Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 171 of 226
Found at i:54709157 original size:24 final size:24
Alignment explanation
Indices: 54709130--54709239 Score: 60
Period size: 26 Copynumber: 4.2 Consensus size: 24
54709120 ATAATATTAT
54709130 TTTAATATTAAATTAAATTTAATA
1 TTTAATATTAAATTAAATTTAATA
54709154 TTT-ATATTGATAGTATTTTATTAATTTAATA
1 TTTAATATT-A-A--A--TTA--AATTTAATA
* * *
54709185 TTAAAATATTAAATTAATTTTATAAGA
1 TT-TAATATTAAATTAA-ATT-TAATA
* * *
54709212 TTTAATATTGAATTTAATCTAATA
1 TTTAATATTAAATTAAATTTAATA
54709236 TTTA
1 TTTA
54709240 TCTTGATAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 24
0.66 0.09 0.24
Matches are distributed among these distances:
23 5 0.08
24 12 0.18
25 3 0.05
26 13 0.20
27 10 0.15
29 4 0.06
31 12 0.18
32 1 0.02
33 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTAATATTAAATTAAATTTAATA
Found at i:54725212 original size:11 final size:11
Alignment explanation
Indices: 54725192--54725287 Score: 57
Period size: 11 Copynumber: 9.4 Consensus size: 11
54725182 TAAAAATTAA
54725192 AAAAAGTATTTT
1 AAAAA-TATTTT
54725204 AAAAATATTTT
1 AAAAATATTTT
54725215 --AAA-A--TT
1 AAAAATATTTT
* *
54725221 AAAAAAAATTT
1 AAAAATATTTT
*
54725232 AAAAGTATTTT
1 AAAAATATTTT
*
54725243 AAAAAAATTTT
1 AAAAATATTTT
54725254 --AAA-ATTTT
1 AAAAATATTTT
*
54725262 AAAAAT-TTAAT
1 AAAAATATT-TT
*
54725273 AAAAGTATTTT
1 AAAAATATTTT
54725284 AAAA
1 AAAA
54725288 TTAAAAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 21
0.69 0.08 0.22
Matches are distributed among these distances:
6 2 0.03
8 9 0.14
9 7 0.11
10 5 0.08
11 36 0.55
12 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54725236 original size:39 final size:40
Alignment explanation
Indices: 54725159--54725287 Score: 152
Period size: 39 Copynumber: 3.1 Consensus size: 40
54725149 ATAAATACCA
*
54725159 AAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATT-AAA-AAAAATT-ATAAAAGTATTTT
54725204 AAAAATATTTTAAAATTAAAAAAAATT-TAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTATAAAAGTATTTT
* ** *
54725243 AAAAAAATTTTAAAATTTTAAAAATTTAATAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATT-ATAAAAGTATTTT
54725284 AAAA
1 AAAA
54725288 TTAAAAAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
39 34 0.44
41 23 0.30
42 3 0.04
43 6 0.08
44 6 0.08
45 5 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAAATTATAAAAGTATTTT
Found at i:54725257 original size:29 final size:28
Alignment explanation
Indices: 54725225--54725295 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 28
54725215 AAAATTAAAA
54725225 AAAATTTAAAAGTATTTTAA-AAAA-ATTTT
1 AAAATTTAAAA--A-TTTAATAAAAGATTTT
54725254 AAAATTTTAAAAATTTAATAAAAGTATTTT
1 AAAA-TTTAAAAATTTAATAAAAG-ATTTT
*
54725284 AAAATTAAAAAA
1 AAAATTTAAAAA
54725296 ATAAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
27 5 0.14
28 5 0.14
29 11 0.30
30 16 0.43
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAATTTAAAAATTTAATAAAAGATTTT
Found at i:54728323 original size:11 final size:11
Alignment explanation
Indices: 54728300--54728335 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
54728290 GATTTACAAC
54728300 TAAATCTGAGCT
1 TAAATC-GAGCT
54728312 TAAATCGAGCT
1 TAAATCGAGCT
*
54728323 TAAATCAAGCT
1 TAAATCGAGCT
54728334 TA
1 TA
54728336 CATAAGCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (11 bp):
TAAATCGAGCT
Found at i:54729229 original size:13 final size:14
Alignment explanation
Indices: 54729211--54729240 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
54729201 TAGATTAGAT
54729211 TTGATTATGTAA-A
1 TTGATTATGTAATA
54729224 TTGATTATGTAATA
1 TTGATTATGTAATA
54729238 TTG
1 TTG
54729241 TAAATCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TTGATTATGTAATA
Found at i:54732973 original size:45 final size:45
Alignment explanation
Indices: 54732923--54733136 Score: 248
Period size: 45 Copynumber: 4.8 Consensus size: 45
54732913 GTTAGAAAAT
* * * *
54732923 CAACACCGGTACATAGTACCTATTGTATGTATATGGCATGATAGT
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * *
54732968 CAACACCGGTACATAGTACCTATTGTATTTATATGGCATGAAAGC
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * * *
54733013 CAACATCGGTAAATAGTACCTGCTGTATGTATATAGCATGATAGC
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * * *
54733058 CAACACCGGTACATAATACTTGCTGTATTTATATAGCATGAAAGC
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * ** *
54733103 CGATACTAGTACATACTACCTGTTGTATGTATAT
1 CAACACCGGTACATAGTACCTGTTGTATGTATAT
54733137 CCTAATTGTT
Statistics
Matches: 145, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 145 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (45 bp):
CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
Found at i:54736780 original size:87 final size:87
Alignment explanation
Indices: 54736634--54736802 Score: 266
Period size: 87 Copynumber: 1.9 Consensus size: 87
54736624 CTTGTTTACA
* * * * *
54736634 AGACTTGTTTGCCTATCTAATTTTGTATAGGATCCAATGCTTCATTTATATACATATTTCCATTC
1 AGACTTGTTTACATATCTAATTTCGTATAGGATCCAATGCTTAATTTATATACATATTTCCATTA
*
54736699 CATGTTTATATGAAAGTACGTG
66 CATGTTGATATGAAAGTACGTG
* *
54736721 AGACTTGTTTACATATCTAATTTCGTATAGGGTCGAATGCTTAATTTATATACATATTTCCATTA
1 AGACTTGTTTACATATCTAATTTCGTATAGGATCCAATGCTTAATTTATATACATATTTCCATTA
54736786 CATGTTGATATGAAAGT
66 CATGTTGATATGAAAGT
54736803 GTGCGGATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (87 bp):
AGACTTGTTTACATATCTAATTTCGTATAGGATCCAATGCTTAATTTATATACATATTTCCATTA
CATGTTGATATGAAAGTACGTG
Found at i:54737207 original size:23 final size:22
Alignment explanation
Indices: 54737181--54737232 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
54737171 ATTATATAAT
54737181 TAAATAATTAGGAATTAATTA-AA
1 TAAATAATTA-GAA-TAATTAGAA
54737204 TAAA-ATATTAGAATAATTAGAA
1 TAAATA-ATTAGAATAATTAGAA
*
54737226 TTAATAA
1 TAAATAA
54737233 CTTCAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (22 bp):
TAAATAATTAGAATAATTAGAA
Found at i:54738993 original size:18 final size:18
Alignment explanation
Indices: 54738972--54739030 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
54738962 GAGAATTATC
54738972 TTAATATGGCGAACTGTA
1 TTAATATGGCGAACTGTA
* * *
54738990 TTAATTTGGTGATCTGTA
1 TTAATATGGCGAACTGTA
54739008 TTAATATGGCGAACTGTA
1 TTAATATGGCGAACTGTA
54739026 TTAAT
1 TTAAT
54739031 TTGCCAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (18 bp):
TTAATATGGCGAACTGTA
Found at i:54739988 original size:36 final size:36
Alignment explanation
Indices: 54739947--54740024 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 36
54739937 GACCATCCCA
54739947 TCACATCATGTGGGGTTAAAAACACCCACCCATCCT
1 TCACATCATGTGGGGTTAAAAACACCCACCCATCCT
54739983 TCACATCATGTGGGGTTAAAAACACCCACCCATCCT
1 TCACATCATGTGGGGTTAAAAACACCCACCCATCCT
54740019 TACACA
1 T-CACA
54740025 CCATATAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 37 0.90
37 4 0.10
ACGTcount: A:0.32, C:0.33, G:0.13, T:0.22
Consensus pattern (36 bp):
TCACATCATGTGGGGTTAAAAACACCCACCCATCCT
Found at i:54741992 original size:17 final size:17
Alignment explanation
Indices: 54741970--54742002 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54741960 ACTGTCATAC
54741970 GCTAATTGGAATGAACT
1 GCTAATTGGAATGAACT
54741987 GCTAATTGGAATGAAC
1 GCTAATTGGAATGAAC
54742003 AGTACATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (17 bp):
GCTAATTGGAATGAACT
Found at i:54743662 original size:21 final size:20
Alignment explanation
Indices: 54743638--54743676 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
54743628 AATGTATCCT
*
54743638 CATTGACACCACAAGAATATA
1 CATTGACACAACAA-AATATA
*
54743659 CATTTACACAACAAAATA
1 CATTGACACAACAAAATA
54743677 AAATATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.23, G:0.05, T:0.21
Consensus pattern (20 bp):
CATTGACACAACAAAATATA
Found at i:54744341 original size:35 final size:35
Alignment explanation
Indices: 54744294--54744392 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 35
54744284 CAGATGTTCA
* * * *
54744294 TAAGAGCCAATCCATCTGAAAGACACCAACGCCCG
1 TAAGAGCTAATCCATCCGAAACACACCAACGCCAG
* * *
54744329 TAAGAGCTAATCCCTCCGAAACACACCAATGCTAG
1 TAAGAGCTAATCCATCCGAAACACACCAACGCCAG
* * *
54744364 TAAGAGCTAGTCTAACCGAAACACACCAA
1 TAAGAGCTAATCCATCCGAAACACACCAA
54744393 AACAAAGAGT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.14
Consensus pattern (35 bp):
TAAGAGCTAATCCATCCGAAACACACCAACGCCAG
Found at i:54747396 original size:41 final size:40
Alignment explanation
Indices: 54747323--54747401 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 40
54747313 GCAAGAATAT
54747323 CAAATAAATAAACAAGATAAACAATAATATAAAAGAAAACA
1 CAAATAAATAAACAAGATAAACAATAATATAAAA-AAAACA
* *
54747364 CAAATTAATAAACAA-ATGAAAGAACTAA-ATAAAAAAAA
1 CAAATAAATAAACAAGAT-AAACAA-TAATATAAAAAAAA
54747402 GAATAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 6 0.18
41 25 0.74
42 3 0.09
ACGTcount: A:0.71, C:0.09, G:0.05, T:0.15
Consensus pattern (40 bp):
