Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 1 of 173
Found at i:31928 original size:9 final size:8
Alignment explanation
Indices: 31911--31940 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
31901 AGACCCCCCC
31911 TTCTTTTT
1 TTCTTTTT
31919 TTCTTTTT
1 TTCTTTTT
31927 TTCTTTTT
1 TTCTTTTT
31935 TT-TTTT
1 TTCTTTT
31941 CATATAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.18
8 18 0.82
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTCTTTTT
Found at i:33641 original size:12 final size:12
Alignment explanation
Indices: 33624--33662 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
33614 AAGATGACCA
*
33624 TTAGAGTTAGAG
1 TTAGAGTTAAAG
*
33636 TTAGAGATAAAG
1 TTAGAGTTAAAG
*
33648 TTAAAGTTAAAG
1 TTAGAGTTAAAG
33660 TTA
1 TTA
33663 AGGTTTTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (12 bp):
TTAGAGTTAAAG
Found at i:34964 original size:25 final size:25
Alignment explanation
Indices: 34936--34987 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
34926 CATAACTTAC
34936 CTCAATAACAATTTAATATGATAAG
1 CTCAATAACAATTTAATATGATAAG
34961 CTCAATAACAATTTAATATGATAAG
1 CTCAATAACAATTTAATATGATAAG
34986 CT
1 CT
34988 ACTAGCTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (25 bp):
CTCAATAACAATTTAATATGATAAG
Found at i:57467 original size:160 final size:161
Alignment explanation
Indices: 57172--57480 Score: 476
Period size: 160 Copynumber: 1.9 Consensus size: 161
57162 TGGTCTTTTC
* * * *
57172 GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTTGATGTTCGAATTAGGCTTCTTGCCTATAGTC
1 GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTCGATATTCAAATTAGGCTTCTTGCC-ATAGTA
* * * *
57237 TATTGGTTCTTGCTTGGATGCTTAACATTTTGTACCGTAGCTATCACTTTTACTTTGGTTTTATC
65 TATTGGTTCTTGCTTGGATGCTTAACATTATGTACCATAGCTAGCACTTTTACTTTGGTTTTACC
57302 ATTATAACTGTGATAATTTAACTGGTCTCACT
130 ATTATAACTGTGATAATTTAACTGGTCTCACT
* * *
57334 GTTCATTAGTTAAGTCTTTAGTTTTCTGTGGCTCGATATTCAAATTAGGTTTCTTGCC-TAGTAT
1 GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTCGATATTCAAATTAGGCTTCTTGCCATAGTAT
* * *
57398 ATTGGTTCTTGCTTGGGTGCTTAACATTATGTACCATTGCTAGCACTTTTTCTTTGGTTTTACCA
66 ATTGGTTCTTGCTTGGATGCTTAACATTATGTACCATAGCTAGCACTTTTACTTTGGTTTTACCA
57463 TTATAACTGTGATAATTT
131 TTATAACTGTGATAATTT
57481 GCTTACTAAA
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
160 81 0.61
162 52 0.39
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (161 bp):
GTTCATTAGTTAAGTCATTAGTTCTCTGTGGCTCGATATTCAAATTAGGCTTCTTGCCATAGTAT
ATTGGTTCTTGCTTGGATGCTTAACATTATGTACCATAGCTAGCACTTTTACTTTGGTTTTACCA
TTATAACTGTGATAATTTAACTGGTCTCACT
Found at i:59456 original size:11 final size:13
Alignment explanation
Indices: 59428--59472 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 13
59418 TTTTACATTC
59428 AATTAAAAATATA
1 AATTAAAAATATA
59441 AATTAAAAA-A-A
1 AATTAAAAATATA
*
59452 AATTAAAAACTATC
1 AATTAAAAA-TATA
59466 AATTAAA
1 AATTAAA
59473 TTTTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.36
12 1 0.04
13 10 0.36
14 7 0.25
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (13 bp):
AATTAAAAATATA
Found at i:72803 original size:17 final size:17
Alignment explanation
Indices: 72781--72814 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
72771 TTACAAAATT
*
72781 AAATCTTATAGGATTAC
1 AAATCTTATAAGATTAC
*
72798 AAATCTTCTAAGATTAC
1 AAATCTTATAAGATTAC
72815 TTTCCTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (17 bp):
AAATCTTATAAGATTAC
Found at i:73325 original size:11 final size:13
Alignment explanation
Indices: 73299--73344 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 13
73289 AAAATAATAC
73299 AAATTATAAACAA
1 AAATTATAAACAA
73312 AAATT-TAAACAA
1 AAATTATAAACAA
*
73324 AAATT-TATA-AA
1 AAATTATAAACAA
73335 AAATTATAAA
1 AAATTATAAA
73345 TTATAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTATAAACAA
Found at i:73500 original size:10 final size:11
Alignment explanation
Indices: 73471--73511 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
73461 TTTATAATTT
73471 TAAATTTTTTG
1 TAAATTTTTTG
73482 TAAATTTTTTG
1 TAAATTTTTTG
*
73493 TAAATTTTTTA
1 TAAATTTTTTG
73504 T-AATTTTT
1 TAAATTTTT
73512 ATGGTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 7 0.24
11 22 0.76
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (11 bp):
TAAATTTTTTG
Found at i:83966 original size:5 final size:5
Alignment explanation
Indices: 83956--84028 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
83946 AAAAAAATAT
* *
83956 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
84002 -A-TA TATTA TATTA TATTA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA TAT
84029 ATCAAAAGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 4 0.07
4 4 0.07
5 32 0.56
6 16 0.28
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:84008 original size:19 final size:17
Alignment explanation
Indices: 83984--84030 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 17
83974 ATTATGTTTT
83984 TATATTATATTATTATTAA
1 TATATTATATTA-TATT-A
84003 TATATTATATTATATTA
1 TATATTATATTATATTA
84020 TATATATATAT
1 TATAT-TATAT
84031 CAAAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTATATTATATTA
Found at i:85577 original size:6 final size:6
Alignment explanation
Indices: 85566--85604 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
85556 TGTCGAATAT
* *
85566 TGTTAC TGTTAC TGTTAC TGCTAC CGTTAC TGTTTAC TG
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TG-TTAC TG
85605 ATCAGGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (6 bp):
TGTTAC
Found at i:85937 original size:13 final size:15
Alignment explanation
Indices: 85909--85937 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
85899 CATTGTTGAG
85909 AAATGAGAAATAAAA
1 AAATGAGAAATAAAA
85924 AAATGA-AAATAAAA
1 AAATGAGAAATAAAA
85938 TGATTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (15 bp):
AAATGAGAAATAAAA
Found at i:93146 original size:21 final size:19
Alignment explanation
Indices: 93109--93147 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
93099 TTCAAATTTT
*
93109 ATTTTTATATAGTTAATAA
1 ATTTTTATATAGATAATAA
93128 ATTTATTATCATAGATAATA
1 ATTT-TTAT-ATAGATAATA
93148 TATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTTTTATATAGATAATAA
Found at i:98854 original size:28 final size:28
Alignment explanation
Indices: 98818--98949 Score: 122
Period size: 28 Copynumber: 4.7 Consensus size: 28
98808 GAATTCGCAT
* * *
98818 GTAAAAGTTTGTATGAATTATCTTTCAA
1 GTAAGAGTTTGTATGGATTATCTTCCAA
* * * * *
98846 GCACGAGTTTGTATGGATTTTCATCCAG
1 GTAAGAGTTTGTATGGATTATCTTCCAA
* ** * *
98874 GTAAGAGTCTACATGAATTATCTTTCAA
1 GTAAGAGTTTGTATGGATTATCTTCCAA
*
98902 G-AACGAGTTTGTATGGATTTTCTTCCAA
1 GTAA-GAGTTTGTATGGATTATCTTCCAA
98930 GTAAGAGTTTGTATGGATTA
1 GTAAGAGTTTGTATGGATTA
98950 GATTTCGAAC
Statistics
Matches: 77, Mismatches: 25, Indels: 4
0.73 0.24 0.04
Matches are distributed among these distances:
27 2 0.03
28 73 0.95
29 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (28 bp):
GTAAGAGTTTGTATGGATTATCTTCCAA
Found at i:98890 original size:56 final size:56
Alignment explanation
Indices: 98830--98937 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 56
98820 AAAAGTTTGT
* *
98830 ATGAATTATCTTTCAAGCACGAGTTTGTATGGATTTTCATCCAGGTAAGAGTCTAC
1 ATGAATTATCTTTCAAGAACGAGTTTGTATGGATTTTCATCCAAGTAAGAGTCTAC
*
98886 ATGAATTATCTTTCAAGAACGAGTTTGTATGGATTTTCTTCCAAGTAAGAGT
1 ATGAATTATCTTTCAAGAACGAGTTTGTATGGATTTTCATCCAAGTAAGAGT
98938 TTGTATGGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (56 bp):
ATGAATTATCTTTCAAGAACGAGTTTGTATGGATTTTCATCCAAGTAAGAGTCTAC
Found at i:101966 original size:3 final size:3
Alignment explanation
Indices: 101958--102025 Score: 84
Period size: 3 Copynumber: 22.3 Consensus size: 3
101948 TAAGTAAATG
*
101958 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ACTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* *
102004 ATTA GTT A-A ATA ATA ATA ATA A
1 A-TA ATA ATA ATA ATA ATA ATA A
102026 AAAGGGACTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.89
4 5 0.09
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:102903 original size:3 final size:3
Alignment explanation
Indices: 102895--102934 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
102885 TTGTATGTAG
102895 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
102935 TAGAAACAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:104069 original size:46 final size:44
Alignment explanation
Indices: 103792--104204 Score: 205
Period size: 43 Copynumber: 9.5 Consensus size: 44
103782 TCAATCTGTA
* *
103792 CCACTGTAACCTCAGGGAGATGAGATCTGAAATTCTTCGGTCTACT
1 CCACTGTAACCTCAGGGAGATAAGA-CTG-AATTCTTCGATCTACT
* *
103838 CCACTGTAACCCCAGGGAGATAAGACATG-A---TGCGATCTACT
1 CCACTGTAACCTCAGGGAGATAAGAC-TGAATTCTTCGATCTACT
** * * ** * *
103879 GTACTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCACT
1 CCACTGTAACCTCAGGGAGATAAGA--CTGAATTCTTCGATCTACT
* * * * * *
103923 CTACTGTAACTTCAGGGAGATAGGA-T-AGTGTCTTGGATCTGCT
1 CCACTGTAACCTCAGGGAGATAAGACTGAAT-TCTTCGATCTACT
* * * * *
103966 CCGCTGTAATCTCAGGGAGAT-AGAAT-AGTGTCTTCGATCTGCT
1 CCACTGTAACCTCAGGGAGATAAGACTGAAT-TCTTCGATCTACT
* * *
104009 CCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACT
1 CCACTGTAACCTCAGGGAGATAAGA-CTG-AATTCTTCGATCTACT
* *
104055 CCACTGTAACCTCAGAGAGATAAGACCTG-A-T-GT-GATCTACT
1 CCACTGTAACCTCAGGGAGATAAGA-CTGAATTCTTCGATCTACT
** * * ** * *
104096 CTGCTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCACT
1 CCACTGTAACCTCAGGGAGATAAGA--CTGAATTCTTCGATCTACT
* * * *
104140 CCACTGTAACTTCAGGGAGATAGGA-T-AGTGTCTTCGATCTGCT
1 CCACTGTAACCTCAGGGAGATAAGACTGAAT-TCTTCGATCTACT
* *
104183 CCGCTGTAATCTCAGGGAGATA
1 CCACTGTAACCTCAGGGAGATA
104205 GGATCTCTAA
Statistics
Matches: 291, Mismatches: 56, Indels: 43
0.75 0.14 0.11
Matches are distributed among these distances:
40 2 0.01
41 62 0.21
42 11 0.04
43 88 0.30
44 62 0.21
45 3 0.01
46 61 0.21
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
CCACTGTAACCTCAGGGAGATAAGACTGAATTCTTCGATCTACT
Found at i:104106 original size:217 final size:218
Alignment explanation
Indices: 103613--104213 Score: 838
Period size: 217 Copynumber: 2.8 Consensus size: 218
103603 TGTGGTTTTA
* * * * ** * *
103613 GTCTGCTCTACTGTAACTTCAGGGAGATAAGA-CTGGATGAGATCTGCTCTACTACATCTTTAGA
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCT-GATGAGATCTACTCTACTGTAACTTCAGA
* * * * *
103677 GAGATAAGATCTTTTGTTTTAATCCGCT-TCGCTGTAACTTCAGGGAGATAGGATAGTATCTTCG
65 GAGATAAGATCCTTTATTTTAATCCACTCT-ACTGTAACTTCAGGGAGATAGGATAGTGTCTTCG
* *
103741 ATCTGCTCCGTTGTAATCTCAGGAAGATA-AGATCTCTAGCTTCAATCTGTACCACTGTAACCTC
129 ATCTGCTCCGCTGTAATCTCAGGGAGATAGAGATCTCTA-CTTCAATCTGTACCACTGTAACCTC
*
103805 AGGGAGATGAGATCTGAAATTCTTCG
193 AGGGAGATAAGATCTGAAATTCTTCG
* * * *
103831 GTCTACTCCACTGTAACCCCAGGGAGATAAGACATGATGCGATCTACTGTACTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGAGATCTACTCTACTGTAACTTCAGAG
*
103896 AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGAT
66 AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
* * * * *
103961 CTGCTCCGCTGTAATCTCAGGGAGATAGA-ATAGTGT-CTTCGATCTGCT-CCGCTGTAATCTCA
131 CTGCTCCGCTGTAATCTCAGGGAGATAGAGAT-CTCTACTTCAATCTG-TACCACTGTAACCTCA
104023 GGGAGATAAGATCTGAAATTCTTCG
194 GGGAGATAAGATCTGAAATTCTTCG
* * *
104048 GTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGTGATCTACTCTGCTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGAGATCTACTCTACTGTAACTTCAGAG
*
104113 AGATAAGATCCTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
66 AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
104178 CTGCTCCGCTGTAATCTCAGGGAGATAG-GATCTCTA
131 CTGCTCCGCTGTAATCTCAGGGAGATAGAGATCTCTA
104214 ATATTCATTA
Statistics
Matches: 340, Mismatches: 36, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
216 2 0.01
217 197 0.58
218 136 0.40
219 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (218 bp):
GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGAGATCTACTCTACTGTAACTTCAGAG
AGATAAGATCCTTTATTTTAATCCACTCTACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
CTGCTCCGCTGTAATCTCAGGGAGATAGAGATCTCTACTTCAATCTGTACCACTGTAACCTCAGG
GAGATAAGATCTGAAATTCTTCG
Found at i:104179 original size:87 final size:90
Alignment explanation
Indices: 103964--104209 Score: 249
Period size: 87 Copynumber: 2.8 Consensus size: 90
103954 CTTGGATCTG
* *
103964 CTCCGCTGTAA-TCTCAGGGAGATAGAATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAACT-TCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAG
** *
104028 ATAAGAT-CTGAAATTCTTCGGTCTA
65 ATAAGATCCTGAAATTCTTCAATCCA
* * * ** * * * *
104053 CTCCACTGTAACCTCAGAGAGATAAGA-CCTGAT-GT-GATCTACTCTGCTGTAA-CTTCAGAGA
1 CTCCACTGTAACTTCAGGGAGATAGGATAGTG-TCTTCGATCTGCTCCGCTGTAATC-TCAGGGA
**
104114 GATAAGATCCT-TTATT-TT-AATCCA
64 GATAAGATCCTGAAATTCTTCAATCCA
104138 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGA
1 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGA
*
104203 TAGGATC
66 TAAGATC
104210 TCTAATATTC
Statistics
Matches: 123, Mismatches: 26, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
85 28 0.23
86 6 0.05
87 61 0.50
88 6 0.05
89 22 0.18
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (90 bp):
CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGA
TAAGATCCTGAAATTCTTCAATCCA
Found at i:104362 original size:3 final size:3
Alignment explanation
Indices: 104354--104394 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
104344 ATGCAGAATT
104354 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
104395 TTGAGAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:116780 original size:3 final size:3
Alignment explanation
Indices: 116722--116763 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
116712 TGAGTAAATG
*
116722 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ACTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA AT
116764 TAGTTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:116784 original size:12 final size:12
Alignment explanation
Indices: 116722--116784 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
116712 TGAGTAAATG
*
116722 ATAATAATAATA
1 ATAATAATAAAA
*
116734 ATAATAATAACA
1 ATAATAATAAAA
116746 ATAATAATAATAA
1 ATAATAATAA-AA
* * *
116759 CTAATTAGT-TAA
1 ATAA-TAATAAAA
116771 ATAATAATAAAA
1 ATAATAATAAAA
116783 AT
1 AT
116785 GGACTAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 3 0.08
12 30 0.75
13 4 0.10
14 3 0.08
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAATAATAAAA
Found at i:117655 original size:3 final size:3
Alignment explanation
Indices: 117647--117677 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
117637 TTGTATGTAG
*
117647 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
117678 TAGAAACAGT
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:119890 original size:27 final size:28
Alignment explanation
Indices: 119858--119917 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
119848 AATTTATAAA
*
119858 ATTTTA-AATT-AATAATTATAAAATTAT
1 ATTTTATAATTCAA-AATAATAAAATTAT
**
119885 ATTTTATTTTTCAAAATAATAAAATTAT
1 ATTTTATAATTCAAAATAATAAAATTAT
119913 ATTTT
1 ATTTT
119918 TACGATGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 20 0.71
29 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTTTATAATTCAAAATAATAAAATTAT
Found at i:120809 original size:24 final size:23
Alignment explanation
Indices: 120764--120809 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
120754 GATTTTAGAC
**
120764 TTAATTTTTTTAATTATAAAAAA
1 TTAATTTTTTTAAAAATAAAAAA
*
120787 TTAATTTCTTTTAAAAATTAAAA
1 TTAATTT-TTTTAAAAATAAAAA
120810 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATTTTTTTAAAAATAAAAAA
Found at i:136367 original size:24 final size:24
Alignment explanation
Indices: 136340--136391 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
136330 TTAGTAAGTC
*
136340 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
136364 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
136388 AAAT
1 AAAT
136392 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:138334 original size:24 final size:24
Alignment explanation
Indices: 138307--138358 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
138297 TTAGTAAGTC
*
138307 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
138331 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
138355 AAAT
1 AAAT
138359 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:139273 original size:26 final size:26
Alignment explanation
Indices: 139244--139295 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
139234 TGGTCTACAC
139244 CCTTTCGATTATATGGAAATTGAAAA
1 CCTTTCGATTATATGGAAATTGAAAA
* *
139270 CCTTTCTATTATATGGAAATTTAAAA
1 CCTTTCGATTATATGGAAATTGAAAA
139296 ATGAACTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (26 bp):
CCTTTCGATTATATGGAAATTGAAAA
Found at i:145911 original size:23 final size:23
Alignment explanation
Indices: 145868--145933 Score: 123
Period size: 23 Copynumber: 2.8 Consensus size: 23
145858 GTTGTTCAAT
145868 CTGTTGACACCATTTTTTTGATAG
1 CTGTTGACACCA-TTTTTTGATAG
145892 CTGTTGACACCATTTTTTGATAG
1 CTGTTGACACCATTTTTTGATAG
145915 CTGTTGACACCATTTTTTG
1 CTGTTGACACCATTTTTTG
145934 GATGAAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 30 0.71
24 12 0.29
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (23 bp):
CTGTTGACACCATTTTTTGATAG
Found at i:147033 original size:43 final size:43
Alignment explanation
Indices: 146985--147067 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
146975 AAATGAGTAA
146985 AATTATAAA-AATAAAAAAAGATATATATATGTACGTATGTTAG
1 AATTATAAAGAATAAAAAAA-ATATATATATGTACGTATGTTAG
* * * * *
147028 AATTATAAAGTATATAAAAAATATGTGTATGTATGTATGT
1 AATTATAAAGAATAAAAAAAATATATATATGTACGTATGT
147068 ATGTATGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 26 0.76
44 8 0.24
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.36
Consensus pattern (43 bp):
AATTATAAAGAATAAAAAAAATATATATATGTACGTATGTTAG
Found at i:147062 original size:4 final size:4
Alignment explanation
Indices: 147053--147084 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
147043 AAAAAATATG
147053 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
147085 AGCTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:147128 original size:8 final size:8
Alignment explanation
Indices: 147107--147177 Score: 58
Period size: 8 Copynumber: 9.1 Consensus size: 8
147097 ATTTATAAAG
*
147107 AGATATGT
