Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 125 of 161
Found at i:39520826 original size:80 final size:79
Alignment explanation
Indices: 39520687--39520852 Score: 219
Period size: 80 Copynumber: 2.1 Consensus size: 79
39520677 GGACTAAGAT
* * **
39520687 CCGAAGGCATTTGTGCGAGTTACTAAATCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT
*
39520751 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAATC
*
39520767 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT
* *
39520831 ATATCCGGTTAAATT
65 AAATCCGGTTAAATC
39520846 CCGAAGG
1 CCGAAGG
39520853 TACGTGATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 16 0.21
80 58 0.76
81 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAATC
Found at i:39528886 original size:40 final size:40
Alignment explanation
Indices: 39528747--39528879 Score: 205
Period size: 40 Copynumber: 3.3 Consensus size: 40
39528737 GGACTAAGAT
39528747 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
39528787 CCGAAGGCATTTGTGTGAGTTACTAAATCCGGGTTAAGTG
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
39528827 TCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
39528867 CCGAAGGCATTTG
1 CCGAAGGCATTTG
39528880 AACGAGTAGC
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 82 0.98
41 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:39528897 original size:80 final size:79
Alignment explanation
Indices: 39528748--39528902 Score: 215
Period size: 80 Copynumber: 1.9 Consensus size: 79
39528738 GACTAAGATC
* ***
39528748 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTAA
1 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAA
39528813 ATCCGGGTTAAGTGT
66 ATCC-GGTTAAGTGT
*
39528828 CGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTA-CT
*
39528891 ATATCCGGTTAA
64 AAATCCGGTTAA
39528903 ATTCCGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
79 8 0.12
80 57 0.85
81 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (79 bp):
CGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGTTAAGTGT
Found at i:39532195 original size:7 final size:7
Alignment explanation
Indices: 39532179--39532208 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
39532169 TTGTGGTTTG
39532179 TGGACTTT
1 TGGAC-TT
39532187 TGGACTT
1 TGGACTT
39532194 TGGACTT
1 TGGACTT
39532201 TGGACTT
1 TGGACTT
39532208 T
1 T
39532209 ACCTCTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.13, C:0.13, G:0.27, T:0.47
Consensus pattern (7 bp):
TGGACTT
Found at i:39532935 original size:11 final size:11
Alignment explanation
Indices: 39532921--39532950 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39532911 TTTATTGCAT
39532921 GATTATCTGTA
1 GATTATCTGTA
*
39532932 GATTATCCGTA
1 GATTATCTGTA
39532943 GATTATCT
1 GATTATCT
39532951 TAAGCATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (11 bp):
GATTATCTGTA
Found at i:39539695 original size:24 final size:25
Alignment explanation
Indices: 39539668--39539717 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
39539658 ATATTAATAA
*
39539668 AATC-AAGATTCTTTCACACCAAAC
1 AATCAAAGATTATTTCACACCAAAC
* *
39539692 AATCAAATATTATTTCACATCAAAC
1 AATCAAAGATTATTTCACACCAAAC
39539717 A
1 A
39539718 TGTTTGTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (25 bp):
AATCAAAGATTATTTCACACCAAAC
Found at i:39542741 original size:18 final size:18
Alignment explanation
Indices: 39542713--39542756 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39542703 AATAGAACTT
**
39542713 ATATGAAAATCCTTGAAGG
1 ATAT-AAAATCCCAGAAGG
*
39542732 ATTTAAAATCCCAGAAGG
1 ATATAAAATCCCAGAAGG
39542750 ATATAAA
1 ATATAAA
39542757 GTTTCTCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (18 bp):
ATATAAAATCCCAGAAGG
Found at i:39546619 original size:17 final size:17
Alignment explanation
Indices: 39546597--39546633 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39546587 AACAAAACAA
39546597 TTTACAAAAACAAAGGT
1 TTTACAAAAACAAAGGT
* *
39546614 TTTACACAAACAAATGT
1 TTTACAAAAACAAAGGT
39546631 TTT
1 TTT
39546634 TTAGAACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (17 bp):
TTTACAAAAACAAAGGT
Found at i:39550467 original size:40 final size:40
Alignment explanation
Indices: 39550423--39550506 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
39550413 AGCAATTCTG
* * * *
39550423 ACTTGTTTGAAAATCACTTT-GATATGTTAAAATTATTTTA
1 ACTTGGTTG-AAATCACTTTGGATAGGCTAAAATCATTTTA
* *
39550463 ACTTGGTTGAAATCATTTTGGCTAGGCTAAAATCATTTTA
1 ACTTGGTTGAAATCACTTTGGATAGGCTAAAATCATTTTA
39550503 ACTT
1 ACTT
39550507 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (40 bp):
ACTTGGTTGAAATCACTTTGGATAGGCTAAAATCATTTTA
Found at i:39550480 original size:20 final size:20
Alignment explanation
Indices: 39550450--39550506 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
39550440 TTTGATATGT
* *
39550450 TAAAATTATTTTAACTTGGT
1 TAAAATCATTTTAACTTGGC
* ** *
39550470 TGAAATCATTTTGGCTAGGC
1 TAAAATCATTTTAACTTGGC
39550490 TAAAATCATTTTAACTT
1 TAAAATCATTTTAACTT
39550507 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (20 bp):
TAAAATCATTTTAACTTGGC
Found at i:39551735 original size:86 final size:86
Alignment explanation
Indices: 39551630--39551886 Score: 399
Period size: 86 Copynumber: 3.0 Consensus size: 86
39551620 TCAAACCCTT
* *
39551630 AAAAAAAACATTTAAGCCCCTATTTTTTTCACTCAATTGGGTATTTAAACTTTCAAAATATATCA
1 AAAAAAAGCAATTAAGCCCCTATTTTTTTCACTCAATTGGGTATTTAAACTTTCAAAATATATCA
39551695 AAAAAGCTCTCAAACTTTTTC
66 AAAAAGCTCTCAAACTTTTTC
39551716 AAAAAAAGCAATTAAGCCCCTATTTTTTTCACTCAATTGGGTATTTAAACTTTCAAAATATATCA
1 AAAAAAAGCAATTAAGCCCCTATTTTTTTCACTCAATTGGGTATTTAAACTTTCAAAATATATCA
39551781 AAAAAGCTCTCAAACTTTTTC
66 AAAAAGCTCTCAAACTTTTTC
* * * * * ** *
39551802 AAAAAAAGCAATTAAGCCCCTATTTTTTTCTCTTACTTGTGTATTTGAACTGCCAAAATGTATC-
1 AAAAAAAGCAATTAAGCCCCTATTTTTTTCACTCAATTGGGTATTTAAACTTTCAAAATATATCA
*
39551866 AAAAAGGTCCTCAAACTTTTT
66 AAAAAGCT-CTCAAACTTTTT
39551887 TTTCAAAAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
85 7 0.04
86 152 0.96
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (86 bp):
AAAAAAAGCAATTAAGCCCCTATTTTTTTCACTCAATTGGGTATTTAAACTTTCAAAATATATCA
AAAAAGCTCTCAAACTTTTTC
Found at i:39557680 original size:67 final size:67
Alignment explanation
Indices: 39557602--39557730 Score: 231
Period size: 67 Copynumber: 1.9 Consensus size: 67
39557592 AGAAATGGAA
39557602 CAAAGGTTGGAAAAATTAGAGCGAATACAGATACAGATACAGGAGCAATTGACCAAATTTCAGCA
1 CAAAGGTTGGAAAAATTAGAGCGAATACAGATACAGATACAGGAGCAATTGACCAAATTTCAGCA
39557667 GG
66 GG
* * *
39557669 CAAAGGTTGGAAAAATTAGAGCGAATGCAGATACAGATGCAGGAGCAATTGATCAAATTTCA
1 CAAAGGTTGGAAAAATTAGAGCGAATACAGATACAGATACAGGAGCAATTGACCAAATTTCA
39557731 ATAGGAAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (67 bp):
CAAAGGTTGGAAAAATTAGAGCGAATACAGATACAGATACAGGAGCAATTGACCAAATTTCAGCA
GG
Found at i:39559817 original size:6 final size:6
Alignment explanation
Indices: 39559808--39559841 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
39559798 TAAAAGTGAT
39559808 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
39559842 TGGAGAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:39559831 original size:18 final size:17
Alignment explanation
Indices: 39559808--39559841 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
39559798 TAAAAGTGAT
39559808 AAAAAGAAAAAGAAAAAG
1 AAAAAG-AAAAGAAAAAG
39559826 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
39559842 TGGAGAGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:39561194 original size:44 final size:44
Alignment explanation
Indices: 39561045--39561551 Score: 458
Period size: 44 Copynumber: 11.6 Consensus size: 44
39561035 GTAGATCAGT
* ** * *
39561045 GAAGATAGCAGGTCCCGTCTTCCTATATTGGTAGGAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCGGAAGTAGATC
* * **
39561089 GAAGAT-GCAGATCTTGTCTTCCCATATTAGT-GGCGGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCGGAAGTAGATC
* * * *
39561131 AAAGAAAGCAGATCTTGTCTTCATTTATTGG-CGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCG-GAAGTAGATC
* * * *
39561175 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCGGAAGTAGATC
* * *
39561219 GAAGATA-CAGATCTTGTCTTCATGTATTAG-CGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCG-GAAGTAGATC
* * * *
39561262 GAAGATAGTAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCG-GAAGTAGATC
* * *
39561307 GAAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCG-GAAGTAGATC
* * * * *
39561351 GAAGAAAGCAGATATTGTCTTCATGTATTGG-CGTAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCG-GAAGTAGATC
* * * * *
39561395 AAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCGGAAGTAGATC
* * *
39561439 GAAGATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCG-GAAGTAGATC
* * * * *
39561483 AAAGAAAGTAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTATATTGGTCG-GAAGTAGATC
*
39561527 GAAGATAGTAGATCTTG-CTTTCCTA
1 GAAGATAGCAGATCTTGTC-TTCCTA
39561552 CACCGACAGC
Statistics
Matches: 367, Mismatches: 84, Indels: 24
0.77 0.18 0.05
Matches are distributed among these distances:
42 13 0.04
43 97 0.26
44 202 0.55
45 55 0.15
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
GAAGATAGCAGATCTTGTCTTCCTATATTGGTCGGAAGTAGATC
Found at i:39561416 original size:220 final size:217
Alignment explanation
Indices: 39561045--39561459 Score: 713
Period size: 220 Copynumber: 1.9 Consensus size: 217
39561035 GTAGATCAGT
*
39561045 GAAGATAGCAGGTCCCGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGATCCCGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * * *
39561110 CCATATTAGTGGCGGTAGATCAAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGATC
66 CCATACTAGTGGCGGTAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAGATC
*
39561175 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTC
131 AAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTC
39561240 ATGTATTAGCGTGAAGTAGATC
196 ATGTATTAGCGTGAAGTAGATC
* *
39561262 GAAGATAGTAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGATCCCGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
39561327 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAG
65 CCCATACTAGTGGCG--GTAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAG
39561392 ATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTC
128 ATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTC
39561457 TTC
193 TTC
39561460 CCATACTGGT
Statistics
Matches: 185, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
217 31 0.17
218 43 0.23
220 111 0.60
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (217 bp):
GAAGATAGCAGATCCCGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATACTAGTGGCGGTAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAGATC
AAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTC
ATGTATTAGCGTGAAGTAGATC
Found at i:39561529 original size:220 final size:218
Alignment explanation
Indices: 39561061--39561543 Score: 700
Period size: 220 Copynumber: 2.2 Consensus size: 218
39561051 AGCAGGTCCC
* *
39561061 GTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTAGTGGCGG
1 GTCTTCATATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTAGTGGCGG
* * * *
39561125 TAGATCAAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
66 TAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAGATCAAAGATAGCAGGTCC
