Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 6 of 204
Found at i:2322117 original size:39 final size:38
Alignment explanation
Indices: 2322049--2322203 Score: 129
Period size: 38 Copynumber: 4.0 Consensus size: 38
2322039 GGTCCATTTT
*
2322049 TATTTTAAAAATTTTAAAAAATTTTAAAAATATTTTAAAAA
1 TATTTT-AAAA-TTTAAAAAA-ATTAAAAATATTTTAAAAA
* *
2322090 TATTTTAAAATTTAAAAAAATTAAAAA-AATTAAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAATATTTTAAAAA
* * ***
2322127 GTATTTTAAAATTAAATTAAAAAGT-ATTTTATTTTAAAAA
1 -TATTTTAAAATTTAA--AAAAATTAAAAATATTTTAAAAA
*
2322167 TATTTTAAAA-TTAAAAAGTATGT-AAAATATTTTAAAA
1 TATTTTAAAATTTAAAAA-AAT-TAAAAATATTTTAAAA
2322204 TTAAAAATAA
Statistics
Matches: 92, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
36 3 0.03
37 9 0.10
38 36 0.39
39 20 0.22
40 18 0.20
41 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (38 bp):
TATTTTAAAATTTAAAAAAATTAAAAATATTTTAAAAA
Found at i:2322125 original size:10 final size:9
Alignment explanation
Indices: 2322096--2322126 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2322086 AAAATATTTT
*
2322096 AAAATTTAA
1 AAAAATTAA
2322105 AAAAATTAA
1 AAAAATTAA
2322114 AAAAATTAA
1 AAAAATTAA
2322123 AAAA
1 AAAA
2322127 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:2322165 original size:17 final size:18
Alignment explanation
Indices: 2322083--2322187 Score: 65
Period size: 17 Copynumber: 5.6 Consensus size: 18
2322073 TAAAAATATT
2322083 TTAAAAA-TATTTTAAAA
1 TTAAAAAGTATTTTAAAA
* **
2322100 TTTAAAAA-AATTAAAAAAA
1 -TTAAAAAGTATT-TTAAAA
2322119 TTAAAAAAGTATTTTAAAATTAAA
1 TT-AAAAAGTATTTT---A--AAA
**
2322143 TTAAAAAGTATTTT-ATT
1 TTAAAAAGTATTTTAAAA
2322160 TTAAAAA-TATTTTAAAA
1 TTAAAAAGTATTTTAAAA
2322177 TTAAAAAGTAT
1 TTAAAAAGTAT
2322188 GTAAAATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
16 6 0.09
17 16 0.24
18 15 0.22
19 9 0.13
20 3 0.04
22 1 0.01
23 12 0.18
24 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TTAAAAAGTATTTTAAAA
Found at i:2322176 original size:11 final size:11
Alignment explanation
Indices: 2322049--2322099 Score: 81
Period size: 11 Copynumber: 4.9 Consensus size: 11
2322039 GGTCCATTTT
2322049 TATTTT-AAAA
1 TATTTTAAAAA
2322059 -ATTTTAAAAA
1 TATTTTAAAAA
2322069 -ATTTTAAAAA
1 TATTTTAAAAA
2322079 TATTTTAAAAA
1 TATTTTAAAAA
2322090 TATTTTAAAA
1 TATTTTAAAA
2322100 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.13
10 14 0.36
11 20 0.51
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:2322192 original size:17 final size:17
Alignment explanation
Indices: 2322140--2322194 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2322130 TTTTAAAATT
*
2322140 AAATTAAAAAGTATTTT
1 AAATTAAAAAGTATTTA
**
2322157 ATTTTAAAAA-TATTTTA
1 AAATTAAAAAGTA-TTTA
*
2322174 AAATTAAAAAGTATGTA
1 AAATTAAAAAGTATTTA
2322191 AAAT
1 AAAT
2322195 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
AAATTAAAAAGTATTTA
Found at i:2322224 original size:27 final size:27
Alignment explanation
Indices: 2322163--2322216 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2322153 TTTTATTTTA
**
2322163 AAAATATTTTAAAATTAAAAAGTATGT
1 AAAATATTTTAAAATTAAAAAGTAAAT
2322190 AAAATATTTTAAAATTAAAAA-TAAAT
1 AAAATATTTTAAAATTAAAAAGTAAAT
2322216 A
1 A
2322217 TATTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
AAAATATTTTAAAATTAAAAAGTAAAT
Found at i:2351111 original size:14 final size:14
Alignment explanation
Indices: 2351037--2351114 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
2351027 ATTTCAAGCA
2351037 ATTTATTTTTA-AT
1 ATTTATTTTTATAT
* * *
2351050 TTCTTATTTTTGTAAA
1 AT-TTATTTTTAT-AT
2351066 ATTTATTTTTATA-
1 ATTTATTTTTATAT
* * *
2351079 ATTTATATATATTT
1 ATTTATTTTTATAT
*
2351093 CTTTATTTTTATAT
1 ATTTATTTTTATAT
2351107 ATTTATTT
1 ATTTATTT
2351115 CCATTTTTTG
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 11 0.23
14 26 0.54
15 9 0.19
16 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (14 bp):
ATTTATTTTTATAT
Found at i:2351122 original size:20 final size:18
Alignment explanation
Indices: 2351079--2351114 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2351069 TATTTTTATA
* *
2351079 ATTTATATATATTTCTTT
1 ATTTTTATATATTTATTT
2351097 ATTTTTATATATTTATTT
1 ATTTTTATATATTTATTT
2351115 CCATTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTATATATTTATTT
Found at i:2351128 original size:27 final size:27
Alignment explanation
Indices: 2351067--2351129 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
2351057 TTTTGTAAAA
*
2351067 TTTATTTTTATAATTTATATATATTTC
1 TTTATTTTTATAATTTATATACATTTC
* *
2351094 TTTATTTTTATATATTTATTTCCATTT-
1 TTTATTTTTATA-ATTTATATACATTTC
*
2351121 TTTGTTTTT
1 TTTATTTTT
2351130 TTAACATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTATTTTTATAATTTATATACATTTC
Found at i:2358074 original size:46 final size:46
Alignment explanation
Indices: 2358022--2358173 Score: 110
Period size: 50 Copynumber: 3.2 Consensus size: 46
2358012 AAATTAGGGT
2358022 TTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGA
1 TTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGA
* * ** ** * ** * *
2358068 TTAGGGTTTAGTGTTTAGGGT-TTTTAAGGAAAAAAATCAAATAAATTAGGA
1 TTAGGG-TTA---CTT-GAGTAAATTAATTATAAATTTTAAAAAAATTA-GA
2358119 TTTAGGGTTACTTGAGTAAATTAATTATAAAATTTT-AAAAAATTAGA
1 -TTAGGGTTACTTGAGTAAATTAATTAT-AAATTTTAAAAAAATTAGA
*
2358166 TTGGGGTT
1 TTAGGGTT
2358174 TAGTATTTAG
Statistics
Matches: 74, Mismatches: 23, Indels: 18
0.64 0.20 0.16
Matches are distributed among these distances:
46 13 0.18
47 8 0.11
48 15 0.20
49 4 0.05
50 20 0.27
51 8 0.11
52 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (46 bp):
TTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGA
Found at i:2358159 original size:97 final size:97
Alignment explanation
Indices: 2357919--2358207 Score: 424
Period size: 98 Copynumber: 3.0 Consensus size: 97
2357909 AAATAAAGGT
* * * * * *
2357919 TTAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTAGAAAATTAGATTAGAGTTTAGAG
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
* *
2357984 TTT-GTGCTTTTTAA-GAAAAAAATTAAATAAA
66 TTTAG-GGTTTTTAAGGAAAAAAATCAAATAAA
2358015 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAGT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTT-AAAAAATTAGATTAGGGTTTAGT
2358080 GTTTAGGGTTTTTAAGGAAAAAAATCAAATAAA
65 GTTTAGGGTTTTTAAGGAAAAAAATCAAATAAA
* *
2358113 TTAGGATTTAGGGTTACTTGAGTAAATTAATTATAAAATTTTAAAAAATTAGATTGGGGTTTAGT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT-AAATTTTAAAAAATTAGATTAGGGTTTAGT
*
2358178 ATTTAGGGTTTTTAAGG--AAAAATCAAATAA
65 GTTTAGGGTTTTTAAGGAAAAAAATCAAATAA
2358208 GTAGTTGTTA
Statistics
Matches: 178, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
96 51 0.29
97 32 0.18
98 88 0.49
99 7 0.04
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.39
Consensus pattern (97 bp):
TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
TTTAGGGTTTTTAAGGAAAAAAATCAAATAAA
Found at i:2363302 original size:25 final size:26
Alignment explanation
Indices: 2363251--2363303 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2363241 CTATTTCATC
* *
2363251 TATTTTTTTTTCTTTTCTAAATTTAT
1 TATTTTATTTTCTTTTCTAAATATAT
2363277 TATTTTATTTTCATTTT-T-AATATAT
1 TATTTTATTTTC-TTTTCTAAATATAT
2363302 TA
1 TA
2363304 AAATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 12 0.50
27 4 0.17
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (26 bp):
TATTTTATTTTCTTTTCTAAATATAT
Found at i:2366113 original size:42 final size:42
Alignment explanation
Indices: 2366066--2366152 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 42
2366056 ACTAAAATAT
*
2366066 TTTAAAGTACAATTAACAATATTTACTCTCAAATATTTATTA
1 TTTAAAGTACAATTAACAATATTAACTCTCAAATATTTATTA
* * *** * *
2366108 TTTAAATTACTATTCGTAGTATTAACTCTTAAATATTTATTA
1 TTTAAAGTACAATTAACAATATTAACTCTCAAATATTTATTA
2366150 TTT
1 TTT
2366153 GAATCCATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48
Consensus pattern (42 bp):
TTTAAAGTACAATTAACAATATTAACTCTCAAATATTTATTA
Found at i:2367614 original size:22 final size:23
Alignment explanation
Indices: 2367588--2367634 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
2367578 ATAACATAGC
*
2367588 TTTAATAAATG-TAGAAAAATCT
1 TTTAATAAATGAAAGAAAAATCT
2367610 TTTAATAAATGAAAAGAAAAATCT
1 TTTAATAAATG-AAAGAAAAATCT
2367634 T
1 T
2367635 AAACTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (23 bp):
TTTAATAAATGAAAGAAAAATCT
Found at i:2368604 original size:42 final size:42
Alignment explanation
Indices: 2368556--2368635 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
2368546 GCAATAATAT
* * *
2368556 TGTCTATACAGAAAAGGAAGCAACTTGGGAAAGCAACATCTA
1 TGTCTATACAAAAAAGAAAGCAACTTGGGAAAACAACATCTA
2368598 TGTCTATACAAAAAAGAAAGCAACTTGGGAAAACAACA
1 TGTCTATACAAAAAAGAAAGCAACTTGGGAAAACAACA
2368636 AGCAAGCTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.17
Consensus pattern (42 bp):
TGTCTATACAAAAAAGAAAGCAACTTGGGAAAACAACATCTA
Found at i:2379469 original size:19 final size:20
Alignment explanation
Indices: 2379430--2379474 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2379420 GAAATAATTA