1 AGATATAT
*
147115 ATATATAT
1 AGATATAT
*
147123 ACATATAT
1 AGATATAT
*
147131 ATATA-AT
1 AGATATAT
147138 AAGATATAT
1 -AGATATAT
147147 AGATATAT
1 AGATATAT
*
147155 ATA-ATA-
1 AGATATAT
*
147161 AGATATAA
1 AGATATAT
147169 AGATATAT
1 AGATATAT
147177 A
1 A
147178 AATAAATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 2 0.04
7 8 0.16
8 39 0.76
9 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (8 bp):
AGATATAT
Found at i:147131 original size:12 final size:11
Alignment explanation
Indices: 147114--147190 Score: 63
Period size: 10 Copynumber: 7.2 Consensus size: 11
147104 AAGAGATATG
147114 TATATATATACA
1 TATATATATA-A
147126 TATATATATAA
1 TATATATATAA
*
147137 TA-AGATATATA
1 TATATATATA-A
*
147148 GATATATATAA
1 TATATATATAA
*
147159 TA-AGATATAA
1 TATATATATAA
*
147169 -AGATATATAA
1 TATATATATAA
*
147179 -ATAAATATAA
1 TATATATATAA
147189 TA
1 TA
147191 GTAATAACAA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 1 0.02
10 28 0.53
11 8 0.15
12 16 0.30
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (11 bp):
TATATATATAA
Found at i:147158 original size:22 final size:22
Alignment explanation
Indices: 147127--147188 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
147117 ATATATACAT
*
147127 ATATATATAATAAGATATATAG
1 ATATATATAATAAGATATAAAG
147149 ATATATATAATAAGATATAAAG
1 ATATATATAATAAGATATAAAG
147171 ATATATA-AATAA-ATATAA
1 ATATATATAATAAGATATAA
147189 TAGTAATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 6 0.15
21 5 0.13
22 28 0.72
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATATATAATAAGATATAAAG
Found at i:147172 original size:30 final size:31
Alignment explanation
Indices: 147100--147190 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 31
147090 AAAAAATATT
* *
147100 TATAAAGAGATAT-GTATATATATACATATATA
1 TATAAAGATATATAG-ATATATATA-ATATAGA
147132 TATAATAAGATATATAGATATATATAATA-AGA
1 TAT-A-AAGATATATAGATATATATAATATAGA
* *
147164 TATAAAGATATATAAATAAATATAATA
1 TATAAAGATATATAGATATATATAATA
147191 GTAATAACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
30 21 0.40
31 1 0.02
32 8 0.15
33 4 0.08
34 17 0.33
35 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (31 bp):
TATAAAGATATATAGATATATATAATATAGA
Found at i:151193 original size:13 final size:13
Alignment explanation
Indices: 151177--151212 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
151167 GAAAATTGTT
*
151177 TTTAGAAAATACC
1 TTTAAAAAATACC
*
151190 TTTAAAAAATACT
1 TTTAAAAAATACC
151203 TTTAAAAAAT
1 TTTAAAAAAT
151213 TTGAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (13 bp):
TTTAAAAAATACC
Found at i:153967 original size:52 final size:48
Alignment explanation
Indices: 153948--154150 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
153938 TGACAAGTGG
* *
153948 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
153994 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
154046 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
154092 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
154138 AAAGTGATAAGTG
1 AAAGTGATAAGTG
154151 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:154002 original size:98 final size:98
Alignment explanation
Indices: 153882--154150 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
153872 TTTGAGTACT
*
153882 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
153947 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
153980 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
154045 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
154078 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
154143 GATAAGTG
65 GAAAAGTG
154151 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:154158 original size:37 final size:37
Alignment explanation
Indices: 154114--154259 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
154104 GATAGCTTTA
*
154114 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
154151 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
154188 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
154225 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
154260 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:158405 original size:16 final size:16
Alignment explanation
Indices: 158372--158405 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
158362 TTTATATGTT
* *
158372 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
158388 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
158404 AA
1 AA
158406 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:161231 original size:21 final size:21
Alignment explanation
Indices: 161205--161245 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
161195 AGACGAGCAA
* *
161205 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
161226 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
161246 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:163181 original size:16 final size:16
Alignment explanation
Indices: 163148--163181 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
163138 GGAGATTGTT
* *
163148 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
163164 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
163180 AA
1 AA
163182 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:174258 original size:23 final size:23
Alignment explanation
Indices: 174232--174280 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
174222 TATTACAAGT
*
174232 ATATTATTTTA-AAATTATAAAAA
1 ATATTATTTAATAAATTA-AAAAA
*
174255 ATATTATTTAATAAATTAAACAA
1 ATATTATTTAATAAATTAAAAAA
174278 ATA
1 ATA
174281 AACATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTATTTAATAAATTAAAAAA
Found at i:183216 original size:42 final size:41
Alignment explanation
Indices: 183053--183246 Score: 174
Period size: 44 Copynumber: 4.5 Consensus size: 41
183043 ATGGCATTAC
* *
183053 ATGATTTCGTATAAGACCATAGCTGGGCTATGACATCGATAT
1 ATGA-TTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
* * * *
183095 ATGAGACTTTGTGTAAGACCATATCTAGGATATGGCATCGATAT
1 AT--GA-TTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
* *
183139 ATGTGATTACGTGTAAGACCATATCTGGAAC-ATTGGCATCGATAT
1 A--TGATT-CGTGTAAGACCATAGCTGG-GCTA-TGGCATCGATAT
*
183184 ATGATTCGTGTAAGACCATAGCTGGGCTATTGGCACCGATAT
1 ATGATTCGTGTAAGACCATAGCTGGGCTA-TGGCATCGATAT
* * *
183226 GTGATAACATGTAAGACCATA
1 ATGAT-TCGTGTAAGACCATA
183247 TGTGGGATAT
Statistics
Matches: 126, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
41 1 0.01
42 37 0.29
43 20 0.16
44 54 0.43
45 13 0.10
46 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
ATGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
Found at i:183239 original size:85 final size:87
Alignment explanation
Indices: 183086--183247 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 87
183076 TGGGCTATGA
* * * * *
183086 CATCGATATATGAGACTTTGTGTAAGACCATATCTAGGATATGGCATCGATATATGTGATTACGT
1 CATCGATATAT-AGACTTCGTGTAAGACCATAGCTAGGATATGGCACCGA-ATATGTGATAACAT
183151 GTAAGACCATATCTGGAACATTGG
64 GTAAGACCATATCTGGAACATTGG
* *
183175 CATCGATATAT-GA-TTCGTGTAAGACCATAGCTGGGCTATTGGCACCG-ATATGTGATAACATG
1 CATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATA-TGGCACCGAATATGTGATAACATG
183237 TAAGACCATAT
65 TAAGACCATAT
183248 GTGGGATATG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
85 24 0.37
86 21 0.32
87 9 0.14
89 11 0.17
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (87 bp):
CATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATATGGCACCGAATATGTGATAACATGT
AAGACCATATCTGGAACATTGG
Found at i:190491 original size:54 final size:54
Alignment explanation
Indices: 190377--190497 Score: 152
Period size: 54 Copynumber: 2.2 Consensus size: 54
190367 TACAGTCTAT
* * * * ** *
190377 TGATTTATGATCATGACCTTTTACTTACGAGATTTTATTAATCTCACGGTCCGC
1 TGATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCACAATCAGC
* * *
190431 TAATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCGCAATTAGC
1 TGATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCACAATCAGC
190485 TGATTTACGATCA
1 TGATTTACGATCA
190498 CAAAATTTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (54 bp):
TGATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCACAATCAGC
Found at i:199988 original size:28 final size:28
Alignment explanation
Indices: 199892--199989 Score: 151
Period size: 28 Copynumber: 3.5 Consensus size: 28
199882 TGACTTTTGA
*
199892 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
199920 CACTAATTGTGCAAGTTTAATTGAAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
199948 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
199976 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
199990 ACTTATTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:202937 original size:3 final size:3
Alignment explanation
Indices: 202929--202953 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
202919 GAAACCTAAT
202929 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
202954 AGAGCACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:205081 original size:32 final size:31
Alignment explanation
Indices: 205019--205080 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
205009 GTCCCATTTT
