Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 157 of 187
Found at i:46419544 original size:9 final size:9
Alignment explanation
Indices: 46419530--46419576 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
46419520 AGGAGAAAAT
46419530 AATAATAAA
1 AATAATAAA
*
46419539 AATAATAAT
1 AATAATAAA
*
46419548 AATAATAAT
1 AATAATAAA
46419557 AA-AAT-AA
1 AATAATAAA
46419564 AATAA-AAA
1 AATAATAAA
46419572 AATAA
1 AATAA
46419577 AAGAACACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 3 0.09
8 12 0.35
9 19 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAATAAA
Found at i:46419783 original size:20 final size:19
Alignment explanation
Indices: 46419758--46419823 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
46419748 CTTGTTTAAA
*
46419758 TTGATTTGGTTCTCAATCTT
1 TTGATTTGATTCTCAATC-T
** * *
46419778 TTGATTTCTTTC-CATTACA
1 TTGATTTGATTCTCAAT-CT
46419797 TTGATTTGATTCTCAATCCT
1 TTGATTTGATTCTCAAT-CT
46419817 TTGATTT
1 TTGATTT
46419824 CTTTCCATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.18, C:0.17, G:0.11, T:0.55
Consensus pattern (19 bp):
TTGATTTGATTCTCAATCT
Found at i:46419802 original size:19 final size:19
Alignment explanation
Indices: 46419778--46419834 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
46419768 TCTCAATCTT
46419778 TTGATTTCTTTCCATTACA
1 TTGATTTCTTTCCATTACA
** * * *
46419797 TTGATTTGATTCTCAATCCT
1 TTGATTTCTTTC-CATTACA
46419817 TTGATTTCTTTCCATTAC
1 TTGATTTCTTTCCATTAC
46419835 TATTTTGCTT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (19 bp):
TTGATTTCTTTCCATTACA
Found at i:46419811 original size:39 final size:39
Alignment explanation
Indices: 46419757--46419834 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
46419747 TCTTGTTTAA
* *
46419757 ATTGATTTGGTTCTCAATCTTTTGATTTCTTTCCATTAC
1 ATTGATTTGATTCTCAATCCTTTGATTTCTTTCCATTAC
46419796 ATTGATTTGATTCTCAATCCTTTGATTTCTTTCCATTAC
1 ATTGATTTGATTCTCAATCCTTTGATTTCTTTCCATTAC
46419835 TATTTTGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (39 bp):
ATTGATTTGATTCTCAATCCTTTGATTTCTTTCCATTAC
Found at i:46420477 original size:44 final size:44
Alignment explanation
Indices: 46420420--46420579 Score: 250
Period size: 44 Copynumber: 3.6 Consensus size: 44
46420410 TTTGTTTACT
* *
46420420 TTCAACCTATTCCACTGCTAACCAGGGAGATAGGATTCTCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
46420464 TTCAGCCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
46420508 TTCAACCTATTCCACTACTGACAAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
46420552 TTCAATCTATTCCACTGCT-ACCTAGGGA
1 TTCAACCTATTCCACTGCTGACC-AGGGA
46420580 AGTAGAATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
43 2 0.02
44 104 0.98
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:46420737 original size:89 final size:89
Alignment explanation
Indices: 46420644--46420810 Score: 307
Period size: 89 Copynumber: 1.9 Consensus size: 89
46420634 GCTATCTTCG
*
46420644 ATCTGCTCCGCTACTGCTTAGGGAGATAATATCTGAAATCTTCAATCTATTCCACTGTTGTCCAG
1 ATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAG
46420709 GGAAGTAAAATTATGCCATCTTTA
66 GGAAGTAAAATTATGCCATCTTTA
**
46420733 ATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTTTAG
1 ATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAG
46420798 GGAAGTAAAATTA
66 GGAAGTAAAATTA
46420811 CTGGCTTCAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (89 bp):
ATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAG
GGAAGTAAAATTATGCCATCTTTA
Found at i:46420825 original size:221 final size:221
Alignment explanation
Indices: 46420531--46420942 Score: 632
Period size: 221 Copynumber: 1.9 Consensus size: 221
46420521 ACTACTGACA
* *
46420531 AGGGAGATAGGATTCACAATCTTCAATCTATTCCACTGCTACCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATTCACAATCTTCAATCTATTCCACTGCTACCTAGGGAAGTAAAATTACTAGCT
*
46420596 TCAATGTACTCCGCTGTAACCACAGAGAGGTAAAAT-TCG-CTATCTTCGATCTGCTCCGCTACT
66 TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCT-GTC-ATCTTCGATCTGCTCCGCTACT
* * *
46420659 GCTTAGGGAGATAATATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAAAATTATG
129 GCTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAAAATTATG
46420724 CCATCTTTAATCTGCTCCGCTACTGCTT
194 CCATCTTTAATCTGCTCCGCTACTGCTT
* * *** *
46420752 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTTTAGGGAAGTAAAATTACTGGC
1 AGGGAGATAAGAT-TCACAATCTTCAATCTATTCCACTGCTACCTAGGGAAGTAAAATTACTAGC
* *
46420816 TTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCTGTCATCTTCGATCTGCTCCGCTACTG
65 TTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGTCATCTTCGATCTGCTCCGCTACTG
* *
46420881 CTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCTAGGGAAGTAGAATTA
130 CTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAAAATTA
46420943 CTGGCTTCAA
Statistics
Matches: 172, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
221 168 0.98
222 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (221 bp):
AGGGAGATAAGATTCACAATCTTCAATCTATTCCACTGCTACCTAGGGAAGTAAAATTACTAGCT
TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGTCATCTTCGATCTGCTCCGCTACTGC
TTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAAAATTATGCC
ATCTTTAATCTGCTCCGCTACTGCTT
Found at i:46420931 original size:44 final size:45
Alignment explanation
Indices: 46420637--46420933 Score: 135
Period size: 44 Copynumber: 6.7 Consensus size: 45
46420627 AAAATTCGCT
* * * * * *
46420637 ATCTTCGATCTGCTCCGCTACTG-CTTAGGGAGATAATATCTGAA
1 ATCTTCAATCTACTCCACTATTGTCTTAGGGAAATAAAATCTGAA
* * * * * **
46420681 ATCTTCAATCTATTCCACTGTTGTC-CAGGGAAGTAAAATTATGCC
1 ATCTTCAATCTACTCCACTATTGTCTTAGGGAAATAAAA-TCTGAA
* * * * * *
46420726 ATCTTTAATCTGCTCCGCTACTG-CTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGTCTTAGGGAAATAAAATCTGAA
* * *
46420770 ATCTTCAATCTATTCCACTGTTGT-TTAGGGAAGTAAAATTACTG--
1 ATCTTCAATCTACTCCACTATTGTCTTAGGGAAATAAAA-T-CTGAA
* * * * *** ** ** **
46420814 -GCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAATCTGTC
1 ATCTTCAATCTACTCCACTATTGTCTTAGGGAAATAAAATCTGAA
* * * * *
46420858 ATCTTCGATCTGCTCCGCTACTG-CTTAGGGAAATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGTCTTAGGGAAATAAAATCTGAA
*
46420902 ATCTTCAATCTATTCCACTATTGTC-TAGGGAA
1 ATCTTCAATCTACTCCACTATTGTCTTAGGGAA
46420934 GTAGAATTAC
Statistics
Matches: 175, Mismatches: 67, Indels: 22
0.66 0.25 0.08
Matches are distributed among these distances:
42 3 0.02
43 17 0.10
44 108 0.62
45 44 0.25
46 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (45 bp):
ATCTTCAATCTACTCCACTATTGTCTTAGGGAAATAAAATCTGAA
Found at i:46421381 original size:132 final size:132
Alignment explanation
Indices: 46420723--46421386 Score: 1085
Period size: 132 Copynumber: 5.0 Consensus size: 132
46420713 GTAAAATTAT
** *
46420723 GCCATCTTTAATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
1 GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
** * * *
46420788 TGTTGTTTAGGGAAGTAAAATTACTGGCTTCAATGTACTCCATTGTAACCACAGGGAGGTAAAAT
66 TGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
*
46420853 CT
131 CC
* * *
46420855 GTCATCTTCGATCTGCTCCGCTACTGCTTAGGGAAATAAGATCTGAAATCTTCAATCTATTCCAC
1 GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
* * *
46420920 TATTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT
66 TGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
46420985 CC
131 CC
* * * *
46420987 ACCATCTTCGATCTACTCCACTACTGCTTAGCGAGATAAGATCTGAAATATTCAATCTATTCCAC
1 GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
*
46421052 TGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
66 TGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
46421117 CC
131 CC
* *
46421119 ACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCTAC
1 GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
*
46421184 TGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
66 TGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
46421249 CC
131 CC
*
46421251 GCCATCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
1 GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
* *
46421316 TGTTGTCCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTATAACCACAGAGAGGTAAAAT
66 TGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
*
46421381 CT
131 CC
46421383 GCCA
1 GCCA
46421387 CCTTTGATAG
Statistics
Matches: 501, Mismatches: 31, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 501 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (132 bp):
GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
TGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
CC
Found at i:46421715 original size:9 final size:9
Alignment explanation
Indices: 46421698--46421734 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46421688 TGAGTTTTTG
46421698 AATTCGAAT
1 AATTCGAAT
*
46421707 AACTCGAAT
1 AATTCGAAT
46421716 AATTCGAAT
1 AATTCGAAT
46421725 AATTCGAAT
1 AATTCGAAT
46421734 A
1 A
46421735 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:46422659 original size:5 final size:5
Alignment explanation
Indices: 46422649--46422674 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46422639 GAACAAATAT
46422649 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
46422675 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:46422774 original size:5 final size:5
Alignment explanation
Indices: 46422764--46422789 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46422754 CTCGAAAATT
46422764 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
46422790 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:46431565 original size:3 final size:3
