Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_pilon, whole genome shotgun sequence
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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 20
Found at i:2522076 original size:5 final size:5
Alignment explanation
Indices: 2522066--2522094 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2522056 TATGTGATAA
2522066 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
2522095 AAATTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:2522130 original size:18 final size:18
Alignment explanation
Indices: 2522075--2522130 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
2522065 ATTTATTTTA
*
2522075 TTTTAT-TTTAT-TTTAT
1 TTTTATATTTATAATTAT
* *
2522091 TTTAAAATTTATAATTAT
1 TTTTATATTTATAATTAT
2522109 TTTTATATTTATAATTAT
1 TTTTATATTTATAATTAT
2522127 TTTT
1 TTTT
2522131 TAAAATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 4 0.12
17 5 0.15
18 24 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATTTATAATTAT
Found at i:2522239 original size:18 final size:19
Alignment explanation
Indices: 2522216--2522283 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
2522206 ATGTGATATT
*
2522216 TTATTT-TAAAATTTATAA
1 TTATTTATAAAATTTAAAA
*
2522234 TTATTTATAAATTTTAAAA
1 TTATTTATAAAATTTAAAA
*
2522253 TT-TGATT-TAAAATATACAAA
1 TTAT--TTATAAAATTTA-AAA
2522273 -TATTTATAAAA
1 TTATTTATAAAA
2522284 ATAAATATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 9 0.22
19 25 0.62
20 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTTATAAAATTTAAAA
Found at i:2522277 original size:149 final size:148
Alignment explanation
Indices: 2521996--2522286 Score: 372
Period size: 149 Copynumber: 2.0 Consensus size: 148
2521986 ATTTTTAATT
*
2521996 TATTTTTATTGTAAATCTTTCATCAATTACAATTTAATATATTAGATTTGTTTAATTATTTATGT
1 TATTTTTATTGTAAATCTTTCATCAATTACAATTTAAAATATTAGATTTGTTTAATTATTTATGT
** * * * * * * *
2522061 GATAATTTATTTTATTTTATTTTATTTTATTTTAAAATTTATAATTATTTTTATATTTATAATTA
66 GATAATTTATTTTA-TAAATTTTATATTATTTTAAAATTTAAAATTATTTTAAAATATACAAATA
* *
2522126 TTTTTTAAAATATAAAATA
130 TTTATAAAAATATAAAATA
* *
2522145 TATTTTTATTGTAAATCTTTTATCAATTACAATTTAAAATATTAGTTTTGTTTAATTATTTATGT
1 TATTTTTATTGTAAATCTTTCATCAATTACAATTTAAAATATTAGATTTGTTTAATTATTTATGT
* *
2522210 GATATTTTATTTTA-AAA-TTTATAATTATTTATAAATTTTAAAATT-TGATTTAAAATATACAA
66 GATAATTTATTTTATAAATTTTAT-ATTATTT-TAAAATTTAAAATTAT--TTTAAAATATACAA
2522272 ATATTTATAAAAATA
127 ATATTTATAAAAATA
2522287 AATATTGTAT
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
146 5 0.04
147 8 0.07
148 12 0.10
149 97 0.80
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (148 bp):
TATTTTTATTGTAAATCTTTCATCAATTACAATTTAAAATATTAGATTTGTTTAATTATTTATGT
GATAATTTATTTTATAAATTTTATATTATTTTAAAATTTAAAATTATTTTAAAATATACAAATAT
TTATAAAAATATAAAATA
Found at i:2523642 original size:19 final size:18
Alignment explanation
Indices: 2523618--2523655 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2523608 TATATATATA
2523618 TATTTAATTATATT-TAATT
1 TATTT-ATT-TATTATAATT
2523637 TATTTATTTATTATAATT
1 TATTTATTTATTATAATT
2523655 T
1 T
2523656 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATTTATTATAATT
Found at i:2523655 original size:10 final size:9
Alignment explanation
Indices: 2523618--2523655 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
2523608 TATATATATA
2523618 TATTTAATT
1 TATTTAATT
2523627 ATATTTAATT
1 -TATTTAATT
2523637 TATTT-ATT
1 TATTTAATT
2523645 TATTATAATT
1 TATT-TAATT
2523655 T
1 T
2523656 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:2523763 original size:13 final size:13
Alignment explanation
Indices: 2523745--2523771 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2523735 TGTTTACTTA
2523745 TTTACTATATTTT
1 TTTACTATATTTT
2523758 TTTACTATATTTT
1 TTTACTATATTTT
2523771 T
1 T
2523772 CTAACGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:2523935 original size:22 final size:20
Alignment explanation
Indices: 2523899--2523955 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
2523889 ACTATTTAGT
*
2523899 ATTTTATTATATTATACATAC
1 ATTTTATT-TTTTATACATAC
* *
2523920 ATTTTTATATTTTTATATATAT
1 A-TTTTAT-TTTTTATACATAC
2523942 ATTTTATTTTTTAT
1 ATTTTATTTTTTAT
2523956 TTTATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.23
21 7 0.23
22 16 0.52
23 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTATTTTTTATACATAC
Found at i:2523951 original size:26 final size:25
Alignment explanation
Indices: 2523922--2523976 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2523912 ATACATACAT
2523922 TTTTATATTTTTATATATA-TATTTTA
1 TTTTATA-TTTTATATATACTA-TTTA
* *
2523948 TTTTTTATTTTATTTATACTATTTA
1 TTTTATATTTTATATATACTATTTA
2523973 TTTT
1 TTTT
2523977 CATTATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTATATTTTATATATACTATTTA
Found at i:2523963 original size:29 final size:30
Alignment explanation
Indices: 2523785--2523976 Score: 93
Period size: 30 Copynumber: 6.5 Consensus size: 30
2523775 ACGTTATATA
2523785 TATATATATATTATTACTTCATTTTATTTTATAT
1 TATATATATATT-TTACTT--TTTTATTTTAT-T
** * * *
2523819 T-TATATGAT-TACTATTTTTTTAGTTAATAT
1 TATATAT-ATATTTTACTTTTTTATTTTAT-T
* *
2523849 TATATGTATA-TTTA-TTTTTCA-TTTATT
1 TATATATATATTTTACTTTTTTATTTTATT
*
2523876 TAT-TAT-TATTATTACTATTTAGTATTTTA-T
1 TATATATATATT-TTACT-TTT-TTATTTTATT
** * *
2523906 TATAT-TATA-CATACATTTTTATATT-TT
1 TATATATATATTTTACTTTTTTATTTTATT
2523933 TATATATATATTTTA-TTTTTTATTTTATT
1 TATATATATATTTTACTTTTTTATTTTATT
*
2523962 TATACTATTTATTTT
1 TATA-TATATATTTT
2523977 CATTATGTTT
Statistics
Matches: 119, Mismatches: 23, Indels: 36
0.67 0.13 0.20
Matches are distributed among these distances:
25 2 0.02
26 3 0.03
27 18 0.15
28 21 0.18
29 20 0.17
30 31 0.26
31 11 0.09
32 4 0.03
33 6 0.05
34 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (30 bp):
TATATATATATTTTACTTTTTTATTTTATT
Found at i:2524637 original size:22 final size:21
Alignment explanation
Indices: 2524597--2524638 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2524587 TATAAAAATT
2524597 AAAATAAATAAAATATATTTA
1 AAAATAAATAAAATATATTTA
* *
2524618 AAAATATAATTAATTATATTT
1 AAAATA-AATAAAATATATTT
2524639 TTACAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATAAATAAAATATATTTA
Found at i:2526042 original size:31 final size:31
Alignment explanation
Indices: 2526006--2526065 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2525996 AACTTAAAAG
* *
2526006 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATATTGAAATTTAAATAATTTT
2526037 AGTTTTACAATATTGAAATTTAAATAATT
1 AGTTTTACAATATTGAAATTTAAATAATT
2526066 CATACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (31 bp):
AGTTTTACAATATTGAAATTTAAATAATTTT
Found at i:2526305 original size:20 final size:20
Alignment explanation
Indices: 2526280--2526318 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2526270 AATTATATGA
2526280 TATTTT-TAGAAAATATTTTT
1 TATTTTATA-AAAATATTTTT
*
2526300 TATTTTATAAAATTATTTT
1 TATTTTATAAAAATATTTT
2526319 ATGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TATTTTATAAAAATATTTTT
Found at i:2526577 original size:20 final size:20
Alignment explanation
Indices: 2526529--2526590 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
2526519 AACTTAAATC
*
2526529 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
2526549 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
2526567 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
2526586 AAAAT
1 AAAAT
2526591 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:2526622 original size:63 final size:58
Alignment explanation
Indices: 2526555--2526744 Score: 172
Period size: 63 Copynumber: 3.1 Consensus size: 58
2526545 ATATAAAATT
2526555 TTAATAA-TATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATATTAAAAA
1 TTAATAATTATATAAAA-AA-TTA-AT-AT-TAAAATT-AATATCTATAATATAATATTAAAAA
*
2526618 TTAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAA
1 TT-A-A--TAA-TTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATT-AAAAA
* * *
2526682 TAATATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATC-A-AATATAATA-TAAAAA
1 T--TA-ATAA-TTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAA
2526741 TTAA
1 TTAA
2526745 ATATAAAACC
Statistics
Matches: 114, Mismatches: 4, Indels: 25
0.80 0.03 0.17
Matches are distributed among these distances:
57 2 0.02
59 6 0.05
60 1 0.01
61 9 0.08
62 1 0.01
63 57 0.50
64 14 0.12
65 5 0.04
66 3 0.03
67 6 0.05
68 2 0.02
69 8 0.07
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (58 bp):
TTAATAATTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAA
Found at i:2526624 original size:18 final size:19
Alignment explanation
Indices: 2526601--2526744 Score: 82
Period size: 18 Copynumber: 7.2 Consensus size: 19
2526591 TAAATATCTA
2526601 TAATA-TAATATTAAAAAT
1 TAATATTAATATTAAAAAT
2526619 TAATATTTAATTTATTTAAAAAAT
1 TAATA-TTAA--TA-TT-AAAAAT
* **
2526643 TAATATTAAAATTAATATCT
1 TAATATTAATATTAA-AAAT
*
2526663 ATAATA-TAATATTAAAAAA
1 -TAATATTAATATTAAAAAT
2526682 TAATATTTAATTTATTTAAAAAAT
1 TAATA-TTAA--TA-TT-AAAAAT
*
2526706 TAATATTAAAATT-AAAAT
1 TAATATTAATATTAAAAAT
*
2526724 CAA-ATATAATA-TAAAAAT
1 TAATAT-TAATATTAAAAAT
2526742 TAA
1 TAA
2526745 ATATAAAACC
Statistics
Matches: 98, Mismatches: 12, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