205019 TATTTTAAAAATTTTAAAAAAATTAAAAAAAG
1 TATTTTAAAAATTTT-AAAAAATTAAAAAAAG
*
205051 TATTTTAAAAATATTT-TAAAATTAAAAAAA
1 TATTTTAAAAAT-TTTAAAAAATTAAAAAAA
205081 AATTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAAG
Found at i:205118 original size:29 final size:30
Alignment explanation
Indices: 205079--205141 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
205069 AAATTAAAAA
* *
205079 AAAATTAAAAAAGTATTTTGAAAA-TATTTT
1 AAAATTAAAAAAAT-TTTTAAAAAGTATTTT
205109 AAAATT-AAAAAATTTTTAAAAAGTATTTT
1 AAAATTAAAAAAATTTTTAAAAAGTATTTT
205138 AAAA
1 AAAA
205142 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 8 0.27
29 16 0.53
30 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (30 bp):
AAAATTAAAAAAATTTTTAAAAAGTATTTT
Found at i:205143 original size:30 final size:30
Alignment explanation
Indices: 205079--205141 Score: 58
Period size: 30 Copynumber: 2.1 Consensus size: 30
205069 AAATTAAAAA
* * *
205079 AAAATTAAAAAAGTATTTTGAAAATATTTT
1 AAAATTAAAAAAGTAATGTAAAAATATTTT
* *
205109 AAAATTAAAAAA-T-TTTTAAAAAGTATTTT
1 AAAATTAAAAAAGTAATGTAAAAA-TATTTT
205138 AAAA
1 AAAA
205142 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 8 0.26
29 11 0.35
30 12 0.39
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (30 bp):
AAAATTAAAAAAGTAATGTAAAAATATTTT
Found at i:205160 original size:30 final size:30
Alignment explanation
Indices: 205126--205190 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
205116 AAAAATTTTT
* * *
205126 AAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAGTATGTAAAAAATATTTTAAAATAA
205156 AAAAAGTATGTAAAAAATATTTTAAAATAA
1 AAAAAGTATGTAAAAAATATTTTAAAATAA
205186 AAAAA
1 AAAAA
205191 AATATTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (30 bp):
AAAAAGTATGTAAAAAATATTTTAAAATAA
Found at i:205182 original size:11 final size:11
Alignment explanation
Indices: 205019--205152 Score: 83
Period size: 11 Copynumber: 12.9 Consensus size: 11
205009 GTCCCATTTT
205019 TATTTT-AAAA
1 TATTTTAAAAA
205029 -ATTTTAAAAA
1 TATTTTAAAAA
* **
205039 AATTAAAAAAA
1 TATTTTAAAAA
205050 GTATTTTAAAAA
1 -TATTTTAAAAA
205062 TATTTT--AAA
1 TATTTTAAAAA
*
205071 -A-TTAAAAAA
1 TATTTTAAAAA
* * *
205080 AAATTAAAAAA
1 TATTTTAAAAA
*
205091 GTATTTTGAAAA
1 -TATTTTAAAAA
205103 TATTTT--AAA
1 TATTTTAAAAA
*
205112 -A-TTAAAAAA
1 TATTTTAAAAA
205121 T-TTTTAAAAA
1 TATTTTAAAAA
205131 GTATTTTAAAAA
1 -TATTTTAAAAA
205143 TATTTTAAAA
1 TATTTTAAAA
205153 TTAAAAAAGT
Statistics
Matches: 98, Mismatches: 12, Indels: 27
0.72 0.09 0.20
Matches are distributed among these distances:
7 4 0.04
8 2 0.02
9 17 0.17
10 12 0.12
11 39 0.40
12 24 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:205184 original size:40 final size:40
Alignment explanation
Indices: 205032--205182 Score: 216
Period size: 41 Copynumber: 3.7 Consensus size: 40
205022 TTTAAAAATT
205032 TTAAAAAA-ATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATATT-AAAAAAGTATTTTAAAAATATTTTAAAA
* *
205072 TTAAAAAAAAATTAAAAAAGTATTTTGAAAATATTTTAAAA
1 TT-AAAAAATATTAAAAAAGTATTTTAAAAATATTTTAAAA
* *
205113 TTAAAAAATTTTTAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATATTAAAAAAGTATTTTAAAAATATTTTAAAA
205153 TTAAAAAAGTATGTAAAAAA-TATTTTAAAA
1 TTAAAAAA-TAT-TAAAAAAGTATTTTAAAA
205183 TAAAAAAAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
40 44 0.44
41 47 0.47
42 9 0.09
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (40 bp):
TTAAAAAATATTAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:210313 original size:23 final size:23
Alignment explanation
Indices: 210287--210355 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
210277 AAGTTAGAAG
*
210287 AGTGAAGAGACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
210310 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
210333 AGTTAAGAGTCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
210356 GGATACACAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.45, C:0.04, G:0.26, T:0.25
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:214789 original size:23 final size:23
Alignment explanation
Indices: 214763--214831 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
214753 AAGTTAGAAG
*
214763 AGTGAAGAGACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
214786 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
214809 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
214832 GGATACACAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.23
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:221105 original size:12 final size:12
Alignment explanation
Indices: 221088--221118 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
221078 GGTCATGTGA
221088 GCCACACGAGCT
1 GCCACACGAGCT
221100 GCCACACGAGCT
1 GCCACACGAGCT
221112 GCCACAC
1 GCCACAC
221119 AGCCATGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.45, G:0.23, T:0.06
Consensus pattern (12 bp):
GCCACACGAGCT
Found at i:227103 original size:23 final size:22
Alignment explanation
Indices: 227051--227103 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
227041 TCCACGTCTT
*
227051 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
227073 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
227096 TTTCTTTT
1 TTTCTTTT
227104 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:240524 original size:44 final size:43
Alignment explanation
Indices: 240448--240646 Score: 201
Period size: 44 Copynumber: 4.6 Consensus size: 43
240438 ATTACATGAT
* * *
240448 TTCGTATAAGACCATAGCTGGGCTA-TGACATCGATATATGAGA
1 TTCGTGTAAGACCATAGCTGGGATATTGGCATCGATATATG-GA
* * *
240491 CTTTGTGTAAGACCATATCTAGGATA-TGGCATCGATATATGTGA
1 -TTCGTGTAAGACCATAGCTGGGATATTGGCATCGATATATG-GA
* *
240535 TTACGTGTAAGACCATATCTGGGACATTGGCATCGATATAT-GA
1 TT-CGTGTAAGACCATAGCTGGGATATTGGCATCGATATATGGA
* *
240578 TTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATATGT-GA
1 TTCGTGTAAGACCATAGCTGGGATATTGGCATCGATATATGGA
* *
240620 TAACATGTAAGACCATATG-TGGGATAT
1 T-TCGTGTAAGACCATA-GCTGGGATAT
240647 GGAATTGTAT
Statistics
Matches: 134, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
42 37 0.28
43 26 0.19
44 57 0.43
45 14 0.10
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (43 bp):
TTCGTGTAAGACCATAGCTGGGATATTGGCATCGATATATGGA
Found at i:240630 original size:85 final size:87
Alignment explanation
Indices: 240454--240647 Score: 229
Period size: 85 Copynumber: 2.3 Consensus size: 87
240444 TGATTTCGTA
* * *
240454 TAAGACCATAGCTGGG-CTATGACATCGATATATGAGACTTTGTGTAAGACCATATCTAGGATAT
1 TAAGACCATATCTGGGACTATGACATCGATATAT-AGACTTCGTGTAAGACCATAGCTAGGATAT
* *
240518 GGCATCGATATATGTGATTACGTG
65 GGCATCGA-ATATGTGATAACATG
* * *
240542 TAAGACCATATCTGGGAC-ATTGGCATCGATATAT-GA-TTCGTGTAAGACCATAGCTGGGCTAT
1 TAAGACCATATCTGGGACTA-TGACATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATA-
240604 TGGCATCG-ATATGTGATAACATG
64 TGGCATCGAATATGTGATAACATG
*
240627 TAAGACCATATGTGGGA-TATG
1 TAAGACCATATCTGGGACTATG
240648 GAATTGTATG
Statistics
Matches: 93, Mismatches: 9, Indels: 12
0.82 0.08 0.11
Matches are distributed among these distances:
84 2 0.02
85 30 0.32
86 21 0.23
87 10 0.11
88 16 0.17
89 14 0.15
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (87 bp):
TAAGACCATATCTGGGACTATGACATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATATG
GCATCGAATATGTGATAACATG
Found at i:247893 original size:54 final size:54
Alignment explanation
Indices: 247786--247904 Score: 166
Period size: 54 Copynumber: 2.2 Consensus size: 54
247776 CAATCTATTG
* * ***
247786 ATTTACGATCATGACCTTTTACTTACGAGATTTTATTAATCTCATGGTCCGCTA
1 ATTTACGATCATGACATTTTACTTACGAGATTTTATGAATCTCACAATCCGCTA
* * *
247840 ATTTACGATCATGACATTTTGCTTACGAGATTTTATGAATCTCGCAATTCGCTA
1 ATTTACGATCATGACATTTTACTTACGAGATTTTATGAATCTCACAATCCGCTA
247894 ATTTACGATCA
1 ATTTACGATCA
247905 CAACCTTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (54 bp):
ATTTACGATCATGACATTTTACTTACGAGATTTTATGAATCTCACAATCCGCTA
Found at i:250170 original size:16 final size:16
Alignment explanation
Indices: 250149--250184 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
250139 TAACTCAGGA
250149 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
250165 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
250181 GCTG
1 GCTG
250185 TGATTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (16 bp):
GCTGCAGGAGTACATG
Found at i:251027 original size:120 final size:120
Alignment explanation
Indices: 250901--251190 Score: 476
Period size: 120 Copynumber: 2.4 Consensus size: 120
250891 AATTATTTTA
* *
250901 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTTATATTT
* *
250965 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
251021 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTAAATTTATATTT
251085 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
251141 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
251191 GTTTAAATAT
Statistics
Matches: 157, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
119 7 0.04
120 147 0.94
121 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:251047 original size:14 final size:14
Alignment explanation
Indices: 251028--251086 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
251018 AAGAATTTTA
251028 TTAAATTATATATT
