Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 29 of 79
Found at i:9924924 original size:16 final size:15
Alignment explanation
Indices: 9924899--9924933 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
9924889 AAAGTTTATA
*
9924899 ATAATTAATATATATT
1 ATAATAAATATA-ATT
9924915 ATAATAAATATAATT
1 ATAATAAATATAATT
9924930 ATAA
1 ATAA
9924934 ACTAGCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:9940198 original size:25 final size:25
Alignment explanation
Indices: 9940096--9940204 Score: 101
Period size: 25 Copynumber: 4.4 Consensus size: 25
9940086 TACACGATCA
* *
9940096 GTGAATCGGTATGCTCTTACGAGCT
1 GTGAATCAGTATGCTCTCACGAGCT
* * *
9940121 GTAAATCAGTATGCTCTCATGATCT
1 GTGAATCAGTATGCTCTCACGAGCT
* * * **
9940146 GTAAATCAATATGCTCTCGCGAATT
1 GTGAATCAGTATGCTCTCACGAGCT
* *
9940171 GTGAATCGGTATGCTCTTACGAGCT
1 GTGAATCAGTATGCTCTCACGAGCT
*
9940196 GTGAGTCAG
1 GTGAATCAG
9940205 AACTTAACTA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (25 bp):
GTGAATCAGTATGCTCTCACGAGCT
Found at i:9944519 original size:24 final size:25
Alignment explanation
Indices: 9944482--9944537 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
9944472 AAAATCTACC
*
9944482 CTAAAAAGAAAAAAGAAAACTTAAA
1 CTAAAAAGAAAAAAGAAAACCTAAA
* *
9944507 CTAAAAA-AGAAAAGAAAACCTAAC
1 CTAAAAAGAAAAAAGAAAACCTAAA
9944531 CTAAAAA
1 CTAAAAA
9944538 CTATAAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.11
Consensus pattern (25 bp):
CTAAAAAGAAAAAAGAAAACCTAAA
Found at i:9946847 original size:20 final size:20
Alignment explanation
Indices: 9946824--9946874 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
9946814 CAACTCATAT
9946824 TATCGATACTTACCTTTGGG
1 TATCGATACTTACCTTTGGG
9946844 TATCGATACTTACCTTTGGG
1 TATCGATACTTACCTTTGGG
9946864 TATCGATACTT
1 TATCGATACTT
9946875 TCTTTTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (20 bp):
TATCGATACTTACCTTTGGG
Found at i:9946881 original size:20 final size:19
Alignment explanation
Indices: 9946778--9946891 Score: 93
Period size: 20 Copynumber: 5.8 Consensus size: 19
9946768 CTAATCTGAG
* *
9946778 CTTTGGGTATCGATACTTT
1 CTTTTGGTATCGATACTTA
* *
9946797 CTTTTGGTATTGATACTCAA
1 CTTTTGGTATCGATACT-TA
** **
9946817 CTCATATTATCGATACTTA
1 CTTTTGGTATCGATACTTA
*
9946836 CCTTTGGGTATCGATACTTA
1 -CTTTTGGTATCGATACTTA
* *
9946856 CCTTTGGGTATCGATACTTT
1 -CTTTTGGTATCGATACTTA
*
9946876 CTTTTGGTACCGATAC
1 CTTTTGGTATCGATAC
9946892 CATTTTAACA
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
19 30 0.40
20 45 0.60
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (19 bp):
CTTTTGGTATCGATACTTA
Found at i:9952682 original size:40 final size:40
Alignment explanation
Indices: 9952616--9952714 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
9952606 TAGGGTAACA
* *
9952616 ACCTTTTTTAACCTTTTAATTGGATATCCATTTCAGATAT
1 ACCTTTTTCAACCTTTTCATTGGATATCCATTTCAGATAT
* * * * *
9952656 ATCTTTTTCAACATTTTCATTTGATATCTATTTCGGATAT
1 ACCTTTTTCAACCTTTTCATTGGATATCCATTTCAGATAT
*
9952696 ACCCTTTTCAACCTTTTCA
1 ACCTTTTTCAACCTTTTCA
9952715 AGAATTCAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.48
Consensus pattern (40 bp):
ACCTTTTTCAACCTTTTCATTGGATATCCATTTCAGATAT
Found at i:9956616 original size:18 final size:18
Alignment explanation
Indices: 9956595--9956633 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9956585 TAGCCATTTA
* *
9956595 TTTGTATTTATTTTTATT
1 TTTGTATTTAGTTTAATT
*
9956613 TTTGTTTTTAGTTTAATT
1 TTTGTATTTAGTTTAATT
9956631 TTT
1 TTT
9956634 ACATTCTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTGTATTTAGTTTAATT
Found at i:9962535 original size:26 final size:24
Alignment explanation
Indices: 9962474--9962551 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 24
9962464 TTATCTATTA
*
9962474 TTATTAGTTATATTA-TATTATTTAT
1 TTATTAGTTATATTATTATT-TTT-C
9962499 TTATT-GTTTATCATCTATTATTTTTC
1 TTATTAG-TTAT-AT-TATTATTTTTC
9962525 TTATTAGTTATATTATTTTATTTTTC
1 TTATTAGTTATATTA--TTATTTTTC
9962551 T
1 T
9962552 AATTCTACTT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
24 3 0.07
25 11 0.24
26 21 0.47
27 6 0.13
28 4 0.09
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.67
Consensus pattern (24 bp):
TTATTAGTTATATTATTATTTTTC
Found at i:9962536 original size:46 final size:46
Alignment explanation
Indices: 9962445--9962547 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 46
9962435 TTGCCCTATT
* * *
9962445 TTATTTATTTATTTGTTTCTTATCTATTATTATTAGTTATATTATA
1 TTATTTATTTATTTGTTTATCATCTATTATTATTACTTATATTATA
*
9962491 TTATTTATTTA-TTGTTTATCATCTATTATT-TTTCTTATTAGTTATA
1 TTATTTATTTATTTGTTTATCATCTATTATTATTACTTA-TA-TTATA
9962537 TTATTTTATTT
1 TTA-TTTATTT
9962548 TTCTAATTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
44 5 0.10
45 19 0.38
46 19 0.38
47 7 0.14
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.67
Consensus pattern (46 bp):
TTATTTATTTATTTGTTTATCATCTATTATTATTACTTATATTATA
Found at i:9964250 original size:5 final size:5
Alignment explanation
Indices: 9964240--9964299 Score: 68
Period size: 5 Copynumber: 11.6 Consensus size: 5
9964230 ATGAGGATCA
* *
9964240 TTTAT TTTAT TTTCT TTCT-T TTTAT TTTAT TTTAT TTTAT TTTAT GTTTTT
1 TTTAT TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT
9964291 TTCTAT TTT
1 TT-TAT TTT
9964300 TAGTCGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
4 1 0.02
5 38 0.79
6 9 0.19
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:9978969 original size:20 final size:20
Alignment explanation
Indices: 9978941--9978987 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9978931 ATATACGTAT
*
9978941 ATATATTATATTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
9978961 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
9978981 ATATATT
1 ATATATT
9978988 TTTCTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:9991617 original size:44 final size:44
Alignment explanation
Indices: 9991520--9991628 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
9991510 GAATAGGGTA
* *
9991520 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTAAAACCAAT
* **
9991564 AATCCTATCTCCCTGAAGTTGAAGTGGAGTGGATTAAAACCACA-
1 AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTAAAACCA-AT
* * *
9991608 GATCTTATCTCTCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTG
9991629 CTGAGAGCAG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 54 0.98
45 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTAAAACCAAT
Found at i:9991711 original size:44 final size:46
Alignment explanation
Indices: 9991647--9991759 Score: 142
Period size: 44 Copynumber: 2.5 Consensus size: 46
9991637 AGTCGCATCT
* * * *
9991647 AGTCTTATCTCCCTAAAGTTGCAGA-GGAGTAGACT-GAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGATGGAGCAGACTCAAGAAAGCA
*
9991691 GGTCTTATCTCCCTGAAGTTGCA-ATGGAGCAGACTCAAGAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGATGGAGCAGACTCAAGAAAGCA
* *
9991736 AGTCTTATCCCCCTGAAATTGCAG
1 AGTCTTATCTCCCTGAAGTTGCAG
9991760 TGGGGTAGGC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 30 0.52
45 27 0.47
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (46 bp):
AGTCTTATCTCCCTGAAGTTGCAGATGGAGCAGACTCAAGAAAGCA
Found at i:9993405 original size:20 final size:20
Alignment explanation
Indices: 9993377--9993423 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9993367 ATATACGTAT
*
9993377 ATATATTATATTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
9993397 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
9993417 ATATATT
1 ATATATT
9993424 TTTCTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:9998921 original size:25 final size:25
Alignment explanation
Indices: 9998893--9998958 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
9998883 CCTATACATT
9998893 TATGCTCAAACGAGCTATGAATCGG
1 TATGCTCAAACGAGCTATGAATCGG
** * *
9998918 TATGCTCTCACGACCTGTGAATCGG
1 TATGCTCAAACGAGCTATGAATCGG
*
9998943 TAAGCTCATAA-GAGCT
1 TATGCTCA-AACGAGCT
9998959 GTGGTGTGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (25 bp):
TATGCTCAAACGAGCTATGAATCGG
Found at i:10001941 original size:50 final size:50
Alignment explanation
Indices: 10001862--10001986 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 50
10001852 NNNNNNAGAT
** *
10001862 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCA-TGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTG-CCAGCGCCATGTCCCAGAC
** *
10001912 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAGCGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAGCGCCATGTCCCAGAC
10001962 ATGGTCTTACATGGGACCTCTCATA
1 ATGGTCTTACATGGGACCTCTCATA
10001987 ACCTCAATGA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
49 3 0.05
50 62 0.95
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATCGGTGCCAGCGCCATGTCCCAGAC
Found at i:10005265 original size:18 final size:18
Alignment explanation
Indices: 10005238--10005275 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10005228 CAAATTAGAG
10005238 CAACAGCCTCAACAACCA
1 CAACAGCCTCAACAACCA
* *
10005256 CAACATCCTCCACAACCA
1 CAACAGCCTCAACAACCA
10005274 CA
1 CA
10005276 CCGAGAGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.47, G:0.03, T:0.08
Consensus pattern (18 bp):
CAACAGCCTCAACAACCA
Found at i:10005946 original size:34 final size:38
Alignment explanation
Indices: 10005881--10005956 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 38
10005871 CAGTTTGTTT
* *
10005881 TTTTTTTTTCTTTCTGTTTTTTTATTGTTTTTATTTGC
1 TTTTTTTTTCCTTCTGTTTTTTTATTGTTTTTATTGGC
*
10005919 TTTTTTTTTCCTT-TG-TTTTTT-TT-TTTTTGTTGGC
1 TTTTTTTTTCCTTCTGTTTTTTTATTGTTTTTATTGGC
10005953 TTTT
1 TTTT
10005957 ATAGTGCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 13 0.37
35 2 0.06
36 6 0.17
37 2 0.06
38 12 0.34
ACGTcount: A:0.03, C:0.08, G:0.09, T:0.80
Consensus pattern (38 bp):
TTTTTTTTTCCTTCTGTTTTTTTATTGTTTTTATTGGC
Found at i:10014991 original size:16 final size:17
