Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 111 of 427
Found at i:29364866 original size:2 final size:2
Alignment explanation
Indices: 29364861--29364898 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
29364851 ATATTTTTCG
29364861 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29364899 GTTTTCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:29365089 original size:22 final size:20
Alignment explanation
Indices: 29365064--29365108 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
29365054 GAATAGTTTT
29365064 TATATTAT-TATCATTTCTAATA
1 TATATTATATAT-ATTT-T-ATA
29365086 TATATTATATATATTTTATA
1 TATATTATATATATTTTATA
29365106 TAT
1 TAT
29365109 TATGTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
21 1 0.05
22 12 0.55
23 3 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATTATATATATTTTATA
Found at i:29365494 original size:21 final size:23
Alignment explanation
Indices: 29365470--29365513 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29365460 CTTTTCTTTA
29365470 ATATCTAT-T-TTATATATATAT
1 ATATCTATATATTATATATATAT
* *
29365491 ATATGTATATATTATGTATATAT
1 ATATCTATATATTATATATATAT
29365514 TTTAACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
ATATCTATATATTATATATATAT
Found at i:29369387 original size:12 final size:12
Alignment explanation
Indices: 29369367--29369402 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
29369357 ATTCATTTGA
*
29369367 CATTTATGCATT
1 CATTCATGCATT
29369379 CATTCATGCATT
1 CATTCATGCATT
*
29369391 CATTCATTCATT
1 CATTCATGCATT
29369403 GCATATCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:29377911 original size:90 final size:88
Alignment explanation
Indices: 29377752--29377914 Score: 256
Period size: 90 Copynumber: 1.8 Consensus size: 88
29377742 TGCCGAGGTA
*
29377752 TTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
1 TTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
29377817 CTGAGGTATTTTTGATTTCCGTC
66 CTGAGGTATTTTTGATTTCCGTC
* *
29377840 TTTTTAATTTATGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCAT-AGGAC
1 TTTTCAATTTATG-T-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCAAGAC
*
29377904 GCACTGAGGTA
63 ACACTGAGGTA
29377915 ATTTCAATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
88 12 0.18
89 1 0.01
90 54 0.79
91 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (88 bp):
TTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
CTGAGGTATTTTTGATTTCCGTC
Found at i:29377970 original size:163 final size:164
Alignment explanation
Indices: 29377693--29378061 Score: 447
Period size: 163 Copynumber: 2.2 Consensus size: 164
29377683 TCCTGTTTTC
* * * *
29377693 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCTCATGCCGAGGTATTTTCA
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCA-GCCGAGGTAATTTCA
* *
29377758 ATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
65 ATTTATGTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAAG
* ** * ** *
29377823 TATTTTTGATTTCCGTCTTTTTAATTTATGCTCTT-
130 AATTTTCAATTGCCGT-TTTCCAAATTATGCTCTTG
* *
29377858 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCAT-AGGACGCA-CTGAGGTAATTTCA
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCAGGACGCAGCCGAGGTAATTTCA
* *** * *
29377921 ATTTCTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAAG
65 ATTTATGTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAAG
* * *
29377986 AATTTTCAATTGCTGTTTTCCAAATTCTGCTTTTG
130 AATTTTCAATTGCCGTTTTCCAAATTATGCTCTTG
* **
29378021 AAAAAAAATTAACTCATATTGCGAGATATGAGTTGAGCCTC
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
29378062 GGGTCACATG
Statistics
Matches: 173, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
162 14 0.08
163 115 0.66
165 43 0.25
166 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (164 bp):
AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCAGCCGAGGTAATTTCAA
TTTATGTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAAGA
ATTTTCAATTGCCGTTTTCCAAATTATGCTCTTG
Found at i:29377993 original size:73 final size:73
Alignment explanation
Indices: 29377861--29378003 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
29377851 TGCTCTTCAA
* * * *
29377861 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCATAGGACGCACTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCATAGGACACACTGAAGTAATTTCAATTGC
29377926 TGTTTGTC
66 TGTTTGTC
* *
29377934 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC-TCAGGGCACGCTGAAG-AATTTTCAATT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCAT-AGGACACACTGAAGTAA-TTTCAATT
29377997 GCTGTTT
64 GCTGTTT
29378004 TCCAAATTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
72 3 0.05
73 59 0.95
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCATAGGACACACTGAAGTAATTTCAATTGC
TGTTTGTC
Found at i:29379338 original size:13 final size:13
Alignment explanation
Indices: 29379320--29379355 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
29379310 TATACCAAAC
29379320 ATACAAAAATATA
1 ATACAAAAATATA
29379333 ATACAAAAATATA
1 ATACAAAAATATA
*
29379346 ACA-AAAAATA
1 ATACAAAAATA
29379356 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.19
Consensus pattern (13 bp):
ATACAAAAATATA
Found at i:29380170 original size:20 final size:20
Alignment explanation
Indices: 29380128--29380166 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29380118 ACTATGTTAA
* *
29380128 GTATATATCTTTATTATTAT
1 GTATATATATTTATTAATAT
29380148 GTATATATATTT-TTAATAT
1 GTATATATATTTATTAATAT
29380167 TGTAGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (20 bp):
GTATATATATTTATTAATAT
Found at i:29380629 original size:17 final size:19
Alignment explanation
Indices: 29380586--29380623 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29380576 TACATAGTAG
*
29380586 TGTATAT-TTTTTCATATA
1 TGTATATGTTTTTAATATA
29380604 TGTATATGTTTTTAATATA
1 TGTATATGTTTTTAATATA
29380623 T
1 T
29380624 TTATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
TGTATATGTTTTTAATATA
Found at i:29380758 original size:24 final size:25
Alignment explanation
Indices: 29380717--29380775 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
29380707 TATGTATATC
*
29380717 TATATAT-TTTTCGTATATAT-TATG
1 TATATATGTTTTCGAATAT-TGTATG
29380741 TATATATGTTTTC-AATATTGTATG
1 TATATATGTTTTCGAATATTGTATG
29380765 TCATATATGTT
1 T-ATATATGTT
29380776 ATTGTGTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 1 0.03
24 16 0.52
25 14 0.45
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (25 bp):
TATATATGTTTTCGAATATTGTATG
Found at i:29380944 original size:9 final size:9
Alignment explanation
Indices: 29380930--29380959 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
29380920 TAATTTCTAA
29380930 TATATATAT
1 TATATATAT
29380939 TATATATAT
1 TATATATAT
*
29380948 TTTATATAT
1 TATATATAT
29380957 TAT
1 TAT
29380960 GTATGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATATATAT
Found at i:29380949 original size:24 final size:22
Alignment explanation
Indices: 29380910--29380956 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
29380900 GAATATTTTT
29380910 TATATTATTATAATTTCTAATATA
1 TATATTATTATAATTT-T-ATATA
29380934 TATATTA-TATATATTTTATATA
1 TATATTATTATA-ATTTTATATA
29380956 T
1 T
29380957 TATGTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTATTATAATTTTATATA
Found at i:29380968 original size:20 final size:20
Alignment explanation
Indices: 29380868--29380971 Score: 67
Period size: 20 Copynumber: 5.2 Consensus size: 20
29380858 TTCATTATTA
*
29380868 TTTATATA-TATGTATGTA-
1 TTTATATATTATGTATATAT
*
29380886 TTTATATAGCGTATG-A-ATAT
1 TTTATATA--TTATGTATATAT
*
29380906 TTTTTATATTAT-TATA-AT
1 TTTATATATTATGTATATAT
*
29380924 TTCTAATATATATATTATATATAT
1 TT-T-ATATAT-TA-TGTATATAT
*
29380948 TTTATATATTATGTATGTAT
1 TTTATATATTATGTATATAT
29380968 TTTA
1 TTTA
29380972 ATGTTATTAG
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
18 16 0.24
19 4 0.06
20 24 0.35
21 8 0.12
22 7 0.10
23 5 0.07
24 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTATATATTATGTATATAT
Found at i:29382039 original size:19 final size:19
Alignment explanation
Indices: 29382015--29382061 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
29382005 CTTCCTTTTG
*
29382015 TTTAAAAAATAAATTTTCT
1 TTTAAAAAATAAAATTTCT
29382034 TTTAAAAAATAAAATTTCT
1 TTTAAAAAATAAAATTTCT
29382053 TTTAAAAAA
1 TTTAAAAAA
29382062 GATGATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAAAAATAAAATTTCT
Found at i:29382792 original size:141 final size:139
Alignment explanation
Indices: 29382353--29382840 Score: 684
Period size: 140 Copynumber: 3.5 Consensus size: 139
29382343 TATTTCTAAA
* * * *
29382353 ATTTTTAAAATTTTCGGATTCTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTTATCTT
1 ATTTCTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA--TTTTTATCTT
*
29382418 A-TTTTAT-TACATAATGTTTCAAATGTATTATTTTAGTATTTTTAAAATAACCCTGATTTTGTC
64 ATTTTTATGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTTAAATAACCCTGATTTTGTC
*
29382481 TCTTTGTTTGT
129 CCTTTGTTTGT
* * *
29382492 ATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTTTTATCT
1 ATTTCTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA---TTTTTATCT
* *
29382557 TA-TTTCA-GTACATAATGTTTCAAATGTATTATTTTA-T-TTTTTTAAAAATAACCCTGACTTT
63 TATTTTTATGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTT--AAATAACCCTGATTTT
*
29382618 ATCCCTTTGTTTGT
126 GTCCCTTTGTTTGT
*
29382632 ATTTCTAAAATATTT-AGATTTTATTATTTAAAATATACTATTTTCGTATTTTATTTTTATCTTA
1 ATTTCTAAAAT-TTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTA
* *
29382696 TTTTGTAATGTACTTAATGTTTCAAATGTATTATTTTAGTATTTTTTAAATAACCCTAATTTTGT
65 TTTT-T-ATGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTTAAATAACCCTGATTTTGT
29382761 CCCTTTGTTTGT
128 CCCTTTGTTTGT
* *
29382773 ATTTTTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTATATTAT
1 ATTTCTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTAT
29382838 TTT
66 TTT
29382841 ATACTATTTT
Statistics
Matches: 315, Mismatches: 22, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
137 11 0.03
138 8 0.03
139 49 0.16
140 122 0.39
141 118 0.37
142 1 0.00
143 6 0.02
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.57
Consensus pattern (139 bp):
ATTTCTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTAT
TTTTATGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTTAAATAACCCTGATTTTGTCCC
TTTGTTTGT
