Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 40 of 235
Found at i:13066200 original size:36 final size:36
Alignment explanation
Indices: 13066118--13066202 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
13066108 GTTAATTTTT
* *
13066118 AAATTTTTTAAAAATTAAAATATATATAAATTATTT
1 AAATTTTTTAAAAATTAAAATATATATAAATAATTA
*
13066154 AAATTATTTAAAAATATATAAA-A-ATATAAA-AATTA
1 AAATTTTTTAAAAAT-TA-AAATATATATAAATAATTA
13066189 ACAATTTTTTAAAA
1 A-AATTTTTTAAAA
13066203 TATGTTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
35 4 0.10
36 32 0.76
37 3 0.07
38 3 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (36 bp):
AAATTTTTTAAAAATTAAAATATATATAAATAATTA
Found at i:13066903 original size:21 final size:21
Alignment explanation
Indices: 13066878--13066918 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
13066868 GAGTAAGTGG
13066878 ATGATAATGGCTTGGTATTTA
1 ATGATAATGGCTTGGTATTTA
13066899 ATGATAATGGCTTGGTATTT
1 ATGATAATGGCTTGGTATTT
13066919 TGTGTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (21 bp):
ATGATAATGGCTTGGTATTTA
Found at i:13073991 original size:21 final size:21
Alignment explanation
Indices: 13073943--13073992 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
13073933 AGCATTGTGG
*
13073943 CAGTTTCAAAGAAAGATAAAC
1 CAGTTCCAAAGAAAGATAAAC
* * * *
13073964 CAATTCCAAGGAAAGATAGAT
1 CAGTTCCAAAGAAAGATAAAC
13073985 CAGTTCCA
1 CAGTTCCA
13073993 TGAGGAGGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (21 bp):
CAGTTCCAAAGAAAGATAAAC
Found at i:13076395 original size:61 final size:61
Alignment explanation
Indices: 13076299--13076427 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
13076289 CACGACCTAG
* * * *
13076299 CACACGGGTGTGTGGCTTGGTTGTGTGACATCTGCACCTATTTAATACAAGTCAGTATGAT
1 CACACGGGCGTGTGGCTTGGCTGTGTGACACCTGCACCTATTTAATACAAGTCAATATGAT
* * * *
13076360 CACACGGGCGTGTGGCTTGGCCT-TGTGACCCCTGCACCTATTTAATGCAAGTTAATATGCT
1 CACACGGGCGTGTGGCTTGG-CTGTGTGACACCTGCACCTATTTAATACAAGTCAATATGAT
13076421 CACACGG
1 CACACGG
13076428 CCTAGCACAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 58 0.98
62 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (61 bp):
CACACGGGCGTGTGGCTTGGCTGTGTGACACCTGCACCTATTTAATACAAGTCAATATGAT
Found at i:13080213 original size:41 final size:41
Alignment explanation
Indices: 13080156--13080234 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
13080146 AATATAAAAG
13080156 TGTAATTTAATATCTTTAAATTTAGTATGACTGTTAATTTT
1 TGTAATTTAATATCTTTAAATTTAGTATGACTGTTAATTTT
13080197 TGTAATTTAATATCTTTAAATTTAGTATGACTGTTAAT
1 TGTAATTTAATATCTTTAAATTTAGTATGACTGTTAAT
13080235 ATCAAAGGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (41 bp):
TGTAATTTAATATCTTTAAATTTAGTATGACTGTTAATTTT
Found at i:13090778 original size:17 final size:17
Alignment explanation
Indices: 13090753--13090786 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13090743 TCATTTAATT
*
13090753 TTATATTAAAAATATAA
1 TTATATTAAAAAAATAA
*
13090770 TTATTTTAAAAAAATAA
1 TTATATTAAAAAAATAA
13090787 ATATCAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATATTAAAAAAATAA
Found at i:13091709 original size:29 final size:29
Alignment explanation
Indices: 13091672--13091728 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
13091662 CACCTTGACA
* * *
13091672 CGAATTCTCAATGAACAAGTTCTTCACCG
1 CGAACTCTCAACGAACAAGTTCTCCACCG
13091701 CGAACTCTCAACGAACAAGTTCTCCACC
1 CGAACTCTCAACGAACAAGTTCTCCACC
13091729 TCTTCCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.33, G:0.12, T:0.23
Consensus pattern (29 bp):
CGAACTCTCAACGAACAAGTTCTCCACCG
Found at i:13096903 original size:39 final size:40
Alignment explanation
Indices: 13096808--13097069 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
13096798 TTGAATGATG
*
13096808 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
13096846 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
13096887 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
13096926 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
13096965 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
13097004 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
13097043 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
13097070 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:13106822 original size:40 final size:39
Alignment explanation
Indices: 13106761--13106836 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
13106751 AAAAACCCCT
**
13106761 AAAAAAGAGCATTAATGGCGCTTCTACA-AAAACGCCACA
1 AAAAAAGAGCATTAACAGCGCTTCTA-AGAAAACGCCACA
* *
13106800 AAAAAACGAGCATTAGCAGCGCTTTTAAGAAAACGCC
1 AAAAAA-GAGCATTAACAGCGCTTCTAAGAAAACGCC
13106837 GCTATAGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 7 0.23
40 24 0.77
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (39 bp):
AAAAAAGAGCATTAACAGCGCTTCTAAGAAAACGCCACA
Found at i:13107540 original size:21 final size:21
Alignment explanation
Indices: 13107516--13107560 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13107506 TAGTTGGAGT
* *
13107516 TTAAGATTTAGGAGTTATGGG
1 TTAAGAATTAGGAGTTAGGGG
*
13107537 TTAAGAATTAGGGGTTAGGGG
1 TTAAGAATTAGGAGTTAGGGG
13107558 TTA
1 TTA
13107561 GTGGATAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (21 bp):
TTAAGAATTAGGAGTTAGGGG
Found at i:13108267 original size:22 final size:22
Alignment explanation
Indices: 13108241--13108283 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13108231 ATTATCATCA
**
13108241 TATTAACATTTATCATCATTAC
1 TATTAACATTTAAAATCATTAC
*
13108263 TATTAATATTTAAAATCATTA
1 TATTAACATTTAAAATCATTA
13108284 ATCTAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTAACATTTAAAATCATTAC
Found at i:13109136 original size:27 final size:28
Alignment explanation
Indices: 13109091--13109146 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
13109081 TCGCTGGATC
*
13109091 CGACCATCTATTGCATCACCATCG-ACT
1 CGACCATCTACTGCATCACCATCGCACT
* * *
13109118 CGACCATCTGCTGCGTCACCGTCGCACT
1 CGACCATCTACTGCATCACCATCGCACT
13109146 C
1 C
13109147 CTCTGCTGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (28 bp):
CGACCATCTACTGCATCACCATCGCACT
Found at i:13110709 original size:22 final size:22
Alignment explanation
Indices: 13110673--13110729 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
13110663 TTTGTTATTA
*
13110673 ATTTTTAATAAAATATTAAATAT
1 ATTTTTAAT-TAATATTAAATAT
**
13110696 ATTTTTAATTAATATTTTATAT
1 ATTTTTAATTAATATTAAATAT
13110718 -TTTTTAAATTAA
1 ATTTTT-AATTAA
13110730 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.17
22 16 0.53
23 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTAATTAATATTAAATAT
Found at i:13111387 original size:64 final size:64
Alignment explanation
Indices: 13111319--13111452 Score: 223
Period size: 64 Copynumber: 2.1 Consensus size: 64
13111309 TAATATTTCT
* *
13111319 ATATTTCTAACACGATTTTTAATAAATTTATTTATTGATATAATATGCCCCATCTAATATACAA
1 ATATTTCTAACACGATTTTTAATAAATTTATTTATTAATATAATATACCCCATCTAATATACAA
* * *
13111383 ATATTTTTATCACGATTTTTAATAAATTTATTTATTAATATAATATATCCCATCTAATATACAA
1 ATATTTCTAACACGATTTTTAATAAATTTATTTATTAATATAATATACCCCATCTAATATACAA
13111447 ATATTT
1 ATATTT
13111453 AATAAAATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.46
Consensus pattern (64 bp):
ATATTTCTAACACGATTTTTAATAAATTTATTTATTAATATAATATACCCCATCTAATATACAA
Found at i:13111465 original size:64 final size:64
Alignment explanation
Indices: 13111332--13111466 Score: 193
Period size: 64 Copynumber: 2.1 Consensus size: 64
13111322 TTTCTAACAC
* * * * *
13111332 GATTTTTAATAAATTTATTTATTGATATAATATGCCCCATCTAATATACAAATATTTTTATCAC
1 GATTTTTAATAAATTTATTTATTAATATAATATACCCCATCTAATATACAAATATTTATATAAA
*
13111396 GATTTTTAATAAATTTATTTATTAATATAATATATCCCATCTAATATACAAATATTTA-ATAAA
1 GATTTTTAATAAATTTATTTATTAATATAATATACCCCATCTAATATACAAATATTTATATAAA
13111459 -ATATTTTA
1 GAT-TTTTA
13111467 TATAGTTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
62 2 0.03
63 8 0.12
64 54 0.84
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (64 bp):
GATTTTTAATAAATTTATTTATTAATATAATATACCCCATCTAATATACAAATATTTATATAAA
Found at i:13111527 original size:24 final size:24
Alignment explanation
Indices: 13111500--13111570 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
13111490 ATTATTATTG
*
13111500 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
*
13111524 AAATATTATCGTCCATTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
13111548 AAATATTATCGTCCGTTTTATCA
1 AAATATTATCGTCCGTTTTATCA
13111571 TTTAAGTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:13111928 original size:9 final size:9
Alignment explanation
Indices: 13111910--13112048 Score: 140
Period size: 9 Copynumber: 15.7 Consensus size: 9
13111900 TAAATATTTA
13111910 ACATAACTT
1 ACATAACTT
*
13111919 ACAAAACTT
1 ACATAACTT
13111928 ACATAACTT
1 ACATAACTT
*
13111937 ATATAACTT
1 ACATAACTT
* *
13111946 AGATAA-AT
1 ACATAACTT
*
13111954 ATATAACTT
1 ACATAACTT
13111963 ACATAACTT
1 ACATAACTT
13111972 ACATAACTT
1 ACATAACTT
*
13111981 ATATAACTT
1 ACATAACTT
* *
13111990 AGATAA-AT
1 ACATAACTT
*
13111998 ATATAACTT
1 ACATAACTT
*
13112007 ACATAA-AT
1 ACATAACTT
* *
13112015 ATATATCATT
1 ACATAAC-TT
13112025 ACATAACTT
1 ACATAACTT
13112034 ACATAACTT
1 ACATAACTT
