Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 118 of 182
Found at i:38156846 original size:20 final size:20
Alignment explanation
Indices: 38156821--38156874 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
38156811 AGTCTTCAAG
38156821 GTATTGGTAGAAGTGAAGTT
1 GTATTGGTAGAAGTGAAGTT
*
38156841 GTATTGGTAGAAGTGGAGTT
1 GTATTGGTAGAAGTGAAGTT
* *
38156861 CTATCGGTAGAAGT
1 GTATTGGTAGAAGT
38156875 CTCACTGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (20 bp):
GTATTGGTAGAAGTGAAGTT
Found at i:38158645 original size:17 final size:17
Alignment explanation
Indices: 38158625--38158665 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
38158615 CGTTTGCCAT
*
38158625 TGCATTTTCCTTGTCAA
1 TGCATTTTCATTGTCAA
* *
38158642 TGCATCTTCATTGTCAT
1 TGCATTTTCATTGTCAA
38158659 TGCATTT
1 TGCATTT
38158666 CCATATATAT
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:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (17 bp):
TGCATTTTCATTGTCAA
Found at i:38163020 original size:32 final size:32
Alignment explanation
Indices: 38162982--38163055 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
38162972 ATTTAAAGTT
38162982 GAGTGTTAGTACTTATCAGAATTGTCTGACAA
1 GAGTGTTAGTACTTATCAGAATTGTCTGACAA
* *
38163014 GAGTGTTAGTACTTGTTAGAATTGTCTGACAA
1 GAGTGTTAGTACTTATCAGAATTGTCTGACAA
*
38163046 GAATGTTAGT
1 GAGTGTTAGT
38163056 GTGCACTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.36
Consensus pattern (32 bp):
GAGTGTTAGTACTTATCAGAATTGTCTGACAA
Found at i:38170261 original size:15 final size:15
Alignment explanation
Indices: 38170243--38170272 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38170233 AAAATAAATA
38170243 AAAAGAATTTAATTT
1 AAAAGAATTTAATTT
*
38170258 AAAAGAATTTCATTT
1 AAAAGAATTTAATTT
38170273 TTAAAAAAAT
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:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (15 bp):
AAAAGAATTTAATTT
Found at i:38172138 original size:40 final size:40
Alignment explanation
Indices: 38172063--38172345 Score: 326
Period size: 40 Copynumber: 7.0 Consensus size: 40
38172053 TTCTCCGACA
* *
38172063 CTTCAATCTGCCATTCTGGATTAAGGGTAAAAGATTGGATGGT
1 CTTCAATCTGCC-CTCTAG-TT-AGGGTAAAAGATTGGATGGT
* *
38172106 CTTCAATCTGCCCTCTCGTTGGGGTAAAAGATTGGATGG-
1 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
* *
38172145 CTTCAATATGCCCATCTGGGTTAGGGGTAAAAGATTGGATGGT
1 CTTCAATCTGCCC-TCT-AGTTA-GGGTAAAAGATTGGATGGT
* *
38172188 CTTCAATCTGCCATCTAGTTAGGGTAAAAGATTTGATGG-
1 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
* * * *
38172227 CTTTAATATGCCC-C-ATGTTTGGGGTAAAAGATTGGAT-GA
1 CTTCAATCTGCCCTCTA-G-TTAGGGTAAAAGATTGGATGGT
*
38172266 CTTCAATCTGCCC-CATGGTTAGGGTAAAAGATTGGATGGT
1 CTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATTGGATGGT
38172306 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
1 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
38172346 TGATAGTATT
Statistics
Matches: 208, Mismatches: 21, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
37 1 0.00
38 3 0.01
39 69 0.33
40 77 0.37
41 10 0.05
42 25 0.12
43 23 0.11
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (40 bp):
CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
Found at i:38172213 original size:82 final size:79
Alignment explanation
Indices: 38172063--38172345 Score: 340
Period size: 82 Copynumber: 3.5 Consensus size: 79
38172053 TTCTCCGACA
* * * * *
38172063 CTTCAATCTGCCATTCTGGATTAAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTCGTTGG
1 CTTCAATATGCC-CTCTGG-TTAGGGGTAAAAGATTGGATGGTCTTCAATCTG-CCTCTAGTTAG
38172128 GGTAAAAGATTGGATGG
63 GGTAAAAGATTGGATGG
38172145 CTTCAATATGCCCATCTGGGTTAGGGGTAAAAGATTGGATGGTCTTCAATCTGCCATCTAGTTAG
1 CTTCAATATGCCC-TCT-GGTTAGGGGTAAAAGATTGGATGGTCTTCAATCTGCC-TCTAGTTAG
*
38172210 GGTAAAAGATTTGATGG
63 GGTAAAAGATTGGATGG
* * * * *
38172227 CTTTAATATGCCC-CAT-GTTTGGGGTAAAAGATTGGAT-GACTTCAATCTGCCCCATGGTTAGG
1 CTTCAATATGCCCTC-TGGTTAGGGGTAAAAGATTGGATGGTCTTCAATCTGCCTC-TAGTTAGG
38172289 GTAAAAGATTGGATGG
64 GTAAAAGATTGGATGG
* *
38172305 TCTTCAATCTGCCCTCTAGTTA-GGGTAAAAGATTGGATGGT
1 -CTTCAATATGCCCTCTGGTTAGGGGTAAAAGATTGGATGGT
38172346 TGATAGTATT
Statistics
Matches: 176, Mismatches: 16, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
77 1 0.01
78 35 0.20
79 48 0.27
80 6 0.03
81 3 0.02
82 81 0.46
83 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (79 bp):
CTTCAATATGCCCTCTGGTTAGGGGTAAAAGATTGGATGGTCTTCAATCTGCCTCTAGTTAGGGT
AAAAGATTGGATGG
Found at i:38172278 original size:39 final size:40
Alignment explanation
Indices: 38172086--38172343 Score: 246
Period size: 39 Copynumber: 6.5 Consensus size: 40
38172076 TTCTGGATTA
*
38172086 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TCG-TT
1 AGGGTAAAAGATTGGAT-GTCTTCAATCTGCCC-CATGGTTT
* * * *
38172126 GGGGTAAAAGATTGGATGGCTTCAATATG-CCCATCTGGGTT
1 AGGGTAAAAGATTGGATGTCTTCAATCTGCCCCA--TGGTTT
* *
38172167 AGGGGTAAAAGATTGGATGGTCTTCAATCTGCCATC-TAG-TT
1 A-GGGTAAAAGATTGGAT-GTCTTCAATCTGCC-CCATGGTTT
* * * *
38172208 AGGGTAAAAGATTTGATGGCTTTAATATGCCCCAT-GTTT
1 AGGGTAAAAGATTGGATGTCTTCAATCTGCCCCATGGTTT
* *
38172247 GGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGG-TT
1 AGGGTAAAAGATTGGATGTCTTCAATCTGCCCCATGGTTT
*
38172286 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG-TT
1 AGGGTAAAAGATTGGAT-GTCTTCAATCTGCCC-CATGGTTT
38172326 AGGGTAAAAGATTGGATG
1 AGGGTAAAAGATTGGATG
38172344 GTTGATAGTA
Statistics
Matches: 183, Mismatches: 22, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 4 0.02
39 73 0.40
40 69 0.38
41 6 0.03
42 18 0.10
43 10 0.05
44 1 0.01
45 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (40 bp):
AGGGTAAAAGATTGGATGTCTTCAATCTGCCCCATGGTTT
Found at i:38173633 original size:27 final size:27
Alignment explanation
Indices: 38173603--38173657 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
38173593 GGCATTAGTT
*
38173603 TGATGTTTATTCTTGTTTTTGCATTCA
1 TGATGTTCATTCTTGTTTTTGCATTCA
38173630 TGATGTTCATTCTTGTTTTTGCATTCA
1 TGATGTTCATTCTTGTTTTTGCATTCA
38173657 T
1 T
38173658 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.58
Consensus pattern (27 bp):
TGATGTTCATTCTTGTTTTTGCATTCA
Found at i:38181140 original size:24 final size:23
Alignment explanation
Indices: 38181112--38181166 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
38181102 ACACAAGTGG
*
38181112 AAGAAGTGGAAGAAGAAGAAGGAA
1 AAGAAGTGAAAGAA-AAGAAGGAA
* *
38181136 AAGAAGAAGAAAGAAAGGAAGGAA
1 AAGAAG-TGAAAGAAAAGAAGGAA
38181160 AAGAAGT
1 AAGAAGT
38181167 CGAGGCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.04
Consensus pattern (23 bp):
AAGAAGTGAAAGAAAAGAAGGAA
Found at i:38181145 original size:15 final size:15
Alignment explanation
Indices: 38181121--38181156 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38181111 GAAGAAGTGG
*
38181121 AAGAAGAAGAAGGAA
1 AAGAAGAAGAAAGAA
38181136 AAGAAGAAGAAAGAA
1 AAGAAGAAGAAAGAA
*
38181151 AGGAAG
1 AAGAAG
38181157 GAAAAGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAGAA
Found at i:38184382 original size:49 final size:49
Alignment explanation
Indices: 38184329--38184686 Score: 414
Period size: 49 Copynumber: 7.3 Consensus size: 49
38184319 CCTTATCTTC
38184329 AGGGTATAAGATTCACCGTT-CTGGCTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCACCGTTAC-GGCTTCAATCTTTCCCTTCACATCTCT
*** * * * *
38184378 AGGGTATAAGATTTGTCATTATGGCTTCAGTCTTTCCCTTTACATCTCT
1 AGGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
*** * *
38184427 AGGGTATAAGATTTGTCATTGCGGCTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
* * *
38184476 AAGGTATAAGATTCATCGTTACGGCTTCAATCTTT-CCTTCTACATTTCT
1 AGGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTC-ACATCTCT
* * ** * * *
38184525 AAGGTATAAGAGTCACTATTCCAGCTTCAATCTTTCCCTCCACATCTCT
1 AGGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
* * * * *
38184574 CGGGTACAAGATTCACCGTTGCGACTTCAATCTTTCCCTCCACATCTCT
1 AGGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
* *
38184623 AGGGTACAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTTT
1 AGGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
*
38184672 AGGGTATACGATTCA
1 AGGGTATAAGATTCA
38184687 ACGTATCCTC
Statistics
Matches: 265, Mismatches: 41, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
48 5 0.02
49 256 0.97
50 4 0.02
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.36
Consensus pattern (49 bp):
AGGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
Found at i:38185894 original size:54 final size:54
Alignment explanation
Indices: 38185812--38185920 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
38185802 TGGCAATGCA
* * *
38185812 ACACAGTTAAAAATAAGTGGACCAAATTCCTTCAATCCCCAAGCAACTTCTGTT
1 ACACAGTTAAAAACAAGTGGACAAAATTCCTTCAATCCCCAAGCAACTTCCGTT
*
38185866 ACACAGTTAAAAACGAGTGGACAAAATTCCTTCAATCCCCAAGCAACTTCCGTT
1 ACACAGTTAAAAACAAGTGGACAAAATTCCTTCAATCCCCAAGCAACTTCCGTT
38185920 A
1 A
38185921 TCTTGCTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.24
Consensus pattern (54 bp):
ACACAGTTAAAAACAAGTGGACAAAATTCCTTCAATCCCCAAGCAACTTCCGTT
Found at i:38186537 original size:26 final size:26
Alignment explanation
Indices: 38186491--38186544 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
38186481 ATTCTGGGCG
38186491 CAATTCTGGACACGTTCATGCAACGA
1 CAATTCTGGACACGTTCATGCAACGA
* * *
38186517 CAATTCTGTACATGTTTATGCAACGA
1 CAATTCTGGACACGTTCATGCAACGA
38186543 CA
1 CA
38186545 TTCCTAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (26 bp):
CAATTCTGGACACGTTCATGCAACGA
Found at i:38186693 original size:36 final size:37
Alignment explanation
Indices: 38186653--38186722 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
38186643 TTCCTGCGGA
* * *
38186653 GACAGTTTT-GGTGTAATCTAGAAGTGCTCATGCGAC
1 GACAGTTTTGGGCGCAATCTAGAAATGCTCATGCGAC
*
38186689 GACAGTTTTGGGCGCAATTTAGAAATGCTCATGC
1 GACAGTTTTGGGCGCAATCTAGAAATGCTCATGC
