Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 116 of 297
Found at i:41570844 original size:17 final size:17
Alignment explanation
Indices: 41570787--41570844 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
41570777 TTTAGTTTTT
*
41570787 TATTGATTAATATTTAATG
1 TATT-ATTAATA-TTAATA
* *
41570806 TTTCTATTAATATTAATC
1 TAT-TATTAATATTAATA
*
41570824 TATTATTAATATTATTA
1 TATTATTAATATTAATA
41570841 TATT
1 TATT
41570845 TATATCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 16 0.48
18 7 0.21
19 9 0.27
20 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTATTAATATTAATA
Found at i:41572843 original size:31 final size:31
Alignment explanation
Indices: 41572795--41572878 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
41572785 TTAGTCTTGA
*
41572795 CATAT-ACTGGGCTGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
41572825 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
41572856 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
41572879 ACTGTAAACG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:41572949 original size:42 final size:42
Alignment explanation
Indices: 41572902--41572993 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
41572892 TGGCCCTTAG
*
41572902 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
41572944 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
41572986 GCCCATTT
1 GCCCATTT
41572994 GGGGAGACTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:41573169 original size:25 final size:25
Alignment explanation
Indices: 41573141--41573210 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41573131 CTCTTTTAAT
*
41573141 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41573166 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41573191 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41573211 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41574037 original size:27 final size:28
Alignment explanation
Indices: 41574006--41574070 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
41573996 TACGGAACAT
*
41574006 AAGGGCATATT-C-GTCATTTTACCATAC
1 AAGGGC-TATTACGGTCACTTTACCATAC
*
41574033 AAGGG-TATTACGGTCACTTTACCCTAC
1 AAGGGCTATTACGGTCACTTTACCATAC
41574060 AAGGGCT-TTAC
1 AAGGGCTATTAC
41574071 AGTCTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 27 0.82
28 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (28 bp):
AAGGGCTATTACGGTCACTTTACCATAC
Found at i:41574080 original size:27 final size:27
Alignment explanation
Indices: 41574018--41574082 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
41574008 GGGCATATTC
*
41574018 GTCATTTTACCATACAAGGGTATTACG
1 GTCATTTTACCATACAAGGGTATTACA
* *
41574045 GTCACTTTACCCTACAAGGGCT-TTACA
1 GTCATTTTACCATACAAGGG-TATTACA
*
41574072 GTCTTTTTACC
1 GTCATTTTACC
41574083 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGTATTACA
Found at i:41574166 original size:27 final size:27
Alignment explanation
Indices: 41574133--41574377 Score: 154
Period size: 27 Copynumber: 9.0 Consensus size: 27
41574123 TTGGTAAATC
41574133 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
** * *
41574160 TGTAAACGAATGGTATTTCTA-TAATTTT
1 TACAAACCAAGGGTATTTC-AGTAA-TTT
* * *
41574188 TAGAAAGTCAAGGGTATTTCTGTAATTT
1 TACAAA-CCAAGGGTATTTCAGTAATTT
** * * **
41574216 TGTAAATCAGGGGTATTTTGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
*** *
41574243 TACAAATTGAGGGTATTTTAGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
* *
41574270 CACAAACC-AGTGGTATTTCGGTAATTT
1 TACAAACCAAG-GGTATTTCAGTAATTT
* * **
41574297 TACAAACTAGGGGTATTTTGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
* * ** *
41574324 TACAAACTAGGGGTATTTTGGTAATTC
1 TACAAACCAAGGGTATTTCAGTAATTT
**
41574351 TATCCTA-CAAGGGTATTTCAGTAATTT
1 TA-CAAACCAAGGGTATTTCAGTAATTT
41574378 CATAATCGAG
Statistics
Matches: 173, Mismatches: 38, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
26 2 0.01
27 140 0.81
28 18 0.10
29 13 0.08
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
TACAAACCAAGGGTATTTCAGTAATTT
Found at i:41574316 original size:81 final size:81
Alignment explanation
Indices: 41574200--41574349 Score: 223
Period size: 81 Copynumber: 1.9 Consensus size: 81
41574190 GAAAGTCAAG
* ** *
41574200 GGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTTAG
1 GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTAG
41574264 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
*
41574281 GGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 GGTATTTCGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAG
41574345 TAATT
65 TAATT
41574350 CTATCCTACA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
80 1 0.02
81 59 0.95
82 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGT
AATTTCACAAACCAGT
Found at i:41574365 original size:54 final size:53
Alignment explanation
Indices: 41574116--41574377 Score: 188
Period size: 54 Copynumber: 4.8 Consensus size: 53
41574106 CATCCTACAA
* * * * ** * *
41574116 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACGAA
1 GGGTATTTTGGTAATTTTACAAA-CAAGGGTATTTTAGTAATTTTACAAACTAG
* * * **
41574170 TGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCT-GTAATTTTGTAAA-TCAG
1 GGGTATTT-TGGTAA-TTTTACAAA--CAAGGGTATTT-TAGTAATTTTACAAACT-AG
** * *
41574226 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTAGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAA-CAAGGGTATTTTAGTAATTTTACAAACTAG
* * * *
41574280 TGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAAC-AAGGGTATTTTAGTAATTTTACAAACTAG
* ** *
41574334 GGGTATTTTGGTAATTCTATCCTACAAGGGTATTTCAGTAATTT
1 GGGTATTTTGGTAATTTTA-CAAACAAGGGTATTTTAGTAATTT
41574378 CATAATCGAG
Statistics
Matches: 163, Mismatches: 35, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
53 1 0.01
54 108 0.66
55 19 0.12
56 35 0.21
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAACAAGGGTATTTTAGTAATTTTACAAACTAG
Found at i:41574366 original size:81 final size:80
Alignment explanation
Indices: 41574196--41574377 Score: 217
Period size: 81 Copynumber: 2.2 Consensus size: 80
41574186 TTTAGAAAGT
* ** *
41574196 CAAGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
1 CAAGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAGGGTATTT
41574261 TAGTAATTTCACAAA
66 TAGTAATTTCACAAA
* *
41574276 CCAGTGGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTA
1 CAAG-GGTATTTCAGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAAA-TAGAGGGTA
* **
41574339 TTTTGGTAA-TTCTATCCTA
63 TTTTAGTAATTTC-A-CAAA
41574358 CAAGGGTATTTCAGTAATTT
1 CAAGGGTATTTCAGTAATTT
41574378 CATAATCGAG
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
80 7 0.08
81 73 0.84
82 7 0.08
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (80 bp):
CAAGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAGGGTATTT
TAGTAATTTCACAAA
Found at i:41574528 original size:26 final size:26
Alignment explanation
Indices: 41574198--41574608 Score: 167
Period size: 27 Copynumber: 15.4 Consensus size: 26
41574188 TAGAAAGTCA
* ** * *
41574198 AGGGTATTTCTGTAATTTTGTAAATC
1 AGGGTATTTCGGTAATTTTACAACTG
* *
41574224 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTCGGTAATTTTAC-AACTG
** * *
41574252 AGGGTATTTTAGTAATTTCACAAAC-C
1 AGGGTATTTCGGTAATTTTAC-AACTG
41574278 AGTGGTATTTCGGTAATTTTACAAACT-
1 AG-GGTATTTCGGTAATTTTAC-AACTG
*
41574305 AGGGGTATTTTGGTAATTTTACAAACT-
1 A-GGGTATTTCGGTAATTTTAC-AACTG
* * * *
41574332 AGGGGTATTTTGGTAATTCTATCCTAC-A
1 A-GGGTATTTCGGTAATT-T-TACAACTG
* * *
41574360 AGGGTATTTCAGTAATTTCATAA-TCG
1 AGGGTATTTCGGTAATTTTACAACT-G
** *
41574386 AGGGTAAAAT-GGTATTTTGTA-AACTG
1 AGGGT-ATTTCGGTAATTT-TACAACTG
** * *
41574412 AGGGTAAAAT-GGTAATTTTATAAATCG
1 AGGGT-ATTTCGGTAATTTTACAACT-G
*** * * * *
41574439 AGGGTAAAACGATAATTCTATAAATCG
1 AGGGTATTTCGGTAATTTTACAACT-G
* * *
41574466 AGGGTATTTTGATAATTTTACAAGTCG
1 AGGGTATTTCGGTAATTTTACAACT-G
*
41574493 AGGGTATTTCAGTAATTTTGA-AACTG
1 AGGGTATTTCGGTAATTTT-ACAACTG
*
41574519 AGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAACT-G
** * *
41574546 AGATTATTTCGGTAATTTTAGAAACCG
1 AGGGTATTTCGGTAATTTTA-CAACTG
*
41574573 GGGGTACTTT-GGTAATTTTACAACTG
1 AGGGTA-TTTCGGTAATTTTACAACTG
*
41574599 GGGGTATTTC
1 AGGGTATTTC
41574609 AGCAATTTGG
Statistics
Matches: 307, Mismatches: 56, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
25 7 0.02
26 73 0.24
27 210 0.68
28 15 0.05
29 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTACAACTG
Found at i:41574535 original size:80 final size:80
Alignment explanation
Indices: 41574451--41574608 Score: 176
Period size: 80 Copynumber: 2.0 Consensus size: 80
41574441 GGTAAAACGA
* * * **
41574451 TAATTCTATAAATCGAGGGTATTTTGATAATTTTACAAGTCGAGGGTA-TTTCAGTAATTTTGA-
1 TAATTCTACAAATCGAGAGTATTTCGATAATTTTACAAACCGAGGGTACTTT-AGTAATTTT-AC
41574514 AACTGAGGGTATTTCGG
64 AACTGAGGGTATTTCGG
* * * * * *
41574531 TAATTTTACAAATCGAGATTATTTCGGTAATTTTAGAAACCGGGGGTACTTTGGTAATTTTACAA
1 TAATTCTACAAATCGAGAGTATTTCGATAATTTTACAAACCGAGGGTACTTTAGTAATTTTACAA
*
41574596 CTGGGGGTATTTC
66 CTGAGGGTATTTC
41574609 AGCAATTTGG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
79 1 0.02
80 60 0.94
81 3 0.05
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (80 bp):
TAATTCTACAAATCGAGAGTATTTCGATAATTTTACAAACCGAGGGTACTTTAGTAATTTTACAA
CTGAGGGTATTTCGG
Found at i:41574539 original size:53 final size:53
Alignment explanation
Indices: 41574136--41574616 Score: 182
Period size: 54 Copynumber: 8.9 Consensus size: 53
41574126 GTAAATCTAC
* * ** *
41574136 AAACCAAGGGTATTTCAGTAATTTTGTAAA-CGAATGGTATTTCTA-TAATTTTTAG
1 AAACCGAGGGTATTT-GGTAATTTTACAAATCG-AGGGTATTTC-AGTAA-TTTTAG
* * * ** ** *
41574191 AAAGTCAAGGGTATTTCTGTAATTTTGTAAATC-AGGGGTATTTTGGTAATTTTAC
1 AAA-CCGAGGGTATTT-GGTAATTTTACAAATCGA-GGGTATTTCAGTAATTTTAG
** * * * * *
41574246 AAATTGAGGGTATTTTAGTAATTTCACAAA-CCAGTGGTATTTCGGTAATTTTAC
1 AAACCGAGGGTA-TTTGGTAATTTTACAAATCGAG-GGTATTTCAGTAATTTTAG
* * ** * *
41574300 AAA-CTAGGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTCTATC
1 AAACCGA-GGGTA-TTTGGTAATTTTACAAATCGA-GGGTATTTCAGTAATTTTA-G
** * * ** *
41574355 CTA-CAAGGGTATTTCAGTAA-TTT-CATAATCGAGGGTAAAAT-GGT-ATTTT-G
1 AAACCGAGGGTATTT-GGTAATTTTACA-AATCGAGGGT-ATTTCAGTAATTTTAG
* ** * *** * *
41574405 TAAACTGAGGGTAAAATGGTAATTTTATAAATCGAGGGTAAAAC-GATAATTCTAT
1 -AAACCGAGGGT-ATTTGGTAATTTTACAAATCGAGGGTATTTCAG-TAATTTTAG
* * *
41574460 AAATCGAGGGTATTTTGATAATTTTACAAGTCGAGGGTATTTCAGTAATTTT-G
1 AAACCGAGGGTA-TTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTAG
* ** *
41574513 AAACTGAGGGTATTTCGGTAATTTTACAAATCGAGATTATTTCGGTAATTTTAG
1 AAACCGAGGGTATTT-GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTAG
* * * *
41574567 AAACCGGGGGTACTTTGGTAATTTTACAACT-GGGGGTATTTCAGCAATTT
1 AAACCGAGGGTA-TTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTT
41574617 GGTAAACTAA
Statistics
Matches: 331, Mismatches: 67, Indels: 58
0.73 0.15 0.13
Matches are distributed among these distances:
51 1 0.00
52 22 0.07
53 90 0.27
54 158 0.48
55 24 0.07
56 35 0.11
57 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (53 bp):
AAACCGAGGGTATTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTAG
Found at i:41576893 original size:31 final size:31
Alignment explanation
Indices: 41576850--41576964 Score: 205
Period size: 31 Copynumber: 3.7 Consensus size: 31
41576840 TTAGTCTTGA
*
41576850 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
41576880 CATATCACTGGGCCAAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
41576911 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
41576942 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
41576965 ACTGTAAACG
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 5 0.06
31 76 0.94