** * *
39561190 TGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTCATGTATTAGCGTGAA
131 TGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTCACATACTAGCGCGAA
* *
39561255 GTAGATCGAAGATAGTAGATCCT
196 GTAGATCAAAGAAAGTAGATCCT
* *
39561278 GTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGA
1 GTCTTCATATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTAGTGGCG-
*
39561343 AGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAGATCAAAGATAGCAGGT
65 -GTAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAGATCAAAGATAGCAGGT
* * *
39561408 CCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGC
129 CCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTCACATACTAG-CGC
*
39561473 GAAGTAGATCAAAGAAAGTAGATCTT
193 GAAGTAGATCAAAGAAAGTAGATCCT
* * * * *
39561499 GTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGTAGATCTTG
1 GTCTTCATATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATCTTG
39561544 CTTTCCTACA
Statistics
Matches: 238, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
217 18 0.08
218 43 0.18
220 131 0.55
221 46 0.19
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (218 bp):
GTCTTCATATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTAGTGGCGG
TAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTAAAGTAGATCAAAGATAGCAGGTCC
TGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTCACATACTAGCGCGAA
GTAGATCAAAGAAAGTAGATCCT
Found at i:39561551 original size:132 final size:133
Alignment explanation
Indices: 39561124--39561540 Score: 572
Period size: 132 Copynumber: 3.2 Consensus size: 133
39561114 ATTAGTGGCG
* * * * * * * * * *
39561124 GTAGATCAAAGAAAGCAGATCTTGTCTTCATTTATTGG-CGTGAAGTAGATCGAAGATAGCAGGT
1 GTAGATCGAAGATAGTAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATA-CAGAT
* * * * * * *
39561188 CCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATA-CAGATCTTGTCTTCATGTATTAGCG
65 CTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCG
39561251 TGAA
130 TGAA
*
39561255 GTAGATCGAAGATAGTAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATC
1 GTAGATCGAAGATAGTAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATC
*
39561320 TTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCGT
66 TTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
*
39561385 AAA
131 GAA
* * *
39561388 GTAGATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATACAGATC
1 GTAGATCGAAGATAGTAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATC
* *
39561452 TTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGTAGATCTTGTCTTCATGTATTGGCGT
66 TTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
39561517 GAA
131 GAA
39561520 GTAGATCGAAGATAGTAGATC
1 GTAGATCGAAGATAGTAGATC
39561541 TTGCTTTCCT
Statistics
Matches: 252, Mismatches: 31, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
131 53 0.21
132 135 0.54
133 64 0.25
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (133 bp):
GTAGATCGAAGATAGTAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATC
TTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
GAA
Found at i:39561738 original size:44 final size:44
Alignment explanation
Indices: 39561672--39561877 Score: 238
Period size: 44 Copynumber: 4.7 Consensus size: 44
39561662 TGACCTCAGC
* * *
39561672 CCTATCTCCTTGGTCAGTAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
39561716 CCTATCTCTCTGGTCAACAGTGGAATAGGGTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
39561760 TCTATCTCCCTGGGCAGTAGTGGAAT-GGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGG-TTGAAGATTGTGA-AT
* *
39561804 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
39561848 CCTATCTCCCTGAGT-AGCAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
39561878 GGAAAATAGC
Statistics
Matches: 135, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
43 3 0.02
44 127 0.94
45 5 0.04
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:39562277 original size:44 final size:44
Alignment explanation
Indices: 39562184--39562299 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
39562174 ATGGCAAATT
* * *
39562184 TTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCGATAATC
1 TTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCGATAATC
* * *
39562228 CTATCTCCCTGAAGTTGCAGTGAAGC-GAATTAAAACC-TTGGATC
1 TTATCTCCCTGAAGTTGCAGTGAAGCAG-ATTAAAACCGAT-AATC
* *
39562272 TTATCTCTCTGAAGTTGCAGAG-AGCAGA
1 TTATCTCCCTGAAGTTGCAGTGAAGCAGA
39562300 ACGCATCTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 6 0.10
44 54 0.90
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCGATAATC
Found at i:39562745 original size:19 final size:19
Alignment explanation
Indices: 39562721--39562793 Score: 110
Period size: 19 Copynumber: 3.7 Consensus size: 19
39562711 TCTTCGAGGC
39562721 TATGCAATCTTAGATATGA
1 TATGCAATCTTAGATATGA
39562740 TATGCAATCTTAGATATGA
1 TATGCAATCTTAGATATGA
39562759 TATTTGCAATCTTAGATATGA
1 TA--TGCAATCTTAGATATGA
* *
39562780 TATGTAATATTAGA
1 TATGCAATCTTAGA
39562794 AGATGTGATT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 31 0.62
21 19 0.38
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (19 bp):
TATGCAATCTTAGATATGA
Found at i:39563152 original size:21 final size:21
Alignment explanation
Indices: 39563108--39563152 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
39563098 AATTAAGTTT
*
39563108 TTTTATTTTTTTAATTTACCA
1 TTTTATTTTTTTAATTTACAA
*
39563129 TTTTATTTATTTTTATTT-CAA
1 TTTTATTT-TTTTAATTTACAA
39563150 TTT
1 TTT
39563153 GGTCTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATTTTTTTAATTTACAA
Found at i:39564401 original size:22 final size:23
Alignment explanation
Indices: 39564353--39564406 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
39564343 CTAGCACGAC
*
39564353 AGTGCTCTCCGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCACATCT
*
39564376 -GTGCTCTCTGTTTAGCAC-TTT
1 AGTGCTCTCTGTTTAGCACATCT
39564397 AGTGCTCTCT
1 AGTGCTCTCT
39564407 ATTCATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.41
Consensus pattern (23 bp):
AGTGCTCTCTGTTTAGCACATCT
Found at i:39568061 original size:301 final size:304
Alignment explanation
Indices: 39567536--39568201 Score: 724
Period size: 301 Copynumber: 2.2 Consensus size: 304
39567526 CATAAGAATT
* * *
39567536 ATTATTATTGG-ATAGT-GGTAAAAAAA--TATTTATAAATC---TAAACACGGGTTCAATC-CT
1 ATTATTATTGGTATAGTAGG-AAAAAAATTTGTTTATAAATCTATTAAACATGGGTTTAATCTC-
* * *
39567593 TAGATATGTTAAATTTTAGTTCTTTTATTTAAAAACTCTATAAAAGTATGAAAAGACAAAAATGT
64 TAGATATGTTAAATTTTAATTCTTTTATTTAAAAACTCTAAAAAAGTATGAAAAGACAAAAAGGT
* *
39567658 ATTAAAATAATAATAGTCATTTAATAAAATGGTATATTATTCATTTCCAAACCGAGTTAGTACCT
129 ATCAAAATAATAATAGTCATTTAATAAAATGGTATATTAGTCATTTCCAAACCGAGTTAGTACCT
* * * * * *
39567723 GATTAACCCATAACATCAACTTAGTCAGGGGTTTTATTAATAGTAT-GATGCACAAATTTGGT-G
194 GATTAACCCATAACACCAACTCAATCAGGGATTTTATTAATAATATAGATACACAAATTTGGTAG
* * * *
39567786 AGAAAAAACATTTTATGTTAAAAG-TT-TTTTTAAGTTGACTCCAGA
259 AGAAAAAACA-ATTACGTTAAAAGTTTATTTTTAAGTTGACTCAAAA
* * * *
39567831 ATTGTTATTGGTGTAGT-GGAAAAGAATTTGTTTATAAATCTATTAAACATGTGTTTAATCTCTA
1 ATTATTATTGGTATAGTAGGAAAAAAATTTGTTTATAAATCTATTAAACATGGGTTTAATCTCTA
* * **
39567895 GATATGTT-AATTTTAATTCTTTTGTTTAAAAATTAC-AAAAAAGTA-GGGAA-A-AAAAAGGTC
66 GATATGTTAAATTTTAATTCTTTTATTTAAAAACT-CTAAAAAAGTATGAAAAGACAAAAAGGT-
* * **
39567955 ATCAAAATAATAGTAGCAATCATTTAATAAAAATGGTATATTAGTCATTTCCTAATTGAGTT-GT
129 ATCAAAATAATAATAG---TCATTTAAT-AAAATGGTATATTAGTCATTTCCAAACCGAGTTAG-
* * *
39568019 TACTTGGTTAACCCATGAA-ACCAACTCAATCAGGTATTTTATTAATAATATAGATACACAAATT
189 TACCTGATTAACCCAT-AACACCAACTCAATCAGGGATTTTATTAATAATATAGATACACAAATT
*
39568083 TGGTAAGAGAAAAAACAATTACGTTAAAAGTTTATTTATTTTTAAGTTTACTCAAAA
253 TGGT-AGAGAAAAAACAATTACGTTAAAAG----TTTATTTTTAAGTTGACTCAAAA
* *
39568140 ATTATTATTGGTATAGTAGTAAAAAAATTTGTTTGTAAATCTATTAAACATGGGTTTAATCT
1 ATTATTATTGGTATAGTAGGAAAAAAATTTGTTTATAAATCTATTAAACATGGGTTTAATCT
39568202 AGACCTGATC
Statistics
Matches: 306, Mismatches: 40, Indels: 35
0.80 0.10 0.09
Matches are distributed among these distances:
295 16 0.05
296 13 0.04
297 26 0.08
298 3 0.01
299 31 0.10
300 35 0.11
301 70 0.23
302 17 0.06
303 11 0.04
304 11 0.04
308 2 0.01
309 31 0.10
310 40 0.13
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (304 bp):
ATTATTATTGGTATAGTAGGAAAAAAATTTGTTTATAAATCTATTAAACATGGGTTTAATCTCTA
GATATGTTAAATTTTAATTCTTTTATTTAAAAACTCTAAAAAAGTATGAAAAGACAAAAAGGTAT
CAAAATAATAATAGTCATTTAATAAAATGGTATATTAGTCATTTCCAAACCGAGTTAGTACCTGA
TTAACCCATAACACCAACTCAATCAGGGATTTTATTAATAATATAGATACACAAATTTGGTAGAG
AAAAAACAATTACGTTAAAAGTTTATTTTTAAGTTGACTCAAAA
Found at i:39570618 original size:50 final size:50
Alignment explanation
Indices: 39570564--39570763 Score: 247
Period size: 50 Copynumber: 3.9 Consensus size: 50
39570554 TTTTCATATA
* * ** *
39570564 GGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTT
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC
39570614 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC
*
39570664 GGTGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATAATCTC
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC
* * * * *
39570717 AATGATGTCAATGCCATGTTCCAGACATGGTCTTACATGGGATCTCT
1 ---GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39570764 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
50 89 0.67
53 5 0.04
56 38 0.29
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC
Found at i:39570633 original size:100 final size:100
Alignment explanation
Indices: 39570516--39570710 Score: 246
Period size: 100 Copynumber: 1.9 Consensus size: 100
39570506 TTTCTTGTAC
* * ** * * *
39570516 TGCCAATGCCATATCCCAGATATGGTATTACATAAGAGTTTTCATATAGGTGCCCATGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTATTACATAAGACCTCTCATATAGGTGCCAACGCCATGTC
*
39570581 CCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
66 CCAGACATGGTCTTACAGGGGACCTCTCATCTTGG
* * ** * *
39570616 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTATTACATAAGACCTCTCATATAGGTGCCAACGCCATGTC
* *
39570681 TCAGACATGGTCTTACATGGGACCTCTCAT
66 CCAGACATGGTCTTACAGGGGACCTCTCAT
39570711 AATCTCAATG
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (100 bp):
TGCCAACGCCATATCCCAGACATGGTATTACATAAGACCTCTCATATAGGTGCCAACGCCATGTC
CCAGACATGGTCTTACAGGGGACCTCTCATCTTGG
Found at i:39572086 original size:10 final size:11
Alignment explanation
Indices: 39572050--39572096 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
39572040 TCTCCACTAC
39572050 TTATTTTATGT
1 TTATTTTATGT
*
39572061 TATATATTATGCT
1 T-TATTTTATG-T
39572074 TTATTTTAT-T
1 TTATTTTATGT
39572084 TTATTTTAT-T
1 TTATTTTATGT
39572094 TTA
1 TTA
39572097 ATTAACCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 14 0.44
11 1 0.03
12 15 0.47
13 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (11 bp):
TTATTTTATGT
Found at i:39590438 original size:22 final size:22
Alignment explanation
Indices: 39590380--39590438 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
39590370 GAATGGTATC
39590380 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
39590402 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
39590425 TACATATCAAATCT
1 TACAAATCAAATCT
39590439 ATGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:39595245 original size:22 final size:22
Alignment explanation