CAAATAAATAAACAAGATAAACAATAATATAAAAAAAACA
Found at i:54747646 original size:30 final size:30
Alignment explanation
Indices: 54747612--54747670 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54747602 GTATAAATAC
*
54747612 AAAAATATTTATTAAAAAAATA-AAATATAG
1 AAAAATATTCA-TAAAAAAATATAAATATAG
54747642 AAAAATATTCATAAAAAAATATAAATATA
1 AAAAATATTCATAAAAAAATATAAATATA
54747671 TATACATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAATATTCATAAAAAAATATAAATATAG
Found at i:54747673 original size:24 final size:24
Alignment explanation
Indices: 54747633--54747678 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
54747623 TTAAAAAAAT
*
54747633 AAAATATAGAAAAATATTCATAAA
1 AAAATATAGAAAAATATACATAAA
*
54747657 AAAATATA-AATATATATACATA
1 AAAATATAGAA-AAATATACATA
54747679 TGTAGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATATAGAAAAATATACATAAA
Found at i:54757752 original size:60 final size:57
Alignment explanation
Indices: 54757681--54757830 Score: 161
Period size: 52 Copynumber: 2.7 Consensus size: 57
54757671 ATTTTATAAT
* * *
54757681 ATTATATATTATGATTT-TTTAATTCATATTTTAATAATAATTAT-TTAAGAATGTTATTAA
1 ATTATATATTAT--TTTATTAAATT-ATA-TTTAATAATAATTATGTTAA-AATATGATTAA
*
54757741 ATTATATATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATGATT-A
1 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
*
54757797 A--AT-TATT-TTTTATTAAAATATATTTAATAATAAT
1 ATTATATATTATTTTATTAAATTATATTTAATAATAAT
54757831 CTTATTAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
52 25 0.30
53 4 0.05
54 2 0.02
56 2 0.02
57 22 0.27
58 9 0.11
59 6 0.07
60 12 0.15
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
Found at i:54757835 original size:26 final size:25
Alignment explanation
Indices: 54757753--54757841 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 25
54757743 TATATATTAT
* *
54757753 TTTATTAAATTGTATTTAATAATAA
1 TTTATTAAAATATATTTAATAATAA
* * * **
54757778 TTATGTTAAAATATGATTAAATTATTT
1 TT-TATTAAAATAT-ATTTAATAATAA
54757805 TTTATTAAAATATATTTAATAATAA
1 TTTATTAAAATATATTTAATAATAA
54757830 TCTTATTAAAAT
1 T-TTATTAAAAT
54757842 TTAATAACAA
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
25 11 0.22
26 28 0.57
27 10 0.20
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (25 bp):
TTTATTAAAATATATTTAATAATAA
Found at i:54758750 original size:21 final size:21
Alignment explanation
Indices: 54758726--54758780 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
54758716 AAAATTATAA
54758726 AAAAATCATAATTTATTTTTT
1 AAAAATCATAATTTATTTTTT
**
54758747 -AAAATCATAAAAATATTTTTT
1 AAAAATCAT-AATTTATTTTTT
*
54758768 AAAAATTATAATT
1 AAAAATCATAATT
54758781 ATACAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 8 0.30
21 12 0.44
22 7 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATCATAATTTATTTTTT
Found at i:54759844 original size:18 final size:19
Alignment explanation
Indices: 54759807--54759847 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
54759797 AATATTATTT
* *
54759807 TAATGTATTATAAATTACA
1 TAATGTATTAAAAATAACA
54759826 TAATGTA-TAAAAATAACA
1 TAATGTATTAAAAATAACA
54759844 TAAT
1 TAAT
54759848 ATAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
TAATGTATTAAAAATAACA
Found at i:54759930 original size:15 final size:15
Alignment explanation
Indices: 54759912--54759941 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54759902 ATGTTCAAGC
54759912 CCATTTCAAACCTAA
1 CCATTTCAAACCTAA
*
54759927 CCATTTCCAACCTAA
1 CCATTTCAAACCTAA
54759942 TATTTTTGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (15 bp):
CCATTTCAAACCTAA
Found at i:54762488 original size:10 final size:11
Alignment explanation
Indices: 54762473--54762501 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
54762463 TGATAATAGA
54762473 AAAAGAAAA-G
1 AAAAGAAAAGG
54762483 AAAAGAAAAGG
1 AAAAGAAAAGG
54762494 AAAAGAAA
1 AAAAGAAA
54762502 CGTTAGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGG
Found at i:54762491 original size:16 final size:16
Alignment explanation
Indices: 54762470--54762501 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54762460 AAATGATAAT
54762470 AGAAAAAGAAAAGAAA
1 AGAAAAAGAAAAGAAA
*
54762486 AGAAAAGGAAAAGAAA
1 AGAAAAAGAAAAGAAA
54762502 CGTTAGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAGAAA
Found at i:54768991 original size:70 final size:70
Alignment explanation
Indices: 54768878--54769017 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
54768868 TTAAAATAAA
54768878 CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
1 CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
54768943 TGATG
66 TGATG
* *
54768948 CTTTAACAAAAGCCAACATTAAATCCAAAAGTACCTGATACTAAATGCCAAAATATCATTAGATG
1 CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
54769013 TGATG
66 TGATG
54769018 GCATTGAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.24
Consensus pattern (70 bp):
CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
TGATG
Found at i:54773925 original size:2 final size:2
Alignment explanation
Indices: 54773913--54773943 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
54773903 GAAATTTTAA
*
54773913 AG AG TG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
54773944 AATTAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
AG
Found at i:54776743 original size:130 final size:130
Alignment explanation
Indices: 54776510--54776743 Score: 459
Period size: 130 Copynumber: 1.8 Consensus size: 130
54776500 AGGGTATTTA
*
54776510 TTTATAACATTGATATGAAACGAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
1 TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
54776575 TGTTGAAACTGAAATCAAATCGTCTGTCAAGGGAAATTTTCATATACTACCTTGAACTTATTTTC
66 TGTTGAAACTGAAATCAAATCGTCTGTCAAGGGAAATTTTCATATACTACCTTGAACTTATTTTC
54776640 TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
1 TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
54776705 TGTTGAAACTGAAATCAAATCGTCTGTCAAGGGAAATTT
66 TGTTGAAACTGAAATCAAATCGTCTGTCAAGGGAAATTT
54776744 AACTTATATC
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 103 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (130 bp):
TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
TGTTGAAACTGAAATCAAATCGTCTGTCAAGGGAAATTTTCATATACTACCTTGAACTTATTTTC
Found at i:54777831 original size:25 final size:25
Alignment explanation
Indices: 54777803--54777861 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
54777793 GAAGCTCTAT
54777803 TTGCAATTCAAGAGGTATTTTATAG
1 TTGCAATTCAAGAGGTATTTTATAG
*
54777828 TTGCAATTCAAGAGGTTTTTTATAG
1 TTGCAATTCAAGAGGTATTTTATAG
54777853 TTGCAATTC
1 TTGCAATTC
54777862 CAGTAAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (25 bp):
TTGCAATTCAAGAGGTATTTTATAG
Found at i:54778105 original size:32 final size:32
Alignment explanation
Indices: 54778064--54778126 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
54778054 GCTTGCACTA
54778064 GTGTATATTCATATACAACGCATTAATTAAAT
1 GTGTATATTCATATACAACGCATTAATTAAAT
54778096 GTGTATATTCATATACAACGCATTAATTAAA
1 GTGTATATTCATATACAACGCATTAATTAAA
54778127 AATATTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (32 bp):
GTGTATATTCATATACAACGCATTAATTAAAT
Found at i:54778409 original size:64 final size:64
Alignment explanation
Indices: 54778243--54778427 Score: 300
Period size: 64 Copynumber: 2.9 Consensus size: 64
54778233 AAATAAAATA
*
54778243 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTTATAACATAT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTGAT-A-ATAT
*
54778308 T
64 G
* *
54778309 AAAATTGGATCATTAGATATAATCAAGTAAATAACTTGATTAAAAAACAATTATTGGAT-ATATG
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATT-GATAATATG
54778373 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATT
54778428 CATTGTTAAT
Statistics
Matches: 112, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
64 57 0.51
66 53 0.47
67 2 0.02
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (64 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTGATAATATG
Found at i:54782061 original size:39 final size:41
Alignment explanation
Indices: 54782016--54782126 Score: 136
Period size: 44 Copynumber: 2.6 Consensus size: 41
54782006 TTTCCTTATG
* *
54782016 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
54782056 C-ATTACGCCTCTATTTCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC----T-ATTCCATTCAACCAAACAAAAGAATTAC
54782101 CTATTACGCCTCTATTCCATTACAAC
1 CTATTACGCCTCTATTCCATT-CAAC
54782127 GAACCAAACG
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
39 9 0.15
40 1 0.02
41 8 0.13
42 5 0.08
43 1 0.02
44 23 0.38
45 4 0.07
46 10 0.16
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:54782096 original size:44 final size:46
Alignment explanation
Indices: 54782029--54782121 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
54782019 TTACACCTCT
* *
54782029 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTTC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
