Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 162 of 172
Found at i:53042197 original size:22 final size:21
Alignment explanation
Indices: 53042147--53042198 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
53042137 CAAACCTTTG
*
53042147 ATTATTTATTATCTGTTTTATT
1 ATTA-TTATTATCTGTTTTATC
*
53042169 ATTATTATTATTTGTATTTATC
1 ATTATTATTATCTGT-TTTATC
53042191 ATTATTAT
1 ATTATTAT
53042199 CACTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
ATTATTATTATCTGTTTTATC
Found at i:53054878 original size:75 final size:75
Alignment explanation
Indices: 53054596--53054955 Score: 465
Period size: 75 Copynumber: 5.0 Consensus size: 75
53054586 AATTTTTGTT
* *
53054596 TTTCAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-AATCACACGCTGAGGTATTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACACACTGAGGTATTT
53054660 TCAATTTATG
66 TCAATTTATG
* *
53054670 TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAATCACGCACTGAGGTATTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACACACTGAGGTATTT
53054735 TCAATTTATG
66 TCAATTTATG
* *
53054745 TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAATCACGCACTGAGGTATTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACACACTGAGGTATTT
* *
53054810 TTAGTTTATG
66 TCAATTTATG
* *** **
53054820 TTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTA--T
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACACACTGAGGTATTT
*
53054883 T---TTTA-A
66 TCAATTTATG
* * **
53054889 TTTC-----TATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTATTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACACACTGAGGTATTT
53054949 TCAATTT
66 TCAATTT
53054956 TTTACTCTTT
Statistics
Matches: 261, Mismatches: 19, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
64 49 0.19
66 2 0.01
69 7 0.03
70 4 0.02
73 2 0.01
74 42 0.16
75 155 0.59
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (75 bp):
TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACACACTGAGGTATTT
TCAATTTATG
Found at i:53054933 original size:64 final size:64
Alignment explanation
Indices: 53054830--53054955 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 64
53054820 TTTCAAAAAA
* ** *
53054830 ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTTAATTTCT
1 ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTATTTTCAATTTCT
53054894 ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTATTTTCAATTT
1 ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTATTTTCAATTT
53054956 TTTACTCTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (64 bp):
ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTATTTTCAATTTCT
Found at i:53056645 original size:3 final size:3
Alignment explanation
Indices: 53056629--53056953 Score: 89
Period size: 3 Copynumber: 107.3 Consensus size: 3
53056619 CTTTATTTTT
* * * * *
53056629 TTA TTT TTA ATA TTA TTA ATA TTA TTA CTA TTA TTT TTA TT- TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*** *
53056674 TTA TTA TTA TTA TTA TTA CCG TTA TTA TTA TT- TTCA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* ** * * * **
53056719 TTT TTA TTA ACA -TA CTA TTA CTAA CTT- TTG CCA -TA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA
* * ** * * *
53056762 TT- TTA -TG TTA TTA TTG TTA TTA ACA TATA TTA TTG TTA GTAA CGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA -TTA
* * * * * * * *
53056808 CTA ATA TTT TCTA TTA TTA TTA TTA TTA CTA ATA TCA CTA TTA TCA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
53056854 TTA TTA TTA TTA TTA TTA CCTT- TT- TTA CTA TCTAA TGTA TTA TTA
1 TTA TTA TTA TTA TTA TTA --TTA TTA TTA TTA T-T-A T-TA TTA TTA
* * * * *
53056899 -TA CCTTT TTA TTA TTA TTA CTA -TA GTA TTA TTG CTA TTA TTA TTA
1 TTA --TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53056944 TTA TTA TTA T
1 TTA TTA TTA T
53056954 ATTTTCCTTT
Statistics
Matches: 231, Mismatches: 69, Indels: 44
0.67 0.20 0.13
Matches are distributed among these distances:
2 20 0.09
3 188 0.81
4 17 0.07
5 6 0.03
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:53057284 original size:3 final size:3
Alignment explanation
Indices: 53057140--53057267 Score: 52
Period size: 3 Copynumber: 43.0 Consensus size: 3
53057130 TGTCTTATGG
* * * * *
53057140 TTA TTA TTA TT- TGTA TTTA TCA TTA TTA TCA CTA TTA TTT TTA TTT
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
53057186 TTA TTA CTA TTA TCA TT- TT- TTA -AA TTA TTA TTA CTA TTA CTC TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
53057230 TTA CCTT- TTA ATA CATA TTA TTA TTA TTA TTA TTA TTA
1 TTA --TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
53057268 GTGTACGATT
Statistics
Matches: 92, Mismatches: 23, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
2 10 0.11
3 74 0.80
4 5 0.05
5 3 0.03
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:53066838 original size:29 final size:29
Alignment explanation
Indices: 53066768--53066825 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
53066758 TTTGCATCAA
53066768 ATTTTGGAACTTGGGGGAGGGGGTTTCTT
1 ATTTTGGAACTTGGGGGAGGGGGTTTCTT
53066797 ATTTTGGAACTTGGGGGAGGGGGTTTCTT
1 ATTTTGGAACTTGGGGGAGGGGGTTTCTT
53066826 TCTTATGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.07, G:0.41, T:0.38
Consensus pattern (29 bp):
ATTTTGGAACTTGGGGGAGGGGGTTTCTT
Found at i:53079005 original size:25 final size:25
Alignment explanation
Indices: 53078971--53079020 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53078961 GTATGTGATG
53078971 GAGGAAGTGTGTTCTAGTAGTTTTA
1 GAGGAAGTGTGTTCTAGTAGTTTTA
53078996 GAGGAAGTGTGTTCTAGTAGTTTTA
1 GAGGAAGTGTGTTCTAGTAGTTTTA
53079021 CTACAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.32, T:0.40
Consensus pattern (25 bp):
GAGGAAGTGTGTTCTAGTAGTTTTA
Found at i:53079212 original size:24 final size:24
Alignment explanation
Indices: 53079185--53079230 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
53079175 TAGAATCTAC
*
53079185 GTCTGCACTTGTATCTGAATCTGT
1 GTCTGCACTTGTATATGAATCTGT
*
53079209 GTCTGCATTTGTATATGAATCT
1 GTCTGCACTTGTATATGAATCT
53079231 AAACATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
GTCTGCACTTGTATATGAATCTGT
Found at i:53080762 original size:30 final size:31
Alignment explanation
Indices: 53080703--53080768 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
53080693 ATTATTAAAG
* * *
53080703 ATAAAATTTTATTTTAATCTTTCTAAAAATA
1 ATAAAAATTTAATTTAATCATTCTAAAAATA
*
53080734 ATAAAAATTTAATTTAATCATT-TAAAAATT
1 ATAAAAATTTAATTTAATCATTCTAAAAATA
53080764 ATAAA
1 ATAAA
53080769 GATATAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAAAAATTTAATTTAATCATTCTAAAAATA
Found at i:53082850 original size:21 final size:22
Alignment explanation
Indices: 53082808--53082850 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
53082798 ATTCTAAATA
*
53082808 ATTTAATAAATTCAACCTTTTT
1 ATTTAATAAATTCAACCATTTT
* *
53082830 ATTT-ATAAATTCTATCATTTT
1 ATTTAATAAATTCAACCATTTT
53082851 TATCCTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTAATAAATTCAACCATTTT
Found at i:53082850 original size:22 final size:22
Alignment explanation
Indices: 53082808--53082853 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
53082798 ATTCTAAATA
*
53082808 ATTTAATAAATTCAACCTTTTT
1 ATTTAATAAATTCAACATTTTT
*
53082830 ATTT-ATAAATTCTATCATTTTT
1 ATTTAATAAATTC-AACATTTTT
53082852 AT
1 AT
53082854 CCTTAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTAATAAATTCAACATTTTT
Found at i:53082936 original size:22 final size:23
Alignment explanation
Indices: 53082911--53082953 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53082901 CCATATCCAT
53082911 AAATTTG-TAAAATTTAAAAAAA
1 AAATTTGATAAAATTTAAAAAAA
*
53082933 AAATTTGATAGAATTTAAAAA
1 AAATTTGATAAAATTTAAAAA
53082954 TAAGAAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
AAATTTGATAAAATTTAAAAAAA
Found at i:53118386 original size:107 final size:106
Alignment explanation
Indices: 53118176--53118389 Score: 320
Period size: 106 Copynumber: 2.0 Consensus size: 106
53118166 GAAAAAAGGG
* *
53118176 TAAGAAGGAATTCAAGAAAACAGACGCAGCAAGAGTCAGACCTTTGTACGAGGAATAAAAAATTT
1 TAAGAAGGAATTCAAGAAAACAGACGCAGCAAGAATCAGACCTTAGTACGAGGAATAAAAAATTT
*
53118241 CTAGGAATAGGCAATCCTTGAGAGGTTGCATATTCTTGAGC
66 CTAGGAACAGGCAATCCTTGAGAGGTTGCATATTCTTGAGC
* ** * * *
53118282 TAAGAAGGAATTCAAGAAAATAGGTGCAGCAATAATCTGACCTTAGTACGAGGAATTAAAACATT
1 TAAGAAGGAATTCAAGAAAACAGACGCAGCAAGAATCAGACCTTAGTACGAGGAA-TAAAAAATT
* *
53118347 TCTAGGTACAGGCAATCCTTGTGAGGTTGCATATTCTTGAGC
65 TCTAGGAACAGGCAATCCTTGAGAGGTTGCATATTCTTGAGC
53118389 T
1 T
53118390 GCTAGAAGCT
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 48 0.50
107 48 0.50
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (106 bp):
TAAGAAGGAATTCAAGAAAACAGACGCAGCAAGAATCAGACCTTAGTACGAGGAATAAAAAATTT
CTAGGAACAGGCAATCCTTGAGAGGTTGCATATTCTTGAGC
Found at i:53121698 original size:15 final size:16
Alignment explanation
Indices: 53121673--53121706 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
53121663 GTAATTTTAA
53121673 TTTATTATTATATATT
1 TTTATTATTATATATT
53121689 TTTA-TATTATATATT
1 TTTATTATTATATATT
53121704 TTT
1 TTT
53121707 TTTTAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTATTATATATT
Found at i:53124267 original size:32 final size:32
Alignment explanation