Indices: 39595187--39595245 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
39595177 GAATGGTATC
39595187 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
39595209 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
39595232 TACATATCAAATCT
1 TACAAATCAAATCT
39595246 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:39603397 original size:63 final size:63
Alignment explanation
Indices: 39603317--39603439 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 63
39603307 CCCAAAGGGT
* * * *
39603317 TAATCACCTAGTGGTGATTATCTCACGGCCGAGGAGCACAGAAGCTGGAATACAAATGGCGCC
1 TAATCACCCAGTGGTGATTATCTCACGACCAAGGAACACAGAAGCTGGAATACAAATGGCGCC
* * * *
39603380 TAATCACCCGGTGGTGATTATTTCGCGACCAAGGAACATAGAAGCTGGAATACAAATGGC
1 TAATCACCCAGTGGTGATTATCTCACGACCAAGGAACACAGAAGCTGGAATACAAATGGC
39603440 ACCGAGAGTC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (63 bp):
TAATCACCCAGTGGTGATTATCTCACGACCAAGGAACACAGAAGCTGGAATACAAATGGCGCC
Found at i:39609642 original size:45 final size:44
Alignment explanation
Indices: 39609534--39609907 Score: 250
Period size: 44 Copynumber: 8.4 Consensus size: 44
39609524 CATCATGGTG
* * * ** **
39609534 AACCTTATCTCTCTGAAGTTGCAGTGGGGCAGGTTGAAGCCACA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGATACA
** * **
39609578 AGTCTTATCTCCCTAAAGTTATAGTGGAGAAGACTGAAGATAACA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGAT-ACA
* * **
39609623 AACCTTATCTCACTGAAGTTGCAGTGGAGCAGGTTGAAGATACA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGATACA
** * * *
39609667 AGTCTTATATCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGATA-CA
* * * * **
39609712 AACCCTATCTCTCTGAAGTTACAGTGTA-ACAGGTTGAAGATACA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGA-AGACTGAAGATACA
** * * * *
39609756 AGTCTTATATCCCTGAAGTTGTAGTGGAGTAGACTGAAGATCGCA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGAT-ACA
* * * *
39609801 AACCCTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGCCAT-C-
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAG--ATACA
* * * * * * *
39609845 AGCCTTATCTACCTAAAGTTACAGTGGAGCAGACTGAGGATAGCG
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGATA-CA
* *
39609890 AATCTTATTTCCCTGAAG
1 AACCTTATCTCCCTGAAG
39609908 CTGTAGTTGA
Statistics
Matches: 248, Mismatches: 72, Indels: 19
0.73 0.21 0.06
Matches are distributed among these distances:
42 2 0.01
44 130 0.52
45 114 0.46
47 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
AACCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGATACA
Found at i:39609903 original size:89 final size:89
Alignment explanation
Indices: 39609534--39610064 Score: 446
Period size: 89 Copynumber: 5.9 Consensus size: 89
39609524 CATCATGGTG
* * ** *
39609534 AACCTTATCTCTCTGAAGTTGCAGTGGGGCAGGTTGAAGCCACAAGTCTTATCTCCCTAAAGTTA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATATCCCTAAAGTTA
* * *
39609599 TAGTGGAGAAGACTGAAGATAACA
66 CAGTGGAGCAGACTGAAGATAGCA
* *
39609623 AACCTTATCTCACTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATATCCCTAAAGTTG
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATATCCCTAAAGTTA
39609688 CAGTGGAGCAGACTGAAGATAGCA
66 CAGTGGAGCAGACTGAAGATAGCA
* * * * * * *
39609712 AACCCTATCTCTCTGAAGTTACAGTGTAACAGGTTGAAGATACAAGTCTTATATCCCTGAAGTTG
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATATCCCTAAAGTTA
* * *
39609777 TAGTGGAGTAGACTGAAGATCGCA
66 CAGTGGAGCAGACTGAAGATAGCA
* * * * * *
39609801 AACCCTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGCCAT-C-AGCCTTATCTACCTAAAGT
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG--ATACAAGTCTTATATCCCTAAAGT
* *
39609864 TACAGTGGAGCAGACTGAGGATAGCG
64 TACAGTGGAGCAGACTGAAGATAGCA
* * * * * * ** * * *
39609890 AATCTTATTTCCCTGAAGCTGTAGTTGAACAAATTGAAGCTATAAATTGCAGATCTTATCTCTCT
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG--ATACA----AG-TCTTATATCCCT
* ** * * *
39609955 GAAGTTGTAGTAGAGCAGA-T---CATATCA
59 AAAGTTACAGTGGAGCAGACTGAAGATAGCA
* * * * *
39609982 AACCTTATCTCCCTGAATTTGCAGTGGAGCAGGTTAAAGATCCCAA-TCTTATCTCACTAAAGTT
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT-ACAAGTCTTATATCCCTAAAGTT
** *
39610046 GTAGTGGAGCAGATTGAAG
65 ACAGTGGAGCAGACTGAAG
39610065 CTAATCCTAT
Statistics
Matches: 357, Mismatches: 71, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
85 28 0.08
86 1 0.00
87 1 0.00
89 261 0.73
90 3 0.01
91 3 0.01
92 33 0.09
95 3 0.01
96 24 0.07
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (89 bp):
AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATATCCCTAAAGTTA
CAGTGGAGCAGACTGAAGATAGCA
Found at i:39610093 original size:85 final size:85
Alignment explanation
Indices: 39609942--39610104 Score: 188
Period size: 85 Copynumber: 1.9 Consensus size: 85
39609932 TAAATTGCAG
* * * ** *
39609942 ATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCATATCAAACCTTATCTCCCTGAATTTGCAGT
1 ATCTTATCTCACTAAAGTTGTAGTAGAGCAGATCATAGCAAACCTTATCTCCCCCAAGTTGCAGT
39610007 GGAGCAGG-TTAAAGATCCCA
66 GGAGC-GGATTAAAGATCCCA
* * * *
39610027 ATCTTATCTCACTAAAGTTGTAGTGGAGCAGATTGA-AGCTAATCC-TATCTCCCCCAAGTTGTA
1 ATCTTATCTCACTAAAGTTGTAGTAGAGCAGA-TCATAGC-AAACCTTATCTCCCCCAAGTTGCA
39610090 GTGGAGCGGATTAAA
64 GTGGAGCGGATTAAA
39610105 ACGATGAATC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
84 2 0.03
85 57 0.88
86 6 0.09
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (85 bp):
ATCTTATCTCACTAAAGTTGTAGTAGAGCAGATCATAGCAAACCTTATCTCCCCCAAGTTGCAGT
GGAGCGGATTAAAGATCCCA
Found at i:39610731 original size:71 final size:71
Alignment explanation
Indices: 39610643--39610783 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
39610633 ACATGCTAAC
* *
39610643 AGTAATGGCAGTAAATATAGGCAGATAAAGGAAAATTTTGATGGTTGTATCTGGCTATAAAGGCC
1 AGTAATGGCAGTAAATATAGGCAGATAAAGGAAAAATTTGATGGTTGTATCCGGCTATAAAGGCC
39610708 TTGATA
66 TTGATA
*
39610714 AGTAATGGCAGTAAATATAGGCAGATAAATGAAAAATTTGATGGTTGTATCCGGCTATAAAGGCC
1 AGTAATGGCAGTAAATATAGGCAGATAAAGGAAAAATTTGATGGTTGTATCCGGCTATAAAGGCC
39610779 TTGAT
66 TTGAT
39610784 CTTTATCTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (71 bp):
AGTAATGGCAGTAAATATAGGCAGATAAAGGAAAAATTTGATGGTTGTATCCGGCTATAAAGGCC
TTGATA
Found at i:39618195 original size:17 final size:17
Alignment explanation
Indices: 39618173--39618211 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
39618163 GTTTTGGTTC
*
39618173 AAATTTAGCGTTAATTT
1 AAATTTAGCATTAATTT
39618190 AAATTTAGCATTAATTT
1 AAATTTAGCATTAATTT
39618207 AAATT
1 AAATT
39618212 ATGTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (17 bp):
AAATTTAGCATTAATTT
Found at i:39624243 original size:39 final size:39
Alignment explanation
Indices: 39624173--39624472 Score: 464
Period size: 39 Copynumber: 7.6 Consensus size: 39
39624163 GCTCCTCGTT
* * *
39624173 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
39624213 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39624252 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39624291 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39624330 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
39624369 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
39624408 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
39624449 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
39624473 CATCATTCAA
Statistics
Matches: 247, Mismatches: 8, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
39 209 0.85
40 29 0.12
41 9 0.04
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:39626341 original size:36 final size:36
Alignment explanation
Indices: 39626281--39626354 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
39626271 AATAAACTCT
*
39626281 ATTCAGTTCAACAGTTTTTCGGATCTATTTTGACTG
1 ATTCAGTTCAACAGCTTTTCGGATCTATTTTGACTG
*
39626317 ATTCAGTTCAATAGACTTTT-GGATCTATTTTGACTG
1 ATTCAGTTCAACAG-CTTTTCGGATCTATTTTGACTG
39626353 AT
1 AT
39626355 GCACTCCTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (36 bp):
ATTCAGTTCAACAGCTTTTCGGATCTATTTTGACTG
Found at i:39639087 original size:56 final size:54
Alignment explanation
Indices: 39639020--39639222 Score: 155
Period size: 56 Copynumber: 3.6 Consensus size: 54
39639010 TTCAAAAATA
* *
39639020 ATATTATTTTAATAGTTTAATATTAAATTAAATTTAATATTTATCTTAATAGTATT
1 ATATTAATTTAATA-TTTAATATTAAATTTAATTTAATATTTATCTTAATA-TATT
* *
39639076 TTATTAATTTAATA-TTAA-ATTAATTATTTTAATATTAA-ATTTATTTTAATCATTCTATT
1 ATATTAATTTAATATTTAATATTAA--A-TTTAAT-TTAATATTTATCTTAAT-A---TATT
* * *
39639135 ATTTTAA--TAATATTTAATATTAAATTTAATTTCATATTTATCTTGATAAATATT
1 ATATTAATTTAATATTTAATATTAAATTTAATTTAATATTTATCTT-A-ATATATT
* * *
39639189 ATATTAAATTAATATTAAAGTGATTAAGTTTAAT
1 ATATTAATTTAATATTTAA-T-ATTAAATTTAAT
39639223 CATAGTTGAA
Statistics
Matches: 118, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
53 5 0.04
54 14 0.12
55 4 0.03
56 51 0.43
57 14 0.12
58 16 0.14
59 14 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (54 bp):
ATATTAATTTAATATTTAATATTAAATTTAATTTAATATTTATCTTAATATATT
Found at i:39639093 original size:11 final size:11
Alignment explanation
Indices: 39639018--39639164 Score: 69
Period size: 11 Copynumber: 13.4 Consensus size: 11
39639008 ATTTCAAAAA
*
39639018 TAATATTATTT
1 TAATATTAATT
39639029 TAATAGTTTAATAT
1 TAATA--TTAAT-T
39639043 TAA-ATTAAATT
1 TAATATT-AATT
*
39639054 TAATATTTATCT
1 TAATATTAAT-T
*
39639066 TAATAGT-ATT
1 TAATATTAATT
39639076 T--TATTAATT
1 TAATATTAATT
*
39639085 TAATATTAAAT
1 TAATATTAATT
*
39639096 T-A-ATTATTT
1 TAATATTAATT
39639105 TAATATTAAATT
1 TAATATT-AATT
*
39639117 T-ATTTTAATCAT
1 TAATATTAAT--T
* *
39639129 T-CTATTATTT
1 TAATATTAATT
*
39639139 TAATAAT-ATT
1 TAATATTAATT
39639149 TAATATTAAATT
1 TAATATT-AATT
39639161 TAAT
1 TAAT
39639165 TTCATATTTA
Statistics
Matches: 103, Mismatches: 16, Indels: 33
0.68 0.11 0.22
Matches are distributed among these distances:
8 3 0.03
9 10 0.10
10 17 0.17
11 33 0.32
12 31 0.30
13 5 0.05
14 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:39639106 original size:20 final size:20
Alignment explanation
Indices: 39639078--39639116 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39639068 ATAGTATTTT
39639078 ATTAATTTAATATTAAATTA
1 ATTAATTTAATATTAAATTA
*
39639098 ATTATTTTAATATTAAATT
1 ATTAATTTAATATTAAATT
39639117 TATTTTAATC
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTAATTTAATATTAAATTA
Found at i:39639112 original size:31 final size:31
Alignment explanation
Indices: 39639077--39639165 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 31
39639067 AATAGTATTT
39639077 TATTAATTTAATATTAAATTAATTATTTTAA
1 TATTAATTTAATATTAAATTAATTATTTTAA
* *
39639108 TATTAAATTT-ATTTTAATCATTCTATTATTTTAA
1 TATT-AATTTAATATTAA--ATT-AATTATTTTAA
*
39639142 TAAT-ATTTAATATTAAATTTAATT
1 TATTAATTTAATATTAAA-TTAATT
39639166 TCATATTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
31 14 0.30
32 11 0.23
33 9 0.19
34 13 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTAATTTAATATTAAATTAATTATTTTAA
Found at i:39639121 original size:17 final size:17
Alignment explanation
Indices: 39639083--39639143 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
39639073 ATTTTATTAA
39639083 TTTAATATTAAATTAATTAT
1 TTTAATATTAAA-T--TTAT
39639103 TTTAATATTAAATTTAT
1 TTTAATATTAAATTTAT
**
39639120 TTTAATCATTCTA-TTAT
1 TTTAAT-ATTAAATTTAT
39639137 TTTAATA
1 TTTAATA