Alignment explanation
Indices: 10014964--10014997 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
10014954 AGATATAGTA
10014964 AAATATTTTAAAAAAAT
1 AAATATTTTAAAAAAAT
10014981 AAATA-TTTAAAAAAAT
1 AAATATTTTAAAAAAAT
10014997 A
1 A
10014998 CATGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATATTTTAAAAAAAT
Found at i:10017474 original size:16 final size:17
Alignment explanation
Indices: 10017447--10017478 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10017437 GCTTAGAAAT
10017447 TATTTTTATCATACTAC
1 TATTTTTATCATACTAC
10017464 TATTTTT-TCATACTA
1 TATTTTTATCATACTA
10017479 ATTAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTATCATACTAC
Found at i:10019123 original size:28 final size:28
Alignment explanation
Indices: 10019091--10019162 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
10019081 TAATGGGATT
* *
10019091 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
10019119 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
10019147 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
10019163 ACTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:10019168 original size:24 final size:24
Alignment explanation
Indices: 10019091--10019171 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 24
10019081 TAATGGGATT
* *
10019091 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGA----AATTATTA
10019119 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGA-A---ATTATTA
*
10019147 AGCACTAAGTGTGCGAACTTATTA
1 AGCACTAAGTGTGCGAAATTATTA
10019171 A
1 A
10019172 ATATTTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 7 0.15
25 1 0.02
27 1 0.02
28 37 0.80
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCACTAAGTGTGCGAAATTATTA
Found at i:10019967 original size:70 final size:70
Alignment explanation
Indices: 10019883--10020052 Score: 268
Period size: 70 Copynumber: 2.4 Consensus size: 70
10019873 TTTGATGCTT
* * * * *
10019883 AAATGCTGCCCAATTCGTTGTATTTATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTGA
1 AAATGTTGCTCAATTCGGTATATATATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTGA
10019948 TGTAA
66 TGTAA
* *
10019953 AAATGTTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGA
1 AAATGTTGCTCAATTCGGTATATATATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTGA
10020018 TGTAA
66 TGTAA
*
10020023 AAATGTTGCTCAATTTGGTATATATATGCT
1 AAATGTTGCTCAATTCGGTATATATATGCT
10020053 GTCCAATTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 93 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (70 bp):
AAATGTTGCTCAATTCGGTATATATATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTGA
TGTAA
Found at i:10020050 original size:47 final size:47
Alignment explanation
Indices: 10019996--10020108 Score: 199
Period size: 47 Copynumber: 2.4 Consensus size: 47
10019986 TAAATTGTTG
10019996 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
*
10020043 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTA
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
* *
10020090 TATATATCCTGCCCAATTT
1 TATATATGCTGTCCAATTT
10020109 GTTGTATATA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (47 bp):
TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
Found at i:10020053 original size:70 final size:70
Alignment explanation
Indices: 10019907--10020053 Score: 285
Period size: 70 Copynumber: 2.1 Consensus size: 70
10019897 TCGTTGTATT
*
10019907 TATGCTACCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
10019972 ATATA
66 ATATA
10019977 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
10020042 ATATA
66 ATATA
10020047 TATGCTG
1 TATGCTG
10020054 TCCAATTTTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 76 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (70 bp):
TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
ATATA
Found at i:10020059 original size:117 final size:118
Alignment explanation
Indices: 10019926--10020156 Score: 401
Period size: 117 Copynumber: 2.0 Consensus size: 118
10019916 TAAATTGTTG
* *
10019926 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCTAAAT
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATCCTGCCCAAAT
*
10019991 TGTTGTATATATGCTGTCCAA-TTTTGATGTAAAAATGTTGCTCAATTTGGTA
66 TGTTGTATATATGCTGTCCAATTTTTGATGTAAAAATGCTGCTCAATTTGGTA
* *
10020043 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTATATATATCCTGCCCAATT
1 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATCCTGCCCAAAT
*
10020108 TGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTT
66 TGTTGTATATATGCTGTCCAATTTTTGATGTAAAAATGCTGCTCAATTT
10020157 TGTTGTGTAT
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
117 82 0.77
118 25 0.23
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (118 bp):
TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATCCTGCCCAAAT
TGTTGTATATATGCTGTCCAATTTTTGATGTAAAAATGCTGCTCAATTTGGTA
Found at i:10020185 original size:72 final size:70
Alignment explanation
Indices: 10020043--10020259 Score: 231
Period size: 72 Copynumber: 3.1 Consensus size: 70
10020033 CAATTTGGTA
* * * * *
10020043 TATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGTATATATATCCTGCCCAATT
1 TATATATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATATATATCCTGACCAAAT
10020108 TGTTG
66 TGTTG
* * * *
10020113 TATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTTGTTGTGTATATGCTGACCAA
1 TATATATGCTGTCCAA-TTTTGGTGTAAAAATGCTGCTCAA-TTTGGTATATATATCCTGACCAA
10020178 ATTGTTG
64 ATTGTTG
* * * * * *
10020185 TATATATGCTGTCCAAATTTTAGTGTGAAAATG-T-CGTCTAGTTTGGTATATAAATGCTGTCCA
1 TATATATGCTGTCC-AATTTTGGTGTAAAAATGCTGC-TC-AATTTGGTATATATATCCTGACCA
*
10020248 AATTGATG
63 AATTGTTG
10020256 TATA
1 TATA
10020260 AGGGCTGTCC
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
70 17 0.14
71 52 0.42
72 53 0.43
73 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (70 bp):
TATATATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATATATATCCTGACCAAAT
TGTTG
Found at i:10026414 original size:23 final size:23
Alignment explanation
Indices: 10026384--10026430 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
10026374 TGCTTAATTA
10026384 TGTTGTATATATGCTGCCCAAAT
1 TGTTGTATATATGCTGCCCAAAT
*
10026407 TGTTGTATATATGCTGTCCAAAT
1 TGTTGTATATATGCTGCCCAAAT
10026430 T
1 T
10026431 TTGGTGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTGTATATATGCTGCCCAAAT
Found at i:10026448 original size:25 final size:25
Alignment explanation
Indices: 10026389--10026478 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 25
10026379 AATTATGTTG
* *
10026389 TATATATGCTGCCCAAATTGTT-GTA
1 TATAAATGCTGTCCAAATT-TTGGTA
*
10026414 TAT--ATGCTGTCCAAATTTTGGTG
1 TATAAATGCTGTCCAAATTTTGGTA
* *
10026437 TGA-AAATGCTGT-C-TAGTTTGGTA
1 T-ATAAATGCTGTCCAAATTTTGGTA
10026460 TATAAATGCTGTCCAAATT
1 TATAAATGCTGTCCAAATT
10026479 GATATATAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
22 3 0.06
23 33 0.65
24 3 0.06
25 12 0.24
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (25 bp):
TATAAATGCTGTCCAAATTTTGGTA
Found at i:10026499 original size:71 final size:72
Alignment explanation
Indices: 10026351--10026499 Score: 160
Period size: 71 Copynumber: 2.1 Consensus size: 72
10026341 TTTGGTACTA
* * * * * *
10026351 TCCAATTTTTGGTGTAAAAATGCTGCTTAATTATGTTGTATATATGCTGCCCAAATTGTTGTATA
1 TCCAAATTTTGGTGTAAAAATGCTGCTTAATTATGGTATATAAATGCTGCCCAAATTGATATATA
*
10026416 TATGCTG
66 TAGGCTG
* * *
10026423 TCCAAATTTTGGTGTGAAAATGCTG-TCTAGTT-TGGTATATAAATGCTGTCCAAATTGATATAT
1 TCCAAATTTTGGTGTAAAAATGCTGCT-TAATTATGGTATATAAATGCTGCCCAAATTGATATAT
*
10026486 A-AGGGTTG
65 ATA-GGCTG
10026494 TCCAAA
1 TCCAAA
10026500 CAGGGTAGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
70 1 0.02
71 36 0.56
72 27 0.42
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (72 bp):
TCCAAATTTTGGTGTAAAAATGCTGCTTAATTATGGTATATAAATGCTGCCCAAATTGATATATA
TAGGCTG
Found at i:10031876 original size:28 final size:28
Alignment explanation
Indices: 10031840--10032726 Score: 1704
Period size: 28 Copynumber: 31.7 Consensus size: 28
10031830 AATTTATGAG
* * *
10031840 ATTAA-CACTAAGTGTGCGAGTTTAATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
* * *
10031867 GTAAAGCACTAAGTGTGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10031895 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10031923 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10031951 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10031979 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032007 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032035 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032063 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032091 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032119 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032147 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032175 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032203 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032231 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032259 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032287 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032315 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032343 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032371 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032399 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032427 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032455 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032483 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032511 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032539 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032567 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032595 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032623 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032651 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