Indices: 53124226--53124291 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
53124216 CAACCCATGG
53124226 TTGTATCAAGCATTGTCACCTTGAAACCTAAC
1 TTGTATCAAGCATTGTCACCTTGAAACCTAAC
53124258 TTGTATCAAGCATTGTCACCTTGAAACCTAAC
1 TTGTATCAAGCATTGTCACCTTGAAACCTAAC
53124290 TT
1 TT
53124292 CCATAGGACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (32 bp):
TTGTATCAAGCATTGTCACCTTGAAACCTAAC
Found at i:53131267 original size:43 final size:42
Alignment explanation
Indices: 53131205--53131287 Score: 148
Period size: 43 Copynumber: 2.0 Consensus size: 42
53131195 AAAGAATTTA
*
53131205 ACTTTTCTCTATCCTATCTATTATAGTGAATTTATTGCCCTG
1 ACTTTTCTCTATCCAATCTATTATAGTGAATTTATTGCCCTG
53131247 ACTTTTCTCCTATCCAATCTATTATAGTGAATTTATTGCCC
1 ACTTTTCT-CTATCCAATCTATTATAGTGAATTTATTGCCC
53131288 GGTTCTCAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 8 0.21
43 31 0.79
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (42 bp):
ACTTTTCTCTATCCAATCTATTATAGTGAATTTATTGCCCTG
Found at i:53131590 original size:15 final size:15
Alignment explanation
Indices: 53131570--53131601 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53131560 GATGTTTATG
53131570 ATTACTTTCTAATTC
1 ATTACTTTCTAATTC
53131585 ATTACTTTCTAATTC
1 ATTACTTTCTAATTC
53131600 AT
1 AT
53131602 GGCGTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTACTTTCTAATTC
Found at i:53136407 original size:15 final size:15
Alignment explanation
Indices: 53136387--53136421 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
53136377 CTTACCTAGC
53136387 TCTTTGACTTCGAAT
1 TCTTTGACTTCGAAT
53136402 TCTTTGACTTCGAAT
1 TCTTTGACTTCGAAT
53136417 TCTTT
1 TCTTT
53136422 TACTAGGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.51
Consensus pattern (15 bp):
TCTTTGACTTCGAAT
Found at i:53137481 original size:21 final size:21
Alignment explanation
Indices: 53137452--53137492 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53137442 TGTTGGACAG
*
53137452 GAGCCGGAATGGGAGTGTTTA
1 GAGCCGGAATGAGAGTGTTTA
*
53137473 GAGCTGGAATGAGAGTGTTT
1 GAGCCGGAATGAGAGTGTTT
53137493 GGTTGCTGGA
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:0.24, C:0.07, G:0.41, T:0.27
Consensus pattern (21 bp):
GAGCCGGAATGAGAGTGTTTA
Found at i:53144854 original size:16 final size:18
Alignment explanation
Indices: 53144819--53144855 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
53144809 AAGGCTTGGG
53144819 TTTCTTATTGTTTATTCT
1 TTTCTTATTGTTTATTCT
*
53144837 TTTCTT-TT-TTTTTTCT
1 TTTCTTATTGTTTATTCT
53144853 TTT
1 TTT
53144856 TGCAAACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTCTTATTGTTTATTCT
Found at i:53157424 original size:52 final size:52
Alignment explanation
Indices: 53157346--53157451 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
53157336 ACAAAAAAAG
53157346 TTGTTCTTTCAAGACAACCAAATTTATAGTGCAATGCTGAAACTAGACTGTA
1 TTGTTCTTTCAAGACAACCAAATTTATAGTGCAATGCTGAAACTAGACTGTA
53157398 TTGTTCTTTCAAGACAACCAAATTTATAGTGCAATGCTGAAACTAGACTGTA
1 TTGTTCTTTCAAGACAACCAAATTTATAGTGCAATGCTGAAACTAGACTGTA
53157450 TT
1 TT
53157452 TTATATTTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (52 bp):
TTGTTCTTTCAAGACAACCAAATTTATAGTGCAATGCTGAAACTAGACTGTA
Found at i:53161553 original size:25 final size:23
Alignment explanation
Indices: 53161508--53161566 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
53161498 ATAATGAAAA
** *
53161508 TTGTAATAAAAATATTGGTACAT
1 TTGTAATAAAAATATACGTACAC
53161531 TTGTAATAAATAGATATACGTACAC
1 TTGTAATAAA-A-ATATACGTACAC
*
53161556 TTGTTATAAAA
1 TTGTAATAAAA
53161567 TAATTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 10 0.33
24 2 0.07
25 18 0.60
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (23 bp):
TTGTAATAAAAATATACGTACAC
Found at i:53171404 original size:28 final size:27
Alignment explanation
Indices: 53171342--53171407 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
53171332 TTTTGAATAG
*
53171342 TTTAAAAATAATAATTTGAAATTTGTAT
1 TTTAAAAAT-ATAATTTCAAATTTGTAT
* *
53171370 TTAAAAAATAT-ATTTCAAATATATGTTT
1 TTTAAAAATATAATTTCAAAT-T-TGTAT
53171398 TTTAAAAATA
1 TTTAAAAATA
53171408 AAATAAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.25
27 3 0.09
28 21 0.66
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (27 bp):
TTTAAAAATATAATTTCAAATTTGTAT
Found at i:53176705 original size:3 final size:3
Alignment explanation
Indices: 53176697--53176722 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53176687 TGGAGAAGCA
53176697 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
53176723 ACCTAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53177818 original size:30 final size:29
Alignment explanation
Indices: 53177782--53177838 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
53177772 CTGAATTTAG
53177782 TTTTTATATTTTTAATTTTAGAAATTTATT
1 TTTTTATATTTTTAATTTTA-AAATTTATT
* *
53177812 TTTTTATTTTTTTATTTTTAAAATTTA
1 TTTTTATATTTTTAATTTTAAAATTTA
53177839 GGTTTAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTTATATTTTTAATTTTAAAATTTATT
Found at i:53177823 original size:7 final size:8
Alignment explanation
Indices: 53177806--53177830 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53177796 ATTTTAGAAA
53177806 TTTATTTT
1 TTTATTTT
53177814 TTTATTTT
1 TTTATTTT
53177822 TTTATTTT
1 TTTATTTT
53177830 T
1 T
53177831 AAAATTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:53180631 original size:40 final size:41
Alignment explanation
Indices: 53180587--53180682 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
53180577 CAATCTCGTA
*
53180587 TCGCACACTTAGTGCC-TCATATAGCCGAGGCTA-TTCCAAC
1 TCGCACACTTAGTGCCAT-ATATAGCCGAAGCTATTTCCAAC
* * * *
53180627 TCGCACACTTAATGCCATTTGTAGCCGAAGCTATTTCGAAC
1 TCGCACACTTAGTGCCATATATAGCCGAAGCTATTTCCAAC
53180668 -CGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
53180683 GAACATAGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 41 0.85
41 7 0.15
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (41 bp):
TCGCACACTTAGTGCCATATATAGCCGAAGCTATTTCCAAC
Found at i:53182979 original size:16 final size:17
Alignment explanation
Indices: 53182948--53182980 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53182938 TTTATAAGTA
53182948 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
53182965 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
53182981 GCACTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:53183328 original size:46 final size:46
Alignment explanation
Indices: 53183278--53183440 Score: 209
Period size: 46 Copynumber: 3.5 Consensus size: 46
53183268 CCATAGTGTA
* * *
53183278 TTTCAACTATGGTCTTACTCATTTTTTGCCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCTTGTCATGTTGCCATGGTATC
* ***
53183324 TTTCAACCATGGTCTTATTCATTTCTTGTCACACTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCTTGTCATGTTGCCATGGTATC
* *** *
53183370 TTTCAACCATGGTCTTATTCATTTCCCATCATGTTGCCATAGTATC
1 TTTCAACCATGGTCTTACTCATTTCTTGTCATGTTGCCATGGTATC
*
53183416 TTTCAACCATGGTCTTACACATTTC
1 TTTCAACCATGGTCTTACTCATTTC
53183441 ATATCAGAGA
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 101 1.00
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACTCATTTCTTGTCATGTTGCCATGGTATC
Found at i:53190697 original size:78 final size:78
Alignment explanation
Indices: 53190564--53190715 Score: 232
Period size: 78 Copynumber: 1.9 Consensus size: 78
53190554 GAGTCACATC
* * * *
53190564 TCATGTAACTGTAGTGAATTAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAAACCTATCCACCTTAAGTTACCAT
53190629 AATGAATCATATA
66 AATGAATCATATA
* * *
53190642 TCATGTAACTGTAGCGAATCAGGATTACCTTTTTAGGTCAAAAGCTATCCGCCTTAAGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAAACCTATCCACCTTAAGTTACCAT
*
53190707 AGTGAATCA
66 AATGAATCA
53190716 GGAATAAATC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (78 bp):
TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAAACCTATCCACCTTAAGTTACCAT
AATGAATCATATA
Found at i:53190755 original size:40 final size:40
Alignment explanation
Indices: 53190686--53190817 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
53190676 AGGTCAAAAG
* * *
53190686 CTATCCGCCTTAAGTTACCATAGTGAATCAGGAATAAATC
1 CTATCCACTTTAAGTTACCATAGTGAATCAGGAACAAATC
* *
53190726 CTATTCACTTTAAATTACCATAGTGAATCAGGAACAAATC
1 CTATCCACTTTAAGTTACCATAGTGAATCAGGAACAAATC
* * ** * *
53190766 CTATCCACTTTGAGGTATTATAGTAAATCAGGAACGAATC
1 CTATCCACTTTAAGTTACCATAGTGAATCAGGAACAAATC
53190806 CTATCCACTTTA
1 CTATCCACTTTA
53190818 TATTCTTGAG
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (40 bp):
CTATCCACTTTAAGTTACCATAGTGAATCAGGAACAAATC
Found at i:53197749 original size:77 final size:78
Alignment explanation
Indices: 53197641--53197793 Score: 247
Period size: 77 Copynumber: 2.0 Consensus size: 78
53197631 TTTACACTAC
* * *
53197641 GTTTAATTTATGATTTTCCCTTTCAAGTATATTAATTTATTCACTTTAAGACTTAGAAGTATTAT
1 GTTTAATTCATGATTTTCCCTTTCAAGTATATTAATTTATTCACATTAAGACTTAAAAGTATTAT
53197706 TCATTATAATTAA
66 TCATTATAATTAA
*
53197719 GTTTAATTCATGA-TTTCCCTTTC-AGTTATATTAATTTATTCACATTAATACTTAAAAGTATTA
1 GTTTAATTCATGATTTTCCCTTTCAAG-TATATTAATTTATTCACATTAAGACTTAAAAGTATTA
53197782 TTCATTATAATT
65 TTCATTATAATT
53197794 TTAGTCTGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
76 2 0.03
77 56 0.80
78 12 0.17
