Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014194.1 Kokia drynarioides strain JFW-HI SEQ_129227, whole genome shotgun sequence
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: 304403
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:10048 original size:18 final size:18
Alignment explanation
Indices: 10035--10090 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
10025 GGTTGCATAC
*
10035 GAGCATGTGATTGCATCT
1 GAGCATGTGACTGCATCT
10053 GAGCATGTGACTGCATCT
1 GAGCATGTGACTGCATCT
10071 GAGCATGTGACTGCATCT
1 GAGCATGTGACTGCATCT
10089 GA
1 GA
10091 TCTTGATGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (18 bp):
GAGCATGTGACTGCATCT
Found at i:13111 original size:42 final size:42
Alignment explanation
Indices: 13053--13426 Score: 502
Period size: 42 Copynumber: 9.2 Consensus size: 42
13043 TATCATCAGA
* *
13053 GTAAGCGATTGAATGATGTCTTCAATCTGCCCCATGGTCGGG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
* * * *
13095 GTAAGAGAATAGATGATGTCTTCAATTTGTCCCATGGTCGGG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
* *
13137 GTAAGAGATTGGATG--G-CTTCAATCTGCCCTATGGTCGAG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
*
13176 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGAG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
* * **
13218 GTAAGAGATTGGATG--GT-TTTAATCTACCCCATGGTCAAG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
*
13257 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTTGGG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
* *
13299 TTAAGAGATTGGATG--GT-TTCAATCTGCCCCATGGTCAGG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
*
13338 GTAAGAGATTGGATGATGTCTTCAATTTGCCCCATGGTCGGG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
*
13380 GTAAGAGATT-GA--ATGGCTTCAATCTGCCCCATGGTCGGG
1 GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
13419 GTAAGAGA
1 GTAAGAGA
13427 CTTGTTGGTA
Statistics
Matches: 294, Mismatches: 29, Indels: 21
0.85 0.08 0.06
Matches are distributed among these distances:
39 135 0.46
40 5 0.02
41 7 0.02
42 147 0.50
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (42 bp):
GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGG
Found at i:13162 original size:81 final size:81
Alignment explanation
Indices: 13067--13426 Score: 549
Period size: 81 Copynumber: 4.4 Consensus size: 81
13057 GCGATTGAAT
* * * * *
13067 GATGTCTTCAATCTGCCCCATGGTCGGGGTAAGAGAATAGATGATGTCTTCAATTTGTCCCATGG
1 GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGG
13132 TCGGGGTAAGAGATTG
66 TCGGGGTAAGAGATTG
* *
13148 GATGGCTTCAATCTGCCCTATGGTCGAGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGG
1 GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGG
*
13213 TCGAGGTAAGAGATTG
66 TCGGGGTAAGAGATTG
* * * **
13229 GATGGTTTTAATCTACCCCATGGTCAAGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGG
1 GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGG
* *
13294 TTGGGTTAAGAGATTG
66 TCGGGGTAAGAGATTG
* * *
13310 GATGGTTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGATGTCTTCAATTTGCCCCATGG
1 GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGG
13375 TCGGGGTAAGAGATTG
66 TCGGGGTAAGAGATTG
*
13391 AATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGA
1 GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGA
13427 CTTGTTGGTA
Statistics
Matches: 254, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 254 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (81 bp):
GATGGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGG
TCGGGGTAAGAGATTG
Found at i:33081 original size:12 final size:13
Alignment explanation
Indices: 33059--33100 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
33049 TGAGGGTGTT
33059 GAAGAAGAAGAGAA
1 GAAG-AGAAGAGAA
33073 -AAGAGAAGAAGAA
1 GAAGAGAAG-AGAA
33086 GGAAGAGAAGAGAA
1 -GAAGAGAAGAGAA
33100 G
1 G
33101 GAAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.20
13 8 0.32
14 4 0.16
15 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (13 bp):
GAAGAGAAGAGAA
Found at i:33091 original size:15 final size:15
Alignment explanation
Indices: 33059--33103 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 15
33049 TGAGGGTGTT
33059 GAAGAAGAAGAGAAAAGA
1 GAAGAAGAAG-G--AAGA
33077 GAAGAAGAAGGAAGA
1 GAAGAAGAAGGAAGA
33092 GAAG-AGAAGGAA
1 GAAGAAGAAGGAA
33104 AAAGAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.30
15 8 0.30
17 1 0.04
18 10 0.37
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGGAAGA
Found at i:33108 original size:17 final size:17
Alignment explanation
Indices: 33059--33115 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 17
33049 TGAGGGTGTT
33059 GAAGAAGAAGAGAAAAGA
1 GAAGAAGAAG-GAAAAGA
33077 GAAGAAGAAGG--AAGA
1 GAAGAAGAAGGAAAAGA
33092 GAAG-AGAAGGAAAA-A
1 GAAGAAGAAGGAAAAGA
*
33107 GAAAAAGAA
1 GAAGAAGAA
33116 AAAGAAGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 6 0.17
15 12 0.34
16 6 0.17
17 1 0.03
18 10 0.29
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAGGAAAAGA
Found at i:40502 original size:51 final size:51
Alignment explanation
Indices: 40426--40611 Score: 237
Period size: 51 Copynumber: 3.6 Consensus size: 51
40416 AGCTATAAAG
* *
40426 AAAGGGCCTGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTGCGGATT
1 AAAGGACCT-ATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
* * *
40478 AAAGGTCCTATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGACCTATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
* * * *
40529 AAAGGACCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGAAGGATT
1 AAAGGACCTATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
* * * * *
40580 AAAGGAGCAATAACTCAGTGTCATCGTGAGTA
1 AAAGGACCTATGACTAAGTGTCATCATGAGTA
40612 TGAATTCCTA
Statistics
Matches: 119, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 111 0.93
52 8 0.07
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (51 bp):
AAAGGACCTATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
Found at i:40560 original size:102 final size:103
Alignment explanation
Indices: 40426--40611 Score: 277
Period size: 102 Copynumber: 1.8 Consensus size: 103
40416 AGCTATAAAG
* * * * * *
40426 AAAGGGCCTGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTG-CGGATTAAAGGTCCTATG
1 AAAGGACCTGATGACTAAGTGTCATCATGAGTAAATGAATCC-ATGAAGGATTAAAGGACCAATA
40490 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
65 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
*
40529 AAAGGACC-GATGACTAAGTGTCATCATGAGTAAATGAATCCATGAAGGATTAAAGGAGCAATAA
1 AAAGGACCTGATGACTAAGTGTCATCATGAGTAAATGAATCCATGAAGGATTAAAGGACCAATAA
*
40593 CTCAGTGTCATCGTGAGTA
66 CTAAGTGTCATCGTGAGTA
40612 TGAATTCCTA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 2 0.03
102 65 0.88
103 7 0.09
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (103 bp):
AAAGGACCTGATGACTAAGTGTCATCATGAGTAAATGAATCCATGAAGGATTAAAGGACCAATAA
CTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:40635 original size:102 final size:101
Alignment explanation
Indices: 40426--40662 Score: 255
Period size: 102 Copynumber: 2.3 Consensus size: 101
40416 AGCTATAAAG
* * * * * *
40426 AAAGGGCCTGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTGCGGATTAAAGGTCCTATGA
1 AAAGGACC-GATGACTAAGTGTCATCATGAGTAAATGAATCCTATGAGGATTAAAGGACCAATAA
* * * **
40491 CTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
65 CTAAGTGTCATCGTGAGT-AATGAATCCTATAAGAACA
*
40529 AAAGGACCGATGACTAAGTGTCATCATGAGTAAATGAATCC-ATGAAGGATTAAAGGAGCAATAA
1 AAAGGACCGATGACTAAGTGTCATCATGAGTAAATGAATCCTATG-AGGATTAAAGGACCAATAA
*
40593 CTCAGTGTCATCGTGAGT-ATGAATTCCTATACAGAACA
65 CTAAGTGTCATCGTGAGTAATGAA-TCCTATA-AGAACA
* * *
40631 AAAGGTCCAATGACTATA-TGTCATCGTGAGTA
1 AAAGGACCGATGACTA-AGTGTCATCATGAGTA