1 TTAAATTATATATT
251042 TTAAATATAATATATT
1 TTAAAT-T-ATATATT
*
251058 TAATAATTAT-TATT
1 TTA-AATTATATATT
251072 TT-AATT-TATATT
1 TTAAATTATATATT
251084 TTA
1 TTA
251087 CAGTATCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
11 1 0.03
12 10 0.26
14 11 0.29
15 3 0.08
16 10 0.26
17 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAAATTATATATT
Found at i:251170 original size:18 final size:17
Alignment explanation
Indices: 251142--251176 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
251132 ATTATTAAGA
*
251142 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
251159 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
251177 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:251291 original size:147 final size:149
Alignment explanation
Indices: 251130--251404 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
251120 ATAAGAATAT
*
251130 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
251195 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
251258 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
251277 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
251342 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
251405 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:251317 original size:18 final size:17
Alignment explanation
Indices: 251289--251323 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
251279 ATTATTAAGA
*
251289 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
251306 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
251324 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:251534 original size:44 final size:45
Alignment explanation
Indices: 251485--251579 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
251475 TTACACCTCT
* * *
251485 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
**
251529 ATTACATTCAACCAAACAGTTGATTTACTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
251574 ATTACA
1 ATTACA
251580 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:260885 original size:33 final size:33
Alignment explanation
Indices: 260804--261024 Score: 158
Period size: 33 Copynumber: 6.7 Consensus size: 33
260794 ACAGGGGAAA
* * * * *
260804 GTGATGTTGAAAGAGTAGAAGTTGATAGAGAGG
1 GTGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
*
260837 ATGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
1 GTGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
* * * *
260870 GTGATGTTGATGGGGT-AGATTTAGATGGGGAAG
1 GTGATGTTGAAGGGGTAAAAGTT-GATGGGGAGG
* * * * * **
260903 GTGTTGTAGAAGAGGTACAAGTTGTTGGGGAAT
1 GTGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
* * * *
260936 GTGATGTTGAAAGGGTAGAAGCTGATGGGTAGG
1 GTGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
* * * **
260969 GTGATGTAGAAGGCGTACAAACTT-ATGAAGAGG
1 GTGATGTTGAAGGGGTA-AAAGTTGATGGGGAGG
* *
261002 GTGATGTAGAAGGTGTAAAAGTT
1 GTGATGTTGAAGGGGTAAAAGTT
261025 AAGGCAAATG
Statistics
Matches: 144, Mismatches: 41, Indels: 7
0.75 0.21 0.04
Matches are distributed among these distances:
32 9 0.06
33 129 0.90
34 6 0.04
ACGTcount: A:0.31, C:0.02, G:0.41, T:0.26
Consensus pattern (33 bp):
GTGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
Found at i:260963 original size:66 final size:65
Alignment explanation
Indices: 260797--260988 Score: 181
Period size: 66 Copynumber: 2.9 Consensus size: 65
260787 GTTGACTACA
* * * * *
260797 GGGGAAAGTGATGTTGAAAGAGTAGAAGTTGATAGAG-AGGATGATGTTGAAGGGGTAAAAGTTG
1 GGGGAAAGTGATGTTGAAAGGGTAGAAGTTGATGGGGAAGG-TGATGTAGAA-GGGTACAAGTTG
260861 AT
64 AT
** ** * *
260863 GGGGAGGGTGATGTTGATGGGGTAG-ATTTAGATGGGGAAGGTGTTGTAGAAGAGGTACAAGTTG
1 GGGGAAAGTGATGTTGAAAGGGTAGAAGTT-GATGGGGAAGGTGATGTAGAAG-GGTACAAGTTG
*
260927 TT
64 AT
* * * *
260929 GGGGAATGTGATGTTGAAAGGGTAGAAGCTGATGGGTAGGGTGATGTAGAAGGCGTACAA
1 GGGGAAAGTGATGTTGAAAGGGTAGAAGTTGATGGGGAAGGTGATGTAGAAGG-GTACAA
260989 ACTTATGAAG
Statistics
Matches: 100, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
65 5 0.05
66 90 0.90
67 5 0.05
ACGTcount: A:0.30, C:0.02, G:0.43, T:0.25
Consensus pattern (65 bp):
GGGGAAAGTGATGTTGAAAGGGTAGAAGTTGATGGGGAAGGTGATGTAGAAGGGTACAAGTTGAT
Found at i:272729 original size:22 final size:23
Alignment explanation
Indices: 272695--272738 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
272685 ACCATCAATG
272695 TATTTAAATAA-TTAATTTTATA
1 TATTTAAATAATTTAATTTTATA
272717 TATTTATAA-AATTTTAATTTTA
1 TATTTA-AATAA-TTTAATTTTA
272739 ATTTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTAAATAATTTAATTTTATA
Found at i:278540 original size:196 final size:196
Alignment explanation
Indices: 278201--278590 Score: 602
Period size: 196 Copynumber: 2.0 Consensus size: 196
278191 CCTTGTAGGA
* *
278201 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTGATTCACTTAAAACTTCTTTGTGCTCTAG
1 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTTCTTTGTGCTCAAG
* *
278266 GGATGGAGAGGGAACACATACTAAATGCACCATGACGTAATTTCTTGGAAGGATATCTTATATTA
66 GGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATTA
* * *
278331 CTAATTATTATAGGTCAAGTTGTGTCGGATTGAAACCACTTGAGATGAAAATGGAATGTGCTTGT
131 CTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTGT
278396 G
196 G
* * * * * *
278397 CTTTTTGTATAAAAGGACATTCTTGTGGTTGTGTTTAATTCACTTTAAGCTTAC-TTGTGCTCAA
1 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTT-CTTTGTGCTCAA
* * * *
278461 GGGATGGAGAGATAACACATACTAAATGTACCTTGACATGATTTCTTGGAAGGATATCTTATATT
65 GGGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATT
*
278526 ACTAATTATTATAGGTCAAATTGCGTTGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTG
130 ACTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTG
278591 CACTTTTTAA
Statistics
Matches: 175, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
196 174 0.99
197 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (196 bp):
CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTTCTTTGTGCTCAAG
GGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATTA
CTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTGT
G
Found at i:282005 original size:14 final size:14
Alignment explanation
Indices: 281986--282013 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
281976 ATCACTCAAC
281986 GAGGTCAACTGGTT
1 GAGGTCAACTGGTT
282000 GAGGTCAACTGGTT
1 GAGGTCAACTGGTT
282014 AAATTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
GAGGTCAACTGGTT
Found at i:284474 original size:33 final size:33
Alignment explanation
Indices: 284436--284505 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
284426 CTGAGGATCT
284436 TCTCTTAATTGTTAAATCATCTTTAGAGACTAA
1 TCTCTTAATTGTTAAATCATCTTTAGAGACTAA
284469 TCTCTTAATTGTTAAATCATCTTTAGAGACTAA
1 TCTCTTAATTGTTAAATCATCTTTAGAGACTAA
284502 -CTCT
1 TCTCT
284506 GATACCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (33 bp):
TCTCTTAATTGTTAAATCATCTTTAGAGACTAA
Found at i:286506 original size:3 final size:3
Alignment explanation
Indices: 286498--286573 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
286488 TTTGTTACTG
* * * *
286498 TTA TTA TTA TCA TTA TAA TTA -AA TT- TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
286544 TTA TTA CTA TTG TTA CTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
286574 CCGCTTTGTG
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:288311 original size:20 final size:19
Alignment explanation
Indices: 288280--288338 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
288270 ACTTGTTTAA
*
288280 AAACAATTTTAACATGATTG
1 AAACAGTTTTAAC-TGATTG
*
288300 AAA-ATGTTTTAACTCAATTG
1 AAACA-GTTTTAACT-GATTG
288320 AAACAGTTTTAACTTGATT
1 AAACAGTTTTAAC-TGATT
288339 TTATCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
AAACAGTTTTAACTGATTG
Found at i:288390 original size:22 final size:24
Alignment explanation
Indices: 288363--288406 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
288353 ATTTTGTTCA
288363 ACTTTAATTT-TTAT-TCAAAAAC
1 ACTTTAATTTGTTATATCAAAAAC
288385 ACTTTAATTTGTTATATCAAAA
1 ACTTTAATTTGTTATATCAAAA
288407 CATATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (24 bp):
ACTTTAATTTGTTATATCAAAAAC
Found at i:290939 original size:31 final size:29
Alignment explanation
Indices: 290904--290983 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
290894 CAACAAATAC
* *
290904 TTATAATTTAAGAACTCAATTAAAACATTAT
1 TTATAATTTAAAAACTCAATTAAAA-AAT-T
* *
290935 TTATAGTTCAAAAACTCAATTAAAAAATT
1 TTATAATTTAAAAACTCAATTAAAAAATT
*
290964 TTAAAATTTAAAAACT-AATT
1 TTATAATTTAAAAACTCAATT
290984 TAAATTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 4 0.10
29 14 0.33
30 2 0.05
31 22 0.52
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (29 bp):
TTATAATTTAAAAACTCAATTAAAAAATT
Found at i:312049 original size:32 final size:32
Alignment explanation
Indices: 312004--312064 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
311994 GAAATAAAAC
* * * *
312004 AACTTTAATTAAAAATAGCTTAAAATAAACTG
1 AACTTAAAGTAAAAATAACGTAAAATAAACTG
*
312036 AACTTAAAGTAAAAGTAACGTAAAATAAA
1 AACTTAAAGTAAAAATAACGTAAAATAAA
312065 AAGTAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.26
Consensus pattern (32 bp):
AACTTAAAGTAAAAATAACGTAAAATAAACTG
Found at i:324586 original size:12 final size:12
