Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 135 of 193
Found at i:42588546 original size:15 final size:17
Alignment explanation
Indices: 42588527--42588567 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
42588517 TAATCATTTA
42588527 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
42588543 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
42588559 AAAATTATA
1 AAAATTATA
42588568 TATTACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:42588560 original size:24 final size:24
Alignment explanation
Indices: 42588527--42588581 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
42588517 TAATCATTTA
* *
42588527 AAAATTATAAAAATATAAATTATT
1 AAAATAATAAAAATATAAATTACT
* *
42588551 AAAATAATAAAATTATATATTACT
1 AAAATAATAAAAATATAAATTACT
42588575 AAAATAA
1 AAAATAA
42588582 AAATATACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAATAAAAATATAAATTACT
Found at i:42589997 original size:22 final size:22
Alignment explanation
Indices: 42589972--42590032 Score: 52
Period size: 26 Copynumber: 2.6 Consensus size: 22
42589962 TTAATCTAAA
*
42589972 TAATAAATATTATTAATTATTT
1 TAATAAATATTATTAATTATCT
*
42589994 TAATCAAAATAATAACTTAATTATCT
1 TAAT--AAAT-ATTA-TTAATTATCT
*
42590020 TAA-AAACATTATT
1 TAATAAATATTATT
42590033 CCAATAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
21 2 0.06
22 7 0.23
23 3 0.10
24 4 0.13
25 3 0.10
26 12 0.39
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAAATATTATTAATTATCT
Found at i:42590832 original size:6 final size:6
Alignment explanation
Indices: 42590821--42590848 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42590811 AACCAGATAA
42590821 AGAGGG AGAGGG AGAGGG AGAGGG AGAG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAG
42590849 AAGGGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:42594767 original size:13 final size:13
Alignment explanation
Indices: 42594749--42594773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42594739 ATTCAATAAA
42594749 ATTTTTTTTTCTG
1 ATTTTTTTTTCTG
42594762 ATTTTTTTTTCT
1 ATTTTTTTTTCT
42594774 TTTTCCAGCT
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:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTTCTG
Found at i:42595800 original size:24 final size:24
Alignment explanation
Indices: 42595773--42595819 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42595763 TGAACTGACC
42595773 TATT-TTTAAGTTTATAATATTTTA
1 TATTATTTAAGTTTAT-ATATTTTA
**
42595797 TATTATTTATTTTTATATATTTT
1 TATTATTTAAGTTTATATATTTT
42595820 GTAGTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TATTATTTAAGTTTATATATTTTA
Found at i:42595978 original size:31 final size:30
Alignment explanation
Indices: 42595930--42595997 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
42595920 AATAAATACA
42595930 AAAAT-ATATACAAA-TTTTAAAATTAAAATT
1 AAAATAATATACAAATTTTTAAAA--AAAATT
42595960 AAAATAATATA-AATATTTTTAAAAAAAATT
1 AAAATAATATACAA-ATTTTTAAAAAAAATT
42595990 AAAA-AATA
1 AAAATAATA
42595998 ATATGAACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
29 4 0.11
30 17 0.49
31 6 0.17
32 8 0.23
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (30 bp):
AAAATAATATACAAATTTTTAAAAAAAATT
Found at i:42595996 original size:32 final size:31
Alignment explanation
Indices: 42595929--42596001 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
42595919 TAATAAATAC
42595929 AAAAAT-ATATACAAATTTTAAAATTAAAATT
1 AAAAATAATATACAAATTTTAAAA-TAAAATT
42595960 -AAAATAATATA-AATATTTTTAAAA-AAAATT
1 AAAAATAATATACAA-A-TTTTAAAATAAAATT
42595990 AAAAAATAATAT
1 -AAAAATAATAT
42596002 GAACGAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
30 13 0.35
31 6 0.16
32 18 0.49
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAAATAATATACAAATTTTAAAATAAAATT
Found at i:42597716 original size:22 final size:22
Alignment explanation
Indices: 42597688--42597732 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
42597678 CCTATTATTG
42597688 TAATTTACCAAAAAAATA-AATT
1 TAATTTA-CAAAAAAATATAATT
*
42597710 TAATTTATAAAAAAATATAATT
1 TAATTTACAAAAAAATATAATT
42597732 T
1 T
42597733 GTGTTTCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATTTACAAAAAAATATAATT
Found at i:42602640 original size:29 final size:29
Alignment explanation
Indices: 42602598--42602854 Score: 103
Period size: 29 Copynumber: 8.8 Consensus size: 29
42602588 ATTTTTGACT
* * *
42602598 TTCGGGGGCAAAAATGTAATTTTGGGAAAA
1 TTCGAGGGTAAAAATGGAATTTT-GGAAAA
* * *
42602628 TTCGTGGTTAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAAATGGAATTTTGGAAAA
* *
42602657 TTCGAGGGT-AAAATGGTAGTTTTTGGTGAAA
1 TTCGAGGGTAAAAATGG-A-ATTTTGG-AAAA
*
42602688 -TCTG-GGTTAAAAATGGAATTTT-GAAAA
1 TTC-GAGGGTAAAAATGGAATTTTGGAAAA
* **
42602715 GTT-TAGGGGT-AAAATGGTAATTTTTTTATGAAA
1 -TTCGA-GGGTAAAAATGG-AA-TTTTGGA--AAA
42602748 TT-G-GGGTTAAAAATGGAATTTT-GAAAA
1 TTCGAGGG-TAAAAATGGAATTTTGGAAAA
* * *
42602775 GTTTGGGGGT---AA-GGTAATTTTTGGCGAAA
1 -TTCGAGGGTAAAAATGG-AA-TTTTGG-AAAA
* *
42602804 -TCGAGGGTAAAAATAGAATTTTGGAAAG
1 TTCGAGGGTAAAAATGGAATTTTGGAAAA
42602832 TTCGAGGGT-AAAATGGTAATTTT
1 TTCGAGGGTAAAAATGG-AATTTT
42602855 TAGGAAGTTT
Statistics
Matches: 173, Mismatches: 25, Indels: 59
0.67 0.10 0.23
Matches are distributed among these distances:
25 2 0.01
26 4 0.02
27 16 0.09
28 26 0.15
29 49 0.28
30 49 0.28
31 15 0.09
32 9 0.05
33 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
TTCGAGGGTAAAAATGGAATTTTGGAAAA
Found at i:42602643 original size:30 final size:30
Alignment explanation
Indices: 42602607--42602710 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 30
42602597 TTTCGGGGGC
*
42602607 AAAAATGTAATTTTGGGAAAATTCGTGGTT
1 AAAAATGGAATTTTGGGAAAATTCGTGGTT
* * *
42602637 AAAAATGGAATTTT-GGAAAGTTCGAGGGT
1 AAAAATGGAATTTTGGGAAAATTCGTGGTT
*
42602666 -AAAATGGTAGTTTTTGGTG-AAA-TC-TGGGTT
1 AAAAATGG-A-ATTTTGG-GAAAATTCGT-GGTT
42602696 AAAAATGGAATTTTG
1 AAAAATGGAATTTTG
42602711 AAAAGTTTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
28 7 0.12
29 18 0.31
30 23 0.39
31 10 0.17
32 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTGGGAAAATTCGTGGTT
Found at i:42602697 original size:59 final size:59
Alignment explanation
Indices: 42602633--42602855 Score: 269
Period size: 59 Copynumber: 3.8 Consensus size: 59
42602623 GAAAATTCGT
* *
42602633 GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAGTTTTTGGTGAAATCTG
1 GGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCTG
* **
42602692 GGTTAAAAATGGAATTTTGAAAAGTT-TAGGGGTAAAATGGTAATTTTTTTATGAAAT-TGG
1 GGTTAAAAATGGAATTTTGAAAAGTTCGA-GGGTAAAATGGTAA-TTTTTGGTGAAATCT-G
* * *
42602752 GGTTAAAAATGGAATTTTGAAAAGTTTGGGGGT--AA-GGTAATTTTTGGCGAAATC-G
1 GGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCTG
* * *
42602807 AGGGTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT
1 -GGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAAAATGGTAATTTTT
42602856 AGGAAGTTTA
Statistics
Matches: 140, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
55 1 0.01
56 38 0.27
57 5 0.04
58 5 0.04
59 49 0.35
60 42 0.30
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (59 bp):
GGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCTG
Found at i:42602823 original size:116 final size:118
Alignment explanation
Indices: 42602633--42602855 Score: 310
Period size: 116 Copynumber: 1.9 Consensus size: 118
42602623 GAAAATTCGT
* * * *
42602633 GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAGTTTTTGGTGAAATCTGGGTTAA
1 GGTTAAAAATGGAATTTTGAAAAGTTCGAGGGT-AAATGGTAATTTTTGGCGAAATCTGGGGTAA
*
42602698 AAATGGAATTTTGAAAAGTTTAG-GGGTAAAATGGTAATTTTTTTATGAAATTGG
65 AAATAGAATTTTGAAAAG-TTAGAGGGTAAAATGGTAATTTTTTTATGAAATTGG
* *
42602752 GGTTAAAAATGGAATTTTGAAAAGTTTGGGGGT-AA-GGTAATTTTTGGCGAAATC-GAGGGTAA
1 GGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAAATGGTAATTTTTGGCGAAATCTG-GGGTAA
* *
42602814 AAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT
65 AAATAGAATTTTGAAAAGTTAGAGGGTAAAATGGTAATTTTT
42602856 AGGAAGTTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
115 4 0.04
116 57 0.61
117 2 0.02
119 30 0.32
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (118 bp):
GGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAAATGGTAATTTTTGGCGAAATCTGGGGTAAA
AATAGAATTTTGAAAAGTTAGAGGGTAAAATGGTAATTTTTTTATGAAATTGG
Found at i:42602863 original size:30 final size:29
Alignment explanation
Indices: 42602787--42602884 Score: 71
Period size: 30 Copynumber: 3.3 Consensus size: 29
42602777 TTGGGGGTAA
*
42602787 GGTAATTTTTGGCGAA-ATCGAGGGTAAAAAT
1 GGTAATTTTT-G-GAAGTTCGAGGGT-AAAAT
*
42602818 AG-AA-TTTTGGAAAGTTCGAGGGTAAAAT
1 GGTAATTTTTGG-AAGTTCGAGGGTAAAAT
*
42602846 GGTAATTTTTAGGAAGTT-TAGGGGTTAAAAT
1 GGTAATTTTT-GGAAGTTCGA-GGG-TAAAAT
42602877 -GTAATTTT
1 GGTAATTTT
42602885 CAAAAATGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
27 1 0.02
28 9 0.16
29 15 0.27
30 22 0.39
31 9 0.16
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
GGTAATTTTTGGAAGTTCGAGGGTAAAAT
Found at i:42602870 original size:116 final size:117
Alignment explanation
Indices: 42602633--42602899 Score: 303
Period size: 116 Copynumber: 2.3 Consensus size: 117
42602623 GAAAATTCGT
* * * * * *
42602633 GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAGTTTTTGGTGAAATCTGGGTTAA
1 GGTTAAAAATGGAATTTTGAAAAGTTTGGGGGT-AAATGGTAATTTTTGGCGAAATCTGGGGTAA
* * *
42602698 AAATGGAATTTTGAAAAGTTTAGGGGTAAAATGGTAATTTTTTTATGAAATTGG
65 AAATAGAATTTTGAAAAGTTGAGGGGTAAAATGGTAA-TTTTTTAGGAAATTGG
42602752 GGTTAAAAATGGAATTTTGAAAAGTTTGGGGGT-AA-GGTAATTTTTGGCGAAATC-GAGGGTAA
1 GGTTAAAAATGGAATTTTGAAAAGTTTGGGGGTAAATGGTAATTTTTGGCGAAATCTG-GGGTAA
* *
42602814 AAATAGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAA-TTTTTAGGAAGTTTAGG
65 AAATAGAATTTTGAAAAGTT-GAGGGGTAAAATGGTAATTTTTTAGGAA-ATT-GG
* *
42602868 GGTT-AAAATGTAATTTTCAAAAATGTTTGGGG
1 GGTTAAAAATGGAATTTT-GAAAA-GTTTGGGG
42602900 TCAAAACATA
Statistics
Matches: 129, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
114 9 0.07
115 15 0.12
116 64 0.50
117 11 0.09
119 30 0.23
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (117 bp):
GGTTAAAAATGGAATTTTGAAAAGTTTGGGGGTAAATGGTAATTTTTGGCGAAATCTGGGGTAAA
AATAGAATTTTGAAAAGTTGAGGGGTAAAATGGTAATTTTTTAGGAAATTGG
Found at i:42603392 original size:17 final size:18
Alignment explanation
Indices: 42603370--42603408 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
42603360 TATATATGGC
42603370 TTCTTTTT-ACTTT-TTTT
1 TTCTTTTTCA-TTTCTTTT
42603387 TTCTTTTTCATTTCTTTT
1 TTCTTTTTCATTTCTTTT
42603405 TTCT
1 TTCT
42603409 CAGAAACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCATTTCTTTT
Found at i:42604540 original size:6 final size:6
Alignment explanation
Indices: 42604523--42604581 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
42604513 TTTGGACATT
* * * * *
42604523 AATTTA ATTTTA AATTTA AATTT- TATGTA AATTTA AATTCA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
42604569 AATTT- AATTTA AA
1 AATTTA AATTTA AA
42604582 AATAAATTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
5 11 0.28
6 29 0.73
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:42604570 original size:17 final size:17
Alignment explanation
Indices: 42604550--42604590 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
42604540 AAATTTTATG
*
42604550 TAAATTTAAATTCAAAA
1 TAAATTTAAATTAAAAA
*
42604567 TAAATTTAATTTAAAAA
1 TAAATTTAAATTAAAAA
42604584 TAAATTT
1 TAAATTT
42604591 TTATCCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTAAAAA
Found at i:42608895 original size:19 final size:18
Alignment explanation
Indices: 42608873--42608912 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42608863 CCGAGAAACG