39639144 ATATTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
16 1 0.03
17 20 0.53
18 4 0.11
19 1 0.03
20 12 0.32
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATATTAAATTTAT
Found at i:39646201 original size:53 final size:53
Alignment explanation
Indices: 39646121--39646225 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
39646111 AAGTTAGTGA
* *
39646121 GTTCAATAATGAAATAATTAATCTTAACATATCATGGAACATGTTTGTAACAT
1 GTTCAACAATGAAATAATTAATCTTAACATATCATAGAACATGTTTGTAACAT
39646174 GTTCAACAATGAAATAATTAATCTTAACATATCATAGAACATGTTTGTAACA
1 GTTCAACAATGAAATAATTAATCTTAACATATCATAGAACATGTTTGTAACA
39646226 AGTCAAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (53 bp):
GTTCAACAATGAAATAATTAATCTTAACATATCATAGAACATGTTTGTAACAT
Found at i:39656208 original size:30 final size:30
Alignment explanation
Indices: 39656174--39656234 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
39656164 AAGCAAAATG
39656174 TCATTGACATATAGAACAAGGAATATATAC
1 TCATTGACATATAGAACAAGGAATATATAC
*
39656204 TCATTGACATATAGAACCAGGAATATATAC
1 TCATTGACATATAGAACAAGGAATATATAC
39656234 T
1 T
39656235 TACTCCCCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (30 bp):
TCATTGACATATAGAACAAGGAATATATAC
Found at i:39658840 original size:20 final size:19
Alignment explanation
Indices: 39658815--39658852 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
39658805 GGAGGAAGAG
39658815 AGGGACAACCAAGGTCTAAA
1 AGGGACAACCAAGG-CTAAA
39658835 AGGGACAACCAAGGCTAA
1 AGGGACAACCAAGGCTAA
39658853 TCAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.45, C:0.21, G:0.26, T:0.08
Consensus pattern (19 bp):
AGGGACAACCAAGGCTAAA
Found at i:39663099 original size:16 final size:16
Alignment explanation
Indices: 39663078--39663125 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
39663068 AGCAGTAACT
39663078 ATATATATATTAAAGC
1 ATATATATATTAAAGC
*
39663094 ATATATACA-TACAAGC
1 ATATATATATTA-AAGC
39663110 -T-TA-ATATTAAAGC
1 ATATATATATTAAAGC
39663123 ATA
1 ATA
39663126 CGTAAACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
13 6 0.23
14 5 0.19
15 3 0.12
16 12 0.46
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.33
Consensus pattern (16 bp):
ATATATATATTAAAGC
Found at i:39663247 original size:13 final size:13
Alignment explanation
Indices: 39663229--39663254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39663219 ATTTTAATAT
39663229 TTAAAACATGAGC
1 TTAAAACATGAGC
39663242 TTAAAACATGAGC
1 TTAAAACATGAGC
39663255 AAACCACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
TTAAAACATGAGC
Found at i:39666681 original size:90 final size:90
Alignment explanation
Indices: 39666514--39666693 Score: 218
Period size: 90 Copynumber: 2.0 Consensus size: 90
39666504 ATATGGATGC
* * * *
39666514 ACTATCACATAACCATTAAGCATATAGCTCGTTTCTTCTTTAATCTTATTTATTCACTGTATTTA
1 ACTATCACATAACCATTAAGCATATAGCTCATTTCTTCTTTAATCTTATTTATTAACTATATATA
* *
39666579 TTTAGAGGTGTGACAAGTGGATTGT
66 TTCAGAGGTGTGACAACTGGATTGT
* * * * * * *
39666604 ACTATCACTTAACCATTGAGCCTGTAGCTTATTTCTTGTTTAATCTTATTTCTTAACTATATATA
1 ACTATCACATAACCATTAAGCATATAGCTCATTTCTTCTTTAATCTTATTTATTAACTATATATA
*
39666669 TTCCAG-GTTGTGACAACTGGATTGT
66 TT-CAGAGGTGTGACAACTGGATTGT
39666694 TGAAAATTCT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
90 73 0.97
91 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (90 bp):
ACTATCACATAACCATTAAGCATATAGCTCATTTCTTCTTTAATCTTATTTATTAACTATATATA
TTCAGAGGTGTGACAACTGGATTGT
Found at i:39671734 original size:68 final size:68
Alignment explanation
Indices: 39671625--39671761 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
39671615 AGAAAGTGTC
*
39671625 AGATTAGTATACAACAAATCAACGTACAATTGTCGAGGTAAGTTCCTCTAACTAAATTATGTATA
1 AGATTAGTATACAACAAATCAACGTAAAATTGTCGAGGTAAGTTCCTCTAACTAAATTATGTATA
39671690 TTT
66 TTT
* *
39671693 AGATTAGTATACAACAAATCAACGTAAAATTGTCGAGGTAAGTTCGTGTAACTAAATTATGTATA
1 AGATTAGTATACAACAAATCAACGTAAAATTGTCGAGGTAAGTTCCTCTAACTAAATTATGTATA
39671758 TTT
66 TTT
39671761 A
1 A
39671762 TATGTTTGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (68 bp):
AGATTAGTATACAACAAATCAACGTAAAATTGTCGAGGTAAGTTCCTCTAACTAAATTATGTATA
TTT
Found at i:39672257 original size:25 final size:24
Alignment explanation
Indices: 39672184--39672289 Score: 90
Period size: 25 Copynumber: 4.4 Consensus size: 24
39672174 TTGCTTGAAC
* **
39672184 CTTCCCGAT-ATGGCTCGTATGAG
1 CTTCCCGTTAATGGCTCACATGAG
* *
39672207 CTTCCCGTTAATGGCTCTC-TAAAG
1 CTTCCCGTTAATGGCTCACAT-GAG
*
39672231 CTTCCCGTTACATGGGTCACATGAG
1 CTTCCCGTTA-ATGGCTCACATGAG
* * *
39672256 CTTCCCATTATATGGCTCAGAAGAG
1 CTTCCCGTTA-ATGGCTCACATGAG
39672281 CTTCCCGTT
1 CTTCCCGTT
39672290 TATGTGCTTG
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 9 0.14
24 19 0.29
25 37 0.56
26 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (24 bp):
CTTCCCGTTAATGGCTCACATGAG
Found at i:39679536 original size:5 final size:5
Alignment explanation
Indices: 39679526--39679569 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
39679516 GCCTAAGATG
* *
39679526 TGAAT TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
39679570 GTTAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:39680286 original size:25 final size:25
Alignment explanation
Indices: 39680198--39680278 Score: 110
Period size: 25 Copynumber: 3.2 Consensus size: 25
39680188 CGGAAGAGAT
* *
39680198 TGGCTCGCATGAGCTTCCTGTTACA
1 TGGCTCACATGAGCTTCCTGTTATA
39680223 TGGCTCACATGAGCTTCCTGTTATA
1 TGGCTCACATGAGCTTCCTGTTATA
* *
39680248 TGGCTCAAAAGAGCTTCCTGTT-TA
1 TGGCTCACATGAGCTTCCTGTTATA
39680272 TGTGCTC
1 TG-GCTC
39680279 GTATGAGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 4 0.08
25 47 0.92
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCTGTTATA
Found at i:39694280 original size:24 final size:24
Alignment explanation
Indices: 39694253--39694299 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
39694243 TAGAACAGTC
* *
39694253 TCAAAAGGAAATGCAGGAGCAGCT
1 TCAAAAGCAAATGAAGGAGCAGCT
*
39694277 TCAAAAGCAAATGAATGAGCAGC
1 TCAAAAGCAAATGAAGGAGCAGC
39694300 AAAAAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (24 bp):
TCAAAAGCAAATGAAGGAGCAGCT
Found at i:39702545 original size:44 final size:43
Alignment explanation
Indices: 39702494--39703044 Score: 245
Period size: 44 Copynumber: 12.6 Consensus size: 43
39702484 GATCGCATCT
* *
39702494 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTAAGAAATTA
1 AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
* ** *
39702538 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGAAAGTA
* * * ** **
39702583 AATCTTGTCTCTCTGAAGTTGCAATGGAGCAGGTTAA-AGCCGATA
1 AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGA-AAG-TA
* ** * ** *
39702628 A-TCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAA-AACCTT
1 AGTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
* * * **
39702670 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCT-
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
* *
39702711 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGAAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
** *
39702755 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGAAAGTA
* ** **
39702800 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCCA-TA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACT-AAG-AAAGTA
* ** * ** *
39702845 A-TCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAA-AACCTT
1 AGTCTTATC-TCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
* * * * * **
39702887 GGATCTTATCTCTTTGAAGTTGCAG-AGAGCAGA-TCA-CATCT-
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
* *
39702928 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
* * ** *
39702972 AGGCTTATCCTCCTGAAGTTGCAGT-GAGGCTGACTGAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGAAAGTA
*
39703017 AATCTTATCTCCCTGAAGTTGCAGTGGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGA
39703045 ACAAATTAAA
Statistics
Matches: 388, Mismatches: 81, Indels: 74
0.71 0.15 0.14
Matches are distributed among these distances:
40 39 0.10
41 18 0.05
42 15 0.04
43 27 0.07
44 179 0.46
45 104 0.27
46 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGTA
Found at i:39702791 original size:217 final size:217
Alignment explanation
Indices: 39702409--39703180 Score: 1179
Period size: 217 Copynumber: 3.5 Consensus size: 217
39702399 CAGTAGCTAG
* *
39702409 TAATCCTATCTCCTTGAAGTTGCAATGGGGTGGATTAAAACCTTGGATCTTGTCTCTCTGAAGTT
1 TAATCCTATCTCCTTGAAGTTGCAATGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
* * * **
39702474 GTAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTAAGAAATTAA
66 GCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGAAAGCAA
* * *
39702539 GTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTGTCTCTCTGAAGTTG
131 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
* *
39702604 CAATGGAGCAGGTTAAAGCCGA
196 CAGTGGAGCAGGTTAAAGCCAA
* *
39702626 TAATCCTATCTTCC-TGAAGTTGCAGTGGAGTGGATTAAAACCTTAGATCTTATCTCTCTGAAGT
1 TAATCCTATC-TCCTTGAAGTTGCAATGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
*
39702690 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGAAAGCA
65 TGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGAAAGCA
39702755 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
130 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
*
39702820 GCAGTGGAGCAGGTTAAAGCCCA
195 GCAGTGGAGCAGGTTAAAGCCAA
* *
39702843 TAATCCTATCTTCC-TGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTTTGAAGT
1 TAATCCTATC-TCCTTGAAGTTGCAATGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
* *
39702907 TGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
65 TGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGAAAGCA
* *
39702972 AGGCTTATCCTCCTGAAGTTGCAGTGAGGCTGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
130 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* ** *
39703037 GCAGTGGAACAAATTAAAACCAA
195 GCAGTGGAGCAGGTTAAAGCCAA
* *
39703060 TAATCATATCTCCTTGAAGTTGCAATGGAGCGGATTAGAACCACAAATCTTGGATCTTATCTCTC
1 TAATCCTATCTCCTTGAAGTTGCAATGGAGTGGATTA-AA--AC----CTTGGATCTTATCTCTC
* *
39703125 TGAAGTCGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGAGGAG
59 TGAAGTTGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
39703181 TAGATTGAAG
Statistics
Matches: 515, Mismatches: 31, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
216 3 0.01
217 435 0.84
218 5 0.01
220 2 0.00
224 70 0.14
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
TAATCCTATCTCCTTGAAGTTGCAATGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
GCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGAAAGCAA
GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGGTTAAAGCCAA
Found at i:39703546 original size:117 final size:117
Alignment explanation
Indices: 39703340--39703572 Score: 448
Period size: 117 Copynumber: 2.0 Consensus size: 117
39703330 GGGCAGTTGT
*
39703340 AATACCCGATTTTTGCCCCGGGTACAAATAATAAACGGGCCCAAATGAAACTGCCCAATTACAAC
1 AATACCCGATTTTTGCCCCGGGTACAAATAATAAACGGGCCCAAATGAAACTACCCAATTACAAC
*
39703405 AAAACCCAGACCCGATTAAACTACAGAGGCCCAAATTAGTGGCCCAAAATAA
66 AAAACCCAAACCCGATTAAACTACAGAGGCCCAAATTAGTGGCCCAAAATAA
39703457 AATACCCGATTTTTGCCCCGGGTACAAATAATAAACGGGCCCAAATGAAACTACCCAATTACAAC
1 AATACCCGATTTTTGCCCCGGGTACAAATAATAAACGGGCCCAAATGAAACTACCCAATTACAAC
