Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 90 of 325
Found at i:28724251 original size:5 final size:5
Alignment explanation
Indices: 28724235--28724308 Score: 53
Period size: 5 Copynumber: 14.6 Consensus size: 5
28724225 ATTATTTACC
* * * * *
28724235 TATAT CTATAT TATAT TTTAT TACAT AATAT T-TAT TATAC TATTT TATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
28724285 TTTAT TAT-T ATATTAT TATAT TAT
1 TATAT TATAT -TA-TAT TATAT TAT
28724309 TTTACACTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
4 5 0.10
5 38 0.73
6 8 0.15
7 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:28724270 original size:24 final size:25
Alignment explanation
Indices: 28724213--28724303 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 25
28724203 AAAAAAACTT
*
28724213 TATTTA-TATATTATTATTTACCTA
1 TATTTATTATATTATTATTTACATA
28724237 TATCTATATTATATT-TTA-TTACATAA
1 TAT-T-TATTATATTATTATTTACAT-A
* *
28724263 TATTTATTATACTA-T-TTTATAT-
1 TATTTATTATATTATTATTTACATA
*
28724285 TTTATTATTATATTATTAT
1 TAT-TTATTATATTATTAT
28724304 ATTATTTTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
22 2 0.04
23 10 0.19
24 18 0.34
25 8 0.15
26 9 0.17
27 6 0.11
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTTATTATATTATTATTTACATA
Found at i:28724288 original size:34 final size:31
Alignment explanation
Indices: 28724235--28724312 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 31
28724225 ATTATTTACC
*
28724235 TATATCTATATTATATTTTATTACATAATATTTAT
1 TATA-CTATTTTATATTTTATT--ATAATA-TTAT
*
28724270 TATACTATTTTATATTTTATTATTATATTAT
1 TATACTATTTTATATTTTATTATAATATTAT
*
28724301 TATATTATTTTA
1 TATACTATTTTA
28724313 CACTTTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.38
32 5 0.12
34 16 0.40
35 4 0.10
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (31 bp):
TATACTATTTTATATTTTATTATAATATTAT
Found at i:28724293 original size:8 final size:8
Alignment explanation
Indices: 28724275--28724312 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
28724265 TTTATTATAC
28724275 TATTTTA-
1 TATTTTAT
28724282 TATTTTAT
1 TATTTTAT
*
28724290 TATTATAT
1 TATTTTAT
*
28724298 TATTATAT
1 TATTTTAT
28724306 TATTTTA
1 TATTTTA
28724313 CACTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TATTTTAT
Found at i:28724295 original size:13 final size:14
Alignment explanation
Indices: 28724275--28724393 Score: 52
Period size: 13 Copynumber: 8.3 Consensus size: 14
28724265 TTTATTATAC
28724275 TATT-TTATATT-T
1 TATTATTATATTAT
28724287 TATTATTATATTAT
1 TATTATTATATTAT
*
28724301 TA-TATTATTTTA-
1 TATTATTATATTAT
* * *
28724313 CACTT-TAATATATGT
1 TA-TTATTATAT-TAT
28724328 TATT-TTATATTAT
1 TATTATTATATTAT
*
28724341 TATTACATCATATTTAT
1 TATT--ATTATA-TTAT
* *
28724358 TATGTATTTTTGTATAT
1 TAT-TA-TTATAT-TAT
28724375 TATTATCTATATTAT
1 TATTAT-TATATTAT
28724390 TATT
1 TATT
28724394 TTGATAGATT
Statistics
Matches: 79, Mismatches: 14, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
12 5 0.06
13 26 0.33
14 12 0.15
15 9 0.11
16 11 0.14
17 15 0.19
18 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (14 bp):
TATTATTATATTAT
Found at i:28730929 original size:51 final size:50
Alignment explanation
Indices: 28730785--28730987 Score: 223
Period size: 50 Copynumber: 4.0 Consensus size: 50
28730775 GCACTTGTAG
* *
28730785 CCGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGG
1 CCGAA-CTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * *
28730836 CCTAACCATCTA-ATACTCATAGTAGCCTGCACTTAGTACTACACACGTGA
1 CCGAACTATC-AGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * *
28730886 TCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA
1 CCGAA-CTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * *
28730937 CCG-ATTAT-ATGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGA
1 CCGAACTATCA-GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
28730986 CC
1 CC
28730988 TCACAATAGC
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 40 0.31
50 44 0.34
51 43 0.34
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (50 bp):
CCGAACTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA
Found at i:28731669 original size:30 final size:30
Alignment explanation
Indices: 28731635--28731694 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28731625 CTTTAATACG
*
28731635 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGACAAAATTACAC-TTTTGCCCCTA
* *
28731665 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
28731695 GCTCAGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:28733023 original size:50 final size:50
Alignment explanation
Indices: 28732948--28733044 Score: 194
Period size: 50 Copynumber: 1.9 Consensus size: 50
28732938 TTAAAAGCCA
28732948 ATTTTGCTCATCTTCTTCAACATGGACGTGTATACCAAGGGAGACTCCAT
1 ATTTTGCTCATCTTCTTCAACATGGACGTGTATACCAAGGGAGACTCCAT
28732998 ATTTTGCTCATCTTCTTCAACATGGACGTGTATACCAAGGGAGACTC
1 ATTTTGCTCATCTTCTTCAACATGGACGTGTATACCAAGGGAGACTC
28733045 AATGGCTAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (50 bp):
ATTTTGCTCATCTTCTTCAACATGGACGTGTATACCAAGGGAGACTCCAT
Found at i:28736925 original size:49 final size:49
Alignment explanation
Indices: 28736848--28737092 Score: 274
Period size: 49 Copynumber: 4.9 Consensus size: 49
28736838 TAGCCGAAGC
* * *
28736848 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * *
28736897 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGGCCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AAT
* * * *
28736947 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
* * * * **
28736998 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTGAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * *
28737047 TATCTGGTACATGTAGTAGCCTACACTTAGTACTATACACGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
28737093 TCACAATAGC
Statistics
Matches: 162, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
49 78 0.48
50 46 0.28
51 38 0.23
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:28736987 original size:28 final size:28
Alignment explanation
Indices: 28736905--28736988 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
28736895 ATTATCCGGT
28736905 ACACGTAGTAGCCTGCACTTAGTACTAC
1 ACACGTAGTAGCCTGCACTTAGTACTAC
* * *
28736933 ACACGT-G--GCCT-AAC-CA-T-CTGAT
1 ACACGTAGTAGCCTGCACTTAGTACT-AC
28736955 ACACGTAGTAGCCTGCACTTAGTACTAC
1 ACACGTAGTAGCCTGCACTTAGTACTAC
28736983 ACACGT
1 ACACGT
28736989 GATCGAAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 2 0.05
25 8 0.19
26 2 0.05
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
ACACGTAGTAGCCTGCACTTAGTACTAC
Found at i:28737031 original size:101 final size:98
Alignment explanation
Indices: 28736861--28737092 Score: 295
Period size: 100 Copynumber: 2.3 Consensus size: 98
28736851 CTGGTACGCA
* * * *
28736861 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTA
*
28736926 GTACTACACACGTG-GCCTAACCATCTGATACACG
66 GTACTACACA--TGCGACTAACCATCTGATACACG
* *
28736960 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACATAGTAGCCTGCACT
* ** * *
28737025 TAGTACTACACATGCGACTGATTATCTGGTACATG
64 TAGTACTACACATGCGACTAACCATCTGATACACG
* *
28737060 TAGTAGCCTACACTTAGTACTATACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
28737093 TCACAATAGC
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
99 32 0.28
100 46 0.40
101 37 0.32
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTA
GTACTACACATGCGACTAACCATCTGATACACG
Found at i:28737774 original size:30 final size:30
Alignment explanation
Indices: 28737740--28737800 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28737730 CTTTAATACG
*
28737740 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGACAAAATTACAC-TTTTGCCCCTA
* *
28737770 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
28737800 A
1 A
28737801 GCTCAGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:28745896 original size:206 final size:205
Alignment explanation
Indices: 28745432--28745978 Score: 862
Period size: 206 Copynumber: 2.7 Consensus size: 205
28745422 GGCTGAGGCA
* *
28745432 AGATCCAAGATGGTTTGGCGTCCTTGTGCTTACAAGGAACAAATCGAAGACATAGTTGATTTGGC
1 AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGC
*
28745497 TTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGATAACAAA
66 TTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
* * * * ** *
28745562 ACAAAGTTTGGTGTCTCATATTCGACAGAGAGCAGACACATAGCAGATCTGGCCTTCAGATGTTT
131 TCGAAGTTTGGCGTCTCATATTCGACAGAGAGCAAACACATAGCAGATCTAACCTTCAGATGCTT
* *
28745627 ATACTGAAGC
196 AGACTAAAGC
* *
28745637 AGGTCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAAAAAATCGAAGACATAGCTGATTTGGC
1 AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGC
*
28745702 TTTCACGTGCTTACGATGAAGCAAATTTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
66 TTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
* *
28745767 TCGAAGTTTGGCGTCTCCATATTCGACAGAGGGCAAACACATAGCGGATCTAACCTTCAGATGCT
131 TCGAAGTTTGGCGTCT-CATATTCGACAGAGAGCAAACACATAGCAGATCTAACCTTCAGATGCT
28745832 TAGACTAAAGC
195 TAGACTAAAGC
* * * *
28745843 AGATCCAGGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGT
1 AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGC
**
28745908 TTTCGTGTGCTTAC-ACTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
66 TTTCACGTGCTTACGA-TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
28745972 ATCGAAG
130 ATCGAAG
28745979 AAGAAGATGT
Statistics
Matches: 314, Mismatches: 26, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
205 138 0.44
206 176 0.56
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (205 bp):
AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGC
TTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
TCGAAGTTTGGCGTCTCATATTCGACAGAGAGCAAACACATAGCAGATCTAACCTTCAGATGCTT
AGACTAAAGC
Found at i:28745998 original size:43 final size:44
Alignment explanation
Indices: 28745936--28746023 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
28745926 AAGCAAATCT
* * *
28745936 AAGATGATTTGGCATCTCTGTATT-GTCAGAGAACAAATCGAAG
