Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 44 of 168
Found at i:12277518 original size:56 final size:51
Alignment explanation
Indices: 12277258--12277554 Score: 244
Period size: 50 Copynumber: 5.8 Consensus size: 51
12277248 GATAATAACA
* * ** * * * *
12277258 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCATGT-A-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAGG
* * * * ** * * *
12277307 TGCCAATGCCATATCCTAGATATGGTCTTACATCGGAGTTCTCATAT-TGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAGG
* * * *** *
12277357 TTCCCATTCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCCTCTC-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAGG
* * *
12277407 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGGCCTCTCGTCT-AGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAGG
12277457 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TCTC-AGG
* * *
12277512 ATGCCAATGCCATGTCCCATACATGGTATTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12277555 TTACCCAAAT
Statistics
Matches: 199, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
49 37 0.19
50 116 0.58
52 1 0.01
53 3 0.02
55 3 0.02
56 39 0.20
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAGG
Found at i:12280066 original size:15 final size:15
Alignment explanation
Indices: 12280042--12280071 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12280032 ACTTAATTCC
12280042 ATTAGCTTTATTTAA
1 ATTAGCTTTATTTAA
*
12280057 ATTAGTTTTATTTAA
1 ATTAGCTTTATTTAA
12280072 TTTCTATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTAGCTTTATTTAA
Found at i:12285984 original size:40 final size:40
Alignment explanation
Indices: 12285939--12286078 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 40
12285929 TTACAAGTTG
* *
12285939 TGTATCAGCAAAGCTCCCCTGTGAGCTTATGGGTAAGCTG
1 TGTATCAGCAAAGCTCCCCTGTGAGCTTATGGATAAGCTA
* * * * *
12285979 CGTATCAACAAATC-CCCCATGTGAGCTTAAGTAATGAAGCTA
1 TGTATCAGCAAAGCTCCCC-TGTGAGCTTATG-GAT-AAGCTA
* * *
12286021 TGTATCAGCAAACCTCCCCTGTAAGCTTATGGATAAGCTT
1 TGTATCAGCAAAGCTCCCCTGTGAGCTTATGGATAAGCTA
*
12286061 TGTTTCAGCAAAGCTCCC
1 TGTATCAGCAAAGCTCCC
12286079 TATATGAGCT
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
39 4 0.05
40 43 0.54
41 3 0.04
42 26 0.32
43 4 0.05
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
TGTATCAGCAAAGCTCCCCTGTGAGCTTATGGATAAGCTA
Found at i:12287954 original size:27 final size:26
Alignment explanation
Indices: 12287924--12287999 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
12287914 GACCCCCGTA
* *
12287924 GGGTTAAATGTTCGAAATACCCTCGAT
1 GGGTAAAAT-TTCGAAATACCCTCAAT
12287951 GGGTAAAATTATCGAAATACCCTCAAT
1 GGGTAAAATT-TCGAAATACCCTCAAT
*
12287978 GGGTAAAATTACTGAAATACCC
1 GGGTAAAATTTC-GAAATACCC
12288000 CCGAAAGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
27 42 0.95
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (26 bp):
GGGTAAAATTTCGAAATACCCTCAAT
Found at i:12288049 original size:27 final size:27
Alignment explanation
Indices: 12287936--12288054 Score: 116
Period size: 27 Copynumber: 4.4 Consensus size: 27
12287926 GTTAAATGTT
* * *
12287936 CGAAATACCCTCGATGGGTAAAATTAT
1 CGAAATACCCTCAATGGGAAAAATTAC
*
12287963 CGAAATACCCTCAATGGGTAAAATTAC
1 CGAAATACCCTCAATGGGAAAAATTAC
* * * * *
12287990 TGAAATACCCCCGAA--AGATACAATGAC
1 CGAAATACCCTC-AATGGGA-AAAATTAC
12288017 CGAAATACCCTCAATGGGAAAAATTAC
1 CGAAATACCCTCAATGGGAAAAATTAC
*
12288044 CAAAATACCCT
1 CGAAATACCCT
12288055 ATATGGTAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
26 3 0.04
27 67 0.91
28 4 0.05
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (27 bp):
CGAAATACCCTCAATGGGAAAAATTAC
Found at i:12289135 original size:4 final size:4
Alignment explanation
Indices: 12289111--12289152 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
12289101 AATTGTATAA
* *
12289111 AAAT AATAT GAAT ACAT AAAT AAAT -AAT AAAT AAAT AAAT AA
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
12289153 TGACATGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:12289142 original size:11 final size:11
Alignment explanation
Indices: 12289107--12289148 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12289097 CAACAATTGT
12289107 ATAAA-AATAA
1 ATAAATAATAA
*
12289117 TATGAATACATAA
1 -ATAAATA-ATAA
12289130 ATAAATAATAA
1 ATAAATAATAA
12289141 ATAAATAA
1 ATAAATAA
12289149 ATAATGACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.59
12 7 0.26
13 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
ATAAATAATAA
Found at i:12289144 original size:15 final size:15
Alignment explanation
Indices: 12289111--12289153 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
12289101 AATTGTATAA
*
12289111 AAATAATATGAATACAT
1 AAATAA-AT-AATAAAT
12289128 AAATAAATAATAAAT
1 AAATAAATAATAAAT
12289143 AAATAAATAAT
1 AAATAAATAAT
12289154 GACATGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 17 0.68
16 2 0.08
17 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATAAATAATAAAT
Found at i:12289465 original size:38 final size:38
Alignment explanation
Indices: 12289392--12289466 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
12289382 TATGTGTTAA
* * * *
12289392 AAAATGAATAGATATTTAGGCATTCTTAGAAATAAAAT
1 AAAATAAATAGATATATACGCATTCATAGAAATAAAAT
*
12289430 AAAATAAATAGATATATACGTATTCATA-AATATAAAA
1 AAAATAAATAGATATATACGCATTCATAGAA-ATAAAA
12289467 CAATATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 2 0.06
38 29 0.94
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (38 bp):
AAAATAAATAGATATATACGCATTCATAGAAATAAAAT
Found at i:12289692 original size:16 final size:16
Alignment explanation
Indices: 12289667--12289699 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12289657 ATAAATAATA
12289667 AAAAAATAATTACATT
1 AAAAAATAATTACATT
*
12289683 AAAAAGTAATTACATT
1 AAAAAATAATTACATT
12289699 A
1 A
12289700 TGGAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAAAATAATTACATT
Found at i:12293256 original size:20 final size:20
Alignment explanation
Indices: 12293229--12293275 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
12293219 CTTTCCAAAT
12293229 TTTC-TTACTTTCATTTGCA
1 TTTCATTACTTTCATTTGCA
*
12293248 TTTCATTACTTTCCTTTGCA
1 TTTCATTACTTTCATTTGCA
*
12293268 TTTTATTA
1 TTTCATTA
12293276 ATTTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.17, C:0.19, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTCATTACTTTCATTTGCA
Found at i:12293931 original size:23 final size:24
Alignment explanation
Indices: 12293913--12293959 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
12293903 TCCTGTACAT
12293913 GTATGCTAACACGAGCTGTGAATAA
1 GTATGCTAACACGAGCTGTGAAT-A
*
12293938 GTATGCTCACACGAGCTGTGAA
1 GTATGCTAACACGAGCTGTGAA
12293960 AATGGGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (24 bp):
GTATGCTAACACGAGCTGTGAATA
Found at i:12295517 original size:16 final size:16
Alignment explanation
Indices: 12295496--12295526 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12295486 ACTTTAGGGG
12295496 CAAAATGTAATTTTTC
1 CAAAATGTAATTTTTC
*
12295512 CAAAATGTGATTTTT
1 CAAAATGTAATTTTT
12295527 GGATTGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (16 bp):
CAAAATGTAATTTTTC
Found at i:12295871 original size:51 final size:50
Alignment explanation
Indices: 12295751--12295935 Score: 176
Period size: 51 Copynumber: 3.7 Consensus size: 50
12295741 AAAGTGATGG
* * * * * * *
12295751 TCACGTGTGTAGTACGATGTGCAGGCTACTACGTGTACCAGAATGGTA-GG
1 TCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAG-ATAGTATGA
* * *
12295801 TCGCATGTGTAGTACTATGTGGAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAGATAG-TAT-GA
* * * *
12295852 TCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCAGATAGTGATGG
1 TCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAGATAGT-ATGA
* *
12295903 TCACATGTGTAGTGCTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGAAGGCTACTATG
12295936 TGAACCAGTA
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 3 0.03
50 36 0.32
51 71 0.64
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGAAGGCTACTATGCGTACCAGATAGTATGA
Found at i:12310175 original size:43 final size:41
Alignment explanation
Indices: 12310128--12310221 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 41
12310118 CAACTCATAA
* *
12310128 CAACCCCTTTCATAATCAAGGATACGGTGGAATCTGCACTTAG
1 CAACCCCTTT-AGAATCAAGAATACGG-GGAATCTGCACTTAG
* *
12310171 CAACCACCTTTAGAATCAATAATTCGGGGAATCTGCACTTAG
1 CAACC-CCTTTAGAATCAAGAATACGGGGAATCTGCACTTAG
12310213 CAACCCCTT
1 CAACCCCTT
12310222 ACATTCAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 4 0.09
42 20 0.43
43 17 0.37
44 5 0.11
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (41 bp):
CAACCCCTTTAGAATCAAGAATACGGGGAATCTGCACTTAG
Found at i:12313541 original size:16 final size:17
Alignment explanation
Indices: 12313515--12313546 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12313505 ATAGAATTTA
12313515 AACATTAATTATTCACC
1 AACATTAATTATTCACC
12313532 AACA-TAATTATTCAC
1 AACATTAATTATTCAC
12313547 TTTAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (17 bp):
AACATTAATTATTCACC
Found at i:12321491 original size:17 final size:17
Alignment explanation
Indices: 12321469--12321503 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12321459 AGTGGCGAGA
12321469 TTATTACTTTGACGAAC
1 TTATTACTTTGACGAAC
*
12321486 TTATTACTTTGGCGAAC
1 TTATTACTTTGACGAAC
12321503 T
1 T
12321504 AGAATGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (17 bp):
TTATTACTTTGACGAAC
Found at i:12323535 original size:43 final size:44
Alignment explanation
Indices: 12323428--12323541 Score: 122
Period size: 43 Copynumber: 2.6 Consensus size: 44
12323418 GTGGCTTCGC
* * *
12323428 CCACAACCTACATGCCAACTTGCCTACAAAAATTGGTGGTTTAT
1 CCACAACCTACATGGCAGCTTGCCTGCAAAAATTGGTGGTTTAT
* * * * * *
12323472 TCACTACCAACATAGTAGCTTGCCTGC-AAATTTGGTGGTTTAT
1 CCACAACCTACATGGCAGCTTGCCTGCAAAAATTGGTGGTTTAT
* *
12323515 CCACAACCTCCATGGCAGCTTGTCTGC
1 CCACAACCTACATGGCAGCTTGCCTGC
12323542 GAATATTGAT
Statistics
Matches: 54, Mismatches: 16, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
43 35 0.65
44 19 0.35
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (44 bp):
CCACAACCTACATGGCAGCTTGCCTGCAAAAATTGGTGGTTTAT
Found at i:12323746 original size:15 final size:15
Alignment explanation
Indices: 12323726--12323758 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12323716 TAAGTATGTG
12323726 CTTATTGTTATTTAA
1 CTTATTGTTATTTAA
12323741 CTTATTGTTATTTAA
1 CTTATTGTTATTTAA
12323756 CTT
1 CTT
12323759 GTTATAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (15 bp):
CTTATTGTTATTTAA
Found at i:12324446 original size:11 final size:12
Alignment explanation
Indices: 12324420--12324448 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12324410 TCTGTATGCA
12324420 TATTTTAAAGAG
1 TATTTTAAAGAG
12324432 TATTTTAAA-AG
1 TATTTTAAAGAG
12324443 TATTTT
1 TATTTT
12324449 GCTATTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (12 bp):
TATTTTAAAGAG
Found at i:12326501 original size:23 final size:23
Alignment explanation
Indices: 12326471--12326531 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
12326461 GGAGTTTTAG
* *
12326471 TATTTATTAGCATATATATTTGA
1 TATTTATTACCATAAATATTTGA
* *
12326494 TATTTATTACCATAAATCTTTGT
1 TATTTATTACCATAAATATTTGA
* *
12326517 TATTTCTTTCCATAA
1 TATTTATTACCATAA
12326532 GTGAAAGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.52
Consensus pattern (23 bp):
TATTTATTACCATAAATATTTGA
Found at i:12342124 original size:98 final size:98
Alignment explanation
Indices: 12341964--12342143 Score: 218
Period size: 98 Copynumber: 1.8 Consensus size: 98
12341954 ATGGCCCGGG
* * * **
12341964 AACGATGATTTTCACTATTTACTCAATTTACCATCTAGGGTGGCCCAACAATGATGGCTTTCACA
1 AACGATGATTTTCACTATTTACACAATTTACCATATACGGTGGCCCAACAACAATGGCTTTCACA
*
12342029 ATTTGCATATTTTACCATCCCAAATTACCTAAC
66 ATTTGCATATTCTACCATCCCAAATTACCTAAC
* * ** **
12342062 AACGATGGTTTTCACTATTTACAC-ATTCTACCATATCCGGTGGCCTGACAACAATGTTTTTCAC
1 AACGATGATTTTCACTATTTACACAATT-TACCATATACGGTGGCCCAACAACAATGGCTTTCAC
* *
12342126 TATTTGTATATTCTACCA
65 AATTTGCATATTCTACCA
12342144 ACCTGGACGA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
97 3 0.04
98 64 0.96
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (98 bp):
AACGATGATTTTCACTATTTACACAATTTACCATATACGGTGGCCCAACAACAATGGCTTTCACA
ATTTGCATATTCTACCATCCCAAATTACCTAAC
Found at i:12343174 original size:22 final size:22
Alignment explanation
Indices: 12343148--12343189 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
12343138 GTAATTATAC
12343148 TTAATTAATTTTGA-TTACATAT
1 TTAATTAATTTT-ATTTACATAT
12343170 TTAATTAATTTTATTTACAT
1 TTAATTAATTTTATTTACAT
12343190 TTCTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAATTAATTTTATTTACATAT
Found at i:12348157 original size:14 final size:15
Alignment explanation
Indices: 12348120--12348157 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12348110 AGCTTGTGAT
12348120 TATTATGATGATTGA
1 TATTATGATGATTGA
*
12348135 TATGATGAT-ATTGA
1 TATTATGATGATTGA
*
12348149 TATTTTGAT
1 TATTATGAT
12348158 TTGTATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (15 bp):
TATTATGATGATTGA
Found at i:12350828 original size:15 final size:15
Alignment explanation
Indices: 12350804--12350835 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12350794 TATGCATTCA
*
12350804 AAATATAAAAGACAT
1 AAATACAAAAGACAT
12350819 AAATACAAAAGACAT
1 AAATACAAAAGACAT
12350834 AA
1 AA
12350836 TAATGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:12351635 original size:26 final size:26