38186723 AGTGACATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 9 0.31
37 20 0.69
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (37 bp):
GACAGTTTTGGGCGCAATCTAGAAATGCTCATGCGAC
Found at i:38190259 original size:16 final size:16
Alignment explanation
Indices: 38190238--38190268 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38190228 ATAATGTGAA
38190238 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
38190254 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
38190269 GGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:38191112 original size:26 final size:26
Alignment explanation
Indices: 38191099--38191153 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
38191089 CCAGCTATAG
*
38191099 TTCTGTACATGTTCATGTAGCGACAA
1 TTCTGTACATGTTCATGCAGCGACAA
38191125 TTCTGTACATGTTCATGCAGCGAC-A
1 TTCTGTACATGTTCATGCAGCGACAA
38191150 TTCT
1 TTCT
38191154 TGGGTGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (26 bp):
TTCTGTACATGTTCATGCAGCGACAA
Found at i:38204510 original size:23 final size:24
Alignment explanation
Indices: 38204471--38204521 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
38204461 TAATAGGGAT
38204471 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
38204494 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
38204518 TTTC
1 TTTC
38204522 CCTTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:38210383 original size:6 final size:6
Alignment explanation
Indices: 38210358--38210396 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
38210348 ACAATTCATA
* * *
38210358 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
38210397 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:38218187 original size:20 final size:20
Alignment explanation
Indices: 38218141--38218188 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
38218131 CTTTTAATTG
38218141 ATGTTTGTGATTTTTGACCA
1 ATGTTTGTGATTTTTGACCA
** *
38218161 ACATTTGCT-ATTTTTTACCA
1 ATGTTTG-TGATTTTTGACCA
38218181 ATGTTTGT
1 ATGTTTGT
38218189 AATCTTTGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (20 bp):
ATGTTTGTGATTTTTGACCA
Found at i:38218225 original size:68 final size:68
Alignment explanation
Indices: 38218151--38218323 Score: 274
Period size: 68 Copynumber: 2.5 Consensus size: 68
38218141 ATGTTTGTGA
*
38218151 TTTTTGACCAACATTTGCTATTTTTTACCAATGTTTGTAATCTTTGGTCATTATTTAATTTTTGC
1 TTTTTGACCAACATTTGCTATTTTTTACCAATGTTTGTAATCTTTGGCCATTATTTAATTTTTGC
38218216 TAT
66 TAT
*
38218219 TTTTTGACCAACATTTGCTATTTTTTACCAATATTTGTAATCTTTGGCCATTATTTAATTTTTGC
1 TTTTTGACCAACATTTGCTATTTTTTACCAATGTTTGTAATCTTTGGCCATTATTTAATTTTTGC
38218284 TAT
66 TAT
* ** ** *
38218287 TTTTTGACCGATTTTTTATATTTTTGACCAATGTTTG
1 TTTTTGACCAACATTTGCTATTTTTTACCAATGTTTG
38218324 CTATCGTTCA
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 96 1.00
ACGTcount: A:0.22, C:0.13, G:0.10, T:0.54
Consensus pattern (68 bp):
TTTTTGACCAACATTTGCTATTTTTTACCAATGTTTGTAATCTTTGGCCATTATTTAATTTTTGC
TAT
Found at i:38218248 original size:20 final size:21
Alignment explanation
Indices: 38218211--38218255 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
38218201 TTATTTAATT
38218211 TTTGCTATTTTTTGACCAACA
1 TTTGCTATTTTTTGACCAACA
*
38218232 TTTGCTATTTTTT-ACCAATA
1 TTTGCTATTTTTTGACCAACA
38218252 TTTG
1 TTTG
38218256 TAATCTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTGCTATTTTTTGACCAACA
Found at i:38218300 original size:21 final size:22
Alignment explanation
Indices: 38218275--38218327 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
38218265 GCCATTATTT
38218275 AATTTTTGCTAT-TTTTTGACC
1 AATTTTTGCTATATTTTTGACC
*
38218296 GATTTTT--TATATTTTTGACC
1 AATTTTTGCTATATTTTTGACC
*
38218316 AATGTTTGCTAT
1 AATTTTTGCTAT
38218328 CGTTCATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 6 0.23
22 3 0.12
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (22 bp):
AATTTTTGCTATATTTTTGACC
Found at i:38219003 original size:99 final size:100
Alignment explanation
Indices: 38218887--38219474 Score: 709
Period size: 100 Copynumber: 5.9 Consensus size: 100
38218877 ATATCAAATT
* *
38218887 AAACTAACAGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCTA-ACCAA
1 AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAA
*
38218951 ATCATATACCACTAAAGTTGTAGAGGGGTGGATTA
66 ATCCTATACCACTAAAGTTGTAGAGGGGTGGATTA
38218986 AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAAT-GAGTGAAGCCACACCAA
1 AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAA
38219050 ATCCTATACCACTAAAGTTGTAGAGGGGTGGATTA
66 ATCCTATACCACTAAAGTTGTAGAGGGGTGGATTA
* * * *
38219085 AAACTAACAGTAACAAATCTCAGTCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGTCACACCAA
1 AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAA
* * * *
38219150 ATCTTATA-TACCTAAAGTTGTAGAGGAGTAGATTA
66 ATCCTATACCA-CTAAAGTTGTAGAGGGGTGGATTA
* * *
38219185 AAACTAACAGTAGCATATCTCAATCTCTACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAA
1 AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAA
* * * **
38219250 ATCCTATACCCCTAAAGTTTTAAAGGGACGGATTA
66 ATCCTATACCACTAAAGTTGTAGAGGGGTGGATTA
* * * ** ** * *
38219285 AAACTAACAGTAGCATATATCAATCTTTACTGAAGTTTTAGTGGAATAGAGTGAAGCCACACTAA
1 AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAA
* ** * *
38219350 ATCCTATACCCCTAAAGTCATAGAGGGGCGAATTA
66 ATCCTATACCACTAAAGTTGTAGAGGGGTGGATTA
* * ** * * * * *
38219385 AAACTAACCGTAACAGATCTTAATCTCC-CAAAAGTTACAATGGAATAGAGTGAAGTTACAAACC
1 AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAG--CCACA-C
*
38219449 CAAATCCTATATCC-CTGAAGTTGTAG
63 CAAATCCTATA-CCACTAAAGTTGTAG
38219475 GGATCGGATT
Statistics
Matches: 426, Mismatches: 55, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
98 10 0.02
99 152 0.36
100 239 0.56
101 3 0.01
102 20 0.05
103 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (100 bp):
AAACTAACAGTAACAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAA
ATCCTATACCACTAAAGTTGTAGAGGGGTGGATTA
Found at i:38219023 original size:53 final size:53
Alignment explanation
Indices: 38218959--38219125 Score: 150
Period size: 53 Copynumber: 3.3 Consensus size: 53
38218949 AAATCATATA
*
38218959 CCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAACAGATCTCAATCT
1 CCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAACAAATCTCAATCT
* * * ** * * * * * * *
38219012 CCACTGAAGTTGCAGTGGAAT-GAGTGAAGC---CA-CACCAAATC-CTAT-A
1 CCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAACAAATCTCAATCT
*
38219058 CCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAACAAATCTCAGTCT
1 CCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAACAAATCTCAATCT
*
38219111 CCACTGAAGTTGTAG
1 CCACTAAAGTTGTAG
38219126 TGGAATGGAG
Statistics
Matches: 80, Mismatches: 27, Indels: 14
0.66 0.22 0.12
Matches are distributed among these distances:
46 16 0.20
47 9 0.11
48 6 0.08
49 2 0.03
50 2 0.03
51 7 0.09
52 8 0.10
53 30 0.38
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (53 bp):
CCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAACAAATCTCAATCT
Found at i:38219103 original size:51 final size:51
Alignment explanation
Indices: 38218948--38219103 Score: 133
Period size: 46 Copynumber: 3.1 Consensus size: 51
38218938 TGAAGCTAAC
*
38218948 CAAATCATATACCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAA
1 CAAATCCTATACCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAA
* * * * * * ** * * * * *
38218999 CAGATCTCAATCTCCACTGAAGTTGCAGTGGAAT-GAGTGAAGC---CA-CAC
1 CAAATC-CTAT-ACCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAA
38219047 CAAATCCTATACCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAA
1 CAAATCCTATACCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAA
38219098 CAAATC
1 CAAATC
38219104 TCAGTCTCCA
Statistics
Matches: 71, Mismatches: 27, Indels: 14
0.63 0.24 0.12
Matches are distributed among these distances:
46 16 0.23
47 9 0.13
48 6 0.08
49 2 0.03
50 2 0.03
51 12 0.17
52 8 0.11
53 16 0.23
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (51 bp):
CAAATCCTATACCACTAAAGTTGTAGAGGGGTGGATTAAAACTAACAGTAA
Found at i:38220081 original size:28 final size:28
Alignment explanation
Indices: 38220049--38220104 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
38220039 GTCCAAATAC
38220049 AATACAAACCCAAATGCCCCAAACCCAA
1 AATACAAACCCAAATGCCCCAAACCCAA
* * *
38220077 AATACAAACTCAAATGCCCTAAGCCCAA
1 AATACAAACCCAAATGCCCCAAACCCAA
38220105 TTTTACAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.36, G:0.05, T:0.11
Consensus pattern (28 bp):
AATACAAACCCAAATGCCCCAAACCCAA
Found at i:38221243 original size:30 final size:30
Alignment explanation
Indices: 38221202--38221274 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
38221192 TTAGTTTAAT
* ** *
38221202 TTTATTTTATTTGTATTTTTAATTT-GTACC
1 TTTAATTTATTTACATTTTCAATTTAGT-CC
38221232 TTTAATTTATTTACATTTTCAATTTAGTCC
1 TTTAATTTATTTACATTTTCAATTTAGTCC
38221262 TTT-ATTTAATTTA
1 TTTAATTT-ATTTA
38221275 ACACCATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 31 0.84
31 2 0.05
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTAATTTATTTACATTTTCAATTTAGTCC
Found at i:38221393 original size:4 final size:4
Alignment explanation
Indices: 38221368--38221554 Score: 52
Period size: 4 Copynumber: 45.8 Consensus size: 4
38221358 TTTGTATTGT
* * * *
38221368 TTTA TTTA -GTA TTTA ATT- TTTA TTTA TTTA TTT- GTTA TTCA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * ** *
38221412 TTTA CGTTA TTTA TATTC TTGCC TTTA TTTAA CTTTA TGTA TTTTA TTTA
1 TTTA -TTTA TTTA T-TTA TT-TA TTTA TTT-A -TTTA TTTA -TTTA TTTA
* * *
38221462 TTT- GTTA TTT- TTTA TGCTA TTTA TACTT- TTGTT TTTA TTTAA TTTTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA T--TTA TT-TA TTTA TTT-A -TTTA
* *
38221509 TTTA TTCA -TTA TTT- TTAA TTTTA TTTTA TTTA TTT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTT
38221555 GTATGTCATT
Statistics
Matches: 135, Mismatches: 25, Indels: 46