1 AAGAAGATGTGGCATCTCTGTATTCGACAGAGAACAAATCGAAG
* * * *
28745979 AAGAAGATGTGGCGTCTCTGTGTTCGACAGAGAGCAGATCGAAG
1 AAGAAGATGTGGCATCTCTGTATTCGACAGAGAACAAATCGAAG
28746023 A
1 A
28746024 TATCAACATG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 20 0.54
44 17 0.46
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (44 bp):
AAGAAGATGTGGCATCTCTGTATTCGACAGAGAACAAATCGAAG
Found at i:28746540 original size:20 final size:20
Alignment explanation
Indices: 28746515--28746568 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
28746505 CCCCGAATCG
28746515 AGGCCATCAATGCACTGTCA
1 AGGCCATCAATGCACTGTCA
*
28746535 AGGCCATCAATGCACTGTCG
1 AGGCCATCAATGCACTGTCA
28746555 AGGCCATCAATGCA
1 AGGCCATCAATGCA
28746569 TTTTCTCAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (20 bp):
AGGCCATCAATGCACTGTCA
Found at i:28747828 original size:5 final size:5
Alignment explanation
Indices: 28747812--28747929 Score: 55
Period size: 5 Copynumber: 23.6 Consensus size: 5
28747802 ATTATTTACC
* * * * *
28747812 TATAT CTATAT TATAT TTTAT TACAT GATAT T-TAT TATAC TATTT TATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* * * * * *
28747862 TTTAT TAT-T T-TAT TATTT TACACT TAAAT ATATGT TATTT TATAT TATTAT
1 TATAT TATAT TATAT TATAT TATA-T TATAT -TATAT TATAT TATAT TA-TAT
* *
28747913 TACAT CATAT T-TAT TAT
1 TATAT TATAT TATAT TAT
28747930 GTATTTTCGT
Statistics
Matches: 81, Mismatches: 24, Indels: 15
0.68 0.20 0.12
Matches are distributed among these distances:
3 1 0.01
4 12 0.15
5 51 0.63
6 17 0.21
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:28747847 original size:24 final size:25
Alignment explanation
Indices: 28747790--28747879 Score: 70
Period size: 24 Copynumber: 3.8 Consensus size: 25
28747780 AAAAAAACTT
*
28747790 TATTTA-TATATTATTATTTACCTA
1 TATTTATTATATTATTATTTACATA
28747814 TATCTATATTATATT-TTA-TTACATGA
1 TAT-T-TATTATATTATTATTTACAT-A
*
28747840 TATTTATTATACTA-T-TTT--ATA
1 TATTTATTATATTATTATTTACATA
*
28747861 T-TTTATTATTTTATTATTT
1 TATTTATTATATTATTATTT
28747880 TACACTTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
20 10 0.19
21 3 0.06
22 5 0.09
24 14 0.26
25 7 0.13
26 9 0.17
27 6 0.11
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (25 bp):
TATTTATTATATTATTATTTACATA
Found at i:28747870 original size:8 final size:8
Alignment explanation
Indices: 28747852--28747881 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
28747842 TTTATTATAC
28747852 TATTTTA-
1 TATTTTAT
28747859 TATTTTAT
1 TATTTTAT
28747867 TATTTTAT
1 TATTTTAT
28747875 TATTTTA
1 TATTTTA
28747882 CACTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TATTTTAT
Found at i:28749843 original size:15 final size:16
Alignment explanation
Indices: 28749823--28749855 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28749813 ATGGACTTCT
28749823 TTATTA-AATTTTAAA
1 TTATTAGAATTTTAAA
*
28749838 TTATTAGTATTTTAAA
1 TTATTAGAATTTTAAA
28749854 TT
1 TT
28749856 GGGTATGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATTAGAATTTTAAA
Found at i:28752800 original size:23 final size:24
Alignment explanation
Indices: 28752724--28752843 Score: 174
Period size: 24 Copynumber: 5.0 Consensus size: 24
28752714 GCTTTATCAT
*
28752724 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
28752749 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
28752774 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28752797 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28752821 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28752844 GCACTTCCTC
Statistics
Matches: 89, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
23 24 0.27
24 34 0.38
25 25 0.28
26 6 0.07
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28752831 original size:47 final size:47
Alignment explanation
Indices: 28752745--28752842 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
28752735 CCTAGCCTCT
28752745 TTTAATAACTGGGGCAAAGCCCTTTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAGCCC-TTTTTAATAACTGGGGCATAAGCCC
28752793 TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCA-AAGCCCTTTTTAATAACTGGGGCATAAGCCC
28752840 TTT
1 TTT
28752843 TGCACTTCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 27 0.55
48 16 0.33
49 6 0.12
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (47 bp):
TTTAATAACTGGGGCAAAGCCCTTTTTAATAACTGGGGCATAAGCCC
Found at i:28752915 original size:9 final size:9
Alignment explanation
Indices: 28752901--28752957 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
28752891 ATCTCGTGTG
28752901 CATATCATA
1 CATATCATA
*
28752910 CATATCATGTG
1 CATATCA--TA
28752921 CATATCATA
1 CATATCATA
* *
28752930 CATGTCATGTG
1 CATATCA--TA
28752941 CATATCATA
1 CATATCATA
28752950 CATATCAT
1 CATATCAT
28752958 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:28752920 original size:20 final size:20
Alignment explanation
Indices: 28752897--28752959 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
28752887 GAACATCTCG
28752897 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
28752917 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
28752937 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
28752957 TGT
1 TGT
28752960 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:28753024 original size:25 final size:25
Alignment explanation
Indices: 28752996--28753043 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28752986 ATATATAAAC
* * *
28752996 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28753021 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28753044 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:28767240 original size:40 final size:40
Alignment explanation
Indices: 28767195--28767331 Score: 175
Period size: 40 Copynumber: 3.4 Consensus size: 40
28767185 CAGTTATTTG
* *
28767195 TGGCACTTAGTGTGCGATACGACATAGCTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTTGGCTATATA
** *
28767235 TGGCACTTAGCATGCGATTCAACATAGCTTTGGCTATATA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTTGGCTATATA
* * * * * *
28767275 TGGCACTTAGTGTGTGATTTGAGATAGTTTTGGCTATGTT
1 TGGCACTTAGTGTGCGATTCGACATAGCTTTGGCTATATA
28767315 TGGCACTTAGTGTGCGA
1 TGGCACTTAGTGTGCGA
28767332 GATATTGAGC
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTCGACATAGCTTTGGCTATATA
Found at i:28767355 original size:28 final size:28
Alignment explanation
Indices: 28767315--28767368 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
28767305 TGGCTATGTT
* *
28767315 TGGCACTTAGTGTGCGAGATATTGAGCA
1 TGGCACTTAGTGTGCAAGACATTGAGCA
28767343 TGGCACTTAGTGTGCAAGACATTGAG
1 TGGCACTTAGTGTGCAAGACATTGAG
28767369 TATTCAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
TGGCACTTAGTGTGCAAGACATTGAGCA
Found at i:28776739 original size:42 final size:43
Alignment explanation
Indices: 28776636--28776753 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
28776626 TTATGTGGAA
*
28776636 AAATGCCACTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
1 AAATGCCACTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * * **
28776679 AAATGCCACTAACGAACATGATCTCTAGCGGTGC-TTTCCTCAC
1 AAATGCCACTAAAGAACATGACCTTTAGCGGCACTTTTCC-CAC
*
28776722 AAATGCC-GTAAAGAACATGACCTTTAGCGGCA
1 AAATGCCACTAAAGAACATGACCTTTAGCGGCA
28776754 TTTGTGGAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
42 24 0.39
43 38 0.61
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
AAATGCCACTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
Found at i:28783854 original size:27 final size:27
Alignment explanation
Indices: 28783823--28783880 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
28783813 ACAATCATAC
28783823 ATCACATAGGGGCATAACAGTCATTTT
1 ATCACATAGGGGCATAACAGTCATTTT
*
28783850 ATCACATAGGGGCATAATAGTCATTTT
1 ATCACATAGGGGCATAACAGTCATTTT
28783877 ATCA
1 ATCA
28783881 ATTAAGGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (27 bp):
ATCACATAGGGGCATAACAGTCATTTT
Found at i:28786321 original size:40 final size:40
Alignment explanation
Indices: 28786267--28786499 Score: 326
Period size: 40 Copynumber: 5.9 Consensus size: 40
28786257 AATATAGCTT
*
28786267 CTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
28786307 CTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* *
28786347 CTAGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* * * *
28786387 CTCACACAATTGCCTTCCGGACTTGGCCCGGTTATAGT-A
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* * * * *
28786426 CTTGCACAAATGCTTTCGGGACTTGGCCCAGATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
28786466 CTCTCACAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
28786500 CAATCCGAAT
Statistics
Matches: 172, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 43 0.25
40 129 0.75
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
Found at i:28786462 original size:119 final size:119
Alignment explanation
Indices: 28786277--28786499 Score: 331
Period size: 119 Copynumber: 1.9 Consensus size: 119
28786267 CTCGCTCAAA
* * * *
28786277 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTAT
1 TGCCTTCCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCAGATAT
*
28786342 AGTAACTAGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAT
66 AGTAACTAGCACAAATGCCTTCGGG-CTTAGCCCGGTTATAGTAACTCACACAAT
* * * *
28786397 TGCCTTCCGGACTTGGCCCGGTTATAGT-ACTTGCACAAATGCTTTCGGGACTTGGCCCAGATAT
1 TGCCTTCCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCAGATAT
**
28786461 AGTAACTCTCACAAATGCCTTCGGGCTTAGCCCGGTTAT
66 AGTAACTAGCACAAATGCCTTCGGGCTTAGCCCGGTTAT
28786500 CAATCCGAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
118 14 0.15
119 52 0.57
120 26 0.28
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (119 bp):
TGCCTTCCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCAGATAT
AGTAACTAGCACAAATGCCTTCGGGCTTAGCCCGGTTATAGTAACTCACACAAT
Found at i:28794354 original size:40 final size:40
Alignment explanation
Indices: 28794300--28794493 Score: 291
Period size: 40 Copynumber: 4.9 Consensus size: 40
28794290 GATATAGCTT
* *