Alignment explanation
Indices: 12351606--12351657 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
12351596 TAGGACAGTC
*
12351606 ATCTTAAGAAAAATGAGAACTTGATA
1 ATCTTAAGAAAAATGAGAACCTGATA
12351632 ATCTTAAGAAAAATGAGAACCTGATA
1 ATCTTAAGAAAAATGAGAACCTGATA
12351658 CAGTCGACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (26 bp):
ATCTTAAGAAAAATGAGAACCTGATA
Found at i:12355468 original size:59 final size:59
Alignment explanation
Indices: 12355371--12355655 Score: 286
Period size: 59 Copynumber: 4.8 Consensus size: 59
12355361 CGACTATGAA
* ** * *
12355371 AATAATGAAAAAGGATAGTTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATC
1 AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGGTGACGACCATC
* * * * * * * **
12355430 AATAATGAAAAGGGATGGTGATGACCATCGAACAATGAAAATGGATAGCT-TC-AGCTGTC
1 AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGAT-GGTGACGA-CCATC
* * * ** * * * * * *
12355489 TAATTATGAAAAGGGATAGTTTCGGCTATTAAATTATGAAAAGGGATAGTGACGGCCATC
1 -AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGGTGACGACCATC
*
12355549 AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGGTGATGACCATC
1 AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGGTGACGACCATC
*
12355608 AACAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGG
1 AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGG
12355656 CTTAGGCTAT
Statistics
Matches: 176, Mismatches: 45, Indels: 10
0.76 0.19 0.04
Matches are distributed among these distances:
58 1 0.01
59 135 0.77
60 40 0.23
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.22
Consensus pattern (59 bp):
AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGGTGACGACCATC
Found at i:12355555 original size:119 final size:119
Alignment explanation
Indices: 12355343--12355594 Score: 353
Period size: 119 Copynumber: 2.1 Consensus size: 119
12355333 ATCCTCGGCT
* ** *
12355343 AATGAAAAGGGATAGCTTC-GACTATGAAAATAATGAAAAAGGATAGTTTCGACTATCAAATTAT
1 AATGAAAAGGGATAGCTTCAG-CTGT-CTAATTATGAAAAAGGATAGTTTCGACTATCAAATTAT
* * * *
12355407 GAAAAGGGATGGTGACGACCATCAATAATGAAAAGGGATGGTGATGACCATCGAAC
64 GAAAAGGGATAGTGACGACCATCAATAATGAAAAAGGATGGTGACGACCATCAAAC
* * * *
12355463 AATGAAAATGGATAGCTTCAGCTGTCTAATTATGAAAAGGGATAGTTTCGGCTATTAAATTATGA
1 AATGAAAAGGGATAGCTTCAGCTGTCTAATTATGAAAAAGGATAGTTTCGACTATCAAATTATGA
* *
12355528 AAAGGGATAGTGACGGCCATCAATAATGAAAAAGGATGGTGACGACCATCAAAT
66 AAAGGGATAGTGACGACCATCAATAATGAAAAAGGATGGTGACGACCATCAAAC
12355582 AATGAAAAGGGAT
1 AATGAAAAGGGAT
12355595 GGTGATGACC
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
119 94 0.81
120 21 0.18
121 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (119 bp):
AATGAAAAGGGATAGCTTCAGCTGTCTAATTATGAAAAAGGATAGTTTCGACTATCAAATTATGA
AAAGGGATAGTGACGACCATCAATAATGAAAAAGGATGGTGACGACCATCAAAC
Found at i:12355620 original size:119 final size:120
Alignment explanation
Indices: 12355343--12355653 Score: 321
Period size: 119 Copynumber: 2.6 Consensus size: 120
12355333 ATCCTCGGCT
* ** *
12355343 AATGAAAAGGGATAGCTTC-GACTATGAAAATAATGAAAAA-GGATAGTTTCGACTATCAAATTA
1 AATGAAAAGGGATAGCTTCAG-CCAT-CTAACAATGAAAAAGGGATAGTTTCGACTATCAAATTA
* * * *
12355406 TGAAAAGGGATGGTGACGACCATCAATAATGAAAAGGGATGGTGATGACCATCGAAC
64 TGAAAAGGGATAGTGACGACCATCAATAATGAAAAAGGATGGTGACGACCATCAAAC
* ** ** * *
12355463 AATGAAAATGGATAGCTTCAGCTGTCTAATTATG-AAAAGGGATAGTTTCGGCTATTAAATTATG
1 AATGAAAAGGGATAGCTTCAGCCATCTAACAATGAAAAAGGGATAGTTTCGACTATCAAATTATG
* *
12355527 AAAAGGGATAGTGACGGCCATCAATAATGAAAAAGGATGGTGACGACCATCAAAT
66 AAAAGGGATAGTGACGACCATCAATAATGAAAAAGGATGGTGACGACCATCAAAC
* * * ** * *
12355582 AATGAAAAGGGAT-G-GTGATGACCATC-AACAATGAAAAA-GGATGGTGACGACCATCAAATAA
1 AATGAAAAGGGATAGCTTCA-G-CCATCTAACAATGAAAAAGGGATAGTTTCGACTATCAAATTA
12355643 TGAAAAGGGAT
64 TGAAAAGGGAT
12355654 GGCTTAGGCT
Statistics
Matches: 159, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
117 2 0.01
118 38 0.24
119 97 0.61
120 21 0.13
121 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (120 bp):
AATGAAAAGGGATAGCTTCAGCCATCTAACAATGAAAAAGGGATAGTTTCGACTATCAAATTATG
AAAAGGGATAGTGACGACCATCAATAATGAAAAAGGATGGTGACGACCATCAAAC
Found at i:12355654 original size:30 final size:30
Alignment explanation
Indices: 12355370--12355655 Score: 258
Period size: 30 Copynumber: 9.6 Consensus size: 30
12355360 TCGACTATGA
* * ** *
12355370 AAATAATGAAAAAGGATAGTTTCGACTATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
*
12355400 AAATTATGAAAAGGGATGGTGACGACCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
*
12355430 -AATAATGAAAAGGGATGGTGATGACCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
* * * * * **
12355459 GAACAATGAAAATGGATAGCT-TC-AGCTGTC
1 AAATAATGAAAAGGGAT-GGTGACGA-CCATC
* * * ** * * *
12355489 TAATTATGAAAAGGGATAGTTTCGGCTATT
1 AAATAATGAAAAGGGATGGTGACGACCATC
* * *
12355519 AAATTATGAAAAGGGATAGTGACGGCCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
*
12355549 -AATAATGAAAAAGGATGGTGACGACCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
*
12355578 AAATAATGAAAAGGGATGGTGATGACCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
* *
12355608 -AACAATGAAAAAGGATGGTGACGACCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
12355637 AAATAATGAAAAGGGATGG
1 AAATAATGAAAAGGGATGG
12355656 CTTAGGCTAT
Statistics
Matches: 209, Mismatches: 40, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
29 80 0.38
30 127 0.61
31 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.22
Consensus pattern (30 bp):
AAATAATGAAAAGGGATGGTGACGACCATC
Found at i:12355679 original size:30 final size:30
Alignment explanation
Indices: 12355645--12355711 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
12355635 TCAAATAATG
* * *
12355645 AAAAGGGATGGCTT-AGGCTATTGAGCTATA
1 AAAAGGGATAGCTTCA-GCTATCGAACTATA
*
12355675 AAAAGGGATAGCTTCAGCTATCGAACTATG
1 AAAAGGGATAGCTTCAGCTATCGAACTATA
12355705 AAAAGGG
1 AAAAGGG
12355712 TTGGAACAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.22
Consensus pattern (30 bp):
AAAAGGGATAGCTTCAGCTATCGAACTATA
Found at i:12355681 original size:178 final size:178
Alignment explanation
Indices: 12355371--12355711 Score: 452
Period size: 178 Copynumber: 1.9 Consensus size: 178
12355361 CGACTATGAA
** * * *
12355371 AATAATGAAAAAGGATAGTTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATCAATAAT
1 AATAATGAAAAAGGATAGTGACGACCATCAAATAATGAAAAGGGATGGTGACGACCATCAACAAT
* * * * * * *
12355436 GAAAAGGGATGGTGATGACCATCGAACAATGAAAATGGATAGCTTCAGCTGTCTAATTATGAAAA
66 GAAAAAGGATGGTGACGACCATCAAACAATGAAAAGGGATAGCTTCAGCTATCTAACTATAAAAA
* * * *
12355501 GGGATAGTTTCGGCTATTAAATTATGAAAAGGGATAGTGACGGCCATC
131 GGGATAGCTTCAGCTATCAAACTATGAAAAGGGATAGTGACGGCCATC
* *
12355549 AATAATGAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGGTGATGACCATCAACAAT
1 AATAATGAAAAAGGATAGTGACGACCATCAAATAATGAAAAGGGATGGTGACGACCATCAACAAT
* * *
12355614 GAAAAAGGATGGTGACGACCATCAAATAATGAAAAGGGATGGCTT-AGGCTAT-TGAGCTATAAA
66 GAAAAAGGATGGTGACGACCATCAAACAATGAAAAGGGATAGCTTCA-GCTATCT-AACTATAAA
*
12355677 AAGGGATAGCTTCAGCTATCGAACTATGAAAAGGG
129 AAGGGATAGCTTCAGCTATCAAACTATGAAAAGGG
12355712 TTGGAACAAC
Statistics
Matches: 139, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
177 2 0.01
178 137 0.99
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (178 bp):
AATAATGAAAAAGGATAGTGACGACCATCAAATAATGAAAAGGGATGGTGACGACCATCAACAAT
GAAAAAGGATGGTGACGACCATCAAACAATGAAAAGGGATAGCTTCAGCTATCTAACTATAAAAA
GGGATAGCTTCAGCTATCAAACTATGAAAAGGGATAGTGACGGCCATC
Found at i:12363582 original size:45 final size:44
Alignment explanation
Indices: 12363533--12363722 Score: 166
Period size: 45 Copynumber: 4.2 Consensus size: 44
12363523 AGATGGATGT
* ** *
12363533 TATGTGCTGATTCCACCTGATATTAATGAAAATAAAGGTGGTTGC
1 TATGTGCTGATTTCACC-GATACCAATGAATATAAAGGTGGTTGC
** *
12363578 TATGTGCTGATTTCACCGAATACCAATGGTTATATAGGTGGTTGC
1 TATGTGCTGATTTCACCG-ATACCAATGAATATAAAGGTGGTTGC
* * * * *
12363623 TATGTGCTTACTTCACCCGGTACCATTGAGTATAAAGGTGGTTGC
1 TATGTGCTGATTTCA-CCGATACCAATGAATATAAAGGTGGTTGC
* * * * * *
12363668 TATGTACTGATTTCACCGAGTACTATTGACTATAAGGGTGG-TAC
1 TATGTGCTGATTTCACCGA-TACCAATGAATATAAAGGTGGTTGC
*
12363712 TGTGTGCTGAT
1 TATGTGCTGAT
12363723 CAACTGTGTA
Statistics
Matches: 118, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
44 15 0.13
45 100 0.85
46 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (44 bp):
TATGTGCTGATTTCACCGATACCAATGAATATAAAGGTGGTTGC
Found at i:12365816 original size:30 final size:31
Alignment explanation
Indices: 12365749--12365939 Score: 160
Period size: 30 Copynumber: 6.3 Consensus size: 31
12365739 TCCTCGGCTA
* * * *
12365749 ATGAAAAGAGATAGCTAT-GGCTTTCAAAATA
1 ATGAAAAGGGATAGCTTTCGGCTATC-AAATT
12365780 ATGAAAAGGGATAG-TTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTTCGGCTATCAAATT
* * *
12365810 ATGAAAAGGGGTAGCTTT-GGCTATCGAATC
1 ATGAAAAGGGATAGCTTTCGGCTATCAAATT
* *
12365840 ATGGAAAGGGATAGC-TTCGGCTATCCAATT
1 ATGAAAAGGGATAGCTTTCGGCTATCAAATT
* ** * * *
12365870 ATGAAAATGGAT-GCTAACGACCATCAAATA
1 ATGAAAAGGGATAGCTTTCGGCTATCAAATT
* * **
12365900 ATGAAAAGGGATAGC-TTCAGCTATCGAGCT
1 ATGAAAAGGGATAGCTTTCGGCTATCAAATT
12365930 ATGAAAAGGG
1 ATGAAAAGGG
12365940 TTGGAGTAAC
Statistics
Matches: 126, Mismatches: 29, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
29 4 0.03
30 98 0.78
31 24 0.19
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (31 bp):
ATGAAAAGGGATAGCTTTCGGCTATCAAATT
Found at i:12365908 original size:60 final size:60
Alignment explanation
Indices: 12365775--12365939 Score: 179
Period size: 60 Copynumber: 2.8 Consensus size: 60
12365765 ATGGCTTTCA
* * ** * *
12365775 AAATAATGAAAAGGGATAGTTTCGGCTATCAAATTATGAAAAGGGGTAGCTTTGGCTATC
1 AAATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATAGCTACGACCATC
* * * * *
12365835 GAATCATGGAAAGGGATAGCTTCGGCTATCCAATTATGAAAATGGAT-GCTAACGACCATC
1 AAATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATAGCT-ACGACCATC
* * **
12365895 AAATAATGAAAAGGGATAGCTTCAGCTATCGAGCTATGAAAAGGG
1 AAATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGG
12365940 TTGGAGTAAC
Statistics
Matches: 85, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 3 0.04
60 82 0.96
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (60 bp):
AAATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATAGCTACGACCATC
Found at i:12367844 original size:50 final size:50
Alignment explanation
Indices: 12367668--12367915 Score: 209
Period size: 49 Copynumber: 4.9 Consensus size: 50
12367658 GAATATAACA
* * * ** * * *
12367668 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * ** *
12367717 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ***
12367767 TGCCCATGCCA-GTCCCAAACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
12367816 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAGTCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--A-TCTC---GG
*
12367872 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA--TCTCATC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
12367916 ACCCAAATGT
Statistics
Matches: 161, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
48 1 0.01
49 75 0.47
50 37 0.23
51 2 0.01
52 2 0.01
53 4 0.02
54 4 0.02
56 36 0.22
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:12370840 original size:17 final size:18
Alignment explanation
Indices: 12370818--12370853 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12370808 AATTATTATT
*
12370818 TTTGTATTCTACAA-ATA
1 TTTGTATTCAACAACATA
12370835 TTTGTATTCAACAACATA
1 TTTGTATTCAACAACATA
12370853 T
1 T
12370854 CAAGAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTGTATTCAACAACATA
Found at i:12372732 original size:19 final size:19
Alignment explanation
Indices: 12372708--12372747 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12372698 CAAACATCAT
*
12372708 ATTAATTTAAATTTATTTG
1 ATTAATTTAAATTTACTTG
*
12372727 ATTAATTTAATTTTACTTG
1 ATTAATTTAAATTTACTTG
12372746 AT
1 AT
12372748 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTAATTTAAATTTACTTG
Found at i:12374457 original size:22 final size:22
Alignment explanation
Indices: 12374432--12374476 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12374422 TTTATGATGA
12374432 TTGATA-ATATGAGATTGATATT
1 TTGATATATATGAGATT-ATATT
* *
12374454 TTGATATGTATGTGATTATATT
1 TTGATATATATGAGATTATATT
12374476 T
1 T
12374477 ATTTTTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (22 bp):
TTGATATATATGAGATTATATT
Found at i:12378239 original size:19 final size:19
Alignment explanation
Indices: 12378217--12378255 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12378207 AGTGTTTAGG
*
12378217 TTAGAATTTATCTAGCGCT
1 TTAGAATTGATCTAGCGCT
12378236 TTAGAATTGATCTAGCGCT
1 TTAGAATTGATCTAGCGCT
12378255 T
1 T
12378256 GCCTCACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (19 bp):
TTAGAATTGATCTAGCGCT
Found at i:12379242 original size:16 final size:16
Alignment explanation
Indices: 12379223--12379277 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
12379213 TTAATCATTT
12379223 TAATATTTAATTAATA
1 TAATATTTAATTAATA
*
12379239 TAATATTT-ATCAATA
1 TAATATTTAATTAATA
*
12379254 TAA-ATATTATATTAATT
1 TAATAT-TTA-ATTAATA
12379271 TAATATT
1 TAATATT
12379278 AAATCTTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.34
16 8 0.25
17 9 0.28
18 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATTTAATTAATA
Found at i:12379278 original size:16 final size:15
Alignment explanation
Indices: 12379221--12379277 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
12379211 ACTTAATCAT