0.66 0.12 0.22
Matches are distributed among these distances:
3 22 0.16
4 75 0.56
5 30 0.22
6 8 0.06
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:38221395 original size:15 final size:15
Alignment explanation
Indices: 38221377--38221556 Score: 58
Period size: 15 Copynumber: 11.7 Consensus size: 15
38221367 TTTTATTTAG
38221377 TATTTAATTT-TTATT
1 TATTT-ATTTGTTATT
38221392 TATTTATTTGTTATT
1 TATTTATTTGTTATT
*
38221407 CATTT-TTTACGTTATT
1 TATTTATTT--GTTATT
* **
38221423 TATATT-CTTG-CCTT
1 TAT-TTATTTGTTATT
*
38221437 TATTTAACTTTATGTATTT
1 TATTT-A-TTTGT-TA-TT
38221456 TATTTATTTGTTATT
1 TATTTATTTGTTATT
*
38221471 T-TTTA--TGCTATT
1 TATTTATTTGTTATT
*
38221483 TATACT-TTTGTT-TT
1 TAT-TTATTTGTTATT
*
38221497 TATTTAATT-TTATT
1 TATTTATTTGTTATT
38221511 TATTCATTATTT-TTAATTT
1 TA-T--TTATTTGTT-A-TT
* *
38221530 TATTTTATTTATTTTT
1 TA-TTTATTTGTTATT
38221546 TATTTATTTGT
1 TATTTATTTGT
38221557 ATGTCATTTA
Statistics
Matches: 125, Mismatches: 18, Indels: 44
0.67 0.10 0.24
Matches are distributed among these distances:
12 7 0.06
13 6 0.05
14 28 0.22
15 30 0.24
16 16 0.13
17 21 0.17
18 4 0.03
19 13 0.10
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.69
Consensus pattern (15 bp):
TATTTATTTGTTATT
Found at i:38221406 original size:26 final size:27
Alignment explanation
Indices: 38221368--38221425 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
38221358 TTTGTATTGT
* *
38221368 TTTATTTAGTATTTAATTTTTA-TTTA
1 TTTATTTAGTATTCAATTTTTACGTTA
*
38221394 TTTATTT-GTTATTCATTTTTTACGTTA
1 TTTATTTAG-TATTCAATTTTTACGTTA
38221421 TTTAT
1 TTTAT
38221426 ATTCTTGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 18 0.67
27 8 0.30
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTATTTAGTATTCAATTTTTACGTTA
Found at i:38221458 original size:60 final size:60
Alignment explanation
Indices: 38221377--38221514 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
38221367 TTTTATTTAG
* *
38221377 TATTTAATTTTTATTTA-TTTATTTGTTAT-TCATTTTTTACGTTATTTATA-TTCTTGCCTT
1 TATTTAA-TTTTATTTATTTTATTTATT-TGTCATTTTTTACGCTATTTATACTT-TTGCCTT
* * * * **
38221437 TATTTAACTTTATGTATTTTATTTATTTGTTATTTTTTATGCTATTTATACTTTTGTTTT
1 TATTTAATTTTATTTATTTTATTTATTTGTCATTTTTTACGCTATTTATACTTTTGCCTT
38221497 TATTTAATTTTATTTATT
1 TATTTAATTTTATTTATT
38221515 CATTATTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
59 8 0.12
60 55 0.85
61 2 0.03
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (60 bp):
TATTTAATTTTATTTATTTTATTTATTTGTCATTTTTTACGCTATTTATACTTTTGCCTT
Found at i:38221534 original size:51 final size:49
Alignment explanation
Indices: 38221452--38221551 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 49
38221442 AACTTTATGT
** *
38221452 ATTTTATTTATTTGTTATTTTTTATGCTATTTATACTTT-TGTTTTTATTTA
1 ATTTTATTTATTCATTATTTTTAATGCTATTT-TA-TTTAT-TTTTTATTTA
**
38221503 ATTTTATTTATTCATTATTTTTAATTTTATTTTATTTATTTTTTATTTA
1 ATTTTATTTATTCATTATTTTTAATGCTATTTTATTTATTTTTTATTTA
38221552 TTTGTATGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
49 13 0.30
50 3 0.07
51 27 0.63
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (49 bp):
ATTTTATTTATTCATTATTTTTAATGCTATTTTATTTATTTTTTATTTA
Found at i:38221548 original size:28 final size:27
Alignment explanation
Indices: 38221435--38221550 Score: 81
Period size: 28 Copynumber: 4.0 Consensus size: 27
38221425 TATTCTTGCC
* *
38221435 TTTATTTAACTTTATGTATTTTATTTATT
1 TTTATTTAATTTTATTTA-TTT-TTTATT
* * *
38221464 TGTTATTT-TTTATGCTATTTATACTTTTGTT
1 T-TTATTTAATT-T--TATTTAT-TTTTTATT
**
38221495 TTTATTTAATTTTATTTATTCATTATT
1 TTTATTTAATTTTATTTATTTTTTATT
*
38221522 TTTAATTTTATTTTATTTATTTTTTATT
1 TTT-ATTTAATTTTATTTATTTTTTATT
38221550 T
1 T
38221551 ATTTGTATGT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
27 7 0.10
28 29 0.43
29 2 0.03
30 14 0.21
31 9 0.13
32 6 0.09
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (27 bp):
TTTATTTAATTTTATTTATTTTTTATT
Found at i:38221717 original size:29 final size:28
Alignment explanation
Indices: 38221676--38221732 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
38221666 GTGTATAATT
*
38221676 AATTAATTTTTATTGTCA-TTATTATTAC
1 AATTAATTGTTATT-TCATTTATTATTAC
*
38221704 AATTGAATTGTTATTTTATTTATTATTAC
1 AATT-AATTGTTATTTCATTTATTATTAC
38221733 TACTCTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (28 bp):
AATTAATTGTTATTTCATTTATTATTAC
Found at i:38229948 original size:20 final size:20
Alignment explanation
Indices: 38229923--38230008 Score: 68
Period size: 20 Copynumber: 4.4 Consensus size: 20
38229913 AGAAAACCTT
*
38229923 TTTACCAAAACATCTAAGGA
1 TTTACCAAAATATCTAAGGA
* *
38229943 TTTACCAATATTTCTAA-GA
1 TTTACCAAAATATCTAAGGA
*
38229962 -CTACCAAAATATCTAAGGA
1 TTTACCAAAATATCTAAGGA
* * * * *
38229981 CTTACTAATATTTCCAAGGA
1 TTTACCAAAATATCTAAGGA
*
38230001 TTTGCCAA
1 TTTACCAA
38230009 TATTTCTAAA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
18 13 0.26
19 4 0.08
20 33 0.66
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (20 bp):
TTTACCAAAATATCTAAGGA
Found at i:38229968 original size:18 final size:19
Alignment explanation
Indices: 38229935--38230017 Score: 69
Period size: 20 Copynumber: 4.3 Consensus size: 19
38229925 TACCAAAACA
*
38229935 TCTAAGGATTTACCAATATT
1 TCTAAGGA-CTACCAATATT
* *
38229955 TCTAA-GACTACCAAAATA
1 TCTAAGGACTACCAATATT
*
38229973 TCTAAGGACTTACTAATATT
1 TCTAAGGAC-TACCAATATT
* * *
38229993 TCCAAGGATTTGCCAATATT
1 TCTAAGGA-CTACCAATATT
38230013 TCTAA
1 TCTAA
38230018 AGTCTTAGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
18 13 0.27
19 5 0.10
20 31 0.63
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (19 bp):
TCTAAGGACTACCAATATT
Found at i:38231416 original size:15 final size:15
Alignment explanation
Indices: 38231396--38231430 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38231386 TGTCATATCC
38231396 TTTTCTTCTGTTTTT
1 TTTTCTTCTGTTTTT
* *
38231411 TTTTCTTTTTTTTTT
1 TTTTCTTCTGTTTTT
38231426 TTTTC
1 TTTTC
38231431 CATGATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (15 bp):
TTTTCTTCTGTTTTT
Found at i:38240562 original size:22 final size:21
Alignment explanation
Indices: 38240484--38240567 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 21
38240474 TTTAATTGAT
* *
38240484 AATTAAGACTTAAGTTTTATTAA
1 AATT-AGATTTAAGGTTT-TTAA
* *
38240507 AATTAAGGTTTAGGGTTTTTAA
1 AATT-AGATTTAAGGTTTTTAA
*
38240529 AATTAGAGTTAAGGTATTTTAA
1 AATTAGATTTAAGGT-TTTTAA
38240551 AA-TAGGATTTAAGGTTT
1 AATTA-GATTTAAGGTTT
38240568 ATTTAATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 12 0.24
22 25 0.49
23 14 0.27
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (21 bp):
AATTAGATTTAAGGTTTTTAA
Found at i:38244188 original size:22 final size:20
Alignment explanation
Indices: 38244142--38244196 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
38244132 AGAGTATTTG
*
38244142 AGAGATTTTTGAGAGTTCAA
1 AGAGAATTTTGAGAGTTCAA
* *
38244162 TGAGAATTTTGAGAGATTTAGA
1 AGAGAATTTTGAGAG-TTCA-A
*
38244184 AGAGAATTGTGAG
1 AGAGAATTTTGAG
38244197 TGAAAAATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 13 0.46
21 3 0.11
22 12 0.43
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (20 bp):
AGAGAATTTTGAGAGTTCAA
Found at i:38257595 original size:2 final size:2
Alignment explanation
Indices: 38257588--38257633 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
38257578 ATGAGTACGA
38257588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38257630 AT AT
1 AT AT
38257634 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38257638 original size:2 final size:2
Alignment explanation
Indices: 38257633--38257657 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38257623 TATATATATA
38257633 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
38257658 TTACTTAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38259614 original size:38 final size:38
Alignment explanation
Indices: 38259572--38259645 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
38259562 AAGATATTTT
* *
38259572 TAAACAGTTACAATTTGACAAAATCAGAATCTAACTTC
1 TAAACAGGTACAATTTGACAAAATCAAAATCTAACTTC
* *
38259610 TAAACGGGTACAATTTGACAAAATTAAAATCTAACT
1 TAAACAGGTACAATTTGACAAAATCAAAATCTAACT
38259646 GTTCAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.28
Consensus pattern (38 bp):
TAAACAGGTACAATTTGACAAAATCAAAATCTAACTTC
Found at i:38266276 original size:21 final size:21
Alignment explanation
Indices: 38266252--38266363 Score: 125
Period size: 21 Copynumber: 5.3 Consensus size: 21
38266242 GACTATGTAA
*
38266252 TGCCCCTGAATAGCACTACAG
1 TGCCCCTGAATAGCACTACGG
* *
38266273 TGCCCTTGAATAGTACTACGG
1 TGCCCCTGAATAGCACTACGG
* * *
38266294 TGCCTCTGAATTGCACTATGG
1 TGCCCCTGAATAGCACTACGG
* * *
38266315 TGCCCATGAAAAGCACTACAG
1 TGCCCCTGAATAGCACTACGG
* *
38266336 TGCCCCTGAATTGCACTATGG
1 TGCCCCTGAATAGCACTACGG
38266357 TGCCCCT
1 TGCCCCT
38266364 ATAAATGGAC
Statistics
Matches: 72, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (21 bp):
TGCCCCTGAATAGCACTACGG
Found at i:38266318 original size:42 final size:42
Alignment explanation
Indices: 38266252--38266361 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 42
38266242 GACTATGTAA
* ** * * * *
38266252 TGCCCCTGAATAGCACTACAGTGCCCTTGAATAGTACTACGG
1 TGCCCCTGAATTGCACTATGGTGCCCATGAAAAGCACTACAG
*
38266294 TGCCTCTGAATTGCACTATGGTGCCCATGAAAAGCACTACAG
1 TGCCCCTGAATTGCACTATGGTGCCCATGAAAAGCACTACAG
38266336 TGCCCCTGAATTGCACTATGGTGCCC
1 TGCCCCTGAATTGCACTATGGTGCCC
38266362 CTATAAATGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (42 bp):
TGCCCCTGAATTGCACTATGGTGCCCATGAAAAGCACTACAG
Found at i:38275267 original size:21 final size:21
Alignment explanation
Indices: 38275243--38275286 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
38275233 CTACACGTAG
*
38275243 AAGT-GAAGCTTCTACCGATAC
1 AAGTAGAAG-TTCTACCGAAAC
*
38275264 AAGTATAAGTTCTACCGAAAC
1 AAGTAGAAGTTCTACCGAAAC
38275285 AA
1 AA