28794300 CTCGCTCAAATGCCTTCAGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
28794340 CTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* * * * *
28794380 CTAGCACAATTTCCTTTGGGACTTGGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* *
28794420 CTCGTACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
28794460 CTCGCACAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
28794494 CAATCCGAAT
Statistics
Matches: 138, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 13 0.09
40 125 0.91
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
Found at i:28800152 original size:32 final size:32
Alignment explanation
Indices: 28800115--28800180 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
28800105 TGGTTAGAAG
28800115 ATAAACAAATTAAAAAGATGAATATTTATCAA
1 ATAAACAAATTAAAAAGATGAATATTTATCAA
28800147 ATAAACAAATTAAAAAGATGAATATTTATCAA
1 ATAAACAAATTAAAAAGATGAATATTTATCAA
28800179 AT
1 AT
28800181 TTTAAAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (32 bp):
ATAAACAAATTAAAAAGATGAATATTTATCAA
Found at i:28801223 original size:42 final size:41
Alignment explanation
Indices: 28801162--28801251 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 41
28801152 TACTATAAAT
28801162 AAAT-ACACATAATTTAGGCATCACAAATAAAGGCAAACTC
1 AAATCACACATAATTTAGGCATCACAAATAAAGGCAAACTC
28801202 AAATCACATCATAATTTAGGCATCACAAATAAAGGCAAACTC
1 AAATCACA-CATAATTTAGGCATCACAAATAAAGGCAAACTC
28801244 AAATCACA
1 AAATCACA
28801252 ACCAAACATA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 4 0.08
41 3 0.06
42 41 0.85
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.20
Consensus pattern (41 bp):
AAATCACACATAATTTAGGCATCACAAATAAAGGCAAACTC
Found at i:28802901 original size:12 final size:10
Alignment explanation
Indices: 28802875--28802901 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28802865 ATCAAAATAT
28802875 AATATATTAA
1 AATATATTAA
28802885 AATATATTAA
1 AATATATTAA
28802895 AATATAT
1 AATATAT
28802902 CATAATGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATATTAA
Found at i:28813738 original size:9 final size:9
Alignment explanation
Indices: 28813726--28813791 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
28813716 TTTTATATAT
28813726 TTATGTAAG
1 TTATGTAAG
*
28813735 TTATGATATG
1 TTATG-TAAG
* * *
28813745 ATATAT-AT
1 TTATGTAAG
28813753 TTATGT-A-
1 TTATGTAAG
28813760 TTATGTAAG
1 TTATGTAAG
28813769 TTATGTAAG
1 TTATGTAAG
28813778 TTATGTAAG
1 TTATGTAAG
28813787 TTATG
1 TTATG
28813792 ATCCAAAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 29 0.62
10 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28813791 original size:34 final size:34
Alignment explanation
Indices: 28813726--28813791 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
28813716 TTTTATATAT
* *
28813726 TTATGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTATGATAAGATATATAGTTATGTA
* *
28813760 TTATGTAAGTTATG-TAAGTTATGTAAGTTATG
1 TTATGTAAGTTATGATAAGATATAT-AGTTATG
28813792 ATCCAAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (34 bp):
TTATGTAAGTTATGATAAGATATATAGTTATGTA
Found at i:28813864 original size:13 final size:13
Alignment explanation
Indices: 28813846--28813871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28813836 GATTATCATA
28813846 TTTAAATTTTAAC
1 TTTAAATTTTAAC
28813859 TTTAAATTTTAAC
1 TTTAAATTTTAAC
28813872 CCTTTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAATTTTAAC
Found at i:28814211 original size:18 final size:18
Alignment explanation
Indices: 28814188--28814236 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
28814178 TCAATTGATC
*
28814188 TAATTTTATTTATATTTT
1 TAATTTTATTTAAATTTT
28814206 TAATTTTA--TAAATTTT
1 TAATTTTATTTAAATTTT
28814222 TAATATTTTATTTAA
1 T-A-ATTTTATTTAA
28814237 TCGAACCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 14 0.54
20 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTATTTAAATTTT
Found at i:28823310 original size:22 final size:22
Alignment explanation
Indices: 28823282--28823356 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
28823272 TTCCACATCC
28823282 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
28823304 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
28823328 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28823351 ATCACA
1 ATCACA
28823357 CATACACATG
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 17 0.45
23 5 0.13
24 5 0.13
25 11 0.29
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28823326 original size:47 final size:47
Alignment explanation
Indices: 28823254--28823901 Score: 928
Period size: 47 Copynumber: 13.6 Consensus size: 47
28823244 CCCCTCGGGA
* * *
28823254 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
28823301 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28823348 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
28823395 CTTATCACACATACT-CA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATA-TACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
28823442 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
28823489 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
28823536 CTTATCACATATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
** *
28823587 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28823634 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28823683 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28823730 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
28823777 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28823826 CTTATCACATATATATACACTTTCACATTCACCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
28823875 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28823902 TATTCAAATA
Statistics
Matches: 569, Mismatches: 20, Indels: 24
0.93 0.03 0.04
Matches are distributed among these distances:
46 2 0.00
47 383 0.67
49 140 0.25
51 43 0.08
52 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:28823647 original size:192 final size:189
Alignment explanation
Indices: 28823254--28823901 Score: 941
Period size: 192 Copynumber: 3.4 Consensus size: 189
28823244 CCCCTCGGGA
* * * *
28823254 CTTATCAC-ATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
* *
28823318 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACATTCATCACA
66 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACA
* *
28823382 TTGGCCATTCGGCCTTATCACACATACT-CA-TGTTCACATTCATCACATTGGCCATTCGGC
130 TTGGCCATTCGGCCTTATCACATATA-TACACT-TTCACATTCATCACATTGGCCATTAGGC
* * * * *
28823442 CTTATCTC-ATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACAC
1 CTTATCACAATATATACACT-TTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
28823505 A-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATATACACTTTCACATTCA
65 ACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC----ATATATACACTTTCACATTCA
**
28823569 TCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
125 TCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
28823634 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
* *
28823699 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
65 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
* *
28823764 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
130 TTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
28823826 CTTATCACATATATATACACTTTCACATTCACCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
28823891 ACTTTCACATT
65 ACTTTCACATT
28823902 TATTCAAATA
Statistics
Matches: 418, Mismatches: 27, Indels: 26
0.89 0.06 0.06
Matches are distributed among these distances:
187 2 0.00
188 91 0.22
190 45 0.11
191 1 0.00
192 192 0.46
193 2 0.00
194 83 0.20
195 2 0.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (189 bp):
CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACAT
TGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:28825413 original size:56 final size:56
Alignment explanation
Indices: 28825346--28825465 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
28825336 TATTAGTTTA
28825346 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
28825402 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
28825458 TTGCCCAT
1 TTGCCCAT
28825466 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:28833301 original size:28 final size:28
Alignment explanation
Indices: 28833238--28833335 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
28833228 ATATTAAGTC
*
28833238 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
28833265 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
28833293 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
28833322 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28833336 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28841585 original size:28 final size:28
Alignment explanation
Indices: 28841522--28841619 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
28841512 ATATTAAGTC
*
28841522 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
28841549 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
28841577 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
28841606 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28841620 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28848713 original size:68 final size:71
Alignment explanation
Indices: 28848640--28848797 Score: 171
Period size: 68 Copynumber: 2.3 Consensus size: 71
28848630 CATCATGTGT
** * * *
28848640 ACAAGAGAGCTACGAGATAG-TATGTAGTAGCTAGGTCAAATGTGTGA-TAC-AG-GATGTATCC
1 ACAAGAGAGCTACGAGATAGATAAAT-GTAGCTAGGTCAAATGTGTGATTACAAGTGAAGGATAC
28848701 CATGTAG
65 CATGTAG
* * * ** *
28848708 ACAAGAGAGCTACGGGAGAGATAAATGTAGTTAGGTCGCATGTGTGATTCCAAGTGAAGGATACC
1 ACAAGAGAGCTACGAGATAGATAAATGTAGCTAGGTCAAATGTGTGATTACAAGTGAAGGATACC
28848773 ATGTAG
66 ATGTAG
*
28848779 ACAAGAGAGCTATGAGATA
1 ACAAGAGAGCTACGAGATA
28848798 AATTGGCTAG
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
68 36 0.50
69 5 0.07
70 2 0.03
71 29 0.40
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (71 bp):