Alignment explanation
Indices: 324569--324594 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
324559 CAAAACATGC
324569 TTTTAGCGGCGT
1 TTTTAGCGGCGT
324581 TTTTAGCGGCGT
1 TTTTAGCGGCGT
324593 TT
1 TT
324595 AGATGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:332117 original size:23 final size:22
Alignment explanation
Indices: 332074--332148 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
332064 CTGGCCTGAA
*
332074 TTATATAT-TAAATATATATATT
1 TTATATATATCAA-ATATATATT
* *
332096 TTATTTTTAATCAAATATATATT
1 TTATATAT-ATCAAATATATATT
*
332119 TTATATATATTAAATATATATAT
1 TTATATATATCAAATATATAT-T
332142 TTA-ATAT
1 TTATATAT
332149 GAGTCAGGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 22 0.50
23 19 0.43
24 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATATATCAAATATATATT
Found at i:332626 original size:13 final size:14
Alignment explanation
Indices: 332608--332636 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
332598 CCAGCCTGTC
332608 TATATAATTT-TTT
1 TATATAATTTATTT
332621 TATATAATTTATTT
1 TATATAATTTATTT
332635 TA
1 TA
332637 AAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATAATTTATTT
Found at i:335541 original size:16 final size:17
Alignment explanation
Indices: 335504--335540 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
335494 TAGTTTTTTG
335504 TTTTTAATTTAATTTAA
1 TTTTTAATTTAATTTAA
*
335521 TTTTTACTTT-ATTT-A
1 TTTTTAATTTAATTTAA
335536 TTTTT
1 TTTTT
335541 TCAGATAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTAATTTAATTTAA
Found at i:337253 original size:215 final size:216
Alignment explanation
Indices: 336835--337267 Score: 546
Period size: 215 Copynumber: 2.0 Consensus size: 216
336825 CTTTAGCTAA
* * * * * *
336835 ATGGTATATTAAGAGTTTTATTAATGCAATTGACGTGGGTTTAAATCCCCTCATATGCATATTTT
1 ATGGTAAATTAAAAGTTTTACTAATGCAATTGACATGGGTTCAAATCCACTCATATGCATATTTT
** * * *
336900 TATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTCGATTAATGTTACTTATTTTAATTACGA
66 TATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTACGA
* *** * *
336965 AAATACATTTTTGTAACTCCCTAACTGAGTTGGTGACCTGGTTAAGGGTGACACCGACTCAGTCA
131 AAAGACATTCCCGTAACTCCCTAACCGAGTTGGTGACCTGGTTAAGGGTGACACCAACTCAGTCA
*
337030 GAAACTTAAATAATATTATAG
196 GAAACTTAAATAATAGTATAG
*
337051 ATGGTAAATTAAAAGTTTTACTAATGCAATTGGCATGGGTTCAAATCTCAC-CATATGCATATTT
1 ATGGTAAATTAAAAGTTTTACTAATGCAATTGACATGGGTTCAAATC-CACTCATATGCATATTT
* * * * * *
337115 TTATTGGTTTTTTTAAAGT-AAAAGACTAACATACCCTAAAATAATATTAATTGTTTTGATTATG
65 TTATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTACG
* * * * * * *
337179 GAAGGACATTCCCGTAACTTCCTAACCGAGTTGGTGACCTGGTTGAGGGTGACGCCAATTTAGTC
130 AAAAGACATTCCCGTAACTCCCTAACCGAGTTGGTGACCTGGTTAAGGGTGACACCAACTCAGTC
*
337244 AGGAACTTAAATAATAGTATAG
195 AGAAACTTAAATAATAGTATAG
337266 AT
1 AT
337268 ATACAATTGA
Statistics
Matches: 183, Mismatches: 33, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
215 110 0.60
216 71 0.39
217 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (216 bp):
ATGGTAAATTAAAAGTTTTACTAATGCAATTGACATGGGTTCAAATCCACTCATATGCATATTTT
TATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTACGA
AAAGACATTCCCGTAACTCCCTAACCGAGTTGGTGACCTGGTTAAGGGTGACACCAACTCAGTCA
GAAACTTAAATAATAGTATAG
Found at i:338126 original size:17 final size:19
Alignment explanation
Indices: 338104--338140 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
338094 GTCTTTTACC
*
338104 AAAATATTA-CAAAA-AAT
1 AAAATAATATCAAAATAAT
338121 AAAATAATATCAAAATAAT
1 AAAATAATATCAAAATAAT
338140 A
1 A
338141 TAAACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATAATATCAAAATAAT
Found at i:338277 original size:19 final size:19
Alignment explanation
Indices: 338250--338286 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
338240 TAGAGGCGGC
338250 ACCAATTGTTCGTATTTTG
1 ACCAATTGTTCGTATTTTG
*
338269 ACCATTTGTTCGTATTTT
1 ACCAATTGTTCGTATTTT
338287 TTTCTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (19 bp):
ACCAATTGTTCGTATTTTG
Found at i:338659 original size:150 final size:151
Alignment explanation
Indices: 338262--338839 Score: 754
Period size: 152 Copynumber: 3.9 Consensus size: 151
338252 CAATTGTTCG
* * **
338262 TATTTTGACCATTTGTTCGTATTTTTTT-CTTGAATTTTATTACTTTT-AAAAAATATACTATTT
1 TATTTCGACCCTTTGTTCGTATTTTTTTCCCAG-ATTTTATTACTTTTAAAAAAATATACTATTT
* * * * *
338325 TATTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTGTGTTT
65 TATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTT
338390 TTAAATAAATTTAAAAAAAACTCT
130 TTAAATAAATTT-AAAAAAAC-CT
* * * *
338414 TATTTCGGCCCTTTGTTCATATTTTTTTCCC-GAATTTTATTACTTTCAATAAAAATATATTATT
1 TATTTCGACCCTTTGTTCGTATTTTTTTCCCAG-ATTTTATTACTTTTAA-AAAAATATACTATT
* * * **
338478 TTCGT-ATTTTATCATTTTACATTATTTTAGTACATCATGTTTGAAATGTATTAATTTACACTTT
64 TT-ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTT
338542 TTTTAAATAAA-TTAAAAAAACCCT
128 TTTTAAATAAATTTAAAAAAA-CCT
* *
338566 TATTTCGACCCTTTGTTCGTA-TTTTTCCCCAGAGTTTATTACTTTTAAAAAAATATACTATTTT
1 TATTTCGACCCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTTAAAAAAATATACTATTTT
*
338630 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTT
66 ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGT-TTTT
338695 TTAAATAAATTTAAAAAAA---
130 TTAAATAAATTTAAAAAAACCT
* * *
338714 -A--AC-ACCCTATGTTCGTATTTTTTTCCCAGATTTTCTTACTTTTAAAAAAATAT--TATTTT
1 TATTTCGACCCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTTAAAAAAATATACTATTTT
*
338773 ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTTTTT
66 ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTT
338838 TA
131 TA
338840 TTGAAAGTAA
Statistics
Matches: 382, Mismatches: 34, Indels: 30
0.86 0.08 0.07
Matches are distributed among these distances:
142 7 0.02
143 64 0.17
144 13 0.03
145 33 0.09
147 1 0.00
149 1 0.00
150 68 0.18
151 35 0.09
152 77 0.20
153 5 0.01
154 77 0.20
155 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (151 bp):
TATTTCGACCCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTTAAAAAAATATACTATTTT
ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTT
TAAATAAATTTAAAAAAACCT
Found at i:339124 original size:153 final size:152
Alignment explanation
Indices: 338843--339332 Score: 713
Period size: 152 Copynumber: 3.2 Consensus size: 152
338833 TTTTTTATTG
* *
338843 AAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGATTTTTTTTTAAATTTA
1 AAAGTAATAAAATTAGGG-AAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTTTAAATTTA
* * *
338908 TTT-AAAAGCACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGCAAAATAATAAA
65 TTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
*
338972 ATTATAAAATAATATATTTTTTA
130 ATTAAAAAATAATATATTTTTTA
338995 AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTTTAAATTTA
1 AAAGTAATAAAAT-TAGGGAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTTTAAATTTA
* * *
339060 TTTAAAAACCACAGTAAATTAATACATTTCAAACATGATGTACTAAAATAATGTAAAATAATAAA
65 TTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
* *
339125 A-TACGAAAATAATATATTTTTATTG
130 ATTA-AAAAATAATATA-TTTT-TTA
* *
339150 AAAGTAATAAAATCAGGGAAAAAATACGAACAAAGGGCCGAAATAAG-GATTTTTTT-AATTTAT
1 AAAGTAATAAAATTAGGGAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTTTAAATTTAT
* * *
339213 TTAAAAAAGACACTAAATTAATACATTTCAAATATAATGTACGAAAATAATGTAAAATAA-AAAA
66 TTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
*
339277 TTAAAAAATAGTATATTTTTTA
131 TTAAAAAATAATATATTTTTTA
* *
339299 GAAGTAATAAAATTCA-GAAAAAAATACGAACAAA
1 AAAGTAATAAAATT-AGGGAAAAAATACGAACAAA
339333 ATGCCAAAAT
Statistics
Matches: 308, Mismatches: 23, Indels: 17
0.89 0.07 0.05
Matches are distributed among these distances:
149 31 0.10
150 5 0.02
151 14 0.05
152 126 0.41
153 80 0.26
154 37 0.12
155 15 0.05
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.29
Consensus pattern (152 bp):
AAAGTAATAAAATTAGGGAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTTTAAATTTAT
TTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
TTAAAAAATAATATATTTTTTA
Found at i:339470 original size:18 final size:19
Alignment explanation
Indices: 339444--339481 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
339434 AAAAAGTTTA
339444 TATTATTTTAGTATT-TTT
1 TATTATTTTAGTATTATTT
* *
339462 TATTTTTTTTGTATTATTT
1 TATTATTTTAGTATTATTT
339481 T
1 T
339482 GGCAAAAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (19 bp):
TATTATTTTAGTATTATTT
Found at i:341601 original size:21 final size:20
Alignment explanation
Indices: 341575--341618 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
341565 TATCTGAAAT
341575 CTTAAACTCCGAACTCTAAAC
1 CTTAAACTCCGAACT-TAAAC
* *
341596 CTTAAACTTCGACCTTAAAC
1 CTTAAACTCCGAACTTAAAC
341616 CTT
1 CTT
341619 GACCTCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.30
Consensus pattern (20 bp):
CTTAAACTCCGAACTTAAAC
Found at i:343894 original size:29 final size:30
Alignment explanation
Indices: 343837--343898 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
343827 ATACATTTTA
343837 ATCACAATCAAAGTTTCATGCCTATAATTGC
1 ATCACAATCAAAGTTTCATG-CTATAATTGC
343868 ATCA-AATCAAAG-TTCATG-TATCAAATTGC
1 ATCACAATCAAAGTTTCATGCTAT--AATTGC
343897 AT
1 AT
343899 ATTAAATCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.10