Found at i:29382824 original size:30 final size:33
Alignment explanation
Indices: 29382782--29382862 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 33
29382772 TATTTTTAAA
29382782 ATTTTCAG-ATTTTATTTTT-TA-A-AATATACT
1 ATTTTC-GTATTTTATTTTTATATATAATATACT
**
29382812 ATTTTCGTATTTTATTTTTATATTATTTTATACT
1 ATTTTCGTATTTTATTTTTATA-TATAATATACT
29382846 ATTTTTCGTATTTTATT
1 A-TTTTCGTATTTTATT
29382863 GTATTTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 17 0.40
31 2 0.05
33 1 0.02
34 7 0.16
35 15 0.35
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (33 bp):
ATTTTCGTATTTTATTTTTATATATAATATACT
Found at i:29382872 original size:20 final size:18
Alignment explanation
Indices: 29382813--29382903 Score: 71
Period size: 17 Copynumber: 5.1 Consensus size: 18
29382803 AAATATACTA
29382813 TTTTCGTATTTTATTTTT
1 TTTTCGTATTTTATTTTT
* * * *
29382831 ATAT--TATTTTATACTAT
1 TTTTCGTATTTTAT-TTTT
29382848 TTTTCGTATTTTATTGTATT
1 TTTTCGTATTTTATT-T-TT
* * *
29382868 TTTTCATATTCTA-TTTC
1 TTTTCGTATTTTATTTTT
29382885 TTTTCGTATTTTATTTTT
1 TTTTCGTATTTTATTTTT
29382903 T
1 T
29382904 CATTAAGATA
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
16 8 0.15
17 16 0.30
18 7 0.13
19 10 0.19
20 12 0.23
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTTCGTATTTTATTTTT
Found at i:29382882 original size:15 final size:15
Alignment explanation
Indices: 29382859--29382906 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
29382849 TTTCGTATTT
*
29382859 TATTGTATTTTTTCA
1 TATTCTATTTTTTCA
*
29382874 TATTCTATTTCTTTTCG
1 TATTCTA-TT-TTTTCA
*
29382891 TATTTTATTTTTTCA
1 TATTCTATTTTTTCA
29382906 T
1 T
29382907 TAAGATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (15 bp):
TATTCTATTTTTTCA
Found at i:29382882 original size:34 final size:35
Alignment explanation
Indices: 29382805--29382899 Score: 99
Period size: 34 Copynumber: 2.7 Consensus size: 35
29382795 ATTTTTTAAA
*
29382805 ATATACTA-TTTTCGTATTTTATTTTTATATTATTT
1 ATATACTATTTTTCGTATTTTA-TTGTATATTATTT
29382840 -TATACTATTTTTCGTATTTTATTGTAT-TT-TTT
1 ATATACTATTTTTCGTATTTTATTGTATATTATTT
*
29382872 CATATTCTATTTCTTTTCGTATTTTATT
1 -ATATACTA--T-TTTTCGTATTTTATT
29382900 TTTTCATTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
32 3 0.06
33 2 0.04
34 18 0.35
35 13 0.25
36 1 0.02
37 15 0.29
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.66
Consensus pattern (35 bp):
ATATACTATTTTTCGTATTTTATTGTATATTATTT
Found at i:29383277 original size:11 final size:10
Alignment explanation
Indices: 29383245--29383278 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
29383235 ATAAATTTAT
29383245 AAATTAAATC
1 AAATTAAATC
29383255 TAAATTAAATC
1 -AAATTAAATC
29383266 AAATTTAAATC
1 AAA-TTAAATC
29383277 AA
1 AA
29383279 CAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTAAATC
Found at i:29383404 original size:18 final size:17
Alignment explanation
Indices: 29383359--29383404 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
29383349 TCCCTCCCTC
*
29383359 TTCTTCTCCTTCTCTTT
1 TTCTTCTCTTTCTCTTT
*
29383376 TTCTTTTTCTTTCTCTTTT
1 TTC-TTCTCTTTCTC-TTT
29383395 TTCTTCTCTT
1 TTCTTCTCTT
29383405 CCCTCACGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 15 0.62
19 6 0.25
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTCTTCTCTTTCTCTTT
Found at i:29383455 original size:18 final size:19
Alignment explanation
Indices: 29383428--29383467 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
29383418 TTGCTCCTTC
*
29383428 TTCTTCTTCTCTTCTTTCT
1 TTCTTCTTCTCTCCTTTCT
29383447 TTCTT-TTCTCTCCTTTCT
1 TTCTTCTTCTCTCCTTTCT
29383465 TTC
1 TTC
29383468 CGAAATGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTCTTCTCTCCTTTCT
Found at i:29383664 original size:19 final size:18
Alignment explanation
Indices: 29383640--29383689 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
29383630 ATCTGTAGCC
*
29383640 TTTTTTTTTGTTTCAGCT
1 TTTTTTTTTGTTTCAACT
29383658 TTTTTTTTTGTTTCAACT
1 TTTTTTTTTGTTTCAACT
29383676 TTTTTTTATTGTTT
1 TTTTTTT-TTGTTT
29383690 TGTGTTAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTGTTTCAACT
Found at i:29386741 original size:12 final size:12
Alignment explanation
Indices: 29386724--29386759 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
29386714 ATTCATTTGA
29386724 CATTCATGCATT
1 CATTCATGCATT
29386736 CATTCATGCATT
1 CATTCATGCATT
*
29386748 CATTCATACATT
1 CATTCATGCATT
29386760 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:29392370 original size:28 final size:28
Alignment explanation
Indices: 29392301--29392401 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
29392291 GACAAGATTG
* * * *
29392301 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
29392331 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
29392359 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
29392388 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
29392402 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:29398302 original size:71 final size:69
Alignment explanation
Indices: 29398204--29398378 Score: 217
Period size: 71 Copynumber: 2.5 Consensus size: 69
29398194 TTTTCGAAGG
* *
29398204 AAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTAAGGTATTTTTAATTTTT
1 AAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCTAAGGTATTTTTAATTTAT
29398268 GTTTT
65 GTTTT
** * * *
29398273 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTA
1 --AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTAAGGTATTTTTAATTTA
29398338 TGTTTT
64 TGTTTT
** * *
29398344 AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
29398379 TTTAATTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
69 31 0.34
71 59 0.64
72 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (69 bp):
AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTAAGGTATTTTTAATTTATG
TTTT
Found at i:29398499 original size:72 final size:71
Alignment explanation
Indices: 29398378--29398543 Score: 235
Period size: 72 Copynumber: 2.3 Consensus size: 71
29398368 GAGTTAAGCC
** * *
29398378 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
29398442 TGAGATA
65 TGAGATA
*
29398449 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAATTTTTGT-TTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
*
29398514 TGAGGTA
65 TGAGATA
* *
29398521 TTTTCAATTTCTGTTTTCAATTT
1 TTTTCAATTTTTGTTTTTAATTT
29398544 ACGTTGTTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 12 0.14
72 69 0.81
73 4 0.05
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT
GAGATA
Found at i:29398639 original size:140 final size:140
Alignment explanation
Indices: 29398476--29399243 Score: 1385
Period size: 140 Copynumber: 5.5 Consensus size: 140
29398466 TTAATTTCAA
29398476 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
29398541 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTTTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
29398606 TCAAAATCAG
131 TCAAAATCAG
29398616 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
29398681 TTTACCTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
29398746 TCAAAATCAG
131 TCAAAATCAG
* * *
29398756 CTCATATTGCGAGAGGCGAGTTGAGCTTCAGGTCACGCTAAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
29398821 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
29398886 TCAAAATCAG
131 TCAAAATCAG
* *
29398896 CTAATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCTATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
29398961 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
29399026 TCAAAATCAG
131 TCAAAATCAG
29399036 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
29399101 TTTATGTTGTTCAAGAATCAACTCACATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
29399166 TCAAAATCAG
131 TCAAAATCAG
*
29399176 CTCATATTGCGAGAGGTGAGTTGAGCCTC-GATTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GTCAC--GCTGAGGTATTTTCAATTTCTGT-TT
29399240 TCAA
62 TCAA
29399244 AAAAAAATTA
Statistics
Matches: 606, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
139 1 0.00
140 576 0.95
142 23 0.04
143 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (140 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAG
Found at i:29399099 original size:13 final size:13
Alignment explanation
Indices: 29399081--29399114 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
29399071 CGCTGAGGTA
*
29399081 TTTTCAATTTCTG
1 TTTTCAATTTATG
29399094 TTTTCAATTTATG
1 TTTTCAATTTATG
29399107 TTGTTCAA
1 TT-TTCAA
29399115 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:29399342 original size:72 final size:72
Alignment explanation
Indices: 29399149--29399383 Score: 251
Period size: 72 Copynumber: 3.2 Consensus size: 72
29399139 GGGTTGAACC
* * ** **
29399149 TTTTAATTTCTACTTTTTCAAAA-TCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCGATTCACA
1 TTTTAATTTCT--GTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-A-AGACA
* *
29399213 TGCTGAGGT-A
62 CGTTGAGGTAA
*
29399223 TTTTCAATTTCTGTCTTTCAAAAAAAAATT-AACTCATATTGCAAGAAATGAGTTGAGCCTCAAG
1 TTTT-AATTTCTGT-TTTC-----AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
29399287 ACACGTTGAGGTAA
59 ACACGTTGAGGTAA
*
29399301 TTTTAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGATTTGAGCCTCAAGACACGTT
1 TTTTAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
29399366 GAGGTAA
66 GAGGTAA
*
29399373 TTTCAATTTCT
1 TTTTAATTTCT
29399384 ATTCAAAATG
Statistics
Matches: 139, Mismatches: 12, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
71 6 0.04
72 56 0.40
73 1 0.01
74 8 0.06
75 7 0.05
76 4 0.03
77 19 0.14
78 6 0.04
79 31 0.22
80 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (72 bp):
TTTTAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
GAGGTAA
Found at i:29399482 original size:121 final size:121
Alignment explanation
Indices: 29399268--29399504 Score: 393
Period size: 121 Copynumber: 2.0 Consensus size: 121
29399258 ATATTGCAAG
* *
29399268 AAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTTAATTTCTGTTTTCAAAATTCAACTCATA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
* * *
29399333 TTGCGAGAAATGATTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTATTCA
66 TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGCAATTTCAATTTCTATTCA
29399389 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
* * * *
29399454 TTGTGAGAAATTAGTTGAGCCTCAAGACATGCTGAGGCATTTTCAATTTCT