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:41577035 original size:42 final size:42
Alignment explanation
Indices: 41576988--41577163 Score: 343
Period size: 42 Copynumber: 4.2 Consensus size: 42
41576978 TGGCCCTTAG
*
41576988 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
41577030 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
41577072 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
41577114 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
41577156 GCCCATTT
1 GCCCATTT
41577164 GGGGAGACTA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 133 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:41577339 original size:25 final size:25
Alignment explanation
Indices: 41577311--41577380 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
41577301 CTCTTTTAAT
41577311 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
41577336 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41577361 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41577381 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 38 0.90
26 4 0.10
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41578208 original size:27 final size:27
Alignment explanation
Indices: 41578177--41578236 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
41578167 TACGGAACAT
*
41578177 AAGGGCA-TATTCGTCATTTTACCATAC
1 AAGGGCATTA-TCGTCACTTTACCATAC
* * *
41578204 AAGGGTATTATGGTCACTTTACCCTAC
1 AAGGGCATTATCGTCACTTTACCATAC
41578231 AAGGGC
1 AAGGGC
41578237 TTTACAGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (27 bp):
AAGGGCATTATCGTCACTTTACCATAC
Found at i:41578386 original size:28 final size:27
Alignment explanation
Indices: 41578311--41578519 Score: 99
Period size: 27 Copynumber: 7.7 Consensus size: 27
41578301 ATCTACAAAC
** *
41578311 CAAGGGTATTTAAGTAATTTT-GTAAAC
1 CAAGGGTATTTCTGTAATTTTAG-AAAT
* *
41578338 CAATGGTA-TTCTATAATTTTTAGAAAGT
1 CAAGGGTATTTCTGTAA-TTTTAGAAA-T
*
41578366 CAAGGGTATTTCTGTAATTTTATAAAT
1 CAAGGGTATTTCTGTAATTTTAGAAAT
* * *
41578393 TAGGGGTATTT-TGGTAATTTTACAAAT
1 CAAGGGTATTTCT-GTAATTTTAGAAAT
** * * *
41578420 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTCTGTAATTTTAGAAAT
* * * *
41578446 CCAGTGGTAATTCGGTAATTTTACAAA-
1 CAAG-GGTATTTCTGTAATTTTAGAAAT
* * *
41578473 CTAGGGGTATTT-TGGTAATTTTACAAAC
1 C-AAGGGTATTTCT-GTAATTTTAGAAAT
*
41578501 CAGGGGTATTT-TGGTAATT
1 CAAGGGTATTTCT-GTAATT
41578520 CTATCCTACA
Statistics
Matches: 149, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
26 8 0.05
27 116 0.78
28 18 0.12
29 7 0.05
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTCTGTAATTTTAGAAAT
Found at i:41578517 original size:81 final size:81
Alignment explanation
Indices: 41578370--41578519 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
41578360 GAAAGTCAAG
* * * * **
41578370 GGTATTTCTGTAATTTTATAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGT
1 GGTAATTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACAGAGGGTATTTCGGT
41578435 AATTTCACAAACCAGT
66 AATTTCACAAACCAGT
*
41578451 GGTAATTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAG-GGGTATTTTGG
1 GGTAATTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAA-CAGAGGGTATTTCGG
41578515 TAATT
65 TAATT
41578520 CTATCCTACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 60 0.98
82 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (81 bp):
GGTAATTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACAGAGGGTATTTCGGT
AATTTCACAAACCAGT
Found at i:41578784 original size:26 final size:27
Alignment explanation
Indices: 41578368--41578787 Score: 188
Period size: 27 Copynumber: 15.7 Consensus size: 27
41578358 TAGAAAGTCA
* * *
41578368 AGGGTATTTCTGTAATTTTATAAA-TT
1 AGGGTATTTCGGTAATTTTACAAACTG
* *
41578394 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTCGGTAATTTTACAAACTG
* *
41578422 AGGGTATTTCGGTAATTTCACAAAC-C
1 AGGGTATTTCGGTAATTTTACAAACTG
*
41578448 AGTGGTAATTCGGTAATTTTACAAACT-
1 AG-GGTATTTCGGTAATTTTACAAACTG
* *
41578475 AGGGGTATTTTGGTAATTTTACAAAC-C
1 A-GGGTATTTCGGTAATTTTACAAACTG
* * **
41578502 AGGGGTATTTTGGTAATTCTATCCTAC--
1 A-GGGTATTTCGGTAATTTTA-CAAACTG
* ** * *
41578529 ATGGGCATTTTAGTAA-TTCACAATCT-
1 A-GGGTATTTCGGTAATTTTACAAACTG
*** * *
41578555 AGGGTAAAACAGTAATTTTACAAGCTG
1 AGGGTATTTCGGTAATTTTACAAACTG
** *
41578582 AGGGTAAAAT-GGTAATCTTT-TAAA-TCG
1 AGGGT-ATTTCGGTAAT-TTTACAAACT-G
*** * *
41578609 AGGGTAAAACGATAATTTTATAAA-TCG
1 AGGGTATTTCGGTAATTTTACAAACT-G
* * *
41578636 AGGGTACTTT-GATAATTTGAC-AAGTCG
1 AGGGTA-TTTCGGTAATTTTACAAACT-G
** *
41578663 AGGGTATTTTAGTAATTTTGCAAACTG
1 AGGGTATTTCGGTAATTTTACAAACTG
*
41578690 AGGGTATTTCGGTAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAACTG
* * * *
41578717 AGGATATTTGGGTAATTTTATAAACCG
1 AGGGTATTTCGGTAATTTTACAAACTG
* *
41578744 GGGGTACTTT-GGTAATTTTAC-AATTG
1 AGGGTA-TTTCGGTAATTTTACAAACTG
* *
41578770 GGGGTATTTCAGTAATTT
1 AGGGTATTTCGGTAATTT
41578788 GGTAAACTAA
Statistics
Matches: 312, Mismatches: 61, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
25 14 0.04
26 42 0.13
27 238 0.76
28 18 0.06
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAACTG
Found at i:41581037 original size:29 final size:29
Alignment explanation
Indices: 41580978--41581035 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
41580968 CAAATAGCCG
* *
41580978 AAGCTAGTTAAATCGTACACTTAATGCCC
1 AAGCTAGTTAAAACGCACACTTAATGCCC
*
41581007 AAGCTAGTTTAAAACGCACACTTAGTGCC
1 AAGCTAG-TTAAAACGCACACTTAATGCC
41581036 AAAACTTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (29 bp):
AAGCTAGTTAAAACGCACACTTAATGCCC
Found at i:41582348 original size:25 final size:25
Alignment explanation
Indices: 41582306--41582541 Score: 238
Period size: 25 Copynumber: 9.4 Consensus size: 25
41582296 GCCATTATTA
* *
41582306 CGATAATACGATCGGTACAAAGCCAT
1 CGATAACA-GATCGGCACAAAGCCAT
* * *
41582332 CGATAACAGATCAGTACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * *
41582357 CAATATCATATCGGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* *
41582382 CGATAACAGATTGGCACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * * *
41582407 CAATATCATATCAGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* *
41582432 CGATAATAGATCGGCACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * *
41582457 CAATATCATATCGGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
*
41582482 CGATAACAGATCGGCACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * * **
41582507 CAATACCATATTAGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
41582532 CGATAACAGA
1 CGATAACAGA
41582542 ATAATTGGCT
Statistics
Matches: 166, Mismatches: 44, Indels: 1
0.79 0.21 0.00
Matches are distributed among these distances:
25 159 0.96
26 7 0.04
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19
Consensus pattern (25 bp):
CGATAACAGATCGGCACAAAGCCAT
Found at i:41582391 original size:50 final size:50
Alignment explanation
Indices: 41582316--41582541 Score: 371
Period size: 50 Copynumber: 4.5 Consensus size: 50
41582306 CGATAATACG
* * *
41582316 ATCGGTACAAAGCCATCGATAACAGATCAGTACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
*
41582366 ATCGGCACAAAGCCATCGATAACAGATTGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
* *
41582416 ATCAGCACAAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
*
41582466 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATACCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
**
41582516 ATTAGCACAAAGCCATCGATAACAGA
1 ATCGGCACAAAGCCATCGATAACAGA
41582542 ATAATTGGCT
Statistics
Matches: 164, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 164 1.00
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19
Consensus pattern (50 bp):
ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
Found at i:41582741 original size:41 final size:41
Alignment explanation
Indices: 41582680--41582803 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 41
41582670 CTTAAAAACC
* * *
41582680 ACCGGTGGAACCACGATCGTCAAGCAACCATGCAATCCTTA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
*
41582721 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
* * *
41582762 ATCGGTGAATCCATGGTCGTCAAGCAACCATGCAATCCTCA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
41582803 A
1 A
41582804 TTTCTTCCTC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (41 bp):
ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
Found at i:41583156 original size:27 final size:27
Alignment explanation
Indices: 41583042--41583295 Score: 176
Period size: 27 Copynumber: 9.4 Consensus size: 27
41583032 TTTCACCCTA
* * * * *
41583042 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTTTCCAAATC
**
41583069 AAGGGTATTTTGGTAATTTTTTAAAGTC
1 AAGGGTATTTTGGTAATTTTCCAAA-TC
* ** *
41583097 AATGGTATTTCT-GTAATTTTGTAAGT-
1 AAGGGTATTT-TGGTAATTTTCCAAATC
* *
41583123 ATGGGGTATTTTTGTAATTTTCCAAATC
1 A-AGGGTATTTTGGTAATTTTCCAAATC
**
41583151 AAGGGTATTTCAGTAATTTTCCAAAT-
1 AAGGGTATTTTGGTAATTTTCCAAATC
* *
41583177 TAGAGGTATTTTGGTAATTTTACAAATC
1 AAG-GGTATTTTGGTAATTTTCCAAATC
* * *
41583205 GAGGGTATTTCGATAA-TTTCACAAATC
1 AAGGGTATTTTGGTAATTTTC-CAAATC
* * **
41583232 AGGGGTATTTTGGTATTTTTAAAAAT-
1 AAGGGTATTTTGGTAATTTTCCAAATC
* * *
41583258 AAGGGGTATTTTGGCAATTTTGCTAATC
1 AA-GGGTATTTTGGTAATTTTCCAAATC
41583286 AAGGGTATTT
1 AAGGGTATTT
41583296 CAATAATTCT
Statistics
Matches: 178, Mismatches: 38, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
26 8 0.04
27 140 0.79
28 29 0.16
29 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTCCAAATC
Found at i:41583185 original size:54 final size:53
Alignment explanation
Indices: 41583071--41583268 Score: 195
Period size: 54 Copynumber: 3.7 Consensus size: 53
41583061 TACAAACCAA
** * ** *
41583071 GGGTATTTTGGTAATTTTTTAAAGTCAATGGTATTTCTGTAATTTT-GTAAGTATG
1 GGGTATTTTGGTAATTTTACAAA-TCAAGGGTATTTC-GTAATTTTCCAAATTA-G
* *
41583126 GGGTATTTTTGTAATTTTCCAAATCAAGGGTATTTCAGTAATTTTCCAAATTAG
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTC-GTAATTTTCCAAATTAG
* * *
41583180 AGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGATAA-TTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCG-TAATTTTC-CAAATTAG
* *
41583234 GGGTATTTTGGTATTTTTAAAAAT-AAGGGGTATTT
1 GGGTATTTTGGTAATTTTACAAATCAA-GGGTATTT
41583269 TGGCAATTTT
Statistics
Matches: 122, Mismatches: 17, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
53 6 0.05
54 92 0.75
55 24 0.20
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.43
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCGTAATTTTCCAAATTAG
Found at i:41583322 original size:27 final size:27
Alignment explanation
Indices: 41583292--41583395 Score: 136
Period size: 27 Copynumber: 3.9 Consensus size: 27
41583282 AATCAAGGGT
41583292 ATTTCAATAATTCTACCCTACAGGGGC
1 ATTTCAATAATTCTACCCTACAGGGGC
* *
41583319 ATTTCAATAATTCTATCCTATAGGGGC
1 ATTTCAATAATTCTACCCTACAGGGGC
* * *
41583346 ATTTTAGTAATTCTACCCTACAGGGGT
1 ATTTCAATAATTCTACCCTACAGGGGC
* * *
41583373 ATTTCAGTAATACTAGCCTACAG
1 ATTTCAATAATTCTACCCTACAG
41583396 ATATGAGATT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (27 bp):
ATTTCAATAATTCTACCCTACAGGGGC
Found at i:41585735 original size:26 final size:26
Alignment explanation
Indices: 41585678--41585762 Score: 113
Period size: 26 Copynumber: 3.3 Consensus size: 26
41585668 AAATCANCCT
41585678 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
*
41585702 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
41585728 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
41585754 AGCCCTTTT
1 AGCCCTTTT
41585763 GCACTTCCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
23 5 0.09
24 7 0.13
25 9 0.17
26 33 0.61
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:41586582 original size:27 final size:28