*
2379430 TTTTAATATATTTAGTGTTT
1 TTTTAATATATTTAGTATTT
*
2379450 TTTTAATATTTTTA-TATTT
1 TTTTAATATATTTAGTATTT
2379469 TTTTAA
1 TTTTAA
2379475 ATTAAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTAATATATTTAGTATTT
Found at i:2380523 original size:6 final size:6
Alignment explanation
Indices: 2380509--2380548 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
2380499 TCCACAAAGA
* *
2380509 ATTATT ATTACT ATTACT ATTACT ACTACT ATTACT ATTA
1 ATTACT ATTACT ATTACT ATTACT ATTACT ATTACT ATTA
2380549 TTTTTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTACT
Found at i:2392929 original size:13 final size:13
Alignment explanation
Indices: 2392911--2392945 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2392901 CTCAAATTTT
2392911 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
2392924 TCAAAAGTACTTT
1 TCAAAAGCACTTC
2392937 TCAAAAGCA
1 TCAAAAGCA
2392946 TTGCCAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:2403264 original size:24 final size:24
Alignment explanation
Indices: 2403216--2403265 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2403206 CCAATCATAT
*
2403216 TAAATTAATTTAATATTATTGTTA
1 TAAATTAATTTAATATTAGTGTTA
2403240 TAAATTAAATGTTAAT-TTAGT-TTA
1 TAAATT-AAT-TTAATATTAGTGTTA
2403264 TA
1 TA
2403266 TTATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 11 0.48
25 7 0.30
26 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TAAATTAATTTAATATTAGTGTTA
Found at i:2405746 original size:3 final size:3
Alignment explanation
Indices: 2405738--2405768 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2405728 TTTACTGAAA
*
2405738 TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2405769 TCCAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:2405760 original size:15 final size:15
Alignment explanation
Indices: 2405740--2405769 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2405730 TACTGAAATA
2405740 TTATTATTATTATTT
1 TTATTATTATTATTT
2405755 TTATTATTATTATTT
1 TTATTATTATTATTT
2405770 CCAATTTTTG
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATTATTATTT
Found at i:2425877 original size:16 final size:17
Alignment explanation
Indices: 2425840--2425878 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
2425830 TTAGATAAAC
*
2425840 ATAAAATTTTAGAATTAG
1 ATAAAATTTTA-AATTAA
2425858 ATAAAATTTT-AATTAA
1 ATAAAATTTTAAATTAA
2425874 ATAAA
1 ATAAA
2425879 TAGTTCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
ATAAAATTTTAAATTAA
Found at i:2436878 original size:15 final size:16
Alignment explanation
Indices: 2436858--2436901 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2436848 AAAATCCAAC
2436858 CCTAAAATCTTATA-T
1 CCTAAAATCTTATAGT
*
2436873 CCTAAAATCATATAGT
1 CCTAAAATCTTATAGT
*
2436889 CGCAAAAATCTTA
1 C-CTAAAATCTTA
2436902 AATATAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 2 0.08
17 9 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (16 bp):
CCTAAAATCTTATAGT
Found at i:2437175 original size:39 final size:40
Alignment explanation
Indices: 2437120--2437208 Score: 135
Period size: 39 Copynumber: 2.2 Consensus size: 40
2437110 TTTACAATAA
**
2437120 ATTATTTTAATTTCCTTTTAAAAAATGGACCCATTTTAGG
1 ATTATTTTAATTTCCTTCCAAAAAATGGACCCATTTTAGG
*
2437160 -TTATTTTAATTTCCTTCCAAGAAATGGACCCATTTTAGG
1 ATTATTTTAATTTCCTTCCAAAAAATGGACCCATTTTAGG
2437199 ATTGATTTTA
1 ATT-ATTTTA
2437209 GCTTTAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 36 0.82
40 2 0.05
41 6 0.14
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (40 bp):
ATTATTTTAATTTCCTTCCAAAAAATGGACCCATTTTAGG
Found at i:2440770 original size:26 final size:25
Alignment explanation
Indices: 2440714--2440771 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
2440704 CCACTTCGTA
*
2440714 TATTTAAAATTTAGTCCCCTACTTT
1 TATTTAAAAATTAGTCCCCTACTTT
*
2440739 TATTTAAGAAATTAGTCTCTCTACTTT
1 TATTTAA-AAATTAGTC-CCCTACTTT
2440766 T-TTTAA
1 TATTTAA
2440772 TTTAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.24
26 13 0.45
27 9 0.31
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (25 bp):
TATTTAAAAATTAGTCCCCTACTTT
Found at i:2442674 original size:18 final size:18
Alignment explanation
Indices: 2442653--2442697 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2442643 TATCACCTCT
* *
2442653 TTCATCTTCATCTTCGCC
1 TTCACCTTCATCTTCACC
*
2442671 TTCAGCTTCATCTTCACC
1 TTCACCTTCATCTTCACC
2442689 TTCACCTTC
1 TTCACCTTC
2442698 GTGGTCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.40, G:0.04, T:0.42
Consensus pattern (18 bp):
TTCACCTTCATCTTCACC
Found at i:2449389 original size:22 final size:20
Alignment explanation
Indices: 2449364--2449413 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
2449354 ATTTATGATA
2449364 AATATATATAATATTTTTTAT
1 AATATATATAATA-TTTTTAT
*
2449385 GAATA-AGTATATTATTTTTAT
1 -AATATA-TATAATATTTTTAT
2449406 AATATATA
1 AATATATA
2449414 ATATTGACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 6 0.24
21 9 0.36
22 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
AATATATATAATATTTTTAT
Found at i:2454597 original size:45 final size:45
Alignment explanation
Indices: 2454425--2455005 Score: 468
Period size: 45 Copynumber: 13.2 Consensus size: 45
2454415 TGAGAAGGCA
** ** * *
2454425 AACAAAGAGATGGCCTCAACAGTGAATAGCTCAGCCGAGAAGATG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* * ** * *
2454470 AAGAATGAGATGGCCATGACAGTAAATAGCTCCA-CTGAGGAGATG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCT-CAGCTGAGAAGATG
* * * *
2454515 AA-AAGAGAGACA-ACTT--CAATAAAGAGCTCAGCGGAGAAGATG
1 AACAA-AGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* * *
2454557 AACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
** * *
2454602 ATGAAAGA-A-A--CAT--CATTAAATAGCTCAGCTGAGAAGATG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* * * *
2454641 AGAC-AAGAGACAG-C-TG-CAGAAAATGGTTCAGCTGAAAAGATG
1 A-ACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* *
2454683 AAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAGAAGATG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* *
2454728 AACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
** ** *
2454773 AACAAAGAGATGGCCAGGACAGTGAATAGCTCAGCTGAGAAGATG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* *
2454818 AGAC-AAGAGACAG-C-T-ACAGTAAATGGCTCGGCTGAGAAGATG
1 A-ACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* * * * *
2454860 AAGAAAGAGACGGCCTTGACAGTAAAAAGCTCGAAC-GAGAAGGTG
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTC-AGCTGAGAAGATG
* * * * *
2454905 AAGAAAGAAACAGCCTTGACAGTAAATAACTCAGCTGAGAAGGTT
1 AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
* * * *
2454950 AAGAAAGAGATC-G-CTTCAACAGTGAATGGCTCAGCTGAGAAGATG
1 AACAAAGAGA-CAGCCTT-GACAGTAAATAGCTCAGCTGAGAAGATG
*
2454995 AAAAAAGAGAC
1 AACAAAGAGAC
2455006 CACTGTGGCA
Statistics
Matches: 433, Mismatches: 78, Indels: 51
0.77 0.14 0.09
Matches are distributed among these distances:
39 28 0.06
40 1 0.00
41 8 0.02
42 93 0.21
43 8 0.02
44 15 0.03
45 274 0.63
46 6 0.01
ACGTcount: A:0.43, C:0.16, G:0.26, T:0.15
Consensus pattern (45 bp):
AACAAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATG
Found at i:2454651 original size:126 final size:126
Alignment explanation
Indices: 2454492--2454728 Score: 311
Period size: 126 Copynumber: 1.9 Consensus size: 126
2454482 GCCATGACAG
* * *
2454492 TAAATAGCTCCACTGAGGAGATGAAAAGAGAGACAACTTCA-ATAAA-GAGCTCAGCGGAGAAGA
1 TAAATAGCTCCACTGAGAAGATGAAAAGAGAGACAACTGCAGA-AAATG-GCTCAGCGGAAAAGA
2454555 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGATGAAAGAAACATCAT
64 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGATGAAAGAAACATCAT
* * * *
2454618 TAAATAGCT-CAGCTGAGAAGATGAGACA-AGAGACAGCTGCAGAAAATGGTTCAGCTGAAAAGA
1 TAAATAGCTCCA-CTGAGAAGATGA-AAAGAGAGACAACTGCAGAAAATGGCTCAGCGGAAAAGA
* * * *
2454681 TGAAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAGAAGATGA
64 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGA
2454729 ACAAAGAGAC
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
125 2 0.02
126 90 0.94
127 4 0.04
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (126 bp):
TAAATAGCTCCACTGAGAAGATGAAAAGAGAGACAACTGCAGAAAATGGCTCAGCGGAAAAGATG
AACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGATGAAAGAAACATCAT
Found at i:2454878 original size:177 final size:173
Alignment explanation
Indices: 2454425--2455005 Score: 622
Period size: 177 Copynumber: 3.3 Consensus size: 173
2454415 TGAGAAGGCA
* * **
2454425 AACAAAGAGATGGCCTCAACAGTGAATAGCTCAGCCGAGAAGATGAAGA-ATGAGATGGCCATGA
1 AACAAAGAGATGG-C-CAACAGTGAATAGCTCAGCTGAGAAGATG-AGACAAGAGACAG-C-T-A
* * ** * *
2454489 CAGTAAATAGCTCCA-CTGAGGAGATGAA-AAGAGAGACAACTT--CAATAAAGAGCTCAGCGGA
60 CAGTAAATGGCT-CAGCTGAGAAGATGAAGAA-AGAGACGCCTTGACAGTAAAAAGCTCAGC-GA
*
2454550 GAAGATGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATG
122 GAAGATGAACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATG
** * * * * * *
2454602 ATGAAAGA-A---ACATCATTAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTGCAGAAA
1 AACAAAGAGATGGCCAACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGTAA
* * * *
2454663 ATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAGAAGATG
66 ATGGCTCAGCTGAGAAGATGAAGAAAGAGAC-GCCTTGACAGTAAAAAGCTCAGC-GAGAAGATG
2454728 AACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATG
129 AACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATG
2454773 AACAAAGAGATGGCCAGGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGT
1 AACAAAGAGATGGCCA--ACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGT
* * *
2454838 AAATGGCTCGGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAGTAAAAAGCTCGAACGAGAAGG
64 AAATGGCTCAGCTGAGAAGATGAAGAAAGAGAC-GCCTTGACAGTAAAAAGCTC-AGCGAGAAGA
* * * * *
2454903 TGAAGAAAGAAACAGCCTTGACAGTAAATAACTCAGCTGAGAAGGTT
127 TGAACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATG
* * * * *
2454950 AAGAAAGAGATCGCTTCAACAGTGAATGGCTCAGCTGAGAAGATGAAAAAAGAGAC
1 AACAAAGAGATGGC--CAACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGAC
2455006 CACTGTGGCA
Statistics
Matches: 340, Mismatches: 49, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
167 2 0.01
168 26 0.08
169 6 0.02
170 4 0.01
171 103 0.30
172 1 0.00
175 2 0.01
176 1 0.00
177 191 0.56
178 2 0.01
179 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.26, T:0.15
Consensus pattern (173 bp):
AACAAAGAGATGGCCAACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGTAA
ATGGCTCAGCTGAGAAGATGAAGAAAGAGACGCCTTGACAGTAAAAAGCTCAGCGAGAAGATGAA
CAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATG
Found at i:2456267 original size:15 final size:14
Alignment explanation
Indices: 2456236--2456274 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2456226 ACAAAATGTT
*
2456236 ATAAATTAAATAAAA
1 ATAAATTACA-AAAA
2456251 ATATAATTACAAAAA
1 ATA-AATTACAAAAA
2456266 ATAAATTAC
1 ATAAATTAC
2456275 TTACTATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 10 0.45
16 6 0.27
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAATTACAAAAA
Found at i:2469364 original size:23 final size:23
Alignment explanation
Indices: 2469306--2469367 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
2469296 TAATATAATA
* *
2469306 AATACTATAATATAATGTATTTTT
1 AATAATAT-ATATAATGTAATTTT
* *
2469330 TAGAGATA-ATATAATGTAATTTT
1 AATA-ATATATATAATGTAATTTT
2469353 AATAATATATATAAT
1 AATAATATATATAAT
2469368 TTTTATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 3 0.10
23 23 0.77
24 2 0.07
25 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (23 bp):
AATAATATATATAATGTAATTTT
Found at i:2469369 original size:18 final size:18
Alignment explanation
Indices: 2469335--2469381 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2469325 TTTTTTAGAG
*
2469335 ATAATATAATGTAATTTTA
1 ATAATAT-ATATAATTTTA
*
2469354 ATAATATATATAATTTTT
1 ATAATATATATAATTTTA
*
2469372 ATAAAATATA
1 ATAATATATA
2469382 ACATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATAATATATATAATTTTA
Found at i:2469479 original size:17 final size:16
Alignment explanation
Indices: 2469448--2469482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2469438 TTCCACATGT
2469448 TATTAAAAACCAATTA
1 TATTAAAAACCAATTA
*
2469464 TATTATAAAACGAATTA
1 TATTA-AAAACCAATTA
2469481 TA
1 TA
2469483 ATAGCTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (16 bp):
TATTAAAAACCAATTA
Found at i:2476313 original size:16 final size:15
Alignment explanation
Indices: 2476286--2476338 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
2476276 CCATTTTTTG
*
2476286 TAAATTAGATTAATA
1 TAAATTAAATTAATA
2476301 TACAATTAAATTAAATA
1 TA-AATTAAATT-AATA
*
2476318 TAAATTAGAGTTAATA
1 TAAATTA-AATTAATA
2476334 TAAAT
1 TAAAT
2476339 GTTATTGTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 2 0.06
16 22 0.67
17 9 0.27
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (15 bp):
TAAATTAAATTAATA
Found at i:2489345 original size:3 final size:3
Alignment explanation
Indices: 2489337--2489388 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2489327 TATTGAGGAG
2489337 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2489385 TAA T
1 TAA T
2489389 TAAGCAGTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2493787 original size:100 final size:101
Alignment explanation
Indices: 2493621--2493823 Score: 345
Period size: 100 Copynumber: 2.0 Consensus size: 101
2493611 GGTATTAAAA
* * **
2493621 AAGTAACTTTAAAATGTATTTTAAATTTAAATTTTTATTATTTATTTTGGATTTGTTGAATTATA
1 AAGTAACTTTAAAATATATTTTAAAATTAAATTTTTATTATTTATTTTGGATTTGTTGAACAATA
2493686 TGCATAGCATGGGATGATATTATTATTTAATTTATG
66 TGCATAGCATGGGATGATATTATTATTTAATTTATG
2493722 AAGTAACTTTAAAATATATTTTAAAATTAAA-TTTTATTATTTATTTTGGATTTGTTGAACAATA
1 AAGTAACTTTAAAATATATTTTAAAATTAAATTTTTATTATTTATTTTGGATTTGTTGAACAATA
* *
2493786 TGCATAGTATGGGATGATATTGTTATTTAATTTATG
66 TGCATAGCATGGGATGATATTATTATTTAATTTATG
2493822 AA
1 AA
2493824 ATATTTTTTT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 67 0.70
101 29 0.30
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (101 bp):
AAGTAACTTTAAAATATATTTTAAAATTAAATTTTTATTATTTATTTTGGATTTGTTGAACAATA
TGCATAGCATGGGATGATATTATTATTTAATTTATG
Found at i:2494392 original size:12 final size:12
Alignment explanation
Indices: 2494375--2494414 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2494365 ATTTCTTGAA
2494375 ATTTATTTTAAT
1 ATTTATTTTAAT
2494387 ATTTATTTTAA-
1 ATTTATTTTAAT
*
2494398 AATTATTTTAAT
1 ATTTATTTTAAT
*
2494410 GTTTA
1 ATTTA
2494415 CATAAAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
ATTTATTTTAAT
Found at i:2494405 original size:11 final size:12
Alignment explanation
Indices: 2494377--2494409 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2494367 TTCTTGAAAT
*
2494377 TTATTTTAATAT
1 TTATTTTAATAA
2494389 TTATTTTAA-AA
1 TTATTTTAATAA
2494400 TTATTTTAAT
1 TTATTTTAAT
2494410 GTTTACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTTTAATAA
Found at i:2496854 original size:72 final size:72
Alignment explanation
Indices: 2496733--2496866 Score: 205
Period size: 72 Copynumber: 1.9 Consensus size: 72
2496723 TGAAAAAGAA
* *
2496733 ATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCTGAGATCGTTTAAAACTTGAGAAA
1 ATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAGAAA
2496798 AAAGGGG
66 AAAGGGG
** * * *
2496805 ATCATGCCCAGTAAGTTAGGACGTGATCTCTTCTTGATTCCCGATATCGTTTAATACTTGAG
1 ATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAG
2496867 TTTGAAAAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (72 bp):
ATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAGAAA
AAAGGGG
Found at i:2497114 original size:39 final size:41
Alignment explanation
Indices: 2497071--2497159 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 41
2497061 CGACGATGGT
* *
2497071 ATAAAGATAATACGAA-CAATAACA-ACGAA-ATTAAGA-CAA
1 ATAAAGATAAAACAAATCAATAACATAC-AATA-TAAGAGCAA
2497110 ATAAAGA-AAAACAAATCAATAACATACAATATAAGAGCAA
1 ATAAAGATAAAACAAATCAATAACATACAATATAAGAGCAA
*
2497150 ATAAAAATAA
1 ATAAAGATAA
2497160 GACATTCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
38 6 0.14
39 22 0.52
40 12 0.29
41 2 0.05
ACGTcount: A:0.65, C:0.11, G:0.08, T:0.16
Consensus pattern (41 bp):
ATAAAGATAAAACAAATCAATAACATACAATATAAGAGCAA
Found at i:2500012 original size:8 final size:8
Alignment explanation
Indices: 2499988--2500027 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
2499978 GACATCAAAA
2499988 TATAATTT
1 TATAATTT
*
2499996 TATTA-TT
1 TATAATTT
*
2500003 TATTATTT
1 TATAATTT
2500011 TATAATTT
1 TATAATTT
2500019 TATAATTT
1 TATAATTT
2500027 T
1 T
2500028 TTAGGTGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TATAATTT
Found at i:2500323 original size:16 final size:16
Alignment explanation
Indices: 2500302--2500344 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2500292 TAGGAGGATG
2500302 TAAATTTTAACCTATT
1 TAAATTTTAACCTATT
* *
2500318 TAAATTTTTTACTTATT
1 TAAA-TTTTAACCTATT
*
2500335 TAAAATTTAA
1 TAAATTTTAA
2500345 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTTTAACCTATT
Found at i:2506472 original size:19 final size:21
Alignment explanation
Indices: 2506450--2506489 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2506440 TTATCGAAAA
2506450 CAAATTT-TATTTC-ATTTAT
1 CAAATTTGTATTTCAATTTAT
*
2506469 CAAATTTGTTTTTCAATTTAT
1 CAAATTTGTATTTCAATTTAT
2506490 AAAAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (21 bp):
CAAATTTGTATTTCAATTTAT
Found at i:2506884 original size:12 final size:12
Alignment explanation
Indices: 2506867--2506891 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2506857 GGTGTTCATT
2506867 CGGTTAACCGAC
1 CGGTTAACCGAC
2506879 CGGTTAACCGAC
1 CGGTTAACCGAC
2506891 C
1 C
2506892 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:2507066 original size:9 final size:9
Alignment explanation
Indices: 2507052--2507146 Score: 120
Period size: 9 Copynumber: 10.4 Consensus size: 9
2507042 TTTGGTTAAA
2507052 AATTACCCG
1 AATTACCCG
2507061 AATTACCCG
1 AATTACCCG
*
2507070 AATTATCCG
1 AATTACCCG
2507079 AATTACCCG
1 AATTACCCG
2507088 AATTACCCG
1 AATTACCCG
* *
2507097 AATTAACCT
1 AATTACCCG