54782073 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
54782119 ATT
1 ATT
54782122 ACAACGAACC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 4 0.09
46 18 0.40
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:54782135 original size:46 final size:42
Alignment explanation
Indices: 54782016--54782126 Score: 131
Period size: 46 Copynumber: 2.6 Consensus size: 42
54782006 TTTCCTTATG
* *
54782016 CTATTACACCTCTATTCCATT--CAACCAAACACAAGAATAC
1 CTATTACGCCTCTATTCCATTCACAACCAAACAAAAGAATAC
*
54782056 C-ATTACGCCTCTATTTCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATTCCATT-CA--CAACCAAACAAAAGAA-TAC
54782101 CTATTACGCCTCTATTCCATT-ACAAC
1 CTATTACGCCTCTATTCCATTCACAAC
54782127 GAACCAAACG
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
39 17 0.28
40 1 0.02
42 4 0.07
44 16 0.27
45 4 0.07
46 18 0.30
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.29
Consensus pattern (42 bp):
CTATTACGCCTCTATTCCATTCACAACCAAACAAAAGAATAC
Found at i:54784864 original size:49 final size:49
Alignment explanation
Indices: 54784789--54784882 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
54784779 TGCTATGCAA
* *
54784789 TGCTAAACTTGGTCTTCAACTGTCTACACTCTTATCACTATTTATACAT
1 TGCTAAACTTAGTCTTCAACTATCTACACTCTTATCACTATTTATACAT
*
54784838 TGCTAAACTTAGTCTTCCACTATCTACACTCTTATCACTATTTAT
1 TGCTAAACTTAGTCTTCAACTATCTACACTCTTATCACTATTTAT
54784883 CCCTTCTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.06, T:0.41
Consensus pattern (49 bp):
TGCTAAACTTAGTCTTCAACTATCTACACTCTTATCACTATTTATACAT
Found at i:54784961 original size:7 final size:7
Alignment explanation
Indices: 54784949--54784974 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54784939 AGAGTGTTAG
54784949 TCCATGC
1 TCCATGC
54784956 TCCATGC
1 TCCATGC
54784963 TCCATGC
1 TCCATGC
54784970 TCCAT
1 TCCAT
54784975 CTACGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.42, G:0.12, T:0.31
Consensus pattern (7 bp):
TCCATGC
Found at i:54786176 original size:18 final size:19
Alignment explanation
Indices: 54786142--54786184 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
54786132 TCTTAATTCA
*
54786142 TCATTTCATATTTCATTTC
1 TCATCTCATATTTCATTTC
54786161 TCATCTCATA-TTCATTTC
1 TCATCTCATATTTCATTTC
54786179 TCATCT
1 TCATCT
54786185 TTGTCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (19 bp):
TCATCTCATATTTCATTTC
Found at i:54793217 original size:11 final size:11
Alignment explanation
Indices: 54793187--54793238 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
54793177 TATTAACCAC
*
54793187 ACCACCACCGG
1 ACCACCACTGG
*
54793198 GCCACCACTGG
1 ACCACCACTGG
**
54793209 ACCACCACTAC
1 ACCACCACTGG
* *
54793220 ACCATCTCTGG
1 ACCACCACTGG
54793231 ACCACCAC
1 ACCACCAC
54793239 CATCACCGCC
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.27, C:0.50, G:0.13, T:0.10
Consensus pattern (11 bp):
ACCACCACTGG
Found at i:54798112 original size:18 final size:19
Alignment explanation
Indices: 54798091--54798126 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
54798081 AATAATTAAT
54798091 GAAAATAAACAAA-GAAAG
1 GAAAATAAACAAACGAAAG
54798109 GAAAATAAACAAACGAAA
1 GAAAATAAACAAACGAAA
54798127 TAAAAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.72, C:0.08, G:0.14, T:0.06
Consensus pattern (19 bp):
GAAAATAAACAAACGAAAG
Found at i:54800958 original size:24 final size:24
Alignment explanation
Indices: 54800930--54800979 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
54800920 GGGTTAAAGT
*
54800930 GATAGATTTTAAGTTTATAACTGA
1 GATAGATTTTAAGTTTAGAACTGA
*
54800954 GATAGATTTTAAGTTTAGAATTGA
1 GATAGATTTTAAGTTTAGAACTGA
54800978 GA
1 GA
54800980 AAAGGACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (24 bp):
GATAGATTTTAAGTTTAGAACTGA
Found at i:54804182 original size:18 final size:18
Alignment explanation
Indices: 54804146--54804181 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
54804136 CCGATACAAC
54804146 ATCAATACCCAACATAAA
1 ATCAATACCCAACATAAA
*
54804164 ATCAATA-CCAACTTAAA
1 ATCAATACCCAACATAAA
54804181 A
1 A
54804182 ACTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (18 bp):
ATCAATACCCAACATAAA
Found at i:54807040 original size:19 final size:19
Alignment explanation
Indices: 54807016--54807052 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
54807006 TCTTTCTAGT
54807016 TTATTTTTCATTT-ATTAAA
1 TTATTTTTC-TTTAATTAAA
54807035 TTATTTTTCTTTAATTAA
1 TTATTTTTCTTTAATTAA
54807053 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTTTCTTTAATTAAA
Found at i:54809436 original size:112 final size:112
Alignment explanation
Indices: 54809197--54809449 Score: 296
Period size: 112 Copynumber: 2.2 Consensus size: 112
54809187 TAGCGACGTT
* * *
54809197 TTTAGCGGCGTTTGGATAA-AAAACGCCGCTAAGGATCGATCATTAGCGGCGCTTTATGGAAAAC
1 TTTAGCGGCGTTT--TTAAGAAAGCGCCGCTAAGGATCGATCATTAGCGGCGATTTATGGAAAAC
*
54809261 ACCGCAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGGGGTA
64 ACCACAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGGGGTA
* * * * * * * *
54809310 GTTAACGGCATTTTTAAGAAAGCGCCGCTAATGATCGATCTTTAGCGGC-ATTTTTGAGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAGGATCGATCATTAGCGGCGATTTATG-GAAAACA
* * * *
54809374 CCACAAAAAACCTAAGCCCAACGATGTCGTTTTTTGAGCTTTCGGGG-A
65 CCAC-AAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGGGGTA
*
54809422 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
54809450 AAAAAAACCT
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
111 8 0.07
112 61 0.52
113 48 0.41
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (112 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAGGATCGATCATTAGCGGCGATTTATGGAAAACAC
CACAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGGGGTA
Found at i:54809485 original size:73 final size:73
Alignment explanation
Indices: 54809350--54809594 Score: 415
Period size: 72 Copynumber: 3.4 Consensus size: 73
54809340 ATGATCGATC
* * *
54809350 TTTAGCGGCATTTTTGAGAAAGCGCCAC-AAAAAACCTAAGCCCAACGATGTCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGTCGTTTTCTGAGCT
54809414 TTCGGGGA
66 TTCGGGGA
54809422 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGTCGTTTTCTGAGCT
54809487 TTCGGGGA
66 TTCGGGGA
54809495 TTTTA-CGGCGTTTTTGAGAAAGCGCCGCAAAAAAA-CTAAGCCCAACGATGTCGTTTTCTGAGC
1 -TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGTCGTTTTCTGAGC
*
54809558 TTTCGAGGA
65 TTTCGGGGA
*
54809567 TTTAGCGGCGTTTTTGAGAAAGTGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
54809595 TAATGCTCAG
Statistics
Matches: 165, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
71 4 0.02
72 84 0.51
73 73 0.44
74 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGTCGTTTTCTGAGCT
TTCGGGGA
Found at i:54809789 original size:14 final size:14
Alignment explanation
Indices: 54809770--54809796 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54809760 GAGTATGGGT
54809770 TTAGGGATTATGGA
1 TTAGGGATTATGGA
54809784 TTAGGGATTATGG
1 TTAGGGATTATGG
54809797 TTTAAGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:54809846 original size:23 final size:22
Alignment explanation
Indices: 54809820--54809863 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
54809810 ATTTAAGGTT
*
54809820 TAGGGGTTTGAGGATTAGGGGTG
1 TAGGGGTTAGAGG-TTAGGGGTG
*
54809843 TAGGGGTTAGATGTTAGGGGT
1 TAGGGGTTAGAGGTTAGGGGT
54809864 TAAGAGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (22 bp):
TAGGGGTTAGAGGTTAGGGGTG
Found at i:54809862 original size:14 final size:14
Alignment explanation
Indices: 54809843--54809875 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54809833 ATTAGGGGTG
54809843 TAGGGGTT-AGATGT
1 TAGGGGTTAAGA-GT
54809857 TAGGGGTTAAGAGT
1 TAGGGGTTAAGAGT
54809871 TAGGG
1 TAGGG
54809876 ATTTAGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.24, C:0.00, G:0.45, T:0.30
Consensus pattern (14 bp):
TAGGGGTTAAGAGT
Found at i:54810100 original size:15 final size:15
Alignment explanation
Indices: 54810062--54810096 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54810052 TATATTTTAA
54810062 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
54810077 GGTTTAGGGATTAT-
1 GGTTTAGGGAGTATG
54810091 GGTTTA
1 GGTTTA
54810097 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:54810266 original size:285 final size:289
Alignment explanation
Indices: 54809895--54810577 Score: 870
Period size: 285 Copynumber: 2.3 Consensus size: 289
54809885 TTAGAGATTT
* *
54809895 AGGGATCGAGTTAGGATTTTGGGCGTTTAGATT-A-A-TTTTTTAATGTATATTTTAAATATGTT
1 AGGG-TCGAGTTAGGGTTTT-GG-GTTTAGATTAATATTTTTTTAATTTATATTTTAAATATGTT
*
54809957 CTTATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATT
63 CTTATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATT
* * *
54810022 TATTTAAGATTTAAAGCCGATTTAGGAGTTTATATTTTAAGGTTTAGGGAGTATGGGTTTAGGGA
128 AATTTAAGATTTAAAGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGA
* *
54810087 TTATGGTTTAAGGG-TT-GGGATTT-G-AGG-TTTATGGGTTAGAGGGTTAAGGGTTTAGGGGTT