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (78 bp):
GTTTAATTCATGATTTTCCCTTTCAAGTATATTAATTTATTCACATTAAGACTTAAAAGTATTAT
TCATTATAATTAA
Found at i:53206294 original size:14 final size:13
Alignment explanation
Indices: 53206267--53206301 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
53206257 TTGTAAGTAA
53206267 TTCAAATTCTTTT
1 TTCAAATTCTTTT
*
53206280 TTCAAATTCCTTT
1 TTCAAATTCTTTT
53206293 TTCACAATT
1 TTCA-AATT
53206302 TCTCGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.26, C:0.20, G:0.00, T:0.54
Consensus pattern (13 bp):
TTCAAATTCTTTT
Found at i:53207963 original size:17 final size:17
Alignment explanation
Indices: 53207943--53207992 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
53207933 ATTGACATAT
53207943 GTGGTAAAAATAATTTC
1 GTGGTAAAAATAATTTC
*
53207960 GTGGTAAAAATAACTTC
1 GTGGTAAAAATAATTTC
*
53207977 GATGTGTATAAATAAT
1 G-TG-GTAAAAATAAT
53207993 ATACATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 17 0.61
18 2 0.07
19 9 0.32
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (17 bp):
GTGGTAAAAATAATTTC
Found at i:53208062 original size:8 final size:8
Alignment explanation
Indices: 53208049--53208085 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
53208039 TTATTATAAT
53208049 ATAATATA
1 ATAATATA
53208057 ATAATATA
1 ATAATATA
53208065 ATAATATA
1 ATAATATA
*
53208073 ATAACATA
1 ATAATATA
53208081 A-AATA
1 ATAATA
53208086 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 3 0.11
8 24 0.89
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (8 bp):
ATAATATA
Found at i:53208081 original size:13 final size:13
Alignment explanation
Indices: 53208043--53208075 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
53208033 AAGTAATTAT
53208043 TATAATATAAT-A
1 TATAATATAATAA
53208055 TAATAATATAATAA
1 T-ATAATATAATAA
53208069 TATAATA
1 TATAATA
53208076 ACATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 16 0.84
14 2 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATAATATAATAA
Found at i:53208164 original size:11 final size:12
Alignment explanation
Indices: 53208143--53208171 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
53208133 AACAGAGAAG
53208143 GAAAAAGGGAAA
1 GAAAAAGGGAAA
53208155 GAAAAA-GGAAA
1 GAAAAAGGGAAA
53208166 GAAAAA
1 GAAAAA
53208172 TTAGGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAAAAGGGAAA
Found at i:53209545 original size:46 final size:46
Alignment explanation
Indices: 53209495--53210443 Score: 1792
Period size: 46 Copynumber: 20.6 Consensus size: 46
53209485 TGCCATAATG
* * *
53209495 TCTTTCAACTATGGTCTTACTCATTTTC-TATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTA
*** * * **
53209541 TCTTTCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209587 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209633 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209679 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209725 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209771 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209817 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209863 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209909 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53209955 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210001 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210047 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210093 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210139 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210185 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210231 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210277 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210323 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210369 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
53210415 TCTTTCAACCATGGTCTTACACATTTCAT
1 TCTTTCAACCATGGTCTTACACATTTCAT
53210444 TTCAGAAAGC
Statistics
Matches: 888, Mismatches: 14, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
45 4 0.00
46 884 1.00
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
Found at i:53214624 original size:25 final size:25
Alignment explanation
Indices: 53214596--53214645 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
53214586 TTTGGCTAGA
*
53214596 CATTTACTAAGCAATATCATATATT
1 CATTTACTAAGCAATATCAAATATT
* * *
53214621 CATTTATTAGGTAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
53214646 GAAATTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:53219109 original size:34 final size:35
Alignment explanation
Indices: 53219071--53219150 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 35
53219061 TTATGGACTT
* *
53219071 TTTTTTTAATTATTTGATA-AT-ATTTTAATAATTA
1 TTTTTTTAATTA-TTAACACATAATTTTAATAATTA
* *
53219105 TTTTTAT-ATTATTAACACATAATTTTAATAATTT
1 TTTTTTTAATTATTAACACATAATTTTAATAATTA
53219139 TTATTTTTAATT
1 TT-TTTTTAATT
53219151 TAAATTATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
32 4 0.11
33 6 0.16
34 20 0.54
35 4 0.11
36 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (35 bp):
TTTTTTTAATTATTAACACATAATTTTAATAATTA
Found at i:53224636 original size:26 final size:25
Alignment explanation
Indices: 53224590--53224639 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
53224580 TTAATAATTG
* **
53224590 TTATATAATTTTTAATTTTTTGAAT
1 TTATATAATTTATAAAATTTTGAAT
53224615 TTATATATATTTATAAAATTTTGAA
1 TTATATA-ATTTATAAAATTTTGAA
53224640 AAAATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TTATATAATTTATAAAATTTTGAAT
Found at i:53246324 original size:113 final size:113
Alignment explanation
Indices: 53246126--53246350 Score: 441
Period size: 113 Copynumber: 2.0 Consensus size: 113
53246116 GGGAAACCTG
53246126 ATGATTGATTATCAGAAGTGCATACTTCTCCTTCATTGGCCTCTTCCATTTTGTTAAAGATCTCG
1 ATGATTGATTATCAGAAGTGCATACTTCTCCTTCATTGGCCTCTTCCATTTTGTTAAAGATCTCG
53246191 ACTTTCTTGTTGTCCATCATGTCTTGAAGTAGTTTTCTAAATACTTCA
66 ACTTTCTTGTTGTCCATCATGTCTTGAAGTAGTTTTCTAAATACTTCA
53246239 ATGATTGATTATCAGAAGTGCATACTTCTCCTTCATTGGCCTCTTCCATTTTGTTAAAGATCTCG
1 ATGATTGATTATCAGAAGTGCATACTTCTCCTTCATTGGCCTCTTCCATTTTGTTAAAGATCTCG
*
53246304 ACTTTCTTGTTGTCCATCATGTCTTGAAGTAGTTTTCTAAATCCTTC
66 ACTTTCTTGTTGTCCATCATGTCTTGAAGTAGTTTTCTAAATACTTC
53246351 GCAAGATTGG
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (113 bp):
ATGATTGATTATCAGAAGTGCATACTTCTCCTTCATTGGCCTCTTCCATTTTGTTAAAGATCTCG
ACTTTCTTGTTGTCCATCATGTCTTGAAGTAGTTTTCTAAATACTTCA
Found at i:53252253 original size:34 final size:36
Alignment explanation
Indices: 53252184--53252293 Score: 109
Period size: 39 Copynumber: 3.1 Consensus size: 36
53252174 GACATATTTC
* * * *
53252184 CAGCACGTAGCCTGCGGACTTTAAGTCCTGTTAT-A
1 CAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
*
53252219 -AGCACATAACCTGCGGACCTTAAGTCCGGATATAA
1 CAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
* *
53252254 TTCCAGCACATAGCCTGCAGACCCTAAGTCCGGATA-AA
1 ---CAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
53252292 CA
1 CA
53252294 TCACTGAATG
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
34 28 0.45
35 3 0.05
38 2 0.03
39 29 0.47
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (36 bp):
CAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
Found at i:53255467 original size:19 final size:19
Alignment explanation
Indices: 53255430--53255469 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
53255420 TATTAATACC
*
53255430 ATAATAAAATAATATACAT
1 ATAATAAAATAATACACAT
53255449 ATAATAAAA-AATAACACAT
1 ATAATAAAATAAT-ACACAT
53255468 AT
1 AT
53255470 GTACAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAATAAAATAATACACAT
Found at i:53255580 original size:18 final size:17
Alignment explanation
Indices: 53255539--53255608 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
53255529 AACAATAGTG
53255539 AAAATAATAAGTATA-ATA
1 AAAAT-ATAA-TATATATA
53255557 ATAAATATAATGATATATA
1 A-AAATATAAT-ATATATA
*
53255576 AAAATAATACTATATATA
1 AAAAT-ATAATATATATA
53255594 AAAAGTAT-ATATATA
1 AAAA-TATAATATATA
53255609 CACGTATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.16
18 25 0.56
19 13 0.29
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAATATAATATATATA
Found at i:53255714 original size:24 final size:25
Alignment explanation
Indices: 53255678--53255742 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
53255668 ATATAATAAT
* *
53255678 AATATGTACATAATATGGTA-TTAA
1 AATATATACATAATATAGTATTTAA
*
53255702 AATATATATATAATATAGTATTTAAAA
1 AATATATACATAATATAGTATTT--AA
*
53255729 AATGTATACATAAT
1 AATATATACATAAT
53255743 TTATATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 17 0.52
25 2 0.06
27 14 0.42
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (25 bp):
AATATATACATAATATAGTATTTAA
Found at i:53256042 original size:22 final size:23
Alignment explanation
Indices: 53255995--53256055 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
53255985 CATAAGATAG
* * *
53255995 TATAAAAAATATATAACTTATGA
1 TATATAAAATATATAACTCATAA
53256018 TAT-TAAAATATAT-ACATCATAA
1 TATATAAAATATATAAC-TCATAA
*
53256040 TATATAAAAAATATAA
1 TATATAAAATATATAA
53256056 TATTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 2 0.06
22 16 0.52
23 12 0.39
24 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (23 bp):