66 TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGCAATTTCAATTTCT
29399505 GTTTTTCAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 107 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (121 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGCAATTTCAATTTCTATTCA
Found at i:29399641 original size:75 final size:75
Alignment explanation
Indices: 29399389--29399741 Score: 446
Period size: 75 Copynumber: 4.7 Consensus size: 75
29399379 TTTCTATTCA
* *
29399389 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTG-TTTTC--AAAATTCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
29399451 ATATTGTGAG
66 ATATTGTGAG
* * *
29399461 AAATTAGTTGAGCCTCAAGACATGCTGAGGCATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTC---AAAAAAATCAA
29399526 CTCATATTGTGAG
63 CTCATATTGTGAG
*
29399539 AAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
*
29399604 ATATTGCGAG
66 ATATTGTGAG
** * * *
29399614 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TTGTCAAAAAAATCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
*
29399678 GTATTGTG-G
66 ATATTGTGAG
*** * * * *
29399687 AGGCGAGTTGAGCCTCAGGTCACGCGCCGAGGTATTTTCAATTTCCGTTTTTCAA
1 AAATGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTCAATTTCTGTTTTTCAA
29399742 TTTCTGTCTT
Statistics
Matches: 250, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
72 41 0.16
73 24 0.10
74 24 0.10
75 85 0.34
76 6 0.02
78 70 0.28
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (75 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
ATATTGTGAG
Found at i:29399740 original size:14 final size:14
Alignment explanation
Indices: 29399721--29399755 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29399711 CGCCGAGGTA
29399721 TTTTCAATTTCCGT
1 TTTTCAATTTCCGT
*
29399735 TTTTCAATTTCTGT
1 TTTTCAATTTCCGT
*
29399749 CTTTCAA
1 TTTTCAA
29399756 AAAAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCCGT
Found at i:29399804 original size:94 final size:93
Alignment explanation
Indices: 29399664--29399835 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 93
29399654 TTCTGTTGTC
* * * *
29399664 AAAAAAATCAACTCGTATTGTGGAGGCGAGTTGAGCCTCAGGTCACGCGCCGAGGTATTTTCAAT
1 AAAAAAAACAACTCATATTGCGGAGGCGAGTTGAGCCTCAGGTCACGCGCCGAGCTATTTTCAAT
*
29399729 TTCCGTTTTTCAATTTCTGTCTTTCAAA
66 TTCCGTCTTTCAATTTCTGTCTTTCAAA
* * *
29399757 AAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCGCTGAGCTATTTTCA
1 AAAAAAAACAACTCATATTGCG-GAGGCGAGTTGAGCCTCAGG-TCACGCGCCGAGCTATTTTCA
*
29399821 ATTTCTGTCTTTCAA
64 ATTTCCGTCTTTCAA
29399836 AAAAAATCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
93 21 0.31
94 47 0.69
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (93 bp):
AAAAAAAACAACTCATATTGCGGAGGCGAGTTGAGCCTCAGGTCACGCGCCGAGCTATTTTCAAT
TTCCGTCTTTCAATTTCTGTCTTTCAAA
Found at i:29399899 original size:80 final size:78
Alignment explanation
Indices: 29399734--29399950 Score: 258
Period size: 78 Copynumber: 2.7 Consensus size: 78
29399724 TCAATTTCCG
* *
29399734 TTTTTCAATTTCTGTCTTTCAAAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG
1 TTTTTCAATTTCTGTCTTTC--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTAG
* * *
29399799 CTCACGCGCTGAGCTA
63 ATCACACACTGAGCTA
29399815 -TTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
1 TTTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTT-AGAT
*
29399879 CACACACTGAGGTA
65 CACACACTGAGCTA
* * * * * **
29399893 TTTTTTCAATTTATATTTTTC-AAAAAAATCAACTCACATTGTGAGATATGAGTTGAGC
1 -TTTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
29399951 CTCGGGTCAC
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
77 3 0.03
78 49 0.41
79 33 0.28
80 35 0.29
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (78 bp):
TTTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTAGATC
ACACACTGAGCTA
Found at i:29399961 original size:79 final size:78
Alignment explanation
Indices: 29399735--29400114 Score: 257
Period size: 78 Copynumber: 4.7 Consensus size: 78
29399725 CAATTTCCGT
* * * * *
29399735 TTTTCAATTTCTGTCTTTCAAAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC
1 TTTTCAATTTATATCTTTC--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA
* *
29399800 TCACGCGCTGAGCTA
64 TCACACACTGAGCTA
* * * *
29399815 TTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
1 TTTTCAATTTATATCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATC
*
29399880 ACACACTGAGGTA
66 ACACACTGAGCTA
* * * ** *
29399893 TTTTTTCAATTTATATTTTTC-AAAAAAATCAACTCACATTGTGAGATATGAGTTGAGCCTCGGG
1 --TTTTCAATTTATATCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA
** * *
29399957 TCACA-TGTCGCGGTA
64 TCACACACT-GAGCTA
* *** * * *
29399972 TTTTCAAAATCTGTTTTTCAGATTCTGTT-TTCAAAAATCAACTTATATTACGAGAAGTGAGTTG
1 TTTTC--AA------TTT-ATA-TCT-TTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* * ***
29400036 AGCCTTGGCTCACGTGCTGAGCTA
55 AGCCTCGGATCACACACTGAGCTA
* *
29400060 TTTTCAATTT-T-TTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTTTCAATTTATATCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
29400115 TTTTTAATTT
Statistics
Matches: 236, Mismatches: 47, Indels: 38
0.74 0.15 0.12
Matches are distributed among these distances:
75 2 0.01
76 33 0.14
77 5 0.02
78 52 0.22
79 48 0.20
80 38 0.16
85 3 0.01
86 4 0.02
87 2 0.01
88 48 0.20
89 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (78 bp):
TTTTCAATTTATATCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATC
ACACACTGAGCTA
Found at i:29400034 original size:245 final size:242
Alignment explanation
Indices: 29399517--29400324 Score: 856
Period size: 245 Copynumber: 3.3 Consensus size: 242
29399507 TTTTCAAAAA
* ** ** * *
29399517 AAAAATCAACTCATATTGTGAGAAATGAGTTGAGCC-T--CAAGACATGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC-TCACGTGCTGAGCTATTTTCAAT
* * *
29399579 TTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCTG
65 TTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTG
* * * * *
29399641 AGGTA-ATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGTG-GAGGCGAGTTGAGCCTCA
130 AGGTATTTTTCAATTTCTTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC-
** * ** * *
29399704 GGTCACGCGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTCTGTCTTTC
194 GGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTCTGT-TTTC
* *
29399754 AAAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
1 -----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
*
29399819 CAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACAC
61 CAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACAC
* * **
29399884 ACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGTGAGATATGAGTTGA
126 ACTGAGGTA-TTTTTCAATTTCT-TTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGA
*
29399949 GCCTCGGGTCACATGTCGCGGTATTTTCAAAATCTGTTTTTC-AGATTCTGTTTTC
189 GCCTC-GGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAG-TTCTGTTTTC
* * *
29400004 AAAAATCAACTTATATTACGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
* * *
29400069 T-T-TTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-ATTTCTGCGA
66 TCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCAGA--TC-AC-A
* * * *
29400131 GAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAG
125 CA-CTGAGGT-A-T-TTTTCAATTTCT-TTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAG
* * ** * * **
29400193 TTGAACCTTCAGTTGCATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAAG-TTTC
185 TTGAGCC-TCGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTCTGTTTTC
29400251 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
29400316 TCTGTTTTT
66 TCTGTTTTT
29400325 AATGTCTGTT
Statistics
Matches: 480, Mismatches: 62, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
242 32 0.07
243 43 0.09
244 30 0.06
245 106 0.22
246 2 0.00
247 80 0.17
248 67 0.14
249 24 0.05
250 43 0.09
251 53 0.11
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (242 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
TCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGA
GGTATTTTTCAATTTCTTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGG
TCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTCTGTTTTC
Found at i:29400132 original size:30 final size:30
Alignment explanation
Indices: 29400096--29400157 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
29400086 CAACTCATAT
29400096 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
29400126 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
29400156 TG
1 TG
29400158 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:29401585 original size:2 final size:2
Alignment explanation
Indices: 29401580--29401612 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29401570 TAAATACTAT
*
29401580 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29401613 TTTAAATACC
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29402897 original size:32 final size:31
Alignment explanation
Indices: 29402859--29402931 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 31
29402849 AAAGTTAAAA
29402859 TAATTTTTTAACA-AGAATACTAACTAAAATAT
1 TAATTTTTTAA-ATA-AATACTAACTAAAATAT
**
29402891 TAATTTTTTAAATACTTACTAACTAAAATAT
1 TAATTTTTTAAATAAATACTAACTAAAATAT
29402922 TAATTTTTTA
1 TAATTTTTTA
29402932 TATACGACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 26 0.68
32 12 0.32
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (31 bp):
TAATTTTTTAAATAAATACTAACTAAAATAT
Found at i:29402911 original size:31 final size:31
Alignment explanation
Indices: 29402876--29402936 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
29402866 TTAACAAGAA
29402876 TACTAACTAAAATATTAATTTTTTAAATACT
1 TACTAACTAAAATATTAATTTTTTAAATACT
*
29402907 TACTAACTAAAATATTAATTTTTTATATAC
1 TACTAACTAAAATATTAATTTTTTAAATAC
29402937 GACAGTCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (31 bp):
TACTAACTAAAATATTAATTTTTTAAATACT
Found at i:29405789 original size:20 final size:20
Alignment explanation
Indices: 29405766--29405805 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29405756 CCTTTACATC
29405766 ATTACACAATTGAAACTTTT
1 ATTACACAATTGAAACTTTT
*
29405786 ATTACATAATTGAAACTTTT
1 ATTACACAATTGAAACTTTT
29405806 TCAGAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTACACAATTGAAACTTTT
Found at i:29406071 original size:14 final size:14
Alignment explanation
Indices: 29406052--29406105 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 14