10032679 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGCGCGAGATTGATT
*
10032707 ATTAAGCACTAAGTGTGCGA
1 ATTAAGCACTAAGTGCGCGA
10032727 ACTTATTAAA
Statistics
Matches: 851, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
27 3 0.00
28 848 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (28 bp):
ATTAAGCACTAAGTGCGCGAGATTGATT
Found at i:10033477 original size:23 final size:23
Alignment explanation
Indices: 10033450--10033571 Score: 66
Period size: 23 Copynumber: 5.3 Consensus size: 23
10033440 TGATGTTTAA
* *
10033450 ATGCTGCCC-AAGTCGTTGTATTT
1 ATGCTGCCCAAACT-GTTGTATAT
*
10033473 ATGCTGCCTAAACTGTTGTATAT
1 ATGCTGCCCAAACTGTTGTATAT
* ** * * *
10033496 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGCCCAA-ACTGTTGTATAT
* * ** * *
10033520 ATGTTGCTCAATTTGGTATATAT
1 ATGCTGCCCAAACTGTTGTATAT
* *
10033543 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCCAAACTGTTGTATAT
10033566 ATGCTG
1 ATGCTG
10033572 TTCAATTTTG
Statistics
Matches: 74, Mismatches: 23, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
23 56 0.76
24 18 0.24
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (23 bp):
ATGCTGCCCAAACTGTTGTATAT
Found at i:10033522 original size:70 final size:70
Alignment explanation
Indices: 10033436--10033591 Score: 213
Period size: 70 Copynumber: 2.2 Consensus size: 70
10033426 TGTTCATGTT
** * * *
10033436 ATTTTGATGTTTAAATGCTGCCCAAGTCGTTGTATTTATGCTGCCTAAACTGTTGTATATATGCT
1 ATTTTGATGTAAAAATGCTGCCCAAGTCGGTATATATATGCTGCCTAAACTGTTGTATATATGCT
10033501 GTCCA
66 GTCCA
* * * * *
10033506 ATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCT
1 ATTTTGATGTAAAAATGCTGCCCAAGTCGGTATATATATGCTGCCTAAACTGTTGTATATATGCT
*
10033571 GTTCA
66 GTCCA
10033576 ATTTTGATGTAAAAAT
1 ATTTTGATGTAAAAAT
10033592 ATTGCTCTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (70 bp):
ATTTTGATGTAAAAATGCTGCCCAAGTCGGTATATATATGCTGCCTAAACTGTTGTATATATGCT
GTCCA
Found at i:10033597 original size:70 final size:70
Alignment explanation
Indices: 10033472--10033614 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 70
10033462 TCGTTGTATT
* *
10033472 TATGCTGCCTAAACTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAACTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATATTGCTCAATTTGAT
10033537 ATATA
66 ATATA
* * *
10033542 TATGCTGCCTAAATTGTTGTATATATGCTGTTCAATTTTGATGTAAAAATATTGCTCTATTTGAT
1 TATGCTGCCTAAACTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATATTGCTCAATTTGAT
10033607 ATATA
66 ATATA
10033612 TAT
1 TAT
10033615 ATATATATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44
Consensus pattern (70 bp):
TATGCTGCCTAAACTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATATTGCTCAATTTGAT
ATATA
Found at i:10033659 original size:23 final size:24
Alignment explanation
Indices: 10033629--10033730 Score: 100
Period size: 23 Copynumber: 4.3 Consensus size: 24
10033619 ATATATATAC
10033629 ATATGCTGCCCAA-TTTGTTGTAT
1 ATATGCTGCCCAATTTTGTTGTAT
* * * *
10033652 ATACGCTGTCCAATTTTTGGTGTAA
1 ATATGCTGCCCAA-TTTTGTTGTAT
* * *
10033677 AAATACTGCTCAATTTTGTTGTAT
1 ATATGCTGCCCAATTTTGTTGTAT
**
10033701 ATATGCTGCCCAA-ACTGTTGTAT
1 ATATGCTGCCCAATTTTGTTGTAT
10033724 ATATGCT
1 ATATGCT
10033731 ATTCAAATTT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 26 0.43
24 19 0.31
25 16 0.26
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
ATATGCTGCCCAATTTTGTTGTAT
Found at i:10036163 original size:41 final size:41
Alignment explanation
Indices: 10036109--10036322 Score: 252
Period size: 41 Copynumber: 5.2 Consensus size: 41
10036099 TACCAATCAT
* * *
10036109 ATAGCTGAAGCTATTACAATTCTGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
* * * *
10036150 CTAGCCGAAGCTATTATAATTCCACAAACTAAGTGCCTTCC
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
*
10036191 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
** * *
10036232 ATAGCCGAAGCTATTATAATTATGCACACTAAGTGCCATAT
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
* ** *
10036273 ATAGCCAAAGCTATTCCAAAT-CGCACACTAAGTGCCATTA-
1 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCC-TTAC
*
10036313 ATAACCGAAG
1 ATAGCCGAAG
10036323 ATATCTCGAA
Statistics
Matches: 147, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
40 22 0.15
41 125 0.85
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (41 bp):
ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
Found at i:10043480 original size:41 final size:41
Alignment explanation
Indices: 10043414--10043609 Score: 218
Period size: 41 Copynumber: 4.8 Consensus size: 41
10043404 CAATGTTTCA
* *
10043414 CACACTAATTGCCAATCATATAGCCGAAGCTATTATAATTCTG
1 CACACTAAGTGCC-TTC-TATAGCCGAAGCTATTATAATTCTG
*
10043457 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCAG
1 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
*
10043498 CACACTAAGTGCCTTAC-ATAGCCGAAGCTATTATAATTCTA
1 CACACTAAGTGCCTT-CTATAGCCGAAGCTATTATAATTCTG
* * * * ** *
10043539 TACACTAAGTGCCATATATAGCCAAAGCTATTCCAAATC-G
1 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
* *
10043579 CACACTAAGTGCCATT-AATAACCGAAGCTAT
1 CACACTAAGTGCC-TTCTATAGCCGAAGCTAT
10043610 CTCGAATTTC
Statistics
Matches: 132, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
40 24 0.18
41 93 0.70
42 3 0.02
43 12 0.09
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (41 bp):
CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
Found at i:10043570 original size:82 final size:81
Alignment explanation
Indices: 10043414--10043609 Score: 250
Period size: 82 Copynumber: 2.4 Consensus size: 81
10043404 CAATGTTTCA
* * * * *
10043414 CACACTAATTGCCAATCATATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCTTCTATAGC
1 CACACTAAGTGCC-ATTA-ATAGCCGAAGCTATTATAATTCTACACACTAAGTGCCATATATAGC
* * *
10043479 CGAAGCTATTATAATTCAG
64 CAAAGCTATTACAAATC-G
*
10043498 CACACTAAGTGCC-TTACATAGCCGAAGCTATTATAATTCTATACACTAAGTGCCATATATAGCC
1 CACACTAAGTGCCATTA-ATAGCCGAAGCTATTATAATTCTACACACTAAGTGCCATATATAGCC
*
10043562 AAAGCTATTCCAAATCG
65 AAAGCTATTACAAATCG
*
10043579 CACACTAAGTGCCATTAATAACCGAAGCTAT
1 CACACTAAGTGCCATTAATAGCCGAAGCTAT
10043610 CTCGAATTTC
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
81 27 0.27
82 60 0.61
84 12 0.12
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (81 bp):
CACACTAAGTGCCATTAATAGCCGAAGCTATTATAATTCTACACACTAAGTGCCATATATAGCCA
AAGCTATTACAAATCG
Found at i:10048521 original size:25 final size:25
Alignment explanation
Indices: 10048475--10048522 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
10048465 CGTTATATGG
*
10048475 CTCTTTGTGAACTTCTCAATTAAAT
1 CTCTTTGTGAACTTCCCAATTAAAT
*
10048500 CTCTTTGTGAGA-TTCCCGATTAA
1 CTCTTTGTGA-ACTTCCCAATTAA
10048523 TGGCTCTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (25 bp):
CTCTTTGTGAACTTCCCAATTAAAT
Found at i:10059854 original size:51 final size:51
Alignment explanation
Indices: 10059799--10059957 Score: 137
Period size: 51 Copynumber: 3.1 Consensus size: 51
10059789 CACGGCTTGT
10059799 GACACAGTCGTGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGA
1 GACACAGTCGTGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGA
* * ** * * * * * * * *
10059850 GACAC-GACTGTGTACCA-AGTCA-ATGAGTTACACGGTCTGGCACACG-GCTTGT
1 GACACAGTC-GTGTGCCATTTTTATTTTAGGTGCA-GGT-T-TCACACGATC-TGA
10059902 GACACAGTCGTGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGA
1 GACACAGTCGTGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGA
10059953 GACAC
1 GACAC
10059958 GACTGTGTAC
Statistics
Matches: 75, Mismatches: 24, Indels: 18
0.64 0.21 0.15
Matches are distributed among these distances:
49 6 0.08
50 7 0.09
51 27 0.36
52 22 0.29
53 7 0.09
54 6 0.08
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (51 bp):
GACACAGTCGTGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGA
Found at i:10059904 original size:103 final size:103
Alignment explanation
Indices: 10059704--10060009 Score: 513
Period size: 103 Copynumber: 3.0 Consensus size: 103
10059694 CACATGACCT
* * * * *
10059704 TGTGTCATTTTTATTTTAGGTGTAGGTTTCACACGGTCTGAGACACGGCCGTGTGTACCAAGTTA
1 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACAC-GAC-TGTGTACCAAGTCA
* *
10059769 GTGACTTACACGGTCTGGCACACGGCTTGTGACACAGTCG
64 ATGAGTTACACGGTCTGGCACACGGCTTGTGACACAGTCG
10059809 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACTGTGTACCAAGTCAAT
1 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACTGTGTACCAAGTCAAT
10059874 GAGTTACACGGTCTGGCACACGGCTTGTGACACAGTCG
66 GAGTTACACGGTCTGGCACACGGCTTGTGACACAGTCG
10059912 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACTGTGTACCAAGTCAAT
1 TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACTGTGTACCAAGTCAAT
* *
10059977 GAGTTACACGGTCTGGCACATGGCTTGCGACAC
66 GAGTTACACGGTCTGGCACACGGCTTGTGACAC
10060010 GACCGTGTGA
Statistics
Matches: 192, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 147 0.77
104 2 0.01
105 43 0.22
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (103 bp):
TGTGCCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACTGTGTACCAAGTCAAT
GAGTTACACGGTCTGGCACACGGCTTGTGACACAGTCG
Found at i:10071076 original size:42 final size:41
Alignment explanation
Indices: 10071010--10071094 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
10071000 TTAGAAAGTA
*
10071010 ATTGATAGATCTTCCCAAAAAAAAAAGAAGAATAAATTTGTT
1 ATTGATAGATCTTCCCAAAAAAAAAAGAAAAAT-AATTTGTT
** * *
10071052 ATTGATAGATCTTCCCCCAGAAAAAAGAAAAATAATTTTTT
1 ATTGATAGATCTTCCCAAAAAAAAAAGAAAAATAATTTGTT
10071093 AT
1 AT
10071095 ATACTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 9 0.24
42 29 0.76
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.31
Consensus pattern (41 bp):
ATTGATAGATCTTCCCAAAAAAAAAAGAAAAATAATTTGTT