40663 TTAAATGAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
100 5 0.04
101 8 0.07
102 93 0.82
103 8 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (101 bp):
AAAGGACCGATGACTAAGTGTCATCATGAGTAAATGAATCCTATGAGGATTAAAGGACCAATAAC
TAAGTGTCATCGTGAGTAATGAATCCTATAAGAACA
Found at i:47774 original size:51 final size:51
Alignment explanation
Indices: 47701--47882 Score: 285
Period size: 51 Copynumber: 3.6 Consensus size: 51
47691 TAAACAAAAG
* *
47701 GGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTGCGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTGTGGATTAAA
* *
47752 GGTCCTATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTGTGGATTAAA
*
47803 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCC-ATGATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTG-TGGATTAAA
* *
47854 TGTCCGATGACTCAGTGTCATCGTGAGTA
1 GGTCCGATGACTAAGTGTCATCGTGAGTA
47883 TGAATTCCTA
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 1 0.01
51 120 0.99
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTGTGGATTAAA
Found at i:47908 original size:102 final size:101
Alignment explanation
Indices: 47701--47933 Score: 274
Period size: 102 Copynumber: 2.3 Consensus size: 101
47691 TAAACAAAAG
* * *
47701 GGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTGCGGATTAAAGGTCCTATGACTAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATGCGGATTAAAGGTCCGATGACTAA
* ** **
47766 GTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
66 GTGTCATCGTGAGT-AATGAATCCTATACAGAACAAA
* * *
47803 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCC-ATGATGGATTAAATGTCCGATGACTC
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATG-CGGATTAAAGGTCCGATGACTA
47867 AGTGTCATCGTGAGT-ATGAATTCCTATACAGAACAAGA
65 AGTGTCATCGTGAGTAATGAA-TCCTATACAGAACAA-A
* * *
47905 GGTCCAATGACCATA-TGTCATCATGAGTA
1 GGTCCGATGACTA-AGTGTCATCGTGAGTA
47934 TTAAATGAAC
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
100 5 0.04
101 12 0.11
102 95 0.84
103 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (101 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATGCGGATTAAAGGTCCGATGACTAA
GTGTCATCGTGAGTAATGAATCCTATACAGAACAAA
Found at i:55735 original size:3 final size:3
Alignment explanation
Indices: 55727--55751 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55717 TAATTTTGTG
55727 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
55752 GAGACCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:55929 original size:14 final size:14
Alignment explanation
Indices: 55910--55939 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55900 TTATATACTA
55910 TGGACTTTGATTTT
1 TGGACTTTGATTTT
*
55924 TGGACTTTGGTTTT
1 TGGACTTTGATTTT
55938 TG
1 TG
55940 CTTTTGGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.27, T:0.57
Consensus pattern (14 bp):
TGGACTTTGATTTT
Found at i:55944 original size:21 final size:21
Alignment explanation
Indices: 55910--55966 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
55900 TTATATACTA
* *
55910 TGGACTTTGATTTTTGGACTT
1 TGGATTTTGATTTTGGGACTT
* *
55931 TGGTTTTTGCTTTTGGGACTT
1 TGGATTTTGATTTTGGGACTT
55952 TGGATTTTGATTTTG
1 TGGATTTTGATTTTG
55967 TAACTTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.11, C:0.07, G:0.26, T:0.56
Consensus pattern (21 bp):
TGGATTTTGATTTTGGGACTT
Found at i:55972 original size:21 final size:21
Alignment explanation
Indices: 55910--55973 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
55900 TTATATACTA
*
55910 TGGACTTTGATTTT-TGGACTT
1 TGGATTTTGATTTTGT-GACTT
* * *
55931 TGGTTTTTGCTTTTGGGACTT
1 TGGATTTTGATTTTGTGACTT
*
55952 TGGATTTTGATTTTGTAACTT
1 TGGATTTTGATTTTGTGACTT
55973 T
1 T
55974 TATGCATGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.12, C:0.08, G:0.23, T:0.56
Consensus pattern (21 bp):
TGGATTTTGATTTTGTGACTT
Found at i:58429 original size:29 final size:29
Alignment explanation
Indices: 58396--58454 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
58386 GCATTCATTA
58396 ACATATAGTATTATAATTGAAACCGATTG
1 ACATATAGTATTATAATTGAAACCGATTG
58425 ACATATAGTATTATAATTGAAACCGATTG
1 ACATATAGTATTATAATTGAAACCGATTG
58454 A
1 A
58455 ATTGACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (29 bp):
ACATATAGTATTATAATTGAAACCGATTG
Found at i:58815 original size:19 final size:18
Alignment explanation
Indices: 58788--58827 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58778 TCACGTCAGC
*
58788 AAATGAATTTAAACTTAAA
1 AAATGAA-TTAAAATTAAA
*
58807 AAATTAATTAAAATTAAA
1 AAATGAATTAAAATTAAA
58825 AAA
1 AAA
58828 CATTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATGAATTAAAATTAAA
Found at i:58877 original size:9 final size:9
Alignment explanation
Indices: 58851--58894 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
58841 TTTGGGACCC
*
58851 ACAATTAAC
1 ACAATTAAA
58860 ACAATTAAA
1 ACAATTAAA
58869 ACAATTAAA
1 ACAATTAAA
58878 A-AA-TAAA
1 ACAATTAAA
58885 ACAAATTAAA
1 AC-AATTAAA
58895 CACTAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 20 0.65
10 4 0.13
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (9 bp):
ACAATTAAA
Found at i:60147 original size:14 final size:15
Alignment explanation
Indices: 60101--60151 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
60091 AAATCAAACT
60101 TATTTAATAATTTTA
1 TATTTAATAATTTTA
*
60116 TTATTTCAAATAAATTTA
1 -TATTT--AATAATTTTA
60134 T-TTTAATAATTTTA
1 TATTTAATAATTTTA
60148 TATT
1 TATT
60152 CTTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
16 8 0.27
17 1 0.03
18 9 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTAATAATTTTA
Found at i:64060 original size:19 final size:19
Alignment explanation
Indices: 64038--64078 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
64028 TGGGCTTAGC
* *
64038 TTAATTTACACAATTGGTA
1 TTAATTGACACAATTGATA
*
64057 TTAATTGACATAATTGATA
1 TTAATTGACACAATTGATA
64076 TTA
1 TTA
64079 TACCAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (19 bp):
TTAATTGACACAATTGATA
Found at i:68334 original size:58 final size:57
Alignment explanation
Indices: 68255--68448 Score: 228
Period size: 59 Copynumber: 3.3 Consensus size: 57
68245 CTTCGAGAAA
* * * *
68255 AAAATGGTAAGTTTCGAAAGGTTCGGGGTTAAAAATGAAAATTTTAAACATCCGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATG-AAATTTTAAACATCAGGGGT
** * * * * *
68313 AAAATGGTAATTTTTGGAAGGTTTAGGATTAAAAATGGAATTTTTAGATATTTAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAAT-GAAATTTTAAACA-TCAGGGGT
*
68372 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAAATTTTAAGACATCTAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTAA-ACATC-AGGGGT
68431 AAAATGGTAA-TTTTGGAA
1 AAAATGGTAATTTTTGGAA
68449 AGTAGAGGTC
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
58 56 0.50
59 57 0.50
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (57 bp):
AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAAATTTTAAACATCAGGGGT
Found at i:68386 original size:59 final size:57
Alignment explanation
Indices: 68308--68827 Score: 447
Period size: 59 Copynumber: 8.8 Consensus size: 57
68298 TTAAACATCC
* * * *
68308 GGGGTAAAATGGTAATTTTTGGAAGGTTTAGGATTAAAAATGGAATTTTTAGATATTTA
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTTAGGGTTAAAAATGGAA-TTTTGGAAATTTA
* ** * * * * *
68367 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAAATTTTAAGACATCTA
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTTAGGGTTAAAAATGGAATTTT-GGAAATTTA
* *
68426 GGGGTAAAATGGTAA-TTTTGGAAAG--TAGAGGTCAAAAAATGGAATTTTGGAAAGATT-
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTTAG-GGT-TAAAAATGGAATTTTGGAAA-TTTA
* * * *
68483 GAGGGTAAAAATATAATTTTTAGAAAGTTTAGGGGTTAAAAATGGAATTTTGGAAAGTTC
1 G-GGGT-AAAATGTAATTTTTGGAAAGTTTA-GGGTTAAAAATGGAATTTTGGAAATTTA
* * *
68543 GAGGATAAAATGTAATTTTTAGAAAGTTTAAGGTTAAAAATGGAATTTTGGAAAGTTTA
1 G-GGGTAAAATGTAATTTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAA-TTTA
* * * * * *
68602 GGGGTAAAAATGTAATTTTTGAAAAGTTCAGGATAAAAAATGGAATTTTAGAAAATTCA
1 GGGGT-AAAATGTAATTTTTGGAAAGTTTAGGGTTAAAAATGGAATTTT-GGAAATTTA
* * * * * * * *
68661 AGGATAAAAATATGATTTTTGGATAGTTCAAGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGT-AAAATGTAATTTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAA-TTTA
* * *
68720 GGGGTAGAAATGTAATTTTTGAAAAGTTTGGGGTTAAAAAATGGAATTTTGGAAAGTTCA
1 GGGGTA-AAATGTAATTTTTGGAAAGTTTAGGGTT-AAAAATGGAATTTTGGAAA-TTTA
* * *
68780 AGGGTAAAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAAATGGAATTTT
1 GGGGT-AAAATGTAATTTTTGGAAAGTTTAGGGTTAAAAATGGAATTTT
68828 TGGATAGTTC
Statistics
Matches: 381, Mismatches: 62, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.00
57 7 0.02
58 79 0.21
59 226 0.59
60 61 0.16
61 6 0.02
62 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (57 bp):
GGGGTAAAATGTAATTTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAATTTA
Found at i:68399 original size:29 final size:30
Alignment explanation
Indices: 68308--68831 Score: 207
Period size: 29 Copynumber: 17.8 Consensus size: 30
68298 TTAAACATCC
68308 GGGGT-AAAATGGTAATTTTTGGAAGGTTTA
1 GGGGTAAAAATGGTAATTTTTGGAAGG-TTA
** * *
68338 GGATTAAAAATGG-AATTTTTAGATA-TTTA
1 GGGGTAAAAATGGTAATTTTTGGA-AGGTTA
*
68367 GGGGT-AAAATGGTAATTTTTGGAAGGTTC
1 GGGGTAAAAATGGTAATTTTTGGAAGGTTA
* **
68396 GGGGTCAAAAAT-GAAATTTTAAGACA--TCTA
1 GGGGT-AAAAATGGTAATTTTTGGA-AGGT-TA
*
68426 GGGGT-AAAATGGTAA-TTTTGGAAAG-TA
1 GGGGTAAAAATGGTAATTTTTGGAAGGTTA
* *
68453 GAGGTCAAAAAATGG-AA-TTTTGGAAAGATT-
1 GGGGT--AAAAATGGTAATTTTTGG-AAGGTTA
* * *
68483 GAGGGTAAAAAT-ATAATTTTTAGAAAGTTTA
1 G-GGGTAAAAATGGTAATTTTT-GGAAGGTTA
* *
68514 GGGGTTAAAAATGG-AA-TTTTGGAAAGTTC
1 GGGG-TAAAAATGGTAATTTTTGGAAGGTTA
* * *
68543 GAGG-ATAAAAT-GTAATTTTTAGAAAGTTTA
1 GGGGTA-AAAATGGTAATTTTT-GGAAGGTTA
* * *
68573 AGGTTAAAAATGG-AA-TTTTGGAAAGTTTA
1 GGGGTAAAAATGGTAATTTTTGG-AAGGTTA
* *
68602 GGGGTAAAAAT-GTAATTTTTGAAAAGTTCA
1 GGGGTAAAAATGGTAATTTTTGGAAGGTT-A
* * **
68632 -GGATAAAAAATGG-AA-TTTTAGAAAATTCA
1 GGGGT-AAAAATGGTAATTTTTGGAAGGTT-A
* * * *
68661 AGGATAAAAAT-ATGATTTTTGGATA-GTTCA
1 GGGGTAAAAATGGTAATTTTTGGA-AGGTT-A
* * * *
68691 AGGTTAAAAATGG-AA-TTTTGGAAAGTTTG
1 GGGGTAAAAATGGTAATTTTTGG-AAGGTTA
* * * *
68720 GGGGTAGAAAT-GTAATTTTTGAAAAGTTT
1 GGGGTAAAAATGGTAATTTTTGGAAGGTTA
*
68749 GGGGTTAAAAAATGG-AA-TTTTGGAAAGTTCA
1 GGGG-T-AAAAATGGTAATTTTTGGAAGGTT-A
* *
68780 AGGGTAAAAATGG-AA-TTTTGGAAAGTTTA
1 GGGGTAAAAATGGTAATTTTTGG-AAGGTTA
68809 GGGGTAAAAATGG-AATTTTTGGA
1 GGGGTAAAAATGGTAATTTTTGGA
68832 TAGTTCAGGG
Statistics
Matches: 375, Mismatches: 69, Indels: 101
0.69 0.13 0.19
Matches are distributed among these distances:
27 9 0.02
28 28 0.07
29 158 0.42
30 136 0.36
31 43 0.11
32 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (30 bp):
GGGGTAAAAATGGTAATTTTTGGAAGGTTA
Found at i:68464 original size:58 final size:58
Alignment explanation
Indices: 68285--68473 Score: 213
Period size: 59 Copynumber: 3.2 Consensus size: 58
68275 GTTCGGGGTT
* ** *
68285 AAAAATGAAAATTTTAA-ACATC-CGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGATT
1 AAAAATG-AAATTTTAAGACATCTAGGGGTAAAATGGTAATTTTTGGAAGGTAGAGG-TC
* * * * * *
68343 AAAAATGGAATTTTTAGATATTTAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTC
1 AAAAATGAAATTTTAAGACATCTAGGGGTAAAATGGTAATTTTTGGAAGG-TAGAGGTC
*
68402 AAAAATGAAATTTTAAGACATCTAGGGGTAAAATGGTAA-TTTTGGAAAGTAGAGGTC
1 AAAAATGAAATTTTAAGACATCTAGGGGTAAAATGGTAATTTTTGGAAGGTAGAGGTC
*
68459 AAAAAATGGAATTTT
1 -AAAAATGAAATTTT
68474 GGAAAGATTG
Statistics
Matches: 110, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
57 13 0.12
58 32 0.29
59 62 0.56
60 3 0.03
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (58 bp):
AAAAATGAAATTTTAAGACATCTAGGGGTAAAATGGTAATTTTTGGAAGGTAGAGGTC
Found at i:69773 original size:21 final size:23
Alignment explanation
Indices: 69732--69779 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
69722 TTTAGAAATC
69732 TAAAATGAGTGTTTCCAAAATTT
1 TAAAATGAGTGTTTCCAAAATTT
*
69755 TAAAATG-G-GTTTCACAAATTTT
1 TAAAATGAGTGTTTC-CAAAATTT
69777 TAA
1 TAA
69780 CTTTTTCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 7 0.30
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (23 bp):
TAAAATGAGTGTTTCCAAAATTT
Found at i:70696 original size:6 final size:6
Alignment explanation
Indices: 70677--70745 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
70667 ATTGTTTAAA
* *
70677 TAAATT TAATTT TAAATT TATAA-- TAAATT TAAATT TCCAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
*
70723 TAAATT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT
70746 CTGTTGGGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.08
5 7 0.14
6 35 0.70
7 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:70709 original size:17 final size:17
Alignment explanation
Indices: 70687--70745 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
70677 TAAATTTAAT
*
70687 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
**
70704 TTTAAATTTCCAATAAA
1 TTTAAATTTAAAATAAA
70721 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
70738 TTTAAATT
1 TTTAAATT
70746 CTGTTGGGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:71337 original size:49 final size:49
Alignment explanation
Indices: 71281--71439 Score: 155
Period size: 49 Copynumber: 3.5 Consensus size: 49
71271 AGTTGGTATA
71281 CTTCTCTGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCG
1 CTTCTCTGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCG
* * *
71330 CTTCTCTGTATCTCATCAGGAAGA--CGAA--T---TTG-----GTCCA
1 CTTCTCTGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCG
** * *
71367 CTTCTCAATATCTCATCAGGAAGATGACC-GCCTCACTTGTTTTAATTCG
1 CTTCTCTGTATCTCATCAGGAAGATG-CCAACCTCACTTGTTTTAATCCG
71416 CTTCTCTGTATCTCATCAGGAAGA
1 CTTCTCTGTATCTCATCAGGAAGA
71440 CGAATTTAGT
Statistics
Matches: 85, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
37 25 0.29
40 1 0.01
41 1 0.01
42 3 0.04
44 3 0.04
45 1 0.01
47 3 0.04
49 48 0.56
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (49 bp):
CTTCTCTGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCG
Found at i:71418 original size:86 final size:86
Alignment explanation
Indices: 71280--71475 Score: 304
Period size: 86 Copynumber: 2.3 Consensus size: 86
71270 GAGTTGGTAT
*
71280 ACTTCTCTGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCGCTTCTCTGTATCTCA
1 ACTTCTCAGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCGCTTCTCTGTATCTCA
*
71345 TCAGGAAGACGAATTTGGTCC
66 TCAGGAAGACGAATTTAGTCC
* * *
71366 ACTTCTCAATATCTCATCAGGAAGATGACC-GCCTCACTTGTTTTAATTCGCTTCTCTGTATCTC
1 ACTTCTCAGTATCTCATCAGGAAGATG-CCAACCTCACTTGTTTTAATCCGCTTCTCTGTATCTC
71430 ATCAGGAAGACGAATTTAGTCC
65 ATCAGGAAGACGAATTTAGTCC
* * *
71452 ACTTCTTAGTATCTAATTAGGAAG
1 ACTTCTCAGTATCTCATCAGGAAG
71476 CTAACCATTT
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 98 0.98
87 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (86 bp):
ACTTCTCAGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCGCTTCTCTGTATCTCA
TCAGGAAGACGAATTTAGTCC
Found at i:71604 original size:287 final size:287
Alignment explanation
Indices: 71081--71610 Score: 812
Period size: 287 Copynumber: 1.8 Consensus size: 287
71071 TTCAGTCTTT
* * * * * *
71081 TTCTCAGTATCTCATCAAGAAGATGATCGCATCCCTTGTTTCAATTCATTTCTTTGTATCTTATC
1 TTCTCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATTCACTTCTCTGTATCTCATC
* *
71146 AGGAAGACGAATTTGGTTCACTTCTCAGTATCTAATCAGGAAGCTAACCATTTTATTACTTCGAC
66 AGGAAGACGAATTTAGTCCACTTCTCAGTATCTAATCAGGAAGCTAACCATTTTATTACTTCGAC
* * * *
71211 CTGCTTCTCAGTATCTCATTAGGAAACTAGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTTG
131 CTGCTTCTCAGTATCTCATCAGGAAACTAGGGTTCAAAGATTTGCTCACATTGAACCTTGAGTTG
* *
71276 GTATACTTCTCTGTATCTCATCAGGAAGATGCCAACCTCACTTGTTTTAATCCGCTTCTCTGTAT
196 GTATACTTCACTGTATCTCATCAGGAAGATACCAACCTCACTTGTTTTAATCCGCTTCTCTGTAT
71341 CTCATCAGGAAGACGAATTTGGTCCAC
261 CTCATCAGGAAGACGAATTTGGTCCAC
* * * *
71368 TTCTCAATATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATTCGCTTCTCTGTATCTCATC
1 TTCTCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATTCACTTCTCTGTATCTCATC
* * *
71433 AGGAAGACGAATTTAGTCCACTTCTTAGTATCTAATTAGGAAGCTAACCATTTTATTGCTTCGAC
66 AGGAAGACGAATTTAGTCCACTTCTCAGTATCTAATCAGGAAGCTAACCATTTTATTACTTCGAC
* *
71498 CTGCTTCTCAGTATCTCATCAGGAAGCT-GAGGTTCAAAGATTTGCTCACATTTAACCTTGAGTT
131 CTGCTTCTCAGTATCTCATCAGGAAACTAG-GGTTCAAAGATTTGCTCACATTGAACCTTGAGTT
*
71562 GGTATACTTCACTGTATCTCATCAGGAAGATTACC-GCCTCACTTGTTTT
195 GGTATACTTCACTGTATCTCATCAGGAAGA-TACCAACCTCACTTGTTTT
71611 GGGTAATTGC
Statistics
Matches: 217, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
286 1 0.00
287 213 0.98
288 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (287 bp):
TTCTCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATTCACTTCTCTGTATCTCATC
AGGAAGACGAATTTAGTCCACTTCTCAGTATCTAATCAGGAAGCTAACCATTTTATTACTTCGAC
CTGCTTCTCAGTATCTCATCAGGAAACTAGGGTTCAAAGATTTGCTCACATTGAACCTTGAGTTG
GTATACTTCACTGTATCTCATCAGGAAGATACCAACCTCACTTGTTTTAATCCGCTTCTCTGTAT
CTCATCAGGAAGACGAATTTGGTCCAC
Found at i:82302 original size:190 final size:189
Alignment explanation
Indices: 81966--82345 Score: 670
Period size: 190 Copynumber: 2.0 Consensus size: 189
81956 TTTGCCTTCC
*
81966 ATGATGAAACTGCCTATCTGGTAATCGAACTTAAATAAACACCTTTTCCTTTTATGATAATGTAA
1 ATGATGAAACTGCCTATCTGGTAATCGAACTTAAATAAACACCTTTTCCTTTTATGATAATGCAA
* *
82031 TGCAAGATAGGAGACAAAACAGAACACGTTAGTAACACATAATAATGTCAGCACACGAGGATATA
66 TGCAAAATAGGAGACAAAACAGAACACGTTAGTAACACATAATAATATCAGCACACGAGGATATA
*
82096 GCAAAGAACCTAAGAAATTGTCTTGGATAACTGCTAAAAGGTTTGGCATAACTCCGTCT
131 GCAAAGAACCTAAGAAATTATCTTGGATAACTGCTAAAAGGTTTGGCATAACTCCGTCT
* *
82155 ATGATGAAACTGCCTATTTGGTAATCGAACTTAAATCAACACCTTTTCCTTTTATGATAATGCAA
1 ATGATGAAACTGCCTATCTGGTAATCGAACTTAAATAAACACCTTTTCCTTTTATGATAATGCAA
* * *
82220 TGCAATAATAGGAGACAAAACATAACACTTTAGTAACACATAATAATATCAGCACACGAGTATAT
66 TGCAA-AATAGGAGACAAAACAGAACACGTTAGTAACACATAATAATATCAGCACACGAGGATAT
82285 AGCAAAGAACCTAAGAAATTATCTTGGATAACTGCTAAAAGGTTTGGCATAACTCCGTCT
130 AGCAAAGAACCTAAGAAATTATCTTGGATAACTGCTAAAAGGTTTGGCATAACTCCGTCT
82345 A
1 A
82346 AGACGAGTAC
Statistics
Matches: 181, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
189 67 0.37
190 114 0.63
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (189 bp):
ATGATGAAACTGCCTATCTGGTAATCGAACTTAAATAAACACCTTTTCCTTTTATGATAATGCAA
TGCAAAATAGGAGACAAAACAGAACACGTTAGTAACACATAATAATATCAGCACACGAGGATATA
GCAAAGAACCTAAGAAATTATCTTGGATAACTGCTAAAAGGTTTGGCATAACTCCGTCT
Found at i:83967 original size:31 final size:29
Alignment explanation
Indices: 83930--84091 Score: 95
Period size: 29 Copynumber: 5.5 Consensus size: 29
83920 TGCTTCGAGA
*
83930 AAAAATGGTAATTTTCGGAAGGTTCGGGGT
1 AAAAATGG-AATTTTCGGAAGGTTCGAGGT
** *
83960 GAAAAATGGAATTTTTAGACA--TCCGACGGT
1 -AAAAATGGAATTTTCGGA-AGGTTCGA-GGT
*
83990 -AAAATGGTAATTTTCGAAAGGTTCGAGGTT
1 AAAAATGG-AATTTTCGGAAGGTTCGAGG-T
**
84020 AAAAATGGAATTTTTAGACA--TTCGATGGT
1 AAAAATGGAATTTTCGGA-AGGTTCGA-GGT
* *
84049 -AAAATGGTAATTTTTGGAAGGTT-TAGGGT
1 AAAAATGG-AATTTTCGGAAGGTTCGA-GGT
*
84078 CAAAATGGAATTTT
1 AAAAATGGAATTTT
84092 TAGACATCTA
Statistics
Matches: 104, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
28 16 0.15
29 37 0.36
30 34 0.33
31 17 0.16
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTCGGAAGGTTCGAGGT
Found at i:84003 original size:28 final size:27
Alignment explanation
Indices: 83962--84112 Score: 101
Period size: 29 Copynumber: 5.2 Consensus size: 27
83952 TTCGGGGTGA
*
83962 AAAATGGAATTTTTAGACATCCGACGGT
1 AAAATGGAATTTTTAGACATTCGA-GGT
* *
83990 AAAATGGTAA-TTTTCGAAAGGTTCGAGGTT
1 AAAATGG-AATTTTTAGACA--TTCGAGG-T
84020 AAAAATGGAATTTTTAGACATTCGATGGT
1 -AAAATGGAATTTTTAGACATTCGA-GGT
* *
84049 AAAATGGTAATTTTTGGA-AGGTT-TAGGGT
1 AAAATGG-AATTTTTAGACA--TTCGA-GGT
* *
84078 CAAAATGGAATTTTTAGACATCTAGGGGT
1 -AAAATGGAATTTTTAGACAT-TCGAGGT
84107 AAAATG
1 AAAATG
84113 ATAATTTTAG
Statistics
Matches: 98, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
28 29 0.30
29 36 0.37
30 19 0.19
31 14 0.14
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (27 bp):
AAAATGGAATTTTTAGACATTCGAGGT
Found at i:84032 original size:30 final size:31
Alignment explanation
Indices: 83930--84033 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
83920 TGCTTCGAGA
* * *
83930 AAAAATGGTAATTTTCGGAAGGTTCGGGGTG
1 AAAAATGGTAATTTTCGAAAGGTTCGAGGTT
* * *
83961 AAAAATGG-AATTTTTAGACA--TCCGACGG-T
1 AAAAATGGTAA-TTTTCGAAAGGTTCGA-GGTT
83990 -AAAATGGTAATTTTCGAAAGGTTCGAGGTT
1 AAAAATGGTAATTTTCGAAAGGTTCGAGGTT
84020 AAAAATGG-AATTTT
1 AAAAATGGTAATTTT
84034 TAGACATTCG
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
28 14 0.25
29 7 0.12
30 15 0.26
31 21 0.37
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.31
Consensus pattern (31 bp):
AAAAATGGTAATTTTCGAAAGGTTCGAGGTT
Found at i:84108 original size:58 final size:59
Alignment explanation
Indices: 83931--84120 Score: 251
Period size: 59 Copynumber: 3.2 Consensus size: 59
83921 GCTTCGAGAA
*
83931 AAAATGGTAATTTTCGGAAGGTTCGGGGTGAAAAATGGAATTTTTAGACATC-CGACGGT
1 AAAATGGTAATTTTCGGAAGGTTCAGGGT-AAAAATGGAATTTTTAGACATCTCGACGGT
* * *
83990 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACAT-TCGATGGT
1 AAAATGGTAATTTTCGGAAGGTTC-AGGGTAAAAATGGAATTTTTAGACATCTCGACGGT
* * * * *
84049 AAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAATGGAATTTTTAGACATCTAG-GGGT
1 AAAATGGTAATTTTCGGAAGGTTCAGGGTAAAAATGGAATTTTTAGACATCTCGACGGT
*
84107 AAAATGATAATTTT
1 AAAATGGTAATTTT
84121 AGAAAGTTTG
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
58 40 0.34
59 73 0.63
60 3 0.03
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTCGGAAGGTTCAGGGTAAAAATGGAATTTTTAGACATCTCGACGGT
Found at i:84139 original size:29 final size:29
Alignment explanation
Indices: 83990--84636 Score: 244
Period size: 29 Copynumber: 22.4 Consensus size: 29
83980 ATCCGACGGT
* * * *
83990 AAAATGGTAATTTTCGAAAGGTTCGAGGTTA
1 AAAAT-GTAATTTTAGAAA-GTTTGAGGGTC
* * * *
84021 AAAATGGAATTTTTAGACA-TTCGATGGT-
1 AAAATGTAA-TTTTAGAAAGTTTGAGGGTC
* *
84049 AAAATGGTAATTTTTGGAAGGTTT-AGGGTC
1 AAAAT-GTAA-TTTTAGAAAGTTTGAGGGTC
* * *
84079 AAAATGGAATTTTTAGACA-TCT-AGGGGT-
1 AAAATGTAA-TTTTAGAAAGTTTGA-GGGTC
84107 AAAATGATAATTTTAGAAAGTTTGA-GGTC
1 AAAATG-TAATTTTAGAAAGTTTGAGGGTC
* * *
84136 AAAAAAAG-AATTTTGGAAAGTTT-AGGGGC
1 --AAAATGTAATTTTAGAAAGTTTGAGGGTC
* *
84165 AAAAATGTAATTTTCAAAAAGTTTG-GAGTC
1 -AAAATGTAATTTT-AGAAAGTTTGAGGGTC
* * * **
84195 AAAAATGGAAATTTGGAAAGTTT-AGGGGA
1 -AAAATGTAATTTTAGAAAGTTTGAGGGTC
*
84224 AAAATGT-ATTGTTAGAAAGTTT-AGGGTTA
1 AAAATGTAATT-TTAGAAAGTTTGAGGG-TC
* * *
84253 AAAATGGAATTTTGGAAAGTTTGGGGGT-
1 AAAATGTAATTTTAGAAAGTTTGAGGGTC
* * *
84281 AAAATTTAATTTTCAAAAAGTTT-AGGGTTA
1 AAAATGTAATTTT-AGAAAGTTTGAGGG-TC
* * *
84311 AAAATGGAATTTTAGAAAGTTCGAGGGTG
1 AAAATGTAATTTTAGAAAGTTTGAGGGTC
*
84340 AAAATATAATTTTTAGAAAGTTTGA-GGTC
1 AAAATGTAA-TTTTAGAAAGTTTGAGGGTC
* * *
84369 AAAAATGTAATTTTGGAAA-TTTTAGGGGTA
1 -AAAATGTAATTTTAGAAAGTTTGA-GGGTC
* * ** * *
84399 AAAATATAAATTTTGGATTG-TTCAAGGTC
1 AAAATGT-AATTTTAGAAAGTTTGAGGGTC
* *
84428 AAAAATGGAATTTT-G--AG--T----GTA
1 -AAAATGTAATTTTAGAAAGTTTGAGGGTC
* *
84449 AAAATGTTATTTTTAGAAAGTTT-AGGGTTA
1 AAAATG-TAATTTTAGAAAGTTTGAGGG-TC
* * * *
84479 AAAATGGAATTTTGGAAAG-TTAAGGG-A
1 AAAATGTAATTTTAGAAAGTTTGAGGGTC
84506 AGAAATGTAATTTTTAGAAAAGTTTG-GGGTC
1 A-AAATGTAA-TTTTAG-AAAGTTTGAGGGTC
* * * * *
84537 AAAAATGGAATTTTGGAAAGTTCGAGTGTA