29406042 AATCTTCAAT
29406052 GATATGCAATCTTA
1 GATATGCAATCTTA
29406066 GATATGATACAATCTTA
1 GATATG---CAATCTTA
29406083 GATATGATGCAATCTTA
1 G--AT-ATGCAATCTTA
29406100 GATATG
1 GATATG
29406106 ATTGCAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.26
15 2 0.06
17 18 0.53
19 2 0.06
20 3 0.09
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (14 bp):
GATATGCAATCTTA
Found at i:29406078 original size:17 final size:17
Alignment explanation
Indices: 29406058--29406126 Score: 111
Period size: 17 Copynumber: 4.0 Consensus size: 17
29406048 CAATGATATG
29406058 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
29406075 CAATCTTAGATATGATG
1 CAATCTTAGATATGATA
*
29406092 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
29406110 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
29406127 TACAGTCTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 32 0.65
18 17 0.35
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:29406080 original size:34 final size:35
Alignment explanation
Indices: 29406055--29406125 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 35
29406045 CTTCAATGAT
29406055 ATGCAATCTTAGATATGA-TACAATCTTAGATATG
1 ATGCAATCTTAGATATGATTACAATCTTAGATATG
*
29406089 ATGCAATCTTAGATATGATTGCAATCTTAGATATG
1 ATGCAATCTTAGATATGATTACAATCTTAGATATG
29406124 AT
1 AT
29406126 ATACAGTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (35 bp):
ATGCAATCTTAGATATGATTACAATCTTAGATATG
Found at i:29409316 original size:10 final size:11
Alignment explanation
Indices: 29409301--29409343 Score: 56
Period size: 10 Copynumber: 4.2 Consensus size: 11
29409291 TTAAGGTTAA
29409301 AAAGAGA-AAG
1 AAAGAGAGAAG
29409311 AAAGAGAGAA-
1 AAAGAGAGAAG
*
29409321 AAAAAGAG-AG
1 AAAGAGAGAAG
29409331 AAAGAGAGAAG
1 AAAGAGAGAAG
29409342 AA
1 AA
29409344 GGTCACGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 1 0.04
10 21 0.75
11 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAGAGAGAAG
Found at i:29409320 original size:12 final size:12
Alignment explanation
Indices: 29409303--29409335 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
29409293 AAGGTTAAAA
29409303 AGAGAAAGAAAG
1 AGAGAAAGAAAG
*
29409315 AGAGAAAAAAAG
1 AGAGAAAGAAAG
29409327 AGAGAAAGA
1 AGAGAAAGA
29409336 GAGAAGAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
AGAGAAAGAAAG
Found at i:29409332 original size:20 final size:20
Alignment explanation
Indices: 29409299--29409340 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29409289 AATTAAGGTT
*
29409299 AAAAAGAGAAAGAAAGAGAG
1 AAAAAAAGAAAGAAAGAGAG
*
29409319 AAAAAAAGAGAGAAAGAGAG
1 AAAAAAAGAAAGAAAGAGAG
29409339 AA
1 AA
29409341 GAAGGTCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAGAAAGAGAG
Found at i:29411331 original size:46 final size:46
Alignment explanation
Indices: 29411278--29411453 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
29411268 GGATTTGGCA
29411278 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
29411324 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
29411371 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
29411417 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29411454 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:29411383 original size:93 final size:93
Alignment explanation
Indices: 29411274--29411445 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
29411264 ACTAGGATTT
* *
29411274 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29411339 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
29411367 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29411432 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
29411446 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:29414421 original size:15 final size:15
Alignment explanation
Indices: 29414401--29414469 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
29414391 GTATCTTGGG
29414401 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
29414416 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
29414431 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
29414446 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
29414461 TTTCTTTAT
1 TTTCTTTAT
29414470 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:29414470 original size:30 final size:30
Alignment explanation
Indices: 29414392--29414479 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
29414382 CATAGTATCG
* * * *
29414392 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
29414422 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
29414452 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
29414480 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:29416911 original size:46 final size:46
Alignment explanation
Indices: 29416861--29417036 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
29416851 GGATGGGGCA
29416861 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
29416907 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
29416954 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
29417000 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29417037 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:29416966 original size:93 final size:93
Alignment explanation
Indices: 29416857--29417028 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
29416847 ACTAGGATGG
* *
29416857 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29416922 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
29416950 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29417015 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
29417029 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:29418733 original size:15 final size:15
Alignment explanation
Indices: 29418709--29418738 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29418699 CATCCATTTC
29418709 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
29418724 AAAAAGAAAAAAAAA
1 AAAAA-AAAAAAAAA
29418739 AGATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:29418735 original size:17 final size:16
Alignment explanation
Indices: 29418709--29418741 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
29418699 CATCCATTTC
29418709 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
29418725 AAAAGAAAAAAAAAAGA
1 AAAA-AAAAAAAAAAGA
29418742 TTATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:29420240 original size:14 final size:14
Alignment explanation
Indices: 29420221--29420286 Score: 91
Period size: 14 Copynumber: 4.8 Consensus size: 14
29420211 ACTTCTATTT
29420221 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
*
29420235 AAAAAAAGAAA-AG
1 AAAAAAAAAAAGAG
*
29420248 -AAAAGAAAAAGAG
1 AAAAAAAAAAAGAG
29420261 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
29420275 AAAAAAGAAAAA
1 AAAAAA-AAAAA
29420287 TGGAGAGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
12 8 0.18
13 4 0.09
14 28 0.62
15 5 0.11
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:29420258 original size:26 final size:25
Alignment explanation
Indices: 29420222--29420280 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
29420212 CTTCTATTTA
29420222 AAAAAAAAAAGAGAAAAAAAGAAAAG
1 AAAAAAAAAAGAGAAAAAAA-AAAAG
*
29420248 AAAAGAAAAAGAGAAAAAAAAAAAG
1 AAAAAAAAAAGAGAAAAAAAAAAAG
*
29420273 AGAAAAAA
1 AAAAAAAA
29420281 GAAAAATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAGAGAAAAAAAAAAAG
Found at i:29421355 original size:84 final size:84
Alignment explanation
Indices: 29421214--29421504 Score: 377
Period size: 84 Copynumber: 3.4 Consensus size: 84
29421204 AAAATTCAGT
* * * * *
29421214 GCCTTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTACGGATCTTATCTCCCTAAGCAGTAG
29421279 TGGAGCAGATCGAAGACTC
66 TGGAGCAGATCGAAGACTC
* *
29421298 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACGGATCTTATCTCCCTAAGTAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTACGGATCTTATCTCCCTAAGCAGTAG
* * *
29421363 CGGAACAGATCAACGATGACTC
66 TGGAGCAGAT---CGAAGACTC
* * * * *
29421385 GCCTTAATCCCTTAAGCAGTAGGGTAACAGGTCAAAATTTCGGATCTTATTTCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTACGGATCTTATCTCCCTAAGCAGTAG
*
29421450 TGGAGTAGATCGAAGA-TGC
66 TGGAGCAGATCGAAGACT-C
* *
29421469 ACCTTAACCCCCTAAGCAATAGGGTAACAGGTTAAA
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAA
29421505 GTATAGCAGA
Statistics
Matches: 177, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
83 1 0.01
84 103 0.58
87 73 0.41
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (84 bp):
GCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTACGGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACTC
Found at i:29421440 original size:44 final size:43
Alignment explanation
Indices: 29421223--29421449 Score: 125
Period size: 43 Copynumber: 5.3 Consensus size: 43
29421213 TGCCTTAATC
* * * *
29421223 CCCTAAGCAGTAGGGTAACAAGT-TAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTCAAAATTT-CGGATCTTATAT
* * * * * *
29421266 CCCTAAGCAGTAGTGG-AGCAGATCGAAGA-CTC-G-CCTTA-ACC
1 CCCTAAGCAGTAG-GGTAACAGGTC-AAAATTTCGGATCTTATA-T
* *
29421307 CCCTAAGCAGTAGGGTAACAGG-CTAAAATTACGGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTC-AAAATTTCGGATCTTATAT
* * * * *
29421350 CCCTAAGTAGTAGCGG-AACAGATCAACGATGACTC-G-CCTTA-AT
1 CCCTAAGCAGTAG-GGTAACAGGTCAA-AAT--TTCGGATCTTATAT
*
29421393 CCCTTAAGCAGTAGGGTAACAGGTCAAAATTTCGGATCTTATTT
1 CCC-TAAGCAGTAGGGTAACAGGTCAAAATTTCGGATCTTATAT
29421437 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
29421450 TGGAGTAGAT
Statistics
Matches: 134, Mismatches: 31, Indels: 38
0.66 0.15 0.19
Matches are distributed among these distances:
40 6 0.04
41 24 0.18
42 3 0.02
43 63 0.47
44 34 0.25
45 3 0.02
46 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGGTCAAAATTTCGGATCTTATAT
Found at i:29421956 original size:207 final size:207
Alignment explanation
Indices: 29421629--29422764 Score: 1819
Period size: 207 Copynumber: 5.5 Consensus size: 207
29421619 CGGTGAGCAG
*
29421629 ATCGAAGACATAGCTGATTTGGCTTTCATGTGTTTACGTTGAAGCAAGTCTAAGATG-TTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* * *
29421693 TCAT-TGTATTGTCAGAGAACAAATCGAAGTTTTGTGTCTCCATATTCGATGGAGGGCAGACACA
66 TC-TCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACA
*
29421757 TAGCAGATCTGGCCTTCAGATGTTTATACTGAAGTAAGATCCAAGATGGTTTGGCATCCTTGTGC
130 TAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGC
29421822 TTACAAGGAACAA
195 TTACAAGGAACAA
*
29421835 ATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* *
29421900 TCTCTGTATTGTTAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
*
29421965 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTACT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
29422030 TACAAGGAACAA
196 TACAAGGAACAA
* *
29422042 ATCGAAAACATAGCTGATTTGGCTTTCACATGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* *
29422107 TCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGTCTCTATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
* *
29422172 AGCAGATCTGGCCTTCAGATGTTTATACTAAAGCAAGATCCAAGATGGTTTGGCATCCTTGTACT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
*
29422237 TACGAGGAACAA
196 TACAAGGAACAA
*
29422249 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACATTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
*
29422314 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
*
29422379 AGCAGATCTGACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
29422444 TACAAGGAACAA
196 TACAAGGAACAA
*
29422456 ATTGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* *
29422521 TCTCTGTATTGTCAGAGAACAAATTGAAGTTTGGTGTCTCCATATTCGACGGATTCGACGGAGGA
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC-G----GA--G-GG-
* * ** * * *
29422586 TAGACATATAGCAGATCTAACCTTCAGATGATTAGACTGAAGC-AGATCCAAGATGGTTTGGTAT
122 CAGACACATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCAT
*
29422650 CCTTGTGCTTACAAGGAGCAA
187 CCTTGTGCTTACAAGGAACAA
** * * *
29422671 ATCGAAGACATAGCTGATTTGGCTTTTGCGTGTTTACGCTGAAGAAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* * *
29422736 TCTTTGTATTGTCAGGGAACAAATTGAAG
66 TCTCTGTATTGTCAGAGAACAAATCGAAG
29422765 AAACAAATCT
Statistics
Matches: 875, Mismatches: 44, Indels: 13
0.94 0.05 0.01
Matches are distributed among these distances:
206 56 0.06
207 648 0.74
208 1 0.00
212 2 0.00
214 1 0.00
215 128 0.15
216 39 0.04
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (207 bp):
ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
TACAAGGAACAA
Found at i:29423161 original size:14 final size:15
Alignment explanation
Indices: 29423142--29423197 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
29423132 AATCTTCAAT
29423142 GATATG-CAATCTTA
1 GATATGACAATCTTA
29423156 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
29423173 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
29423191 GATATGA
1 GATATGA
29423198 TATACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:29423168 original size:17 final size:17
Alignment explanation
Indices: 29423148--29423211 Score: 92
Period size: 17 Copynumber: 3.6 Consensus size: 17
29423138 CAATGATATG
29423148 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
29423165 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
29423183 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
29423202 CAATCTTAGA
1 CAATCTTAGA
29423212 AGATATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.36
18 15 0.36
19 11 0.26
20 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:29423186 original size:35 final size:37
Alignment explanation
Indices: 29423140--29423218 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
29423130 ATAATCTTCA
29423140 ATGATATGCAATCTTAGATATG-ATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGAATACAATCTTAGAT
29423176 ATGAT-TGCAATCTTAGATATGATATACAATCTTAGA-
1 ATGATATGCAATCTTAGATATGA-ATACAATCTTAGAT
29423212 A-GATATG
1 ATGATATG
29423219 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 19 0.47
36 8 0.20
37 13 0.32
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGAATACAATCTTAGAT
Found at i:29427397 original size:21 final size:22
Alignment explanation
Indices: 29427373--29427479 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 22
29427363 AATAAAGATA
*
29427373 AATATAAATAACATAATAA-AT
1 AATATAAATAAAATAATAATAT
*
29427394 AATATATGATAAAAT-ATAA-AT
1 AATATA-AATAAAATAATAATAT
*
29427415 AA-AT-AAT-AGATAATATATAT
1 AATATAAATAAAATAATA-ATAT
* *
29427435 AATAGACAAGATAACATAATAATAT
1 AAT--ATAA-ATAAAATAATAATAT
29427460 AAATATATAATAAAATAATA
1 -AATATA-AATAAAATAATA
29427480 TACGATAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 21
0.69 0.08 0.22
Matches are distributed among these distances:
17 3 0.05
18 5 0.08
19 1 0.02
20 6 0.09
21 14 0.21
22 6 0.09
23 1 0.02
24 13 0.20
25 7 0.11
26 10 0.15
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (22 bp):
AATATAAATAAAATAATAATAT
Found at i:29427469 original size:57 final size:54
Alignment explanation
Indices: 29427351--29427479 Score: 137
Period size: 57 Copynumber: 2.4 Consensus size: 54
29427341 TTACAAGTGT
29427351 TAAAAT-T-ATAATAATAA-AGATAAATATAAATAACATAATAAATAATATATGA
1 TAAAATATAATAA-AATAATAGATAAATATAAATAACATAATAAATAATATATGA
29427403 TAAAATATAA-ATAAATAATAGATAATATATATAATAGACA-AGATAACATAATA-AT-A
1 TAAAATATAATA-AAATAATAGATAA-ATATA-AATA-ACATA-ATAA-ATAATATATGA
29427459 TAAATATATAATAAAATAATA
1 TAAA-ATATAATAAAATAATA
29427480 TACGATAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 17
0.80 0.00 0.20
Matches are distributed among these distances:
52 6 0.09
53 7 0.11
54 8 0.12
55 5 0.08
56 10 0.15
57 23 0.35
58 7 0.11
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (54 bp):
TAAAATATAATAAAATAATAGATAAATATAAATAACATAATAAATAATATATGA
Found at i:29427524 original size:17 final size:17
Alignment explanation
Indices: 29427484--29427525 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
29427474 ATAATATACG
*
29427484 ATAAATAATTTTTATAT
1 ATAAATAATGTTTATAT
*
29427501 ATGAATAATGTTTATAGT
1 ATAAATAATGTTTATA-T
29427519 A-AAATAA
1 ATAAATAA
29427526 ATAATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (17 bp):
ATAAATAATGTTTATAT
Found at i:29427558 original size:22 final size:21
Alignment explanation
Indices: 29427518--29427577 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 21
29427508 ATGTTTATAG
29427518 TAAAATAAATAATATATAAAATATT
1 TAAAATAAAT-A-A-ATAAAA-ATT
29427543 TAAAATAAATAAATAAAAATT
1 TAAAATAAATAAATAAAAATT
*
29427564 TAGAAATATATAAA
1 TA-AAATAAATAAA
29427578 AAAGGATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 5 0.15
22 16 0.48
23 1 0.03
24 1 0.03
25 10 0.30
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAATAAATAAATAAAAATT
Found at i:29429156 original size:80 final size:79
Alignment explanation
Indices: 29429011--29429214 Score: 241
Period size: 80 Copynumber: 2.6 Consensus size: 79
29429001 AGTCTTGAGT
** ** * **
29429011 TCTTCGATTTGCTCCCCGTTGAATACAGAGACACCCAAATCATCTTGAATCAGCCTTGATGAAGG
1 TCTTCGATTTGCTCCCCGTCAAATACAGAGATGCCCAAATCATCTTGAATCAGCCTCGAAAAAGG
29429076 TCAGATCTACTAAT-
66 TCAGATCTACT-ATG
* * * * *
29429090 TCCTTCGATTTGCTCTCCGTCCATTACAGAGATGCCCAAATCATCTTGGATCTGCCTCGAAAAAG
1 T-CTTCGATTTGCTCCCCGTCAAATACAGAGATGCCCAAATCATCTTGAATCAGCCTCGAAAAAG
*
29429155 GTCAGATCTGCTATG
65 GTCAGATCTACTATG
* *
29429170 TCTTTGATTTGCTCCCCATCAAATACAGAGATG-CCAAATCATCTT
1 TCTTCGATTTGCTCCCCGTCAAATACAGAGATGCCCAAATCATCTT
29429215 CTTGGTTTTG
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
78 12 0.11
79 30 0.28
80 64 0.60
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (79 bp):
TCTTCGATTTGCTCCCCGTCAAATACAGAGATGCCCAAATCATCTTGAATCAGCCTCGAAAAAGG
TCAGATCTACTATG
Found at i:29429245 original size:44 final size:44
Alignment explanation
Indices: 29429170--29429346 Score: 194
Period size: 44 Copynumber: 4.0 Consensus size: 44
29429160 ATCTGCTATG
* * *
29429170 TCTTTGATTTGCTCCCCATCAAATACAGAGATGCCAAATCATCT
1 TCTTGGATTTGCTCCCCATCGAATACGGAGATGCCAAATCATCT
* * * * *
29429214 TCTTGGTTTTGCTCCCCGTCGAATACGGAGATGCCGAATCTGTCA
1 TCTTGGATTTGCTCCCCATCGAATACGGAGATGCCAAATC-ATCT
* * * * **
29429259 TCTTGGATCTACT-CCCGTCGAATACGGGGATGCCAAATCCGCT
1 TCTTGGATTTGCTCCCCATCGAATACGGAGATGCCAAATCATCT
* *
29429302 TCTTGGATTTGCTCCTCATCGAATACGAAGATGCCAAATCATCT
1 TCTTGGATTTGCTCCCCATCGAATACGGAGATGCCAAATCATCT
29429346 T
1 T
29429347 GGATCTGCTC
Statistics
Matches: 107, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
43 12 0.11
44 83 0.78
45 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTTGGATTTGCTCCCCATCGAATACGGAGATGCCAAATCATCT
Found at i:29429743 original size:26 final size:26
Alignment explanation
Indices: 29429710--29429817 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
29429700 TGATACAAAT
29429710 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
29429736 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29429762 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29429788 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29429814 TGAT
1 TGAT
29429818 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29435185 original size:297 final size:297
Alignment explanation
Indices: 29434651--29435249 Score: 1135
Period size: 297 Copynumber: 2.0 Consensus size: 297
29434641 ATATTTGCAT
29434651 TTAAGATTTAGAGACATTACTTGTACGGAGAAAGGTGTATTATATACACTGACCATAAGAGTCTT
1 TTAAGATTTAGAGACATTACTTGTACGGAGAAAGGTGTATTATATACACTGACCATAAGAGTCTT
29434716 AAGTATTTGTTGACTCAAAAGGAGCTGAACCTTAGGCAAAAGAGATGGATTGAGTTGCTTAATGA
66 AAGTATTTGTTGACTCAAAAGGAGCTGAACCTTAGGCAAAAGAGATGGATTGAGTTGCTTAATGA
*
29434781 TTATGACTGTTCGATCGAGTATCACCTAGGCAAGGCTAATGTGGTAGCCGATGCTCTAAGTCGCA
131 TTATGACTGTTCGATCGAGTATCACCCAGGCAAGGCTAATGTGGTAGCCGATGCTCTAAGTCGCA
29434846 GAGCTATATCTGATCTGAGAGCAATGTTTGCTCGTCTGAGTCTGTATGATGATGGAAGTCTGTTG
196 GAGCTATATCTGATCTGAGAGCAATGTTTGCTCGTCTGAGTCTGTATGATGATGGAAGTCTGTTG
*
29434911 GCTGAGTTACAAGTGAGGCCAACCTTGGTGGATCAGA
261 GCTGAGTTACAAGTGAGGCCAACCTGGGTGGATCAGA
29434948 TTAAGATTTAGAGACATTACTTGTACGGAGAAAGGTGTATTATATACACTGACCATAAGAGTCTT
1 TTAAGATTTAGAGACATTACTTGTACGGAGAAAGGTGTATTATATACACTGACCATAAGAGTCTT
* ** *
29435013 AAGTATTTGTTGACTCAGAAGGAGCTGATGCTTAGGCAAAAGATATGGATTGAGTTGCTTAATGA
66 AAGTATTTGTTGACTCAAAAGGAGCTGAACCTTAGGCAAAAGAGATGGATTGAGTTGCTTAATGA
*
29435078 TTATGACTGTTCGATCGAGTATCACCCAGGCAAGGCTAATGTGGTAGCCGATGCTCTAAGTCGTA
131 TTATGACTGTTCGATCGAGTATCACCCAGGCAAGGCTAATGTGGTAGCCGATGCTCTAAGTCGCA
29435143 GAGCTATATCTGATCTGAGAGCAATGTTTGCTCGTCTGAGTCTGTATGATGATGGAAGTCTGTTG
196 GAGCTATATCTGATCTGAGAGCAATGTTTGCTCGTCTGAGTCTGTATGATGATGGAAGTCTGTTG
29435208 GCTGAGTTACAAGTGAGGCCAACCTGGGTGGATCAGA
261 GCTGAGTTACAAGTGAGGCCAACCTGGGTGGATCAGA
29435245 TTAAG
1 TTAAG
29435250 GAAAAGCAGT
Statistics
Matches: 295, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