42608873 GTCTCGGGGCAGCAGAGGA
1 GTCTC-GGGCAGCAGAGGA
* *
42608892 GTCTCGGGTAGTAGAGGA
1 GTCTCGGGCAGCAGAGGA
42608910 GTC
1 GTC
42608913 AACGGTCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.20, C:0.17, G:0.45, T:0.17
Consensus pattern (18 bp):
GTCTCGGGCAGCAGAGGA
Found at i:42608972 original size:16 final size:16
Alignment explanation
Indices: 42608951--42608992 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
42608941 CTGACGTGAC
42608951 GCTGATGTGGACACAT
1 GCTGATGTGGACACAT
*
42608967 GCTGATGTGGACATAT
1 GCTGATGTGGACACAT
*
42608983 GATGATGTGG
1 GCTGATGTGG
42608993 CAGCTGACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.29
Consensus pattern (16 bp):
GCTGATGTGGACACAT
Found at i:42608999 original size:28 final size:28
Alignment explanation
Indices: 42608967--42609031 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
42608957 GTGGACACAT
* *
42608967 GCTGATGTGGACATATGATGATGTGGCA
1 GCTGACGTGGACATATGATAATGTGGCA
*
42608995 GCTGACGTGGACATGTGATAATGTGGCA
1 GCTGACGTGGACATATGATAATGTGGCA
42609023 GCTGACGTG
1 GCTGACGTG
42609032 ACGACGGCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.14, G:0.37, T:0.26
Consensus pattern (28 bp):
GCTGACGTGGACATATGATAATGTGGCA
Found at i:42609702 original size:98 final size:98
Alignment explanation
Indices: 42609556--42609922 Score: 398
Period size: 98 Copynumber: 3.8 Consensus size: 98
42609546 TTTGAGATTT
* * * * * * * * ** *
42609556 GCCATTATGGCTTCAATCTTTCCTTTTATGTCTTCGTGGTACTAGATTCATCGTTGTGGCTTGAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
* *
42609621 TATTTCCCTTCGTGCTTTTGAGGTATAAGGTTC
66 TCTTTCCCTTCATGCTTTTGAGGTATAAGGTTC
* *** * * * **
42609654 GCCGTTACGGCTTAAACCTTTCCCTTAACATCTTTGGGGTACTGGATTCGCTGTTGTAACTTAAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
*
42609719 TCTTACCCTTCAT--TTTTGAGGTACT-AGGTTC
66 TCTTTCCCTTCATGCTTTTGAGGTA-TAAGGTTC
* * * *
42609750 GCCATTATGGCTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTGGCCGTTGCGGCTTAAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
* *
42609815 TCTTTCCCTTTATGCCTTTGAGGTATAAGGTTC
66 TCTTTCCCTTCATGCTTTTGAGGTATAAGGTTC
* * * * *
42609848 GTCATTGCGACTTAAACTTTTCCCTTTGTATCTTCGCGGTTCTGGATTCGCCGTTGTGGCTTAAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
42609913 TCTTTCCCTT
66 TCTTTCCCTT
42609923 AATTATTCGT
Statistics
Matches: 221, Mismatches: 44, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
96 80 0.36
97 2 0.01
98 139 0.63
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (98 bp):
GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
TCTTTCCCTTCATGCTTTTGAGGTATAAGGTTC
Found at i:42609704 original size:49 final size:49
Alignment explanation
Indices: 42609564--42610068 Score: 296
Period size: 49 Copynumber: 10.4 Consensus size: 49
42609554 TTGCCATTAT
* * * * * ** *
42609564 GGCTTCAATCTTTCCTTTTATGTCTTCGTGGTACTAGATTCATCGTTGT
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACTGGATTCGCCGTTGC
* * ** * * *
42609613 GGCTTGAATATTTCCCTTCGT-GCTTTTGAGGTA-TAAGG-TTCGCCGTTAC
1 GGCTTAAATCTTTCCCTTTATATC-TTCGAGGTACT--GGATTCGCCGTTGC
* * * * * * *
42609662 GGCTTAAACCTTTCCCTTAACATCTTTGGGGTACTGGATTCGCTGTTGT
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACTGGATTCGCCGTTGC
** * * * * **
42609711 AACTTAAATCTTACCCTTCAT-T-TTTGAGGTACTAGG-TTCGCCATTAT
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACT-GGATTCGCCGTTGC
* * * *
42609758 GGCTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTGGCCGTTGC
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACTGGATTCGCCGTTGC
** * * *
42609807 GGCTTAAATCTTTCCCTTTATGCCTTTGAGGTA-TAAGG-TTCGTCATTGC
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACT--GGATTCGCCGTTGC
* * * * *
42609856 GACTTAAA-CTTTTCCCTTTGTATCTTCGCGGTTCTGGATTCGCCGTTGT
1 GGCTTAAATC-TTTCCCTTTATATCTTCGAGGTACTGGATTCGCCGTTGC
* * * *
42609905 GGCTTAAATCTTTCCCTTAAT-TATTCGTGGTACTGGATTCACCGTTGC
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACTGGATTCGCCGTTGC
* * ** * * *
42609953 GGCTTAAATCTTTTCCTTCATGCCTTTGAGGTA-TAAGG-TTCGTCATTGC
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACT--GGATTCGCCGTTGC
* * * * *
42610002 GACTTAAACCTTTCCCTTTGTATCTTCGCGGTACTAGATTCGCCGTTGC
1 GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACTGGATTCGCCGTTGC
*
42610051 GGCTTAAATCTTTTCCTT
1 GGCTTAAATCTTTCCCTT
42610069 CGTGGTAATG
Statistics
Matches: 338, Mismatches: 97, Indels: 42
0.71 0.20 0.09
Matches are distributed among these distances:
47 33 0.10
48 57 0.17
49 238 0.70
50 10 0.03
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (49 bp):
GGCTTAAATCTTTCCCTTTATATCTTCGAGGTACTGGATTCGCCGTTGC
Found at i:42609764 original size:47 final size:48
Alignment explanation
Indices: 42609636--42609775 Score: 142
Period size: 47 Copynumber: 2.9 Consensus size: 48
42609626 CCCTTCGTGC
*
42609636 TTTTGAGGTA-TAAGGTTCGCCGTTACGGCTTAAACCTTTCCCTTAACAT
1 TTTTGAGGTACT-AGGTTCGCCGTTATGGCTTAAACCTTTCCCTT-ACAT
* * * * ** * *
42609685 CTTTGGGGTACT-GGATTCGCTGTTGTAACTTAAATCTTACCCTT-CAT
1 TTTTGAGGTACTAGG-TTCGCCGTTATGGCTTAAACCTTTCCCTTACAT
*
42609732 TTTTGAGGTACTAGGTTCGCCATTATGGCTTAAACCTTTCCCTT
1 TTTTGAGGTACTAGGTTCGCCGTTATGGCTTAAACCTTTCCCTT
42609776 TGTATCTTCG
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
47 35 0.50
48 4 0.06
49 30 0.43
50 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTTGAGGTACTAGGTTCGCCGTTATGGCTTAAACCTTTCCCTTACAT
Found at i:42609895 original size:194 final size:194
Alignment explanation
Indices: 42609556--42609922 Score: 464
Period size: 194 Copynumber: 1.9 Consensus size: 194
42609546 TTTGAGATTT
* * * * * * *
42609556 GCCATTATGGCTTCAATCTTTCCTTTTATGTCTTCGTGGTACTAGATTCATCGTTGTGGCTTGAA
1 GCCATTATGGCTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCACCGTTGCGGCTTAAA
* * * *
42609621 TATTTCCCTTCGTGCTTTTGAGGTATAAGGTTCGCCGTTACGGCTTAAACCTTTCCCTTAACATC
66 TATTTCCCTTCATGCCTTTGAGGTATAAGGTTCGCCATTACGACTTAAACCTTTCCCTTAACATC
* * *
42609686 TTTGGGGTACTGGATTCGCTGTTGTAACTTAAATCTTACCCTTCATTTTTGAGGTACTAGGTTC
131 TTCGCGGTACTGGATTCGCCGTTGTAACTTAAATCTTACCCTTCATTTTTGAGGTACTAGGTTC
* * **
42609750 GCCATTATGGCTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTGGCCGTTGCGGCTTAAA
1 GCCATTATGGCTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCACCGTTGCGGCTTAAA
* * * * * ***
42609815 TCTTTCCCTTTATGCCTTTGAGGTATAAGGTTCGTCATTGCGACTTAAACTTTTCCCTTTGTATC
66 TATTTCCCTTCATGCCTTTGAGGTATAAGGTTCGCCATTACGACTTAAACCTTTCCCTTAACATC
* ** *
42609880 TTCGCGGTTCTGGATTCGCCGTTGTGGCTTAAATCTTTCCCTT
131 TTCGCGGTACTGGATTCGCCGTTGTAACTTAAATCTTACCCTT
42609923 AATTATTCGT
Statistics
Matches: 143, Mismatches: 30, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
194 143 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (194 bp):
GCCATTATGGCTTAAACCTTTCCCTTTATATCTTCGTGGTACTAGATTCACCGTTGCGGCTTAAA
TATTTCCCTTCATGCCTTTGAGGTATAAGGTTCGCCATTACGACTTAAACCTTTCCCTTAACATC
TTCGCGGTACTGGATTCGCCGTTGTAACTTAAATCTTACCCTTCATTTTTGAGGTACTAGGTTC
Found at i:42609959 original size:146 final size:147
Alignment explanation
Indices: 42609738--42610068 Score: 511
Period size: 146 Copynumber: 2.3 Consensus size: 147
42609728 TCATTTTTGA
* * * * ** * **
42609738 GGTACTAGGTTCGCCATTATGGCTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTGGCCG
1 GGTACTAGATTCGCCGTTGTGGCTTAAATCTTTCCCTTAATATATTCGTGGTACTGGATTCACCG
* *
42609803 TTGCGGCTTAAATCTTTCCCTTTATGCCTTTGAGGTATAAGGTTCGTCATTGCGACTTAAACTTT
66 TTGCGGCTTAAATCTTTCCCTTCATGCCTTTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTT
42609868 TCCCTTTGTATCTTCGC
131 TCCCTTTGTATCTTCGC
* *
42609885 GGTTCTGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTAAT-TATTCGTGGTACTGGATTCACCG
1 GGTACTAGATTCGCCGTTGTGGCTTAAATCTTTCCCTTAATATATTCGTGGTACTGGATTCACCG
*
42609949 TTGCGGCTTAAATCTTTTCCTTCATGCCTTTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTT
66 TTGCGGCTTAAATCTTTCCCTTCATGCCTTTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTT
42610014 TCCCTTTGTATCTTCGC
131 TCCCTTTGTATCTTCGC
* *
42610031 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTTCCTT
1 GGTACTAGATTCGCCGTTGTGGCTTAAATCTTTCCCTT
42610069 CGTGGTAATG
Statistics
Matches: 166, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
146 133 0.80
147 33 0.20
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.40
Consensus pattern (147 bp):
GGTACTAGATTCGCCGTTGTGGCTTAAATCTTTCCCTTAATATATTCGTGGTACTGGATTCACCG
TTGCGGCTTAAATCTTTCCCTTCATGCCTTTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTT
TCCCTTTGTATCTTCGC
Found at i:42609966 original size:98 final size:96
Alignment explanation
Indices: 42609556--42609970 Score: 350
Period size: 98 Copynumber: 4.3 Consensus size: 96
42609546 TTTGAGATTT
* * * * * * * * ** *
42609556 GCCATTATGGCTTCAATCTTTCCTTTTATGTCTTCGTGGTACTAGATTCATCGTTGTGGCTTGAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
* **
42609621 TATTTCCCTTCGTGCTTTTGAGGTA-TAAGGTTC
66 TCTTTCCCTTAAT--TTTTGAGGTACT-AGGTTC
* *** * * * **
42609654 GCCGTTACGGCTTAAACCTTTCCCTTAACATCTTTGGGGTACTGGATTCGCTGTTGTAACTTAAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
* *
42609719 TCTTACCCTTCATTTTTGAGGTACTAGGTTC
66 TCTTTCCCTTAATTTTTGAGGTACTAGGTTC
* * * *
42609750 GCCATTATGGCTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTGGCCGTTGCGGCTTAAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
* *
42609815 TCTTTCCCTTTATGCCTTTGAGGTA-TAAGGTTC
66 TCTTTCCCTTAAT--TTTTGAGGTACT-AGGTTC
* * * * *
42609848 GTCATTGCGACTTAAACTTTTCCCTTTGTATCTTCGCGGTTCTGGATTCGCCGTTGTGGCTTAAA
1 GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
* *
42609913 TCTTTCCCTTAATTATTCGTGGTACT-GGATTC
66 TCTTTCCCTTAATT-TTTGAGGTACTAGG-TTC
* * * * *
42609945 ACCGTTGCGGCTTAAATCTTTTCCTT
1 GCCATTACGGCTTAAACCTTTCCCTT
42609971 CATGCCTTTG
Statistics
Matches: 255, Mismatches: 55, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
96 82 0.32
97 31 0.12
98 142 0.56
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (96 bp):
GCCATTACGGCTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCGCCGTTGTGGCTTAAA
TCTTTCCCTTAATTTTTGAGGTACTAGGTTC
Found at i:42611183 original size:21 final size:22
Alignment explanation
Indices: 42611157--42611293 Score: 134
Period size: 23 Copynumber: 6.0 Consensus size: 22
42611147 ACGGAACAAG
* *
42611157 CAGAGAGTAC-CAAAGTACTAA
1 CAGAGAGCACACAAAGTGCTAA
*
42611178 CAGAGAGCACA-TAAGTGCTGGGTAA
1 CAGAGAGCACACAAAGTGC----TAA
* *
42611203 TAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCT-AA
*
42611226 CAGAGAGCACACAAAGTACTAA
1 CAGAGAGCACACAAAGTGCTAA
42611248 TCAGAGAGCACACAAAGTGCTAA
1 -CAGAGAGCACACAAAGTGCTAA
*
42611271 TCAGAGAGCACACACAGTGCTAA
1 -CAGAGAGCACACAAAGTGCTAA
42611294 TAACAGAGAG
Statistics
Matches: 97, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
21 14 0.14
22 3 0.03
23 62 0.64
25 13 0.13
26 5 0.05
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (22 bp):
CAGAGAGCACACAAAGTGCTAA
Found at i:42611231 original size:48 final size:45
Alignment explanation
Indices: 42611176--42611327 Score: 137
Period size: 46 Copynumber: 3.2 Consensus size: 45
42611166 CCAAAGTACT
*
42611176 AACAGAGAGCACATAAGTGCTGGGTAATAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACAAAAGTGCT---TAATAGAGAGCACACACAGTGCTA
* *
42611224 AACAGAGAGCACACAAAGTAC-TAATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACA-AAAGTGCTTAAT-AGAGAGCACACACAGTGCTA
* * * * *
42611270 ATCAGAGAGCACACACAGTGCTAATAACAGAGAGCATGAGAC-GTGCTA
1 AACAGAGAGCACA-AAAGTGCT--TAATAGAGAGCA-CACACAGTGCTA
42611318 AACAGAGAGC
1 AACAGAGAGC
42611328 GCGCTAGTGT
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
45 4 0.05
46 37 0.43
48 36 0.41
49 10 0.11