*
2507106 AATTAACCG
1 AATTACCCG
2507115 AATTA-CCG
1 AATTACCCG
*
2507123 AAAAATACCCG
1 --AATTACCCG
2507134 AATTACCCG
1 AATTACCCG
2507143 AATT
1 AATT
2507147 TTTTTATTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
8 3 0.04
9 66 0.87
10 4 0.05
11 3 0.04
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:2516226 original size:2 final size:2
Alignment explanation
Indices: 2516210--2516257 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2516200 CTCAAATGAT
*
2516210 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2516251 TA TA TA T
1 TA TA TA T
2516258 CTGCTCTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2530653 original size:2 final size:2
Alignment explanation
Indices: 2530646--2530697 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2530636 TAATTGATAA
2530646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2530688 AT AT AT AT AT
1 AT AT AT AT AT
2530698 TAACTACTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2534334 original size:19 final size:21
Alignment explanation
Indices: 2534295--2534338 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
2534285 TTTTACTTTC
2534295 TGTTCAGCTCTTACAAGTTTA
1 TGTTCAGCTCTTACAAGTTTA
*
2534316 TGTTCAGCT-TT-CGAGTTTA
1 TGTTCAGCTCTTACAAGTTTA
2534335 TGTT
1 TGTT
2534339 GGCGTATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 9 0.41
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (21 bp):
TGTTCAGCTCTTACAAGTTTA
Found at i:2539001 original size:131 final size:131
Alignment explanation
Indices: 2538767--2539030 Score: 528
Period size: 131 Copynumber: 2.0 Consensus size: 131
2538757 TAACGATGTC
2538767 AATAATTGGACTTGATTTTCAAATTTGAAAAGTAGAGGGACTAAATTCTTGAAAATAAAAGTATA
1 AATAATTGGACTTGATTTTCAAATTTGAAAAGTAGAGGGACTAAATTCTTGAAAATAAAAGTATA
2538832 AAGACTAAATTGCAAATTTGTGAAGAGTACATAGACTTATAACAAATTTTAACTTTTATACTACA
66 AAGACTAAATTGCAAATTTGTGAAGAGTACATAGACTTATAACAAATTTTAACTTTTATACTACA
2538897 A
131 A
2538898 AATAATTGGACTTGATTTTCAAATTTGAAAAGTAGAGGGACTAAATTCTTGAAAATAAAAGTATA
1 AATAATTGGACTTGATTTTCAAATTTGAAAAGTAGAGGGACTAAATTCTTGAAAATAAAAGTATA
2538963 AAGACTAAATTGCAAATTTGTGAAGAGTACATAGACTTATAACAAATTTTAACTTTTATACTACA
66 AAGACTAAATTGCAAATTTGTGAAGAGTACATAGACTTATAACAAATTTTAACTTTTATACTACA
2539028 A
131 A
2539029 AA
1 AA
2539031 CATTTATTAT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 133 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (131 bp):
AATAATTGGACTTGATTTTCAAATTTGAAAAGTAGAGGGACTAAATTCTTGAAAATAAAAGTATA
AAGACTAAATTGCAAATTTGTGAAGAGTACATAGACTTATAACAAATTTTAACTTTTATACTACA
A
Found at i:2539052 original size:15 final size:15
Alignment explanation
Indices: 2539032--2539083 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
2539022 ACTACAAAAC
2539032 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
2539047 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
2539066 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
2539081 ATT
1 ATT
2539084 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:2539766 original size:32 final size:32
Alignment explanation
Indices: 2539728--2539798 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
2539718 AATTATATAT
*
2539728 ATAATAAAA-AAATTCAAATAATAGTTAAAAA-
1 ATAATAAAATAAATT-AAATAATAATTAAAAAG
* *
2539759 ATTAATAAAATATATTAAATTATAATTAAAAAG
1 A-TAATAAAATAAATTAAATAATAATTAAAAAG
2539792 ATAATAA
1 ATAATAA
2539799 TATTATTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 28 0.82
33 5 0.15
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (32 bp):
ATAATAAAATAAATTAAATAATAATTAAAAAG
Found at i:2546042 original size:3 final size:3
Alignment explanation
Indices: 2546034--2546091 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
2546024 TTTCAGATAT
2546034 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2546082 ATA ATA ATA A
1 ATA ATA ATA A
2546092 ATAAGAGTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2549145 original size:13 final size:13
Alignment explanation
Indices: 2549127--2549152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2549117 CCTATCCAAT
2549127 TATTTTATGTCAC
1 TATTTTATGTCAC
2549140 TATTTTATGTCAC
1 TATTTTATGTCAC
2549153 GTCAACAACT
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:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TATTTTATGTCAC
Found at i:2549449 original size:23 final size:24
Alignment explanation
Indices: 2549406--2549456 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
2549396 AAGTTCGTTC
2549406 CTATTTTTAATGATTAAAATT-AA
1 CTATTTTTAATGATTAAAATTCAA
**
2549429 CTATTTTTAA-GATTTTTAATTCAA
1 CTATTTTTAATGA-TTAAAATTCAA
2549453 CTAT
1 CTAT
2549457 GAAATAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 16 0.67
24 6 0.25
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (24 bp):
CTATTTTTAATGATTAAAATTCAA
Found at i:2550480 original size:43 final size:44
Alignment explanation
Indices: 2550419--2550506 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 44
2550409 TCCCATTCTT
2550419 GACAGAGAATTAAAA-TTTTTATAAATAAATCGTAAATGGATCA
1 GACAGAGAATTAAAATTTTTTATAAATAAATCGTAAATGGATCA
2550462 GACAGAGAATTAAAATTTTTTTATAAATAAATCGTAAATGGATCA
1 GACAGAGAATTAAAA-TTTTTTATAAATAAATCGTAAATGGATCA
2550507 TGTGCTTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 15 0.35
45 28 0.65
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (44 bp):
GACAGAGAATTAAAATTTTTTATAAATAAATCGTAAATGGATCA
Found at i:2554516 original size:18 final size:17
Alignment explanation
Indices: 2554495--2554528 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2554485 TAAAATTGCG
2554495 ATAATTAAGAATTTAAAA
1 ATAATT-AGAATTTAAAA
*
2554513 ATAATTATAATTTAAA
1 ATAATTAGAATTTAAA
2554529 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATTAGAATTTAAAA
Found at i:2554528 original size:152 final size:152
Alignment explanation
Indices: 2554260--2554548 Score: 399
Period size: 152 Copynumber: 1.9 Consensus size: 152
2554250 TTAGAAAAAG
* * *
2554260 TTTTGAACTAACAAAAATAATATTTATTTTTATCATTTATTAAATTTACATTTAAAATAATTATA
1 TTTTGAACTAACAAAAATAACATTTATTTTCATCATTTATTAAAATTACATTTAAAATAATTATA
* * * * *
2554325 ATTTAATAAAAATTATGGTAATTACAAATTTAAAAAATAATTGAAACTTAAATTGCAATTATTAA
66 AATTAATAAAAATTACGATAATTACAAATTTAAAAAATAATTGAAACTTAAATTACAATTATCAA
2554390 TTAAAAATGTGCTAATTTAAAC
131 TTAAAAATGTGCTAATTTAAAC
2554412 TTTTGAACTATA-AAAAATAACATTTATTCTTCATCATATTATTAAAATTACATTTAAAATAATT
1 TTTTGAACTA-ACAAAAATAACATTTATT-TTCATCAT-TTATTAAAATTACATTTAAAATAATT
* *
2554476 ATAAATTAAT-AAAATTGCGATAATTA-AGAATTT-AAAAATAATT-ATAATTTAAATTACAATT
63 ATAAATTAATAAAAATTACGATAATTACA-AATTTAAAAAATAATTGA-AACTTAAATTACAATT
*
2554537 ATCCATTAAAAA
126 ATCAATTAAAAA
2554549 ATTGTGTTAA
Statistics
Matches: 121, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
151 1 0.01
152 60 0.50
153 26 0.21
154 34 0.28
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (152 bp):
TTTTGAACTAACAAAAATAACATTTATTTTCATCATTTATTAAAATTACATTTAAAATAATTATA
AATTAATAAAAATTACGATAATTACAAATTTAAAAAATAATTGAAACTTAAATTACAATTATCAA
TTAAAAATGTGCTAATTTAAAC
Found at i:2555293 original size:19 final size:19
Alignment explanation
Indices: 2555269--2555306 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2555259 TTTTTTACAT
2555269 AAATAATACAAAAAAAATA
1 AAATAATACAAAAAAAATA
* *
2555288 AAATAATACTAAAATAATA
1 AAATAATACAAAAAAAATA
2555307 CAACAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAATAATACAAAAAAAATA
Found at i:2555829 original size:30 final size:30
Alignment explanation
Indices: 2555795--2555857 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2555785 AATTTTAATT
* * * *
2555795 TTTATGTTATGTACATTCTATGTTTTTTTA
1 TTTATGTTACGTACATACTATGTCTTATTA
2555825 TTTATGTTACGTACATACTATGTCTTATTA
1 TTTATGTTACGTACATACTATGTCTTATTA
2555855 TTT
1 TTT
2555858 TATTATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTATGTTACGTACATACTATGTCTTATTA
Found at i:2555872 original size:12 final size:12
Alignment explanation
Indices: 2555852--2555882 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2555842 CTATGTCTTA
*
2555852 TTATTTTATTAT
1 TTATGTTATTAT
2555864 TTATGTTATTAT
1 TTATGTTATTAT
2555876 TTATGTT
1 TTATGTT
2555883 GTGTACATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTATGTTATTAT
Found at i:2556064 original size:17 final size:17
Alignment explanation
Indices: 2556044--2556076 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2556034 GTTTATGAAA
*
2556044 AAATAAAATATGAAAAG
1 AAATAAAAAATGAAAAG
2556061 AAATAAAAAATGAAAA
1 AAATAAAAAATGAAAA
2556077 TAGTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AAATAAAAAATGAAAAG
Found at i:2556313 original size:151 final size:149
Alignment explanation
Indices: 2556063--2556367 Score: 427
Period size: 151 Copynumber: 2.0 Consensus size: 149
2556053 ATGAAAAGAA
* * *
2556063 ATAAAAAATGAAAATAGTATATTTACTAAAAGTAATAAAATCTGAAAAAAAAATACGAATAAATG
1 ATAAAAAACGAAAATAGTATATTTACTAAAAGTAATAAAATCTGAAAAAAAAATACGAACAAATA
* * * *
2556128 GCCAAAATAATGGGTTTTTTTACTAAATTTATATAAAACA-CACACTAAAATAGTACATTTCAAA
66 ACCAAAATAATGGGTTTTTTTACTAAATTTATATAAAAAAGCACACCAAAATAATACATTTCAAA