39703522 AAAACCCAAACCCGATTAAACTACAGAGGCCCAAATTAGTGGCCCAAAATA
66 AAAACCCAAACCCGATTAAACTACAGAGGCCCAAATTAGTGGCCCAAAATA
39703573 GTCAAAAACC
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.41, C:0.27, G:0.15, T:0.17
Consensus pattern (117 bp):
AATACCCGATTTTTGCCCCGGGTACAAATAATAAACGGGCCCAAATGAAACTACCCAATTACAAC
AAAACCCAAACCCGATTAAACTACAGAGGCCCAAATTAGTGGCCCAAAATAA
Found at i:39703888 original size:142 final size:142
Alignment explanation
Indices: 39703732--39704018 Score: 520
Period size: 142 Copynumber: 2.0 Consensus size: 142
39703722 GCAAATTTCT
39703732 TTTATTATTTCTCTATTTCATTCGGCTATAAAATAGCCATTTCAATACTGTAAACGGGATCCCCC
1 TTTATTATTTCTCTATTTCATTCGGCTATAAAATAGCCATTTCAATACTGTAAACGGGATCCCCC
* * *
39703797 GAATCCGAAATCAATAAAAATACACAAGTATTTTCACAAAAAACAGAGAGTAAATCGGACTCAAA
66 GAATCCGAAATCAATAAAAACAAACAAGTATTTTCACAAAAAACAGAGAGTAAATCGGAATCAAA
39703862 GGTTGATATACA
131 GGTTGATATACA
*
39703874 TTTATTATTTCTCTATTTCATTCGGCTATAAAATAGCCATTTCAATACTGTAAGCGGGATCCCCC
1 TTTATTATTTCTCTATTTCATTCGGCTATAAAATAGCCATTTCAATACTGTAAACGGGATCCCCC
* *
39703939 GAATCCGAAATCAATAAAAACAAACAAGTATTTTCACAACAAACAGAGAGTAAATTGGAATCAAA
66 GAATCCGAAATCAATAAAAACAAACAAGTATTTTCACAAAAAACAGAGAGTAAATCGGAATCAAA
39704004 GGTTGATATACA
131 GGTTGATATACA
39704016 TTT
1 TTT
39704019 TCGTTTTACT
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (142 bp):
TTTATTATTTCTCTATTTCATTCGGCTATAAAATAGCCATTTCAATACTGTAAACGGGATCCCCC
GAATCCGAAATCAATAAAAACAAACAAGTATTTTCACAAAAAACAGAGAGTAAATCGGAATCAAA
GGTTGATATACA
Found at i:39706331 original size:36 final size:36
Alignment explanation
Indices: 39706291--39706360 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
39706281 ATATAAAATA
39706291 TAAAATACAGTAAAAACATTAAAACAAATGTTTCCC
1 TAAAATACAGTAAAAACATTAAAACAAATGTTTCCC
* * * *
39706327 TAAAATACATTAAAAATATTGAAATAAATGTTTC
1 TAAAATACAGTAAAAACATTAAAACAAATGTTTC
39706361 TTAATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (36 bp):
TAAAATACAGTAAAAACATTAAAACAAATGTTTCCC
Found at i:39713539 original size:6 final size:6
Alignment explanation
Indices: 39713515--39713558 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
39713505 TGACACATTC
* * *
39713515 TCCCCTT TCCCCT TTCCCT TCCCCT TCCCGT TTCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
39713559 GGGTTGCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.57, G:0.02, T:0.41
Consensus pattern (6 bp):
TCCCCT
Found at i:39713548 original size:18 final size:18
Alignment explanation
Indices: 39713515--39713558 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
39713505 TGACACATTC
39713515 TCCCCTTTCCCCTTTCCCT
1 TCCCC-TTCCCCTTTCCCT
*
39713534 TCCCCTTCCCGTTTCCCT
1 TCCCCTTCCCCTTTCCCT
39713552 TCCCCTT
1 TCCCCTT
39713559 GGGTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.57, G:0.02, T:0.41
Consensus pattern (18 bp):
TCCCCTTCCCCTTTCCCT
Found at i:39713907 original size:11 final size:11
Alignment explanation
Indices: 39713891--39713916 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39713881 TTGCTGGATG
39713891 ATATTTTGGTT
1 ATATTTTGGTT
39713902 ATATTTTGGTT
1 ATATTTTGGTT
39713913 ATAT
1 ATAT
39713917 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:39716335 original size:22 final size:20
Alignment explanation
Indices: 39716292--39716330 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39716282 TAATTTAAAA
39716292 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
39716312 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
39716331 ATGTAAAAAC
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:39716475 original size:34 final size:34
Alignment explanation
Indices: 39716417--39716482 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
39716407 CAAACACCAG
39716417 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTAC-GAAAAGT
39716452 AAAATATTTTCCAG-AAATCATTTTACGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACGAAAA
39716483 ACATTTTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 5 0.16
34 12 0.39
35 14 0.45
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (34 bp):
AAAATATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:39717200 original size:31 final size:30
Alignment explanation
Indices: 39717163--39717220 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
39717153 TTTTAAATTA
*
39717163 ATAAATA-TAAAATTATATTTTAACTCCTGAT
1 ATAAATATTAAAATT-TAATTTAA-TCCTGAT
39717194 ATAAATATTAAAATTTAATTTAATCCT
1 ATAAATATTAAAATTTAATTTAATCCT
39717221 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 4 0.16
31 14 0.56
32 7 0.28
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (30 bp):
ATAAATATTAAAATTTAATTTAATCCTGAT
Found at i:39718202 original size:51 final size:51
Alignment explanation
Indices: 39718132--39718232 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
39718122 ATAGAGAAAG
*
39718132 GAAGCGTTGCAAACAAAAAGTTGACTATTTTTGTTAAAAGAAAGGGAGAAC
1 GAAGCGTTGCAAACAAAAAGTTGACTATTTTGGTTAAAAGAAAGGGAGAAC
39718183 GAAGCGTTGCAAACAAAAAGTTGACTATTTTGGTTAAAAGAAAGGGAGAA
1 GAAGCGTTGCAAACAAAAAGTTGACTATTTTGGTTAAAAGAAAGGGAGAA
39718233 ACGCTCTTAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.23
Consensus pattern (51 bp):
GAAGCGTTGCAAACAAAAAGTTGACTATTTTGGTTAAAAGAAAGGGAGAAC
Found at i:39724563 original size:2 final size:2
Alignment explanation
Indices: 39724551--39724585 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
39724541 GTAATACTCG
* *
39724551 TA TA TA AA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39724586 GATGTACTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39726078 original size:15 final size:15
Alignment explanation
Indices: 39726055--39726121 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 15
39726045 ATTATTTTAA
* *
39726055 ATTAATTTTATTGTT
1 ATTATTTTTATTATT
39726070 ATTATTTTTA-TATT
1 ATTATTTTTATTATT
** *
39726084 AAAATTTTTATTTTT
1 ATTATTTTTATTATT
*
39726099 A-TATCTTTTATTATA
1 ATTAT-TTTTATTATT
39726114 ATT-TTTTT
1 ATTATTTTT
39726122 CATAAATTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
14 17 0.41
15 23 0.56
16 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (15 bp):
ATTATTTTTATTATT
Found at i:39729682 original size:18 final size:18
Alignment explanation
Indices: 39729659--39729694 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39729649 CACCATATCG
39729659 ATATTTGAATCGTAGCTT
1 ATATTTGAATCGTAGCTT
39729677 ATATTTGAATCGTAGCTT
1 ATATTTGAATCGTAGCTT
39729695 GGAACTCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (18 bp):
ATATTTGAATCGTAGCTT
Found at i:39730991 original size:15 final size:15
Alignment explanation
Indices: 39730958--39731008 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
39730948 TAGTATGCAT
39730958 AATATTTAGATGT-TTA
1 AATATTT-GAT-TATTA
39730974 AATATTTGATTATTA
1 AATATTTGATTATTA
39730989 AAT-TCTTG-TTATTA
1 AATAT-TTGATTATTA
39731003 AATATT
1 AATATT
39731009 ATTGTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (15 bp):
AATATTTGATTATTA
Found at i:39731431 original size:51 final size:51
Alignment explanation
Indices: 39731355--39731456 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
39731345 TAGAACTCAT
*
39731355 AACACATTCAGAGAATTTTGTGTTTACGTTTTGAGGGTTCTTTGTTTTTCG
1 AACACATTCAGAGAATTTTGTGTTTACGTTTTGAGGGTTATTTGTTTTTCG
39731406 AACACATTCAGAGAATTTTGTGTTTACGTTTTGAGGGTTATTTGTTTTTCG
1 AACACATTCAGAGAATTTTGTGTTTACGTTTTGAGGGTTATTTGTTTTTCG
39731457 GGTTTTCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.21, C:0.11, G:0.22, T:0.47
Consensus pattern (51 bp):
AACACATTCAGAGAATTTTGTGTTTACGTTTTGAGGGTTATTTGTTTTTCG
Found at i:39737279 original size:50 final size:50
Alignment explanation
Indices: 39737222--39737345 Score: 160
Period size: 50 Copynumber: 2.5 Consensus size: 50
39737212 TCTTCCAAGC
*
39737222 TGAATAACGAGAAGCTCATGCGAGTTGAATAACGGGAAGTTCATGCGAGT
1 TGAATAACGAGAAGCTCATGCGAGTTGAATAACGGGAAGCTCATGCGAGT
* * * *
39737272 TGAATAACGGGAAACTCATGCGAGTTGAATATCGGGAAGCTCATGTGAGT
1 TGAATAACGAGAAGCTCATGCGAGTTGAATAACGGGAAGCTCATGCGAGT
* * *
39737322 TGTAA-ATCGAAAAGCTCATACGAG
1 TG-AATAACGAGAAGCTCATGCGAG
39737346 CTGTGGTGTG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 61 0.97
51 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (50 bp):
TGAATAACGAGAAGCTCATGCGAGTTGAATAACGGGAAGCTCATGCGAGT
Found at i:39737330 original size:25 final size:25
Alignment explanation
Indices: 39737222--39737323 Score: 159
Period size: 25 Copynumber: 4.1 Consensus size: 25
39737212 TCTTCCAAGC
*
39737222 TGAATAACGAGAAGCTCATGCGAGT
1 TGAATAACGGGAAGCTCATGCGAGT
*
39737247 TGAATAACGGGAAGTTCATGCGAGT
1 TGAATAACGGGAAGCTCATGCGAGT
*
39737272 TGAATAACGGGAAACTCATGCGAGT
1 TGAATAACGGGAAGCTCATGCGAGT
* *
39737297 TGAATATCGGGAAGCTCATGTGAGT
1 TGAATAACGGGAAGCTCATGCGAGT
39737322 TG
1 TG
39737324 TAAATCGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (25 bp):
TGAATAACGGGAAGCTCATGCGAGT
Found at i:39737336 original size:25 final size:25
Alignment explanation
Indices: 39737222--39737345 Score: 108
Period size: 25 Copynumber: 5.0 Consensus size: 25
39737212 TCTTCCAAGC
* *
39737222 TGAATAACGAGAAGCTCATGCGAGT
1 TGAATATCGAAAAGCTCATGCGAGT
* ** *
39737247 TGAATAACGGGAAGTTCATGCGAGT
1 TGAATATCGAAAAGCTCATGCGAGT
* *
39737272 TGAATAACGGGAAA-CTCATGCGAGT
1 TGAATATC-GAAAAGCTCATGCGAGT
** *
39737297 TGAATATCGGGAAGCTCATGTGAGT
1 TGAATATCGAAAAGCTCATGCGAGT
*
39737322 TGTAA-ATCGAAAAGCTCATACGAG
1 TG-AATATCGAAAAGCTCATGCGAG
39737346 CTGTGGTGTG
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
24 4 0.05
25 75 0.88
26 6 0.07
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (25 bp):
TGAATATCGAAAAGCTCATGCGAGT
Found at i:39738167 original size:4 final size:4
Alignment explanation
Indices: 39738158--39738184 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39738148 CATGATTAGG
39738158 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
39738185 TTTGGTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:39742987 original size:16 final size:15
Alignment explanation
Indices: 39742957--39742992 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
39742947 AAAAATTATT
*
39742957 TATATTTAGCAATAA
1 TATATTTAACAATAA
39742972 TATATTATAACAATAA
1 TATATT-TAACAATAA
39742988 TATAT
1 TATAT
39742993 ACATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATTTAACAATAA
Found at i:39744418 original size:15 final size:15
Alignment explanation
Indices: 39744398--39744426 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39744388 CTTTTGTGGT
39744398 TTCTGTTTTGTATGG
1 TTCTGTTTTGTATGG
39744413 TTCTGTTTTGTATG
1 TTCTGTTTTGTATG
39744427 TTTGTATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.24, T:0.62
Consensus pattern (15 bp):
TTCTGTTTTGTATGG
Found at i:39745554 original size:29 final size:29
Alignment explanation
Indices: 39745512--39745583 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
39745502 ATTGTTGCAA
39745512 TGGAAATTGTCTGCAGTTTTCAATGAAAC
1 TGGAAATTGTCTGCAGTTTTCAATGAAAC
* *
39745541 TGGAAATTGTCTGCTGTTTTTAATGAAAC
1 TGGAAATTGTCTGCAGTTTTCAATGAAAC
39745570 TGGAAATTGT-TGCA
1 TGGAAATTGTCTGCA
39745584 TTTGTTTAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (29 bp):
TGGAAATTGTCTGCAGTTTTCAATGAAAC
Found at i:39746084 original size:13 final size:13
Alignment explanation
Indices: 39746066--39746090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39746056 TTTATTAGTG