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (45 bp):
AACAGAGAGCACAAAAGTGCTTAATAGAGAGCACACACAGTGCTA
Found at i:42611234 original size:23 final size:23
Alignment explanation
Indices: 42611204--42611327 Score: 151
Period size: 23 Copynumber: 5.3 Consensus size: 23
42611194 GCTGGGTAAT
42611204 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACACAGTGCTAAAC
* * *
42611227 AGAGAGCACACAAAGTACTAATC
1 AGAGAGCACACACAGTGCTAAAC
* *
42611250 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACACAGTGCTAAAC
42611273 AGAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACACAGTGCT-A-AAC
* *
42611298 AGAGAGCATGAGAC-GTGCTAAAC
1 AGAGAGCA-CACACAGTGCTAAAC
42611321 AGAGAGC
1 AGAGAGC
42611328 GCGCTAGTGT
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
23 70 0.78
24 2 0.02
25 15 0.17
26 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAAAC
Found at i:42613375 original size:12 final size:12
Alignment explanation
Indices: 42613360--42613390 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42613350 TGCAACTGCG
42613360 CTTGCATTTGTT
1 CTTGCATTTGTT
42613372 CTTGCATTTGTT
1 CTTGCATTTGTT
42613384 CTTGCAT
1 CTTGCAT
42613391 CTCTTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.19, G:0.16, T:0.55
Consensus pattern (12 bp):
CTTGCATTTGTT
Found at i:42619123 original size:16 final size:16
Alignment explanation
Indices: 42619102--42619146 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
42619092 ACATAGAGCT
*
42619102 TGCTGACATGGACACA
1 TGCTGACGTGGACACA
42619118 TGCTGACGT-GACACA
1 TGCTGACGTGGACACA
42619133 TGCTGACGTGGACA
1 TGCTGACGTGGACA
42619147 TGTGATGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (16 bp):
TGCTGACGTGGACACA
Found at i:42619620 original size:60 final size:61
Alignment explanation
Indices: 42619473--42619866 Score: 339
Period size: 60 Copynumber: 6.5 Consensus size: 61
42619463 GCTTATGAAA
* * * * * *
42619473 TTTTTGTCAGAT-AAAAAATAC-AATTTTTTTGTGTTAGCCATTGC-ATGGTCGACA-TCCC
1 TTTTTATCAGATAAAAAAATTCAAATTTTTTGGTGTTGGCCA-TGCAATGGCCGACACCCCC
* * * *
42619531 TTTTTAATCTGATAAAAAAAATCAAATTTTTAGGTGTTGGCCATGTAATGGCCGACACCCCC
1 TTTTT-ATCAGATAAAAAAATTCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* *
42619593 TTTTTTATCAGAT-AAAAAA-TCTAA-TTTTTGGATGTTGTCCATGCAATGGCCGACACCCCC
1 -TTTTTATCAGATAAAAAAATTCAAATTTTTTGG-TGTTGGCCATGCAATGGCCGACACCCCC
* * * *
42619653 -TTCTCTCAGATAAAAAATTTCAAATTTTTTTGGTGTTAGG-CATGCAATGGCCGACACTCCC
1 TTTTTATCAGATAAAAAAATTCAAA-TTTTTTGGTGTT-GGCCATGCAATGGCCGACACCCCC
* * * * * *
42619714 -TGTTCTCAAATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGCTATGGCTGACACCCCC
1 TTTTTATCAGATAAAAAAA-TTC-AAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* **
42619776 --TTT-TCAGATAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACAATCCC
1 TTTTTATCAGATAAAAAAA-TTCAAA-TTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* * *
42619836 -TTTTCTCAAATAAAAAATTTCAAAATTTTTT
1 TTTTTATCAGATAAAAAAATTC-AAATTTTTT
42619867 TCGTGTTGAC
Statistics
Matches: 278, Mismatches: 39, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
58 14 0.05
59 19 0.07
60 89 0.32
61 84 0.30
62 64 0.23
63 8 0.03
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (61 bp):
TTTTTATCAGATAAAAAAATTCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
Found at i:42619836 original size:122 final size:123
Alignment explanation
Indices: 42619617--42619866 Score: 384
Period size: 122 Copynumber: 2.0 Consensus size: 123
42619607 AAAAATCTAA
42619617 TTTTTGGATGTTGTCCATGCAATGGCCGACACCCCCTTCTCTCAGATAAAAAATTTCAAATTTTT
1 TTTTTGGATGTTGTCCATGCAATGGCCGACACCCCCTTCTCTCAGATAAAAAATTTCAAATTTTT
*
42619682 TTGGTGTTAGGCATGCAATGGCCGACACTCCCTGTTCTCAAATAAAAAAATTTCAAAAT
66 TTGGTGTTAGGCATGCAATGGCCGACAATCCCTGTTCTCAAAT-AAAAAATTTCAAAAT
* * *
42619741 TTTTTGG-TGTTGGT-CATGCTATGGCTGACACCCCCTT-T-TCAGATAAAAAAATTTTAAATTT
1 TTTTTGGATGTT-GTCCATGCAATGGCCGACACCCCCTTCTCTCAGAT-AAAAAATTTCAAATTT
*
42619802 TTTTGGTGTT-GGCCATGCAATGGCCGACAATCCCTTTTCTCAAATAAAAAATTTCAAAAT
64 TTTTGGTGTTAGG-CATGCAATGGCCGACAATCCCTGTTCTCAAATAAAAAATTTCAAAAT
42619862 TTTTT
1 TTTTT
42619867 TCGTGTTGAC
Statistics
Matches: 118, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
121 28 0.24
122 56 0.47
123 25 0.21
124 9 0.08
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (123 bp):
TTTTTGGATGTTGTCCATGCAATGGCCGACACCCCCTTCTCTCAGATAAAAAATTTCAAATTTTT
TTGGTGTTAGGCATGCAATGGCCGACAATCCCTGTTCTCAAATAAAAAATTTCAAAAT
Found at i:42619993 original size:62 final size:62
Alignment explanation
Indices: 42619917--42620070 Score: 211
Period size: 62 Copynumber: 2.5 Consensus size: 62
42619907 TGTGTCAGCC
* * * *
42619917 TTTGGTGTTTGCCATGCCATGGCCGATACCCCCT-TTTTCAGATAAAAAAATTTCAAAATTTT
1 TTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCAGATAAAAAAATTTC-AAATTTT
* * *
42619979 TTTGGTGTTGGCCATGCAATGGTCAACACCCCCTGTTCTCAGATAAGAAAATTTCAAATTTT
1 TTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCAGATAAAAAAATTTCAAATTTT
* *
42620041 TTTGATGTTGGCCATGTAATGGCCGACACC
1 TTTGGTGTTGGCCATGCAATGGCCGACACC
42620071 AACTTCTCAT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 62 0.77
63 18 0.22
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
TTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCAGATAAAAAAATTTCAAATTTT
Found at i:42624055 original size:85 final size:86
Alignment explanation
Indices: 42623721--42624202 Score: 785
Period size: 86 Copynumber: 5.6 Consensus size: 86
42623711 ATTTAAAATT
* * * *
42623721 AATTTAACATTATTTAAATAAAAAA-ATTATTATTATATTATAATTTATATCAAATATTGTGTTT
1 AATTTAA-A-TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
*
42623785 ATTTGACAAGACATTATTTA-TCA
64 ATTTGACAATACATTATTTACT-A
** *
42623808 AATTTTTATATTTAAATAAAAAAGATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
42623873 TTGACAATACATTATTTACTA
66 TTGACAATACATTATTTACTA
*
42623894 AATTTAAATATTTAAATAAAAAAGATTGTTATTATATTACAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
42623959 TTGACAATACATTATTTACTA
66 TTGACAATACATTATTTACTA
*
42623980 AATTTAAATATTTAAATAAAAAA-ATTATTATTATATTACAATTTTTATCAAATAATATGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
42624044 TTGACAATACATTATTTACTA
66 TTGACAATACATTATTTACTA
*
42624065 AATTTAAATATTTAAAT-AAAAA-ATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
42624128 TTGACAATACATTATTTACTA
66 TTGACAATACATTATTTACTA
* *
42624149 AATTTAAATATTTAAATAAAAAAGATTATTATCATATTACAATTTTTATTAAAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAAT
42624203 TTTAAATTTA
Statistics
Matches: 373, Mismatches: 18, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
84 82 0.22
85 97 0.26
86 188 0.50
87 6 0.02
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (86 bp):
AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
TTGACAATACATTATTTACTA
Found at i:42624188 original size:255 final size:259
Alignment explanation
Indices: 42623721--42624202 Score: 821
Period size: 255 Copynumber: 1.9 Consensus size: 259
42623711 ATTTAAAATT
* * * *
42623721 AATTTAACATTATTTAAATAAAAAAATTATTATTATATTATAATTTATATCAAATATTGTGTTTA
1 AATTTAACATTATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATAATATGTTGA
**
42623786 TTTGACAAGACATTATTTATCAAATTTTTATATTTAAATAAAAAAGATTATTATTATATTAAAAT
66 TTTGACAAGACATTATTTATCAAATTTAAATATTTAAATAAAAAAGATTATTATTATATTAAAAT
42623851 TTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAAA
131 TTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAAA
* *
42623916 AGATTGTTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
196 AGATTATTATCATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
*
42623980 AATTTAA-A-TATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGA
1 AATTTAACATTATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATAATATGTTGA
*
42624043 TTTGACAATACATTATTTA-CTAAATTTAAATATTTAAAT-AAAAA-ATTATTATTATATTAAAA
66 TTTGACAAGACATTATTTATC-AAATTTAAATATTTAAATAAAAAAGATTATTATTATATTAAAA
42624105 TTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAA
130 TTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAA
*
42624170 AAGATTATTATCATATTACAATTTTTATTAAAT
195 AAGATTATTATCATATTACAATTTTTATCAAAT
42624203 TTTAAATTTA
Statistics
Matches: 211, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
255 113 0.54
256 6 0.03
257 84 0.40
258 1 0.00
259 7 0.03
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (259 bp):
AATTTAACATTATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATAATATGTTGA
TTTGACAAGACATTATTTATCAAATTTAAATATTTAAATAAAAAAGATTATTATTATATTAAAAT
TTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAAA
AGATTATTATCATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
Found at i:42625238 original size:22 final size:20
Alignment explanation
Indices: 42625187--42625238 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
42625177 CTCGATTTTA
42625187 TATTTTTTAATTTTATTAAT
1 TATTTTTTAATTTTATTAAT
* *
42625207 TATTATTTT--TATT-CTAAT
1 TATT-TTTTAATTTTATTAAT
42625225 TATTTTTTAATTTT
1 TATTTTTTAATTTT
42625239 TCAGATGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
17 4 0.15
18 8 0.31
19 6 0.23
20 4 0.15
21 4 0.15
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTTTAATTTTATTAAT
Found at i:42626628 original size:28 final size:29
Alignment explanation
Indices: 42626578--42626645 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
42626568 ATATCGTTTT
42626578 TATTTTAAATTTAATTTCCAATTTCCAGTA
1 TATTTT-AATTTAATTTCCAATTTCCAGTA
* * *
42626608 TATTTTAATTT-TTTTCTAATTTCCTGTA
1 TATTTTAATTTAATTTCCAATTTCCAGTA
*
42626636 TATTCTAATT
1 TATTTTAATT
42626646 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 23 0.68
29 5 0.15
30 6 0.18
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (29 bp):
TATTTTAATTTAATTTCCAATTTCCAGTA
Found at i:42627571 original size:58 final size:58
Alignment explanation
Indices: 42627460--42627579 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 58
42627450 GGGAAGTTGA
* * **
42627460 TGTCGGTCATTACATGGCCAACACAAAAAATTTTAATTTTTTACCAAATAAAAAGGGG
1 TGTCGGCCATTACATGGCCAACAAAAAAAATTGAAATTTTTTACCAAATAAAAAGGGG
* * *
42627518 TGTCGGCCATTACATGGCCAATACAAAAAAAATTGAAATTTTTTATCTAA-AAAAGGGGG
1 TGTCGGCCATTACATGGCC-A-ACAAAAAAAATTGAAATTTTTTACCAAATAAAAAGGGG
42627577 TGT
1 TGT
42627580 TGACCATGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 18 0.34
59 12 0.23
60 23 0.43
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (58 bp):
TGTCGGCCATTACATGGCCAACAAAAAAAATTGAAATTTTTTACCAAATAAAAAGGGG
Found at i:42627674 original size:98 final size:94
Alignment explanation
Indices: 42627541--42627725 Score: 264
Period size: 98 Copynumber: 1.9 Consensus size: 94
42627531 ATGGCCAATA
* * *
42627541 CAAAAAAAATTGAAATTTTTTATCTAAAAAAGGGGGTGTTGACCATGGTATGG-CTAACACCAAA
1 CAAAAAAAATTGAAATTTTTTAACTAAAAAAGGGGGTGTCGACCATGGCATGGTC-AACACCAAA
*
42627605 AAATTTTGAAATTTTTTTATCTGAGAACAGG
65 AAAATTTG-AATTTTTTTATCTGAGAACAGG
* *
42627636 CAAAAAAAATTTGAAATTTTTTTAACTGAGAAAAGGGGGTGTCGACCATTGCATGGTCAACACCA
1 CAAAAAAAA-TTGAAA-TTTTTTAACT-AAAAAAGGGGGTGTCGACCATGGCATGGTCAACACCA
42627701 AAAAAATTTGAATTTTTTTATCTGA
63 AAAAAATTTGAATTTTTTTATCTGA
42627726 AAAGGGGTGT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
95 9 0.11
96 6 0.08
97 24 0.30
98 40 0.50
99 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (94 bp):
CAAAAAAAATTGAAATTTTTTAACTAAAAAAGGGGGTGTCGACCATGGCATGGTCAACACCAAAA
AAATTTGAATTTTTTTATCTGAGAACAGG
Found at i:42627817 original size:62 final size:60
Alignment explanation
Indices: 42627638--42627903 Score: 319
Period size: 60 Copynumber: 4.4 Consensus size: 60
42627628 AGAACAGGCA
* *
42627638 AAAAAAATTTGAAATTTTTTTAACTGAGAAAAGGGGGTGTCGACCATTGCATGGTCAACACC