ACAAGAGAGCTACGAGATAGATAAATGTAGCTAGGTCAAATGTGTGATTACAAGTGAAGGATACC
ATGTAG
Found at i:28850794 original size:42 final size:43
Alignment explanation
Indices: 28850692--28850841 Score: 166
Period size: 44 Copynumber: 3.5 Consensus size: 43
28850682 ATGTGTTTTC
28850692 GTGTAAGACCACGA-CTGGGACATTGGCATCG-ACTTATGATTTAT
1 GTGTAAGACCAC-ATCTGGGACATTGGCATCGTA-TT-TGATTTAT
28850736 GTGTAAGACCACATCTGGGACATTGGCATCGTATTTGATTT-T
1 GTGTAAGACCACATCTGGGACATTGGCATCGTATTTGATTTAT
* * * *
28850778 GTGTAAGACGC-TATCTGGGATAGTGGCATCGATATTTGA-TTAC
1 GTGTAAGAC-CACATCTGGGACATTGGCATCG-TATTTGATTTAT
* *
28850821 ATGTAAGACCACGTCTGGGAC
1 GTGTAAGACCACATCTGGGAC
28850842 GTTCACATTG
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
42 30 0.33
43 30 0.33
44 31 0.34
45 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCACATCTGGGACATTGGCATCGTATTTGATTTAT
Found at i:28850838 original size:43 final size:43
Alignment explanation
Indices: 28850692--28850841 Score: 164
Period size: 42 Copynumber: 3.5 Consensus size: 43
28850682 ATGTGTTTTC
* *
28850692 GTGTAAGACCACGACTGGGACATTGGCATCGACT-TATGATTTAT
1 GTGTAAGACCACGTCTGGGACATTGGCATCGA-TATTTGA-TTAT
* *
28850736 GTGTAAGACCACATCTGGGACATTGGCATCG-TATTTGATTTT
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTAT
* * *
28850778 GTGTAAGACGCTA--TCTGGGATAGTGGCATCGATATTTGATTAC
1 GTGTAAGAC-C-ACGTCTGGGACATTGGCATCGATATTTGATTAT
*
28850821 ATGTAAGACCACGTCTGGGAC
1 GTGTAAGACCACGTCTGGGAC
28850842 GTTCACATTG
Statistics
Matches: 90, Mismatches: 10, Indels: 13
0.80 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 30 0.33
43 29 0.32
44 30 0.33
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTAT
Found at i:28855421 original size:24 final size:24
Alignment explanation
Indices: 28855389--28855435 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
28855379 CTGTCAGGAG
28855389 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
28855413 AGGATTTAGGAGTTGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
28855436 GGAAATCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:28855446 original size:24 final size:23
Alignment explanation
Indices: 28855389--28855460 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
28855379 CTGTCAGGAG
*
28855389 AGGATTTAGGAGTTGATAAGGGA
1 AGGATCTAGGAGTTGATAAGGGA
*
28855412 TAGGATTTAGGAGTTGATAAGGG-
1 -AGGATCTAGGAGTTGATAAGGGA
* *
28855435 AGGAAATCTAGGAGCTGATAAAGGA
1 AGG--ATCTAGGAGTTGATAAGGGA
28855460 A
1 A
28855461 CAAGAGGTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.07
24 38 0.90
25 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.36, T:0.24
Consensus pattern (23 bp):
AGGATCTAGGAGTTGATAAGGGA
Found at i:28856891 original size:27 final size:26
Alignment explanation
Indices: 28856851--28856962 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
28856841 AGGAAGCGTC
*
28856851 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
28856878 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAT-TATCTGA-T
*
28856905 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
28856933 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
28856959 CTGG
1 CTGG
28856963 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
26 8 0.11
27 49 0.66
28 16 0.22
29 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28856955 original size:54 final size:54
Alignment explanation
Indices: 28856851--28856962 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
28856841 AGGAAGCGTC
*
28856851 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATT
* * * * *
28856905 CTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTATT
28856959 CTGG
1 CTGG
28856963 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATT
Found at i:28863274 original size:24 final size:24
Alignment explanation
Indices: 28863208--28863267 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
28863198 CTGTCAGGAG
28863208 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
28863232 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
28863256 AGGATTTAGGAG
1 AGGATTTAGGAG
28863268 CAGATAAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:28864738 original size:27 final size:26
Alignment explanation
Indices: 28864698--28864802 Score: 129
Period size: 27 Copynumber: 3.9 Consensus size: 26
28864688 AGGAAGCGTC
*
28864698 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
28864725 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
28864752 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* *
28864780 CTGGTGACTCTGTCACATTATCT
1 CTGGTGGCTCTGCCACATTATCT
28864803 ATTCTGGCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.03
27 50 0.74
28 16 0.24
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28864802 original size:54 final size:54
Alignment explanation
Indices: 28864698--28864809 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
28864688 AGGAAGCGTC
* *
28864698 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATT
* * * *
28864752 CTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTATT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTATT
28864806 CTGG
1 CTGG
28864810 CAACCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATT
Found at i:28868455 original size:27 final size:27
Alignment explanation
Indices: 28868425--28868678 Score: 309
Period size: 27 Copynumber: 9.4 Consensus size: 27
28868415 ATTACCAAAG
* *
28868425 TACCATCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28868452 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
28868479 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
28868506 TACCCTCGATTTACAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
**
28868533 TACCCTCGATTT-CTAGAATTACCATTT
1 TACCCTCGATTTAC-AGAATTACTGTTT
*
28868560 TACCCTCGATTTATAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
*
28868587 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * **
28868614 TACCCTTGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28868641 TACCCTC-AGTTTACAAAATTACTGTTT
1 TACCCTCGA-TTTACAGAATTACTGTTT
28868668 TACCCTCGATT
1 TACCCTCGATT
28868679 GTGAAATTAC
Statistics
Matches: 198, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.01
27 195 0.98
28 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:28868490 original size:54 final size:54
Alignment explanation
Indices: 28868425--28868678 Score: 341
Period size: 54 Copynumber: 4.7 Consensus size: 54
28868415 ATTACCAAAG
* * *
28868425 TACCATCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTA-CTGTTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATC-GTTT
*
28868479 TACCCTTGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTT
* * *
28868533 TACCCTCGATTTCTAGAATTACCATTTTACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTT
* * * * *
28868587 TACCCTCGATTTACAGAATTACCGTTTTACCCTTGATTTACAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTT
* * *
28868641 TACCCTC-AGTTTACAAAATTACTGTTTTACCCTCGATT
1 TACCCTCGA-TTTATAGAATTACCGTTTTACCCTCGATT
28868679 GTGAAATTAC
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.01
54 177 0.99
55 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTT
Found at i:28868524 original size:81 final size:81
Alignment explanation
Indices: 28868425--28868678 Score: 343
Period size: 81 Copynumber: 3.1 Consensus size: 81
28868415 ATTACCAAAG
* * **
28868425 TACCATCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTTGATTTACAGAATTACCATTTTACCCTTGATT
28868490 TATAGAATTACCGTTT
66 TATAGAATTACCGTTT
* *
28868506 TACCCTCGATTTACAGAATTA-TCGTTTTACCCTCGATTT-CTAGAATTACCATTTTACCCTCGA
1 TACCCTCGATTTACAGAATTACT-GTTTTACCCTTGATTTAC-AGAATTACCATTTTACCCTTGA
*
28868569 TTTATAGAATTATCGTTT
64 TTTATAGAATTACCGTTT
* * *
28868587 TACCCTCGATTTACAGAATTACCGTTTTACCCTTGATTTACAAAATTACCATTTTACCC-TCAGT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTTGATTTACAGAATTACCATTTTACCCTTGA-T
* * *
28868651 TTACAAAATTACTGTTT
65 TTATAGAATTACCGTTT
28868668 TACCCTCGATT
1 TACCCTCGATT
28868679 GTGAAATTAC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
80 3 0.02
81 148 0.97
82 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTACTGTTTTACCCTTGATTTACAGAATTACCATTTTACCCTTGATT
TATAGAATTACCGTTT
Found at i:28868721 original size:27 final size:26
Alignment explanation
Indices: 28868682--28868779 Score: 81
Period size: 27 Copynumber: 3.7 Consensus size: 26
28868672 CTCGATTGTG
** *
28868682 AAATTACTGAAATACCCTTGTAGGATA
1 AAATTACCAAAATACCCTAGTAGG-TA
* **
28868709 GAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATA-CCCTAGTAGGTA
*
28868736 AAATTACCAAAATACCCCTAGCT-TGTA
1 AAATTACCAAAATA-CCCTAG-TAGGTA
*
28868763 AGATTACCAAAATACCC
1 AAATTACCAAAATACCC
28868780 CTGATTTGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.05
27 50 0.82
28 8 0.13
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (26 bp):
AAATTACCAAAATACCCTAGTAGGTA
Found at i:28868788 original size:27 final size:27
Alignment explanation
Indices: 28868710--28868862 Score: 134
Period size: 27 Copynumber: 5.7 Consensus size: 27
28868700 TGTAGGATAG
28868710 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
28868737 AATTACCAAAATACCCCTAGCTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
28868764 GATTACCAAAATACCCCT-GATTTGTGA
1 AATTACCAAAATACCCCTAG-TTTGTAA
*** * *
28868791 AATTATTGAAATA-CTCTCGATTTGTAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
* * * *
28868818 AA-TATCGAAATA-CCCTTGTAATGTAA
1 AATTACCAAAATACCCCTAGT-TTGTAA
*
28868844 AAATACCAAAATACCCCTA
1 AATTACCAAAATACCCCTA
28868863 TAGGGTAAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.01
26 24 0.23
27 75 0.72
28 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:28868803 original size:54 final size:55
Alignment explanation
Indices: 28868677--28868804 Score: 147
Period size: 54 Copynumber: 2.4 Consensus size: 55
28868667 TTACCCTCGA
*
28868677 TTGTGAAATTACTGAAATA-CCCTTGTAGGATAGAATTACCAAAATACCCCTAGT
1 TTGTGAAATTACTGAAATACCCCTAGTAGGATAGAATTACCAAAATACCCCTAGT
* ** * *
28868731 TTGTAAAATTACCAAAATACCCCTAGCTTGTA-AG-ATTACCAAAATACCCCT-GAT
1 TTGTGAAATTACTGAAATACCCCTAG-TAGGATAGAATTACCAAAATACCCCTAG-T