39746066 AAAGAGTACATAA
1 AAAGAGTACATAA
39746079 AAAGAGTACATA
1 AAAGAGTACATA
39746091 CAAATTTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (13 bp):
AAAGAGTACATAA
Found at i:39749492 original size:16 final size:16
Alignment explanation
Indices: 39749471--39749512 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39749461 TTATTAAATT
*
39749471 ATATATTTTAATTATA
1 ATATATTTTAATAATA
39749487 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
39749502 AT-TATGTTTAA
1 ATATAT-TTTAA
39749513 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:39749497 original size:15 final size:15
Alignment explanation
Indices: 39749462--39749503 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39749452 TTAAGAATTT
*
39749462 TATTAAATTAT-ATA
1 TATTTAATTATAATA
39749476 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
39749490 TATTTAATAATAAT
1 TATTTAATTATAAT
39749504 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:39749747 original size:16 final size:16
Alignment explanation
Indices: 39749726--39749758 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39749716 TTGATTTGCT
39749726 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
39749742 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
39749758 A
1 A
39749759 ATATAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:39750096 original size:15 final size:15
Alignment explanation
Indices: 39750076--39750105 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39750066 ATCTATAAAG
39750076 ACATAATAAATTGTT
1 ACATAATAAATTGTT
39750091 ACATAATAAATTGTT
1 ACATAATAAATTGTT
39750106 TATCTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
ACATAATAAATTGTT
Found at i:39755562 original size:18 final size:18
Alignment explanation
Indices: 39755513--39755581 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
39755503 ACTCAGGTCG
* * *
39755513 CAAAGCTGCGAGCCCATC
1 CAAAGTTGCGAGCTCATA
* *
39755531 CAAACTTGCGAGCTCATT
1 CAAAGTTGCGAGCTCATA
39755549 CAAAGTTGCGAGCTCA-A
1 CAAAGTTGCGAGCTCATA
*
39755566 CAAAGATGCGAGCTCA
1 CAAAGTTGCGAGCTCA
39755582 ACCAAGATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 15 0.34
18 29 0.66
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (18 bp):
CAAAGTTGCGAGCTCATA
Found at i:39755575 original size:17 final size:17
Alignment explanation
Indices: 39755537--39755590 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
39755527 CATCCAAACT
* *
39755537 TGCGAGCTCATTCAAAGT
1 TGCGAGCTCA-ACAAAGA
39755555 TGCGAGCTCAACAAAGA
1 TGCGAGCTCAACAAAGA
*
39755572 TGCGAGCTCAACCAAGA
1 TGCGAGCTCAACAAAGA
39755589 TG
1 TG
39755591 TTATCAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 23 0.70
18 10 0.30
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (17 bp):
TGCGAGCTCAACAAAGA
Found at i:39761149 original size:58 final size:58
Alignment explanation
Indices: 39761027--39761149 Score: 167
Period size: 57 Copynumber: 2.1 Consensus size: 58
39761017 ATACAAATTG
**
39761027 TGAAAATGGAGAAATGAGAAACATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
1 TGAAAATCAAGAAATGAGAAACATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
* * * * *
39761085 TAAAAATCAAGAAATGA-AAATATTTGGAATTGAATGTGGTTTTCTCCAAAATGAAAAA
1 TGAAAATCAAGAAATGAGAAACATTTGGAAATGAATATGATTTTCTCCAAAATG-AAAA
39761143 TGAAAAT
1 TGAAAAT
39761150 GACTTGGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 32 0.57
58 24 0.43
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.28
Consensus pattern (58 bp):
TGAAAATCAAGAAATGAGAAACATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
Found at i:39761157 original size:45 final size:46
Alignment explanation
Indices: 39761087--39761174 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
39761077 AATGAAAATA
* * *
39761087 AAAATCAAGAAATGAAAATATTTGGAATTGAA-TGTGGTTTTCTCC
1 AAAATCAAGAAATGAAAATACTTGGAAATGAATTATGGTTTTCTCC
*
39761132 AAAATGAA-AAATGAAAATGACTTGGAAATGAATTATGGTTTTC
1 AAAATCAAGAAATGAAAAT-ACTTGGAAATGAATTATGGTTTTC
39761175 AAATTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 10 0.27
45 18 0.49
46 9 0.24
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (46 bp):
AAAATCAAGAAATGAAAATACTTGGAAATGAATTATGGTTTTCTCC
Found at i:39764290 original size:51 final size:51
Alignment explanation
Indices: 39764217--39764321 Score: 156
Period size: 51 Copynumber: 2.1 Consensus size: 51
39764207 ACTATTTACT
* * *
39764217 TATATGATCATTCAAAGTTGTCTACTAGAGTTATTGTTACTAAATTATTTA
1 TATATGATCATTCAAAGCTGTCTACTAGAGTCATTGTCACTAAATTATTTA
* * *
39764268 TATATGATCATTTAGAGCTGTCTACTTGAGTCATTGTCACTAAATTATTTA
1 TATATGATCATTCAAAGCTGTCTACTAGAGTCATTGTCACTAAATTATTTA
39764319 TAT
1 TAT
39764322 CTTGAGCTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (51 bp):
TATATGATCATTCAAAGCTGTCTACTAGAGTCATTGTCACTAAATTATTTA
Found at i:39768825 original size:26 final size:26
Alignment explanation
Indices: 39768796--39768858 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
39768786 CTACCTACAA
*
39768796 TAGTTTCAGAATATCATAACATTTAT
1 TAGTTTCAGAATATCATAACATGTAT
* *
39768822 TAGTTTCAGATTATCATAGCATGTAT
1 TAGTTTCAGAATATCATAACATGTAT
*
39768848 CAGTTTCAGAA
1 TAGTTTCAGAA
39768859 CACTTACAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (26 bp):
TAGTTTCAGAATATCATAACATGTAT
Found at i:39769610 original size:34 final size:34
Alignment explanation
Indices: 39769566--39769633 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
39769556 GCACAGTTGA
* *
39769566 ACAGTCTTGGGCCTAAGCCCTTTTCAATATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATATCAATAT-AGTG
*
39769601 ACAGT-TTGGGCCTTAGCCCATATCAATATAGTG
1 ACAGTCTTGGGCCTAAGCCCATATCAATATAGTG
39769634 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 4 0.13
34 21 0.70
35 5 0.17
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATATCAATATAGTG
Found at i:39771019 original size:92 final size:92
Alignment explanation
Indices: 39770856--39771029 Score: 249
Period size: 92 Copynumber: 1.9 Consensus size: 92
39770846 TAATTTTCAC
* * *
39770856 TTATTTCTCTTATGTCTCAAAAACAAGCAATTTCAGCTTTTCACCGAATCCTATTTTTTGCATTT
1 TTATATCTCTTATGTCTCAAAAACAAGCAATTTCAGCTTTTCACCAAATCCCATTTTTTGCATTT
*
39770921 TAGGTACACACCTGTATTGTTTTTGCT
66 CAGGTACACACCTGTATTGTTTTTGCT
* * * * * *
39770948 TTATATCTCTTATTTCTCGAAAACAAGTAATTTTAGCTTTTCATCAAATCCCATTTTTTGTATTT
1 TTATATCTCTTATGTCTCAAAAACAAGCAATTTCAGCTTTTCACCAAATCCCATTTTTTGCATTT
*
39771013 CGGGTACACACCTGTAT
66 CAGGTACACACCTGTAT
39771030 CATTTTCGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
92 71 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.44
Consensus pattern (92 bp):
TTATATCTCTTATGTCTCAAAAACAAGCAATTTCAGCTTTTCACCAAATCCCATTTTTTGCATTT
CAGGTACACACCTGTATTGTTTTTGCT
Found at i:39778686 original size:28 final size:28
Alignment explanation
Indices: 39778605--39778686 Score: 65
Period size: 28 Copynumber: 2.8 Consensus size: 28
39778595 ACAAAATGAT
*
39778605 TAGTTGGGTGACCAAAAAAGAAACAAATCCA
1 TAGTTAGGTGA-CAAAAAAG-AA-AAATCCA
* * **** *
39778636 TAGCTAGGTGACCAATTTTAAAAATTCA
1 TAGTTAGGTGACAAAAAAGAAAAATCCA
39778664 TAGTTAGGTGACAAAAAAGAAAA
1 TAGTTAGGTGACAAAAAAGAAAA
39778687 TGACTCATAG
Statistics
Matches: 37, Mismatches: 14, Indels: 3
0.69 0.26 0.06
Matches are distributed among these distances:
28 23 0.62
29 2 0.05
30 3 0.08
31 9 0.24
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (28 bp):
TAGTTAGGTGACAAAAAAGAAAAATCCA
Found at i:39785515 original size:22 final size:22
Alignment explanation
Indices: 39785480--39785528 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
39785470 TATTGTTTAA
*
39785480 AAATATATAAATAATTTTATTT
1 AAATATATAAATAATTTCATTT
* * *
39785502 AAATATTTATATAATTTCGTTT
1 AAATATATAAATAATTTCATTT
39785524 AAATA
1 AAATA
39785529 AAAAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
AAATATATAAATAATTTCATTT
Found at i:39785624 original size:49 final size:49
Alignment explanation
Indices: 39785567--39785668 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
39785557 GTAAAATGGA
39785567 GAATTTAGATAGGGAAAGTTGGGTTTGAGTCTAAAATTAATTTTTTTTG
1 GAATTTAGATAGGGAAAGTTGGGTTTGAGTCTAAAATTAATTTTTTTTG
**
39785616 GAATTTAGATAGGGAAAGTTGGGTTTGAGTCTAAAATTTTTTTTTTTTG
1 GAATTTAGATAGGGAAAGTTGGGTTTGAGTCTAAAATTAATTTTTTTTG
39785665 GAAT
1 GAAT
39785669 CACGCCTGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (49 bp):
GAATTTAGATAGGGAAAGTTGGGTTTGAGTCTAAAATTAATTTTTTTTG
Found at i:39787425 original size:9 final size:8
Alignment explanation
Indices: 39787409--39787435 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
39787399 TTCATTTGTG
39787409 TATTTTTT
1 TATTTTTT
39787417 TATTTTTT
1 TATTTTTT
39787425 TATTTTTT
1 TATTTTTT
39787433 TAT
1 TAT
39787436 GTCTAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:39787662 original size:20 final size:20
Alignment explanation
Indices: 39787637--39787683 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
39787627 ACCTTATATC
39787637 TATATATCTT-TATATCTTAT
1 TATATAT-TTATATATCTTAT
*
39787657 TATATATTTATATGTCTTAT
1 TATATATTTATATATCTTAT
39787677 TATATAT
1 TATATAT
39787684 ATATCTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATATTTATATATCTTAT
Found at i:39787666 original size:18 final size:18
Alignment explanation
Indices: 39787630--39787683 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 18
39787620 TATATATACC
*
39787630 TTATATC-TA-TATATCT
1 TTATATCTTATTATATAT
39787646 TTATATCTTATTATATAT
1 TTATATCTTATTATATAT
39787664 TTATATGTCTTATTATATAT
1 TTATA--TCTTATTATATAT
39787684 ATATCTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 7 0.21
17 2 0.06
18 11 0.33
20 13 0.39
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATATCTTATTATATAT
Found at i:39787686 original size:18 final size:19
Alignment explanation
Indices: 39787637--39787692 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
39787627 ACCTTATATC
* *
39787637 TATATATCTTTATATCTTAT
1 TATATAT-TATATCTCTTAT
*
39787657 TATATATTTATATGTCTTAT
1 TATATA-TTATATCTCTTAT
39787677 TATATA-TATATCTCTT
1 TATATATTATATCTCTT
39787693 TTACATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 9 0.28
20 22 0.69
21 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (19 bp):
TATATATTATATCTCTTAT
Found at i:39788777 original size:137 final size:137
Alignment explanation
Indices: 39788531--39788806 Score: 516
Period size: 137 Copynumber: 2.0 Consensus size: 137
39788521 CGTAACCGAC
39788531 TCCCGAACCCGTTTTCTAAATTCCGTGGACCAAAATCGTTGTTTTAATAAAATCAAACCGTTTAT
1 TCCCGAACCCGTTTTCTAAATTCCGTGGACCAAAATCGTTGTTTTAATAAAATCAAACCGTTTAT
*
39788596 TAAAAACAATCACTTTTCGAGGTGATCCAATCACACCTCATTAAAAAGGATTGGTGGCGACTCCC
66 TAAAAACAACCACTTTTCGAGGTGATCCAATCACACCTCATTAAAAAGGATTGGTGGCGACTCCC
39788661 GTTTTTT
131 GTTTTTT
* *
39788668 TCCCGAACCCGTTTTCTGAATTTCGTGGACCAAAATCGTTGTTTTAATAAAATCAAACCGTTTAT
1 TCCCGAACCCGTTTTCTAAATTCCGTGGACCAAAATCGTTGTTTTAATAAAATCAAACCGTTTAT
39788733 TAAAAACAACCACTTTTCGAGGTGATCCAATCACACCTCATTAAAAAGGATTGGTGGCGACTCCC
66 TAAAAACAACCACTTTTCGAGGTGATCCAATCACACCTCATTAAAAAGGATTGGTGGCGACTCCC
*
39788798 TTTTTTT
131 GTTTTTT
39788805 TC
1 TC
39788807 GTTTTCGTCA
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (137 bp):
TCCCGAACCCGTTTTCTAAATTCCGTGGACCAAAATCGTTGTTTTAATAAAATCAAACCGTTTAT
TAAAAACAACCACTTTTCGAGGTGATCCAATCACACCTCATTAAAAAGGATTGGTGGCGACTCCC