193 TTATGGATT-AGGGATTAGGG-TTTAGTAGGATTTAAGGGTTAG-GGGTTAAGGGTTTAGGGGTT
*
54810147 AGACGTGCTAGGGGTT-A-A-A-AA-TTAGGGATTCA
255 AGA--TACTAGGGGTTAATAGATAAGTTAGGGATTCA
54810179 AGGGTCGAGTTAGGGTTTTGGGTTTAGATTAACTATTTTTTTAATTTATATTTTAAATATGTTCT
1 AGGGTCGAGTTAGGGTTTTGGGTTTAGATTAA-TATTTTTTTAATTTATATTTTAAATATGTTCT
54810244 TATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAA
65 TATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAA
* *
54810309 TTTAAGATTTAAGGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATT
130 TTTAAGATTTAAAGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATT
* * * *
54810374 ATGGATTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGGGTTAGGGGTTTAGGGGTTA
195 ATGGATTAGGGATTAGGGTTT-A--G-TAGGATTTAAGGGTTAGGGGTTAAGGGTTTAGGGGTTA
*
54810439 GATATTAGGGGTTAAGAGATAGGGATTTAAGGTTTAGGGATTCA
256 GATACTAGGGGTT---A-ATA--GA--TAA-G-TTAGGGATTCA
* * * * *
54810483 GGGGTCAAGTTAAGGTTTTGAGTTTAGATTAATTATTTTTCTAATTTATATTTTAAATATGTTCT
1 AGGGTCGAGTTAGGGTTTTGGGTTTAGATTAA-TATTTTTTTAATTTATATTTTAAATATGTTCT
54810548 TATATAATTGTAAAAGAGATAATAATAAAT
65 TATATAATTGTAAAAGAGATAATAATAAAT
54810578 CAAATAGATT
Statistics
Matches: 349, Mismatches: 22, Indels: 36
0.86 0.05 0.09
Matches are distributed among these distances:
281 9 0.03
282 3 0.01
283 14 0.04
284 9 0.03
285 163 0.47
286 2 0.01
289 10 0.03
291 24 0.07
292 10 0.03
294 1 0.00
295 1 0.00
298 1 0.00
301 2 0.01
304 100 0.29
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (289 bp):
AGGGTCGAGTTAGGGTTTTGGGTTTAGATTAATATTTTTTTAATTTATATTTTAAATATGTTCTT
ATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAAT
TTAAGATTTAAAGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATTA
TGGATTAGGGATTAGGGTTTAGTAGGATTTAAGGGTTAGGGGTTAAGGGTTTAGGGGTTAGATAC
TAGGGGTTAATAGATAAGTTAGGGATTCA
Found at i:54810384 original size:14 final size:15
Alignment explanation
Indices: 54810349--54810395 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 15
54810339 TATTTTAAGG
*
54810349 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
54810364 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
54810379 -TTAGGGATTATGG-
1 TTTAGGGATTATGGA
54810392 TTTA
1 TTTA
54810396 AGGGTTGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 16 0.53
15 14 0.47
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:54810431 original size:15 final size:15
Alignment explanation
Indices: 54810411--54810439 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54810401 TGGGATTTAA
54810411 GGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
54810426 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
54810440 ATATTAGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:54811008 original size:138 final size:137
Alignment explanation
Indices: 54810852--54811121 Score: 452
Period size: 138 Copynumber: 2.0 Consensus size: 137
54810842 AATTTTTAGC
* * *
54810852 ATAGCAAAACGGCATCATTTTGTTCAAAGTGAAATAATATTTTGCAGCGTTTTTATGAAAAACGC
1 ATAGCAAAACGGCATCATTTTGTTCAAAATGAAATAATATTTCGCAGCGTTTTTATAAAAAACGC
* *
54810917 CGCAAAAGATAAGCAATAGCGGCGTTTTCTAT-AAAAACGCTGCAAAAAATAAATCAATTTATAA
66 CGCAAAAGATAAGCAATAGCGGCGTTTT-TATAAAAAACACCGC-AAAAATAAATCAATTTATAA
54810981 AAAAACAAA
129 AAAAACAAA
* *
54810990 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTCGCGGCGTTTTTATAAAAAACGC
1 ATAGCAAAACGGCATCATTTTGTTCAAAATGAAATAATATTTCGCAGCGTTTTTATAAAAAACGC
54811055 CGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAACACCGCAAAAATAAATCAATTTATAAAA
66 CGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAACACCGCAAAAATAAATCAATTTATAAAA
54811120 AA
131 AA
54811122 TAAAATAAAA
Statistics
Matches: 124, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
137 27 0.22
138 97 0.78
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (137 bp):
ATAGCAAAACGGCATCATTTTGTTCAAAATGAAATAATATTTCGCAGCGTTTTTATAAAAAACGC
CGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAACACCGCAAAAATAAATCAATTTATAAAA
AAACAAA
Found at i:54811254 original size:77 final size:77
Alignment explanation
Indices: 54811111--54811255 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 77
54811101 AATAAATCAA
* * * ** *
54811111 TTTATAAAAAATAAAATAAAAAATTTTTTAGCGGGGGGAAACGGTGTCAATTTGTTCAAAGGGAA
1 TTTATAAAAAAAAAAATAAAAAATTTTTTAGCAGAGCAAAACGGTGTCAATTTGTTCAAAAGGAA
54811176 ATAGCGACGTTT
66 ATAGCGACGTTT
* * *
54811188 TTTATAAAAAACAAAAATAAAAAA-TTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAAAATGA
1 TTTATAAAAAA-AAAAATAAAAAATTTTTTAGCAGAGCAAAACGGTGTCAATTTGTTCAAAAGGA
54811252 AATA
65 AATA
54811256 AGTTTTTGCG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 47 0.81
78 11 0.19
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (77 bp):
TTTATAAAAAAAAAAATAAAAAATTTTTTAGCAGAGCAAAACGGTGTCAATTTGTTCAAAAGGAA
ATAGCGACGTTT
Found at i:54811374 original size:219 final size:223
Alignment explanation
Indices: 54810990--54811416 Score: 578
Period size: 219 Copynumber: 1.9 Consensus size: 223
54810980 AAAAAACAAA
54810990 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTCGCGGCGTTTTTATAAAAAACGC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTCGCGGCGTTTTTATAAAAAACGC
* *
54811055 CGCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAACACCGCAAAAATAAATCAATTTATAAAA
66 CGCAAAAGAAAAGCAATAGCGGCGTTTTTAT-----A-A-CGCAAAAATAAATCAATGTATAAAA
* * * ** *
54811120 AATAAAATAAAAAATTTTTTAGCGGGGGGAAACGGTGTCAATTTGTTCAAAGGGAAATAGCGACG
124 AATAAAATAAAAAAATTTTTAGCAGAGCAAAACGGTGTCAATTTGTTCAAAAGGAAATAGCGACG
*
54811185 TTTTTTATAAAAAACAAAAATAAAAAATTTTTAGC
189 CTTTTTATAAAAAACAAAAATAAAAAATTTTTAGC
* * *
54811220 ATAGCAAAACGGTGTCATTTTGTTCAAAATGAAATAAGT-TTTTGCGGCGTTTTTAT-AAAAATG
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAA-TATTTCGCGGCGTTTTTATAAAAAACG
*
54811283 CCGCAAAAGAAAAGCAATAGCGGTG-TTTT-T-A-GCAAAAATAAATCAATGTATAAAAAAATAA
65 CCGCAAAAGAAAAGCAATAGCGGCGTTTTTATAACGCAAAAATAAATCAATGTAT-AAAAAATAA
* * * *
54811344 AATAAAAAAATTTTTAGCATAGCAAAACGGTGTTAATTTGTTCAAAATGAAATAGCGGCGCTTTT
129 AATAAAAAAATTTTTAGCAGAGCAAAACGGTGTCAATTTGTTCAAAAGGAAATAGCGACGCTTTT
54811409 TATAAAAA
194 TATAAAAA
54811417 CGCCGCAAAA
Statistics
Matches: 178, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
218 19 0.11
219 71 0.40
220 1 0.01
227 1 0.01
228 4 0.02
229 29 0.16
230 52 0.29
231 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (223 bp):
ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTCGCGGCGTTTTTATAAAAAACGC
CGCAAAAGAAAAGCAATAGCGGCGTTTTTATAACGCAAAAATAAATCAATGTATAAAAAATAAAA
TAAAAAAATTTTTAGCAGAGCAAAACGGTGTCAATTTGTTCAAAAGGAAATAGCGACGCTTTTTA
TAAAAAACAAAAATAAAAAATTTTTAGC
Found at i:54814939 original size:15 final size:15
Alignment explanation
Indices: 54814904--54814955 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54814894 TTAAGAATTT
*
54814904 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54814918 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54814932 TATTTAATAATAAT-
1 TATTTAATTATAATA
54814946 TATGTTAATT
1 TAT-TTAATT
54814956 TATATTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54815087 original size:116 final size:119
Alignment explanation
Indices: 54814849--54815186 Score: 594
Period size: 116 Copynumber: 2.9 Consensus size: 119
54814839 AGCAATAACA
*
54814849 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
*
54814914 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTGTAGT
66 TATATTTTAATTATAATATATTTAATAATAATTATG-TAATTTATATTTTATAGT
*
54814969 ATCATATATTATGACTTGAGTAAATTCATATAAG-ATATTGATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
*
54815033 TAT-CTTTAA-TAT-ATATATTTAATAATAATTATGTAATTTTATATTTTATAGT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTAA-TTTATATTTTATAGT
54815085 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
54815150 TATATTTTAATTATAATATATTTAATAATAATTATGT
66 TATATTTTAATTATAATATATTTAATAATAATTATGT
54815187 TTAAATATGA
Statistics
Matches: 207, Mismatches: 6, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
115 3 0.01
116 68 0.33
117 36 0.17
118 10 0.05
119 35 0.17
120 55 0.27
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (119 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
TATATTTTAATTATAATATATTTAATAATAATTATGTAATTTATATTTTATAGT
Found at i:54815170 original size:16 final size:16
Alignment explanation
Indices: 54815149--54815190 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
54815139 TTATTAAATT
*
54815149 ATATATTTTAATTATA
1 ATATATTTTAATAATA
54815165 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
54815180 AT-TATGTTTAA
1 ATATAT-TTTAA
54815191 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:54815175 original size:15 final size:15
Alignment explanation
Indices: 54815140--54815181 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54815130 TTAAGAATTT
*
54815140 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54815154 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54815168 TATTTAATAATAAT
1 TATTTAATTATAAT