1 AAAAAAATTTG-AATTTTTTTATCTGAGAAAA-GGGGTGTCGACCATTGCATGGCCAACACC
*
42627700 AAAAAAATTTGAATTTTTTTATCT--GAAAAGGGGTGTCGACCATTGCATGACCAACACC
1 AAAAAAATTTGAATTTTTTTATCTGAGAAAAGGGGTGTCGACCATTGCATGGCCAACACC
* *
42627758 AAAAAATTTTGAAATTTTTTTATCTGAGAAAAGGGGGTGTCAACCATTGCATGGCCAACACC
1 AAAAAAATTTG-AATTTTTTTATCTGAGAAAA-GGGGTGTCGACCATTGCATGGCCAACACC
* * * * * *
42627820 -CAAAAATTTGATTTTTTTTATCAGATTAAAAGGGGTGTCGGCCA-TGCAATGGCCAACA-T
1 AAAAAAATTTGAATTTTTTTATCTGA-GAAAAGGGGTGTCGACCATTGC-ATGGCCAACACC
* *
42627879 AAAAAAAATTGTA-TTTTTTATCTGA
1 AAAAAAATTTGAATTTTTTTATCTGA
42627904 CAAATGGCTG
Statistics
Matches: 178, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
58 37 0.21
59 32 0.18
60 42 0.24
61 29 0.16
62 38 0.21
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (60 bp):
AAAAAAATTTGAATTTTTTTATCTGAGAAAAGGGGTGTCGACCATTGCATGGCCAACACC
Found at i:42628018 original size:16 final size:18
Alignment explanation
Indices: 42627988--42628021 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
42627978 CTCGTATTTT
42627988 CGTATATTAATAAAATAC
1 CGTATATTAATAAAATAC
42628006 CGTAT-TTAA-AAAATAC
1 CGTATATTAATAAAATAC
42628022 ATAGGTGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (18 bp):
CGTATATTAATAAAATAC
Found at i:42628372 original size:20 final size:20
Alignment explanation
Indices: 42628347--42628385 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42628337 GAATTTAACT
*
42628347 TAAAAAATTTTCGAATCAAA
1 TAAAAAAATTTCGAATCAAA
*
42628367 TAAAAAAATTTCGAGTCAA
1 TAAAAAAATTTCGAATCAA
42628386 GTTAACGAAT
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:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (20 bp):
TAAAAAAATTTCGAATCAAA
Found at i:42629878 original size:19 final size:20
Alignment explanation
Indices: 42629835--42629878 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42629825 TTACCTTCAT
* * *
42629835 TTTTATAAGGAAAACTTGAA
1 TTTTACAAGGAAAAATCGAA
42629855 TTTTACAAGGAAAAATCG-A
1 TTTTACAAGGAAAAATCGAA
42629874 TTTTA
1 TTTTA
42629879 TTTTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTACAAGGAAAAATCGAA
Found at i:42636731 original size:5 final size:6
Alignment explanation
Indices: 42636713--42636738 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42636703 GAAAAAACAC
42636713 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
42636739 GGTGTTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:42637547 original size:8 final size:9
Alignment explanation
Indices: 42637514--42637544 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
42637504 TGATTTAGAT
42637514 TTTTTAAAA
1 TTTTTAAAA
42637523 TTTTTAAAA
1 TTTTTAAAA
42637532 TTTTTAAAA
1 TTTTTAAAA
42637541 TTTT
1 TTTT
42637545 AAATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:42639730 original size:3 final size:3
Alignment explanation
Indices: 42639722--42639759 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42639712 TGTATTGGGT
42639722 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
42639760 GTGGTGGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:42643823 original size:3 final size:3
Alignment explanation
Indices: 42643817--42643845 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
42643807 ATTAATAATA
42643817 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42643846 GGAACTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:42644713 original size:36 final size:36
Alignment explanation
Indices: 42644666--42644738 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
42644656 ATTGGCAAGC
42644666 TAAGATGCAATTATCGACGGCTGATCAAGCTTAGTA
1 TAAGATGCAATTATCGACGGCTGATCAAGCTTAGTA
42644702 TAAGATGCAATTATCGACGGCTGATCAAGCTTAGTA
1 TAAGATGCAATTATCGACGGCTGATCAAGCTTAGTA
42644738 T
1 T
42644739 GTATTAACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (36 bp):
TAAGATGCAATTATCGACGGCTGATCAAGCTTAGTA
Found at i:42645488 original size:61 final size:61
Alignment explanation
Indices: 42645355--42645493 Score: 183
Period size: 61 Copynumber: 2.3 Consensus size: 61
42645345 TCCTCAATAT
* * * * * *
42645355 AAAATATTCAACAAACTTAGCCCTCAATGTTTACAAAATTTATCATTTTAGTTTGAATTCTG
1 AAAA-ATTCAATAAATTTAGCCCTCAATATTTACAAAAATTATCAATTTAGTTTCAATTCTG
42645417 AAAAATTCAATAAATTTAGCCCTCAATATTTACAAAAAATT-TCAATTTAGTTTCAATTCT-
1 AAAAATTCAATAAATTTAGCCCTCAATATTTAC-AAAAATTATCAATTTAGTTTCAATTCTG
42645477 AAAAAGTTCAATAAATT
1 AAAAA-TTCAATAAATT
42645494 AATTTTTGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 5 0.07
61 54 0.78
62 10 0.14
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.37
Consensus pattern (61 bp):
AAAAATTCAATAAATTTAGCCCTCAATATTTACAAAAATTATCAATTTAGTTTCAATTCTG
Found at i:42654694 original size:25 final size:23
Alignment explanation
Indices: 42654642--42654695 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
42654632 CCTATGGATT
* *
42654642 TATTATTATTATTATTTTTGAATA
1 TATT-TTATTATAAGTTTTGAATA
42654666 -ATTTTATTATAAGTTTTGATCATA
1 TATTTTATTATAAGTTTTGA--ATA
42654690 TATTTT
1 TATTTT
42654696 TTTTACAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 14 0.56
23 3 0.12
24 3 0.12
25 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (23 bp):
TATTTTATTATAAGTTTTGAATA
Found at i:42655707 original size:22 final size:22
Alignment explanation
Indices: 42655679--42655720 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
42655669 ATTATTTCAT
42655679 TTTTTTCTATTATATTTGTGCA
1 TTTTTTCTATTATATTTGTGCA
42655701 TTTTTTCTATTATATTTGTG
1 TTTTTTCTATTATATTTGTG
42655721 TATATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (22 bp):
TTTTTTCTATTATATTTGTGCA
Found at i:42655733 original size:22 final size:22
Alignment explanation
Indices: 42655684--42655733 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
42655674 TTCATTTTTT
* *
42655684 TCTATTATATTTGTGCATTTTT
1 TCTATTATATTTGTGCATTATA
*
42655706 TCTATTATATTTGTGTATATATA
1 TCTATTATATTTGTGCAT-TATA
42655729 T-TATT
1 TCTATT
42655734 TATGAAGGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.62
Consensus pattern (22 bp):
TCTATTATATTTGTGCATTATA
Found at i:42661669 original size:6 final size:5
Alignment explanation
Indices: 42661639--42661668 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
42661629 AGGAGTGACA
42661639 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
42661669 AACATGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:42662139 original size:20 final size:21
Alignment explanation
Indices: 42662116--42662156 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42662106 TAAATTAAAA
*
42662116 TTCAAA-TCCGAACCTTGAAC
1 TTCAAATTCCAAACCTTGAAC
*
42662136 TTCAAATTTCAAACCTTGAAC
1 TTCAAATTCCAAACCTTGAAC
42662157 CAATATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (21 bp):
TTCAAATTCCAAACCTTGAAC
Found at i:42677644 original size:31 final size:31
Alignment explanation
Indices: 42677597--42677667 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
42677587 GAAATTCATG
*
42677597 ATAAAAAATGACCTAAATTA-TATGTAAATAA
1 ATAAAAAATGACCTAAAATATTAT-TAAATAA
*
42677628 CATAAAAAATTA-CTAAAATATTATTAAATAA
1 -ATAAAAAATGACCTAAAATATTATTAAATAA
*
42677659 TTAAAAAAT
1 ATAAAAAAT
42677668 AATCATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.23
31 14 0.40
32 13 0.37
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (31 bp):
ATAAAAAATGACCTAAAATATTATTAAATAA
Found at i:42677676 original size:21 final size:22
Alignment explanation
Indices: 42677622--42677680 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
42677612 AATTATATGT
* *
42677622 AAATAA-CATAAAAAATTACTA
1 AAATAATCATAAATAATTACAA
*
42677643 AAAT-ATTATTAAATAATTA-AA
1 AAATAATCA-TAAATAATTACAA
42677664 AAATAATCATAAATAAT
1 AAATAATCATAAATAAT
42677681 ATAATGAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.03
21 18 0.58
22 12 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAATCATAAATAATTACAA
Found at i:42680425 original size:12 final size:12
Alignment explanation
Indices: 42680365--42680432 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
42680355 AAACAGTAAC
42680365 AATCAAAATCC-
1 AATCAAAATCCA
*
42680376 AATCAAAATCGA
1 AATCAAAATCCA
42680388 AAT-AACAAT--A
1 AATCAA-AATCCA
**
42680398 AATCGAAAATAAA
1 AATC-AAAATCCA
42680411 AATCAAAATCCA
1 AATCAAAATCCA
*
42680423 AATCGAAATC
1 AATCAAAATC
42680433 GAATAAACCC
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.09
11 15 0.32
12 23 0.49
13 5 0.11
ACGTcount: A:0.60, C:0.18, G:0.04, T:0.18
Consensus pattern (12 bp):
AATCAAAATCCA
Found at i:42680454 original size:47 final size:46
Alignment explanation
Indices: 42680365--42680463 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 46
42680355 AAACAGTAAC
*
42680365 AATCAAAATCCAATCAAAATCGAAATAACAATAAATCGAAAATAAA
1 AATCAAAATCCAATCAAAATCGAAATAACAATAAATCAAAAATAAA
* ** * *
42680411 AATCAAAATCCAAATCGAAATCG-AATAAACCCTAAATCAAAAATCAC
1 AATCAAAATCC-AATCAAAATCGAAAT-AACAATAAATCAAAAATAAA
42680458 AATCAA
1 AATCAA
42680464 TATCGACATC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 14 0.31
47 31 0.69
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (46 bp):
AATCAAAATCCAATCAAAATCGAAATAACAATAAATCAAAAATAAA
Found at i:42680681 original size:31 final size:31
Alignment explanation
Indices: 42680646--42680744 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
42680636 AAAATTAAGA
*
42680646 TTAAATTGACAGAATATTTAAATATTGAGGG
1 TTAAATTAACAGAATATTTAAATATTGAGGG
* ** * * *
42680677 TTAAATTTATTGAAAATCTTAAA-ATCG-GGA
1 TTAAATTAACAGAATAT-TTAAATATTGAGGG
* ** *
42680707 TTAAATTAACAAAATGGTTAAATATTGAAGG
1 TTAAATTAACAGAATATTTAAATATTGAGGG
42680738 TTAAATT
1 TTAAATT
42680745 TACTATTATA
Statistics
Matches: 49, Mismatches: 16, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
29 5 0.10
30 15 0.31
31 24 0.49
32 5 0.10
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.36
Consensus pattern (31 bp):
TTAAATTAACAGAATATTTAAATATTGAGGG
Found at i:42680823 original size:31 final size:31
Alignment explanation
Indices: 42680788--42680851 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
42680778 TTTATTTGAA
*
42680788 TTTGATGTCG-ATATTGATTGTGATTTTCGAT
1 TTTGAT-TCGAATATTGATTGTCATTTTCGAT
* * *
42680819 TTTGATTTGAATTTTGATTTTCATTTTCGAT
1 TTTGATTCGAATATTGATTGTCATTTTCGAT
42680850 TT
1 TT
42680852 AGGGTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (31 bp):
TTTGATTCGAATATTGATTGTCATTTTCGAT
Found at i:42680825 original size:6 final size:6
Alignment explanation
Indices: 42680782--42680851 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
42680772 TTTGTGTTTA
* * * * *
42680782 TTTGAA TTTGAT GTCGAT ATTGAT TGTGAT TTTCGAT TTTGA- TTTGAAT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTT-GAT TTTGAT TTTG-AT
*
42680831 TTTGAT TTTCAT TTTCGAT TT
1 TTTGAT TTTGAT TTT-GAT TT
42680852 AGGGTTATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
5 4 0.08
6 32 0.64
7 14 0.28
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (6 bp):
TTTGAT
Found at i:42680839 original size:18 final size:18
Alignment explanation
Indices: 42680782--42680844 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
42680772 TTTGTGTTTA
*
42680782 TTTGAATTTGA-TGTCGAT
1 TTTG-ATTTGATTTTCGAT
*
42680800 ATTGATTGTGATTTTCGAT
1 TTTGATT-TGATTTTCGAT
42680819 TTTGATTTGAATTTT-GAT
1 TTTGATTTG-ATTTTCGAT
*
42680837 TTTCATTT
1 TTTGATTT
42680845 TCGATTTAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 3 0.08
18 18 0.47
19 17 0.45
ACGTcount: A:0.21, C:0.05, G:0.17, T:0.57
Consensus pattern (18 bp):
TTTGATTTGATTTTCGAT
Found at i:42699614 original size:19 final size:19
Alignment explanation
Indices: 42699592--42699631 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42699582 GATGGTTGAG
