copynumber: 3.0 Consensus size: 43
19877005 CATAGGATTC
*
19877015 TGATATGTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 TGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
19877058 CG--ATTTGATATTTACGTGTAAGACC-CTGTCTAGGAAAG-TGGCAT
1 TGATATTTG--ATTT-CGTGTAAGACCAC-GTCT-GGGACGTTGGCAT
*
19877102 TGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
1 TGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
19877145 TG
1 TG
19877147 TACGATCTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
41 4 0.06
42 4 0.06
43 28 0.39
44 27 0.38
45 4 0.06
46 5 0.07
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
TGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:19894374 original size:4 final size:4
Alignment explanation
Indices: 19894365--19894405 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
19894355 GAAATTTGAC
19894365 AATA AATA AA-A AATA AATA AAT- -ATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
19894406 GACGAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 29 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:19894394 original size:14 final size:14
Alignment explanation
Indices: 19894365--19894403 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
19894355 GAAATTTGAC
19894365 AATAAATAAAAAATA
1 AATAAAT-AAAAATA
*
19894380 AATAAATATAAATA
1 AATAAATAAAAATA
19894394 AATAAATAAA
1 AATAAATAAA
19894404 TAGACGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:19894398 original size:18 final size:17
Alignment explanation
Indices: 19894370--19894405 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
19894360 TTGACAATAA
19894370 ATAAAAAATAAATAAAT
1 ATAAAAAATAAATAAAT
19894387 ATAAATAAATAAATAAAT
1 ATAAA-AAATAAATAAAT
19894405 A
1 A
19894406 GACGAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAAAATAAATAAAT
Found at i:19894893 original size:3 final size:3
Alignment explanation
Indices: 19894849--19894873 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19894839 TTAAAATACT
19894849 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
19894874 TTGGAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:19896249 original size:31 final size:30
Alignment explanation
Indices: 19896211--19896272 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
19896201 ATCTTTTAGG
*
19896211 CATATATTTAGGAATATATTATATATGTTTT
1 CATATATTTAGGAACATATTATATAT-TTTT
19896242 CATATATTTAGGAACATATTATATATTTTT
1 CATATATTTAGGAACATATTATATATTTTT
19896272 C
1 C
19896273 CTATTCCTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.50
Consensus pattern (30 bp):
CATATATTTAGGAACATATTATATATTTTT
Found at i:19896735 original size:19 final size:19
Alignment explanation
Indices: 19896695--19896736 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19896685 TGGATAATTT
*
19896695 AAAATAAAAATTTTAAAGA
1 AAAATAAAAATTTAAAAGA
*
19896714 AAAATAAAACA-TTAAAATA
1 AAAATAAAA-ATTTAAAAGA
19896733 AAAA
1 AAAA
19896737 AGTAAGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAAAAATTTAAAAGA
Found at i:19896908 original size:21 final size:19
Alignment explanation
Indices: 19896858--19896909 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
19896848 CGTTTTAGTT
19896858 TTTTATTTTTCATTTTAAC
1 TTTTATTTTTCATTTTAAC
*
19896877 TTCTCTTTTTTTCATTTTAAC
1 TT-T-TATTTTTCATTTTAAC
*
19896898 ATTTTAGTTTTC
1 -TTTTATTTTTC
19896910 TTTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.07
20 7 0.26
21 16 0.59
22 2 0.07
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATTTTTCATTTTAAC
Found at i:19897659 original size:2 final size:2
Alignment explanation
Indices: 19897652--19897679 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19897642 TTACAGCTAG
19897652 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19897680 TTAATGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19915801 original size:31 final size:31
Alignment explanation
Indices: 19915766--19915831 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
19915756 ACCAAAACTA
*
19915766 TATATATCAACTTTAGTTTAACATGTAATAT
1 TATATATCAACTTTAGTTTAACATGTAATAC
* * *
19915797 TATATATTAATTTTGGTTTAACATGTAATAC
1 TATATATCAACTTTAGTTTAACATGTAATAC
19915828 TATA
1 TATA
19915832 AATGAGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (31 bp):
TATATATCAACTTTAGTTTAACATGTAATAC
Found at i:19920370 original size:42 final size:44
Alignment explanation
Indices: 19920320--19920502 Score: 252
Period size: 43 Copynumber: 4.3 Consensus size: 44
19920310 TTTGATAAAT
*
19920320 AAACGCCGCTAAAGACCA-AGA-CTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
*
19920362 AAACGCCGCTAAAGACCATA-ACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