*
28868785 TTGTGAAATTATTGAAATAC
1 TTGTGAAATTACTGAAATAC
28868805 TCTCGATTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
53 1 0.02
54 50 0.82
55 7 0.11
56 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (55 bp):
TTGTGAAATTACTGAAATACCCCTAGTAGGATAGAATTACCAAAATACCCCTAGT
Found at i:28868842 original size:26 final size:26
Alignment explanation
Indices: 28868813--28868890 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
28868803 ACTCTCGATT
28868813 TGTAAAATATCGAAATACCCTTGTAA
1 TGTAAAATATCGAAATACCCTTGTAA
* * * * *
28868839 TGTAAAAATACCAAAATACCCCTATAG
1 TGT-AAAATATCGAAATACCCTTGTAA
* *
28868866 GGTAAAATTATCGAGATACCCTTGT
1 TGTAAAA-TATCGAAATACCCTTGT
28868891 GGGGTAAAAG
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
26 7 0.18
27 32 0.82
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (26 bp):
TGTAAAATATCGAAATACCCTTGTAA
Found at i:28869146 original size:25 final size:25
Alignment explanation
Indices: 28869108--28869226 Score: 186
Period size: 25 Copynumber: 4.8 Consensus size: 25
28869098 AGGAAGTGCT
* *
28869108 AAAAAGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
28869133 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
28869158 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* * *
28869183 AAAAAGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
28869208 AAAAGGG-TTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28869227 ATTAAAAGAG
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
24 12 0.14
25 76 0.86
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:28869250 original size:49 final size:50
Alignment explanation
Indices: 28869108--28869251 Score: 152
Period size: 50 Copynumber: 2.9 Consensus size: 50
28869098 AGGAAGTGCT
* * **
28869108 AAAAA-GGCTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACC
1 AAAAAGGGCTTTGCCCCAGTTTACCGAAAAAGGCTAGGCCCCAGTTTACC
* ** *
28869157 GAAAAGGGCTTTGCCCCAGTTTACCGAAAAAGGCTTTGCCCCAGTTTATC
1 AAAAAGGGCTTTGCCCCAGTTTACCGAAAAAGGCTAGGCCCCAGTTTACC
**
28869207 AAAAAGGG-TTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAAGGGCTTTGCCCCAGTTTACCGAAAA-AGGCTAGGCC-CCAGTT
28869252 ATATGATAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
47 4 0.05
48 11 0.13
49 20 0.24
50 48 0.58
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (50 bp):
AAAAAGGGCTTTGCCCCAGTTTACCGAAAAAGGCTAGGCCCCAGTTTACC
Found at i:28875133 original size:42 final size:42
Alignment explanation
Indices: 28875076--28875199 Score: 126
Period size: 42 Copynumber: 2.9 Consensus size: 42
28875066 TCCGATATGT
*
28875076 ATTTTCGTTTAAGACCATGTCTAGGACGTTGGCATTGTATTTG
1 ATTTT-GTGTAAGACCATGTCTAGGACGTTGGCATTGTATTTG
* * *
28875119 ATTTTGTGTAAGACCCTGTCTCGGACAG-TGGCATCGATATTTG
1 ATTTTGTGTAAGACCATGTCTAGGAC-GTTGGCATTG-TATTTG
*** * *
28875162 ATTACATGTAAGACCACGTCTA-GATGTTGGCATTGTAT
1 ATTTTGTGTAAGACCATGTCTAGGACGTTGGCATTGTAT
28875200 GAGCTTTTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
41 4 0.06
42 34 0.52
43 28 0.42
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (42 bp):
ATTTTGTGTAAGACCATGTCTAGGACGTTGGCATTGTATTTG
Found at i:28884616 original size:47 final size:47
Alignment explanation
Indices: 28884407--28884614 Score: 308
Period size: 47 Copynumber: 4.4 Consensus size: 47
28884397 ATTGATGTAC
* *
28884407 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
*
28884454 AAGTATATATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
1 AAG--TGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
* *
28884503 AAGTGTATATATGTGATAGGGTCGAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
* * * *
28884550 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
*
28884597 AAGTGTATAAATGTGATA
1 AAGTGTATATATGTGATA
28884615 AGTCCCGAAG
Statistics
Matches: 148, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
47 102 0.69
49 46 0.31
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
Found at i:28888187 original size:43 final size:43
Alignment explanation
Indices: 28888087--28888209 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 43
28888077 AATTAAGAAG
* * * * * **
28888087 TCCAAACTCATTAAGTGGTCCGGGTTCGTTATATATG-TGGCA
1 TCCAAGCTCATTGAGTGGTCCGAGTTCATTATAGATGCAAGCA
28888129 TCCAAGCTCATTGAGTGGTCCGAGTTCATTATAGATGCAAGCA
1 TCCAAGCTCATTGAGTGGTCCGAGTTCATTATAGATGCAAGCA
* * * * *
28888172 TCCGAGCTTATTGAGTGGTCTGAGTTCATAATGGATGC
1 TCCAAGCTCATTGAGTGGTCCGAGTTCATTATAGATGC
28888210 GATACATGTG
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 32 0.47
43 36 0.53
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
TCCAAGCTCATTGAGTGGTCCGAGTTCATTATAGATGCAAGCA
Found at i:28891874 original size:42 final size:43
Alignment explanation
Indices: 28891792--28891890 Score: 112
Period size: 42 Copynumber: 2.3 Consensus size: 43
28891782 TCCCGGATGT
* * ** *
28891792 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCTCAGACAG
1 GGTCTTACACGTAAGTCAATATCGATGCCAATGTCCCAGACAG
*
28891835 GGTCTTACACG-AAGTCAGATA-CGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAAGTCA-ATATCGATGCCAATGTCCCAGACAG
*
28891877 GGTCTTATACGTAA
1 GGTCTTACACGTAA
28891891 ATCTCAATCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 32 0.68
43 15 0.32
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
GGTCTTACACGTAAGTCAATATCGATGCCAATGTCCCAGACAG
Found at i:28891991 original size:47 final size:47
Alignment explanation
Indices: 28891920--28892013 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
28891910 TCCCAGACAC
*
28891920 AGTCTTATACGATGTCTCAAACAGATGTCAACTTTTCTCTAGAAACA
1 AGTCTTATACGATATCTCAAACAGATGTCAACTTTTCTCTAGAAACA
* *
28891967 AGTCTTATACGATATCTCAGACAGATGTCAACTTTTCTTTAGAAACA
1 AGTCTTATACGATATCTCAAACAGATGTCAACTTTTCTCTAGAAACA
28892014 TACAGAGCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (47 bp):
AGTCTTATACGATATCTCAAACAGATGTCAACTTTTCTCTAGAAACA
Found at i:28893990 original size:27 final size:28
Alignment explanation
Indices: 28893953--28894036 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
28893943 CAGAGTAAGC
*
28893953 ACAGTTTGGGCCTAAGCCC-TTTCAGTA
1 ACAGTTAGGGCCTAAGCCCATTTCAGTA
* *
28893980 ACAGTTAGGGCCTTAA-CCCATTTTAGTT
1 ACAGTTAGGGCC-TAAGCCCATTTCAGTA
* *
28894008 ACAATTAGGGCCTTAGCCCATTTCAGTA
1 ACAGTTAGGGCCTAAGCCCATTTCAGTA
28894036 A
1 A
28894037 TAGTAGCAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 16 0.34
28 31 0.66
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (28 bp):
ACAGTTAGGGCCTAAGCCCATTTCAGTA
Found at i:28894066 original size:34 final size:34
Alignment explanation
Indices: 28894028--28894097 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
28894018 CCTTAGCCCA
* *
28894028 TTTCAGTAATAGTAGCAATCTGGGCCTGAGCCTG
1 TTTCAGTAACAGTAGCAATCTGGGCCTAAGCCTG
* *
28894062 TTTCAGTAACAGTAGCAGTGTGGGCCTAAGCCTG
1 TTTCAGTAACAGTAGCAATCTGGGCCTAAGCCTG
28894096 TT
1 TT
28894098 AACATATCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (34 bp):
TTTCAGTAACAGTAGCAATCTGGGCCTAAGCCTG
Found at i:28894574 original size:192 final size:192
Alignment explanation
Indices: 28894247--28894630 Score: 714
Period size: 192 Copynumber: 2.0 Consensus size: 192
28894237 CTAAAACAGT
28894247 ATTTGTAGCAAAGATGCCAGTAATAGGCTTATAGACTTTTAGTACACTTCCTCCAAGATCATATA
1 ATTTGTAGCAAAGATGCCAGTAATAGGCTTATAGACTTTTAGTACACTTCCTCCAAGATCATATA
* *
28894312 TCCTACACCATGCAATGCTACATAATATGAATGTAAATACAATAAGAATGGCATGCTCAAATAGT
66 TCCCACACCATGCAATGCTACATAATATGAATGTAAATACAATAAGAATGGCATGCTCAAACAGT
*
28894377 CATACATCACATAAGGGTAAAATCGTCATCTTACCAAAATAAGGGTCCAGGTACACTTACCG
131 CATACATCACATAAGGGTAAAATCATCATCTTACCAAAATAAGGGTCCAGGTACACTTACCG
* *
28894439 ATTTGTAGCAAATATGCCAGTAATAGGCTTATAGACTTTTAGTACACTTCCTCCAATATCATATA
1 ATTTGTAGCAAAGATGCCAGTAATAGGCTTATAGACTTTTAGTACACTTCCTCCAAGATCATATA
*
28894504 TCCCACCCCATGCAATGCTACATAATATGAATGTAAATACAATAAGAATGGCATGCTCAAACAGT
66 TCCCACACCATGCAATGCTACATAATATGAATGTAAATACAATAAGAATGGCATGCTCAAACAGT
28894569 CATACATCACATAAGGGTAAAATCATCATCTTACCAAAATAAGGGTCCAGGTACACTTACCG
131 CATACATCACATAAGGGTAAAATCATCATCTTACCAAAATAAGGGTCCAGGTACACTTACCG
28894631 GCCCAACAGT
Statistics
Matches: 186, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
192 186 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (192 bp):
ATTTGTAGCAAAGATGCCAGTAATAGGCTTATAGACTTTTAGTACACTTCCTCCAAGATCATATA
TCCCACACCATGCAATGCTACATAATATGAATGTAAATACAATAAGAATGGCATGCTCAAACAGT
CATACATCACATAAGGGTAAAATCATCATCTTACCAAAATAAGGGTCCAGGTACACTTACCG
Found at i:28910862 original size:13 final size:13
Alignment explanation
Indices: 28910844--28910871 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28910834 CATATATGCA
28910844 CATATTTACAAAC
1 CATATTTACAAAC
28910857 CATATTTACAAAC
1 CATATTTACAAAC
28910870 CA
1 CA
28910872 AAACATATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (13 bp):
CATATTTACAAAC
Found at i:28911206 original size:12 final size:12
Alignment explanation
Indices: 28911189--28911213 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28911179 TAACAAACCT
28911189 TTCATATGCTTA
1 TTCATATGCTTA
28911201 TTCATATGCTTA
1 TTCATATGCTTA
28911213 T
1 T
28911214 ATGCAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TTCATATGCTTA
Found at i:28911423 original size:39 final size:39
Alignment explanation
Indices: 28911328--28911468 Score: 210
Period size: 40 Copynumber: 3.6 Consensus size: 39
28911318 CGATATCTTT
* * *
28911328 CACACTAAGTGCCATAAATAGCCGAAGCTATCTCAAATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTC-GATCG
* * *
28911368 TATACTAAGTGCCATATATAGCTGAAGCTATGTCGATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGATCG
28911407 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATGTCG-ATCG
28911447 CACACTAAGTGCCATATATAGC
1 CACACTAAGTGCCATATATAGC
28911469 AGATTTGTCG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 36 0.40
40 55 0.60
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (39 bp):
CACACTAAGTGCCATATATAGCCGAAGCTATGTCGATCG
Found at i:28913123 original size:25 final size:27
Alignment explanation
Indices: 28913086--28913138 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28913076 TCAAACATGC