12379221 TTTAATATTTAATTAA
1 TTTAATATTT-ATTAA
* *
12379237 TATAATATTTATCAA
1 TTTAATATTTATTAA
*
12379252 TATAAATATTATATTAA
1 T-TTAATATT-TATTAA
12379269 TTTAATATT
1 TTTAATATT
12379278 AAATCTTACT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 5 0.15
16 22 0.67
17 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATATTTATTAA
Found at i:12379367 original size:20 final size:18
Alignment explanation
Indices: 12379320--12379368 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
12379310 CAAGATAAAC
12379320 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
12379337 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
12379357 ATTAAATTAATA
1 ATTAAATTAATA
12379369 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:12389143 original size:4 final size:4
Alignment explanation
Indices: 12389125--12389158 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
12389115 TTAATAATTC
12389125 TATT TATT CTA-T TATT TATT TATT TATT TATT TA
1 TATT TATT -TATT TATT TATT TATT TATT TATT TA
12389159 CTTTTTACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 24 0.86
5 2 0.07
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:12389632 original size:106 final size:106
Alignment explanation
Indices: 12389447--12389878 Score: 670
Period size: 106 Copynumber: 4.1 Consensus size: 106
12389437 TTCTAATTCA
* * * *
12389447 AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATTGAGAAAACATGCCCTAACGTGTTGG
1 AAAATTTCAAAGCAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
* *
12389512 GTTTTGATTTCTCGTTCGACCAAATAGTCAAATATCCTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* * * *
12389553 AAAATTTCAAAGCAAGGAAATATTTTGCGTTTGGAAATTTGAGAAAATGTGCCCTAACGTGCTGG
1 AAAATTTCAAAGCAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
12389618 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* *
12389659 AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAATGTGCTGG
1 AAAATTTCAAAGCAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
* *
12389724 GTTTTGATTTCTCGTTCGACCAAATAGCCAAATATCCTATT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* * * *
12389765 -AAATTTCAAAGCAAGGTAATATTTTGCGTTGGGAAATTCGAGAAAACGTGCCCTAACTTGCTGG
1 AAAATTTCAAAGCAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
* *
12389829 GTTTCGATTTCTCGTTTGACCAAATAGCCAAATATCCTCTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
12389870 -AAATTTCAA
1 AAAATTTCAA
12389879 TCCATGTTAT
Statistics
Matches: 301, Mismatches: 25, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
105 105 0.35
106 196 0.65
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (106 bp):
AAAATTTCAAAGCAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
Found at i:12397265 original size:21 final size:21
Alignment explanation
Indices: 12397239--12397280 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12397229 CATTATTTTC
12397239 TTCTTT-TTTTACTGTCTTGTT
1 TTCTTTATTTT-CTGTCTTGTT
*
12397260 TTCTTTATTTTCTTTCTTGTT
1 TTCTTTATTTTCTGTCTTGTT
12397281 CTTTAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (21 bp):
TTCTTTATTTTCTGTCTTGTT
Found at i:12397823 original size:3 final size:3
Alignment explanation
Indices: 12397817--12397873 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
12397807 GTTATCTTTG
*
12397817 TTA TTA -TA TTA TATA TTA CTA TTA TTA TTA -TA TTAA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
**
12397862 TGG TTA TTA TTA
1 TTA TTA TTA TTA
12397874 CCATTTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:12397868 original size:24 final size:24
Alignment explanation
Indices: 12397816--12397871 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
12397806 TGTTATCTTT
*
12397816 GTTATTATATTATATATTACTATT
1 GTTATTATATTATATATTACTATG
* *
12397840 ATTATTATATTA-ATTATTATTATG
1 GTTATTATATTATA-TATTACTATG
12397864 GTTATTAT
1 GTTATTAT
12397872 TACCATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (24 bp):
GTTATTATATTATATATTACTATG
Found at i:12398040 original size:18 final size:18
Alignment explanation
Indices: 12398003--12398036 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12397993 TACATATATT
*
12398003 TATGTTTTATAATATTTA
1 TATGTTTTACAATATTTA
12398021 TATGTTTT-CAATATTT
1 TATGTTTTACAATATTT
12398037 TATAATCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (18 bp):
TATGTTTTACAATATTTA
Found at i:12405185 original size:26 final size:25
Alignment explanation
Indices: 12405129--12405188 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
12405119 TTGAGCCAGT
*
12405129 ATTCTTTTATTCTTTTTTCAAGTAATT
1 ATTCTTTTATTCTTTTTTC-A-TAATC
12405156 ATTCTTTTATTCTTTTTTGC-TACATC
1 ATTCTTTTATTCTTTTTT-CATA-ATC
12405182 ATTCTTT
1 ATTCTTT
12405189 ATTAATTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.07
26 9 0.30
27 18 0.60
28 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.63
Consensus pattern (25 bp):
ATTCTTTTATTCTTTTTTCATAATC
Found at i:12408830 original size:9 final size:9
Alignment explanation
Indices: 12408804--12408844 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
12408794 ACTTTTCTTA
12408804 AAAAAAAAG
1 AAAAAAAAG
* *
12408813 GAAAGAAAG
1 AAAAAAAAG
12408822 AAAAAAAAG
1 AAAAAAAAG
12408831 AAAAAAAAGG
1 AAAAAAAA-G
12408841 AAAA
1 AAAA
12408845 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
9 22 0.81
10 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:12410147 original size:83 final size:84
Alignment explanation
Indices: 12410044--12410411 Score: 299
Period size: 83 Copynumber: 4.4 Consensus size: 84
12410034 CAGAAGAAAT
* * *
12410044 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTG
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTCCTGAAGTTG
*
12410109 CAG-AGAGCAGATCATATC
66 CAGTAGAGCAGATCACATC
* ** * *
12410127 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CA-ATCCTATCTCCCTGAA
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGC-G---GATTAACATCCAGATCTTATCTTCCTGAA
* * *
12410189 GTTGCAGTGGAGCGGATTAACATC
62 GTTGCAGTAGAGCAGA-TCACATC
** * * **
12410213 CAGATCTTATCTTTCTGAGGTTGCAG-AGAGC--ATATCGCATCCAG-TCTTAT-TTCCCTGAAG
1 CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGAT-TAACATCCAGATCTTATCTT-CCTGAAG
* * *
12410273 TTGCAGTGGAGCAGATAGAAGAAAT-
63 TTGCAGTAGAGCAGAT----CACATC
* * * * **
12410298 AAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAACATCCAGATCTTATCTTTCTGTGGTTG
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTCCTGAAGTTG
*
12410363 CAG-AGAGCAGATCGCATC
66 CAGTAGAGCAGATCACATC
12410381 CAATCTTATCTCCCTGAAGTTGCAGTGGAGC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGC
12410412 AGACTAAAAA
Statistics
Matches: 218, Mismatches: 45, Indels: 44
0.71 0.15 0.14
Matches are distributed among these distances:
80 1 0.00
82 6 0.03
83 85 0.39
84 39 0.18
85 12 0.06
86 32 0.15
87 41 0.19
88 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (84 bp):
CAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTCCTGAAGTTG
CAGTAGAGCAGATCACATC
Found at i:12410200 original size:44 final size:44
Alignment explanation
Indices: 12410003--12410413 Score: 235
Period size: 44 Copynumber: 9.7 Consensus size: 44
12409993 GAAACTTCAG
*
12410003 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAAT-CAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG-CAGAAGAAATCCAA
* **
12410047 TCCTATCTCCCTGAAGTTGCAGTGGAGC-G--GATTAACATCCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAAGAA-ATCCA-A
** * ** * *
12410090 TCTTATCTTTCTGAGGTTGCA---GAG-AGCAGATCATATCCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAAGAAATCCAA
12410130 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAT-CAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG-CAGAAGAAATCCAA
* **
12410174 TCCTATCTCCCTGAAGTTGCAGTGGAGC-G--GATTAACATCCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAAGAA-ATCCA-A
** * * * * *
12410217 TCTTATCTTTCTGAGGTTGCA---GAG-AGCATATCG-CATCCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGA-AGAAATCCAA
* * *
12410257 TCTTATTTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAAT-AAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG-CAGAAGAAATCCAA
* * **
12410301 TCCTATCTCCCTGAAGTTGCAGT-GA--AGCGGATTAACATCCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAAGAA-ATCCA-A
** ** * *
12410344 TCTTATCTTTCTGTGGTTGCA---GAG-AGCAGATCG-CATCCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGA-AGAAATCCAA
12410384 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG
12410414 ACTAAAAATA
Statistics
Matches: 274, Mismatches: 60, Indels: 66
0.69 0.15 0.17
Matches are distributed among these distances:
40 73 0.27
41 25 0.09
42 15 0.05
43 66 0.24
44 84 0.31
45 11 0.04
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAAGAAATCCAA
Found at i:12410226 original size:127 final size:127
Alignment explanation
Indices: 12410000--12410415 Score: 742
Period size: 127 Copynumber: 3.3 Consensus size: 127
12409990 GGTGAAACTT
*
12410000 CAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
**
12410065 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCATATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
12410127 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
*
12410192 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCATATCGCATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
* * *
12410254 CAGTCTTATTTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAATAAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
* *
12410319 GCAGTGAAGCGGATTAACATCCAGATCTTATCTTTCTGTGGTTGCAGAGAGCAGATCGCATC
66 GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
*
12410381 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
12410416 TAAAAATAGC
Statistics
Matches: 276, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 276 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (127 bp):
CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
GCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
Found at i:12412028 original size:2 final size:2
Alignment explanation
Indices: 12411969--12412009 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
12411959 TATGATCCAA
*
12411969 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12412010 CACGTTAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12412131 original size:16 final size:15
Alignment explanation
Indices: 12412110--12412146 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
12412100 ATTACTAATA
12412110 TATTATGTTTATACAT
1 TATTATGTTTAT-CAT
*
12412126 TATTATGTTTATTAT
1 TATTATGTTTATCAT
12412141 TATTAT
1 TATTAT
12412147 TTTTTAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (15 bp):
TATTATGTTTATCAT
Found at i:12417469 original size:44 final size:43
Alignment explanation
Indices: 12417401--12417690 Score: 175
Period size: 44 Copynumber: 6.7 Consensus size: 43
12417391 TCGCATCCAG
* *
12417401 TCTTATATACCTGAAGTTGCAGTGGAGCAGAAATAAGAAACCA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG--ATAAGAAACCACA
* * * *
12417445 TCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTA-AAACCACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAGAAACCACA
* * * * * * **
12417487 TGTGTTATCTCTCTGAAGTTGCAGTAGAGCAGAT-CG-CATCAGT
1 --TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAGAAACCACA
* * *
12417530 TCTTATCTCCCTGAAGTTGTAGTGGAGGAGACAGAAGAAACCA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG--ATAAGAAACCACA
* * *
12417574 TCATATCTCCCTGAAGTTGCAGTGGAGCGGATTA-AAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAGAAACCAC--A
** * ** * *
12417618 TCTTATCTTTCTGAAGTTGCAGTAGAGCAG-TTTG-CATCA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAGAAACCACA
* *
12417658 GCCTTATCTCCCTGAAGTTGCAGCGGAGCAGAT
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
12417691 TGAAGCTATT
Statistics
Matches: 186, Mismatches: 46, Indels: 30
0.71 0.18 0.11
Matches are distributed among these distances:
40 1 0.01
41 62 0.33
42 7 0.04
43 9 0.05
44 104 0.56
45 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAGAAACCACA
Found at i:12417544 original size:41 final size:41
Alignment explanation
Indices: 12417362--12417690 Score: 123
Period size: 44 Copynumber: 7.7 Consensus size: 41
12417352 ACCACATACA
* * *
12417362 TTATCTCTCTAAAGTTGCAGTAGAGCATATCGCATCCAG-TC
1 TTATCTCCCTGAAGTTGCAGTAGAGCAGATCGCAT-CAGATC
* * * * * *
12417403 TTATATACCTGAAGTTGCAGTGGAGCAGAAATAAGAAACCA-ATC
1 TTATCTCCCTGAAGTTGCAGTAGAGCAG--AT-CG-CATCAGATC
* * * * *** * * *
12417447 CTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACATGTG
1 TTATCTCCCTGAAGTTGCAGTAGAGCAGA-TCGCATCAGA--TC
* *
12417491 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAGTTC
1 TTATCTCCCTGAAGTTGCAGTAGAGCAGATCGCATCAGATC
* * * *
12417532 TTATCTCCCTGAAGTTGTAGTGGAGGAGACAGA-AGAAACCA-ATC
1 TTATCTCCCTGAAGTTGCAGT--A-GAG-CAGATCG-CATCAGATC
* * *
12417576 ATATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAC-CA-CAGATC
1 TTATCTCCCTGAAGTTGCAGTAGAGCAGA-T----CGCATCAGATC
** * * *
12417620 TTATCTTTCTGAAGTTGCAGTAGAGCAGTTTGCATCA-AGCC
1 TTATCTCCCTGAAGTTGCAGTAGAGCAGATCGCATCAGA-TC
**
12417661 TTATCTCCCTGAAGTTGCAGCGGAGCAGAT
1 TTATCTCCCTGAAGTTGCAGTAGAGCAGAT
12417691 TGAAGCTATT
Statistics
Matches: 211, Mismatches: 53, Indels: 48
0.68 0.17 0.15
Matches are distributed among these distances:
40 6 0.03
41 78 0.37
42 3 0.01
43 11 0.05
44 105 0.50
45 8 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
TTATCTCCCTGAAGTTGCAGTAGAGCAGATCGCATCAGATC
Found at i:12417568 original size:129 final size:128
Alignment explanation
Indices: 12417336--12417739 Score: 513