* * * *
19920405 AAACACCACTAAAGACCA-AGACCTTTAGCGGTGCTTTTCAGAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
* *
19920448 AAACGCCGCTATAGA--ATTGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
19920490 AAACGCCGCTAAA
1 AAACGCCGCTAAA
19920503 AATATATCTT
Statistics
Matches: 125, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
41 1 0.01
42 54 0.43
43 70 0.56
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (44 bp):
AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
Found at i:19920424 original size:85 final size:85
Alignment explanation
Indices: 19920328--19920502 Score: 246
Period size: 85 Copynumber: 2.1 Consensus size: 85
19920318 ATAAACGCCG
*
19920328 CTAAAGACCAAGA-CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-TAACCTTTAGC
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTAAAGA--ATTAACCTTTAGC
*
19920391 GGCGCTTTTCCCACAAACACCA
64 GGCGCTTTTCACACAAACACCA
* * * *
19920413 CTAAAGACCAAGACCTTTAGCGGTGCTTTTCAGACAAACGCCGCTATAGAATTGACCTTTAGCGG
1 CTAAAGACCAAGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTAAAGAATTAACCTTTAGCGG
* *
19920478 CGCTTTTCACACAAACGCCG
66 CGCTTTTCACACAAACACCA
19920498 CTAAA
1 CTAAA
19920503 AATATATCTT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 1 0.01
85 47 0.59
86 32 0.40
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (85 bp):
CTAAAGACCAAGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTAAAGAATTAACCTTTAGCGG
CGCTTTTCACACAAACACCA
Found at i:19920825 original size:43 final size:43
Alignment explanation
Indices: 19920759--19920849 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
19920749 ACATATGCAA
* * * *
19920759 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
19920802 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
19920845 -GTAAT
1 GGTAAT
19920850 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:19921688 original size:25 final size:26
Alignment explanation
Indices: 19921648--19921753 Score: 92
Period size: 25 Copynumber: 4.2 Consensus size: 26
19921638 AAGTTATGTA
* *
19921648 TTATGTAAGATATGTAAGT-TGTATT
1 TTATGTAAGTTATGTAAGTATGTATG
* *
19921673 TTATGTAAGTTCTGT-ATTATGTATG
1 TTATGTAAGTTATGTAAGTATGTATG
* * *
19921698 TTATGTAAGTTGTGT-AGAATGTAAG
1 TTATGTAAGTTATGTAAGTATGTATG
* * *
19921723 CTATGTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATGTAAG-TATGTATG
19921750 TTAT
1 TTAT
19921754 TATGTAAGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 2 0.03
25 51 0.78
26 2 0.03
27 10 0.15
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (26 bp):
TTATGTAAGTTATGTAAGTATGTATG
Found at i:19921758 original size:12 final size:12
Alignment explanation
Indices: 19921741--19921765 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19921731 GTTATATAAG
19921741 TTATGTAAGTTA
1 TTATGTAAGTTA
19921753 TTATGTAAGTTA
1 TTATGTAAGTTA
19921765 T
1 T
19921766 GCAAGCTTAT
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:19921766 original size:9 final size:9
Alignment explanation
Indices: 19921638--19921753 Score: 95
Period size: 9 Copynumber: 13.8 Consensus size: 9
19921628 TAGTTCAGAG
19921638 AAGTTATGT
1 AAGTTATGT
19921647 -A-TTATGT
1 AAGTTATGT
*
19921654 AAGATATGT
1 AAGTTATGT
19921663 AAG-T-TGT
1 AAGTTATGT
**
19921670 ATTTTATGT
1 AAGTTATGT
*
19921679 AAGTTCTGT
1 AAGTTATGT
19921688 -A-TTATGT
1 AAGTTATGT
*
19921695 ATGTTATGT
1 AAGTTATGT
*
19921704 AAGTTGTGT
1 AAGTTATGT
*
19921713 -AG-AATGT
1 AAGTTATGT
*
19921720 AAGCTATGT
1 AAGTTATGT
*
19921729 AAGTTATAT
1 AAGTTATGT
19921738 AAGTTATGT
1 AAGTTATGT
19921747 AAGTTAT
1 AAGTTAT
19921754 TATGTAAGTT
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
7 18 0.22
8 9 0.11
9 56 0.67
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (9 bp):
AAGTTATGT
Found at i:19921807 original size:8 final size:8
Alignment explanation
Indices: 19921791--19921846 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
19921781 TATATATAAG
19921791 TTATG-TA
1 TTATGTTA
19921798 TTATGTTA
1 TTATGTTA
19921806 TTATGTTA
1 TTATGTTA
*
19921814 TTAT-ATA
1 TTATGTTA
19921821 TTATG-TA
1 TTATGTTA
19921828 --AT-TTA
1 TTATGTTA
19921833 TTATGTTA
1 TTATGTTA
19921841 TTATGT
1 TTATGT
19921847 AAGTTATGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
5 4 0.10
7 15 0.36
8 23 0.55
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (8 bp):
TTATGTTA
Found at i:19923672 original size:24 final size:24
Alignment explanation
Indices: 19923593--19923672 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
19923583 TGTATCTTTC
* * *
19923593 ATTTAAATAATTAATTACATGTCT
1 ATTTAAATAATTAATTACCTATTT
* *
19923617 ACTTAAATAATTAATTACCTAAAAATTA
1 ATTTAAATAATTAATTACCT----ATTT