GTTTTTT
Found at i:39791938 original size:7 final size:7
Alignment explanation
Indices: 39791926--39791962 Score: 53
Period size: 6 Copynumber: 5.7 Consensus size: 7
39791916 CTGATCGAAA
39791926 AAAAATC
1 AAAAATC
39791933 AAAAATC
1 AAAAATC
39791940 -AAAATC
1 AAAAATC
39791946 -AAAATC
1 AAAAATC
39791952 AAAAA-C
1 AAAAATC
39791958 AAAAA
1 AAAAA
39791963 AGAAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAATC
Found at i:39791951 original size:19 final size:19
Alignment explanation
Indices: 39791927--39791994 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
39791917 TGATCGAAAA
*
39791927 AAAATCAAAAATCAAAATC
1 AAAAGCAAAAATCAAAATC
* **
39791946 AAAATCAAAAA-CAAAAAAG
1 AAAAGCAAAAATC-AAAATC
* *
39791965 AAAAGAAAAAATCAAAGTC
1 AAAAGCAAAAATCAAAATC
39791984 AAAAGCAAAAA
1 AAAAGCAAAAA
39791995 AGAGAAATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 1 0.03
19 37 0.95
20 1 0.03
ACGTcount: A:0.74, C:0.12, G:0.06, T:0.09
Consensus pattern (19 bp):
AAAAGCAAAAATCAAAATC
Found at i:39791986 original size:26 final size:27
Alignment explanation
Indices: 39791946--39792030 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 27
39791936 AATCAAAATC
**
39791946 AAAATCAAAAACAAAA-AAGAAAAGA-A
1 AAAATCAAAGTCAAAACAA-AAAAGAGA
39791972 AAAATCAAAGTCAAAAGCAAAAAAGAGA
1 AAAATCAAAGTCAAAA-CAAAAAAGAGA
* *
39792000 AATCAATCAAAGTCAAAATAAAATAG-GA
1 AA--AATCAAAGTCAAAACAAAAAAGAGA
39792028 AAA
1 AAA
39792031 GAGAAAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
26 15 0.30
27 6 0.12
28 9 0.18
29 6 0.12
30 14 0.28
ACGTcount: A:0.71, C:0.09, G:0.11, T:0.09
Consensus pattern (27 bp):
AAAATCAAAGTCAAAACAAAAAAGAGA
Found at i:39792010 original size:30 final size:30
Alignment explanation
Indices: 39791940--39792017 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 30
39791930 ATCAAAAATC
*
39791940 AAAATCAAAATCAAAAACAAAAAAGAAAAGAA
1 AAAATCAAAGTCAAAAACAAAAAAG--AAGAA
*
39791972 AAAATCAAAGTCAAAAGCAAAAAAG-AGAA
1 AAAATCAAAGTCAAAAACAAAAAAGAAGAA
*
39792001 ATCAATCAAAGTCAAAA
1 A-AAATCAAAGTCAAAA
39792018 TAAAATAGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 5 0.12
30 14 0.33
32 23 0.55
ACGTcount: A:0.71, C:0.12, G:0.09, T:0.09
Consensus pattern (30 bp):
AAAATCAAAGTCAAAAACAAAAAAGAAGAA
Found at i:39793829 original size:131 final size:131
Alignment explanation
Indices: 39793659--39794853 Score: 1860
Period size: 131 Copynumber: 9.2 Consensus size: 131
39793649 TCGGTGAAAT
* * * *
39793659 CACAAGTCCTATGTCCCTAACCAGCAGCGGAATAGGTTGGAAATTACAGATCTCGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
*
39793724 CAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39793789 C
131 C
*
39793790 CACAAGTCCTATGTCCCTGACCGGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
*
39793855 CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39793920 C
131 C
** * *
39793921 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTATAGATATTGTCTTCCTAAA
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCT-AA
* *
39793986 G-AGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAA
65 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAA
39794050 GC
130 GC
* * * *
39794052 CACAAGTCCTATGTCCCTGACCGGCAGTGAAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAA
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* * *** *
39794117 CAGTAGCGGAGTAGATCGAAGACGGCGGATCTTATCTTCTTTAGGAGCAGGGAAACAGA-TTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39794181 C
131 C
* * * *
39794182 CACAAGTCCTATGTACC-GACCAGCAGTGTAATAGGTTGGAAATTGTATATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
** * *
39794246 CAGTAGCGGAGCAGATCGAAGACAACGAATCTTATCTTCCCAAGGAGTAGGG-AACAGATTTAAA
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39794310 C
131 C
39794311 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* *
39794376 TAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39794441 C
131 C
*
39794442 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAAATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* * *
39794507 CAGTAGCGGAACAGATCGAAGACGGCGAATCTTATTTTCCCCAAGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39794572 C
131 C
* * * *
39794573 CACAAGTCCTATGCCCCTGACCAGTAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* * *
39794638 CAGTAGCGGAGTAGATCGAAGACAGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39794703 C
131 C
* ** *
39794704 CACAAGTCCTATGTCCTTGACCAATAGTGG-ATAGGTTGGAAATTGCAGATCTTGTCTCCATAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* * *
39794768 CAATAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAAGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39794833 C
131 C
* * *
39794834 CACGAGTCCTTTCTCCCTGA
1 CACAAGTCCTATGTCCCTGA
39794854 GGTTACAGTG
Statistics
Matches: 971, Mismatches: 88, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
128 6 0.01
129 106 0.11
130 222 0.23
131 634 0.65
132 3 0.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (131 bp):
CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
C
Found at i:39794958 original size:652 final size:650
Alignment explanation
Indices: 39793659--39794972 Score: 1849
Period size: 652 Copynumber: 2.0 Consensus size: 650
39793649 TCGGTGAAAT
39793659 CACAAGTCCTATGTCCCTAACCAGCAGCGGAATAGGTTGGAAATTACAGATCTCGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTAACCAGCAGCGGAATAGGTTGGAAATTACAGATCTCGTCTCCCTAAG
*
39793724 CAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
* *
39793789 CCACAAGTCCTATGTCCCTGACCGGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAA
131 CCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAAATCTTGTCTCCCTAA
* *
39793854 GCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAA
196 GCAGTAGCGGAACAGATCGAAGACGGCAAATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAA
* * * *
39793919 GCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTATAGATATTGTCTTCCTA
261 GCCACAAGTCCTATGCCCCTGACCAGCAGTGGAATAGGTTAGAAATTACAGATATTGTCTCCCTA
* *
39793984 AAGAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTA
326 AAGAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTA
** *
39794049 AGCCACAAGTCCTATGTCCCTGACCGGCAGTGAAATAGGTTGGAAATTACAGATCTTGTCTCCCT
391 AGCCACAAGTCCTATGTCCCTGACCAACAGTGAAATAGGTTGGAAATTACAGATCTTGTCTCCAT
* * * * *** *
39794114 AAACAGTAGCGGAGTAGATCGAAGACGGCGGATCTTATCTTCTTTAGGAGCAGGGAAACAGATTA
456 AAACAATAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGCAAGGAAACAGATTA
* * * ** * * * *
39794179 AGCCACAAGTCCTATGTACCGACCAGCAGTGTAATAGGTTGGAAATTGTATATCTTGTCTCCCTA
521 AGCCACAAGTCCTATCTACCGACCAGCAGTGGAACAGACT-GAAATAGCAGATCTTATCTCCCTA
* *
39794244 AGCAGTAGCGGAGCAGATCGAAGACAACGAATCTTATCTTCCCAAGGAGTAGGGAACAGATTTAA
585 AGCAGTAGCGGAGCAGATCGAAGACAACGAATCTTATATT-CCAAGGAGTAAGGAACAGATTTAA
39794309 AC
649 AC
* * * *
39794311 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTAACCAGCAGCGGAATAGGTTGGAAATTACAGATCTCGTCTCCCTAAG
* *
39794376 TAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
39794441 CCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAAATCTTGTCTCCCTAA
131 CCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAAATCTTGTCTCCCTAA
* *
39794506 GCAGTAGCGGAACAGATCGAAGACGGCGAATCTTATTTTCCCCAAGAGTAGGGAAACAGATTTAA
196 GCAGTAGCGGAACAGATCGAAGACGGCAAATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAA
* *
39794571 GCCACAAGTCCTATGCCCCTGACCAGTAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCT-
261 GCCACAAGTCCTATGCCCCTGACCAGCAGTGGAATAGGTTAGAAATTACAGATATTGTCTCCCTA
*
39794635 AAGCAGTAGCGGAGTAGATCGAAGAC-AGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATT
326 AAG-AGTAGCGGAGCAGATCGAAGACGA-CAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATT
* * * *
39794699 TAAGCCACAAGTCCTATGTCCTTGACCAATAGTG-GATAGGTTGGAAATTGCAGATCTTGTCTCC
389 TAAGCCACAAGTCCTATGTCCCTGACCAACAGTGAAATAGGTTGGAAATTACAGATCTTGTCTCC
* *
39794763 ATAAGCAATAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAAGGAAACAGAT
454 ATAAACAATAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGCAAGGAAACAGA-
* * * ** * *
39794828 TTAAGCCACGAGTCCTTTCTCCCTGAGGTTA-CAGTGGAACAGACT-AAGTAAGCAGGTCTTATC
518 TTAAGCCACAAGTCCTATCTACC-GA--CCAGCAGTGGAACAGACTGAAAT-AGCAGATCTTATC
*** *
39794891 -CCTCTGAAGTTGCAGT-G-GGA-CAGATCGAAGATGGCGAATCTTATATT-CAA-GTGTAAGGA
579 TCC-CT-AA---GCAGTAGCGGAGCAGATCGAAGACAACGAATCTTATATTCCAAGGAGTAAGGA
*
39794950 AGCAGATTTAAGC
639 A-CAGATTTAAAC
*
39794963 CACGAGTCCT
1 CACAAGTCCT
39794973 TTCTCCTTGA
Statistics
Matches: 586, Mismatches: 63, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
651 93 0.16
652 436 0.74
653 12 0.02
654 35 0.06
655 4 0.01
656 1 0.00
657 5 0.01
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (650 bp):
CACAAGTCCTATGTCCCTAACCAGCAGCGGAATAGGTTGGAAATTACAGATCTCGTCTCCCTAAG
CAGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
CCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAAATCTTGTCTCCCTAA
GCAGTAGCGGAACAGATCGAAGACGGCAAATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAA
GCCACAAGTCCTATGCCCCTGACCAGCAGTGGAATAGGTTAGAAATTACAGATATTGTCTCCCTA
AAGAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTA
AGCCACAAGTCCTATGTCCCTGACCAACAGTGAAATAGGTTGGAAATTACAGATCTTGTCTCCAT
AAACAATAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGCAAGGAAACAGATTA
AGCCACAAGTCCTATCTACCGACCAGCAGTGGAACAGACTGAAATAGCAGATCTTATCTCCCTAA
GCAGTAGCGGAGCAGATCGAAGACAACGAATCTTATATTCCAAGGAGTAAGGAACAGATTTAAAC
Found at i:39795019 original size:129 final size:129
Alignment explanation
Indices: 39794779--39795223 Score: 638
Period size: 129 Copynumber: 3.4 Consensus size: 129
39794769 AATAGCGGAG
* * * *
39794779 CAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAAGGAAACAGATTTAAGCCACGAGTCCT
1 CAGATCGAAGACGGCGAATCTTATCTT---CAAGTGTAAGGAAGCAGATTTAAGCCACGAGTCCT
* *
39794844 TTCTCCCTGAGGTTACAGTGGAACAGACTAAGTAAGCAGGTCTTATCCCTCTGAAGTTGCAGTGG
63 TTCTCCCTGAGGTTACAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCACTGAAGTTGCAGTGG
39794909 GA
128 GA
* *
39794911 CAGATCGAAGATGGCGAATCTTATATTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTCCTTTC
1 CAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTCCTTTC
* * * * * *
39794976 TCCTTGAGGTTACAGTGGAGCGGACTAAGTAAGTAGGTTTTATCCCCCTGAAGTTGCAGTGGAA
66 TCCCTGAGGTTACAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCACTGAAGTTGCAGTGGGA
*
39795040 CAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAACGAAGCAGATTTAAGCCACGAGTCCTTTC
1 CAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTCCTTTC
* * * * * *
39795105 TCCCTGAAGTTGCAGTAGAGCAGATTAAGTAAGCAGGTCTTATCTCGACTGAAGTAGCAGTGGGA
66 TCCCTGAGGTTACAGTGGAGCAGACTAAGTAAGCAGGTCTTATC-CCACTGAAGTTGCAGTGGGA
* * *
39795170 CAGATCGAAGACAGCGAATCTTATCTTCAAGCGTAAGGAAGCAAATTTAAGCCA
1 CAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
39795224 TAAATCCTAT
Statistics
Matches: 280, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
129 190 0.68
130 66 0.24
132 24 0.09
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (129 bp):
CAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTCCTTTC
TCCCTGAGGTTACAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCACTGAAGTTGCAGTGGGA
Found at i:39795289 original size:259 final size:258
Alignment explanation
Indices: 39794779--39795294 Score: 631
Period size: 259 Copynumber: 2.0 Consensus size: 258