Found at i:10078728 original size:25 final size:24
Alignment explanation
Indices: 10078699--10078779 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 24
10078689 AAGCTCTTTC
*
10078699 GAGCTGAATAATGGGAAGATCATG
1 GAGCTGAATAATGGGAAGCTCATG
*
10078723 TGAGCTGAATAATGGGAAGCTCATAC
1 -GAGCTGAATAATGGGAAGCTCAT-G
* *
10078749 GAGCTAAATAACGGGAAGCTCATAG
1 GAGCTGAATAATGGGAAGCTCAT-G
10078774 GAGCTG
1 GAGCTG
10078780 TGGTGTGTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.20
Consensus pattern (24 bp):
GAGCTGAATAATGGGAAGCTCATG
Found at i:10081134 original size:45 final size:45
Alignment explanation
Indices: 10081083--10081173 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
10081073 CTAGACATGT
10081083 TCTTTCCCATTACCACATCACTTTATTTTTTCTATTGAAGAGGCA
1 TCTTTCCCATTACCACATCACTTTATTTTTTCTATTGAAGAGGCA
10081128 TCTTTCCCATTACCACATCACTTTATTTTTTCTATTGAAGAGGCA
1 TCTTTCCCATTACCACATCACTTTATTTTTTCTATTGAAGAGGCA
10081173 T
1 T
10081174 TGAGCTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (45 bp):
TCTTTCCCATTACCACATCACTTTATTTTTTCTATTGAAGAGGCA
Found at i:10088538 original size:22 final size:23
Alignment explanation
Indices: 10088498--10088544 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
10088488 TCAAAAGCCT
10088498 GAAGGCTGAACTTAAGCTCATGA
1 GAAGGCTGAACTTAAGCTCATGA
10088521 GAAGGCTGAAC-TAAGCTCATGA
1 GAAGGCTGAACTTAAGCTCATGA
10088543 GA
1 GA
10088545 GCTAAACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (23 bp):
GAAGGCTGAACTTAAGCTCATGA
Found at i:10096192 original size:36 final size:36
Alignment explanation
Indices: 10096145--10096218 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
10096135 AGCAAGCTCT
*
10096145 ATTCAATTCAGTAGCCTCTT-GGATCTATTCTGACTG
1 ATTCAATTCAGTAGCCT-TTCGGATCTATTCTAACTG
10096181 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
1 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
10096217 AT
1 AT
10096219 ATGCTCATCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (36 bp):
ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
Found at i:10098661 original size:69 final size:69
Alignment explanation
Indices: 10098561--10099043 Score: 426
Period size: 69 Copynumber: 7.1 Consensus size: 69
10098551 GTTCTGGTTT
* * ** * **
10098561 TTCATCTGCAAACCTTAATATGACAACTGGGAGTTTTGCTCTTACTAACTGTTTTGGAGGTTGC-
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
*
10098625 GATTC
66 G-CTC
** * * * * *
10098630 TTCACCTGTAAACCTTATTATGATAGTTGGGAGCTTTGCTCTCGTTAA-TTTTTATGGAGGTTGT
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTT-TGGAGGTTGC
*
10098694 GGCTC
65 AGCTC
* * * ** * *
10098699 TTCACCTGTGAACCTTAATATTACAATTGGGAGCTTTATTGTCGCTAACTATTTTGGAGGTTGCA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
10098764 GCTC
66 GCTC
* * * * * * * *
10098768 TTCACTTGCGAACTTTAATATGACAGCTGAGAGCTTTACTCTCGCTAATTTTTTTGGAGGTTACA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
10098833 GCTC
66 GCTC
* * * * *
10098837 TTCGCCTGCGAACATTAATATGACAGTTGGGAGCTTTGCTCTCACTAACAGTTTTGGAGGTTGTA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
*
10098902 GTTC
66 GCTC
** * * * ** * *
10098906 TTTGCCTACGAACTTTAACATGACAACTGGGAGCTTTGCTTTCGCTAACTGTTTTAGAGGTT--A
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
10098969 ---C
66 GCTC
* * * *
10098970 -T-GCCTGCGAGCCTTAATATGACAGTTGTGAGCTTTGCTCTCGCTAACTGCTTTGGAGGTTGCA
1 TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
10099033 GCTC
66 GCTC
*
10099037 TTTACCT
1 TTCACCT
10099044 TTAAACCTTA
Statistics
Matches: 333, Mismatches: 71, Indels: 20
0.79 0.17 0.05
Matches are distributed among these distances:
62 49 0.15
63 1 0.00
64 2 0.01
67 2 0.01
68 5 0.02
69 269 0.81
70 5 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (69 bp):
TTCACCTGCGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCA
GCTC
Found at i:10115188 original size:262 final size:262
Alignment explanation
Indices: 10114729--10115200 Score: 600
Period size: 262 Copynumber: 1.8 Consensus size: 262
10114719 AAATAAGAAC
* * * * * *
10114729 ATATCCCCAAAACTAAGATGGGAATTTTAAAGTCAAATTGTACAATTCTGAAACTTTAAATTTAG
1 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTCAAATTTAG
* * *
10114794 GAGAAAATGAAAAAGTATGACATTAGCTTTCTCATAGATTTTATGATTACAAAGAGCTAAAGTTA
66 GAGAAAATGAAAAAGTATAACATTAGCTTTCTCATAGAATTTATGATTACAAAGAGCAAAAGTTA
*
10114859 TGCCACAAAATTTTCATCAGCCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
131 TGCCACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
*
10114924 AGTCAGTAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
196 AGTCAGGAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
10114989 AT
261 AT
*
10114991 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAATTTGCACAATTCTAAAAATTCAAATTTTC
1 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTCAAA-TTT-
* *
10115056 A-GAGAAAATGAAGAAGTATAACGTTAGCTTTCTGGCA-A-AATTTATG-TTAGCAGAA-AGTCA
64 AGGAGAAAATGAAAAAGTATAACATTAGCTTTCT--CATAGAATTTATGATTA-CA-AAGAG-CA
* ** * * * * * *
10115116 AAATTTATGCTGCAAATTTTTCATCAACCGATAATTATGCCACCTATATAACCAGAAA-C-TGAC
124 AAAGTTATGCCACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGAC
*
10115179 T-CTATCTAGTTAGGAAAACTCT
189 TAC-ATCTAGTCAGGAAAACTCT
10115201 CTAGTCCCAA
Statistics
Matches: 178, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
261 1 0.01
262 77 0.43
263 44 0.25
264 54 0.30
265 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (262 bp):
ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTCAAATTTAG
GAGAAAATGAAAAAGTATAACATTAGCTTTCTCATAGAATTTATGATTACAAAGAGCAAAAGTTA
TGCCACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
AGTCAGGAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
AT
Found at i:10121308 original size:9 final size:9
Alignment explanation
Indices: 10121294--10121334 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
10121284 ACAAATTAAG
10121294 AAAGAAAAA
1 AAAGAAAAA
10121303 AAAGAAAAA
1 AAAGAAAAA
10121312 AAAGAAAGAA
1 AAAGAAA-AA
*
10121322 AAAGAAAAG
1 AAAGAAAAA
10121331 AAAG
1 AAAG
10121335 GGAGAAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:10121341 original size:19 final size:19
Alignment explanation
Indices: 10121294--10121334 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
10121284 ACAAATTAAG
10121294 AAAGAAA-AAAAAGAAAAA
1 AAAGAAAGAAAAAGAAAAA
*
10121312 AAAGAAAGAAAAAGAAAAG
1 AAAGAAAGAAAAAGAAAAA
10121331 AAAG
1 AAAG
10121335 GGAGAAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAAAGAAAAA
Found at i:10122019 original size:16 final size:16
Alignment explanation
Indices: 10122000--10122032 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10121990 TTTGGCACTT
10122000 TTATA-TTGAATTGAAA
1 TTATAGTTG-ATTGAAA
10122016 TTATAGTTGATTGAAA
1 TTATAGTTGATTGAAA
10122032 T
1 T
10122033 GGATTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (16 bp):
TTATAGTTGATTGAAA
Found at i:10123285 original size:21 final size:22
Alignment explanation
Indices: 10123261--10123307 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
10123251 TAGAATGATA
10123261 GTTTTG-GCATGTTTTGAGTGT
1 GTTTTGAGCATGTTTTGAGTGT
* *
10123282 G-TTTGATCGTGTTTTGAGTGT
1 GTTTTGAGCATGTTTTGAGTGT
10123303 GTTTT
1 GTTTT
10123308 TGAGTTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.09, C:0.04, G:0.32, T:0.55
Consensus pattern (22 bp):
GTTTTGAGCATGTTTTGAGTGT
Found at i:10123308 original size:12 final size:11
Alignment explanation
Indices: 10123270--10123312 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
10123260 AGTTTTGGCA
10123270 TGTTTTGAGTG
1 TGTTTTGAGTG
10123281 TG-TTTGA-TCG
1 TGTTTTGAGT-G
10123291 TGTTTTGAGTG
1 TGTTTTGAGTG
10123302 TGTTTTTGAGT
1 TG-TTTTGAGT
10123313 TGCTTAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.04
10 8 0.29
11 10 0.36
12 9 0.32
ACGTcount: A:0.09, C:0.02, G:0.33, T:0.56
Consensus pattern (11 bp):
TGTTTTGAGTG
Found at i:10128182 original size:14 final size:14
Alignment explanation
Indices: 10128163--10128201 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
10128153 TCTCTTCACG
10128163 TAATTTTCTCTCTA
1 TAATTTTCTCTCTA
10128177 TAATTTTCTCTCTA
1 TAATTTTCTCTCTA
*
10128191 TAACTTTCTCT
1 TAATTTTCTCT
10128202 TGAATTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTTCTCTCTA
Found at i:10128687 original size:37 final size:40
Alignment explanation
Indices: 10128588--10128696 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 40
10128578 ATCTACATGA
* *
10128588 TAAACATTAAATTTAAT-TT-AA-TATTCAGATAATCACT
1 TAAATATTAAATTTAATATTAAATTATTAAGATAATCACT
*
10128625 TAAATATTAAA-TTAATA-AAATATTATTAAGATAAGT-A-T
1 TAAATATTAAATTTAATATTAA-ATTATTAAGATAA-TCACT
*
10128663 T-AA-ATTAAATTTAATATTAAATTATTAAAATAAT
1 TAAATATTAAATTTAATATTAAATTATTAAGATAAT
10128697 ATGATTTTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
36 12 0.20
37 31 0.52
38 5 0.08
39 11 0.18
40 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (40 bp):
TAAATATTAAATTTAATATTAAATTATTAAGATAATCACT
Found at i:10131198 original size:30 final size:31
Alignment explanation
Indices: 10131162--10131221 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
10131152 AAACCTTTTA
*
10131162 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
10131192 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
10131222 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:10132139 original size:101 final size:102
Alignment explanation
Indices: 10132024--10132208 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
10132014 AAAGTGATGG
* ** *
10132024 TCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCAGAATGAT-A-GGTTGCATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAAGCTACTACGAGTATC-GAATGATAATGGTCACATGTATAGT
10132087 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* * * *
10132125 TCACGTGTGTAGTACTATGTGCAGGCTATTACGAGTATCGGATGATAATGGTCACATGTATAGTA
1 TCACATGTGTAGTACTATGTGCAAGCTACTACGAGTATCGAATGATAATGGTCACATGTATAGTA