19923645 ATTTAAATAATTAATTACCTATTT
1 ATTTAAATAATTAATTACCTATTT
19923669 ATTT
1 ATTT
19923673 GTTTATTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
24 25 0.56
28 20 0.44
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (24 bp):
ATTTAAATAATTAATTACCTATTT
Found at i:19924808 original size:43 final size:42
Alignment explanation
Indices: 19924690--19924843 Score: 197
Period size: 41 Copynumber: 3.7 Consensus size: 42
19924680 TTTTATTATT
* * * *
19924690 ATTAGCGGCGC-TTTTGAGAAAGCGCCGCTAAAGGTCCGAGC
1 ATTAGCGGCGCTTTTTAAAAAAACGCCGCTGAAGGTCCGAGC
* *
19924731 ATTAGCGGCGCGTTTT-AAAAAACGCCGCTGAAGGTCCGAAC
1 ATTAGCGGCGCTTTTTAAAAAAACGCCGCTGAAGGTCCGAGC
* *
19924772 ATTAGCGGCTCTTTTTAAAAAAAACGCTGCTGAAGGTCCGAGC
1 ATTAGCGGCGCTTTTT-AAAAAAACGCCGCTGAAGGTCCGAGC
*
19924815 ATTAGCGGCGCTTTTT-GAAAAACGCCGCT
1 ATTAGCGGCGCTTTTTAAAAAAACGCCGCT
19924844 AAAAGCCCCC
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
41 57 0.58
42 4 0.04
43 38 0.38
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (42 bp):
ATTAGCGGCGCTTTTTAAAAAAACGCCGCTGAAGGTCCGAGC
Found at i:19931907 original size:43 final size:42
Alignment explanation
Indices: 19931828--19931940 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 42
19931818 GTACATAAGT
* * * * *
19931828 GCTAAACAGAAACCCATAATGATTGAACGGAAGCTCATAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTCAAAAGA
* * *
19931870 GCTGAACGGAAAACCCATAAGGGTTAAACTGATGCTCAAAAGA
1 GCTAAACGG-AAACCCATAAGGGTTAAACGGAAGCTCAAAAGA
* * *
19931913 GCTAAATGGAAACTCATTAGGGTTAAAC
1 GCTAAACGGAAACCCATAAGGGTTAAAC
19931941 AAAAACTCAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 24 0.41
43 34 0.59
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (42 bp):
GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTCAAAAGA
Found at i:19939545 original size:21 final size:21
Alignment explanation
Indices: 19939516--19939556 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19939506 AAGCCCGAAG
* *
19939516 GCTACACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
*
19939537 GCTAAACAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
19939557 GGTTGAACGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.12
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:19939577 original size:42 final size:42
Alignment explanation
Indices: 19939525--19939659 Score: 141
Period size: 42 Copynumber: 3.2 Consensus size: 42
19939515 GGCTACACAG
* * *
19939525 AAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGA
1 AAGCTCATAAGTGCTAAACGGAAACCCATAAGGGTTAAACGA
* *
19939567 AAGCTCATAAGAT-CTAAATGGAAACCCATAAGGGTTAAATTG-
1 AAGCTCATAAG-TGCTAAACGGAAACCCATAAGGGTTAAA-CGA
* * * *
19939609 AAGCTTAAAAGAGCTAAACGGAAACCCATTAGGGTTAAACGGA
1 AAGCTCATAAGTGCTAAACGGAAACCCATAAGGGTTAAAC-GA
19939652 AA-CTCATA
1 AAGCTCATA
19939660 TGAGTTAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
42 71 0.95
43 4 0.05
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (42 bp):
AAGCTCATAAGTGCTAAACGGAAACCCATAAGGGTTAAACGA
Found at i:19939605 original size:21 final size:21
Alignment explanation
Indices: 19939530--19939659 Score: 75
Period size: 21 Copynumber: 6.2 Consensus size: 21
19939520 CACAGAAGCA
* * *
19939530 CATAAGTGCTAAACAGAAACC
1 CATAAGGGTTAAACGGAAACC
* *
19939551 CATAAGGGTTGAAC-GAAAGCT
1 CATAAGGGTTAAACGGAAA-CC
* *
19939572 CATAA-GATCTAAATGGAAACC
1 CATAAGGGT-TAAACGGAAACC
** * *
19939593 CATAAGGGTTAAATTGAAGCT
1 CATAAGGGTTAAACGGAAACC
* * * *
19939614 TAAAAGAGCTAAACGGAAACC
1 CATAAGGGTTAAACGGAAACC
* *
19939635 CATTAGGGTTAAACGGAAACT
1 CATAAGGGTTAAACGGAAACC
19939656 CATA
1 CATA
19939660 TGAGTTAATT
Statistics
Matches: 78, Mismatches: 27, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
20 6 0.08
21 66 0.85
22 6 0.08
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (21 bp):
CATAAGGGTTAAACGGAAACC
Found at i:19939666 original size:21 final size:21
Alignment explanation
Indices: 19939618--19939667 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19939608 GAAGCTTAAA
*
19939618 AGAGCTAAACGGAAACCCATT
1 AGAGTTAAACGGAAACCCATT
* *
19939639 AGGGTTAAACGGAAACTCA-T
1 AGAGTTAAACGGAAACCCATT
19939659 ATGAGTTAA
1 A-GAGTTAA
19939668 TTGAAGCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
AGAGTTAAACGGAAACCCATT
Found at i:19943506 original size:29 final size:30
Alignment explanation
Indices: 19943473--19943529 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19943463 TCCGAGCCTT
*
19943473 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
*
19943502 GGGGAAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
19943530 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:19943760 original size:13 final size:13