17 3 0.03
18 28 0.29
19 3 0.03
20 20 0.20
21 7 0.07
22 4 0.04
23 12 0.12
24 21 0.21
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATATTAATATTAAAAAT
Found at i:2526746 original size:18 final size:18
Alignment explanation
Indices: 2526700--2526752 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2526690 AATTTATTTA
2526700 AAAAATT-AATATTAAAAT
1 AAAAATTAAATA-TAAAAT
* * *
2526718 TAAAATCAAATATAATAT
1 AAAAATTAAATATAAAAT
2526736 AAAAATTAAATATAAAA
1 AAAAATTAAATATAAAA
2526753 CCTCTTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATTAAATATAAAAT
Found at i:2528167 original size:141 final size:142
Alignment explanation
Indices: 2527910--2528193 Score: 349
Period size: 141 Copynumber: 2.0 Consensus size: 142
2527900 ACTATAATTA
* * * * * *
2527910 AAAATTAGCTGATCCTATTCTTATATGTAATGTGGTGAGGAGGTAGGGTAGTAGGCTGTGACTCC
1 AAAATTAGCTGA-CCTATTCTCATATGTAATGTGATGAGGAGATAAGATAGTAGGC-ATGACTCC
* *
2527975 AATGTCAAGTTGAGAACAACTTCCGTAGAAGATCTCCGACAGTCAGAATTATGAATTGTCCACCG
64 AATGTCAAGTTAAGAACAACTTCCGTAGAAGATCTCCGACAGTCAAAATTATGAATTGTCCACCG
*
2528040 TGAGTCTCGATCCT
129 TGAGACTCGATCCT
* *
2528054 AAAATTAGCTTG-CCTATTCTCATATGTAATGTGATGAGGAGATAAGATATTAGG-ATGCCTCCA
1 AAAATTAGC-TGACCTATTCTCATATGTAATGTGATGAGGAGATAAGATAGTAGGCATGACTCCA
* * * * * *
2528117 ATGTCAAGTTAAGAGCAATTTTCGTATAAGA-CTTCTGGCAGTCAAAATTATGAATTGTCCACCG
65 ATGTCAAGTTAAGAACAACTTCCGTAGAAGATC-TCCGACAGTCAAAATTATGAATTGTCCACCG
*
2528181 TGGGACTCGATCC
129 TGAGACTCGATCC
2528194 CATGATCACA
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
140 1 0.01
141 72 0.60
143 36 0.30
144 9 0.08
145 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (142 bp):
AAAATTAGCTGACCTATTCTCATATGTAATGTGATGAGGAGATAAGATAGTAGGCATGACTCCAA
TGTCAAGTTAAGAACAACTTCCGTAGAAGATCTCCGACAGTCAAAATTATGAATTGTCCACCGTG
AGACTCGATCCT
Found at i:2532116 original size:35 final size:35
Alignment explanation
Indices: 2532065--2532144 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
2532055 AACACAATTA
* *
2532065 TCAATTATATTCTAAACCCCAAATTTCAAAATATT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATATT
* * **
2532100 TTAATTACATTTTAAACTTCAAATTCCAAAATATT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATATT
2532135 TCAATTACAT
1 TCAATTACAT
2532145 GTCCAACCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATATT
Found at i:2532159 original size:35 final size:34
Alignment explanation
Indices: 2532065--2532160 Score: 84
Period size: 35 Copynumber: 2.7 Consensus size: 34
2532055 AACACAATTA
* * * *
2532065 TCAATTATATTCTAAACCCCAAATTTCAAAATATT
1 TCAATTACATTC-CAACCCTAAATTCCAAAATATT
* ** * *
2532100 TTAATTACATTTTAAACTTCAAATTCCAAAATATT
1 TCAATTACATTCCAACCCT-AAATTCCAAAATATT
2532135 TCAATTACATGTCCAACCCTAAATTC
1 TCAATTACAT-TCCAACCCTAAATTC
2532161 ATATTTCATT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
34 3 0.07
35 38 0.83
36 5 0.11
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.38
Consensus pattern (34 bp):
TCAATTACATTCCAACCCTAAATTCCAAAATATT
Found at i:2532525 original size:143 final size:142
Alignment explanation
Indices: 2532316--2532594 Score: 472
Period size: 143 Copynumber: 2.0 Consensus size: 142
2532306 TACTCAATTC
* * * *
2532316 AGTTTATAAAATATTTGACTCGATTTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGTTTAAT
1 AGTTTATAAAATAGTTGACACGATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
*
2532381 TGAATCTTT-GAGTTT-TAGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATTTGA
66 TGAAT-TTTCGAGTTTCT-GTTTAAATTTAATTATAAATATTTATAATATTATAATATTATTTGA
2532444 TTCTAATTCAGTTT
129 TTCTAATTCAGTTT
2532458 AGTTTATAAAATAGTTGACACGAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAA
1 AGTTTATAAAATAGTTGACACG-ATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAA
2532523 TTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATATTATTTGAT
65 TTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATATTATTTGAT
2532588 TCTAATT
130 TCTAATT
2532595 TAAATATTTT
Statistics
Matches: 129, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
142 23 0.18
143 105 0.81
144 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (142 bp):
AGTTTATAAAATAGTTGACACGATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
TGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATATTATTTGATT
CTAATTCAGTTT
Found at i:2533108 original size:35 final size:35
Alignment explanation
Indices: 2533062--2533157 Score: 131
Period size: 35 Copynumber: 2.7 Consensus size: 35
2533052 AATGGATTAT
* *
2533062 GAATTTGAGGTTGGGCATATAATTGAAGTATTTTG
1 GAATTTGAGGTTGAGAATATAATTGAAGTATTTTG
* *
2533097 GAATTTGAGGTTTATAATATAATTGAAGTATTTTG
1 GAATTTGAGGTTGAGAATATAATTGAAGTATTTTG
*
2533132 GAATTT-AGGGTTTAGAATATAATTGA
1 GAATTTGA-GGTTGAGAATATAATTGA
2533158 TGATTATGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 1 0.02
35 54 0.98
ACGTcount: A:0.33, C:0.01, G:0.24, T:0.42
Consensus pattern (35 bp):
GAATTTGAGGTTGAGAATATAATTGAAGTATTTTG
Found at i:2537556 original size:50 final size:49
Alignment explanation
Indices: 2537498--2537639 Score: 164
Period size: 50 Copynumber: 2.9 Consensus size: 49
2537488 TTGTGAGCAC
*
2537498 CATTTTAATTTACACTCCAAACCCAAATAAAAAAAACCCAAACCCTTTTA
1 CATTTTAATTTACAC-CCAAACCCAAATAAAAAAAACCCAAACCCATTTA
*
2537548 CATTTTAATTTACACCCAAAAACCCAACT-AAAAAAA-CCAAACCCATTTA
1 CATTTTAATTTACACCC--AAACCCAAATAAAAAAAACCCAAACCCATTTA
** * *
2537597 CATTTT-ATTTTTACCCAAAGCCCAAACCAAATAAAACCCAAAC
1 CATTTTAATTTACACCCAAA-CCCAAA-TAAAAAAAACCCAAAC
2537640 TGTCCAAACC
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
46 3 0.04
47 5 0.06
48 8 0.10
49 26 0.33
50 28 0.35
51 9 0.11
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (49 bp):
CATTTTAATTTACACCCAAACCCAAATAAAAAAAACCCAAACCCATTTA
Found at i:2540922 original size:26 final size:27
Alignment explanation
Indices: 2540892--2540955 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
2540882 TAACAACAAC
2540892 AATAATATTTTCTTT-TCTAAAAATAA
1 AATAATATTTTCTTTCTCTAAAAATAA
* * * *
2540918 GATAAGATATTCTTTCTGTAAAAATAA
1 AATAATATTTTCTTTCTCTAAAAATAA
2540945 AAT-ATATTTTC
1 AATAATATTTTC
2540956 CTAATAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (27 bp):
AATAATATTTTCTTTCTCTAAAAATAA
Found at i:2547108 original size:22 final size:22
Alignment explanation
Indices: 2547065--2547108 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2547055 AATGCCAGAG
*
2547065 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* * *
2547087 GGGAATCGATTCCCCTAAAGGA
1 GGGAACCGATACCCCCAAAGGA
2547109 AAATGTTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.32, C:0.30, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:2547735 original size:31 final size:31
Alignment explanation
Indices: 2547697--2547881 Score: 336
Period size: 31 Copynumber: 6.0 Consensus size: 31
2547687 GGGTCGAGGG
2547697 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2547728 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2547759 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2547790 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2547821 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
2547852 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
2547882 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:2551547 original size:21 final size:21
Alignment explanation
Indices: 2551521--2551565 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2551511 GATTTCTGGG
* *
2551521 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2551542 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2551563 CAA
1 CAA
2551566 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2552278 original size:31 final size:31
Alignment explanation
Indices: 2552240--2552424 Score: 336
Period size: 31 Copynumber: 6.0 Consensus size: 31
2552230 GGGTCGAGGG
2552240 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2552271 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2552302 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2552333 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2552364 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
2552395 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
2552425 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:2560032 original size:17 final size:16
Alignment explanation
Indices: 2559999--2560031 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2559989 ATCAAATGAA
2559999 TAAAAAAATTGATTTT
1 TAAAAAAATTGATTTT
2560015 TAAAAAAATTGATTTT
1 TAAAAAAATTGATTTT
2560031 T
1 T
2560032 TTCCATTCAT
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:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TAAAAAAATTGATTTT
Found at i:2562049 original size:2 final size:2
Alignment explanation
Indices: 2562042--2562076 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2562032 ACACTATACA
2562042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2562077 CCGATGTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2562538 original size:20 final size:21
Alignment explanation
Indices: 2562499--2562538 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2562489 ATACTAAAAT
* *
2562499 ATATTAAAGTTAATAGTTTAA
1 ATATTAAAGTAAATAATTTAA
2562520 ATATTAAA-TAAATAATTTA
1 ATATTAAAGTAAATAATTTA