*
10132190 CTATGTGCAGGTTACTATG
66 CTATGTGCAGGCTACTATG
10132209 TGAACCGAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
100 6 0.08
101 36 0.49
102 31 0.42
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTGCAAGCTACTACGAGTATCGAATGATAATGGTCACATGTATAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:10132189 original size:51 final size:50
Alignment explanation
Indices: 10132020--10132206 Score: 198
Period size: 51 Copynumber: 3.7 Consensus size: 50
10132010 AGTGAAAGTG
* * *
10132020 ATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCAGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATC-GGATGAT
** * * *
10132071 A-GGTTGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATCGGATGA-T
* * * *
10132120 TTCGATCACGTGTGTAGTACTATGTGCAGGCTATTACGAGTATCGGATGAT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATCGGATGAT
* *
10132171 AATGGTCACATGTATAGTACTATGTGCAGGTTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
10132207 TGTGAACCGA
Statistics
Matches: 109, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
48 1 0.01
49 4 0.04
50 35 0.32
51 67 0.61
52 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGAGTATCGGATGAT
Found at i:10132281 original size:45 final size:45
Alignment explanation
Indices: 10132217--10132302 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
10132207 TGTGAACCGA
* *
10132217 ACATCATTAATTAGGAAGGTGGTTGCTATGTGCTGATTCCAGCAG
1 ACATCATTAATTAAGAAGGTGGTTGCTATGTGCTGAATCCAGCAG
* *
10132262 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1 ACATCATTAATTAAGAAGGTGGTTGCTATGTGCTGAATCCA
10132303 CCAAGTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (45 bp):
ACATCATTAATTAAGAAGGTGGTTGCTATGTGCTGAATCCAGCAG
Found at i:10136602 original size:34 final size:34
Alignment explanation
Indices: 10136559--10136628 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
10136549 TTAAAGATTG
10136559 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
1 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
10136593 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
1 TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
10136627 TA
1 TA
10136629 TGTTAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (34 bp):
TAAATGTTGCCATTGATGAATCTTGTGATTTTTT
Found at i:10143874 original size:66 final size:65
Alignment explanation
Indices: 10143795--10143930 Score: 236
Period size: 66 Copynumber: 2.1 Consensus size: 65
10143785 TGAGATAGGT
* *
10143795 AATTAAAATAAAATTGCTAACCGAGGTTTCCATGGTTCTATTTCTAGAAAATAAATAAAAAAATA
1 AATTAAAATAAAATTGCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAAT-AAAAAATA
10143860 A
65 A
*
10143861 AATTAAAATAAAATTTCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAATAAAAAATAA
1 AATTAAAATAAAATTGCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAATAAAAAATAA
10143926 AATTA
1 AATTA
10143931 CATAGTTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 14 0.21
66 53 0.79
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.32
Consensus pattern (65 bp):
AATTAAAATAAAATTGCTAACCAAGGTTTCCATGGTTCTATTTATAGAAAATAAATAAAAAATAA
Found at i:10143961 original size:25 final size:25
Alignment explanation
Indices: 10143933--10143980 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
10143923 TAAAATTACA
10143933 TAGTTTTTCACCACAAGGCATTCCT
1 TAGTTTTTCACCACAAGGCATTCCT
*
10143958 TAGTTTTTCACCACAAGTCATTC
1 TAGTTTTTCACCACAAGGCATTC
10143981 ATTGGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (25 bp):
TAGTTTTTCACCACAAGGCATTCCT
Found at i:10143989 original size:26 final size:25
Alignment explanation
Indices: 10143933--10143992 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
10143923 TAAAATTACA
*
10143933 TAGTTTTTCACCACAAGGCATTCCT
1 TAGTTTTTCACCACAAGGCATTCAT
*
10143958 TAGTTTTTCACCACAAGTCATTCAT
1 TAGTTTTTCACCACAAGGCATTCAT
* *
10143983 TGGGTTTTCA
1 TAGTTTTTCA
10143993 GCCGCCATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (25 bp):
TAGTTTTTCACCACAAGGCATTCAT
Found at i:10144824 original size:37 final size:36
Alignment explanation
Indices: 10144764--10144839 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
10144754 CTTAATCACT
*
10144764 TTAATATTAAATTAATAAAAAACTATTAAGATAAGTA
1 TTAATATTAAATTAATAAAAAACTATTAAAATAA-TA
**
10144801 TTAA-ATTAAATTTAATATTAAACTATTAAAATAATA
1 TTAATATTAAA-TTAATAAAAAACTATTAAAATAATA
10144837 TTA
1 TTA
10144840 TTTTGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 11 0.31
37 24 0.69
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAAAACTATTAAAATAATA
Found at i:10145878 original size:91 final size:90
Alignment explanation
Indices: 10145716--10145907 Score: 226
Period size: 91 Copynumber: 2.1 Consensus size: 90
10145706 CACTAGTGAG
* * * * *
10145716 TTATCCACAAAATTATTGGCAGCTTTTATATGCAAACATGTTGTGTATTCACAGCCTAATGACAG
1 TTATCCACAAAATTATTGGCAACTTTTATATGCAAACATATTGTGCATTCACAACCTAATGACAA
* *
10145781 CGTATTAACATGCAATCACTGGTGGT
66 CATATTAACATACAAT-ACTGGTGGT
* * * *
10145807 TTATCCACAAATTTATTGGCAACTTTTATCTGCAAACCTATTGTGCATTCACAATCTACCA-G-C
1 TTATCCACAAAATTATTGGCAACTTTTATATGCAAACATATTGTGCATTCACAACCTA--ATGAC
*
10145870 AACATATTAACCTACAATACTGGTGGT
64 AACATATTAACATACAATACTGGTGGT
*
10145897 TCATCCACAAA
1 TTATCCACAAA
10145908 CTAGAGTGTC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
90 19 0.22
91 65 0.76
92 1 0.01
93 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (90 bp):
TTATCCACAAAATTATTGGCAACTTTTATATGCAAACATATTGTGCATTCACAACCTAATGACAA
CATATTAACATACAATACTGGTGGT
Found at i:10173834 original size:38 final size:39
Alignment explanation
Indices: 10173766--10173851 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 39
10173756 CTTATTCTTT
*
10173766 AAAAAAATAAAAAGCAAAAAGCGCAAAAAAAAAACCGCAA
1 AAAAAAAGAAAAAGCAAAAAGCGC-AAAAAAAAACCGCAA
10173806 AAAAAAAGAAAAAGCAAAAAGCGC-AAAAAAAACCGCAA
1 AAAAAAAGAAAAAGCAAAAAGCGCAAAAAAAAACCGCAA
10173844 AAAAAAAG
1 AAAAAAAG
10173852 TTGCCTACCT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 22 0.49
40 23 0.51
ACGTcount: A:0.73, C:0.14, G:0.12, T:0.01
Consensus pattern (39 bp):
AAAAAAAGAAAAAGCAAAAAGCGCAAAAAAAAACCGCAA
Found at i:10186002 original size:31 final size:32
Alignment explanation
Indices: 10185939--10186002 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
10185929 TAATAAGGTA
10185939 AGATTTCTATCCTTAATTATAGGGATTCCAAC
1 AGATTTCTATCCTTAATTATAGGGATTCCAAC
*
10185971 AGATTTCTATCCTTAATTATA-GGATTTCAAC
1 AGATTTCTATCCTTAATTATAGGGATTCCAAC
10186002 A
1 A
10186003 CTCCCTCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (32 bp):
AGATTTCTATCCTTAATTATAGGGATTCCAAC
Found at i:10193381 original size:20 final size:20
Alignment explanation
Indices: 10193353--10193395 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
10193343 CAAATGTTAC
*
10193353 AATAATTTATATAATTGAAT
1 AATAATTTATAAAATTGAAT
* *
10193373 AATATTTTATAAAATTGTAT
1 AATAATTTATAAAATTGAAT
10193393 AAT
1 AAT
10193396 TATATAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AATAATTTATAAAATTGAAT
Found at i:10201323 original size:21 final size:22
Alignment explanation
Indices: 10201282--10201327 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
10201272 CATACTTGAT
10201282 TTCTTTCAAATTGATTTAATTC
1 TTCTTTCAAATTGATTTAATTC
10201304 TTCTTTCAAATTGA-TTAATTC
1 TTCTTTCAAATTGATTTAATTC
10201325 TTC
1 TTC
10201328 ATGCATAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.54
Consensus pattern (22 bp):
TTCTTTCAAATTGATTTAATTC
Found at i:10208967 original size:42 final size:42
Alignment explanation
Indices: 10208854--10209017 Score: 204
Period size: 43 Copynumber: 3.8 Consensus size: 42
10208844 CAAAAAGCTC
* *
10208854 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
* * *
10208896 ATAACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAT
1 AT-ACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
*
10208939 ATACGATGCCAATGTCCCAAACATGGTCTTACACGTAAATCGCAA
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACGT-AAT--CAA
* * *
10208984 AT-CGATGCCAATTTCCCAGACGTTGTCTTACACG
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACG
10209018 ATATCACATA
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.31
43 40 0.38
44 28 0.27
45 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
Found at i:10210124 original size:13 final size:13
Alignment explanation
Indices: 10210106--10210130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10210096 ACAAACGATA
10210106 AAATTTTCACACG
1 AAATTTTCACACG
10210119 AAATTTTCACAC
1 AAATTTTCACAC
10210131 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:10212383 original size:16 final size:16
Alignment explanation
Indices: 10212359--10212390 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10212349 TGAACATGAC
*
10212359 AATTGATTCAATTAAA
1 AATTCATTCAATTAAA
10212375 AATTCATTCAATTAAA
1 AATTCATTCAATTAAA
10212391 GTCTATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTCATTCAATTAAA
Found at i:10222210 original size:26 final size:26
Alignment explanation
Indices: 10222174--10222226 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
10222164 AATTGGAGAG
*
10222174 TGACATAAGAGAATCGAATATATATA
1 TGACATAAGAGAATAGAATATATATA
10222200 TGACATAAGAGAATAGAATATATATA
1 TGACATAAGAGAATAGAATATATATA
10222226 T
1 T
10222227 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (26 bp):
TGACATAAGAGAATAGAATATATATA
Found at i:10222224 original size:2 final size:2
Alignment explanation
Indices: 10222217--10222249 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
10222207 AGAGAATAGA
10222217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10222250 TGCTAAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10224740 original size:359 final size:359
Alignment explanation
Indices: 10224081--10224802 Score: 1435
Period size: 359 Copynumber: 2.0 Consensus size: 359
10224071 TATACCATGA