Alignment explanation
Indices: 19943742--19943772 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19943732 TTCCAGCAAC
19943742 TATGAATTTATTT
1 TATGAATTTATTT
19943755 TATGAATTTATTT
1 TATGAATTTATTT
*
19943768 GATGA
1 TATGA
19943773 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:19943945 original size:50 final size:50
Alignment explanation
Indices: 19943867--19944129 Score: 206
Period size: 50 Copynumber: 4.8 Consensus size: 50
19943857 ATTTGGGTAA
*
19943867 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
19943917 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
19943967 ATGGCATTGG-CACCGA-GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 A--G-A--GGTC-CC-ATG-T-A-A-G-ACCA----------TGTCTGGGACATGGCATTGGCAC
19944030 CGAGATG
44 CGAGATG
* * * * *
19944037 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
19944087 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19944130 TGTTATTATC
Statistics
Matches: 172, Mismatches: 16, Indels: 49
0.73 0.07 0.21
Matches are distributed among these distances:
50 78 0.45
51 34 0.20
52 1 0.01
53 1 0.01
54 1 0.01
55 5 0.03
56 2 0.01
57 1 0.01
58 1 0.01
59 1 0.01
60 6 0.03
61 1 0.01
62 1 0.01
63 1 0.01
64 1 0.01
65 4 0.02
66 1 0.01
67 1 0.01
68 1 0.01
70 30 0.17
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:19943972 original size:20 final size:20
Alignment explanation
Indices: 19943947--19943987 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
19943937 TGTCTGGGAC
19943947 ATGGCATTGGCACCGAGATG
1 ATGGCATTGGCACCGAGATG
19943967 ATGGCATTGGCACCGAGATG
1 ATGGCATTGGCACCGAGATG
19943987 A
1 A
19943988 GAGGTCCCAT
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:0.27, C:0.20, G:0.34, T:0.20
Consensus pattern (20 bp):
ATGGCATTGGCACCGAGATG
Found at i:19944010 original size:70 final size:70
Alignment explanation
Indices: 19943897--19944037 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
19943887 TGTTTGGGAC
19943897 ATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
1 ATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
19943962 AGATG
66 AGATG
*
19943967 ATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG
1 ATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
19944032 AGATG
66 AGATG
19944037 A
1 A
19944038 GAGGTCCCCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.20
Consensus pattern (70 bp):
ATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
AGATG
Found at i:19946199 original size:31 final size:32
Alignment explanation
Indices: 19946161--19946236 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
19946151 GAATCACCCC
*
19946161 GTGTTTACTATCCCGA-CGGACTATCTATTCT
1 GTGTTTACTATCCCGAGCAGACTATCTATTCT
* * *
19946192 GTGTTTACTGT-CCTAGCAGACTATCTATTTT
1 GTGTTTACTATCCCGAGCAGACTATCTATTCT
19946223 GTGTTTACTATCCC
1 GTGTTTACTATCCC
19946237 AATGAACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 3 0.08
31 33 0.87
32 2 0.05
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (32 bp):
GTGTTTACTATCCCGAGCAGACTATCTATTCT
Found at i:19946246 original size:31 final size:30
Alignment explanation
Indices: 19946161--19946246 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
19946151 GAATCACCCC
* *
19946161 GTGTTTACTATCCCGACGGACTATCTATTCT
1 GTGTTTACTATCCC-AAGAACTATCTATTCT
* * *
19946192 GTGTTTACTGT-CCTAGCAGACTATCTATTTT
1 GTGTTTACTATCCCAAG-A-ACTATCTATTCT
19946223 GTGTTTACTATCCCAATGAACTAT
1 GTGTTTACTATCCCAA-GAACTAT
19946247 TTTTGTAGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
29 1 0.02
30 2 0.05
31 36 0.82
32 4 0.09
33 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (30 bp):
GTGTTTACTATCCCAAGAACTATCTATTCT
Found at i:19948062 original size:10 final size:10
Alignment explanation
Indices: 19948049--19948130 Score: 59
Period size: 10 Copynumber: 8.4 Consensus size: 10
19948039 GAAAAGTTAT
19948049 AAAATTATTCA
1 AAAATTATT-A
*
19948060 AAACTT-TTA
1 AAAATTATTA
19948069 AAAATTA-TA
1 AAAATTATTA
19948078 AGAAATTA-TA
1 A-AAATTATTA
*
19948088 AAAATTTATTT
1 AAAA-TTATTA
*
19948099 AAAAGTA--A
1 AAAATTATTA
19948107 AAAA-TATTTA
1 AAAATTA-TTA
19948117 AAAATTATTA
1 AAAATTATTA
19948127 AAAA
1 AAAA
19948131 AATTCTTGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.03
8 4 0.07
9 12 0.21
10 28 0.48
11 12 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATTATTA
Found at i:19948129 original size:20 final size:19
Alignment explanation
Indices: 19948040--19948130 Score: 62
Period size: 19 Copynumber: 4.7 Consensus size: 19
19948030 AAAATTACAG
* * *
19948040 AAAAGTTATAAAATTATTC
1 AAAAATTATAAAAATATTT
* * *
19948059 AAAACTTTTAAAAAT-TAT
1 AAAAATTATAAAAATATTT