**
42699592 ATTCAAAATGATTAAAAAA
1 ATTCAAAATGACAAAAAAA
*
42699611 ATTCAAAGTGACAAAAAAA
1 ATTCAAAATGACAAAAAAA
42699630 AT
1 AT
42699632 AGGGGCTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (19 bp):
ATTCAAAATGACAAAAAAA
Found at i:42702601 original size:30 final size:29
Alignment explanation
Indices: 42702567--42702639 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
42702557 AATTTACAAG
42702567 AATTGAATCAAATCAAAATTTCATGTATAC
1 AATTGAATCAAATCAAAATTTC-TGTATAC
* * *
42702597 AATTGCA-CAAAATCAAAGTTTCTGTATAT
1 AATTGAATC-AAATCAAAATTTCTGTATAC
42702626 AATTGCACATCAAA
1 AATTG-A-ATCAAA
42702640 CCATAGTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
29 12 0.34
30 18 0.51
31 4 0.11
32 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (29 bp):
AATTGAATCAAATCAAAATTTCTGTATAC
Found at i:42702623 original size:29 final size:30
Alignment explanation
Indices: 42702576--42702634 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
42702566 GAATTGAATC
42702576 AAATCAAAATTTCATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATACAATTGCACA
* *
42702606 AAATCAAAGTTTC-TGTATATAATTGCACA
1 AAATCAAAATTTCATGTATACAATTGCACA
42702635 TCAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATACAATTGCACA
Found at i:42707877 original size:18 final size:18
Alignment explanation
Indices: 42707856--42707893 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
42707846 TAAATTTTCG
42707856 AATTCAAAT-AACTCGAAT
1 AATTCAAATAAACT-GAAT
42707874 AATTCAAATAAACTGAAT
1 AATTCAAATAAACTGAAT
42707892 AA
1 AA
42707894 AATTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (18 bp):
AATTCAAATAAACTGAAT
Found at i:42710351 original size:40 final size:37
Alignment explanation
Indices: 42710307--42710393 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
42710297 TAAAAAGTAT
* *
42710307 TTATATTAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAA-A-TA-AATAAATAAAATAAATATTTTA
42710347 TTATATTAAAAAATAAATAAATAAAATAAATATTTTA
1 TTATATTAAAAAATAAATAAATAAAATAAATATTTTA
*
42710384 GTATATTAAA
1 TTATATTAAA
42710394 TATAAACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 29 0.66
38 2 0.05
39 1 0.02
40 12 0.27
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (37 bp):
TTATATTAAAAAATAAATAAATAAAATAAATATTTTA
Found at i:42713619 original size:29 final size:29
Alignment explanation
Indices: 42713574--42713632 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
42713564 GAGAATGGTT
*
42713574 TAATATATATTTGGTAATTAACTTTCATA
1 TAATATATATTTAGTAATTAACTTTCATA
42713603 TAATATATATTTAGTAATTAACTTTCATA
1 TAATATATATTTAGTAATTAACTTTCATA
42713632 T
1 T
42713633 TCTTTCGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (29 bp):
TAATATATATTTAGTAATTAACTTTCATA
Found at i:42716541 original size:31 final size:30
Alignment explanation
Indices: 42716485--42716542 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
42716475 TAGTAAAGTT
* *
42716485 AACAATAAAACAAGAGTTATACAATATCCA
1 AACAATAAAACAAGAATAATACAATATCCA
42716515 AACAATAACAACAA-AATAATAGCAATAT
1 AACAATAA-AACAAGAATAATA-CAATAT
42716543 AATAGCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (30 bp):
AACAATAAAACAAGAATAATACAATATCCA
Found at i:42716544 original size:22 final size:22
Alignment explanation
Indices: 42716518--42716595 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
42716508 ATATCCAAAC
42716518 AATAACAACAAAATAATAGCAA
1 AATAACAACAAAATAATAGCAA
* * * *
42716540 TATAATAGCGAAATAATAGCAA
1 AATAACAACAAAATAATAGCAA
* * * *
42716562 AACAACAACAAAATGACAGCGA
1 AATAACAACAAAATAATAGCAA
*
42716584 AACAACAACAAA
1 AATAACAACAAA
42716596 CGAACATTAC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.63, C:0.17, G:0.09, T:0.12
Consensus pattern (22 bp):
AATAACAACAAAATAATAGCAA
Found at i:42721255 original size:2 final size:2
Alignment explanation
Indices: 42721248--42721378 Score: 262
Period size: 2 Copynumber: 65.5 Consensus size: 2
42721238 AAATTCTTAA
42721248 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42721290 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42721332 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42721374 TC TC T
1 TC TC T
42721379 TTTCTAACTA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 129 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:42725715 original size:17 final size:17
Alignment explanation
Indices: 42725693--42725731 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
42725683 AGGTGGAGAA
* *
42725693 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
42725710 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
42725727 CTTGT
1 CTTGT
42725732 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:42726520 original size:6 final size:6
Alignment explanation
Indices: 42726495--42726576 Score: 54
Period size: 6 Copynumber: 14.8 Consensus size: 6
42726485 ACCAAATTAT
* **
42726495 TTTAAA ATTAAA TTT--A -TTAAA TTTAAA TTT-AA TTTAAA TTTGGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
42726539 TTT-AA TATAAA TTTAAA GTT--A TTATAAA TTT-AA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAA
42726577 TGTCCAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
3 2 0.03
4 3 0.05
5 15 0.26
6 35 0.60
7 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:42726530 original size:11 final size:11
Alignment explanation
Indices: 42726514--42726576 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
42726504 AAATTTATTA
42726514 AATTTAAATTT
1 AATTTAAATTT
42726525 AATTTAAATTT
1 AATTTAAATTT
* *
42726536 GGATTT-AATATA
1 -AATTTAAAT-TT
*
42726548 AATTTAAAGTT
1 AATTTAAATTT
42726559 -ATTATAAATTT
1 AATT-TAAATTT
42726570 AATTTAA
1 AATTTAA
42726577 TGTCCAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
10 3 0.07
11 28 0.68
12 10 0.24
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:42726531 original size:17 final size:17
Alignment explanation
Indices: 42726495--42726577 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
42726485 ACCAAATTAT
*
42726495 TTTAAAATTAAATTT-A
1 TTTAAATTTAAATTTAA
42726511 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
**
42726527 TTTAAATTTGGATTTAA
1 TTTAAATTTAAATTTAA
* *
42726544 TATAAATTTAAAGTT-A
1 TTTAAATTTAAATTTAA
42726560 TTATAAATTT-AATTTAA
1 TT-TAAATTTAAATTTAA
42726577 T
1 T
42726578 GTCCAAATAC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
15 13 0.24
16 7 0.13
17 34 0.63
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:42727198 original size:18 final size:18
Alignment explanation
Indices: 42727158--42727210 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 18
42727148 TGAGTACCTT
*
42727158 TAATATTATTATTAATTA
1 TAATATTATTATTAATAA
*
42727176 GAATATTATTTATTATAATAA
1 TAATATTA-TTA-T-TAATAA
*
42727197 TAATAATATTATTA
1 TAATATTATTATTA
42727211 TTATTAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 9 0.32
19 4 0.14
20 4 0.14
21 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATATTATTATTAATAA
Found at i:42727259 original size:22 final size:20
Alignment explanation
Indices: 42727225--42727266 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
42727215 TAAATGAGGG
42727225 TATTAAATAATATTAATAAT
1 TATTAAATAATATTAATAAT
42727245 TATTAATATTAATATTAATAAT
1 TATTAA-A-TAATATTAATAAT
42727267 AAATATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTAAATAATATTAATAAT
Found at i:42728271 original size:29 final size:28
Alignment explanation
Indices: 42728239--42728528 Score: 112
Period size: 29 Copynumber: 10.0 Consensus size: 28
42728229 TTGACCCAAA
** *
42728239 AACTTCCCAAAATTGTATTTTTACCCCC
1 AACTTCCCAAAATTCCATTTTTAACCCC
* *
42728267 GAACTTTCTAAAATTCCATTTTTAACCCC
1 -AACTTCCCAAAATTCCATTTTTAACCCC
* *
42728296 AATTTCACCAAAAATTACCA-TTTT-GCCCC
1 AACTTC-CC-AAAATT-CCATTTTTAACCCC
* * *
42728325 GAACTTTCCAAAATTCCATTTTTGATCCC
1 -AACTTCCCAAAATTCCATTTTTAACCCC
* *
42728354 AATTTCACCAAAAATTACCATTTTT--CCTTCA
1 AACTTC-CC-AAAATT-CCATTTTTAACC--CC
*
42728385 AAC-TCTCCAAAATTTCATTTTTAACCCC
1 AACTTC-CCAAAATTCCATTTTTAACCCC
* * * *
42728413 GATTTCACCAAAATTTACATTTTT-ACCCTTA
1 AACTTC-CCAAAA-TTCCATTTTTAACCC--C
* * *
42728444 AACTTTCCAAACTTCCA-TTTTGACCCC
1 AACTTCCCAAAATTCCATTTTTAACCCC
* *
42728471 GATTTCACCAAAAATTACCA-TTTT-ACCCC
1 AACTTC-CC-AAAATT-CCATTTTTAACCCC
* * *
42728500 TAAACTTTCTAAAATTTCATTTTTAACCC
1 --AACTTCCCAAAATTCCATTTTTAACCC
42728529 TAATTTTATC
Statistics
Matches: 195, Mismatches: 41, Indels: 49
0.68 0.14 0.17
Matches are distributed among these distances:
27 6 0.03
28 35 0.18
29 82 0.42
30 52 0.27
31 20 0.10
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.37
Consensus pattern (28 bp):
AACTTCCCAAAATTCCATTTTTAACCCC
Found at i:42728556 original size:59 final size:59
Alignment explanation
Indices: 42728257--42728557 Score: 358
Period size: 58 Copynumber: 5.1 Consensus size: 59
42728247 AAAATTGTAT
** *
42728257 TTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCA
* * * *
42728316 TTTTGCCCC-GAACTTTCCAAAATTCCATTTTTGATCCCAATTTCACCAAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCA
* * * * * *
42728374 TTTT-TCCTTCAAACTCTCCAAAATTTCATTTTTAACCCCGATTTCACCAAAATTTA-CA
1 TTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCA
* * * *
42728432 TTTTTACCCTTAAACTTTCCAAACTTCCA-TTTTGACCCCGATTTCACCAAAAATTACCA
1 -TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCA
* * * * *
42728491 TTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCCTAATTTTATCAAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCA
42728550 TTTTACCC
1 TTTTACCC
42728558 TCGAAAGTTT
Statistics
Matches: 208, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
57 2 0.01
58 101 0.49
59 101 0.49
60 4 0.02
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (59 bp):
TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCA
Found at i:42728557 original size:29 final size:28
Alignment explanation
Indices: 42728479--42728558 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
42728469 CCGATTTCAC
42728479 CAAAAATTACCATTTTACCCCTAAACTTT
1 CAAAAATTACCATTTTA-CCCTAAACTTT
* * **
42728508 CTAAAATT-TCATTTTTAACCCTAATTTTAT
1 CAAAAATTACCA-TTTT-ACCCTAAACTT-T
42728538 CAAAAATTACCATTTTACCCT
1 CAAAAATTACCATTTTACCCT
42728559 CGAAAGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 2 0.05
29 24 0.59
30 13 0.32
31 2 0.05
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (28 bp):
CAAAAATTACCATTTTACCCTAAACTTT
Found at i:42728588 original size:117 final size:117
Alignment explanation
Indices: 42728257--42728573 Score: 385
Period size: 117 Copynumber: 2.7 Consensus size: 117
42728247 AAAATTGTAT
** * *
42728257 TTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTGC
1 TTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* *
42728322 CC-CG-AACTTTCCAAAATTCCATTTTTGATCCCAATTTCACCAAAAATTACCA
66 CCTCGAAACTTT-CAAAATTCCA-TTTTGACCCCGATTTCACCAAAAATTACCA
* * * * * *
42728374 TTTT-TCCTTCAAACTCTCCAAAATTTCATTTTTAACCCCGATTTCACCAAAATTTA-CATTTTT
1 TTTTACCCCT-AAACTTTCTAAAATTTCATTTTTAACCCCAATTTCACCAAAAATTACCA-TTTT
* *
42728437 ACCCT-TAAACTTTCCAAACTTCCATTTTGACCCCGATTTCACCAAAAATTACCA
64 ACCCTCGAAACTTT-CAAAATTCCATTTTGACCCCGATTTCACCAAAAATTACCA
* * *
42728491 TTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCCTAATTTTATCAAAAATTACCATTTTAC
1 TTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
*
42728556 CCTCGAAAGTTT-AAAATT
66 CCTCGAAACTTTCAAAATT
42728574 ACTATTTTCC
Statistics
Matches: 167, Mismatches: 26, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
116 9 0.05
117 131 0.78
118 27 0.16
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (117 bp):
TTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
CCTCGAAACTTTCAAAATTCCATTTTGACCCCGATTTCACCAAAAATTACCA
Found at i:42734147 original size:24 final size:24
Alignment explanation
Indices: 42734099--42734165 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
42734089 GAACTCAGAT
*
42734099 ACAATGAAGAAAAACAAATAA-AAAAA
1 ACAA-GAAGAAAAA-AAA-AAGCAAAA
*
42734125 AGAAG-AGAAAAAAAAAAGCAAAA
1 ACAAGAAGAAAAAAAAAAGCAAAA
*
42734148 ACAAGAAGAAAAATAAAA
1 ACAAGAAGAAAAAAAAAA
42734166 TAGAAAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.06
23 11 0.31
24 18 0.51
25 1 0.03
26 3 0.09
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (24 bp):
ACAAGAAGAAAAAAAAAAGCAAAA
Found at i:42735526 original size:50 final size:49
Alignment explanation
Indices: 42735462--42735964 Score: 238
Period size: 50 Copynumber: 10.3 Consensus size: 49
42735452 AAAACATAAA
42735462 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATGG
1 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA-AAGCATGG
* * * ** * * *
42735512 AAGGGAAAGATCTAAGATCGTAACGGCGGATTC-AATACCGCAAA-AATAGAA
1 AAGGGAAAGGTCTAAG-TCGCAACGGCGGA-CCGTGTACCTCAAAGCAT-G-G
*
42735563 AAGGGAAAGGTTTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATGG
1 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA-AAGCATGG
* * * * * * * ***
42735613 AAGGGAAAGATTTAAGACCGCAATGGCAGATCC-AGTACCGCCAAAGCACAT
1 AAGGGAAAGGTCTAAG-TCGCAACGGCGGA-CCGTGTACC-TCAAAGCATGG
* **** **
42735664 AAGGGAAAGGTCTAAGTCGCAACGGCGAACCGTGTAAGGGAAAG-ATCT
1 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAAAGCATGG
** * * * ***
42735712 AA--G-ACCG-C-AA-TGGCAGATC--CAGTACC--G---C-CAAAACACAA
1 AAGGGAAAGGTCTAAGTCGCA-A-CGGC-GGACCGTGTACCTCAAAGCATGG
*
42735750 AAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGCAT-G
1 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA-AAGCATGG
* * * * * * * ***
42735799 AAGGGAAAGATCTAAGATTGCAATGGCAGATCC-AGTACCGCAAAAACACAA
1 AAGGGAAAGGTCTAAG-TCGCAACGGCGGA-CCGTGTACCTC-AAAGCATGG
* *
42735850 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAGACATGA
1 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAAAG-CATGG
* * *
42735900 AAGGGAAAGATCTAAGTCGCAATGGCGGATCGTGTACCTCAGAAGCAT-G
1 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA-AAGCATGG
*
42735949 AAGGGAAAGATCTAAG
1 AAGGGAAAGGTCTAAG
42735965 GCCACAATGA
Statistics
Matches: 335, Mismatches: 81, Indels: 75
0.68 0.16 0.15
Matches are distributed among these distances:
37 3 0.01
38 3 0.01
40 1 0.00
41 3 0.01
42 7 0.02
43 14 0.04
44 7 0.02
45 3 0.01
46 1 0.00
48 5 0.01
49 46 0.14
50 146 0.44
51 89 0.27
52 7 0.02
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.14
Consensus pattern (49 bp):
AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAAAGCATGG
Found at i:42735652 original size:101 final size:100
Alignment explanation
Indices: 42735452--42735699 Score: 352
Period size: 101 Copynumber: 2.5 Consensus size: 100
42735442 AGTACCACAA
42735452 AAAACATAAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATGGAAGGG
1 AAAA-ATAAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATGGAAGGG
* * * *
42735517 AAAGATCTAAGATCGTAACGGCGGATTCAATACCGC
65 AAAGATCTAAGACCGCAACGGCAGATCCAATACCGC
*
42735553 AAAAATAGAAAAGGGAAAGGTTTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATGGAAGGG
1 AAAAATA-AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATGGAAGGG
* * *
42735618 AAAGATTTAAGACCGCAATGGCAGATCCAGTACCGC
65 AAAGATCTAAGACCGCAACGGCAGATCCAATACCGC
* ** * *
42735654 CAAAGCACATAAGGGAAAGGTCTAAGTCGCAACGGCGAACCGTGTA
1 AAAAATA-AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTA
42735700 AGGGAAAGAT
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 3 0.02
101 128 0.98
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.15
Consensus pattern (100 bp):
AAAAATAAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATGGAAGGGA
AAGATCTAAGACCGCAACGGCAGATCCAATACCGC
Found at i:42735758 original size:86 final size:86
Alignment explanation
Indices: 42735613--42735785 Score: 301
Period size: 86 Copynumber: 2.0 Consensus size: 86
42735603 AGAAGCATGG
* * *
42735613 AAGGGAAAGATTTAAGACCGCAATGGCAGATCCAGTACCGCCAAAGCACATAAGGGAAAGGTCTA
1 AAGGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCCAAAACACAAAAGGGAAAGGTCTA
*
42735678 AGTCGCAACGGCGAACCGTGT
66 AGTCGCAACGACGAACCGTGT
42735699 AAGGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCCAAAACACAAAAGGGAAAGGTCTA
1 AAGGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCCAAAACACAAAAGGGAAAGGTCTA
*
42735764 AGTCGCAACGACGGACCGTGT
66 AGTCGCAACGACGAACCGTGT
42735785 A
1 A
42735786 CCTCAGAAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.13
Consensus pattern (86 bp):
AAGGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCCAAAACACAAAAGGGAAAGGTCTA
AGTCGCAACGACGAACCGTGT
Found at i:42735872 original size:100 final size:101
Alignment explanation
Indices: 42735699--42735930 Score: 389
Period size: 100 Copynumber: 2.3 Consensus size: 101
42735689 CGAACCGTGT
* *
42735699 AAGGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCCAAAACACAAAAGGGAAAGGTCTA
1 AAGGGAAAGATCTAAGATCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTA
42735764 AGTCGCAACGACGGACCGTGTACCTCAGA-AGCATG-
66 AGTCGCAACGACGGACCGTGTACCTCAGAGA-CATGA
*
42735799 AAGGGAAAGATCTAAGATTGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTA
1 AAGGGAAAGATCTAAGATCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTA
*
42735864 AGTCGCAACGGCGGACCGTGTACCTCAGAGACATGA
66 AGTCGCAACGACGGACCGTGTACCTCAGAGACATGA
*
42735900 AAGGGAAAGATCTAAG-TCGCAATGGCGGATC
1 AAGGGAAAGATCTAAGATCGCAATGGCAGATC
42735931 GTGTACCTCA
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
100 107 0.86
101 17 0.14
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (101 bp):
AAGGGAAAGATCTAAGATCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTA
AGTCGCAACGACGGACCGTGTACCTCAGAGACATGA
Found at i:42735973 original size:50 final size:49
Alignment explanation
Indices: 42735750--42735964 Score: 245
Period size: 50 Copynumber: 4.3 Consensus size: 49
42735740 CAAAACACAA
* * *
42735750 AAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGCATG
1 AAGGGAAAGATCTAAGTCGCAATGGCGGACCGTGTACCTCAGAAGCATG
* * * * * * **
42735799 AAGGGAAAGATCTAAGATTGCAATGGCAGATCC-AGTACCGCAAAAACACAA
1 AAGGGAAAGATCTAAG-TCGCAATGGCGGA-CCGTGTACCTCAGAAGCA-TG
* *
42735850 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAG-AGACATG
1 AAGGGAAAGATCTAAGTCGCAATGGCGGACCGTGTACCTCAGAAG-CATG
*
42735899 AAAGGGAAAGATCTAAGTCGCAATGGCGGATCGTGTACCTCAGAAGCATG
1 -AAGGGAAAGATCTAAGTCGCAATGGCGGACCGTGTACCTCAGAAGCATG
42735949 AAGGGAAAGATCTAAG
1 AAGGGAAAGATCTAAG
42735965 GCCACAATGA
Statistics
Matches: 135, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
49 34 0.25
50 82 0.61
51 19 0.14
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.15
Consensus pattern (49 bp):
AAGGGAAAGATCTAAGTCGCAATGGCGGACCGTGTACCTCAGAAGCATG
Found at i:42735993 original size:150 final size:151
Alignment explanation
Indices: 42735749--42736054 Score: 436
Period size: 150 Copynumber: 2.0 Consensus size: 151
42735739 CCAAAACACA
*
42735749 AAAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGCATGAAGGGAAAGATCTAA
1 AAAGGGAAAGATCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGCATGAAGGGAAAGATCTAA
*** * * * *
42735814 GATTGCAATGGCAGATCCAGTACCGCAAAAACAC-AAAAGGGAAAGGTCTAAGTCGCAACGGCGG
66 GACCACAATGACAGATCCAGTACCACAAAAACACAAAAAGGGAAAGGTCTAAGTCGCAACGACGA
*
42735878 A-CCGTGTACCTCAGAGACATG
131 ACCCGT-TACCTCAGAAACATG
* * *
42735899 AAAGGGAAAGATCTAAGTCGCAATGGCGGATCGTGTACCTCAGAAGCATGAAGGGAAAGATCTAA
1 AAAGGGAAAGATCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGCATGAAGGGAAAGATCTAA
* * * *
42735964 GGCCACAATGACATATCCAGTACCACAAAAATACAAAAAGGGAAAGGTTTAAGTCGCAACGACGA
66 GACCACAATGACAGATCCAGTACCACAAAAACACAAAAAGGGAAAGGTCTAAGTCGCAACGACGA
*
42736029 ACCCGTTACCTTAGAAACATG
131 ACCCGTTACCTCAGAAACATG
42736050 AAAGG
1 AAAGG
42736055 TCAAACCCAC
Statistics
Matches: 137, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
150 87 0.64
151 46 0.34
152 4 0.03
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (151 bp):
AAAGGGAAAGATCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGCATGAAGGGAAAGATCTAA
GACCACAATGACAGATCCAGTACCACAAAAACACAAAAAGGGAAAGGTCTAAGTCGCAACGACGA
ACCCGTTACCTCAGAAACATG
Found at i:42736425 original size:11 final size:11
Alignment explanation
Indices: 42736413--42736505 Score: 68
Period size: 11 Copynumber: 8.5 Consensus size: 11
42736403 ACCAAATTAT
*
42736413 TTTAAATTTAT
1 TTTAAATTTAA
*
42736424 TTTAAAATTAAA
1 TTT-AAATTTAA
*
42736436 TTT--ATTAAA
1 TTTAAATTTAA
42736445 TTTAAATTTAA
1 TTTAAATTTAA
*
42736456 TTTAAATTTGGA
1 TTTAAATTT-AA
*
42736468 TTT-AATATAAA
1 TTTAAAT-TTAA
*
42736479 TTTAAAGTT-A
1 TTTAAATTTAA
42736489 TTATAAATTTAA
1 TT-TAAATTTAA
42736501 TTTAA
1 TTTAA
42736506 TGTCCAAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
9 9 0.14
10 3 0.05
11 34 0.52
12 19 0.29
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:42736449 original size:6 final size:6
Alignment explanation
Indices: 42736413--42736505 Score: 60
Period size: 6 Copynumber: 16.8 Consensus size: 6
42736403 ACCAAATTAT
* *
42736413 TTTAAA TTT-AT TTTAAA ATTAAA TTT--A -TTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
42736456 TTTAAA TTTGGA TTT-AA TATAAA TTTAAA GTT--A TTATAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
42736501 TTTAA
1 TTTAA
42736506 TGTCCAAATA
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
3 2 0.03
4 3 0.05
5 19 0.29
6 39 0.59
7 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:42736462 original size:17 final size:17
Alignment explanation
Indices: 42736413--42736506 Score: 97
Period size: 17 Copynumber: 5.7 Consensus size: 17
42736403 ACCAAATTAT
*
42736413 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
*
42736430 ATTAAATTT-A-TTAAA
1 TTTAAATTTAATTTAAA
42736445 TTTAAATTTAATTTAAA
1 TTTAAATTTAATTTAAA
** *
42736462 TTTGGATTTAATATAAA
1 TTTAAATTTAATTTAAA
*
42736479 TTTAAAGTT-ATTATAAA
1 TTTAAATTTAATT-TAAA
42736496 TTT-AATTTAAT
1 TTTAAATTTAAT
42736507 GTCCAAATAC
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
15 13 0.21
16 7 0.11
17 42 0.68
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:42738313 original size:29 final size:29
Alignment explanation
Indices: 42738261--42738485 Score: 112
Period size: 29 Copynumber: 7.6 Consensus size: 29
42738251 AAATTATCCA
* *
42738261 AAAATTACA-TTTTGACCCAAAAAC-TTCC
1 AAAATTCCATTTTTGACCC-CAAACTTTCC
* *
42738289 TAAAATTGCATTTTTGCCCCCAAACTTTCC
1 -AAAATTCCATTTTTGACCCCAAACTTTCC
42738319 AAAATTCCATTTTTGACCCC-AA-TTTCACC
1 AAAATTCCATTTTTGACCCCAAACTTT--CC
*
42738348 AAAAATTACCA-TTTT-ACCCCCGAACTTTCC
1 -AAAATT-CCATTTTTGA-CCCCAAACTTTCC
* ***
42738378 AAAATTCCATTTTT-AACCTTGA-TTTCACC
1 AAAATTCCATTTTTGACCCCAAACTTT--CC
* *
42738407 AAAAATTACCATTTTTGACCTC-GA-TTTCACC
1 -AAAATT-CCATTTTTGACCCCAAACTTT--CC
* *
42738438 AAAAATTACATTTTT-ACCCTCAAACTTTCA
1 -AAAATTCCATTTTTGACCC-CAAACTTTCC
*
42738468 AAAATTTCATTTTTGACC
1 AAAATTCCATTTTTGACC
42738486 TTGATTTTAC
Statistics
Matches: 160, Mismatches: 17, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
27 6 0.04
28 8 0.05
29 62 0.39
30 46 0.29
31 30 0.19
32 8 0.05
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTGACCCCAAACTTTCC
Found at i:42738333 original size:59 final size:58
Alignment explanation
Indices: 42738261--42738421 Score: 148
Period size: 59 Copynumber: 2.7 Consensus size: 58
42738251 AAATTATCCA
* * * *
42738261 AAAATTACA-TTTTGACCCAAAAACTT-CCTAAAATT-GCATTTTTGCCCCCAAACTTTCC