TATATAAAATATATAACTCATAA
Found at i:53256055 original size:16 final size:16
Alignment explanation
Indices: 53256036--53256066 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53256026 TATATACATC
53256036 ATAATATATAAAAAAT
1 ATAATATATAAAAAAT
*
53256052 ATAATATTTAAAAAA
1 ATAATATATAAAAAA
53256067 ATGTACATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATATATAAAAAAT
Found at i:53256106 original size:23 final size:21
Alignment explanation
Indices: 53255995--53256107 Score: 63
Period size: 23 Copynumber: 5.2 Consensus size: 21
53255985 CATAAGATAG
*
53255995 TATAAAAAATATATA-ACTTA
1 TATAAAAAATATATATACATA
* *
53256015 TGATATTAAAATATATACATCATAA
1 T-ATA-AAAAATATATATA-CAT-A
*
53256040 TATATAAAA-A-ATATA-ATA
1 TATAAAAAATATATATACATA
* * *
53256058 TTTAAAAAAATGTACATAACATA
1 TAT-AAAAAATATATAT-ACATA
53256081 TATAAAAATATATATATACATAA
1 TATAAAAA-ATATATATACAT-A
53256104 TATA
1 TATA
53256108 GTATTAAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 21
0.70 0.10 0.21
Matches are distributed among these distances:
18 3 0.04
19 7 0.10
20 1 0.01
21 10 0.14
22 21 0.30
23 22 0.31
24 5 0.07
25 2 0.03
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
TATAAAAAATATATATACATA
Found at i:53256202 original size:21 final size:21
Alignment explanation
Indices: 53256173--53256244 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 21
53256163 TAATGCTACA
*
53256173 TAAATATATACATATATATAT
1 TAAAAATATACATATATATAT
*
53256194 TAAAAATAT--ATACATATAT
1 TAAAAATATACATATATATAT
* *
53256213 AAAAAATATACACTAATATATAA
1 TAAAAATATACA-T-ATATATAT
*
53256236 TAATAATAT
1 TAAAAATAT
53256245 TGAAATACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 17 0.43
21 9 0.22
22 1 0.03
23 13 0.32
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAATATACATATATATAT
Found at i:53256232 original size:19 final size:18
Alignment explanation
Indices: 53256184--53256224 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
53256174 AAATATATAC
*
53256184 ATATATATAT-TAAAAAT
1 ATATACATATATAAAAAT
53256201 ATATACATATATAAAAA-
1 ATATACATATATAAAAAT
53256218 ATATACA
1 ATATACA
53256225 CTAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATACATATATAAAAAT
Found at i:53256486 original size:149 final size:146
Alignment explanation
Indices: 53256261--53256670 Score: 510
Period size: 149 Copynumber: 2.8 Consensus size: 146
53256251 ACAAAAAGCA
* * * **
53256261 AATATAATAAAGATATTAAAATAAAGTAATAAAAAAATAATACTATATATAAATATATATACATA
1 AATATAATAATGATATTAAAATAAAGTAAT-TAAAAATAGTGTTATATATAAATATATAT--AT-
* *
53256326 TACATG--TATAATAAAAATATACACTAATATATAATAATGATAATAATACTA-ACAATAGCAAT
62 TACATGTATATAATAAAAATATACACTAATATATAATAATAATAATAATACTAGA-AATAACAAT
*
53256388 GAAATACAAAAAAAAGTAAATAT
126 GAAATAC-AAAAAAA-TAAACAT
*
53256411 AATATAATAATGATATTAAAATAAAGTAATTAAAAATAGTGTTATATATAACTATATATATTCAC
1 AATATAATAATGATATTAAAATAAAGTAATTAAAAATAGTGTTATATATAAATATATATATT-AC
* *
53256476 ATGTATATAATAAGAAA-ATACACTATTAATAATAATAATAATAATATAATACTAGAAATAATAA
65 ATGTATATAATAA-AAATATACACTAAT-AT-ATAATAATAAT-A-ATAATACTAGAAATAACAA
53256540 TGAAATACAAAAAAATAAACAT
125 TGAAATACAAAAAAATAAACAT
* *
53256562 AATATAATAAT-AT-TAAAAATAAAGTAATTAAAAATAGTGTTATATATAAGTATATATA-TACA
1 AATATAATAATGATATTAAAATAAAGTAATTAAAAATAGTGTTATATATAAATATATATATTACA
* *
53256624 CGTATATAATAAGAATATACACTAATATAGTAATAATAATAATAATA
66 TGTATATAATAAAAATATACACTAATATA-TAATAATAATAATAATA
53256671 ATATTGATTA
Statistics
Matches: 233, Mismatches: 16, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
144 6 0.03
145 2 0.01
146 15 0.06
147 30 0.13
148 1 0.00
149 84 0.36
150 36 0.15
151 27 0.12
152 8 0.03
153 23 0.10
154 1 0.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (146 bp):
AATATAATAATGATATTAAAATAAAGTAATTAAAAATAGTGTTATATATAAATATATATATTACA
TGTATATAATAAAAATATACACTAATATATAATAATAATAATAATACTAGAAATAACAATGAAAT
ACAAAAAAATAAACAT
Found at i:53256525 original size:20 final size:20
Alignment explanation
Indices: 53256502--53256540 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53256492 AATACACTAT
53256502 TAATAATA-ATAATAATAATA
1 TAATAATAGA-AATAATAATA
*
53256522 TAATACTAGAAATAATAAT
1 TAATAATAGAAATAATAAT
53256541 GAAATACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
TAATAATAGAAATAATAATA
Found at i:53256705 original size:18 final size:16
Alignment explanation
Indices: 53256661--53256708 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
53256651 TAGTAATAAT
53256661 AATAATAATAATATTG
1 AATAATAATAATATTG
*
53256677 ATTAGATTAATAATATTAG
1 AATA-A-TAATAATATT-G
53256696 AAATAATAATAAT
1 -AATAATAATAAT
53256709 GATATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 17 0.65
19 2 0.08
20 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AATAATAATAATATTG
Found at i:53258557 original size:26 final size:26
Alignment explanation
Indices: 53258518--53258627 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
53258508 TGATACAAAT
*
53258518 TGATAATAGATTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
53258544 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
53258570 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
53258596 TGATAATGGGTTAGGTTAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
53258622 TGATAA
1 TGATAA
53258628 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:53259900 original size:26 final size:26
Alignment explanation
Indices: 53259871--53259923 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
53259861 TTTACAGTTT
53259871 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
53259897 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
53259923 T
1 T
53259924 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:53260028 original size:22 final size:22
Alignment explanation
Indices: 53260002--53260055 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
53259992 GACGGAGGAA
53260002 GTACTGGAGGTGGCTTGTCCAC
1 GTACTGGAGGTGGCTTGTCCAC
53260024 GTACTGGAGGTGGCTTGTCCAC
1 GTACTGGAGGTGGCTTGTCCAC
53260046 GTACTGGAGG
1 GTACTGGAGG
53260056 CTTTGCCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.15, C:0.20, G:0.39, T:0.26
Consensus pattern (22 bp):
GTACTGGAGGTGGCTTGTCCAC
Found at i:53262794 original size:15 final size:15
Alignment explanation
Indices: 53262776--53262805 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53262766 AAATTTTAAT
*
53262776 TTTTTATAGTTTATA
1 TTTTTATAATTTATA
53262791 TTTTTATAATTTATA
1 TTTTTATAATTTATA
53262806 AAGGATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTATA
Found at i:53274087 original size:38 final size:38
Alignment explanation
Indices: 53274044--53274133 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 38
53274034 ATTTAATCCT
53274044 AAAAATTATTAAAATTTTATAAATTATAATAA-ATT-T-A
1 AAAAATT-TTAAAATTTTATAAATTATAA-AATATTATGA
* *
53274081 GAAAAA-TGTAAAATTTTATATATTATAAAATATTATGA
1 -AAAAATTTTAAAATTTTATAAATTATAAAATATTATGA
53274119 AAAAATTTTAAAATT
1 AAAAATTTTAAAATT
53274134 ATAGACAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
35 2 0.04
36 22 0.49
37 7 0.16
38 14 0.31
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (38 bp):
AAAAATTTTAAAATTTTATAAATTATAAAATATTATGA
Found at i:53274109 original size:17 final size:17
Alignment explanation
Indices: 53274046--53274116 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
53274036 TTAATCCTAA
53274046 AAATTATTAAAATTTTAT
1 AAATTA-TAAAATTTTAT
* *
53274064 AAATTATAATAAATTTAGA
1 AAATTATAA-AATTTTA-T
* *
53274083 AAAATGTAAAATTTTAT
1 AAATTATAAAATTTTAT
* *
53274100 ATATTATAAAATATTAT
1 AAATTATAAAATTTTAT
53274117 GAAAAAATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
17 16 0.39
18 18 0.44
19 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTATAAAATTTTAT
Found at i:53274688 original size:15 final size:15
Alignment explanation
Indices: 53274670--53274701 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53274660 TTAAGTGTCG
53274670 AAAATTTAAATATTA
1 AAAATTTAAATATTA
53274685 AAAATTTAAATATTA
1 AAAATTTAAATATTA
53274700 AA
1 AA
53274702 TTTAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTTAAATATTA
Found at i:53276932 original size:14 final size:15
Alignment explanation
Indices: 53276913--53276945 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53276903 ATTATTAACA
53276913 TTGTTAAATTT-TTT
1 TTGTTAAATTTGTTT
*
53276927 TTGTTACATTTGTTT
1 TTGTTAAATTTGTTT
53276942 TTGT
1 TTGT
53276946 GACATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.15, C:0.03, G:0.12, T:0.70
Consensus pattern (15 bp):
TTGTTAAATTTGTTT
Found at i:53276944 original size:15 final size:14
Alignment explanation
Indices: 53276913--53276953 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
53276903 ATTATTAACA
*
53276913 TTGTTAAATTTTTT
1 TTGTTACATTTTTT
53276927 TTGTTACATTTGTTT
1 TTGTTACATTT-TTT
*
53276942 TTGTGACATTTT
1 TTGTTACATTTT
53276954 GAAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (14 bp):
TTGTTACATTTTTT
Found at i:53293594 original size:132 final size:131
Alignment explanation
Indices: 53293430--53293685 Score: 358
Period size: 132 Copynumber: 1.9 Consensus size: 131
53293420 TTTAGAAAAT
* * * *
53293430 ATGAGTGAAATTCAAAAGGGACGTTCGATTATTTTGAACAAATG-GAAAATTGCAACCCAGCACG
1 ATGAGTGAAATTCAAAAGGAACATTCAATTATTTTGAACAAACGAG-AAATTGCAACCCAGCACG
* *