2562539 CCCTTAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATTAAAGTAAATAATTTAA
Found at i:2562792 original size:15 final size:16
Alignment explanation
Indices: 2562751--2562798 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
2562741 ATAAGATAAA
2562751 TTATG-TATTTAGTAT
1 TTATGTTATTTAGTAT
**
2562766 TTAAATTA-TTAGT-T
1 TTATGTTATTTAGTAT
2562780 TTATGTTATTTAGTAT
1 TTATGTTATTTAGTAT
2562796 TTA
1 TTA
2562799 AATATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 7 0.27
15 13 0.50
16 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.60
Consensus pattern (16 bp):
TTATGTTATTTAGTAT
Found at i:2562804 original size:15 final size:15
Alignment explanation
Indices: 2562756--2562805 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2562746 ATAAATTATG
2562756 TATTTAGTATTTAAA
1 TATTTAGTATTTAAA
**
2562771 T-TATTAGT-TTTATGT
1 TAT-TTAGTATTTA-AA
2562786 TATTTAGTATTTAAA
1 TATTTAGTATTTAAA
2562801 TATTT
1 TATTT
2562806 TAAAAATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
14 5 0.19
15 17 0.63
16 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
TATTTAGTATTTAAA
Found at i:2564003 original size:20 final size:20
Alignment explanation
Indices: 2563978--2564016 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2563968 TGCACACAAA
*
2563978 AGGGAATTCACGTGGTGAGC
1 AGGGAATTCACGGGGTGAGC
2563998 AGGGAATTCACGGGGTGAG
1 AGGGAATTCACGGGGTGAG
2564017 ATGATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.44, T:0.18
Consensus pattern (20 bp):
AGGGAATTCACGGGGTGAGC
Found at i:2567670 original size:173 final size:172
Alignment explanation
Indices: 2567372--2567719 Score: 599
Period size: 173 Copynumber: 2.0 Consensus size: 172
2567362 TTTATGTTGA
2567372 TCCTATTACTTTTTTAATGTTTTTGTTTAGTAGTGTTACTTTATAAAATTAATACTTTTATAAAT
1 TCCTATTACTTTTTTAATGTTTTTGTTTAGTAGTGTTACTTTATAAAATTAATACTTTTATAAAT
*
2567437 TTTCTTTTAACAATAACAAAATTTTCTTTTATAAAATGTGCTTTTGTTTAATGTAGGCCCCAATG
66 TTTCTTTTAACAATAACAAAATTTTCTTTTATAAAATGTGCTTTTATTTAATGTAGGCCCCAATG
*
2567502 TTTTTGCAAAATTTTATAAAGTG-TGCATTTTATATAAAATTT
131 CTTTTGCAAAATTTTATAAAGTGATG-ATTTTATATAAAATTT
* * *
2567544 TCCTGTTACTTTTTTTAATGTTTTTGTTTAGTAGTGTTAGTTTATAAAATTAATGCTTTTATAAA
1 TCCTATTAC-TTTTTTAATGTTTTTGTTTAGTAGTGTTACTTTATAAAATTAATACTTTTATAAA
*
2567609 TTTTCTTTTAACAATAACAAACTTTTCTTTTATAAAATGTGCTTTTATTTAATGTAGGCCCCAAT
65 TTTTCTTTTAACAATAACAAAATTTTCTTTTATAAAATGTGCTTTTATTTAATGTAGGCCCCAAT
*
2567674 GCTTTTGCAAAATTTTATAAAGTGTATGTTTTTATATAAAATTT
130 GCTTTTGCAAAATTTTATAAAGTG-ATGATTTTATATAAAATTT
2567718 TC
1 TC
2567720 TTTGGCATTA
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
172 8 0.05
173 139 0.84
174 17 0.10
175 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.50
Consensus pattern (172 bp):
TCCTATTACTTTTTTAATGTTTTTGTTTAGTAGTGTTACTTTATAAAATTAATACTTTTATAAAT
TTTCTTTTAACAATAACAAAATTTTCTTTTATAAAATGTGCTTTTATTTAATGTAGGCCCCAATG
CTTTTGCAAAATTTTATAAAGTGATGATTTTATATAAAATTT
Found at i:2567848 original size:33 final size:33
Alignment explanation
Indices: 2567802--2567884 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
2567792 ATTAGCACGA
*
2567802 TGAAGAAGACGCCGAGAACTCCACCTCCAAGGC
1 TGAAGAAGACGCCGAGAACTCCACCCCCAAGGC
* *
2567835 TGATGAAGACGCCGAGAATTCCACCCCCAAGGC
1 TGAAGAAGACGCCGAGAACTCCACCCCCAAGGC
2567868 TGAAGAAGACGCCGAGA
1 TGAAGAAGACGCCGAGA
2567885 GATCCTGCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.34, C:0.30, G:0.27, T:0.10
Consensus pattern (33 bp):
TGAAGAAGACGCCGAGAACTCCACCCCCAAGGC
Found at i:2568567 original size:12 final size:12
Alignment explanation
Indices: 2568550--2568574 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2568540 GTTATGAAAG
2568550 GTTAATTTAAAT
1 GTTAATTTAAAT
2568562 GTTAATTTAAAT
1 GTTAATTTAAAT
2568574 G
1 G
2568575 ATCAACAATA
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (12 bp):
GTTAATTTAAAT
Found at i:2569059 original size:6 final size:6
Alignment explanation
Indices: 2569007--2569048 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
2568997 ATATTTTTTT
**
2569007 ACCCTAA ACCCAA ACCCAA ACCCAA ACCTGA ACCCAA ACCCA
1 ACCC-AA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCA
2569049 TCCTAAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.45, C:0.48, G:0.02, T:0.05
Consensus pattern (6 bp):
ACCCAA
Found at i:2569640 original size:18 final size:20
Alignment explanation
Indices: 2569605--2569654 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2569595 TGTTAGAAAG
2569605 AAAATAAAA-AAAACATAA-
1 AAAATAAAATAAAACATAAT
*
2569623 AAAATAAAATAATA-ATAAT
1 AAAATAAAATAAAACATAAT
*
2569642 GAAATAAAATAAA
1 AAAATAAAATAAA
2569655 TCAAGGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAAACATAAT
Found at i:2569716 original size:10 final size:9
Alignment explanation
Indices: 2569698--2569743 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
2569688 AACTAAATAA
2569698 AAAAAAAAT
1 AAAAAAAAT
2569707 AAAGAAAAAT
1 AAA-AAAAAT
2569717 AAAATAAAA-
1 AAAA-AAAAT
*
2569726 GAAAAAAAT
1 AAAAAAAAT
2569735 AAAAAAAAT
1 AAAAAAAAT
2569744 TGTTAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 4 0.12
9 15 0.47
10 13 0.41
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:2571097 original size:2 final size:2
Alignment explanation
Indices: 2571090--2571128 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2571080 ACAAAGCATA
2571090 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 A
2571129 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2571213 original size:39 final size:38
Alignment explanation
Indices: 2571166--2571526 Score: 181
Period size: 39 Copynumber: 9.3 Consensus size: 38
2571156 AATAATATAC
2571166 TATATATATTTTTAAAAATATTTACCCAAAAC-A-ATAATA
1 TATATATATTTTTAAAAATATTT---CAAAACTATATAATA
* * *
2571205 TATATATATTTTCAAATAATATTTTAAAACTATATATTA
1 TATATATATTTTTAAA-AATATTTCAAAACTATATAATA
* * *
2571244 TATATATATATTTAAAAATGTTTTCAAAATTATATATATATA
1 TATATATATTTTTAAAAAT-ATTTCAAAA--CTATATA-ATA
* * *
2571286 TATATATATAGTTTTCAAAACGT-TTTAAAAACTATATATTA
1 TATATATAT--TTTT-AAAA-ATATTTCAAAACTATATAATA
* * * *
2571327 TATATATATTTTCAAAATGTTTTTAAAAAC-ATAT-AT-
1 TATATATATTTTTAAAA-ATATTTCAAAACTATATAATA
* * * ** *
2571363 TATATATATTTTTAAAATGTTTTTAAAAAAAACAT-ATA
1 TATATATATTTTTAAAA-ATATTTCAAAACTATATAATA
* * *
2571401 T-TGTATAATTTTTCAAAATGTTTTCAAAAACTATAT-A-A
1 TATATAT-ATTTTTAAAAAT-ATTTC-AAAACTATATAATA
* * * *
2571439 TATATACATTTTCAAAAATCGTTTTCAAAAACTATATATTA
1 TATATATATTTTTAAAAAT--ATTTC-AAAACTATATAATA
** **
2571480 TATATATATTTCGAAATGT-TTTCAAAACTATAT-AT-
1 TATATATATTTTTAAAAATATTTCAAAACTATATAATA
2571515 TATATATATTTT
1 TATATATATTTT
2571527 CGAAAACCGA
Statistics
Matches: 262, Mismatches: 39, Indels: 46
0.76 0.11 0.13
Matches are distributed among these distances:
35 11 0.04
36 29 0.11
37 26 0.10
38 44 0.17
39 81 0.31
40 7 0.03
41 32 0.12
42 17 0.06
44 10 0.04
45 4 0.02
46 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATATATTTTTAAAAATATTTCAAAACTATATAATA
Found at i:2571281 original size:32 final size:33
Alignment explanation
Indices: 2571240--2571305 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
2571230 AAAACTATAT
*
2571240 ATTATATATATATATTTAAAAAT-GTTTTCAAA
1 ATTATATATATATATATAAAAATAGTTTTCAAA
* *
2571272 ATTATATATATATATATATATATAGTTTTCAAA
1 ATTATATATATATATATAAAAATAGTTTTCAAA
2571305 A
1 A
2571306 CGTTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (33 bp):
ATTATATATATATATATAAAAATAGTTTTCAAA
Found at i:2571451 original size:37 final size:37
Alignment explanation
Indices: 2571280--2571532 Score: 291
Period size: 39 Copynumber: 6.6 Consensus size: 37
2571270 AAATTATATA
*
2571280 TATATATATATATATAGTTTTCAAAACGTTTT-AAAAAC
1 TATATAT-TATATATA-TTTTCAAAATGTTTTCAAAAAC
*
2571318 TATATATTATATATATATTTTCAAAATGTTTTTAAAAAC
1 TATATA-T-TATATATATTTTCAAAATGTTTTCAAAAAC
* *
2571357 -ATATATTATATATATTTTTAAAATGTTTTTAAAAAAAAC
1 TATATATTATATATATTTTCAAAATG-TTTT--CAAAAAC
*
2571396 -ATATATTGTATA-ATTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATA-TTTTCAAAATGTTTTCAAAAAC
* *
2571432 TATATAATATATACATTTTCAAAAATCGTTTTCAAAAAC
1 TATATATTATATATATTTTC-AAAAT-GTTTTCAAAAAC
*
2571471 TATATATTATATATATATTTCGAAATGTTTTC-AAAAC
1 TATATATTATATATAT-TTTCAAAATGTTTTCAAAAAC
2571508 TATATATTATATATATTTTCGAAAA
1 TATATATTATATATATTTTC-AAAA
2571533 CCGATTTTTA
Statistics
Matches: 191, Mismatches: 12, Indels: 25
0.84 0.05 0.11
Matches are distributed among these distances:
36 28 0.15
37 44 0.23
38 42 0.22
39 73 0.38
40 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAAAC
Found at i:2579166 original size:17 final size:17
Alignment explanation
Indices: 2579136--2579168 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2579126 TAAATATTAT
2579136 TAAAATATTAAACAATG
1 TAAAATATTAAACAATG
2579153 TAAATATATT-AACAAT
1 TAAA-ATATTAAACAAT
2579169 ATTTTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATATTAAACAATG
Found at i:2580706 original size:2 final size:2
Alignment explanation
Indices: 2580699--2580745 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2580689 ATACATGATA
2580699 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2580740 AT AT AT
1 AT AT AT
2580746 TGTTTTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2583470 original size:21 final size:21
Alignment explanation
Indices: 2583446--2583485 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2583436 AAGACTTTAT