54815182 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54815413 original size:16 final size:16
Alignment explanation
Indices: 54815392--54815424 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54815382 TTGATTTGCT
54815392 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
54815408 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
54815424 A
1 A
54815425 ATATAGCGAA
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:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:54816719 original size:29 final size:29
Alignment explanation
Indices: 54816676--54816732 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
54816666 AGAAACTCTT
*
54816676 AATTATTGCTGTTGTTCTCGAGTAGCAAC
1 AATTATTGCTATTGTTCTCGAGTAGCAAC
* * *
54816705 AATTATTTCTATTGTTCTTGATTAGCAA
1 AATTATTGCTATTGTTCTCGAGTAGCAA
54816733 AAAAGGTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (29 bp):
AATTATTGCTATTGTTCTCGAGTAGCAAC
Found at i:54818117 original size:19 final size:21
Alignment explanation
Indices: 54818079--54818117 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54818069 CAGTGATATT
*
54818079 TTTTTATATATTGTTCTAAAG
1 TTTTTATATATTCTTCTAAAG
54818100 TTTTTATAT-TTCTT-TAAA
1 TTTTTATATATTCTTCTAAA
54818118 TTTGCATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTTATATATTCTTCTAAAG
Found at i:54818485 original size:21 final size:21
Alignment explanation
Indices: 54818459--54818498 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54818449 TTTATTTTAG
*
54818459 TATGTACGAATGTTAGGTTAT
1 TATGTACGAAGGTTAGGTTAT
54818480 TATGTACGAAGGTTAGGTT
1 TATGTACGAAGGTTAGGTT
54818499 TAGCTTCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40
Consensus pattern (21 bp):
TATGTACGAAGGTTAGGTTAT
Found at i:54819847 original size:43 final size:43
Alignment explanation
Indices: 54819768--54819948 Score: 233
Period size: 43 Copynumber: 4.3 Consensus size: 43
54819758 ATTATGTTTT
* *
54819768 TAGCGGCATTTGTGAAAAAAGCGCCGCT--AGGTCATGGTCTG
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
54819809 TAGCGGCGTTTGTGGGAAAAA-CGCCGCTAAAGGCCATGGTCTA
1 TAGCGGCGTTTGT-GAAAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
54819852 TAGCGGCATTTGTAAAAAAAGCGACGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGGTCTA
* **
54819895 TAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGGTCTA
*
54819938 TAGCGACGTTT
1 TAGCGGCGTTT
54819949 ATTTCTAAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 19 0.16
42 11 0.09
43 91 0.75
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:54819910 original size:86 final size:84
Alignment explanation
Indices: 54819768--54819942 Score: 278
Period size: 86 Copynumber: 2.1 Consensus size: 84
54819758 ATTATGTTTT
* * * *
54819768 TAGCGGCATTTGTGAAAAAAGCGCCGCTAGGTCATGGTCTGTAGCGGCGTTTGTGGGAAAAACGC
1 TAGCGGCATTTGTAAAAAAAGCGACGCTAGGTCATGGTCTATAGCGACGTTTGTGGGAAAAACGC
54819833 CGCTAAAGGCCATGGTCTA
66 CGCTAAAGGCCATGGTCTA
*
54819852 TAGCGGCATTTGTAAAAAAAGCGACGCTAAAGGTCATGGTCTATAGCGACGTTTGTGGGAAAAGC
1 TAGCGGCATTTGTAAAAAAAGCGACGCT--AGGTCATGGTCTATAGCGACGTTTGTGGGAAAAAC
*
54819917 GCCGCTAAAGGTCATGGTCTA
64 GCCGCTAAAGGCCATGGTCTA
54819938 TAGCG
1 TAGCG
54819943 ACGTTTATTT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 26 0.31
86 57 0.69
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (84 bp):
TAGCGGCATTTGTAAAAAAAGCGACGCTAGGTCATGGTCTATAGCGACGTTTGTGGGAAAAACGC
CGCTAAAGGCCATGGTCTA
Found at i:54826600 original size:26 final size:26
Alignment explanation
Indices: 54826571--54826622 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
54826561 AAGTGACGAA
54826571 TCTCATCTACTTGAAGCCTTGGTGGC
1 TCTCATCTACTTGAAGCCTTGGTGGC
54826597 TCTCATCTACTTGAAGCCTTGGTGGC
1 TCTCATCTACTTGAAGCCTTGGTGGC
54826623 CCAATGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (26 bp):
TCTCATCTACTTGAAGCCTTGGTGGC
Found at i:54828065 original size:15 final size:16
Alignment explanation
Indices: 54828040--54828069 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54828030 GTATAATATG
54828040 AAATAGAAAAAAATTA
1 AAATAGAAAAAAATTA
54828056 AAAT-GAAAAAAATT
1 AAATAGAAAAAAATT
54828070 CACTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAATAGAAAAAAATTA
Found at i:54828455 original size:20 final size:20
Alignment explanation
Indices: 54828420--54828465 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
54828410 GTATCAATCC
* *
54828420 GGTATCGATACTTTTCTTAG
1 GGTATCGATACTTTTCCTAA
54828440 GGTATCGATA-TATTTCCTAA
1 GGTATCGATACT-TTTCCTAA
54828460 GGTATC
1 GGTATC
54828466 TATTAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
GGTATCGATACTTTTCCTAA
Found at i:54830741 original size:20 final size:20
Alignment explanation
Indices: 54830716--54830763 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
54830706 TTAATTTAGT
54830716 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* *
54830736 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
54830756 TCAGCTCA
1 TCAGCTCA
54830764 ATCTTAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:54830761 original size:10 final size:10
Alignment explanation
Indices: 54830715--54830765 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
54830705 TTTAATTTAG
54830715 TTCAGCTC-A
1 TTCAGCTCAA
*
54830724 CTCGAGCTCAA
1 TTC-AGCTCAA
*
54830735 GTCAGCTC-A
1 TTCAGCTCAA
54830744 TTCGAGCTCAA
1 TTC-AGCTCAA
54830755 TTCAGCTCAA
1 TTCAGCTCAA
54830765 T
1 T
54830766 CTTAACCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 5 0.14
10 23 0.66
11 7 0.20
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:54834114 original size:23 final size:23
Alignment explanation
Indices: 54834050--54834149 Score: 87
Period size: 23 Copynumber: 4.3 Consensus size: 23
54834040 ACATGTAATG
* * *
54834050 TTCTGTAAAGCCTTTGTGACTTG
1 TTCTGTAAAGCCTTTGTGGCGTA
*
54834073 TT-TGGTAAAG-CTTGTGTGGCATA
1 TTCT-GTAAAGCCTT-TGTGGCGTA
54834096 TTCTGTAAAGCCTTTGTGGCGTA
1 TTCTGTAAAGCCTTTGTGGCGTA
* * * * *
54834119 TTCTATGATGCCTATGTGGCGTG
1 TTCTGTAAAGCCTTTGTGGCGTA
54834142 TTCTGTAA
1 TTCTGTAA
54834150 CGCCCTTGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
22 4 0.06
23 54 0.87
24 4 0.06
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (23 bp):
TTCTGTAAAGCCTTTGTGGCGTA
Found at i:54839253 original size:18 final size:18
Alignment explanation
Indices: 54839230--54839265 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54839220 TCATACTTAT
54839230 TCTAAATAAACAAAATTA
1 TCTAAATAAACAAAATTA
54839248 TCTAAATAAACAAAATTA
1 TCTAAATAAACAAAATTA
54839266 AGTCATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (18 bp):
TCTAAATAAACAAAATTA
Found at i:54841188 original size:23 final size:23
Alignment explanation
Indices: 54841145--54841254 Score: 107
Period size: 23 Copynumber: 4.7 Consensus size: 23
54841135 TAATGTTCAA
**
54841145 GAACATGTTCATTTAAC-TTAATC
1 GAACATGTTCA-CGAACATTAATC
*
54841168 GAACATGTTCACGAACATTAAAC
1 GAACATGTTCACGAACATTAATC
* *
54841191 GAATATGTTCACGAACACTAAAT-
1 GAACATGTTCACGAACA-TTAATC
* * *
54841214 GAACATGTTCATGAACATATAGTT
1 GAACATGTTCACGAACAT-TAATC
54841238 GAACATGTTCACGAACA
1 GAACATGTTCACGAACA
54841255 ATGTTAATAA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
22 4 0.06
23 49 0.68
24 19 0.26
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (23 bp):
GAACATGTTCACGAACATTAATC
Found at i:54841280 original size:15 final size:15
Alignment explanation
Indices: 54841260--54841293 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54841250 GAACAATGTT
*
54841260 AATAAATAATAAACA
1 AATAAACAATAAACA
*
54841275 AATAAACAATAAATA
1 AATAAACAATAAACA
54841290 AATA
1 AATA
54841294 CATATGCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAAACAATAAACA
Found at i:54843831 original size:24 final size:24
Alignment explanation
Indices: 54843804--54843858 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
54843794 TCATTAATAA
* *
54843804 ATAAACGAGTCAATAAATGAGTTT
1 ATAAACGAGCCAATAAATGAGCTT
54843828 ATAAACGAGCCAATAAATGAGCTT
1 ATAAACGAGCCAATAAATGAGCTT
54843852 A-AAACGA
1 ATAAACGA
54843859 ACCGAACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (24 bp):
ATAAACGAGCCAATAAATGAGCTT
Found at i:54851441 original size:11 final size:10
Alignment explanation
Indices: 54851427--54851515 Score: 53
Period size: 10 Copynumber: 9.0 Consensus size: 10
54851417 ATTTATAAAA
54851427 AAAATATTAAT
1 AAAATATT-AT
*
54851438 AAAAT-TTCT
1 AAAATATTAT
54851447 AGAAATATTAT
1 A-AAATATTAT
54851458 AAAA-ATTAT
1 AAAATATTAT
*
54851467 AAAAAATT-T
1 AAAATATTAT
** *
54851476 CCAATAATA-
1 AAAATATTAT
54851485 AAAATTATT-T
1 AAAA-TATTAT
*
54851495 AAAAAATTAT
1 AAAATATTAT
54851505 AAAATCATTAT
1 AAAAT-ATTAT
54851516 TAAACAATCT
Statistics
Matches: 59, Mismatches: 11, Indels: 16
0.69 0.13 0.19
Matches are distributed among these distances:
9 21 0.36
10 24 0.41
11 14 0.24
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (10 bp):
AAAATATTAT
Found at i:54851473 original size:21 final size:22