53293494 ATAGGGCACGATTCCCCGAATTG-CTAAGCATCGAACGTT-TCCTTCATTTTAAAGAATTTTTTA
65 ATAGGGCACGATT-CCCGAATTGTC-AAACATCGAACATTGT-CTTCATTTTAAAGAATTTTTTA
53293557 AAGAC
127 AAGAC
*
53293562 ATGAGTGAAATTCCAAAA-GAATATTCAATTATTTTGAACAAACGAGAAATTGCAACCCAGCACG
1 ATGAGTGAAATT-CAAAAGGAACATTCAATTATTTTGAACAAACGAGAAATTGCAACCCAGCACG
**
53293626 ATAGGGCACGATTCCCGAATTGTCAAACATCGAACATTGTCTTTGTTTTAAAGAATTTTT
65 ATAGGGCACGATTCCCGAATTGTCAAACATCGAACATTGTCTTCATTTTAAAGAATTTTT
53293686 AAATGAATAA
Statistics
Matches: 111, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
131 39 0.35
132 66 0.59
133 6 0.05
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (131 bp):
ATGAGTGAAATTCAAAAGGAACATTCAATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGA
TAGGGCACGATTCCCGAATTGTCAAACATCGAACATTGTCTTCATTTTAAAGAATTTTTTAAAGA
C
Found at i:53307643 original size:31 final size:31
Alignment explanation
Indices: 53307608--53307672 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
53307598 TAATATATGG
*
53307608 TTTAGTATTTAGATTTAAC-TTCAATATTTAA
1 TTTAGTATTTAAATTTAACATTCAA-ATTTAA
* * *
53307639 TTTAGTGTTTAAATTTGACATTCAAGTTTAA
1 TTTAGTATTTAAATTTAACATTCAAATTTAA
53307670 TTT
1 TTT
53307673 TAATGTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.52
Consensus pattern (31 bp):
TTTAGTATTTAAATTTAACATTCAAATTTAA
Found at i:53322353 original size:27 final size:27
Alignment explanation
Indices: 53322323--53322374 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
53322313 TATAATATGG
*
53322323 ATTTAAAAAATAATTTTTATAATTTTT
1 ATTTAAAAAATAATATTTATAATTTTT
* * *
53322350 ATTTATAAAATTATATTTGTAATTT
1 ATTTAAAAAATAATATTTATAATTT
53322375 ACGTTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTTAAAAAATAATATTTATAATTTTT
Found at i:53327795 original size:28 final size:27
Alignment explanation
Indices: 53327656--53327803 Score: 87
Period size: 28 Copynumber: 5.4 Consensus size: 27
53327646 AAATAAATAA
*
53327656 ATAAAAATACATAAATATTTTCAAAAAA-
1 ATAAAAATAGATAAA-ATTTT-AAAAAAT
*
53327684 AT-ATAATA-ATAAAA-TTTAAAAAAT
1 ATAAAAATAGATAAAATTTTAAAAAAT
*
53327708 ACATAAAAATA-A-AAAGATTGTTGACAGGAAAT
1 --ATAAAAATAGATAAA-ATT-TT-A-A-AAAAT
* *
53327740 AT--TAATATATAAAATTTTAAAAAAT
1 ATAAAAATAGATAAAATTTTAAAAAAT
*
53327765 ATAAAAATAGATAAATATTTTAAAAAGT
1 ATAAAAATAGATAAA-ATTTTAAAAAAT
*
53327793 ATAATAATAGA
1 ATAAAAATAGA
53327804 ATTAAAAATA
Statistics
Matches: 96, Mismatches: 9, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
23 6 0.06
24 3 0.03
25 7 0.07
26 11 0.11
27 22 0.23
28 30 0.31
29 6 0.06
30 6 0.06
31 1 0.01
32 4 0.04
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.30
Consensus pattern (27 bp):
ATAAAAATAGATAAAATTTTAAAAAAT
Found at i:53327801 original size:55 final size:53
Alignment explanation
Indices: 53327645--53327801 Score: 142
Period size: 55 Copynumber: 2.8 Consensus size: 53
53327635 ATTGTAAAAA
53327645 TAAATAAATAAATAAAAATACATAAATATTTTCAAAAA-AAT-ATAATAATAAAATT
1 TAAA-AAAT-AATAAAAATA-ATAAATATTTT-AAAAAGAATAATAATAATAAAATT
* * * * *
53327700 TAAAAAATACATAAAAATAA-AAAGATTGTTGACAGGAAATATTAATATATAAAATTT
1 TAAAAAATA-ATAAAAATAATAAATATT-TTAAAAAG-AATAATAATA-ATAAAA-TT
*
53327757 TAAAAAAT-ATAAAAATAGATAAATATTTTAAAAAGTATAATAATA
1 TAAAAAATAATAAAAATA-ATAAATATTTTAAAAAGAATAATAATA
53327802 GAATTAAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
52 8 0.10
53 4 0.05
54 16 0.20
55 26 0.32
56 12 0.15
57 16 0.20
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (53 bp):
TAAAAAATAATAAAAATAATAAATATTTTAAAAAGAATAATAATAATAAAATT
Found at i:53327821 original size:20 final size:19
Alignment explanation
Indices: 53327757--53327823 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
53327747 TATAAAATTT
*
53327757 TAAA-AAATATAAAAATAGA
1 TAAATAAAT-TAAAAATAAA
**
53327776 TAAATATTTTAAAAAGTATAA
1 TAAATAAATTAAAAA-TA-AA
53327797 T-AATAGAATTAAAAATAAA
1 TAAATA-AATTAAAAATAAA
53327816 TAAATAAA
1 TAAATAAA
53327824 AATCCCCCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 15 0.39
20 14 0.37
21 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAATAAATTAAAAATAAA
Found at i:53329190 original size:30 final size:30
Alignment explanation
Indices: 53329147--53329206 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
53329137 TTAAAATACC
53329147 CCCAATTAAAATATAAAAGCTCCCATCCTA
1 CCCAATTAAAATATAAAAGCTCCCATCCTA
* *
53329177 CCCAGTTACAATATAAAAGCTCCCATCCTA
1 CCCAATTAAAATATAAAAGCTCCCATCCTA
53329207 AACCTAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.32, G:0.05, T:0.23
Consensus pattern (30 bp):
CCCAATTAAAATATAAAAGCTCCCATCCTA
Found at i:53332262 original size:18 final size:18
Alignment explanation
Indices: 53332241--53332276 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53332231 GAAATTAATT
*
53332241 AAATATCAATTAATTAAA
1 AAATATCAATAAATTAAA
*
53332259 AAATATTAATAAATTAAA
1 AAATATCAATAAATTAAA
53332277 GTTATATAAC
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:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATCAATAAATTAAA
Found at i:53333669 original size:16 final size:16
Alignment explanation
Indices: 53333648--53333681 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
53333638 TATATTTATC
53333648 TATTTA-AATTTAGTTT
1 TATTTATAATTTA-TTT
53333664 TATTTATAATTTATTT
1 TATTTATAATTTATTT
53333680 TA
1 TA
53333682 ATATTGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TATTTATAATTTATTT
Found at i:53343156 original size:175 final size:174
Alignment explanation
Indices: 53342866--53343220 Score: 615
Period size: 175 Copynumber: 2.0 Consensus size: 174
53342856 GCAATTTGCT
53342866 TCATTTGTGAGAGCTAATCACCATGGTCTCTTTATCCTTCTTGGGTGTGCTGTAATTTCATGTGA
1 TCATTTGTGAGAGCTAATCACCATGGTCTCTTTATCCTTCTTGGGTGTGCTGTAATTTCATGTGA
* * *
53342931 AGATGTAACAACATTTGGGTGATTGTTTTCATCGTGGCTCTCTAATATGTTGGTGTCTTGCTTCA
66 AGATGCAACAACATTTAGGTGATTGTTTTCACCGTGGCTCTCTAATATGTTGGTGTCTTGCTTCA
* *
53342996 ATCGATAATTTGTTGCTGCAATTTCGTTAAAATACTTGATGCAC
131 ATCAAGAATTTGTTGCTGCAATTTCGTTAAAATACTTGATGCAC
53343040 TCATTTGTGAGAGCTAATCACCATGGTCTCTCTCTATCCTTCTT-GGTGTGCTGTAATTTCATGT
1 TCATTTGTGAGAGCTAATCACCATGGTCTCT-T-TATCCTTCTTGGGTGTGCTGTAATTTCATGT
* *
53343104 GAAGATGCAACAGCATTTAGGTGATTGTTTTCACCGTGGCTCTTTAATATGTTGGTGTCTTGCTT
64 GAAGATGCAACAACATTTAGGTGATTGTTTTCACCGTGGCTCTCTAATATGTTGGTGTCTTGCTT
53343169 CAATCAAGAATTTGTTGCTGCAATTTCGTTAAAATACTTGATGCAC
129 CAATCAAGAATTTGTTGCTGCAATTTCGTTAAAATACTTGATGCAC
53343215 -CATTTG
1 TCATTTG
53343221 CTCAATTTTG
Statistics
Matches: 172, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
174 37 0.22
175 125 0.73
176 10 0.06
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.40
Consensus pattern (174 bp):
TCATTTGTGAGAGCTAATCACCATGGTCTCTTTATCCTTCTTGGGTGTGCTGTAATTTCATGTGA
AGATGCAACAACATTTAGGTGATTGTTTTCACCGTGGCTCTCTAATATGTTGGTGTCTTGCTTCA
ATCAAGAATTTGTTGCTGCAATTTCGTTAAAATACTTGATGCAC
Found at i:53351731 original size:17 final size:17
Alignment explanation
Indices: 53351702--53351734 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53351692 TTATCTATCA
53351702 TTATTGTTATTATTTAT
1 TTATTGTTATTATTTAT
53351719 TTATATGTT-TTATTTA
1 TTAT-TGTTATTATTTA
53351735 CATTTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
TTATTGTTATTATTTAT
Found at i:53354828 original size:22 final size:21
Alignment explanation
Indices: 53354792--53354832 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
53354782 ATATAGTAAA
*
53354792 TAAATAATGTATTTTTAAAAAT
1 TAAATAATATA-TTTTAAAAAT
*
53354814 TAAATAATATGTTTTAAAA
1 TAAATAATATATTTTAAAA
53354833 CAGTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAATAATATATTTTAAAAAT
Found at i:53357514 original size:19 final size:19
Alignment explanation
Indices: 53357471--53357508 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
53357461 TTTAAAAAAA
53357471 TATAAA-ATTTGAAATTTT
1 TATAAATATTTGAAATTTT
*
53357489 TATAAATATTTGGAATTTT
1 TATAAATATTTGAAATTTT
53357508 T
1 T
53357509 GAAAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TATAAATATTTGAAATTTT
Found at i:53360576 original size:22 final size:22
Alignment explanation
Indices: 53360551--53360639 Score: 101
Period size: 22 Copynumber: 4.0 Consensus size: 22
53360541 GCACTATTAA
53360551 ACAGAGAGCACTAATGTGCTAT
1 ACAGAGAGCACTAATGTGCTAT
*
53360573 ACAGAGAGCACAAATGTGCTA-
1 ACAGAGAGCACTAATGTGCTAT
53360594 A-AGGAGAGCACTAATGTGCTAAT
1 ACA-GAGAGCACTAATGTGCT-AT
* *
53360617 AATCAGATAGCACTAACGTGCTA
1 -A-CAGAGAGCACTAATGTGCTA
53360640 ATAATCAGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.02
21 17 0.30
22 21 0.37
24 2 0.04
25 15 0.26
26 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (22 bp):
ACAGAGAGCACTAATGTGCTAT
Found at i:53360602 original size:21 final size:21
Alignment explanation
Indices: 53360550--53360615 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
53360540 TGCACTATTA
53360550 AACAGAGAGCACTAATGTGCT
1 AACAGAGAGCACTAATGTGCT
*
53360571 ATACAGAGAGCACAAATGTGCT
1 A-ACAGAGAGCACTAATGTGCT
53360593 AA-AGGAGAGCACTAATGTGCT
1 AACA-GAGAGCACTAATGTGCT
53360614 AA
1 AA
53360616 TAATCAGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.02
21 20 0.49
22 20 0.49
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (21 bp):
AACAGAGAGCACTAATGTGCT
Found at i:53360637 original size:25 final size:25
Alignment explanation