28913086 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
28913112 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
28913138 A
1 A
28913139 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:28914658 original size:26 final size:26
Alignment explanation
Indices: 28914628--28914683 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
28914618 TGAAATGCCC
28914628 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28914654 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
28914680 ATCA
1 ATCA
28914684 ATTTTTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28918008 original size:48 final size:48
Alignment explanation
Indices: 28917943--28918189 Score: 431
Period size: 48 Copynumber: 5.1 Consensus size: 48
28917933 GCTGAAATTG
*
28917943 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
28917991 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28918039 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-AT
* *
28918089 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28918137 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
28918185 ATGTA
1 ATGTA
28918190 GGCGATGTGT
Statistics
Matches: 189, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
48 142 0.75
49 4 0.02
50 43 0.23
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:28918123 original size:98 final size:98
Alignment explanation
Indices: 28917943--28918186 Score: 429
Period size: 98 Copynumber: 2.5 Consensus size: 98
28917933 GCTGAAATTG
* *
28917943 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATGAGATATGT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGT
*
28918006 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
66 ATATGTGGTAAAGCCGAATGGCTAATATGAAAT
*
28918039 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATATATGAGATATGT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGT
28918104 ATATGTGGTAAAGCCGAATGGCTAATATGAAAT
66 ATATGTGGTAAAGCCGAATGGCTAATATGAAAT
*
28918137 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
28918187 GTAGGCGATG
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
96 42 0.30
97 2 0.01
98 96 0.69
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (98 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGT
ATATGTGGTAAAGCCGAATGGCTAATATGAAAT
Found at i:28918444 original size:37 final size:37
Alignment explanation
Indices: 28918336--28918444 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
28918326 GGAAATATAT
*
28918336 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATA
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTA
*
28918373 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTA
* * * *
28918410 TTCGGGTAAGACTCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
28918445 CATCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTA
Found at i:28919743 original size:40 final size:40
Alignment explanation
Indices: 28919700--28920018 Score: 431
Period size: 40 Copynumber: 8.0 Consensus size: 40
28919690 GAGAGTTATA
* *
28919700 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
28919740 TATATCCGGGTTAAGTACCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
*
28919780 TATATCCGGGCTAAGTCCCGAAGAACATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * *
28919820 TATATCCGGGCTAAGTCCCGAAGATCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * * *
28919860 TGTATCCAGGCTAAGTCCCGAAGAGCATTAGTCCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * * * *
28919900 TATATCCGGGCTAAGTCTCAAAGAGCATTTGTGCTAGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
28919940 TATATCAGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * * *
28919980 TATATCCGGGCTAGGTCCCGAAGACCAATCATGCTGGTG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
28920019 ATGTGTATTC
Statistics
Matches: 241, Mismatches: 38, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 241 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
Found at i:28920232 original size:25 final size:25
Alignment explanation
Indices: 28920182--28920232 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
28920172 TGTGTAACAA
* *
28920182 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
28920207 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
28920232 C
1 C
28920233 GAGTTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:28923536 original size:48 final size:48
Alignment explanation
Indices: 28923471--28923717 Score: 440
Period size: 48 Copynumber: 5.1 Consensus size: 48
28923461 GCTGAAATTG
*
28923471 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
28923519 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28923567 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-AT
*
28923617 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28923665 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
28923713 ATGTA
1 ATGTA
28923718 GGCGATGTGT
Statistics
Matches: 191, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
48 143 0.75
49 4 0.02
50 44 0.23
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.32
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:28923651 original size:98 final size:98
Alignment explanation
Indices: 28923471--28923714 Score: 438
Period size: 98 Copynumber: 2.5 Consensus size: 98
28923461 GCTGAAATTG
* *
28923471 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATGAGATATGT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGT
28923534 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
66 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28923567 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATATATGAGATATGT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGT
28923632 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
66 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
28923665 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
28923715 GTAGGCGATG
Statistics
Matches: 141, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
96 42 0.30
97 2 0.01
98 97 0.69
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.32
Consensus pattern (98 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGT
ATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:28923972 original size:37 final size:37
Alignment explanation
Indices: 28923869--28923972 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
28923859 TATATTCCGA
* *
28923869 GTAAGACCCGATGACTACGTGTGGAGATTATATCCGG
1 GTAAGACCCGATGACTACGTGTGGAGATTTTATCCAG
* *
28923906 GTAAGACCCGATGACTACGTATGGAGATTTTGTCCAG
1 GTAAGACCCGATGACTACGTGTGGAGATTTTATCCAG
* * *
28923943 GTAAGACTCGATAACTTCGTGTGGAGATTT
1 GTAAGACCCGATGACTACGTGTGGAGATTT
28923973 CATCTGAGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (37 bp):
GTAAGACCCGATGACTACGTGTGGAGATTTTATCCAG
Found at i:28927796 original size:42 final size:42
Alignment explanation
Indices: 28927737--28927820 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
28927727 CCTCGCGCTA
28927737 TTTGTACGGGTTGCATAGCCCTTTGTTCAACCACTTGAGCCT
1 TTTGTACGGGTTGCATAGCCCTTTGTTCAACCACTTGAGCCT
28927779 TTTGTACGGGTTGCATAGCCCTTTGTTCAACCACTTGAGCCT
1 TTTGTACGGGTTGCATAGCCCTTTGTTCAACCACTTGAGCCT
28927821 GAGCTGGCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (42 bp):
TTTGTACGGGTTGCATAGCCCTTTGTTCAACCACTTGAGCCT
Found at i:28930418 original size:25 final size:27
Alignment explanation
Indices: 28930381--28930433 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28930371 TCAAACATGC
28930381 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
28930407 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
28930433 A
1 A
28930434 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:28935246 original size:34 final size:33
Alignment explanation
Indices: 28935208--28935273 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
28935198 ATTTCAATCA
* * * *
28935208 GGGCCTTAGCCCATTACAGTATCAGTATCAGTGT
1 GGGCCTGAGCCAATCACAGTAACAGTAT-AGTGT
28935242 GGGCCTGAGCCAATCACAGTAACAGTATAGTG
1 GGGCCTGAGCCAATCACAGTAACAGTATAGTG
28935274 CAGATATGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (33 bp):
GGGCCTGAGCCAATCACAGTAACAGTATAGTGT
Found at i:28938495 original size:2 final size:2
Alignment explanation
Indices: 28938490--28938532 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28938480 TATATATATA
28938490 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28938532 T
1 T
28938533 AGTCAACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:28952734 original size:31 final size:31
Alignment explanation
Indices: 28952692--28952755 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
28952682 CCTTTTCATA
*
28952692 TTTCATTTTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
28952723 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
28952754 TT
1 TT
28952756 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:28952996 original size:24 final size:24
Alignment explanation
Indices: 28952969--28953090 Score: 205
Period size: 24 Copynumber: 5.2 Consensus size: 24
28952959 GCCTAGCCTG
28952969 TTTTAATAACTGGGGCA-AAGCCC
1 TTTTAATAACTGGGGCATAAGCCC
28952992 TTTTTAATAACT-GGGCATAAGCCC
1 -TTTTAATAACTGGGGCATAAGCCC
28953016 -TTTAATAACTGGGGCATAAGCCC
1 TTTTAATAACTGGGGCATAAGCCC
28953039 TTTTAATAACTGGGGCATAAGCCC
1 TTTTAATAACTGGGGCATAAGCCC
*
28953063 TTTTAATAACTGGGGCGTAAGCCC
1 TTTTAATAACTGGGGCATAAGCCC
28953087 TTTT
1 TTTT
28953091 GCACTTCCTC
Statistics
Matches: 94, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
22 10 0.11
23 17 0.18
24 67 0.71
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (24 bp):
TTTTAATAACTGGGGCATAAGCCC
Found at i:28953023 original size:46 final size:48
Alignment explanation
Indices: 28952969--28953090 Score: 196
Period size: 46 Copynumber: 2.6 Consensus size: 48
28952959 GCCTAGCCTG
28952969 TTTTAATAACTGGGGCAAAGCCCTTTTTAATAACT-GGGCATAAGCCC
1 TTTTAATAACTGGGGCAAAGCCCTTTTTAATAACTGGGGCATAAGCCC
28953016 -TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