38275287 CCAATACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (21 bp):
AAGTAGAAGTTCTACCGAAAC
Found at i:38275973 original size:24 final size:24
Alignment explanation
Indices: 38275940--38276167 Score: 296
Period size: 24 Copynumber: 9.5 Consensus size: 24
38275930 ACAACAACCC
*
38275940 ATATATGTTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
*
38275964 ATATTCGTTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
38275988 ATATACGTTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
*
38276012 ATATATGTTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
** * *
38276036 GCACACATTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
*
38276060 ATATACGTTTACGCTCGTCAACTT
1 ATATACGTTTACGCTCGTCAGCTT
* * *
38276084 -TCACACATTTACGCTCGTCAACTT
1 AT-ATACGTTTACGCTCGTCAGCTT
* *
38276108 ATATATGTTTACACTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
** *
38276132 GCACACGTTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
38276156 ATATACGTTTAC
1 ATATACGTTTAC
38276168 AATATTCATA
Statistics
Matches: 173, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
23 1 0.01
24 171 0.99
25 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (24 bp):
ATATACGTTTACGCTCGTCAGCTT
Found at i:38276168 original size:48 final size:48
Alignment explanation
Indices: 38275946--38276167 Score: 336
Period size: 48 Copynumber: 4.6 Consensus size: 48
38275936 ACCCATATAT
* ** *
38275946 GTTTACGCTCGTCAGCTTATATTCGTTTACGCTCGTCAGCTTATATAC
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACAC
*
38275994 GTTTACGCTCGTCAGCTTATATATGTTTACGCTCGTCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACAC
* * *
38276042 ATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAACTTTCACAC
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACAC
* * * *
38276090 ATTTACGCTCGTCAACTTATATATGTTTACACTCGTCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACAC
38276138 GTTTACGCTCGTCAGCTTATATACGTTTAC
1 GTTTACGCTCGTCAGCTTATATACGTTTAC
38276168 AATATTCATA
Statistics
Matches: 157, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 157 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (48 bp):
GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACAC
Found at i:38277977 original size:34 final size:33
Alignment explanation
Indices: 38277933--38277996 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
38277923 TTTTTAAACA
38277933 GTTACAATTTGACAAAATCAGAATCTAGGTTCTT
1 GTTACAATTTGACAAAATCAGAATCT-GGTTCTT
* * *
38277967 GTTACCATTTGATAAAATTAGAATCTGGTT
1 GTTACAATTTGACAAAATCAGAATCTGGTT
38277997 GTTGAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (33 bp):
GTTACAATTTGACAAAATCAGAATCTGGTTCTT
Found at i:38280706 original size:21 final size:21
Alignment explanation
Indices: 38280681--38280777 Score: 169
Period size: 21 Copynumber: 4.7 Consensus size: 21
38280671 CCAAGAAAAC
*
38280681 AAACAGAACACATAAAAAATG
1 AAACAGAACACATAACAAATG
38280702 AAACAGAACACATAACAAATG
1 AAACAGAACACATAACAAATG
38280723 AAACAGAACACATAACAAATG
1 AAACAGAACACATAACAAATG
*
38280744 AAACAGAATACATAACAAATG
1 AAACAGAACACATAACAAATG
38280765 AAACAG-ACACATA
1 AAACAGAACACATA
38280778 TTTATTGACA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
20 6 0.08
21 67 0.92
ACGTcount: A:0.63, C:0.18, G:0.09, T:0.10
Consensus pattern (21 bp):
AAACAGAACACATAACAAATG
Found at i:38281673 original size:33 final size:33
Alignment explanation
Indices: 38281612--38281680 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
38281602 GGATTTAAGA
**
38281612 TTTGAGTTTGGGTTTAGTGTTTAGGGTTCGAGG
1 TTTGAGTTTGGGTTTAAAGTTTAGGGTTCGAGG
*
38281645 TTTGAGTTTGGGTTTAAAGTTT-GTGGTTCGTGG
1 TTTGAGTTTGGGTTTAAAGTTTAG-GGTTCGAGG
38281678 TTT
1 TTT
38281681 AAAGTTTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.12, C:0.03, G:0.36, T:0.49
Consensus pattern (33 bp):
TTTGAGTTTGGGTTTAAAGTTTAGGGTTCGAGG
Found at i:38281726 original size:20 final size:21
Alignment explanation
Indices: 38281703--38281747 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
38281693 TTAAGGTTCG
38281703 GGGTTTAATGGTTGG-GTTTA
1 GGGTTTAATGGTTGGTGTTTA
* *
38281723 GGG-TTCATGTTTGGTGTTTA
1 GGGTTTAATGGTTGGTGTTTA
38281743 GGGTT
1 GGGTT
38281748 CGAGGTTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 9 0.43
20 11 0.52
21 1 0.05
ACGTcount: A:0.11, C:0.02, G:0.40, T:0.47
Consensus pattern (21 bp):
GGGTTTAATGGTTGGTGTTTA
Found at i:38282913 original size:18 final size:20
Alignment explanation
Indices: 38282858--38282924 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 20
38282848 TAAAAAATAA
38282858 TCAAAATAA-TTATTCAAAAAT
1 TCAAAATAATTTA-T-AAAAAT
* *
38282879 TGAAAATAATTT-TTAAAAT
1 TCAAAATAATTTATAAAAAT
38282898 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTTATAAAAAT
38282917 TCTAAAAT
1 TC-AAAAT
38282925 TTGTATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.10
19 19 0.49
20 6 0.15
21 8 0.21
22 2 0.05
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.37
Consensus pattern (20 bp):
TCAAAATAATTTATAAAAAT
Found at i:38303616 original size:16 final size:18
Alignment explanation
Indices: 38303590--38303623 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
38303580 TATTATTTAT
38303590 TAAATTAATTTTC-CAAC
1 TAAATTAATTTTCTCAAC
38303607 TAAA-TAATTTTCTCAAC
1 TAAATTAATTTTCTCAAC
38303624 CCAAGTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAC
Found at i:38306231 original size:21 final size:21
Alignment explanation
Indices: 38306207--38306246 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38306197 ACTGTTGGAA
*
38306207 GAGGAAGAGGAGGAGGAAGTG
1 GAGGAAGAAGAGGAGGAAGTG
38306228 GAGGAAGAAGAGGAGGAAG
1 GAGGAAGAAGAGGAGGAAG
38306247 AGTCGGAGTA
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:0.42, C:0.00, G:0.55, T:0.03
Consensus pattern (21 bp):
GAGGAAGAAGAGGAGGAAGTG
Found at i:38306245 original size:12 final size:12
Alignment explanation
Indices: 38306210--38306247 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
38306200 GTTGGAAGAG
*
38306210 GAAGAGGAGGAG
1 GAAGAGGAGGAA
*
38306222 GAAGTGGAGGAA
1 GAAGAGGAGGAA
38306234 GAAGAGGAGGAA
1 GAAGAGGAGGAA
38306246 GA
1 GA
38306248 GTCGGAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.53, T:0.03
Consensus pattern (12 bp):
GAAGAGGAGGAA
Found at i:38311826 original size:15 final size:15
Alignment explanation
Indices: 38311808--38311854 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
38311798 ATTTTTTGAA
38311808 TTATTTATATTAATT
1 TTATTTATATTAATT
* * *
38311823 TTATTGATGTGAATT
1 TTATTTATATTAATT
38311838 TTATTTATTATT-ATT
1 TTATTTA-TATTAATT
38311853 TT
1 TT
38311855 TTGTTTTTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
TTATTTATATTAATT
Found at i:38311942 original size:28 final size:28
Alignment explanation
Indices: 38311899--38311953 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
38311889 GTTTAGAAGG
* *
38311899 TATTTTTAGATGGTGATATAAAACATAA
1 TATTTTTAGATAGTGAGATAAAACATAA
* *
38311927 TATTTTTAGGTAGTGAGATAAAGCATA
1 TATTTTTAGATAGTGAGATAAAACATA
38311954 TTTAGGCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (28 bp):
TATTTTTAGATAGTGAGATAAAACATAA
Found at i:38312769 original size:28 final size:28
Alignment explanation
Indices: 38312738--38312792 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
38312728 ATTTAAAAGG
*
38312738 TATTTTTAGATGGTGAGATAAAACATAA
1 TATTTTTAGATAGTGAGATAAAACATAA
*
38312766 TATTTTTAGGTAGTGAGATAAAACATA
1 TATTTTTAGATAGTGAGATAAAACATA
38312793 TTTAGGCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (28 bp):
TATTTTTAGATAGTGAGATAAAACATAA
Found at i:38319333 original size:26 final size:26
Alignment explanation
Indices: 38319282--38319333 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
38319272 TTCTATGGTT
* *
38319282 TAGAAAATTCTAAAAAGATATGAAAA
1 TAGAAAATTCTAAAAAAATATCAAAA
38319308 TAGAAAATTCTAATAAAAAT-TCAAAA
1 TAGAAAATTCTAA-AAAAATATCAAAA
38319334 GTCAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.25
Consensus pattern (26 bp):
TAGAAAATTCTAAAAAAATATCAAAA
Found at i:38327508 original size:18 final size:17
Alignment explanation
Indices: 38327476--38327521 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
38327466 AAAATTTAAA
*
38327476 AATATTTTTATAATTCTTT
1 AATA-TTTTAAAATT-TTT
38327495 AATATTTTAAAATTTTT
1 AATATTTTAAAATTTTT
38327512 AATAATTTTA
1 AAT-ATTTTA
38327522 TTTTTTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 4 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
AATATTTTAAAATTTTT
Found at i:38328849 original size:26 final size:27
Alignment explanation
Indices: 38328820--38328870 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
38328810 TAGTATTCAA
* *
38328820 TTATCACTTTGATA-TTTAATTTTTTT
1 TTATCAATTTGATACTTTAAATTTTTT
38328846 TTATCAATTTGATACTTTAAATTTT
1 TTATCAATTTGATACTTTAAATTTT
38328871 CAATCCGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (27 bp):
TTATCAATTTGATACTTTAAATTTTTT
Found at i:38333770 original size:14 final size:14
Alignment explanation
Indices: 38333751--38333779 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38333741 ATAATGGATT
38333751 GCATGCTCAGACAA
1 GCATGCTCAGACAA
38333765 GCATGCTCAGACAA
1 GCATGCTCAGACAA
38333779 G
1 G
38333780 GAATCTTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.24, T:0.14
Consensus pattern (14 bp):
GCATGCTCAGACAA
Found at i:38347130 original size:2 final size:2
Alignment explanation
Indices: 38347123--38347167 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
38347113 AGTTTATTCA
38347123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38347165 AT A
1 AT A
38347168 AGTATATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38347365 original size:28 final size:28
Alignment explanation
Indices: 38347334--38347395 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
38347324 AAATTCTTGG
* *
38347334 TTTTTTATAAAATT-ATATATTTTTCTAA
1 TTTTTTAAAAAATTGAGAT-TTTTTCTAA
* *
38347362 TTTTTGAAAAAATTGAGATTTTTTTTAA