Period size: 129 Copynumber: 3.1 Consensus size: 128
12417326 TGGAGCAGAC
* ** * *
12417336 AGTGGAGTGGATTAAAACCACATACATTATCTCTCTAAAGTTGCAGTAGAGCATATCGCATCCAG
1 AGTGGAGCGGATTAAAACCACATGTATTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCAT-CAG
* * *
12417401 TCTTATATACCTGAAGTTGCAGTGGAGCAGAAATAAGAAACCAATCCTATCTCCCTGAAGTTGT
65 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAAAGAAGAAACCAATCCTATCTCCCTGAAGTTGT
*
12417465 AGTGGAGCGGATTAAAACCACATGTGTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAGT
1 AGTGGAGCGGATTAAAACCACATGTATTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAG-
* * * * *
12417530 TCTTATCTCCCTGAAGTTGTAGTGGAGGAGACAGAAGAAACCAATCATATCTCCCTGAAGTTGC
65 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAAAGAAGAAACCAATCCTATCTCCCTGAAGTTGT
* * * *
12417594 AGTGGAGCGGATTAAAACCACA-GATCTTATCTTTCTGAAGTTGCAGTAGAGCAGTTTGCATCAA
1 AGTGGAGCGGATTAAAACCACATG-TATTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATC-A
* * ** ** ** *
12417658 GCCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGCTATTAATCCTATCTCCCTGAAGCTGT
64 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAAAGAAGAAACCAATCCTATCTCCCTGAAGTTGT
*
12417723 AATGGAGCGGATTAAAA
1 AGTGGAGCGGATTAAAA
12417740 TGATGAATCC
Statistics
Matches: 240, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
128 4 0.02
129 234 0.98
130 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (128 bp):
AGTGGAGCGGATTAAAACCACATGTATTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAGT
CTTATCTCCCTGAAGTTGCAGTGGAGCAGAAAGAAGAAACCAATCCTATCTCCCTGAAGTTGT
Found at i:12417760 original size:129 final size:128
Alignment explanation
Indices: 12417362--12417867 Score: 454
Period size: 129 Copynumber: 3.9 Consensus size: 128
12417352 ACCACATACA
* * *
12417362 TTATCTCTCTAAAGTTGCAGTAGAGCA-TATCGCATCCAGTCTTATATACCTGAAGTTGCAGTGG
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGT-TCGCAT-CAGTCTTATCTCCCTGAAGTTGCAGTGG
12417426 AGCAGAAAT-AAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACATG-
64 AGCAG-AATGAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAA--ACATGA
*
12417489 -TG
126 ATC
* *
12417491 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAGTTCTTATCTCCCTGAAGTTGTAGTGGA
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGTTCGCATCAG-TCTTATCTCCCTGAAGTTGCAGTGGA
* * *
12417556 GGAGACA-GAAGAAACCAATCATATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA-G-A
65 GCAGA-ATGAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAA--ACATGAA
12417618 TC
127 TC
* * * *
12417620 TTATCTTTCTGAAGTTGCAGTAGAGCAGTTTGCATCAAGCCTTATCTCCCTGAAGTTGCAGCGGA
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGTTCGCATC-AGTCTTATCTCCCTGAAGTTGCAGTGGA
* ** ** * * **
12417685 GCAGATTGAAGCTATTAATCCTATCTCCCTGAAGCTGTAATGGAGCGGATTAAAATGATGAATC
65 GCAGAATGAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAAACATGAATC
* * * *
12417749 CTATAC-CTCTGAAGTTGTAGTAG-GTCGGATTAAATCTACCATGACAAGTCTTATCTCCCTGAA
1 TTAT-CTCTCTGAAGTTGCAGTAGAG-C--AGT---TC--GCAT--C-AGTCTTATCTCCCTGAA
* ** * * * *
12417812 GTTACAGTGGAGCAGGCTGAAGATACCAGTCGTATCTCCCTGAAGTTGCAGTGGAG
54 GTTGCAGTGGAGCAGAATGAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAG
12417868 TGAATCGAAG
Statistics
Matches: 311, Mismatches: 46, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
127 1 0.00
128 7 0.02
129 232 0.75
130 3 0.01
131 2 0.01
134 1 0.00
136 3 0.01
138 62 0.20
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (128 bp):
TTATCTCTCTGAAGTTGCAGTAGAGCAGTTCGCATCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
CAGAATGAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAAACATGAATC
Found at i:12419951 original size:106 final size:106
Alignment explanation
Indices: 12419809--12420347 Score: 875
Period size: 106 Copynumber: 5.1 Consensus size: 106
12419799 TTCTAATTCA
* * *
12419809 AAAATTTCAAAGTAAGACAATATTTTGCGTTCGGAAAATCGAGAAAACGTGGCCTAACGTGCTGG
1 AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
*
12419874 TTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
*
12419915 AAAATTTCAACGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
* * *
12419980 GTTTTGATTTGTCGTTCGACCAAATAGCCAAATATTCTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* *
12420021 AAAATTTCAAAGCAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
12420086 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* * *
12420127 AAAATTTCAACGTAAGGCAATATTTTACGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGTTGG
1 AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
*
12420192 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATACTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* * * *
12420233 AAAATTTCAAAGCAAGGTAATATTTTGCGTTTGGAAATTTGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
* *
12420298 GTTT-GTTTTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
66 GTTTCG-ATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
12420339 -AAATTTCAA
1 AAAATTTCAA
12420348 TCCATGTTAT
Statistics
Matches: 402, Mismatches: 30, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
105 10 0.02
106 392 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (106 bp):
AAAATTTCAAAGTAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
Found at i:12421942 original size:18 final size:18
Alignment explanation
Indices: 12421919--12421956 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12421909 GTTGAAATAG
* *
12421919 ATTTTTTATTATTTTTTA
1 ATTTTTAATAATTTTTTA
12421937 ATTTTTAATAATTTTTTA
1 ATTTTTAATAATTTTTTA
12421955 AT
1 AT
12421957 CTAACCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTAATAATTTTTTA
Found at i:12423541 original size:34 final size:36
Alignment explanation
Indices: 12423478--12423551 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 36
12423468 TATATTTTTT
*
12423478 AAAATGAAAAAGTAAAAAAAACTTATTAAA-ATTAA
1 AAAATGAAAAAGTAAAAAAAACTTATTAAATATAAA
* *
12423513 AAAAT-AAAAA-TAAAAATAAATTTTTTAAATATAAA
1 AAAATGAAAAAGTAAAAA-AAACTTATTAAATATAAA
12423548 AAAA
1 AAAA
12423552 ATTTCAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 6 0.18
34 15 0.44
35 13 0.38
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (36 bp):
AAAATGAAAAAGTAAAAAAAACTTATTAAATATAAA
Found at i:12423546 original size:21 final size:20
Alignment explanation
Indices: 12423517--12423555 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12423507 AATTAAAAAA
12423517 TAAAAATAAAAATAAATTTTT
1 TAAAAATAAAAA-AAATTTTT
*
12423538 TAAATATAAAAAAAATTT
1 TAAAAATAAAAAAAATTT
12423556 CAAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAAAAAAAATTTTT
Found at i:12424341 original size:21 final size:20
Alignment explanation
Indices: 12424304--12424344 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12424294 TAACATATTC
* *
12424304 AAACATAGAATTTATAATAA
1 AAACATAAAATTGATAATAA
12424324 AAACAATAAAATTGATAATAA
1 AAAC-ATAAAATTGATAATAA
12424345 TTTCTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (20 bp):
AAACATAAAATTGATAATAA
Found at i:12446039 original size:20 final size:19
Alignment explanation
Indices: 12446016--12446080 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
12446006 TATGTGCATT
12446016 CAGGGGTATCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
* * * **
12446036 CAGGGGCACGATGTGCATT
1 CAGGGGTACGAAGTACAAA
12446055 CAGGGGTACCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
12446075 CAGGGG
1 CAGGGG
12446081 CACGTATGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.32, C:0.18, G:0.35, T:0.14
Consensus pattern (19 bp):
CAGGGGTACGAAGTACAAA
Found at i:12446129 original size:41 final size:40
Alignment explanation
Indices: 12445921--12446217 Score: 380
Period size: 40 Copynumber: 7.4 Consensus size: 40
12445911 TATCAAGCGA
* ** *
12445921 GCACGTATATGCATTCAAAGGTATCGAAGTACAAATAGGG
1 GCACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
* * * *
12445961 GCGCGTATGTGCATTCAGGGGTACCGAAGTATAAATAGGG
1 GCACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
*
12446001 GCACATATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
1 GCACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
*
12446041 GCACG-ATGTGCATTCAGGGGTACCGAAGTACAAACAGGG
1 GCACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
* * **
12446080 GCACGTATGTGCATTCAGAGAGTATTGAAGTACAAACAGCA
1 GCACGTATGTGCATTCAG-GGGTATCGAAGTACAAACAGGG
* * * *
12446121 GCATGTATGTGCATTTAGGGGTACCGAAGTATAAACAGGG
1 GCACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
* * *
12446161 GCACGTGTGTGCATTCAGGGGTATCGAAGTAGAAAAAGGG
1 GCACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
*
12446201 GCACATATGTGCATTCA
1 GCACGTATGTGCATTCA
12446218 AGCAATAATT
Statistics
Matches: 221, Mismatches: 34, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 38 0.17
40 150 0.68
41 33 0.15
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (40 bp):
GCACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
Found at i:12446184 original size:160 final size:160
Alignment explanation
Indices: 12445921--12446217 Score: 443
Period size: 160 Copynumber: 1.9 Consensus size: 160
12445911 TATCAAGCGA
* ** *
12445921 GCACGTATATGCATTCAAAGGTATCGAAGTACAAATAGGGGCGCGTATGTGCATTCAGGGGTACC
1 GCACGTATATGCATTCAAAGGTATCGAAGTACAAACAGCAGCACGTATGTGCATTCAGGGGTACC
* *
12445986 GAAGTATAAATAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAACAGGGGCAC-GATGT
66 GAAGTATAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAAAAGGGGCACAGATGT
12446050 GCATTCAGGGGTACCGAAGTACAAACAGGG
131 GCATTCAGGGGTACCGAAGTACAAACAGGG
* * * * *
12446080 GCACGTATGTGCATTCAGAGAGTATTGAAGTACAAACAGCAGCATGTATGTGCATTTAGGGGTAC
1 GCACGTATATGCATTCAAAG-GTATCGAAGTACAAACAGCAGCACGTATGTGCATTCAGGGGTAC
* * * *
12446145 CGAAGTATAAACAGGGGCACGTGTGTGCATTCAGGGGTATCGAAGTAGAAAAAGGGGCACATATG
65 CGAAGTATAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAAAAGGGGCACAGATG
12446210 TGCATTCA
130 TGCATTCA
12446218 AGCAATAATT
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
159 18 0.15
160 92 0.76
161 11 0.09
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (160 bp):
GCACGTATATGCATTCAAAGGTATCGAAGTACAAACAGCAGCACGTATGTGCATTCAGGGGTACC
GAAGTATAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAAAAGGGGCACAGATGT
GCATTCAGGGGTACCGAAGTACAAACAGGG
Found at i:12451255 original size:27 final size:26
Alignment explanation
Indices: 12451189--12451258 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
12451179 TTTACATCAT
* *
12451189 TGCTCACACGAGTTGTGAAATGGATC
1 TGCTCACACGAGCTGTGAAATGGACC
* *
12451215 TGCTCACACAAGCTGTGAAATGGGCCC
1 TGCTCACACGAGCTGTGAAAT-GGACC
12451242 T-CTTCACACGAGCTGTG
1 TGC-TCACACGAGCTGTG
12451259 GGTCAGAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.54
27 17 0.46
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGACC
Found at i:12456122 original size:40 final size:40
Alignment explanation
Indices: 12456078--12456158 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
12456068 AATGTTCTCG
* *
12456078 GAGGTAGCATAA-TACAATCATGAGCACGTATATGCATTCA
1 GAGGTAGCA-AATTACAAACAGGAGCACGTATATGCATTCA
* * *
12456118 GAGGTATCAAATTACAAACAGGGGCACGTATGTGCATTCA
1 GAGGTAGCAAATTACAAACAGGAGCACGTATATGCATTCA
12456158 G
1 G
12456159 GCATACTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (40 bp):
GAGGTAGCAAATTACAAACAGGAGCACGTATATGCATTCA
Found at i:12456176 original size:40 final size:40
Alignment explanation
Indices: 12456101--12456279 Score: 211
Period size: 40 Copynumber: 4.5 Consensus size: 40
12456091 ACAATCATGA
* * *
12456101 GCACGTATATGCATTCAGAGG-TATCAAATTACAAACAGGG
1 GCACGTATGTGCATTCAG-GGATATCGAAGTACAAACAGGG
* *
12456141 GCACGTATGTGCATTCAGGCATA-CTGAAGTGCAAACAGGG
1 GCACGTATGTGCATTCAGGGATATC-GAAGTACAAACAGGG
* * *
12456181 GCACGTATGTG-AGTTTAGGGATATCGGAGTACAAACAGTG
1 GCACGTATGTGCA-TTCAGGGATATCGAAGTACAAACAGGG
* *
12456221 ACACGTATGTGCATTCAGGGGTATCGAAGTACAAACAGGG
1 GCACGTATGTGCATTCAGGGATATCGAAGTACAAACAGGG
*
12456261 GCACATATGTGCATTCAGG
1 GCACGTATGTGCATTCAGG
12456280 TAATAGTTAT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.03
40 112 0.96
41 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.22
Consensus pattern (40 bp):
GCACGTATGTGCATTCAGGGATATCGAAGTACAAACAGGG
Found at i:12457998 original size:43 final size:43
Alignment explanation
Indices: 12457951--12458360 Score: 450
Period size: 43 Copynumber: 9.8 Consensus size: 43
12457941 AAAAGTCATT
* *
12457951 ACCTTTAGCGGCGCTTTTCTCGCAAACGCCGCTATAGACCACG
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
* * *
12457994 ACCTTTAGCAGCGCTTTTCCTGA-AAACGCCACTATAGACCACG
1 ACCTTTAGCGGCGCTTTTCC-CACAAACGCCGCTATAGACCACG
12458037 ACCTTTA-----------CCCACAAACGCCGCTATAGACCACG
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
* *
12458069 ATCTTTTGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
12458112 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
* *
12458155 ACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTATAAACCACG
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
* * *
12458198 ACCTTTAGTGGCGCTTTTGCCACAAACGCCGCTATAGACCATG
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
** * * * *
12458241 ACCTTTAATGGCGCTTTTCCCACAAATGCCGCTAAAGATCATG
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
* ** * * * * *
12458284 ACCTTTAGCGACGCTTTTTATCATAAACGCCACTAAAGAACA-A
1 ACCTTTAGCGGCGC-TTTTCCCACAAACGCCGCTATAGACCACG
* * *
12458327 ACCTTTAGCGGCGCTTCTCGCAAAAACGCCGCTA
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
12458361 AAAACATAAC
Statistics