1 AAAATTCCATTTTTGACCC--AAACTTACCAAAAATTACCA-TTTTACCCCCAAACTTTCC
* * *
42738319 AAAATTCCATTTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTGACCCAAACTT-ACCAAAAATTACCATTTTACCCCCAAACTTTCC
* *** *
42738378 AAAATTCCATTTTTAACCTTGATTTCACCAAAAATTACCATTTT
1 AAAATTCCATTTTTGACCCAAACTT-ACCAAAAATTACCATTTT
42738422 TGACCTCGAT
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
57 4 0.05
58 8 0.09
59 74 0.84
60 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCAAACTTACCAAAAATTACCATTTTACCCCCAAACTTTCC
Found at i:42738444 original size:90 final size:90
Alignment explanation
Indices: 42738319--42738511 Score: 291
Period size: 90 Copynumber: 2.2 Consensus size: 90
42738309 CAAACTTTCC
* *
42738319 AAAATT-CCATTTTTGACCCCAATTTCACCAAAAATTACCA-TTTTACCCCCGAACTTTCCAAAA
1 AAAATTACCATTTTTGACCCCAATTTCACCAAAAATTA-CATTTTTACCCCCAAACTTTCAAAAA
42738382 TTCCATTTTTAACCTTGATTTCACCA
65 TTCCATTTTTAACCTTGATTTCACCA
* * *
42738408 AAAATTACCATTTTTGACCTCGATTTCACCAAAAATTACATTTTTACCCTCAAACTTTCAAAAAT
1 AAAATTACCATTTTTGACCCCAATTTCACCAAAAATTACATTTTTACCCCCAAACTTTCAAAAAT
* * *
42738473 TTCATTTTTGACCTTGATTTTACCA
66 TCCATTTTTAACCTTGATTTCACCA
42738498 AAAATTACCATTTT
1 AAAATTACCATTTT
42738512 GTCCCCGAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
89 8 0.09
90 86 0.91
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (90 bp):
AAAATTACCATTTTTGACCCCAATTTCACCAAAAATTACATTTTTACCCCCAAACTTTCAAAAAT
TCCATTTTTAACCTTGATTTCACCA
Found at i:42738512 original size:30 final size:31
Alignment explanation
Indices: 42738319--42738511 Score: 160
Period size: 30 Copynumber: 6.5 Consensus size: 31
42738309 CAAACTTTCC
* *
42738319 AAAATT-CCATTTTTGACCCCAATTTCACCA
1 AAAATTACCATTTTTGACCTCGATTTCACCA
*
42738349 AAAATTACCA-TTTT-ACCCCCGAACTTT--CC-
1 AAAATTACCATTTTTGA-CCTCG-A-TTTCACCA
* *
42738378 AAAATT-CCATTTTTAACCTTGATTTCACCA
1 AAAATTACCATTTTTGACCTCGATTTCACCA
42738408 AAAATTACCATTTTTGACCTCGATTTCACCA
1 AAAATTACCATTTTTGACCTCGATTTCACCA
*
42738439 AAAATTA-CATTTTT-ACCCTCAAACTTT---CA
1 AAAATTACCATTTTTGA-CCTC-GA-TTTCACCA
* * *
42738468 AAAATT-TCATTTTTGACCTTGATTTTACCA
1 AAAATTACCATTTTTGACCTCGATTTCACCA
42738498 AAAATTACCATTTT
1 AAAATTACCATTTT
42738512 GTCCCCGAAA
Statistics
Matches: 135, Mismatches: 9, Indels: 37
0.75 0.05 0.20
Matches are distributed among these distances:
27 6 0.04
28 5 0.04
29 35 0.26
30 43 0.32
31 40 0.30
32 6 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (31 bp):
AAAATTACCATTTTTGACCTCGATTTCACCA
Found at i:42738529 original size:59 final size:60
Alignment explanation
Indices: 42738405--42738539 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 60
42738395 CTTGATTTCA
*
42738405 CCAAAAATTACCATTTTTGACCTCGATTTCACCAAAAATTACATTTTTACCCTCAAACTT
1 CCAAAAATTACCATTTTTGACCTCGATTTCACCAAAAATTACATTTTTACCCTCAAACGT
* * * *
42738465 TCAAAAATT-TCATTTTTGACCTTGATTTTACCAAAAATTACCATTTTGT-CCC-CGAAA-GT
1 CCAAAAATTACCATTTTTGACCTCGATTTCACCAAAAATTA-CATTTT-TACCCTC-AAACGT
*
42738524 CC-AAAATTACTATTTT
1 CCAAAAATTACCATTTT
42738540 ACCCCCGAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
58 6 0.10
59 36 0.57
60 20 0.32
61 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (60 bp):
CCAAAAATTACCATTTTTGACCTCGATTTCACCAAAAATTACATTTTTACCCTCAAACGT
Found at i:42745491 original size:21 final size:21
Alignment explanation
Indices: 42745448--42745514 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 21
42745438 ATTTAATTTA
*
42745448 TATTTT-ATTAAAAACAGTTAAT
1 TATTTTAATT-AAAATA-TTAAT
42745470 TATTTTAATTAAAATATTAAT
1 TATTTTAATTAAAATATTAAT
*
42745491 T-TTTTAATT-TAATATTAAT
1 TATTTTAATTAAAATATTAAT
42745510 TATTT
1 TATTT
42745515 CACGTTCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.24
20 11 0.27
21 6 0.15
22 11 0.27
23 3 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TATTTTAATTAAAATATTAAT
Found at i:42745494 original size:19 final size:19
Alignment explanation
Indices: 42745465--42745510 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
42745455 TTAAAAACAG
42745465 TTAATTATTTTAATTAAAATA
1 TTAATT-TTTTAATT-AAATA
*
42745486 TTAATTTTTTAATTTAATA
1 TTAATTTTTTAATTAAATA
42745505 TTAATT
1 TTAATT
42745511 ATTTCACGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATTTTTTAATTAAATA
Found at i:42748315 original size:16 final size:16
Alignment explanation
Indices: 42748268--42748385 Score: 83
Period size: 17 Copynumber: 6.9 Consensus size: 16
42748258 GTTTTTTTTT
*
42748268 AATTTATTTTAAAATTA
1 AATTTA-TTTAAATTTA
* *
42748285 AATTTGATATGAATTTA
1 AATTT-ATTTAAATTTA
*
42748302 GATTTATTTAAATTTA
1 AATTTATTTAAATTTA
*
42748318 AATTTAAATTAAACTTTA
1 AATTT-ATTTAAA-TTTA
* * *
42748336 AATTTGAATTTGAGTCTA
1 AATTT--ATTTAAATTTA
42748354 AATTTATTTTAAATTTAA
1 AATTTA-TTTAAATTT-A
*
42748372 AATTAATTTAAATT
1 AATTTATTTAAATT
42748386 AAAGTCCAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
16 14 0.18
17 36 0.46
18 24 0.30
19 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:42748316 original size:6 final size:6
Alignment explanation
Indices: 42748307--42748385 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
42748297 ATTTAGATTT
* * * *
42748307 ATTTAA ATTTAA ATTTAA A-TTAA ACTTTAA ATTTGA ATTTGA GTCTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA
* *
42748355 ATTT-A TTTTAA ATTTAA AATT-A ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
42748386 AAAGTCCAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 13 0.22
6 41 0.69
7 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (6 bp):
ATTTAA
Found at i:42749040 original size:16 final size:15
Alignment explanation
Indices: 42749012--42749046 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
42749002 TTCATTAGCA
42749012 TTAATAATAATATCT
1 TTAATAATAATATCT
*
42749027 TTAATAATTAATATGT
1 TTAATAA-TAATATCT
42749043 TTAA
1 TTAA
42749047 ATAAAGTATA
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:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
TTAATAATAATATCT
Found at i:42750106 original size:30 final size:30
Alignment explanation
Indices: 42750070--42750151 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
42750060 AAATTGTCCA
* **
42750070 AAAATTACATTTCAACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
42750100 AAAATTATATTTTTACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
42750130 AAAATTACATTTTAACCCCAAA
1 AAAATTACATTTTAACCCCAAA
42750152 CTTCCCTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:42750213 original size:59 final size:56
Alignment explanation
Indices: 42750128--42750316 Score: 159
Period size: 59 Copynumber: 3.3 Consensus size: 56
42750118 CAAAACTTTT
* * * *
42750128 CCAAAATTA-CATTTTAACCCCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTT-GCCTCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCA
* * * * ** **
42750185 CCAAAACTTACCGTTTTGCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGATTTTG
1 CCAAAA-TTACCATTTTGCCT-CAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCA
* *
42750244 CCAAAATTTACCATTTTATTCCTCAAACTTTCCAAATTCCA-TTTTAGCCCCGATTTCA
1 CCAAAA-TTACCA-TTT-TGCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCA
42750302 -CAAAATTACCATTTT
1 CCAAAATTACCATTTT
42750317 ACCCCTAAAA
Statistics
Matches: 103, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
54 1 0.01
55 3 0.03
56 6 0.06
57 11 0.11
58 16 0.16
59 50 0.49
60 12 0.12
61 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.37
Consensus pattern (56 bp):
CCAAAATTACCATTTTGCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCA
Found at i:42762186 original size:76 final size:75
Alignment explanation
Indices: 42762060--42762864 Score: 970
Period size: 76 Copynumber: 11.0 Consensus size: 75
42762050 CACCAAGATT
* * * * *
42762060 ATTTCTTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGCCTTTATCTCTAAAATTGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
42762125 AGAGCAACGTC
66 AGAGCAA-GTC
*
42762136 ATTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
42762201 AGAGCAAGATC
66 AGAGCAAG-TC
* *
42762212 A-TGCCATATCCTCTTGAAATTGAAGTAGAG-TGG--AACACGTTTTTATCTCTGAAATTGAAGT
1 ATTTCC-TATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGT
*
42762273 AGGAGCAAGATC
65 AAGAGCAAG-TC
* *
42762285 -TTTCCCTGTCCTCTTGAAATTGAAGTAGAG-TGG--AACACGTCTTTACCTCTGAAATTGAAGT
1 ATTT-CCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGT
* *
42762346 AGGAGCGAGATC
65 AAGAGCAAG-TC
* * *
42762358 TTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
42762422 AGAGCAACGTC
66 AGAGCAA-GTC
42762433 A----C---CCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
42762491 AGAGCAACGTC
66 AGAGCAA-GTC
42762502 A----C---CCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
42762560 AGAGCAA--C
66 AGAGCAAGTC
* * * *
42762568 --GT-C-ATCCTCTTGAAATTGAAGTAGAG-TGGATAACATGTCTTTACCTCT-AAAATGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
*
42762627 AGAGCAAAATC
66 AGAGC-AAGTC
* *
42762638 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
*
42762703 AGAGCAAAATC
66 AGAGC-AAGTC
* * *
42762714 ATTTCCTATCCTCTTGAAATTAAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
42762779 AGAGCAAGATC
66 AGAGCAAG-TC
* * * * * * *
42762790 ATTTCCTATCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTTTGAAATTGAAG
1 ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTAT--CTCTGAAATTGAAG
42762855 TAAGAGCAAG
64 TAAGAGCAAG
42762865 ATGGAGCACC
Statistics
Matches: 662, Mismatches: 42, Indels: 48
0.88 0.06 0.06
Matches are distributed among these distances:
66 1 0.00
67 16 0.02
68 42 0.06
69 130 0.20
70 1 0.00
71 1 0.00
72 1 0.00
73 130 0.20
74 28 0.04
75 62 0.09
76 227 0.34
78 23 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (75 bp):
ATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
AGAGCAAGTC
Found at i:42762192 original size:38 final size:37
Alignment explanation
Indices: 42762150--42762778 Score: 277
Period size: 38 Copynumber: 17.4 Consensus size: 37
42762140 CCTATCCGCT
42762150 TGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTC
* * * **
42762188 TGAAATTGAAGTA-AGAGCA-AGATCATG-CCATATCCTC
1 TGAAATTGAAGTAGAGTGGATA-A-CACGTCTTTAT-CTC
*
42762225 TTGAAATTGAAGTAGAGTGG--AACACGTTTTTATCTC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
* * ** ** *
42762261 TGAAATTGAAGTAG-GAGCA-AGATC-TTTCCCTGTCCTC
1 TGAAATTGAAGTAGAGTGGATA-A-CACGTCTTTAT-CTC
*
42762298 TTGAAATTGAAGTAGAGTGG--AACACGTCTTTACCTC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
* *** * *
42762334 TGAAATTGAAGTAGGAGCGAGAT--CTTTTC-CTATCCGC
1 TGAAATTGAAGTA-GAGTG-GATAACACGTCTTTAT-CTC
*
42762371 TTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
** ****
42762409 TGAAATTGAAGTA-A---GAGCA-ACGTCACCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
42762440 TGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTC
** ****
42762478 TGAAATTGAAGTA-A---GAGCA-ACGTCACCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
42762509 TGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTC
** * **
42762547 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
* *
42762578 TGAAATTGAAGTAGAGTGGATAACATGTCTTTACCTC
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
* * * * ** *
42762615 T-AAAATGAAGTA-AGAGCAAAATCATTTC-CTATCCTC
1 TGAAATTGAAGTAGAGTGGATAA-CACGTCTTTAT-CTC
* *
42762651 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
1 -TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTC
* * * ** *
42762690 TGAAATTGAAGTA-AGAGCAAAATCATTTC-CTATCCTC
1 TGAAATTGAAGTAGAGTGGATAA-CACGTCTTTAT-CTC
* * *
42762727 TTGAAATTAAAGTAGAGTTGGATAACAAGTCTTCATCTC
1 -TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTC
42762766 TGAAATTGAAGTA
1 TGAAATTGAAGTA