1 TTTTAATAACTGGGGCA-AAGCCCTTTTTAATAACTGGGGCATAAGCCC
*
28953063 TTTTAATAACTGGGGCGTAAGCCCTTTT
1 TTTTAATAACTGGGGC-AAAGCCCTTTT
28953091 GCACTTCCTC
Statistics
Matches: 69, Mismatches: 1, Indels: 8
0.88 0.01 0.10
Matches are distributed among these distances:
46 27 0.39
47 18 0.26
48 21 0.30
49 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (48 bp):
TTTTAATAACTGGGGCAAAGCCCTTTTTAATAACTGGGGCATAAGCCC
Found at i:28953164 original size:20 final size:20
Alignment explanation
Indices: 28953136--28953206 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
28953126 GCATTTATGA
*
28953136 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
28953156 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
28953176 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
28953196 ACAGATCATGT
1 ACATATCATGT
28953207 TTATCAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:28953171 original size:11 final size:11
Alignment explanation
Indices: 28953141--28953195 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
28953131 TATGAACATC
28953141 TCATGTGCATA
1 TCATGTGCATA
*
28953152 TCA--TACATA
1 TCATGTGCATA
28953161 TCATGTGCATA
1 TCATGTGCATA
* *
28953172 TCA--TACATG
1 TCATGTGCATA
28953181 TCATGTGCATA
1 TCATGTGCATA
28953192 TCAT
1 TCAT
28953196 ACAGATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:28953271 original size:25 final size:25
Alignment explanation
Indices: 28953243--28953290 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28953233 ATATATAAAC
* *
28953243 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGTAAAACGGTCATTTTTA
28953268 CCTAGGGGTAAAACGGTCATTTT
1 CCTAGGGGTAAAACGGTCATTTT
28953291 CATATTATAA
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:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGTAAAACGGTCATTTTTA
Found at i:28958638 original size:47 final size:47
Alignment explanation
Indices: 28958469--28958890 Score: 731
Period size: 47 Copynumber: 8.9 Consensus size: 47
28958459 CAAATCAAGC
* *
28958469 TCACATATA-A-ACTTTCACATTCATCACATCAGCCATTAGGCCCTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
28958514 TCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGCCCTA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
28958563 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28958612 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
28958659 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCATTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28958706 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
28958753 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCATTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28958800 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28958847 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
28958891 ATACTATCAT
Statistics
Matches: 367, Mismatches: 6, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
45 4 0.01
47 275 0.75
48 1 0.00
49 87 0.24
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:28962518 original size:39 final size:40
Alignment explanation
Indices: 28962411--28962747 Score: 348
Period size: 40 Copynumber: 8.5 Consensus size: 40
28962401 AGCATGATTA
* * * *
28962411 CTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* ** * *
28962451 CTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
*
28962491 CTCTTC-GAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* * *
28962530 CTCCTCGGGACTTAGCCCGGATATATCACTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
28962570 CTCTTCGGAACTTAG-CCGGATACATCACTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
28962609 CTCTTC-GGACTTAGCCCGGATACATCGCTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
** * * *
28962648 CTCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACCAATG
1 CTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAATG
* ** *
28962688 C-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAATG
28962728 C-CTTCGGGACTTAGCCCGGA
1 CTCTTCGGGACTTAGCCCGGA
28962748 CATCATTCGA
Statistics
Matches: 251, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
38 10 0.04
39 106 0.42
40 127 0.51
41 8 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
Found at i:28962524 original size:79 final size:79
Alignment explanation
Indices: 28962396--28962666 Score: 348
Period size: 79 Copynumber: 3.4 Consensus size: 79
28962386 CGAATACACG
* * * * * * * * *
28962396 TCACCAGCATGATTACTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTTGGGG
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTC-TTGGGA
* *
28962461 TTTAGCACGGATATA
65 CTTAGCCCGGATATA
* *
28962476 TCACTAGCACGAATGCTCTTC-GAACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCT-CTTGGGA
28962540 CTTAGCCCGGATATA
65 CTTAGCCCGGATATA
* *
28962555 TCACTAGCATGAATGCTCTTCGGAACTTAG-CCGGATACATCACTAGCATGAATGCTCTTCGGAC
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTGGGAC
*
28962619 TTAGCCCGGATACA
66 TTAGCCCGGATATA
* *
28962633 TCGCTAGCATGAATGCTCTTCGGGACTTAGCCCG
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCG
28962667 ATTTAGTAAC
Statistics
Matches: 168, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
78 47 0.28
79 95 0.57
80 26 0.15
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTGGGAC
TTAGCCCGGATATA
Found at i:28962624 original size:118 final size:118
Alignment explanation
Indices: 28962415--28962709 Score: 378
Period size: 118 Copynumber: 2.5 Consensus size: 118
28962405 TGATTACTCT
* * * * *** *
28962415 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTTGGGGTTTAGCACGGATATATCAC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGC-CGGATACATCAC
28962480 TAGCACGAATGCTCTTCGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
65 TAGCACGAATGCTCTTCGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
*
28962534 TCGGGACTTAGCCCGGATATATCACTAGCATGAATGCTCTTCGGAACTTAGCCGGATACATCACT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCGGATACATCACT
* * * * *
28962599 AGCATGAATGCTCTTCGGACTTAGCCCGGATACATCGCTAGCATGAATGCTCT
66 AGCACGAATGCTCTTCGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
* * * * *
28962652 TCGGGACTTAGCCC-GATTTAGTAACTCGCACCAATGC-CTTCGGATCTTAGTCCGGATA
1 TCGGGACTTAGCCCGGATATA-TCACTAGCACGAATGCTCTTCGGAACTTAG-CCGGATA
28962710 TGGTCACTTA
Statistics
Matches: 154, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
117 17 0.11
118 93 0.60
119 44 0.29
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (118 bp):
TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCGGATACATCACT
AGCACGAATGCTCTTCGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
Found at i:28962733 original size:118 final size:117
Alignment explanation
Indices: 28962415--28962747 Score: 368
Period size: 118 Copynumber: 2.8 Consensus size: 117
28962405 TGATTACTCT
* * * * ***
28962415 TCGGGACCTAGCCCGGATATA-ACACCAGCACGAATGCTCTTTGGGGTTTAGCACGGATATATCA
1 TCGGGACTTAGCCCGGATATATA-ACTAGCACCAATGCTCTTCGGAACTTAGC-CGGATATATCA
*
28962479 CTAGCACGAATGCTCTTCGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
64 CTAGCAC-AATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCC
* ** *
28962534 TCGGGACTTAGCCCGGATATATCACTAGCATGAATGCTCTTCGGAACTTAGCCGGATACATCACT
1 TCGGGACTTAGCCCGGATATATAACTAGCACCAATGCTCTTCGGAACTTAGCCGGATATATCACT
* * * *
28962599 AGCATGAATGCTCTTCGGACTTAGCCCGGATACATCGCTAGCATGAATGCTCT
66 AGCA-CAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCC
* * * *
28962652 TCGGGACTTAGCCC-GATTTAGTAACTCGCACCAATGC-CTTCGGATCTTAGTCCGGATATGGTC
1 TCGGGACTTAGCCCGGATATA-TAACTAGCACCAATGCTCTTCGGAACTTAG-CCGGATAT-ATC
*
28962715 ACTTAGCACAAAGC-CTTCGGGACTTAGCCCGGA
63 AC-TAGCACAATGCTCTTC-GGACTTAGCCCGGA
28962748 CATCATTCGA
Statistics
Matches: 183, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
117 17 0.09
118 96 0.52
119 65 0.36
120 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (117 bp):
TCGGGACTTAGCCCGGATATATAACTAGCACCAATGCTCTTCGGAACTTAGCCGGATATATCACT
AGCACAATGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCC
Found at i:28963091 original size:29 final size:29
Alignment explanation
Indices: 28963052--28963130 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
28963042 CTTAATAATC
*
28963052 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
28963082 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
28963111 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28963131 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:28963173 original size:43 final size:43
Alignment explanation
Indices: 28963112--28963214 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
28963102 TGCATTTCAA
28963112 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
28963155 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
28963198 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
28963215 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:28965126 original size:37 final size:37
Alignment explanation
Indices: 28965076--28965154 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28965066 TTATTACGAA
* * *
28965076 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
28965113 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
28965150 GTCTT
1 GTCTT
28965155 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:28965345 original size:47 final size:47
Alignment explanation
Indices: 28965271--28965678 Score: 732
Period size: 47 Copynumber: 8.7 Consensus size: 47
28965261 GCCCTTCGGG
*
28965271 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
28965319 ACTTTCACATTCATCACATCAGCCATTAGGCC-TATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
28965367 ACTTTCACATTCATCACATCGGCCATTAGGCC-TATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
28965413 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
28965460 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
28965507 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
28965554 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
28965601 ACTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