Alignment explanation
Indices: 46431557--46431613 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
46431547 NNNNNNNNNN
46431557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46431605 TAA TAA TAA
1 TAA TAA TAA
46431614 AAGAACACAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46431817 original size:20 final size:18
Alignment explanation
Indices: 46431792--46431857 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 18
46431782 CTTGTTTACA
46431792 TTGATTTGATTCTCAATCTT
1 TTGATTTGATTC-CAATC-T
** * *
46431812 TTGATTTCTTTCCATTACA
1 TTGATTTGATTCCAAT-CT
46431831 TTGATTTGATTCACAATCCT
1 TTGATTTGATTC-CAAT-CT
46431851 TTGATTT
1 TTGATTT
46431858 CTTTCCGTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (18 bp):
TTGATTTGATTCCAATCT
Found at i:46431841 original size:39 final size:39
Alignment explanation
Indices: 46431787--46431868 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
46431777 AAAATCTTGT
* *
46431787 TTACATTGATTTGATTCTCAATCTTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCACAATCCTTTGATTTCTTTCCA
*
46431826 TTACATTGATTTGATTCACAATCCTTTGATTTCTTTCCG
1 TTACATTGATTTGATTCACAATCCTTTGATTTCTTTCCA
46431865 TTAC
1 TTAC
46431869 TGTTTTGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.21, C:0.20, G:0.09, T:0.51
Consensus pattern (39 bp):
TTACATTGATTTGATTCACAATCCTTTGATTTCTTTCCA
Found at i:46440633 original size:18 final size:18
Alignment explanation
Indices: 46440610--46440689 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
46440600 ACCACTATAA
46440610 TATATTTTATATAATATT
1 TATATTTTATATAATATT
* * *
46440628 TATATTTTGTAT-GTAAT
1 TATATTTTATATAATATT
* *
46440645 TAT-TTTTCTATTAAAATT
1 TATATTTTATA-TAATATT
*
46440663 TATTTTATATATATAATA-T
1 TATATT-T-TATATAATATT
46440682 TATATTTT
1 TATATTTT
46440690 TAAATTTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
16 6 0.13
17 8 0.17
18 17 0.36
19 8 0.17
20 5 0.11
21 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATTTTATATAATATT
Found at i:46446861 original size:9 final size:9
Alignment explanation
Indices: 46446847--46446872 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
46446837 GGAATACGTG
46446847 GTTGTACAC
1 GTTGTACAC
46446856 GTTGTACAC
1 GTTGTACAC
46446865 GTTGTACA
1 GTTGTACA
46446873 AAGCTTATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (9 bp):
GTTGTACAC
Found at i:46449483 original size:20 final size:21
Alignment explanation
Indices: 46449458--46449504 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
46449448 GAAAATATAA
46449458 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTGAAATTTTTGA-AAATT
46449478 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
46449498 ATTTTGA
1 ATTTTGA
46449505 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:46449489 original size:19 final size:20
Alignment explanation
Indices: 46449458--46449509 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
46449448 GAAAATATAA
46449458 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTG-AATTTTTGA-AAATT
46449478 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
46449498 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
46449510 TTTTTGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:46450234 original size:6 final size:6
Alignment explanation
Indices: 46450223--46450251 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
46450213 TTAAAATTTT
46450223 AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAAT
46450252 TCCATGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:46451444 original size:18 final size:19
Alignment explanation
Indices: 46451401--46451445 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
46451391 ATTTTCGAAA
* *
46451401 TTTTTATATTTTTTTGTAT
1 TTTTTAAATTATTTTGTAT
*
46451420 ATTTTAAATTATTTT-TAT
1 TTTTTAAATTATTTTGTAT
46451438 TTTTTAAA
1 TTTTTAAA
46451446 ATTTTAAATA
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:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTAAATTATTTTGTAT
Found at i:46452295 original size:47 final size:47
Alignment explanation
Indices: 46452226--46452321 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
46452216 ACTAACTCAA
46452226 TTCGAGTTGAATTTCACAATTCGAATAACATATTAGTGTAAATACCT
1 TTCGAGTTGAATTTCACAATTCGAATAACATATTAGTGTAAATACCT
*
46452273 TTCGAGTTGAATTTCACAATTCGAATAACATATTAGTGTAAATTCCT
1 TTCGAGTTGAATTTCACAATTCGAATAACATATTAGTGTAAATACCT
46452320 TT
1 TT
46452322 TTGGTCAGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (47 bp):
TTCGAGTTGAATTTCACAATTCGAATAACATATTAGTGTAAATACCT
Found at i:46452397 original size:25 final size:23
Alignment explanation
Indices: 46452368--46452433 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 23
46452358 CTCTCATAAC
46452368 AAAAAATTTAAAAATAAATTATTT
1 AAAAAATTTAAAAATAAATT-TTT
* *
46452392 ATAAAAATTTCAAAATTTATATTTTT
1 A-AAAAATTT-AAAA-ATAAATTTTT
46452418 AAAAAATTATAAAAAT
1 AAAAAATT-TAAAAAT
46452434 TCTAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 19 0.54
26 9 0.26
27 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAAAATTTAAAAATAAATTTTT
Found at i:46452446 original size:2 final size:2
Alignment explanation
Indices: 46452439--46452465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46452429 AAAATTCTAA
46452439 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46452466 AAGTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46452954 original size:2 final size:2
Alignment explanation
Indices: 46452947--46452988 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
46452937 ATAAAATGTA
46452947 CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT
46452989 TTAACTAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:46455423 original size:21 final size:21
Alignment explanation
Indices: 46455399--46455438 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46455389 AAGGTTGAAA
46455399 CTAGCCTTGATGGGTTAGATG
1 CTAGCCTTGATGGGTTAGATG
**
46455420 CTAGGGTTGATGGGTTAGA
1 CTAGCCTTGATGGGTTAGA
46455439 GGCTGGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.10, G:0.38, T:0.33
Consensus pattern (21 bp):
CTAGCCTTGATGGGTTAGATG
Found at i:46455447 original size:21 final size:21
Alignment explanation
Indices: 46455405--46455449 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
46455395 GAAACTAGCC
*
46455405 TTGATGGGTTAGATGCTAGGG
1 TTGATGGGTTAGAGGCTAGGG
*
46455426 TTGATGGGTTAGAGGCTGGGG
1 TTGATGGGTTAGAGGCTAGGG
46455447 TTG
1 TTG
46455450 CTAGGATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.04, G:0.47, T:0.33
Consensus pattern (21 bp):
TTGATGGGTTAGAGGCTAGGG
Found at i:46456082 original size:15 final size:12
Alignment explanation
Indices: 46456046--46456086 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
46456036 TCAAAAGAAA
46456046 AAAATAAATAAT
1 AAAATAAATAAT
46456058 AAAATAAATAAT
1 AAAATAAATAAT
46456070 AACAATGATAATAAT
1 AA-AAT-A-AATAAT
46456085 AA
1 AA
46456087 TAGTGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.54
13 3 0.12
14 1 0.04
15 8 0.31
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:46456155 original size:4 final size:4
Alignment explanation
Indices: 46456146--46456175 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
46456136 TAAGGACAAG
*
46456146 TAAA TAAA TAAA TAAA TACA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
46456176 TAGAGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:46456297 original size:19 final size:19
Alignment explanation
Indices: 46456256--46456297 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
46456246 AATTTGTAAT
*
46456256 AAAATAGATAATAATAGAT
1 AAAATAGATAATAATAGAA
*
46456275 AAAATA-ATAATAGTGAGAA
1 AAAATAGATAATAAT-AGAA
46456294 AAAA
1 AAAA
46456298 ACAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (19 bp):
AAAATAGATAATAATAGAA
Found at i:46456348 original size:4 final size:4
Alignment explanation
Indices: 46456313--46456359 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
46456303 AATAAAAAGG
* ** *
46456313 AAAT AAAT AGAT AAAT GTAT AAAT ATAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
46456360 AAGGGAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:46463272 original size:24 final size:25
Alignment explanation
Indices: 46463244--46463398 Score: 104
Period size: 24 Copynumber: 6.2 Consensus size: 25
46463234 ATGTCACAGA
*
46463244 AAGCTCATAAGAGCC-TTAATCGGG
1 AAGCTCATAAGAGCCATTAATCAGG
** * *
46463268 AAGCTCATTTGAGCCAAT-ATCGGG
1 AAGCTCATAAGAGCCATTAATCAGG
* * *
46463292 AAGCTCATGAGAGATCCTTTTATCAGG
1 AAGCTCAT-A-AGAGCCATTAATCAGG
* * *
46463319 AAGCT-TTGGAGAGCCAATT-ATCAAG
1 AAGCTCAT-AAGAGCC-ATTAATCAGG
* * *
46463344 AAGCTCATATGAGCCA-TAAACGGG
1 AAGCTCATAAGAGCCATTAATCAGG
*
46463368 AAGCTCAAAAGAGCCATTAATCAGG
1 AAGCTCATAAGAGCCATTAATCAGG
46463393 AAGCTC
1 AAGCTC
46463399 GTGAGAGTCA
Statistics
Matches: 99, Mismatches: 24, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
23 1 0.01
24 45 0.45
25 33 0.33
26 10 0.10
27 10 0.10
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (25 bp):
AAGCTCATAAGAGCCATTAATCAGG
Found at i:46463381 original size:49 final size:50
Alignment explanation
Indices: 46463328--46463424 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 50
46463318 GAAGCTTTGG
46463328 AGAGCCAATT-ATCAAGAAGCTCAT-ATGAGCCATA-AACGGGAAGCTCAAA
1 AGAGCC-ATTAATCAAGAAGCTCATGA-GAGCCATATAACGGGAAGCTCAAA
* * * *
46463377 AGAGCCATTAATCAGGAAGCTCGTGAGAGTCATATAACGGGATGCTCA
1 AGAGCCATTAATCAAGAAGCTCATGAGAGCCATATAACGGGAAGCTCA
46463425 TTAAAGCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 3 0.07
49 25 0.61
50 13 0.32