1 -AAAATGTAATTTTAGAAAGTTTGAGGGTC
* *
84567 AAAATGGAATTTT-GAGAAGTTTGGGGGT-
1 AAAATGTAATTTTAGA-AAGTTTGAGGGTC
* * *
84595 AAAATGGAATTTTGGAAAGTTTGAGGGTA
1 AAAATGTAATTTTAGAAAGTTTGAGGGTC
*
84624 AAAATATAATTTT
1 AAAATGTAATTTT
84637 TGGAAAATTT
Statistics
Matches: 475, Mismatches: 89, Indels: 106
0.71 0.13 0.16
Matches are distributed among these distances:
20 6 0.01
21 7 0.01
22 1 0.00
24 2 0.00
25 1 0.00
26 2 0.00
27 4 0.01
28 106 0.22
29 200 0.42
30 119 0.25
31 26 0.05
32 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAGTTTGAGGGTC
Found at i:84147 original size:58 final size:59
Alignment explanation
Indices: 83931--84149 Score: 223
Period size: 59 Copynumber: 3.7 Consensus size: 59
83921 GCTTCGAGAA
* * * * *
83931 AAAATGGTAATTTTCGGAAGGTTCGGGGTGAAAAATGGAATTTTTAGACATC-CGACGGT
1 AAAATGGTAATTTT-AGAAAGTTTGAGGTCAAAAATGGAATTTTTAGACATCTCGACGGT
* * * *
83990 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACAT-TCGATGGT
1 AAAATGGTAATTTTAGAAA-GTTTGAGGTCAAAAATGGAATTTTTAGACATCTCGACGGT
* * * *
84049 AAAATGGTAATTTTTGGAAGGTTT-AGGGTC-AAAATGGAATTTTTAGACATCTAG-GGGT
1 AAAATGGTAA-TTTTAGAAAGTTTGA-GGTCAAAAATGGAATTTTTAGACATCTCGACGGT
* **
84107 AAAATGATAATTTTAGAAAGTTTGAGGTCAAAAAAAGAATTTT
1 AAAATGGTAATTTTAGAAAGTTTGAGGTCAAAAATGGAATTTT
84150 GGAAAGTTTA
Statistics
Matches: 137, Mismatches: 16, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
57 15 0.11
58 48 0.35
59 67 0.49
60 7 0.05
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTAGAAAGTTTGAGGTCAAAAATGGAATTTTTAGACATCTCGACGGT
Found at i:84197 original size:59 final size:57
Alignment explanation
Indices: 84049--84636 Score: 412
Period size: 59 Copynumber: 10.2 Consensus size: 57
84039 ATTCGATGGT
* * * * * *
84049 AAAATGGTAATTTTTGGAAGGTTTAGG-GTC-AAAATGGAATTTTTAGACA-TCTAGGGGT
1 AAAAT-GTAA-TTTTAGAAAGTTT-GGAGTCAAAAATGGAA-TTTTGGAAAGTTTAGGGGA
**
84107 AAAATGATAATTTTAGAAAGTTT-GAGGTCAAAAAAAGAATTTTGGAAAGTTTAGGGGCA
1 AAAATG-TAATTTTAGAAAGTTTGGA-GTCAAAAATGGAATTTTGGAAAGTTTAGGGG-A
* *
84166 AAAATGTAATTTTCAAAAAGTTTGGAGTCAAAAATGGAAATTTGGAAAGTTTAGGGGA
1 AAAATGTAATTTT-AGAAAGTTTGGAGTCAAAAATGGAATTTTGGAAAGTTTAGGGGA
* * *
84224 AAAATGT-ATTGTTAGAAAGTTTAGG-GTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGTAATT-TTAGAAAGTTT-GGAGTCAAAAATGGAATTTTGGAAAGTTTAGGGGA
* * * * *
84281 AAAATTTAATTTTCAAAAAGTTTAGG-GTTAAAAATGGAATTTTAGAAAGTTCGAGGGTG-
1 AAAATGTAATTTT-AGAAAGTTT-GGAGTCAAAAATGGAATTTTGGAAAGTT-TAGGG-GA
* * *
84340 AAAATATAATTTTTAGAAAGTTT-GAGGTCAAAAATGTAATTTTGGAAATTTTAGGGGTA
1 AAAATGTAA-TTTTAGAAAGTTTGGA-GTCAAAAATGGAATTTTGGAAAGTTTAGGGG-A
* * ** ** *
84399 AAAATATAAATTTTGGATTG-TTCAAGGTCAAAAATGGAATTTT-G--AG--T---GTA
1 AAAATGT-AATTTTAGAAAGTTTGGA-GTCAAAAATGGAATTTTGGAAAGTTTAGGGGA
* * *
84449 AAAATGTTATTTTTAGAAAGTTTAGG-GTTAAAAATGGAATTTTGGAAAG-TTAAGGGA
1 AAAATG-TAATTTTAGAAAGTTT-GGAGTCAAAAATGGAATTTTGGAAAGTTTAGGGGA
* * * *
84506 AGAAATGTAATTTTTAGAAAAGTTTGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGTGTA
1 A-AAATGTAA-TTTTAG-AAAGTTTGGAGTCAAAAATGGAATTTTGGAAAGTT-TAGGGGA
* * *
84567 AAAATGGAATTTT-GAGAAGTTTGGGGGT--AAAATGGAATTTTGGAAAGTTTGAGGGTA
1 AAAATGTAATTTTAGA-AAGTTT-GGAGTCAAAAATGGAATTTTGGAAAGTTT-AGGGGA
*
84624 AAAATATAATTTT
1 AAAATGTAATTTT
84637 TGGAAAATTT
Statistics
Matches: 434, Mismatches: 56, Indels: 81
0.76 0.10 0.14
Matches are distributed among these distances:
50 30 0.07
51 5 0.01
53 2 0.00
54 2 0.00
55 1 0.00
56 1 0.00
57 114 0.26
58 106 0.24
59 152 0.35
60 17 0.04
61 4 0.01
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTAGAAAGTTTGGAGTCAAAAATGGAATTTTGGAAAGTTTAGGGGA
Found at i:85586 original size:21 final size:23
Alignment explanation
Indices: 85545--85592 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
85535 TTTAGAAATC
85545 TAAAATAGGTGTTTCCAAAATTT
1 TAAAATAGGTGTTTCCAAAATTT
*
85568 TAAAAT-GG-GTTTCACAAATTTT
1 TAAAATAGGTGTTTC-CAAAATTT
85590 TAA
1 TAA
85593 CTTTTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 12 0.52
23 6 0.26
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (23 bp):
TAAAATAGGTGTTTCCAAAATTT
Found at i:91078 original size:31 final size:31
Alignment explanation
Indices: 91040--91105 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
91030 AAATTTTTTG
91040 ATACTTTATGAAAAGTATCGATACCAGATCA
1 ATACTTTATGAAAAGTATCGATACCAGATCA
* *
91071 ATACTTTATGAAAAGTATTGATACCAGATCG
1 ATACTTTATGAAAAGTATCGATACCAGATCA
91102 ATAC
1 ATAC
91106 CTAAATGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (31 bp):
ATACTTTATGAAAAGTATCGATACCAGATCA
Found at i:91753 original size:20 final size:19
Alignment explanation
Indices: 91718--91767 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
91708 ATTTTGAAAC
* *
91718 CAAATTAAAATGATTTCAA
1 CAAATCAAAATAATTTCAA
*
91737 CAAAGTCAAAATAATTTTAA
1 CAAA-TCAAAATAATTTCAA
*
91757 CACATCAAAAT
1 CAAATCAAAAT
91768 GACTTTCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.54, C:0.14, G:0.04, T:0.28
Consensus pattern (19 bp):
CAAATCAAAATAATTTCAA
Found at i:95478 original size:30 final size:30
Alignment explanation
Indices: 95425--95496 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
95415 AAATTTCAAG
* *
95425 TTAATCCCTAAATTCCTCAAAAATTC-TAAT
1 TTAATCCTTAAATTCCACAAAAA-TCATAAT
* *
95455 TTAATCCTTAAATTTCACTAAAATCATAAT
1 TTAATCCTTAAATTCCACAAAAATCATAAT
*
95485 TAAATCCTTAAA
1 TTAATCCTTAAA
95497 ATAAATTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (30 bp):
TTAATCCTTAAATTCCACAAAAATCATAAT
Found at i:97004 original size:24 final size:24
Alignment explanation
Indices: 96952--97005 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
96942 AAGTGTTGGA
* *
96952 CTCACAAGTTCGGGTTGAGTCGGG
1 CTCACAAGTTCAGGTTGAGTCAGG
* *
96976 CTCACGAGTTCAGGTTGAGTTAGG
1 CTCACAAGTTCAGGTTGAGTCAGG
*
97000 TTCACA
1 CTCACA
97006 GGCATGGGTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (24 bp):
CTCACAAGTTCAGGTTGAGTCAGG
Found at i:98992 original size:21 final size:21
Alignment explanation
Indices: 98968--99007 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
98958 ATACTTGGGA
98968 AAGTTCTACC-GATACAAGTGT
1 AAGTTCTACCAGA-ACAAGTGT
98989 AAGTTCTACCAGAACAAGT
1 AAGTTCTACCAGAACAAGT
99008 CATACTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (21 bp):
AAGTTCTACCAGAACAAGTGT
Found at i:100686 original size:20 final size:19
Alignment explanation
Indices: 100652--100693 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
100642 ACTTTCATGA
* *
100652 TTAACTTACTTAATCATCT
1 TTAACTTAATTAATCATAT
100671 TTAACTCTAATTAATCATAT
1 TTAACT-TAATTAATCATAT
100691 TTA
1 TTA
100694 TAAGTCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAACTTAATTAATCATAT
Found at i:105267 original size:29 final size:29
Alignment explanation
Indices: 105235--105302 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
105225 AATTAAAACT
* * *
105235 TAGTTTAGTCCCTAAGTTTAACAAATTTC
1 TAGTTTAGTCCCTAAATTCAACAAAATTC
* **
105264 TAG-TTAATCCCTAAATTCCTCAAAATTC
1 TAGTTTAGTCCCTAAATTCAACAAAATTC
105292 TAGTTTAGTCC
1 TAGTTTAGTCC
105303 TTTAATTTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (29 bp):
TAGTTTAGTCCCTAAATTCAACAAAATTC
Found at i:105699 original size:42 final size:42
Alignment explanation
Indices: 105639--105723 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
105629 CAAGCCACCG
* *
105639 TTGATATTATTTTGTGGACAAGCCACCACTGATGTGTAGATA
1 TTGATATAATTTTGTGGACAAGCCACCACTGATGTGCAGATA
* *
105681 TTGATATAATTTTTTGGACTAGCCACCACTGATGTGCAGATA
1 TTGATATAATTTTGTGGACAAGCCACCACTGATGTGCAGATA
105723 T
1 T
105724 ACTACCACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (42 bp):
TTGATATAATTTTGTGGACAAGCCACCACTGATGTGCAGATA
Found at i:120594 original size:32 final size:32
Alignment explanation
Indices: 120554--120634 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 32
120544 TGAAATTAGT