Alignment explanation
Indices: 41586551--41586646 Score: 94
Period size: 27 Copynumber: 3.6 Consensus size: 28
41586541 TACGGAACAT
*
41586551 AAGGGCATATT-C-GTCATTTTACCATAC
1 AAGGGC-TATTACAGTCACTTTACCATAC
*
41586578 AAGGG-TATTACAGTCACTTTACCCTAC
1 AAGGGCTATTACAGTCACTTTACCATAC
* *
41586605 AAGGGCT-TTACGGTCACTTTACCCTAC
1 AAGGGCTATTACAGTCACTTTACCATAC
* *
41586632 AGGGGCT-TTATAGTC
1 AAGGGCTATTACAGTC
41586647 TTTTTACCTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
25 4 0.07
26 1 0.02
27 54 0.90
28 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (28 bp):
AAGGGCTATTACAGTCACTTTACCATAC
Found at i:41586656 original size:26 final size:27
Alignment explanation
Indices: 41586563--41586646 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
41586553 GGGCATATTC
* *
41586563 GTCATTTTACCATACAAGGG-TATTACA
1 GTCACTTTACCCTACAAGGGCT-TTACA
*
41586590 GTCACTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCCTACAAGGGCTTTACA
* *
41586617 GTCACTTTACCCTACAGGGGCTTTATA
1 GTCACTTTACCCTACAAGGGCTTTACA
41586644 GTC
1 GTC
41586647 TTTTTACCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (27 bp):
GTCACTTTACCCTACAAGGGCTTTACA
Found at i:41586691 original size:27 final size:25
Alignment explanation
Indices: 41586563--41586696 Score: 67
Period size: 27 Copynumber: 5.0 Consensus size: 25
41586553 GGGCATATTC
* **
41586563 GTCATTTTACCATACAAGGGTATTACA
1 GTCA-TTTACCCTACAAGGGT-TTTTA
*
41586590 GTCACTTTACCCTACAAGGG-CTTTA
1 GTCA-TTTACCCTACAAGGGTTTTTA
* *
41586615 CGGTCACTTTACCCTACAGGGGCTTTATA
1 --GTCA-TTTACCCTACAAGGG-TTTTTA
*
41586644 GTCTTTTTA-CCTA-ATAGGGGTATTTTA
1 GTC-ATTTACCCTACA-A-GGGT-TTTTA
41586671 GTCATTTCACCCTACAAGGGTGTTTT
1 GTCATTT-ACCCTACAAGGGT-TTTT
41586697 GGTAAATCTA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
25 3 0.04
26 8 0.10
27 63 0.76
28 5 0.06
29 4 0.05
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (25 bp):
GTCATTTACCCTACAAGGGTTTTTA
Found at i:41586862 original size:53 final size:54
Alignment explanation
Indices: 41586685--41586924 Score: 180
Period size: 53 Copynumber: 4.4 Consensus size: 54
41586675 TTTCACCCTA
* * * * *
41586685 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATCTTGT-TAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAAT-TT-TACAAAC
* *** * * * ** *
41586740 CAATGGTATTTCCATAATTTTTAGAAAGTCAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTTTGGTAA-TTTTACAAA-CCAAGGGTATTT-TAGTAATTTTACAAAC
* * *
41586796 CAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTACAGA-
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAAC
* ** * * **
41586849 CTAGGGTATTTTGGTAATTTTACTGATCAAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAAC
*
41586903 CAAGGGTATTTTAGTAATTTTA
1 CAAGGGTATTTTGGTAATTTTA
41586925 TAAATCGAGG
Statistics
Matches: 143, Mismatches: 36, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
53 44 0.31
54 39 0.27
55 21 0.15
56 24 0.17
57 15 0.10
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAAC
Found at i:41586924 original size:54 final size:54
Alignment explanation
Indices: 41586685--41586964 Score: 215
Period size: 54 Copynumber: 5.1 Consensus size: 54
41586675 TTTCACCCTA
* * * * * * * *
41586685 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATCTTGTTAAAC
1 CAAGGGTATTTTGGTAATTTTACTAATCAAGGGTATTTTAGTAATTTTG-TAAAT
* *** ** *
41586740 CAATGGTATTTCCATAATTTTTAGAAAGTCAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTTTGGTAA-TTTTACTAA-TCAAGGGTATTT-TAGTAATTTTGTAAAT
* * * * ** *
41586796 CAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTACAGA-
1 CAAGGGTATTTTGGTAATTTTACTAATCAAGGGTATTTTAGTAATTTTGTAAAT
* * * *
41586849 CTAGGGTATTTTGGTAATTTTACTGATCAAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACTAATCAAGGGTATTTTAGTAATTTTGTAAAT
* * ***
41586903 CAAGGGTATTTTAGTAATTTTA-TAAATCGAGGGTAAAATAGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACT-AATCAAGGGTATTTTAGTAATTTTGTAAAT
41586957 CAAGGGTA
1 CAAGGGTA
41586965 AAATAGTAAT
Statistics
Matches: 175, Mismatches: 44, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
53 45 0.26
54 70 0.40
55 20 0.11
56 22 0.13
57 18 0.10
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACTAATCAAGGGTATTTTAGTAATTTTGTAAAT
Found at i:41586928 original size:27 final size:27
Alignment explanation
Indices: 41586685--41586991 Score: 192
Period size: 27 Copynumber: 11.3 Consensus size: 27
41586675 TTTCACCCTA
* * * * * *
41586685 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAT
* *
41586712 CAAGGGTATTTCAGTAATCTTGT-TAAAC
1 CAAGGGTATTTTAGTAAT-TT-TATAAAT
* * *
41586740 CAATGGTATTTCCA-TAATTTTTAGAAAGT
1 CAAGGGTATTT-TAGTAA-TTTTATAAA-T
* *
41586769 CAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTTTATAAAT
* * * *
41586796 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAT
* * *
41586823 CAGGGGTATTTTAGTAATTTTACAGA-
1 CAAGGGTATTTTAGTAATTTTATAAAT
* * *
41586849 CTAGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTAGTAATTTTA-TAAAT
* * *
41586876 CAAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAT
41586903 CAAGGGTATTTTAGTAATTTTATAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAT
* *** *
41586930 CGAGGGTAAAATAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAT
*** *
41586957 CAAGGGTAAAATAGTAATTCTATAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAT
*
41586984 CGAGGGTA
1 CAAGGGTA
41586992 AAACGATAAT
Statistics
Matches: 228, Mismatches: 41, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
26 23 0.10
27 158 0.69
28 29 0.13
29 18 0.08
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTATAAAT
Found at i:41586990 original size:81 final size:79
Alignment explanation
Indices: 41586913--41587099 Score: 203
Period size: 81 Copynumber: 2.3 Consensus size: 79
41586903 CAAGGGTATT
* * *
41586913 TTAGTAATTTTATAAATCGAGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAATAGTAATTCT
1 TTAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCT
*
41586978 ATAAATCGAGGGTA
66 ACAAATCGAGGGTA
** * * * * *
41586992 AAACGATAATTCTGTAATTCTAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAGTAATT
1 TTA-G-TAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACAGTAATT
*
41587057 CTACAAATCGGGGGTA
64 CTACAAATCGAGGGTA
* * *
41587073 CGTTGGTAATTTTACAAGTCGAGGGTA
1 --TTAGTAATTTTATAAATCGAGGGTA
41587100 TTTCAATAAT
Statistics
Matches: 84, Mismatches: 20, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
79 1 0.01
80 1 0.01
81 81 0.96
82 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (79 bp):
TTAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCT
ACAAATCGAGGGTA
Found at i:41586992 original size:27 final size:27
Alignment explanation
Indices: 41586914--41587072 Score: 203
Period size: 27 Copynumber: 5.9 Consensus size: 27
41586904 AAGGGTATTT
*
41586914 TAGTAATTTTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* * *
41586941 TAGTAATTTTGTAAATCAAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
41586968 TAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* * * *
41586995 -CGATAATTCTGTAATTCTAGGGTAAAA
1 TAG-TAATTCTATAAATCGAGGGTAAAA
41587022 TAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* * *
41587049 CAGTAATTCTACAAATCGGGGGTA
1 TAGTAATTCTATAAATCGAGGGTA
41587073 CGTTGGTAAT
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 1 0.01
27 112 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (27 bp):
TAGTAATTCTATAAATCGAGGGTAAAA
Found at i:41587083 original size:54 final size:54
Alignment explanation
Indices: 41586889--41587058 Score: 234
Period size: 54 Copynumber: 3.1 Consensus size: 54
41586879 GGGTATTTTG
* * *** * *
41586889 GTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
*
41586943 GTAATTTTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAAC-
1 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
* *
41586996 GATAATTCTGTAATTCTAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
1 G-TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
41587051 GTAATTCT
1 GTAATTCT
41587059 ACAAATCGGG
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.01
54 103 0.98
55 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.34
Consensus pattern (54 bp):
GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
Found at i:41588184 original size:50 final size:50
Alignment explanation
Indices: 41588109--41588383 Score: 285
Period size: 50 Copynumber: 5.6 Consensus size: 50
41588099 GGATGTTACA
*
41588109 GTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATGACAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATGAGAGCTAGT
* *
41588159 GTAAGACCATGACTGGGACATGGCATC-AGCCTCGAGATATAAGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGA-CCTCGAGATATGAGAGCTAGT
* * *
41588209 GTAAGACCATGTCTGGGACATGGCATCGA-CT--TGATAT--GTGTTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATGAGAGCTAGT
* * * * * * * *
41588254 GTAGGACCATGTCTAGGACATGGCATCGGCATCGATAGATGAGAGCCAAT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATGAGAGCTAGT
* * * * * *
41588304 GTAAGACCATGTCTGGGACATGGAATTGGCCTCGATATACGAGAG-TCAAT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATGAGAGCT-AGT
* *
41588354 GTAAGACCATGTTTGGAACATGGCATCGAC
1 GTAAGACCATGTCTGGGACATGGCATCGAC
41588384 TTTGATGTGT
Statistics
Matches: 186, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
45 32 0.17
46 1 0.01
47 5 0.03
48 3 0.02
49 3 0.02
50 141 0.76
51 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATGAGAGCTAGT
Found at i:41588299 original size:95 final size:98
Alignment explanation
Indices: 41588109--41588326 Score: 280
Period size: 95 Copynumber: 2.2 Consensus size: 98
41588099 GGATGTTACA
*
41588109 GTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATGACAGCTAGTGTAAGACCATGACTG
1 GTAAGACCATGTCTGGGACATGGCATCGACCTC-AGATATGA-AGCTAGTGTAAGACCATGACTA
* * * *
41588174 GGACATGGCATCAGCCTCGAGATATAAGAGCTAGT
64 GGACATGGCATCAGCATCGAGAGATAAGAGCCAAT
* * * * *
41588209 GTAAGACCATGTCTGGGACATGGCATCGA-CT-TGATATG-TGTTAGTGTAGGACCATGTCTAGG
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCAGATATGAAGCTAGTGTAAGACCATGACTAGG
* * *
41588271 ACATGGCATCGGCATCGATAGATGAGAGCCAAT
66 ACATGGCATCAGCATCGAGAGATAAGAGCCAAT
41588304 GTAAGACCATGTCTGGGACATGG
1 GTAAGACCATGTCTGGGACATGG
41588327 AATTGGCCTC
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
95 68 0.65
97 6 0.06
99 2 0.02
100 29 0.28
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (98 bp):
GTAAGACCATGTCTGGGACATGGCATCGACCTCAGATATGAAGCTAGTGTAAGACCATGACTAGG
ACATGGCATCAGCATCGAGAGATAAGAGCCAAT
Found at i:41588365 original size:145 final size:146
Alignment explanation
Indices: 41588113--41588394 Score: 370
Period size: 145 Copynumber: 1.9 Consensus size: 146
41588103 GTTACAGTAA
* * * * *
41588113 GACCATGTCTGGGACATGGCATCGACCTCGAGATATGACAGCTAGTGTAAGACCATGACTGGGAC
1 GACCATGTCTAGGACATGGCATCGACATCGAGAGATGACAGCCAATGTAAGACCATGACTGGGAC
* * * *
41588178 ATGGCATCAGCCTCGAGATATAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTG
66 ATGGAATCAGCCTCGAGATACAAGAGCTAATGTAAGACCATGTCTGGAACATGGCATCGACTTTG
41588242 ATATGTGTTAGTGTAG
131 ATATGTGTTAGTGTAG
* * * *
41588258 GACCATGTCTAGGACATGGCATCGGCATCGATAGATGAGAGCCAATGTAAGACCATGTCTGGGAC
1 GACCATGTCTAGGACATGGCATCGACATCGAGAGATGACAGCCAATGTAAGACCATGACTGGGAC
** * * *
41588323 ATGGAATTGGCCTCGATATACGAGAG-TCAATGTAAGACCATGTTTGGAACATGGCATCGACTTT
66 ATGGAATCAGCCTCGAGATACAAGAGCT-AATGTAAGACCATGTCTGGAACATGGCATCGACTTT
*
41588387 GATGTGTG
130 GATATGTG
41588395 AGCCAATGTA
Statistics
Matches: 116, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
144 1 0.01
145 106 0.91
146 9 0.08
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (146 bp):
GACCATGTCTAGGACATGGCATCGACATCGAGAGATGACAGCCAATGTAAGACCATGACTGGGAC