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.19
Consensus pattern (50 bp):
AGAGCCATTAATCAAGAAGCTCATGAGAGCCATATAACGGGAAGCTCAAA
Found at i:46465396 original size:23 final size:22
Alignment explanation
Indices: 46465353--46465396 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
46465343 TTCTAAGTCG
46465353 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
46465376 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
46465397 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:46465507 original size:45 final size:45
Alignment explanation
Indices: 46465442--46465534 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
46465432 ATAGATACTC
* *
46465442 GGTGGATTCAGCACAAAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGAATCAGCACAAAGCAACCACCTTACTAATCAATGATGTCT
* *
46465487 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTT
1 GGTGGAATCAGCACAAAGCAACCACCTTACTAATCAATGATGTCT
46465532 GGT
1 GGT
46465535 TCACATAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (45 bp):
GGTGGAATCAGCACAAAGCAACCACCTTACTAATCAATGATGTCT
Found at i:46465598 original size:51 final size:50
Alignment explanation
Indices: 46465539--46465676 Score: 163
Period size: 51 Copynumber: 2.7 Consensus size: 50
46465529 TTTGGTTCAC
* *
46465539 ATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATATACG
1 ATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCG--ATACG
* * * * *
46465591 -TAGTAGCCTGCACATGGTACTACACACGTGATCGA-AACTATCTGGTACG
1 ATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCGATACG
46465640 TATAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 -ATAGTAGCCTGCACATAGTACTACACACGTGACCAT
46465677 CACTTTCACT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
49 4 0.05
50 2 0.03
51 65 0.89
52 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
ATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATACG
Found at i:46465696 original size:51 final size:50
Alignment explanation
Indices: 46465537--46465706 Score: 155
Period size: 51 Copynumber: 3.3 Consensus size: 50
46465527 TGTTTGGTTC
* * * *
46465537 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATAT
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATCC-TTAT
* * * **
46465588 ACGTAGTAGCCTGCACATGGTACTACACACGTGATCGA-AACTAT-CTGGT
1 ACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACTATCCTTAT
* * *
46465637 ACGTATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTTTCACTTTT
1 AC--ATAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATC-CTTAT
* *
46465690 ACATAGTGGCCTACACA
1 ACATAGTAGCCTGCACA
46465707 CAATCCGTGC
Statistics
Matches: 95, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
49 3 0.03
50 3 0.03
51 82 0.86
52 2 0.02
53 5 0.05
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATCCTTAT
Found at i:46469149 original size:21 final size:21
Alignment explanation
Indices: 46469087--46469174 Score: 61
Period size: 21 Copynumber: 4.1 Consensus size: 21
46469077 CCTGATCAGT
* *
46469087 ATACGACACA-TAAGTGCCTG
1 ATACGACACACGAGGTGCCTG
* ** *
46469107 AAACGACACACGAGACGTCTG
1 ATACGACACACGAGGTGCCTG
*
46469128 ATACGACATACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
** *
46469149 AAATACGACACATAAAGTGCCTG
1 --ATACGACACACGAGGTGCCTG
46469172 ATA
1 ATA
46469175 TGCAACACAT
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
20 9 0.18
21 24 0.48
23 17 0.34
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.17
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:46469196 original size:23 final size:23
Alignment explanation
Indices: 46469142--46469196 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
46469132 GACATACGAG
* *
46469142 GTGCCTGAAATACGACACATAAA
1 GTGCCTGATATACAACACATAAA
* *
46469165 GTGCCTGATATGCAACACATCAA
1 GTGCCTGATATACAACACATAAA
46469188 GTGCCTGAT
1 GTGCCTGAT
46469197 CGAAAAAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (23 bp):
GTGCCTGATATACAACACATAAA
Found at i:46470238 original size:6 final size:6
Alignment explanation
Indices: 46470227--46470259 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
46470217 TTTTCCTTCC
46470227 TTTTCT TTTTCT TTTTC- TTTTCT TCTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTT
46470260 CCCCTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:46470246 original size:17 final size:18
Alignment explanation
Indices: 46470226--46470259 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
46470216 TTTTTCCTTC
46470226 CTTTTCTT-TTTCTTTTT
1 CTTTTCTTCTTTCTTTTT
46470243 CTTTTCTTCTTTCTTTT
1 CTTTTCTTCTTTCTTTT
46470260 CCCCTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
CTTTTCTTCTTTCTTTTT
Found at i:46476555 original size:25 final size:26
Alignment explanation
Indices: 46476530--46476708 Score: 81
Period size: 25 Copynumber: 7.1 Consensus size: 26
46476520 CCCATGCGAG
***
46476530 CATGTAATCAGGAAGCTCTTTTGAGC
1 CATGTAATCAGGAAGCTCAAGTGAGC
* *
46476556 CATATAA-CGGGAAGCTCAAGTGAGC
1 CATGTAATCAGGAAGCTCAAGTGAGC
*
46476581 CATGTAAT-AGGAAGCTCATA-AGAGC
1 CATGTAATCAGGAAGCTCA-AGTGAGC
* * *
46476606 C--GTAATCGGGAAGCTCATGAGAGC
1 CATGTAATCAGGAAGCTCAAGTGAGC
* *
46476630 CAT-T-ATC-GAAAAGCTCATGAGAGAGC
1 CATGTAATCAG-GAAGCTCA--AGTGAGC
* * **
46476656 C-TTTTATTGGGAAGCTCAAGTGAGC
1 CATGTAATCAGGAAGCTCAAGTGAGC
* * * *
46476681 TAT-TAATCGGGAAGCTCATGAGAGC
1 CATGTAATCAGGAAGCTCAAGTGAGC
46476706 CAT
1 CAT
46476709 ATAACGAGAT
Statistics
Matches: 119, Mismatches: 21, Indels: 27
0.71 0.13 0.16
Matches are distributed among these distances:
23 6 0.05
24 25 0.21
25 62 0.52
26 16 0.13
27 9 0.08
28 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (26 bp):
CATGTAATCAGGAAGCTCAAGTGAGC
Found at i:46476622 original size:24 final size:24
Alignment explanation
Indices: 46476590--46476706 Score: 85
Period size: 24 Copynumber: 4.7 Consensus size: 24
46476580 CCATGTAATA
*
46476590 GGAAGCTCATAAGAGCCGTAATCG
1 GGAAGCTCATAAGAGCCTTAATCG
*
46476614 GGAAGCTCATGAGAGCCATT-ATCG
1 GGAAGCTCATAAGAGCC-TTAATCG
** * *
46476638 AAAAGCTCATGAGAGAGCCTTTTATTG
1 GGAAGCTCAT-A-AGAGCC-TTAATCG
* *
46476665 GGAAGCTCA-AGTGAGCTATTAATCG
1 GGAAGCTCATA-AGAGC-CTTAATCG
*
46476690 GGAAGCTCATGAGAGCC
1 GGAAGCTCATAAGAGCC
46476707 ATATAACGAG
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
24 28 0.39
25 25 0.35
26 8 0.11
27 10 0.14
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCTTAATCG
Found at i:46476670 original size:27 final size:27
Alignment explanation
Indices: 46476608--46476704 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 27
46476598 ATAAGAGCCG
*
46476608 TAATCGGGAAGCTCAT--GAGAGCCAT
1 TAATCGGGAAGCTCATGAGAGAGCTAT
**
46476633 T-ATCGAAAAGCTCATGAGAGAGCCT-T
1 TAATCGGGAAGCTCATGAGAGAG-CTAT
* * *
46476659 TTATTGGGAAGCTCA--AGTGAGCTAT
1 TAATCGGGAAGCTCATGAGAGAGCTAT
46476684 TAATCGGGAAGCTCATGAGAG
1 TAATCGGGAAGCTCATGAGAG
46476705 CCATATAACG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
24 14 0.25
25 20 0.36
26 7 0.13
27 14 0.25
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (27 bp):
TAATCGGGAAGCTCATGAGAGAGCTAT
Found at i:46477094 original size:12 final size:12
Alignment explanation
Indices: 46477077--46477124 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
46477067 ATAAATACCA
46477077 AAAAATTATTTT
1 AAAAATTATTTT
*
46477089 AAAAATTA---A
1 AAAAATTATTTT
*
46477098 AAAAAGTATTTT
1 AAAAATTATTTT
46477110 AAAAA-TATTTT
1 AAAAATTATTTT
46477121 AAAA
1 AAAA
46477125 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
9 7 0.23
11 10 0.33
12 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:46477102 original size:21 final size:21
Alignment explanation
Indices: 46477076--46477115 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
46477066 AATAAATACC
*
46477076 AAAAAATTATTTTAAAAATTA
1 AAAAAAGTATTTTAAAAATTA
46477097 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
46477116 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAAAGTATTTTAAAAATTA
Found at i:46477130 original size:17 final size:17
Alignment explanation
Indices: 46477108--46477207 Score: 94
Period size: 17 Copynumber: 5.7 Consensus size: 17
46477098 AAAAAGTATT
46477108 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
46477125 TTAAAAAAATTTTAAAA
1 TTAAAAATATTTTAAAA
***
46477142 TTAAAAA-ATAAAAAAATA
1 TTAAAAATAT-TTTAAA-A
46477160 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTTAAAA
* *
46477179 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTTAAAA
*
46477196 TTTAAAATATTT
1 TTAAAAATATTT
46477208 ATTATATCAG
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
16 2 0.03
17 51 0.76
18 1 0.01
19 1 0.01
20 10 0.15
21 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:46477179 original size:10 final size:11
Alignment explanation
Indices: 46477153--46477178 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
46477143 TAAAAAATAA
46477153 AAAAATATTTT
1 AAAAATATTTT
46477164 AAAAATATTTT
1 AAAAATATTTT
46477175 AAAA
1 AAAA
46477179 TTAAAAAAAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:46477186 original size:55 final size:55
Alignment explanation
Indices: 46477087--46477202 Score: 198
Period size: 54 Copynumber: 2.1 Consensus size: 55
46477077 AAAAATTATT
* *
46477087 TTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAA
1 TTAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAA
46477142 TTAAAAAATAAAAAAA-TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAA
1 TTAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAA
*
46477196 TTTAAAA
1 TTAAAAA
46477203 TATTTATTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
54 43 0.74
55 15 0.26