Indices: 53360600--53360648 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
53360590 GCTAAAGGAG
*
53360600 AGCACTAATGTGCTAATAATCAGAT
1 AGCACTAACGTGCTAATAATCAGAT
53360625 AGCACTAACGTGCTAATAATCAGA
1 AGCACTAACGTGCTAATAATCAGA
53360649 GAGCGCGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (25 bp):
AGCACTAACGTGCTAATAATCAGAT
Found at i:53361015 original size:28 final size:28
Alignment explanation
Indices: 53360980--53361035 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
53360970 ATATAACATA
*
53360980 ATTCAATACTTATTAATATTCTAAAATT
1 ATTCAATACTTATTAATATTCCAAAATT
53361008 ATTCAATACTTATTAATATTCCAAAATT
1 ATTCAATACTTATTAATATTCCAAAATT
53361036 CACTACAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTCAATACTTATTAATATTCCAAAATT
Found at i:53362985 original size:20 final size:21
Alignment explanation
Indices: 53362943--53362986 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
53362933 CCTTTTTTAG
* *
53362943 AATAATAATTAAATATACGAA
1 AATAATAATTAAATACACAAA
*
53362964 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
53362984 AAT
1 AAT
53362987 GTATATAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:53363195 original size:20 final size:19
Alignment explanation
Indices: 53363165--53363203 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
53363155 TAACATTAAG
53363165 AATATATATATACAATATA
1 AATATATATATACAATATA
53363184 AATATAATATATACAATATA
1 AATAT-ATATATACAATATA
53363204 CACATATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATATATATACAATATA
Found at i:53364386 original size:18 final size:18
Alignment explanation
Indices: 53364363--53364413 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
53364353 AGGGTTTCTT
53364363 GGTTTTTTTGGGGGGTTA
1 GGTTTTTTTGGGGGGTTA
***
53364381 GGTTTTTTTTTTGGGTTA
1 GGTTTTTTTGGGGGGTTA
53364399 GGTTTTTTTGGGGGG
1 GGTTTTTTTGGGGGG
53364414 GCTTAATGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.04, C:0.00, G:0.41, T:0.55
Consensus pattern (18 bp):
GGTTTTTTTGGGGGGTTA
Found at i:53364516 original size:18 final size:17
Alignment explanation
Indices: 53364484--53364525 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
53364474 AAATGGGTCA
*
53364484 TGGGTTAAGGGTTTTAG-
1 TGGGTTTAGGGTTTT-GT
53364501 TGGGTTTAGAGGTTTTGT
1 TGGGTTTAG-GGTTTTGT
53364519 TGGGTTT
1 TGGGTTT
53364526 TGATATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (17 bp):
TGGGTTTAGGGTTTTGT
Found at i:53366668 original size:8 final size:8
Alignment explanation
Indices: 53366657--53366739 Score: 51
Period size: 8 Copynumber: 9.8 Consensus size: 8
53366647 AAAATTTTAA
53366657 TAAAAATT
1 TAAAAATT
*
53366665 TAAATA-T
1 TAAAAATT
53366672 TAAAAATT
1 TAAAAATT
* *
53366680 AGAAAAATA
1 -TAAAAATT
53366689 TAAAAATTGT
1 TAAAAA-T-T
53366699 TAAAAAATT
1 T-AAAAATT
*
53366708 ATAAAATTT
1 -TAAAAATT
*
53366717 TAAAATTT
1 TAAAAATT
*
53366725 TAAAAGTT
1 TAAAAATT
53366733 GTAAAAA
1 -TAAAAA
53366740 AAATATAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
7 6 0.10
8 26 0.44
9 19 0.32
10 3 0.05
11 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (8 bp):
TAAAAATT
Found at i:53366701 original size:27 final size:25
Alignment explanation
Indices: 53366666--53366729 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
53366656 ATAAAAATTT
*
53366666 AAATATTAAAAATTAGAAAAATATAA
1 AAATTTTAAAAATTA-AAAAATATAA
* * *
53366692 AAATTGTTAAAAAATTATAAAATTTTA
1 AAATT-TT-AAAAATTAAAAAATATAA
53366719 AAATTTTAAAA
1 AAATTTTAAAA
53366730 GTTGTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 4 0.12
26 6 0.19
27 14 0.44
28 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (25 bp):
AAATTTTAAAAATTAAAAAATATAA
Found at i:53366714 original size:36 final size:36
Alignment explanation
Indices: 53366670--53366766 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 36
53366660 AAATTTAAAT
* *
53366670 ATTA-AAAATTAGAAAAATATAAAAATTGTTAAAAA
1 ATTATAAAATTATAAAAATATAAAAATTGTAAAAAA
* * * *
53366705 ATTATAAAATTTTAAAATTTTAAAAGTTGTAAAAAA
1 ATTATAAAATTATAAAAATATAAAAATTGTAAAAAA
* *
53366741 AATATAAAATATATAGAAATATAAAA
1 ATTATAAAAT-TATAAAAATATAAAA
53366767 TTTTATAAAG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
35 4 0.08
36 34 0.69
37 11 0.22
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (36 bp):
ATTATAAAATTATAAAAATATAAAAATTGTAAAAAA
Found at i:53366777 original size:46 final size:47
Alignment explanation
Indices: 53366717--53366813 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 47
53366707 TATAAAATTT
** * *
53366717 TAAAATTTTAAAAGTTGTAA-AAAA-AATATAAAATATATAGAAATA
1 TAAAATTTTAAAAGTCATAAGAAAATAATACAAAATATAAAGAAATA
* *
53366762 TAAAATTTTATAAAGTCATAAGAAAATTATACAAAATGTAAAGAAATA
1 TAAAATTTTA-AAAGTCATAAGAAAATAATACAAAATATAAAGAAATA
53366810 TAAA
1 TAAA
53366814 TTTCGTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
45 10 0.23
46 8 0.19
47 4 0.09
48 21 0.49
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (47 bp):
TAAAATTTTAAAAGTCATAAGAAAATAATACAAAATATAAAGAAATA
Found at i:53366889 original size:21 final size:20
Alignment explanation
Indices: 53366858--53366901 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
53366848 AAAAGAAGCA
53366858 TTTTATAATTTTTCTATAAT
1 TTTTATAATTTTTCTATAAT
* *
53366878 TTTTATTAATTTTTTTATCAT
1 TTTTA-TAATTTTTCTATAAT
53366899 TTT
1 TTT
53366902 CGCCACATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATAATTTTTCTATAAT
Found at i:53367056 original size:18 final size:18
Alignment explanation
Indices: 53367035--53367094 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
53367025 AACTTAATTT
53367035 TTTATATTTTTATTAAAA
1 TTTATATTTTTATTAAAA
*
53367053 TTTAATAATTTTT-CTAAAA
1 TTT-AT-ATTTTTATTAAAA
*
53367072 TTTAT-TATTTATTATAAA
1 TTTATATTTTTATTA-AAA
53367090 TTTAT
1 TTTAT
53367095 TTATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 4 0.11
17 2 0.06
18 13 0.37
19 10 0.29
20 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATATTTTTATTAAAA
Found at i:53367064 original size:19 final size:19
Alignment explanation
Indices: 53367042--53367093 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
53367032 TTTTTTATAT
53367042 TTTTATTAAAATTTAATAA
1 TTTTATTAAAATTTAATAA
*
53367061 TTTT-TCTAAAATTT-ATTA
1 TTTTAT-TAAAATTTAATAA
53367079 -TTTATTATAAATTTA
1 TTTTATTA-AAATTTA
53367094 TTTATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 5 0.18
18 11 0.39
19 12 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATTAAAATTTAATAA
Found at i:53383028 original size:18 final size:18
Alignment explanation
Indices: 53383005--53383054 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
53382995 AAATTTATAC
53383005 TTTTTATAAATTTATTTA
1 TTTTTATAAATTTATTTA
53383023 TTTTTA-AAGATATT-TTTA
1 TTTTTATAA-AT-TTATTTA
*
53383041 TTTTT-TTAATTTAT
1 TTTTTATAAATTTAT
53383055 GCTCGTTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
16 2 0.07
17 5 0.19
18 18 0.67
19 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTATAAATTTATTTA
Found at i:53395373 original size:18 final size:18
Alignment explanation
Indices: 53395352--53395392 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
53395342 AATTTTACAA
53395352 AAAATGCTTAGATAAATC
1 AAAATGCTTAGATAAATC
53395370 AAAATGCTTAGATAAATC
1 AAAATGCTTAGATAAATC
53395388 AAAAT
1 AAAAT
53395393 AGATGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (18 bp):
AAAATGCTTAGATAAATC
Found at i:53396183 original size:3 final size:3
Alignment explanation
Indices: 53396175--53396304 Score: 93
Period size: 3 Copynumber: 40.3 Consensus size: 3
53396165 TGTATAAACA
53396175 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * **
53396220 AAT CAG AAT AAT ATAT AAGT ACAA AAT GGGT AAT AAAT AAAT AGAT GAAT
1 AAT AAT AAT AAT A-AT AA-T A-AT AAT -AAT AAT -AAT -AAT A-AT -AAT
*
53396270 AAAT AAT AAT AAT GAT AAT AAT AGAT AAT AA- AAT A
1 -AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A
53396305 CCAATGATAA
Statistics
Matches: 103, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
2 3 0.03
3 73 0.71
4 25 0.24
5 2 0.02
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:53396351 original size:18 final size:18
Alignment explanation
Indices: 53396328--53396363 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53396318 AGACATAGAT
* *
53396328 AAAATGAACGACTAATAA
1 AAAATGAAAGAATAATAA
53396346 AAAATGAAAGAATAATAA
1 AAAATGAAAGAATAATAA
53396364 GTGAATACAA
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:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (18 bp):
AAAATGAAAGAATAATAA
Found at i:53401056 original size:46 final size:46
Alignment explanation
Indices: 53400743--53401056 Score: 450
Period size: 46 Copynumber: 6.8 Consensus size: 46
53400733 TGATGTCATA
* * * * *
53400743 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCAGGTTGCCATG
* *** *
53400789 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
*
53400836 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
53400882 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
53400928 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
53400974 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
53401020 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
53401057 AGAGCACACT
Statistics
Matches: 251, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 212 0.84