ATGGAATCAGCCTCGAGATACAAGAGCTAATGTAAGACCATGTCTGGAACATGGCATCGACTTTG
ATATGTGTTAGTGTAG
Found at i:41590537 original size:22 final size:22
Alignment explanation
Indices: 41590509--41590550 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
41590499 CTTATTGAGT
41590509 CTAGTTTTATTAGAAACAAATA
1 CTAGTTTTATTAGAAACAAATA
41590531 CTAGTTTTATTAGAAACAAA
1 CTAGTTTTATTAGAAACAAA
41590551 CGACATAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (22 bp):
CTAGTTTTATTAGAAACAAATA
Found at i:41591640 original size:28 final size:28
Alignment explanation
Indices: 41591580--41591643 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
41591570 TGGGAAGTAG
* *
41591580 TTGGGCCTGATGCGCCATATGAATGTGA
1 TTGGGCCTGATGCGCCATATGAACGAGA
* * *
41591608 CTGGGCCTGATGGGCCATGTGAACGAGA
1 TTGGGCCTGATGCGCCATATGAACGAGA
41591636 TTGGGCCT
1 TTGGGCCT
41591644 AAAGGGGCCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.19, C:0.20, G:0.36, T:0.25
Consensus pattern (28 bp):
TTGGGCCTGATGCGCCATATGAACGAGA
Found at i:41591994 original size:27 final size:27
Alignment explanation
Indices: 41591964--41592299 Score: 288
Period size: 27 Copynumber: 12.5 Consensus size: 27
41591954 TAAGAGAAAG
*
41591964 TACCGAAATACCC-CTGGTTTGTAAAAT
1 TACCGAAATACCCTC-GATTTGTAAAAT
* * *
41591991 TACCGAAGTACCCCCTG-CTTGTAAAAT
1 TACCGAAATACCCTC-GATTTGTAAAAT
* * *
41592018 TATCGAAATATCCTAGATTTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* *
41592045 TACTGAAACACCCTCGA-TTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
** * *
41592071 TATTGGAATGCCCTCGATTTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
*
41592098 TACCGAAATACCCTCGATTTGTGAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* *
41592125 TACCGAAATACCCTCAATTTTTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* *
41592152 TACTGAAACACCCTCGATTTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* *
41592179 TACC-AAACTACTCTCAATTTGTAAAAT
1 TACCGAAA-TACCCTCGATTTGTAAAAT
** **
41592206 TACTAAAATACCCTTAATTTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
** * *
41592233 TATTGAAATACCCTTG-TAGTGTAAAAT
1 TACCGAAATACCCTCGAT-TTGTAAAAT
* * *
41592260 TACCAAAATACCCT-TATAGTGTAAAAT
1 TACCGAAATACCCTCGAT-TTGTAAAAT
* *
41592287 GACCGACATACCC
1 TACCGAAATACCC
41592300 CTGTAGGGTA
Statistics
Matches: 255, Mismatches: 47, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
26 27 0.11
27 222 0.87
28 6 0.02
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (27 bp):
TACCGAAATACCCTCGATTTGTAAAAT
Found at i:41592167 original size:107 final size:108
Alignment explanation
Indices: 41591981--41592180 Score: 298
Period size: 107 Copynumber: 1.9 Consensus size: 108
41591971 ATACCCCTGG
* * *
41591981 TTTGTAAAATTACCGAAGTACCCCCTGCTTGTAAAATTATCGAAATATCCTAGATTTGTAAAATT
1 TTTGTAAAATTACCGAAATACCCCCTGCTTGTAAAATTACCGAAATACCCTAGATTTGTAAAATT
41592046 ACTGAAACACCCTCGA-TTGTAAAATTATTGGAATGCCCTCGA
66 ACTGAAACACCCTCGATTTGTAAAATTATTGGAATGCCCTCGA
* * * *
41592088 TTTGTAAAATTACCGAAATACCCTC-GATTTGTGAAATTACCGAAATACCCTCA-ATTTTTAAAA
1 TTTGTAAAATTACCGAAATACCCCCTG-CTTGTAAAATTACCGAAATACCCT-AGATTTGTAAAA
41592151 TTACTGAAACACCCTCGATTTGTAAAATTA
64 TTACTGAAACACCCTCGATTTGTAAAATTA
41592181 CCAAACTACT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
106 1 0.01
107 70 0.84
108 12 0.14
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (108 bp):
TTTGTAAAATTACCGAAATACCCCCTGCTTGTAAAATTACCGAAATACCCTAGATTTGTAAAATT
ACTGAAACACCCTCGATTTGTAAAATTATTGGAATGCCCTCGA
Found at i:41592180 original size:81 final size:81
Alignment explanation
Indices: 41592009--41592273 Score: 320
Period size: 81 Copynumber: 3.3 Consensus size: 81
41591999 TACCCCCTGC
* * * * *
41592009 TTGTAAAATTATCGAAATATCCTAGATTTGTAAAATTACTGAAACACCCTCGA-TTGTAAAATTA
1 TTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGAAATACCCTCAATTTGTAAAATTA
* *
41592073 TTGGAATGCCCTCGAT
66 TTGAAATACCCTCGAT
* * *
41592089 TTGTAAAATTACCGAAATACCCTCGATTTGTGAAATTACCGAAATACCCTCAATTTTTAAAATTA
1 TTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGAAATACCCTCAATTTGTAAAATTA
* *
41592154 CTGAAACACCCTCGAT
66 TTGAAATACCCTCGAT
* * * *
41592170 TTGTAAAATTACC-AAACTACTCTCAATTTGTAAAATTACTAAAATACCCTTAATTTGTAAAATT
1 TTGTAAAATTACCGAAA-TACCCTCGATTTGTAAAATTACTGAAATACCCTCAATTTGTAAAATT
*
41592234 ATTGAAATACCCTTG-T
65 ATTGAAATACCCTCGAT
* *
41592250 AGTGTAAAATTACCAAAATACCCT
1 -TTGTAAAATTACCGAAATACCCT
41592274 TATAGTGTAA
Statistics
Matches: 157, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
80 50 0.32
81 104 0.66
82 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (81 bp):
TTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGAAATACCCTCAATTTGTAAAATTA
TTGAAATACCCTCGAT
Found at i:41592283 original size:54 final size:54
Alignment explanation
Indices: 41592198--41592313 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
41592188 ACTCTCAATT
* * * ** *
41592198 TGTAAAATTACTAAAATACCCTTAATTTGTAAAATTATTGAAATACCCTTGTAG
1 TGTAAAATTACCAAAATACCCTTAATGTGTAAAATGACCGAAATACCCCTGTAG
*
41592252 TGTAAAATTACCAAAATACCCTT-ATAGTGTAAAATGACCGACATACCCCTGTAG
1 TGTAAAATTACCAAAATACCCTTAAT-GTGTAAAATGACCGAAATACCCCTGTAG
*
41592306 GGTAAAAT
1 TGTAAAAT
41592314 AATTGTTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 2 0.04
54 51 0.96
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (54 bp):
TGTAAAATTACCAAAATACCCTTAATGTGTAAAATGACCGAAATACCCCTGTAG
Found at i:41592310 original size:27 final size:27
Alignment explanation
Indices: 41592238--41592313 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
41592228 AAAATTATTG
*
41592238 AAATACCCTTGTAGTGTAAAATTACCA
1 AAATACCCTTGTAGTGTAAAATGACCA
* *
41592265 AAATACCCTTATAGTGTAAAATGACCG
1 AAATACCCTTGTAGTGTAAAATGACCA
* * *
41592292 ACATACCCCTGTAGGGTAAAAT
1 AAATACCCTTGTAGTGTAAAAT
41592314 AATTGTTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (27 bp):
AAATACCCTTGTAGTGTAAAATGACCA
Found at i:41592885 original size:27 final size:26
Alignment explanation
Indices: 41592829--41592886 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
41592819 AGGCTAAGAT
* * *
41592829 GGGCTAGACCCAATTGATTCTGTTAT
1 GGGCTAGACCCAAATGATTCTGTAAC
41592855 GGGCTATGACCCAAATGATAT-TGTAAC
1 GGGCTA-GACCCAAATGAT-TCTGTAAC
41592882 GGGCT
1 GGGCT
41592887 TTGGCCCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.22
27 20 0.74
28 1 0.04
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (26 bp):
GGGCTAGACCCAAATGATTCTGTAAC
Found at i:41595260 original size:28 final size:28
Alignment explanation
Indices: 41595228--41595293 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
41595218 TGGGAAGTAG
* *
41595228 TTGGGCCTAATGGGCCATATGAATGTGA
1 TTGGGCCTAATGGGCCATATGAACGAGA
*
41595256 TTGGGCCTAATGGGCCATGTGAACGAGA
1 TTGGGCCTAATGGGCCATATGAACGAGA
41595284 TTGGGCCTAA
1 TTGGGCCTAA
41595294 AGGGGCCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAACGAGA
Found at i:41595649 original size:26 final size:27
Alignment explanation
Indices: 41595608--41595780 Score: 201
Period size: 26 Copynumber: 6.5 Consensus size: 27
41595598 TAATAAAGAG
*
41595608 AAATTACCGAAATACCCTC-AGTTTGTA
1 AAATTACTGAAATACCCTCGA-TTTGTA
* * * *
41595635 AAA-TATTGAAGTACCCTTGGTTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
41595661 AAATTACTGAAATACCC-CGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
41595687 AAATTACTGAAAAACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
41595714 AAATTACTGAAACACCCTCGA-TTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
41595740 AAATTACTAAAATACACTCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
41595767 AAATTACCGAAATA
1 AAATTACTGAAATA
41595781 GAAACACCAC
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 64 0.52
27 59 0.48
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:41595704 original size:53 final size:54
Alignment explanation
Indices: 41595608--41595780 Score: 194
Period size: 53 Copynumber: 3.3 Consensus size: 54
41595598 TAATAAAGAG
* ** * *
41595608 AAATTACCGAAATACCCTC-AGTTTGTAAAA-TATTGAAGTACCCTTGGTTTGTA
1 AAATTACCGAAATACCCTCGA-TTTGTAAAATTACTGAAAAACCCTCGATTTGTA
*
41595661 AAATTACTGAAATACCC-CGATTTGTAAAATTACTGAAAAACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACTGAAAAACCCTCGATTTGTA
* * * * *
41595714 AAATTACTGAAACACCCTCGA-TTGTGAAATTACT-AAAATACACTCAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACTGAAAA-ACCCTCGATTTGTA
41595767 AAATTACCGAAATA
1 AAATTACCGAAATA
41595781 GAAACACCAC
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
52 14 0.13
53 87 0.84
54 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (54 bp):
AAATTACCGAAATACCCTCGATTTGTAAAATTACTGAAAAACCCTCGATTTGTA
Found at i:41595826 original size:27 final size:27
Alignment explanation
Indices: 41595796--41595857 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
41595786 ACCACCGATT
41595796 TGTAAAATTATCAAAATACCCTTGTAA
1 TGTAAAATTATCAAAATACCCTTGTAA
* *
41595823 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTATCAAAATACCCTTGTAA
41595850 TGTAAAAT
1 TGTAAAAT
41595858 GACCGACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (27 bp):
TGTAAAATTATCAAAATACCCTTGTAA
Found at i:41595868 original size:27 final size:27
Alignment explanation
Indices: 41595809--41595884 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
41595799 AAAATTATCA
* * *
41595809 AAATACCCTTGTAATGTAAAATTATCG
1 AAATACCCTTGTAGTGTAAAATGACCG
41595836 AAATACCCTTGTAGTGTAAAATGACCG
1 AAATACCCTTGTAGTGTAAAATGACCG
* * *
41595863 ACATACCCCTGTAGGGTAAAAT
1 AAATACCCTTGTAGTGTAAAAT
41595885 AACTATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (27 bp):
AAATACCCTTGTAGTGTAAAATGACCG
Found at i:41601579 original size:46 final size:46
Alignment explanation
Indices: 41601492--41601579 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
41601482 GCTTAGTATT
* * *
41601492 CCTATACTCTCGAGTCCGCAACATATGTAGGAGGTCGGAACCAATA
1 CCTATACTCTCAAGTCCGCAACATATGTAGGAGCTCAGAACCAATA
* * * *
41601538 CCTATATTCTCAAGTTCGCAACATATGTTGGAGCTTAGAACC
1 CCTATACTCTCAAGTCCGCAACATATGTAGGAGCTCAGAACC
41601580 TATTCCTGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (46 bp):
CCTATACTCTCAAGTCCGCAACATATGTAGGAGCTCAGAACCAATA
Found at i:41604652 original size:42 final size:43
Alignment explanation
Indices: 41604592--41604696 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 43
41604582 ATGATTTACG
*
41604592 TGTAAGACCATGTTTGGGAC-ATCGGCATCG-TATTTGATTTGA
1 TGTAAGACCATGTCTGGGACAAT-GGCATCGATATTTGATTTGA
* **
41604634 TGTAAGATCC-TGTCTGGGACAATGGTATCGATATTTGATTACA
1 TGTAAGA-CCATGTCTGGGACAATGGCATCGATATTTGATTTGA
* * *
41604677 TGCAAAACCACGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
41604697 GTTGGCATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
42 24 0.46
43 28 0.54
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAATGGCATCGATATTTGATTTGA
Found at i:41617330 original size:10 final size:10
Alignment explanation
Indices: 41617314--41617371 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
41617304 CAACTCCGAC
41617314 CAGCTCAATT
1 CAGCTCAATT
* *
41617324 GAGCTCATTT
1 CAGCTCAATT
41617334 CAGCTCAA-T
1 CAGCTCAATT
41617343 CGAGCTCAATT
1 C-AGCTCAATT
*
41617354 TAGCTACAATT
1 CAGCT-CAATT
41617365 CAGCTCA
1 CAGCTCA
41617372 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:41617337 original size:20 final size:20
Alignment explanation
Indices: 41617314--41617374 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41617304 CAACTCCGAC
41617314 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
41617334 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
41617355 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
41617375 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:41628978 original size:41 final size:41
Alignment explanation