Alignment explanation
Indices: 54851425--54851473 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
54851415 AAATTTATAA
* *
54851425 AAAAAATATTAATAAAATTTCT
1 AAAAAATATTAATAAAAATTAT
*
54851447 -AGAAATATT-ATAAAAATTAT
1 AAAAAATATTAATAAAAATTAT
54851467 AAAAAAT
1 AAAAAAT
54851474 TTCCAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAAATATTAATAAAAATTAT
Found at i:54866591 original size:13 final size:12
Alignment explanation
Indices: 54866572--54866605 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
54866562 GATTTATGCC
*
54866572 AAAAGAAGAACA
1 AAAAGAACAACA
54866584 ACAAAGAACAACA
1 A-AAAGAACAACA
54866597 AAAAGAACA
1 AAAAGAACA
54866606 CTCGCAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.74, C:0.15, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAACAACA
Found at i:54868467 original size:16 final size:17
Alignment explanation
Indices: 54868446--54868478 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54868436 AGATTTTATG
54868446 AAATAAA-ATCAAACAA
1 AAATAAACATCAAACAA
54868462 AAATAAACATCAAACAA
1 AAATAAACATCAAACAA
54868479 TGCCATCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAACATCAAACAA
Found at i:54870679 original size:14 final size:14
Alignment explanation
Indices: 54870660--54870686 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54870650 TAGCTTTAGT
54870660 TTTAATTAGTTTAA
1 TTTAATTAGTTTAA
54870674 TTTAATTAGTTTA
1 TTTAATTAGTTTA
54870687 TCATTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTAATTAGTTTAA
Found at i:54870788 original size:25 final size:25
Alignment explanation
Indices: 54870739--54870788 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54870729 CTCTAGTAGA
* * *
54870739 CTAATAATTATTTTCTATAAGTAAC
1 CTAATAATAATTTTCTACAAATAAC
*
54870764 CTAATAATAATTTTCTCCAAATAAC
1 CTAATAATAATTTTCTACAAATAAC
54870789 AATACCTTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (25 bp):
CTAATAATAATTTTCTACAAATAAC
Found at i:54875892 original size:25 final size:25
Alignment explanation
Indices: 54875863--54875912 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
54875853 CAAATGAAAC
* * *
54875863 ATTAAGTGCAGAAGATAGTGAAAGT
1 ATTAAGTGAACAAAATAGTGAAAGT
54875888 ATTAAGTGAACAAAATAGTGAAAGT
1 ATTAAGTGAACAAAATAGTGAAAGT
54875913 GAAAGGTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (25 bp):
ATTAAGTGAACAAAATAGTGAAAGT
Found at i:54879243 original size:14 final size:14
Alignment explanation
Indices: 54879226--54879255 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54879216 AATACGAAGA
54879226 AAGAAATGTTTGAT
1 AAGAAATGTTTGAT
54879240 AAGAAATGTTTGAT
1 AAGAAATGTTTGAT
54879254 AA
1 AA
54879256 TCACAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (14 bp):
AAGAAATGTTTGAT
Found at i:54879483 original size:48 final size:48
Alignment explanation
Indices: 54879412--54879511 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
54879402 ATGGGACTCT
**
54879412 TTCTCTGACCGGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
1 TTCTCTGACAAGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
*
54879460 TTCTCTGACAAGCTATTTGATGTTTGCAATATGTTATTGTCATTCACA
1 TTCTCTGACAAGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
54879508 TTCT
1 TTCT
54879512 TACAGCTCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (48 bp):
TTCTCTGACAAGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
Found at i:54881074 original size:28 final size:28
Alignment explanation
Indices: 54881003--54881084 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
54880993 AGTGGTGGAT
** *
54881003 AATCCAAAGTACAAGTGAAAGTGACGAAC
1 AATCC-AAGTACAAGCCAAAGTGGCGAAC
* *
54881032 AGTCCAAGTATAAGCCAAAGTGGCGAAC
1 AATCCAAGTACAAGCCAAAGTGGCGAAC
* * *
54881060 AATCCCAGTGCAAGCCAATGTGGCG
1 AATCCAAGTACAAGCCAAAGTGGCG
54881085 GATAGTCCGA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
28 39 0.91
29 4 0.09
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (28 bp):
AATCCAAGTACAAGCCAAAGTGGCGAAC
Found at i:54881097 original size:28 final size:27
Alignment explanation
Indices: 54881043--54881119 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
54881033 GTCCAAGTAT
*
54881043 AAGCCAAAGTGGCGAACAATCCCAGTGC
1 AAGCC-AAGTGGCGGACAATCCCAGTGC
* * * *
54881071 AAGCCAATGTGGCGGATAGTCCGAGTGT
1 AAGCCAA-GTGGCGGACAATCCCAGTGC
*
54881099 AAGACAAGATGGCGGACAATC
1 AAGCCAAG-TGGCGGACAATC
54881120 TAACCACCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 3 0.08
28 36 0.92
ACGTcount: A:0.34, C:0.22, G:0.30, T:0.14
Consensus pattern (27 bp):
AAGCCAAGTGGCGGACAATCCCAGTGC
Found at i:54883615 original size:43 final size:43
Alignment explanation
Indices: 54883551--54883668 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
54883541 CTGATAAGTG
* *
54883551 TTTTCGTGTAATAGCACGTCTGGGACGTTGGCATCGACTTGT-A
1 TTTTCGTGTAAGA-CCCGTCTGGGACGTTGGCATCGACTTGTGA
** *
54883594 TTTTCGTGTAAGACCCTGTCTGGGACAATGGCATCGATTTGTGA
1 TTTTCGTGTAAGACCC-GTCTGGGACGTTGGCATCGACTTGTGA
* *
54883638 -TTACATGTAAGACCACGTCTGGGACGTTGGC
1 TTTTCGTGTAAGACC-CGTCTGGGACGTTGGC
54883669 GTTGTACGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
42 2 0.03
43 59 0.94
44 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.32
Consensus pattern (43 bp):
TTTTCGTGTAAGACCCGTCTGGGACGTTGGCATCGACTTGTGA
Found at i:54885582 original size:2 final size:2
Alignment explanation
Indices: 54885575--54885615 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
54885565 GTAATGCTGC
54885575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54885616 AGAACAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54886559 original size:30 final size:29
Alignment explanation
Indices: 54886525--54886595 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
54886515 ACCATGCAAC
54886525 AGTGGTGGACAAGCCAAAAGTACAAGCCAA
1 AGTGGTGGACAAGCC-AAAGTACAAGCCAA
* *
54886555 AGTGGCGGACAATCCAAAGTACAAGCCAA
1 AGTGGTGGACAAGCCAAAGTACAAGCCAA
* *
54886584 AATGGTGAACAA
1 AGTGGTGGACAA
54886596 TCCCAGTGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (29 bp):
AGTGGTGGACAAGCCAAAGTACAAGCCAA
Found at i:54886583 original size:29 final size:29
Alignment explanation
Indices: 54886525--54886629 Score: 95
Period size: 29 Copynumber: 3.6 Consensus size: 29
54886515 ACCATGCAAC
* *
54886525 AGTGGTGGACAAGCCAAAAGTACAAGCCAA
1 AGTGGCGGACAATCC-AAAGTACAAGCCAA
54886555 AGTGGCGGACAATCCAAAGTACAAGCCAA
1 AGTGGCGGACAATCCAAAGTACAAGCCAA
* * * * * *
54886584 AATGGTGAACAATCC-CAGTGCAAGCTAA
1 AGTGGCGGACAATCCAAAGTACAAGCCAA
* * *
54886612 TGTGGCAGACAGTCCAAA
1 AGTGGCGGACAATCCAAA
54886630 TGTGGCGAAC
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
28 19 0.32
29 27 0.46
30 13 0.22
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (29 bp):
AGTGGCGGACAATCCAAAGTACAAGCCAA
Found at i:54886633 original size:18 final size:18
Alignment explanation
Indices: 54886610--54886676 Score: 100
Period size: 18 Copynumber: 3.7 Consensus size: 18
54886600 AGTGCAAGCT
54886610 AATGTGGC-AGACAGTCCA
1 AATGTGGCGA-ACAGTCCA
*
54886628 AATGTGGCGAACAATCCA
1 AATGTGGCGAACAGTCCA
54886646 AATGTGGCGAACAGTCCA
1 AATGTGGCGAACAGTCCA
*
54886664 AATGTGGTGAACA
1 AATGTGGCGAACA
54886677 ATCTAAGAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 44 0.98
19 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (18 bp):
AATGTGGCGAACAGTCCA
Found at i:54886690 original size:36 final size:36
Alignment explanation
Indices: 54886610--54886679 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
54886600 AGTGCAAGCT
54886610 AATGTGGC-AGACAGTCCAAATGTGGCGAACAATCCA
1 AATGTGGCGA-ACAGTCCAAATGTGGCGAACAATCCA
*
54886646 AATGTGGCGAACAGTCCAAATGTGGTGAACAATC
1 AATGTGGCGAACAGTCCAAATGTGGCGAACAATC
54886680 TAAGAGTGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.19
Consensus pattern (36 bp):
AATGTGGCGAACAGTCCAAATGTGGCGAACAATCCA
Found at i:54898649 original size:18 final size:18
Alignment explanation
Indices: 54898584--54898651 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
54898574 AAAATGACTA
*
54898584 AAAATCATTAAAAATAGG
1 AAAATTATTAAAAATAGG
* *
54898602 AACATTATAAAAAATA--
1 AAAATTATTAAAAATAGG
* *
54898618 AAATAGATACTAAAAATAGG
1 AAA-A-TTATTAAAAATAGG
54898638 AAAATTATTAAAAA
1 AAAATTATTAAAAA
54898652 CTCAAAAACT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
16 2 0.05
17 1 0.03
18 30 0.81
19 1 0.03
20 3 0.08
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (18 bp):
AAAATTATTAAAAATAGG
Found at i:54899002 original size:17 final size:19
Alignment explanation
Indices: 54898982--54899022 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
54898972 TTACTAAGAT
54898982 AAAAACCTTGT-AA-GAAA
1 AAAAACCTTGTGAAGGAAA
*
54898999 AAAATCCTTGTGAAGGAAA
1 AAAAACCTTGTGAAGGAAA
54899018 AAAAA
1 AAAAA
54899023 GTACACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.50
18 2 0.10
19 8 0.40
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.17
Consensus pattern (19 bp):
AAAAACCTTGTGAAGGAAA
Found at i:54899020 original size:18 final size:16