10224081 ATTTTATTGAATGGTTTTTGATGTTAAATGCTAGATTATAAATCTTTGTTGATAAATAAACAAGT
1 ATTTTATTGAATGGTTTTTGATGTTAAATGCTAGATTATAAATCTTTGTTGATAAATAAACAAGT
10224146 TTTACAAAGCGATTTTTGATGAATTTTAGAAATTAGGGACTAAATTGTTAAAGGTATGAATTCTA
66 TTTACAAAGCGATTTTTGATGAATTTTAGAAATTAGGGACTAAATTGTTAAAGGTATGAATTCTA
10224211 GGGTTTTAATGTGAAATGATGATAAAAATGGGTTGTTTCAAGGTCCCTTGCATATTTGGTTAACA
131 GGGTTTTAATGTGAAATGATGATAAAAATGGGTTGTTTCAAGGTCCCTTGCATATTTGGTTAACA
10224276 TATATTGAGATTAAAATGATTAGATTTAAAGTTATAAGCTTAAGGACTAAATTGTGAAAAAGTTA
196 TATATTGAGATTAAAATGATTAGATTTAAAGTTATAAGCTTAAGGACTAAATTGTGAAAAAGTTA
10224341 AAATGTTAGAGGTAAAATGGTAATTTTGCATAAATCTGAAATGTGGATTGAATTGAATTTTTAAG
261 AAATGTTAGAGGTAAAATGGTAATTTTGCATAAATCTGAAATGTGGATTGAATTGAATTTTTAAG
10224406 GTTAATTGAAGTACTTAATTGAATATAATTATCT
326 GTTAATTGAAGTACTTAATTGAATATAATTATCT
10224440 ATTTTATTGAATGGTTTTTGATGTTAAATGCTAGATTATAAATCTTTGTTGATAAATAAACAAGT
1 ATTTTATTGAATGGTTTTTGATGTTAAATGCTAGATTATAAATCTTTGTTGATAAATAAACAAGT
10224505 TTTACAAAGCGATTTTTGATGAATTTTAGAAATTAGGGACTAAATTGTTAAAGGTATGAATTCTA
66 TTTACAAAGCGATTTTTGATGAATTTTAGAAATTAGGGACTAAATTGTTAAAGGTATGAATTCTA
*
10224570 GGGTTTTAATGTGAAATGATGATAAAAATGGGTTGTTTCAAGGTCCCTTGCATTTTTGGTTAACA
131 GGGTTTTAATGTGAAATGATGATAAAAATGGGTTGTTTCAAGGTCCCTTGCATATTTGGTTAACA
10224635 TATATTGAGATTAAAATGATTAGATTTAAAGTTATAAGCTTAAGGACTAAATTGTGAAAAAGTTA
196 TATATTGAGATTAAAATGATTAGATTTAAAGTTATAAGCTTAAGGACTAAATTGTGAAAAAGTTA
10224700 AAATGTTAGAGGTAAAATGGTAATTTTGCATAAATCTGAAATGTGGATTGAATTGAATTTTTAAG
261 AAATGTTAGAGGTAAAATGGTAATTTTGCATAAATCTGAAATGTGGATTGAATTGAATTTTTAAG
10224765 GTTAATTGAAGTACTTAATTGAATATAATTATCT
326 GTTAATTGAAGTACTTAATTGAATATAATTATCT
10224799 ATTT
1 ATTT
10224803 AGATCAAGAT
Statistics
Matches: 362, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
359 362 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (359 bp):
ATTTTATTGAATGGTTTTTGATGTTAAATGCTAGATTATAAATCTTTGTTGATAAATAAACAAGT
TTTACAAAGCGATTTTTGATGAATTTTAGAAATTAGGGACTAAATTGTTAAAGGTATGAATTCTA
GGGTTTTAATGTGAAATGATGATAAAAATGGGTTGTTTCAAGGTCCCTTGCATATTTGGTTAACA
TATATTGAGATTAAAATGATTAGATTTAAAGTTATAAGCTTAAGGACTAAATTGTGAAAAAGTTA
AAATGTTAGAGGTAAAATGGTAATTTTGCATAAATCTGAAATGTGGATTGAATTGAATTTTTAAG
GTTAATTGAAGTACTTAATTGAATATAATTATCT
Found at i:10226569 original size:187 final size:187
Alignment explanation
Indices: 10226237--10226619 Score: 579
Period size: 187 Copynumber: 2.0 Consensus size: 187
10226227 TGTATTCAAG
*
10226237 TCAGTGAGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTATACGGCCCAGCA
1 TCAGT-AGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTACACGGCCCAGCA
* * *
10226302 CACGAGCGTGTGACACGACCGTGTGACCCTACTTAGAGAGTTACACAGGTAAGAACACAGGCTGA
65 CACGAGCATGTGACACGACCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGA
** * * *
10226367 GACACAGTAGTGTGTCCCTAGTTCGAAGGCTACACAGCCTGAGACACGGGCGTGTGTC
130 GACACAACAGTGTGTCCCGAGTTCAAAGGCTACACAGCCTGAGACACGGACGTGTGTC
* * **
10226425 TCAGTAGTTACAAGGCCTAGCACACGGGCGTATGGGGCAACTTAGAGAGTTACACGGCCTGGCAC
1 TCAGTAGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTACACGGCCCAGCAC
* *
10226490 ACGAGCATGTGACACTG-TCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGG
66 ACGAGCATGTGACAC-GACCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGA
* * *
10226554 GACACAACCGTGTGTCTCGAGTTCAAAGGCTACATAGCCTGAGACACGGACGTGTGTC
130 GACACAACAGTGTGTCCCGAGTTCAAAGGCTACACAGCCTGAGACACGGACGTGTGTC
10226612 TCAGTAGT
1 TCAGTAGT
10226620 GTGAGGTACA
Statistics
Matches: 176, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
187 170 0.97
188 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.29, T:0.19
Consensus pattern (187 bp):
TCAGTAGTTACAAGGCCTAGCACACGGGCGTATAGGGCAACTCAGAGAGTTACACGGCCCAGCAC
ACGAGCATGTGACACGACCGTGTGACCCTACTTAAAGAGTTACACAGGTAAGAACACAGGCCGAG
ACACAACAGTGTGTCCCGAGTTCAAAGGCTACACAGCCTGAGACACGGACGTGTGTC
Found at i:10232311 original size:20 final size:20
Alignment explanation
Indices: 10232286--10232324 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10232276 AACTACTTTT
*
10232286 AGAATGCTCCTTTTGTACAC
1 AGAATGCTCCTTTTATACAC
*
10232306 AGAATGCTCTTTTTATACA
1 AGAATGCTCCTTTTATACA
10232325 TAAACCTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (20 bp):
AGAATGCTCCTTTTATACAC
Found at i:10234913 original size:54 final size:53
Alignment explanation
Indices: 10234735--10234901 Score: 208
Period size: 54 Copynumber: 3.1 Consensus size: 53
10234725 CATGGTAAGC
* * * * * *
10234735 GAATACCATATAGTGTAAGGCCTAGCCATTTGCAATGACTTTATATTGAGAAAT
1 GAATACCATATAGTGTAAGGCCTAG-CGTTTGCTATGACATCATATGGGGAAAT
* * * *
10234789 AAATACCATATAGTGTAAGCCCTAGACGTTTGTTATGGCATCATATGGGGAAAT
1 GAATACCATATAGTGTAAGGCCTAG-CGTTTGCTATGACATCATATGGGGAAAT
*
10234843 GAAGACCATATAGTGTAAGGCCTAGCTGTTTGCTATGACATCATATGGGGAAAT
1 GAATACCATATAGTGTAAGGCCTAGC-GTTTGCTATGACATCATATGGGGAAAT
10234897 GAATA
1 GAATA
10234902 ATACATAGTG
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 1 0.01
54 94 0.99
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (53 bp):
GAATACCATATAGTGTAAGGCCTAGCGTTTGCTATGACATCATATGGGGAAAT
Found at i:10234921 original size:54 final size:54
Alignment explanation
Indices: 10234744--10234921 Score: 144
Period size: 54 Copynumber: 3.3 Consensus size: 54
10234734 CGAATACCAT
* ** * * * * * * * * *
10234744 ATAGTGTAAGGCCTAGCCATTTGCAATGACTTTATATTGAGAAATAAATACCAT
1 ATAGTGTAAGACCTAGCTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
* * * * *
10234798 ATAGTGTAAGCCCTAGAC-GTTTGTTATGGCATCATATGGGGAAATGAAGACCAT
1 ATAGTGTAAGACCTAG-CTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
* * *
10234852 ATAGTGTAAGGCCTAGCTGTTTGCTATGACATCATATGGGGAAATGAATAATAC
1 ATAGTGTAAGACCTAGCTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
10234906 ATAGTGTATA-ACCTAG
1 ATAGTGTA-AGACCTAG
10234922 TCTAGGACTA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.01
54 99 0.97
55 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (54 bp):
ATAGTGTAAGACCTAGCTGTTTGCTATGACATCATATGGGGAAATGAAGAACAC
Found at i:10235302 original size:29 final size:31
Alignment explanation
Indices: 10235254--10235313 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
10235244 TAATGATATA
*
10235254 TGGACGCCTCTATGGCTATCTA-AG-TCAAG
1 TGGACGCCTCTATGGATATCTATAGATCAAG
* *
10235283 TGGACGCCTTTGTGGATATCTATAGATCAAG
1 TGGACGCCTCTATGGATATCTATAGATCAAG
10235314 CAAGTGTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 19 0.73
30 2 0.08
31 5 0.19
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (31 bp):
TGGACGCCTCTATGGATATCTATAGATCAAG
Found at i:10235611 original size:6 final size:6
Alignment explanation
Indices: 10235575--10235609 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10235565 CTCTACCCCA
* *
10235575 CCCTTT CCCTCT CCCTCT CCCTCT CCCTCC CCCTC
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
10235610 CCAACATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCTCT
Found at i:10238670 original size:16 final size:16
Alignment explanation
Indices: 10238649--10238684 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
10238639 GATTTGCTAT
10238649 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
10238665 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
10238681 TACA
1 TACA
10238685 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:10241137 original size:12 final size:13
Alignment explanation
Indices: 10241107--10241136 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10241097 ATAAGGGCTT
*
10241107 TTTTTATTTAATA
1 TTTTTATATAATA
10241120 TTTTTATATAATA
1 TTTTTATATAATA
10241133 TTTT
1 TTTT
10241137 AAATAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATATAATA
Found at i:10241321 original size:20 final size:20
Alignment explanation
Indices: 10241293--10241336 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10241283 CCAAATTTAT
*
10241293 AATACTTTAAA-TACATTAAA
1 AATACTTTAAACT-CAGTAAA
*
10241313 AATAGTTTAAACTCAGTAAA
1 AATACTTTAAACTCAGTAAA
10241333 AATA
1 AATA
10241337 TTTCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (20 bp):
AATACTTTAAACTCAGTAAA
Found at i:10248574 original size:16 final size:16
Alignment explanation
Indices: 10248553--10248602 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
10248543 AAAAAATTTA
10248553 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
*
10248569 TAAGTTA---A-CATG
1 TAAGTTATGTATTATG
10248581 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
10248597 TAAGTT
1 TAAGTT
10248603 TACATATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:10248585 original size:28 final size:28
Alignment explanation
Indices: 10248551--10248619 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
10248541 AAAAAAAATT
10248551 TATAAGTTATGTATTATGTAAGTTAACA
1 TATAAGTTATGTATTATGTAAGTTAACA
* *
10248579 TGTAAGTTATGTATTATGTAAGTTTACA
1 TATAAGTTATGTATTATGTAAGTTAACA
10248607 TATAAGTTTATGT
1 TATAAG-TTATGT
10248620 GATAGTTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 31 0.84
29 6 0.16
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (28 bp):
TATAAGTTATGTATTATGTAAGTTAACA
Found at i:10249820 original size:15 final size:15
Alignment explanation
Indices: 10249800--10249828 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10249790 TGATAACAGT
10249800 AAATTAGTACCAAAG
1 AAATTAGTACCAAAG
10249815 AAATTAGTACCAAA
1 AAATTAGTACCAAA
10249829 TACTTCAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (15 bp):
AAATTAGTACCAAAG
Found at i:10251897 original size:13 final size:14
Alignment explanation
Indices: 10251872--10251915 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
10251862 CATAAATTCT
10251872 AAACCTTAAACCCCA
1 AAACC-TAAACCCCA
10251887 AAACC-AAACCCCA
1 AAACCTAAACCCCA
*
10251900 AACCCTAAACCCCA
1 AAACCTAAACCCCA
10251914 AA
1 AA
10251916 TCCCAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 12 0.44
14 10 0.37
15 5 0.19