29 14 0.48
30 8 0.28
31 4 0.14
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (30 bp):
ATCACAATCAAAGTTTCATGCTATAATTGC
Found at i:344663 original size:12 final size:12
Alignment explanation
Indices: 344646--344670 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
344636 TTGACCTGAA
344646 GAGTGAACTGTT
1 GAGTGAACTGTT
344658 GAGTGAACTGTT
1 GAGTGAACTGTT
344670 G
1 G
344671 TTCCTCCACC
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:0.08, G:0.36, T:0.32
Consensus pattern (12 bp):
GAGTGAACTGTT
Found at i:346717 original size:29 final size:29
Alignment explanation
Indices: 346678--346737 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
346668 AATTCATATC
346678 TTTATAATTTTAAAAAATTAAATAAAATT
1 TTTATAATTTTAAAAAATTAAATAAAATT
* * *
346707 TTTATTATTTTAAATAATTAAGTAAAATT
1 TTTATAATTTTAAAAAATTAAATAAAATT
346736 TT
1 TT
346738 ATCATTACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTATAATTTTAAAAAATTAAATAAAATT
Found at i:348668 original size:129 final size:129
Alignment explanation
Indices: 348438--348695 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
348428 CCTCGCTCCT
348438 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
1 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
348503 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
66 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
348567 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
1 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
348632 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
66 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
348696 GGATTAGACA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (129 bp):
TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
Found at i:353205 original size:12 final size:12
Alignment explanation
Indices: 353185--353218 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
353175 TTCTTTTTGG
353185 TATATATATAAA
1 TATATATATAAA
*
353197 TATAAATATAAA
1 TATATATATAAA
353209 TATATATATA
1 TATATATATA
353219 TTGGATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATATATATAAA
Found at i:353219 original size:6 final size:6
Alignment explanation
Indices: 353185--353218 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
353175 TTCTTTTTGG
* *
353185 TATATA TATAAA TATAAA TATAAA TATATA TATA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATA
353219 TTGGATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TATAAA
Found at i:353313 original size:59 final size:59
Alignment explanation
Indices: 353248--353365 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
353238 TGCACTTAAG
353248 TTTGGTAGTGTAAATATGAACTATAAATATTTAACAAAAATGTTATAAAGTAAATGAAT
1 TTTGGTAGTGTAAATATGAACTATAAATATTTAACAAAAATGTTATAAAGTAAATGAAT
353307 TTTGGTAGTGTAAATATGAACTATAAATATTTAACAAAAATGTTATAAAGTAAATGAAT
1 TTTGGTAGTGTAAATATGAACTATAAATATTTAACAAAAATGTTATAAAGTAAATGAAT
353366 GAATGTGATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (59 bp):
TTTGGTAGTGTAAATATGAACTATAAATATTTAACAAAAATGTTATAAAGTAAATGAAT
Found at i:354619 original size:7 final size:7
Alignment explanation
Indices: 354607--354638 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
354597 AAAAGGGGTC
354607 AAAAATG
1 AAAAATG
354614 AAAAATG
1 AAAAATG
354621 AAAAATG
1 AAAAATG
354628 AAAAATG
1 AAAAATG
354635 AAAA
1 AAAA
354639 GCAATTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:354684 original size:2 final size:2
Alignment explanation
Indices: 354677--354701 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
354667 CCACAGAAGA
354677 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
354702 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:362118 original size:24 final size:24
Alignment explanation
Indices: 362048--362121 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
362038 ATAATTATAC
* * *
362048 GTATATATAATATA-TTTTACAAT
1 GTATATATTATAAACTTTTACATT
* * *
362071 CT-TATATTATATAAC-CTTATATT
1 GTATATATTATA-AACTTTTACATT
362094 GTATATATTATAAACTTTTACATT
1 GTATATATTATAAACTTTTACATT
362118 GTAT
1 GTAT
362122 CATAAATGTC
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
22 8 0.21
23 11 0.29
24 19 0.50
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
GTATATATTATAAACTTTTACATT
Found at i:363078 original size:22 final size:22
Alignment explanation
Indices: 363051--363126 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
363041 AATGCGGTTA
363051 AAATTGTAGACAATGCAACTAG
1 AAATTGTAGACAATGCAACTAG
* *
363073 AAATTGCAGTTAAAATTGCCAAC-AG
1 AAATTGTAG--ACAA-TG-CAACTAG
*
363098 ATAATCGTAGACAATGCAACTAG
1 A-AATTGTAGACAATGCAACTAG
363121 AAATTG
1 AAATTG
363127 CAGTTTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
22 16 0.38
23 5 0.12
24 6 0.14
25 5 0.12
26 10 0.24
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (22 bp):
AAATTGTAGACAATGCAACTAG
Found at i:363702 original size:43 final size:43
Alignment explanation
Indices: 363655--363969 Score: 149
Period size: 43 Copynumber: 7.3 Consensus size: 43
363645 TCAAGGTCTT
* * *
363655 TAGCGGCGTTTTTTTCTCAAACGCCGCAATAGACCCTGATCTA
1 TAGCGGCGCTTTCTCCTCAAACGCCGCAATAGACCCTGATCTA
** * * * * *
363698 TAGCGGCGCTTTGACCACAAACGCCACTAA-AGAACCTAATCTT
1 TAGCGGCGCTTTCTCCTCAAACGCCGC-AATAGACCCTGATCTA
* *
363741 TAGCGGTGCTTTCTCCTAAAACGCCGCAATAGACCCTGATCTA
1 TAGCGGCGCTTTCTCCTCAAACGCCGCAATAGACCCTGATCTA
* * * * * * *
363784 TAGCGGCAC-TTCGACCACAAAACGCCACTAA-AGAACCTAATCTT
1 TAGCGGCGCTTTC-TCCTC-AAACGCCGC-AATAGACCCTGATCTA
* * * * * *
363828 TAGCGGCGC-TTCGACCACAAAACGCCACTAA-AGAACCTAATCTT
1 TAGCGGCGCTTTC-TCCTC-AAACGCCGC-AATAGACCCTGATCTA
* * ** * * *
363872 TAGGGGCGCTTTCCCCAAAAATGCCGCTAA-AGACCATGATCTT
1 TAGCGGCGCTTTCTCCTCAAACGCCGC-AATAGACCCTGATCTA
* * * * * *
363915 TAGTGGCGCTTTTTCCACAAACGCCGCTAA-AGACTCTTATCTT
1 TAGCGGCGCTTTCTCCTCAAACGCCGC-AATAGACCCTGATCTA
*
363958 TAACGGCGCTTT
1 TAGCGGCGCTTT
363970 GACCAAAAAC
Statistics
Matches: 220, Mismatches: 46, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
42 5 0.02
43 136 0.62
44 74 0.34
45 5 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (43 bp):
TAGCGGCGCTTTCTCCTCAAACGCCGCAATAGACCCTGATCTA
Found at i:363980 original size:43 final size:42
Alignment explanation
Indices: 363693--363989 Score: 281
Period size: 43 Copynumber: 6.9 Consensus size: 42
363683 ATAGACCCTG
* *
363693 ATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAG-ACCTA
* ** * * *
363736 ATCTTTAGCGGTGCTTTCTCCTAAAACGCCGC-AATAGACCCTG
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAA-AGA-CCTA
* * *
363779 ATCTATAGCGGCACTTCGACCACAAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTGACCA-AAAACGCCACTAAAG-ACCTA
*
363823 ATCTTTAGCGGCGCTTCGACCACAAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTGACCA-AAAACGCCACTAAAG-ACCTA
* ** * * *
363867 ATCTTTAGGGGCGCTTTCCCCAAAAATGCCGCTAAAGACCATG
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACC-TA
* ** * * *
363910 ATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACTCTT
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGAC-CTA
*
363953 ATCTTTAACGGCGCTTTGACCAAAAACGCCACTAAAG
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAG
363990 GCCAACACCT
Statistics
Matches: 209, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
42 6 0.03
43 125 0.60
44 75 0.36
45 3 0.01
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (42 bp):
ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCTA
Found at i:364014 original size:86 final size:86
Alignment explanation
Indices: 363651--363989 Score: 344
Period size: 86 Copynumber: 3.9 Consensus size: 86
363641 TAGATCAAGG
* * * *
363651 TCTTTAGCGGCGTTTTTTTCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAC
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAA
*
363716 AAACGCCACTAAAGAACCTAA
66 AAACGCCACTAAAGAACCAAA
* * * *
363737 TCTTTAGCGGTGCTTTCTCCTA-AAACGCCGCAATAGACCCTGATCTATAGCGGCACTTCGACCA
1 TCTTTAGCGGCGCTTTTTCC-ACAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCA
*
363801 CAAAACGCCACTAAAGAACCTAA
65 -AAAACGCCACTAAAGAACCAAA
*** * * * * * **
363824 TCTTTAGCGGCGCTTCGACCACAAAACGCCACTAA-AGAACCTAATCTTTAGGGGCGCTTTCCCC
1 TCTTTAGCGGCGCTTTTTCCAC-AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACC
* * *
363888 AAAAATGCCGCTAAAG-ACCATGA
64 AAAAACGCCACTAAAGAACCA-AA
* * * * *
363911 TCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAA-AGACTCTTATCTTTAACGGCGCTTTGACCA
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCA
363975 AAAACGCCACTAAAG
65 AAAACGCCACTAAAG
363990 GCCAACACCT
Statistics
Matches: 208, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
86 107 0.51
87 69 0.33
88 30 0.14
89 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTTTCCACAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAA
AAACGCCACTAAAGAACCAAA
Found at i:364023 original size:86 final size:86
Alignment explanation
Indices: 363701--364031 Score: 213
Period size: 86 Copynumber: 3.8 Consensus size: 86
363691 TGATCTATAG
* * * * * ** * *
363701 CGGCGCTTTGACCACAAACGCCACTAAAGAACCTA-ATCTTTAGCGGTGCTTTCTCCTAAAACGC
1 CGGCGCTTTCACCAAAAACGCCACTAAAG-ACCAACACCTTTAGTGACGCTTTTTCCAAAAACGC
* * * * *
363765 CGC-AATAGACCCTGATCTATAG