47 39 0.16
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:53409356 original size:7 final size:8
Alignment explanation
Indices: 53409339--53409367 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53409329 GACCTTCTCC
53409339 TTTTTATT
1 TTTTTATT
53409347 TTTTTATT
1 TTTTTATT
53409355 TTTTTATT
1 TTTTTATT
53409363 TTTTT
1 TTTTT
53409368 TTACATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTATT
Found at i:53410166 original size:18 final size:18
Alignment explanation
Indices: 53410143--53410179 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53410133 CTAAAGTCTT
53410143 ATTTCAATATTT-TTATAC
1 ATTTCAAT-TTTATTATAC
53410161 ATTTCAATTTTATTATAC
1 ATTTCAATTTTATTATAC
53410179 A
1 A
53410180 CACTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTCAATTTTATTATAC
Found at i:53411250 original size:26 final size:25
Alignment explanation
Indices: 53411186--53411235 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53411176 ATTCAAAATC
53411186 TATTTATTATTTTTCTTAAAAACAA
1 TATTTATTATTTTTCTTAAAAACAA
53411211 TATTTATTATTTTTCTTAAAAACAA
1 TATTTATTATTTTTCTTAAAAACAA
53411236 CTTTTTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTATTATTTTTCTTAAAAACAA
Found at i:53422841 original size:3 final size:3
Alignment explanation
Indices: 53422833--53422857 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53422823 TGCTGTTGTG
53422833 GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT G
53422858 ATGGGCATCA
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:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:53424943 original size:30 final size:31
Alignment explanation
Indices: 53424876--53424947 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
53424866 AATACATAAT
* * *
53424876 ATTATTATAATATAAACATTAAAAAATTAAG
1 ATTATTATAATACAAACATTAAAAAATAAAA
*
53424907 ATTATTAT-ATACAAA-ATATAATAAATAAAA
1 ATTATTATAATACAAACAT-TAAAAAATAAAA
53424937 ATTATTA-AATA
1 ATTATTATAATA
53424948 TTAAATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 2 0.06
30 25 0.71
31 8 0.23
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (31 bp):
ATTATTATAATACAAACATTAAAAAATAAAA
Found at i:53431854 original size:29 final size:29
Alignment explanation
Indices: 53431822--53431885 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
53431812 ATGAATAAGC
*
53431822 AAAATAATAATTAAATAATGCATGATATA
1 AAAATAATAATCAAATAATGCATGATATA
* *
53431851 AAAACAATAATCAAATAATGTATGATATA
1 AAAATAATAATCAAATAATGCATGATATA
*
53431880 CAAATA
1 AAAATA
53431886 GAAGAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (29 bp):
AAAATAATAATCAAATAATGCATGATATA
Found at i:53432082 original size:7 final size:7
Alignment explanation
Indices: 53432070--53432095 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53432060 AAATAGTATT
53432070 TAATATA
1 TAATATA
53432077 TAATATA
1 TAATATA
53432084 TAATATA
1 TAATATA
53432091 TAATA
1 TAATA
53432096 ACAAGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATATA
Found at i:53432313 original size:20 final size:19
Alignment explanation
Indices: 53432275--53432317 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
53432265 ACAATTTACA
53432275 AATTTAAAATAATATATAT
1 AATTTAAAATAATATATAT
53432294 AATTTAAACATAA-ATAATAT
1 AATTTAAA-ATAATAT-ATAT
53432314 AATT
1 AATT
53432318 GGTAAATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTAAAATAATATATAT
Found at i:53439656 original size:12 final size:12
Alignment explanation
Indices: 53439639--53439669 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53439629 GAAGCAGGGG
53439639 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
53439651 AGAAAAAGGGAA
1 AGAAAAAGAGAA
53439663 AGAAAAA
1 AGAAAAA
53439670 TAAAAGAGAA
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:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:53440035 original size:18 final size:18
Alignment explanation
Indices: 53440014--53440054 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
53440004 AAAAAAAAAG
53440014 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
53440032 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
53440050 AGAAA
1 AGAAA
53440055 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:53440565 original size:20 final size:20
Alignment explanation
Indices: 53440542--53440579 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53440532 GTTATTAAGT
53440542 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
53440562 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
53440580 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:53441644 original size:25 final size:25
Alignment explanation
Indices: 53441610--53441660 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
53441600 GATTGAGCAG
53441610 GTATGCTTTAGAATATATTCCAACC
1 GTATGCTTTAGAATATATTCCAACC
*
53441635 GTATGCTTTAGAATATGTTCCAACC
1 GTATGCTTTAGAATATATTCCAACC
53441660 G
1 G
53441661 AGGCTGATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (25 bp):
GTATGCTTTAGAATATATTCCAACC
Found at i:53448560 original size:18 final size:18
Alignment explanation
Indices: 53448537--53448572 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53448527 ATAACAAGTA
*
53448537 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
53448555 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
53448573 ATGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.58, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:53448588 original size:29 final size:29
Alignment explanation
Indices: 53448555--53448617 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
53448545 GAGTTAGTGG
53448555 GGGTGATGGAGGTAGTGGAT-GGTTTAGTA
1 GGGTGATGGAGGTAGTGG-TCGGTTTAGTA
*
53448584 GGGTGATGGAGTTAGTGGTCGGTTTAGTA
1 GGGTGATGGAGGTAGTGGTCGGTTTAGTA
53448613 GGGTG
1 GGGTG
53448618 TTTAATTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.17, C:0.02, G:0.49, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGTCGGTTTAGTA
Found at i:53448985 original size:85 final size:85
Alignment explanation
Indices: 53448855--53449157 Score: 450
Period size: 85 Copynumber: 3.6 Consensus size: 85
53448845 AACGAAAATA
53448855 AGATCTGT-AATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
* **
53448919 CACCACTGCTCGGAGAG-TT
66 CACCACTGCTCGGCGAGCCC
* *
53448938 AGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGCTAAGGCGAGTCTTTGACCTGCT
1 A-GATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCT
*
53449003 CCACCACTGTTCGGCGAGCCC
65 CCACCACTGCTCGGCGAGCCC
* * * *
53449024 A-AGTCTATAAACTTTAGCCTCTTACCCTACTGCTTAGGGAGTTAAGGCGAGTCTTCGACCTGCT
1 AGA-TCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCT
* *
53449088 CCGCCAATGCTCGGCGAGCCC
65 CCACCACTGCTCGGCGAGCCC
*
53449109 AGATCTGTAAATTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCG
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG
53449158 TGTATCTTTG
Statistics
Matches: 195, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
83 1 0.01
84 8 0.04
85 184 0.94
86 2 0.01
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.29
Consensus pattern (85 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
CACCACTGCTCGGCGAGCCC
Found at i:53449351 original size:87 final size:86
Alignment explanation
Indices: 53448854--53449351 Score: 319
Period size: 85 Copynumber: 5.8 Consensus size: 86
53448844 CAACGAAAAT
* * *
53448854 AAGATCTGTAA-TTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC-GAG-TCTTCGACCTG
1 AAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTG-GTTCTTTGATCTG
* * *
53448916 CTCCACCA-CTGC-T-CGGAGAGTT
65 CTCCACTATC-GCTTAAGGAGA--C
* * * * *
53448938 AGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGCTAAGGC-GAG-TCTTTGACCTG
1 AAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTG-GTTCTTTGATCTG
* ** *
53449001 CTCCACCA-CTG-TTCGGCGAGCCC
65 CTCCACTATC-GCTTAAG-GAG-AC
* ** * * * * *
53449024 AAG-TCTATAAACTTTAGCCTCTTACCCTACTGCTTAGGGAGTTAAGGC-GAG-TCTTCGACCTG
1 AAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTG-GTTCTTTGATCTG
* * ** *
53449086 CTCCGCCAAT-GC-TCGGCGAGCC
65 CTCC-ACTATCGCTTAAG-GAGAC
* * * *
53449108 CAGATCTGTAAATTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGC-GTGTATCTTTGATCT
1 AAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTG-GT-TCTTTGATCT
* * *
53449172 GCTCCGCTATTGCTTAAGGAGAT
64 GCTCCACTATCGCTTAAGGAGAC
* * * * * * *
53449195 AAGATCTATAATCTTCAGCTTGTTACCCTATTGCTTAGGGAGTTAA-AGCGTGTTTCTTTGATCT
1 AAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGA-C-TGGTTCTTTGATCT
*
53449259 ACTCCACTATCGCTTAAGGAGAC
64 GCTCCACTATCGCTTAAGGAGAC
* **
53449282 AAGATCTGTAGTTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTGGTGGTTTGAATCTG
1 AAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTGGTTCTTTG-ATCTG
53449347 CTCCA
65 CTCCA
53449352 TTGCCGATAC
Statistics
Matches: 340, Mismatches: 56, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
84 14 0.04
85 169 0.50
86 15 0.04
87 137 0.40
88 4 0.01
89 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (86 bp):
AAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTGGTTCTTTGATCTGC
TCCACTATCGCTTAAGGAGAC
Found at i:53450554 original size:29 final size:29
Alignment explanation
Indices: 53450512--53450570 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