Indices: 41628921--41629004 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
41628911 GTATAGCTTA
41628921 TAAGCTTGAATTTGGTTGATAATAATATGGTATGAATGATG
1 TAAGCTTGAATTTGGTTGATAATAATATGGTATGAATGATG
41628962 TAAGCTTGAATTTGGTTGATAATAATATGGTATGAATGATG
1 TAAGCTTGAATTTGGTTGATAATAATATGGTATGAATGATG
41629003 TA
1 TA
41629005 TGATTTGGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (41 bp):
TAAGCTTGAATTTGGTTGATAATAATATGGTATGAATGATG
Found at i:41638988 original size:18 final size:18
Alignment explanation
Indices: 41638946--41638988 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
41638936 GCCCATTCCG
*
41638946 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
41638964 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
41638982 AAGTATG
1 AAGTATG
41638989 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:41639510 original size:27 final size:28
Alignment explanation
Indices: 41639426--41639523 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
41639416 CATGAGATTG
* * *
41639426 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
41639455 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
41639483 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41639510 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
41639524 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41639537 original size:29 final size:27
Alignment explanation
Indices: 41639454--41639537 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
41639444 TAAATTGTTC
* *
41639454 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
41639482 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
41639509 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
41639538 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:41644615 original size:15 final size:16
Alignment explanation
Indices: 41644595--41644632 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
41644585 TATTTTCTTC
41644595 TGGATTTCCT-TATGT
1 TGGATTTCCTATATGT
*
41644610 TGGATTT-CTATATTT
1 TGGATTTCCTATATGT
41644625 TGGATTTC
1 TGGATTTC
41644633 TCCGTTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (16 bp):
TGGATTTCCTATATGT
Found at i:41646719 original size:16 final size:16
Alignment explanation
Indices: 41646698--41646728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41646688 AGTTTAGGGG
41646698 CAAAAATATAATTTTT
1 CAAAAATATAATTTTT
*
41646714 CAAAAATATGATTTT
1 CAAAAATATAATTTT
41646729 GAGTCGATTT
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:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
CAAAAATATAATTTTT
Found at i:41647587 original size:608 final size:608
Alignment explanation
Indices: 41646433--41648259 Score: 3600
Period size: 608 Copynumber: 3.0 Consensus size: 608
41646423 ACCGATGTGT
*
41646433 GACATGCATGCATTTTGATGTCTAATGGTAGAAAATGAGTGTTGGGTGTTAAATAAACAACTTTT
1 GACATGCATGCATTTTGATATCTAATGGTAGAAAATGAGTGTTGGGTGTTAAATAAACAACTTTT
41646498 ACTAAGCGATTTTCGACGAAAACGTCCGAAAGGACTGTTTTGTAAAAGTTATAAAAATGGTATAA
66 ACTAAGCGATTTTCGACGAAAACGTCCGAAAGGACTGTTTTGTAAAAGTTATAAAAATGGTATAA
41646563 AAGCGTGTAATGATGAGAATTGTATTTTTCTATATTTATGAAAATGGTTCGGCTAAGCTTATAGA
131 AAGCGTGTAATGATGAGAATTGTATTTTTCTATATTTATGAAAATGGTTCGGCTAAGCTTATAGA
41646628 ATGGGAAAATTGAATAAAAATCATTTTACGAGCCTAAGGGCAAAAGTGTAATTTCAACAAAGTTT
196 ATGGGAAAATTGAATAAAAATCATTTTACGAGCCTAAGGGCAAAAGTGTAATTTCAACAAAGTTT
41646693 AGGGGCAAAAATATAATTTTTCAAAAATATGATTTTGAGTCGATTTGAATAATTTGAGTCCTAAA
261 AGGGGCAAAAATATAATTTTTCAAAAATATGATTTTGAGTCGATTTGAATAATTTGAGTCCTAAA
41646758 TAGGCTATCTTTGAAATAATAGATCAAGGAAATCGAGATTTGGGCTTAAATCTGGAAAATACAAG
326 TAGGCTATCTTTGAAATAATAGATCAAGGAAATCGAGATTTGGGCTTAAATCTGGAAAATACAAG
41646823 TTTTGGACTAAAATGGTAATTTTACCGTTTCCATATTCGAGGTAAGTTCGCGTGATTTAATAAGC
391 TTTTGGACTAAAATGGTAATTTTACCGTTTCCATATTCGAGGTAAGTTCGCGTGATTTAATAAGC
41646888 ATATTATTCATGTTATTATTGTTATGCATGAAATATATCTTGCTATGATTGTATTGAATTTGATG
456 ATATTATTCATGTTATTATTGTTATGCATGAAATATATCTTGCTATGATTGTATTGAATTTGATG
41646953 TTAATGGACATTTAATGGAAATTGACATTTTAAATGAAATGAATAAGTTTGTATGAAAACTAGGT
521 TTAATGGACATTTAATGGAAATTGACATTTTAAATGAAATGAATAAGTTTGTATGAAAACTAGGT
41647018 GATACGTTATTTTTGGTTGTATG
586 GATACGTTATTTTTGGTTGTATG
41647041 GACATGCATGCATTTTGATATCTAATGGTAGAAAATGAGTGTTGGGTGTTAAATAAACAACTTTT
1 GACATGCATGCATTTTGATATCTAATGGTAGAAAATGAGTGTTGGGTGTTAAATAAACAACTTTT
41647106 ACTAAGCGATTTTCGACGAAAACGTCCGAAAGGACTGTTTTGTAAAAGTTATAAAAATGGTATAA
66 ACTAAGCGATTTTCGACGAAAACGTCCGAAAGGACTGTTTTGTAAAAGTTATAAAAATGGTATAA
41647171 AAGCGTGTAATGATGAGAATTGTATTTTTCTATATTTATGAAAATGGTTCGGCTAAGCTTATAGA
131 AAGCGTGTAATGATGAGAATTGTATTTTTCTATATTTATGAAAATGGTTCGGCTAAGCTTATAGA
41647236 ATGGGAAAATTGAATAAAAATCATTTTACGAGCCTAAGGGCAAAAGTGTAATTTCAACAAAGTTT
196 ATGGGAAAATTGAATAAAAATCATTTTACGAGCCTAAGGGCAAAAGTGTAATTTCAACAAAGTTT
* * *
41647301 AAGGGCAAAACTATAATTTTTCAAAAATATGATTTTGAGTCGGTTTGAATAATTTGAGTCCTAAA
261 AGGGGCAAAAATATAATTTTTCAAAAATATGATTTTGAGTCGATTTGAATAATTTGAGTCCTAAA
41647366 TAGGCTATCTTTGAAATAATAGATCAAGGAAATCGAGATTTGGGCTTAAATCTGGAAAATACAAG
326 TAGGCTATCTTTGAAATAATAGATCAAGGAAATCGAGATTTGGGCTTAAATCTGGAAAATACAAG
41647431 TTTTGGACTAAAATGGTAATTTTACCGTTTCCATATTCGAGGTAAGTTCGCGTGATTTAATAAGC
391 TTTTGGACTAAAATGGTAATTTTACCGTTTCCATATTCGAGGTAAGTTCGCGTGATTTAATAAGC
41647496 ATATTATTCATGTTATTATTGTTATGCATGAAATATATCTTGCTATGATTGTATTGAATTTGATG
456 ATATTATTCATGTTATTATTGTTATGCATGAAATATATCTTGCTATGATTGTATTGAATTTGATG
41647561 TTAATGGACATTTAATGGAAATTGACATTTTAAATGAAATGAATAAGTTTGTATGAAAACTAGGT
521 TTAATGGACATTTAATGGAAATTGACATTTTAAATGAAATGAATAAGTTTGTATGAAAACTAGGT
41647626 GATACGTTATTTTTGGTTGTATG
586 GATACGTTATTTTTGGTTGTATG
41647649 GACATGCATGCATTTTGATATCTAATGGTAGAAAATGAGTGTTGGGTGTTAAATAAACAACTTTT
1 GACATGCATGCATTTTGATATCTAATGGTAGAAAATGAGTGTTGGGTGTTAAATAAACAACTTTT
41647714 ACTAAGCGATTTTCGACGAAAACGTCCGAAAGGACTGTTTTGTAAAAGTTATAAAAATGGTATAA
66 ACTAAGCGATTTTCGACGAAAACGTCCGAAAGGACTGTTTTGTAAAAGTTATAAAAATGGTATAA
41647779 AAGCGTGTAATGATGAGAATTGTATTTTTCTATATTTATGAAAATGGTTCGGCTAAGCTTATAGA
131 AAGCGTGTAATGATGAGAATTGTATTTTTCTATATTTATGAAAATGGTTCGGCTAAGCTTATAGA
*
41647844 ATGGGAAAATTGAATAAAAATCATTTTCCGAGCCTAAGGGCAAAAGTGTAATTTCAACAAAGTTT
196 ATGGGAAAATTGAATAAAAATCATTTTACGAGCCTAAGGGCAAAAGTGTAATTTCAACAAAGTTT
41647909 AGGGGCAAAAATATAATTTTTCAAAAATATGATTTTGAGTCGATTTGAATAATTTGAGTCCTAAA
261 AGGGGCAAAAATATAATTTTTCAAAAATATGATTTTGAGTCGATTTGAATAATTTGAGTCCTAAA
41647974 TAGGCTATCTTTGAAATAATAGATCAAGGAAATCGAGATTTGGGCTTAAATCTGGAAAATACAAG
326 TAGGCTATCTTTGAAATAATAGATCAAGGAAATCGAGATTTGGGCTTAAATCTGGAAAATACAAG
41648039 TTTTGGACTAAAATGGTAATTTTACCGTTTCCATATTCGAGGTAAGTTCGCGTGATTTAATAAGC
391 TTTTGGACTAAAATGGTAATTTTACCGTTTCCATATTCGAGGTAAGTTCGCGTGATTTAATAAGC
41648104 ATATTATTCATGTTATTATTGTTATGCATGAAATATATCTTGCTATGATTGTATTGAATTTGATG
456 ATATTATTCATGTTATTATTGTTATGCATGAAATATATCTTGCTATGATTGTATTGAATTTGATG
41648169 TTAATGGACATTTAATGGAAATTGACATTTTAAATGAAATGAATAAGTTTGTATGAAAACTAGGT
521 TTAATGGACATTTAATGGAAATTGACATTTTAAATGAAATGAATAAGTTTGTATGAAAACTAGGT
*
41648234 GATATGTTATTTTTGGTTGTATG
586 GATACGTTATTTTTGGTTGTATG
41648257 GAC
1 GAC
41648260 TAATGCCCAA
Statistics
Matches: 1210, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
608 1210 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (608 bp):
GACATGCATGCATTTTGATATCTAATGGTAGAAAATGAGTGTTGGGTGTTAAATAAACAACTTTT
ACTAAGCGATTTTCGACGAAAACGTCCGAAAGGACTGTTTTGTAAAAGTTATAAAAATGGTATAA
AAGCGTGTAATGATGAGAATTGTATTTTTCTATATTTATGAAAATGGTTCGGCTAAGCTTATAGA
ATGGGAAAATTGAATAAAAATCATTTTACGAGCCTAAGGGCAAAAGTGTAATTTCAACAAAGTTT
AGGGGCAAAAATATAATTTTTCAAAAATATGATTTTGAGTCGATTTGAATAATTTGAGTCCTAAA
TAGGCTATCTTTGAAATAATAGATCAAGGAAATCGAGATTTGGGCTTAAATCTGGAAAATACAAG
TTTTGGACTAAAATGGTAATTTTACCGTTTCCATATTCGAGGTAAGTTCGCGTGATTTAATAAGC
ATATTATTCATGTTATTATTGTTATGCATGAAATATATCTTGCTATGATTGTATTGAATTTGATG
TTAATGGACATTTAATGGAAATTGACATTTTAAATGAAATGAATAAGTTTGTATGAAAACTAGGT
GATACGTTATTTTTGGTTGTATG
Found at i:41647935 original size:16 final size:16
Alignment explanation
Indices: 41647914--41647944 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41647904 AGTTTAGGGG
41647914 CAAAAATATAATTTTT
1 CAAAAATATAATTTTT
*
41647930 CAAAAATATGATTTT
1 CAAAAATATAATTTT
41647945 GAGTCGATTT
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:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
CAAAAATATAATTTTT
Found at i:41653477 original size:11 final size:11
Alignment explanation
Indices: 41653461--41653485 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41653451 TATCATGGAC
41653461 CATAAAATAAT
1 CATAAAATAAT
41653472 CATAAAATAAT
1 CATAAAATAAT
41653483 CAT
1 CAT
41653486 TTCTATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (11 bp):
CATAAAATAAT
Found at i:41654551 original size:22 final size:24
Alignment explanation
Indices: 41654523--41654566 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41654513 ATTTTGTTCA
41654523 ACTTTAAATT-TTAT-TCAAAAAC
1 ACTTTAAATTGTTATATCAAAAAC
*
41654545 ACTTTAATTTGTTATATCAAAA
1 ACTTTAAATTGTTATATCAAAA
41654567 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAAATTGTTATATCAAAAAC
Found at i:41656804 original size:26 final size:27
Alignment explanation
Indices: 41656775--41656850 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 27
41656765 TCAATTTAAC
* *
41656775 CCTAGGGGTATTTTAGTAATTTTGC-A
1 CCTAGGGGTATTATAGTAATTTTCCAA
* *
41656801 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATTATAGTAATTTTCCA-A
*
41656829 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATTATAGTAATTT
41656851 AGCTATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 21 0.51
28 20 0.49
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (27 bp):
CCTAGGGGTATTATAGTAATTTTCCAA
Found at i:41658330 original size:26 final size:26
Alignment explanation
Indices: 41658299--41658432 Score: 225
Period size: 26 Copynumber: 5.2 Consensus size: 26
41658289 TGAAATGCCC
41658299 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
41658325 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
41658351 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
41658377 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
41658403 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
41658429 ATCA
1 ATCA
41658433 ATTTGTACCA
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
25 3 0.03
26 99 0.97
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:41665208 original size:16 final size:17
Alignment explanation
Indices: 41665187--41665218 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41665177 ACTATGGTAT
41665187 ATGAAATAT-TGATATA
1 ATGAAATATATGATATA
41665203 ATGAAATATATGATAT
1 ATGAAATATATGATAT
41665219 GTGTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
ATGAAATATATGATATA
Found at i:41676441 original size:75 final size:75
Alignment explanation
Indices: 41676351--41676500 Score: 273
Period size: 75 Copynumber: 2.0 Consensus size: 75
41676341 CATGGGATTG
*
41676351 GGGTATTGATGGAGGAAGTATTGAAAGCGGTTCATCCATGTACTGGAGGCTTTGCCTCAACTTAC
1 GGGTATTGATGGAGGAAGTATTGAAAGCGGTTCATCCACGTACTGGAGGCTTTGCCTCAACTTAC
*
41676416 TGATATTTGA
66 TGACATTTGA
*
41676426 GGGTATTGATGGAGGAAGTATTGAAAGTGGTTCATCCACGTACTGGAGGCTTTGCCTCAACTTAC
1 GGGTATTGATGGAGGAAGTATTGAAAGCGGTTCATCCACGTACTGGAGGCTTTGCCTCAACTTAC
41676491 TGACATTTGA
66 TGACATTTGA
41676501 ACAGCGTTGC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (75 bp):
GGGTATTGATGGAGGAAGTATTGAAAGCGGTTCATCCACGTACTGGAGGCTTTGCCTCAACTTAC
TGACATTTGA
Found at i:41682087 original size:26 final size:25
Alignment explanation
Indices: 41682058--41682148 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 25
41682048 GCTATGATGG
* *
41682058 GTAAGCTCCTTTTGAGCT-GATGAACA
1 GTAAGCTCCTATCGAGCTGGA--AACA
41682084 GTAAGCT-CTATCGAGCTGGAAACA
1 GTAAGCTCCTATCGAGCTGGAAACA