13112043 ACATAA
1 ACATAA
13112049 TACTTAAATA
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
8 17 0.16
9 83 0.78
10 6 0.06
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (9 bp):
ACATAACTT
Found at i:13111969 original size:35 final size:35
Alignment explanation
Indices: 13111912--13112048 Score: 150
Period size: 35 Copynumber: 3.9 Consensus size: 35
13111902 AATATTTAAC
* * *
13111912 ATAACTTACAAAACTTACATAACTTATATAACTTAG
1 ATAA-TTACATAACTTACATAACTTACATAACTTAT
* *
13111948 ATAAATATATAACTTACATAACTTACATAACTTAT
1 ATAATTACATAACTTACATAACTTACATAACTTAT
* * * *
13111983 ATAACTTAGATAA-ATATATAACTTACATAAATATAT
1 ATAA-TTACATAACTTACATAACTTACATAACT-TAT
*
13112019 ATCATTACATAACTTACATAACTTACATAA
1 ATAATTACATAACTTACATAACTTACATAA
13112049 TACTTAAATA
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
35 53 0.63
36 31 0.37
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (35 bp):
ATAATTACATAACTTACATAACTTACATAACTTAT
Found at i:13111980 original size:53 final size:52
Alignment explanation
Indices: 13111910--13112048 Score: 145
Period size: 53 Copynumber: 2.6 Consensus size: 52
13111900 TAAATATTTA
* * * * *
13111910 ACATAACTTACAAAACTTACATAACTTATATAACTTAGATAA-ATATATAACTT
1 ACATAACTTACATAACTTACATAACTTACATAA-ATAGATAACATACATAA-AT
* * * *
13111963 ACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTACATAAAT
1 ACATAACTTACATAACTTACATAACTTACATAAATAGATAACATACATAAAT
* *
13112015 ATATATCATTACATAACTTACATAACTTACATAA
1 ACATAAC-TTACATAACTTACATAACTTACATAA
13112049 TACTTAAATA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
52 12 0.17
53 60 0.83
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (52 bp):
ACATAACTTACATAACTTACATAACTTACATAAATAGATAACATACATAAAT
Found at i:13112010 original size:44 final size:44
Alignment explanation
Indices: 13111912--13112012 Score: 193
Period size: 44 Copynumber: 2.3 Consensus size: 44
13111902 AATATTTAAC
*
13111912 ATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATAT
13111956 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATAT
13112000 ATAACTTACATAA
1 ATAACTTACATAA
13112013 ATATATATCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.35
Consensus pattern (44 bp):
ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATAT
Found at i:13112031 original size:44 final size:44
Alignment explanation
Indices: 13111912--13112039 Score: 170
Period size: 44 Copynumber: 2.9 Consensus size: 44
13111902 AATATTTAAC
*
13111912 ATAACTTACA-AAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAAA-TTACATAACTTACATAACTTAGATAAATAT
* *
13111956 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAAATTACATAACTTACATAACTTAGATAAATAT
* * *
13112000 ATAACTTACATAAA-TATATATCATTACATAACTTACATAA
1 ATAACTTACATAAATTACATAAC-TTACATAACTTAGATAA
13112040 CTTACATAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
43 6 0.08
44 68 0.89
45 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (44 bp):
ATAACTTACATAAATTACATAACTTACATAACTTAGATAAATAT
Found at i:13113932 original size:12 final size:12
Alignment explanation
Indices: 13113915--13113939 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13113905 AAGATCGAGG
13113915 GATGAATCTGAT
1 GATGAATCTGAT
13113927 GATGAATCTGAT
1 GATGAATCTGAT
13113939 G
1 G
13113940 GAGAGGATGA
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:0.08, G:0.28, T:0.32
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:13117273 original size:13 final size:14
Alignment explanation
Indices: 13117257--13117285 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13117247 TTCTAAATAT
13117257 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
13117270 TTATAATTGTTTAA
1 TTATAATTGTTTAA
13117284 TT
1 TT
13117286 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:13117739 original size:21 final size:20
Alignment explanation
Indices: 13117715--13117796 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 20
13117705 AGCAAAAAAG
*
13117715 GAGGCAGCGACAGTAGCGAGA
1 GAGGCAGCGGCAG-AGCGAGA
*
13117736 GAGGCAGCGGCAGCAGCGAGG
1 GAGGCAGCGGCAG-AGCGAGA
*
13117757 GAGGCAGAGGCACGAGCGAGA
1 GAGGCAGCGGCA-GAGCGAGA
*
13117778 GAGGCAGAGGCAGCAGCGA
1 GAGGCAGCGGCAG-AGCGA
13117797 TGGCAGCAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 52 0.96
22 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.48, T:0.01
Consensus pattern (20 bp):
GAGGCAGCGGCAGAGCGAGA
Found at i:13117760 original size:42 final size:42
Alignment explanation
Indices: 13117714--13117796 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
13117704 CAGCAAAAAA
* *
13117714 GGAGGCAGCGACA-GTAGCGAGAGAGGCAGCGGCAGCAGCGAG
1 GGAGGCAGAGACACG-AGCGAGAGAGGCAGAGGCAGCAGCGAG
*
13117756 GGAGGCAGAGGCACGAGCGAGAGAGGCAGAGGCAGCAGCGA
1 GGAGGCAGAGACACGAGCGAGAGAGGCAGAGGCAGCAGCGA
13117797 TGGCAGCAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.48, T:0.01
Consensus pattern (42 bp):
GGAGGCAGAGACACGAGCGAGAGAGGCAGAGGCAGCAGCGAG
Found at i:13118233 original size:43 final size:43
Alignment explanation
Indices: 13118198--13118290 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 43
13118188 AAGTCATGGA
* *
13118198 TTTTAGCAGCGCTTTCCCAACAAACACCGCTAAAAGCCATTAC
1 TTTTAGCAGCACTTTCCCAACAAACACCGCTAAAAGCCATGAC
* * ** *
13118241 TTTTAACGGCACTTTTTCAACAAACGCCGCTAAAAGCCATGAC
1 TTTTAGCAGCACTTTCCCAACAAACACCGCTAAAAGCCATGAC
13118284 TTTTAGC
1 TTTTAGC
13118291 GGTGTTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (43 bp):
TTTTAGCAGCACTTTCCCAACAAACACCGCTAAAAGCCATGAC
Found at i:13128433 original size:15 final size:14
Alignment explanation
Indices: 13128404--13128446 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
13128394 ATTCCATCAC
*
13128404 TTTTGTTTAAATTT
1 TTTTATTTAAATTT
13128418 TTTTATTTAGAATTT
1 TTTTATTTA-AATTT
13128433 TTTATATGTTAAAT
1 TTT-TAT-TTAAAT
13128447 ATAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 8 0.32
16 6 0.24
17 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (14 bp):
TTTTATTTAAATTT
Found at i:13129235 original size:16 final size:15
Alignment explanation
Indices: 13129203--13129231 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13129193 CGTGTCTCTC
13129203 TTTTTTAAATATTTA
1 TTTTTTAAATATTTA
13129218 TTTTTTAAATATTT
1 TTTTTTAAATATTT
13129232 TATTATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTAAATATTTA
Found at i:13131508 original size:19 final size:18
Alignment explanation
Indices: 13131486--13131528 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
13131476 ATTAGAACTC
*
13131486 ATTAATTTAATTATATAAT
1 ATTAATTTAATT-TAAAAT
*
13131505 ATTATCTTTAATTTAAAAT
1 ATTA-ATTTAATTTAAAAT
13131524 ATTAA
1 ATTAA
13131529 AATAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATTTAATTTAAAAT
Found at i:13132429 original size:2 final size:2
Alignment explanation
Indices: 13132422--13132465 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
13132412 AACACTCTTT
*
13132422 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13132464 TC
1 TC
13132466 ACTCATTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:13132470 original size:10 final size:10
Alignment explanation
Indices: 13132422--13132470 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
13132412 AACACTCTTT
*
13132422 TCTCTCTCTC
1 TCTCTCTCAC
*
13132432 TCTCTCTCTC
1 TCTCTCTCAC
*
13132442 TCTCTCTCTC
1 TCTCTCTCAC
13132452 TCTCTCTCAC
1 TCTCTCTCAC
*
13132462 TCTCACTCA
1 TCTCTCTCA
13132471 TTGGCATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.45
Consensus pattern (10 bp):
TCTCTCTCAC
Found at i:13139107 original size:2 final size:2
Alignment explanation
Indices: 13139097--13139129 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13139087 TGTACTTTTT
*
13139097 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
13139130 TTGGTCACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:13143653 original size:20 final size:20
Alignment explanation
Indices: 13143628--13143673 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
13143618 GTATTTACTA
13143628 TTTTAGATATCACAACCAAG
1 TTTTAGATATCACAACCAAG
13143648 TTTTAGATATCACAACCAAG
1 TTTTAGATATCACAACCAAG
13143668 TTTTAG
1 TTTTAG
13143674 TTTTGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (20 bp):
TTTTAGATATCACAACCAAG
Found at i:13145761 original size:26 final size:26
Alignment explanation
Indices: 13145732--13145839 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
13145722 TGATACAAAT
*
13145732 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
13145758 TGATAATAGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13145784 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
13145810 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13145836 TGAT
1 TGAT
13145840 GGGAATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:13147353 original size:26 final size:26
Alignment explanation
Indices: 13147324--13147376 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
13147314 TTTACAGTTT
13147324 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
13147350 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
13147376 T
1 T
13147377 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:13147898 original size:137 final size:136
Alignment explanation