19948077 AAGAAATTATAAAAATTTATTT
1 AA-AAATTATAAAAA--TATTT
*
19948099 -AAAAGTA-AAAAATATTT
1 AAAAATTATAAAAATATTT
19948116 AAAAATTATTAAAAA
1 AAAAATTA-TAAAAA
19948131 AATTCTTGGA
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
17 5 0.09
18 9 0.16
19 27 0.49
20 10 0.18
21 2 0.04
22 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.35
Consensus pattern (19 bp):
AAAAATTATAAAAATATTT
Found at i:19949042 original size:43 final size:43
Alignment explanation
Indices: 19948923--19949043 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
19948913 TTGCAGCGTT
* * *
19948923 TAATGTTCTTTAGCGGCGCTTGGTA-AAAAAACGCCGCTATAGA
1 TAATGTTCTTTAGCGGCGCTT-TTATAAAAAACGCCGCAAAAGA
* * * **
19948966 TCATGTTCTTTAGCGGCGCTTTCATCACGAACGCCGCGAAAAG-
1 TAATGTTCTTTAGCGGCGCTTTTATAAAAAACGCCGC-AAAAGA
19949009 TAATGTTCTTTAGCGGCGCTTTTATAAAAAACGCC
1 TAATGTTCTTTAGCGGCGCTTTTATAAAAAACGCC
19949044 ACTAATTTTG
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.02
43 59 0.94
44 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (43 bp):
TAATGTTCTTTAGCGGCGCTTTTATAAAAAACGCCGCAAAAGA
Found at i:19949459 original size:21 final size:21
Alignment explanation
Indices: 19949432--19949480 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
19949422 GTTTCTCTCA
19949432 CTGCTTCTCGCACTGCAGCCT
1 CTGCTTCTCGCACTGCAGCCT
* * *
19949453 TTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCGCACTGCAGCCT
19949474 CTGCTTC
1 CTGCTTC
19949481 CCTCGTTGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.41, G:0.18, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCGCACTGCAGCCT
Found at i:19949485 original size:21 final size:21
Alignment explanation
Indices: 19949444--19949496 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
19949434 GCTTCTCGCA
* *
19949444 CTGCAGCCTTTGCTTCTCTCG
1 CTGCAGCCTCTGCTTCCCTCG
19949465 CTGCAGCCTCTGCTTCCCTCG
1 CTGCAGCCTCTGCTTCCCTCG
* *
19949486 TTGCCGCCTCT
1 CTGCAGCCTCT
19949497 ACTTTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.04, C:0.43, G:0.19, T:0.34
Consensus pattern (21 bp):
CTGCAGCCTCTGCTTCCCTCG
Found at i:19950653 original size:114 final size:114
Alignment explanation
Indices: 19950448--19950907 Score: 760
Period size: 114 Copynumber: 4.0 Consensus size: 114
19950438 TAAATTATTT
* *
19950448 TAAATCCCTGAGTATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
*
19950513 GGCGTCGTTGGGCTTAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* *
19950562 TAAAGCCCTGAGCTTTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
* *
19950627 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTACCAAAAACGCCGT
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
19950676 TAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCATTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
19950741 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
19950790 CATAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTTAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
* * *
19950855 GGCGTCGTTGGGCTGAGGT-TTTTTGTGGCGCTTCTCTCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTT-TCCCAAAAACGCCGC
19950904 TAAA
1 TAAA
19950908 TCCCCGAAAG
Statistics
Matches: 322, Mismatches: 23, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
113 13 0.04
114 309 0.96
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (114 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:19950907 original size:73 final size:72
Alignment explanation
Indices: 19950807--19950978 Score: 218
Period size: 73 Copynumber: 2.4 Consensus size: 72
19950797 CTGAGCATTA
* * * * *
19950807 GCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTTAGAAAACGGCGTCGTTGGGCTGAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAG
*
19950872 GTTTTTT
66 GTATTTT
* * *
19950879 GTGGCGCTTCTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCGGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTT-TCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGA
19950944 GGTATTTT
65 GGTATTTT
* ** *
19950952 GCGGTGCTTTCTGGAAAATGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
19950979 TGCTTATTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 23 0.27
73 62 0.73
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAG
GTATTTT
Found at i:19953291 original size:7 final size:7
Alignment explanation
Indices: 19953279--19953305 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19953269 TTATTATGCC
19953279 TATTATA
1 TATTATA
19953286 TATTATA
1 TATTATA
19953293 TATTATA
1 TATTATA
19953300 TATTAT
1 TATTAT
19953306 TTGTTAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTATA
Found at i:19961053 original size:45 final size:45