2583446 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
2583467 TTTCAAAATTTAAAAATGA
1 TTTCAAAATACAAAAATGA
2583486 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:2589830 original size:19 final size:19
Alignment explanation
Indices: 2589806--2589845 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2589796 AGGCAGATTG
2589806 CCCAGAAGGTACCAATACC
1 CCCAGAAGGTACCAATACC
* *
2589825 CCCAGAGGGTACCGATACC
1 CCCAGAAGGTACCAATACC
2589844 CC
1 CC
2589846 TATGTAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.40, G:0.20, T:0.10
Consensus pattern (19 bp):
CCCAGAAGGTACCAATACC
Found at i:2591441 original size:31 final size:31
Alignment explanation
Indices: 2591403--2591489 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
2591393 GACCTATCCG
*
2591403 TATGTCCCGAAGGACATAGGTAACTTGT-TCA
1 TATGTCCCGAAGGACATAGGTAACCTGTCT-A
2591434 TATGTCCCGAAGGACATAGGTAACCTGTCTA
1 TATGTCCCGAAGGACATAGGTAACCTGTCTA
*
2591465 CATGTCCCGAAGGACATAGGTAACC
1 TATGTCCCGAAGGACATAGGTAACC
2591490 CTCGAATCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
31 52 0.98
32 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (31 bp):
TATGTCCCGAAGGACATAGGTAACCTGTCTA
Found at i:2591851 original size:6 final size:6
Alignment explanation
Indices: 2591835--2591884 Score: 55
Period size: 6 Copynumber: 7.7 Consensus size: 6
2591825 CATATAACAT
*
2591835 ATATAAC ATATAC ATATAC ATATAC ATATCAC ATAACAC ATAATAC ATAT
1 ATAT-AC ATATAC ATATAC ATATAC ATAT-AC AT-ATAC AT-ATAC ATAT
2591885 CATGCACATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 20 0.51
7 18 0.46
8 1 0.03
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (6 bp):
ATATAC
Found at i:2592402 original size:21 final size:21
Alignment explanation
Indices: 2592378--2592433 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
2592368 AATTCAGAAT
2592378 TATGGTATCGATACTCATTCA
1 TATGGTATCGATACTCATTCA
2592399 TATGGTATCGATACTCATTCA
1 TATGGTATCGATACTCATTCA
2592420 TATGGTATCGATAC
1 TATGGTATCGATAC
2592434 CCCTATTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (21 bp):
TATGGTATCGATACTCATTCA
Found at i:2595474 original size:31 final size:31
Alignment explanation
Indices: 2595431--2595526 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
2595421 ATCCCGAATG
* *
2595431 ACCTATCCATATGTCCCGAAGGATATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
*
2595462 ACCTGTCCATATGTCCTGAAGGACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
*
2595493 ACCTGTCTATATGTCCCGAAGGACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
2595524 ACC
1 ACC
2595527 CTCGACTCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (31 bp):
ACCTGTCCATATGTCCCGAAGGACATAGGTA
Found at i:2597657 original size:37 final size:37
Alignment explanation
Indices: 2597462--2597835 Score: 479
Period size: 37 Copynumber: 10.2 Consensus size: 37
2597452 GGGTATGATG
* * * * **
2597462 GTTTAAAGAGAAACCGTCTCAAGAGAGAC-AAAACTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
* * * * **
2597498 CTTTCAAGGGAAACCGT-TAAAAGAGAGAC-AAAACTT
1 GTTTCAAGGGAAACTGTCT-CAAGGGAGACGAAATTTT
* * *
2597534 GTTTTAAGAGAAACTATCTCAAGGGAGAC-AAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
* *
2597570 GTTTCAAGAGAAACTGTCTCAAGGGAGATGAAA-TTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
*
2597606 CTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
*
2597643 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
* * *
2597680 GTTTCAAGGGAAACTGTTTCAAGGCAGACAAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
*
2597717 GTTTCAAGGGAAATTGTCTCAAGGGAGACGAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
* *
2597754 GTTTCATGGGAAACTGTCTCAAGGGAGACAAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
2597791 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
2597828 GTTTCAAG
1 GTTTCAAG
2597836 AGAGACAAAA
Statistics
Matches: 302, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
35 1 0.00
36 114 0.38
37 187 0.62
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (37 bp):
GTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTT
Found at i:2597965 original size:66 final size:66
Alignment explanation
Indices: 2597854--2598050 Score: 215
Period size: 66 Copynumber: 3.0 Consensus size: 66
2597844 AATACGTTCC
* * *
2597854 AAGGGAAACATTCTCAAAG-TTTATGTTTCAAGAGAAATTGTCTCAAGGAAGACAATTTTTTTTT
1 AAGGGAAACATACTTAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAATTTTTTTTT
2597918 A
66 A
* *
2597919 AAGGGAAACATACTTAAAGACTTT-TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAA-CTTTGT
1 AAGGGAAACATACTTAAAGA-TTTATGTTTCAAGAGAAACTGTCTCAAGGA-AGACAATTTTTTT
*
2597981 TTC
64 TTA
* * * * *
2597984 AAGGGAAATAGA-TTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTGT
1 AAGGGAAACATACTT-AAAGA-TTTATGTTTCAAGAGAAACTGTCTCAAGGAAGAC-AATTTTTT
2598048 TTT
63 TTT
2598051 GAGTAAAATT
Statistics
Matches: 111, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
64 2 0.02
65 43 0.39
66 55 0.50
67 6 0.05
68 5 0.05
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (66 bp):
AAGGGAAACATACTTAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAATTTTTTTTT
A
Found at i:2598642 original size:4 final size:4
Alignment explanation
Indices: 2598635--2598674 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
2598625 TGGGTTGATA
2598635 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2598675 AGGGGAATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2599734 original size:38 final size:38
Alignment explanation
Indices: 2599680--2599753 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
2599670 TTGCTTTAGT
* * *
2599680 GGAATAGCTCAGCTTTATCACACACACACATACACAAC
1 GGAATAGATCAACTTTATCACACACACACACACACAAC
2599718 GGAATAGATCAACTTTATCACACACACACACACACA
1 GGAATAGATCAACTTTATCACACACACACACACACA
2599754 CACACACACA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.31, G:0.09, T:0.18
Consensus pattern (38 bp):
GGAATAGATCAACTTTATCACACACACACACACACAAC
Found at i:2599743 original size:2 final size:2
Alignment explanation
Indices: 2599736--2599805 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
2599726 TCAACTTTAT
2599736 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2599778 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2599806 TACATACGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2601743 original size:25 final size:25
Alignment explanation
Indices: 2601704--2601762 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
2601694 AGCAAGGTAT
* **
2601704 TAAAAATAATTAAAACAA-CAAATTA
1 TAAAAATAA-TAAAAAAACCAAAAAA
*
2601729 TAAAAATAGTAAAAAAACCAAAAAA
1 TAAAAATAATAAAAAAACCAAAAAA
2601754 TAAAAATAA
1 TAAAAATAA
2601763 AATAAGTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.19
Consensus pattern (25 bp):
TAAAAATAATAAAAAAACCAAAAAA
Found at i:2603178 original size:13 final size:14
Alignment explanation
Indices: 2603151--2603195 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
2603141 GTAATTTTTT
2603151 TAAT-ATAATAATAA
1 TAATAATAA-AATAA
2603165 TAATAA-AAAATAA
1 TAATAATAAAATAA
*
2603178 TAA-AATTAAATAA
1 TAATAATAAAATAA
2603191 TAATA
1 TAATA
2603196 GTCTTTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.07
13 17 0.63
14 7 0.26
15 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:2603178 original size:16 final size:16
Alignment explanation
Indices: 2603157--2603195 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2603147 TTTTTAATAT
2603157 AATAATAATAA-TAAAA
1 AATAATAA-AATTAAAA
*
2603173 AATAATAAAATTAAAT
1 AATAATAAAATTAAAA
2603189 AATAATA
1 AATAATA
2603196 GTCTTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAATAAAATTAAAA
Found at i:2603572 original size:25 final size:25
Alignment explanation
Indices: 2603543--2603602 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
2603533 TAATTGTGCC
2603543 ATTATTTTTCGTCAATATAATAAAT
1 ATTATTTTTCGTCAATATAATAAAT
* * *
2603568 ATTATTTTTTGTGATTATAATAAAT
1 ATTATTTTTCGTCAATATAATAAAT
*
2603593 ATCATTTTTC
1 ATTATTTTTC
2603603 TACTGAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (25 bp):
ATTATTTTTCGTCAATATAATAAAT
Found at i:2603830 original size:38 final size:38
Alignment explanation
Indices: 2603788--2603863 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
2603778 TTTCCTGTTC
*
2603788 AACCACCAACCTACT-TATATTATTAATGGATAATTAAT
1 AACCACCAACCTACTCGA-ATTATTAATGGATAATTAAT
*
2603826 AACCACCAACCTACTCGAGTTATTAATGGATAATTAAT
1 AACCACCAACCTACTCGAATTATTAATGGATAATTAAT
2603864 TGTGCCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (38 bp):
AACCACCAACCTACTCGAATTATTAATGGATAATTAAT
Found at i:2604198 original size:301 final size:300
Alignment explanation
Indices: 2603568--2604204 Score: 745
Period size: 302 Copynumber: 2.1 Consensus size: 300
2603558 TATAATAAAT
* * *
2603568 ATTATTTTTTGTGATTATAATAAATATCATTTTTCTACTGAAATATTATTTATCCTTGCAAAAAA
1 ATTATTTTTTGTCATTATAATAAATATTATTTTTCTACTGAAATATTATTTAACCTTGCAAAAAA
* * * * * *
2603633 TGTAAATATATTAACAATATGTTTTTTTATAAAAATAATACTTAAATATTATGATTATATTATAA
66 TGTAAATATATTAACAATA-GATATTTTATAAAAACAATACTTAAATACTATGATTACATTACAA
2603698 TAATGATTAAATTTATTACTTCGGATTTTTTATAACTACTTATTAATACTTCGAATTTATTACTC
130 TAATGATTAAATTTATTACTTCGGATTTTTTATAACTACTTATTAATACTTCGAATTTATTACTC
* ** * ** * * * *