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (14 bp):
AAACCTAAACCCCA
Found at i:10251900 original size:7 final size:7
Alignment explanation
Indices: 10251879--10251923 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
10251869 TCTAAACCTT
10251879 AAACCCC
1 AAACCCC
*
10251886 AAA-ACC
1 AAACCCC
10251892 AAACCCC
1 AAACCCC
*
10251899 AAACCCT
1 AAACCCC
10251906 AAACCCC
1 AAACCCC
*
10251913 AAATCCC
1 AAACCCC
10251920 AAAC
1 AAAC
10251924 TGAAATATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.49, C:0.47, G:0.00, T:0.04
Consensus pattern (7 bp):
AAACCCC
Found at i:10251911 original size:14 final size:14
Alignment explanation
Indices: 10251872--10251915 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
10251862 CATAAATTCT
*
10251872 AAACCTTAAACCCC
1 AAACCCTAAACCCC
*
10251886 AAAACC-AAACCCC
1 AAACCCTAAACCCC
10251899 AAACCCTAAACCCC
1 AAACCCTAAACCCC
10251913 AAA
1 AAA
10251916 TCCCAAACTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (14 bp):
AAACCCTAAACCCC
Found at i:10251923 original size:14 final size:13
Alignment explanation
Indices: 10251879--10251923 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
10251869 TCTAAACCTT
*
10251879 AAACCCCAAAACC
1 AAACCCCAAACCC
10251892 AAACCCCAAACCC
1 AAACCCCAAACCC
10251905 TAAACCCCAAATCCC
1 -AAACCCCAAA-CCC
10251920 AAAC
1 AAAC
10251924 TGAAATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 12 0.41
14 14 0.48
15 3 0.10
ACGTcount: A:0.49, C:0.47, G:0.00, T:0.04
Consensus pattern (13 bp):
AAACCCCAAACCC
Found at i:10252449 original size:81 final size:80
Alignment explanation
Indices: 10252297--10252452 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 80
10252287 AACCATTAAC
* * *
10252297 CCCTAACTACTAACCCTAACCTTATTTAATATACAAATTAAAAATATTAATTAATCAAAACCCTA
1 CCCTAACCACTAACCCTAACCTTATTTAATATACAAATTAAAAACACTAATTAATCAAAACCCTA
10252362 AATCCTAACCCGAAT
66 AATCCTAACCCGAAT
* * *
10252377 CCCTAACCCCTAACCCTTAAACCTTATTTCATA-A-AAATTAAAACACACTAATTAATCTAAACC
1 CCCTAACCACTAACCC-T-AACCTTATTTAATATACAAATTAAAA-ACACTAATTAATCAAAACC
10252440 CTAAATCCTAACC
63 CTAAATCCTAACC
10252453 TGACACCGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 23 0.34
81 31 0.46
82 13 0.19
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.28
Consensus pattern (80 bp):
CCCTAACCACTAACCCTAACCTTATTTAATATACAAATTAAAAACACTAATTAATCAAAACCCTA
AATCCTAACCCGAAT
Found at i:10253467 original size:115 final size:114
Alignment explanation
Indices: 10252967--10253547 Score: 628
Period size: 114 Copynumber: 5.1 Consensus size: 114
10252957 CGCTTCAACA
* * * *
10252967 AAAATGCCGCTAAAGCCCTAAGCATTAGCGGCGCATT-CTT-AAAACGCCGCTAAAGCCCACGAA
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTACTTAAAAACGCCACTAAATCCC-CGAA
* * ** * * * *
10253030 TTG-TCAGAAAATAGTGTAGTTCGG-TTTAGTTTTTGTTGTGGCGCTTTCTCA
64 -AGCTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTT-TTGTGGCGCTTTCTCG
*
10253081 AAAACGCCGCTAAAGCCCTGAACATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
* *
10253146 CTCAAAAAACAGCATCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTC-
66 CTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCG
*
10253194 AAAA-GCACTGCTAAAG-CCTGAGCATTAGCGGCGCTTACCTAAAAACGCCACTAAATCCCCGAA
1 AAAACGC-C-GCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAA
* * * * * *
10253257 TGCTCAGAAAACGGCGTCATTGGGC-TTAGGTATTTTT-TCGCTGCTTTCCCG
64 AGCTCAAAAAACGGCGTCGTTGGGCTTTA-GTTTTTTTGTGGC-GCTTTCTCG
* * * * *
10253308 AAAACGCTGCTAAAGCCCTGAGCATTAGCGGTG-TCTACTAAAAAATGCCATTAAATCCCCGAAA
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT-TACTTAAAAACGCCACTAAATCCCCGAAA
*
10253372 GCTCAAAAAACGGCGTCGTTGGGCTTTGGTTTTTTTTGTGGCGCTTTCTCG
65 GCTCAAAAAACGGCGTCGTTGGGCTTTAG-TTTTTTTGTGGCGCTTTCTCG
* * * *
10253423 AAAACGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAG
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
* ** * * * *
10253488 CTCGAAAAACGGCGTCGTTATGC-TTAGGTATTTTGCGGCGCTTTAT-G
66 CTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCG
*
10253535 GAAACGCCGCTAA
1 AAAACGCCGCTAA
10253548 TGCTTATTTT
Statistics
Matches: 398, Mismatches: 53, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
112 21 0.05
113 110 0.28
114 145 0.36
115 118 0.30
116 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (114 bp):
AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAG
CTCAAAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCG
Found at i:10255160 original size:21 final size:22
Alignment explanation
Indices: 10255135--10255175 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10255125 TTTAATTATT
10255135 TTTA-TAACATCTTTGGAAAGA
1 TTTATTAACATCTTTGGAAAGA
* *
10255156 TTTATTAATATCTTTTGAAA
1 TTTATTAACATCTTTGGAAA
10255176 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTATTAACATCTTTGGAAAGA
Found at i:10255550 original size:15 final size:16
Alignment explanation
Indices: 10255529--10255564 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
10255519 GCTATGGATT
10255529 ATTAAAGTAAAGACCC
1 ATTAAAGTAAAGACCC
10255545 -TTAAAGTAAAGACCC
1 ATTAAAGTAAAGACCC
10255560 ATTAA
1 ATTAA
10255565 TAAGATAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (16 bp):
ATTAAAGTAAAGACCC
Found at i:10256612 original size:43 final size:42
Alignment explanation
Indices: 10256519--10256681 Score: 211
Period size: 43 Copynumber: 3.8 Consensus size: 42
10256509 AGGGTTTCCA
* *
10256519 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATCTA
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
*
10256561 AGACTT-CGTGTAAGACCATATCTGGGACATTGGCATCGATATG
1 AGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATG
* * ** *
10256604 TGATTTCGTGTAAGACCATGGCTGGGATATTGGCATCGATACG
1 AGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATG
*
10256647 AGATTACATGTAAGACCATATCTGGGATATGGCAT
1 AGATTACGTGTAAGACCATATCTGGGATATGGCAT
10256682 TGTTACGGTA
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.31
43 72 0.69
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
Found at i:10258252 original size:12 final size:12
Alignment explanation
Indices: 10258232--10258264 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10258222 GGCAATAATA
10258232 AGTTAAAAA-CG
1 AGTTAAAAATCG
10258243 AGTGTAAAAATCG
1 AGT-TAAAAATCG
10258256 AGTTAAAAA
1 AGTTAAAAA
10258265 GGCATAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 12 0.60
13 5 0.25
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (12 bp):
AGTTAAAAATCG
Found at i:10258926 original size:25 final size:23
Alignment explanation
Indices: 10258872--10258914 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10258862 AATGCTTGGG
10258872 TTATATA-GTTTTGGTCATGATA
1 TTATATATGTTTTGGTCATGATA
10258894 TATATATATGTTTTGG-CATGA
1 T-TATATATGTTTTGGTCATGA
10258915 AGTAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.05
23 11 0.58
24 7 0.37
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (23 bp):
TTATATATGTTTTGGTCATGATA
Found at i:10266581 original size:43 final size:42
Alignment explanation
Indices: 10266486--10266650 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 42
10266476 TTAGGGTTAT
* *
10266486 TGAGATTACGTGTAAGACCATATCTAGGATATGACATCGATA
1 TGAGATTACGTGTAAGACCATATCTAGGACATGGCATCGATA
* * *
10266528 TGAGACTT-CGTGTAACACCATGTCTGGGACATTGGCATCGATA
1 TGAGA-TTACGTGTAAGACCATATCTAGGACA-TGGCATCGATA
* * **
10266571 TGTGATTTCGTGTAAGACCATGGCTAGG-CTATTGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTAGGAC-A-TGGCATCGATA
* * * *
10266614 CGAGATTACTTGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTACGTGTAAGACCATATCTAGGACATGGCAT
10266651 TGTTACGGTA
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 33 0.33
43 68 0.67
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTAGGACATGGCATCGATA
Found at i:10272579 original size:40 final size:40
Alignment explanation
Indices: 10272534--10272699 Score: 199
Period size: 40 Copynumber: 4.2 Consensus size: 40
10272524 TCTGTTTGGT
* * *
10272534 GTGTTTC-AGTTAGATTAGCTCTTATAAGCTTCTGTCTGGC
1 GTGTTTCGA-TTAGATTAACTCTTATGAGCTTCTGTCTAGC
* *
10272574 ATGTTTCGATTAGATTAACTCTTGTGAGCTTCTGTCTAGC
1 GTGTTTCGATTAGATTAACTCTTATGAGCTTCTGTCTAGC
* * *
10272614 GTGTTTCGATTAGATTAACTCTTGTGAGCTTTTTTCTAGC
1 GTGTTTCGATTAGATTAACTCTTATGAGCTTCTGTCTAGC
* * * * *
10272654 GTGTTTCGGTTGGATTAGCTCTTATGAGCTTCTGTCTGGT
1 GTGTTTCGATTAGATTAACTCTTATGAGCTTCTGTCTAGC
10272694 GTGTTT
1 GTGTTT
10272700 GGTTGATTTG
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
40 108 0.99
41 1 0.01
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (40 bp):
GTGTTTCGATTAGATTAACTCTTATGAGCTTCTGTCTAGC
Found at i:10275009 original size:35 final size:34
Alignment explanation
Indices: 10274963--10275035 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
10274953 AATGATGTTA
* ** *
10274963 AATTGAATGTATTTATTATGTATATAGCCGAATTG
1 AATTGAATGTATGTA-TAACTACATAGCCGAATTG
* *
10274998 AATTGTATGTATGTATAACTACATTGCCGAATTG
1 AATTGAATGTATGTATAACTACATAGCCGAATTG
10275032 AATT
1 AATT
10275036 TGGCATGGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 19 0.59
35 13 0.41
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.41
Consensus pattern (34 bp):
AATTGAATGTATGTATAACTACATAGCCGAATTG
Found at i:10275264 original size:42 final size:43
Alignment explanation
Indices: 10275164--10275315 Score: 139
Period size: 43 Copynumber: 3.5 Consensus size: 43
10275154 TTTCGTGTAG
* * * *
10275164 GACCACGTCTGGGACGTTGGCATCGATTTGAGATTTACGTGTAA
1 GACCATGTCTGGGACATTGGCATCGATAT-AGATTTACGTATAA
*
10275208 GACCATGTCTGGGACATTGGCATCG-TATATGATTT-TGTATAA
1 GACCATGTCTGGGACATTGGCATCGATATA-GATTTACGTATAA
* * * * *
10275250 GACCTTGTCTGGGACAGTGGCATCGATAGTTGA-TTACATGTAA
1 GACCATGTCTGGGACATTGGCATCGATA-TAGATTTACGTATAA
** *
10275293 GACCACATCTGGGACGTTGGCAT
1 GACCATGTCTGGGACATTGGCAT
10275316 TGTACGAGCT
Statistics
Matches: 88, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 31 0.35