*
41682108 GTAAGCT-CTGA-CGAGCT-GAGAATA
1 GTAAGCTCCT-ATCGAGCTGGA-AACA
*
41682132 GTAAGCTCTTA-CGAGCT
1 GTAAGCTCCTATCGAGCT
41682149 AATAAATCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.04
24 36 0.63
25 10 0.18
26 9 0.16
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (25 bp):
GTAAGCTCCTATCGAGCTGGAAACA
Found at i:41682111 original size:24 final size:24
Alignment explanation
Indices: 41682071--41682148 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
41682061 AGCTCCTTTT
41682071 GAGCTGATGAACAGTAAGCTCTATC
1 GAGCTGA-GAACAGTAAGCTCTATC
41682096 GAGCTG-GAAACAGTAAGCTCTGA-C
1 GAGCTGAG-AACAGTAAGCTCT-ATC
*
41682120 GAGCTGAGAATAGTAAGCTCT-TAC
1 GAGCTGAGAACAGTAAGCTCTAT-C
41682144 GAGCT
1 GAGCT
41682149 AATAAATCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
23 1 0.02
24 38 0.81
25 8 0.17
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (24 bp):
GAGCTGAGAACAGTAAGCTCTATC
Found at i:41685276 original size:32 final size:31
Alignment explanation
Indices: 41685240--41685311 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
41685230 TACTCAATTG
*
41685240 AATTTCCGTGCATACCTGTACCATATTGTTCC
1 AATTTCCGTGCATA-CTGTACCATATTGTACC
*
41685272 AATTTCCATGCATACTGTACCATATTGTACC
1 AATTTCCGTGCATACTGTACCATATTGTACC
41685303 AATTTCCGT
1 AATTTCCGT
41685312 AGATACCGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (31 bp):
AATTTCCGTGCATACTGTACCATATTGTACC
Found at i:41685457 original size:56 final size:56
Alignment explanation
Indices: 41685380--41685541 Score: 190
Period size: 56 Copynumber: 2.9 Consensus size: 56
41685370 TGAATATTCA
* *
41685380 ATGTATCGCACACT-AGATGCCATACCCGATACCTT-GCACACTAAGTGTCATTCTGG
1 ATGTTTCGCACACTAAG-TGCCAT-CCCGATACCTTCGCACACTAAGTGCCATTCTGG
*
41685436 ATGTTTCGCACACTAAGTGCCATCCTCGTTA-CTTCGCACACTAAGTGCCATTCTGG
1 ATGTTTCGCACACTAAGTGCCATCC-CGATACCTTCGCACACTAAGTGCCATTCTGG
* **
41685492 ATGTATT-GCACATTAAGTGCCATCCCCGATA-CTTCGCACGTTAAGTGCCA
1 ATGT-TTCGCACACTAAGTGCCAT-CCCGATACCTTCGCACACTAAGTGCCA
41685542 CATATAATTA
Statistics
Matches: 94, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
55 5 0.05
56 83 0.88
57 6 0.06
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (56 bp):
ATGTTTCGCACACTAAGTGCCATCCCGATACCTTCGCACACTAAGTGCCATTCTGG
Found at i:41685530 original size:28 final size:28
Alignment explanation
Indices: 41685385--41685541 Score: 126
Period size: 28 Copynumber: 5.6 Consensus size: 28
41685375 ATTCAATGTA
41685385 TCGCACACT-AGATGCCATACC-CGATACCT
1 TCGCACACTAAG-TGCCAT-CCTCGATA-CT
* * * **
41685414 T-GCACACTAAGTGTCATTCTGGATGTT
1 TCGCACACTAAGTGCCATCCTCGATACT
*
41685441 TCGCACACTAAGTGCCATCCTCGTTACT
1 TCGCACACTAAGTGCCATCCTCGATACT
* *
41685469 TCGCACACTAAGTGCCATTCTGGATGTA-T
1 TCGCACACTAAGTGCCATCCTCGA--TACT
* *
41685498 T-GCACATTAAGTGCCATCCCCGATACT
1 TCGCACACTAAGTGCCATCCTCGATACT
**
41685525 TCGCACGTTAAGTGCCA
1 TCGCACACTAAGTGCCA
41685542 CATATAATTA
Statistics
Matches: 102, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
26 2 0.02
27 5 0.05
28 88 0.86
29 5 0.05
30 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (28 bp):
TCGCACACTAAGTGCCATCCTCGATACT
Found at i:41690899 original size:16 final size:16
Alignment explanation
Indices: 41690878--41690909 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41690868 TTTGTAACGC
41690878 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
*
41690894 CCCAAAAATCCTGAAA
1 CCCAAAAATCCCGAAA
41690910 TCCTGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:41692413 original size:29 final size:29
Alignment explanation
Indices: 41692371--41692475 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 29
41692361 ATAATATGAT
* * **
41692371 TTGGGCCTAATGGGCCATAGGAATGGGAA
1 TTGGGCCTAGTGGGCCATAAGAATAAGAA
*
41692400 TTGGGCCTAGTGGGCCATAAGAATATGAA
1 TTGGGCCTAGTGGGCCATAAGAATAAGAA
* * **
41692429 CTGGGCC-AGATAGGCCATTTGAATAAG-A
1 TTGGGCCTAG-TGGGCCATAAGAATAAGAA
41692457 TTGGGCCTAGTGGGCCATA
1 TTGGGCCTAGTGGGCCATA
41692476 TACATGTATG
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
28 16 0.26
29 46 0.74
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.23
Consensus pattern (29 bp):
TTGGGCCTAGTGGGCCATAAGAATAAGAA
Found at i:41700919 original size:25 final size:25
Alignment explanation
Indices: 41700890--41700937 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
41700880 TTATAATATG
* *
41700890 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTTTACCCCTAGGTA
41700915 AAAATGACCATTTTACCCCTAGG
1 AAAATGACCATTTTACCCCTAGG
41700938 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (25 bp):
AAAATGACCATTTTACCCCTAGGTA
Found at i:41700999 original size:11 final size:10
Alignment explanation
Indices: 41700967--41701020 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 10
41700957 GCATGAGATT
41700967 TGATAT-ACA
1 TGATATGACA
*
41700976 TGATTTGACA
1 TGATATGACA
41700986 TGATATGCACA
1 TGATATG-ACA
*
41700997 TGATATG-TA
1 TGATATGACA
41701006 TGATATGCACA
1 TGATATG-ACA
41701017 TGAT
1 TGAT
41701021 GTATTCATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
9 13 0.35
10 9 0.24
11 15 0.41
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:41701094 original size:26 final size:27
Alignment explanation
Indices: 41701065--41701138 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
41701055 TGGAGGAAGT
*
41701065 GAAAAAGGGC-TATGCCCCAGTTTACC
1 GAAAAAGGGCTTTTGCCCCAGTTTACC
*
41701091 GAAAAA-GGCTTTTGCCCCAGTTTATC
1 GAAAAAGGGCTTTTGCCCCAGTTTACC
41701117 -AAAAAGGGCTTTTGCCCCAGTT
1 GAAAAAGGGCTTTTGCCCCAGTT
41701139 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.18
26 36 0.82
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (27 bp):
GAAAAAGGGCTTTTGCCCCAGTTTACC
Found at i:41701120 original size:25 final size:25
Alignment explanation
Indices: 41701077--41701151 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 25
41701067 AAAAGGGCTA
*
41701077 TGCCCCAGTTTACCGAAAAAGGCTTT
1 TGCCCCAGTTTATC-AAAAAGGCTTT
41701103 TGCCCCAGTTTATCAAAAAGGGCTTT
1 TGCCCCAGTTTATCAAAAA-GGCTTT
*
41701129 TGCCCCAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAA-AGGCT
41701152 AGGCCTCCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
25 17 0.38
26 28 0.62
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (25 bp):
TGCCCCAGTTTATCAAAAAGGCTTT
Found at i:41701361 original size:31 final size:31
Alignment explanation
Indices: 41701323--41701407 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
41701313 TTGCATGTAT
41701323 TATGGATAATGAAAAGGCTTCGGCCCAGTGA
1 TATGGATAATGAAAAGGCTTCGGCCCAGTGA
41701354 TATGGATAATGAAAAGGCTTCGGCCCAGTGA
1 TATGGATAATGAAAAGGCTTCGGCCCAGTGA
* **
41701385 TATGAATAATGTGAAGGCTTCGG
1 TATGGATAATGAAAAGGCTTCGG
41701408 TCGAGTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (31 bp):
TATGGATAATGAAAAGGCTTCGGCCCAGTGA
Found at i:41706427 original size:50 final size:48
Alignment explanation
Indices: 41706314--41706489 Score: 190
Period size: 50 Copynumber: 3.5 Consensus size: 48
41706304 CTGGTACGCA
* * * * *
41706314 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCGA-TACACG
**
41706363 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATC-GATACACG
* * * * *
41706413 TAGTAGCCTACACTTAGTACTACACACGTGATCGAATTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATC-GATACACG
41706464 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
41706490 TGCGACCTCA
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
49 30 0.28
50 42 0.39
51 35 0.33
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCGATACACG
Found at i:41710562 original size:40 final size:40
Alignment explanation
Indices: 41710495--41710701 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41710485 CCTTCGGAGT
* *
41710495 TTAG-CCGGATATAGCT-ACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
* *
41710534 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGAAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
41710574 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
41710614 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-C
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* * *
41710653 TTAGCCCGGA-ATTAGTCACTAGAACAAATGCCTTCGGGAC
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAC
41710693 TTAGCCCGG
1 TTAGCCCGG
41710702 TTATCAATCC
Statistics
Matches: 155, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
38 1 0.01
39 39 0.25
40 115 0.74
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:41711213 original size:37 final size:37
Alignment explanation
Indices: 41711163--41711235 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
41711153 TCATGTGCAC
41711163 GTTTATGACCGAATACACACATCATTAACCTAATATT
1 GTTTATGACCGAATACACACATCATTAACCTAATATT
*
41711200 GTTTATGATCGAATACACACATCATTAACCTAATAT
1 GTTTATGACCGAATACACACATCATTAACCTAATAT
41711236 CAATTAACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (37 bp):
GTTTATGACCGAATACACACATCATTAACCTAATATT
Found at i:41718251 original size:79 final size:79
Alignment explanation
Indices: 41718153--41718430 Score: 279
Period size: 79 Copynumber: 3.3 Consensus size: 79
41718143 GCTACTAGCT
* *
41718153 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
41718218 ATTAGTCACTAGAA
66 ATTAGTCACTAGAA
41718232 CAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
* * * *
41718297 ATATACTTAGCCCGGTTATAG
66 AT-TA-GT--CAC---TAGAA
* * * ***
41718318 TAACTCGCCCAAAT-GCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGC
1 CAAAT-G-CC--TTCG-GGAC-----TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGC
*
41718382 TTAGCCCGGAATTAGTCACTAGCA
56 TTAGCCCGGAATTAGTCACTAGAA
41718406 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
41718431 TTATCAATCC
Statistics
Matches: 158, Mismatches: 23, Indels: 36
0.73 0.11 0.17
Matches are distributed among these distances:
79 74 0.47
80 2 0.01
81 1 0.01
83 2 0.01
84 2 0.01
85 1 0.01
86 8 0.05
87 2 0.01
88 7 0.04
89 1 0.01
90 2 0.01
91 2 0.01
93 1 0.01
94 2 0.01
95 51 0.32
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
ATTAGTCACTAGAA
Found at i:41718301 original size:40 final size:40
Alignment explanation
Indices: 41718120--41718301 Score: 214
Period size: 40 Copynumber: 4.6 Consensus size: 40
41718110 AAACCAAGTA
* * *
41718120 CCTTCGGAGTTTAG-CC-GAATATAGCTACTAGCTCAAATG
1 CCTTCGG-GCTTAGCCCGGAATATAGCAACTAGCACAAATG
* * *
41718159 CCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGAATATAGCAACTAGCACAAATG
*
41718199 CCTTCGGGCTTAGCCCGGAAT-TAGTC-ACTAGAACAAATG
1 CCTTCGGGCTTAGCCCGGAATATAG-CAACTAGCACAAATG
*
41718238 CCTTCGGGACTTAGCCCGG-ATATAGCAACTCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGAATATAGCAACTAGCACAAATG
41718278 CCTTCGGGCTTAGCCCGGAATATA
1 CCTTCGGGCTTAGCCCGGAATATA
41718302 CTTAGCCCGG
Statistics
Matches: 122, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
38 1 0.01
39 56 0.46
40 64 0.52
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGCTTAGCCCGGAATATAGCAACTAGCACAAATG
Found at i:41718331 original size:55 final size:55
Alignment explanation
Indices: 41718246--41718356 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
41718236 TGCCTTCGGG
41718246 ACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAATAT
1 ACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATAT
* * *
41718301 ACTTAGCCCGGTTATAGTAACTCGCCCAAATGCCTTCGGGACTTAGCCCGGATAT
1 ACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
41718356 A
1 A
41718357 GCAACTCGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 42 0.81
56 10 0.19
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (55 bp):
ACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
Found at i:41718357 original size:40 final size:40
Alignment explanation
Indices: 41718301--41718430 Score: 192