2603763 TCTAATTCATTATATTTTCCTGTTCAACCACCAACCTACTTATATTATTAATGGATAATTAATAA
195 CCTAATTCACCAAACATCCCTGTTCAAACACCAACCTACTTACATTATTAATGGATAATT-ACAA
* *
2603828 CCACCAACCTACTCGAGTTATTAATGGATAATTAATTGTGCC
259 CCACCAACCTACCCGAGTTATTAATGGATAATTAATGGTGCC
*
2603870 ATTATTTTTTGTTATTATAATAAATATTATTTTTCTACT-ACAATATTATTTAACCTTGCAAAAA
1 ATTATTTTTTGTCATTATAATAAATATTATTTTTCTACTGA-AATATTATTTAACCTTGCAAAAA
2603934 ATGTAAATATATTAACAATA-ATATTTTATAAAAACAATGA-TTAAATACTATGATTACATTACA
65 ATGTAAATATATTAACAATAGATATTTTATAAAAACAAT-ACTTAAATACTATGATTACATTACA
* * * *
2603997 ATAGTGATTAAATTTATTATTTCGGA-TTTTTATAACTACTTATTATTAC-TCTTAATTTATTAC
129 ATAATGATTAAATTTATTACTTCGGATTTTTTATAACTACTTATTAATACTTC-GAATTTATTAC
* *** * ***
2604060 TCCCTAATTCTCAACCAAAGCATCCCAT-TTTATAACATCTCAGGGTA-TT-CATTA-TACTTTC
193 TCCCTAA-T-TC-ACCAAA-CATCCC-TGTTCA-AACA-C-CAACCTACTTACATTATTAATGGA
** *
2604121 TCGTT-CAACCACCAACCTACCCGGGTTATTAATGGATAATTAATGGTGCC
250 TAATTACAACCACCAACCTACCCGAGTTATTAATGGATAATTAATGGTGCC
*
2604171 ATTATTTTTCGTCATTATAATAAATATTATTTTT
1 ATTATTTTTTGTCATTATAATAAATATTATTTTT
2604205 TGACATTATA
Statistics
Matches: 286, Mismatches: 38, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
298 2 0.01
299 38 0.13
300 60 0.21
301 77 0.27
302 82 0.29
303 12 0.04
304 8 0.03
305 3 0.01
306 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (300 bp):
ATTATTTTTTGTCATTATAATAAATATTATTTTTCTACTGAAATATTATTTAACCTTGCAAAAAA
TGTAAATATATTAACAATAGATATTTTATAAAAACAATACTTAAATACTATGATTACATTACAAT
AATGATTAAATTTATTACTTCGGATTTTTTATAACTACTTATTAATACTTCGAATTTATTACTCC
CTAATTCACCAAACATCCCTGTTCAAACACCAACCTACTTACATTATTAATGGATAATTACAACC
ACCAACCTACCCGAGTTATTAATGGATAATTAATGGTGCC
Found at i:2604199 original size:25 final size:25
Alignment explanation
Indices: 2604171--2604230 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
2604161 TAATGGTGCC
*
2604171 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCGACATTATAATAAAT
*
2604196 ATTATTTTTTGACATTATAATAAAT
1 ATTATTTTTCGACATTATAATAAAT
2604221 ATTATTTTTC
1 ATTATTTTTC
2604231 TACTAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (25 bp):
ATTATTTTTCGACATTATAATAAAT
Found at i:2604788 original size:7 final size:7
Alignment explanation
Indices: 2604776--2604800 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2604766 ATTTCTCGTT
2604776 CAACCAC
1 CAACCAC
2604783 CAACCAC
1 CAACCAC
2604790 CAACCAC
1 CAACCAC
2604797 CAAC
1 CAAC
2604801 ATACCTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
CAACCAC
Found at i:2606705 original size:15 final size:15
Alignment explanation
Indices: 2606687--2606719 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2606677 ATTTTTTGAA
2606687 ATTTTATAAATTTTT
1 ATTTTATAAATTTTT
2606702 ATTTTATAAATTTTT
1 ATTTTATAAATTTTT
2606717 ATT
1 ATT
2606720 CTTTAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTATAAATTTTT
Found at i:2607502 original size:2 final size:2
Alignment explanation
Indices: 2607489--2607519 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2607479 ACTCCTATTG
2607489 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
2607520 TAAACTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2608183 original size:2 final size:2
Alignment explanation
Indices: 2608176--2608246 Score: 87
Period size: 2 Copynumber: 37.5 Consensus size: 2
2608166 ACAATCTTAT
2608176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2608218 T- TA T- TA -A AA TA TA TA T- TA AA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2608247 GTAAATGATT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
1 4 0.07
2 56 0.93
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2608497 original size:16 final size:17
Alignment explanation
Indices: 2608467--2608500 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2608457 GTTTTCGGTT
2608467 TTTCCCCACCCCAATTG
1 TTTCCCCACCCCAATTG
2608484 TTTCCCCA-CCCAATTG
1 TTTCCCCACCCCAATTG
2608500 T
1 T
2608501 CATCCCTACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.18, C:0.44, G:0.06, T:0.32
Consensus pattern (17 bp):
TTTCCCCACCCCAATTG
Found at i:2608506 original size:17 final size:17
Alignment explanation
Indices: 2608469--2608506 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2608459 TTTCGGTTTT
*
2608469 TCCCCACCCCAATTGTT
1 TCCCCACCCCAATTGTA
2608486 TCCCCA-CCCAATTGTCA
1 TCCCCACCCCAATTGT-A
2608503 TCCC
1 TCCC
2608507 TACGAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.18, C:0.50, G:0.05, T:0.26
Consensus pattern (17 bp):
TCCCCACCCCAATTGTA
Found at i:2608936 original size:20 final size:20
Alignment explanation
Indices: 2608908--2608948 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2608898 TGGATTTTCA
* *
2608908 AAATTTATTTTTGAAATTAT
1 AAATATATTTTTAAAATTAT
2608928 AAATATATTTTTAAAATTAT
1 AAATATATTTTTAAAATTAT
2608948 A
1 A
2608949 TTTAAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATATATTTTTAAAATTAT
Found at i:2617569 original size:46 final size:46
Alignment explanation
Indices: 2617493--2617592 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
2617483 TTTTGTGTTC
* *
2617493 AAATTCAAGTTTTATGGACTTTGAACTATTTTTGAAAACTTTGAAT
1 AAATTCAAGTTTTATGGACTTGGAACTATTTTTAAAAACTTTGAAT
*
2617539 AAATTCAAGTTTTATGGACTTGGAATTATTTTTAAAAACTTTGAAT
1 AAATTCAAGTTTTATGGACTTGGAACTATTTTTAAAAACTTTGAAT
2617585 AAATTCAA
1 AAATTCAA
2617593 TTGAGTCCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (46 bp):
AAATTCAAGTTTTATGGACTTGGAACTATTTTTAAAAACTTTGAAT
Found at i:2621192 original size:20 final size:20
Alignment explanation
Indices: 2621167--2621212 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2621157 TAGGTCTCGG
2621167 TACCAACATCCCGGTATCGA
1 TACCAACATCCCGGTATCGA
2621187 TACCAACATCCCGGTATCGA
1 TACCAACATCCCGGTATCGA
2621207 TACCAA
1 TACCAA
2621213 ATGTGCAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.20
Consensus pattern (20 bp):
TACCAACATCCCGGTATCGA
Found at i:2621917 original size:5 final size:5
Alignment explanation
Indices: 2621907--2622100 Score: 388
Period size: 5 Copynumber: 38.8 Consensus size: 5
2621897 TCATGTGACT
2621907 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2621957 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2622007 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2622057 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT
2622101 GTTTTTAAAA
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 189 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:2624862 original size:23 final size:23
Alignment explanation
Indices: 2624818--2624862 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2624808 AACATATTAG
**
2624818 GTAGCGCTTATATAATGTAATAT
1 GTAGCGCTTATATAATAAAATAT
2624841 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
2624863 GGCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAT
Found at i:2624924 original size:87 final size:87
Alignment explanation
Indices: 2624778--2624940 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
2624768 AATGTTATAT
* * *
2624778 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATATGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGAAGCGCTTATATAATGTAATAGGT
2624843 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
2624865 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGAAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGAAGCGCTTATATAATGTAATAGGT
2624930 AGCGCTTATAT
66 AGCGCTTATAT
2624941 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGAAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:2625538 original size:162 final size:162
Alignment explanation
Indices: 2625220--2625547 Score: 380
Period size: 162 Copynumber: 2.0 Consensus size: 162
2625210 TATACTTATG
*
2625220 GGTTTCGATGTTTCCGGGATCGATACATTTTATAAATGTATCGACACTTTATGGTTGCACCCTTT
1 GGTTTCGATGTTTCCGGGATCGATACATTTTATAAATGTATCGACACTTTATGGTTACACCCTTT
* * * ** * * *
2625285 TTGGTATTTATTTTGGACCAAAAGTATCGACACAAATTTAGCAAGTGTCGATACTTTACGCTGAC
66 GTGGCATTCATCCTGGAACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTACGCTGAC
* * *
2625350 CTATTTTATCATAAAACTGATATATTTATATC
131 CTATTTTATAATAAAACCGATATATTTATACC
**
2625382 GGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCG-TACACCTC
1 GGTTTCGATGTTTCCGGGATCGATACATTTT-ATAAATGTATCGACACTTTATG-GTTACACC-C
*
2625445 GTTTGT-GCATTCATCCT-GAACAATAAGTATCGACACAAA-TTACACAAGTGTCGATACATTAT
63 -TTTGTGGCATTCATCCTGGAACAA-AAGTATCGACACAAATTTA-ACAAGTGTCGATACATTAC
* * * * *
2625507 GTTGACCTGTTTTCTAAT-TAACCGGTATATTTATACC
125 GCTGACCTATTTTATAATAAAACCGATATATTTATACC
2625544 GGTT
1 GGTT
2625548 ATATTGTTAA
Statistics
Matches: 140, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
161 4 0.03
162 78 0.56
163 54 0.39
164 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (162 bp):
GGTTTCGATGTTTCCGGGATCGATACATTTTATAAATGTATCGACACTTTATGGTTACACCCTTT
GTGGCATTCATCCTGGAACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTACGCTGAC
CTATTTTATAATAAAACCGATATATTTATACC
Found at i:2628536 original size:199 final size:199
Alignment explanation
Indices: 2628159--2628701 Score: 770
Period size: 199 Copynumber: 2.7 Consensus size: 199
2628149 TTTATTTACA
* * *
2628159 AAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGATTATATTA
*
2628224 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACACTTTTAATAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAAT
* * *
2628289 GTATCGACACTTTGTACGTTCATCCTTTCTGGCATCCATTCTGAAAAAAAGTATCGACGCAA-AT
131 GTATCGACACTTTATACGTTCACCCTTTCTGGCATCCATTCTGAAAAAAAGTATCGACACAATA-
2628353 TTAAC
195 TTAAC
* * ** * *
2628358 AAGTGTCGCTACATGTTATAGACATATTCTCTCATAAAACCAATATATTTATACCGATTACATTG
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGATTATATTA
* * * * * *
2628423 TAAATTTACGTATTACATTATAATTATGGGTTT-TATGTTTTTGGGATTGACACTATTTGA-AAA
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACT-TTTAATAAA
* ** * **
2628486 TGTATCGACATTTTATGTGTTCACCCTTTTTGGCATCCATTCTGGAAAAAACTTATCGACACAAT
130 TGTATCGACACTTTATACGTTCACCCTTTCTGGCATCCATTCT-GAAAAAAAGTATCGACACAAT
*
2628551 ATTAAG
194 ATTAAC
* *
2628557 AAGTGTCGATACATATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGATTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGATTATATTA
2628622 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAAT
2628687 GTATCAGA-ACTTTAT
131 GTATC-GACACTTTAT
2628702 GCGTGAAACC
Statistics
Matches: 297, Mismatches: 41, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
198 58 0.20
199 202 0.68
200 35 0.12
201 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (199 bp):
AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGATTATATTA
CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAAT
GTATCGACACTTTATACGTTCACCCTTTCTGGCATCCATTCTGAAAAAAAGTATCGACACAATAT
TAAC
Found at i:2628918 original size:251 final size:252
Alignment explanation
Indices: 2628461--2628914 Score: 670
Period size: 251 Copynumber: 1.8 Consensus size: 252
2628451 GGTTTTATGT
* *
2628461 TTTTGGGATTGACACTATTTGAAAATGTATCGACATTTTATGTGTTCACCCTTTTTGGCATCCAT
1 TTTTGGGATTGACACTATATGAAAATGTATCAACATTTTATGTGTTCACCCTTTTTGGCATCCAT
* * * *
2628526 TCTGGAAAAAACTTATCGACACAATATTAAGAAGTGTCGATACATATTATAGACCTATTCTCTCA
66 TCTGGAAAAAACGTATCGACACAATACTAAGAAGTGTCGATAAATATTATAGACATATTCTCTCA
* * *
2628591 TAAAACCGGTATATGTATACCGATTATATTACAAAATTACCTATTACATTATAATTATGGGTTTC
131 TAAAACCGGTATATGTATACCGATTACATTAAAAAATTACCCATTACATTATAATTATGGGTTTC
2628656 GATGTTTTTGGGATCGACACTTTTAATAAATGTATCAGAACTTTATGCGTGAAACCC
196 GATGTTTTTGGGATCGACACTTTTAATAAATGTATCAGAACTTTATGCGTGAAACCC
*
2628713 TTTT-GGATTGACACTCTATGAAAATGTATCAACACTTTGTA-G-GTTCACCCTTTTTGGCATCC
1 TTTTGGGATTGACACTATATGAAAATGTATCAACA-TTT-TATGTGTTCACCCTTTTTGGCATCC
* * * *
2628775 ATTCTGGACAAAAA-GTATCGACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATT-TT
64 ATTCTGGA-AAAAACGTATCGACACAATACTAAGAAGTGTCGATAAATATTATAGACATATTCTC
*
2628838 TCATAAAACC-GTCATATTTATACC-AGTTACATTAAAAAATTACCCATTACATTATAATTATGG
128 TCATAAAACCGGT-ATATGTATACCGA-TTACATTAAAAAATTACCCATTACATTATAATTATGG
*
2628901 GTTTTGATGTTTTT
191 GTTTCGATGTTTTT
2628915 TGGGTTGTTA
Statistics
Matches: 181, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
249 3 0.02
250 68 0.38
251 95 0.52
252 13 0.07
253 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (252 bp):
TTTTGGGATTGACACTATATGAAAATGTATCAACATTTTATGTGTTCACCCTTTTTGGCATCCAT
TCTGGAAAAAACGTATCGACACAATACTAAGAAGTGTCGATAAATATTATAGACATATTCTCTCA
TAAAACCGGTATATGTATACCGATTACATTAAAAAATTACCCATTACATTATAATTATGGGTTTC
GATGTTTTTGGGATCGACACTTTTAATAAATGTATCAGAACTTTATGCGTGAAACCC
Found at i:2630229 original size:3 final size:3
Alignment explanation
Indices: 2630221--2630273 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
2630211 ACTTGTTTGG
* * * *
2630221 ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
2630269 TTC AT
1 ATC AT
2630274 TGACCACTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:2631467 original size:15 final size:15
Alignment explanation
Indices: 2631428--2631468 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2631418 AGGAGGTTGT
*
2631428 GGTTGAGAAAAACTG
1 GGTTGAGAAGAACTG
2631443 GGTTGAGAAGAACTG
1 GGTTGAGAAGAACTG
2631458 GGTTGAGAAGA
1 GGTTGAGAAGA
2631469 GCTTTGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.37, C:0.05, G:0.39, T:0.20
Consensus pattern (15 bp):
GGTTGAGAAGAACTG
Found at i:2632099 original size:201 final size:201
Alignment explanation
Indices: 2631754--2632496 Score: 1315
Period size: 201 Copynumber: 3.7 Consensus size: 201
2631744 TATTTAAATT
*
2631754 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGAT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * *
2631819 ATATTTATACCGATTACATTAAAAATTTACCTATTACATTATACTTATAGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
2631884 GGATCGATACTTTTTATAAATGTATCGACACTTTATGGATGCACCCTTTTTGGCATTCATTCTGG
131 GGATTGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
2631949 ACCAAA
196 ACCAAA
* *
2631955 AGTATCGATACAAAATTAAAAAAGTGTCGATACATGTTGTAAACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
2632020 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTA
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
2632085 GGATTGATACTTTTTATAAATGTATTGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTAG
131 GGATTGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
2632150 ACCAAA
196 ACCAAA
**
2632156 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTAGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
2632221 ATATTTATATCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
2632286 GGATTGATACTTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTG
131 GGATTGATAC-TTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTG
2632351 GACCAAA
195 GACCAAA
* *
2632358 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAATCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
2632423 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTATG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
2632488 GGATCGATA
131 GGATTGATA
2632497 AATTTTACCT
Statistics
Matches: 515, Mismatches: 26, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
201 324 0.63
202 191 0.37
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATTGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
ACCAAA
Found at i:2632784 original size:19 final size:19
Alignment explanation
Indices: 2632760--2632804 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
2632750 TTACATTCAC
2632760 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
2632779 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
2632798 ATA-AAAA
1 ATACAAAA
2632805 AATTAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:2634632 original size:33 final size:33
Alignment explanation
Indices: 2634595--2634660 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2634585 CATCTTAAGA
*
2634595 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
**
2634628 TCACCCCTCAACACCTTTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
2634661 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:2634718 original size:21 final size:21
Alignment explanation
Indices: 2634693--2634758 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
2634683 TCCCCTTATG
* *
2634693 TCTCTCAAGTGTATCTTCGAC
1 TCTCTCAAGTTTCTCTTCGAC
2634714 TCTCTCAAGTTTCTCTTCGAC
1 TCTCTCAAGTTTCTCTTCGAC
2634735 TCTCTCAAGTTTCTCTTCGAC
1 TCTCTCAAGTTTCTCTTCGAC
2634756 TCT
1 TCT
2634759 TGATTGTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.15, C:0.32, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTCTCAAGTTTCTCTTCGAC
Found at i:2635172 original size:22 final size:24
Alignment explanation
Indices: 2635144--2635223 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
2635134 AACCTGCATT
*
2635144 TATAATAA-AAT-TTATAATTTTA
1 TATAATAACAATACTATAATTTTA
* *
2635166 TATAATAACTATACTATCATTTTA
1 TATAATAACAATACTATAATTTTA
* *
2635190 TATAATAACTATACTATCATTTTA
1 TATAATAACAATACTATAATTTTA
*
2635214 TATAAAAACA
1 TATAATAACA
2635224 CAAAAAAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 8 0.16
23 2 0.04
24 41 0.80
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAATAACAATACTATAATTTTA
Found at i:2635192 original size:24 final size:24
Alignment explanation
Indices: 2635160--2635218 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
2635150 AAAATTTATA
2635160 ATTTTATATAATAACTATACTATC
1 ATTTTATATAATAACTATACTATC
2635184 ATTTTATATAATAACTATACTATC
1 ATTTTATATAATAACTATACTATC
2635208 ATTTTATATAA
1 ATTTTATATAA
2635219 AAACACAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTTATATAATAACTATACTATC
Found at i:2637296 original size:182 final size:182
Alignment explanation
Indices: 2636971--2637302 Score: 529
Period size: 182 Copynumber: 1.8 Consensus size: 182
2636961 GCTTTATCGA
*
2636971 TTTTATCATATTTTTACCTATTATATCATTGTGGATCGATACATTTTTATAAAGCATCGACACTT
1 TTTTATCATATTTTTACCTATTATATCATTGTGGATCGATACATTTTTATAAAACATCGACACTT
* * **
2637036 TATAGGCGCTAAAACTGCTTCTCTTTTAAATTCATAAAGTGTCGTTACTTATATTAAAGTACCGA
66 TATAGGCGCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGACACTTATATTAAAGTACCGA
*
2637101 CACTTTAAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGATACCAC
131 CACATTAAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGATACCAC
* * * *
2637153 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACTT
1 TTTTATCATATTTTTACCTATTATATCATTGTGGATCGATACATTTTTATAAAACATCGACACTT
* * *
2637218 TATAGGCGTTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGACCCTTATATTAAAGTATCGA
66 TATAGGCGCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGACACTTATATTAAAGTACCGA
* *
2637283 CACATTCAATATATCTGGTA
131 CACATTAAATATATCCGGTA