Indices: 13147624--13147909 Score: 475
Period size: 137 Copynumber: 2.1 Consensus size: 136
13147614 GAGTAGTCTC
* *
13147624 CCCAAATGGGCTTGTATATGTTATTGATGTTGCAGGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCAGGTATTTTGAAATGGGCCTATGGGCCATACT
13147689 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
13147754 CTATTA
131 CTATTA
* *
13147760 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTG-AATGGGCCTATGGGCCATAT
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCAGGTATTTTGAAATGGGCCTATGGGCCATAC
*
13147824 TGTTATCTGAATAAGGGGCTAAGGCCTCAGTTTATTGTAATTTGAAAAGGGCTCTGGCCCAGTAC
65 TGTTATCTGAATAAGGGGCTAAGGCC-CAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTAC
*
13147889 CACTGTTA
129 CACTATTA
**
13147897 CCTGAATGGGCTT
1 CCCAAATGGGCTT
13147910 AGGCCCAATG
Statistics
Matches: 140, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
136 64 0.46
137 76 0.54
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCAGGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTATTA
Found at i:13152010 original size:17 final size:18
Alignment explanation
Indices: 13151976--13152011 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13151966 TGAATTTCTA
13151976 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
13151994 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
13152011 T
1 T
13152012 AACTCATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:13156882 original size:6 final size:6
Alignment explanation
Indices: 13156871--13156915 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
13156861 TAAGTCTACG
* *
13156871 AAAATA AAAATA AACATA AACATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
13156916 GAAAACAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:13161120 original size:3 final size:3
Alignment explanation
Indices: 13161107--13161167 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
13161097 TAAATAACGT
*
13161107 ATA AAA ATA ATA ATA ATA ATA A-A GA-A ATA A-A ATA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA
*
13161151 ATA ATT ATA ATA GATA A
1 ATA ATA ATA ATA -ATA A
13161168 CAAATAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:13161154 original size:38 final size:42
Alignment explanation
Indices: 13161107--13161191 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 42
13161097 TAAATAACGT
* *
13161107 ATAAAAATAATAATAATA-ATAA-AGA-AATAAAATAA-TAA
1 ATAATAATAATAATAATAGATAACAAATAATAAAATAATTAA
* *
13161145 ATAATAATAATTATAATAGATAACAAATAATTAAATAATTAA
1 ATAATAATAATAATAATAGATAACAAATAATAAAATAATTAA
13161187 ATAAT
1 ATAAT
13161192 TAAATAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 16 0.41
39 4 0.10
40 2 0.05
41 9 0.23
42 8 0.21
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (42 bp):
ATAATAATAATAATAATAGATAACAAATAATAAAATAATTAA
Found at i:13165809 original size:304 final size:304
Alignment explanation
Indices: 13165260--13165867 Score: 1117
Period size: 304 Copynumber: 2.0 Consensus size: 304
13165250 TCAAAATACA
13165260 GCATTTACTTAAAAAATCATATAACAATCACAATTATTTAATTGTTCAATTCGTAGACAAATTCC
1 GCATTTACTTAAAAAATCATATAACAATCACAATTATTTAATTGTTCAATTCGTAGACAAATTCC
*
13165325 TTATACTAATTCAATTCTTGTCATCTATTAAACCAATAGCTTTTCTCAATAAATTCACAAATCAT
66 TTATACTAATTCAATTCTTGTCATCTATTAAACCAATAGCTTTTCACAATAAATTCACAAATCAT
*
13165390 TAGAGCAATAATATTCTTCATTCACATCCAATTCAGAGATACTTAATTCATGTGCCTTATTCATA
131 TAGAACAATAATATTCTTCATTCACATCCAATTCAGAGATACTTAATTCATGTGCCTTATTCATA
* *
13165455 CTTTAGTTCACTGTTTAATTTCAATAAATATTATTCAACAATTCACTTGTCAATCAATATTCTGT
196 ATTTAGTTCACTGTTCAATTTCAATAAATATTATTCAACAATTCACTTGTCAATCAATATTCTGT
* *
13165520 ACTCATTCATTCCAATAATAGTTAGTATTTTCAATATTAATCAC
261 ACTCATTCATTCCAATAACAATTAGTATTTTCAATATTAATCAC
13165564 GCATTTACTTAAAAAATCATATAACAATCACAATTATTTAATTGTTCAATTCGTAGACAAATTCC
1 GCATTTACTTAAAAAATCATATAACAATCACAATTATTTAATTGTTCAATTCGTAGACAAATTCC
*
13165629 TTATACTAATTCAATTCTTGTCATCTATTAACCCAATAGCTTTTCACAATAAATTCACAAATCAT
66 TTATACTAATTCAATTCTTGTCATCTATTAAACCAATAGCTTTTCACAATAAATTCACAAATCAT
* *
13165694 TAGAACAATAATATTCTTCATTCATATCCAATTCAGAGATACTTAATTCATGTGTCTTATTCATA
131 TAGAACAATAATATTCTTCATTCACATCCAATTCAGAGATACTTAATTCATGTGCCTTATTCATA
* *
13165759 ATTTAGTTCACTGTTCAATTTTAATAAATATTATTTAACAATTCACTTGTCAATCAATATTCTGT
196 ATTTAGTTCACTGTTCAATTTCAATAAATATTATTCAACAATTCACTTGTCAATCAATATTCTGT
13165824 ACTCATTCATTCCAATAACAATTAGTATTTTCAATATTAATCAC
261 ACTCATTCATTCCAATAACAATTAGTATTTTCAATATTAATCAC
13165868 TTTATCAATT
Statistics
Matches: 293, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
304 293 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.40
Consensus pattern (304 bp):
GCATTTACTTAAAAAATCATATAACAATCACAATTATTTAATTGTTCAATTCGTAGACAAATTCC
TTATACTAATTCAATTCTTGTCATCTATTAAACCAATAGCTTTTCACAATAAATTCACAAATCAT
TAGAACAATAATATTCTTCATTCACATCCAATTCAGAGATACTTAATTCATGTGCCTTATTCATA
ATTTAGTTCACTGTTCAATTTCAATAAATATTATTCAACAATTCACTTGTCAATCAATATTCTGT
ACTCATTCATTCCAATAACAATTAGTATTTTCAATATTAATCAC
Found at i:13165920 original size:18 final size:18
Alignment explanation
Indices: 13165880--13166085 Score: 225
Period size: 18 Copynumber: 11.4 Consensus size: 18
13165870 TATCAATTTC
*
13165880 ATTCAGTAAC-GATCAATT
1 ATTCAGTAACAG-TCAGTT
* *
13165898 GTTCAGTAACAGTCGGTT
1 ATTCAGTAACAGTCAGTT
* *
13165916 ATTCAGTAATAGTCATTT
1 ATTCAGTAACAGTCAGTT
*
13165934 ATTCAGTAACAGTCAATT
1 ATTCAGTAACAGTCAGTT
* *
13165952 ATTCAGTAATAATCAGTT
1 ATTCAGTAACAGTCAGTT
* *
13165970 ATTCAATAACAGTCATTT
1 ATTCAGTAACAGTCAGTT
*
13165988 ATTCAGTAACAGTCATTT
1 ATTCAGTAACAGTCAGTT
* *
13166006 ATTCAGTAATAATCAGTT
1 ATTCAGTAACAGTCAGTT
*
13166024 ATTCAGTAACAGTCATTT
1 ATTCAGTAACAGTCAGTT
* * *
13166042 ATTTAGTAACAGTTAATT
1 ATTCAGTAACAGTCAGTT
* *
13166060 ATTCAGTAGCAGTTAGTT
1 ATTCAGTAACAGTCAGTT
13166078 ATTCAGTA
1 ATTCAGTA
13166086 CCTTTATTTA
Statistics
Matches: 158, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
18 157 0.99
19 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTCAGTAACAGTCAGTT
Found at i:13165939 original size:54 final size:54
Alignment explanation
Indices: 13165875--13166085 Score: 280
Period size: 54 Copynumber: 3.9 Consensus size: 54
13165865 CACTTTATCA
* * * *
13165875 ATTTCATTCAGTAAC-GATCAATTGTTCAGTAACAGTCGGTTATTCAGTAATAGTC
1 ATTT-ATTCAGTAACAG-TCAATTATTCAGTAACAATCAGTTATTCAGTAACAGTC
* *
13165930 ATTTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATTCAATAACAGTC
1 ATTTATTCAGTAACAGTCAATTATTCAGTAACAATCAGTTATTCAGTAACAGTC
* *
13165984 ATTTATTCAGTAACAGTCATTTATTCAGTAATAATCAGTTATTCAGTAACAGTC
1 ATTTATTCAGTAACAGTCAATTATTCAGTAACAATCAGTTATTCAGTAACAGTC
* * * * *
13166038 ATTTATTTAGTAACAGTTAATTATTCAGTAGCAGTTAGTTATTCAGTA
1 ATTTATTCAGTAACAGTCAATTATTCAGTAACAATCAGTTATTCAGTA
13166086 CCTTTATTTA
Statistics
Matches: 140, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
54 135 0.96
55 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (54 bp):
ATTTATTCAGTAACAGTCAATTATTCAGTAACAATCAGTTATTCAGTAACAGTC
Found at i:13167511 original size:15 final size:14
Alignment explanation
Indices: 13167485--13167514 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
13167475 CCTATTTCTC
13167485 CCTTTTCTTTCTTT
1 CCTTTTCTTTCTTT
13167499 CCTTTTCCTTTCTTT
1 CCTTTT-CTTTCTTT
13167514 C
1 C
13167515 TTTCTCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
CCTTTTCTTTCTTT
Found at i:13168080 original size:23 final size:24
Alignment explanation
Indices: 13168049--13168105 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
13168039 ATATATTTTT
13168049 ATACATTTGTACAATATCAATACC
1 ATACATTTGTACAATATCAATACC
*
13168073 ATAC-TTTGTTCAATATCAATACC
1 ATACATTTGTACAATATCAATACC
*
13168096 ATACAATTGT
1 ATACATTTGT
13168106 CATACTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (24 bp):
ATACATTTGTACAATATCAATACC
Found at i:13178281 original size:3 final size:3
Alignment explanation
Indices: 13178273--13178298 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13178263 ATGAAGATAA
13178273 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
13178299 ATGGCAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:13179998 original size:30 final size:31
Alignment explanation
Indices: 13179964--13180034 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
13179954 TGCAATTCCC
*
13179964 TTTATAATTTTTAA-A-ACATTAAATTAAAAT
1 TTTAT-ATTTTTAAGAGACATTAAAGTAAAAT
* *
13179994 TTTATCA-TTTTAAGAGAGATTAAAGTATAAT
1 TTTAT-ATTTTTAAGAGACATTAAAGTAAAAT
13180025 TTTATATTTT
1 TTTATATTTT
13180035 ACTAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 6 0.18
30 8 0.24
31 20 0.59
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
TTTATATTTTTAAGAGACATTAAAGTAAAAT
Found at i:13184616 original size:25 final size:25
Alignment explanation
Indices: 13184571--13184620 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13184561 CACCCAAATT
* **
13184571 CAATTTTAAATTTTATTTTTTTATA
1 CAATTTTAAATTATAAATTTTTATA
13184596 CAATTTTAAATTATAAATTTTTATA
1 CAATTTTAAATTATAAATTTTTATA
13184621 TTCTAAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
CAATTTTAAATTATAAATTTTTATA
Found at i:13186223 original size:20 final size:21
Alignment explanation
Indices: 13186184--13186223 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
13186174 CACCAAGTGA
13186184 AAGCATTTACATAAACAACTTC