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (55 bp):
TTAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAA
Found at i:46477207 original size:9 final size:9
Alignment explanation
Indices: 46477154--46477208 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
46477144 AAAAAATAAA
46477154 AAAATATTTT
1 AAAATA-TTT
46477164 AAAAATATTT
1 -AAAATATTT
* *
46477174 TAAA-ATTA
1 AAAATATTT
*
46477182 AAAAAATTT
1 AAAATATTT
46477191 AAAA-ATTT
1 AAAATATTT
46477199 AAAATATTT
1 AAAATATTT
46477208 A
1 A
46477209 TTATATCAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 14 0.37
9 15 0.39
10 3 0.08
11 6 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAATATTT
Found at i:46485660 original size:20 final size:21
Alignment explanation
Indices: 46485615--46485660 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
46485605 TTACCCCAAA
*
46485615 CTCCCAAAACTCTTTACTTTC
1 CTCCCAAAACTCTTTACTTCC
46485636 C-CCCAAAACT-TTTACTTCC
1 CTCCCAAAACTCTTTACTTCC
46485655 CTCCCA
1 CTCCCA
46485661 TCCGTTGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 13 0.57
21 1 0.04
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (21 bp):
CTCCCAAAACTCTTTACTTCC
Found at i:46487342 original size:18 final size:19
Alignment explanation
Indices: 46487308--46487343 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
46487298 TTAATTCTAA
46487308 AAAATGAAAATAAATAAAG
1 AAAATGAAAATAAATAAAG
*
46487327 AAAATTAAAA-AAATAAA
1 AAAATGAAAATAAATAAA
46487344 ATGGTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAATGAAAATAAATAAAG
Found at i:46487623 original size:21 final size:21
Alignment explanation
Indices: 46487599--46487640 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
46487589 TCTATCAAAC
*
46487599 TTCAGGTTTTTCCTGTAAAAA
1 TTCAAGTTTTTCCTGTAAAAA
*
46487620 TTCAAGTTTTTCCTTTAAAAA
1 TTCAAGTTTTTCCTGTAAAAA
46487641 CCTGAGTAAT
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:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (21 bp):
TTCAAGTTTTTCCTGTAAAAA
Found at i:46489909 original size:2 final size:2
Alignment explanation
Indices: 46489904--46489939 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46489894 ACACACACAC
46489904 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
46489940 TCTTGACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46498033 original size:27 final size:27
Alignment explanation
Indices: 46497995--46498049 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
46497985 CATTACTCTC
46497995 GGCAATATCACTATGTATCATAGAAAG
1 GGCAATATCACTATGTATCATAGAAAG
46498022 GGCAATATCACTATGTATCATAGAAAG
1 GGCAATATCACTATGTATCATAGAAAG
46498049 G
1 G
46498050 CTTAATGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (27 bp):
GGCAATATCACTATGTATCATAGAAAG
Found at i:46501837 original size:20 final size:20
Alignment explanation
Indices: 46501785--46501874 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
46501775 AGAGGCGTCT
46501785 AGTGCAAGACAGAGGCA-TAA
1 AGTGCAA-ACAGAGGCACTAA
* ** *
46501805 TTGTGCAGTCAGAGGCATTAA
1 -AGTGCAAACAGAGGCACTAA
*
46501826 AGTGCAAACAGAGACACTAA
1 AGTGCAAACAGAGGCACTAA
** * *
46501846 AGTGTGAACAAAGGCACCAA
1 AGTGCAAACAGAGGCACTAA
46501866 AGTGCAAAC
1 AGTGCAAAC
46501875 CCATACAAGT
Statistics
Matches: 53, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 45 0.85
21 8 0.15
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (20 bp):
AGTGCAAACAGAGGCACTAA
Found at i:46506658 original size:15 final size:15
Alignment explanation
Indices: 46506638--46506668 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46506628 AAATATTTTT
46506638 ATTTTTTATTTTTAA
1 ATTTTTTATTTTTAA
46506653 ATTTTTTATTTTTAA
1 ATTTTTTATTTTTAA
46506668 A
1 A
46506669 ATACTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTTTATTTTTAA
Found at i:46506698 original size:15 final size:15
Alignment explanation
Indices: 46506646--46506698 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
46506636 TTATTTTTTA
46506646 TTTTTAAATTT-TTT
1 TTTTTAAATTTATTT
* *
46506660 ATTTTTAAA-ATACTT
1 -TTTTTAAATTTATTT
46506675 TTTTT--ATTTATTT
1 TTTTTAAATTTATTT
46506688 TTTTTAAATTT
1 TTTTTAAATTT
46506699 TGGTGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 1 0.03
13 9 0.30
14 6 0.20
15 14 0.47
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTAAATTTATTT
Found at i:46507800 original size:16 final size:18
Alignment explanation
Indices: 46507767--46507800 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
46507757 TATTAATAGG
46507767 GTGAATTTTGTGTTAATT
1 GTGAATTTTGTGTTAATT
46507785 GTGAA-TTTGT-TTAATT
1 GTGAATTTTGTGTTAATT
46507801 TTACATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (18 bp):
GTGAATTTTGTGTTAATT
Found at i:46511998 original size:17 final size:18
Alignment explanation
Indices: 46511968--46512001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46511958 TCCCAGATGA
*
46511968 GTTTTTCCATTAAAAAGT
1 GTTTTTCCACTAAAAAGT
46511986 GTTTTTCC-CTAAAAAG
1 GTTTTTCCACTAAAAAG
46512002 CAATAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (18 bp):
GTTTTTCCACTAAAAAGT
Found at i:46512573 original size:13 final size:13
Alignment explanation
Indices: 46512552--46512613 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
46512542 ACACTCAAAT
46512552 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
46512565 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
46512578 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
*
46512591 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
46512604 TTTTCAAAAG
1 TTTTCAAAAG
46512614 TATTGCCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 3 0.07
13 34 0.83
14 4 0.10
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:46515212 original size:64 final size:64
Alignment explanation
Indices: 46515091--46515212 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
46515081 TCGAACCATA
* * * *
46515091 CACATATGTATGTAAAATTCATAAATTGAATTCAGCTTAAGAACTTTATAACCTATATTTGAAT
1 CACATATGTATATAAAATTCATAAATTGAATTCAGCTCAAGAACTTTAAAACATATATTTGAAT
* * *
46515155 CACATATGTATATAAAATTCGTACATT-AATTTCAGCTCAAGAACTTTAAAATATATAT
1 CACATATGTATATAAAATTCATAAATTGAA-TTCAGCTCAAGAACTTTAAAACATATAT
46515213 ATATTCAAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 48 0.96
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (64 bp):
CACATATGTATATAAAATTCATAAATTGAATTCAGCTCAAGAACTTTAAAACATATATTTGAAT
Found at i:46518312 original size:13 final size:14
Alignment explanation
Indices: 46518286--46518314 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46518276 TGACTTTAAC
46518286 AAATAAAGAAATAA
1 AAATAAAGAAATAA
46518300 AAATAAA-AAATAA
1 AAATAAAGAAATAA
46518313 AA
1 AA
46518315 TTATAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (14 bp):
AAATAAAGAAATAA
Found at i:46526128 original size:24 final size:24
Alignment explanation
Indices: 46526082--46526128 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
46526072 TGAATTGAAA
*
46526082 ATGATGAAATGTAAATTGAGTTAT
1 ATGATGAAATGGAAATTGAGTTAT
*
46526106 ATGATGAATTGGATAATTG-GTTA
1 ATGATGAAATGGA-AATTGAGTTA
46526129 CCTTAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (24 bp):
ATGATGAAATGGAAATTGAGTTAT
Found at i:46530894 original size:15 final size:16
Alignment explanation
Indices: 46530845--46530894 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
46530835 TCAACATTAC
46530845 TATT-TTAATAATAAA
1 TATTATTAATAATAAA
*
46530860 TATTTATTAAAATTATAAA
1 TA-TTATT--AATAATAAA
46530879 TA-TATTAATAATAAA
1 TATTATTAATAATAAA
46530894 T
1 T
46530895 GTTTTGTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
17 6 0.21
19 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTATTAATAATAAA
Found at i:46532674 original size:27 final size:26
Alignment explanation
Indices: 46532635--46532685 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
46532625 TACAAGGACT
46532635 TATGACATATTTTAACTTAGTATAAAAA
1 TATGACATATTTTAA-TTA-TATAAAAA
46532663 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTTAATTATATAAA
46532686 TATGAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 3 0.13
27 9 0.39
28 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
TATGACATATTTTAATTATATAAAAA
Found at i:46536325 original size:24 final size:24
Alignment explanation
Indices: 46536298--46536347 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
46536288 AATTTAATCT
46536298 TTGAAGTTTATATTTTTTA-TTAAA
1 TTGAAGTTTA-ATTTTTTAGTTAAA
**
46536322 TTGATTTTTAATTTTTTAGTTAAA
1 TTGAAGTTTAATTTTTTAGTTAAA
46536346 TT
1 TT
46536348 TAATCATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (24 bp):
TTGAAGTTTAATTTTTTAGTTAAA
Found at i:46537402 original size:13 final size:14
Alignment explanation
Indices: 46537378--46537406 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46537368 TTTCATCTCC
46537378 TTCTTCTTTTCTTT
1 TTCTTCTTTTCTTT
46537392 TTCTT-TTTTCTTT
1 TTCTTCTTTTCTTT
46537405 TT
1 TT
46537407 ATAACAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTCTTTTCTTT
Found at i:46555127 original size:30 final size:30
Alignment explanation
Indices: 46555093--46555159 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
46555083 AAAATGAATA
*
46555093 TTTCATGTTTATATTTG-AACACAATCAAAG
1 TTTCATGTTTATAATTGCAACA-AATCAAAG
* *
46555123 TTTCATCTTTATAATTGCATCAAATCAAAG
1 TTTCATGTTTATAATTGCAACAAATCAAAG
46555153 TTT-ATGT
1 TTTCATGT
46555160 ATCAAATTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 26 0.81
31 3 0.09
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (30 bp):
TTTCATGTTTATAATTGCAACAAATCAAAG
Found at i:46556014 original size:23 final size:23