Alignment explanation
Indices: 54898966--54899021 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
54898956 CTGCCTCATT
* *
54898966 AAAACCTTACTAAGATA
1 AAAACCTT-GTAAGAAA
54898983 AAAACCTTGTAAGAAA
1 AAAACCTTGTAAGAAA
54898999 AAAATCCTTGTGAAGGAAA
1 AAAA-CCTTGT-AA-GAAA
54899018 AAAA
1 AAAA
54899022 AGTACACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 10 0.29
17 14 0.41
18 2 0.06
19 8 0.24
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (16 bp):
AAAACCTTGTAAGAAA
Found at i:54909294 original size:38 final size:38
Alignment explanation
Indices: 54909237--54909311 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
54909227 GGTGAAATTC
* *
54909237 AGGCTTAGTGATTACCAGGCTTTGTGCTGATGTTATTT
1 AGGCTTAGTGATTACCAGGCTTGGTGCCGATGTTATTT
* *
54909275 AGGCTTAGTG-TCTAGCAGGCTTGGTGCCGGTGTTATT
1 AGGCTTAGTGAT-TACCAGGCTTGGTGCCGATGTTATT
54909312 AGTGCCGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.16, C:0.15, G:0.31, T:0.39
Consensus pattern (38 bp):
AGGCTTAGTGATTACCAGGCTTGGTGCCGATGTTATTT
Found at i:54909318 original size:15 final size:15
Alignment explanation
Indices: 54909298--54909326 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54909288 AGCAGGCTTG
54909298 GTGCCGGTGTTATTA
1 GTGCCGGTGTTATTA
54909313 GTGCCGGTGTTATT
1 GTGCCGGTGTTATT
54909327 CAGGCTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.14, G:0.34, T:0.41
Consensus pattern (15 bp):
GTGCCGGTGTTATTA
Found at i:54909348 original size:16 final size:16
Alignment explanation
Indices: 54909327--54909393 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 16
54909317 CGGTGTTATT
54909327 CAGGCTTAGTGCCTAG
1 CAGGCTTAGTGCCTAG
*
54909343 CAGGCTTAGTGCCGGTGCTATC
1 CAGGCTTAGTG-C----CTA-G
*
54909365 CAGGCTTCGTGCCTAG
1 CAGGCTTAGTGCCTAG
54909381 CAGGCTTAGTGCC
1 CAGGCTTAGTGCC
54909394 GGTGTGTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
16 23 0.56
17 4 0.10
21 4 0.10
22 10 0.24
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.25
Consensus pattern (16 bp):
CAGGCTTAGTGCCTAG
Found at i:54909359 original size:38 final size:38
Alignment explanation
Indices: 54909310--54909398 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
54909300 GCCGGTGTTA
*
54909310 TTAGTGCCGGTGTTATTCAGGCTTAGTGCCTAGCAGGC
1 TTAGTGCCGGTGTTATCCAGGCTTAGTGCCTAGCAGGC
* *
54909348 TTAGTGCCGGTGCTATCCAGGCTTCGTGCCTAGCAGGC
1 TTAGTGCCGGTGTTATCCAGGCTTAGTGCCTAGCAGGC
54909386 TTAGTGCCGGTGT
1 TTAGTGCCGGTGT
54909399 GTAACAGCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.30
Consensus pattern (38 bp):
TTAGTGCCGGTGTTATCCAGGCTTAGTGCCTAGCAGGC
Found at i:54909360 original size:22 final size:22
Alignment explanation
Indices: 54909335--54909397 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
54909325 TTCAGGCTTA
54909335 GTGCCTAGCAGGCTTAGTGCCG
1 GTGCCTAGCAGGCTTAGTGCCG
*
54909357 GTG-CTATCCAGGC-T--T--C-
1 GTGCCTA-GCAGGCTTAGTGCCG
54909373 GTGCCTAGCAGGCTTAGTGCCG
1 GTGCCTAGCAGGCTTAGTGCCG
54909395 GTG
1 GTG
54909398 TGTAACAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 16
0.63 0.04 0.33
Matches are distributed among these distances:
16 8 0.26
17 5 0.16
19 2 0.06
21 5 0.16
22 11 0.35
ACGTcount: A:0.13, C:0.27, G:0.35, T:0.25
Consensus pattern (22 bp):
GTGCCTAGCAGGCTTAGTGCCG
Found at i:54909393 original size:91 final size:91
Alignment explanation
Indices: 54909233--54909398 Score: 224
Period size: 91 Copynumber: 1.8 Consensus size: 91
54909223 ATGAGGTGAA
* * * * ** * *
54909233 ATTCAGGCTTAGTGATTACCAGGCTTTGTGCTGATGTTATTTAGGCTTAGTGTCTAGCAGGCTTG
1 ATTCAGGCTTAGTGACTACCAGGCTTAGTGCCGATGCTATCCAGGCTTAGTGCCTAGCAGGCTTA
54909298 GTGCCGGTGTTATTAGTGCCGGTGTT
66 GTGCCGGTGTTATTAGTGCCGGTGTT
* * * *
54909324 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCGGTGCTATCCAGGCTTCGTGCCTAGCAGGCTTA
1 ATTCAGGCTTAGTGACTACCAGGCTTAGTGCCGATGCTATCCAGGCTTAGTGCCTAGCAGGCTTA
54909389 GTGCCGGTGT
66 GTGCCGGTGT
54909399 GTAACAGCTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
91 63 1.00
ACGTcount: A:0.15, C:0.20, G:0.31, T:0.34
Consensus pattern (91 bp):
ATTCAGGCTTAGTGACTACCAGGCTTAGTGCCGATGCTATCCAGGCTTAGTGCCTAGCAGGCTTA
GTGCCGGTGTTATTAGTGCCGGTGTT
Found at i:54909649 original size:12 final size:12
Alignment explanation
Indices: 54909634--54909666 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
54909624 AACAGAACCG
54909634 TAAATATTTTTA
1 TAAATATTTTTA
54909646 TAAATATTTTTA
1 TAAATATTTTTA
54909658 TAAATATTT
1 TAAATATTT
54909667 ACGGAGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:54910514 original size:287 final size:287
Alignment explanation
Indices: 54909998--54910576 Score: 1095
Period size: 287 Copynumber: 2.0 Consensus size: 287
54909988 CATTGTTAAA
54909998 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCCTA
1 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCCTA
54910063 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCGTTTTTGAATTTG
66 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCGTTTTTGAATTTG
54910128 TTAAAGATTTTAAATGTTGCCATTGATGAACCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
131 TTAAAGATTTTAAATGTTGCCATTGATGAACCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
54910193 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
196 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
*
54910258 AAATTGCTAAAGGAATAATAATTCAAG
261 AAATTGCTAAAGGAATAATAAGTCAAG
* * *
54910285 GACTTTGAAGCTTCGGCCAAGCTTTAATGTATTCATGTAAGTCCATTTTGAACTCGTTTCTCGTA
1 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCCTA
*
54910350 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCTCGTACCTTCGTTTTTGAATTTG
66 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCGTTTTTGAATTTG
*
54910415 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
131 TTAAAGATTTTAAATGTTGCCATTGATGAACCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
*
54910480 AGTATTAGTTTTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
196 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
54910545 AAATTGCTAAAGGAATAATAAGTCAAG
261 AAATTGCTAAAGGAATAATAAGTCAAG
54910572 GACTT
1 GACTT
54910577 GATGTGAAAT
Statistics
Matches: 285, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
287 285 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (287 bp):
GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCCTA
ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCGTTTTTGAATTTG
TTAAAGATTTTAAATGTTGCCATTGATGAACCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
AAATTGCTAAAGGAATAATAAGTCAAG
Found at i:54912474 original size:54 final size:53
Alignment explanation
Indices: 54912385--54912494 Score: 148
Period size: 54 Copynumber: 2.1 Consensus size: 53
54912375 GAGTTTCTTA
* * * * * *
54912385 GTGTTTCAAGTCAGTGAGTTACACGGCTTAGCACACGGCCTGGCACATGGGCAT
1 GTGTTGCAACTCAGAGAGTTACACGGCCTAACACAC-GCCTGGCACAAGGGCAT
*
54912439 GTGTTGCAACTCAGAGAGTTACACGGCCTAACACACGCCTGGCACAAGGGCGT
1 GTGTTGCAACTCAGAGAGTTACACGGCCTAACACACGCCTGGCACAAGGGCAT
54912492 GTG
1 GTG
54912495 GGACATCTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 18 0.37
54 31 0.63
ACGTcount: A:0.24, C:0.25, G:0.30, T:0.21
Consensus pattern (53 bp):
GTGTTGCAACTCAGAGAGTTACACGGCCTAACACACGCCTGGCACAAGGGCAT
Found at i:54912516 original size:53 final size:54
Alignment explanation
Indices: 54912395--54912517 Score: 151
Period size: 53 Copynumber: 2.3 Consensus size: 54
54912385 GTGTTTCAAG
* * * *
54912395 TCAGTGAGTTACACGGCTTAGCACACGGCCTGGCACATGGGCATGTGTTGCAAC
1 TCAGTGAGTTACACGGCCTAACACACGGCCTGGCACAAGGGCATGTGTGGCAAC
* * *
54912449 TCAGAGAGTTACACGGCCTAACACAC-GCCTGGCACAAGGGCGTGTG-GGACATC
1 TCAGTGAGTTACACGGCCTAACACACGGCCTGGCACAAGGGCATGTGTGG-CAAC
*
54912502 TCAGTGAGTAACACGG
1 TCAGTGAGTTACACGG
54912518 GTGAGGACAC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.02
53 35 0.59
54 23 0.39
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.19
Consensus pattern (54 bp):
TCAGTGAGTTACACGGCCTAACACACGGCCTGGCACAAGGGCATGTGTGGCAAC
Found at i:54916483 original size:22 final size:22
Alignment explanation
Indices: 54916455--54916498 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54916445 GAGGCTCTTG
54916455 GTACTAAACTTAATTTCAGTAT
1 GTACTAAACTTAATTTCAGTAT
54916477 GTACTAAACTTAATTTCAGTAT
1 GTACTAAACTTAATTTCAGTAT
54916499 AGCGTATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
GTACTAAACTTAATTTCAGTAT
Found at i:54921107 original size:23 final size:23
Alignment explanation
Indices: 54921051--54921117 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
54921041 GGGTGTTACA
*
54921051 ATTCTGCTATGCCTTTGTGGTGT
1 ATTCTGCAATGCCTTTGTGGTGT
*
54921074 ATTCTGTAATGCCTTTGTGGCT-T
1 ATTCTGCAATGCCTTTGTGG-TGT
* **
54921097 ATTTTGCAATGTTTTTGTGGT
1 ATTCTGCAATGCCTTTGTGGT
54921118 AAGTTCTGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.12, C:0.13, G:0.24, T:0.51
Consensus pattern (23 bp):
ATTCTGCAATGCCTTTGTGGTGT
Found at i:54926544 original size:24 final size:23
Alignment explanation