1 AAGCATTTA-ATAAACAACTTC
*
13186206 AAGCATTT-ATATACAACT
1 AAGCATTTAATAAACAACT
13186224 ATGTTCTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (21 bp):
AAGCATTTAATAAACAACTTC
Found at i:13189117 original size:26 final size:26
Alignment explanation
Indices: 13189080--13189213 Score: 241
Period size: 26 Copynumber: 5.2 Consensus size: 26
13189070 TGATACAAAT
*
13189080 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
13189106 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13189132 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13189158 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
13189184 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13189210 TGAT
1 TGAT
13189214 GGGCATTTCA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:13190728 original size:26 final size:26
Alignment explanation
Indices: 13190699--13190751 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
13190689 TTTACAGTTT
13190699 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
13190725 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
13190751 T
1 T
13190752 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:13200722 original size:35 final size:35
Alignment explanation
Indices: 13200682--13200752 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
13200672 TCTAGGATCA
*
13200682 CATATCTTTGAAGATCAGC-TTCCATATTTGCCAAG
1 CATATCTTTGAAGATCA-CTTTCCATATTTACCAAG
*
13200717 CATATCTTTGAATATCACTTTCCATATTTACCAAG
1 CATATCTTTGAAGATCACTTTCCATATTTACCAAG
13200752 C
1 C
13200753 TCCGGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (35 bp):
CATATCTTTGAAGATCACTTTCCATATTTACCAAG
Found at i:13203416 original size:9 final size:9
Alignment explanation
Indices: 13203402--13203433 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
13203392 ACATTAACAT
*
13203402 ATTATTTGA
1 ATTATTTAA
13203411 ATTATTTAA
1 ATTATTTAA
13203420 ATTATTTAA
1 ATTATTTAA
13203429 ATTAT
1 ATTAT
13203434 AAAATTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (9 bp):
ATTATTTAA
Found at i:13204827 original size:19 final size:18
Alignment explanation
Indices: 13204779--13204829 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
13204769 CCTTGATCCG
13204779 ATACATGATTAGAAAATTTA
1 ATACATGA-T-GAAAATTTA
*
13204799 A-ACGAAGATGAAGAATTTA
1 ATAC-ATGATGAA-AATTTA
13204818 ATACATGATGAA
1 ATACATGATGAA
13204830 CTTAAAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.12
19 17 0.65
20 6 0.23
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (18 bp):
ATACATGATGAAAATTTA
Found at i:13218133 original size:2 final size:2
Alignment explanation
Indices: 13218126--13218236 Score: 59
Period size: 2 Copynumber: 62.0 Consensus size: 2
13218116 TACTGCTGCT
* *
13218126 TC TC TC TC TC -C TC TC TC TC TC CC TT TC -C T- TC TC -C T- TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
13218163 TC -C T- TT TC TC TC -C TC TC TC TC TC -C T- TT TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
13218200 TC -C TC TC -C T- TC TC TC TC TC TT TC TC TT TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13218237 CTTATCCCTA
Statistics
Matches: 82, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
1 13 0.16
2 69 0.84
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13218158 original size:27 final size:27
Alignment explanation
Indices: 13218128--13218225 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 27
13218118 CTGCTGCTTC
*
13218128 TCTCTCTCCTCTCTCTCTCCCTTTCCT
1 TCTCTCTCCTCTCTCTCTCCCTCTCCT
*
13218155 TCTCCTTCTCCT-TTTCTCTCCTCTCTCTCT
1 TCT-C-TCTCCTCTCTCTCTCC-CTCTC-CT
* *
13218185 CCT-TTTCC-CTCTCTCT-CCTCTCCT
1 TCTCTCTCCTCTCTCTCTCCCTCTCCT
*
13218209 TCTCTCT-CTCTTTCTCT
1 TCTCTCTCCTCTCTCTCT
13218226 TTCTCTTTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
24 5 0.09
25 14 0.25
26 1 0.02
27 13 0.23
28 9 0.16
29 10 0.18
30 4 0.07
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (27 bp):
TCTCTCTCCTCTCTCTCTCCCTCTCCT
Found at i:13218173 original size:39 final size:39
Alignment explanation
Indices: 13218130--13218265 Score: 125
Period size: 39 Copynumber: 3.5 Consensus size: 39
13218120 GCTGCTTCTC
13218130 TCTCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCCTTT
1 TCTCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCCTTT
* * *
13218169 TCTCTCCTCTCTCTCTCCTTTTCCCTCT-C-TCTCCTCT
1 TCTCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCCTTT
* * * * * *
13218206 CCT-TCTCTCTCTCTTTCTCTTTCTCTTTCTCCTTATCCCTA
1 TCTCTC-CTCTCTCTCTCCCTTTC-C-TTCTCCTTCTCCTTT
* *
13218247 TCTCTCCTTTCTCTTTCCC
1 TCTCTCCTCTCTCTCTCCC
13218266 NCTCTATCTT
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
36 2 0.03
37 23 0.30
38 2 0.03
39 29 0.38
40 1 0.01
41 17 0.22
42 2 0.03
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.51
Consensus pattern (39 bp):
TCTCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCCTTT
Found at i:13218237 original size:35 final size:35
Alignment explanation
Indices: 13218125--13218263 Score: 101
Period size: 35 Copynumber: 3.9 Consensus size: 35
13218115 CTACTGCTGC
* *
13218125 TTCTCTCTCTCCTCTCTCTCTCCCTTTC-C-TTCTCC
1 TTCTC-CTCTCCT-TCTCTCTCTCTTTCTCTTTCTCT
*
13218160 TTCTCCT-T--TTCTCTCCTCTCTCTCTCCTTTTCCCTCT
1 TTCTCCTCTCCTTCTCT-CTCTCTTTCT-C-TTT--CTCT
*
13218197 CTCTCCTCTCCTTCTCTCTCTCTTTCTCTTTCTCT
1 TTCTCCTCTCCTTCTCTCTCTCTTTCTCTTTCTCT
* * *
13218232 TTCTCCTTATCCCTATCTCTC-CTTTCTCTTTC
1 TTCTCC-TCTCCTTCTCTCTCTCTTTCTCTTTC
13218264 CCNCTCTATC
Statistics
Matches: 84, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
30 5 0.06
31 8 0.10
33 2 0.02
34 2 0.02
35 27 0.32
36 11 0.13
37 12 0.14
38 2 0.02
39 9 0.11
40 6 0.07
ACGTcount: A:0.01, C:0.46, G:0.00, T:0.53
Consensus pattern (35 bp):
TTCTCCTCTCCTTCTCTCTCTCTTTCTCTTTCTCT
Found at i:13218237 original size:51 final size:54
Alignment explanation
Indices: 13218138--13218254 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 54
13218128 TCTCTCTCCT
* *
13218138 CTCTCTCTCCCTTTCCTTCTCCTTCTCCTTTTCTCTCCTCTCTCTCTCCTTTTCC
1 CTCTCTCT-CCTCTCCTTCTCCTTCTCCTTTTCTCTCCTCTCTCTCTCCTTATCC
* *
13218193 CTCTCTCTCCTCTCCTTCT-C-TCT-CTCTTTCTCT-TTCTCTTTCTCCTTATCC
1 CTCTCTCTCCTCTCCTTCTCCTTCTCCT-TTTCTCTCCTCTCTCTCTCCTTATCC
*
13218244 CTATCTCTCCT
1 CTCTCTCTCCT
13218255 TTCTCTTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
51 27 0.48
52 10 0.18
53 1 0.02
54 10 0.18
55 8 0.14
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (54 bp):
CTCTCTCTCCTCTCCTTCTCCTTCTCCTTTTCTCTCCTCTCTCTCTCCTTATCC
Found at i:13222361 original size:33 final size:33
Alignment explanation
Indices: 13222331--13222404 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
13222321 TTAGTCACTA
13222331 AAATTTAAGCAATTGTGACAAAAAATGTCACAT
1 AAATTTAAGCAATTGTGACAAAAAATGTCACAT
* * **
13222364 ATATTTAATCTTTTGTGACAAAAAATGTCACAT
1 AAATTTAAGCAATTGTGACAAAAAATGTCACAT
*
13222397 ATATTTAA
1 AAATTTAA
13222405 TCTTTTGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (33 bp):
AAATTTAAGCAATTGTGACAAAAAATGTCACAT
Found at i:13222405 original size:33 final size:33
Alignment explanation
Indices: 13222343--13222415 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
13222333 ATTTAAGCAA
13222343 TTGTGACAAAAAATGTCACATATATTTAATCTT
1 TTGTGACAAAAAATGTCACATATATTTAATCTT
13222376 TTGTGACAAAAAATGTCACATATATTTAATCTT
1 TTGTGACAAAAAATGTCACATATATTTAATCTT
13222409 TTGTGAC
1 TTGTGAC
13222416 TAAATTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (33 bp):
TTGTGACAAAAAATGTCACATATATTTAATCTT
Found at i:13225024 original size:22 final size:22
Alignment explanation
Indices: 13224999--13225045 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
13224989 TTTCAGTTCC
13224999 TTATCTATTTGAACTCAGGCTT
1 TTATCTATTTGAACTCAGGCTT
13225021 TTATCTATTTGAACTCAGGCTT
1 TTATCTATTTGAACTCAGGCTT
13225043 TTA
1 TTA
13225046 CTTACATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (22 bp):
TTATCTATTTGAACTCAGGCTT
Found at i:13225352 original size:15 final size:15
Alignment explanation
Indices: 13225332--13225361 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13225322 ATTATGAAAG
13225332 ATATGTTTTGGATTA
1 ATATGTTTTGGATTA
*
13225347 ATATGTTTTGTATTA
1 ATATGTTTTGGATTA
13225362 GAATTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTA
Found at i:13225982 original size:41 final size:42
Alignment explanation
Indices: 13225923--13226048 Score: 139
Period size: 41 Copynumber: 3.0 Consensus size: 42
13225913 TAGGATTTCT
* *
13225923 GATATGTGATTACATGTAAAACCATGTCTGGGACATTGGCATC
1 GATATGTGATT-GATGTAAGACCATGTCTGGGACATTGGCATC
* * *
13225966 G-TATTTGATTCG-TGTAAGACCCTGTCTGGGACAATGGCATC
1 GATATGTGATT-GATGTAAGACCATGTCTGGGACATTGGCATC
* * *
13226007 GATATGTGATTGTATGTAAGACCACGTTTGGGACTTTGGCAT
1 GATATGTGATTG-ATGTAAGACCATGTCTGGGACATTGGCAT
13226049 TGTACGATAT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 28 0.41
42 16 0.24
43 24 0.35
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (42 bp):
GATATGTGATTGATGTAAGACCATGTCTGGGACATTGGCATC
Found at i:13230589 original size:34 final size:35
Alignment explanation
Indices: 13230550--13230623 Score: 141
Period size: 34 Copynumber: 2.1 Consensus size: 35
13230540 CTATATTGCC
13230550 ATTATCAATGTTAGTTTCTACAATATTTTTAATGT