Period size: 40 Copynumber: 3.3 Consensus size: 40
41718291 CCCGGAATAT
* *
41718301 ACTTAGCCCGGTTATAGTAACTCGCCCAAATGCCTTCGGG
1 ACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG
*
41718341 ACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGG
1 ACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG
* *
41718381 -CTTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGG
1 ACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGG
41718420 ACTTAGCCCGG
1 ACTTAGCCCGG
41718431 TTATCAATCC
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
38 1 0.01
39 34 0.41
40 47 0.57
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (40 bp):
ACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG
Found at i:41720133 original size:36 final size:37
Alignment explanation
Indices: 41720093--41720165 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
41720083 TTCCGACTAG
*
41720093 GGTCACTTTAGGGCTGTCACAACTC-TCCCCCACTTA
1 GGTCAATTTAGGGCTGTCACAACTCTTCCCCCACTTA
41720129 GGTCAATTTAGGGCTGTCACAACTCTTCCCCCACTTA
1 GGTCAATTTAGGGCTGTCACAACTCTTCCCCCACTTA
41720166 AGAAATTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 24 0.69
37 11 0.31
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (37 bp):
GGTCAATTTAGGGCTGTCACAACTCTTCCCCCACTTA
Found at i:41720173 original size:36 final size:36
Alignment explanation
Indices: 41720099--41720173 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
41720089 CTAGGGTCAC
* *
41720099 TTTAGGGCTGTCACAACTCTCCCCCACTTAGGTCAA
1 TTTAGGGCTGTCACAACTCTCCCCCACTTAAGTAAA
41720135 TTTAGGGCTGTCACAACTCTTCCCCCACTTAAG-AAA
1 TTTAGGGCTGTCACAACTC-TCCCCCACTTAAGTAAA
41720171 TTT
1 TTT
41720174 TCGTCCCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 24 0.67
37 12 0.33
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (36 bp):
TTTAGGGCTGTCACAACTCTCCCCCACTTAAGTAAA
Found at i:41722681 original size:46 final size:46
Alignment explanation
Indices: 41722614--41722704 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
41722604 TTCTGAAAGC
* *
41722614 AGTTTTGGGTATATCCGAATCTCGAATTCGCAACTGGTAATAACCT
1 AGTTTTGGGTATATCCGAATCTCGAATTCACAACTGATAATAACCT
41722660 AGTTTTGGGTATATCCGAATCTCGAATTCACAACTGATAATAACC
1 AGTTTTGGGTATATCCGAATCTCGAATTCACAACTGATAATAACC
41722705 CGATCTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (46 bp):
AGTTTTGGGTATATCCGAATCTCGAATTCACAACTGATAATAACCT
Found at i:41724407 original size:43 final size:43
Alignment explanation
Indices: 41724347--41724429 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
41724337 CTGATATACT
41724347 TTTTTCGAAACTCAGTTTGGAAAAACTCCCAAGTTACTTGATC
1 TTTTTCGAAACTCAGTTTGGAAAAACTCCCAAGTTACTTGATC
41724390 TTTTTCGAAACTCAGTTTGGAAAAACTCCCAAGTTACTTG
1 TTTTTCGAAACTCAGTTTGGAAAAACTCCCAAGTTACTTG
41724430 CTCTCGGGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (43 bp):
TTTTTCGAAACTCAGTTTGGAAAAACTCCCAAGTTACTTGATC
Found at i:41726480 original size:40 final size:40
Alignment explanation
Indices: 41726426--41726619 Score: 336
Period size: 40 Copynumber: 4.9 Consensus size: 40
41726416 GATATAGCTT
*
41726426 CTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
41726466 CTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* *
41726506 CTCGCACAATTGCCTTCGGGACTTGGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
41726546 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
41726586 CTCGCACAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
41726620 CAATCCGAAT
Statistics
Matches: 147, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
39 13 0.09
40 134 0.91
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
Found at i:41726535 original size:80 final size:80
Alignment explanation
Indices: 41726399--41726619 Score: 340
Period size: 80 Copynumber: 2.8 Consensus size: 80
41726389 AAGCCAAGTA
** * *
41726399 CCTTCGGGGTTTAG-CCGGATATAGCT-TCTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATA
*
41726462 GTAACTCGCACAATTG
65 GTAACTCGCACAAATG
* * *
41726478 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTGGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
41726543 TAACTCGCACAAATG
66 TAACTCGCACAAATG
41726558 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
41726620 CAATCCGAAT
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
79 26 0.20
80 103 0.80
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAATG
Found at i:41756933 original size:43 final size:43
Alignment explanation
Indices: 41756886--41756971 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
41756876 AGGGTATATC
*
41756886 CAACAACCC-ATGTTTATCTTCTCCTCTT-TTTAAATTCTTTTTT
1 CAACAACCCAATATTT-TCTTCTCCT-TTCTTTAAATTCTTTTTT
*
41756929 CAACAACCCAATATTTTCTTTTCCTTTCTTTAAATTCTTTTTT
1 CAACAACCCAATATTTTCTTCTCCTTTCTTTAAATTCTTTTTT
41756972 TCTAGGATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 2 0.05
43 32 0.82
44 5 0.13
ACGTcount: A:0.22, C:0.24, G:0.01, T:0.52
Consensus pattern (43 bp):
CAACAACCCAATATTTTCTTCTCCTTTCTTTAAATTCTTTTTT
Found at i:41760534 original size:50 final size:50
Alignment explanation
Indices: 41760458--41760594 Score: 197
Period size: 50 Copynumber: 2.8 Consensus size: 50
41760448 AATGATCTAT
**
41760458 TGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGA-
1 TGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAC
* *
41760507 TGGTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAC
1 T-GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAC
* *
41760558 TGT-TGGTCGTATGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
41760595 TGCATACCAG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
49 31 0.40
50 46 0.59
51 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (50 bp):
TGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAC
Found at i:41774908 original size:12 final size:12
Alignment explanation
Indices: 41774891--41774955 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
41774881 AAGAAACATT
41774891 ATCAAAA-CTAGA
1 ATCAAAATC-AGA
*
41774903 ATCAAAATGAGA
1 ATCAAAATCAGA
*
41774915 ATCAGAATCAGA
1 ATCAAAATCAGA
* *
41774927 ATC-AAGTGACAAA
1 ATCAAAAT--CAGA
41774940 ATCAAAATCAGA
1 ATCAAAATCAGA
41774952 ATCA
1 ATCA
41774956 GAATTAGGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 2 0.05
12 30 0.73
13 6 0.15
14 3 0.07
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.17
Consensus pattern (12 bp):
ATCAAAATCAGA
Found at i:41774923 original size:6 final size:6
Alignment explanation
Indices: 41774900--41775009 Score: 64
Period size: 6 Copynumber: 17.8 Consensus size: 6
41774890 TATCAAAACT
* * * * *
41774900 AGAATC AAAATG AGAATC AGAATC AGAATC A-AGTGAC AAAATC AAAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * *
41774949 AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGTATC AGGTAAT- AGAATC
1 AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC A-G-AATC AGAATC
*
41774999 AGAATT AGAAT
1 AGAATC AGAAT
41775010 ATGAATGCAA
Statistics
Matches: 81, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
5 6 0.07
6 64 0.79
7 6 0.07
8 5 0.06
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:41774949 original size:31 final size:31
Alignment explanation
Indices: 41774905--41774987 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
41774895 AAACTAGAAT
*
41774905 CAAAATGAGAATCAGAATCAGAATCAAGTGA
1 CAAAATCAGAATCAGAATCAGAATCAAGTGA
* * *
41774936 CAAAATCAAAATCAGAATCAGAATTAGGTGA
1 CAAAATCAGAATCAGAATCAGAATCAAGTGA
* *
41774967 CAGAATCAGAATCAGTATCAG
1 CAAAATCAGAATCAGAATCAG
41774988 GTAATAGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (31 bp):
CAAAATCAGAATCAGAATCAGAATCAAGTGA
Found at i:41774973 original size:25 final size:25
Alignment explanation
Indices: 41774945--41775009 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
41774935 ACAAAATCAA
* *
41774945 AATCAGAATCAGAATTAGGTGACAG
1 AATCAGAATCAGAATCAGGTAACAG
* *
41774970 AATCAGAATCAGTATCAGGTAATAG
1 AATCAGAATCAGAATCAGGTAACAG
*
41774995 AATCAGAATTAGAAT
1 AATCAGAATCAGAAT
41775010 ATGAATGCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTAACAG
Found at i:41775932 original size:27 final size:27
Alignment explanation
Indices: 41775900--41775991 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
41775890 GGGGTAAAAT
* *
41775900 GGTAATTTTACCCCA-AGAGGGTATCTC
1 GGTAATTTTACCCTACAG-GGGTATTTC
* * *
41775927 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
*
41775954 GGTAATTTTACCTTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
41775981 GGTAATTTTAC
1 GGTAATTTTAC
41775992 AAATTAGGGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 54 0.96
28 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAGGGGTATTTC
Found at i:41775976 original size:54 final size:54
Alignment explanation
Indices: 41775900--41776018 Score: 125
Period size: 54 Copynumber: 2.2 Consensus size: 54
41775890 GGGGTAAAAT
**
41775900 GGTAATTTTACCCCAAGAGGGTATCTCGATAATTCTAC-CCTATAGGGGTATTTC
1 GGTAATTTTACCCCAAGAGGGTATCTCGATAATTCTACAAAT-TAGGGGTATTTC
** * * * *
41775954 GGTAATTTTACCTTACAG-GGGTATTTCGGTAATTTTACAAATTAGGGGTATTTT
1 GGTAATTTTACCCCA-AGAGGGTATCTCGATAATTCTACAAATTAGGGGTATTTC
*
41776008 TGTAATTTTAC
1 GGTAATTTTAC
41776019 AAATTAGGGG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
54 51 0.94
55 3 0.06
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.39
Consensus pattern (54 bp):
GGTAATTTTACCCCAAGAGGGTATCTCGATAATTCTACAAATTAGGGGTATTTC
Found at i:41776000 original size:27 final size:27
Alignment explanation
Indices: 41775942--41776096 Score: 179
Period size: 27 Copynumber: 5.7 Consensus size: 27
41775932 TTCTACCCTA
* *
41775942 TAGGGGTATTTCGGTAATTTTAC--CT
1 TAGGGGTATTTTGGTAATTTTACAAAT
*
41775967 TACAGGGGTATTTCGGTAATTTTACAAAT
1 T--AGGGGTATTTTGGTAATTTTACAAAT
*
41775996 TAGGGGTATTTTTGTAATTTTACAAAT
1 TAGGGGTATTTTGGTAATTTTACAAAT
* *
41776023 TAGGGGTATTTTGGTAATTTTGCTAAT
1 TAGGGGTATTTTGGTAATTTTACAAAT
* * *
41776050 TAAGGGTATTTTGGTAATTTTGCTAAT
1 TAGGGGTATTTTGGTAATTTTACAAAT
* *
41776077 CAAGGGTATTTTGGTAATTT
1 TAGGGGTATTTTGGTAATTT
41776097 GGTAAACTAA
Statistics
Matches: 118, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
25 1 0.01
27 115 0.97
29 2 0.02
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (27 bp):
TAGGGGTATTTTGGTAATTTTACAAAT
Found at i:41776096 original size:81 final size:81
Alignment explanation
Indices: 41775942--41776096 Score: 197
Period size: 81 Copynumber: 1.9 Consensus size: 81
41775932 TTCTACCCTA
* * *
41775942 TAGGGGTATTTCGGTAATTTTACCTTACAGGGGTATTTCGGTAATTTTACAAATTAGGGGTATTT
1 TAGGGGTATTTCGGTAATTTTACATTACAGGGGTATTTCGGTAATTTTACAAATCAAGGGTATTT
*
41776007 TTGTAATTTTACAAAT
66 TGGTAATTTTACAAAT
* * * * *
41776023 TAGGGGTATTTTGGTAATTTTGCTAATTA-A-GGGTATTTTGGTAATTTTGCTAATCAAGGGTAT
1 TAGGGGTATTTCGGTAATTTTAC--ATTACAGGGGTATTTCGGTAATTTTACAAATCAAGGGTAT
41776086 TTTGGTAATTT
64 TTTGGTAATTT
41776097 GGTAAACTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 59 0.94
82 1 0.02
83 3 0.05
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (81 bp):
TAGGGGTATTTCGGTAATTTTACATTACAGGGGTATTTCGGTAATTTTACAAATCAAGGGTATTT
TGGTAATTTTACAAAT
Found at i:41784672 original size:8 final size:8
Alignment explanation
Indices: 41784661--41784688 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41784651 GGCAAATCTT
41784661 GAAATGCC
1 GAAATGCC
41784669 GAAATGCC
1 GAAATGCC
41784677 GAAATGCC
1 GAAATGCC
41784685 GAAA
1 GAAA
41784689 AGCCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (8 bp):
GAAATGCC
Found at i:41792200 original size:46 final size:46
Alignment explanation
Indices: 41792133--41792361 Score: 458
Period size: 46 Copynumber: 5.0 Consensus size: 46
41792123 AAGATGAGAC
41792133 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