Matches: 314, Mismatches: 39, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
31 1 0.00
32 26 0.08
42 15 0.05
43 251 0.80
44 21 0.07
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.23
Consensus pattern (43 bp):
ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCACG
Found at i:12462893 original size:30 final size:29
Alignment explanation
Indices: 12462823--12462894 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
12462813 ATTATAAAAA
*
12462823 TAAAAGTTTAAAATCTTTTTAAAATTTTT
1 TAAAAATTTAAAATCTTTTTAAAATTTTT
*
12462852 AAAAAGATTTAAAATC-TTTTAAAATTCATTT
1 TAAAA-ATTTAAAATCTTTTTAAAATT--TTT
*
12462883 TAAAATTTTAAA
1 TAAAAATTTAAA
12462895 TCACGAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 14 0.39
30 15 0.42
31 7 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (29 bp):
TAAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:12462894 original size:20 final size:20
Alignment explanation
Indices: 12462829--12462891 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
12462819 AAAATAAAAG
*
12462829 TTTAAAATCTTTTTAAAATT
1 TTTAAAATCATTTTAAAATT
**
12462849 TTTAAAAAGA-TTTAAAATCT
1 TTTAAAATCATTTTAAAAT-T
12462869 TTTAAAATTCATTTTAAAATT
1 TTTAAAA-TCATTTTAAAATT
12462890 TT
1 TT
12462892 AAATCACGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.23
20 15 0.43
21 4 0.11
22 8 0.23
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAAAATCATTTTAAAATT
Found at i:12464469 original size:41 final size:41
Alignment explanation
Indices: 12464410--12464523 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 41
12464400 AGATTTTATT
*
12464410 ATTAGCGGCGCTTTTTCAAAAACGCTGCTAAAGGTACGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTACGAGC
* * *
12464451 ATTAGCGGCGCTTCTTCAAAAACACCGTTAAAGGTACGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTACGAGC
*
12464492 ATTAGCGGCGCTTTTTCAAAAACGCCACTAAA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
12464524 TGCCCCAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTACGAGC
Found at i:12465589 original size:12 final size:13
Alignment explanation
Indices: 12465563--12465595 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12465553 AAAGACAAAG
12465563 ATAAAAATGAAAA
1 ATAAAAATGAAAA
*
12465576 ATGAAAAT-AAAA
1 ATAAAAATGAAAA
12465588 ATAAAAAT
1 ATAAAAAT
12465596 TTTAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (13 bp):
ATAAAAATGAAAA
Found at i:12476481 original size:52 final size:52
Alignment explanation
Indices: 12476403--12476507 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
12476393 GATCATACCC
*
12476403 AAGGGAGGAGAATACTAAATTAATCCTAACCTAAGCATAAATAGAGGTAATT
1 AAGGGAGGAGAATACTAAATTAATCCTAACCTAAGCATAAATAGAGCTAATT
* *
12476455 AAGGGAGGATAATACTAAATTAATCCTAACCTAAGTATAAATAGAGCTAATT
1 AAGGGAGGAGAATACTAAATTAATCCTAACCTAAGCATAAATAGAGCTAATT
12476507 A
1 A
12476508 GTACTTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (52 bp):
AAGGGAGGAGAATACTAAATTAATCCTAACCTAAGCATAAATAGAGCTAATT
Found at i:12476891 original size:23 final size:23
Alignment explanation
Indices: 12476857--12476904 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12476847 CTAGATGTCC
*
12476857 AATACCCTGAAAATTACTACTGT
1 AATACCCTGAAAATTACTACAGT
12476880 AATA-CCTCGAAAATTACTACAGT
1 AATACCCT-GAAAATTACTACAGT
12476903 AA
1 AA
12476905 GAAAGTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (23 bp):
AATACCCTGAAAATTACTACAGT
Found at i:12480097 original size:50 final size:50
Alignment explanation
Indices: 12479979--12480265 Score: 294
Period size: 50 Copynumber: 5.6 Consensus size: 50
12479969 TGTGAGCCAG
* * *
12479979 TGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAAATTATGAGAGATCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CG--A-GATGAGAGATCCCA
* *
12480035 TGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATCCCA
* * * *
12480085 TGTAAGACCATGTATGGGACATGGCGTTGGCATCGGGATGAGAGGTCCC-
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATCCCA
* * *
12480134 TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGA-ACTCCCA
1 T-GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGA-TCCCA
* * * * * *
12480185 TGTAAGACCATATCTGGGATATGGCGTTGGCA--GTACATGAAACATCTCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATGAGAGATCCCA
*
12480234 TGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCA
12480266 TGTTATTATC
Statistics
Matches: 200, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.00
49 40 0.20
50 125 0.62
51 2 0.01
53 1 0.00
55 1 0.00
56 30 0.15
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATCCCA
Found at i:12480184 original size:150 final size:153
Alignment explanation
Indices: 12479980--12480266 Score: 379
Period size: 149 Copynumber: 1.9 Consensus size: 153
12479970 GTGAGCCAGT
* *
12479980 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAAATTATGAGAGATCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCA-CG-AATTATGAGAGATCCCATGTAAGACCA
* * * * **
12480045 TGTCTGGGACATGGTGTTGGCACCG-AGATGAGAGGTCCCATGTAAGACCATGTATGGGACATGG
64 TATCTGGGACATGGCGTTGGCA--GTACATGAAACATCCCATGTAAGACCATGTATGGGACATGG
12480109 CGTTGGCATCGGGATGAGAGGTCCCTC
127 CGTTGGCATCGGGATGAGAGGTCCCTC
12480136 GTAAGACCATGTCTGGGACATGGCATGGGCA-C-CG-A-TATGAGA-ACTCCCATGTAAGACCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCACGAATTATGAGAGA-TCCCATGTAAGACCAT
* * * *
12480196 ATCTGGGATATGGCGTTGGCAGTACATGAAACATCTCATGTAAGACCATGTCTGGGACATGGCTT
65 ATCTGGGACATGGCGTTGGCAGTACATGAAACATCCCATGTAAGACCATGTATGGGACATGGCGT
12480261 TGGCAT
130 TGGCAT
12480267 GTTATTATCA
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
148 1 0.01
149 42 0.36
150 41 0.35
151 1 0.01
153 1 0.01
155 1 0.01
156 30 0.26
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (153 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCACGAATTATGAGAGATCCCATGTAAGACCATA
TCTGGGACATGGCGTTGGCAGTACATGAAACATCCCATGTAAGACCATGTATGGGACATGGCGTT
GGCATCGGGATGAGAGGTCCCTC
Found at i:12481771 original size:23 final size:23
Alignment explanation
Indices: 12481741--12481791 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
12481731 GGGAGAGAAA
12481741 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
*
12481764 TGTAATATCCTGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
*
12481787 AGTAA
1 TGTAA
12481792 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:12510505 original size:54 final size:54
Alignment explanation
Indices: 12510379--12510549 Score: 256
Period size: 54 Copynumber: 3.2 Consensus size: 54
12510369 GCTAGTGTAA
* * *
12510379 TTGGTGAACCGGTGTTCTCCAGGTAAGGTGCCGATTGGGGGTTC-CCAGTCTAT
1 TTGGTGAACCGATGTTCTCCAGGTAAGGTGTCGACTGGGGGTTCACCAGTCTAT
*
12510432 TTGGCGAACCGGA-GTTCTCCAGGTAAGGTGTCGACTGGGGGTTCACCAGTCTAT
1 TTGGTGAACC-GATGTTCTCCAGGTAAGGTGTCGACTGGGGGTTCACCAGTCTAT
* *
12510486 TTGGTGAACCGATGTTCTCCAGGTAAGGTGTCGACTTGGGTTTCACCAGTCTAT
1 TTGGTGAACCGATGTTCTCCAGGTAAGGTGTCGACTGGGGGTTCACCAGTCTAT
*
12510540 TTAGTGAACC
1 TTGGTGAACC
12510550 AGTTCGCCAG
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
53 40 0.37
54 67 0.63
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (54 bp):
TTGGTGAACCGATGTTCTCCAGGTAAGGTGTCGACTGGGGGTTCACCAGTCTAT
Found at i:12516947 original size:50 final size:50
Alignment explanation
Indices: 12516836--12517083 Score: 271
Period size: 50 Copynumber: 4.8 Consensus size: 50
12516826 ATTCGGGTAA
* * *
12516836 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
12516892 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
12516942 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
12516992 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * ** *
12517042 AGAACTCTCATGTAAGACCATATCTAAGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12517084 GTACAAGAAA
Statistics
Matches: 168, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
50 126 0.75
53 3 0.02
55 1 0.01
56 38 0.23
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:12517552 original size:43 final size:43
Alignment explanation
Indices: 12517485--12517775 Score: 332
Period size: 43 Copynumber: 6.8 Consensus size: 43
12517475 AACGCCGCTA
* * *
12517485 AAGACTCTTTAGCGGCGCTCTTCCCAAAAACGCCGCTAAAGACT
1 AAGAC-CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
** *
12517529 AAGACCTTTAGTAGCGCTTTTCCCACAAACGCCGTTAAAGACC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
* *
12517572 AAGACCTTGAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
* *
12517615 ATGACCTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
* * *
12517658 ATGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAAC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
* * ** * ** * *
12517701 ATGAACTTTAGCGATGCATACCCCACAAACGTCGCTAAAGAAC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
* * **
12517744 TA-ATCTTTAGCGGCGCTTTTATCACAAACGCC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
12517776 ACTTAAAATT
Statistics
Matches: 210, Mismatches: 37, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 21 0.10
43 184 0.88
44 5 0.02
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.21
Consensus pattern (43 bp):
AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
Found at i:12518751 original size:2 final size:2
Alignment explanation
Indices: 12518746--12518799 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
12518736 AATAAGAAAC
12518746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12518788 TA TA TA TA TA TA
1 TA TA TA TA TA TA
12518800 ATGCAAAGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12519987 original size:24 final size:24
Alignment explanation
Indices: 12519955--12520014 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
12519945 CGTTGAAGGC
12519955 AGAAATAGATAACTTAAACAAATT
1 AGAAATAGATAACTTAAACAAATT
* *
12519979 AGAAATAGATAAATTAAACAACTT
1 AGAAATAGATAACTTAAACAAATT
*
12520003 AG-ACTAGATAAC
1 AGAAATAGATAAC
12520015 AGTAGTCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 8 0.25
24 24 0.75
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (24 bp):
AGAAATAGATAACTTAAACAAATT
Found at i:12522656 original size:20 final size:19
Alignment explanation
Indices: 12522627--12522668 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
12522617 AATTTTAACT
*
12522627 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
12522646 AATAGTAAATAGACAAATAA
1 AATA-TAAATAAACAAATAA
12522666 AAT
1 AAT
12522669 GTTTTTGCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:12522739 original size:41 final size:41
Alignment explanation
Indices: 12522675--12522815 Score: 149
Period size: 41 Copynumber: 3.4 Consensus size: 41
12522665 AAATGTTTTT
*
12522675 GCGGCGCTTTTTCAAAAACGCCGCTAAATCCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAATCCCCGAGCATTA
** * *
12522716 GCGGCGCTTCTTGGAAAATGCCGCTAAATCCCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAATCCCCGAGCATTA
* * * * * *
12522757 GCGGTGCATT-TTTAAAAACGCAGCTAAAGCTCTGAGCATTA
1 GCGGCGC-TTCTTCAAAAACGCCGCTAAATCCCCGAGCATTA
* *
12522798 GCGACGCTTTTTCAAAAA
1 GCGGCGCTTCTTCAAAAA
12522816 TGCTGTCAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 2 0.02
41 79 0.95
42 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAATCCCCGAGCATTA
Found at i:12522979 original size:40 final size:40
Alignment explanation
Indices: 12522925--12523017 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
12522915 CACTTTCCTG
*
12522925 AAAGCACCGCTAATGCTCGATCTTTAGCGGTGTTTTATGT-
1 AAAGCACCGCTAATGCTCGATCTTTAGCGGCGTTTT-TGTC
* * * *
12522965 AAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTTGTC
1 AAAGCACCGCTAATGCTCGATCTTTAGCGGCGTTTTTGTC
*
12523005 AAAACACCGCTAA
1 AAAGCACCGCTAA
12523018 AAATGCCGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.07
40 42 0.93
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
AAAGCACCGCTAATGCTCGATCTTTAGCGGCGTTTTTGTC
Found at i:12528645 original size:50 final size:50
Alignment explanation
Indices: 12528520--12528760 Score: 295
Period size: 50 Copynumber: 4.7 Consensus size: 50
12528510 ATTTGGGTAA
* * * *
12528520 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
* * * *
12528576 AGAGATCCCATGTAAGACCACGTCTGGGAGATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
12528626 AAATGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
12528676 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCCCCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
12528726 TGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGC
12528761 ATGGATACCT
Statistics
Matches: 167, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.01
50 125 0.75
53 3 0.02
56 38 0.23
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:12528777 original size:100 final size:100
Alignment explanation
Indices: 12528525--12528815 Score: 284
Period size: 100 Copynumber: 2.9 Consensus size: 100
12528515 GGTAAAGAGA
* *
12528525 TCCCATGTAAGACCATGTCTGGGACATGAC-ATTGGCATCATTGAGATTATGAGAGATCCCATGT
1 TCCCATGTAAGACCATGTCTGGGACATGGCGA-TGGCA-C----CGA-TATGAGAGATCCCATGT
* * * * *
12528589 AAGACCACGTCTGGGAGATGGCGTTGGCATCGAGATGAAATG
59 AAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAAAGG
* * *
12528631 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGATATGAGAGATCCCATGTAAGACCA
* **
12528696 TGTCTGGGACATGGCGTTGGCCCCAAGATGTGAGG
66 TGTCTGGGACATGGCGTTGGCACCAAGATGAAAGG
* * **
12528731 TCCC-TCGTAAGACCATGTCTGGGACATGGC-ATGGATACCTATATGAGA-ACTTTCATGTAAGA
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCGATGG-CACCGATATGAGAGA-TCCCATGTAAGA
* * *
12528793 CCATATCTGGGATATGGCATTGG
63 CCATGTCTGGGACATGGCGTTGG
12528816 TAGTACAAGA
Statistics