120554 TTGTTGGAT-TGTGAAATTATTATGTTTTAAAG-
1 TTGTTGGATAT-TGAAATTATTATGTTTT-AAGC
*
120586 TTGTTGGATATTGAATTTATTATGTTTTAAGC
1 TTGTTGGATATTGAAATTATTATGTTTTAAGC
120618 TTGTTGGATATTGAAAT
1 TTGTTGGATATTGAAAT
120635 GATTGACAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.07
32 41 0.91
33 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.51
Consensus pattern (32 bp):
TTGTTGGATATTGAAATTATTATGTTTTAAGC
Found at i:121175 original size:14 final size:14
Alignment explanation
Indices: 121158--121190 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
121148 AATAAAAATC
121158 CTAAAAGACTAAAA
1 CTAAAAGACTAAAA
*
121172 CTAAAAGTCTAAAA
1 CTAAAAGACTAAAA
121186 -TAAAA
1 CTAAAA
121191 CATCCCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (14 bp):
CTAAAAGACTAAAA
Found at i:121334 original size:23 final size:24
Alignment explanation
Indices: 121308--121353 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
121298 TTCATGAACC
*
121308 ATCTGACGT-CCACCAGTCACACT
1 ATCTGACGTCCCACCAATCACACT
*
121331 ATCTGGCGTCCCACCAATCACAC
1 ATCTGACGTCCCACCAATCACAC
121354 CGTCCGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
ATCTGACGTCCCACCAATCACACT
Found at i:127424 original size:17 final size:17
Alignment explanation
Indices: 127392--127425 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
127382 TGATTCAATA
*
127392 CTTTAATTCGATTAATT
1 CTTTAATTCGAGTAATT
*
127409 CTTTAATTCGGGTAATT
1 CTTTAATTCGAGTAATT
127426 TGAGTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (17 bp):
CTTTAATTCGAGTAATT
Found at i:128502 original size:21 final size:21
Alignment explanation
Indices: 128477--128519 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
128467 ATATTTTATA
* *
128477 TTTTTACCCCAAATCTTTTAC
1 TTTTTACCCAAAAACTTTTAC
*
128498 TTTTTTCCCAAAAACTTTTAC
1 TTTTTACCCAAAAACTTTTAC
128519 T
1 T
128520 CCTTCTCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTTACCCAAAAACTTTTAC
Found at i:128972 original size:27 final size:27
Alignment explanation
Indices: 128934--128995 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
128924 ATCTTCGGAT
128934 CTACGCCCCGAAACATTTCGTCGCTTA
1 CTACGCCCCGAAACATTTCGTCGCTTA
128961 CTACGCCCCGAAACATTTCGTCGCTTA
1 CTACGCCCCGAAACATTTCGTCGCTTA
128988 CTACGCCC
1 CTACGCCC
128996 TTCCTCATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.21, C:0.40, G:0.15, T:0.24
Consensus pattern (27 bp):
CTACGCCCCGAAACATTTCGTCGCTTA
Found at i:129217 original size:19 final size:19
Alignment explanation
Indices: 129193--129249 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
129183 CTATTTATAT
*
129193 TATTGAATTTTTTTAATAA
1 TATTGAATTTTTATAATAA
* *
129212 TATTGAATATTTATATTAA
1 TATTGAATTTTTATAATAA
* *
129231 AATTGAATTGTTAATAATA
1 TATTGAATT-TTTATAATA
129250 CCATAAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
TATTGAATTTTTATAATAA
Found at i:129846 original size:102 final size:102
Alignment explanation
Indices: 129719--130123 Score: 675
Period size: 102 Copynumber: 3.9 Consensus size: 102
129709 ACTTGGATAA
129719 TATTATTAATTTATAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTGGAC
1 TATTATTAATTTATAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTGGAC
129784 GATATTGTAGTTATCACGTGGTGTAATACTAGTTATG
66 GATATTGTAGTTATCACGTGGTGTAATACTAGTTATG
*
129821 TATTATTAATTTGTAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTGGAC
1 TATTATTAATTTATAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTGGAC
129886 GATATTGTAGTTATCACGTGGTGTAATACTAGTTATG
66 GATATTGTAGTTATCACGTGGTGTAATACTAGTTATG
129923 TATTATTAATTTATAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTGGAC
1 TATTATTAATTTATAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTGGAC
* * *
129988 GATATTGTAATTATCATGTGATGTAATACTAGTTATG
66 GATATTGTAGTTATCACGTGGTGTAATACTAGTTATG
** * *
130025 TACTTAGAAAATATTGTAGTTATCATGTGGTGTACTATTAATTTGTAATATTAGTTATGCACTTG
1 TA-TTA-TTAAT-TTATAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTG
* * * *
130090 GATGATATTGTAGTTATCATGTTGTGTACTACTA
63 GACGATATTGTAGTTATCACGTGGTGTAATACTA
130124 ATTTATAATA
Statistics
Matches: 286, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
102 201 0.70
103 3 0.01
104 3 0.01
105 79 0.28
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.44
Consensus pattern (102 bp):
TATTATTAATTTATAGTTATCATGTGGTGTACTACTAATTTGTAATATTAGTTATGCACTTGGAC
GATATTGTAGTTATCACGTGGTGTAATACTAGTTATG
Found at i:129848 original size:43 final size:42
Alignment explanation
Indices: 129788--129870 Score: 121
Period size: 43 Copynumber: 2.0 Consensus size: 42
129778 TTGGACGATA
* *
129788 TTGTAGTTATCACGTGGTGTAATACTAGTTATGTATTATTAAT
1 TTGTAGTTATCACGTGGTGTAATACTAATT-TGTAATATTAAT
* *
129831 TTGTAGTTATCATGTGGTGTACTACTAATTTGTAATATTA
1 TTGTAGTTATCACGTGGTGTAATACTAATTTGTAATATTA
129871 GTTATGCACT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 9 0.25
43 27 0.75
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (42 bp):
TTGTAGTTATCACGTGGTGTAATACTAATTTGTAATATTAAT
Found at i:130013 original size:46 final size:46
Alignment explanation
Indices: 129963--130064 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
129953 ACTACTAATT
* **
129963 TGTAATATTAGTTATGCACTTGGACGATATTGTAATTATCATGTGA
1 TGTAATATTAGTTATGCACTTAGAAAATATTGTAATTATCATGTGA
* * * *
130009 TGTAATACTAGTTATGTACTTAGAAAATATTGTAGTTATCATGTGG
1 TGTAATATTAGTTATGCACTTAGAAAATATTGTAATTATCATGTGA
*
130055 TGTACTATTA
1 TGTAATATTA
130065 ATTTGTAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (46 bp):
TGTAATATTAGTTATGCACTTAGAAAATATTGTAATTATCATGTGA
Found at i:130101 original size:59 final size:59
Alignment explanation
Indices: 130009--130136 Score: 184
Period size: 59 Copynumber: 2.2 Consensus size: 59
129999 TATCATGTGA
* * *
130009 TGTAATACTAGTTATGTACTTAGAAAATATTGTAGTTATCATGTGGTGTACTATTAATT
1 TGTAATATTAGTTATGCACTTAGAAAATATTGTAGTTATCATGTGGTGTACTACTAATT
* ** *
130068 TGTAATATTAGTTATGCACTTGGATGATATTGTAGTTATCATGTTGTGTACTACTAATT
1 TGTAATATTAGTTATGCACTTAGAAAATATTGTAGTTATCATGTGGTGTACTACTAATT
*
130127 TATAATATTA
1 TGTAATATTA
130137 ATTGTGGTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.45
Consensus pattern (59 bp):
TGTAATATTAGTTATGCACTTAGAAAATATTGTAGTTATCATGTGGTGTACTACTAATT
Found at i:130351 original size:21 final size:19
Alignment explanation
Indices: 130313--130357 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
130303 ATTTAAATAT
130313 AAAAAAATATTAACTTTTCC
1 AAAAAAATATTAACTTTT-C
* *
130333 AAAAAAATAATTTATTTTTC
1 AAAAAAAT-ATTAACTTTTC
130353 AAAAA
1 AAAAA
130358 TTATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAAATATTAACTTTTC
Found at i:131641 original size:15 final size:15
Alignment explanation
Indices: 131621--131650 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
131611 CACCGGAATT
131621 TTTAATTGAGTAACC
1 TTTAATTGAGTAACC
*
131636 TTTAATTTAGTAACC
1 TTTAATTGAGTAACC
131651 ATTTTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (15 bp):
TTTAATTGAGTAACC
Found at i:133083 original size:24 final size:24
Alignment explanation
Indices: 133046--133139 Score: 102
Period size: 24 Copynumber: 3.9 Consensus size: 24
133036 CTTCCAGAAT
* *
133046 TTAGCTCATACGAG-CCAGATAGAA
1 TTAGCTCTTACGAGACCAGATAG-G
*
133070 TTAACTCTTACGAGACCAGATAGG
1 TTAGCTCTTACGAGACCAGATAGG
* *
133094 TTAGCTCTTATGAG-CCTAAATAGG
1 TTAGCTCTTACGAGACC-AGATAGG
*
133118 TTAGCTCTTACGAGCCCAGATA
1 TTAGCTCTTACGAGACCAGATA
133140 AAGTTTAACT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
23 2 0.03
24 47 0.80
25 10 0.17
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (24 bp):
TTAGCTCTTACGAGACCAGATAGG
Found at i:133098 original size:48 final size:48
Alignment explanation
Indices: 133046--133139 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
133036 CTTCCAGAAT
*
133046 TTAGCTCATACGAGCC-AGATAGAATTAACTCTTACGAGACCAGATAGG