Alignment explanation
Indices: 19960989--19961083 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
19960979 TTCTTCTTCA
* *
19960989 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
1 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
19961034 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
1 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
19961079 TCTTC
1 TCTTC
19961084 ATCATCTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (45 bp):
TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
Found at i:19961092 original size:45 final size:45
Alignment explanation
Indices: 19960998--19961093 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
19960988 ATCTTCGTTT
* * * **
19960998 TCTTCTGCTGGATGTAATGATTCCATCAATGGATATTCTTCGTTT
1 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
19961043 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
1 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
19961088 TCTTCT
1 TCTTCT
19961094 TCCCCTGCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.43
Consensus pattern (45 bp):
TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
Found at i:19964321 original size:15 final size:14
Alignment explanation
Indices: 19964282--19964320 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19964272 GGGTTGTTAA
*
19964282 TTTTGATTTTAATTT
1 TTTTG-TTTTTATTT
*
19964297 ATTTGTTTTTATTT
1 TTTTGTTTTTATTT
19964311 TTTTGTTTTT
1 TTTTGTTTTT
19964321 TTCAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (14 bp):
TTTTGTTTTTATTT
Found at i:19966997 original size:45 final size:44
Alignment explanation
Indices: 19966812--19966999 Score: 167
Period size: 45 Copynumber: 4.2 Consensus size: 44
19966802 ATACTCGAAT
* *
19966812 AATCACATATATCGAACAATGCCAACGTCCCAGACGTGGTCTTACATG
1 AATCACATATATCG----ATGCCATCGTCCCAGACGTGGTCTTACACG
* *
19966860 -CT-ATATCATATCGATGCCA-CTGTCCCAGACAG-GGTCTTACACG
1 AATCACAT-ATATCGATGCCATC-GTCCCAGAC-GTGGTCTTACACG
* *
19966903 AATCA-A-ATA-CGATGCCAAT-GTCCTAGACATGGTCTTACACG
1 AATCACATATATCGATGCC-ATCGTCCCAGACGTGGTCTTACACG
19966944 TAATCACATATATCGATGCCATCGTCCCAGACGTGGTCTTACACG
1 -AATCACATATATCGATGCCATCGTCCCAGACGTGGTCTTACACG
*
19966989 AGAACACATAT
1 A-ATCACATAT
19967000 TGGAAATCCT
Statistics
Matches: 117, Mismatches: 9, Indels: 31
0.75 0.06 0.20
Matches are distributed among these distances:
41 26 0.22
42 10 0.09
43 26 0.22
44 9 0.08
45 36 0.31
46 3 0.03
47 7 0.06
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (44 bp):
AATCACATATATCGATGCCATCGTCCCAGACGTGGTCTTACACG
Found at i:19967914 original size:28 final size:31
Alignment explanation
Indices: 19967882--19967940 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
19967872 TGTTTTGTTT
19967882 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
19967910 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
19967941 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:19976751 original size:22 final size:23
Alignment explanation
Indices: 19976720--19976765 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
19976710 AAAATTATTA
19976720 AATATTAAATATTAATTAAAAAT
1 AATATTAAATATTAATTAAAAAT
**
19976743 AATA-TAAATATTTTTTAAAAAT
1 AATATTAAATATTAATTAAAAAT
19976765 A
1 A
19976766 GGTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATTAAATATTAATTAAAAAT
Found at i:19977505 original size:41 final size:39
Alignment explanation
Indices: 19977459--19977597 Score: 136
Period size: 40 Copynumber: 3.5 Consensus size: 39
19977449 GGCGTTTGGA
*
19977459 TAAAAAATGCCGCTAAAAATCAAGCATTAGCGACGCTTT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGACGCTTT
* * *
19977498 TCAAAAAACGCCGCTAAAGATCGAAGCATTAGTGGCGCTTT
1 T-AAAAAACGCCGCTAAAAATC-AAGCATTAGCGACGCTTT
** * * *
19977539 TTGAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTCT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGACGCTT-T
* *
19977578 TAGAAAAGCGCCGCAAAAAA
1 TA-AAAAACGCCGCTAAAAA
19977598 CCTAATCCCA
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
38 14 0.17
39 3 0.04
40 48 0.59
41 17 0.21
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (39 bp):
TAAAAAACGCCGCTAAAAATCAAGCATTAGCGACGCTTT
Found at i:19977692 original size:41 final size:40
Alignment explanation
Indices: 19977635--19977743 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 40
19977625 ACCTTTCGGG
* *
19977635 GCTTTAGCCGCGTTTTTAAAAAAACGCCACTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTC-GA
** ** * *
19977676 GCTTTAGCGGCGTTTTTGGAAAAGCGCTGCTAATTCTCGG
1 GCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTCGA
*
19977716 GATTTAGCGGCGTTTTTAAAAAAGCGCC
1 GCTTTAGCGGCGTTTTTAAAAAAGCGCC
19977744 GCAAAAACAT