Matches: 158, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
99 4 0.03
100 117 0.74
101 2 0.01
105 1 0.01
106 34 0.22
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (100 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGATATGAGAGATCCCATGTAAGACCA
TGTCTGGGACATGGCGTTGGCACCAAGATGAAAGG
Found at i:12540542 original size:27 final size:27
Alignment explanation
Indices: 12540512--12540568 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12540502 TTCACCATAG
* *
12540512 AGGCTA-TCATTTCATATTTTGTCACAA
1 AGGCTACTC-TTTCATATTTCGCCACAA
*
12540539 AGGCTACTCTTTCTTATTTCGCCACAA
1 AGGCTACTCTTTCATATTTCGCCACAA
12540566 AGG
1 AGG
12540569 TGTTGCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (27 bp):
AGGCTACTCTTTCATATTTCGCCACAA
Found at i:12546294 original size:19 final size:19
Alignment explanation
Indices: 12546259--12546295 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12546249 TTATGAGCAT
*
12546259 AAATTAATTATGATTAATG
1 AAATTAATTAAGATTAATG
*
12546278 AAATTAATTAAGTTTAAT
1 AAATTAATTAAGATTAAT
12546296 TAACTCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
AAATTAATTAAGATTAATG
Found at i:12549453 original size:22 final size:23
Alignment explanation
Indices: 12549405--12549454 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
12549395 AACTTTTGCT
*
12549405 AAATATAAGTACCACATTAGAAA
1 AAATACAAGTACCACATTAGAAA
12549428 AAATACAAGTACCACATTA-AAA
1 AAATACAAGTACCACATTAGAAA
12549450 AAATA
1 AAATA
12549455 TTAAAATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.60, C:0.14, G:0.06, T:0.20
Consensus pattern (23 bp):
AAATACAAGTACCACATTAGAAA
Found at i:12556126 original size:24 final size:23
Alignment explanation
Indices: 12556099--12556173 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
12556089 TATATATTTC
12556099 AATAAATATTAAAAAATTATAAAA
1 AATAAA-ATTAAAAAATTATAAAA
* *
12556123 AATAAAATTTATTAAAATTTTAAAA
1 AATAAAA-TTA-AAAAATTATAAAA
* *
12556148 ACATAAAA-AATAAAAATTATAGAA
1 A-ATAAAATTA-AAAAATTATAAAA
12556172 AA
1 AA
12556174 CTATATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
23 2 0.05
24 22 0.52
25 12 0.29
26 6 0.14
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (23 bp):
AATAAAATTAAAAAATTATAAAA
Found at i:12556173 original size:16 final size:16
Alignment explanation
Indices: 12556110--12556173 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
12556100 ATAAATATTA
12556110 AAAAATTATAAAAAAT
1 AAAAATTATAAAAAAT
* **
12556126 AAAATTTATTAAAATTTT
1 AAAAATTA-TAAAA-AAT
*
12556144 AAAAA-CATAAAAAAT
1 AAAAATTATAAAAAAT
12556159 AAAAATTATAGAAAA
1 AAAAATTATA-AAAA
12556174 CTATATTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
15 6 0.17
16 15 0.42
17 10 0.28
18 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAATTATAAAAAAT
Found at i:12556188 original size:50 final size:49
Alignment explanation
Indices: 12556110--12556207 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 49
12556100 ATAAATATTA
*
12556110 AAAAATTATAAAAAATAAAATTTATTAAAATTTTAAAAACATAAAAAAT
1 AAAAATTATAAAAAATAAAATTTATTAAAAATTTAAAAACATAAAAAAT
* * * * **
12556159 AAAAATTATAGAAAACTATATTTTTTTAAAAATTTAAAATTATAAAAAA
1 AAAAATTATA-AAAAATAAAATTTATTAAAAATTTAAAAACATAAAAAA
12556208 AGTAAAACTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 10 0.24
50 31 0.76
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (49 bp):
AAAAATTATAAAAAATAAAATTTATTAAAAATTTAAAAACATAAAAAAT
Found at i:12558267 original size:59 final size:60
Alignment explanation
Indices: 12558194--12558317 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 60
12558184 GTTAGGTAGA
* * * * *
12558194 GGTCATCCAACTATGAAAAGTTACAAAATGATTACTCTACTATTCAATTTTGT-TTTTTT
1 GGTCATCCAACTATGAAAAGTTACAAAACGATCACCCAACTATTCAATTTTATCTTTTTT
* *
12558253 GGTCATTCAACTATGAAAAGTTACAAAACGATCACCCAACTATTTAATTTTATCTTTTTT
1 GGTCATCCAACTATGAAAAGTTACAAAACGATCACCCAACTATTCAATTTTATCTTTTTT
*
12558313 AGTCA
1 GGTCA
12558318 CCAGCTTGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 46 0.82
60 10 0.18
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (60 bp):
GGTCATCCAACTATGAAAAGTTACAAAACGATCACCCAACTATTCAATTTTATCTTTTTT
Found at i:12560235 original size:29 final size:30
Alignment explanation
Indices: 12560201--12560275 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 30
12560191 CCAGAAGGTC
*
12560201 GTGTGGTAGGCCGTGTGCAACACA-TGACA
1 GTGTGGTAGGCCGTGTGCAACACACAGACA
* *
12560230 GTGTGGTACGCCGTGTGCAACACACAGCCA
1 GTGTGGTAGGCCGTGTGCAACACACAGACA
*
12560260 -TGTGATAGGCCGTGTG
1 GTGTGGTAGGCCGTGTG
12560276 TGACATACGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 37 0.93
30 3 0.08
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (30 bp):
GTGTGGTAGGCCGTGTGCAACACACAGACA
Found at i:12561129 original size:17 final size:18
Alignment explanation
Indices: 12561086--12561129 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
12561076 CAACTGATAA
12561086 AACAGTTTTTCTGAAAAT
1 AACAGTTTTTCTGAAAAT
* *
12561104 AAGAATTTTTCT-AAAAT
1 AACAGTTTTTCTGAAAAT
12561121 AACAGTTTT
1 AACAGTTTT
12561130 CAAGAAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (18 bp):
AACAGTTTTTCTGAAAAT
Found at i:12571198 original size:20 final size:20
Alignment explanation
Indices: 12571170--12571211 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12571160 TACTCAGCTA
*
12571170 AAATTGAACCATCATCAGAC
1 AAATCGAACCATCATCAGAC
12571190 AAATCGAACCATCATCAGAC
1 AAATCGAACCATCATCAGAC
12571210 AA
1 AA
12571212 CGTCAGTCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.17
Consensus pattern (20 bp):
AAATCGAACCATCATCAGAC
Found at i:12575266 original size:17 final size:17
Alignment explanation
Indices: 12575244--12575276 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12575234 CACTAACACT
*
12575244 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
12575261 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
12575277 GTTCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:12577707 original size:9 final size:9
Alignment explanation
Indices: 12577693--12577717 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12577683 ATGAGGAAAT
12577693 ACTTCGACA
1 ACTTCGACA
12577702 ACTTCGACA
1 ACTTCGACA
12577711 ACTTCGA
1 ACTTCGA
12577718 AAGGTCCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTTCGACA
Found at i:12582895 original size:48 final size:48
Alignment explanation
Indices: 12582776--12582972 Score: 161
Period size: 48 Copynumber: 4.1 Consensus size: 48
12582766 TACTATGCGT
* * *
12582776 ACCGATAATCTGTTATA-ACACAAGGGTGGCACGGAATGTGTGCAGGCC
1 ACCGATATTCTATTA-AGACACAAGGGTGGCACGGACTGTGTGCAGGCC
** *
12582824 ACCGATATTCTATTGTGACACAAGGGTGGCACGGACTGTGTGTAGGCC
1 ACCGATATTCTATTAAGACACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * *
12582872 A-CTA-ATTACTTGTTAAGATACAAGGGTGGCACGGACTATGTACAGGCC
1 ACCGATATT-C-TATTAAGACACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * * *
12582920 ACCGAGAATCTGTTATTAGGCA-AA-GGTGGTACGGGCTGTGTGCAGGCC
1 ACCGATATTCTATTA--AGACACAAGGGTGGCACGGACTGTGTGCAGGCC
12582968 ACCGA
1 ACCGA
12582973 GAAATCTCTT
Statistics
Matches: 120, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
46 3 0.03
47 3 0.03
48 104 0.87
49 5 0.04
50 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (48 bp):
ACCGATATTCTATTAAGACACAAGGGTGGCACGGACTGTGTGCAGGCC
Found at i:12582959 original size:96 final size:96
Alignment explanation
Indices: 12582795--12582969 Score: 224
Period size: 96 Copynumber: 1.8 Consensus size: 96
12582785 CTGTTATAAC
* * * * * *
12582795 ACAAGGGTGGCACGGAATGTGTGCAGGCCACCGATATTCTATTGTGACACAAGGGTGGCACGGAC
1 ACAAGGGTGGCACGGAATATGTACAGGCCACCGAGAATCTATTATGACACAAAGGTGGCACGGAC
*
12582860 TGTGTGTAGGCCACTAATTACTTGTTAAGAT
66 TGTGTGCAGGCCACTAATTACTTGTTAAGAT
* * * ** * *
12582891 ACAAGGGTGGCACGGACTATGTACAGGCCACCGAGAATCTGTTATTAGGCAAAGGTGGTACGGGC
1 ACAAGGGTGGCACGGAATATGTACAGGCCACCGAGAATCTATTATGACACAAAGGTGGCACGGAC
12582956 TGTGTGCAGGCCAC
66 TGTGTGCAGGCCAC
12582970 CGAGAAATCT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
96 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (96 bp):
ACAAGGGTGGCACGGAATATGTACAGGCCACCGAGAATCTATTATGACACAAAGGTGGCACGGAC
TGTGTGCAGGCCACTAATTACTTGTTAAGAT
Found at i:12590564 original size:96 final size:96
Alignment explanation
Indices: 12590402--12590577 Score: 244
Period size: 96 Copynumber: 1.8 Consensus size: 96
12590392 CTGTTATGGC
* * * * * * *
12590402 ACAAGGGTGGCACAGACTGTGTGGAGGCCACTGATATTCTGTTGTGACACAAGGGTGGCACGGAC
1 ACAAGGGTGGCACAGACTATGTGCAGGCCACCGAGAATCTGTTATGACACAAAGGTGGCACGGAC
12590467 TGTGTGCAGGCCACCAATTACTTGTTAAGAT
66 TGTGTGCAGGCCACCAATTACTTGTTAAGAT
* * * * *
12590498 ACAAGGGTGGCACGGACTATGTGCAGGTCACCGAGAATCTGTTATTAGACAAAGGTGGTACGGAC
1 ACAAGGGTGGCACAGACTATGTGCAGGCCACCGAGAATCTGTTATGACACAAAGGTGGCACGGAC
12590563 TGTGTGCAGGCCACC
66 TGTGTGCAGGCCACC
12590578 GAGAAATCTC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 68 1.00
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (96 bp):
ACAAGGGTGGCACAGACTATGTGCAGGCCACCGAGAATCTGTTATGACACAAAGGTGGCACGGAC
TGTGTGCAGGCCACCAATTACTTGTTAAGAT
Found at i:12590578 original size:48 final size:48
Alignment explanation
Indices: 12590383--12590582 Score: 208
Period size: 48 Copynumber: 4.2 Consensus size: 48
12590373 TACTATGCAT
* * *
12590383 ACCGATAATCTGTTATG-GCACAAGGGTGGCACAGACTGTGTGGAGGCC
1 ACCGAGAATCTGTTATGAG-ACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * *
12590431 ACTGATATTCTGTTGTGACACAAGGGTGGCACGGACTGTGTGCAGGCC
1 ACCGAGAATCTGTTATGAGACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * *
12590479 ACC-A-ATTACTTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGTC
1 ACCGAGAAT-C-TGTTATGAGACAAGGGTGGCACGGACTGTGTGCAGGCC
* * *
12590527 ACCGAGAATCTGTTATTAGACAAAGGTGGTACGGACTGTGTGCAGGCC
1 ACCGAGAATCTGTTATGAGACAAGGGTGGCACGGACTGTGTGCAGGCC
12590575 ACCGAGAA
1 ACCGAGAA
12590583 ATCTCTTTTT
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
46 3 0.02
47 2 0.02
48 118 0.93
49 2 0.02
50 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (48 bp):
ACCGAGAATCTGTTATGAGACAAGGGTGGCACGGACTGTGTGCAGGCC
Found at i:12594405 original size:29 final size:30
Alignment explanation
Indices: 12594349--12594408 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
12594339 AGCCAAAGCG
*
12594349 ATCCCTTTTCATAATTTTGATGGTCGTCACC
1 ATCCCTTTTCAT-ATGTTGATGGTCGTCACC
12594380 ATCCCTTTTCAT-TGTTGATGGTCGTCACC
1 ATCCCTTTTCATATGTTGATGGTCGTCACC
12594409 GTCATTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 16 0.57
31 12 0.43
ACGTcount: A:0.17, C:0.27, G:0.15, T:0.42
Consensus pattern (30 bp):
ATCCCTTTTCATATGTTGATGGTCGTCACC
Found at i:12594417 original size:29 final size:29
Alignment explanation
Indices: 12594365--12594420 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12594355 TTTCATAATT
*
12594365 TTGATGGTCGTCACCATCCCTTTTCATTG
1 TTGATGGTCGTCACCATCACTTTTCATTG
* *
12594394 TTGATGGTCGTCACCGTCATTTTTCAT
1 TTGATGGTCGTCACCATCACTTTTCAT
12594421 AGTTTGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (29 bp):
TTGATGGTCGTCACCATCACTTTTCATTG
Found at i:12594568 original size:120 final size:120
Alignment explanation
Indices: 12594354--12594570 Score: 299
Period size: 120 Copynumber: 1.8 Consensus size: 120
12594344 AAGCGATCCC
* * * * *
12594354 TTTTCATAATTTTGATGGTCGTCACCATCCCTTTTCATTGTTGATGGTCGTCACCGTCATTTTTC
1 TTTTCATAATTTTGATGGTAGTCACCATCCCTGTTCATTGTTGATGGTCATCACCATCACTTTTC
* * * * * *
12594419 ATAGTTTGATAGTAAGAGTTGTCCTTTTTCATGACTTGGTAGCTGAAGCTACCCT
66 ATAGCTCGATAGCAAGAGCTATCCCTTTTCATGACTTGGTAGCTGAAGCTACCCT
* *
12594474 TTTTCATAATTTTGATGGTAGTCACCATCCCTGTTCATTGTTGATTGTCATCACCATCCCTTTTC
1 TTTTCATAATTTTGATGGTAGTCACCATCCCTGTTCATTGTTGATGGTCATCACCATCACTTTTC
**
12594539 ATAGCTCGATAGCCGGAGCTATCCCTTTTCAT
66 ATAGCTCGATAGCAAGAGCTATCCCTTTTCAT
12594571 TTTTCAATGA
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
120 82 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (120 bp):
TTTTCATAATTTTGATGGTAGTCACCATCCCTGTTCATTGTTGATGGTCATCACCATCACTTTTC
ATAGCTCGATAGCAAGAGCTATCCCTTTTCATGACTTGGTAGCTGAAGCTACCCT
Found at i:12602785 original size:735 final size:734
Alignment explanation
Indices: 12601842--12604741 Score: 4071
Period size: 735 Copynumber: 4.0 Consensus size: 734
12601832 NNNNNNNNNN
*
12601842 TCGCATGGTTGTGTGTCACACACGATTGTGACACACGCCCGTGTCTTACCGTGTGCACAAGAAAT
1 TCGCATGGTTGTGTGTCACACACGATCGTGACACACGCCCGTGTCTTACCGTGTGCACAAGAAAT
**
12601907 TGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAACTTGCGTATAT
66 TGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAACTTGCCCATAT
12601972 AATTAAGACCTTAAAACATACCTAAACATCAATAATACGACCAATTCAAATGACCAAATTCCATT
131 AATTAAGACCTTAAAACATACCTAAACATCAATAATACGACCAATTCAAATGACCAAATTCCATT
12602037 AAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAA
196 AAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAA
*
12602102 ATTAATTTTGATGAAGAAAAATTGTAAC-CCCTTAACCTATATTTCTAACCGAAATAGGGTTACG
261 ATTAATTTTGATGAAGAAAAATTGTAACACCCTTAACCTATATCTCTAACCGAAATAGGGTTACG
* * * * *
12602166 GAGCATTACCGTAAATCCGGAACATCACAACATTCATTTCTGAGA-ATTTCATTAAGCATAGGAT
326 GAGCATTACCGTAAAACCAGAACATCACAACATTCATTTCT-AAACATTTCATTAAGCATAGCAA
* * *
12602230 AGTCCACACGTACACATACTTGTTGTCCCTTAATCGAGCCTTCTACGCCCTAGAAACACTTTAGA
390 AGTCCACACATACACATACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGA
12602295 AACAATTCGGGACTAAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTG
455 AACAATTCGGGACTAAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTG
* * * *
12602360 CAGGGGTCACAGGGCTGAGAAACATGCCCGTCTCTCAAGCCATTTAAAATTTGAAATAGGGACAC
520 CAGGGGTCACACGACTGAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACAC
*
12602425 ACAGCTGTGTCGCAGCCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGCTACACGGTCAACCT
585 ACAGCTGTGTCGCAGCCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCT
* **
12602490 TGAAAATCACCTTACATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAATA-CCACATTTAAAATG
650 TCAAAATCACCTTACATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAA-AGCCACATTTAAAACC
*
12602554 TATAGGGGACACATGGCCGTG
714 TATAGGGGACACACGGCCGTG
* * *
12602575 TCGCATGGTTGTGTGTCACACTCGGTCGTGACACAC-CCTCGTGTCTTAGGCCGTGTGGACAAGA
1 TCGCATGGTTGTGTGTCACACACGATCGTGACACACGCC-CGTGTCTTA--CCGTGTGCACAAGA
* * *
12602639 AATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGATTTGCCCA
63 AATTGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAACTTGCCCA
*
12602704 TATAATTAAGACCTTAAAACATACCTAAACAT-ACATAATATGACCAATTCAAATGACCAAATTC
128 TATAATTAAGACCTTAAAACATACCTAAACATCA-ATAATACGACCAATTCAAATGACCAAATTC
* * * *
12602768 CATTAAACTAATATGCCATATAATTTTCTTAAAAAATTATTTTCGAAAATCTAAGTAATTTTTTG
192 CATTAAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGG
* * * * ** * * * *
12602833 GAAAATTAATTTTGATTACGTAAAATTCTAACACCCCGAACCTGTATCTATCACCGGAATAGGGT
257 GAAAATTAATTTTGATGAAGAAAAATTGTAACACCCTTAACCTATATCTCTAACCGAAATAGGGT
* * * * *
12602898 TATGGAGCATTACCGTAAAACCATAATATCACAACGTTCATTTCTAAATATTTCATTAAGCATAG
322 TACGGAGCATTACCGTAAAACCAGAACATCACAACATTCATTTCTAAACATTTCATTAAGCATAG
* * * *
12602963 CAAAGTCCACACATACACATGCTTATTGCCCCTTAATTGAGCCTTCCAGGCCCTAGAAACACTTT
387 CAAAGTCCACACATACACATACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTT
* * *
12603028 AGAAACAATTCGGGACTAAATC-AGGAATATTTAAAACATTAAAGAGAAAGATAGAAAAATTTAA
452 AGAAACAATTCGGGACTAAATCGA-GAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAA
** * * * * *
12603092 GCTGCAGGGGTCACGTGGCTGGGAAACACGCTCGTGTCTCAAGCCATGTAAAATTAGAAATAGGG
516 GCTGCAGGGGTCACACGACTGAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGG
* * ** * * * * * *
12603157 ACACACAACAGTGTCATAGCCCTTGTCCGTGCTCATGTAACTCTATGACTTGGGTTGCACGGTGA
581 ACACACAGCTGTGTCGCAGCCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCA
* * ** *
12603222 ACCTTCAAAATGACCTTACATGCCCGTGTGCC-AGTCGTGTAACTTTTGAAAAGAAACCTTTAAA
646 ACCTTCAAAATCACCTTACATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAAAGCCACATTTAAA
**
12603286 ACCTATAGGGGACATGCGGCCGTG
711 ACCTATAGGGGACACACGGCCGTG
*
12603310 TCGCATGGTTGTGTGTCACACACGATTGTGACACACGCCCGTGTCTTACCGTGTGCACAAGAAAT
1 TCGCATGGTTGTGTGTCACACACGATCGTGACACACGCCCGTGTCTTACCGTGTGCACAAGAAAT
*
12603375 TGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAA----G-------AATTAACTTGCGCATAT
66 TGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAACTTGCCCATAT
*
12603429 AATTAAGACCTTAAAACATACCTAAACATCAATAATACGACCAATTCAAATGACCAAACTCCATT
131 AATTAAGACCTTAAAACATACCTAAACATCAATAATACGACCAATTCAAATGACCAAATTCCATT
12603494 AAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAA
196 AAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAA
*
12603559 ATTAATTTTGATGAAGAAAAATTGTAAC-CCCTTAACCTATATTTCTAACCGAAATAGGGTTACG
261 ATTAATTTTGATGAAGAAAAATTGTAACACCCTTAACCTATATCTCTAACCGAAATAGGGTTACG
* * * * *
12603623 GAGCATTACCGTAAATCCGGAACATCACAACATTCATTTCTGAGA-ATTTCATTAAGCATAGGAT
326 GAGCATTACCGTAAAACCAGAACATCACAACATTCATTTCT-AAACATTTCATTAAGCATAGCAA
* * *
12603687 AGTCCACACGTACACATACTTGTTGTCCCTTAATCGAGCCTTCTACGCCCTAGAAACACTTTAGA
390 AGTCCACACATACACATACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGA
12603752 AACAATTCGGGACTAAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTG
455 AACAATTCGGGACTAAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTG
* * * *
12603817 CAGGGGTCACACGACGGAGAAACATGCCCGTCTCTCAAGCCATTTAAAATTTGAAATAGGGGCAC
520 CAGGGGTCACACGACTGAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACAC
* *
12603882 ACAGCTGTGTCGCAACCCGTGTCCCTACTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCT
585 ACAGCTGTGTCGCAGCCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCT
**
12603947 TCAAAATCACCTTACATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAATA-CCACATTTAAAATG
650 TCAAAATCACCTTACATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAA-AGCCACATTTAAAACC
*
12604011 TATAGGGGACACATGGCCGTG
714 TATAGGGGACACACGGCCGTG
* * * *
12604032 TCGCATGGTTGTGTGTCACACTCGGTCGTGACACACCCCCGTGTCTTAGGCCGTGTGGACAAGAA
1 TCGCATGGTTGTGTGTCACACACGATCGTGACACACGCCCGTGTCTTA--CCGTGTGCACAAGAA
* *
12604097 ATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGACTTGCCCAT
64 ATTGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAACTTGCCCAT
* *
12604162 ATAATTAAGACCTTAAAACATACCTAAACAT-ACATAATATGACCAATTCAAATGAACAAATTCC
129 ATAATTAAGACCTTAAAACATACCTAAACATCA-ATAATACGACCAATTCAAATGACCAAATTCC
12604226 ATTAAACTAATATGCCATATAATTTTC--------TT-A-----AAAA---AT-TAA-TTTT--G
193 ATTAAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGG
* * * * *
12604270 ---ATTAA----G-T-----AAAATTGTAACACCCTTAACTTGTATCTGTCACCGGAATAGGGTT
258 AAAATTAATTTTGATGAAGAAAAATTGTAACACCCTTAACCTATATCTCTAACCGAAATAGGGTT
* * *
12604322 AC-GACGCATTACCTTAAAACCATAACATCACAACATTCATTTCTAAACATTTCATTAGGCATAG
323 ACGGA-GCATTACCGTAAAACCAGAACATCACAACATTCATTTCTAAACATTTCATTAAGCATAG
* * * * * * * *
12604386 CAAAGTCCACACATGCACGTGCTTATTGTCGCTTAATCGAGCATTCCAGGCCCTAGAACCACTTC
387 CAAAGTCCACACATACACATACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTT
* * *
12604451 AGAAATAATTCGGGACTAAATCGAGAATATTTGAAACATTAAGGAGAAAGTTAGAAAAATTTAAG
452 AGAAACAATTCGGGACTAAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAG
* * * *
12604516 CTGCAGGGGTCACACGACTGAGAAACACGCCCATGTCTCAGGCCATGTAAAATTTGAAGTAGGGA
517 CTGCAGGGGTCACACGACTGAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGA
* * *
12604581 CACACAGCTGTGTCCCAGCCCATGTCCGTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAA
582 CACACAGCTGTGTCGCAGCCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAA
*
12604646 CCTTCAAAATCACCTTACATGCCTGTGTGCCAGGTCGTGTAACTTTTGAAAAGCCACATTTAAAA
647 CCTTCAAAATCACCTTACATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAAAGCCACATTTAAAA
12604711 CCTATAGGGGACACACGGCCGTG
712 CCTATAGGGGACACACGGCCGTG
12604734 TCGC-TGGT
1 TCGCATGGT
12604742 AGCTATCGTT
Statistics
Matches: 1928, Mismatches: 207, Indels: 96
0.86 0.09 0.04
Matches are distributed among these distances:
701 20 0.01
702 396 0.21
706 1 0.00
707 1 0.00
711 5 0.00
714 1 0.00
716 4 0.00
717 3 0.00
718 2 0.00
721 336 0.17
722 253 0.13
723 2 0.00
724 51 0.03
726 1 0.00
727 2 0.00
728 1 0.00
729 1 0.00
732 2 0.00
733 93 0.05
734 3 0.00
735 413 0.21
736 337 0.17
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (734 bp):
TCGCATGGTTGTGTGTCACACACGATCGTGACACACGCCCGTGTCTTACCGTGTGCACAAGAAAT
TGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAACTTGCCCATAT
AATTAAGACCTTAAAACATACCTAAACATCAATAATACGACCAATTCAAATGACCAAATTCCATT
AAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAA
ATTAATTTTGATGAAGAAAAATTGTAACACCCTTAACCTATATCTCTAACCGAAATAGGGTTACG
GAGCATTACCGTAAAACCAGAACATCACAACATTCATTTCTAAACATTTCATTAAGCATAGCAAA
GTCCACACATACACATACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGAA
ACAATTCGGGACTAAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGC
AGGGGTCACACGACTGAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACACA
CAGCTGTGTCGCAGCCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTT
CAAAATCACCTTACATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAAAGCCACATTTAAAACCTA
TAGGGGACACACGGCCGTG
Found at i:12604496 original size:702 final size:708
Alignment explanation
Indices: 12602119--12604741 Score: 3398
Period size: 702 Copynumber: 3.7 Consensus size: 708
12602109 TTGATGAAGA
* *
12602119 AAAATTGTAACCCCTTAACCTATATTTCTAACCGAAATAGGGTTACGGAGCATTACCGTAAATCC
1 AAAATTGTAACCCCTTAACCTATATCTCTAACCGAAATAGGGTTACGGAGCATTACCGTAAAACC
* * * * *
12602184 GGAACATCACAACATTCATTTCTGAGAATTTCATTAAGCATAGGATAGTCCACACGTACACATAC
66 AGAACATCACAACATTCATTTCTGAAAATTTCATTAAGCATAGCAAAGTCCACACATACACATAC
* *
12602249 TTGTTGTCCCTTAATCGAGCCTTCTACGCCCTAGAAACACTTTAGAAACAATTCGGGACTAAATC
131 TTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGAAACAATTCGGGACTAAATC
* * *
12602314 GAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGCAGGGGTCACAGGGCTGAG
196 GAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGCAGGGGTCACACGACGGAG
* *
12602379 AAACATGCCCGTCTCTCAAGCCATTTAAAATTTGAAATAGGGACACACAGCTGTGTCGCAGCCCG
261 AAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACACACAGCTGTGTCGCAGCCCG
* *
12602444 TGTCCCTGCTCATGTAACTCTCTGACCTGGGCTACACGGTCAACCTTGAAAATCACCTTACATGC
326 TGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTTCAAAATCACCTTACATGC
** *
12602509 CTGTGTGCCAAGTCGTGTAACTTTTGAAATA-CCACATTTAAAATGTATAGGGGACACATGGCCG
391 CTGTGTGCCAAGTCGTGTAACTTTTGAAA-AGCCACATTTAAAACCTATAGGGGACACACGGCCG
*
12602573 TGTCGCATGGTTGTGTGTCACACTCGGTCGTGACACACCCTCGTGTCTTAGGCCGTGTGGACAAG
455 TGTCGCATGGTTGTGTGTCACACTCGGTCGTGACACACCCCCGTGTCTTAGGCCGTGTGGACAAG
*
12602638 AAATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGATTTGCCC
520 AAATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGACTTGCCC
12602703 ATATAATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTC
585 ATATAATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTC
12602768 CATTAAACTAATATGCCATATAATTTTCTTAAAAAATTATTTTCGAAAATCTAAGTAATTTTTTG
650 CATTAAACTAATATGCCATATAATTTTCTT----AA-TA------AAAA--T-A-TAA-TTTTTG
12602833 GAAAATTAATTTTGATTACGT
699 G--AATT-A-----A-T--GT
* ** * * * * *
12602854 AAAATTCTAACACCCCGAACCTGTATCTATCACCGGAATAGGGTTATGGAGCATTACCGTAAAAC
1 AAAATTGTAAC-CCCTTAACCTATATCTCTAACCGAAATAGGGTTACGGAGCATTACCGTAAAAC
* * *
12602919 CATAATATCACAACGTTCATTTCT-AAATATTTCATTAAGCATAGCAAAGTCCACACATACACAT
65 CAGAACATCACAACATTCATTTCTGAAA-ATTTCATTAAGCATAGCAAAGTCCACACATACACAT
* * * *
12602983 GCTTATTGCCCCTTAATTGAGCCTTCCAGGCCCTAGAAACACTTTAGAAACAATTCGGGACTAAA
129 ACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGAAACAATTCGGGACTAAA
* * * ** *
12603048 TC-AGGAATATTTAAAACATTAAAGAGAAAGATAGAAAAATTTAAGCTGCAGGGGTCACGTGGCT
194 TCGA-GAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGCAGGGGTCACACGAC-
* * * * * **
12603112 GG-GAAACACGCTCGTGTCTCAAGCCATGTAAAATTAGAAATAGGGACACACAACAGTGTCATAG
257 GGAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACACACAGCTGTGTCGCAG
* * * * * * *
12603176 CCCTTGTCCGTGCTCATGTAACTCTATGACTTGGGTTGCACGGTGAACCTTCAAAATGACCTTAC
322 CCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTTCAAAATCACCTTAC
* ** * **
12603241 ATGCCCGTGTGCC-AGTCGTGTAACTTTTGAAAAGAAACCTTTAAAACCTATAGGGGACATGCGG
387 ATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAAAGCCACATTTAAAACCTATAGGGGACACACGG
* * * * *
12603305 CCGTGTCGCATGGTTGTGTGTCACACACGATTGTGACACACGCCCGTGTCTTA--CCGTGTGCAC
452 CCGTGTCGCATGGTTGTGTGTCACACTCGGTCGTGACACACCCCCGTGTCTTAGGCCGTGTGGAC
* *
12603368 AAGAAATTGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAA----G-------AATTAACTTG
517 AAGAAATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGACTTG
* *
12603422 CGCATATAATTAAGACCTTAAAACATACCTAAACAT-CAATAATACGACCAATTCAAATGACCAA
582 CCCATATAATTAAGACCTTAAAACATACCTAAACATAC-ATAATATGACCAATTCAAATGACCAA
*
12603486 ACTCCATTAAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTT
646 ATTCCATTAAACTAATATGCCATATAATTTTCTT----AA-T-A-----AAAA--TA--TAATTT
12603551 TTGGGAAAATTAATTTTGAT
696 TT-GG--AATTAA---TG-T
*
12603571 GAAGAAAAATTGTAACCCCTTAACCTATATTTCTAACCGAAATAGGGTTACGGAGCATTACCGTA
1 -----AAAATTGTAACCCCTTAACCTATATCTCTAACCGAAATAGGGTTACGGAGCATTACCGTA
* * * * * *
12603636 AATCCGGAACATCACAACATTCATTTCTGAGAATTTCATTAAGCATAGGATAGTCCACACGTACA
61 AAACCAGAACATCACAACATTCATTTCTGAAAATTTCATTAAGCATAGCAAAGTCCACACATACA
* *
12603701 CATACTTGTTGTCCCTTAATCGAGCCTTCTACGCCCTAGAAACACTTTAGAAACAATTCGGGACT
126 CATACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGAAACAATTCGGGACT
12603766 AAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGCAGGGGTCACACGA
191 AAATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGCAGGGGTCACACGA
* * *
12603831 CGGAGAAACATGCCCGTCTCTCAAGCCATTTAAAATTTGAAATAGGGGCACACAGCTGTGTCGCA
256 CGGAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACACACAGCTGTGTCGCA
* *
12603896 ACCCGTGTCCCTACTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTTCAAAATCACCTTA
321 GCCCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTTCAAAATCACCTTA
** *
12603961 CATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAATA-CCACATTTAAAATGTATAGGGGACACAT
386 CATGCCTGTGTGCCAAGTCGTGTAACTTTTGAAA-AGCCACATTTAAAACCTATAGGGGACACAC
12604025 GGCCGTGTCGCATGGTTGTGTGTCACACTCGGTCGTGACACACCCCCGTGTCTTAGGCCGTGTGG
450 GGCCGTGTCGCATGGTTGTGTGTCACACTCGGTCGTGACACACCCCCGTGTCTTAGGCCGTGTGG
12604090 ACAAGAAATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGACT
515 ACAAGAAATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGACT
*
12604155 TGCCCATATAATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGAACA
580 TGCCCATATAATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCA
12604220 AATTCCATTAAACTAATATGCCATATAATTTTCTT-A-AAAAAT-TAA-TTTT-G-ATTAA-GT
645 AATTCCATTAAACTAATATGCCATATAATTTTCTTAATAAAAATATAATTTTTGGAATTAATGT
* * * * * *
12604277 AAAATTGTAACACCCTTAACTTGTATCTGTCACCGGAATAGGGTTAC-GACGCATTACCTTAAAA
1 AAAATTGTAAC-CCCTTAACCTATATCTCTAACCGAAATAGGGTTACGGA-GCATTACCGTAAAA
* * * *
12604341 CCATAACATCACAACATTCATTTCT-AAACATTTCATTAGGCATAGCAAAGTCCACACATGCACG
64 CCAGAACATCACAACATTCATTTCTGAAA-ATTTCATTAAGCATAGCAAAGTCCACACATACACA
* * * * * * *
12604405 TGCTTATTGTCGCTTAATCGAGCATTCCAGGCCCTAGAACCACTTCAGAAATAATTCGGGACTAA