42762779 AGAGCAAGAT
Statistics
Matches: 429, Mismatches: 107, Indels: 110
0.66 0.17 0.17
Matches are distributed among these distances:
31 39 0.09
32 29 0.07
33 9 0.02
34 2 0.00
35 40 0.09
36 68 0.16
37 72 0.17
38 133 0.31
39 25 0.06
40 12 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (37 bp):
TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
Found at i:42762444 original size:31 final size:31
Alignment explanation
Indices: 42762402--42762590 Score: 130
Period size: 31 Copynumber: 5.7 Consensus size: 31
42762392 TAACACGTCT
42762402 TCAT-CTC-TGAAATTGAAGTAAGAGCAACG
1 TCATCCTCTTGAAATTGAAGTAAGAGCAACG
* **
42762431 TCACCCTCTTGAAATTGAAGTAGAGTTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A----GAGCA-ACG
* **
42762468 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
* **
42762500 TCACCCTCTTGAAATTGAAGTAGAGTTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A----GAGCA-ACG
* **
42762537 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
42762569 TCATCCTCTTGAAATTGAAGTA
1 TCATCCTCTTGAAATTGAAGTA
42762591 GAGTGGATAA
Statistics
Matches: 120, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
29 3 0.03
30 3 0.03
31 39 0.32
32 19 0.16
33 6 0.05
36 6 0.05
37 18 0.15
38 26 0.22
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (31 bp):
TCATCCTCTTGAAATTGAAGTAAGAGCAACG
Found at i:42762477 original size:69 final size:69
Alignment explanation
Indices: 42762365--42762785 Score: 569
Period size: 69 Copynumber: 5.9 Consensus size: 69
42762355 ATCTTTTCCT
*
42762365 ATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
42762429 CGTC
66 CGTC
* *
42762433 ACCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
42762498 CGTC
66 CGTC
* *
42762502 ACCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
42762567 CGTC
66 CGTC
* * * *
42762571 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACATGTCTTTACCTCT-AAAATGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC--
*
42762634 AATCATTTCC
64 AA-C--GT-C
*
42762644 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 -ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC-
*
42762709 AAATCATTTCC
64 -AA-C--GT-C
* *
42762720 TATCCTCTTGAAATTAAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 -ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
42762785 A
65 A
42762786 GATCATTTCC
Statistics
Matches: 330, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
67 15 0.05
68 41 0.12
69 137 0.42
70 1 0.00
72 1 0.00
73 1 0.00
74 25 0.08
75 19 0.06
76 90 0.27
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (69 bp):
ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
CGTC
Found at i:42762808 original size:38 final size:37
Alignment explanation
Indices: 42762620--42762825 Score: 159
Period size: 38 Copynumber: 5.4 Consensus size: 37
42762610 ACCTCTAAAA
*
42762620 TGAAGTAAGAGCAAAATCATTTCCTATCCTCTTGAAAT
1 TGAAGT-AGAGCAAGATCATTTCCTATCCTCTTGAAAT
*** ** *
42762658 TGAAGTAGAGTTGGATAACAAGT-CT-TCATCTCTGAAAT
1 TGAAGTAGAGCAAGAT--CATTTCCTATCCTCT-TGAAAT
*
42762696 TGAAGTAAGAGCAAAATCATTTCCTATCCTCTTGAAAT
1 TGAAGT-AGAGCAAGATCATTTCCTATCCTCTTGAAAT
* *** ** *
42762734 TAAAGTAGAGTTGGATAACAAGT-CT-TCATCTCTGAAAT
1 TGAAGTAGAGCAAGAT--CATTTCCTATCCTCT-TGAAAT
42762772 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAAT
1 TGAAGT-AGAGCAAGATCATTTCCTATCCTCTTGAAAT
*
42762810 TGAAGTAGAGCTAGAT
1 TGAAGTAGAGCAAGAT
42762826 ATCAAGCCTT
Statistics
Matches: 126, Mismatches: 30, Indels: 25
0.70 0.17 0.14
Matches are distributed among these distances:
37 37 0.29
38 60 0.48
39 29 0.23
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (37 bp):
TGAAGTAGAGCAAGATCATTTCCTATCCTCTTGAAAT
Found at i:42762854 original size:40 final size:40
Alignment explanation
Indices: 42762803--42762947 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 40
42762793 TCCTATCCTC
42762803 TTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCT
1 TTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCT
* * *
42762843 TTGAAATTGAAGTAAGAGCAAGATGGAGCACCGACATCTTT-TCCTATCCT
1 TTGAAATTGAAGT-AGAGCTAGAT--ATCA-AG-C--CTTTGT-C---CCT
* *
42762893 CTTGAAATTGAAGTAGAGTTGGATATCAAGCCTTTGTCCCT
1 -TTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCT
*
42762934 CTGAAATTGAAGTA
1 TTGAAATTGAAGTA
42762948 AGAGTAAGAT
Statistics
Matches: 83, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
40 26 0.31
41 12 0.14
43 3 0.04
44 6 0.07
45 2 0.02
46 2 0.02
47 6 0.07
48 3 0.04
50 10 0.12
51 13 0.16
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCT
Found at i:42762946 original size:91 final size:91
Alignment explanation
Indices: 42762791--42762958 Score: 300
Period size: 91 Copynumber: 1.8 Consensus size: 91
42762781 AGCAAGATCA
*
42762791 TTTCCTATCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTTTGAAATTGAAGT
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTCTGAAATTGAAGT
42762856 AAGAGCAAGATGGAGCACCGACATCT
66 AAGAGCAAGATGGAGCACCGACATCT
* *
42762882 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGT
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTCTGAAATTGAAGT
*
42762947 AAGAGTAAGATG
66 AAGAGCAAGATG
42762959 AAACACCAAC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (91 bp):
TTTCCTATCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTCTGAAATTGAAGT
AAGAGCAAGATGGAGCACCGACATCT
Found at i:42762985 original size:91 final size:91
Alignment explanation
Indices: 42762792--42762994 Score: 284
Period size: 91 Copynumber: 2.2 Consensus size: 91
42762782 GCAAGATCAT
* *
42762792 TTCCTATCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTTTGAAATTGAAGTA
1 TTCCTACCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTA
* * * *
42762857 AGAGCAAGATGGAGCACCGACATCTT
66 AGAGCAAGATGAAACACCAACATCTC
* * *
42762883 TTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTA
1 TTCCTACCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTA
*
42762948 AGAGTAAGATGAAACACCAACATCATC
66 AGAGCAAGATGAAACACCAACATC-TC
*
42762975 TTCGT-CCCTC-TGAAATTGAA
1 TTCCTACCCTCTTGAAATTGAA
42762995 TAAGAGCAAG
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
90 10 0.10
91 86 0.85
92 5 0.05
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (91 bp):
TTCCTACCCTCTTGAAATTGAAGTAGAGCTAGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTA
AGAGCAAGATGAAACACCAACATCTC
Found at i:42763308 original size:16 final size:16
Alignment explanation
Indices: 42763261--42763378 Score: 83
Period size: 17 Copynumber: 6.9 Consensus size: 16
42763251 GCTTTTTTTT
*
42763261 AATTTATTTTAAAATTA
1 AATTTA-TTTAAATTTA
* *
42763278 AATTTGATATGAATTTA
1 AATTT-ATTTAAATTTA
*
42763295 GATTTATTTAAATTTA
1 AATTTATTTAAATTTA
*
42763311 AATTTAAATTAAACTTTA
1 AATTT-ATTTAAA-TTTA
* * *
42763329 AATTTGAATTTGAGTCTA
1 AATTT--ATTTAAATTTA
42763347 AATTTATTTTAAATTTAA
1 AATTTA-TTTAAATTT-A
*
42763365 AATTAATTTAAATT
1 AATTTATTTAAATT
42763379 AAAGTCCAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
16 14 0.18
17 36 0.46
18 24 0.30
19 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:42763309 original size:6 final size:6
Alignment explanation
Indices: 42763300--42763378 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
42763290 ATTTAGATTT
* * * *
42763300 ATTTAA ATTTAA ATTTAA A-TTAA ACTTTAA ATTTGA ATTTGA GTCTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA
* *
42763348 ATTT-A TTTTAA ATTTAA AATT-A ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
42763379 AAAGTCCAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 13 0.22
6 41 0.69
7 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (6 bp):
ATTTAA
Found at i:42764025 original size:15 final size:16
Alignment explanation
Indices: 42764005--42764039 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42763995 TTCATTAGCA
42764005 TTAATAA-TAATATCT
1 TTAATAATTAATATCT
*
42764020 TTAATAATTAATATTT
1 TTAATAATTAATATCT
42764036 TTAA
1 TTAA
42764040 ATAAGAATGT
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATAATTAATATCT
Found at i:42764981 original size:30 final size:30
Alignment explanation
Indices: 42764947--42765233 Score: 255
Period size: 30 Copynumber: 9.6 Consensus size: 30
42764937 AAATTGTCCA
* *
42764947 AAAATTACATTTCGACCTTAAAACTTTCTG
1 AAAATTACATTTTGACCCTAAAACTTTCTG
* *
42764977 AAAATTATATTTTGACCCTAAAACTTTTTG
1 AAAATTACATTTTGACCCTAAAACTTTCTG
* * *
42765007 AAAATTACATTTTAACCCTTAAACTTT-TCC
1 AAAATTACATTTTGACCCTAAAACTTTCT-G
* * *
42765037 AAAATTATATTTTGACCCCAAAACTTT-TCC
1 AAAATTACATTTTGACCCTAAAACTTTCT-G
* **
42765067 AATATTACATTTCAACCCTAAAACTTTCTG
1 AAAATTACATTTTGACCCTAAAACTTTCTG
* *
42765097 AAAATTATATTTTGACCCCT-AAACTTTTCCG
1 AAAATTACATTTTGA-CCCTAAAAC-TTTCTG
* * *
42765128 -AAATTATATTTTGACCCCAAAACTTT-TCC
1 AAAATTACATTTTGACCCTAAAACTTTCT-G
** *
42765157 AAAATTACATTTCAACCCTAAAACTTTCTA
1 AAAATTACATTTTGACCCTAAAACTTTCTG
* * *
42765187 AAAATTATACTTTGACCCTAAAACTTTC-A
1 AAAATTACATTTTGACCCTAAAACTTTCTG
42765216 AAAATTACCATTTT-ACCC
1 AAAATTA-CATTTTGACCC
42765234 CCAAACTTCC
Statistics
Matches: 211, Mismatches: 37, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
29 19 0.09
30 181 0.86
31 11 0.05
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTAAAACTTTCTG
Found at i:42765100 original size:90 final size:90
Alignment explanation
Indices: 42764977--42765241 Score: 372
Period size: 90 Copynumber: 3.0 Consensus size: 90
42764967 AAACTTTCTG
* ** * * *
42764977 AAAATTATATTTTGACCCTAAAACTTTTTGAAAATTACATTTTAACCCTTAAACTTTTCCAAAAT
1 AAAATTACATTTCAACCCTAAAACTTTCTGAAAATTATATTTTGACCCTTAAACTTTTCCAAAAT
42765042 TATATTTTGACCCCAAAACTTTTCC
66 TATATTTTGACCCCAAAACTTTTCC
* * *
42765067 AATATTACATTTCAACCCTAAAACTTTCTGAAAATTATATTTTGACCCCTAAACTTTTCCGAAAT
1 AAAATTACATTTCAACCCTAAAACTTTCTGAAAATTATATTTTGACCCTTAAACTTTTCCAAAAT
42765132 TATATTTTGACCCCAAAACTTTTCC
66 TATATTTTGACCCCAAAACTTTTCC
* * * *
42765157 AAAATTACATTTCAACCCTAAAACTTTCTAAAAATTATACTTTGACCCTAAAAC-TTTCAAAAAT
1 AAAATTACATTTCAACCCTAAAACTTTCTGAAAATTATATTTTGACCCTTAAACTTTTCCAAAAT
* *
42765221 TACCATTTT-ACCCCCAAACTT
66 TA-TATTTTGACCCCAAAACTT
42765242 CCCTAAATCT
Statistics
Matches: 156, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
89 21 0.13
90 135 0.87
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (90 bp):
AAAATTACATTTCAACCCTAAAACTTTCTGAAAATTATATTTTGACCCTTAAACTTTTCCAAAAT
TATATTTTGACCCCAAAACTTTTCC
Found at i:42765277 original size:59 final size:57
Alignment explanation
Indices: 42765214--42765407 Score: 201
Period size: 59 Copynumber: 3.3 Consensus size: 57
42765204 CTAAAACTTT
*
42765214 CAAAAATTACCATTTTACCCCCAAACTTCCCTAAATCTCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAAT-TCATTTTTAACCCCGATTTCAC
* * * * * ** **
42765273 CAAAACTTACCGTTTTACCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGATTTTGC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAA-TTCATTTTTAACCCCGATTTCAC
* * * *
42765332 CAAAATTTTCCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCATTTTA-CCCCCAAACTTTCCAAATT-CATTTTTAACCCCGATTTCAC
42765390 CAAAAATTACCATTTTAC
1 CAAAAATTACCATTTTAC
42765408 TCCTAAAAAT
Statistics
Matches: 106, Mismatches: 26, Indels: 8
0.76 0.19 0.06
Matches are distributed among these distances:
58 17 0.16
59 77 0.73
60 12 0.11
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTCATTTTTAACCCCGATTTCAC
Found at i:42767149 original size:3 final size:3
Alignment explanation
Indices: 42767141--42767165 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42767131 GCTTTATGCC
42767141 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
42767166 TAATTTCAAC
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Done.