Indices: 54926500--54926545 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
54926490 TTTTTATTTC
*
54926500 TTAAAAATTTATTTAATTAAAAT
1 TTAAAAATTTATTTAAATAAAAT
54926523 TTAAAACATTT-TTTAAAATAAAA
1 TTAAAA-ATTTATTT-AAATAAAA
54926546 CAAACGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAAATTTATTTAAATAAAAT
Found at i:54932679 original size:11 final size:13
Alignment explanation
Indices: 54932659--54932690 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54932649 AATAAATTAA
54932659 TAAAATATCAT-T
1 TAAAATATCATAT
54932671 TAAAA-ATCATAT
1 TAAAATATCATAT
54932683 TAAAATAT
1 TAAAATAT
54932691 TAATCAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:54934453 original size:49 final size:50
Alignment explanation
Indices: 54934398--54934493 Score: 167
Period size: 49 Copynumber: 1.9 Consensus size: 50
54934388 TCGTTTTCTC
54934398 GATGCCATAGTCCAACTATGGTCTTACACGTAATCACA-AATCACATACT
1 GATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAATCACATACT
* *
54934447 GATGCCATAGTCTAGCTATGGTCTTACACGTAATCACATAATCACAT
1 GATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAATCACAT
54934494 GTTCACATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 36 0.82
50 8 0.18
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (50 bp):
GATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAATCACATACT
Found at i:54935374 original size:33 final size:33
Alignment explanation
Indices: 54935323--54935659 Score: 126
Period size: 33 Copynumber: 9.7 Consensus size: 33
54935313 TTATCCGTTA
* *
54935323 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* *
54935357 TCGGGGAATCAGCACTTAGTAACCCCTTTCACATTCAAAGAT
1 TCGGGGAATCAGCACTTAGCAA---C---CAC---CAATGAT
* * *
54935399 AT-GGTGGAATTAGCACTCAGCAACCACCAATAAT
1 -TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* *
54935433 TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAAT
1 TCGGGGAATCAGCACTTAGCAA-CCAC--CA-A--T--GAT
* * *
54935474 ACGGTGGAATCAACACTTAGCAACCACCAATGAA
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
54935508 TCGGGGAATCAGCACTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
* *
54935535 T-GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAAT
1 TCGGGGAATCAGCACTTAGCAA-CCAC--CA-A--T--GAT
* * * *
54935575 ACGATGGAATCAACACTTAGCAACCACCAATGAA
1 TCG-GGGAATCAGCACTTAGCAACCACCAATGAT
*
54935609 TCGGGGAATCAACACTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
*
54935636 TGGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
54935660 CCCTTTATAT
Statistics
Matches: 235, Mismatches: 31, Indels: 81
0.68 0.09 0.23
Matches are distributed among these distances:
26 20 0.09
27 25 0.11
28 1 0.00
30 1 0.00
32 4 0.02
33 72 0.31
34 21 0.09
36 5 0.02
37 4 0.02
38 2 0.01
39 8 0.03
40 2 0.01
41 13 0.06
42 41 0.17
43 16 0.07
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:54935521 original size:75 final size:76
Alignment explanation
Indices: 54935324--54935533 Score: 307
Period size: 76 Copynumber: 2.8 Consensus size: 76
54935314 TATCCGTTAT
* * * * *
54935324 CGGTGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGTAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTCAC
54935389 ATTCAAAGATA
66 ATTCAAAGATA
* * *
54935400 TGGTGGAATTAGCACTCAGCAACCACCAAT-AATTCGGGGAATCAGCACTTAGCAACCCCCTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAA-TCGGGGAATCAGCACTTAGCAACCCCCTTCA
*
54935464 CATTTAAA-ATA
65 CATTCAAAGATA
*
54935475 CGGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
54935534 TTGGGGAATC
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
75 56 0.47
76 63 0.53
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTCAC
ATTCAAAGATA
Found at i:54935539 original size:26 final size:26
Alignment explanation
Indices: 54935510--54935559 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
54935500 CCAATGAATC
54935510 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
54935536 GGGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
54935560 CTTCACATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTT
Found at i:54935586 original size:101 final size:102
Alignment explanation
Indices: 54935435--54935664 Score: 435
Period size: 101 Copynumber: 2.3 Consensus size: 102
54935425 CCAATAATTC
*
54935435 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGATGGAATCAACACTTAGCAACCA
*
54935500 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT-
66 CCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
54935536 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGATGGAATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGATGGAATCAACACTTAGCAACCA
54935601 CCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
54935638 GGGGAATCAGCACTTAGCAACCCCCTT
1 GGGGAATCAGCACTTAGCAACCCCCTT
54935665 TATATTCAAT
Statistics
Matches: 126, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
101 99 0.79
102 27 0.21
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGATGGAATCAACACTTAGCAACCA
CCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
Found at i:54937839 original size:11 final size:13
Alignment explanation
Indices: 54937819--54937850 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54937809 AATAAATTAA
54937819 TAAAATATCAT-T
1 TAAAATATCATAT
54937831 TAAAA-ATCATAT
1 TAAAATATCATAT
54937843 TAAAATAT
1 TAAAATAT
54937851 TAATCAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:54938768 original size:37 final size:37
Alignment explanation
Indices: 54938720--54938804 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
54938710 TTTAAATAAG
* *
54938720 AAGTATTTGGTTGTTTGATAAGTGAAGGGAAATGAAT
1 AAGTATATGGTTGTTTGATAAGTGAACGGAAATGAAT
* *
54938757 AAGTATATGGTTGTTTGATATGTGTACGGAAATGAAT
1 AAGTATATGGTTGTTTGATAAGTGAACGGAAATGAAT
54938794 AAGTATATGGT
1 AAGTATATGGT
54938805 GAAACACTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.34, C:0.01, G:0.28, T:0.36
Consensus pattern (37 bp):
AAGTATATGGTTGTTTGATAAGTGAACGGAAATGAAT
Found at i:54941369 original size:14 final size:15
Alignment explanation
Indices: 54941350--54941379 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54941340 CTTGTTAATG
54941350 ACTTGAAAT-TGATT
1 ACTTGAAATATGATT
54941364 ACTTGAAATATGATT
1 ACTTGAAATATGATT
54941379 A
1 A
54941380 AGTTCACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
ACTTGAAATATGATT
Found at i:54942172 original size:12 final size:12
Alignment explanation
Indices: 54942157--54942198 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
54942147 ACACGGGTGA
54942157 GGACACAGGCTG
1 GGACACAGGCTG
*
54942169 GGACAC-GGGTG
1 GGACACAGGCTG
54942180 AGGACACAGGCTG
1 -GGACACAGGCTG
54942193 GGACAC
1 GGACAC
54942199 GGCCATGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 18 0.69
13 4 0.15
ACGTcount: A:0.26, C:0.24, G:0.43, T:0.07
Consensus pattern (12 bp):
GGACACAGGCTG
Found at i:54942174 original size:24 final size:24
Alignment explanation
Indices: 54942147--54942200 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
54942137 TCAGAGAGTT
54942147 ACACGGGTGAGGACACAGGCTGGG
1 ACACGGGTGAGGACACAGGCTGGG
54942171 ACACGGGTGAGGACACAGGCTGGG
1 ACACGGGTGAGGACACAGGCTGGG
54942195 ACACGG
1 ACACGG
54942201 CCATGTGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.22, G:0.44, T:0.07
Consensus pattern (24 bp):
ACACGGGTGAGGACACAGGCTGGG
Found at i:54944997 original size:42 final size:42
Alignment explanation
Indices: 54944889--54944998 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
54944879 ACGGCCTGGC
* *
54944889 ACATGGGCATGTGG-CACGACCGTATAACCCTACTCAGTAAGTT
1 ACATGGGC-TG-GGACACGACCGTGTGACCCTACTCAGTAAGTT
* * ** *
54944932 ACACGGGCTGGGACATGGTCGTGTGACCCTATTCAGTAAGTT
1 ACATGGGCTGGGACACGACCGTGTGACCCTACTCAGTAAGTT
54944974 ACATGGGCTGGGACACGACCGTGTG
1 ACATGGGCTGGGACACGACCGTGTG
54944999 TCTCTAGTTC
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.04
42 46 0.84
43 7 0.13
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.23
Consensus pattern (42 bp):
ACATGGGCTGGGACACGACCGTGTGACCCTACTCAGTAAGTT
Found at i:54948577 original size:23 final size:23
Alignment explanation
Indices: 54948534--54948578 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54948524 AGTTATTTTG
*
54948534 GATGTTCATGATATTGGTATAAT
1 GATGTTCATGATAGTGGTATAAT
*
54948557 GATGTTGATGAT-GTGGATATAA
1 GATGTTCATGATAGTGG-TATAA
54948579 GTGTAATGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (23 bp):
GATGTTCATGATAGTGGTATAAT
Found at i:54951344 original size:24 final size:24
Alignment explanation
Indices: 54951311--54951384 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
54951301 AATCATACGT
* * *
54951311 CCTGGAACACGGGCTGTCACACAG
1 CCTGGGACACTGGCTATCACACAG
* *
54951335 CCTGGGACACTGGCTATCATACGG
1 CCTGGGACACTGGCTATCACACAG
54951359 CCTGGGACACTGGCTATCACACAG
1 CCTGGGACACTGGCTATCACACAG
54951383 CC
1 CC
54951385 ACCCCAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.27, T:0.16
Consensus pattern (24 bp):
CCTGGGACACTGGCTATCACACAG
Done.