Alignment explanation
Indices: 46555965--46556015 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
46555955 TTGTTTCATA
*
46555965 AGTCTTTTCTTTTAGAAATTTTT
1 AGTCTTGTCTTTTAGAAATTTTT
* *
46555988 -GTCTTGTCTTTTATAGATTTTT
1 AGTCTTGTCTTTTAGAAATTTTT
46556010 AGTCTT
1 AGTCTT
46556016 ACTTTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.61
Consensus pattern (23 bp):
AGTCTTGTCTTTTAGAAATTTTT
Found at i:46556020 original size:22 final size:22
Alignment explanation
Indices: 46555973--46556021 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
46555963 TAAGTCTTTT
*
46555973 CTTTTAGAAATTTTTGTCTTGT
1 CTTTTAGAAATTTTTGTCTTGA
* *
46555995 CTTTTATAGATTTTTAGTCTT-A
1 CTTTTAGAAATTTTT-GTCTTGA
46556017 CTTTT
1 CTTTT
46556022 GCAAGTGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.61
Consensus pattern (22 bp):
CTTTTAGAAATTTTTGTCTTGA
Found at i:46559390 original size:7 final size:7
Alignment explanation
Indices: 46559380--46559437 Score: 80
Period size: 7 Copynumber: 8.3 Consensus size: 7
46559370 ACCTTGAATG
46559380 TCAAACC
1 TCAAACC
46559387 TCAAACC
1 TCAAACC
46559394 TCAAACC
1 TCAAACC
46559401 TCAAACC
1 TCAAACC
* *
46559408 TTAAACA
1 TCAAACC
46559415 TCAAACC
1 TCAAACC
*
46559422 TCGAACC
1 TCAAACC
*
46559429 CCAAACC
1 TCAAACC
46559436 TC
1 TC
46559438 GAATCCCAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.41, C:0.41, G:0.02, T:0.16
Consensus pattern (7 bp):
TCAAACC
Found at i:46559445 original size:14 final size:14
Alignment explanation
Indices: 46559383--46559446 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 14
46559373 TTGAATGTCA
* *
46559383 AACCTCAAACCTCA
1 AACCCCAAACCTCG
* **
46559397 AACCTCAAACCTTA
1 AACCCCAAACCTCG
**
46559411 AACATCAAACCTCG
1 AACCCCAAACCTCG
46559425 AACCCCAAACCTCG
1 AACCCCAAACCTCG
*
46559439 AATCCCAA
1 AACCCCAA
46559447 GTTCAAAGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.42, C:0.41, G:0.03, T:0.14
Consensus pattern (14 bp):
AACCCCAAACCTCG
Found at i:46567799 original size:15 final size:14
Alignment explanation
Indices: 46567780--46567823 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
46567770 TTTCTTCTTC
*
46567780 TTTTTTTTTCTCAG
1 TTTTTTTTTCTCAA
*
46567794 TGTTTTTTTTTTCAA
1 T-TTTTTTTTCTCAA
*
46567809 TTATTTTTTCTCAA
1 TTTTTTTTTCTCAA
46567823 T
1 T
46567824 CTACCCTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTTTTTTTCTCAA
Found at i:46577933 original size:113 final size:113
Alignment explanation
Indices: 46577794--46578008 Score: 285
Period size: 113 Copynumber: 1.9 Consensus size: 113
46577784 CGATATCAAG
* * *
46577794 AAGGGTATCGATAAATTTTGAAAGGTA-CTGATACT-TTGTTAAGGGTATCGGTACTTTTGATTT
1 AAGGGTATCGATAAATTTTGAAAGGTATC-AATA-TGTTGTTAAAGGTATCGATACTTTTGATTT
*
46577857 TTGTTC-AATTTTCT-AACAAATTGAAGCTCAAATTGGTATTGATACCAGGC
64 TTGCTCGAATTTTCTGAAC--ATTGAAGCTCAAATTGGTATTGATACCAGGC
* * *
46577907 AAGGGTATTGATAATTTTTGCAAGGTATCAATATGTTGTTAAAGGTATCGATACTTTTGATTTTT
1 AAGGGTATCGATAAATTTTGAAAGGTATCAATATGTTGTTAAAGGTATCGATACTTTTGATTTTT
* *
46577972 GCTCGATTTTTCTGAACTTTGAAGCTCAAATTGGTAT
66 GCTCGAATTTTCTGAACATTGAAGCTCAAATTGGTAT
46578009 CAATACTTGG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
112 1 0.01
113 77 0.87
114 8 0.09
115 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (113 bp):
AAGGGTATCGATAAATTTTGAAAGGTATCAATATGTTGTTAAAGGTATCGATACTTTTGATTTTT
GCTCGAATTTTCTGAACATTGAAGCTCAAATTGGTATTGATACCAGGC
Found at i:46581133 original size:8 final size:9
Alignment explanation
Indices: 46581113--46581137 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46581103 ATTAATTTTT
46581113 AAAAATTCA
1 AAAAATTCA
46581122 AAAAATTCA
1 AAAAATTCA
46581131 AAAAATT
1 AAAAATT
46581138 ATTTCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATTCA
Found at i:46582034 original size:21 final size:19
Alignment explanation
Indices: 46581989--46582036 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
46581979 ATTTAAATAA
*
46581989 TAAAAAT-TTAAATTTAAT
1 TAAAAATATTAAATTCAAT
46582007 TATAAAATATATAAATATCAAT
1 TA-AAAATAT-TAAAT-TCAAT
46582029 TAAAAATA
1 TAAAAATA
46582037 AAATTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 1 0.04
21 11 0.44
22 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATATTAAATTCAAT
Found at i:46583805 original size:34 final size:34
Alignment explanation
Indices: 46583762--46583829 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
46583752 TTCCAAATAT
46583762 CCTATCATAGTATTATTTTACTAAAAAATGAGAA
1 CCTATCATAGTATTATTTTACTAAAAAATGAGAA
46583796 CCTATCATAGTATTATTTTACTAAAAAATGAGAA
1 CCTATCATAGTATTATTTTACTAAAAAATGAGAA
46583830 GATGAAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (34 bp):
CCTATCATAGTATTATTTTACTAAAAAATGAGAA
Found at i:46585383 original size:50 final size:50
Alignment explanation
Indices: 46585255--46585496 Score: 175
Period size: 50 Copynumber: 4.7 Consensus size: 50
46585245 GATAATAACA
* * ** * * *
46585255 TGCCAAAGCCATGTCCCAGACACGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * * **
46585304 TACCAATGTCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
46585354 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGG
* * * **
46585404 TGCCAACGCCATGTCCCAGATAAGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* *
46585460 TGCTAATGCCATGTGCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
46585497 TCTCATTCCC
Statistics
Matches: 148, Mismatches: 35, Indels: 13
0.76 0.18 0.07
Matches are distributed among these distances:
48 1 0.01
49 36 0.24
50 76 0.51
51 1 0.01
53 2 0.01
56 32 0.22
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:46585966 original size:35 final size:35
Alignment explanation
Indices: 46585920--46585994 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
46585910 TTCATCCCTT
46585920 ATTCTTATGTTTTATGACATGTTGAACATTTTTCC
1 ATTCTTATGTTTTATGACATGTTGAACATTTTTCC
46585955 ATTCTTATGTTTTATGACATGTTGAACATTTTTCC
1 ATTCTTATGTTTTATGACATGTTGAACATTTTTCC
46585990 ATTCT
1 ATTCT
46585995 ATGGCAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.52
Consensus pattern (35 bp):
ATTCTTATGTTTTATGACATGTTGAACATTTTTCC
Found at i:46592835 original size:5 final size:5
Alignment explanation
Indices: 46592827--46592886 Score: 120
Period size: 5 Copynumber: 12.0 Consensus size: 5
46592817 TTAAAATTTA
46592827 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
46592877 ATATT ATATT
1 ATATT ATATT
46592887 TGACTTGTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:46593970 original size:41 final size:40
Alignment explanation
Indices: 46593882--46594072 Score: 132
Period size: 40 Copynumber: 4.7 Consensus size: 40
46593872 TGCTAGTATG
* * * *
46593882 AAAACGCCGCAAAAGGTTAGAGC-TATAGCGGTGTTTATGACA
1 AAAACGCCGCAAAAGGTCA-AGCAT-TAGCGGCGCTTAT-AAA
46593924 AAAACGCCGCAAAAGGTCAAGCATTAGCGGCGCTTATAAA
1 AAAACGCCGCAAAAGGTCAAGCATTAGCGGCGCTTATAAA
* * * * * **
46593964 ACAAACGTCGCTATAGGTCGAGCATTAGCGGCGCTTTTTGA
1 A-AAACGCCGCAAAAGGTCAAGCATTAGCGGCGCTTATAAA
* * * * * * **
46594005 AAAACGCCGCTATAGATCAAGCATTAGTGACGCTTTTTGA
1 AAAACGCCGCAAAAGGTCAAGCATTAGCGGCGCTTATAAA
* * * *
46594045 AAAACGCCGCTATAGATCGAGCATTAGC
1 AAAACGCCGCAAAAGGTCAAGCATTAGC
46594073 TGCGTTTTTT
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 63 0.49
41 47 0.36
42 19 0.15
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCAAAAGGTCAAGCATTAGCGGCGCTTATAAA
Found at i:46594008 original size:81 final size:81
Alignment explanation
Indices: 46593923--46594088 Score: 208
Period size: 81 Copynumber: 2.0 Consensus size: 81
46593913 TGTTTATGAC
* * * *
46593923 AAAAACGCCGCAAAAGGTCAAGCATTAGCGGCGCTTATAAAACAAACGTCGCTATAGGTCGAGCA
1 AAAAACGCCGCAAAAGATCAAGCATTAGCGACGCTTATAAAA-AAACGCCGCTATAGATCGAGCA
46593988 TTAGCGGCG-CTTTTTG
65 TTAGCGGCGTCTTTTTG
* * * * **
46594004 AAAAACGCCGCTATAGATCAAGCATTAGTGACGCTTTTTGAAAAACGCCGCTATAGATCGAGCAT
1 AAAAACGCCGCAAAAGATCAAGCATTAGCGACGCTTATAAAAAAACGCCGCTATAGATCGAGCAT
* *
46594069 TAGCTGCGTTTTTTTG
66 TAGCGGCGTCTTTTTG
46594085 AAAA
1 AAAA
46594089 CGTTGCAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 28 0.39
81 44 0.61
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (81 bp):
AAAAACGCCGCAAAAGATCAAGCATTAGCGACGCTTATAAAAAAACGCCGCTATAGATCGAGCAT
TAGCGGCGTCTTTTTG
Found at i:46594028 original size:40 final size:40
Alignment explanation
Indices: 46593923--46594088 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
46593913 TGTTTATGAC
* * * * **
46593923 AAAAACGCCGCAAAAGGTCAAGCATTAGCGGCGCTTATAA
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* * *
46593963 AACAAACGTCGCTATAGGTCGAGCATTAGCGGCGCTTTTTG
1 AA-AAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* *
46594004 AAAAACGCCGCTATAGATCAAGCATTAGTGACGCTTTTTG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* * *
46594044 AAAAACGCCGCTATAGATCGAGCATTAGCTGCGTTTTTTTG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCG-CTTTTTG
46594085 AAAA
1 AAAA
46594089 CGTTGCAAAA
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
40 64 0.60
41 43 0.40
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
Found at i:46594176 original size:40 final size:40
Alignment explanation
Indices: 46594132--46594260 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
46594122 AGCTTTAGTG
* * * *
46594132 GCATTAGCGGCACTTTTTAAAAAACGCCACAATTGATCGA
1 GCATTAGCGGCACTTTTTGAAAAACGCCGCTATAGATCGA
* * *
46594172 GCATTAACGGCGA-TATTTGAAAAACACCGCTATAGATCGA
1 GCATTAGCGGC-ACTTTTTGAAAAACGCCGCTATAGATCGA
* * *
46594212 GCATTAGCGGCGCTTTATCGAAAAACGTCGCTATAGATCGA
1 GCATTAGCGGCACTTT-TTGAAAAACGCCGCTATAGATCGA
46594253 GCATTAGC
1 GCATTAGC
46594261 AGTGCTTTTC