39794769 AATAGCGGAG
* *
39794779 CAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAAGGAAACAGATTTAAGCCACGAGTCCT
1 CAGATCAAAGACGGCGAATCTTATCTT--CCAAGAGTAACGAAACAGATTTAAGCCACGAGTCCT
* * * *
39794844 TTCTCCCTGAGGTTACAGTGGAACAGACTAAGTAAGCAGGTCTTATCCCTCTGAAGTTGCAGTGG
64 TTCTCCCTGAAGTTACAGTAGAACAGACTAAGTAAGCAGGTCTTATCCCACTGAAGTAGCAGTGG
** * * * * *
39794909 GACAGATCGAAGATGGCGAATCTTATATTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTCCTT
129 GACAGATCGAAGACAGCGAATCTTATATTCAAGCGTAAGGAAGCAAATTTAAGCCACAAATCCTA
* * * * ** ** *
39794974 TCTCCTTGAGGTTACAGTGGAGCGGACTAAGTAAGTAGGTTTTATCCCCCTGAAGTTGCAGTGGA
194 TCTCCCTAAAGTTACAGTGGAGCAGACTAAG-AACCACATTTCATCCCCCTGAAGTTGCAGTGGA
39795039 A
258 A
* * *
39795040 CAGATCGAAGACGGCGAATCTTATCTT-CAAGTGTAACGAAGCAGATTTAAGCCACGAGTCCTTT
1 CAGATCAAAGACGGCGAATCTTATCTTCCAAGAGTAACGAAACAGATTTAAGCCACGAGTCCTTT
* * * *
39795104 CTCCCTGAAGTTGCAGTAGAGCAGATTAAGTAAGCAGGTCTTATCTCGACTGAAGTAGCAGTGGG
66 CTCCCTGAAGTTACAGTAGAACAGACTAAGTAAGCAGGTCTTATC-CCACTGAAGTAGCAGTGGG
* *
39795169 ACAGATCGAAGACAGCGAATCTTATCTTCAAGCGTAAGGAAGCAAATTTAAGCCATAAATCCTAT
130 ACAGATCGAAGACAGCGAATCTTATATTCAAGCGTAAGGAAGCAAATTTAAGCCACAAATCCTAT
** * * **
39795234 CTCCCTAAAGTTGTAGTGGAGCAGATTAA-AACCACATATCTCATCTCTTTGAAGTTGCAGT
195 CTCCCTAAAGTTACAGTGGAGCAGACTAAGAACCACAT-T-TCATCCCCCTGAAGTTGCAGT
39795295 AGAGGGGATT
Statistics
Matches: 215, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
257 4 0.02
258 74 0.34
259 111 0.52
261 26 0.12
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (258 bp):
CAGATCAAAGACGGCGAATCTTATCTTCCAAGAGTAACGAAACAGATTTAAGCCACGAGTCCTTT
CTCCCTGAAGTTACAGTAGAACAGACTAAGTAAGCAGGTCTTATCCCACTGAAGTAGCAGTGGGA
CAGATCGAAGACAGCGAATCTTATATTCAAGCGTAAGGAAGCAAATTTAAGCCACAAATCCTATC
TCCCTAAAGTTACAGTGGAGCAGACTAAGAACCACATTTCATCCCCCTGAAGTTGCAGTGGAA
Found at i:39795374 original size:85 final size:86
Alignment explanation
Indices: 39795226--39795431 Score: 213
Period size: 85 Copynumber: 2.4 Consensus size: 86
39795216 TTAAGCCATA
* * * *
39795226 AATCCTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAACCACATATCTCATCTCTTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACATATCTCATCTCCTTGAAGTTG
* *
39795291 CAGTAGAGGGGATTACA-T-T
66 CAGTAGAGCGGATTAAAGTAT
* ** *
39795310 GAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGACA-ATC-CTATCTCCTTGAAG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAACCACATATCTC-ATCTCCTTGAAG
* *
39795373 TTGTAGTGGAGCGGATTAAAGTAAT
63 TTGCAGTAGAGCGGATTAAAGT-AT
* *
39795398 AGATCTTATCTCTCTGAAGTTGCAGCGGAGCAGA
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
39795432 CTGAGAAAAC
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
84 1 0.01
85 61 0.61
86 7 0.07
87 1 0.01
88 30 0.30
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (86 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACATATCTCATCTCCTTGAAGTTG
CAGTAGAGCGGATTAAAGTAT
Found at i:39795381 original size:44 final size:44
Alignment explanation
Indices: 39795226--39795608 Score: 171
Period size: 44 Copynumber: 8.8 Consensus size: 44
39795216 TTAAGCCATA
* * ** *
39795226 AATCCTATCTCCCTAAAGTTGTAGTGGAGCAGATT-AAAACCAC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGAC
** * ** *
39795269 ATAT-CTCATCTCTTTGAAGTTGCAGTAGAGGGGATT-ACA-TTG--
1 A-ATCCT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGTCGAC
* *
39795311 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGAC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGAC
* * * * * *
39795355 AATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGT-AAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGAC
* * * * ***
39795398 AGATCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTG-AGAAAAC
1 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGAC
* *** * * **
39795442 AAGTCTTATC-CACCTGAAGTCATAGTGGGGCAGACTGAAGAAG-C
1 AA-TCCTATCTC-CCTGAAGTTGCAGTGGAGCAGATTGAAGTCGAC
* * *
39795486 ACATCTTATCTCCCT-AAGGTTGCAGTGGAGCAGATTGAATTCGAT
1 A-ATCCTATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAAGTCGAC
* * * * *
39795531 AATCCTATCTCCCTGGAGTTGTAGTGGAGCGGATT-ACAGT-AAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGTCGAC
* * **
39795574 AGATCTTATCTCTCTGAAGTTGCAGAAGAGCAGAT
1 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
39795609 CGCAGTAAGT
Statistics
Matches: 255, Mismatches: 65, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
41 26 0.10
42 5 0.02
43 15 0.06
44 200 0.78
45 9 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGAC
Found at i:39795430 original size:88 final size:88
Alignment explanation
Indices: 39795312--39795608 Score: 314
Period size: 88 Copynumber: 3.4 Consensus size: 88
39795302 ATTACATTGA
* *
39795312 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGACAATCCTATCTCCTTGAAGTTGT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGACAATCCTATCTCCCTGAAGTTGT
39795377 AGTGGAGCGGATTAAAGTAATAG
66 AGTGGAGCGGATTAAAGTAATAG
* * * *** * *
39795400 ATCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTG-AGAAAACAAGTCTTATC-CACCTGAAGTC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGACAA-TCCTATCTC-CCTGAAGTT
* * * * * * *
39795463 ATAGTGGGGCAGACTGAAG-AAGCAC
64 GTAGTGGAGCGGATTAAAGTAA-TAG
* * *
39795488 ATCTTATCTCCCT-AAGGTTGCAGTGGAGCAGATTGAATTCGATAATCCTATCTCCCTGGAGTTG
1 ATCTTATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAAGTCGACAATCCTATCTCCCTGAAGTTG
*
39795552 TAGTGGAGCGGATTACAGTAATAG
65 TAGTGGAGCGGATTAAAGTAATAG
* **
39795576 ATCTTATCTCTCTGAAGTTGCAGAAGAGCAGAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
39795609 CGCAGTAAGT
Statistics
Matches: 162, Mismatches: 39, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
87 11 0.07
88 142 0.88
89 9 0.06
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (88 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGACAATCCTATCTCCCTGAAGTTGT
AGTGGAGCGGATTAAAGTAATAG
Found at i:39795919 original size:11 final size:11
Alignment explanation
Indices: 39795889--39795925 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39795879 GCCCGAGCAC
39795889 AAATATTAAAA-
1 AAATA-TAAAAT
39795900 AAA-ATAAAAT
1 AAATATAAAAT
39795910 AAATATAAAAT
1 AAATATAAAAT
39795921 AAATA
1 AAATA
39795926 AAATGTTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.21
10 4 0.17
11 15 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:39795924 original size:20 final size:21
Alignment explanation
Indices: 39795889--39795929 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
39795879 GCCCGAGCAC
39795889 AAATATTAAAAAAAATAAAAT
1 AAATATTAAAAAAAATAAAAT
*
39795910 AAATA-TAAAATAAATAAAAT
1 AAATATTAAAAAAAATAAAAT
39795930 GTTCAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATATTAAAAAAAATAAAAT
Found at i:39813222 original size:6 final size:6
Alignment explanation
Indices: 39813213--39813238 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39813203 CTTAATTCTA
39813213 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
39813239 AAAACCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:39816507 original size:15 final size:16
Alignment explanation
Indices: 39816487--39816516 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39816477 ATGTTTGTTC
39816487 ATTAAGCTTT-AATTA
1 ATTAAGCTTTGAATTA
39816502 ATTAAGCTTTGAATT
1 ATTAAGCTTTGAATT
39816517 TGCTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (16 bp):
ATTAAGCTTTGAATTA
Found at i:39819516 original size:17 final size:17
Alignment explanation
Indices: 39819494--39819529 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39819484 CTCATTTTTC
*
39819494 TATTTTGATACTTAAAT
1 TATTTTGATACTCAAAT
*
39819511 TATTTTGGTACTCAAAT
1 TATTTTGATACTCAAAT
39819528 TA
1 TA
39819530 AAAAAATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (17 bp):
TATTTTGATACTCAAAT
Found at i:39823683 original size:16 final size:16
Alignment explanation
Indices: 39823662--39823718 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
39823652 TTTGGTTCGT
*
39823662 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
39823678 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
39823694 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
39823710 TGTAATGGA
1 TGTAATGGA
39823719 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:39823985 original size:18 final size:17
Alignment explanation
Indices: 39823964--39823998 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39823954 TTATTATTAA
*
39823964 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39823982 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39823999 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39824006 original size:79 final size:79
Alignment explanation
Indices: 39823923--39824166 Score: 220
Period size: 79 Copynumber: 3.1 Consensus size: 79
39823913 TTATTATCAA
39823923 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
39823988 TTTAATAAAATTCT
66 TTTAATAAAATTCT
* * * * **** * * *
39824002 TAATAATTAGCA-TAAAT-TTGTTTTGGTA-AATTATTATT--GT-TATTGTT-ATTTAAAT-TT
1 TAATAAATA--ATTTAATCATATTTAAACATAATTATTATTAAATATATT-TTAATTAAAATATA
* * *
39824059 TAA--TAAGATTAATATCAA
63 TAATTTAATA-AAAT-TC-T
*
39824077 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
39824142 TTTAATAAAATTCT
66 TTTAATAAAATTCT
*
39824156 TAATAATTAAT
1 TAATAAATAAT
39824167 ATTCTTATAT
Statistics
Matches: 119, Mismatches: 30, Indels: 32
0.66 0.17 0.18
Matches are distributed among these distances:
72 4 0.03
73 4 0.03
74 10 0.08
75 24 0.20
76 13 0.11
78 12 0.10
79 34 0.29
80 10 0.08
81 4 0.03
82 4 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (79 bp):
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
TTTAATAAAATTCT
Found at i:39824135 original size:16 final size:16
Alignment explanation
Indices: 39824098--39824139 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39824088 TTAATCATAT
*
39824098 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
39824114 TT-AAATATATTATAA
1 TTAAAATATATTATAA
39824129 TTAAAATATAT
1 TTAAAATATAT
39824140 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:39824137 original size:154 final size:156
Alignment explanation
Indices: 39823851--39824164 Score: 578
Period size: 154 Copynumber: 2.0 Consensus size: 156
39823841 TAGAATACCC
39823851 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
39823916 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
39823981 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAATAA
* *
39824008 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
39824071 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
39824136 ATATAATTTAATAAAATTCTTAATAA
131 ATATAATTTAATAAAATTCTTAATAA
39824162 TTA
1 TTA
39824165 ATATTCTTAT
Statistics
Matches: 154, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 93 0.60
155 1 0.01
157 60 0.39
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAA
Found at i:39824146 original size:14 final size:15
Alignment explanation
Indices: 39824107--39824148 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39824097 TTTAAACATA
*
39824107 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39824122 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
39824136 A-TATAATTTAATA
1 ATTATAATTAAATA
39824149 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Done.