1 TTAGCTCATACGAGCCTAAATAG-ATTAACTCTTACGAGACCAGATAGG
* * * * *
133094 TTAGCTCTTATGAGCCTAAATAGGTTAGCTCTTACGAGCCCAGATA
1 TTAGCTCATACGAGCCTAAATAGATTAACTCTTACGAGACCAGATA
133140 AAGTTTAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 34 0.87
49 5 0.13
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (48 bp):
TTAGCTCATACGAGCCTAAATAGATTAACTCTTACGAGACCAGATAGG
Found at i:134028 original size:331 final size:332
Alignment explanation
Indices: 133426--134086 Score: 1085
Period size: 331 Copynumber: 2.0 Consensus size: 332
133416 GCTCCAAGCT
*
133426 TGACATCTTGTTTTTTCATTCGCTTCCCAATCTTCTCAAGCATTCAACCTTCTTTGAGTGGCTAC
1 TGACATCTTGTTTCTTCATTCGCTTCCCAATCTTCTCAAGCATTCAACCTTCTTTGAGTGGCTAC
* * *
133491 AACAATAATGAATACACAAAGGAATATTTCAATGAATATAAATTAACACTACGAACTTACCGGAT
66 AACAATAATGAATACACAAAGGAATATTTCAATGAATATAAACTAACACTACAAACTTACCGGAC
** * *
133556 GGAATTGTAATTTGAGTGGAACTCTAGGAACTATTCTGAAAATTTCCCTTTTCCACGATCAGTGG
131 AAAATTGTAATTTGAGTGGAACTCTAGGAACTATTATGAAAATTTCCCTTTTCCACGATCAGTGA
* *
133621 CTCTTTCTCGATCTAAATCAATAATTCAATCATTTCTCTCATTAAATCATGGAATTTGATCAATT
196 CTCTTTCTCGATCTAAATCAATAATTCAATAATTTCTCTCATTAAATCATGCAATTTGATCAATT
*
133686 TATACATATAAG-CCTTTTTTGGAAATTTACAAAATTACCCCTAACCTTTGCATTTTTATTCAAT
261 TATACATATAAGCCCTTTTTGGGAAATTTACAAAATTACCCCTAACCTTTGCATTTTTATTCAAT
133750 TTAGGCC
326 TTAGGCC
*
133757 TGACATCTTGTTTCTTCATTCGCTTCCCAATCTTCTCGAGCATTCAACCTTCTTTGAGTGGCTAC
1 TGACATCTTGTTTCTTCATTCGCTTCCCAATCTTCTCAAGCATTCAACCTTCTTTGAGTGGCTAC
* * **
133822 AACAATAATGAATACACAAAGGAATATTTCAATGAATATAAACTAACACTGCAAATTTATTGGAC
66 AACAATAATGAATACACAAAGGAATATTTCAATGAATATAAACTAACACTACAAACTTACCGGAC
* * *
133887 AAAATTGTAGTTTGAGTGGAACTCTAGTG-ATTATTAT-AAAATTTTCCCTTTTCCACGATCGGT
131 AAAATTGTAATTTGAGTGGAACTCTAG-GAACTATTATGAAAA-TTTCCCTTTTCCACGATCAGT
133950 GACTCTTTCTCGATCTAAATCAATAATTCAATAATTTCTCTCATTAAATCATGCAATTTGATCAA
194 GACTCTTTCTCGATCTAAATCAATAATTCAATAATTTCTCTCATTAAATCATGCAATTTGATCAA
* *
134015 TTTATACATATAAGCCCCTTTTTGGGAAATTTACAAAATTACCTCTAGCCTTTGCATTTTTATTC
259 TTTATACATATAAG-CCCTTTTTGGGAAATTTACAAAATTACCCCTAACCTTTGCATTTTTATTC
134080 AATTTAG
323 AATTTAG
134087 TCCTTAAGTA
Statistics
Matches: 305, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
330 4 0.01
331 247 0.81
332 1 0.00
333 53 0.17
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (332 bp):
TGACATCTTGTTTCTTCATTCGCTTCCCAATCTTCTCAAGCATTCAACCTTCTTTGAGTGGCTAC
AACAATAATGAATACACAAAGGAATATTTCAATGAATATAAACTAACACTACAAACTTACCGGAC
AAAATTGTAATTTGAGTGGAACTCTAGGAACTATTATGAAAATTTCCCTTTTCCACGATCAGTGA
CTCTTTCTCGATCTAAATCAATAATTCAATAATTTCTCTCATTAAATCATGCAATTTGATCAATT
TATACATATAAGCCCTTTTTGGGAAATTTACAAAATTACCCCTAACCTTTGCATTTTTATTCAAT
TTAGGCC
Found at i:150743 original size:23 final size:22
Alignment explanation
Indices: 150696--150750 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
150686 TAATAAATAC
* *
150696 AAATAACAT-ATTTAAAAACAT
1 AAATAACATAACTTAAAAACAA
*
150717 AAATAACATAACTTAAAAAGGAA
1 AAATAACATAACTTAAAAA-CAA
*
150740 AAATATCATAA
1 AAATAACATAA
150751 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 9 0.32
22 8 0.29
23 11 0.39
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.24
Consensus pattern (22 bp):
AAATAACATAACTTAAAAACAA
Found at i:151525 original size:18 final size:19
Alignment explanation
Indices: 151491--151527 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
151481 ATTCGAAACA
*
151491 AATTCAAGTTGACTCGATT
1 AATTCAAGTTAACTCGATT
151510 AATTCAA-TTAACTCGATT
1 AATTCAAGTTAACTCGATT
151528 CGAATAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
AATTCAAGTTAACTCGATT
Found at i:158304 original size:17 final size:17
Alignment explanation
Indices: 158273--158307 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
158263 CATTTTAATT
**
158273 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
158290 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
158307 T
1 T
158308 AAAAATACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:158821 original size:3 final size:3
Alignment explanation
Indices: 158815--158842 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
158805 TCAAATCTTC
158815 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
158843 TGGTATGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:159662 original size:15 final size:15
Alignment explanation
Indices: 159639--159668 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
159629 ATAAATTAAA
159639 TTATCTTTCATATCT
1 TTATCTTTCATATCT
*
159654 TTATTTTTCATATCT
1 TTATCTTTCATATCT
159669 CTTTTCCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATCTTTCATATCT
Found at i:163267 original size:11 final size:11
Alignment explanation
Indices: 163237--163277 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
163227 AAAAAATCTA
*
163237 AAATTATATA-
1 AAATTATAAAT
163247 AAATTA-AAAT
1 AAATTATAAAT
163257 AAATTATAAAT
1 AAATTATAAAT
*
163268 AAATAATAAA
1 AAATTATAAA
163278 AATATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 2 0.07
10 12 0.44
11 13 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTATAAAT
Found at i:165795 original size:69 final size:70
Alignment explanation
Indices: 165681--165811 Score: 156
Period size: 69 Copynumber: 1.9 Consensus size: 70
165671 TAGCTCCCCT
* * *
165681 TGTGTCGCGACAAACCTGTAAGTCTTGATATTCCAGTAATCTGA-CCCTTTGTCATAACATAGCG
1 TGTGTCGCGACAAACCTATAAGTCTTGAAATTCCAGCAATCTGACCCCTTTGTCATAACATAGCG
165745 TCTTC
66 TCTTC
* * ** * * * *
165750 TGTGTCGCGACAAACCTATCAGTTTTGAAATTTTAGCAGTTTGACCCCTTTTTCGTAACATA
1 TGTGTCGCGACAAACCTATAAGTCTTGAAATTCCAGCAATCTGACCCCTTTGTCATAACATA
165812 AAAAGGGGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
69 35 0.70
70 15 0.30
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (70 bp):
TGTGTCGCGACAAACCTATAAGTCTTGAAATTCCAGCAATCTGACCCCTTTGTCATAACATAGCG
TCTTC
Found at i:167029 original size:15 final size:16
Alignment explanation
Indices: 167009--167038 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
166999 AGATTCCCAA
167009 ATCTTCAT-AATATCC
1 ATCTTCATAAATATCC
167024 ATCTTCATAAATATC
1 ATCTTCATAAATATC
167039 ATCATCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (16 bp):
ATCTTCATAAATATCC
Found at i:186799 original size:17 final size:17
Alignment explanation
Indices: 186774--186827 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
186764 TATAATAACA
*
186774 AATGAAAATGCAATGAC
1 AATGAAAATGTAATGAC
* *
186791 AATGCAAATGTAGTGAC
1 AATGAAAATGTAATGAC
*
186808 AATTAAAATGTAATGAC
1 AATGAAAATGTAATGAC
186825 AAT
1 AAT
186828 AGGAATGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (17 bp):
AATGAAAATGTAATGAC
Found at i:209541 original size:12 final size:12
Alignment explanation
Indices: 209524--209557 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
209514 GATGAAGAAC
209524 AAAAGGATGAAG
1 AAAAGGATGAAG
209536 AAAAGGATGAAG
1 AAAAGGATGAAG
**
209548 TGAAGGATGA
1 AAAAGGATGA
209558 CAAACACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.12
Consensus pattern (12 bp):
AAAAGGATGAAG
Found at i:215515 original size:142 final size:142
Alignment explanation
Indices: 215298--215563 Score: 380
Period size: 142 Copynumber: 1.9 Consensus size: 142
215288 TATCTATTTT
* * *
215298 ATTTACTTTTTCAAAATTTTGATAATTCTTAATATTAAATTATAAATTAAATTTTATAATTTATA
1 ATTTAATTTTTCAAAATTTTGATAATCCTTAATATTAAATTATAAATTAAATTTCATAATTTATA
* * *
215363 TTAGTTATTAT-AAGAA-TTTGAATCAAAACTTGTTTTCTTTAAA-ATTTTGAATTTAAATAAAG
66 TTAATCATTATCAA-AAGTTTGAATCAAAA--T-TTGT-TTTAAATATTTTGAATTTAAATAAAG
215425 TTTTTCATTTAAACTTA
126 TTTTTCATTTAAACTTA
215442 ATTTAATTTTTC-AAATTTTGATAATCCTTAATATT-AATTATAAATTAAATTTCATAATTTATA
1 ATTTAATTTTTCAAAATTTTGATAATCCTTAATATTAAATTATAAATTAAATTTCATAATTTATA
* *
215505 TTAATCATTATCAAAAGTTTGAATTAGAATTTGTTTTAAATATTTTGAATTTAAATAAA