128 TACTTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGAAACAATTCGGGACTAA
* * *
12604470 ATCGAGAATATTTGAAACATTAAGGAGAAAGTTAGAAAAATTTAAGCTGCAGGGGTCACACGACT
193 ATCGAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGCAGGGGTCACACGACG
* * * * *
12604535 GAGAAACACGCCCATGTCTCAGGCCATGTAAAATTTGAAGTAGGGACACACAGCTGTGTCCCAGC
258 GAGAAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACACACAGCTGTGTCGCAGC
* *
12604600 CCATGTCCGTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTTCAAAATCACCTTACA
323 CCGTGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTTCAAAATCACCTTACA
*
12604665 TGCCTGTGTGCCAGGTCGTGTAACTTTTGAAAAGCCACATTTAAAACCTATAGGGGACACACGGC
388 TGCCTGTGTGCCAAGTCGTGTAACTTTTGAAAAGCCACATTTAAAACCTATAGGGGACACACGGC
12604730 CGTGTCGC-TGGT
453 CGTGTCGCATGGT
12604742 AGCTATCGTT
Statistics
Matches: 1664, Mismatches: 184, Indels: 114
0.85 0.09 0.06
Matches are distributed among these distances:
701 20 0.01
702 396 0.24
706 1 0.00
707 1 0.00
711 5 0.00
714 1 0.00
716 6 0.00
717 4 0.00
718 2 0.00
720 3 0.00
721 339 0.20
722 239 0.14
723 2 0.00
724 51 0.03
727 1 0.00
728 1 0.00
729 1 0.00
730 1 0.00
733 51 0.03
734 1 0.00
735 203 0.12
736 334 0.20
737 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (708 bp):
AAAATTGTAACCCCTTAACCTATATCTCTAACCGAAATAGGGTTACGGAGCATTACCGTAAAACC
AGAACATCACAACATTCATTTCTGAAAATTTCATTAAGCATAGCAAAGTCCACACATACACATAC
TTATTGTCCCTTAATCGAGCCTTCCACGCCCTAGAAACACTTTAGAAACAATTCGGGACTAAATC
GAGAATATTTAAAACATTAAGGAGAAAGTTACAAAAATTTAAGCTGCAGGGGTCACACGACGGAG
AAACACGCCCGTCTCTCAAGCCATGTAAAATTTGAAATAGGGACACACAGCTGTGTCGCAGCCCG
TGTCCCTGCTCATGTAACTCTCTGACCTGGGTTACACGGTCAACCTTCAAAATCACCTTACATGC
CTGTGTGCCAAGTCGTGTAACTTTTGAAAAGCCACATTTAAAACCTATAGGGGACACACGGCCGT
GTCGCATGGTTGTGTGTCACACTCGGTCGTGACACACCCCCGTGTCTTAGGCCGTGTGGACAAGA
AATTGGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTGACTTGCCCA
TATAATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTCC
ATTAAACTAATATGCCATATAATTTTCTTAATAAAAATATAATTTTTGGAATTAATGT
Found at i:12616501 original size:736 final size:735
Alignment explanation
Indices: 12614822--12616505 Score: 2906
Period size: 735 Copynumber: 2.3 Consensus size: 735
12614812 TTAACAGTCT
* *
12614822 CATGGTTGTGTGTCACACACGGTCGTGACACACCCCCGTGTCTTAGGCCATGTGGACAAGAAATT
1 CATGGTTGTGTGTCACACACGGTTGTGACACACCCCCGTGTCTTAGGCCGTGTGGACAAGAAATT
* *
12614887 GGCTAAAATTCAAGTCATTTCTTTCACCCATTCAAGCTTGAACCTACAATT-GACTTGCCCATAT
66 GGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAG-CTTGCACATAT
* * *
12614951 AATTAAGAACTTAAAACATACCTAAACATACATAATATGACCAATTTAAATGACCAAATTCCATT
130 AATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTTCATT
*
12615016 AAACTAATATGCCATATAATTTTCTTAAAAATTTAATTTGGAAAATCTATGTAATTTTTGGGAAA
195 AAACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAA
*
12615081 ATTAATTTTGATTAAGTAAAATTGTAACACCCTTAACCTGTATCTGTCACTGGAATAGGGTTACG
260 ATTAATTTTGATTAAGTAAAATTGTAACACCCTTAACCTGTATCTGTCACTGGAATAGGGTTACA
*
12615146 GAGCATTACCGTAAAACCATAACATCACAACATTCATTTCTAAACATTTCAATATGCATAGCAAA
325 GAGCATTACCGTAAAACCATAACATCACAACATTCATTTCTAAACATTTCAATAGGCATAGCAAA
* *
12615211 GTCCACACATACACATGCTTATTGTCGCTTAATAGAGCCTTCCAGGCCCTAGAACAATTTTAGAA
390 GTCCACACATACACATACTTATTGTCGCTTAATAGAGCCTTCCAGGCCCTAGAACAACTTTAGAA
* *
12615276 ATAATTCGGGACTAAATTGGGGATATTTAAAACATTAAGGAGAAAGTTAGAAAAATTTAAGCTGC
455 ATAATTCGGGACTAAATCGGGAATATTTAAAACATTAAGGAGAAAGTTAGAAAAATTTAAGCTGC
* * *
12615341 AGGGGTCACACGACTGAGAAACAGGCCCATGTCTCAGGCCATGCAAAATTTGAAGTAGGGACACA
520 AGGGGTCACACGACTGAGAAACACGCCCATGCCTCAGGCCATGCAAAATTTGAAATAGGGACACA
* *
12615406 CAACTGTGTCCCAGCCCGTGTCCGTGCTCATGTAACTCTCTGACTTGGTTACACAGTCAACCTTC
585 CAACTGTGTCCCAGCCCGTGTCCGTGCTCATGTAACTCTCTAACTTGGTTACACAGTCAACATTC
* *
12615471 AAGATGACCTTGCACGCACGTGTGCCAGGTCGTGTTACTTTTGAAAAGCAACCTTTAAAACCTAC
650 AAGATGACCTTGCACGCACGTGTGCCAGGTCGTGTAACTTTTGAAAACCAACCTTTAAAACCTAC
12615536 AGGGGACACACGGTCGTGTCG
715 AGGGGACACACGGTCGTGTCG
*
12615557 AATGGTTGTGTGTCACACACGGTTGTGACACACCCCCGTGTCTTAGGCCGTGTGGACAAGAAATT
1 CATGGTTGTGTGTCACACACGGTTGTGACACACCCCCGTGTCTTAGGCCGTGTGGACAAGAAATT
* * * * * *
12615622 GGCTAAAATTCAAGCAATTTCTTTCCCCCTTTCAAGCTTGAGCATACAATTAACTTGCACATATA
66 GGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAGCTTGCACATATA
*
12615687 ATTAAGACCTTAAAACATACCTAAACATACATAATATTACCAATTCAAATGACCAAATTTCATTA
131 ATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTTCATTA
*
12615752 AACTAATATGCCATATAATTTTCTTAAAAAATTAATTTTGAAAATCTATGTAATTTTTGGGAAAA
196 AACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAAA
*
12615817 TTAATTTTGATTAAGTAAAATTGTAACACCCTTAACTTGTATCTGTCACTGGAATAGGGTTACAG
261 TTAATTTTGATTAAGTAAAATTGTAACACCCTTAACCTGTATCTGTCACTGGAATAGGGTTACAG
*
12615882 AGCATTACCGTAAAACCATAACATCACAACATTCATTTCTAAACATTTCATTAGGCATAGCAAAG
326 AGCATTACCGTAAAACCATAACATCACAACATTCATTTCTAAACATTTCAATAGGCATAGCAAAG
*
12615947 TCCACACATACACATACTTATTGTCGCTTAATCGAGCCTTCCAGGCCCTAGAA-ACACTTTAGAA
391 TCCACACATACACATACTTATTGTCGCTTAATAGAGCCTTCCAGGCCCTAGAACA-ACTTTAGAA
12616011 ATAATTCGGGACTAAATCGGGAATATTTAAAACATTAAGGAGAAAGTTAGAAAAATTTAAGCTGC
455 ATAATTCGGGACTAAATCGGGAATATTTAAAACATTAAGGAGAAAGTTAGAAAAATTTAAGCTGC
* *
12616076 AGGGGTCACACGATTGAGAAACACGCCCATGCCTCAGGCCATGTAAAATTTGAAATAGGGACACA
520 AGGGGTCACACGACTGAGAAACACGCCCATGCCTCAGGCCATGCAAAATTTGAAATAGGGACACA
** * * **
12616141 CAGTTGTGTCCCAGTCCGTGTCCGTGCTCATGTAACTCTTTAACTTGGATTACATGGTCAACATT
585 CAACTGTGTCCCAGCCCGTGTCCGTGCTCATGTAACTCTCTAACTTGG-TTACACAGTCAACATT
*
12616206 CAAGATGACCTTGCACGCCCGTGTGCCAGGTCGTGTAACTTTTGAAAACCAACCTTTAAAACCTA
649 CAAGATGACCTTGCACGCACGTGTGCCAGGTCGTGTAACTTTTGAAAACCAACCTTTAAAACCTA
*
12616271 CAGGGGATACACGGTCGTGTCG
714 CAGGGGACACACGGTCGTGTCG
*
12616293 CATGGTTGTGTGTCACACATGGTTGTGACAC-CTCCCCGTGTCTTAGGCCGTGTGGACAAGAAAT
1 CATGGTTGTGTGTCACACACGGTTGTGACACAC-CCCCGTGTCTTAGGCCGTGTGGACAAGAAAT
*
12616357 TGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGATTGAACCTACAATTAGCTTGCACATAT
65 TGGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAGCTTGCACATAT
12616422 AATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTTCATT
130 AATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTTCATT
12616487 AAACTAATATGCCATATAA
195 AAACTAATATGCCATATAA
12616506 GGTACCACAA
Statistics
Matches: 892, Mismatches: 53, Indels: 7
0.94 0.06 0.01
Matches are distributed among these distances:
734 1 0.00
735 594 0.67
736 297 0.33
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (735 bp):
CATGGTTGTGTGTCACACACGGTTGTGACACACCCCCGTGTCTTAGGCCGTGTGGACAAGAAATT
GGCTAAAATTCAAGCCATTTCTTTCACCCATTCAAGCTTGAACCTACAATTAGCTTGCACATATA
ATTAAGACCTTAAAACATACCTAAACATACATAATATGACCAATTCAAATGACCAAATTTCATTA
AACTAATATGCCATATAATTTTCTTAAAAAATTAATTTGGAAAATCTATGTAATTTTTGGGAAAA
TTAATTTTGATTAAGTAAAATTGTAACACCCTTAACCTGTATCTGTCACTGGAATAGGGTTACAG
AGCATTACCGTAAAACCATAACATCACAACATTCATTTCTAAACATTTCAATAGGCATAGCAAAG
TCCACACATACACATACTTATTGTCGCTTAATAGAGCCTTCCAGGCCCTAGAACAACTTTAGAAA
TAATTCGGGACTAAATCGGGAATATTTAAAACATTAAGGAGAAAGTTAGAAAAATTTAAGCTGCA
GGGGTCACACGACTGAGAAACACGCCCATGCCTCAGGCCATGCAAAATTTGAAATAGGGACACAC
AACTGTGTCCCAGCCCGTGTCCGTGCTCATGTAACTCTCTAACTTGGTTACACAGTCAACATTCA
AGATGACCTTGCACGCACGTGTGCCAGGTCGTGTAACTTTTGAAAACCAACCTTTAAAACCTACA
GGGGACACACGGTCGTGTCG
Found at i:12619525 original size:41 final size:38
Alignment explanation
Indices: 12619466--12619732 Score: 225
Period size: 41 Copynumber: 6.6 Consensus size: 38
12619456 GACTTTTTGG
*
12619466 GGCCTTTAGCGGCATTTTTGAAGATGCACAGCTAATGCTC
1 GGCCTTTAGCGGCGTTTTTGAAGATGC-CA-CTAATGCTC
* **
12619506 GGTCCTTTAGCGGCGTTTTTAGAGAAACACCACTAATGCTC
1 GG-CCTTTAGCGGCGTTTTT-GA-AGATGCCACTAATGCTC
* *
12619547 AGGCCTTTAGCGACGTTTTTGAAGGAGCGCCACTAATGCTC
1 -GGCCTTTAGCGGCGTTTTTGAA-GA-TGCCACTAATGCTC
* *
12619588 GAGCCTTTAGCGGCGTTTTTGAAAATTTGCCACTAATGCTTA
1 G-GCCTTTAGCGGCGTTTTTGAAGA--TGCCACTAATGC-TC
* *
12619630 GGCCTTTAGCGGCGTTTTTGAAAATGCGCCGCTAATGCTC
1 GGCCTTTAGCGGCGTTTTTGAAGAT--GCCACTAATGCTC
* * * *
12619670 GGTCCTTTAGCGGTGTTTTTAGAGAAACGCCGCTAATGCTC
1 GG-CCTTTAGCGGCGTTTTT-GA-AGATGCCACTAATGCTC
12619711 GGGCC---AGCGGCGTTTTTGAAGA
1 -GGCCTTTAGCGGCGTTTTTGAAGA
12619733 AGCGCCGCAA
Statistics
Matches: 194, Mismatches: 18, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
36 2 0.01
37 2 0.01
38 11 0.06
39 2 0.01
40 10 0.05
41 149 0.77
42 12 0.06
43 6 0.03
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (38 bp):
GGCCTTTAGCGGCGTTTTTGAAGATGCCACTAATGCTC
Found at i:12619603 original size:82 final size:82
Alignment explanation
Indices: 12619466--12619738 Score: 321
Period size: 82 Copynumber: 3.4 Consensus size: 82
12619456 GACTTTTTGG
* * *
12619466 GGCCTTTAGCGGCATTTTTGAAGATGC-ACAGCTAATGCTCGGTCCTTTAGCGGCGTTTTTAGAG
1 GGCCTTTAGCGGCGTTTTTGAAAATGCGCCA-CTAATGCTCGGTCCTTTAGCGGCGTTTTTAGAG
*
12619530 AAACACCACTAATGCTCA
65 AAACGCCACTAATGCTCA
* *
12619548 GGCCTTTAGCGACGTTTTTGAAGGA-GCGCCACTAATGCTCGAG-CCTTTAGCGGCGTTTTT-GA
1 GGCCTTTAGCGGCGTTTTTGAA-AATGCGCCACTAATGCTCG-GTCCTTTAGCGGCGTTTTTAGA
* *
12619610 -AAATTTGCCACTAATGCTTA
64 GAAA--CGCCACTAATGCTCA
* *
12619630 GGCCTTTAGCGGCGTTTTTGAAAATGCGCCGCTAATGCTCGGTCCTTTAGCGGTGTTTTTAGAGA
1 GGCCTTTAGCGGCGTTTTTGAAAATGCGCCACTAATGCTCGGTCCTTTAGCGGCGTTTTTAGAGA
* *
12619695 AACGCCGCTAATGCTCG
66 AACGCCACTAATGCTCA
12619712 GGCC---AGCGGCGTTTTTGAAGAA-GCGCC
1 GGCCTTTAGCGGCGTTTTTGAA-AATGCGCC
12619739 GCAAAAACAT
Statistics
Matches: 167, Mismatches: 14, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
79 20 0.12
80 5 0.03
81 4 0.02
82 128 0.77
83 7 0.04
84 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.29
Consensus pattern (82 bp):
GGCCTTTAGCGGCGTTTTTGAAAATGCGCCACTAATGCTCGGTCCTTTAGCGGCGTTTTTAGAGA
AACGCCACTAATGCTCA
Found at i:12619688 original size:123 final size:123
Alignment explanation
Indices: 12619467--12619730 Score: 296
Period size: 123 Copynumber: 2.2 Consensus size: 123
12619457 ACTTTTTGGG
* * *
12619467 GCCTTTAGCGGCATTTTTGAAGATGCACAGCTAATGCTCGGTCCTTTAGCGGCGTTTTTAGAGAA
1 GCCTTTAGCGGCGTTTTTGAAAATGCACAGCTAATGCTAGGTCCTTTAGCGGCGTTTTTAGAGAA
* *
12619532 ACACCACTAATGCTCAGGCCTTTAGCGACGTTTTT-GAAGGAGCGCCACTAATGCTCGA
66 ACACCACTAATGCTCAGGCCTTTAGCGACGTTTTTAG-AGAAACGCCACTAATGCTCGA
12619590 GCCTTTAGCGGCGTTTTTGAAAATTTGC-CA-CTAATGCTTAGG-CCTTTAGCGGCGTTTTT-GA
1 GCCTTTAGCGGCGTTTTTGAAAA--TGCACAGCTAATGC-TAGGTCCTTTAGCGGCGTTTTTAGA
* * ** * *
12619651 -AAATGCGCCGCTAATGCTC-GGTCCTTTAGCGGTGTTTTTAGAGAAACGCCGCTAATGCTCGG
63 GAAA--CACCACTAATGCTCAGG-CCTTTAGCGACGTTTTTAGAGAAACGCCACTAATGCTCGA
12619713 GCC---AGCGGCGTTTTTGAA
1 GCCTTTAGCGGCGTTTTTGAA
12619731 GAAGCGCCGC
Statistics
Matches: 123, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
120 15 0.12
121 3 0.02
122 4 0.03
123 92 0.75
124 6 0.05
125 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (123 bp):
GCCTTTAGCGGCGTTTTTGAAAATGCACAGCTAATGCTAGGTCCTTTAGCGGCGTTTTTAGAGAA
ACACCACTAATGCTCAGGCCTTTAGCGACGTTTTTAGAGAAACGCCACTAATGCTCGA
Found at i:12620155 original size:14 final size:15
Alignment explanation
Indices: 12620127--12620159 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
12620117 AAGGTTTATA
12620127 GATTATGGAATTAGG
1 GATTATGGAATTAGG
12620142 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
12620156 GATT
1 GATT
12620160 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:12620204 original size:7 final size:7
Alignment explanation
Indices: 12620194--12620381 Score: 79
Period size: 7 Copynumber: 26.0 Consensus size: 7
12620184 GTTTAATATT
12620194 GGTTAGG
1 GGTTAGG
12620201 GGTTAGG
1 GGTTAGG
*
12620208 GGTTAGA
1 GGTTAGG
**
12620215 GGTTAAA
1 GGTTAGG
*
12620222 AGTTAGG
1 GGTTAGG
*
12620229 AGTTTAGG
1 -GGTTAGG
*
12620237 GGTTAGA
1 GGTTAGG
**
12620244 GGTTAAA
1 GGTTAGG
*
12620251 AGTTAGG
1 GGTTAGG
*
12620258 AGTTTAGG
1 -GGTTAGG
*
12620266 GGTTAGA
1 GGTTAGG
**
12620273 GGTTAAA
1 GGTTAGG
*
12620280 AGTTAGG
1 GGTTAGG
* *
12620287 AGTTTAAG
1 -GGTTAGG
* *
12620295 GTTTATTG
1 GGTTA-GG
*
12620303 GTTTAGG
1 GGTTAGG
12620310 GGTTAGG
1 GGTTAGG
*
12620317 TGTTAGG
1 GGTTAGG
*
12620324 GATTTAGG
1 G-GTTAGG
*
12620332 GGTTAAG
1 GGTTAGG
*
12620339 TGTTAGG
1 GGTTAGG
*
12620346 GGTTTGG
1 GGTTAGG
*
12620353 GGTTCGG
1 GGTTAGG
*
12620360 GATTTAGG
1 G-GTTAGG
12620368 GGTTAGG
1 GGTTAGG
*
12620375 AGTTAGG
1 GGTTAGG
12620382 AATTTAGTGT
Statistics
Matches: 134, Mismatches: 41, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
7 103 0.77
8 31 0.23
ACGTcount: A:0.23, C:0.01, G:0.42, T:0.34
Consensus pattern (7 bp):
GGTTAGG
Found at i:12620305 original size:29 final size:29
Alignment explanation
Indices: 12620195--12620292 Score: 180
Period size: 29 Copynumber: 3.4 Consensus size: 29
12620185 TTTAATATTG
*
12620195 GTTAGG-GGTTAGGGGTTAGAGGTTAAAA
1 GTTAGGAGTTTAGGGGTTAGAGGTTAAAA
12620223 GTTAGGAGTTTAGGGGTTAGAGGTTAAAA
1 GTTAGGAGTTTAGGGGTTAGAGGTTAAAA
12620252 GTTAGGAGTTTAGGGGTTAGAGGTTAAAA
1 GTTAGGAGTTTAGGGGTTAGAGGTTAAAA
12620281 GTTAGGAGTTTA
1 GTTAGGAGTTTA
12620293 AGGTTTATTG
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
28 6 0.09
29 62 0.91
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.32
Consensus pattern (29 bp):
GTTAGGAGTTTAGGGGTTAGAGGTTAAAA
Found at i:12620330 original size:22 final size:22
Alignment explanation
Indices: 12620304--12620356 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
12620294 GGTTTATTGG
*
12620304 TTTAGGGGTTAGGTGTTAGGGA
1 TTTAGGGGTTAAGTGTTAGGGA
*
12620326 TTTAGGGGTTAAGTGTTAGGGG
1 TTTAGGGGTTAAGTGTTAGGGA
12620348 TTT-GGGGTT
1 TTTAGGGGTT
12620357 CGGGATTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (22 bp):
TTTAGGGGTTAAGTGTTAGGGA
Done.