1 TTTTTTAAAAAATTGAGATTTTTTCTAA
38347390 TTTTTT
1 TTTTTT
38347396 TTGGAAAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTTTAAAAAATTGAGATTTTTTCTAA
Found at i:38349458 original size:28 final size:28
Alignment explanation
Indices: 38349427--38349516 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
38349417 AAAGTTCAGG
38349427 TAGAGCTATGATCTACTTACGTCTCGTT
1 TAGAGCTATGATCTACTTACGTCTCGTT
* * **
38349455 TAGAGC-ATAATGCCA-TGTACAG-CTCGGG
1 TAGAGCTATGAT-CTACT-TAC-GTCTCGTT
* * *
38349483 TAGAGCTATGATCTGCTTACATCTCTTT
1 TAGAGCTATGATCTACTTACGTCTCGTT
38349511 TAGAGC
1 TAGAGC
38349517 GTAATACCAT
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
27 5 0.11
28 34 0.76
29 6 0.13
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (28 bp):
TAGAGCTATGATCTACTTACGTCTCGTT
Found at i:38349458 original size:56 final size:56
Alignment explanation
Indices: 38349365--38349685 Score: 365
Period size: 56 Copynumber: 5.7 Consensus size: 56
38349355 TGAAGGACAG
* * *
38349365 CTCGAGTAGAGCTATGATTTACTTACGTCTCGGTTAGAGCGTAATGCCATGTA-AA
1 CTCGGGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCGTAATGCCATGTACAA
* * * * * *
38349420 GTTCAGGTAGAGCTATGATCTACTTACGTCTCGTTTAGAGCATAATGCCATGTACAG
1 -CTCGGGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCGTAATGCCATGTACAA
* ** *
38349477 CTCGGGTAGAGCTATGATCTGCTTACATCTCTTTTAGAGCGTAATACCATGTACAA
1 CTCGGGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCGTAATGCCATGTACAA
* *
38349533 CTCGGGTAGAGCTATGATCTGTTTACGTCTTGGTTAGAGCGTAATGCCATGTACAA
1 CTCGGGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCGTAATGCCATGTACAA
* * * * * * * *
38349589 CTCGGGTAAAGCTATAACCTGCTTACATCTTGATTAGAGCATAATGCCATGCACAA
1 CTCGGGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCGTAATGCCATGTACAA
** * * * *
38349645 CTCAAGTAGAGCTATGTTTTTCTTATGTCTCGGTTAGAGCG
1 CTCGGGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCG
38349686 CAAGGTTATG
Statistics
Matches: 222, Mismatches: 42, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
56 221 1.00
57 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (56 bp):
CTCGGGTAGAGCTATGATCTGCTTACGTCTCGGTTAGAGCGTAATGCCATGTACAA
Found at i:38349542 original size:28 final size:28
Alignment explanation
Indices: 38349511--38349596 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
38349501 ACATCTCTTT
38349511 TAGAGCGTAATACCATGTACAACTCGGG
1 TAGAGCGTAATACCATGTACAACTCGGG
* ** * *
38349539 TAGAGC-T-ATGATC-TGTTTACGTCTTGGT
1 TAGAGCGTAAT-ACCATG--TACAACTCGGG
*
38349567 TAGAGCGTAATGCCATGTACAACTCGGG
1 TAGAGCGTAATACCATGTACAACTCGGG
38349595 TA
1 TA
38349597 AAGCTATAAC
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 28 0.68
29 2 0.05
30 4 0.10
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (28 bp):
TAGAGCGTAATACCATGTACAACTCGGG
Found at i:38352123 original size:14 final size:13
Alignment explanation
Indices: 38352099--38352146 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
38352089 TCAAATGTAC
38352099 AATATAATTAAAT
1 AATATAATTAAAT
38352112 AATATAAATTAAAT
1 AATAT-AATTAAAT
38352126 --TA-AATTAAAT
1 AATATAATTAAAT
*
38352136 AATTTAATTAA
1 AATATAATTAA
38352147 TATTTACCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 8 0.27
12 3 0.10
13 11 0.37
14 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATAATTAAAT
Found at i:38352137 original size:19 final size:18
Alignment explanation
Indices: 38352104--38352146 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
38352094 TGTACAATAT
38352104 AATTAAATAATATAAATTA
1 AATTAAATAATAT-AATTA
*
38352123 AATTAAATTAA-ATAATTT
1 AATTAAA-TAATATAATTA
38352141 AATTAA
1 AATTAA
38352147 TATTTACCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTAAATAATATAATTA
Found at i:38352732 original size:22 final size:22
Alignment explanation
Indices: 38352707--38352774 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
38352697 TATCACCAAA
38352707 TATTAAAATTAAAAGATAAAAT
1 TATTAAAATTAAAAGATAAAAT
* *
38352729 TATTAAAATTAACAGATACAAT
1 TATTAAAATTAAAAGATAAAAT
38352751 TATTAAAATTAAAAGATAAAAT
1 TATTAAAATTAAAAGATAAAAT
38352773 TA
1 TA
38352775 ACAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (22 bp):
TATTAAAATTAAAAGATAAAAT
Found at i:38360821 original size:18 final size:18
Alignment explanation
Indices: 38360798--38360837 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38360788 CATAGATAAT
**
38360798 ATGCGATCACATGATCAG
1 ATGCGATCACAAAATCAG
38360816 ATGCGATCACAAAATCAG
1 ATGCGATCACAAAATCAG
38360834 ATGC
1 ATGC
38360838 ATTCATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (18 bp):
ATGCGATCACAAAATCAG
Found at i:38384357 original size:24 final size:24
Alignment explanation
Indices: 38384321--38384388 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
38384311 CTAGACAACT
**
38384321 TTAGCTCACACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
38384345 TTAGCTCTTACGAGCCTACAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
38384369 TTAGCTCTTACGAGCCCAGA
1 TTAGCTCTTACGAGCCCAGA
38384389 CAGAGTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:38392453 original size:17 final size:17
Alignment explanation
Indices: 38392430--38392477 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
38392420 CGATCTTCAT
38392430 CAATGTTGGCTATTCCA
1 CAATGTTGGCTATTCCA
* *
38392447 TAATGTT-G-AAGTTCCA
1 CAATGTTGGCTA-TTCCA
38392463 CAATGTTGGCTATTC
1 CAATGTTGGCTATTC
38392478 ACGATTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
15 1 0.04
16 12 0.50
17 10 0.42
18 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (17 bp):
CAATGTTGGCTATTCCA
Found at i:38402759 original size:25 final size:25
Alignment explanation
Indices: 38402708--38402759 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
38402698 CATTAATTAC
* *
38402708 ATTAATTAAAAATATAACGTTTAAA
1 ATTAATTAAAAATATAACATGTAAA
*
38402733 ATTAATTAAAAAT-TAAACATGTGAA
1 ATTAATTAAAAATAT-AACATGTAAA
38402758 AT
1 AT
38402760 CAAATACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (25 bp):
ATTAATTAAAAATATAACATGTAAA
Found at i:38402844 original size:2 final size:2
Alignment explanation
Indices: 38402837--38402868 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38402827 ATTTAATCTC
38402837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38402869 GAACAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38403913 original size:11 final size:11
Alignment explanation
Indices: 38403899--38403923 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38403889 TTTATTTTAG
38403899 AATTATAAAAA
1 AATTATAAAAA
38403910 AATTATAAAAA
1 AATTATAAAAA
38403921 AAT
1 AAT
38403924 AAATAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATTATAAAAA
Found at i:38404248 original size:10 final size:9
Alignment explanation
Indices: 38404228--38404345 Score: 50
Period size: 9 Copynumber: 13.1 Consensus size: 9
38404218 AATAAATTAT
38404228 TTTTATAAA
1 TTTTATAAA
38404237 TTTTATAGAA
1 TTTTATA-AA
38404247 -TTTAT-AA
1 TTTTATAAA
*
38404254 TTTTAATGAA
1 TTTT-ATAAA
38404264 TTTT-TAATAA
1 TTTTAT-A-AA
38404274 TTTTATAAAA
1 TTTTAT-AAA
* ***
38404284 TTTAATTGT
1 TTTTATAAA
38404293 TTTTAT-AA
1 TTTTATAAA
*
38404301 TTTTAATGAA
1 TTTT-ATAAA
*
38404311 TTTTATAAT
1 TTTTATAAA
* **
38404320 TTTTTTATT
1 TTTTATAAA
38404329 TTTTAT-AA
1 TTTTATAAA
38404337 TTTTA-AAA
1 TTTTATAAA
38404345 T
1 T
38404346 GCATTTAGAC
Statistics
Matches: 84, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
7 2 0.02
8 16 0.19
9 36 0.43
10 27 0.32
11 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTATAAA
Found at i:38404285 original size:47 final size:44
Alignment explanation
Indices: 38404228--38404322 Score: 127
Period size: 47 Copynumber: 2.1 Consensus size: 44
38404218 AATAAATTAT
*
38404228 TTTTATAAATTTTATAGAATTTATAATTTTAATGAATTTTTAATAA
1 TTTTATAAATTTAATAGAATTTATAATTTTAATGAA-TTTT-ATAA
* **
38404274 TTTTATAAAATTTAATTGTTTTTATAATTTTAATGAATTTTATAA
1 TTTTAT-AAATTTAATAGAATTTATAATTTTAATGAATTTTATAA
38404319 TTTT
1 TTTT
38404323 TTTATTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
45 8 0.18
46 10 0.23
47 26 0.59
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (44 bp):
TTTTATAAATTTAATAGAATTTATAATTTTAATGAATTTTATAA
Found at i:38404303 original size:37 final size:38
Alignment explanation
Indices: 38404226--38404318 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 38
38404216 ATAATAAATT
*
38404226 ATTTTT-ATAAATTTTATAGAATTTATAATTTTAATGA
1 ATTTTTAATAAATTTTATAAAATTTATAATTTTAATGA
** *
38404263 ATTTTTAAT-AATTTTATAAAATTTAATTGTTTTTAT-A
1 ATTTTTAATAAATTTTATAAAATTT-ATAATTTTAATGA
*
38404300 A-TTTTAATGAATTTTATAA
1 ATTTTTAATAAATTTTATAA
38404319 TTTTTTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 7 0.14
37 32 0.65
38 10 0.20
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (38 bp):
ATTTTTAATAAATTTTATAAAATTTATAATTTTAATGA
Found at i:38404319 original size:18 final size:17
Alignment explanation
Indices: 38404235--38404342 Score: 74
Period size: 18 Copynumber: 5.9 Consensus size: 17
38404225 TATTTTTATA
*
38404235 AATTTTATAGAATTT-AT
1 AATTTTATA-ATTTTAAT
38404252 AATTTTAATGAATTTTTAAT
1 AATTTT-AT-AA-TTTTAAT
*
38404272 AATTTTATAAAATTTAATT
1 AATTTTAT-AATTTTAA-T
**
38404291 GTTTTTATAATTTTAAT
1 AATTTTATAATTTTAAT
**
38404308 GAATTTTATAATTTTTTT
1 -AATTTTATAATTTTAAT
*
38404326 ATTTTTTATAATTTTAA
1 A-ATTTTATAATTTTAA
38404343 AATGCATTTA
Statistics
Matches: 71, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
17 8 0.11
18 40 0.56
19 15 0.21
20 8 0.11
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (17 bp):
AATTTTATAATTTTAAT
Found at i:38404882 original size:18 final size:18
Alignment explanation
Indices: 38404861--38404940 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
38404851 TAATATTATA
38404861 AAAAATTATAAAATTTTT
1 AAAAATTATAAAATTTTT
* *
38404879 AAAAATTGTTAAAA-TATT
1 AAAAATT-ATAAAATTTTT
* * *
38404897 AAAATTCTTTAAAAATTCTT