65 CACTAA-AGAACCTAATCTTTAA
* * * * * ***
363787 CGGCAC-TTCGACCACAAAACGCCACTAAAGAACCTA-ATCTTTAGCGGCGCTTCGACCACAAAA
1 CGGCGCTTTC-ACCA-AAAACGCCACTAAAG-ACCAACACCTTTAGTGACGCTTTTTCCA-AAAA
*
363850 CGCCACTAAAGAACCTAATCTTTAG
62 CGCCACTAAAGAACCTAATCTTTAA
* * * * ** * * *
363875 GGGCGCTTTCCCCAAAAATGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCC
1 CGGCGCTTTCACCAAAAACGCCACTAAAGACCAACACCTTTAGTGACGCTTTTTCCAAAAACGCC
* *
363940 GCTAAAG-ACTCTTATCTTTAA
66 ACTAAAGAAC-CTAATCTTTAA
* * * **
363961 CGGCGCTTTGACCAAAAACGCCACTAAAGGCCAACACCTTTAGTGACGTTTTTTTTAAAAACGCC
1 CGGCGCTTTCACCAAAAACGCCACTAAAGACCAACACCTTTAGTGACGCTTTTTCCAAAAACGCC
364026 ACTAAA
66 ACTAAA
364032 TTTGGCAGAT
Statistics
Matches: 196, Mismatches: 42, Indels: 14
0.78 0.17 0.06
Matches are distributed among these distances:
85 4 0.02
86 90 0.46
87 68 0.35
88 29 0.15
89 5 0.03
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (86 bp):
CGGCGCTTTCACCAAAAACGCCACTAAAGACCAACACCTTTAGTGACGCTTTTTCCAAAAACGCC
ACTAAAGAACCTAATCTTTAA
Found at i:364363 original size:21 final size:21
Alignment explanation
Indices: 364334--364426 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
364324 TTTGACGCTG
*
364334 CTCTACTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
364355 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
364376 CTCTGCTTCCCTCACTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
364397 CTATACTTCTCTAGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
364418 CTCTGCTTC
1 CTCTGCTTC
364427 TTTTACTGCC
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.09, C:0.44, G:0.14, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:364579 original size:66 final size:66
Alignment explanation
Indices: 364456--364586 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
364446 TTAAGCTGCT
* * *
364456 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCACTGCTGCATCTGCTTTTAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCACTGCTGCATCCGCTTTAAGTTGT
364521 A
66 A
* * * *
364522 GCTGGAGTTCTTCATATCTTT-TTTGAACCTTAACTTCTCTCGA-TGTTGCCTCCGCTTTAAGTT
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAACTTCTCTC-ACTGCTGCATCCGCTTTAAGTT
364585 GT
64 GT
364587 GTAATTTGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 51 0.91
67 5 0.09
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCACTGCTGCATCCGCTTTAAGTTGT
A
Found at i:370094 original size:9 final size:9
Alignment explanation
Indices: 370080--370174 Score: 94
Period size: 9 Copynumber: 11.2 Consensus size: 9
370070 TAAGGGATAT
370080 TTATGTAAG
1 TTATGTAAG
370089 TTATGTAAG
1 TTATGTAAG
370098 TTATGT-A-
1 TTATGTAAG
* *
370105 TTAAGTAAA
1 TTATGTAAG
370114 TTATGTAAG
1 TTATGTAAG
370123 TTATGT-A-
1 TTATGTAAG
* *
370130 TTAAGTAGG
1 TTATGTAAG
*
370139 TTATGTAAT
1 TTATGTAAG
*
370148 TTATGT--C
1 TTATGTAAG
370155 TTATGTAAG
1 TTATGTAAG
370164 TTATGTAAG
1 TTATGTAAG
370173 TT
1 TT
370175 GTTGTTTTGT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
7 16 0.23
8 3 0.04
9 51 0.73
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:370112 original size:25 final size:25
Alignment explanation
Indices: 370084--370174 Score: 137
Period size: 25 Copynumber: 3.6 Consensus size: 25
370074 GGATATTTAT
370084 GTAAGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
*
370109 GTAAATTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* * * *
370134 GTAGGTTATGTAATTTATGTCTTAT
1 GTAAGTTATGTAAGTTATGTATTAA
370159 GTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTT
370175 GTTGTTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (25 bp):
GTAAGTTATGTAAGTTATGTATTAA
Found at i:370132 original size:16 final size:17
Alignment explanation
Indices: 370080--370170 Score: 82
Period size: 16 Copynumber: 5.4 Consensus size: 17
370070 TAAGGGATAT
370080 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
* *
370098 TTATGTA-TTAAGTAAA
1 TTATGTAGTTATGTAAG
370114 TTATGTAAGTTATGT-A-
1 TTATGT-AGTTATGTAAG
* *
370130 TTAAGTAGGTTATGTAAT
1 TTATGTA-GTTATGTAAG
*
370148 TTATGT-CTTATGTAAG
1 TTATGTAGTTATGTAAG
370164 TTATGTA
1 TTATGTA
370171 AGTTGTTGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.02
16 39 0.65
17 4 0.07
18 16 0.27
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (17 bp):
TTATGTAGTTATGTAAG
Found at i:370239 original size:12 final size:12
Alignment explanation
Indices: 370222--370264 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
370212 TGGTTATGTA
370222 TTATTATGTAAG
1 TTATTATGTAAG
* *
370234 TTATTATTTAGG
1 TTATTATGTAAG
370246 TTATTATGTAAG
1 TTATTATGTAAG
*
370258 TCATTAT
1 TTATTAT
370265 ATATGTTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.53
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:370496 original size:16 final size:16
Alignment explanation
Indices: 370471--370525 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
370461 TGCAAGATAT
370471 TTATGTAAGTGGTGTA
1 TTATGTAAGTGGTGTA
* *
370487 TTATGCAAGT--TAT-
1 TTATGTAAGTGGTGTA
370500 TTATGTAAGTGGTGTA
1 TTATGTAAGTGGTGTA
370516 TTATGTAAGT
1 TTATGTAAGT
370526 TATGTACGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 2 0.06
16 19 0.59
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTGGTGTA
Found at i:370500 original size:29 final size:29
Alignment explanation
Indices: 370454--370528 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
370444 ACGTAGGCTA
*
370454 TGTATTATGCAAGATATTTATGTAAGTGG
1 TGTATTATGCAAGTTATTTATGTAAGTGG
370483 TGTATTATGCAAGTTATTTATGTAAGTGG
1 TGTATTATGCAAGTTATTTATGTAAGTGG
*
370512 TGTATTATGTAAGTTAT
1 TGTATTATGCAAGTTAT
370529 GTACGCTATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (29 bp):
TGTATTATGCAAGTTATTTATGTAAGTGG
Found at i:370531 original size:16 final size:16
Alignment explanation
Indices: 370420--370531 Score: 65
Period size: 16 Copynumber: 7.2 Consensus size: 16
370410 ACGTAAGTGG
370420 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
* * * *
370436 AGTAAGTTACGTAGGCTA
1 TGT-A-TTATGTAAGTTA
*
370454 TGTATTATGCAAG--A
1 TGTATTATGTAAGTTA
* **
370468 TAT-TTATGTAAGTGG
1 TGTATTATGTAAGTTA
*
370483 TGTATTATGCAAGTTA
1 TGTATTATGTAAGTTA
**
370499 --T-TTATGTAAGTGG
1 TGTATTATGTAAGTTA
370512 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
370528 TGTA
1 TGTA
370532 CGCTATGTAT
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
13 17 0.25
14 4 0.06
15 3 0.04
16 31 0.46
17 2 0.03
18 11 0.16
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (16 bp):
TGTATTATGTAAGTTA
Found at i:370616 original size:9 final size:9
Alignment explanation
Indices: 370596--370624 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
370586 TATAAGTTTC
370596 TATGTA-GT
1 TATGTAGGT
370604 TATGTAGGT
1 TATGTAGGT
370613 TATGTAGGT
1 TATGTAGGT
370622 TAT
1 TAT
370625 TATTTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (9 bp):
TATGTAGGT
Found at i:370780 original size:13 final size:13
Alignment explanation
Indices: 370735--370785 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
370725 TATCAAATTT
370735 TATTATGTAACTG
1 TATTATGTAACTG
* * * *
370748 TATGATATGATTG
1 TATTATGTAACTG
370761 TTATTATGTAACTG
1 -TATTATGTAACTG
370775 TATTATGTAAC
1 TATTATGTAAC
370786 AGTTACATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (13 bp):
TATTATGTAACTG
Found at i:370790 original size:27 final size:27
Alignment explanation
Indices: 370734--370790 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
370724 TTATCAAATT
* **
370734 TTATTATGTAACTGTATGATATGATTG
1 TTATTATGTAACTGTATGATATAACAG
* *
370761 TTATTATGTAACTGTATTATGTAACAG
1 TTATTATGTAACTGTATGATATAACAG
370788 TTA
1 TTA
370791 CATATATAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (27 bp):
TTATTATGTAACTGTATGATATAACAG
Found at i:372041 original size:29 final size:29
Alignment explanation
Indices: 371915--372042 Score: 111
Period size: 29 Copynumber: 4.6 Consensus size: 29
371905 GCAAATAAAT
* *
371915 CCTCACCGACAAAAAATTATAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
*
371944 CCTCACCGAAAAAACATTAAAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
*** * * * ***
371973 CCTCTGTGA-ATAACATCATAAATTGTCG
1 CCTCACCGACAAAACATTAAAAATTGAAA
*
372001 CTTCA--G-CAAAACATTAAAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
372027 CCTCACCGACAAAACA
1 CCTCACCGACAAAACA
372043 AAAAAGAAAA
Statistics
Matches: 74, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
26 18 0.24
28 17 0.23
29 39 0.53
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.21
Consensus pattern (29 bp):
CCTCACCGACAAAACATTAAAAATTGAAA
Found at i:372800 original size:47 final size:49
Alignment explanation
Indices: 372715--372812 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 49
372705 CATAGTTTTG
*
372715 TTAAGTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
1 TTAACTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
*
372764 TTAACTAATATTTATAA-AT-T-TTAGATAAAATTATAAATTTTAGTGTT
1 TTAACTAATATTTATAATATATAGTAG-TAAAATTATAAATTTTAGTGTT
372811 TT
1 TT
372813 TATTTTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 3 0.07
47 25 0.54
48 2 0.04
49 16 0.35
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (49 bp):
TTAACTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
Done.