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
40 43 0.59
41 30 0.41
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (40 bp):
GCATTAGCGGCACTTTTTGAAAAACGCCGCTATAGATCGA
Found at i:46594235 original size:41 final size:40
Alignment explanation
Indices: 46594166--46594260 Score: 129
Period size: 41 Copynumber: 2.4 Consensus size: 40
46594156 CGCCACAATT
*
46594166 GATCGAGCATTAACGGCGATATTTGAAAAACACCGCTATA
1 GATCGAGCATTAGCGGCGATATTTGAAAAACACCGCTATA
* **
46594206 GATCGAGCATTAGCGGCGCT-TTATCGAAAAACGTCGCTATA
1 GATCGAGCATTAGCGGCGATATT-T-GAAAAACACCGCTATA
46594247 GATCGAGCATTAGC
1 GATCGAGCATTAGC
46594261 AGTGCTTTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.04
40 19 0.39
41 28 0.57
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (40 bp):
GATCGAGCATTAGCGGCGATATTTGAAAAACACCGCTATA
Found at i:46594268 original size:41 final size:41
Alignment explanation
Indices: 46594190--46594268 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
46594180 GGCGATATTT
*
46594190 GAAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTATC
1 GAAAAACACCGCTATAGATCGAGCATTAGCAGCGCTTTATC
** *
46594231 GAAAAACGTCGCTATAGATCGAGCATTAGCAGTGCTTT
1 GAAAAACACCGCTATAGATCGAGCATTAGCAGCGCTTT
46594269 TCGGGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (41 bp):
GAAAAACACCGCTATAGATCGAGCATTAGCAGCGCTTTATC
Found at i:46594415 original size:198 final size:186
Alignment explanation
Indices: 46593987--46594427 Score: 506
Period size: 198 Copynumber: 2.3 Consensus size: 186
46593977 TAGGTCGAGC
* * * *
46593987 ATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCAAGCATTAGTGACGCTTTTTGAAAAACGC
1 ATTAGCGGCGC-TTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGC
*** * *
46594052 CGCTATAGATCGAGCATTAGCTGCGTTTTTTTGAAAACGTTGCAAAAAAGTTGAGCAAAACATGT
65 CGCTATAGATCGAGCATTAGCTGCGTTTTCGGGAAAACATCGCAAAAAAGTTGAGCAAAACATGT
* * *
46594117 TGTTGAGCTTTAGTGGCATTAGCGGCACTTTTTAAAAAACGCCACAATTGATCGAGC
130 TGTTGAGCTTTAGTGGCATTAGCGGCACTTTTTAAAAAACGCCACAATAGATAGAGA
* * *
46594174 ATTAACGGCGATATTTGAAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTATCGAAAAACG
1 ATTAGCGGCGCT-TTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTT-TCGAAAAACG
* * *
46594239 TCGCTATAGATCGAGCATTAGCAGTGC-TTTTCGGGAAAATATCGTAAAAAAGTTGAGCAAATTA
64 CCGCTATAGATCGAGCATTAGC--TGCGTTTTCGGGAAAACATCGCAAAAAAGTTGAGC-AA--A
* ** ** * *
46594303 ACGTCGTTTGTTGTTGAGCTTTAGTGGCATTAGCGGCGTTTTTTTTTAAAATGTCACAATAGATA
124 A---C--ATGTTGTTGAGCTTTAGTGGCATTAGCGGC-ACTTTTTAAAAAACGCCACAATAGATA
46594368 GAGA
183 GAGA
*
46594372 ATTAGCTGCGCTTGTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTC
1 ATTAGCGGCGCTT-TTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTC
46594428 ACAAAATGCT
Statistics
Matches: 211, Mismatches: 29, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
186 1 0.00
187 46 0.22
188 30 0.14
189 24 0.11
190 5 0.02
192 2 0.01
195 1 0.00
197 32 0.15
198 70 0.33
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (186 bp):
ATTAGCGGCGCTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCC
GCTATAGATCGAGCATTAGCTGCGTTTTCGGGAAAACATCGCAAAAAAGTTGAGCAAAACATGTT
GTTGAGCTTTAGTGGCATTAGCGGCACTTTTTAAAAAACGCCACAATAGATAGAGA
Found at i:46594621 original size:21 final size:21
Alignment explanation
Indices: 46594597--46594638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46594587 TCAGATATAA
* *
46594597 TGTTTATTATTTTGGGATTAG
1 TGTTTATGATTTAGGGATTAG
*
46594618 TGTTTATGATTTAGGGTTTAG
1 TGTTTATGATTTAGGGATTAG
46594639 GATTTAGGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (21 bp):
TGTTTATGATTTAGGGATTAG
Found at i:46594636 original size:14 final size:14
Alignment explanation
Indices: 46594614--46594657 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
46594604 TATTTTGGGA
*
46594614 TTAGTGTTTATGAT
1 TTAGGGTTTATGAT
*
46594628 TTAGGGTTTAGGAT
1 TTAGGGTTTATGAT
*
46594642 TTAGGGTTTATTAT
1 TTAGGGTTTATGAT
46594656 TT
1 TT
46594658 TATAGTTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:46594858 original size:7 final size:7
Alignment explanation
Indices: 46594848--46594994 Score: 63
Period size: 7 Copynumber: 20.9 Consensus size: 7
46594838 TATGGTTTGG
46594848 GGTTTAA
1 GGTTTAA
*
46594855 GGTTTAT
1 GGTTTAA
*
46594862 GATTT-A
1 GGTTTAA
46594868 -GTGTTAA
1 GGT-TTAA
46594875 GAGTTT-A
1 G-GTTTAA
*
46594882 GTGTTTAC
1 G-GTTTAA
*
46594890 GGTTTAG
1 GGTTTAA
*
46594897 GGTGTAA
1 GGTTTAA
*
46594904 -GTTTAT
1 GGTTTAA
*
46594910 GGCTT-A
1 GGTTTAA
*
46594916 GTGTTTAT
1 G-GTTTAA
*
46594924 GGTTTAG
1 GGTTTAA
*
46594931 GGTTTAG
1 GGTTTAA
46594938 GGTTTAA
1 GGTTTAA
*
46594945 AGTTT-A
1 GGTTTAA
* *
46594951 GTATTTAT
1 G-GTTTAA
46594959 GGTTTAA
1 GGTTTAA
*
46594966 GGGTTATA
1 GGTTTA-A
46594974 GAGTTTAA
1 G-GTTTAA
46594982 GGTTTAA
1 GGTTTAA
46594989 GGTTTA
1 GGTTTA
46594995 GGGTCCAAGT
Statistics
Matches: 103, Mismatches: 25, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
5 1 0.01
6 8 0.08
7 79 0.77
8 9 0.09
9 6 0.06
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.46
Consensus pattern (7 bp):
GGTTTAA
Found at i:46594941 original size:14 final size:14
Alignment explanation
Indices: 46594836--46594998 Score: 85
Period size: 14 Copynumber: 11.6 Consensus size: 14
46594826 AAGGTATATT
* *
46594836 TTTATGGTTTGGGG
1 TTTAGGGTTTAGGG
* * *
46594850 TTTAAGGTTTATGA
1 TTTAGGGTTTAGGG
* * *
46594864 TTTAGTGTTAAGAG
1 TTTAGGGTTTAGGG
* *
46594878 TTTAGTGTTTACGG
1 TTTAGGGTTTAGGG
* *
46594892 TTTAGGGTGTA-AG
1 TTTAGGGTTTAGGG
* * *
46594905 TTTATGGCTTAGTG
1 TTTAGGGTTTAGGG
*
46594919 TTTATGGTTTAGGG
1 TTTAGGGTTTAGGG
**
46594933 TTTAGGGTTTAAAG
1 TTTAGGGTTTAGGG
** *
46594947 TTTAGTATTTATGG
1 TTTAGGGTTTAGGG
*
46594961 TTTAAGGGTTATAGAG
1 TTT-AGGGTT-TAGGG
* *
46594977 TTTAAGGTTTAAGG
1 TTTAGGGTTTAGGG
46594991 TTTAGGGT
1 TTTAGGGT
46594999 CCAAGTGGCC
Statistics
Matches: 109, Mismatches: 37, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
13 9 0.08
14 85 0.78
15 9 0.08
16 6 0.06
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:46594949 original size:21 final size:21
Alignment explanation
Indices: 46594836--46594998 Score: 105
Period size: 21 Copynumber: 7.7 Consensus size: 21
46594826 AAGGTATATT
* * *
46594836 TTTATGGTTTGGGGTTTAAGG
1 TTTAAGGTTTAGGGTTTAGGG
* * * * *
46594857 TTTATGATTTAGTGTTAAGAG
1 TTTAAGGTTTAGGGTTTAGGG
*
46594878 TTT-AGTGTTTACGGTTTAGGG
1 TTTAAG-GTTTAGGGTTTAGGG
* * * *
46594899 TGTAA-GTTTATGGCTTAGTG
1 TTTAAGGTTTAGGGTTTAGGG
*
46594919 TTTATGGTTTAGGGTTTAGGG
1 TTTAAGGTTTAGGGTTTAGGG
* ** *
46594940 TTTAAAGTTTAGTATTTATGG
1 TTTAAGGTTTAGGGTTTAGGG
* *
46594961 TTTAAGGGTTATAGAGTTTAAGG
1 TTTAA-GGTT-TAGGGTTTAGGG
46594984 TTTAAGGTTTAGGGT
1 TTTAAGGTTTAGGGT
46594999 CCAAGTGGCC
Statistics
Matches: 106, Mismatches: 31, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
20 16 0.15
21 68 0.64
22 8 0.08
23 14 0.13
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTAGGG
Found at i:46600144 original size:43 final size:43
Alignment explanation
Indices: 46599871--46600141 Score: 305
Period size: 43 Copynumber: 6.3 Consensus size: 43
46599861 GAATGGTACT
* * * *
46599871 TTTAGCAGCGTTTGTGATAAAAGTGCTGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* ** * * *
46599914 TTTAGCGACGTTTGTGA-AAAAAAGCTGTTAAAAGTCAT-TCTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGT-TC
*
46599956 TATAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* *
46599999 TTCAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * * *
46600042 TTTAGTGGTGTTCGTGGGTAAAA-CGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCATGTTC
* *
46600085 TTTAGCGGCGTTTTTTTATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCG-TTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* *
46600129 TATAGCGTCGTTT
1 TTTAGCGGCGTTT
46600142 TTTCACATAA
Statistics
Matches: 191, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 33 0.17
43 119 0.62
44 38 0.20
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:46601541 original size:19 final size:20
Alignment explanation
Indices: 46601504--46601541 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46601494 TATAGGAATA
46601504 ATATTTAAATATGATTTTTG
1 ATATTTAAATATGATTTTTG
*
46601524 ATATTTAAA-ATTATTTTT
1 ATATTTAAATATGATTTTT
46601542 AATTGTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
ATATTTAAATATGATTTTTG
Found at i:46606519 original size:12 final size:12
Alignment explanation
Indices: 46606498--46606527 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46606488 TACTGAAACA
46606498 ATTGCAATTGCG
1 ATTGCAATTGCG
*
46606510 ATTGCGATTGCG
1 ATTGCAATTGCG
46606522 ATTGCA
1 ATTGCA
46606528 TTTAATGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (12 bp):
ATTGCAATTGCG
Found at i:46610927 original size:22 final size:22
Alignment explanation
Indices: 46610885--46610927 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
46610875 TGAAAATTTT
*
46610885 TATTTTAATATTAAAGTATAAA
1 TATTTTAATATTAAAGAATAAA
*
46610907 TATTTTAAATTTTAAA-AATAA
1 TATTTT-AATATTAAAGAATAA
46610928 TATACAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTTTAATATTAAAGAATAAA
Found at i:46617814 original size:18 final size:18
Alignment explanation
Indices: 46617791--46617830 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
46617781 TATTATTTTA
46617791 AAAAATA-TATAATACATC
1 AAAAATACTA-AATACATC
46617809 AAAAATACTAAATACATC
1 AAAAATACTAAATACATC
46617827 AAAA
1 AAAA
46617831 TAAATATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATACTAAATACATC
Found at i:46617957 original size:30 final size:30
Alignment explanation