1 ATTATCAATGTTAGTTTCTACAATATTTTTAATGT
13230585 -TTATCAATGTTAGTTTCTACAATATTTTTAATGT
1 ATTATCAATGTTAGTTTCTACAATATTTTTAATGT
13230619 ATTAT
1 ATTAT
13230624 ATATATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (35 bp):
ATTATCAATGTTAGTTTCTACAATATTTTTAATGT
Found at i:13237980 original size:2 final size:2
Alignment explanation
Indices: 13237973--13237998 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13237963 AGCATTTAAA
13237973 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
13237999 TTTGACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13240080 original size:30 final size:30
Alignment explanation
Indices: 13240045--13240104 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
13240035 TTTTTTATTA
13240045 TTAATTTTGTTATAATTTTAGAGGCATTTG
1 TTAATTTTGTTATAATTTTAGAGGCATTTG
* *
13240075 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATAATTTTAGAGGCATTTG
13240105 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATAATTTTAGAGGCATTTG
Found at i:13242177 original size:18 final size:18
Alignment explanation
Indices: 13242150--13242223 Score: 103
Period size: 18 Copynumber: 4.1 Consensus size: 18
13242140 TACGACCATT
*
13242150 TACGGTACTATTCACATA
1 TACGGCACTATTCACATA
**
13242168 TACGGCACTATTCATGTA
1 TACGGCACTATTCACATA
* *
13242186 TACGGTACTATTCACGTA
1 TACGGCACTATTCACATA
13242204 TACGGCACTATTCACATA
1 TACGGCACTATTCACATA
13242222 TA
1 TA
13242224 TACGGTACTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (18 bp):
TACGGCACTATTCACATA
Found at i:13242197 original size:36 final size:37
Alignment explanation
Indices: 13242150--13242244 Score: 147
Period size: 36 Copynumber: 2.6 Consensus size: 37
13242140 TACGACCATT
* *
13242150 TACGGTACTATTCACATATACGGCACTATT-CATGTA
1 TACGGTACTATTCACGTATACGGCACTATTACATATA
13242186 TACGGTACTATTCACGTATACGGCACTATTCACATATA
1 TACGGTACTATTCACGTATACGGCACTATT-ACATATA
*
13242224 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
13242245 AGTAGTTGGG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 29 0.54
38 25 0.46
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (37 bp):
TACGGTACTATTCACGTATACGGCACTATTACATATA
Found at i:13248572 original size:29 final size:31
Alignment explanation
Indices: 13248499--13248581 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
13248489 TCATAATTAC
* * *
13248499 AAAAGTATAGGGACTAAAAGTGAGCAATTTG
1 AAAAGTATAAGGACTAAAATTGAGCAATATG
* * *
13248530 AAAAGTACATGGACTAAAATTGATCAA-AT-
1 AAAAGTATAAGGACTAAAATTGAGCAATATG
*
13248559 AAAAGTATAAGGACTAAATTTGA
1 AAAAGTATAAGGACTAAAATTGA
13248582 AACTTTTACA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.45
30 1 0.02
31 23 0.52
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.24
Consensus pattern (31 bp):
AAAAGTATAAGGACTAAAATTGAGCAATATG
Found at i:13249195 original size:23 final size:21
Alignment explanation
Indices: 13249169--13249217 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
13249159 ATTTAACCAA
13249169 AAAAAGAAAAGAA-AAGAAAGTTT
1 AAAAA-AAAAGAAGAAGAAA--TT
*
13249192 AAAAAAGAAGAAGAAGAAATT
1 AAAAAAAAAGAAGAAGAAATT
13249213 AAAAA
1 AAAAA
13249218 TTAATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.10
Consensus pattern (21 bp):
AAAAAAAAAGAAGAAGAAATT
Found at i:13251772 original size:5 final size:6
Alignment explanation
Indices: 13251757--13251781 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13251747 ATAAGTCTTG
13251757 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
13251782 GTTGAACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:13253993 original size:10 final size:10
Alignment explanation
Indices: 13253971--13254004 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
13253961 TTGTTAACTA
13253971 AAAAATATATT
1 AAAAATAT-TT
13253982 AAAAATATTT
1 AAAAATATTT
13253992 AAAAATA-TT
1 AAAAATATTT
13254001 AAAA
1 AAAA
13254005 TAAATATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.26
10 9 0.39
11 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATATTT
Found at i:13256082 original size:18 final size:18
Alignment explanation
Indices: 13256061--13256343 Score: 142
Period size: 18 Copynumber: 15.3 Consensus size: 18
13256051 GAACAATTAT
13256061 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
13256079 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
13256097 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
13256115 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
13256141 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
13256159 TTATTAAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
13256176 ATATTCAGTAACAATTAAG
1 TTATTCAGTAAC-AGTCAG
*
13256195 TTATTCAGTAACAATCA-
1 TTATTCAGTAACAGTCAG
** *
13256212 TTCATTCAGCGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* * *
13256231 TTATTCAATAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
13256249 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
13256267 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
13256285 ATATTCAGTAATAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
13256303 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
13256321 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
13256339 TTATT
1 TTATT
13256344 TTATACTTTT
Statistics
Matches: 197, Mismatches: 52, Indels: 32
0.70 0.19 0.11
Matches are distributed among these distances:
17 16 0.08
18 146 0.74
19 19 0.10
21 2 0.01
22 1 0.01
23 2 0.01
26 11 0.06
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:13256101 original size:36 final size:36
Alignment explanation
Indices: 13256048--13256343 Score: 197
Period size: 36 Copynumber: 8.0 Consensus size: 36
13256038 TCATTAACAC
* * *
13256048 TCAG-AACAATTATTTATTCAGTAACAGTCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
13256083 TCGGTAACAATCAATTATTCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
13256119 TCAGTATCGATCAATTGATCGGTTATCCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATT-A-----T-T-CAGTAACAATCAGTTAT
* *
13256163 TAAGTAA-AATCAGA-TATTCAGTAACAATTAAGTTAT
1 TCAGTAACAATCA-ATTATTCAGTAACAA-TCAGTTAT
**
13256199 TCAGTAACAATC-ATTCATTCAGCGACAATCAGTTAT
1 TCAGTAACAATCAATT-ATTCAGTAACAATCAGTTAT
* ** * *
13256235 TCAATAATGATCAATTATTCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
13256271 TCAGTAACAGTCTAA-TATTCAGTAATAGTCAATTAT
1 TCAGTAACAATC-AATTATTCAGTAACAATCAGTTAT
* * * *
13256307 CCGGTAACAGTCAATTATTCAGTAATAATCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
13256343 T
1 T
13256344 TTATACTTTT
Statistics
Matches: 201, Mismatches: 43, Indels: 33
0.73 0.16 0.12
Matches are distributed among these distances:
35 14 0.07
36 140 0.70
37 21 0.10
42 2 0.01
43 6 0.03
44 18 0.09
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (36 bp):
TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
Found at i:13256204 original size:54 final size:54
Alignment explanation
Indices: 13256141--13256343 Score: 187
Period size: 54 Copynumber: 3.8 Consensus size: 54
13256131 AATTGATCGG
* * *
13256141 TTATCCAGTAACAGTCAATTATTAAGTAA-AATCAGATATTCAGTAACAATTAA
1 TTATCCAGTAACAGTCAATTATTCAGTAACAATCAGATATTCAGTAATAATCAA
* * ** * * *
13256194 GTTATTCAGTAACAATC-ATTCATTCAGCGACAATCAGTTATTCAATAATGATCAA
1 -TTATCCAGTAACAGTCAATT-ATTCAGTAACAATCAGATATTCAGTAATAATCAA
* * * * * *
13256249 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA-ATATTCAGTAATAGTCAA
1 TTATCCAGTAACAGTCAATTATTCAGTAACAATC-AGATATTCAGTAATAATCAA
* * *
13256303 TTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TTATCCAGTAACAGTCAATTATTCAGTAACAATCAGATATT
13256344 TTATACTTTT
Statistics
Matches: 116, Mismatches: 28, Indels: 10
0.75 0.18 0.06
Matches are distributed among these distances:
53 4 0.03
54 90 0.78
55 22 0.19
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (54 bp):
TTATCCAGTAACAGTCAATTATTCAGTAACAATCAGATATTCAGTAATAATCAA
Found at i:13256263 original size:10 final size:10
Alignment explanation
Indices: 13256250--13256297 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
13256240 AATGATCAAT
13256250 TATTCAGTAA
1 TATTCAGTAA
13256260 TATTCAGT--
1 TATTCAGTAA
13256268 TATTCAGTAA
1 TATTCAGTAA
* *
13256278 CAGTC--TAA
1 TATTCAGTAA
13256286 TATTCAGTAA
1 TATTCAGTAA
13256296 TA
1 TA
13256298 GTCAATTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
8 14 0.47
10 16 0.53
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (10 bp):
TATTCAGTAA
Found at i:13256600 original size:51 final size:51
Alignment explanation
Indices: 13256507--13256644 Score: 143
Period size: 51 Copynumber: 2.7 Consensus size: 51
13256497 ACAAATCTGG
* * * * **
13256507 AACAGTACCAGTAACAGTATTCAATACACAAAGTGCTAAATCGATAACGGT
1 AACAGTAACAGTAACAGTATTCGACACACAAAGTGCCAAATCGATAAAAGT
* * *
13256558 AACAGTAGCAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAAAGT
1 AACAGTAACAGTAACAGTATTCGACACACAAAGTGCCAAATCGATAAAAGT
* * * * *
13256609 AACGGTAACAGTAGCAGTAGTCGGCACA-TAAGTGCC
1 AACAGTAACAGTAACAGTATTCGACACACAAAGTGCC
13256645 TGATCAGTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 7 0.10
51 66 0.90
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (51 bp):
AACAGTAACAGTAACAGTATTCGACACACAAAGTGCCAAATCGATAAAAGT
Found at i:13257119 original size:38 final size:38
Alignment explanation