43 33 0.38
44 24 0.27
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GACCATGTCTGGGACATTGGCATCGATATAGATTTACGTATAA
Found at i:10278505 original size:40 final size:40
Alignment explanation
Indices: 10278461--10278542 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
10278451 CCATGTAAGA
*
10278461 CCATGTTTGGGACATGGCGTTGGCACCGAGATAAGAGGTC
1 CCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGGTC
*
10278501 CCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGGTC
10278541 CC
1 CC
10278543 CCGTAAGACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (40 bp):
CCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGGTC
Found at i:10278599 original size:50 final size:49
Alignment explanation
Indices: 10278501--10278667 Score: 156
Period size: 50 Copynumber: 3.4 Consensus size: 49
10278491 ATAAGAGGTC
* * * ** **
10278501 CCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGA
1 CCATGTCTGGGACATGGCATTGGCACCAACATGA-AAATCCCATGTAAGA
* *
10278551 CCATGTCTGGGACATGGCATGGGCACCAATATGAAAATTCCCATGTAAGA
1 CCATGTCTGGGACATGGCATTGGCACCAACATGAAAA-TCCCATGTAAGA
** * ** *
10278601 CCATAACTGGGATATGGCATTGGCA-GTACAGGAAACATCCCATGTAAGA
1 CCATGTCTGGGACATGGCATTGGCACCAACATGAAA-ATCCCATGTAAGA
*
10278650 CCATGTCTGGAACATGGC
1 CCATGTCTGGGACATGGC
10278668 TTTAGCATGT
Statistics
Matches: 95, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
49 33 0.35
50 62 0.65
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (49 bp):
CCATGTCTGGGACATGGCATTGGCACCAACATGAAAATCCCATGTAAGA
Found at i:10278667 original size:49 final size:50
Alignment explanation
Indices: 10278545--10278667 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 50
10278535 GAGGTCCCCC
* *
10278545 GTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAAAATTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCAACAGGAAAATTCCCAT
** * * **
10278595 GTAAGACCATAACTGGGATATGGCATTGGCA-GTACAGGAAACA-TCCCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCAACAGGAAA-ATTCCCAT
*
10278644 GTAAGACCATGTCTGGAACATGGC
1 GTAAGACCATGTCTGGGACATGGC
10278668 TTTAGCATGT
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
49 32 0.53
50 28 0.47
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACCAACAGGAAAATTCCCAT
Found at i:10284457 original size:36 final size:35
Alignment explanation
Indices: 10284381--10284451 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
10284371 TAATATTATA
*
10284381 AATGTATTTTAATCTATTATATAATTTTTTTCTTGT
1 AATGTATTTTAATCTATTATATAA-TATTTTCTTGT
* *
10284417 AATGTTTTTTTATCTATTATATAA-ATTTTCTTGT
1 AATGTATTTTAATCTATTATATAATATTTTCTTGT
10284451 A
1 A
10284452 GAATGTCCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 10 0.31
36 22 0.69
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (35 bp):
AATGTATTTTAATCTATTATATAATATTTTCTTGT
Found at i:10287026 original size:17 final size:17
Alignment explanation
Indices: 10287004--10287067 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
10286994 AATAGAGAAT
10287004 ATTATGTAGTAATTTTA
1 ATTATGTAGTAATTTTA
*
10287021 ATTATGT-GTTAATTTCAA
1 ATTATGTAG-TAATTT-TA
**
10287039 GACTTATGTAGTGTTTTTA
1 -A-TTATGTAGTAATTTTA
10287058 ATTATGTAGT
1 ATTATGTAGT
10287068 GATTAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.03
17 22 0.58
18 2 0.05
19 2 0.05
20 10 0.26
21 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.52
Consensus pattern (17 bp):
ATTATGTAGTAATTTTA
Found at i:10288786 original size:102 final size:102
Alignment explanation
Indices: 10288605--10288814 Score: 375
Period size: 102 Copynumber: 2.1 Consensus size: 102
10288595 CTACAATAGT
*
10288605 TAAAAATGAAATTAGTGCTTGTAATTGTAATAGTTAAAGGCAAAATATGAAAAGTCTCACATAGG
1 TAAACATGAAATTAGTGCTTGTAATTGTAATAGTTAAAGGCAAAATATGAAAAGTCTCACATAGG
*
10288670 CAGTTTAATAGTCACAAAAGTGCCTATAAATATCCTC
66 CAGTTGAATAGTCACAAAAGTGCCTATAAATATCCTC
* * *
10288707 TAAACATGAAATTAGTGCTTGTAATTGTACTAGTTAAAGGCCAACTATGAAAAGTCTCACATAGG
1 TAAACATGAAATTAGTGCTTGTAATTGTAATAGTTAAAGGCAAAATATGAAAAGTCTCACATAGG
10288772 CAGTTGAATAGTCACAAAAGTGCCTATAAATATCCTC
66 CAGTTGAATAGTCACAAAAGTGCCTATAAATATCCTC
10288809 TAAACA
1 TAAACA
10288815 AAACTTTGAT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (102 bp):
TAAACATGAAATTAGTGCTTGTAATTGTAATAGTTAAAGGCAAAATATGAAAAGTCTCACATAGG
CAGTTGAATAGTCACAAAAGTGCCTATAAATATCCTC
Found at i:10297628 original size:22 final size:22
Alignment explanation
Indices: 10297603--10297644 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10297593 AAAGTGACCC
*
10297603 AAAATAAGAATTCATTAGTGGG
1 AAAAGAAGAATTCATTAGTGGG
**
10297625 AAAAGAAGTGTTCATTAGTG
1 AAAAGAAGAATTCATTAGTG
10297645 TACCTGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (22 bp):
AAAAGAAGAATTCATTAGTGGG
Found at i:10297710 original size:6 final size:6
Alignment explanation
Indices: 10297699--10297734 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
10297689 GTAAAAAAAA
10297699 TTATAT TTATAT TTATAT TTATAT ATATATAT TTAT
1 TTATAT TTATAT TTATAT TTATAT -T-TATAT TTAT
10297735 GATTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.75
7 2 0.07
8 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:10298047 original size:7 final size:7
Alignment explanation
Indices: 10298035--10298060 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
10298025 AGTTTTCCAG
10298035 TCCCCAC
1 TCCCCAC
10298042 TCCCCAC
1 TCCCCAC
10298049 TCCCCAC
1 TCCCCAC
10298056 TCCCC
1 TCCCC
10298061 CTTTATGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.73, G:0.00, T:0.15
Consensus pattern (7 bp):
TCCCCAC
Found at i:10301743 original size:20 final size:20
Alignment explanation
Indices: 10301718--10301757 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10301708 TAGGATCAAA
10301718 TTGGGGAGTGGATATTATGG
1 TTGGGGAGTGGATATTATGG
10301738 TTGGGGAGTGGATATTATGG
1 TTGGGGAGTGGATATTATGG
10301758 AAGATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (20 bp):
TTGGGGAGTGGATATTATGG
Found at i:10310169 original size:4 final size:4
Alignment explanation
Indices: 10310160--10310198 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
10310150 ACTTTCTTCT
* **
10310160 TTAC TTAC TTTC TTAC TTGT TTAC TTAC TTAC TTAC TTA
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTA
10310199 AATAACTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.56
Consensus pattern (4 bp):
TTAC
Found at i:10310176 original size:8 final size:8
Alignment explanation
Indices: 10310148--10310198 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
10310138 ATCATGATCT
10310148 TTACTTTC
1 TTACTTTC
10310156 TT-CTTTAC
1 TTACTTT-C
10310164 TTACTTTC
1 TTACTTTC
10310172 TTACTTGT-
1 TTACTT-TC
*
10310180 TTACTTAC
1 TTACTTTC
*
10310188 TTACTTAC
1 TTACTTTC
10310196 TTA
1 TTA
10310199 AATAACTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 4 0.11
8 29 0.76
9 5 0.13
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.59
Consensus pattern (8 bp):
TTACTTTC
Found at i:10310184 original size:20 final size:20
Alignment explanation
Indices: 10310148--10310197 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
10310138 ATCATGATCT
* *
10310148 TTACTTTCTTCTTTACTTAC
1 TTACTTACTTGTTTACTTAC
*
10310168 TTTCTTACTTGTTTACTTAC
1 TTACTTACTTGTTTACTTAC
10310188 TTACTTACTT
1 TTACTTACTT
10310198 AAATAACTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60
Consensus pattern (20 bp):
TTACTTACTTGTTTACTTAC
Found at i:10320025 original size:45 final size:45
Alignment explanation
Indices: 10319933--10320027 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
10319923 ATACTTTCAT
* * * * **
10319933 ATGATGCCATACCGTCTTTTAGCTATGGTCTTACTCATTTTTCTC
1 ATGATGCCATACCATCTTTCAGCTATGGCCTTACTCATCTTAATC
* *
10319978 ATGATGCCATAGCATCTTTCAGCTATGGCCTTACTTATCTTAATC
1 ATGATGCCATACCATCTTTCAGCTATGGCCTTACTCATCTTAATC
10320023 ATGAT
1 ATGAT
10320028 CTCAAAATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (45 bp):
ATGATGCCATACCATCTTTCAGCTATGGCCTTACTCATCTTAATC
Found at i:10326254 original size:25 final size:26
Alignment explanation
Indices: 10326226--10326276 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
10326216 CGTCCGTACC
* *
10326226 ATAGT-CCACAAATAATAATAATAAA
1 ATAGTCCCAAAAATAACAATAATAAA
*
10326251 ATAGTCCCAAAAATACCAATAATAAA
1 ATAGTCCCAAAAATAACAATAATAAA
10326277 GTTTAGCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.59, C:0.16, G:0.04, T:0.22
Consensus pattern (26 bp):
ATAGTCCCAAAAATAACAATAATAAA
Found at i:10326729 original size:23 final size:24
Alignment explanation
Indices: 10326697--10326741 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
10326687 CACTTGTTAG
10326697 CGTTGAGGACAAGACAC-CAATAT
1 CGTTGAGGACAAGACACTCAATAT
* *
10326720 CGTTGTGGACAAGCCACTCAAT
1 CGTTGAGGACAAGACACTCAAT
10326742 TTTGCAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
CGTTGAGGACAAGACACTCAATAT
Found at i:10327786 original size:22 final size:18
Alignment explanation
Indices: 10327758--10327803 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 18
10327748 CATTACTAAC
10327758 AAATGGATGAAAAGAATGAGA
1 AAATGGA-GAAAA-AAT-AGA
10327779 GAAATGGAGAAAAAATAGA
1 -AAATGGAGAAAAAATAGA
10327798 AAATGG
1 AAATGG
10327804 TGGTGGTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 3 0.12
21 5 0.21
22 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (18 bp):
AAATGGAGAAAAAATAGA
Found at i:10332732 original size:30 final size:33
Alignment explanation
Indices: 10332698--10332757 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
10332688 TTTAAATGTA
*
10332698 TTGAATCA-AATCAAAA-TTT-TGTATATACAT
1 TTGAACCACAATCAAAATTTTATGTATATACAT
*
10332728 TTGAACCACATTCAAAATTTTATGTATATA
1 TTGAACCACAATCAAAATTTTATGTATATA
10332758 TTACACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 7 0.28
32 3 0.12
33 8 0.32
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (33 bp):
TTGAACCACAATCAAAATTTTATGTATATACAT
Done.