Indices: 46617914--46617972 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
46617904 CTTAACAAGC
*
46617914 AAATGCCTCTAAAATAATAGCAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
* *
46617944 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
46617973 CAATAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:46629771 original size:19 final size:18
Alignment explanation
Indices: 46629749--46629806 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
46629739 TTACAAAATC
46629749 AATT-AAAATAATTTTCAAA
1 AATTCAAAATAATTTT--AA
46629768 AATTCAAAATAAATTTTAA
1 AATTCAAAAT-AATTTTAA
46629787 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTT-TAA
46629805 AA
1 AA
46629807 AAAATCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.11
18 5 0.14
19 16 0.44
20 5 0.14
21 6 0.17
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTCAAAATAATTTTAA
Found at i:46629807 original size:19 final size:19
Alignment explanation
Indices: 46629749--46629859 Score: 77
Period size: 21 Copynumber: 5.5 Consensus size: 19
46629739 TTACAAAATC
46629749 AATT-AAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
46629768 AATTCAAAATAAATTTT-AA
1 AATTCAAAAT-AATTTTAAA
46629787 AATTCAAAAT-ATTTATAAAAA
1 AATTCAAAATAATTT-T--AAA
*
46629808 AAATCAAAATTTATATTTTTAAA
1 AATTCAAAA--TA-A-TTTTAAA
* *
46629831 AATTCTAAAAAAAATTTAAA
1 AATTC-AAAATAATTTTAAA
46629851 AATT-AAAAT
1 AATTCAAAAT
46629860 TTTAAATTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
17 4 0.05
18 5 0.07
19 16 0.21
20 15 0.20
21 17 0.23
22 1 0.01
23 8 0.11
24 4 0.05
25 2 0.03
26 3 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:46629811 original size:64 final size:62
Alignment explanation
Indices: 46629743--46629863 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 62
46629733 CAAAAATTAC
* *
46629743 AAAATCAATTAAAATA-ATTTTCAAAAATTC-AAAATAAATTTTAAAATTCAAAATATTTATAAA
1 AAAATCAA--AAAATATATTTTCAAAAATTCTAAAAAAAATTTAAAAATT-AAAAT-TTTATAAA
46629806 A
62 A
** *
46629807 AAAATCAAAATTTATATTTTTAAAAATTCTAAAAAAAATTTAAAAATTAAAATTTTA
1 AAAATCAAAAAATATATTTTCAAAAATTCTAAAAAAAATTTAAAAATTAAAATTTTA
46629864 AATTTTTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 8 0.16
63 18 0.36
64 24 0.48
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (62 bp):
AAAATCAAAAAATATATTTTCAAAAATTCTAAAAAAAATTTAAAAATTAAAATTTTATAAAA
Found at i:46636815 original size:26 final size:28
Alignment explanation
Indices: 46636750--46636821 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
46636740 ATAAGAAAAT
* *
46636750 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
*
46636780 TTATTATTAAATTATATGTAATAATA-A
1 TTATTATTAAATTATATGAAATAATATA
46636807 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
46636822 CAAATTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 14 0.36
29 1 0.03
30 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:46636986 original size:120 final size:120
Alignment explanation
Indices: 46636862--46637154 Score: 493
Period size: 120 Copynumber: 2.4 Consensus size: 120
46636852 AATTATTTTA
* * *
46636862 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
46636925 TTAT-AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TT-TCAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
*
46636982 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
46637047 TCAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
66 TCAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
46637102 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
46637155 TAAATATGAT
Statistics
Matches: 164, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
119 6 0.04
120 156 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
TCAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:46637022 original size:15 final size:15
Alignment explanation
Indices: 46636987--46637038 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
46636977 TTAAGAATTT
*
46636987 TATTAAATTAT-ATA
1 TATTTAATTATAATA
46637001 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
46637015 TATTTAATAATAAT-
1 TATTTAATTATAATA
46637029 TATGTTAATT
1 TAT-TTAATT
46637039 TATATTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:46637131 original size:18 final size:17
Alignment explanation
Indices: 46637103--46637137 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
46637093 ATTATTAAGA
*
46637103 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
46637120 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
46637138 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:46637255 original size:157 final size:157
Alignment explanation
Indices: 46637091--46637407 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
46637081 ATAAGAATAT
*
46637091 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTAAATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
46637156 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
*
46637221 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
46637248 TAATTATTAAGAATTTTATTAAATTAAATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTAAATATTTTAATTAAAATATATTTAATAATAATTATGTTT
46637313 AAATATGATTAAATTATTTATTATTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
*
46637378 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
46637405 TAA
1 TAA
46637408 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTAAATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATATTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:46643421 original size:23 final size:22
Alignment explanation
Indices: 46643378--46643421 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
46643368 TTTCAAGTAA
46643378 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
46643401 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
46643422 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:46643582 original size:44 final size:45
Alignment explanation
Indices: 46643505--46643589 Score: 111
Period size: 46 Copynumber: 1.9 Consensus size: 45
46643495 CACGATGGAT
* *
46643505 TCAACACACAGCAATCACCCTTAGTAATCAATGATATCCGGTGAGA
1 TCAAAACACAGCAACCACCCTTAGTAATCAATGATA-CCGGTGAGA
* *
46643551 TCAAAACATAGCAACCA-CCTTA-TAATTAATGATACCGGT
1 TCAAAACACAGCAACCACCCTTAGTAATCAATGATACCGGT
46643590 TCACATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.14
44 11 0.31
45 5 0.14
46 14 0.40
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.24
Consensus pattern (45 bp):
TCAAAACACAGCAACCACCCTTAGTAATCAATGATACCGGTGAGA
Found at i:46643660 original size:51 final size:51
Alignment explanation
Indices: 46643598--46643777 Score: 213
Period size: 51 Copynumber: 3.5 Consensus size: 51
46643588 GTTCACATAA
* * *
46643598 TAGCCTACACATAGTACTACACATGTGATCATCA-CTATCCGATACATGTAG
1 TAGCCTGCACATAGTACTACACACGTGATCAT-AGCTATCCGGTACATGTAG
*
46643649 TAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCGGTACATATAG
1 TAGCCTGCACATAGTACTACACACGTGATC-ATAGCTATCCGGTACATGTAG
* * * * * * * *
46643700 TAGCCTGCACATGGTACTACACATGCGA-CCTATCTTTCTGGTACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGATCATAGCTATCCGGTACATGTAG
46643750 TAGCCTGCACATAGTACTACACACGTGA
1 TAGCCTGCACATAGTACTACACACGTGA
46643778 CCATCACTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 41 0.37
51 68 0.62
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (51 bp):
TAGCCTGCACATAGTACTACACACGTGATCATAGCTATCCGGTACATGTAG
Found at i:46643801 original size:101 final size:101
Alignment explanation
Indices: 46643585--46643777 Score: 253
Period size: 101 Copynumber: 1.9 Consensus size: 101
46643575 ATTAATGATA
* * * *
46643585 CCGGTTCACATAATAGCCTACACATAGTACTACACATGTGATCATCACTATCCGATACATGTAGT
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCGATACACGTAGT
*
46643650 AGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
65 AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
* * * * * * *
46643687 CCGGTACATATAGTAGCCTGCACATGGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGT
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCGATACACGTAGT
46643751 AGCCTGCACATAGTACTACACACGTGA
65 AGCCTGCACATAGTACTACACACGTGA
46643778 CCATCACTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
100 1 0.01
101 42 0.53
102 36 0.46
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (101 bp):
CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCCGATACACGTAGTA
GCCTGCACATAGTACTACACACGTGATCCAAGCTAT
Found at i:46649630 original size:106 final size:106
Alignment explanation
Indices: 46649437--46649674 Score: 431
Period size: 106 Copynumber: 2.2 Consensus size: 106
46649427 AAAAATAATA
* * *
46649437 AAATTTTCAAAATAAGGCAATATTTTACGTTTGGAGAATCGAGGAAACGTGCCCTAACGTGTTGG
1 AAATTTT-AAAATAAGGCAATGTTTTACGTTTGAAAAATCGAGGAAACGTGCCCTAACGTGTTGG
46649502 GTGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
65 GTGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
*
46649544 AAGTTTTAAAATAAGGCAATGTTTTACGTTTGAAAAATCGAGGAAACGTGCCCTAACGTGTTGGG
1 AAATTTTAAAATAAGGCAATGTTTTACGTTTGAAAAATCGAGGAAACGTGCCCTAACGTGTTGGG
46649609 TGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
66 TGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
46649650 AAATTTTAAAATAAGGCAATGTTTT
1 AAATTTTAAAATAAGGCAATGTTTT
46649675 GTATTTGGAA
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
106 120 0.95
107 6 0.05
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (106 bp):
AAATTTTAAAATAAGGCAATGTTTTACGTTTGAAAAATCGAGGAAACGTGCCCTAACGTGTTGGG
TGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
Found at i:46663885 original size:88 final size:88
Alignment explanation