2556192 CATTATGTACTAAAA-AAT
131 CATTATGTACTAAAATAAT
* ** * *
2556210 ATAAAATACGAAAATAGTATATTTTTTTAAAGTAATAAAATTTGAAAATAAGAAAAATACGAACA
1 ATAAAAAACGAAAATAGTATATTTACTAAAAGTAATAAAATCTG--AA-AA-AAAAATACGAACA
*
2556275 AATAACCAAAAT-ATGGGTTTTTTTTACTAAATTTATATAAAAAAGCACACCAAATTAATACATT
62 AATAACCAAAATAATGGG-TTTTTTTACTAAATTTATATAAAAAAGCACACCAAAATAATACATT
2556339 TCAAACATTATGTACTAAAATAAT
126 TCAAACATTATGTACTAAAATAAT
2556363 ATAAA
1 ATAAA
2556368 TTAATACATT
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
147 38 0.28
149 2 0.01
150 7 0.05
151 47 0.34
152 36 0.26
153 8 0.06
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (149 bp):
ATAAAAAACGAAAATAGTATATTTACTAAAAGTAATAAAATCTGAAAAAAAAATACGAACAAATA
ACCAAAATAATGGGTTTTTTTACTAAATTTATATAAAAAAGCACACCAAAATAATACATTTCAAA
CATTATGTACTAAAATAAT
Found at i:2556980 original size:13 final size:13
Alignment explanation
Indices: 2556962--2556988 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2556952 CCGCAATGTG
2556962 ACGGATGCAATAA
1 ACGGATGCAATAA
2556975 ACGGATGCAATAA
1 ACGGATGCAATAA
2556988 A
1 A
2556989 AAAATTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (13 bp):
ACGGATGCAATAA
Found at i:2557104 original size:3 final size:3
Alignment explanation
Indices: 2557096--2557147 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2557086 TAACTAACAC
2557096 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2557144 AAT A
1 AAT A
2557148 GTTTTGTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2557898 original size:16 final size:16
Alignment explanation
Indices: 2557860--2557899 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2557850 AATATGCGAA
2557860 TAATATTATTTAAAAT
1 TAATATTATTTAAAAT
*
2557876 TATTATT-TTTAAAACT
1 TAATATTATTTAAAA-T
2557892 TAATATTA
1 TAATATTA
2557900 AAATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATTATTTAAAAT
Found at i:2557912 original size:18 final size:19
Alignment explanation
Indices: 2557885--2557920 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2557875 TTATTATTTT
2557885 TAAAACTT-AATATTAAAA
1 TAAAACTTAAATATTAAAA
*
2557903 TAAAATTTAAATATTAAA
1 TAAAACTTAAATATTAAA
2557921 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAACTTAAATATTAAAA
Found at i:2557932 original size:31 final size:29
Alignment explanation
Indices: 2557895--2557960 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
2557885 TAAAACTTAA
*
2557895 TATTAAAATAA-AATTTAAATATTAAATAATT
1 TATTAAAATAATAAATT--ATATT-AATAATT
2557926 TATTAAAAATAATAAATTATATTAATAATT
1 TATT-AAAATAATAAATTATATTAATAATT
2557956 TATTA
1 TATTA
2557961 TATGACTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.03
30 11 0.34
31 9 0.28
32 7 0.22
33 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TATTAAAATAATAAATTATATTAATAATT
Found at i:2558959 original size:11 final size:11
Alignment explanation
Indices: 2558945--2558975 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2558935 TTAAAACAGT
2558945 TTTAATTTTTA
1 TTTAATTTTTA
*
2558956 TTTAAATTTTA
1 TTTAATTTTTA
2558967 TTTAATTTT
1 TTTAATTTT
2558976 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTAATTTTTA
Found at i:2560585 original size:22 final size:22
Alignment explanation
Indices: 2560555--2560608 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2560545 CAATTTATGA
*
2560555 ATTAAAATTTAA-ACTATAAAAT
1 ATTAAAATTAAATACT-TAAAAT
* *
2560577 ATTATAATTAAATACTTAAAGT
1 ATTAAAATTAAATACTTAAAAT
*
2560599 ATTAATATTA
1 ATTAAAATTA
2560609 TTTTGACCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTAAAATTAAATACTTAAAAT
Found at i:2565230 original size:16 final size:15
Alignment explanation
Indices: 2565175--2565228 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
2565165 TGTGTTTAGT
2565175 ATTATTTTT-AATAA
1 ATTATTTTTAAATAA
2565189 A-TATTTTTGAAATAAA
1 ATTATTTTT-AAAT-AA
**
2565205 AGCATTTTTAAATAA
1 ATTATTTTTAAATAA
2565220 ATTATTTTT
1 ATTATTTTT
2565229 TAGAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 7 0.21
14 1 0.03
15 12 0.36
16 7 0.21
17 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (15 bp):
ATTATTTTTAAATAA
Found at i:2570773 original size:18 final size:18
Alignment explanation
Indices: 2570750--2570792 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2570740 ACTCAATCTA
**
2570750 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
2570768 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
2570786 AACCCAA
1 AACCCAA
2570793 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:2570914 original size:9 final size:9
Alignment explanation
Indices: 2570900--2570948 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
2570890 ATAGTGATTC
*
2570900 AATTTGGTT
1 AATTCGGTT
*
2570909 AATTTGGTT
1 AATTCGGTT
*
2570918 AATTCGGGT
1 AATTCGGTT
*
2570927 AATTCGGGT
1 AATTCGGTT
2570936 AATTCGGTT
1 AATTCGGTT
2570945 AATT
1 AATT
2570949 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:2573608 original size:40 final size:40
Alignment explanation
Indices: 2573563--2573681 Score: 163
Period size: 39 Copynumber: 3.0 Consensus size: 40
2573553 ACCAAAAATT
2573563 TATTTTAAAATTAAAACAAAATT-AAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAA-AAAATTAAAAAAGTATTTTAAAAA
2573603 TATTTTAAAATT-AAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
* **
2573642 -AATTTAAAATTTAAAAAATTTTAAAAAAAGTATTTTAAAA
1 TATTTTAAAA-TTAAAAAAAATT-AAAAAAGTATTTTAAAA
2573682 TTTTAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
38 14 0.19
39 22 0.31
40 19 0.26
41 17 0.24
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:2573634 original size:28 final size:28
Alignment explanation
Indices: 2573580--2573640 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
2573570 AAATTAAAAC
* *
2573580 AAAATTAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAG-AATTAAAAAATATTTT
2573609 AAAATTAAAAA-AATTAAAAAAGTATTTT
1 AAAATTAAAAAGAATTAAAAAA-TATTTT
2573637 AAAA
1 AAAA
2573641 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.28
28 10 0.34
29 11 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTAAAAAGAATTAAAAAATATTTT
Found at i:2573647 original size:10 final size:10
Alignment explanation
Indices: 2573609--2573670 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
2573599 AAAATATTTT
2573609 AAAA-TTAAA
1 AAAATTTAAA
2573618 AAAA-TTAAA
1 AAAATTTAAA
2573627 AAAGTATTTTAAA
1 AAA--A-TTTAAA
2573640 AAAATTT---
1 AAAATTTAAA
2573647 AAAATTTAAA
1 AAAATTTAAA
*
2573657 AAATTTTAAA
1 AAAATTTAAA
2573667 AAAA
1 AAAA
2573671 GTATTTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
7 7 0.16
9 12 0.27
10 15 0.34
11 2 0.05
13 8 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:2573656 original size:17 final size:17
Alignment explanation
Indices: 2573634--2573667 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2573624 AAAAAAGTAT
2573634 TTTAAAAAAATTTAAAA
1 TTTAAAAAAATTTAAAA
*
2573651 TTTAAAAAATTTTAAAA
1 TTTAAAAAAATTTAAAA
2573668 AAAGTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAAAAAAATTTAAAA
Found at i:2573706 original size:39 final size:39
Alignment explanation
Indices: 2573564--2573707 Score: 134
Period size: 39 Copynumber: 3.7 Consensus size: 39
2573554 CCAAAAATTT
* *
2573564 ATTTT-AAAATTAAAACAAAAT-TAAAAAGTATTTTAAAA
1 ATTTTAAAAATTAAAA-ATAATAAAAAAAGTATTTTAAAA
* *
2573602 ATATTTTAAAATTAAAAA-AATTAAAAAAGTATTTTAAAAA
1 AT-TTTAAAAATTAAAAATAATAAAAAAAGTATTTT-AAAA
* * **
2573642 AATTTAAAATTTAAAAAATTTTAAAAAAAGTATTTT-AAA
1 ATTTTAAAAATT-AAAAATAATAAAAAAAGTATTTTAAAA
*
2573681 ATTTTAAAAAATAATAAATAATAAAAA
1 ATTTTAAAAATTAA-AAATAATAAAAA
2573708 TACTTATTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
38 7 0.08
39 46 0.53
40 20 0.23
41 14 0.16
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (39 bp):
ATTTTAAAAATTAAAAATAATAAAAAAAGTATTTTAAAA
Found at i:2579274 original size:20 final size:20
Alignment explanation
Indices: 2579231--2579274 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2579221 TTAAAATACT
* **
2579231 TTTAAAATAAATTTTTTATT
1 TTTAAAATAAATTTTTAACG
2579251 TTTAAAATAAATTTTTAACG
1 TTTAAAATAAATTTTTAACG
2579271 TTTA
1 TTTA
2579275 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAAAATAAATTTTTAACG
Found at i:2580205 original size:2 final size:2
Alignment explanation
Indices: 2580198--2580225 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2580188 AAGTACTTAC
2580198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2580226 GAATATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2585319 original size:18 final size:18
Alignment explanation
Indices: 2585280--2585340 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
2585270 TGTATTATGA
*
2585280 TTTTAGTAAATTCATATA-
1 TTTTATTAAATT-ATATAT
*
2585298 TTTTGTTAAATTATATAT
1 TTTTATTAAATTATATAT
*
2585316 TTTTATTGAATTATATAT
1 TTTTATTAAATTATATAT
2585334 TATTTAT
1 T-TTTAT
2585341 ATTAATAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 5 0.14
18 27 0.73
19 5 0.14
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:2585498 original size:39 final size:40
Alignment explanation
Indices: 2585442--2585546 Score: 124