1 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
41792179 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
1 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
41792225 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
1 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
41792271 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
1 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
41792317 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATC
1 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATC
41792362 AGCATCGTGA
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 183 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (46 bp):
ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCG
Found at i:41792459 original size:138 final size:135
Alignment explanation
Indices: 41792133--41792450 Score: 379
Period size: 138 Copynumber: 2.3 Consensus size: 135
41792123 AAGATGAGAC
* * *
41792133 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGACGAGAGCTAG
1 ACATGAAGACGACAGCCAGTGTAAGACATGTCTGGGA-A-GCATCGACATTAAGACGAGAGCTAG
*
41792198 TGTAAGACATGTCTGGGACATGCATCGACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGAC
64 TGTAAGACATGTCTGGGACATGCATCGACATTAAGAC-AGAGCTAGTGTAAAACATGTCTGGGAC
41792263 ATGCATCG
128 ATGCATCG
* * *
41792271 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGACGAGAGCTAG
1 ACATGAAGACGACAGCCAGTGTAAGACATGTCTGGGA-A-GCATCGACATTAAGACGAGAGCTAG
* * *
41792336 TGTAAGACATGTCTGGGACATGCATC-AGCATCGTGATATAC-GAGCTAGTGTAAAACCTTTCTG
64 TGTAAGACATGTCTGGGACATGCATCGA-CAT--T-A-AGACAGAGCTAGTGTAAAACATGTCTG
41792399 GGACATGGCATCG
124 GGACAT-GCATCG
* * * *
41792412 GCACTGACAGATGACAGCCAGTGTAAGACTTGTTTGGGA
1 ACA-TGA-AGACGACAGCCAGTGTAAGACATGTCTGGGA
41792451 CACGACATTG
Statistics
Matches: 161, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
137 1 0.01
138 94 0.58
140 26 0.16
141 9 0.06
142 5 0.03
143 26 0.16
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (135 bp):
ACATGAAGACGACAGCCAGTGTAAGACATGTCTGGGAAGCATCGACATTAAGACGAGAGCTAGTG
TAAGACATGTCTGGGACATGCATCGACATTAAGACAGAGCTAGTGTAAAACATGTCTGGGACATG
CATCG
Found at i:41792502 original size:98 final size:95
Alignment explanation
Indices: 41792133--41792549 Score: 328
Period size: 92 Copynumber: 4.4 Consensus size: 95
41792123 AAGATGAGAC
* * * * *
41792133 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATC-GACAT--T-A-AGACGAGA
1 ACATGAAGACGACAGCCAGTGTAAGACATGTCTGGGACACGCATCAG-CATCGTGATATAC-A-A
41792193 GCTAGTGTAAGACATGTCTGGGACAT-GCATCG
63 GCTAGTGTAAGACATGTCTGGGACATGGCATCG
* * * * *
41792225 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATC-GACAT--T-A-AGACGAGA
1 ACATGAAGACGACAGCCAGTGTAAGACATGTCTGGGACACGCATCAG-CATCGTGATATAC-A-A
41792285 GCTAGTGTAAGACATGTCTGGGACAT-GCATCG
63 GCTAGTGTAAGACATGTCTGGGACATGGCATCG
* * * * *
41792317 ACATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGTGATATACGAGCT
1 ACATGAAGACGACAGCCAGTGTAAGACATGTCTGGGACACGCATCAGCATCGTGATATACAAGCT
* * *
41792382 AGTGTAAAACCTTTCTGGGACATGGCATCG
66 AGTGTAAGACATGTCTGGGACATGGCATCG
* * * * ** *
41792412 GCACTGACAGATGACAGCCAGTGTAAGACTTGTTTGGGACACGACATTGGCCTCGAT-ATATGA-
1 ACA-TGA-AGACGACAGCCAGTGTAAGACATGTCTGGGACACG-CATCAGCATCG-TGATAT-AC
*
41792475 AAG-TCAGTGTAAGACATGTCTGGGACATGGCATTG
61 AAGCT-AGTGTAAGACATGTCTGGGACATGGCATCG
* *
41792510 ACTTTAATG-CG-CTAGCCAGTGTAAGACCATGTCTGGGACA
1 ACATGAA-GACGAC-AGCCAGTGTAAGA-CATGTCTGGGACA
41792550 TGGCGTCAGC
Statistics
Matches: 283, Mismatches: 27, Indels: 25
0.84 0.08 0.07
Matches are distributed among these distances:
92 140 0.49
93 1 0.00
94 25 0.09
95 10 0.04
96 20 0.07
97 44 0.16
98 41 0.14
99 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (95 bp):
ACATGAAGACGACAGCCAGTGTAAGACATGTCTGGGACACGCATCAGCATCGTGATATACAAGCT
AGTGTAAGACATGTCTGGGACATGGCATCG
Found at i:41792509 original size:49 final size:48
Alignment explanation
Indices: 41792334--41792507 Score: 140
Period size: 49 Copynumber: 3.6 Consensus size: 48
41792324 GACGAGAGCT
* * *
41792334 AGTGTAAGACATGTCTGGGACAT-GCATCAGCATCG-TGATAT-ACGAGC
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAT-ATATGA-AAGC
* * * * * *
41792381 TAGTGTAAAACCTTTCTGGGACATGGCATCGGCACT-GACAGATGACAGCC
1 -AGTGTAAGACATGTCTGGGACATGGCATCGGC-CTCGATATATGAAAG-C
* * * * *
41792431 AGTGTAAGACTTGTTTGGGACACGACATTGGCCTCGATATATGAAAGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGATATATGAAAG-C
41792480 AGTGTAAGACATGTCTGGGACATGGCAT
1 AGTGTAAGACATGTCTGGGACATGGCAT
41792508 TGACTTTAAT
Statistics
Matches: 97, Mismatches: 23, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
48 22 0.23
49 72 0.74
50 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGATATATGAAAGC
Found at i:41794961 original size:32 final size:30
Alignment explanation
Indices: 41794914--41795239 Score: 149
Period size: 32 Copynumber: 10.6 Consensus size: 30
41794904 TAAGATATTC
*
41794914 ATAACAAAAATTAATATAAACTAATAAAAATT
1 ATAATAAAAA-TAATA-AAACTAATAAAAATT
* * *
41794946 ATACTAAAAAGTAATAAAAACTTATAAATATT
1 ATAATAAAAA-TAAT-AAAACTAATAAAAATT
* * *
41794978 ATAATAAATATAATAAATCTAAT--AATTT
1 ATAATAAAAATAATAAAACTAATAAAAATT
* * *
41795006 ATAA-AAAAATATTATATAAAATTATAAATATT
1 ATAATAAAAATA--ATA-AAACTAATAAAAATT
*
41795038 AT-A-AAAAATAA-AAAACGAA-AAAAATT
1 ATAATAAAAATAATAAAACTAATAAAAATT
* * * *
41795064 AAAAATAGGAAAATTATTAAAAAATCATAAAAATT
1 -ATAATA--AAAA-TAAT-AAAACTAATAAAAATT
* * *
41795099 ATTAAAAATTAAAATTAATATAAACTTATAAATATT
1 A-T---AA-TAAAAATAATA-AAACTAATAAAAATT
* *
41795135 ATAATAAAAAATAATAAAAACTTATAAATATT
1 ATAAT-AAAAATAAT-AAAACTAATAAAAATT
* *
41795167 ATAATAAATATAATAAATCTAAT--AAATT
1 ATAATAAAAATAATAAAACTAATAAAAATT
41795195 AT-A-AAAAATAATATAAACGT-ATAAAAATT
1 ATAATAAAAATAATA-AAAC-TAATAAAAATT
*
41795224 AT-A-AAAAATCATAAAA
1 ATAATAAAAATAATAAAA
41795240 AAATTGAACT
Statistics
Matches: 227, Mismatches: 40, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
26 15 0.07
27 17 0.07
28 19 0.08
29 22 0.10
30 19 0.08
31 25 0.11
32 70 0.31
33 2 0.01
34 6 0.03
35 9 0.04
36 16 0.07
37 3 0.01
38 2 0.01
39 2 0.01
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (30 bp):
ATAATAAAAATAATAAAACTAATAAAAATT
Found at i:41794963 original size:22 final size:21
Alignment explanation
Indices: 41794919--41794971 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
41794909 TATTCATAAC
*
41794919 AAAAATTA-ATATAAACTAAT
1 AAAAATTATATAAAAACTAAT
*
41794939 AAAAATTATACTAAAAAGTAAT
1 AAAAATTATA-TAAAAACTAAT
41794961 AAAAACTTATA
1 AAAAA-TTATA
41794972 AATATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 1 0.04
22 14 0.50
23 5 0.18
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAATTATATAAAAACTAAT
Found at i:41794965 original size:10 final size:10
Alignment explanation
Indices: 41794919--41794994 Score: 57
Period size: 10 Copynumber: 7.3 Consensus size: 10
41794909 TATTCATAAC
41794919 AAAAATTAAT
1 AAAAATTAAT
* *
41794929 ATAAACTAAT
1 AAAAATTAAT
41794939 AAAAATTATACT
1 AAAAATTA-A-T
*
41794951 AAAAAGTAAT
1 AAAAATTAAT
41794961 AAAAACTT-AT
1 AAAAA-TTAAT
*
41794971 AAATATT-AT
1 AAAAATTAAT
41794980 AATAAATATAAT
1 AA-AAAT-TAAT
41794992 AAA
1 AAA
41794995 TCTAATAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
9 6 0.12
10 29 0.56
11 5 0.10
12 12 0.23
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (10 bp):
AAAAATTAAT
Found at i:41795189 original size:18 final size:19
Alignment explanation
Indices: 41795168--41795203 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41795158 ATAAATATTA
*
41795168 TAATAAA-TATAATAAATC
1 TAATAAATTATAAAAAATC
41795186 TAATAAATTATAAAAAAT
1 TAATAAATTATAAAAAAT
41795204 AATATAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATTATAAAAAATC
Found at i:41795228 original size:9 final size:9
Alignment explanation
Indices: 41795011--41795240 Score: 83
Period size: 9 Copynumber: 25.6 Consensus size: 9
41795001 AATTTATAAA
41795011 AAAATATTAT
1 AAAA-ATTAT
41795021 ATAAAATTAT
1 A-AAAATTAT
*
41795031 AAATATTAT
1 AAAAATTAT
*
41795040 AAAAAATA-
1 AAAAATTAT
**
41795048 AAAAACGA-
1 AAAAATTAT
*
41795056 AAAAAAT-T
1 AAAAATTAT
*
41795064 AAAAA-TAG
1 AAAAATTAT
*
41795072 GAAAATTATT
1 AAAAATTA-T
*
41795082 AAAAAATCAT
1 -AAAAATTAT
41795092 AAAAATTATT
1 AAAAATTA-T
41795102 AAAAA-T-T
1 AAAAATTAT
41795109 -AAAATTAAT
1 AAAAATT-AT
*
41795118 ATAAACTTAT
1 A-AAAATTAT
*
41795128 AAATATTAT
1 AAAAATTAT
41795137 ---AA-TA-
1 AAAAATTAT
*
41795141 AAAAATAAT
1 AAAAATTAT
41795150 AAAAACTTAT
1 AAAAA-TTAT
*
41795160 AAATATTAT
1 AAAAATTAT
41795169 AATAAA-TAT
1 AA-AAATTAT
41795178 AATAAATCTA-
1 AA-AAAT-TAT
*
41795188 ATAAATTAT
1 AAAAATTAT
*
41795197 AAAAAATAAT
1 -AAAAATTAT
**
41795207 ATAAACGTAT
1 A-AAAATTAT
41795217 AAAAATTAT
1 AAAAATTAT
*
41795226 AAAAAATCAT
1 -AAAAATTAT
41795236 AAAAA
1 AAAAA
41795241 AATTGAACTA
Statistics
Matches: 165, Mismatches: 30, Indels: 51
0.67 0.12 0.21
Matches are distributed among these distances:
5 2 0.01
6 5 0.03
7 5 0.03
8 23 0.14
9 66 0.40
10 48 0.29
11 16 0.10
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:41795241 original size:10 final size:10
Alignment explanation
Indices: 41795073--41795241 Score: 77
Period size: 10 Copynumber: 17.4 Consensus size: 10
41795063 TAAAAATAGG
41795073 AAAATTATTAA
1 AAAATTA-TAA
*
41795084 AAAATCAT-A
1 AAAATTATAA
*
41795093 AAAATTATTA
1 AAAATTATAA
41795103 AAAA-T-T--
1 AAAATTATAA
*
41795109 AAAATTAATAT
1 AAAATT-ATAA
*
41795120 AAACTTATAA
1 AAAATTATAA
* *
41795130 ATATTATAATAA
1 A-A-AATTATAA
*
41795142 AAAATAATAA
1 AAAATTATAA
*
41795152 AAACTTAT-A
1 AAAATTATAA
*
41795161 AATATTATAA
1 AAAATTATAA
*
41795171 TAAA-TATAA
1 AAAATTATAA
* *
41795180 TAAA-TCTAA
1 AAAATTATAA
*
41795189 TAAATTATAA
1 AAAATTATAA
* *
41795199 AAAATAATAT
1 AAAATTATAA
**
41795209 AAACGTAT-A
1 AAAATTATAA
41795218 AAAATTATAA
1 AAAATTATAA
*
41795228 AAAATCATAA
1 AAAATTATAA
41795238 AAAA
1 AAAA
41795242 ATTGAACTAG
Statistics
Matches: 121, Mismatches: 26, Indels: 23
0.71 0.15 0.14
Matches are distributed among these distances:
6 4 0.03
7 1 0.01
8 1 0.01
9 40 0.33
10 56 0.46
11 13 0.11
12 6 0.05
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:41797864 original size:19 final size:20
Alignment explanation
Indices: 41797840--41797877 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41797830 GGTACCACCA
41797840 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
41797859 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
41797878 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:41798218 original size:46 final size:46
Alignment explanation
Indices: 41798101--41798228 Score: 145
Period size: 46 Copynumber: 2.8 Consensus size: 46
41798091 TAACCCGCCC
41798101 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * * * * *
41798149 CTCA-CGAACTCAGACTCAACTCAACGAGTTTGGA-C-ATTTGCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
41798192 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -C-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41798229 TGCTCAACCA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 6 0.09
44 2 0.03
45 2 0.03
46 27 0.40
47 27 0.40
48 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:41798247 original size:46 final size:45
Alignment explanation
Indices: 41798104--41798247 Score: 118
Period size: 46 Copynumber: 3.1 Consensus size: 45
41798094 CCCGCCCCTA
41798104 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * * * *
41798151 CA-CGAACTCAGACTCAACTCAACGAGTTTGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCT
41798197 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
41798243 AGTGA
1 AGTGA
41798248 CATGTCACTT
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 31 0.41
47 29 0.39
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Done.