53450502 NNNNNNNNNN
53450512 GATGGAGGTAGTGGAT-GGTTTAGTAGGGT
1 GATGGAGGTAGTGG-TCGGTTTAGTAGGGT
*
53450541 GATGGAGTTAGTGGTCGGTTTAGTAGGGT
1 GATGGAGGTAGTGGTCGGTTTAGTAGGGT
53450570 G
1 G
53450571 TTTAATTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.32
Consensus pattern (29 bp):
GATGGAGGTAGTGGTCGGTTTAGTAGGGT
Found at i:53451101 original size:170 final size:171
Alignment explanation
Indices: 53450819--53451197 Score: 575
Period size: 170 Copynumber: 2.2 Consensus size: 171
53450809 GATCTGTAAT
*
53450819 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACCACTGCTCG
1 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACCAATGCTCG
** *
53450884 GAGAGTTAGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGCTAAGGCGAG-TCTTT
66 GAGAGCCAGGATCTGTAAATTTTAGCCTGTTACCCTACTACTTAGGGGGCTAAGGCGAGATCTTT
*
53450948 GACCTGCTCCACCACTGTTCGGCGAGCCCA-AGTCTATAAAC
131 GACCTGCTCCACCACTGCTCGGCGAGCCCAGA-TCTATAAAC
* * *
53450989 TTTAGCCTCTTACCCTACTGCTTAGGGAGTTAAGGCGAGTCTTCGACCTGCTCCGCCAATGCTCG
1 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACCAATGCTCG
* * *
53451054 GCGAGCCCA-GATCTGTAAATTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCGTGTATCT
66 GAGAG-CCAGGATCTGTAAATTTTAGCCTGTTACCCTACTACTTAGGGGGCTAAGGCGAG-ATCT
* * * *
53451118 TTGATCTGCTCCGCCACTGCTCGGCGAGCCCAGATCTTTAAAT
129 TTGACCTGCTCCACCACTGCTCGGCGAGCCCAGATCTATAAAC
53451161 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG
1 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG
53451198 TGTATCTTTG
Statistics
Matches: 188, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
170 112 0.60
171 1 0.01
172 74 0.39
173 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (171 bp):
TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACCAATGCTCG
GAGAGCCAGGATCTGTAAATTTTAGCCTGTTACCCTACTACTTAGGGGGCTAAGGCGAGATCTTT
GACCTGCTCCACCACTGCTCGGCGAGCCCAGATCTATAAAC
Found at i:53451160 original size:87 final size:85
Alignment explanation
Indices: 53450808--53451368 Score: 585
Period size: 87 Copynumber: 6.5 Consensus size: 85
53450798 AACGAAAATA
*
53450808 AGATCTGT-AATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGCTC
* **
53450872 CACCACTGCTCGGAGAG-TT
66 CACCACTGCTCGGCGAGCCC
*
53450891 AGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGCTAAGGCGAGTCTTTGACCTGCT
1 A-GATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGCT
*
53450956 CCACCACTGTTCGGCGAGCCC
65 CCACCACTGCTCGGCGAGCCC
* * * * *
53450977 A-AGTCTATAAACTTTAGCCTCTTACCCTACTGCTTAGGGAGTTAAGGCGAGTCTTCGACCTGCT
1 AGA-TCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGCT
* *
53451041 CCGCCAATGCTCGGCGAGCCC
65 CCACCACTGCTCGGCGAGCCC
* * *
53451062 AGATCTGTAAATTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCGTGTATCTTTGATCTGC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAG--TCTTTGACCTGC
*
53451127 TCCGCCACTGCTCGGCGAGCCC
64 TCCACCACTGCTCGGCGAGCCC
* * *
53451149 AGATCTTTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTGC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAG--TCTTTGACCTGC
* * ** ***
53451214 TCCACTATTGCTTAAG-GAGATA
64 TCCACCACTGC-TCGGCGAGCCC
* * * * * * * * *
53451236 AGATCTAT-AATCTTCAGCTTGTTACCCTATTGCTTAGGGAGTTAAAGCGTGTTTCTTTGATCTA
1 AGATCTGTAAAT-TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAG--TCTTTGACCTG
* * ** * *
53451300 CTCCACTACCGCTTAAG-GAGACA
63 CTCCACCACTGC-TCGGCGAGCCC
**
53451323 AGATCTGTAGTTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
53451369 ACTGGTGGTT
Statistics
Matches: 415, Mismatches: 53, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.00
84 8 0.02
85 185 0.45
86 5 0.01
87 213 0.51
88 3 0.01
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (85 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGCTC
CACCACTGCTCGGCGAGCCC
Found at i:53451459 original size:44 final size:44
Alignment explanation
Indices: 53451411--53451497 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
53451401 CATGGAGATA
* *
53451411 AGATCCGCTGAAATTTGATCTGTTCCACTCCTGC-CAGTGGGATG
1 AGATCCGCT-AAATTTAACCTGTTCCACTCCTGCTCAGTGGGATG
** *
53451455 AGATCTTCTATATTTAACCTGTTCCACTCCTGCTCAGTGGGAT
1 AGATCCGCTAAATTTAACCTGTTCCACTCCTGCTCAGTGGGAT
53451498 AACGCTGGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 21 0.57
44 16 0.43
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (44 bp):
AGATCCGCTAAATTTAACCTGTTCCACTCCTGCTCAGTGGGATG
Found at i:53451488 original size:132 final size:134
Alignment explanation
Indices: 53451335--53451858 Score: 613
Period size: 132 Copynumber: 4.0 Consensus size: 134
53451325 ATCTGTAGTT
* * * *
53451335 TTTAGCCTGTTACC-CTACTGCTTAGGGGGTTAAGACTGGTGGTTTG-AATCTGCTCCATTGCCG
1 TTTAGCCTGTT-CCACTCCTGCTCAGGGGGATAAGGCTGGTGG-TTGAAATCTGCTCCATTGCCG
* * *
53451398 ATACATGGAGATAAGATCCGCTGAAATTTGATCTGTTCCACTCCTGC-CAGTG-GGATGAGATCT
64 ATACATGGAGATAAGATCCGCTAAAATTTGATCTGCTCCACTCCTGCTCAGTGAGGATAAGATCT
53451461 TCTATA
129 TCTATA
* * * *
53451467 TTTAACCTGTTCCACTCCTGCTCAGTGGGATAACGCTGGTGGTTTG-AATCTGCTCTATTGCCGA
1 TTTAGCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTGGTGG-TTGAAATCTGCTCCATTGCCGA
* * *
53451531 TACATAGAGATAAGATTCG-TCAAAATTTGATCTGCTCCACTCCTGCTCAGTGAAGATAAGA---
65 TACATGGAGATAAGATCCGCT-AAAATTTGATCTGCTCCACTCCTGCTCAGTGAGGATAAGATCT
*
53451592 TCTAGA
129 TCTATA
* * * ** * *
53451598 GTTTAGCCTGCTCAACTTCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATATGCTCCATTGCCG
1 -TTTAGCCTGTTCCACTCCTGCTCAG-GGGGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCG
* * * *
53451663 ATACATGGAGATAAGATCCGCTGAAATTTGATCTGTTCCCCTCCTGC-CAGTG-GGATGAGATCT
64 ATACATGGAGATAAGATCCGCTAAAATTTGATCTGCTCCACTCCTGCTCAGTGAGGATAAGATCT
*
53451726 GCTATA
129 TCTATA
*
53451732 TTTAGCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTTGTGG-TGAAATCTGCTCCATTGCCGAT
1 TTTAGCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGAT
* * ** *
53451796 ACATGGAGATAAGATTCGCCAAAATTTGATCTGCTCGGCTCCTGCTCAGCGAGGATAAGATCT
66 ACATGGAGATAAGATCCGCTAAAATTTGATCTGCTCCACTCCTGCTCAGTGAGGATAAGATCT
53451859 GTCGAAATTT
Statistics
Matches: 329, Mismatches: 50, Indels: 25
0.81 0.12 0.06
Matches are distributed among these distances:
131 74 0.22
132 139 0.42
133 105 0.32
134 11 0.03
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (134 bp):
TTTAGCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTGGTGGTTGAAATCTGCTCCATTGCCGAT
ACATGGAGATAAGATCCGCTAAAATTTGATCTGCTCCACTCCTGCTCAGTGAGGATAAGATCTTC
TATA
Found at i:53451891 original size:177 final size:178
Alignment explanation
Indices: 53451671--53452124 Score: 736
Period size: 177 Copynumber: 2.6 Consensus size: 178
53451661 CGATACATGG
* * *
53451671 AGATAAGATCCG-CTGAAATTTGATCTGTTCCCCTCCTGCCAGTGGGATGAGATCTGCTATATTT
1 AGATAAGATCTGTC-GAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATCTGCTATATTT
53451735 AGCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTTGTGG-TGAAATCTGCTCCATTGCCGATACA
65 AGCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTGCCGATACA
* *
53451799 TGGAGATAAGATTCGCCAAAATTTGATCTGCTCGGCTCCTGCTCAGCGA
130 TGGAGATAAGATTCGCCAAAATTTGATCTGCTCCGCTCCTGATCAGCGA
*
53451848 GGATAAGATCTGTCGAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATCTGCTATATTTA
1 AGATAAGATCTGTCGAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATCTGCTATATTTA
* * * * *
53451913 GCCTGCTT-CACTCCTACTCA-GTGAAGAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACA
66 GCCTG-TTCCACTCCTGCTCAGGGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTGCCGATACA
* *
53451976 TGGAGGTAAGATTTGCCAAAATTTGATCTGCTCCGCTCCTGATCAGCGA
130 TGGAGATAAGATTCGCCAAAATTTGATCTGCTCCGCTCCTGATCAGCGA
53452025 AGATAAGATCTGTCGAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATCTGCTATATTTA
1 AGATAAGATCTGTCGAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATCTGCTATATTTA
*
53452090 GCCTGTTCCACTCCTGCTCAGTGGGATAAGGCTTG
66 GCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTTG
53452125 CCGAATCTGT
Statistics
Matches: 252, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
176 15 0.06
177 225 0.89
178 12 0.05
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (178 bp):
AGATAAGATCTGTCGAAATTTGATCTGTTCCACTCCAGCCAGTGGGATGAGATCTGCTATATTTA
GCCTGTTCCACTCCTGCTCAGGGGGATAAGGCTTGTGGCTGAAATCTGCTCCATTGCCGATACAT
GGAGATAAGATTCGCCAAAATTTGATCTGCTCCGCTCCTGATCAGCGA
Found at i:53453397 original size:24 final size:24
Alignment explanation
Indices: 53453370--53453417 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
53453360 TCACCTTGGC
*
53453370 CTCTCATTTGCTTTTCTTTTCTTT
1 CTCTCATTTGCTTTTCTCTTCTTT
** *
53453394 CTCTTTTTTGTTTTTCTCTTCTTT
1 CTCTCATTTGCTTTTCTCTTCTTT
53453418 TTCCTTTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.23, G:0.04, T:0.71
Consensus pattern (24 bp):
CTCTCATTTGCTTTTCTCTTCTTT
Found at i:53453455 original size:25 final size:25
Alignment explanation
Indices: 53453404--53453459 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
53453394 CTCTTTTTTG
*
53453404 TTTTTCTCTTCTTTTTCCTTTTCCT
1 TTTTTCTCTTCTTTTTCCTCTTCCT
*
53453429 TTTTTCTCTTTCCTTTTT-CTCTTCTT
1 TTTTTCTC-TT-CTTTTTCCTCTTCCT
53453455 TTTTT
1 TTTTT
53453460 TTTTTGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 8 0.30
26 13 0.48
27 6 0.22
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTCTCTTCTTTTTCCTCTTCCT
Done.