Period size: 44 Copynumber: 2.5 Consensus size: 40
2585432 TTTCCTTTTT
*
2585442 CTATTACACCTCTATTCCATTCAACCAAACACAA-GAATAC
1 CTATTACGCCTCTATTCCATTCAACCAAACA-AATGAATAC
*
2585482 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAATGATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAATGAATAC
2585526 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
2585547 ACGCATGTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
39 13 0.23
40 6 0.11
43 2 0.04
44 21 0.38
45 14 0.25
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30
Consensus pattern (40 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAATGAATAC
Found at i:2585541 original size:45 final size:44
Alignment explanation
Indices: 2585459--2585548 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
2585449 ACCTCTATTC
2585459 CATTCAACCAAACACAAGAATACCATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGAATACCATTACGCCTCTATTCCATTA
*
2585503 CATTCAACCAAACA-AATGATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAA-GAATACC-ATTACGCCTCTATTCCATTA
2585548 C
1 C
2585549 GCATGTATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 2 0.05
44 20 0.47
45 21 0.49
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.28
Consensus pattern (44 bp):
CATTCAACCAAACACAAGAATACCATTACGCCTCTATTCCATTA
Found at i:2585549 original size:16 final size:16
Alignment explanation
Indices: 2585528--2585579 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
2585518 ATGATTACCT
2585528 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* *
2585544 ATTACGCATGTATTCC
1 ATTACGCCTCTATTCC
*
2585560 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
2585576 ATTA
1 ATTA
2585580 TAGCCAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:2594745 original size:3 final size:3
Alignment explanation
Indices: 2594737--2594788 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2594727 CGAACATTAC
2594737 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2594785 AGA A
1 AGA A
2594789 ACAGGACCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2596158 original size:20 final size:19
Alignment explanation
Indices: 2596133--2596177 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2596123 CAACATGGAT
*
2596133 AATTTTTTCTAAAATTTTAA
1 AATTTTTTAT-AAATTTTAA
*
2596153 AATTTTTTATTAATTTTAA
1 AATTTTTTATAAATTTTAA
2596172 AATTTT
1 AATTTT
2596178 AAAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTTATAAATTTTAA
Found at i:2596350 original size:6 final size:7
Alignment explanation
Indices: 2596325--2596349 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2596315 TCATTATGAG
2596325 AAAAATA
1 AAAAATA
2596332 AAAAATA
1 AAAAATA
2596339 AAAAATA
1 AAAAATA
2596346 AAAA
1 AAAA
2596350 TCCAATCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2597034 original size:63 final size:62
Alignment explanation
Indices: 2596927--2597226 Score: 281
Period size: 63 Copynumber: 4.9 Consensus size: 62
2596917 TGAACTGCTG
* *
2596927 GCTCCTGTTGAGTAGTCGCGGAAGGTCCCGGTGCTGTTATACTGTAATGTATGGTAAGAGGTT
1 GCTCCTGTTGAGGAGTCGCGGAAGGTCCC-GTGCTGCTATACTGTAATGTATGGTAAGAGGTT
* * * * * ***
2596990 GGTCCTGTTGAGGAGTCACGGAAGGTCCTGATGCTGCTACACTGTAATGCATGGCCTGAGGTT
1 GCTCCTGTTGAGGAGTCGCGGAAGGTCCCG-TGCTGCTATACTGTAATGTATGGTAAGAGGTT
* * * * *
2597053 GTTCCTGTTGAGGAATTGCCGAAGGTCCCGGTGCTGCTATACTGTAATGTATGGTCAGAGGTT
1 GCTCCTGTTGAGGAGTCGCGGAAGGTCCC-GTGCTGCTATACTGTAATGTATGGTAAGAGGTT
* * * ** *
2597116 GCT-CTGGTTGAGGAGCCGTGGAAGGTCCCG-G-AGCTACGCTGTAATGTATGG-ACTGAGGTT
1 GCTCCT-GTTGAGGAGTCGCGGAAGGTCCCGTGCTGCTATACTGTAATGTATGGTA-AGAGGTT
* * *
2597176 GCTCTTGTTG-GTGAGTCACTGAAGGTCCC--GCTGCTATACTGTAATGTATGG
1 GCTCCTGTTGAG-GAGTCGCGGAAGGTCCCGTGCTGCTATACTGTAATGTATGG
2597227 ACCGAGGTCG
Statistics
Matches: 191, Mismatches: 39, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
59 2 0.01
60 60 0.31
61 2 0.01
62 4 0.02
63 122 0.64
64 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (62 bp):
GCTCCTGTTGAGGAGTCGCGGAAGGTCCCGTGCTGCTATACTGTAATGTATGGTAAGAGGTT
Found at i:2597179 original size:60 final size:60
Alignment explanation
Indices: 2597088--2597234 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
2597078 TCCCGGTGCT
* * *
2597088 GCTATACTGTAATGTATGGTCAGAGGTTGCTCTGGTTGAG-GAG-C-CGTGGAAGGTCCCGGA
1 GCTACACTGTAATGTATGGACAGAGGTTGCTCTGGTTG-GTGAGTCAC-T-GAAGGTCCCGCA
* * * *
2597148 GCTACGCTGTAATGTATGGACTGAGGTTGCTCTTGTTGGTGAGTCACTGAAGGTCCCGCT
1 GCTACACTGTAATGTATGGACAGAGGTTGCTCTGGTTGGTGAGTCACTGAAGGTCCCGCA
* *
2597208 GCTATACTGTAATGTATGGACCGAGGT
1 GCTACACTGTAATGTATGGACAGAGGT
2597235 CGTGTTGCCT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 70 0.95
61 2 0.03
62 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (60 bp):
GCTACACTGTAATGTATGGACAGAGGTTGCTCTGGTTGGTGAGTCACTGAAGGTCCCGCA
Found at i:2600105 original size:21 final size:21
Alignment explanation
Indices: 2600076--2600115 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2600066 CCCCCTGAAT
* *
2600076 TTTTTAAAATCTTCATTAGAC
1 TTTTAAAAATCTTAATTAGAC
*
2600097 TTTTAAAAATTTTAATTAG
1 TTTTAAAAATCTTAATTAG
2600116 GTCCCTCAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTAAAAATCTTAATTAGAC
Found at i:2605249 original size:63 final size:63
Alignment explanation
Indices: 2605167--2605298 Score: 203
Period size: 63 Copynumber: 2.1 Consensus size: 63
2605157 GATGCCTTCC
* *
2605167 GTTGAGGAGTTGCGGAAGGTCCCGGTGCTGCTATACTGTAATGTATGGTAAGAGGCTGCTCCT-
1 GTTGAGGAGTCGCAGAAGGTCCCGGTGCTGCTATACTGTAATGTATGGTAAGAGGCTGCT-CTG
* * *
2605230 GTTGAGGAGTCGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGGTATGAGGTTGCTCTG
1 GTTGAGGAGTCGCAGAAGGTCCCGGTGCTGCTATACTGTAATGTATGGTAAGAGGCTGCTCTG
2605293 GTTGAG
1 GTTGAG
2605299 TCATGGAAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 2 0.03
63 61 0.97
ACGTcount: A:0.19, C:0.15, G:0.36, T:0.30
Consensus pattern (63 bp):
GTTGAGGAGTCGCAGAAGGTCCCGGTGCTGCTATACTGTAATGTATGGTAAGAGGCTGCTCTG
Found at i:2605391 original size:60 final size:59
Alignment explanation
Indices: 2605167--2605391 Score: 188
Period size: 63 Copynumber: 3.7 Consensus size: 59
2605157 GATGCCTTCC
* *
2605167 GTTGAGGAGTTGCGGAAGGTCCCGGTGCTGCTATACTGTAATGTATGGTAAGAGG-CTGCTCCT
1 GTTGAAGAGTTGC-GAAGGTCCC---GCTGCTATACTGTAATGTATGGTATGAGGTC-GCTCCT
* * * *
2605230 GTTGAGGAGTCGCAGAAGGTCCTGGTGCTGCTATACTGTAATGTATGGTATGAGGTTGCT-CT
1 GTTGAAGAGTTGC-GAAGGTCC---CGCTGCTATACTGTAATGTATGGTATGAGGTCGCTCCT
*** * * * ** *
2605292 GGTTG-AGTCATG-GAAAGTCCCGATGCTACACTGTAATGTATGGCCTGAGGTCCCTCCT
1 -GTTGAAGAGTTGCGAAGGTCCCGCTGCTATACTGTAATGTATGGTATGAGGTCGCTCCT
2605350 GTTGAAGAGTTGCTGAAGGTCCCGCTGCTATACTGTAATGTA
1 GTTGAAGAGTTGC-GAAGGTCCCGCTGCTATACTGTAATGTA
2605392 CAGCCCGAGG
Statistics
Matches: 129, Mismatches: 24, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
57 32 0.25
58 6 0.05
60 32 0.25
62 4 0.03
63 55 0.43
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (59 bp):
GTTGAAGAGTTGCGAAGGTCCCGCTGCTATACTGTAATGTATGGTATGAGGTCGCTCCT
Found at i:2615418 original size:23 final size:22
Alignment explanation
Indices: 2615392--2615435 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2615382 AAATAATTTA
*
2615392 AAATTATAAAAATATTTAAAAAT
1 AAATTATAAAAA-ATATAAAAAT
*
2615415 AAATTTTAAAAAATATAAAAA
1 AAATTATAAAAAATATAAAAA
2615436 AATTCAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATTATAAAAAATATAAAAAT
Found at i:2615611 original size:31 final size:31
Alignment explanation
Indices: 2615553--2615614 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2615543 ACAATTAAGC
** *
2615553 TTTTTTTTTAAAAATTGATGGTCAATTTTAA
1 TTTTTTTTTAAAAATTGACAGTAAATTTTAA
*
2615584 TTTTTTTTTAAATATTGACAGTAAATTTTAA
1 TTTTTTTTTAAAAATTGACAGTAAATTTTAA
2615615 CTAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (31 bp):
TTTTTTTTTAAAAATTGACAGTAAATTTTAA
Found at i:2622868 original size:7 final size:7
Alignment explanation
Indices: 2622856--2622901 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
2622846 AAGTCAATTT
2622856 AGGGTTA
1 AGGGTTA
*
2622863 AGGGTTT
1 AGGGTTA
2622870 AGGGTTA
1 AGGGTTA
*
2622877 AAGGTTA
1 AGGGTTA
2622884 AGGGTTTA
1 AGGG-TTA
*
2622892 AGGTTTA
1 AGGGTTA
2622899 AGG
1 AGG
2622902 TCTAAGGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.39, T:0.33
Consensus pattern (7 bp):
AGGGTTA
Found at i:2622872 original size:14 final size:14
Alignment explanation
Indices: 2622853--2622908 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
2622843 TCTAAGTCAA
2622853 TTTAGGGTTAAGGG
1 TTTAGGGTTAAGGG
*
2622867 TTTAGGGTTAAAGG
1 TTTAGGGTTAAGGG
*
2622881 TTAAGGGTTTAA-GG
1 TTTAGGG-TTAAGGG
*
2622895 TTTAAGGTCTAAGG
1 TTTAGGGT-TAAGG
2622909 AATAGAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.03
14 29 0.83
15 5 0.14
ACGTcount: A:0.27, C:0.02, G:0.36, T:0.36
Consensus pattern (14 bp):
TTTAGGGTTAAGGG
Found at i:2622884 original size:21 final size:21
Alignment explanation
Indices: 2622858--2622908 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
2622848 GTCAATTTAG
*
2622858 GGTTAAGGGTTTAGGGTTAAA
1 GGTTAAGGGTTTAAGGTTAAA
*
2622879 GGTTAAGGGTTTAAGGTTTAA
1 GGTTAAGGGTTTAAGGTTAAA