1 AAAAAT-TAT-AAAATTTTT
*
38404917 AAAATATTA-AAAAGTTTT
1 AAAA-ATTATAAAATTTTT
38404935 AAAAAT
1 AAAAAT
38404941 ATCAAAACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
17 2 0.04
18 28 0.57
19 10 0.20
20 8 0.16
21 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAAATTATAAAATTTTT
Found at i:38404883 original size:10 final size:10
Alignment explanation
Indices: 38404870--38404940 Score: 53
Period size: 10 Copynumber: 7.5 Consensus size: 10
38404860 AAAAAATTAT
38404870 AAAATTTTTA
1 AAAATTTTTA
*
38404880 AAAATTGTT-
1 AAAATTTTTA
*
38404889 AAAA-TATT-
1 AAAATTTTTA
38404897 AAAATTCTTTA
1 AAAATT-TTTA
*
38404908 AAAATTCTT-
1 AAAATTTTTA
*
38404917 AAAA-TATTA
1 AAAATTTTTA
*
38404926 AAAAGTTTTA
1 AAAATTTTTA
38404936 AAAAT
1 AAAAT
38404941 ATCAAAACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 10 0.20
9 13 0.27
10 20 0.41
11 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:38404908 original size:28 final size:27
Alignment explanation
Indices: 38404869--38404940 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 27
38404859 TAAAAAATTA
*
38404869 TAAAATTTTTAAAAATTGTTAAAATAT
1 TAAAATTTTTAAAAATTCTTAAAATAT
38404896 TAAAATTCTTTAAAAATTCTTAAAATAT
1 TAAAATT-TTTAAAAATTCTTAAAATAT
*
38404924 TAAAAAGTTTTAAAAAT
1 T-AAAATTTTTAAAAAT
38404941 ATCAAAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.17
28 29 0.71
29 5 0.12
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (27 bp):
TAAAATTTTTAAAAATTCTTAAAATAT
Found at i:38405312 original size:30 final size:28
Alignment explanation
Indices: 38405278--38405345 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
38405268 TACAATTTTA
* **
38405278 ACTTATTTGATTCTATTTAATTGTATAAAG
1 ACTTATTT-ATTC-ATTGAATAATATAAAG
38405308 ACTTAGTTTATTCATTGAATAATATAAAG
1 ACTTA-TTTATTCATTGAATAATATAAAG
*
38405337 ACTAATTTA
1 ACTTATTTA
38405346 ATCCAATCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.12
29 17 0.52
30 9 0.27
31 3 0.09
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (28 bp):
ACTTATTTATTCATTGAATAATATAAAG
Found at i:38413515 original size:22 final size:22
Alignment explanation
Indices: 38413487--38413537 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
38413477 CAAAATAATC
*
38413487 TATTTTGTTGTTGTTTCATTGT
1 TATTTTGTTGTTGTTTCACTGT
38413509 TATTTTGTTGTTGTTTCACTGT
1 TATTTTGTTGTTGTTTCACTGT
*
38413531 TGTTTTG
1 TATTTTG
38413538 CTACCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.08, C:0.06, G:0.20, T:0.67
Consensus pattern (22 bp):
TATTTTGTTGTTGTTTCACTGT
Found at i:38416850 original size:20 final size:20
Alignment explanation
Indices: 38416827--38416865 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38416817 TATTCAAACT
*
38416827 ATATTACTTGAATAATTATA
1 ATATTACATGAATAATTATA
*
38416847 ATATTAGATGAATAATTAT
1 ATATTACATGAATAATTAT
38416866 GTCTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (20 bp):
ATATTACATGAATAATTATA
Found at i:38420641 original size:39 final size:40
Alignment explanation
Indices: 38420582--38420659 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 40
38420572 GAGAATTACT
38420582 AATTGTAAGTAAATGTCAACTTACCTGAGGAAGAAGTGAG
1 AATTGTAAGTAAATGTCAACTTACCTGAGGAAGAAGTGAG
38420622 AATT-TAAGTAAATGTCAACTTACCTGAGGAAGAAGTGA
1 AATTGTAAGTAAATGTCAACTTACCTGAGGAAGAAGTGA
38420660 ACCCATCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (40 bp):
AATTGTAAGTAAATGTCAACTTACCTGAGGAAGAAGTGAG
Found at i:38436023 original size:21 final size:21
Alignment explanation
Indices: 38435999--38436044 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
38435989 AGCATGTAAG
38435999 GTTTTTACAATGGATCAACCA
1 GTTTTTACAATGGATCAACCA
38436020 GTTTTTACAATGGATCAACCA
1 GTTTTTACAATGGATCAACCA
38436041 GTTT
1 GTTT
38436045 CAGCCCCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
GTTTTTACAATGGATCAACCA
Found at i:38438431 original size:14 final size:14
Alignment explanation
Indices: 38438412--38438442 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38438402 TTTTCAAGCA
*
38438412 TGTGATATTATTTG
1 TGTGATATTAGTTG
38438426 TGTGATATTAGTTG
1 TGTGATATTAGTTG
38438440 TGT
1 TGT
38438443 AAGTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (14 bp):
TGTGATATTAGTTG
Found at i:38440234 original size:20 final size:20
Alignment explanation
Indices: 38440209--38440248 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38440199 ATCTTCGTTG
38440209 ATTCTTTAGCATAAGTAGAC
1 ATTCTTTAGCATAAGTAGAC
38440229 ATTCTTTAGCATAAGTAGAC
1 ATTCTTTAGCATAAGTAGAC
38440249 CTAACTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
ATTCTTTAGCATAAGTAGAC
Found at i:38440588 original size:20 final size:20
Alignment explanation
Indices: 38440546--38440588 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
38440536 ATTAATTCTA
**
38440546 TTAAACAATAAATGATATTT
1 TTAAACAATAAATGATAACT
* *
38440566 TTAAATAATAAATGTTAACT
1 TTAAACAATAAATGATAACT
38440586 TTA
1 TTA
38440589 TTTCAATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
TTAAACAATAAATGATAACT
Found at i:38448705 original size:19 final size:19
Alignment explanation
Indices: 38448681--38448720 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
38448671 CGAGATATGT
38448681 ATTAATATTATGAATTAAA
1 ATTAATATTATGAATTAAA
*
38448700 ATTAATATTATTAATTAAA
1 ATTAATATTATGAATTAAA
38448719 AT
1 AT
38448721 AATTAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTAATATTATGAATTAAA
Found at i:38463252 original size:15 final size:15
Alignment explanation
Indices: 38463218--38463251 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
38463208 GAGAAAATCG
38463218 AAAAATAATTTAAAT
1 AAAAATAATTTAAAT
*
38463233 TAAAAT-ATTTAAAT
1 AAAAATAATTTAAAT
38463247 AAAAA
1 AAAAA
38463252 AATGAATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAATAATTTAAAT
Found at i:38463590 original size:21 final size:22
Alignment explanation
Indices: 38463553--38463593 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38463543 AGGGCCAAAT
*
38463553 TTAAATTTTGGAATGTTGGAGG
1 TTAAATTTTGAAATGTTGGAGG
38463575 TTAAATTTT-AAATGTTGGA
1 TTAAATTTTGAAATGTTGGA
38463594 AAGTTTAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (22 bp):
TTAAATTTTGAAATGTTGGAGG
Found at i:38463609 original size:30 final size:29
Alignment explanation
Indices: 38463497--38463604 Score: 114
Period size: 29 Copynumber: 3.7 Consensus size: 29
38463487 GTTAAAAATG
* *
38463497 AAATTTTGGAAAGTTTGGGGGCCAAATTC
1 AAATTTTGGAAAGTTTAGGGGCCAAATTT
38463526 AAATTTTTGGAAAGTTTA-GGGCCAAATTT
1 AAA-TTTTGGAAAGTTTAGGGGCCAAATTT
* **
38463555 AAATTTTGGAATG-TT-GGAGGTTAAATTTT
1 AAATTTTGGAAAGTTTAGG-GGCCAAA-TTT
*
38463584 AAATGTTGGAAAGTTTAGGGG
1 AAATTTTGGAAAGTTTAGGGG
38463605 TTAAAATATG
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.05
28 14 0.21
29 30 0.45
30 17 0.26
31 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (29 bp):
AAATTTTGGAAAGTTTAGGGGCCAAATTT
Found at i:38464346 original size:16 final size:16
Alignment explanation
Indices: 38464321--38464356 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
38464311 TTTCCGAAAT
*
38464321 AAAT-AATAAAAATAA
1 AAATAAATAAAAACAA
38464336 AAATAAATAAAAACAA
1 AAATAAATAAAAACAA
38464352 AAATA
1 AAATA
38464357 TATACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAATAAATAAAAACAA
Found at i:38465627 original size:123 final size:122
Alignment explanation
Indices: 38465393--38465980 Score: 771
Period size: 123 Copynumber: 4.8 Consensus size: 122
38465383 CCGACATCTT
* *
38465393 TGTATCTCATCAGGAAGATGGAGTTTGAAGTTTCACTCACATTGAGCTCCACTTCGTTGATTTGG
1 TGTATCTCATCAGGAAGATGG-GTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGATTTGG
* * ** * * * *
38465458 TCCTCTTCTCTATATCTCATCAAAAAGATGATCGCTTCATTGTTTTGACCCACTTCTC
65 TCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACTTCTC
* ** * *
38465516 TGTATCTCATCAGGAAGATAGGGTTTGAAGTTTTACTCGTATTGAGCTTCGCTTCATTGTTTTGG
1 TGTATCTCATCAGGAAGAT-GGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGATTTGG
*** *
38465581 TGTTCTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACTTCTC
65 TCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACTTCTC
* * * * * * *
38465639 TTTATCTCATCAGGAAAATGGGGTTTAAAGTTTCATTCGCATTGAGCTCTGCTTCATTAATTTGG
1 TGTATCTCATCAGGAAGAT-GGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGATTTGG
* * * *
38465704 TCCACTTCTTTGTATCTCATCAGGAAGATGACCGCTTTATCATTTTGATCCACTTCTC
65 TCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACTTCTC
* *
38465762 TGTATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTCCGCTTCATTGATTTG
1 TGTATCTCATCAGGAAGAT--GGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGATTTG
* * * *
38465827 GTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTTATTGTTTTGACCCACTTCTT
64 GTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACTTCTC
**
38465886 TGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTTGTTGATTTGG
1 TGTATCTCATCAGGAAGATG-GGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGATTTGG
*
38465951 TCCACTTCTCTGTATCTCATCAAGAAGATG
65 TCCACTTCTCTGTATCTCATCAGGAAGATG
38465981 GGGTTTGAAG
Statistics
Matches: 404, Mismatches: 58, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
122 1 0.00
123 293 0.73
124 110 0.27
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (122 bp):
TGTATCTCATCAGGAAGATGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGATTTGGT
CCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACTTCTC
Found at i:38465900 original size:247 final size:246
Alignment explanation
Indices: 38465389--38465980 Score: 862
Period size: 247 Copynumber: 2.4 Consensus size: 246
38465379 TTGGCCGACA
* *
38465389 TCTTTGTATCTCATCAGGAAGATGGAGTTTGAAGTTTCACTCACATTGAGCTCCACTTCGTTGAT
1 TCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCGTTGAT
* * * * **
38465454 TTGGTCCTCTTCTCTATATCTCATCAAAAAGATGATCGCTTCATTGTTTTGACCCACTTCTCTGT
66 TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATCATTTTGACCCACTTCTCTGT
* ** * * * *