297 295 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (297 bp):
TTAAGATTTAGAGACATTACTTGTACGGAGAAAGGTGTATTATATACACTGACCATAAGAGTCTT
AAGTATTTGTTGACTCAAAAGGAGCTGAACCTTAGGCAAAAGAGATGGATTGAGTTGCTTAATGA
TTATGACTGTTCGATCGAGTATCACCCAGGCAAGGCTAATGTGGTAGCCGATGCTCTAAGTCGCA
GAGCTATATCTGATCTGAGAGCAATGTTTGCTCGTCTGAGTCTGTATGATGATGGAAGTCTGTTG
GCTGAGTTACAAGTGAGGCCAACCTGGGTGGATCAGA
Found at i:29437068 original size:26 final size:26
Alignment explanation
Indices: 29437029--29437136 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
29437019 TTGATACAAT
29437029 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
29437055 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29437081 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29437107 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29437133 TGAT
1 TGAT
29437137 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29439875 original size:44 final size:44
Alignment explanation
Indices: 29439827--29439932 Score: 185
Period size: 44 Copynumber: 2.4 Consensus size: 44
29439817 CAAAATACGA
* *
29439827 AGATGCCAAATCTACTGTCTTCGATCTGCTTTCTGACAATACAG
1 AGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGACAATACAG
*
29439871 AGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAG
1 AGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGACAATACAG
29439915 AGATGCCAAATCTGCTGT
1 AGATGCCAAATCTGCTGT
29439933 AACACCCCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
AGATGCCAAATCTGCTGTCTTCGATCTGCTCTCTGACAATACAG
Found at i:29440971 original size:27 final size:28
Alignment explanation
Indices: 29440867--29440979 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 28
29440857 CTATTCAGAA
* **
29440867 ATCAGTGTTAA-CTGGGCTTTAGCCCAT
1 ATCAGTATTAATCTGGGCCATAGCCCAT
* *
29440894 ATCAATATTAATCTGGGCCATAGCCCCT
1 ATCAGTATTAATCTGGGCCATAGCCCAT
*
29440922 -TACAGTATTAGAGTATATTGGGCC-TAGCCCAT
1 AT-CAGTATT--A--AT-CTGGGCCATAGCCCAT
*
29440954 ATCAGTATTAATCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCCATAGCCC
29440980 TATTACAAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
27 16 0.24
28 27 0.40
30 2 0.03
32 16 0.24
33 7 0.10
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (28 bp):
ATCAGTATTAATCTGGGCCATAGCCCAT
Found at i:29440999 original size:60 final size:60
Alignment explanation
Indices: 29440886--29441015 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
29440876 AACTGGGCTT
* ** *
29440886 TAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATTAGAGTATATTGGGCC
1 TAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACAGTACGAGAGTATATTGCGCC
* *
29440946 TAGCCCATATCAGTATTAATCTGGGCCGTAGCCCTATTACAAGT-CGAGA-TATATTGCGCC
1 TAGCCCATATCAATATTAATCTGGGCCATAGCCC-ATTAC-AGTACGAGAGTATATTGCGCC
*
29441006 TTGCCCATAT
1 TAGCCCATAT
29441016 TAACACAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
60 51 0.84
61 7 0.11
62 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (60 bp):
TAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACAGTACGAGAGTATATTGCGCC
Found at i:29443057 original size:12 final size:12
Alignment explanation
Indices: 29443040--29443064 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29443030 AACATATTAA
29443040 ATAATAATAATC
1 ATAATAATAATC
29443052 ATAATAATAATC
1 ATAATAATAATC
29443064 A
1 A
29443065 AAACATCCAA
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATAATAATC
Found at i:29446816 original size:44 final size:44
Alignment explanation
Indices: 29446753--29446906 Score: 236
Period size: 44 Copynumber: 3.5 Consensus size: 44
29446743 GGGGCGTTAG
* * *
29446753 ATCTGCTATCTTCAATCTGCTCTCTGGCAATACAAAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAA
*
29446797 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACACCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAA
* * *
29446841 ATCTGCTACCTTCTATGTGCTCTCTGACAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAA
*
29446885 ATCTGCTATTTTCGATCTGCTC
1 ATCTGCTATCTTCGATCTGCTC
29446907 CTTGTAAACG
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 98 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAA
Found at i:29447184 original size:220 final size:219
Alignment explanation
Indices: 29446882--29447332 Score: 663
Period size: 220 Copynumber: 2.1 Consensus size: 219
29446872 ACAGAGACGC
* *
29446882 CAAATCTGCTAT--TTTCGATCTGCTCCTTGTAAACGCAAGGATGCTAAATCATCTTGGATCTGC
1 CAAATCTGCTATGCCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTGC
* * *
29446945 TTCTAAACAAAAAATCTGAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCATCGAATATAGA
66 TTCGAAACAAAAAATCTGAAGGTTAGATCTACTATGTCTTCGATCTGATCTCCATCGAATATAGA
* * * *
29447010 GATGCCAAATCTATTTCTTCGATTTGTTCTCTGACAATTCAGAGACGCCAAATCATCTTGGATCT
131 GATGCCAAATCTATTTCTTCGATTTGCTCTCTGACAATACAAAGACGCCAAATCATCTTAGATCT
* **
29447075 GCTTCAGCGTTAACATTTGAAGGT
196 GCTTCAGCGTAAACACCTGAAGGT
* * * *
29447099 CAGATCTGCTATGCCTTCGATCTGCTCCTTGTAAATGTAAGGATGCCAAATCATCTTGGATTTGC
1 CAAATCTGCTATGCCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTGC
** * * *
29447164 TTCGATGCAAAAACATCTGAAGGTTAGATCTACTATGTCTTTGATCTGATCTCCGTCGAATATGG
66 TTCGAAACAAAAA-ATCTGAAGGTTAGATCTACTATGTCTTCGATCTGATCTCCATCGAATATAG
* * *
29447229 AGATGCCAAATCTGTTTCTTCGATTTGCTCTCTGATAATACAAAGATGCCAAATCATCTTAGATC
130 AGATGCCAAATCTATTTCTTCGATTTGCTCTCTGACAATACAAAGACGCCAAATCATCTTAGATC
29447294 TGCTTCAGCGTAAACACCTGAAGGT
195 TGCTTCAGCGTAAACACCTGAAGGT
29447319 CAAATCTGCTATGC
1 CAAATCTGCTATGC
29447333 TTTGGCCTAT
Statistics
Matches: 206, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
217 11 0.05
219 56 0.27
220 139 0.67
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (219 bp):
CAAATCTGCTATGCCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTGC
TTCGAAACAAAAAATCTGAAGGTTAGATCTACTATGTCTTCGATCTGATCTCCATCGAATATAGA
GATGCCAAATCTATTTCTTCGATTTGCTCTCTGACAATACAAAGACGCCAAATCATCTTAGATCT
GCTTCAGCGTAAACACCTGAAGGT
Found at i:29451047 original size:68 final size:64
Alignment explanation
Indices: 29450982--29451189 Score: 206
Period size: 67 Copynumber: 3.2 Consensus size: 64
29450972 CATCATGTGT
29450982 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTACGAG--A-TAT-ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
29451047 TAG
62 TAG
* * * * * * *
29451050 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGT
29451115 AG
63 AG
* * * * *
29451117 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATA-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
29451179 TACAAGAGAGC
1 -ACAAGAGAGC
29451190 CGAACTTTAT
Statistics
Matches: 117, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.16
64 21 0.18
65 11 0.09
66 17 0.15
67 31 0.26
68 17 0.15
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.22
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
Found at i:29455473 original size:68 final size:67
Alignment explanation
Indices: 29455401--29455550 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
29455391 CATCATGTGT
* * * *
29455401 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
29455463 ATGTAG
62 ATGTAG
** * *
29455469 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
29455534 AG
66 AG
29455536 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
29455551 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:29455506 original size:64 final size:64
Alignment explanation
Indices: 29455425--29455608 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
29455415 AGACATTATG
* *
29455425 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
29455489 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29455554 AA
63 AA
* * * *
29455556 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
29455609 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:29463181 original size:40 final size:40
Alignment explanation
Indices: 29463125--29463292 Score: 184
Period size: 40 Copynumber: 4.2 Consensus size: 40
29463115 CAATTGAATG
* *
29463125 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-CTT
29463166 -TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGCTT
* * *
29463205 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGT-CGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGC-TT
** *
29463245 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTGCTT
29463285 ATATCCGG
1 ATATCCGG
29463293 TTGTATTCCG
Statistics
Matches: 110, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
39 8 0.07
40 98 0.89
41 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGCTT
Found at i:29463258 original size:80 final size:79
Alignment explanation
Indices: 29463125--29463292 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 79
29463115 CAATTGAATG
* *
29463125 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
*
29463190 TTCGTGCAAGTTGTT
65 TTCGTGCAAGTGGTT
* *
29463205 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
29463269 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
29463285 ATATCCGG
1 ATATCCGG
29463293 TTGTATTCCG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 2 0.03
80 76 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:29471718 original size:39 final size:39
Alignment explanation
Indices: 29471603--29471799 Score: 250
Period size: 39 Copynumber: 5.0 Consensus size: 39
29471593 TCGTTCAAAC
* * ** * **
29471603 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
29471643 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
29471683 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
29471722 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
* * *
29471761 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
29471800 CACTTAGCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 101 0.73
40 38 0.27
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:29474452 original size:40 final size:40
Alignment explanation
Indices: 29474396--29474563 Score: 166
Period size: 40 Copynumber: 4.2 Consensus size: 40
29474386 CAATTGAATG
* *
29474396 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-CTT
29474437 -TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGCTT
* * * *
29474476 ATATCCGGGTTAATACCCGAAGGCATTTGTGCGAGT-CGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGC-TT
* ** *
29474516 ATATCTGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTGCTT
29474556 ATATCCGG
1 ATATCCGG
29474564 TTGTATTCCG
Statistics