2622900 GGTCTAAGG
1 GGT-TAAGG
2622909 AATAGAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.33
Consensus pattern (21 bp):
GGTTAAGGGTTTAAGGTTAAA
Found at i:2625451 original size:9 final size:9
Alignment explanation
Indices: 2625437--2625744 Score: 262
Period size: 9 Copynumber: 34.4 Consensus size: 9
2625427 TTCAAATTAA
2625437 ATAACTTAC
1 ATAACTTAC
*
2625446 ATAACTTAA
1 ATAACTTAC
2625455 ATAACTTAC
1 ATAACTTAC
2625464 ATAA--TAC
1 ATAACTTAC
2625471 ATAACCTT-C
1 ATAA-CTTAC
*
2625480 CTAACTTAC
1 ATAACTTAC
* *
2625489 ATTATTTAC
1 ATAACTTAC
2625498 ATAA--TAC
1 ATAACTTAC
2625505 ATAACTTAGTAC
1 ATAAC-T--TAC
2625517 ATAACTTAC
1 ATAACTTAC
* *
2625526 ATAATTTTTTCTAA
1 ATAA----CT-TAC
2625540 ATAACTTAC
1 ATAACTTAC
* *
2625549 ATAAATTAA
1 ATAACTTAC
2625558 ATAACTTAC
1 ATAACTTAC
* *
2625567 ATAAATTAA
1 ATAACTTAC
2625576 ATAACTTAC
1 ATAACTTAC
2625585 ATAACTTAC
1 ATAACTTAC
* *
2625594 ATAAATTAA
1 ATAACTTAC
2625603 ATAACTTAC
1 ATAACTTAC
2625612 ATAACTTAC
1 ATAACTTAC
*
2625621 ATAACTTAA
1 ATAACTTAC
2625630 ATAACTTAC
1 ATAACTTAC
2625639 ATAA--TAC
1 ATAACTTAC
2625646 ATAACTCT-C
1 ATAACT-TAC
*
2625655 CTAACTTAC
1 ATAACTTAC
* *
2625664 ATTATTTAC
1 ATAACTTAC
2625673 ATAA--TAC
1 ATAACTTAC
* *
2625680 ATAGCCTAC
1 ATAACTTAC
2625689 ATAACTTAC
1 ATAACTTAC
2625698 ATAACTTAC
1 ATAACTTAC
*
2625707 ATAACTCAC
1 ATAACTTAC
2625716 ATAA--TAC
1 ATAACTTAC
*
2625723 ACAACTTAC
1 ATAACTTAC
2625732 ATAACTTAC
1 ATAACTTAC
2625741 ATAA
1 ATAA
2625745 TACATAAAAA
Statistics
Matches: 240, Mismatches: 37, Indels: 44
0.75 0.12 0.14
Matches are distributed among these distances:
7 32 0.13
8 4 0.02
9 185 0.77
10 3 0.01
11 1 0.00
12 8 0.03
13 1 0.00
14 6 0.03
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:2629837 original size:21 final size:21
Alignment explanation
Indices: 2629788--2629837 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
2629778 GGATAAGAAT
2629788 TTAT-AATGAAATTATTCAAA
1 TTATAAATGAAATTATTCAAA
* *
2629808 TAAATAAATGTAATTATTCAAA
1 T-TATAAATGAAATTATTCAAA
2629830 TTATAAAT
1 TTATAAAT
2629838 TAAACCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 8 0.32
22 16 0.64
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (21 bp):
TTATAAATGAAATTATTCAAA
Found at i:2632206 original size:28 final size:28
Alignment explanation
Indices: 2632133--2632215 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
2632123 GGGTCCAAAA
*
2632133 TCTAGAG-TCTGTGGTCCAAGGTTTAAGG
1 TCTAGAGTTC-GTGGTCTAAGGTTTAAGG
* *
2632161 TTTAGAGTTTC-TGGTCTAAGGTTTAGGG
1 TCTAGAG-TTCGTGGTCTAAGGTTTAAGG
* *
2632189 TCTAGAGTTCGTGATCTAAGATTTAAG
1 TCTAGAGTTCGTGGTCTAAGGTTTAAG
2632216 ATCCAAAGTC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.07
28 40 0.89
30 2 0.04
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (28 bp):
TCTAGAGTTCGTGGTCTAAGGTTTAAGG
Found at i:2633055 original size:34 final size:34
Alignment explanation
Indices: 2633000--2633065 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
2632990 CAAACACCAG
* *
2633000 AAAATATTTTCCTGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCCGTAAATCATTTTAC-GAAAAGT
2633035 AAAACATTTTCCCG-AAATCATTTTACGAAAA
1 AAAACATTTTCCCGTAAATCATTTTACGAAAA
2633066 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (34 bp):
AAAACATTTTCCCGTAAATCATTTTACGAAAAGT
Found at i:2636011 original size:16 final size:16
Alignment explanation
Indices: 2635974--2636013 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2635964 TAAATAAAAT
* *
2635974 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
2635990 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
2636006 TAAAATTA
1 TAAAATTA
2636014 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:2636098 original size:9 final size:9
Alignment explanation
Indices: 2636086--2636129 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
2636076 ATTATCAAAT
2636086 TATTAATTG
1 TATTAATTG
2636095 TATTAATTG
1 TATTAATTG
2636104 --TTAATTG
1 TATTAATTG
*
2636111 AATTAATTG
1 TATTAATTG
2636120 TATTAATTG
1 TATTAATTG
2636129 T
1 T
2636130 TGTAACAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 7 0.22
9 25 0.78
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (9 bp):
TATTAATTG
Found at i:2636107 original size:16 final size:16
Alignment explanation
Indices: 2636083--2636120 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2636073 AAAATTATCA
* *
2636083 AATTATTAATTGTATT
1 AATTGTTAATTGAATT
2636099 AATTGTTAATTGAATT
1 AATTGTTAATTGAATT
2636115 AATTGT
1 AATTGT
2636121 ATTAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
AATTGTTAATTGAATT
Found at i:2636226 original size:68 final size:68
Alignment explanation
Indices: 2636117--2636252 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
2636107 ATTGAATTAA
*
2636117 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAATAAACTTGATATTTTATTATT
1 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATATTTTATTATT
2636182 ATT
66 ATT
*
2636185 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
1 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATATTTTATTATT
2636250 ATT
66 ATT
2636253 ATTATTTTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (68 bp):
TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATATTTTATTATT
ATT
Found at i:2636250 original size:3 final size:3
Alignment explanation
Indices: 2636242--2636272 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2636232 ACTTGATGTT
2636242 TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2636273 TTGTAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2636262 original size:17 final size:17
Alignment explanation
Indices: 2636240--2636272 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2636230 AAACTTGATG
2636240 TTTTATTATTATTATTA
1 TTTTATTATTATTATTA
2636257 TTTTATTATTATTATT
1 TTTTATTATTATTATT
2636273 TTGTAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTATTATTA
Found at i:2636264 original size:14 final size:14
Alignment explanation
Indices: 2636245--2636274 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2636235 TGATGTTTTA
2636245 TTATTATTATTATT
1 TTATTATTATTATT
2636259 TTATTATTATTATT
1 TTATTATTATTATT
2636273 TT
1 TT
2636275 GTAACAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:2640738 original size:46 final size:46
Alignment explanation
Indices: 2640671--2640763 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
2640661 TAGTCTTTAT
2640671 ATATTGAAAAAATAGGTATATTAGCCCGATGAATCTCTTGTTAAAA
1 ATATTGAAAAAATAGGTATATTAGCCCGATGAATCTCTTGTTAAAA
2640717 ATATTGAAAAAATAGGTATATTAGCCCGATGAATCTCTTGTTAAAA
1 ATATTGAAAAAATAGGTATATTAGCCCGATGAATCTCTTGTTAAAA
2640763 A
1 A
2640764 ATTACCGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (46 bp):
ATATTGAAAAAATAGGTATATTAGCCCGATGAATCTCTTGTTAAAA
Found at i:2655539 original size:13 final size:13
Alignment explanation
Indices: 2655521--2655545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2655511 TTTTAGGTGC
2655521 CTAAAATGAAAAT
1 CTAAAATGAAAAT
2655534 CTAAAATGAAAA
1 CTAAAATGAAAA
2655546 CTTTTTACAG
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:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (13 bp):
CTAAAATGAAAAT
Found at i:2657893 original size:18 final size:18
Alignment explanation
Indices: 2657852--2657895 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2657842 CGCAACCGTG
* *
2657852 ATAGGGAACGTGATCGAG
1 ATAGGGAACGGGATCGAC
* *
2657870 ACAGGGATCGGGATCGAC
1 ATAGGGAACGGGATCGAC
2657888 ATAGGGAA
1 ATAGGGAA
2657896 GACAAAGACA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.39, T:0.14
Consensus pattern (18 bp):
ATAGGGAACGGGATCGAC
Found at i:2671296 original size:33 final size:33
Alignment explanation
Indices: 2671259--2671424 Score: 278
Period size: 33 Copynumber: 5.0 Consensus size: 33
2671249 AGGGCCAGGA
2671259 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
* *
2671292 GCTCCACCACCAGGAGGTGGTGGCGGAGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
2671325 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
*
2671358 GCTCCTCCACCAGGAGGTGGTGGCGGAGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
* * *
2671391 GCTCCTCCTCCTGGAGGTGGTGGTGGCGGTGGT
1 GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
2671424 G
1 G
2671425 GTCCAACTCC
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 124 1.00
ACGTcount: A:0.10, C:0.24, G:0.46, T:0.20
Consensus pattern (33 bp):
GCTCCTCCTCCAGGAGGTGGTGGCGGAGGTGGT
Found at i:2671442 original size:33 final size:33
Alignment explanation
Indices: 2671405--2671519 Score: 110
Period size: 33 Copynumber: 3.6 Consensus size: 33
2671395 CTCCTCCTGG
* *
2671405 AGGTGGTGGTGGCGGTGGTGGTCCAACTCCAAA
1 AGGTGGCGGTGGAGGTGGTGGTCCAACTCCAAA
* * * * *
2671438 AGGTGGCGCTGGAAGTGGTGGTTCAATTCCAAG
1 AGGTGGCGGTGGAGGTGGTGGTCCAACTCCAAA
* * * *
2671471 AGGCGGCGGTGGAGGTGGCGGT---ACCCCAGA
1 AGGTGGCGGTGGAGGTGGTGGTCCAACTCCAAA
2671501 AGGTGGCGGTGGAGGTGGT
1 AGGTGGCGGTGGAGGTGGT
2671520 TCTCCAATAG
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
30 21 0.32
33 44 0.68
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.19