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
40 25 0.45
41 31 0.55
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (40 bp):
GCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTCGA
Found at i:19978168 original size:15 final size:14
Alignment explanation
Indices: 19978148--19978191 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
19978138 AAGGTTTATA
19978148 GATTATGGAATTAAG
1 GATTATGG-ATTAAG
*
19978163 GATTATGGATTAGG
1 GATTATGGATTAAG
* *
19978177 GATTCTGGTTTAAG
1 GATTATGGATTAAG
19978191 G
1 G
19978192 GTTGTGATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (14 bp):
GATTATGGATTAAG
Found at i:19978339 original size:7 final size:7
Alignment explanation
Indices: 19978327--19978385 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
19978317 TAAATAATGT
19978327 TTAGGGG
1 TTAGGGG
19978334 TTAGGGG
1 TTAGGGG
*
19978341 TTGGGGG
1 TTAGGGG
**
19978348 TTAGTAG
1 TTAGGGG
19978355 TTAGGGG
1 TTAGGGG
*
19978362 TTTGGGG
1 TTAGGGG
19978369 TTAGGGG
1 TTAGGGG
*
19978376 TTAGAGG
1 TTAGGGG
19978383 TTA
1 TTA
19978386 AGAGTTAGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.15, C:0.00, G:0.51, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:19978525 original size:21 final size:22
Alignment explanation
Indices: 19978498--19978544 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
19978488 ATTGTAAAAG
19978498 AGGGGTT-AGGGATTAG-AGGTT
1 AGGGGTTAAGGG-TTAGTAGGTT
*
19978519 AGGGGTTAAGGGTTAGTAGTTT
1 AGGGGTTAAGGGTTAGTAGGTT
19978541 AGGG
1 AGGG
19978545 TTTATGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.23, C:0.00, G:0.47, T:0.30
Consensus pattern (22 bp):
AGGGGTTAAGGGTTAGTAGGTT
Found at i:19979272 original size:113 final size:113
Alignment explanation
Indices: 19979112--19979316 Score: 329
Period size: 113 Copynumber: 1.8 Consensus size: 113
19979102 GCGTTTTATA
* * * ** *
19979112 AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCCATTTTATATAGCAAAATTGTGT
1 AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCAATTTTACAAAGCAAAACAGTAT
*
19979177 CGTTTTATTTCAAATGAAATAATTTTTGCGTAAGCAATAGCGGCGTTT
66 CGTTTTATTCCAAATGAAATAATTTTTGCGTAAGCAATAGCGGCGTTT
* *
19979225 AAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGTGCAATTTTACAAAGCAAAACAGTAT
1 AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCAATTTTACAAAGCAAAACAGTAT
19979290 CGTTTTATTCCAAATGAAATAATTTTT
66 CGTTTTATTCCAAATGAAATAATTTTT
19979317 TACAAAGCAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 83 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (113 bp):
AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCAATTTTACAAAGCAAAACAGTAT
CGTTTTATTCCAAATGAAATAATTTTTGCGTAAGCAATAGCGGCGTTT
Found at i:19979295 original size:23 final size:23
Alignment explanation
Indices: 19979269--19979341 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
19979259 AATAGTGCAA
19979269 TTTTACAAAGCAAAACAGTATCG
1 TTTTACAAAGCAAAACAGTATCG
19979292 TTTTATTCCAAATG-AAATA-A-T-T--
1 TTTTA---CAAA-GCAAA-ACAGTATCG
19979314 TTTTACAAAGCAAAACAGTATCG
1 TTTTACAAAGCAAAACAGTATCG
19979337 TTTTA
1 TTTTA
19979342 TTCCAAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 22
0.64 0.00 0.36
Matches are distributed among these distances:
18 2 0.05
19 8 0.21
20 1 0.03
21 1 0.03
22 5 0.13
23 10 0.26
24 1 0.03
25 1 0.03
26 8 0.21
27 2 0.05
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (23 bp):
TTTTACAAAGCAAAACAGTATCG
Found at i:19979319 original size:45 final size:45
Alignment explanation
Indices: 19979269--19979362 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
19979259 AATAGTGCAA
19979269 TTTTACAAAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATT
1 TTTTACAAAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATT
19979314 TTTTACAAAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATT
1 TTTTACAAAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATT
19979359 TTTT
1 TTTT
19979363 GCGGCGTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (45 bp):
TTTTACAAAGCAAAACAGTATCGTTTTATTCCAAATGAAATAATT
Found at i:19979904 original size:11 final size:11
Alignment explanation
Indices: 19979888--19979913 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19979878 TTTTCCTCAT
19979888 TTTTCTTTTTG
1 TTTTCTTTTTG
19979899 TTTTCTTTTTG
1 TTTTCTTTTTG
19979910 TTTT
1 TTTT
19979914 GTTCTACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:19980192 original size:6 final size:5
Alignment explanation
Indices: 19980157--19980191 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
19980147 TTAATGTGGG
19980157 TTTAT TTTAT TTTAT TTTATT TTTATT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTAT TTT