2637303 AGGATTTACC
Statistics
Matches: 135, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
182 135 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (182 bp):
TTTTATCATATTTTTACCTATTATATCATTGTGGATCGATACATTTTTATAAAACATCGACACTT
TATAGGCGCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGACACTTATATTAAAGTACCGA
CACATTAAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGATACCAC
Found at i:2641236 original size:80 final size:79
Alignment explanation
Indices: 2641100--2641278 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 79
2641090 TCCTCGGATG
2641100 AGTTCTTCTCATTATGAAC-TCTCTACTGGAAATATTGATCCACCTCCTTCTATGATGGAATCGA
1 AGTTCTTCTCATTATGAACTTCTCTACTGGAAATATTGATCCACCTCCTTCTATGATGGAATCGA
***
2641164 TTGAAATGTTGAACA
66 ACCAAA-GTTGAACA
* * * * * * *
2641179 AGTTCTGCTCATTAGGAACTTCT-TCATTGGAAATGTTGATCCACCTCCTTTTGTGATGTAATCG
1 AGTTCTTCTCATTATGAACTTCTCT-ACTGGAAATATTGATCCACCTCCTTCTATGATGGAATCG
2641243 AACCAAAGTTGAACA
65 AACCAAAGTTGAACA
2641258 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
2641279 ATTCTCCCTT
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 45 0.52
80 41 0.48
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (79 bp):
AGTTCTTCTCATTATGAACTTCTCTACTGGAAATATTGATCCACCTCCTTCTATGATGGAATCGA
ACCAAAGTTGAACA
Found at i:2646068 original size:23 final size:23
Alignment explanation
Indices: 2646027--2646100 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
2646017 TCGAGGGTTC
* **
2646027 TATGTGCTCCTTCGGGACAAAAT
1 TATGTGGTCCTTCAAGACAAAAT
* **
2646050 TATGTGGTCTTTCAAGACAAACC
1 TATGTGGTCCTTCAAGACAAAAT
*
2646073 TATGTGGTCCTTCAGGAC--AAT
1 TATGTGGTCCTTCAAGACAAAAT
2646094 TATGTGG
1 TATGTGG
2646101 CACTCCGGTG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 8 0.20
23 33 0.80
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCAAGACAAAAT
Found at i:2649309 original size:7 final size:7
Alignment explanation
Indices: 2649297--2649334 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2649287 GTCAAAGAAA
2649297 GTCAACG
1 GTCAACG
2649304 GTCAACG
1 GTCAACG
*
2649311 GTCAACA
1 GTCAACG
2649318 GTCAACG
1 GTCAACG
2649325 GTCAACG
1 GTCAACG
2649332 GTC
1 GTC
2649335 GGGTCGATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2649361 original size:9 final size:9
Alignment explanation
Indices: 2649347--2649380 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2649337 GTCGATTCAG
2649347 ACCGGTCAA
1 ACCGGTCAA
*
2649356 ACCGGTTCAG
1 ACCGG-TCAA
2649366 ACCGGTCAA
1 ACCGGTCAA
2649375 ACCGGT
1 ACCGGT
2649381 TTTCCAGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2649364 original size:19 final size:19
Alignment explanation
Indices: 2649342--2649381 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2649332 GTCGGGTCGA
2649342 TTCAGACCGGTCAAACCGG
1 TTCAGACCGGTCAAACCGG
2649361 TTCAGACCGGTCAAACCGG
1 TTCAGACCGGTCAAACCGG
2649380 TT
1 TT
2649382 TTCCAGCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (19 bp):
TTCAGACCGGTCAAACCGG
Found at i:2656622 original size:26 final size:26
Alignment explanation
Indices: 2656592--2656641 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2656582 GGTCGGGTCG
* *
2656592 GGTCAGACCGGGTCAGACTGGTCACC
1 GGTCAAACCGGGTCAGACCGGTCACC
*
2656618 GGTCAAACCGGTTCAGACCGGTCA
1 GGTCAAACCGGGTCAGACCGGTCA
2656642 AACCGGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (26 bp):
GGTCAAACCGGGTCAGACCGGTCACC
Found at i:2656627 original size:9 final size:9
Alignment explanation
Indices: 2656615--2656648 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2656605 CAGACTGGTC
2656615 ACCGGTCAA
1 ACCGGTCAA
*
2656624 ACCGGTTCAG
1 ACCGG-TCAA
2656634 ACCGGTCAA
1 ACCGGTCAA
2656643 ACCGGT
1 ACCGGT
2656649 TTTCCAGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2661679 original size:23 final size:23
Alignment explanation
Indices: 2661627--2661707 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
2661617 GTTGAGGGTT
* *
2661627 CTATGTGGTCCTT-GGGGCAAAA
1 CTATGTGGTCCTTCGGGACAAAC
* *
2661649 TTAAGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
*
2661672 CTATGTGGTCCTTCGAGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
2661695 CTATGTGGTCCTT
1 CTATGTGGTCCTT
2661708 TAGGACAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 11 0.22
23 40 0.78
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:2676329 original size:45 final size:45
Alignment explanation
Indices: 2676274--2676494 Score: 363
Period size: 45 Copynumber: 4.9 Consensus size: 45
2676264 AATTTCTTAT
2676274 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
*
2676319 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATATTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
2676364 CAATATACTTACAATTTATCACATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
2676409 CAATATACTTATCATTTATCCCATAAGCTCGTAAGTTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
** *
2676454 CAATATACTTGTCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
2676495 GTATATTTAT
Statistics
Matches: 165, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 25 0.15
45 140 0.85
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:2680536 original size:29 final size:29
Alignment explanation
Indices: 2680494--2680563 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 29
2680484 ATCTATCATC
*
2680494 TTTTTCCTTCTTTTTT--TCTTC-TTGTTG
1 TTTTTTCTT-TTTTTTCATCTTCTTTGTTG
*
2680521 TTTTTTCTATTTTTTTCATCTTCTTTTTTG
1 TTTTTTCT-TTTTTTTCATCTTCTTTGTTG
2680551 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
2680564 AAGCTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 13 0.35
28 1 0.03
29 10 0.27
30 13 0.35
ACGTcount: A:0.03, C:0.14, G:0.04, T:0.79
Consensus pattern (29 bp):
TTTTTTCTTTTTTTTCATCTTCTTTGTTG
Found at i:2683237 original size:45 final size:45
Alignment explanation
Indices: 2683182--2683447 Score: 441
Period size: 45 Copynumber: 5.9 Consensus size: 45
2683172 AATTTCTTAT
2683182 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
2683227 CAATATACTTACCATTTAT-TCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCT-CATAAGCTCGTAAGCTTATTTTAC
* *
2683272 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATATTAC
1 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
*
2683317 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
2683362 CAATATACTTACCATTTATC-CTATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCTC-ATAAGCTCGTAAGCTTATTTTAC
*
2683407 CAATATACTTGCCA-TTAT-TCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATCT-CATAAGCTCGTAAGCTTATTT
2683448 GTATATTTAT
Statistics
Matches: 212, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
44 26 0.12
45 186 0.88
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
Found at i:2683358 original size:25 final size:25
Alignment explanation
Indices: 2683285--2683358 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
2683275 TATACTTACC
2683285 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
* *
2683310 ATATTA-CCAATATA-CT--T-A-C-C
1 AT-TTATCCCATA-AGCTCGTAAGCTT
2683330 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
2683355 ATTT
1 ATTT
2683359 TACCAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 4 0.11
20 9 0.25
21 1 0.03
22 2 0.06
23 2 0.06
24 1 0.03
25 13 0.36
26 4 0.11
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (25 bp):
ATTTATCCCATAAGCTCGTAAGCTT
Found at i:2686000 original size:43 final size:44
Alignment explanation
Indices: 2685711--2686027 Score: 352
Period size: 44 Copynumber: 7.2 Consensus size: 44
2685701 TTTTTTATGA
* * * *
2685711 AAACGCCGCAATAGGTCTAGTATTTAGCGGCGTTTTTAGGGTAC
1 AAACGCCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * *
2685755 AAACGCCGCTATAGGACTGGAATATAGCGGCATTTTTAGGATAC
1 AAACGCCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * *
2685799 AAACGCTGCGATAGGTCAGGTATATAGCGGCGTTTTTAGGATAC
1 AAACGCCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * * * * *
2685843 AAATGCCGCGATAGGTCAGGTATATAACGACATTTTTAGGATAC
1 AAACGCCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
*
2685887 AAACGCCACTATAGGT-TAGGTATATAGCGGCGTTTTTAGGATAC
1 AAACGCCGCTATAGGTCT-GGTATATAGCGGCGTTTTTAGGATAC
* * *
2685931 AAACG-CGCGATAGGTCTGCTATATAGCGACGTTTTTAGGATAC
1 AAACGCCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * * * * **
2685974 AAATGCCGCTAAAAGT-TGGTACATAGCGGCATTTTTCTGATAC
1 AAACGCCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
*
2686017 AAACGCAGCTA
1 AAACGCCGCTA
2686028 AATATGTGAC
Statistics
Matches: 229, Mismatches: 41, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
43 66 0.29
44 163 0.71
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
AAACGCCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
Found at i:2690909 original size:41 final size:41
Alignment explanation
Indices: 2690864--2691062 Score: 131
Period size: 41 Copynumber: 4.8 Consensus size: 41
2690854 TTTTTTGCAC
*
2690864 AAACGCCACTATAAACAATACTATTGCGGCGTTTGTTTG-AT
1 AAACGCCACTATAAACAATACTATTGCGGCGTTTG-TTGAAA
* ** * * * * * *
2690905 AAACGCCGCTA-AATTACTTCTTTATAGTGTCGTTTGTTGAAC
1 AAACGCCACTATAAACAATAC--TATTGCGGCGTTTGTTGAAA
* * * *
2690947 AAACGCCACTATAAACAACACTATAGCGGCATTTG-TGTAA
1 AAACGCCACTATAAACAATACTATTGCGGCGTTTGTTGAAA
* * *
2690987 AAACGCCAC-AAAATTACCACT-CTATTGCGGTGTTTGTTGAAA