Consensus pattern (33 bp):
AGGTGGCGGTGGAGGTGGTGGTCCAACTCCAAA
Found at i:2671987 original size:42 final size:42
Alignment explanation
Indices: 2671859--2671992 Score: 132
Period size: 42 Copynumber: 3.3 Consensus size: 42
2671849 TATCGATGGG
* * *
2671859 GGAGGAGGTTGGGTGTTAGATGTTGATGGGGGCGGTGGAGAT
1 GGAGGAGGTGGGGTGCTAGATGTTGATGGGGGTGGTGGAGAT
** ** * * *
2671901 GGAGGAGGTGGGGCACTAG-TCGTCAAAGTGGTTGGT-GA-A-
1 GGAGGAGGTGGGGTGCTAGAT-GTTGATGGGGGTGGTGGAGAT
*
2671940 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
1 GGAGGAGGTGGGGTGCTAGATGTTGATGGGGGTGGTGGAGAT
2671982 GGAGGAGGTGG
1 GGAGGAGGTGG
2671993 AGGGAGTAGG
Statistics
Matches: 69, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
39 26 0.38
40 4 0.06
41 4 0.06
42 35 0.51
ACGTcount: A:0.19, C:0.04, G:0.54, T:0.22
Consensus pattern (42 bp):
GGAGGAGGTGGGGTGCTAGATGTTGATGGGGGTGGTGGAGAT
Found at i:2672063 original size:207 final size:206
Alignment explanation
Indices: 2671808--2672567 Score: 822
Period size: 207 Copynumber: 3.7 Consensus size: 206
2671798 ACTAGTTGAA
* * * *
2671808 AAAGTGGTTGATAAAGGTGAAGGAGGAAGTGAAGCACTAGATATCGATGGGGGAGGAGGTTGGGT
1 AAAGTGGTTGGTGAAGGTGAAGGAGGAAGTGAAGCACTAGACATCGATGGGGGAGGAGGTGGGGT
* * *
2671873 GTTAGATGTTGATGGGGGCGGTGGAGATGGAGGAGGTGGGGCACTAGTCGTCAAAGTGGTTGGTG
66 GCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGGGCACTAGTCGTCAAAGTGGTTGGTG
*
2671938 AAGGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGAGGGAGTAGG
131 AAGGAGGAGGTGGGGTGCTAGATATTGATGAGGGTGGTGGAGATGGAGGAGGTGGA-GGAGTAGG
2672003 GCACTAGTCATC
195 GCACTAGTCATC
** *
2672015 AAAGTATTTGGTGAAGGTGAAGGAGGAATTGAAGCACTAGACATCGATGGGGGAGGAGGTGGGGT
1 AAAGTGGTTGGTGAAGGTGAAGGAGGAAGTGAAGCACTAGACATCGATGGGGGAGGAGGTGGGGT
* * * *
2672080 GCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGCTGGGGTACTAGTCATCGAAGTGGTTGGTG
66 GCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGGGCACTAGTCGTCAAAGTGGTTGGTG
* *
2672145 AAGGAGGAGGTGGGGTGCTAGATATTGAAGAAGGTGGTGGAGAT---GGA---GGA-G-GTAGGG
131 AAGGAGGAGGTGGGGTGCTAGATATTGATGAGGGTGGTGGAGATGGAGGAGGTGGAGGAGTAGGG
**
2672202 CACTAGTTGTC
196 CACTAGTCATC
* * * * * * *
2672213 AAAGTGGTTGGTGAAGGAGAACGAGGAATTGAAGCACTAGACATCGATGAGGGAAGAGGTTGGAT
1 AAAGTGGTTGGTGAAGGTGAAGGAGGAAGTGAAGCACTAGACATCGATGGGGGAGGAGGTGGGGT
* * *** * *
2672278 GCTAGATATTGATAGGGGTGATGGAGACAAAAGAGGTGGGGCACTAGTCGTTGCAGAG-GG-TGG
66 GCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGGGCACTAGTCG-T-CAAAGTGGTTGG
* * ** * *
2672341 TGAAGATGGAGGAGGAAGTGGG-GCAGTAGACATCAATGTGGGAGGTGGAGATGGTAGTGAAGGT
129 TG-A-A-GGAGGAGG-TG-GGGTGC--TAGATATTGATGAGGGTGGTGGAGATGG-AG-G-AGGT
* *
2672405 GAAGGAGGTGGGGCACTAGTCATC
184 GGAGGA-GTAGGGCACTAGTCATC
* * * * * * * *
2672429 AAAGTGGTTGGCGAAAGTGAAAGAGGAAGTGGAGCACTAGATACCGACGGGGGAGGAAGTGGGGT
1 AAAGTGGTTGGTGAAGGTGAAGGAGGAAGTGAAGCACTAGACATCGATGGGGGAGGAGGTGGGGT
* * ** *
2672494 GTTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGGGCACTAGTTGTCAAAAAGGGTGGTG
66 GCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGGGCACTAGTCGTCAAAGTGGTTGGTG
*
2672559 AAGGTGGAG
131 AAGGAGGAG
2672568 CAGGAAACGA
Statistics
Matches: 455, Mismatches: 75, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
198 118 0.26
199 5 0.01
200 4 0.01
201 11 0.02
202 3 0.01
203 3 0.01
204 22 0.05
207 157 0.35
208 1 0.00
209 1 0.00
210 1 0.00
213 8 0.02
214 5 0.01
215 4 0.01
216 112 0.25
ACGTcount: A:0.27, C:0.07, G:0.46, T:0.20
Consensus pattern (206 bp):
AAAGTGGTTGGTGAAGGTGAAGGAGGAAGTGAAGCACTAGACATCGATGGGGGAGGAGGTGGGGT
GCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGGGCACTAGTCGTCAAAGTGGTTGGTG
AAGGAGGAGGTGGGGTGCTAGATATTGATGAGGGTGGTGGAGATGGAGGAGGTGGAGGAGTAGGG
CACTAGTCATC
Found at i:2672112 original size:39 final size:39
Alignment explanation
Indices: 2672069--2672193 Score: 119
Period size: 39 Copynumber: 3.1 Consensus size: 39
2672059 CGATGGGGGA
* *
2672069 GGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
1 GGAGGTGGGGTGCTAGATATTGAAGAGGGTGGTGGAGAT
* * * * *
2672108 GGAGGAGCTGGGGTACTAG-TCATCGAAGTGGTTGGTGAAGGA-
1 GGA-G-G-TGGGGTGCTAGAT-ATTGAAGAGGGTGGTGGA-GAT
*
2672150 GGAGGTGGGGTGCTAGATATTGAAGAAGGTGGTGGAGAT
1 GGAGGTGGGGTGCTAGATATTGAAGAGGGTGGTGGAGAT
2672189 GGAGG
1 GGAGG
2672194 AGGTAGGGCA
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
38 2 0.03
39 31 0.46
40 3 0.04
41 3 0.04
42 26 0.39
43 2 0.03
ACGTcount: A:0.22, C:0.05, G:0.50, T:0.22
Consensus pattern (39 bp):
GGAGGTGGGGTGCTAGATATTGAAGAGGGTGGTGGAGAT
Found at i:2672112 original size:42 final size:42
Alignment explanation
Indices: 2672066--2672197 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 42
2672056 CATCGATGGG
* *
2672066 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGAT
1 GGAGGAGGTGGGGTGCTAGATATTGAAGAGGGTGGTGGAGAT
* * * * *
2672108 GGAGGAGCTGGGGTACTAG-TCATCGAAGTGGTTGGT-GA-A-
1 GGAGGAGGTGGGGTGCTAGAT-ATTGAAGAGGGTGGTGGAGAT
*
2672147 GGAGGAGGTGGGGTGCTAGATATTGAAGAAGGTGGTGGAGAT
1 GGAGGAGGTGGGGTGCTAGATATTGAAGAGGGTGGTGGAGAT
2672189 GGAGGAGGT
1 GGAGGAGGT
2672198 AGGGCACTAG
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
39 28 0.38
40 4 0.05
41 4 0.05
42 37 0.51
ACGTcount: A:0.23, C:0.05, G:0.51, T:0.22
Consensus pattern (42 bp):
GGAGGAGGTGGGGTGCTAGATATTGAAGAGGGTGGTGGAGAT
Found at i:2672160 original size:81 final size:81
Alignment explanation
Indices: 2672066--2672231 Score: 251
Period size: 81 Copynumber: 2.0 Consensus size: 81
2672056 CATCGATGGG
* ** * *
2672066 GGAGGAGGTGGGGTGCTAGATATTGATGGGGGTGGTGGAGATGGAGGAGCTGGGGTACTAGTCAT
1 GGAGGAGGTGGGGTGCTAGATATTGAAGAAGGTGGTGGAGATGGAGGAGCTAGGGCACTAGTCAT
*
2672131 CGAAGTGGTTGGTGAA
66 CAAAGTGGTTGGTGAA
* **
2672147 GGAGGAGGTGGGGTGCTAGATATTGAAGAAGGTGGTGGAGATGGAGGAGGTAGGGCACTAGTTGT
1 GGAGGAGGTGGGGTGCTAGATATTGAAGAAGGTGGTGGAGATGGAGGAGCTAGGGCACTAGTCAT
2672212 CAAAGTGGTTGGTGAA
66 CAAAGTGGTTGGTGAA
2672228 GGAG
1 GGAG
2672232 AACGAGGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.23, C:0.05, G:0.49, T:0.22
Consensus pattern (81 bp):
GGAGGAGGTGGGGTGCTAGATATTGAAGAAGGTGGTGGAGATGGAGGAGCTAGGGCACTAGTCAT
CAAAGTGGTTGGTGAA
Found at i:2672584 original size:216 final size:216
Alignment explanation
Indices: 2672191--2672640 Score: 535
Period size: 216 Copynumber: 2.1 Consensus size: 216
2672181 GTGGAGATGG
** * * * *
2672191 AGGAGGTAGGGCACTAGTTGTCAAAGTGGTTGGTGAAGGAGAACGAGGAATTGAAGCACTAGACA
1 AGGAGGTAGGGCACTAGTCATCAAAGTGGTTGGCGAAAGAGAAAGAGGAAGTGAAGCACTAGACA
* * * *
2672256 TCGATGAGGGAAGAGGTTGGATGCTAGATATTGATAGGGGTGATGGAGACAAAAGAGGTGGGGCA
66 CCGACGAGGGAAGAAGTGGGATGCTAGATATTGATAGGGGTGATGGAGACAAAAGAGGTGGGGCA
*** * * ** *
2672321 CTAGTCGTTGCAGAGGGTGGTGAAGATGGAGGAGGAAGTGGGGCAGTAGACATCAAT-GTGGGAG
131 CTAGTCGTCAAAAAGGGTGGTGAAGATGGAGCAGGAAACGAGGCAGTAGACATCAATAG-GGGAG
2672385 GTGGAGATGGTAGT-GAAGGTGA
195 GTGGAGATGGTAGTGGAA-GTGA
* * * *
2672407 AGGAGGTGGGGCACTAGTCATCAAAGTGGTTGGCGAAAGTGAAAGAGGAAGTGGAGCACTAGATA
1 AGGAGGTAGGGCACTAGTCATCAAAGTGGTTGGCGAAAGAGAAAGAGGAAGTGAAGCACTAGACA
* * * * * * *** *
2672472 CCGACGGGGGAGGAAGTGGGGTGTTAGATATTGATGGGGGTGGTGGAGATGGAGGAGGTGGGGCA
66 CCGACGAGGGAAGAAGTGGGATGCTAGATATTGATAGGGGTGATGGAGACAAAAGAGGTGGGGCA
* *
2672537 CTAGTTGTCAAAAAGGGTGGTGAAGGTGGAGCAGGAAACGAGGCAGTAGACATCAATAGGGGAGG
131 CTAGTCGTCAAAAAGGGTGGTGAAGATGGAGCAGGAAACGAGGCAGTAGACATCAATAGGGGAGG
* *
2672602 TGGAGATGGTGGTGGAATTGA
196 TGGAGATGGTAGTGGAAGTGA
*
2672623 AGGAGGTAAGGCACTAGT
1 AGGAGGTAGGGCACTAGT
2672641 AACCGAAGAA
Statistics
Matches: 194, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
216 190 0.98
217 4 0.02
ACGTcount: A:0.30, C:0.08, G:0.44, T:0.19
Consensus pattern (216 bp):
AGGAGGTAGGGCACTAGTCATCAAAGTGGTTGGCGAAAGAGAAAGAGGAAGTGAAGCACTAGACA
CCGACGAGGGAAGAAGTGGGATGCTAGATATTGATAGGGGTGATGGAGACAAAAGAGGTGGGGCA
CTAGTCGTCAAAAAGGGTGGTGAAGATGGAGCAGGAAACGAGGCAGTAGACATCAATAGGGGAGG
TGGAGATGGTAGTGGAAGTGA
Found at i:2672745 original size:84 final size:85
Alignment explanation
Indices: 2672646--2672925 Score: 338
Period size: 84 Copynumber: 3.3 Consensus size: 85
2672636 CTAGTAACCG
* * * * * * *
2672646 AAGAAGGTGGTGAAGGTGGAGGAAGTGAAGCACTAGACATTGATGGGAGTTGTGGAGCTGGAGGA
1 AAGAGGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGAGTGGTGGAGATGGAGGA
* *
2672711 GATG-GGACAATATTAG-TCA
66 GACGAGG-CAATAGTAGTTCA
* *
2672730 AAGAGGGTGGTGAAGGCGGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGTGGAGATGGAGGA
1 AAGAGGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGAGTGGTGGAGATGGAGGA
*
2672795 GACGAGGCAATAGTAGTTGA
66 GACGAGGCAATAGTAGTTCA
**
2672815 AA-AGGGTGGTGAAAATGGAGGAAGTGGAGTACTACACATTGGT-GGAGGTGGTGGAGATGGAGG
1 AAGAGGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGA-GTGGTGGAGATGGAGG
*
2672878 AGACGAGGCAATAGTAGTTGA
65 AGACGAGGCAATAGTAGTTCA
* *
2672899 AA-AAGGTGGTG-AGGTTAGAGGAAGTGG
1 AAGAGGGTGGTGAAGG-TGGAGGAAGTGG
2672926 GACAGTAGTC
Statistics
Matches: 172, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
83 3 0.02
84 163 0.95
85 6 0.03
ACGTcount: A:0.31, C:0.06, G:0.44, T:0.19
Consensus pattern (85 bp):
AAGAGGGTGGTGAAGGTGGAGGAAGTGGAGTACTACACATTGGTGGGAGTGGTGGAGATGGAGGA
GACGAGGCAATAGTAGTTCA
Done.