19980192 TTTGAGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:19981595 original size:18 final size:18
Alignment explanation
Indices: 19981572--19981607 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19981562 TATTTTTCAT
*
19981572 TTGCTTCAATTTCTATGC
1 TTGCTTCAATTTCCATGC
*
19981590 TTGCTTTAATTTCCATGC
1 TTGCTTCAATTTCCATGC
19981608 CTTACAATAA
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:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (18 bp):
TTGCTTCAATTTCCATGC
Found at i:19982668 original size:43 final size:42
Alignment explanation
Indices: 19982618--19982722 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 42
19982608 GTGTTTGTAA
** *
19982618 AAAAGCGTCGCTAAAGGTCAT-TCTTTATAGTGGCGTTTGTGGT
1 AAAAGCGTCGCTAAAGGTCATATC-TT-TAGCAGCGTTTGTGGG
* * *
19982661 AGAAGCGTCGCAAAAAGTCATGATCTTTAGCAGCGTTTGTGGG
1 AAAAGCGTCGCTAAAGGTCAT-ATCTTTAGCAGCGTTTGTGGG
*
19982704 AAAAGCGCCGCTAAAGGTC
1 AAAAGCGTCGCTAAAGGTC
19982723 CTGGCTTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
43 46 0.92
44 2 0.04
45 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.27
Consensus pattern (42 bp):
AAAAGCGTCGCTAAAGGTCATATCTTTAGCAGCGTTTGTGGG
Found at i:19984770 original size:3 final size:3
Alignment explanation
Indices: 19984762--19984812 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
19984752 CTTTATTACT
19984762 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
19984810 ATC
1 ATC
19984813 GCAACTATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:19986500 original size:23 final size:23
Alignment explanation
Indices: 19986486--19986529 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19986476 CACCGATGTG
19986486 CCAAAATGAATTGCACCGTAGGT
1 CCAAAATGAATTGCACCGTAGGT
* *
19986509 CCAAAATGAATTACATCGTAG
1 CCAAAATGAATTGCACCGTAG
19986530 TGCTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (23 bp):
CCAAAATGAATTGCACCGTAGGT
Found at i:19987398 original size:30 final size:30
Alignment explanation
Indices: 19987363--19987497 Score: 135
Period size: 30 Copynumber: 4.5 Consensus size: 30
19987353 TTCAAACCAA
* * * *
19987363 ATCATATCATAACAAAACATATTATAATGT
1 ATCATATCATATCATAACGTATTATAACGT
* ** * *
19987393 ATCATATCATATCGTAACGTAACATAGCAT
1 ATCATATCATATCATAACGTATTATAACGT
19987423 ATCATATCATATCATAACGTATTATAACGT
1 ATCATATCATATCATAACGTATTATAACGT
** * ** *
19987453 ATCATATCATATCATGTCATATCGTAACAT
1 ATCATATCATATCATAACGTATTATAACGT
19987483 ATCATATCATATCAT
1 ATCATATCATATCAT
19987498 GTCCTACCCC
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (30 bp):
ATCATATCATATCATAACGTATTATAACGT
Found at i:19987400 original size:5 final size:5
Alignment explanation
Indices: 19987392--19987497 Score: 95
Period size: 5 Copynumber: 21.2 Consensus size: 5
19987382 TATTATAATG
* * * * * * *
19987392 TATCA TATCA TATCG TAACG TAACA TAGCA TATCA TATCA TATCA TAACG
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
* * * * * *
19987442 TATTA TAACG TATCA TATCA TATCA TGTCA TATCG TAACA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
19987492 TATCA T
1 TATCA T
19987498 GTCCTACCCC
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 80 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (5 bp):
TATCA
Found at i:20011071 original size:159 final size:160
Alignment explanation
Indices: 20010777--20011097 Score: 509
Period size: 159 Copynumber: 2.0 Consensus size: 160
20010767 CGGACTAAAA
* * **
20010777 TCGATCTTGACTTTCTATCGAATAGCCTTATCAGTTAATTCTCAAATTACGAACTGCTTTGAGTG
1 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTAATTCTCAAACCACGAACTGCTTTGAGTG
* * * * *
20010842 TGTGCTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTTACTTTTAGTAGGAAGG
66 TATACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGG
*
20010907 CTAATTCTCTCTATAAACGGAAACTATGCG
131 CTAATTCTCTCTATAAACGAAAACTATGCG
*
20010937 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTT-ATTCTCAAACCACGAATTGCTTTGAGTG
1 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTAATTCTCAAACCACGAACTGCTTTGAGTG
*
20011001 TATACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAATTTTATTAACTTTCAGAAGGAAGG
66 TATACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGG
* *
20011066 TTAATTCTCTCTATGAACGAAAACTATGCG
131 CTAATTCTCTCTATAAACGAAAACTATGCG
20011096 TC
1 TC
20011098 TTTGAAATTA
Statistics
Matches: 147, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
159 113 0.77
160 34 0.23
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (160 bp):
TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTAATTCTCAAACCACGAACTGCTTTGAGTG
TATACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGG
CTAATTCTCTCTATAAACGAAAACTATGCG
Done.