38465519 ATCTCATCAGGAAGATAGGGTTTGAAGTTTTACTCGTATTGAGCTTCGCTTCATTGTTTTGGTGT
131 ATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTAAGCTCCGCTTCATTGATTTGGTCT
* * *
38465584 TCTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACT
196 ACTTCTCTATATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACT
* * * * * * *
38465635 TCTCTT-TATCTCATCAGGAAAATGGGGTTTAAAGTTTCATTCGCATTGAGCTCTGCTTCATTAA
1 TCT-TTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCGTTGA
* * * *
38465699 TTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCGCTTTATCATTTTGATCCACTTCTCTG
65 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATCATTTTGACCCACTTCTCTG
*
38465764 TATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTCCGCTTCATTGATTTGGT
130 TATCTCATCAGGAAGATA-GGGTTTGAAGTTTCACTCACATTAAGCTCCGCTTCATTGATTTGGT
*
38465829 CTACTTCTCTATATCTCATCAGGAAGATGACCACTTTATTGTTTTGACCCACT
194 CTACTTCTCTATATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACT
* *
38465882 TCTTTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTTGTTGAT
1 TCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCGTTGAT
38465947 TTGGTCCACTTCTCTGTATCTCATCAAGAAGATG
66 TTGGTCCACTTCTCTGTATCTCATCAAGAAGATG
38465981 GGGTTTGAAG
Statistics
Matches: 301, Mismatches: 42, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
246 126 0.42
247 175 0.58
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (246 bp):
TCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCGTTGAT
TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATCATTTTGACCCACTTCTCTGT
ATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTAAGCTCCGCTTCATTGATTTGGTCT
ACTTCTCTATATCTCATCAGGAAGATGACCACTTTATTATTTTGACCCACT
Found at i:38466005 original size:75 final size:75
Alignment explanation
Indices: 38465877--38466056 Score: 306
Period size: 75 Copynumber: 2.4 Consensus size: 75
38465867 TTGTTTTGAC
* * *
38465877 CCACTTCTTTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTTG
1 CCACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
38465942 TTGATTTGGT
66 TTGATTTGGT
* *
38465952 CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTCCGCTTCG
1 CCACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
38466017 TTGATTTGGT
66 TTGATTTGGT
*
38466027 CTACTTCTCTGTATCTCATCAAGAAGATGA
1 CCACTTCTCTGTATCTCATCAAGAAGATGA
38466057 CTGCTTCATT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 98 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (75 bp):
CCACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
TTGATTTGGT
Found at i:38466034 original size:198 final size:198
Alignment explanation
Indices: 38465747--38466178 Score: 650
Period size: 198 Copynumber: 2.2 Consensus size: 198
38465737 GCTTTATCAT
* *
38465747 TTTGATCCACTTCTCTGTATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTC
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCACATTAAGCTC
* * *
38465812 CGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTTATTGTTTTGA-
65 CGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACTTCATTATTTTGAT
* * * * *
38465876 CCCACTTCTTTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTT
130 CCC-CTTCTCTGTACCTCATCAGGAAGATGAGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTC
38465941 GTTGA
194 GTTGA
* * *
38465946 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTCC
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTAAGCTCC
* * **
38466011 GCTTCGTTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACTGCTTCATTATTTTGATC
66 GCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACTTCATTATTTTGATC
* * *
38466076 CCTTTCTCTGTACCTTATCAGGAAGATGGGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCGT
131 CCCTTCTCTGTACCTCATCAGGAAGATGAGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCGT
38466141 TGA
196 TGA
*
38466144 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATG
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATG
38466179 ACTGCTTCAT
Statistics
Matches: 210, Mismatches: 22, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
198 176 0.84
199 34 0.16
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (198 bp):
TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTAAGCTCC
GCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACTTCATTATTTTGATC
CCCTTCTCTGTACCTCATCAGGAAGATGAGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCGT
TGA
Found at i:38466268 original size:245 final size:245
Alignment explanation
Indices: 38465952--38466421 Score: 712
Period size: 245 Copynumber: 1.9 Consensus size: 245
38465942 TTGATTTGGT
* *
38465952 CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTCCGCTTCG
1 CCACTTCTCTGTAACTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
* * *
38466017 TTGATTTGG-TCTACTTCTCTGTATCTCATCAAGAAGATGACTGCTTCATTATTTTGATCCC-TT
66 TTGATTTGGTTC-ACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTATTTT-AACCCACT
* * *
38466080 TCTCTGTACCTTATCAGGAAGATGGGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCGTTGAT
129 TCTCTGTACCTCATCAGGAAGAT-AGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCATTGAT
38466145 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGTTTTGAC
193 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGTTTTGAC
* * *
38466198 CCACTTTTCTGTAACTCATCAAGAAGAT-GGGTTTGAAGTTTCACTCGCATTGAGCTCCGCTTCT
1 CCACTTCTCTGTAACTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
*
38466262 TTGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAACCCACTTC
66 TTGATTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTATTTTAACCCACTTC
* * ** *
38466327 TCTGTATCTCATCAGGAAGATAGGTTTGAAGTTTCACTCGTATTGAGCTCCGCTTCATTGATTTG
131 TCTGTACCTCATCAGGAAGATAGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCATTGATTTG
* * *
38466392 GTTCACTTCTCTGTATCTCATTAGGAAGAT
196 GTCCACTTCTCTATATCTCATCAGGAAGAT
38466422 AAGGTTTGAA
Statistics
Matches: 202, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
244 69 0.34
245 105 0.52
246 28 0.14
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (245 bp):
CCACTTCTCTGTAACTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
TTGATTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTATTTTAACCCACTTC
TCTGTACCTCATCAGGAAGATAGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCATTGATTTG
GTCCACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGTTTTGAC
Found at i:38466287 original size:122 final size:123
Alignment explanation
Indices: 38465952--38466421 Score: 687
Period size: 122 Copynumber: 3.8 Consensus size: 123
38465942 TTGATTTGGT
*
38465952 CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTCCGCTTCG
1 CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
*
38466017 TTGATTTGG-TCTACTTCTCTGTATCTCATCAAGAAGATGACTGCTTCATTATTTTGATC
66 TTGATTTGGTTC-ACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTGA-C
* * * * * *
38466076 CC-TTTCTCTGTACCTTATCAGGAAGATGGGGTTTAAAGTTTCACTCACATTAAGCTCCGCTTCG
1 CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
* * *
38466140 TTGATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGTTTTGAC
66 TTGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTGAC
* * * *
38466198 CCACTTTTCTGTAACTCATCAAGAAGAT-GGGTTTGAAGTTTCACTCGCATTGAGCTCCGCTTCT
1 CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
* *
38466262 TTGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAAC
66 TTGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTGAC
* * ** *
38466320 CCACTTCTCTGTATCTCATCAGGAAGAT-AGGTTTGAAGTTTCACTCGTATTGAGCTCCGCTTCA
1 CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
*
38466384 TTGATTTGGTTCACTTCTCTGTATCTCATTAGGAAGAT
66 TTGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGAT
38466422 AAGGTTTGAA
Statistics
Matches: 312, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
122 183 0.59
123 126 0.40
124 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (123 bp):
CCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCG
TTGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTGAC
Found at i:38466463 original size:75 final size:74
Alignment explanation
Indices: 38466321--38466496 Score: 282
Period size: 75 Copynumber: 2.4 Consensus size: 74
38466311 TATTTTAACC
* *
38466321 CACTTCTCTGTATCTCATCAGGAAGATAGGTTTGAAGTTTCACTCGTATTGAGCTCCGCTTCATT
1 CACTTCTCTGTATCTCATCAGGAAGATAGGTTTGAAGTTTCACTCGCATTGAGCTACGCTTCATT
38466386 GATTTGGTT
66 GATTTGGTT
* *
38466395 CACTTCTCTGTATCTCATTAGGAAGATAAGGTTTGAAGTTTCACTCGCATTGAGTTACGCTTTC-
1 CACTTCTCTGTATCTCATCAGGAAGAT-AGGTTTGAAGTTTCACTCGCATTGAGCTACGC-TTCA
38466459 TTGATTTGGTT
64 TTGATTTGGTT
*
38466470 CTCTTCTCTGTATCTCATCAGGAAGAT
1 CACTTCTCTGTATCTCATCAGGAAGAT
38466497 GACCGCTTCA
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
74 26 0.28
75 65 0.69
76 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (74 bp):
CACTTCTCTGTATCTCATCAGGAAGATAGGTTTGAAGTTTCACTCGCATTGAGCTACGCTTCATT
GATTTGGTT
Found at i:38466675 original size:42 final size:42
Alignment explanation
Indices: 38466628--38466736 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
38466618 TAGGGATGTA
* * *
38466628 AGATTTTCCTTTGCAACTTCAATTTAGCCCTTTAC-ATTTTCG
1 AGATTTACCTTTGCGACTTCAATTTAGCCCTCTACTATTTT-G
* * ***
38466670 AGATTTACCTTTGCGGCTTCAATCTATTTCTCTACTATTTTG
1 AGATTTACCTTTGCGACTTCAATTTAGCCCTCTACTATTTTG
**
38466712 AGATTCGCCTTTGCGACTTCAATTT
1 AGATTTACCTTTGCGACTTCAATTT
38466737 GCTTCATCTT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 49 0.91
43 5 0.09
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (42 bp):
AGATTTACCTTTGCGACTTCAATTTAGCCCTCTACTATTTTG
Found at i:38467004 original size:49 final size:49
Alignment explanation
Indices: 38466766--38467032 Score: 137
Period size: 49 Copynumber: 5.5 Consensus size: 49
38466756 ATATTTGCCA
* * ** *
38466766 TTACGGTC-TCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTTGCTA
1 TTACGG-CATCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTCACTG
* * * ** * * * * * *
38466815 TTGCGACCTTGACCTTTCTCTGCACATCTTTAGGGTTCAAGATTCACCG
1 TTACGGCATCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTCACTG
* ** * ** * * * * * *
38466864 TTACGGCTTCAATC-TGGCTTTCTTATTTCTAAGGTATAAGGTTCGCCG
1 TTACGGCATCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTCACTG
** *
38466912 TTGTGGCCTCAA-CATTTCCCTTCACATCTCTAGGGTACAAGATTCACTG
1 TTACGGCATCAATC-TTTCCCTTCACATCTCTAGGGTACAAGATTCACTG
* * ** **
38466961 TTGCGGCATCAATCTTTTCCTTCACAT-TCCTAGGGTATGAGATTCGTTG
1 TTACGGCATCAATCTTTCCCTTCACATCT-CTAGGGTACAAGATTCACTG
*
38467010 TTACGGCCTCAATCTTTCCCTTC
1 TTACGGCATCAATCTTTCCCTTC
38467033 TCGTCTTTAG
Statistics
Matches: 154, Mismatches: 59, Indels: 10
0.69 0.26 0.04
Matches are distributed among these distances:
47 1 0.01
48 31 0.20
49 121 0.79
50 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (49 bp):
TTACGGCATCAATCTTTCCCTTCACATCTCTAGGGTACAAGATTCACTG
Found at i:38468874 original size:18 final size:20
Alignment explanation
Indices: 38468839--38468884 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
38468829 CCTTGCGGGT
38468839 TTTTTTTTATCATCTTGACC
1 TTTTTTTTATCATCTTGACC
*
38468859 TTTTTTTT-TC-TTTTGACC
1 TTTTTTTTATCATCTTGACC
38468877 TCTTTTTT
1 T-TTTTTT
38468885 GATAACACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
20 8 0.33
ACGTcount: A:0.09, C:0.17, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTTTTATCATCTTGACC
Found at i:38473261 original size:30 final size:29
Alignment explanation
Indices: 38473217--38473293 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
38473207 GTCAAAAACA
38473217 AAATTTTGGAAAGTTTAGGAGCCAAATTC
1 AAATTTTGGAAAGTTTAGGAGCCAAATTC
* * * *
38473246 AAAGTTTTAGAAAGTTAAGGGGTCAAATTC
1 AAA-TTTTGGAAAGTTTAGGAGCCAAATTC
38473276 TAAATTTTGGAAAGTTTA
1 -AAATTTTGGAAAGTTTA
38473294 AAGGTCAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.08
30 34 0.85
31 3 0.08
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (29 bp):
AAATTTTGGAAAGTTTAGGAGCCAAATTC
Found at i:38473300 original size:30 final size:29
Alignment explanation
Indices: 38473217--38473302 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
38473207 GTCAAAAACA
*
38473217 AAATTTTGGAAAGTTT-AGGAGCCAAATTC
1 AAATTTTGGAAAGTTTAAGG-GTCAAATTC
*
38473246 AAAGTTTTAGAAAG-TTAAGGGGTCAAATTC
1 AAA-TTTTGGAAAGTTTAA-GGGTCAAATTC
*
38473276 TAAATTTTGGAAAGTTTAAAGGTCAAA
1 -AAATTTTGGAAAGTTTAAGGGTCAAA
38473303 ATATGATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
29 5 0.10
30 34 0.71
31 9 0.19
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (29 bp):
AAATTTTGGAAAGTTTAAGGGTCAAATTC
Found at i:38479218 original size:16 final size:16
Alignment explanation
Indices: 38479197--38479228 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38479187 AGAAATTTTT
*
38479197 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
38479213 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
38479229 TTTGTAATGA
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:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:38480956 original size:21 final size:21
Alignment explanation
Indices: 38480908--38480959 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
38480898 AGAGTTTTTA
38480908 GTATCGGTAGAAACATTACAT
1 GTATCGGTAGAAACATTACAT
* * *
38480929 GTTTCGGTAGAACTCA-TACTT
1 GTATCGGTAGAA-ACATTACAT
38480950 GTATCGGTAG
1 GTATCGGTAG
38480960 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAACATTACAT
Found at i:38485874 original size:21 final size:21
Alignment explanation
Indices: 38485850--38485889 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38485840 CGGTAGAGGA
* *
38485850 GTCACATGTGTCGGTAGAACT
1 GTCACATATATCGGTAGAACT
*
38485871 GTCACTTATATCGGTAGAA
1 GTCACATATATCGGTAGAA
38485890 ATATGCACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (21 bp):
GTCACATATATCGGTAGAACT
Found at i:38489088 original size:36 final size:36
Alignment explanation
Indices: 38489041--38489141 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 36
38489031 GGTAACAGGC
* *
38489041 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGAATA
*
38489077 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGAATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGAATA
* * *
38489113 AGGATCTTTGGGGTCAATAGGGAGTAAAA
1 ATGACCTTT-GGGTCAACAGGGAGTAAAA
38489142 CGAATAACGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 40 0.69
37 18 0.31
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.22
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAGAATA
Found at i:38489778 original size:92 final size:92
Alignment explanation
Indices: 38489632--38489812 Score: 283
Period size: 92 Copynumber: 2.0 Consensus size: 92
38489622 GGTAGAACTC
* * * **
38489632 ATGCTTGTATCGGTAGAAGTATAGGGTAGAAGAGAGGTTTTTCTCTGACCTGAGTTGTTTCGGTA
1 ATGCTTGTATCAGTAGAAGTATAGGGTAGAAGAGAGGTTGTTCTCAGACCTGAGTTGTTTCAATA
38489697 GTTGTATAACAGGTATCGGTAGTTTAA
66 GTTGTATAACAGGTATCGGTAGTTTAA
*
38489724 ATGCTTGTATCAGTAGAAGTATAGGGTA-AGAGAGAGGTTGTTCTCAGACTTGAGTTGTTTCAAT
1 ATGCTTGTATCAGTAGAAGTATAGGGTAGA-AGAGAGGTTGTTCTCAGACCTGAGTTGTTTCAAT
*
38489788 AGTTGTATTACAGGTATCGGTAGTT
65 AGTTGTATAACAGGTATCGGTAGTT
38489813 CTGTACATTG
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 1 0.01
92 80 0.99
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (92 bp):
ATGCTTGTATCAGTAGAAGTATAGGGTAGAAGAGAGGTTGTTCTCAGACCTGAGTTGTTTCAATA
GTTGTATAACAGGTATCGGTAGTTTAA
Found at i:38489911 original size:116 final size:116
Alignment explanation
Indices: 38489707--38489975 Score: 448
Period size: 116 Copynumber: 2.3 Consensus size: 116
38489697 GTTGTATAAC
* * *
38489707 AGGTATCGGTAGTTTAAATGCTTGTATCAGTAGAAGTATAGGGTAAGAGAGAGGTTGTTCTCAGA
1 AGGTATCGGTAGTTTAAATACTTGTATCGGTAGAAGTATAGGGTAAAAGAGAGGTTGTTCTCAGA
* * *
38489772 CTTGAGTTGTTTCAATAGTTGTATTACAGGTATCGGTAGTTCTGTACATTG
66 CTTGAGTTGTTTCAATAGTTGTATAACAAGTATCGGTAGTTCTATACATTG
*
38489823 AGGTATCGGTAGTTTAAATACTTGTATCGGTAGAAGTATAGGGTAAAAGAGAGGTTGTTCTCTGA
1 AGGTATCGGTAGTTTAAATACTTGTATCGGTAGAAGTATAGGGTAAAAGAGAGGTTGTTCTCAGA
* *
38489888 CTTGAGTTGTTTCAGTAGTTGTATAACAAGTATCGGTAGTTTTATACATTG
66 CTTGAGTTGTTTCAATAGTTGTATAACAAGTATCGGTAGTTCTATACATTG
*
38489939 AGGTATCGATAGTTTAAATACTTGTATCGGTAGAAGT
1 AGGTATCGGTAGTTTAAATACTTGTATCGGTAGAAGT
38489976 TGCAGGGTAG
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 143 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (116 bp):
AGGTATCGGTAGTTTAAATACTTGTATCGGTAGAAGTATAGGGTAAAAGAGAGGTTGTTCTCAGA
CTTGAGTTGTTTCAATAGTTGTATAACAAGTATCGGTAGTTCTATACATTG
Found at i:38490038 original size:21 final size:21
Alignment explanation
Indices: 38490012--38490063 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
38490002 GGAGTTTTTA
38490012 GTATCGGTAGTAGTATAACTT
1 GTATCGGTAGTAGTATAACTT
* * *
38490033 GTATCGGTAGTTGTCTCACTT
1 GTATCGGTAGTAGTATAACTT
*
38490054 GTATCAGTAG
1 GTATCGGTAG
38490064 AACTGTCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (21 bp):
GTATCGGTAGTAGTATAACTT
Found at i:38492319 original size:24 final size:24
Alignment explanation
Indices: 38492292--38492348 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
38492282 CTGTTACCTG
* *
38492292 AAAGGATATCTATGAAAAGGTTAA
1 AAAGGATATCAAGGAAAAGGTTAA
* *
38492316 AAAGGATAGCAAGGAAAAGGTTCA
1 AAAGGATATCAAGGAAAAGGTTAA
38492340 AAAGGATAT
1 AAAGGATAT
38492349 TATTCGAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.51, C:0.05, G:0.25, T:0.19
Consensus pattern (24 bp):
AAAGGATATCAAGGAAAAGGTTAA
Found at i:38492333 original size:63 final size:63
Alignment explanation
Indices: 38492266--38492410 Score: 220
Period size: 63 Copynumber: 2.3 Consensus size: 63
38492256 CTGAATTCTT
* *
38492266 GAAAAGGTTGAAAAGGCTGTTAC-CTGAAAGGATATCTATGAAAAGGTTAAAAAGGATAGCAAG
1 GAAAAGGTTGAAAAGGATATTACTC-GAAAGGATATCTATGAAAAGGTTAAAAAGGATAGCAAG
* * * *
38492329 GAAAAGGTTCAAAAGGATATTATTCGAAAGGATATCTATGAAAAGGTTGAAAAGGATAGCAAT
1 GAAAAGGTTGAAAAGGATATTACTCGAAAGGATATCTATGAAAAGGTTAAAAAGGATAGCAAG
38492392 GAAAAGGTTGAAAAGGATA
1 GAAAAGGTTGAAAAGGATA
38492411 GCAATGAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
63 73 0.99
64 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.21
Consensus pattern (63 bp):
GAAAAGGTTGAAAAGGATATTACTCGAAAGGATATCTATGAAAAGGTTAAAAAGGATAGCAAG
Found at i:38492382 original size:24 final size:24
Alignment explanation
Indices: 38492355--38492423 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
38492345 ATATTATTCG
* *
38492355 AAAGGATATCTATGAAAAGGTTGA
1 AAAGGATAGCAATGAAAAGGTTGA
38492379 AAAGGATAGCAATGAAAAGGTTGA
1 AAAGGATAGCAATGAAAAGGTTGA
38492403 AAAGGATAGCAATGAAAAGGT
1 AAAGGATAGCAATGAAAAGGT
38492424 CGGTATCTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.49, C:0.04, G:0.28, T:0.19
Consensus pattern (24 bp):
AAAGGATAGCAATGAAAAGGTTGA
Found at i:38492396 original size:15 final size:15
Alignment explanation
Indices: 38492376--38492422 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
38492366 ATGAAAAGGT
38492376 TGAAAAGGATAGCAA
1 TGAAAAGGATAGCAA
38492391 TGAAAAGG-T-----
1 TGAAAAGGATAGCAA
38492400 TGAAAAGGATAGCAA
1 TGAAAAGGATAGCAA
38492415 TGAAAAGG
1 TGAAAAGG
38492423 TCGGTATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
14 1 0.04
15 16 0.62
ACGTcount: A:0.51, C:0.04, G:0.30, T:0.15
Consensus pattern (15 bp):
TGAAAAGGATAGCAA
Found at i:38492398 original size:39 final size:40
Alignment explanation
Indices: 38492315--38492398 Score: 91
Period size: 39 Copynumber: 2.1 Consensus size: 40
38492305 GAAAAGGTTA
** *
38492315 AAAAGGATAGCAAGGAAAAGGTTCAAAAGGATATTATTCG
1 AAAAGGATAGCAAGGAAAAGGTTCAAAAGGATAGCAATCG
* * * *
38492355 -AAAGGATATCTATGAAAAGGTTGAAAAGGATAGCAAT-G
1 AAAAGGATAGCAAGGAAAAGGTTCAAAAGGATAGCAATCG
38492393 AAAAGG
1 AAAAGG
38492399 TTGAAAAGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.49, C:0.06, G:0.26, T:0.19
Consensus pattern (40 bp):
AAAAGGATAGCAAGGAAAAGGTTCAAAAGGATAGCAATCG
Done.