28965647 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
28965679 ATACTATCAT
Statistics
Matches: 350, Mismatches: 6, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
46 91 0.26
47 210 0.60
48 49 0.14
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:28968516 original size:31 final size:31
Alignment explanation
Indices: 28968474--28968537 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
28968464 CCTTTTCGTA
* *
28968474 TTTCATTTTTCATAACACTGGGCTGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
28968505 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
28968536 TT
1 TT
28968538 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:28968807 original size:23 final size:24
Alignment explanation
Indices: 28968731--28968874 Score: 213
Period size: 24 Copynumber: 6.0 Consensus size: 24
28968721 GCTTTATCAT
*
28968731 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
28968756 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
28968781 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
28968804 ATAACTAGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28968828 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28968852 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28968875 GCACTTCCTC
Statistics
Matches: 111, Mismatches: 3, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
23 23 0.21
24 57 0.51
25 25 0.23
26 6 0.05
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28968946 original size:9 final size:9
Alignment explanation
Indices: 28968932--28968988 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
28968922 ATCTCGTGTG
28968932 CATATCATA
1 CATATCATA
*
28968941 CATATCATGTG
1 CATATCA--TA
28968952 CATATCATA
1 CATATCATA
* *
28968961 CATGTCATGTG
1 CATATCA--TA
28968972 CATATCATA
1 CATATCATA
28968981 CATATCAT
1 CATATCAT
28968989 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:28968951 original size:20 final size:20
Alignment explanation
Indices: 28968928--28968990 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
28968918 GAACATCTCG
28968928 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
28968948 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
28968968 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
28968988 TGT
1 TGT
28968991 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:28972857 original size:55 final size:53
Alignment explanation
Indices: 28972770--28973026 Score: 235
Period size: 55 Copynumber: 4.9 Consensus size: 53
28972760 ATTAGGGTTT
*
28972770 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAA-GG
* * * * * *
28972825 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAACTTACTATAAGG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGG
* * * *
28972879 CAAAGG-TCCCATATAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGG
1 --AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGG
* *
28972932 CAAGGATACCATGTAAGACCATGTCAAGACATGGGAA-TGGTAAGTTTC-AA--
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGG
* * *
28972982 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT
28973027 ACCCGCGTAT
Statistics
Matches: 166, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
49 41 0.25
52 7 0.04
53 37 0.22
54 14 0.08
55 63 0.38
56 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGG
Found at i:28972997 original size:49 final size:49
Alignment explanation
Indices: 28972933--28973026 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
28972923 TTCATAAGGC
* * *
28972933 AAGGATACCATGTAAGACCATGTCAAGACATGGGAATGGTAAGTTTCAA
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGTTTCAA
*
28972982 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAGTT
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGTT
28973027 ACCCGCGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (49 bp):
AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGTTTCAA
Found at i:28973227 original size:4 final size:4
Alignment explanation
Indices: 28973218--28973265 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
28973208 AAATTTGATC
** * * *
28973218 AAGT AAGT AAGT ATTT AAGT AAGT GAGT AAGT GAGT AAGT GAGT AAGT
1 AAGT AAGT AAGT AAGT AAGT AAGT AAGT AAGT AAGT AAGT AAGT AAGT
28973266 GAAGAAGTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (4 bp):
AAGT
Found at i:28973246 original size:8 final size:8
Alignment explanation
Indices: 28973235--28973267 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
28973225 TAAGTATTTA
28973235 AGTAAGTG
1 AGTAAGTG
28973243 AGTAAGTG
1 AGTAAGTG
28973251 AGTAAGTG
1 AGTAAGTG
28973259 AGTAAGTG
1 AGTAAGTG
28973267 A
1 A
28973268 AGAAGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.24
Consensus pattern (8 bp):
AGTAAGTG
Found at i:28975961 original size:25 final size:24
Alignment explanation
Indices: 28975892--28976070 Score: 105
Period size: 25 Copynumber: 7.2 Consensus size: 24
28975882 AGCTGTTACA
28975892 CTTTTCATAAGATTAGCCACAAAGG
1 CTTTTCATAA-ATTAGCCACAAAGG
* * *
28975917 C-ATTC-TAGATAATACACCACAAAGG
1 CTTTTCATA-A-ATTA-GCCACAAAGG
**
28975942 CTTTTCATAACATTAGCCACAAATT
1 CTTTTCATAA-ATTAGCCACAAAGG
* *
28975967 CTTTCCAGATAA-TACGCCACAAAGG
1 CTTTTCATA-AATTA-GCCACAAAGG
*
28975992 CTTTCCATAATATTAGCCACAAAGG
1 CTTTTCATAA-ATTAGCCACAAAGG
* * *
28976017 -TTTTCCAGATAATTCGCCAAAAAGG
1 CTTTT-CATA-AATTAGCCACAAAGG
* * *
28976042 ATTTTCATAAGATTAACCATAAAGG
1 CTTTTCATAA-ATTAGCCACAAAGG
28976067 CTTT
1 CTTT
28976071 CCAAATAATA
Statistics
Matches: 118, Mismatches: 24, Indels: 24
0.71 0.14 0.14
Matches are distributed among these distances:
23 2 0.02
24 14 0.12
25 85 0.72
26 15 0.13
27 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (24 bp):
CTTTTCATAAATTAGCCACAAAGG
Found at i:28975977 original size:50 final size:50
Alignment explanation
Indices: 28975892--28976107 Score: 263
Period size: 50 Copynumber: 4.3 Consensus size: 50
28975882 AGCTGTTACA
* * *
28975892 CTTTTCATAAGATTAGCCACAAAGGCATTCTAGATAATACACCACAAAGG
1 CTTTTCATAAGATTAGCCACAAAGGCTTTCCAGATAATACGCCACAAAGG
* **
28975942 CTTTTCATAACATTAGCCACAAATTCTTTCCAGATAATACGCCACAAAGG
1 CTTTTCATAAGATTAGCCACAAAGGCTTTCCAGATAATACGCCACAAAGG
* * * * *
28975992 CTTTCCATAATATTAGCCACAAAGGTTTTCCAGATAATTCGCCAAAAAGG
1 CTTTTCATAAGATTAGCCACAAAGGCTTTCCAGATAATACGCCACAAAGG
* * * * *
28976042 ATTTTCATAAGATTAACCATAAAGGCTTTCCAAATAATACTCCACCAAA-G
1 CTTTTCATAAGATTAGCCACAAAGGCTTTCCAGATAATACGCCA-CAAAGG
*
28976092 CTTTTCATAAGTTTAG
1 CTTTTCATAAGATTAG
28976108 GGTTTAGTTT
Statistics
Matches: 139, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
50 136 0.98
51 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (50 bp):
CTTTTCATAAGATTAGCCACAAAGGCTTTCCAGATAATACGCCACAAAGG
Found at i:28984833 original size:23 final size:23
Alignment explanation
Indices: 28984807--28984852 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28984797 TATTGGAAGA
28984807 TTTAGTGTTTAGAGCTCAAGTTG
1 TTTAGTGTTTAGAGCTCAAGTTG
28984830 TTTAGTGTTTAGAGCTCAAGTTG
1 TTTAGTGTTTAGAGCTCAAGTTG
28984853 AATTTAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (23 bp):
TTTAGTGTTTAGAGCTCAAGTTG
Found at i:29003052 original size:47 final size:47
Alignment explanation
Indices: 29002994--29003124 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
29002984 ATCACTCGAT
* *
29002994 AAGTACCTATACCATGGCCCGTAGCTAAATAAAGGTAACTTATCTTG
1 AAGTACCTATACCATGGCCCGTAGCTAAATAAAGGTAACTCATCTTC
* * * * * *
29003041 GAGTACTTATACCATGGCCCATAGCCAAATCAAGGTAACTCCTCTTC
1 AAGTACCTATACCATGGCCCGTAGCTAAATAAAGGTAACTCATCTTC
* * *
29003088 AAATACCTATATCATGGCCCGTAGCTAAATTAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCTAAATAAAGGTA
29003125 TTATTCACAC
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCTAAATAAAGGTAACTCATCTTC
Found at i:29012085 original size:15 final size:15
Alignment explanation
Indices: 29012065--29012095 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29012055 ACTTGTCTTT
*
29012065 ATTACATTTTTATGG
1 ATTACAATTTTATGG
29012080 ATTACAATTTTATGG
1 ATTACAATTTTATGG
29012095 A
1 A
29012096 ATGATTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
ATTACAATTTTATGG
Found at i:29013180 original size:42 final size:41
Alignment explanation
Indices: 29013134--29013288 Score: 175
Period size: 42 Copynumber: 3.7 Consensus size: 41
29013124 CAAAGACTAT
*
29013134 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
*
29013176 GTGTAAAACCATATCTGGGATATGGCATCGATATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
*** * * * **
29013218 GTGTAAGGTTATATATGGGCTATTGGCATTGATACAAGATTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATT-C
*
29013261 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
29013289 TGGTATAGTA
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 63 0.68
43 30 0.32
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTC
Found at i:29014400 original size:20 final size:20
Alignment explanation
Indices: 29014375--29014426 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
29014365 CCGGTTAGGG
*
29014375 ACACGGGCGTGTTCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
29014395 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
29014415 ACACGGGCGTGT
1 ACACGGGCGTGT
29014427 GGCTCTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.35, G:0.33, T:0.13
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:29017804 original size:2 final size:2
Alignment explanation
Indices: 29017797--29017837 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
29017787 TTTCTTTTCA
* *
29017797 TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29017838 TGAGAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:29017820 original size:14 final size:14
Alignment explanation
Indices: 29017797--29017837 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
29017787 TTTCTTTTCA
*
29017797 TCTCTCTCTCTCTC
1 TCTCTTTCTCTCTC
29017811 TCTCTTTCTCTCTC
1 TCTCTTTCTCTCTC
29017825 TCTCTTTCTCTCT
1 TCTCTTTCTCTCT
29017838 TGAGAAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (14 bp):
TCTCTTTCTCTCTC
Done.