Indices: 13257068--13257142 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
13257058 ATAAATAAAA
*
13257068 ACCTTGGCCACCTACTCCACCACCTTTGTTGGCCACCC
1 ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACCC
13257106 ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACC
1 ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACC
13257143 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.17, C:0.47, G:0.12, T:0.24
Consensus pattern (38 bp):
ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACCC
Found at i:13266118 original size:58 final size:59
Alignment explanation
Indices: 13266028--13266144 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 59
13266018 ACAAGAATTA
13266028 CCCCCGCCGCTACTCCAAAAGGAGGTTCGAGGTTTTCTAGGAAGGCTGAACTATATTGC
1 CCCCCGCCGCTACTCCAAAAGGAGGTTCGAGGTTTTCTAGGAAGGCTGAACTATATTGC
13266087 CCCCCGCCGCTACT-CAAAAGGAGGTTCGAGGTTTTCTAGGAAGGCTGAACTATATTGC
1 CCCCCGCCGCTACTCCAAAAGGAGGTTCGAGGTTTTCTAGGAAGGCTGAACTATATTGC
13266145 TCGGTTCATC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 44 0.76
59 14 0.24
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (59 bp):
CCCCCGCCGCTACTCCAAAAGGAGGTTCGAGGTTTTCTAGGAAGGCTGAACTATATTGC
Found at i:13268299 original size:51 final size:51
Alignment explanation
Indices: 13268223--13268321 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
13268213 CTTGGTAGAA
*
13268223 GAAAAGAGGTTAAAAGCTATTCGTCATGGTCAGATGTATCAGAAACGAGAG
1 GAAAAGAGGTCAAAAGCTATTCGTCATGGTCAGATGTATCAGAAACGAGAG
13268274 GAAAAGAGGTCAAAAGCTATTCGTCATGGTCAGATGTATCAGAAACGA
1 GAAAAGAGGTCAAAAGCTATTCGTCATGGTCAGATGTATCAGAAACGA
13268322 ATGATGCGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.21
Consensus pattern (51 bp):
GAAAAGAGGTCAAAAGCTATTCGTCATGGTCAGATGTATCAGAAACGAGAG
Found at i:13268815 original size:47 final size:47
Alignment explanation
Indices: 13268746--13268839 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
13268736 ACTACACCTG
13268746 AATCGCAAGAAAGAGTAGGTGACATCTTGGGGTATCGACAAAATACT
1 AATCGCAAGAAAGAGTAGGTGACATCTTGGGGTATCGACAAAATACT
* *
13268793 AATCGGAAGAAGGAGTAGGTGACATCTTGGGGTATCGACAAAATACT
1 AATCGCAAGAAAGAGTAGGTGACATCTTGGGGTATCGACAAAATACT
13268840 GTAGATTCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (47 bp):
AATCGCAAGAAAGAGTAGGTGACATCTTGGGGTATCGACAAAATACT
Found at i:13269325 original size:46 final size:46
Alignment explanation
Indices: 13269272--13269363 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
13269262 AAGGAAGAGT
*
13269272 CCAAGTCGGGACTATCCTTTCAGATTTTGTTGTCCAAACATTGACA
1 CCAAGTCGGGACTATCCTTTCAAATTTTGTTGTCCAAACATTGACA
13269318 CCAAGTCGGGACTATCCTTTCAAATTTTGTTGTCCAAACATTGACA
1 CCAAGTCGGGACTATCCTTTCAAATTTTGTTGTCCAAACATTGACA
13269364 AGATGTCGTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (46 bp):
CCAAGTCGGGACTATCCTTTCAAATTTTGTTGTCCAAACATTGACA
Found at i:13270282 original size:131 final size:131
Alignment explanation
Indices: 13269972--13270602 Score: 1118
Period size: 131 Copynumber: 4.8 Consensus size: 131
13269962 TCATGTATTG
* * *
13269972 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGCAGATCGAA
1 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
* ** *
13270037 GATAGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAGGATGCAGAGCTTGTCTTCCCA
66 GATAACAGGTCCTATCTTCCTATATTGATAGG-AGTGGATCCAATATGCAGATCTTGTCTTCCCA
13270102 TA
130 TA
13270104 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
1 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
13270169 GATAACAGGTCCTATCTTCCTATATTGATAGGAGTGGATCCAATATGCAGATCTTGTCTTCCCAT
66 GATAACAGGTCCTATCTTCCTATATTGATAGGAGTGGATCCAATATGCAGATCTTGTCTTCCCAT
13270234 A
131 A
13270235 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
1 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
13270300 GATAACAGGTCCTATCTTCCTATATTGATAGGAGTGGATCCAATATGCAGATCTTGTCTTCCCAT
66 GATAACAGGTCCTATCTTCCTATATTGATAGGAGTGGATCCAATATGCAGATCTTGTCTTCCCAT
13270365 A
131 A
13270366 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
1 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
13270431 GATAACAGGTCCTATCTTCCTATATTGATAGGAGTGGATCCAATATGCAGATCTTGTCTTCCCAT
66 GATAACAGGTCCTATCTTCCTATATTGATAGGAGTGGATCCAATATGCAGATCTTGTCTTCCCAT
13270496 A
131 A
* *
13270497 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAA
1 TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
* * * * *
13270562 GGTAGCAGATCCTATCTTTCTATATTGGTAGGAAGTGGATC
66 GATAACAGGTCCTATCTTCCTATATTGATAGG-AGTGGATC
13270603 GAAATCTTGT
Statistics
Matches: 484, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
131 383 0.79
132 101 0.21
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (131 bp):
TTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAA
GATAACAGGTCCTATCTTCCTATATTGATAGGAGTGGATCCAATATGCAGATCTTGTCTTCCCAT
A
Found at i:13270665 original size:80 final size:80
Alignment explanation
Indices: 13270529--13270682 Score: 254
Period size: 80 Copynumber: 1.9 Consensus size: 80
13270519 AAAGCAGATA
* * * *
13270529 TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTATATTGGTAGG
1 TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATATTCCTATATTGATAGG
13270594 AAGTGGATCGAAATC
66 AAGTGGATCGAAATC
* *
13270609 TTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGATAGG
1 TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATATTCCTATATTGATAGG
13270674 AAGTGGATC
66 AAGTGGATC
13270683 CAATATGCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (80 bp):
TTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATATTCCTATATTGATAGG
AAGTGGATCGAAATC
Found at i:13270763 original size:132 final size:132
Alignment explanation
Indices: 13270606--13271012 Score: 706
Period size: 132 Copynumber: 3.1 Consensus size: 132
13270596 GTGGATCGAA
13270606 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGAT
1 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGAT
13270671 AGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
66 AGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
13270736 AG
131 AG
13270738 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGAT
1 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGAT
13270803 AGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
66 AGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
13270868 AG
131 AG
* * * *
13270870 ATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGCCCTATCTTCCTATATTGAT
1 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGAT
* * * * * **
13270935 AGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGATTGC
66 AGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
13271000 AG
131 AG
*
13271002 ATCTTGCCTTC
1 ATCTTGTCTTC
13271013 CTNNNNNNNN
Statistics
Matches: 262, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 262 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (132 bp):
ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGAT
AGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
AG
Found at i:13270765 original size:212 final size:211
Alignment explanation
Indices: 13270395--13270814 Score: 750
Period size: 212 Copynumber: 2.0 Consensus size: 211
13270385 CAGAAAGCAG
*
13270395 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAACAGGTCCTATCTTCCTATATTGAT
1 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAACAGGTCCTATATTCCTATATTGAT
13270460 AGGAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCA
66 AGGAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCA
* * * *
13270525 GATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTATATTGG
131 GATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATATTCCTATATTGA
13270590 TAGGAAGTGGATCGAA
196 TAGGAAGTGGATCGAA
*
13270606 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGAT
1 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAACAGGTCCTATATTCCTATATTGAT
13270671 AGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
66 AGG-AGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
* * *
13270736 AGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTG
130 AGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATATTCCTATATTG
13270801 ATAGGAAGTGGATC
195 ATAGGAAGTGGATC
13270815 CAATATGCAG
Statistics
Matches: 199, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
211 66 0.33
212 133 0.67
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (211 bp):
ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAACAGGTCCTATATTCCTATATTGAT
AGGAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCA
GATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATATTCCTATATTGA
TAGGAAGTGGATCGAA
Found at i:13270932 original size:44 final size:44
Alignment explanation
Indices: 13270606--13271014 Score: 281
Period size: 44 Copynumber: 9.3 Consensus size: 44
13270596 GTGGATCGAA
* * *
13270606 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGAGTGAAGTAGATCGAAGATAGCAG
* * * * * * * *
13270650 GTCCTATATTCCTATATTGATAG-GAAGTGGATCCAATAT-GCAG
1 ATCTTGTCTTCCTATATTG-GAGTGAAGTAGATCGAAGATAGCAG
* * * * *
13270693 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAG
1 ATCTTGTCTTCCTATATTGG-AGTGAAGTAGATCGAAGATAGCAG
* * *
13270738 ATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGAGTGAAGTAGATCGAAGATAGCAG