Matches: 106, Mismatches: 13, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
39 8 0.08
40 94 0.89
41 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGCTT
Found at i:29474529 original size:80 final size:79
Alignment explanation
Indices: 29474396--29474563 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 79
29474386 CAATTGAATG
*
29474396 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
*
29474461 TTCGTGCAAGTTGTT
65 TTCGTGCAAGTGGTT
* * *
29474476 ATATCCGGGTTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
29474540 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
29474556 ATATCCGG
1 ATATCCGG
29474564 TTGTATTCCG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 2 0.03
80 76 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (79 bp):
ATATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:29481745 original size:29 final size:29
Alignment explanation
Indices: 29481683--29481784 Score: 91
Period size: 33 Copynumber: 3.3 Consensus size: 29
29481673 AAAGATAAAG
29481683 ATAAATAACATAATAAATAATATATGATAAAAT
1 ATAAATAACATAAT-AATAATATAT-AT--AAT
29481716 ATAAATAA-ATAATAGATAATATATATAAT
1 ATAAATAACATAATA-ATAATATATATAAT
* *
29481745 AGACAAGATAACATAATAATATAAATATATAAT
1 --ATAA-ATAACATAATAATA-ATATATATAAT
29481778 A-AAATAA
1 ATAAATAA
29481785 TATACGATAA
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
29 7 0.11
30 2 0.03
31 7 0.11
32 21 0.34
33 24 0.39
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (29 bp):
ATAAATAACATAATAATAATATATATAAT
Found at i:29483185 original size:18 final size:18
Alignment explanation
Indices: 29483162--29483198 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29483152 TTAAATAGAC
*
29483162 TGTTTAATTTTATTTTTT
1 TGTTTAATTTCATTTTTT
29483180 TGTTTAATTTCATTTTTT
1 TGTTTAATTTCATTTTTT
29483198 T
1 T
29483199 AATTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (18 bp):
TGTTTAATTTCATTTTTT
Found at i:29485050 original size:15 final size:15
Alignment explanation
Indices: 29485030--29485060 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29485020 GGATGTTGTA
*
29485030 TGTAATTCGTCTATT
1 TGTAATTCATCTATT
29485045 TGTAATTCATCTATT
1 TGTAATTCATCTATT
29485060 T
1 T
29485061 CAGTAGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.55
Consensus pattern (15 bp):
TGTAATTCATCTATT
Found at i:29486945 original size:30 final size:30
Alignment explanation
Indices: 29486896--29486954 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
29486886 TACAATTTTG
* * *
29486896 TTTTATTTTTATTTTAATTTGGCCCTAATA
1 TTTTATATTTATTTCAATTTAGCCCTAATA
* *
29486926 TTTTATATTTGTTTCAATTTAGTCCTAAT
1 TTTTATATTTATTTCAATTTAGCCCTAAT
29486955 GGCTATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (30 bp):
TTTTATATTTATTTCAATTTAGCCCTAATA
Found at i:29487254 original size:17 final size:16
Alignment explanation
Indices: 29487229--29487286 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
29487219 ATACGTTTCT
*
29487229 TATAGATTTTTGTTATA
1 TATATATTTTT-TTATA
29487246 TATATATTTTACTTTATA
1 TATATATTTT--TTTATA
29487264 TAT-TATTTATTTTACTA
1 TATATATTT-TTTTA-TA
29487281 TATATA
1 TATATA
29487287 AAATTATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 4 0.11
17 19 0.54
18 11 0.31
19 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TATATATTTTTTTATA
Found at i:29487263 original size:16 final size:17
Alignment explanation
Indices: 29487241--29487286 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
29487231 TAGATTTTTG
29487241 TTATATATATATTTTACT
1 TTATATATATA-TTTACT
*
29487259 TTATATAT-TATTTATT
1 TTATATATATATTTACT
29487275 TTACTATATATA
1 TTA-TATATATA
29487287 AAATTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 10 0.40
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATATATATTTACT
Found at i:29487276 original size:21 final size:20
Alignment explanation
Indices: 29487242--29487286 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
29487232 AGATTTTTGT
*
29487242 TATATATATATTTTACTTTA
1 TATATATATATTTTACTATA
*
29487262 TATATTATTTATTTTACTATA
1 TATA-TATATATTTTACTATA
29487283 TATA
1 TATA
29487287 AAATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATATATATTTTACTATA
Found at i:29487392 original size:11 final size:12
Alignment explanation
Indices: 29487369--29487421 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 12
29487359 CCAATATGTT
*
29487369 TTATTCATTATA
1 TTATTTATTATA
29487381 TTATTT-TTATA
1 TTATTTATTATA
*
29487392 TATATTATATTGTA
1 T-TATT-TATTATA
29487406 TTATTTATT-TA
1 TTATTTATTATA
29487417 TTATT
1 TTATT
29487422 ATGTACATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 13 0.36
12 13 0.36
13 5 0.14
14 5 0.14
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (12 bp):
TTATTTATTATA
Found at i:29487399 original size:27 final size:25
Alignment explanation
Indices: 29487369--29487423 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
29487359 CCAATATGTT
29487369 TTATTCATTATATTATTT-TTATATATA
1 TTATT-ATTATATTATTTATT-TAT-TA
*
29487396 TTA-TATTGTATTATTTATTTATTA
1 TTATTATTATATTATTTATTTATTA
29487420 TTAT
1 TTAT
29487424 GTACATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
24 5 0.20
25 14 0.56
26 3 0.12
27 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TTATTATTATATTATTTATTTATTA
Found at i:29499804 original size:220 final size:220
Alignment explanation
Indices: 29499433--29499856 Score: 616
Period size: 220 Copynumber: 1.9 Consensus size: 220
29499423 AGATCTGACC
* * *
29499433 TTCAGGTGTTTACGCTGAAGCAGATCCAAAATGATTTGGCATCTTTGTATTACTAGAGAACAAAT
1 TTCACGTGTTTACACTGAAGCAGATCCAAAATGATTTGGCATCTCTGTATTACTAGAGAACAAAT
* * *
29499498 AGAAGAAACAAATTTGGCATCTCCGTATTTGACAGAGAGTAGATCGGAGACATAGCAGATCTAAC
66 AGAAGAAACAAATTTGGCATCTCCATATTTGACAGAGAGCAGATCGAAGACATAGCAGATCTAAC
* * *
29499563 CTTCAGATGTTTTCACATCGAAATAGATCCAAGATGATTTGGCATCCTTGCATTTACAAGGAGCA
131 CTTCAAATATTTTCACATCGAAACAGATCCAAGATGATTTGGCATCCTTGCATTTACAAGGAGCA
**
29499628 GGTCGAAGACAAAGCAGATTTGGCT
196 AATCGAAGACAAAGCAGATTTGGCT
* ** * * *
29499653 TTCACGTGTTTACACTGAAGCAGATCTAAGTTGATTTGGCATCTCTGTATT-GTCAGAGAGCAAC
1 TTCACGTGTTTACACTGAAGCAGATCCAAAATGATTTGGCATCTCTGTATTACT-AGAGAACAAA
* * * *
29499717 TCGAAGAAACAGATTTGGCATCTCCATATTTGACGGAGAGCAGATTGAAGACATAGCAGATCTAA
65 TAGAAGAAACAAATTTGGCATCTCCATATTTGACAGAGAGCAGATCGAAGACATAGCAGATCTAA
** *
29499782 CCTTCAAATATTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTTGCATTTACAAGGAGC
130 CCTTCAAATATTTTCACATCGAAACAGATCCAAGATGATTTGGCATCCTTGCATTTACAAGGAGC
29499847 AAATCGAAGA
195 AAATCGAAGA
29499857 TAGCAGACTT
Statistics
Matches: 179, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
219 1 0.01
220 178 0.99
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (220 bp):
TTCACGTGTTTACACTGAAGCAGATCCAAAATGATTTGGCATCTCTGTATTACTAGAGAACAAAT
AGAAGAAACAAATTTGGCATCTCCATATTTGACAGAGAGCAGATCGAAGACATAGCAGATCTAAC
CTTCAAATATTTTCACATCGAAACAGATCCAAGATGATTTGGCATCCTTGCATTTACAAGGAGCA
AATCGAAGACAAAGCAGATTTGGCT
Found at i:29499891 original size:44 final size:44
Alignment explanation
Indices: 29499843--29500223 Score: 575
Period size: 44 Copynumber: 8.7 Consensus size: 44
29499833 CATTTACAAG
* *
29499843 GAGCAAATCGAAGATAGCAGACTTGGCGTCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
* *
29499887 GAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGG
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
*
29499931 GAGCAGATCGAAGATAGCAGATTTGGCGTCGCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
* *
29499975 GAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGTCAGAA
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAG-A
* *
29500020 GAGTAGATTGAAGATAG-AGATTTGGCGTCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
* * * *
29500063 GAGCAAATCAAAGATAGCAGATTTGACATCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
* * *
29500107 GAACAGATCGAAGATAGCAGATTTAGTGTCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
29500151 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
* * *
29500195 GAGCAGATAGAAGATAACAGATCTGGCGT
1 GAGCAGATCGAAGATAGCAGATTTGGCGT
29500224 TCCTGAGTTT
Statistics
Matches: 302, Mismatches: 33, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
43 14 0.05
44 273 0.90
45 15 0.05
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (44 bp):
GAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
Found at i:29502055 original size:40 final size:40
Alignment explanation
Indices: 29501962--29502111 Score: 171
Period size: 39 Copynumber: 3.8 Consensus size: 40
29501952 AAATTGAATG
* * * *
29501962 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
* **
29502001 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
* *
29502041 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGT-TTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAATT
* *
29502080 AAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
29502112 AAATCGTGAT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
39 60 0.63
40 35 0.37
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
Found at i:29510241 original size:40 final size:39
Alignment explanation
Indices: 29510076--29510259 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
29510066 AAATTGAATG
* * *
29510076 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
29510116 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
29510156 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
29510196 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
29510235 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29510260 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:29510284 original size:80 final size:81
Alignment explanation
Indices: 29510116--29510304 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
29510106 GCTGGAAATT
* * * *
29510116 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
29510181 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
29510197 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
29510260 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29510276 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29510305 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29516339 original size:16 final size:16
Alignment explanation
Indices: 29516318--29516350 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29516308 AGTATGGTAT
29516318 GGTTAGATTAAACTAA
1 GGTTAGATTAAACTAA
29516334 GGTTAGATTAAACTAA