1 AAACGCCACTATAA--A-CAATACTATTGCGGCGTTTGTTGAAA
*
2691029 AAACGTCACTATAAAC-ATATCTATTGCGGCGTTT
1 AAACGCCACTATAAACAATA-CTATTGCGGCGTTT
2691063 TAGCTATAAT
Statistics
Matches: 116, Mismatches: 31, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
39 4 0.03
40 18 0.16
41 51 0.44
42 36 0.31
43 7 0.06
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (41 bp):
AAACGCCACTATAAACAATACTATTGCGGCGTTTGTTGAAA
Found at i:2691115 original size:83 final size:80
Alignment explanation
Indices: 2690786--2691118 Score: 281
Period size: 83 Copynumber: 4.0 Consensus size: 80
2690776 TAATATAAAT
* * * * ** * *
2690786 GCCACGATAAACAA-CATATTGCGGCGTTTTTAGGATAAATGCCGCTATATTATTACTCTATTAC
1 GCCACTATAAACAATC-TATTGCGGCG-TTTT-GTATAAACGCCGCTAAATTACCACTTTATTGC
* * * *
2690850 GGCATTTTTTGCACAAAC
63 GGCGTTTGTTGAAAAAAC
* ** * *
2690868 GCCACTATAAACAATACTATTGCGGCGTTTGTTTGATAAACGCCGCTAAATTACTTCTTTATAGT
1 GCCACTATAAACAAT-CTATTGCGGCGTTT-TGT-ATAAACGCCGCTAAATTACCACTTTATTGC
* *
2690933 GTCGTTTGTTGAACAAAC
63 GGCGTTTGTTGAAAAAAC
* * * * * * *
2690951 GCCACTATAAACAACACTATAGCGGCATTTGTGTAAAAACGCCACAAAATTACCACTCTATTGCG
1 GCCACTATAAACAA-TCTATTGCGGCGTTT-TGTATAAACGCCGCTAAATTACCACTTTATTGCG
*
2691016 GTGTTTGTTGAAAAAAC
64 GCGTTTGTTGAAAAAAC
* *
2691033 GTCACTATAAACATATCTATTGCGGCGTTTTAGCTATAATCGCCGCTAAATTACCACTTTATTGC
1 GCCACTATAAACA-ATCTATTGCGGCGTTTT-G-TATAAACGCCGCTAAATTACCACTTTATTGC
* *
2691098 GGCGTCTGTTTAAAAAAC
63 GGCGTTTGTTGAAAAAAC
2691116 GCC
1 GCC
2691119 GCTAAAGTAT
Statistics
Matches: 200, Mismatches: 43, Indels: 15
0.78 0.17 0.06
Matches are distributed among these distances:
81 1 0.00
82 78 0.39
83 120 0.60
84 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (80 bp):
GCCACTATAAACAATCTATTGCGGCGTTTTGTATAAACGCCGCTAAATTACCACTTTATTGCGGC
GTTTGTTGAAAAAAC
Found at i:2691424 original size:17 final size:17
Alignment explanation
Indices: 2691393--2691433 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2691383 GACCACCAGG
*
2691393 GTGAGCTACCAAAAAAA
1 GTGAGTTACCAAAAAAA
* *
2691410 GTTAGTTACCCAAAAAA
1 GTGAGTTACCAAAAAAA
2691427 GTGAGTT
1 GTGAGTT
2691434 CCAGTCGGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.22
Consensus pattern (17 bp):
GTGAGTTACCAAAAAAA
Found at i:2697029 original size:5 final size:6
Alignment explanation
Indices: 2696992--2697026 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2696982 ATAAAAAAGA
*
2696992 AAAAAG AAAACAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT AAAA
2697027 TAAGCATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (6 bp):
AAAAAT
Found at i:2697035 original size:6 final size:6
Alignment explanation
Indices: 2696999--2697047 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
2696989 AGAAAAAAGA
* * * *
2696999 AAACAT AAAAAT AAAAAT AAAAAT AAA-AT AAGCAT AAACAT AAACAT
1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT
2697046 AA
1 AA
2697048 GGAACAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.16
Consensus pattern (6 bp):
AAACAT
Found at i:2697035 original size:17 final size:18
Alignment explanation
Indices: 2697015--2697048 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2697005 AAAAATAAAA
2697015 ATAAAAATAAA-ATAAGC
1 ATAAAAATAAACATAAGC
*
2697032 ATAAACATAAACATAAG
1 ATAAAAATAAACATAAG
2697049 GAACAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.09, G:0.06, T:0.18
Consensus pattern (18 bp):
ATAAAAATAAACATAAGC
Found at i:2698500 original size:17 final size:17
Alignment explanation
Indices: 2698478--2698515 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2698468 GTTTTTTTAA
* *
2698478 ATAATAATATTTATAAT
1 ATAATAATAATAATAAT
2698495 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
2698512 ATAA
1 ATAA
2698516 GGGTAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:2699255 original size:16 final size:16
Alignment explanation
Indices: 2699231--2699274 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
2699221 GTTTTCTTAC
2699231 TTTTTAGAAAAGTCAG
1 TTTTTAGAAAAGTCAG
*
2699247 TTTTCAGAAAAGTCAG
1 TTTTTAGAAAAGTCAG
2699263 TTTTTAGAAAAG
1 TTTTTAGAAAAG
2699275 ATTTAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (16 bp):
TTTTTAGAAAAGTCAG
Found at i:2701996 original size:19 final size:19
Alignment explanation
Indices: 2701974--2702036 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
2701964 CTCTGAACTT
2701974 TGATATATGTTCTGATCTC
1 TGATATATGTTCTGATCTC
* * *
2701993 TGATTTTTATTCTGATCTC
1 TGATATATGTTCTGATCTC
* * * * *
2702012 AGATCTCTGCTCTGATTTC
1 TGATATATGTTCTGATCTC
2702031 TGATAT
1 TGATAT
2702037 CTCTATTTAC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.49
Consensus pattern (19 bp):
TGATATATGTTCTGATCTC
Found at i:2703269 original size:25 final size:27
Alignment explanation
Indices: 2703241--2703296 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
2703231 ATTTTATATT
2703241 TTAAATT-AA-ATTTATTAA-ATAATCA
1 TTAAATTGAATATTT-TTAATATAATCA
*
2703266 TTAAATTGAATATTTTTAATATAATTA
1 TTAAATTGAATATTTTTAATATAATCA
2703293 TTAA
1 TTAA
2703297 GTTTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 7 0.26
26 6 0.22
27 14 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAATTGAATATTTTTAATATAATCA
Found at i:2709576 original size:2 final size:2
Alignment explanation
Indices: 2709565--2709609 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
2709555 GACTTAATTA
2709565 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2709605 A- AT AT
1 AT AT AT
2709610 TTTTTAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2718248 original size:26 final size:26
Alignment explanation
Indices: 2718214--2718266 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2718204 CAAAGTCAAC
* * *
2718214 GGGTTGGGTTAAAGCAGTTCGGGTCG
1 GGGTCGGGTCAAAGCAGTTCAGGTCG
*
2718240 GGGTCGGGTCAAGGCAGTTCAGGTCG
1 GGGTCGGGTCAAAGCAGTTCAGGTCG
2718266 G
1 G
2718267 ACAGACGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.15, C:0.15, G:0.47, T:0.23
Consensus pattern (26 bp):
GGGTCGGGTCAAAGCAGTTCAGGTCG
Found at i:2720253 original size:24 final size:24
Alignment explanation
Indices: 2720216--2720270 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
2720206 TGAACCAGTG
2720216 AACCGGTACTATGGCCGGTTCACT
1 AACCGGTACTATGGCCGGTTCACT
2720240 AACCGGTAGC-ATGGCCGGTTCACT
1 AACCGGTA-CTATGGCCGGTTCACT
2720264 AACCGGT
1 AACCGGT
2720271 CCGGTTCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (24 bp):
AACCGGTACTATGGCCGGTTCACT
Found at i:2725631 original size:23 final size:22
Alignment explanation
Indices: 2725595--2725646 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
2725585 CATTGCAGTG
2725595 CCACATA-TTTGTCCCGAAAGA
1 CCACATAGTTTGTCCCGAAAGA
* *
2725616 CCACATAGTTTTGTCCTGAAGGA
1 CCACATAG-TTTGTCCCGAAAGA
2725639 CCACATAG
1 CCACATAG
2725647 AACCCTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 7 0.26
23 20 0.74
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (22 bp):
CCACATAGTTTGTCCCGAAAGA
Found at i:2726615 original size:53 final size:53
Alignment explanation
Indices: 2726535--2726638 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
2726525 CGTGAAGAGG
*
2726535 CACACGCATAGAGCAGAAAAATCAGATTTTTATTTCCTTTTTTCTTTTCTTAT
1 CACACGCATAGAGCAGAAAAATCAGATTTTTATTTCCTTTTTCCTTTTCTTAT
2726588 CACACGCATAGAGCAGAAAAATCAGATTTTTATTTCCTTTTTCCTTTTCTT
1 CACACGCATAGAGCAGAAAAATCAGATTTTTATTTCCTTTTTCCTTTTCTT
2726639 CTTCATTGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (53 bp):
CACACGCATAGAGCAGAAAAATCAGATTTTTATTTCCTTTTTCCTTTTCTTAT
Found at i:2726709 original size:25 final size:25
Alignment explanation
Indices: 2726680--2726737 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
2726670 CCAAGGAGTG
2726680 GCGAGCTAGGTGCCAAGAAGAGCTA
1 GCGAGCTAGGTGCCAAGAAGAGCTA
* *
2726705 GCGAGCTAGGTGCCGAGAGGAGCTA
1 GCGAGCTAGGTGCCAAGAAGAGCTA
2726730 GCGAGCTA
1 GCGAGCTA
2726738 AAGTGATTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.40, T:0.12
Consensus pattern (25 bp):
GCGAGCTAGGTGCCAAGAAGAGCTA
Found at i:2735416 original size:11 final size:11
Alignment explanation
Indices: 2735400--2735431 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2735390 ATTGCATGGC
2735400 ATTTAGTTTAT
1 ATTTAGTTTAT
2735411 ATTTAGTTTAT
1 ATTTAGTTTAT
*
2735422 ATTTGGTTTA
1 ATTTAGTTTA
2735432 GTTCTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (11 bp):
ATTTAGTTTAT
Found at i:2742769 original size:23 final size:22
Alignment explanation
Indices: 2742720--2742771 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
2742710 CACTGAAGTG
*
2742720 CCACATA-TTTGTCCTGAAAGA
1 CCACATAGTTTGTCCCGAAAGA
* *
2742741 CTACATAGTTTTGTCCCGAATGA
1 CCACATAG-TTTGTCCCGAAAGA
2742764 CCACATAG
1 CCACATAG
2742772 AACCCTCGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 6 0.24
23 19 0.76
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (22 bp):
CCACATAGTTTGTCCCGAAAGA
Found at i:2746547 original size:28 final size:28
Alignment explanation
Indices: 2746488--2746541 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2746478 ATTAAACATA
*
2746488 TTTTTATTTTAACAATACTTTTGTGTAC
1 TTTTTATTATAACAATACTTTTGTGTAC
* * *
2746516 TTTTTCTTATAACTATATTTTTGTGT
1 TTTTTATTATAACAATACTTTTGTGT
2746542 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.61
Consensus pattern (28 bp):
TTTTTATTATAACAATACTTTTGTGTAC
Done.