* * * * * * * *
13270782 GTCCTATATTCCTATATTGATAG-GAAGTGGATCCAATAT-GCAG
1 ATCTTGTCTTCCTATATTG-GAGTGAAGTAGATCGAAGATAGCAG
* * * * *
13270825 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAG
1 ATCTTGTCTTCCTATATTGG-AGTGAAGTAGATCGAAGATAGCAG
* * * *
13270870 ATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGAGTGAAGTAGATCGAAGATAGCAG
** * * * * *
13270914 GCCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAGAT-GCAG
1 ATCTTGTCTTCCTATATTG-GAGTGAAGTAGATCGAAGATAGCAG
* * * * *
13270957 ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGATTGCAG
1 ATCTTGTCTTCCTATATTGG-AGTGAAGTAGATCGAAGATAGCAG
*
13271002 ATCTTGCCTTCCT
1 ATCTTGTCTTCCT
13271015 NNNNNNNNNN
Statistics
Matches: 268, Mismatches: 85, Indels: 23
0.71 0.23 0.06
Matches are distributed among these distances:
43 56 0.21
44 153 0.57
45 59 0.22
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (44 bp):
ATCTTGTCTTCCTATATTGGAGTGAAGTAGATCGAAGATAGCAG
Found at i:13271013 original size:88 final size:89
Alignment explanation
Indices: 13270606--13271014 Score: 330
Period size: 88 Copynumber: 4.7 Consensus size: 89
13270596 GTGGATCGAA
*** * * * *
13270606 ATCTTGTCTTCATGTATTGGT-GTGAAGTAGATCGAAGATAGCAGGTCCTATATTCCTATATTGA
1 ATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGA
* *
13270670 TAG-GAAGTGGATCCAATATGCAG
66 TAGCGAAGTAGATCCAAGATGCAG
* * * * * *
13270693 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGG
1 ATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGA
* *
13270758 T-GTGAAGTAGATCGAAGATAGCAG
66 TAGCGAAGTAGATCCAAGAT-GCAG
* * * * * * * * * * * *
13270782 GTCCTATATTCCTATATTGATAG-GAAGTGGATCCAATAT-GCAGATCTTGTCTTCCCATATTGG
1 ATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGA
* *
13270845 TGGCGAAGTAGATCGC-AGAAAGCAG
66 TAGCGAAGTAGATC-CAAG-ATGCAG
* *** * ** * *
13270870 ATATTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGCCCTATCTTCCTATATTGA
1 ATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGA
*
13270934 TAG-GAAGTGGATCCAAGATGCAG
66 TAGCGAAGTAGATCCAAGATGCAG
* * * *
13270957 ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGATTGCAGATCTTGCCTTCCT
1 ATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCT
13271015 NNNNNNNNNN
Statistics
Matches: 244, Mismatches: 68, Indels: 19
0.74 0.21 0.06
Matches are distributed among these distances:
87 63 0.26
88 140 0.57
89 41 0.17
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (89 bp):
ATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGA
TAGCGAAGTAGATCCAAGATGCAG
Found at i:13280201 original size:22 final size:24
Alignment explanation
Indices: 13280152--13280201 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
13280142 TTATTGGGGT
*
13280152 AAAAAAACTTAAAATAAATTTATA
1 AAAAAAACTTAAAATAAATTCATA
* *
13280176 AAAAAAA-TTATAAT-AATTCATG
1 AAAAAAACTTAAAATAAATTCATA
13280198 AAAA
1 AAAA
13280202 GTGATTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 6 0.26
24 7 0.30
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAAAACTTAAAATAAATTCATA
Found at i:13280201 original size:23 final size:23
Alignment explanation
Indices: 13280151--13280201 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
13280141 ATTATTGGGG
* *
13280151 TAAAAAAACTTAAAATAAATTTA
1 TAAAAAAAATTAAAATAAATTCA
*
13280174 TAAAAAAAATTATAAT-AATTCA
1 TAAAAAAAATTAAAATAAATTCA
*
13280196 TGAAAA
1 TAAAAA
13280202 GTGATTGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAAAAAAATTAAAATAAATTCA
Found at i:13281956 original size:17 final size:17
Alignment explanation
Indices: 13281936--13281968 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13281926 TTTTGAATAA
13281936 TTTAATTTTTTATTTTT
1 TTTAATTTTTTATTTTT
*
13281953 TTTATTTTTTTATTTT
1 TTTAATTTTTTATTTT
13281969 CCTTTTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTAATTTTTTATTTTT
Found at i:13282002 original size:122 final size:125
Alignment explanation
Indices: 13281876--13282108 Score: 427
Period size: 122 Copynumber: 1.9 Consensus size: 125
13281866 CCTCCCTTTT
*
13281876 ATTTTTCTATGTTTTTCATTTGTTAAAACTAATCCCTATATTTTTA-TTTTTTTTGAATAATTTA
1 ATTTTTCTATGTTTTTCATTTGTTAAAACTAATCCCTATACTTTTATTTTTTTTTGAATAATTTA
13281940 ATTTTTTA-TTT-TTTTTATTTTTTTATTTTCCTTTTCTTCTTCCATCTCTTTTAACTTA
66 ATTTTTTATTTTATTTTTATTTTTTTATTTTCCTTTTCTTCTTCCATCTCTTTTAACTTA
13281998 ATTTTTCTATGTTTTTCATTTGTTAAAACTAATCCCTATACTTTTATTTTTTTTTGAATAATTTA
1 ATTTTTCTATGTTTTTCATTTGTTAAAACTAATCCCTATACTTTTATTTTTTTTTGAATAATTTA
13282063 ATTTTTTATTTTTATTTTTATTTTTTTATTTTCCTTTTCTTCTTCC
66 ATTTTTTA-TTTTATTTTTATTTTTTTATTTTCCTTTTCTTCTTCC
13282109 CTTTTAGTTT
Statistics
Matches: 106, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
122 45 0.42
123 26 0.25
125 3 0.03
126 32 0.30
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (125 bp):
ATTTTTCTATGTTTTTCATTTGTTAAAACTAATCCCTATACTTTTATTTTTTTTTGAATAATTTA
ATTTTTTATTTTATTTTTATTTTTTTATTTTCCTTTTCTTCTTCCATCTCTTTTAACTTA
Found at i:13282100 original size:20 final size:20
Alignment explanation
Indices: 13282059--13282100 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13282049 TTTTGAATAA
*
13282059 TTTAATTTTTTATTTTTATT
1 TTTAATTTTTTATTTTCATT
* *
13282079 TTTATTTTTTTATTTTCCTT
1 TTTAATTTTTTATTTTCATT
13282099 TT
1 TT
13282101 CTTCTTCCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTAATTTTTTATTTTCATT
Found at i:13282210 original size:10 final size:10
Alignment explanation
Indices: 13282195--13282223 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
13282185 AGCAGAAGAG
13282195 AAAGAAAAAT
1 AAAGAAAAAT
13282205 AAAGAAAAAT
1 AAAGAAAAAT
13282215 AAAGAAAAA
1 AAAGAAAAA
13282224 AATTAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (10 bp):
AAAGAAAAAT
Found at i:13287944 original size:6 final size:6
Alignment explanation
Indices: 13287933--13287962 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
13287923 CTATAAAAAA
13287933 AACAAT AACAAT AACAAT AACAAT AACAAT
1 AACAAT AACAAT AACAAT AACAAT AACAAT
13287963 GCCTTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
AACAAT
Found at i:13299976 original size:5 final size:6
Alignment explanation
Indices: 13299953--13299986 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
13299943 CCCAAAACCA
13299953 AAAAAT AAAAAACT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT -AAAAA-T AAAAAT AAAAAT AAAAAT AA
13299987 CATTAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 15 0.58
7 10 0.38
8 1 0.04
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:13301457 original size:4 final size:4
Alignment explanation
Indices: 13301448--13301555 Score: 53
Period size: 4 Copynumber: 27.0 Consensus size: 4
13301438 CTTTAATCCT
* * *
13301448 TTTA TTTA TTTA TTTA CTTA TTTA CTTGA -TTA TTTA TTCA -TTA TTCT-
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TT-TA
* * * * * * * *
13301495 TTTCA TTTTA CTCA TTTA TTTG TTTA CTTA TTTA TTCA TATA -TCA TTAA
1 TTT-A -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
13301544 TTTA TTTA TTTA
1 TTTA TTTA TTTA
13301556 CCTTTTATTT
Statistics
Matches: 75, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
3 6 0.08
4 61 0.81
5 5 0.07
6 3 0.04
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (4 bp):
TTTA
Found at i:13301748 original size:3 final size:3
Alignment explanation
Indices: 13301742--13301800 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
13301732 GCATATACAT
*
13301742 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TT- TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
13301787 TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TT
13301801 GTCCACTCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:13308625 original size:29 final size:29
Alignment explanation
Indices: 13308557--13308616 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
13308547 ATTAATTAAA
*
13308557 CTAATTAAA-TTAATGAACCTAAAATAAC
1 CTAATGAAATTTAATGAACCTAAAATAAC
* * *
13308585 CTAATGAAATTTAATTAACCTAAGATATC
1 CTAATGAAATTTAATGAACCTAAAATAAC
13308614 CTA
1 CTA
13308617 CTAGAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (29 bp):
CTAATGAAATTTAATGAACCTAAAATAAC
Found at i:13311277 original size:29 final size:30
Alignment explanation
Indices: 13311217--13311277 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
13311207 AACTAATTAA
*
13311217 TTAATTTAACCTAAAATAACCTAATGGAAT
1 TTAATTTAACCTAAAATAACCTAATAGAAT
* *
13311247 TTAA-TTAACCTAAGATATCCTAATAGAAT
1 TTAATTTAACCTAAAATAACCTAATAGAAT
13311276 TT
1 TT
13311278 TCTATTCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (30 bp):
TTAATTTAACCTAAAATAACCTAATAGAAT
Found at i:13311695 original size:16 final size:15
Alignment explanation
Indices: 13311674--13311707 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
13311664 ACGAAAGATA
13311674 AATAAAGAAATAAAAG
1 AATAAAGAAA-AAAAG
*
13311690 AATAAAGGAAAAAAG
1 AATAAAGAAAAAAAG
13311705 AAT
1 AAT
13311708 GTTCATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (15 bp):
AATAAAGAAAAAAAG
Found at i:13314740 original size:27 final size:27
Alignment explanation
Indices: 13314702--13314829 Score: 166
Period size: 27 Copynumber: 4.7 Consensus size: 27
13314692 TTATCTGACT
* *
13314702 GTAATACCCCTGTAGGGTAAAATGATC
1 GTAATACCCCTGTAGGGTAAAATAACC