1 GGTTAGATTAAACTAA
29516350 G
1 G
29516351 CTAATTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (16 bp):
GGTTAGATTAAACTAA
Found at i:29522652 original size:40 final size:40
Alignment explanation
Indices: 29522567--29522717 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
29522557 AATTGAATGA
* * * **
29522567 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTCA-TAC
* *
29522607 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT--CATAC
*
29522648 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATAC
*
29522687 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
29522718 ACGTGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 1 0.01
39 5 0.05
40 84 0.91
41 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATAC
Found at i:29522731 original size:40 final size:40
Alignment explanation
Indices: 29522604--29522733 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
29522594 ATGCTGGAAA
* * *
29522604 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
29522644 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
29522684 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
29522724 TTATATCCGG
1 TTATATCCGG
29522734 TTATATTCCG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:29528344 original size:39 final size:38
Alignment explanation
Indices: 29528290--29528492 Score: 298
Period size: 39 Copynumber: 5.2 Consensus size: 38
29528280 AACCCAAGTA
* **
29528290 CCTTCGGGATTTAGCCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATATAGTAACT-GCACAAATG
29528329 CCTTCGGGACTTAGCCCGGATATAGTAACTGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTGCACAAATG
29528368 CCTTCGGGACTTAGCCCGGATATAGTAACTGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTGCACAAATG
*
29528407 CCTTCGGGACTTAACCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATATAGTAACT-GCACAAATG
* *
29528446 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTT-AGCCGGATATAGTAACT-GCACAAATG
29528486 CCTTCGG
1 CCTTCGG
29528493 ATCTTAGTCC
Statistics
Matches: 154, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
38 15 0.10
39 95 0.62
40 44 0.29
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (38 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTGCACAAATG
Found at i:29536327 original size:40 final size:40
Alignment explanation
Indices: 29536258--29536461 Score: 333
Period size: 40 Copynumber: 5.2 Consensus size: 40
29536248 AACCCAAGTA
* **
29536258 CCTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29536297 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29536337 CCTTCGGGACTTAGCCCGGATATAGTAACT-GCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29536376 CCTTCGGGACTTA-CCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
29536415 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29536455 CCTTCGG
1 CCTTCGG
29536462 ATCTTAGTCC
Statistics
Matches: 157, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
38 16 0.10
39 57 0.36
40 84 0.54
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29542058 original size:68 final size:70
Alignment explanation
Indices: 29541986--29542183 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
29541976 ACACCCTGTA
* * * *
29541986 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
29542048 ATAAAT
65 ATAAAT
*
29542054 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
29542119 ATAAAT
65 ATAAAT
*
29542125 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
29542184 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:29542097 original size:41 final size:41
Alignment explanation
Indices: 29542052--29542169 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
29542042 TGAAAGATAA
29542052 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
29542093 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29542123 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29542164 ATGTAG
1 ATGTAG
29542170 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:29542109 original size:71 final size:71
Alignment explanation
Indices: 29542020--29542183 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
29542010 GAGATGTATC
29542020 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29542085 AGGACA
66 AGGACA
29542091 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29542156 AGGACA
66 AGGACA
29542162 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29542184 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:29549610 original size:68 final size:70
Alignment explanation
Indices: 29549538--29549735 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
29549528 ACACCCTGTA
* * * *
29549538 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
29549600 ATAAAT
65 ATAAAT
*
29549606 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
29549671 ATAAAT
65 ATAAAT
*
29549677 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
29549736 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:29549649 original size:41 final size:41
Alignment explanation
Indices: 29549604--29549721 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
29549594 TGAAAGATAA
29549604 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
29549645 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29549675 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
29549716 ATGTAG
1 ATGTAG
29549722 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:29549661 original size:71 final size:71
Alignment explanation
Indices: 29549572--29549735 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
29549562 GAGATGTATC
29549572 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29549637 AGGACA
66 AGGACA
29549643 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29549708 AGGACA
66 AGGACA
29549714 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29549736 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:29551276 original size:40 final size:40
Alignment explanation
Indices: 29551164--29551316 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
29551154 GGATATAGCG
* * * * ***
29551164 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* * *
29551204 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* **
29551244 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGGGA
*
29551284 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
29551317 CATCATTCGA
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.03
40 78 0.85
41 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
Found at i:29559257 original size:40 final size:40
Alignment explanation
Indices: 29559145--29559297 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
29559135 GGATATAGCG
* * * * ***
29559145 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* * *
29559185 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* **
29559225 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGGGA
*
29559265 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
29559298 CATCATTCGA
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.03
40 78 0.85
41 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
Found at i:29564737 original size:39 final size:39
Alignment explanation
Indices: 29564677--29564800 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
29564667 CAGTGATGTT
* *
29564677 TATCCGGACTTAGGGTTCGCAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
*
29564716 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTAGAATTA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* * * *
29564755 TAACCTGACTTAAGGTCCGCAGGCTACGTGCTGGAAATA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
*
29564794 TGTCCGG
1 TATCCGG
29564801 GCTAAATTCC
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:29571948 original size:12 final size:12
Alignment explanation
Indices: 29571931--29571955 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29571921 TTAGAGGCTC
29571931 AATATCAAATAA
1 AATATCAAATAA
29571943 AATATCAAATAA
1 AATATCAAATAA
29571955 A
1 A
29571956 TCTAGCATAA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AATATCAAATAA
Found at i:29596754 original size:40 final size:40
Alignment explanation
Indices: 29596699--29596777 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
29596689 TTATAGTACC
*
29596699 ACTTGGTGTGTAGGGCTGGATAGGTCGATTTTCTCCCCAT
1 ACTTGGTGTGTAGGGCTGGATAGGTCGATTTTATCCCCAT
* *
29596739 ACTTGGTGTGTAGGGCTGGGTGGGTCGATTTTATCCCCA
1 ACTTGGTGTGTAGGGCTGGATAGGTCGATTTTATCCCCA
29596778 CATGGTGTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.34
Consensus pattern (40 bp):
ACTTGGTGTGTAGGGCTGGATAGGTCGATTTTATCCCCAT
Found at i:29599419 original size:38 final size:38
Alignment explanation
Indices: 29599368--29599597 Score: 343
Period size: 38 Copynumber: 6.0 Consensus size: 38
29599358 AGCACTCGAT
29599368 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
* *
29599406 ATATATCCAGGTTAAGTCTCGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
* *
29599444 ATATATTCGGGTTAAGTCCCGTAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
* *
29599482 ATATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
*
29599520 ATATATCCGGGTTAAAGTCCCGCAGGCTTAGTGCTGGTA
1 ATATATCCGGGTT-AAGTCCCGCAGGCTTCGTGCTGGTA
* * *
29599559 TTATATCCGAGCTTAAAGTCCCGCAGGCTTTGTGCTGGT
1 ATATATCCG-GGTT-AAGTCCCGCAGGCTTCGTGCTGGT
29599598 GATTGGATTC
Statistics
Matches: 174, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
38 117 0.67
39 30 0.17
40 27 0.16
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (38 bp):
ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
Found at i:29603570 original size:45 final size:45
Alignment explanation
Indices: 29603521--29603687 Score: 162
Period size: 45 Copynumber: 3.7 Consensus size: 45
29603511 TGAGCATCGA
29603521 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGTCCG
* * * *
29603566 AACTCATTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-T--G--TCCG
** * **
29603613 AACTCGTTGAGTTGAGTTTGAGTTCATTTATGGATGCGAATCCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AATGTCCG
*
29603659 AGCTCGTTGAGTTGAGTCC-AGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
29603688 GGGGCGGGTT
Statistics
Matches: 97, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
42 6 0.06
43 1 0.01
44 2 0.02
45 34 0.35
46 19 0.20
47 26 0.27
48 2 0.02
50 5 0.05
51 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGTCCG
Done.