66 TTAATCATTATCAAAAGTTTGAATCAAAATTTGTTTTAAATATTTTGAATTTAAATAAA
215564 AAATGAGTTT
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
139 6 0.05
140 21 0.19
141 1 0.01
142 38 0.34
143 34 0.31
144 11 0.10
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (142 bp):
ATTTAATTTTTCAAAATTTTGATAATCCTTAATATTAAATTATAAATTAAATTTCATAATTTATA
TTAATCATTATCAAAAGTTTGAATCAAAATTTGTTTTAAATATTTTGAATTTAAATAAAGTTTTT
CATTTAAACTTA
Found at i:217008 original size:18 final size:18
Alignment explanation
Indices: 216966--217009 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
216956 TTTTGTTAAA
*
216966 GAAGAAAAAGAAGACTCT
1 GAAGAAGAAGAAGACTCT
*
216984 GAAGAAGAAGAGGACTCT
1 GAAGAAGAAGAAGACTCT
*
217002 GAGGAAGA
1 GAAGAAGA
217010 CCCTAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.50, C:0.09, G:0.32, T:0.09
Consensus pattern (18 bp):
GAAGAAGAAGAAGACTCT
Found at i:226752 original size:20 final size:18
Alignment explanation
Indices: 226716--226759 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
226706 TAAGAAGTGG
226716 AAGAAGAAGAAGAAGGAA
1 AAGAAGAAGAAGAAGGAA
226734 AAGAAGAAGAGAGGAAGGAA
1 AAGAAGAAGA-A-GAAGGAA
*
226754 AGGAAG
1 AAGAAG
226760 TCGAGGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (18 bp):
AAGAAGAAGAAGAAGGAA
Found at i:227235 original size:17 final size:17
Alignment explanation
Indices: 227205--227249 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
227195 ATTGCTTTTA
* * *
227205 ATTGTCACTACATTTGC
1 ATTGTCATTGCATTTCC
227222 ATTGTCATTGCATTTCC
1 ATTGTCATTGCATTTCC
227239 ATTTGTCATTG
1 A-TTGTCATTG
227250 TAAATTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (17 bp):
ATTGTCATTGCATTTCC
Found at i:227835 original size:23 final size:22
Alignment explanation
Indices: 227803--227845 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
227793 TCACATATAA
227803 AAAAAAAAGAAAAGAGAAAAAGG
1 AAAAAAAAGAAAAGA-AAAAAGG
*
227826 AAAAAGAAGAAAAGAAAAAA
1 AAAAAAAAGAAAAGAAAAAA
227846 TATATATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAAAAGAAAAAAGG
Found at i:227845 original size:15 final size:13
Alignment explanation
Indices: 227801--227844 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
227791 GGTCACATAT
227801 AAAA-AAAAAAGA
1 AAAAGAAAAAAGA
*
227813 AAAGAGAAAAAGGA
1 AAA-AGAAAAAAGA
227827 AAAAGAAGAAAAGA
1 AAAAGAA-AAAAGA
227841 AAAA
1 AAAA
227845 ATATATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 5 0.19
14 19 0.70
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:229561 original size:29 final size:29
Alignment explanation
Indices: 229519--229587 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
229509 ATGTGAGCCT
229519 TTGAAGCCAACCCTAATAAATGATATTCC
1 TTGAAGCCAACCCTAATAAATGATATTCC
229548 TTGAAGCCAACCCTAATAAATGATATTCC
1 TTGAAGCCAACCCTAATAAATGATATTCC
229577 TTGAAGCCAAC
1 TTGAAGCCAAC
229588 TTTGAGACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.26
Consensus pattern (29 bp):
TTGAAGCCAACCCTAATAAATGATATTCC
Found at i:230553 original size:40 final size:40
Alignment explanation
Indices: 230498--230578 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
230488 GAAGAAAAGG
*
230498 TATTTCTAAACTTTTATTATTACATTGATTATTACTTATC
1 TATTTCTAAACTTTTATTATTACATTGATTATTACTCATC
230538 TATTTCTAAACTTTTATTATTACATTGATTATTACTCATC
1 TATTTCTAAACTTTTATTATTACATTGATTATTACTCATC
230578 T
1 T
230579 TCTACTCGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.54
Consensus pattern (40 bp):
TATTTCTAAACTTTTATTATTACATTGATTATTACTCATC
Found at i:233764 original size:21 final size:22
Alignment explanation
Indices: 233728--233786 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
233718 TCTTTATTTA
*
233728 TTAGTATTTTTATTGTTTAGTT
1 TTAGTATTTTTGTTGTTTAGTT
*
233750 TTAGTA-TTTTGTTGTTTATTT
1 TTAGTATTTTTGTTGTTTAGTT
*
233771 TTCAATATTTTTGTTG
1 TT-AGTATTTTTGTTG
233787 CTTTTGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.47
22 9 0.28
23 8 0.25
ACGTcount: A:0.17, C:0.02, G:0.14, T:0.68
Consensus pattern (22 bp):
TTAGTATTTTTGTTGTTTAGTT
Found at i:235482 original size:21 final size:22
Alignment explanation
Indices: 235458--235498 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
235448 CTAACCTCTT
*
235458 TGTCGTGACA-CGACTCCTATG
1 TGTCATGACATCGACTCCTATG
235479 TGTCATGACATCGACTCCTA
1 TGTCATGACATCGACTCCTA
235499 GACACGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (22 bp):
TGTCATGACATCGACTCCTATG
Found at i:240540 original size:22 final size:22
Alignment explanation
Indices: 240512--240555 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
240502 CCAAGCTCAC
240512 AAGGTCCGTGCTCGCATTATTA
1 AAGGTCCGTGCTCGCATTATTA
240534 AAGGTCCGTGCTCGCATTATTA
1 AAGGTCCGTGCTCGCATTATTA
240556 GTGTTAGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (22 bp):
AAGGTCCGTGCTCGCATTATTA
Found at i:270484 original size:23 final size:22
Alignment explanation
Indices: 270454--270497 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
270444 AAAGAAATAA
270454 AATTAACCCAAATTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
270476 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
270498 GAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:271500 original size:21 final size:21
Alignment explanation
Indices: 271476--271515 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
271466 TTCCGAGTAA
271476 TATTTTTTTTCTT-CTTTTTGG
1 TATTTTTTTT-TTACTTTTTGG
271497 TATTTTTTTTTTACTTTTT
1 TATTTTTTTTTTACTTTTT
271516 AACTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.80
Consensus pattern (21 bp):
TATTTTTTTTTTACTTTTTGG
Found at i:280360 original size:16 final size:15
Alignment explanation
Indices: 280315--280348 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
280305 AAAAAGATGA
280315 AAAATA-AACAAAAAT
1 AAAATATAA-AAAAAT
280330 AAAATATAAAAAAAT
1 AAAATATAAAAAAAT
280345 AAAA
1 AAAA
280349 ACTAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATATAAAAAAAT
Found at i:286518 original size:173 final size:166
Alignment explanation
Indices: 286220--286558 Score: 518
Period size: 173 Copynumber: 2.0 Consensus size: 166
286210 AGTGAAATAG
* * *
286220 GAAAATTAATATGGTATACGAACTTTAGTATAGCTAGAAAGAGAAAAACAATAAAAATCAAAAAG
1 GAAAATTAATAAGGAATACGAACTTTAGTATAGCTAGAAAGAGAAAAACAATAAAAATAAAAAAG
**
286285 AAAATAAAATTTGAGTAGAAACAAGAGAAAAAAATACATGAGTGAGAAAACATGTGAAAAGTGAC
66 AAAATAAAAAATGAGTAGAAACAAGAGAAAAAAATACATGAGTGAGAAAACATGTGAAAAGTGAC
286350 AAAGTCACAAAAATACCAAAAAGAAGAAAAATCTTA
131 AAAGTCACAAAAATACCAAAAAGAAGAAAAATCTTA
* **
286386 GAAAATTAATAAGGAATATGAACTTTAGTATAGCTAGAAAGAGAAAAGTAATAAACAAATAAAAA
1 GAAAATTAATAAGGAATACGAACTTTAGTATAGCTAGAAAGAGAAAAACAAT-AA-AAAT-AAAA
286451 AAGAAAATAAAAAAAAAT-AGTAGAAACAAAAGAGAAAAAAATACATGAGTGAGAAAACATGTGA
63 AAGAAAAT---AAAAAATGAGTAGAAAC--AAGAGAAAAAAATACATGAGTGAGAAAACATGTGA
*
286515 AAAGTGACAAAGTCACAAAAATACCAAAAGGAAGAAAAATCTTA
123 AAAGTGACAAAGTCACAAAAATACCAAAAAGAAGAAAAATCTTA
286559 CTCAAGAAAT
Statistics
Matches: 156, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
166 47 0.30
167 2 0.01
168 4 0.03
169 11 0.07
171 9 0.06
172 5 0.03
173 78 0.50
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.17
Consensus pattern (166 bp):
GAAAATTAATAAGGAATACGAACTTTAGTATAGCTAGAAAGAGAAAAACAATAAAAATAAAAAAG
AAAATAAAAAATGAGTAGAAACAAGAGAAAAAAATACATGAGTGAGAAAACATGTGAAAAGTGAC
AAAGTCACAAAAATACCAAAAAGAAGAAAAATCTTA
Found at i:286653 original size:21 final size:21
Alignment explanation
Indices: 286628--286667 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
286618 CCTAAGTGGA
*
286628 GAGAAA-AGGAAGGTAGAGAAG
1 GAGAAATAAGAAGGT-GAGAAG
286649 GAGAAATAAGAAGGTGAGA
1 GAGAAATAAGAAGGTGAGA
286668 TGGAATGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.40, T:0.07
Consensus pattern (21 bp):
GAGAAATAAGAAGGTGAGAAG
Done.