*
13314729 GTAATACCCCTGTAGGCTAAAATAACC
1 GTAATACCCCTGTAGGGTAAAATAACC
* *
13314756 ATAATAACCCTGTAGGGTAAAATAACC
1 GTAATACCCCTGTAGGGTAAAATAACC
* * *
13314783 GTAATGCTCCTGTAGGGTAAAATGACC
1 GTAATACCCCTGTAGGGTAAAATAACC
* *
13314810 GTAATGCCCCTGCAGGGTAA
1 GTAATACCCCTGTAGGGTAA
13314830 TATGGCGATT
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (27 bp):
GTAATACCCCTGTAGGGTAAAATAACC
Found at i:13320798 original size:9 final size:9
Alignment explanation
Indices: 13320784--13320814 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13320774 AGCGGCCTCG
13320784 ATGGGCCGA
1 ATGGGCCGA
13320793 ATGGGCCGA
1 ATGGGCCGA
*
13320802 ATGGGCCCA
1 ATGGGCCGA
13320811 ATGG
1 ATGG
13320815 CCCGCATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.42, T:0.13
Consensus pattern (9 bp):
ATGGGCCGA
Found at i:13321211 original size:27 final size:27
Alignment explanation
Indices: 13321154--13321222 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
13321144 ATTATCTGAT
* **
13321154 CGTAATACCTCTGTAGGGTAAAATGGT
1 CGTAATACCCCTGTAGGGTAAAATGAC
* *
13321181 CGTATTACCCTTGTAGGGTAAAATGAC
1 CGTAATACCCCTGTAGGGTAAAATGAC
13321208 CGTAATACCCCTGTA
1 CGTAATACCCCTGTA
13321223 TGTTAATATG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (27 bp):
CGTAATACCCCTGTAGGGTAAAATGAC
Found at i:13321452 original size:27 final size:26
Alignment explanation
Indices: 13321370--13321453 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 26
13321360 ATGGAGGAAG
* *
13321370 TACTATACTGGTGACTATGTCACATT
1 TACTATACTGGTGGCTATGCCACATT
* * * *
13321396 CACTGTTACTGGTGGCTATGCCATAAT
1 TACT-ATACTGGTGGCTATGCCACATT
*
13321423 TACTAATACTGGTGGCTTTGCCACATT
1 TACT-ATACTGGTGGCTATGCCACATT
13321450 TACT
1 TACT
13321454 GCTCTGGCAA
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
26 3 0.07
27 42 0.93
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (26 bp):
TACTATACTGGTGGCTATGCCACATT
Found at i:13325802 original size:13 final size:13
Alignment explanation
Indices: 13325786--13325820 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
13325776 AATAAAATAA
13325786 TAAAATATTTTAT
1 TAAAATATTTTAT
*
13325799 TAAAATATCTTAT
1 TAAAATATTTTAT
13325812 TAAAATATT
1 TAAAATATT
13325821 AATAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAAATATTTTAT
Found at i:13327103 original size:26 final size:26
Alignment explanation
Indices: 13327074--13327142 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 26
13327064 ATCTACCTTT
13327074 ACATAGCTTGATACAATGACAACTTC
1 ACATAGCTTGATACAATGACAACTTC
*
13327100 ACATAGCTTGA-A-TA-GAC--CTTC
1 ACATAGCTTGATACAATGACAACTTC
13327121 ACATAGCTTGATACAATGACAA
1 ACATAGCTTGATACAATGACAA
13327143 GTCTTGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
21 15 0.42
22 1 0.03
23 4 0.11
24 4 0.11
25 1 0.03
26 11 0.31
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (26 bp):
ACATAGCTTGATACAATGACAACTTC
Found at i:13328989 original size:15 final size:15
Alignment explanation
Indices: 13328953--13329008 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
13328943 TATAAACACT
13328953 ATATAAAAAAATAAA
1 ATATAAAAAAATAAA
* * *
13328968 TTGTAAATAAATAAA
1 ATATAAAAAAATAAA
13328983 ATATAAAAAAATGTATAA
1 ATATAAAAAAA--TA-AA
13329001 ATATAAAA
1 ATATAAAA
13329009 TATTTTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 20 0.62
17 2 0.06
18 10 0.31
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
ATATAAAAAAATAAA
Found at i:13329690 original size:15 final size:15
Alignment explanation
Indices: 13329670--13329777 Score: 62
Period size: 15 Copynumber: 7.2 Consensus size: 15
13329660 TTTATGGAAA
13329670 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
13329685 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
13329699 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
**
13329715 ATC-AA-ATAGTGGAA
1 ATCAAAGATA-TGGGT
*
13329729 AGTCAAATATATGGGT
1 A-TCAAAGATATGGGT
* **
13329745 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
13329759 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
13329775 ATC
1 ATC
13329778 GAGATATTGG
Statistics
Matches: 68, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
13 3 0.04
14 14 0.21
15 34 0.50
16 14 0.21
17 3 0.04
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:13329707 original size:30 final size:30
Alignment explanation
Indices: 13329663--13329777 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
13329653 ATCCATATTT
*
13329663 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
13329693 ATAGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
13329723 GTGGAAAGTCAAATATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
13329753 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
13329778 GAGATATTGG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:13334390 original size:30 final size:30
Alignment explanation
Indices: 13334355--13334568 Score: 392
Period size: 30 Copynumber: 7.1 Consensus size: 30
13334345 TCCATATTTA
* *
13334355 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
13334385 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
13334415 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
13334445 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
13334475 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
13334505 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
13334535 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
13334566 TGG
1 TGG
13334569 CATAATAAAA
Statistics
Matches: 180, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
30 172 0.96
31 8 0.04
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:13356569 original size:19 final size:18
Alignment explanation
Indices: 13356545--13356628 Score: 61
Period size: 19 Copynumber: 4.7 Consensus size: 18
13356535 AAAGAACTTA
13356545 TTATAAATTTTTATAATAT
1 TTATAAATTTTTA-AATAT
* *
13356564 TTATAACTTTTTATGA-AT
1 TTATAAATTTTTA-AATAT
* *
13356582 TT-T--ATTTTTAGATGT
1 TTATAAATTTTTAAATAT
13356597 TTATATAATTTTTAATATAT
1 TTATA-AATTTTTAA-ATAT
13356617 TTAT-AATTTTTA
1 TTATAAATTTTTA
13356629 CAAGAAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.04
15 9 0.17
16 1 0.02
17 1 0.02
18 12 0.23
19 21 0.40
20 7 0.13
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.61
Consensus pattern (18 bp):
TTATAAATTTTTAAATAT
Found at i:13358937 original size:20 final size:18
Alignment explanation
Indices: 13358900--13358938 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
13358890 TTCCGCTAGA
*
13358900 TTTCCTTTTCTTTCTTAT
1 TTTCCTTTTCTTTATTAT
13358918 TTTCCTTTTGACTTTATTAT
1 TTTCCTTTT--CTTTATTAT
13358938 T
1 T
13358939 CGATGATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTCCTTTTCTTTATTAT
Found at i:13360930 original size:39 final size:39
Alignment explanation
Indices: 13360887--13360964 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
13360877 TAGATGTGGA
*
13360887 AGTGAATCAACATTGGGCAATCAAGCTTACATTTTTTTC
1 AGTGAATCAAAATTGGGCAATCAAGCTTACATTTTTTTC
13360926 AGTGAATCAAAATTGGGCAATCAAGCTTACATTTTTTTC
1 AGTGAATCAAAATTGGGCAATCAAGCTTACATTTTTTTC
13360965 TCCCTAGAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (39 bp):
AGTGAATCAAAATTGGGCAATCAAGCTTACATTTTTTTC
Found at i:13362530 original size:2 final size:2
Alignment explanation
Indices: 13362523--13362555 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13362513 CTTCATTATT
13362523 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13362556 TTTCATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13365150 original size:31 final size:31
Alignment explanation
Indices: 13365112--13365173 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
13365102 CTAGGAAAGG
13365112 TGCATTGATTAGCGCCCTTTACTCAATCTAA
1 TGCATTGATTAGCGCCCTTTACTCAATCTAA
13365143 TGCATTGATTAGCGCCCTTTACTCAATCTAA
1 TGCATTGATTAGCGCCCTTTACTCAATCTAA
13365174 GTTGCTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (31 bp):
TGCATTGATTAGCGCCCTTTACTCAATCTAA
Found at i:13370988 original size:21 final size:21
Alignment explanation
Indices: 13370947--13370988 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13370937 ATCCAATATG
*
13370947 GCTAGTTAACTGGTCATGTCA
1 GCTAGTTAACTGGTCACGTCA
13370968 GCTAGTTAACTGG-CTACGTCA
1 GCTAGTTAACTGGTC-ACGTCA
13370989 CCTGTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (21 bp):
GCTAGTTAACTGGTCACGTCA
Found at i:13374611 original size:15 final size:15
Alignment explanation
Indices: 13374579--13374612 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13374569 GTTCAACGAA
*
13374579 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
13374594 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
13374609 GAGG
1 GAGG
13374613 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:13380387 original size:26 final size:26
Alignment explanation
Indices: 13380366--13380429 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
13380356 ACCGCCATAG
*
13380366 AGGCTTCCATTTCAGATACGCCACAA
1 AGGCTTCCATTTCAAATACGCCACAA
*
13380392 AAGCTTCCATTTCAAATACGCCACAA
1 AGGCTTCCATTTCAAATACGCCACAA
13380418 AGGCTTCCATTT
1 AGGCTTCCATTT
13380430 TCTGACATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (26 bp):
AGGCTTCCATTTCAAATACGCCACAA
Done.