Indices: 46663763--46664235 Score: 621
Period size: 88 Copynumber: 5.4 Consensus size: 88
46663753 TATCCAGTCC
* *
46663763 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATCCTATCTCCCTAAGCAGTAGTGG
** *
46663828 AGC-GAGTCGAAGATAG-AAGATCT
66 AGCAGA-TCGAAGACGGCGA-ATCT
* *
46663851 TATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATCCTATCTCCCTAAGCAGTAGTGG
*
46663916 AGAAGATCGAAGACGGCGAATCT
66 AGCAGATCGAAGACGGCGAATCT
* *
46663939 TATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATCCTATCTCCCTAAGCAGTAGTGG
*
46664004 AGAAGATCGAAGACGGCGAATCT
66 AGCAGATCGAAGACGGCGAATCT
* * * * ** ** ** *
46664027 TATCTTCCTAAGCATTAGTGAAGCAGATTTAAGCCA-CCGGTCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATCCTATCTCCCTAAGCAGTAGTGG
* * * *
46664091 AGCAGGTCGAAGATGG-TAGATCC
66 AGCAGATCGAAGACGGCGA-ATCT
* *
46664114 TATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATCCTATCTCCCTAAGCAGTAGTGG
46664179 AGCAGATCGAAGACGGCGAATCT
66 AGCAGATCGAAGACGGCGAATCT
* *
46664202 TATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGA
46664236 CGGCGAATCT
Statistics
Matches: 334, Mismatches: 46, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
86 1 0.00
87 67 0.20
88 262 0.78
89 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (88 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATCCTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGCGAATCT
Found at i:46663973 original size:132 final size:132
Alignment explanation
Indices: 46663763--46664235 Score: 648
Period size: 132 Copynumber: 3.6 Consensus size: 132
46663753 TATCCAGTCC
* * *
46663763 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG-TAGATCCTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-ATCCTATCTCCCTAAGCAGTAGTG
46663827 GAGC-GAGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAG
65 GAGCAG-GTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAG
46663891 ATCT
129 ATCT
* *
46663895 TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGAATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCTATCTCCCTAAGCAGTAGTGG
* ** * * **
46663960 AGCGGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGA-CGGCGAA
66 AGCAGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAG-A
46664024 TCT
130 TCT
* * * ** * ** *
46664027 TATCTTCCTAAGCATTAGTGAAGCAGATTTAAGCCACCG-GTCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCTATCTCCCTAAGCAGTAGTGG
* * *
46664091 AGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGAT
66 AGCAGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGAT
46664156 CT
131 CT
* *
46664158 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCTATCTCCCTAAGCAGTAGTGG
*
46664223 AGCAGATCGAAGA
66 AGCAGGTCGAAGA
46664236 CGGCGAATCT
Statistics
Matches: 292, Mismatches: 44, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
131 110 0.38
132 180 0.62
133 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (132 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCTATCTCCCTAAGCAGTAGTGG
AGCAGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGAT
CT
Found at i:46664147 original size:219 final size:219
Alignment explanation
Indices: 46663763--46664311 Score: 703
Period size: 219 Copynumber: 2.5 Consensus size: 219
46663753 TATCCAGTCC
* * * * *
46663763 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG-TAGATC-CTATCTCCCTAAGCAGTAGT
1 TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGA-ATCTC-ATCTTCCTAAGCAGTAGT
* ** ** ** * *
46663826 GGAGC-GAGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAA
64 GAAGCAGA-TTTAAGCCACCAG-TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAA
* **
46663890 GATCTTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGAC-GGCGAATCTTATCTCCCTAAGCAG
127 GATCCTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACAGAAG-ATCTTATCTCCCTAAGCAG
* *
46663954 TAGTGGAGCGGGTCGAAGATAGAAG-ATCT
191 TAGTGGAGCAGATCGAAGA-AGAAGAATCT
* *
46663983 TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGAATCTTATCTTCCTAAGCATTAGTGA
1 TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAGTAGTGA
* * *
46664048 AGCAGATTTAAGCCACCGGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATC
66 AGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATC
** * *
46664113 CTATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGATCTTATCTCCCTAAGCAGTAGTG
131 CTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACAGAAGATCTTATCTCCCTAAGCAGTAGTG
* **
46664178 GAGCAGATCGAAGACGGCGAATCT
196 GAGCAGATCGAAGAAGAAGAATCT
* *
46664202 TATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAGTAGTGA
1 TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAGTAGTGA
*
46664267 AGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGTAGTAGTGGAG
66 AGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAG
46664312 AAGACAGAAT
Statistics
Matches: 287, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
218 2 0.01
219 217 0.76
220 65 0.23
221 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (219 bp):
TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAGTAGTGA
AGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGAAGATC
CTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACAGAAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGAAGAAGAATCT
Found at i:46664272 original size:44 final size:44
Alignment explanation
Indices: 46663763--46664273 Score: 561
Period size: 44 Copynumber: 11.6 Consensus size: 44
46663753 TATCCAGTCC
* * *
46663763 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGGAGATCT
* *
46663807 TATCTCCCTAAGCAGTAGTGGAGC-GAGTCGAAGATAGAAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGA-TCGAAGATGGGAGATCT
* * * *
46663851 TATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGGAGATCT
* *
46663895 TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGA-ATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-GAGATCT
* * * *
46663939 TATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGGAGATCT
* *
46663983 TATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGCGA-ATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-GAGATCT
* * * ** ** *
46664027 TATCTTCCTAAGCATTAGTGAAGCAGATTTAAGCCA-CCG-G-TCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG--ATGGGAGATCT
* * *
46664070 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGGAGATCT
* * * *
46664114 TATCTCCCTAAGCAGTAGTGGAGCGGGTCGAAGATAGAAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGGAGATCT
*
46664158 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-ATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-GAGATCT
* *
46664202 TATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-ATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-GAGATCT
* * *
46664246 CATCTTCCTAAGCAGTAGTGAAGCAGAT
1 TATCTCCCTAAGCAGTAGTGGAGCAGAT
46664274 TTAAGCCACC
Statistics
Matches: 402, Mismatches: 53, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.00
43 32 0.08
44 364 0.91
45 4 0.01
46 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (44 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGGAGATCT
Found at i:46666827 original size:106 final size:106
Alignment explanation
Indices: 46666579--46666816 Score: 431
Period size: 106 Copynumber: 2.2 Consensus size: 106
46666569 AAAAATAATA
* *
46666579 AAATTTTCAAAATAAGGCAATATTTTACGTTTGGAGAATCGAGGAAACGTGCCCTAACGTGTTGG
1 AAATTTT-AAAATAAGGCAATGTTTTACGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGG
46666644 GTGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
65 GTGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
*
46666686 AAGTTTTAAAATAAGGCAATGTTTTACGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGG
1 AAATTTTAAAATAAGGCAATGTTTTACGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGG
*
46666751 TGTCGATTACTCGTTTAACGAAATAGTCGAATATCCTTTCG
66 TGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
46666792 AAATTTTAAAATAAGGCAATGTTTT
1 AAATTTTAAAATAAGGCAATGTTTT
46666817 GTATTTGGAA
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
106 120 0.95
107 6 0.05
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (106 bp):
AAATTTTAAAATAAGGCAATGTTTTACGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGG
TGTCGATTACTCGTTTAACCAAATAGTCGAATATCCTTTCG
Found at i:46670510 original size:32 final size:32
Alignment explanation
Indices: 46670474--46670534 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
46670464 TTTTGGAATC
* *
46670474 TAGTCCCTATGCTTTTATTTTTAAGAATTTAT
1 TAGTCCCTATACTTTTATTTTCAAGAATTTAT
*
46670506 TAGTCCCTGTACTTTTATTTTCAAGAATT
1 TAGTCCCTATACTTTTATTTTCAAGAATT
46670535 CAGTCCCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.51
Consensus pattern (32 bp):
TAGTCCCTATACTTTTATTTTCAAGAATTTAT
Found at i:46673659 original size:21 final size:21
Alignment explanation
Indices: 46673634--46673700 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
46673624 GTCACCTCTT
46673634 TTTAAATTAAAATATTATTTC
1 TTTAAATTAAAATATTATTTC
* ** * *
46673655 TTTAATTTATTATTTTATTTG
1 TTTAAATTAAAATATTATTTC
** *
46673676 TTTTTATTAAAATATTATTTT
1 TTTAAATTAAAATATTATTTC
46673697 TTTA
1 TTTA
46673701 TAAGTAGTGC
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (21 bp):
TTTAAATTAAAATATTATTTC
Found at i:46675733 original size:13 final size:13
Alignment explanation
Indices: 46675715--46675747 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
46675705 AACAAACTTT
46675715 TCAAAAGTATTTC
1 TCAAAAGTATTTC
*
46675728 TCAAAAGTATTTT
1 TCAAAAGTATTTC
46675741 TCAAAAG
1 TCAAAAG
46675748 CAATGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (13 bp):
TCAAAAGTATTTC
Done.